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1
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2342616849
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Role of the tautomerism of 2-azaadenine and 2-azahypoxanthine in substrate recognition by xanthine oxidase
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Hernandez B, Orozco M, Luque FJ. Role of the tautomerism of 2-azaadenine and 2-azahypoxanthine in substrate recognition by xanthine oxidase. J Comput Aided Mol Des. 11:1997;153-162.
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J Comput Aided Mol des
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Hernandez, B.1
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Luque, F.J.3
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2
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0000497455
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Conformational and solvation aspects of the chorismate-perphenate rearrangement studies by ab initio electronic structure and simulation methods
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of special interest. This paper compares the results of continuum and explicit solvation on the conformational energetics and activation barrier of the Claisen rearrangement of chorismate to prephenate. The detailed comparison of quantum and classical simulation results, and the succesful comparison with experiments, are of significant interest.
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Davidson MM, Guest JM, Craw JS, Hillie IH, Vincent MA. Conformational and solvation aspects of the chorismate-perphenate rearrangement studies by ab initio electronic structure and simulation methods. of special interest J Chem Soc Perkin Trans. 2:1997;1395-1400 This paper compares the results of continuum and explicit solvation on the conformational energetics and activation barrier of the Claisen rearrangement of chorismate to prephenate. The detailed comparison of quantum and classical simulation results, and the succesful comparison with experiments, are of significant interest.
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(1997)
J Chem Soc Perkin Trans
, vol.2
, pp. 1395-1400
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Davidson, M.M.1
Guest, J.M.2
Craw, J.S.3
Hillie, I.H.4
Vincent, M.A.5
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3
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0030970225
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A conformational study of 2-oxanol: Insight into the role of ring distortion on enzyme-catalyzed glycosidic bond cleavage
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Smith BJ. A conformational study of 2-oxanol: insight into the role of ring distortion on enzyme-catalyzed glycosidic bond cleavage. J Am Chem Soc. 119:1997;2699-2706.
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(1997)
J Am Chem Soc
, vol.119
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Smith, B.J.1
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6
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0000133152
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Ab initio calculations on neutral and alkaline hydrolyses of β-lactam antibiotics. A theoretical study including solvent effects
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Pitarch J, Ruiz-Lopez MF, Pascual-Ahuir J-L, Silla E, Tuñón I. Ab initio calculations on neutral and alkaline hydrolyses of β-lactam antibiotics. A theoretical study including solvent effects. J Phys Chem B. 101:1997;3581-3588.
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J Phys Chem B
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Pitarch, J.1
Ruiz-Lopez, M.F.2
Pascual-Ahuir J-L3
Silla, E.4
Tuñón, I.5
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7
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0030937423
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Role of active site tyrosine in glutathione S-transferase: Insights from a theoretical study of model systems
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Zheng Y-J, Ornstein RL. Role of active site tyrosine in glutathione S-transferase: insights from a theoretical study of model systems. J Am Chem Soc. 119:1997;1523-1528.
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J Am Chem Soc
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Zheng Y-J1
Ornstein, R.L.2
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8
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0030767647
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A Theoretical examination of the factors controlling the catalytic efficiency of a transmethylation enzyme: Cathechol O-methyltransferase
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Zheng Y-J, Bruice TC. A Theoretical examination of the factors controlling the catalytic efficiency of a transmethylation enzyme: cathechol O-methyltransferase. J Am Chem Soc. 119:1997;8137-8145.
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(1997)
J Am Chem Soc
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Zheng Y-J1
Bruice, T.C.2
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9
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0030921325
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On the dehalogenation mechanism of 4-chlorobenzoyl CoA by 4-chlorobenzoyl CoA dehalogenase: Insight from study based on the nonenzymatic reaction
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Zheng Y-J, Bruice TC. On the dehalogenation mechanism of 4-chlorobenzoyl CoA by 4-chlorobenzoyl CoA dehalogenase: insight from study based on the nonenzymatic reaction. J Am Chem Soc. 119:1997;3868-3877.
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J Am Chem Soc
, vol.119
, pp. 3868-3877
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Zheng Y-J1
Bruice, T.C.2
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10
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84961974330
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Triosephosphate isomerase (TIM)-catalysed proton abstraction from carbon acid: An analysis on the origin of the catalytic activity
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Peräkylä M. Triosephosphate isomerase (TIM)-catalysed proton abstraction from carbon acid: an analysis on the origin of the catalytic activity. Chem Commun. 1996;361-362.
