Journal of Molecular Structure-theochem最新文献

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.

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.

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.

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.

We report a theoretical work on the electronic excitation spectrum of two heparins like disaccharides. Time dependent density functional theory (TD-DFT) calculated spectra for these sulfated and carboxylated disaccharides are presented. The orbitals involved in the observed electronic excitations are analyzed. ππ∗ excitations involving the acidic functions lead to a strong optical absorption of these compounds between 270 and 220 nm, which is in agreement with experimental spectra reported previously [16].

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.

The ground and three low-lying excited electronic states of the GeO molecule, including Σ⁺, Σ⁻ and Π symmetry with singlet and triplet spin multiplicities, have been investigated employing the full valence complete active space self-consistent field (CASSCF) method followed by the highly accurate valence internally contracted multireference configuration interaction (MRCI) approach. The potential energy curves (PECs) of these states have been calculated with the cc-pV5Z basis set. And the effect on the PECs by the relativistic corrections has been taken into considerations. The way to consider the relativistic corrections is to use the second-order Douglas–Kroll Hamiltonian approximation. For the four electronic states, the spectroscopic parameters (T_e, D₀, D_e, R_e, ω_e, ω_ex_e, α_e and B_e) of 10 isotopes (⁷⁰Ge¹⁶O, ⁷²Ge¹⁶O, ⁷³Ge¹⁶O, ⁷⁴Ge¹⁶O, ⁷⁶Ge¹⁶O, ⁷⁰Ge¹⁸O, ⁷²Ge¹⁸O, ⁷³Ge¹⁸O, ⁷⁴Ge¹⁸O, ⁷⁶Ge¹⁸O) have been determined. The spectroscopic parameters have been compared with those of previous investigations reported in the literature, and excellent agreement has been found between the present results and the available data. With the PECs determined here, the first 30 vibrational states for each species are computed for the four electronic states when the rotational quantum number J equals zero (J = 0). The vibrational level G(υ), inertial rotation constant B_υ and centrifugal distortion constant D_υ are determined when J = 0, which are in excellent agreement with the available experimental data. The ro-vibrational levels have been calculated for these low-lying electronic states of 10 isotopes when J ⩽ 29. And the transition lines are evaluated according to the transition rule. Comparison with the available experimental observations shows that the present ro-vibrational levels are reliable.

We are presenting a density functional calculation utilizing Beck three parameters hybrid, correlation functional of Lee, Yang and Parr (B3LYP), MP2 and G2MP2 levels of theory to probe the influence of R1, R2 and R3 substitutions on 3-mercapto-propenethial, estimating (i) The π-electron delocalization parameter (Q) as a geometrical indicator of a local aromaticity, (ii) the geometry-based HOMA index and (iii) intramolecular hydrogen-bond strength. The effects of F, H, Cl, CH₃, OH, and NH₂ as substituents are examined. Furthermore the topological properties of the electron density distributions for S–H⋯intramolecular bridges are analyzed in terms of the Bader theory of atoms in molecules (AIM). The electron density (ρ) and Laplacian (∇²ρ) properties, estimated by AIM calculations, indicate that S⋯H bond possesses low ρ and positive ∇²ρ values which are in agreement with electrostatic character of the HBs, whereas S–H bonds have covalent character (∇²ρ < 0). Natural population analysis data, the electron density and Laplacian properties, as well as, υ_(S–H) and γ_(S–H) have been used to evaluate the hydrogen bonding interactions.