Noncovalent interactions in the gas-phase conformers of anionic iduronate (methyl 2-O-sulfo-α-L-iduronate): Variation of subconformer versus ring conformer energetics for a prototypical anionic monosaccharide studied using computational methods

Journal of Physical Chemistry A

Volumn 114, Issue 42, 2010, Pages 11153-11160

  Taylor, Christopher J ^a   Nix, Michael G D ^a   Dessent, Caroline E H ^a  

^a UNIVERSITY OF YORK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANOMERIC EFFECT; COMPUTATIONAL LEVEL; COMPUTATIONAL STUDIES; CONFORMATIONAL PREFERENCES; FUNCTIONALS; GASPHASE; HYDROGEN BONDING INTERACTIONS; MP2 CALCULATIONS; NON-COVALENT INTERACTION; NONCOVALENT; PENDANT FUNCTIONAL GROUP; RELATIVE ENERGIES; SIDE CHAINS;

FUNCTIONAL GROUPS; GLUCOSE; HYDROGEN; QUANTUM CHEMISTRY; SUGAR (SUCROSE);

HYDROGEN BONDS;

ANION; DRUG DERIVATIVE; IDURONIC ACID; METHYL 2 O SULFO ALPHA L IDURONATE; METHYL 2-O-SULFO-ALPHA-L-IDURONATE;

ARTICLE; CHEMISTRY; CONFORMATION; GAS; MOLECULAR DYNAMICS;

ANIONS; CARBOHYDRATE CONFORMATION; GASES; IDURONIC ACID; MOLECULAR DYNAMICS SIMULATION;

EID: 77958486249     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp102657t     Document Type: Article

References (48)

