Mm3 modeling of aldopentose pyranose rings
TLDR
In this paper, the authors studied the ring conformations of d-xylopyranose, d-lyxopyrnose, and d-arabinopyrynose and found that the energy surfaces exhibit low-energy regions corresponding to chair and skew forms with high energy barriers between these regions.About:
This article is published in Journal of Carbohydrate Chemistry.The article was published on 2002-05-31 and is currently open access. It has received 12 citations till now. The article focuses on the topics: Pyranose & Conformational isomerism.read more
Citations
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Journal ArticleDOI
Conformation, dynamics, solvation and relative stabilities of selected β-hexopyranoses in water: a molecular dynamics study with the gromos 45A4 force field
TL;DR: Good agreement is found with available experimental and theoretical data on the structural, dynamical, solvation and energetic properties of these compounds, but this detailed comparison also reveals some discrepancies, suggesting the need for further refinement.
Journal ArticleDOI
The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases
TL;DR: Ab initio conformational free energy landscapes, together with molecular dynamics simulations, enable to predict the catalytic itineraries of β-xylanase enzymes.
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Synthesis, conformation and biology of naphthoxylosides.
Anna Siegbahn,Ulrika Aili,Agata Ochocinska,Martin Olofsson,Jerk Rönnols,Katrin Mani,Göran Widmalm,Ulf Ellervik +7 more
TL;DR: A new synthetic protocol, based on acetal protection and selective benzylation, for modification of the three hydroxyl groups in xylose is developed, which synthesized twelve analogs of 2-naphthyl β-d-xylopyranoside (XylNap), where each hydroxym group has been epimerized or replaced by methoxy, fluoro, or hydrogen.
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Determining the solution conformational entropy of oligosaccharides by SEC with on-line viscometry detection.
TL;DR: The accuracy and precision of SEC/VISC were found to be excellent, as was the sensitivity of the viscometer in the oligomeric region, and an hypothesis is advanced to explain the unexpectedly high sensitivity of viscometric detection for low-molar-mass analytes.
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Modeling ring puckering in strained systems: application to 3,6-anhydroglycosides.
TL;DR: Results show the preponderance of a distorted chair conformation over that of the distorted boat, though the energy difference is lower and the distortions are larger for the compound with the beta-D-galacto configuration.
References
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The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
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General definition of ring puckering coordinates
Dieter Cremer,John A. Pople +1 more
TL;DR: In this article, a unique mean plane is defined for a general monocyclic puckered ring, which is described by amplitude and phase coordinates which are generalizations of those introduced for cyclopentane by Kilpatrick, Pitzer, and Spitzer.
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Molecular mechanics. The MM3 force field for hydrocarbons. 1
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The relationship between proton-proton NMR coupling constants and substituent electronegativities—I : An empirical generalization of the karplus equation
TL;DR: In this paper, a new coupling constant-torsion angle relation for the three-bond 1H-1H spin-spin coupling constant is formulated, which includes a correction for the electronegativity of substituents.
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Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons
Jenn Huei Lii,Norman L. Allinger +1 more
TL;DR: The van der Waals' potentials used for interactions between carbon and hydrogen in both aliphatic and aromatic systems have been improved from those available in MM2, and the new values are used in MM3 as mentioned in this paper.