A reoptimized GROMOS force field for hexopyranose‐based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers

This article presents a reoptimization of the GROMOS 53A6 force field for hexopyranose‐based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate systems) into a new version 56ACARBO (nearly equivalent to 53A6 for non‐carbohydrate systems). This reoptimization was found necessary to repair a number of shortcomings of the 53A6 (45A4) parameter set and to extend the scope of the force field to properties that had not been included previously into the parameterization procedure. The new 56ACARBO force field is characterized by: (i) the formulation of systematic build‐up rules for the automatic generation of force‐field topologies over a large class of compounds including (but not restricted to) unfunctionalized polyhexopyranoses with arbritrary connectivities; (ii) the systematic use of enhanced sampling methods for inclusion of experimental thermodynamic data concerning slow or unphysical processes into the parameterization procedure; and (iii) an extensive validation against available experimental data in solution and, to a limited extent, theoretical (quantum‐mechanical) data in the gas phase. At present, the 56ACARBO force field is restricted to compounds of the elements C, O, and H presenting single bonds only, no oxygen functions other than alcohol, ether, hemiacetal, or acetal, and no cyclic segments other than six‐membered rings (separated by at least one intermediate atom). After calibration, this force field is shown to reproduce well the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers. As a result, the 56ACARBO force field should be suitable for: (i) the characterization of the dynamics of pyranose ring conformational transitions (in simulations on the microsecond timescale); (ii) the investigation of systems where alternative ring conformations become significantly populated; (iii) the investigation of anomerization or epimerization in terms of free‐energy differences; and (iv) the design of simulation approaches accelerating the anomerization process along an unphysical pathway. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

[1]  Zaida Ann Luthey-Schulten,et al.  Barriers to Forced Transitions in Polysaccharides , 2000 .

[2]  J. T. Vázquez,et al.  Rotational population dependences of the hydroxymethyl group in alkyl glucopyranosides: Anomers comparison , 1997 .

[3]  Jens Ø. Duus,et al.  A Conformational Study of Hydroxymethyl Groups in Carbohydrates Investigated by 1H NMR Spectroscopy , 1994 .

[4]  Alexander D. MacKerell.  Empirical force fields for biological macromolecules: Overview and issues , 2004, J. Comput. Chem..

[5]  F. Pederiva,et al.  On the calculation of puckering free energy surfaces. , 2009, The Journal of chemical physics.

[6]  B. E. Hudson,et al.  Structural Determination of cis- and trans-1,3-Dibromocyclohexane1 , 1963 .

[7]  Michael J. S. Dewar,et al.  Ground states of molecules. XXV. MINDO/3. Improved version of the MINDO semiempirical SCF-MO method , 1975 .

[8]  Michael J. Frisch,et al.  Self‐consistent molecular orbital methods 25. Supplementary functions for Gaussian basis sets , 1984 .

[9]  Walter.  Polysaccharide Association Structures in Food , 1998 .

[10]  E. Havinga,et al.  Conformation of non-aromatic ring compounds—XLVII , 1968 .

[11]  G. Guella,et al.  Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation. , 2010, The Journal of chemical physics.

[12]  S B Engelsen,et al.  A molecular builder for carbohydrates: application to polysaccharides and complex carbohydrates. , 1998, Biopolymers.

[13]  Serge Pérez,et al.  Conformation, dynamics and ion-binding properties of single-chain polyuronates: a molecular dynamics study , 2008 .

[14]  Wilfred F van Gunsteren,et al.  Theoretical Investigation of Solvent Effects on Glycosylation Reactions: Stereoselectivity Controlled by Preferential Conformations of the Intermediate Oxacarbenium-Counterion Complex. , 2010, Journal of chemical theory and computation.

[15]  Wilfred F van Gunsteren,et al.  Multiple free energies from a single simulation: extending enveloping distribution sampling to nonoverlapping phase-space distributions. , 2008, The Journal of chemical physics.

[16]  E. Eliel,et al.  Conformational Analysis. II. Esterification Rates of Cyclohexanols1 , 1957 .

[17]  G. Skjåk‐Braek,et al.  Mechanical properties of C-5 epimerized alginates. , 2008, Biomacromolecules.

[18]  Alain Laederach,et al.  Modeling protein recognition of carbohydrates , 2005, Proteins.

[19]  R. J. Abraham,et al.  Conformational analysis. Part 19 —conformational analysis of 6‐deoxy‐6‐fluoro‐D‐glucose (6DFG) in solution , 1992 .

[20]  Mark J. Forster,et al.  Molecular dynamics study of iduronate ring conformation , 1993 .

[21]  G. A. Jeffrey,et al.  Crystallographic studies of carbohydrates. , 1990, Acta crystallographica. Section B, Structural science.

[22]  C. Beeson,et al.  A comprehensive description of the free energy of an intramolecular hydrogen bond as a function of solvation: NMR study , 1993 .

[23]  Massimo Ragazzi,et al.  A force‐field study of the conformational characteristics of the iduronate ring , 1986, Journal of computational chemistry.

[24]  Jenn-Huei Lii,et al.  Alcohols, ethers, carbohydrates, and related compounds. III. The 1,2‐dimethoxyethane system , 2003, J. Comput. Chem..

[25]  Vojtech Spiwok,et al.  Modelling of beta-D-glucopyranose ring distortion in different force fields: a metadynamics study. , 2010, Carbohydrate research.

[26]  H. Berendsen,et al.  COMPUTER-SIMULATION OF MOLECULAR-DYNAMICS - METHODOLOGY, APPLICATIONS, AND PERSPECTIVES IN CHEMISTRY , 1990 .

[27]  Gregory S. Tschumper,et al.  Intrinsic conformational preferences of substituted cyclohexanes and tetrahydropyrans evaluated at the CCSD(T) complete basis set limit: implications for the anomeric effect. , 2005, The journal of physical chemistry. A.

[28]  J. Kowalewski,et al.  Dynamical Behavior of Carbohydrates As Studied by Carbon-13 and Proton Nuclear Spin Relaxation , 1996 .

[29]  Kenneth M. Merz,et al.  A force field for monosaccharides and (1 → 4) linked polysaccharides , 1994, J. Comput. Chem..

[30]  The conformational properties of glycosidic linkages , 1974 .

[31]  J. Brewer,et al.  Conformational Preferences for Solvated Hydroxymethyl Groups in Hexopyranose Structures , 1973 .

[32]  Robert M. Giuliano,et al.  Structure of methyl 6-deoxy-α-d-idopyranoside , 1989 .

[33]  Molecular modeling of interfaces between cellulose crystals and surrounding molecules: Effects of caprolactone surface grafting , 2008 .

