Journal of Molecular Structure-theochem最新文献

Ab initio and density functional calculations were used to analyze the O₃–HNCO and O₃–HCNO clusters in the gas phase. Interaction of O₃ with HNCO and HCNO have been investigated at the B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) computational levels. Three isomers were found for each system in both methods. The NH⋯O, CH⋯O, O⋯O, N⋯O and C⋯O interactions are predicted in the optimized structures. The atoms in molecules (AIM) theory were also applied to explain the nature of the interaction in predicted clusters.

The assessment of the C–N bond dissociation energies is performed by using the various density functionals at 6-31+g(d,p) level. CBS-QB3 method was used to provide the theoretical benchmark values. The present results show that the three hybrid meta GGA functionals, BB1K, MPWB1K and M06 reproduce the experimental values well. M06-2X could normally overestimate the homolytic C–N bond dissociation energies. For the hybrid functionals, B3P86 and PBE1PBE can also behave almost as well as the above meta GGA functionals. Thus, they should be recommended as the most reliable method to estimate the energetic C–N bond dissociation energies.

Second-order non-linear optical (NLO) properties of dehydrogenated hydrogen cyanide borane(1) oligomers (up to dodecamers) are investigated by the Hartree–Fock, hybrid DFT (including long-range corrected functionals) and MP2 approaches. Due to one-dimensional extension of the systems the longitudinal component of the properties is addressed with focus on the electronic contributions. Direct and indirect electron correlation effects are evaluated at the MP2 level paying particular attention to the basis set effects. Unit-cell asymmetry and delocalization effects in the NLO responses are discussed in terms of the evolution of the bond-length alternation parameter, dipole moment and polarizability (reduced per unit cell) with the increasing chain length. It was found that suitable combination of the unit-cell asymmetry and electron delocalization leads to extremely large NLO response (MP2/6-311++G(d,p) value for the dodecamer is 43.7 × 10³ a.u. per unit cell) what makes the conjugated BCN oligomers (if one takes into account their thermodynamic stability) a promising material for NLO applications.

The structures and relative stabilities of C_nB₃ (n = 1–8) clusters are explored and analyzed at the CCSD(T)/6-311+G(d)//B3LYP/6-311+G(d) level. For low-lying isomers of C_nB₃ (n = 1–8), cyclic structures are more favorable in energy than branch as well as linear structures, and rings with exocyclic chains. For most isomers of C_nB₃ (n = 1–8), the structures with doublet states are lower in energy than the ones with quartet states. The lowest-energy isomers of C_nB₃ are all cyclic structures. The lowest-energy structures of C_nB₃ (n = 1–3) appear to be similar to those of pure boron clusters which have polycylic structures, while the lowest-energy structures of C_nB₃ (n = 4–8) tend to be analogous to the corresponding geometries of pure carbon, C_nB, and C_nB₂ clusters which possess single-ring structures. The most stable structures of planar C_nB₃ (n = 3–8) clusters can be derived from combining a B–C–B–C–C–B building unit and a carbon chain. Some physical properties, such as the binding energy per atom, incremental binding energy, and second order energy difference suggest that for C_nB₃ clusters, odd-n clusters are more stable than even-n clusters. Results from NBO and molecular orbital analysis illustrate that the formation of the delocalized π MOs, the σ-radial and σ-tangential MOs are favorable to the stabilization of structures for lowest-energy isomers. It is interesting to find from the valence molecular orbital and NBO analyses that for the most stable isomers of C_nB₃ (n = 1–8), the numbers of π electrons for C_nB₃ (n = 1–8) is (n + 1) with an exception of C₄B₃ (6 π electrons), suggesting that CB₃, C₄B₃ and C₅B₃ may have aromaticity, which is consistent with the results of the nucleus independent chemical shifts (NICS).

Structural and electronic properties of solid adamantane in a FCC lattice form have been investigated using density functional theory (DFT). One, two, three and four tertiary hydrogen atoms have been substituted with Na to form C₁₀H_16-nNa_n. Although, pristine adamantane shows a wide band gap and can be categorized as an insulator but, it is shown that under Na doping process, the band gap reduces and finally it become semi metallic or metallic. The same scenario in gas phase has been calculated and the results are compared with the lattice phase.

