Journal of Theoretical and Computational Chemistry

Cysteine dioxygenase (CDO) catalyzes the oxidation of cysteine to cysteine sulfinate, which has crucial roles in the metabolism and bioconversion. The catalyzed reaction mechanism of CDO is currently disputed. Herein, a high-spin "Fe-proximal oxygen" catalytic mechanism of rat CDO is theoretically investigated with an energy barrier of 15.7 kcal⋅mol^-1. In the mechanism, the Fe-proximal oxygen atom firstly attacks the sulfur atom of cysteine by the swing of O(1)–O(2) bond, and this makes the Fe-proximal oxygen atom O(1) accessible to S and Fe-terminal oxygen atom O(2) be closed to Fe. Then the generated seven-membered ring intermediate has smaller tension and could help the reaction take place easily. The reaction ends in the formation of the product cysteine sulfinic acid with the second oxygen atom O(2) transferred to S. This study gives an additional insight of the reaction mechanism of CDO, where the "Fe-proximal oxygen" and "Fe-terminal oxygen" mechanisms are both favorable in the catalytic process.

Based on four physicochemical descriptors (the rigidness descriptor R^OM resulted by hydrogen-bonding moieties group and/or rings, the chain mobility n, the molecular average polarizability α and the net charge of the most negative atom q^-) derived from the polymers' monomers structure, the support vector regression (SVR) approach combined with particle swarm optimization (PSO), is proposed to construct a model for prediction of the glass transition temperature T_g of three classes of vinyl polymers, including polystyrenes, polyacrylates and polymethacrylates. The mean absolute error (MAE = 13.68 K), mean absolute percentage error (MAPE = 4.22%) and correlation coefficient (R² = 0.9252) calculated by SVR are superior to those (MAE = 16.74 K, MAPE = 5.30% and R² = 0.9059) achieved by S-SAR model, and (MAE = 16.83 K, MAPE = 5.27% and R² = 0.9057) achieved by ANN model for the identical training set (124 vinyl polymers), whereas the MAE = 15.09 K, MAPE = 4.82% and R² = 0.9253 calculated by SVR are also better than those of MAE = 17.96 K, MAPE = 5.94% and R² = 0.8952 achieved by S-SAR, and MAE = 16.603 K, MAPE = 5.4% and R² = 0.9120 achieved by ANN for the same 68 test samples. Furthermore, the MAE, MAPE and R² for an independent set (10 vinyl polymers) predicted by SVR also reached 14.132 K, 4.25% and 0.9475, respectively. The results strongly support that the comprehensive modeling and prediction ability of SVR model surpass those of S-SAR and ANN models by applying identical training, test and independent samples. It is demonstrated that the established SVR model is more suitable to be used for prediction of the T_g values for unknown vinyl polymers possessing similar structure than S-SAR model or ANN model.

The insertion reactions of the germylenoid H₂GeLiF with RH (R = Cl, SH, PH₂) were studied for the first time by using the DFT B3LYP and QCISD methods. The geometries of the stationary points on the potential energy surfaces of the reactions were optimized at the B3LYP/6-311+G (d,p) level of theory. The calculated results indicated that the mechanisms of the insertion reactions of H₂GeLiF with HCl, H₂S, and PH₃ are identical to each other. The QCISD/6-311++G(d,p)//B3LYP/6-311+G(d,p) calculated potential energy barriers of the three reactions are 81.80, 123.39 and 205.56 kJ/mol, and the reaction energies for the three reactions are -58.74, -33.51 and -13.35 kJ/mol, respectively. Under the same situation, the insertion reactions should occur easily in the following order H–Cl > H–SH > H–PH₂. The insertion reaction in THF solution is easier than in gas phase.

The asymmetric Michael reaction of aldehydes and nitrostyrene catalyzed by a new (S)-tertbutyl-diphenyl-silyl-pyrrolidine catalyst has been investigated by using density functional theory calculations. The Re face of the enamine is effectively shielded, because of the bulky 2-substituent group on the pyrrolidine ring. For acetaldehyde, there are two different conformers of enamines. Based on the two conformers of enamines, four different reaction pathways have been considered. The calculated enantiomeric excess value is 80.27% in favor of the (R)-configuration product. For propanal, eight different reaction pathways have been considered and the eight corresponding transition states have been located. The calculated enantiomeric excess value is 98.96% in favor of the (2S, 3R)-configuration product. These calculated results are in good agreement with the experimental observations. In addition, the calculations also show that both the used solvent and the enamines play important roles in determining the stereochemical outcome of the product.

