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Gas phase structures and molecular constants of dimers and molecules determined using microwave spectroscopy

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GAS PHASE STRUCTURES AND MOLECULAR CONSTANTS OF DIMERS
AND MOLECULES DETERMINED USING MICROWAVE SPECTROSCOPY
by
Adam Michael Daly
___________________________
A Dissertation Submitted to the Faculty of the
DEPARTMENT OF CHEMISTRY AND BIOCHEMISTRY
In Partial Fulfillment of the Requirements
For the Degree of
DOCTOR OF PHILOSOPHY
WITH A MAJOR IN CHEMISTRY
In the Graduate College
THE UNIVERSITY OF ARIZONA
2010
UMI Number: 3434347
All rights reserved
INFORMATION TO ALL USERS
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In the unlikely event that the author did not send a complete manuscript
and there are missing pages, these will be noted. Also, if material had to be removed,
a note will indicate the deletion.
UMI 3434347
Copyright 2011 by ProQuest LLC.
All rights reserved. This edition of the work is protected against
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2
THE UNIVERSITY OF ARIZONA
GRADUATE COLLEGE
As members of the Dissertation Committee, we certify that we have read the dissertation
prepared by Adam M. Daly
entitled Partial Structures and Molecular Constants of Gas Phase Dimers and Molecules using
Microwave Spectroscopy
and recommend that it be accepted as fulfilling the dissertation requirement for the Degree of
Doctor of Philosophy
____________________________________________________________Date: 11/08/10
Dr. Stephen G. Kukolich
____________________________________________________________Date: 11/08/10
Dr. John H. Enemark
____________________________________________________________Date: 11/08/10
Dr. Dennis L. Lichtenberger
____________________________________________________________Date: 11/08/10
Dr. Andrei Sanov
____________________________________________________________Date: 11/08/10
Dr. Lucy M. Ziurys
Final approval and acceptance of this dissertation is contingent upon the candidate's submission
of the final copies of the dissertation to the Graduate College.
I hereby certify that I have read this dissertation prepared under my direction and recommend
that it be accepted as fulfilling the dissertation requirement.
___________________________________________________Date: 11/08/10
Dissertation Director: Dr. Stephen G. Kukolich
3
STATEMENT BY AUTHOR
This dissertation has been submitted in partial fulfillment of requirements
for an advanced degree at the University of Arizona and is deposited in the
University Library to be made available to borrowers under rules of the Library.
Brief quotations from this dissertation are allowable without special
permission, provided that accurate acknowledgment of source is made.
Requests for permission for extended quotation from or reproduction of this
manuscript in whole or in part may be granted by the head of the major
department or the Dean of the Graduate College when in his or her judgment the
proposed use of the material is in the interests of scholarship. In all other
instances, however, permission must be obtained from the author.
SIGNED: Adam M. Daly
4
ACKNOLWLEDGEMENTS
I would like to sincerely acknowledge the significant efforts of many people
that collaborated and/or aided in the work described in this dissertation.
Noteworthy is the work of Dr. Chakree Tanjaroon, Bryan Sargus, Alison Holden,
Daniel Sanchez, Erica Weidenschilling, Kostya Pichugin and Dr. Stephen
Kukolich. The department and division should be acknowledged with many kind
words for the inspirational classes of Dr. Andei Sanov, Dr. Dennis Lichtenberger
and Dr. Ron Salzman. In addition, my classmates also found ways to inspire me
during this journey with notable influences from Emily R. Grumbling, Aaron
Vannucci and Michael Blumenfeld.
It is a great honor to acknowledge the superior education I received at
Humboldt State University and Brookhaven National Laboratories. The effort
necessary to be successful in the laboratories at those institutions has provided
guidance for success at every stage of my personal and professional endeavors
as both citizen and scientist.
Personally, I would like to acknowledge the training by Mr. Otto Campos,
who showed many ways that the discipline of science can be transformed into
the discipline of life. The foundation that my family set was a tremendous asset
and has become a spring board for self-understanding, trust and love. Although I
may have survived this life without a guitar or a passport, Greg Reiter assured
that I would never know that path. My personal journey has had many twists,
turns and escapades. The unique path has been a source of strength and would
like to say Thank You to my friends and family.
And not least I would like to acknowledge, the University of Arizona, the
agencies that promote scientific research and the country in general for making
the work that is described in this dissertation possible.
5
DEDICATION
To my mother Barbara
6
TABLE OF CONTENTS
LIST OF FIGURES…………………………………………………………………….11
LIST OF TABLES……………………………………………………………………...13
ABSTRACT………………………………………………………………………….....17
1. INTRODUCTION……………………………………………………………………18
2. EXPERIMENTAL METHODS…,,…………………………………………………28
2.1 Introduction…………………………………………………………...……28
2.2 Autoscan 6.0……………………………………………………………….35
2.3 Glassware………………………………………………………………….41
3. THEORY AND CALCULATIONS………………………………………………..42
3.1 Angular Momentum ……………………………………………….……...42
3.1.1. The rigid symmetric top energy levels………….……………42
3.1.2 The rigid asymmetric top energy levels……….………….…..44
3.1.3. The distortable rotor………….………………………….……..47
3.1.4 The microwave spectrum………………………………….…...48
3.1.5 Nuclear quadrupole and the microwave spectrum……..……50
3.2 Computational Methods……………..……………………………………52
3.3 Structure Fits………………………………………………………………53
4. HYDROGEN BONDED HETERODIMERS……………………………………..55
4.1 Introduction………………………………………………………………...55
4.2. Formamide-Formic Acid Dimer………………………………………….56
4.2.1. Introduction……………………………………………………...56
7
TABLE OF CONTENTS - Continued
4.2.2. Calculations…………………………………………………….60
4.2.3 Experimental…………………………………………………….64
4.2.4 Data Summary…………………………………………………..65
4.2.5 Discussion……………………………………………………….68
4.3. Propiolic Acid-Formic Acid Dimer……………………………………….81
4.3.1. Introduction……………………………………………………...81
4.3.2. DFT and Ab-initio calculations………………………………..84
4.3.3 Experimental Methods …………………………………….......85
4.3.3.1 Experiments at the University of Arizona ……...…..85
4.3.3.2 Experiments at the University of Virginia……….….86
4.3.4 Data Analysis and Results …………………………………….87
4.3.4.1 Microwave Spectrum…………………………………87
4.3.4.2 Structure Determination……………………………...88
4.3.4.3 One Dimensional Potential Well…………………….90
4.3.5 Discussion……………………………………………………….91
5. QUADRUPOLE COUPLING AND STRUCTURE OF SMALL INORGANIC
MOLECULES…………………………………………………………………………109
5.1. Introduction………………………………………………………………109
5.2 Azaborine………………………………………………………………....110
5.2.1 Introduction……………………………………………………..110
5.2.2 Calculations…………………………………………………….113
8
TABLE OF CONTENTS - Continued
5.2.3 Experimental…………………………………………………...115
5.2.4 Data Summary………………………………………………....116
5.2.4.1 Microwave Spectrum………………………………..116
5.2.4.2 Structure Determination…………………………….119
5.2.4.3 Townes-Dailey Population Analysis……………….121
5.2.5 Discussion……………………………………………………...124
5.3 Mercaptopyridine-N-oxide………………………………………………137
5.3.1. Introduction…………………………………………………….137
5.3.2 Experimental…………………………………………………...139
5.3.3 Data Summary…………………………………………………139
5.3.4 Results………………………………………………………….145
5.4 Arsenic Triphosphide……………………………………………………147
5.4.1 Introduction……………………………………………………..147
5.4.2 Experimental…………………………………………………...148
5.4.2.1 Synthesis of AsP3…………………………………...148
5.4.3 Data Summary…………………………………………………149
6. LOOSELY BOUND COMPLEXES OF ORGANOMETALLIC
MOLECULES…………………..……………………………………………………..153
6.1 Introduction……………………………………………………………….153
6.2. Ar-CpTl…………………………………………………………………...156
6.3 Ferrocene-HCl……………………………………………………………158
9
TABLE OF CONTENTS - Continued
6.3.1 Introduction……………………………………………………..158
6.3.2 Experimental…………………………………………………...159
6.3.3 Calculations…………………………………………………….159
6.3.4 Results………………………………………………………….160
6.4 Methyl Rhenium Trioxide Complexes………………………………..162
6.4.1 Introduction……………………………………………………..162
6.4.2 Gas Phase complexes of MTO………………………………164
7. STRUCTURE AND MOLECULAR PARAMETERS OF (η7-C7H7)Ti(η5C5H5)…………….…………………………………………………………………….166
7.1 Introduction……………………………………………………………….166
7.2 Experimental……………………………………………………………..167
7.3 Calculations………………………………………………………………168
7.4 Data Analysis and Results……………………………………………...169
7.4.1 (η7-C7H7)48Ti(η5-C5H5)………………………………………...169
7.4.2 (η7-C7H7)47Ti(η5-C5H5)………………………………………...170
8. CONCLUSIONS AND FUTURE DIRECTIONS………………………………..175
9. SUPPLEMENTAL MATERIAL…………………………………………………...179
9.1 Board Layouts for pulse box……………………………………………179
9.2 The AutoScan Code……………………………………………………. 181
9.3 Example fit codes for method of least squares……………………….209
9.4 Example job file for ICE Cluster – Batch Job…………………………214
10
TABLE OF CONTENTS - Continued
9.5 Example files for using Pickett’s SPCAT and SPFIT………………...215
WORKS CITED…..………………………………………………………………..…218
11
LIST OF FIGURES
Figure 2.1. Components of the spectrometer hardware………………….…..…...29
Figure 2.2. Output of the pulse box ……………………………………..……........31
Figure 2.3. The circuit diagram of the non-automated pulse box………..……....32
Figure 2.4. Homodyne microwave circuitry……………………………...………....34
Figure 2.5. The control circuit used in the pulse box………………………….......36
Figure 2.6. The motor control circuit ……………………………………..………....37
Figure 2.7. Board layout of the automated pulse box …………………..……......38
Figure 2.8. Sample cell for small yield reactions……………..……………....…....41
Figure 4.1. Formamide-Formic Acid complex……………………………...……....57
Figure 4.2 Gas phase structure calculated using MP2/6-311++G** for the dimer
between formamide-formic acid……………………………………………..............59
Figure 4.3 Calculated structure of the dimer between formic acid –propiolic-acid
using MP2/6311++G**…………………...……………….………………..……........83
Figure 4.4 Parameters used in the fit of propiolic acid-formic acid………...........94
Figure 5.1 Azaborine with parameters used in the fit…………………….….......112
Figure 5.2 Parameters used in the least squares............... ……………...........120
Figure 5.3. Electron density maps for the MP2 optimized structures of 1,2dihydro-1,2-azaborine and benzene mapped with the electrostatic potential (Iso
Val = 0.001) from the total SCF density………………...…………………………136
Figure 5.4 A) N-hydroxypyridine-2(1H)-thione , B) 2-mercaptopyridine-Noxide..................................................................................................................138
12
LIST OF FIGURES – Continued
Figure 5.5 Parameters and results from a four parameter fit……………...…...145
Figure 5.6 Arsenic triphosphide………………………………...……………......148
Figure 6.1 Plot of the binding energy (cm-1) as a function of r(Ar-Cp) for MP2 and
DFTcalculations…………………………………………………............................156
Figure 6.2 Potential energy surface profile for Ar-CpTl evaluated at the MP2/augcc-pVTZ-PP (Thallium)/aug-cc-pVTZ(Ar, C, H).....………………......................157
Figure 6.3 Axis system for calculations of the Ferrocene-HCl dimer………......159
Figure 6.4 Graph of results with HCl-Ferrocene…………………………...........161
Figure 6.5 Axis system for methylrhenium trioxide used in calculations……....164
Figure 8.1 Predictions of the gas phase dimer of 2-hydroxy-pyridine/2-pyridone
and formic acid………………………………………………….…………………....176
13
LIST OF TABLES
Table 1.1 Binding energies of gas phase dimers…………………………………..21
Table 3.1 Matrix elements of the symmetric top…………………………………..43
Table 3.2 Matrix elements needed for equation 3.8………………………………45
Table 3.3 Mapping of the rotational constants to the coefficients
in equation 3.8………………………………………………………………………….46
Table 3.4 The distortable rotor for both quartic and sextic in both A and S
representations………………………………………………………………………...48
Table 3.5 Symmetry of rotation energy levels……………………………………..49
Table 3.6 Allowed transitions for an asymmetric top………………………………50
Table 4.1 . Predicted and experimental values for molecular geometry
parameters, rotational constants and quadrupole coupling constants using 6311++G**……………………………………………………………………………….61
Table 4.2. Comparison of Mulliken charges on the atoms calculated for the
monomer and the complex using MP2/6-311++G** in units of (e)………………63
Table 4.3. Rotational transition frequencies measured for the normal
isotopologue, HCOOH-H214NCHO, and H13COOH-H214NCHO with deviations
from the best fit values (o-c = observed - calculated) in MHz………………….…71
Table 4.4. Measured rotational transition frequencies (MHz) for four
isotopologues of HCOOH-H215NCHO. The first group is a-dipole transitions and
the second b-dipole transitions……………………………………………………….73
14
LIST OF TABLES - Continued
Table 4.5. Experimental rotational constants (MHz) and centrifugal distortion
(kHz) constants………………………………………………………………………...75
Table 4.6. Experimental rotational and quadrupole coupling constants for
H12COOH-H214NCHO and H13COOH-H214NCHO in MHz…………………………77
Table 4.7. Best fit-results for the adjustable parameters used in the
structure fit…………………………………………………………………………….78
Table 4.8. Coordinates determined by least squares structure fit, Kraitchman
analysis and as predicted by CCSD in Å…………………………………………..79
Table 4.9. Summary of calculated and experimental key molecular and structural
parameters…………………………………………………………………………….95
Table 4.10. Results from the fit of a and b-type dipole transitions………………96
Table 4.11. Rotational and distortion constants for the Propiolic-Formic dimer
and the measured isotopomers……………………………………………………...97
Table 4.12. Barrier height calculations and transition state geometry………..…98
Table 4.13. The measured transitions of ProFA from 1.7 GHz to 21.3 GHz……99
Table 4.14. Propiolic Acid- Formic Acid (C13) results……………………………103
Table 4.15. Summary of the isotopic substitution of deuterium……………..…105
Table 4.16. Summary of results from the structure fit with Propiolic Acid angle
fixed and Formic Acid deviation angle from the monomer fit with rotation of
Formic acid and monomers centers of mass separation…………………….…..107
15
LIST OF TABLES - Continued
Table 4.17. Coordinates for Kraitchman analysis and the results of two structure
fits. Fit I is a three parameter fit with the propiolic <(C-O1-H1) angle fixed…..107
Table 4.18. Summary of results using the ANHARM program for a minima
separation of 0.7Å and fit to V(Z)=A*(Z4-B*Z2)…………………………………..108
Table 5.1. Spectroscopic constants for1,2-dihydro-1,2-Azaborine. …………..128
Table 5.2. Structural parameters from the least squares fit to the experimental
rotational constants………………………………………………………………….129
Table 5.3. B-N bond distances reported in the literature……………………….129
Table 5.4. Azaborine line list of measured frequencies (obs) for the normal
isotopomer, H6B11-N14C4………………………………………………………..….130
Table 5.5. Azaborine line list for H6B10-N14C4. Frequencies are
given in MHz………………………………………………………………………...133
Table 5.6. Azaborine line list for H5B11-N14DC4……………………………........135
Table 5.7 Summary of the calculated rotational constants and quadrupole
coupling constant…………………………………………………………………….140
Table 5.8 Results of the three isotopomers……………………………………….140
Table 5.9 C5H432S14NOH line list (o-c) is observed-calculated in kHz………..141
Table 5.10 Line list for C5H432S14NOD……………………………………………143
Table 5.11 Line list for C5H434S14NOH……………………………………………144
Table 5.12. Results of fits to the three sets of constants……………………….149
Table 5.13 Line list for the strongest measured transitions……………………..150
Table 5.14 Line list of next set of transitions assigned…………………………..151
16
LIST OF TABLES - Continued
Table 5.15 Measured transitions from the third fit………………………………..152
Table 6.1 Results of Calculated binding energy and rotational constants
compare with theory………………………………………………………………….155
Table 6.3 Summary of binding energy, rotational constants and dipole moment
magnitude for the ferrocene-HCl dimer……………………………………………160
Table 6.4 MTO monomer with DFT and MP2 predictions of structure and
quadrupole coupling constant………………………………………………………163
Table 6.5 Summary of calculations of dimers and MTO………………………..165
Table 7.1 Results of CHT-X-Cp using B3PW91/Hay Wadt (n+1) on metal/631+G(d) on carbon and hydrogen………………………………………………….168
Table 7.2 Summary of Isotopic studies with (η7-C7H7)Ti(η5-C5H5)………….….169
Table 7.3 Results from Least Squares Fit………………………………………...170
Table 7.4 Results of 47Ti fit and comparisons to Keck and Calculations………171
Table 7.5 1-d-CHT-Ti-Cp……………………………………………………………172
Table 7.6
13
CHT-Ti-Cp results……………………………………………………..173
Table 7.7 CHT-Ti-13Cp results………………………………………………………173
Table 7.8 Results of 47Ti in CHT-Ti-Cp…………………………………………….174
17
ABSTRACT
Gas phase structures and other molecular parameters have been
investigated for several molecules and dimers using pulsed beam Fourier
Transform Microwave Spectroscopy. An automated control system has been
designed and implemented for the microwave spectrometer that has allowed a
systematic observation of the microwave spectrum for many molecules. The
theoretical models that are available to the gas phase structural chemist, density
functional theory and ab-initio methods, are described with detailed comparisons
to experimental results. Experimental data was generated for systems involving
hydrogen bonded dimers, organic molecules, inorganic molecules and
organometallic molecules. Rotational constants and quadrupole coupling
constants were determined using the microwave spectra. This data and isotopic
investigations have been used to determine key structural parameters and
molecular properties.
18
1.
INTRODUCTION
High resolution spectroscopy of molecules in the gas phase is a valuable
probe into the predictive power of theoretical models. The refinement of
theoretical models is an important effort for 21st century science as the
computational power has increased and interesting molecular systems have
increased in size. This dissertation reports the gas phase measurements of
inorganic and organometallic molecules and dimers of organic and
organometallic molecules using pulsed beam fourier transform microwave
spectroscopy (PBFTMW). The systems described here span a wide range of
chemical systems and offer a valuable comparison of experimental results with
theoretical prediction. The level of theory presently available to the structural
chemist is unprecedented and has its roots in the achievements of many
branches of science: quantum theory, numerical methods and computer science.
These branches play significant roles in the advancement and accessibility in
integrating the highest levels of theory with the biggest molecular systems of
interest. This dissertation describes experimental results and a subset of
theoretical predictions for a number of gas phase systems. The connection
between the two composes the territory for the experimental scientist. The
scientist who desires to make a significant contribution needs to develop the
19
motivation and interpretation of laboratory results in the framework of the current
theoretical models.
Several systems that present interesting experimental and theoretical
approaches are summarized in this dissertation. There are theoretical
predictions for each system that helped guide the interpretation of results and
effort has been made to perform calculations with both density functional theory
(DFT) and ab initio methods when possible. In the first experiment described in
this dissertation, covered in chapter 4, several theoretical papers existed on the
gas phase dimer between formamide and formic acid1.
The heterodimer had been predicted but not observed until our experiments.
The formamide-formic acid system is a doubly hydrogen bonded system made
from the simplest amide, formamide, with the simplest carboxylic acid, formic
acid. The exchange of protons had been shown to be asymmetric because the
result is the less stable formamidic acid-formic acid dimer. This species was not
observed in our experiments, the more stable formamide-formic acid dimer was
observed and several isotopic species were measured.
20
The second system reported in chapter 4 did not have any theoretical
papers that described the existence of the dimer between propiolic acid and
formic acid (Pro-FA).
HO
O
H
HC
OH
O
Formic Acid-Propiolic Acid
A similar system had been studied by many theoretical groups2 and
experimentally by Havenith3 who published the rotational constants of the ground
and first vibrational state. The energy difference between the ground and first
vibrational states was also reported for formic (HCOOH) and the deuterated
(DCOOH)2 dimers. The experiment used high resolution infrared spectroscopy
and the authors claim to have determined the energy “splitting” that is predicted
in a symmetric double well potential. The tunneling motion of the proton can be
modeled by a double well potential. Formic acid dimer is symmetric by definition
and the perfect system to study the symmetric double well potential.
Unfortunately, this system does not have a permanent dipole moment and can
not be studied using microwave spectroscopy. An effort was undertaken to
identify a system that has a dipole moment and whose tunneling motion involved
a symmetric well. On the advice of Dr. Robin Polt, calculations with propiolic and
formic acid were performed and compared to formic-formic acid dimer
21
calculations. Additionally, several other systems 2-pyridone-formic acid, benzoic
acid-formic acid and acetic acid-formic-acid were studied.
Table 1.1 Binding energies of gas phase dimers
Dimer
Method
Formic_Formic
MP2
FormicTrifluoroacetic
MP2
Formamide_Trifluoroacetic
MP2
Formic 2-hydroxypyridine
MP2
Formic-2-Pyridone
MP2
Formic- Propiolic
MP2
Formic – Benzoic
MP2
Formic – Formamide
B3Pw91
Formic – Formamide
HCTH407
Formic – Formamide
TPSSTPSS
Propiolic_H2O
MP2
Propiolic-Propiolic
MP2
*corrected for basis set superposition error
Basis Set
6-311++G**
6-311++G**
6-311++G**
6-311++G**
6-311++G**
6-311++G**
6-311++G**
6-311++G**
6-311++G**
6-311++G**
6-311++G**
6-311++G**
Binding
Energy* /cm-1
-4754
-5492
-7026
-5512
-6320
-4857
-5053
-5639
-5347
-6072
-3073
-4928
The results of these calculations led to a successful experiment with
propiolic acid-formic acid4. The spectrum shows evidence of a concerted proton
exchange that is very similar to the phenomenon observed with formic-formic
acid. The ground state and first vibrational state rotational constants were
obtained. With the help of data collected at the University of Virginia, the energy
difference between the two states and the magnitude of the dipole moment were
obtained. Details of this work are in chapter 4 and are stated here to introduce
the interplay of theory and experiments.
Microwave spectroscopy is a technique that uses electromagnetic
radiation in the 1 to 1000 GHz region to probe molecules by exciting transitions
that can be described by application of quantum mechanics to angular
momentum. This technique has led to the determination of important structural
22
and molecular parameters of stable molecules, gas phase dimers and reactive
species. A successful measurement requires a coordinated effort of many
components which are described in chapter 2. Briefly, a chamber must be kept
between 10-6 to 10-7 Torr and a sample is “injected” into a Fabry-Perot resonator.
Light is then sent into the cavity and if it coincides with a transition, a free
induction decay (FID) is observed. This signal is transformed and the frequency
is obtained. Due to the high resolution of the technique and small bandwidth the
difference between the molecular signal and predicted signal can be several
hundred megahertz. The most efficient way to observe a signal is to scan a
region where there is a prediction of a transition. In an effort to make this as
efficient as possible, an automated program was developed that scans a region
of interest and saves the datafiles. An “on the fly” algorithm was developed to
detect signals and save the results in a summary file that is generated after every
run. This system has been extremely successful at recording the spectrum in
fixed frequency windows and the details are given in chapter 2.
Angular momentum is a quantity with a rich history and powerful
applications in both modern and classical physics. The sources of angular
momentum in a molecule can be rotation about the center of mass, the nuclear
spin angular momentum and electronic spin angular momentum. In microwave
spectroscopy, the interpretation of the spectrum comes from knowledge of the
symmetry, the vibrational state and the isotopic masses in the molecule. In
chapter 3 the useful results of energy levels as a function of structure is detailed.
23
The assignment of quantum numbers to the different energy transitions is
essential to reveal the gas phase structure, gas phase dynamics and electronic
environments near nuclei. Application of the current state of theory can
sometimes give reasonable values for each of the three molecular properties
mentioned above. The typical experiment involves an iterative process where
initial values for the structure, dynamics and electronic environments near nuclei
for a molecule are estimated using molecular orbital theory’s solutions to the
Schrödinger equation modeled as Gaussian wave functions using the Gaussian
program run on the ICE cluster at the University of Arizona. The experiment is
performed where a sample is pulsed into an evacuated chamber and the
spectrum is obtained. The spectrum is predicted using the best molecular
calculations and the comparison of the predicted and the measured spectrum
provide an analysis of the a priori information obtained from calculations. The
correct assignment of quantum numbers to transitions allows the determination
of the rotational constants, distortion constants, and quadrupole coupling
constants for a particular vibrational state. Usually, only the ground vibrational
state is observed using pulsed beam microwave spectroscopy.
Using the theory of angular momentum with quantum mechanics, the
connection between the molecular structure and the general features (neglecting
the hyperfine, quadrupole and vibrational structure) of the microwave spectrum
has been determined. The energy levels are combinations of the reciprocal of
the moments of inertia and for the molecules reported in this dissertation, the
24
general approach and results will be described in Chapter 3. The connection of
the proper quantum number assignments to the moments of inertia is the key to
the structural fits used to determine bond lengths and angles. The moments of
inertia are products of the isotopic mass and the square of coordinates, which
can be utilized using Kraitchman’s equations or least squares analysis to
determine substitution structures. Often the moment of inertia itself is not
reported but the reciprocal of the moment of inertia times a constant, the
rotational constant, is utilized a great deal. The purpose of the analysis of a
molecule’s spectrum is to extract out the isotopic rotational constants for the
determination of important structural features of the molecule.
Chapter 4 discusses the progress made on understanding the structure
and dynamics of amides and carboxylic acids in the gas phase. The motivation
of the work involves the rapidly developing arm of computational biochemistry.
Soon, the dynamics within supermolecules will be studied with techniques that
have only been possible with smaller molecules, 100 amu. Systems like
formamide-formic acid and propiolic-formic acid are great systems that help
reveal the subtle structural and dynamic possibilities in doubly hydrogen bonded
systems.
The focus of Chapter 5 is the analysis of the quadrupole coupling constant
and its usefulness in quantifying aromaticity in azaborine,
25
NH
BH
Azaborine
identification of isomers in N-hydroxy-pyridinethione
OH
N
S
2-mercaptopyridine-N-oxide
and the interesting analysis of the effect of vibrational state on the quadrupole
coupling constant on arsenic triphosphide
.
These three systems offer a look into the diversity of the rich spectrum of
molecules with at least one atom containing a nucleus with an isotope of I >1.
The coupling of the quadrupole moment of the nucleus and the electric field
gradient at that nucleus gives an excellent insight into the degree in which
calculations can predict the electronic environment near nuclei and this is
summarized in the chapter.
26
Chapter 6 is a summary of the work that is half computational and half
laboratory results. The calculations of the first rare gas-organometallic complex
are reported for argon-cyclopentadienylthallium (CpTl). The second project
reports the experimental efforts to find the complex predicted between HCl and
ferrocene.
Fe
H
Cl
Ferrocene-HCl
Several transitions were observed and possibilities of chemical reactions
occurring have hampered the analysis of this system. The last project reported
involves the computational work performed to model methyl rhenium trioxide.
The spectrum of an organometallic complex, η7-cycloheptatriene titanium
η5-cyclopentadienyl, has been measured and the experiment has been described
in Chapter 7.
27
Ti
CpTiCHT
A re-evaluation of the quadrupole coupling constant is given for the only
assignments of the titanium-47 isotope. The gas phase structure was
constructed from measurements of 13C in both rings and singly deuterated
cycloheptatriene. Calculations for other metals in this moiety and a summary of
the subtle structural changes predicted are given.
The dissertation concludes with general statements about the work
presented and a short summary of the data that was not presented in the thesis
but could aid future work in their respective areas.
28
2. EXPERIMENTAL METHODS
2.1 Introduction
The technique used in the experiments described in this dissertation
involves the use of three main parts: a Flygare-Balle pulsed beam microwave
spectrometer, electronics with computer control and carefully handled samples.
The successful convergence of these three components is required for
experiments performed in our laboratory. The main aspects of the experiments
will be described generally here and components that I changed will be given in
considerable more detail. I expanded or introduced into the laboratory the
automation of the pulsed beam fourier transform microwave spectrometer
(PBFTMW) and the introduction of glassware that has been used successfully in
experiments.
The flygare-balle pulsed beam microwave spectrometer5 is the instrument
used to measure the spectrum of the systems described in the dissertation. The
experimental details have been published6and will be mentioned here. Figure
2.1 gives the essential components of the spectrometer. There is a Fabry-Perot
cavity with 2 12” mirrors labeled K that are mounted to a chamber that can be
evacuated using the diffusion pump labeled E and fore pump labeled H.
29
Figure 2.1. A). Gas handling system (not shown) feeding a General Valve 9. B). Fabry Perot
mirrors 12” C). Water circulation to chiller D). Heat Element E). Diffusion Pump F). Vacuum
plumbing G). Motor drivers through baffle that moves mirror H) Fore Pump Welch (10-3 Torr)
I). Antenna made of a 90° angle of conductor fed through a flange (not shown) J). Vacuum
container made of stainless steel. K) Fixed mirror that also contains the antenna.
30
The coordinated sequence of events needed to effectively use the
microwave spectrometer in the Kukolich laboratory begins with a sharp (50 μs)
TTL signal to the valve driver which houses the elements of a high voltage RLC
circuit with the valve as the inductor. The signal sent from the pulse box to the
solenoid valve driver represents t=0 and closes the circuit to ground shown in
figure 2.2. This discharges a capacitor that is held at a voltage from 130 to 180 V
to open the solenoid valve. Magnetic induction produced in the windings pull the
armature into the solenoid, whereby the poppet is separated by the faceplate and
is opened into the cavity. The general valve 9 was used for most of the data
given in this dissertation except as described when various fuel injectors were
used toward the latter stages of research. The delays shown in figure 2.3 control
the onset of the signals sent to the microwave switch, Herley MDI switch and
digitization by the PICO digital oscilloscope.
31
Transmit
Receive Delay
Valve Signal
Receive Signal
Transmit
Figure 2.2. Output of the pulse box. The valve signal is generated by a 555 and
runs at half the frequency of the transmit signal. The delay between transmit and
receive and valve and receive are adjusted using potentiometers located on the front
panel.
32
Figure 2.3. The circuit diagram of the non-automated pulse box in which two
different oscillators control the timing of the pulsed beam relative to the radiation
signal and digitization.
There are two modes of operation and when data is being taken, it
operates as described above. The valve opens and a 1 ms delay later a short (1
μs) signal is sent to the switch and a burst of microwave radiation fills the cavity
(5 dBm) and is dispersed across ±1 MHz frequency range due to the uncertainty
33
principle. An adjustable time later (10 μs) the PICO is triggered to take 100 μs of
data.
