Crystal Water Dynamics of Guanosine Dihydrate: Analysis of Atomic Displacement Parameters, Time Profile of Hydrogen-Bonding Probability, and Translocation of Water by MD Simulation
| Autor: | Shigetaka Yoneda, Yoko Sugawara, Hisako Urabe |
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| Rok vydání: | 2004 |
| Předmět: |
Models
Molecular Time Factors Guanosine Hydrogen bond Electric potential energy Water Hydrogen Bonding Crystallography X-Ray Molecular physics Surfaces Coatings and Films Crystal Kinetics chemistry.chemical_compound Crystallography Molecular dynamics Models Chemical chemistry Coincident Orientation (geometry) Materials Chemistry Molecule Computer Simulation Physical and Theoretical Chemistry Crystallization |
| Zdroj: | The Journal of Physical Chemistry B. 109:1304-1312 |
| ISSN: | 1520-5207 1520-6106 |
| DOI: | 10.1021/jp046258j |
| Popis: | The dynamics of crystal water molecules of guanosine dihydrate are investigated in detail by molecular dynamics (MD) simulation. A 2 ns simulation is performed using a periodic boundary box composed of 4 x 5 x 8 crystallographic unit cells and using the particle-mesh Ewald method for calculation of electrostatic energy. The simulated average atomic positions and atomic displacement parameters are remarkably coincident with the experimental values determined by X-ray analysis, confirming the high accuracy of this simulation. The dynamics of crystal water are analyzed in terms of atomic displacement parameters, orientation vectors, order parameters, self-correlation functions of the orientation vectors, time profiles of hydrogen-bonding probability, and translocations. The simulation clarifies that the average structure is composed of various stable and transient structures of the molecules. The simulated guanosine crystal forms a layered structure, with four water sites per asymmetric unit, classified as either interlayer water or intralayer water. From a detailed analysis of the translocations of water molecules in the simulation, columns of intralayer water molecules along the c axis appear to represent a pathway for hydration and dehydration by a kind of molecular valve mechanism. |
| Databáze: | OpenAIRE |
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