COMPUTATIONAL STUDY OF VIBRATIONAL

PROPERTIES OF GLUTAMIC ACID

A PROJECT WORK SUBMITTED TO THE

DEPARTMENT OF PHYSICS
ST. XAVIER’S COLLEGE
INSTITUTE OF SCIENCE AND TECHNOLOGY
TRIBHUVAN UNIVERSITY
NEPAL

FOR THE AWARD OF

BACHELOR OF SCIENCE (B.Sc.) IN
PHYSICS
BY
AVISESH BHANDARI
SYMBOL NO: 502820039
T.U. REGISTRATION NO: 5-2-282-34-2018

JULY, 2023
 RECOMMENDATION

This is to recommend that Avisesh Bhandari, (symbol no: 502820039, TU Registration

no. : 5-2-282-34-2018), has carried out project work entitled “ Study on Vibrational
properties of Glutamic Acid” for the requirement to the project work in Bachelor of
Science (B.Sc.) degree in Physics under my supervision in the Department of Physics ,
Saint Xavier’s college, Institute of Science and Technology (IoST), Tribhuvan University
(T.U), Nepal.

To my knowledge, this work has not been submitted for any other degree.

He has fulfilled all the requirements laid down by the Institute of Science and Technology
(IoST), Tribhuvan University (T.U) , Nepal for the submission of the project work for the
partial fulfillment of Bachelor of Science (B.Sc.) degree.

..............................
Mr.Kiran Pudasainee
Supervisor
Department of
Physics St. Xavier’s
College

15, JULY, 2023

i
 DECLARATION

This project work entitled “Computational study of vibrational properties of Glutamic

Acid” is being Submitted to the Department of Physics, St. Xavier’s College, Institute of
Science and Technology (IoST), Tribhuvan University (T.U), Nepal for the fulfillment of
the requirement to the project work in Bachelor of Science (B.Sc.) degree in Physics. This
project work is carried out by me under the supervision of Mr. Kiran Pudasainee in the
Department of Physics, St. Xavier’s College, Institute of science and technology (IoST),
Tribhuvan University (T.U), Nepal.

This work is original and has not been submitted earlier in part or full in this or any form
to any university or institute, here or elsewhere, for the award of any degree.

………………………
Signature
Name of Student: Avisesh Bhandari
Symbol No.: 502820039
T.U. Registration No.: 5-2-282-34-2018

ii
 LETTER OF FORWARD

27-June-2023

On the recommendation of Mr. Kiran Pudasainee, this project work is submitted by

Avisesh Bhandari Symbol No.: 502820039, T.U Registration No.: 5-2-282-34-2018,
entitled ‘‘Computational study of Vibrational properties of Glutamic Acid” is
forwarded by the Department of physics, St. Xavier’s college, for the approval to the
Evaluation Committee, Institute of Science and Technology (IoST), Tribhuvan University
(T.U), Nepal

He has fulfilled all the requirements laid down by the Institute of Science and Technology
(IoST), Tribhuvan University (T.U), Nepal for the project work.

……………………………..
Dr. Binod Adhikari
Head of Department
Department of
Physics St. Xavier’s
college Tribhuvan
University

iii
 BOARD OF EXAMINATION AND
CERTIFICATE OF APPROVAL

This project work (PRO-406) entitled “Computational study of the vibrational

properties of Glutamic Acid” by Mr. Avisesh Bhandari (Symbol No.:502820039 and
T.U. Registration No.: 5-2-282-34-2018) under the supervision of Mr. Kiran Pudasainee in
the department of Physics, St. Xavier’s College, Institute of Science and Technology
(IoST), Tribhuvan University (T.U.), is hereby submitted for the partial fulfillment of
Bachelor of Science (B.Sc.) degree in Physics. This report has been accepted and
forwarded to the Controller of Examination, Institute of Science and Technology,
Tribhuvan University, Nepal for the legal procedure.

……………………….
Mr. Kiran Pudasainee
Supervisor
Department of Physics
St. Xavier’s College

……………………… ……………………..
External Examiner Internal Examiner
….…...…….…………….
Dr. Binod Adhikari
Head of Department
Department of
Physics St. Xavier’s
College Tribhuvan
University

iv
 ACKNOWLEDGEMENTS

First of all, I would like to thank my respected supervisor, Dr. Kiran Pudasainee sir
for his constant guidance and supervision throughout the process. I am obliged to
thank him for his consistent help and support without which the project wouldn’t
have been completed. He has helped me out in case of difficulties and provided
valuable suggestions for better research work.

It is my honor to thank Fr. Principal Dr. Augustine Thomas S.J. for his time
facilitating St. Xavier’s college which made this research possible.

Moreover, it is an honor to receive insightful comments and advice from our Vice
Principal Ms. Saluja Chand which made my project much easier to carry out.
I also like to thank our Head of Department, Dr. Binod Adhikari,whose
encouraging remarks have motivated us to work hard on this project.
Furthermore, I would like to thank the research co-ordinator, Dr. Basudev Ghimire,
whose unwavering dedication, hard work and support provided us with much
inspiration.

My Sincere thanks to my friend Simanta Sankhi and Pradip Khadka who helped me
with constant encouragement and support in this research.
Finally, I would like to express my gratitude to my family, faculty members,
teachers, mentors and friends for their endless help and support.

…...............................
Avisesh Bhandari
Symbol No: 502820039
T.U. Registration No: 5-2-282-34-2018

v
 ABSTRACT

The primary aim of this research was to investigate the stability order of Glutamic Acid by
examining its bond length, bond angle, and dihedral angle, as well as conducting IR
spectroscopy analysis. These properties were studied computationally using software such as
GaussView and Gaussian. The 6-311+G(d) basis set and the B3LYP approximation within the
framework of Density Functional Theory (DFT) was applied. Additionally, the ground state
energy was determined to be -15012.43593 eV. The IR spectroscopy analysis of Glutamic Acid
was performed for three states: anion, cation and neutral states, within a certain frequency
range. Notably, significant frequency peaks were observed in the vicinity of 1800 cm-1. The
investigation of bond length, bond angle, and dihedral angle indicated the crucial role of carbon
atoms in the stability of Glutamic Acid.

Keywords : DFT, bond length, bond angle, dihedral angle, IR spectroscopy.

vi
 zf]w;f/

o; cg';Gwfgsf] k|fylds p2]Zo Un'6flds Pl;8sf] :yfloTj qmdnfO{ o;sf]

aG8 nDafO, aG8 sf]0f, / 8fOx]8«n sf]0f hfFr u/]/, ;fy} IR :k]S6«f]:sf]kL

ljZn]if0f ;~rfng ug{] lyof]. oL u'0fx¿ uf};Eo" / uf}l;og h:tf ;km\6j]o/ k|

of]u u/]/ u0fgfTds ¿kdf cWoog ul/Psf] lyof]. 6-311+G(d) cfwf/ ;]6 / 3gTj
sfo{fTds l;4fGt (DFT) sf] ¿k/]vf leq B3LYP cg'dfg nfu" ul/of]. yk ¿kdf, u|
fp08 :6]6 pmh{f -15012.43593 eV lgw{f/0f ul/Psf] lyof]. Un'6flds Pl;8 sf] IR
:k]S6«f]:sf]kL ljZn]if0f tLg :6]6x¿sf] nfuL k|bz{g ul/Psf] lyof] (Sofzg,
Go"6«n / Plgog :6]6x¿), Ps lglZrt cfj[lQ bfo/f leq. pn\n]vgLo ¿kdf,
dxQ\jk"0f{ lk|mSj]G;L lzv/x¿ 1800 cm-1 sf] j/k/ cjnf]sg ul/Psf] lyof]. aG8
nDafO, aG8 sf]0f, / 8fOx]8«n sf]0fsf] cg';Gwfgn] Un'6flds Pl;8sf]
l:y/tfdf sfa{g k/df0f'x¿sf] dxQ\jk"0f{ e"ldsfnfO{ ;+s]t uo{f].

Keywords : DFT, bond length, bond angle, dihedral angle, IR spectroscopy.

vii
 LIST OF ACRONYMS

a.u: Atomic Unit

Å: Angstrom
B3LYP: Becke, Three-parameters, Lee-Yang-Parr exchange-correlation functional
DFT: Density Functional Theory
eV: Electron Volt
HF: Hatree-Fock
IR: Infrared

viii
 LIST OF SYMBOLS

ρ(r): probability of finding any of the N electrons within the infinitesimal volume element,
dr.
ri: position of electron
e: electron charge
m: electron mass
ħ: reduced planck’s constant
∇: operator nabla
RA: position of nuclei
ZA: atomic number of atom A
ZB: atomic number of atom B
MA: mass of atom A
MB: mass of atom B

(Atom A and Atom B are the supposed atom represented in the formula
calculating the total Hamiltonian.)

ix
 LIST OF TABLES

Page No.
Table 1: Dihedral Angle and Ground state Energy of Glutamic Acid ..................... 13
Table 2: Bond Length of various bonds across the Structure of Glutamic Acid ....... 21
Table 3: Bond Angle of various bonds across the Structure of Glutamic Acid ......... 23
Table 4: Dihedral Angle of various bonds across the Structure of Glutamic Acid..... 24

x
 LIST OF FIGURES

Page No.

