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Volumn 8, Issue 2, 1998, Pages 257-262

Quantum mechanical calculations on biological systems

Author keywords

[No Author keywords available]

Indexed keywords

METAL;

EID: 0032054613     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(98)80048-1     Document Type: Article
Times cited : (106)

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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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    • 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.
    • 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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    • 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.
    • 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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    • Merz K.M., Jr.1    Banci, L.2
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    • A simulation of the catalytic mechanism of aspartylglucosaminidase using ab initio quantum mechanics and molecular dynamics
    • 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.
    • 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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    • Peräkylä, M.1    Kollman, P.A.2
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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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    • 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.
    • 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.
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    • Davidson, M.M.1    Gould, I.R.2    Hillier, I.H.3
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    • Bash, P.A.1    Field, M.J.2    Karplus, M.3


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