Theory of Intermolecular Interaction

IRIS: intermolecular RNA interaction search.

Here we present IRIS, a method for prediction of RNA-RNA interactions that is based on dynamic programming and extends current RNA secondary structure prediction approaches. Using this method we have found a number of interesting refinements to the structures of RNA-RNA complexes that have been studied previously and predicted novel targets for several known regulatory RNAs in E. coli. The comp...

Intermolecular interaction in tetramethylurea solutions

Dependence of the Intermolecular Electrostatic Interaction Energy on the Level of Theory and the Basis Set.

As electrostatic forces play a prominent role in the process of folding and binding of biological macromolecules, an examination of the method dependence of the electrostatic interaction energy is of great importance. An extensive analysis of the basis set and method dependence of electrostatic interaction energies (Ees) in molecular systems using six test dimers of α-glycine is presented. A nu...

DFT study of the intermolecular interaction of 3,4-dinitropyrazole (DNP) and H2O

In the present work, the sensitivity to the moisture (hygroscopisity) is studied for 3,4-dinitropyrazole (DNP) as a famous energetic molecule. All of the DNP-H2O complex systems (1-3) as well as individual molecules were optimized and bond lengths, bond angles, dihedral angles, charge transfer and stability via NBO analysis, corrected interaction energies with ZPE + BSSE and hydrogen bonds anal...

SAPT A Program for Many Body Symmetry Adapted Perturbation Theory Calculations of Intermolecular Interaction Energies