Parameterization of the approximate valence bond (AVB) method to describe potential energy surface in the reaction catalyzed by HIV-1 protease

Trylska, Joanna; Grochowski, Paweł; Geller, Maciej

doi:10.1002/1097-461x(2001)82:2<86::aid-qua1024>3.0.co;2-e

Cited by 11 publications

(23 citation statements)

References 24 publications

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“…Chatfield et al used an ab initio QM/MM approach with CHARMM for the MM part to determine a minimum energy path for the reaction in the enzyme (255,256). Trylska et al (257) presented a parameterization of a 23 × 23 approximate valence bond description of the complete enzymatic reaction catalyzed by HIV-1 protease. HYDROGENASE Amara et al (258) used a B3LYP/effective core potential treatment of a 30-atom quantum subsystem joined by link atoms to a CHARMM subsystem of 10,000 atoms in residues within 27Å of the active site to optimize reactant structures of Ni-Fe hydrogenase.…”

Section: Haloalkane Dehalogenasementioning

confidence: 99%

QUANTUMMECHANICALMETHODS FORENZYMEKINETICS

Gao

Truhlar

2002

Annu. Rev. Phys. Chem.

775

632

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This review discusses methods for the incorporation of quantum mechanical effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model. We emphasize three aspects: (a) use of quantum mechanical electronic structure methods such as molecular orbital theory and density functional theory, usually in conjunction with molecular mechanics; (b) treating vibrational motions quantum mechanically, either in an instantaneous harmonic approximation, or by path integrals, or by a three-dimensional wave function coupled to classical nuclear motion; (c) incorporation of multidimensional tunneling approximations into reaction rate calculations.

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Section: Haloalkane Dehalogenasementioning

confidence: 99%

QUANTUMMECHANICALMETHODS FORENZYMEKINETICS

Gao

Truhlar

2002

Annu. Rev. Phys. Chem.

775

632

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“…The use of valence-bond (VB) theory to study these reactions quantitatively is less common because of the higher computational cost and slow convergence (with respect to adding configurations) of VB calculations, but VB theory has the advantage of providing unique insight into the electronic structure 54–59. Examples of nucleophilic substitution reactions studied using VB methodology include the identity X − + RX′ → XR + X′ − reactions (R = alkyl; X, X′ = F, Cl, Br, I);54–57,60–68 nonidentity versions of these reactions (X not the same as X′);54–57 the Cl − + CH 3 SH 2 + → ClCH 3 + SH 2 and H 3 N + CH 3 SH 2 + → H 3 NCH 3 + + SH 2 reactions;61 the particular case CH 3 Cl + NH 3 →Cl − + CH 3 NH 3 + of the general Menshutkin reaction;55,58,69–72 reactions of esters and ketyl radical anions;56,73 reactions at peptide bonds;74 and reaction at phosphorus 75…”

Section: Introductionmentioning

confidence: 99%

Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase S_N2 Reaction of Acetate Ion with 1,2-Dichloroethane