[34]  P. Sundararajan,et al.  Theoretical studies on the conformation of aldopyranoses , 1972 .

[35]  Raymond A. Dwek,et al.  Glycobiology: Toward Understanding the Function of Sugars. , 1996, Chemical reviews.

[36]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[37]  Joshua Jortner,et al.  Modelling of Biomolecular Structures and Mechanisms , 1995 .

[38]  Pablo G. Debenedetti,et al.  Structure and dynamics in concentrated, amorphous carbohydrate--water systems by molecular dynamics simulation , 1999 .

[39]  W. Voelter,et al.  Durch Molybdationen katalysierte Reaktionen bei Kohlenhydraten, V. Epimerisierung von L‐Rhamnose , 1972 .

[40]  Hanoch Senderowitz,et al.  Carbohydrates: United Atom AMBER* Parameterization of Pyranoses and Simulations Yielding Anomeric Free Energies , 1996 .

[41]  P. Hünenberger,et al.  The influence of polyhydroxylated compounds on a hydrated phospholipid bilayer: a molecular dynamics study , 2008 .

[42]  Karl N. Kirschner,et al.  Solvent interactions determine carbohydrate conformation , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[43]  S. Angyal.  The Composition of Reducing Sugars in Solution: Current Aspects , 1991 .

[44]  J. Brady,et al.  A revised potential-energy surface for molecular mechanics studies of carbohydrates. , 1988, Carbohydrate research.

[45]  W. V. Gunsteren,et al.  Validation of the 53A6 GROMOS force field , 2005, European Biophysics Journal.

[46]  Göran Widmalm,et al.  Hydroxymethyl group conformation in saccharides: structural dependencies of (2)J(HH), (3)J(HH), and (1)J(CH) spin-spin coupling constants. , 2002, The Journal of organic chemistry.

[47]  R. Sjöholm,et al.  Complete assignments of the (1)H and (13)C chemical shifts and J(H,H) coupling constants in NMR spectra of D-glucopyranose and all D-glucopyranosyl-D-glucopyranosides. , 2008, Carbohydrate research.

[48]  N. Zefirov,et al.  The gauche effect , 1978 .

[49]  Seiichiro Ogawa,et al.  A 1H- and 13C-n.m.r. spectroscopic analysis of six pseudohexoses , 1988 .

[50]  Wilfred F. van Gunsteren,et al.  A Molecular Dynamics Simulation Study of Liquid Carbon Tetrachloride , 1996 .

[51]  A. McNaught.  Nomenclature of carbohydrates (IUPAC Recommendations 1996) , 1996, Advances in carbohydrate chemistry and biochemistry.

[52]  Richard G. Haverkamp,et al.  Stretching single polysaccharide molecules using AFM: A potential method for the investigation of the intermolecular uronate distribution of alginate? , 2008 .

[53]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[54]  Alexander D. MacKerell,et al.  CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. , 2009, Journal of chemical theory and computation.

[55]  S. Engelsen,et al.  Modeling polysaccharides: present status and challenges. , 1996, Journal of molecular graphics.

[56]  R. Rittner,et al.  1,3-Diaxial steric effects and intramolecular hydrogen bonding in the conformational equilibria of new cis-1,3-disubstituted cyclohexanes using low temperature NMR spectra and theoretical calculations. , 2005, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

[57]  Serge Stoll,et al.  Explicit-Solvent Molecular Dynamics Simulations of the β(1→3)- and β(1→6)-Linked Disaccharides β-Laminarabiose and β-Gentiobiose in Water , 2004 .

[58]  G. Davies,et al.  Mechanistic insights into glycosidase chemistry. , 2008, Current opinion in chemical biology.

[59]  Jhih-Wei Chu,et al.  Reaction Path Optimization with Holonomic Constraints and Kinetic Energy Potentials. , 2009, Journal of chemical theory and computation.

[60]  R. E. Reeves.  The Shape of Pyranoside Rings , 1950 .

[61]  E. Juaristi,et al.  Conformational analysis of 5-substituted 1,3-dioxanes. 6. Study of the attractive gauche effect in O-C-C-O segments , 1992 .

[62]  H. Künsch.  The Jackknife and the Bootstrap for General Stationary Observations , 1989 .

[63]  Robert J Woods,et al.  Reconciling solvent effects on rotamer populations in carbohydrates - A joint MD and NMR analysis. , 2006, Canadian journal of chemistry.

[64]  A. Becke.  Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[65]  M. Frisch,et al.  Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields , 1994 .

[66]  Davis,et al.  Carbohydrate Recognition through Noncovalent Interactions: A Challenge for Biomimetic and Supramolecular Chemistry. , 1999, Angewandte Chemie.

[67]  H. Hori,et al.  Conformational Analysis of Hydroxymethyl Group of D-Mannose Derivatives Using (6S)- and (6R)-(6-2H1)-D-Mannose , 1990 .

[68]  Hirotaka Kawashima,et al.  Conformational properties of and a reorientation triggered by sugar-water vibrational resonance in the hydroxymethyl group in hydrated beta-glucopyranose. , 2006, The journal of physical chemistry. B.

[69]  E. Corey,et al.  Computer-assisted synthetic analysis. A rapid computer method for the semiquantitative assignment of conformation of six-membered ring systems. 1. Derivation of a preliminary conformational description of the six-membered ring , 1980 .

[70]  K. Woerpel,et al.  Stereochemical Reversal of Nucleophilic Substitution Reactions Depending upon Substituent: Reactions of Heteroatom-Substituted Six-Membered-Ring Oxocarbenium Ions through Pseudoaxial Conformers , 2000 .

[71]  P. Grootenhuis,et al.  Parametrization and application of CHEAT95, and extended atom force field for hydrated oligosaccharides , 1995 .

[72]  R. Friesner,et al.  Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† , 2001 .

[73]  Yuan-Ping Pang,et al.  Polysaccharide elasticity governed by chair–boat transitions of the glucopyranose ring , 1998, Nature.

[74]  Wilfred F van Gunsteren,et al.  Sampling of rare events using hidden restraints. , 2006, The journal of physical chemistry. B.

[75]  Markus Christen,et al.  The GROMOS software for biomolecular simulation: GROMOS05 , 2005, J. Comput. Chem..

[76]  Norman L. Allinger,et al.  Molecular mechanics. The MM3 force field for hydrocarbons. 2. Vibrational frequencies and thermodynamics , 1989 .

[77]  Hiroshi Ohrui,et al.  1H-NMR studies of (6r)- and (6s)-deuterated d-hexoses: assignment of the preferred rotamers about C5C6 bond of D-glucose and D-galactose derivatives in solutions , 1984 .

