Journal of Theoretical and Computational Chemistry

A MP2/6-31++G(d,p)//B3LYP/6-31++G(d,p) method was used to investigate the mechanisms of α-H and proton transfers of glycine induced by Mg²⁺. Eight complexes were obtained, six of which were neutral and the other two were zwitterionic. Among them, the zwitterion with a binding energy of 159.4 kcal/mol was the most stable structure. Conformation transformations of the complexes caused by the rotation of single bond and the transfers of α-H and proton were completed via seven transition states. The inductive effect of Mg²⁺ made the electron cloud of glycine deviate to Mg²⁺, which activated the covalent bond involving the transferred proton. The neutral complex can be turned into the zwitterionic one by the transfers of both carboxyl hydrogen and α-H, and the energy barrier of each reaction was less than 9.2 kcal/mol. After the transfer of α-H, a delocalized π bond was formed in glycine skeleton and the α-C atom took 0.19 positive charges. So the chemical activity of the glycine enhanced, and glycine was readily available for addition and nucleophilic substitution reactions. The path from the most stable glycine conformer G1 to the zwitterionic conformation I is G1 → G1–G3 → G3 → G3–G4 → G4 → G2–G4 → G2 → VI → I–VI → I, and the highest energy barrier of this path is 9.2 kcal/mol.

Calculations based on density functional theory (DFT) have been carried out for the gas-phase ion-molecule reactions of CS₂ with CHX^•- (X = F, Cl, and Br) to investigate the effect of the halogen-substituent on the reaction mechanism. The doublet potential energy surfaces (PESs), involving two striking reaction patterns named by the middle-C attack and the end-S attack in terms of anion attack on the C and S atoms of CS₂, have been explored and characterized in detail. Compared with the results of the end-S attack, reaction with the middle-C attack pattern displays more efficiency on PES. For a given reaction pattern, the reactions of CHCl^•- and CHBr^•- occur with similar efficiencies and reactivity trends. The CHF^•- anion displays remarkably different reactivity, which is traced to its lower electron binding energy and the effect of the electronegative fluorine substituent. This is in good agreement with the experimental observation. According to the property of the product branching ratios in experiment, dynamical effect is used to evaluate the reason that the end-S attack with less energetically favorable obtained in our theoretical studies is comparable to the middle-C attack.

A theoretical investigation of the mechanism, kinetics and probable product analysis of the Cl-initiated oxidation reaction of methyl methacrylate (MMA) is presented in this paper. The major degradation pathway of MMA is the Cl-addition to the terminal carbon of the olefinic bond. Beside this, energetic and mechanism of other possible reaction pathways are discussed in detail. In addition, the mechanism for the secondary reactions in presence of O₂ and NO has also been presented. Cl-addition to the double bond takes place via formation of the pre-reactive complex as these reaction channel passes through negative activation barrier. Energetics and thermochemical analysis have been studied at the MP2=Full/6-311++g(d,p) level of theory. The rate constant of the Cl-addition reaction has been calculated using conventional transition state theory (CTST) at 1 atm pressure and 250–350 K temperature range.

Oligo- and polythiophenes on surfaces play a fundamental role in building molecular circuits and organic-based electronics and may be assembled via interaction of the monomer units with the surface. In this framework, the nature of interaction of 2-vinyl thiophene (2VTP), a conjugated heteroaromatic monomer unit, with the Si(100) surface was studied by means of density functional theory (DFT). In particular, structural optimizations were performed comparing the effects of the inclusion of van der Waals (VdW) forces. It came out that the adsorption through the double bond is energetically favored, if VdW forces are included, whereas the adsorption through both aromatic ring and double bond simultaneously is more stable, if they are excluded. Physisorbed states were singled out and the barriers between two of them and the corresponding chemisorbed states were calculated along with the imaginary frequencies of the transition states. Also the transition energies have different values if the VdW forces are included.

KcsA potassium channel is a membrane protein that allows the passage of potassium ions and water molecules across the cellular membrane. Using molecular dynamics (MD) simulation method, the effect of an applied GHz oscillating electric field of strength 0.004 V/nm on the dynamics of K⁺ and water molecules in a KcsA channel was modeled. It was found that the application of GHz range electric field caused a change in the potential energy profile of the water molecules in the filter sites, causing an increase in the delay time of the water molecules in these sites. Therefore, exposing the channel to the GHz fields can perturb the dynamics of the water molecules in the filter, and consequently, the channel operation may be disturbed. Furthermore, the results show that the applied field has no major effects on the dipole orientation of water molecules in the channel.

To understand the reaction mechanism involving hydrogen transfers through hydrogen-bond bridge, we carried out both Self-Consistent Charge Density Functional Tight-Binding (SCC-DFTB) calculations of bulk nitromethane and Density Functional Theory (DFT) calculations of singlet ground state/triplet excited state molecular nitromethane using B3LYP functional. Firstly, we tuned the repulsive parameters of the SCC-DFTB method for nitromethane with dataset calculated from DFT at B3LYP/6-311g level. The molecular dynamics simulations are carried out with tuned parameters to get the dynamical properties of the bulk nitromethane, and the static calculations are intended to give energy profile of the reaction process. These calculations indicate the excitation of nitromethane molecule making the proton transfer reactions possible, and lowering the reaction barrier.

Electronic and topological properties of hexane (C₆H₁₄) and its five geometric isomers are systematically studied quantum mechanically using several techniques such as positron–electron annihilation gamma-ray spectra, C1s binding energy spectra and carbon nuclear magnetic resonance (NMR) spectra, as well as information derived from graph theory. It is revealed that the Doppler-shift in the gamma-ray spectra of the hexane isomers is in the vicinity of the n-hexane molecule with small structural dependency, in agreement with the fact that the measured Doppler-shifts of other linear alkanes are in the vicinity of hexane. The present study further reveals the electronic structures of hexane isomers, which are deeply rooted into the carbon core electrons, more than mere properties in the valence space. The calculations show that the highest occupied molecular orbitals (HOMOs) of the isomers exhibit less important roles in gamma-ray spectra; whereas the electron–positron annihilation is dominated by the electrons of the lowest occupied valence orbitals (LOVOs) and other valence electrons underneath the HOMO electrons, in agreement with previous findings. The present study further reveals that the C1s binding energies of the isomers exhibit association with the nodes of the isomers using graph theory. That is, more branched carbons likely engage with larger chemical shift, which is indicated by the largest eigenvalues (LEVs) of the adjacency matrix (AM) from graph theory. The chemical shift of the carbon NMR spectra is revealed by the LEVs of the Laplacian matrix (LM) obtained from chemical graph theory.