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.

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.

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.

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.

The origin of the optical properties of the firstly reported stable luminescent $\left[\text{Cu}\right(\text{PP}{)}_2{]}^{+}$ complex $\left[\text{Cu}\right(\text{dppb}{)}_2{]}^{+}[\text{dppb}=1\text{,}2-\text{bis}(\text{diphenylphosphino}\left)\text{benzene}\right]$ is investigated using the exchange–correlation functional PBE0. The choice of the basis set used is discussed and a comparison with the results obtained by other functionals is performed. The role played by the bisphosphine ligands within the complex is elucidated by considering the electronic properties of the ligand alone to evidence how both the geometrical changes and the electronic interactions, induced by the inclusion of the metal cation, affect the electronic behavior of the whole system. The NBO analysis shows how the aryl groups of the ligands act as a reservoir of electrons within the complex. The electronic excitations of both the complex and of the ligand, calculated by including the solvation effects, allow to assign the lowest energy absorption broad band, recorded in CH₂Cl₂ solution. The peculiar contribution of the phosphorus atoms to the description of the high occupied MOs and the participation of the copper cation to the description of the lowest singlet excited state, is pointed out. The origin of the observed phosphorescence of the complex is attributed to a triplet state, whose SOMO is characterized by the contributions of the valence 4s and of the Rydberg 5s AOs of the metal cation, along with the lone pair orbitals of the P atoms.

A computational study predicts a number of unusual Be- and Mg-containing compounds with general formula X–M–N₂–Li (X = F, Cl, Br; M = Be, Mg). Generally, the X–Be–N₂–Li species were found to be energetically stable with respect to the LiX + Be + N₂ fragments and with respect to the LiBeX + N₂ fragments, whereas the Mg-containing species by comparison were found to be unstable. Harmonic vibrational frequencies and various bonding parameters were also computed and found useful in rationalizing the relative stabilities and trends (for varying X) of these unusual compounds. The high stability of X–Be–N₂–Li is thought to be due mainly to strong electrostatic interactions between the constituent atoms and especially the Be atom in its +2 valence state.

Alkali metal amides may exist in solution, the solid phase, and even the gas phase. Based on a theoretical model of a Li₃N system which adsorbs and desorbs two hydrogen molecules, we examine the possible pathways of the ${\text{Li}}_3\text{N}+2{\text{H}}_2\leftrightarrow {\text{LiNH}}_2+2\text{LiH}$ reversible reaction. The dehydrogenation process can be separated into two-step reactions, ${\text{Li}}_2\text{NH}+\text{LiH}\to {\text{Li}}_3\text{N}+{\text{H}}_2$ (−9.5 kcal/mol exothermic) and ${\text{LiNH}}_2+\text{LiH}\to {\text{Li}}_2\text{NH}+{\text{H}}_2$ (+0.7 kcal/mol endothermic). Along the reaction pathway, two intermediates and a transition state for each reaction were found in our ab initio molecular orbital calculations at the MP2 and CCSD(T) levels of theory. A total of two H₂ molecules can be stored and released at normal temperature and pressure if there are means to substantially raise the energy of the two stable intermediates. Reaction energy profiles from our calculations support the much higher temperature of the first step reaction in experiment.