Exploring 3D-QSPR models of human skin permeability for a diverse dataset of chemical compounds.

The control of permeation is vital not only for the topical application of lotions, creams, and ointments but also for the toxicological and risk assessment of materials from environmental and occupational hazards. To understand the effects of physicochemical properties of a variety of 211 compounds on skin permeability, we developed a three-dimensional quantitative structure-property relationship (3 D-QSPR) model. Alignment free GRid-INdependent Descriptors (GRINDs), which were derived from molecular interaction fields (MIFs) contributed to the regression models. Kennard-Stone algorithm was employed to split data set to a training set of 159 molecules and a test set of 52 molecules. Fractional factorial design (FFD), genetic algorithm (GA) and successive projection algorithm (SPA) were applied to select the most relevant 3 D molecular descriptors. The descriptors selected using various feature selection were correlated with skin permeability constants by partial least squares (PLS) and support vector machine (SVM). SPA-SVM model gave prominent statistical values with the correlation coefficient of [Formula: see text]= 0.96, Q2= 0.73 and R2pred=0.76. According to the analysis results, the hydrogen bonding donor and acceptor properties of the investigated compounds can influence the penetration into the human skin. Furthermore, it was found that permeability was enhanced by increasing the hydrophobicity and was diminished by increasing the molecular weight. In addition, the presence of hydrophobic groups in the target molecule, as well as their shape and position, can affect the skin permeability.

A comprehensive adsorption study and modeling of antibiotics as a pharmaceutical waste by graphene oxide nanosheets.

The adsorption behavior of tetracycline (TCN), doxycycline (DCN) as the most common antibiotics in veterinary and ciprofloxacin (CPN) onto graphene oxide nanosheets (GOS) in aqueous solution was evaluated. The four factors influencing the adsorption of antibiotics (initial concentration, pH, temperature and contact time) were studied. The results showed that initial pH ∼ 6 to 7 and contact time ∼ 100 - 200min are optimum for each drug. The monolayer adsorption capacity was reduced with the increasing temperature from 25°C to 45°C. Non-linear regressions were carried out in order to define the best fit model for every system. To do this, eight error functions were applied to predict the optimum model. Among various models, Hill and Toth isotherm models represented the equilibrium adsorption data of antibiotics while the kinetic data were well fitted by pseudo second-order (PSO) kinetic model (DCN and TCN) and Elovich (CPN) models. The maximum adsorption capacity (qmax) is found to be in the following order: CPN >> DCN > TCN, obtained from sips equation at the same temperature. The GOS shows highest adsorption capacity towards CPN up to 173.4mgg-1. The study showed that GOS can be removed more efficiently from water solution.

Oxidation of nickel surfaces through the energetic impacts of oxygen molecules: Reactive molecular dynamics simulations.

Molecular dynamics approach accompanied by reactive force field is used to study the characteristics of the oxide growth process on Ni(100) and Ni(111) surfaces at the temperatures of 300, 600, and 900 K and 5 eV as the energy of the O2 impacts. The exposure of Ni surfaces to the high-energy O2 impacts indicates that the primary oxide nuclei can be formed on any impact site. The results of kinetic studies clarify that the oxide growth kinetics cannot be accurately explained with the island growth model and increasing the surface temperature raises failure of the model. Under the present conditions, the growth kinetics is found to obey a Langmuir growth model. Increasing the surface temperature from 300 to 900 K results in ∼18.75% and ∼23% more oxygen consumption by (100) and (111) surfaces of Ni, respectively. The structure of nickel oxide (NiO) film formed after 200 successive O2 impacts per surface super-cell is investigated utilizing radial distribution functions and oxygen density profiles. These calculations demonstrate that the structure of the formed NiO film is amorphous. Moreover, the charge profiles in Ni/NiO system are illustrated and discussed.

Communication: Striking dependence of diffusion kinetics in Ag-Cu nanoalloys upon composition and quantum effects.

The kinetics of elemental inter-diffusion in Ag-Cu nanoalloys of 32-34 atoms around 80:20 composition is theoretically investigated by combining analytic-potential and first-principles calculations. An extremely varied behavior is found, with transformation times ranging from tens of nanoseconds to weeks at room temperature in a narrow interval of size and composition, also depending on quantum effects in magic clusters. Predictions are consistent with time-of-flight experiments and suggest their interpretation in a new light.

A highly efficient and sustainable photoabsorber in solar-driven seawater desalination and wastewater purification.

