Incorporation of hydration effects within the semiempirical molecular orbital framework. AM1 and MNDO results for neutral molecules, cations, anions, and reacting systems

Ford, George P.; Wang, Bingze

doi:10.1021/ja00052a061

Cited by 67 publications

(49 citation statements)

References 7 publications

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“…tial MEP in the semiempirical approximation, that is, the same as used by Wang and Ford 28,29 and Chudinov et al 30 in their semiempirical SCRF models. Note that these definitions of the MEP do not employ a density matrix ''deorthogonalization'' procedure.…”

mentioning

confidence: 99%

Coupled semiempirical molecular orbital and molecular mechanics model (QM/MM) for organic molecules in aqueous solution

Cummins

Gready

1997

J. Comput. Chem.

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A coupled quantum mechanical and molecular mechanical (QM/MM) model based on the AM1, MNDO, and PM3 semiempirical molecular orbital methods and the TIP3P molecular mechanics model for liquid water is presented. The model was parameterized for each of the three molecular orbital methods using the aqueous solvation free energies of a wide range of neutral organic molecules, many of which are representative of amino acid side chains. The fit to the experimental solvation free energies was achieved by varying the radii in the van der Waals (vdW) terms for interactions between the solute, which was treated quantum mechanically, and the molecular mechanics (TIP3P) solvent molecules. It is assumed that the total free energy can be obtained as the sum of components derived from the electrostatic terms in the Hamiltonian plus a generally smaller “nonelectrostatic” term. The electrostatic contributions to the solvation free energies were computed using molecular dynamics (MD) simulation and thermodynamic integration techniques; the nonelectrostatic contributions were taken from the literature. It was found that the experimental free energies could be reproduced accurately (to within 1 kcal/mol) from the MD simulations, provided that the vdW parameter associated with hydrogen bonding (H bonding) was allowed to have different values depending on the QM method (AM1, MNDO, or PM3) and the type of functional group involved in the H bonding. Moreover, the radial distribution functions obtained from the MD simulations using such a parameterization scheme showed the expected H‐bonded structures between the solute and molecules of the solvent. The solvent‐induced dipole moments also compared favorably with the results of other QM/MM model calculations. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1496–1512, 1997

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confidence: 99%

Coupled semiempirical molecular orbital and molecular mechanics model (QM/MM) for organic molecules in aqueous solution

Cummins

Gready

1997

J. Comput. Chem.

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“…Each (1 -At)-'Br, product is always less than Partial closure approximation consists of neglecting the last terms in eq. (17). In the present work, two levels of truncation have been considered: CLS1-PCM and CLS2-PCM, respectively, shown in eqs.…”

Section: The New Formulation: Partial Closure Cls-pcmmentioning

confidence: 99%

On the evaluation of the solvent polarization apparent charges in the polarizable continuum model: A new formulation

1995

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A new formulation (CLS-PCM) for the calculation of the apparent surface charges in the framework of the ab initio polarizable continuum model of the solvent (PCM) is introduced. Its performance is compared with that of the original iterative version (ITER-PCM) of the method as well as with a matricial alternative formulation (matrix-BEM-PCM) of the same problem. Both CLS-PCM and matrix-BEM-PCM have shown to be computationally more efficient than ITER-PCM without presenting any problems associated with the convergence of the process. Although for small and medium-size solutes the use of matrix-BEM-PCM is recommended, for neutral solutes of larger size the use of CLS2 becomes computationally more convenient. Finally, for very large-size systems, compromise between matrix storage requirements, time of calculation, and exactness of the results may make preferable the use of the more approximate CLSl formalism, possibly in conjunction with semiempirical or semiclassical descriptions of the solute.

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“…Although originally developed for ab initio methods, the PCM has recently been introduced to semiempirical methods. 7,25,26 In the present work we present the implementation of the PCM into the SINDO1 method 27 ᎐ 29 in combination with the asymptotic Ž . 30 density model ADM for the molecular electro-Ž .…”

Section: Introduction He Theoretical Description Of Solution Effectsmentioning

confidence: 99%

Solvation effects in SINDO1: Application to organic molecules

Kölle

Jug

1997

J. Comput. Chem.

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Incorporation of hydration effects within the semiempirical molecular orbital framework. AM1 and MNDO results for neutral molecules, cations, anions, and reacting systems

Cited by 67 publications

References 7 publications

Coupled semiempirical molecular orbital and molecular mechanics model (QM/MM) for organic molecules in aqueous solution

Coupled semiempirical molecular orbital and molecular mechanics model (QM/MM) for organic molecules in aqueous solution

On the evaluation of the solvent polarization apparent charges in the polarizable continuum model: A new formulation

Solvation effects in SINDO1: Application to organic molecules

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