Abstract
Correct prediction of the structure and energetics along the reaction pathway of the formation or dissociation of the glycosidic bond in sugar phosphates is crucial for the understanding of catalytic mechanism and for the determination of transition state structures of sugar-phosphate processing enzymes. The performance of seven density functional theory (DFT) methods (BLYP, B3LYP, MPW1PW91, MPW1K, MPWB1K, M05 and M05-2X) and two wave function methods (HF and MP2) was tested using four structural models with the activated sugar-phosphate α-glycosidic linkage. The models were chosen based on the crystal structure of the retaining glycosyltransferase LgtC complex with methyl α-d-galactopyranose diphosphate and its 2-fluoro derivative. Results of the MP2 method were used as a benchmark for the other methods. Two structural trends were observed in the calculations: predicted length of the activated C1-O1 glycosidic bond of 1.49–1.63 Å was significantly larger than values of a standard C1-O1 glycosidic bond in crystal structures of carbohydrates (1.39–1.48 Å), and the calculated value depended on the DFT method used. The MPW1K, M05 and M05-2X functionals provided results in closest agreement with those from the MP2 method, the difference being less than 0.02 Å in the calculated glycosidic bond lengths. On the contrary, the BLYP and B3LYP functionals failed to predict sugar diphosphate in the (-sc) conformation as a stable structure. Instead, the only stationary points localized along the C1-O1 dissociation coordinate were oxocarbenium ions at the distance of approximately 2.8 Å. The M05-2X, MPW1K and MPWB1K functionals gave the most reasonable prediction of the thermochemical kinetic parameters, where the formation of the oxocarbenium ion has a slightly endothermic character (0.4–1.7 kJ mol−1) with an activation barrier of 7.9–9.2 kJ mol−1.
[1] Adamo, C., & Barone, V. (1998). Exchange functionals with improved long-range behavior and adiabatic connection methods without adjustable parameters: The mPW and mPW1PW models. Journal of Chemical Physics, 108, 664–675. DOI: 10.1063/1.475428. http://dx.doi.org/10.1063/1.47542810.1063/1.475428Search in Google Scholar
[2] André, I., Tvaroška, I., & Carver, J. P. (2000). Effects of the complexation by the Mg2+ cation on the stereochemistry of the sugar-diphosphate linkage. Ab initio modeling on nucleotide-sugars. Journal of Physical Chemistry A, 104, 4609–4617. DOI: 10.1021/jp000028x. http://dx.doi.org/10.1021/jp000028x10.1021/jp000028xSearch in Google Scholar
[3] André, I., Tvaroška, I., & Carver, J. P. (2003). On the reaction pathways and determination of transition-state structures for retaining α-galactosyltransferases. Carbohydrate Research, 338, 865–877. DOI: 10.1016/S0008-6215(03)00050-8. http://dx.doi.org/10.1016/S0008-6215(03)00050-810.1016/S0008-6215(03)00050-8Search in Google Scholar
[4] Becke, A. D. (1993). Density-functional thermochemistry. 3. The role of exact exchange. Journal of Chemical Physics, 98, 5648–5652. DOI: 10.1063/1.464913. http://dx.doi.org/10.1063/1.46491310.1063/1.464913Search in Google Scholar
