Overview and Goals learn are applicable to any size system.However,we have used methods and basis sets which are appropriate to research-level calculations.Nevertheless,virtually all of the exercises can be run under any post-1994 version of Gaussian,including Windows versions such as Gaussian 94W(although some jobs may have elapsed times of hours or even days on slower PC's).Readers with limited computing resources may want to reduce the level of theory and/or basis set size for some or all jobs. A long study Examples and exercises involving particularly computationally-intensive studies have (>30 mins.on been marked with one of the icons in the margin.We provide a complete list of all the reference examples and exercises,together with their associated job files and CPU times on a computer) reference computer system,beginning on page xiv.We haven't even attempted to cover all of Gaussian's features.Instead,we've tried to focus on those of most general A very long study (>2 hrs.) applicability.Once you understand these,you'll be in a position to explore the rest of Gaussian's capabilities on your own. Input Files for the Examples and Exercises Input files for all examples and exercises are included with Gaussian(although you will probably want to try setting up your own first for the exercises).In Gaussian 94, they are stored in the following default directory locations: System Type Directory Location File Extension UNIX systems $g94root/g94/explore com VMS systems Disk:[G94.Explore] .COM Windows systems X:\G94W\Explore .GJF Example 0: For VMS and Windows systems,the appropriate disk name must be prepended to the Sample Example directory location.There are subdirectories under the explore directory named file:sample examples and exercise,which hold the input files for the examples in the text and for the exercises at the end of each chapter,respectively (the corresponding filename is given in the margin at the start of each example and exercise);the input files for the Quick Start section are located in the subdirectory quick in the same location.If you do not find these files in the designated location on your system, contact your system administrator for assistance in determining where Gaussian is installed. Exploring Chemistry with Electronic Structure Methods xxvii
Along study 1>30 mins. on the reference computerl Awwy long study 1>2 hrs} Overview and Goals learn are applicable to any size system. However, we have used methods and basis sets which are appropriate to research-level calculations. Nevertheless, virtually all of the exercises can be run under any post-1994 version of Gaussian, including Windows versions such as Gaussian 94W (although some jobs may have elapsed times of hours or even days on slower PC's). Readers with limited computing resources may want to reduce the level of theory and/or basis set size for some or all jobs. Examples and exercises involving particularly computationally-intensive studies have been marked with one of the icons in the margin. We provide a complete list of aU examples and exercises, together with their associated job files and CPU times on a reference computer system, beginning on page xiv. We haven't even attempted to cover all of Gaussian's features. Instead, we've tried to focus on those of most general applicability. Once you understand these, you'll be in a position to explore the rest of Gaussian's capabilities on your own. Input Files for the Examples and Exercises Input files for all examples and exercises are included with Gaussian (although you wiH probably want to try setting up your own first for the exercises). In Gaussian 94, they are stored in the following default directory locations: System Type UNIX systems VMS systems Windows systems Directory Location $g94root/g94/explore Disk: [G9 4. Explore] X: \G94W\Explore File Extension .com .COM .GJF Example 0: Sample Exampl. file: lampl_ For VMS and Windows systems, the appropriate disk name must be prepended to the directory location. There are subdirectories under the explore directory named examples and exercise, which hold the input files for the examples in the text and for the exercises at the end of each chapter, respectively (the corresponding ftIename is given in the margin at the start of each example and exercise}; the input ftIes for the Quick Start section are located in the subdirectory qui ck in the same location. If you do not find these files in the designated location on your system, contact your system administrator for assistance in determining where Gaussian is installed. Exploring Chemistry with Electronic Structure Methods xxvii
Preface About This Work Organizational Structure This book begins with a Gaussian Quick Start tutorial designed to help new Gaussian users begin using the program right away.The remainder of the work is divided into three main parts: Part 1,Essential Concepts Techniques,introduces computational chemistry and the principal sorts of predictions which can be made using electronic structure theory.It presents both the underlying theoretical and philosophical approach to electronic structure calculations taken by this book and the fundamental procedures and techniques for performing them. ◆ Part 2,Model Chemistries,provides an in-depth examination of the accuracy,scope of applicability and other characteristics and trade-offs of all of the major well-defined electronic structure models.It also gives some general recommendations for selecting the best model for investigating a particular problem. Part 