The second mode involves the tuning of the cavity and is often described
as FAST or TUNE. In the case of tuning, a fast, 550 Hz signal is introduced into
the cavity that does not send a signal to the valve or have a receive delay. The
reflected signal is sent through a directional coupler and converted into a voltage
using a diode detector and split. One signal is sent to an amplifier then to the
DAQ board and the other signal is sent to an oscilloscope. At a given frequency,
the motor is moved until the cavity is in resonance. At the resonant condition a
power decrease is detected due to the coupling of the radiation with the cavity
and the reflected signal going to a minimum. During the autoscan procedure, the
amplified signal from the detector is digitized over a 2 MHz range and the
minimum is set to be the stimulation frequency for that motor position. The path
the radiation takes to enter the cavity and exit to be digitized is shown in figure
2.4 using the homodyne detection scheme.
The homodyne system makes use of a power divider that sends the pulse
of radiation into the cavity by the fast acting switch, 1 μs, Herley MDI switch .
This will stimulate molecules in a ±1 MHz range (with different efficiencies of
detection) and the signal appearing at the antenna about 10 μs after the radiation
has been turned off is digitized. If a rotational transition is in this frequency
window, a superposition of the two states is created and when the radiation is
34
turned off a loss of phase occurs. This results in a decay of the emitted radiation
at a frequency equal to the separation energy of the two levels.
Figure 2.4. Homodyne microwave circuitry used in all the experiments performed in
this dissertation.
35
2.2 AutoScan 6.0
The project to automate the scanning operation with the microwave
spectrometer was performed in the Fall of 2008. It consists of a C++ program,
AutoScan 6.0 and hardware to connect the computer to the key elements in the
microwave circuitry. The program was built out of Chris Dannemiller’s TRW 3.0
program. The key features are the computer controlled DAQ board,
Measurement Computing LS1208, a PROLOGIX usb-gpib connector and
additional circuitry to the pulse box described above. The pulse box circuit
described above needed to be modified to allow computer control over the
TUNE/SCAN state and MOTOR ENABLE. A key element was developed to add
to the pulse box, the control circuit given in Figure 2.5. This allows that one
switch, CONTROL, could allow the TUNE/SCAN switch and MOTOR ENABLE to
be controlled independently by either the computer or by the operator. There are
two such control circuits in the pulse box. With the control switch set to
MANUAL, the operator has control and can use Scan 2.0 to obtain and save data
in the same manner as the TRW 3.0 performed in the past.
36
Operator
Computer
Control
Control
1
2
Output
H
H
H
L
L
H
H
L
H
H
L
H
H
L
H
L
H
L
L
H
H
L
L
H
L
H
H
L
H
H
L
H
H
L
H
L
H
L
H
H
L
H
H
L
L
H
H
H
L
L
L
L
H
H
H
L
Figure 2.5. The control circuit used in the pulse box with the truth table of its
operation. The function of this circuit is to control which signal gets passed to
the output by using a switch, Operator/Computer control of the pulse box. In
the pulse box this is either SCAN/TUNE or motor ENABLE.
37
The motor board has circuit shown in Figure 2.6. The motor is controlled by
pulse-width modulation using a 555 and LS123. The 555 triggers the one-shot
that has an adjustable dutycycle from 1 to 90% and will be passed to the motor
enable line on the L6202 if either the Operator Enable or Computer Enable goes
high.
Figure 2.6. The motor control circuit using a L6202 motor driver that is utilizing a
pulse-width modulation derived from an oscillator (555) driving a one-shot (LS123)
whose range varies from 1 to 99% dutycycle. Only when the operator or computer
signal is high will the pulse width modulation signal arrive at the motor control.
38
Figure 2.7. Board layout of the automated pulse box. 1) Clock board (Figure 2.3) 2)
Control Board and Pulse Width Modulation 3)Motor Board 4) Power Supply (5V) 5)
Line Driver board (LS244) 6) BNC connections for Valve, Transmit and Receive
(trigger) Signals. The valve frequency, Transmit delay and Transmit width, Receive
delay and motor pulsewidth are adjusted with potentiometers located on the front
panel. See 9.1 for details about boards 1-3. Wiring diagrams in a separate
document
39
The hardware used during the automation is controlled by the C++ program
Autoscan 6.0 and is given in 9.2. The changes made to the original program,
TRW, involve a control loop that is based on the frequency condition. The
condition is based on a comparison between the stimulation frequency and the
final frequency. The stimulation frequency is the frequency at the minimum
voltage recorded from sweeping the mode (± 1 MHz). The data acquisition loop
will run until the preset number of shots is met. In this loop an algorithm is
implemented where radiation is sent in twice the rate of molecular pulses. Each
acquisition is digitized by the PICO and stored in the array g_pDATA. The
“empty” shot is subtracted from the molecular pulse and stored in, g_pSum. This
array is added to g_pDraw and sent to the fast fourier transform subprogram in
GFX.h. The function DrawPlots brings in the time domain signal to the
subprogram and the function FTandDraw produces the fourier transform and
displays it. The DrawPlots array is saved in a file with the stimulating frequency
as its name. After the file is saved a signal to pulse the motor for 150 ms is sent
from the DAQ board. This pulse to the motor causes a movement of the mirror
and a new resonant condition for the microwaves. The loop will repeat until the
stop frequency is obtained.
At the start of the winmain program it searches for a file, config.ini, that
contains the start and stop frequency, number of shots per frequency. named.
Here is the format for the file:
40
Start Frequency in MHz
Stop Frequency in MHz
Goal for step in frequency in MHz
Line Criteria
Number of Shots per frequency
The motor pulse length
The goal for the step in frequency, line criteria and motor pulse length are
usually not changed in normal operation of automatic scanning. The line criteria,
which is defined below, is an “on the fly” analysis program that was developed
empirically after measurement of several files. The datafile consists of 512
samples at 5 MHz and signals have a distinct maximum and minimum due to the
free induction decay signal. When a line is encountered the maximum and
minimum’s difference can exceed 3 times the noise limit of 1500 in arbitrary
units. If the difference is 4500 or greater the Lines Detected field is incremented
and the updated value of “Lines detected” appears on the screen. Also, a
summary file is generated that has the frequencies tested and the result of the
line criteria test.
41
2.3 Glassware
The standard sample cell used by our group had already been designed.
It is has ¼” glass tubing that is connected to a reservoir that holds a sample. A
carrier gas is introduced on one end that is connected to the gas handling system
and the other end is connected by Swagelok to the valve.
Products of organometallic syntheses usually require a sublimation to obtain the
product. The cold finger used in the sublimation is scraped in the dry box and
placed into a sample cell. Often, there is not enough product on the cold finger
to transfer into a sample cell. Due to this, a new sample cell was designed so
that the entire contents of the cold finger could be directly analyzed on the
spectrometer.
Figure 2.8. Sample cell for small yield reactions product obtained by sublimation.
42
3. THEORY AND CALCULATIONS
3.1 Angular Momentum
This section describes the origin of the quantum number assignments
made in this dissertation. It is not exhaustive in the development of the solutions
to the symmetric top or asymmetric top but cursory to introduce the fundamental
results that result from the solution of the angular wave equation without an
external potential for two cases, the prolate symmetric top and the asymmetric
top. The full development of the solutions is well described in Gordy and Cook7,
Kroto8 and Wollrab9. The approach of Kroto will be used to introduce the
approach theoretically. Dr. Herb Pickett’s SPCAT and SPFIT10 program
integrates the solutions of the distorted symmetric and asymmetric top and were
used to generate the spectra and fitted parameters from analysis of the spectra.
3.1.1 The rigid symmetric top energy levels
The Hamiltonian for a molecule rotating about its center of mass can be
written as
⎛ Ja2 Jb2 Jc2 ⎞
⎜
⎟
⎜ 2 I + 2 I + 2 I ⎟Ψ (θ , φ ) = Ψ (θ , φ )E
b
c ⎠
⎝ a
(3.1)
43
The components of the angular momentum lie along the principle axes., a,
b and c.. It is convenient to define three quantities, the rotational constants. A, B
and C and are defined as A=ħ2/2Ia. B=ħ2/2Ib and C=ħ2/2Ic. In the prolate
symmetric top, the angular momentum components along b and c principle axis
are identical and the equation can be reduced to
(BJ
2
)
+ ( A − B )J a Ψ (θ , φ ) = Ψ (θ , φ )E
2
(3.2).
The other case is the oblate top where A=B and the equation is given as
(BJ
2
)
+ (C − B )J a Ψ (θ , φ ) = Ψ (θ , φ )E
2
(3.3)
The eigenfunctions of angular momentum operators J2 and Ja are the
associated Legendre polynomials and are represented in the dirac notation as
Ψ = JK M
.
(3.4).
K is the projection of the total angular momentum onto the symmetry axis of
the molecule. M is the projection of the total angular momentum onto the
laboratory axis, z, which is useful when an external electric field is applied.
Table 3.1 Matrix elements of the symmetric top
J , K , M | J 2 | J , K , M = h 2 J ( J + 1)
J , K , M | J a | J , K , M = hK
J , K , M | J z | J , K , M = hM
44
The energy levels can be derived using the results from Table 3.1 The
solutions for the two cases, prolate and oblate top, are given as
E=BJ(J+1)+(B-C)K2
(3.5)
E=BJ(J+1)+(C-B)K2
(3.6)
The selection rules are ΔJ=0,±1 and ΔK=0 for the rigid symmetric top rotor
and the spectrum is identical to the linear molecule with transition spacing equal
to 2B. B is the rotational constant along the b-axis, perpendicular to the
symmetry axis. Molecules are not rigid and distortion proportional to powers of J
and K occur but are small compared to the separation between J levels and are
treated using perturbation methods. The two methods developed by Watson are
discussed after the rigid asymmetric top.
3.1.2 The rigid asymmetric top energy levels
.The
energy levels of the asymmetric top are more complicated because all
three moments of inertia are different. The general approach involves
rearranging equation 3.1 to
Η=
(
)
(
1
(a + b ) J a2 + J b2 + cJ c2 1 (a − b ) J a2 − J b2
2
2
)
(3.7)
Which is reduced to
(
Η = αJ 2 + β J c2 + γ J +2 + J −2
)
(3.8)
45
Using
α=
1
(a + b ), β = C − 1 (a + b ) , γ = 1 (a − b )
2
2
4
(3.9)
Table 3.2 Matrix elements needed for equation 3.8
J , K , M | J | J , K , M = h 2 [J ( J + 1)]
2
J , K , M | J 2 c | J , K , M = hK 2
2
J , K , M | J − | J , K + 2, M = h 2 ( J − K )( J + K + 1)( J − K − 1)( J + K + 2)
2
J , K , M | J + | J , K − 2, M = h 2 ( J + K )( J − K + 1)( J + K − 1)( J − K + 2)
46
The symmetry of the molecule determines which rotational constants the
coefficients, α, β and γ, get mapped to help facilitate diagonalization. The usual
cases are summarized in Table 3.3
Table 3.3 Mapping of the rotational constants to the coefficients in equation 3.8
Case
Coefficient
Rotational Constant
Near prolate
a,b,c
B,C,A
Very asymmetric
a,b,c
C,A,B
Near oblate
a,b,c
A,B,C
The Hamiltonian is diagonal in J with dimension (2J+1)x(2J+1). Offdiagonal terms appear that mix states that are ± 2 in K. The result is a matrix that
is symmetric on both diagonals because of the K degeneracy and can be
transformed into basis functions given in equation
Ψ=
[
1
J+ K ± J− K
2
]
(3.10)
using the Wang matrix. A new scheme to identify the energy levels is necessary
to identify the prolate and oblate symmetric top solutions that correlate to the
asymmetric top energy level. This is designated using Ka, the prolate limit, and
Kc, the oblate limit and given as JKaKc. The energy levels solutions can be
47
obtained in closed form for low J and numerically determined for higher J. For
the purpose of generating microwave spectra used in this dissertation, Herb
Pickett’s program SPCAT and SPFIT were used.
3.1.3 The distortable rotor
The deviation of a molecule from a perfectly rigid system must be
parameterized to account for the small change in the predicted energy levels as
a function of J and K. There are two reduced forms that were proposed by
Watson11, Asymmetric (A) and Symmetric (S), representations. The quartic and
sextic terms in the Hamiltonian for both are given in Table 3.4. Both
representations are implemented in Herb Pickett’s SPCAT/SPFIT program. Most
of the molecules reported in this dissertation are slightly asymmetric and the Srepresentation was used. The three most frequently used distortion constants
are the fourth power terms, DJ and DJK. The term HR term is the rigid rotor
solutions given in the previous sections except that effective rotational constants
are used. The rotational constants are readily obtained from the constants
determined in the fit.
48
Table 3.4 The distortable rotor for both quartic and sextic in both A and S
representations.
A-reduced Hamiltonian H(A)=HR+Hd(4)+Hd(6)
Hd(4)=ΔJJ4-ΔJKJ2Jz2-ΔK Jz4-2δjJ2(Jx2-Jy2)-δk[Jz2(Jx2-Jy2)+(Jx2-Jy2) Jz2]
Hd(6)=ΦJJ6-ΦJKJ4Jz2-ΦKJ J2Jz4- ΦKJz6+2φjJ4(Jx2-Jy2)-φjkJ2[Jz2(Jx2-Jy2)+(Jx2-Jy2)
Jz2] +φk[Jz4(Jx2-Jy2)+(Jx2-Jy2) Jz4]
S-reduced Hamiltonian H(S)=HR+Hd(4)+Hd(6)
Hd(4)=DJJ4-DJKJ2Jz2-DK Jz4+d1J2(J+2-J-2)+d2[(J+4-J-4)]
Hd(6)=HJJ6-HJKJ4Jz2-HKJ J2Jz4- HKJz6+2h1jJ4(J+2-J-2)-h2J2[(J+4-J-4)]
+h3[(Jx6-Jy6)]
3.1.4 The microwave spectrum
Microwave spectroscopy uses the information from the spectrum which is the
difference between energy levels. If the electric dipole moment matrix element is
non-zero, a transition can occur. The electric dipole moment may have
components on one or all three of the principle axes, μa, μb and μc for an
asymmetric top. The symmetry of the cross product of Γ(Ψ”)x Γ(μ)x Γ(Ψ’) must
be A. The Hamiltonian is invariant to the rotation about any one of the axes
because it is a sum of squares of the angular momentum operator and its
components. A simultaneous change in sign of any two components leave the
49
Hamiltonian unchanged. The D2 character table can be used for the asymmetric
top and the Γ(μa)=B1, Γ(μb)=B2 and Γ(μc)=B3. The energy levels symmetry are
summarized in table 3.5 and the following selection rules are obtained.
Table 3.5 Symmetry of rotation energy levels
KaKc
Symmetry
even-even
A
even-odd
B1
odd-odd
B2
odd-even
B3
The cross products that are non-zero for different dipole moment
components are summarized in table 3.6
50
Table 3.6 Allowed transitions for an asymmetric top
Dipole moment
μa≠0
Selection rule
ΔKa=0, ±2,·
ΔKc= ±1, ±3
μb≠0
ΔKa=±1, ±3 ·
ΔKc= ±1, ±3 ··
μc≠0
ΔKa=±1, ±3 ··
ΔKc= 0, ±2·
·
3.1.5 Nuclear quadrupole and the microwave spectrum
The spin angular momentum of nuclei can couple with the molecular
rotation and produce considerable changes to the spectrum. If the nuclear
angular momentum, I, is one or greater a distinguishable pattern arises that is
specific to each half integer of nuclear spin. Rotational assignments were made
of molecules and dimers that included the nuclei nitrogen-14 (I=1), boron-10
(I=3), boron-11 (I=3/2), titanium-47(I=5/2) and arsenic (I=3/2) in this dissertation.
To analyze the spectrum with a nucleus having I>1 requires the introduction of
several new concepts regarding the coupling of the spin angular momentum and
the molecular rotation.
The interaction originates from the quadrupole moment of the nucleus and
the electric field gradient near the nucleus. The first term in the expansion is the
51
nuclear monopole which does not interact with molecular rotation. The second
term is the nuclear dipole and if present, can be neglected (this term is used in
the Stark effect). The third term is the integral of the nuclear quadrupole times
the second derivative of the potential.
HQ =
1
( 2)
Vij Qij( 2 )
∑
6 ij
(3.11)
Where Vij(2) and Qij(2) are second-rank symmetric tensors that represent the
gradient of the electric field by electrons in orbitals that are not spherically
symmetric and the nuclear charge distribution. The two terms in HQ have been
shown by Casimir to
HQ =
( )
( )
1
eqJ Q
⎡ ˆ ˆ 2 3 ˆ ˆ ˆ2 ˆ 2 ⎤
3I ⋅J + I ⋅J −I J ⎥
2
2 (I )(2 I − 1)J (2 J − 1) ⎢⎣
⎦
(3.12)
Q is the quadrupole moment of the nucleus and qJ is the molecular field gradient
averaged over the rotational state in the ground vibrational state.
52
3.2 Computational Methods
Computers have greatly enhanced the predictive power of theoretical
models in chemistry. For most molecular systems, exact solutions to the
Schrödinger equation are not possible. The molecular systems that are studied
in this thesis range from small organic molecules to gas phase heterodimers of
organometallic molecules. The smallest system studied in the dissertation is
arsenic triphosphide with four atoms and 78 electrons. Ab initio methods such as
MP2 scale as N5 and CCSD scale as N7 in computational time with number of
electrons. 12 These methods offer better results than DFT for gas phase
structures of loosely bound dimers. Density functional theory (DFT) is a powerful
theory that has a celebrated history of predicting the structure of transition metal
complexes and scales more favorably with number of electrons, N4. The
diversity in DFT approaches center around the different ways to handle electron
correlation. An assumption of DFT is that the electron density does not vary
rapidly and the gas phase dimers are poorly described by this assumption. In
this dissertation several chemical systems are studied and where possible DFT
and ab initio methods are compared to experimental results. All of the
calculations performed used the Gaussian 03 or Gaussian 09 suite run on the
Marin and Ice clusters located at the University of Arizona. Details of the specific
calculations are given in the respective chapters.
The goal of the calculations performed before an experiment is to produce
coordinates for the nuclei in a molecule. The moments of inertia can be
53
produced from the coordinates of the atoms and the masses. First the center of
mass is determined and the coordinates are then produced from the origin
placed at the center of mass. The principle axes of the system can be
determined by diagonalizing the moment of inertia matrix.
Once the moments of inertia are determined for the principle axes, the
rotational constants can be determined. The symmetric and asymmetric top
spectra are known combinations of the rotational constants. The program
SPCAT can be used to generate the spectrum from the rotational constants.
This prediction will be the starting point for all the molecules reported in this
dissertation.
3.3 Structure fits
The primary objective of the spectroscopy performed in this dissertation is to
determine detailed information about the gas phase structure through isotopic
substitution. The most powerful tool for determination of optimized parameters of
a molecule is the method multiple regression.
A least squares approach has been implemented in the fortran program
STRFT and an example is given in Appendix 9.3.. The geometry is constructed
from either calculations or literature values and angles and distances of interest
are parameterized. An iterative method is performed to find the best values of
the parameters. These optimized values when used to generate the structure,
54
represent the best fit to the experimental rotational constants. The standard
deviation is reported as
σ=
∑Y
i
− Ycalc
i
N−p
(3.11)
Yi is the set of experimental rotational constant, N is the number of
rotational constants and p is the number of parameters. Two subprograms fita2.f
and rotsub.f must be compiled with the program. The program fita2.f is used to
generate the best value of the parameters and correlation matrix. This is done
by generating an error matrix, labeled C in the program. This matrix is
diagonalized and subtracted from the parameters and runs again. The number
of iterations is determined by the user. Rotsub is a program that generates the
rotational constants from the new coordinates that are generated from the refined
parameters and isotopic substitutions.
The output is generated in two files, the geometry is in fort.10. The output
file contains the final parameter values and the residual value from the fit of each
rotational constant. The sum of squares is the numerator in equation 3.11.
55
4. HYDROGEN BONDED HETERODIMERS
4.1 Introduction
Hydrogen bonds play key roles in biological and chemical processes. The
experimental determination of gas phase structures which involve hydrogen
bonds can help provide benchmark systems that can be utilized to evaluate and
improve theoretical models. Hydrogen bonding interactions have substantial
effects on phase transition temperatures, conformations, and interactions of
proteins and nucleic acids. The recognition of hydrogen-bonded base pairs for
DNA is essential to the replication, transcription and translation of the genetic
information. An understanding of the dynamics of hydrogen bonding at the
quantum level may even shed some light on the nature of genetic mutations13.
The secondary and tertiary structure in protein folding is largely determined by
hydrogen bonding and other weak interactions between the amino acids chains.
Gas phase dimers have been studied using microwave spectroscopy to
investigate model systems that may help theoretical efforts that are aimed at
understanding the structure and dynamics of hydrogen bonding. The dimers
studied include: Formic Acid-Formamide, Formic Acid-Propiolic Acid, Formic
Acid-Acetic Acid and Formic Acid-Benzoic Acid. Partial Gas phase structures
were determined for Formic Acid-Formamide, Formic Acid-Propiolic Acid. A
summary of the experiments performed with Formic Acid-Acetic Acid and Formic
Acid-Benzoic Acid is given at the end of the chapter.
56
4.2 Formamide-Formic Acid Dimer
4.2.1 Introduction
Microwave spectroscopy has a well documented history14 of providing
accurate, detailed gas-phase structures of small molecules. The complete
substitution structures for both of the monomers, formic acid15 and formamide16
have been published, and observations of structural changes occurring upon
forming a complex can provide valuable additional information on hydrogenbonding dynamics in the Formamide-Formic Acid (FM-FA) complex. Gas-phase
carboxylic acid-pairs have been studied previously using microwave and infrared
spectroscopy. These pairs include: formic with formic acid17, trifluoroactetic with
acetic and with trimethyl acetic acid18 and trifluoroacetic acid with formic and with
acetic acid19. Formamide has been extensively studied as a monomer20 and also
as a hydrogen-bonded complex with water and methanol21. The FM-FA
heterodimer was discussed in previous literature, particularly with respect to
computational work using DFT and ab initio methods.22,23. However, to the best
of our knowledge, the microwave spectrum for this complex has not been
measured. We have found that maintaining two sample cells (one for each
57
________________________________________________________________
Figure 4.1. Formamide-Formic Acid complex. The angle β is the sum of the
∠ (C-O-H) = 106.8˚ for the monomer plus the deviation γ from the structure fit,
The fifth variable, η, is not shown, it is the z-component (out of plane coordinate)
of H2.
58
monomer) in series, at different temperatures, enabled the formation of the
complex in sufficient quantities to facilitate successful microwave measurements.
Formic acid is the simplest carboxylic acid and formamide is similar to the
“backbone” in polypeptides. Hopefully, the study of the FM-FA complex can
provide information which will be helpful in analyzing the structure and energetics
of proteins and nucleic acids and provide potential parameters for semi-empirical
modeling programs.
We report the gas phase measurements of six isotopologues of the
formamide-formic acid (FM-FA) hydrogen-bonded heterodimer using microwave
spectroscopy measurements over the range of 5 to 15 GHz. These
measurements were used to determine structural parameters which were then
compared with the results of MP2 and DFT calculations. The present
experimental results for the FM-FA complex provide constraints and data to
evaluate recent theoretical calculations to predict the binding energy, structure
and the possibility of a formic-formamidic acid tautomer22. Another theoretical
paper24 discussed the proton exchange associated with the tautomerization of
formamide to formamidic acid. A search for the formic-formamidic acid complex
based on theoretical predictions for the structure of the second tautomer was
conducted, without finding evidence for this tautomer. This search was not
exhaustive and the possibility of finding this tautomer cannot be ruled out.
59
Figure 4.2 Gas phase structure calculated using MP2/6-311++G** for the
dimer between formamide-formic acid.
60
4.2.2 Calculations
Ab initio (MP225, CCSD26) and Density Functional theory27 (DFT) calculations
were performed to determine the optimum geometry for the FM-FA complex
using the Gaussian 03 suite28. The published, gas-phase monomer geometries
for formic acid and formamide were used to determine a starting geometry for the
calculations, but all internal coordinates were allowed to vary to determine the
optimized structure. Binding energies were calculated using the counterpoise
correction developed by Boys and Bernardi29. All calculated values were
determined using Pople’s 6-311++G**30 basis set as described by Hazra, et al,22
who found binding energies similar to the present results. Rotational constants
and key structural parameters determined using these methods are shown in
Table 4.1.
61
Table 4.1 . Predicted and experimental values for molecular geometry
parameters, rotational constants and quadrupole coupling constants using 6311++G**._____________________________________________________
R(O1··O2) (Å)
TPSSTPSS HCTH407 B3PW91
2.64
2.74
2.64
R(O3··N) (Å)
2.86
3.03
2.88
R(O3··H1) (Å)
1.85
2.04
1.88
R(O1··H4) (Å)
1.62
1.74
1.63
(C-O-H)
111.4º
110.9º
111.5º
A (MHz)
5793.624
5862.57
5906.2
B (MHz)
2170.317
2013.782
2164.74
C (MHz)
1578.868
1498.911
1584.13
eQqaa (MHz)
1.14
1.36
1.18
eQqbb-eQqcc
(MHz)
5.59
5.76
5.56
-0.0001
-0.0003
-0.0001
I (amu Å2)
a) ∠ (C-O-H) = 106.8˚ for HCOOH monomer15
62
Table 4.1 cont._________________________________________
CCSD
R(O1··O2) (Å)
MP2
2.68
2.71
Experiment
2.78
R(O3··N) (Å)
2.93
2.96
2.75
R(O3··H1) (Å)
R(O1··H4) (Å)
(C-O-H)
1.93
1.69
109.7º
1.98
1.73
109.9 º
5901.792
1.8
1.78
121.3º
A (MHz)
5861.012
5889.465(2)
2065.473
B (MHz)
2104.76
2148.7409(7)
1531.598
C (MHz)
1550.185
eQqaa (MHz)
1.22
eQqbb-eQqcc
(MHz)
5.47
2
ΔI (amu Å )
-0.3277
1575.1234(6)
1.38
5.89
-0.3425
1.02(1)
4.98(2)
-0.158
Density functional theory has been shown to predict binding energies and
geometries for strongly bound complexes reasonably well using appropriate
adapted functionals31. TPSS32, HCTH40733 and B3PW9134 were used in the
present work and found to predict the rotational constants to within 1-2% and
quadrupole coupling constants to within 15-65%. The DFT calculations, using
this basis set, predict a planar dimer structure which was not observed in this
study. The ab initio methods (MP2-CCSD) used in this study predict a dimer
structure where the formamide is not planar. The N atom is lifted out of the plane
by c = 0.07 Å and the H2 and H4 coordinates are decreased by 0.1 Å. The
resulting difference in the N and H2 c-coordinates is 0.17 Å, similar to the trend
63
from the structural fit. These findings are also reflected in the inertial defect (ΔI)
values.
The results of the MP2/6-311++G** calculations for the Mulliken atomic
charges are summarized in Table 4.2, for the monomers and the dimer.
Table 4.2. Comparison of Mulliken charges on the atoms calculated for the
monomer and the complex using MP2/6-311++G** in units of (e).
Atom
Monomer
Complex
N
- 0.43
- 0.56
O1
- 0.46
- 0.56
C1
0.23
0.29
H1
0.28
0.41
H2
0.26
0.27
H3
0.11
0.14
C2
0.35
0.25
O2
- 0.26
- 0.41
O3
- 0.38
- 0.47
H4
0.29
0.45
H5
0.00
0.16
It is clear from these values that there is a significant redistribution of charge in
the monomers on complex formation. This charge redistribution is the most likely
64
cause in the reduction in N quadrupole coupling strength for the dimer. Both
molecules remain neutral in the dimer so there is no significant charge transfer
predicted.
4.2.3 Experimental
Formic Acid (88%) was purchased from Alfa Aesar.
14
N-formamide, from
Pierce Laboratories, was obtained from the Miesfeld laboratory at the University
of Arizona and used without purification. H13COOH, HCOOD, DCOOD and
H215NCHO were purchased from Cambridge Isotope Labs and used without
purification. DCOOH was made by placing equal amounts of HCOOH with
DCOOD and placing the mixture into a sample cell.
The samples were placed in two custom glass holders and maintained at
different temperatures. The sample holders contained two stopcocks that
allowed evacuation and ease of fitting the samples together to maintain
temperatures. Each sample was evacuated below 1 torr and held at liquid
nitrogen temperature when connected to the spectrometer. They were then
allowed to come to their respective temperatures slowly with neon added to 0.81.0 atm. Neon was passed over the formic acid held at 0˚C and allowed to mix
with formamide maintained at 80˚C. The resulting mixture was introduced into a
Flygare-Balle35 microwave spectrometer using a general valve pulsed at 2 Hz.
The main cavity chamber was maintained at 10-6 to 10-7 torr, and a homodyne
detection system was employed, as described elsewhere36. The formamide and
65
formic acid monomer spectra have been well characterized and care was taken
to assure that the monomer line intensities were optimized.
4.2.4
Data Summary
The transitions were measured from 5 to 15 GHz for the first isotopologue
studied, H12COOH-H214NCHO. Quadrupole splittings of the asymmetric top
transitions were observed since IN=1. A total of 59 transitions were recorded
involving 12 asymmetric top a-type dipole and b-dipole rotational transitions and
are listed in Table 4.3. The quadrupole hyperfine structure was completely
absent, as anticipated, for the isotopologues involving H215NCHO, leaving only
the single-line asymmetric top transitions, which are listed in Table 4.4.
The transitions for all isotopologues were fit using the SPFIT37 program in
the S-reduced representation and results are given in Table 4.5. Transitions for
all the isotopologue combinations were quickly found by scaling the calculated
rotational constants using the ratios of the experimental rotational constants
found for the first isotopologue to the calculated rotational constants as predicted
using MP2. The three rotational constants, A, B and C, quadrupole coupling
constants, eQqaa , eQq bb , eQqcc and distortion constants, DJ, DJK and DK , were
determined in the fit for H12COOH-H214NCHO. There were not enough
transitions measured to fit the distortion constants of the H13COOH-H214NCHO
complex. For these fits the distortion constants were fixed to the H12COOHH214NCHO (normal isotopologue) values. The measured transitions are given in
66
Table 4.3 and the results of the two fits with 14N are summarized in Table 4.6.
Both a-type and b-type transitions were measured and could be observed with a
single beam pulse. The predicted dipole moments are μa=2 D and μb=2 D using
MP2/6-311++G** calculations.
The least squares structure fit was initially performed using three
adjustable parameters. Each monomer was allowed to rotate, by angles φ and θ,
about their respective centers of mass and the distance between the centers of
mass, RCM was optimized to obtain the best fit to the measured rotational
constants. The parameters are shown in Figure 4.1 and summarized in Table
4.7. The starting geometry was the orientation predicted using the MP2/6311++G** calculations. The fit was significantly improved by including a fourth
variable parameter γ. This parameter represents a deviation from the gas phase
monomer angle. The total angle then becomes this value plus the gas phase
monomer angle determined ∠ (C-O-H) for formic acid. The optimum value was
determined to be 14(2)˚. When added to the monomer gas phase angle of 107˚
this gives a total ∠ (C-O-H) = 121˚ for the complex. Using the rotational
constants, the inertial defect was determined to be Δ = -0.158 amu Å2 and a fifth
parameter was used in the fit that ultimately gave us a fit standard deviation of
0.42 MHz. This fifth parameter is the z-coordinate (out of plane deviation) for the
proton on the formamide nitrogen, (H2). The value obtained in the fit was 0.27(4)
Å, giving an angle of 15° out of the plane of the remaining atoms in the complex
for the N-H bond. Based on the results from the CCSD calculation, an additional
67
fit was performed that used the fifth parameter,η, to add to the c coordinate of H2
and H3 in formamide and subtract from N. The standard deviation is slightly
lower 0.41 MHz and is consistent with the prediction made by the CCSD
calculation. The other parameters in the fit were left unchanged. These
coordinates are summarized in Table 4.8. Both fits are consistent with a nonplanar structure of formamide in the FM-FA dimer.
