Literature DB >> 18444612

Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl)tetrahydropyran.

H Lee Woodcock1, Bernard R Brooks, Richard W Pastor.   

Abstract

High level ab initio computations in vacuum and with the IEFPCM implicit solvent model are carried out on 5-(hydroxymethyl)tetrahydropyran to investigate the effects of water on the exocyclic torsional surface. Rotamer populations evaluated from the omega(C-C-C-O), theta(C-C-C-O) solvent surface agree almost quantitatively with experimental values for the closely related methyl 4-deoxy-alpha-D-xylohexopyranoside. Potentials of mean force obtained from the two surfaces show substantial solvent stabilization of the TG (omega = 180 +/- 60 degrees) rotamer and the barriers at omega= 120 and 240 degrees but solvent destabilization at the cis barrier (omega = 0 degrees). Natural bond orbital analyses indicate that energetics of these effects are largely explained by overstabilization of the vacuum GT (omega= 60 +/- 60 degrees) and GG (omega = 300 +/- 60 degrees) rotamers. Solvent stabilization of theta conformations provides entropic stabilization.

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Year:  2008        PMID: 18444612      PMCID: PMC2935315          DOI: 10.1021/ja077633z

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  16 in total

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Journal:  J Am Chem Soc       Date:  2003-11-26       Impact factor: 15.419

2.  Crystal structure and hydrogen-bonding system in cellulose Ibeta from synchrotron X-ray and neutron fiber diffraction.

Authors:  Yoshiharu Nishiyama; Paul Langan; Henri Chanzy
Journal:  J Am Chem Soc       Date:  2002-08-07       Impact factor: 15.419

Review 3.  Empirical force fields for biological macromolecules: overview and issues.

Authors:  Alexander D Mackerell
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

4.  Hydroxymethyl group conformation in saccharides: structural dependencies of (2)J(HH), (3)J(HH), and (1)J(CH) spin-spin coupling constants.

Authors:  Roland Stenutz; Ian Carmichael; Göran Widmalm; Anthony S Serianni
Journal:  J Org Chem       Date:  2002-02-08       Impact factor: 4.354

5.  Hydroxymethyl rotamer populations in disaccharides.

Authors:  Alfredo Roën; Juan I Padrón; Jesús T Vázquez
Journal:  J Org Chem       Date:  2003-06-13       Impact factor: 4.354

6.  Further characterization of the antithrombin-binding sequence in heparin.

Authors:  L Thunberg; G Bäckström; U Lindahl
Journal:  Carbohydr Res       Date:  1982-03-01       Impact factor: 2.104

7.  B3LYP/6-311++G** study of monohydrates of alpha- and beta-D-glucopyranose: hydrogen bonding, stress energies, and effect of hydration on internal coordinates.

Authors:  F A Momany; M Appell; G Strati; J L Willett
Journal:  Carbohydr Res       Date:  2004-02-25       Impact factor: 2.104

8.  Theoretical study of the relative stability of rotational conformers of alpha and beta-D-glucopyranose in gas phase and aqueous solution.

Authors:  Jose C Corchado; María L Sánchez; Manuel A Aguilar
Journal:  J Am Chem Soc       Date:  2004-06-16       Impact factor: 15.419

9.  Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran.

Authors:  H Lee Woodcock; Damian Moran; Richard W Pastor; Alexander D MacKerell; Bernard R Brooks
Journal:  Biophys J       Date:  2007-07-01       Impact factor: 4.033

10.  Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations.

Authors:  Michelle Kuttel; J W Brady; Kevin J Naidoo
Journal:  J Comput Chem       Date:  2002-10       Impact factor: 3.376

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  1 in total

1.  Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types.

Authors:  Jeffery B Klauda; Richard M Venable; J Alfredo Freites; Joseph W O'Connor; Douglas J Tobias; Carlos Mondragon-Ramirez; Igor Vorobyov; Alexander D MacKerell; Richard W Pastor
Journal:  J Phys Chem B       Date:  2010-06-17       Impact factor: 2.991

  1 in total

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