Solvent Dependence of Conformational Distribution, Molecular Geometry, and Electronic Structure in Adenosine
2009 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 4, 1012-1021 p.Article in journal (Refereed) Published
Solvation dynamics of adenosine in water and chloroform solvents under ambient conditions has been investigated using both force-field molecular dynamics (MD) and first-principles Car-Parrinello molecular dynamics (CPMD) calculations. First, the solvent dependence of the equilibria between anti-syn forms, C((3'))-endo-C((2'))-endo conformations, and carbinol group rotamers has been discussed from MD calculations. We find that in both the solvents the adenosine molecule can remain either in anti or syn conformations. But, the anti-syn interconversion occurs relatively faster in water solvent than in chloroform solvent. Because of the relatively larger time scale for the interconversion, anti and syn conformational states of adenosine are studied separately in water and chloroform solvents using CPMD calculations. The dipole moments calculated from CPMD and MD calculations for adenosine in water are significantly larger than in chloroform solvent. On the basis of the CPMD calculations, the syn form of adenosine in water has a larger dipole moment than the anti form. Moreover, the molecular geometry of anti and syn forms of adenosine in these two solvents is reported. We report a remarkable solvent effect on the geometry of the anti form of the adenosine, which is attributed to differences in the intermolecular and intramolecular hydrogen-bonding, stabilization. We also report the solvent effect on the frontier Kohn-Sham orbitals and energy gaps for anti-syn conformational states. Finally, we report the solvation shell structure of adenosine in both the solvents, and we find that the solvent-solute interaction is site-specific in the case of water while in chloroform solvent the interaction is globular isotropic in nature.
Place, publisher, year, edition, pages
2009. Vol. 113, no 4, 1012-1021 p.
proton-magnetic-resonance, crystal-structure, protein-structure, aqueous-solution, sugar ring, dynamics, nucleosides, density, state, water
IdentifiersURN: urn:nbn:se:kth:diva-18120DOI: 10.1021/jp803058gISI: 000262665500023ScopusID: 2-s2.0-61949335115OAI: oai:DiVA.org:kth-18120DiVA: diva2:336166
QC 201005252010-08-052010-08-052013-03-14Bibliographically approved