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Volumn 29, Issue 2, 2010, Pages 246-255

Hierarchical approach to conformational search and selection of computational method in modeling the mechanism of ester ammonolysis

Author keywords

Computational chemistry; Conformational search; Reaction mechanisms; Transition states

Indexed keywords

AMMONOLYSIS; AUTOMATED PROCEDURES; BASIS SETS; COMPUTATIONAL INVESTIGATION; CONFORMATIONAL FREEDOM; CONFORMATIONAL SEARCH; ENERGY DATA; ETHANEDIOL; EXPERIMENTAL VALUES; HIERARCHICAL APPROACH; INITIAL STRUCTURES; QUANTUM MECHANICAL METHOD; REACTION MECHANISM; REACTION PATHS; REACTION SYSTEM; STATISTICAL ANALYSIS; TRANSITION STATE; UNKNOWN GEOMETRY;

EID: 77956278300     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2010.07.006     Document Type: Article
Times cited : (5)

References (57)
  • 2
    • 70349270612 scopus 로고    scopus 로고
    • Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM
    • Banáš P., Jurečka P., Walter N.G., Šponer J., Otyepka M. Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods 2009, 49:202-216.
    • (2009) Methods , vol.49 , pp. 202-216
    • Banáš, P.1    Jurečka, P.2    Walter, N.G.3    Šponer, J.4    Otyepka, M.5
  • 3
    • 48249153490 scopus 로고    scopus 로고
    • Metal binding affinity and selectivity in metalloproteins: insights from computational studies
    • Dudev T., Lim C. Metal binding affinity and selectivity in metalloproteins: insights from computational studies. Ann. Rev. Biophys. 2008, 37:97-116.
    • (2008) Ann. Rev. Biophys. , vol.37 , pp. 97-116
    • Dudev, T.1    Lim, C.2
  • 4
    • 33748584863 scopus 로고    scopus 로고
    • Mechanisms and free energies of enzymatic reactions
    • Gao J., Ma S., Major D.T., Nam K., Pu J., Truhlar D.G. Mechanisms and free energies of enzymatic reactions. Chem. Rev. 2006, 106:3188-3209.
    • (2006) Chem. Rev. , vol.106 , pp. 3188-3209
    • Gao, J.1    Ma, S.2    Major, D.T.3    Nam, K.4    Pu, J.5    Truhlar, D.G.6
  • 6
    • 66849115073 scopus 로고    scopus 로고
    • Theoretical studies of structure, function and reactivity of molecules-a personal account
    • Morokuma K. Theoretical studies of structure, function and reactivity of molecules-a personal account. Proc. Jpn. Acad. B 2009, 85:167-182.
    • (2009) Proc. Jpn. Acad. B , vol.85 , pp. 167-182
    • Morokuma, K.1
  • 7
    • 61649087892 scopus 로고    scopus 로고
    • Ethylene conversion to ethylidyne over Pd(111): revisiting the mechanism with first-principles calculations
    • Moskaleva L.V., Chen Z.-X., Aleksandrov H.A., Mohammed A.B., Sun Q., Rösch N. Ethylene conversion to ethylidyne over Pd(111): revisiting the mechanism with first-principles calculations. J. Phys. Chem. C 2009, 113:2512-2520.
    • (2009) J. Phys. Chem. C , vol.113 , pp. 2512-2520
    • Moskaleva, L.V.1    Chen, Z.-X.2    Aleksandrov, H.A.3    Mohammed, A.B.4    Sun, Q.5    Rösch, N.6
  • 8
    • 70449122678 scopus 로고    scopus 로고
    • Fast prediction of selectivity in heterogeneous catalysis from extended brønsted-evans-polanyi relations: a theoretical insight
    • Loffreda D., Delbecq F., Vigné F., Sautet P. Fast prediction of selectivity in heterogeneous catalysis from extended brønsted-evans-polanyi relations: a theoretical insight. Angew. Chem., Int. Ed. 2009, 48:8978-8980.