The monomer center of mass separation distance, RCM was determined to
be 3.118(4) Å and the angles of rotation from the calculated orientation are both
positive (clockwise) with values of θ = 3.1(7)° and φ = 4.9(7)° for formic acid and
formamide respectively, as summarized in Table 4.7 and shown in Figure 4.1.
The other angles and distances were fixed to the monomer gas phase structure
values. This fit yielded a O3··H1 distance of 1.78 Å and H4··O1 distance of 1.79
Å, which differs from the predicted structure. All the methods used in this study
predict an asymmetric structure with O3··H larger than H4··O1 by about 0.2 Å. A
Kraitchman analysis was carried out using the singly substituted isotopologues to
obtain principal axis coordinates for N, C2, H4 and H5 and the results are listed
in Table 4.8. Also included in Table 4.8 are the principal-axis Cartesian
coordinates from the structural fit and from the ab-initio calculations. The a and b
coordinates of these atoms from the Kraitchman analysis are in excellent
agreement with the corresponding values from the structure fit. The coordinates
from the structure fit of 1.53 Å and -1.08 Å for nitrogen are consistent with
kratichman-determined values of 1.5(4) Å and 1.1(3) Å. It is important to note
68
that the b coordinate of H4 from the structure fit of 1.30 Å is in excellent
agreement with the value 1.3(1) Å from the Kraitchman analysis. This provides
excellent support for the reliability of the ∠ (C-O-H) and γ = 14(2)˚ from the
structure fit.
4.2.5 Discussion
The formamide-formic acid complex has been considered a model system
studied by computational chemists, and now gas phase structural parameters
have been determined. The results presented here are consistent with a strongly
bound dimer with two hydrogen bonds of less than 2 Å bond length. Heavy atom
distances of R(O3-N) of 2.78 Å and R(O2-O1) of 2.75 Å were obtained from the
least squares analysis. These distances are very close to the Formic AcidTrifluoroacetic Acid R(O-O) distances of 2.700 Å and 2.702 Å19.
Density functional theory and ab initio calculations provided rotational
constants and quadrupole coupling constants consistent with the gas phase
measurements when using the 6-311++G** basis set. DFT and ab-initio
predictions for the geometry provided very similar results and indicate a strongly
bound dimer but predicted a planar complex. Calculations given in the
literature22 also indicate a strongly bound dimer with a reported binding energy of
43 kcal/mol and this value was obtained by our calculations using Gaussian 03.
The change in geometry of formic acid on complex formation is interesting
and larger than the value reported by Martinache, et al19 for the formic acid-
69
trifluoroacetic acid complex. In their paper the ∠ (C-O-H) of formic acid was
increased from 106 in the monomer to 109 in the complex. The present
structural results indicate that this angle is greater and may be due to the larger
structure of formamide, however the calculations do not predict this big of a
change in the formic ∠ (C-O-H). The increase in the angle is supported by the
excellent agreement of the b coordinates for H4 from the fit and the Kraitchman
analysis. It is important to note that the Kraitchman-derived coordinates are not
subject to the possible correlation errors in the structure fit values associated the
fixing of other atom coordinates. The two independent methods of determining
the coordinates offer a good check to support the larger value for ∠ (C-O-H)
found in formic acid in this complex.
Comparing the difference in the eQqcc values of the formamide monomer
and that of the complex reveals a decrease in magnitude of 0.8 MHz from the
monomer value of -3.848 MHz reported in Kukolich, et al20 and the value
reported here of -3.00 MHz. The formamide monomer structure is described by
Constain, et al16 as having the N-CHO fragment most likely planar with a shallow
pyramid on the H2N portion of the molecule. This is in agreement with our
structure for formamide in the complex. Compared with the monomer, there was
a 20% decrease in the quadrupole coupling strength along the c-axis. Analysis
of the structures indicates that the original c-axis of the formamide monomer
coincides with the c-axis of the FM-FA dimer to with in a few degrees, so this
rotation is an unlikely cause for the eQqcc reduction in the complex. It is more
70
likely due to modification of the electronic structure of formamide in the complex.
We speculate that the complex may draw some electron density to the nitrogen
from the H1 proton, which changes the electric field gradient at the nitrogen
nucleus. This is supported by present calculations which predict a similar
reduction from -4.09 MHz for the monomer to -3.44 MHz for the complex. The
most likely cause of this reduction is the significant redistribution of charge on
complex formation as discussed above (Section II) and shown in Table 2.
In conclusion, the formamide-formic acid gas phase dimer has been
observed. Six isotopologues have been fit and the data was used to perform a
least squares analysis of the gas phase structure. This has provided important
structure information about the complex.
71
Table 4.3. Rotational transition frequencies measured for the normal
isotopologue, HCOOH-H214NCHO, and H13COOH-H214NCHO with deviations
from the best fit values (o-c = observed - calculated) in MHz.______________
JKaKc’
212
212
212
212
212
202
202
202
202
202
111
111
111
413
413
413
303
303
303
303
211
211
211
211
211
514
514
514
313
313
313
212
212
F’ JKaKc” F”
1
111 1
3
111 2
2
111 1
1
111 0
2
111 2
1
101 1
3
101 2
2
101 1
1
101 0
2
101 2
0
000 1
2
000 1
1
000 1
4
404 4
3
404 4
5
404 5
3
212 2
4
212 3
2
212 1
3
212 3
1
110 0
2
110 2
3
110 2
2
110 1
1
110 1
5
505 5
6
505 6
4
505 4
4
212 3
3
212 2
3
212 3
1
101 1
3
101 2
H12COOH-H214NCHO
observed
o-c
6872.826
-0.001
6873.959
0.001
6874.328
0.001
6874.328
0.012
6874.922
-0.001
7386.071
-0.002
7386.624
0.004
7386.752
-0.001
7386.839
0.005
7387.056
-0.001
7463.582
-0.001
7464.474
-0.003
7465.068
-0.004
7592.602
0.002
7593.164
-0.002
7593.885
0.007
7703.412
0.002
7703.760
0.003
7704.074
-0.003
7704.371
-0.003
8020.289
-0.004
8020.656
0.006
8021.292
0.004
8021.563
0.013
8022.539
-0.004
9770.561
-0.003
9771.942
-0.008
9772.236
0.004
10274.699
-0.003
10274.850
-0.006
10275.817
-0.003
10613.778
-0.006
10614.621
-0.003
H13COOH-H214NCHO
observed
o-c
6784.644
-0.002
6785.778
-0.001
6786.147
0.010
6786.147
-0.002
6786.744
-0.002
7286.049
-0.001
7286.599
0.002
7286.729
0.002
7286.815
0.001
7287.029
-0.003
7444.652
0.001
7445.546
0.000
7446.141
-0.001
72
Table 4.3 cont._________________________________________________________
JKaKc’
212
212
303
303
303
303
303
303
322
322
322
322
322
322
321
321
321
321
312
312
615
615
615
414
404
404
F’ JKaKc” F”
2
101 1
2
101 2
2
202 2
2
202 2
4
202 3
4
202 3
3
202 2
3
202 2
2
221 1
2
221 3
4
221 3
3
221 3
2
221 2
3
221 2
2
220 1
4
220 3
3
220 2
2
220 2
2
211 1
4
211 3
6
606 6
7
606 7
5
606 5
5
313 4
5
303 4
4
303 3
H12COOH-H214NCHO
observed
o-c
10615.306
0.022
10615.577
-0.011
10931.104
-0.005
10931.109
0.001
10931.768
0.007
10931.768
0.007
10931.926
-0.015
10931.947
0.006
11171.136
0.003
11171.320
0.006
11171.320
0.006
11171.320
0.006
11171.640
0.000
11171.640
0.000
11410.930
0.012
11411.051
-0.012
11411.220
-0.001
11411.590
-0.007
11991.305
-0.014
11991.486
0.001
12527.955
0.001
12529.395
0.003
12529.633
-0.002
13637.244
-0.005
14322.368
0.007
14322.577
0.005
73
Table 4.4. Measured rotational transition frequencies (MHz) for four isotopologues of HCOOHH215NCHO. The first group is a-dipole transitions and the second b-dipole transitions.
Transition
HCOOH-H215NCHO
HCOOD-H215NCHO
J’KaKc
J”KaKc
Observed
o-c
Observed
o-c
212
111
6799.902
-0.001
6768.088
-0.001
202
101
7308.258
0.001
7279.844
0.010
211
110
7938.745
-0.002
7919.704
-0.015
313
212
10163.495
-0.002
10114.064
0.006
303
202
10814.156
-0.001
10764.585
0.002
322
221
11053.855
0.002
-
-
321
220
11293.682
0.008
312
211
11867.610
-0.003
11836.986
-0.001
414
313
13488.952
-0.002
-
-
404
303
14165.802
-0.003
14089.518
-0.003
423
322
14690.757
0.011
-
-
432
331
14848.938
-0.007
-
-
111
000
7365.504
0.003
-
-
212
101
10480.722
-0.002
10343.812
-0.002
303
212
7641.690
-0.001
7700.605
0.002
413
404
7510.392
-0.001
7471.072
0.005
514
505
9676.015
0.000
9676.944
-0.002
-
74
Table 4.4 cont.____________________________________________________
Transition
DCOOH-H215NCHO
H13COOH-H215NCHO
J’KaKc
J”KaKc
Observed
o-c
Observed
o-c
212
111
6590.311
-0.016
6712.190
-0.001
202
101
7070.478
0.009
7208.761
0.000
211
110
7656.042
-0.017
7820.259
0.000
313
212
9853.999
0.003
10034.020
0.000
303
202
10477.176
-0.003
10673.389
0.001
322
221
-
-
10899.209
0.007
321
220
-
-
11125.141
-0.003
312
211
11449.300
0.020
11692.346
0.000
414
313
13084.273
0.008
13319.737
0.000
404
303
13747.380
-0.014
13991.296
0.000
423
322
-
-
-
-
432
331
-
-
-
-
111
000
-
-
7346.539
-0.002
212
101
10349.011
0.006
10425.603
-0.002
303
212
7198.645
0.002
-
-
413
404
7297.908
-0.003
7420.055
-0.001
514
505
-
-
9512.998
-0.001
75
Table 4.5. Experimental rotational constants (MHz) and centrifugal distortion
(kHz) constants. Values in square brackets [ ] were held constant.________
Isotopologue
H12COOH –
H214NCHO
H12COOH –
H215NCHO
H13COOH –
H215NCHO
A
5889.466(2)
5807.886(3)
5807.006(1)
B
2148.7409(7) 2127.056(1) 2093.5867(4)
C
1575.1234(6) 1557.628(1) 1539.5470(3)
DJ
0.66(3)
0.68(3)
0.665(9)
DJK
5.7(1)
5.24(9)
5.3(2)
DK
0.185(5)
0.20(2)
0.188(4)
N
σ
59
6
17
4
12
1
76
Table 4.5 cont.____________________________________________________
Isotopologue H12COOD –
H215NCHO
D12COOH – H13COOH –
H215NCHO
H214NCHO
A
5699.64(1)
5805.93(3)
5888.721(2)
B
2123.898(3)
2047.24(1)
2115.121(1)
C
1548.077(2) 1514.369(6) 1556.941(3)
DJ
0.57(7)
0.6 (1)
DJK
7(1)
3(2)
DK
0.19(3)
0.3(2)
-
N
σ
11
6
11
11
12
3
[0.66]
[5.7]
77
Table 4.6. Experimental rotational and quadrupole coupling constants for
H12COOH-H214NCHO and H13COOH-H214NCHO in MHZ, except for N(number of
lines) and σ._____________________________________________________________
HCOOH-
H13COOH-
H214NCHO
H214NCHO
A
5889.465(2)
5888.721(2)
B
2148.7409(7)
2115.121(1)
C
1575.1234(6)
1556.941(3)
eQqaa
1.014(5)
1.01(1)
eQqbb
1.99(1)
1.99(3)
eQqcc
-3.00(1)
-3.01(3)
N
59
12
σ/ kHz
6
3
Parameter
78
Table 4.7. Best fit-results for the adjustable parameters used in the structure fit.
Parameter
Value
θ
3.1(7)˚
φ
4.9(7)˚
R
3.118(4)Å
γ
14(2)˚
η
0.08(1) Å
σ
0.41 MHz
79
Table 4.8. Coordinates determined by least squares structure fit, Kraitchman
analysis and as predicted by CCSD in Å.______________________________
Structure Fit
Kraitchman
Atom
a
b
c
|a|
|b|
|c|
N
1.55
-1.07
0.04
1.5(4)
1.1(3)
-
O1
1.19
1.16
0.00
-
-
-
C1
1.95
0.24
-0.02
2.0(6)
0.11(4)
0.022(7)
H1
0.57
-1.28
-0.03
-
-
-
H2
2.22
-1.81
-0.13
-
-
-
H3
3.04
0.37
-0.10
-
-
-
C2
-1.96
-0.18
-0.00
-
-
-
O2
-1.55
1.07
0.01
-
-
-
O3
-1.23
-1.17
-0.02
-
-
-
H4
-0.58
1.30
0.01
0.59(5)
1.3(1)
0.046(4)
H5
-3.06
-0.22
0.00
3.05(6)
0.135(3)
0.112(2)
80
Table 4.8. Cont.___________________________________________________
CCSD/6-311++G**
Atom
a
b
c
N
1.65
1.10
0.07
O1
1.20
-1.14
-0.02
C1
1.99
-0.20
-0.04
H1
0.66
1.34
0.05
H2
2.34
1.80
-0.08
H3
3.08
-0.38
-0.13
C2
-1.97
0.16
0.00
O2
-1.51
-1.08
0.03
O3
-1.31
1.17
-0.05
H4
-0.52
-1.06
0.02
H5
-3.07
0.17
0.02
81
4.3 Propiolic Acid-Formic Acid Dimer
4.3.1 Introduction
Hydrogen bonding interactions have substantial effects on phase
transition temperatures and conformations and interactions of proteins and
nucleic acids. In DNA the hydrogen-bonded base pair recognition is the key to
the transcription and translation of the genetic messages. This recognition relies
on specific doubly and triply hydrogen-bonded base pairing interactions. The
suggestion that the hydrogen bonded protons could tunnel between base pairs
may play an important role in mutagenisis has been discussed by Löwdin38 and
Catala´n and Kasha39. Calculations of concerted proton tunneling in hydrogenbonded base pair interactions are reported by Scheiner and Kern40 where they
describe the concerted proton tunneling as “a simultaneous and synchronous
motion of two protons” in a double-well potential. This concerted proton
tunneling has been studied experimentally for the formic acid dimer by Havenith,
et al41,42,43. High resolution IR spectroscopy of the formic-formic dimer has
revealed that (DCOOH)2 has a spectrum that can be fit to four sets of rotational
constants and it has been proposed that two pairs are for the upper and lower
levels of splittings due to tunneling in the double well potential for both the
ground and first excited vibrational state. The dimer between propiolic acid and
formic acid (Prop-FA) is a similar system that should exhibit tunneling properties
of the formic acid dimer. The microwave spectrum of the gas phase dimer
82
between (Prop-FA) has been measured from 1-20 GHz using pulsed beam
microwave spectroscopy and indeed we report two sets of rotational constants
for the ground vibrational state for both the parent and carbon-13 formic acid with
propiolic acid.
The (Pro-FA) system has a permanent electric dipole and is predicted to
be a prolate top with an a-dipole moment of 0.82 D and b-dipole of -0.10 D.
Calculations of double well potentials in the literature are quite extensive 44,45,46,
but to our knowledge no published results on this system are available. The
model of the proton motion has been the subject of debate in theoretical
approaches. A concerted proton exchange is a possible mechanism and we
report calculations that estimate the potential well with a barrier height reached
with the protons equidistant from the two opposting oxygen atoms.
The rotation-vibrational interaction has been studied by Herb M. Pickett47
using rotating axes and solutions that couple the two vibrational states have been
implemented in his program SPFIT48. The formulism has been extended by
Turner, et al.49 and applied to malonaldehyde and by Tanaka50 to tropolone. This
analysis can be used to fit the parameters ΔE01 and Fc, the difference in energy
between the ground and first excited state and the coefficient of interaction
amongst the ground and first vibrational state μab·(PaPb+PbPa), respectively.
83
Figure 4.3 Calculated structure of the dimer between Formic Acid –PropiolicAcid using MP2/6-311++G**
84
4.3.2 DFT and Ab-initio calculations
Density functional theory and MP251 calculations were performed to
estimate the binding energy, gas phase structure and energy barrier to proton
exchange. Table 4.9 gives the results of the predicted rotational constants and
key structural parameters by method. The calculations were done using the
Gaussian 0352 suite running on the University of Arizona ICE high performance
computing cluster.
Using MP2/6-311++G**the binding energy, removing basis set
superposition error, an estimate of the binding energy in the Formic-Formic dimer
was determined, -56.9 kJ/mol and compared to the Prop-FA dimer that was
calculated to be -58.1 kJ/mol. Density functional theory methods B3LYP53,
B3PW9154, HCTH40755 and TPSSTPSS56 were also used to compute gas phase
structures and compute vibrational frequencies.
To obtain an estimate for the energy barrier to proton exchange, the
(TS,calcFC) option was used with the keyword opt using the Gaussian program
with the results in Table 4 using B3LYP, B3PW91 and MP2. The procedure used
the starting point from optimized structure obtained while performing. Steps of
0.10 Å were made with the OH bond on propiolic acid and the OH formic acid
was stepped within each value to construct a 2D potential energy surface. One
of the settings converged to a structure that has R(O—O) at 2.4 Ǻ with the proton
at 1.2 Ǻ in the middle. The energy difference between the equilibrium energy
85
and at proton equidistant point was obtained and used as an estimate of the
barrier height of a two well potential. These values compare very well with the
formic-formic dimer (reference here). Higher levels of theory were also used,
MP2/aug-cc-pVDZ and CCSD57/6-311++G** and compared to the experimentally
determined rotational constants and structure.
4.3.3 Experimental Methods
4.3.3.1
Experiments at the University of Arizona
Measurements in the frequency range of 1 to 14 GHz were done using
two pulsed beam Fourier transform microwave spectrometers. Measurements in
the 4 to 14 GHz range were performed using a conventional spectrometer
discussed previously58. To prepare the sample for microwave experiment, the
sample cell was loaded onto the spectrometer sample chamber and
subsequently placed into a liquid nitrogen bath to freeze the liquid sample. This
cell was then evacuated, charged to 1.2 atm with neon, and allowed to come
to -10˚C. The temperature of -10˚C was then maintained by placing the cell in a
bath with an ethanol/water mixture and dry ice. Propiolic acid and formic acid
seeded in neon were introduced into the spectrometer cavity transverse to the
microwave cavity axis at 2 Hz pulse rate, using a pulsed valve (General valve
series 9). The pressure inside the spectrometer chamber was maintained at 106
-10-7 Torr prior to the valve opening and the backing pressure of neon was kept
at about 0.9 to 1.2 atm during the frequency scanning. Following the molecular
pulse (about 1 ms delay), a π/2 microwave excitation pulse (1μs duration) was
86
injected into the resonator to coherently excite the molecules, using a Herley
SPDT microwave switch. The molecular FID signal was transmitted via the same
SPDT switch, passed to a Miteq 6-18 GHz low noise amplifier, and sent to the
RF circuit for further signal processing. Initially, the samples were kept in
separate cells and each monomer spectrum was observed while the other was
frozen out with an optimum signal observed for both ~-10˚C. Given the similar
properties of the acids, we added both samples to the same cell and obtained all
the isotopic data using a single cell.
4.3.3.2
Experiments at the University of Virginia
he experimental setup consisted of a Balle-Flygare type Fourier transform
microwave spectrometer59 based on the recent NIST60 design. The carrier gas
(80/20 Ne/He) was passed through a steel sample cell placed outside the
vacuum chamber which contained 4:1 mixture of propiolic acid to formic acid.
The nozzle (General Valve series 9, 1mm orifice) was heated to 50 °C.
FTMW-pusled-MW double resonance spectroscopy was used to aid in the
assignment of the pure rotational transitions and to locate the much weaker
tunneling-rotation splittings. It is analogous to the work by the Endo group where
the second microwave source is used to destroy the coherence of the monitored
rotational transition61. The timing was set up such that the second microwave
pulse (~5 μs duration) followed directly (500 ns delay) after the cavity microwave
pulse (4 μs duration). A 1 Watt power amplifier (DBS) was used to amplify the
87
cavity microwave pulse for optimal excitation for the low dipole moment tunneling
transitions (b-dipole transitions), see Figure 3.
The dipole moment was determined using a chirped-broadband spectrometer62
with a stark cage63 that was calibrated with OCS (0.1% in H2/Ar) at 12kV giving a
field of 464.4 V/cm. The propiolic acid-formic acid sample was the same as
described above.
4.3.4 Data Analysis and Results
4.3.4.1
Microwave Spectrum
The propiolic acid-formic acid dimer is a prolate asymmetric top which
exhibits splittings of the rotational transitions due to proton tunneling effects. The
a-dipole spectrum consists of pairs of transitions that are separated between 1 to
3 MHz with splittings which depend on the difference in rotational constants for
the two tunneling vibrational states. 138 a-dipole transitions were observed for
HCOOH···HOOCCCH. These provide information on the A, B and C rotational
constants and centrifugal distortion constants for the upper and lower tunneling
states. 28 b-dipole combination transitions, which connect different tunneling
vibrational states, were ultimately fit in a combined fit using Herb Pickett’s
SPFIT64 with Watson’s A representation, see Table 4.10 for a summary and
Table 4.13 for the frequencies measured. The Coriolis term, Fc·(Pa Pb+ Pb Pa),
where Fc is a constant and ΔE01 were adjustable parameters in this fit.
88
Using the ab ninitio barrier heights and difference energy spacing, the
equilibrium coordinate for the tunneling proton position can be obtained and is
given in the results.
The C-13 formic substituted isotopomer spectrum also consisted of pairs of lines
with similar spacing as the parent and only a-type dipole transitions were
recorded and are summarized in Table 4.14. The C-13 isotopically enriched set
of data also contains two distinct spectra. Centrifugal distortion constants were
fixed to the parent values and a good fit to the rotational constants was obtained.
Only one set of rotational constants were observed for the isotopes that
contain deuterium substitution for either, or both protons 1 and 2. The transitions
are summarized in Table 4.15. A search of another set of possible splitting of
these transitions was performed and not observed. The b-type transitions were
observed and found to fit a ground state only spectrum. The transitions were fit,
see Table 4.11, with the “center of gravity” of the unresolved deuterium splitting
assigned to the transition frequency. The weak signal obtained with the
isotopomer DCOOH···HOOCCCH is thought to be the reason that the second set
of rotational constants were not observed for this isotopomer.
4.3.4.2
Structure Determination
A structural fit from the 12 B and C rotational constants obtained from the
6 isotopomer combinations given in Tables 4.9 and 4.11 was performed with
three parameters. The parameters used in the least-squares regression analysis
89
were the monomer’s centers of mass separation, Rcm, and rotation angle for
formic monomer about its centers of mass,θ, and the deviation <(C-O4-H2)
angle on formic acid, ε (see Figure 4.4). The gas phase structures of propiolic
and formic acid monomers pointing at each other were used as the starting point
for the structural analysis.
The structural fit indicates that the <(C-O-H) on both carboxylic acids may
open up from the monomer angles of 106°. The deviation from the monomer
formic acid angle <(C-O4-H2), ε , was used in the fit. The propiolic acid angle
<(C-O1-H1) was stepped in 2 degree increments and a structure was obtained
and a summary of the results are in Table 4.16. When the propiolic acid angle is
held at the monomer value of 106° <(C-O4-H2),) angle was fit to 118°. Using
109° for the <(C-O1-H1) angle and 109° for the <(C-O4-H2) angle gives a σ=1.7
MHz. Interestingly, the lowest standard deviation, 0.3 MHz, is obtained in a four
parameter fit with the deviation, φ , from the monomer angle <(C-O1-H1) of
propiolic acid. The result is that the proton rotates almost 180° in the ab plane.
The coordinates are consistent with the absolute values of obtained in the
Kraitchman analysis given in Table 4.17. In Fit I with the fixed . <(C-O1-H1)
angle, the coordinates obtained in the structure fit are very different than
obtained with the Kraitchman analysis for a coordinate of the H1 atom. The
structure that results from Fit I that is summarized in Table 8 gives a symmetric
(O1-H1··O3) and (O2··H2-O4) distances of 1.65 Å.
90
Isotopic substitution on H3 would help the structure fit by adding
information about the propiolic acid orientation in the dimer. Efforts are
underway to exchange on H3 and obtain the spectrum.
4.3.4.3
One Dimensional Potential Well
The two-well potential is a famous problem and if modeled using a
potential of the form V=a*X4+b*X2, the energy levels can be solved using Kisiel’s
ANHARM65 program that is based on the work of Laane. The double well’s
dimensions are constructed from the structure obtained in the structure fit. The
O—O distance was determined to be 2.7Å and the O-H distance is taken to be
1Å. Using this information the protons are 0.35 Å from the barrier maximum.
Several calculations were run to estimate the barrier height. The values ranged
from 2000 cm-1 using DFT to 3800 cm-1 using MP2 and the basis set 6311++G**. There are three independent parameters in the construction of the
energy levels using this model: the reduced mass, the barrier height and the
position of the two minima. To obtain a barrier height of 4000 cm-1 using 0.35Å
as the spacing from the barrier maximum to the minimum, an equation of
265,000*X4-65115*X2 was used. The reduced mass for the vibration of the
concerted O-H vibration was estimated to be 2 amu which is consistent with the
concerted motion of the two protons. This information was transformed in the
91
reduced coordinates as described by Laane as, V(z)=141.5*(-10.1*Z2 + Z4). The
results of the ANHARM calculation gives the difference between the first two
energy levels as 0.0034 cm-1, 243 MHz. A summary of the predicted splitting at 1
and 2 amu for barrier heights of 2000, 4000 and 8000 cm-1 is given in Table 4.18.
The 1 amu reduced mass was investigated because frequency calculations
performed with Gaussian gave the reduced mass in vibration 31, the coordinated
OH stretch, 1.07 amu. The results from this model indicate that a barrier height
of greater than 8000 cm-1 would be necessary to obtain the 240 cm-1 obtained in
this experiment.
Using these parameters with a reduced mass of 4 amu gives .00002 cm-1,
0.3 MHz. This value can be resolved and will be examined in the future by our
laboratory.
4.3.5 Discussion
The first evidence of a concerted proton exchange between two carboxylic
acids has been measured in the microwave region between Propiolic Acid and
Formic Acid. The parent isotope was studied extensively with three different
spectrometers spanning 1-21 GHz. Using microwave double resonance, the btype transitions which occur between vibrational levels give a clear connection to
a closely spaced vibrational level near the ground state. The closely spaced
vibrational levels are consistent with the theory of the double well potential. The
lack of this pattern upon deuteration of the H1 or H2 atoms also gives evidence
92
that the parent’s spectrum is influenced by proton tunneling. The symmetry is
broken due to the presence of a deuterium atom. We have shown that the singly
deuterated isotopomers show a spectrum of only one set of a-type transitions
and b-type transitions that fit to rotational constants of the vibrational ground
state.
The structural information obtained in the study reveal a tightly bound
dimer that has symmetric hydrogen bond distances of 1.65 Å. A second fit does
not reflect a probable structure with the H1 atom on the other side of the oxygen.
Calculations using MP2/aug-cc-pVDZ and CCSD/6-311++G** give a structure
similar to the Fit I with both <(C-O-H) angles at 109°. Substitution with 18O at O1
or O2 and 2H at H3 would help refine the orientation of propiolic acid in the dimer.
In this study there is only one substitution of propiolic acid and three on formic
acid. This is thought to be the reason that rotation of propiolic acid about its
center of mass does not affect the fit and was fixed. Fit I improves with an
increase of <(C-O1-H1) from the monomer value of 106° and more isotopic
substitutions may make this angle more reliably determined.
The one-coordinate double well potential model for the concerted proton
tunneling has been investigated for this system. The reduced mass and the
potential height are the most significant variables. Both the structure fit and
calculations give the distance of 0.70 as the distance between well minima. The
ground state and the next vibrational state splitting was determined to be 240 cm1
and the model predicts that at 1 amu the barrier height is close to 8000 cm-1.
93
Calculations with MP2/6-311++G** and B3PW91/6-311++G** give between 2000
and 4000 cm-1. A reduced mass of 2 reproduces the energy difference obtained
from the global fit of a intravibrational and b intervibrational transitions of 241.
The reduced mass of 2 could be a consequence of the double proton exchange
necessary for the tunneling to occur.
