Ukrainian American Laboratory of Computational Chemistry

Kharkiv, Ukraine

Ukrainian American Laboratory of Computational Chemistry

Kharkiv, Ukraine
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Turovskij N.A.,Donetsk National University | Turovskij N.A.,Ukrainian American Laboratory of Computational Chemistry | Pasterna E.N.,Ukrainian Academy of Sciences | Raksha E.V.,Donetsk National University | And 5 more authors.
Oxidation Communications | Year: 2010

Activated decomposition of lauroyl peroxide in the presence of tetraalkylammonium bromides (Alk4NBr) has been studied. The ammonium salts show catalytic properties in the system. The initiation efficiency of the binary system lauroyl peroxide -Alk4NBr has been studied. The causes of peroxide bond chemical activation are considered on the basis of experimental results and results of molecular modelling of the activated peroxide decomposition. The supramolecular mechanism is proposed for the peroxide decomposition in the presence of tetraalkylammonium bromides.

Shishkin O.V.,Ukrainian Academy of Sciences | Shishkin O.V.,Ukrainian American Laboratory of Computational Chemistry | Dopieralski P.,Wrocław University | Palamarchuk G.V.,Ukrainian Academy of Sciences | And 2 more authors.
Chemical Physics Letters | Year: 2010

Theoretical investigation of the conformation of 2′-deoxyriboadenosine monophosphate protonated at the N7 atom and stabilized by a very strong C8-H⋯O-P hydrogen bond indicates that this hydrogen bond may be disrupted by rotation of the adenine moiety around the glycosidic bond. A B3LYP/aug-cc-pVDZ scan of the relaxed potential energy surface demonstrates that this rotation is a multi-stage process, accompanying proton transfer from the N7 atom of adenine to the oxygen atom of the phosphate group with a change of conformation of the nucleotide from south/anti to north/syn conformation. Car-Parrinello molecular dynamics simulation indicates that rotation around the glycosidic bond is the preferred way for relaxation of the molecular geometry of this conformer. Both processes, i.e. conformational transition and proton transfer, are strongly coupled. However, the conformer containing a strong C-H⋯O hydrogen bond also corresponds to a local minimum on the Gibbs free energy surface. A specific property of this hydrogen bond is the large variation of the H⋯O distance (ranging from 1.3 to 2.2 Å), which is not caused by proton movement between the carbon and oxygen atoms, but rather by relative motions of the adenine and phosphate moieties. © 2010 Elsevier B.V. All rights reserved.

Kyrychenko A.,University of Kharkiv | Kyrychenko A.,University of Kansas Medical Center | Kyrychenko A.,Ukrainian American Laboratory of Computational Chemistry | Wu F.,University of Houston | And 3 more authors.
Journal of Physical Chemistry B | Year: 2010

Fluorescence of environment-sensitive dyes is widely applied to monitor local structure and solvation dynamics of biomolecules. It has been shown that, in comparison with a parent indole fluorophore, fluorescence of 2-(2′-pyridyl)-5-methylindole (5M-PyIn-0) and 2-[2′-(4′, 6′-dimethylpyrimidyl)]-indole (DMPmIn-0) is remarkably sensitive to hydrogen bonding with protic partners. Strong fluorescence, observed for these compounds in nonpolar and polar aprotic solvents, is efficiently quenched in aqueous solution. This study demonstrates that 5M-PyIn-0 and DMPmIn-0, which are almost nonemitting in aqueous solution, become highly fluorescent upon titrating with phospholipid vesicles. The fluorescence enhancement is accompanied by a significant blue shift of emission maximum. The Gibbs free energy of membrane partitioning, measured by the increase in the steady-state fluorescence intensities during transfer from an aqueous environment to a lipid bilayer, is very favorable for both compounds, being in a range from -7.1 to -8.0 kcal/mol and depending only slightly on lipid composition of the membrane. The fluorescence enhancement upon membrane partitioning is indicative of the loss of the specific hydrogen-bonding interactions between the excited fluorophore and water molecules, causing efficient fluorescence quenching in bulk water. This conclusion is supported by atomistic molecular dynamics (MD) simulations, demonstrating that both 5M-PyIn-0 and DMPmIn-0 bind rapidly and partition deeply into a lipid bilayer. MD simulations also show a rapid, nanosecond-scale decrease in the probability of solute-solvent hydrogen bonding during passive diffusion of the probe molecules from bulk water into a lipid bilayer. At equilibrium conditions, both 5M-PyIn-0 and DMPmIn-0 prefer deep localization within the hydrophobic, water-free region of the bilayer. A free energy profile of penetration across a bilayer estimated using MD umbrella sampling shows that both indole derivatives favor residence in a rather wide potential energy well located 10-15 Å from the bilayer center. © 2010 American Chemical Society.

