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Surname, Initial(s). (2012) Title of the thesis or dissertation. PhD. (Chemistry)/ M.Sc. (Physics)/ M.A. (Philosophy)/M.Com. (Finance) etc. [Unpublished]: University of Johannesburg. Retrieved from: https://ujcontent.uj.ac.za/vital/access/manager/Index?site_name=Research%20Output (Accessed: Date).

FORMATION OF IN THE :

COMPUTATIONAL STUDIES ON VARIOUS POSSIBLE REACTION PATHS

by

ZANELE PRECIOUS NHLABATSI

Student Number: 200826464

Thesis

Submitted in fulfilment of the requirement for the degree

PHILOSOPHIAE DOCTOR

in

CHEMISTRY

in the

FACULTY OF SCIENCE

of the

UNIVERSITY OF JOHANNESBURG

Supervisor:

Dr. SANYASI SITHA

DECLARATION

I hereby declare that this thesis, which I herewith submit for the research qualification

DOCTORAL DEGREE IN CHEMISTRY to the University of Johannesburg, Department of Chemistry, is apart from the recognised assistance of my supervisors, my own work and has not previously been submitted by me to another institution to obtain a research diploma or degree.

______on this ____ day of ______

(Candidate)

______on this ____ day of ______

(Supervisor)

i

DEDICATION

I dedicate this work, firstly to GOD ALMIGHTY who made all this possible, my dad Samson

Masayidi Nhlabatsi, my mother Zodwa Norah Bhembe, my late sister, Winile Lungile

Nhlabatsi (rest in peace Mantini waLanga),and my loving fiancé, and soon to be Husband,

Derrick Themba Khumalo. I truly thank you all for your love and support. Last but not least, to the Holy Spirit, who is my counselor, helper and my comforter.

Ephesians 3:20

………………….Now to Him Who is able to do immeasurably more than ALL we ask or imagine, according to His POWER that is at work in us.

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ACKNOWLEDGMENTS

Special thanks to God Almighty for HIS loving support and guidance.

I wish to greatly acknowledge the following people for their contributions towards the success of this project:

 Dr. Sanyasi Sitha for his great supervision, advice and mentorship and guidance

throughout this work.

 Prof. I. D. Isabirye (North-West Universty). Prof. R. W. M. Krause (Rhodes

University) and Prof. L. M. Cele (Tshwana University of Technology).

 Apostle Bheki and Pastor Zandile Thwala for their vital spiritual guidance together

with Pastor Andrew Mwaikambo and Pastor Themba Manana (LGTG).

 Computational Chemistry Group Priya Bhasi and Vijay Miriyala for their assistance

in many ways.

 Mr Ali Ilunga Kabeya. Thanks for your all your assistance.

 Mr Martin Magu and Ephraim Marondedze for your assistance.

 Everyone who is part of the Department of Chemistry.

 My siblings, both brothers and sisters, Mduduzi and Thuli Dlamini, and all my family

members.

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 My dad, Nhlanhla Nhlabatsi and all the Nhlabatsi members, my friends, Refiloe Mota,

Noluthando Dlamini, Samkelisiwe Motsa, Dumsile Nyembe, and Xolile Mkoko (for being good friends).

 National Research Foundation (NRF) for financial support, and the University of

Johannesburg for support.

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The work presented in this thesis has been published in peer reviewed journals and presented in national and international conferences for poster presentations.

1. PUBLICATIONS

1. Zanele P. Nhlabatsi, Priya Bhasi and Sanyasi Sitha, “Possible interstellar

formation of glycine from the reaction of CH2=NH, CO and H2O: catalysis by extra

through the relay transport” Physical Chemistry Chemical

Physics 18 (2016) 375-381.

2. Zanele P. Nhlabatsi, Priya Bhasi and Sanyasi Sitha, “Possible interstellar

formation of glycine through a concerted mechanism: a computational study on the

reaction of CH2=NH, CO2 and H2” Physical Chemistry Chemical Physics, 18 (2016)

20109-20117.

2. OTHER PUBLICATIONS

1. Lungile P. Lukhele, Rui W.M. Krause, Zanele P. Nhlabatsi, Bhekie

B. Mamba, Z Maggy NB Momba “Copper and Silver Impregnated

Nanotubes incorporated into Cyclodextrin Polyurethanes for the Removal of

Bacterial and Organic Pollutants in Water” Desalination and Water

Treatment27 (2011) 299-307.

2. Sanyasi Sitha, Linda L. Jewell, Priya Bhasi, Zanele P. Nhlabatsi,

Vijay M. Miriyala “Potential surface of the cation-neutral

hydroamination reaction: a computational study on the role of an -

complex in the reaction pathway” Tetrahedron70 (2014) 7906-7911.

3. Priya Bhasi, Zanele P. Nhlabatsi, Sanyasi Sitha, “Reaction between

HN and SN: a possible channel for the interstellar formation of N2 and SH in

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the cold interstellar clouds”Physical Chemistry Chemical Physics17 (2015)

32455-32463.

4. Priya Bhasi, Zanele P. Nhlabatsi and Sanyasi Sitha, Possible

interstellar formation of phosphorus analogue of hydrazoic acid: A

computational study on the reaction between HN and PN” Computational and

Theoretical Chemistry1078 (2016) 129–137.

5. Priya Bhasi, Zanele P. Nhlabatsi and Sanyasi Sitha, “ Expanding the

applicability of electrostatic potentials to the realm of transition states”

Physical Chemistry Chemical Physics, 18 (2016) 13002-13009.

3. CONFERENCES

1. Z. P. Nhlabatsi, P. Bhasi, S. Sitha, Pontential energy surface of OH + NO2

HOONO reaction: A computational study, 41st National Convention of the South

African Chemical Institute, Poster Presentation, 1-6 December 2013, WSU (Water

Sisulu University), South Africa.

2. Z. P. Nhlabatsi, P. Bhasi, S. Sitha, A Computational study on dipole moment

and hyperpolarizability of pyridine-borobenzine adduct, 10th Theoretical Chemistry

Conference in Africa, Poster Presentation, 6–11 April 2014, University of Venda,

Thohoyandou, South Africa.

3. Z. P. Nhlabatsi, P. Bhasi, S. Sitha, Computational study on the Formation of

Glycine in the Interstellar Medium (ISM), 10TH Congress of the World Association of

Theoretical and Computational Chemists WATOC 2014, Poster Presentation, 5-10

October 2014, Santiago,Chile.

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4. Z. P. Nhlabatsi, P. Bhasi, S. Sitha, Computational study on the Formation of

Glycine, CHPC (Centre for High Performance Computing) National Meeting 2015,

30TH November – 4TH December 2015, Poster Presentation, CSIR (Council of Scientific

and Industrial Research) International Convention Centre, South Africa.

4. WORKSHOPS ATTENDED

1. Workshop hosted by Centre for High Performance Computing (CHPC) and

Nelson Mandela Metropolitan University (NMMU), 26TH June – 2ND July 2016.Course

covered the concepts and theory of parallel computers, and programming for parallel

systems with MPI and OpenMP, and possibly CUDA or other co-processors, using the

C, Fortran or python programming languages.

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ABSTRACT

“How the most essential elements, i.e., amino-acids, were formed in the interstellar medium (ISM)?” and “What are their roles in the evolution of life in our ?” are the two most intriguing questions, which are not yet answered exclusively as indicated in the works of many researchers. Among all the natural amino-acids, glycine (H2N-CH2-COOH) is not only an important biologically active molecule but also is the simplest as well as smallest amino-acid that can be found in all the biological entities found in the . The era of the astronomical search for glycine began as soon as the laboratory spectra for it were made available in 1978. Since then astrophysicists have been searching for this glycine in the ISM and many decades have been passed but still without any success. This is in spite of the fact that many amino-acid including the glycine have been found on , and moreover the distinct isotopic signature of those amino-acids are indicative of their extraterrestrial origin.However, detection of glycine in the interstellar medium is still ambiguous and the major problem arising in the analysis of a large cluster of weak lines collected through various high resolution telescopes. In this present work, using computational calculations many possible as well as favourable reaction paths, which can lead to the formation of

Glycine in the interstellar conditions, have been investigated. Detailed mechanisms of those possible reaction paths have been investigated and also aptness of their feasibilities in the

ISM has been discussed in the light of the prevailing interstellar conditions.

From the mechanistic analysis of these possible reaction paths, it was observed that two of them show concerted type of mechanism, whereas others proceed through multi-stepped paths. One such concerted reaction discussed in this thesis encompasses the reaction of

CH2=NH, CO and H2O leading to the formation of glycine. It was observed that this reaction

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proceeds through a large barrier and thus indicating it’s feasible only in the hot-cores of interstellar medium. When the same reaction was investigated in the excess of water molecules where discrete water molecules were treated explicitly as part of reactants, it was surprising to find that with the presence of three or more water molecules, the barrier height reduced so drastically that the reaction behaves like a barrierless type of reaction.

Mechanistic study indicates that the extra water molecules exhibit catalytic role through the hydrogen transport relay effect. As barrierless types of reactions are most suitable reactions for the cold-cores or cold interstellar clouds, the feasibility of this reaction can be predicted at the cold water- surfaces.

Another concerted reaction path studied in this thesis is the reaction between CH2=NH, CO2 and H2 leading to the formation of glycine. Detailed mechanism of the reaction as well as feasibility of such a reaction in drastic interstellar temperature conditions has also been discussed. On one hand the large barrier height for this reaction predicts its feasibility only in the high temperature conditions of the hot-cores of ISM. On the other hand analysis of the of transition state indicates the presence of prominent hydrogen , i.e., a prominent tunnelling effect, and thus advocating the cold-core possibility of this reaction. In other words intrinsic phenomenon of tunnelling observed in the transition state, supported by a tunnelling ready like state as a low lying van der Waals’ complex will propel this reaction to happen in the cold interstellar clouds.

The multi-stepped paths discussed in this study includes the reaction of either CO + H2O or

CO2 + H2 that proceed via a dihydroxycarbene intermediate resulting to highly endothermic reactions with large barrier heights, whereas the subsequent step of interaction of this carbene with CH2=NH to give glycine is exothermic as well as barrierless. On the basis of this observation it was proposed that the formation of glycine via the carbene route as a least favourable or even unfavourable for its thermochemical feasibility in the ISM as the large

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barrier height can act as a bottleneck to this reaction. Additional multi-step paths involves two reaction paths, H2C=O + NH3 and H2C=NH + H2O reaction paths passing through a hemiaminal intermediate (α-hydroxy amine) and a subsequent step interaction with CO respectively to form glycine. Even though our calculations reveal that both paths are thermodynamically favourable in the ISM, further analysis indicate that these two paths are feasible only in hot-cores, but not in the cold interstellar clouds in the interstellar conditions.

Reaction path H2C=O + NH3 that pass through a hemiaminal intermediate (α-hydroxy amine) and following interaction with CO was further suggested to be carried out as one-pot synthesis for the laboratory synthesis of glycine subjected under the condition that the reaction is performed at a controlled temperature. This research study can further be extended to the preparation of other α-amino-acids with the suitable choice of aldehyde and even based on the mechanism it can be expected to possibly give an enantiomeric excess. We therefore trust that this study will not only be able to enrich our future understanding about glycine (or

α-amino-acids) formation in interstellar medium, but also suggests other paths for laboratory synthesis of the glycine (or α-amino-acids) using the ingredients of either Strecker’s synthesis or Miller’s experiment.

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TABLE OF CONTENTS

DECLARATION ...... i

DEDICATION ...... ii

ACKNOWLEDGMENTS ...... iii

ABSTRACT ...... viii

CHAPTER 1 INTRODCUTION ...... 1

1.1 Problem statement ...... 1 1.2 Justification ...... 4 1.2.1. Plausible Formation Processes of Glycine in the ISM ...... 7 1.3 Objectives of study ...... 8 1.4 Thesis outline ...... 9 1.5 References ...... 12

CHAPTER 2 LITERATURE REVIEW ...... 19

2.1 Introduction ...... 19 2.2 Life on Earth...... 19 2.2.1 Origin of life on Earth ...... 20 2.2.1.1 ...... 21 2.3 Interstellar Medium (ISM) ...... 23 2.3.1 Interstellar clouds ...... 25 2.3.1.1. Diffuse interstellar clouds ...... 26

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2.3.1.2 Dense molecular clouds ...... 27 2.3.1.2.1 Dense cores ...... 29 2.4 Interstellar Chemistry ...... 33 2.4.1 -Phase Chemistry ...... 34 2.4.1.1 Gas-Phase Chemical Reactions in the Diffuse Clouds ..... 35 2.4.1.2 Gas-Phase Chemical Reactions in Cold Dense Molecular Clouds 42 2.4.2 Grain-Surface Processes ...... 46 2.5 Formation of amino-acids in the ISM ...... 51 2.5.1 Formation of amino-acids through solid-phase reactions in the ISM...... 51 2.5.2 Formation of amino-acids through gas-phase reactions in the ISM ...... 54 2.5.3 The origin of in amino-acids and its role in the evolution of life 58

2.5.4 General description of Glycine (NH2CH2COOH) ...... 61 2.5.4.1 Conformers of Glycine ...... 61

2.5.4.1.1 The most stable conformers of Glycine (NH2CH2COOH) ...... 63

2.5.4.2 Plausible formation Processes of Glycine (NH2CH2COOH) in the ISM ...... 65

2.5.4.3 Detectability of Glycine (NH2CH2COOH) in the ISM ...... 67 2.6 References ...... 70

CHAPTER 3 THEORETICAL METHODOLOGY ...... 110

3.1 Basic principles of theory used ...... 110 3.1.1 The Born-Oppenheimer approximation ...... 110 3.1.1.1 Independent approximation ...... 111 3.1.2 The Slater determinants ...... 111 3.1.3 Variational principle ...... 112 3.2 Hartree-Fock Theory ...... 112 3.2.1 Self-Consistent Field (SCF) ...... 113 3.3 Post-Hartree-Fock (Correlation) Methods ...... 114 3.3.1 Moller-Plesset (MPn) Perturbation Theory (MPPT) ...... 115 3.3.2 Coupled Cluster (CC) method ...... 116 3.3.3 Composite Quantum Chemistry Methods ...... 117 3.4 Functional Theory (DFT) ...... 118 xii

3.4.1 Description of Equations of Elements of Theory used in this thesis ...... 119 3.4.1.1 Schrodinger Equation and Born-Oppenheimer approximation ...... 119 3.4.1.2 The Hartree-Fock Approximation ...... 120 3.4.1.3 Density Functional Theory ...... 124 3.4.1.5 Generalized Gradient Approximation and Hybrids ...... 127 3.5 Gaussian Functions ...... 128 3.5.1 Gaussian Functions as Basis Sets ...... 129 3.5.1.1 Minimal Basis Set ...... 130 3.5.1.2 Split Valence Basis Set ...... 131 3.5.1.3 Polarization Functions ...... 131 3.5.1.4 Diffuse Functions ...... 132 3.5.1.5 Effective Core Potential Basis Sets ...... 132 3.5.1.6 Correlation-Consistent Basis Sets ...... 133 3.6 Software ...... 134 3.7 References ...... 134

CHAPTER 4 POSSIBLE INTERSTELLAR FORMATION OF GLYCINE FROM

THE REACTION OF CH2=NH, CO AND H2O: CATALYSIS BY EXTRA WATER

MOLECULES THROUGH THE HYDROGEN RELAY TRANSPORT ...... 143

4.1 Introduction ...... 144 4.2 Computational Methods ...... 145 4.3 Results and discussions ...... 146

4.3.1 PES for CH2=NH + CO + H2O → Glycine reaction ...... 146 4.3.2 Reactant Complex ...... 147 4.3.3 Transition state ...... 149 4.3.4 Catalysis by an extra water molecule ...... 150 4.3.5 Effect of excess water molecules ...... 153 4.3.6 Possible Interstellar Applications: ...... 155 4.4 Conclusions ...... 157 4.5 References ...... 159

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CHAPTER 5 POSSIBLE INTERSTELLAR FORMATION OF GLYCINE

THROUGH A CONCERTED MECHANISM: A COMPUTATIONAL STUDY ON

THE REACTION OF CH2=NH, CO2 AND H2 ...... 164

5.1 Introduction ...... 165

5.2 Computational Methods ...... 168

5.3 Results and Discussions ...... 169 5.3.1 Formation of Glycine via the carbene route ...... 169 5.3.2 Formation of Glycine via concerted mechanism ...... 172

5.3.2.1 PES of the reaction, CH2=NH +H2 + CO2 → Glycine ...... 172 5.3.2.2 Structure and nature of interactions in the TS for reaction 4 174 5.3.2.3 Effects of temperature of the transition state ...... 176 5.3.2.4 Effects of various methods on the PES of the reaction 4 178 5.3.3 Interstellar possibility of the glycine formation ...... 179 5.3.3.1 Interstellar feasibility of glycine formation via the carbene route 180 5.3.3.2 Interstellar feasibility of formation of glycine via the concerted route ...... 182 5.4 Conclusions ...... 186 5.5 References ...... 188

CHAPTER 6 AN ALTERNATE AND SHORTEST ROUTE FOR THE FORMATION

OF GLYCINE USING EITHER STRECKER’S OR MILLER’S INGREDIENTS: A

COMPUTATIONAL STUDY ON THE HEMIAMINAL INTERMEDIATE ROUTE

...... 196

6.1 Introduction ...... 197

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6.2 Computational Methods ...... 199 6.3 Results and discussions ...... 201

6.3.1 PES of the Reaction 1 (H2C=O + NH3 → H2N-CH2-OH) ...... 201

6.3.2 PES of the Reaction 2 (H2N-CH2-OH + CO → H2N-CH2-COOH) ...... 205

6.3.3 PES of the Reaction 3 (H2C=NH + H2O → H2N-CH2-OH) ...... 208 6.3.4 Possible applications in the laboratory synthesis of Glycine ...... 211 6.3.5 Possible application in the Interstellar Formation of Glycine ...... 214 6.3.5.1 Availabilities of the ingredients in the ISM ...... 214 6.3.5.2 Extreme Temperature conditions of ISM ...... 215 6.3.5.3 Possibility of Glycine formation in the ISM ...... 216 6.4 Conclusions ...... 218 6.5 References ...... 222

CHAPTER 7 CONCLUSIONS AND RECOMMENDATIONS ...... 229

7. 1 Conclusions ...... 229 7.2 Recommendations and future work ...... 231

APPENDIX A Supporting Information (Chapter 4) ...... 233

APPENDIX B Supporting Information (Chapter 5) ...... 250

APPENDIX C Supporting Information (Chapter 6) ...... 266

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LIST OF FIGURES

CHAPTER 2:

Figure 2. 1: Experimental set-up of the Urey-Miller experiment.[16, 18]...... 22

Figure 2. 2: The formation of H2 on the surface of dust grains in molecular clouds described by Langumuir-Hinshelwood and Eley-Rideal mechanisms [Credit: Kaiser (2002)] [245]...... 48

Figure 2. 3: Most stable conformers structures of glycine optimized by MP2/6-311++G**

level of theory. Torsional angles Φ = (Φ1,Φ2,Φ3) indicate coordinates of twisting

motion about the C-C bond (Φ1), C-O single bond (Φ2), and C-N bond (Φ3). (a) conformers reported to have been observed experimentally. [Credit : Csaszar (1992) and Miller et al. (2004) [355] ]...... 64

CHAPTER 3:

Figure 3. 1: Schematic diagram that explains the Self-Consistent Field...... 114

CHAPTER 4:

Figure 4. 1: B3LYP/6-31++G(3df,2pd) optimized PES for the CH2=NH + CO + H2O → Glycine, reaction. All the are in kcal/mol and the diagram is not to scale...... 146

Figure 4. 2: (a) B3LYP/6-31++G(3df,2pd) optimized structure of the reactant complex with

important interaction distances. (b) Computed ESP maps of CH2=NH, CO and

H2O (oriented in the similar fashion like that of the reactant complex) calculated from the B3LYP/6-31++G (3df,2pd) method at 0.001 au electron density surfaces [ESP colour scheme: Red (negative) - Positive (blue)]...... 148

Figure 4. 3: B3LYP/6-31++G(3df,2pd) optimized structure of the reactant complex with important interaction distances...... 149

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Figure 4. 4: B3LYP/6-31++G(3df,2pd) optimized PES for the CH2=NH + CO + 2H2O → Glycine, reaction. All the energies are in kcal/mol and the diagram is not to scale...... 151

Figure 4. 5: B3LYP/6-31G optimized geometries of the transition states, (a) with three water molecules as reactants and (b) with four water molecules as reactants...... 154

CHAPTER 5:

Figure 5. 1: PES of the reactions, (a) CO + H2O → ꞉C(OH)2, (b) CO2 + H2 → ꞉C(OH)2, and

(c) ꞉C(OH)2 + CH2=NH → Glycine, calculated using B3LYP/6-31++G(d,p) method. All the energies reported here are ZPVE corrected and are in the units of kcal/mol. Diagram is not to scale...... 170

Figure 5. 2: PES for the reaction, CH2=NH + CO2 + H2 → Glycine, calculated using B3LYP/6-31++G(3df,3pd) method. All the energies reported here are ZPVE corrected and are in the units of kcal/mol. Diagram is not to scale...... 173

Figure 5. 3: Computed ESP maps of CH2=NH, CO2 and H2calculated from the B3LYP/6- 31++G (3df,3pd) method at 0.001 au electron density surfaces. Quantitative values of electrostatic potentials are also in au...... 175

CHAPTER 6:

Figure 6. 1: B3LYP/6-31++G(3df,2pd) optimized PES for the H2C=O + NH3 → H2N-CH2- OH (α-hydroxy amine), reaction. All the energies are ZPVE corrected and are in kcal/mol. The diagram is not to scale...... 202

Figure 6. 2: Computed ESP maps of H2C=O and NH3 calculated using B3LYP/6-31++G(d,p) method at 0.02 au electron density surfaces. Quantitative values of electrostatic potentials are also in au...... 203

Figure 6. 3: B3LYP/6-31++G(3df,2pd) optimized PES for the H2N-CH2-OH + CO → H2N-

CH2-COOH (glycine), reaction. All the energies are ZPVE corrected and are in kcal/mol. The diagram is not to scale...... 205

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Figure 6. 4: Computed ESP maps of H2N-CH2-OH and CO calculated using B3LYP/6- 31++G(d,p) method at 0.02 au electron density surfaces. Quantitative values of electrostatic potentials are also in au...... 206

Figure 6. 5: B3LYP/6-31++G(3df,2pd) optimized PES for the H2C=NH + H2O → H2N-CH2- OH (α-hydroxy amine), reaction. All the energies are ZPVE corrected and are in kcal/mol. The diagram is not to scale...... 208

Figure 6. 6: Computed ESP maps of H2C=NH and H2O calculated using B3LYP/6- 31++G(d,p) method at 0.02 au electron density surfaces. Quantitative values of electrostatic potentials are also in au...... 209

Supporting Information (CHAPTER 4)

Figure S4. 1: Schematic diagram of energy differences for H2O + CO +

CH2NH→NH2CH2COOH reaction, with optimized structures of reactants, complex, transition state and product for the termolecular reactions leading to the formation of glycine performed at MP2/6-31++G(3df,2pd)...... 233

Figure S4. 2: Schematic diagram of energy differences for H2O + H2O + CO +

CH2NH→NH2CH2COOH reaction, with optimized structures of reactants, complex, transition state and product for the quaterrmolecular reactions leading to the formation of glycine performed at MP2/6-31++G(3df,2pd). .. 234

Figure S4. 3: Schematic diagram of energy differences for H2O-H2O complex + CO +

CH2NH→NH2CH2COOH reaction, with optimized structures of reactants, complex, transition state and product for the quatermolecular reactions leading to the formation of glycine performed at B3LYP/6-31++G(3df,2pd)...... 234

Figure S4. 4: Schematic diagram of energy differences for H2O-H2O complex + CO +

CH2NH→NH2CH2COOH reaction, with optimized structures of reactants, complex, transition state and product for the quatermolecular reactions leading to the formation of glycine performed at MP2/6-31++G(3df,2pd)...... 235

Figure S4. 5: Mechanism for H2O + CO + CH2NH→NH2CH2COOH reaction, optimized geometries of the complex, transition state and product involved in the termolecular reactions for the formation of glycine at B3LYP/6- 31++G(3df,2pd)...... 235

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Figure S4. 6: Mechanism for H2O + CO + CH2NH→NH2CH2COOH reaction, optimized geometries of the complex, transition state and product involved in the termolecular reactions for the formation of glycine at MP2/6-31++G(3df,2pd)...... 236

Figure S4. 7: Mechanism for H2O + H2O + CO + CH2NH→NH2CH2COOH reaction, optimized geometries of the complex, transition state and product involved in the quatermolecular reactions for the formation of glycine at B3LYP/6- 31++G(3df,2pd)...... 236

Figure S4. 8: Mechanism for H2O + H2O + CO + CH2NH→NH2CH2COOH reaction, optimized geometries of the complex, transition state and product involved in the quatermolecular reactions for the formation of glycine at MP2/6- 31++G(3df,2pd)...... 237

Supporting Information (CHAPTER 5)

Figure S5. 1: B3LYP/6-31G(3df,2pd) optimized geometries of the reactants, transition state and product...... 250

Figure S5. 2: MP2/6-31G(3df,2pd) optimized geometries of the reactants, transition state and product...... 250

Figure S5. 3: MP2/6-31G(3df,2pd) PES for the CH2=NH + CO2 + H2 → Glycine, reaction. All the energies are in kcal/mol and the diagram is not to scale.(Colour Code: Pink=Hydrogen, Grey=Carbon, Blue=, Red=)...... 251

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LIST OF TABLES

CHAPTER 2:

Table 2. 1: Summary of physical factors found in the interstellar medium (ISM)...... 32

Table 2. 2: Important Gas-Phase reactions occurring in the interstellar medium (credit to Carbo et al. (1985)...... 35

Table 2. 3: Gas-phase chemistry proposed mechanisms for the formation of some certain species in diffuse clouds...... 38

CHAPTER 5:

Table 5. 1: Results of effect of temperature (in ) on activation energy of the CH2=NH

+ CO2 + H2 → Glycine reaction. Thermal energy corrected total energies (ET = Sum of the electronic and thermal energies) are in Hartrees and relative energies are in kcal/mol calculated using the B3LYP/6-31++G(d,p) method...... 177

Table 5. 2: Results of effect of various methods on the potential energy surface of the

CH2=NH + CO2 + H2 → Glycine reaction. Where ΔE1 = ETS – EREACTANTS, ΔE2 =

ETS – EPRODUCT and ΔE3 = EREACTANTS – EPRODUCT.All the energies reported here are ZPVE corrected and are in the units of kcal/mol...... 178

Supporting Information (CHAPTER 4)

Table S4. 1: Optimized transition state structure for the bond lengths in angstroms and bond angles in degrees for different methods using 6-31++G(3df,2pd) basis set...... 237

Table S4. 2: Optimized transition state structure for the bond lengths in angstroms and bond angles in degrees for different methods using 6-31G++(3df,2pd) basis set...... 239

Table S4. 3: Results of effect of various basis sets (for B3LYP Method) on the potential

energy surface of the CH2=NH + CO + H2O → Glycine reaction. Where ΔE1 =

EReactant – EReactant Complex , ΔE2 = ETS – EReactant Complex, ΔE3 = ETS – EProduct and ∆E4

= EReactant Complex – EProduct.All the energies are ZPE corrected and are in kcal/mol...... 241

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Table S4. 4: Results of effect of various methods on the potential energy surface of the

CH2=NH + CO + H2O → Glycine reaction. Where ΔE1 = EReactant – EReactant Complex

, ΔE2 = ETS – EReactant Complex, ΔE3 = ETS – EProduct and ∆E4 = EReactant Complex –

EProduct.All the energies are ZPE corrected and are in kcal/mol...... 243

Table S4. 5: Results of effect of various basissets (for B3LYP Method) on the potential

energy surface of the CH2=NH + CO + 2H2O → Glycine reaction. Where ΔE1 =

EReactant – EReactant Complex , ΔE2 = ETS – EReactant Complex, ΔE3 = ETS – EProduct Complex,

∆E4 = EReactant Complex – EProduct Complex and ∆E5 = EProduct – EProduct Complex.All the energies are ZPE corrected and are in kcal/mol...... 244

Table S4. 6: Results of effect of various methods on the potential energy surface of the

CH2=NH + CO + 2H2O → Glycine reaction. Where ΔE1 = EReactant – EReactant

Complex , ΔE2 = ETS – EReactant Complex, ΔE3 = ETS – EProduct Complex, ∆E4 = EReactant

Complex – EProduct Complex and ∆E5 = EProduct – EProduct Complex.All the energies are ZPE corrected and are in kcal/mol...... 246

Supporting Information (CHAPTER 5)

Table S5. 1: Results of effect of various basissets (with B3LYP method) on the potential

energy surface of the CH2=NH + CO2 + H2 → Glycine reaction. Where ΔE1 =

ETS – EREACTANTS, ΔE2 = ETS – EPRODUCT and ΔE3 = EREACTANTS – EPRODUCT.All the energies are ZPE corrected and are in kcal/mol...... 251

Table S5. 2: Effect of various methods on the geometry of the transition state for the reaction,

CH2=NH + CO2 + H2 → Glycine. Some important geometric data are shown [Basisset used is 6-31++G(3df,2pd)]...... 252

Table S5. 3: Effect of various Basissets on the geometry of the transition state. Some important geometric data are shown (Method used is B3LYP)...... 253

Supporting Information (CHAPTER 6)

Table S6. 1: Results of effect of various methods on the potential energy surface of the NH3 +

H2CO → H2N-CH2-OH (Reaction 1). Where ΔE1 = EREACTANTS – ECOMPLEX, ΔE2

= ETS – ECOMPLEX and ΔE3 = ECOMPLEX – EPRODUCT.All the energies are ZPE corrected and are in kcal/mol...... 266

xxi

Table S6. 2: Results of effect of various methods on the potential energy surface of the H2N-

CH2-OH + CO → NH2CH2COOH (Reaction 2). Where ΔE1 = EREACTANTS –

ECOMPLEX, ΔE2 = ETS – ECOMPLEX and ΔE3 = ECOMPLEX – EPRODUCT.All the energies are ZPE corrected and are in kcal/mol...... 267

Table S6. 3: Results of effect of various methods on the potential energy surface of the

NH=CH2 + H2O → H2N-CH2-OH (Reaction 3). Where ΔE1 = EREACTANTS –

ECOMPLEX, ΔE2 = ETS – ECOMPLEX and ΔE3 = ECOMPLEX – EPRODUCT.All the energies are ZPE corrected and are in kcal/mol...... 267

Table S6. 4: Results of effect of various basis sets (with B3LYP method) on the potential

energy surface of the NH3 + H2CO → H2N-CH2-OH (Reaction 1). Where ΔE1 =

EREACTANTS – ECOMPLEX, ΔE2 = ETS – ECOMPLEX and ΔE3 = ECOMPLEX –

EPRODUCT.All the energies are ZPE corrected and are in kcal/mol...... 268

Table S6. 5: Results of effect of various basis sets (with B3LYP method) on the potential

energy surface of the H2N-CH2-OH + CO → NH2CH2COOH (Reaction 2).

Where ΔE1 = EREACTANTS – ECOMPLEX, ΔE2 = ETS – ECOMPLEX and ΔE3 = ECOMPLEX

– EPRODUCT.All the energies are ZPE corrected and are in kcal/mol...... 268

Table S6. 6: Results of effect of various basis sets (with B3LYP method) on the potential

energy surface of the NH=CH2 + H2O → H2N-CH2-OH (Reaction 3). Where ΔE1

= EREACTANTS – ECOMPLEX, ΔE2 = ETS – ECOMPLEX and ΔE3 = ECOMPLEX –

EPRODUCT.All the energies are ZPE corrected and are in kcal/mol...... 269

Table S6. 7: Results of effect of various methods for all molecules on the potential energy

surface of i) H2CO → HCHO--NH3 (complex) → H2NCH2OH + CO →

H2NCH2OH—CO (complex) → NH2CH2COOH, and ii) NH=CH2 + H2O →

NHCH2-H2O (complex) → H2NCH2OH + CO → H2NCH2OH—CO (complex)

→ NH2CH2COOH. All the energies are ZPE corrected and these total energies are in Hartrees...... 269

Table S6. 8: Results of effect of various basis sets (with B3LYP method) for all molecules on

the potential energy surface of i) H2CO → HCHO--NH3 (complex) →

H2NCH2OH + CO → H2NCH2OH—CO (complex) → NH2CH2COOH, and ii)

NH=CH2 + H2O → NHCH2-H2O (complex) → H2NCH2OH + CO →

H2NCH2OH—CO (complex) → NH2CH2COOH. All the energies are ZPE corrected and these total energies are in Hartrees...... 271

xxii

LIST OF ABBREVIATIONS

AGB AO ATOMIC ORBITALS aug-cc-pVXZ AUGUMENTED ORRELATED CONSISTED POLARIZED, WHERE

X=D, T, Q, 5…., ZETA

B- HYDROGEN-BURNING STAR OF SPECTRAL TYPE B B3LYP BECKE 3 TERM WITH LEE, YANG, PARR EXCHANGE B3PW91 BECKE EXCHANGE, PERDEW AND WANG CORRELATION COMPLETE BASIS SETS METHODS WHERE THE BASIS CBS-QB3 FUNCTION EXTRAPOLATED TO INFINITY CASSCF COMPLETE SPACE SELF CONSISTENCE CC COUPLED CLUSTER CCD COUPLED CLUSTER DOUBLE CCSD COUPLED CLUSTER SINGLE DOUBLE CD CIRCULAR DICHROISM CGF CONTRACTED GAUSSIAN FUNCTIONS CI CONFIGURATION INTERACTION CPL CIRCULAR POLARIZED LIGHT 2D 2 DIMENTIONAL DAB DIAMOND ACIDS DIAMINOBUTYRIC DAP DIAMINOPROPIONIC DFT DENSITY FUNCTIONAL THEORY EACA ε-AMINO-n-CAPRIOC ACID ECP EFFECTIVE CORE POTENTIAL Ee ENANTIOMERIC EXCESS ESP ELECTROSTATIC POTENTIAL G2 GAUSSIAN 2 G3 GAUSSIAN 3 G4 GAUSSIAN 4 (GAUSSIAN THEORY) A METHOD FOR ETRAPOLATING FROM G3MP2B3 AB INITIO RESULTS TO AN ESTIMATION OF THE EXACT ENERGY

xxiii

(GAUSSIAN THEORY) A METHOD FOR EXTRAPOLATING G4MP2 FROM AB INITIO RESULTS TO AN ESTIMATION OF THE EXACT ENERGY GC-MS GAS CHROMATOGRAPHY- SPECTROMETRY GGA GENERALIZED GRADIENT APPROXIMATION GGC GUANOSINE GUANOSINE CYTIDINE GGG GUANOSINE GUANOSINEGUANOSINE GGU GUANOSINE GUANOSINE URIDINE GMC GIANT MOLECULAR CLOUDS GTO GAUSSIAN TYPE ORBITALS HF HATREE FOCK HPLC HIGH PERFORMANCE LIQUID CHROMATOGHY IRAS ASTRONOMICAL SATELLITE IRC INTRINSIC REACTION COORDINATES ISM INTERSTELLAR MEDIUM LDA LOCAL DENSITY APPROXIMATION M OF MASS (SOLAR MASS) MAG MAGNITUDE MCSCF MULTI CONFIGURATIONAL SELF CONSITENT FIELD Mh MILLIHATREE MO MOLECULAR ORBITALS MOLECULAR ORBITALS-LINEAR COMBIANTION OF ATOMIC MO-LCAO ORBITALS MPn MØLLER PLESSET MPPT MØLLER PLESSET PERTUBATION THEORY NASA NATIONAL AERONAUTICS AND SPACE ADMINISTRATION KL KLEINMANN-LOW O-STAR BLUE WHITE STAR OF SPECTRAL TYPE O P86 PERDEW 1986 PAHs POLYCYCLIC AROMATICS HYDROCARBONS Pc PES POTENTIAL ENERGY SURFACE PW91 PERDUE AND WANG 1991 pKa NEGATIVE LOGARITH OF THE IONIZATION CONSTANT (ka)

xxiv

R RIGHT HANDED MOLECULES RH ROOTHAAN HALL RHF RESTRICTED HARTREE FOCK RNA RIBONUCLEIC ACID SCF SELF CONSISTENT FIELD SEST SWEDISH-ESO SUBMILLIMETRE TELESCOPE Sgr-B2 SAGITARIUS B2 STO SLATER TYPE ORBITALS T TEMPERATURE THz TERAHERTZ TMC-1 DARK CLOUD IN TAURUS TOC TABLE OF CONTENTS TS TRANSITION STATE UHF UNRESTRICTED HATREE FOCK ULIRG ULTRALUMINOUS INFRARED UV ULTRA VIOLET vdw complex VAN DAN WAALS COMPLEX EXTENDED HYDRID FUNCTION COMBINED WITH LEE-YANG- X3LYP PARR CORRELATION FUNCTIONAL ZPE ZERO POINT ENERGY ZPVE ZERO POINT VIBRATIONAL ENERGY

xxv

Chapter 1

CHAPTER 1

INTRODCUTION

1.1 Problem statement

One of the most fundamental questions “How was life created?”, which directly relates to the origin of life in the earth, still remains an unanswered including to scientists of all fields [1,

2]. It is well-known that amino-acids are building blocks of all the biological systems. Not only the simplest and smallest, but also the most important among all the amino-acids, is glycine NH2CH2COOH, found in all the living entities on earth. Glycine belongs to a special class of amino-acids commonly known as α-amino-acids. Other higher homologous amino- acids of this class can be derived from glycine by replacing one of the hydrogen of the central unit(-CH2-) with suitable organic functional group modifications[3].

Glycine can exist either as a completely neutral molecule or as a zwitterionic form and it is well known that at ambient conditions there exists a dynamic equilibrium between the two

[4]. Coming back to the original question stated in the beginning of the problem statement, one technical question to be asked would be “How are these vital elements of life, i.e. the amino acids; with glycine, NH2CH2COOH, being the simplest of them all, formed?” [5, 6].

The era of the astronomical search for glycine began with the availability of the laboratory spectra for it [7] and from then on astronomers have tried to search the glycine for decades in interstellar space, but have not yet succeeded [6, 8-10]. Kuan et al. (2005) analysed 27 lines of glycine in 19 different spectral bands with column of about 1014 cm-1[8] and were able to put forward proof that the neutral form of glycine might exist in three hot molecular cores:Sgr B2 (N-LMH), Orion KL, and W51 el/e2 [11]. They also estimated the relative

1

Chapter 1 abundance of glycine to hydrogen to be around 2.1 x 10-1 for Sgr B2, 1.5 x 10-9 for Orion and

2.1 X 10-10 for W51 [5].Nonetheless, new laboratory measurements and analysis techniques were used by Snyder et al. (2005)[10] for a glycine rotor to identify glycine in the interstellar medium (ISM). In their study, they concluded that the necessary crucial lines to detect glycine in the ISM have not yet been found. This is because glycine occurs in a diversity of rotational conformations [12] which give rise to relatively weak lines which are hard to distinguish in dense, warm cores, even when using present day observational tools. The confusion is caused by the contamination of spectra by weak lines coming from a huge number of species available in the ISM that puts a question mark on the unambiguous detection of glycine [8].

