Optimization of parameters for semiempirical methods II. Applications

Stewart, James J. P.

doi:10.1002/jcc.540100209

Cited by 4,029 publications

(2,078 citation statements)

References 31 publications

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“…Molecular geometry was optimized and quantum chemical descriptors were calculated using the PM3 Hamiltonian (1989) contained in the quantum chemical computation software MOPAC (Version 6.0, Stewart, 1989. Frank J. Seiler Research Laboratory, US Air Force Academy, Co 80840).…”

Section: Methodsmentioning

confidence: 99%

Quantitative structure–property relationships (QSPRs) on direct photolysis of PCDDs

Chen

Quan

Schramm³

et al. 2001

Chemosphere

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Section: Methodsmentioning

confidence: 99%

Quantitative structure–property relationships (QSPRs) on direct photolysis of PCDDs

Chen

Quan

Schramm³

et al. 2001

Chemosphere

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“…2 With these response properties, the polarized charge of QM atom α is computed as (18) The superscript ref designates the reference state in the absence of the perturbation. The electrostatic interaction between the QM and MM subsystems is the simple Coulombic interaction between point charges (19) The intenial energy of the QM sub system is defined as (20) which can be computed as 2 (21) That is, the energy is expanded to second order of perturbations around the initial conformation (denoted as ) and the initial electrostatic potential it bears denoted as ). With the definitions of Eq.…”

Section: Reaction Path Potential With a Mean MM Fieldmentioning

confidence: 99%

QM/MM Minimum Free-Energy Path: Methodology and Application to Triosephosphate Isomerase

Yang

2007

J. Chem. Theory Comput.

139

198

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Structural and energetic changes are two important characteristic properties of a chemical reaction process. In the condensed phase, studying these two properties is very challenging because of the great computational cost associated with the quantum mechanical calculations and phase space sampling. Although the combined quantum mechanics/molecular mechanics (QM/MM) approach significantly reduces the amount of the quantum mechanical calculations and facilitates the simulation of solution phase and enzyme catalyzed reactions, the required quantum mechanical calculations remain quite expensive and extensive sampling can be achieved routinely only with semiempirical quantum mechanical methods. QM/MM simulations with ab initio QM methods, therefore, are often restricted to narrow regions of the potential energy surface such as the reactant, product and transition state, or the minimum energy path. Such ab initio QM/MM calculations have previously been performed with the QM/MM-Free Energy (QM/MM-FE) method of Zhang et al. 1 to generate the free energy profile along the reaction coordinate using free energy perturbation calculations at fixed structures of the QM subsystems. Results obtained with the QM/MM-FE method depend on the determination of the minimum energy reaction path, which is based on local conformations of the protein/solvent environment and can be difficult to obtain in practice. To overcome the difficulties associated with the QM/MM-FE method and to further enhance the sampling of the MM environment conformations, we develop here a new method to determine the QM/MM minimum free energy path (QM/MM-MFEP) for chemical reaction processes in solution and in enzymes. Within the QM/MM framework, we express the free energy of the system as a function of the QM conformation, thus leading to a simplified potential of mean force (PMF) description for the thermodynamics of the system. The free energy difference between two QM conformations is evaluated by the QM/MM free energy perturbation method. The free energy gradients with respect to the QM degrees of freedom are calculated from molecular dynamics simulations at given QM conformations. With the free energy and free energy gradients in hand, we further implement chain-of-conformation optimization algorithms in the search for the reaction path on the free energy surface without specifying a reaction coordinate. This method thus efficiently provides a unique minimum free energy path for solution and enzyme reactions, with structural and energetic properties being determined simultaneously. To further incorporate the dynamic contributions of the QM subsystem into the simulations, we develop the reaction path potential of Lu, et al. 2 for the minimum free energy path. The combination of the methods developed here presents a comprehensive and accurate treatment for the simulation of reaction processes in solution and in enzymes with ab initio QM/MM methods. The method has been demonstrated on the first step of the reaction of the enzyme triosephosphate isome...

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“…Owing to the large size of the ions, the initial survey calculations were performed by using the PM3 [30,31] semi-empirical algorithm, which was obtained as part of the Spartan '02 for Linux package (Wavefunction, Inc.). The starting points of the investigation were the protonated ions of compounds 1, 5 and 9 [3], to which we limited the calculations.…”

Section: Theoretical Calculationsmentioning

confidence: 99%

Protonated nitro group as a gas-phase electrophile: Experimental and theoretical study of the cyclization of o-nitrodiphenyl ethers, amines, and sulfides

Moolayil

George

Srinivas

et al. 2007

J. Am. Soc. Mass Spectrom.

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A novel gas-phase electrophilic cyclization, initiated by the protonation of a nitro group, occurs for 2-nitrophenyl phenyl ether and for the analogous sulfide and amine, leading to heterocyclic intermediates in each case. Subsequently, the cyclic intermediates dissociate via two pathways: (1) unusual step-wise eliminations of two OH radicals to afford heterocyclic cations, [phenoxazine − H] + , [phenothiazine − H] + and [phenazine + H] + , and (2) expulsion of H 2 O, to yield a heterocyclic ketone, followed by loss of CO. The proposed structures of the gas-phase product ions and reaction mechanisms are supported by chemical substitution, deuterium labeling, accurate mass measurements at high mass resolving power, product-ion mass spectra obtained by tandem mass spectrometry, mass spectra of reference compounds, and molecular orbital calculations. Using a mass spectrometer as a reaction vessel, we demonstrate that, upon protonation, a nitro group becomes an electrophile and participates in cyclization reactions in the gas-phase.

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Optimization of parameters for semiempirical methods II. Applications

Cited by 4,029 publications

References 31 publications

Quantitative structure–property relationships (QSPRs) on direct photolysis of PCDDs

Quantitative structure–property relationships (QSPRs) on direct photolysis of PCDDs

QM/MM Minimum Free-Energy Path: Methodology and Application to Triosephosphate Isomerase

Protonated nitro group as a gas-phase electrophile: Experimental and theoretical study of the cyclization of o-nitrodiphenyl ethers, amines, and sulfides

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