Keiko Takano

DFT Study of Internal Alkyne-to-Disubstituted Vinylidene Isomerization in [CpRu(PhC≡CAr)(dppe)]+

Internal alkyne-to-vinylidene isomerization in the Ru complexes ([CpRu(η(2)-PhC≡CC(6)H(4)R-p)(dppe)](+) (Cp = η(5)-C(5)H(5); dppe = Ph(2)PCH(2)CH(2)PPh(2); R = OMe, Cl, CO(2)Et)) has been investigated using a combination of quantum mechanics and molecular mechanics methods (QM/MM), such as ONIOM(B3PW91:UFF), and density functional theory (DFT) calculations. Three kinds of model systems (I-III), each having a different QM region for the ONIOM method, revealed that considering both the quantum effect of the substituent of the aryl group in the η(2)-alkyne ligand and that of the phenyl groups in the dppe ligand is essential for a correct understanding of this reaction. Several plausible mechanisms have been analyzed by using DFT calculations with the B3PW91 functional. It was found that the isomerization of three complexes (R = OMe, CO(2)Et, and Cl) proceeds via a direct 1,2-shift in all cases. The most favorable process in energy was path 3, which involves the orientation change of the alkyne ligand in the transition state. The activation energies were calculated to be 13.7, 15.0, and 16.4 kcal/mol, respectively, for the three complexes. Donor-acceptor analysis demonstrated that the aryl 1,2-shift is a nucleophilic reaction. Furthermore, our calculation results indicated that an electron-donating substituent on the aryl group stabilizes the positive charge on the accepting carbon rather than that on the migrating aryl group itself at the transition state. Therefore, unlike the general nucleophilic reaction, the less-electron-donating aryl group has an advantage in the migration.

Site‐specific fragmentation following Si:2p core‐level photoexcitation of F3SiCH2Si(CH3)3 in the vapor phase

Site‐specific fragmentation following Si:2p photoexcitation of (trifluorosilyl) (trimethylsilyl)methane [F3SiCH2Si(CH3)3 (FSMSM)] has been studied by means of photoelectron‐photoion and photoion–photoion coincidence techniques. The total photoionization efficiency curve of FSMSM has only one broad peak near the Si:2p core‐ionization threshold and no evidence is obtained for the occurrence of selective excitation of each of the two Si atoms. From the results of ab initio calculations of FSMSM, it is found that the magnitude of the Coulomb interaction between the valence electrons and the Si:2p core electrons is very similar at the two Si sites. As a result, the difference in the chemical shift of the 2p core level between the two Si sites is very small. However, the evidence for site‐specific fragmentation of the molecule following the Si:2p core‐level photoexcitation is obtained by analyzing the photoion–photoion coincidence spectra; the relative yields of H+–SiF+ and CH+n–SiF+3 (n=1–3) ion pairs are enha...

A Novel Method for Characterization of Three-Dimensional Reaction Fields Based on Electrostatic and Steric Interactions toward the Goal of Quantitative Analysis and Understanding of Organic Reactions

A novel characterization method named FRAU (Field-characterization for reaction analysis and understanding), which numerically characterizes field around molecules based on electrostatic and steric interactions with pseudoreactant, has been developed for giving numeric measures of factors controlling reactions. FRAU estimates three kinds of features (FRAU features), i.e., extent of reaction field, electrostatic features, and steric features. Power of the FRAU features as discriminators recognizing similarities and differences of characteristics of structures and roles of reagents in reactions have been examined by 39 reagents containing Mg or B atoms. Similarities in these features were analyzed with the help of a self-organizing map (SOM). Good correspondences were found between the features, structures, and the role of the reagents in reaction. The results show abilities of FRAU to give useful numeric characterization of reagents.

Ab initio molecular orbital dynamic reaction path simulations of HNC⇌HCN isomerization reaction: election of the reaction mode in a thermally excited system

Abstract Dynamic reaction path (DRP) simulation of the HNC⇌HCN isomerization reaction has been carried out at the HF/6-31 G ** level to search for an intramolecular vibrational energy redistribution (IVR) process converging to the reaction mode of vibration having an imaginary frequency near the transition state (TS). Starting at the TS, a molecule was pushed forward or backward with the least necessary excess energy in the direction of the reaction mode. The thus started DRP, proposed here as intrinsic dynamic reaction path (IDRP), was analyzed in terms of vibration mixing and vibration mapping methods, giving an example of the IVR process to build up the reaction mode from randomly distributed vibration modes.

Quantum chemical interpretation of oxidation number as applied to carbon and oxygen compounds. Numerical analysis of the electron distribution with ab initio molecular orbital wave functions

Analyse des distributions electroniques autour des atomes C, O et F dans les trois series: 1) CH 4 , CH 3 OH, HCHO, HCOOH, CO 2 ; 2) H 2 O,H 2 O 2 ; 3) F 2 O,F 2 O 2 , a partir de calculs MO ab initio

Affinity of HIV-1 antibody 2G12 with monosaccharides: a theoretical study based on explicit and implicit water models.