Figure 1: Molecular structure of Glutamic Acid ......................................... 2

Figure 2: Preview of the Gaussian setup ...................................................... 8
Figure 3: Glutamic Acid molecule in Gauss view ...................................... 9
Figure 4: Graph plot presentation of Dihedral Angle Vs Energy ................ 15
Figure 5: IR spectrum of Glutamic Acid in Cation State ............................. 17
Figure 6: IR spectrum of Glutamic Acid in Anion State .............................. 18
Figure 7: IR spectrum of Glutamic Acid in Neutral State ............................. 19
Figure 8: Graphical representation of the Highest Peak in IR spectrum ....... 20

xi
 TABLE OF CONTENTS

Page No.

Cover Page

Recommendation i

Declaration ii

Letter of Forward iii

Board of Examination and Certificate of Approval iv

Acknowledgements v

Abstract vi

List of Acronyms and Abbreviations vii

List of Symbols viii

List of Tables ix

List of Figures x

CHAPTER 1: INTRODUCTION

1.1 General Introduction 1

1.2 Rationale 2

1.3 Objectives 2

xii
CHAPTER 2: LITERATURE REVIEW 3

CHAPTER 3: MATERIALS AND METHOD

3.1 Materials

3.1.1. Gaussian 6

3.1.2 MS-Excel and Gauss View 5.0 8

3.1.3 Data processing, Plotting and analysis 9

3.2 Method 10

4. RESULT AND DISCUSSION

4.1.1 Ground state Energy of Glutamic Acid 13

4.1.2 IR spectroscopy 17

4.1.3 Highest peak region in IR spectrum 19

4.2 Bond Length, Bond angle, Dihedral angle of Glutamic Acid. 21

5. CONCLUSION AND RECOMMENDATION

5.1 Conclusion 26

5.2 Novelty and National Prosperity aspect of Project work 26

5.3 Limitations of the work 37

5.4 Recommendations for future work 28

REFERENCES 30

xiii
APPENDIX 32

xiv
 CHAPTER 1

1. INTRODUCTION

1.1 General Introduction:

Glutamic acid is an α-amino acid that is used by almost all living being for the biosynthesis
of proteins[L-Glutamic acid CAS#: 56-86-0". www.chemicalbook.com]. Its molecular
formula is C5H9NO4. Amino acids are constituents of the larger systems of peptides (short
chain of amino acids) and protein chains, thus their experimental properties and
computational modeling of their behavior in different media or in different electrolytic
solutions that mimics the media, represents a point for developing an convienient models
for describing the conforming changes of the protein chains and to assess their global
properties and their thermodynamic behavior[S. Grimme et al., (2003)]. Researchers have
done work on the computation of the molecular structure, harmonic and anharmonic
vibrational frequencies or ionization equilibria of L-glutamic acid[B. C. Gosh et al.,
(2013)].This project aims to supplement it. The substance (Glutamic Acid) was discovered
and identified in the year 1866 by the German chemist Karl Heinrich Ritthausen, who
treated wheat gluten (for which it was named) with sulfuric acid [Pilmmer et al., (1912)].
We plan to report on the IR spectra of glutamic acid dipeptides and/or similar protein
chains upon which we base our characterization of the vibrational properties of the
glutamic acid. Peptides containing huge concentrations of the amino acids has not been
studied in depth from a vibrational point of view yet. Our goal is help in the further
research which approach a large system of such amyloid peptides which are usually
formed by around 40-42 amino acid units, into small subsystems and computing them with
different models and tools as presented in the objectives. [Stefaniu et al.,].

1
 Figure 1. Molecular Structure of Glutamic Acid
(source: https://healthjade.net/glutamic-acid/)

1.2 Rationale:

The main purpose of this study is to study the vibrational properties of glutamic acid using
Gaussian. To set up model study, to inspect and compute the data on the glutamic acid
molecule and then embedding, and correlating the information globally which is important
as such unit are the subsystems of the larger peptides (chain of amino acid) and
characterization of their vibrational properties helps us to better understand about the
thermodynamic properties and it’s behavior in different interactions and provide a better
insight regarding the dynamics of the peptides constituting of such molecules.

1.3 Objectives:
Computational study using Gaussian software has helped researchers to learn, assess and
model various parameters of a molecular structure. This work aims to study with following
objectives:
a) To study the optimized molecule’s ground state Energy of Glutamic Acid in every
dihedral angle.
b) To assess the highest peak of vibration in Anion, Cation and Neutral State.
c) To assess the Bond angle, Bond length and Dihedral of the optimized molecule.

2
 CHAPTER 2

2. LITERATURE REVIEW

In 1980, Wilson et al., published a book on the theory of IR and Raman vibration spectra.
It explains how the theory of IR and Raman vibration spectra involves the interaction of
electromagnetic radiation with molecules, where absorption or scattering of light
corresponds to the vibrational modes of the molecule. The use of molecular symmetry and
group theory helps determine the allowed vibrational modes and their symmetries, leading
to the interpretation of the observed spectra.

In 1994, Chhiba et al., published a paper on how to reproduce the structures and vibrational
frequencies of a number of acids using the SPASIBA spectroscopic potential: acidic
corrosive, pivalic corrosive, succinic corrosive, adipic corrosive and l-glutamic corrosive.
Typical direction examinations have been performed on acidic, pivalic, succinic and adipic
corrosive dimers (counting their deutero analogs) and the l-glutamic corrosive dimer. It is
shown that the determined potential energy surfaces and consonant vibrational frequencies
are in awesome agreement with the trial results. Examination with past tasks underlines a
semi understanding for the four previous particles. Interestingly, new tasks are given for a
few vibrational groups of l-glutamic corrosive.

In 1995, Navaratte, J. L. et al., published a paper on the vibrational study of aspartic acid
and glutamic acid dipeptides. The infrared and Raman spectra of glutamic corrosive
dipeptide and aspartic corrosive dipeptide as strong examples were enlisted and
estimated. An overall task for the key vibrations has been proposed in the premise of past
works about their monomers and different examinations on the trademark frequencies for
the peptide linkage. A connection between's the tasks of the two peptides was likewise
done, showing comparative vibrational properties.

3
In 1995, Ramirez et al., distributed a paper on the power field and typical direction
estimations for glutamic corrosive. The MNDO-scaled consonant power field of glutamic
corrosive is gotten in about a bunch of non-repetitive neighborhood symmetrized inner
directions. A bunch of scaling factors is moved from aspartic corrosive. The hypothetical
vibrational frequencies for the basics are effectively contrasted and the noticed qualities,
and the frequencies of the 5N and d4 isotopic subsidiaries are additionally determined and
contrasted and the tests. For the majority of the observed bands, these findings and the
description of the normal modes, followed by the mean of the potential energy distribution,
agree with the previous assignments that were proposed, demonstrating a substantial
coupling between the skeletal stretching and bending coordinates.

In 2003, Grimme, S. et al., published a paper on the Improved second-order Møller–Plesset

perturbation theory by separate scaling of parallel-and antiparallel-spin pair correlation
energies. A modified version of MP2 is proposed to improve the accuracy of calculating
molecular ground state energies. It partitions the correlation energy into parallel- and
antiparallel-spin components, which are scaled independently. The scaling factors are
optimized using reaction energies from different molecules. Compared to standard MP2,
the modified method shows significant improvements, reducing errors and deviations. It
performs better than DFT/B3LYP and QCISD/QCISD(T) for systems with strong
correlation effects. The modified MP2 method also enhances bond lengths and vibrational
frequencies. Overall, it is a robust and valuable approach for quantum chemical
calculations.

In 2012, Dittrich, B. et al., distributed a paper on the dependable estimations of dipole

minutes from single-precious stone diffraction information and evaluation of an in-gem
upgrade. Utilizing seven instances of top notch informational indexes of amino acids it is
demonstrated the way that exact sub-atomic dipole minutes can be acquired from trial
diffraction information. Proposals for commonsense displaying decisions are given while
utilizing the Hansen/Coppens multipole model. Multipole-model outcomes, including
those from invariom refinement, are viewed as less precise than results from a premise set

4
depiction. The inquiry whether a sub-atomic dipole-second upgrade in the strong state is
reality or relic is concentrated on by various methods: A hypothetical particle implanted in
a bunch of point-charges gives a significant improvement, in concurrence with Hirshfeld

molecule refinement with point charges and dipoles. The exploratory procedures, multipole
refinement and wavefunction fitting, lead to more modest dipole-second improvements
than the hypothetical forecasts.

