Exploring Chemistry with Electronic Structure Methods Second Edition James B. Foresman £leen Frisch G Gaussian, Inc. Pittsburgh, PAQuick Topic Finder Accuracies of Model Chemistries Atomic Charges . CASSCF Method Complete Basis Set Methods ... Density Functional Theory .. Excited States . Frequency Calculations G2 Calculations Hyperfine Coupling Constants. IRC Calculations... Isodesmic Reactions .. Methods Accuracies Compared .. Relative Costs ... ‘Model Chemistries Selection Recommendations 96 Molecular Orbitals NMR Properties Optimizations Performing. sno ‘Advanced Techniques .. . Characterizing Stationary Points .. Locating Transition Structures Potential Energy Surface Scans Reaction Path Following .. Resource Requirements Scale Factors for Frequencies/ZPEs SN2 Reactions Solvent Effects Stability Calculations Thermochemistry wnnrneren ‘Transition Structure Optimizations 146, 157 Exploring Chemistry with Electronic Structure Methods itTable of Contents List of Examples and Exercise Table of Input Files... List of “To the Teacher” Boxes... Acknowledgments Preface: About This Worl Who Should Read This Book? Overview and Goals.. Examples and Exercises. Organizational Structure... Where to Get Additional Information. ‘Typographic and Graphical Conventions. Quick Start: Running Gaussian .. Tutorial for UNIX and VMS Systems. Converting a Structure from a Graphics Program. Batch Processing... Tutorial for Windows Systems....... Converting a Structure from a Graphics Program. ae, Drag-and-Drop Execution... A Quick Tour of Gaussian Output. Part 1: Essential Concepts & Techniques Chapter 1: Computational Models & Model Chemistries ‘An Overview of Computational Chemistry... Molecular Mechanics. Electronic Structure Methods.. Model Chemistries.... Defining Model Chemistries. References... Exploring Chemistry with Electronic Structure Methods vTable of Contents Chapter 2: Single Point Energy Calculations Setting Up Energy Calculations non The Route Section... The Title Section The Molecule Specification Section. ‘Multi-Step Jobs... Locating Results in Gaussian Cau . Standard Orientation Geometry Energy... Molecular Orbitals and Orbital Energies Charge Distribution... . Dipole and Higher Multipole Moments... CPU Time and Other Resource Usage.. Predicting NMR Properties Exercises References.. Chapter 3: Geometry Optimizations ... Potential Energy Surfaces Locating Minima.. Convergence Criteria Preparing Input for Geometry Optimizations .. Examining Optimization Outpu Locating Transition Structures Handling Difficult Optimization Cases Exercises References Chapter 4: Frequency Calculations... Predicting IR and Raman Spectra Input for Frequency Jobs. Frequencies and Intensities Normal Modes. Thermochemistry. Zero-Point Energy and Thermal Energy . Polarizability and Hyperpolarizability.. Characterizing Stationary Points Exercises . Reference: wi Exploring Chemistry with Electronic Structure MethodsTable of Contents Part 2: Model Chemistries Introduction. . Model Chemistries.... Terminology. Recommendations for Selecting Research Models. Chapter 5: Basis Set Effects Minimal Basis Sets... Split Valence Basis Sets.... Polarized Basis Sets.. Diffuse Functions... High Angular Momentum Basis Sets. Basis Sets for Post-Third-Row Atoms. Exercises. References ... 