27 ps DFT molecular dynamics simulation of α-maltose: A reduced basis set study

Journal of Computational Chemistry

Volumn 31, Issue 11, 2010, Pages 2087-2097

  Schnupf, Udo ^a   Willett, J L ^a   Momany, Frank A ^a  

^a NATIONAL CENTER FOR AGRICULTURAL UTILIZATION RESEARCH   (United States)

Author keywords

4 31G; B3lyp 6 31+g*; DFTMD; Dynamics; Maltose

Indexed keywords

4-31G; ATOM INTERACTION; BASIS SETS; BOND ANGLE; CONFORMATIONAL TRANSITIONS; DFT METHOD; ELECTRONIC STRUCTURE CALCULATIONS; END EFFECTS; EXPERIMENTAL VALUES; HYDROGEN BONDING NETWORK; IMPLICIT SOLVENTS; MOLECULAR DYNAMICS SIMULATIONS; REDUCED BASIS; REDUCING ENDS; TIME SEGMENTS; TRANSITION STATE; VELOCITY CORRELATION FUNCTIONS; VIBRATIONAL FREQUENCIES;

CARBOHYDRATES; CONFORMATIONS; ELECTRONIC STRUCTURE; FOURIER TRANSFORMS; HYDROGEN BONDS; MALTOSE; MOLECULAR DYNAMICS; WAVELET TRANSFORMS;

DYNAMICS;

EID: 77954303909     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21495     Document Type: Article

References (61)

