Journal of Theoretical and Computational Chemistry

The adsorption of $\alpha$-AminoTiophene on Si(100)2$\times$1 was investigated by van der Waals corrected DFT and climbing image nudged-elastic band, in view of potential applications in silicon-based technologies. The overall scenario indicates that dissociative states are more favorable than the molecular ones, the one occurring through N–C bond breakage and Si–N and Si–C bond formation, having the largest adsorption energy (2.71eV). Furthermore, this configuration is also kinetically easily accessible, being connecting to one of the physisorbed states (Phys1) by a nearly barrierless transition. Also the molecular states are relatively easily kinetically accessible, with transition barriers from the corresponding physisorbed states in the 0.05–0.30eV range. At variance with this, the transitions to the dissociative state characterized by N–H bond breakage and Si–N and Si–H bond formation (N–H Diss) either from physisorbed or from molecular states are all significantly higher, i.e. in the 0.63–2.70eV range. Finally, the effects of the coverage on the adsorption energy were evaluated for the N–H Diss configuration and indicating a gain, whose extent depends both on the coverage and on the surface arrangement, i.e. whether cis or trans. The trend is different if the vdW forces are excluded.

A theoretical study of the antioxidant behavior of N${}^{\prime }$-(2-hydroxy-3-methoxy-benzylidene)-4-tert-buty-lenzohydrazide (1), N${}^{\prime }$-(5-bromo-2-hydroxy-benzylidene)-4-tert-butyl benzohydrazide (2) and N${}^{\prime }$-(2-hydroxy-3-methoxybenzylidene)-4-methyl-benzene-sulfonohydrazide (3) and their tautomers 1 ${}^{\prime }$ –3 ${}^{\prime }$ have been carried out at B3LYP/6-31$++$G(2d,2p). The numerical values of descriptors, namely, bond dissociation enthalpy, proton affinity (PA), electron transfer enthalpy (ETE), ionization potential, and proton dissociation enthalpy (PDE) have been calculated in gas phase and media solution (EtOH, DMSO and water). The obtained results show that the hydrogen atom transfer (HAT) mechanism is more favored thermodynamically in gas phase, whereas the sequential proton loss electron transfer (SPLET) mechanism is more preferred in solvents. Moreover, the couple (3,3${}^{\prime }$) is found to be the most potent antioxidant as expected experimentally. Furthermore, the BDE values of compound 3 ${}^{\prime }$ is much lower than that of ascorbic acid (AA), indicating that the tautomerization of compounds 1–3 has great influence on the antioxidant activity of these compounds. The antioxidant power of compounds (3.3${}^{\prime }$) was also rationalized by the calculation of the atomic spin density. In addition, the molecular docking study of compounds 1–3 and 1${}^{\prime }$ –3${}^{\prime }$ on xanthine oxidase (XO) as the protein target revealed important interactions between active compounds and amino acids. Moreover, compound 3 is predicted to be a potential inhibitor with higher activity.

Martini coarse-grained force field simulations have been carried out to estimate the free energy profiles of the spontaneous membrane-translocating peptide TP2 and one negative control peptide ONEG with POPC as the model bilayer. The results show that the free energy minimum of TP2 is $-$20kJ/mol lower than that of ONEG. In addition, the minimum of TP2 shifts slightly to the bilayer center compared with ONEG. The translocation barrier height for TP2 and ONEG are 119.0kJ/mol and 155.7kJ/mol, respectively. The lower central energy barrier of TP2 facilitates the transition between two leaflets of POPC. Both translocating peptides induce the formation of funnel-shaped structures at the bilayer center, but TP2 has a more compact structure and brings less perturbation compared with ONEG. Subsequently all atom molecular simulations testify the findings. It is indicated that compared with its negative control ONEG, TP2 binds better with lipid and penetrates deeper into bilayer with less perturbation to the bilayer structure. Our findings may shed light on the design and virtual screening of spontaneous membrane-translocating peptides.

Group 4 metallocene-mediated cationic ring-opening polymerizations of a series of lactones and cyclic carbonates, with different ring sizes ($n=4$–8) have been theoretically studied. Using the “naked cation” approach in combination with density functional theory, the activated chain-end mechanism and the influence of transition metals, solvent and monomer ring size on the polymerizability were explored in detail. The results showed that the cationic metallocene–monomer complex, [catalyst][monomer]${}^{+}$, is formed, generating cationic (carbocation ion) species responsible for polymer chain growth. We found that poor polymerizability of five-membered lactone and six-membered ring carbonate depends not only on the nature of the monomer ring size but also the relative stability of the complex, which was found to correlate well with the ring strain. Subsequently, several propagation steps take place through an SN₂ reaction which involves ring opening of an active monomer, via alkyl–oxygen bond cleavage. Based on the computed activation energies of all metallocene systems, the first propagation was found to be the rate-determining step of the overall propagation and the hafnocene was found to be most active with the energy barrier of 17.6kcal/mol, followed by zirconocene (18.6kcal/mol) and titanocene (19.5kcal/mol), respectively. The mechanistic study may be applicable to the cationic ROP of lactides and other related monomers.

