Listed Alphabetically
AIM – (Atoms In Molecule) An analysis method based upon the shape of the total electron density; used to define bonds, atoms, etc. Atomic charges computed using this theory are probably the most justifiable theoretically, but are often quite different from those from older analyses, such as Mulliken populations.
AO – (Atomic Orbital) An orbital described by wavefunction for a single electron centered on a single atom.
AOM – (Angular Overlap Model)
AM1 – (Austin Model 1) Dewar's NDDO semiempirical parameterization.
ASE – (Aromatic Stabilization Energy)
BAC-MP4 – (Bond Additive Corrections to energies from Møller-Plesset 4th order perturbation theory) empirical corrections to calculated energy based (exponentially) on bond lengths.
Bader's analysis – see AIM
Basis Set – finite set of functions used to approximately express the Molecular Orbital wavefunction(s) of system, normally atom centered, consisting of AOs differing in local angular momentum for each atom.
BCUT – (Burden CAS University of Texas) topological molecular similarity index of Burden.
BDE – (Bond Dissociation Energy)
BSSE – (Basis Set Superposition Error) error introduced when the energy of two molecules modeled together is lower than the sum of the energies when modeled separately, because more basis sets are available for each fragment (more degrees of freedom) during the calculation. Minimal basis sets can have less BSSE because only diffuse functions can span a to b. A particular problem for binding energies of weakly bonded molecular complexes, less with more complete basis sets.
BLYP – (Becke-Lee-Yang-Parr)
bohr - One atomic unit of distance, equal to 0.5292 Å.
CADPAC – (Cambridge Analytical Derivatives PACkage)
CAS – (Complete Active Space)
CASPT – (Complete Active Space Perturbation Theory)
CASSCF – (Complete Active Space Self-Consistent Field) popular variant of the MCSCF method, using a specific choice of configurations. One selects a set of active orbitals and active electrons, then forms all of the configurations possible by placing the active electrons in the active orbitals, consistent with the proper spin and space symmetry requirements. Essentially equivalent to the FORS method.
CBS-QCI – (Complete Basis Set Quadratic Configuration Interaction) alternative extrapolation algorithm to complete basis set.
CC – (Coupled Cluster) A perturbation theory of electron correlation with an excited configuration that is "coupled" to the reference configuration. Complete to infinite order, but only for a subset of possible excitations (doubles, for CCD). Newer than CI.
CCD – (Coupled Cluster, Doubles only.) Complete to infinite order for doubles excitations.
CCSD – (Coupled Cluster, Singles and Doubles only.) Complete to ° order for singles & doubles excitations.
CCSD(T) – (Coupled Cluster, Singles and Doubles with Triples treated approximately.) Size consistent. ΔHdiss ± 1.0 kcal/mol
CCSDT – (Coupled Cluster, Singles, Doubles and Triples)
CCSS – (Correlated Capped Small Systems) Special case of IMOMO. See Truhlar's and Hass's work.
CEPA – (Coupled Electron Pair Approximation)
CFF – (Consistent Force Field) Class II force field based on ab initio data developed by Biosym Consortium/MSI.
CFMM – (Continuous Fast Multipole Method) linear scaling method for matrix formation for DFT.
CFSE – (Crystal Field Stabilization Energy)
CHA – (Chemical Hamiltonian Approach) excludes BSSE effects from wavefunction w/ BSSE free Hamiltonian.
CHF – (Coupled Hartree-Fock method)
CHELP – (CHarges from Electrostatic Potential) an attempt to obtain atomic charges by fitting the electrostatic potential to a set of atomic point charges. The key component to the CHELP method is that it is non-iterative, rather using a Lagrangian multiplier method.
chemical shift tensor – representation of the chemical shift. 3x3 matrix field felt in a direction induced by current due to applied field in b direction.
CI – (Configuration Interaction) The simplest variational approach to incorporate dynamic electron correlation. Combination of the Hartree-Fock configuration (Slater determinant) and a large set of other configurations is used as a many e- basis set. The expansion coefficients are determined (in principal) by diagonalizing the Hamiltonian matrix and variationally minimizing the total energy of the CI wavefunction. Not size consistent.
CID – (Configuration Interaction, Doubles substitution only) post-Hartree-Fock method that involves configuration interaction where the included configurations are the Hartree-Fock configuration and all configurations derived from doubles substitution.