In 2013, B. C. Ghosh et al., published a paper on the investigation on the ionization

equilibria in L-Aspartic and L–Glutamic acid in water at microscopic level by DFT
method. pKa values of dissociable groups in L-Aspartic and L-Glutamic acids were
estimated using DFT methods in vacuum and aqueous environments with optimized
structures including H-bonded water molecules. Tautomers were considered in cyclic
equilibrium. In aqueous medium, zwitterionic forms had a significant contribution. Gibbs
energy changes for the cyclic equilibria were calculated to determine overall pKa values,
which showed good agreement with experimental data for both amino acids.

In 2016, Stefaniu et al., published a paper on the computational study of the L-aspartic
and L-Glutamic acid. It employs a linear scaling approach, optimizing the 3D structures of
the amino acids and comparing various properties in vacuum and water. The findings
provide insights into electronic effects, molecular deformability, steric factors, and
reactivity. This approach has potential in predicting protein-ligand interactions for drug
design and protein engineering.

5
 CHAPTER 3

3. MATERIALS AND METHODS

3.1 Materials

1. Gaussian
Gaussian 09W is a widely used software package for computational chemistry. It provides
a comprehensive suite of tools for various types of calculations related to molecular
structure, properties, and reactions. Here is a short report on Gaussian 09W software and
its uses:

1. Molecular Modeling and Quantum Chemical Calculations:

Gaussian 09W enables researchers to perform a range of quantum chemical calculations,
such as geometry optimization, energy calculations, and electronic structure analysis. It
employs a variety of methods, including Hartree-Fock (HF), density functional theory
(DFT), post-HF methods (MP2, CCSD(T)), and more advanced methodologies.

2. Spectroscopic Predictions:
Gaussian 09W facilitates the prediction of various spectroscopic properties, such as
infrared (IR) and Raman spectra, UV-Vis absorption spectra, and nuclear magnetic
resonance (NMR) chemical shifts. These predictions aid in the interpretation and analysis
of experimental data.

3. Reaction Mechanism Studies:

The software allows researchers to investigate reaction mechanisms and kinetics by
performing transition state searches, calculating reaction energetics, and analyzing reaction
pathways. This is valuable for understanding and predicting chemical reactions.

6
4. Solvent Effects:
Gaussian 09W incorporates solvation models to study the influence of solvents on
molecular properties and reactions. It enables the calculation of solvent effects using
continuum solvation models like the polarizable continuum model (PCM) and conductor-
like screening model (COSMO).

5. Excited States and Photochemistry:

Gaussian 09W offers capabilities for studying excited states and photochemical
processes, including the calculation of electronic excited states, optical spectra, and
photochemical reaction pathways. This is particularly useful for investigating light-induced
phenomena and photoactive materials.

6. Materials Science and Solid-State Chemistry:

The software supports calculations on extended systems, including periodic boundary
conditions and crystal structures. This allows for the study of materials properties, crystal
structures, phase transitions, and electronic band structures.

7. High-Performance Computing:
Gaussian 09W is designed to efficiently utilize high-performance computing resources,
allowing calculations to be performed on clusters and supercomputers. This enables
complex and computationally demanding calculations to be carried out in a timely manner.

In conclusion, Gaussian 09W is a versatile and powerful software package extensively

used in the field of computational chemistry. It provides a wide range of tools and
methodologies for studying molecular properties, reactions, and spectroscopy. Its
applications extend to various areas, including molecular modeling, reaction mechanism
studies, spectroscopic predictions, and materials science. With its robust capabilities and
efficient use of computational resources, Gaussian 09W has become an essential tool for
researchers in the field of computational chemistry.
7
 Figure 2: Preview of Gaussian setup.

2. MS-Excel and GaussView 5.0

GaussView 5.0 is a graphical interface software used alongside Gaussian for visualizing
and analyzing computational chemistry results. It aids in molecular structure building,
input file preparation, visualization of properties, analysis of results, reaction pathway
analysis, surface modeling, and serves as an educational tool. Its user-friendly interface
and visualization capabilities make it a valuable resource for researchers and students in
the field of computational chemistry. In order to manage data manipulations like arithmetic
operations, spreadsheets like Microsoft Excel use a grid of cells arranged in numbered

8
rows and letter-named columns. Also for this study, I'm using MS-Excel to plot various
graphs of glutamic acid molecule's IR spectroscopy.

Figure 3 : Glutamic Acid molecule in Gauss View 5.0

3. Data processing, Plotting and analysis

Quantum chemical calculations were conducted using the Gaussian 09W software
package. The DFT/B3LYP method with the 6-311+G(d) basis set was employed to
determine optimized geometrical parameters and vibrational frequencies of the molecule.
Molecular visualization and analysis were carried out using GaussView 5.0.

9
 3.2 Methods

Vibrational properties of glutamic molecule was studied using Gaussian 09W. Here, the
calculated vibrational properties of several modes of peptides was presented. From the
calculated vibrational mode frequency and intensity, we were be able to construct IR
spectra, a realistic looking IR spectra are obtained which we call absorbance spectra.

Here we studied vibrational frequency band position and intensities.

Different computational methods were developed in order to solve the quantum
mechanical problem that could deal with many electron systems with considerable
accuracy. Standing on the ground of various quantum theories and approximations, a wide
range of quantum computational software have been developed which help for solving the
quantum mechanical system in less time with more accuracy.

A molecular system is composed of mutually interacting electrons and nuclei and the
dynamics of these particles, in general, cannot be considered separately. Many properties
of the interacting system can be obtained by determining the eigen function which is the
fundamental problem in many-body problems. The Hamiltonian is a system of N mutually
interacting electrons and M nuclei can be written as,

H =

( ) ( ) Z A e2 Z A ZB e2
N 2 M 2 N M N ❑ M ❑
−ℏ −ℏ e2
∑ ❑ 2 m ∇i + ∑ ❑ 2 M ∇ A −∑ ❑ ∑ ❑ r ⃑ −R ⃑ +∑ ❑∑ ❑ r ⃑ – r ⃑ + ∑ ❑ ∑ ❑ R ⃑ − R ⃑
2 2

i=1 A =1 A i=1 A=1 |i A | i=1 j>i |i j | A=1 B>A | A B |

Where, the indices i, j refer to the electrons; A, B refer to the nuclei; MA, MB and ZA and

10
ZB refer to the masses and of the nuclei and atomic numbers of atoms A and B
respectively. e and m are the electron charge and mass, r i and RA are the position of
electron and nuclei respectively.

The first two terms in the equation above represent the kinetic energy of electrons and
nuclei respectively. The third term represents the coulomb attraction between the electrons
and nuclei; the fourth term is the coulomb repulsion between the electrons and nuclei and
the last term denotes the coulomb repulsion between nuclei. The expression for the
interactions between electrons and protons includes a sum on the indices i and j, with the
self-interaction terms i = j clearly excluded. The expression for the interactions between
nuclei also includes a sum on the indices A and B, with self-interaction terms A = B
clearly excluded. Nevertheless, obtaining the exact solutions of the Schrӧdinger’s equation
of N-electrons system using the Hamiltonian (H) as given by above equation is somewhat
taxing job and hence needs to be subjected to certain approximation like DFT.

Density Functional Theory

The density functional theory is a computational quantum mechanical modeling method

used to investigate the electronic structure of many-body problems. The properties of a
many-electron system can be determined using the functionals i.e. functions of another
function which is spatially dependent electron density in this case.

The density functional theory is used to treat many-body systems and is used to learn
electron correlations. It is likewise viewed as a speculation of Thomas-Fermi technique
and is respected to be a piece of The Standard Model for occasional solids. For his central
role in developing the density functional method, Walter Kohn received a chemistry Nobel
Prize in 1998.

The density functional theory is categorized into two parts. The part is derived from a
basic theorem of P. Hohenberg and W. Kohn upon which the whole theory is based. This
theory
11
reduces the solution of a one-particle Schrӧdinger-like equation for the electron density.
The information needed is contained in the electron density. The density functional theory
is used for calculating the binding energies, lattice parameters and bulk moduli of metals.
The application includes atoms, molecules, semiconductors, insulators, surfaces and
defects. DFT also demonstrates that an electron's ground state electrical configuration can
only be identified by electron. If one knows the exact electron density(𝑟), then the joining
of this density would occur at the position of nuclei. A knowledge of |(𝑟)| at the nuclei
will give the nuclear charge. Then, ρ(r) is given by,

2
ρ(r) = N∫ … ∫ | 𝜑 (𝑥1, 𝑥2,……𝑥N) | d𝑥1, d𝑥2, … ,d𝑥N

𝑤ℎ𝑒𝑟𝑒, ρ(r) represents the probability of finding any of N electrons within the
volume element, dr. Commonly, it is called the electron density.

