We study the behavior of lipid bilayers composed of SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) with different concentrations of cholesterol, ranging from 10 mol% to 50 mol% at 273 K. To this end, we carry out extensive atomistic molecular dynamic simulations with the aid of the Slipid force field aiming at computing basic bilayer parameters, as well as thermodynamic properties and structural characteristics. The obtained results are compared to available relevant experimental data and the outcome of atomistic simulations performed on bilayers composed of analogous phospholipids. Our results show a good quantitative, as well as qualitative, agreement with the main trends associated with the concentration increase in cholesterol. Moreover, it comes out that a change in the behavior of the bilayer is brought about at a concentration of about 30 mol% cholesterol. At this very concentration, some of the bilayer properties are found to exhibit a saturation and a significant long-range ordering of the lipid molecules in the membrane shows up.

Folate and its synthetic analogues, called antifolates, are known to have diverse bio-applications, for example as cell proliferation stimulators or anticancer drugs. Their molecular structure is important for performing the required biological activity. Since all folate-derived ligands contain a peptide-like amide bond, its configuration is one of the key components for the functional fitness of such compounds. During the modelling of folate and three of its derivatives – methotrexate, 5-methyl tetrahydrofolate, and pteroyl ornithine, we registered significant population of the cis isomers along the amide bond. The properties of the cis and trans forms of the ligands in saline are studied in detail by classical atomistic molecular dynamics and by quantum chemical methods. The calculations predict high probability for coexistence of the cis isomers for two of the ligands. The energetic instability of the cis form is explained with a σ-character admixture into the CO(π) bond, while its magnitude is attributed to the pattern of local electron density redistribution. The cis forms of all molecules have markedly slower structural dynamics than the trans ones, which might affect their behavior in vivo.

The present study proposes an atomistic molecular dynamics model system of a magnetite (Fe₃O₄) {111} surface. The effect of temperature on the adsorption process of ammonia (NH₃) at low concentrations in the aqueous phase has been considered. The molecular dynamics simulations were carried out using the Clay force field (Clay FF) with a modification for the iron atoms in the NPT ensemble at a pressure of 90 bar. The considered system was heated in a temperature range from 293 to 473 K, and additional relaxations were performed at temperatures of interest. Within the scope of this study, the basic parameters of the magnetite surface were calculated and the distances between the ammonia molecules and the surface were determined. A general idea of the degree and rate of adsorption at specific temperatures was obtained. The calculation results were compared to the experimental data where possible and to other available simulations of adsorption processes on metal oxides.