Acronyms & Definitions
Listed Alphabetically 

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<b>AIM</b> - (Atoms In Molecule)

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<b>AO</b> - (Atomic Orbital) An atomic orbital is the wavefunction for a single electron centered on a single atom.

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<b>AOM</b> - (Angular Overlap Model)

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<b>AM1</b> - (Austin Model 1) Dewars NDDO semiempirical parameterization.

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<b>ASE</b> - (Aromatic Stabilization Energy)

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<b>BAC-MP4</b> - (Bond Additive Corrections to energies from Moller-Plesset 4th order perturbation theory) empirical corrections to calculated energy based (exponentially) on bond lengths.

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<b>Bader's analysis</b> -

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<b>Basis Set</b> - finite set of functions used to approximately express wavefunction(s) of system, normally atom centered, consisting of AOs differing in local angular momentum for each atom.

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<b>BCUT</b> - (Burden CAS University of Texas) topological molecular similarity index of Burden.

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<b>BDE</b> - (Bond Dissociation Energy)

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<b>BSSE</b> - (Basis Set Superposition Error) The energy of two molecules modeled together can be 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. 

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<b>BLYP</b> - (Becke-Lee-Yang-Parr)

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<b>CADPAC</b> - (Cambridge Analytical Derivatives PACkage)

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<b>CAS</b> - (Complete Active Space)

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<b>CASPT</b> - (Complete Active Space Perturbation Theory)

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<b>CASSCF</b> - (Complete Active Space Self-Consistent Field) Perhaps the most popular variant of the MCSCF method. CACSF is an MCSCF method with a specific choice of configurations. In essence, one selects a set of active orbitals and active electrons. The CASSCF procedure is to then form all of the configurations possible by placing the active electrons in the active orbitals, consistent with the proper spin and space symmetry requirements. It is essentially equivalent to the FORS method.

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<b>CBS-QCI</b> - (Complete Basis Set Quadratic Configuration Interaction) alternative extrapolation algorithm to complete basis set.

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<b>CC</b> - (Coupled Cluster)

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<b>CCD</b> - (Coupled Cluster, Doubles only.)

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<b>CCSD</b> - (Coupled Cluster, Singles and Doubles only.)

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<b>CCSD(T)</b> - (Coupled Clusters, Singles and Doubles with Triples treated approximately.) ?Hdiss ± 1.0 kcal/mol

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<b>CCSS</b> - (Correlated Capped Small Systems) Special case of IMOMO. See Truhlar's and Hass's work.

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<b>CEPA</b> - (Coupled Electron Pair Approximation)

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<b>CFF</b> - (Consistent Force Field) Class II force field based on ab initio data developed by Biosym Consortium/MSI.

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<b>CFMM</b> - (Continuous Fast Multipole Method) linear scaling method for matrix formation for DFT.

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<b>CFSE</b> - (Crystal Field Stabilization Energy)

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<b>CHF</b> - (Coupled Hartree-Fock method)

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<b>CHELP</b> - (CHarges from ELectrostatic Potential) One of many attempts to obtain atomic charges, this approach is to fit 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.

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<b>Chemical Shift Tensor</b> - representation of the chemical shift. 3x3 matrix field felt in a direction induced by current due to applied filed in b direction.

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<b>CI</b> - (Configuration Interaction) The simplest variational approach to incorporate dynamic electron correlation is the Configuration Interaction method. The CI wavefunction includes the Hartree-Fock configuration and a select set of other configurations, with the expansion coefficients determined (in principal) by diagonalizing the Hamiltonian matrix. The choice of configurations to include is left to the user; two popular methods are the CID and CISD methods.

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<b>CID</b> - (Configuration Interaction, Doubles Substitution Only) The post-Hartree-Fock method that involves configuration interaction where the included configurations are the Hartree-Fock configuration and all configuration derived from doubles substitution.

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<b>CIDEP</b> - (Chemically Induced Dynamic Electron Polarization)

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<b>CIDNP</b> - (Chemically Induced Dynamic Nuclear Polarization)

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<b>CISD</b> - (Configuration Interaction, Singles and Doubles Substitution Only) The 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.

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<b>CKFF</b> - (Cotton-Kraihanzel Force Field)

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<b>CNDO</b> - (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.

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<b>Combinatorial Chemistry</b> - testing a large number of related compounds (as a mixture?) to find a compound that is active.

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<b>CoMFA</b> - (Comparative Molecular Field Analysis) technique used to establish 3-D similarity of molecular structure in relation to a target property.

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<b>COOP</b> - (Crystal Overlap pOPulation)

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<b>Correspondence Principle</b> - classical mechanics becomes a special case of quantum mechanics at larger masses/scale.