    • (2009) Angew. Chem., Int. Ed. , vol.48 , pp. 8978-8980
    • Loffreda, D.1    Delbecq, F.2    Vigné, F.3    Sautet, P.4
  • 9
    • 0032500320 scopus 로고    scopus 로고
    • Density-functional approach to hardness evaluation and its use in the study of the maximum hardness principle
    • Mineva T., Sicilia E., Russo N. Density-functional approach to hardness evaluation and its use in the study of the maximum hardness principle. J. Am. Chem. Soc. 1998, 120:9053-9058.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9053-9058
    • Mineva, T.1    Sicilia, E.2    Russo, N.3
  • 10
    • 21944439368 scopus 로고    scopus 로고
    • Treatment of substitution and rearrangement mechanisms of transition metal complexes with quantum chemical methods
    • Rotzinger F.P. Treatment of substitution and rearrangement mechanisms of transition metal complexes with quantum chemical methods. Chem. Rev. 2005, 105:2003-2037.
    • (2005) Chem. Rev. , vol.105 , pp. 2003-2037
    • Rotzinger, F.P.1
  • 12
    • 77954212942 scopus 로고    scopus 로고
    • Assessment of a new hybrid functional on thermochemistry, metal-ligand bonding and reaction barriers
    • Heron Press, Sofia
    • Proynov E., Kong J. Assessment of a new hybrid functional on thermochemistry, metal-ligand bonding and reaction barriers. Theoretical Aspects of Catalysis 2009, vol. 3:1-9. Heron Press, Sofia.
    • (2009) Theoretical Aspects of Catalysis , vol.3 , pp. 1-9
    • Proynov, E.1    Kong, J.2
  • 14
    • 84962359533 scopus 로고    scopus 로고
    • Quantum chemical model study of the acyl migration in 2'(3')-formylnucleosides
    • Rangelov M.A., Vayssilov G.N., Petkov D.D. Quantum chemical model study of the acyl migration in 2'(3')-formylnucleosides. Int. J. Quant. Chem. 2006, 106:1346-1356.
    • (2006) Int. J. Quant. Chem. , vol.106 , pp. 1346-1356
    • Rangelov, M.A.1    Vayssilov, G.N.2    Petkov, D.D.3
  • 16
    • 76649094618 scopus 로고    scopus 로고
    • The transition state for peptide bond formation reveals the ribosome as a water trap
    • Wallin G., Åqvist J. The transition state for peptide bond formation reveals the ribosome as a water trap. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:1888-1893.
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 1888-1893
    • Wallin, G.1    Åqvist, J.2
  • 17
    • 33646141185 scopus 로고    scopus 로고
    • The syn-oriented 2-OH provides a favorable proton transfer geometry in 1,2-diol monoester aminolysis: implications for the ribosome mechanism
    • Rangelov M.A., Vayssilov G.N., Yomtova V.M., Petkov D.D. The syn-oriented 2-OH provides a favorable proton transfer geometry in 1,2-diol monoester aminolysis: implications for the ribosome mechanism. J. Am. Chem. Soc. 2006, 128:4964-4965.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 4964-4965
    • Rangelov, M.A.1    Vayssilov, G.N.2    Yomtova, V.M.3    Petkov, D.D.4
  • 20
    • 40949152731 scopus 로고    scopus 로고
    • Synthesis of isotopically labeled P-site substrates for the ribosomal peptidyl transferase reaction
    • Zhong M.H., Strobel S.A. Synthesis of isotopically labeled P-site substrates for the ribosomal peptidyl transferase reaction. J. Org. Chem. 2008, 73:603-611.
    • (2008) J. Org. Chem. , vol.73 , pp. 603-611
    • Zhong, M.H.1    Strobel, S.A.2
  • 21
    • 77956282875 scopus 로고    scopus 로고
    • MolRan, Version 1.8. More information about the program can be obtained from the author via e-mail: mran@orgchm.bas.bg.
    • M.A. Rangelov, MolRan, Version 1.8, 2008. More information about the program can be obtained from the author via e-mail: mran@orgchm.bas.bg. mailto:mran@orgchm.bas.bg.
    • (2008)
    • Rangelov, M.A.1
  • 23
    • 84986444438 scopus 로고
    • Theoretical models incorporating electron correlation
    • Pople J.A., Binkley J.S., Seeger R. Theoretical models incorporating electron correlation. Int. J. Quant. Chem. 1976, 10:1-19.
