Replica sub-permutation method for molecular dynamics and monte carlo simulations

We propose an improvement of the replica-exchange and replica-permutation methods, which we call the replica sub-permutation method (RSPM). Instead of considering all permutations, this method uses a new algorithm referred to as sub-permutation to perform parameter transition. The RSPM succeeds in reducing the number of combinations between replicas and parameters without the loss of sampling efficiency. For comparison, we applied the replica sub-permutation, replica-permutation, and replica-exchange methods to a β-hairpin mini protein, chignolin, in explicit water. We calculated the transition ratio and number of tunneling events in the parameter space, the number of folding–unfolding events, the autocorrelation function, and the autocorrelation time as measures of sampling efficiency. The results indicate that among the three methods, the proposed RSPM is the most efficient in both parameter and conformational spaces. © 2019 Wiley Periodicals, Inc.     

A hybrid density-functional study of the one-dimensional ferromagnetic ordering of (BDTA)[Ni(mnt)2]

The one-dimensional intermolecular ferromagnetic interaction of a charge-transfer (CT) complex, (BDTA)[Ni(mnt)₂] (BDTA: 1,3,2-benzodithiazolyl, mnt: maleonitriledithiolate), is studied by the Kohn–Sham hybrid density functional method, in order to understand the mechanism of the magnetism. All possible effective exchange integrals, J, between the spin pairs of the system indicate that a ferromagnetic interaction (J = 172 cm⁻¹) exists along the b-axis. Magnetic susceptibility, simulated with the ab initio determined J values by the quantum Monte Carlo (QMC) method, is qualitatively consistent with that measured experimentally.     

Synthesis of donor-acceptor chromophores by the [2 + 2] cycloaddition of arylethynyl-2H-cyclohepta[b]furan-2-ones with 7,7,8,8-tetracyanoquinodimethane

Arylethynyl-2H-cyclohepta[b]furan-2-ones reacted with 7,7,8,8-tetracyanoquinodimethane (TCNQ) in a formal [2 + 2] cycloaddition reaction, followed by ring opening of the initially formed cyclobutene derivatives, to afford the corresponding dicyanoquinodimethane (DCNQ) chromophores in excellent yields. The intramolecular charge-transfer (ICT) interactions between the 2H-cyclohepta[b]furan-2-one ring and DCNQ acceptor moiety were investigated by UV/Vis spectroscopy and theoretical calculations. The redox behavior of the novel DCNQ derivatives was examined by cyclic voltammetry (CV) and differential pulse voltammetry (DPV), which revealed their multistep electrochemical reduction properties depended on the number of DCNQ units in the molecule. Moreover, a significant color change was observed by visible spectroscopy under electrochemical reduction conditions.     

Synthesis of redox-active, intramolecular charge-transfer chromophores by the [2+2] cycloaddition of ethynylated 2H-cyclohepta[b]furan-2-ones with tetracyanoethylene

Ethynylated 2H-cyclohepta[b]furan-2-ones 5-15 have been prepared by Pd-catalyzed alkynylation of 3-iodo-5-isopropyl-2H-cyclohepta[b]furan-2-one (2) with the corresponding ethynylarenes or the reaction of 2-iodothiophene with 3-ethynyl-5-isopropyl-2H-cyclohepta[b]furan-2-one (4) under Sonogashira-Hagihara conditions. Compounds 5-15 reacted with tetracyanoethylene in a formal [2+2] cycloaddition reaction, followed by ring opening of the initially formed [2+2] cycloadducts, cyclobutenes, to afford the corresponding 1,1,4,4-tetracyanobutadienyl (TCBD) chromophores 16-26 in excellent yields. The intramolecular charge-transfer interactions between the 2H-cyclohepta[b]furan-2-one ring and TCBD acceptor moiety were investigated by UV/Vis spectroscopy and theoretical calculations. The redox behavior of the novel TCBD derivatives 16-26 was examined by cyclic voltammetry and differential pulse voltammetry, which revealed multistep electrochemical reduction properties, depending on the number of TCBD units in the molecule. Moreover, a significant color change was observed by UV/Vis spectroscopy under electrochemical reduction conditions.     

