Intermolecular propargyl/allenyl group transfer from Pd(II) to Pt(0) and Pt(II) to Pd(0). Key reaction in metal-catalyzed isomerization between propargyl and allenyl metal complexes

Isomerization of phenyl-substituted propargylplatinum(II) complex, trans-Pt(CH₂CCPh)(Cl)(PPh₃)₂ (1) to allenyl complex, trans-Pt(CPh=C=CH₂)(Cl)(PPh₃)₂ (2) was found to be catalyzed by zerovalent complex Pd(PPh₃)₄. The reaction was proposed to proceed through the transfer of the propargyl/allenyl ligand both from Pt(II) to Pd(0) and Pd(II) to Pt(0). The former transfer, which seemingly has a thermodynamic disadvantage, has unambiguously been confirmed to take place; treatment of 1 with Pd(PPh₃)₄ or a mixture of Pd₂(dba)₃ and PPh₃ resulted in the formation of Pd(I) complex, Pd₂(μ-PhCCCH₂)(μ-Cl)(PPh₃)₂ which lies in equilibrium with a mixture of propargyl/allenylpalladium(II) and Pd(0) complexes.     

Synthesis and mesomorphic properties of new chiral banana-shaped liquid crystals with chiral 3-(alkoxy)propoxy terminal groups

New chiral banana-shaped liquid crystals with chiral 3-(alkoxy)propoxy terminal groups (Pn-O-PIMB5*-4O, n = 7, 8, 9 and 10) were synthesized and their mesomorphic properties and phase structures investigated by means of electro-optic measurements, polarizing optical microscopy, differential scanning calorimetry, and second harmonic generation measurements. Most of these chiral bent-core mesogens (n = 7-9) showed the antiferroelectric B2 phase, whereas P10-O-PIMB5*-4O exhibited the B7 phase. Comparing with the previously reported homologue Pn-O-PIMB(n-2)*, we conclude that the terminal chain structure, particularly the position of chiral centres, plays an important role in the emergence of particular phase structures.     

Feedback control of instability waves in a transitional flat-plate boundary layer

A semi-automatic and active control of T-S waves and oblique waves in a transitional flat plate boundary layer is carried out in a wind-tunnel experiment and a numerical simulation. An array of piezo-ceramic actuators attached on a surface is used to generate counter waves that cancel the incoming instability waves. The actuator’s operating amplitudes and phases are successively updated using the velocity fluctuations monitored downstream by a rake of hotwires. Experimental results show that the system is effective in weakening these waves when their inclination angles are less than 15 degrees. However, the system encountered difficulty in controlling the waves of large inclination angles. In the numerical simulation, it is shown that the control can be accomplished much easier. The numerical results show that controllability of the large inclination angle waves can be improved by shortening the spanwise length each actuator piece. The danger of pursuing this kind of research solely by a numerical simulation is pointed out.     

A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor

We have developed a new docking method to consider receptor flexibility, a hybrid method of molecular dynamics and harmonic dynamics. The global motions of the whole receptor were approximately introduced into those of the receptor in the docking simulation as harmonic dynamics. On the other hand, the local flexibility of the side chains was also considered by conventional molecular dynamics. We confirmed that this new method can reproduce the fluctuations of the whole receptor by making a comparison of the directions and amplitudes of the global fluctuations. Then this method was applied to the docking of HIV-1 protease and its ligand. As a result, we observed a docking process where the ligand enters into the binding pocket well, which implies that this method is effective enough to reproduce a molecular complex formation.     

Virtual‐system‐coupled adaptive umbrella sampling to compute free‐energy landscape for flexible molecular docking

A novel enhanced conformational sampling method, virtual‐system‐coupled adaptive umbrella sampling (V‐AUS), was proposed to compute 300‐K free‐energy landscape for flexible molecular docking, where a virtual degrees of freedom was introduced to control the sampling. This degree of freedom interacts with the biomolecular system. V‐AUS was applied to complex formation of two disordered amyloid‐β (Aβ_30–35) peptides in a periodic box filled by an explicit solvent. An interpeptide distance was defined as the reaction coordinate, along which sampling was enhanced. A uniform conformational distribution was obtained covering a wide interpeptide distance ranging from the bound to unbound states. The 300‐K free‐energy landscape was characterized by thermodynamically stable basins of antiparallel and parallel β‐sheet complexes and some other complex forms. Helices were frequently observed, when the two peptides contacted loosely or fluctuated freely without interpeptide contacts. We observed that V‐AUS converged to uniform distribution more effectively than conventional AUS sampling did. © 2015 Wiley Periodicals, Inc.     

New syntheses and spectral properties of pteridine‐related heterocycles from 2,5‐diamino‐3,6‐dicyanopyrazine

The reaction of 2,5‐diamino‐3,6‐dicyanopyrazine ( 1 ) as a new pyrazine raw material with alkyl isocyanate in the presence of sodium hydride gave novel heptahydroirnidazo[4,5‐g]pteridine‐2,6,8‐trione ( 2 ), but with tertiary butyl isocyanate gave trihydroimidazo[4,5‐b]pyrazine‐2‐ones ( 3 ). Similar reaction of 1 with alkyl thioisocyanate followed by alkyl iodide gave tetrahydropyrimido[4,5‐g]pteridines ( 4 ). The reac tion of 1 with alkylamine gave the amine‐adduct of the cyano groups which was further reacted with arylaldehyde to give the pyrimido[4,5‐g]pteridine ( 10 ). The products prepared are all of interest as potential pesticides and fluorescent chromophores.     

A Virtual Active Compound Produced from the Negative Image of a Ligand-binding Pocket, and its Application to in-silico Drug Screening

We developed a new structure-based in-silico screening method using a negative image of a ligand-binding pocket and a multi-protein–compound interaction matrix. Based on the structure of the ligand pocket of the target protein, we designed a negative image, which consists of virtual atoms whose radii are close to those of carbon atoms. The virtual atoms fit the pocket ideally and achieve an optimal Coulomb interaction. A protein–compound docking program calculates the protein–compound interaction matrix for many proteins and many compounds including the negative image, which can be treated as a virtual compound. With specific attention to a vector of docking scores for a single compound with many proteins, we selected a compound whose score vector was similar to that of the negative image as a candidate hit compound. This method was applied to representative target proteins and showed high database enrichment with a relatively quick procedure.     

Noise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening

We developed a new method to improve the accuracy of molecular interaction data using a molecular interaction matrix. This method was applied to enhance the database enrichment of in silico drug screening and in silico target protein screening using a protein-compound affinity matrix calculated by a protein-compound docking software. Our assumption was that the protein-compound binding free energy of a compound could be improved by a linear combination of its docking scores with many different proteins. We proposed two approaches to determine the coefficients of the linear combination. The first approach is based on similarity among the proteins, and the second is a machine-learning approach based on the known active compounds. These methods were applied to in silico screening of the active compounds of several target proteins and in silico target protein screening.