Rapid QM/MM approach for biomolecular systems under periodic boundary conditions: Combination of the density‐functional tight‐binding theory and particle mesh Ewald method

A quantum mechanical/molecular mechanical (QM/MM) approach based on the density‐functional tight‐binding (DFTB) theory is a useful tool for analyzing chemical reaction systems in detail. In this study, an efficient QM/MM method is developed by the combination of the DFTB/MM and particle mesh Ewald (PME) methods. Because the Fock matrix, which is required in the DFTB calculation, is analytically obtained by the PME method, the Coulomb energy is accurately and rapidly computed. For assessing the performance of this method, DFTB/MM calculations and molecular dynamics simulation are conducted for a system consisting of two amyloid‐β(1‐16) peptides and a zinc ion in explicit water under periodic boundary conditions. As compared with that of the conventional Ewald summation method, the computational cost of the Coulomb energy by utilizing the present approach is drastically reduced, i.e., 166.5 times faster. Furthermore, the deviation of the electronic energy is less than . © 2016 Wiley Periodicals, Inc.     

Arenophile‐Mediated Dearomative Reduction

A dearomative reduction of simple arenes has been developed which employs a visible‐light‐mediated cycloaddition of arenes with an N‐N‐arenophile and in situ diimide reduction. Subsequent cycloreversion or fragmentation of the arenophile moiety affords 1,3‐cyclohexadienes or 1,4‐diaminocyclohex‐2‐enes, compounds that are not synthetically accessible using existing dearomatization reactions. Importantly, this strategy also provides numerous opportunities for further derivatization as well as site‐selective functionalization of polynuclear arenes.     

Carbohydrate-appended curdlans as a new family of glycoclusters with binding properties both for a polynucleotide and lectins

Beta-1,3-glucans having carbohydrate-appendages (alpha-D-mannoside, N-acetyl-beta-D-glucosaminide and beta-lactoside) at the C6-position of every repeating unit can be readily prepared from curdlan (a linear beta-1,3-glucan) through regioselective bromination/azidation to afford 6-azido-6-deoxycurdlan followed by chemo-selective Cu(i)-catalyzed [3 + 2]-cycloaddition with various carbohydrate modules having a terminal alkyne. The resultant carbohydrate-appended curdlans can interact with polycytosine to form stable macromolecular complexes consistent with two polysaccharide strands and one polycytosine strand. Furthermore, these macromolecular complexes show strong and specific affinity toward carbohydrate-binding proteins (lectins). Therefore, one can utilize these carbohydrate-appended curdlans as a new family of glycoclusters.     

Hydrogen generation from weak acids: electrochemical and computational studies of a diiron hydrogenase mimic

Extended investigation of electrocatalytic generation of dihydrogen using [(mu-1,2-benzenedithiolato)][Fe(CO)3]2 has revealed that weak acids, such as acetic acid, can be used. The catalytic reduction producing dihydrogen occurs at approximately -2 V for several carboxylic acids and phenols resulting in overpotentials of only -0.44 to -0.71 V depending on the weak acid used. This unusual catalytic reduction occurs at a potential at which the starting material, in the absence of a proton source, does not show a reduction peak. The mechanism for this process and structures for the intermediates have been discerned by electrochemical and computational analysis. These studies reveal that the catalyst is the monoanion of the starting material and an ECEC mechanism occurs.     

Relocation of active acetylcholinesterase to liposome-gel conjugate

Relocation of a glycosylphosphatidylinositol (GPI)-anchored protein acetylcholinesterase (AChE) in its enzymatically active form from proteovesicles containing human erythrocyte ghost membrane proteins onto a liposome-gel conjugate was examined. Liposomes of 1,2-dimyristoylphosphatidylcholine (DMPC) were immobilized on Sephacryl S-1000 gel that was chemically modified to bear hydrophobic octyl moieties. Upon coincubation of the liposome-gel conjugate with freely suspended proteovesicles prepared from erythrocyte ghosts, 50% of the AChE left the proteovesicles and immobilized onto the liposome-gel conjugate in 18 h. When the proteovesicles were immobilized and interacted with freely suspended plain liposomes, approximately 2% of the AChE appeared in the liposome fraction. The relocation of AChE apparently possesses strong preference for the liposome-gel conjugate, suggesting that the hydrophobic moieties on the gel could assist the relocation.     

