Constructing and evaluating energy surfaces of crystalline disaccharides

Journal of Molecular Graphics and Modelling

Volumn 18, Issue 2, 2000, Pages 95-107

  French, Alfred D ^a   Kelterer, Anne Marie ^b   Johnson, Glenn P ^a   Dowd, Michael K ^a   Cramer, Christopher J ^c  

^a SOUTHERN REGIONAL RESEARCH CENTER   (United States)

^b GRAZ UNIVERSITY OF TECHNOLOGY   (Austria)

^c UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Carbohydrate; Conformation; Laminarabiose; Maltose; Molecular mechanics; Quantum mechanics; Sucrose; Tetrahydropyran; Trehalose

Indexed keywords

CRYSTALLOGRAPHY; ELECTRIC POWER MEASUREMENT; HYDROGEN BONDS; PERMITTIVITY; POTENTIAL ENERGY; QUANTUM THEORY; SUGAR (SUCROSE); CONFORMATIONS; CRYSTALLINE MATERIALS; FIELD PLOTTING; GLUCOSE; MALTOSE; MOLECULAR DYNAMICS;

DISACCHARIDES; ENERGY SURFACES; LAMINARABIOSE; TETRAHYDROPYRAN; TREHALOSE;

MOLECULAR GRAPHICS; SUGAR (SUCROSE);

DISACCHARIDE; MALTOSE; SUCROSE; TETRAHYDROPYRAN DERIVATIVE; TREHALOSE;

ANALYTIC METHOD; ARTICLE; CARBOHYDRATE METABOLISM; COMPUTER SIMULATION; CRYSTAL STRUCTURE; CRYSTALLIZATION; CRYSTALLOGRAPHY; DIELECTRIC CONSTANT; HYDROGEN BOND; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; QUANTUM MECHANICS; SURFACE PROPERTY;

CARBOHYDRATE CONFORMATION; CRYSTALLOGRAPHY; DISACCHARIDES; HYDROGEN BONDING; MALTOSE; MODELS, MOLECULAR; QUANTUM THEORY; SOFTWARE; SUCROSE; THERMODYNAMICS;

EID: 0034351346     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(00)00041-3     Document Type: Article

References (58)

1. Stereochemical criteria for polypeptides and proteins
2. Phi/Psi-chology: Ramachandran revisited
3. A molecular mechanics force field (MM3) for alcohols and ethers
4. Use of umbrella sampling in the calculation of the potential of mean force for maltose in vacuum from molecular dynamics simulations
5. Molecular dynamics studies of the hydration of α,α-trehalose
6. The conformation of sucrose in water: A molecular dynamics approach
7. A comparison and chemometric analysis of several molecular mechanics force fields and parameter sets applied to carbohydrates
8. A QM/MM conformational analysis of crystalline sucrose moieties
9. Overlapping anomeric effects in a sucrose analogue
10. Ab initio-MIA and molecular mechanics studies of the distorted sucrose linkage of raffinose
11. Exploration of disaccharide conformations by molecular mechanics
12. HF/6-31G* energy surfaces for disaccharide analogs
13. Carbohydrate force fields
14. Anomeric and exo-anomeric effects in carbohydrate chemistry
15. Ab initio and density functional theory study of structures and energies for dimehtoxymethane as a model for the anomeric effect
16. Carbohydrates: United atom AMBER* parameterization of pyranoses and simulations yielding anomeric free energies
17. The consistent force field. 4. An optimized set of potential energy functions for aliphatic and alicyclic ethers and anomeric carbon atoms
18. A molecular mechanical force field for the conformational analysis of oligosaccharides: Comparison of theoretical and crystal structures of Manαl-3Manβl-4GlcNAc
19. Derivation of class II force fields. VI. Carbohydrate compounds and anomeric effects
20. A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives
21. Relative stability of alternative chair forms and hydroxymethyl conformations of β-D-glucopyranose
22. Factors controlling the relative stability of anomers and hydroxymethyl conformers of glucopyranose
23. B3LYP/6-31G*, HF/6-31G* and MM3 heats of formation for disaccharide analogs
24. Heats of formation of organic molecules calculated by density functional theory: II. Alkanes
25. The importance of selecting the proper basis set in the quantum mechanical studies of the potential energy surfaces of carbohydrates
26. 1 chair forms of β-D-glucose: A density functional study
27. 4 α-L-fucose
28. Theoretical study of alternative ring forms of α-L-fucopyranose
29. Conformational analysis of a disaccharide (cellobiose) with the molecular mechanics program (MM2)
30. General atomic and molecular electronic structure system
31. Sucrose. X-ray refinement and comparison with neutron refinement
32. Conformations of hydroxymethyl group in crystalline aldopyranoses
33. Monosachcarides: Geometry and dynamics
34. Heteronuclear coupling constants of hydroxyl protons in a water solution of oligosaccharides: Trehalose and sucrose
35. Use of locally enhanced sampling in free energy calculations: Testing and application to the αβ anomerization of glucose
36. Disaccharide conformational maps: How adiabatic is an adiabatic map?
37. Modeling of alddopyranosyl ring puckering with MM3(92)
38. Pitfalls in the use of the torsion angle driving method for the calculation of conformational interconversions
39. Conformational analysis of a disaccharide (cellobiose) with the molecular mechanics program (MM2)
40. Miniature crystal models of cellulose polymorphs and other carbohydrates
41. The consistent force field. 5. PEF95SAC: Optimized potential energy function for alcohols and carbohydrates
42. Accurate bond and angle parameters for X-ray protein structure refinement
43. Can statistical analysis of structural parameters from different crystal environments lead to quantitative energy relationships?
44. Chemical reaction paths. 8. Stereoisomerization path for triphenylphosphine oxide and related molecules: Indirect observation of the structure of the transition state