    • (1976) Int. J. Quant. Chem. , vol.10 , pp. 1-19
    • Pople, J.A.1    Binkley, J.S.2    Seeger, R.3
  • 25
    • 36849115659 scopus 로고
    • Self-consistent molecular-orbital methods. IX. An extended gaussian-type basis for molecular-orbital studies of organic molecules
    • Ditchfield R., Hehre W.J., Pople J.A. Self-consistent molecular-orbital methods. IX. An extended gaussian-type basis for molecular-orbital studies of organic molecules. J. Chem. Phys. 1971, 54:724-728.
    • (1971) J. Chem. Phys. , vol.54 , pp. 724-728
    • Ditchfield, R.1    Hehre, W.J.2    Pople, J.A.3
  • 26
    • 0347170005 scopus 로고
    • Self-consistent molecular orbital methods. XII. Further extensions of gaussian-type basis sets for use in molecular orbital studies of organic molecules
    • Hehre W.J., Ditchfield R., Pople J.A. Self-consistent molecular orbital methods. XII. Further extensions of gaussian-type basis sets for use in molecular orbital studies of organic molecules. J. Chem. Phys. 1972, 56:2257-2261.
    • (1972) J. Chem. Phys. , vol.56 , pp. 2257-2261
    • Hehre, W.J.1    Ditchfield, R.2    Pople, J.A.3
  • 27
    • 0000812163 scopus 로고
    • n equilibrium geometries by single determinant molecular orbital theory
    • n equilibrium geometries by single determinant molecular orbital theory. Mol. Phys. 1974, 27:209-214.
    • (1974) Mol. Phys. , vol.27 , pp. 209-214
    • Hariharan, P.C.1    Pople, J.A.2
  • 28
    • 85022583881 scopus 로고
    • The isomers of silacyclopropane
    • Gordon M.S. The isomers of silacyclopropane. Chem. Phys. Lett. 1980, 76:163-168.
    • (1980) Chem. Phys. Lett. , vol.76 , pp. 163-168
    • Gordon, M.S.1
  • 29
    • 33748545144 scopus 로고
    • The influence of polarization functions on molecular orbital hydrogenation energies
    • Hariharan P.C., Pople J.A. The influence of polarization functions on molecular orbital hydrogenation energies. Theor. Chim. Acta 1973, 28:213-222.
    • (1973) Theor. Chim. Acta , vol.28 , pp. 213-222
    • Hariharan, P.C.1    Pople, J.A.2
  • 30
    • 84987093700 scopus 로고
    • Approximate fourth-order perturbation theory of the electron correlation energy
    • Krishnan R., Pople J.A. Approximate fourth-order perturbation theory of the electron correlation energy. Int. J. Quant. Chem. 1978, 14:91-100.
    • (1978) Int. J. Quant. Chem. , vol.14 , pp. 91-100
    • Krishnan, R.1    Pople, J.A.2
  • 31
    • 0000649832 scopus 로고
    • Contribution of triple substitutions to the electron correlation energy in fourth order perturbation theory
    • Krishnan R., Frisch M.J., Pople J.A. Contribution of triple substitutions to the electron correlation energy in fourth order perturbation theory. J. Chem. Phys. 1980, 72:4244-4245.
    • (1980) J. Chem. Phys. , vol.72 , pp. 4244-4245
    • Krishnan, R.1    Frisch, M.J.2    Pople, J.A.3
  • 32
    • 84987097935 scopus 로고
    • Electron correlation theories and their application to the study of simple reaction potential surfaces
    • Pople J.A., Krishnan R., Schlegel H.B., Binkley J.S. Electron correlation theories and their application to the study of simple reaction potential surfaces. Int. J. Quant. Chem. 1978, 14:545-560.
    • (1978) Int. J. Quant. Chem. , vol.14 , pp. 545-560
    • Pople, J.A.1    Krishnan, R.2    Schlegel, H.B.3    Binkley, J.S.4
  • 33
    • 2442617487 scopus 로고
    • Self-consistent molecular orbital methods. 21. Small split-valence basis sets for first-row elements
    • Binkley J.S., Pople J.A., Hehre W.J. Self-consistent molecular orbital methods. 21. Small split-valence basis sets for first-row elements. J. Am. Chem. Soc. 1980, 102:939-947.
