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The interactions between thirteen Li atoms and graphyne (GY) and boron nitride (BN-yne) were investigated by the density functional theory (DFT). The electronic and structural properties of the interactions between the hollow sites of GY and BN-yne with Li atoms were unveiled within the quantum theory of atoms in molecules (QTAIM) framework. Theoretical understanding of the interactions between Li atoms and extended carbon-based network structures is crucial for the development of new materials. Herein, calculations to explore the impact of Li decoration on the GY and BN-yne are reported. It was predicted that Li decoration would increase the density of state of these sheets. Owing to strong interactions between Li and the GY and BNyne, dramatic changes in the electronic properties of the sheets together with large band gap variations have been observed. The present study sheds deep insight into the chemical properties of the novel carbon–based two-dimensional (2D) structures beyond the graphene sheet.

To investigate the potential energy surfaces and the coupling between the adiabatic states of SO2 molecules, it is necessary to consider the non-adiabatic coupling terms (NACTs), where the Born–Oppenheimer approximation breaks down. In this work, we analyze the conical intersections between 1 1A1 and 1 1B2 states (the A′ states in Cs symmetry) and 1 1A2 and 1 1B1 states (the A′′ states in Cs symmetry) using NACTs and adiabatic-to-diabatic transformation (ADT) angles. Our results confirm reasonable interaction between 1 1A1 and 1 1B2 states and strong interaction between 1 1A2 and 1 1B1 states. [ABSTRACT FROM AUTHOR]

Topological analyses of the electron density using the quantum theory of atoms in molecules (QTAIM) have been carried out at the B3PW91/6-31g (d) theoretical level, on bis(pyrazol-1-yl)methanes derivatives 9-(4-(di (1H-pyrazol-1-yl)-methyl)phenyl)-9H-carbazole (L) and its zinc(II) complexes: ZnLCl2 (1), ZnLBr2 (2) and ZnLI2 (3). The topological parameters derived from Bader theory were also analyzed; these are characteristics of Zn-bond critical points and also of ring critical points. The calculated structural parameters are the frontier molecular orbital energies highest occupied molecular orbital energy (EHOMO), lowest unoccupied molecular orbital energy (ELUMO), hardness (η), softness (S), the absolute electronegativity (χ), the electrophilicity index (ω) and the fractions of electrons transferred (ΔN) from ZnLX2 complexes to L. The numerous correlations and dependencies between energy terms of the Symmetry Adapted Perturbation Theory approach (SAPT), geometrical, topological and energetic parameters were detected and described.

In F2O+ cation the first (2B2) and second excited (2A1) electronic states can be coupled with each other by anti‐symmetric stretching mode and thus conical intersection and non‐adiabatic dynamics play an important role in characterizing molecular properties. In this work, we tried to find a suitable computational method for determining equilibrium structures and harmonic vibrational frequencies of the three lowest electronic states of F2O+. To understand non‐adiabatic dynamics at conical intersections, we calculated the probability of electronic population on 2B2 and 2A1 excited electronic states using linear vibronic coupling Hamiltonian mode including all three vibrational modes (bending (ω1), symmetric stretching (ω2) and anti‐symmetric stretching (ω3)).The amount of vibronic coupling constant between these states is obtained 0.08 eV at multi reference configuration interaction/Aug‐cc‐pVQZ level of theory. [ABSTRACT FROM AUTHOR]

In this study, adsorption of photosynthetic pigments on the inner and outer surfaces of single-walled carbon nanotube (15, 15) has been investigated using molecular dynamics simulation. The binding free energy is calculated by using the linear interaction energy algorithm, that its value indicates the adsorption of all pigments is desirable in both positions. Also, despite the high similarity between each category of these pigments, their interaction with the nanotube is different, that this result can be useful to separate these pigments from one another. According to Lennard-Jones potential energy between the pigments and carbon nanotube, the interaction on the inner surface is stronger than that on the outer surface for all pigments. The chlorophylls phytol tail interacts more strongly with the nanotube compared with the porphyrin ring of chlorophylls. The ability of carotenoids to institute π-π stacking is attributed to conjugated system. Furthermore, xanthophylls due to hydrogen bonded to oxygen atom form semi-hydrogen bonds with carbon nanotube. [ABSTRACT FROM AUTHOR]