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(1996)
Chem Commun
, pp. 361-362
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Peräkylä, M.1
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11
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0004573289
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Ab initio calculations on 2-, 3- and 4-substituted quinolines in relation with their activity as protein tyrosine kinase inhibitors
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Thomson C, Zwaans R. Ab initio calculations on 2-, 3- and 4-substituted quinolines in relation with their activity as protein tyrosine kinase inhibitors. J Mol Struct. 362:1996;51-68.
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(1996)
J Mol Struct
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Thomson, C.1
Zwaans, R.2
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12
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0030912339
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A proficient enzyme revisited: The predicted mechanism for orotidine monophosphate decarboxylase
-
of outstanding interest. This paper proposes a specific mechanistic explanation using quantum chemical modeling for a reaction that is dramatically accelerated by the enzyme. Although the quantum chemistry is not particularly high level, nor on a large model of the enzyme active site, the mechanistic proposal is an interesting one that can be tested experimentally.
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Lee JK, Houk KN. A proficient enzyme revisited: the predicted mechanism for orotidine monophosphate decarboxylase. of outstanding interest Science. 276:1997;942-945 This paper proposes a specific mechanistic explanation using quantum chemical modeling for a reaction that is dramatically accelerated by the enzyme. Although the quantum chemistry is not particularly high level, nor on a large model of the enzyme active site, the mechanistic proposal is an interesting one that can be tested experimentally.
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(1997)
Science
, vol.276
, pp. 942-945
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Lee, J.K.1
Houk, K.N.2
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13
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0030858487
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- attack in phosphate ester hydrolysis is not fully justified
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of special interest. This paper investigates phosohate ester hydrolysis using ab initio quantum chemical techniques and shows that the proposed pathway is inconsistent with these calculations. Of interest here is the use of calculations in order to rule out a proposed mechanistic pathway for a biologically important system.
-
- attack in phosphate ester hydrolysis is not fully justified. of special interest J Am Chem Soc. 119:1997;5473-5474 This paper investigates phosohate ester hydrolysis using ab initio quantum chemical techniques and shows that the proposed pathway is inconsistent with these calculations. Of interest here is the use of calculations in order to rule out a proposed mechanistic pathway for a biologically important system.
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(1997)
J Am Chem Soc
, vol.119
, pp. 5473-5474
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Florian, J.1
Warshe, A.2
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14
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0030180875
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New model for calculation of solvation free energies: Correction of self-consistent reaction field continuum dielectric theory for short range hydrogen bonding effects
-
of special interest. This paper shows that dielectric continuum methods have systematic inaccuracies due to the incorrect treatment of hydrogen bonding, and develops a systematic empirical protocol to correct this deficiency. The same problems can also be observed in molecular mechanics force fields, which rely primarily on an electrostatic description of hydrogen bonding.
-
Marten B, Kim K, Cortis C, Friesner RA, Murphy RB, Ringnalda MN, Sitkoff D, Honig B. New model for calculation of solvation free energies: correction of self-consistent reaction field continuum dielectric theory for short range hydrogen bonding effects. of special interest J Phys Chem. 100:1996;11775-11788 This paper shows that dielectric continuum methods have systematic inaccuracies due to the incorrect treatment of hydrogen bonding, and develops a systematic empirical protocol to correct this deficiency. The same problems can also be observed in molecular mechanics force fields, which rely primarily on an electrostatic description of hydrogen bonding.
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(1996)
J Phys Chem
, vol.100
, pp. 11775-11788
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Marten, B.1
Kim, K.2
Cortis, C.3
Friesner, R.A.4
Murphy, R.B.5
Ringnalda, M.N.6
Sitkoff, D.7
Honig, B.8
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15
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84962464697
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Quantum mechanical geometry optimization in solution using a finite element continuum electrostatics method
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Cortis C, Langlois JM, Beachy M, Friesner R. Quantum mechanical geometry optimization in solution using a finite element continuum electrostatics method. J Chem Phys. 105:1996;5472-5484.
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(1996)
J Chem Phys
, vol.105
, pp. 5472-5484
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Cortis, C.1
Langlois, J.M.2
Beachy, M.3
Friesner, R.4
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16
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Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent
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Tomasi J, Persico M. Molecular interactions in solution: an overview of methods based on continuous distributions of the solvent. Chem Rev. 94:1994;2027-2094.