[78]  Robert Stern,et al.  Carbohydrate polymers at the center of life's origins: the importance of molecular processivity. , 2008, Chemical reviews.

[79]  Esben Thormann,et al.  Force pulling of single cellulose chains at the crystalline cellulose-liquid interface: a molecular dynamics study. , 2009, Langmuir : the ACS journal of surfaces and colloids.

[80]  Wilfred F van Gunsteren,et al.  Conformational and dynamical properties of disaccharides in water: a molecular dynamics study. , 2006, Biophysical journal.

[81]  Udo Kaatze,et al.  Ultrasonic relaxation and fast chemical kinetics of some carbohydrate aqueous solutions , 1997 .

[82]  I. Alabugin.  Stereoelectronic Interactions in Cyclohexane, 1,3-Dioxane, 1,3-Oxathiane, and 1,3-Dithiane: W-Effect, σC-X ↔ σ*C-H Interactions, Anomeric EffectWhat Is Really Important? , 2000 .

[83]  Norman L. Allinger,et al.  Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons , 1989 .

[84]  H. Isbell,et al.  Mutarotation of sugars in solution. 1. History, basic kinetics, and composition of sugar solutions. , 1968, Advances in carbohydrate chemistry and biochemistry.

[85]  N. D. Epiotis,et al.  Open Shell Interactions, Nonbonded Attraction, and Aromaticity. Implications for Regiochemistry , 1974 .

[86]  P. Wertz,et al.  Anatomy of a complex mutarotation. Kinetics of tautomerization of .alpha.-D-galactopyranose and .beta.-D-galactopyranose in water , 1981 .

[87]  J. Brady,et al.  Computer Modeling of Carbohydrates: An Introduction , 1990 .

[88]  Alessandro Laio,et al.  The conformational free energy landscape of beta-D-glucopyranose. Implications for substrate preactivation in beta-glucoside hydrolases. , 2007, Journal of the American Chemical Society.

[89]  Wilfred F van Gunsteren,et al.  Enveloping distribution sampling: a method to calculate free energy differences from a single simulation. , 2007, The Journal of chemical physics.

[90]  S. Pérez,et al.  The exo-anomeric effect: experimental evidence from crystal structures , 1978 .

[91]  G. Torrie,et al.  Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling , 1977 .

[92]  D. Peter Tieleman,et al.  A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field , 2003, European Biophysics Journal.

[93]  Gabriel Cuevas,et al.  Recent studies of the anomeric effect , 1992 .

[94]  F. Anet.  The Use of Remote Deuteration for The Determination of Coupling Constants and Conformational Equilibria in Cyclohexane Derivatives , 1962 .

[95]  U. Kaatze,et al.  Conformational kinetics of disaccharides in aqueous solutions. , 2004, The Journal of chemical physics.

[96]  Diego A. Navarro,et al.  Modeling ring puckering in strained systems: application to 3,6-anhydroglycosides. , 2005, Carbohydrate research.

[97]  William L. Jorgensen,et al.  OPLS all‐atom force field for carbohydrates , 1997 .

[98]  L. Lerner,et al.  Origin and Quantitative Modeling of Anomeric Effect , 1993 .

[99]  S. Angyal.  Conformational analysis in carbohydrate chemistry. I. Conformational free energies. The conformations and α : β ratios of aldopyranoses in aqueous solution , 1968 .

[100]  Wilfred F. van Gunsteren,et al.  An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase , 2001, J. Comput. Chem..

[101]  D. Cremer,et al.  General definition of ring puckering coordinates , 1975 .

[102]  S. Immel,et al.  Synthesis, Structure, and Conformational Features of α-Cycloaltrin: A Cycloeligosaccharide with Alternating 4C1/1C4 Pyranoid Chairs† , 1997 .

[103]  R. Rittner,et al.  The relevant effect of an intramolecular hydrogen bond on the conformational equilibrium of cis-3-methoxycyclohexanol compared to trans-3-methoxycyclohexanol and cis-1,3-dimethoxycyclohexane. , 2005, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

[104]  J. Zajicek,et al.  Acyclic forms of [1-(13)C]aldohexoses in aqueous solution: quantitation by (13)C NMR and deuterium isotope effects on tautomeric equilibria. , 2001, The Journal of organic chemistry.

[105]  Jesús Jiménez-Barbero,et al.  Conformation of 1,2-O-alkylidenehexopyranoses: tri-O-acetyl derivatives of D-allose and D-gulose , 1986 .

[106]  J. L. Willett,et al.  Computational studies on carbohydrates: in vacuo studies using a revised AMBER force field, AMB99C, designed for alpha-(1-->4) linkages. , 2000, Carbohydrate research.

[107]  D. Baldisseri,et al.  Septanose Carbohydrates: Synthesis and Conformational Studies of Methyl α-d-glycero-d-Idoseptanoside and Methyl β-d-glycero-d-Guloseptanoside , 2005 .

[108]  Mahmoud E S Soliman,et al.  Mechanism of glycoside hydrolysis: A comparative QM/MM molecular dynamics analysis for wild type and Y69F mutant retaining xylanases. , 2009, Organic & biomolecular chemistry.

[109]  C. Hardacre,et al.  Glucose solvation by the ionic liquid 1,3-dimethylimidazolium chloride: a simulation study. , 2007, The journal of physical chemistry. B.

[110]  Theoretical studies on the conformation of saccharides , 1986 .

[111]  Piotr E Marszalek,et al.  Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides. , 2004, Biophysical journal.

[112]  G. Sheldrick,et al.  Effect of Peracylation of β-Cyclodextrin on the Molecular Structure and on the Formation of Inclusion Complexes: An X-ray Study , 2001 .

[113]  G. Davies,et al.  Mapping the conformational itinerary of β-glycosidases by X-ray crystallography , 2003 .

[114]  G. Csonka.  Proper basis set for quantum mechanical studies of potential energy surfaces of carbohydrates , 2002 .

[115]  Hiroshi Ohrui,et al.  1H NMR Analyses of Rotameric Distribution of C5-C6 bonds of D-Glucopyranoses in Solution , 1988 .

[116]  P. Sanderson,et al.  Conformational equilibria of alpha-L-iduronate residues in disaccharides derived from heparin. , 1987, The Biochemical journal.

[117]  Molecular dynamics simulations of the interaction between polyhydroxylated compounds and Lennard-Jones walls: preferential affinity/exclusion effects and their relevance for bioprotection , 2010 .

