A density functional theory study on structure and mechanism of some isomerization and cycloaddition reactions

Vrije Universiteit Brussel Faculteit Wetenschappen Onderzoeksgroep Algemene Chemie Vrije Universiteit Brussel Faculteit Wetenschaid Alge A Density Functional Theory Study on Structure and Mechanism of some Isomerization and Cycloaddition Reactions Loc Thanh Nguyen Promotors: Prof Dr Paul Geerlings, Vrije Universiteit Brussel Prof Dr Minh Tho Nguyen, Katholieke Universiteit Leuven Proefschrift voorgelegd tot het behalen van de wettelijke graad van Doctor in de Wetenschappen October 2002 Acknowledgements The story of this thesis started in September 1997 with the “Interuniversity Program for Education in Computational Chemistry in Vietnam” supported by the Flemish Government (project VIET/97-4) Professor Minh Tho Nguyen at the Katholieke Universiteit Leuven (KULeuven), the main promoter of this project, together with professor Paul Geerlings at the Vrije Universiteit Brussel (VUB) and professor Kris Van Alsenoy of the Universiteit van Antwerpen (UIA), has opened a door for me to enter the fascinating field of computational chemistry when providing me an opportunity to join two of the research groups involved, first the KULeuven group, then the VUB one At the beginning, every quantum theory was new for me But, from that time, both professors had tried hard not only to give me a sound background but also to look for financial resources Finally they used their own research funds, namely the Geconcerteerde Onderzoeksacties (GOA) and the DFT Research community of the Fund for Scientific Research (FWO-Vlaanderen), along with the kind support of their colleagues (professor Luc Vanquickenborne, professor Arnout Ceulemans, professor Kristine Pierloot, professor Marc Hendrickx (KULeuven) and professor Frank De Proft (VUB)), to give me a unique chance to perform research at the doctoral level in the department of chemistry, VUB, but on a joint research project between both VUB and KULeuven quantum chemistry groups The last doctoral year fellowship was granted by the Vrije Universiteit Brussel Therefore, I would first like to express my sincere thanks to both universities, the research funds, professors Nguyen and Geerlings as well as their colleagues for their kind support I would like to express my deep gratitude to professor Paul Geerlings and professor Minh Tho Nguyen for their constant encouragement, scientific guidance and patient supervision of my research work This work would not have been achievable without the friendly support and efficient help from many other people In particular, I wish to acknowledge professor Frank De Proft (VUB), Dr Wilfried Langenaeker (VUB; now at Janssen Pharmaceutica) and Dr Asit Kumar Chandra (KULeuven, now in India) for patiently answering my technical problems and valuable help I would also like to thank professor Kalidas Sen (India) for uncomplainingly explaining my theoretical questions during his short visiting day at VUB A special thank is also sent to professor Kris Van Alsenoy for helping me with the Hirshfeld charge calculations I am particularly grateful to Dr Hans Vansweevelt (KULeuven) for computational help and to the VUB Computer Center for support Mrs Rita Jungbluth (KULeuven) and Mrs Martine De Valck (VUB) are also acknowledged for administrative help The days would have passed far more slowly without the support of my friends, both at the KULeuven and VUB, providing me such a rich source of conversation, education and entertainment My warmest gratitude goes to my friends Trung Ngoc Le, Hung Thanh Le, Hue Minh Thi Nguyen, Thanh Lam Nguyen, Nam Cam Pham, Nguyen ii Acknowledgement Nguyen Pham-Tran, David Delaere, Dr Annelies Delabie, Dr Steven Creve, Dr Raman Sumathy (KULeuven), Ricardo Vivas-Reyes, Bennasser Safi, Dr Gregory Van Lier, Pierre Mignon, Dr Frederik J C Tielens, Dr Robert Balawender, Dr Stefan Loverix, Greet Boon, Goedele Roos, Jan Baert, Montserrat Cases Amat (VUB) … and many more I could not have asked for a better working environment and friendship Furthermore I also owe a debt of thanks to Mr Diet Van Tran and his family, Mrs Mai Phuong Le and her two nice daughters, my friends (Nho Hao Dinh, Chau Ngan Nguyen-Vo, Ngoc Lien Truong, Phuong Khuong Ong, Minh Tri Nhan, Chi Thanh Truong, Thu Phong Phan-Vo, Lam Thanh Nguyen, Thai An Mai, Thi Xuan Tran … and many more), who have no direct relation with my research, but they have given me much concern and useful help during my stays in Belgium My thanks also extend to my home university in Vietnam, the Faculty of Chemical Engineering, HoChiMinh