CIDEP – (Chemically Induced Dynamic Electron Polarization)
CIDNP – (Chemically Induced Dynamic Nuclear Polarization)
CIS – (Configuration Interaction with Singles excitations) simplest method for calculating electronically excited states; limited to singly-excited states. Contains no e- correlation and has no effect on the ground state (Hartree-Fock) energy.
CISD – (Configuration Interaction, Singles and Doubles substitution only) post-Hartree-Fock method that involves configuration interaction where the included configurations are the Hartree-Fock configuration and all configuration derived from singles and doubles substitution. Comparable to MP2.
CKFF – (Cotton-Kraihanzel Force Field)
CNDO – (Complete Neglect of Differential Overlap) The simplest of the semi-empirical methods. The principle feature is the total neglect of overlap between different orbitals. In other words, the overlap matrix S is the unit matrix. The only two-electron integrals kept are those where electron 1 is in just one orbital and electron 2 is in just one orbital. Like all semiempirical methods the integrals are evaluated empirically.
Combinatorial Chemistry – testing a large number of related compounds (as a mixture?) to find a compound that is active.
CoMFA – (Comparative Molecular Field Analysis) technique used to establish 3-D similarity of molecular structure in relation to a target property.
COMPASS – (Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies) Molecular Mechanics force field derived from Class II force field, but optimized for condensed phase properties.
contraction – the particular choice of scheme for generating the linear combinations of Gaussian functions that constitute a contracted basis set. A "generally-contracted" basis set is one in which each primitive is used in many basis functions. A "segmented" basis set, in contrast, is one in which each primitive is used in only one (or maybe two) contracted function.
COOP – (Crystal Overlap pOPulation)
Correspondence Principle – classical mechanics becomes a special case of quantum mechanics at larger masses/scale.
COSMO – (Conductor-Like Screening Model) implicit solvation model of Andreas Klamt. Considers macroscopic dielectric continuum around solvent accessible surface of solute. Less sensitive to outlying charges then PCM.
COSMO-RS – (COSMO for Realistic Solvents) describes solute and solvent on the same footing. Allows for realistic calculations of fluid thermodynamics: partition coefficients, solubilities, activity coefficients, vapor pressures, & phase diagrams.
Coulomb integral – 1-center, 2 electron integral in Hamiltonian. Represents localized contribution of e- pair (in A+B- or A-B+) to bonding.
CP – (Counter Poise) correction method for BSSE based on assumption of additivity of effects caused by BSSE on intermolecular interactions. The BSSE is approximated as the energy difference between (1) an isolated fragment and (2) t fragment accompanied by the basis functions, but not the atoms, of its companion fragment(s).
CPHF – (Coupled Perturbed Hartree-Fock )
CVFF – (Consistent Valence Force Field)
Density Matrix –
DFT – (Density Functional Theory) ab initio electronic method from solid state physics. Tries to find best approximate functional to calculate energy from e- density. Scales as 2nd power times a large number. Static correlation built in. Not variational. Believed to be size consistent.
diffuse – refers to basis functions that are typically of low angular momentum (unlike polarization functions) but with much smaller exponents, so that they spread more thinly over space. Usually essential for calculations involving negative ions or Rydberg states.
DIIS – (Direct Inversion in the Iterative Space) Pulay's extremely efficient, extrapolation procedure, to accelerate the convergence of the SCF in Hartree-Fock calculations.
DISCO –
DOS – (Density Of States)
dynamic correlation – All the correlation energy or correlation effect that is not considered "nondynamic" or "static." Essential for dispersion interactions.
DZ – (Double-Zeta) A basis set for which there are twice as many basis functions as are minimally necessary. "Zeta" (Greek letter z) is the usual name for the exponent that characterizes a Gaussian function.
DZP – (Double-Zeta with Polarization functions added) A polarization set generally has an angular momentum one unit higher than the highest valence function. So a polarization set on carbon is a set of d-functions.
ECP = pseudopotential – (Effective Core Potential) The core electrons have been replaced by an effective potential. Saves computational expense. May sacrifice some accuracy, but can include some relativistic effects for heavy elements.
EFFF – (Energy Factored Force Field)
EHT – (Extended Hückel Theory)
electron correlation – explicitly considering the effect of the interactions of specific e- pairs, rather than the effect each e- feels from the average of all the other e-. High correlation effects for e- rich systems, transition states, "unusual" coordination numbers, no unique Lewis structure, condensed multiple bonds, radicals, & biradicals.