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Chem Rev
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Tomasi, J.1
Persico, M.2
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17
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0030857280
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Acylation of β-lactamase: An ab initio theoretical study on the effects of the oxy-anion hole
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of special interest. This paper incorporates explicit amino acid residues from the active site into the quantum chemical model and calculates the activation energy for the proposed enzymatic pathway at the Hartree - Fock level. The paper is noteworthy for the large size of the quantum chemical model.
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Wladkowski BD, Chenoweth SA, Sanders JN, Krauss M, Stevens WJ. Acylation of β-lactamase: an ab initio theoretical study on the effects of the oxy-anion hole. of special interest J Am Chem Soc. 119:1997;6423-6431 This paper incorporates explicit amino acid residues from the active site into the quantum chemical model and calculates the activation energy for the proposed enzymatic pathway at the Hartree - Fock level. The paper is noteworthy for the large size of the quantum chemical model.
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(1997)
J Am Chem Soc
, vol.119
, pp. 6423-6431
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Wladkowski, B.D.1
Chenoweth, S.A.2
Sanders, J.N.3
Krauss, M.4
Stevens, W.J.5
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18
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0030254780
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2 receptor. I. Theoretical investigations of histamine binding to an oligopeptide mimicking a part of the fifth transmembrane α-helix
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of special interest. This paper presents ab initio modeling of receptor - ligand binding using quite a large model, by current literature standards, for the receptor active site. From the calculations, a proposal for the binding site of the ligand is presented.
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2 receptor. I. Theoretical investigations of histamine binding to an oligopeptide mimicking a part of the fifth transmembrane α-helix. of special interest J Comput Aided Mol Des. 10:1996;461-478 This paper presents ab initio modeling of receptor - ligand binding using quite a large model, by current literature standards, for the receptor active site. From the calculations, a proposal for the binding site of the ligand is presented.
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(1996)
J Comput Aided Mol des
, vol.10
, pp. 461-478
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Nederkoorn, P.H.J.1
Van Lenthe, J.H.2
Van Der Goot, H.3
Donné-Op Den Kelder, G.M.4
Timmerman, H.5
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19
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0029775587
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Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A
-
of special interest. This paper describes a state of the art ab initio molecular dynamics calculation on a biologically relevant system, specifically investigating proton transfer in an on channel.
-
Sagnella DE, Laasonen K, Klein ML. Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A. of special interest Biophys J. 71:1996;1172-1178 This paper describes a state of the art ab initio molecular dynamics calculation on a biologically relevant system, specifically investigating proton transfer in an on channel.
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(1996)
Biophys J
, vol.71
, pp. 1172-1178
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Sagnella, D.E.1
Laasonen, K.2
Klein, M.L.3
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20
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77956779984
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Density-functional thermochemistry. (I.) The effect of the exchange-only gradient correction
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Becke AD. Density-functional thermochemistry. (I.) The effect of the exchange-only gradient correction. J Chem Phys. 96:1992;2155-2160.
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(1992)
J Chem Phys
, vol.96
, pp. 2155-2160
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Becke, A.D.1
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21
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0001161681
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Density-functional thermochemistry. (II.) The effect of the Perdew-Wang generalized gradient correlation correction
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Becke AD. Density-functional thermochemistry. (II.) The effect of the Perdew-Wang generalized gradient correlation correction. J Chem Phys. 97:1992;9173-9177.
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(1992)
J Chem Phys
, vol.97
, pp. 9173-9177
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Becke, A.D.1
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0000189651
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Density-functional thermochemistry. (III.) The role of exact exchange
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Becke AD. Density-functional thermochemistry. (III.) The role of exact exchange. J Chem Phys. 98:1993;5648-5652.
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(1993)
J Chem Phys
, vol.98
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Becke, A.D.1
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23
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34250817103
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A new mixing of Hartree-Fock and local density-functional theories
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Becke AD. A new mixing of Hartree-Fock and local density-functional theories. J Chem Phys. 98:1993;1372-1377.
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(1993)
J Chem Phys
, vol.98
, pp. 1372-1377
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Becke, A.D.1
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24
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0031591331
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Investigation of the use of B3LYP zero-point energies and geometries in the calculation of enthalpies of formation
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Curtiss LA, Raghavachari K, Redfern PC, Pople JA. Investigation of the use of B3LYP zero-point energies and geometries in the calculation of enthalpies of formation. Chem Phys Lett. 270:1997;419-426.
