Physical Chemistry Research
Volume:6 Issue: 1, Winter 2018

In this research, the interaction of pyrimidine molecule with pristine B12N12 nanocluster is studied in different phases to understand the effect of environment on the electronic properties of the designated adsorption complexes. To this end, the pyrimidine adsorption over B12N12 in the gas phase and water medium is investigated using density functional theory (DFT) at the B97D/6-31+G(d,p) level of theory. Geometry and electronic structures of the fragments and their interacting systems are studied, and then natural bond orbitals (NBO) analysis is applied to interpret the perturbation caused by molecular adsorption. Our results confirm a chemical adsorption between pyrimidine molecule and exterior surface of pristine B12N12 One of the interesting features of this interaction is that pyrimidine adsorption in water medium is more favorable than that in the gas phase and exhibits an increase in adsorption energy (Eads) compared to gas phase, from 120.44 to -141.85 kJ/mol. It is hoped that pristine B12N12 will be used in designing novel materials for potential applications to detect pyrimidine molecule in the gas phase and water medium.

The structures of boron-doped fullerene B-C59 (1) as a drug delivery system (DDS), two phosphoramides (2 and 3) which were analogous to the cyclophosphamide anticancer prodrug as well as their covalently bonded structures to B-C59 (4 and 5) were optimized by DFT computations at B3LYP level of theory using 6-31G(d) basis set. Comparing compounds 4 and 5 revealed that the chloro derivative (-1429544.59 kcal/mol) was more stable than its bromo analogue (-1429531.23 kcal/mol). The dipole moments of isolated drugs had almost half values compared with those of their related covalently bonded compounds with B-C59 reflecting attachment of drugs to the B-C59 considerably enhanced the polarity of the whole systems which was a desired property for drug delivery in biological media. The negative ΔGinteraction values for compounds 4 and 5 confirmed that attachments of both drugs on the surface of B-C59 were spontaneously taken place. The negative ΔHinteraction values for both compounds 4 and 5 reflected these interactions were exothermic (ΔHinteraction<0). The density of states (DOS) spectra disclosed that there were very strong hybridizations between the orbitals of B-C59 and the drug molecules. The oxygen atoms of P=O and P–O bonds revealed  values about 5.0 and 10.0 MHz, respectively that might be because of more positive oxygen atoms in P–O bonds that had a greater interaction with EFG tensor. It was established that the DDS 4 was preferred for the cancer therapy applications due to its greater Ebinding, ΔHinteraction and ΔGinteraction values compared with those of DDS 5.

In this research, the effects of Al&S doped on the HCN interaction with beryllium oxide nanotube (BeONTs) are investigated by using density functional theory at the cam-B3LYP/6-31G (d) level of theory. Inspection of computational results reveals that the adsorption energies of all considered models are in range of −1.39 to −31.84 Kcal/mol and exothermic in view of thermodynamic approach. Due to doping Al and Al&S atoms, the adsorption energy, and the gap energy of BeONTs/HCN complex alter significantly from original values and so the conductivity and activity of nanotube increases significantly from pristine values. The natural bonding orbital (NBO) and molecular electrostic potential (MEP) results demonstrate that the HCN molecule has a donor electron effect. The computational results indicate that doping of Al, S and Al&S increase the sensivity of the BeONTs to detect and adsorb of HCN molecule.

The effect of NiO nanoparticles on the rheological and volumetric properties of dilute solutions of starch-NaOH-H2O, PEG400-PEG2000 and PEG400-PEG6000 were investigated. Achieve this aim requires to prepare the stable nanofluids. Therefore, nanoparticles of NiO were added to these solutions and dispersed by a shaker and an ultrasonic bath for making the homogeneous nanofluids. The UV-Vis spectroscopy, zeta potential and dynamic light scattering have been used to specify the stability and particle size distribution of colloidal solutions studied. Fluid flow and suspense structure of NiO nanoparticles in the solutions of starch-NaOH-H2O, PEG400-PEG2000 and PEG400-PEG6000 were studied by measuring the magnetorheological properties at T=298.15 K. Bingham plastic, Herschel-Bulkley and Carreau-Yasuda models have been applied for modeling the magnetorheological properties of nanofluids. Density values of NiO-starch-NaOH-H2O, NiO-PEG400-PEG2000 and NiO-PEG400-PEG6000 nanofluids have also been measured at T = (298.15, 308.15 and 318.15) K. The excess molar volumes were calculated from the density data for highlighting the interparticle interactions occurred in nanofluids. Singh et al. equation was used for fitting the excess molar volume values.

A theoretical study was performed to evaluate the defersirox potency to chelate aluminum (Al) and gallium (Ga) as the toxic metals in biological systems. Deferasirox as an important class of chelators, which binds to the metallic center with the ratio of 1:2, is used to remove the toxic metals in the case of iron overload disease. The effects of water and DMSO as the solvent on the electronic nanostructures of [Al(DFX)2]3- and [Ga(DFX)2]3- were investigated by using the density functional theory and compared with the gas phase results. Natural bond orbital and quantum theory of atoms in molecules analyses was carried out to understand the nature of the complex bond character in the complexes. Topological analysis verified that deferasirox –aluminum complex is more stable than gallium complex, which is in good agreement with the experimental data. Natural charge analysis revealed that aluminum has a more positive character in comparison to gallium, therefore electron-donor atoms of the deferasirox bind to aluminum more favorable than gallium. TD-DFT studies showed a blue shift in the absorption spectra for the complexes in the presence of solvent. Based on different analyses, deferasirox is considered as a good chelator to remove aluminum and gallium cations in the biological systems.