94
Figure 4.4 Parameters used in the fit of Propiolic Acid-Formic Acid
95
Table 4.9. Summary of calculated and experimental key molecular and structural
parameters
A /MHz
B / MHz
C / MHz
R(O1H1—O3)
/Å
R(O2—H2O4)
/Å
<(C-O4-H2) / °
<(C-O1-H1) / °
|μa| / D
MP2
6-311++G**
5962.207
910.541
789.907
MP2
aug-cc-pVDZ
5880.107
914.236
791.218
HCTH407
6-311++G**
5952.353
896.513
779.16
Expt
5988.7
927.782
803.72
1.73
1.69
1.77
1.65
1.71
108.7
108.6
1.67
109
109
1.76
109.8
109.5
1.65
109
109
0.88
0.77
0.8
0.579(4)
Table 4.9. cont.__________________________________________________________
A /MHz
B / MHz
C / MHz
R(O1H1—O3)
/Å
R(O2—H2O4)
/Å
<(C-O4-H2) / °
<(C-O1-H1) / °
|μa| / D
B3PW91
6-311++G**
6024.614
934.822
809.253
B3LYP
6-311++G**
5991.895
920.436
797.872
TPSSTPSS
6-311++G**
5903.03
933.095
805.732
Expt
5988.7
927.782
803.72
1.66
1.7
1.64
1.65
1.64
110.1
109.9
1.68
110.3
110.1
1.63
109.8
109.6
1.65
109
109
0.78
0.81
0.84
0.579(4)
96
Table 4.10. Results from the fit of a and b-type dipole transitions
v
0
1
0
1
0
1
0
1
0
1
0
1
Fit
Parameter
A / MHz
A / MHz
B / MHz
B / MHz
C / MHz
C / MHz
ΔE / MHz
Fc / MHz
DJ / kHz
DJ / kHz
DJK / kHz
DJK kHz
dJ / kHz
dJ / kHz
σ / kHz
Ν
Value
6005.289(3)
6005.275(3)
930.553(3)
930.546(3)
803.9948(3)
803.9907(2)
291.4318(25)
120.688(59)
0.0749(4)
0.0755(4)
0.700(7)
0.691(7)
0.0108(5)
0.0086(4)
4
166
97
Table 4.11. Rotational and distortion constants for the Propiolic-Formic dimer and the
measured isotopomers___________________________________________________
Pro-FAC13
5987.5(4)
915.2551(4)
794.3132(4)
ProFAC13_2
5987.4(3)
915.2604(3)
794.6304(3)
Pro-FAOD
5912.5(2)
925.6587(3)
800.7534(3)
ProOD-FA
5918.4(3)
923.4015(4)
799.1703(5)
DJ /kHz
DJK
/kHz
[0.12(3)]
[0.12(3)]
0.064(4)
0.059(5)
[-5.0(5)]
[-5.0(5)]
0.99(8)
0.9(1)
δJ /kHz
[0.05(1)]
[0.05(1)]
-
-
δK /kHz
[52(5)]
[52(5)]
-
-
φjk /kHz
N
σ /kHz
[-0.15(2)]
11
4
[-0.15(2)]
11
3
16
2
16
3
A /MHz
B/MHz
C/MHz
Table 4.11 cont._______________________________________________________
ProFAODCD
5920(5)
901.600(2)
782.699(2)
Pro-FACD
5898.2(8)
903.130(3)
786.026(1)
ProODFAOD
5824.5(8)
921.5312(6)
796.0334(6)
DJ /kHz
DJK
/kHz
0.12(7)
[0.12(3)]
0.09(1)
-6(3)
[-5.0(5)]
2.8(6)
δJ /kHz
-
[0.05(1)]
-
δK /kHz
-
[52(5)]
-
φjk /kHz
N
σ /kHz
7
5
[-0.15(2)]
8
13
8
1
A /MHz
B/MHz
C/MHz
98
Table 4.12. Barrier height calculations and transition state geometry
Method
Delta/(cm-1)a
R(O--O)/Ǻ
R(O--H)/Ǻ
B3LYP/6-311++G**
2504
2.42
1.2
B3PW91/6-311++G**
1978
2.41
1.2
MP2/6-311++G**
3755
2.44
1.2
a
Difference in optimized (global minimum)energy and converged transition state, 3652 cm-1 in
reference (Havenith) for Formic-Formic dimer
99
Table 4.13. The measured transitions of ProFA from 1.7 GHz to 21.3 GHz.__
J’KaKc
10,1
10,1
21,2
21,2
20,2
20,2
21,1
21,1
31,3
31,3
30,3
30,3
32,2
32,1
31,2
31,2
11,1
41,4
41,4
40,4
40,4
42,3
43,2
43,1
42,2
11,1
41,3
21,2
51,5
51,5
50,5
50,5
52,4
52,4
52,3
21,2
51,4
51,4
31,3
v’
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
0
1
0
1
0
1
0
0
1
1
0
0
1
0
1
0
1
0
1
1
1
0
0
J”KaKc
00,0
00,0
11,1
11,1
10,1
10,1
11,0
11,0
21,2
21,2
20,2
20,2
22,1
22,0
21,1
21,1
00,0
31,3
31,3
30,3
30,3
32,2
33,1
33,0
32,1
00,0
31,2
10,1
41,4
41,4
40,4
40,4
42,3
42,3
42,2
10,1
41,3
41,3
20,2
v”
1
0
1
0
1
0
1
0
1
0
1
0
1
1
1
0
1
1
0
1
0
1
0
0
1
0
0
1
1
0
1
0
1
0
1
0
1
0
1
Frequency
/ MHz
1731.493
1731.834
3339.166
3340.174
3460.747
3461.44
3586.851
3587.202
5007.364
5008.881
5185.527
5186.594
5194.49
5203.43
5378.861
5379.394
6520.902
6673.937
6675.966
6903.622
6905.096
6924.239
6931.678
6931.827
6946.562
7103.387
7169.857
8129.58
8338.397
8340.95
8612.895
8614.821
8652.493
8654.204
8697.007
8710.748
8957.035
8957.967
9677.711
o-c
/ kHz
-0.6
0.1
-1.6
-0.4
-0.5
-0.1
1.1
-0.1
-1.2
-0.6
-0.1
0.1
1.3
-1
1.8
-0.4
4.7
1
-1.3
0
-0.8
0.4
-0.3
-1.7
-0.4
-18.5
-2.4
1.5
2.1
0.8
-0.4
0.5
2
-1.6
2.1
9.1
-1.4
1.8
-2
100
Table 4.13 cont._____________________________________________________
J’KaKc
31,3
61,6
61,6
31,3
60,6
60,6
60,6
80,8
62,5
62,5
62,5
63,4
63,3
63,4
63,3
62,4
62,4
62,4
62,4
61,5
61,5
41,4
71,7
71,7
41,4
90,9
70,7
70,7
70,7
72,6
72,6
73,5
73,5
73,4
73,4
72,5
72,5
71,6
71,6
51,5
51,5
v’
0
1
0
1
1
0
0
1
1
1
0
1
1
0
0
1
1
0
0
1
0
0
1
0
1
0
1
0
0
1
0
1
0
1
0
1
0
1
0
0
0
J”KaKc
20,2
51,5
51,5
20,2
50,5
50,5
50,5
71,7
52,4
52,4
52,4
53,3
53,2
53,3
53,2
52,3
52,3
52,3
52,3
51,4
51,4
30,3
61,6
61,6
30,3
81,8
60,6
60,6
60,6
62,5
62,5
63,4
63,4
63,3
63,3
62,4
62,4
61,5
61,5
40,4
40,4
v”
1
1
0
0
1
0
0
0
1
1
0
1
1
0
0
1
1
0
0
1
0
1
1
0
0
1
1
0
0
1
0
1
0
1
0
1
0
1
0
1
1
Frequency
/ MHz
9677.719
10000.3
10003.39
10256.67
10311.37
10313.8
10313.8
10319.46
10378.87
10378.88
10380.95
10400.5
10401.91
10402.46
10403.86
10456.35
10456.36
10458.02
10458.02
10741.88
10743.02
11168.16
11659.3
11662.92
11744.01
11782.18
11997.36
12000.35
12000.35
12103.02
12105.46
12137.38
12139.65
12140.56
12142.79
12225.91
12227.72
12522.9
12524.28
12605.45
12605.48
o-c
/ kHz
6.3
-2.7
-0.2
5.2
-2.1
-1.8
0.7
-0.8
-0.3
1.4
0.5
0.7
-0.2
0
-0.4
-1
1.7
-7.1
-1.1
-0.9
0.1
4.9
-1.2
-3.9
3.6
0.4
-2
0.9
1.2
3.1
2.3
-0.1
0.5
0
-0.7
-2.7
-3.1
1.5
0.3
-25.5
4.5
101
Table 4.13 cont._____________________________________________________
J’KaKc
51,5
51,5
81,8
81,8
80,8
80,8
82,7
82,7
83,6
83,6
83,5
83,5
61,6
82,6
82,6
62,4
72,5
52,3
81,7
81,7
100,10
42,2
61,6
62,4
32,1
52,3
91,9
91,9
90,9
90,9
71,7
32,2
22,0
92,8
92,8
94,6
94,5
94,6
94,5
93,7
93,7
v’
1
1
1
0
1
0
1
0
1
0
1
0
0
1
0
0
1
0
1
0
1
0
1
1
0
1
1
0
1
0
0
0
1
1
0
1
1
0
0
1
0
J”KaKc
40,4
40,4
71,7
71,7
70,7
70,7
72,6
72,6
73,5
73,5
73,4
73,4
50,5
72,5
72,5
61,5
71,6
51,4
71,6
71,6
91,9
41,3
50,5
61,5
31,2
51,4
81,8
81,8
80,8
80,8
60,6
31,3
21,1
82,7
82,7
84,5
84,4
84,5
84,4
83,6
83,6
v”
0
0
1
0
1
0
1
0
1
0
1
0
1
1
0
1
0
1
1
0
0
1
0
0
1
0
1
0
1
0
1
1
0
1
0
1
1
0
0
1
0
Frequency
/ MHz
13177.31
13177.31
13315.06
13319.24
13669.64
13673.25
13824.56
13827.38
13875.54
13878.09
13881.87
13884.38
13995.98
14006.52
14008.41
14014.39
14289.43
14298.25
14299.28
14300.92
14327.19
14556.79
14562.79
14587.8
14778.12
14874.47
14967.35
14972.11
15327.62
15331.91
15347.54
15510.04
15534.69
15543.13
15546.33
15604.54
15604.73
15607.42
15607.61
15614.92
15617.75
o-c
/ kHz
3.4
3.4
1
-2.5
-1
-0.6
2.2
5.2
1.5
-0.7
2.9
-0.4
0.5
0.6
1.4
-2.7
-4.6
-0.7
1.7
0.1
-2.3
-3.5
-0.9
-3.8
-7
-1.2
0.9
-1
-2.1
-3.2
1.8
11.7
7.5
2.9
5
-4.1
-1.6
0.2
1.2
3.1
-1.4
102
Table 4.13 cont._____________________________________________________
J’KaKc
93,6
93,6
92,7
92,7
71,7
91,8
91,8
101,10
101,10
81,8
100,10
100,10
102,9
102,9
104,7
104,6
104,7
104,6
103,8
103,8
103,7
102,8
102,8
101,9
101,9
111,11
111,11
110,11
110,11
112,10
112,10
113,9
113,9
113,8
113,8
112,9
112,9
111,10
111,10
121,12
121,12
v’
1
0
1
0
1
1
0
1
0
0
1
0
1
0
1
1
0
0
1
0
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
J”KaKc
83,5
83,5
82,6
82,6
60,6
81,7
81,7
91,9
91,9
70,7
90,9
90,9
92,8
92,8
94,6
94,5
94,6
94,5
93,7
93,7
93,6
92,7
92,7
91,8
91,8
101,10
101,10
100,10
100,10
102,9
102,9
103,8
103,8
103,7
103,7
102,8
102,8
101,9
101,9
111,11
111,11
v”
1
0
1
0
0
1
0
1
0
1
1
0
1
0
1
1
0
0
1
0
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
Frequency
/ MHz
15626.49
15629.24
15798.35
15800.28
15908.29
16070.07
16072
16616.03
16621.37
16669.43
16971.46
16976.49
17258.38
17261.98
17342.97
17343.37
17346.13
17346.53
17355.4
17358.51
17378.12
17600.84
17602.79
17834.28
17836.53
18261.01
18266.97
18602.12
18607.92
18969.96
18973.97
19096.78
19100.17
19128.71
19131.85
19412.6
19414.54
19590.76
19593.38
19902.28
19908.91
o-c
/ kHz
0.9
-1.8
-2.8
-2.5
0.9
-0.7
-2.7
2.6
-3
5.8
0.2
0.4
8
7
0.1
-1.9
1.5
1
3.6
-1.7
-1.7
-4.4
-4.9
-1
-1
4.4
-2.8
0
-0.1
10.8
8.9
3
2.1
-1.4
-2.9
-8.2
-6.3
2.6
-0.8
-8.9
-4.1
103
Table 4.13 cont._____________________________________________________
J’KaKc
120,12
120,12
121,11
121,11
v’
1
0
1
0
J”KaKc
110,11
110,11
111,10
111,10
v”
1
0
1
0
Table 4.14. Propiolic Acid- Formic Acid (C13) results
J'KaKc
J"KaKc
Pro-FA13C v=1
Pro-FA13C v=0
Frequency
Frequency
o-c
-
o-c
-
30,3
20,2
5120.198
0.008
5121.209
0.008
31,2
21,1
5308.486
0.004
5308.989
0.000
6594.586
0.002
41,4
31,3
6592.647
0.002
-
40,4
30,3
6817.054
0.003
6818.453
0.003
-
41,3
31,2
7075.435
0.000
7076.122
0.002
8239.428
0.003
8507.359
0.000
51,5
41,4
8236.985
0.001
-
50,5
40,4
8505.529
0.002
Frequency
/ MHz
20221.26
20227.87
21338.3
21341.34
o-c
/ kHz
2.5
-1
1.6
2.9
104
Table 4.14 cont._____________________________________
Pro-FA13C v=1
Pro-FA13C v=0
J'KaKc
J"KaKc
Frequency
o-c
Frequency
o-c
51,4
41,3
8840.141
0.000
8841.025
0.003
-
61,6
51,5
9878.904
0.006
9881.850
0.002
60,6
50,5
10183.744
0.002
10186.052
0.001
61,5
51,4
10601.948
0.001
10603.039
0.001
105
Table 4.15. Summary of the isotopic substitution of deuterium
ProFAOD
ProOD
-FA
ProFACD
J'KaKc
J"KaKc
obs
o-c
obs
o-c
obs
o-c
31,3
21,2
4990.429
-1
4979.931
-8
-
-
30,3
20,2
-
-
-
-
5059.377
0
31,2
21,1
5365.113
-6
5352.602
-6
-
-
41,4
31,3
6651.259
0
6637.306
3
6518.853
-3
40,4
30,3
6882.509
0
6867.432
0
6736.415
-9
42,3
32,2
-
-
6888.464
0
-
-
42,2
32,1
6926.922
1
6911.304
2
-
-
41,3
31,2
7150.724
5
7134.075
4
-
-
51,5
41,4
8309.898
1
8292.506
3
8144.944
-6
50,5
40,4
8585.927
1
8567.293
3
8405.498
6
52,4
42,3
8626.840
0
-
-
-
-
52,3
42,2
8672.939
-1
8653.242
-1
-
-
51,4
41,3
8933.861
2
8913.106
0
-
-
61,6
51,5
9965.893
0
9945.092
-1
9768.731
20
60,6
50,5
10278.18
-3
10256.12
1
10064.79
14
61,5
51,4
10713.82
-2
10689.01
-1
-
-
71,7
61,6
11618.86
0
11594.69
0
-
-
70,7
60,6
11957.58
1
11932.23
-1
11712.72
-11
106
Table 4.15 cont._________________________________________________________
ProODFAOD
ProFAODCD
J'KaKc
J"KaKc
obs
o-c
obs
o-c
31,3
21,2
-
-
4873.273
0
30,3
20,2
-
-
-
-
31,2
21,1
-
-
-
-
41,4
31,3
6614.545
0
-
-
40,4
30,3
6846.504
2
6716.320
-4
42,3
32,2
-
-
-
-
42,2
32,1
-
-
-
-
41,3
31,2
7116.369
2
6970.767
0
51,5
41,4
8263.894
-1
8115.342
0
50,5
40,4
8540.464
-3
8379.865
-5
52,4
42,3
-
-
-
-
52,3
42,2
-
-
-
-
51,4
41,3
8890.79
-2
-
-
61,6
51,5
9910.536
1
-
-
60,6
50,5
10223
1
10033.31
61,5
51,4
-
-
-
-
71,7
61,6
-
-
-
-
70,7
60,6
-
-
-
-
-2
107
Table 4.16. Summary of results from the structure fit with Propiolic Acid angle fixed and
Formic Acid deviation angle from the monomer fit with rotation of Formic acid and
monomers centers of mass separation.
Propiiolic Acid
Formic Acid
Fit standard deviation
<(C-O1-H1)*
<(C-O4-H2)
(MHz)
106
118
1.88
109
116
1.85
109
109
1.88
106
106
1.97
*If the angle is included in fit the value is 287° and σ=0.3 MHz
Table 4.17. Coordinates for Kraitchman analysis and the results of two structure fits. Fit
I is a three parameter fit with the propiolic <(C-O1-H1) angle fixed.
Kraitchman Results
Structure Fit I
Atom
a
b
c
a
b
C
C1
2.7(3)
0.054(7)
0.12(2)
2.74
-0.10
0.0
H1
1.6(1)
1.00(9)
0.063(6)
0.41
-1.05
0.0
H2
1.1(2)
1.0(2)
.07(1)
1.32
1.08
0.0
H3
3.72(2)
0.544(3)
1.019(6)
3.84
-0.11
0.0
108
Table 4.18. Summary of results using the ANHARM program for a minima separation of
0.7Å and fit to V(Z)=A*(Z4-B*Z2)
Barrier Height (cm-1)
Reduced Mass (amu)
v1-v0 (MHz)
2000
1
210000
2000
2
9500
4000
1
19000
4000
2
261
8000
1
480
8000
2
1.2
109
5. QUADRUPOLE COUPLING AND STRUCTURE OF SMALL INORGANIC
MOLECULES
5.1 Introduction
This chapter will detail the efforts of three molecules in which the
experimentally determined quadrupole coupling constant has led to significant
insight into aromaticity in azaborine, molecular structure of N-hydroxypyridine2(H)-thione and the effect of vibrational state on the quadrupole coupling
constant in arsenic triphosphide. Each system contains at least one atom with
spin 1 or greater and resulted in a rich spectrum. The theoretical framework of
one and two quadrupole nuclei in a symmetric and asymmetric top has already
been given66 and is now fully implemented in the Dr. Herb Pickett’s
SPCAT/SPFIT programs. The goal in this introduction is to introduce the key
elements of the theory so that the notation and results are successfully described
and communicated.
The nuclear quadrupole coupling analysis quantifies an extremely
valuable molecular parameter, the electric field gradient. The electronic
environment near a nucleus of spin, I, greater than 1 can be probed using
microwave spectroscopy due to the low J states and high resolution available.
The measurements of ammonia’s inversion spectrum in the microwave region
provided the first measurements of the quadrupole interaction in molecules67 and
110
have been a successful parameter in the identification of isomers68, population in
p-orbitals69 and determination of ionic properties of molecules70. This
dissertation describes the work in quantifying the quadrupole coupling constants
and the comparison to theory for several molecules and dimers: azaborine,
mercaptopyridine-N-oxide, arsenic triphosphide, formamide-formic acid and
C7H747TiC5H5.
5.2 Azaborine
5.2.1 Introduction
Liu and co-workers have reported the synthesis, NMR and UV spectrum of 1,2dihydro-1,2-azaborine but a crystal structure was not obtained. Calculations
comparing 1,2-dihydro-1,2-azaborine with borazine and benzene have been
published, 71 and gas phase experimental data on these heterocyclic ring
systems have remained largely elusive to date.72 Here, we report microwave
spectroscopy measurements and structural parameters for 1,2-dihydro-1,2azaborine. Rotational transitions for 1,2-dihydro-1,2-azaborine and its 10B and 2H
isotopologues were measured in 7-15 GHz to obtain rotational constants and
nuclear quadrupole coupling strengths for the ground electronic and vibrational
state. Results from our microwave molecular beam experiments can be directly
compared with ab initio theory.
111
Microwave spectroscopy has been the most accurate and useful method
for the determination of gas phase structures of many small molecules. Some
examples containing boron and nitrogen are H2NBH2,73 H3NBF3,74 and BH3NH375.
Studies of amine-boron complexes have revealed a very strong interaction
between boron and nitrogen. In the HCN-BF3 dimer, a very short van der Waals
bond distance between boron and nitrogen has been observed.76 Microwave
spectroscopy of borazine is not possible due to the lack of permanent dipole
moment. 1,2-Dihydro-1,2-azaborine on the contrary has a strong permanent
dipole moment (2 D) and thus its microwave spectrum can be readily measured.
Another advantage of microwave spectroscopy is the high sensitivity which
allows measurements of the minor 10B isotopic species in natural abundance,
thus providing additional data for structure determination. Our work
complements the detailed work of Marwitz, et al. and provides new experimental
data on the bond lengths and nuclear quadrupole coupling constants for this
molecule.
Experimental determination of the nuclear quadrupole coupling constants
for 14N, 11B and 10B allow the determination of the valence p-orbital electron
occupation on those atoms from the Townes-Daily model.77 The latter is
especially of interest to compare with the calculated natural bond orbital
occupation for boron and nitrogen. The experimental molecular parameters and
the π electron occupancies on boron and nitrogen can provide additional
information regarding the aromaticity for 1,2-dihydro-1,2-azaborine.
112
Figure 5.1 Azaborine with parameters used in the fit.
113
5.2.2 Calculations
Quantum electronic structure calculations were performed to obtain a
starting structure for microwave frequency predictions. The predicted structure
and derived rotational constants were accurate and reduced the effort in
searching for transitions. The calculations were done using the Gaussian 0378
suite running on the University of Arizona ICE high performance computing
cluster. The structure, nuclear quadrupole coupling constants, and rotational
constants for 1,2-dihydro-1,2-azaborine were computed using the Møller-Plesset
2nd order perturbation theory (MP2). Sufficiently large double and triple zeta
atomic basis sets, 6-31+G(d,p) and 6-311G+(d,p) were chosen to accurately
describe the wavefunctions and to study the optimization performance of the
basis sets.79 Geometry optimizations were done in redundant internal
coordinates at tight convergence criteria without any symmetry constraints.
Harmonic frequency calculations were computed on a fine grid to verify that the
optimized structure is at the global minimum. Theoretical rotational constants
and nuclear quadrupole coupling constants obtained for the optimized structures
at the MP2/6-31+G(d,p) and MP2/6-311+G(d,p) levels of calculations are given in
Table 1. The ground state geometry of 1,2-dihydro-1,2-azaborine was predicted
to be planar and a near-oblate asymmetric-top rotor. As shown in Figure 5.1, the
nitrogen atom lies very close to the a-inertial axis and the boron atom lies near
the b-inertial axis (The c-inertial axis is perpendicular to the molecular plane).
114
Calculations indicate that both a and b dipole rotational transitions are
allowed. The predicted dipole strengths are a = 1.6 D and b = 1.4 D for 1,2dihydro-1,2-azaborine, and both types were observed in this experiment as
described below. Several accounts of electronic structure calculations for
BNC4H6 exist in the literature for direct comparison with our results.80 The
present computations of the BNC4H6 structure are in good agreement with the
earlier calculations, including those employing higher order electron correlation
methods. Calculated bond lengths and angles for the C-C-C-C portion of the
molecule did not change significantly when larger basis sets (i.e. 6-311+G(d,p))
were used in the calculations. However, nuclear quadrupole coupling constants
determined by MP2 seemed to depend somewhat on the basis set size for boron
but were more consistent for nitrogen. Natural bond analysis (NBO) was carried
out using the MP2 method to study valence p-electron occupancy in B-N bond
environment and the relation to the nuclear quadrupole coupling interaction
strengths.
To better understand the relationship between the molecular structure and
π-electron density distribution, we investigated the total electron density
distribution and provide an electrostatic potential map (see Fig. 5.3) for the
azaborine molecule. For these calculations, the isosurface of total electron
density was computed at the MP2/6-31+G(d,p) level. The illustrated isosurface
was mapped with the electrostatic potential from total SCF density (Iso Val =
0.001) to provide qualitative data on the electronic charge density distribution.
115
For direct comparison, a mapped isosurface of benzene was computed at the
same level of calculations. Figure 5.3 shows the results of the isosurface plots
for benzene and 1,2-dihydro-1,2-azaborine, where red color indicates most
negative (most electron rich) regions and blue color indicates most positive (most
electron poor) regions. The overall dipole moment for 1, 2-dihydro-azaborine
and is predicted to lie along a line connecting the two carbons that are adjacent
to nitrogen (C1) and boron (C4) (See Fig. 5.1 ). The calculated dipole moment is
2 D, pointing from C1 (most negative, adjacent to B) toward C4 (most positive,
adjacent to N) (This is the Physics convention, not the same as many chemistry
text books). From the Mulliken charges it is observed that the carbon nearest
boron (C1) has a region of strongest negative charge, -0.5e, and the carbon
closest to nitrogen (C4) to have +0.2e. This is in agreement with the charge
isosurface plot (Fig. 5.3) The Mulliken charges on N (-0.3e) and B (0.2e) give a
B-N bond dipole in a direction opposite the overall dipole moment for the
molecule.. The NBO (from MP2) charges indicate a more polarized B-N bond,
with B (0.5e) and N (-0.7e).
5.2.3 Experimental
1,2-dihydro-1,2-Azaborine arrived as a clear liquid (in dodecane) from the Liu
laboratory at the University of Oregon, in a two-neck sample cell that allowed for vacuum
transfers. Details of the synthesis of the compound are reported in Marwitz et al81. 1deutero-2-hydro-1,2-azaborine was prepared simply by adding small concentration of
116
CH3OD to 1,2-dihydro-1,2-azaborine and allowing the mixture to exchange at room
temperature to make D-NBC4H5. The D-enriched sample that was shipped to our
laboratory had a yellowish color and might have contained some impurities or
decomposition products. We were able to obtain some spectra for this D-substituted
isotopomer.
To prepare the sample for microwave measurements, the sample cell was
loaded onto the spectrometer sample chamber and subsequently placed into a liquid
nitrogen bath to freeze the liquid sample. This cell was then evacuated, charged to 0.81.0 atm with neon, and allowed to warm to 0˚C. The temperature of 0˚C was then
maintained by placing the cell in the ice bath. The azaborine molecules seeded in neon
were introduced into the spectrometer resonator cavity with the nozzle beam transverse
to the microwave radiation, at 2 Hz using a pulsed valve (General valve series 9). The
pressure inside the spectrometer chamber was maintained at 10-6-10-7 torr prior to the
valve opening and the backing pressure of neon was kept at about 0.8 atm during the
frequency scanning. Following the molecular pulse (about 1 ms delay), a π/2 microwave
excitation pulse (1μs duration) was injected into the resonator to coherently excite the
molecules, using a Herley SPDT microwave switch. The molecular FID signal was
transmitted via the same SPDT switch, passed to a Miteq 6-18 GHz low noise amplifier,
and sent to the RF circuit for further signal processing. The details of the homodyne
mixing and detection system and spectrometer have been given previously.82
5.2.4 Data Summary
5.2.4.1 Microwave spectrum
117
1,2-Dihydro-1,2-azaborine displayed an asymmetric-top spectrum with
complicated nuclear quadrupole hyperfine splittings. Many of the observed atype and b-type lines appeared fairly congested due to the unresolved hyperfine
splittings. The J=0→1 line was observed for both a-type and b-type dipole
transitions which aided spectral assignment for the fit. Nine distinct a-type and btype rotational transitions for the parent 1,2-dihydro-1,2-azaborine species were
measured in 7-15 GHz. We were able to assign a total of 92 resolved hyperfine
components to the parent species. Eight a-type and b-type rotational transitions
were measured for the 10B isotopologue in natural abundance and 39 hyperfine
components were assigned to this isotopomer. Our spectral assignment of 10B
isotopologue in natural abundance helped to confirm unambiguously the identity
of the parent species. The measured transition frequencies and deviations for
the spectral fits are given in Tables 5.4 and 5.5.. Also, the observed 14N nuclear
quadruple coupling constants for 10B and 11B isotopologues are nearly identical
and agree within the experimental error limits. The larger fit standard deviation
obtained for the 10B isotopologue is largely due to the measurement uncertainty
as spectral lines for this isotopomer are weaker and more likely to be blended
with other transitions. Our experimental line widths (FWHM) are 10-20 kHz with
a measurement uncertainty of about 5 kHz for resolved transitions. We have
high confidence that our current spectral assignment is correct, although some
hyperfine components were not assigned due largely to the spectral line
congestion. Only three rotational transitions were observed for the D-enriched
118
species. Further frequency searches using refined rotational constants were
performed for the D-enriched species, but no additional lines were found.
Nuclear quadrupole coupling of two nuclei, 11B (I=3/2) and 14N (I=1), and
10
B (I=3) and 14N, with the molecular rotation yielded rich hyperfine spectral
patterns. This quadrupole data (i.e., the hyperfine splittings) allows us to
determine the electric field gradient environment and p valence electron density
at the B and N nuclei. The 10B nuclear quadrupole moment is approximately
twice as large as that of 11B. Herb Pickett’s SPFIT83 program was used to
analyze and fit the observed hyperfine splittings. Resolved hyperfine transitions
were assigned and fit using a rigid Watson’s s-reduced Hamiltonian in the Ir
representation. The variable parameters are A, B, C, eQqaa and eQqbb-eQqcc.
The off-diagonal element eQqab, which could be non-zero for a planar molecule,
was not determined from the current fits. The angular momentum coupling
scheme used in this analysis is the IB+J=F1, IN + F1 = F coupling scheme. In this
coupling scheme, the boron nucleus is coupled to the rotational angular
momentum to give IB+J=F1. The nitrogen nucleus was coupled to F1 to give
IN+F1=F. Table 5.4 lists the observed hyperfine transition frequencies for
11
B14NC4H6 , Table 5.5 lists the observed hyperfine transition frequencies for
10
B14NC4H6 and Table 5.6 lists the three transitions observed for 11B14NC4H5D.
The assignments are specified by the quantum numbers |J Ka Kc F1 F 〉 where F
represents the total angular momentum. The molecular parameters determined
by fitting the experimental transition frequencies are given in Table 5.1.
119
5.2.4.2 Structure Determination
It was not possible to experimentally determine all of the structural
parameters since the rotational constants for only three isotopologues were
measured. Because the molecule has low molecular symmetry, a complete
analysis of the ring structure would require five isotopologues with different ring
substitutions. In the present analysis a number of the important structural
parameters for the ring are obtained. Since the 10B and 2H isotopologues were
measured, we can accurately determine some structural parameters by fitting the
effective moments of inertia. The identified structural parameters, which depend
on the boron position, are the bond distances R(B-C) and R(B-N). We performed
a least-squares structure fit analysis to determine the polar coordinates of boron
and nitrogen from the carbon atom indicated in Figure 5.2.
120
Figure 5.2 Parameters used in the least squares fit. The N-C bond length was a
parameter and the B-N bond length was obtained from the B and N coordinates
The variable parameters R(B-C), R(C-N), θ, and φ can be used to determine the
R(B-N) bond length. Using the structure with the best fit to the nine rotational
constants, the R(B-C) distance and internal angles (α, β, γ, δ) shown in Figure
5.1, were obtained with results given in Table 5.2. In this least-squares analysis,
the structural parameters R(B-H), and R(N-H) were varied incrementally. It was
found that changing the R(N-H) bond length from the calculated value did not
significantly improve the fit and so was fixed 1.02 Å. This value was obtained
from the MP2/6-31+G(d) calculation and agreed with the value of 1.02 Å obtained
121
from the structure fit. The value for R(B-H) obtained using it as a fit parameter is
1.19 Å. Correlation effects are reduced and we prefer the value of 1.21 Å
obtained by incrementing fixed values for R(B-H) and looking for the lowest
standard deviation for the fit. The difference in these values is not significant.