This is besides the fact that several amino-acids including glycine have been found in meteorites and in . In the Murchison alone over 70 different amino-acids have been detected with varying structure and complexities[13-25].One crucial discovery is that of glycine in the pristine cometary samples returned by the NASA mission

[26], and furthermore the distinct isotopic signature of those amino-acids are suggestive of their extraterrestrial origin [6, 25]. This is because most of the amino-acids found in meteorites have a high (D) enrichment which is perhaps the most convincing molecular evidence that they once inhabited the ISM, as deuterium fractionation is high and efficient at low temperatures in dense molecular clouds grain mantles [27].Due to the lack of deuterium in meteorites, it has been theorized that the primitive essential material for pre- biotic chemistry of amino-acids may have originated in the ISM and then transported to meteorites [25]. These remarkable findings bring forward the most apparent question: “how are these complex molecules formed in galactic clouds like the interstellar medium?”[6]

2

Chapter 1

The question arises as a consequence of the fact that despite these exciting discoveries, our knowledge on the formation of glycine through various chemical pathways seems to be either incomplete or inconclusive [1, 9, 10]. There are well known reported bio-molecule precursors in the ISM that can form amino-acids like the simplest amino-acid, glycine. These include carbon and nitrogen based molecules, NH (imidyl radical), NH2 (amide) CH2 (methylene),

+ HCO (formal radical), CO (), HOCO (protonated CO2), CH3 (), CN (cyanide radical) together with other molecules like OH () and many more. Amino-acids such as glycine are the basic units for and they are therefore key elements of life [28]. Although the detection of glycine in the ISM has been in dispute, a suitable combination of the above precursors might be able to form the glycine in the ISM.

There have been a variety of potential mechanisms postulated for the formation of glycine in the ISM, which include the Strecker mechanism, radical-radical mechanism, and gas-phase formation of interstellar amino-acids through ion-molecule interaction schemes occurring in both gaseous phase and grains, with some of the studies done both theoretically as well as experimentally. There are two widely exploited approaches that can be found in the literature which discuss the formation of glycine in the laboratory. The first is Strecker’s synthesis [29,

30], where the synthesis of glycine is described as a multi-step process starting from (HCHO) as main reactant. The second is the Urey-Miller experiment, where the final few steps are the same as the Strecker’s synthesis [5, 31-33], but the starting reactants differ.

The problem associated with all these potential mechanisms is due to the inconsistencies between the projected products and the amino-acids detected in meteoritic compounds [30],

3

Chapter 1 i.e. all the laboratory synthetic methods result in a racemic mixture while meteoritic samples show L-enantiomeric excess [27]. Another challenge faced by most scientists is that replication of the ISM conditions in the laboratory for the formation and reactions of amino- acids and their precursors is a challenging task to accomplish [29, 30]. Therefore, it is essential to suggest reaction mechanisms that can take place at extremely low temperatures to overcome the thermodynamic challenges existing in the ISM. One of the most challenging issues is to find suitable chemical channels that are thermodynamically feasible and viable to account for the formation of glycine in the ISM. Computational Chemistry is however a good tool for studying very complex chemical reactions because intermediates and transition states that are difficult to detect and identify experimentally, can be calculated. Hence, employing computational chemistry as a tool may be useful to clarify how glycine is formed in the ISM.

In this study, we propose six new possible potential mechanisms for the formation of glycine

(CH2NH2COOH), the simplest amino-acid with specific simple precursor molecules that have been identified in the ISM. These new reaction mechanisms are aimed at predicting more thermodynamically feasible products that can verify the formation of glycine in the ISM.

High level quantum chemical calculations have been performed to trace reaction paths in the reaction potential energy surfaces. Various stationary points in the reaction paths including all possible transition states as well as intermediates were analysed in detail to account for a precise predictive view for the viability and formation of glycine in the ISM.

1.2 Justification

A great deal of attention has been focused by many researchers around the world to identify interstellar pre-biotic molecules that may provide crucial understanding of our solar system

4

Chapter 1 and even the evidence of the origin of life outside, i.e., the interstellar medium (ISM).This is mainly because the ISM is enriched with large varieties of molecules/fragments ranging from very simple to complex forms, with astrobiological importance, which might have undergone evolution and recycling continuously and repeatedly, and may be able to provide valuable insight to the origin of life [34, 35].

The interstellar medium (ISM) is the that exists in the space among the in a galaxy, which for us is the . The matter in ISM exists in gaseous form (ionic, molecular, atomic or form), as dusts or clouds and as high energy particles like cosmic rays. The ISM constitutes about 99.9% hydrogen (H2) and (He), with other elements making up the remaining 0.1%. Carbon, nitrogen and oxygen represent the majority of this remaining 0.1%, with heavier elements being even less abundant [36]. In the very early stage of the , interstellar reactions like nuclear fusion of H and He might have given rise to the evolution and formation of heavier elements like C, N, O, etc. We are now able to detect a large number of molecules in the ISM and circumstellar environments, which are capable of transforming themselves via a single or multiple pathways to breed many important organic molecules like amino-acids [2].

These simple chemical entities which can give rise to other complex chemical entities by the process of chemical transformations were initially thought to be impossible in the unfavourable ISM conditions [37, 38]. The first hindrance was thought to be the low temperatures of about 10 to 100K typical of interstellar dust grains, which rules out all endothermic reactions in addition to exothermic reactions which have any significant reaction barrier [39, 40]. The second problem was thought to be the low number densities in

5

Chapter 1 interstellar clouds which may lead to a very small collision frequency (estimated to be less than one collision every two weeks) [2, 41, 42].

Additionally, reactions which are both exothermic and barrier-less can only proceed very slowly leading to almost zero reaction rates [43, 44]. Nevertheless, there are some mitigating factors which must also be considered. For example, the lifetime of a typical is approximately 105–106 years [2, 45]. Hence, while the collisional rate is slow by terrestrial standards, it is still sufficiently fast on an astronomical timescale for reactions to occur efficiently. Additionally, many of the chemical species which exist within interstellar clouds are or radicals. Both radical-radical and ion-neutral reactions are often thought to proceed with almost no activation barriers [46-48]. Furthermore, the rate of collisions between ions and neutral species is typically a factor of 10–100 times larger than the corresponding rate for two neutral species [2, 49, 50]. This enhanced collisional rate for ions with neutral species is a consequence of the attractive ion-induced dipole interactions between the ion and neutral species [50]. In view of the above arguments, it is clear that gas phase reactions can, in some cases, proceed efficiently even under the conditions of the interstellar low densities.

Indeed, the abundances of many species observed in the interstellar medium are well explained by gas phase reaction networks [51, 52]. To date, over 200 molecules and ions have been detected in the interstellar medium, from simple diatomic to large organic molecules [36, 53]. Furthermore, the rate of detection of species in the interstellar medium has been consistent since 1970 [54]. With new and more sensitive telescopes being expected to come in future, it is very likely that many more ions and molecules will be detected. It is clear that with the given number and complexity of interstellar molecules/fragments detected

6

Chapter 1 so far, the interstellar medium can be said to be very rich in chemistry [2, 42, 55].

Understanding the formation mechanisms of interstellar species, as well as the reactions which they may undergo, has therefore attracted considerable interest, not only due to the fact that such interstellar chemical reactions determine the materials available for the formation of planetary systems, but also because of the potential for prebiotic molecules to be formed in the interstellar medium [34, 55, 56].

1.2.1. Plausible Formation Processes of Glycine in the ISM

Several reaction mechanisms have been postulated for the formation of glycine in extraterrestrial environments. Blagojlvich et al. (2002)[36] studied gas-ion-molecule reactions of the interstellar medium. They suggested that the glycine can be produced by reacting with ionized and protonated hydroxylamine. Their mechanism suggests that the neutral glycine could be formed from dissociation-recombination and electron transfer reactions due to the high affinity of glycine [57]. They have also indicated that the dissociation-recombination channel is the most favoured one.

Glycine is also reported to be formed in the laboratory from ice mixtures of water (H2O), carbon monoxide (CO), (NH3), and (CH4)via UV photo processing.

Radical-radical reactions are said to be generated by UV ranging from 4 to 13 eV

. . that yield radicals such as methyl (H3C ), hydroxyl ( OH) and amino (NH2) species, essentially without any barrier. Visible quantities of amino-acids have also been formed by the irradiation of a mixture of water (H2O), (CH3OH), ammonia (NH3), carbon

15 -1 monoxide (CO), (CO2), with a flux of 1.5 x 10 s for 24 hours [24,

7

Chapter 1

58]. It was concluded that the abundance of glycine in these products shows that glycine can be produced in one out of 30 000 photons (i.e. with low quantum yields)[24].

The Strecker-type synthesis is also another reaction process that was postulated and involves a reaction in liquid water between HCN [], NH3 [ammonia], and an aldehyde [RCHO]. Other potential mechanisms have also been tried both experimentally and theoretically and these include the recombination of the COOH radical with CH2NH2, where (CH3NH2) is believed to be the source for CH2NH2 in the ISM. A quantum chemical study was performed by Largo and co-workers [24] whereby they used acetic acid

+ (CH3COOH), and the ion (NH4 ) in their chemical mechanism to produce glycine. Another theoretical study was done by Barrientos et al. (2012)[59]on the formation of glycine in the ISM by reacting acetic acid (CH3COOH) with hydroxylamine (NH2OH).

Though many precursor molecules/fragments have been already detected in the ISM which can lead to the formation of glycine, many of them have not been tried to establish reaction pathways both experimentally as well as theoretically. It is stated that the reaction efficiencies of these molecules/fragments in the ISM are mostly reliant on their abundances. Therefore, based on the abundances of the reactants some of the reaction pathways maybe considered as more favoured than others in the gas phase as well as interstellar clouds [28]. To find new reaction pathways that will be favourable to occur in both extremely low temperatures and at low densities is very important to this field of research.

1.3 Objectives of study

The aim of this work is to use computational chemistry to study the possible formation pathways of glycine in the interstellar medium by following the steps below:

8

Chapter 1

 Propose new reaction schemes for the possible interstellar formation of

glycine (NH2CH2COOH), from readily available potential precursors already

existing in the interstellar medium.

 Thorough analysis of some already proposed schemes for interstellar

formation of glycine (NH2CH2COOH), studying the implications of suitable

partial alteration to the scheme on the mechanism, thermodynamics and

overall feasibility.

 Test the proposed hypothesis by applying many computational

techniques and methodologies. Strategies include analysis of all the plausible

reaction channels in the reaction potential energy surfaces, interactions of the

reactants involved in the crucial steps, etc.

1.4 Thesis outline

The thesis outline shown below gives a brief description of what will be discussed in the next chapters.

Chapter 2

This chapter provides an extensive overall review of the study field. Detailed literature on the structure of the interstellar medium (ISM) with a focus on the extra-terrestrial environment related to this research is also provided. Also discussed is the main interstellar chemistry

9

Chapter 1 occurring in this medium. Other aspects covered include in-depth interstellar pre-biotic molecules of astrobiological importance that may have resulted in the formation of essential organic molecules like amino-acids, with glycine (NH2CH2COOH, simplest amino-acid) being the main focus. Plausible formation processes obtained from both theoretical and experimental work are considered together with the detectability of glycine in the ISM are discussed generally in this section of the thesis.

Chapter 3

This chapter provides a brief background on the theoretical methodology used in this research work. It explains concisely most of the basic principles of the underlying theory of ab initio and DFT methods.

Chapter 4

This chapter provides a detailed account of the results, discussions and conclusions drawn from using different computational methods to predict the possible interstellar formation of glycine from the reaction of CH2=NH, CO and H2O.

Chapter 5

The results, discussion and conclusions are expanded in this section of the thesis, whereby different ab initio and DFT methods were used to predict the possible interstellar formation of glycine through a concerted mechanism of CH2=NH, CO2 and H2.

10

Chapter 1

Chapter 6

This chapter gives a well-defined simple two-step path as an alternate and shortest route for the formation of glycine compared to the multi-step pathways suggested in the Strecker’s or

Miller’s synthesis.

Chapter 7

This chapter gives a summary of all the conclusions made from the individual chapters together with recommendations and future work.

Appendix A

Supplementary information for chapter 4 on the potential energy surfaces (PESs) for both

CH2=NH+CO+1H2O and CH2=NH+CO+2H2O plus the reaction CH2=NH+CO+H2O-H2O

(binary complex) is provided in Appendix A. It also includes optimized structures with crucial geometric parameters for both MP2 and B3LYP methods. Tables summarizing optimized geometries of the two reactions, CH2=NH+CO+1H2O and CH2=NH+CO+2H2O, are given together with tables summarising various basissets and methodologies for the two reactions respectively.

Appendix B

Chapter 5 supplementary information for optimized geometries for the reactants, transition states (TSs) and products for reaction 4 are illustrated in Appendix B, including the PES for

11

Chapter 1 the MP2 method. Tables comprising energetic data showing the effect of various basissets with the B3LYP of theory and various methods is also provided. Optimized geometries of the stationary points for reactions 1 and 3 are shown together with some Cartesian coordinates of stationary points for reaction 4.

Appendix C

Provides supplementary information for the thermodynamic data related to the PES discussed in chapter 6. It also gives tables showing the effect of varying methods and basissets for the three reactions described in this chapter. The total energies for the PES along with optimized geometries in Cartesian coordinates of all stationary points calculated using theB3LYP/6-

3++G(3df,2pd) level of theory are also given.

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34. Ehrenfreund, P., et al., Astrophysical and astrochemical insights into the origin of life.

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35. Ehrenfreund, P. and K.M. Menten, From molecular clouds to the origin of life. 2002:

Springer.

36. Blagojevic, V., S. Petrie, and D.K. Bohme, Gas-phase syntheses for interstellar

carboxylic and amino acids. Monthly Notices of the Royal Astronomical Society,

2003. 339(1): p. L7-L11.

37. Vidali, G., et al., Laboratory studies of formation of molecules on dust grain

analogues under ISM conditions. Journal of Geophysical Research: , 2004.

109(E7).

38. Stahl, F., et al., Reaction of the , C2H, with methylacetylene,

CH3CCH, under single collision conditions: Implications for . The

Journal of Chemical Physics, 2001. 114(8): p. 3476-3487.

39. Flower, D., Molecular collisions in the interstellar medium. Vol. 42. 2007:

Cambridge University Press.

40. Fillion, J., et al. Gas-surface interactions and heterogeneous chemistry on interstellar

grains analogues. in EPJ Web of Conferences. 2011. EDP Sciences.

41. Flower, D. and G.P. des Forêts, The influence of grains on the propagation and

structure of C-type shock waves in interstellar molecular clouds. Monthly Notices of

the Royal Astronomical Society, 2003. 343(2): p. 390-400.

42. Tielens, A.G., The physics and chemistry of the interstellar medium. 2005: Cambridge

University Press.

43. Jalbout, A.F. and M.A.H. Shipar, The ribose and glycine Maillard reaction in the

interstellar medium (ISM): A theoretical study. Journal of Chemical Sciences, 2008.

120(3): p. 329-337.

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44. Carl, S.A., et al., No barrier for the gas-phase C2H+ NH3 reaction. The Journal of

Physical Chemistry A, 2004. 108(17): p. 3695-3698.

45. Kwan, J., The mass spectrum of interstellar clouds. The Astrophysical Journal, 1979.

229: p. 567-577.

46. Snow, T.P. and V.M. Bierbaum, Ion chemistry in the interstellar medium. Annu. Rev.

Anal. Chem., 2008. 1: p. 229-259.

47. Duley, W., Chemical evolution of carbonaceous material in interstellar clouds. The

Astrophysical Journal, 2000. 528(2): p. 841.

48. Klemperer, W., Interstellar chemistry. Proceedings of the National Academy of

Sciences, 2006. 103(33): p. 12232-12234.

49. Herbst, E. and W. Klemperer, The formation and depletion of molecules in dense

interstellar clouds. The Astrophysical Journal, 1973. 185: p. 505-534.

50. Oppenheimer, M. and A. Dalgarno, The fractional ionization in dense interstellar

clouds. The Astrophysical Journal, 1974. 192: p. 29-32.

51. Garrod, R.T., S.L.W. Weaver, and E. Herbst, Complex chemistry in star-forming

regions: an expanded gas-grain warm-up chemical model. The Astrophysical Journal,

2008. 682(1): p. 283.

52. Wakelam, V., et al., Reaction networks for interstellar chemical modelling:

improvements and challenges. Space science reviews, 2010. 156(1-4): p. 13-72.

53. Wilson, T. and R. Rood, Abundances in the interstellar medium. Annual Review of

Astronomy and Astrophysics, 1994. 32: p. 191-226.

54. Watson, W.D., Interstellar molecule reactions. Reviews of Modern Physics, 1976.

48(4): p. 513.

17

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55. Ehrenfreund, P. and S.B. Charnley, Organic molecules in the interstellar medium,

comets, and meteorites: a voyage from dark clouds to the early Earth. Annual Review

of Astronomy and Astrophysics, 2000. 38(1): p. 427-483.

56. Caro, G.M., et al., Amino acids from ultraviolet irradiation of interstellar ice

analogues. Nature, 2002. 416(6879): p. 403-406.

57. Pilling, S., et al., Formation routes of interstellar glycine involving carboxylic acids:

possible favoritism between gas and solid phase. Astrobiology, 2011. 11(9): p. 883-

893.

+ 58. Largo, L., et al., The reaction between NH3 and CH3COOH: a possible process for

the formation of glycine precursors in the interstellar medium. Astronomy &

Astrophysics, 2010. 516: p. A79.

59. Barrientos, C., et al., Gas-phase synthesis of precursors of interstellar glycine: A

computational study of the reactions of acetic acid with hydroxylamine and its ionized

and protonated derivatives. The Astrophysical Journal, 2012. 748(2): p. 99.

18

Chapter 2

CHAPTER 2

LITERATURE REVIEW

2.1 Introduction

This chapter gives a brief review of life on Earth and highlights some crucial understanding of our solar system which may help provide evidence of the origin of life outside our

Earth, and this includes the interstellar medium (ISM), which is the major extra-terrestrial focus of this research. Aspects covered in detail also include interstellar pre-biotic molecules with astrobiological importance that might have undergone evolution and recycling to produce important organic molecules like amino-acids with glycine (NH2CH2COOH, simplest amino- acid) being the main thrust of this study. Although our research is explicitly theoretical, this chapter takes into account both theoretical and experimental work that has been done to predict the possible formation pathways of glycine (NH2CH2COOH) and its detectability in the ISM.

2.2 Life on Earth

Life is an ambiguous term that most scientists and philosophers have difficulty defining. It can be defined as characteristic distinctive physical units that possess and maintain signalling and self-sustainable biological processes making it different from dead or inanimate entities that lack these functionalities. Different forms of life are known to exist on our planet ‘Earth’ and these include plants, animals, fungi, protists, archaea and bacteria. These different forms are at times confusingly defined which could lead to the right or wrong description of viruses, viroid or potential synthetic life as existing [1, 2]. An organism is the known smallest

19

Chapter 2 contiguous unit of life composed of one or many cells that undergoes metabolism, hence maintaining homeostasis and can grow and respond to stimuli. The prime science concerned with the study of life in general is biology with many other fields of science involved. All of these various selections of organisms are a carbon and water based-cellular with intricate organization and inborn hereditary material [2]. The organism reproduces either sexually

(reproduction that occurs through the unification of male and female gametes) or asexually

(reproduction that occurs without the union of male and female gametes, e.g. budding or binary fission), and adapts to its environment in successive generations through evolution.

2.2.1 Origin of life on Earth

There are several scientific theories which are used as basis to explain the origins of life on our Planet Earth. It is believed that life on Earth started more than three billion years ago, developing from microbes into an interesting arrangement of multifaceted organizations over time [3-5]. There is however no definite evidence which can prove exclusively that these theories are indeed true. Some scientists trust that life came into being at the time when our planet’s environment was sufficiently balanced to sustain it [6-9]. Overall, the science community has been long baffled by the origin of life on Earth with almost all of these theories contradicting the biblical perspective of the book of Genesis. The bible proclaims that life can only “propagate according to its own kind” and therefore not accepting the concept of life arising from non-living matter [10]. A definite answer with incontestable evidence can assist in filling in one of the gaps in origin of life in scientific research that has remained a mystery to most scientists. Although there is no consensus as to how life originated on our Planet Earth, the majority of scientists believe that the origin of life on

Earth developed from some parallel natural progression and advanced through a multistep

20

Chapter 2 process over the duration of a million of years until the first single-celled life was created

[11-15].

2.2.1.1 Abiogenesis

The idea of a natural process that presumes that life originated from non-living matter such as organic compounds is known as abiogenesis [16, 17]. There are three main aspects that are considered in the study of abiogenesis, and these include the geophysical, the chemical and the biological aspects, although some studies consider all the three approaches. The concept of abiogenesis was first proposed in 1924 by Alexandra Oparin, a Russian biochemist who proposed that living cells arose from non-living material through a sequence of non-living organisms. This process is believed to have occurred on Planet Earth more than 3 billion years ago, and has been studied extensively with no conclusive results that make rational speculations about whether primordial chemical reactions may have given rise to living systems [5, 6, 18-21]. This was done by performing both laboratory experiments and by similarly deducing genetic information of modern organisms. Oparin suggested that the atmosphere of our primitive Earth contained which when excited with lightening or other sources of energy would react to form organic compounds. The compounds formed are believed to have self-assembled successively to form complex molecules like proteins that would henceforth organize themselves into living cells [22-25]. This hypothesis was later tested by two scientists, Stanley Miller supervised by Harold Urey in the year 1953 who conducted an experiment that simulated the atmospheric conditions of primitive Earth. Their experimental procedure consisted of methane (CH4), ammonia (NH3), water (H2O) and hydrogen (H2) being boiled into vapour at the bottom of a sterile 5 litre glass flask which was then passed through a 500 ml flask that was half filled with water [26-30]. The resulting

21

Chapter 2 mixture was subjected to a 50,000 volt spark between electrodes to mimic lightening in the water vapour and gas mixture followed by the cooling of the simulated atmosphere to enable the water condensed to be collected in the U-shaped trap at the bottom of the apparatus.

Examination of the results by Urey and Miller revealed a tar-like substance, which after removing impurities by some chemical processes and the use of paper chromatography revealed the presence of amino-acids, the well-known building blocks of life [31, 32].

Figure 2. 1: Experimental set-up of the Urey-Miller experiment.[16, 18].

Nonetheless all forms of abiogenesis methods have not been supported scientifically [33].

The conditions believed to have existed in the early earth have shown an inability to the building blocks required for life, which proves to be self-contradictory[34]. Moreover, everything that is known from science seems to prove that abiogenesis could not have transpired under any possible natural conditions. Besides the Urey-Miller experiment, there have been many other approaches done to investigate the process of abiogenesis that are very

22

Chapter 2 complex with some more outrageously unlikely than others, but with the majority studying how molecules self-replicate, and how their components came into existence. It is however generally assumed that the existing life on planet Earth came from the RNA world, albeit

RNA life may not have been the very first life to have existed on Earth [32, 35, 36]. Other approaches focused their attention on how the process of catalysis in chemical systems may have provided precursor molecules that are required for the self-replicating process [37].

Another intriguing discovery was that complex organic molecules are the necessary starting materials for the advancement of life on Earth [38]. These organic molecules were found in the Solar system in space between , called the interstellar space and also known as the interstellar medium [39].

2.3 Interstellar Medium (ISM)

The interstellar medium is the region in space between star systems in a galaxy, which is the

Milky Way [3, 40, 41]. The matter in ISM exists as dust, or in gaseous form (ionic, molecular, atomic or plasma) and as high energy particles like cosmic rays. The ISM blends smoothly into the adjoining intergalactic space and fills up the interstellar space. The type of energy found in the in the form of electromagnetic radiation is called interstellar radiation [2,

42, 43].

Multiple phases constitute the interstellar medium depending on whether the matter found is ionic, atomic, or molecular, together with the temperature and density of the matter. Gases make up a bulk of the ISM matter, composed mainly of H2 and He that constitute about 99%

[44, 45]. The interstellar medium consists of ~91% hydrogen with ~9% helium by number of atoms respectively, and only 0.1% being atoms denser than either hydrogen or helium. By

23

Chapter 2

mass this amounts to 70% H2, 28% He, with other elements making up the remaining 2%.

Carbon, nitrogen and oxygen represent a majority of the final 2% with heavier elements being less abundant. Both hydrogen and helium are known to have resulted from primordial , whereas the heavier elements, also known as “” in astronomical parlance, are a result of enhancement from the process [46, 47].

The dust is a mixture of grains produced in dying stars and is reformed in the ISM [48-50]. It plays a substantial part in the interstellar chemistry of the ISM although it is encompassing only a trivial amount of the interstellar material of about 1% by mass. The dust of the ISM matter absorbs and scatters photons that have penetrated the gas matter of the ISM from near- ultraviolet to the far-infrared, a process called [51-55]. It can therefore serve as a buffer to ultraviolet light especially in denser regions of the ISM making it possible for more complex reactions to occur on the grains themselves in surface mediated regions and in the surrounding gas [56, 57]. The temperature and density of the ISM varies and differs between two types of clouds that are traditionally distinguished per their physical properties and chemical properties. It varies from extremely hot (10,000 K) diffuse clouds (1 cm-3) which are easily penetrated by starlight, to extremely cold (10 K) dark cloud (> 104 atoms/molecules cm-3) which are dense and impermeable to starlight [58], conditions that permit the existence of more complex chemical species [59, 60]. Starlight extinction results from the absorbance and scattering of energy by the solid material in the ISM [61-65].

Nonetheless, all phases of the ISM are extremely tenuous by earthly standards [66-68].

The unfavourable conditions of the ISM according to terrestrial standards were perceived to be a hindrance for the simple chemical entities found in the ISM to give rise to other complex chemical entities by the process of chemical transformation [69-72]. This reasoning was first

24

Chapter 2 based on the low temperatures of the ISM of about 10 to 100 K typical for interstellar dust grains, which could rule out all endothermic reactions in addition to exothermic reactions which have any significant reaction barriers [42, 67, 73, 74]. The second hindrance was perceived to be the low number densities in the interstellar clouds which may lead to a very small collision frequency of approximately one collision per two weeks. However modern chemistry has revealed otherwise; several spectral observations detected from the intervening space using a number of techniques and instruments have shown an abundance of information with many more discoveries made each year, and the rate of detection of species in the ISM has been approximately constant since 1970 [67, 74-76]. To date, over 200 molecules and ions are being detected in the interstellar medium, from simple diatomic to large organic molecules. The conditions of the ISM though understood to be unusual according to terrestrial laboratory standards, have allowed the on-going existence of unstable

+ + and reactive species such as HCO , N2H , CH, etc. and radicals like HC4, OH, etc.[74, 77-

79]. For this reason, the ISM may be viewed as a unique synthetic laboratory.

2.3.1 Interstellar clouds

The interstellar medium is a complex clumpy structure that is not homogeneous at all [58,

80]. These clumpy structures of the ISM are known as the interstellar clouds, a general name given to the accumulation of neutral matter of gas phase and particulate phase (dust) concentrated along the spiral arms found in both our halo above and below the and also in other galaxies. These interstellar clouds are denser than the average region of the

ISM and are continually developed from the formation of new stars with their enhancement occurring during stellar nucleosynthesis process when material from dying stars is ejected into them [2, 60, 81, 82]. They are classified according to the cloud’s size, density and

25

Chapter 2 temperature and they are neither dynamically dormant nor identical on long time scales [2].

Two main different kinds of interstellar clouds are found in the ISM, namely; diffuse and dense clouds with hydrogen (most abundant element) present in all the clouds. Hydrogen gas is either present as neutral atomic hydrogen in H I regions or ionized hydrogen in H II regions usually in diffuse clouds, or molecular hydrogen (molecular clouds) in the dense clouds [83].

Interstellar clouds also containing of helium with heavy elements occurring in very small amounts. Diffuse clouds have low-densities and high temperatures in which UV radiation readily penetrates, while dense clouds have higher densities and are much colder than the diffuse clouds, also dark and impermeable to visible and UV radiation [2, 59, 81, 82, 84].

2.3.1.1 Diffuse interstellar clouds

Diffuse clouds are of very low density of roughly 100-300 cm-3 with moderate extinctions (<1 mag), dominated by high radiation fields. These clouds form the first step in

2 evolutionary passage and are comprised primarily of H atoms and H2 molecules of about 10 cm-3 with a gas temperature of 50 K combined with low yet observable micron-sized concentration of “dust” particles having a dust temperature of 20 K that are stellar visible [2,

59, 81, 85, 86]. They can be described as transition objects between the atomic and molecular phases that can also be penetrated by ultra-violet light without total weakening of the UV rays, and thus can be treated as simple laboratory for the crucial chemical process

[87].Almost the entire extent of a diffuse cloud is easily penetrated by the UV photons triggering a gas phase composition that results from photochemical reactions that only allow the formation of fairly simple molecules [86]. The use of ground based telescopes has helped

26

Chapter 2 in the detection of interstellar species like CH, CN and CH+ which were the first to be detected in these clouds due to their distinctive absorption spectra in the visible region of the spectrum [86, 88]. At a certain , interstellar extinction measured in magnitude

(mag) [86] reflects the captivated starlight and disseminated by dust grains and extents to the dimmed viewer [88-91].

However, detection of molecules in diffuse clouds was quite difficult until the advent of satellites and sensitive enough equipment was introduced after the year 1951, which helped researchers in the field to detect more molecules in the diffuse clouds by using UV absorption via absorption line observation of bright background continuum sources, which provided a suitable background source [92-95]. Other diatomic molecules

+ such as CO and H2 together with polyatomic species like HCO , C3H2 and H2CO have been detected in diffuse clouds with heavy elements mainly residing in dust grains except for N and S [90, 91].Molecules that can survive in the interstellar diffuse clouds are thus limited to simple diatomic species, with a few polyatomic species due to the harsh UV light that is able to penetrate and heat the diffuse clouds, thus making the ambient temperatures of these clouds relatively high ranging to about 100-200 K [89]. The temperatures in diffuse clouds are an outcome of the thermal balance between heating and radiative cooling, whereby heating of the clouds is through photo electron emission from dust, polycyclic aromatic hydrocarbons (PAHs) and C atoms, while cooling is mainly through fine-structure radiation transitions of C+ and O [91, 96, 97].

2.3.1.2 Dense molecular clouds

The interstellar dense molecular clouds form part of the composition of the ISM where stars of different and their planetary systems are born [88,89]. Dense molecular clouds are

27

Chapter 2 thought to have developed from diffuse interstellar clouds from the dissipation of interstellar turbulence in shock waves [98-101]. These dense clouds consist mainly of H2 and He and have a density of approximately 10-4 – 10-6 cm-3 containing a greater concentration of dust grains than diffuse clouds [86]. Dust grains contained in dense molecular clouds have a high extinction efficiency that results in the shielding of the innermost interior of these clouds from the destructive interstellar radiation that affects these clouds. Additionally, most of the photons capable of dissociating H2 and other elements are absorbed at cloud surfaces, which results in the available H being converted to H2 by grain catalysis [102-105].

+ Nonetheless, dense molecular clouds can be penetrated by cosmic particles producing H3 ,

He+ and that heat the gas. However, since most of the gas phase ‘C’ is available as

CO, dense clouds cool off through emitting radiation corresponding to the rotational lines of the CO molecule excited by collision with H2 and He. Both the heating and cooling off processes causes the temperature of the dense molecular clouds to be very low, ranging from about <100 K with some clouds having a temperature of about 10 K [102, 106, 107]. Even though external UV photons do not significantly penetrate dense clouds, a weak UV flux that results from the excitation of H2 by energetic electrons produced in cosmic-ray impacts most likely exists throughout the interiors of the molecular cloud [108]. This flux is capable of photodissociating and photoionizing interstellar molecules and can considerably influence the richness of some atomic ‘C’ and other species [109].

To date there have been discoveries of more than 140 molecules in dense molecular clouds and analogous interstellar gas and grain chemistry being the primary building blocks for protostellar disk, after which planets, comets, and a wide range of complex macroscopic bodies are believed to have been formed[110]. Analogous gas and grain are also

28

Chapter 2 believed to produce a variety of complex organic species [111, 112]. Therefore complex polyatomic molecules and a huge diversity of gas phase organic molecules have been detected in dense molecular clouds using observational frequencies in the infrared, radio, millimeter and sub-millimeter ranges [106, 113]. Classes of molecules found in the dense molecular clouds include aldehydes, alcohols, acids, ketones, amides, amines, ethers, nitriles, together with long-chain hydrogen compounds [88,89]. Thus, the most abundant atoms in these clouds consist of H, He, O, N, C, S, and P in which most reactions happen and formation of molecules results from their chemical reactions [114-118]. The dense component of molecular clouds consists of cold atomic HI clouds having temperatures of about 100K together with giant molecular clouds (GMC) that have temperatures of about 10-

20 K that have clumpy sub-structures. A significant quantity of matured molecular clouds comprises a condensed phase in the form of dust or grains that are generally composed of various silicates. The particles at low temperatures develop mantles of other molecules e.g. at temperatures below 150 K, water ices condenses into grains [119-122].

2.3.1.2.1 Dense cores

The existence of micrometre (µm) size grains in dense condensations regions inside dense molecular cloud cores at temperatures of about 10 K specified as cloud cores or dense cores

[123, 124]. These dust grains play a pivotal part in some of the important physical processes of the ISM. On one hand, dust materials and grain size distribution reflects the dependence of wavelength on the optical depth for dust absorption and scattering, particularly known as the extinction curve [124-126]. Again, some molecular species, especially H2 are mainly formed on dust surfaces [127, 128]. Dependence of both the extinction curve and the total grain surface area on grain size distribution, results to the rate of dust surface reaction relative to

29

Chapter 2 the total surface of dust grains [124, 129, 130]. Therefore, in the ISM it is of particular importance to understand the roles of dust so that their mechanisms are elucidated and regulated. It has been shown that deuterium-bearing species are exceptional probes of these cold regions before takes place. Two key molecules of importance for star

+ + formation studies include H2D and D2H as evident from the unfamiliar transitions near 1.4

+ + THz indicating that they are not diminished on to the grains. This making H2D and D2H as best tracers of the dense gas in the central star forming cores and ammonia isotopologues.

The first two are assumed to be plentiful in dense regions that can be studied in absorption alongside resilient continuum sources or in emission in these regions [131-139].

It is also documented that low-mass star formation happens within cloud cores whereby much of the hydrogen is in the molecular (H2), nebulae referred to as molecular clouds, whereby much higher densities of more than104 cm-3 are found in small scale of about 0.1 parsec (pc).

For star formation to occur in this region the gravitational force acting to collapse the cloud is supposed to surpass the interior that are acting outward to avoid a collapse [122,

140-142]. On the other hand, the physics of molecular clouds is still contested as it is poorly understood. It is believed that turbulent motions that are highly supersonic turbulence in a cold, magnetized gas govern the internal motions of such clouds. This highly supersonic turbulences are said to be comparable to the speeds of magnetic disturbances which are assumed to cause a rapid energy loss that involves a total collapse or a balanced reinjection of energy [101].

Formation of the low-mass stars was first detected inside the coldest clouds in the infrared region of the spectra by observers and also detected at the surface of the clouds in visible light when the cloud disintegrates [122, 143-146]. The mechanism for the formation of stars

30

Chapter 2

with masses more than 8 M☉ is not yet well understood, however, it is speculated that unabundant quantity of radiation is emitted by gigantic stars which thrusts against subsiding material [147-150]. This postulation has resulted in the formulation of many theories in an attempt to elucidate this fact. One of them suggests that some massive are surrounded by the disks and this is supported by many evidences, with the most prominent one being competitive accretion, several others still need to be tested observationally [151-153]. Competitive accretion suggest that the gigantic protostars are seeded with low-mass protostars competing with other protostars to lure in matter from the whole parent molecular cloud [150]. Nonetheless, clouds are documented to be disrupted by the effects of massive stars before a noteworthy portion of their masses become stars [100,

147, 154, 155]. It is therefore clear that it is not possible to describe star formation in only a few sentences, since these are multifaceted, time-dependent extremes of hot and cold with different types of material falling from different parts of the solar system that preserve slight record of the gas and grains from which they formed [128, 150, 156].

It is in the dense cores that significant active gas-phase chemistry occurs that is crucial in setting the preliminary chemical inventory of volatile species obtainable in the protosolar nebula [157]. It is also in this region whereby evolutionary chemical sequence originates from the asymptotic giant branch (AGB) envelopes and the diffuse ISM. This is basically the region where interstellar chemistry begins to have a direct relevance for cometary compositions, e.g. the molecular ice mantles can form on siliceous and carbonaceous dust grains, and a lot of chemical pathways can be opened from the processing of these ices [119,

128, 129, 157-160].

31

Chapter 2

Table 2. 1: Summary of physical factors found in the interstellar medium (ISM).

Region Molecules Density (cm-3) Temperatures (K)

Simple molecules H2 , + 2 Diffuse clouds CH , CH, CN, C2, OH, 10-10 100-120 CO, HCO+, HCN

Simple molecules H2, + 2 3 Translucent clouds CH , CH, CN, C2, OH, 10 -10 50-100 CO, HCO+, HCN, C Saturated molecules

CH3OH, C2HOH,

C2HCN, CH3COCH,

CH, NH, H2O Hot molecular No carbon-rich linear 104-109 100-300 clouds molecules. Vibrationally excited

HCCCN/C2H3CN Large deuterium fractionation Carbon-rich, carbon clusters and hydrogen- Circumstellar terminated clusters, variable 10-4500 envelops oxygen-rich, small oxygen-bearing species Carbon-rich, di- and Planetary nebulae variable 200-3000 triacetylene,

32

Chapter 2

2.4 Interstellar Chemistry

Due to the drastic differences in physical conditions found in the ISM that contrast severely with those present on the Earth, it is inevitable that the chemistry in the ISM is substantially different from the one that occurs on Earth [161]. There is an ever growing catalogue of interstellar molecules that stimulates astrochemists to give themselves time to do research with their qualitative and quantitative models, which would help them to understand how molecules are formed and destroyed in the interstellar environment [2, 58, 77]. A lot of work has been done leading to the clarification of some pending questions related to interstellar chemistries, since the studies of Spitzer and Bates concerning CH and CH+ [58, 162, 163].

Generally, from previous studies it has been shown that the qualitative depiction of the interstellar chemistry is sensible whereas the quantitative feature is still not as yet clear [58].

The main physical conditions that prevail in the ISM comprise very low densities and temperatures resulting in interstellar chemistry being limited to the following processes: (i) exothermic reactions, since these are highly probable reactions if they have a reasonably high rate constant ‘r’ (due to the activation Ea being comparable to the thermic energy kT of the

Arrhenius equation r = A e-Ea/kT, whereby A is the pre-exponential factor); (ii) bimolecular reactions (three-body collisions are a relatively rare occurrence) [58, 81, 164, 165]. Similarly, due to the low temperatures of the ISM, the Gibbs free energy (ΔG = ΔH – TΔS) that governs stellar atmosphere chemistry is almost equivalent to enthalpy, ΔH [166, 167]. Therefore the results of many chemical reactions in the ISM can be projected from the enthalpies of the atoms and molecules that are involved [168-170].

33

Chapter 2

Simple molecules in the ISM are formed by gas-phase chemistry based on positive ion molecule reactions with some molecules like H2O and CO2 formed more efficiently on the surfaces of grains [171, 172]. Other more complex molecules like C2H2OH and

CH3OH are formed solely by grain catalysis, more of what have been identified in cold molecular clouds and some in warmer regions of forming protostars [173, 174].

2.4.1 Gas-Phase Chemistry

Different reaction types are evidently involved in the gas-phase chemistry of the ISM, with positive ions and neutral species reactions assumed as most probable relative to neutral- neutral reactions, since they need less or zero activation energy to occur. On the other hand, the gas-phase chemistry of interstellar molecules for both diffuse and dark clouds is regulated by diverse processes and is therefore conveniently and properly discussed by being treated differently [58, 78, 128, 175, 176]. A qualitative list of some of the important type of reactions that occurs in the ISM is shown in Table 2.2:

34

Chapter 2

Table 2. 2: Important gas-phase reactions occurring in the interstellar medium (credit to

Carbo et al. (1985) [58].