    • (1980) J. Am. Chem. Soc. , vol.102 , pp. 939-947
    • Binkley, J.S.1    Pople, J.A.2    Hehre, W.J.3
  • 34
    • 0141509423 scopus 로고
    • Contracted Gaussian basis sets for molecular calculations. I. Second row atoms, Z=11-18
    • McLean A.D., Chandler G.S. Contracted Gaussian basis sets for molecular calculations. I. Second row atoms, Z=11-18. J. Chem. Phys. 1980, 72:5639-5648.
    • (1980) J. Chem. Phys. , vol.72 , pp. 5639-5648
    • McLean, A.D.1    Chandler, G.S.2
  • 36
    • 0038276407 scopus 로고    scopus 로고
    • An evaluation of the MM+force field
    • Hocquet A., Langgård M. An evaluation of the MM+force field. J. Mol. Model. 1998, 4:94-112.
    • (1998) J. Mol. Model. , vol.4 , pp. 94-112
    • Hocquet, A.1    Langgård, M.2
  • 39
    • 33645861085 scopus 로고    scopus 로고
    • Hydrogen bonds in molecular mechanics force fields
    • Hermans J. Hydrogen bonds in molecular mechanics force fields. Adv. Protein Chem. 2005, 72:105-119.
    • (2005) Adv. Protein Chem. , vol.72 , pp. 105-119
    • Hermans, J.1
  • 40
    • 0000695985 scopus 로고
    • A reinvestigation of the structure of monomer and dimer formic acid by gas electron diffraction technique
    • Almenningen A., Bastiansen O., Motifeldt T. A reinvestigation of the structure of monomer and dimer formic acid by gas electron diffraction technique. Acta Chem. Scand. 1969, 23:2848-2864.
    • (1969) Acta Chem. Scand. , vol.23 , pp. 2848-2864
    • Almenningen, A.1    Bastiansen, O.2    Motifeldt, T.3
  • 43
    • 0001480124 scopus 로고
    • Quantum chemical studies of a model for peptide bond formation: formation of formamide and water from ammonia and formic acid
    • Oie T., Loew G.H., Burt S.K., Binkley J.S., MacElroy R.D. Quantum chemical studies of a model for peptide bond formation: formation of formamide and water from ammonia and formic acid. J. Am. Chem. Soc. 1982, 104:6169-6174.
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 6169-6174
    • Oie, T.1    Loew, G.H.2    Burt, S.K.3    Binkley, J.S.4    MacElroy, R.D.5
  • 44
    • 0347486647 scopus 로고
    • Uncatalyzed peptide bond formation in the gas phase
    • Jensen J.H., Baldridge K.K., Gordon M.S. Uncatalyzed peptide bond formation in the gas phase. J. Phys. Chem. 1992, 96:8340-8351.
    • (1992) J. Phys. Chem. , vol.96 , pp. 8340-8351
    • Jensen, J.H.1    Baldridge, K.K.2    Gordon, M.S.3
  • 45
    • 0035961095 scopus 로고    scopus 로고
    • Computer simulation of amide bond formation in aqueous solution
    • Chalmet S., Harb W., Ruiz-Lopez M.F. Computer simulation of amide bond formation in aqueous solution. J. Phys. Chem. A 2001, 105:11574-11581.
    • (2001) J. Phys. Chem. A , vol.105 , pp. 11574-11581
    • Chalmet, S.1    Harb, W.2    Ruiz-Lopez, M.F.3
  • 46
    • 77956285480 scopus 로고    scopus 로고
    • Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab initio MO calculations
    • Takahashi O., Kohno Y., Nishio M. Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab initio MO calculations. Chem. Rev. 2010, 10.1021/cr100072x.
    • (2010) Chem. Rev.
    • Takahashi, O.1    Kohno, Y.2    Nishio, M.3
  • 47
    • 43049141516 scopus 로고    scopus 로고
    • The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals
    • Zhao Y., Truhlar D. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor. Chem. Acc. 2008, 120:215-241.
