Rapidly calculated DFT relaxed iso-potential ϕ/ψ maps: β-cellobiose
Source abstract
Abstract
New cellobiose ϕH/ψH maps are generated using a mixed basis set DFTr method, found to achieve a high level of confidence while reducing computer resources dramatically. Relaxed iso-potential maps are created for different conformational states of cellobiose, showing how glycosidic bond dihedral angles vary as different sets of hydroxymethyl rotamers and hydroxyl directions are examined. These maps are generated, fixing the dihedral ϕH and ψH values at ten degree intervals and energy optimizing the remaining geometry using the B3LYP/6-31+G* functional for all atoms except carbon atoms, where the functional B3LYP was used with the mixed basis set, 4-31G. Mapping results are compared between in vacuo structures using the mixed basis set, in vacuo using the full basis set, and those in which the implicit solvent method, COSMO, is included with the mixed basis set. Results show significant changes in position of energy minima with variation in hydroxyl rotamers and with application of solvent. Unique to this study is the mapping of the hydration energy at each ϕH/ψH point on the map using the energy derived at each point by applying COSMO. Using hydration gradients as a guide one observes directional solvent driven changes in the minimum energy positions. Interesting internal coordinate variances are described.
Source: openaire · Quality: candidate unverified · Source record ↗
Research context
OpenAlex topics: Molecular spectroscopy and chirality · Advanced Chemical Physics Studies · Nonlinear Optical Materials Research
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References (71)
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1. Andrianov VM, Zhbankov RG, Dashevski VG (1980) A theoretical study of the vibrational spectrum of cellobiose within the framework of the additive model of interatomic interactions. J Struct Chem 21:320–32410.1007/BF00746852 ↗
2. Asensio JL, Jimenez-Barbero J (1995) The use of the AMBER force field in conformational analysis of carbohydrate molecules: Determination of the solution conformation of methyl α-lactoside by NMR spectroscopy, assisted by molecular mechanics and dynamics calculations. Biopolymers 35:55–7310.1002/bip.360350107 ↗
3. Asensio JL, Martin-Pastor M, Jimenez-Barbero J (1997) The use of the MM3* and ESFF force fields in conformational analysis of carbohydrate molecules in solution: the methyl α-lactoside case. J Mol Struct (Theochem) 395–396; 245–27010.1016/S0166-1280(96)04956-1 ↗
4. Bosma WB, Appell M, Willett JL, Momany FA (2006a) 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) 776:13–31
5. Bosma WB, Appell M, Willett JL, Momany FA (2006b) Stepwise hydration of cellobiose by DFT methods: 2. Energy contributions to relative stabilities of cellobiose (H2O)1–4 complexes. J Mol Struct (THEOCHEM) 776:1–1110.1016/j.theochem.2006.07.024 ↗
6. Cheetham NWH, Dasgupta P, Ball GE (2003) NMR and modeling studies of disaccharide conformation. Carbohydr Res 338:955–96210.1016/S0008-6215(03)00069-7 ↗
7. Chen JY-J, Naidoo KJ (2003) Evaluating intra-molecular hydrogen bond strengths in (1–4) linked disaccharides from electron density relationships. J Phys Chem B 107:9558–956610.1021/jp035574f ↗
8. Christensen NJ, Hansen PI, Larsen FH, Folkerman T, Motawia MS, Engelsen SB (2010) A combined nuclear magnetic resonance and molecular dynamics study of the two structural motifs for mixed-linkage β-glucans: methyl β-cellobioside and methyl β-laminarabioside. Carbohydr Res 345:474–48610.1016/j.carres.2009.12.009 ↗
9. Chu SSC, Jeffrey GA (1968) The refinement of the crystal structures of β-d-glucose and cellobiose. Acta Cryst B24:830–838
10. Cocinero EJ, Gamblin DP, Davis BG, Simons JP (2009) The building blocks of cellulose: the intrinsic conformational structures of cellobiose, its epimer, lactose and their singly hydrated complexes. J Am Chem Soc 131:11117–1112310.1021/ja903322w ↗
