Young - Computational chemistry

A.6 SPECIAL-PURPOSE PROGRAMS 357

number of input keywords, which the user must be familiar with to use all the features, but almost every keyword has a default value that is recommended by the authors. So, if the user is willing to accept the default, it is not necessary to understand all the options. The program output is a well-formatted ASCII ®le.

The reaction-rate calculations available include TST, CVT, ICVT, and mVT. A number of options to account for anharmonicity are available. Semiclassical corrections for tunneling and nonclassical re¯ection can also be included, and in fact the small-curvature and large-curvature multidimensional tunneling corrections available in this program are one of its key features. Dual-level calculations allow for additional corrections to energetics or both energetics and frequencies using levels of theory too time-consuming to apply to the entire potential energy surface.

The documentation is very thorough, although it does assume some familiarity with transition-state theory. New users can expect to spend some time with the manual, which is nearly 500 pages long! A collection of example ®les is also included.

Price category: free

Client platforms: Unix, Linux

Contact information: Benjamin Lynch or Donald G. Truhlar Department of Chemistry

University of Minnesota

207 Pleasant Street SE

Minneapolis, MN 55455 http://comp.chem.umn.edu/polyrate/ [e-mail]

A.6.7 QCPE

QCPE (the Quantum Chemistry Program Exchange) is a repository for programs that have been contributed by many authors. Hundreds of programs are available with source code. There is no acceptance criteria for including a program, so programs range from those that are simplistic or di½cult to use to ones that are very well written and powerful pieces of software. The catalogue is on the Web page listed below and can be searched interactively by opening a telnet session to qcpe6.chem.indiana.edu (using the login ``anonymous'' and then typing ``./Catsrch''). For a small fee, updates listing new software submissions can be received.

Price category: student, individual

Platforms: varies from one program to the next

Contact information: QCPE

358 APPENDIX A SOFTWARE PACKAGES

Creative Arts Bldg. 181 Indiana University Bloomington, IN 47405 [phone]

http://server.ccl.net/cca/html pages/qcpe/index.shtml [e-mail]

A.6.8 SynTree

SynTree (we tested Version 3.0) is a program for ®nding organic synthesis routes. It uses a retrosynthetic algorithm and a database of known reactions. The database of reactions includes 450 reactions typically included in an undergraduate organic curriculum. The algorithm includes the ability to recognize when protective groups are needed. There are utility programs to add additional reactions.

The program is used by ®rst building the target molecule. It then generates a list of possible precursors. The user can choose which precursor to use and then obtain a list of precursors to it. The reaction name and conditions can also be displayed. Once a satisfactory synthesis route is found, it can be printed without all the other possible precursors included. The drawing mode worked well and the documentation was well written.

This program is marketed as an exploratory tool for undergraduate organic chemistry students. As an educational tool, it is well designed. The program, as is, might also serve as a reminder of possible options for synthetic chemists. It could also be useful to the research community if more reactions are included in future versions.

Price category: student, individual Platforms: PC, Macintosh

Contact information: Trinity Software, Inc. 607 Tenney Mountain Hwy.

Suite 215

Plymouth, NH 03264 [phone]

http://www.trinitysoftware.com/

[e-mail]

BIBLIOGRAPHY

Other listings of chemistry software packages are

D. B. Boyd, Rev. Comput. Chem. 11, 373 (1997).

BIBLIOGRAPHY 359

Computational Thermochemistry K. K. Irikura, D. J. Frurip, Eds., Appendix A., American Chemical Society, Washington (1998).

Encyclopedia of Computational Chemistry John Wiley & Sons, New York (1998). Some software packages are mentioned in sequence in this encyclopedia and others are collected at the end of volume 5.

http://server.ccl.net/

http://www.chamotlabs.com/cl/Freebies/Software.html

http://nhse.npac.syr.edu:8015/rib/repositories/csir/catalog/index.html J. P. Bays, J. Chem. Ed. 69, 209 (1992).

Reviews of individual packages are sometimes published in Journal of Computational Chemistry.

Software can be purchased directly from the company that makes it or through catalogues, such as the following. Some of these have paper catalogues as well as web stores.

http://genamics.com/software/

http://www.ChemStore.com/

http://www.chemsw.com/

http://www.falconsoftware.com/

http://www.biosoft.com/

http://www.trinitysoftware.com/

http://chemweb.com/

http://www.claessen.net/chemistry/soft en.html

http://www.sciquest.com/

Computational Chemistry: A Practical Guide for Applying Techniques to Real-World Problems. David C. Young Copyright ( 2001 John Wiley & Sons, Inc.