City University of Technology (HUT), for administrative support I would like to acknowledge professor Van Luong Dao for scientific guidance and valuable advice of my research work in Vietnam I am indebted to professor Van Bon Pham, professor Huu Nieu Nguyen, professor Van Lua Nguyen, professor Van Hang Tong, professor Huu Khiem Mai, professor Thuong Truong Le, professor Khac Chuong Tran, professor Viet Hoa Thi Tran, professor Minh Tan Phan, Msc Dinh Pho Nguyen, Mrs Thi Dung Huynh, Msc Ba Minh Vu, Mr Hung Dung Tran, Msc Minh Nam Hoang, Msc Thanh Son Thanh Do, Mr Van Co Ngo, Msc Thanh Trung Duong, Msc Huu Thao Vo, Dr Dac Thanh Nguyen, Dr Van Phuoc Nguyen, Dr Ngoc Hanh Nguyen, Mrs Thi Thu Nguyen, Mrs Kim Anh Thi Lam, Mrs Ngoc Phu Thi Nguyen (HUT) and Mr Cat Si Thanh Le (HoChiMinh City) for their continuous support and valuable help Many thanks also go to my colleagues and my friends in HUT for their cooperation, friendship and encouragement Especially, I would express heartfelt thanks to my parents, my parents-in-law, my brothers, my sisters and their families, for their love, invaluable help and support throughout my life Finally, I would like to give my special thanks to my wife, Dieu Chan Thi Truong, and our two children, Huong Lan Ngoc Nguyen and Thanh Triet Nguyen, for their love, patience and encouragement that enabled me to complete this work Table of Contents Acknowledgments i Table of Contents iii Summary vii Samenvatting ix Chapter Introduction 1.1 Computational Chemistry 1.1.1 Current Situation 1.1.2 Methods 1.2 Structures and reaction mechanism in organic chemistry 1.3 Scope of the Thesis 10 1.4 References 11 Chapter Theoretical Background 13 2.1 Wave function Ab Initio methods 13 2.1.1 Schrödinger equation 13 2.1.2 The Hartree-Fock theory 14 2.1.2.1 Restricted closed-shell Hartree-Fock: The Roothaan-Hall equations 16 2.1.2.2 Unrestricted open-shell Hartree-Fock: The Pople-Nesbet equations 17 2.1.3 Post Hartree-Fock methods 18 2.1.3.1 The Configuration Interaction method 19 2.1.3.2 The Coupled Cluster method 20 2.1.3.3 The Møller-Plesset Perturbation method 20 2.1.4 Basis sets 22 2.1.4.1 Minimal basis sets 22 2.1.4.2 Scaling the orbital by splitting the minimal basis set 23 2.1.4.2.1 Split valence basis sets 23 2.1.4.2.2 Double zeta basis sets 23 2.1.4.3 Extended basis sets 24 2.1.4.3.1 Polarization basis functions 24 2.1.4.3.2 Diffuse basis functions 24 2.1.4.4 Dunning's correlation consistent basis sets 24 2.1.5 Molecular quantities 25 2.1.5.1 The electron density function 25 2.1.5.2 Atomic charges 25 2.1.5.2.1 The Mulliken population analysis method 25 2.1.5.2.2 The natural population analysis 26 2.1.5.2.3 The electrostatic potential derived charges 27 2.2 Density Functional Theory 27 iv 2.2.1 2.2.2 2.2.3 2.2.3.1 2.2.3.2 2.2.3.3 2.2.4 2.2.4.1 2.2.4.2 2.2.4.3 2.2.4.4 2.3 2.3.1 2.3.2 2.3.2.1 2.3.2.2 2.3.3 2.3.3.1 2.3.3.2 2.4 Table of Contents The Thomas-Fermi-Dirac theory 28 The Kohn-Sham method 28 The exchange-correlation energy functional 30 Local Density methods 30 Gradient Corrected methods 30 Hybrid methods 30 DFT-based chemical concepts 31 The chemical potential 31 Hardness and Softness 32 The Fukui function and local softness 33 The Local Hard and Soft Acids and Bases principle 34 Solvent effect 34 Introduction 34 Solvation models 35 Explicit solvation models 35 Implicit solvation models 36 The PCM model 37 Introduction 37 Model Implementation 37 References 39 Chapter Computational Details 41 3.1 Software and Hardware 41 3.2 References 43 Chapter Application of Density Functional Theory (DFT) in constructing the Potential Energy Surface for Simple Isomerization and Fragmentation Reactions 45 4.1 Introduction 45 4.2 Theoretical study of the CH3 + NS and related reactions: mechanism of HCN formation 48 4.2.1 Introduction 48 4.2.2 Methods of Calculations 48 4.2.3 Results and Discussion 48 4.2.4 Conclusions 55 4.3 Theoretical Study of the Potential Energy Surface Related to NH2 + NS Reaction: N2 versus H2 Elimination 56 4.3.1 Introduction 56 4.3.2 Methods of Calculations 56 4.3.3 Results and Discussion 57 4.3.4 Conclusions 65 4.4 General Conclusion 66 4.5 References 67 Chapter Application of Density Functional Theory (DFT) in studying Cycloaddition Reactions 71 5.1 Introduction 71 Table of Contents 5.2 v Mechanism of [2+1] Cycloadditions of Hydrogen Isocyanide to Acetylenes 76 5.2.1 Introduction 76 5.2.2 Methods of Calculation 77 5.2.3 Results and Discussion 77 5.2.3.1 Preliminary analysis of frontier orbital interactions 77 5.2.3.2 Addition of the unsubstituted system HN≡C + HC≡CH (Reaction H) 78 5.2.3.3 Addition of