Kazuya Ishimura

Accuracy of the three‐body fragment molecular orbital method applied to Møller–Plesset perturbation theory

The three‐body energy expansion in the fragment molecular orbital method (FMO) was applied to the 2nd order Møller–Plesset theory (MP2). The accuracy of both the two and three‐body expansions was determined for water clusters, alanine n‐mers (α‐helices and β‐strands) and one synthetic protein, using the 6‐31G* and 6‐311G* basis sets. At the best level of theory (three‐body, two molecules/residues per fragment), the absolute errors in energy relative to ab initio MP2 were at most 1.2 and 5.0 mhartree, for the 6‐31G* and 6‐311G* basis sets, respectively. The relative accuracy was at worst 99.996% and 99.96%, for 6‐31G* and 6‐311G*, respectively. A three‐body approximation was introduced and the optimum threshold value was determined. The protein calculation (6‐31G*) at the production level (FMO2/2) took 3 h on 36 3.2‐GHz Pentium 4 nodes and had the absolute error in the MP2 correlation energy of only 2 kcal/mol.

Dilithioplumbole: A Lead-Bearing Aromatic Cyclopentadienyl Analog

Aromatic Lead The bond stabilization, or aromaticity, observed in cyclic carbon molecules, such as benzene, relies on delocalization of electrons around the ring. Although electron distributions in heavier elements can complicate this arrangement, Saito et al. (p. 339) show that even lead, one of the heaviest metals, is able to participate in an otherwise carbon-based aromatic network. In an analog of the well-studied cyclopentadienyl anion, one carbon atom was replaced with lead, and the framework stabilized by appending phenyl groups to the other four carbons. Crystallography revealed a planar structure, which together with spectroscopic data and theoretical calculations confirmed the aromatic character of the product. Lead can participate in the delocalized electron network of an aromatic carbon ring. Although the concept of aromaticity has long played an important role in carbon chemistry, it has been unclear how applicable the stabilizing framework is to the heaviest elements. Here we report the synthesis of dilithiotetraphenylplumbole by reduction of hexaphenylplumbole. X-ray crystallography revealed a planar structure with no alternation of carbon–carbon bond lengths in the five-membered ring core. Nuclear magnetic resonance spectra and relativistic theoretical calculations show considerable aromatic character in the molecule, thus extending aromaticity to carbon’s heaviest congener.

A new parallel algorithm of MP2 energy calculations.

A new parallel algorithm has been developed for second‐order Møller–Plesset perturbation theory (MP2) energy calculations. Its main projected applications are for large molecules, for instance, for the calculation of dispersion interaction. Tests on a moderate number of processors (2–16) show that the program has high CPU and parallel efficiency. Timings are presented for two relatively large molecules, taxol (C47H51NO14) and luciferin (C11H8N2O3S2), the former with the 6‐31G* and 6‐311G** basis sets (1032 and 1484 basis functions, 164 correlated orbitals), and the latter with the aug‐cc‐pVDZ and aug‐cc‐pVTZ basis sets (530 and 1198 basis functions, 46 correlated orbitals). An MP2 energy calculation on C130H10 (1970 basis functions, 265 correlated orbitals) completed in less than 2 h on 128 processors.

Analytic energy gradient for second-order Møller-Plesset perturbation theory based on the fragment molecular orbital method

The first derivative of the total energy with respect to nuclear coordinates (the energy gradient) in the fragment molecular orbital (FMO) method is applied to second order Møller-Plesset perturbation theory (MP2), resulting in the analytic derivative of the correlation energy in the external self-consistent electrostatic field. The completely analytic energy gradient equations are formulated at the FMO-MP2 level. Both for molecular clusters (H(2)O)(64) and a system with fragmentation across covalent bonds, a capped alanine decamer, the analytic FMO-MP2 energy gradients with the electrostatic dimer approximation are shown to be complete and accurate by comparing them with the corresponding numeric gradients. The developed gradient is parallelized with the parallel efficiency of about 97% on 32 Pentium4 nodes connected by Gigabit Ethernet.