Type of reaction mechanism Example of the reaction mechanism

Ion-molecule a) Charge transfer A+ + B → B+ + A b) Radiative association A+ + B → AB+ + h c) Atom transfer A+ + BC → AB+ + C AB+ + C → A+ + BC Electron recombination reactions Radiative A+ + e- → A + hѵ Dissociative AB+ + e- → A + B

Photochemical reactions a) AB+ + hѵ → A+ + B b) Photoionization A + hѵ → A+ + e-

Neutral-neutral reactions a) Atom (or atom group) transfer A + BC → AB + C b) Radiative association A + B → AB + hѵ c) Chemionization A + B → AB+ + e-

Other reactions a) Ion-ion neutralization A+ + B- → AB b) Negative ion-neutral A- + B → AB + e- A- + BC → AB- + C

2.4.1.1 Gas-Phase Chemical Reactions in the Diffuse Clouds

Diffuse cloud chemistry primarily forms simple molecules due to the permeation of a high ultraviolet flux that is usually around 1000-2000 Å wavelength range. The ionization and

35

Chapter 2 destruction processes of atoms and molecules within the cloud are governed by these UV photons, which act as a principle external energy source [177-180].

A crucial role in the gas-phase chemistry of diffuse clouds is played by molecular hydrogen, but due to the low densities and temperatures of these clouds, H2 cannot be produced from them. For instance, a three-body reaction pathway known to produce H2would have to be excluded here since it cannot occur in diffuse clouds, but can only happen in high energy, dense environments such as in the of novae or supernovae. Nonetheless, production of

H2 in diffuse clouds occurs by the colliding, sticking, or migrating of H atoms on the surfaces

+ of dust grains [181, 182]. The formation of H2 from recombination of H has been demonstrated by experimental studies to be slower on similar surfaces known to be present in diffuse clouds compared to ones predicted in theory. Although it is understood that the H2 production in diffuse clouds is difficult by experimental studies, the H/H2 ratio attained in the clouds is a balance between the formation of H2 on dust and the photo-destruction of UV, which is controlled by the nonlinear self-shielding of H2.The H2 produced also escapes into the gas and adds to the heating of the gas [86, 181-183].

A wavelength greater than 912 Å (13.6 eV) corresponding to hydrogen ionization potential of atomic hydrogen absorption reduces the spectrum of light to photons, separating the energetic barrier into two groups; (i) elements with less than 13.6 eV that exist mainly as ions like carbon, (ii) and those remaining in neutral form with an ionization potential that is greater than 13.6 eV like oxygen and nitrogen [42, 94, 184]. Moreover, the nitrogen available in diffuse clouds is in the form of N0 and N+ while that available in dense clouds is in the form of N2 [95, 185-187]. The chemical composition of diffuse clouds was thought to be very simple, with only diatomic molecules present in these clouds such as NO, OH, CH etc.Recent

36

Chapter 2 observations have proven otherwise, having shown the presence of polyatomic species in diffuse clouds, with their origin uncertain at present [94, 188-190].

Knowledge of the presence and form of the major elements in diffuse clouds are mainly based on ionization potentials and the interstellar energy spectrum UV field. Those elements with less than 13.6 eV are easily photoionized [94, 191, 192] as shown in Eqn 2.1:

C + hν → C+ + e− (Eqn. 2.1)

Accepted formation mechanisms for some of the available species in the diffuse interstellar clouds have been proposed [193] and are illustrated in Table 2.3.Elements like C, S and refractory metals like Na, Mg, etc. are practically fully ionized, while elements such as O and

N require more energetic photons to be ionized than are readily available in the clouds.

37

Chapter 2

Table 2. 3: Gas-phase chemistry proposed mechanisms for the formation of various species in diffuse clouds.

Formation of H2O and OH species: H+ + O → O+ + H + O + H2 → OH + H + + OH + H2 → H2O + H + H2O + H2 → H3O + H + − H3O + e → H2O + H

H2O + H → OH + H2

H2O + hν → OH + H [194]

Formation of HD: H+ + D → H + D+ + + D + H2 → HD + H [195]

Formation of CO: C+ + OH → CO+ + H + + CO + H2 → HCO + H HCO+ + e− → CO + H

Formation of CH and CH+: + + C + H2 → CH + H C + H → CH + hν CH+ + e− → CH + hν [194] CH + hν → C + H [196] + + C + H2 → CH + H + + CH + H2 → CH2 + H + + CH2 + H2 → CH3 + H + − CH2 + e → CH + H + − CH3 + e → CH2 + H

CH2 + H → CH + H2 [196]

38

Chapter 2

Elements like nitrogen cannot be completely ionized in the diffuse clouds due to the unavailability of sufficient energetic photons to ionize them, while carbon and several refractory elements that include Na, Mg etc. are completely ionized [197-199]. However, cosmic-rays present in these clouds are capable of ionizing H and H2, and He atoms. From some of the mechanisms mentioned in Table 2.3, it is evident that H can be ionized to H+,

+ + while H2 ionized to H2 , while He, though not mentioned in Table 2.3 is ionized to He . In

+ + most cases, a production of H3 is consequently caused by the fast reaction of H2 with H2, which later transfers a proton to other atomic entities than H2[200-202]. This causes the loss of electrons produced through radiative recombination reactions like that seen in Eqn 2.2:

C+ + e− → C + hν (Eqn. 2.2)

or sometimes in dissociative recombination reactions like the ones shown in Eqn 2.3

+ − H3 + e → H2 + H, or 3H (Eqn. 2.3)

+ OH and H2O are then produced by the dissociative recombination of H3O is initiated by a sequence of exchange reactions with H2 that is caused by the charge transfer of processes described by the first chemical reactions in Table 2.3and Eqn 2.4 below

H+ + O → O+ + H (Eqn. 2.4)

and followed by the reaction in Eqn 2.5

+ + O + H2 → OH (Eqn. 2.5)

39

Chapter 2

And also continues according the proposed reaction mechanism and the steps followed in

Table 2.3.

Another interesting and controversial gas-phase interstellar chemistry is that of the CH and

CH+ species which was discovered about 30 years ago and yet remains an unresolved problem of the diffuse interstellar medium [58, 203]. The abundance of CH+ remains a mystery as no models have been able to reproduce its abundance even though all observational limitations are obeyed. Most of the CH+ is usually discovered alongside sight lines towards bright O and B stars; recent literature has reported its column density to being ≥

1013 cm-2. Even though other chemical models of the clouds are able to reproduce the column densities of many other species, the abundance of CH+ still remains baffling because CH+ is demolished by atomic and molecular hydrogen and the only known chemical mechanism to form CH+ proceeds under temperatures of ≥ 1000 K or more as shown in Eqn 2.6 [204-207]:

∆E C+ + H → CH+ + H = −4640 K endoergic (1)[208] (Eqn. 2.6) 2 k

Some models have proposed solution to this problem by invoking the additional energy source to overcome the 4640 K [86]. They have taken advantage of the fact that when diffuse gas is heated and compressed by hydrodynamic or magneto hydrodynamic shock waves originating in explosions, it becomes ionized due to collision showing high oxidation states of oxygen as O6+ or others[209]. This constituent is known as the coronal gas due to its physical state as it is the same as that of the stellar coronae. The hot gas then cools off through adiabatic expansion and emits X-rays. This is believed be a component where most of the chemical reactions with activation energy barriers or endothermic processes can

40

Chapter 2 occur. However, both the hydrodynamic and magneto hydrodynamic mechanisms are still not able to resolve the CH+ matter without causing other problems [204]. These include the observed abundance of OH molecules and the rotational populations of H2 for hydrodynamic shocks. Another limitation is that in these plasmas some magneto hydrodynamic waves are known to travel faster than the sound speed which means there is a huge difference in the velocities of the ions and neutrals giving rise to C-shocks [205, 210]. In C-shocks all variables are unceasing across the shock structure and have also been shown to produce CH+ with varied attainment. Refer to Gredel (1997) for a detailed outline of these mechanisms with some complications aspect that defies their detection [211].

One promising idea is the intermittent dissipation of interstellar turbulence that occurs in shocks, pioneered by Falgarone et al. (1995) [212]. This mechanism involves the heating of small sections within diffuse clouds to temperatures of about ≥ 1000 K crucial to enable equation 2.6 to proceed. Degradation to thermal energy within a small volume results from the heating efficiency that occurs from the available energy from the dissipation of turbulence. This model has been successful in explaining the observation of high(> 1013 cm-3)

CH+ column densities that is normally detected in the diffuse molecular sight lines [204].

While the “CH+ problem” still persists, ongoing research with different approaches is continuing to attempt to improve on it as it has proven to have had much success than the other entire proposed ones. The study of the physics and chemistry of diffuse clouds can be significantly impacted by resolving the origin of CH+ [205, 211].

41

Chapter 2

2.4.1.2 Gas-Phase Chemical Reactions in Cold Dense Molecular Clouds

It is well established that molecular clouds have higher densities of gas and dust than their apparent precursors, diffuse clouds. Cold dense molecular clouds being opaque to ultraviolet starlight, are penetrated by cosmic rays (a unique external energetic source), that pierce into the deepest cloud interiors [78, 213]. The cosmic rays are highly energetic nuclei of 1-100

MeV/nucleon and they are present throughout the entire Galaxy [214, 215]. They are the ones

+ + responsible in producing H3 and He , and electrons that heat the gas by first initially ionizing the predominant elements found in the ISM, hydrogen and helium, following the reaction mechanisms in Eqn 2.7 and Eqn 2.8[168, 216-218]:

+ − + H2 → H2 + e (Eqn. 2.7)

Cosmic ray + He → He+ + e− (Eqn. 2.8)

+ This reaction results to the production of H3 , a highly reactive and most crucial ion from the

+ reaction of molecular hydrogen H2 and other species as seen in Eqn 2.9.

+ + H2 + H2 → H3 + H (Eqn. 2.9)

A chemistry of ion-molecule and neutral-neutral reactions stirred by cosmic-ray ionization transforms a substantial portion of heavy elements to molecular forms; other reactions include ion-electron dissociative reactions and radiative recombination reactions. This results in the existence of C as CO, even though a substantial amount of atomic C is available as

(C/CO ≈ 0.1) [219], and from chemical models, O is assumed to be atomic, not O2 [220].

42

Chapter 2

+ H3 reacts by readily transferring a proton to other species present in these clouds to produce hydrogenated molecular ions, therefore playing a pivotal role in dense molecular cloud

+ chemistry [168]. Detection of the abundance of N2H in the clouds confirms that the available nitrogen present is in the form N2[221, 222]. Some of the reaction mechanisms that take place

+ from the reaction of H3 with other species in the dense molecular clouds are shown in Eqn

2.10:

+ + H3 + A → AH + H2 (Eqn. 2.10)

+ + + + + where A = C2, CO, O, N, N2and AH = HCO , N2H , OH , C2H , NH

The proton transfer reactions resulting in the production and observation of HCO+ and DCO+ are sometimes used for the estimation of electron density and or for the substantial

+ abundances of some molecules like N2H (that is sometimes not easy to detect) and regularly

+ + used to trace N2. Detection of N2H and HCO also strongly supports these based mechanisms [223, 224]. Many S-bearing molecules are produced in abundance in dense clouds which suggests that atomic sulphur is perhaps the main source of this element [220].

It is important to note that interstellar molecule synthesis is started by charge transfer from

+ H and O atoms, through an ion-molecule reaction with H2 that leads to the production of

OH. This also leads to the formation of the most abundant molecules CO and N2, after H2, with some major molecules in abundance being NH3, SO and OH [225-227]. It takes several million years to accomplish a chemically stable state in such processes, to make sure that the entire content of C is combined with O and become fused into CO and O2. As high atomic C and low O2abundance are detected in the molecular clouds gives the indication that the

43

Chapter 2 lifetimes of the clouds are not prolonged or that the above mentioned process is not as prevailing in the ISM[219, 228].

Moreover, as He (helium) atoms are in turn ionized by cosmic-rays, neutral molecules are significantly destroyed by He+ dissociative charge transfer reactions. Similarly, dust particles are said to efficiently destroy external photons from outside the molecular clouds, though marginal UV photons do not aggressively penetrate these clouds, a small, weak residual flux exists throughout the molecular interiors that play a major role [229]. This flux is reported to be resultant from excitation of H2 by energetic electrons produced in cosmic-ray impacts. The consequent UV emission is assumed to photodissociate and photoionize interstellar molecules and hence influencing the considerable amount of some species [230, 231]. Some of the chemical reactions that include the dissociation of molecules that produce atomic atoms by helium ions include the ones shown in Eqn 2.11:

AB + He+ → A+ + B + He (Eqn. 2.11)

+ + + + + where, AB = C2, CO, O2, N2 and A = C , O , N , N2

With molecular hydrogen being the most common species in the dark molecular clouds, ionic molecular species tend to react with it to produce a large amount of hydrogenated species

[58] and some of the reactions mechanisms include the ones seen in Eqn 2.12:

44

Chapter 2

+ + A + H2 → AH + H (Eqn. 2.12)

+ + + + + + + + + + + + + + where, A = O , N , CH , CH2 , OH , H2O , NH and AH = H2O , H3O , CH , CH2 , CH3 ,

+ + + + NH , NH2 , NH4 , OH

A lot of the neutral-neutral reactions have notable rate coefficients at low temperatures. Long carbon-chains molecules like are particularly produced by C atoms and CN radicals with reactions involving various hydrocarbons like C2H2 [175, 218]. Such reactions can in turn produce innumerable hydrocarbons and complex cyanopolyenes and a lot of hydrocarbon chains that are sometimes detected in molecular clouds, like in the TMC-1 in Taurus. Additionally, molecular zero-point energies are a pivotal factor in the gas-phase kinetics of extremely cold temperatures in dense clouds [232]. Therefore noteworthy fractionation of isotopes of H, C, and N can form in these regions with deuterium enhanced in

+ H3 [233] since the reverse of the reaction is shown in Eqn 2.13;

+ + H3 + HD → H2D + H2(very slow at 10 K) (Eqn. 2.13)

+ The D atoms formed can be distributed throughout the molecular chemistry with H2D initiating the distribution. Various chemical reactions lead to the enhancement of chemical fractionation to occur in extremely cold temperatures of dense clouds [234]. Sensitivity to enhanced chemical fractionation in these cold regions is the primary reason that has given enlightenment to the origin isotopic fractionation in comets and meteorites [235].

Many chemical reactions transpiring in dense clouds control the amount of ionization, which later regulates the magnetic development of these clouds via rate loss of magnetic flux by

45

Chapter 2

+ + ambipolar diffusion [94]. HCO and N2H with electron fractions comparable to

H nuclei (~ 10-8 -10-7) are the most prevalent ions [236]. Nonetheless various searches for various hydrides and oxides have been to no avail [237] and has therefore verified that elements heavier than He, like refractory metals, Na, Mg, Fe, etc. are not found in the dense gas and have been suggested to be completely merged into/onto dust grains [91].

2.4.2 Grain-Surface Processes

Construction of a “dirty” ice mantle that covers a more refractory siliceous/carbonaceous core transpires at gas and dust temperatures that are close to 10 K. At this temperature, efficient adsorption of atoms and molecules from gas occurs succeeded by surface diffusion and reaction of atoms with other surface species [238, 239]. The resultant siliceous and carbonaceous micrometre and sub-micrometre-sized dust particles produced from outflows of late-type asymptotic giant branch (AGB) stars suggest a possible rich catalytic chemistry as revealed by infrared observations of these dark clouds and consequent analyses. These ices are extremely sensitive to various kinds of energetic processes like UV photolysis, cosmic- ray impacts and heating near protostars[239].

Molecules contained in abundance in the ices are H2O, with CO, CO2, with the second copious molecule being CH3OH (containing ~5% to 40% of the ice). Some observations have however revealed excesses of CH3OH ice in conditions of low-star formation. Many other molecules are only present in small amounts, these include NH3, H2CO, CH4, OCS, and

HCOOH [238].

46

Chapter 2

Cold grain-surface kinetics is said to happen in two subsequent steps resulting to a Langmuir-

Hinshelwood catalytic model. Atoms and molecules first adsorb to the surface and subsequently diffuse between surface binding sites by either quantum mechanical tunnelling or by thermal hopping [81] see Figure 2.2. The particles are reported to accrete at a rate of about one per day from the gas at typical molecular cloud densities. At 10 K, the sticking coefficients for most of the species have been calculated to be close to unity, with heavy molecules like CO, suggested to be relatively immobile on the surface [238, 240]. Some of the present atoms diffuse and react with some of the immobile ones or amongst themselves

[241]. Smaller or lighter atoms like hydrogen atoms and D atoms are known to rapidly explore the surfaces by quantum-mechanical tunnelling whereby experiments have shown that quantum diffusion of the is most rapid once a monolayer has formed.

Although heavier atoms like C and O diffuse by thermal hopping, H atoms are known to scan the entire surface to discover any available co-reactants [241, 242].

Hydrogen jumps over the irregularities of grain surfaces (hopping) or easily moves through the grain surfaces (tunnelling) because it is very light and mobile. Formation of molecular H2 from two hydrogen atoms by hopping and tunnelling may be described (vide infra) by the

Langmuir –Hinshelwood mechanism [241, 243] shown in Figure 2.2. Another mechanism for the formation of H2 which occurs during the collision of a hydrogen atom from the gas phase with another one from the grain dust grain is also shown by the Eley-Rideal mechanism [244] in Figure 2.2. Other atoms that react with the hydrogen atom while absorbed on the dust grain include atoms oxygen (O), nitrogen (N) and carbon (C) which later form ice mantles of very simple molecules like CH3, H2O and CH4[238].

47

Chapter 2

Figure 2. 2: The formation of H2 on the surface of dust grains in molecular clouds described

by Langmuir-Hinshelwood and Eley-Rideal mechanisms [Credit: Kaiser (2002)]

[245].

Lighter atoms generally diffuse faster than heavier molecules resulting in a chemistry of mostly exothermic atom-atom reactions, atom-molecular radical reactions, atom-molecular radical reactions, and reactions involving activation barriers with atoms adding to molecules having several bonds [238]. The successive addition on grain surfaces of H atoms to accreted

O, N, S and C yields H2S, NH3, CH4 and H2O [246]. Moreover, accreted CO molecules can be deuterated, oxidized and reduced by D, O and H atoms respectively through activation energy barriers. Additions involving C atoms as known from the basic kinetic scheme in CO reduction arrangement, with an additional constraint of radical stability, is known to result to surface reactions which is believed to form aldehydes, ketones, alcohols, sugars, etc. which are well-known interstellar molecules [173, 238].

48

Chapter 2

The accreted atoms that slowly react chemically and convert to various molecules later result in the formation of ice mantles. Formation of a thick ice mantle results in further “energetic processing” that includes UV absorption of photons and cosmic-ray influences. The contribution of photolysis and radiolysis is still not yet considered as characteristic for the interstellar inventory even though many experimental studies have been done. One important aspect of the ISM chemistry by energetic processing is thermal heating, preceding comprehensive desorption of the icy mantle leading to molecular rearrangement [247]. This has been well defined in a study by Blake et al. (1991) and experimentally shown in a study done by Ehrenfreund et al. (1998)[158, 248].

An “accretion catastrophe” can happen if there is no efficient means to return molecules to gas, which completely removes the heavy element component from molecular gas from on an

5 4 -3 accretion timescale of about 10 years at a density of nH ≈ 10 cm . However, with molecular clouds older than this, this accretion catastrophe is usually resolved by a presumed desorption mechanism or mechanisms that are not yet unequivocally known [118, 249]. A reaction product with sensibly high but unknown efficiency to be retained is inevitable as ice forms, though some desorption processes do occur and they are usually divided into passive and active modes [123, 250]. Willacy and Millar (1998) described passive desorption by considering processes that are directly linked to surface and bulk chemistry acting to eliminate molecules [251]. These may use excess energy from exothermic atom-hydrogen atom additions to break weak surface bonds. An in-depth account of other mechanisms is given in the works ofBergin et al. (1998), and Charnley et al. (2001a)[118, 121].

Likewise, UV photons or cosmic rays absorption may result in mantle molecules being directly ejected with such energetic processes that result in minor population of highly

49

Chapter 2 reactive species in bulk ice. These in turn experience spontaneous explosions which later lead to the loss of mantle material. The reported ultraviolet irradiations have been shown to produce amphiphiles, aromatic ketones and amino-acids also found in meteorites [238].

Active desorption is sometimes exhibited by the grain mantle material determined by the external physical environment, Herbst (2000)[252].

More than 200 molecules and ions have been reported to date in the ISM, with most complex molecules having 13 atoms. The list includes simple diatomics to large organic molecules.

This includes simple sugar molecules of astrobiological importance like .

Furthermore, the detection rate of species in the ISM has been constant since 1970.

Introduction of new and more sensitive telescopes coming online in the next decade, it is highly likely that many more ions and molecules will be detected over the coming years [128,

183, 245]. Given the number and complexity of interstellar molecules detected so far, it is evident that the interstellar medium has a very rich chemistry. Therefore, understanding the formation mechanisms of interstellar species, as well as the reactions which they may undergo, has attracted considerable interest, and not only due to the fact that such interstellar chemical reactions determine the materials available for the formation of planetary systems, but also because of the potential for prebiotic molecules to be formed in the ISM [195].

Additionally, the origin of many celestial bodies including planets, comets, asteroids may have been from atoms and molecules produced in the ISM, along with dust grains that may have been incorporated in the solar nebulae and have therefore acted as building blocks for these celestial materials [113, 253]. During the late heavy bombardment presumed to have initiated the delivery of these molecules to the preliminary Earth and about 4.5-3.8 billion years ago, amino-acids are probable molecules that played a fundamental role as they

50

Chapter 2 are known to be the building blocks of proteins and enzymes, and hence have effects to life’s origin [113].

2.5 Formation of amino-acids in the ISM

The origin of amino-acids (basic units of proteins) in the prebiotic environment of early Earth is an interesting subject because these elements are the crucial building blocks of biological systems. Since amino-acids are elementary constituents of proteins, and thus vital components for all living organisms, the search for the mechanism of formation of these key elements and their prebiotic precursor molecules is crucial to help reveal the chemistry that may have led to the origin of life [254]. However, it is still one of the most challenging tasks to modern astronomers and astrologists with quite a number of interesting perceived views on how amino-acids are formed in the ISM [113, 254-257].

2.5.1 Formation of amino-acids through solid-phase reactions in the ISM

Formation of amino-acids in solid-phase reactions by energetic processing on interstellar ice grains, a) through irradiation of grain mantles with Lyman-α line ultraviolet photons form neighbouring stars or via galactic cosmic rays UV induced photons, b) by excited particles like cosmic rays and c) via thermal processing in hot molecular cores diffusing to the cold clouds [113, 258]. Following the temperatures in these regions known to be extremely low, about <50 K, where atoms and molecules accrete on to the surface of dust grains in the gas phase leading to the formation of ice mantles [259]. Accreted atoms diffuse resulting in surface reactions that form more additional interstellar ice species mainly composed of CO,

51

Chapter 2

CO2, H2O, CH4, NH3 and CH3OH and other species therein, following irradiation of the grain mantles by UV photons and cosmic rays which may change its composition [260-262].

Although the exact pathway for the formation of amino-acids in ice mantles is not yet known, there have been many theoretical and laboratory simulation studies done to ascertain the evolution of these icy organic mantles thought to give an idea about the chemical composition of the organic material of ancient carbonaceous meteorites and comets [113,

259, 263, 264]. Examples of laboratory simulations of interstellar ice analogues irradiated at low temperatures of <10 K for the production of amino-acids include the use of galactic cosmic ray particles by Holtom et al. (2005) to irradiate an ice mixture that contained CO2 and CH3NH2 to produce HOCO and CH2NH2 radicals [265]. However, recombination of the two radicals is believed to produce glycine and its isomer CH3NHCOOH [261]. Other laboratory simulations include UV-irradiation of a combination of CO:H2O:NH3 (5:5:1) at 12

K for 24 hours done by Briggs et al. (1992) to produce an organic residue, with one of the products being 0.27% glycine [266]. Another experiment was done by Bernstein et al. (2002) whereby they irradiated an initial gas mixture having water, methanol, ammonia and hydrogen cyanide (H2O:CH3OH:NH3:HCN) in molar composition of 20:2:1:1 and afterwards identified three amino-acids namely glycine, serine and alanine in racemic mixtures, using

HPLC based analysis [256]. Munoz Caro et al (2002) also irradiated a mixture of

13 13 13 H2O: CH3OH:NH3: CO: CO2 = 2:1:1:1:1 with ultraviolet photons and identified 16 amino- acids using enantioselective GC-MS analysis with six proteinogenic amino-acids contained within the 16, namely glycine, alanine, serine, aspartic, and proline [255]. High concentrations of two amino groups were also detected such as the diaminopropionic acid

(DAP) and the diaminobutyric acid (DAB) after confirmation of the analytic results by

52

Chapter 2 isotopic 13C-labeled reactants to eliminate any contamination by trace terrestrial composites

[267].

It has also been shown through quantum chemical calculations that amino-acids may be produced from the fusion of two radicals COOH and CH2NH2 formed by the respective of H2O and CH3OH and hydrogenation of HCN [258, 268]. Another theoretical modelling study predicted the formation of glycine via a radical-radical sequence in interstellar ices [269] which follow reaction pathway shown in Eqn 2.14, 2.15 and 2.16:

CO + CH2 → CH2CO (Eqn. 2.14)

CH2CO + OH → CH2COOH (Eqn. 2.15)

CH2COOH + NH3 → NH2CH2COOH (Eqn. 2.16)

Conversely, it appears that interstellar medium amino-acids have a short life span as they are highly susceptible to UV-photon destruction, even at relatively low energy UV-photons exposure [270, 271]. Complementary to this is that bound-amino-acids have been found to show a higher photo-stability against γ-rays and UV irradiation compared to the free formed amino-acids [272]. It is therefore suggested that amino-acid precursors that are formed in an interstellar ice matrix are partially protected from the destructive UV radiation, e.g., formation of amino [113, 265]. From most of the experiments performed to form amino-acids, it has been shown that; a) if elements C, O, H and N are available, amino-acids form autonomously from initial ice mixture structure, b) the number of formed molecules/100 eV in high-energy radioactive process does not depend on the type of particle such as

53

Chapter 2 electrons, alpha particles or . And lastly c) if high-molecular-weight-residues are not treated with acidic hydrolysis, they contain various precursor molecules of amino-acids, nucleic acids, biological cofactors, sugars like glycolamide, and heterocyclic and polycyclic hydrocarbons all easily detected by Curie-point pyrolysis that is coupled to GC-

MS [255, 273].

Moreover, a prerequisite for most of the radical-radical reactions described above involve the diffusion of the radicals into and /or onto ice mantles, which can only happen at temperatures

≥ 100 K [113, 258, 274]. In summary, it has been demonstrated that UV light effectively promotes photochemical processes in interstellar ice analogues that results in the production of organic molecules such as amino and di-amino-acids in the semi-refractory residue [255,

275]. Contrary to the fact that the amino-acids have a low resistance to UV photolysis, this still raises questions on whether amino-acids can be formed in interstellar ices by UV photolysis [276], therefore further detailed studies of UV light, γ-rays and energetic bombardment on interstellar ice analogues are still required to effectively comprehend the development and transformation of interstellar ices to produce amino-acids.

2.5.2 Formation of amino-acids through gas-phase reactions in the ISM

Besides formation of amino-acids through the solid-phase reactions, it is also postulated that the amino-acids can form in the ISM through specific gas-phase reactions in dark clouds through ion-molecule reactions [128, 176, 254]. Although most experimental results specify that the amino-acids formed in gas-phase will be destroyed in the typical life time of an interstellar cloud, it is also believed that the amino-acids potentially formed in this

54

Chapter 2 environment can exist as transient gas-phase species and can survive in a sufficiently low UV flux of about 300 mag of visual extinction [258, 276, 277].

The long-term electrostatic interaction between reactants in ion-molecule reactions guarantees high reaction efficiency in producing complex interstellar molecules, even at interstellar temperatures of about 10-100 K molecular environments [254, 278]. It has been shown by Blagojevic et al. (2003) that the reaction of acetic acid with ionized and protonated

+ + hydroxylamine formed by electron transfer to CO and proton transfer CH5 , correspondingly produced ionized and protonated glycine through reaction mechanisms as shown in Eqn 2.17 and 2.18[176]:

+ + NH2OH + CH3COOH → NH2CH2COOH + H2O (Eqn. 2.17)

+ + NH2OH + CH3COOH → NH2OH (CH3COOH)(Eqn. 2.18)

The same procedure was used to produce alanine, whereby propanoic acid was used in the place of acetic acid and the reaction proceeded as shown in Eqn 2.19 and 2.20 below:

+ + NH2OH + CH3COOH → NH2CH2CH2COOH + H2O (Eqn. 2.19)

+ + NH2OH + CH3COOH → NH2OH (CH3CH2COOH)(Eqn. 2.20)

It is also reported that the survival of extra-terrestrial glycine and other amino-acids may have resulted from the examination of interplanetary dust particles and of carbonaceous meteorites of asteroidean and cometary origin [176, 279, 280]. Yet synthesis of interstellar amino-acids have mostly concentrated on the formation of α-amino-acids which are crucial for life,

55

Chapter 2 carbonaceous meteorites analysis on the other hand have demonstrated to contribute a significant amount of β- and γ-amino-acids with β-alanine being the most abundant one

[279]. Experiments have also shown that dissociative recombination may produce neutral amino-acids for the above reaction.

Amino-acids may also be produced in hot molecular cores by alcohols, formic acid and amino-alcohols that have evaporated from interstellar grains via exothermic alkyl and aminoalkyl cation transfer reactions [258, 281]. Charnley et al. (2001)undertooke a study to produce protonated glycine and β-alanine by performing aminoalkyl cation transfer from aminomethanol and aminoethanol to HCOOH respectively following the reaction below in

Eqn 2.21 and 2.22[282]:

+ + NH2CH2OH2 + HCOOH → NH2CH2COOH2 + H2O (Eqn. 2.21)

+ + NH2(CH2)2OH2 + HCOOH → NH2(CH2)2COOH2 + H2O (Eqn. 2.22)

Neutral amino-acids can be formed by an electron recombination with further alkylation capable of producing various amino-acids through water molecule elimination [176, 283,

284].

Whether synthesized via solid-phase or gas-phase reactions, amino-acids, after being formed need to be resilient and be able to survive exposure to both UV and cosmic radiation in the interstellar medium. However, a laboratory study that simulates ISM conditions of both interstellar gas and grains investigated by Ehrenfreund et al. (2001) to test amino-acid’s stability against UV photolysis irradiated in frozen Ar, N2 and H2O revealed that amino-acids in gas-phase will probably be destroyed in the lifetime of a characteristic interstellar cloud

56

Chapter 2

[254, 285]. Although amino-acids may exist as transient gas-phase species in relatively low

UV radiation as mentioned above, their durability in icy grain mantles and comets and planetary surface layers is more restricted to the presence of UV radiation [254]. Their rate of demolition is therefore insensitive to the structure of the amino-acid and also to the ice matrix [259, 276, 286].

Nevertheless, more than 80 amino-acids have been detected in Murchison meteorites [287,

288]. The amino-acids found in meteorites have an excess of levo-rotatory amino-acids and also non-terrestrial isotopic ratios[256]. These isotopic enrichments observed in the meteoritic amino-acids are best explained by supposing that the precursor prebiotic molecules may have originated from the ISM [289, 290]. High deuterium enrichment of the meteoritic amino-acids is a plausible evidence that support the previous statement, whereby fractionation of deuterium is known to be efficient and elevated at very low temperatures in dense molecular clouds in grain mantles and in numerous gas-phase interstellar molecules

[256, 291]. These include amino-acid precursors like ammonia and formaldehyde, which may indicate that meteoritic amino-acids are formed in the ISM, because Murchison meteorites are known for their deuterium deficiency. These amino-acids are assumed to have been transported from the ISM to meteorites and are likely to be delivered to Earth by meteorites

(asteroids and comets) and may have played an essential role in the origin of life [254, 256,

275, 292].

Primitive meteorites may be considered as closet entities to find an answer to the question related to the origin of life [258]. The planet Earth and other planetary systems are indicated to have formed from the collapse of an interstellar dense molecule made of gas and sub- micrometre sized grains [256, 275, 293, 294]. There have been several postulated plausible

57

Chapter 2 mechanisms for the formation of amino-acids in the ISM which might help provide insight into the formation of life on Earth [284, 295, 296]. Even so, most of the mechanisms postulated still have limited knowledge in explaining the amino-acid levo-rotatory excess on

Earth (the origin of homochirality) as they lack complete clarification of the exact conditions of the primitive Earth [265, 275, 297-299].

2.5.3 The origin of homochirality in amino-acids and its role in the evolution of life

One of the most intriguing phenomena in Biology, Chemistry, and Physics is the origin of homochirality in biomolecules and its role in the evolution of life in our solar system, which remains unknown [113, 300, 301]. It is well established that homochirality of amino-acids is imperative to their functions in proteins, with the L-forms of amino-acids primarily serving as the building blocks of proteins [302-306]. About the nature’s choice for exclusive homochirality and the preference towards only the L-amino-acids (left-handed), which is found in almost all the living organism in this world, two contradicting theories can be found in the literature [298, 306, 307]. One theory explains that life was initially composed of racemates, but slowly the evolution was biased only to a specific optical isomer [308, 309]; at the same time the second theory suggests that carbonaceous chondrites which contain some

L-amino-acids in enantiomeric excess (ee), where ee = (R-S)/(R+S) and R and S are concentrations of the right and left hand molecules, might have implanted the primitive earth with the necessary amino-acids which are crucial for life [310-313].

According to the second theory, the choice of homochirality might be an inheritance from the primordial carbonaceous chondrites and such a signature chemical phenomenon which might have been transported directly to the earth[314, 315]. To support the second theory, there

58

Chapter 2 ismuch strong evidence that can be found in the literature where either the net optical rotation measurements of Murchison meteorite extracts or the measurement of enantiomeric ratio of many chiral amino-acids suggests that the nature’s choice might not be accidental at all [308,

316, 317]. At the same time the phenomenon of disparity in the enantiomeric ratio found on those carbonaceous chondrites was not able to find a tangible explanation till date, and this enigma created an open question for many researchers [297, 318-320].

Among the numerous suggestions found in many review articles, the widely accepted suggestion is the impact of circularly polarized light, commonly known as CPL, to induce the enantiomeric excess [264, 301, 321]. This enantioselective photolysis mechanism is based on variant absorption of circularly polarized light by amino-acid enantiomers that lead to the formation of ee. A number of photochemical models have been suggested which are efficient in prompting enantiomer-enrichments in chiral organic molecules [316, 322, 323]. In one particular model, it was shown that by extending circular dichroism (CD) spectroscopy to the vacuum-ultraviolet spectral range, significant circular dichroic transitions in amino-acids were observed, which confirmed that CPL is capable of inducing ee’s of alpha-methylated amino-acids found in carbonaceous meteorites having an 18.5% ee[113]. Another interesting study was done by Nahon et al. (2004) whereby they irradiated condensed C1- and N1- unit precursor molecules such as NH3, CH3OH and H2O under replicated interstellar/circumstellar conditions on solid nitrogen cooled surface at 80 K with UV-CPL. Results revealed a high percentage yield rate of up to1.34% amino-acids that were recovered [324].

Another study was performed by Bonner et al. (1977) in which he irradiated a racemic mixture of normal amino-acid with right CPL in the ultraviolet, that led a selective destruction of D-enantiomers and resulted in a mixture of a few percent L-enantiomeric

59

Chapter 2 ee’s[325]. Albeit evidence to prove the CPL may have resulted in the formation of L- enantiomers on Earth is still not that convincing as it is known that short wavelength required for absorption of amino-acids could not have penetrated the prebiotic carbon dioxide atmosphere of Earth [302, 311]. In consideration of recent findings, it has been presumed that prebiotic organic molecules including amino-acids may have first formed on interstellar dust grains in dense molecular clouds (protostellar regions of space), therefore resulting in the accretion of the grains that in turn produced several debris such as chondritic meteorites, asteroids and comets [326, 327]. These were then suggested to be the main vehicles that delivered life’s molecular seeds to primordial Earth [327].

Therefore, the one important question of the origin of the single-handedness of biological molecules that are either molecular or macromolecular is still a property of all living organism and seems to be a pre-requisite to life [28]. Even though several viable models have been invoked that are both chemical and physical for the amplification of enantiomeric excess, there is still yet a need to weave salient aspects to validate how the complexity in organic molecules like amino-acids are necessary for the development of life that might have arisen in chemical reactions under plausible prebiotic conditions that elucidate accurately the chain of proceedings that led to life on Earth today [328, 329].

A thermodynamically feasible mechanism for the formation and study of the simplest of all amino-acids, glycine (NH2CH2COOH), in which higher homologues can be derived from it by substituting an organic group in the place of one hydrogen of the methylene group may assist to elucidate and provide evidence for the origin of biological homochirality and the formation of life on Earth [265, 330].

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2.5.4 General description of Glycine (NH2CH2COOH)

Glycine is one of the simplest 20 amino-acids (building blocks of all biological systems), commonly found as basic units for proteins consisting of codons GGU, GGC, GGA, GGG, of the genetic code which are key elements of life [331-334]. Although uncertain, denoting that it can be inside or outside of the molecule, generally it can exist either as a completely neutral molecule or predominantly zwitterion form in aqueous solution or at near neutral pH

[335-338]. In ambient conditions there exists a dynamic equilibrium between the two. The pKas of the two ionizable groups, the amino group and the carboxylic acid group, are the central determining factors of the isoelectric point or isoelectric pH of glycine which has a hydrogen substituent as its side chain [338-341].

Glycine is considered to be unique among the proteinogenic amino-acids which can fit in both hydrophilic and hydrophobic environments, and at the same time achiral in nature [342-

344]. The discovery of glycine was first observed in 1820 by Henri Braconnot, who first isolated it from gelatine; he boiled a gelatinous object with sulphuric acid [345]. Most of the glycine is produced by Strecker’s amino-acid synthesis [275, 346].

2.5.4.1 Conformers of Glycine

It is important to understand gas-phase properties of complex structures like amino-acids as many biological phenomena can be traced to have origin in those molecular properties [347].

Therefore understanding the electronic charge redistribution in the outer valence orbitals during structural and conformational manipulations is another important property to help understand the true structure of glycine [348-350]. The chemical point of view associated with the conformational flexibility in producing many local minimum structures on the 61

Chapter 2

torsional potential-energy surfaces of the amino-acids, (e.g., NH2CH2COOH) is due to the saturated chemical backbone [351-353].

The diversity of conformational structures of amino-acids is an important factor that assists to determine the three-dimensional structure of proteins whereby their dynamics can be controlled [347]. Large energy barriers associated with these amino-acids imply that they generally exist as single conformers, whilst very small energy barriers make conformer isolation a huge challenge. Glycine though the simplest amino-acids, it’s dynamic conformational behaviour has brought many difficulties to experimental and theoretical investigations [347, 354].

Quantum mechanical calculations performed by Csaszar (1992) confirmed that glycine has

13 neutral glycine conformers which includes 8 possible conformers with planar heavy-atom arrangements with only a few of these observed experimentally due to their thermal variability [355]. Glycine has 3 internal rotational degrees of freedom (Φ, Ψ and θ associated with C-N, C-C and C-O respectively [356]. In its neutral state, glycine has Cs symmetry consisting of 8 rotational isomers. Different intramolecular H-bonds of varying strengths are also present that form and assist in stabilizing a particular form of conformer [357-360].

