Journal of Theoretical and Computational Chemistry

In this work, the product polarization characteristics are reported for the reaction F + LiH (v = 0 - 2, j = 0) → LiF + H at the collision energy of 35 kcal/mol, by using the QCT method on the Aguado–Paniagua-potential energy surface (see Aguado et al.). The distribution of P(θ_r) which represents the K (reagent relative velocity vector) and J′ (product rotational angular momentum vector) correlation, the dihedral angle distribution of K-K′ (product relative velocity vector)-J′ P(φ_r), the angular distribution P(θ_r, φ_r) and the four polarization-dependent differential cross sections (2π/σ)(dσ₀₀/dω_t), (2π/σ)(dσ₂₀/dω_t), (2π/σ)(dσ₂₂₊/dω_t), (2π/σ)(dσ_21-/dω_t) in each initial state are presented and discussed.

Time-dependent density functional theory (TDDFT) and second-order coupled cluster method with resolution-of-the-identity approximation (RICC2) were used to investigate the photolysis dynamics of 9-fluorenol (FOH) in alcohols. In this work, a novel mechanism for the accelerated photolysis dynamics of FOH in alcohols is proposed for the first time. The two hydrogen bonds present different effects in the dissociation process of C₉–O bond in MeOH⋯FOH⋯MeOH trimer: formation of hydrogen bond MeOH⋯FOH could weaken the C₉–O bond, while, hydrogen bond FOH⋯MeOH fastens the bond. Moreover, the thermodynamic equilibrium can be accomplished in both ground and excited states between hydrogen-bonded complexes, since the hydrogen bond reorganization occurs in hundreds of femtosecond upon the excitation. The excited-state potential energy (PE) curves along C₉–O bond have been optimized in S₁ state. The cleavage of C₉–O bond upon the photoexcitation would be facilitated effectively in MeOH⋯FOH dimer. This leads the thermodynamic equilibrium between hydrogen-bonded complexes leaning to the side of MeOH⋯FOH dimer to quench the fluorescence. Therefore, the photolysis of 9-fluorenol in alcohols can be facilitated effectively by MeOH⋯FOH hydrogen bond via excited-state hydrogen bond reorganization. Additionally, the excited-state hydrogen bond reorganization is also the rate-controlling step in photolysis of FOH in alcohols, since there is no barrier in the PE curve of MeOH⋯FOH dimer.

We have performed a systematic density functional study on the ground-state electronic structure and excited states of a representative D-σ-A dyad, i.e. EDT-TTF-Im-F₄TCNQ π-radical, in vacuo and in different conventional solvents (toluene, THF, DMF and DMSO) by using some popular hybrid density functionals (B3LYP, M05, M05-2X, PBE0 and BMK). It has been shown that the M05 and B3LYP functionals perform the best in predicting the intramolecular charge-transfer (ICT) pertaining to both the ground state and excited states of the dyad. The amphoteric dyad is liable to solvent-promoted ICT from its EDT-TTF-Im donor (D) to F₄TCNQ acceptor (A), adopting a charge-unseparated ground state D-A^• in vacuo, a partially zwitterionic ground state [D-A]^• in nonpolar toluene solvent, and a fully zwitterionic ground state D^•+-A^- in such polar solvents as THF, DMF and DMSO. Owing to its solvent-dependent chameleon ground state, excited states of the dyad in solvents also exhibit remarkable dependence on solvent polarity, as revealed by TDDFT calculations. Furthermore, cluster model calculations revealed that intermolecular charge-transfer readily occurs between the dyads, accounting for the observed zwitterionic charge state in solid state and solid-state semiconductivity.

A theoretical study of the reactivity and regioselectivity of the addition of the triplet oxygen atom O(³P) to a series of unsymmetrical substituted alkenes has been performed at the PMP2/6-311++G (d,p) level of theory. Two reaction pathways, namely, the addition to the substituted carbon atom (α-site) and addition to the non-substituted carbon atom (β-site), have been studied. Our calculations show that the β-addition products are kinetically more favored; whereas the α-addition products are found to be thermodynamically more stable. The regioselectivity (α vs. β) of the addition of the O(³P) to the carbon–carbon double bond is predicted by means of the relative energies of the localized transition states and also by the calculation of spin densities of the ³ππ* states of reactants and Fukui indices corresponding to the radical attack to alkenes. Our calculations are in good agreement with experimental outcomes.

We present a new three-dimensional potential energy surface for Xe–CO₂ including the Q₃ normal mode for the υ₃ antisymmetric stretching vibration of the CO₂ molecule. Two vibrationally adiabatic potentials with CO₂ in both the ground (υ₃ = 0) and the first excited (υ₃ = 1) states are generated by the integration of this potential over the Q₃ coordinate. Each potential is found to have a T-shaped global minimum. The radial DVR/angular FBR method and the Lanczos algorithm are employed to calculate the rovibrational energy levels. The calculated band origin shifts, microwave and infrared spectra based on the two averaged potentials are in good agreement with the available experimental data.

