Journal of Theoretical and Computational Chemistry

DFT B3LYP method was employed to calculate the second-order nonlinear optical (NLO) responses of the derivatives of disubstituted seven-vertex cobaltacarborane metallocenyl. The results show that cobaltacarborane metallocenyl plays a pushing/pulling role and a bridge role to transfer electron in these molecules. The five-membered ring of cyclopentadiene is more beneficial to increase second-order NLO response than the five-membered ring composed of two C atoms and three B atoms in cobaltacarborane. Moreover, the second-order NLO response is more powerful when one substituent containing electron donor group and one substituent containing electron acceptor group are located at meta position. Accordingly, among the nine models, model c2 is the optimum model with largest value of β_tot. The calculation results also show that cobaltacarborane metallocenyl and ferrocene parts play the same roles to increase second-order NLO response. Thus, cobaltacarborane metallocenyl can be a promising second-order NLO material.

The reaction mechanism for methane hydroxylation catalyzed by mimic methane monooxygenase (MMO) with bis(μ-oxo)dimanganese core has been investigated on the septet and nonet potential energy surfaces by hybrid density functional method B3LYP. The key reactive compound Q of MMO was modeled by trans-(H₂CNH)(COOH) Mn(μ-O)₂(μ-HCOO)₂Mn(H₂CNH)(COOH). The ground state of Q is located on the septet state, which has a diamond-core structure with two Mn(IV) atoms. It is shown that the reaction proceeds via a radical-rebound mechanism, in which the step of C–H cleavage is the rate-determining step both in the gas phase and solution. Furthermore, the reaction may proceed more easily as the polarity of solution is larger. On the other hand, the kinetic isotope effects (KIEs) for H atom abstraction from methane are taken into account on the basis of transition state theory with Wigner tunneling corrections. The mimic MMO with bis(μ-oxo)dimanganese core might be an effective mimic catalyst for methane hydroxylation.

A systematic study of torsional potential curves in electronic ground state based on second-order Møller–Plesset energy (MP2), density functional theory (DFT), and Austin mode 1 (AM1) methods is presented for para-phenylenevinylene oligomers constructed from two to four aromatic rings. The semiempirical AM1 approach gives the correct location of potential energy minima in comparison with the reference MP2 calculations and literature data. However, the semiempirical AM1 energy barriers at perpendicular orientation are ca. 30% smaller than the MP2 ones. The DFT calculations indicate optimal planar structures and the barriers are three times higher than MP2 values. Excited-state potential energy curves evaluated from vertical excitations at the time-dependent density functional theory (TD-DFT) and ab initio CI levels exhibit much steeper increase of values in the vicinity of perpendicular orientation than in the semiempirical Zerner's intermediate neglect of differential overlap (ZINDO) and ab initio RI-CC2 cases. The effects of vibrational motion of phenylene rings on the torsional broadening of absorption spectra were estimated from semi-classical molecular dynamics simulations and harmonic oscillator sampling. The simulated spectra agree well with the experiment and allow estimating the conformer distribution of the molecules.

The reaction of CH₃SH with Cl atoms has been theoretically studied using dual-level direct dynamics method. Three reaction channels, two H-abstraction (from the –SH and –CH₃ groups) and one substitution channel, have been found. The optimized geometries and frequencies of all the stationary points are calculated at the MP2/6-311+G(d,p) level, and the potential-energy profile along each reaction path is refined by the single-point calculation at the CCSD(T)/6-311+G(d,p) level. The rate constants for the two H-abstraction channels are evaluated by the improved canonical variational transition-state theory (ICVT) with the small-curvature tunneling (SCT) correction over a wide temperature range of 193–1000 K. The calculated ICVT/SCT rate constants are in good agreement with available experimental values and exhibit negative temperature dependence below 500 K. The present calculations indicate that the H-abstraction from the –SH group is the major channel for the title reaction, while the H-abstraction from the –CH₃ group should be taken into account only at high temperatures.