In this study, the transfer of L-ascorbic acid by UlaA through Escherichia coli ( E. coli) membrane was evaluated using density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulation methods. DFT calculations at the B3lyp/6311G(p,d) level were performed to investigate the interaction properties and molecular descriptors. The physical properties, such as chemical potential, chemical hardness, and chemical electrophilicity of all studied molecules, were investigated. Natural population analysis was employed to describe the state of charge transfer between interactions using the natural bond orbital (NBO). The atoms in molecules (AIM) theory was used to examine the properties of the bond critical points such as their electron densities and Laplacians. Molecular docking studies showed that L-ascorbic acid was bounded to the internal cavity of UlaA. It was found that there were some hydrogen bond interactions between L-ascorbic acid and active sites of UlaA. The results of the MD simulation showed that the root mean square deviation (RMSD) of UlaA and L-ascorbic acid bound-UlaA reached equilibrium after 3.7ns. An evaluation of the radius of gyration () revealed that UlaA and L-ascorbic acid bound-UlaA were stabilized around 10,000ns. Finally, analysis of the RMS fluctuations suggested that the structure of the L-ascorbic acid binding site remained approximately rigid during simulation. All obtained results shed light on the special manner of L-ascorbic acid transfer through E. coli membrane, and confirmed the results of previous studies on this issue. [ABSTRACT FROM AUTHOR]

We show that the time-correlation function formalism can be applied to calculate nonadiabatic electronic population dynamics on the two vibronically coupled diabatic displaced-distorted harmonic potential energy surfaces through conical intersection. We present general formulas for the time-evolved electronic populations at finite temperature with initial sampling from both initial thermal equilibrium and nonequilibrium nuclear distributions. The validity of our formalism is verified through comparison with previous work in a certain limit of our results for case of displaced harmonic oscillator. Finally for illustration, the derived expressions have been applied to determine the electronic population dynamics at conical intersections for SO2 and trans-1,3,5-hexatriene molecules. [ABSTRACT FROM AUTHOR]

We present the kinetics and mechanism of the reaction of O (3P) with CH3NH2. Geometries of all the stationary points involved in the reaction have been investigated at the B3LYP/6-311+G (d, p) level. We report the potential energy surface for all of the possible pathways by the Gaussian-2 G3B3 method. This is the first time one has gained a conclusive insight into the detailed mechanism and kinetics for this reaction. Using the Rice-Ramsperger-Kassel-Marcus (RRKM) theory, we have computed the rate constants for channels leading to several products over the temperature range 298-440 K. The main reaction channel is found to be addition of an oxygen atom to CH3NH2 followed by migration of an H atom from N to O atoms and loss of H2O, which agrees with experimental results (Slagle, Dudich, and Gutman (1979) J.Phys.Chem., 83). As experimental data are available for this reaction, we are able to conclude that our thermal rate constants are in agreement over a wide range of temperatures. [ABSTRACT FROM AUTHOR]