Kraitchman analysis was less useful for this study because it only provides
values for the coordinates of boron in the center of mass system. Measurements
using isotopically labeled 13C and 15N isotopologues would allow refinement of
R(B-C), R(B-N), and R(N-H) bond lengths and angles in the ring. However,
because no isotopologues were measured for any ring carbon and nitrogen
atoms in this work, the bond distances and angles in C-C-C-C part of the
azaborine ring could not be directly obtained and were fixed to the theoretical
values MP2/6-31+G(d,p). The results of this least-squares fit analysis are given
in Table 5.2. Error limits for the angles are only reported for γ and β, as they are
the only angles completely determined from the fit. The errors for the angles
were determined two ways. The first way involved the propagation of error
through the parameters using the law of sines and second, by moving the
nitrogen atom 2σ along R(N-C) in each direction to determine the effect on γ and
β. Both give similar results with an upper limit 2σ estimate for the errors to be 3˚.
5.2.4.3 Townes-Dailey Population Analysis
122
The measured nuclear quadrupole coupling constants were used to
determine the pc valence electron occupancy in boron and nitrogen using an
extended Townes-Dailey population analysis.77 Because the electric field
gradients are primarily dependent on the p-electron density, useful information
about the p-electron occupancy can be directly determined from the measured
eQq values. Boron has 3 electrons to form the three sigma bonds (sp2
hybridized), but has an empty, unhybridized pc orbital. Nitrogen has two
electrons occupying the pc orbital and is expected to have p valence electron
occupancy pc closer to 2 e, given a model where three sp2 orbitals are formed to
make three sigma bonds. A natural bond orbital calculation at the MP2/6311+G(d,p) shows electron density in the valence pc orbital of 11B to be 0.35 and
that of 14N to be 1.6. The occupancy of the orbital can be experimentally
determined by comparison of the molecular coupling constants and the atomic
coupling constants. With the constraint that the sum of pa, pb and pc populations
be 2 for 11B and 4 for 14N, the experimental populations of pc were experimentally
determined to be 0.3 for 11B and 1.3 for 14N. It is expected that the hybridization
adds one electron from the s into the p-orbitals giving a total of 2 for boron and 4
for nitrogen. Results from this simple model are surprisingly close to calculated
occupations for nitrogen and boron and reveal that contributions to the coupling
constants along the a and b axes by the hybridized orbitals have atomic p-orbital
character. These pc orbital electron densities may have been modified by the
delocalized π-bonding in the ring.
123
An additional analysis for nitrogen can be performed if we assume that the
nitrogen atom has pyrrole-like hybridization and that the eQqzz (14N) = eQqcc (14N)
(i.e., the inertial c-axis is parallel to the z-axis of the molecule; the molecule lies
in the xy plane and that N lies on the y-axis). We can estimate the pc electron
occupation number and πc, the amount of pi bonding in the nitrogen pc orbital (the
2p orbital that lies orthogonal to the molecular plane). The following TownesDailey equation can be applied to 1,2-azaborine: eQqzz/eQq210 = (1 - 0.375iσ(NC)
-0.375iσ(NB)- 0.25 iσ(NH) - πc) ⁄ (1+0.3[c-])84. The best estimate of eQq210 for a
single 2p electron in atomic nitrogen is -11.2(2) MHz85 and c-, the negative
charge on nitrogen, is taken from the natural bond orbital estimate of 0.3.
iσ(NC), iσ(NB) and iσ(NH) are the ionic character for the sigma bond, which can
be obtained from the electronegativites using the relation, iσ= |xa-xb|/2, giving
iσ(NC)=.25 and iσ(NH)= iσ(NB) = 0.5. The pc occupation number is expressed as
nz = 2 - πc. From these equations, we obtained the amount of pi bonding πc = 0.5,
clearly indicating delocalization of pi electrons. Thus, the value of electron
occupation number in pc orbital is nz = 1.5. The value of nz = 1.5 is in good
agreement with the theoretical value (1.6) and is only slightly larger than the 1.3
obtained using an extended Townes-Dailey analysis discussed above.
Bonding around the nitrogen in 1,2-dihydro-1,2-azaborine is in principle
quite similar to that of pyrrole. Pyrrole86 thus serves as an excellent molecule for
comparison of quadrupole coupling strengths of the nitrogen nucleus along the c-
124
axis. In both molecules, the nuclear quadrupole coupling constant along the cinertial axis, eQqcc, is perpendicular to the ring plane; the nitrogen atom is sigma
bonded to hydrogen. The measured eQqcc for 1,2-dihydro-1,2-azaborine is 1.25
MHz and for pyrrole it is given86 as 1.292 MHz Thus, the electric field gradients
at the nitrogen nucleus orthogonal to the ring plane are very similar for the
aromatic molecule pyrrole and 1,2-dihydro-1,2-azaborine. This implies that pelectron electronic charge distribution around the nitrogen atom of 1,2-dihydro1,2-azaborine is very similar to that of pyrrole. The observed similarities indicate
that, for both molecules, a nitrogen unshared electron pair, which lies orthogonal
to the ring plane, participates in π-electron system.
5.2.5 Discussion
The microwave spectrum for 1,2-dihydro-1,2-azaborine has been
measured in 7-18 GHz range, providing important structural parameters for the
isolated BNC4H6 molecule. Analysis of the rotational spectrum has shown that
this molecule is a near-oblate asymmetric top (asymmetry parameter κ = 0.79).
Measured rotational constants and nuclear quadrupole coupling constants for the
ground state structure are in good agreement with the theoretical calculations.
The r0 structural parameters R(B-N) = 1.45(3) Å, R(B-C) = 1.51(1) Å and R(N-C)
= 1.37 (3) Å have been determined from the least-squares fit analysis.
Measured quadrupole coupling constants of 14N, 10B and 11B are consistent with
previous measurements on small B-N molecules. The nuclear quadrupole
125
moments of boron and nitrogen have the same sign with the value for 11B being
twice and 10B four times that of 14N. The measured nitrogen quadrupole coupling
constants for the 2 boron isotopomers in the principal axis system are essentially
the same within the given uncertainty limit. As expected, these 14N eQq values
should not change for the different boron isotopomers.
Our measurements of rotational constants permitted us to directly
measure the planarity of this molecule from the inertial defect. From the
measured rotational constants, we calculated the ground state inertial defect to
be Δ0 = 0.02 amu⋅Å2. The observed near zero and positive inertial defect
indicates that the molecular structure of 1,2-dihydro-1,2-azaborine is planar. If
the ring were to be non-planar or have large anharmonicity, a negative inertial
defect would have been observed. Frequency calculations (MP2/6-311+G**)
showed there are three ring-puckering modes that can distort the molecule from
planarity. These three modes have anharmonic vibration frequencies ranging
from 325-465 cm-1 and contribute little to the total zero-point vibrational energy.
We estimated the vibrational temperature in the molecular beam to be about 10
Kelvin for our experiment. The calculated asymmetrically reduced distortion
constant for 1, 2-dihydro-1,2-azaborine is ΔJ = 0.7 kHz. Data from both
experiment and theory suggested that the ring is planar with a very small
centrifugal distortional constant.
126
Several theoretical calculations predicted that 1,2-dihydro-1,2-azaborine
would show more aromatic character than borazine but would have
approximately half the aromatic stabilization energy as benzene. Studies by
Martitz, et al87. confirmed that this is most likely to be the case. A key aspect of
the present work was to provide high resolution spectroscopic data that would
provide additional information to support the current hypothesis regarding the
aromatic properties of 1,2-dihydro-1,2-azaborine. One requirement of aromaticity
for a heterocyclic ring molecule is that the ring must be planar. We have shown
that this is the case for 1,2-dihydro-1,2-azaborine (see above discussion).
Because the ring is planar, we can infer that there is some π-electron overlap in
the B-N bond. Our least-squares fit analysis of the BNC4H6 structure showed the
measured bond distance between boron and nitrogen, R(B-N) = 1.45 Å. This
distance is closer to the double bond found in H2NBH2 (R(B-N) = 1.39 Å) than the
single bond found in H3NBH3 (R(B-N) = 1.65 Å). The measured bond length R(BC) = 1.51 Å is longer compared with the C-C bond distance in benzene due to
the increased atomic radius of boron. The gas-phase bond lengths for BNC4H6
are in good agreement with the bond lengths determined by single crystal X-ray
diffraction of substituted 1,2-azaborine derivatives .
Our interpretation of the nuclear quadupole coupling constants reveals
additional information regarding the aromaticity. The component perpendicular
to the c-axis for nitrogen is consistent with other nitrogen-containing aromatic
molecules. The electric field gradients experienced by nitrogen in 1,2-dihydro-
127
1,2-azaborine and pyrrole are nearly equal. Additionally, using an extended
Townes-Daily analysis, we ‘see’ approximately 0.3 e- in the boron valence pc
orbital. This result is consistent with a π-electron delocalized structure for 1,2dihydro-1,2-azaborine.
128
Table 5.1. Spectroscopic constants for1,2-dihydro-1,2-Azaborine. Values in MHz. The
ground state inertia defect (Δ = Icc – Iaa –Ibb) is Δ0 = 0.02 amu⋅Å2 for H6B11N14C4.______
Parameter
H6B11N14C4
H6B10N14C4
H5B11DN14C4 MP2/ 6-
MP2/
31+G(d,p)
6-311+G(d,p)
A
5657.335(1)
5794.049(3)
5642.9571
5635.595
5633.597
B
5349.2807(5) 5352.383(1)
5059.2583
5354.980
5344.391
C
2749.1281(4) 2781.7927(6) 2669.6747
2745.937
2742.593
Βχaa
-1.71(1)
-3.42(2)
-
-1.51
-1.6
Βχbb
-1.33(2)
-1.83(5)
-
-1.32
-1.4
Βχcc
3.03(2)
5.26(3)
-
2.83
3.0
Νχaa
0.46(1)
0.43(1)
-
0.50
0.47
Νχbb
0.78(6)
0.79(3)
-
0.55
0.57
Νχcc
-1.25(6)
-1.22(3)
-
-1.05
-1.0
σ kHz
8
17
-
-
-
Ntotal/Ndistinct
139/92
73/58
3
-
-
129
Table 5.2. Structural parameters from the least squares fit to the experimental rotational
constants. The listed error limits are 2σ______________________________________.
Parameter
Microwave
MP2/6-31+G(d,p)
MP2/6-311+G(d,p)
r(B-N)
1.45(3) Å
1.438 Å
1.437 Å
r(B-C)
1.51(1) Å
1.510 Å
1.516 Å
r(N-C)
1.37(3) Å
1.369 Å
1.368 Å
α
119˚
119.2˚
119.1˚
β
115(3)˚
114.3˚
114.5˚
γ
123(3)˚
124.4˚
124.1˚
δ
120˚
120.4
120.4˚
σ
0.9 MHz
-
-
Table 5.3. B-N bond distances reported in the literature
Molecule
R(B-N)/ Å
H2NBH2
1.391(2)a
H3NBF3
1.59b
BH3NH3
1.6576(16)c
HCN-BF3*
1.60(2)d
a
ref 85
b
ref 86
c
ref 87
d
ref 88
130
Table 5.4. Azaborine line list of measured frequencies (obs) for the normal isotopomer,
H6B11-N14C4. The frequencies are given in MHz. The column (o-c) lists the deviations of
the “best fit” calculated frequencies ( c ) from the measured frequencies (o).__________
J" Ka" Kc" F1" F" J' Ka' Kc' F1' F '
1
0
1
2
2 0 0
0
2
2
1
0
1
2
2 0 0
0
2
3
1
0
1
2
3 0 0
0
2
2
1
0
1
2
3 0 0
0
2
3
1
0
1
2
1 0 0
0
2
1
1
0
1
2
1 0 0
0
2
2
1
0
1
3
4 0 0
0
2
3
1
0
1
3
3 0 0
0
2
2
1
0
1
3
3 0 0
0
2
3
1
0
1
1
2 0 0
0
2
1
1
0
1
1
2 0 0
0
2
2
1
0
1
1
2 0 0
0
2
3
1
1
1
2
2 0 0
0
2
1
1
1
1
2
2 0 0
0
2
2
1
1
1
2
2 0 0
0
2
3
1
1
1
2
3 0 0
0
2
2
1
1
1
2
3 0 0
0
2
3
1
1
1
2
1 0 0
0
2
1
1
1
1
2
1 0 0
0
2
2
1
1
1
3
2 0 0
0
2
1
1
1
1
3
2 0 0
0
2
3
1
1
1
3
4 0 0
0
2
3
1
1
1
1
1 0 0
0
2
1
1
1
1
1
1 0 0
0
2
2
1
1
1
1
2 0 0
0
2
1
1
1
1
1
2 0 0
0
2
2
1
1
1
1
2 0 0
0
2
3
2
1
1
3
3 2 1
2
3
2
2
1
1
3
2 2 1
2
3
3
2
1
1
2
2 2 1
2
3
2
2
1
1
2
3 2 1
2
3
3
2
1
1
4
5 2 1
2
3
4
2
1
1
4
5 2 1
2
3
4
2
1
1
2
2 2 1
2
3
3
2
1
1
3
2 2 1
2
2
1
obs
8097.956
8097.956
8098.072
8098.072
8098.168
8098.168
8098.458
8098.580
8098.580
8098.869
8098.869
8098.869
8405.945
8405.945
8405.945
8406.217
8406.217
8406.346
8406.346
8406.439
8406.439
8406.493
8406.816
8406.816
8406.883
8406.883
8406.883
7801.448
7801.369
7801.141
7801.068
7801.015
7801.003
7800.952
7800.936
o-c
-0.004
-0.004
-0.005
-0.005
0.012
0.012
-0.013
0.003
0.003
0.000
0.000
0.000
-0.018
-0.018
-0.018
0.013
0.013
0.008
0.008
0.005
0.005
0.003
0.004
0.004
-0.005
-0.005
-0.005
0.002
0.003
-0.007
-0.005
0.003
-0.009
-0.008
-0.003
131
Table 5.4 cont.__________________________________________________
J" Ka" Kc" F1" F" J' Ka' Kc' F1' F '
2
1
1
1
2 2 1
2
3
2
2
1
1
4
4 2 1
2
3
3
2
1
1
3
3 2 1
2
2
2
2
1
1
3
4 2 1
2
4
5
2
1
1
3
4 2 1
2
4
3
2
1
1
4
3 2 1
2
2
3
2
1
1
2
2 2 1
2
2
2
2
1
1
3
4 2 1
2
4
4
2
1
1
4
3 2 1
2
2
2
2
1
1
1
2 2 1
2
2
3
2
1
1
1
2 2 1
2
4
3
2
1
1
3
3 2 0
2
3
2
2
1
1
2
1 2 0
2
3
2
2
1
1
4
3 2 0
2
3
4
2
1
1
3
2 2 0
2
2
3
2
1
1
3
4 2 0
2
2
3
2
1
1
4
4 2 0
2
3
3
2
1
1
3
3 2 0
2
2
2
2
1
1
3
4 2 0
2
4
5
2
1
1
3
4 2 0
2
4
3
2
1
1
2
2 2 0
2
2
1
2
1
1
4
3 2 0
2
2
3
2
1
1
2
3 2 0
2
4
3
2
1
1
4
3 2 0
2
2
2
2
1
1
3
3 2 0
2
4
4
2
1
1
4
3 2 0
2
4
3
2
1
1
3
2 2 0
2
1
2
2
1
1
1
2 2 0
2
2
2
2
1
1
1
2 2 0
2
4
3
2
1
1
2
2 2 0
2
1
2
2
1
1
4
3 2 0
2
1
2
3
2
1
4
3 3 2
2
4
3
3
2
1
4
3 3 2
2
2
2
3
2
1
4
3 3 2
2
3
2
3
2
1
4
3 3 2
2
3
3
3
2
1
4
3 3 2
2
4
3
3
2
1
4
5 3 2
2
3
4
3
2
1
4
5 3 2
2
4
5
3
2
1
4
5 3 2
2
5
4
3
2
1
4
5 3 2
2
5
6
3
2
1
4
4 3 2
2
2
3
3
2
1
4
4 3 2
2
3
4
obs
7800.809
7800.737
7800.658
7800.617
7800.518
7800.415
7800.374
7800.246
7800.246
7800.177
7799.879
7827.221
7827.056
7826.695
7826.695
7826.611
7826.511
7826.437
7826.381
7826.301
7826.301
7826.198
7826.106
7826.026
7826.026
7825.893
7825.793
7825.793
7825.660
7825.403
7825.294
7355.761
7355.761
7355.761
7355.761
7355.761
7355.629
7355.629
7355.629
7355.629
7355.523
7355.523
o-c
-0.008
0.010
-0.003
0.014
0.011
-0.003
0.012
0.007
-0.016
-0.010
0.013
-0.003
0.000
0.001
-0.008
0.005
0.003
-0.007
-0.001
0.010
-0.009
0.002
0.011
-0.020
0.011
0.011
-0.017
-0.021
0.010
-0.001
-0.010
0.006
0.006
0.006
0.006
0.006
-0.012
-0.013
-0.013
-0.013
0.005
0.005
132
Table 5.4 cont.__________________________________________________
J" Ka" Kc" F1" F" J' Ka' Kc' F1' F '
3
2
1
4
4 3 2
2
4
4
3
2
1
4
4 3 2
2
5
4
3
2
1
4
4 3 2
2
5
5
3
2
1
3
2 3 2
2
2
1
3
2
1
3
2 3 2
2
2
2
3
2
1
3
2 3 2
2
3
2
3
2
1
3
2 3 2
2
3
3
3
2
1
2
1 3 2
2
2
1
3
2
1
2
1 3 2
2
2
2
3
2
1
5
6 3 2
2
4
5
3
2
1
5
6 3 2
2
5
5
3
2
1
5
6 3 2
2
5
6
3
2
1
5
4 3 2
2
4
4
3
2
1
5
4 3 2
2
3
3
3
2
1
5
4 3 2
2
4
5
3
2
1
5
4 3 2
2
5
4
2
1
2
3
3 1 1
1
3
2
2
1
2
3
2 1 1
1
2
2
2
1
2
2
3 1 1
1
3
4
2
1
2
3
3 1 1
1
2
2
2
1
2
2
2 1 1
1
2
3
2
1
2
1
2 1 1
1
1
2
2
1
2
2
1 1 1
1
2
2
2
1
2
2
3 1 1
1
2
2
2
1
2
1
2 1 1
1
1
1
2
1
2
4
3 1 1
1
2
3
2
0
2
2
2 1 1
1
3
3
2
0
2
2
3 1 1
1
3
4
2
0
2
3
3 1 1
1
2
2
2
0
2
2
2 1 1
1
2
3
2
0
2
2
1 1 1
1
2
2
2
0
2
2
3 1 1
1
2
2
2
0
2
1
1 1 1
1
1
2
2
0
2
1
2 1 1
1
1
1
2
0
2
1
1 1 1
1
1
1
2
0
2
2
2 1 1
1
2
2
2
0
2
1
2 1 1
1
3
3
2
0
2
3
3 1 0
1
3
3
2
0
2
3
3 1 0
1
3
4
2
0
2
3
3 1 0
1
3
2
2
0
2
2
3 1 0
1
1
2
2
0
2
3
3 1 0
1
2
3
obs
7355.523
7355.523
7355.523
7355.492
7355.492
7355.492
7355.492
7355.038
7355.038
7355.141
7355.141
7355.141
7355.084
7355.084
7355.084
7355.084
13596.162
13596.443
13596.544
13596.632
13596.997
13597.040
13597.040
13597.067
13597.113
13597.153
13570.718
13570.764
13570.848
13571.203
13571.264
13571.293
13571.325
13571.325
13571.401
13571.434
13571.475
13878.223
13878.325
13878.389
13878.389
13878.744
o-c
0.005
0.005
0.005
0.002
0.002
0.002
0.002
0.016
0.016
0.002
0.002
0.002
-0.014
-0.014
-0.014
-0.014
0.008
0.006
0.004
0.006
0.014
0.004
-0.012
0.000
-0.001
0.005
-0.004
0.002
0.004
0.004
-0.011
0.004
-0.001
-0.007
-0.003
-0.006
0.012
-0.008
-0.011
0.010
0.006
0.013
133
Table 5.4 cont.__________________________________________________
J" Ka" Kc" F1" F" J' Ka' Kc' F1' F '
2
0
2
2
3 1 0
1
3
2
2
0
2
2
2 1 0
1
3
3
2
0
2
2
1 1 0
1
2
1
2
0
2
2
3 1 0
1
2
3
2
1
2
3
4 1 0
1
3
3
2
1
2
3
3 1 0
1
3
3
2
1
2
2
1 1 0
1
1
1
2
1
2
4
3 1 0
1
1
2
2
1
2
2
1 1 0
1
3
2
2
2
1
2
2 2 1
2
1
2
2
2
1
4
5 2 1
2
4
4
2
2
1
1
1 2 1
2
2
2
2
2
1
2
3 2 1
2
4
4
2
2
1
3
2 2 1
2
1
2
2
2
1
2
2 2 1
2
4
3
obs
13878.822
13878.822
13879.080
13879.171
13903.952
13904.002
13904.175
13904.476
13904.580
8723.804
8724.054
8724.108
8724.157
8724.180
8724.379
o-c
-0.001
-0.004
-0.002
-0.004
-0.007
-0.010
-0.001
-0.006
-0.007
-0.002
0.013
0.001
0.003
-0.009
-0.001
Table 5.5. Azaborine line list for H6B10-N14C4. Frequencies are given in MHz.
J'
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
Ka'
0
0
0
0
0
0
0
0
0
0
1
1
1
1
1
1
1
0
0
0
0
Kc'
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
F1
3
3
3
3
3
4
4
4
2
2
4
4
4
3
3
3
3
3
3
2
2
F
3
3
3
4
4
5
4
4
2
2
5
4
4
4
4
2
2
4
2
2
2
J"
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
1
1
1
Ka"
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Kc"
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
1
1
1
F1"
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
4
4
2
2
F"
2
3
4
4
3
4
3
4
2
3
4
3
4
4
3
2
3
3
3
3
1
Frequency
8133.594
8133.594
8133.594
8133.693
8133.693
8134.331
8134.403
8134.403
8134.608
8134.608
8575.871
8576.067
8576.067
8575.561
8575.561
8575.678
8575.678
14086.77
14086.77
14086.86
14086.96
o-c
0.0259
0.0259
0.0259
0.0077
0.0077
0.0043
-0.0098
-0.0098
-0.0055
-0.0055
-0.0216
-0.0033
-0.0033
-0.025
-0.025
0.0218
0.0217
-0.0034
-0.0057
-0.0146
0.0211
134
Table 5.5 cont._______________________________________
J'
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
Ka'
0
0
0
0
0
0
0
0
0
0
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
Kc'
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
1
1
2
2
1
1
1
1
F1
2
3
5
1
4
5
5
3
4
3
3
3
3
4
5
2
2
2
2
5
5
2
2
1
2
1
2
2
3
5
1
5
5
3
5
3
3
2
1
2
2
5
F
1
3
5
1
5
6
4
3
5
4
3
2
2
4
4
3
3
1
1
6
4
3
1
0
3
1
2
2
3
5
0
4
4
3
5
3
2
1
1
1
3
5
J"
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
1
1
2
2
2
2
Ka"
0
0
0
0
0
0
0
0
0
0
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
0
0
0
0
0
0
0
0
1
1
0
0
0
0
0
0
Kc"
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
1
1
2
2
2
2
F1"
2
3
4
2
3
4
4
3
4
2
2
2
3
3
2
2
2
2
2
4
4
3
3
2
3
2
2
2
3
4
2
4
4
3
4
2
3
2
1
1
1
5
F"
1
3
5
2
4
5
3
2
5
3
2
1
2
3
3
3
2
2
1
5
3
2
2
1
4
2
2
1
2
4
1
3
5
3
4
2
2
1
2
1
2
5
Frequency
14087.2
14087.46
14087.74
14087.86
14087.15
14087.42
14087.5
14087.26
14086.52
14086.41
14086.36
13697.22
13697.56
13697.64
13697.71
13697.73
13697.82
13697.82
13697.92
13697.99
13698.13
13698.3
13698.3
13698.37
13698.37
13698.47
14139.07
14139.07
14139.46
14139.84
14139.86
14139.67
14139.61
14139.61
7712.085
7711.826
14139.5
14139.37
7762.598
7762.794
7762.794
7763.01
o-c
-0.0168
0.0104
0.0047
0.0255
-0.0018
0.0167
0.0072
-0.0335
0.0071
-0.0061
-0.0402
0.0209
-0.0041
-0.0071
-0.0177
-0.0093
0.0016
-0.0001
-0.0071
-0.0054
-0.017
0.0107
0.0089
-0.0248
0.0128
-0.0058
0.0203
-0.0268
-0.0088
0.0211
0.0105
0.0091
0.0036
-0.0146
-0.0142
-0.0318
0.0096
-0.0136
0.0282
-0.0088
-0.0026
-0.0086
135
Table 5.5 cont.____________________________________________
J'
2
2
2
2
2
2
2
2
2
2
Ka'
1
1
1
1
0
0
0
0
0
0
Kc'
1
1
1
1
2
2
2
2
2
2
F1
3
1
1
4
3
5
1
5
1
5
F
3
2
0
4
3
5
0
4
2
4
J"
2
2
2
2
1
1
1
1
1
1
Ka"
0
0
0
0
1
1
1
1
1
1
Kc"
2
2
2
2
1
1
1
1
1
1
F1"
1
2
2
5
3
4
2
4
2
2
F"
2
3
1
5
2
4
1
5
2
3
Frequency
7763.14
7763.256
7763.317
7763.585
13645.35
13646.02
13646.23
13645.9
13646.27
13645.54
o-c
0.0132
0.0291
-0.0176
0.0086
-0.0121
0.0297
-0.0145
0.0269
0.0028
-0.0197
Table 5.6. Azaborine line list for H5B11-N14DC4. Frequencies are given in MHz.
J’
1
1
2
Ka’
0
1
0
Kc’
1
1
2
J"
0
0
1
Ka"
0
0
0
Kc"
0
0
1
obs
7728.933
8312.632
13557.518
136
Figure 5.3. Electron density maps for the MP2 optimized structures of 1,2-dihydro-1,2azaborine and benzene mapped with the electrostatic potential (Iso Val = 0.001) from
the total SCF density. Center (dark part) is most negative (electron rich) and the edge is
most positive. In the top, right, B atom is lightest, N atom blue(darker).
137
5.3 Mercaptopyridine-N-oxide
5.3.1 Introduction
The interest in 2-mercaptopyridine-N-oxide originates from Eric Block at
the University of Albany. He has been studying the sulfur-containing molecules
in plants for many years88 and contacted our laboratory about possibly detecting
2-mercapto-pyridine-N-oxide or its tautomer N-hydroxypyridine-2(1H)-thione.
The first step in this collaboration was to determine the microwave spectrum and
to identify the species in a pure sample.
The equilibrium between 2-mercaptopyridine-N-oxide and Nhydroxypyridine-2(1H)-thione has been of studied by many groups89. This
section provides experimental evidence that the N-hydroxypyridine-2(1H)-thione
has been observed and a partial gas phase structure consistent with Nhydroxypyridine-2(1H)-thione has been determined using isotopes of sulfur and
hydrogen. The object of this project is to provide an analysis of the monomer
that can be used to identify the species in a mixture present in plant samples.
138
A
B
Erel = 0
Erel = 1400 cm-1
μa=5.0D
μa=3.8
μb=0.3D
μa=3.0
Figure 5.4 A) N-hydroxypyridine-2(1H)-thione , B) 2-mercaptopyridine-N-oxide
Calculated structures and total energies using MP2/6-31+G(d,p),
139
5.3.2 Experimental
2-mercaptopyridine-N-oxide was purchased from sigma Aldrich and used
without purification. The first experiments were run at 70C and discoloration of
the sample was observed within a couple of hours. Eventually, 45C gave
sufficient vapor pressure to take all the data reported here. The 34S was
measured in natural abundance (4.3%) and the OD isotopomer was made by
placing 0.250 mg of 2-mercaptopyridine-N-oxide in 1 mL of d4-methanol and
allowed to stir overnight. The d4-methanol was pumped off and single shot signal
strength of the singly deuterated sample was observed. The spectrometer has
been described in chapter two and the Bosch fuel injector was used for this.
5.3.3 Data Summary
The measured microwave spectrum obtained consisted of only a-type
dipole transition with the predicted spectrum of N-hydroxypyridine-2(1H)-thione.
61 transitions were assigned to one species that exhibited a rich spectrum that
could be fit using Herb Pickett’s SPFIT program. The spectrum used the
quadrupole coupling of nitrogenThe most telling feature of the predicted spectra
involve the quadrupole coupling constant for nitrogen. The nitrogen quadrupole
coupling constant was fit three times in the experiment and a good determination
of all three components has been obtained. The predicted nitrogen quadrupole
coupling constant is twenty times lower in 2-mercaptopyridine-N-oxide than Nhydroxypyridine-2(1H)-thione. The lack of b-dipole transitions and the magnitude
140
of the quadrupole coupling constant suggest that the molecule observed is Nhydroxypyridine-2(1H)-thione.
Table 5.7 Summary of the calculated rotational constants and quadrupole
coupling constant_______________________________________________
A
B
C
χaa
χbb
χcc
N
σ
/ MHz
/ MHz
/ MHz
/ MHz
/ MHz
/ MHz
/ kHz
MP2/6-31+G(d,p)
SH
3200.02
1586.64
1060.07
0.048
0.71
-0.75
-
MP2/6-31+G(d,p)
OH
3197.71
1596.93
1065.05
0.97
1.75
-2.72
-
32
S / 1H
3212.10(1)
1609.328(7)
1072.208(6)
1.15(1)
2.00(1)
-3.09(1)
61
8
Table 5.8 Results of the three isotopomers
32
A
B
C
DJ/
DJK/
χaa
χbb
χcc
N
σ
/ MHz
/ MHz
/ MHz
/ kHz
/ kHz
/ MHz
/ MHz
/ MHz
/ kHz
S / 1H
3212.10(1)
1609.328(7)
1072.208(6)
0.021(8)
0.25(9)
1.15(1)
2.00(1)
-3.09(1)
61
8
32
S / 2H
3166.49(2)
1596.440(1)
1061.412(1)
0.01(1)
0.4(2)
1.21(2)
1.91(2)
-3.12(2)
47
14
34
S/1H
3200.81(4)
1566.132(2)
1051.632(2)
0.23(8)
-5(2)
1.09(3)
1.93(3)
-3.08(3)
20
5
141
Table 5.9 C5H432S14NOH line list (o-c) is observed-calculated in kHz.