[118]  Robert Langer,et al.  Pyranose Ring Flexibility. Mapping of Physical Data for Iduronate in Continuous Conformational Space , 1998 .

[119]  R. Woods,et al.  Three-dimensional structures of oligosaccharides. , 1995, Current opinion in structural biology.

[120]  M. Tanner,et al.  Mechanistic aspects of enzymatic carbohydrate epimerization. , 2002, Natural product reports.

[121]  Robert J. Woods,et al.  Molecular Mechanical and Molecular Dynamic Simulations of Glycoproteins and Oligosaccharides. 1. GLYCAM_93 Parameter Development , 1995 .

[122]  Jan Kroon,et al.  Improved carbohydrate force field for gromos: ring and hydroxymethyl group conformations and exo-anomeric effect , 1999 .

[123]  A. Becke,et al.  Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.

[124]  Igor Tvaroska,et al.  Quantum mechanical and NMR spectroscopy studies on the conformations of the hydroxymethyl and methoxymethyl groups in aldohexosides. , 2002, Carbohydrate research.

[125]  de Nk Koen Vries,et al.  Different rotamer populations around the C-5C-6 bond for α- and β-d-galactopyranosides through the combined interaction of the gauche and anomeric effects: A 300-MHz 1H-n.m.r. and mndo study , 1987 .

[126]  J. R. Dixon,et al.  Structural information from OH stretching frequencies—conformations of cyclohexanol and cyclohexandiols , 1989 .

[127]  Herbert M. Pickett,et al.  Conformational structure, energy, and inversion rates of cyclohexane and some related oxanes , 1970 .

[128]  R. Bentley.  Configurational and conformational aspects of carbohydrate biochemistry. , 1972, Annual review of biochemistry.

[129]  J. Robyt.  Essentials of carbohydrate chemistry , 1997 .

[130]  L. Kenne,et al.  1H NMR studies on the hydrogen-bonding network in mono-altro-β-cyclodextrin and its complex with adamantane-1-carboxylic acid , 2005 .

[131]  H. Limbach,et al.  Multi-scale modelling of polymers: Perspectives for food materials , 2006 .

[132]  Raymond A Dwek,et al.  Conformational studies of oligosaccharides and glycopeptides: complementarity of NMR, X-ray crystallography, and molecular modelling. , 2002, Chemical reviews.

[133]  K. Kamiński,et al.  Dielectric studies on mobility of the glycosidic linkage in seven disaccharides. , 2008, The journal of physical chemistry. B.

[134]  Peter A. Kollman,et al.  Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the α → β Anomerization of Glucose , 1998 .

[135]  J. Pople,et al.  Self‐consistent molecular orbital methods. XX. A basis set for correlated wave functions , 1980 .

[136]  J. Brady,et al.  Molecular Dynamics Simulations of Carbohydrates and Their Solvation , 1990 .

[137]  Reko Leino,et al.  Conformation of the galactose ring adopted in solution and in crystalline form as determined by experimental and DFT 1H NMR and single-crystal X-ray analysis. , 2004, The Journal of organic chemistry.

[138]  J. Pierce,et al.  Anomerization of furanose sugars: kinetics of ring-opening reactions by proton and carbon-13 saturation-transfer NMR spectroscopy , 1982 .

[139]  I. Tvaroška,et al.  Angular dependence of vicinal carbon-proton coupling constants for conformational studies of the hydroxymethyl group in carbohydrates , 1995 .

[140]  J. E. Mark,et al.  Conformational energies and the random-coil dimensions and dipole moments of the polyoxides CH3O[(CH2)yO]xCH3 , 1976 .

[141]  Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling. , 2010, Journal of chemical theory and computation.

[142]  G. Widmalm,et al.  Oligosaccharides display both rigidity and high flexibility in water as determined by 13C NMR relaxation and 1H,1H NOE spectroscopy: evidence of anti-phi and anti-psi torsions in the same glycosidic linkage. , 2001, Chemistry.

[143]  Frank A. Momany,et al.  B3LYP/6-311++G** study of α- and β-d-glucopyranose and 1,5-anhydro-d-glucitol: 4C1 and 1C4 chairs, 3,OB and B3,O boats, and skew-boat conformations , 2004 .

[144]  Benito Casu,et al.  Evidence for conformational equilibrium of the sulfated L-iduronate residue in heparin and in synthetic heparin mono- and oligo-saccharides: NMR and force-field studies , 1986 .

[145]  Christopher B. Barnett,et al.  Calculating Ring Pucker Free Energy Surfaces From Reaction Coordinate Forces , 2009 .

[146]  J. R. Snyder,et al.  D-Talose anomerization: NMR methods to evaluate the reaction kinetics , 1989 .

[147]  Mohsen Tafazzoli,et al.  New Karplus equations for 2JHH, 3JHH, 2JCH, 3JCH, 3JCOCH, 3JCSCH, and 3JCCCH in some aldohexopyranoside derivatives as determined using NMR spectroscopy and density functional theory calculations. , 2007, Carbohydrate research.

[148]  G. Scuseria,et al.  Gaussian 03, Revision E.01. , 2007 .

[149]  Ian H. Williams,et al.  Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformation for the substrate: QM/MM molecular dynamics studies of wild-type and mutant xylanases. , 2009, Organic & biomolecular chemistry.

[150]  Alan E. Mark,et al.  The GROMOS96 Manual and User Guide , 1996 .

[151]  W. M. Haynes.  CRC Handbook of Chemistry and Physics , 1990 .

[152]  J. Praly,et al.  Influence of solvent on the magnitude of the anomeric effect , 1987 .

[153]  Roland Stenutz,et al.  Correlated C-C and C-O bond conformations in saccharide hydroxymethyl groups: parametrization and application of redundant 1H-1H, 13C-1H, and 13C-13C NMR J-couplings. , 2004, Journal of the American Chemical Society.

[154]  Matthias Rief,et al.  Single-molecule force spectroscopy on polysaccharides by AFM – nanomechanical fingerprint of α-(1,4)-linked polysaccharides , 1999 .

[155]  Norman L. Allinger,et al.  Theoretical Studies of the Potential Energy Surfaces and Compositions of the d-Aldo- and d-Ketohexoses , 1998 .

[156]  S. L. Mayo,et al.  DREIDING: A generic force field for molecular simulations , 1990 .

[157]  Edward M. Eyring,et al.  Molecular Dynamics and Kinetics of Monosaccharides in Solution. A Broadband Ultrasonic Relaxation Study , 2000 .

[158]  G. Widmalm,et al.  Determination of the Conformational Flexibility of Methyl α-Cellobioside in Solution by NMR Spectroscopy and Molecular Simulations , 2004 .