A density functional theory (DFT) study concerning the atomistic detail of the interaction between surfactant molecules and II–IV semiconductor nanoparticles is presented. As a corollary effort, we investigated the adsorption of H₂O, NaOH and KOH on the (II–IV)_n nanostructure with n = 12, 48, 60 under the vacuum and solvent conditions. Different solvent environments like water, methanol and ethanol were considered using a conductor-like screening model (COSMO) method. Results showed that the adsorption reaches a fairly strong due to electrostatic interactions. The strength of interaction is increased in the order of anionic molecule (strong base) > anionic molecule (weak base) > non-ionic molecule, which explains the experimental results clearly. Moreover, the system was found to be more stable under solvent than vacuum environments.

Reptation quantum Monte Carlo (RQMC) is a Markov chain and Metropolis-Hastings type algorithm. In this paper RQMC-variants are implemented for the ground-state of water molecule, whereby adjustments are made to the Metropolis decision to utilize the trial density at strategic reptile locations and to impose microscopic reversibility on the electron moves. Our objective is to identify the adjustment which gives one-electron properties of the water molecule which best agree with highly-accurate determinations in the literature. Other than for the energy, RQMC, when implemented with a single-$\zeta$ STO guiding function, does not significantly improve the variational estimates. For a double-$\zeta$ STO case, the RQMC-HT variant that adjusts the Metropolis decision at where new scales are being added clearly provides the most precise estimates with negligible bias. For double-$\zeta$ and triple-$\zeta$ cases, each with polarization, RQMC-HT still outperforms the others, but, as expected, to a much lesser extent.

Structure and vibrational characteristics of biologically important 3,7-dihydro-purine-2,6-dione (xanthine) and its 7- or 9-substituted methyl derivatives derived from the second order MØller–Plesset perturbation theory have been analyzed using the molecular electron density (MED) topography. Successive substitution of methyl group at 9 position engender carbonyl stretching vibrations at higher wavenumber compared to those in X₇ tautomer along the series. The C–O bond distance in 7-substituted xanthine tautomers correlate well to electron density at the bond critical point (bcp) in the MED topography.

Histidine as a natural amino acid is found to be biologically important and is known to function as a nucleophile or enzyme co-factor, or in proton transfer process. The properties of gaseous aromatic amino acid histidine depend on the structural forms it may take in gas-phase. Ab initio method has been used to characterize the gas-phase conformer/tautomers of histidine. Wide range of possible structures for histidine was surveyed at the MM level, and then the geometries of the unique conformers were refined at the B3LYP/6-311++G (d,p) levels.

At this theoretical level, 25 conformers were located for both tautomers of histidine i.e., His [N^πH] and His [N^τH]. The MM level provides a poor description of the relative energies. Calculations at the B3LYP/6-311++G (d,p) level represent a significant improvement. Ab initio dipole moments are reported for all the conformers/tautomers. The results are compared to previous studies of amino acids and are analyzed in terms of intramolecular hydrogen-bonding interactions and Newman projections. In addition, we calculated the infrared frequencies and intensities of the most stable structures in order to assist in the assignment of hydrogen-bonding. Furthermore, Ramachandran backbone potential energy surfaces (PES) of 25 conformers of His [N^πH] and His [N^τH] tautomers of histidine were considered.

The stationary points characterizing the potential energy profile of the various conformers/tautomers of histidine were investigated by the same density functional theory B3LYP/6-311++G (d,p). Minima and transition states characterizing the energetic paths for the interconversion of various structures of histidine were explored in detail.

The influence of spatial confinement on the electric properties: dipole moment (μ), dipole polarizability (α), first hyperpolarizability (β) and second hyperpolarizability (γ) of the LiH molecule was studied. The confining model potential is assumed in the form of a penetrable spherical box. The properties in question were calculated within the finite field approach, with an accurate, explicitly correlated wave function. We found all studied properties diminished under confinement.