Journal of Molecular Structure-theochem最新文献

In this paper, we carried out the calculations to study the dynamics properties of Sr+CH₃Br reaction system by using quasi-classical trajectory (QCT) method, based on the extended London-Eyring-Polanyi-Sato (LEPS) potential energy surface (PES). We have obtained the vibrational distribution, rotational distribution, reaction cross section and the product rotational alignments. The calculated rotational alignments are in good agreement with the experimental ones [3]. When the collision energy is 0.57 eV, the peak values of the vibrational and rotational distributions are located at v = 7 and j = 70, respectively. The reaction cross sections decrease with the increasing collision energy when the collision energy changes from 0.1 to 1.0 eV.

Under the generalized gradient approximation (GGA), the magnetic and electronic properties have been investigated for a Fe atom chain wrapped in armchair (n,n) carbon nanotubes (CNTs) (2 ≤ n ≤ 6)) by using the first-principles projector-augmented wave (PAW) potential within the density function theory (DFT) framework. After simply moving the Fe atom chain parallel to tube axis to make Fe atom locates on the perpendicular of the tube wall through the center of a hexagon by carbon–carbon bonds, all Fe@(n,n) systems including the narrow Fe@(2,2) and Fe@(3,3) systems exhibit metallic character and the Fe atom chain maintains its magnetic moment. Total density of states (DOS) and projected densities of states (PDOS) analyses show that the spin polarization and the magnetic moment of Fe@(n,n) systems come mostly from the Fe atom chain. And with increasing n and thus tube diameter, the difference between the minority spin and the majority spin at the Fermi level increases for the PDOS onto Fe atom and thus for the DOS of Fe@(n,n) systems. This trend is also indicated quantitatively by the magnetic moment on Fe atom and spin polarization for Fe@(n,n) systems. The higher magnetic moment and spin polarization of the Fe@(6,6) system show it can be used as magnetic nanostructure possessing potential current and future applications in permanent magnetism, magnetic recording, and spintronics.

We report the molecular mechanism of protein–RNA complex stabilization based on the electronic state calculation. Fragment molecular orbital (FMO) method based quantum mechanical calculations were performed for neuro-oncological ventral antigen (NOVA)–RNA complex system. The inter-molecular interactions and their effects on the electronic state of NOVA were examined in the framework of ab initio quantum calculation. The strength of inter-molecular interactions was evaluated using inter-fragment interaction energies (IFIEs) associated with residue–RNA base and residue–RNA backbone interactions. Under the influence of inter-molecular interactions, the change of electronic state of NOVA upon the complex formation was examined based on IFIE values associated with intra-NOVA residue–residue interactions and the change of atomic charges by each residue. The results indicated that non-specifically recognized bases contributed to the stability of the complex as well as specifically recognized bases and that the secondary structure of NOVA was remarkably associated with the change of electronic state upon the complex formation.

Results of B3LYP/6-31+G(d,p) calculations are reported. Special emphasis is put on the effect of the environment on relative stability and structures of different isomers and tautomers of methylamino- and phenylamino-substituted cyclic azaphospholine, oxaphospholine and thiaphospholine in gas and aqueous phases. In the gas phase, the imino forms are found to be the most stable species for the cyclic azaphospholines and thiaphospholines, whereas for oxaphospholines, the amino species are predicted to be more stable. The calculations in the aqueous media were done by considering two different models, i.e., the PCM–SCRF and the Microsolvated/SCRF model. It is found that solvation shifts the stability towards the amino forms, except for the phenyl-substituted cyclic azaphospholine and thiaphospholine, for which the imino forms are more stable in solution. The molecular geometries change only little when going from the gas phase to the aqueous phase. The stability in gas phase and in PCM–SCRF is attributed to the presence of intramolecular hydrogen bonding. In the Microsolvated/SCRF model, the presence of intermolecular hydrogen bonds affects the relative stability of tautomers and isomers.

Density-functional theory (DFT) and Marcus charge transport theory were employed to investigate the hole transport property of N,N′-diphenyl-N,N′-bis(3-methylphenyl)-(1,1′-biphenyl)-4,4′-diamine (TPD) which is a prototype of good hole-transporting materials. Using an incoherent transport model we calculated its hole mobility (μ). Both reorganization energy and electronic coupling, especially the electronic couplings are considered and calculated in detail. The factors influencing its electronic coupling are revealed. It has high hole transport efficiency (μ = 1.26 × 10⁻² cm²/(V s)) and the reason was explained in terms of the spatial extent of the frontier orbitals.

The kernel energy method (KEM) provides a way to calculate the ab initio energy of very large biological molecules. The results are accurate, and the computational time reduced. However, by use of a list of double kernel interactions a significant additional reduction of computational effort may be achieved, still retaining ab initio accuracy. A numerical comparison of the indices that name the known double interactions in question, allow one to list higher order interactions having the property of topological continuity within the full molecule of interest. When, that list of interactions is unpacked, as a kernel expansion, which weights the relative importance of each kernel in an expression for the total molecular energy, high accuracy, and a further significant reduction in computational effort results. A KEM molecular energy calculation based upon the HF/STO3G chemical model, is applied to the protein insulin, as an illustration.

The gas-phase reactions of fluorocarbon compounds CH_4 – nF_n (n = 1–3) with Pt (³D, ¹S) have been systematically explored via density functional theory (DFT) in order to investigate the mechanisms of these reactions. The results indicate that a reaction of CH₃F with Pt (³D, ¹S) experiences a rearrangement process to generate counterintuitive production (CH₂F−PtH). CH₂F₂ and CHF₃ activation by Pt (³D, ¹S) yields high-oxidation-state complexes with carbon–metal double bonds. Moreover, the attack of platinum atoms on fluorine atoms in different fluorocarbon compounds involves intersystem crossing (ISC) between triplet and singlet state Potential Energy Surfaces (PESs). The crossing points (CPs) have been located by the intrinsic reaction coordinate (IRC) approach used by Yoshizawa et al. and corresponding minimum energy crossing points (MECPs) obtained by the mathematical algorithm proposed by Harvey et al. have also been used. Additionally, possible spin inversion processes are discussed using spin–orbit coupling (SOC) calculations.