Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P. Comparisons are made with experimental thermodynamic and structural data including the recent neutron diffraction results of Thiessen and Narten. The computed densities and potential energies are in reasonable accord with experiment except for the original BF model, which yields an 18% overestimate of the density and poor structural results. The TIPS2 and TIP4P potentials yield oxygen–oxygen partial structure functions in good agreement with the neutron diffraction results. The accord with the experimental OH and HH partial structure functions is poorer; however, the computed results for these functions are similar for all the potential functions. Consequently, the discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons are also made for self‐diffusion coefficients obtained from molecular dynamics simulations. Overall, the SPC, ST2, TIPS2, and TIP4P models give reasonable structural and thermodynamic descriptions of liquid water and they should be useful in simulations of aqueous solutions. The simplicity of the SPC, TIPS2, and TIP4P functions is also attractive from a computational standpoint.

Comparison of simple potential functions for simulating liquid water

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

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

Previous attempts to combine Hartree–Fock theory with local density‐functional theory have been unsuccessful in applications to molecular bonding. We derive a new coupling of these two theories that maintains their simplicity and computational efficiency, and yet greatly improves their predictive power. Very encouraging results of tests on atomization energies, ionization potentials, and proton affinities are reported, and the potential for future development is discussed.

A New Mixing of Hartree-Fock and Local Density-Functional Theories

Polarization functions are added in two steps to a split-valence extended gaussian basis set: d-type gaussians on the first row atoms C. N, O and F and p-type gaussians on hydrogen. The same d-exponent of 0.8 is found to be satisfactory for these four atoms and the hydrogen p-exponent of 1.1 is adequate in their hydrides. The energy lowering due to d functions is found to depend on the local symmetry around the heavy atom. For the particular basis used, the energy lowerings due to d functions for various environments around the heavy atom are tabulated. These bases are then applied to a set of molecules containing up to two heavy atoms to obtain their LCAO-MO-SCF energies. The mean absolute deviation between theory and experiment (where available) for heats of hydrogenation of closed shell species with two non-hydrogen atoms is 4 kcal/mole for the basis set with full polarization. Estimates of hydrogenation energy errors at the Hartree-Fock limit, based on available calculations, are given.

The influence of polarization functions on molecular orbital hydrogenation energies

In preceding papers the energies associated with the internal rotations in the sugar–phosphate–sugar complex were described with an analytical potential consisting of a Lennard-Jones 6–12 term and an intrinsic torsional term and representing the best fit to a large number of energies computed with a quantum mechanical ab initio technique. The complex considered there (of 37 atoms and with the chemical formula C10H18O8P) is repesentative of deoxyribonucleic acids. In this paper we apply our potential to evaluating the intramolecular energies of the 39-atom complex C10H18O10P, representative of the ribonucleic acids. The potential energies for the internal rotations (considered independent from one another) and the energy maps for rotations about consecutive bonds of the backbone chain are critically compared, both with those obtained for the deoxy system and with those obtained from different theoretical approaches as available from literature. It is shown that, at least for certain combinations of the internal rotation angles, the choice of the starting geometry for the sugarphosphate–sugar molecule (bond lengths and valence angles) strongly affects the value of the computed energy. If a proper geometry is used, very low energies are predicted by our potential in correspondence of the sets of torsional angles found in various RNAs by x-ray crystallography.

Conformational studies on polynucleotide chains. IV. Backbone structure of ribonucleic acids.

We have performed detailed ab initio SCF calculations on the intermolecular interaction energies for one Na+ ion and one water molecule with two molecular fragments, one exemplifying a phospholipid (PL) head (PLHD) and the other, a phospholipid tail (PLTL). A 6-12-1 atom-atom pair potential for the interaction of a Na+ ion and water with a lysophosphatidyl-ethanolamine (LPEA) was derived from these results by a fitting procedure. This fitted potential was used to obtain isoenergy maps that provide energy profiles of the Na+ ion and the water around the phospholipids. The interaction of the Na+ ion with PL, as well as the interaction of water with the PL, can be visualized from these maps, which, as expected, show regions of hydrophilicity and hydrophobicity for the water and indicate a very strong binding site for the Na+ ion on the phosphate. It appears to be a stationary site that would limit the Na+ ion mobility. This binding site is located near the double-bonded oxygen atom of the phosphate group; its binding energy for Na+ is 67 kcal/mol. On the other hand the NH+ group of PLHD ahows strong electrostatic repulsion of Na+ while interacting with water with a binding energy of 13 kcal/mol. This potential energy well region for water is separated from another of similar depth near the phosphate by a barrier and both regions are expected to act as binding sites for water.

Interaction of phospholipids (Lysophosphatidylethanolamines) with water and sodium cation

http://link.springer.com/content/pdf/10.1007/978-94-011-3032-5_21.pdf

Molecular Dynamics Simulations with ab initio Interaction Potentials

Our interest in parallel processing systems has been motivated by the need to solve large scale computational problems occuring in theoretical chemistry, biophysics, and more recently in engineering. We have been experimenting with a loosely coupled system, that uses a master processor to control a group of independent slave processors. This architecture was designed to meet the following objectives: the initial system 

1)

should be classifiable as a “supercomputer”,




2)

be easily extended to higher computing speeds,




3)

be flexible and fault tolerant,




4)

permit easy migration of large codes to parallel execution




5)

be relatively inexpensive.

Solution of Large Scale Engineering Problems Using a Loosely Coupled Array of Processors

http://link.springer.com/content/pdf/10.1007/978-94-009-3117-6_12.pdf

Enrico Clementi

Papers

Conformational studies on polynucleotide chains. IV. Backbone structure of ribonucleic acids.

Interaction of phospholipids (Lysophosphatidylethanolamines) with water and sodium cation

Molecular Dynamics Simulations with ab initio Interaction Potentials

Solution of Large Scale Engineering Problems Using a Loosely Coupled Array of Processors

Electronic Devices from Molecules: Overview, Prospects and Theoretical Chemistry