Physical Chemistry Research
Volume:4 Issue: 4, Autumn 2016

In this study, functionalized β-cyclodextrin (β-CD) by aldehyde group was investigated as an oxidase enzyme mimic for the amino phenol oxidation. All calculations were performed by GAUSSIAN 09 package using two layers ONIOM method at the ONIOM (MPW1PW91/6-311(d,p)/UFF) level. In the first step, H2O2 is encapsulated in the hydrophobic cavity. In the second step, H2O2 molecule oxidized the aldehyde group of the functionalized β-CD, through the wide edge of β-CD. This step is the Rate Determining Step (RDS) with the activation energy of 54.4 kcal mol-1. Natural population analysis has been performed for calculation of the global electron density transfer of the atoms involved at the center of the reaction. In order to have a knowledge of the intermolecular interactions, HOMO-LUMO analysis has been done and showed a reduction in the chemical hardness during the reaction. Topological analysis of the structures at the RDS confirmed that the ratio of the potential to the kinetic energy density for the O-O bond at the transition state is covalent in nature.

Hydrogen is considered as a unique choice for future world’s resources. The important parameter in the process of hydrogen production is the value of reduction potential for the used catalyst, in direct contact with consumed energy in process. The application of computational methods to design and modify molecular catalysts is highly regarded. This study sought to explore Density Functional Theory (DFT), employing an effective core potential basis set (LanL2DZ) for metals, as an applicable method used to calculate molecular geometries and electronic structures of the redox forms of two new super-efficient catalysts, CoP4N2 and FeP4N2. The reduction potential related to CoP4N2 catalyst in the presence of water solvent is measured using a reference isodesmic reaction. The calculated data revealed that obtained theoretical value for the reduction potential of catalyst, -0.58V, is in an excellent agreement with its experimental value, -0.50 V. The results confirmed that water molecules coordinated with Co or Fe core in catalyst structure play the main role in H2 gas production.

The present study describes the fragmentation under electron ionization (EI) of gas phase serine and threonine amino acids. Ab initio methods were performed to calculate the fragmentation paths and interpret the mass spectra. The six lowest energy conformers of L-serine, L-threonine and L-allo-threonine were obtained with B3LYP, G3MP2 and MP2 methods. The adiabatic and vertical ionization energies of the most stable conformers are reported. The structures of fragment ions and neutral species formed by direct bond cleavages as well as rearrangement reactions were obtained. Appearance energies (AE) were calculated for the formation of particular fragment ions at 200 °C. The order of peak intensities were compared with the theoretical calculated AEs, and a complementary explanation was provided about the relative abundance of fragmentation products.

In this study, kinetics and mechanism of the sulfur dioxide adsorption on the single-walled carbon nanotubes (CNT) are investigated. Three single-walled carbon nanotubes, including the armchair (6,6), chiral (6,5) and zigzag (6,0) CNTs were chosen as the models and the different orientations of SO2 molecule relative to the CNT axis were considered. The B3LYP functional within the 6-31G(d) basis set was used for the theoretical calculations. For all orientations, reaction Gibbs free energies (ΔG˚) were calculated and the transition state structures were investigated for the spontaneous reactions. Chiral single-walled carbon nanotube (6,5) showed the least activation energy (11.72 kcal mol-1) while the armchair model showed the highest one (17.93 kcal mol-1). Natural bond orbital analysis showed that the electronic charge is transferred from CNT to sulfur dioxide. Topological analysis confirmed the C-S bond formation at the transition state. Density of states analysis showed that Fermi level energy is increased in armchair model. The application of the external electric field indicated that the CNTs stability and the functionalization energies are improved. Based on the obtained data, by using the electric field, it is possible to elevate the conductivity of CNT and the functionalization rate of SWCNT for industrial applications.

The conformational analysis of the organic compounds specially the biologically active natural products has attracted the consideration of different research groups. Therefore, in the present study the MP2/6-311(d,p)//B3LYP/6-311(d,p) level of theory was used to study the conformations of dapdiamide D. The identity of interactions in selected conformers was studied using atom in molecule approach. The energies of hydrogen bonding and Van der Waals interactions were calculated using the potential energy density V(r) at the bond critical point. An interaction between carbonyl and nitrogen of the amide functional group is evident, in most of the cases. This interaction creates a boat-like seven member-ring. The interaction between amine and hydrogen of the amide functional groups is important as well. This interaction forms a five-member ring. The results showed that the potential energy density V(r) and electron density at the bond critical points can be used as a criteria to determine the strength of the interactions.