11. da Silva CO, Nascimento MAC (2004) Ab initio conformational maps for disaccharides in gas phase and aqueous solution. Carbohydr Res 339:113–12210.1016/j.carres.2003.09.037 ↗
12. Duus JO, Bock K, Ogawa S (1994) An NMR spectroscopic and conformational study of 12 pseudo-disaccharides (d-glucopyranosyl-5a-carba-d- and–l-gluco- pyranoses). Carbohydr Res 252:1–18
13. French AD (1988) Rigid- and relaxed-residue conformational analyses of cellobiose using the computer program MM2. Biopolymers 27:1519–152510.1002/bip.360270914 ↗
14. French AD, Dowd MK (1993) Exploration of disaccharide conformations by molecular mechanics. J Mol Struct (THEOCHEM) 286:183–20110.1016/0166-1280(93)87162-7 ↗
15. French AD, Johnson GP (2004) Advanced conformational energy surfaces for cellobiose. Cellulose 11:449–46210.1023/B:CELL.0000046409.37326.b1 ↗
16. French AD, Johnson GP (2006) Quantum mechanics studies of cellobiose conformations. Can J Chem 84:603–61210.1139/v06-050 ↗
17. French AD, Johnson GP (2008) Roles of starting geometries in quantum mechanics studies of cellobiose. Mol Simul 34:365–37210.1080/08927020701663347 ↗
18. French AD, Johnson GP (2009) Cellulose and the twofold screw axis: modeling and experimental arguments. Cellulose 16:959–97310.1007/s10570-009-9347-4 ↗
19. French AD, Kelterer AM, Johnson GP, Dowd MK, Cramer CJ (2000) Construction and evaluating energy surfaces of crystalline disaccharides. J Mol Graph Model 18:95–10710.1016/S1093-3263(00)00041-3 ↗
20. French AD, Kelterer A-M, Johnson GP, Dowd MK, Cramer CJ (2001) HF/6–31G* energy surfaces for disaccharide analogs. J Comp Chem 22:65–7810.1002/1096-987X(20010115)22:1<65::AID-JCC7>3.0.CO;2-R ↗
21. Gessler K, Krauss N, Steiner T, Betzel C, Sarko A, Saenger W (1995) β-d-cellotetraose hemihydrate as a structural model for cellulose II. An X-ray diffraction study. J Am Chem Soc 117:11397–1140610.1021/ja00151a003 ↗
22. Ham JT, Williams DG (1970) The crystal and molecular structure of methyl-β-cellobioside-methanol. Acta Cryst B26:1373–138310.1107/S0567740870004132 ↗
23. Hamer GK, Balza F, Cyr N, Perlin AS (1978) A conformational study of methyl β-cellobioside-d8 by 13C nuclear magnetic resonance spectroscopy: Dihedral angle dependence of 3JC, H in 13C-O-C-1H arrays. Can J Chem 56:3109–311610.1139/v78-508 ↗
24. Hardy BJ, Sarko AJ (1993a) Conformational analysis and molecular dynamics simulation of cellobiose and larger cellooligomers. J Comput Chem 14:831–84710.1002/jcc.540140709 ↗
25. Hardy BJ, Sarko AJ (1993b) Molecular dynamics simulation of cellobiose in water. J Comput Chem 14:848–85710.1002/jcc.540140710 ↗
26. Hardy BJ, Gutierrez A, Lesiak K, Seidl E, Widmalm G (1996) Structural analysis of the solution conformation of methyl-4-O-b-d-glucopyranosyl-a-d-glucospyranoside by molecular mechanics and ab initio calculation, stochastic dynamics simulation, and NMR spectroscopy. J Phys Chem 100:9187–919210.1021/jp953139i ↗
27. Hirotsu K, Shimada A (1974) The crystal and molecular structure of β-lactose. Bull Chem Soc Jpn 47:1872–187910.1246/bcsj.47.1872 ↗
28. Homans SW (1993) Conformation and dynamics of oligosaccharides in solution. Glycobiology 3:551–55510.1093/glycob/3.6.551 ↗
29. Horii F, Hirai A, Kitamaru R (1982) Solid-state high-resolution 13C-NMR studies of regenerated cellulose samples with different crystallinities. Polym Bull 8:163–17010.1007/BF00263023 ↗
30. Horii F, Hirai A, Kitamaru R (1983) Solid-state 13C-NMR study of conformations of oligosaccharides and cellulose. Polym Bull 10:357–36110.1007/BF00281948 ↗
31. Hyperchem v8.0.2 (2007) Hypercube, Inc. 115 NW 4th Street, Gainesville, FL, 32602. USA
32. Johnson GP, Petersen L, French AD, Reilly PJ (2009) Twisting of glycosidic bonds by hydrolases. Carbohydr Res 344:2157–216610.1016/j.carres.2009.08.011 ↗
33. Kirschner KN, Woods RJ (2001) Solvent interactions determine carbohydrate conformation. Proc Natl Acad Sci 11:10541–1054510.1073/pnas.191362798 ↗