3,Applications,discusses electronic structure calculations in the context of real-life research situations,focusing on how it can be used to illuminate a variety of chemical problems. Contents of this Work Each of the chapters in this work is described briefly below: ◆ Chapter 1,"Computational Models and Model Chemistries,"provides an overview of the computational chemistry field and where electronic structure theory fits within it.It also discusses the general theoretical methods and procedures employed in electronic structure calculations(a more detailed treatment of the underlying quantum mechanical theory is given in Appendix A). ◆ Chapter 2,"Single Point Energy Calculations,"discusses computing energies at specific molecular structures,as well as the related molecular properties that may be predicted at the same time. Note that much of the discussion of Gaussian input has been moved to Appendix B in this second edition. Chapter 3,"Geometry Optimizations,"describes how to locate equilibrium structures of molecules,or,more technically,stationary points on the potential energy surface.It includes an overview of the various commonly used optimization techniques and a consideration of optimizing transition structures as well as minimizations. Chapter 4,"Frequency Calculations,"discusses computing the second derivatives of the energy and using it to predict IR and Raman frequencies and intensities and vibrational normal modes.It also considers other uses ovi浦 Exploring Chemistry with Electronic Structure Methods
Preface I About This Work Organizational Structure This book begins with a Gaussian Quick Start tutorial designed to help new Gaussian users begin using the program right away. The remainder of the work is divided into three main parts: .. Part 1, Essential Concepts & Techniques, introduces computational chemistry and the principal sorts of predictions which can be made using electronic structure theory. It presents both the underlying theoretical and philosophical approach to electronic structure calculations taken by this book and the fundamental procedures and techniques for performing them. .. Part 2, Model Chemistries, provides an in-depth examination of the accuracy, scope of applicability and other characteristics and trade-offs of all ofthe major well-defined electronic structure models. It also gives some general recommendations for selecting the best model for investigating a particular problem. .. Part 3, Applications, discusses electronic structure calculations in the context of real-life research situations, focusing on how it can be used to illuminate a variety of chemical problems. Contents of this Work Each of the chapters in this work is described briefly below: .. Chapter 1, "Computational Models and Model Chemistries," provides an overview of the computational chemistry field and where electronic structure theory fits within it. It also discusses the general theoretical methods and procedures employed in electronic structure calculations (a more detailed treatment of the underlying quantum mechanical theory is given in Appendix A). .. Chapter 2, "Single Point Energy Calculations," discusses computing energies at specific molecular structures, as well as the related molecular properties that may be predicted at the same time. Note that much of the discussion of Gaussian input has been moved to Appendix Bin this second edition. ... Chapter 3, "Geometry Optimizations," describes how to locate equilibrium structures of molecules, or, more technically, stationary points on the potential energy surface. It includes an overview of the various commonly used optimization techniques and a consideration of optimizing transition structures as well as minimizations. ... Chapter 4, "Frequency Calculations," discusses computing the second derivatives of the energy and using it to predict IR and Raman frequencies and intensities and vibrational normal modes. It also considers other uses xxviii Exploring Chemistry with Electronic Structure Methods
Overview and Goals of second derivatives,including characterizing stationary points found during optimizations as minima or transition states. ◆ Part 2,"Model Chemistries,"begins with Chapter 5,"Basis Set Effects." This chapter discusses the most important standard basis sets and presents principles for basis set selection.It also describes the distinction between open shell and closed shell calculations. ◆ Chapter 6,"Selecting an Appropriate Theoretical Method,"discusses the model chemistry concept introduced in Chapter I in detail.It covers the strengths,computational cost and limitations of a variety of popular methods,beginning with semi-empirical models and continuing through Hartree-Fock,Density Functional Theory,and electron correlation methods. Chapter 7,"High Accuracy Energy Models,"describes several research procedures for predicting very accurate thermodynamic and energetic properties of systems,including G1,G2,G2(MP2)and several Complete Basis Set (CBS)models. Part3,“Applications,”begins with Chapter8,“Studying Chemical Reactions and Reactivity,"which discusses using electronic structure theory to investigate chemical problems.It includes consideration of reaction path features to investigate the routes between transition structures and the equilibrium structures they connect on the reaction's potential energy surface. ◆ Chapter 9,"Modeling Excited States,"discusses predicting the properties of excited states of molecules,including structures and vibrational frequencies.An exercise in the advanced track considers CASSCF methods. Chapter 10,"Modeling Systems in Solution,"discusses how to model systems in solution.It describes available solvation models and the sorts of systems and properties which may be studied with them. Appendix A,"The Theoretical Background,"contains an overview of the quantum mechanical theory underlying Gaussian.It also includes references to the several detailed treatments available. Appendix B,"Overview of Gaussian Input,"provides a summary of the Gaussian input file format.It also discusses techniques for creating Z-matrix representations of molecular systems. Exploring Chemistry with Electronic Structure Methods xxix
