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- •COMPUTATIONAL CHEMISTRY
- •CONTENTS
- •PREFACE
- •1.1 WHAT YOU CAN DO WITH COMPUTATIONAL CHEMISTRY
- •1.2 THE TOOLS OF COMPUTATIONAL CHEMISTRY
- •1.3 PUTTING IT ALL TOGETHER
- •1.4 THE PHILOSOPHY OF COMPUTATIONAL CHEMISTRY
- •1.5 SUMMARY OF CHAPTER 1
- •REFERENCES
- •EASIER QUESTIONS
- •HARDER QUESTIONS
- •2.1 PERSPECTIVE
- •2.2 STATIONARY POINTS
- •2.3 THE BORN–OPPENHEIMER APPROXIMATION
- •2.4 GEOMETRY OPTIMIZATION
- •2.6 SYMMETRY
- •2.7 SUMMARY OF CHAPTER 2
- •REFERENCES
- •EASIER QUESTIONS
- •HARDER QUESTIONS
- •3.1 PERSPECTIVE
- •3.2 THE BASIC PRINCIPLES OF MM
- •3.2.1 Developing a forcefield
- •3.2.2 Parameterizing a forcefield
- •3.2.3 A calculation using our forcefield
- •3.3 EXAMPLES OF THE USE OF MM
- •3.3.2 Geometries and energies of polymers
- •3.3.3 Geometries and energies of transition states
- •3.3.4 MM in organic synthesis
- •3.3.5 Molecular dynamics and Monte Carlo simulations
- •3.4 GEOMETRIES CALCULATED BY MM
- •3.5 FREQUENCIES CALCULATED BY MM
- •3.6 STRENGTHS AND WEAKNESSES OF MM
- •3.6.1 Strengths
- •3.6.2 Weaknesses
- •3.7 SUMMARY OF CHAPTER 3
- •REFERENCES
- •EASIER QUESTIONS
- •HARDER QUESTIONS
- •4.1 PERSPECTIVE
- •4.2.1 The origins of quantum theory: blackbody radiation and the photoelectric effect
- •4.2.2 Radioactivity
- •4.2.3 Relativity
- •4.2.4 The nuclear atom
- •4.2.5 The Bohr atom
- •4.2.6 The wave mechanical atom and the Schrödinger equation
- •4.3.1 Introduction
- •4.3.2 Hybridization
- •4.3.3 Matrices and determinants
- •4.3.4 The simple Hückel method – theory
- •4.3.5 The simple Hückel method – applications
- •4.3.6 Strengths and weaknesses of the SHM
- •4.4.1 Theory
- •4.4.2 An illustration of the EHM: the protonated helium molecule
- •4.4.3 The extended Hückel method – applications
- •4.4.4 Strengths and weaknesses of the EHM
- •4.5 SUMMARY OF CHAPTER 4
- •REFERENCES
- •EASIER QUESTIONS
- •5.1 PERSPECTIVE
- •5.2.1 Preliminaries
- •5.2.2 The Hartree SCF method
- •5.2.3 The HF equations
- •5.2.3.1 Slater determinants
- •5.2.3.2 Calculating the atomic or molecular energy
- •5.2.3.3 The variation theorem (variation principle)
- •5.2.3.4 Minimizing the energy; the HF equations
- •5.2.3.5 The meaning of the HF equations
- •5.2.3.6a Deriving the Roothaan–Hall equations
- •5.3 BASIS SETS
- •5.3.1 Introduction
- •5.3.2 Gaussian functions; basis set preliminaries; direct SCF
- •5.3.3 Types of basis sets and their uses
- •5.4 POST-HF CALCULATIONS: ELECTRON CORRELATION
- •5.4.1 Electron correlation
- •5.4.3 The configuration interaction approach to electron correlation
- •5.5.1 Geometries
- •5.5.2 Energies
- •5.5.2.1 Energies: Preliminaries
- •5.5.2.2 Energies: calculating quantities relevant to thermodynamics and to kinetics
- •5.5.2.2a Thermodynamics; “direct” methods, isodesmic reactions
- •5.5.2.2b Thermodynamics; high-accuracy calculations
- •5.5.2.3 Thermodynamics; calculating heats of formation
- •5.5.2.3a Kinetics; calculating reaction rates
- •5.5.2.3b Energies: concluding remarks
- •5.5.3 Frequencies
- •Dipole moments
- •Charges and bond orders
- •Electrostatic potential
- •Atoms-in-molecules