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(1997)
Chem Phys Lett
, vol.270
, pp. 419-426
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Curtiss, L.A.1
Raghavachari, K.2
Redfern, P.C.3
Pople, J.A.4
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25
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0000109748
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Assessment of Gaussian-2 and density functional theories for the computation of enthalpies of formation
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Curtiss LA, Raghavachari K, Redfern PC, Pople JA. Assessment of Gaussian-2 and density functional theories for the computation of enthalpies of formation. J Chem Phys. 106:1997;1063-1079.
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(1997)
J Chem Phys
, vol.106
, pp. 1063-1079
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Curtiss, L.A.1
Raghavachari, K.2
Redfern, P.C.3
Pople, J.A.4
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26
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16444375810
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The performance of a family of density functional methods
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Johnson BG, Gill PMW, Pople JA. The performance of a family of density functional methods. J Chem Phys. 98:1993;5612-5626.
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(1993)
J Chem Phys
, vol.98
, pp. 5612-5626
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Johnson, B.G.1
Gill, P.M.W.2
Pople, J.A.3
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27
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0030567425
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Linear scaling density functional calculations via the continuous fast multipole method
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of special interest. This is the first paper on linear scaling density functional theory (DFT), which has the potential to extend DFT to very large systems. The paper is primarily technical, but will be of interest to readers who want to understand what is involved in using quantum chemistry for ultralarge computations.
-
White CA, Johnson BG, Gill PMW, Head Gordon M. Linear scaling density functional calculations via the continuous fast multipole method. of special interest Chem Phys Lett. 253:1996;268-278 This is the first paper on linear scaling density functional theory (DFT), which has the potential to extend DFT to very large systems. The paper is primarily technical, but will be of interest to readers who want to understand what is involved in using quantum chemistry for ultralarge computations.
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(1996)
Chem Phys Lett
, vol.253
, pp. 268-278
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White, C.A.1
Johnson, B.G.2
Gill, P.M.W.3
Head Gordon, M.4
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28
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0000485335
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The local correlation treatment. II. Implementation and tests
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Saebó S, Pulay P. The local correlation treatment. II. Implementation and tests. J Chem Phys. 88:1988;1884-1890.
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(1988)
J Chem Phys
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Saebó, S.1
Pulay, P.2
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29
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0001049403
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Consistent generalization of the Møller-Plesset partitioning to open-shell and multiconfigurational SCF reference states in many-body perturbation theory
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Wolinski K, Sellers H, Pulay P. Consistent generalization of the Møller-Plesset partitioning to open-shell and multiconfigurational SCF reference states in many-body perturbation theory. Chem Phys Lett. 140:1987;225-231.
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Chem Phys Lett
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, pp. 225-231
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Wolinski, K.1
Sellers, H.2
Pulay, P.3
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30
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0001053989
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Pseudospectral localized Møller-Plesset methods: Theory and calculation of conformational energies
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Murphy M, Beachy MD, Friesner RA, Ringnalda MN. Pseudospectral localized Møller-Plesset methods: theory and calculation of conformational energies. J Chem Phys. 103:1996;1481-1490.
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(1996)
J Chem Phys
, vol.103
, pp. 1481-1490
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Murphy, M.1
Beachy, M.D.2
Friesner, R.A.3
Ringnalda, M.N.4
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31
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0001465661
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Pseudospectral localized generalized Møller-Plesset methods with a generalized valence bond reference wave function: Theory and calculation of conformational energies
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3 scaling, that provides uniformly high accuracies for conformational energies. Such methods will be crucial in designing the next generation of force fields in which quantitative agreement with quantum chemical data is enforced.
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3 scaling, that provides uniformly high accuracies for conformational energies. Such methods will be crucial in designing the next generation of force fields in which quantitative agreement with quantum chemical data is enforced.
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(1997)
J Chem Phys
, vol.106
, pp. 5073-5084
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Murphy, R.B.1
Pollard, W.T.2
Friesner, R.A.3
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32
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84986532404
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Calculation of molecular geometries, relative conformational energies, dipole moments, and molecular electrostatic potential fitted charges of small organic molecules of biochemical interest by density functional theory
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St-Amant A, Cornell WD, Kollman PA, Halgren TA. Calculation of molecular geometries, relative conformational energies, dipole moments, and molecular electrostatic potential fitted charges of small organic molecules of biochemical interest by density functional theory. J Comput Chem. 16:1995;1483-1506.
