This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To
Urea: An ab initio and force field study of the gas and solid phases
โ Scribed by H. Sun; P. W.-C. Kung
- Publisher
- John Wiley and Sons
- Year
- 2005
- Tongue
- English
- Weight
- 90 KB
- Volume
- 26
- Category
- Article
- ISSN
- 0192-8651
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โฆ Synopsis
Abstract
We have studied the gaseous and solid phases of urea using both quantum mechanics calculation and force field simulation methods. Our ab initio calculations confirmed experimental observations that urea structure is planar in the crystal, but nonplanar in the gas phase. Based on electron structure analysis, we suggest that the significant difference between these two structures in different environments can be qualitatively explained by two resonance structures. The planar structure is more polarized than the nonplanar one, and the former is stabilized in the solid phases due to strong electrostatic interactions. We found classical force field method is incapable to represent such strong polarization effect. Using molecular dynamics simulations with a force field optimized for condensed phases, we calculated the crystalline structures of urea in the temperature range of 12 to 293 K. The densities as well as cell parameters are within 2% deviation from the experimental data in the temperature range. ยฉ 2004 Wiley Periodicals, Inc. J Comput Chem 26: 169โ174, 2005
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