101 103 10 Mm ur M3 14 Chapter 6: Selecting an Appropriate Theoretical Method .. Using Semi-Empirical Methods... Limitations of Semi-Empirical Methods Electron Correlation and Post-SCF Method: The Limits of Hartree-Fock Theory... us ‘The MPn Methods a 116 Coupled Cluster and Quadratic Configuration Interaction Methods. 117 Density Functional Theory Methods. us Resource Usage Exercises .. 139 References... Chapter 7: High Accuracy Energy Models........ M1 Predicting Thermochemistry. 4d ui M2 43 143 Atomization Energies.. Electron Affinities Ionization Potentials. Proton Affinities... Evaluating Model Chemistries 144 ‘The G2 Molecule Set (and Pitfalls in Its Interpretation) so 44 Relative Accuracies of Selected Model Chemistries..... 146 Exploring Chemistry with Electronic Structure Methods vibTable of Contents Compound Methods. Gaussian-1 and Gaussian-2 Theories... Complete Basis Set Methods.. Exercises .. References..... Part 3: Applications Chapter 8: Studying Chemical Reactions and Reactivity .. Interpreting the Electron Density. ‘Computing Enthalpies of Reactior Studying Potential Energy Surfac Potential Energy Surface Scans. Reaction Path Following... Running IRC Calculations. Exploring a Potential Energy Surface Molecular Dissociation of Formaldehyde. The 1,2 Hydrogen Shift Reaction. A Final Note on IRC Calculations. Isodesmic Reactions. Limitations of Isodesmic Reactions. Exercise References Chapter 9: Modeling Excited States Running Excited State Calculations. Cl-Singles Output Excited State Optimizations and Frequencies Chapter 10: Modeling Systems in Solution Reaction Field Models of Solvation Limitations of the Onsager Model... Running SCRF Calculation Molecular Volume Calculations Locating Results in Gaussian Output. Exercises. References Exploring Chemistry with Electronic Structure MethodsTable of Contents Appendices Appendix A: The Theoretical Background The Schrdinger Equation eunsennnnen The Molecular Hamiltonian. Atomic Units... sea ‘The Born-Oppenheimer Approximation... Restrictions on the Wavefunction. Hartree-Fock Theory. Molecular Orbital: Basis Sets The Variational Principle The Roothaan-Hall Equations Open Shell Methods... Electron Correlation Methods .. Configuration Interaction. Moller-Plesset Perturbation Theory... Density Functional Theory.... The Complete Basis Set Extrapolation nin-nsnonsn References nnn Appendix B: Overview of Gaussian Input. Input File Sections. The Route Section, More Complex Z-Matrices Using Variables in a Z-matrix. Multi-Step Jobs. Index. ara Physical Constants & Conversion Factors inside back cover Exploring Chemistry with Electronic Structure Methods ixExercise QS.1: Exercise QS.2: Exercise QS.3: Example 2.1: Example 2.2: Exercise 2.1 Exercise 2.2: Exercise 2.3 Bxercise 24: Exercise 2.5: Advanced Exercise 2.6: Advanced Exercise 2.7: Advanced Exercise 2.8: Example 3.1 Example 3.2: Examiple 3.3: Exercise 3.1: Exercise 3.2: Exercise 3.3 Exercise 3.4: Advanced Exercise 3.5: Advanced Exercise 3.6: Advanced Exercise 3.7: Advanced Exercise 3.8: Example 4.1: Example 4.2: Exercise 4.1 Exercise 4.2: List of Examples and Exercises Water Single Point Energy... oxi Converting a PDB File.. RXV Sample Gaussian Output, oti Formaldehyde Single Point Energy... 16 Methane NMR Shielding Constants 21 Propene Single Point Energy.. 22 1,2-Dichloro-1,2-Difluoroethane Conformer Energies... 24 ‘Acetone Compared to Formaldehyde... 