Production of a positron microprobe using a transmission remoderator.

A production method for a positron microprobe using a beta+-decay radioisotope (22Na) source has been investigated. When a magnetically guided positron beam was extracted from the magnetic field, the combination of an extraction coil and a magnetic lens enabled us to focus the positron beam by a factor of 10 and to achieve a high transport efficiency (71%). A 150-nm-thick Ni(100) thin film was mounted at the focal point of the magnetic lens and was used as a remoderator for brightness enhancement in a transmission geometry. The remoderated positrons were accelerated by an electrostatic lens and focused on the target by an objective magnetic lens. As a result, a 4-mm-diameter positron beam could be transformed into a microprobe of 60 microm or less with 4.2% total efficiency. The S parameter profile obtained by a single-line scan of a test specimen coincided well with the defect distribution. This technique for a positron microprobe is available to an accelerator-based high-intensity positron source and allows 3-dimensional vacancy-type defect analysis and a positron source for a transmission positron microscope.     

Role of OH-stretch/torsion coupling and quantum yield effects in the first OH overtone spectrum of cis-cis HOONO

A joint theoretical and experimental investigation is undertaken to study the effects of OH-stretch/HOON torsion coupling and of quantum yield on the previously reported first overtone action spectrum of cis-cis HOONO (peroxynitrous acid). The minimum energy path along the HOON dihedral angle is computed at the coupled cluster singles and doubles with perturbative triples level with correlation consistent polarized quadruple zeta basis set, at the structure optimized using the triple zeta basis set (CCSD(T)/cc-pVQZ//CCSD(T)/cc-pVTZ). The two-dimensional ab initio potential energy and dipole moment surfaces for cis-cis HOONO are calculated as functions of the HOON torsion and OH bond length about the minimum energy path at the CCSD(T)/cc-pVTZ and QCISD/AUG-cc-pVTZ (QCISD-quadratic configuration interaction with single and double excitation and AUG-augmented with diffuse functions) level of theory/basis, respectively. The OH-stretch vibration depends strongly on the torsional angle, and the torsional potential possesses a broad shelf at approximately 90 degrees , the cis-perp conformation. The calculated electronic energies and dipoles are fit to simple functional forms and absorption spectra in the region of the OH fundamental and first overtone are calculated from these surfaces. While the experimental and calculated spectra of the OH fundamental band are in good agreement, significant differences in the intensity patterns are observed between the calculated absorption spectrum and the measured action spectrum in the 2nu(OH) region. These differences are attributed to the fact that several of the experimentally accessible states do not have sufficient energy to dissociate to OH+NO(2) and therefore are not detectable in an action spectrum. Scaling of the intensities of transitions to these states, assuming D(0)=82.0 kJ/mol, is shown to produce a spectrum that is in good agreement with the measured action spectrum. Based on this agreement, we assign two of the features in the spectrum to Deltan=0 transitions (where n is the HOON torsion quantum number) that are blue shifted relative to the origin band, while the large peak near 7000 cm(-1) is assigned to a series of Deltan=+1 transitions, with predominant contributions from torsionally excited states with substantial cis-perp character. The direct absorption spectrum of cis-cis HOONO (6300-6850 cm(-1)) is recorded by cavity ringdown spectroscopy in a discharge flow cell. A single band of HOONO is observed at 6370 cm(-1) and is assigned as the origin of the first OH overtone of cis-cis HOONO. These results imply that the origin band is suppressed by over an order of magnitude in the action spectrum, due to a reduced quantum yield. The striking differences between absorption and action spectra are correctly predicted by the calculations.     