Exact diagonalization studies on two-band minimal model for iron-based superconductors

In order to explore a superconducting mechanism on iron-based superconductors, we numerically study a two-band minimal model considering two degenerate d_xz and d_yz orbitals on Fe atom. We perform exact diagonalization on a two-band and two-leg square ladder totally composed of 10 lattice sites, which is computationally equivalent to 4-leg 20-sites square-Hubbard-ladder. Consequently, we find that a robust pairing occurs in a wide parameter range when the intra-orbital repulsive interaction becomes smaller than the inter-orbital one. Moreover, the obtained binding energy can grow into much larger value than that obtained in the single band Hubbard model depending on the parameter range.     

Multibaric-multithermal ensemble molecular dynamics simulations

We present new generalized-ensemble molecular dynamics simulation algorithms, which we refer to as the multibaric-multithermal molecular dynamics. We describe three algorithms based on (1) the Nosé thermostat and the Andersen barostat, (2) the Nosé-Poincaré thermostat and the Andersen barostat, and (3) the Gaussian thermostat and the Andersen barostat. The multibaric-multithermal simulations perform random walks widely both in the potential-energy space and in the volume space. Therefore, one can calculate isobaric-isothermal ensemble averages in wide ranges of temperature and pressure from only one simulation run. We test the effectiveness of the multibaric-multithermal algorithm by applying it to a Lennard-Jones 12-6 potential system.     

In-Line Reactions and Ionizations of Vaporized Diphenylchloroarsine and Diphenylcyanoarsine in Atmospheric Pressure Chemical Ionization Mass Spectrometry

We propose detecting a fragment ion (Ph₂As⁺) using counter-flow introduction atmospheric pressure chemical ionization ion trap mass spectrometry for sensitive air monitoring of chemical warfare vomiting agents diphenylchloroarsine (DA) and diphenylcyanoarsine (DC). The liquid sample containing of DA, DC, and bis(diphenylarsine)oxide (BDPAO) was heated in a dry air line, and the generated vapor was mixed into the humidified air flowing through the sampling line of a mass spectrometer. Humidity effect on the air monitoring was investigated by varying the humidity of the analyzed air sample. Evidence of the in-line conversion of DA and DC to diphenylarsine hydroxide (DPAH) and then BDPAO was obtained by comparing the chronograms of various ions from the beginning of heating. Multiple-stage mass spectrometry revealed that the protonated molecule (MH⁺) of DA, DC, DPAH, and BDPAO could produce Ph₂As⁺ through their in-source fragmentation. Among the signals of the ions that were investigated, the Ph₂As⁺ signal was the most intense and increased to reach a plateau with the increased air humidity, whereas the MH⁺ signal of DA decreased. It was suggested that DA and DC were converted in-line into BDPAO, which was a major source of Ph₂As⁺.

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Photo‐Induced Anomalous Deformation of Poly(N‐Isopropylacrylamide) Gel Hybridized with an Inorganic Nanosheet Liquid Crystal Aligned by Electric Field

Poly‐(N‐isopropylacrylamide) (PNIPA) hydrogel films doped with uniaxially aligned liquid crystalline (LC) nanosheets adsorbed with a dye are synthesized and its anomalous photothermal deformation is demonstrated. The alignment of the nanosheet LC at the cm‐scale is easily achieved by the application of an in‐plane or out‐of‐plane AC electric field during photo‐polymerization. A photoresponsive pattern is printable onto the gel with μm‐scale resolution by adsorption of the dye through a pattern‐holed silicone rubber. When the gel is irradiated with light, only the colored part is photothermally deformed. Interestingly, the photo‐irradiated gel shows temporal expansion along one direction followed by anisotropic shrinkage, which is an anomalous behavior for a conventional PNIPA gel.

     

Effect of geometrical imperfections on swelling-induced buckling patterns in gel films with a square lattice of holes

In this study, we investigate the effect of geometrical imperfections on swelling-induced buckling patterns in gel films with a square lattice of holes. Finite element analysis is performed using the inhomogeneous field theory of polymeric gels in equilibrium proposed by Hong et al. (2009). Periodic units consisting of 2 × 2 and 10 × 10 unit cells are analyzed under a generalized plane strain assumption. Geometrical imperfections are introduced using randomly oriented elliptical holes. The 2 × 2 unit cells show that the resulting buckling patterns are sensitive to imperfections; three different buckling patterns are obtained, and the most dominant one is the diamond plate pattern observed in experiments, which cannot be described using the model without imperfections. The 10 × 10 unit cells reveal that random imperfections are responsible for inducing homogeneous transformation into the diamond plate pattern. Furthermore, domain wall formation is simulated using a 10 × 10 unit cell model containing two elliptic holes.