    • (2008) Theor. Chem. Acc. , vol.120 , pp. 215-241
    • Zhao, Y.1    Truhlar, D.2
  • 48
    • 71549159258 scopus 로고    scopus 로고
    • A structural view on the mechanism of the ribosome-catalyzed peptide bond formation
    • Simonović M., Steitz T.A. A structural view on the mechanism of the ribosome-catalyzed peptide bond formation. Biochim. Biophys. Acta 2009, 1789:612-623.
    • (2009) Biochim. Biophys. Acta , vol.1789 , pp. 612-623
    • Simonović, M.1    Steitz, T.A.2
  • 49
    • 0038508659 scopus 로고    scopus 로고
    • Peptide bond formation on the ribosome: structure and mechanism
    • Rodnina M.V., Wintermeyer W. Peptide bond formation on the ribosome: structure and mechanism. Curr. Opin. Struct. Biol. 2003, 13:334-340.
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 334-340
    • Rodnina, M.V.1    Wintermeyer, W.2
  • 50
    • 34247589630 scopus 로고    scopus 로고
    • The ribosomal peptidyl transferase
    • Beringer M., Rodnina M.V. The ribosomal peptidyl transferase. Mol. Cell. 2007, 26:311-321.
    • (2007) Mol. Cell. , vol.26 , pp. 311-321
    • Beringer, M.1    Rodnina, M.V.2
  • 52
    • 77956273204 scopus 로고    scopus 로고
    • Catalytic Role of Vicinal OH in Ester Aminolysis - Proton Shuttle versus Hydrogen-Bonds Stabilization, submitted for publication.
    • M.A. Rangelov, G.P. Petrova, V.M. Yomtova, G.N. Vayssilov, Catalytic Role of Vicinal OH in Ester Aminolysis - Proton Shuttle versus Hydrogen-Bonds Stabilization, submitted for publication.
    • Rangelov, M.A.1    Petrova, G.P.2    Yomtova, V.M.3    Vayssilov, G.N.4
  • 53
    • 0001361466 scopus 로고
    • The mechanism of the aminolysis of methyl formate
    • Blackburn G.M., Jencks W.P. The mechanism of the aminolysis of methyl formate. J. Am. Chem. Soc. 1968, 90:2638-2645.
    • (1968) J. Am. Chem. Soc. , vol.90 , pp. 2638-2645
    • Blackburn, G.M.1    Jencks, W.P.2
  • 54
    • 0011245414 scopus 로고
    • Gas-phase pathways for ester hydrolysis
    • Takashima K., Riveros J.M. Gas-phase pathways for ester hydrolysis. J. Am. Chem. Soc. 1978, 100:6128-6132.
    • (1978) J. Am. Chem. Soc. , vol.100 , pp. 6128-6132
    • Takashima, K.1    Riveros, J.M.2
  • 55
    • 84962374950 scopus 로고    scopus 로고
    • Computational study of the aminolysis of esters. The reaction of methylformate with ammonia
    • Ilieva S., Galabov B., Musaev D.G., Morokuma K., Schaefer H.F. Computational study of the aminolysis of esters. The reaction of methylformate with ammonia. J. Org. Chem. 2003, 68:1496-1502.
    • (2003) J. Org. Chem. , vol.68 , pp. 1496-1502
    • Ilieva, S.1    Galabov, B.2    Musaev, D.G.3    Morokuma, K.4    Schaefer, H.F.5
  • 56
    • 0002606725 scopus 로고
    • A new method of constrained optimization and a comparison with other methods
    • Box M.J. A new method of constrained optimization and a comparison with other methods. Comput. J. 1965, 8:42-52.
    • (1965) Comput. J. , vol.8 , pp. 42-52
    • Box, M.J.1
  • 57
    • 34248512588 scopus 로고    scopus 로고
    • Unambiguous evidence for efficient chemical catalysis of adenosine ester aminolysis by its 2'/3'-OH
    • Bayryamov S.G., Rangelov M.A., Mladjova A.P., Yomtova V., Petkov D.D. Unambiguous evidence for efficient chemical catalysis of adenosine ester aminolysis by its 2'/3'-OH. J. Am. Chem. Soc. 2007, 129:5790-5791.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 5790-5791
    • Bayryamov, S.G.1    Rangelov, M.A.2    Mladjova, A.P.3    Yomtova, V.4    Petkov, D.D.5


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