A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. © John Wiley & Sons, Inc.

General atomic and molecular electronic structure system

Scaling factors for obtaining fundamental vibrational frequencies, low-frequency vibrations, zero-point vibrational energies (ZPVE), and thermal contributions to enthalpy and entropy from harmonic frequencies determined at 19 levels of theory have been derived through a least-squares approach. Semiempirical methods (AM1 and PM3), conventional uncorrelated and correlated ab initio molecular orbital procedures [Hartree−Fock (HF), Moller−Plesset (MP2), and quadratic configuration interaction including single and double substitutions (QCISD)], and several variants of density functional theory (DFT:  B-LYP, B-P86, B3-LYP, B3-P86, and B3-PW91) have been examined in conjunction with the 3-21G, 6-31G(d), 6-31+G(d), 6-31G(d,p), 6-311G(d,p), and 6-311G(df,p) basis sets. The scaling factors for the theoretical harmonic vibrational frequencies were determined by a comparison with the corresponding experimental fundamentals utilizing a total of 1066 individual vibrations. Scaling factors suitable for low-frequency vib...

Harmonic Vibrational Frequencies: An Evaluation of Hartree−Fock, Møller−Plesset, Quadratic Configuration Interaction, Density Functional Theory, and Semiempirical Scale Factors

To make practical the molecular dynamics simulation of large scale reactive chemical systems (1000s of atoms), we developed ReaxFF, a force field for reactive systems. ReaxFF uses a general relationship between bond distance and bond order on one hand and between bond order and bond energy on the other hand that leads to proper dissociation of bonds to separated atoms. Other valence terms present in the force field (angle and torsion) are defined in terms of the same bond orders so that all these terms go to zero smoothly as bonds break. In addition, ReaxFF has Coulomb and Morse (van der Waals) potentials to describe nonbond interactions between all atoms (no exclusions). These nonbond interactions are shielded at short range so that the Coulomb and van der Waals interactions become constant as Rij → 0. We report here the ReaxFF for hydrocarbons. The parameters were derived from quantum chemical calculations on bond dissociation and reactions of small molecules plus heat of formation and geometry data for...

http://www.wag.caltech.edu/publications/sup/pdf/471.pdf

ReaxFF: A Reactive Force Field for Hydrocarbons

Several modifications that have been made to the NDDO core-core interaction term and to the method of parameter optimization are described. These changes have resulted in a more complete parameter optimization, called PM6, which has, in turn, allowed 70 elements to be parameterized. The average unsigned error (AUE) between calculated and reference heats of formation for 4,492 species was 8.0 kcal mol−1. For the subset of 1,373 compounds involving only the elements H, C, N, O, F, P, S, Cl, and Br, the PM6 AUE was 4.4 kcal mol−1. The equivalent AUE for other methods were: RM1: 5.0, B3LYP 6–31G*: 5.2, PM5: 5.7, PM3: 6.3, HF 6–31G*: 7.4, and AM1: 10.0 kcal mol−1. Several long-standing faults in AM1 and PM3 have been corrected and significant improvements have been made in the prediction of geometries.

/pdf/optimization-of-parameters-for-semiempirical-methods-v-597lxcumix.pdf

Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements.

MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics (MD) or Monte Carlo (MC) simulations. Several implicit solvation models are available with MMPBSA.py, including the Poisson–Boltzmann Model, the Generalized Born Model, and the Reference Interaction Site Model. Vibrational frequencies may be calculated using normal mode or quasi-harmonic analysis to approximate the solute entropy. Specific interactions can also be dissected using free energy decomposition or alanine scanning. A parallel implementation significantly speeds up the calculation by dividing frames evenly across available processors. MMPBSA.py is an efficient, user-friendly program with the flexibility to accommodate the needs of users performing end-state free energy calculations. The source code can be downloaded at http://ambermd.org/ with AmberTools, rele...

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.

A new method for obtaining optimized parameters for semiempirical methods has been developed and applied to the modified neglect of diatomic overlap (MNDO) method. The method uses derivatives of calculated values for properties with respect to adjustable parameters to obtain the optimized values of parameters. The large increase in speed is a result of using a simple series expression for calculated values of properties rather than employing full semiempirical calculations. With this optimization procedure, the rate-determining step for parameterizing elements changes from the mechanics of parameterization to the assembling of experimental reference data.

Optimization of parameters for semiempirical methods I. Method

MNDO/AM1‐type parameters for twelve elements have been optimized using a newly developed method for optimizing parameters for semiempirical methods. With the new method, MNDO‐PM3, the average difference between the predicted heats of formation and experimental values for 657 compounds is 7.8 kcal/mol, and for 106 hypervalent compounds, 13.6 kcal/mol. For MNDO the equivalent differences are 13.9 and 75.8 kcal/mol, while those for AM1, in which MNDO parameters are used for aluminum, phosphorus, and sulfur, are 12.7 and 83.1 kcal/mol, respectively. Average errors for ionization potentials, bond angles, and dipole moments are intermediate between those for MNDO and AM1, while errors in bond lengths are slightly reduced.

Optimization of parameters for semiempirical methods II. Applications

Before we start, we need a working definition for MOPAC. The following description has been used many times to describe MOPAC: MOPAC is a general-purpose, semiempirical molecular orbital program for the study of chemical reactions involving molecules, ions, and linear polymers. It implements the semiempirical Hamiltonians MNDO, AM 1, MINDO/3, and MNDOPM3, and combir_es the calculations of vibrational spectra, thermodynamic quantities, isotopic substitution effects, and force constants in a fully integrated program. Elements parameterized at the MNDO level include H, Li, Be, B, C, N, O, F, A1, Si, P, S, C1, Ge, Br, Sn, Hg, Pb, and I; at the PM3 level the elements H, C, N, O, F, A1, Si, P, S, C1, Br, and I are available. Within the electronic part of the calculation, molecular and localized orbitals, excited states up to sextets, chemical bond indices, charges, etc. are computed. Both intrinsic and dynamic reaction coordinates can be calculated. A transition-state location routine and two transition-state optimizing routines are available for studying chemical reactions.

MOPAC: A semiempirical molecular orbital program

: A finite field method for the calculation of polarizabilities and hyperpolarizabilities is developed based on both an energy expansion and a dipole moment expansion. This procedure is implemented in the MOPAC semiempirical program. Values and components of the dipole moment (mu), polarizability (alpha), first hyperpolarizability (beta), and second hyperpolarizability (gamma) are calculated as an extension of the usual MOPAC run. Applications to benzene and substituted benzenes are shown as test cases utilizing both MNDO and AM1 Hamiltonians.

Calculation of the nonlinear optical properties of molecules

Using a recently developed procedure for optimizing parameters for semiempirical methods,1 PM3 has been extended to a total of 28 elements. Average ΔHf errors for the newly parameterized elements are Be: 8.6, Mg: 8.4, Zn: 5.8, Ga: 14.9, Ge: 11.4, As: 8.5, Se: 11.1, Cd: 2.6, In: 11.3, Sn: 9.0, Sb: 13.7, Te: 11.3, Hg: 6.8, Tl: 6.5, Pb: 7.4, and Bi: 10.9 kcal/mol. For some elements the paucity of data has resulted in a method, which, while highly accurate, is likely to be only poorly predictive.

James J. P. Stewart

Papers

Optimization of parameters for semiempirical methods I. Method

Optimization of parameters for semiempirical methods II. Applications

MOPAC: A semiempirical molecular orbital program

Calculation of the nonlinear optical properties of molecules

Optimization of parameters for semiempirical methods. III. Extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb, and Bi