Computational Chemistry Lab

Since the presence of hydrogen bonds is a prerequisite for the existence of living organisms, theoretical analysis is focused on hydrogen-bonded systems. Quantum-chemical calculations are performed with the Gaussian 09 program package. The presence of X-H×××Y hydrogen bonds is reflected in the shape of infrared spectra, i.e. it predominantly affects the position and the shape of the X-H stretching band. Due to the strong anharmonic couplings among vibrational degrees of freedom, analysis of the system’s dynamics and calculation of IR spectra requires construction of multi-dimensional potential energy surfaces. Such models are investigated with the MCTDH program (Multi-Configurational Time Dependent Hartree). Since water is one of the main constituents of the environment in which biomolecules are embedded, its presence is included either implicitly (polarizable continuum model) or by adding explicit water molecules.

Besides hydrogen bonding, we are interested in the analysis of other non-covalent interactions, like p-p stacking. Although weak, these interactions determine the structure of biomolecules, but are also important for numerous processes in biological systems, like molecular recognition. Such relatively weak interactions are successfully analysed using the QTAIM approach (Quantum Theory of Atoms in Molecules). We perform this analysis with the AIMAll suite of programs.


For more information regarding these topics and collaboration, please contact Asst. Prof. Milena Petković, PhD: