Acceleration of self‐consistent field convergence in ab initio molecular dynamics simulation with multiconfigurational wave function

The Lagrange interpolation of molecular orbital (LIMO) method, which reduces the number of self‐consistent field iterations in ab initio molecular dynamics simulations with the Hartree–Fock method and the Kohn–Sham density functional theories, is extended to the theory of multiconfigurational wave functions. We examine two types of treatments for the active orbitals that are partially occupied. The first treatment, as denoted by LIMO(C), is a simple application of the conventional LIMO method to the union of the inactive core and the active orbitals. The second, as denoted by LIMO(S), separately treats the inactive core and the active orbitals. Numerical tests to compare the two treatments clarify that LIMO(S) is superior to LIMO(C). Further applications of LIMO(S) to various systems demonstrate its effectiveness and robustness. © 2014 Wiley Periodicals, Inc.     

Three Distinct Redox States of an Oxo‐Bridged Dinuclear Ruthenium Complex

A series of [{(terpy)(bpy)Ru}(μ‐O){Ru(bpy)(terpy)}]ⁿ⁺ ( [RuORu]ⁿ⁺ , terpy=2,2′;6′,2′′‐terpyridine, bpy=2,2′‐bipyridine) was systematically synthesized and characterized in three distinct redox states (n=3, 4, and 5 for Ru^II,III₂ , Ru^III,III₂ , and Ru^III,IV₂ , respectively). The crystal structures of [RuORu]ⁿ⁺ (n=3, 4, 5) in all three redox states were successfully determined. X‐ray crystallography showed that the Ru? O distances and the Ru‐O‐Ru angles are mainly regulated by the oxidation states of the ruthenium centers. X‐ray crystallography and ESR spectra clearly revealed the detailed electronic structures of two mixed‐valence complexes, [Ru^IIIORu^IV]⁵⁺ and [Ru^IIORu^III]³⁺ , in which each unpaired electron is completely delocalized across the oxo‐bridged dinuclear core. These findings allow us to understand the systematic changes in structure and electronic state that accompany the changes in the redox state.     

Function and association of CyanoP in photosystem II of Synechocystis sp. PCC 6803

The CyanoP protein is a cyanobacterial homolog of the PsbP protein, which is an extrinsic subunit of photosystem II (PSII) in green plant species. The molecular function of CyanoP has been investigated in mutant strains of Synechocystis but inconsistent results have been reported by different laboratories. In this study, we generated and characterized a Synechocystis mutant in which entire region of the CyanoP gene was eliminated. After repeated subculture in CaCl₂-depleted medium, growth retardation was clearly observed for a CyanoP knockout mutant of Synechocystis sp. PCC 6803 (?P). The PSII-mediated oxygen-evolving activity of the ?P cells was more susceptible to depletion of CaCl₂ than that of wild-type cells. The 77 K fluorescence emission spectra indicated that energy coupling between phycobilisome and PSII was perturbed in both wild-type and ?P cells under CaCl₂-depleted conditions, and was more evident for the ?P mutant. To examine the association of CyanoP with PSII complexes, we tested several detergents for solubilization of thylakoid membranes and showed that CyanoP was partly included in fractions containing large protein complexes in gel-filtration analysis. These results indicate that CyanoP constitutively stabilizes PSII functionality in vivo.     

Precise determination of bromine in PP resin pellet by instrumental neutron activation analysis using internal standardization

Instrumental neutron activation analysis with the internal standardization was applied to the precise determination of Br in polypropylene resin of candidate certified reference material. The known amount of ¹⁹⁷Au was used as an internal standard to compensate for neutron flux inhomogeneity, to improve the γ ray measurement uncertainty and the linearity of the calibration curves. The reliability of the proposed method validated using analytical results of BCR-681. The analytical result of Br in the sample was consistent with that obtained by ID-ICPMS. The relative expanded uncertainty (k = 2) was 1.5 %, and it was equivalent to that of ID-ICPMS.     

Imaging mass spectrometry distinguished the cancer and stromal regions of oral squamous cell carcinoma by visualizing phosphatidylcholine (16:0/16:1) and phosphatidylcholine (18:1/20:4)

Most oral cancers are oral squamous cell carcinoma (OSCC). The anatomical features of OSCC have been histochemically evaluated with hematoxylin and eosin. However, the border between the cancer and stromal regions is unclear and large portions of the cancer and stromal regions are resected in surgery. To reduce the resected area and maintain oral function, a new method of diagnosis is needed. In this study, we tried to clearly distinguish the border on the basis of biomolecule distributions visualized by imaging mass spectrometry (IMS). In the IMS dataset, eleven signals were significantly different in intensity (p?<?0.01) between the cancer and stromal regions. Two signals at m/z 770.5 and m/z 846.6 were distributed in each region, and a clear border was revealed. Tandem mass spectrometric (MS/MS) analysis identified these signals as phosphatidylcholine (PC) (16:0/16:1) at m/z 770.5 in the cancer region and PC (18:1/20:4) at m/z 846.6 in the stromal region. Moreover, the distribution of PC species containing arachidonic acid in the stromal region suggests that lymphocytes accumulated in response to the inflammation caused by cancer invasion. In conclusion, the cancer and stromal regions of OSCCs were clearly distinguished by use of these PC species and IMS analysis, and this molecular identification can provide important information to elucidate the mechanism of cancer invasion.     

Revisiting the extrapolation of correlation energies to complete basis set limit

The extrapolation scheme of correlation energy is revisited to evaluate the complete basis set limit from double‐zeta (DZ) and triple‐zeta levels of calculations. The DZ level results are adjusted to the standard asymptotic behavior with respect to the cardinal number, observed at the higher levels of basis sets. Two types of adjusting schemes with effective scaling factors, which recover errors in extrapolations with the DZ level basis set, are examined. The first scheme scales the cardinal number for the DZ level energy, while the second scheme scales the prefactor of the extrapolation function. Systematic assessments on the Gaussian‐3X and Gaussian‐2 test sets reveal that these calibration schemes successfully and drastically reduce errors without additional computational efforts. © 2015 Wiley Periodicals, Inc.     

Structure activity relationships of quinoxalin-2-one derivatives as platelet-derived growth factor-beta receptor (PDGFbeta R) inhibitors, derived from molecular modeling

We previously reported a quinoxalin-2-one compound (Compound 1) that had inhibitory activity equivalent to existing platelet-derived growth factor-beta receptor (PDGFbeta R) inhibitors. Lead optimization of Compound 1 to increase its activity and selectivity, using structural information regarding PDGFbeta R-ligand interactions, is urgently needed. Here we present models of the PDGFbeta R kinase domain complexed with quinoxalin-2-one derivatives. The models were constructed using comparative modeling, molecular dynamics (MD) and ligand docking. In particular, conformations derived from MD, and ligand binding site information presented by alpha-spheres in the pre-docking processing, allowed us to identify optimal protein structures for docking of target ligands. By carrying out molecular modeling and MD of PDGFbeta R in its inactive state, we obtained two structural models having good Compound 1 binding potentials. In order to distinguish the optimal candidate, we evaluated the structural activity relationships (SAR) between the ligand-binding free energies and inhibitory activity values (IC50 values) for available quinoxalin-2-one derivatives. Consequently, a final model with a high SAR was identified. This model included a molecular interaction between the hydrophobic pocket behind the ATP binding site and the substitution region of the quinoxalin-2-one derivatives. These findings should prove useful in lead optimization of quinoxalin-2-one derivatives as PDGFb R inhibitors.     

Oxidative rearrangement of tertiary allylic alcohols employing oxoammonium salts

Practical and highly efficient methods for oxidative rearrangement of tertiary allylic alcohols to beta-substituted alpha,beta-unsaturated carbonyl compounds employing oxoammonium salts are described. The methods developed are applicable to acyclic substrates as well as medium membered ring substrates and macrocyclic substrates. The counteranion of the oxoammonium salt plays crucial roles on this oxidative rearrangement.