Table of Input Files Corresponding CPUTime Input File Example/Exercise Description of Job (hrs:mins:secs:) Chaptor 10 10_02 Exercise 10.2 Formaldehyde optimization in cyclohexane 0:01:49.8 10_03a Exercise 10.3 Acetaldehyde frequencies in acetonitrile 0:04:38.0 10_036 Exercise 10.3 Acrolein frequencies in acetonitrile 0:17:55.3 1003c Exercise 10.3 Formamide frequencies in acetonitrile 0:04:52.3 1003d Exercise 10.3 Acetone frequencies in acetonitrile 0:16:9.8 1003e Exercise 10.3 Acetyl chloride frequencies in acetonitrile 0:18:58.3 1003f Exercise 10.3 Methyl acetate frequencies in acetonitrile 0:38:19.1 1004a Exercise 10.4 N-methyl-(2-nitrovinyl)amine E form 2:40:11.5 10.04h Exercise 10.4 N-methyl-(2-nitrovinyl)amine Z form 2:09:36.6 1004c Exercise 10.4 N-methyl-(2-nitrovinyl)amine rot.TS 4:28:53.4 10_05a Exercise 10.5 Furfuraldehyde(anti)in solution 4:08:21.0 1005b Exercise 10.5 Furfuraldehyde(syn)in solution 4:02:58.7 Appendix A ea_0la Example A.1 SisH12 with different integration grids 0:12:39.8 ea_0lb Example A.1 AlP4 with different integration grids 0:25:40.6 ea_0lc Example A.1 AlP4 without symmetry 0:34:22.2 Exploring Chemistry with Electronic Structure Methods xix
-"--- Table ofInput Files Corresponding CPU Time Input File Example/Exercise Description of Job (hrs:mins:secs:) Chapter 10 10_02 Exercise 10.2 Formaldehyde optimization in cyclohexane 0:01:49.8 10_030 Exercise 10.3 Acetaldehyde frequencies in acetonitrile 0:04:38.0 10_03b Exercise 10.3 Acrolein frequencies in acetonitrile 0:17:55.3 10_03c Exercise 10.3 Formamide frequencies in acetonitrile 0:04:52.3 10_03d Exercise 10.3 Acetone frequencies in acetonitrile 0:16:9.8 ------ lO_03e Exercise 10.3 Acetyl chloride frequencies in acetonitrile 0:18:58.3 10_03f Exercise 10.3 Methyl acetate frequencies in acetonitrile 0:38:19.1 10_040 Exercise lOA N-methyl-(2-nitrovinyl)amine E form 2:40:11.5 10_04b Exercise 10.4 N-methyl-(2-nitrovinyl)amine Z form 2:09:36.6 10_04c Exercise 10.4 N-methyl-(2-nitrovinyl)amine rot. TS 4:28:53.4 10_05a Exercise 10.5 Furfuraldehyde (anti) in solution 4:08:21.0 10_05b Exercise 10.5 Furfuraldehyde (syn) in solution 4:02:58.7 Appendix A ea_Ola Example A.I SisH12 with different integration grids 0:12:39.8 ------ ea_Olb Example A.I Al4P4 with different integration grids 0:25:40.6 ea_Olc Example A.I Al4P4 without symmetry 0:34:22.2 Exploring Chemistry ~ith Electronic Structure Methods xix
List of“To the Teacher”Boxes About This Guide.XXi Molecular Orbitals....9 Magnetic PrOperties............30 Further Substitutions. .45 The Harmonic Oscillator....... …62 Connecting Thermochemistry to Statistical Mechanics67 Transition State Optimizations. .77 Additional Modes Discussion............. .78 Interpreting Gas Phase Frequencies......... .83 Further Frequency Discussion........ 88 Basis Set Details… .99 Further Investigation of the SiHPES. .203 Additional Isodesmic Reactions206 Charge Distribution Difference Density.2 CI vs.One-Particle Dipole Moments...222 Carbonyl Stretch in Cyclohexane.....246 Exploring Chemistry with Electronic Structure Methods xxi
111f----~-L-l-·S-t0-'1-'-'T(-o-t-he-Te-a-ch-er"-B~o~es About This Guide xxxi Molecular Orbitals 19 Magnetic Properties 30 Further Substitutions 45 The Harmonic Oscillator 62 Connecting Thermochemistry to Statistical Mechanics 67 Transition State Optimizations 77 Additional Modes Discussion 7R Interpreting Gas Phase Frequencies 83 Further Frequency Discussion 8R Basis Set Details 99 Further Investigation ofthe Si2H4+ PES 203 Additional Isodesmic Reactions 206 Charge Distribution Difference Density 220 CI vs. One-Particle Dipole Moments 222 Carbonyl Stretch in Cyclohexane 246 Explorirlg Chemistry with Electrorlic Structure Methods xxi
