Interaction of OH− with xylan and its hydrated complexes: structures and molecular dynamics study using elongation method

Journal of Molecular Modeling

Volumn 21, Issue 5, 2015, Pages

  Jin, Lin ^a   Liu, Kai ^a   Aoki, Yuriko ^a,b  

^a KYUSHU UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Alkali; Elongation (ELG) method; Hydrated complex; Molecular dynamics simulations; Xylan

Indexed keywords

HYDROXIDE; XYLAN;

ALGORITHM; ARTICLE; CALCULATION; CHEMICAL INTERACTION; CHEMICAL REACTION; GEOMETRY; HIGH TEMPERATURE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTON TRANSPORT; REACTION ANALYSIS; ROOM TEMPERATURE; TEMPERATURE;

EID: 84928391341     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-015-2666-5     Document Type: Article

References (47)

1. Hosoya T, Nakao Y, Sato H, Sakaki S (2010) Theoretical study of 1,6-anhydrosugar formation from phenyl D-glucosides under basic condition: reasons for higher reactivity of β-anomer. J Org Chem 75:8400–8409
2. Dimmel DR, Willenbrink HJ, Vreede PV (2001) Influence of carbohydrate physical state on pulping and bleaching chemistry. J Wood Chem Technol 21:211–225
3. Kaylor RM, Dimmel DR, Ragauskas AJ, Liotta CL (1995) A new model compound for studying alkaline cellulose chain cleavage reactions. J Wood Chem Technol 15:431–452
4. Schroeder LR, Wylie TR (1998) Alkaline degradation of 1,5-anhydro-4-O-β-D-glucopyranosyl-2,3,4-tri-O-methyl-D-glucitol. J Wood Chem Technol 18:107–127
5. Tanaka T, Huang WC, Noguchi M, Kobayashi A, Shoda S (2009) Direct synthesis of 1,6-anhydro sugars from unprotected glycopyranoses by using 2-chloro-1,3-dimethylimidazolinium chloride. Tetrahedron Lett 50:2154–2157
6. Lu S, Li X, Wang A (2000) A new chiral diphosphine ligand and its asymmetric induction in catalytic hydroformylation of olefins. Catal Today 63:531–536
7. Moody W, Richards GN (1981) A re-investigation of the kinetics of alkaline degradation of phenyl β-D-glucopyranoside and some other glycosides. Carbohydr Res 93:83–90
8. Lai YZ, Ontto DE (1979) Kinetics of base-catalyzed degradation of phenyl d-gluco-pyranosides. Carbohydr Res 75:51–59
9. Blythe DA, Schroeder LR (1985) Degradation of a nonreducing cellulose model, L,5-anhydro-4-O-β-D-glucopyranosyl-D-glucitol, under kraft pulping conditions. J Wood Chem Technol 5:313–334
10. Lai YZ (1972) Kinetic evidence of anionic intermediates in the base-catalyzed cleavage of glycosidic bonds in the methyl D-glucopyranosides. Carbohydr Res 24:57–65
11. Brooks RD, Thompson NS (1966) Degradation of 1,5-anhydroribitol and 1,5-anhydroxylitol by oxygen in aqueous sodium hydroxide solutions. Tappi 49:362–366
12. McCloskey CM, Coleman GH (1945) A proposed inversion mechanism for the formation of levoglucosan from phenyl β-D-glucoside and trimethylglucosylammonium compounds. J Org Chem 10:184–193
13. Tsai CS, Reyes-Zamora C (1972) Mechanisms of alkaline hydrolysis of p-nitrophenyl glucopyranosides. J Org Chem 37:2725–2729
14. Molinarolo WE, Dimmel DR, Malcolm EW, Schroeder LR (1990) High-temperature alkaline degradation of phenyl β-D-glucopyranoside. J Wood Chem Technol 10:209–231
15. Adams R, Voorhees V (1921) Furfural. Org Synth 1:49–52
16. Yi GS, Zhang YG (2012) One-pot selective conversion of hemicellulose (xylan) to xylitol under mild conditions. ChemSusChem 5:1383–1387
17. Beg Q, Kapoor M, Mahajan L, Hoondal G (2001) Microbial xylanases and their industrial applications: a review. Appl Microbiol Biotechnol 56:326–338
18. Xie HB, Gerber RB (2012) Interaction and reaction of the hydroxyl ion with β-D-galactose and its hydrated complex: an ab initio molecular dynamics study. Phys Chem Chem Phys 14:12086–12089
19. Suzuki T (2008) The hydration of glucose: the local configurations in sugar–water hydrogen bonds. Phys Chem Chem Phys 10:96–105
20. Heyden M, Brundermann E, Heugen U, Niehues G, Leitner DM, Havenith M (2008) Long range influence of carbohydrates on the solvation dynamics of water–answers from THz absorption measurements and molecular modeling simulations. J Am Chem Soc 130:5773–5779
21. Aviles-Moreno JR, Demaison J, Huet TR (2006) Conformational flexibility in hydrated sugars: the glycolaldehyde-water complex. J Am Chem Soc 128:10467–10473