[5] Biarnés, X., Ardèvol, A., Planas, A., Rovira, C., Laio, A., & Parrinello, M. (2007). The conformational free energy landscape of β-d-glucopyranose. Implications for substrate preactivation in β-glucoside hydrolases. Journal of the American Chemical Society, 129, 10686–10693 DOI: 10.1021/ja068411o. http://dx.doi.org/10.1021/ja068411o10.1021/ja068411oSearch in Google Scholar
[6] Biarnés, X., Nieto, J., Planas, A., & Rovira, C. (2006). Substrate distortion in the Michaelis complex of Bacillus 1,3-1,4-β-glucanase: Insight from first principles molecular dynamics simulations. Journal of Biological Chemistry, 281, 1432–1441. DOI: 10.1074/jbc.M507643200. http://dx.doi.org/10.1074/jbc.M50764320010.1074/jbc.M507643200Search in Google Scholar
[7] Bottoni, A., Miscione, G. P., & De Vivo, M. (2005). A theoretical DFT investigation of the lysozyme mechanism: Computational evidence for a covalent intermediate pathway. Proteins-Structure Function and Bioinformatics, 59, 118–130. DOI: 10.1002/prot.20396. http://dx.doi.org/10.1002/prot.2039610.1002/prot.20396Search in Google Scholar
[8] Brooks, S. A., Dwek, M. V., & Schumacher, U. (2002). Functional & molecular glycobiology (1st ed.) (pp. 287–327). Oxford: BIOS Scientific Publishers Ltd. Search in Google Scholar
[9] Coskuner, O. (2007). Preferred conformation of the glycosidic linkage of methyl β-mannose. Journal of Chemical Physics, 127, 015101. DOI: 10.1063/1.2747238. 10.1063/1.2747238Search in Google Scholar
[10] Csonka, G. I. (2002). Proper basis set for quantum mechanical studies of potential energy surfaces of carbohydrates. Journal of Molecular Structure: THEOCHEM, 584, 1–4. DOI: 10.1016/S0166-1280(02)00096-9. http://dx.doi.org/10.1016/S0166-1280(02)00096-910.1016/S0166-1280(02)00096-9Search in Google Scholar
[11] Dkhissi, A., & Blossey, R. (2007). Performance of DFT/MPWB1K for stacking and H-bonding interactions. Chemical Physics Letters, 439, 35–39. DOI: 10.1016/j.cplett.2007.03.065. http://dx.doi.org/10.1016/j.cplett.2007.03.06510.1016/j.cplett.2007.03.065Search in Google Scholar
[12] Fabian, W. M. F. (2007). Metal binding induced conformational interconversions in methyl β-d-xylopyranoside. Theoretical Chemistry Accounts, 117, 223–229. DOI: 10.1007/s00214-006-0130-4. http://dx.doi.org/10.1007/s00214-006-0130-410.1007/s00214-006-0130-4Search in Google Scholar
[13] Fois, E. S., Penman, J. I., & Madden, P. A. (1993). Self-interaction corrected density functionals and the structure of metal clusters. Journal of Chemical Physics, 98, 6352–6360. DOI: 10.1063/1.464828. http://dx.doi.org/10.1063/1.46482810.1063/1.464828Search in Google Scholar
[14] Frisch, M. J., Headgordon, M., & Pople, J. A. (1990a). A direct MP2 gradient-method. Chemical Physics Letters, 166, 275–280. DOI: 10.1016/0009-2614(90)80029-D. http://dx.doi.org/10.1016/0009-2614(90)80029-D10.1016/0009-2614(90)80029-DSearch in Google Scholar
[15] Frisch, M. J., Headgordon, M., & Pople, J. A. (1990b). Semidirect algorithms for the MP2 energy and gradient. Chemical Physics Letters, 166, 281–289. DOI: 10.1016/0009-2614(90)80030-H. http://dx.doi.org/10.1016/0009-2614(90)80030-H10.1016/0009-2614(90)80030-HSearch in Google Scholar
[16] 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. (2005). Gaussian 03, Revision D.02 and E.01 [computer software]. Wallingford, CT: Gaussian, Inc. Search in Google Scholar