HN≡C to HC≡C-CH3 (Reaction M) 82 5.2.3.4 Addition of HN≡C to HC≡C-NH2 (Reaction A) 84 5.2.3.5 Addition of HN≡C to HC≡C-F (Reaction F) 87 5.2.3.6 Asynchronism in Addition 90 5.2.4 Conclusions 98 5.3 [2+1] Cycloadditions of CO and CS to Acetylenes 99 5.3.1 Cyclopropenones and cyclopropenethiones: decomposition via intermediates 99 5.3.1.1 Introduction 99 5.3.1.2 Methods of Calculation 100 5.3.1.3 Results and Discussion 100 5.3.1.3.1 Analysis of the nature of the reaction partners 100 5.3.1.3.2 Reaction of H-C≡C-H with C=X (X = O, S) 101 5.3.1.3.2.1 Potential energy surfaces 101 5.3.1.3.2.2 Solvent effect 107 5.3.1.3.2.3 Estimation of the vertical first excitation energies 107 5.3.1.3.3 Reaction of H-C≡C-F with C=X (X = O, S) 108 5.3.1.3.4 Reaction of F-C≡C-F with C=X (X = O, S) 111 5.3.1.3.5 Profiles of hardness, polarizability and activation energy along an IRC path 113 5.3.1.4 Conclusions 115 5.3.2 [2 + 1] Cycloaddition of CO and CS to Acetylenes forming Cyclopropenones and Cyclopropenethiones 116 5.3.2.1 Introduction 116 5.3.2.2 Methods of Calculation 117 5.3.2.3 Results and Discussion 118 5.3.2.3.1 Classification of the reactants as nucleophile or electrophile 118 5.3.2.3.2 Potential Energy Surfaces 119 5.3.2.3.2.1 Reaction of H-C≡C-CH3 with CX (X = O, S) 119 5.3.2.3.2.2 Reaction of H-C≡C-OH 123 5.3.2.3.2.3 Reaction of H-C≡C-NH2 124 5.3.2.3.2.4 Reaction of H-C≡C-C6H5 125 5.3.2.3.2.5 Reaction of HO-C≡C-CH3 127 5.3.2.3.2.6 Reaction of HO-C≡C-C6H5 128 5.3.2.3.3 Effects of substituents on the aromaticity of cyclo-propenones and cyclopropenethiones 132 5.3.2.3.4 Site selectivity in the initial attack of the addition 133 5.3.2.4 Conclusions 136 5.4 1,3-Dipolar cycloadditions of thionitroso compounds (R–N=S) 138 5.4.1 Introduction 138 vi Table of Contents 5.4.2 5.4.3 5.4.3.1 5.4.3.1.1 5.4.3.1.2 5.4.3.1.3 5.4.3.1.4 5.4.3.2 5.4.3.3 5.4.4 5.5 Details of calculations 138 Results and discussion 139 Structure and energetics 139 The HC≡N+–O- + HN=S addition (A) 139 The HC≡N+–O- + H2N–N=S addition (B) 140 The HN=N+=N- + HN=S addition (C) 141 Additions of substituted systems 143 Regiochemistry of the addition: testing the local HSAB principle 144 Testing the maximum hardness principle 147 Conclusions 149 Nitrous Oxide as a 1,3-Dipole: A Study of Its Cycloaddition Mechanism 150 5.5.1 Introduction 150 5.5.2 Details of Calculation 152 5.5.3 Results and Discussion 152 5.5.3.1 Frontier Molecular Orbital Analysis 152 5.5.3.2 The 1,3-DC of N2O to acetylene 154 5.5.3.3 The 1,3-DC of N2O to substituted alkynes 157 5.5.3.3.1 Geometries 157 5.5.3.3.2 Energy barriers and solvent effect 159 5.5.3.3.3 Regioselectivity 161 5.5.4 Conclusions 166 5.6 1,3-Dipolar cycloadditions of diazoalkanes, hydrazoic acid and nitrous oxide to acetylenes, phosphaalkynes and cyanides: a regioselectivity study 168 5.6.1 Introduction 168 5.6.2 Details of Calculation 171 5.6.3 Results and Discussion 171 5.6.3.1 The 1,3-DC of Diazoalkanes 171 5.6.3.2 The 1,3-DC of Hydrazoic acid and Nitrous Oxide 178 5.6.4 Conclusions 182 5.7 General Conclusion 184 5.8 References 187 Chapter General Conclusions 197 Appendices 199 A1 List of Symbols and Abbreviations 199 A2 List of supplementary Tables and Figures in §5.3.2 and §5.6 201 A3 List of Publications 212 Summary In this thesis we apply the Density Functional Theory (DFT) in its Kohn Sham formulation using the B3LYP functional, for constructing of the potential energy surface (PES) for some isomerization and fragmentation reactions and studying a number of [2+1] and 1,3-dipolar cycloadditions The PES constructions for the isomerization and fragmentation reactions involving two NS moieties, [CH3NS] and [NH2NS] show that, with respect to the CCSD(T) values, the B3LYP method tends to overestimate the energy gaps between equilibrium structures relative to the starting structures (CH3NS or NH2NS) The energy ordering however remains almost unchanged Moreover, the most significant chemical results of the theoretical studies are a prediction on the preferential formation of HCN in the CH3 + NS reaction and the fact that both radicals NH2 and NS can go through an initial barrierfree nitrogen-nitrogen association giving NH2NS, which in turn tends to follow a lowenergy two-step path leading to the stable products, N2 and H2S A one-step elimination of H2 seems to be a more energy-demanding process The theoretical studies of the [2+1] cycloaddition of hydrogen isocyanide (HN≡C), CX (X = O, S) to acetylenes demonstrates that these reactions proceed in two steps: addition of the carbon atom in HN≡C or CX to a carbon atom of the acetylenes giving rise to an