Producing freshwater from seawater and wastewater is of great importance through interfacial solar steam generation (ISSG). Herein, the three-dimensional (3D) carbonized pine cone, CPC1, was fabricated via a one-step carbonization process as a low-cost, robust, efficient, and scalable photoabsorber for the ISSG of seawater as well as a sorbent/photocatalyst for use in wastewater purification. Taking advantage of the large solar-light-harvesting ability of CPC1 due to the presence of carbon black layers on the 3D structure, its inherent porosity, rapid water transportation, large water/air interface, and low thermal conductivity, a conversion efficiency of 99.8% and evaporation flux of 1.65 kg m-2 h-1 under 1 sun (kW m-2) illumination were achieved. After carbonization of the pine cone, its surface becomes black and rough, which leads to an increase in its light absorption in the UV-Vis-NIR region. The photothermal conversion efficiency and evaporation flux of CPC1 did not change significantly during 10 evaporation-condensation cycles. CPC1 exhibited good stability under corrosive conditions without significant change in its evaporation flux. More importantly, CPC1 can be used to purify seawater or wastewater by the removal of organic dyes as well as by the reduction of polluting ions, like nitrate ions in sewage.

Using the Semiempirical Quantum Mechanics in Improving the Molecular Docking: A Case Study with CDK2.

In this study, we use some modified semiempirical quantum mechanics (SQM) methods for improving the molecular docking process. To this end, the three popular SQM Hamiltonians, PM6, PM6-D3H4X, and PM7 are employed for geometry optimization of some binding modes of ligands docked into the human cyclin-dependent kinase 2 (CDK2) by two widely used docking tools, AutoDock and AutoDock Vina. The results were analyzed with two different evaluation metrics: the symmetry-corrected heavy-atom RMSD and the fraction of recovered ligand-protein contacts. It is shown that the evaluation of the fraction of recovered contacts is more useful to measure the similarity between two structures when interacting with a protein. It was also found that AutoDock is more successful than AutoDock Vina in producing the correct ligand poses (RMSD≤2.0 Å) and ranking of the poses. It is also demonstrated that the ligand optimization at the SQM level improves the docking results and the SQM structures have a significantly better fit to the observed crystal structures. Finally, the SQM optimizations reduce the number of close contacts in the docking poses and successfully remove most of the clash or bad contacts between ligand and protein.

Insights into doxycycline adsorption onto graphene nanosheet: a combined quantum mechanics, thermodynamics, and kinetic study.

Recently, pharmaceutically active compounds including antibiotics have been detected in drinking water at very low levels, mostly nanogram/liter concentrations, proposing that these materials were unaffected by water treatment processes. Adsorption processes were suggested to play a significant role in the removal of antibiotics. In this study, the adsorption behavior of doxycycline (DC) in aqueous solution was evaluated. The four factors influencing the adsorption of DC onto graphene nanosheet (GNS) were studied. The results showed that initial pH âˆ¼ 6 to 7 and contact time ∼ 200 min are optimum. The monolayer adsorption capacity was reduced with the increasing temperature from 25 to 45 °C. Nonlinear regressions were carried out to define the best fit model for every system. Among various models, the Hill isotherm model represented the equilibrium adsorption data of antibiotics while the kinetic data were well fitted by the Elovich kinetic model. The maximum adsorption capacity (q max) was 110 mg.g-1, obtained from the Hill equation. Semiempirical molecular orbital theory was used to investigate the molecular interaction of the adsorption system. The experiments and semiempirical computation have systematically demonstrated that DC could be adsorbed onto GNS by π- π and electrostatic interactions. It was shown that there is a good compromise with the experimental results. Graphical abstract Insights into doxycycline adsorption onto graphene nanosheet: quantum mechanics, thermodynamics, and kinetic study.

Isomorphic Viscosity Equation of State for Binary Fluid Mixtures.

The thermodynamic behavior of the simple binary mixtures in the vicinity of critical line has a universal character and can be mapped from pure components using the isomorphism hypothesis. Consequently, based upon the principle of isomorphism, critical phenomena and similarity between P-ρ-T and T-η-(viscosity)-P relationships, the viscosity model has been developed adopting two cubic, Soave-Redlich-Kwong (SRK) and Peng-Robinson (PR), equations of state (EsoS) for predicting the viscosity of the binary mixtures. This procedure has been applied to the methane-butane mixture and predicted its viscosity data. Reasonable agreement with the experimental data has been observed. In conclusion, we have shown that the isomorphism principle in conjunction with the mapped viscosity EoS suggests a reliable model for calculating the viscosity of mixture of hydrocarbons over a wide pressure range up to 35 MPa within the stated experimental errors.

Calculation of the second self-diffusion and viscosity virial coefficients of Lennard-Jones fluid by equilibrium molecular dynamics simulations.

The second self-diffusion and viscosity virial coefficients of the Lennard-Jones (LJ) fluid were calculated by a detailed evaluation of the velocity and shear-stress autocorrelation functions using equilibrium molecular dynamics simulations at low and moderate densities. Accurate calculation of these coefficients requires corresponding transport coefficient values with low degrees of uncertainty. These were obtained via very long simulations by increasing the number of particles and by using the knowledge of correlation functions in the Green-Kubo method in conjunction with their corresponding generalized Einstein relations. The values of the self-diffusion and shear viscosity coefficients have been evaluated for systems with reduced densities between 0.0005 and 0.05 and reduced temperatures from 0.7 to 30.0. This provides a new insight into the transport coefficients beyond what can be offered by the Rainwater-Friend theory, which has not been developed for the self-diffusion coefficient.