[17] Gibson, R. P., Tarling, C. A., Roberts, S., Withers, S. G., & Davies, G. J. (2004). The donor subsite of trehalose-6-phosphate synthase: Binary complexes with UDP-glucose and UDP-2-deoxy-2-fluoro-glucose at 2 Å resolution. Journal of Biological Chemistry, 279, 1950–1955. DOI: 10.1074/jbc.M307643200. http://dx.doi.org/10.1074/jbc.M30764320010.1074/jbc.M307643200Search in Google Scholar
[18] Hohenstein, E. G., Chill, S. T., & Sherrill, C. D. (2008). Assessment of the performance of the M05-2X and M06-2X exchange-correlation functionals for noncovalent interactions in biomolecules. Journal of Chemical Theory and Computation, 4, 1996–2000. DOI: 10.1021/ct800308k. http://dx.doi.org/10.1021/ct800308k10.1021/ct800308kSearch in Google Scholar
[19] Hricovíni, M., Scholtzová, E., & Bízik, F. (2007). B3LYP/6-311++G** study of structure and spin-spin coupling constant in heparin disaccharide. Carbohydrate Research, 342, 1350–1356. DOI: 10.1016/j.carres.2007.03.020. http://dx.doi.org/10.1016/j.carres.2007.03.02010.1016/j.carres.2007.03.020Search in Google Scholar
[20] Ikeda, Y., & Takahashi, M. (2007). Glycosyltransferases and glycosidases: Enzyme mechanisms. In J. P. Kamerling, G. J. Boons, Y. C. Lee, A. Suzuki, N. Taniguchi, & A. G. J. Voragen (Eds.), Comprehensive glycosciense (Vol. 3, pp. 115–127). Oxford: Elsevier. Search in Google Scholar
[21] Ionescu, A. R., Whitfield, D. M., Zgierski, M. Z., & Nukada, T. (2006). Investigations into the role of oxocarbenium ions in glycosylation reactions by ab initio molecular dynamics. Carbohydrate Research, 341, 2912–2920. DOI: 10.1016/j.carres.2006.09.027. http://dx.doi.org/10.1016/j.carres.2006.09.02710.1016/j.carres.2006.09.027Search in Google Scholar
[22] Johnson, B. G., Gonzales, C. A., Gill, P. M. W., & Pople, J. A. (1994). A density-functional study of the simplest hydrogen abstraction reaction. Effect of self-interaction correction. Chemical Physics Letters, 221, 100–108. DOI: 10.1016/0009-2614(94)87024-1. http://dx.doi.org/10.1016/0009-2614(94)87024-110.1016/0009-2614(94)87024-1Search in Google Scholar
[23] Jones, P. G., & Kirby, A. J. (1979). Linear relationship between bond length and reactivity. Journal of Chemical Society, Chemical Communications, 1979, 288–289. DOI: 10.1039/C39790000288. http://dx.doi.org/10.1039/c3979000028810.1039/c39790000288Search in Google Scholar
[24] Jones, P. G., & Kirby, J. (1982). Evidence from crystal structures for an incipient fragmentation reaction. Journal of Chemical Society, Chemical Communications, 1982, 1365–1366. DOI: 10.1039/C39820001365. http://dx.doi.org/10.1039/c3982000136510.1039/c39820001365Search in Google Scholar
[25] Karamat, S., & Fabian, W. M. F. (2006). Computational study of the conformational space of methyl 2,4-diacetyl-β-d-xylopyranoside: 4C1 and 1C4 chairs, skew-boats (2SO, 1S3), and B3,O boat forms. Journal of Physical Chemistry A, 110, 7477–7484. DOI: 10.1021/jp061024g. http://dx.doi.org/10.1021/jp061024g10.1021/jp061024gSearch in Google Scholar
[26] Kozmon, S., & Tvaroška, I. (2006). Catalytic mechanism of glycosyltransferases: Hybrid quantum mechanical/molecular mechanical study of inverting N-acetylglucosaminyltransferase I. Journal of American Chemical Society, 128, 16921–16927. DOI: 10.1021/ja065944o. http://dx.doi.org/10.1021/ja065944o10.1021/ja065944oSearch in Google Scholar