intermediate, followed by a ring closure step of the latter to form at last the cycloadducts The intermediate has the properties of a semi-carbene, semi-zwitterion and its structure is best described as a resonance hybrid between a carbene and a zwitterion In all cases acetylenes behave as nucleophiles The investigation of the hardness and polarizability profiles along the IRC reaction paths shows that there is a maximum in the polarizability profile besides an inverse relationship between hardness and polarizability In the cycloadditions of CX to acetylenes, it is also shown that the promotion of an electron from the ground state to an excited state for any reaction partner requires a large amount of energy As such, all investigated reactions are expected to take place in the ground state rather than in an excited state We also show that the solvent effect is small on the reactions, and tends to stabilize all the isomers Different reactivity criteria such as Frontier Molecular Orbital (FMO) coefficients, local softness, hardness, polarizability and nucleus-independent chemical shifts (NICS) are used to predict the site selectivity in all studied cases, and the NICS, FMO coefficients, local softness seem to yield the best results among them The 1,3-dipolar cycloadditions (1,3-DC) of fulminic acid (HCNO) and the simple azides (XNNN, X=H, CH3, NH2) to thionitroso compounds (R-N=S, R = H, NH2) are generally characterized by their rather low energy barriers In the cases of azides, the reaction is not stereospecific In all cases, they show a certain regioselectivity favoring the formation of a cycloadduct The 1,3-DC reactions of diazoalkanes, hydrazoic acid and nitrous oxide to the polar viii Summary dipolarophiles considered are concerted but asynchronous processes When approaching a polar dipolarophile partner either the C-end of a diazo derivative, or the N(R) of an azide or the O-atom of nitrous oxide, consistently acts as a new bond donor and the other molecular terminus being the new bond acceptor As a consequence, the lone pair of the central nitrogen, formed upon bending of the dipole, originates from the triple N≡N bond Those cycloaddition reactions are essentially orbital-controlled, which is supported by the successful prediction of the regioselectivity based on reactivity criteria that are basically generalized forms of FMO theory The local softness differences and FMO coefficient products remain the criteria of choice in predicting the regioselectivity of cycloaddition reactions Among available population analysis methods to define the atomic charges, the Natural Population Analysis (NPA) seems to give the best support to the local Hard and Soft Acids and Bases (HSAB) principle In the cycloadditions of nitrous oxide to acetylenes, in general, the shape of the potential energy surface appears not to be affected by the polarity of the solvent Although all Ts’s are aromatic, their aromaticity does not influence the regioselectivity of the reactions In this study the less aromatic, more polar and more asynchronous Ts is the Ts-normal Samenvatting In deze thesis wordt Density Functional Theory (DFT) toegepast in de Kohn Sham formulering, met gebruik van de B3LYP functionaal, om het Potentiële Energie Oppervlak (PES) van een aantal isomerisatie en fragmentatiereacties te bestuderen, alsook een aantal [2+1] en 1,3-dipolaire cycloaddities De PES constructie voor de isomerisatie en fragmentatiereacties voor twee NS entiteiten bevattende species, [CH3NS] en [NH2NS], toont aan dat, in vergelijking met CCSD(T), de B3LYP methode de energieverschillen overschat tussen evenwichtsstructuren, transitietoestanden en de startstructuren (CH3NS of NH2NS) De ordening van de energieën daarentegen is bijna steeds onveranderd De meest significante chemische resultaten van de theoretische studie zijn enerzijds een voorspelling van de voorkeur van vorming van HCN in de CH3 + NS reactie, anderzijds het feit dat beide radicalen, NH2 en NS, een initiële barrièrevrije stikstof-stikstof associatie vertonen, aanleiding gevend tot NH2NS Op zijn beurt volgt NH2NS een laagenergetisch tweestapsmechanisme leidend tot de stabiele eindproducten N2 en H2S Een eenstapseliminatie van H2 blijkt een energetisch minder gunstig proces te zijn De theoretische studie van de [2+1] cycloadditie van waterstofisocyanide (HN≡C) en CX (X = O, S) aan acetylenen toont aan dat deze reacties in twee stappen verlopen : additie van het koolstofatoom in HN≡C of CX aan een koolstofatoom van de acetylenen wat aanleiding geeft tot een intermediair, gevolgd door een ringsluiting met finaal vorming van