- •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
Literature, Software, Books and Websites 455
and 3 should largely cancel out energy differences due to ring strain. The two magnetic properties calculated [33] arise from the presence of a diatropic ring current [27], which tends to push an aromatic molecule out of a magnetic field (calculated property: magnetic susceptibility, and which exerts NMR shielding on a proton at or above the ring center (calculated property: nucleus-independent chemical shift, NICS). NICS values are obtained from the calculated NMR shielding (section 5.5.5) of a “ghost nucleus” [34] with no charge, electrons or basis functions, placed at or above [35] the ring center. Calculation of the changes in and in NICS along the reaction coordinate for the known reaction, the isomerization of diademane to triquinacene (Fig. 8.9), showed that the transition state, but neither the reactant nor the product, was aromatic. Homoaromaticity in a few neutral, ground-state molecules has been claimed [36].
The absence of homoaromaticity in triquinacene is probably due to the three pairs of nonbonded carbons being too far apart, 2.533 Å, from X-ray diffraction; in the transition state (Fig. 8.9), in contrast, the nonbonded CC distance has been reduced to 1.867 Å according to a calculation (section 7.2.3.4c).
Significantly, the measured C–C length, 1.319 Å, is close to the normal C–C length (calculated and measured parameters of triquinacene are cited in [33]).
8.2 TO THE LITERATURE
A feast of information on computational chemistry is available, a small selection of which is given below.
8.2.1Books
Listed in chronological order; readers should use their judgement to decide in which order to read them.
Essentials of Computational Chemistry. Theories and Models, C. J. Cramer, Wiley, New York, 2002.
Covers a wide range of topics. The level is sometimes quite advanced. Critical discussions of the literature.
Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems, D. Young, Wiley, New York, 2001.
456 |
Computational Chemistry |
||
A |
“meta-book” |
in that |
it lists several books on computational chemistry; it |
also lists many |
websites |
concerned with computational chemistry, and many |
computational chemistry programs. The material of this book is available at http://server.ccl.net/cca/documents/dyoung/
A Chemist’s Guide to Density Functional Theory, W. Koch and M. C. Holthausen, Wiley-VCH, New York, 2000.
Detailed introduction to the theory and applications of DFT.
Quantum Chemistry, 5th edn, I. N. Levine, Prentice Hall, Upper Saddle River, NJ, 2000.
Chapters 15, 16, and 17 give many references to the original literature, to books, to programs, and to websites. Enormously useful book on quantum chemistry in general.
Series of books from Wavefunction, Inc, makers of the Spartan computational chemistry program 2000 and earlier. For available books contact Wavefunction, http://www.wavefun.com/
These books, oriented toward Wavefunction’s Spartan program, are very useful introductions to the practice of computational chemistry.
Introduction to Computational Chemistry, F. Jensen, Wiley, New York, 1999. Good general introduction. Goes fairly deeply into theory.
Computational Thermochemistry, K. K. Irikura and D. J. Frurip, Eds., American Chemical Society, Washington, DC, 1998.
Useful source of information on the calculation of energy quantities: heats of formation, reaction energies, bond energies, activation energies, high-accuracy methods (G2, CBS, etc.), energies of solvation.
The Encyclopedia of Computational Chemistry, 5 volumes, P. von R. Schleyer, Ed., Wiley, New York, 1998.
A convenient source of information, but pricey (ca. $3000).
Molecular Mechanics Across Chemistry, A. K. Rappé and C. J. Casewit, University Science Books, Sausalito, CA, 1997.
Detailed presentation of the applications of MM, particularly in biochemistry and drug design.
Exploring Chemistry with Electronic Structure Methods, 2nd edn, J. Foresman and Æ. Frisch, Gaussian, Inc., Pittsburgh, PA, 1996.
Very useful hands-on guide; oriented toward Gaussian 94, but very useful for Gaussian 98 too.
Molecular Modelling. Principles and Applications, A. R. Leach, Longman, Essex, England 1996.
Good general introduction. Goes reasonably deeply into theory.
Modern Quantum Chemistry. Introduction to Advanced Electronic Structure Theory,
A. Szabo and N. S. Ostlund, 1st edn, revised, McGraw-Hill, New York, 1989.
A detailed, very advanced introduction to basic Hartree–Fock, CI, and MP theory.