Acknowledgments Many people helped with this work.We are grateful to the many readers who read all or part of the manuscript of the second edition:K.B.Wiberg (Yale University), George Petersson (Wesleyan University),Mike Robb (King's College,London), Berny Schlegel and his research group(Wayne State University and Gaussian,Inc.), Doug Fox and David Moses(Gaussian,Inc.),John Montgomery,Jim Cheeseman, Mike Frisch and Gary Trucks(Lorentzian,Inc.),Andrew Livelsberger(York College of PA;Rice University),Joe Uchterski and Carlos Sosa(Cray Research),and Krishnan Raghavachari (AT&T Bell Laboratories/Lucent Technologies).We also continue to thank the readers of the first edition of this book:Ken Fountain (Northeast Missouri State University),Robert Higgins (Fayetteville State University),James Lobue(Ursinus College),John Ranck(Elizabethtown College), Arlen Viste(Augustana College),Martin Head-Gordon(University of California, Berkeley),Bill Ellis (Lorentzian,Inc.),and David Turner(Scientific Computing Associates).Arlen Viste,Michael Tsai(Univiversity of Alabama,Birmingham), Errol Lewars(Trent University),and Ross Nobes(Molecular Simulations)provided helpful bug reports on the first edition.The errors that remain are our own. John Montgomery,Mike Robb,K.B.Wiberg,Gustavo Scuseria(Rice University), lan Carmichael(University of Notre Dame),Sason Shaik(University of Rochester), M.W.(Richard)Wong (University of Queensland),Krishnan Raghavachari, Charlie Bauschlicher (NASA),Carlos Sosa (Cray Research)and David Tozer (Cambridge University),and Jim Cheeseman,Mike Frisch and Gary Trucks were also extremely helpful in developing some of the examples and exercises in this book.We thank them for their inspirational scientific work,their patience,and their quick email responses. John Carpenter and Carlos Sosa of Cray Research generously provided the computer time and technical assistance for the resource use study in Chapter 6. The figures of the C600 isomers in Chapter 3 are reprinted by permission from Chem.Phys.Letters. This book also benefits from the excellent copy editing of Carolyn Ball and Laura Lasala.Laura Lasala,Gina Onushco,Judy Loukides and Christine Ashline also provided invaluable assistance in the production process. Finally,the authors thank all of the important people in their lives who allowed this project to be a central focus for such a long time. Exploring Chemistry with Electronic Structure Methods xxiii
III~--~~--~~---~-~-~- ~---~ Acknowledgments Many people helped with this work. We are grateful to the many readers who read all or part of the manuscript of the second edition: K. B. Wiberg (Yale University), George Petersson (Wesleyan University), Mike Robb (King's College, London), Berny Schlegel and his research group (Wayne State University and Gaussian, Inc.), Doug Fox and David Moses (Gaussian, Inc.), John Montgomery, Jim Cheeseman, Mike Frisch and Gary Trucks (Lorentzian, Inc.), Andrew Livelsberger (York College of PA; Rice University), Joe Ochterski and Carlos Sosa (Cray Research), and Krishnan Raghavachari (AT&T Bell Laboratories/Lucent Technologies). We abo continue to thank the readers of the first edition of this book: Ken Fountain (Northeast Missouri State University), Robert Higgins (Fayetteville State University), James Lobue (Ursinus College), John Ranck (Elizabethtown College), Arlen Viste (Augustana College), Martin Head-Gordon (University of California, Berkeley), Bill Ellis (Lorentzian, Inc.), and David Turner (Scientific Computing Associates). Arlen Viste, Michael Tsai (Univiversity of Alabama, Birmingham), Errol Lewars (Trent University), and Ross Nobes (Molecular Simulations) provided helpful bug reports on the first edition. The errors that remain are our own. John Montgomery, Mike Robb, K. B. Wiberg, Gu~tavo Sctlseria (Rice lJniver$ity), Ian Carmichael (University of Notre Dame), Sason Shaik (University of Rochester), M. W. (Richard) Wong (University of Queensland), Krishnan Raghavachari, Charlie Bauschlicher (NASA), Carlos Sosa (Cray Research) and David Tozer (Cambridge University), and Jim Cheeseman, Mike Frisch and Gary Trucks were also extremely helpful in developing some of the examples and exercises in this book. We thank them for their inspirational scientific work, their patience, and their quick email responses. John Carpenter and Carlos Sosa of Cray Research generously provided the computer time and technical assistance for the resource use study in Chapter 6. The figures of the C600 isomers in Chapter 3 are reprinted by permission from Chern. Phys. Letters. This book also benefits from the excellent copy editing of Carolyn Ball and Laura Lasala. Laura Lasala, Gina Onushco, Judy Loukides and Christine Ashline also provided invaluable assistance in the production process. Finally, the authors thank all ofthe important people in their lives who allowed this project to be a central focus for such a long time. Exploring Chemistry with Electronic Structure Methods xxiii