JKaKc
212
212
212
212
202
202
202
202
211
211
211
211
211
313
313
313
313
303
303
303
322
322
322
322
322
322
321
321
321
321
321
312
312
312
312
312
414
414
414
414
404
404
404
F
1
3
2
2
1
3
2
2
1
2
3
2
1
2
4
3
3
2
4
3
2
3
4
2
3
2
3
4
2
3
2
2
4
3
2
2
3
5
4
4
3
5
3
JKaKc
111
111
111
111
101
101
101
101
110
110
110
110
110
212
212
212
212
202
202
202
221
221
221
221
221
221
220
220
220
220
220
211
211
211
211
211
313
313
313
313
303
303
303
F
1
2
1
2
1
2
1
2
0
2
2
1
1
2
3
2
3
2
3
2
1
3
3
3
2
2
3
3
1
2
2
1
3
2
3
2
3
4
3
4
3
4
2
measured
4824.697
4825.825
4826.247
4826.819
5248.434
5249.107
5249.347
5249.688
5899.131
5899.571
5900.198
5900.481
5901.435
7172.46
7173.86
7174.056
7175.04
7618.24
7619.122
7619.452
8044.316
8044.52
8044.52
8044.52
8044.897
8044.897
8469.475
8469.977
8469.832
8470.07
8470.739
8769.579
8769.762
8769.919
8769.919
8770.549
9461.592
9463.119
9463.258
9464.446
9802.572
9803.757
9803.757
o-c
-1.2
-1.8
7.6
1.4
-1.4
0.6
2.5
-2.7
-0.4
16.5
23.9
1.8
-8.2
6.1
0.8
3
-3.6
-1.1
-7.1
20.9
5.7
1.6
1.5
1.4
3.7
3.5
-5
-2.4
2.3
5.6
0.2
-2.8
-2.1
-1.6
-7.3
3
-1.8
-1
-6.7
-3.1
-2.1
-2.5
-7.1
142
Table 5.9 cont.______________________________________
JKaKc
404
423
423
423
432
432
432
431
431
431
413
413
413
422
422
515
515
505
505
505
606
606
514
514
F
4
5
4
4
3
5
4
3
5
4
3
5
4
5
4
5
5
6
5
5
7
6
6
5
JKaKc
303
322
322
322
331
331
331
330
330
330
312
312
312
321
321
414
414
404
404
404
505
505
413
413
F
4
4
3
4
2
4
3
2
4
3
2
4
3
4
4
4
5
5
4
5
6
5
5
4
measured
9804.922
10636.49
10636.71
10636.71
10914.66
10914.78
10915.04
11004.83
11004.94
11005.12
11521.37
11521.48
11521.66
11557.13
11556.56
11698.95
11700.29
11903.47
11903.69
11904.86
13999.16
13999.32
14090.21
14090.41
o-c
-1.2
-13
0.5
0.5
0.7
6.7
0.2
-4
7.7
-6.1
-18.3
5.2
5.8
1.6
-11.7
0.8
5.6
-5.4
13.7
17
15.2
27.2
29.3
1
143
Table 5.10 Line list for C5H432S14NOD
JKaKc
313
313
313
313
303
303
303
303
322
322
322
322
321
321
321
312
312
312
312
414
414
414
414
404
404
404
404
423
423
423
432
432
413
413
413
413
422
422
515
515
505
505
505
F
4
2
3
3
2
4
3
3
2
3
4
2
3
2
4
4
2
3
2
5
3
4
4
3
5
4
4
5
4
4
5
4
3
5
4
3
4
3
6
5
6
4
5
JKaKc
212
212
212
212
202
202
202
202
221
221
221
221
220
220
220
211
211
211
211
313
313
313
313
303
303
303
303
322
322
322
331
331
312
312
312
312
321
321
414
414
404
404
404
F
3
1
2
3
2
3
2
3
1
3
3
3
3
1
3
3
3
2
2
4
2
3
4
3
4
3
4
4
3
4
4
3
2
4
3
3
3
2
5
4
5
3
4
measured
7105.354
7105.486
7105.544
7106.562
7543.638
7544.572
7544.868
7545.484
7973.236
7973.486
7973.486
7973.486
8401.934
8402.264
8402.451
8694.602
8694.785
8694.785
8695.374
9371.144
9371.221
9371.296
9372.504
9702.933
9704.151
9704.435
9705.338
10540.804
10541.031
10541.031
10821.461
10821.731
11418.868
11418.98
11419.158
11419.493
11466.231
11466.231
11583.465
11583.588
11781.472
11781.546
11781.718
o-c
-7.5
-11.8
-17.4
-2.4
-10.2
0.7
-7.2
2.6
-6.2
26.6
26.6
26.4
11.3
-3.9
23.1
-3.9
21.4
16
-2.6
-0.2
3.1
3.9
9.1
2.7
4.7
8.4
1.4
-29.5
-22.6
-22.6
7.3
-2.7
-19.6
3.9
0.6
-2.3
11.1
-3.8
2.6
3
-18.4
34.6
17.8
144
Table 5.10 cont.
JKaKc
505
616
616
606
F
5
5
6
6
JKaKc
404
515
515
505
F
5
4
5
5
measured
11782.879
13756.095
13756.209
13856.543
o-c
-11.4
-35.9
9.4
16.8
Table 5.11 Line list for C5H434S14NOH
JKaKc
F
313
313
313
303
303
303
303
312
312
312
414
414
404
404
404
413
413
515
505
JKaKc
2
4
3
2
4
3
3
2
4
3
5
4
5
4
4
3
5
4
6
F
212
212
212
202
202
202
202
211
211
211
313
313
303
303
303
312
312
414
404
2
3
3
2
3
2
3
1
3
2
4
3
4
3
4
2
4
3
5
measured
7020.763
7022.167
7023.353
7463.234
7464.101
7464.396
7464.945
8552.205
8552.386
8552.538
9268.916
9269.041
9618.251
9618.528
9619.38
11249.05
11249.14
11464.9
11682.79
o-c
-2.5
-3.7
2.7
-3
6.9
7.4
-1.5
-1
-3.5
1.2
12.3
-3.8
-1.4
-6.3
-6.8
2.4
-0.4
-6.6
16.4
145
5.3.4 Results
Using the results from Table 5.7 a fit of four parameters was performed
and are summarized in figure 5.5. The structure is consistent with Nhydroxypyridine-2(1H)-thione and not 2-mercaptopyridine-N-oxide. There is a tilt
of the sulfur towards the OH as predicted using MP2/6-31+G(d,p).
Figure 5.5 Parameters and results from a four parameter fit using three sets of
rotational constants given in Table 5.7.
________________________________________________________________
The initial goal of the project has been met. The spectrum has been identified
and if this molecule can be extracted from the plant, it can be uniquely identified.
146
The 34S signal was very strong and could also be used to help identify the
mixture that may come from the plant.
147
5.4 Arsenic Triphosphide
5.4.1 Introduction
Arsenic triphosphide (AsP3) has been analyzed using microwave
spectroscopy to assign the quadrupole spectrum and obtain data on an
interesting analog of ammonia. It was anticipated that (AsP3) would not behave
in the manner ammonia has received much attention, the tunneling of arsenic
through the plane of the phosphorous, but may reveal something interesting in
the assignment of the quadrupole spectrum.
This molecule had remained elusive until Cossairt, et al90 were able to
reliably synthesize the compound using a niobium catalyst. Their paper on the
physical properties and reactivity of AsP391 was complemented by their next
paper that explored the electronic and molecular structure.92 This work
complements the inquiries into electronic structure by determining the
quadrupole coupling constant and comparing the value to theory.
148
Figure 5.6 Arsenic triphosphide
5.4.2 Experimental
5.4.2.1
Synthesis of AsP3
The sample arrived from Dr. Christopher Cummins laboratory where Dr. Brandi
Cossairt performed the synthesis. Here is her procedure:
All manipulations, unless otherwise noted, were performed in a Vacuum
Atmospheres model MO-40M glovebox under an inert atmosphere of purified N2.
All solvents were obtained anhydrous and oxygen-free by bubble degassing (Ar)
and purification using a Glass Contours Solvent Purification
System built by SG Water. Celite 435 (EM Science) were dried by heating
above 200 °C under a dynamic vacuum for at least 24 h prior to use. All reagents
were purchased from Aldrich chemical company and were used without further
purification. {[Na·3THF][P3Nb(ODipp)3]} was prepared
according to literature procedures
[AsP3]
[Na][P3Nb(ODipp)3] + AsCl3 → AsP3 + Cl2Nb(ODipp)3 + NaCl
Procedure
{[Na·3THF][P3Nb(ODipp)3]} 93(2.91 g, 3.04 mmol) is dissolved in 50 mL of THF in
a 100 mL round bottom flask equipped with a Teflon coated stir bar. This solution
is frozen in the glove box cold well along with a vial containing [AsCl3] (547 mg,
149
3.04 mmol) in 5 mL of THF. Upon thawing the [AsCl3] solution was added to the
THF solution of {[Na·3THF][P3Nb(ODipp)3]}. The reaction mixture was allowed
warm
to room temperature and is allowed to stir for 45 minutes. After the reaction time
had elapsed, the reaction mixture is filtered through a pad of Celite and the
volatile components are removed under reduced pressure. The resulting residue
is isolated and placed into a sublimation apparatus. The residue is sublimed with
the exclusion of light at 70 °C under dynamic vacuum for 5 h. A constant stream
of cold water should be kept running through the cold finger during the
sublimation to ensure no loss of [AsP3].
After cooling, the sublimation apparatus can be returned to the glove box and the
crystalline [AsP3] isolated from the cold finger, with pure orange
[Cl2Nb(ODipp)3(THF)] in the bottom of the sublimation
apparatus. Yield after sublimation: 65%.
5.4.3 Data Summary
Arsenic triphosphide has a complicated microwave spectrum that is still under
analysis. There is only one isotope combination as arsenic (75As), I=3/2, has one
stable isotope as does phosphorus (31P). It was expected that the 0-1 transition
would contain three transitions due to arsenic having a spin of great than 1. 11
transitions were detected between 4412 and 4344 MHz. Nine were assigned
rotational quantum numbers and the results of the three fits are given below in
Table 5.12.
Fit
B
χaa
DJ
DJK
HJ
N
σ
I
2201.3899(4)
48.73(1)
49
9
II
2192.257(4)
48.62(3)
6.5(9)
-75(1)
-210(50)
20
30
III
2183.640(6)
48.53(3)
92.6(8)
43(2)
14
12
150
Table 5.13 Line list for the strongest measured transitions.
J’
1
1
1
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
K’
0
0
0
1
0
1
-1
1
-1
0
0
-1
1
-1
1
-1
1
2
0
-1
1
-2
-2
2
-2
2
-1
1
-1
1
0
0
0
2
-2
2
-1
1
-1
F’
1
3
2
1
2
2
2
4
4
4
1
3
3
2
2
3
3
3
2
2
2
3
5
5
4
4
3
3
5
5
4
5
3
3
2
2
4
4
3
J”
0
0
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
K”
0
0
0
-1
0
-1
1
-1
1
0
0
1
-1
1
-1
1
-1
0
0
1
-1
2
2
-2
2
-2
1
-1
1
-1
2
0
2
-2
2
-2
1
-1
1
F”
2
2
2
1
2
1
1
3
3
3
1
3
3
2
2
2
2
3
1
2
2
3
4
4
4
4
3
3
4
4
3
4
2
2
2
2
3
3
2
Observed
frequency
/ MHz
4390.619
4400.356
4412.542
8793.413
8795.839
8799.498
8799.498
8802.612
8802.612
8804.525
8805.569
8808.711
8808.711
8810.459
8810.459
8814.806
8814.806
8816.713
8817.765
13201.03
13201.03
13202.08
13204.85
13204.85
13204.85
13204.85
13205.81
13205.81
13207.03
13207.03
13207.76
13207.76
13208.34
13208.34
13208.34
13208.34
13210.07
13210.07
13210.17
o-c /
kHz
9.4
7.3
7.5
9.9
11
11
11
7
7
7.9
9.7
6
6
9.4
9.4
8.5
8.5
11.6
12.1
-3.4
-3.4
-0.2
-15.1
-15.1
-24.7
-24.7
-9.3
-9.3
-8.7
-8.7
0.3
-0.5
-3.9
-3.9
-17.9
-17.9
-11.7
-11.7
6.2
151
Table 5.13 cont________________________________________.
J’
3
3
3
3
3
3
3
3
3
3
K’
1
0
-2
-1
1
0
2
-2
2
0
F’
3
2
3
4
4
3
3
4
4
4
J”
2
2
2
2
2
2
2
2
2
2
K”
-1
0
0
1
-1
0
-2
0
-2
0
F”
2
1
2
4
4
3
3
3
3
4
Observed
frequency
/ MHz
13210.17
13210.77
13210.77
13216.17
13216.17
13217.04
13217.04
13217.04
13217.04
13219.94
o-c /
kHz
6.2
-4.6
2.5
-8.7
-8.7
-5.7
-5.7
-12.3
-12.3
-0.8
Table 5.14 Line list of next set of transitions assigned____________
J’
1
1
1
2
2
2
2
2
2
2
2
2
2
2
2
2
3
3
3
3
K’
0
0
0
0
1
-1
-1
1
0
2
1
-1
-1
1
2
0
0
0
0
1
F’
1
3
2
2
2
2
4
4
4
3
2
3
3
3
3
2
5
3
2
3
J”
0
0
0
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
K”
0
0
0
0
-1
1
1
-1
0
0
-1
1
1
-1
0
0
0
0
0
-1
F”
2
2
2
2
1
1
3
3
3
2
2
3
2
2
3
1
4
2
1
3
Observed
frequency
/ MHz
4372.342
4382.059
4394.219
8759.043
8763.031
8763.031
8766.154
8766.154
8767.705
8767.705
8773.971
8772.239
8778.311
8778.311
8779.863
8780.917
13151.96
13154.99
13154.99
13150.38
o-c / kHz
0.6
-0.8
-0.2
-20.1
16
16
27.3
27.3
-29.2
-27.3
16.2
25.3
17.3
17.3
-29.1
-24.4
24.7
46.9
39.7
-68.1
152
Table 5.15 Measured transitions from the third fit (weakest measured)
J’
1
1
1
2
2
2
2
2
2
2
2
2
K’
0
0
0
-1
0
-1
-1
0
0
-1
1
1
F’
1
3
2
1
2
2
4
4
1
3
2
3
J”
0
0
0
1
1
1
1
1
1
1
1
1
K”
0
0
0
1
0
1
1
0
0
1
-1
-1
F”
2
2
2
1
2
1
3
3
1
3
2
2
Observed
frequency
/ MHz
4354.783
4364.486
4376.63
8719.321
8721.905
8725.401
8728.465
8730.558
8731.596
8734.532
8736.289
8740.643
2
2
3
1
0
3
8742.699
o-c / kHz
-3.6
-1.2
4.9
5.5
0.9
25.7
-16.8
-2.2
-2.1
-25.1
-6.1
16.8
3.4
153
6. LOOSELY BOUND COMPLEXES OF ORGANOMETALLIC MOLECULES
6.1 Introduction
An effort to characterize the structure of loosely bound organometallic
complexes was begun after the success of accurately predicting the structure
of cyclopentadienyl thallium, η5-(C5H5)Tl, with argon94. The objective was to
determine a suitable system whose structure could be experimentally
determined using organometallic complexes of ferrocene (Cp2Fe), methyl
rhenium trioxide (MTO), butadiene iron tricarbonyl η4-(C4H6)Fe(CO)3 and
small molecules like carbon monoxide, ethylene and HCl. There exists a rich
literature reporting the effectiveness of MP2 calculations of gas phase dimers
of small molecules95. There is an equally extensive body of work on the
success of DFT to predict organometallic structure and reactivity96. Absent in
the literature are calculations of dimers that mix organometallic complexes
with small molecules. There exists comparisons of MP2 and DFT predictions
of structures and dipole moments of molecules97 and is the basis of my
approach to study these complex systems. The calculations reported here
begin to address an additional level of complexity, transition metal complexes.
While not much attention has been given to predicting the structure of loosely
bound dimers of organometallic complexes and small molecules, it is
anticipated that benchmark experimental results will catalyze future interest.
Given the amount of choices of basis set, method and geometry, only a
154
subset was calculated for each system. Hopefully, this work can stimulate
experimental work in this area and provide a path for the full blossoming of
this field.
Calculations of transition metals in the literature are very diverse. Density
functional theory has been found to accurately describe metal bonding in
solids98 and has been extended to molecules by the development of
generalized gradient approximation (GGA) methods99, most notably the
success of B3LYP and B3PW91. The traditional emphasis of DFT with
organometallic complexes can be opened to MP2 similar to the work of
Johnson, et al100. Calculations using MP2 can take considerable time with
optimizations and frequency calculations. There are two strategies regarding
the geometry of the organometallic monomer. The structure can be optimized
using each method or the gas phase structure can be used. If the gas phase
organometallic monomer is used with each method and a partial optimization
is performed, the binding energy may not represent a good comparison
amongst methods. For the calculations listed, with the exception of the CpTl,
a total optimization was performed. The results of the monomer calculations
using each method can give an indication of the effectiveness in predicting
the ground state geometry and molecular parameters if applicable. That is
stated with some caution because the bonding in the monomer may not be a
good indication of the dimer energy environment.
155
The diversity of approaches can be grouped into three categories:
method, basis set and geometry. There exist many DFT functionals that
could be tested but the best place to start was to use the traditionally
successful methods for organometallic structure, B3PW91 and B3LYP, and
compare them to MP2 (if possible). DFT methods have been developed to
better predict gas phase dimers such as HCTH407 and TPSS/TPSS and for
ferrocene-HCl were calculated.
Rare gas -organic molecule dimers have been in the literature since for 3
decades. The Moller-Plesset theory (MP2) with the 6-31+G basis set was
explored for model systems and are and given in Table 6-1.
Table 6.1 Results of Calculated binding energy and rotational constants
compare with theory.
Complex
Benzene HCl
Benzene HCl
Ethylene-HCl
Ethylene-HCl
Furan-HCl
Furan-HCl
Method
mp2/6-31G(d)
Expt101
mp2/6-31+G
Expt102
mp2/6-31+G
Expt103
Interaction
Energy/cm-1
-907.57
-720.00
-611.74
-575.00
-1696.47
-883.00
A
2830.22
22201.68
25457.00
8846.03
9420.00
B
1240.00
1237.70
2303.14
2308.00
1041.76
1003.99
C
1239.97
2140.08
2168.00
933.21
904.48
156
6.2 Ar-CpTl
MP2 calculations were used to study argon-cyclopentadienyl thallium104.
The loosely bound system was found to have a structure that was consistent
with MP2 calculations.
Figure 6.1 Plot of the binding energy (cm-1) as a function of r(Ar-Cp) for MP2
and DFT calculations
157
Figure 6.2 Potential energy surface profile for Ar-CpTl evaluated at the
MP2/aug-cc-pVTZ-PP (Thallium)/aug-cc-pVTZ(Ar, C, H). The binding energy
for the lowest energy structure is 4.6 kJ /mol.
158
6.3 Ferrocene-HCl
6.3.1 Introduction
Ferrocene’s structure, both electronic and molecular, has been analyzed
in many experiments as has the structure of loosely bound dimers of HCl with
organic molecules. The dimer between ferrocene and HCl provides a system
that is at the reach of high level ab initio calculations. The many choices of
methods and basis sets allow a description of the energy environment as a
function “approach”. Density functional theory is a natural starting point when a
transition metal is being studied. The number of electrons on the metal alone
provide ample complexity for any theory. The use of HCl as part of a dimer
immediately brings to mind MP2 or CCSD to predict binding energies and
equilibrium geometries.
It is of great interest to characterize the performance of DFT versus MP2.
Most studies have relied on the body of literature to compare the calculation
results with experiment. To further this analysis, organometallic complexes
represent a formidable energy landscape to probe with small molecules using the
current theoretical models.
The structure of ferrocene is known from many sources105 and the focus of
the calculations with ferrocene was to calculate the most stable structure of a
complex with HCl.
159
6.3.2 Experimental
Several weeks of experiments were performed using ferrocene and HCl.
Freshly sublimed ferrocene was placed into a sample cell and a 1-3% HCl in
Neon was passed over the sample and injected into the microwave
spectrometer. The sample was heated to 40 degrees and after a day, a green
deposition occurred in the cell.
6.3.3 Calculations
Many calculations were performed to predict the lowest energy geometry
of the dimer between ferrocene and HCl using DFT and MP2 methods. The
geometry is given in Figure 6.3.
Figure 6.3 Axis system for calculations of the Ferrocene-HCl dimer
160
Table 6.3 Summary of binding energy, rotational constants and dipole
moment magnitude for the ferrocene-HCl dimer. Basis Set Fe Hay-Wadt (n+1)
VDZ and C,H,O 6-311+G.
Orientation
ClH
ClH
ClH
ClH
ClH
ClH
ClH
HCl
HCl
HCl
HCl
HCl
HCl
HCl
HClp
Angle /˚
Method
0
0
0
0
90
90
90
90
90
90
90
0
0
0
90
MP2
B3PW91
B971
HCTH407
B3PW91
B971
HCTH407
MP2
B3PW91
B971
HCTH407
B3PW91
B971
HCTH407
HCTH407
Binding
Energy
-142.38
300.37
42.77
-130.84
41.25
-248.21
-916.10
-955.01
-889.83
-1448.48
-858.25
-717.26
-1192.93
-558.03
-364.26
A / MHz
1146.68
2182.79
2167.76
2174.93
1045.75
1015.08
1071.64
2123.68
1033.97
1007.09
1060.41
2178.73
2164.78
2173.15
1067.77
B/ MHz
628.85
347.23
372.59
366.71
455.18
553.58
567.03
409.39
714.24
704.08
612.12
376.04
367.58
316.62
524.76
C/ MHz
502.03
347.22
372.58
366.70
371.04
429.11
447.03
409.32
524.02
512.49
472.49
376.04
367.58
316.62
419.79
μ/D
1.80
1.85
1.76
1.81
1.99
1.95
1.87
2.90
3.19
3.06
2.70
2.88
2.84
2.42
1.40
6.3.4. Results
Large parts of the spectrum was covered and 58 lines were measured and
remain unassigned. Figure 6.4 is a graph of the transitions found so far and their
intensities. The potential reaction occurring in the cell made assignments very
difficult. Possible species involved C5H5FeClH and C5H4Cl. The experiment was
postponed until a sophisticated mixing valve106 could be constructed. If the
samples only met during the expansion into the microwave cavity, then the
possibility of observing dimers instead of reaction product would increase.
161
0.2
'FCHCLO~1.DAT'
0.18
Predicted Intensity
0.16
0.14
0.12
0.1
0.08
0.06
4000
5000
6000
7000
8000
Frequency / MHz
9000
Figure 6.4 Graph of results with HCl-Ferrocene
10000
11000
162
6.4 Methyl Rhenium Trioxide Complexes
6.4.1 Introduction
With the success of the Ar-CpTl calculations, similar calculations were performed
with MTO with argon, carbon monoxide and ethylene and ammonia. One system
in the literature has received much attention, methyl rhenium trioxide and
ethylene. The epoxiation of ethylene by MTO is a significant
The quadrupole coupling constant along the a-axis for 187Re in MTO was
calculated using B3LYP, B3PW91, M06, TPSS/TPSS, HCTH407 and MP2 using
the basis sets 6-31+G(d,p) and cc-pVDZ. The B3LYP and B3PW91 are two
methods that are commonly used for transition metal complexes. M06,
TPSSTPSS and HCTH407 are functionals that have been developed for gas
phase dimers.
163
Table 6.4 MTO monomer with DFT and MP2 predictions of structure and
quadrupole coupling constant.
Method
basis set C,H,O
B3PW91
cc-pVDZ
HCTH407
cc-pVDZ
M06
cc-pVDZ
MP2
cc-pVDZ
MP2
6-31+G(d,p)
TPSS/TPSS
cc-pVDZ
B3LYP
cc-pVDZ
χΨaa= 716.55(2) MHz
Ж
ŧ
χΨaa /MHz BЖ / MHz
-2.2
3467.97
-1.7
3429.8
-2.7
3479.7
13.0
3303.33
14.0
3305.37
-0.6
3401.42
-2.0
3435.53
Re-C / Re-Oŧ Å
2.07 / 1.70
2.08 / 1.71
2.07 / 1.70
2.07 / 1.75
2.09 / 1.75
2.09 / 1.72
2.09 / 1.71
Bexpt=3466.964(2)107
Re-C / Re-Oexpt = 2.074(4) / 1.703(2) Å108
The quadrupole coupling constant is very interesting. All the DFT calculations
run give the opposite sign of MP2 and the experimentally determined value.
MP2 is an order of magnitude away also. The results are from full optimizations
of methylrhenium trioxide. The geometries are very consistent with the gas
phase structure and there does not seem to be a correlation between predicted
geometry and the predicted quadrupole coupling constant.
164
6.4.2 Gas Phase complexes of MTO
Several small molecule dimers with MTO were calculated with MP2 and
the basis set listed in Table 6.5. The axis system of MTO is given in Figure 6.6.
Figure 6.5 Axis system for methylrhenium trioxide used in calculations
165
Table 6.5 Summary of calculations of dimers and MTO
Dimer
Orientation
Binding
Basis set on C,H,O*
Energy
cm-1
A/ MHz
B/ MHz C / MHz
μ/D
Ar
180
6-31+G(d)aVDZ
-112.67
3717.9
836.1
836.1
2.22
CO
180
6-31+G(d)
-368.24
3660.5
895.3
895.2
1.63
CO
90
6-31+G(d)
-409.47
3239.4
947.4
913.3
2.30
H2
180
6-31+G(d)
-95.27
3392.8
2873.2
2670.8
2.36
H2O
180
-2389.40 6-31+G(d)/aVDZ
3439.7
1878.1
1866.6
2
NH3
180
6-31+G(d)
-5133.20
2953.2
2171.8
1941.2
1.88
OC
180
6-31+G(d)
-271.88
3706.3
991.5
991.5
2.30
OC
90
6-31+G(d)
-59.30
3324.0
975.9
946.1
4.20
Ar
90
6-31+G(d)/aVDZ
-199.21
3409.0
638.8
628.9
2.32
C2H2
180
6-31+G(d)
-677.41
0.30
0.69
0.66
2.24
C2H4
180/90
6-31+G(d)
1957.66
3151.91
1163.6
1128.3
1.49
NF3
90
6-31+G(d)
-163.56
2252.52
524.4
524.4
2.37
* If Argon is present than aug-cc-pVDZ was used for Ar and the basis set listed was used for
C,H,O
166
7. STRUCTURE AND MOLECULAR PARAMETERS OF (η7-C7H7)Ti(η5-C5H5)
7.1 Introduction
The structural changes of organic ligands has been studied in for many
transition metal complexes109. The (η7-cycloheptatriene)Ti(η5-cyclopentadienyl),
(CHT)Ti(Cp), has been studied by our group110, but no structural information was
determined in that study. X-ray diffraction111 had produced a structure of the
carbon ring (CHT)- Ti-carbon ring (Cp) and that can now be compared to the
experimentally determined Ti-C distances. A second feature of the structure that
is interesting involves the “droop” of hydrogen towards the metal. The many
combinations of theory can produce an array of estimates of the angle (see figure
7-1). The goal of this experiment is to determine this angle and provide an
analysis of the results from several theoretical models. Also, a comparison of
similar molecules of zirconium, hafnium, chromium, molybdenum and tungsten
has been performed to report the trend predicted as we go down a row with 16eand 18e-complexes.
The first paper by our group also published the first 47Ti quadrupole coupling
constant assignments in a molecule. The molecule is a symmetric top and many
transitions were observed closely spaced. The K structure was assigned for the
48
Ti isotope and remaining lines were assigned to 47Ti quadrupole transitions. A
167
re-evaluation of this data has been performed because of predictions made by
high level theory that reveal a different sign and 4 to 8 times greater in magnitude
than reported in the first paper.
7.2 Experimental
The parent, (CHT)Ti(Cp), was synthesized as described by Keck, et al.
Two flasks containing CpTiCl3 in THF and freshly distilled cycloheptatriene and
magnesium turnings in THF are made and kept under a nitrogen environment.
The contents of the first flask CpTiCl3 in THF are added dropwise over an hour to
the second flask with stirring. Immediate green color is observed and after 1
hour from the addition of all the CpTiCl3 the solution turns darker green to blue.
The solution is allowed to sit overnight with stirring. The solvent is removed
under reduced pressure and the product is acquired by sublimation onto a cold
finger below 1 mTorr at 100C.
1-d-cycloheptatriene was made by addition of tropyllium tetrafluoroborate
and sodium borodeuteride in THF112. The solution is kept under nitrogen and
stirred overnight. The sample was filtered under an inert atmosphere and added
to a flask with magnesium turnings. This solution was reacted as described
above.
168
7.3 Calculations
The CHT-X-Cp motif was explored using Ti, Zr, Hf, Cr, Mo and W with
DFT calculations. The hybrid functional of Becke, Perdew and Wang (B3PW91)
was used with the Hay-Wadt (n+1) VDZ core potential on the metal and Pople’s
6-31+G(d) on carbon and hydrogen. The prediction of the tilt angle of the
hydrogen atom in the cycloheptatriene ring and the ring centroid to metal
distances are reported in Table 7.1.
Table 7.1 Results of CHT-X-Cp using B3PW91/Hay Wadt (n+1) on metal/631+G(d) on carbon and hydrogen. The angle is taken as centroid-carbonhydrogen deviation from 180 degrees towards the metal.
X
D(CHT-X)
D(Cp-X)
<(Cent-C-H)
Ti
1.47
1.98
8.5
Zr
1.69
2.2
5.6
Hf
1.62
2.16
6.1
Cr
1.43
1.80
10.1
Mo
1.60
2.00
8.0
W
1.59
1.98
8.9
169
7.4 Data Analysis and Results
The data taken for the this project is composed of additional measurements of
the parent and a new analysis of the 47Ti isotope in the parent complex.
7.4.1 (η7-C7H7)48Ti(η5-C5H5)
Three asymmetric top species were recorded, 13CC6H7-Ti-C5H5, 1-dC7H6TiC5H5 and C7H7Ti13CC4H5. The results are summarized in Table 7.2 and
the raw data located in tables 7.2-7.4.
Table 7.2 Summary of Isotopic studies with (η7-C7H7)Ti(η5-C5H5)
A
B
C
DJ
DJK
N
σ
/MHz
/MHz
/MHz
/kHz
/kHz
/kHz
Cp-13C
1270(5)
767.0142(9)
765.323(1)
[0.0429]
[0.364]
9
21
CHT-13C
1720(4)
769.269(1)
766.131(1)
0.04(2)
0.4(3)
12
7
1-d-CHT
1773(2)
769.6931(4)
761.1789(5)
0.030(6)
0.04(5)
16
4
The results from the isotopic studies can be used to perform a structure fit
with three parameters. Only the B and C rotational constants are used because
the parent does not have A determined and the fits of the isotopes have poorly
determined A rotational constants. The three parameters are the a coordinate of
the ring of carbon in the cycloheptatriene ring, cyclopentadienyl ring and
hydrogen in the cycloheptatriene ring. The results of the fit are given in table 7.3.
170
Table 7.3 Results from Least Squares Fit
Atom
a-coordinate
this study
a-coordinate
Calculated*
C-CHT
-1.48(3)
-1.47
H-CHT
-1.33(3)
-1.30
C-Cp
2.01(3)
1.98
24 kHz
σ
* as described in 7.3
The a-coordinate of the hydrogen has been determined to be 0.17Å smaller
than the carbon. Using 1 Å as the bond length, a droop of 9.8° is obtained for the
C-H bond from the plane the carbon ring. The deviation in the fit of 24 kHz
indicates that rings are most likely planar.
