Journal of Theoretical and Computational Chemistry

Hund's state conservation rule predicts (1 × 6) [N (⁴S) + O(-)(²P)] plus 9 × 9 [(³P) N(-) + O(³P)] = 87 spin states for NO(-). The experimental E_a(NO), 0.92(2)-0.16(2) eV are assigned to the (3 + 27) bonding states with anion bond orders, 0.80-1.15. The E_a(NO) 0.026(5)-0.14(2) eV are assigned to seven of the 27 nonbonding states with anion bond orders about one. The negative E_a(NO) for the 20 other nonbonding and 30 antibonding states are estimated. Ionic Morse potentials are calculated for 87 predicted states for NO(-) and the 54 bonding and antibonding states of superoxide.

The selective excitation of the high ground vibrational state of rotationless HF in an unobserved quasi-resonant thermal environment under the control of a single pulse and pulse train is studied using the reduced density matrix theory. It is shown that the pulse train can enhance the population transfer probability. The numerical results reveal that the vibrational relaxation process is affected by the distribution of the environment frequency and the molecule–environment coupling intensity. The effects of the molecule–environment coupling parameter and the overlapping pulses on the population of the target state of HF are also discussed.

The electronic density of states (DOS) and energy bands of doped anatase TiO₂ are studied by the full potential linearized augmented plane wave (FPLAPW) method based on the density functional theory. After doping with transition metal atoms, the band gap of TiO₂ is narrowed, doping with transition metal cation makes both valence bands and conduction bands move towards lower position.

A theoretical survey on the potential energy surface for the CH (X²Π) + CH₂CO reaction has been carried out. The geometries and energies of all stationary points involved in the reaction are calculated at the UB3LYP/6-311+G(d, p) level. And the more accurate energy information is provided by single point calculations at the UCCSD(T)/6-311++G(2d, 2p) level. Relationships of the reactants, transition states, intermediates, and products are confirmed by the intrinsic reaction coordinate (IRC) calculations. Our calculations demonstrate that this reaction is most likely initiated by carbon-to-olefinic carbon attack manners. The results suggest that P1 (C₂H₃ + CO) is the most important product through two competitive channels R → IM1 → TS1/P1 → P1(C₂H₃ + CO) and R → IM1 → TS1/6 → IM6 → TS6/P1 → P1(C₂H₃ + CO). This study presents highlights of the mechanism of the title reaction, which is in good agreement with experimental results.

The energy levels and wavefunctions for all rovibrational bound states of HO₂ are systematically computed, for all total angular momentum values J = 0–10. The calculations are performed using ScalIT, a suite of software modules designed to enable quantum dynamics and related calculations to be performed on massively parallel computing architectures. This is the first-ever application of ScalIT to a real (and very challenging) molecular application. The codes, and in particular, the algorithms (optimal separable basis, preconditioned inexact spectral transform, phase space optimized discrete variable representation basis) are so efficient that in fact, the entire calculation can be performed on a single CPU — although parallel scalability over a small number of CPUs is also evaluated, and found to be essentially perfect in this regime. For the lowest 11 vibrational states, the rotational levels for J = 0–10 fit fairly well to a rigid rotor model, with all vibrational-state-dependent rotational constants, B_eff(v), close to values obtained from a previous calculation for J = 0 and 1 [J Chem Phys107:2705, 1997]. However, comparatively larger discrepancies with the rigid-rotor model are found at the higher J values, manifesting in the observed K-splitting (along the O–O bond) of rovibrational levels. This supports earlier work [J Chem Phys113:11055, 2000] suggesting that Coriolis coupling is quite important for this system.

A series of norbornane-based HIV-1 protease (PR) inhibitors are designed theoretically to displace the tetrahedrally coordinated internal water molecule that bridges inhibitor to flaps via hydrogen bonds. These designed inhibitors use the norbornenone oxygen atom to mimic this structural water molecule and contain diols to interact with the carboxylate oxygens of catalytic aspartates. The binding free energies were estimated by modified linear interaction energy approach [Zoete H, Michielin O, Karplus M, J Comput Aided Mol Des17:861, 2003], in which the binding free energy is written as a linear combination of the electrostatic interaction energy between PR and the ligand, E_elec, the van der Waals interaction energy between PR and the ligand, E_vdW, and the difference of the solvation free energies of the complex, the receptor, and the isolated ligand, ΔG_solv. The equation obtained in previous work [Da W. Zhang, Philip Lin Huang, Sylvia Lee-Huang, John Z. H. Zhang, J Theor Comput Chem7:485, 2008] is applied directly to calculate the binding free energy of designed norbornane-based HIV-1 PR inhibitors.