In this paper, we report simulations of laser-driven many-electron dynamics by means of the time-dependent configuration interaction singles (TD-CIS) approach. Photoionization is included by a heuristic model within calculations employing standard Gaussian basis sets. Benzo[g]-N-methyl-quinolinium-7-hydroxylate (BMQ7H) serves as a test system to generate predefined wave packets, i.e. a superposition between the ground and fifth excited state, in a large molecule. For this molecule, these two states have a very similar geometry, which enables us to use the fixed nuclei approximation. Furthermore, this geometric stability would also prevent a dephasing of the electron wave packet due to nuclear dynamics in an experimental realization of our simulations. We also simulate the possible detection of such a wave packet by ultra short probe laser pulses, i.e. pump-probe spectra.

We present a theoretical scheme for achieving the field-free molecular orientation in dissipative media by a combination of femtosecond and THz laser pulses. Numerical calculations are performed by solving the quantum Liouville equation based on multilevel Bloch model. The molecular orientation degree is sensitive to the carrier-envelope phase of the THz pulse and the delay time between the two pulses. The orientation and the rotational population of CO molecules in dissipative environment are computed at different pressures and temperatures. The influence of pure decoherence on the molecular orientation is also discussed.

C-doped TiO₂ nanotubes (NTs) with anatase structure, prepared by anodizing the polished Ti foils, were characterized using X-ray diffraction (XRD), field-emission scanning electron microscope (FE-SEM), and synchrotron-based X-ray photoemission spectroscopy (XPS). XPS results show electron losses in C atoms, no electron change in Ti atoms, and two doping energy levels appeared in band gaps. Structural geometries, DOSs, PDOSs, and Bader charge analyses of C-doped TiO₂ anatase are predicted by periodic DFT calculations. Eight doping positions were taken into consideration: two substitutional cases (in oxygen and titanium sites) and six interstitial cases. We found that the interstitial carbon doping type is the most stable one, whereas the substitutional cases are rather unstable. Band-gap modifications can also be found in oxygen substitution, but not in titanium substitution. Both band-gap modification and non-band-gap modification are found in the interstitial carbon doping. In these eight C-doping systems, only the C atom in the oxygen substitution case gains electrons, 1.14 e, and others present electron losses within 0.5–4.00 e. The results of XPS measurements, DOSs calculations, and Bader charge analyses show that carbon interstitial is the most likely doping type for the C-doped TiO₂ NTs.

Stereodynamics of the reaction Li + HF (v = 0,j = 0) → LiF + H and its isotopic variants on the ground electronic state (1²A′) potential energy surface (PES) are studied by employing the quasiclassical trajectory (QCT) method. At a collision energy of 2.2 kcal/mol, product rotational angular momentum distributions, P(θ_r) and P(ϕ_r), are calculated in the center-of-mass (CM) frame. The results demonstrate that the product rotational angular momentum j^′ is not only aligned along the direction perpendicular to the reagent relative velocity vector k, but also oriented along the negative y-axis. The four generalized polarization-dependent differential cross sections (PDDCSs) are also computed. The PDDCS₀₀ distribution shows a sideways scattering for the reaction Li + HF and a strongly backward scattering for the reaction Li + DF. However, it displays both the forward and backward scatterings for the reaction Li + TF. These features demonstrate that the Li + HF and Li + DF reactions proceed predominantly through the direct reaction mechanism. However, the Li + TF reaction undergoes both the direct and indirect reaction mechanisms. The PDDCS_21- distribution indicates that the product angular distributions are anisotropic.

