Kh. T. Kholmurodov

The determination of the limiting partial molar volume of solutions of monocarboxylic acids in benzene by molecular dynamics simulation

A molecular dynamics simulation of the limiting solutions of monocarboxylic acids (oleic, stearic, and myristic) in benzene was performed. The radial distribution functions between benzene and dissolved acid atoms were obtained. The functions were used to calculate the limiting partial molar volumes of solutions of the acids. The results were compared with the experimental limiting molar partial volumes of solutions of the acids obtained by precision vibrational densimetry and small-angle neutron scattering.

Molecular dynamics simulation analysis of small-angle neutron scattering by a solution of stearic acid in benzene

Data of small-angle neutron scattering by a diluted solution of stearic acid in deuterated benzene have been analyzed using the results of molecular dynamics simulation. The molecular dynamics simulation approach has been used to calculate the time-averaged distribution of the neutron scattering length density at the interface between the acid molecule and the solvent. It has been shown that the organization of the solvent at the interface with the acid molecule leads to a modulation of the neutron scattering length density and makes a significant contribution to the scattering. This contribution should be taken into account when interpreting the experimental small-angle neutron scattering curves for both the considered system and its analogues.

Calculating the bulk properties of decalins and fatty acids in decalin according to data from molecular dynamics simulation

Pure solutions of decalin with different contents of its isomeric forms are studied by molecular dynamics simulation. Limiting solutions of fatty acids with different carbon chain length in decalin are considered. Comparison of the features of structural organization of decalin isomers in the vicinity of saturated (myristic, stearic) and unsaturated (oleic) acids molecules are performed. Limiting partial molar volumes of acids are determined using a radial distribution function of atoms in the solution. In contrast to earlier data for benzene, a considerable difference in the volumes of stearic and oleic acids is obtained that is explained by the more complex structure of decalin, which is sensitive to bending of unsaturated acid.

Solute-solvent interaction in nonpolar solutions of oleic acid as revealed by molecular dynamics simulation

Limiting solutions of oleic acid (CH3(CH2)7CH=CH(CH2)7COOH) in deuterated benzene (C6D6) and decalin (C10D18) are examined by molecular-dynamics simulation. To elucidate the possible effect of the interaction of a solvent with an acid on small-angle thermal neutron scattering, the time-averaged spatial distributions of the scattering-length density (SLD) of neutrons in the vicinity of acid molecule in mentioned solutions are constructed and analyzed. A difference is found in the SDL distributions in the inner and outer field of the bend of the oleic-acid molecule, depending on the effective size of the solvent molecule.

Molecular dynamics simulation of the substitution of serine for the conserved glycine in the G-loop in the cdc28-srm yeast mutant using the crystal lattice of human CDK2 kinase

Two-nanosecond molecular dynamics simulations of the crystal lattice of an active complex of pT160-CDK2 kinase/cyclin A/ATP-Mg2+/substrate were performed. The simulations showed that the structures of the wild-type CDK2 complex and the mutant CDK2 complex involving the substitution G16S-CDK2 corresponding to the yeast substitution G20S-CDC28 differ noticeably and the differences between the structural conformations are most pronounced in the regions that play a key role in the kinase functioning. The results of the computer calculations were used to consider the structural elements that may affect the kinase activity, the regulatory phosphorylation, and the binding of protein kinase with cyclins and substrates.

Molecular dynamics studies of the interaction between water and oxide surfaces

The water-surface interaction is a research target of great importance for a broad spectrum of technological applications and fundamental scientific disciplines. In the present study, a comparative analysis is performed to clarify the structural and diffusion properties of water on a number of oxide surfaces. Based on the molecular dynamics (MD) simulation method, the water-surface interaction mechanism was investigated for the oxide materials TiO2 (anatase), Al2O3 (corundum), and Fe2O3 (hematite). A comparison of the water-TiO2 interaction with the water-Al2O3 and water-Fe2O3 systems demonstrates the specificity of the adsorption and layer formation on the atomic/molecular level scale. The obtained MD analysis data point to a considerable enhancement of water-TiO2 surface adsorption and a relatively high density distribution profile near the surface. The novel data on water structure and diffusion on oxide surfaces are discussed from the point of view of possible material innovation and design.

Molecular dynamics study of perovskite structures with modified interatomic interaction potentials

The structure of compounds with the perovskite structure ABX3 (A and B are cations, X are anions O2—, F—, Cl—, Br—, and I—), which are widely used in engineering due to unique electrical, optical, and photovoltaic properties, has been considered. Hybrid organic—inorganic halide perovskites important for photovoltaics of a new generation are worth mentioning; they contain cations of organic nitrogen bases as monovalent cations. A molecular dynamics (MD) study of the CaTiO3 base structure (Ca2+, Ti4+, and O2—) has been performed in order to develop the methodology of computer simulation and optimization of the shape and parameters of atomic potentials for perovskite systems.

Molecular dynamics simulations of formamide interaction with hydrocyanic acid on a catalytic surface TiO2

The behavior of water—formamide and hydrocyanic acid—formamide solutions on an anatase surface have been studied using molecular dynamics (MD) simulation method. The interaction activation energies have been estimated for the temperature range from 250 up to 400 K. The diffusion coefficients and structural radial distribution functions have been calculated for the formamide, water and hydrocyanic acid on an anatase surface. The calculated activation energies of the water—formamide—anatase and hydrocyanic acid—formamide—anatase systems were analyzed and compared. A comparative analysis of the systems under investigation was performed and a possible correlation between the obtained MD results and the molecular mechanism involving the formamide’s interaction with dioxide titan adsorbing surface were discussed.

Studies on the conformational state of the chromophore group (11-cis-retinal) in rhodopsin by computer molecular simulation methods

The molecular dynamics of the rhodopsin chromophore (11-cis-retinal) has been followed over a 3-ns path, whereby 3 × 106 discrete conformational states of the molecule were recorded. It is shown that within a short time, 0.3–0.4 ns from the start of simulation, the retinal β-ionone ring rotates about the C6–C7 bond through ∼60° relative to the initial configuration, and the whole chromophore becomes twisted. The results of ab initio quantum chemical calculations indicate that for the final conformation of the chromophore center (t = 3 ns) the rhodopsin absorption maximum is shifted by 10 nm toward longer wavelengths as compared with the initial state (t = 0). In other words, the energy of transition of such a system into the excited singlet state S1 upon photon capture will be lower than that for the molecule where the β-ionone ring of the chromophore is coplanar to its polyene chain.

Molecular physiology of rhodopsin: Computer simulation

Computer simulation is used for comparative investigation of the molecular dynamics of rhodopsin containing the chromophore group (11-cis-retinal) and free opsin. Molecular dynamics is traced within a time interval of 3000 ps; 3 × 106 discrete conformational states of rhodopsin and opsin are obtained and analyzed. It is demonstrated that the presence of the chromophore group in the chromophore center of opsin influences considerably the nearest protein environment of 11-cis-retinal both in the region of the β-ionone ring and in the region of the protonated Schiff base bond. Based on simulation results, a possible intramolecular mechanism of keeping rhodopsin as a G-protein-coupled receptor in the inactive state, i.e., the chromophore function as an efficient ligand antagonist, is discussed.