[27] Lairson, L. L., Chiu, C. P. C., Ly, H. D., He, S. M., Wakarchuk, W. W., Strynadka, N. C. J., & Withers, S. G. (2004). Intermediate trapping on a mutant retaining α-galactosyltransferase identifies an unexpected aspartate residue. Journal of Biological Chemistry, 279 28339–28344. DOI: 10.1074/jbc.M400451200. http://dx.doi.org/10.1074/jbc.M40045120010.1074/jbc.M400451200Search in Google Scholar
[28] Lairson, L. L., Henrissat, B., Davies, G. J., & Withers, S. G. (2008). Glycosyltransferases: Structures, functions, and mechanism. Annual Reviews of Biochemistry, 77, 521–555. DOI: 10.1146/annurev.biochem.76.061005.092322. http://dx.doi.org/10.1146/annurev.biochem.76.061005.09232210.1146/annurev.biochem.76.061005.092322Search in Google Scholar
[29] Lee, C. T., Yang, W. T., & Parr, R. G. (1988). Development of the Colle-Salvetti correlation-energy formula into a functional of the electron-density. Physical Review B, 37, 785–789. DOI: 10.1103/PhysRevB.37.785. http://dx.doi.org/10.1103/PhysRevB.37.78510.1103/PhysRevB.37.785Search in Google Scholar
[30] Lii, J. H., Ma, B. Y., & Allinger, N. L. (1999). Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates. Journal of Computational Chemistry, 20, 1593–1603. DOI: 10.1002/(SICI)1096-987X(19991130)20:15〈1593::AID-JCC1〉3.0.CO;2-A. http://dx.doi.org/10.1002/(SICI)1096-987X(19991130)20:15<1593::AID-JCC1>3.0.CO;2-A10.1002/(SICI)1096-987X(19991130)20:15<1593::AID-JCC1>3.0.CO;2-ASearch in Google Scholar
[31] Lynch, B. J., Fast, P. L., Harris, M., & Truhlar, D. G. (2000). Adiabatic connection for kinetics. Journal of Physical Chemistry A, 104, 4811–4815. DOI: 10.1021/jp000497z. http://dx.doi.org/10.1021/jp000497z10.1021/jp000497zSearch in Google Scholar
[32] Miehlich, B., Savin, A., Stoll, H., & Preuss, H. (1989). Results obtained with the correlation-energy density functionals of Becke and Lee, Yang and Parr. Chemical Physics Letters, 157, 200–206. DOI: 10.1016/0009-2614(89)87234-3. http://dx.doi.org/10.1016/0009-2614(89)87234-310.1016/0009-2614(89)87234-3Search in Google Scholar
[33] Mohr, M., Bryce, R. A., & Hillier, I. H. (2001). Quantum chemical studies of carbohydrate reactivity: Acid catalyzed ring opening reactions. Journal of Physical Chemistry A, 105, 8216–8222. DOI: 10.1021/jp010901+. http://dx.doi.org/10.1021/jp010901+10.1021/jp010901+Search in Google Scholar
[34] Møller, C., & Plesset, M. S. (1934). Note on an approximation treatment for many-electron systems. Physical Review, 46, 618–622. DOI: 10.1103/PhysRev.46.618. http://dx.doi.org/10.1103/PhysRev.46.61810.1103/PhysRev.46.618Search in Google Scholar
[35] Momany, F. A., Appell, M., Willett, J. L., Schnupf, U., & Bosma, W. B. (2006). DFT study of α- and β-d-galactopyranose at the B3LYP/6-311++G** level of theory. Carbohydrate Research, 341, 525–537. DOI: 10.1016/j.carres.2005.12.006. http://dx.doi.org/10.1016/j.carres.2005.12.00610.1016/j.carres.2005.12.006Search in Google Scholar PubMed
[36] Momany, F. A., Schnupf, U., Willett, J. L., & Bosma, W. B. (2007). DFT study of α-maltose: influence of hydroxyl orientations on the glycosidic bond. Structural Chemistry, 18, 611–632. DOI: 10.1007/s11224-007-9191-9. http://dx.doi.org/10.1007/s11224-007-9191-910.1007/s11224-007-9191-9Search in Google Scholar