Potential energy curve for ring-opening reactions: comparison between broken-symmetry and multireference coupled cluster methods

The spin-unrestricted Hartree-Fock (UHF)-based coupled cluster singles and doubles (UHF-CCSD) and Mukherjee's state-specific multireference CCSD (MkCCSD) methods are applied to four ring-opening reactions. The spin-restricted Hartree-Fock (RHF)-based CCSD (RHF-CCSD) calculations are also performed for comparison. In the case of the UHF-CCSD method, an approximate spin-projection (AP) method is applied to the broken-symmetry (BS) singlet solution to remove the spin contamination effect. For potential energy curves (PECs) of all reactions presented in this study, the results of RHF-CCSD and UHF-CCSD are substantially different from those of MkCCSD, while the results after the AP method (AP-UCCSD) reproduce the MkCCSD results well. It strongly suggests that the spin contamination effect should be removed by the AP correction even at the UHF-CCSD level to predict reliable energetics of these reactions.     

Cross-chiral examinations of molecular enantioselective recognition by fast atom bombardment mass spectrometry: Host–guest complexations between chiral crown ethers and chiral organic ammonium ions

Using fast atom bombardment (FAB) mass spectrometry (MS), cross-chiral relationships were confirmed for the first time for the diasteromeric host-guest complexations between the chiral crown ether host (1) and the chiral organic ammonium ion guest (2) on the basis of the relative peak intensities (RPI). Both host–guest combinations (R, R, R, R) – 1, (R) – 2 and (S, S, S, S) – 1, (S) – 2 obviously provided larger RPI values than the combination of both (R, R, R, R) – 1, (S) – 2 and (S, S, S, S) – 1, (R) – 2 by a factor of 1.6 as an averaged value: 1.87 (n = 4)/1.16 (n = 4) = 1.6. These results are consistent with the expected stabilities of the host-guest complexations by CPK model examinations. Successfully observed cross-chiral examinations strongly suggest a potentially useful FABMS/RPI methodology for rapidly searching newly designed and synthesized crown ether-like host compounds with a higher degree of enantioselectivity.     

Carbon Monoxide Oxidation by Polyoxometalate‐Supported Gold Nanoparticulate Catalysts: Activity,Stability, and Temperature‐ Dependent Activation Properties

Nanoparticulate gold supported on a Keggin‐type polyoxometalate (POM), Cs₄[α‐SiW₁₂O₄₀]?n H₂O, was prepared by the sol immobilization method. The size of the gold nanoparticles (NPs) was approximately 2 nm, which was almost the same as the size of the gold colloid precursor. Deposition of gold NPs smaller than 2 nm onto POM (Au/POM) was essential for a high catalytic activity for CO oxidation. The temperature for 50 % CO conversion was ?67 °C. The catalyst showed extremely high stability for at least one month at 0 °C with full conversion. The catalytic activity and the reaction mechanism drastically changed at temperatures higher than 40 °C, showing a unique behavior called a U‐shaped curve. It was revealed by IR measurement that Au^δ+ was a CO adsorption site and that adsorbed water promoted CO oxidation for the Au/POM catalyst. This is the first report on CO oxidation utilizing Au/POMs catalysts, and there is a potential for expansion to various gas‐phase reactions.     

Peumusolide A, unprecedented NES non-antagonistic inhibitor for nuclear export of MEK

A new polyketide peumusolide A was disclosed as an unprecedented NES non-antagonistic inhibitor for nuclear export of MEK, a promising scaffold for antitumor agents with novel mechanism of action, from Peumus boldus Molina. The absolute stereostructure as well as optical purity was established by use of the two synthesized enantiomeric model lactones. In addition, the Δε values in their CD spectra were demonstrated to be the conclusive index for determination of not only configuration at C-3 but also optical purity of natural congeneric polyketides. Peumusolide A was revealed to show NES non-antagonistic action by the biotinylated probe and to inhibit proliferation of MEK-activated tumor cells selectively.