Embedded Cluster – Sauer's (and Teunissen's and others) approach to modeling large/extended systems, using a high accuracy (QM) method for the important site, and a less accurate (MM) method for the environment. Subtract out duplicated overlap term, in case of extended system. See also IMOMM, and CCSS.
ESFF – (Extensible & Systematic Force Field) Rule based force field designed for generality rather than accuracy by Biosym/MSI.
ESP – (ElectroStatic Potential) The electrical potential due to the nuclei and electrons in the molecule, as experienced by a test charge.
exchange energy – Also called "exchange correlation energy." The energy associated with the correlation among the positions of electrons of like spin. This is included in Hartree-Fock calculations.
Exchange integral – integral in Hamiltonian centered on 2 atoms. Corresponds to covalent bond term.
FMO – (Frontier Molecular Orbital Theory) reaction controlled by interaction and overlap (energy, symmetry, accessibility) of frontier MO. Fukui calculation of weighted contributions, but dominated by HOMO for electrophilic, LUMO for nucleophilic susceptibility, closest energy for free radical superdelocalizability.
Fock Matrix – 1 particle/e- Hamiltonian; matrix of 1 e-, 2 e- Coulomb, & 2 e- Exchange integrals in total energy
Fock Operator – replaces the Hamiltonian Operator in the Schrödinger equation for a spin orbital/single electron in a mean field of the other electrons
FORS – (Fully Optimized Reaction Space) The FORS method, first proposed by Ruedenberg and coworkers, is essentially equivalent to the CASSCF method, except for the implementation of the MCSCF.
G1, G2 – (Gaussian 1 theory, Gaussian 2 theory) empirical algorithm to extrapolate to complete basis set and full correlation (beyond MP2/6-31G**) from combination of lower level calculations: HF/6-31G(d) frequencies; MP2/6-311G(dp) geometries; single point energies of MP4SDTQ w/ 6-311G**, 6-311+G** & 6-311G**(2df) and QCISD(T)/6-311G**. Practical up to ~7 heavy atoms. Cons: Cl, F BDE's. ΔHf ± 1.93 kcal/mol
G3 – (Gaussian 3 "slightly empirical" theory) extension of G2, add systematic correction for each paired e- (3.3 mHa) & each unpaired e- (3.1 mHa). ΔHf ± 1.45 kcal/mol
Gaussians – functions frequently used as primitive functions to expand total wave function. Typically defined with Cartesian coordinates w/ respect to a point in space.
GAPT – (Generalized Atomic Polar Tensor) A method for determining atomic charge on the basis of dipole moment derivatives.
GGA – (Generalized Gradient Approximation) Corrects local density approximation by including a functional of the density gradient (i.e., f[grad rho]) in addition to the local functional. Favors greater densities and inhomogeneity, overcomes LDA tendency to overbind. Uses scale factors from density & 1st derivative of density. Adds ~20% to compute time.
ghost function – A basis function that is not accompanied by an atomic nucleus, usually for counterpoise corrections for BSSE.
GIAO – (Gauge Independent Atomic Orbitals) Ditchfield's method for canceling out the arbitrariness of the choice of origin & form (gauge) of the vector potential used to introduce the magnetic field in the Hamiltonian when calculating chemical shielding and chemical shift tensor. An exponential term containing the vector potential is included with each atomic orbital. Originally developed based on Hartree-Fock, improved by Pulay w/ DFT to be faster, also used w/MP2 & CCSD. Pros: less basis set dependence than IGAIM
Green's Function – inverse of the Hessian Matrix.
GTO – (Gaussian-Type Orbital) Basis function consisting of a Gaussian function, i.e., exp(-r2), multiplied by an angular function. If the angular function is "Cartesian", there are six d-functions, ten f-functions, etc. (6d, 10f). If the angular function is spherical, there will the usual number of functions (5d, 7f).
GUGA – (Graphical Unitary Group Approximation)
GVB – (Generalized Valence Bond) Bill Goddard's "laid back Southern California wavefunctions." Equivalent to MCSCF correlation treatment: 2 configurations used to represent each e- pair and solved for 2 associated orthogonal functions. Excitations are taken within an electron pair but not between orbitals in different pairs Dissociation-consistent. If restricted to doubles, is called "perfect pairing" (GVB-PP). If includes both singles and doubles, is called "restricted configuration interaction" (GVB-RCI).