[159]  E. Kleinpeter.  Conformational Analysis of Saturated Heterocyclic Six-Membered Rings , 2004 .

[160]  Z. Pakulski.  Seven Membered Ring Sugars: A Decade Update , 2006 .

[161]  Andrew E. Torda,et al.  Local elevation: A method for improving the searching properties of molecular dynamics simulation , 1994, J. Comput. Aided Mol. Des..

[162]  Christopher B. Barnett,et al.  Free Energies from Adaptive Reaction Coordinate Forces (FEARCF): an application to ring puckering , 2009 .

[163]  P. Hünenberger,et al.  Interaction of the sugars trehalose, maltose and glucose with a phospholipid bilayer: a comparative molecular dynamics study. , 2006, The journal of physical chemistry. B.

[164]  L. D. Hayward,et al.  A Symmetry rule for the Circular Dichroism of reducing sugars, and the proportion of Carbonyl forms in Aqueous solutions thereof , 1977 .

[165]  I. Tvaroška,et al.  Ab Initio Molecular Orbital Calculation of Carbohydrate Model Compounds. 6. The Gauche Effect and Conformations of the Hydroxymethyl and Methoxymethyl Groups , 1997 .

[166]  H. Berendsen,et al.  Interaction Models for Water in Relation to Protein Hydration , 1981 .

[167]  J. Gasteiger,et al.  ITERATIVE PARTIAL EQUALIZATION OF ORBITAL ELECTRONEGATIVITY – A RAPID ACCESS TO ATOMIC CHARGES , 1980 .

[168]  Alexander D. MacKerell,et al.  Additive empirical force field for hexopyranose monosaccharides , 2008, J. Comput. Chem..

[169]  J. A. Mills,et al.  Cyclitols. XXXV. Tridentate complexing of some C-methyl- and C-hydroxymethyl-cyclitols with borate ions , 1974 .

[170]  Chris Oostenbrink,et al.  An improved nucleic acid parameter set for the GROMOS force field , 2005, J. Comput. Chem..

[171]  J. D. Stevens,et al.  THE PROTON MAGNETIC RESONANCE SPECTRA AND TAUTOMERIC EQUILIBRIA OF ALDOSES IN DEUTERIUM OXIDE , 1966 .

[172]  M. Kabayama,et al.  THE THERMODYNAMICS OF MUTAROTATION OF SOME SUGARS: II. THEORETICAL CONSIDERATIONS , 1958 .

[173]  F. D. Leeuw,et al.  The relationship between proton-proton NMR coupling constants and substituent electronegativities—I : An empirical generalization of the karplus equation , 1980 .

[174]  Riccardo Baron,et al.  Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling. , 2010, Carbohydrate research.

[175]  F. Lichtenthaler,et al.  4,6-di-O-benzoyl-3-O-benzyl-alpha-D-arabino-hexo-pyranos-2-ulosyl bromide: a conveniently accessible glycosyl donor for the expedient construction of diantennary beta-D-mannosides branched at O-3 and O-6. , 1997, Carbohydrate research.

[176]  U. Salzner,et al.  Ab Initio Examination of Anomeric Effects in Tetrahydropyrans, 1,3-Dioxanes, and Glucose , 1994 .

[177]  S. Angyal,et al.  The interaction energy between an axial methyl and an axial hydroxyl group in pyranoses , 1966 .

[178]  Milos Hricovíni,et al.  Structural aspects of carbohydrates and the relation with their biological properties. , 2004, Current medicinal chemistry.

[179]  Chang Yong Lee,et al.  Mutarotation of d-glucose and d-mannose in aqueous solution , 1969 .

[180]  F. Anet,et al.  Spectroscopic detection of the twist-boat conformation of cyclohexane. Direct measurement of the free energy difference between the chair and the twist-boat , 1975 .

[181]  W. Bailey,et al.  Conformational Studies in the Cyclohexane Series. 1. Experimental and Computational Investigation of Methyl, Ethyl, Isopropyl, and tert-Butylcyclohexanes. , 1999, The Journal of organic chemistry.

[182]  P. Salvadori,et al.  A conformational model of per-O-acetyl-cyclomaltoheptaose (-beta-cyclodextrin) in solution: detection of partial inversion of glucopyranose units by NMR spectroscopy. , 2003, Carbohydrate research.

[183]  F. Cañada,et al.  Conformational insights on the molecular recognition processes of carbohydrate molecules by proteins and enzymes: A 3D view by using NMR , 2006 .

[184]  Serge Pérez,et al.  Conformations of the hydroxymethyl group in crystalline aldohexopyranoses , 1979 .

[185]  Sj Angyal,et al.  Equilibria between pyranoses and furanoses. II. Aldoses , 1972 .

[186]  M Paluch,et al.  Identification of the molecular motions responsible for the slower secondary (beta) relaxation in sucrose. , 2008, The journal of physical chemistry. B.

[187]  S. Osanai.  Nickel(II)-Catalyzed Rearrangements of Free Sugars , 2001 .

[188]  J. R. Snyder,et al.  D-Idose: a one- and two-dimensional NMR investigation of solution composition and conformation , 1986 .

[189]  Roberto D. Lins,et al.  A new GROMOS force field for hexopyranose‐based carbohydrates , 2005, J. Comput. Chem..

[190]  T. Straatsma,et al.  Interaction between the CBM of Cel9A from Thermobifida fusca and cellulose fibers , 2009, Journal of molecular recognition : JMR.

[191]  J. Lehmann.  Carbohydrates: Structure and Biology , 1997 .

[192]  Sajjad Karamat,et al.  Computational study of the conformational space of methyl 2,4-diacetyl-beta-D-xylopyranoside: 4C1 and 1C4 chairs, skew-boats (2SO, 1S3), and B3,O boat forms. , 2006, The journal of physical chemistry. A.

[193]  Piotr E Marszalek,et al.  Identification of sugar isomers by single-molecule force spectroscopy. , 2006, Journal of the American Chemical Society.

[194]  H. P. Ramesh,et al.  Carbohydrates—The Renewable Raw Materials of High Biotechnological Value , 2003, Critical reviews in biotechnology.

[195]  I. C. O. B. Nomenclature.  IUPAC-IUB Commission on Biochemical Nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains. Tentative rules (1969). , 1970, Biochemistry.

[196]  L. Poppe.  Modeling carbohydrate conformations from NMR data : maximum entropy rotameric distribution about the C5-C6 bond in gentiobiose , 1993 .

[197]  T. Bruce Grindley,et al.  Effect of Solvation on the Rotation of Hydroxymethyl Groups in Carbohydrates , 1998 .