12
 CHAPTER 4

4. RESULTS AND DISCUSSIONS

The main objective of this research or study is to examine and interpret the characteristics
of Glutamic Acid based on its structure. In this study, various properties of Glutamic Acid,
such as Energy, IR Spectroscopy, Highest frequency region and its graph, Bond length,
Bond Angle, and Dihedral Angle, were analyzed in detail. This investigation involved
computational work using software programs like Gaussian, Gauss View, and MS-Excel.
The properties were calculated using Density-Functional Theory with the application of the
B3LYP approximation and the 6-311+G(d) basis sets.

4.1.1 Ground State Energy of Glutamic Acid:

We have carried out DFT level of approximation with 6-311+G(d), B3LYP basis set
calculation to obtain the total ground state energy of Glutamic Acid molecule to get the
optimized structures which are shown in table:

Table 1: Optimized structure of total ground state energy of Glutamic Acid.

Angle(Degree) Energy(a.u) Energy(eV)

0 -551.69509339 -15012.35425006
10 -551.69464734 -15012.34211245
20 -551.69299248 -15012.29708152
30 -551.68802711 -15012.16196722
40 -551.68305452 -15012.02665646
50 -551.67760950 -15011.87849026
60 -551.67281341 -15011.74798230
70 -551.66922275 -15011.65027568
80 -551.66678542 -15011.58395270
90 -551.66623933 -15011.56909287
100 -551.66912317 -15011.64756598

13
110 -551.67546562 -15011.82015244
120 -551.68271037 -15012.01729169
130 -551.68790348 -15012.15860309
140 -551.69008129 -15012.21786418
150 -551.68996770 -15012.21477325
160 -551.68888038 -15012.18518583
170 -551.68778234 -15012.15530671
180 -551.68735187 -15012.14359305
190 -551.68773461 -15012.15400791
200 -551.68888779 -15012.18538747
210 -551.69045830 -15012.22812312
220 -551.69196895 -15012.26922991
230 -551.69293702 -15012.29557238
240 -551.69209627 -15012.27269446
250 -551.69209627 -15012.27269446
260 -551.69209627 -15012.27269446
270 -551.68798000 -15012.16068530
280 -551.68798000 -15012.16068530
290 -551.68446113 -15012.06493218
300 -551.68435307 -15012.06199173
310 -551.68782567 -15012.15648577
320 -551.68777652 -15012.15514834
330 -551.69047585 -15012.22860068
340 -551.69299248 -15012.29708152
350 -551.69464734 -15012.34211245
360 -551.69509339 -15012.35425006

14
 Energy Vs Dihedral Angle
-15011.50

-15011.60

-15011.70

-15011.80
Energy (in

-15011.90

-15012.00
eV)

-15012.10

-15012.20

-15012.30

-15012.40 0 50 100 150 200 250 300 350 400

Dihedral Angle (in degrees)

Figure 4 : Graph representing dihedral angle vs energy

Through the utilization of software such as Gauss View and Gaussian, employing the 6-
311+G(d) basis set and the B3LYP Approximation within the framework of Density
Functional Theory (DFT), the energy of the system was investigated computationally. A
graphical representation was presented, depicting the relationship between the angle (on
the horizontal axis) and the energy (on the vertical axis). It was observed that the minimum
energy occurred at specific angles, namely 0, 230, 350, and 360 degrees. Among these
values, the energy reached its lowest point at 0 degrees, measuring approximately -
15012.43593 electron volts (eV).

A cation is an ion that carries a positive charge. It is formed when an atom loses electrons,
leading to a net positive charge due to an excess of protons. In contrast, an anion is an ion
that carries a negative charge. It is formed when an atom gains electrons, resulting in a net
negative charge caused by an excess of electrons. On the other hand, a neutral atom is an
atom that possesses an equal number of protons and electrons, resulting in a net charge of

15
zero. Consequently, neutral atoms do not carry any electrical charge. In summary, cations
have a positive charge due to electron loss, anions have a negative charge due to electron
gain, and neutral atoms have an overall neutral charge. In such situation, there are less
electron-electron repulsion and the net nuclear attraction per electron is higher. So, the
newly formed ions becomes a more condensed and/or compact version of its original
neutral atom. So we have to calculate this behavior and we use the IR spectroscopy of the
cation, anion and neutral structure with the help of Gaussian and plot the IR graph.

16
4.1.2 IR-Spectroscopy

To examine the structure and IR spectra of Glutamic Acid, calculations were

conducted using the B3LYP/6-311+G(d) configuration. Infrared spectroscopy, which
investigates the interaction between matter and infrared radiation, was employed for
this purpose. The resulting IR spectrum can be graphically represented, showing the
intensity of infrared light (measured in arbitrary absorbance or transmittance units)
on the vertical axis and the frequency or wavelength on the horizontal axis.
Typically, IR spectra measure frequency in reciprocal centimeters (cm -1). The figure
below presents the IR spectroscopy of Glutamic Acid in three states: cation, neutral,
and anion states, with frequencies upto 2000 cm -1. The accompanying figure
provides a visual representation of the relevant IR spectroscopy of Glutamic Acid.

Cation IR Spectrum
4000
3500
3000
2500
2000
Intensity(a.u)

1500
1000
500
0

0 500 1000 1500 2000

Wavenumber (cm-1)

Figure 5: IR Spectrum of Glutamic Acid in Cation state.

17
 Anion IR spectrum
9100
8400
7700
7000
6300
Intensity (a.u)

5600
4900
4200
3500
2800
2100
1400
700
0

0 500 1000 1500 2000

Wavenumber (cm-1)

Figure 6: IR spectrum of Glutamic Acid molecule in Anion state.

18
 IR spectrum for neutral state
2500

2000
Intensity(a.u)

1500

1000

500

0
0 500 1000 1500 2000
Wavenumber(cm-1)

Figure 7: IR spectrum of Glutamic Acid in Neutral state.

4.1.3 Highest Peak Region in the IR Spectrum of Glutamic acid:

After analyzing the Glutamic Acid molecule using Gaussian software, its IR spectrum was
obtained, as depicted in figure 3. An IR spectrum is typically represented as a graph that
plots the intensity of infrared light (measured in arbitrary units) on the vertical axis against
the wavenumber (frequency of a wavelength) on the horizontal axis. Notably, in the
frequency range around 1800 cm-1, there are significant peaks indicating intense vibration
and absorption within the Glutamic Acid molecule. To highlight these high-frequency peak
regions, a graph was created, as presented below.

19
 1000 1200 1400 1600 1800
Wavenumber (cm-1)

Legends:
Anion ----
Cation ----
Neutral ----

Figure 8: Graph of Highest Peak region of Glutamic Acid in Anion, Cation and Neutral states

20
It is plotted with wavenumber on the X-axis and intensity on the Y-axis. In this region
vibration of whole Glutamic Acid molecule structure has occurred. From the figure itself it
shows that around (1000 to 1800) cm−1 region the peaks are maximum and are highly
absorbed. Region where the peak is running smoothly which shows that this region has caused
little vibration to the structure of Glutamic Acid. After onwards the peaks are increasing very
rapidly from region (1000 to1800) cm−1 which shows that this region has caused maximum
vibration in the structure of Glutamic Acid molecule.

4.2 Bond length, Bond Angle and Dihedral Angle of Glutamic Acid:

The bond length refers to the average distance between the centers of two atoms that are
bonded together in a molecule. On the other hand, a bond angle represents the angle
formed by three atoms, with at least two bonds connecting them. It describes the three-
dimensional arrangement of the atoms within the molecule. Lastly, a dihedral angle is
the angle between two bonds that originate from different atoms, and its value ranges
from -180 to 180 degrees. In the case of Glutamic Acid, its structure comprises 5 carbon
atoms, 4 oxygen atoms, 9 hydrogen atoms, and 1 nitrogen atom. The following tables
provide information on the bond lengths, bond angles, and dihedral angles within the
Glutamic Acid molecule.

Table 2: Bond length of various bonds across the structure of Glutamic Acid:

Bond Bond Bond Bond length

between length in between in Å
atoms Å atoms

O1-C9 1.3519 C6-C7 1.5437

O1-H18 0.9707 C6-C8 1.5281
O2-C10 1.3564 C6-H11 1.0944

21
O2-H19 0.9706 C6-H12 1.0935
O3=C9 1.2074 C7-C9 1.522
O4=C10 1.208 C7-H13 1.1039
N5-C7 1.4595 C8-C10 1.5078
N5-H16 1.0156 C8-H14 1.0971
N5-H17 1.0138 C8-H15 1.0958

22
Electronegativity plays a crucial role in determining the bond length between atoms. It
refers to an atom's ability to attract a shared pair of electrons towards itself. In the context
of the elements involved—Carbon, Hydrogen, Oxygen, and Nitrogen—Oxygen exhibits
the highest electronegativity, indicating its strong electron-attracting tendency. Nitrogen
follows oxygen in terms of electronegativity. Carbon is less electronegative than both
oxygen and nitrogen but still more electronegative than hydrogen, which possesses the
lowest electronegativity among these elements. As electronegativity increases, bond length
tends to decrease. Therefore, the bond between Hydrogen and Carbon (H-C) is more stable
due to the higher electronegativity of Carbon.