In this paper the Szeged and revised Szeged indices of an infinite family of IPR fullerenes with 50 + 10n carbon atoms and D_5h point group symmetry are computed. It seems that some chemico-physical properties of these fullerenes are derived from the mentioned topological invariants.

We performed the nonadiabatic time-dependent wave packet calculation on the four diabatic potential energy surfaces, which have the different barrier height, to investigate the contribution of the noncollinear channel for the F (²P) + H₂/D₂ (v = j = 0) reactions. The reaction probabilities, integral cross-sections, and rate constants are presented. The results indicate that the probabilities as the function of the collision energy have an obvious translation. The reactive activity of the reactions comes from the noncollinear reactive channel. The bent barrier height would decrease the reactive activity. The integral cross-sections are in the order of AWS < LWA-5 < LWA-78 ≈ MASW, which is opposite to that of the bent barrier height. At the lower temperature, the difference of the rate constants is unambiguous. As the temperature increases, the difference reduces. At the higher temperature, the rate constants computed on the four potential energy surfaces are close.

As the only metabolizing enzyme for the degradation of second messenger cAMP and cGMP, phosphodiesterase (PDE) has been the clinical target of various human diseases. But the hydrolysis procedure of PDE is still unclear. To investigate the mechanism of PDE catalysis, three types of PDE (PDE4d, PDE5a and PDE10a) were selected and studied by using molecular dynamics (MD) simulation and quantum mechanics (QM) calculation methods. MD Simulation results indicate that different PDEs share a similar hydrolysis area in the active sites, and the phosphate parts of cyclic nucleotides take the same orientation and are partly surrounded by water molecules. Based on the statistical data of MD simulation, the QM calculation models were built. The calculation results indicate that in aqueous solution, the nucleophile hydroxide ion that attacks the phosphor atom of the cyclic nucleotide in the hydrolysis may migrate between the two metal ions in the active site. To help the ring-open reaction, it is the water molecule that provides proton to the O3′ atom of cyclic nucleotide, and generates another hydroxide ion complexed with the metal ion.

Hydrogen bond is a key factor in the determination of structures and properties of room-temperature ionic liquids. Connections of these hydrogen bonds form a network. In this work, we analyzed the hydrogen bond network of 1-alkyl-3-methylimidazolium ionic liquids using network theory. A two-dimensional view of the hydrogen bond network has been generated, the connection pattern shown that the average length of line shape connection is 2.44 to 2.77 for six 1-alkyl-3-methylimidazolium ionic liquids, and the connection patterns are different for short and long alkyl side chain length. The degree of each ion was calculated and analyzed. The nodes with zero degree were adopted to detect the boundary of the clusters in the ionic liquids, which have no hydrogen bond connected with neighbor ions. This work indicates that the network analysis method is useful for understanding and predicting the structure and function of RTILs.

The low-lying states of an organic donor-σ-acceptor dyad, i.e. tetrathiafulvalene-σ-tetracyano-p-quinodimethane (TTF-σ-TCNQ), in gas phase and in various solvents have been investigated by means of hybrid DFT calculations in combination with the conductor-like polarizable continuum model to describe solvent effects. It has been shown that the dyad, though preferring a closed-shell singlet ground state with an eclipsed conformation in gas phase, adopts the charge-separated zwitterionic states with an extended conformation (TTF⁺-σ-TCNQ^-), i.e. open-shell singlet biradical ground state immediately followed by triplet biradical state, in polar solvent (CH₃CN and CH₂Cl₂) as a result of the intramolecular electron transfer (ET) stimulated by solvent polarization. The degree of such intramolecular ET is so strongly dependent on the polarity (dielectric constant) of solvent that the zwitterionic biradical states become more stable with respect to the closed-shell singlet state with increasing polarity of the solvent. As such, the dyad should show a higher ratio of biradicals in more polar solvent and/or at higher temperature and, hence, is chameleonic in nature.