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<b>COSMO</b> - (Conductor-Like Screening Model) implicit solvation model of Andreas Klamt. Less sensitive to outlying charges then PCM.

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<b>Coulomb</b> - 1-center, 2 electron integral.

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<b>CPHF</b> - (Coupled Perturbed Hartree-Fock )

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<b>CVFF</b> - (Consistent Valence Force Field)

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<b>DFT</b> - (Density Functional Theory) ab initio electronic method from solid state physics. Assumes exact wavefunction and tries to find best approximate functional. Scales as 2nd power times a large number. Correlation built in. Not variational. Believed to be size consistent.

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<b>DIIS</b> - (Direct Inversion in the Iterative Space) Pulay's extremely efficient to accelerate the convergence of the SCF in Hartree-Fock calculations.

DISCO -

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<b>DOS</b> - (Density Of States)

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<b>DZ</b> - (Double-Zeta)

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<b>ECP</b> - (Effective Core Potential)

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<b>EFFF</b> - (Energy Factored Force Field)

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<b>EHT</b> - (Extended Huckel Theory)

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<b>Electron Correlation</b> - 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.

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<b>Embedded Cluster</b> - Sauer's (and Teunissen's and others) approach to modeling real 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.

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<b>ESFF</b> - (Extensible & Systematic Force Field) Rule based force field designed for generality rather than accuracy by Biosym/MSI.

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<b>FMO</b> - (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 electrophylic, LUMO for nucleophylic susceptibility, closest energy for free radical superdelocalizability. 

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<b>Fock Matrix</b> - 1 e- Hamiltonian?

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<b>FORS</b> - (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.

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<b>G1, G2</b> - (Gaussian 1 theory, Gaussian 2 theory) empirical algorithm to extrapolate to full 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**. ?Hf ± 2.4 kcal/mol

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<b>Gaussians</b> - functions frequently used as primitive functions to expand total wave function. Typically defined with Cartesian coordinates w/ respect to point in space.

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<b>GAPT</b> - (Generalized Atomic Polar Tensor) A method for determining atomic charge on the basis of dipole moment derivatives.

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<b>GGA</b> - (Generalized Gradient Approximation) Adds nonlocal gradient corrections to local density approximation. Favors greater densities and inhomogeneity, overcomes LDA tendency to overbind. Uses scale factors from density & 1st derivative of density. Adds ~20% to compute time.

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<b>GIAO</b> - (Gauge Including 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 based on Hartree-Fock, improved by Pulay w/ DFT to be faster.

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<b>GTO</b> - (Gaussian-Type Orbital)

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<b>GUGA</b> - (Graphical Unitary Group Approximation)

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<b>GVB</b> - (Generalized Valence Bond) Bill Goddards "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.

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<b>Hamiltonian</b> - Matrix of bare nucleus, 0 e- Fock Matrix. Matrix that operates on wavefunction to calculate the energy in Schrodingers equation.

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<b>Hessian</b> - Matrix of 2nd derivatives of energy with respect to nuclear displacement. Diagonalized to determine normal modes & calculate vibrational frequencies.

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<b>HF</b> - (Hartree-Fock) Named after the developers of the most widely practiced method for solving the Schrodinger Equation for multi-electronic systems. The Hartree-Fock approximation (sometimes called the Self-Consistent Field Approximation) assumes a single determinant wavefunction, or in other terms, the standard molecular orbital model. (approximate molecular all e- wavefunction as product of single e- wavefunctions, and approximate molecular wavefunctions as LCAO.) 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 Schroedinger's equation, and tries to find the best approximate wavefunction. Scales as n^3-4.

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<b>HMO</b> - (Huckel Molecular Orbital theory)

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<b>HOMO</b> - (Highest Occupied Molecular Orbital) The occupied molecular orbital having the greatest energy is referred to as the HOMO. In Frontier Molecular Orbital theory the HOMO plays a significant role in determining the course and barrier to reactions.

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<b>HONDO</b> -

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<b>IEHT</b> - (Iterative Extended Huckel Theory)

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<b>IEPA</b> - (Independent Electron Pair Approximation) An alternative method to the CI approach for 
obtaining electron correlation, the Independent Electron Pair Approximation assumes the correlation energy is pair-wise additive. Thus, the correlation energy for each pair of electrons is obtained independent 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).

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<b>IGLO</b> - (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

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<b>IMOMM</b> - (Integrated Molecular Orbital & Molecular Mechanics) Morokuma's method to extrapolate to high level calculation on large systems by adding ?E between real and model systems at low level (MM) to the energy of the model calculated at a high level (MO).