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(1995)
J Comput Chem
, vol.16
, pp. 1483-1506
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St-Amant, A.1
Cornell, W.D.2
Kollman, P.A.3
Halgren, T.A.4
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33
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0037571112
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Merck Molecular Force Field. I. Basis, form, scope, parameterization, and performance of MMFF94
-
of outstanding interest. of special interest. This paper describes a new molecular modeling force field, MMFF, with wide coverage of pharmaceutical compounds, using extensive fitting to good quality quantum chemical data. The MMFF force field is one of the two best performers in the tests carried out in [41] concerning the prediction of tetrapeptide energetics.
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of outstanding interest Halgren TA. Merck Molecular Force Field. I. Basis, form, scope, parameterization, and performance of MMFF94. of special interest J Comput Chem. 17:1996;490-519 This paper describes a new molecular modeling force field, MMFF, with wide coverage of pharmaceutical compounds, using extensive fitting to good quality quantum chemical data. The MMFF force field is one of the two best performers in the tests carried out in [41] concerning the prediction of tetrapeptide energetics.
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(1996)
J Comput Chem
, vol.17
, pp. 490-519
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Halgren, T.A.1
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34
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Merck Molecular Force Field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions
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Halgren TA. Merck Molecular Force Field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions. J Comput Chem. 17:1996;520-552.
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(1996)
J Comput Chem
, vol.17
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Halgren, T.A.1
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35
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Merck Molecular Force Field. III. Molecular geometrics and vibrational frequencies for MMFF94
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Halgren TA. Merck Molecular Force Field. III. Molecular geometrics and vibrational frequencies for MMFF94. J Comput Chem. 17:1996;553-586.
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(1996)
J Comput Chem
, vol.17
, pp. 553-586
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Halgren, T.A.1
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36
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Merck Molecular Force Field. IV. Conformational Energies and Geometries for MMFF94
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Halgren TA, Nachbar RB. Merck Molecular Force Field. IV. Conformational Energies and Geometries for MMFF94. J Comput Chem. 17:1996;587-615.
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(1996)
J Comput Chem
, vol.17
, pp. 587-615
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Halgren, T.A.1
Nachbar, R.B.2
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37
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Merck Molecular Force Field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules
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Halgren TA. Merck Molecular Force Field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules. J Comput Chem. 17:1996;616-641.
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J Comput Chem
, vol.17
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Halgren, T.A.1
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38
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0029912748
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Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
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of outstanding interest. This paper describes a new molecular modeling force field, OPLS-AA, which is extensively fit to both quantum chemical data and liquid state thermodynamics. OPLS-AA is one of the two best performers in the tests carried out in [41], and simultaneously provides excellent prediction of liquid state properties.
-
Jorgensen WL, Maxwell DS, TiradoRives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. of outstanding interest J Am Chem Soc. 118:1996;11225-11236 This paper describes a new molecular modeling force field, OPLS-AA, which is extensively fit to both quantum chemical data and liquid state thermodynamics. OPLS-AA is one of the two best performers in the tests carried out in [41], and simultaneously provides excellent prediction of liquid state properties.
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(1996)
J Am Chem Soc
, vol.118
, pp. 11225-11236
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Jorgensen, W.L.1
Maxwell, D.S.2
Tiradorives, J.3
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39
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0029011701
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A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
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Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, aiFerguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc. 117:1995;5179-5197.
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(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
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Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz K.M., Jr.5
Aiferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
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40
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6344260593
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An all-atom empirical energy function for the simulation of nucleic acids
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Mackerell AD Jr, Wiórkiewicz-Kuczera J, Karplus M. An all-atom empirical energy function for the simulation of nucleic acids. J Am Chem Soc. 117:1995;11946-11975.
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(1995)
J Am Chem Soc
, vol.117
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MacKerell A.D., Jr.1
Wiórkiewicz-Kuczera, J.2
Karplus, M.3
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41
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0030745939
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Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields
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of outstanding interest. This paper tests the transferability of protein force fields with large scale accurate quantum chemistry calculations. The energies of 10 conformations of an alanine tetrapeptide were computed at a accurate quantum chemical level and the results compared against a comprehensive list of protein molecular mechanics force fields. A preliminary assessment of the accuracy of the force fields tested is provided.
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Beachy M, Chasman D, Murphy R, Halgren T, Friesner R. Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields. of outstanding interest J Am Chem Soc. 119:1997;5908-5920 This paper tests the transferability of protein force fields with large scale accurate quantum chemistry calculations. The energies of 10 conformations of an alanine tetrapeptide were computed at a accurate quantum chemical level and the results compared against a comprehensive list of protein molecular mechanics force fields. A preliminary assessment of the accuracy of the force fields tested is provided.