26 Ethylene and Formaldehyde Molecular Orbitals.. ee NMR Properties of Alkanes, Alkenes and Alkynes suru 29 Cog Single Point Energy wns 31 CPU Resource Usage by Calculation Size... 31 SCE Stability Calculations... eT] Ethylene Optimization .. 42 Fluoroethylene Optimization. 45 Transition State Optimization... 46 Optimizations of Propene Conformers.. 49 Optimizations of Vinyi Alcohol Conformers... 50 Planar Vinyl Amine Optimization. 31 Chromium Hexacarbonyl Optimization... 52 NMR Isotropic Chemical Shift for Benzene... 53 Optimization of Cog0 Isomers... 54 ‘A.1,1 Elimination Transition State Optimization. 56 Comparing Optimization Procedures. Formaldehyde Frequencies... Characterizing Stationary Points.. Frequencies of Vinyl Alcohol Isomers.. Characterizing Planar Vinyl Amine. Exploring Chemistry with Electronic Structure Methods xtList of Examples and Exercises xii Exercise 4.3: Exercise 4.4 Advanced Exercise 4.5: Advanced Exercise 4.6: Example 5.1: Example 5.2: Exercise 5.1: Exercise 5.2: Advanced Exercise 5.3: Advanced Exercise 5.4 Advanced Exercise 5.5: Advanced Exercise 5.6: Example 6.1: Example 6.2: Example 6.3: Example 6.4: Example 6.5: Example 6.6: Exercise 6.1: Exercise 6.2: Exercise 6.3 Exercise 6.4: Exercise 6.5: Advanced Exercise 6.6: Advanced Exercise 6.7: Advanced Exercise 6.8: Advanced Exercise 6.9 Example 7.1: Example 7.2: Example 7.3: Example 7.4 Example 7.5: Example 7.6: Exercise 7.1 Advanced Exercise 7.2: Vinyl Series Frequencies. Carbonyl Stretch by Substituent Strained Hydrocarbons.....oninnonennennn A 1,3 Hydrogen Shift on the CsHsF Potential Energy Surface Methanol vs. Methoxide Anion Optimizations PO Bond Distance... HE Bond Length nnn Periodic Trends in Transition Metal Complexes. Basis Set Effects on NMR Calculations (Benzene) Geometry of N,N-Dimethylformamide... Basis Set Definitions... Comparing 6-31G(d) and 6-31Gt 101 103 105 107 M2 13 us Optimization of Ozone... ale CO; Structure and Atomization Energy. M9 Ey” Structure and Frequencies. .urnsnn 121 Butane-Iso-Butane Isomerization Energy... sow 124 Rotational Barrier of N-Butane.. 12S 126 128 Malonaldehyde Optimization Optimization of FOOF wn. ‘Acetaldchyde-Ethylene Oxide Isomerization Enetgy..u.m:m Spin Polarization in Heterosubstituted Allyl Radicals. 130 133, MTFy” Structures and Frequencies Hyperfine Coupling Constants Ozone Destruction by Atomic Chlorine... Atomization Energy of PH). Electron Affinity of PH Ionization Potential of PH). Proton Affinity of PH. G2 Proton Affinity of PH3.. CBS-4 and CBS-Q Proton Affinities of PH)... CBS-4 Thermochemistry ‘Ozone Destruction by Atomic Chlorine Revisited. Exploring Chemistry with Electronic Structure MethodsExample 8.1: Example 8.2: Example 8.3: Example 8.4: Example 8.5: Example 8.6: Example 8.7: Exercise 8.1: Exercise 8.2: Exercise 8.3: Exercise 8.4: Exercise 8.5: Advanced Exercise 8.6: Advanced Exercise 8.7: Advanced Exercise 8.8: Advanced Exercise 8.9: Advanced Exercise 8.10: Example 9.1: Example 9.2: Exercise 9.1: Exercise 9.2: Exercise 9.3: Advanced Exercise 9.4: Advanced Exercise 9.5: Advanced Exercise 9.6: Example 10.1 Example 10.2: Exercise 10.1: Exercise 10.2: Exercise 10.3: Advanced Exercise 10.4: Advanced Exercise 10.5: Example A.1: Exercise B.1: Exercise B.2: List of Eeamples and Exercises Electron Densities of Substituted Benzenes. Hydration Reactions unm (CHO + Hy + COIRC CH,0 > HCOH IRC AH for an Isodesmic Reaction. 