1. Momany, F. A.; Willett, J. L.; Schnupf, U. DFT molecular dynamic (DFTMD) simulations of carbohydrates: COSMO solvated α-maltose. J. Mol. Struct. THEOCHEM (submitted).
2. Schnupf, U.; Willett, J. L.; Bosma, W. B.; Momany, F. A. DFT conformation and energies of amylose fragments at atomic resolution. Part 1: Syn forms of α-maltotetraose. Carbohydr Res 2009, 344, 362.
3. Schnupf, U.; Willett, J. L.; Momany, F. A. DFT conformation and energies of amylose fragments at atomic resolution. Part 2: 'Band-flip' and 'kink' forms of α-maltotetraose. Carbohydr Res 2009, 344, 374.
4. Schnupf, U.; Willett, J. L.; Bosma, W. B.; Momany, F. A. DFT conformational studies of α-maltotriose. J Comput Chem 2008, 29, 1103.
5. Momany, F. A.; Schnupf, U.; Willett, J. L.; Bosma, W. B. DFT study of α-maltose: Influence of hydroxyl orientations on the glycosidic bond. Struct Chem 2007, 18, 611.
6. Schnupf, U.; Willett, J. L.; Bosma, W. B.; Momany, F. A. DFT study of α- and β-D-allopyranose at the B3LYP/6-311 + +G**level of theory. Carbohydr Res 2007, 342, 196.
7. Schnupf, U.; Willett, J. L.; Bosma, W. B.; Momany, F. A. DFT studies of the disaccharide, α-maltose: Relaxed isopotential maps. Carbohydr Res 2007, 342, 2270.
8. Momany, F. A.; Willett, J. L.; Bosma, W. B.; Schnupf, U. Abstracts of Papers, 233rd ACS National Meeting, Chicago, IL, United States, March 25-29, 2007, COMP-58.
9. Bosma, W. B.; Appell, M.; Willett, J. L.; Momany, F. A. Stepwise hydration of cellobiose by DFT methods: 2. Energy contributions to relative stabilities of cellobiose-(H2O)1-4 complexes. J Mol Struct: THEOCHEM 2006, 776, 1.
10. Bosma, W. B.; Appell, M.; Willett, J. L.; Momany, F. A. Stepwise hydration of cellobiose by DFT methods: 1. Conformational and structural changes brought about by the addition of one to four water molecules. J Mol Struct: THEOCHEM. 2006, 776, 13.
11. Momany, F. A.; Appell, M..; Willett, J. L.; Schnupf, U.; Bosma, W. B. DFT Study of α- and β-D-galactopyranose at the B3LYP/6311 + +G** level of theory. Carbohydr Res 2006, 341, 525.
12. Schnupf, U.; Momany, F. A.; Willett, J. L.; Bosma, W.B.Abstracts of Papers, 232nd ACS National Meeting, San Francisco, CA, United States, September 10-14, 2006, CARB-105.
13. Appell, M.; Willett, J. L.; Momany, F. A. DFT Study of α- and β-DMannopyranose at the B3LYP/6-311 ++G** level. Carbohydr Res 2005, 340, 459.
14. Momany, F. A.; Appell, M.; Willett, J. L.; Bosma, W. B. B3LYP/6311+ +G geometry-optimization study of pentahydrates of α- and βD-glucopyranose. Carbohydr Res 2005, 340, 1638.
15. 3,0 boats, and skew-boat conformations. Carbohydr Res 2004, 339, 537.
16. Momany, F. A.; Appell, M. A.; Strati, G. L.; Willett, J. L. B3LYP/ 6-311 + +G** study of monohydrates of α- and β-D-glucopyranose: Hydrogen bonding, stress energies, and effect of hydration on internal coordinates. Carbohydr Res 2004, 339, 553.
17. Strati, G. L.; Willett, J. L.; Momany, F. A. Ab Initio computational study of β-cellobiose conformers using B3LYP/6-311 + +G**. Carbohydr Res 2002, 337, 1833.
18. Strati, G. L.; Willett, J. L.; Momany, F. A. A DFT/ab initio study of hydrogen bonding and conformational preference in model cellobiose analogs using B3LYP/6-311 + +G**. Carbohydr Res 2002, 337, 1851.
19. Momany, F. A.; Willett, J. L. Computational studies on carbohydrates: 1. Density functional ab initio geometry optimization on maltose conformations. J Comput Chem 2000, 21, 1204.
20. French, A. D.; Johnson, G. P. Roles of starting geometries in quantum mechanics studies of cellobiose. Mol Simul 2008, 34, 365.
21. French, A. D.; Johnson, G. P. Quantum mechanics studies of cellobiose conformations. Can J Chem 2006, 84, 603.
22. Navarro, D. A.; Stortz, C. A. DFT/MM modeling of the five membered ring in 3,6-anhydrogalactose derivatives and its influence on disaccharide adiabatic maps. Carbohydr Res 2008, 343, 2292.
23. (a) Novoa, J. J.; Sosa, C. J Chem Phys 1995, 99, 15837;
24. (b) Sirois, S.; Proynov, E. I.; Nguyen, D. T.; Salahub, D. R. J Chem Phys 1997, 107, 6770;
25. (c) Paizs, B.; Shuai, S. J Comput Chem 1998, 19, 575;
26. (d) Hagemeister, F. C.; Gruenloh, C. J.; Zwier, T. S. J Phys Chem A 1998, 102, 82.
27. (a) Csonka, G. I. Proper basis set for quantum mechanical studies of potential energy surfaces of carbohydrates. J Mol Struct THEOCHEM. 2002, 584, 1;
28. (b) Csonka, G. I., et al. Evaluation of density functionals and basis sets for carbohydrates. J Chem Theory Comp 2009, 5, 679.
29. (a) Klamt, A; Schuurmann, G. J. COSMO: A new approach to dielectric screening in solvents with explicit expressions for the Screening energy and its gradient. J Chem Soc Perkin Trans2 1993, 799;
30. (b) Andzelm, J.; Kölmel, C.; Klamt, A. Incorporation of solvent effects into density functional calculations of molecular energies and geometries. J Chem Phys 1995, 103, 9312;
31. (c) Klamt, A.; Mennucci, B.; Tomasi, J.; Barone, V.; Curutchet, C.; Orozco, M.; Luque, F. J. On the performance of continuum solvation methods. A comment on "Universal Approaches to Solvation Modeling." Acc Chem Res 2009, 42, 489.
32. Parallel Quantum Solutions.Ab Initio Program Package, Parallel Quantum Solutions, 2013 Green Acres, Suite E, Fayetteville, AR 72703, USA.
33. (a) Verlet, L. Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys Rev 1967, 159, 98;
