Decomposition of the solvation free energies of deoxyrilbonuceoside triphosphates using the free energy perturbation method

Article Abstract:

Free energy perturbation (FEP) calculations using the Amber 95 force field and the TIP3P water model were conducted to evaluate the solvation free energy of deoxyribonucleoside triphosphates in aqueous solution. Structural origins of the relative solvation free energies of deoxyrilbonuclcoside-phosphates are examined by calculating the contribution of the interaction of the base moiety with its surrounding.

Electric properties, Phosphates, Solvation, Aqueous solution reactions

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Molecular dynamics simulations of [beta]-cyclodextrin-aziadamantane complexes in water

Article Abstract:

Force-field-based atomistic simulations of host-guest supramolecular complexes between [beta]-cyclodextrin and aziadamantane derivatives in water are analyzed with respect to relative orientation and interaction energies. The orientation angle and inclusion depth are correlated and the enthalpy of complex formation is calculated for the unsubstituted aziadamantane.

Molecular dynamics, Thermal properties, Cyclodextrins, Azo compounds, Chemical properties

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