Human epidermal growth factor receptor 2 (HER2) is a member of the epidermal growth factor receptor family having tyrosine kinase activity. Overexpression of HER2 usually causes malignant transformation of cells and is responsible for the breast cancer. In this work, the virtual screening, molecular docking, quantum mechanics and molecular dynamics methods were employed to study protein–ligand interactions to be applied for drug design. The virtual screening was performed by docking among 762 chemicals derived from ZINC library to find specific inhibitors for active sites in HER2 intracellular. Among the best-ranked compounds in comparison with the crystallographic inhibitor pyrrolo [3, 2-d] pyrimidine, five compounds resulted and compound 1was further tested by molecular dynamics simulation and also quantum theory of atoms in molecules. The obtained results indicated that the interactions of compound 1 with the active site of HER2 TK are stronger than those of pyrrolo [3, 2-d] pyrimidine. Root mean square deviation, root mean square fluctuation, radius of gyration and binding free energy were calculated to check and evaluate the stability and mobility of the simulated system

Reverse micellar systems are nanofluids with unique properties that make them attractive in high selectivity separation processes, especially for biological compounds. Understanding the phase behavior and thermodynamic properties of these nanosystems is the first step in process design. Separation of components by these nanosystems is performed upon contact of aqueous and reverse micellar phases. Due to the complexities of components molecular interactions, phase behavior studies of these solutions are different from regular liquid-liquid systems, and few thermodynamic models have been developed to describe distribution of extract between phases. In this study, a thermodynamic model with φ-φ approach and use of equations of states (EOS) is developed for the first time to describe the protein phase equilibria in reverse micellar systems. The developed model assumes that some reverse micelles act as active surfaces which can adsorb protein molecules. Also, the non-ideal behavior of micellar solution was modeled by three EOS, i.e. vdW, PR, and SRK. Results showed that SRK EOS shows the best match with experimental data of Bovine Serum Albomin (BSA) extraction from aqueous solution using reverse micellar solution of CTAB, a cationic surfactant. In addition, results indicate that the proposed thermodynamic model can describe the changes in electrostatic forces and increase in active surfaces on equilibrium protein extraction. Also, the standard deviation shows an excellent match between experimental data and model predictions.

The interactions between N-hydroxyurea (NHU) as anticancer drug and SWCNTs (pure and Fe-doped) were investigated with density functional theory. In this study, large long-range corrected CAM-B3LYP and B3LYP were employed to investigate the stability of the different NHU-CNT and NHU/Fe-CNT complexes in the gas phase and solution (water). The presence of an iron atom would create suitable space on the nanotube surface for the adsorption between drug and nanotubes. The results revealed that the adsorption of drugs on the outer surface of both nanotubes was energetically favorable and the reactivity of Fe doped complexes increased compared to pristine nanotubes. Results indicated that adsorption is dependent on the sites of the drug. NBO, QTAIM and NCI-RDG analyses were applied for further understanding of the adsorption process. The data suggested that the doping of iron atom increases adsorption ability

The electronic structures and the electrostatic potential of some amino derivatives of adamantane have been studied using the density functional theory. The partial atomic charges and nuclear quadrupole coupling constants (NQCC) of 14N nucleus of the considered molecules have been reported. The partial atomic charges are calculated with two methods for 14N nucleus: Mulliken charges and natural bond orbital (NBO). All of the computations were carried out with the Gaussian 03 program and the B3LYP/6-311++G (d, p) level of theory. The results of both methods have reasonably good correlation with NQCC parameter, but the correlation between NBO charges and NQCC of 14N nucleus has been suggested is much better.

In this theoretical research, the mechanism of the C2H + C2H2 reaction is studied by high-level quantum-chemical methods and kinetics of the reaction is investigated by statistical rate theories. High-level electronic structure calculation methods including M06-2X, CCSD(T), CBS-Q and G4 methods are employed to explore the doublet potential energy surface of the reaction and compute the molecular properties necessary for carrying out the statistical rate theory calculations. After locating stationary points of the reaction, steady-state approximation to the chemically-activated intermediates along with some statistical manipulations are applied to derive some practical integral equations for the rate constants of formation of all possible products of the reaction. Unimolecular rate constants are computed by RRKM theory. VRC-TST is used to compute the sum of quantum states for internal degrees of freedom of loose transition states. The present calculations reveal that the product HCCCCH + H (P8) is the dominant product over whole pressure and temperature range considered in the present study. Nonetheless, at low temperatures and high pressures, other intermediate products especially HCC(H)CCH and H2CCCCH, become significant. The overall computed rate constants are nearly constant over the temperature range 100-500 K and slightly increase at higher temperatures.