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<b>IMOMO</b> - (Integrated Molecular Orbital & Molecular Orbital) same as IMOMM with high (ab initio) and low level (semiempirical) MO calculations.

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<b>INDO</b> - (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 and the restriction that the monocentric two-electron integrals all be equal is lifted.

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<b>IRC</b> - (Intrinsic Reaction Coordinate)

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<b>LCAO</b> - (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 Schrodinger equation, typically in the Hartree-Fock approximation.

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<b>Level Shifting</b> - method to avoid oscillations during SCF convergence by artificially raising the energies of the virtual orbitals to separate the different states.

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<b>LFER</b> - (Linear Free Energy Relationship)

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<b>LNDO</b> - (Local Neglect of Differential Overlap)

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<b>LORG</b> - (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.

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<b>LST</b> - (Linear Synchronous Transit) 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.

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<b>LUMO</b> - (Lowest Unoccupied Molecular Orbital) The unoccupied molecular orbital having the lowest energy is referred to as the LUMO. In Frontier Molecular Orbital theory the LUMO plays a significant role in determining the course and barrier to reactions.

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<b>Madelung Potential</b> - a set of point charges used to represent a solid continuum.

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<b>MBPT</b> - (Many Body Perturbation Theory)

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<b>MC</b> - (Monte Carlo) method of sampling based on generating random numbers.

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<b>MCPF</b> - (Modified Couple Pair Functional)

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<b>MCSCF</b> - (MultiConfiguration Self-Consistent Field) A simple extension of the SCF approach to include non-dynamic electron correlation, the correlation of electrons that has to do with the dissociation of a system into fragments. In the MCSCF method, a number of configurations are chosen in some manner. The expansion coefficients and the orbital coefficients are then optimized.

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<b>MD</b> - (Molecular Dynamics) method of sampling based on Newtonian laws of motion.

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<b>MEP</b> - (Molecular Electrostatic Potential)

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<b>MERP</b> - (Minimum Energy Reaction Path)

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<b>MINDO</b> - (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.

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<b>Minimal Basis Set</b> - The smallest # of functions needed to hold all electrons and still be spherical.

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<b>MM</b> - (Molecular Mechanics)

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<b>MM2</b> - (Molecular Mechanics, Allinger Force Field version 2)

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<b>MMFF</b> - (Merck Molecular Force Field)

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<b>MMP2</b> - (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.

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<b>MM3</b> - (Molecular Mechanics, Allinger Force Field version 3)

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<b>MNDO</b> - (Modified Neglect of Diatomic Overlap) Dewar's first parametrization of the NDDO semiempirical method. The method was first incorporated into the MOPAC program. 

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<b>MNDOC</b> - (Modified Neglect of Diatomic Overlap Correlated) Thiel's version of MNDO which includes limited configuration interaction.

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<b>MNDO/d</b> - (MNDO with d-orbitals) Thiels version of MNDO with extra set of orbitals for second row transition and main group elements.

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<b>MO</b> - (Molecular Orbital) A molecular orbital is the wavefunction for a single electron in a molecule. This wavefunction is usually delocalized across the entire molecule. Usually, molecular orbitals are constructed as combinations of atomic orbitals.

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<b>MP2</b> - (Moller-Plesset Theory, Second Order) Moller 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. 

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<b>MP3</b> - (Moller-Plesset Theory, Third 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 -(Moller-Plesset Theory, Fourth 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. MP4SDTQ means that triples are included as well.

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<b>MPA</b> - ( Mulliken Population Analysis)

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<b>MR</b> - (Multi-Reference)

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<b>Mulliken Charges</b> - Charges are assigned to each atom from an electronic calculation, by 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.

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<b>NAO</b> - (Natural Atomic Orbital)

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<b>NBO</b> - (Natural Bond Orbitals)

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<b>NDDO</b> - (Neglect of Differential Diatomic Overlap) This semiempirical method keeps all terms of the Fock matrix except those involving diatomic differential overlap. This means that the only two-electron terms that are kept are those where electron 1 is in one orbital on atom A and electron 2 is in one orbital on atom B.

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<b>NPA</b> - (Natural Population Analysis) A method for determining atomic charge distributions in a molecule. The method is based on creating atomic natural orbitals from the molecular orbitals, by finding eigenfunctions of atomic sub-blocks of the molecular density matrix.

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<b>OPLS</b> - (Optimized Potentials for Liquid Simulations) Electrostatic only for H-bond, "Disappearing L-J" H-bond.

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<b>ONIOM</b> - (Our own N-layered Integrated molecular Orbital molecular Mechanics method) Morokuma's method. Model critical part of chemical system with a high accurate/level method, intermediate region with a less expensive method, outer region approximately.

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<b>Pauling Point</b> - calculation that gives a good result because errors cancel out.