Also present are N and O lone pairs in some planar forms that causes repulsion and steric strain with a destabilizing effect that is usually reduced by small torsional changes. This effect may cause some of the planar forms to correspond to saddle points rather than the local energy minima on the potential energy surface of glycine which cause the C1 symmetry to be also considered in the study of glycine conformers. Minor changes in the entire energy of the system are expected to be produced due to these conformational changes that are caused by the balance between the steric and H-bond effects [355, 361, 362].

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2.5.4.1.1 The most stable conformers of Glycine (NH2CH2COOH)

From extensive theoretical analysis of glycine it has been revealed that most of the glycine isomers have relative energies of less than 1000 cm-1. The results indicate that the non-planar structures are more stable for some low-energy isomers than the planar forms [355].

However, results obtained from high level ab-initio calculations have predicted that five glycine conformers exist within 10 kJ/mol of global potential minimum [347, 359] has presented in Figure 2.3.

Conversely, using both ab initio and DFT methods, the conformational processes of glycine in space done by Nguyen et al. (1997) and Herrera et al. (2004) established that both

B3LYP/6-11G** and MP2/6-311G** models described conformational energies together with geometrical parameters and vertical ionization quite accurately in comparison to photoelectron spectroscopy (PES), which is an experimental method [363, 364]. The two levels of theory predicted that the five lowest conformers of glycine having either the Cs and

C1 symmetry and lie within 6kcal/mol of the global minimum compared to the least stable of the glycine [347].

Several theoretical calculations done that include sophisticated calculations and the use of large basis sets and configuration-interaction (CI), Møller-Plesset (MP) perturbation theory or density-functional (DFT) comprising the Hatree-Fock (HF) exchange theory have generally revealed that conformer I is the lowest energy conformer, making it the most stable and most populated of the five conformers having a Cs symmetry geometry [347]. Conformer II on the hand, depending on the level of theory employed, may exhibit a symmetry plane, though inclusion of larger basis sets (with inclusion of polarization and diffuse functions) and

63

Chapter 2 electron correlation results in the strengthening of hydrogen-bonding interactions that distort the minimized geometry [365, 366]. The heavy atoms found in conformer III-V are non- planar and it is also evident that each glycine structure that possesses C1 symmetry displays a mirror-image structure with inverted angles of equivalent energy [347, 356].

Figure 2. 3: Most stable conformers structures of glycine optimized by MP2/6-311++G**

level of theory. Torsional angles Φ = (Φ1,Φ2,Φ3) indicate coordinates of twisting

motion about the C-C bond (Φ1), C-O single bond (Φ2), and C-N bond (Φ3). (a)

conformers reported to have been observed experimentally. [Credit : Csaszar

(1992) and Miller et al. (2004)[355] ].

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2.5.4.2 Plausible formation Processes of Glycine (NH2CH2COOH) in the ISM

Glycine is the single pre-biotic molecule claimed to be observed in the interstellar medium

(ISM) [367]. Even though its detection in the ISM is not unambiguous to date [128, 281, 368,

369], but considering available precursor molecules/fragments in the ISM, formation and detection of this molecule cannot be completely ruled out; and is the main driving force of researchers in this field. First spectrum of glycine was established in a laboratory experiment by Brown et al. (1978), in which in subsistent years they also tried to search for it in galactic molecular clouds with their findings still remaining inconclusive compelling many researchers to devote their time in understanding the origin and distribution of amino-acids in extraterrestrial space [150, 370]. Nonetheless, the controversy is still prevalent on whether amino-acid, glycine (NH2CH2COOH) is really detected in the ISM.

However, several formation mechanisms have been postulated for the formation of glycine in extraterrestrial environments, these include neutral-neutral as well as radical-radical and radical-molecules pathways [367]. Woon (2002) considered the reaction between HCN and

CH2NH2 for the radical-radical and radical-molecular pathways for formation of glycine on

UV irradiated ices. He proposed that CH2NH2 is formed through sequential hydrogenation of

HCN and COOH, whereby COOH originates from the results from the reaction between CO and OH with a rate coefficient of 1.13 x 10-17 cm3 s-1, with OH produced primarily from OH hydrolysis. The COOH is said to recombine with CH2NH2 to form interstellar glycine at a rate coefficient 1.82 x 10-19 cm3 s-1[371]. Blagojevic et al. (2003) studied gas-ion-molecule reactions of the interstellar medium [176]. He proved that glycine can be formed from the reactions of acetic acid with ionized and protonated hydroxylamine. He also stated that that since glycine has a high proton affinity; it can therefore be suggested that neutral glycine

65

Chapter 2 could be formed from the dissociation recombination and electron transfer reaction. He also proved that the dissociation recombination channel is the most favoured one [176, 261, 265].

Glycine is also reported to be formed in the ice mixtures through the UV photo processing of water (H2O), methane (CH4), ammonia (NH3), and carbon monoxide (CO). Radical-radical reactions are said to be generated by UV photons ranging from 4 to 13 eV that generate

. . radicals such as methyl (H3C ), hydroxyl ( OH) and amino (NH2) species., with no entrance barrier essentially [265]. Detectable quantities of amino-acids have also been produced from the irradiation of a mixture of water (H2O), methanol (CH3OH), ammonia (NH3), carbon

15 -1 monoxide (CO), carbon dioxide (CO2), with a photon flux of 1.5 x 10 s for 24 hours. It was concluded that the abundance of glycine in these products revealed that glycine can be produced in one out of the 30 000 photons.

The Streckertype synthesis is also another reaction that was postulated which involves a reaction in liquid water between, hydrogen cyanide (HCN), ammonia (NH3), and an aldehyde

(RCHO) [275, 372, 373]. Other potential mechanisms have been tried both experimentally and theoretically and these include the recombination of carboxylic radical (COOH) with

CH2NH2 and methylamine (CH3NH2) being the most obvious source for CH2CH2 detected in the ISM [258, 367, 374]. A quantum chemical study was performed by Largo and co-

+ workers, where they used acetic acid (CH3COOH) and the ammonium ion (NH4 ) in their chemical mechanism to produce glycine [375]. Another theoretical study was done by

Barrientos et al. (2012) for the formation of glycine in the ISM through the reaction of acetic acid (CH3COOH) with hydroxylamine (NH2OH) [376].

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Though a lot of the precursors have been detected in the ISM that leads to the formation of glycine, with some precursor reaction pathways tried both experimentally and theoretically, it is stated that their reaction efficiency in the ISM is mostly dependent on the abundance and survival in the presence of a field reaction [254, 377-379]. Therefore, this confirms that some reaction pathways maybe highly more favoured than others in the gas phase and solid phase

[378]. The problem about almost all these potential mechanisms is the inconsistencies between the expected products and the amino-acids detected in the meteoritic compounds

[254, 275, 279]. Thus, it is still necessary for researchers in this field to propose new reaction mechanisms that can take place at extremely low temperatures and very low densities.

2.5.4.3 Detectability of Glycine (NH2CH2COOH) in the ISM

Astronomical detection of glycine in the interstellar medium is still unclear and the reason is due the large partition function of glycine that results in the analysis of a large cluster of weak lines, which makes it hard to detect in warm, dense cloud cores [281]. Moreover, a cluster of other weak lines coming from other available molecules in the same region can also interfere with the spectrum of glycine. Such interference is believed to be the root cause of the confusion as to whether glycine is actually detected in the ISM [281, 380].

While the findings for the spectrum of glycine for the first time in the laboratory by Brown et al. (1978), Brown et al. (1979) and Brown et al (1988) were not conclusive [150, 370, 381], it has not stopped researchers in the field to continue in their pursuit to understand the origin and distribution of amino-acids in extra-terrestrial space, despite the controversy still prevalent for glycine. Kuan et al. (2003)analyzed 27 lines of glycine in 19 different spectral bands with column densities of about 1014 cm-1 and they were able to put forward some

67

Chapter 2 evidence that neutral glycine might exist in three hot molecular cores; Sgr B2 (N-LMH),

Orion KL, and W51 el/e2. They also estimated the relative abundance of glycine to hydrogen to be around 2.1 x 10-1 for Sgr B2, 1.5 x 10-9 for Orion and 2.1 x 10-1 for W51. Their detection reports were supported with rotational diagrams for all the three sources [281].

Nevertheless, new laboratory measurements and straightforward analysis techniques were used by Snyder et al. (2005) for a glycine rotor to identify glycine in the ISM [380]. In their study they used laboratory measurements of glycine as a basis for the analysis technique to their 12 m telescope data and Swedish-ESO Submillimetre Telescope [SEST] data that was previously published, of Numemelin and colleagues. The researchers concluded that the necessary crucial lines to detect glycine in the ISM have not yet been found. Some common molecular candidates were identified that they suggested to be examined further as they thought they could be likely carriers of several lines that could be reported as glycine. This is because glycine exists in a variety of conformations which give rise to relative weak lines which are difficult to detect in dense, warm molecular clouds, even when using present day observational tools. The confusion was also confirmed to be caused by the contamination of spectra due to weak lines coming from large number of species present in the ISM that give rise to unambiguous detection of glycine. Additionally, these researchers mentioned that the rotational temperature diagrams used in Kuan et al. (2003) detection reports were used without the support of correct spectroscopic assignments and are consequently not a reliable tool for the identification of interstellar molecules [281, 380].

Likewise, Friedel et al. (2005) in their study for the detection of interstellar in the

Orion-KL hot core mention that due to the detection of 54 transitions of interstellar (CH3)2CO toward the Orion hot core, it is most likely that the transitions ascribed to glycine by Kuan et

68

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al. could be due to (CH3)2CO [281, 382]. Hence the search for glycine in the ISM, though unambiguous and inconclusive, is still an on-going research.

Massive protostars are reported to be favourable sites for the formation and survival of complex molecules as they are well-known to harbour these molecules [383]. Nonetheless, less luminous solar type protostars have been stated to plausibly harbour these complex molecules more favourably than the former [156]. A search was done by Ceccarelli et al.

(2000) on solar type , IRAS 16293-2433 to see if it emitted an emission line of glycine. Even though the researchers did not detect any emission associated with glycine from this solar type protostar, based on their observation, they claimed that glycine column density was less than ~ 5 x 10-12. The researchers were also able to derive the upper limit to the glycine abundance when basing their observations on the structure of the envelope surrounding this solar type protostar. They assigned the upper limit to glycine abundance to be ~ 1 x 10-10 in cold outer envelope and ~ 7 x 10-9 in hot core, respectively, which challenged some theoretical estimates glycine abundance in solar type protostars which were recently found [384].

Cometary samples returned to Earth by NASA’s Stardust spacecraft revealed various amines and amino-acids with their origin not absolutely verified [385]. Nonetheless, comets are alleged to contain interstellar material that has been mildly to greatly processed in the solar nebular [128]. The two most abundant amino-acids identified in the cometary Stardust- returned foil samples were the stable carbon isotopic ratios of glycine and ε-amino-n-caproic acid [EACA]. These two were identified by measuring with gas chromatography-mass spectrometry coupled with isotope ratio mass spectrometry. The ϛ13 values of glycine and

EACA are +29± 6‰ and -25± 2‰ respectively, the glycine value strongly suggested an

69

Chapter 2 extraterrestrial origin while the EACA value showed a terrestrial Nylon-6 contamination during curation [385].

Many other researchers have pursued the search for glycine in the ISM [254, 256, 275, 285,

371, 386] which has still remained to be a controversial issue due to the limitation of spectral lines as in indicated by Snyder et al. (2005)[380] with Ehrenfreund et al. (2001a) suggesting that glycine detection is still not firmly verified due to the lack of insufficient sensitive spectroscopic detection methods [285]. However, the possible existence of glycine in the ISM is still of specific interest because it can assist in the role of prebiotic organic inventory from which life developed, as it is the well-known simplest amino-acid that is pervasive in biochemistry [386].

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373. Keyhani, A. and V.A. Yaylayan, Elucidation of the mechanism of pyrazinone

formation in glycine model systems using labeled sugars and amino acids. Journal of

Agricultural and Food Chemistry, 1996. 44(9): p. 2511-2516.

374. Liebster, J. and J. Kopoldova, The Radication Chemistry of Amino Acids. Advances in

Radiation Biology, 2013. 1: p. 157.

375. Largo, L., et al., The reaction between NH3+ and CH3COOH: a possible process for

the formation of glycine precursors in the interstellar medium. Astronomy &

Astrophysics, 2010. 516: p. A79.

376. Barrientos, C., et al., Gas-phase synthesis of precursors of interstellar glycine: A

computational study of the reactions of acetic acid with hydroxylamine and its ionized

and protonated derivatives. The Astrophysical Journal, 2012. 748(2): p. 99.

377. Largo, A., P. Redondo, and C. Barrientos, Theoretical study of possible ion‐molecule

reactions leading to precursors of glycine in the interstellar medium. International

journal of quantum chemistry, 2004. 98(4): p. 355-360.

378. Singh, A., A. Misra, and P. Tandon, Quantum chemical analysis for the formation of

glycine in the interstellar medium. Research in Astronomy and Astrophysics, 2013.

13(8): p. 912.

379. Redondo, P., A. Largo, and C. Barrientos, Is the reaction between formic acid and

protonated aminomethanol a possible source of glycine precursors in the interstellar

medium? Astronomy & Astrophysics, 2015. 579: p. A125.

380. Snyder, L.E., et al., A rigorous attempt to verify interstellar glycine. The

Astrophysical Journal, 2005. 619(2): p. 914.

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381. Brown, R.D., et al., A search for interstellar glycine. Monthly Notices of the Royal

Astronomical Society, 1979. 186(1): p. 5P-8P.

382. Friedel, D., et al., Detection of interstellar acetone toward the Orion-KL hot core. The

Astrophysical Journal Letters, 2005. 632(2): p. L95.

383. Largo, L., et al., Gas-Phase Reaction of NH2+ with Acetic Acid: Implications in

Astrochemistry. Journal of chemical theory and computation, 2008. 4(12): p. 2085-

2093.

384. Ceccarelli, C., et al., Search for glycine in the solar type protostar IRAS 16293-2422.

Astronomy and Astrophysics, 2000. 362: p. 1122-1126.

385. Elsila, J.E., D.P. Glavin, and J.P. Dworkin, Cometary glycine detected in samples

returned by Stardust. Meteoritics & Planetary Science, 2009. 44(9): p. 1323-1330.

386. Crovisier, J., The molecular complexity of comets, in Astrobiology: Future

Perspectives. 2004, Springer. p. 179-203.

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Chapter 3

CHAPTER 3

THEORETICAL METHODOLOGY

3.1 Basic principles of theory used

It is well established that the Schrödinger equation is the foundation of theoretical chemistry.

Thus, to decipher the Schrödinger equation for a molecule is an intricate issue [1]. A molecule with N variables has many degrees of freedom involved. The general strategies are based on the standard nuclei and n electrons, we have 3(N + n) degrees of freedoms to divide and conquer! This can be resolved separately by dividing the large problem into several smaller problems. This universal melody is reiterated many times throughout quantum chemistry [1, 2]. Errors are usually introduced by dividing the system, as it will be revealed, which can be successively amended after the minor, simpler problems are dealt with. The essential steps in resolving the molecular problem can be summarized as follows:

3.1.1 The Born-Oppenheimer approximation

The Born-Oppenheimer approximation [3] separates the nuclear problem from the electronic problem. This approximation was shown by Born-Oppenheimer in 1927 that the nuclei in a molecule with respect to the electrons are fixed [4]. This can be assumed to be a qualitative expression of the principle, thus mathematically; as stated by the approximation, the

Schrödinger equation for a molecule may be divided into an electronic and nuclear equation

[3, 5]. In simply terms the nuclei and electrons are not independent, they are uncorrelated.

This is sensible since the nucleus is much denser than the electron (approximately 1900 times more), hence its movements when compared to the electrons is trivial. In this situation, the

110

Chapter 3 nucleus can be considered to be frozen with its set to zero thus only contributing to the potential energy of the system [3].

3.1.1.1 Independent electron approximation

This approximation separates one n-electron problem into n single-electron problems, and does not consider electron-electron interaction in a molecule. Due to a number of reasons it is quite a challenge to treat electron-electron interactions in comparison to ion-electron interaction [6]. For an example, (1) the potential due to ion-electron interactions is not periodic, also (2) considering all electron dynamics at once is a challenge since (3) we are not aware of the positions of the electrons (wavefunctions). However, single electron approach is not reasonable and results in the omission of electron correlation and to fulfil the Pauli

Exclusion Principle (‘no two electrons can occupy the same state’), and hence the wavefunctions are modelled as stated Slater determinants [7, 8].

3.1.2 The Slater determinants

The Slater determinants of single electron wavefunctions named spin orbitals each having a single electron [6]. To satisfy the quantum-mechanical generalisation of the Pauli’s Exclusion

Principle, the spin orbital comprises a spatial part, known as the molecular orbital (MO) and with a spin (up/down or ↿/⇂). When particular (spin) orbitals are occupied by electrons leaving others empty, this is called the electron configuration [9, 10]. A single Slater determinant signifies one electron configuration, i.e. the Slater determinant is the same as the electron configuration.

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3.1.3 Variational principle

The variational principle asserts that the estimated wavefunction that affords a solution closest to the precise one is that for which the quantum mechanical energy is a minimum [11, 12]. The procedure to attain the estimated solutions to the Schrödinger equation is to employ the energy minimization path (with the help of various minimization mathematical procedures). Through enhanced wavefunction, the above stated minimum energy will be systematically approached. The combination of the variational principle with the Slater determinant wavefunction results in the Hartree-Fock equations [7].

3.2 Hartree-Fock Theory

The Hartree-Fock theory is essentially an electronic structure theory. It can also be described as the field theory whereby every electron has its own individual wavefunction (orbital) that conforms to a tangible 1-electron Schrödinger equation [13]. This means that an individual electron’s motion is defined by a single-particle wavefunction (orbital) that is not explicitly dependent on the rapid movements of other electrons but is only dependent on an average field created by all electrons. These orbitals are result of mathematical approximations with relatively high accuracy, whereas only for hydrogen atom or He+, one-electron wavefuntions have exact eigenfunctions of the full electronic Hamiltonian [11]. This effective Hamiltonian

(Fock-operator) is the one that encompasses the average field (Coulomb and exchange) of the overall electrons in the system, indicating that the electron-electron repulsion is preserved in a mean field way. Therefore the overall electronic wavefunction for the molecule is a product of the orbitals, and this simply ignores the complications that are brought by the Pauli’s

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Exclusion Principle [14], i.e. the density for a given electron is not dependent on the positions of all other electrons, and hence electron motions are more intimately correlated.

As a result, the Hartree-Fock theory is usually a good starting point for multi-body perturbation theory and single-reference configuration interactions which are examples of more intricate theoretical methods that are improved electronic Schrödinger equation approximations [15, 16]. Molecular orbitals (MOs) are constructed as a linear combination of atomic orbitals (AOs) known as the MO-LCAO, with adjustable coefficients [2, 17].

Therefore, to finally solve the Hartree-Fock equation two methods can be used depending on the situation encountered. For a system that contains an even number of electrons with all of them paired, the system is solved by using the RHF formalism (Restricted HartreeFock) [18], while for a system having an odd number of electrons or even number but with electrons unpaired, then the UHF formalism (Unrestricted HartreeFock) is applied [16]. The variation

(minimization) of the energy with the coefficients leads to the Roothan-Hall equation in the first case, RHF [19-21]. Whereas in the second case, the equation is resolved using the

Berthier-Pople-Nesbert equation [22].

3.2.1 Self-Consistent Field (SCF)

Iterative approaches can be used to get the solutions to the Hartree-Fock (Roothan-Hall and

Pople-Nesbert) equations. A preliminary guess of the LCAO coefficients is achieved and either the Hartree-Fock (Roothan-Hall or Pople-Nesbert) equations are solved giving a new set of coefficients, which are substituted back into the equations, repeating the cycle until self-consistency is reached [11, 23]. Self-consistency is attained when the coefficients do not change, meaning that the energy is no longer reducing. The SCF procedure produces the

113

Chapter 3 optimal LCAO coefficients, which are then utilised to create the MOs. Electrons occupy MOs

(two by two with opposed spins) which are plugged into the Slater determinant, therefore by the postulates of the quantum mechanics, the Slater determinant is the wavefunction which has the entire information about the system [11, 24].

Yes

Figure 3. 1: Schematic diagram that explains the Self-Consistent Field method.

3.3 Post-Hartree-Fock (Correlation) Methods

Hartree-Fock (synonymous with the SCF) calculations can be employed as an initial point for higher-level methods. However, one key challenge in the Hartree-Fock method is that it totally disregards electron correlations with the same spin (beyond exchange) [2]. Even though the electron correlation energy is a trivial fraction to the overall energy, it still crucially contributes to numerous physical and chemical systems of interest.

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Post-Hartree-Fock methods aim to improve the Hartree-Fock method by correcting for the neglect of electron correlation by always considering it in their calculations; hence they are called correlated methods [25, 26]. Examples of correlated methods include configuration interaction (CI), multi-configurational SCF (MCSCF) usually applied as complete space SCF

(CASSCF), Møller-Plesset perturbation theory (MPn) and coupled cluster theory (CC).

Electron correlation in the Møller-Plesset perturbation theory is treated in a perturbative way, while in the coupled cluster method it is controlled by using the cluster operator [25]. Both the CI and MCSCF or CASSCF methods were not used in this research, and will not be further discussed. However, the Møller-Plesset perturbation theory, coupled cluster and composite quantum chemistry methods will be explained concisely.

3.3.1 Møller-Plesset(MPn) Perturbation Theory (MPPT)

This is a non-variational method in which the principle of perturbation is generally started from a plain model that has been solved precisely or approximately [27]. Small

“perturbations” are progressively added to the model that may result to the calculated energy of the system to be lower than the ground state energy [28]. The MPPT uses the nth order perturbation theory (n=2 and higher) to accurately determine electron correlation, hence computational cost increases strongly with each successive order [29, 30]. Therefore, at infinite order the energy should be equal to the accurate solution of the Schrödinger equation

(for a given basis set-still to be discussed).

Generally, MP2 is recommended as it is not too slow, but has shown improvements over the

Hartree-Fock in various respects in electronic structure calculations [31]. One instance is that the MP2 can capture the weak non-covalent while Hartree-Fock fails dismally to

115

Chapter 3 do that [32, 33]. However, Møller-Plesset perturbation theory also has its own shortfalls; there is no guarantee that the series is actually convergent [34], e.g. it is not suitable for strictly metallic systems and for certain molecular properties like spectroscopic constants that are not necessarily converged at higher orders [35]. This means that MP4, MP5 or MP25 do not necessarily provide improved results over MP2. Hence, MP2 is extensively used in molecular system in electronic structure calculations as it is a useful and powerful method due to its accuracy and scaling (N5) [36, 37].

3.3.2 Coupled Cluster (CC) method

The CC method was invented by Coester and Kummel and was later introduced in 1960 into quantum chemistry by Cizek and Paldus [38]. This method appeared as possibly the greatest efficient yet computationally reasonable method for approximate solution of the electronic

Schrödinger equation and for predicting molecular properties [39-42]. It is a non-variational method that uses an exponential operator in constructing the expansion of determinants that result to accurate and compact wavefunction expansions that produce accurate electronic energies [43].

It is well established that precise description of atoms and molecules involve a very precise assimilation of the utmost crucial effects of electron correlations, in which quantum chemists target to calculate correlation energies to the precision of one milli-Hartree (1mH) [44]. The

CC method is believed to be at a computational stage of meeting this purpose more intricate polyatomic molecules, and for an extensive variety of properties and phenomena of chemical importance which therefore makes it progressively the first best method for a variety of problems associated with molecular structure and molecular spectra [45].

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CC method use variants that are the simplest implementation of this method which are coupled cluster double (CCD) approximation that includes the total bi-excited clusters with respect to specific a antisymmetric Slater determinant (single-reference) state [46]. Mono- excited clusters similarly vanish only once the reference state is an anti-symmetrized produce of alleged maximum overlap orbitals; or else their assimilation along with the bi-excited clusters is achieved by the coupled cluster singles and doubles (CCSD) approximation, a common variant[45]. A complete coupled cluster singles, doubles and triplet (CCSD(T)) result was first reported by Noga and Bartlett [47] by comparing the CC method and configuration-interaction (CI) wavefunctions of the molecular system BH3 molecule by making use of a small basis set. Their study was based on the fact that tri-excited clusters contributed to a larger extent to the energy, and the authors were therefore able to demonstrate the most pivotal contributions came from (linked) triple excitations which could not be decomposed into (disconnected) single or double excitation constituents. Using the

CCSD(T) method with large basis sets can generally provide highly accurate results; thermochemistry within a chemical precision of about 1 kcal/mol can often be achieved [48].

3.3.3 Composite Quantum Chemistry Methods

These are methods that combine results of several calculations for high-accuracy thermochemical calculations. The main aim of these calculations is to approximate the energy at a high level of theory and large basis sets by executing many smaller calculations. They do this by combining methods with a high level of theory and a smaller basis set together with methods that use a lower level of theory with larger basis sets [49, 50]. The main purpose of

117

Chapter 3 composite methods is to achieve chemical precision which is frequently within 1 kcal/mol of the experimental value [51].

One example of the composite method is the Guassian-2 (G2) theory which involves an order of distinct ab initio molecular orbital calculations aimed at getting the total energy of a particular molecular species [52]. In this method, second-order Møller-Plesset perturbation theory is used to determine geometries with correlation level calculations performed by using both the Møller-Plesset perturbation theory up to the fourth order and quadratic configuration interaction [53, 54]. Correlation calculations also include large basis sets that comprise various sets of polarization functions; therefore a series of additivity approximations makes this technique justifiably extensively applicable [55].

Composite methods are thus commonly used to calculate enthalpies of formation, ionization potential, electron affinities and proton affinities [55, 56]. The Gaussian-n of the composite methods include Gaussian-1 (G1) presented by John Pople, which was the first systematic model chemistry, Gaussian-2 (G2), the second, Gaussian-3 (G3) and Gaussian-4 (G4) [49].

3.4 Density Functional Theory (DFT)

DFT was introduced to avoid the wavefunction (known to be intricate, elusive and not observable experimentally), hence making it much better to work with the real and physically observable electron density [57]. Nevertheless, in order to create the electron density, DFT requires the wavefunction and basis sets. The calculation is therefore accomplished via an

SCF technique comparable to the HF method, however, the Hamiltonian is not the same since it includes for electron correlation [58].

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3.4.1 Description of Equations of Elements of Theory used in this thesis

Two basic theories which are for most of the methodologies, viz, Hartree-Fock theory and the density functional theories are founded on the solution of the Schrödinger equation:

ĤѰ = EѰ (Eqn. 3.1)

3.4.1.1 Schrödinger Equation and Born-Oppenheimer approximation

In the year 1930, Schrödinger presented a non-relativistic wave equation which ruled the motion of nuclei and electrons in molecules in the time-independent form. It is shown in Eqn. 3.1 where Ĥ is the Hamiltonian operator and  is the wave function of a particular state. E is the total energy of this state. Writing out all the terms in atomic units, the

Hamiltonian looks like,

N M N M N N M M 1 2 1 2 ZA 1 ZAZB Ĥ = − ∑ ∇i − ∑ ∇A − ∑ ∑ + ∑ ∑ + ∑ ∑ (Eqn. 3.2) 2 2MA riA rij RAB I=1 A=1 i=A A=1 i=1 j>푖 A=1 B>퐴

The first two terms in Eqn. 3.2 are the kinetic energy of the N electrons and the M nuclei, respectively. MA is the ratio of the mass of nucleus A to the mass of an electron. The

Coulomb attraction between the electrons and the nuclei is denoted by term three, and the fourth and fifth terms define the repulsion between electrons and between nuclei, respectively. Thus, Eqn. 3.1 with the Hamiltonian in Eqn. 3.2 will produce a set of coupled

119

Chapter 3 differential equations. To be able to solve these equations, it is essential to make approximations both for the Hamiltonian and the wave function.

Since the mass of the nuclei is much greater than the mass of the electrons, the nuclei move much slower than the electrons. Hence, the second and the last term can be neglected. This is called the Born-Oppenheimer approximation. The remaining terms are called the electronic

Hamiltonian, describing the motion of N electrons in the field of M point charges,

N N M N N 1 2 ZA 1 퐻푒푙 = − ∑ ∇i − ∑ ∑ + ∑ ∑ (Eqn. 3.3) 2 riA rij I=1 i=A A=1 i=1 j>푖

Hartree-Fock or Density functional methods can be used to solve Eqn. 3.1 within the Born-

Oppenheimer approximation.

3.4.1.2 The Hartree-Fock Approximation

A many particle wave function describing electrons is required to follow Pauli principle, i.e., no electrons in the same system are permissible to have the same set of quantum numbers, or the wave function needs to be antisymmetric. One such wave function is the Slater determinant,

푥1(x1) 푥2(x1) … 푥N(x1) 1 푥1(x2)푥2(x2) …푥N(x2) Ѱ(x1, x2, … , xN) = × | | (Eqn.3.4) √N! ⋮ ⋮ ⋮ 푥1(xN)푥2(xN) …푥N(xN)

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Chapter 3

describing N electrons occupying N spin orbitals (1, 2,…… N). A spin orbital is a product

of a spatial orbital,  i r  , and one of the two orthonormal functions  and describing spin

up and spin down, respectively. The factor 1/N! is the normalization constant and xi indicates both spatial and spin coordinates. The overall energy of the system can be expressed

(variation method) as,

E = ⟨Ѱ|Hel|Ѱ⟩ (Eqn. 3.5)

By changing the spatial part of the Slater determinant, i.e., the molecular orbitals, can influence the overall energy. The value of the energy that is obtained is an upper bound of the exact solution according to the variational principle. This is known as the Hartree-Fock approximation. The solution is an approximation due to the fact that the Coulomb interaction between electrons cannot be separated. Thus, the exact solution cannot be a product of one- particle wave functions. The Hartree-Fock approximation was made more practical for numerical solutions by Roothaan in 1951 who introduced the concept of basis sets. The molecular orbitals are represented as a linear combination of prescribed three-dimensional

one-electron functions j ,

K

Ѱa = ∑ Cajɸj (Eqn. 3.6) j=1

where K is an integer larger than the number of electrons in the system. This results in a set of algebraic equations (see Eqn. 3.13 in the later page), where the coefficients caj are varied to minimize the energy. In the minimization of Eqn. 3.5 the constraint that the spin orbitals

121

Chapter 3 remain orthonormal needs to be kept. Therefore, the Lagrangian, L, with this constrain included is studied,

ℒ = ⟨Ѱ|Hel|Ѱ⟩ − ∑ εa,b(⟨xa|xb⟩ − δa,b) (Eqn. 3.7) a,b

where ,ba are Lagrange multipliers. The minimization of Eqn. 3.7 yields the condition,

ƒ(푖)|푥푎⟩ = ∑ 휀푎,푏|푥푏⟩ (Eqn. 3.8) 푏=1

where f (i) is the Fock operator for an arbitrary electron i,

푀 푁 1 2 푍퐴 ƒ(푖) = − ∇푖 − ∑ + ∑ ℐ푏(푖) − Ƙ푏(푖) (Eqn. 3.9) 2 푟푖퐴 퐴=1 푏=1

ℐb(i) is the Coulomb operator describing the Coulomb interaction acting on an electron in

spin orbital  a due to one of the other N-1 electrons in the system. The exchange operator,

 b i  has no classical interpretation. By a unitary transformation, Eqn. 3.8 can be written in a diagonal form,

ƒ(i)|푥a⟩ = εa|푥a⟩ (Eqn. 3.10)

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Chapter 3

This is known as the Hartee-Fock equation.  a is interpreted as the orbital energy of  a .

Hence, the task is to find spin orbitals that are eigenfunctions of the Fock operator.

Introduction of a basis set, i.e., Eqn. 3.6 yields,

퐾 퐾

ƒ(푖) ∑ 퐶푎푗|ɸ푗⟩ = 휀푎 ∑ 퐶푎푗|ɸ푗⟩ (Eqn. 3.11) 푗=1 푗=1

and multiplication with a results in

K K

∑ Caj⟨ɸa|ƒ(i)|ɸj⟩ = εa ∑ Caj⟨ɸa|ɸj⟩ (Eqn. 3.12) j=1 j=1

where there are K such equations, a = 1, 2, ….K. Writing these in a matrix equation yields the

Roothaan equation

퐹퐶 = 푆퐶퐸 (Eqn. 3.13)

where,

Faj = ⟨ɸa|f(i)|ɸj⟩ (Eqn. 3.14)

Sa = ⟨ɸa|ɸj⟩ (Eqn. 3.15)

Eaj = εaδaj (Eqn. 3.16)

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Chapter 3

By using a starting estimate of the wave function, C, Eqn. 3.13 can be solved iteratively, a so called Self Consistent Field (SCF) procedure. For each iteration, the factor of normalization of the new wave function is compared to the previous one, and at a chosen precision the iteration is stopped.

3.4.1.3 Density Functional Theory

In the Hartree-Fock approximation the Slater determinant is introduced and used to define the wave functions for the system that is under consideration. Knowing the wave functions, it is possible to determine the property of interest. Another approach is to consider the electron density,n , defined by,

2 n(r) = N ∫ … ∫ |Ѱ(x1, x2, … , xN)| ds1dx2 … dxN (Eqn. 3.17)

where  (x1, x2,…. XN) is the ground states of many particle wave functions describing the

N electrons. The ground state density, rn  , is the density which minimizes the energy functional E [rn  ]. It is possible to show that the total energy, , can be expressed as the functional of ,

E[n(r)] = T[n(r)] + V[n(r)] + U[n(r)] (Eqn. 3.17)

where T represent the kinetic energy of the system,V an external potential and U the electron-electron interaction. If the explicit form of [ ] was known, it would be

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Chapter 3 possible to minimize it with respect to the density. However, this is not the case and an approximate approach is needed.

If the many particle kinetic operator,T , is replaced by the known single particle kinetic operator and the true electron-electron interaction is replaced by the Coulomb repulsion, E can be written as

1 n(r)n(r′) E[n(r)] = T [n(r)] + ∫ n(r)v(r)d3 r + ∬ d3rd3r′ + E [n(r)] (Eqn. 3.19) sp 2 |r − r′| xc

where rv  is an external potential, e.g., a Coulomb potential that originates from atom cores

in a molecule. E XC [rn  ] is defined by,

1 n(r)n(r′) E[n(r)] = T[n(r)] + U[n(r)] − 푇 [n(r) − ∬ d3rd3r′ (Eqn. 3.20) 푠푝 2 |r − r′|

The three first terms in Eqn. 3.19 are possible to calculate numerically. The remaining problem is to find an expression for the exchange and correlation energy, [ ], since it contains the two unknown functionals [ ] and U [ ]. Various approximations have been proposed.

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Chapter 3

Local Density Approximation

In the Local Density Approximation, LDA, the exchange-correlation energy is approximated by,

3 Exc[n(r)] = ∫ εxc(n(r))n(r)d r (Eqn. 3.21)

where  XC is the exchange and correlation energy per electron of a uniform electron gas of density n . The energy functional, Eqn. 3.19, may now be minimized with respect to the electron density. By solving the single-particle Schrödingerequation,

∇2 (− + V (r)) ψ = ε ψ (Eqn. 3.22) 2 n i i i

and setting,

푁 2 푛(푟) = ∑ |휓푖 | (퐸푞푛. 3.23) 푖=1

will minimize the energy. Eqn. 3.22 are known as the Kohn-Sham equations for the Kohn-

Sham orbitals,  i . The potential in Eqn. 3.22 is,

n(r′) V (r) = v(r) + ∫ d3r′ + μ (n(r)) (Eqn. 3.24) n |r − r′| xc

where,

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Chapter 3

ϑ((n(r)εxc(n(r))) μxc(n(r)) = (Eqn. 3.25) ϑn(r)

is the exchange and correlation contribution to the chemical potential of a uniform gas of densityn . Introducing a basis set for the Kohn-Sham orbitals,

K

ψi = ∑ Cijɸj (Eqn. 3.26) j=1

Eqn. 3.22 can be solved using an SCF procedure similar to the Hartree-Fock method.

3.4.1.5 Generalized Gradient Approximation and Hybrids

The disadvantage with the LDA approximation, Eqn. 3.21, is that it does not give the precise asymptotic performance of the exchange energy. Becke introduced a correction to this problem [57], which includes the gradient of the density. Combination of Becke's functional and the correlation energy functional derived by Lee, Yang and Parr is referred to as the

BLYP functional [59]. This is a semi-empirical functional containing five parameters chosen so that it models closed shell atoms correctly. Functionals that depend on the density and the gradient of the density are called Generalized Gradient Approximations (GGA's).

Introducing the Hartree-Fock exchange energy, i.e., the eigenvalue of the exchange operator

b iK  in Eqn. 3.9, in the BLYP functional, an exact description of the exchange energy is obtained. Thus, the exchange and correlation energy terms are divided into two terms, one

127

Chapter 3 exact description of the exchange energy and a term containing all other contributions. This functional is denoted as B3LYP. Functionals which include exact exchange are often called hybrid methods.

Other functionals are combinations including the functionals of Perdew et al. (1996)[60] which are known as P86 and PW91. These are derived from the properties of the electron gas, and are thus appropriate for metals.

3.5 Gaussian Functions

Employing Gaussian functions in the calculations of chemical problems has become very common. In fact almost all electronic structure methods nowadays essentially rely on an expansion on the unknown wavefunction in terms of a set of basis function. Another important concept, the basis set is also required to solve the electronic Schrödinger equation besides the basic ingredients of quantum chemistry methods (e.g. MP2, CC, composite methods, etc.). Although any type of these basis functions may in principle be used like Slater type orbitals, Gaussian, numerical atomic orbitals, polynomial, spline, exponential, plane wave, there are still some important issues that one needs to consider when selecting them.

These include:

 Economical - the wavefunction/density has to be described accurately by basis

function with as low a computational cost as possible.

 Specific – basis functions behaviour will preferably capture some of the physics of the

problem. One example is that when the distance between the nucleus and the electron

becomes large for bound atomic or molecular systems, functions should go to zero.

Specific Gaussian orbital basis sets used in this thesis will be discussed.

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Chapter 3

3.5.1 Gaussian Functions as Basis Sets

The crucial role of basis sets is to find the solution to the Hartree-Fock (HF) equation.

Atomic orbitals (AO) or molecular are created from basis-functions and are usually expanded as a linear combination of such functions with the coefficients to be determined [61]. The basis-functions can be divided into two main significant which will be briefly described in

Eqn 3.27.

Slater type orbitals, also called STOs are centred on an atom with each MO Ѱ푖, expressed as a linear combination of STO centred on each of the atoms, having an exponential dependence: 푒−휁푟with their mathematical expression very close to the real AO:

푛−1 −휁푟푎 푚푥 푚 휓푆푇푂 = 푁푟푎 푒 (푌푙 ± 푌푖 )⁄√2 (Eqn 3.27)

Nevertheless, when two atoms are present, it causes difficulties to evaluate the needed integrals. To simply molecular integral evaluation, Gaussian-type orbitals (GTOs) were proposed by Boys [62] instead of STOs in the linear combination of atomic orbital wavefunction. A Cartesian Gaussian centred on an atom is defined by Eqn. 3.28:

1 푚 푛 −휁푟2 Ѱ퐺푇푂 (푥, 푦, 푧) = 푥 푦 푧 푒 (Eqn. 3.28)

where x,y and z are local (atom centered) Cartesian coordinates.