Kyrychenko A.,University of Kharkiv | Kyrychenko A.,Ukrainian American Laboratory of Computational Chemistry | Kyrychenko A.,The Jackson Laboratory | Karpushina G.V.,University of Kharkiv | And 7 more authors.
Journal of Physical Chemistry C | Year: 2012

Understanding the interaction of fluorescent dyes with monolayer-protected gold nanoparticles (AuNPs) is of fundamental importance in designing new fluorescent nanomaterials. Among a variety of molecular sensors and reporters, fluorescent probes based on a 3-hydroxychromone (3HC) skeleton appear to be very promising. They exhibit the phenomenon of dual band emission, resulting from excited-state intramolecular proton transfer (ESIPT), known to be highly sensitive to a nature of microenvironment surrounding a fluorophore. In this study, dodecanethiol-protected gold nanoparticles were synthesized, and, owing to the transmission electron micrograph imaging, their average diameter was found to be ∼1.4 nm. Fluorescence titrations of the 3HC ESIPT probes with AuNPs in toluene solutions demonstrate significant changes in the intensity ratio of their normal and tautomeric emission bands, suggesting that the probe molecules become noncovalently bound to a dodecanethiol layer of AuNPs. Despite expected fluorescence quenching induced by close proximity to the metal surface, no fluorescence lifetime decrease was observed, indicating that a bound-fluorophore is shielded from a nanoparticle core. Further spectral analysis revealed that the ratiometric fluorescence changes could be interpreted as a consequence of intermolecular hydrogen bonding between a probe and residual ethanol molecules, trapped into the dodecanethiol shell of AuNPs during the synthesis. Evidences for residual traces of ethanol in the ligand shell of the nanoparticles were also observed in NMR spectra, suggesting that alkylthiol-coated gold nanoparticles may not be as hydrophobic as one could expect. To elucidate structural features of dodecanethiol-stabilized gold nanoparticles at the supramolecular level, a molecular dynamics (MD) model of AuNP was developed. The model was based on the all-atom CHARMM27 force field parameters and parametrized according to available experimental data of the synthesized AuNPs. Our MD simulations show that in bulk toluene the 3HC probe molecule becomes weakly bound to a dodecanethiol monolayer, so that a fluorophore favors residence in an outer shell of AuNP. In addition, MD simulations of transfer of AuNP from bulk ethanol to toluene demonstrate that a small population of ethanol molecules are able to penetrate deeply into the dodecanethiol layer and may indeed be trapped into the ligand shell of alkylthiol-functionalized gold nanoparticles. The results of our fluorescence experiments and molecular dynamics simulation suggest that 3-hydroxychromones can be used as a noncovalent fluorescent labeling agent for alkylthiol- stabilized noble metal nanoparticles. © 2012 American Chemical Society.

Kyrychenko A.,University of Kharkiv | Kyrychenko A.,Ukrainian American Laboratory of Computational Chemistry | Kyrychenko A.,The Jackson Laboratory | Karpushina G.V.,University of Kharkiv | And 5 more authors.
Computational and Theoretical Chemistry | Year: 2011

Thiol-stabilized metal nanoparticles possess unique properties in the comparison with larger-scale materials, which enable their use in many promising chemical and biological applications. We have synthesized thiol-coated colloidal gold nanoparticles (AuNP) soluble in non-polar organic solvents by a simplified procedure, in which AuCl4- was initially reduced in aqueous phase and then coated with thiol residues and transferred to organic phase. Using the transmission electron micrograph (TEM) imaging, the average diameter of a dodecanethiol-stabilized AuNP was estimated to be 3.75±0.06. nm. Based on the experimental TEM data, a new coarse-grained molecular dynamics model of AuNP was developed. The model was applied for studying self-assembly of AuNPs on a flat graphite surface, enabling further elucidating the structure and packing of the ligand shell around the spherical nanoparticle core. © 2011 Elsevier B.V.

Iliashenko R.Y.,University of Kharkiv | Zozulia O.S.,University of Kharkiv | Doroshenko A.O.,University of Kharkiv | Doroshenko A.O.,Ukrainian American Laboratory of Computational Chemistry
Central European Journal of Chemistry | Year: 2011

A series of novel nitro-substituted ortho-analogs of POPOP was synthesized. Like the most of the other known compounds of this class, the synthesized molecules demonstrate high Stokes shift fluorescence emission owing to the planarization of their molecules at electronic excitation. Significant fluorescence quenching in polar solvents was described as the "energy gap law" action rather than the specific effect of the dialkylamino group excited state twisting. © Versita Sp. z o.o.

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