Valero

Song

Gao

et al. 2008

J. Chem. Theory Comput.

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Diabatic models are widely employed for studying chemical reactivity in condensed phases and enzymes, but there has been little discussion of the pros and cons of various diabatic representations for this purpose. Here we discuss and contrast six different schemes for computing diabatic potentials for a charge rearrangement reaction. They include (i) the variational diabatic configurations (VDC) constructed by variationally optimizing individual valence bond structures and (ii) the consistent diabatic configurations (CDC) obtained by variationally optimizing the ground-state adiabatic energy, both in the nonorthogonal molecular orbital valence bond (MOVB) method, along with the orthogonalized (iii) VDC-MOVB and (iv) CDC-MOVB models. In addition, we consider (v) the fourfold way (based on diabatic molecular orbitals and configuration uniformity), and (vi) empirical valence bond (EVB) theory. To make the considerations concrete, we calculate diabatic electronic states and diabatic potential energies along the reaction path that connects the reactant and the product ion-molecule complexes of the gas-phase bimolecular nucleophilic substitution (SN2) reaction of 1,2-dichloethane (DCE) with acetate ion, which is a model reaction corresponding to the reaction catalyzed by haloalkane dehalogenase. We utilize ab initio block-localized molecular orbital theory to construct the MOVB diabatic states and ab initio multi-configuration quasidegenerate perturbation theory to construct the fourfold-way diabatic states; the latter are calculated at reaction path geometries obtained with the M06-2X density functional. The EVB diabatic states are computed with parameters taken from the literature. The MOVB and fourfold-way adiabatic and diabatic potential energy profiles along the reaction path are in qualitative but not quantitative agreement with each other. In order to validate that these wave-function-based diabatic states are qualitatively correct, we show that the reaction energy and barrier for the adiabatic ground state, obtained with these methods, agree reasonably well with the results of high-level calculations using the composite G3SX and G3SX(MP3) methods and the BMC-CCSD multi-coefficient correlation method. However, a comparison of the EVB gas-phase adiabatic ground-state reaction path with those obtained from MOVB and with the fourfold way reveals that the EVB reaction path geometries show a systematic shift towards the products region, and that the EVB lowest-energy path has a much lower barrier. The free energies of solvation and activation energy in water reported from dynamical calculations based on EVB also imply a low activation barrier in the gas phase. In addition, calculations of the free energy of solvation using the recently proposed SM8 continuum solvation model with CM4M partial atomic charges lead to an activation barrier in reasonable agreement with experiment only when the geometries and the gas-phase barrier are those obtained from electronic structure calculations, i.e., methods i–v. These comparis...

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“…A detailed description of the AVB method has been previously presented 2, 3. Below we describe only basic approximations.…”

Section: Outline Of the Avb Methodsmentioning

confidence: 99%

“…The AVB method was parameterized to precisely reproduce more advanced density functional theory (DFT) calculations for smaller molecular systems and/or fragments of enzyme active sites 2, 3. The AVB parameters were also refined using experimental data in the vapor state, for example, dissociation energies of molecular fragments, when available.…”

Section: Introductionmentioning

confidence: 99%

“…AVB has already been merged with conventional molecular dynamics (MD) and serves as a fast quantum mechanical generator of the potential energy function either for classic dynamics or quantum dynamics in a classic biomolecular environment. The parallelized quantum classic molecular dynamics (QCMD) code has been applied to phospholipase A 2 4, 5 and HIV‐protease 3, allowing simulation of the entire enzymatic process in the first case and the most important steps in the second. A similar empirical valence bond (EVB) method was earlier developed and applied to a number of enzymatic processes by Warshel and coworkers 6–8.…”

Section: Introductionmentioning

confidence: 99%

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DFT calculations and parameterization of the approximate valence bond method to describe the phosphoryl transfer reaction in a model system

Ginalski¹,

Grochowski²,

Lesyng³

et al. 2002

Int J of Quantum Chemistry

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Density functional theory (DFT) calculations have been performed at the B3LYP/6-31Gϩ(d,p) level for a model phosphodiester system to describe a transphosphorylation reaction that mimics the phosphoryl transfer process in serine/threonine protein kinases. The DFT energy and electrostatic potential data have been used to extend the parameterization of the approximate valence bond (AVB) method. AVB mimics well the DFT results and is planned for use as a fast potential energy generator to simulate phosphoryl transfer processes in protein kinases using the quantum classic molecular dynamics approach.

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Parameterization of the approximate valence bond (AVB) method to describe potential energy surface in the reaction catalyzed by HIV-1 protease

Cited by 11 publications

References 24 publications

QUANTUMMECHANICALMETHODS FORENZYMEKINETICS

QUANTUMMECHANICALMETHODS FORENZYMEKINETICS

Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase S_N2 Reaction of Acetate Ion with 1,2-Dichloroethane

DFT calculations and parameterization of the approximate valence bond method to describe the phosphoryl transfer reaction in a model system

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Parameterization of the approximate valence bond (AVB) method to describe potential energy surface in the reaction catalyzed by HIV-1 protease

Cited by 11 publications

References 24 publications

QUANTUMMECHANICALMETHODS FORENZYMEKINETICS

QUANTUMMECHANICALMETHODS FORENZYMEKINETICS

Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase SN2 Reaction of Acetate Ion with 1,2-Dichloroethane

DFT calculations and parameterization of the approximate valence bond method to describe the phosphoryl transfer reaction in a model system

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Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase S_N2 Reaction of Acetate Ion with 1,2-Dichloroethane