[37] Nyerges, B., & Kovács, A. (2005). Density functional study of the conformational space of 4C1d-glucuronic acid. Journal of Physical Chemistry A, 109, 892–897. DOI: 10.1021/jp047451g. http://dx.doi.org/10.1021/jp047451g10.1021/jp047451gSearch in Google Scholar PubMed
[38] Perdew, J. P., Burke, K., & Wang, Y. (1996). Generalized gradient approximation for the exchange-correlation hole of a many-electron system. Physical Review B, 54, 16533–16539. DOI: 10.1103/PhysRevB.54.16533. http://dx.doi.org/10.1103/PhysRevB.54.1653310.1103/PhysRevB.54.16533Search in Google Scholar PubMed
[39] Perdew, J. P., Chevary, J. A., Vosko, S. H., Jackson, K. A., Pederson, M. R., Singh, D. J., & Fiolhais, C. (1992). Atoms, molecules, solids, and surfaces — applications of the generalized gradient approximation for exchange and correlation. Physical Review B, 46, 6671–6687. DOI: 10.1103/Phys-RevB.46.6671. http://dx.doi.org/10.1103/PhysRevB.46.6671Search in Google Scholar
[40] Persson, K., Ly, H. D., Dieckelmann, M., Wakarchuk, W. W., Withers, S. G., & Strynadka, N. C. J. (2001). Crystal structure of the retaining galactosyltransferase LgtC from Neisseria meningitidis in complex with donor and acceptor sugar analogs. Nature Structural Biology, 8, 166–175. DOI: 10.1038/84168. http://dx.doi.org/10.1038/8416810.1038/84168Search in Google Scholar PubMed
[41] Petrova, P., Koča, J., & Imberty, A. (1999). Potential energy hypersurfaces of nucleotide sugars: Ab initio calculations, force-field parametrization, and exploration of the flexibility. Journal of the American Chemical Society, 121, 5535–5547. DOI: 10.1021/ja983854g. http://dx.doi.org/10.1021/ja983854g10.1021/ja983854gSearch in Google Scholar
[42] Raab, M., Kozmon, S., & Tvaroška, I. (2005). Potential transition-state analogs for glycosyltransferases. Design and DFT calculations of conformational behavior. Carbohydrate Research, 340, 1051–1057. DOI: 10.1016/j.carres.2005.01.041. http://dx.doi.org/10.1016/j.carres.2005.01.04110.1016/j.carres.2005.01.041Search in Google Scholar PubMed
[43] Roothaan, C. C. J. (1951). New developments in molecular orbital theory. Reviews of Modern Physics, 23, 69–76. DOI: 10.1103/RevModPhys.23.69. http://dx.doi.org/10.1103/RevModPhys.23.6910.1103/RevModPhys.23.69Search in Google Scholar
[44] Salzner, U., & von Ragué Schleyer, P. (1994). Ab initio examination of anomeric effects in tetrahydropyrans, 1,3-dioxanes, and glucose. Journal of Organic Chemistry, 59, 2138–2155. DOI: 10.1021/jo00087a035. http://dx.doi.org/10.1021/jo00087a03510.1021/jo00087a035Search in Google Scholar
[45] Sarkar, M., & Schachter, H. (2001). Cloning and expression of Drosophila melanogaster UDP-GlcNAc:α-3-d-mannoside β1,2-N-acetylglucosaminyltransferase I. Biological Chemistry, 382, 209–217. DOI: 10.1515/BC.2001.028. http://dx.doi.org/10.1515/BC.2001.02810.1515/BC.2001.028Search in Google Scholar PubMed
[46] Schneider, B., Kabelac, M., & Hobza, P. (1996). Geometry of the phosphate group and its interactions with metal cations in crystals and ab initio calculations. Journal of the American Chemical Society, 118, 12207–12217. DOI: 10.1021/ja9621152. http://dx.doi.org/10.1021/ja962115210.1021/ja9621152Search in Google Scholar
[47] Schultz, N. E., Zhao, Y., & Truhlar, D. G. (2008). Benchmarking approximate density functional theory for s/d excitation energies in 3d transition metal cations. Journal of Computational Chemistry, 29, 185–189. DOI: 10.1002/jcc.20717. http://dx.doi.org/10.1002/jcc.2071710.1002/jcc.20717Search in Google Scholar PubMed