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(1997)
J Am Chem Soc
, vol.119
, pp. 5908-5920
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Beachy, M.1
Chasman, D.2
Murphy, R.3
Halgren, T.4
Friesner, R.5
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42
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0030606884
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The cupric geometry of blue copper proteins is not strained
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of special interest. This paper presents ab initio quantum chemical calculations on an active site model for blue copper proteins, using both density functional theory and multirefence perturbation theory methods, and concludes that the active site geometry around the copper center is not strained. The use of multireference perturbation theory, a highly accurate quantum chemical method, on a reasonable size active site model, is particularly noteworthy here.
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Ryde U, Olsson MHM, Pierloot K, Roos BO. the cupric geometry of blue copper proteins is not strained. of special interest J Mol Biol. 261:1996;586-596 This paper presents ab initio quantum chemical calculations on an active site model for blue copper proteins, using both density functional theory and multirefence perturbation theory methods, and concludes that the active site geometry around the copper center is not strained. The use of multireference perturbation theory, a highly accurate quantum chemical method, on a reasonable size active site model, is particularly noteworthy here.
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(1996)
J Mol Biol
, vol.261
, pp. 586-596
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Ryde, U.1
Olsson, M.H.M.2
Pierloot, K.3
Roos, B.O.4
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43
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0030755238
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A quantum chemical study of hydrogen abstraction from manganese-coordinated water by a tyrosyl radical: A model for water oxidation in photosystem II
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of special interest. This paper provides ab initio quantum chemical calculations on a large transition metal active site model using density functional theory, with a specific mechanism proposed for key steps of water oxidation in photosystem II. This is a biologically important problem and the calculations provide support for a proposed physical mechanism.
-
Blomberg MRA, Siegbahn PEM, Styring S, Babcock GT, Akermaker B, Korall P. A quantum chemical study of hydrogen abstraction from manganese-coordinated water by a tyrosyl radical: a model for water oxidation in photosystem II. of special interest J Am Chem Soc. 119:1997;8285-8292 This paper provides ab initio quantum chemical calculations on a large transition metal active site model using density functional theory, with a specific mechanism proposed for key steps of water oxidation in photosystem II. This is a biologically important problem and the calculations provide support for a proposed physical mechanism.
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(1997)
J Am Chem Soc
, vol.119
, pp. 8285-8292
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Blomberg, M.R.A.1
Siegbahn, P.E.M.2
Styring, S.3
Babcock, G.T.4
Akermaker, B.5
Korall, P.6
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44
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0001272489
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Density-functional and electrostatic calculations for a model of a manganese superoxide dismutase active site in aqueous solution
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Fisher CL, Chen J-L, Li J, Bashford D, Noodleman L. Density-functional and electrostatic calculations for a model of a manganese superoxide dismutase active site in aqueous solution. J Phys Chem. 100:1996;13498-13505.
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(1996)
J Phys Chem
, vol.100
, pp. 13498-13505
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Fisher, C.L.1
Chen J-L2
Li, J.3
Bashford, D.4
Noodleman, L.5
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45
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0030986743
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Mechanism of C-H activation by diiron methane monoxygenases: Quantum chemical studies
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of outstanding interest. This paper presents ab initio quantum chemical calculations on a large transition metal active site model of methane monooxygenase using density functional theory, with proposals for the pathway by which the enzyme catalyzes the transformation of methane to methanol. Particularly noteworthy here is the use of large basis sets for the DFT calculations. This is a major step forward in obtaining more reliable results for energetics as compared to previous work in the literature.
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Siegbahn PEM, Crabtree RH. Mechanism of C-H activation by diiron methane monoxygenases: quantum chemical studies. of outstanding interest J Am Chem Soc. 119:1997;3103-3113 This paper presents ab initio quantum chemical calculations on a large transition metal active site model of methane monooxygenase using density functional theory, with proposals for the pathway by which the enzyme catalyzes the transformation of methane to methanol. Particularly noteworthy here is the use of large basis sets for the DFT calculations. This is a major step forward in obtaining more reliable results for energetics as compared to previous work in the literature.
-
(1997)
J Am Chem Soc
, vol.119
, pp. 3103-3113
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Siegbahn, P.E.M.1
Crabtree, R.H.2
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46
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0029997138
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2-peroxo- and bis(u-oxo)dicopper cores
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of special interest. This paper describes ab initio quantum chemical calculations on small active site models of the conformational energetics of dicopper cores. The calculations use multireference perturbation theory, and are thus high quality calculations, and also a dielectric continuum solvation model.