- •5.5.5 Miscellaneous properties – UV and NMR spectra, ionization energies, and electron affinities
- •5.5.6 Visualization
- •5.6 STRENGTHS AND WEAKNESSES OF AB INITIO CALCULATIONS
- •5.7 SUMMARY OF CHAPTER 5
- •REFERENCES
- •EASIER QUESTIONS
- •HARDER QUESTIONS
- •6.1 PERSPECTIVE
- •6.2 THE BASIC PRINCIPLES OF SCF SE METHODS
- •6.2.1 Preliminaries
- •6.2.2 The Pariser-Parr-Pople (PPP) method
- •6.2.3 The complete neglect of differential overlap (CNDO) method
- •6.2.4 The intermediate neglect of differential overlap (INDO) method
- •6.2.5 The neglect of diatomic differential overlap (NDDO) method
- •6.2.5.2 Heats of formation from SE electronic energies
- •6.2.5.3 MNDO
- •6.2.5.7 Inclusion of d orbitals: MNDO/d and PM3t; explicit electron correlation: MNDOC
- •6.3 APPLICATIONS OF SE METHODS
- •6.3.1 Geometries
- •6.3.2 Energies
- •6.3.2.1 Energies: preliminaries
- •6.3.2.2 Energies: calculating quantities relevant to thermodynamics and kinetics
- •6.3.3 Frequencies
- •6.3.4 Properties arising from electron distribution: dipole moments, charges, bond orders
- •6.3.5 Miscellaneous properties – UV spectra, ionization energies, and electron affinities
- •6.3.6 Visualization
- •6.3.7 Some general remarks
- •6.4 STRENGTHS AND WEAKNESSES OF SE METHODS
- •6.5 SUMMARY OF CHAPTER 6
- •REFERENCES
- •EASIER QUESTIONS
- •HARDER QUESTIONS
- •7.1 PERSPECTIVE
- •7.2 THE BASIC PRINCIPLES OF DENSITY FUNCTIONAL THEORY
- •7.2.1 Preliminaries
- •7.2.2 Forerunners to current DFT methods
- •7.2.3.1 Functionals: The Hohenberg–Kohn theorems
- •7.2.3.2 The Kohn–Sham energy and the KS equations
- •7.2.3.3 Solving the KS equations
- •7.2.3.4a The local density approximation (LDA)
- •7.2.3.4b The local spin density approximation (LSDA)
- •7.2.3.4c Gradient-corrected functionals and hybrid functionals
- •7.3 APPLICATIONS OF DENSITY FUNCTIONAL THEORY
- •7.3.1 Geometries
- •7.3.2 Energies
- •7.3.2.1 Energies: preliminaries
- •7.3.2.2 Energies: calculating quantities relevant to thermodynamics and kinetics
- •7.3.2.2a Thermodynamics
- •7.3.2.2b Kinetics
- •7.3.3 Frequencies
- •7.3.6 Visualization
- •7.4 STRENGTHS AND WEAKNESSES OF DFT
- •7.5 SUMMARY OF CHAPTER 7
- •REFERENCES
- •EASIER QUESTIONS
- •HARDER QUESTIONS
- •8.1 FROM THE LITERATURE
- •8.1.1.1 Oxirene
- •8.1.1.2 Nitrogen pentafluoride
- •8.1.1.3 Pyramidane
- •8.1.1.4 Beyond dinitrogen
- •8.1.2 Mechanisms
- •8.1.2.1 The Diels–Alder reaction
- •8.1.2.2 Abstraction of H from amino acids by the OH radical
- •8.1.3 Concepts
- •8.1.3.1 Resonance vs. inductive effects
- •8.1.3.2 Homoaromaticity
- •8.2 TO THE LITERATURE
- •8.2.1 Books
- •8.2.2 The Worldwide Web
- •8.3 SOFTWARE AND HARDWARE
- •8.3.1 Software
- •8.3.2 Hardware
- •8.3.3 Postscript
- •REFERENCES
- •INDEX
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406 Computational Chemistry
the HNC isomerization: 0.035Å (1.383 Å cf. 1.348 Å) and 3.3° (70.8° cf. 67.5°). The consistency of the two DFT methods and their good agreement with MP2 (the “errors” for the HNC reaction transition state should not affect any qualitative conclusions one might draw) suggest that these DFT methods are quite comparable to MP2/6-31G* in calculating transition state geometries.