34. (b) Verlet, L. Computer "experiments" on classical fluids. II. Equilibrium correlation functions. Phys Rev 1968, 165, 201.
35. HyperChem 8.0 (2008) Hypercube, Inc., 115 NW 4th Street, Gainesville, FL 32601, USA.
36. ORIGIN 8.0 (2008) OriginLab Corporation, One Roundhouse Plaza, Northampton, MA 01060, USA.
37. Noid, D. W.; Koszykowski, M. L.; Marcus, R. A. A spectral analysis method of obtaining molecular spectra from classical trajectories. J Chem Phys 1977, 67, 414.
38. Berens, P. H.; Wilson, K. R. Molecular dynamics and spectra: I. Diatomic rotation and vibration. J Chem Phys 1981, 74, 4872.
39. Fredkin, D. R.; Komornicki, A.; White, S. R.; Wilson, K. R. Ab initio infrared and Raman spectra. J Chem Phys 1983, 78, 7077.
40. Vasko, P. D.; Blackwell, J.; Fredkin, J. L. Infrared and Raman spectroscopy of carbohydrates: Part I: Identification of O-H and C-H related vibrational modes for o-glucose, maltose, cellobiose, and dextran by deuterium substitution methods. Carbohydr Res 1971, 19, 297.
41. (a) Gress, M. A.; Jefferey, G. A. A neutron diffraction refinement of crystal structure of β-maltose monohydrate. Acta Cryst B 1977, 33, 2490;
42. (b) Gress, M. E.; Jeffrey, G. A. The crystal structure of D-glucaro-l,4-lactone monohydrate. Carbohydr Res 1976, 50, 159.
43. Momany, F. A.; Willett, J. L. Computational studies on carbohydrates: In vacuo studies using a revised AMBER force field, AMB99C, designed for alpha-(1->4)linkages. Carbohydr Res 2000, 326, 194.
44. Momany, F. A.; Willett, J. L. Computational studies on carbohydrates: Solvation studies on maltose and cyclomaltooligosaccharides (cyclodextrins) using a DFT/ab initio-derived empirical force field, AMB99C. Carbohydr Res 2000, 326, 210.
45. Ha, S. N.; Madsen, L. J.; Brady, J. W. Conformational analysis and molecular dynamics simulations of maltose. Biopolymers 1988, 27, 1927.
46. Brady, J. W.; Schmidt, R. K. The role of hydrogen bonding in carbohydrates: Molecular dynamics simulations of maltose in aqueous solution. J Phys Chem 1993, 97, 958.
47. Schmidt, R. K.; Teo, B.; Brady, J. W. Use of umbrella sampling in the calculation of the potential of mean force for maltose in vacuum from molecular dynamics simulations. J Phys Chem 1995, 99, 11339.
48. Ott, K.-H.; Meyer, B. Parameterization of GROMOS force field for oligosaccharides and assessment of efficiency of molecular dynamics simulations. J Comput Chem 1996, 17, 1068.
49. Ott, K.-.H.; Meyer, B. Molecular dynamics simulations of maltose in water. Carbohydr Res 1996, 281, 11.
50. Pereira, C. S.; Kony, D.; Baron, R.; Muller, M.; van Gunsteren, W. Conformational and dynamical properties of disaccharides in water: A molecular dynamics study. Biophys J 2006, 90, 4337.
51. Wang, C. X.; Chen, W. Z.; Tran, V.; Douillard, R. Analysis of interfacial water structure and dynamics in alpha-maltose solution by molecular dynamics simulation. Chem Phys Lett 1996, 251, 268.
52. Sakurai, M.; Murata, M.; Inoue, Y.; Hino, A.; Kobayashi, S. Molecular-dynamics study of aqueous solution of trehalose and maltose: Implication for the biological function of trehalose. Bull Chem Soc Jpn 1997, 70, 847.
53. -45. (a) Naidoo, K. J.; Kuttel, M. Water structure about the dimer and hexamer repeat units of amylose from molecular dynamics computer simulations. J Comput Chem 2001, 22, 445; (Pubitemid 33640783)
54. (b) Kuttel, M. M.; Naidoo, K. J. Free energy surfaces for the α(1-≤4)-glycosidic linkage: Implications for polysaccharide solution structure and dynamics. J Phys Chem. B 2005, 109, 7468.
55. -46. Engelsen, S. B.; Monteiro, C.; Herve de Penhoat, C.; Perez, S. The diluted aqueous solvation of carbohydrates as inferred from molecular dynamics simulations and NMR spectroscopy. Biophys Chem 2001, 93, 103. (Pubitemid 34142181)
56. Best, R. B.; Jackson, G. E.; Naidoo, K. J. Molecular dynamics and NMR study of the α(1-→4) and α(1-→6) glycosidic linkages: maltose and isomaltose. J Phys Chem B 2001, 105, 4742.
57. Corzana, F.; Motawia, M.; Herve du Penhoat, C.; Perez, S.; Tschampel, S. M.; Woods, R. J.; Engelsen, S. B. A hydration study of (1-→4) and (1-→6) linked α-glucans by comparative 10 ns molecular dynamics simulations and 500-MHz NMR. J Comput Chem 2004, 25, 573.
58. Umemura, M.; Hayashi, S.; Nakagawa, T.; Yamanaka, S.; Urakawa, H.; Kajiwara, K. Structure of water molecules in aqueous solutions of di-and penta-D-glucopyranoses using molecular dynamics simulation. J Mol Struct: THEOCHEM 2003, 624, 129.
59. Umemura, M.; Hayashi, S.; Nakagawa, T.; Urakawa, H.; Kajiwara, K. Structure of water molecules in aqueous maltose and cellobiose solutions using molecular dynamics simulation. II. Dynamics. J Mol Struct: THEOCHEM. 2003, 624, 215.
60. Yu, H.; Amann, M.; Hansson, T.; Kohler, J.; Wich, G.; van Gunsteren, W. F. Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: A molecular dynamics study. Carbohydr Res 2004, 339, 1697.
61. -52. Lerbret, A.; Bordat, P.; Affouard, F.; Guinet, Y.; Hedoux, A.; Paccou, L.; Prevost, D.; Descamps, M. Influence of homologous disaccharides on the hydrogen-bond network of water: Complementary raman scattering experiments and molecular dynamics simulations. Carbohydr Res 2005, 340, 881. (Pubitemid 40380823)