No abstract

Structural properties, electronic structure and UV absorption spectra of mercury(ii) mediated metal-DNA complex, thymine-mercury(ii)-thymine base pair (T-Hg(II)-T), were theoretically and computationally investigated along with experimental data [Ono et al., J. Am. Chem. Soc., 2006, 128(7), 2172-2173]. The results were obtained by density functional theory (DFT) calculations for ground state and time-dependent DFT (TD-DFT) calculations for excited states associated with the polarized continuum model (PCM) in order to account for the bulk solvent effect. The LUMO of T-Hg(II)-T was stabilized due to the presence of Hg(II) since an unoccupied 6p orbital interacted with the 2p orbitals of thymine N3 atoms in the same way as in a pi-conjugated system. Thus, excitations in T-Hg(II)-T involve transitions qualitatively different from those of the thymine-thymine mismatch base pair (T-T). Since conventional DFT functionals lack correct description of dispersion forces, a method previously developed in our research group which combines DFT and a van der Waals correction functional was introduced to study multiple stacking nucleobase pairs. Based on the evaluated distance and the interaction energy between two stacking nucleobase pairs, the selective capturing of Hg(II) ion by T-T compared to other metal ions is explained. The calculated UV absorption spectra of multiple stacking nucleobase pairs reproduced the decrease of absorption around 260 nm and the red-shift of the main peak experimentally observed in the presence of Hg(II) ion. Detailed analysis of the electronic structure revealed that the metal-metal interaction between two Hg(II) in multiple stacking T-Hg(II)-T is the origin of the significant changes in UV absorption spectra.

No abstract

The authors have derived coupled equations of motion of cumulants that consist of a symmetric-ordered product of the position and momentum fluctuation operators in one dimension. The key point is the utilization of a position shift operator acting on a potential operator, where the expectation value of the shift operator is evaluated using the cumulant expansion technique. In particular, the equations of motion of the second-order cumulant and the expectation values of the position and momentum operators are given. The resultant equations are expressed by those variables and a quantal potential that consists of an exponential function of the differential operators and the original potential. This procedure enables us to perform quantal (semiclassical) dynamics in one dimension. In contrast to a second-order quantized Hamilton dynamics by Prezhdo and Pereverzev which conserves the total energy only with an odd-order Taylor expansion of the potential [J. Chem. Phys. 116, 4450 (2002); 117, 2995 (2002)], the present quantal cumulant dynamics method exactly conserves the energy, even if a second-order approximation of the cumulants is adopted, because the present scheme does not truncate the given potential. The authors propose three schemes, (i) a truncation, (ii) a summation of derivatives, and (iii) a convolution method, for evaluating the quantal potentials for several types of potentials. The numerical results show that although the truncation method preserves the energy to some degree, the trajectory obtained gradually deviates from that of the summation scheme after 2000 steps. The phase space structure obtained by the truncation scheme is also different from that of the summation scheme in a strongly anharmonic region.

No abstract

The reaction mechanism of the reduction of dinitrogen coordinated side-on to a binuclear Zr complex, [(eta(5)-C(5)Me(4)H)(2)Zr](2)(mu(2),eta(2),eta(2)-N(2)) (T1), was investigated theoretically using a model complex, [(eta(5)-C(5)H(5))(2)Zr](2)(mu(2),eta(2),eta(2)-N(2)) (A1), employing density functional theory calculations. The effectiveness of A1 in describing T1 was confirmed by comparing the structures, distributions of charge, and frontier molecular orbitals. Our calculations showed that A1 has a twisted structure, resembling that of T1, which results in similar properties. The calculations for A1 and its derivatives on H(2) addition clearly explain the reaction mechanism and the reaction path that T1 follows, as well as the experimentally required reaction conditions. The immediate reaction of the first and second H(2) additions produces [(eta(5)-C(5)Me(4)H)(2)ZrH](2)(mu(2),eta(2),eta(2)-N(2)H(2)) (T2), and this is explained by the barrier heights of the reaction, which were calculated to be 20.4 and 10.9 kcal/mol, respectively. The latter barrier was below that of A1 + 2H(2). Complex T2 may be the initial complex for further H(2) addition under proper conditions, or it could lose one H(2) molecule followed by H migration from the Zr site to the N site. Both reactions are expected to occur, because of the closeness of the barrier heights (25.1 and 36.5 kcal/mol, respectively). Gentle warming is required for further H(2) additions, which can be understood from the energetics as well. The high reactivity of T1 with H(2) has been discussed by the comparison of the calculation of A1 and another complex with different ligands, presenting an interesting indication on the effects of the ligands. These theoretical results and discussion explaining the experiment should provide insight into the nature of the hydrogenation mechanism.

We give closed formulas for all vectors of the canonical basis of a level 2 irreducible integrable representation of U v (sl ∞ ). These formulas coincide at v = 1 with Lusztig's formulas for the constructible characters of the Iwahori-Hecke algebras of type B and D.

We give some closed formulas for certain vectors of the canonical bases of the Fock space representation of U v ( s l n ) U_v(\mathfrak {sl}_n) . As a result, a combinatorial description of certain parabolic Kazhdan-Lusztig polynomials for affine type A A is obtained.