In the present study, the cooperative and diminutive interplay between halogen, hydride, and cation-σ interactions are studied in HMgH···Li(Na)···NCCl, Li(Na)···HMgH···ClCN and HMgH···ClCN···Li(Na) complexes by means of ab initio calculations. To better understand the cooperative or diminutive effects in the ternary systems, the corresponding binary complexes are also considered. The estimated cooperative energies (Ecoop) are all negative for the systems with CNCl in the central location, while positive in the other systems. In addition, complexes involving cation-σ interactions have the largest stability energy among studied complexes. The electronic properties of the complexes are analyzed using parameters derived from the quantum theory of atoms in molecules methodology.

DFT calculations were used to investigate adsorptionof F-, Cl-, Li and Na ions on the exterior surface of Mg12O12 nanocage in the gas phase and water media. The most favorite position for adsorption of the studied anions and cations are atop of Mg and O atoms of Mg12O12, respectively. The strongest interaction is obtained when fluoride is located atop of Mg atom with the adsorption energy of -2.92 eV. In water media, adsorption energy of ions is reduced due hydration of ions and nanocage. Adsorption of the studied ions on the Mg12O12 nanocage is compared with adsorption of these ions on AlNNT surface. It is shown that Mg12O12 is more convenient adsorbent for fluoride ion than AlNNT.

The present paper aims to investigate the role of open metal site metal-organic frameworks (MOFs) on hydrogen adsorptivity using periodic boundary condition (PBC) density functional theory (DFT). Hence, MIL-47-M (M = V and Fe) were selected and one hydrogen molecule adsorptivity was calculated in different orientations on them. Four different chemical sites were identified in every cluster section of these MOFs, and molecular hydrogen adsorption was studied in these sites. In these MOFs, V has fewer electrons than Fe in its valence layer. Results demonstrated that when dihedral angle of M-O-H-H is 0̊, the binding energy of hydrogen adsorption is higher than that in other orientations in both MILs (-26.16 and -19.73 kJ mol-1 for V and Fe, respectively). In this orientation, hydrogen molecule has a head-to-head interaction with O in M-O-M. Also, hydrogen desorption in various orientations in MIL-Fe was found, and minimum distances between the hydrogen molecule and one atom of MILs were calculated in all the orientations. It was revealed that there are not significant differences in all orientations and the best adsorptivity condition is hydrogen molecule in a head-to-head orientation with O, (M-O-M), which is 2.419 and 2.338 Å for V and Fe, respectively. According to PBC-DFT results, hydrogen adsorption on MIL-V is energitically more stable than that on MIL-Fe. Findings indicate that MOFs with an open metal site are more proper candidates for hydrogen adsorptions.

In the present study we search potential of Pt-decorated graphene (PtG) as a new nanostructure adsorbent for nitrous oxide (N2O) using density functional theory (DFT). After fully relaxation of different possible orientations of N2O-PtG complex, we distinguished two optimized configurations for this system; 1- terminal N-side of gas is oriented towards Pt so that the molecule axis is perpendicular to the surface (P1), and 2- O-side of the molecule is closing to Pt while the axis of molecule has an angular configuration to the surface (P2). Our results showed high adsorption of N2O on PtG, however there is a significant difference between the value of adsorption for P1 compared to that for P2 (-113.6 (-88.7 BSSE) vs. -41.2 (-32.0 BSSE) kJ mol-1). Results of the charge analyses reveled interesting net charge transfer; the direction of charge is from N2O to PtG for P1 configuration and the reverse is found for P2.

A comprehensive study on the structural, electronic and nonlinear optical (NLO) properties of alumina nanostructures (Al2O3)n with n = 2-5 belonging to the groups III and VI dopants carried out by density functional theory. The NBO charges exhibit dopant atoms caused to the increasing charge transfer and introduces acceptor-donor model for NLO response of alumina nanostructures. Under the influence of doping S and Se, the energy gap decreases, because high energy level is formed as the new HOMO orbitals in the primary gap of pristine nanostructures. Furthermore, the results of the present study show that dopant atoms enhance NLO response in the alumina nanostructures and the greatest values are obtained for a, b0 and γtot through doping Se in Al10O15.