In order to develop potential ligands to HIV-1 antibody 2G12 toward HIV-1 vaccine, binding mechanisms of the antibody 2G12 with the glycan ligand of D-mannose and D-fructose were theoretically examined. D-Fructose, whose molecular structure is slightly different from D-mannose, has experimentally shown to have stronger binding affinity to the antibody than that of D-mannose. To clarify the nature of D-fructoses higher binding affinity over D-mannose, we studied interaction between the monosaccharides and the antibody using ab initio fragment molecular orbital (FMO) method considering solvation effect as implicit model (FMO-PCM) as well as explicit water model. The calculated binding free energies of the glycans were qualitatively well consistent with the experimentally reported order of their affinities with the antibody 2G12. In addition, the FMO-PCM calculation elucidated the advantages of D-fructose over D-mannose in the solvation energy as well as the entropic contribution term obtained by MD simulations. The effects of explicit water molecules observed in the X-ray crystal structure were also scrutinized by means of FMO methods. Significant pair interaction energies among D-fructose, amino acids, and water molecules were uncovered, which indicated contributions from the water molecules to the strong binding ability of D-fructose to the antibody 2G12. These FMO calculation results of explicit water model as well as implicit water model indicated that the strong binding of D-fructose over D-mannose was due to the solvation effects on the D-fructose interaction energy.

A theoretical study of tautomerism in hexa-aza macrocycles containing 2,2′-bipyridine and 1,10-phenanthroline and their ability to form lithium complexes

Abstract Calculations using ab initio restricted Hartree–Fock molecular orbital (RHF MO) theory and the density functional theory (DFT) are reported for several structural isomers of hexa-aza macrocycles 1 – 3 containing 2,2′-bipyridine and 1,10-phenanthroline, as well as their lithium complexes. Based on the computational results, we describe the geometries, imine/amine tautomerism, and lithium complexation of these hexa-aza macrocycles. Metal-free macrocycles have the most stable imine form with planar structures, whereas their lithium complexes tend to be in the amine form. We discuss protonation/deprotonation processes with proton transfer in a cavity of macrocycles as a means of interpreting imine/amine tautomerism. Deprotonation and the subsequent geometric changes in tautomeric isomers lead to structural changes, i.e. macrocycles 2 and 3 having 2,2′-bipyridines become non-planar; this theoretical result is consistent with observed experimental behaviors. The present results indicate that unlike macrocycle 1 , macrocycles 2 and 3 with 2,2′-bipyridine have the capacity for amine/imine tautomerism, as well as the ability to form complexes with lithium.

Novel sulfated gangliosides, high-affinity ligands for neural siglecs, inhibit NADase activity of leukocyte cell surface antigen CD38.

Three kinds of novel sulfated gangliosides structurally related to the Chol-1 (alpha-series) ganglioside GQ1balpha were synthesized. These sulfated gangliosides were potent inhibitors of NADase activity of leukocyte cell surface antigen CD38. Among the synthetic gangliosides, GSC-338 (II(3)III(6)-disulfate of iso-GM1b) was surprisingly found to be the most potent structure in both the NADase inhibition and MAG-binding activity. The present study indicates that the sulfated gangliosides are useful to study the recognition of the internal tandem sialic acid residues alpha2-3-linked to Gal(II(3)) as well as the siglec-dependent recognition including a terminal sialic acid residue.

Water molecules inside protein structure affect binding of monosaccharides with HIV-1 antibody 2G12.

Water molecules inside biomolecules constitute integral parts of their structure and participate in the functions of the proteins. Some of the X‐ray crystallographic data are insufficient for analyzing a series of ligand–protein complexes in the same condition. We theoretically investigated antibody binding abilities of saccharide ligands and the effects of the inner water molecules of ligand–antibody complexes. Classical molecular dynamics and quantum chemical simulations using a model with possible water molecules inside the protein were performed with saccharide ligands and Human Immunodeficiency Virus 1 neutralizing antibody 2G12 complexes to estimate how inner water molecules of the protein affect the dynamics of the complexes as well as the ligand–antibody interaction. Our results indicate the fact that d‐fructoses strong affinity to the antibody was partly due to the good retentiveness of solvent water molecules of the ligand and its stability of the ligands conformation and relative position in the active site.

CHEMICAL DESCRIPTION OF THE INTERACTION BETWEEN GLYCAN LIGAND AND SIGLEC-7 USING AB INITIO FMO METHOD AND CLASSICAL MD SIMULATION

We clarified in detail the theoretical features of the interaction between the glycan ligand containing α(2,8)-disialyl residue and a lectin called Siglec (sialic acid Ig-like binding lectin)-7 by ab initio fragment molecular orbital (FMO) calculations and classical molecular dynamics (MD) simulations. By comparing the ligand–Siglec-7 interaction of the wild-type Siglec-7 and those of mutant-Siglec-7s, we herein describe protein–glycan interactions thoroughly, and provide fundamentals to elucidate ligand-recognition mechanism. The experimentally observed decrease in ligand binding produced by mutagenesis at residues in non-active site was explained with MD simulations; both Trp85 and Trp74 residues are fundamental in structural stability of the Siglec-7, which is involved in the binding of the glycan ligand. The interaction energies obtained by the FMO method were consistent with the experimental ligand-binding results. The glycan ligand preferentially interacted with Siglec-7 via sialic acid residues. The stabilization by the dispersion interaction between the neutral parts of the ligand was also considerable in the binding.