[48] Stubbs, J. M., & Marx, D. (2003). Glycosidic bond formation in aqueous solution: On the oxocarbenium intermediate. Journal of the American Chemical Society, 125, 10960–10962. DOI: 10.1021/ja035600n. http://dx.doi.org/10.1021/ja035600n10.1021/ja035600nSearch in Google Scholar PubMed
[49] Sugawara, Y., & Iwasaki, H. (1984). Structure of disodium uridine diphosphoglucose dihydrate, C15H22N2O17P 22−.2Na+.2H2O, and refinement of dipotassium glucose 1-phosphate dihydrate, C6H11O9P2−.2K+.2H2O (monoclinic form). Acta Crystallographica Section C, 40, 389–393. DOI: 10.1107/S010827018400425X. 10.1107/S010827018400425XSearch in Google Scholar
[50] Tvaroška, I. (2005). Structural insights into the catalytic mechanism and transition state of glycosyltransferases using ab initio molecular modeling. Trends in Glycoscience and Glycotechnology, 17, 177–190. 10.4052/tigg.17.177Search in Google Scholar
[51] Tvaroška, I., André, I., & Carver, J. P. (1999). Ab initio molecular orbital study of the conformational behavior of the sugar-phosphate linkage. Toward an understanding of the catalytic mechanism of glycosyltransferases. Journal of Physical Chemistry B, 103, 2560–2569. DOI: 10.1021/jp984226o. http://dx.doi.org/10.1021/jp984226o10.1021/jp984226oSearch in Google Scholar
[52] Tvaroška, I., André, I., & Carver, J. P. (2000). Ab initio molecular orbital study of the catalytic mechanism of glycosyltransferases: Description of reaction pathways and determination of transition-state structures for inverting N-acetylglucosaminyltransferases. Journal of the American Chemical Society, 122, 8762–8776. DOI: 10.1021/ja001525u. http://dx.doi.org/10.1021/ja001525u10.1021/ja001525uSearch in Google Scholar
[53] Tvaroška, I., & Carver, J. P. (1994a). Ab-initio molecular-orbital calculation of carbohydrate model compounds. 2. Conformational analysis of axial and equatorial 2-methoxytetrahydropyrans. Journal of Physical Chemistry, 98, 9477–9485. DOI: 10.1021/j100089a020. http://dx.doi.org/10.1021/j100089a02010.1021/j100089a020Search in Google Scholar
[54] Tvaroška, I., & Carver, J. P. (1994b). Ab-initio molecular-orbital calculation on carbohydrate model compounds. 1. The anomeric effect in fluoro and chloro derivatives of tetrahydropyran. Journal of Physical Chemistry, 98, 6452–6458. DOI: 10.1021/j100077a006. http://dx.doi.org/10.1021/j100077a00610.1021/j100077a006Search in Google Scholar
[55] Tvaroška, I., & Carver, J. P. (1998). The anomeric and exoanomeric effects of a hydroxyl group and the stereochemistry of the hemiacetal linkage. Carbohydrate Research, 309, 1–9. DOI: 10.1016/S0008-6215(98)00114-1. http://dx.doi.org/10.1016/S0008-6215(98)00114-110.1016/S0008-6215(98)00114-1Search in Google Scholar
[56] Tvaroška, I., Taravel, F. R., Utille, J. P., & Carver, J. P. (2002). Quantum mechanical and NMR spectroscopy studies on the conformations of the hydroxymethyl and methoxymethyl groups in aldohexosides. Carbohydrate Research, 337, 353–367. DOI: 10.1016/S0008-6215(01)00315-9. http://dx.doi.org/10.1016/S0008-6215(01)00315-910.1016/S0008-6215(01)00315-9Search in Google Scholar