Hamiltonian – Matrix of bare nucleus, 0 e- Fock Matrix. Matrix that operates on wavefunction to calculate the energy in Schrödingers equation.
hartree – One atomic unit of energy, equal to 2625.5 kJ/mol, 627.5 kcal/mol, 27.211 eV, and 219474.6 cm-1.
Hessian – Matrix of mass normalized 2nd derivatives of energy with respect to nuclear displacement in Cartesian coordinates. Diagonalized to determine normal modes & calculate vibrational frequencies.
HF – (Hartree-Fock) Named after the developers of the most widely practiced method for solving the Schrödinger Equation for multi-electronic systems. The Hartree-Fock approximation (sometimes called the Self-Consistent Field Approximation) assumes a single (Slater) determinant wavefunction, or in other terms, the standard molecular orbital model. Approximates the molecular, all e- wavefunction as product of single e- wavefunctions, and approximate molecular wavefunctions as LCAO. Orbitals that contain e- are occupied, those that are vacant are called "virtual." The orbital for each electron is determined in the average field of the other electrons, and iterated until self-consistency is achieved. Uses exact form of the (electronic) Hamiltonian Operator in Schrödinger’s equation, and tries to find the best approximate wavefunction. Scales as n^3-4.
HMO – (Hückel Molecular Orbital theory)
HOMO – (Highest Occupied Molecular Orbital) The occupied molecular orbital having the greatest energy. In Frontier Molecular Orbital theory the HOMO plays a significant role in determining the course and barrier to reactions. The energy of this orbital approximates the ionization energy of the molecule by Koopman's Theorem.
HONDO –
IEHT – (Iterative Extended Hückel Theory)
IEPA – (Independent Electron Pair Approximation) An alternative method to the CI approach for obtaining electron correlation. Assumes the correlation energy is pair-wise additive: the correlation energy for each pair of electrons is obtained independently of all other electrons and then summed up. The method was developed by Sinanoglu (who called it Many-Electron Theory or MET) and Nesbet (who called it Bethe-Goldstone Theory).
IGLO – (Individual Gauge for Localized Orbitals) Kutzelnigg & Schiendler's method for canceling out the arbitrariness of the choice of origin & form (gauge) of the vector potential used to introduce the magnetic field in the Hamiltonian when calculating chemical shielding & chemical shift tensors at nuclei. An exponential term containing the vector potential premultiplies MOs that have been localized in real space. Faster than HF based GIAO
IMOMM – (Integrated Molecular Orbital & Molecular Mechanics) Morokuma's method to extrapolate to high level calculation on large systems by integrating addition of ΔE between large system and small model systems calculated at low level (MM), to the energy of the small model calculated at a high level (MO).
IMOMO – (Integrated Molecular Orbital & Molecular Orbital) same as IMOMM with high (ab initio) and low level (semiempirical) MO calculations.
INDO – (Intermediate Neglect of Differential Overlap) A semiempirical method closely related to the CNDO method, where all terms of the Fock matrix used in CNDO are included, but the restriction that the monocentric two-electron integrals all be equal is lifted.
internal coordinates – Bond lengths, bond angles, and dihedral (torsional) angles; sometimes called "natural coordinates."
IRC – (Intrinsic Reaction Coordinate) An optimized reaction path that is followed downhill, starting from a transition state, to approximate the course (mechanism) of an elementary reaction step. (Ignores tunneling, contribution of vibrationally excited modes/partition function, etc.)
isodesmic – a chemical reaction that conserves types of chemical bond. Due to better cancellation of systematic errors, energy changes computed using such reactions are expected to be more accurate than those computed using reactions that do not conserve bond types.
isogyric – a chemical reaction that conserves net spin. Due to better cancellation of systematic errors, energy changes computed using such reactions are expected to be more accurate than those computed using reactions that do not conserve spin.
Koopman's Theorem – the ionization potential can be approximated by the energy of the HOMO. Errors from neglect of e- correlation & e- relaxation tend to cancel for IP, but compound for trying to approximate EA from LUMO energy.
LCAO – (Linear Combination of Atomic Orbitals) Molecular orbitals are usually constructed as a linear combination of atomic orbitals. The coefficients in this expansion are determined by solving the Schrödinger equation, typically in the Hartree-Fock approximation.
LDA = LSDA – (Local Density/Spin-Density Approximation) A DFT method involving only local functionals: those that depend only upon the value of the density, f[rho]: no dependence upon the gradient of the electron density.
level shifting – method to avoid oscillations during SCF convergence by artificially raising the energies of the virtual orbitals to separate the different states.