165 176 179 182 182 183 185 186 191 Limitations of Isodesmic Reactions Hydration Reactions. Bond Dissociation HCO Potential Energy Surface ‘Atomic Charge Analysis. Group Charges “ ‘Atoms in Molecules Charges and Bond Orders. Sit + Silane Potential Energy Surface 198 Isodesmic Reactions... Heats of Formation via Isodesmic Reactions An Sy? Reaction ern Ethylene Excited States Formaldehyde Excited State Optimizatior Methylenecyclopropene Excited States.. Formaldehyde Excited State Optimization. Acrolein Excited State Optimization Benzene Excitation Energies .new Using the CASSCF Method to Study Excited State System: Using CASSCF to Study Butadiene Photochemistry... Dichloroethane Conformer Energy Difference by Solvent. 24 216 218 220 23 224 28 232 Formaldehyde Frequencies in Acetonitril Dichloroethane Conformer Energy Differences. Formaldehyde Frequencies. Carbonyl Stretch in Solution.. Rotational Barrier in Solution for N-Methyl-2-Nitrovinylamine.. ‘Comparing SCRF Methods on Furfuraldehyd Comparing Integration Grids. Z-Matrices for 1,2-Dichloro-1,2-Difluoroethane Isomers.. ‘Mixed Cartesian and Internal Coordinates nnn 21 m2 293 Exploring Chemistry with Electronic Structure Methods iidList of Examples and Exercises Table of Input Files ‘The following table lists the input files corresponding to the various examples and exercises in this work. These files are located in the subdirectories quick, exomples and ‘exercise of the explore subdirectory of the Gaussian directory tree. Files have the extension .com on UNIX and VMS systems, and .GJF on Windows systems. The final column of the table lists the CPU time required for running the job on our reference computer system, a DEC AlphaServer 2100°?%; all jobs were run using a single processor. For multi-step jobs, the timing figure indicates the total CPU time for all job steps. Filenames and CPU times for long jobs (> 30 minutes) are in boldface type, and filenames and CPU times for very long jobs (> 2 hours) are in boldface red type. ‘Corresponding ‘CPU Time Input File _Example/Exercise Description of Job (hrsminssecs:) Quick Stort Gs Exercise QS1 Water single point energy 10:00:08.2 waterpdb Exercise QS2__ Convertinga PDB file 0:00:08.2 Chapter 2 e2_01 Example 2.1 Formaldehyde energy 0:00:09.1 2.02 Example 2.2__ Methane NMR properties Zor Exercise 21 Propene energy 2.020 Exercise 22 Dichl ethane (RR form) “202 _Exercise22__Dichloro-difluoro-ethane (SS form) 001:068 70% Exercise 22 __Dichloro-difluoro-ethane (meso form) 2.03 Exercise 23 Acetone energy 2.04 Exercise 2.4 Ethylene energy ; 2.050 Exercise 25 Butane NMR proper 0:03:01.8 Exercise 25 Trans 2-butene NMR properties ___—=—=—«0-02:45.2_ Exercise 25 __2-Butyne NMR properties Co energy ‘Conventional vs.direct CPU usage study Exercise 2.8 Stability of oxygen Exercise 28 ‘of ozone Example 3.1 Ethylene geometry optimization Example 3.2 Fluoroethylene optimization ~_ 0:01:56.4 Example3.3__ HiyCO—H,COH TS opt. (QST2) 0:02:07. Exercise 3.1 Propene optimization (180°) Exercise 3.1 Propene optimization (0°) xiv Exploring Chemistry with Electronic Structure MethodsChapter 3 Chapter 4 Table of Input Files ‘Corresponding CPU Time Input File _Example/Exercise Description of Job (hrssminssecs) 3.02a Exercise 3.2 Vinyl alcohol optimization (0°) 3.02% Exercise 3.2 wv alcohol optimization (1 “3.02e Exercise 3.2 Acetaldehyde optimization 3.03 Exercise 3.3 Planar vinyl amine optimization “304 Exercise 3.4 Chromium hexacarbonyl optimization 3.050 Exercise 3.5 Benzene optimization & NMR props. 