: Unwanted water production from oil and gas reservoirs is a serious problem for producers. Preformed particle gel (PPG) treatment is a benefit approach to control excess water production. Swelling percentage of PPG samples in saline water is a key factor affecting the efficiency of the water conformance process. In this study, an efficient series of PPGs were synthesized and their swelling behaviors were studied. The design of experiments (DOE) software was used to design synthesis experiments and optimum swelling percentage of PPGs in BaCl2 salt solution. Results showed that the optimized range of the dominant factors including mole ratio of acrylamide (AAm) to acrylic acid (AA), the mole percentage of N,N'-methylenebisacrylamide (MBA) and time were found to be 6.8 to 7.4, 4.2 to 4.5 percent and 179.8 to 180 min, respectively. Additionally, PPGs had the maximum swelling percentage of 529% in the optimum conditions. In the end, for the first time, an empirical correlation was proposed by the software that predicts the swelling percentage of PPGs in BaCl2 salt solution, which had good compatibility with the laboratory data.

Although catalyst deactivation rate greatly varies depending on many factors, including the catalyst structure, reactor feed composition, and operating conditions; it is usually inevitable. Since catalyst deactivation modeling has so far been poorly addressed in the literature, in the present study, nine experimental sets of cobalt based Fischer-Tropsch catalysts activity-time data were considered to be modeled using an innovative sigmoidal pattern with amazingly meaningful parameters. Such theoretical models for catalyst life significantly facilitate the control of reactors during petrochemical industrial applications, where a constant reactor product flow rate is necessary. Five types of statistics were used to validate the goodness of the regression model. The results showed that the sigmoid model perfectly predicts the activity of the whole catalyst life for a wide range types of catalyst which is capable of being utilized as an important part of a reaction rate. For process conditions within the range of T=220–230 0C, P=20 bar, and H2/CO ratio=2, the two important constants of the model average 0.6 ± 0.1 and 0.42 ± 0.06 for steady-state activity and total loss of activity, respectively. The proposed model offers a significant advance over the existing macroscopic deactivation models, since different catalyst deactivation trends can be covered.

Fluid velocity has the potential to cause severe erosion damage to oil & gas production infrastructure. In order to avoid or alleviate damage due to erosion, the American Petroleum Institute Recommended Practice (API RP) 14E recommends a threshold fluid velocity for production tubing and pipelines. However, field and laboratory data have proven that the applied empirical constants, known as C-factors, within the formula are not valid for all conditions. In many cases the calculated API RP 14E erosional velocity is significantly underestimated or overestimated due to insufficient consideration of fluid characteristics. In addition, accurate field data on erosional velocity can assist proper pipe sizing calculations for prospective oilfield projects. Oversizing of tubing unnecessarily increases construction costs whilst underestimating required size of tubulars can lead to catastrophic erosion/corrosion failures. In this study new values for erosional velocity constants, beyond those suggested by API RP 14E, are proposed based on experimental data achieved from sidestream pilot test units. The experimental pilot test units were installed on four different gas condensate production fields in the south of Iran. Electrical Resistance (ER) probes were employed to gather online erosion-corrosion data from the pilot units, each of which was in service for about nine months. The results showed that higher C-factors can be safely applied for these gas condensate fields in comparison with those recommended by API RP 14E. Furthermore, it was revealed that pilot test units exposed to a higher Condensate Gas Ratio (CGR) experienced a greater rate of erosion.

The antioxidant properties of coumarin derivatives using the 2,2ˈ -diphenyl-1- picrylhydrazyl (DPPH) radical scavenging assay were investigated by the application of Quantitative Structure Activity Relationship (QSAR) studies. The molecular structures were optimized and submitted for the generation of quantum chemical and molecular descriptors. Genetic Function Algorithm (GFA) was employed in model development. Also the applicability domain of the developed models were accessed by the leverage approach. The Variation Inflation Factor (VIF), Mean Effect (MF) and Degree of Contribution (DC) of these descriptors were estimated. Five predictive QSAR models were developed and subjected to various validation tests. The developed models gave highly encouraging results upon validation (R=0.938, R^2=0.879, Q^2=0.845, 〖R^2〗_pred=0.700 and cR_p^2= 0.832. This research indicates that the most crucial descriptors that influence the free radical scavenging activities and essential in the design of new set of the coumarin antioxidants are the HBDCount (hydrogen-bond donor count), AATS3e (Average Broto-Moreau autocorrelation - lag 3 / weighted by Sanderson electronegativities), and the MW (Molecular weight) descriptors.

Analytic expressions were derived for the compressibility factor and residual internal energy of the square-well plus Sutherland fluid. In this derivation, we used the second order Barker-Henderson perturbation theory based on the macroscopic compressibility approximation together with an analytical expression for radial distribution function of the reference hard sphere fluid. These properties are expressed in terms of density, temperature, and the potential parameters. Derived equations successfully applied to hard-core Lennard-Jones fluid. It is found that the agreement between theory and simulation is quite good for both the compressibility factor and the residual internal energy for a wide range of densities and temperature.