Spherical orbitals like hygrogen orbitals are usually given by l=m=n=0, a px orbital is given by l=1, m=n=0, a dx orbital is given by l=m=1, n=0 e.t.c. Contrary to hydrogen atom orbitals,

GTOs are without radial nodes with radial nodes only obtainable by combining different 129

Chapter 3

GTOs. Though, GTOs have these shortfalls, they are still a better compromise because a product of two of them centred on two different atoms is a third one situated between them.

Therefore a number of GTOs can be combined to appropriate a STO, making it more efficent than using STOs which are very difficult to handle computationally due to the four-center- two-electron integrals which are time consuming.

Hence, the precision of a basis set is described by the number of contracted Gaussian functions employed to represent each atomic orbital [63-66]. Therefore, quite often, an atomic basis function is actually a static linear combination of GTOs referred to as contracted

Gaussian functions (CGF).

3.5.1.1 Minimal Basis Set

The term minimal basis set denotes the smallest possible basis set that only has one orbital to be contracted. An orbital is usually thought of as an atom that sometimes consists of unoccupied orbitals. A well-known minimal basis set is the STO-3G, where G indicates a combination of contracted Gaussian Functions, these are formed by a linear combination of three GCF for each basis function so as to resemble an STO. However, STO-3G is also more difficult to compute. Even though, GTO may give a good approximation to an atomic orbital, they are still not flexible enough to expand or shrink in the existence of other atoms in a molecule, giving less accurate results.

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3.5.1.2 Split Valence Basis Set

To get a better description of a system with good precision of a system, two or more functions can be used to describe each type of orbital. For an example, double zeta and triple zeta basis sets. Double zeta basis sets in this case is if we have twice as many basis functions as in a minimum basis (exponent in the STO gives the zeta ζ). It is more vital to have a flexible description of the valence electrons because they are the ones that change the most in a chemical reaction. Hence, basis sets where the core and the valence orbitals are treated separately are stated as split valence basis sets. One example of a split valence is the 6-31G basis set, nomenclature of this type of basis set is given as: X-YZG. In this instance, X denotes the number of primitives GTO used to describe one single contracted Gaussian function of the core. While Y and Z (with many more added for better precision) denotes the number of primitives GTOs describing the valence orbitals. Therefore 6-31G has two functions with three primitives and the other one only having one.

3.5.1.3 Polarization Functions

A deformation of the electronic cloud around each atom results when atoms bond, called polarization. To allow for this, higher-angular momentum basis functions are often added to increase flexibility. For an example, the highest angular momentum orbital for hydrogen atom is an s orbital; the “polarization” of this atom can be defined by adding p function as polarization functions. Similarly, a d-function can be added to a basis set consisting of p valence orbitals, f-functions for d-valence orbitals. One well-known example of a split- valence double zeta plus polarization is the 6-31G* (Pople’s basis set) [67-70]. This notion can be defined as the core orbitals designated by a contraction of 6 Gaussian functions, while

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Chapter 3 the valence orbitals is described by two functions, one made of a contraction of 3 Gaussian functions and one having a single contracted Gaussian function. The star (*) denotes polarization functions on non-hydrogen atoms. Moreover, to get more precise results, the polarization function can be better defined by the addition of p and d polarization to 6-31G basis set of hydrogen atom, which can later become 6-31G(d,p).

3.5.1.4 Diffuse Functions

Diffuse functions describe the part of atomic orbitals distant from the nuclei that have a very crucial role when considering anions or electronic clouds in second or third row transition metals. Therefore, since normal basis functions that are we use are sometimes inadequate, basis functions that are more spread out, i.e. GTOs with small exponents are used to model these correctly. The GTOs are added as singles without contracting them together. For example, these diffuse functions are indicated by a + or ++, e.g. 6-31+G or 6-31++G.

Additionally, the diffuse functions can also be added along with polarization functions leading to basis sets like 6-31+G*, 6-31+G**, and 6-31++G*.

3.5.1.5 Effective Core Potential Basis Sets

Another crucial fact to consider is that transition metals and other systems involving electrons of elements in the third row or higher in the periodic table have a large number of inner core electrons. Though inner core electrons are not pivotal in a chemical sense, they still need a great number of basis functions to enlarge the corresponding orbitals be in order to properly describe the valence orbitals, otherwise it would lead to poor depiction of electron-electron repulsion.

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The core electrons of elements in the lower half of the periodic table reach velocities sufficiently near the speed of light that may manifest relativistic effects that a non-relativistic

Hamiltonian operator cannot account for. Thus, in order to resolve this challenge, Effective

Core Potentials (ECP) (also called Pseudopotentials) is introduced to replace those basis functions. The ECP is capable of modelling the effects of the nucleus and the electrons from the inner shell on the valence electrons as an average effect. Since these basis functions are generated from relativistic atomic calculations, some relativistic effects can also be included besides just allowing the reduction of big computational calculations.

3.5.1.6 Correlation-Consistent Basis Sets

Dunning and associates [67, 71-73] developed the correlation consistent basis set which has become the contemporary state of art for correlated calculations, and are thus widely used.

Such basis sets are constructed by adding shells of functions to the core of Hatree-Fock functions, with every function in a shell providing the same amount of electron correlation energy in an atomic calculation. Correlated consistent basis sets use correlated wavefunctions for optimization and were designed to converge systematically to the complete basis set also known as CBS limit using extrapolation technique.

For the first and subsequent row atoms, the basis sets are cc-pVNZ, where “cc” corresponds to correlation consistent, p corresponds to polarized, and V designates that they are valence only basis sets, N=D, T, Q, 5, …., where D denotes double zeta, T is triple zeta, Q is quadruple zeta, 5 is quintuple zeta etc. To illustrate this, the cc-pVDZ basis set for the first row and succeeding row adds 1s, 1p and 1d function, while the cc-pVTZ basis set adds

133

Chapter 3 another s, p, d and an f function etc. An addition of the prefix ‘aug’ is done which means that the basis is augmented with diffuse functions, for example, cc-pVXZ becomes aug-cc-pVXZ.

For functions that describe core correlations, ‘C’ is also included in the basis set, e.gaug-cc- pVXZ becomes aug-cc-pCVXZ basis set which denotes that the core electrons are not frozen but contribute to the electron correlation.

3.6 Software

All calculations described in this thesis were done using the Gaussian 09 suite of programmes.

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CHAPTER 4

POSSIBLE INTERSTELLAR FORMATION OF GLYCINE FROM THE

REACTION OF CH2=NH, CO AND H2O: CATALYSIS BY EXTRA

WATER MOLECULES THROUGH THE HYDROGEN RELAY

TRANSPORT

Abstract: “How the fundamental life elements are created in the interstellar medium (ISM)?, is one of the intriguing questions related to genesis of life. Using computational calculations, we have discussed the reaction of CH2=NH, CO and H2O for the formation of glycine, the simplest life element. This reaction proceeds through a concerted mechanism with reasonably large barriers for the cases with one and two water molecules as reactants. For the two water case we found that the extra water molecule exhibits some catalytic role through hydrogen transport relay effect and the barrier height is reduced substantially compared to the case with one water molecule. These two cases can be treated as ideal cases for the hot-core formation of the interstellar glycine. With increasing number of water molecules as the reactants, we found that when the numbers of water molecules are three or more than three, the barrier height reduced so drastically that the transition states were more stable than the reactants.

Such a situation gives a clear indication that with excess water molecules as the reactants, this reaction will be feasible even in the low temperature conditions existing in the cold interstellar clouds and the exothermic nature of the reaction will be driving force.

Keywords: Glycine, Interstellar Medium, ISM, CH2=NH, Methanimine, CO, H2O.

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4.1 Introduction

There exist one fundamental question related to the origin of life and that is “How life is created?” or more technically “How the essential life elements, i.e., the amino acids are formed?” [1, 2]To find answers for this question; chemists, biologists, astronomers and geologists are trying with their full potentials by considering all possible angles. Among the various amino-acids, glycine, (H2N-CH2-COOH) is one of the simplest amino-acid found in the earth. The era of the astronomical search for glycine begins with the availability of the laboratory spectra for it [3], but its presence in the interstellar medium (ISM) is still controversial [4-6]. On the other side, many amino-acids including glycine have been found on meteorites [7-18]. In a recent discovery glycine is being detected even in comets, as evidenced from the pristine cometary samples reverted back by NASA STARDUST mission

[18], which can be treated as a validation for its extraterrestrial origin. On the other hand our knowledge on its formation in the extraterrestrial space through various chemical pathways seems to be either incomplete or inconclusive [1]. To imitate the synthesis in laboratory, there are two most widely exploited approaches can be found in the literature. First one is the

Strecker’s synthesis [19], and the second one is the Miller experiment [20], where in both the cases it is believed that the key intermediate is the HCHO (formaldehyde). Similar to formaldehyde, another important reactant, Methanimine (CH2=NH) which is isoelectronic with HCHO is also suggested as a potential prebiotic precursor for glycine [21-24]. Starting with this Methanimine, in this work using computational calculations, we have carried out a complete potential energy surface (PES) analysis of CH2=NH + CO + H2O → Glycine reaction. In a recent work, “Discovering chemistry with an ab initio nano reactor” [25]by

Wang et al. (2014) also indicates the possibility of such a reaction, but without any further discussions. With a detailed potential energy surface analysis, we have shown that the

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Chapter 4 reaction suggested by Wang et al. [25] proceeds through a concerted type of reaction mechanism from CH2=NH, CO and H2O to give glycine as the end product. Also we have discussed about the cooperative and catalytic role of extra water molecules for this reaction through hydrogen relay transport phenomena. The role of water acting as proton transfer helper was first described by Radom and co-workers [26-28]. But, such phenomena are less investigated for the interstellar formation of Glycine [24, 29-32]. In the recent work by

Rimola et al. (2012)[32] where they have carried out computational studies on the formation of glycine from the reaction CH2=NH and CO on radical surfaces of water-ice dust particles, indicates a clear catalytic role exhibited by the water molecules of the water-ice cluster.

Moreover the work of Rimola et al. (2012)[32], they have shown how the defects formed in the water-ices is capable of making the reaction feasible and the mechanism proposed is multi-stepped in nature. The work discussed here shows a concerted type of mechanism for the formation of glycine, also with discussions related to the catalytic role of extra water molecules, which is capable of bring down the reaction barrier drastically.

4.2 Computational Methods

All the calculations have been carried out using Gaussian software package [33]. We have carried out calculations using various methods like, B3LYP, B3PW91, CBS-QB3, MP2, and also various composite methods which are known for accurate energy predictions, like,

G3B3, G3MP2B3, G4 and G4MP2. For the B3LYP method we have also tested the effect of various basis sets. The true minima and the transition states were confirmed from analysis of their frequencies by ensuring that all frequencies were positive for the minimum, with there is only one imaginary frequency for the transition state. We have also carried out the analysis of the displacement vectors for the imaginary frequency to ascertain that the TS is a structurally

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Chapter 4 true TS and also confirmed by the IRC analysis. All the thermodynamic quantities were calculated from the zero point energy (ZPE) corrected energies of the stationary points in the

PES. As all the methods predict similar kind of trend, in the main text we have limited our discussion only to B3LYP/6-31++G(3df,3pd) method only with a very little discussions on effects of methodologies and basissets.

4.3 Results and discussions

4.3.1 PES for CH2=NH + CO + H2O → Glycine reaction

The PES of the termolecular reaction between CH2=NH, CO and H2O to form glycine is shown in Figure 4.1 PES for the MP2 method is provided in the supporting information.

Figure 4. 1: B3LYP/6-31++G(3df,2pd) optimized PES for the CH2=NH + CO + H2O →

Glycine, reaction. All the energies are in kcal/mol and the diagram is not to

scale.

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Analysis of the PES shows that a well synchronized approach of the three reactants first leads to the formation of a stable hydrogen-bonded complex, which ultimately passes through a transition state to reach the product, glycine. Energetics of the PES shows that the complex is around 4.6 kcal/mol more stable than the corresponding reactants. The complex then passes through a transition state, where the TS is 41.0 kcal/mol higher in energy than the complex

(36.4 kcal/mol is higher in energy compared to the reactants). Analysis of the product, glycine shows that it is 25.3 kcal/mol more stable compared to the reactant complex or 29.9 kcal/mol more stable compared to the reactants. The PES for the MP2 method shows similar kind of behaviour like that of the B3LYP surface with a little difference in the energetics. The exothermic nature of this reaction is a clear indication for the thermochemical feasibility of this reaction ISM, but the reasonably large barrier may act as a bottleneck. We have also investigated the effect of various basissets with the B3LYP method for the PES of this reaction and also the effect of various methodologies for the PES of this reaction. The detailed discussions related to these are provided in the supporting information. As the reactant complex and transition state, are vital to the feasibility of this reaction in the interstellar conditions, a concise discussion about their structures and nature of interactions are shown below.

4.3.2 Reactant Complex

There are two major possibilities for the approach of the CO+H2O towards the planar

CH2=NH; (1) above or below the plane of the molecule (perpendicular to the π-cloud of molecule), (2) in-plane from one side of the methanimine. The optimized structure of the reactant-complex is shown in Figure 4.2. (a). Analysis of the reactant-complex shows that approach of the reactants towards CH2=NH is almost in-plane and also is in the same side of

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the plane. CO molecule is placed in the side of CH2 of the methanimine and makes a hydrogen bonded interaction with one of the H-atom of CH2 unit (C-H-O hydrogen bonding.

Hydrogen bond distance is 2.895 Å). On the other hand H2O molecule is in the NH unit side of the methanimine, where one of the H-atom of the water molecule is interacting with the N- atom of the methanimine and the nature of interaction is hydrogen bonding (O-H-N hydrogen bonding. Hydrogen bond distance is 1.941 Å). Besides these two major interactions there exist so many van der Waals type of interaction in the reactant complex.

Figure 4. 2: (a) B3LYP/6-31++G(3df,2pd) optimized structure of the reactant complex with

important interaction distances. (b) Computed ESP maps of CH2=NH, CO and

H2O (oriented in the similar fashion like that of the reactant complex) calculated

from the B3LYP/6-31++G (3df,2pd) method at 0.001 au electron density

surfaces [ESP colour scheme: Red (negative) - Positive (blue)].

To study the nature of interaction existing in the complex we have analyzed the electrostatic potential (ESP) maps of the reactants [Figure 4.2(b)]. Analysis of the ESP maps shows that;

(1) for CO: there is a maximum negative potential around the C-atom and a smaller negative

148

Chapter 4 potential around the O-atom, which are capable of interacting with positive potential regions of other reactants, (2) For H2O: two ends with H-atoms have positive potentials and region around the central O-atom is having the negative potential, (3) for CH2=NH: except the region around N-atom (showing negative potential) all other regions have positive potentials.

Analysis of the geometry of the reactant-complex shows a well synchronized approach of the reactions from electrostatic potential point of view.

4.3.3 Transition state

Optimized structure of the TS is shown in Figure 4.3 Analysis of the TS shows that it is a distorted cyclic 5-membered ring and at the TS all the three reactants are arranged in a nonplanar three dimensional way (imaginary frequency: 777.3i cm-1).

Figure 4. 3: B3LYP/6-31++G(3df,2pd) optimized structure of the reactant complex with

important interaction distances.

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Structure of the TS shows that the molecular structural characteristics of CO and CH2=NH are almost retained in the TS, and at the same time one of the H-O bond in H2O is largely elongated. Further analysis of the structure of the TS shows that the approach of the CO+H2O towards the CH2=NH is perpendicular to the plane of CH2=NH (perpendicular to the π-cloud of CH2=NH). To know the nature of interaction existing at the TS, we have analyzed the

ESPs of the reactants again. It can be seen that again the H2O in the TS is in the side of NH unit of CH2=NH, with one of the H-atom (with positive potential) of H2O sandwiched between the negative potentials of N-atom of NH and O-atom of H2O. On the other hand the

CO and the OH of H2O are interacting with the π-hole regions [34] of the CH2=NH rather than interacting with each other. In other word π-hole regions [34] of the CH2=NH provides a well synchronized positioning of these two reactants in the TS.

4.3.4 Catalysis by an extra water molecule

Rimola et al. (2012)have carried out computational studies on the formation of glycine on radical surfaces of water-ice dust particles which involves CH2=NH and CO as reactants [32].

In their work they have used a cluster of water molecule where many water molecules are interlinked with each other [32]. Though the mechanism predicted in their work is a step-wise mechanism, but their work clearly indicates the prominent hydrogen transport catalytic effect exhibited by those interlinked water molecules. Similarly, Wang et al. (2014) in their recent work also indicated the possible catalytic effect for this reaction, but without any further details on the mechanistic aspect of this reaction [25]. So in this work we have carried out calculations related to PES of the reaction between the CH2=NH, CO and two molecules of

H2O to study the mechanistic aspect of this reaction. In our study we have placed the two water molecules adjacent to each other and at the same time also interlinked with each other.

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This inter linked system also sometimes can be viewed as a H2O-H2O binary complex. We have compared our results of the reaction PES consisting of two individual molecules of water with that of the reaction PES for H2O-H2O binary complex. The potential energy surface of the reaction between CH2=NH, CO, with two water molecules is shown in Figure

4.4 PES related to H2O-H2O binary complex for both the MP2 and B3LYP methods are provided in the supporting information.

Figure 4. 4:B3LYP/6-31++G(3df,2pd) optimized PES for the CH2=NH + CO + 2H2O →

Glycine, reaction. All the energies are in kcal/mol and the diagram is not to

scale.

Analysis of the potential energy surface shows that a well-coordinated approach of the four reactants leads to the formation of a stable hydrogen bonded reactant-complex (multiple hydrogen bonding situations can be seen in the complex) at the entry channel of this reaction.

This complex ultimately passes through a transition state to reach a stable product-complex, an exit channel complex for this reaction. This exit channel complex then endothermically dissociates to give glycine and water as final products. Without any further discussion about

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Chapter 4 the structures of the all the stationary points in the PES we have only discussed the energetics of this reaction PES to account for the extent of catalytic effect by extra water molecule as reactant. More details about the optimized structures of these stationary points can be found in the supporting information. Analysis of the reactant complex shows that it is highly stable

(around 10.2 kcal/mol more stable than the corresponding reactants). The extra stability of the reactant complex is coming from the more number of well synchronized H-bonded interactions existing in the complex than the previous case as discussed above for one water molecule. Instead of the two separate water molecules, we have extended our discussions for the

H2O-H2O complex reacting with CH2=NH and CO and this is based on the fact that the binary complex of H2O also being detected in the ISM [35]. Now, with H2O-H2O binary complex as one of the reactant, the reactant complex is 7.0 kcal/mol stable compared to the reactants. The loss in the stability is hidden in the H2O-H2O binary complexation energy.

The complex then passes through a transition state and analysis of the TS shows that it is a distorted cyclic 8-membered ring. At the TS all the four reactants are arranged in a nonplanar three dimensional way. Energetics of the TS shows that it is 34.0 kcal/mol higher in energy than the reactant complex (23.8 kcal/mol higher in energy compared to the reactants). This clearly shows a 7.0 kcal/mol of decrease in energy compared to the uncatalyzed case

(~12 kcal/mol compared to the reactants in the un-catalyzed case) and a direct indication of the prominent catalytic activity by the extra water molecule for this reaction [25]. In the TS, the catalytic effect of the extra H2O molecule can be considered as being facilitated by the relay effect it is exhibiting in transporting the H-atom to the N-atom site of CH2=NH [36]. In the transition state the water molecule close to the N-atom of the CH2=NH acts as the communicator in relay transporting the H-atom from the other water molecule placed close to

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Chapter 4 the CO molecule to the N-atom of the methanimine. Though prominent hydrogen transport is happening in the transition state, the low value of imaginary frequency of the TS clearly gives an indication of negligible chances for the low temperature tunnelling mechanism to happen for this reaction [37]. While descending from the TS towards the product in the PES, we observed a product-complex formation (complex between Glycine and water). In the complex the hydrogen bonding complexation of the H2O seems to be with both NH2 and COOH groups of the glycine. Interestingly we found that the exit channel product complex to be marginally more stable (0.1 kcal/mol) than that the glycine and water alienated. Being a stable complex it might help to prevent the photochemical degradation of glycine, a phenomenon needs separate and further investigations. At the end, under suitable conditions, product-complex will dissociate endothermically to give the glycine and water separated. We have also investigated the effect of various basissets with the B3LYP method for the PES of this reaction and also the effect of various methodologies for the PES of this reaction. The detailed discussions related to these are provided in the supporting information.

4.3.5 Effect of excess water molecules

As we have seen in the earlier case of two water molecules, the catalytic effect exhibited by the extra water molecule is very significant in reducing the barrier by an amount of around

12.6 kcal/mol. So to have some preliminary idea about the above mentioned catalytic effect when the water is in excess, we extended our investigation for three and four water molecules. Without going further detail into the PES, we tried to optimize the transition states for these two cases. The optimized structure of the transition states for three and four water molecules are shown in Figure 4.5. With the limited computational resource available with us, first we optimized both the transition states using B3LYP/6-31G method. Then to

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Chapter 4 compare with our results of the other two PESs as discussed above, we did only the energy calculations at B3LYP/6-31++G(3df,2pd) level, using those optimized geometries. Then the energies were corrected for ZPVE with the zero point energies obtained during the B3LYP/6-

31G optimizations.

Figure 4. 5: B3LYP/6-31G optimized geometries of the transition states, (a) with three water

molecules as reactants and (b) with four water molecules as reactants.

As it can be seen from the two transition state structures, by adding extra water molecules to the reaction, the relay transport of hydrogen are happening over a longer and longer distances. Besides these the major differences observed are in the structure of the transition state, i.e. the positioning of the CO molecule. For the one H2O case, the CO and H2O are in the same side of the plane, and for the two H2O case, though the CO position is shifted a little bit, the two H2O molecules and the CO are still in the same side of the plane (this is perpendicular to the molecular plane of the CH2=NH, or we can say, above the molecular plane of the CH2=NH). With the three H2O and four H2O, the situations are quite similar in the sense that all the H2O and the CO are above the molecular plane of the CH2=NH. The major differences as stated earlier are with respect to the positions of CO molecules in these

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two cases. For 3H2O, the CO molecule is just above the C-N bond axis of the CH2=NH molecule, whereas for 4H2O, the CO molecule is away from the C-N bond axis of the

CH2=NH molecule. For the 4H2O case, the 4H2O are in one side and the CO is in the opposite side with respect to the C-N bond axis of the CH2=NH molecule. Thus it can be imagined that this drastic shift in the positions of the CO molecules in these two cases might have some significant effect on the energetics of these two transition states. After comparing the energetics of these two transition states, we found that the results were quite surprising and indicate that both the transition states are now more stable than the reactants. For the case of 3H2O as reactants, the transition state [Figure 4.5(a)] is around 10.0 kcal/mol below the reactants, and for 4H2O, the transition state [Figure 4.5(b)] is around 13.8 kcal/mol below the reactants. Such a situation gives a clear indication that with excess water molecules as the reactants, will definitely has a significant catalytic effect in making the reaction feasible in the low temperature conditions.

4.3.6 Possible Interstellar Applications:

Though the interstellar time scale is large, still these kinds of reactions are kinetically less probable owing to the large number of molecules involved in the reaction process. As the reaction proceeds through the formation of a stable complex (a super molecule), the kinetic behavior of the reaction can be expected to be unimolecular. The only problem arises here is the probability of the formation of this super molecule or the stable complex and this largely depends on the molecular composition of the ISM. It is well known that the CO and H2O are among the most abundant molecules in the ISM (in fact it is believed that CO is the second most abundant molecule in the ISM) besides the hydrogen [38-40]. On the basis of this, along with the large concentrations of the H2O available in ISM, formation of this complex is fairly

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Chapter 4 probable. Once the complex is formed the reaction will precede towards a unimolecular kinetics pathway to give glycine as an end product.

As extreme temperature conditions are prevailing in the ISM, we tried to explore the possibility of this reaction in both hot-cores and cold interstellar clouds. As part of this we first tried to find whether the reactants are available in those hot-cores and cold interstellar clouds, or not? Methanimine (CH2NH) was first detected in Sgr B2 by Godfrey et al.

(1973)[21], then subsequently has been found in many other hot core sources [22], and also recently Salter et al. detected it in the ultraluminous infrared galaxy (ULIRG) Arp 200 which is 250 million light years away, with the Arecibo ; certainly a remarkable discovery [23]. Interestingly, besides the availability in hot cores, CH2=NH was also observed to be present in the quiesceny gas at the so-called “radical-ion peak” along the

Orion ridge, where the temperature is about 20K and also expected to be present even at regions of 10K or low temperatures [22]. Availability of CO and H2O in the through the ISM are well known [38-40]. In the interstellar medium (ISM), hot cores are the dense and warm regions consisting of gases and dusts, which are rich in exotic gas chemistries [39, 40]. High temperature in those hot cores (around 200K - 1000K) is capable of facilitating most of the high barrier reactions [39]. Analysis of the PES shows that there is a reasonably large barrier for this reaction for the cases of one and two water molecules. We believe that with the existing condition in the hot-cores of ISM and where water is not in very large excess the reaction might proceed through the paths shown in Figure 4.1 and Figure4.4 and the large reaction barriers will not be able to act as a bottleneck to this reaction to happen. On the other hand the feasibility of this reaction in the cold interstellar clouds, where a large amount of water exists as water-ice and the temperature is extremely low, is affirmative only if there are three or more water molecules involved in the reaction. Our preliminary results on the

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Chapter 4 transition state analysis for three water molecules involved in the reaction process shows that, the transition state is even more stable than the reactants. This makes the entire process thermodynamically favourable to happen in the extreme low temperature conditions existing in the cold interstellar clouds. In the low temperature conditions, these transition states being lower in energies comparted to the reactants, the exothermic nature of the reaction will drive the reaction. Moreover though probability of tunnelling can be expected to extremely low

[37], but owing to the exhibited prominent proton dynamics, such a phenomenon can’t be completely ruled out [36].

4.4 Conclusions

We have discussed a reaction for the possible interstellar formation of glycine from CH2=NH,

CO and H2O using computation calculations. We have carried out the complete PES analysis for this reaction using various methodologies. Our calculations show that the reaction is having a large barrier height, indicating that such a reaction is only feasible in the hot core regions of the ISM. We have also shown the catalytic role of an extra water molecule in reducing the barrier height, which can further enhance the rate and thus a clear indication that excess water is going to assist the reaction strongly in the hot core regions of ISM. The catalytic role of the extra water molecule is explained by the relay hydrogen transport effect of the water. With the expectations that more number of water molecules as reactants (more than two water molecules) will be able to reduce the barrier significantly to a very low value, we carried out some preliminary investigation for the cases with three and four water molecules as reactants. Our preliminary studies related to finding the transition states for these two cases indicates that the respective transition states were found to be more stable than the reactants. Now with the transition states being lower in energy compared to the

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Chapter 4 reactant, we can predict that this reaction will also be feasible in the cold interstellar clouds, and the exothermic nature of the reaction will be the driving force for this reaction to happen in such extreme low temperature conditions. A more detailed PES analysis of the reactions related to three and four water molecules needs further investigations to have an idea about the complete reaction profile. We hope that this work will be able to contribute to our future understanding of the formation of glycine in the ISM as well as its synthesis in the laboratory.

Supplementary Information: Potential energy surfaces for the MP2 method for the reaction,

CH2=NH+CO+1H2O and CH2=NH+CO+2H2O are shown in Appendix A, Figures S4.1 and

S4.2 respectively. Similarly, for the reaction CH2=NH+CO+H2O-H2O (binary complex) the

PESs for B3LYP and MP2 methods are shown in Figures S4.3 and S4.4 respectively.

Optimized structures with important geometric parameters for MP2 as well as B3LYP methods are shown in Figures S4.5-S4.8. Table S4.1 summarizes the optimized geometries of the TS for the CH2=NH+CO+1H2O reaction for various methodologies and Table S4.2 summarizes the optimized geometries of the TS for the CH2=NH+CO+2H2O reaction case for various methodologies. Table S4.3 and S4.4 are related to the effect of various basissets and methodologies respectively for the reaction of CH2=NH, CO with one H2O. Similarly,

Table S4.5 and S4.6 are related to the effect of various basissets and methodologies respectively for the reaction of CH2=NH, CO with two H2O.

TOC Graphics

Possible interstellar formation glycine from the reaction of CH2=NH, CO and H2O: Catalysis by extra water molecules through the hydrogen relay transport

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4.5 References

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3. Brown, R.D., et al., Microwave spectrum and conformation of glycine. Journal of the

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4. Kuan, Y.-J., et al., Interstellar glycine. The Astrophysical Journal, 2003. 593(2): p.

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5. Hollis, J.M., et al., A sensitive very large array search for small-scale glycine

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6. Snyder, L.E., et al., A rigorous attempt to verify interstellar glycine. The

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7. Pizzarello, S., The chemistry of life's origin: A carbonaceous meteorite perspective.

Accounts of Chemical Research, 2006. 39(4): p. 231-237.

8. Burton, A.S., et al., Understanding prebiotic chemistry through the analysis of

extraterrestrial amino acids and nucleobases in meteorites. Chemical Society

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9. Schmitt-Kopplin, P., et al., High molecular diversity of extraterrestrial organic matter

in Murchison meteorite revealed 40 years after its fall. Proceedings of the National

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10. Cronin, J.R. and S. Pizzarello, Enantiomeric excesses in meteoritic amino acids.

Science, 1997. 275(5302): p. 951-955.

11. Engel, M.H. and B. Nagy, Distribution and enantiomeric composition of amino acids

in the Murchison meteorite. 1982.

12. Kvenvolden, K., et al., Evidence for extraterrestrial amino-acids and hydrocarbons in

the Murchison meteorite. 1970.

13. Engel, M., S. Macko, and J. Silfer, Carbon isotope composition of individual amino

acids in the Murchison meteorite. 1990.

14. Callahan, M.P., et al., A search for amino acids and nucleobases in the Martian

meteorite Roberts Massif 04262 using liquid chromatography‐mass spectrometry.

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15. Brown, P.G., et al., The fall, recovery, orbit, and composition of the Tagish Lake

meteorite: A new type of carbonaceous chondrite. Science, 2000. 290(5490): p. 320-

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16. Hiroi, T., M.E. Zolensky, and C.M. Pieters, The Tagish Lake meteorite: A possible

sample from a D-type asteroid. Science, 2001. 293(5538): p. 2234-2236.

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17. Lawless, J.G., et al., Amino acids indigenous to the Murray meteorite. Science, 1971.

173(3997): p. 626-627.

18. Elsila, J.E., D.P. Glavin, and J.P. Dworkin, Cometary glycine detected in samples

returned by Stardust. Meteoritics & Planetary Science, 2009. 44(9): p. 1323-1330.

19. Strecker, A., Ueber die künstliche Bildung der Milchsäure und einen neuen, dem

Glycocoll homologen Körper. Justus Liebigs Annalen der Chemie, 1850. 75(1): p. 27-

45.

20. Miller, S.L., A production of amino acids under possible primitive earth conditions.

Science, 1953. 117(3046): p. 528-529.

21. Godfrey, P., et al., Discovery of interstellar methanimine (formaldimine).

Astrophysical Letters, 1973. 13: p. 119.

22. Dickens, J., et al., Hydrogenation of interstellar molecules: A survey for

methylenimine (CH2NH). The Astrophysical Journal, 1997. 479(1): p. 307.

23. Salter, C., et al., The Arecibo Arp 220 Spectral Census. I. Discovery of the Pre-Biotic

Molecule Methanimine and New cm-Wavelength Transitions of Other Molecules. The

Astronomical Journal, 2008. 136(1): p. 389.

24. Koch, D.M., et al., A theoretical study of the formation of the aminoacetonitrile

precursor of glycine on icy grain mantles in the interstellar medium. The Journal of

Physical Chemistry C, 2008. 112(8): p. 2972-2980.

25. Wang, L.-P., et al., Discovering chemistry with an ab initio nanoreactor. Nature

chemistry, 2014. 6(12): p. 1044-1048.

26. Gauld, J.W., et al., Water-catalyzed interconversion of conventional and distonic

radical cations: methanol and methyleneoxonium radical cations. Journal of the

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27. Chalk, A.J. and L. Radom, Proton-transport catalysis: a systematic study of the

rearrangement of the isoformyl cation to the formyl cation. Journal of the American

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28. Gauld, J.W. and L. Radom, Effects of Neutral Bases on the Isomerization of

+ + Conventional Radical Cations CH3X to Their Distonic Isomers CH2X H (X= F, OH,

NH2): Proton-Transport Catalysis and Other Mechanisms. Journal of the American

Chemical Society, 1997. 119(41): p. 9831-9839.

29. Woon, D.E., Ab initio quantum chemical studies of reactions in astrophysical ices 3.

Reactions of HOCH2NH2 formed in H2CO/NH3/H2O ices. The Journal of Physical

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+ 30. Rimola, A., et al., Is the peptide bond formation activated by Cu2 interactions?

Insights from density functional calculations. The Journal of Physical Chemistry B,

2007. 111(20): p. 5740-5747.

31. Rimola, A., M. Sodupe, and P. Ugliengo, Deep-space glycine formation via Strecker-

type reactions activated by ice water dust mantles. A computational approach.

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32. Rimola, A., M. Sodupe, and P. Ugliengo, Computational study of interstellar glycine

formation occurring at radical surfaces of wáter-ice dust particles. The Astrophysical

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33. Gaussian09, R.A., 1, MJ Frisch, GW Trucks, HB Schlegel, GE Scuseria, MA Robb, JR

Cheeseman, G. Scalmani, V. Barone, B. Mennucci, GA Petersson et al., Gaussian.

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σ/π‐Hole Interactions. ChemPhysChem, 2015. 16(12): p. 2496-2517.

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35. Scherer, M., et al., A search for (H2O)2 in the Galaxy and toward comet Hale-Bopp.

Astronomy and Astrophysics, 1998. 335: p. 1070-1076.

36. Meng, X., et al., Direct visualization of concerted proton tunnelling in a water

nanocluster. Nature Physics, 2015. 11(3): p. 235-239.

37. Shannon, R.J., et al., Accelerated chemistry in the reaction between the hydroxyl

radical and methanol at interstellar temperatures facilitated by tunnelling. Nature

chemistry, 2013. 5(9): p. 745-749.

38. Dyson, J.E. and D.A. Williams, The physics of the interstellar medium. 1997: CRC

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39. Garrod, R.T. and S.L. Widicus Weaver, Simulations of Hot-Core Chemistry.

Chemical reviews, 2013. 113(12): p. 8939-8960.

40. van Dishoeck, E.F. and G.A. Blake, Chemical evolution of star-forming regions.

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CHAPTER 5

POSSIBLE INTERSTELLAR FORMATION OF GLYCINE THROUGH

A CONCERTED MECHANISM: A COMPUTATIONAL STUDY ON

THE REACTION OF CH2=NH, CO2 AND H2

Abstract: Glycine being the simplest amino acid and also having significant astrobiological implications; intensive investigations have been carried out in the past, starting from its detection in the interstellar medium (ISM), to analysis of meteorites and cometary samples, to laboratory synthesis as well as computational studies, on the possible reaction paths. In this present work quantum chemical calculations have been performed to investigate possible interstellar formation of glycine via two different paths;(1) in a two-step process via a dihydroxycarbene intermediate and (2) through a one-step concerted mechanism, starting from the reactants like, CH2=NH, CO, CO2, H2O and H2. For the two reactions representing the carbene route, it was observed that the formation of dihydroxycarbene from either CO +

H2O or CO2 + H2 are highly endothermic with large barrier heights, whereas the subsequent step of interaction of this carbene with CH2=NH to give glycine is exothermic as well as barrier less. Based on this observation it is suggested that the formation of glycine via the carbene route as a least favourable or even unfavourable path. On the other hand the two reactions, CH2=NH + CO + H2O and CH2=NH + CO2 + H2 representing the concerted paths were found to be favourable in leading to the formation of glycine. After an extensive study on the first concerted reaction in our previous work (Phys. Chem. Chem. Phys. 2016,18, 375-

381), in this work a detailed investigation has been carried out for the second concerted reaction, CH2=NH + CO2 + H2 which can possibly lead to the interstellar formation of glycine. It was observed that this reaction proceeds through a large barrier and at the same time the transition state shows prominent hydrogen dynamics, indicating a tunnelling

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Chapter 5 possibility for this reaction. Based on these observations possible formation of glycine via this reaction in hot-cores and in cold interstellar clouds has been proposed. The cold-core possibility of this reaction is argued on the basis of phenomenon of tunnelling assisted by a van der Waals’ complex.

Keywords: Glycine, Interstellar Medium, ISM, CH2=NH, Methanimine, CO2, H2.

5.1 Introduction

One of the intriguing questions associated with the genesis of life is related to the formation of essential life elements, i.e., the amino-acids [1, 2]. Among the various amino-acids, glycine, (H2N-CH2-COOH) is one of the simplest amino-acid found in the earth. The era of the astronomical glycine begins with the availability of the laboratory spectra for it [3] and since then astronomers have been searching for the glycine for decades, but without any precise conclusions [4-6]. This is in spite of the fact that many amino-acids including the glycine have been found on meteorites and even in comets, and moreover the distinct isotopic signature of those amino-acids are indicative of their extraterrestrial origin [7-18]. One of the key discovery is the detection of glycine in the pristine cometary samples reverted back by

NASA STARDUST mission [18]. These interesting discoveries put forward a most obvious question on “how these complex molecules are formed in the interstellar medium?” To find an answer to this, many experimental as well as theoretical studies have been carried out in the past and various reaction paths have been proposed for the interstellar formation of glycine [1, 19-32]. In a recent study “Discovering chemistry with an ab initio nano-reactor”

Wang et al. (2014)have shown that the formation of glycine is possible via numerous pathways [33]. This study deals with a highly accelerated first-principle molecular dynamics

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simulation of the classic Urey-Miller experiment, where the initial reactants were H2, CO,

H2O, NH3 and CH4[33]. As shown in their study, there are two competing channels for the formation of Glycine from CO, H2O and CH2=NH (Methanimine) [33].

Step−2 Step−1 → Reaction 1: CO + H2O → HO − C̈ − OH Glycin푒 +CH2 = NH

Reaction 2: CH2 = NH + CO + H2O → Glycine

Reaction 1 shows that the first step is the formation of a dihydroxycarbene from the reaction between CO and H2O, which in the subsequent step (step-2) reacts with CH2=NH to give glycine as the end product. On the other hand, as shown in reaction 2, CO, H2O and CH2=NH react with each other through a concerted reaction mechanism to produce glycine directly.

Similar to the above two proposed reaction channels, we have proposed two more reaction channels which are not studied in the work of Wang et al. (2014)[33] and are shown below.