Table 3: Bond Angle of various bonds across the structure of Glutamic Acid.

Bond Bond angle Bond Bond angle

between in degree between in degree
atoms atoms
C9-O1-H18 106.9457 N5-C7-H13 112.7949
C10-O2-H19 106.8073 C6-C7-C9 113.2869
C7-N5-H16 110.6173 C6-C7-H13 106.7323
C7-N5-H17 111.0958 C9-O7-C13 103.9149
H16-N5-H17 108.8071 O6-C8-H10 113.0179
C7-C6-C8 113.04 C6-C8-H14 109.8704
C7-C6-H11 107.6295 C6-C8-H15 112.0798
C7-C6-H12 109.5697 C10-C8-H14 107.4612
C8-C6-H11 109.1398 C10-C8-H15 107.977
C8-C6-H12 110.5885 H14-C8-H15 106.0986
H11-C6-H12 106.6275 O1-C9=O3 122.4996
N5-C7-C6 111.0659 O1-C9-C7 112.2916
N5-C7-C9 108.8942 O3=C9-C7 125.1747
O2-C10-C8 111.5974 O2-C10=O4 122.0932
O4=C10-C8 126.3048 - -

23
The different bond angle found in the structure of Glutamic Acid are tabulated in above
table. Most carbon atoms in the bond angle structure indicates that it plays an important
role in stability of any structure. Also, the electronegativity of oxygen is higher than
that of hydrogen and carbon and electronegativity of carbon is higher than that of
hydrogen. The reason behind these stability orders is due to the electron density or
cloud of electrons which play an important role in configuration of these atoms.

Table 4: Dihedral Angle of various bonds across the structure of Glutamic Acid.

Bond between Dihedral Bond between Dihedral

atoms angle in atoms angle in
degree degree
H18-O1-C9=O3 0.7379 C7-C6-C8-H14 -49.0468
H18-O1-C9-C7 -177.243 C7-C6-C8-H15 68.6496
H19-O2-C10=O4 0.8974 H11-C6-C8-C10 -49.3259
H19-O2-C10-C8 -178.3714 H11-C6-C8-H14 70.6873
H16-N5-C7-C6 -153.7952 H11-C6-C8-H15 -171.6163
H16-N5-C7-C9 -28.3721 H12-C6-C8-C10 67.6701
H16-N5-C7-13 86.4339 H12-C6-C8-H14 -172.3167
H17-N5-C7-C6 85.2524 H12-C6-C8-H15 -54.6203
H17-N5-C7-C9 -149.3244 N5-C7-C9-O1 -170.8653
H17-N5-C7-H13 -34.5184 N5-C7-C9=O3 11.2181
C8-C6-C7-N5 61.8754 C6-C7-C9-O1 -46.7462
C8-C6-C7-C9 -61.0517 C6-C7-C9=O3 135.3371
C8-C6-C7-H13 -174.8033 H13-C7-C9-O1 68.6922
H11-C6-C7-N5 -58.7224 H13-C7-C9=O3 -109.2245
H11-C6-C7-C9 178.3505 C6-C8-C10-O2 -168.9163
H11-C6-C7-H13 64.5989 C6-C8-C10=O4 11.8523
H12-C6-C7-N5 -174.2932 H14-C8-C10-O2 69.6996
H12-C6-C7-C9 62.7797 H14-C8-C10=O4 -109.5318
H12-C6-C7-H13 -50.9718 H15-C8-C10-O2 -44.3591
C7-C6-C8-C10 -169.06 H15-C8-C10=O4 136.4095

24
Dihedral Angle of various atoms across the structure of Glutamic Acid is listed in
the table above. This dihedral angle is in the range of [-180,180] which agrees with
the theoretical result. Most of the Carbon attached dihedral angle are in positive
range which shows that how these carbon atoms play important role in the stability.

25
 CHAPTER 5

5. CONCLUSION AND RECOMMENDATION

5.1 Conclusions
The computational analysis of the glutamic acid molecule using Gaussian software
involved examining its various features. Basis sets 6-311+G(d) and the B3LYP
approximation were utilized, and software tools like GaussView and Gaussian were
employed. Several parameters were observed, including IR spectroscopy, bond length,
bond angle, dihedral angle, and ground state energy. The energy was found to be -
15012.43593 eV. Glutamic acid's IR spectroscopy exhibited distinct patterns in three
states: cation, neutral, and the differences between the cation and neutral states. The
observed frequency peaks in the vicinity of 1800 cm-1 were notably high.

5.2 Novelty and National Prosperity aspect of Project work

Computational study of the vibrational properties of glutamic acid is innovative in a sense

that it examines the behavior of a glutamic acid molecule in the simulation, which may
help us understand its characteristics and prospective uses.

Utilizing this knowledge, we could contribute to national prosperity as the understanding

of the vibrational properties of glutamic acid aids in drug discovery and design efforts. It
enables the identification of optimal binding sites, prediction of drug efficacy, and the
development of targeted therapeutics, contributing to advancements in the pharmaceutical
industry and national healthcare. Also, the study of vibrational properties has practical
applications in various biotechnological fields. It assists in the design of enzymes,
catalysts, biocompatible materials, and the development of biosensors and diagnostic tools,
fostering innovation and economic growth.

26
5.3 Limitations of the work :

Some limitations of this work are mentioned below:

While Gaussian software offers a wide range of capabilities for computational studies, it
also has certain limitations that researchers should be aware of. Some of the limitations of
computational studies in Gaussian software include:

1. Approximations and Methods: Computational calculations in Gaussian software rely on

various approximations and methods to solve the quantum mechanical equations. These
approximations can introduce errors and limitations in the accuracy of the results obtained.
Researchers need to carefully select appropriate methods and consider the potential
limitations associated with them.

2. Computational Resources: The accuracy and complexity of calculations in Gaussian

software depend on the available computational resources, including processing power and
memory. Large and complex systems may require substantial computational resources,
leading to increased computational time and costs. Researchers need to consider the
limitations of their computational infrastructure for performing accurate and efficient
calculations.

3. Size Limitations: Gaussian software has certain limitations in terms of the size of
systems that can be effectively studied. As the size of the system increases, the
computational cost and memory requirements also increase significantly. This limitation
may restrict the study of large molecular systems or extended systems, such as crystals or
nanoparticles, within the capabilities of the software.

4. Potential Convergence Issues: Certain calculations, such as geometry optimizations and

transition state searches, may encounter convergence issues in Gaussian software. This can
result in difficulties in obtaining accurate and reliable results. Researchers need to
27
carefully

28
monitor convergence criteria and employ appropriate strategies to address convergence
problems when encountered.

5. Inherent Simplifications: Computational models in Gaussian software involve

simplifications and assumptions to make calculations tractable. These simplifications may
neglect certain effects or interactions that can be important in real-world systems.
Researchers should be aware of these simplifications and understand their potential impact
on the accuracy and applicability of the results.

6. Sensitivity to Parameters: The accuracy and reliability of results obtained from Gaussian
software can be sensitive to various parameters, such as basis sets, functionals, and
convergence criteria. Careful selection and optimization of these parameters are necessary
to obtain meaningful and accurate results. Researchers need to thoroughly validate and
verify their chosen parameters to ensure the reliability of their computational study.

It is important for researchers to be aware of these limitations and carefully consider them
when interpreting and drawing conclusions from computational studies performed using
Gaussian software.

5.4 Recommendations for future work

Understanding the vibrational properties of the glutamic acid molecule is highly

significant across multiple research areas. Here are a few recommendations highlighting
the prospects for any future work:

1. Functional Group Analysis: Glutamic acid contains various functional groups. The
vibrational properties enable the characterization and differentiation of these groups
based on their unique vibrational signatures, providing insights into their functional roles
and interactions.

29
2. Protein Structure and Folding: Glutamic acid plays a crucial role in protein structure
and folding. Studying its vibrational properties sheds light on conformational changes,
hydrogen bonding patterns, and intermolecular interactions involved in protein folding
processes.

3. Drug Design and Interaction Studies: Glutamic acid is a target for drug design in
various biological processes. Investigating its vibrational properties helps understand the
interactions between glutamic acid and potential drug molecules, aiding in rational drug
design.

4. Biochemical Reactions and Catalysis: Glutamic acid participates in enzymatic

reactions and catalytic processes. Exploring its vibrational properties provides insights
into reaction mechanisms, transition states, and active site interactions, enhancing our
understanding of biochemical reactions and facilitating efficient catalyst design.

