Journal of Molecular Structure-theochem最新文献

In this investigation we discussed one possible mechanism of the photoinduced cyclodimerization of two malonaldehyde molecules to form the “face-to-back” cyclodimer. Linear interpolation in internal coordinates approach was applied to study the excited-state relaxation mechanisms at the TD DFT level with aug-cc-pVDZ basis functions. It was found that the formation of the cyclodimer occurs through the first ¹ππ∗ excited state which has a charge transfer character. We also found a radiationless relaxation path of the ¹ππ∗ excited state mediated by a S_o–S₁ conical intersection.

A simple formula for the standard enthalpy of perfect-gas molecules, $\Delta H_f^{\circ }={\sum }_{K}F\left(K\right)+\mathrm{ZPE}+H_T-H_0-{\sum }_{k<l}{\epsilon }_{\mathrm{kl}}-\left(\mathrm{CNE}-E_{\mathrm{nb}}^{\mathrm{KL}}\right)$, is illustrated by novel applications and over 100 examples and comparisons with experimental results. The propounded model views molecules as constructs of chemical groups, K, L, … , etc. (such as CH₃, COOH, for example) characterized once and for all, independently of their belonging to one or another host, by fixed numbers $F\left(K\right)\text{,}F\left(L\right)\text{,}\dots$, etc. ZPE + H_T − H₀ is the familiar sum of zero-point + heat-content energy, ε_kl is the intrinsic energy (at 0 K) of the bond connecting K and L, CNE (for Charge Neutralization Energy) takes care of the fact that K, L, … , are usually not electroneutral in the host molecule, and $E_{\mathrm{nb}}^{\mathrm{KL}}$ measures nonbonded interactions summed over all pairs of groups K and L. New parameters, $F\left[\mathrm{CH}\right(X\left)\right]$ with X = CH₃, NH₂, OH, CHO, COOH, Cl, Br and SH, are described and an amazingly simple formula for carbon–hydrogen bonds, giving ${\epsilon }_{\mathrm{CH}}^{\ast }={\epsilon }_{\mathrm{CH}}+\mathrm{CNE}$, turns out to be most useful any time a fragment CH(X) is bonded to one hydrogen atom at least.

In this paper, we calculated a series of halogen-bonded complexes. The halogen bond donor is CF_nH_3−nCl, and the halogen bond acceptors are NH₃, H₂O, H₂S, and Br⁻. Ten stable halogen-bonded complexes were obtained and the C–Cl bond length was contracted in all of these complexes. We carried out AIM and NBO analysis under the MP2/aug-cc-PVDZ optimized structures. The variation of the electron density at the bond critical point of C–Cl bond correlates well with Δr(C–Cl). A balance among intra- and inter-hyperconjugation and rehybridization determined the contracted C–Cl bond.

The anticoagulent drug warfarin exhibits chameleon-like isomerism, where the environment-dependent composition of the ensemble of structures greatly influences its bioavailability. Here, the mechanism of conversion between the major isomeric forms is studied. The dramatic differences in transition state energies, as determined by density functional calculations, highlight the necessity for the involvement of intermolecular interactions in the key proton transfer step. A viable model for the mechanism underlying the isomerization reactions is presented.

The gas phase enthalpies of formation of C₁–C₄ mononitroalkanes were calculated using different multilevel (G1, G2, G3, G3B3, CBS-QB3) and density functional theory (DFT)-based B3LYP techniques. The enthalpies of the C–N bond dissociation of these nitroalkanes were also calculated. The calculated values of the formation and reaction enthalpies were compared with available experimental data. It was found that the G3 and G3B3 procedures gave accurate results for the formation enthalpy of nitroalkanes and radical products. The agreement of the CBS-QB3 calculations with experiment is also satisfactory, whereas less accurate than G3 and G3B3 estimations. The G3 and G3B3 multilevel techniques showed good results for the reaction enthalpies of the C–N bond dissociation.