Step−2 Step−1 → Reaction 3: CO2 + H2 → HO − C̈ − OH Glycine + CH2 = NH

Reaction 4: CH2 = NH + CO2 + H2 → Glycine

Reaction 3 is very much similar to the reaction 1, where in the first step formation of a dihydroxycarbene happens to be from the reaction between CO2 and H2 and the second step is same as reaction 1. On the other hand, though reaction 4 proceeds through a concerted mechanism to form glycine as the end product like that of the reaction 2, but the initial reactants are CO2, H2 and CH2=NH instead. In our previous work using computational calculations we have already studied the detailed mechanistic aspect of the reaction 2 and

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Chapter 5 proposed the interstellar feasibility of this reaction [34]. Analysis of reactions 1 and 3 shows that, the first step in both the reactions is the formation of dihydroxycarbene. A search of the earlier literature showed few studies related to the dissociation of this carbene, where some cases leads to H2O + CO and some other cases leads to H2 + CO2[35-38]. So, in this work we have carried out the computational studies of the potential energy surfaces of [H2O + CO] and [H2 + CO2] leading to the formation of dihydroxycarbene. The second step for both the reaction 1 and 3, is the formation of glycine from the interaction of the dihydroxycarbene with methanimine. A search of the earlier literature showed that mass spectral fragmentation of glycine leads to the CH2=NH and dihydroxycarbene combinations [39]. So in this work we have carried out computation studies on the potential energy surface of [CH2=NH + ꞉C(OH)2] leading to the formation of glycine. On the other hand we were not able to find any studies related to the formation of glycine via reaction 4 in a concerted way. So, to know whether such a reaction is feasible of not, we found some interesting evidences. Interestingly some of the works by Miller it has been shown that glycine is the only amino-acid formed from the

CO and CO2 model atmospheres [40]. In their prebiotic synthesis experiments they have shown that, when the H2/CO2 ratio is < 1.0, the yields reduce drastically [40, 41]. Besides these works of Miller [40, 41], three recent works, one, “Low energy fragmentation of protonated glycine” of Rogalewicz et al. (2000), [42] second, “Soft x-ray ionization induced fragmentation of glycine” by Itala et al. (2014)[43] and the third one “X-ray induced irradiation effects in glycine thin films: A time-dependent XPS and TPD study” by

Tzvetkov et al. (2010)[44] also suggest the formation of CO2 as well as H2 from the fragmentations of glycine. So, in this work we have carried out computational calculations for the potential energy surface of the reaction and discussed its interstellar feasibility.

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5.2 Computational Methods

All quantum-chemical calculations have been performed using Gaussian 09 package and the geometries of all the stationary points in the PES have been visualized using GaussView program [45]. In this work, all DFT (density functional theory) calculations were performed by using the B3LYP exchange–correlation functionalities theoretical level [46, 47], using 6-

31++G(d,p) basis set, unless otherwise mentioned. Harmonic vibrational frequencies were computed to evaluate the zero-point vibrational energy (ZPVE) corrections, which have been included in all the reported energies in this work. It is notable that no imaginary frequencies were found for all the minima in the PES at all of the theoretical levels investigated in this work. At the same time transition states were confirmed from the analysis of their frequencies, by ensuring that only one imaginary frequency for each of those transition states.

We have also carried out analysis of the displacement vectors for the imaginary frequencies of those transition states, to ascertain that the transition states were structurally true transition states, and also confirmed them from their IRC (intrinsic reaction coordinates) analysis [48].

As reaction 4 is crucial to this study, so only for this reaction calculations using various methods like, B3LYP [46, 47], X3LYP [49], B3PW91 [46, 50], HF, O3LYP [51], CBSQB3

[52], MP2 [53, 54], MP2(Full)[53, 54] and various composite methods which are known for accurate energy predictions, like, G3[55], G3B3[56], G3MP2[57], G3MP2B3[56] have also been carried out. When computed data for various methods were analysed it was observed that they all predict a similar kind of behaviour in the PES.

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5.3 Results and Discussions

5.3.1 Formation of Glycine via the carbene route

Both reactions 1 and reaction 3 represent the formation of glycine via dihydroxycarbene route. In case of reaction 1, this carbene is formed from the reaction of CO with H2O and in case of reaction 3, it is formed from the reaction of CO2+H2. The second step in both the reactions is the subsequent reaction of this dihydroxycarbene with CH2=NH to give glycine.

The computed PESs for all these steps involved in the reactions 1 and 3 are shown in Figure

5.1.

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(a) (b)

(c)

Figure 5. 1:PES of the reactions, (a) CO + H2O → ꞉C(OH)2, (b) CO2 + H2 → ꞉C(OH)2, and

(c) ꞉C(OH)2 + CH2=NH → Glycine, calculated using B3LYP/6-31++G(d,p)

method. All the energies reported here are ZPVE corrected and are in the units

of kcal/mol. Diagram is not to scale.

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Optimized geometries of all the stationary points in these PESs are provided in the supporting information. Analysis of the PESs shows that the formation of dihydroxycarbene, either from the CO + H2O [Figure 5.1(a)] or from CO2 + H2 [Figure 5.1(b)] reactions, is endothermic in nature. In the former case, the product dihydroxycarbene is 31.7 kcal/mol higher in energy compared to the reactants, and in the latter case, the dihydroxycarbene is 45.8 kcal/mol higher in energy compared to the reactants. Two barriers in these two reaction surfaces were also located, and it was observed that the barrier of transformation from CO + H2O and CO2

+ H2 leading to the formation of dihydroxycarbene are 64.0 kcal/mol and 72.4 kcal/mol respectively with respect to their respective reactants. Also worth to mention here is that both the reaction passes through the formations of pre-reaction complexes in their respective reaction paths. In the case of CO + H2O leading to the formation of dihydroxycarbene, the pre-reaction complex is 0.6 kcal/mol stable than the reactants and at the same time the nature of interaction existing in this pre-reaction complex can be considered as a hydrogen bonded type of interaction a favourable Keesom type of interaction (the distance between the H-atom of H2O and the C-atom of CO is 2.369 Å). Whereas in the case of CO2 + H2 leading to the formation of dihydroxycarbene, the pre-reaction complex is seems to be 0.5 kcal/mol higher in energy than the reactants and the destabilizing nature of interaction (distance between the

H-atom of the H2 and the O-atom of the CO2 is 2.992 Å) in this pre-reaction complex can be attributed to the non-existent dipole moments of these two interacting molecules. Analysis of the reaction step leading to the formation of glycine from the interaction of the dihydroxycarbene with CH2=NH [Figure 5.1(c)] shows that the reaction passes through the formation of stable complex (10.9 kcal/mol stable compared to the reactants. The stability of the pre-reaction complex can be attributed to the strong hydrogen bonding interaction between the H-atom of the dihydroxycarbene and N-atom of the CH2=NH. The nature of the

H-bonding is very strong as can be evidenced from the small H-bond distance of 1.711 Å)

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Chapter 5 and a low lying transition state (the transition state is 1.8 kcal/mol below the reactants).

Though the transition state of the reaction is below the reactants, presence of a pre-reaction complex in its reaction path shows that the reaction is not truly barrierless. This reaction step was found to be exothermic in nature, where the product, glycine was found to be 63.7 kcal/mol more stable than the reactants. By analysing the energetics, we can say that endothermic nature of the reactions along with large barrier heights, leading to the formation of the dihydroxycarbene can put a question mark on the possibility of the formation of glycine via the carbene route. Detailed investigations on the feasibility of glycine formation via this carbene route can be found in the section 5.3.3.

5.3.2 Formation of Glycine via concerted mechanism

Reactions 2 and 4 represent the formation of glycine via a concerted mechanism. In our previous work we have carried out a thorough computational study on the reaction 2

(formation of glycine from CO + H2O + CH2=NH) and discussed its interstellar significance

[34]. So, this work is only focused on the reaction 4, which represents the formation of glycine via concerted mechanism from the reaction of CO2 + H2 + CH2=NH.

5.3.2.1 PES of the reaction, CH2=NH +H2 + CO2 → Glycine

Computed PES for the reaction 4, i.e. the reaction of CO2 + H2 + CH2=NH leading to the formation of glycine is shown in Figure 5.2 As this reaction is central to this study, investigations have been carried out to know the effect of various basissets on the PES and the results discussed here are from the B3LYP/6-31++G(3df,3pd) method [a comparison of the effects of various basissets on the PES of this reaction is provided in the supporting

172

Chapter 5 information]. Also, if required the B3LYP/6-31++G(d,p) results for this reaction can be compared directly with the results of the reactions 1 and 3. Besides the effects of various basissets, an effort has been made to evaluate the effect of various methods on the PES of this reaction (discussed in the section 5.3.2.3).

Figure 5. 2:PES for the reaction, CH2=NH + CO2 + H2 → Glycine, calculated using

B3LYP/6-31++G(3df,3pd) method. All the energies reported here are ZPVE

corrected and are in the units of kcal/mol. Diagram is not to scale.

Analysis of the PES shows that interaction of the reactants first leads to the formation of a marginally stable pre-reaction van der Waals’ complex (vdw-complex), which subsequently passes through an energetically large barrier to reach the product, glycine. Analysis of the structures of the reactants show that CH2=NH has a fully planar structure (Linear structures of CO2 and H2 are well known). Analysis of the structure of the vdw-complex shows that linearity of CO2 is still conserved and there exist many van der Waals types of interactions between the reactants. Analysis of the structure of the transition state (TS) indicates that it is

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Chapter 5 a 6-membered cyclic transition state. As this TS central to this reaction a detailed discussion related to the structure as well as existing nature of interactions is provided in the section

5.3.2.2. Analysis of the product structure indicates a three dimensional structure for glycine.

Structures of all the stationary points are provided in the supporting information.

Energetically, the pre-reaction complex was found to be 1.0 kcal/mol stable compared to the reactants (3.1 kcal/mol in MP2 method. See Supporting information), indicating a marginally stable vdw-complex. At the same time TS was found to be 71.4 kcal/mol higher in energy than the reactants (72.4 kcal/mol above the pre-reaction complex). This is a clear indication that the forward reaction proceeds through a very large barrier and presence of such a large barrier in the reaction path leading to the formation of glycine, might act as a bottleneck to this reaction. Interstellar feasibility of this reaction is discussed in details in the section 5.3.3.

Analysis of the product shows that it is only 10.3 kcal/mol more stable compared to the reactants (9.3 kcal/mol more stable with respect to the pre-reaction complex), indicating that the reaction is reasonably exothermic in nature. Thus, we can say that at the time when the exothermic nature of the reaction predicts the thermodynamic feasibility of this reaction, the large activation energy puts a question mark on the kinetics of this reaction.

5.3.2.2 Structure and nature of interactions in the TS for reaction 4

Structure of the TS (Figure 5.2) shows a well synchronized placing of the reactants, where the C-atom of the CO2 is close to the C-atom of the CH2=NH, and at the same time H2 is in the close proximity of both CO2 and CH2=NH. In the TS, while the geometry of the H2 molecule is almost intact (a slight increase in the bond distance compared to the reactant H2),

CO2 and CH2=NH show some structural deviations. In the TS, interestingly CO2 is now has a slightly bent structural arrangement rather than its original linear structure. On the other hand,

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in the TS, CH2=NH is no more planar, rather the CH2-unit of the molecule shows some pyramidality. Further analysis of the structure of the TS shows that the approach of the CO2 +

H2 towards the CH2=NH is perpendicular to the CH2=NH molecular plane (perpendicular to the π-cloud of CH2=NH). To know the nature of interaction existing in the TS, electrostatic potentials of the reactants were analyzed and the ESP maps for the reactants are shown in

Figure 5.3.

Figure 5. 3: Computed ESP maps of CH2=NH, CO2 and H2calculated from the B3LYP/6-

31++G (3df,3pd) method at 0.001 au electron density surfaces. Quantitative

values of electrostatic potentials are also in au.

Analysis of the ESP maps shows that: (I) For H2: two ends have positive potentials and the central bond region is having the negative potential, (II) for CO2: two Oxygen ends have negative potentials and the central C-atom has positive potential, (3) for CH2=NH: except the region around N-atom (showing negative potential) all other regions have positive potentials.

Fitting these ESP maps with the TS structure shows a well synchronized approach of the

H2+CO2 towards CH2=NH, where: (i) For H2, while one of the H-atom is interacting with the

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N-atom of CH2=NH, the other H-atom is interacting with one of the O-atom of the CO2. (ii)

For CO2, interestingly which shows bent structure (might have arisen due to reduce in bond order, thus reducing the positive potential in the central carbon region), the other O-atom interacting with the H-atom of the CH2-unit of the CH2=NH (exhibiting a kind of CHO hydrogen bonding type of interaction and the hydrogen bond distance is 2.580 Å). Thus it can be said that the bent structure of the CO2 and pyramidality of the CH2-unit of the CH2=NH, facilitates a well synchronized electrostatic approach of the reactants towards each other.

5.3.2.3 Effects of temperature of the transition state

To account for the effect of temperature on the transition state calculations have been carried out using B3LYP/6-31++G(d,p) optimized geometry of the transition state. Without further geometric optimization we have carried out only the thermal energy corrections to the transition state energies at various temperatures (taking the optimized geometry obtained in the above method, single point energy and thermochemistry calculations have been carried out at the same level of theory using various temperature conditions). Results related to these calculations are shown in Table 5.1.

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Table 5. 1: Results of effect of temperature (in Kelvin) on activation energy of the CH2=NH

+ CO2 + H2 → Glycine reaction. Thermal energy corrected total energies (ET = Sum of the electronic and thermal energies) are in Hartrees and relative energies are in kcal/mol calculated using the B3LYP/6-31++G(d,p) method.

Temperature ET Relative Energy

20 -284.238432 -3.2

50 -284.238137 -3.0

100 -284.237548 -2.6

150 -284.236793 -2.2

200 -284.235840 -1.6

250 -284.234679 -0.8

298.15 -284.233360 0.0

350 -284.231723 +1.0

400 -284.229944 +2.1

450 -284.227983 +3.4

500 -284.225855 +4.7

550 -284.223577 +6.1

600 -284.221162 +7.7

Analysis of the results from the Table 5.1 shows that compared to the room temperature condition, the barrier height getting reduced smoothly when approaching the lower temperature conditions. At 20 K the barrier height is reduced only by 3.2 kcal/mol and may not be considered as a significant. On the other hand when approaching the higher temperature conditions, the barrier height is becoming larger and larger continuously. At 600

K the barrier height is increased by 7.7 kcal/mol compared to the standard room temperature

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Chapter 5 condition. In the light of this observation for the higher temperature conditions, one can say that the limiting value of the barrier height has not yet reached.

5.3.2.4 Effects of various methods on the PES of the reaction 4

To account for the accuracies in the energetics, calculations have been carried out on the PES of the reaction 4 using various methodologies and the results are shown in Table 5.2. Based on our observations related to effect of various basissets on the B3LYP method, during the calculations using various methods, where required a basisset like, 6-31++G(3df,2pd) was used. Analysis of the results shows that all the methods predict more or less similar trend in the energetics of the reaction surface except for the Hartree-Fock method.

Table 5. 2:Results of effect of various methods on the potential energy surface of the

CH2=NH + CO2 + H2 → Glycine reaction. Where ΔE1 = ETS – EREACTANTS, ΔE2 = ETS –

EPRODUCT and ΔE3 = EREACTANTS – EPRODUCT.All the energies reported here are ZPVE corrected and are in the units of kcal/mol.

Methods ∆E1 ∆E2 ∆E3 Methods ∆E1 ∆E2 ∆E3

HF 110.7 117.6 6.9 Full MP2 70.8 85.9 15.1

B3LYP 70.4 80.1 9.7 CBS-QB3 75.5 91.4 15.9

X3LYP 67.9 81.1 13.2 G3 75.8 87.5 11.7

O3LYP 73.0 78.3 5.3 G3MP2 76.7 86.7 10.0

B3PW91 67.0 81.2 14.2 G3B3 76.5 87.9 11.4

MP2(FC) 71.7 85.1 13.4 G3MP2B3 77.3 87.1 9.8

For HF method which doesn’t account for electron correlations, the deviations are large and the barrier height of 110.7 kcal/mol for the forward reaction seems to be highly

178

Chapter 5 overestimated. Among the DFT methods O3LYP methods predicts a slightly large barrier approximately

2.5 kcal/mol higher compared to B3LYP method. On the hand X3LYP and B3PW91 methods predict a slightly lower in barrier height by approximately 2.5 and 3.5 kcal/mol respectively compared to B3LYP method. Analysis of the results from MP2 methods shows that while full

MP2 method predicts a similar barrier like that of B3LYP method, the frozen core approximation of MP2 predicts the barrier to be approximately 1.3 kcal/mol higher compared to B3LYP method. But, on the other hand the MP2 methods predict a comparatively more exothermic nature of the reaction like that of the X3LYP and B3PW91 methods, compared to the B3LYP method. Analysis of the results of the complete basisset method, CBS-QB3 shows that the reaction is more exothermic in nature and proceeds through a comparatively larger barrier (around 5 kcal/mol higher) as compared to the B3LYP method. Results from various composite methods show that the barrier height is larger compared to B3LYP method

(approximately 5.5 kcal/mol higher for G3 and 7.0 kcal/mol higher for G3MP2B3 methods).

Analysis of all these results gives a clear indication that the trend is similar and also the reaction proceeds through a large barrier definitely.

5.3.3 Interstellar possibility of the glycine formation

As extreme temperature conditions are prevailing in the ISM, we tried to explore the possibility of formation of the glycine in both hot-cores as well as cold interstellar clouds, via the carbene route and via the concerted route. In the interstellar medium (ISM), hot-cores are the dense and warm regions consisting of gases and dusts, which are rich in exotic gas chemistries [58, 59]. High temperature in those hot cores can facilitate most of the high barrier reactions and sometimes even the endothermic reactions [58]. On the other hand

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Chapter 5 interstellar clouds have varied properties depending on the temperature of the gas cloud, but are usually have extremely low temperatures [2]. Occasionally gas clouds are found close to a very hot star which heats the gas to about 10,000 Kelvin and thus can facilitate many high energy barrier reactions as well as endothermic reactions, which are practically impossible in the low temperature conditions[60]. At the same time, in the coldest and densest regions of the interstellar medium one can find clouds whose cores contain molecular gases, primarily molecular hydrogen (H2) gas and these molecular clouds have temperatures of only about 10

Kelvin [2, 60].

5.3.3.1 Interstellar feasibility of glycine formation via the carbene route

As discussed earlier, reactions 1 and 3 represent the interstellar formation of the glycine via the carbene route. In both the reactions the first step is the formation a dihydroxycarbene. For both the reactions the second step is same, where the generated carbene react with CH2=NH to give glycine. In both the reactions it was found that the second step is highly exothermic in nature and also at the same time, located pre-reaction complex and the transition state being lower in energy than the reactants. Such a situation can make the reaction very much feasible in both hot-cores as well as cold interstellar clouds. But, the real problem arises in the first steps of both the reactions. As shown in Figure 5.1(a) and (b), for both the reactions formation of the dihydroxycarbene highly endothermic in nature and also are associated with large reaction barriers. As reactions with a barrier or any endothermic reactions are completely forbidden to happen in the interstellar clouds, where the temperatures are extremely low [2]; one can say that the formation of the dihydroxycarbene in those cold interstellar clouds will definitely not happen either via the CO + H2O reaction or via the CO2

+ H2 reaction. But, on the other hand owing to the prominent hydrogen dynamics exhibited

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Chapter 5 by all the transition states in the carbene route and in the light of some recent studies related to possibility of tunnelling in endothermic reactions at very low temperature condition

(powered by Tunnelling Ready States) [61-63], possible formation of glycine via the carbene route assisted by tunnelling needs a separate investigation to give it a second thought. But, at this stage one can say that formation of glycine through the carbene route via the reactions 1 and 3 seems impossible in the cold interstellar clouds. With the hope that presence of other molecules in these reaction paths might be able to bring some changes to the course of these reactions, we have tried to introduce the water molecule in the reaction path in order to know whether it is going to reduce the barrier heights for the reactions shown in Figure 1(a), (b) and (c) or even the nature of these reactions. After many attempts with various possible input geometric orientations of the reactants, we were not able to locate any transition states in the reaction potential energy surfaces of these three reactions. As we have not carried out similar investigations with any other molecules rather than water, hence a definite conclusion can’t be made at this stage on the role of other molecules on these routes of formation of Glycine.

On the other side, in the extreme high temperatures of the hot-cores or in the gas clouds which are close to a very hot star, the feasibility of this reaction can be expected. But, analysis of the dissociation reactions of the dihydroxycarbene [reverse reactions in Figure

1(a) and (b)] to CO + H2O and CO2 + H2 shows that they are 32.3 kcal/mol and 26.6 kcal/mol respectively. This gives very clear indication that the dihydroxycarbene will have very short life time and sometimes being highly unstable it might readily dissociate back to the reactants. With this stability issue associated with the dihydroxycarbene, we can say that formation of glycine via the carbene route is still doubtful even in the hot-cores of the interstellar medium.

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5.3.3.2 Interstellar feasibility of formation of glycine via the concerted route

As discussed earlier, reaction 2 and 4 represent the interstellar formation of the glycine via the concerted mechanism. From these two concerted paths leading to the formation of glycine, reaction 2, where CO and H2O are involved is already discussed in great details in our previous work [34]. There we have shown the possible interstellar formation of glycine via this route in both hot-cores as well as in cold interstellar clouds[34]. We have also discussed the catalytic role of the water molecules to show how this reaction behaves like a barrierless reaction in the presence of excess water and thus making it possible to happen in the cold interstellar clouds [34]. So, in this work we have discussed only the fate of the reaction 4 in the drastic interstellar conditions. Though the interstellar time scale is large, still the reactions where large numbers of molecules are involved in the reaction process can be expected to be kinetically less probable. As the reaction 4, proceeds through the formation of a stable pre-reaction vdw-complex (a super molecule), the kinetic behavior of the reaction can be expected to be unimolecular. The only problem arises here is the probability of the formation of this super molecule and this largely depends on the molecular composition of the ISM. It is well known that hydrogen covers around 90% of the universe by number density and 75% by mass density [64]. Also, it is well known that CO2 is one of the most abundant molecules in the ISM besides CO and H2O [65, 66]. Though CO2 is not quite evenly distributed in the ISM, but a large abundance of CO2 can be found in many hot cores

[65] as well as colder regions of ISM as CO2-ice[66]. Methanimine (CH2NH) was first detected in Sgr B2 by Godfrey et al. (1973)[67], then subsequently has been found in many other hot core sources [68], and also recently Salter et al. detected it in the ultraluminous infrared galaxy (ULIRG) Arp 200 which is 250 million light years away, with the Arecibo radio telescope; certainly a remarkable discovery [69]. Interestingly, besides the availability

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in hot cores, CH2=NH was also observed to be present in the quiesceny gas at the so-called

“radical-ion peak” along the Orion ridge, where the temperature is about 20K and also expected to be present even at regions of 10K or low temperatures [68]. On the basis of this, along with the large concentrations of the H2 and CO2 available in ISM, formation of this complex is fairly probable. Once the complex is formed the reaction will precede towards a unimolecular kinetics pathway to give glycine as an end product.

As discussed earlier, reaction 4 leading to the formation of glycine proceeds through a very high barrier, which we believed can act as a bottleneck to the possibility of the reaction in the

ISM. But, owing to the availability of all the three reactants in the hot-core regions [64, 65,

67-69], powered by the high energies of the hot cores [58], the reaction can be expected to be very much feasible. Thus one can say that the formation of glycine in the hot-core regimes of the ISM is quite feasible. On the other hand, as the reaction 4 proceeds through a very high barrier, this large barrier height can act as a bottleneck to this reaction to happen in the extremely low temperature conditions existing in the interstellar clouds. Also as discussed in the section 5.2.2.3., the decrease in the barrier height at lower temperature is not at all significant and thus eliminating the classical way of approaching the product by climbing the barrier. The only way this reaction will be possible at such low temperatures, if there is an operative tunnelling mechanism. To analyse the possibility tunnelling mechanism, our first check was the imaginary frequency of the TS. It is known that, one can have some qualitative information about the width of a barrier from its imaginary frequency [70], where the lower value of the TS imaginary frequency is associated with a gentler and broader barrier, and the higher value of imaginary frequency corresponds to a sharper and narrower barrier [70]. The value of imaginary frequency of the TS here was found to be around 1600i cm-1. This indicates that the barrier might not be as sharper as expected. We believe that this might be

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Chapter 5 due to the simultaneous proton dynamics arising from the two H-atoms. Analysis of the displacement vectors related to vibrations due to the imaginary frequency shows that two concurrent movements of H-atoms with almost sole contributions to the vibrational coefficients and that to in partially opposite vectorial directions. Such a situation might have some effect on widening the barrier to a little extent. Nevertheless owing to the considerably large value of the imaginary frequency (1600i cm-1) arising from the protuberant movements of the two light H-atoms, one can happily advocate for the effects of tunnelling, especially at very low temperatures [70].

Though the above discussion related to the imaginary frequency of the TS advocates for a tunnelling phenomenon to happen in the low temperature conditions, but it is generally believed that presence of an entry channel weakly bound complex might be able to facilitate the process further [70, 71]. As mentioned by Smith et al. (2002), existence of such a pre- reaction complex can manifest itself in terms of the negative temperature dependence, i.e. show the significant deviation from the Arrhenius behaviour at extremely low temperatures

[71]. The vdw-complex shown in the PES of the reaction 4 (Figure 5.2) may not play a significant role while dealing with high temperature conditions for the reaction, but its presence will have a vital effect in extremely low temperature conditions and probably could help in facilitating the tunnelling to happen for this reaction. Though the reaction is having a very large barrier, the prominent effect of tunnelling will be able to make this reaction feasible and thus the formation of the glycine in the low temperature regime of the ISM through this concerted mechanism will possible happen. In this work qualitatively we predicted about the possibility of tunnelling from the quantitative value of the imaginary frequency of the transition state. Due to unavailability of the required computing softwares to carry out the kinetics calculations, we were unable to exactly confirm our qualitative

184

Chapter 5 prediction about the possibility of tunnelling. But, in view of the prominent proton dynamics, a tunnelling possibility can be advocated for this reaction at low temperature conditions.

It is generally believed that in the ISM, CH2=NH on hydrogenation reaction produces

Methylamine, CH3-NH2[68]. This methyl amine then subsequent reaction with CO2 produces

+ - methylammonium methylcarbamate ([CH3NH3 ] [CH3NHCOO ]), which after UV irradiation

+ - evolve into ([CH3NH3 ] [NH2CH2COO ]), a glycine salt precursor, instead of glycine [72].

Though this proposed multiple-step process was not able to produce glycine as an end product, still starting with the same reactants, for the first time we were able to show a single- step reaction for the formation of glycine in the ISM. Moreover we have shown the universality of this reaction irrespective of the divergent temperature conditions existing in the ISM. Owing to the interstellar conditions, we believe that single-step reactions have advantages over the multi-step processes and hope this finding will have much more interstellar significance. Moreover with the hope that presence of other molecules in this reaction path might be able to bring some changes to the course of this reaction, we have tried to introduce the water molecule in the reaction path in order to know whether it is going to reduce the barrier height for the reactions 4. After many attempts with various possible input geometric orientations of the reactants, we were not able to locate any transition state in the reaction potential energy surface of this reaction. As we have not carried out similar investigations with any other molecules rather than water, hence a definite conclusion can’t be made at this stage on the role of other molecules on this route of formation of Glycine.

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5.4 Conclusions

In conclusion, in this work, using computational calculations, we have analyzed two different routes, (1) via a carbene intermediate, and (2) via a concerted reaction path for the possible interstellar formation of glycine. Based on the analysis of the potential energy surfaces for those reactions which proceed though the carbene intermediate paths, it has been suggested that the formation of glycine via this route seems impossible in the interstellar medium. The background for these suggestions comes from the endothermic of the reactions steps leading to the formation of this dihydroxycarbene. On the other hand one of the reactions studied in this work, CH2=NH + CO2 + H2 → Glycine, which proceeds through a concerted mechanism, has been suggested as favorable path for the interstellar formation of glycine. It was found that this reaction is having a very large energy barrier and has been proposed that it will be very much feasible in the hot-core regions of ISM. At the same time, by the analysis of the nature of the barrier for this reaction, from its imaginary frequency and also the prominent proton dynamics it is exhibiting, we have advocated for the tunnelling to happen.

With the aid from an entry channel vdW-complex and the proposed tunnelling to happen, the reaction is also suggested to form glycine easily in the colder regions of ISM, thus demonstrating its universality. The reaction though exothermic in nature, owing to the lower value of enthalpy of formation, a detailed kinetics calculations/experiment will probably be able to give an exact picture of the rate constant for this reaction for the hot-core formation of glycine. On the other hand, for the kinetics related to low temperature formation of glycine, where tunnelling plays a vital role, the simultaneous movement of the two H-atoms in the TS for this case can be viewed as a correlated many body tunnelling type [73] and also need further experimental as well as computational investigations.

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Supplementary Information: Optimized geometries for the reactants, TS, and product for the reaction 4 are shown in Figure S5.1 (for B3LYP method), Figure S5.2 (For MP2 method) and Potential energy surface for the MP2 method is shown in Figure S5.3.

Thermodynamic data for effect of various basissets for B3LYP method on the PES of reaction 4 are shown in Table S5.1. Geometries of TS for various methods are shown in

Table S5.2 (and effect of basissets in Table S5.3) and also the optimized Cartesian coordinates of the stationary points are provided. Besides reaction 4, optimized geometries of the stationary points for reaction 1 and 3 are also provided.

TOC Graphics

Possible interstellar formation of Glycine through a concerted mechanism: A computational study on the reaction of CH2=NH, CO2 and H2

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CHAPTER 6

AN ALTERNATE AND SHORTEST ROUTE FOR THE FORMATION

OF GLYCINE USING EITHER STRECKER’S OR MILLER’S

INGREDIENTS: A COMPUTATIONAL STUDY ON THE

HEMIAMINAL INTERMEDIATE ROUTE

Abstract: Using computational chemistry calculations, we have discussed two simple two-

+퐶푂 step paths (Path-I: 퐻2퐶 = 푂 + 푁퐻3 → α − hydroxy amine → 퐺푙푦푐푖푛푒, Path-II: 퐻2퐶 =

+퐶푂 푁퐻 + 퐻2푂 → α − hydroxy amine → 퐺푙푦푐푖푛푒) for the formation of glycine, which passes through a hemiaminal intermediate (α-hydroxy amine). Our calculations show that both the paths are thermodynamically favourable. Further analysis shows that in the interstellar conditions these two paths are feasible only in hot-cores, but not in the cold interstellar clouds

(Cold-core formation of glycine is possible only if CH2=NH, H2O and CO of Path-II, react in a concreted manner in the presence of excess water). For the laboratory synthesis of glycine, the possibility has been suggested via Path-I subjected to the condition that the reaction is being carried out as one-pot synthesis at a controlled temperature. This study can further be extended to the preparation of other α-amino-acids with a suitable choice of the aldehyde and even based on the mechanism it can be even predicted to give an enantiomeric excess. We think that this work not only will be able to enrich our future understanding about glycine (or

α-amino-acids) formation in interstellar medium, but also suggests alternative paths for laboratory synthesis of the glycine (or α-amino-acids) using the ingredients of either

Strecker’s synthesis or Miller’s experiment.

Keywords: Glycine, Interstellar Medium, ISM, CH2=NH, HCHO, NH3, CO, H2O.

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6.1 Introduction

The fundamental question associated with the genesis of life is related to the formation of the essential life elements, i.e., the amino-acids of the nature [1-3]. Among all the amino-acids, glycine, (H2N-CH2-COOH) is the simplest amino-acid found in the earth. Astronomical search for glycine began as soon as the laboratory spectra for it were available [4]. Till date presence of this simplest amino-acid in the interstellar medium (ISM) is still in dispute [5-7].

But on the other hand, many amino-acids including glycine have been found on meteorites samples collected by various researchers [8-19]. In a recent discovery glycine is being detected even in comets, as evidenced from the pristine cometary samples reverted back by

NASA STARDUST mission [18], which can be treated as a validation for its extraterrestrial origin. On the other hand our knowledge on its possible formation in the extraterrestrial space through various chemical pathways is ever expanding with the advent many new researches.

To imitate the synthesis of glycine in laboratory, there are two most widely exploited approaches can be found in the literature. First one is the Strecker’s synthesis [20, 21], and the second one is the Miller experiment [22-24], where in both the cases it is believed that the key reactant is the HCHO (formaldehyde). If both the reactions are viewed from the step where the H2C=O reacts with the NH3 and then it can be said that in both the case it results in the formation of a most important intermediate, the amino nitrile compound. This amino nitrile compound with a multiple hydrolysis step then produces an α–amino-acid, which is glycine. Thus in both the cases the overall process leading to the formation of glycine comprises of many steps. In a recent study “Discovering chemistry with an ab initio nano- reactor” Wang et al. (2014), have shown that the formation of glycine is possible via numerous pathways and they have used highly accelerated first-principle molecular dynamics

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simulation of the classic Urey-Miller experiment, where the initial reactants were H2, CO,

H2O, NH3 and CH4[25]. From the various possible pathways, one of the pathways represents the formation of glycine through the formation of a stable intermediate, α-hydroxy amine

(belongs to the general class called “Hemiaminals” or “Carbinolamines”) and seems to us as quite simple and comprises only two steps [25]. As discussed in their work, formation of this stable intermediate, α-hydroxy amine can be achieved by a simple reaction of formaldehyde with the ammonia, as shown in Reaction 1 [25]. At the same time formation of glycine from the α-hydroxy amine can be achieved also from a simple reaction between this α-hydroxy amine with CO directly [25]. Interestingly comparison of the chemical composition of α- hydroxy amine with the glycine, it can be found that they differ from each other by a unit of

‘CO’.

Reaction 1

HCHO NH3 H2N-CH2-OH + → (Formaldehyde) (Ammonia) (α-hydroxy amine)

Reaction 2

H2N-CH2-OH CO H2N-CH2-COOH + → (α-hydroxy amine) (Carbon monoxide) (Glycine)

Now looking again at the starting reactants, the intermediate α-hydroxy amine and the final product, glycine, the question arises here is that, instead of the multiple steps involved either in the Strecker’s[20, 21] synthesis or Miller’s experiment [22-24]“will it be possible to get the glycine directly from the reaction of α-hydroxy amine with CO?” In other words, will it be possible to get the glycine just from the two-step reaction as shown above, using either

198

Chapter 6 the Strecker’s or Miller’s ingredients used for the synthesis of glycine? To the best of our knowledge, no one till-date has tried to study this reaction experimentally. Only in the recent work of Wang et al. (2014) [25] it is only indicated that such a reaction is possible but without further detailed discussion about either the complete reaction profile and its implications either in the interstellar context or in the laboratory synthesis. So, in this work using computational calculations, we have tried to explore the feasibility of such reaction steps. We have analyzed the complete potential energy surfaces of these two reaction steps

(Reaction 1 and Reaction 2) leading to the formation of Glycine. We have also carried out computations and discussed an alternative reaction path for the Reaction 1, where instead of the reaction between HCHO and NH3 leading to the formation of α-hydroxy amine, CH2=NH

(which is known as Methanimine and is isoelectronic with the HCHO. Also this is an important intermediate in the imine route of synthesis of glycine via Strecker’s synthesis [20,

21]) and H2O reacts with each other to give the same product α-hydroxy amine (Reaction 3).

The reverse reaction of Reaction 3, i.e., dissociation of α-hydroxy amine to Methanimine and water is also indicated in the same work of Wang et al. (2014)[25]. Besides its significance either in the Miller’s experiment or in the Strecker’s synthesis, the other motivation behind considering this alternative reaction step leading to the formation of α-hydroxy amine is based on its interstellar importance.

Reaction 3:

H2C=NH H2O H2N-CH2-OH + → (Methanimine) (Water) (α-hydroxy amine)

6.2 Computational Methods

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All quantum-chemical calculations have been performed using Gaussian 09 package and the geometries of all the stationary points in the PES have been visualized using GaussView program [26]. In this work, all DFT (density functional theory) calculations reported were performed at the B3LYP [27, 28] exchange–correlation functionalities theoretical level and using a large basisset like, 6-31++G(3df,2pd). Calculation related to test the effects of various basisset using the B3LYP methods were also performed. Besides the B3LYP method, we have also carried out calculations using various composite methods (which are known for accurate energy predictions) like, G3 [29], G3B3 [30], G3MP2 [31], G3MP2B3 [30] and

G4MP2 [32]. Harmonic vibrational frequencies were computed to evaluate the zero-point vibrational energy (ZPVE) corrections, which have been included in all the obtained energies.

It is notable that no imaginary frequencies were found for the minima, which verify that the minima obtained in the PES were true minima at all of the theoretical levels. Transition states were confirmed from analysis of their frequencies by ensuring that only one imaginary frequency for each of these transition states. We have also carried out the analysis of the displacement vectors for the imaginary frequency to ascertain that the obtained transition states were structurally true TS and also confirmed by the IRC (intrinsic reaction coordinates) analysis [33]. The energies of the transition states were also compared with the energies of the reactants to ascertain that the obtained transition states are also energetically true transition states. The data reported in the main text of the article are mainly from the

B3LYP/6-31++G(3df,2pd) calculations, unless otherwise mentioned specified, and the data from other methods are provided in the supporting information.

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6.3 Results and discussions

6.3.1 PES of the Reaction 1 (H2C=O + NH3 → H2N-CH2-OH)

Computed potential energy surface of the reaction of HCHO with the NH3 leading to the formation of the stable intermediate α-hydroxy amine (Reaction 1) is shown in Figure 6.1.

Though there are theoretical studies available in the literature for the Reaction 1 [34], still we have revisited this step to show the complete potential energy diagram of the process leading to the formation of glycine with the same method of study used for other reactions. As shown in the PES, the interaction of the formaldehyde with the ammonia leads to the formation of a pre-reaction complex first (this pre-reaction complex was found to be a potential well in the reaction potential energy surface), which subsequently passes through a transition state leading to the formation of α-hydroxy amine, a hemiaminal intermediate as the final product.

This α-ydroxy amine is regarded as the important intermediate in the Strecker’s synthesis as well as in the famous Urey-Miller experiment. Formation of the α-hydroxy amine through the path as shown in Figure 6.1 was found to be slightly exothermic, which indicates the feasibility of the reaction from the thermodynamic or energetic point of view.

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Figure 6. 1: B3LYP/6-31++G(3df,2pd) optimized PES for the H2C=O + NH3 → H2N-CH2-

OH (α-hydroxy amine), reaction. All the energies are ZPVE corrected and are in

kcal/mol. The diagram is not to scale.

Analysis of the association complex between the formaldehyde and ammonia (which is the pre-reaction complex) shows that the distance between the C-atom of the H2C=O and N-atom of the NH3 is 2.936 Å. The complex was found to be only 1.3 kcal/mol below the reactants,

HCHO and NH3. From the orientations of the two reactants as seen in the geometry of the complex and also from the large distance between the two reactants, the nature of interaction can be regarded as physical type of interaction in nature. To have a qualitative idea about the nature of interaction we have computed the electrostatic potentials (ESP) of the reactants and the computed ESP maps are shown in Figure 6.2. Analysis of the ESP maps of the CH2=O shows that there are negative potentials around the O-atom and positive potentials around the

CH2-unit. Similarly, analysis of the ESP maps of the NH3 shows that there are negative potentials around the N-atom and positive potentials around the three H-atoms. Now, incorporating the ESP maps into the geometric orientation of the complex, the nature of interaction seems more like electrostatic interaction in nature [35]. The HNO angle away

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Chapter 6 from 90 o and the large distance between the reactants can be explained considering the ESP maps of the reactants. It can be seen that when NH3 approaches the HCHO either in a perpendicular way or with any angle small than 90 o and are close to each other the negative potentials around the O-atom of HCHO will exert an repulsion to the negative potentials around the N-atom of the NH3. Such a repulsive interaction is prominent due to the short C-O distance (1.206 Å) and thus the geometry of the complex is arising as a result of the balance between such repulsive interactions to that of the attractive electrostatic interaction between the positive ESP around the C-atom of the HCHO and the negative ESP around the N-atom of the NH3.

Figure 6. 2: Computed ESP maps of H2C=O and NH3 calculated using B3LYP/6-31++G(d,p)

method at 0.02 au electron density surfaces. Quantitative values of electrostatic

potentials are also in au.