1. Bernfield, M.; Götte, M.; Park, P. W.; Reizes, O.; Fitzgerald, M. L.; Lincecum, J.; Zako, M. Annu. Rev. Biochem. 1999, 68, 729
2. Berg, M.; Tymoczko, J. L.; Stryer, L.; Biochemistry, Fifth ed.; W.H Freeman & Company: 2002.
3. Drouin, L.; Stanca-Kaposta, E. C.; Saundh, P.; Fairbanks, A. J.; Kemper, S.; Claridge, T. D. W.; Simons, J. P. Chem.-Eur. J. 2009, 15, 4057
4. Petitou, M.; van Boeckel, C. A. A. Angew. Chem., Int. Ed. 2004, 43, 3118
5. Lindahl, U.; Backstrom, G.; Hook, M.; Thunberg, L.; Fransson, L. A.; Linker, A. Proc. Natl. Acad. Sci. 1979, 76, 3198
6. Shriver, Z.; Raman, R.; Venkataraman, G.; Drummond, K.; Turnbull, J.; Toida, T.; Linhardt, R.; Biemann, K.; Sasisekharan, R. Biochemistry 2000, 97, 10359
7. Pope, R. M.; Raska, C. S.; Thorp, S. C.; Liu, J. Glycobiology 2001, 11, 505
8. Venkataraman, G.; Shriver, Z.; Raman, R.; Sasisekharan, R. Science 1999, 286, 537
9. Kuberan, B.; Lech, M.; Zhang, L.; Wu, Z. L.; Beeler, D. L.; Rosenberg, R. D. J. Am. Chem. Soc. 2002, 124, 8707
10. Desaire, H.; Leary, J. A. J. Am. Soc. Mass Spectrom. 2000, 11, 916
11. Jin, L.; Barran, P. E.; Deakin, J. A.; Lyon, M.; Uhrin, D. Phys. Chem. Chem. Phys. 2005, 7, 3464
12. Taylor, C. J.; Burke, R. M.; Wu, B.; Panja, S.; Nielsen, S. B.; Dessent, C. E. H. Int. J. Mass. Spec. 2009, 285, 70
13. Linhardt, R. J.; Capila, I. Angew. Chem., Int. Ed. 2002, 41, 390
14. Hunig, I.; Painter, A. J.; Jockusch, R. A.; Carcabal, P.; Marzluff, E. M.; Snoek, L. C.; Gamblin, D. P.; Davis, B. G.; Simons, J. P. Phys. Chem. Chem. Phys. 2005, 7, 2474
15. Cocinero, E. J.; Stanca-Kaposta, E. C.; Scarlan, E. M.; Gamblin, D. P.; Davis, B. G.; Simons, J. P. Chem.-Eur. J. 2008, 14, 8947
16. Raju, R. K.; Ramraj, A.; Vincent, M. A.; Hillier, I. A.; Burton, N. A. Phys. Chem. Chem. Phys. 2008, 10, 6500
17. Raju, R. K.; Ramraj, A.; Hillier, I. H.; Vincent, M. A.; Burton, N. A. Phys. Chem. Chem. Phys. 2009, 11, 3411
18. Hricovini, M. Carbohydr. Res. 2006, 341, 2575
19. Remko, M.; von der Lieth, C. W. J. Chem. Inf. Model. 2006, 46, 1194
20. Hemmingson, L.; Madsen, D. E.; Esbensen, A. L.; Olsen, L.; Engelsen, S. B. Carbohydr. Res. 2004, 339, 937
21. Barrows, S. E.; Dulles, F. J.; Cramer, C. J.; French, A. D.; Truhlar, D. G. Carbohydr. Res. 1995, 276, 219
22. Weldon, A. J.; Vickerey, T. L.; Tschumper, G. S. J. Phys. Chem. A 2005, 109, 11073
23. Johnson, E. R.; Becke, A. D. Chem. Phys. Lett. 2006, 432, 600
24. Cerny, J.; Hobza, P. Phys. Chem. Chem. Phys. 2007, 9, 5291
25. Kubar, T.; Jurecka, P.; Cerny, J.; Rezac, J.; Otyepka, M.; Valdes, H.; Hobza, P. J. Phys. Chem. A 2007, 111, 5642
26. Hobza, P.; Zahradnik, R.; Muller-Dethlefs, K. Collect. Czech. Chem. Commun. 2006, 71, 443
27. Zhao, Y.; Truhlar, D. G. J. Chem. Theory Comput. 2007, 3, 289
28. Zhao, Y.; Schultz, N. E.; Truhlar, D. G. J. Chem. Theory Comput. 2006, 2, 364
29. Grimme, S. J. J. Comput. Chem. 2006, 27, 1787
30. Deppmeier, B. J.; Driessen, A. J.; Hehre, T. S.; Hehre, W. J.; Johnson, J. A.; Klunzinger, P. E.; Leonard, J. M.; Ohlinger, W. S.; Pham, I. N.; Pietro, W. J.; Yu, J. PC Spartan Pro; Wavefunction, Inc.: Irvine, CA, 2000.
31. Halgren, T. A. J. Comput. Chem. 1996, 17, 490
32. Stortz, C. A.; Johnson, G. P.; French, A. D.; Csonka, G. I. Carbohyd. Res. 2009, 344, 2217
33. Kaminsky, J.; Jensen, F. J. Chem. Theory. Comput., 2007, 3, 1774
34. Burke, R. M.; Pearce, J. K.; Boxford, W. E.; Bruckmann, A.; Dessent, C. E. H. J. Phys. Chem. A 2005, 109, 9775
35. Burke, R. M.; Dessent, C. E. H. J. Phys. Chem. A. 2009, 113, 2683
36. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision C.01; Gaussian, Inc.: Pittsburgh, PA, 2003.
37. Tsuzuki, S.; Lüthi, H. P. J. Chem. Phys. 2001, 114, 3949
38. Yang, Y.; Pan, W.; Yang, W. J. Chem. Phys. 1997, 107, 7291
39. Wesolowski, T. A.; Parisel, O.; Ellinger, Y.; Weber, J. J. Phys. Chem. A 1997, 101, 7818
40. Patey, M. D.; Dessent, C. E. H. J. Phys. Chem. A 2002, 106, 4623
41. Joint Commission on Biochemical Nomenclature (JCBN), Eur. J. Biochem. 2005, 111, 295.
42. The term "hydrogen bond" is applied to any pair-wise interaction between an electron-pair donating atom and an electron-pair accepting hydrogen atom. We define typical hydrogen bonds as having bond lengths of <3Å and bond angles of 180 ± 25°, with loose "hydrogen-bond-like" interactions having bond lengths of <3.5 Å and bond angles of 180 ± 65°.
43. Jurecka, P.; Sponer, J.; Cerny, J.; Hobza, P. Phys. Chem. Chem. Phys. 2006, 8, 1985
44. Csonka, G. I.; French, A. D.; Johnson, G. P.; Stortz, C. A. J. Chem. Theory Comput. 2009, 5, 679
45. 1-V according to the naming scheme adopted in Figure 3.
46. Raghuraman, A.; Liang, A.; Krishnasamy, C.; Lauck, T.; Gunnarsson, G. T.; Desai, U. R. Eur. J. Med. Chem. 2009, 44, 2626
47. Dowd, M. K.; French, A. D.; Reilly, P. J. Carbohyd. Res. 1994, 264, 1
48. van Mourik, T. J. Chem. Theory Comput. 2008, 10, 1610