het cycloadduct Het intermediair blijkt de eigenschappen van een semicarbeen, semi-zwitterion te hebben Zijn structuur wordt het best beschreven als een resonantiehybride tussen een carbeen en een zwitterion In alle gevallen blijken acetylenen zich als nucleofiel te gedragen Het onderzoek van de hardheid en de polariseerbaarheidsprofielen langsheen het IRC reactiepad toont aan dat er een maximum in het polariseerbaarheidsprofiel is Een inverse relatie tussen hardheid en polarisabiliteit wordt vastgesteld Bij de cycloaddities van CX op acetylenen wordt ook aangetoond dat de overgang van de electronische grondtoestand naar een aangeslagen toestand voor elk van de reactiepartners veel energie vergt Men kan daarom verwachten dat alle reacties plaatsgrijpen vanuit de grondtoestand en niet vanuit een aangeslagen toestand Ook wordt aangetoond dat het solvent effect op deze reacties klein is en dat het alle isomeren stabiliseert Verschillende reactiviteitscriteria zoals de "Frontier Molecular Orbital" (FMO) coëfficiënten en de lokale zachtheid, hardheid, polariseerbaarheid en de "nucleusindependent chemical shifts" (NICS) worden gebruikt om de "site selectivity" te voorspellen in alle beschouwde gevallen De NICS, FMO coëfficiënten en de lokale zachtheid blijken hierbij de beste resultaten op te leveren De 1,3-dipolaire cycloaddities (1,3-DC) van HCNO en eenvoudige azides (XNNN, X = H, CH3, NH2) op thionitroso verbindingen (R-N=S, R = H, NH2) worden over het 192 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 Chapter Middleton, W J J Am Chem Soc 1966, 88, 3842 Roesky, H W.; Emmert, R.; Isenberg, W.; Schmidt, M.; Sheldrick, G M J Chem Soc., Dalton Trans 1983, 183 Leroy, G.; Sana, M.; Burke, L A.; Nguyen, M T Contribution to the theoretical study of reaction mechanisms In Quantum Theory of Chemical Reactions; Daudel, R.; Pullman, A.; Salem, L.; Veillard, A., Eds.; Reidel, D Publishing: 1979; Vol 1, p 91-144 Nguyen, M T J Mol Struct (THEOCHEM) 1983, 105, 343 Regitz, M Chem Rev 1990, 90, 191 Nyulaszi, L.; Varnai, P.; Eisfeld, W.; Regitz, M J Comput Chem 1997, 18, 609 Sengupta, D.; Chandra, A K.; Nguyen, M T J Org Chem 1997, 62, 6404 Méndez, F.; Tamariz, J.; Geerlings, P J Phys Chem A 1998, 102, 6292 Rastelli, A.; Gandolfi, R.; Amade, M S J Org Chem 1998, 63, 7425 Politzer, P.; Murray, J S.; Grice, M E Charge capacities and shell structures of atoms In Chemical Hardness, Structure and Bonding; Springer-Verlag: Berlin, 1993; Vol 80, p 101-114 Ghanty, T K.; Ghosh, S K J Phys Chem 1993, 97, 4951 Pal, S.; Chandra, A K J Phys Chem 1995, 99, 13865 Chattaraj, P K.; Sengupta, S J Phys Chem A 1997, 101, 7893 Cárdenas-Jirón, G I.; Lahsen, J.; Toro-Labbé, A J Phys Chem 1995, 99, 5325 Eger, E I., II Nitrous oxide/N2O; Elsevier: New York, 1985 Grant, W J Medical Gases : Their Properties and Uses; Year Book Medical Publishers: Chicago, 1978 Zeidifard, E.; Godfrey, S.; Davies, E E J Appl Physiol 1976, 41, 433 Hahn, C E W.; Black, A M S.; Barton, S A.; Scott, I J Appl Physiol 1993, 75, 1863 Frumkin, A N.; Petrii, O A.; Damaskin, B B In Comprehensive Treatise in Electrochemistry; Bockris, J O M.; Conway, B E.; Yeager, E., Eds.; Plenum Press: New York, 1980; Vol 1, p 221-289 Conway, B E In Modern Aspects of Electrochemistry; Conway, B E.; Bockris, J O M., Eds.; Plenum Press: New York, 1972; Vol 7, p 83-142 Simpler, C A.; Webster, R C Industrial Users of Nitrous Oxide - No Laughing Matter In Clinical Anaesthesia: Nitrous oxide 1/1964; Eastwood, D W., Ed.; Davis Co.: Philadelphia, 1964 Schmidt, H H H W.; Hofmann, H.; Schindler, U.; Shutenko, Z S.; Cunningham, D D.; Feelisch, M Proc Natl Acad Sci U S A 1996, 93, 14492 Sojka, Z.; Che, M J Phys Chem 1996, 100, 14776 Delahay, G.; Coq, B.; Kieger, S.; Neveu, B Catal Today 1999, 54, 431 Bange, H W Nature 2000, 408, 301 Prather, M In Climate Change 1995: The Science of Climate Change, Contribution of Working Group I to the Second Assessment Report of the Intergovernmental Panel on Climate Change; Houghton, J T., Ed.; Cambridge University Press: Cambridge, 1996, p 86-103 Wayne, R P Chemistry of Atmospheres; Clarendon Press: Oxford, 1991 Seiler, W.; Conrad, R J Air Pollut Control 1981, 31, 767 Chapter 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 193 McMahon, P B.; Bruce, B W.; Becker, M F.; Pope, L M.; Dennehy, K F Environ Sci Technol 2000, 34, 4873 Becker, K H.; Lorzer, J C.; Kurtenbach, R.; Wiesen, P.; Jensen, T E.; Wallington, T J Environ Sci Technol 1999, 33, 4134 Eichner, M J J Environ Qual 1990, 19, 272 Czepiel, P.; Crill, P.; Harriss, R Environ Sci Technol 1995, 29, 2352 Ronen, D.; Magaritz, M.; Almon, E Nature 