The pre-reaction complex then passes through a transition state with a barrier height of

32.8 kcal/mol. Analysis of the geometry of the transition state shows that it is structurally close to the pre-reaction complex. The one major difference is at the CH2-unit of CH2=O, which was fully planer in the pre-reaction complex now became slightly pyramidal in the transition state. The other differences are: one of the N-H bonds of the NH3 in the transition

203

Chapter 6 state is now elongated (this elongated bond distance is 1.187 Å), the distance between N- atom of NH3 and the C-atom of the HCHO is 1.575 Å, and the distance between the elongated H-atom of NH3 and the O-atom of the HCHO is 1.415 Å. Analysis of the displacement vectors associated with the imaginary frequency of the transition state shows a prominent proton dynamics. In the light of this observation, to see if there is any possibility of tunnelling mechanism, our first check was the imaginary frequency of the TS. It is known that, one can have some qualitative information about the width of a barrier from its imaginary frequency [36-38], where the lower value of the TS imaginary frequency is associated with a gentler and broader barrier, and the higher value of imaginary frequency corresponds to a sharper and narrower barrier [36-38]. The value of imaginary frequency of the TS here was found to be around 1530i cm-1, which indicates that, the barrier is in fact sharper. Such a sharp and narrow barrier found in this case advocates for the phenomena of tunnelling to happen in this reaction leading to the formation of α-hydroxy amine. The geometry of the α-hydroxy amine is shown in the Figure 6.1, where the NH2 unit is pyramidal and the molecule is stabilized by many favorable intramolecular hydrogen bonding interactions existing between the –NH2 and –OH substituents. The product α-hydroxy amine was found to slightly stable than the reactants (7.2 kcal/mol) or the pre-reaction complex (5.9 kcal/mol) and thus making the overall transformation reaction to be exothermic as well as thermodynamically favorable. We have also observed that the effect of basissets and methods

(energetics data provided in the supporting information) on the PES are much less pronounced.

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6.3.2 PES of the Reaction 2 (H2N-CH2-OH + CO → H2N-CH2-COOH)

Figure 6. 3: B3LYP/6-31++G(3df,2pd) optimized PES for the H2N-CH2-OH + CO → H2N-

CH2-COOH (glycine), reaction. All the energies are ZPVE corrected and are in

kcal/mol. The diagram is not to scale.

Computed potential energy surface of the reaction of the α-hydroxy amine which was formed in the reaction 1, with the carbon monoxide leading to the formation of the glycine is shown in Figure 6.3. In the other words, the computed PES of the Reaction 2 is shown in Figure

6.3. As shown in the PES, the interaction of the α-hydroxy amine with the carbon monoxide leads to the formation of a pre-reaction complex first (this pre-reaction complex was found to be a potential well in the reaction potential energy surface), which subsequently passes through a transition state leading to the formation of glycine as the final product. Formation of the glycine through the path as shown in Figure 6.3 was found to be exothermic, which indicates the feasibility of the reaction from the thermodynamic or energetic point of view.

Also feasibility of this reaction step indicates that one can be able to get the glycine in very few steps from the Miller’s ingredients using the alternative pathways discussed in this work.

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Figure 6. 4: Computed ESP maps of H2N-CH2-OH and CO calculated using B3LYP/6-

31++G(d,p) method at 0.02 au electron density surfaces. Quantitative values of

electrostatic potentials are also in au.

Analysis of the association complex between the α-hydroxy amine and CO (which is the pre-reaction complex) shows that though it is a potential well in the reaction PES, but it is only

0.1 kcal/mol more stable than the reactants. From the geometry of the complex it was observed that all the interaction distances between the two reactants are all > 4.0 Å, which is a clear indication of the fact that the nature of interactions existing between the two reactants are merely of physical interaction in nature. To have some qualitative idea about the nature of interactions existing between the two, we have computed the ESPs of the two reactants and are shown in Figure 6.4. Analysis of the ESP map of the α-hydroxy amine shows that there are negative potentials around the N-atom and O-atoms, positive potentials around all the H- atoms and slightly positive potentials around the CH2-unit. On the other hand, analysis of the

ESP map of the CO shows that there are negative potentials around both C- and N-atoms.

The central bond region has positive potentials. Incorporating the ESP maps of the reactants

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Chapter 6 into the geometry of the pre-reaction complex, it can be seen that though there are favorable interactions, still negative potentials of the O-atom of the CO is experiencing an enormous repulsion from the negative potentials around the N-atom of the α-hydroxy amine, thus making the reactants separated by a large distance.

This pre-reaction weak association complex then passes through a transition state to give glycine as the end product. The barrier height for this transformation with respect to the pre-reaction complex was found to be 57.7 kcal/mol. In the transition state the CO moves close to the σ-hole region of the C-N bond of the α-hydroxy amine, making the C-atom of the α-hydroxy amine and C-atom of the CO to interact with each other. Also, at the same time, due to the close proximity of the –OH substituent after it being detached, is now able interact with the C-atom of the CO with its O-atom. Such an interaction also may be due to the fact that now the –OH is also close to the σ-hole region (the C-C-O angle was found

o to be 34.3 ) [35, 39-42]. In the transition state the CH2 unit was found to be planar (it was in the pyramidal shape in the α-hydroxy amine) and the transition state interaction is a three membered cyclic ring between C-C-O atoms. We found the distances between the C-atom of the α-hydroxy amine and C-atom of CO to be 2.704 Å, the distance between the O-atom of the OH and C-atom of the CO to be 1.523 Å, and the distance between O-atom of the OH and the C-atom of the α-hydroxy amine to be 2.301 Å. Analysis of the displacement vectors associated with the imaginary frequency of the transition state shows a complex vibration with the value of imaginary frequency as 404i cm-1. In the light of this observation and based on this behavior, phenomena of tunnelling can be completely ruled out, and the barrier can be predicted to gentle and broader [36-38]. The optimized structure of the product, glycine is shown in Figure 6.3 and also discussed in details in our pervious works related to the possible interstellar formations of glycine [38]. The product glycine was found to 19.0

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Chapter 6 kcal/mol stable than the reactants or 18.9 kcal/mol stable than the pre-reaction complex, and thus making the overall transformation reaction to be exothermic as well as thermodynamically favorable. We have also observed that the effect of basissets and methods

(energetics data provided in the supporting information) on the PES are much less pronounced.

6.3.3 PES of the Reaction 3 (H2C=NH + H2O → H2N-CH2-OH)

Figure 6. 5:B3LYP/6-31++G(3df,2pd) optimized PES for the H2C=NH + H2O → H2N-CH2-

OH (α-hydroxy amine), reaction. All the energies are ZPVE corrected and are in

kcal/mol. The diagram is not to scale.

Computed potential energy surface of the reaction between Methanimine with water

(Reaction 3) is shown in Figure 6.5. As discussed earlier Reaction 3 is an alternative reaction path for the Reaction 1. The reverse reaction of Reaction 3, i.e., the endothermic dissociation of α-hydroxy amine to Methanimine and water is also indicated in the same work of Wang et al. (2014)[25], but without further detailed discussion about its complete reaction profile.

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This alternative path has an advantage and that is the reactant H2O is abundantly available in interstellar space than the NH3. As shown in the PES, the interaction of the CH2=NH with the

H2O leads to the formation of a pre-reaction complex first (this pre-reaction complex was found to be a potential well in the reaction potential energy surface), which subsequently passes through a transition state leading to the formation of α-hydroxy amine as the final product. Formation of the α-hydroxy amine through the path as shown in Figure 6.5 was found to be exothermic, which indicates the feasibility of the reaction from the thermodynamic or energetic point of view.

Figure 6. 6:Computed ESP maps of H2C=NH and H2O calculated using B3LYP/6-

31++G(d,p) method at 0.02 au electron density surfaces. Quantitative values of

electrostatic potentials are also in au.

Analysis of the association complex between CH2=NH and H2O shows that it is a stable H- bonded complex, which is energetically 3.9 kcal/mol below the reactants. The interaction distance between the two was found to be 1.956 Å, indicating a strong hydrogen bonding type of interaction. To have an idea about the nature of interaction existing in this complex,

ESPs were computed and the ESP maps are shown in Figure 6.6. Analysis of the ESP maps

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show that there are negative potentials around the N-atom of CH2=NH and all other atoms mostly have positive potentials around them. At the same time for H2O, negative potentials are around the O-atom and positive potentials are around the two H-atoms. Fitting the ESP maps of the two reactants into the complex geometry, a highly favorable electrostatic interaction between the two reactants can be visualized for the pre-reaction complex.

This pre-reaction complex then passes through a barrier of height 46.0 kcal/mol to give the final product, α-hydroxy amine. Analysis of the transition state geometry shows that, while moving from the complex to the transition state, the water molecule which was previously almost in the same plane of the CH2=NH, now moved to a plane almost perpendicular to the plane of the CH2=NH and also one of the O-H bond is elongated to 1.654 Å. The other two major parameters in the transition state are, the distance between the N-atom of the CH2=NH and elongated H-atom the H2O which is 1.070 Å, and the distance between the O-atom of the

H2O and C-atom of the CH2=NH which is 2.274 Å. Analysis of the displacement vectors associated with the imaginary frequency of the transition state shows a prominent proton dynamics, but the value of the imaginary frequency was found to be around 585i cm-1, which is an indication that the barrier is gentle and broader [36-38]. We have attempted to explain such a broadening of barrier width based on the sudden transformation of the geometry while moving from the complex to the transition state. Analysis of the structures of the stationary points in the PES indicates that the geometries of the transition state and product (3D structures) are quite different to that of the complex (pseudo-2D structure). Thus we think, the presence of the pre-reaction complex creates the geometric constraints by the directionality nature of its hydrogen bonding and renders no geometric synergy between the

TS and the complex. This lack of synergy in the orientations or geometries between the complex-TS-product might be the factor responsible for broadening of the transition state

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Chapter 6 width in this case. Thus one can say that, when the protuberant movement of the H-atom of the H2O advocates for the possibility of tunnelling phenomena, at the same time the lower value of imaginary frequency, stands as a difficulty for the tunnelling phenomena to happen

[36]. Based on these two observations, in our view the phenomena of tunnelling for this reaction can’t be completely ruled out, instead we can say that the tunnelling might be able to assist the reaction at lower temperature conditions, but the tunnelling rates might be very small. The geometry of the α-hydroxy amine has been discussed already in the section 6.3.1.

In this case, the α-hydroxy amine was also found to slightly stable than the reactants (9.2 kcal/mol) or the pre-reaction complex (5.3 kcal/mol) and thus making the overall transformation reaction to be exothermic as well as thermodynamically favorable. We have also observed that the effect of basissets and methods (energetics data provided in the supporting information) on the PES are much less pronounced for this reaction potential energy surface.

6.3.4 Possible applications in the laboratory synthesis of Glycine

As discussed in the introduction, in this two-step reaction leading to the formation of glycine, the intermediate α-hydroxy amine can be considered as a very important intermediate [25]. In this work we have proposed two different routes (Reaction 1 and Reaction 3) for the formation of this intermediate compound. In the Reaction 1, where the formation of glycine is from the HCHO and NH3 reaction passes through a barrier of 32.8 kcal/mol high and at the same time being exothermic it is thermodynamically favorable. On the other hand, Reaction

2, where the formation of glycine is from the reaction of CH2=NH, the imine with H2O, which is also being exothermic in nature again thermodynamically favorable, but the reaction passes through a barrier of 46.0 kcal/mol. Comparing these two different reactions leading to

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Chapter 6 the formation of α-hydroxy amine it can be said that Reaction 1 is more favorable and also more preferable over Reaction 2. The other disadvantage associated with the Reaction 2 is that this simplest and the smallest imine, CH2=NH is not stable and is in fact a transient molecule. Thus, to make this Reaction 2 possible, one need to generate this imine in-situ, this then can react with the water and will be able to produce the α-hydroxy amine. Whereas the advantages associated with the Reaction 1 is that both the reactants HCHO and NH3 are very stable and also readily available. As in both the reactions, the product, α-hydroxy amine is marginally stable compared to their respective starting reactants, at elevated temperature which is necessary to surpass the barrier, stability of the α-hydroxy amine is an issue needs to be taken into account [42-50]. From the analysis of the structure of the α-hydroxy amine it can be said that it is more susceptible to undergo a water elimination reaction, i.e., with an elimination of water molecule, this hemiaminal will be converted to an imine [42-50]. This water elimination process is nothing but the reverse process of the Reaction 3, [25] where the barrier height for the water elimination reaction can be regarded as 47.4 kcal/mol. Thus it can be said that, both the forward (for which the barrier height is 46.0 kcal/mol) as well as reverse reaction steps for the Reaction 3 will be very much competing with each other at elevated temperature. In the other words the α-hydroxy amine formed via Reaction 3 might dissociates back to the reactants immediately at elevated temperature conditions. Also, from the analysis of the Reaction 1, it can be said that at elevated temperature conditions in this case also the α- hydroxy amine will dissociate to CH2=NH + H2O rather than to HCHO + NH3. In favor of this argument we can infer to the nature of the barriers in both the reaction potential energy surfaces, where for the Reaction 1 the barrier is sharp and narrow, and for the Reaction 3, the barrier is smooth and broader. Owing to the existing nature of the barriers present in the potential energy surfaces of the two reactions, i.e., Reaction 1 and Reaction 3, one can say that they are definitely going to intersect with each other at some point close to the α-

212

Chapter 6 hydroxyamine. Now, if this water elimination reaction acts as a reverse process for the

Reaction 1, then the reverse process for the reaction has to pass through a barrier of 47.4 kcal/mol. But, the barrier height for the forwards process of the Reaction 1 is of

32.8 kcal/mol. Thus, with a large difference in the barrier height for the forward and reverse process of the Reaction 1, a controlled temperature condition will be able to make the reaction realizable in the laboratory.

The next step in the path leading to the formation of glycine is the reaction of this α-hydroxy amine with CO. Now, CO being commercially available and the Reaction 2 being thermodynamically favorable, this reaction can be predicted to be efficient enough to produce glycine. But, for this reaction to happen it has to pass through a barrier of around 57.6 kcal/mol and thus elevated temperature conditions are necessary to make the reactant surpass the barrier. Now with the final product in this reaction step, i.e., glycine, which is around 19.0 kcal/mol more stable than the reactants, it can be said that with a controlled temperature condition, one will be able to produce glycine through this reaction with much efficiency.

From the previous discussion, it is known that at such an elevated temperature (which is required to at-least to surpass the barrier height of 57.6 kcal/mol) it might be quite possible that the reactant, α-hydroxy amine might dissociate to give CH2=NH + H2O (the barrier for this dissociation is 47.4 kcal/mol). Thus, in our view instead of the step by step reaction, the

HCHO, NH3 and CO can be mixed in one pot (one-pot synthesis) or in the other words mixture of the NH3 and CO can be made pass through the liquid formaldehyde to make the formation of glycine more feasible. The major advantage in such a one-pot synthesis approach can be that as soon as the α-hydroxy amine produced in the reaction pot, instead of going through a dissociation process it can immediately react with the large excess of CO present in the reaction pot to produce glycine. From the above discussion we can say that

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using HCHO, NH3 and CO as the starting reactants, one can be able to produce glycine efficiently in a one-pot synthetic process via a two-step mechanism. In our view such a two- step path is definitely going to advantageous over the multi-step paths proposed either in the

Miller’s experiment[22-24] or in the Strecker’s[20, 21] synthesis of glycine. Based on the analysis of the nature of the transition state in the Reaction 1, it can be said that with a substitution in the aldehyde, the energetics of the reaction path might get affected, but nevertheless the mechanism of formation of substituted α-hydroxy amine will be same (or in other words the reaction of a substituted aldehyde with ammonia will pass through a similar kind of transition state as shown in Figure 6.1). Thus it can be said that with a suitable choice of the substituted aldehyde, many important α-amino-acids (for example, Alanine, etc.) can also be synthesized using the same one-pot synthesis approach as discussed above for the glycine.

6.3.5 Possible application in the Interstellar Formation of Glycine

6.3.5.1 Availabilities of the ingredients in the ISM

The reactants in the Reaction 1 are formaldehyde and ammonia, which are already detected in the interstellar medium (ISM) [51-55]. As discussed in the work of Snyder et al., Interstellar formaldehyde (H2CO) has been detected in absorption against numerous galactic and extragalactic radio sources [56]. At the same time, the detection of ammonia in the interstellar space has been discussed in the works of Nguyen-Q-Rieu et al.[57] andZiurys (2006)[58].

Similarly, for the Reaction 3 which also produces the α-hydroxy amine like that of the

Reaction 1, the two reactants are CH2=NH and H2O and at the same time CO is the reactant in the Reaction 2. Methanimine (CH2NH) was first detected in Sgr B2 by Godfrey et

214

Chapter 6 al.(1973)[59] and also has been found in many other hot core sources [60]. It was Salter et al. who also recently detected it in the ultraluminous infrared galaxy (ULIRG) Arp 200 which is

250 million light years away, with the Arecibo radio telescope; certainly a remarkable discovery [61]. Availability of CO and H2O in the ISM are well known [62-64]. It is well known that the CO and H2O are among the most abundant molecules in the ISM (in fact it is believed that CO is the second and the third most abundant molecules in the ISM) besides the hydrogen [62-64].

6.3.5.2 Extreme Temperature conditions of ISM

It is well known that extreme temperature conditions exist in the interstellar medium, where in one hands hot-cores have extremely high temperatures at the same time in the other hand cold interstellar clouds have extremely low temperature conditions almost close to absolute zero. In the interstellar medium (ISM), hot-cores are the dense and warm regions consisting of gases and dusts, which are rich in exotic gas chemistries [63, 64]. High temperature in those hot cores can facilitate most of the high barrier reactions and sometimes even the endothermic reactions [63]. On the other hand interstellar clouds have varied properties depending on the temperature of the gas cloud, but are usually have extremely low temperatures [2]. Occasionally gas clouds are found close to a very hot star which heats the gas to about 10,000 Kelvin and thus can facilitate many high energy barrier reactions or even many endothermic reactions, which are practically impossible in the low temperature conditions[65]. At the same time, in the coldest and densest regions of the interstellar medium one can find clouds whose cores contain molecular gases, these molecular clouds have temperatures of as low as 10 Kelvin [2, 65].

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6.3.5.3 Possibility of Glycine formation in the ISM

Analysis of the Reactions 1-3 shows that all of them proceed through reasonably large barrier. We believe that with the existing condition in the hot-cores of ISM it will not be able to act as a bottleneck to these reactions to happen [63]. Now, owing to the availability of the reactants, HCHO, NH3 and CH2=NH in the ISM coupled with very high temperature conditions existing in the hot cores, the reasonably large barriers observed for the Reactions

1-3 may not act as bottlenecks to these reactions. Thus interstellar formation of glycine in the hot-core regions if ISM can be viewed as a feasible process through these reaction paths. The only problem associated with these reactions, especially with the Reaction 1 and Reaction 3, and also to some extent the Reaction 2, is that the respective products formed in each case are very much prone to undergo dissociation. Thus though the exact nature of the kinetics of the reactions can’t be predicted at this time, still the formation of glycine in the hot-cores via these reaction steps can’t be ruled out completely.

It is well known that reactions in the cold-cores or cold interstellar clouds in the ISM (where the temperature is quite low and even close to 10 K) are quite complicated [2]. It is generally believed that, when the temperature conditions are almost close to absolute zero [2], even a small barrier if present in the reaction path, it can act as a bottleneck to that reaction. It has been proposed in the literature that such reactions at extreme low temperature conditions are only feasible if there is an operative tunnelling mechanism [36-38]. The other way-out which we have also discussed extensively in our previous works [38, 66, 67] is where (i) all the stationary points (including the transition state in the reaction path) are energetically below the reactants, (ii) the overall reaction is highly exothermic in nature and (iii) all the elementary steps in the reaction path are also exothermic in nature. Analysis of the Reactions

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1-3 indicates that the barriers present in their respective PESs are all far above the reactants.

Thus, the cold-core possibilities of these reactions can be argued only on the basis if there is an operative tunnelling mechanism. As discussed earlier, Reaction 1 only shows prominent tunnelling, whereas Reaction 2 shows no tunnelling probability and for Reaction 3 has some tunnelling probability, but the tunnelling rates can be expected to be very low for the

Reaction 3. Based on this observation we can say that the formation of the intermediate α- hydroxy amine either via either the Reaction 1 or the Reaction 3 is possible. In the cold interstellar clouds, while Reaction 1 will be more preferable in view of the prominent tunnelling effect it is exhibiting, in the other hand Reaction 3 will have also significant contribution as the amount of water available in the interstellar medium is far more in quantities than ammonia [62-64]. But, the real difficulty arises with the Reaction 2, where the product is glycine. As the tunnelling probability can be completely ruled out for the Reaction

2, formation of glycine in the conditions existing in the cold interstellar seems impossible.

퐸푥푐푒푠푠 푊푎푡푒푟 푎푛푑 퐶표푛푐푒푟푡푒푑 푅푒푎푐푡푖표푛 4: 퐶퐻2 = 푁퐻 + 퐶푂 + 퐻2푂 → 퐺푙푦푐푖푛푒 [66]

Thus formation of glycine either through the Reactions 1 and 2 combinations, or through the

Reactions 3 and 2 combinations is not possible in the low temperature conditions of the interstellar clouds. But, analysis of the Reactions 3 and 2 combinations it can be seen that the reactants are CH2=NH, H2O and CO. Though cold-core formation of glycine is not possible in this combination two-step process, but with the availability of all the three reactants in the cold interstellar clouds, a concerted way where all the three reactants are reacting with each other simultaneously to form glycine in the presence of excess water as proposed in our earlier work (Reaction 4) can be advocated as the only way of formation of glycine in the cold interstellar clouds [66]. Thus we can say that, the formation of glycine in the laboratory

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is only possible from the reactants HCHO, NH3 and CO in the two-step process as discussed in this work. Whereas in the interstellar conditions, especially in the cold interstellar clouds, formation of glycine is only possible from the reactants CH2=NH, H2O and CO through a concerted mechanism in the presence of excess water as discussed in our earlier work

(Reaction 4) [66].

6.4 Conclusions

Using computational calculations, we have analyzed the complete potential energy surfaces of two alternative and shortest paths leading to the formation of glycine. One path (let’s say

Path-I) starts with the reaction of H2C=O with NH3 to form α-hydroxy amine (an hemiaminal) in the first step, which on the subsequent step reacts with CO to form glycine.

The other path (let’s say Path-II) starts with the reaction of H2C=NH with H2O in the first step to form α-hydroxy amine, which then reacts with the CO in the second step to form glycine. We found that both the paths are exothermic in nature and thus can be regarded as thermodynamically favorable. But, analysis shows that both the paths leading to the formation of glycine are only possible at elevated temperature conditions. We have analyzed the difficulties associated with these two reaction paths at elevated temperature conditions and found that the Path-I might be the preferable path over the Path-II. With the Path-I being favorable over the Path-II and also the stability issue associated with the key intermediate α- hydroxy amine (the hemiaminal), we have proposed that in the laboratory, with a suitable temperature condition still synthesis of the glycine may not be regarded as an efficient way, if the two steps are carried out separately. Rather it is proposed that with a suitable temperature conditions, if the two steps are carried out concurrently in a one-pot synthesis, then the efficient synthesis of glycine in the laboratory might be expected. As this one-pot synthesis is

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Chapter 6 a two-step process, it might be regarded as advantageous over the multi-step process of synthesis as suggested in the Strecker’s synthesis and Miller’s experiment. Also it can be regarded as an alternative and shortest route for the synthesis of glycine using the same ingredients as used either in the Strecker’s synthesis and Miller’s experiment. We have also analyzed the interstellar possibilities of the two paths (Path-I and Path-II). Thermochemical analysis of the reaction paths indicates the possibility for both the paths in the hot-cores of the

ISM. In the other side, we found that though in both the paths the first step seems to be favorable in the cold interstellar conditions, the second step in both the paths seems to be act as a bottleneck. Thus we have suggested that formation of glycine in the cold interstellar cloud is not possible through either of the paths. But, in our view we think that as the ingredients used in the second path, i.e., CH2=NH, H2O and CO which are all available in the cold interstellar clouds, a concerted reaction of these three in the presence of excess water interstellar formation of glycine could be possible as suggested in our previous work [66].

We anticipate that this work will be able to contribute to our future understanding of the formation of glycine in the ISM as well as its synthesis in the laboratory. It is well known that glycine belongs to the most important class of amino-acids, known as α-amino-acids observed in the nature. Thus we can say that this study can also be extended further to prepare many such α-amino-acids in the laboratory just with a suitable choice of appropriately substituted aldehyde. Also, as shown in the reaction step, α-hydroxy amine +

CO → glycine, analysis of the nature of the transition state, it can be expected that such a reaction step might be able to produce preferably one enantiomer. (Reasoning: In the transition state, the CH2-unit is planar like a carbocation, but instead of the interaction of the

OH+CO above or below the plane of the CH2-unit, it is from one side of the CH2-unit and is specific due to their close proximity to the α-hole region. Such a situation will probably be able to eliminate the process of inversion assisted racemization and may preferably give rise

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Chapter 6 to only one enantiomer.) In the other words, with the mechanism involved in the reaction process, an enantiomeric excess can be expected for the other α-amino-acids formations, in contrast to the racemic mixture usually one gets, when either Strecker’s synthesis or Miller’s experiment is carried out. As such a claim needs further experimental verifications and validations. Thus at this stage we can only say that this study can be expected to have applications in the preparation of other higher α-amino-acids, but predicting the possibility of getting an enantiomeric excess is still contentious.

Supplementary Information: Energetics data related to the potential energy surfaces for the three reactions discussed in the article, i.e., Reactions 1-3, calculated using various methods and basissets, as discussed in the computational section, are tabulated in Tables S6.1 – S6.6.

We have also provided the total energies of all the stationary points found in the potential energy surfaces of these three reactions (Tables S6.7 – S6.8). Along with the energetics data we have also provided the optimized Cartesian geometries in coordinates for all those stationary points calculated using B3LYP/6-31++G(3df,2pd) level of theory.

Supplementary Information: Energetics data related to the potential energy surfaces for the three reactions discussed in the article, i.e., Reactions 1-3, calculated using various methods and basissets, as discussed in the computational section, are tabulated in Tables S6.1 – S6.6.

We have also provided the total energies of all the stationary points found in the potential energy surfaces of these three reactions (Tables S6.7 – S6.8). Along with the energetics data we have also provided the optimized Cartesian geometries in coordinates for all those stationary points calculated using B3LYP/6-31++G(3df,2pd) level of theory.

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TOC Graphics

An alternate and shortest route for the formation of glycine using either Strecker’s or Miller’s ingredients: A computational study on the Hemiaminal intermediate route

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228

APPENDIX A

CHAPTER 7

CONCLUSIONS AND RECOMMENDATIONS

7. 1 Conclusions

The project’s objectives were to explicitly use theoretical calculations to investigate some new proposed channels leading to the possible formation of glycine in the interstellar medium. The manifolds of approaches for this study was either to use multistep pathways or a concerted reaction mechanisms which were achieved. We believe that our results will shed some light on the mechanistic part of interstellar research related to the formation of glycine and may also serve as a benchmark for various astronomical observations related to the quest for ISM glycine. The study was completed successfully and the following conclusions can be made from this research project:

1. We were able to successfully propose two concerted type of reaction

mechanisms for the interstellar formation of glycine from a) CH2=NH, CO and H2O,

b) CH2=NH, CO2 and H2, respectively for the first time using detailed computational

chemistry calculations of the reaction potential energy surfaces.

2. For the reaction 1.a), it was observed that the reaction between CH2=NH, CO

and H2O has a large barrier height, indicating that this reaction will only be feasible in

hot core regions of the ISM. We were also able to show a catalytic role of an extra

water molecule explained by the relay transport effect in reducing the barrier height.

This further enhanced the rate and hence is believed to assist the reaction in the hot

229

APPENDIX A core regions of the ISM. Furthermore, carrying out some preliminary studies to find the transition states when adding three or four water molecules as reactants was found to significantly reduce the barrier height to a very low value. This resulted in the respective transition states being more stable than the reactants and thus providing a plausible reason to the prediction that this reaction will be feasible in cold interstellar clouds. The exothermic nature of the reaction would be the driving force for this reaction under the extremely low temperatures of this region.

3. For the reaction 1.b), it was observed that the reaction between CH2=NH, CO2 and H2 also has a very large energy barrier making it feasible only in hot core regions of the ISM. However, analysis of the barrier for this reaction shows that it is sharp and narrow while the imaginary frequency shows prominent proton dynamics indicative of tunnelling occurring. Hence, with the proposed tunnelling assisted by the formation a van der Waals’ complex, the reaction is also suggested to yield glycine in the colder regions of the ISM, and thus proving its universality.

4. Two different pairs of multistep reaction mechanisms have been calculated to investigate the possible formation of glycine via two different paths: a) the reaction from either CO + H2O or CO2 + H2 in a two-step process via a dihydroxycarbene intermediate followed by a subsequent step involving interaction with CH2=NH to give glycine; b) the reaction from either H2C=O + NH3 or H2C=NH + H2O which passes through a hemiaminal intermediate (α-hydroxy amine) followed by a subsequent step of interaction of theα-hydroxy amine with CO to form glycine.

230

APPENDIX A

5. The formation of the dihydroxycarbene from the reactions mentioned in 4.a)

from CO + H2O or CO2 + H2 was observed to be highly endothermic with large

barrier heights. The subsequent step involving interaction of the dihydroxycarbene

with CH2=NH to give glycine is exothermic and barrier less for the reactions. It was

therefore concluded that the formation of glycine via the carbene route is least

favourable or even unfavourable path from the observations made above.

6. Analysis of the PESs for the two-step pathsfrom either H2C=O + NH3 or

H2C=NH + H2O passing through a hemiaminal intermediate (α-hydroxy amine)

followed by a subsequent step involving an interaction with CO mentioned in reaction

4.b) reveal that both paths are thermodynamically favourable. Nonetheless, in the

interstellar conditions, these two reactions are only feasible in hot core regions of the

ISM, and not in cold interstellar clouds.

7.2 Recommendations and future work

1. While our preliminary studies of the concerted type of mechanism for the

reaction of CH2=NH, CO and H2O showed positive results as explained in section

7.1, 2), a more detailed analysis of the PES with implicit and explicit consideration

ofwater should be carried out to further examine the complete reaction profile.Further

calculations related to the kinetics of this reaction would provide much more insight

into the reaction.

231

APPENDIX A

2. Likewise, even though the concerted reaction between CH2=NH, CO2 and H2 was predicted to be exothermic nature owing to the lower enthalpy of formation. A comprehensive calculation of the kinetics and even an experimental study is still needed to give a proper understanding of the rate constant for this reaction. On the other hand, the reaction involves the controlled splitting of a hydrogen molecule (H2) without any catalyst viewed as a correlated many body tunnelling type, a phenomenon not reported to date. Hence, kinetics related to low temperature formation of glycine where tunnelling plays an essential role still needs to be explored to provide a more inclusive computational and experimental investigation.

3. Glycine belongs to the most essential class of amino-acids known as α-amino- acids observed in nature. The reaction of 퐻2퐶 = 푂 + 푁퐻3 → α − hydroxy amine

+퐶푂 → 퐺푙푦푐푖푛푒,can be suggested for the laboratory synthesis of glycine. This reaction can be carried out as a one pot synthesis at a controlled elevated temperature. A further extension of the study to the preparation of other α-amino-acids with an appropriate choice of aldehyde is also recommended. Also, based on the mechanism determined here in the reaction can be predicted to give an enantiomeric excess, which is in contrast to the racemic mixture that usually results from carrying out either Strecker’s synthesis or Miller’s experiment. Hence this claim still requires experimental verification and validation.

232

APPENDIX A

APPENDIX A

Supporting Information (Chapter 4)

Possible interstellar hot-core formation glycine from the reaction of CH2=NH, CO and H2O:

Catalysis by extra water molecule through the hydrogen relay transport effect.

Figure S4. 1: Schematic diagram of energy differences for H2O + CO +

CH2NH→NH2CH2COOH reaction, with optimized structures of reactants,

complex, transition state and product for the quatermolecular reactions

leading to the formation of glycine performed at MP2/6-31++G(3df,2pd).

233

APPENDIX A

Figure S4. 2: Schematic diagram of energy differences for H2O + H2O + CO +

CH2NH→NH2CH2COOH reaction, with optimized structures of reactants,

complex, transition state and product for the quatermolecular reactions

leading to the formation of glycine performed at MP2/6-31++G(3df,2pd).

Figure S4. 3: Schematic diagram of energy differences for H2O-H2O complex + CO +

CH2NH→NH2CH2COOH reaction, with optimized structures of reactants,

complex, transition state and product for the quatermolecular reactions

leading to the formation of glycine performed at B3LYP/6-31++G(3df,2pd).

234

APPENDIX A

Figure S4. 4: Schematic diagram of energy differences for H2O-H2O complex + CO +

CH2NH→NH2CH2COOH reaction, with optimized structures of reactants,

complex, transition state and product for the quatermolecular reactions leading

to the formation of glycine performed at MP2/6-31++G(3df,2pd).

Figure S4. 5: Mechanism for H2O + CO + CH2NH→NH2CH2COOH reaction, optimized

geometries of the complex, transition state and product involved in the

termolecular reactions for the formation of glycine at B3LYP/6-

31++G(3df,2pd).

235

APPENDIX A

Figure S4. 6: Mechanism for H2O + CO + CH2NH→NH2CH2COOH reaction, optimized

geometries of the complex, transition state and product involved in the

termolecular reactions for the formation of glycine at MP2/6-31++G(3df,2pd).

Figure S4. 7: Mechanism for H2O + H2O + CO + CH2NH→NH2CH2COOH reaction,

optimized geometries of the complex, transition state and product involved in

the quatermolecular reactions for the formation of glycine at B3LYP/6-

31++G(3df,2pd).

236

APPENDIX A

Figure S4. 8: Mechanism for H2O + H2O + CO + CH2NH→NH2CH2COOH reaction,

optimized geometries of the complex, transition state and product involved in

the quatermolecular reactions for the formation of glycine at MP2/6-

31++G(3df,2pd).

Table S4. 1: Optimized transition state structure for the bond lengths in angstroms and bond angles in degrees for different methods using 6-31++G(3df,2pd) basis set.

Figure SF9: Tansition state for the reaction 1H2O + CO + CH2NH→NH2CH2COOH. Methods Bond length Bond angles C-O =1.941 Ǻ a = 90.466º O-H = 1.404 Ǻ b = 82.603º X3LYP N-H = 1.135 Ǻ c = 96.946º d = 106.629º C-C = 2.244 Ǻ e = 147.623º C-O = 1.933 Ǻ a = 87.037º B3PW91 O-H = 1.204 Ǻ b = 87.393º

237

APPENDIX A

N-H = 1.288 Ǻ c = 103.125º d = 99.685º C-C = 2.010 Ǻ e = 154.256º C-O = 1.991 Ǻ a = 84.886º O-H = 1.172 Ǻ b = 89.061º O3LYP N-H =1.324 Ǻ c = 106.986º d = 98.867º C-C = 1.910 Ǻ e = 155.726º C-O = 1.906 Ǻ a = 90.803º O-H = 1.370 Ǻ b = 83.494º CBS-QB3 N-H = 1.156 Ǻ c = 96.862º d = 148.932º C-C = 2.23 Ǻ e = 147.779º C-O = 1.910 Ǻ a = 89.056º O-H = 1.287 Ǻ b = 85.872º G3B3 N-H = 1.223 Ǻ c = 98.966º d = 102.885º C-C = 2.142 Ǻ e = 151.755º C-O = 1.908 Ǻ a = 88.097º O-H = 1.261 Ǻ b = 86.783º G4 N-H =1.236 Ǻ c = 100.585º d = 101.507º C-C =2.083 Ǻ e = 153.043º C-O = 1.908 Ǻ a = 88.097º O-H = 1.261 Ǻ b = 86.783º G4MP2 N-H = 1.236 Ǻ c = 100.585º d = 101.507º C-C = 2.083 Ǻ e = 153.043º

238

APPENDIX A

Table S4. 2: Optimized transition state structure for the bond lengths in angstroms and bond angles in degrees for different methods using 6-31G++(3df,2pd) basis set.

Figure SF10: Tansition state for the reaction 2H2O + CO + CH2NH→NH2CH2COOH. Type of method Bond length Bond angles (11)C-(7)O = 2.047 Ǻ a = 82.014 º (7)O-(8)H = 1.337 Ǻ b = 122.509º (8)H-(9)O = 1.111 Ǻ c = 168.056º X3LYP (9)O-(2)H = 1.475 Ǻ d = 93.079º (2)H-(1)N = 1.097 Ǻ e = 162.373º (1)N-(4)C = 1.288 Ǻ f = 118.124º (4)C-(11)C = 2.418 Ǻ g = 108.905º (11)C-(7)O = 1.962 Ǻ a = 91.744º (7)O-(8)H = 1.206 Ǻ b = 117.705º (8)H-(9)O = 1.209 Ǻ c = 171.042º B3PW91 (9)O-(2)H = 1.345 Ǻ d = 93.881º (2)H-(1)N = 1.159 Ǻ e = 163.323º (1)N-(4)C = 1.296 Ǻ f = 117.147º (4)C-(11)C = 2.251 Ǻ g = 108.476º (11)C-(7)O = 1.972 Ǻ a = 93.827º (7)O-(8)H = 1.217 Ǻ b = 115.937º (8)H-(9)O = 1.203 Ǻ c = 171.545º O3LYP (9)O-(2)H = 1.353 Ǻ d = 94.759º (2)H-(1)N = 1.157 Ǻ e = 163.574º (1)N-(4)C = 1.300 Ǻ f = 117.630º (4)C-(11)C = 2.277 Ǻ g = 108.059º

239

APPENDIX A

(11)C-(7)O = 2.100 Ǻ a = 75.038º (7)O-(8)H = 1.458 Ǻ b = 120.767º (8)H-(9)O = 1.050 Ǻ c = 165.608º M06 (9)O-(2)H = 1.593 Ǻ d = 92.545º (2)H-(1)N = 1.062 Ǻ e = 159.726º (1)N-(4)C = 1.285 Ǻ f = 117.814º (4)C-(11)C = 2.431 Ǻ g = 109.843º (11)C-(7)O = 2.014 Ǻ a = 79.510º (7)O-(8)H = 1.343 Ǻ b = 117.552º (8)H-(9)O = 1.109 Ǻ c = 167.728º CBS-QB3 (9)O-(2)H = 1.440Ǻ d = 94.219º (2)H-(1)N = 1.117Ǻ e = 162.390º (1)N-(4)C = 1.289Ǻ f = 116.855º (4)C-(11)C = 2.447Ǻ g = 108.958º (11)C-(7)O = 1.920 Ǻ a = 93.038º (7)O-(8)H = 1.207 Ǻ b = 113.717º (8)H-(9)O = 1.228 Ǻ c = 171.257º G3B3 (9)O-(2)H = 1.309 Ǻ d = 95.557º (2)H-(1)N = 1.197 Ǻ e = 163.637º (1)N-(4)C = 1.304 Ǻ f = 116.271º (4)C-(11)C = 2.224 Ǻ g = 108.704º (11)C-(7)O = 1.920 Ǻ a = 93.015º (7)O-(8)H = 1.207 Ǻ b = 113.716º (8)H-(9)O = 1.228 Ǻ c = 171.263º G3MP2B3 (9)O-(2)H = 1.309 Ǻ d = 95.544º (2)H-(1)N = 1.197 Ǻ e = 163.616º (1)N-(4)C = 1.304 Ǻ f = 116.270º (4)C-(11)C = 2.243 Ǻ g = 108.701º (11)C-(7)O = 1.923 Ǻ a = 91.411º (7)O-(8)H = 1.226 Ǻ b = 116.322º G4 (8)H-(9)O = 1.195 Ǻ c = 171.127º (9)O-(2)H = 1.321 Ǻ d = 94.935º (2)H-(1)N = 1.180 Ǻ e = 163.759º

240

APPENDIX A

(1)N-(4)C = 1.299 Ǻ f = 116.273º (4)C-(11)C = 2.261 Ǻ g = 108.725º (11)C-(7)O = 1.923 Ǻ a = 91.435º (7)O-(8)H = 1.226 Ǻ b = 116.329º (8)H-(9)O = 1.195 Ǻ c = 171.124º G4MP2 (9)O-(2)H = 1.320 Ǻ d = 94.728º (2)H-(1)N = 1.181 Ǻ e = 163.769º (1)N-(4)C = 1.299 Ǻ f = 116.272º (4)C-(11)C = 2.260 Ǻ g = 108.722º

Effect of various basissets on PES of reaction; CH2=NH + CO + H2O → Glycine

To test the effect of various basissets on the energetics of the stationary points in the PES, we have carried out calculations using B3LYP method with the combinations of various basissets. The results related to these calculations are summarized in Table S4.3.