LFER – (Linear Free Energy Relationship)
LNDO – (Local Neglect of Differential Overlap)
LORG – (Localized Orbitals, Local Origin) Hansen & Bouman Gauge invariant method for calculating chemical shielding & chemical shift tensors: expanding angular momentum terms relative to local origin for each orbital so no reference to gauge origin. Similar to IGLO.
LST – (Linear Synchronous Transit) An interpolative method to provide an initial guess for a transition state. Assumes each atom position in the transition state is in a direct line between its position in the reactants and its position in the products.
LUMO – (Lowest Unoccupied Molecular Orbital) The unoccupied molecular orbital having the lowest energy. In Frontier Molecular Orbital theory the LUMO plays a significant role in determining the course and barrier to reactions. The energy of the LUMO is a poor approximation of the EA.
Madelung Potential – a set of point charges used to represent a solid continuum.
MBPT = Møller-Plesset Perturbation Theory – (Many Body Perturbation Theory)
MC – (Monte Carlo) method of sampling based on generating random numbers.
MCCM – (Multi Coefficient Correction Method) Truhlar's method to scale each component of the correlation energy to extrapolate to full correlation: HF, MP2, and MP4 terms.
MCPF – (Modified Couple Pair Functional)
MCSCF – (MultiConfiguration Self-Consistent Field) A limited type of CI. A simple extension of the SCF approach to include non-dynamic electron correlation, with the added feature of orbital optimization. A number of configurations are chosen in some manner, then both the expansion coefficients and the orbital coefficients are optimized.
MD – (Molecular Dynamics) method of sampling geometries based on Newtonian laws of motion.
MEP – (Molecular Electrostatic Potential)
MERP – (Minimum Energy Reaction Path)
MINDO – (Modified Intermediate Neglect of Differential Overlap) Refers to the parametrization set (and computer code) developed by the Dewar group for performing INDO calculations. The most useful of the MINDO series is MINDO/3.
Minimal Basis Set – The smallest # of functions needed to hold all electrons and still be spherical. Commonly refers to STO-3G.
MM – (Molecular Mechanics) classical description of molecules as atoms held together by spring-like bonds. Chemical "Hamiltonian" based on force constants.
MM2 – (Molecular Mechanics, Allinger Force Field version 2) one of the earliest, and probably the best known and tested Molecular Mechanics force field for organic molecules.
MMFF – (Merck Molecular Force Field)
MMP2 – (Molecular Mechanics, Allinger Force Field version 2 with Pi electrons handled quantum mechanically). Pi bond stretch calculated on the fly based on simple SCF bond order.
MM3 – (Molecular Mechanics, Allinger Force Field version 3)
MNDO – (Modified Neglect of Diatomic Overlap) Dewar’s first parametrization of the NDDO semiempirical method. First incorporated into the MOPAC program.
MNDOC – (Modified Neglect of Diatomic Overlap Correlated) Thiel’s version of MNDO which includes limited configuration interaction.
MNDO/d – (MNDO with d-orbitals) Thiel's version of MNDO with extra set of orbitals for second row transition and main group elements.
MO – (Molecular Orbital) An orbital described by the wavefunction for a single electron in a molecule, usually delocalized across the entire molecule. Usually, molecular orbitals are constructed as combinations of atomic orbitals.
MP2 – (Møller-Plesset theory, 2nd order) Møller-Plesset developed the perturbative approximation to include electron correlation, using the Hartree-Fock wavefunction as the zeroth order wavefunction. MP2 refers to the second order energy correction. Comparable to CISD.
MP3 – (Møller-Plesset Theory, 3rd order) A perturbative approximation for including electron correlation, using the Hartree-Fock wavefunction as the zeroth order wavefunction. MP3 refers to the third-order energy correction.
MP4 –(Møller-Plesset Theory, 4th order) A perturbative approximation for including electron correlation, using the Hartree-Fock wavefunction as the zeroth order wavefunction. MP4 refers to the fourth order energy correction. MP4 as implemented in GAUSSIAN can be calculated using various configurations. For example, MP4SDQ means that all terms involving singles, doubles and quadruples configurations are included through fourth order.
MPA – ( Mulliken Population Analysis)
MR – (Multi-Reference)
MRCI – (Multi-Reference Configuration Interaction) CI using more that one reference determinant, instead of the usual single Hartree-Fock reference (ie. the ground state wavefunction). Among multi-reference theories, MR-CISD (singles and doubles CI) is popular and high-level (but not dissociation consistent).
