Young - Computational chemistry

GLOSSARY 367

PES (potential energy surface) space of energies corresponding to locations of nuclei ignoring vibrational motion

PLS (partial least-squares) algorithm used for 3D QSAR calculations PM3 (parameterization method three) a semiempirical method

PMF (potential of mean force) a solvation method for molecular dynamics calculations

potential energy energy that a particle has due to its position, particularly because of Coulombic interactions with other particles

population analysis a method of partitioning the wave function in order to give an understanding of where the electrons are in the molecule

PPP (Pariser±Parr±Pople) a simple semiempirical method

PRDDO (partial retention of diatomic di¨erential overlap) a semiempirical method

PRISM (polymer reference interaction-site model) method for modeling homopolymer melts

PW91 (Perdew, Wang 1991) a gradient corrected DFT method

QCI (quadratic con®guration interaction) a correlated ab initio method QMC (quantum Monte Carlo) an explicitly correlated ab initio method QM/MM a technique in which orbital-based calculations and molecular

mechanics calculations are combined into one calculation

QSAR (quantitative structure±activity relationship) a technique for computing chemical properties, particularly as applied to biological activity

QSPR (quantitative structure±property relationship) a technique for computing chemical properties

quadratic con®guration interaction (QCI) a correlated ab initio method quantum mechanics a mathematical method for predicting the behavior of

fundamental particles, which is considered to be rigorously correct when applicable (where the e¨ects of relativity are negligible)

quantum Monte Carlo (QMC) an explicitly correlated ab initio method radial distribution function a function that gives the probability of ®nding a

particle at a given distance from another particle

RAM (random access memory) volatile computer memory

random ¯ight (or freely jointed chain) a polymer simulation technique RECP (relativistic e¨ective core potential) a potential function for represent-

ing the core electrons in an ab initio calculation

relativity mathematical theory for describing behavior of particles near the speed of light

restricted (spin-restricted) assumption that particles of di¨erent spins can be described by the exact same spatial function, rigorously correct for singlet systems

RIS (rotational isomeric state) a polymer simulation technique

368 GLOSSARY

RHF (restricted Hartree±Fock) ab initio method for singlet systems

ROHF (restricted open-shell Hartree±Fock) ab initio method for open-shell systems

RPA (random-phase approximation) ab initio method used for computing nonlinear optical properties

SAC (symmetry-adapted cluster) a variation on the coupled cluster ab initio method

SACM (statistical adiabatic channel model) method for computing reaction rates

SAM1 (semi-ab initio method one) a semiempirical method

SASA (solvent-accessible surface area) algorithm for computing solvation e¨ects

SCF (self-consistent ®eld) procedure for solving the Hartree±Fock equations SCI-PCM (self-consistent isosurface-polarized continuum method) an ab

initio solvation method

SCR (structurally conserved regions) sections of a biopolymer sequence that are identical to that of another sequence, for which there is a known threedimensional structure

SCRF (self-consistent reaction ®eld) method for including solvation e¨ects in ab initio calculations

SDS (synthesis design system) a program for predicting a synthesis route self-consistent ®eld (SCF) procedure for solving the Hartree±Fock equations semiempirical methods that are based on quantum mechanics, but also in-

clude values obtained through an empirical parameterization

simulated annealing algorithm consisting of a molecular dynamics simulation with a gradually decreasing temperature

SINDO (symmetrically orthogonalized intermediate neglect of di¨erential overlap) a semiempirical method

size-consistent a method is size-consistent if the energy obtained for two molecular fragments at large separation will be equal to the sum of the energies of those fragments computed separately

size-extensive a method is size-extensive if the energy is a linear function of the number of electrons

Slater type orbital (STO) mathematical function for describing the wave function of an electron in an atom, which is rigorously correct for atoms with one electron

SM1±SM5 solvation methods for use with semiempirical and ab initio calculations

SMILES (simpli®ed molecular-input line-entry speci®cation) a way of specifying a molecular formula and connectivity, but not the three-dimensional geometry

GLOSSARY 369

solvation e¨ects changes in the behavior of a solute due to the presence of the solvent

SOS (sum over states) an algorithm that averages the contributions of various states of the molecule

spin contamination an error sometimes occurring in unrestricted calculations spin-restricted (restricted) assumption that particles of di¨erent spins can be

described by the exact same spatial function, rigorously correct for singlet systems

spin-unrestricted (unrestricted) calculation in which particles of di¨erent spins are described by di¨erent spatial functions

statistical mechanics mathematical theory for computing thermodynamic properties from atomic-scale properties

STO (Slater type orbital) mathematical function for describing the wave function of an electron in an atom, which is rigorously correct for atoms with one electron

TDGI (time-dependent gauge-invariant) ab initio method used for computing nonlinear optical properties

TDHF (time-dependent Hartree±Fock) ab initio method used for computing nonlinear optical properties

thermodynamics mathematical system for describing energy and entropy in macroscopic chemical systems

theoretical chemistry mathematical means for predicting chemistry

time complexity a way of denoting how much additional computational resources, particularly CPU time, will be used as the size of the system being modeled is increased

TNDO (typed neglect of di¨erential overlap) a semiempirical method for computing NMR chemical shifts

trajectory a sequence of geometries produced by a molecular dynamics simulation

transition structure geometry of a molecular system corresponding to the energy maximum (saddle point) that must be traversed in going from reactants to products

Tripos a molecular mechanics force ®eld, also the name of a company that sells computational chemistry software

TST (transition state theory) method for computing rate constants UHF (unrestricted Hartree±Fock)

UFF (universal force ®eld) a molecular mechanics force ®eld

unrestricted (spin unrestricted) calculation in which particles of di¨erent spins are described by di¨erent spatial functions

VTST (variational transition state theory) method for predicting rate constants

370 GLOSSARY

VWN (Vosko, Wilks, and Nusair) a DFT method

wave function a function used to describe the electron distribution in a quantum mechanical scheme; the wave function is also called the probability amplitude because the square of the wave function gives the probability of ®nding an electron

Xa (X alpha) a DFT method

YETI a molecular mechanics force ®eld

zero point energy the energy di¨erence between the minimum on a potential energy surface and the ®rst vibrational energy level

ZINDO (Zerner's intermediate neglect of di¨erential overlap, synonymous with INDO/S) a semiempirical method

Z-matrix a way of writing a molecular geometry

BIBLIOGRAPHY

Other sources that have computatonal chemistry de®nitions are

M. F. Schlecht, Molecular Modeling on the PC Wiley-VCH, New York (1998).

P.W. Atkins, R. S. Friedman, Molecular Quantum Mechanics 315, Oxford, Oxford (1997).

P. W. Atkins, Quanta Oxford, Oxford (1991).

http://www.mathub.com/glossary/index.html

http://www.iupac.org/recommendations/1996/6802brown/