5. Biophysical and Biomedical Studies: The vibrational properties of glutamic acid have
applications in biophysical and biomedical research. They can be utilized to monitor
and characterize glutamic acid in biological samples, study its behavior under different
conditions, and investigate its involvement in diseases and metabolic pathways.

30
 REFERENCES

Chhiba, M., Derreumaux, P., & Vergoten, G. (1994). The use of the SPASIBA spectroscopic
potential for reproducing the structures and vibrational frequencies of a series of acids:
acetic acid, pivalic acid, succinic acid, adipic acid and l-glutamic acid. Journal of
molecular structure, 317(1-2), 171-184.

Destrade, C., & Garrigoulagrange, C. (1976). use of calculation of normal vibration modes for
determination of conformation of glycylglycine and triglycine in aqueous-solution.
journal of molecular structure, 31(2), 301-317.

Dittrich, B., & Jayatilaka, D. (2012). Reliable measurements of dipole moments from single-
crystal diffraction data and assessment of an in-crystal enhancement. Electron Density
and Chemical Bonding II, 27-45.
Ghosh, B. C., & Mukherjee, A. K. (2013). Investigation of ionization equilibria of L- aspartic
and L-glutamic acids in water at a microscopic level by DFT method. Molecular
Physics, 111(7), 851-859.

Grimme, S. (2003). Improved second-order Møller–Plesset perturbation theory by separate

scaling of parallel-and antiparallel-spin pair correlation energies. The Journal of
chemical physics, 118(20), 9095-9102.

Navarrete, J. L., Hernandez, V., & Ramirez, F. J. (1995). Vibrational study of aspartic acid
and glutamic acid dipeptides. Journal of molecular structure, 348, 249-252.
Plimmer, R. H. A. (1912). RHA Plimmer; FG Hopkins, eds. The Chemical Constitution of the
Protein. Monographs on biochemistry. Part I. Analysis (2nd ed.). London: Longmans,
Green and Co, 114.

Ramirez, F. J., & Navarrete, J. L. (1995). Force field and normal coordinate calculations

31
for glutamic acid. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy,
51(2), 293-302.

Stefaniu, A., Savoiu, V. G., Lupescu, I., & Iulian, O. (2016). Computational study on 3D
structure of L-aspartic acid and L-glutamic acid: Molecular descriptors and properties.
Ovidius Univ. Ann. Chem, 27, 48-52.

Wilson, E. B., Decius, J. C., & Cross, P. C. (1980). Molecular vibrations: the theory of
infrared and Raman vibrational spectra. Courier Corporation.
https://healthjade.net/glutamic-acid/ (source for image of Molecular structure of
Glutamic Acid)

32
 APPENDIX

******************************************
Gaussian 09: IA32W-G09RevA.02 11-Jun-2009
03-Jul-2023
******************************************

OPTIMIZATION

Item Value Threshold Converged?

Maximum Force 0.000286 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.039368 0.001800 NO
RMS Displacement 0.010239 0.001200 NO
Predicted change in Energy=-1.064424D-05

Input orientation:

Center Atomic Atomic Coordinates (Angstroms)

Numbe Number Type X Y Z
r

1 8 0 1.838145 1.487673 -0.910955

2 8 0 -3.089051 0.685160 1.096353
3 8 0 2.867592 0.534994 0.840902
4 8 0 -3.006885 -0.503516 -0.805839
5 7 0 1.473092 -1.795406 0.588964
6 6 0 -0.146355 -0.556916 -0.816541
7 6 0 1.337600 -0.808601 -0.478701
8 6 0 -0.940576 0.006592 0.361194
9 6 0 2.091538 0.452405 -0.080518
10 6 0 -2.428992 0.015259 0.119368
11 1 0 -0.584037 -1.512881 -1.120740
12 1 0 -0.218231 0.107784 -1.681678
13 1 0 1.829221 -1.123306 -1.416160
14 1 0 -0.753862 -0.591827 1.261112
15 1 0 -0.635484 1.029819 0.608524
16 1 0 2.349228 -1.663762 1.085629

33
 17 1 0 1.447612 -2.738442 0.217473
18 1 0 2.391705 2.228507 -0.616043
19 1 0 -4.034560 0.631364 0.884056

Stoichiometry C5H9NO4
Framework group C1[X(C5H9NO4)]
Deg. of freedom 51
Full point group C1 NOp 1
Largest Abelian subgroup C1 NOp 1
Largest concise Abelian subgroup C1 NOp 1
Standard orientation:

Center Atomic Atomic Coordinates (Angstroms)

Number Number Type X Y Z

1 8 0 1.875799 -1.524515 0.840455

2 8 0 -3.109572 -0.776832 -1.017263
3 8 0 2.834158 -0.542203 -0.935086
4 8 0 -2.996567 0.418623 0.878881
5 7 0 1.432269 1.775019 -0.603822
6 6 0 -0.136459 0.496495 0.824110
7 6 0 1.335630 0.769834 0.451402
8 6 0 -0.953521 -0.062537 -0.340028
9 6 0 2.089870 -0.477879 0.013535
10 6 0 -2.434825 -0.094362 -0.059359
11 1 0 -0.577455 1.443490 1.150605
12 1 0 -0.178507 -0.179493 1.682414
13 1 0 1.848193 1.075559 1.380247
14 1 0 -0.798938 0.551652 -1.235480
15 1 0 -0.640968 -1.077398 -0.611237
16 1 0 2.289400 1.651508 -1.134731
17 1 0 1.422427 2.711467 -0.215228
18 1 0 2.425305 -2.256627 0.517668
19 1 0 -4.050060 -0.735187 -0.781365

Rotational constants (GHZ): 2.3679697 0.6445029 0.6056191

Standard basis: 6-31+G(2d,p) (6D, 7F)
There are 295 symmetry adapted basis functions of A symmetry.
Integral buffers will be 262144 words long.
Raffenetti 2 integral format.
34
35
 Two-electron integral symmetry is turned on.
295 basis functions, 443 primitive gaussians, 295 cartesian basis functions
39 alpha electrons 39 beta electrons
nuclear repulsion energy 545.7777620388 Hartrees.
NAtoms= 19 NActive= 19 NUniq= 19 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=F Big=F
One-electron integrals computed using PRISM.
NBasis= 295 RedAO= T NBF= 295
NBsUse= 295 1.00D-06 NBFU= 295

anion vibration calc.

Symbolic Z-matrix:
Charge = -1 Multiplicity =
2
O 2.24818 -1.63437 0.36373
O -3.75559 0.53915 0.15966
O 3.46866 0.10219 -0.36735
O -2.70864 -1.36582 -0.40179
N 1.36074 1.83057 -0.24977
C -0.12073 -0.15358 -0.21644
C 1.17341 0.49821 0.31581
C -1.38709 0.56169 0.25225
C 2.42029 -0.33173 0.04554
C -2.64587 -0.21412 -0.04271
H -0.14089 -1.18859 0.13872
H -0.08606 -0.19811 -1.30847
H 1.09465 0.50817 1.4169
H -1.34539 0.72146 1.33685
H -1.48918 1.55567 -0.1976
H 2.34583 2.07699 -0.2658
H 0.8579 2.52864 0.28653
H 3.09619 -2.07898 0.20429
H -4.51923 -0.03123 -0.02361

Atomic-Atomic Spin Densities.