34. Klamt A, Schüürmann GJ (1993) COSMO-A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J Chem Soc Perkin Tran II:799–80510.1039/P29930000799 ↗
35. Korolik EV, Ivanova NV, Kolosova TE, Zhbankov RG (1985) Investigation of the IR spectra of cellobiose and O-deuterated cellobiose at the temperature of liquid helium. J Appl Spectrosc 42:551–55310.1007/BF00661405 ↗
36. Larsson EA, Staaf M, Soderman P, Hoog C, Widmalm G (2004) Determination of the conformational flexibility of methyl α-cellobioside in solution by NMR spectroscopy and molecular simulations. J Phys Chem A 108:3932–393710.1021/jp049714c ↗
37. Leung F, Chanzy HD, Perez S, Marchessault RH (1976) Crystal structure of β-d-acetyl cellobiose, C28H38O19. Can J Chem 54:1365–137110.1139/v76-195 ↗
38. Mackie ID, Rohrling J, Gould RO, Pauli J, Jager C, Walkinshaw M, Potthast A, Rosenau T, Kosma P (2002) Crystal and molecular structure of methyl 4-O-methyl-β-d-glucopyranosyl-(1 → 3)-β-d-glucopyranoside. Carbohydr Res 337:161–16610.1016/S0008-6215(01)00299-3 ↗
39. Mendonca S, Johnson GP, French AD, Laine RA (2002) Conformational analyses of native and permethylated disaccharides. J Phys Chem A 106:4115–412410.1021/jp013290u ↗
40. Momany FA, Schnupf U (2011) DFTMD studies of b-cellobiose: conformational preference using implicit solvent. Carbohydr Res 340:619–630
41. Olsson U, Serianni AS, Stenutz R (2008) Conformational analysis of β-glycosidic linkages in 13C-labeled glucobioside using inter-residue scalar coupling constants. J Phys Chem B112:4447–445310.1021/jp710977k ↗
42. Origin v8.0 (2009) OriginLab Corporation, Northampton, MA
43. Peralta-Inga Z, Johnson GP, Dowd MK, Rendleman JA, Stevens ED, French AD (2002) The crystal structure of the α-cellobiose 2 NaI·2 H2O complex in the context of related structures and conformational analysis. Carbohydr Res 337:851–86110.1016/S0008-6215(02)00041-1 ↗
44. Pereira CS, Kony D, Baron R, Muller M, van Gunsteren WF, Hunenberger PH (2006) Conformational and dynamical properties of disaccharides in water: a molecular dynamics study. Biophys J 90:4337–434410.1529/biophysj.106.081539 ↗
45. Peters T, Meyer B, Stuike-Prill R, Somorjai R, Brisson J-R (1993) A Monte Carlo method for conformational analysis of saccharides. Carbohydr Res 238:49–7310.1016/0008-6215(93)87005-D ↗
46. PQS, Ab Initio Program Package v3.3 (2009) Parallel Quantum Solutions, 2013 Green Acres, Suite E, Fayetteville, AR 72703, USA
47. Raymond S, Henrissat B, Qui DT, Kvick A, Chanzy H (1995) The crystal structure of methyl β-cellotrioside monohydrate 0.25 ethanolate and its relationship to cellulose II. Carbohydr Res 277:209–22910.1016/0008-6215(95)00219-J ↗
48. Rencurosi A, Rohrling J, Pauli J, Potthast A, Jager C, Perez S, Kosma P, Imberty A (2002) Polymorphism in the crystal structure of the cellulose fragment analogue methyl 4-O-methyl-β-d-glucopyranosyl-(1–4)-β-d-glucopyranoside. Angew Chem Int Ed 41:4277–428110.1002/1521-3773(20021115)41:22<4277::AID-ANIE4277>3.0.CO;2-I ↗
49. Schnupf U, Willett JL, Bosma WB, Momany FA (2007) DFT studies of the disaccharide, α-maltose: relaxed isopotential maps. Carbohydr Res 342:2270–228510.1016/j.carres.2007.06.026 ↗
50. Schnupf U, Willett JL, Momany FA (2011) 27 ps DFT molecular dynamics simulation of a-maltose: a reduced basis set study. J Comput Chem 31:2087–209710.1002/jcc.21495 ↗
51. Sergeyev I, Moyna G (2005) Determination of the three-dimensional structure of oligosaccharides in the solid state from experimental 13C NMR data and ab initio chemical shift surfaces. Carbohydr Res 340:1165–117410.1016/j.carres.2005.02.022 ↗
52. Shen T, Langan P, French AD, Johnson GP, Gnanakaran S (2009) Conformational flexibility of soluble cellulose oligomers: chain length and temperature dependence. J Am Chem Soc 131:14786–1479410.1021/ja9034158 ↗
