Journal of Computational Chemistry

Mazur, Alexey K.

doi: 10.1002/(SICI)1096-987X(199708)18:11<1354::AID-JCC3>3.0.CO;2-Kpmid: N/A

Conventional molecular dynamics simulations of macromolecules require long computational times because the most interesting motions are very slow compared to the fast oscillations of bond lengths and bond angles that limit the integration time step. Simulation of dynamics in the space of internal coordinates, that is, with bond lengths, bond angles, and torsions as independent variables, gives a theoretical possibility of eliminating all uninteresting fast degrees of freedom from the system. This article presents a new method for internal coordinate molecular dynamics simulations of macromolecules. Equations of motion are derived that are applicable to branched chain molecules with any number of internal degrees of freedom. Equations use the canonical variables and they are much simpler than existing analogs. In the numerical tests the internal coordinate dynamics are compared with the traditional Cartesian coordinate molecular dynamics in simulations of a 56 residue globular protein. For the first time it was possible to compare the two alternative methods on identical molecular models in conventional quality tests. It is shown that the traditional and internal coordinate dynamics require the same time step size for the same accuracy and that in the standard geometry approximation of amino acids, that is, with fixed bond lengths, bond angles, and rigid aromatic groups, the characteristic step size is 4 fs, which is 2 times higher than with fixed bond lengths only. The step size can be increased up to 11 fs when rotation of hydrogen atoms is suppressed. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 1354–1364, 1997

Chen, Zhuo‐Min; Çağin, Tahir; Goddard, William A.

doi: 10.1002/(SICI)1096-987X(199708)18:11<1365::AID-JCC4>3.0.CO;2-Jpmid: N/A

This work considers ways to increase calculation speed for Ewald crystal summations in cases where standard combination rules do not apply. This also increases speed of free‐energy perturbation theory calculations. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 1365–1370, 1997

Liang, Guyan; Chen, Xiannong; Dustman, J. A.; Lewin, Anita H.; Bowen, J. Phillip

doi: 10.1002/(SICI)1096-987X(199708)18:11<1371::AID-JCC5>3.0.CO;2-Ipmid: N/A

The geometries and vibrational frequencies of 11 training molecules containing the ammonium ion moiety were calculated at the MP2/6‐31+G* level of theory. Various torsional energy profiles were also calculated using this basis set. From those ab initio calculations, a molecular mechanics (MM3) force field was developed using our Parameter Analysis and Refinement Toolkit System (PARTS). Using this set of parameters, the MM3 force field was found to well reproduce the molecular geometries and vibrational spectra for the all training molecules. CPU time was reduced from days to seconds. The availability of this new force field dramatically increases the feasibility of the computer‐assisted drug design involving ammonium and protonated amino groups. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 1371–1391, 1997

Freeman, Fillmore; Lee, Choonsun; Hehre, Warren J.; Po, Henry N.

doi: 10.1002/(SICI)1096-987X(199708)18:11<1392::AID-JCC6>3.0.CO;2-Gpmid: N/A

Optimized geometries and total energies for 3,4‐dihydro‐1,2‐dioxin (1), 3,6‐dihydro‐1,2‐dioxin (2), 4H‐1,3‐dioxin (1,3‐diox‐4‐ene, 3), and 2,3‐dihydro‐1,4‐dioxin (1,4‐dioxene, 4) were calculated using ab initio 3‐21G, 6‐31G*, and MP2/6‐31G*//6‐31G* methods. The half‐chair conformers of 1 (C1), 2 (C2), 3 (C1), and 4 (C2) are more stable than their respective planar structures (1 (Cs), 2 (C2v), 3 (Cs), and 4 (C2v)). Among the four isomers 1–4, the half‐chair conformer of 3 is the most stable. It is 53.1, 54.6, and 3.4 kcal mol−1 more stable than 1, 2, and 4, respectively. The largest energy difference (19.0 kcal mol−1) is observed between the half‐chair and planar conformers of 2. The boat conformers of 2 and 4 are less stable than their respective half‐chair conformers, but are more stable than their planar structures. Hyperconjugative orbital interactions (anomeric effects) contribute to the greater stability of 3(nO(3) →σ*C(2)—O(1), nO(3)→σ* C(2)—H ax,n O(3)→σ* C(2)—H ax ) and of 4 (nO(1)→ σ* C(2)—H ax). The ab initio calculated structural features of the half‐chair conformations of the dihydrodioxins 1–4 are compared with the half‐chair conformations of cyclohexene and the chair conformations of cyclohexane, oxacyclohexane (tetrahydropyran), 1,2‐dioxacyclohexane (1,2‐dioxane), 1,3‐dioxacyclohexane (1,3‐dioxane), and 1,4‐dioxacyclohexane (1,4‐dioxane) © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 1392–1406, 1997

Magela E Silva, Geraldo; Acioli, Paulo Hora; Pedroza, Antonio Carlos

doi: 10.1002/(SICI)1096-987X(199708)18:11<1407::AID-JCC7>3.0.CO;2-Ppmid: N/A

The electronic correlation energy of diatomic molecules and heavy atoms is estimated using a back propagation neural network approach. The supervised learning is accomplished using known exact results of the electronic correlation energy. The recall rate, that is, the performance of the net in recognizing the training set, is about 96%. The correctness of values given to the test set and prediction rate is at the 90% level. We generate tables for the electronic correlation energy of several diatomic molecules and all the neutral atoms up to radon (Rn). © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 1407–1414, 1997

Möhle, Kerstin; Gußmann, Martin; Hofmann, Hans‐Jörg

doi: 10.1002/(SICI)1096-987X(199708)18:11<1415::AID-JCC8>3.0.CO;2-Opmid: N/A

A systematic quantum chemical study on the structure and stability of the major types of β‐turn structures in peptides and proteins was performed at different levels of ab initio MO theory (MP2/6‐31G*, HF/6‐31G*, HF/3‐21G) considering model turns of the general type Ac(SINGLE BOND)Xaa(SINGLE BOND)Yaa(SINGLE BOND)NHCH3 with the amino acids glycine, l‐ and d‐alanine, aminoisobutyric acid, and l‐proline. The influence of correlation effects, zero‐point vibration energies, thermal energies, and entropies on the turn formation was examined. Solvent effects on the turn stabilities were estimated employing quantum chemical continuum approaches (Onsager's self‐consistent reaction field and Tomasi's polarizable continuum models). The results provide insight into the geometry and stability relations between the various β‐turn subtypes. They show some characteristic deviations from the widely accepted standard rotation angles of β turns. The stability order of the β‐turn subtypes depends strongly on the amino acid type. Thus, the replacement of l‐amino acids in the two conformation‐determining turn positions by d‐ or α,α‐disubstituted amino acid residues generally increases the turn formation tendency and can be used to favor distinct β‐turn subtypes in peptide and protein design. The β‐turn subtype preferences, depending on amino acid structure modifications, can be well illustrated by molecular dynamics simulations in the gas phase and in aqueous solution. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 1415–1430, 1997