[198]  D. G. Streefkerk,et al.  P.M.R studies on fully methylated aldohexopyranosides and their 6-deoxy analogues using lanthanide shift reagents , 1976 .

[199]  Bernd Meyer,et al.  Further justification for the exo-anomeric effect. Conformational analysis based on nuclear magnetic resonance spectroscopy of oligosaccharides , 1982 .

[200]  J. C. Martin,et al.  Solvation effects on conformational equilibria. Studies related to the conformational properties of 2-methoxytetrahydropyran and related methyl glycopyranosides , 1969 .

[201]  P. Graczyk,et al.  Anomeric Effect: Origin and Consequences , 1994 .

[202]  A. Barbetta,et al.  Comparative studies on solution characteristics of mannuronan epimerized by C-5 epimerases , 2005 .

[203]  Chang Yong Lee,et al.  Thermodynamics and kinetics of D-galactose tautomers during mutarotation , 1969 .

[204]  R. J. Abraham,et al.  Conformational analysis. Part 21. Conformational isomerism in cis-cyclohexane-1,3-diol , 1993 .

[205]  P. Hünenberger,et al.  Trehalose–protein interaction in aqueous solution , 2004, Proteins.

[206]  Roger A. Laine,et al.  Invited Commentary: A calculation of all possible oligosaccharide isomers both branched and linear yields 1.05 × 1012 structures for a reducing hexasaccharide: the Isomer Barrier to development of single-method saccharide sequencing or synthesis systems , 1994 .

[207]  F. R. Jensen,et al.  Conformational Preferences in Cyclohexanes and Cyclohexenes , 1971 .

[208]  A. Oberhauser,et al.  Atomic levers control pyranose ring conformations. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[209]  Lars Olsen,et al.  Evaluation of carbohydrate molecular mechanical force fields by quantum mechanical calculations. , 2004, Carbohydrate research.

[210]  W. Saenger,et al.  A molecular dynamics simulation of crystalline α-cyclodextrin hexahydrate , 1987, European Biophysics Journal.

[211]  Minke Tang,et al.  Stabilization of Dry Mammalian Cells: Lessons from Nature1 , 2005, Integrative and comparative biology.

[212]  Vojtech Spiwok,et al.  Conformational free energy surface of alpha-N-acetylneuraminic acid: an interplay between hydrogen bonding and solvation. , 2009, The journal of physical chemistry. B.

[213]  P. Agrawal,et al.  NMR spectroscopy in the structural elucidation of oligosaccharides and glycosides. , 1992, Phytochemistry.

[214]  S. Angyal.  A short note on the epimerization of aldoses , 1997 .

[215]  Jan Kroon,et al.  Solvent effect on the conformation of the hydroxymethyl group established by molecular dynamics simulations of methyl‐β‐D‐glucoside in water , 1990 .

[216]  R. Marchessault,et al.  Carbon-13 nuclear magnetic resonance relaxation of amylose and dynamic behavior of the hydroxymethyl group , 1991 .

[217]  C. Podlasek,et al.  [13C]Enriched Methyl Aldopyranosides: Structural Interpretations of 13C-1H Spin-Coupling Constants and 1H Chemical Shifts , 1995 .

[218]  Andrew E. Torda,et al.  The GROMOS biomolecular simulation program package , 1999 .

[219]  J. Jiménez-Barbero,et al.  Medicinal chemistry based on the sugar code: fundamentals of lectinology and experimental strategies with lectins as targets. , 2000, Current medicinal chemistry.

[220]  C. Sagui,et al.  Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water. , 2009, The Journal of chemical physics.

[221]  A. J. Bennet,et al.  Transition states for glucopyranose interconversion. , 2006, Journal of the American Chemical Society.

[222]  D Lamba,et al.  Evidence for a boat-chair equilibrium in the glucuronate residue of chondrosine. , 1991, Carbohydrate research.

[223]  Lukas D. Schuler,et al.  On the Choice of Dihedral Angle Potential Energy Functions for n-Alkanes , 2000 .

[224]  Chris Oostenbrink,et al.  A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 , 2004, J. Comput. Chem..

[225]  M. Brochier-Salon,et al.  Conformational analysis of 6‐deoxy‐6‐iodo‐D‐glucose in aqueous solution , 2000 .

[226]  M. Manoharan,et al.  Homoanomeric effects in six-membered heterocycles. , 2003, Journal of the American Chemical Society.

[227]  Jenn-Huei Lii,et al.  Alcohols, ethers, carbohydrates, and related compounds. IV. carbohydrates , 2003, J. Comput. Chem..

[228]  M. Huggins.  Bond Energies and Polarities1 , 1953 .

[229]  J. Vliegenthart,et al.  Estimation of the persistence length of polymers by MD simulations on small fragments in solution. Application to cellulose , 1997 .

[230]  Roberto D Lins,et al.  Interaction of the disaccharide trehalose with a phospholipid bilayer: a molecular dynamics study. , 2004, Biophysical journal.

[231]  J. Jiménez-Barbero,et al.  Chemical Biology of the Sugar Code , 2004, Chembiochem : a European journal of chemical biology.

[232]  Philippe H Hünenberger,et al.  Effect of trehalose on a phospholipid membrane under mechanical stress. , 2008, Biophysical journal.

[233]  John W. Brady,et al.  Molecular dynamics simulations of .alpha.-D-glucose in aqueous solution , 1989 .

[234]  Saul Wolfe,et al.  Gauche effect. Stereochemical consequences of adjacent electron pairs and polar bonds , 1972 .

[235]  Tim N. Heinz,et al.  Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations , 2001 .

[236]  R. E. Reeves.  Cuprammonium-Glycoside Complexes. VII. Glucopyranoside Ring Conformations in Amylose , 1954 .

[237]  T. Straatsma,et al.  Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution. , 2008, Journal of chemical theory and computation.

[238]  Wilfred F. van Gunsteren,et al.  An improved OPLS–AA force field for carbohydrates , 2002, J. Comput. Chem..

[239]  G. P. Johnson,et al.  Comparison of different force fields for the study of disaccharides. , 2009, Carbohydrate research.

[240]  S. Nozaki,et al.  SYNTHESIS OF [2-SERINE, 8-VALINE]-HUMAN CALCITONIN , 1974 .

[241]  J. R. Grigera,et al.  On the sweetness properties of aldoses: characterization of molecular active sites by computer simulation , 1996 .

[242]  S. Inagaki,et al.  A new theory for the anti-periplanar effect. , 1986 .