53. Sivchik VV, Zhbankov RG (1977) Theoretical investigation of the vibrational spectrum of cellobiose. Translated from Zhurnal Prikladnoi Spektroskopii 27:853–859
54. Stortz CA, Cerezo AS (2002) Disaccharide conformational maps: 3D contours or 2D plots? Carbohydr Res 337:1861–187110.1016/S0008-6215(02)00257-4 ↗
55. Stortz CA, Cerezo AS (2003) Depicting the MM3 potential energy surfaces of trisaccharides by single contour maps: application to β-cellotriose and α-maltotriose. Carbohydr Res 338:95–10710.1016/S0008-6215(02)00360-9 ↗
56. Stortz CA, French AD (2008) Disaccharide conformational maps: adiabaticity in analogues with variable ring shapes. Mol Simul 34:373–38910.1080/08927020701663339 ↗
57. Stortz CA, Johnson GP, French AD, Csonka GI (2009) Comparison of different force fields for the study of disaccharides. Carbohydr Res 344:2217–222810.1016/j.carres.2009.08.019 ↗
58. Strati GL, Willett JL, Momany FA (2002a) Ab initio computational study of β-cellobiose conformers using B3LYP/6–311++G**. Carbohydr Res 337:1833–184910.1016/S0008-6215(02)00267-7 ↗
59. Strati GL, Willett JL, Momany FA (2002b) A DFT/ab initio study of hydrogen bonding and conformational preference in model cellobiose analogs using B3LYP/6–311++G**. Carbohydr Res 337:1851–185910.1016/S0008-6215(02)00269-0 ↗
60. Sugiyama H, Hisamichi K, Usui T, Sakai K, Ishiyama J-i (2000) A study of the conformation of β-1, 4-linked glucose oligomers, cellobiose to cellohexaose, in solution. J Mol Struct (THEOCHEM) 556:173–17710.1016/S0022-2860(00)00630-X ↗
61. Suzuki S, Horii F, Kurosu H (2009) Theoretical investigations of 13C chemical shifts in glucose, cellobiose, and native cellulose by quantum chemistry calculations. J Mol Struct (THEOCHEM) 921:219–22610.1016/j.molstruc.2009.01.002 ↗
62. Tvaroska I (1984) Theoretical studies on the conformation of saccharides. VIII. Solvent effect on the stability of β-cellobiose conformers. Biopolymers 23:1951–196010.1002/bip.360231011 ↗
63. Tvaroska I, Taravel FR (1992) One-bond carbon-proton coupling constants: angular dependence in β-linked oligosaccharides. J Biomol NMR 2:421–43010.1007/BF02192806 ↗
64. Umemura M, Hayashi S, Nakagawa T, Yamanaka S, Urakawa H, Kajiwara K (2003a) Structure of water molecules in aqueous maltose and cellobiose solutions using molecular dynamics simulation. I. Statics. J Mol Struct (THEOCHEM) 624:129–14410.1016/S0166-1280(02)00717-0 ↗
65. Umemura M, Hayashi S, Nakagawa T, Urakawa H, Kajiwara K (2003b) Structure of water molecules in aqueous maltose and cellobiose solutions using molecular dynamics simulation. II. Dynamics. J Mol Struct (THEOCHEM) 636:215–22810.1016/S0166-1280(03)00477-9 ↗
66. Umemura M, Yuguchi Y, Hirotsu T (2005) Hydration at glycosidic linkages of malto- and cello-oligosaccharides in aqueous solution from molecular dynamics simulation: effect of conformational flexibility. J Mol Struct (THEOCHEM) 730:1–810.1016/j.theochem.2005.05.034 ↗
67. Vietor RJ, Mazeau K, Lakin M, Perez S (2000) A priori crystal structure prediction of native celluloses. Biopolymers 54:342–35410.1002/1097-0282(20001015)54:5<342::AID-BIP50>3.0.CO;2-O ↗
68. Wacowich-Sgarbi SA, Ling CC, Otter A, Bundle DR (2001) A tethered disaccharide trapped as its anti-conformer calibrates the Karplus relationship for 3JC, H coupling constants. J Am Chem Soc 123:4362–436310.1021/ja005901m ↗
69. Yoneda Y, Mereiter K, Jaeger C, Brecker L, Kosma P, Rosenau T, French A (2008) van der Waals versus hydrogen-bonding forces in a crystalline analog of cellotetraose: cyclohexyl 4′-O-cyclohexyl β-d-cellobioside cyclohexane solvent. J Am Chem Soc 130:16678–1669010.1021/ja805147t ↗
70. York WS, Yi X (2004) CONDORR-CONstrained dynamics of rigid residues: a molecular dynamics program for constrained molecules. J Mol Model 10:271–289
71. Zhang W, Zhao W, Carmichael H, Serianni AS (2009) An NMR investigation of putative inter-residue H-bonding in methyl α-cellobioside in solution. Carbohydr Res 344:1582–158710.1016/j.carres.2009.06.007 ↗