7.4.2 (η7-C7H7)47Ti(η5-C5H5)
An analysis of the 47Ti isotopomer has produced a fit of 28 lines compared to 17
lines in the published fit by Keck, see Table 7.4.
171
Table 7.4 Results of 47Ti fit and comparisons to Keck and Calculations
This Study
Keck
Calculated
B / MHz
771.7836(5)
771.7902(3)
780.682
χaa / MHz
-16.6(2)
8.19(4)
55.65
DJ / kHz
0.016(5)
0..040
-
DJK / kHz
-.125
1.64
-
σ / kHz
4
14
-
N
28
17
-
Using Gaussian 09, a single point calculation of the 47Ti isotope in the geometry
of the optimized structure gives χaa=+55.7 MHz. An analysis of the data for the
47
Ti gives χaa=-16.6 MHz. This is significantly different from the prediction and
the fit in the Keck paper of +8.2 MHz.
172
Table 7.5 1-d-CHT-Ti-Cp
J’ Ka’ Kc’ J” Ka” Kc” Measured
3
0
3
2
0
2
4592.4014
4
1
4
3
1
3
6106.3457
4
0
4
3
0
3
6122.9395
4
2
3
3
2
2
6123.4346
4
3
1
3
3
0
6123.5854
4
1
3
3
1
2
6140.4014
5
1
5
4
1
4
7632.8257
5
0
5
4
0
4
7653.2661
5
3
2
4
3
1
7654.5342
5
2
3
4
2
2
7655.293
5
1
4
4
1
3
7675.3926
6
1
6
5
1
5
9159.2383
6
0
6
5
0
5
9183.3193
6
1
5
5
1
4
9210.3154
7
1
7
6
1
6
10685.5713
7
0
7
6
0
6
10713.043
o-c /
KHz
4.4
1.2
-1.3
-2.7
-0.8
1.2
0.2
-0.2
4.6
-9.9
0.4
0.7
-0.1
4.3
3.1
-4.4
173
Table 7.6
13
CHT-Ti-Cp results
J’ Ka’ Kc’ J” Ka” Kc” Measured
5
1
5
4
1
4
7669.0869
4
1
4
3
1
3
6135.29
6
1
6
5
1
5
9202.8838
5
1
4
4
1
3
7684.7773
4
1
3
3
1
2
6147.8384
7
0
7
6
0
6
10747.2891
6
1
5
5
1
4
9221.709
6
0
6
5
0
5
9212.1045
5
0
5
4
0
4
7676.8257
4
0
4
3
0
3
6141.5093
4
2
3
3
2
2
6141.568
6
2
5
5
2
4
9212.3105
o-c /
KHz
0.0003
0.002
0.0141
0.0025
-0.0002
-0.0138
0.0138
0.017
0.0061
0.0013
0.0086
0.0216
Table 7.7 CHT-Ti-13Cp results
J’ Ka’ Kc’ J” Ka” Kc” Measured
4
0
4
3
0
3
6129.2524
4
1
3
3
1
2
6132.709
5
1
5
4
1
4
7657.4185
5
0
5
4
0
4
7661.5537
5
1
4
4
1
3
7665.874
6
1
6
5
1
5
9188.8994
6
0
6
5
0
5
9193.8604
6
1
5
5
1
4
9199.042
5
2
4
4
2
3
7661.6343
o-c /
KHz
-0.0425
0.0035
0.0057
-0.0272
0.0073
0.0262
0.0184
0.0244
-0.003
174
Table 7.8 Results of 47Ti in CHT-Ti-Cp
J'
3
3
3
4
4
4
5
5
5
5
5
5
5
6
6
6
6
6
7
7
7
7
7
7
7
8
8
K'
0
0
0
0
0
1
0
0
-1
0
0
1
1
0
0
-1
0
1
0
0
0
0
0
-1
-1
0
0
F'
6
5
1
7
6
6
3
8
3
7
6
5
6
4
9
8
7
7
9
10
6
5
8
8
10
11
10
J"
2
2
2
3
3
3
4
4
4
4
4
4
4
5
5
5
5
5
6
6
6
6
6
6
6
7
7
K"
0
0
0
0
0
-1
0
0
1
0
0
-1
-1
0
0
1
0
-1
0
0
0
0
0
1
1
0
0
F"
5
4
1
6
5
5
2
7
2
6
6
4
5
3
8
7
6
6
8
9
5
4
7
7
9
10
9
measured
4630.862
4631.065
4630.692
6174.369
6174.488
6174.301
7717.622
7717.877
7717.818
7718.008
7717.414
7717.548
7717.702
9261.254
9261.439
9261.439
9261.368
9261.323
10805.01
10804.99
10804.77
10804.85
10804.96
10804.91
10805.01
12348.53
12348.57
o-c
kHz
-30.8
13.4
-2.6
-15.2
2.9
12.1
-0.6
-30.2
22.3
31
-9.5
4.3
11.3
0
-5.2
-8.1
-1.1
-0.8
-17.2
0.8
-10.3
2.4
22.8
-0.6
-6.2
-1.6
4.9
175
8. CONCLUSIONS AND FUTURE DIRECTIONS
Pulsed beam microwave spectrometry is a high resolution technique that
can probe the structure of gas phase dimers and molecular properties near the
nuclei that have spin greater than 1. The systems reported in this dissertation
span many degrees of complexity from the preparation of the experimental
sample to the analysis of reaction products when HCl comes in contact with an
organometallic complex.
Hydrogen bonded dimers are a rich field to investigate with microwave
spectroscopy. There are only two studies to date that can quantify the energy
barrier to the concerted proton tunneling. In Chapter 4, the case has been made
that propiolic acid-formic acid is such a system. Another system that could show
interesting features in its spectrum is the dimer between 2-hydroxy-pyridine/2pyridone and formic acid. Calculations have already been run on this system
and are summarized in figure 8.1.
176
Parameter
2-Pyridone-Formic Acid
2-Hydroxy-Pyridine-Formic Acid
A / MHz
3000.51
2775.25
B / MHz
741.89
790.92
C / MHz
595.95
615.51
μa/ D
3.1
2.3
μb / D
2.5
2.3
0
800
ΔE /cm-1
Figure 8.1 Predictions of the gas phase dimer of 2-hydroxy-pyridine/2-pyridone
and formic acid
Also, as was presented in the introduction, there exist many acid dimers that
have high binding energy. Formic Acid-Benzoic acid is a good candidate to
study possible tunneling phenomena. The potential well is symmetric and should
177
be similar to propiolic acid-formic acid. An interesting difference is the
temperature at which the monomer signal for benzoic acid can be seen.
Preliminary experiments with benzoic acid show that the sample cell needs to be
heated to 90 C while formic acid and propiolic acid can be run -20 C to 0 C. A
special cell has been designed to study such a sample but has not been shown
to work very well.
Azaborine, N-hydroxypridine-2(1H)-thione, arsenic triphosphide and (η7C7H7)47Ti(η5-C5H5) have been analyzed using microwave spectroscopy. Each
molecule has at least one atom with I > 1. The assignments were greatly aided
by the well known intensity patterns of the isotopes. A simple model of p-orbital
occupancy has shed light on the partial aromatic character of azaborine and this
result is confirmed using theory. The impressive change on nitrogen’s
quadrupole coupling constant between the two isomers was very useful in
making the assignment. With that information a structure fit was produced that
has opened a new field here in the laboratory, detection of organic molecules in
plants. Our experiment with arsenic triphosphide will hopefully complement the
many ways that small molecule has been studied. The possibility of low lying
vibrational states affecting the spectrum is exciting. If the spectrum could be
assigned, including the vibrational quantum number, then the results could refine
the ro-vibrational coupling constants.
The last system whose quadrupole coupling constant was studied, (η7C7H7)47Ti(η5-C5H5), contains results that is not receiving very much attention in
178
the literature. The worst predicted parameter in a molecule is the quadrupole
coupling constant. It can be an order of magnitude off from experiment or, as in
the case of methylrhenium trioxide, can have the opposite sign of the
experimentally determined value as stated in section 6.4.
The gas phase dimers have provided a very formidable challenge with
sample preparation and predictions. There needs to be a benchmark system
and it could be the organometallic complexes studied here using CpTl, MTO or
ferrocene. A concentrated effort with mixing valves and a little luck could open
this field to use very powerful theoretical models and sensitive experimental
techniques.
179
9 SUPPLEMENTAL MATERIAL
Additional detail is given here regarding the electronics in the pulse box, 9.1,
the Autoscan 6.0 code, 9.2, Structure Fit codes for molecules given in the
thesis, 9.3, Example job file for running Gaussian 09 on the ICE cluster, 9.4
and Example files for use of Pickett (Appendix 9.5).
9.1 Board layouts for the pulse box
Figure 9.1 Clock Board Layout from figure 2.7 labeled board 1
180
Figure 9.2 Pulse Width Modulation and Control Board layout. This is board
labeled 2 in figure 2.7.
Figure 9.3 Motor driver board layout. This is labeled 3 in figure 2.7 and has the
operation described in figure 2.6.
181
9.2 Autoscan 6.0 code
Located here is the code that is named winmain.cpp which contains the
main program for Autoscan. There are several files that need to be
included to run properly. It is to be run using Microsoft Visual C++ 6.0 and
will have to undergo significant changes to run using other versions of
C++.
9.2.1 // Include files
#include <time.h> // this is necessary to access the sleep command
#include "windecl.h" // GPIB library
#include "trw.h" Included by C. Dannemiller for all c++ graphics and FFT
calculations needed to run what was called TRW 3.0 and is now called
Scan 2.0
//
#include <windows.h>
// For Windows support
#include <ddraw.h>
// For DirectDraw
#include <stdio.h>
// For standard Input/Ouput routines
#include <stdarg.h>
// for the va_*() funtions
#include <winreg.h>
// For registry suppot
#include <string.h>
// for string operations
#include <mmsystem.h>
// for VK_*
#include <math.h>
// for sin/cos
#include "winmain.h"
// Main windows
#include "registry.h"
// Registry data
#include "resource.h"
// Resource data
#include "adc200.h"
// for the ADC200 box of the real kind
#include "fmemory.h"
// Fast memory routines
#include "FSWindow.h"
// Full screen window's handler
#include "gfx.h"
// Graphics wrapper FFT calculated here
#include "adc200wp.h"
// Wrapper for adc200 box
//#include <fstream>
//
#include "stdafx.h" include file for standard system include files
#include "comport.h" // Comport USB header file
#include "stdio.h"// standard file commands needed here
#include "usb1208.h" // original stdafx.h from Measurement computing
#include "cbw.h" // header from Measurement Computing
182
#include "time.h" // to access the clock wait feature of motor control
#include "MoveFrequency.h" // header provided for frequency finder
algorithm
Also, there are other *.cpp files that need to included in the project.
9.2.2 C++ files that need to included in the project
adc200wp.cpp // A simple ADC-200 Wrapper that allows for the
programmer to more easily acess ADC-200 functionality
Comport.cpp // program provided to talk to Prologix USB-GPIB
Configure.cpp // This file handles the configuration dialog box
FSWindow.cpp // This code will allow you to update a window in
DirectDraw full-screen.
MoveFrequency.cpp // Program to sweep mode and find frequency at the
minimum voltage read in by DAQ board from the diode during automated
tune mode.
REGISTRY.cpp// Macro to ease data reading
STDAfx.cpp // #include "usb1208.h"
9.2.3 AutoScan 6.0
//------------------------------------------------------------------// PROJECT: AutoScan
183
//
// Revision: 6.0
// By Adam Daly and Sarko
//
// winmain.cpp
//
// This part of the program handles most of the program contorls. and
// Interfrances with the rest of the system.
//
// a header file was renamed, stdafx.h, to usb1208.h so that comport.cpp
// would be happy and that I could keep the definitions
// ------------------------------------------------------------// changes from 5.0 include:
// creation of an ini file that reads in the following parameters:
// fFreq_start Starting frequency
// fFreq_max Maximum frequency of the scan
// fFreq_step Stepping frequency during scan
// Line_CRIT Criteria of MaxIntensity-MinimumIntensity for
//
Is_There_A_Line array that is summarized in the
//
"Ffreq_Max"f text file
// MaxCounts Maximum number of shots during a scan at one frequency
//
// Ffreq_Max text file that summarizes based on number of scans whether
//
the line criteria was met. frequency can be determined
// by step number* step size + Ffreq_start
//
//
// Also, g_pSum needed to cleared at the end of file save so that
// an aggregate of all the arrays was not carried through which is present in
// all versions prior to this one
//
// k should also be reset to 0xff prior to reset
//
// In addition, the box stops taking data during the file and array
// comparisons to minimize unwanted data in the initial arrays
// the original program did not have any significant delays upon
// restart, but this program as several GPIB (slow!) callouts during that
// time.
//
// Additional feature from Autoscan 5.2, step motor and use frequency as tuning
// mechanism
//
//------------------------------------------------------------------// Include files
//------------------------------------------------------------------#include <time.h>
#include "windecl.h"
#include "trw.h"
#include "stdafx.h"
#include "comport.h"
#include "stdio.h"
#include "usb1208.h" // original stdafx.h from Measurement computing
#include "cbw.h" // header from Measurement Computing
184
#include "time.h" // to access the clock wait feature of motor control
#include "MoveFrequency.h" // header provided for frequency finder algorithm
//#include <sstream>
//#include <iostream.h> // additional headers for ascii open
//float MaxIntensity; // global maximum intensity for analysis use
float VAMP;
// global access to mode information in ReadScope
//------------------------------------------------------------------// String Data
//------------------------------------------------------------------#if !(NDEBUG) || (FORCE_LOG)
char szDebugFile[] = "debug.log";
// File to log debuging
data
#endif // !(NDEBUG) || (FORCE_LOG)
// Program Name and title
char szName[] = "TRW";
char szTitle[] = "TRW v3.0";
//------------------------------------------------------------------// Global Data
//------------------------------------------------------------------HWND
g_hWnd = NULL;
HWND
g_hWndDlg = NULL;
GFX
*TRWGfx = NULL;
// TRW Gfx
BOOL
g_bQuiting = FALSE;
char
ShutDownLoop=1;
double
SecretVariable=0;
//------------------------------------------------------------------// Local Data
//------------------------------------------------------------------static HINSTANCE
g_hInstance = NULL;
static BOOL
g_bUseLines = TRUE;
static BOOL
g_bDrawShot = FALSE;
static BOOL
g_bDrawFFT = TRUE;
static BOOL
g_bDlgActive = FALSE;
static BOOL
g_bActive = FALSE;
// Is Application
up un Runnin?
static BOOL
g_bObjsAvil = TRUE;
static short
*g_pData = NULL;
static long
*g_pSum = NULL;
static int
*g_pDraw = NULL;
static int
*g_pFreqy=NULL;
static ULONG
g_ulLoopCount = 0;
static int
g_nShift = 0;
// Shifting rate
static BOOL
g_bUseGPIB = TRUE;
static BOOL
g_bLocked = FALSE;
//------------------------------------------------------------------// Name: BigSI()
// Desc: Handles SI for unsigned longs
185
//------------------------------------------------------------------static char pSI[] = { 'k', 'M', 'G', 'T', 'P', 'E', 'Z', 'Y' };
static char szBigSITemp[20];
char *BigSI(unsigned long s)
{
int si = 0;
while(s > 1000)
{
si++;
s/=1000;
}
if(si == 0)
sprintf(szBigSITemp,"%ld ", s);
else
sprintf(szBigSITemp,"%f %c", s, pSI[si-1]);
return szBigSITemp;
}
//------------------------------------------------------------------// Name: CleanUp()
// Desc: Clean up all data from memory
//------------------------------------------------------------------static void CleanUp(void)
{
// Graphics class Allready Loaded?
if(TRWGfx != NULL)
delete TRWGfx;
FreeMemory(g_pData);
FreeMemory(g_pSum);
FreeMemory(g_pDraw);
FreeMemory(g_pFreqy);
g_bObjsAvil = FALSE;
}
//------------------------------------------------------------------// Name: ResetTRW()
// Desc: Resets various TRW stats
//------------------------------------------------------------------void ResetTRW()
{
TRW_STOP();
// Clear the g_pSum field
ZeroMemory(g_pSum, g_nBufferSize * sizeof(long));
g_ulLoopCount = 0;
g_nShift = 0;
g_bLocked = FALSE;
186
// Reset data collection
TRW_RUN(g_nBufferSize);
}
void HardResetTRW(int nNewBufferSize)
{
if(g_pSum != NULL)
free(g_pSum);
if(g_pData != NULL)
free(g_pData);
if(g_pDraw != NULL)
free(g_pDraw);
if(g_pFreqy != NULL)
free(g_pFreqy);
ADC200ReOpenBox();
g_nBufferSize = nNewBufferSize;
g_pData
g_pSum
g_pDraw
g_pFreqy
= new short[g_nBufferSize];
= new long [g_nBufferSize];
= new int [g_nBufferSize];
= new int [g_nBufferSize];
ResetTRW();
// Let this reset the rest
}
//------------------------------------------------------------------// Name: DebugLog()
// Desc: Logs data to debug.log
//------------------------------------------------------------------// Only debug to log if in debug mode or force log flag on
#if !(NDEBUG) || (FORCE_LOG)
void DebugLog(BOOL bAppend, char *szMessage, ...)
{
char szBuffer[128];
char szDate[20], szTime[20];
va_list vl;
FILE *pfDebug;
va_start(vl, szMessage);
vsprintf(szBuffer, szMessage, vl);
va_end(vl);
// if bAppend appened it to error.log, else over write
if(bAppend)
{
// Appened to file
187
if((pfDebug = fopen(szDebugFile, "at")) == NULL)
return;
fseek(pfDebug, 0, SEEK_END);
} else {
// overwrite
if((pfDebug = fopen(szDebugFile, "wt")) == NULL)
return;
}
_strdate(szDate);
_strtime(szTime);
fprintf(pfDebug, "%s-%s : %s\n", szDate, szTime, szBuffer);
fclose(pfDebug);
}
#endif // !(NDEBUG) || (FORCE_LOG)
//------------------------------------------------------------------// Name: ProgramError()
// Desc: Called upon when initalization failed or another error
//
occured that requires the program to quit.
//------------------------------------------------------------------HRESULT
ProgramError(HWND hWnd, HRESULT hRet, LPCSTR szError, ...)
{
char szBuff[128];
va_list vl;
va_start(vl, szError);
vsprintf(szBuff, szError, vl);
MessageBox(hWnd, szBuff, szTitle, MB_OK | MB_ICONSTOP);
DebugLog(TRUE, szBuff);
DebugLog(TRUE, "hRet = 0x%08x", hRet);
DestroyWindow(hWnd);
va_end(vl);
CleanUp();
g_bActive = FALSE;
// Tell the program to goto hell'n'die
return hRet;
}
//------------------------------------------------------------------// Name: ReadStimFreq()
// Desc: Make a connection to the GPIB card, then contact the HP5340a
//
and retrive the data for Frequency. Then reset the HP5340a box
//
so that it still gates on its own.
//------------------------------------------------------------------int ReadStimFreq()
{
//
188
static int i=100;
int finalfreq;
i++;
finalfreq=i;
// Original code to speak to the frequency counter
//
int dev;
//
char buffer[17], newby[17], frecy[17];
//
//
dev = ibfind("HP5340a");
//
//
ibrd(dev, buffer, 16);
//
//
buffer[16] = '\0';
//
int x = (int)(strchr(buffer, 0x0a) - buffer) + 1;
//
if(x == 16) x = 0;
//
if(x == 0) // yippe no bariner
//
{
//
strcpy(newby, buffer);
//
newby[14] = 0x00;
//
} else {
// Oh crap well ok handle it
//
memcpy(newby, buffer+x, 16-x);
//
memcpy(newby+(16-x), buffer, x);
//
newby[14] = 0x00;
//
}
//
//
if(newby[1] == 'O') {
// Overflow
//
return -1.;
//
}
//
//
strcpy(frecy, newby+3);
//
//
int exp = 3;
//
//
frecy[strlen(frecy)-3] = '\0';
//
//
double finalfreq = atoi(frecy);
//
//
while(exp != 0)
//
{
//
finalfreq /= 10.;
//
exp--;
//
}
//
ibwrt(dev,"H\r\n",3);
return finalfreq;
}
//----------------------------------------------------------------// Name: ReadASCII(char*, float, float, float)
189
//----------------------------------------------------------------void ReadASCII(char* fname, float &Ffreq_start, float &Ffreq_max, float &Ffreq_step){
//
ifstream fin;
char tmp[256];
const int numParamsToRead = 3;
int numParamsRead= 0;
char *endptr;
//
//
//
Ffreq_start = 7000;
Ffreq_max =
7001;
Ffreq_step= 0.225;
FILE *pfile;
pfile=fopen(fname, "r");
// Assume some default values
//
//
//
//
//
//
//
//
if(!fin.is_open()){
fin.close();
ofstream out;
out.open(fname, ios_base::out);
out << Ffreq_start << endl;
out << Ffreq_max << endl;
out << Freq_step << endl;
out.close();
fclose(pfile);
}
//------------------------------------------------------------------// Name: WriteStimFreq()
// Desc: Make a connection to the GPIB card, then contact the P8673D
// write new frequency.
//------------------------------------------------------------------void WriteStimFreq(char *cmd)
{
// TODO: Specify Virtual COM port
char* port = "COM3";
// char outs[50];
char buffer[ 256 ];
// char readr[256];
char f_number[50];
char *endptr;
// static double freq=10000;
int i, address;
address=0;
//
int freq_max=6000;
// char cmd[ 253 ];
DWORD error = 0;
190
do
{
// Open port
error = PxSerialOpen( port );
if ( error != 0 )
{
printf( "Error %08x opening %s.\n", error, port );
break;
}
// Append CR and LF
char f_buffer[256];
sprintf( f_buffer, "%s\r\n", cmd );
// Write command to port
DWORD written = 0;
error = PxSerialWrite( f_buffer, (DWORD)strlen( f_buffer ), &written );
if ( error != 0 )
{
printf( "Error %08x writing %s.\n", error, port );
break;
}
// TODO: Adjust timeout as needed
//
const DWORD TIMEOUT = 1500;
//
//
// Millisec
DWORD elapsedTime = 0;
DWORD lastRead = timeGetTime();
// Read until TIMEOUT time has elapsed since last
// successful read.
// while ( elapsedTime <= TIMEOUT )
//
{
//
DWORD bytesRead;
//
//
error = PxSerialRead( buffer, sizeof( buffer ) - 1, &bytesRead );
//
if ( error != 0 )
//
{
//
printf( "Error %08x reading %s.\n", error, port );
//
break;
//
}
//
//
//
//
//
//
//
//
if ( bytesRead > 0 )
{
buffer[ bytesRead ] = 0;
printf( "%s", buffer );
// Append NULL to print to console
lastRead = timeGetTime();
}
191
//
//
elapsedTime = timeGetTime() - lastRead;
}
}
while ( 0 );
// printf( "\n" );
// Close port
error = PxSerialClose();
if ( error != 0 )
{
printf( "Error %08x closing %s.\n", error, port );
}
//
return address;
}
//------------------------------------------------------------------// Here are the various dialog procdures
//------------------------------------------------------------------// Name: AboutDLGProc()
// Desc: Handles messages for the about Dialog.
//------------------------------------------------------------------LRESULT CALLBACK AboutDLGProc(HWND hDlg,
UINT uMsg,
WPARAM wParam,
LPARAM lParam)
{
switch(uMsg)
{
case WM_COMMAND:
switch (LOWORD(wParam))
{
case IDCANCEL:
case IDOK:
ResetTRW();
Missed shots data has become invalid
FSWindow_End();
EndDialog(hDlg, TRUE);
return TRUE;
}
break;
case WM_CLOSE:
g_hWndDlg = (HWND )NULL;
FSWindow_End();
break;
}
return FALSE;
}
//------------------------------------------------------------------// Name: FreqancyDLGProc()
// Desc: Handles data for the freqancy dialog box
//-------------------------------------------------------------------
//
192
LRESULT CALLBACK SaveDLGProc(HWND hDlg,
UINT uMsg,
WPARAM wParam,
LPARAM lParam)
{
char szText[128];
float fFreqancy = 1;
int freq=1 ; //new by A. Daly to start the file naming
switch(uMsg)
{
case WM_INITDIALOG: //originally called to read in StimFrequency for the dialog box
if(g_bUseGPIB)
{
sprintf(szText, "%.3f", ReadStimFreq()); //original
fFreqancy = (float)atof(szText);
SendDlgItemMessage(hDlg, IDC_EDITFREQANCY, WM_SETTEXT, 0,
(LONG)szText); //original
if(fFreqancy == 0.0)
{
MessageBox(hDlg, "Error in freqancy value:\n\nString must be a
floatin point number > 0", szTitle, MB_OK | MB_ICONEXCLAMATION);
SetFocus(GetDlgItem(hDlg, IDC_EDITFREQANCY));
return TRUE;
}
freq++;
sprintf(szText, "Tr%i", ReadStimFreq()); //original
SendDlgItemMessage(hDlg, IDC_EDITFILENAME, WM_SETTEXT, 128,
(LONG)szText);
// changed to WM_SETTEXT TO POSITION IN BOX
if(!strcmp(szText, ""))
{
MessageBox(hDlg, "Error in file name:\n\nMust enter a file
name", szTitle, MB_OK | MB_ICONEXCLAMATION);
SetFocus(GetDlgItem(hDlg, IDC_EDITFILENAME));
return TRUE;
}
if(strchr(szText, '.') == NULL)
strcat(szText, ".plt");
FILE *pFile;
if((pFile = fopen(szText, "wt")) == NULL)
{
MessageBox(hDlg, "Error creating file", szTitle, MB_OK |
MB_ICONEXCLAMATION);
SetFocus(GetDlgItem(hDlg, IDC_EDITFILENAME));
193
return TRUE;
}
fprintf(pFile, "Points: %5d\n\n", g_nBufferSize);
for(ULONG i = 0; i < g_nBufferSize; i++)
fprintf(pFile, "Channel: %5d Voltage: %10ld\n", i, g_pSum[i]);
fprintf(pFile, "\nCycles: %10lu\n", g_ulLoopCount);
fprintf(pFile, "Stim Frequency: %i\n", fFreqancy);
fprintf(pFile, "Voltage: %10.3f\n", ((float)g_nACD200Voltage)/1000);
#ifndef EMULATE_ADC200_BOX
fprintf(pFile, "Sample Frequency: %sHz",
BigSI(g_ulADC200Frequancy));
#else
fprintf(pFile, "Sample Frequency: 10MHz");
#endif
fclose(pFile);
g_bLocked = FALSE;
FSWindow_End();
EndDialog(hDlg, TRUE);
return TRUE;
}
case WM_COMMAND:
switch (LOWORD(wParam))
{
case IDCANCEL:
FSWindow_End();
EndDialog(hDlg, TRUE);
g_bLocked = TRUE;
return TRUE;
case IDOK:
SendDlgItemMessage(hDlg, IDC_EDITFREQANCY, WM_GETTEXT,
128, (LONG)szText);
fFreqancy = (float)atof(szText);
194
if(fFreqancy == 0.0)
{
MessageBox(hDlg, "Error in freqancy value:\n\nString must be a
floatin point number > 0", szTitle, MB_OK | MB_ICONEXCLAMATION);
SetFocus(GetDlgItem(hDlg, IDC_EDITFREQANCY));
return TRUE;
}
// ADDED BY A. DALY TO INCREMENT FILE NAMES AFTER 'OK'
freq++;
sprintf(szText, "T%.3f", freq); //original
SendDlgItemMessage(hDlg, IDC_EDITFILENAME, WM_SETTEXT, 128,
(LONG)szText);
if(!strcmp(szText, ""))
{
MessageBox(hDlg, "Error in file name:\n\nMust enter a file
name", szTitle, MB_OK | MB_ICONEXCLAMATION);
SetFocus(GetDlgItem(hDlg, IDC_EDITFILENAME));
return TRUE;
}
if(strchr(szText, '.') == NULL)
strcat(szText, ".plt");
FILE *pFile;
if((pFile = fopen(szText, "wt")) == NULL)
{
MessageBox(hDlg, "Error creating file", szTitle, MB_OK |
MB_ICONEXCLAMATION);
SetFocus(GetDlgItem(hDlg, IDC_EDITFILENAME));
return TRUE;
}
fprintf(pFile, "Points: %5d\n\n", g_nBufferSize);
for(ULONG i = 0; i < g_nBufferSize; i++)
fprintf(pFile, "Channel: %5d Voltage: %10ld\n", i, g_pSum[i]);
fprintf(pFile, "\nCycles: %10lu\n", g_ulLoopCount);
fprintf(pFile, "Stim Frequency: %4.2f\n", fFreqancy);
fprintf(pFile, "Voltage: %10.3f\n", ((float)g_nACD200Voltage)/1000);
#ifndef EMULATE_ADC200_BOX
fprintf(pFile, "Sample Frequency: %sHz",
BigSI(g_ulADC200Frequancy));
#else
fprintf(pFile, "Sample Frequency: 10MHz");
#endif
fclose(pFile);
195
g_bLocked = FALSE;
FSWindow_End();
EndDialog(hDlg, TRUE);
return TRUE;
}
break;
case WM_CLOSE:
g_hWndDlg = (HWND )NULL;
FSWindow_End();
break;
}
return FALSE;
}
//------------------------------------------------------------------// Name: WindowProc()
// Desc: The Main Window Procdure, Mainly handles stuff like
// user input
//------------------------------------------------------------------long FAR PASCAL
WindowProc(HWND hWnd, UINT uMessage, WPARAM wParam, LPARAM lParam)
{
switch (uMessage)
{
case WM_ACTIVATEAPP:
// Pause if minimized or not the top window
g_bActive = (wParam == WA_ACTIVE) || (wParam == WA_CLICKACTIVE);
break;
case WM_DESTROY:
// Clean up and close the app
g_bQuiting = TRUE;
PostQuitMessage(0);
return (0);
// We are dying
// Post Successs
case WM_KEYDOWN:
// Handle any non-accelerated key commands
switch (wParam)
{
case VK_ESCAPE:
ShutDownLoop=0;
PostMessage(hWnd, WM_CLOSE, 0, 0);
return 0L;
case 'D':
if(g_bUseLines)
g_bUseLines = FALSE;
else
g_bUseLines = TRUE;
break;
case 'H':
196
if(g_bDrawShot)
g_bDrawShot = FALSE;
else
g_bDrawShot = TRUE;
break;
case 'S':
g_hWndDlg = CreateDialog(g_hInstance,
MAKEINTRESOURCE(IDD_SAVEDLG),
g_hWnd, (DLGPROC) SaveDLGProc);
ShowWindow(g_hWndDlg, SW_SHOWNORMAL);
FSWindow_Begin(g_hWndDlg, FALSE);
break;
case 'R':
// Reset values
ResetTRW();
break;
case 'F':
// Draw FFT
g_bDrawFFT = (g_bDrawFFT) ? FALSE : TRUE;
break;
case 'C':
// Congiguation
g_hWndDlg = CreateDialog(g_hInstance,
MAKEINTRESOURCE(IDD_CONFIG),
g_hWnd, (DLGPROC) ConfigureDialogProc);
ShowWindow(g_hWndDlg, SW_SHOWNORMAL);
FSWindow_Begin(g_hWndDlg, TRUE);
break;
case VK_F1:
// Help
g_hWndDlg = CreateDialog(g_hInstance,
MAKEINTRESOURCE(IDD_ABOUTBOX),
g_hWnd, (DLGPROC) AboutDLGProc);
ShowWindow(g_hWndDlg, SW_SHOWNORMAL);
FSWindow_Begin(g_hWndDlg, FALSE);
break;
}
break;
case WM_SETCURSOR:
// Turn off the cursor since this is a full-screen app, unless we doing a
dialog
if(g_bActive && !FSWindow_IsActive())
{
SetCursor(NULL);
return TRUE;
}
}
return DefWindowProc(hWnd, uMessage, wParam, lParam);
}
//------------------------------------------------------------------// Name: InitApp()
// Desc: Initalize Application
//------------------------------------------------------------------static HRESULT
197
InitApp(HINSTANCE hInstance, int nCmdShow)
{
HWND
hWnd;
WNDCLASS
wc;
// Set up and register window class
wc.style = 0;
// No styles for speed
wc.lpfnWndProc = WindowProc;
wc.cbClsExtra = 0;
wc.cbWndExtra = 0;
wc.hInstance = hInstance;
wc.hIcon = LoadIcon(NULL, IDC_ICON);
wc.hCursor = LoadCursor(NULL, IDC_ARROW);
wc.hbrBackground = (HBRUSH) GetStockObject(BLACK_BRUSH);
wc.lpszMenuName = NULL;
wc.lpszClassName = szName;
RegisterClass(&wc);
// Create a window
hWnd = CreateWindowEx(WS_EX_TOPMOST,
szName,
szTitle,
WS_POPUP,
0, 0,
0, 0,
NULL,
NULL,
hInstance,
NULL);
if(!hWnd)
{
MessageBox(GetDesktopWindow(), "Could not create window for DirectDraw",
szTitle, MB_OK | MB_ICONEXCLAMATION);
return FALSE;
}
ShowWindow(hWnd, nCmdShow);
UpdateWindow(hWnd);
SetFocus(hWnd);
g_hWnd = hWnd;
Registry_Start();
TRWGfx = new GFX(Registry_ReadInteger("Width", 640),
Registry_ReadInteger("Height", 480),
g_nBufferSize);
Registry_End();
g_bObjsAvil = TRUE;
g_bActive = TRUE;
return DD_OK; // Well if we got this far everthing is okey dokey
// and honkey dory
198
}
//------------------------------------------------------------------// Name: IsMMX()
// Desc: Check to see if processor has MMX Support.