ISBNs: 0-471-33368-9 (Hardback); 0-471-22065-5 (Electronic)

Glossary

The following are de®nitions of terms relevant to computational chemistry. These de®nitions are based on common usage in this ®eld. They do not necessarily re¯ect the dictionary de®nitions or those in other branches of science.

mVT (microcanonical variational theory) a variational transition state theory technique

ab initio a calculation that may use mathematical approximations, but does not utilize any experimental chemical data either in the calculation or the original creation of the method

accuracy how close a computed value is to the experimental value

adiabatic process a chemical process in which the system does not make a transition from one electronic state to another

Ahhrenius equation mathematical equation for predicting reaction rate constants

AI (arti®cial intelligence) computer algorithms that mimic some aspects of how people think

AIM (atoms in molecules) a population analysis technique AM1 (Austin model 1) a semiempirical method

AMBER (assisted model building with energy re®nement) a molecular mechanics force ®eld

amu (atomic mass unit) atomic unit of mass

ANO (atomic natural orbital) a way of deriving basis functions antisymmetric function a function that only changes sign when the identities of

two electrons are switched

approximation a numerical estimation of a solution to a mathematical problem

APW (augmented plane wave) a band structure computation method atomic mass unit (amu) atomic unit of mass

atomic units a system of units convenient for formulating theoretical derivations with a minimum number of constants in the equations

B3LYP (Becke 3 term, Lee Yang, Parr) a hybrid DFT method basis set a set of functions used to describe a wave function B96 (Becke 1996) a gradient corrected DFT method

360

GLOSSARY 361

band structure the electronic structure of a crystalline solid beads individual units in a mesoscale simulation

BLYP (Becke, Lee, Yang, Parr) a gradient corrected DFT method Bohr atomic unit of length

Boltzmann distribution statistical distribution of how many systems will be in various energy states when the system is at a given temperature

Born±Oppenheimer approximation assumption that the motion of electrons is independent of the motion of nuclei

boson a fundamental particle with an integer spin

BSSE (basis set superposition error) an error introduced when using an incomplete basis set

CAOS (computer aided organic synthesis) a program for predicting a synthesis route

Cartesian coordinates system for locating points in space based on three coordinates, which are usually given the symbols x, y, z or i, j, k

CBS (complete basis set) an ab initio method

CC (coupled cluster) a correlated ab initio method

CFF (consistent force ®eld) a class of molecular mechanics force ®elds CFMM (continuous fast multipole method) a method for fast DFT calcula-

tions on large molecules

CHAIN a relaxation method for obtaining reaction paths from semiempirical calculations

charge density (electron density, number density) number of electrons per unit volume at a point in space

CHARMM (chemistry at Harvard macromolecular mechanics) a molecular mechanics force ®eld

CHEAT (carbohydrate hydroxyls represented by external atoms) a molecular mechanics force ®eld

CHelp an electrostatic charge calculation method CHelpG an electrostatic charge calculation method

CI (con®guration interaction) a correlated ab initio method

CNDO (complete neglect of di¨erential overlap) a semiempirical method computational chemistry computer-automated means for predicting chemistry con®guration interaction (CI) a correlated ab initio method

conventional integral evaluation algorithm that stores integrals in a ®le convergence criteria for completion of a self-consistent ®eld calculation convex hull a molecular surface that is determined by running a planar probe

over a molecule

COOP (crystal orbital overlap population) a plot analogous to population analysis for band-structure calculations

362 GLOSSARY

correlation name for the statement that there is a higher probability of ®nding electrons far apart than close to one another, which is re¯ected by some but not all ab initio calculations

COSMO (conductor-like screening model) a method for including solvation e¨ects in orbital-based calculations

Coulomb's law the statement that like charges repel and unlike charges attract along with the equations for predicting the magnitude of those interactions

coupled cluster (CC) a correlated ab initio method

CPHF (coupled perturbed Hartree±Fock) ab initio method used for computing nonlinear optical properties

CPU (central processing unit) the part of a computer that does mathematical and logical operations.