The density functional theory (DFT) was used to investigate some toxic derivatives of aromatic hydrocarbons adsorption on perfect graphene (pG) and graphene-doped with B/Al/Ga (BG/AlG/GaG). And the parallel and vertical adsorptions were considered for the position relation between the adsorbent and adsorbate. The adsorption energy, adsorption distance, charge transfer and density of states (DOS) were discussed in optimized structures. The greater adsorption energy, shorter adsorption distance and more charge transfer were found in AlG by studying the four kinds of molecules (phenol/m-cresol/PCP/p-NP) adsorption on pG/BG/AlG/GaG. Then, 10 derivatives adsorption on AlG were reported, and the adsorption energy increased in the order of pentachlorophenol $<$ 2,4,6-trichlorophenol $<$ 2,4-dichlorophenol $<$ p-cresol $<$ m-cresol $<$ phenol $<$ o-chlorophenol $<$ o-cresol $<$ 2,4,6-trintrotoluene $<$ para-nitrophenol. The interaction between these derivatives and the substrate was chemisorption for AlG and physisorption for pG. The oxygen atom in nitro group was more closer to the substrate than in hydroxyl group about optimized structures.

Over the past years, an interest has arisen in resolving the problems of the increased carbon monoxide and carbon dioxide emissions, leading to the serious air pollution and many detrimental effects. A convenient solution would be a process that could utilize metal oxide nanoparticles such as TiO₂ to control the concentration of atmospheric pollutants. The chemisorption of CO and CO₂ molecules over the semiconductor titanium dioxide (TiO${}_2)$ is such a process. In this way, density functional theory (DFT) calculations were performed to investigate CO and CO₂ adsorptions on undoped and N-doped TiO₂ anatase nanoparticles. The supercell approach is conducted to construct the considered nanoparticles and the adsorption of CO_x molecule was simulated by use of these chosen nanoparticles. By including van der Waals (vdW) interactions between CO_x molecule and TiO₂ nanoparticle, we found that both CO and CO₂ molecules can bind strongly to the N-doped nanoparticles. The adsorption on the five-fold coordinated titanium site of TiO₂ nanoparticles including the bond lengths, bond angles, adsorption energies, density of states (DOSs), Mulliken population analysis and molecular orbitals has been broadly studied in this work. Based on the obtained results, it can be concluded that the adsorption on the N-doped nanoparticle is more energetically favorable than the adsorption on the pristine one, representing the higher tendency of N-doped nanoparticles for CO_x detention, compared to the undoped ones. Therefore, the results indicate that the N-doped TiO₂ would be an ideal CO_x gas sensor in the environment.

The validity of the “Koopmans in DFT” (KID) procedure have been assessed by means of the calculation of several Conceptual DFT reactivity descriptors calculated through a $\mathrm{\Delta }$SCF procedure compared with the results of the HOMO and LUMO energies of the neutral system. Three resveratrol derivatives were considered: cis- and trans-piceid and resveratrone-6-O-$\beta$ glucoside. The Minnesota latest family of density functionals have been considered for the calculations in connection with water as a solvent simulated with the SMD parametrization. It is shown that the range-separated hybrids MN12SX and N12SX fulfill the KID procedure with great accuracy.

This study used mpw1pw91 quantum chemical calculations in gas and solution phases to clarify the interaction between C₂₀ and Cr(CO)₅ fragment. It also sought to clarify the effects of solvent polarity on dipole moment, structural parameters, and frontier orbital energies of the complex. Energy decomposition analysis (EDA) was applied to analyze the bonding interaction between the C₂₀ and Cr(CO)₅ fragment. Percentage composition in terms of the defined groups of frontier orbitals for the complex was evaluated to characterize the metal–ligand bonds. The Cr–C bonds within the complex were examined using quantum theory of atoms in molecules (QTAIM) analysis. In order to determine the back-bonding effects in these bonds, QTAIM analysis was applied to calculate of the quadrupole polarization of the carbon atom.

The Mepivacaine drug is used as a local anesthetic in dentistry, which could exist as three different tautomers. Herein, geometry, energy behavior as well as tautomerization of these tautomers have been investigated by employing density functional theory (DFT) and considering the solvent effects with the polarizable continuum model (PCM) model. The most stable tautomer of the Mepivacaine has a carbonyl and an –NH amine groups in its structure. The frontier orbitals and the energy gap of the molecule have been computed using the natural bond orbital analysis (NBO). Also, the armchair (5,5) single wall carbon nanotube (SWCNT) was used for investigation of the noncovalent interactions of the Mepivacaine molecule with the pristine SWCNT and the –COOH functionalized SWCNT in several forms. Geometries of the possible forms have been optimized. The most stable form for noncovalent interactions of the drug with each of the pristine and functionalized SWCNTs have been determined. The intermolecular H-bonds have essential role in energy behavior of the noncovalent interactions between the Mepivacaine drug and the investigated SWCNTs.