[243]  U. Kaatze,et al.  Molecular dynamics and conformational kinetics of mono- and disaccharides in aqueous solution. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

[244]  O. Runquist,et al.  Conformational analysis of some 2-alkoxytetrahydropyrans , 1968 .

[245]  Akihiro Abe,et al.  Gas phase NMR of 1,2-dimethoxyethane , 1991 .

[246]  M. Robb,et al.  The Gauche Effect. A Study of Localized Molecular Orbitals and Excited-State Geometries in FCH2OH , 1973 .

[247]  Kevin J. Naidoo,et al.  Carbohydrate solution simulations: Producing a force field with experimentally consistent primary alcohol rotational frequencies and populations , 2002, J. Comput. Chem..

[248]  Preparing relaxed systems of amorphous polymers by multiscale simulation: Application to cellulose , 2004 .

[249]  Karl-Heinz Ott,et al.  Parametrization of GROMOS force field for oligosaccharides and assessment of efficiency of molecular dynamics simulations , 1996, J. Comput. Chem..

[250]  P. Lillford,et al.  Isomeric equilibria of monosaccharides in solution. Influence of solvent and temperature , 1989 .

[251]  D. Lightner,et al.  Steric Size in Conformational Analysis. Steric Compression Analyzed by Circular Dichroism Spectroscopy , 2000 .

[252]  S. David,et al.  Hexopyranose sugars conformation revised , 1984 .

[253]  J. T. Vázquez,et al.  CD and 1H NMR Study of the Rotational Population Dependence of the Hydroxymethyl Group in .beta. Glucopyranosides on the Aglycon and Its Absolute Configuration , 1995 .

[254]  Gaio Paradossi,et al.  Gel-like structure of a hexadecyl derivative of hyaluronic acid for the treatment of osteoarthritis. , 2009, Macromolecular bioscience.

[255]  Donald G. Truhlar,et al.  Quantum Chemical Conformational Analysis of Glucose in Aqueous Solution , 1993 .

[256]  Z. Hricovíniová.  The effect of microwave irradiation on Mo(VI) catalyzed transformations of reducing saccharides. , 2006, Carbohydrate research.

[257]  Andrea Barbetta,et al.  Ionic gel formation of a (pseudo)alginate characterised by an alternating MG sequence produced by epimerising mannuronan with AlgE4 , 2007 .

[258]  H. Hori,et al.  1H-NMR Studies on (6R)- and (6S)-deuterated (1–6)-linked disaccharides: assignment of the preferred rotamers about C5–C6 bond of (1–6)-disaccharides in solution , 1985 .

[259]  S. Pérez,et al.  Shapes and interactions of polysaccharide chains , 1999 .

[260]  Roland H. Hertwig,et al.  On the parameterization of the local correlation functional. What is Becke-3-LYP? , 1997 .

[261]  L. Petruš,et al.  The Bílik Reaction , 2001 .

[262]  O. Hassel,et al.  The Structure of Molecules Containing Cyclohexane or Pyranose Rings. , 1947 .

[263]  Philip J. Hajduk,et al.  Picosecond dynamics of simple monosaccharides as probed by NMR and molecular dynamics simulations , 1993 .

[264]  Robert J Woods,et al.  Computational carbohydrate chemistry: what theoretical methods can tell us , 1998, Glycoconjugate Journal.

[265]  Norman L. Allinger,et al.  Molecular mechanics. The MM3 force field for hydrocarbons. 1 , 1989 .

[266]  Chris Oostenbrink,et al.  An effective force field for molecular dynamics simulations of dimethyl sulfoxide and dimethyl sulfoxide-water mixtures , 2004 .

[267]  Philippe H. Hünenberger,et al.  Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water , 2010, J. Comput. Chem..

[268]  C. Rovira,et al.  Mechanism of cellulose hydrolysis by inverting GH8 endoglucanases: a QM/MM metadynamics study. , 2009, The journal of physical chemistry. B.

[269]  N. S. Zefirov,et al.  Stereochemical studies—XX: Conformations of 1,2-trans-disubstituted cyclohexanes , 1976 .

[270]  Wilfred F. van Gunsteren,et al.  A generalized reaction field method for molecular dynamics simulations , 1995 .

[271]  B. Perly,et al.  Conformer populations of L-iduronic acid residues in glycosaminoglycan sequences. , 1990, Carbohydrate research.

[272]  Alexander D. MacKerell,et al.  CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose. , 2009, The journal of physical chemistry. B.

[273]  Hm Henk Buck,et al.  Solvent dependence of the rotamer population around the interglycosidic C(5)-C(6) bond of (1 ® 6)-b-linked digalactopyranosides , 2010 .

[274]  S. Pérez.  Molecular modeling and electron diffraction of polysaccharides. , 1991, Methods in enzymology.

[275]  B. Coxon,et al.  Boat conformations synthesis, NMR spectroscopy, and molecular dynamics of methyl 4,6-O-benzylidene-3-deoxy-3-phthalimido-alpha-D-altropyranoside derivatives. , 2001, Carbohydrate research.

[276]  H. Verli,et al.  GROMOS96 43a1 performance on the characterization of glycoprotein conformational ensembles through molecular dynamics simulations. , 2009, Carbohydrate research.

[277]  O. Subbotin,et al.  Application of carbon-13 nuclear magnetic resonance spectrometry to the study of isomer and conformer ratios of dichlorocyclohexanes in their mixtures , 1976 .

[278]  J. Kroon,et al.  Molecular dynamics study of conformational equilibria in aqueous d-glucose and d-galactose , 1997 .

[279]  S. J. Angyal,et al.  The Composition and Conformation of Sugars in Solution , 1969 .

[280]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[281]  Hans-Joachim Gabius,et al.  The sugar code: functional lectinomics. , 2002, Biochimica et biophysica acta.

[282]  Bruce Tidor,et al.  Solvent effect on the anomeric equilibrium in D-glucose: a free energy simulation analysis , 1991 .

[283]  P. Hünenberger,et al.  pH-Dependent Stability of a Decalysine α-Helix Studied by Explicit-Solvent Molecular Dynamics Simulations at Constant pH , 2004 .

[284]  H. Berendsen,et al.  Simulations of Proteins in Water a , 1986, Annals of the New York Academy of Sciences.

[285]  Alexander D. MacKerell,et al.  CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol. , 2009, Journal of chemical theory and computation.

[286]  S. H. Vosko,et al.  Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis , 1980 .

[287]  J. Wieruszeski,et al.  Primary structure of four human milk octa-, nona-, and undeca-saccharides established by 1H- and 13C-nuclear magnetic resonance spectroscopy. , 1992, Carbohydrate research.

[288]  A. Imberty,et al.  Oligosaccharide structures: theory versus experiment. , 1997, Current opinion in structural biology.