Mulliken Charges – Charges are assigned to each atom from an electronic calculation, by arbitrarily attributing the e- density of the diagonal terms (single atom terms) to each atom, plus half of the e- density of each off-diagonal term for that atom. Very sensitive (<100%) to basis set.
NAO – (Natural Atomic Orbital)
natural orbital – those orbitals for which the first-order density matrix is diagonal; each will contain some non-integer number of electrons between 0 and 2. Usually discussed in the context of a correlated calculation. RHF calculations give molecular orbitals that are also natural orbitals. The NOs are the orbitals for which the CI expansion converges fastest. Particularly valuable in modeling organometallic complexes.
NEMD – (Non Equilibrium Molecular Dynamics) MD w/ applied forces, such as shear.
NBO –
NDDO – (Neglect of Differential Diatomic Overlap) This semiempirical method that keeps all terms of the Fock matrix except those involving diatomic differential overlap: the only two-electron terms, are those where e- 1 is in one orbital on atom A and e- 2 is in one orbital on atom B.
NPA – (Natural Population Analysis) A method for determining atomic charge distributions in a molecule. Based on creating atomic natural orbitals from the molecular orbitals, by finding eigenfunctions of atomic sub-blocks of the molecular density matrix, based on chemical concepts of bonds, lone pairs, etc. Fairly independent of basis set.
OPLS – (Optimized Potentials for Liquid Simulations) force field for condensed (aqueous) simulations. Electrostatic only for H-bond, "Disappearing L-J" H-bond.
ONIOM – (Our own N-layered Integrated molecular Orbital molecular Mechanics method) Morokuma's generalized method for modeling large/condensed systems. Model critical part of chemical system with a high accurate/level method, intermediate region with a less expensive method, outer region approximately.
orbital – the wavefunction describing where an e- is in an atom or molecules. Usually an eigenfunction of a one-electron Hamiltonian, e.g., from Hartree-Fock theory. A spin orbital has an explicit spin and a spatial orbital does not. Orbitals are probably the most useful concept from quantum chemistry: one can think of an atom or molecule as having a set of orbitals that are filled with electrons (occupied) or vacant (unoccupied or "virtual").
Pauling point – calculation that gives a good result because systematic, but opposed errors cancel out.
PCI – (Parameterized Configuration Interaction) empirical scaling of contribution of dynamic correlation to bond strengths. See Siegbahn, Blomberg, et. al.
PCM – (Polar Continuum Model) implicit solvation model of Tomasi.
PES – (Potential Energy Surface) The 3N-6 (or 3N-5, for linear molecules) dimensional function that indicates how the molecule's energy depends upon its geometry.
Perturbation Theory – approximation to include electron correlation, based on Taylor Series expansion of the Hartree-Fock wavefunction (1 e- Hamiltonian) as the 0th order wavefunction, for E in Schrödinger equation, truncated after n terms.
PM3 – (Parametric Method number 3) A re-parameterized version of AM1 by Stewart.
PMO – (Perturbation Molecular Orbital theory)
PNDO – (Partial Neglect of Differential Overlap)
polarized – basis set that includes functions that are of higher angular momentum than is minimally required. (Combination of p-orbitals added to the valence s-orbitals, or d-orbitals in addition to valence p-orbitals on carbon, for instance.) The added functions are often called "polarization functions." Polarization functions help to account for the fact that atoms within molecules are not spherical.
PPP – (Pariser-Parr-Pople)
PRDDO – (Partial Retention of Diatomic Differential Overlap)
primitive – individual Gaussian functions used singly to produce a contracted basis function: a set of p-functions is three basis functions, but may be many primitives (3n, where there are n primitives in the cGTO).
PRISM – (Polymer Reference Interaction Site Model) Adaptation of RISM theory for liquid polymers by Schweizer & Curro. Based on single chain conformational statistics and interaction potentials.
PUHF – (spin-Projected UHF) An approximation to provide the energy that would result from a UHF calculation, if it did not suffer spin-contamination. The PUHF energy is usually lower than the UHF energy because the contributions of higher-multiplicity states, which usually have high energies, have been (approximately) subtracted.
QCI – (Quadratic Configuration Interaction) CI method with terms added to confer size-consistency. An approximation to coupled-cluster theory.
QCISD(T) – (Quadratic Configuration Interaction with all Single and Double excitations and perturbative inclusion of Triple excitations) post Hartree-Fock method. Similar results to QCISDT, used in G2. Scales as n^7.
