
- •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

312 Computational Chemistry
thus called a zero-flux surface (the gradient vector field is analogous to an electric field whose “flux lines” point along the direction of attraction of a positive charge toward a central negative charge). The space within a molecule bounded by one (for a diatomic molecule) or more zero-flux surfaces is an atomic basin (away from the nuclei the basin extends outward to infinity, becoming shallower as the electron density fades toward zero). The nucleus and the electron density in an atomic basin constitute an atom in a molecule. Even for molecules other than homonuclear diatomics, atoms are still defined by atomic basins partitioned off by unique zero-flux surfaces, as illustrated in Fig. 5.43.
In the AIM (atoms-in-molecules method), the charge on an atom is calculated by integrating the electron density function over the volume of its atomic basin; the charge is the algebraic sum of the electronic charge and the nuclear charge (the atomic number of the nucleus minus the number of electrons in the basin). An AIM bond order can be defined in terms of the electron density [172], and the bond order
for two particular atoms A and B is then defined by an empirical equation obtained by fitting
to a few accepted A–B bond orders. For example, for nitrogen/nitrogen bonds a linear equation correlates
and
for, say,
HN=NH and N=N; from this equation bond orders can be assigned to other nitrogen/nitrogen bonds from their
values.
5.5.5Miscellaneous properties – UV and NMR spectra, ionization energies, and electron affinities
A few other properties that can be calculated by ab initio methods are briefly treated here.

Ab initio calculations 313
UV spectra
Ultraviolet spectra result from the promotion of an electron in an occupied MO of a ground electronic state molecule into a virtual MO, thus forming an electronically excited state [152] (excited state-to-excited state spectra are not normally studied by experimentalists). Calculation of UV spectra with reasonable accuracy requires some method of dealing with excited states. Simply equating energy differences between HOMO and LUMO with does not give satisfactory results for the absorption frequency/wavelength, because the energy of a virtual orbital, unlike that of an occupied one, is not a good measure of its energy (of the energy needed to remove an electron from it; this is dealt with in connection with ionization potentials and electron affinities) and because this method ignores the energy difference between a singlet and a triplet state.
Electronic spectra of moderate accuracy can be calculated by the configuration interaction CIS method (section 5.4.3) [173]. Compare, for example, the UV spectra of methylenecyclopropene calculated by the CIS/6-31+G* method (diffuse functions appear to be desirable in treating excited states, as the electron cloud is relatively extended) with the experimental spectrum [173], in Table 5.20. The agreement in wavelength is not particularly good for the longest-wavelength band, although this result can be made more palatable by noting that both calculation and experiment agree reasonably well on relative intensities (the two bands that were not observed are calculated to be relatively weak and to lie very near the strongest band). The CIS approach to excited states has been said [173] to be analogous to the HF approach to ground states in that both give at least qualitatively useful results.
NMR spectra
NMR spectra result from the transition of an atomic nucleus in a magnetic field from a low-energy to a high-energy state [152]. Quantum-mechanical calculations of NMR spectra focus on predicting the chemical shift (magnetic field strength needed for the transition relative to that needed for some reference) of a nucleus. This requires calculation of the magnetic shielding of the nuclei of the molecule of interest, and of the reference nuclei, usually those of tetramethylsilane, TMS. The chemical shift of the

314 Computational Chemistry
or
nucleus is then its (absolute) shielding value minus that of the TMS
or
nucleus. The theory of magnetic shielding of nuclei involves a treatment of how the energy of a nucleus varies with a magnetic field and with nuclear magnetic moments [174]. NMR spectra can be calculated with remarkable accuracy even at the HF level [175] (although there is some evidence that improved results are obtained using the
Ab initio calculations 315
MP2 method [175b,176]), as is clearly shown by the results in Fig. 5.44. The remarkable shielding effect of a benzene ring in [7]paracyclophane [177] is nicely reproduced. The calculation of NMR spectra has become an important tool in probing the electronic structure of theoretically interesting molecules [178],
Ionization energies and electron affinities
Ionization energies (also called ionization potentials) and electron affinities are related in that both involve transfer of an electron between a molecular orbital and infinity: in one case (IE) we have removal of an electron from an occupied orbital and in the other (EA) addition of an electron to a virtual (or a half-occupied) orbital. The IE for an orbital is defined as the energy needed to remove an electron from the orbital (to infinite separation), while the EA of an orbital is the energy released when the orbital accepts an electron from infinity [179]. The term IE when applied to a molecule normally means the minimum energy needed to remove an electron to infinity, i.e. to form the radical (for an originally closed-shell molecule) cation, and the term electron affinity normally means the maximum energy released when the molecule accepts an electron to form the radical anion (for an originally closed-shell molecule). The IE of a “stable” species, i.e. any molecule or atom that can exist (a relative minimum on the potential energy surface), is always positive. The EA of a molecule is positive if the accepted electron is bound, i.e. if it is not spontaneously ejected; if the new electron is ejected in microseconds or less (is unbound), the molecule has a negative EA (is a “resonance state” – this has nothing to do with the term resonance as in resonance hybrid).
IEs and EAs may be vertical or adiabatic: the energy difference between the precursor molecule and the species
formed by removing or adding an electron gives the vertical value if
is at the same geometry as
while the adiabatic value is obtained if
has its own actual, equilibrium geometry. Since the equilibrium geometry of
is clearly of lower energy than the unrelaxed geometry corresponding to
vertical IEs are larger than adiabatic IEs, and vertical EAs are smaller than adiabatic EAs. Experimental IEs and EAs may be vertical or adiabatic. The adiabatic values appear to be of more interest to chemists, since it is these that represent the energy difference between two “stable” molecules (the neutral and the charged; at least in those cases where the charged species does not instantly decompose), but compilations of IEs and EAs often do not state explicitly whether their listed values are adiabatic or vertical; a welcome exception is the book by Levin and Lias [ 180]. A good brief discussion of IEs and EAs, including various measurement techniques, is to be found in the compilation by Lias et al. [130b]. Many IEs and EAs are available on the worldwide web [130a].
lonization energies and electron affinities can be calculated simply as the energy difference between the neutral and the ion. Approximate IEs can be obtained by applying Koopmans’ (not Koopman’s) theorem [181], which says that the energy required to remove an electron from an orbital is the negative of the orbital energy. Thus the IE of a molecule is approximately the negative of the energy of its HOMO (the principle does not work as well for ionization ofelectrons more tightly bound than those in the HOMO). This makes it simple to obtain approximate IEs for comparison with photoelectron spectroscopy [182] results. Unfortunately, the principle does not work well for EAs: the EA of a molecule is not reasonably well approximated as the negative of the LUMO energy. In fact, ab initio calculations normally give virtual MOs (vacant MOs) positive