[289]  Karl Nicholas Kirschner,et al.  GLYCAM06: A generalizable biomolecular force field. Carbohydrates , 2008, J. Comput. Chem..

[290]  Michael Schlenkrich,et al.  Force field parameters for carbohydrates , 1996 .

[291]  V. Tolstoguzov.  Why Were Polysaccharides Necessary? , 2004, Origins of life and evolution of the biosphere.

[292]  R. Rittner,et al.  Conformer dipole moment and syn-1,3-diaxial steric effect on the conformational equilibrium of the cis isomer of some 1,3-disubstituted cyclohexanes , 2005 .

[293]  R. J. Abraham,et al.  Conformational analysis. Part 20 —conformational analysis of 4‐deoxy‐4‐fluoro‐D‐glucose and 6‐deoxy‐6‐fluoro‐D‐galactose in solution , 1994 .

[294]  V S Rao,et al.  Theoretical studies on the conformation of aldohexopyranoses. , 1971, Carbohydrate research.

[295]  Tim N. Heinz,et al.  Combining the lattice-sum and reaction-field approaches for evaluating long-range electrostatic interactions in molecular simulations. , 2005, The Journal of chemical physics.

[296]  A. Shashkov,et al.  Computation techniques in the conformational analysis of carbohydrates , 2008, Russian Journal of Bioorganic Chemistry.

[297]  Siewert J Marrink,et al.  Martini Coarse-Grained Force Field: Extension to Carbohydrates. , 2009, Journal of chemical theory and computation.

[298]  Thomas N Huckerby,et al.  Conformational equilibrium of unsulphated iduronate in heparan sulphate tetrasaccharides , 2005, Glycoconjugate Journal.

[299]  Wilfred F. van Gunsteren,et al.  A molecular dynamics simulation study of chloroform , 1994 .

[300]  L. Berglund,et al.  Dynamics of cellulose-water interfaces: NMR spin-lattice relaxation times calculated from atomistic computer simulations. , 2008, The journal of physical chemistry. B.

[301]  S. Pérez,et al.  Structure, conformation, and dynamics of bioactive oligosaccharides: theoretical approaches and experimental validations. , 2000, Chemical reviews.

[302]  J. Stenger,et al.  Chair–chair conformational flexibility, pseudorotation, and exocyclic group isomerization of monosaccharides in water , 2002 .

[303]  A. Tunnacliffe,et al.  Resurrecting Van Leeuwenhoek's rotifers: a reappraisal of the role of disaccharides in anhydrobiosis. , 2003, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[304]  E. Corey,et al.  Computer-assisted synthetic analysis. A rapid computer method for the semiquantitative assignment of conformation of six-membered ring systems. 2. Assessment of conformational energies , 1980 .

[305]  K. Gekko,et al.  Vacuum-ultraviolet circular dichroism study of saccharides by synchrotron radiation spectrophotometry. , 2004, Carbohydrate research.

[306]  J. T. Vázquez,et al.  Experimental evidence on the hydroxymethyl group conformation in alkyl β-d-mannopyranosides , 2004 .

[307]  J. Marth,et al.  A genetic approach to Mammalian glycan function. , 2003, Annual review of biochemistry.

[308]  K. Woerpel,et al.  Stereochemistry of nucleophilic substitution reactions depending upon substituent: evidence for electrostatic stabilization of pseudoaxial conformers of oxocarbenium ions by heteroatom substituents. , 2003, Journal of the American Chemical Society.

[309]  V. Schramm,et al.  Conformational equilibrium isotope effects in glucose by (13)C NMR spectroscopy and computational studies. , 2001, Journal of the American Chemical Society.

[310]  Kathleen A. Durkin,et al.  Alcohols, ethers, carbohydrates, and related compounds. II. The anomeric effect , 2003, J. Comput. Chem..

[311]  P. Hajduk,et al.  Solution dynamics of the 1,2,3,4,6-penta-O-acetyl-α-D-idopyranose ring , 1997, Glycoconjugate Journal.

[312]  Stephen J. Angyal,et al.  The composition of reducing sugars in solution , 1984 .

[313]  Serge Pérez,et al.  Prospects for glycoinformatics. , 2005, Current opinion in structural biology.

[314]  K. Rice,et al.  Experimental determination of oligosaccharide three-dimensional structure , 1993 .

[315]  Rengaswami Chandrasekaran,et al.  Conformation of Carbohydrates , 1998 .

[316]  I. Tvaroška,et al.  The anomeric and exo-anomeric effects of a hydroxyl group and the stereochemistry of the hemiacetal linkage , 1998 .

[317]  Kjeld Rasmussen,et al.  A comparison and chemometric analysis of several molecular mechanics force fields and parameter sets applied to carbohydrates , 1998 .

[318]  Cornelis Altona,et al.  Relationship between protonproton NMR coupling constants and substituent electronegativities. V —Empirical substituent constants deduced from ethanes and propanes , 1989 .

[319]  Cornelis Altona,et al.  Relationship between proton—proton NMR coupling constants and substituent electronegativities. IV —An extended karplus equation accounting for interactions between substituents and its application to coupling constant data calculated by the Extended Hückel method , 1989 .

[320]  MM3(92) ANALYSIS OF INOSITOL RING PUCKERING , 1996 .

[321]  Cornelis Altona,et al.  Empirical group electronegativities for vicinal NMR proton–proton couplings along a CC bond: Solvent effects and reparameterization of the Haasnoot equation , 1994 .

[322]  Wilfred F van Gunsteren,et al.  Simple, Efficient, and Reliable Computation of Multiple Free Energy Differences from a Single Simulation: A Reference Hamiltonian Parameter Update Scheme for Enveloping Distribution Sampling (EDS). , 2009, Journal of chemical theory and computation.

[323]  S. Pérez,et al.  A database of three-dimensional structures of monosaccharides from molecular-mechanics calculations , 1991 .

[324]  P. Hünenberger,et al.  Conformation, dynamics, solvation and relative stabilities of selected beta-hexopyranoses in water: a molecular dynamics study with the GROMOS 45A4 force field. , 2007, Carbohydrate research.

[325]  David A. Dixon,et al.  Ab initio conformational analysis of cyclohexane , 1990 .

[326]  Wilfred F. van Gunsteren,et al.  Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation , 2009, J. Comput. Chem..

[327]  Piotr E. Marszalek,et al.  Atomic cranks and levers control sugar ring conformations , 2005 .

[328]  Paramita Dasgupta,et al.  NMR and modelling studies of disaccharide conformation. , 2003, Carbohydrate research.