[57] Whitfield, D. M. (2007). DFT studies of the ionization of alpha and beta glycopyranosyl donors. Carbohydrate Research, 342, 1726–1740. DOI: 10.1016/j.carres.2007.05.012. http://dx.doi.org/10.1016/j.carres.2007.05.01210.1016/j.carres.2007.05.012Search in Google Scholar
[58] Withers, S. G., Rupitz, K., Street, I. P. (1988). 2-Deoxy-2-fluoro-d-glycosyl fluorides. A new class of specific mechanismbased glysosidase inhibitors. Journal of Biological Chemistry, 263, 7929–7932. 10.1016/S0021-9258(18)68421-2Search in Google Scholar
[59] Zea, C. J., Camci-Unal, G., & Pohl, N. L. (2008). Thermodynamics of binding of divalent magnesium and manganese to uridine phosphates: implications for diabetes-related hypomagnesaemia and carbohydrate biocatalysis. Chemistry Central Journal, 2, 15. DOI: 10.1186/1752-153X-2-15. http://dx.doi.org/10.1186/1752-153X-2-1510.1186/1752-153X-2-15Search in Google Scholar PubMed PubMed Central
[60] Zhang, Y., & Yang, W. (1998). A challenge for density functionals: Self-interaction error increases for systems with a noninteger number of electrons. Journal of Chemical Physics, 109, 2604–2608. DOI: 10.1063/1.476859. http://dx.doi.org/10.1063/1.47685910.1063/1.476859Search in Google Scholar
[61] Zhao, Y., Schultz, N. E., & Truhlar, D. G. (2005). Exchange-correlation functional with broad accuracy for metallic and nonmetallic compounds, kinetics, and noncovalent interactions. Journal of Chemical Physics, 123, 161103. DOI: 10.1063/1.2126975. 10.1063/1.2126975Search in Google Scholar PubMed
[62] Zhao, Y., Schultz, N. E., & Truhlar, D. G. (2006). Design of density functionals by combining the method of constraint satisfaction with parametrization for thermochemistry, thermochemical kinetics, and noncovalent interactions. Journal of Chemical Theory and Computation, 2, 364–382. DOI: 10.1021/ct0502763. http://dx.doi.org/10.1021/ct050276310.1021/ct0502763Search in Google Scholar PubMed
[63] Zhao, Y., & Truhlar, D. G. (2004). Hybrid meta density functional theory methods for thermochemistry, thermochemical kinetics, and noncovalent interactions: The MPW1B95 and MPWB1K models and comparative assessments for hydrogen bonding and van der Waals interactions. Journal of Physical Chemistry A, 108 6908–6918. DOI: 10.1021/jp048147q. http://dx.doi.org/10.1021/jp048147q10.1021/jp048147qSearch in Google Scholar
[64] Zhao, Y., & Truhlar, D. G. (2008a). Density functionals with broad applicability in chemistry. Accounts of Chemical Research, 41, 157–167. DOI: 10.1021/ar700111a. http://dx.doi.org/10.1021/ar700111a10.1021/ar700111aSearch in Google Scholar PubMed
[65] Zhao, Y., & Truhlar, D. G. (2008b). Exploring the limit of accuracy of the global hybrid meta density functional for main-group thermochemistry, kinetics, and noncovalent interactions. Journal of Chemical Theory and Computation, 4, 1849–1868. DOI: 10.1021/ct800246v. http://dx.doi.org/10.1021/ct800246v10.1021/ct800246vSearch in Google Scholar PubMed
[66] Zheng, J., Zhao, Y., & Truhlar, D. G. (2007). Representative benchmark suites for barrier heights of diverse reaction types and assessment of electronic structure methods for thermochemical kinetics. Journal of Chemical Theory and Computation, 3, 569–582. DOI: 10.1021/ct600281g. http://dx.doi.org/10.1021/ct600281g10.1021/ct600281gSearch in Google Scholar PubMed
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