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2-peroxo- and bis(u-oxo)dicopper cores. of special interest J Am Chem Soc. 118:1996;11283-11287 This paper describes ab initio quantum chemical calculations on small active site models of the conformational energetics of dicopper cores. The calculations use multireference perturbation theory, and are thus high quality calculations, and also a dielectric continuum solvation model.
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(1996)
J Am Chem Soc
, vol.118
, pp. 11283-11287
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Cramer, C.J.1
Smith, B.A.2
Tolman, W.B.3
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47
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0000680353
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Carbonic anhydrase reactivity, mutation, and inhibition probed with a model of ab initio quantum chemistry within a protein
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Garmer DR. Carbonic anhydrase reactivity, mutation, and inhibition probed with a model of ab initio quantum chemistry within a protein. J Phys Chem. 101:1997;2945-2953.
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(1997)
J Phys Chem
, vol.101
, pp. 2945-2953
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Garmer, D.R.1
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48
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1842299316
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Binding of bicarbonate to human carbonic anhydrase II: A continuum of binding states
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of special interest. This paper presents QM/MM simulations using a semi-empirical QM Hamiltonian on the binding of bicarbonate to carbonic anhydrase. It is a good example of how a QM/MM calculation can address qualitative questions reasonably well, even though the model is probably not highly precise. With a transition metal-binding site, conventional force fields are problematic, and QM/MM even at the semi-empirical level is likely the best alternative.
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Merz KM Jr, Banci L. Binding of bicarbonate to human carbonic anhydrase II: a continuum of binding states. of special interest J Am Chem Soc. 119:1997;863-871 This paper presents QM/MM simulations using a semi-empirical QM Hamiltonian on the binding of bicarbonate to carbonic anhydrase. It is a good example of how a QM/MM calculation can address qualitative questions reasonably well, even though the model is probably not highly precise. With a transition metal-binding site, conventional force fields are problematic, and QM/MM even at the semi-empirical level is likely the best alternative.
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(1997)
J Am Chem Soc
, vol.119
, pp. 863-871
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Merz K.M., Jr.1
Banci, L.2
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49
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84962428702
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Chemical reaction mechanisms in vacuo, in solution and in enzyme fields: Isomerization catalyzed by triose phosphate- isomerase (TIM)
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Alagona G, Ghio C, Kollman PA. Chemical reaction mechanisms in vacuo, in solution and in enzyme fields: isomerization catalyzed by triose phosphate- isomerase (TIM). J Mol Struct. 371:1996;287-298.
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(1996)
J Mol Struct
, vol.371
, pp. 287-298
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Alagona, G.1
Ghio, C.2
Kollman, P.A.3
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50
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1842410903
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A simulation of the catalytic mechanism of aspartylglucosaminidase using ab initio quantum mechanics and molecular dynamics
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of special interest. This paper uses a QM/MM approach in which simulations are carried out at the MD level. Key structures are then extracted from the simulations and calculated at the QM level using Hartree - Fock and MP2 levels of theory, treating the protein environment as point charges and using a continuum model for solvation. The QM calculations allow an evaluation of transition state energetics that would be unavailable from the MM force field. An explanation of the catalytic mechanism is provided from the calculations.
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Peräkylä M, Kollman PA. A simulation of the catalytic mechanism of aspartylglucosaminidase using ab initio quantum mechanics and molecular dynamics. of special interest J Am Chem Soc. 119:1997;1189-1196 This paper uses a QM/MM approach in which simulations are carried out at the MD level. Key structures are then extracted from the simulations and calculated at the QM level using Hartree - Fock and MP2 levels of theory, treating the protein environment as point charges and using a continuum model for solvation. The QM calculations allow an evaluation of transition state energetics that would be unavailable from the MM force field. An explanation of the catalytic mechanism is provided from the calculations.
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(1997)
J Am Chem Soc
, vol.119
, pp. 1189-1196
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Peräkylä, M.1
Kollman, P.A.2
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51
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0030124161
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The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations
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Ryde U. The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations. J Comput Aided Mol Des. 10:1996;153-164.
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(1996)
J Comput Aided Mol des
, vol.10
, pp. 153-164
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Ryde, U.1
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52
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0002709949
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Transition-state structural refinement with GRACE and CHARMm: Realistic modelling of lactate dehydrogenase using a combined quantum/classical method
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Moliner V, Turner AJ, Williams IH. Transition-state structural refinement with GRACE and CHARMm: realistic modelling of lactate dehydrogenase using a combined quantum/classical method. Chem Commun. 1997;1271-1272.
