The diffusion and concentration effects of formamide on a TiO₂surface in the presence of a water solvent

The formamide-titanium oxide interaction mechanism is a research target of great importance for understanding the elementary events of the origin of life: the synthesis of nucleoside bases and formation of biological molecules needed for life. Titanium oxide (TiO2) can act as a strongly adsorbing surface or a catalytic material. In the present study, a comparative molecular dynamics analysis performed to clarify the adsorbing and diffusion properties of liquid formamide on a TiO2 surface in the presence of water molecules. The structural features of the formamide concentration effect (the accumulation of molecules) on a TiO2 surface in the presence and absence of water solvent are cleared up. Modification of the formamide diffusion abilities mediated by a water solvent is observed to correlate with the formamide-water concentration distribution on the surface.

Molecular dynamics simulation of the interaction of ethanol-water mixture with a Pt surface

An analysis of the molecular dynamics of ethanol solvated by water molecules in the absence and presence of a Pt surface has been performed using DL_POLY_2.19 code. The structure and diffusion properties of an ethanol–water system have been studied at various temperatures from 250 to 600 K. We have measured the self-diffusion coefficients of the 50:50% ethanol–water solution;in the absence of a Pt surface our results show an excellent agreement–within an error of 7.4% – with the experimental data. An increase in the self-diffusion coefficients with the inclusion of a Pt surface has been observed. The estimation of the diffusion coefficients of both water and ethanol in the presence of a Pt surface shows that they obey the Arrhenius equation;the calculated activation energies of diffusion of ethanol and water are 2.47 and 2.98 Kcal/mole, respectively. The radial distribution function graphs and density profiles have been built;their correlations with the self-diffusion coefficients of both ethanol and water molecules are also illustrated.

MD Simulations of the P53 oncoprotein structure: the effect of the Arg273→His mutation on the DNA binding domain

A comparative molecular dynamics (MD) simulation study was performed on the p53 oncoprotein to investigate the effect of the Arg273His (R273H) mutation on the p53→DNA Binding Domain (DBD). The two p53 dimer structures of the wild-type and mutant Arg273His (R273H) were simulated with the same thermodynamic and environmental parameters. The obtained results demonstrate that the induced Arg273His mutation has a considerable effect on the p53→DNA close contact interaction and changes the picture of hydrogen formation. The Arg273His mutation, in some cases, destroys the existing native hydrogen bond, but, in other cases, forms a strong p53→DNA hydrogen bond, which is not proper for the native protein. The MD simulation results illustrate some molecular mechanism of the conformational changes of the Arg273His key amino acid residue in the p53→DNA binding domain, which might be important for the understanding of the physiological functioning of the p53 protein and the origin of cancer.

Molecular dynamics simulations of a DNA photolyase protein: High-mobility and conformational changes of the FAD molecule at low temperatures

A molecular dynamics (MD) simulation is performed on a DNA photolyase to study the conformational behavior of the photoactive cofactor flavin adenine dinucleotide (FAD) inside the enzyme pocket. A DNA photolyase is a highly efficient light-driven enzyme that repairs the UV-induced cyclobutane pyrimidine dimer in damaged DNA. In this work, the FAD conformational and dynamic changes were studied within the total complex structure of a DNA photolyase protein (containing FADH–, MTHF, and DNA molecules) embedded in a water solvent. We aimed to compare the conformational changes of the FAD cofactor and other constituent fragments of the molecular system under consideration. The obtained results were discussed to gain insight into the light-driven mechanism of DNA repair by a DNA photolyase enzyme—based on the enzyme structure, the FAD mobility, and conformation shape.

Molecular dynamics simulations of valinomycin interactions with potassium and sodium ions in water solvent

The aim of this work is to estimate the value of the electric field (potentials) for the system of valinomycin + К+ and Na+ ions based on a molecular dynamics (MD) study. An analysis has been performed of the interaction processes for the system of valinomycin + К+(Na+) ion in water solvent. It is obtained that capturing a К+(Na+) ion in the valinomycin cavity is not possible for all values of the electric field strength. Each of the two kinds of ions (К+ or Na+) has its own critical electric field associated with ion binding to valinomycin, for which to exist, the ion has to remain localized inside the valinomycin cavity. The results obtained for the electrical potential reveal a stronger valinomycin binding—especially with the potassium ion. Valinomycin’s molecular structure efficiently surrounds the K+ ion, as this structure has to exactly correspond to the K+ ion in size. MD simulation results could be a prerequisite for studying a more complex scenario—for estimating ion transport in the cell membrane or physiological electric potential which is formed in the membrane or inside the cell relative to its surrounding medium.

Molecular dynamics simulations of the interaction of carbon nanotube and a carbon disulfide solvent

An analysis of the molecular dynamics (МD) of the interaction between a carbon nanotube (CNT) and a carbon disulfide active solvent (CS2) has been carried out. The aim of the present work is to estimate the dynamical and structural behavior of the CNTCS2 system at different relative atomic concentrations and under temperature changes. The structural radial distribution functions and the dynamical configurations have been built for a CNT interacting with a CS2 solvent. A nontrivial observation for the CNTCS2 system is that the solvent carbon disulfide atoms make up a patterned (layered) formation around the carbon nanotube.