Variational electrostatic projection (VEP) methods for different modeling of the macromolecular electrostatic and solvation environment in activated dynamics simulations

Article Abstract:

New methods for the efficient calculation of electrostatic interactions between the active dynamical region and surrounding solvated macromolecular environment in hybrid quantum mechanical/molecular mechanical (QM/MM) calculations are presented. The variational electrostatic projection (VEP) method, and related variational reverse-mapping procedure (VEP-RVM) utilize an expansion in Gaussian surface elements for representation of electrostatic interactions.

Electrostatics

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Shuttling process in [2]rotaxenes. Modeling by molecular dynamics and free energy perturbation simulations

Article Abstract:

The first application of a methodology previously developed and tested on pseudorotaxanes is presented in the study of the structure and the energetics of [2]rotaxane. This model correctly reproduced the experimentally observed free energy difference between the two translational isomers of [2]rotaxane (computed delta G = 1.06 plusmn kcal mol(super -1)).

Analysis, Force and energy, Energy (Physics)

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Insights into the structure of large-ring cyclodextrins through molecular dynamics simulations in solution

Article Abstract:

Molecular dynamics simulations are carried out using the AMBER parm99 force field and explicit water molecules to gain insight into the structural deformations and energetic of several large-ring cycoldextrins in solution. The results support the hypothesis for the existence of more than one cavity in large-ring cyclodextrins.

Cyclodextrins, Structure

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