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(1997)
Chem Commun
, pp. 1271-1272
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Moliner, V.1
Turner, A.J.2
Williams, I.H.3
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53
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0031193019
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Hybrid quantum and molecular mechanical (QM/MM) studies on the pyruvate to L-lactate interconversion in L-lactate dehydrogenase
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Ranganathan S, Gready JE. Hybrid quantum and molecular mechanical (QM/MM) studies on the pyruvate to L-lactate interconversion in L-lactate dehydrogenase. J Phys Chem B. 101:1997;5614-5618.
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(1997)
J Phys Chem B
, vol.101
, pp. 5614-5618
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Ranganathan, S.1
Gready, J.E.2
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54
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0030887896
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Simulation of the enzyme mechanism of malate dehydrogenase
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Cunningham MA, Ho LL, Nguyen DT, Gillilan RE, Bash PA. Simulation of the enzyme mechanism of malate dehydrogenase. Biochemistry. 36:1997;4800-4816.
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(1997)
Biochemistry
, vol.36
, pp. 4800-4816
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Cunningham, M.A.1
Ho, L.L.2
Nguyen, D.T.3
Gillilan, R.E.4
Bash, P.A.5
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55
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0000235210
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The mechanism of the catalysis of the Claisen rearrangement of chorismate to perphenate by the chorismate mutase from Bacillus subtilis. A molecular mechanics and hybrid quantum mechanical/molecular mechanical study
-
of special interest. This paper investigates the role of the active site of the enzyme chorismate mutase in catalyzing the Claisen rearrangement of chorismate to prephenate. Here, QM structures (computed at the Hartree - Fock level) along the reaction path are docked into the active site and the energies are evaluated via a mixed QM/MM Hamiltonian. This is yet another approach to deploying QM/MM technology, and leads to reasonable qualitative agreement with experiments in terms of the ability of the enzyme to lower the barrier to reaction.
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Davidson MM, Gould IR, Hillier IH. The mechanism of the catalysis of the Claisen rearrangement of chorismate to perphenate by the chorismate mutase from Bacillus subtilis. A molecular mechanics and hybrid quantum mechanical/molecular mechanical study. of special interest J Chem Soc Perkin Trans. 2:1996;525-532 This paper investigates the role of the active site of the enzyme chorismate mutase in catalyzing the Claisen rearrangement of chorismate to prephenate. Here, QM structures (computed at the Hartree - Fock level) along the reaction path are docked into the active site and the energies are evaluated via a mixed QM/MM Hamiltonian. This is yet another approach to deploying QM/MM technology, and leads to reasonable qualitative agreement with experiments in terms of the ability of the enzyme to lower the barrier to reaction.
-
(1996)
J Chem Soc Perkin Trans
, vol.2
, pp. 525-532
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Davidson, M.M.1
Gould, I.R.2
Hillier, I.H.3
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56
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0030598997
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A combined quantum/classical molecular dynamics study of the catalytic mechanism of HIV protease
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Liu H, Müller-Plathe F, van Gunsteren WF. A combined quantum/classical molecular dynamics study of the catalytic mechanism of HIV protease. J Mol Biol. 261:1996;454-469.
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(1996)
J Mol Biol
, vol.261
, pp. 454-469
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Liu, H.1
Müller-Plathe, F.2
Van Gunsteren, W.F.3
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57
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0000049872
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Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I. Theoretical considerations
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Eurenius KP, Chatfield DC, Brooks BR, Hodoscek M. Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I. Theoretical considerations. Int J Quantum Chem. 60:1996;1189-1200.
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(1996)
Int J Quantum Chem
, vol.60
, pp. 1189-1200
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Eurenius, K.P.1
Chatfield, D.C.2
Brooks, B.R.3
Hodoscek, M.4
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58
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33845283509
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Free energy perturbation method for chemical reactions in the condensed phase: A dynamical approach based on a combined quantum and molecular mechanics potential
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Bash PA, Field MJ, Karplus M. Free energy perturbation method for chemical reactions in the condensed phase: a dynamical approach based on a combined quantum and molecular mechanics potential. J Am Chem Soc. 109:1987;8092-8094.
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(1987)
J Am Chem Soc
, vol.109
, pp. 8092-8094
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Bash, P.A.1
Field, M.J.2
Karplus, M.3
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