1988, 335, 57 McMahon, P B.; Dennehy, K F Environ Sci Technol 1999, 33, 21 Cole, J J.; Caraco, N F Environ Sci Technol 2001, 35, 991 Perry, R A.; Miller, J A Int J Chem Kinet 1996, 28, 217 Centi, G.; Generali, P.; dall'Olio, L.; Perathoner, S.; Rak, Z Ind Eng Chem Res 2000, 39, 131 Poh, S.; Hernandez, R.; Inagaki, M.; Jessop, P G Org Lett 1999, 1, 583 Bruning, F.; Matejcik, S.; Illenberger, E.; Chu, Y N.; Senn, G.; Muigg, D.; Denifl, G.; Mark, T D Chem Phys Lett 1998, 292, 177 Kryachko, E S.; Vinckier, C.; Nguyen, M T J Chem Phys 2001, 114, 7911 Lein, I.; Potzinger, P Organometallics 2000, 19, 4701 Bridson-Jones, F S.; Buckley, G D.; Levy, W J J Chem Soc 1951, 3009 Bridson-Jones, F S.; Buckley, G D.; Cross, L H.; Driver, A P J Chem Soc 1951, 2999 Buckley, G D.; Levy, W J J Chem Soc 1951, 3016 Houk, K N J Am Chem Soc 1972, 94, 8953 Sana, M.; Leroy, G.; Dive, G.; Nguyen, M T J Mol Struct (THEOCHEM) 1982, 6, 147 Gothelf, K V.; Jorgensen, K A Chem Rev 1998, 98, 863 Di Valentin, C.; Freccero, M.; Gandolfi, R.; Rastelli, A J Org Chem 2000, 65, 6112 Chandra, A K.; Uchimaru, T.; Nguyen, M T J Chem Soc., Perkin Trans 1999, 2117 Chandra, A K.; Michalak, A.; Nguyen, M T.; Nalewajski, R F J Phys Chem A 1998, 102, 10182 Parr, R G.; Pearson, R G J Am Chem Soc 1983, 105, 7512 Hu, Y F.; Houk, K N Tetrahedron 2000, 56, 8239 Schwerdtfeger, P.; Dolg, M.; Schwarz, W H E.; Bowmaker, G A.; Boyd, P D W J Chem Phys 1989, 91, 1762 Bergner, A.; Dolg, M.; Kuchle, W.; Stoll, H.; Preuss, H Mol Phys 1993, 80, 1431 Glukhovtsev, M N.; Pross, A.; McGrath, M P.; Radom, L J Chem Phys 1995, 103, 1878 Nguyen, M T.; Chandra, A K.; Sakai, S.; Morokuma, K J Org Chem 1999, 64, 65 Keith, T A.; Bader, R F W Chem Phys Lett 1992, 194, Keith, T A.; Bader, R F W Chem Phys Lett 1993, 210, 223 Koch, W.; Holthausen, M C A Chemist's Guide to Density Functional Theory; 2nd ed.; Wiley-VCH: Weinheim, 2001 Nguyen, M T.; Hegarty, A F.; Elguero, J Angew Chem., Int Ed Engl 1985, 24, 713 Nguyen, L T.; De Proft, F.; Nguyen, M T.; Geerlings, P J Org Chem 2001, 66, 4316 194 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 Chapter Fieser, L F.; Fieser, M Advanced Organic Chemistry; Reinhold Pubblishing Corporation: New York, 1961 Streitwieser, A., Jr.; Heathcock, C H Introduction to Organic Chemistry; 3rd ed.; Macmillan Publishing Company: New York, 1985 Papakondylis, A.; Mavridis, A J Phys Chem A 1999, 103, 1255 Leroy, G.; Sana, M Tetrahedron 1975, 31, 2091 Leroy, G.; Sana, M Tetrahedron 1976, 32, 709 Leroy, G.; Nguyen, M T.; Sana, M Tetrahedron 1976, 32, 1529 Leroy, G.; Sana, M Tetrahedron 1976, 32, 1379 March, J Advanced Organic Chemistry: Reactions, Mechanisms, and Structures; 4th ed.; Wiley: New York, 1992 Gandolfi, R.; Tonoletti, G.; Rastelli, A.; Bagatti, M J Org Chem 1993, 58, 6038 Bagatti, M.; Ori, A.; Rastelli, A.; Burdisso, M.; Gandolfi, R J Chem Soc., Perkin Trans 1992, 1657 Burdisso, M.; Gamba, A.; Gandolfi, R.; Toma, L.; Rastelli, A.; Schiatti, E J Org Chem 1990, 55, 3311 Muray, E.; Alvarez-Larena, A.; Piniella, J F.; Branchadell, V.; Ortuno, R M J Org Chem 2000, 65, 388 Sustmann, R.; Sicking, W.; Felderhoff, M Tetrahedron 1990, 46, 783 Annunziata, R.; Benaglia, M.; Cinquini, M.; Raimondi, L Tetrahedron 1993, 49, 8629 Branchadell, V.; Muray, E.; Oliva, A.; Ortuno, R M.; Rodriguez-Garcia, C J Phys Chem A 1998, 102, 10106 Blavins, J J.; Karadakov, P B.; Cooper, D L J Org Chem 2001, 66, 4285 Leggio, A.; Liguori, A.; Napoli, A.; Siciliano, C.; Sindona, G J Org Chem 2001, 66, 2246 Sustmann, R.; Sicking, W.; Huisgen, R J Org Chem 1993, 58, 82 Ortuno, R M.; Ibarzo, J.; AlvarezLarena, A.; Piniella, J F Tetrahedron Lett 1996, 4059 Diaz, M.; Branchadell, V.; Oliva, A.; Ortuno, R M Tetrahedron 1995, 51, 11841 Saladino, R.; Stasi, L.; Crestini, C.; Nicoletti, R.; Botta, M Tetrahedron 1997, 53, 7045 Karadakov, P B.; Cooper, D L J Phys Chem A 2001, 105, 10946 Nguyen, M T.; Chandra, A K.; Uchimaru, T.; Sakai, S J Phys Chem A 2001, 105, 10943 Harcourt, R D J Phys Chem A 2001, 105, 10947 Harcourt, R D.; Schulz, A J Phys Chem A 2000, 104, 6510 Daudel, R.; Leroy, G.; Peeters, D.; Sana, M Quantum Chemistry; Wiley: New York, 1983 Karadakov, P B.; Cooper, D L.; Gerratt, J Theor Chem Acc 1998, 100, 222 Klicic, J J.; Friesner, R A J Phys Chem A 1999, 103, 1276 Korchowiec, J.; Chandra, A K.; Uchimaru, T J Mol Struct (THEOCHEM) 2001, 572, 193 Abu-Orabi, S T Molecules 2002, 7, 302 Kadaba, P K Synlett 1990, 349 Nguyen, L T.; De Proft, F.; Chandra, A K.; Uchimaru, T.; Nguyen, M T.; Geerlings, P J Org Chem 2001, 66, 6096 Chandra, A K.; Nguyen, M T Int J Mol Sci 2002, 3, 310 Reed, A E.; Weinstock, R B.; Weinhold, F