𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Conformational properties of penicillins: Quantum chemical calculations and molecular dynamics simulations of benzylpenicillin

✍ Scribed by Natalia Díaz; Dimas Suárez; Tomás L. Sordo

Publisher
John Wiley and Sons
Year
2003
Tongue
English
Weight
318 KB
Volume
24
Category
Article
ISSN
0192-8651

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

Herein, we present theoretical results on the conformational properties of benzylpenicillin, which are characterized by means of quantum chemical calculations (MP2/6‐31G* and B3LYP/6‐31G*) and classical molecular dynamics simulations (5 ns) both in the gas phase and in aqueous solution. In the gas phase, the benzylpenicillin conformer in which the thiazolidine ring has the carboxylate group oriented axially is the most favored one. Both intramolecular CH · · · O and dispersion interactions contribute to stabilize the axial conformer with respect to the equatorial one. In aqueous solution, a molecular dynamics simulation predicts a relative population of the axial:equatorial conformers of 0.70:0.30 in consonance with NMR experimental data. Overall, the quantum chemical calculations as well as the simulations give insight into substituent effects, the conformational dynamics of benzylpenicillin, the frequency of ring‐puckering motions, and the correlation of side chain and ring‐puckering motions. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1864–1873, 2003

📜 SIMILAR VOLUMES

Molecular Dynamics Simulations of Cellul
Molecular Dynamics Simulations of Cellulose Oligomers: Conformational Analysis
✍ Séverine Queyroy; Florian Müller-Plathe; David Brown 📂 Article 📅 2004 🏛 John Wiley and Sons 🌐 English ⚖ 345 KB

## Abstract **Summary:** The results of classical molecular simulations of cellulose oligomers are presented here. The conformations of the chains in the high temperature melt, room temperature quenched melt and gas phase are compared with respect to various geometrical parameters including square

Calculations of a list of neighbors in M
Calculations of a list of neighbors in Molecular Dynamics simulations
✍ Virginia Yip; Ron Elber 📂 Article 📅 1989 🏛 John Wiley and Sons 🌐 English ⚖ 650 KB

The algorithm is based on a grid search and on partitioning of the atoms into boxes rather than on calculations of distances. The effort associated with the generation of the box list grows only linearly with the number of atoms. The algorithm is particularly advantageous for solvated systems. Test

Dynamic structures of phosphodiesterase-
Dynamic structures of phosphodiesterase-5 active site by combined molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations
✍ Ying Xiong; Hai-Ting Lu; Chang-Guo Zhan 📂 Article 📅 2008 🏛 John Wiley and Sons 🌐 English ⚖ 511 KB

## Abstract Various quantum mechanical/molecular mechanical (QM/MM) geometry optimizations starting from an x‐ray crystal structure and from the snapshot structures of constrained molecular dynamics (MD) simulations have been performed to characterize two dynamically stable active site structures o