22. Ditzler MA, Otyepka M, Sponer J, Walter NG (2010) Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in. Acc Chem Res 43:40–47
23. Jin L, Simons JP, Gerber RB (2011) Structures of the xylose–water complex: energetics, transitions between conformers and spectroscopy. Chem Phys Lett 518:49–54
24. Jin L, Simons JP, Gerber RB (2012) Monosaccharide-water complexes: vibrational spectroscopy and anharmonic potentials. J Phys Chem A 116:11088–11094
25. Aoki Y, Gu FL (2012) An elongation method for large systems toward bio-systems. Phys Chem Chem Phys 14:7640–7668
26. Imamura A, Aoki Y, Maekawa K (1991) A theoretical synthesis of polymers by using uniform localization of molecular orbitals: proposal of an elongation method. J Chem Phys 95:5419–5431
27. Aoki Y, Imamura A (1992) Local density of states of aperiodic polymers using the localized orbitals from an ab initio elongation method. J Chem Phys 97:8432–8440
28. Aoki Y, Suhai S, Imamura A (1994) An efficient cluster elongation method in density-functional theory and its application to poly-hydrogen-bonding molecules. J Chem Phys 101:10808–10823
29. Korchowiec J, Gu FL, Imamura A, Kirtman B, Aoki Y (2005) Elongation method with cutoff technique for linear SCF scaling. Int J Quantum Chem 102:785–794
30. Korchowiec J, Silva P, Makowski M, Gu FL, Aoki Y (2010) Elongation cutoff technique at kohn-sham level of theory. Int J Quantum Chem 110:2130–2139
31. Korchowiec J, Gu FL, Aoki Y (2006) Elongation method for linear scaling SCF calculations of polymers. J Comput Meth Sci Eng 6:189–200
32. Korchowiec J, Lewandowski J, Makowski M, Gu FL, Aoki Y (2009) Elongation cutoff technique armed with quantum fast multipole method for linear scaling. J Comput Chem 30:2515–2525
33. Liu K, Yan Y, Gu FL, Aoki Y (2013) A modified localization scheme for the three-dimensional elongation method applied to large systems. Chem Phys Lett 565:143–147
34. Chaban G, Schmidt MW, Gordon MS (1997) Approximate second order method for orbital optimization of SCF and MCSCF wavefunctions. Theor Chem Accounts 97:88–95
35. Makowski M, Korchowiec J, Gu FL, Aoki Y (2006) Efficiency and accuracy of the elongation method as applied to the electronic structures of large systems. J Comput Chem 27:1603–1619
36. Orimoto Y, Gu FL, Imamura A, Aoki Y (2007) Efficient and accurate calculations on the electronic structure of B-type poly(dG)-poly(dC) DNA by elongation method: first step toward the understanding of the biological properties of aperiodic DNA. J Chem Phys 126:215104
37. Xie P, Liu K, Gu FL, Aoki Y (2011) Counter-ion effects of A- & B-type poly(dG)·poly(dC) and poly(dA)·poly(dT) DNA by elongation method. Int J Quantum Chem 112:230–239
38. Chen W, Yu GT, Gu FL, Aoki Y (2009) Investigation on nonlinear optical properties of ladder-structure polydiacetylenes derivatives by using the elongation finite-field method. Chem Phys Lett 474:175–179
39. Chen W, Yu GT, Gu FL, Aoki Y (2009) Investigation on the electronic structures and nonlinear optical properties of pristine boron nitride and BN/C heterostructured single-wall nanotubes by the elongation method. J Phys Chem C 113:8447–8454
40. Xie P, Orimoto Y, Aoki Y (2013) An efficient local molecular dynamics polymerization simulation combined with an ab initio MO method. Materials 6:870–885
41. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su SJ, Windus TL, Dupuis M, Montgomery JA (2003) GAMESS Version 14 (Iowa State University, Iowa, 2003) General atomic and molecular electronic structure system. J Comput Chem 14:1347–1363
42. Gu FL, Aoki Y, Korchowiec J, Imamura A, Kirtman B (2004) A new localization scheme for the elongation method. J Chem Phys 121:10385–10391
43. Allen MP, Tildesley DJ (1987) Computer simulation of liquids. Oxford University Press, Oxford
44. Sadus RJ (1999) Molecular Simulation of fluids: theory, algorithms and object-orientation. Elsevier, New York
45. Berendsen HJC, Postma JPM, Vangunsteren WF, Dinola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690
46. Nieduszynski I, Marchessault RH (1971) Structure of β-D-(1,4’)-xylan hydrate. Nature 232:46–47
47. Sarkar A, Pérez S (2012) PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides. BMC Bioinforma 13:302