Young D.C. - Computational chemistry (2001)(en)
.pdfGLOSSARY 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
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multireference con®guration interaction |
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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
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/