Preface About This Work Exploring Chemistry with Electronic Structure Methods serves as an introduction to the capabilities of and procedures for this variety of computational chemistry.It is designed to teach you how to use electronic structure modeling to investigate the chemical phenomena of interest to you.This work was developed using the Gaussian series of computational chemistry programs for all of its specific examples and exercises(specifically Gaussian 94).Other program(s)could be substituted,provided that the necessary features and capabilities were available. Gaussian is capable of predicting many properties of molecules and reactions, including the following: ◆ Molecular energies and structures ◆ Energies and structures oftransition states ◆ Bond and reaction energies ◆ Molecular orbitals ◆ Multipole moments ◆ Atomic charges and electrostatic potentials ◆ Vibrational frequencies ◆ IR and Raman spectra ◆NMR properties Polarizabilities and hyperpolarizabilities Thermochemical properties Reaction pathways Computations can be carried out on systems in the gas phase or in solution,and in their ground state or in an excited state.Gaussian can serve as a powerful tool for exploring areas of chemical interest like substituent effects,reaction mechanisms, potential energy surfaces,and excitation energies. Who Should Read This Book? Several different types of chemists will benefit from reading this work: Experimental research chemists with little or no experience with computational chemistry may use this work as an introduction to electronic structure calculations.They will discover how electronic structure theory can be used as an adjunct to their experimental research to provide new insights into chemical problems. Exploring Chemistry with Electronic Structure Methods V
About This Work Exploring Chemistry with Electronic Structure Methods serves as an introduction to the capabilities of and procedures for this variety of computational chemistry. It is designed to teach you how to use electronic structure modeling to investigate the chemical phenomena ofinterest to you. This work was developed using the Gaussian series of computational chemistry programs for all of its specific examples and exercises (specifically Gaussian 94). Other program(s} could be substituted, provided that the necessary features and capabilities were available. Gaussian is capable of predicting many properties of molecules and reactions, including the following: • Molecular energies and structures • Energies and structures oftransition states • Bond and reaction energies • Molecular orbitals • Multipole moments • Atomic charges and electrostatic potentials • Vibrational frequencies • IR and Raman spectra • NMR properties • Polarizabilities and hyperpolarizabilities • Thermochemical properties • Reaction pathways Computations can be carried out on systems in the gas phase or in solution, and in their ground state or in an excited state. Gaussian can serve as a powerful tool for exploring areas of chemical interest like substituent effects, reaction mechanisms, potential energy surfaces, and excitation energies. Who Should Read This Book? Several different types of chemists will benefit from reading this work: • Experimental research chemists with litde or no experience with computational chemistry may use this work as an introduction to electronic structure calculations. They will discover how electronic structure theory can be used as an adjunct to their experimental research to provide new insights into chemical problems. 1 Exploring Chon',,,,, with EI""on,, S"",tu", Mdhod