New parallel algorithm for MP2 energy gradient calculations

A new parallel algorithm has been developed for calculating the analytic energy derivatives of full accuracy second order Møller‐Plesset perturbation theory (MP2). Its main projected application is the optimization of geometries of large molecules, in which noncovalent interactions play a significant role. The algorithm is based on the two‐step MP2 energy calculation algorithm developed recently and implemented into the quantum chemistry program, GAMESS. Timings are presented for test calculations on taxol (C47H51NO14) with the 6‐31G and 6‐31G(d) basis sets (660 and 1032 basis functions, 328 correlated electrons) and luciferin (C11H8N2O3S2) with aug‐cc‐pVDZ and aug‐cc‐pVTZ (530 and 1198 basis functions, 92 correlated electrons). The taxol 6‐31G(d) calculations are also performed with up to 80 CPU cores. The results demonstrate the high parallel efficiency of the program.

First-principles computational visualization of localized surface plasmon resonance in gold nanoclusters.

Cluster-size dependence of localized surface plasmon resonance (LSPR) for Aun nanoclusters (n = 54, 146, 308, 560, 922, 1414) is investigated by using our recently developed computational program of first-principles calculations for photoinduced electron dynamics in nanostructures. The size of Au1414 (3.9 nm in diameter) is unprecedentedly large in comparison with those addressed in previous first-principles calculations of optical response in nanoclusters. These computations enable us to clearly see that LSPR gradually grows and the LSPR peaks red shift with increasing cluster size. The growth of LSPR is visualized in real space, demonstrating that electron charge distributions oscillate in a collective manner around the outermost surface region of the clusters. We further illustrate that the core d electrons screen the collective oscillation of the conduction-like s electrons.

Ionized and excited states of ferrocene: Symmetry adapted cluster-configuration-interaction study

The ground state, singlet, and triplet excited states, and ionized states of ferrocene Fe(C5H5)2 were studied by the symmetry adapted cluster (SAC)/SAC–configuration–interaction method. The calculated ionization energies and intensities fairly well reproduced the observed photoelectron spectrum in the wide region of 6–14 eV. In particular, the first two peaks (2E2′ and 2A1′) were assigned to the ionizations from the occupied 3d orbitals of Fe, mixed already with the two-electron shake-up processes. This is the first ab initio quantitative assignment that is consistent with the experimental data. For the singlet states, three d–d transitions were calculated at 2.12, 2.26, and 4.02 eV, which correspond to the experimental peaks observed at 2.69, 2.97, and 3.82 eV. We propose possible assignments for other absorption bands in the range of 2.12–6.57 eV. In another three triplet d–d transition states we calculated, we found that the energy order of these states (1 3E1″, 1 3E2″, 2 3E1″) differs from that of sin...

Dichlorocarbene Addition to C60 from the Trichloromethyl Anion: Carbene Mechanism or Bingel Mechanism?

The reactions of C(60) and trichloromethyl anion (CCl(3)(-)) via both the Bingel mechanism and the carbene mechanism were comparably studied by means of density functional theory (DFT) computations. The Bingel mechanism is highly competitive as compared with the carbene mechanism that leads to the formation of C(60)(CCl(2)). Unlike the carbene mechanism with a weak regioselectivity and solvent sensitivity, the Bingel mechanism yields the [6,6]-C(60)(CCl(2)) isomer as the exclusive product and favors highly polar solvents. The results receive strong experimental support and simultaneously rationalize these experimental findings.

Facile Synthesis of Dibenzopentalene Dianions and Their Application as New π-Extended Ligands

Reduction of phenyl(silyl)ethynes with potassium followed by quenching with iodine gave dibenzopentalenes in moderate yields. The intermediates of the reactions, dipotassium dibenzopentalenides, were isolated. The first dibenzopentalene-transition-metal complex was successfully synthesized. The ruthenium atoms are located above the six-membered rings. However, X-ray diffraction analysis and theoretical calculations revealed that the aromatic nature of the five-membered rings was retained. The cyclic voltammetry of the Ru complex revealed two oxidation waves with relatively large separation.

Synthesis, Structures, and Properties of Plumboles

Reactions of 1,4-dilithio-1,2,3,4-tetraphenyl-1,3-butadiene with dichlorodiphenylplumbane gave hexaphenylplumbole 1 and spirobiplumbole 2. These structures were determined by X-ray diffraction analysis. Electronic structures of 1 and 2 were discussed by the aid of NMR analysis and theoretical calculations. The compounds 1 and 2 were found to be the first fluorescent organolead compounds.