Dependency of ligand free energy landscapes on charge parameters and solvent models

We performed replica-exchange molecular dynamics (REMD) simulations of six ligands to examine the dependency of their free energy landscapes on charge parameters and solvent models. Six different charge parameter sets for each ligand were first generated by RESP and AM1-BCC methods using three different conformations independently. RESP charges showed some conformational dependency. On the other hand, AM1-BCC charges did not show conformational dependency and well reproduced the overall trend of RESP charges. The free energy landscapes obtained from the REMD simulations of ligands in vacuum, Generalized-Born (GB), and TIP3P solutions were then analyzed. We found that even small charge differences can produce qualitatively different landscapes in vacuum condition, but the differences tend to be much smaller under GB and TIP3P conditions. The simulations in the GB model well reproduced the landscapes in the TIP3P model using only a fraction of the computational cost. The protein-bound ligand conformations were rarely the global minimum states, but similar conformations were found to exist in aqueous solution without proteins in regions close to the global minimum, local minimum or intermediate states.     

Non-extractable photoinitiators based on thiol-functionalized benzophenones and thioxanthones

Non-extractable photoinitiators could be advantageous for use in biological, electronic, and food packaging applications. Therefore, thioxanthone and benzophenone derivatives were synthesized from 1,6-hexane dithiol and chlorinated benzophenone or thioxanthone. The efficiency of thiol-functionalized photoinitiators in combination with amine co-initiators was compared to benzophenone and isopropylthioxanthone with amine co-initiators, and the cleavage of photoinitiator 2,2-dimethoxy-1,2-diphenylethan-1-one in acrylic resins. The reaction kinetics were analyzed using photo-differential scanning calorimetry and real-time FTIR. Coating physical properties were evaluated by pendulum and pencil hardness, steel-wool scratch and mandrel bend tests. The non-extractable photoinitiators had higher absorbance than their benzophenone or isopropylthioxanthone counterparts due to the sulfide substitution on the phenyl ring, and the free thiol groups reacted with the acrylate by either an amine catalyzed Michael addition or a free-radical chain process. The combination of thiol-functionalized photoinitiators with secondary amines provides an efficient photoinitiator system that is locked into the photopolymerized network and cannot be extracted with typical solvents.     

Small-span bending test for determination of elastic-plastic properties of ultrathin Pt wires

A mechanical testing methodology for determination of elastic-plastic properties of very thin metallic wires using small-span bending under lateral load is described. Sufficient strain is locally developed in the tested section of wire by unsymmetrical bending with two opposite probes where one end of the wire is fixed on a substrate with rigid joint by Joule heat welding. From the load-displacement relationships obtained experimentally, Young’s modulus is determined by analytical formulation. Moreover, yield stress and hardening modulus of the wire are identified using an optimization strategy with finite-element analyses. The thin Pt wires with a nominal diameter of about 625 nm are examined by the testing scheme and the wires are found to have higher yield stress compared to bulk Pt.     

Public policy structuring incorporating reciprocal expectation analysis

This paper proposes a method of structuring public policy by incorporating reciprocal expectation analysis. The proposed method is characterized by three components: identification of the problem structure perceived by stakeholders using cognitive maps, policy structuring analysis with a value–driver matrix and a reciprocal expectation matrix, and feasibility analysis of agreements among the stakeholders. The three types of relationship among stakeholders are derived from the feasibility analysis, which are “Dosho-imu”, “Isho-imu”, and “Domu”. Three tests of feasibility to reach the agreement are then proposed: “information-sharing test”, “bargaining test”, and “reframing test”. A case study is presented, applying the method to strategic transportation planning in the Kanto region of Japan. Finally, the potential functions of the proposed method in practice are discussed.     

Total synthesis of (±)-erythravine based on ring closing dienyne metathesis

The first total synthesis of (±)-erythravine was achieved in thirteen steps from 3,4-dimethoxyphenethylamine using ring closing dienyne metathesis as the key step.     

The effect of UV irradiation on the reduction of Au(III) ions adsorbed on manganese dioxide.

The effect of UV (ultraviolet) irradiation on the adsorption of Au(III) ions on manganese dioxide and their reduction to Au(0) (gold with 0 valence state) was investigated using XPS (X-ray photoelectron spectroscopy) and 197Au M?ssbauer spectroscopy. The UV irradiation accelerated the adsorption and the reduction. From the fact that the proportion of Au(0) estimated from Au 4f XPS spectra for surface analysis was significantly smaller than that from 197Au M?ssbauer spectra for bulk analysis, we deduced that Au(0) was interpenetrated to the inside of manganese dioxide (into deeper places than about 30 A) where XPS is impossible to detect. The content of surface hydroxyl groups on manganese dioxide also increased due to the UV irradiation. The relationship between the charge in the content of hydroxyl groups and the interpenetration of Au(0) is discussed.     

Diffuse mode bifurcation of soil causing convection-like shear investigated by group-theoretic image analysis

Diffuse mode bifurcation of soil under plane-strain compression test is shown, by means of an image analysis based on group-theoretic bifurcation theory, to trigger convection-like shear and to precede shear band formation. First digital photos of Toyoura sand specimens are processed by PIV (particle image velocimetry) to gather digitized images of deformation. Next bifurcation from a uniform state is detected by expanding these images into the double Fourier series and finding a predominant harmonic diffuse bifurcation mode based on that theory. This harmonic bifurcation mode, which is the mixture of a few harmonic functions, expresses complex convection-like shear. Last bifurcation from a non-uniform state is detected by decomposing each image into a few images with different symmetries to extract non-harmonic diffuse bifurcation modes. Diffuse modes of bifurcation, which hitherto were hidden behind predominant uniform compressive deformation, have thus been made transparent by virtue of the group-theoretic image analysis proposed. A possible course of deformation suggested herein is the evolution of diffuse mode bifurcation with a convection-like bifurcation mode breaking uniformity and symmetry, followed by the formation of shear bands through localization.     

Efficient calculation of two‐electron integrals for high angular basis functions

The computation of electron repulsion integrals (ERIs) is the most time‐consuming process in the density functional calculation using Gaussian basis set. Many temporal ERIs are calculated, and most are stored on slower storage, such as cache or memory, because of the shortage of registers, which are the fastest storage in a central processing unit (CPU). Moreover, the heavy register usage makes it difficult to launch many concurrent threads on a graphics processing unit (GPU) to hide latency. Hence, we propose to optimize the calculation order of one‐center ERIs to minimize the number of registers used, and to calculate each ERI with three or six co‐operating threads. The performance of this method is measured on a recent CPU and a GPU. The proposed approach is found to be efficient for high angular basis functions with a GPU. When combined with a recent GPU, it accelerates the computation almost 4‐fold. © 2014 Wiley Periodicals, Inc.