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Molecular dynamics study of solvation effects on acid dissociation in aprotic media (1996)

Laria, Daniel ; Kapral, Raymond ; Estrin, Darío ; [et al.]

College Park, Md. : American Institute of Physics (AIP)

The Journal of Chemical Physics 104 (1996), S. 6560-6568

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ISSN: 1089-7690

Source: AIP Digital Archive

Topics: Physics , Chemistry and Pharmacology

Notes: Acid ionization in aprotic media is studied using molecular dynamics techniques. In particular, models for HCl ionization in acetonitrile and dimethylsulfoxide are investigated. The proton is treated quantum mechanically using Feynman path integral methods and the remaining molecules are treated classically. Quantum effects are shown to be essential for the proper treatment of the ionization. The potential of mean force is computed as a function of the ion pair separation and the local solvent structure is examined. The computed dissociation constants in both solvents differ by several orders of magnitude which are in reasonable agreement with experimental results. Solvent separated ion pairs are found to exist in dimethylsulfoxide but not in acetonitrile. Dissociation mechanisms in small clusters are also investigated. Solvent separated ion pairs persist even in aggregates composed of rather few molecules, for instance, as few as 30 molecules. For smaller clusters or for large ion pair separations cluster finite-size effects come into play in a significant fashion. © 1996 American Institute of Physics.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1063/1.471375

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Molecular dynamics study of a monomeric heme undecapeptide of cytochromec (1995)

Melchionna, Simone ; Barteri, Mario ; Ciccotti, Giovanni

Springer

Journal of computer-aided materials design 2 (1995), S. 9-22

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ISSN: 1573-4900

Keywords: Molecular dynamics ; Microperoxidase ; Conformational calculations

Source: Springer Online Journal Archives 1860-2000

Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics

Notes: Summary Molecular dynamics simulations were performed to predict the structure of the monomeric heme-containing peptide microperoxidase-11 (MP-11). The simulations were carried out both in vacuo and in water solvent, taking as starting coordinates those of the corresponding amino acid sequence in the crystal structure of cytochrome c, since the crystallographic structure of MP-11 is not known. The structural data, including the H-bond network, are reported and visualised with the aid of graphical tools. The structure predicted is consistent with what is known experimentally on MP-11. This agreement suggests that molecular dynamics simulations might be useful in the prediction of the catalytic activity or reactivity of microperoxidases.