QCPE – (Quantum Chemistry Program Exchange) The Quantum Chemistry Program Exchange is a warehouse of chemistry computer codes. They have operated since 1962, providing a depository of what is now well over 600 different programs. QCPE can be contacted at QCPE Creative Arts Building 181 Indiana University Bloomington, IN 47405 USA telephone: (812)855-4784 fax: (812)855-5539 E-mail: qcpe@ucs.indiana.edu anonymous ftp access: qcpe6.hem.indiana.edu
QMC – (Quantum Monte Carlo) ab initio method using explicitly correlated wave functions, and evaluating integrals numerically via Monte Carlo integration.
QSAR – (Quantitative Structure-Activity Relationship) correlation developed between chemical structure and (biological) activity. Typically used to design drugs & predict activity.
QSPR – (Quantitative Structure-Activity Relationship) correlation developed between chemical structure and (physical) properties. Typically used to design materials and predict properties.
RECP – (Relativistic Effective Core Potential) Core electrons have been replaced by an effective potential that is based upon relativistic quantum calculations of the free atoms. Saves cost because of fewer explicit electrons and also includes some relativistic effects, especially the contraction of core s- and p-orbitals.
reference – As in "single-reference" or "multi-reference," refers to the number of configurations (or Slater determinants) in the 0th-order description of the wavefunction. Most methods that don't begin with "MR," "MC," or "CAS" are single-reference methods
RHF – (Restricted Hartree-Fock) The standard HF-SCF method where every spatial orbital is doubly occupied, i.e. every spin up electron has a spatially equivalent spin down electron. This generally implies a closed-shell wavefunction, though restricted open-shell SCF can be done.
RIS – (Rotational Isomeric State) Build representative polymer models by sequentially considering rotational isomers of next bond along backbone to add each monomer. Statistical weights fitted to experiment.
RISM – (Reference Interaction Site Model) Chandler & Anderson's theory of small molecule liquids based on interaction potentials.
ROHF – (Restricted Open-shell Hartree-Fock) Restricted Hartree-Fock theory for open shell systems. a electron of spin up and b electron of spin down with a>b, and for electrons 1,2...b use the identical spatial form of the orbitals for the up and down spins. No spin contamination, but singly occupied orbital energies don't obey Koopman's Theorem.
RRKM – (Rice-Ramsperger-Kassel-Marcus) kinetic theory for reaction rates
SAC – (Scaling All-Correlation) empirical scaling of contribution of dynamic correlation to bond strengths. See Truhlar, Gordon, et. al.
SALC – (Symmetry Adapted Linear Combinations)
SAM1 – (Semiempirical Ab initio Method version 1) Andy Holder’s extension of AM1 in Ampac by the addition of d-orbitals in the Hamiltonian. More theoretically consistent.
scaling – Multiplying calculated results by an empirical fudge factor in the hope of getting a more accurate prediction. Very often done for vibrational frequencies computed at the HF/6-31G* level, for which the accepted scaling factor is 0.893.
SCEP – (Self-Consistent Electron Pairs)
SCF – (Self Consistent Field) The most widely practiced method for solving the Schrödinger Equation for multi-electron systems. The Self-Consistent Field Approximation (typically referred to as the Hartree-Fock Approximation, but also applies to most DFT and all MCSCF calculations) assumes a single determinant wavefunction, or in other terms, the standard molecular orbital model. The orbital (ie. the coefficients of the atomic basis functions in each molecular orbital) for each electron is adjusted in the average field of the other electrons, and iterated until self-consistency is achieved.
SCI-PCM – (Self Consistent Isodensity surface Polar Continuum Model) enhanced solvation method of Tomasi.
SCREEP – (Surface Charge Representation of the Electrostatic Embedding Potential) Truong's representation of effect of surrounding charge on closed surface around a cluster.
SCRF – (Self-Consistent Reaction Field) an implicit solvation model.
semiempirical – An approximate version of Hartree-Fock theory in which the more computationally expensive integrals are replaced by adjustable parameters, which are determined by fitting experimental atomic and molecular data. Different choices of parameterization lead to different specific theories (e.g., MNDO, AM1, PM3).
secular equation –
SINDO – (Symmetrically orthogonalized INDO method)
size-consistent – a calculation that gives the same energy for two atoms (or molecular fragments) separated by a large distance as is obtained from summing the energies for the atoms (or molecular fragments) computed separately. So for a size-consistent method, the bond energy in N2 is ΔEdiss = 2E(N) - E(N2). For a method that is not size-consistent, a "supermolecule" calculation with a big distance (e.g., 100 Å) is required: ΔEdiss = E(N......N) - E(N2).
