
- •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

450 Computational Chemistry
minimum with a barrier of for its lowest-energy isomerization path, to the tricyclic carbene, which lies
above it. This presents us with the astonishing possibility that the exotic hydrocarbon may be isolable at room temperature. The threshold barrier for isolability at room temperature is about
for example, (E)-cycloheptene, with a barrier of
to isomerization, has a roomtemperature halflife of about 47 s [8], and the halflife rises steeply with the barrier. Other properties of pyramidane, including ionization energy and electron affinity (section 5.5.5), heat of formation (section 5.5.2.2c), and NMR spectra (section 5.5.5) were calculated [7b].
8.1.1.4 Beyond dinitrogen
There has in recent years been considerable interest in the possibility of making allotropes of nitrogen with more than two atoms per molecule. Curiously, almost all (the cation has been made [9, 10]) the work reported has been computational rather than experimental. These compounds are interesting because to any chemist with imagination the idea of a form of pure nitrogen that is not a gas at room temperature is fascinating, and because any such compound would be thermodynamically very unstable with respect to decomposition to dinitrogen.
Perhaps the first serious computational study of nitrogen oligomers was by Engelke, who studied the analogues of the benzene isomers in Fig. 8.4, first at the uncorrelated [11] then at the MP2 [12] level. The uncorrelated calculations suggested that 1–5 were “stable”, i.e. kinetically stable, although thermodynamically much higher in energy than dinitrogen. However, on the MP2/6-31G* potential energy surface 1 is a hilltop (section 2.2) and 5 is a transition state (section 2.2). This illustrates the not-so-rare fact that optimistic predictions at low levels of theory may not be sustained at higher levels. Noncorrelated ab initio, and in particular, semiempirical (chapter 6) calculations, tend to be too permissive in granting reality to exotic molecules.
8.1.2Mechanisms
We have seen, above, that computational chemistry can sometimes tell us with good reliability whether a molecule can exist. Another important application is to indicate how one molecule gets to be another: how chemical reactions occur. Indeed, the prime architect of one of the most useful computational tools, the AM1 method (chapter 6), questioned “whether the mechanism of any organic reaction was really known” [13] before the advent of computational chemistry! This skepticism was

Literature, Software, Books and Websites 451
engendered by the difficulties and ambiguities in studying very transient intermediates, and the impossibility (at the time) of observing transition states.
8.1.2.1 The Diels–Alder reaction
This is one of the most important reactions in all of organic synthesis, as it unites two moieties in a predictable stereochemical relationship, with the concomitant formation of two carbon–carbon bonds (Fig. 8.5) [14]. The reaction has been used in the synthesis of complex natural products, for example, in an efficient synthesis of the antihypertensive drug reserpine [15]. Such a reaction seems to be well worth studying.
The Diels–Alder reaction and related pericyclic reactions, which can be treated qualitatively by the Woodward–Hoffmann rules (section 4.3.5), have been reviewed in the context of computational chemistry [16]. The reaction is clearly nonionic, and the main controversy was whether it proceeds in a concerted fashion (as indicated in Fig. 8.5) or through a diradical, in which one bond has formed and two unpaired electrons have yet to form the other bond. A subtler question was whether the reaction, if concerted, was synchronous or asynchronous: whether both new bonds were formed to the same extent as the reaction proceeded, or whether the formation of one ran ahead of the formation of the other. Using the CASSCF method (section 5.4.3) Li and Houk [17] concluded that the butadiene–ethene reaction is concerted and synchronous, and chided Dewar and Jie [18] for stubbornly adhering to the diradical (biradical) mechanism. A DFT (chapter 7) study also supported the concerted mechanism [19].
8.1.2.2Abstraction of H from amino acids by the OH radical
This reaction seems more esoteric than the Diels–Alder, and although not “used” at all, may be very important. Proteins are combinations of amino acid residues, and