CVT (canonical variational theory) a variational transition state theory technique

Davidson±Fletcher±Powell (DFP) a geometry optimization algorithm

De Novo algorithms algorithms that apply arti®cial intelligence or rational techniques to solving chemical problems

density functional theory (DFT) a computational method based on the total electron density

determinant a mathematical procedure for converting a matrix into a function or number

DFP (Davidson±Fletcher±Powell) a geometry optimization algorithm

DFT (density functional theory) a computational method based on the total electron density

DHF (Dirac±Hartree±Fock) relativistic ab initio method

DHF (derivative Hartree±Fock) a means for calculating nonlinear optical properties

diabatic process (nonadiabatic) a process in which the lowest-energy path is followed, even if it is necessary to change from one electronic state to another

di¨use functions basis functions that describe the wave function far from the nucleus

DIIS (direct inversion of the iterative subspace) algorithm used to improve SCF convergence

DIM (diatomics-in-molecules) a semiempirical method used for representing potential energy surfaces

Dirac equation one-electron relativistic quantum mechanics formulation direct integral evaluation algorithm that recomputes integrals when needed distance geometry an optimization algorithm in which some distances are held

®xed

DM (direct minimization) an algorithm for forcing SCF calculations to converge

GLOSSARY 363

DPD (dissipative particle dynamics) a mesoscale algorithm DREIDING a molecular mechanics force ®eld

dummy atom an atom type, usually given the symbol X, used in specifying a molecular to specify a point in space at which no atom is located

ECEPP (empirical conformational energy program for peptides) a molecular mechanics force ®eld

ECP (e¨ective core potential) a potential function for representing the core electrons in an ab initio calculation

EF (eigenvector following) a geometry optimization algorithm EFF (empirical force ®eld) a molecular mechanics force ®eld eigenvector following (EF) a geometry optimization algorithm

electron density (charge density, number density) number of electrons per unit volume at a point in space

electronic structure the arrangement of electrons in a molecule electrostatics results that are implications of Coulomb's law

electrostatic potential …f† a function that gives the energy of interaction with an in®nitesimal charge at any position in space (if we assume polarizability is negligible)

empirical a procedure not based purely on mathematical theory ensemble a conceptual collection of identical chemical systems

ESP (electrostatic potential) normally used to denote charges derived from the electrostatic potential

Fenske±Hall a semiempirical method

Fermi contact density the electron density at the nucleus of an atom (if we assume that the nucleus is an in®nitesimal point with a given mass and charge)

fermion a fundamental particle with a half-integer spin Fletcher±Powell (FP) a geometry optimization algorithm

FMM (fast multipole method) a method for fast DFT calculations on large molecules

force ®eld a set of functions and associated constants that de®nes the energy expression for molecular mechanics calculations

FP (Fletcher±Powell) a geometry optimization algorithm

freely jointed chain (or random ¯ight) a polymer simulation technique

G1, G2, G3 (Gaussian theory) a method for extrapolating from ab initio results to an estimation of the exact energy

G96 (Gill 1996) a DFT method

Gaussian theory (G1, G2, G3) a method for extrapolating from ab initio results to an estimation of the exact energy

Gaussian-type orbital (GTO) mathematical function for describing the wave function of an electron in an atom

364 GLOSSARY

GAPT (generalized atomic polar tensor) a charge calculation method GB/SA (generalized Born/surface area) method for computing solvation

e¨ects

generalized valence bond (GVB) an ab initio method

genetic algorithm an optimization algorithm based on a collection (population) of solutions that combine, mutate, and die to produce subsequent populations by a survival-of-the-®ttest process

GIAO (gauge-independent atomic orbitals) technique for removing dependence on the coordinate system when computing NMR chemical shifts or optical activity

GROMOS (Gronigen molecular simulation) a molecular mechanics force ®eld, also the name of a computer program

group additivity an empirical method for computing chemical properties GTO (Gaussian type orbital) mathematical function for describing the wave

function of an electron in an atom

GVB (generalized valence bond) an ab initio method

half-electron approximation an algorithm for open-shell semiempirical calculations

Hamiltonian quantum mechanical operator for energy.

hard sphere assumption that atoms are like hard billiard balls, which is implemented by having an in®nite potential inside the sphere radius and zero potential outside the radius

Hartree atomic unit of energy

Hartree±Fock (HF) an ab initio method based on averaged electron±electron interactions

Hessian matrix the matrix of second derivatives of energy with respect to nuclear motion

HF (Hartree±Fock) an ab initio method based on averaged electron±electron interactions

HFS (Hartree±Fock±Slater) a DFT method

homology an algorithm that looks for similar molecules, particularly sequences of peptides or nucleotides