//
- From the CDX engine
//------------------------------------------------------------------#ifdef MMX_SUPPORT
// Dont include this code with non-MMX compiles
BOOL IsMMX(void)
{
SYSTEM_INFO si;
int nCPUFeatures=0;
GetSystemInfo(&si);
if (si.dwProcessorType != PROCESSOR_INTEL_386 && si.dwProcessorType !=
PROCESSOR_INTEL_486)
{
try
{
__asm
{
; we must push/pop the registers << CPUID>> writes to, as the
; optimiser doesn't know about << CPUID>> , and so
doesn't expect
; these registers to change.
push eax
push ebx
push ecx
push edx
; << CPUID>>
; eax=0,1,2 -> CPU info in eax,ebx,ecx,edx
mov eax,1
_emit 0x0f
_emit 0xa2
mov nCPUFeatures,edx
pop edx
pop ecx
pop ebx
pop eax
}
}
catch(...) // just to be sure...
{
return false;
}
}
return (nCPUFeatures & 0x00800000) != 0;
}
#endif // MMX_SUPPORT
//------------------------------------------------------------------// Name: WinMain()
199
// Desc: Initalizeation, and Message Loop
//------------------------------------------------------------------int PASCAL
WinMain(HINSTANCE hInstance,
HINSTANCE hPrevInstance,
LPSTR lpCmdLine,
int nCmdShow)
{
char scan[10];
int Result[1000];
float Resultm[100000];
float Resultf[100000];
char move[10];
char szText[128];
char ins[256];
char outs[256];
char cmd[256];
//
float VAMP;
int number[50];
float freq_scan=10000;
//
int i;
float fFreqancy, mode;
int freq=1 ; //new by A. Daly to start the file naming
ULONG nCount;
ULONG liner=0;
unsigned char k;
static int f=0;
char *endptr;
char freq_start[10];
char freq_min[10];
char freq_step[10];
float Ffreq_start=7511;
float Ffreq_min=7513;
float Ffreq_step=0.225 ;
long MaxIntensity;
float MODE_CRIT;
float modedepth;
long MinIntensity;
long Diff_Intensity=0;
long Line_Crit = 3000;
long y=0;
float nPause;
int loop;
int watch;
int rready;
long w=0;
long z=0;
int Is_There_A_Line;
long MaxCount =50;
MSG msg;
static unsigned long freq_scan_display = 0;
200
FILE *pfile;
pfile=fopen("config.ini", "r");
fscanf(pfile,"%f", &Ffreq_start);
fscanf(pfile,"%f", &Ffreq_min);
fscanf(pfile,"%f", &Ffreq_step); // wait while motor is on in milliseconds
fscanf(pfile, "%ld", &Line_Crit);
fscanf(pfile, "%ld", &MaxCount);
fscanf(pfile, "%f", &nPause);
fclose(pfile);
MoveFrequency(1, &modedepth); // initialization of MeasComp daq, GPIB and
synthesizer
DebugLog(FALSE, "Program Started");
char *pMoving = strtok(lpCmdLine, " ");
while(pMoving != NULL)
{
if(!stricmp("-nogpib", pMoving))
g_bUseGPIB = FALSE;
pMoving = strtok(NULL, " ");
}
#ifdef MMX_SUPPORT
// If we supporting MMX, then make sure this
if(!IsMMX())
// computer supports MMX extensions
{
MessageBox(NULL, "This program reqires MMX Support, or\nrecompile this
program turing of the MMX_SUPPORT define", szTitle, MB_OK | MB_ICONSTOP);
return 0L;
}
#endif
DebugLog(TRUE, "Atemepting to open ADC200 Box");
// Initalize ACD-200 Box
if(!ADC200ReOpenBox())
{
MessageBox(NULL, "Could not talk to the ADC200 Box. Check cables\nand or
configuration", szTitle, MB_OK | MB_ICONSTOP);
return 0L;
}
g_hInstance = hInstance;
DebugLog(TRUE, "Creating window");
// Initalize windows stuff
if(InitApp(hInstance, nCmdShow) != DD_OK)
return FALSE;
201
DebugLog(TRUE, "Initalizing memory");
g_pData = new short[g_nBufferSize];
g_pSum = new long [g_nBufferSize];
g_pDraw = new int [g_nBufferSize];
//
g_pFreqy = new int [g_nBufferSize];
k = 0xff;
// Used to ossolate the addtion subtionration ru
// Clear the g_pSum field
ZeroMemory(g_pSum, g_nBufferSize * sizeof(long)); // clear initially
// buffer
// Start running the ADC200-BOX now.
TRW_RUN(g_nBufferSize);
DebugLog(TRUE, "Begin program loop");
while(g_bActive) // loop of acquisition that is true when not locked -A.Daly
{
SetBPort(0);
// stop motor (just in case), switch clock to fast
while ((Ffreq_start> Ffreq_min) && ShutDownLoop) // this will be the frequency
< frequency_max condition -A.Daly
{
Ffreq_start=MoveFrequency(Ffreq_start, &modedepth);
SecretVariable = Ffreq_start;
SetBPort(2);
// switch clock to slow
while (g_ulLoopCount < MaxCount) // this will be max_counts -A.Daly
{
#ifndef NDEBUG
// Check for for force a quit key, for debug only
if(GetAsyncKeyState(VK_F12))
{
PostMessage(g_hWnd, WM_CLOSE, 0, 0);
}
#endif
// We peek at message (don't wait)
// objects to see if there is one there
if(PeekMessage(&msg, NULL, 0, 0, PM_REMOVE))
{
// Someone wants us ota here so goodbye.
if(msg.message == WM_QUIT)
break;
// If the dialog is showing, translate messages for it since
it's
// a modeless dialog.
if (g_hWndDlg == (HWND )NULL ||
!IsDialogMessage(g_hWndDlg, &msg))
{
202
// Translate and dispatch the message
TranslateMessage(&msg);
DispatchMessage(&msg);
}
}
if (FSWindow_IsActive())
{
FSWindow_Update();
}
else if(TRW_READY() &&
// Are we ready
to read data
g_bADC200Opened)
// from the
if(!g_bLocked)
// Not ensuring
ADC-200 box
{
good save
// takin data
{
TRW_STOP();
TRW_GETA_CHANNEL(g_pData,
g_nBufferSize);
TRW_RUN(g_nBufferSize);
// Draw pico stuff YEAH
#ifndef STAVG
k ^= 0xff;
#endif
if(g_bObjsAvil == FALSE)
// If memory was released during loop stop now
continue;
// If statment on lower block for speed purposes
// After the first line the two loops should handle
the exact same
if(!k)
for(nCount = 0; nCount < g_nBufferSize;
nCount++)
{
g_pSum[nCount] +=
g_pData[nCount];
g_pDraw[nCount] =
(g_pSum[nCount]) >> g_nShift;
if(ABS(g_pDraw[nCount]) >
2047)
{
203
g_pSum[nCount] -=
g_pData[nCount];
g_nShift++; nCount--;
}
}
else
for(nCount = 0; nCount <
g_nBufferSize; nCount++)
{
g_pSum[nCount] -=
g_pData[nCount];
g_pDraw[nCount] =
(g_pSum[nCount]) >> g_nShift;
if(ABS(g_pDraw[nCount]) > 2047)
{
g_pSum[nCount] += g_pData[nCount];
g_nShift++;
nCount--;
}
}
}
// Lock trw memory down
if(TRWGfx->Lock() != NULL)
// Only if we got
it down
{
// Make screen black!
TRWGfx->ClearBackup();
//
TRWGfx>DrawPlots(g_nBufferSize, g_pFreqy, TRWGfx->m_bColorGreen, g_bUseLines,
g_bDrawFFT);
TRWGfx->DrawPlots(g_nBufferSize, g_pDraw,
TRWGfx->m_bColorGreen, g_bUseLines, g_bDrawFFT);
if(g_bDrawShot)
TRWGfx->DrawPlots(g_nBufferSize,
g_pData, TRWGfx->m_bColorRed, g_bUseLines, g_bDrawFFT);
if(g_bDrawFFT)
TRWGfx->FTAndDraw(g_nBufferSize,
g_pDraw, TRWGfx->m_bColorYellow);
// Unlock V Mem
TRWGfx->Unlock();
204
// Do text drawing last or the lock/unlock
sequance will
// overwrite it!
if(TRWGfx->StartDC())
{
TRWGfx->WriteString(TRWGfx>m_nWidth - 240, 20,
RGB(0xff, 0xff, 0xff),
RGB(0x00, 0x00, 0x00),
"Count: %d", g_ulLoopCount);
#ifndef EMULATE_ADC200_BOX
TRWGfx->WriteString(TRWGfx>m_nWidth - 240, 40,
RGB(0xff, 0xff, 0xff),
RGB(0x00, 0x00, 0x00),
"Lines found: %s",BigSI(liner));
#else
TRWGfx->WriteString(TRWGfx>m_nWidth - 240, 40,
RGB(0xff, 0xff, 0xff),
RGB(0x00, 0x00, 0x00),
"Frequency: Forced To
10MHz");
#endif
if(g_bLocked)
TRWGfx->WriteString(TRWGfx>m_nWidth - 240, 60,
RGB(0xff, 0x00, 0x00),
RGB(0x00, 0x00, 0x00),
"LOCKED!!!");
TRWGfx->EndDC();
}
if(!TRWGfx->Flip())
ProgramError(g_hWnd, DD_OK, "Lost
DirectDraw Surface");
}
if(!g_bLocked)
g_ulLoopCount++; // increment number of shots
}
} // end for the while loop, now want to initiate save
// increment loop of frequency
g_bLocked = TRUE; // turn off acquisition
205
SetBPort(1); // turn on motor
Sleep(nPause); // wait for time specified in MoveFrequency algorithm
SetBPort(0); // turn off motor
Sleep(500); // wait until motor stops completely (0.5sec)
fFreqancy = Ffreq_start;
sprintf(szText, "%.2f", fFreqancy); //read in 'frequency' as integer
//
SendDlgItemMessage(hDlg, IDC_EDITFILENAME,
WM_SETTEXT, 128, (LONG)szText);
//
if(!strcmp(szText, ""))
//
{
//
MessageBox(hDlg, "Error in file name:\n\nMust enter a
file name", szTitle, MB_OK | MB_ICONEXCLAMATION);
//
SetFocus(GetDlgItem(hDlg, IDC_EDITFILENAME));
//
return TRUE;
//
}
if(strchr(szText, '.') == NULL)
strcat(szText, ".plt");
// Make sure it does not contain additional period
// add suffix of .plt using string append
FILE *pFile;
pFile = fopen(szText, "wt");
// Open file with name from ReadStimFreq()
//
{
//
MessageBox(hDlg, "Error creating file", szTitle, MB_OK |
MB_ICONEXCLAMATION);
//
SetFocus(GetDlgItem(hDlg, IDC_EDITFILENAME));
//
return TRUE;
//
}
MaxIntensity= -10000;
for(ULONG j = 0; j < g_nBufferSize ; j++)
{
if(MaxIntensity < g_pSum[j])
MaxIntensity = g_pSum[j];
}
MinIntensity= 10000;
for(ULONG r = 0; r < g_nBufferSize ; r++)
{
if(MinIntensity > g_pSum[r])
206
MinIntensity=g_pSum[r];
}
Diff_Intensity = MaxIntensity - MinIntensity;
if(Diff_Intensity > Line_Crit)
{
Is_There_A_Line = 1;
liner++;
}
else
Is_There_A_Line = 0;
Result[y]=Is_There_A_Line;
y++;
fprintf(pFile, "Points: %5d\n\n", g_nBufferSize); // beginning of data writing
// Aaron's modifications below:
//
float tempDraw[g_nBufferSize] = TRWGfx.pDataIntens;
// Try something like that, we need the data from pDataIntens here!!!
for(ULONG i = 0; i < g_nBufferSize; i++)
// This following line was changed to g_pDraw from g_pSum:
fprintf(pFile, "Channel: %5d Voltage: %10ld\n", i, g_pSum[i]);
fprintf(pFile, "\nCycles: %10lu\n", g_ulLoopCount);
fprintf(pFile, "Stim Frequency: %4.2f\n", fFreqancy);// problem here not coming through
fprintf(pFile, "Max Intensity: %i\n", MaxIntensity);
fprintf(pFile, "Min Intensity: %i\n", MinIntensity);
fprintf(pFile, "Voltage: %10.3f\n", ((float)g_nACD200Voltage)/1000);
#ifndef EMULATE_ADC200_BOX
fprintf(pFile, "Sample Frequency: %sHz", BigSI(g_ulADC200Frequancy));
#else
fprintf(pFile, "Sample Frequency: 10MHz");
#endif
207
fclose(pFile);
g_bLocked = FALSE;
//
//
//
//
FSWindow_End();
EndDialog(hDlg, TRUE);
return TRUE;
}
fFreqancy = (float)atof(szText); // store frequency as double
Resultm[y]=VAMP;
w++;
Resultf[z]=fFreqancy;
z++;
f++;
k = 0xff; // reset the acquisition toggle
// Clear the g_pSum field
ZeroMemory(g_pSum, g_nBufferSize * sizeof(long)); // necessary
// to clear the buffer before next one obtained
ResetTRW();
} // end of the frequency loop
sprintf(szText, "%fr", fFreqancy); //read in 'frequency' as integer
if(strchr(szText, '.') == NULL) // Make sure it does not contain additional period
strcat(szText, ".txt");
// add suffix of .plt using string append
FILE *pFile;
pFile = fopen(szText, "wt");
// Open file with name from ReadStimFreq()
for(int i = 0; i < f; i++)
fprintf(pFile, "Frequency %3f : Mode:%3f Line:%3ld\n", Resultf[i], Resultm[i], Result[i]);
//PostMessage(hWnd, WM_CLOSE, 0, 0);
MoveFrequency(-1, &modedepth); // shutdown command
CleanUp();
TRW_STOP();
DebugLog(TRUE, "Program ended");
return msg.wParam;
// Stop Data collection
208
} // end for the g_active loop
//PostMessage(hWnd, WM_CLOSE, 0, 0);
MoveFrequency(-1, &modedepth); // shutdown command
CleanUp();
TRW_STOP();
DebugLog(TRUE, "Program ended");
return msg.wParam;
}
// Stop Data collection
209
9.3 Example fit codes for method of least squares
The codes will be listed as given in the thesis giving the order formamide-formic
7
dimer, propiolic-formic dimer, azaborine, 2-mercaptopyridine-N-oxide and (η -
C7H7)Ti(η5-C5H5). The first part of the program sets up the arrays that ship the
data from the different subprograms. One should make sure that your arrays are
big enough and should have at least one MORE than the number of atoms in the
molecule/complex. The second part is to assign the masses to each atom by
defining the elements in the array which is labeled F. At line 60 the isotopes are
specified and should be consistent with the input file that has the isotopic
rotational constants. The F array is updated with new masses as a function of
reading in the input file. The last part involves the three other arrays which are
the X, Y and Z coordinates of the atoms. The same index is used as was defined
in the creation of the mass array, F. Usually some fraction of the coordinates are
fixed by values known by calculation and atoms of interest can have coordinates
parameterized. The number of parameters and the initial value (interation zero)
are given in the input file.
9.3.1
Formamide-Formic Acid
9.3.1.1
Structure Fit
C STRUCTURE FIT - FMA_FA - GSUB - ftbz7.f
C ** NEW FCNDP FOR
C LINK - FTHCO, FITB1, ROTSUB, CFAC
SUBROUTINE FCNDP(NP,ND,NV,NDATA,X1,P0,W,CM)
IMPLICIT REAL*8(A-H,O-Z)
DIMENSION X1(ND,NV),W(ND),P0(NP),CM(ND,NP)
DIMENSION FO(12),ZO(12),YO(12),XO(12), PP(12)
DIMENSION F(12),X(12),Y(12),Z(12)
DIMENSION AN(12), BN(12), CN(12)
NCYC = NCYC + 1
DELTA = 1.0D-06
N=11
ISW=0
SYM=2
C NX = 0
CCC-----MASSES----------C ADD MASS OF NITROGEN/OXYGEN AND ISOTOPES HERE
MASSH = 1.007825
FMC = 13.0033544
210
FMN = 14.003074
FMD = 2.014102
C**********ASSIGN MASSES TO STRUCTURE***************
DO 17, I=1,2
FO(I)=12.
17 F(I)=12.
DO 18, I=3,7
FO(I) = 1.007825
18 F(I) = 1.007825
DO 19, I=8,10
FO(I)=15.994915
19 F(I)=15.994915
FO(11)=15.000108
F(11)=15.000108
C----------------------------------------C*********USE PARAMATERS TO OBTAIN GEOMETRY********
DO 50, I=1,5
PP(I)=P0(I)
50
CONTINUE
CALL GSUB(NP,PP,X,Y,Z)
DO 20, L=1,N
XO(L)=X(L)
YO(L)=Y(L)
ZO(L)=Z(L)
20
CONTINUE
C**********CYCLE THROUGH DATA SETS****************************
DO 100, NQ=1,16,3
DO 60, L=1,N
F(L)=FO(L)
60
CONTINUE
IF(NQ.EQ.4) F(11)=FMN
IF(NQ.EQ.7) F(6)=FMD
IF(NQ.EQ.10) F(7)=FMD
IF(NQ.EQ.13) F(2)=FMC
61
CONTINUE
ISW=1
IF(NCYC.EQ.9)ISW=1
CALL ROTCONST(N,SYM,F,X,Y,Z,A,B,C,ASYMK,ISW)
ISW=0
W(NQ)=A
W(NQ+1)=B
W(NQ+2)=C
DO 40, K=1,10
PP(K)=P0(K)+DELTA
CALL GSUB(NP,PP,X,Y,Z)
PP(K)=P0(K)
62
CONTINUE
C
IF(NQ.EQ.4) F(1)=FMC
C
IF(NQ.EQ.7) F(3)=FMC
C
IF(NQ.EQ.10) F(5)=FMC
CALL ROTCONST(N,SYM,F,X,Y,Z,AN(K),BN(K),CN(K),ASYMK,ISW)
40
CONTINUE
DO 70, L=1,N
211
X(L)=XO(L)
Y(L)=YO(L)
Z(L)=ZO(L)
70
CONTINUE
DO 30, K=1,10
CM(NQ,K)=(AN(K)-A)/DELTA
CM(NQ+1,K)=(BN(K)-B)/DELTA
CM(NQ+2,K)=(CN(K)-C)/DELTA
30
CONTINUE
100
CONTINUE
RETURN
END
SUBROUTINE GSUB(NP,PP,X,Y,Z)
IMPLICIT REAL*8(A-H,O-Z)
DIMENSION X(12),Y(12),Z(12),PP(12)
DO 2, I1=1,11
2 Z(I1) = 0.
Z(3)=PP(5)
Z(11)=-PP(5)
Z(5)=PP(5)
C#########################################
RMM = PP(1)
THT = PP(3)
PHI = PP(4)
C
PHI = 0.005
C
THT = 0.0
C
BET= PP(6)
GAM = PP(2)
C
RH= PP(5)
RH= 0.9
X(1)= 0.41053*DCOS(PHI) - 0.106287*DSIN(PHI)
Y(1)= 0.106287*DCOS(PHI) + 0.41053*DSIN(PHI)
X(2)= -0.41559*DCOS(THT) + 0.0745*DSIN(THT)-RMM
Y(2)= -0.0745*DCOS(THT) - 0.41559*DSIN(THT)
X(3)= -1.16489*DCOS(PHI) + 1.21802*DSIN(PHI)
Y(3)= -1.21802*DCOS(PHI) - 1.16489*DSIN(PHI)
X(4)= 0.405593*DCOS(PHI) + 1.967967*DSIN(PHI)
Y(4)= -1.967967*DCOS(PHI) + 0.405593*DSIN(PHI)
X(5)= 1.512286*DCOS(PHI) - 0.083508*DSIN(PHI)
Y(5)= 0.083508*DCOS(PHI) + 1.512286*DSIN(PHI)
X(6)= 0.1287*DCOS(THT) -1.1248*DSIN(THT)+0.9917*DCOS(GAM)-RMM
Y(6)= 1.1248*DCOS(THT) + 0.1287*DSIN(THT)+0.9917*DSIN(GAM)
X(7)= -1.5102*DCOS(THT) + 0.0025*DSIN(THT)- RMM
Y(7)= -0.0025*DCOS(THT) - 1.5102*DSIN(THT)
X(8)= -0.215079*DCOS(PHI) - 1.118557*DSIN(PHI)
Y(8)= 1.118557*DCOS(PHI) - 0.215079*DSIN(PHI)
X(9)= 0.129*DCOS(THT) - 1.125*DSIN(THT)- RMM
Y(9)= +1.125*DCOS(THT) + 0.129*DSIN(THT)
X(10)= 0.20932*DCOS(THT) + 1.1316*DSIN(THT)- RMM
Y(10)= -1.1316*DCOS(THT) + 0.20932*DSIN(THT)
X(11)= -.160327*DCOS(PHI) + 1.145458*DSIN(PHI)
Y(11)= -1.145458*DCOS(PHI) - 0.160327*DSIN(PHI)
212
C
Z(11)= 1.157*DSIN(BET)
RETURN
END
213
9.3.1.2
Input file
fmfaft
5 15 1 15
3.12 0.0 0.0 0.0 0.1
5807.886
0
2127.056
0
1557.628
0
5889.466
0
2148.7409 0
1575.1234 0
5699.64
0
2123.898
0
1548.077
0
5805.93
0
2047.24
0
1514.369
0
5807.006
0
2093.5867 0
1539.5470 0
0
0
0
0
0
0
0
0
0
0
214
9.4 Example Job file for using ICE cluster – Batch Job
9.4.1
Batch commands and executables
#!/bin/csh
#PBS -N MTOQ
// Name of calculation for Batch
#PBS -l ncpus=1
// Number of CPU’s
#PBS -q windfall // priority
//1000 hours default per month, unlimited windfall
#PBS -l cput=400:0:0 //total amount of hours given to calculation walltime x ncpus)
#PBS -l walltime=100:0:0
//total amount of hours per processor
#PBS -W group_list=kukolich
// group name
#PBS -m bea //
#PBS -M adaly@email.arizona.edu
// email for start and stop of job
#
source /usr/share/modules/init/csh
// Gaussian files called
module load Gaussian
// Gaussian files called
module list
// Gaussian files called
set SCR = /scr3/adaly
// Scratch directory must be made (See >hottip Xdisk)
setenv g03root /uaopt/g09
// Gaussian files called
setenv GAUSS_ARCDIR $SCR
// Gaussian files called
setenv GAUSS_EXEDIR /uaopt/g09
// Gaussian files called
setenv GAUSS_SCRDIR $SCR
// Gaussian files called
setenv LD_LIBRARY_PATH /uaopt/g09
// Gaussian files called
#
cd /home2/u26/adaly/MTO
// directory where file is located
#
Date
// date calculation started
$GAUSS_EXEDIR/g09 MTO_1_ccsd_6p.com
// file to be executed
Date
// date at end of calculation
215
9.5 Example files for using Pickett’s SPCAT and SPFIT
There are many resources for this program and a couple are listed here.
The program can be found at:
http://spec.jpl.nasa.gov/ftp/pub/calpgm/spinv.html
A very handy crib-sheet can be found at:
http://www.ifpan.edu.pl/~kisiel/asym/pickett/crib.htm run by Dr. Kisiel
Or everything you wanted to know about Pickett but were afraid to ask
(University of Koln)
http://www.astro.uni-koeln.de/site/vorhersagen/pickett/
9.5.1
SPCAT
The SPCAT program has been utilized in every experiment used to generate the
spectrum for every system discussed here from rotational constants obtained by
calculations. The purpose of SPCAT is to generate a spectrum from rotational
constants, distortion constants and quadrupole coupling constants. There are many
other features this program offers but these three types of constants were used
exclusively. The input is the *.var file and *.int file.
9.6.1.1 *.var file
Here is an example file from Formamide-Formic Acid. The key parameters are the
rotational constants and if there is at least one nucleus with I>1, the quadrupole
coupling constants and distortion constants.
Formamide - formic acid
Tue Jul 06 05:32:06 2010
8 59 99 0 0.0000E+000 1.0000E+006 1.0000E+000 1.0000000000
s 3 1 0 12 0 1,,,,,,,,,
10000
5.88946E+003
3.21705895E-003 / A /
20000
2.1487409E+003
1.04114209E-003 / B /
30000
1.5751233E+003
8.99049833E-004 / C /
110010000
1.5211618E+000
1.10727459E-002 / (1.5*χaa)
110040000
1.246714E+000
3.43891113E-003 / 0.25*(χbb--χcc)
200
-6.5735512E-004
3.92112241E-005 / -DJ /
1100
-5.6495341E-003
2.03712485E-004 / -DJK/
40100
-1.84753174E-004
7.61465794E-006 / -DK /
9.6.1.2 *.int file
The *.int file specifies the dipole direction, the maximum F value, the minimum
logarithm of the intensity and maximum frequency.
216
Formamide-Formic Complex
0011 00001 93.3106 0 7 -6. -6.
001
2.0000000
/ a dipole
002
2.0000000
/ b dipole
003
0.0000000
/ c dipole
9.5.2
15.
5.
SPFIT
The SPFIT program is designed to perform a regression to find the best values of
the constants given the assignments made in the *.lin file. There is another file
named *.par that is identical to the *.var file. The output of the fit is a *.fit file that
details the results of each iteration. An example of the *.lin file is given with and
without quadrupole coupling. The formamide-formic acid project has both fits
due to the work with 15N(I=1/2) and 14N(I=1) formamide.
9.5.2.1
*.par file
The *.par file closely resembles the *.var except that the uncertainties aren’t
due to the fit as in the *.var but are controls to restrict the range of values. An
exponent of E+037 means the value can be fit to wherever the regression
takes it. One can freeze a value by setting it to E-037. Or one can restrict it
to an order of magnitude of the actual parameter.
Formamide - formic acid
Tue Jul 06 05:32:06 2010
8 59 99 0 0.0000E+000 1.0000E+006 1.0000E+000 1.0000000000
s 3 1 0 12 0 1,,,,,,,,,
10000
5.88946565E+003
1.00000000E+037 / A /
20000
2.14874093E+003
1.00000000E+037 / B /
30000
1.57512338E+003
1.00000000E+037 / C /
110010000
1.5211618E+000
1.00000000E+037 / 1.5*χaa)
110040000
1.24671420E+000
1.00000000E+037 / 0.25*(χbb--χcc)
200
-6.573551E-004
1.00000000E+037 / -DJ /
1100
-5.6495341E-003
1.00000000E+037 / -DJK/
40100
-1.847531E-004
1.00000000E+037 / -DK /
217
9.5.2.2 *. lin file
This file is highly structured and great care should be taken in using the format given
here. There are two files shown below, one with quadrupole coupling and one
without.
21211111
21231112
21221111
21211110
21221112
212111
202101
211110
313212
6872.8262
6873.9594
6874.3281
6874.3281
6874.9219
6712.190
7208.761
7820.259
10034.020
218
WORKS CITED
1
A. M. Daly, B. A. Sargus and S.G. Kukolich J. Chem. Phys. 133 174304 (2010)
2
N. Shida, P. F. Barbara and J. Almlöf, J. Chem. Phys. 94, 3633 (1991)
3
F. Madeja and M. Havenith, J. Chem. Phys. 117,. 7162 (2002)
4
A. M. Daly; P.R. Bunker, S.G. Kukolich J. Chem. Phys. 132, 201101/1 (2010)
5
T. J. Balle, W. H.Flygare,. Rev. Sci. Instrum. 52 33 (1981)
6
B. S Tackett,.; C. Karunatilaka,.; A. M. Daly, S.G Kukolich,. Organometallics 26,
2070 (2007),
7
W. Gordy, and R.L. Cook, Microwave Molecular Spectra, Wiley-Interscience, New
York, 1984.
8
H.W. Kroto,; Molecular Rotational Spectra, Dover Publications, Inc. New York, 1992
9
J. E. Wollrab, Rotational Spectra and Molecular Structure Academic Press, New York,
1967.
10
. M. Pickett, J. Mol. Spectrosc. 148, 371 (1991).(see also
http://spec.jpl.nasa.gov/ftp/pub/calpgm/spinv.html).
11
J. K. G Watson,.. J. Chem. Phys. 45 1360 (1966), J. K. G Watson,.. J. Chem. Phys.46
1935 (1967).
12
R. A. Fiesner, R. B. Murphy, M. D. Beachy, M. N. Ringualda, W. T. Pllard, B.D.
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