Pavel Hobza

Noncovalent interactions play important role in chemistry, physics and especially in biosciences. They determine structure of biomacromolecules such as nucleic acids and proteins, and they are also responsible for molecular-recognition process. They are extremely important in the formation of the functional complexes, and their high fidelity represents one of the most important features of life. Proper understanding of the role of molecular interactions belongs to important goals of modern physical chemistry, biochemistry and structural molecular biology. It is a difficult task, considering the astonishing complexity of biomolecular interactions and the tiny balance of all the contributing noncovalent forces.

Computational studies of the intrinsic interactions of biomolecular building blocks should always start with the gas phase calculations, in which the effects of the environment are eliminated. Quantum chemical studies provide a full description of molecular interactions including data on geometry, stabilization energy, electric properties, IR, visible and UV spectra, etc. In some situations, theoretical and numerical demands in treatment of a dynamical flexibility of biomolecules may lead to problems which require designing of ad hoc approximate theoretical models. In such cases, we usually rely on the adiabatic separation of the dynamical degrees of freedom possessing different contents of energy.

In order to fully understand the role of molecular interactions in biomolecules the range of computational techniques must be enriched by solid and verified methods capable to treat solvated biologically functional systems. Explicit solvent molecular dynamics simulation represents the gold standard in contemporary modeling. Simulation provides unprecedented detail information about the picosecond scale time development of all aspects of the three-dimensional structure of the single simulated molecule including exact dynamical positions of all solvent and ion molecules. Moreover, the inclusion of the solvent, as well as of other parts of surrounding environment, is required in order to determine the free energy changes in biomolecular systems.