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

We present the theoretical and technical foundations of the Amsterdam Density Functional (ADF) program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order-N scaling, QM/MM) and its functionality (e.g., NMR chemical shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency-dependent (hyper)polarizabilities, atomic VDD charges). In the Applications section we discuss the physical model of the electronic structure and the chemical bond, i.e., the Kohn–Sham molecular orbital (MO) theory, and illustrate the power of the Kohn–Sham MO model in conjunction with the ADF-typical fragment approach to quantitatively understand and predict chemical phenomena. We review the “Activation-strain TS interaction” (ATS) model of chemical reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochemistry (structure and bonding of DNA) and of time-dependent density functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the analysis of chemical phenomena. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 931–967, 2001

Chemistry with ADF

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

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CHARMM: the biomolecular simulation program.

The activation strain or distortion/interaction model is a tool to analyze activation barriers that determine reaction rates. For bimolecular reactions, the activation energies are the sum of the energies to distort the reactants into geometries they have in transition states plus the interaction energies between the two distorted molecules. The energy required to distort the molecules is called the activation strain or distortion energy. This energy is the principal contributor to the activation barrier. The transition state occurs when this activation strain is overcome by the stabilizing interaction energy. Following the changes in these energies along the reaction coordinate gives insights into the factors controlling reactivity. This model has been applied to reactions of all types in both organic and inorganic chemistry, including substitutions and eliminations, cycloadditions, and several types of organometallic reactions.

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Analyzing Reaction Rates with the Distortion/Interaction‐Activation Strain Model

The electrophilic/nucleophilic character of a series of captodative (CD) ethylenes involved in polar cycloaddition reactions has been studied using DFT methods at the B3LYP/6-31G(d) level of theory. The transition state structures for the electrophilic/nucleophilic interactions of two CD ethylenes toward a nucleophilically activated ethylene, 2-methylene-1,3-dioxolane, and an electrophilically activated ethylene, 1,1-dicyanoethyelene, have been studied, and their electronic structures have been characterized using both NBO and ELF methods. Analysis of the reactivity indexes of the CD ethylenes explains the reactivity of these species. While the electrophilicity of the molecules accounts for the reactivity toward nucleophiles, it is shown that a simple index chosen for the nucleophilicity, Ν, based on the HOMO energy is useful explaining the reactivity of these CD ethylenes toward electrophiles.

Understanding the reactivity of captodative ethylenes in polar cycloaddition reactions. A theoretical study.

A new algorithm is presented for obtaining points on a steepest descent path from the transition state of the reactants and products. In mass‐weighted coordinates, this path corresponds to the intrinsic reaction coordinate. Points on the reaction path are found by constrained optimizations involving all internal degrees of freedom of the molecule. The points are optimized so that the segment of the reaction path between any two adjacent points is given by an arc of a circle, and so that the gradient at each point is tangent to the path. Only the transition vector and the energy gradients are needed to construct the path. The resulting path is continuous, differentiable and piecewise quadratic. In the limit of small step size, the present algorithm is shown to take a step with the correct tangent vector and curvature vector; hence, it is a second order algorithm. The method has been tested on the following reactions: HCN→CNH, SiH2+H2→SiH4, CH4+H→CH3+H2, F−+CH3F→FCH3+F−, and C2H5F→C2H4+HF. Reaction paths calculated with a step size of 0.4 a.u. are almost identical to those computed with a step size of 0.1 a.u. or smaller.

An improved algorithm for reaction path following

Our previous algorithm for following reaction paths downhill (J. Chem. Phys. 1989, 90, 2154), has been extended to use mass-weighted internal coordinates. Points on the reaction path are round by constrained optimizations involving the internal degrees or freedom or the molecule. The points are optimized so that the segment or the reaction path between any two adjacent points is described by an arc or a circle in mass-weighted internal coordinates, and so that the gradients (in mass-weighted internals) at the end points or the arc are tangent to the path. The algorithm has the correct tangent vector and curvature vectors in the limit or small step size but requires only the transition vector and the energy gradients; the resulting path is continuous, differentiable, and piecewise quadratic

Reaction Path Following in Mass-Weighted Internal Coordinates

The primary processes in methane combustion include hydrogen abstraction by radicals to form CH{sub 3}. Ab initio molecular orbital calculations have been used to study three important reactions contributing to the formation of the methyl radical: CH{sub 4} + X {yields} CH{sub 3} + HX, where X = OH, H, and {sup 3}O. Optimized geometries and harmonic vibrational frequencies have been calculated for all reactants, transition states, and products at the HF/6-31G** and UMP2/6-31G** levels. Barriers and heats of reaction have been estimated by fourth-order Moeller-Plesset perturbation theory with spin projection (PMP4(SDTQ)) using the 6-311G** basis set.

Ab initio study of the reactions between methane and OH, H, and 3O

A detailed study of the potential energy surfaces for methyl radical plus ethylene and methyl radical plus formaldehyde has been carried out with the 3-21G and 6-31G* basis sets at the Hartree-Fock level. Heats of reaction and barrier heights have been computed with the Moeller-Plesset perturbation theory up to the fourth order with and without annihilation of spin contamination. The results of the calculations indicate the formation of an early transition state with reactant-like structure for both reactions. In the case of methyl radical plus ethylene, spin annihilation lowers the barrier height by 7 kcal/mol, while in the reaction between methyl radical and formaldehyde the barrier is lowered by 6 kcal/mol when spin annihilation is considered. A comparison between the calculated and experimental values of the barrier height for the methyl addition to ethylene (6.8 kcal/mol vs 7.9 kcal/mol) and formaldehyde (6.3 kcal/mol vs. 6.8 kcal/mol) indicates very good agreement between theory and experiment.

Ab initio study of the addition reaction of the methyl radical to ethylene and formaldehyde

Analytical gradients were used to optimize the polarization function exponents in the 6-31G(d) and 6-31G(d, p) basis sets for the reactants, transition structures and products in the reactions H2SO → HSOH and CH3SH → CH2SH2. The optimizedd exponents on the heavy atoms change by ±10% in the course of the reactions and depend on the bonding of the heavy atoms. Thep exponents on the hydrogens change by as much as a factor of 5 and depend on the element to which the hydrogen is bonded and its valency. The effect of exponent optimization on the relative energies is small (±3 kcal/mol). With the 6-31G(d, p) basis set, optimization of the polarization exponents can make some of the bonds significantly more polar, as judged by the Mulliken charges.

Carlos Gonzalez

Papers

An improved algorithm for reaction path following

Reaction Path Following in Mass-Weighted Internal Coordinates

Ab initio study of the reactions between methane and OH, H, and 3O

Ab initio study of the addition reaction of the methyl radical to ethylene and formaldehyde

Gradient optimization of polarization exponents in ab initio MO calculations on H2SO→HSOH and CH3SH→CH2SH2