1:00:06.4 3.05b Exercise 3.5 TMS optimization & NMP properties 1:45:01.8 3.060 Exercise 3.6 Cg0 optimizations (PM3) 320 3.065 Exercise 3.6 Cgg0 optimizations (HF) ‘i 3.07 “Exercise 3.7 SiH + Hy > Sift, TS optimization 2 3.08 Exercise 38 Bicyclo[2.2.2Joctane optimizations with different coordinate systems e401 Formaldehyde frequencies ed 020 2 Trans I-fluoropropene (0°) freqs. (026 Example 4.2 Trans 1-fluoropropene (180°) freqs. e4_02c Example 4.2 __ Cis 1-fluoropropene (0°) freqs. e4 02d Example 4.2 __Cis-TransTS for 1-fluoropropene ‘401e Exercise 4.1 Vinyl alcohol (180) frequencies ‘4016 Exercise 4.1 Vinyl alcohol (0°) frequencies 4020 Exercise 4.2 Vinyl amine (planar) frequencies 0:02:44.7 4026 ‘Exercise 42 Vinyl amine TS opt. + frequencies 0:03:21.3 4030 Exercise 4.3 Ethylene frequencies 00-41. 4.036 Exercise 4.3 Fluoroethylene frequencies : 0:01:54.1 403 Exercise 4.3 Propene frequencies = 0:02:53.7 404a Exercise 4.4 Acetaldehydefrequencies —_ 4.04b_Exercise4.4 —_Acrolein frequencies ‘40d Exercise 4.4 Formamide frequencies _ a 404d Exercise 4.4 Acetone frequencies “A0de Exercise 4.4 Acetyl chloride frequencies 04 Exercise 4.4 Methyl acetate frequencies 4050 Exercise 4.5 Strained hydrocarbons frequencies 0:55:19.1 4056 Exercise 45 Larger strained hydrocarbons freqs. BOE. 4060 Exercise 46 __3-Fluoropropene optimization 0:14:53.9 Exploring Chemistry with Electronic Structure Methods = x¥List of Examples and Exercises Corresponding CPUTime | 7 Input File _Example/Exercise_ Description of Job (besiminssecs) | { Chapter 4 “4066 Exercise 46 ___ CHyF-CH=CH @ CHF=CH-CH, TS 0:20:25.7_! Chapter 5 e5_01 Example5.1 Methanol vs. methoxide anion 0:01:12.2 : e502 “Example 5.2 Optimization of PO 501 Exercise 5.1 is set effects on H-F bond length 5.02 Exercise 5.2 )g optimizations (LANL2DZ) Exercise 5.3 Benzene NMR properties by basis set ~_ Brercise 5.3 es by basis Exercise 5 iyi-formamide opt. + freq. Exercise 5.5 Basis set structure (via methanol) Exercis 6-31G"* vs, 631GHT basis sets Chapter 6 ‘Exampl TPP AMI molecular orbitals ~0:1:40.3 x Example 6.2 HF Dimer semi-empirical study 0:05:12.8 Example 6.3 HF bond energy ~0:05:07.5 Example 6.4 Ozone optimizations 3:30:31.6 Example 6.5 CO, atomization energy: HF Example 6.5 CO atomization energy: SVWN_ Example 6.5 CO atomization energy: SVWNS Example6.3 CO, atomization energy: BLYP Example6.5 CO, atomization energy: B3LYE Example 6.5 CO, atomization energy: a1 0:09:35.6 Example65 CO, atomization energy: MP2 10:05:25.7 Example 6.6 F3~ frequencies 3 Exercise 6.1 __ Isobutane and n-butane AMI opts. Exercise 6.1 Isobutane and n-butane PM3 opts. Exercise 6.1 Isobutane and n-butane HF opts. Exercise 6.2 __N-butane (anticlinal) AMI opt. Exercise 6.2 N-butane (anticlinal) HF opt. ~ Exercise 6.3 Malonaldehyde optimizations Exercise 63 Malonaldehyde optimization (B3LYP) Exercise 6.4 FOOF optimizations — Exercise 65 Acetaldehyde QCISD(T) energy 0:11:22.6 Exercise 65 __ Ethylene oxide QCISD(T) energy :13:04.9 Exercise 66 __Cyano radical spin polarization 135347 xxvi_—_Exploring Chemistry with Electronic Structure Methods