Preface About This Work Students of physical chemistry,at the advanced undergraduate or beginning graduate level,will find this work a useful complement to standard texts,enabling them to experiment with the theoretical construct discussed there. Experienced Gaussian users may use this book to acquaint themselves with the program's newest features. Overview and Goals This work is structured as a study guide,and it employs a hands-on approach to teaching you how to use electronic structure theory to investigate chemical systems.It is suitable for either individual,self-paced study or dlassroom use.Naturally,not every section will be relevant to all readers.Accordingly,chapters are designed to be as self-contained as possible;you should focus on those parts which address your research needs and interests. Examples and Exercises Each chapter focuses on a single topic,and includes explanations of the chemical properties or phenomena under consideration and the relevant computational procedures,one or two detailed examples of setting up such calculations and interpreting their results,and several exercises designed to both provide practice in the area and to introduce its more advanced aspects.Full solutions are provided for all exercises. Many exercises include new material that expands on themes first introduced in the text.Accordingly,you may find it beneficial to read through each problem and solution even if you do not choose to complete every exercise.For this second edition, we have added new exercises covering advanced aspects of the current topic to most chapters.This material constitutes an advanced track through the work.Experienced researchers may wish to examine the advanced track even in the earlier,more elementary chapters where the basic concepts are very familiar. The molecules considered in both the worked examples in the text and the exercises have been chosen to minimize the amount of CPU time necessary to complete a non-trivial calculation of each type.We've deliberately chosen systems that,for the most part,can be modeled with minimal cost because our goal here is to focus on the chemistry,rather than on Gaussian's features and research capabilities.Note,however, that although the molecules we will consider are relatively small,the methods you will xxvi Exploring Chemistry with Electronic Structure Methods
Overview and Goals pretacel About This Work • Students of physical chemistry, at the advanced undergraduate or beginning graduate level, will find this work a useful complement to standard texts, enabling them to experiment ~ith the theoretical constructs discussed there. • Experienced Gaussian users may use this book to acquaint themselves with the program's newest features. This work is structured as a study guide, and it employs a hands-on approach to teaching you how to use electronic structure theory to investigate chemical systems. It is suitable for either individual, self-paced study or classroom usc. Naturally, not every section will be relevant to all readers. Accordingly, chapters arc designed to be aI self-contained as possible; you should focus on those parts which address your research needs and interests. Examples and Exercises Each chapter focuses on a single topic, and includes explanations of the chemical properties or phenomena under consideration and the relevant computational procedures, one or two detailed examples of setting up such calculations and interpreting their results, and several exercises designed to both provide practice in the area and to introduce its more advanced aspects. Full solutions are provided for aD exercises. Many exercises include new material that expands on themes first introduced in the text. Accordingly, you may find it beneficial to read through each problem and solution even ifyou do not choose to complete every exercise. For this second edition, we have added new exercises covering advanced aspects of the current topic to most chapters. This material constitutes an advanced track through the work. Experienced researchers may wish to examine the advanced track even in the earlier, more elementary chapters where the basic concepts are very familiar. The molecules considered in both the worked examples in the text and the exercises have been chosen to minimize the amount of CPU time necessary to complete a non-trivial calculation of each type. We've deliberately chosen systems that, for the most part, can be modeled with minimal cost because our goal here is to focus on the chemistry, rather than on Gaussian's features and research capabilities. Note, however, that although the molecules we will consider are relatively small, the methods you will xxvi Exploring Chemistry with Electronic Structure Methods 'l! t¢.,'~'i' ~~~~~~~ i