Slater Determinant – a trial guess for the electronic wavefunction in the form of a determinant describing the Hartree-Fock configuration
SOMO – (Singly Occupied Molecular Orbital) for radicals
SOS-DFPT – (Sum Over States Density Functional Perturbation Theory)
SPCA – (Single Point Charge Extended) model of water.
SPC water – (Simple Point Charge) MM model of water with charge, Van der Waals, and angle terms.
spin-contamination – calculations with UHF wavefunctions that are not eigenfunctions of spin, and are contaminated by states of higher spin multiplicity (which usually raises the energy).
spin density – The amount of excess alpha (over beta) spin. Identifies the location of unpaired electrons in radicals and for interpreting ESR experiments.
Spin Orbital – single electron/particle function: eigenfunction to 1 particle Hamiltonian
Split Valence – basis set that is more than minimal for the valence orbitals. At least VDZ. In Gaussian nomenclature, 3-21G is a split valence basis, and 6-311G is a triple-split-valence basis.
static correlation = nondynamic correlation – The part of the correlation that is ascribed to the "multireference" nature of the problem at hand, i.e., to the qualitative failure of Hartree-Fock theory to describe the dissociation of a system into fragments. The best-known stable molecule with important nondynamic correlation is singlet methylene, CH2 (ã 1A1), for which two configurations are important: (a1)2(b1)0 and (a1)0(b1)2. In many cases, the distinction between nondynamic and dynamic correlation is rather arbitrary. When nondynamic correlation is important, single-reference theories may be unreliable.
STO – (Slater-Type Orbital) Basis function with an exponential radial function, i.e., exp(- zeta r). Also used to denote a fit to such a function using other functions, such as Gaussians. For example, STO-3G is an MBS that uses 3 Gaussians to fit an exponential. Exponentials are probably better basis functions than Gaussian, but are so much more difficult computationally that they were abandoned by most people a long time ago.
TCSCF – (Two-Configuration Self-Consistent Field)
TIP3P – MM model of water with charge, Van der Waals, and angle terms.
Transition State Theory – the transition state is a maximum along the vibrationless potential energy surface. The activation energy is taken as the difference between the energies of the ground state and the transition state.
TZ – (Triple Zeta)
UFF – (Universal Force Field) Force field of Rappe & Landis to include all elements.
UGA – ( Unitary Group Approach)
UHF – (Unrestricted Hartree-Fock) The self-consistent field method without the restriction of pairing up and down electrons. Unlike the restricted case, where the spin-orbitals are defined such that each spin up and spin down pair have the same spatial form, in the unrestricted space every spin-orbital has different spatial forms. The drawback to this approach is that the UHF wavefunction does not have to be an eigenfunction of the S^2 operator, while the RHF will always be an eigenfunction of the S^2 operator.
Variational Transition State Theory – transition state is at the maximum in free energy along the reaction path. Takes into account the shape of the PES in kinetic calculations. An essential definition for bond cleavage.
VB – (Valence Bond)
VDZ – (Valence double-zeta) A minimal basis is used to describe core electrons, but the valence electrons have twice the minimum number of functions.
VSEPR – (Valence Shell Electron Pair Repulsion)
Wigner correction – approximate correction to transition state theory for tunneling, based on the imaginary frequency at the transition state.
ZDO – (Zero Differential Overlap)
Z-matrix – common format for specifying molecular geometry in terms of internal coordinates. Each atom is described in terms of its distance from some other atom (normally one it is bonded to), the angle it makes with that atom and a previously defined atom, and the dihedral angle between those 3 atoms and a 4th atom.
ZPVE – (Zero-Point Vibrational Energy, also ZPE)
(Grain of Salt)
This dictionary of Computational Chemistry terms has been assembled over several years from a variety of sources, including my own interpretation of published useage, as well as a compilation and/or paraphrasing of definitions from other sources. Some of these come from Dictionaries published on the Internet, which are no longer available. Two similar, extensive dictionaries/glossaries which are still available on the Internet are:
Karl Irikura's Glossary of Common Terms and Abbreviations in Quantum Chemistry.
and a, Dictionary of Computational Chemistry by Martin Grayson.
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