Overview and Goals of second derivatives, including characterizing stationary points found during optimizations as minima or transition states. • Part 2, "Model Chemistries," begins with Chapter 5, "Basis Set Effects." This chapter discusses the most important standard basis sets and presents principles for basis set selection. It also describes the distinction between open shell and closed shell calculations. • Chapter 6, "Selecting an Appropriate Theoretical Method," discusses the model chemistry concept introduced in Chapter I in detail. It covers the strengths, computational cost and limitations of a variety of popular methods, beginning with semi-empirical models and continuing through Hartree-Fock, Density Functional Theory, and electron correlation methods. • Chapter 7, "High Accuracy Energy Models," describes several research procedures for predicting very accurate thermodynamic and energetic properties of systems, including GI, G2, G2(MP2) and several Complete Basis Set (CBS) models. • Part 3, "Applications," begins with Chapter R, "Studying Chemical Reactions and Reactivity," which discusses using electronic structure theory to investigate chemical problems. It includes consideration of reaction path features to investigate the routes between transition structures and the equilibrium structures they connect on the reaction's potential energy surface. • Chapter 9, "Modeling Excited States," discusses predicting the properties of excited states of molecules, including structures and vibrational frequencies. An exercise in the advanced track considers CASSCF methods. • Chapter 10, "Modeling Systems in Solution," discusses how to model systems in solution. It describes available solvation models and the sorts of systems and properties which may be studied with them. • Appendix A, "The Theoretical Background," contains an overview of the quantum mechanical theory underlying Gaussian. It also includes references to the several detailed treatments available. • Appendix B, "Overview of Gaussian Input," provides a summary of the Gaussian input file format. It also discusses techniques for creating Z-matrix representations of molecular systems. Explorilrg CI,emistry with ElectrOlrie Strudure Methods xxix
Preface About This Work Where to Get Additional Information We hope that the discussions here will stimulate your interest in computational chemistry in general and Gaussian in particular.Each chapter provides references to the original studies from which the examples and exercises are drawn as well as to other works of related interest. More detailed information about the Gaussian 94 program can be found in the Gaussian 94 User's Reference and Gaussian 94 Programmer's Reference. Typographic and Graphical Conventions In this book,we have used the following typographical and graphical conventions. Full or partial Gaussian input sets are set in fixed-width type and are set off from normal text like this: RHF/STO-3G Opt SCF=Direct Test Similarly,general syntax statements for Gaussian input are set off from the text,set in fixed-width type.Within syntax statements,literal keywords appear in fixed-width type while replaceable parameters-items for which you must substitute the appropriate value-are set in normal italic type: method/basis_set [Test] Optional items appear in square brackets(which are not themselves typed when the item is included). When Gaussian input keywords,like RHF,appear within normal text,they are set in boldface sans-serif type.Basis set names when referred to as keywords are also set in boldface sans-serif type.Basis set names used in a generic way are set in normal type. Gaussian output is also set off from normal text,set in fixed-width type,and endosed in a shadowed box.Comments about the output are set in red sans-serif type and appear to the left of the output: Comment on the SCFD0NE:E(RHP)=-74.9607165382 A.U.AFTER 8 CYCLES Gaussian output CONVG 0.2843D-09 -V/T=2.0050 S**2 =0.0000 A few UNIX and VMS command examples appear in the text,mostly in the Gaussian Quick Start section,which precedes the text proper.These commands are set off from XXX Exploring Chemistry with Electronic Structure Methods