Antioxidants are compounds which can prevent biological and chemical substances from oxidative damage by reactive oxygen species. Flavonoids are the most important class of polyphenolic compounds that because of their antioxidant characters possess biological activities and pharmacological effects. Chrysin-6-C-fucopyranoside and chrysin-3-malonyl-6-C-fucopyranoside are mono C-glycosyl derivatives of chrysin and flavonoid metabolites in leaves of Cyclanthera pedata. In order to study the effect of glycoside group on the antioxidant ability of chrysin, theoretical parameters including bond dissociation enthalpy (BDE), energy gap (∆E) and spin density for three above mentioned flavonoids are calculated using DFT method at the B3LYP/6-311** level in gas phase. In order to consider the various environments, solvent effects in water and DMSO using self-consistent reaction field (SCRF) and the polarizable continuum model (PCM) at B3LYP/6-311** level are performed. Obtained results show that solvent is able to cause significant change in the reaction enthalpies but no significant change on energy gap (∆E) and spin density. Our results indicate that BDE values due to its space prevention and presence of intra hydrogen bond between O atom of glycoside group (O-C1gg) in chrysin derivatives and 7OH have a low inverse effect on the BDE and so on antioxidant ability. We use Bader’s atoms in molecules (AIM) theory to perform a topological study on chrysin and its derivatives to emphasize the presence of intra hydrogen bonds. Base on AIM analyses, these hydrogen bonds have covalent nature. Energy gap (∆E) and spin density of flavonoid radicals almost do not change in the presence of glycoside group in gas phase, as well as in water and DMSO solvents. So, linked glycoside agent to chrysin does not improve its antioxidant ability.

Cobalt ferrite (CoFe2O4) nanorods were synthesized by iron chloride (FeCl3.6H2O) and cobalt sulfate hexahydrate (CoSO4.7H2O) as precursor in the presence of ethylene glycol agent and poly vinyl pyrrolidone (PVP) surfactant. The samples were characterized to identify the physical properties. XRD pattern of cobalt ferrite samples showed the structure of body center cubic (bcc) structure. The diameter of as-prepared samples was determined about 20 nm and annealed one was about 30 and 50 nm in diameter at 500 °C and 1100 °C, respectively. The TEM studies showed that the particles change from rod shaped to sphere-liked shaped particles by increasing annealing temperature. Peaks in the FTIRspectrum determined the element of Fe-Co nanoparticles. EDS shows peaks of iron and cobalt with fewer impurities in prepared samples and Fe/Co ratio was also decreased with increasing annealing temperature. The result of magnetic measurements showed saturation magnetization around 59.5 emu g-1 for annealed samples.

Experimental determination of solubility and ternary phase diagram of chiral compound are of tedious and time consuming tasks, and in many cases, there is not enough experimental data for different enantiomeric compositions to access the experimental ternary phase diagram. Using thermodynamic models with predictive capability, having less dependency on experimental data, affords a great advantage for ternary phase diagram modeling of these compounds. In this study, NRTL-SAC model, as one of the known and famous predictive models in the solubility modeling of pharmaceutical compounds, has been applied to ternary phase diagram modeling of chiral medetomidine salts in alcohols. NRTL-SAC molecular parameters of each chiral compound were calculated just by using racemic point solubility data before being used for the solubility prediction of other enantiomeric compositions. The results of thermodynamic modeling and the predictive data are compared with those of the experimental data. Root mean square error (RMSE) is also calculated for each compound. It was observed that, there is a small deviation between predictive and experimental ternary phase diagrams. The eutectic points of chiral compounds in both racemic and conglomerate forms are also well predicted through this method.

Densities and viscosities of binary mixtures of methyl tert-butyl ether (MTBE) with 1-alkanols include 1-butanol, or pentanol, or hexanol, or heptanol were measured as a function of composition from 293.15 to 308.15 K at atmospheric pressure. The temperatures studied were 293.15, 298.15, 303.15 and 308.15 K. The experimental results have been used to calculate the viscosity deviation Dh and volumetric properties such as , and . Both and Dh values were negative over the entire range of mole fraction for all temperatures and systems studied. The results for all volumetric and viscometric properties are discussed on the basis of molecular interactions between the components of the mixtures.

The interaction of a nitrosyl hydride (HNO) molecule with B12N12 nanocage was explored by means of density functional calculations. It was found that HNO prefers to be adsorbing on a boron atom of the cage with adsorption energy of -0.65 eV. This adsorption process significantly shifts the HOMO-LUMO gap (Eg) of the cage to lower energies, thereby reducing Eg of the cage from 6.84 to 2.45 eV. Time-dependent density functional theory (TDDFT) calculations show a high intensity peak in 381.38 nm in the most stable complexes of HNO with B12N12. The change in electronic properties of the B12N12 nanocage on HNO adsorption is significant enough to consider it a potential sensor for HNO detection.