The first quasi-classical trajectory (QCT) calculation for the exothermic reaction Sr + CH₃Br is carried out based on a constructed London–Eyring–Polanyi–Sato (LEPS) potential energy surface (PES). By QCT calculation, the product SrBr vibration distributions are obtained. The result is in good comparison with the experimental one by Keijzer JF et al. [Chem. Phys.207:261, 1996]. Furthermore, the reaction product SrBr angular distribution and rotational alignment are also obtained. The products are dominantly forward-scattered and the alignment effect is obvious. Fast dynamics mechanism is proposed upon the calculation results.

A molecular recognition mechanism based on dimeric model for cyclic dipeptide Cyclo[(S)-His-(S)-Phe] (abridged CHP) catalyzed autoinduction is proposed according to the inference of previous experimental findings, which is supported by theoretical calculation with Oniom(B3LYP/3-21G*:AM1) method. The most unstable CHP dimer whose intermolecular hydrogen bonds are immensely lessened by two intramolecular hydrogen bonds is defined as the highest active component (IIa) existing in solid among the three possible dimers (Ia, IIa, and IIb). The carbonyl group of benzaldehyde coordinates to CHP dimer (IIa) by a hydrogen bond with Phe–N_αH rather than His–N_αH and HCN interacted with the imidazole moiety of His residue to form cyanide ion. In view of the theoretical calculation and experimental results, the structures of the nine-ring complexes derived from interaction between catalytic active dimer CHP(IIa) and cyanohydrins were postulated to explain the enantioselective autoinduction: The structure of no nitrile involved six-ring complex derived from interaction between catalytic active dimer CHP(IIa) and cyanohydrins were postulated to explain the elimination of enantioselective autoinduction.

Our interest in conjugation effects in substituted phenyl compounds has turned our attention to the highly reactive compounds phenyl ketene, azide, and isocyanate, which due to their reactivity are of utmost importance in organic synthesis. We performed local density functional theory (DFT) calculations using a 6-311G** basis set to calculate the structures and potential functions of the internal rotation. Further for the minimum structures we computed the vibrational infrared and Raman spectra of the three molecules. In order to confirm that DFT works rather well in these systems we performed the geometry optimizations also using ab initio Moeller–Plesset perturbation theory of second order (MP2) in the same basis set. As expected there exist just two minimum structures for each of the molecules which both correspond to planar structures and are identical due to the symmetry of the phenyl ring. The transitions states (TS) of the internal rotations are the perpendicular ones. We expect conjugation to play no major role in these molecules since extensive conjugation effects would imply a large reduction of the aromatic character of the phenyl ring which in turn would greatly destabilize the systems. However, although the rotational barriers appear to be rather small in these systems conjugation must play at least some role in stabilizing the planar ground state. As detailed later, the relative heights of the rotational barriers can all be explained naturally. Experimental vibrational spectra could be obtained only for phenyl isocyanate and azide, but not for the ketene because of the high reactivity of this molecule. Since in the former cases the calculated spectra agree fairly well with the measured ones, we present those of the other molecule as theoretical prediction, which could be useful to detect spectroscopically in a reaction mixture residual reactant. On the basis of potential energy distribution (PED) calculations we present a complete assignment of the vibrational lines to symmetry coordinates, where, for example, ring breathing must show up with rather large intensities in the Raman spectra of the molecules.

Equilibrium geometries and harmonic vibrational frequencies of two isomers of a new substituted dioxirane, C₂O₄, are reported. Molecular geometric characteristics, vibrational frequencies, and local atomic charges, are compared with its analog, CO₄. It is found that C₂O₄ is structurally and chemically similar to CO₄: one isomer shows the dioxirane rings like most substituted dioxiranes and the other isomer retains a CO₃ ring. Equilibrium geometries and vibrational frequencies of two energetically low-lying triplet states of C₂O₄ are predicted and analyzed.