1 2 3 4 5 6
1O 0.675909 0.000238 0.120225 -0.001825 0.158897 -1.397248
2O 0.000238 0.872940 -0.000208 0.270252 0.054419 -0.839467
3O 0.120225 -0.000208 0.124380 0.000104 -0.073780 0.027864
36
4 O -0.001825 0.270252 0.000104 0.255759 0.003178 -0.254635
5 N 0.158897 0.054419 -0.073780 0.003178 2.310963 -5.960171
6 C -1.397248 -0.839467 0.027864 -0.254635 -5.960171 29.727076
7 C 1.253893 0.134750 0.192577 0.049293 0.872051 -10.382371
8 C 0.250588 -0.088007 -0.034466 -0.029796 1.852332 -8.738226
9 C -1.099488 0.020350 -0.354993 0.008803 0.251600 1.484397
10 C 0.048859 -0.479904 -0.008044 -0.347136 0.479487 -2.437251
11 H 0.004887 0.001879 -0.000249 0.000130 0.011826 -0.141950
12 H 0.003604 0.002216 -0.000765 0.000459 0.024658 -0.184650
13 H -0.004763 -0.000346 0.002141 0.000170 -0.045447 0.174945
14 H -0.000017 -0.003254 0.000042 -0.000426 -0.005746 0.043768
15 H 0.000001 0.001450 -0.000008 0.000146 0.002704 -0.013064
16 H -0.002131 -0.000020 0.004783 0.000010 -0.053927 0.085850
17 H -0.001755 -0.001130 0.006469 0.000068 -0.240679 0.369058
18 H -0.178995 -0.000006 -0.030908 0.000120 -0.014538 0.197892
19 H 0.000002 -0.148855 0.000000 -0.044786 -0.000816 0.038713
7 8 9 10 11 12
1 O 1.253893 0.250588 -1.099488 0.048859 0.004887 0.003604
2 O 0.134750 -0.088007 0.020350 -0.479904 0.001879 0.002216
3 O 0.192577 -0.034466 -0.354993 -0.008044 -0.000249 -0.000765
4 O 0.049293 -0.029796 0.008803 -0.347136 0.000130 0.000459
5 N 0.872051 1.852332 0.251600 0.479487 0.011826 0.024658
6 C -10.382371 -8.738226 1.484397 -2.437251 -0.141950 -0.184650
7 C 6.919150 2.620259 -2.619178 0.661809 0.072150 0.067436
8 C 2.620259 3.035588 -0.098235 1.002799 0.041951 0.056375
9 C -2.619178 -0.098235 2.699116 0.005683 -0.010564 0.005997
10 C 0.661809 1.002799 0.005683 1.119032 0.014526 0.017346
11 H 0.072150 0.041951 -0.010564 0.014526 0.002314 0.001114
12 H 0.067436 0.056375 0.005997 0.017346 0.001114 0.003806
13 H -0.076557 -0.051031 0.014036 -0.012396 -0.000400 -0.000177
14 H -0.006195 -0.025405 0.000597 -0.002299 -0.000115 -0.000053
15 H 0.000408 0.003963 0.000580 0.003995 0.000007 0.000037
16 H -0.002238 -0.021756 -0.010985 -0.003076 -0.000020 -0.000088
17 H 0.062513 -0.129595 -0.051704 -0.029219 -0.000126 -0.000475
18 H -0.224752 -0.028748 0.273493 -0.004964 -0.000414 -0.000130
19 H -0.005943 0.045684 -0.000608 0.116473 -0.000023 -0.000021
13 14 15 16 17 18
1 O -0.004763 -0.000017 0.000001 -0.002131 -0.001755 -0.178995
2 O -0.000346 -0.003254 0.001450 -0.000020 -0.001130 -0.000006
3 O 0.002141 0.000042 -0.000008 0.004783 0.006469 -0.030908
4 O 0.000170 -0.000426 0.000146 0.000010 0.000068 0.000120
5 N -0.045447 -0.005746 0.002704 -0.053927 -0.240679 -0.014538

37
 6 C 0.174945 0.043768 -0.013064 0.085850 0.369058 0.197892
7 C -0.076557 -0.006195 0.000408 -0.002238 0.062513 -0.224752
8 C -0.051031 -0.025405 0.003963 -0.021756 -0.129595 -0.028748
9 C 0.014036 0.000597 0.000580 -0.010985 -0.051704 0.273493
10 C -0.012396 -0.002299 0.003995 -0.003076 -0.029219 -0.004964
11 H -0.000400 -0.000115 0.000007 -0.000020 -0.000126 -0.000414
12 H -0.000177 -0.000053 0.000037 -0.000088 -0.000475 -0.000130
13 H 0.007800 0.000233 -0.000003 0.000462 0.002043 0.000327
14 H 0.000233 0.001487 -0.000255 0.000004 0.000182 0.000001
15 H -0.000003 -0.000255 -0.000756 -0.000001 -0.000108 0.000000
16 H 0.000462 0.000004 -0.000001 0.005074 0.005019 0.000067
17 H 0.002043 0.000182 -0.000108 0.005019 0.040870 0.000023
18 H 0.000327 0.000001 0.000000 0.000067 0.000023 0.064386
19 H 0.000001 0.000053 -0.000020 0.000000 0.000001 0.000000
19
1O 0.000002
2O -0.148855
3O 0.000000
4O -0.044786
5N -0.000816
6C 0.038713
7C -0.005943
8C 0.045684
9C -0.000608
10 C 0.116473
11 H -0.000023
12 H -0.000021
13 H 0.000001
14 H 0.000053
15 H -0.000020
16 H 0.000000
17 H 0.000001
18 H 0.000000
19 H 0.043754

Anisotropic Spin Dipole Couplings in Principal Axis System

Atom a.u. MegaHertz Gauss 10(-4) cm-1 Axes

Baa -0.0536 3.881 1.385 1.295 0.6112 -0.4093 0.6774

1 O(17) Bbb -0.0266 1.926 0.687 0.642 0.6632 0.7319 -0.1562

38
 Bcc 0.0803 -5.807 -2.072 -1.937 -0.4319 0.5448 0.7188

Baa -0.0340 2.460 0.878 0.820 -0.5995 -0.2278 0.7672

2 O(17) Bbb -0.0192 1.393 0.497 0.465 -0.3000 0.9527 0.0485
Bcc 0.0532 -3.853 -1.375 -1.285 0.7420 0.2011 0.6395

Baa -0.0482 3.489 1.245 1.164 0.7935 -0.5915 0.1429

3 O(17) Bbb -0.0404 2.925 1.044 0.976 0.6026 0.7310 -0.3202
Bcc 0.0886 -6.414 -2.289 -2.139 0.0849 0.3402 0.9365

Baa -0.0231 1.670 0.596 0.557 0.8328 0.4416 -0.3338

4 O(17) Bbb -0.0115 0.835 0.298 0.279 -0.2966 0.8651 0.4045
Bcc 0.0346 -2.505 -0.894 -0.835 0.4674 -0.2379 0.8514

Baa -0.0081 -0.312 -0.111 -0.104 0.9085 0.1972 -0.3683

5 N(14) Bbb -0.0061 -0.237 -0.084 -0.079 0.3783 -0.0138 0.9256
Bcc 0.0142 0.549 0.196 0.183 -0.1775 0.9803 0.0871

Baa -0.0056 -0.746 -0.266 -0.249 0.3829 0.8664 -0.3204

6 C(13) Bbb -0.0018 -0.238 -0.085 -0.079 0.6019 0.0291 0.7980
Bcc 0.0073 0.983 0.351 0.328 0.7008 -0.4984 -0.5103

Baa -0.0153 -2.050 -0.731 -0.684 -0.5272 0.6393 0.5597

7 C(13) Bbb -0.0108 -1.455 -0.519 -0.485 0.7361 0.6727 -0.0750
Bcc 0.0261 3.505 1.251 1.169 0.4245 -0.3725 0.8253

Baa -0.0129 -1.731 -0.618 -0.577 0.6526 -0.0763 0.7538

8 C(13) Bbb -0.0088 -1.175 -0.419 -0.392 0.4154 0.8681 -0.2718
Bcc 0.0217 2.906 1.037 0.969 0.6337 -0.4905 -0.5982

Baa -0.0475 -6.377 -2.276 -2.127 0.3871 0.8475 -0.3631

9 C(13) Bbb -0.0440 -5.905 -2.107 -1.970 0.8655 -0.4698 -0.1738
Bcc 0.0915 12.282 4.383 4.097 0.3179 0.2469 0.9154

Baa -0.0155 -2.085 -0.744 -0.695 -0.4948 0.7997 0.3401

10 C(13) Bbb -0.0134 -1.799 -0.642 -0.600 0.8690 0.4568 0.1903
Bcc 0.0289 3.884 1.386 1.295 0.0032 -0.3897 0.9210

Baa -0.0011 -0.587 -0.210 -0.196 0.0786 0.2110 0.9743

11 H(1) Bbb -0.0004 -0.192 -0.069 -0.064 -0.6049 0.7869 -0.1216
Bcc 0.0015 0.780 0.278 0.260 0.7924 0.5798 -0.1895

39
 Baa -0.0026 -1.406 -0.502 -0.469 0.1497 0.9886 -0.0182
12 H(1) Bbb 0.0001 0.028 0.010 0.009 0.8832 -0.1419 -0.4470
Bcc 0.0026 1.378 0.492 0.460 0.4445 -0.0508 0.8943

