Journal of Computational Chemistry

Forster, Mark J.

doi: 10.1002/jcc.540120303pmid: N/A

Various algorithms for solving the Solomon equations describing nuclear Overhauser effects (nOes) in NMR spectroscopy have been compared. The applicability of the eigenvalue/eigenvector and the numerical integration approaches have been investigated. The eigenvalue/eigenvector approach is not a computationally efficient means of simulating nOe experiments in which a saturating radiofrequency field is applied during the time course. For experiments in which nOes develop in the absence of an RF field, this approach should only be used in simulating a full NOESY spectrum. Integration schemes have been found to be more efficient at simulating nOe experiments in which the nOe evolves in the presence of a saturating field, at simulating a partial set of initial perturbation experiments and at simulating a few rows or columns in a NOESY spectrum. Various integration schemes were applied to a two‐spin system for which an analytic solution is available and to a model B‐DNA oligonucleotide hexamer. The previously unused Taylor series algorithm was found to be superior to the Euler, midpoint, and fourth‐order Runge–Kutta methods with regard to integration accuracy/computation time. An adaptive step size control routine for the Taylor series integration scheme was developed. Integration schemes can be speeded up in a simple fashion by introducing a distance cutoff for the dipolar interaction. Using a cutoff of 8 Å the Taylor series algorithm was able to compute the NOESY spectrum more rapidly than the eigenvalue/eigenvector algorithm for large spin systems at short mixing times. At longer mixing times the eigenvalue/eigenvector approach becomes the more efficient scheme.

Bonaccorsi, Rosanna; Cammi, Roberto; Tomasi, Jacopo

doi: 10.1002/jcc.540120304pmid: N/A

We present several variants of methods for the automatic search of optimum geometries of solutes via ab initio SCF procedures. The physical meaning of geometry optimization in solution is discussed. Advantages and disadvantages of the different variants are shown making use of calculations on the HF dimer with different basis sets, supplemented by information on the computational times. Suggestions for the most convenient strategies (which in part depend on the nature of the solute) are also done.

Zimmermann, Karel

doi: 10.1002/jcc.540120305pmid: N/A

A molecular mechanics energy minimizer is presented whose main features are the “floating blocks” and “isles” option, the “a‐NOE” distance inequality constraints and the variable storage first derivative minimization method. The program possibilities are illustrated by examples of molecular docking, energy barrier estimation, modeling of infinite structures, and DNA bending simulations.

Stewart, James J. P.

doi: 10.1002/jcc.540120306pmid: N/A

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.

Wilson, Stephen R.; Cui, Weili; Moskowitz, Jules W.; Schmidt, Kevin E.

doi: 10.1002/jcc.540120307pmid: N/A

We describe in this article our solution to the global minimum problem which uses the simulated annealing algorithm of Kirkpatrick. This method is a Metropolis (e‐ΔE/kT) Monte Carlo sampling of conformation space with simultaneous constraint of the search by lowering the temperature T so that the search converges on the global minimum. The Anneal‐Conformer program has been extensively tested with peptides and organic molecules using either the Amber or MM2 force fields. A history file of the simulated annealing process allows reconstruction of the random walk in conformation space for subsequent examination. Thus plots of distance and dihedral angle changes during the search for the global minimum can be examined to deduce molecular shape and flexibility. A separate program Conf‐Gen reads the history file and extracts all low energy conformations visited during the run.

Davis, Larry P.; Burggraf, Larry W.; Storch, Donn M.

doi: 10.1002/jcc.540120308pmid: N/A

The AM1 semiempirical molecular orbital method has been used to calculate successive heats of hydration of small anions, including hydride, hydroxide, and the halogen ions, for cluster sizes up to 11 water molecules surrounding the central anion. Heats of hydration agree with available experimental data to within a few kcal/mol. Structures, however, do not always agree well with available ab initio calculations on clusters with one or two water molecules. The results indicate that the AM1 semiempirical technique applied to finite‐sized clusters must be used with caution in understanding how hydration affects the chemical reactions of anions.

Kitao, Akio; Gō, Nobuhiro

doi: 10.1002/jcc.540120309pmid: N/A

Effects of different treatments of the degrees of freedom of bond length stretching and bond angle bending in computational analysis of conformational dynamics of proteins and polypeptides are assessed. More specifically, the normal mode analysis of conformational dynamics of α‐helix of deca‐alanine has been carried out both in the dihedral angle space (DAS) and in the Cartesian coordinate space (CCS). Almost perfect one‐to‐one correspondence has been found between normal modes in the CCS with frequencies less than 128 cm−1 and those in the DAS with frequencies less than 164 cm−1. Patterns of atomic displacements in the corresponding modes are very similar. This indicates that the effects of fixing degrees of freedom of bond length stretching and bond angle bending on the very‐low‐frequency normal modes in the CCS with frequencies less than 128 cm−1 are almost solely to increase the frequencies by about 20%. The conclusion indicates that the different treatment of these degree does not lead to qualitatively different results as long as low‐frequency motions are concerned. Based on the results of calculation, mechanical property of the α‐helix of deca‐alanine is discussed.

Mullay, John

doi: 10.1002/jcc.540120310pmid: N/A

A previously developed method for calculating atomic charge in neutral molecules is modified so as to account for charged molecular species. The method is based on the orbital electronegativity (EN) concept and utilizes an EN equalization principal. Since only one linear equation is required per bond in the molecule, the scheme is extremely simple to use and thus is readily applicable to larger molecules of interest to biochemistry. Atom charge results are compared to ab initio calculations as well as experimental data from NMR and X‐ray diffraction studies. It is shown that the method compares very well even with higher level theoretical methods for a variety of charged molecules including alanine and protonated adenine. It is also shown that NMR chemical shift data for charged amino acids are correlated quite well with atomic charges from the present method. In addition charges obtained from X‐ray diffraction data for both ionic alanine and 2′‐deoxycytidine‐5′‐monophosphate are also reproduced very well.