Background: The aim of this study was to investigate interaction between vanillin and alpha-, beta- and gamma-cyclodextrin carriers for targeted drug delivery and compare the performance between them using theoretical methods. Methods: All theoretical calculations were performed on a Intel® Core™ i5 Processors computer at Kerman University using Gaussian 09 program package (Gaussian, Inc., Wallingford, USA) in a three month period (February 2014 to May 2014). Starting geometries were generated employing Gauss View software, version 5 (Gaussian, Inc., Wallingford, USA) and then the resulting coordinates were optimized using density functional theory (DFT) calculations. The natural bond orbital method (NBO program, under Gaussian 09 program package) was carried out to study charge transfer energy associated with the intermolecular interactions. The quantum theory of atoms in molecules was applied for DFT results to get insight in the nature of interaction existing in the investigated systems. The calculations were carried out with AIM 2000 program and AIMAll 14.10.27 package (Todd A. Keith, TK Gristmill software, Overland Park KS, USA) to find and characterize bond critical points. Results: The vanillin molecule is adsorbed on the surface of carriers by hydrogen bonding between its oxygen atom and hydrogen atoms of cyclodextrin. The hydrogen of - OH group on the cyclodextrin can form hydrogen bond to the oxygen atom of carbonyl group of vanillin molecule. This study indicates a decrease of total energy with increasing surface of cyclodextrin. So gamma-cyclodextrin and its complex with the maximum surface in between carriers have the highest stabilities. The gamma-cyclodextrin shows the strongest interaction with vanillin. In all complexes of vanillin-cyclodextrin, the direction of charge transfer is from drug to carrier. Conclusion: Due to the high solubility of gamma-cyclodxtrin and its stronger interaction with the molecule vanillin, it can be the best option as drug carrier. [ABSTRACT FROM AUTHOR]

The recently presented ab initio calculations for the reaction system of CH3Cl + OH (Dehestani and Shojaie, Int J Quantum Chem, in press) are applied to the vibrational mode analysis. Extending previous work, we use the vibrational mode analysis to elucidate the relationships of the reactants, the transition state, the intermediates (IM), and the products. The extensive investigation shows that the reaction mechanism is reliable. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011 [ABSTRACT FROM AUTHOR]

The kinetics and mechanism of the reaction of OH with CH3Cl have been theoretically studied. The potential energy surface for each possible pathway has been investigated by the G2MP2 method. The rate constants for channels leading to several products have been calculated by multichannel-Rice-Ramsperger-Kassel-Marcus (RRKM) theory over a temperature range 200-2000 K. The results show the major channel is hydrogen abstraction mechanism. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012 [ABSTRACT FROM AUTHOR]

In this work, we examine nonadiabatic population dynamics for 11B1 and 11A2 states of ozone molecule (O3). In O3, two lowest singlet excited states, 1A2 and 1B1, can be coupled. Thus, population transfer between them occurs through the seam involving these two states. At any point of the seam (conical intersection), the Born‐Oppenheimer approximation breaks down, and it is necessary to investigate nonadiabatic dynamics. We consider a linear vibronic coupling Hamiltonian model and evaluate vibronic coupling constant, diabatic frequencies for three modes of O3, bilinear and quadratic coupling constants for diabatic potentials, displacements, and Huang‐Rhys coupling constants using ab initio calculations. The electronic structure calculations have been performed at the multireference configuration interaction and complete active space with second‐order perturbation theory with a full‐valence complete active space self‐consistent field methods and augmented Dunning's standard correlation‐consistent‐polarized quadruple zeta basis set to determine ab initio potential energy surfaces for the ground state and first two excited states of O3, respectively. We have chosen active space comprising 18 electrons distributed over 12 active orbitals. Our calculations predict the linear vibronic coupling constant 0.123 eV. We have obtained the population on the 11B1 and 11A2 excited electronic states for the first 500 fs after photoexcitation. [ABSTRACT FROM AUTHOR]

To investigate the potential energy surfaces and the coupling between the adiabatic states of SO 2 molecules, it is necessary to consider the non-adiabatic coupling terms (NACTs), where the Born-Oppenheimer approximation breaks down. In this work, we analyze the conical intersections between 1 1 A 1 and 1 1 B 2 states (the A' states in C s symmetry) and 1 1 A 2 and 1 1 B 1 states (the A'' states in C s symmetry) using NACTs and adiabatic-to-diabatic transformation (ADT) angles. Our results confirm reasonable interaction between 1 1 A 1 and 1 1 B 2 states and strong interaction between 1 1 A 2 and 1 1 B 1 states.