Hehre has compared bond lengths calculated by the DFT non-gradient-corrected SVWN method, B3LYP, and MP2, using the 6-31G (no polarization functions) and 6-31G* basis sets [59]. This work confirms the necessity of using polarization functions with the correlated (DFT and MP2) methods to obtain reasonable results, and also shows that for equilibrium structures (i.e. structures that are not transition states) there is little advantage to correlated over HF methods as far as geometry is concerned, a conclusion presented in section 5.5.1. Hehre and Lou [48] carried out extensive comparisons of HF, MP2, and DFT (SVWN, pBP, B3LYP) methods with 6-31G* and larger basis sets, and the numerical DN* and DN** bases. For a set of 16 hydrocarbons, MP2/6-311 + G(2d,p), B3LYP/6-311 + G(2d, p), pBP/DN**, and pBP/DN* calculations gave errors of 0.005, 0.006, 0.010, and 0.010Å, respectively. HF/6-311 + G(2d, p) and SVWN calculations also gave errors of 0.010Å. For 14 C–N, C–O and C–O bond lengths B3LYP and pBP (errors of 0.007 and 0.008 Å) were distinctly better than HF and SVWN (errors of 0.022 and 0.014 Å, respectively). The overall indication from the literature and the results in Figs 7.1 and 7.2 and Table 7.1 is that B3LYP/6-31G* calculations give excellent geometries and pBP/DN* calculations give good geometries. Larger basis sets may increase the accuracy, but the increase in time may not make this worthwhile. DFT calculations appear to be “saturated” more quickly by using bigger basis sets than are ab initio calculations: Merrill et al. noted that “Once the double split-valence level is reached, further improvement in basis set quality offers little in the way of structural or energetic improvement.” [34]; Stephens et al. report that “Our results also show that B3LYP calculations converge rapidly with increasing basis set size and that the cost-to-benefit ratio is optimal at the 6-31G* basis set level. 6-31G* will be the basis
set of choice in B3LYP calculations on much larger molecules [than |
[49]. |
The results in section 7.3.2.2b, regarding Fig. 7.3, support the view that the 6-31G* basis nearly saturates gradient-corrected functionals.
7.3.2Energies
7.3.2.1Energies: preliminaries
Usually, we seek from a DFT calculation, as from an ab initio or semiempirical one, geometries (preceding section) and energies. Like an ab initio energy, a DFT energy is relative to the energy of the nuclei and electrons infinitely separated and at rest, i.e. it is the negative of the energy needed to dissociate the molecule into its nuclei and electrons. AM1 and PM3 semiempirical energies (section 6.3.2) are heats of formation, and by parameterization include zero-point energies. In contrast, an ab initio (section 5.2.3.6d) or DFT molecular energy, the energy printed out at the end of any calculation, is the energy of the molecule sitting motionless at a stationary point (section 2.2) on the potential energy surface; it is the purely electronic energy plus the internuclear