Baa -0.0054 -2.863 -1.022 -0.955 -0.2088 0.8257 -0.5241

13 H(1) Bbb -0.0048 -2.554 -0.911 -0.852 0.8514 0.4172 0.3179
Bcc 0.0102 5.417 1.933 1.807 -0.4811 0.3798 0.7901

Baa -0.0049 -2.592 -0.925 -0.865 -0.5480 0.8176 0.1767

14 H(1) Bbb -0.0039 -2.069 -0.738 -0.690 0.6744 0.5568 -0.4849
Bcc 0.0087 4.662 1.663 1.555 0.4948 0.1465 0.8565

Baa -0.0040 -2.135 -0.762 -0.712 0.6533 -0.5500 -0.5203

15 H(1) Bbb -0.0010 -0.553 -0.197 -0.185 0.7498 0.3747 0.5453
Bcc 0.0050 2.689 0.959 0.897 0.1050 0.7464 -0.6572

Baa -0.0020 -1.056 -0.377 -0.352 0.2566 0.2072 0.9441

16 H(1) Bbb -0.0004 -0.210 -0.075 -0.070 0.0996 0.9659 -0.2390
Bcc 0.0024 1.266 0.452 0.422 0.9614 -0.1554 -0.2272

Baa -0.0039 -2.098 -0.748 -0.700 0.8216 0.4368 0.3663

17 H(1) Bbb -0.0023 -1.244 -0.444 -0.415 -0.1578 0.7917 -0.5901
Bcc 0.0063 3.342 1.192 1.115 -0.5478 0.4271 0.7194

Baa -0.0059 -3.121 -1.114 -1.041 -0.2003 -0.1474 0.9686

18 H(1) Bbb -0.0056 -2.971 -1.060 -0.991 0.4396 0.8700 0.2233
Bcc 0.0114 6.093 2.174 2.032 0.8756 -0.4705 0.1095

Baa -0.0056 -2.964 -1.058 -0.989 -0.5916 0.7868 0.1761

19 H(1) Bbb -0.0043 -2.320 -0.828 -0.774 0.0755 -0.1634 0.9837
Bcc 0.0099 5.284 1.886 1.763 0.8027 0.5953 0.0373

cation Vibration calc.

Symbolic Z-matrix:
Charge = 1 Multiplicity = 2

40
 O 2.24818 -1.63437 0.36373
O -3.75559 0.53915 0.15966
O 3.46866 0.10219 -0.36735
O -2.70864 -1.36582 -0.40179
N 1.36074 1.83057 -0.24977
C -0.12073 -0.15358 -0.21644
C 1.17341 0.49821 0.31581
C -1.38709 0.56169 0.25225
C 2.42029 -0.33173 0.04554
C -2.64587 -0.21412 -0.04271
H -0.14089 -1.18859 0.13872
H -0.08606 -0.19811 -1.30847
H 1.09465 0.50817 1.4169
H -1.34539 0.72146 1.33685
H -1.48918 1.55567 -0.1976
H 2.34583 2.07699 -0.2658
H 0.8579 2.52864 0.28653
H 3.09619 -2.07898 0.20429
H -4.51923 -0.03123 -0.02361

Condensed to atoms (all electrons):

1 2 3 4 5 6
1 O 8.464071 -0.000011 -0.122336 -0.000561 0.009871 0.022192
2 O -0.000011 8.415478 -0.000005 -0.094155 0.000082 0.054024
3 O -0.122336 -0.000005 8.160819 -0.000004 -0.020569 -0.026549
4 O -0.000561 -0.094155 -0.000004 8.080277 -0.000283 0.038094
5 N 0.009871 0.000082 -0.020569 -0.000283 7.040817 -0.073991
6 C 0.022192 0.054024 -0.026549 0.038094 -0.073991 7.489118
7 C -0.139638 0.004593 -0.078732 0.020182 -0.100896 -1.252895
8 C -0.024103 0.010455 -0.003736 -0.090317 0.056886 -0.759334
9 C 0.193205 - 0.000096 0.449408 -0.002715 0.113221 0.170044
10 C 0.001693 0.004288 0.000813 0.348276 0.000586 0.001597
11 H 0.004089 0.000508 0.000481 0.004313 0.007277 0.349664
12 H -0.001054 -0.000166 -0.000040 0.000878 0.001035 0.390905
13 H -0.001496 -0.000020 -0.001398 0.000119 -0.040170 -0.056166
14 H -0.000052 0.001353 -0.000026 0.000828 -0.003054 -0.052094
15 H -0.000003 0.002358 0.000039 0.003067 0.009487 -0.086295
16 H 0.002058 0.000002 0.024015 0.000006 0.274483 0.051820
17 H -0.000364 -0.000049 0.000151 -0.000010 0.264700 -0.061858
18 H 0.159874 0.000000 0.008515 0.000004 -0.001275 -0.004578
19 H 0.000001 0.155334 0.000000 0.007110 0.000004 -0.001986

41
1 O -0.139638 -0.024103 0.193205 0.001693 0.004089 -0.001054
2O 0.004593 0.010455 -0.000096 0.004288 0.000508 -0.000166
3 O -0.078732 -0.003736 0.449408 0.000813 0.000481 -0.000040
4O 0.020182 -0.090317 -0.002715 0.348276 0.004313 0.000878
5 N -0.100896 0.056886 0.113221 0.000586 0.007277 0.001035
6 C -1.252895 -0.759334 0.170044 0.001597 0.349664 0.390905
7C 8.350046 0.344847 -1.033940 -0.107245 -0.021610 -0.056271
8 C 0.344847 7.227041 -0.163050 -0.511567 -0.016921 -0.060728
9 C -1.033940 -0.163050 5.852005 -0.086422 -0.020221 0.026436
10 C -0.107245 -0.511567 -0.086422 5.602758 0.000791 0.003339
11 H -0.021610 -0.016921 -0.020221 0.000791 0.426769 -0.021443
12 H -0.056271 -0.060728 0.026436 0.003339 -0.021443 0.446771
13 H 0.360734 -0.021931 -0.000096 0.006707 -0.001580 0.003510
14 H 0.003096 0.356001 0.005790 -0.012004 -0.002689 0.003423
15 H -0.012594 0.398619 -0.010191 0.006468 0.003307 -0.003438
16 H -0.067092 -0.002198 -0.018903 0.001155 -0.000102 -0.000216
17 H 0.042495 0.010592 0.008135 -0.000760 -0.000062 0.000051
18 H 0.065198 0.001944 -0.040616 -0.000002 0.000060 -0.000049
19 H 0.000593 0.030868 -0.000055 -0.008163 -0.000003 -0.000005
13 14 15 16 17 18
1O -0.001496 -0.000052 -0.000003 0.002058 -0.000364 0.159874
2O -0.000020 0.001353 0.002358 0.000002 -0.000049 0.000000
3O -0.001398 -0.000026 0.000039 0.024015 0.000151 0.008515
4O 0.000119 0.000828 0.003067 0.000006 -0.000010 0.000004
5N -0.040170 -0.003054 0.009487 0.274483 0.264700 -0.001275
6C -0.056166 -0.052094 -0.086295 0.051820 -0.061858 -0.004578
7C 0.360734 0.003096 -0.012594 -0.067092 0.042495 0.065198
8C -0.021931 0.356001 0.398619 -0.002198 0.010592 0.001944
9C -0.000096 0.005790 -0.010191 -0.018903 0.008135 -0.040616
10 C 0.006707 -0.012004 0.006468 0.001155 -0.000760 -0.000002
11 H -0.001580 -0.002689 0.003307 -0.000102 -0.000062 0.000060
12 H 0.003510 0.003423 -0.003438 -0.000216 0.000051 -0.000049
13 H 0.450052 0.004340 0.000231 0.001027 -0.003328 -0.000222
14 H 0.004340 0.457870 -0.026933 -0.000028 0.000080 -0.000001
15 H 0.000231 -0.026933 0.453760 0.000059 -0.000369 0.000000
16 H 0.001027 -0.000028 0.000059 0.284325 -0.021220 -0.000049
17 H -0.003328 0.000080 -0.000369 -0.021220 0.315225 0.000005
18 H -0.000222 -0.000001 0.000000 -0.000049 0.000005 0.276392
19 H 0.000000 -0.000249 -0.000113 0.000000 0.000000 0.000000

1 O 0.000001

42
 3O 0.000000
4O 0.007110
5N 0.000004
6C -0.001986
7C 0.000593
8C 0.030868
9C -0.000055
10 C -0.008163
11 H -0.000003
12 H -0.000005
13 H 0.000000
14 H -0.000249
15 H -0.000113
16 H 0.000000
17 H 0.000000
18 H 0.000000
19 H 0.294145

Mulliken atomic
charges: 1
1O -0.567436
2O -0.553973
3O -0.390845
4O -0.315109
5N -0.538210
6C -0.191712
7C -0.320869
8C -0.783370
9C 0.558061
10 C 0.747693
11 H 0.287371
12 H 0.267062
13 H 0.299686
14 H 0.264348
15 H 0.262540
16 H 0.470857
17 H 0.446586
18 H 0.534799
19 H 0.522520
Sum of Mulliken atomic charges = 1.00000

43
44
 Mulliken charges with hydrogens summed into heavy
atoms: 1
1O -0.032637
2O -0.031453
3O -0.390845
4O -0.315109
5N 0.379232
6C 0.362721
7C -0.021183
8C -0.256482
9C 0.558061
10 C 0.747693
Sum of Mulliken charges with hydrogens summed into heavy atoms = 1.00000

The diagram of the labeled molecule which was used as the reference label in bond length, bond angle and dihedral calculations.

45