A 3D-QSAR study using comparative molecular field analysis (CoMFA) was carried out on anti-tubulin agents with indole as a nucleus core. The structures of the compounds were obtained using docking calculations, and were then subjected to alignment procedures. CoMFA calculations for the 42 ligands that were examined as the training set gave a q² value of 0.623 in correlation with experimental IC₅₀ values for the inhibition of MKN-45 gastric cancer cells. Calculation for the test set of 17 ligands resulted in an r² value of 0.714. The calculated results suggest that the R3 functional group site (see structure in Fig. 1) favored bulky groups while R1, R2, and R4 sites favored the opposite. At the R5 and R6 sites, parts of the region favored bulky groups while other parts favored the opposite. As for the electrostatic aspect, the R3 site was found to favor groups with a negative partial charge. At the R2 site, part of the region favored the group with a negative partial charge while other regions favored groups with a positive partial charge. The R4 and R5 sites favored groups with negative and positive partial charges, respectively, with a less favorable magnitude when compared with the R2 and R3 sites. The R1 and R6 sites did not exhibit significant electrostatic favor. Correlation of the results with IC₅₀ values of ligands were analyzed and discussed.

We explore the pattern of time evolution of a harmonically confined single carrier 2-d quantum dot when an external time varying polychromatic radiation field is switched on. The radiation field is composed of four mutually prime "nonresonant" frequencies. For given strengths of the confining field, cyclotron frequency, intensities, and oscillation frequencies of the external field, the system reveals a counter-intuitive long-time dynamics leading to a kind of localization in the unperturbed state space. The presence of cubic and quartic anharmonicity in the confining fields, and phase shifts in the external radiation fields, bring in new features in the dynamics. Time dependent Hellman–Feynmann theorem is invoked to gain insight into the frequency resolved absorption spectrum.

We report ReaxFF molecular dynamic simulations of structure change of crystalline nitromethane and the formation of hydrogen bond under high pressure. Under high pressure, the angles between C–N bonds and X, Y and Z axes have changed. Through the calculation of g(r) of O and H atoms, we found a new peak near 1.6 Å, which indicates the formation of the hydrogen bond between O and H atoms. We calculated the distribution of the angles of the C–N bonds orientations, the distribution of the dihedral angle of CNOO, and the charge distribution of nitromethane molecules under various pressures, and made a comparison between low and high pressures. The effects of hydrogen bonding in high explosive materials are discussed.

The product angular momentum polarization of the Cl + C₂D₆ → DCl + C₂D₅ reaction is calculated via the quasiclassical trajectory (QCT) method at the collision energy of 0.25 eV. A new London–Eyring–Polanyi–Sato (LEPS) potential energy surface (PES) is used in this reaction. There is a "late" barrier and a "deep" well on this new LEPS PES. The four polarization-dependent "generalized" differential cross sections (PDDCSs) are presented in the center-of-mass frame. In the meantime, the distributions of P(ϕ_r), P(θ_r), and P(θ_r, ϕ_r) are calculated. The calculations are in good agreement with the experimental data. In addition, the rotational alignment factors , , and in the stationary-target frame (STF) are also calculated.

