- •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
Density Functional Calculations 411
Mathieu developed an economical way of calculating heats of formation by performing BP/DN* calculations on molecular mechanics geometries; rms deviations from experiment were about for a variety of compounds [65]. Ventura et al. found DFT to be better than CCSD(T) (a high-level ab initio method) for studying the thermochemistry of compounds with the O–F bond [66].
7.3.2.2b Kinetics
Consider the reaction profiles in Fig. 7.2. In all four cases, the B3LYP/6-31G* and
pBP/DN* activation energies differ by no more than |
(224/200, 126/121, |
|
|
and give a reasonable indication of the height of the barrier. |
|
The worst case is that of the ethenol (vinyl alcohol, |
isomerization, where |
|
the calculated barrier differs from the reported experimental one by from |
||
(B3LYP) to |
(pBP) (but the experimental barrier could be significantly in |
|
error [61a]). |
|
|
Let us compare the activation energies for the reactions in Fig. 7.2 with highaccuracy (section 5.5.2.2d) energy difference values. We will compare the 0 K activation enthalpies, which is what these energy differences are (section 2.2), of the CBS-Q and G2 methods, two of the best high-accuracy methods, with the corresponding activa-
tion energies, in Fig. |
For unimolecular reactions Arrhenius activation |
||
energies |
exceed enthalpy differences |
by RT (Eq. (5.180)), but this is only |
|
|
even at room temperature, 298 K. |
|
CBS-Q, 237; G2, 237; B3LYP, 224; pBP, 200; exp, 282
HCN reaction
CBS-Q, 128; G2, 124; B3LYP, 126; pBP, 121; exp 129
CBS-Q, 164; G2, 161, B3LYP, 164; pBP, 159; exp, 161
Cyclopropylidene reaction
CBS-Q, 22; G2, 22, B3LYP, 25; pBP, 12.5; exp 13 –20
For the isomerization the B3LYP/6-31G* activation energy is a little lower than the CBS-Q and G2 values (which are somewhat lower than the reported experimental value, which as stated above could be significantly in error). For the HCN isomerization the B3LYP/6-31G*, CBS-Q, G2 and experimental values are essentially the same. For theisomerization the B3LYP/6-31G*, CBS-Q, G2 and experimental values are again essentially the same, and for the cyclopropylidene isomerization the B3LYP/6-31G*, CBS-Q and G2 values are again essentially the same and equal to the higher end of the reported experimental values. In all cases the pBP/DN* activation energies are a little less than the CBS-Q, G2 and B3LYP values.
412 Computational Chemistry
Figure 7.3 compares the results of BP86/6-31G*, BP86/6-311G*, and pBP/DN* calculations on the and reaction profiles. The BP86/6-31G* and BP86/6-311G* geometries are very similar and the relative energies are nearly identical, indicating that basis set saturation (section 7.3.1) has been essentially reached. The pBP/DN* geometries and energies resemble the BP86 ones quite closely, matching the BP86/6-311G* results a little more closely than the BP86/6-31G*. These results suggest that B3LYP/6-31 G* activation energies are similar to those from the more timedemanding (below) CBS-Q and G2 methods, and are close to the experimental values; pBP/DN* and BP86/6-31G* (and BP86/6-311G*) activation energies may be a little (perhaps lower than those from B3LYP/6-31G*. Here are the times required for some DFT, CBS-Q, and G2 calculations (optimization + frequencies), in each case starting from an AM1 geometry; the jobs were run with Gaussian 94 [54] on a 600 MHz Pentium III computer:
Ethenol (vinyl |
alcohol, |
BP86/6-31G* |
30.0 minutes, relative time 1 |
B3LYP/6-31G* |
30.0 minutes, relative time 1.0 |
CBS-Q |
53.4 minutes, relative time 1.8 |
G2 |
142.6 minutes, relative time 4.8 |
In a study of alkene epoxidation with peroxy acids, B3LYP/6-31G* gave an activation energy similar to that calculated with MP4/6-31G*//MP2/6-31G* but yielded kinetic isotope effects in much better agreement with experiment than did the ab initio calculation [69]. Even better activation energies than from B3LYP (which it is said tends to underestimate barriers [70,71]) have been reported for the BH&H-LYP functional [71–74]. In a study by Baker et al. [75] of 12 organic reactions using seven methods (semiempirical, ab initio, and DFT), B3PW91/6-31G* was best (average and maximum errors 15.5 and and B3LYP/6-31G* second best (average and maximum errors 25 and Jursic studied 28 reactions and recommended “B3LYP or B3PW91 with an appropriate basis set”, but warned that highly exothermic reactions with a small barrier involving hydrogen radicals “are particularly difficult to reproduce.” [76]. Barriers “above [ca. 40kJ should be reliable. Lower activation energies should be underestimated by [76]. As with thermodynamic energy differences (i.e. energy differences not involving a transition state), consistently obtaining activation energies accurate to with some confidence requires one of the high-accuracy methods.
Density functional transition states and activation energies have their problems. Merrill et al. found that for the fluoride ion-induced elimination of HF from
none of the 11 functionals tested (including B3LYP) was satisfactory, by comparison with high-level ab initio calculations. Transition states were often looser and stabler than predicted by ab initio, and in several cases a transition state could not even be found. They concluded that hybrid functionals offer the most promise, and that “the ability of density functional methods to predict the nature of TSs demands a great deal more attention than it has received to date.” [34]. Note that it is assumed here that