Journal of Theoretical and Computational Chemistry

The heat capacities and Joule–Thomson coefficients have been evaluated using three known analytical expressions for radial distribution functions (RDFs). Using such approach not only tests the power of distribution functions theory in predicting the heat capacities and Joule–Thomson coefficients, but also specifies better expressions in determining these properties. To calculate these quantities, the variation of RDF with density and temperature is required. Therefore, we should have analytical expressions which explicitly present RDF as a function of temperature, density, and interparticle distance. It is shown that if an expression is used which properly presents RDFs as a function of interparticle distance, density, and temperature, it is possible to calculate heat capacities and Joule–Thomson coefficients from distribution function theory.

The interaction of ladder polyethers of marine origin, like ciguatoxin 3C and brevenal, as well as hypothetic ent-brevenal, with the human voltage-gated Kv1.5 potassium ion channel is investigated in this work using homology modeling, automated docking, and energy scoring from molecular dynamics (MD) simulations. A 3D homology model of the pore region of the Kv1.5 channel, previously developed from the 2.9 Å resolution crystal structure of the mammalian Kv1.2 channel — which has a very similar pore sequence — is used here. While ciguatoxin 3C did not enter the pore, both brevenal and ent-brevenal were found into the pore, the latter one with the best score. Binding is attended by notable strain in the ligands, and the corresponding energy increase was evaluated for ent-brevenal by self consistent field (SCF) and density functional theory (DFT) procedures. Egress of ent-brevenal from the pore, as a microscopical reversal of the ingress, was investigated by a smart form of biased MD simulations. While this study indicates ample room and attractive interactions for both brevenal and its enantiomer into the pore, whether these molecules will be found to inhibit voltage-gated potassium ion currents depends upon the barriers in the real system to access the pore, with their thermodynamic and kinetic requirements.

A DFT/B3LYP study was performed to calculate ¹⁵N chemical shielding tensors in (benzamide)_{n = 1-6} clusters. We found that N–H⋯O hydrogen bonds around the benzamide molecule in crystalline lattice have significant influences on the ¹⁵N chemical shielding tensors. For (benzamide)_n clusters, the n-dependent trend in ¹⁵N chemical shielding appears to be correlated with cooperative effects in R_[N–H⋯O] bond distance. Natural bonding orbital (NBO) analysis was used to rationalize the chemical shielding results in terms of charge delocalization effects in the benzamide clusters. This suggests that ¹⁵N chemical shielding measurements can provide a useful probe of electron delocalization phenomena in both gaseous and condensed media.

The gas-phase identity bimolecular nucleophilic substitution reactions, Cl^- + CH₃ Cl → ClCH₃ + Cl^- and Cl^- + SiH₃Cl → ClSiH₃ + Cl^-, are investigated in terms of the ab initio method, potential acting on an electron in a molecule (PAEM) and molecular face (MF) theory. The computations have been performed at the CCSD(T)/aug-cc-pVTZ//MP2/6-311+G(3df,3pd) and CISD/aug-cc-pVDZ level. Based on the ab initio calculation, according to the PAEM theory, the strength of a chemical bond during forming or rupturing may be characterized by the D_pb, which is a new physical quantity relating to the barrier height of the PAEM along a chemical bond. According to the MF theory, the interesting pictures of electron transfer and interpolarization effect between the reactants are clearly demonstrated to provide visualized spatial changing features of the MF for the title reactions along the IRC routes. The reason why [Cl⋯CH₃⋯Cl]^- is a high-energy transition state is also analyzed in comparison with the stable low-energy intermediate [Cl⋯SiH₃⋯Cl]^-.

We present reaction probabilities, branching ratios and vibrational product quantum state distributions for the reaction O(¹D)+HCl → OH+Cl (OCl+H), Boltzmann averaged over initial rotational quantum states at a temperature of 300 K and also for the deuterium isotopic variant. The quantum scattering dynamics are performed using the potential energy surfaces for all three contributing electronic states. Comparisons are presented with results computed using only the ground electronic state potential energy surface, with results computed using only the j = 0 initial rotational state and also with results obtained using an equal weighting for the lowest 10 rotational states. Inclusion of the higher initial rotational states significantly changes the form of the reaction probability as a function of collision energy, reducing the threshold for reaction on the 1A" and 2A' excited electronic states. We found that the combined inclusion of higher initial rotational states and all three contributing electronic states is crucial for obtaining a branching ratio that is within the range and trend given by experiment from our J = 0 calculations. Isotopic effects range from tunnelling effects for the hydrogen variant and enhancement of reactivity for the production of OD on the excited electronic states.

