Research area of Prof. P.Hobza

• Accurate calculations of stabilization energies of DNA base pairs and aminoacid pairs; many-body terms
• Determination of structure and geometry of model and biomolecular complexes
• "On-the-fly" ab initio molecular dynamic simulations on isolated systems, and molecular and biomolecular complexes; evaluation of anharmonic vibration spectra
• Structure, stabilization energies and thermodynamic characteristics of DNA...ligand and protein...ligand complexes
• Blue-shifting H-bonding

Research area of O.Bludský

Probe molecules (e.g., CO, H₂) are often used for characterization of complex molecular environments (molecular sieves, molecular matrices). Assignment of spectral characteristics to particular structure is difficult and in many cases impossible. Our goal is to link the spectral features to particular structure type based on the overlap of experimental and theoretical spectra.

Research area of M.Kabeláč

• Exploration of conformational landscapes of biomolecules
• Hydration and solvation of biomolecules
• Highly accurate ab initio calculations of noncovalent interactions in biological systems

Research area of P.Nachtigall

Metal-exchanged zeolites (M⁺/zeolite) are intensively investigated for their interesting sorption and catalytic properties. We investigate the coordination and localization of metal cation sites in zeolites and their interaction with adsorbed molecules. The period DFT or a hybrid QM/MM models are used for the description of the system.

Metal cation sites in zeolites with different topology (including MFI, FER, IFR, LTA) and composition are systematically investigated. It is our goal to understand the correlation between the cation coordination and its adsorption and catalytic properties. Vibrational dynamics of molecules adsorbed on M⁺/zeolites is investigated theoretically. Vibrational frequencies of small molecules adsorbed inside the zeolite channels can be calculated with spectroscopic accuracy, using a recently developed ω/r scaling method together with the periodic model of zeolite. Therefore, details of experimental IR spectra can be interpreted based on these calculations.

Theoretical investigation of properties of Cu-containing zeolites, in particular, electronic excitation energies (UV-vis spectra), vibrational dynamics of adsorbed probe molecules, and catalytic activity.

Research area of D.Nachtigallová

The behavior of nucleic acid bases in their excited states has been subject of several experimental and theoretical studies. The aim of these studies is to explain their photochemical behavior in order to prevent the nucleic acid bases against UV damage. In our group we are interested in the calculations of electronically excited states of nucleic acid bases in the stacked conformation to investigate the excited state energy transfer between DNA bases. The aim of these studies is to evaluate the interaction of DNA bases in their excited states depending on the sequence of bases and their mutual orientation. The calculations of the relevant small models are also performed to understand these phenomena based on the results obtained with precise methods which are not always possible in the calculations of DNA bases.

Research area of V.Špirko

Quantum-mechanical studying of large molecular rearangements opposed by nonharmonic (multiple minima) potential energy functions (conformational dynamics, isomerizations, proton transfers, dynamical corrections for molecular properties). Theoretical studying of highly excited and continuum ro-vibrational states of small molecular systems (density and statistical properties of molecular states, energy clustering and "hidden" symmetries, elementary chemical reactions). Approximate methods for quantum-mechanical calculations (adiabatic separation approaches, numerical integration of coupled Schrödinger equations).

Research area of J.Šponer

Computational chemistry of nucleic acids, structural molecular biology and biophysics, molecular modeling, atomistic simulations of biopolymers, quantum chemistry, bioinormatics.

Structural studies of functional RNA molecules. These studies include investigations of several ribozymes (Hepatitis Delta Virus r., Hairpin r. and Hammerhead r.) and are presently aimed towards MD and QM/MM analyzes of the reaction mechanism. Major attention is paid to structural dynamics of key ribosomal RNA segments, such as the A-site finger, L7/L12 stalk and L1 stalk, which play essential role in tRNA binding and movement throughout ribosome during protein synthesis. Studies of DNA (B-DNA, quadruplexes and others) and their complexes with drugs and proteins. Theoretical studies of the basic principles of molecular interactions of nucleic acids including metal cation interactions, with a special attention paid to RNA folding.

Research area of J.Vondrášek

• Stabilization of protein molecules and a consequence with protein folding
• De novo design of functional peptides and small proteins bearing desired biological functions
• Structural bioinformatics based on high level ab initio calculations