We present an ab initio investigation on the chiral discrimination of 2-methylol oxirane (M-olOx)· · · ethanol (EtOH) complexes, for the sake of comparison with previous report on propylene oxide (PO)· · · EtOH complexes. Second-order Møller–Plesset perturbation theory (MP2) with the 6-311++G(d,p) basis set was used to elucidate the diastereomeric interactions between ethanol (EtOH), a transient chiral alcohol, and the chiral molecule 2-methylol oxirane (R). Six complexes of M-olOx· · · EtOH have been identified and their structures as well as their calculated stability ordering have been determined. The six complexes were defined in a similar way as for PO· · · EtOH. The primary O–H· · · O hydrogen bonds are predicted to be important contributions to chiral discrimination in M-olOx· · · EtOH. The three syn structures, with ethanol and the methylol group on the same side of the oxirane ring, are energetically favored over the three anti structures. The larger chirodiastaltic energy between synG- and synG+ is 0.52 kJ mol^-1. The largest diastereofacial energy between synG- and antiG- is 13.90 kJ mol^-1. The obtained results are compared with previously reported results on the PO· · · EtOH complexes and the mechanisms of chiral discrimination in PO· · · EtOH and M-olOx· · · EtOH are discussed. The harmonic frequencies, IR intensities, rotational constants, and dipole moments for the M-olOx· · · EtOH complexes are also presented. Such a theoretical study should be valuable to further spectroscopic investigations on M-olOx· · · EtOH complexes.

A series of diamond nanoparticles with different surface terminations, (I) CH_n (n = 1, 2) and (II) CH_n (n = 1–3) species, have been investigated by means of density functional theory (DFT) to probe the effects of the terminated CH_n species on the geometric and electronic structures and related properties. Our results show that quantum confinement effects of HOMO–LUMO gap occurs for the series I particles with size up to 1.1 nm, in contrast to the much weaker decay of the gap for larger size. With the existence of additional CH₃ species, for size larger than 1 nm, the series II particles have larger gaps than the series I counterparts, which may be even larger than that of bulk diamond. The compositions of HOMO and LUMO are responsible for the different behaviors in the quantum confinement, which agrees with the experimentally observed spectral feature in the X-ray absorption measurement. In addition, our results show that the negative electron affinity is strongly dependent on the C/H ratio for the hydrogenated diamond nanoparticles.

The interaction of the K⁺-sparing agent amiloride — a synthetic chlorinated pyrimidine derivative — with the hASIC1a ion channel is investigated here along homology modeling of the pore region (using the crystal structure of the cASIC1 channel as a template and the known sequence of hASIC1a), automated docking (using the NMR solution structure of amiloride and its conjugated acid, refined by computations), and molecular dynamics simulations. This represents the first modeling and computational chemistry of the pore region of ASIC/DEG/ENaCs/FaNaCh channels. The results agree with the putative amiloride binding site for alphaENaC channel chimeras once the amiloride free base is considered, while its conjugated acid — in contrast with literature beliefs — is poorly scored on a nearby protein pocket. Different protonation conditions of the pore region are irrelevant because histidine residues are far from the binding sites. Mapping the amino acids of the homology model closest to amiloride can have heuristic value in stimulating in silico search of new pore-blocking agents, experimental studies of ASIC channels themselves, and development of code for constant-pH MD simulations.

Density-functional B3LYP and ab initio HF calculations are used to study three isomeric systems including: borepin I, boranorbornadiene II, and boranorcaradiene III as well as their X-substituted analogues at two different positions (X = F, Cl, Br, CH₃, OCH₃, CF₃, CN, and NH₂). Geometries, enthalpies, and energy barriers for two series of interconversions, III_X → I_X and III_X → II_X, are calculated using 6-311G* basis set. The B3LYP calculated relative stability is in the order: I (0.00 kcal/mol) > II (23.33 kcal/mol) > III (39.07 kcal/mol). Except for NH₂, the electronic effects of the substituents are generally insignificant on the relative stability. At B3LYP, the gas-phase activation enthalpies for III → I and III → II interconversions are estimated to be very small (0.6 and 0.75 kcal/mol, respectively). The reverse conversions, I → III and II → III, have activation energies of 39.67 and 16.49 kcal/mol, respectively. These energies rule out the possibility of a rapid interconversion of the isomers in the gas phase. Again, none of the substituents, X, can change this situation. Two pathways are proposed for the possible [1, 3]-suprafacial sigmatropic shifts of III_X → II_X. The partial aromatic characters of planar borepins are estimated using magnetic (NICS) and structural criteria (bond length alternation).