This article gives a trajectory-following method for the steady state of chemical reaction rate equations. In order to avoid wasting unnecessary computing time during the steady-state phase and get roughly accurate solutions during the transient-state phase, this method is realized via adopting the semi-implicit Euler formula as the stepping direction and adaptively adjusting the time-step size by an analogous trust-region technique. Under some standard assumptions, its global convergence analysis and local superlinear convergence analysis are also given. Finally, some numerical experiments of this method, in comparison with the traditional optimization methods and ordinary differential equation methods, are reported. The numerical results show that this trajectory-following method is a promising solution for this class of problems.

Using quasi-classical trajectory (QCT) method, the vector correlation between products and reagents for the exothermic reaction Ba + CH₃I → BaI + CH₃ has been studied on the extended Lond–Eyring–Polanyi–Sato (LEPS) potential energy surface (PES) at three collision energies of 1.6, 3.3, and 5.6 kcal/mol. The P(θ_r) distribution of the products describing the k-j' correlation and the dihedral angle distribution P(ϕ_r) describing k-k'-j' correlation are calculated in center-of-mass (CM) frame. Four polarization dependent generalized differential cross-sections (2π/σ)(dσ₀₀/dω_t), (2π/σ)(dσ₂₀/dω_t), (2π/σ)(dσ₂₂₊/dω_t), and (2π/σ)(dσ_21-/dω_t) have also been presented in the CM frame as well. The results indicate that the product rotational angular momentum j^' is not only aligned, but also oriented along the direction perpendicular to the scattering plane. In addition, the alignment and the orientation of the BaI product rotational angular momentum depend very sensitively on the collision energy.

Theoretical insight into the mechanism of C8 adducts formation in a series of complicated carcinogenic reactions has been provided in a previous work. However, two important issues involved in this mechanism still need to be elucidated in detail. Hence, in this paper, we first present a new theoretical model to study the direct formation mechanism of C8 adduct. It is found that this model can well reflect the actual interactions in the real carcinogenic reactions. Thus, a better theoretical model to simulate other properties of these complicated reactions is found using ab initio and density functional theory (DFT) methods. Second, we simulate the formation process of C8 adduct in this new theoretical model using ABEEM/MM-MD method. According to the MD study, we approve that the higher aqueous-phase activation energy for transition state in this kind of reaction contributes to weaker interactions between central sites of reaction and water compared with those for reactants. This study once more supports the mechanism of formation of C8 adducts in the actual carcinogenic reactions where arylnitrenium ions directly attack at C8 positions of nucleoside bases in DNA.

In this paper, the two-dimensional (2D) site and the three-dimensional (3D) cube representations [Sun MT, J Chem Phys124: 054903, 2006] have been further developed to study the charge transfer during excited-state relaxation. With these newly developed representations, we theoretically investigate the excited-state intramolecular electron transfer (ESIET) in enol excited-state geometry relaxation, and ESIET coupled with excited-state intramolecular proton transfer (ESIPT) in phototautomerization (in enol to keto transformation). The energy levels of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of HBODC in enol and keto absorption and fluorescence are compared to understand photoinduced ESIET and ESIPT process. The excited regions of molecule (where arrangement of electron density takes place during excited-state relaxation) are located with 2D site representation. 3D cube representations visualize the character of charge transfer (CT) in those regions. Results of the research indicate that the ability of charge transfer during enol excited-state geometry relaxation is much stronger than that in phototautomerization.

The reaction mechanism of CuI-catalyzed formation of ethyl 2-phenylacetoacetate by arylation of ethyl acetoacetate has been investigated by density functional theory (DFT) using Becke's three-parameter nonlocal exchange functional and the Lee, Yang, and Parr nonlocal correlation functional (B3LYP). The geometries of the reactants, intermediates, transition states, and products have been optimized and verified by means of vibration frequency calculations. According to our assumption, this reaction can be divided into two stages. The rate-determining step is found to be the 3 → 4-TS procedure, which is the first procedure of stage 1. The low energy barrier of 39.85 kcal/mol indicates that this reaction can be carried out, which is in accordance with the experimental facts. For comparison, we have investigated the reaction mechanism of the same chemical reaction without CuI catalyst, whose energy barrier of rate-determining step is 212.76 kcal/mol higher than that with CuI catalyst. This fact suggests that CuI catalyst accelerates the reaction by remarkably lowering the energy barrier. The solvation effects on the barriers of the reaction are important. But the energetic order in DMSO solvent seems to be almost the same as that in gas-phase, which indicates that our conclusion achieved in gas-phase is believable. Our findings reveal the microscopic catalytic mechanism of CuI and are in agreement with the experimental facts.