J Chem Phys 1985, 83, 735 Reed, A E.; Curtiss, L A.; Weinhold, F Chem Rev 1988, 88, 899 Hirshfeld, F L Isr J Chem 1977, 16, 198 Hirshfeld, F L Theor Chim Acta 1977, 44, 129 Chapter 174 175 176 177 178 179 180 195 Nalewajski, R F.; Parr, R G Proc Natl Acad Sci U S A 2000, 97, 8879 Nalewajski, R F Int J Mol Sci 2002, 3, 237 Olah, J.; Van Alsenoy, C.; Sannigrahi, A B J Phys Chem A 2002, 106, 3885 De Proft, F.; Van Alsenoy, C.; Peeters, A.; Langenaeker, W.; Geerlings, P J Comp Chem., in press Langenaeker, W.; De Decker, M.; Geerlings, P.; Raeymaekers, P J Mol Struct (THEOCHEM) 1990, 207, 115 Bach, R D.; Glukhovtsev, M N.; Gonzalez, C.; Marquez, M.; Estevez, C M.; Baboul, A G.; Schlegel, H B J Phys Chem A 1997, 101, 6092 Kadaba, P K.; Colturi, T F J Heterocycl Chem 1969, 6, 829 Regitz, M In Multiple Bonds and Low Coordination in Phosphorus Chemistry; Regitz, M.; Scherer, O J.; Appel, R., Eds.; G Thieme Verlag: Stuttgart, 1990, p 58 General Conclusions In this thesis Density Functional Theory (DFT) has been applied in the study of “Structure and Mechanism” for some isomerization and cycloaddition reactions The study of the isomerization and fragmentation reactions of the [CH3NS] and [NH2NS] moieties indicates that the accuracy of DFT/B3LYP values for all isomers on the potential energy surface is only semi-quantitative as compared to the CCSD(T) (for energy barriers) or the MP2 (for geometrical parameters) methods The identification of the most favored channel in transforming the reactant partners shows that HCN will be formed preferentially in the CH3 + NS reaction; the elimination of N2 is more favorable than that of H2 in the NH2 + NS one B3LYP studies point out that the [2+1] cycloaddition reactions of HNC, CO and CS to acetylenes are stepwise The existence of the intermediates has been confirmed by the CCSD(T) computations The hardness and polarizability profiles along the IRC reaction paths clearly indicate an inverse relationship between hardness and polarizability The cycloadditions of CO and CS to acetylenes are shown to occur in the ground state rather than in an excited state The solvent effect is small and tends to uniformly stabilize all the isomers The investigations of the 1,3-dipolar cycloaddition reactions of HCNO and XNNN to R-N=S; and RC2NN, HNNN and N2O to polar dipolarophiles show that the B3LYP method can be used to determine the energy-favored paths, which are in the same energy ordering as that obtained from the CCSD(T) calculations In the reactions of N2O with acetylenes, in general, the shape of the potential energy surface seems not to be influenced by the polarity of the solvent Moreover, although all the transition structures (Ts) in these reactions are aromatic, their aromaticity does not contribute to the regio-specificity of the reactions It is observed that the less aromatic, more polar and more asynchronous Ts is preferred The prediction of the site selectivity by using DFT-based reactivity descriptors such as local softness, hardness, polarizability together with Frontier Molecular Orbital (FMO) coefficients, and nucleus-independent chemical shifts (NICS) reveals that the NICS, FMO coefficients and local softness using natural population analysis (NPA) charges yield the best results In summary, this thesis can be considered as a contribution to the understanding of “Structure and Mechanism”, a fundamental problem in physical organic chemistry This work also illustrates a way of applying computational chemistry to “real” chemical problems, in line with the growing tendency of computerizing all branches of science Furthermore, as already stated in chapter 1, the area of this dissertation belongs both to the conceptual DFT and computational DFT Our study shows that DFT methods, at some extents of acceptable accuracy, can be satisfactorily applied in locating structures and energy barriers with a favorable quality/cost ratio as compared to wave function 198 Chapter methods such as MP2, CCSD(T) … It also reveals that the concepts derived from DFT, especially the local softness, are very useful in rationalizing and predicting reactivity of molecules In a near future, the rapid development of information technology will lead to new high performance computers Coupled to the further development of theoretical methods (e.g better functionals in DFT) and further optimization of algorithms, this will allow us to perform more accurate calculations on much larger systems It is certain that in the coming years, quantum/computational chemistry will play an even more indispensable role in determining structures, interpreting