Search PubMed⌕ Search

Biomedical subjects

Petr Slavícek

Publications and source records attributed to Petr Slavícek.

3 recordsLinked to original sources

Multicentered valence electron effective potentials: a solution to the link atom problem for ground and excited electronic states.

We introduce a multicentered valence electron effective potential (MC-VEEP) description of functional groups which succeeds even in the context of excited electronic states. The MC-VEEP is formulated within the ansatz which is familiar for effective core potentials in quantum chemistry, and so can be easily incorporated in any quantum chemical calculation. By demanding that both occupied and virtual orbitals are described correctly on the MC-VEEP, we are able to ensure correct behavior even when the MC-VEEP borders an electronically excited region. However, the present formulation does require that the electrons represented by the MC-VEEP are primarily spectators and not directly participating in the electronic excitation. We point out the importance of separating the electrostatic and exchange-repulsion components of the MC-VEEP in order that interactions between the effective potential and other nuclei can be modeled correctly. We present a MC-VEEP for methyl radical with one active electron which is tested in several conjugated molecules. We discuss the use of the MC-VEEP as a solution to the "link atom" problem in hybrid quantum mechanical/molecular mechanical methods. We also discuss the limitations and further development of this approach.

Journal Article↗

Solvent-mediated folding of a doubly charged anion.

The microsolvation of the suberate dianion, -O2C(CH2)6CO2-, with two separate charge centers was studied by photoelectron spectroscopy and molecular dynamics simulation one solvent molecule at a time for up to 20 waters. It is shown that the two negative charges are solvated in the linear suberate alternately. As the solvent number increases, the negative charges are screened and a conformation change occurs at 16 waters, where the cooperative hydrogen bonding of water is large enough to overcome the Coulomb repulsion and pull the two negative charges closer through a water bridge. This conformation change, revealed both from the experiment and from the simulation, is a manifestation of the hydrophilic and hydrophobic forces at the molecular level.

Journal Article↗

Optical pump-terahertz probe spectroscopy of dyes in solutions: probing the dynamics of liquid solvent or solid precipitate?

The optical pump-terahertz probe spectroscopy was used together with ab initio calculations and molecular dynamics simulations to investigate ultrafast dynamics following electronic excitation of Coumarin 153 and TBNC (2,11,20,29-tetra-tert-butyl-2,3-naphtalocyanine) dyes in polar solvents. By scanning the terahertz waveform for different pump-probe delays this experimental technique allows us to obtain two dimensional spectra directly reflecting the temporal response of the system. A distinct signal was obtained for TBNC in chloroform, 2-propanol, and n-butanol, while no signal was recorded for Coumarin 153 in either of these solvents. We explain the nonequilibrium signal detected in TBNC solutions by the presence of a solid, polycrystalline phase of the dye resulting from irradiating the solution by intense optical pulses.

Journal Article↗