Molecular mechanics and the camseq processor

Potenzone, Rudolph; Cavicchi, Elizabeth; Weintraub, Herschel J. R.; Hopfinger, A. J.

doi:10.1016/0097-8485(77)85009-2

Cited by 63 publications

(18 citation statements)

References 9 publications

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“…The most likely explanation for the limited matching was that molecular dynamics permitted variations in bond lengths and especially bond angles that CONGEN could not permit, and this greatly increased the number of possible conformation^.^^'^^ The rms fluctuations in bond angles computed from trajectory samples every 0.978 ps were 4.6" at 500 K, 5.8" at 800 K, and 7.8" at 1500 K. One peculiar aspect of the distribution of matches was the improvement seen when the temperature reaches 1500 K. The higher temperatures appear to cover conformational space more thoroughly and thereby approached closer to the CONGEN generated conformations. Table VI shows the converse comparison, namely how close each dynamics conformation was to some CONGEN-generated conformation.…”

Section: Table IV Summary Of Torsion Angle Histograms"mentioning

confidence: 99%

Conformational sampling using high‐temperature molecular dynamics

1990

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High-temperature molecular dynamics as a method for conformational search was explored on the antigen combining site of McPC 603, a phosphorylcholine binding immunoglobulin. Simulations at temperatures of 500, 800, and 1500 K were run for 111.5, 101.7, and 76.3 ps, respectively. The effectiveness of the search was assessed using a variety of methods. For the shorter hypervariable loops, molecular dynamics explored an appreciable fraction of the conformational space as evidenced by a comparison to a simple theoretical model of the size of the conformational space. However, for the longer loops and the antigen combining site as a whole, the simulation times were too short for a complete search. The simulations at 500 and 800 K both generated conformations that minimized to energies 200 kcal/mole lower than the crystal structure. However, the 1500 K simulation produced higher energy structures, even after minimization; in addition, this highest temperature run had many cis-trans peptide isomerizations. This suggests that 1500 K is too high a temperature for unconstrained conformational sampling. Comparison of the results of high temperature molecular dynamics with a direct conformational search method, [R. E. Bruccoleri & M. Karplus (1987) Biopolymers 26, 137-168]. showed that the two methods did not overlap much in conformational space. Simple geometric measures of the conformational space indicated that the direct method covered more space than molecular dynamics at the lower temperature, but not at 1500 K. The results suggest that high-temperature molecular dynamics can aid in conformational searches.

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Section: Table IV Summary Of Torsion Angle Histograms"mentioning

confidence: 99%

Conformational sampling using high‐temperature molecular dynamics

1990

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“…The conformational calculations for the silane molecule was carried out using our molecular mechanics software system LCHfAB (formerly Camseq-lI) (24). The built-in potential energy function between an atom pair i,j is represented in the following form: where the atomic polarizability a for Silicon is taken from Benderson et al (26).…”

Section: Conformational Energy Calculationsmentioning

confidence: 99%

The structure of an aminosilane coupling agent in aqueous solutions and partially cured solids

Ishida

Naviroj

Tripathy

et al. 1982

J. Polym. Sci. Polym. Phys. Ed.

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The molecular structures of partially cured polyaminopropylsilsesquioxane and aminopropyltriethoxysilane in water have been studied using Fourier‐transform infrared, laser Raman, and quasielastic laser light‐scattering spectroscopy. A multiply hydrogen‐bonded structure is proposed for the intramolecularly interacting amine and silanol groups on the basis of isotope exchange experiment and conformational energy calculations. Conformational restrictions are rather low for the proposed structure, which is thus suitable for the partially cured solid where there are slight perturbations by the surrounding amine and silanol groups. The O.…N distance was experimentally determined to be in the range 2.70–2.67 Å and estimated theoretically as 2.49–2.45 Å. The aminosilane in very dilute solution is found to be mostly monomeric. The isolated monomer‐oligomer transition lies around 0.15% by weight and this transition influences the amount of silane uptake by glass fibers. It is also proposed that this phenomenon may be general for surface treatments by silane coupling agents. Hydrolyzed aminosilane oligomers exist in part as submicron aggregates which can be broken up by the addition of an alcohol. The neutralized aminosilane hydrolyzes very slowly although it dissolves in water instantaneously. Micelle formation is also proposed.

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“…In addition, CIS has data referral capability (5) and a data analysis software system (6). It can be thought of as having five main areas.…”

Section: Structure Of Cismentioning

confidence: 99%

Environmental Uses of the NIH-EPA Chemical Information System

Milne

Fisk

Heller

et al. 1982

Science

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A publicly accessible computer system for chemical information has been developed jointly by a number of agencies of the U.S. government. The system contains spectroscopic, crystallographic, toxicological, and regulatory data for more than 200,000 chemicals. The entire data base may be searched for a particular chemical structure or substructure, whose properties may then be retrieved. Alternatively, searching with numeric properties data is possible, permitting the identification of chemicals. Access is by local telephone call, and the system is used on a fee-for-service basis by organizations in over 20 countries. An important application of the system is to problems of chemical pollution.

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Molecular mechanics and the camseq processor

Cited by 63 publications

References 9 publications

Conformational sampling using high‐temperature molecular dynamics

Conformational sampling using high‐temperature molecular dynamics

The structure of an aminosilane coupling agent in aqueous solutions and partially cured solids

Environmental Uses of the NIH-EPA Chemical Information System

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