Journal of Computational Chemistry

doi: 10.1002/jcc.540171601pmid: N/A

Juffer, A. H.; Argos, P.; de Vlieg, J.

doi: 10.1002/(SICI)1096-987X(199612)17:16<1783::AID-JCC1>3.0.CO;2-Jpmid: N/A

A computer model has been developed to simulate the adsorption of proteins onto charged surfaces displaying an electric double layer. Coadsorption of ions onto the surface is included by means of explicit ions. Only electrostatic interactions are considered. Monte Carlo simulations in the canonical ensemble of the enzyme cutinase and 15 variants (modeled from the X‐ray tertiary structure of the wild‐type) were performed. Adsorption free energies for all variants were calculated by the thermodynamic integration method. Distributions of the electric moment and the vector pointing toward the protein active site and parallel to its central β‐sheet were determined to elucidate the mean orientation of the protein with respect to the surface as a function of its distance from the surface. It was found that the free energy of adsorption varied linearly with the total charge of the protein, while the electric moment (dipole moment) had a second‐order but significant effect. Though an increase of the electric moment generally resulted in a slightly increased affinity of the protein for the surface, close to the surface the mean force acting on the protein clearly varied linearly with the strength of the electric moment, such that a clear correlation between the latter and the protein orientation with respect to the surface could be established. Wild‐type cutinase displayed the highest affinity for the charged surface amongst all proteins having the same total charge, even though it did not have the largest electric moment. © 1996 by John Wiley & Sons, Inc.

Kovács, Attila; Kolossváry, István; Csonka, Gábor I.; Hargittai, István

doi: 10.1002/(SICI)1096-987X(199612)17:16<1804::AID-JCC2>3.0.CO;2-Rpmid: N/A

The conformational behavior of 2‐trifluoromethylphenol was investigated by means of theoretical calculations. Four characteristic structures have been found on the potential energy hypersurface of the compound: anti form (local minimum), in which the hydroxy hydrogen points away from the trifluoromethyl group; and three syn forms (the hydrogen points towards the trifluoromethyl group), with different trifluoromethyl torsions (global minimum, one low and another one high lying saddle‐point). The geometry of these conformers were optimized by ab initio calculations using 6‐31G** basis set. The effects of electron correlation were investigated by MP2 and various DFT methods. To investigate the intramolecular interaction in the syn forms, the electron density distribution was calculated at the MP2 level of theory. In the structure corresponding to the global minimum at the MP2/6‐31G** level a bond critical point was found in Bader's sense between the hydroxy hydrogen and a fluorine of the trifluoromethyl group indicating hydrogen bonding interaction. The length of the hydrogen bond, 1.98 Å, corresponds to medium strength interaction. The O(SINGLE BOND)H bond is slightly twisted and the C(SINGLE BOND)F bond, interacting with it, is considerably twisted out of the plane of the benzene ring to the same side of the ring. The most pronounced geometrical consequence of the hydrogen bond is the 0.02‐Å lengthening of the C(SINGLE BOND)F bond participating in its formation. All the other geometrical changes in 2‐trifluoromethylphenol, as compared with trifluoromethylbenzene and phenol, are also consistent with the phenomenon of resonance‐assisted hydrogen bonding. © 1996 by John Wiley & Sons, Inc.

Ionova, Irina V.; Carter, Emily A.

doi: 10.1002/(SICI)1096-987X(199612)17:16<1836::AID-JCC4>3.0.CO;2-Opmid: N/A

Based on Banach's principle, we formally obtain possible choices for an error vector in the direct inversion in the iterative subspace (DIIS) method. These choices not only include all previously proposed error vectors, but also a new type of error vector which is computationally efficient and applicable to much wider range of problems. The error vector analysis also reveals a strong connection between DIIS and damping, thus adding to understanding of the reasons behind DIIS's effect on convergence. We illustrate our conclusions with several examples. © 1996 by John Wiley & Sons, Inc.

Hunt, Nathan G.; Cohen, Fred E.

doi: 10.1002/(SICI)1096-987X(199612)17:16<1857::AID-JCC6>3.0.CO;2-Mpmid: N/A

We describe novel lookup tables for the rapid calculation of interatomic interactions. The tables have nonuniform distributions of bin widths tailored to minimize numerical error and maximize computational speed. Since interaction energies are precalculated, computer time requirements are essentially independent of the form of the potential function used. In test calculations using the AMBER force field and an internal coordinate Monte Carlo algorithm, the lookup table runs 15% faster than direct calculation of nonbonded interactions. The method is more advantageous for more complicated energy functions. As an example of a more complicated potential function, we have tested a pairwise approximation to accessible surface area. In this case, the use of the lookup table results in a speedup of a factor of two. The method is straightforward to implement and should be widely applicable. © 1996 by John Wiley & Sons, Inc.