The dynamic reaction pathways after passing the initial barrier for the reaction of atomic oxygen radical anion (O⁻) with ethylene (CH₂CH₂) have been investigated with Born–Oppenheimer molecular dynamics (BOMD) simulations. The BOMD simulations initiated at this [O⋯H⋯CHCH₂]⁻ barrier on the exit-channel potential energy surface (PES) reveal several different types of dynamic reaction pathways leading to various anionic products. In particular, as the energy added on the transition vector of the [O⋯H⋯CHCH₂]⁻ transition state increases remarkably, the OH⁻ and CH₂CH become the dominant products instead of the CH₂CHO⁻ and H. As a result, animated images are displayed and more extensive reaction mechanisms are illuminated for the title reaction from the perspective of the dynamic reaction pathways.

The interactions of the Br₂ with hydrogen halide have been investigated by performing calculations at the second-order perturbation theory based on the Møller–Plesset partition of the Hamiltonian with the Sadlej PVTZ basis set. The X–Br type geometry and hydrogen-bonded geometry are investigated in these interactions. The calculated interaction energies show that the X–Br type structures are more stable than the corresponding hydrogen-bonded structures. To study the nature of the intermolecular interactions, symmetry-adapted perturbation theory (SAPT) calculations were carried out and the results indicate that the X–Br interactions are dominantly electrostatic and dispersion energy in nature, while dispersion energy governs the hydrogen bonding interactions.

The H-abstraction reactions of CHX⁻ (X = halogen) with CH₂Cl₂ have been investigated in detail using ab initio theoretical method. Optimized geometries and frequencies of all stationary points on PES are obtained at the MP2/6-311++G(d, p)/RECP level of theory, and then the energy profiles are refined at the QCISD(T)/6-311++G(3df, 2p)/RECP by using the MP2/6-311++G(d, p)/RECP optimized geometries. Our calculated findings suggest that the reactivity of the title reactions presents an increasing trend CHI⁻ + CH₂Cl₂ < CHBr⁻ + CH₂Cl₂ < CHCl⁻ + CH₂Cl₂ < CHF⁻ + CH₂Cl₂. This result was further analyzed by the NBO charges, the Activation Strain model and the correlations of activation barrier with both PA and IE, respectively. As an additional study, it is found that the entropy has little effect on the reactivity of the H-abstraction reactions.

In order to understand cellulose pyrolysis mechanism, the pyrolysis of β-d-glucopyranose was investigated using density functional theory methods at B3LYP/6-31++G(d,p) level. Four possible pyrolytic pathways were proposed and geometries of reactants, transition states, intermediates and products were fully optimized. In pathway 1, the products are glycolicaldehyde, acetol, CO and H₂O; in pathway 2, the products are 5-hydroxymethylfurfural and H₂O; in pathway 3, the products are levoglucosan and H₂O; in pathway 4, the products are 3,4-anhydroaltrose and H₂O. The standard thermodynamic and kinetic parameters in each reaction pathway were calculated at different temperatures. The calculation results show that all reactions are endothermic and can take place spontaneously when reaction temperature exceeds 550 K. The changes of Gibbs free energies and the activation energies of rate-determining steps in reaction pathways 1 and 2 are less than that in reaction pathways 3 and 4. The activation energy of rate-determining step in pathway 1 is 297.0 kJ/mol and the activation energy of rate-determining step in pathway 2 is 284.5 kJ/mol. Based on thermodynamics and kinetic analysis, reaction pathways 1 and 2 are major pyrolysis reaction channels and the major products of β-d-glucopyranose pyrolysis are low molecular weight compounds such as glycolicaldehyde, 5-hydroxymethylfurfural, acetol and CO. The above results are in accordance with the related experimental results.

The reaction mechanism of atomic oxygen radical anion (O⁻) with pyridine (C₅H₅N) has been investigated at the G3MP2B3 level of theory. Three different entrance potential energy surfaces are explored, respectively, as atomic oxygen radical anion attacks γ-, β- and α-H atoms of pyridine. Possible thermodynamic product channels are examined subsequently. Based on the calculated G3MP2B3 energies and optimized geometries of all species for the title reaction, it has been demonstrated that the oxide anion formation channel is dominant, and the C₅H₃N⁻ + H₂O channel is also favorable in thermodynamics, whereas the H-abstraction and H⁺-abstraction channels are inaccessible at room temperature. The present conclusions are consistent qualitatively with the previous experimental results. The secondary reactions of the anionic products are expected to be responsible for the contradiction of branching ratios between present calculation and previous experiments.