mechanisms and above all, predicting chemical phenomena The further development of new generations of exchange-correlation functionals probably will consolidate DFT as the method of choice in studying this kind of problems in chemistry When completing, guiding and sometimes replacing experiments, computational chemistry thereby becomes an essential tool in a broad domain of chemical research Structure Site attack C-(O) to C-H C-(O) to C-CH3 H-C≡C-NH2 C-(O) to C-H C-(O) to C-NH2 C-(O) to C-H H-C≡C-OH C-(O) to C-OH C-(O) to C-H H-C≡C-F C-(O) to C-F H-C≡C-C6H5 C-(O) to C-H C-(O) to C-C6H5 HO-C≡C-C6H5 C-(O) to C-OH C-(O) to C-C6H5 HO-C≡C-CH3 C-(O) to C-OH C-(O) to C-CH3 H-C≡C-CH3 Eact B3LYP/6-311G(d,p) NICS(+1) values taken from GIAO/B3LYP/6-311G(d,p) C from HF/STO-3G Eact ΔNPA (kJ/mol) 122.5 150.3 82.0 136.2 176.8 119.7 181.9 96.4 121.8 180.4 92.9 167.0 94.4 75.4 0.20 0.38 0.05 1.20 0.04 0.79 0.12 0.60 0.27 1.39 0.67 0.84 0.73 0.13 C NICS (+1) 0.50 0.48 0.63 0.40 0.64 0.45 0.63 0.53 0.43 0.29 0.39 0.41 0.47 0.62 -10.8 -8.2 -9.0 -7.8 -4.4 -8.2 -3.8 -6.4 -8.3 -3.7 -6.5 -3.7 -8.5 -11.0 Structure H-C≡C-NH2 Site attack O-to-C(-H) O-to-C(-NH2) O-to-C(-H) H-C≡C-PH2 O-to-C(-PH2) O-to-C(-H) H-C≡C-SH O-to-C(-SH) O-to-C(-H) H-C≡C-SiH3 O-to-C(-SiH3) H-C≡C-COOH O-to-C(-H) O-to-C(-COOH) CH3-C≡C-CHO O-to-C(-CH3) O-to-C(-CHO) O-to-C(-H) H-C≡C-CHO O-to-C(-CHO) Eact 103.7 94.4 107.5 106.5 111.0 109.4 106.7 105.0 114.1 111.7 109.9 114.1 107.0 105.0 Δ 0.625 0.092 0.593 0.130 0.790 0.192 0.157 0.118 0.498 0.102 0.744 0.266 0.766 0.249 C NICS(+1) 0.375 -17.84 0.462 -10.62 0.259 -18.80 0.294 -17.76 0.235 -18.62 0.294 -17.64 0.353 -19.18 0.358 -18.20 0.349 -17.96 0.359 -17.33 0.491 -15.61 0.485 -16.70 0.494 -17.83 0.504 -17.21 Structure Site attack H-C≡C-CH3 O-to-C(-H) O-to-C(-CH3) O-to-C(-H) H-C≡C-F O-to-C(-F) H-C≡C-Cl O-to-C(-H) O-to-C(-Cl) H-C≡C-Br O-to-C(-H) O-to-C(-Br) O-to-C(-H) H-C≡C-I O-to-C(-I) H-C≡C-OH O-to-C(-H) O-to-C(-OH) Eact 110.9 105.2 109.7 104.1 117.1 112.8 115.0 111.0 112.4 111.4 114.4 108.2 Δ 0.143 0.023 0.262 0.000 0.386 0.029 0.480 0.068 0.670 0.150 0.469 0.030 C 0.551 0.565 0.503 0.547 0.452 0.478 0.313 0.351 0.194 0.224 0.436 0.511 NICS(+1) -18.32 -16.61 -17.03 -15.57 -18.11 -16.58 -18.37 -16.66 -18.69 -17.58 -17.47 -16.14 Structure C1H3-C2H=C3H-C4H=O C1H3-C2H=C3H-C4H=NH Site attack (N) to C2 (N) to O (N) to C2 (N) to N Eact 6.1 36.9 11.0 48.4 ΔNPA 0.976 3.234 2.487 2.369 C 0.542 0.546 0.599 0.601 Table Differences (in eV) in LUMO – HOMO energies and (IE – EA) of Hydrogen Isocyanide (HN≡C) and related structures N Structure EHOMOa b (IE ) a b ELUMO(HNC) – EHOMO(R)a {IE (R) – EA(HNC)b} ELUMO(R) – EHOMO(HNC)a {IE(HNC) – EA(R)b} HN≡C -13.0 (12.2) HC≡C-CH3 -10.4 (10.3) 16.0 (13.8) 19.2 (15.2) HC≡C-NH2 -9.3 (9.0) 15.0 (12.5) 18.9 (14.7) HC≡C-F -11.2 (11.3) 16.9 (14.8) 19.9 (15.6) Values obtained from HF/6-31G(d) wavefunctions in eV Values calculated using B3LYP/6-311G(d,p) in eV Table Activation Energies (kJ/mol) and square of the softness differences Δ (a.u.) No Structure H-C≡C-CH3 H-C≡C-NH2 H-C≡C-F a d Site attack in TS Eact Δa Δb C-(NH) to C-H C-(NH) to C-CH3 C-(NH) to C-H C-(NH) to C-NH2 C-(NH) to C-H C-(NH) to C-F 100 132 74 114 85 79 0.082 0.852 0.000 1.913 0.116 0.799 0.136 0.293 0.020 1.049 0.070 0.494 Δ values obtained from electrostatic potential driven (ESP) charges Δ values obtained from natural population analysis (NPA) charges CO + R1-C≡C-R2 CS + R1-C≡C-R2 R1 R2 ΔNPA C NICS(+1) R1 R2 ΔNPA H H H H H OH OH CH3 NH2 OH F C6H5 C6H5 CH3 x x o o x x x x x o o x o x x x x x x x x H H H H H OH OH CH3 NH2 OH F C6H5 C6H5 CH3 x x x o x x x C NICS(+1) x x x o x o x x x x o x o x N2O + R1-C≡C-R2 R1 R2 ΔNPA C NICS(+1) H H H H H H H H H H H H CH3 CH3 F Cl Br I OH NH2 PH2 SH SiH3 COOH CHO CHO x x x x x x x x x x x x o x x x x x x x x x x x x x o o o o o o o o o o o o o H H H H H H H H H H H H CH3 CH3 F Cl Br I OH Structure NH2 PH2 SH SiH3 COOH CHO CHO Δ x x x x x x C x x x x x x Δ x x x x x x o NICS(+1) o o o o o o C x x x x x x x NICS(+1) o o o o o o o ... potential energy surface (PES) for some isomerization and fragmentation reactions and studying a number of [2+1] and 1,3-dipolar cycloadditions The PES constructions for the isomerization and fragmentation... concentration of reactants, catalysts and the rate of the reaction, which are summarized Chapter in the rate law The relationship between a kinetic expression and a reaction mechanism can be evaluated... as a resonance hybrid between a carbene and a zwitterion In all cases acetylenes behave as nucleophiles The investigation of the hardness and polarizability profiles along the IRC reaction paths