DFT calculations are applied to evaluate the effects of atomic arrangements of dopant atoms on electronic features of the most stable structures of C_60−nN_n(n = 1–12) fullerenes. Our study reveals that ¹³C isotropic chemical shifts (δ_iso) of the nuclei at C–N pentagon–hexagon (ph) junctions appear at downfield values while there are no tangible values of δ_iso for the nuclei at C–N hexagon–hexagon (hh) junctions; the carbon sites attached to the first neighbors of nitrogen at hh junctions (the second neighboring effect) yield upfield values of δ_iso. Moreover, compensation between diatropic and paratropic ring currents leads to slightly less negative NICS value in C₅₉N heterofullerene (-3.6) compared to the parent fullerene C₆₀ (-4.25). However, with incorporating more nitrogen atoms into the cage the aromaticity first increases, up to the 66π-system C₅₄N₆ and C₅₃N₇, yielding the most negative NICS values of -26.3 and -26.8, respectively, and then decreases so that NICS finally reaches the value of -6.6 ppm for C₄₈N₁₂ heterofullerene. On the basis of distinct value predicted for each heterofullerene, one expects that NICS values may also be useful for identification of the molecules through their endohedral ³He NMR chemical shifts.

Photodetachment of near a soft reflecting surface is investigated by using theoretical imaging method. Analytical expressions are derived for detached electron flux and photodetachment cross section. The surface strongly affects the results and induces oscillation in the detached electron spectra. The photodetachment cross section is double of the H^- near a plane wall. For a very large distance between the surface and (R → ∞) the cross section reduces to the cross section of two center system in free space.

Classical molecular dynamics (MD) simulations are employed to study the thermal conductivity of carbon nanotube/natural rubber (CNT/NR) composite. An aligned CNT/NR system is constructed by atomic potential function and periodic boundary condition and the anisotropic thermal conductivity is predicted in three main directions. The highest thermal conductivity of 80 W/(mK) is predicted along the axial direction of CNT. However, the transverse thermal conductivity perpendicular to the CNT axis is only about 0.6 W/(mK). For obtaining thermal conductivity of randomly oriented CNT/NR composite, an isotropic algorithm is provided from thermal resistance analysis method and results indicate the thermal conductivity improvement of randomly oriented CNT/NR composite is negligible. It is deduced therefore aligning CNTs in NR matrix can be a promising method in thermal management of CNT/NR composite.

In this paper, the weak interaction between aromatic rings (ARs) and rare gas (Rg) atoms has been studied using ab initio calculation and density functional theory (DFT). The augmented Dunning basis sets were used, and the convergence test was performed up to aug-cc-pV5Z. Among the computationally feasible methods, ωB97XD performed the best for these non-covalent systems. NBO analysis was performed to investigate the nature of the Rg/AR interactions. In this type of weak interaction, the induced and instantaneous dipole and charge transfer character both contribute to the interaction energies and equilibrium distances.

This theoretical work applied density functional theory (DFT) to study the ground state of the indigo molecule and the effects of substituents. B3LYP was employed with the 6-31G[d,p] basis set. The obtained energies were used to describe the local reactivity [Δf(r)]. The effects of the substituents on the local reactivity were dependent on the molecular positions of the substituents.

The difficulty of achieving p-type conductance has severely limited the application of ZnO to electronic devices. In this work, we propose a simple and effective way to achieving p-type semiconducting ZnO nanowires (NWs) through density functional theory computations. Adsorption of tetrathiafulvalene (TTF) during synthetic procedures leads to lower formation energies, and accordingly higher concentration of p-type defects; after the formation of ZnO NWs and the desorption of TTF, p-type ZnO NWs can be achieved. Also, we present a facile synthesis route on basis of previous experiments, which provides some guidance for the realization of p-type ZnO NWs.

The quasi-classical trajectory (QCT) calculations have been carried out for the reaction N + NH (v = 0–3, j=0) → N₂ + H on the ground state of double many-body expansion (DMBE) potential energy surface [Caridade, PJSB, Poveda LA, Rodrigues SPJ, Varandas AJC, J Phys Chem A111:1172, 2007]. The influence of reagent vibrational excitation on reaction probability for total angular momentum J = 0 and integral cross section (ICS) at collision energies ranging from 0.1 eV to 1.0 eV has been investigated. The reaction probability tends to decrease with increasing collision energy and increase with the rising of initial vibration state, although some fluctuations appear. The ICS declines monotonously with the increase of collision energy and v. The product rotational alignment factor 〈P₂(j′•k)〉 has also been calculated, and its value has a declining trend with the increase of collision energy. In spite of that, the results still show that the product is highly aligned. In addition, the vibrational excitation effect on the product polarization has also been studied. All the distributions of P(ϕ_r), P(θ_r), and the generalized polarization dependent differential cross sections indicate dependent behaviors on v.