Table S4. 3: Results of effect of various basis sets (for B3LYP Method) on the potential energy surface of the CH2=NH + CO + H2O → Glycine reaction. Where ΔE1 = EReactant –

EReactant Complex , ΔE2 = ETS – EReactant Complex, ΔE3 = ETS – EProduct and ∆E4 = EReactant Complex –

EProduct.All the energies are ZPE corrected and are in kcal/mol.

Basissets ∆E1 ∆E2 ∆E3 ∆E4

6-31G 11.4 26.2 61.3 35.0

6-31G(d) 7.8 36.5 68.8 32.3

6-31+G(d) 5.9 39.5 67.6 28.1

6-31++G(d) 5.9 39.5 67.6 28.1

6-31++G(d,p) 5.7 39.9 66.3 26.4

6-31++G(2df,2p) 4.7 41.0 66.3 25.3

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APPENDIX A

6-31++G(2df,2pd) 4.8 41.0 66.2 25.2

6-31++G(3df,2pd) 4.6 41.0 66.3 25.3

6-31++G(3df,3pd) 4.6 40.9 66.2 25.3

aug-cc-pvdz 4.8 40.3 65.9 25.3

aug-cc-pvtz 4.5 41.9 64.0 23.8

From the table it can be seen that moving from the 6-31G basisset to 6-31G(d) basisset the energetics values shows large fluctuations, but slowly the fluctuation becomes less and less prominent when we reach up to the 6-31++G(3df,3pd) basisset. It is interesting to note that after (2df,2p) adding more d and f functions has almost no significant effects on the energetics. At the same time the energetics related to aug-cc-pvnz basissets are more or less similar to that of the 6-31++G(3df,2pd) basisset. So, when testing for the effect of methodologies we have carried out all the calculations using 6-31++G(3df,2pd) basisset.

Effect of various methodologies on PES of reaction; CH2=NH + CO + H2O → Glycine

To account for the effect of various methodologies on the energetics of the PES, we have carried out calculations using various methods as shown in Table S4.4. For all these calculations, we have used the 6-31++G(3df,2pd) basisset.

242

APPENDIX A

Table S4. 4: Results of effect of various methods on the potential energy surface of the

CH2=NH + CO + H2O → Glycine reaction. Where ΔE1 = EReactant – EReactant Complex , ΔE2 = ETS

– EReactant Complex, ΔE3 = ETS – EProduct and ∆E4 = EReactant Complex – EProduct.All the energies are

ZPE corrected and are in kcal/mol.

Methods ∆E1 ∆E2 ∆E3 ∆E4

B3LYP 4.6 41.0 66.3 25.3

B3PW91 3.6 36.6 69.6 32.9

MP2 6.6 45.3 70.2 24.9

CBS-QB3 5.4 48.2 72.2 23.9

G3B3 5.3 47.5 70.7 23.2

G3MP2B3 4.8 48.8 70.6 21.8

G4 5.0 48.8 71.4 22.6

G4MP2 4.6 50.0 71.2 21.2

From the table it can be seen that all these methods show similar kind of trend in the energetics of the reaction. Comparatively large stability for the reactant complex is shown by the MP2 method and lower stability is shown by the B3PW91 method. Composite method

G4MP2 shows that the reactant complex is 4.6 kcal/mol more stable compared to the reactants and is very much similar to that of the B3LYP method. The lowest barrier height for the reaction (from the reactant complex to the TS) is again shown by the B3PW91 method, whereas the all the composite methods, MP2 method and even the CBS-QB3 method show a comparatively larger barrier than both B3LYP and B3PW91 method. The lowest value of the barrier height for the reverse reaction is obtained for the B3LYP method followed by the

B3PW91 method. All other methods predict a 4-5 kcal/mol larger barrier height for the reverse reaction. From the table it can be seen that by combining ∆E1 and ∆E4 gives the

243

APPENDIX A enthalpy of the reaction. It can be seen that the lowest enthalpy of the reaction values are predicted by the composite methods, whereas highest value for this is predicted by the

B3PW91 method. MP2 and B3LYP methods predict similar enthalpy of the reaction.

Analysis of all these results show that various methods have some effect on the energetics of the reaction PES, but nevertheless they all predict similar kind of behaviour and trend.

Effect of various basissets on PES of reaction; CH2=NH + CO + 2H2O → Glycine

Similar to the previous case of the PES analysis for the case of one water molecule as reactant, here also we have carried out calculations with various basissets using B3LYP method to have an idea about the energetics of the stationary points in the PES. The results related to these calculations are summarized in Table S4.5.

Table S4. 5: Results of effect of various basissets (for B3LYP Method) on the potential energy surface of the CH2=NH + CO + 2H2O → Glycine reaction. Where ΔE1 = EReactant –

EReactant Complex , ΔE2 = ETS – EReactant Complex, ΔE3 = ETS – EProduct Complex, ∆E4 = EReactant Complex –

EProduct Complex and ∆E5 = EProduct – EProduct Complex.All the energies are ZPE corrected and are in kcal/mol.

Method ∆E1 ∆E2 ∆E3 ∆E4 ∆E5

6-31G 25.4 15.2 42.6 27.2 6.4

6-31G(d) 17.8 30.0 55.7 25.6 3.3

6-31+G(d) 13.2 32.6 54.8 22.1 1.3

6-31++G(d) 13.2 32.7 54.7 22.0 1.3

6-31++G(d,p) 12.7 32.0 52.3 20.4 1.0

6-31++G(2df,2p) 10.5 33.7 53.4 19.7 0.2

244

APPENDIX A

6-31++G(2df,2pd) 10.7 33.5 53.0 19.5 0.2

6-31++G(3df,2pd) 10.2 34.0 53.8 19.8 0.1

6-31++G(3df,3pd) 10.1 33.8 53.7 19.9 0.1

aug-cc-pvdz 10.6 33.2 53.2 20.0 0.2

aug-cc-pvtz 9.8 34.5 52.9 18.4 0.1

From the table it can be seen that moving from the 6-31G basisset to 6-31G(d) basisset the energetics values shows large fluctuations, but slowly the fluctuation becomes less and less prominent when we reach up to the 6-31++G(3df,3pd) basisset. At the same time the energetics related to aug-cc-pvnz basissets are more or less similar to that of the 6-

31++G(2df,2pd) basisset. All most all the reasonably larger basissets predict close energetics values and also same trend of the PES. So, when testing for the effect of methodologies we have carried out all the calculations with a comparatively larger basisset like 6-

31++G(3df,2pd).

Effect of various methodologies on PES of reaction; CH2=NH + CO + 2H2O → Glycine

Similar to the previous case of PES with one water molecule as reactant, here also we have carried out calculations with various methods with 6-31++G(3df,2pd) basisset, to test the effect of various methodologies on the energetics of the stationary points in the PES. The results related to these calculations are summarized in Table S4.6.

245

APPENDIX A

Table S4. 6: Results of effect of various methods on the potential energy surface of the

CH2=NH + CO + 2H2O → Glycine reaction. Where ΔE1 = EReactant – EReactant Complex , ΔE2 =

ETS – EReactant Complex, ΔE3 = ETS – EProduct Complex, ∆E4 = EReactant Complex – EProduct Complex and ∆E5

= EProduct – EProduct Complex.All the energies are ZPE corrected and are in kcal/mol.

Method ∆E1 ∆E2 ∆E3 ∆E4 ∆E5

B3LYP 10.2 34.0 53.8 19.8 0.1

B3PW91 8.7 30.6 57.5 26.9 0.2

MP2 13.07 41.4 61.6 20.2 1.7

CBS-QB3 11.6 41.0 59.8 18.9 1.1

G3B3 11.8 41.7 59.5 17.8 1.1

G3MP2B3 10.9 49.8 66.3 16.6 0.8

G4 10.9 42.4 59.7 17.2 0.6

G4MP2 10.1 44.4 60.4 16.0 0.3

From the table it can be seen that all these methods show similar kind of trend in the energetics of the reaction. MP2 method predicts a comparatively higher stability for both the reactant-complex and product complex, whereas B3PW91 method predicts the least stability for those two complexes. Nevertheless all the methods predict that both the complexes are stable complexes. Analysis of the barrier heights for the forward reaction shows that all the methods in this case predict a lowering of barrier height (catalytic effect) compared to the reaction with one H2O case, with the exception with the G3MP2B3 method which predicts a slightly increase in the barrier height. On the other hand all the methods predict also a decrease in the barrier heights for the reveres reaction in this case compared to the previous case of this reaction with one water molecule, which is again an indication of the catalytic effect of the extra water molecule. Analysis of all these results show that though various

246

APPENDIX A methods have some effect on the energetics of the reaction PES, but nevertheless they all predict similar kind of behaviour and trend.

B3LYP/6-31G optimized geometries of the transition states with 3H2O and 4H2O in

Cartesian Co-ordinates

For 3H2O case:

N -1.871415 -1.556388 -0.256537

H -2.203825 0.020099 -0.493682

H -2.374775 -2.317047 -0.727587

C -0.858946 -1.910831 0.455431

H -0.260712 -1.149447 0.969122

H -0.549008 -2.955640 0.562702

O -0.089571 2.156264 0.025459

H -1.003378 1.802248 -0.255517

O -2.305436 1.036111 -0.598661

H -3.153997 1.353925 -0.249877

C 2.275846 -0.987751 -0.635329

O 2.956681 -0.088905 -0.898162

H 0.396395 2.534032 -0.725266

O 0.924980 0.308463 1.525707

H 1.256031 0.609855 2.389163

H 0.598538 1.092715 0.971336

247

APPENDIX A

For 4H2O case:

N -0.320303 -1.979345 0.441072

H -1.807150 -1.826695 -0.093324

H 0.349729 -2.723785 0.221889

C 0.161722 -0.974355 1.082040

H -0.492111 -0.134606 1.304416

H 1.202209 -0.879713 1.380012

O -2.796595 0.984480 -0.810928

H -2.854965 -0.026744 -0.653588

O -2.750894 -1.518543 -0.385610

H -3.459292 -2.015704 0.052939

C 3.258813 -0.815706 -0.268192

O 3.944472 -0.114854 -0.883307

H -2.970598 1.213646 -1.737437

O -0.950155 2.122580 0.526802

H -1.305049 2.704041 1.217891

H -1.695310 1.708465 -0.040583

O 1.563157 1.390125 0.335259

H 2.056405 1.947552 -0.292114

H 0.615163 1.719028 0.411580

Optimized structure and Cartesian co-ordinates of the most stable structure of the

glycine:

248

APPENDIX A

249

APPENDIX B

APPENDIX B

Supporting Information (Chapter 5)

Possible interstellar formation of Glycine through a concerted mechanism:

A computational study on the reaction of CH2=NH, CO2 and H2

Figure S5. 1: B3LYP/6-31G(3df,2pd) optimized geometries of the reactants, transition state

and product.

Figure S5. 2: MP2/6-31G(3df,2pd) optimized geometries of the reactants, transition state and

product.

250

APPENDIX B

Figure S5. 3: MP2/6-31G(3df,2pd) PES for the CH2=NH + CO2 + H2 → Glycine, reaction.

All the energies are in kcal/mol and the diagram is not to scale.(Colour Code:

Pink=Hydrogen, Grey=Carbon, Blue=Nitrogen, Red=Oxygen).

Table S5. 1: Results of effect of various basissets (with B3LYP method) on the potential energy surface of the CH2=NH + CO2 + H2 → Glycine reaction. Where ΔE1 = ETS –

EREACTANTS, ΔE2 = ETS – EPRODUCT and ΔE3 = EREACTANTS – EPRODUCT.All the energies are

ZPE corrected and are in kcal/mol.

Basissets ∆E1 ∆E2 ∆E3 6-31G 62.0 86.4 24.4 6-31G* 69.8 76.5 6.7 6-31++G(d,p) 69.0 85.3 16.3 6-31++G(2df,2p) 70.8 80.2 9.4 6-31++G(3df,2pd) 70.4 80.1 9.7 6-31++G(3df,3pd) 70.3 80.1 9.8 aug-cc-pvdz 67.0 80.6 13.6 aug-cc-pvtz 71.3 79.8 8.5

251

APPENDIX B

Table S5. 2: Effect of various methods on the geometry of the transition state for the reaction,

CH2=NH + CO2 + H2 → Glycine. Some important geometric data are shown [Basisset used is

6-31++G(3df,2pd)].

Methods Bond length Bond angles

H-H = O.880 Ǻ a = 111.334º

N-H = 1.366 Ǻ b = 111.940º X3LYP O-H = 1.490 Ǻ c = 108.819º

C-C = 1.979 Ǻ d = 144.866º

H-H = 0.877 Ǻ a = 111.640º

N-H = 1.367 Ǻ b = 112.315º B3PW91 O-H = 1.506 Ǻ c = 108.531º

C-C = 1.981 Ǻ d = 145.674º

H-H = 0.866 Ǻ a = 112.611º

N-H = 1.394 Ǻ b = 110.478º HF O-H = 1.419 Ǻ c = 108.567º

C-C = 1.957 Ǻ d = 145.622º

H-H = 0.878 Ǻ a = 111.337º

N-H = 1.352 Ǻ b = 112.300º O3LYP O-H = 1.525 Ǻ c = 118.587º

C-C = 1.983 Ǻ d = 145.134º

252

APPENDIX B

H-H = 0.904 Ǻ a = 111.039º

N-H = 1.285 Ǻ b = 113.148º MP2=full O-H = 1.493 Ǻ c = 108.234º

C-C = 1.982 Ǻ d = 146.184º

H-H = 0.891 Ǻ a = 110.910º

N-H = 1.343 Ǻ b = 111.813º CBS-QB3 O-H = 1.489 Ǻ c = 108.681º

C-C = 1.981 Ǻ d = 114.584º

H-H = 0.881 Ǻ a = 109.682º

N-H = 1.374 Ǻ b = 110.968º G3B3 O-H = 1.500 Ǻ c = 110.082º

C-C = 1.942 Ǻ d = 142.944º

H-H = 0.881 Ǻ a = 109.682º

N-H = 1.374 Ǻ b = 110.968º G3MP2B3 O-H = 1.500 Ǻ c = 110.080º

C-C = 1.942 Ǻ d = 142.944º

Table S5. 3: Effect of various Basissets on the geometry of the transition state. Some important geometric data are shown (Method used is B3LYP).

Basissets Bond length Bond angles H-H = O.882 Ǻ a = 110.552º N-H = 1.361 Ǻ b = 111.346º 6-31G O-H = 1.557 Ǻ c = 110.468º C-C = 1.961 Ǻ d = 142.490º H-H = O.881 Ǻ a = 109.682º N-H = 1.374 Ǻ b = 110.968º 6-31G(d) O-H = 1.500 Ǻ c = 110.082º C-C = 1.942 Ǻ d = 142.944º 6-31+G(d) H-H = 0.875 Ǻ a = 110.274º

253

APPENDIX B

N-H = 1.378 Ǻ b = 111.352º O-H = 1.517 Ǻ c = 110.062º C-C = 1.946 Ǻ d = 143.080º H-H = 0.877 Ǻ a = 110.324º N-H = 1.375 Ǻ b = 111.415º 6-31++G(d) O-H = 1.516 Ǻ c = 110.000º C-C = 1.948 Ǻ d = 143.158º H-H = 0.877 Ǻ a = 111.142º N-H = 1.365 Ǻ b = 111.733º 6-31++G(d,p) O-H = 1.514 Ǻ c = 109.279º C-C = 1.974 Ǻ d = 144.127º H-H = 0.882 Ǻ a = 111.266º N-H = 1.357 Ǻ b = 111.934º 6-31++G(2df,2p) O-H = 1.498 Ǻ c = 108.949º C-C = 1.976 Ǻ d = 144.519º H-H = 0.882 Ǻ a = 111.317º N-H = 1.360 Ǻ b = 111.954º 6-31++G(2df,2pd) O-H = 1.493 Ǻ c = 108.824º C-C = 1.983 Ǻ d = 144.726º H-H = 0.881 Ǻ a = 111.252º N-H = 1.367 Ǻ b = 111.887º 6-31++G(3df,2pd) O-H = 1.490 Ǻ c = 108.885º C-C = 1.980 Ǻ d = 144.701º H-H = 0.880 Ǻ a = 111.286º N-H = 1.368 Ǻ b = 111.877º 6-31++G(3df,3pd) O-H = 1.489 Ǻ c = 108.838º C-C = 1.981 Ǻ d = 144.726º H-H = 0.890 Ǻ a = 111.651º N-H = 1.365 Ǻ b = 112.087º aug-cc-pvdz O-H = 1.514 Ǻ c = 109.056º C-C = 1.981 Ǻ d = 144.570º H-H = 0.885 Ǻ a = 111.509º N-H = 1.357 Ǻ b = 111.921º aug-cc-pvtz O-H =1.486 Ǻ c = 108.710º C-C = 1.987 Ǻ d = 144.630º

254

APPENDIX B

Cartesian Coordinates of stationary points

[From B3LYP/6-31++G(3df,2pd) optimized geometries]

vdW-Complex

C -2.203213 -0.336688 0.001473

N -1.280195 0.551229 -0.010608

H -1.611679 1.525427 -0.022085

H -3.278983 -0.131151 0.000174

H -1.907027 -1.383933 0.014057

H 0.595324 3.116494 0.039220

H 0.277356 3.788759 0.052167

C 1.234283 -0.378808 -0.000894

O 0.826328 -1.496510 0.012374

O 1.761166 0.686357 -0.013968

Transition State

C -0.862934 -0.842765 -0.036846

H -0.638687 -1.360943 -0.963695

H -0.628966 -1.362549 0.886707

O 1.721333 -0.754475 0.014891

C 0.881010 0.094701 0.006462

O 0.682131 1.295036 0.013443

H -0.768861 1.618030 -0.081691

N -1.926940 -0.024242 -0.067513

255

APPENDIX B

H -2.261122 0.169088 0.878724

H -1.549954 1.269967 -0.291813

Methanimine (CH2=NH)

C 0.586885 0.028877 -0.000014

H 1.245720 -0.839259 0.000030

H 1.076099 1.007625 0.000028

N -0.667824 -0.154020 0.000003

H -1.168363 0.736515 0.000004

Product (Glycine)

C 0 0.745907 -0.750143 0.000094

O 0 -1.672056 -0.714322 -0.000069

H 0 0.764079 -1.412175 -0.869017

H 0 0.764093 -1.411864 0.869445

H 0 1.949029 0.692680 0.812616

H 0 1.949047 0.692359 -0.812971

N 0 1.931433 0.088161 -0.000058

C 0 -0.634976 -0.097365 0.000002

O 0 -0.590688 1.257176 0.000038

H 0 -1.509914 1.564093 -0.000001

256

APPENDIX B

Optimized structure and Cartesian co-ordinates of the most stable structure of the

glycine [B3LYP/6-31++G(3df,2pd)]:

B3LYP/6-31++G(d,p) Optimized structures and the geometric parameters of the

various stationary points (in the reaction 1 and 3 (for reaction 2, see the reference 35)

R(1,2) 1.1373

R(1,2) 0.7438

257

APPENDIX B

R(1,2) 0.9653

R(1,3) 0.9653

A(2,1,3) 105.7192

R(1,2) 1.1694

R(1,3) 1.1694

A(2,1,3 ) 180.0000

R(1,2) 1.3132

R(1,3) 1.3436

R(2,4) 0.9855

R(3,5) 0.9679

A(2,1,3) 107.2889

A(1,2,4) 112.1525

A(1,3,5) 107.9239

258

APPENDIX B

D(3,1,2,4) -0.0236

D(2,1,3,5) 180.0107

Transition state for CO + H2O →DihydroxyCarbene in Cartesian coordinates

C 0.331554 0.724044 -0.009582

O 1.028719 -0.303161 0.024499

O -1.053836 -0.138371 -0.092728

H -0.038883 -0.895925 0.053308

H -1.749501 0.083921 0.550012

Transition state for CO2 + H2 → DihydroxyCarbene in Cartesian co-ordinates

C 0.000000 0.154507 0.000000

O -0.858268 -0.769092 0.000000

O 1.143441 0.438118 0.000000

259

APPENDIX B

H -1.414272 0.426526 0.000000

H -0.867110 1.294223 0.000000

R(1,2) 1.093

R(1,3) 1.0985

R(1,4) 1.272

R(4,5) 1.0252

A(2,1,3) 116.1708

A(2,1,4) 118.8487

A(3,1,4) 124.9805

A(1,4,5) 110.9655

D(2,1,3,4) 180.0

D(2,1,4,5) 180.0

D(3,1,4,5) 0.0

260

APPENDIX B

R(1,3) 1.0965

R(1,4) 1.0965

R(1,7) 1.4489

R(1,8) 1.5255

R(2,8) 1.3566

R(2,10) 0.9726

R(5,7) 1.0163

R(6,7) 1.0163

R(8,9) 1.2125

A(3,1,4) 105.6019

A(3,1,7) 109.8916

A(3,1,8) 107.5308

A(4,1,7) 109.8917

A(4,1,8) 107.532

A(7,1,8) 115.8688

A(8,2,10) 107.4783

A(1,7,5) 110.6883

A(1,7,6) 110.6881

A(5,7,6) 106.4526

A(1,8,2) 111.5141

261

APPENDIX B

A(1,8,9) 125.709

A(2,8,9) 122.7769

D(3,1,7,5) -178.9936

D(3,1,7,6) 63.2173

D(4,1,7,5) -63.203

D(4,1,7,6) 179.008

D(8,1,7,5) 58.9025

D(8,1,7,6) -58.8865

D(3,1,8,2) 56.6567

D(3,1,8,9) -123.3429

D(4,1,8,2) -56.6458

D(4,1,8,9) 123.3546

D(7,1,8,2) -179.9951

D(7,1,8,9) 0.0054

D(10,2,8,1) -179.9986

D(10,2,8,9) 0.001

Transition state for CH2=NH + DihydroxyCarbene → Glycine in Cartesian co-ordinates

262

APPENDIX B

C 1.559382 0.831178 0.114655

H 1.255435 1.191327 1.091298

H 1.792364 1.589295 -0.633570

N 1.842668 -0.436990 -0.035242

H 2.193751 -0.645546 -0.969736

C -0.789193 0.223403 -0.068325

O -0.511287 -1.004661 0.121062

O -2.091138 0.495747 -0.088378

H 0.669602 -1.007492 0.164719

H -2.611566 -0.324829 0.054532

Pre-reaction complex for CO2 + H2 → DihydroxyCarbene in Cartesian co-ordinates

C 0.377868 -0.000850 -0.000039

263

APPENDIX B

O -0.791581 -0.005607 -0.000119

O 1.547023 0.003856 0.000047

H -4.527355 0.012111 -0.002479

H -3.783386 0.006997 0.003295

Pre-reaction complex for CO + H2O → DihydroxyCarbene in Cartesian coordinates

C 0.984844 0.102639 0.006397

O 2.109682 -0.050449 -0.004060

O -2.325829 -0.127510 -0.000966

H -2.795790 0.715065 -0.010819

H -1.384095 0.092773 0.012644

Pre-reaction Complex for CH2=NH + DihydroxyCarbene → Glycine in Cartesian co- ordinates

C 2.293978 -0.713912 0.000111

H 1.500801 -1.462698 -0.000956

H 3.333583 -1.057367 0.001456

264

APPENDIX B

N 1.957264 0.515099 -0.000215

H 2.754434 1.154577 0.001053

C -1.146396 -0.420505 -0.000513

O -0.731561 0.832590 -0.000012

O -2.471699 -0.427343 0.000271

H 0.275487 0.832108 -0.000749

H -2.824561 0.492213 0.001044

265

APPENDIX C

APPENDIX C

Supporting Information (Chapter 6)

An alternate and shortest route for the formation of glycine using either Strecker’s or Miller’s ingredients: A computational study on the Hemiaminal intermediate route.

Table S6. 1: Results of effect of various methods on the potential energy surface of the NH3 +

H2CO → H2N-CH2-OH (Reaction 1). Where ΔE1 = EREACTANTS – ECOMPLEX, ΔE2 = ETS –

ECOMPLEX and ΔE3 = ECOMPLEX – EPRODUCT.All the energies are ZPE corrected and are in kcal/mol.

Methods ∆E1 ∆E2 ∆E3 B3LYP/6-31++G(3df,2pd) 1.258 32.741 5.921 G3B3 1.660 33.531 7.241 G3MP2 1.893 34.869 6.513 G3MP2B3 1.524 34.178 6.858 G3 2.016 34.170 6.923 G4MP2 1.612 33.955 6.728

266

APPENDIX C

Table S6. 2: Results of effect of various methods on the potential energy surface of the H2N-

CH2-OH + CO → NH2CH2COOH (Reaction 2). Where ΔE1 = EREACTANTS – ECOMPLEX, ΔE2 =

ETS – ECOMPLEX and ΔE3 = ECOMPLEX – EPRODUCT.All the energies are ZPE corrected and are in kcal/mol.

Methods ∆E1 ∆E2 ∆E3 B3LYP/6-31++G(3df,2pd) 0.070 57.709 18.964 G3B3 0.808 66.642 16.433 G3MP2 0.821 67.825 15.514 G3MP2B3 0.685 67.383 15.528 G3 0.954 67.114 16.463 G4MP2 0.603 68.203 14.793

Table S6. 3: Results of effect of various methods on the potential energy surface of the

NH=CH2 + H2O → H2N-CH2-OH (Reaction 3). Where ΔE1 = EREACTANTS – ECOMPLEX, ΔE2 =

ETS – ECOMPLEX and ΔE3 = ECOMPLEX – EPRODUCT.All the energies are ZPE corrected and are in kcal/mol.

Methods ∆E1 ∆E2 ∆E3 B3LYP/6-31++G(3df,2pd) 3.920 46.042 5.312 G3B3 3.838 49.554 5.732 G3MP2 4.127 51.713 4.657 G3MP2B3 3.624 50.210 5.109 G3 4.322 51.017 5.355 G4MP2 3.426 50.151 5.142

267

APPENDIX C

Table S6. 4: Results of effect of various basis sets (with B3LYP method) on the potential energy surface of the NH3 + H2CO → H2N-CH2-OH (Reaction 1). Where ΔE1 = EREACTANTS

– ECOMPLEX, ΔE2 = ETS – ECOMPLEX and ΔE3 = ECOMPLEX – EPRODUCT.All the energies are ZPE corrected and are in kcal/mol.

Methods ∆E1 ∆E2 ∆E3 B3LYP/6-31G 2.791 29.631 7.435 B3LYP/6-31G* 2.510 33.259 5.180 B3LYP/6-31+G* (a) - - - B3LYP/6-31++G* (a) - - - B3LYP/6-31++G** (a) - - - B3LYP/6-31++G(2df,2p) 1.337 32.893 5.819 B3LYP/6-31++G(2df,2pd) 1.389 32.779 5.791 B3LYP/6-31++G(3df,2pd) 1.258 32.741 5.921 (a)There were convergence problems with some parts of the calculations. Hence are not reported here.

Table S6. 5: Results of effect of various basis sets (with B3LYP method) on the potential energy surface of the H2N-CH2-OH + CO → NH2CH2COOH (Reaction 2). Where ΔE1 =

EREACTANTS – ECOMPLEX, ΔE2 = ETS – ECOMPLEX and ΔE3 = ECOMPLEX – EPRODUCT.All the energies are ZPE corrected and are in kcal/mol.

Methods ∆E1 ∆E2 ∆E3 B3LYP/6-31G 1.206 46.681 25.936 B3LYP/6-31G* 0.987 60.490 22.192 B3LYP/6-31+G* 0.224 56.626 19.982 B3LYP/6-31++G* 0.240 56.574 19.876 B3LYP/6-31++G** 0.221 56.121 19.896 B3LYP/6-31++G(2df,2p) 0.068 57.748 18.540 B3LYP/6-31++G(2df,2pd) 0.075 57.592 18.589 B3LYP/6-31++G(3df,2pd) 0.070 32.741 18.965

268

APPENDIX C

Table S6. 6: Results of effect of various basis sets (with B3LYP method) on the potential energy surface of the NH=CH2 + H2O → H2N-CH2-OH (Reaction 3). Where ΔE1 =

EREACTANTS – ECOMPLEX, ΔE2 = ETS – ECOMPLEX and ΔE3 = ECOMPLEX – EPRODUCT.All the energies are ZPE corrected and are in kcal/mol.

Methods ∆E1 ∆E2 ∆E3 B3LYP/6-31G 7.491 38.048 10.233 B3LYP/6-31G* 5.414 44.023 9.874 B3LYP/6-31+G* 4.869 44.047 7.454 B3LYP/6-31++G* 4.849 44.023 7.478 B3LYP/6-31++G** 4.753 44.664 5.721 B3LYP/6-31++G(2df,2p) 4.089 45.668 5.675 B3LYP/6-31++G(2df,2pd) 4.123 45.623 5.545 B3LYP/6-31++G(3df,2pd) 3.920 46.042 5.312

Table S6. 7: Results of effect of various methods for all molecules on the potential energy surface of i) H2CO → HCHO--NH3 (complex) → H2NCH2OH + CO → H2NCH2OH—CO

(complex) → NH2CH2COOH, and ii) NH=CH2 + H2O → NHCH2-H2O (complex) →

H2NCH2OH + CO → H2NCH2OH—CO (complex) → NH2CH2COOH. All the energies are

ZPE corrected and these total energies are in Hartrees.

Molecules B3LYP/6- G3B3 G3MP2 G3MP2B G3 G4MP2 31++G(3df,2p 3 d) HCHO -114.495050 - - - - - 114.43375 114.35303 114.35802 114.43106 114.37158 9 7 8 1 4

NH3 -56.541164 - -56.470142 - - - 56.508289 56.473014 56.507021 56.478971 HCHO-NH3- -171.038189 - - - - - complex 170.94469 170.82619 170.83347 170.94129 170.85312 4 6 1 5 4 HCHO-NH3- -170.986012 - - - - -

269

APPENDIX C

TS 170.89125 170.77062 170.77900 170.88684 170.79901 9 9 5 2 4

CH2=NH -94.610218 - -94.480174 - - - 94.557256 94.484839 94.554867 94.537389

H2O -76.422694 - -76.342403 - - - 76.383726 76.345644 76.382040 76.355851

CH2NH-H2O- -171.023960 - - - - - complex 170.94709 170.82915 170.83625 170.94379 170.85565 8 3 9 5 1

CH2NH-H2O- -170.965786 - - - - - TS 170.86812 170.74674 170.75624 170.86249 170.77573 8 3 5 4 1

NH2CH2OH -171.047624 - - - - - 170.95623 170.83657 170.84440 170.95232 170.86384 3 5 0 8 6 CO -113.323038 - - - - - 113.26996 113.18887 113.19328 113.26736 113.20766 9 3. 8 7 4

NH2CH2OH- -284.278810 284.22749 - - - - CO-complex 0 284.02675 284.03878 284.22121 284.07247 7 0 5 1

NH2CH2- -284.278810 - - - - - COOHTS 284.12129 283.91867 283.93139 283.11426 283.96378 0 1 8 2 2

NH2CH2COO -284.400997 - - - - - H 284.25367 284.05148 284.06352 284.24745 284.09604 7 0 5 0 5

270

APPENDIX C

Table S6. 8: Results of effect of various basis sets (with B3LYP method) for all molecules on the potential energy surface of i) H2CO → HCHO--NH3 (complex) → H2NCH2OH + CO →

H2NCH2OH—CO (complex) → NH2CH2COOH, and ii) NH=CH2 + H2O → NHCH2-H2O

(complex) → H2NCH2OH + CO → H2NCH2OH—CO (complex) → NH2CH2COOH. All the energies are ZPE corrected and these total energies are in Hartrees.

Molecules 6-31G 6-31G* 6- 6- 6- 6- 6- 31+G* 31++G* 31++G* 31++G(2df 31++G(2 * ,2p) df,2pd) HCHO ------114.434 114.473 114.482 114.482 114.484 114.493799 114.49448 299 648 078 178 956 0

NH3 ------56.536246 - 56.4978 56.5134 56.5224 56.5226 56.5327 56.537878 29 11 71 48 25 HCHO------

NH3- 170.936 170.936 171.032175 171.03457 complex 575 575 2 HCHO------

NH3-TS 170.889 170.938 170.954 170.954 170.969 170.979756 170.98233 355 058 516 855 418 5

CH2=NH ------94.605236 - 94.6102 94.5871 94.5941 94.5943 94.6008 94.606636 18 61 65 69 72

H2O ------76.420651 - 76.3655 76.3877 76.4014 76.4016 171.013 76.421757 61 90 75 08 727

CH2NH------

H2O- 170.932 170.983 171.003 171.003 171.021 171.032404 171.03496 complex 116 578 400 704 302 3

CH2NH------

H2O-TS 170.871 170.913 170.933 170.933 170.950 170.959628 170.96225 483 423 206 549 125 8

NH2CH2O ------H 170.948 170.993 171.015 171.015 171.030 171.041448 171.04380

271

APPENDIX C

424 140 278 621 419 0 CO ------133.254 113.304 113.312 113.312 113.312 113.323059 113.32305 472 423 306 306 306 9

NH2CH2O ------H-CO- 284.204 284.305 284.327 284.328 284.343 284.364615 284.36697 complex 818 310 941 309 077 8

NH2CH2------COOHTS 284.130 284.208 284.237 284.238 284.253 284.272587 284.27520 427 913 701 152 642 0

NH2CH2C ------OOH 284.246 284.340 284.359 284.359 284.374 284.394161 284.39660 150 675 784 983 783 1

Optimized Cartesian coordinates of all the stationary points, in the Potential energy surfaces of the Reactions 1-3.

HCHO (Formaldehyde)

B3LYP/6-31++G(3df,2pd)

C 0.528119 0.000000 0.000031

O -0.674798 -0.000001 -0.000032

H 1.114828 0.938152 0.000056

H 1.114840 -0.938145 0.000017

272

APPENDIX C

NH3 (Ammonia)

B3LYP/6-31++G(3df,2pd)

N 0.000000 0.000000 0.114000

H 0.000000 0.940626 -0.266000

H -0.814606 -0.470313 -0.266000

H 0.814606 -0.470313 -0.266000

HCHO - NH3 ---Transition State (Reaction 1)

B3LYP/6-31++G(3df,2pd)

N -1.069209 -0.210105 -0.000003

H -0.190654 -1.008490 -0.000062

H -1.644251 -0.131399 -0.835357

H -1.644155 -0.131511 0.835426

C 0.269698 0.619214 0.000005

O 1.103466 -0.436154 -0.000002

H 0.258798 1.258039 -0.900064

H 0.258808 1.258041 0.900071

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APPENDIX C

NH2CH2OH (α-hydroxy amine)

B3LYP/6-31++G(3df,2pd)

N -1.230231 -0.160947 -0.018716

H 1.318877 -0.819526 0.660978

H -1.304500 -0.705460 -0.870185

H -1.368917 -0.780835 0.770534

C 0.028043 0.535881 0.047106

O 1.206558 -0.264669 -0.117391

H 0.075295 1.255446 -0.769359

H 0.070142 1.079072 0.995535

HCHO - NH3 --- Complex (Reaction 1)

B3LYP/6-31++G(3df,2pd)

C 0.000000 1.121142 0.000000

O 1.205641 1.122181 0.000000

H -0.589228 1.128162 0.933696

H -0.589228 1.128162 -0.933696

N -0.868153 -1.684002 0.000000

H 0.128118 -1.880048 0.000000

H -1.258858 -2.146283 0.814745

H -1.258858 -2.146283 -0.814745

274

APPENDIX C

CO (Carbon monoxide)

B3LYP/6-31++G(3df,2pd)

C 0.000000 0.000000 -0.646001

O 0.000000 0.000000 0.484501

NH2CH2OH - CO --- Complex (Reaction 2)

B3LYP/6-31++G(3df,2pd)

C 1.403026 -0.377175 0.195060

C -2.663753 -0.625720 -0.296749

O -3.233453 0.203498 0.219676

H 1.072748 -1.236003 -0.387730

H 1.267108 -0.601461 1.256978

N 0.576543 0.755701 -0.136713

H 0.782437 1.562801 0.440520

H 0.695599 1.021340 -1.107719

H 3.195908 0.381899 0.492653

O 2.797798 -0.253638 -0.110623

275

APPENDIX C

NH2CH2-CO - OH --- Transition State (Reaction 2)

B3LYP/6-31++G(3df,2pd)

C 1.448796 0.068145 0.664711

C -1.125995 -0.450633 0.023700

O -2.320153 -0.431030 0.004060

H 0.866905 -0.631905 1.241341

H 1.587269 1.086792 0.986404

N 2.120087 -0.369237 -0.368329

H 1.922313 -1.292185 -0.727214

H 2.590933 0.269077 -0.989840

O -0.497183 0.913648 -0.226216

H -1.206142 1.586862 -0.285604

NH2CH2COOH (Glycine)

B3LYP/6-31++G(3df,2pd)

C 0.746250 -0.749948 0.000127

C -0.635145 -0.097326 0.000020

O -1.671956 -0.714670 -0.000069

H 0.764088 -1.412146 -0.868908

H 0.764138 -1.411726 0.869487

N 1.931708 0.088210 -0.000096

276

APPENDIX C

H 1.949186 0.692703 -0.812928

H 1.949226 0.693074 0.812458

O -0.591169 1.257122 0.000032

H -1.510230 1.564656 -0.000024

CH2=NH(Methylamine)

B3LYP/6-31++G(3df,2pd)

C 0.586885 0.028877 -0.000014

H 1.245720 -0.839259 0.000030

H 1.076099 1.007625 0.000028

N -0.667824 -0.154020 0.000003

H -1.168363 0.736515 0.000004

H2O (Water)

B3LYP/6-31++G(3df,2pd)

O 0.000000 0.000000 0.117016

H 0.000000 0.763067 -0.468064

H 0.000000 -0.763067 -0.468064

277

APPENDIX C

NHCH2 - H2O --- Transition State (Reaction 3)

B3LYP/6-31++G(3df,2pd)

N 0.859197 -0.617840 -0.112063

H 1.286486 -1.115916 0.657276

H -0.106253 -0.948286 -0.424368

C 0.768613 0.678462 -0.016951

H 1.309697 1.215396 0.754763

H 0.260834 1.221958 -0.793516

O -1.382526 -0.035379 0.091405

H -2.316614 0.163992 -0.039244

CH2NH - H2O --- Complex (Reaction 3)

B3LYP/6-31++G(3df,2pd)

N -0.789582 0.563114 0.007867

H -1.308125 1.437704 -0.077181

H 1.131814 0.200538 -0.025763

C -1.555949 -0.447455 0.017474

H -2.644683 -0.395164 -0.054274

H -1.115113 -1.439478 0.100148

O 2.035834 -0.158264 -0.094813

H 2.512202 0.205446 0.655656

278