HuÈckel one of the simplest semiempirical methods

ICVT (improved canonical variational theory) a variational transition state theory technique

IGAIM (individual gauges for atoms in molecules) technique for removing dependence on the coordinate system when computing NMR chemical shifts IGLO (individual gauge for localized orbitals) technique for removing depen-

dence on the coordinate system when computing NMR chemical shifts in-core integral evaluation algorithm that stores integrals in memory

INDO (intermediate neglect of di¨erential overlap) a semiempirical method

GLOSSARY 365

initial guess an approximate wave function used as the starting point for an SCF calculation

intrinsic reaction coordinate (IRC, MEP, minimum-energy path) the lowestenergy route from reactants to products in a chemical process

IPCM (isosurface polarized continuum method) an ab initio solvation method IRC (intrinsic reaction coordinate, MEP, minimum-energy path) the lowest-

energy route from reactants to products in a chemical process kinetic energy energy that a particle has due to its motion

Klein±Gordon equation for describing relativistic behavior of spin zero particles

Kohn±Sham orbitals functions for describing the electron density in density functional theory calculations

Koopman's theorem a means for obtaining the ionization potential from a Hartree±Fock calculation

LCAO (linear combination of atomic orbitals) refers to construction of a wave function from atomic basis functions

LDA (local density approximation) approximation used in some of the more approximate DFT methods

level shifting algorithm used to improve SCF convergence

LMP2 (local second-order Mùller±Plesset) an ab initio perturbation theory technique

LORG (localized orbital-local origin) technique for removing dependence on the coordinate system when computing NMR chemical shifts

LSDA (local spin-density approximation) approximation used in more approximate DFT methods for open-shell systems

LSER (linear solvent energy relationships) method for computing solvation energy

MCSCF (multicon®gurational self-consistent ®eld) a correlated ab initio method

MEP (IRC, intrinsic reaction coordinate, minimum-energy path) the lowestenergy route from reactants to products in a chemical process

MIM (molecules-in-molecules) a semiempirical method used for representing potential energy surfaces

MINDO (modi®ed intermediate neglect of di¨erential overlap) a semiempirical method

minimum-energy path (IRC, MEP, intrinsic reaction coordinate) the lowestenergy route from reactants to products in a chemical process

MK (Mertz±Singh±Kollman) an electrostatic charge calculation method MMFF (Merck molecular force ®eld) a molecular mechanics force ®eld MMn (MM1, MM2, MM3, MM4, MMX, MM‡) names of a family of

similar molecular mechanics force ®elds

366 GLOSSARY

MNDO (modi®ed neglect of diatomic overlap) a semiempirical method model a simple way of describing something that is actually more complex

than the model

molecular dynamics a time-dependent calculation in which a molecular mechanics force ®eld is combined with classical equations of motion

molecular mechanics an empirical method for predicting molecular shape and interactions

Mùller±Plesset (MPn) correlated ab initio method based on perturbation theory

MOMEC a molecular mechanics force ®eld with a semiempirical term for describing transition metals

Monte Carlo a simulation technique that incorporates a random movement of atoms or molecules

Morse potential a function used to describe the energy change due to bond stretching

MPn (Mùller±Plesset nth-order) correlated ab initio method based on perturbation theory

MRCI (multireference con®guration interaction) a correlated ab initio method

multicon®gurational self-consistent ®eld	(MCSCF)	a	correlated	ab	initio
method
multireference con®guration interaction	(MRCI)	a	correlated	ab	initio
method

NBO (natural bond order) the name of a set of population analysis techniques NDO (neglect of di¨erential overlap) the fundamental assumption behind

many semiempirical methods

neural networks computer algorithms that simulate how the brain works by having many simple units, analogous to neurons in the brain

Newton±Raphson a geometry optimization algorithm

NMR (nuclear magnetic resonance) an analytical chemistry technique

NPA (natural population analysis) one of the NBO population analysis techniques

OPLS (optimized potentials for liquid simulation) a molecular mechanics force ®eld

OPW (orthogonalized plane wave) a band-structure computation method P89 (Perdew 1986) a gradient corrected DFT method

parallel computer a computer with more than one CPU Pariser±Parr±Pople (PPP) a simple semiempirical method

PCM (polarized continuum method) method for including solvation e¨ects in ab initio calculations

perturbation theory an approximation method based on corrections to a solution for a portion of a mathematical problem