- •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 457
Ab Initio Molecular Orbital Theory, W. J. Hehre, L. Radom, P. von R. Schleyer, and J. A. Pople, Wiley, New York, 1986.
Still a good introduction to ab initio calculations, although one should realize that there have been considerable advances since 1986. Basic theory, advice, and extensive collections of calculated and experimental geometries, energies, and frequencies.
A Handbook of Computational Chemistry, T. Clark, Wiley, New York, 1985. Still useful, although dated. A revised edition will be welcome.
Book series:
Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., WileyVCH, New York; volume 1 appeared in 1990, volume 17 is currently (July 2001) in preparation.
A volume in this series typically has from four to eleven chapters, each a kind of tutorial on the theory and application of some computational method. For tables of contents and other information see http://chem.iupui.edu/~boyd/rcc.html.
8.2.2 The Worldwide Web
Information on even specialized scientific topics can often be obtained from ordinary search engines. For example, a popular search engine gave information (ten hits for each) on these five topics, using the keywords shown: Hartree Fock, potential energy surface, molecular mechanics, Huckel, Extended Huckel. In several cases the hypertext leads one to tutorials, and to free programs.
Many websites are given in the books by Young and by Levine, above; some useful ones are:
http://ccl.osc.edu/ccl/cca.html
CCL, the computational chemistry list. A truly extraordinarily helpful forum for exchanging ideas, asking questions and getting help. If you join the network you can expect typically 5–10 messages a day.
http://www.chem.swin.esu.au/chem_ref.html
Gives links to sites for general chemistry, chemistry education, computational chemistry, etc.
qcldb.ims.ac.jp/index.html
A database of the literature of ab initio and DFT calculations.
www.ccdc.cam.ac.uk/
The Cambridge Crystallographic data Centre; contains the Cambridge Structural Database, which has X-ray or neutron diffraction structures of more than 230 000 compounds.
8.3 SOFTWARE AND HARDWARE
Many programs are described in the books by Young and by Levine, above; I mention here only a few that may be of particular interest to people getting into computational chemistry.
458 Computational Chemistry
8.3.1 Software
SPARTAN
Wavefunction, http://www.wavefun.com/
This is a suite of programs with MM (SYBYL and MMFF), ab initio, semiempirical (MNDO, AM1, PM3), and DFT, with its own superb graphical user interface (GUI) for building molecules for calculations, and for viewing the resulting geometries, vibrational frequencies, orbitals, electrostatic potential distributions, etc. SPARTAN is a complete package in the sense that one does not need to buy add-on programs like, say, a GUI. The program is very easy to use and its algorithms are robust – they usually accomplish their task, e.g. the sometimes tricky job of finding a transition state usually works with SPARTAN. Versions of the program are available for PCs running under Windows NT and LINUX, for Macs, and for UNIX workstations. It has some high-level correlated ab initio methods and is nevertheless extremely useful for research, not to mention teaching.
GAUSSIAN www.gaussian.com/
The most widely used computational chemistry program. Actually a suite of programs with MM (AMBER, DREIDING, UFF), ab initio, semiempirical (CNDO, INDO, MINDO/3, MNDO, AM1, PM3) and DFT, and all the usual high-level correlated ab initio methods. The common high-accuracy methods are available simply by keywords. There is a large number of basis sets and functionals. Electronically excited states can be calculated. GAUSSIAN has appeared in improved versions every few years from 1970 (…G92, G94, G98). It is now available in versions for PCs running under Windows NT and LINUX, and for UNIX workstations. GAUSSIAN does not have an integrated GUI, but there are several graphics programs for creating input files and for viewing the results of calculations. GaussView, expressly designed for GAUSSIAN 98, is highly recommended as the solution to all GAUSSIAN graphics problems.
GAMESS (General Atomic and Molecular Electronic Structure System) www.msg.ameslab.gov/GAMESS/GAMESS.html
Not as many options as GAUSSIAN but free. Versions are available for PCs, Macs, UNIX workstations and supercomputers.
HyperChem http://www.hyper.com
Has MM (MM+, AMBER, BIO+, OPLS), semiempirical (extended Hückel, CNDO, INDO, MINDO/3, MNDO, ZINDO/1, ZINDO/S, AM1, PM3), Hartree-Fock, and single-point MP2. Available for PCs with Windows 95, 98, NT and 2000, and UNIX workstations.
Q-Chem www.q-chem.com/
“The first commercially available quantum chemistry program capable of analyzing large structures in practical amounts of time.” For ab initio (including high-level
Literature, Software, Books and Websites 459
correlated methods) and DFT. Q-Chem is available for PCs running under LINUX, for UNIX workstations, and for supercomputers.
JAGUAR www.psgvb.com
Made by Schrödinger, Inc., JAGUAR is an ab initio (Hartree Fock and MP2) and DFT package that uses sophisticated algorithms to speed up ab initio calculations. It is said to be particularly good at handling transition metals, solvation, and conformational searching. The Jaguar algorithms combined with the SPARTAN GUI are available as TITAN from the makers of JAGUAR and SPARTAN.
ACES II www.qtp.ufl.edu/Aces2/
Particularly recommended for MP2 calculations and for CCSD(T) optimizations + frequencies, which latter are perhaps the most reliable calculations that can currently be done on molecules of reasonable size (up to about 10 heavy atoms). CCSD(T) optimizations and frequencies tend to be considerably slower with some other programs. Available for UNIX workstations and supercomputers.
MOLPRO www.tc.bham.ac.uk/molpro/
Intended for high-level correlated ab initio calculations (multiconfiguration SCF, multireference CI, and CC). “The emphasis is on highly accurate computations … accurate ab initio calculations can be performed for much larger molecules than with most other programs.” MOLPRO has been run on a variety of machines with UNIX-type operating systems.
8.3.2 Hardware
Someone beginning computational chemistry, who intends to use it extensively enough to warrant having one’s own machine (strongly recommended), might wish to get a high-end PC running under Windows NT or LINUX: such a machine is fairly cheap and it will do even sophisticated correlated ab initio calculations. A 1.5 MHz Pentium with 1GB of memory and 40GB or more of disk space is now not unusual (soon it may be substandard). While this is a reasonable choice for general computational chemistry, certain jobs will run faster on other configurations of machine and operating system. Using standard Gaussian 94 test jobs and various operating systems, and varying software and hardware parameters, Nicklaus et al. comprehensively compared a wide range of “commodity computers” [37]. These are personal computers like those of the Pentium series, and machines in a similar price range (the costliest was about U.S. $5000 and most were less than $3000, ca. 1998). They concluded that “commoditytype computers have … surpassed in power the more powerful workstations and even supercomputers ….Their price/performance ratios will make them extremely attractive for many chemists who do not have an unlimited budget, …”