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<b>PCI</b> - (Parameterized Configuration Interaction) empirical scaling of contribution of dynamic correlation to bond strengths. See Siegbahn, Blomberg, et. al.

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<b>PCM</b> - (Polar Continuum Model) implicit solvation model of Tomasi.

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<b>PES</b> - (Potential Energy Surface)

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<b>PM3</b> - (Parametric Method number 3) A re-parameterized version of AM1 by Stewart.

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<b>PMO</b> - (Perturbation Molecular Orbital theory)

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<b>PNDO</b> - (Partial Neglect of Differential Overlap)

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<b>PPP</b> - (Pariser-Parr-Pople)

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<b>PRDDO</b> - (Partial Retention of Diatomic Differential Overlap)

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<b>Primitive</b> - Gaussian functions used singly in Basis set.

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<b>PRISM</b> - (Polymer Reference Interaction Site Model) Adaptation of RISM theory for liquid polymers by Schweizer & Curro. Based on single chain conformational statistics and interaction potentials.

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<b>QCISD(T)</b> - (Quadratic Configuration Interaction with all Single and Double excitations and perturbative inclusion of Triple excitations) post Hartree-Fock method. Scales as n^7.

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<b>QCPE</b> - (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 There is also a connection to the QCPE through the Other Chemistry Gopher port in the NIU Chemistry Gopher.

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<b>QMC</b> - (Quantum Monte Carlo) ab initio method using explicitly correlated wave functions, and evaluating integrals numerically via Monte Carlo integration.

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<b>QSAR</b> - (Quantitative Structure-Activity Relationship)

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<b>QSPR</b> - (Quantitative Structure-Activity Relationship)

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<b>RHF</b> - (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.

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<b>RIS</b> - (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.

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<b>RISM</b> - (Reference Interaction Site Model) Chandler & Anderson's theory of small molecule liquids based on interaction potentials.

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<b>ROHF</b> - (Restricted Open-shell Hartree-Fock) Restricted Hartree-Fock theory for open shell systems. Suppose we have a electron of spin up and b electron of spin down with a>b. For the electron number 1,2...b the spatial form of the orbitals will be identical for the up and down spins. No spin contamination, but singly occupied orbital energies don't obey Koopman's Theorem.

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<b>RRKM</b> - (Rice-Ramsperger-Kassel-Marcus) kinetic theory

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<b>SAC</b> - (Scaling All-Correlation) empirical scaling of contribution of dynamic correlation to bond strengths. See Truhlar, Gordon, et. al.

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<b>SALC</b> - (Symmetry Adapted Linear Combinations)

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<b>SAM1</b> - (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.

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<b>SCEP</b> - (Self-Consistent Electron Pairs)

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<b>SCF</b> - (Self Consistent Field) The most widely practiced method for solving the Schrodinger Equation for multi-electronic systems. The Self-Consistent Field Approximation (also referred to as the Hartree-Fock Approximation) assumes a single determinant wavefunction, or in other terms, the standard molecular orbital model. The orbital for each electron is determined in the average field of the other electrons, and iterated until self-consistency is achieved.

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<b>SCI-PCM</b> - (Self Consistent Isodensity surface Polar Continuum Model) enhanced solvation method of Tomasi.

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<b>SCRF</b> - (Self-Consistent Reaction Field) an implicit solvation model.

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<b>SINDO</b> - (Symmetrically orthogonalized INDO method)

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<b>SOMO</b> - (Singly Occupied Molecular Orbital)

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<b>SOS-DFPT</b> - (Sum Over States Density Functional Perturbation Theory)

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<b>SPCA</b> - (Single Point Charge Extended) model of water.

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<b>SPC Water</b> - (Simple Point Charge) MM model of water with charge, Van der Waals, and angle terms.

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<b>Split Valence</b> - basis set with combination of p-orbitals added to the valence s-orbitals, or d-orbitals in addition to valence p-orbitals

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<b>STO</b> - (Slater-Type Orbital)

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<b>TCSCF</b> - (Two-Configuration Self-Consistent Field)

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<b>TIP3P</b> - MM model of water with charge, Van der Waals, and angle terms.

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<b>TZ</b> - (Triple Zeta)

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<b>UFF</b> - (Universal Force Field) Force field of Rappe & Landis to include all elements.

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<b>UGA</b> - ( Unitary Group Approach)

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<b>UHF</b> - (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.

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<b>VB</b> - (Valence Bond)

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<b>VSEPR</b> - (Valence Shell Electron Pair Repulsion)

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<b>ZDO</b> - (Zero Differential Overlap)

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<b>ZPVE</b> - (Zero-Point Vibrational Energy, also ZPE)