We present a systematic study of the electronic, geometric, and magnetic properties of the actinide dioxides, UO₂, PuO₂, AmO₂, U_0.5Pu_0.5O₂, U_0.5Am_0.5O₂ and Pu_0.5Am_0.5O₂. For UO₂, PuO₂ and AmO₂, both density functional and hybrid density functional theory (DFT and HDFT) have been used. The fractions of exact Hartree–Fock (HF) exchange chosen were 25% and 40% for the hybrid density functional. For U_0.5Pu_0.5O₂, U_0.5Am_0.5O₂ and Pu_0.5Am_0.5O₂, only HDFT with 40% exact HF exchange was used. Each compound has been studied at the nonmagnetic, ferromagnetic and anti-ferromagnetic configurations, with and without spin–orbit coupling (SOC). The lattice parameters, magnetic structures, bulk moduli, band gaps and density of states have been computed and compared to available experimental data and other theoretical results. Pure DFT fails to provide a satisfactory qualitative description of the electronic and magnetic structures of the actinide dioxides. On the other hand, HDFT performs very well in the prediction and description of the properties of the actinide dioxides. Our total energy calculations clearly indicate that the ground-state structures are anti-ferromagnetic for all actinide dioxides considered here. The lattice constants and the band gaps expand with an increase of HF exchange in HDFT. The influence of SOC is found to be significant.

The structures of 5,5′-bis(naphth-2-yl)- 2,2′-bithiophene (NaT2), 5,5″-bis(naphth-2-yl)-2,2′:5′,2′-terthiophene (NaT3), 5,5‴-bis(naphth-2-yl)-2,2′:5′,2″:5″,2‴-tetrathiophene (NaT4), 5,5″″-bis(naphth-2-yl)-2,2′:5′,2″:5″,2‴:5‴,2″″-quinquethiophene (NaT5) and 5,5′″″-bis(naphth-2-yl)-2,2′:5′,2″:5″,2‴:5‴,2″″:5″″,2′″″-sexithiophene (NaT6) have been optimized at PBE1PBE/6-31G* level of theory. By increasing the chain length (thiophene units) energy gap decreases. The hole reorganization energy also decreases from NaT2–NaT6. We have observed that mobility of NaT5 and NaT6 can be enhanced by minimizing the polarization and relaxation. The end-capped naphthyl groups have been rotated from 0°–60° in the case study of NaT2, it was found that hole reorganization energy increases with the increment in angle. Furthermore the charge transport properties of 5,5′-bis(thionaphth-2-yl)-2,2′-bithiophene (TNT2), 5,5″-bis(thionaphth-2-yl)-2,2′:5′,2″-terthiophene (TNT3), and 5,5‴-bis(thionaphth-2-yl)-2,2′:5′,2″:5″,2‴-quaterthiophene (TNT4) have been investigated at the same level of theory. It has been studied that cis isomers have higher hole reorganization energies as compared to trans ones thus these isomers would diminish the mobility.

A new analytical solution is developed for the one- and two- dimensional generalized discrete time random walk with discrete and finite length of jumping. It is shown that the ensemble average of the mean square displacement has a linear relation with time. This result is general and independent of mathematical form of distribution function but magnitude of diffusion coefficient depends on the distribution function. This result confirms our previous numerical work. The truncated Levy flight is studied as a special case and the diffusion coefficient for different maximum length of jump is calculated numerically. The obtained results are in good agreement with the analytical solution.

The proton assisted isomerization reactions of 1H-imidazo(4,5-b)pyridine (IMP) derivatives have been studied by using B3LYP/6-31G + (d,p) calculations, and the transition states of the reactions are analyzed with B3LYP/6-31+G(d,p) opt=qst3 route. It has been found that the prototropic transformation could be the feasible pathway of isomerization, since the energy gaps between the various protonated isomers are found closer compared to free molecules. The conversion of IMP-a1 to IMP-b1 may pass through several protrotopic isomerization, since the activation energy as well as the relative energy levels of these isomers are not small compared to other pathways. However, the results suggest that some of the reactions may take place simultaneously through protrotopic transformation. The relative variations of energy gaps in the excited states are smaller than the ground states. The protrotropic transformation in the excited states may be more feasible than the ground state.

Quasiclassical trajectory (QCT) calculations for the title reaction are carried out by employing the recent developed accurate potential energy surface of the 1²A′ ground state. Two angular distributions, P(θ_r) and P(ϕ_r), with θ_r, ϕ_r being the polar angles of the product angular momentum, and two commonly used polarization dependent differential cross sections, (2π/σ)(dσ₀₀/dω_t) and (2π/σ)(dσ₂₀/dω_t), with ω_t being the polar coordinates of the product velocity, are generated in the center-of-mass frame. It was found that the product rotational angular momentum j′ is not only aligned, but also oriented along the negative direction of y-axis. We also investigated the product state distributions in the present work, and found that the vibrational and rotational state distributions are inverted. Influences of collision energies on the product polarization and state distributions are also shown and discussed.

The suitability of a recently developed extension to the polyspherical parametrization of protein complexes has been investigated by molecular dynamic simulations. The extension makes it possible to study the motion of proteins consisting of several chains, which are internally covalently bonded. Tests indicate that time steps of up to at least 10 fs for simulations lasting up to 100 ps are possible, at least for small proteins.