Oversampling Free Energy Perturbation Simulation in Determination of the Ligand-Binding Free Energy

Determination of the ligand-binding affinity is an extremely interesting problem. Normally, the free energy perturbation (FEP) method provides an appropriate result. However, it is of great interest to improve the accuracy and precision of this method. In this context, temperature replica exchange molecular dynamics implementation of the FEP computational approach, which we call replica exchange free energy perturbation (REP) was proposed. In particular, during REP simulations, the system can easily escape from being trapped in local minima by exchanging configurations with high temperatures, resulting in significant improvement in the accuracy and precision of protein–ligand binding affinity calculations. The distribution of the decoupling free energy was enlarged, and its mean values were decreased. This results in changes in the magnitude of the calculated binding free energies as well as in alteration in the binding mechanism. Moreover, the REP correlation coefficient with respect to experiment ( R^REP = 0.85 ± 0.15 ) is significantly boosted in comparison with the FEP one ( R^FEP = 0.64 ± 0.30 ). Furthermore, the root-mean-square error (RMSE) of REP is also smaller than FEP, RMSE^REP = 4.28 ± 0.69 versus RMSE^FEP = 5.80 ± 1.11 kcal/mol, respectively. © 2019 Wiley Periodicals, Inc.     

γ‐Glutamylcysteine‐ and Cysteinylglycine‐Directed Growth of Chiral Gold Nanoparticles and their Crystallographic Analysis

Chiral optical metamaterials with delicate structures are in high demand in various fields because of their strong light–matter interactions. Recently, a scalable strategy for the synthesis of chiral plasmonic nanoparticles (NPs) using amino acids and peptides has been reported. Reported herein, 3D chiral gold NPs were synthesized using dipeptide γ‐Glu‐Cys and Cys‐Gly and analyzed crystallographically. The γ‐Glu‐Cys‐directed NPs present a cube‐like outline with a protruding chiral wing. In comparison, the NPs synthesized with Cys‐Gly exhibited a rhombic dodecahedron‐like outline with curved edges and elliptical cavities on each face. Morphology analysis of intermediates indicated that γ‐Glu‐Cys generated an intermediate concave hexoctahedron morphology, while Cys‐Gly formed a concave rhombic dodecahedron. NPs synthesized with Cys‐Gly are named 432 helicoid V because of their unique morphology and growth pathway.     

Triterpene glycosides from the Vietnamese sea cucumber Holothuria edulis

Abstract

From the MeOH extract of the Vietnamese sea cucumber Holothuria edulis, eight triterpene glycosides (1–8), including one new compound namely holothurin A₅ (1), were isolated by using various chromatographic separations. Their structures were established by spectroscopic experiments including 1D, 2D NMR and HR-ESI-MS. Holothurin A₅ (1) has a hydroperoxy group at C-25. To the best of our knowledge, this is the first report of this group in triterpene saponins obtained from sea cucumbers to date. In addition, the in vitro cytotoxicity against five human cancer cell lines (HepG2, KB, LNCaP, MCF7 and SK-Mel2) of all isolated compounds was also evaluated using SRB assays.     

Optical modes in nanoscale one-dimensional spin chains

The spin chain systems with one-dimensional magnetic ordering are promising candidates for quantum optical devices. This paper shows how the optical excitation can induce various phonon modes in an ideal Cu-O chain at various lengths. The calculation was carried out at different level theories including configuration interaction singles for excited states, density functional theory and second-order Möller-Plesset perturbation. In general, the number of modes increases with chain length due to growing asymmetry of atomic positions when chain exceeds 5 nm. There were, however, only two basic modes: one is associated with the symmetric oscillation of oxygen and another with the asymmetric motion of the same along the chain. At the length below 4.3 nm, the Raman activity of the symmetric mode (440 cm⁻¹) dominates. From analysis of density of states, this mode may be associated with the excitation across the lowest LUMO bands with changing in spin state.     

Observation of B-->K(0)(S)pi(+)pi(-) and Evidence for B-->K(*+/-)pi(-/+)

We report on a search for charmless hadronic B decays to the three-body final states K(0)(S)h(+)pi(-), K(+)h(-)pi(0), K(0)(S)h(+)pi(0) (h(+/-) denotes a charged pion or kaon), and their charge conjugates, using 13.5 fb(-1) of integrated luminosity produced near sqrt[s]=10.6 GeV, and collected with the CLEO detector. We observe the decay B-->K0pi(+)pi(-) with a branching fraction (50(+10)(-9)(stat.)+/-7(syst.))x10(-6) and the decay B-->K(*+)(892)pi(-) with a branching fraction (16(+6)(-5)(stat.)+/-2(syst.))x10(-6).     

Decoherence in josephson phase qubits from junction resonators

Although Josephson junction qubits show great promise for quantum computing, the origin of dominant decoherence mechanisms remains unknown. Improving the operation of a Josephson junction based phase qubit has revealed microscopic two-level systems or resonators within the tunnel barrier that cause decoherence. We report spectroscopic data that show a level splitting characteristic of coupling between a two-state qubit and a two-level system. Furthermore, we show Rabi oscillations whose "coherence amplitude" is significantly degraded by the presence of these spurious microwave resonators. The discovery of these resonators impacts the future of Josephson qubits as well as existing Josephson technologies.     

Observation of eta'c production in gammagamma fusion at CLEO

We report on the observation of the eta(')(c)(2(1)S0), the radial excitation of the eta(c)(1(1)S0) ground state of charmonium, in the two-photon fusion reaction gammagamma-->eta(')(c)-->K(0)(S)K+/-pi(-/+) in 13.6 fb(-1) of CLEO II/II.V data and 13.1 fb(-1) of CLEO III data. We obtain M(eta(')(c))=3642.9+/-3.1(stat)+/-1.5(syst) MeV and M(eta(c))=2981.8+/-1.3(stat)+/-1.5(syst) MeV. The corresponding values of hyperfine splittings between 1S0 and 3S1 states are DeltaM(hf)(1S)=115.1+/-2.0 MeV and DeltaM(hf)(2S)=43.1+/-3.4 MeV. Assuming that the eta(c) and eta(')(c) have equal branching fractions to K(S)Kpi, we obtain Gamma(gammagamma)(eta(')(c))=1.3+/-0.6 keV.     

A nondestructive method for estimation of the fracture toughness of CrMoV rotor steels based on ultrasonic nonlinearity

The objective of this paper is to develop a nondestructive method for estimating the fracture toughness (K(IC)) of CrMoV steels used as the rotor material of steam turbines in power plants. To achieve this objective, a number of CrMoV steel samples were heat-treated, and the fracture appearance transition temperature (FATT) was determined as a function of aging time. Nonlinear ultrasonics was employed as the theoretical basis to explain the harmonic generation in a damaged material, and the nonlinearity parameter of the second harmonic wave was the experimental measure used to be correlated to the fracture toughness of the rotor steel. The nondestructive procedure for estimating the K(IC) consists of two steps. First, the correlations between the nonlinearity parameter and the FATT are sought. The FATT values are then used to estimate K(IC) using the K(IC) versus excess temperature (i.e., T-FATT) correlation that is available in the literature for CrMoV rotor steel.     

Room-temperature multiwavelength erbium-doped fiber ring laser employing sinusoidal phase-modulation feedback

An effective method for achieving a room-temperature multiwavelength erbium-doped fiber ring laser is presented. Simultaneous multiwavelength lasing with 0.5-nm intervals is achieved both experimentally and theoretically by addition of sinusoidal phase modulation in the ring cavity to prevent single-wavelength oscillation.