Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation

Article Abstract:

The study describes the extension of a conductor-like screening model for solvation to a d-ortibal semiempirical framework (MNDO/d-SCOSMO) with analytic gradients that can be used for geometry optimization, transition state search and molecular dynamics simulations. MNDO/d-SCOSMO seems to have considerable advantages over hybrid quantum mechanical/ molecular methods with explicit solvation.

Molecular dynamics, Solvation

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The resting state of P450(sub cam): A QM/MM study

Article Abstract:

The combined quantum mechanical/molecular mechanical (QM/MM) calculations are used to study the substrate-free form of P450(sub cam) (CYP101). The results of QM/MM are compared to analogous results for the isolated QM subsystem in the gas-phase and the effects of the protein environment on the central iron-aqua complex are reported.

Chemistry, Physical and theoretical, Physical chemistry, Cytochrome P-450

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A QM/MM study of the Bergman reaction of dynemicin A in the minor groove of DNA

Article Abstract:

The QM/MM investigation results of the Bergmann cyclization of the natural enediyne dynemicin A in its triggered form bound to the minor groove of DNA is reported.

Biological Product (except Diagnostic) Manufacturing, Drugs, Deoxyribonucleic Acid, DNA, Mechanical properties, Enthalpy, Natural products, Ring formation (Chemistry), Cyclization (Chemistry), Structure, Chemical properties

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