Preface III - About This Work Where to Get Additional Information We hope that the discussions here will stimulate your interest in computational chemistry in general and Gaussian in particular. Each chapter provides references to ;; the original studies from which the examples and exercises are drawn as well as to !' other works of related interest. More detailed information about the Gaussian 94 program can be found in the Gaussian 94 User's Reference and Gaussian 94 Programmer's Reference. .~ Typographic and Graphical Conventions ... .~ In this book, we have used the following typographical and graphical conventions. , Full or partial Gaussian input sets are set in fixed-width type and are set off from normal text like this: j # RHF/STO-3G Opt SCF=Direct Test Similarly, general syntax statements for Gaussian input are set off from the text, set in ~. fixed-width type. Within syntax statements, literal keywords appear in fixed-width i type while replaceable parameters-items for which you must substitute the f appropriate value-are set in normal italic type: . # method/basis_set [Test] Optional items appear in square brackets (which are not themselves typed when the item is included). A few UNIX and VMS command examples appear in the text, mostly in the Gaussian Quick Start section, which precedes the text proper. These commands are set offfrom Gaussian output is also set offfrom normal text, set in fixed-width type, and enclosed in a shadowed box. Comments about the output are set in red sans-serif type and appear to the left ofthe output: When Gaussian input keywords, like RHF, appear within normal text, they are set in boldface sans-serif type. Basis set names when referred to as keywords are abo set in boldface sans-seriftype. Basis set names used in a generic way are set in normal type. A.U. AFTER 8 CYCLES -V/T = 2.0050 -74.9607165382 = 0.2843D-09 0.0000 E(RHF) CONVG 8**2 Comment on 8CF DONE: the Gauuian output Exploring Chemistry with Electronic Structure Methods
Typographic and Graphical Conventions normal text and set in fixed-width type (but have no box surrounding them). Commands that the user must type appear in boldface fixed-width type,and computer prompts and messages appear in normal fixed-width type: grep "SCF DONE tut000.log SCFD0NE:E(RHF)--74.9607165382.. When UNIX and VMS commands and file or pathnames appear within normal text, they are set in bold and normal sans-serif type(respectively). Gaussian 94W menu options and display labels are set in boldface sans-serif type, following the usual Windows convention. Italic type is used to indicate special terms,like basis set,the first time they appear in the text.Italicized terms will be defined immediately following their introduction. Finally,we have included advice to teachers at appropriate points throughout this work.They are enclosed in a red shaded box.The first one of these "To The Teacher" boxes appears at the end of this section. To The Teacher:About This Guide It is our intention that this book might be used as an instructional unit in a variety of undergraduate and graduate chemistry courses (in addition to serving as an overview of electronic structure theory for research chemists). Accordingly,we have provided To The Teacher boxes such as this one at appropriate points throughout the text.They will contain hints for introducing and discussing material in the cassroom,suggestions for further exercises,clarification of answers given in the text,and pointers to additional reference material. Note that the exercises in this work are not ordered and can be used in other sequences.Omitting earlier exercises will not generally affect later ones.The exercises are suitable as either homework or laboratory exercises,and they have been designed so that the work may be easily divided among a group of students. We'd love to hear about your experiences using this book for educational purposes.Please also feel free to let us know how this book could better meet the needs of your students and courses.You can contact us at explore@gaussian.com. Exploring Chemistry with Electronic Structure Methods d
Typographic and Grnphical Conventions normal text and set in fIxed-width type (but have no box surrounding them). Commands that the user must type appear in boldface fixed-width type, and computer prompts and messages appear in normal fixed-width type: % grep "SCI' DOO" tutOOO.log SCF DONE: E(RHF) -74.9607165382 When UNIX and VMS commands and file or palhnamcs appear within norma) ttXt, they are set in bold and normal sans-seriftype (respectively). Gaussian 94W menu options and display labels are set in boldface sans-serif type, following the usual Windows convention. Italic type is used to indicate special terms, like basis set, the fIrst time they appear in the text. Italicized terms will be defIned immediately following their introduction. Finally, we have included advice to teachers at appropriate points throughout this work. They are enclosed in a red shaded box. The first one ofthese "To The Teacher" boxes appears at the end ofthis section. To The Teacher: About This Guide It isoudntention that this book might be used as an instructional unit in a variety of undergraduate and graduate chemistry courses (in addition to servingasanoverviewofelectronic structure theory for research chemists). Acconiingly•. We have provided To· The TelUher boxes such as this one at approptiate l'oints throughout the text. They wUl contain hints for introdudngallddiKussing mllterial in the classroom. suggestions for furtherexercises.darlfitation.ofallswersgiven in the text, and pointers to additioi1;ll.reference material. Note that theexerdsesinthis work are not ordered and can be used in other sequences. Omitting earlier etetclseswill not generally affect later ones. The exer~isesaresuitableaseitherhomework odaboratory exercises. and they have been deslgned sO thatthe workmay be easily divided among agroup of students~ We'd }ovetoheariaboutyOurexpenences using this book for educational purp()ses. PlcasealsoJetl free to let knowhow this book could better meet the needs of youI students and courses. You can contact us at explore@gattssiatt.tottt. Exploring Chemistry with Electronic Structure Methods JOUd A!