Draft Genome Sequence of Amphibacillus jilinensis Y1T,a Facultatively Anaerobic,Alkaliphilic and Halotolerant Bacterium

The genus Amphibacillus was established in 1990, and seven additional species were described in the past two decades. Amphibacillus jilinensis Y1^T is a facultatively anaerobic and alkaliphilic bacterium isolated from a soda lake in China. Here we describe the structural and genetic features of the draft genome about the type strain Y1^T (3,831,075 bp, with a G+C content of 37.27%). This is the first genome report of the Amphibacillus genus.     

N+ ion beam implantation of tannase-producing Aspergillus niger and optimization of its process parameters under submerged fermentation

Low-energy ion implantation as a novel mutagen has been increasingly applied in the microbial mutagenesis for its higher mutation frequency and wider mutation spectra. In this work, N⁺ ion beam implantation was used to enhance Aspergillus niger TA9701 in tannase yield. The optimization of process parameters under submerged fermentation was carried out to further improve the tannase yield of the mutant, Aspergillus niger J-T18. The results indicate that an excellent mutant J-T18 with a yield of 38.5 IU/mL, that is five times that of the original strain, was achieved by nine successive implantations under the conditions of 10 keV and 30–40 (×2.6?×?10¹³) ions/cm². This optimization further increased the yield of the mutant by 42 %, i.e. 53.6 U/mL which occurred in the mutant cultivated in the optimal fermentation culture medium composed of: rice flour 5 %; ammonium sulfate 1 %; tannic acid 2 %; calcium carbonate 0.5 %; manganese sulfate 0.1 %; and dipotassium phosphate 0.3 %; incubated at 30°C and 180 rpm for 72 h.     

A theoretical study on 1,5-diazido-3-nitrazapentane (DANP) and 1,7-diazido-2,4,6-trinitrazaheptane (DATNH): molecular and crystal structures, thermodynamic and detonation properties, and pyrolysis mechanism

1,5-Diazido-3-nitrazapentane (DANP) and 1,7-diazido-2,4,6-trinitrazaheptane (DATNH) are two energetic plasticizers. To better understand them, a detailed theoretical investigation was carried out using density functional theory and molecular mechanics methods. The crystal structures, spectra, thermodynamic properties, heats of formation, detonation velocity, detonation pressure, specific impulse and thermal stability were estimated. Possible initiation steps of pyrolysis were discussed by considering the bond breaking of N–NO₂, C–N₃, and N–N₂ (via hydrogen transfer) for both compounds and the cyclization of the adjacent nitro and azido groups for DATNH. Results show that the rupture of N–NO₂ and N–N₂ (via hydrogen transfer) may happen simultaneously as the initial step of pyrolysis. Both crystals have P-1 symmetry as was observed experimentally. DANP has higher stability than DATNH, while DATNH has better detonation performance than DANP. In addition, DANP has a lower while DATNH has a higher specific impulse than RDX, which shows their prospects as propellant components.     

Triterpenoids from the Stem Bark of Melia toosendan and Determination of Their Absolute Configurations at C(24)

Six new triterpenoids, meliasenins S–X ( 1 – 6 , resp.), were isolated from the stem bark of Melia toosendan. Their structures were elucidated by mass spectrometry, NMR experiments, and comparison with the known compounds. Particularly, the absolute configuration at C(24) in new compounds was determined through their CD spectra of the [Pr(FOD)₃] complex (fod=1,1,1,2,2,3,3,7,7,7‐decafluoroheptane‐4,6‐dione) in CCl₄, as well as by using Mosher's method.     

First-principles study of the structural transformation, electronic structure, and optical properties of crystalline 2,6-diamino-3,5-dinitropyrazine-1-oxide under high pressure

Periodic first-principles calculations have been performed to study the effect of high pressure on the geometric, electronic, and absorption properties of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) under hydrostatic pressures of 0–50 GPa. Obvious irregular changes in lattice constants, unit-cell angles, bond lengths, bond angles, and band gaps showed that crystalline LLM-105 undergoes four structural transformations at 8, 17, 25, and 42 GPa, respectively. The intramolecular H-bonds were strong at pressures of 0–41 GPa but weakened in the range 42–50 GPa. The lengths of the intermolecular H-bonds (<1.47 Å) indicated that these H-bonds have covalent character and tend to induce the formation of a new twelve-membered ring. Analysis of the DOS showed that the interactions between electrons, especially the valence electrons, strengthen under the influence of pressure. The p states play a very important role in chemical reactions of LLM-105. The absorption spectrum of LLM-105 displayed more bands—as well as stronger bands—in the fundamental absorption region when the pressure was high rather than low. A new absorption peak due to O–H stretching appeared at 18.3 eV above 40 GPa, indicating that covalent O–H bonds and a new twelve-membered ring are present in LLM-105.     

A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions

Halogen bonding, a non-covalent interaction between the halogen σ-hole and Lewis bases, could not be properly characterized by majority of current scoring functions. In this study, a knowledge-based halogen bonding scoring function, termed XBPMF, was developed by an iterative method for predicting protein-ligand interactions. Three sets of pairwise potentials were derived from two training sets of protein-ligand complexes from the Protein Data Bank. It was found that two-dimensional pairwise potentials could characterize appropriately the distance and angle profiles of halogen bonding, which is superior to one-dimensional pairwise potentials. With comparison to six widely used scoring functions, XBPMF was evaluated to have moderate power for predicting protein-ligand interactions in terms of “docking power”, “ranking power” and “scoring power”. Especially, it has a rather satisfactory performance for the systems with typical halogen bonds. To the best of our knowledge, XBPMF is the first halogen bonding scoring function that is not dependent on any dummy atom, and is practical for high-throughput virtual screening. Therefore, this scoring function should be useful for the study and application of halogen bonding interactions like molecular docking and lead optimization.

Binding selectivity studies of PKBα using molecular dynamics simulation and free energy calculations

Designing selective protein kinase B (PKB/Akt) inhibitor is an area of intense research to develop potential anticancer drugs. In the present study, the molecular basis governing PKB-selective inhibition has been investigated using molecular dynamics simulation. The binding free energies calculated by MM/PBSA gave a good correlation with the experimental biological activity and a good explanation of the activity difference of the studied inhibitors. The decomposition of free energies by MM/GBSA indicates that the ethyl group on pyrrolo[2,3-d]pyrimidine ring of inhibitor Lig1 (N-{[(3S)-3-amino-1-(5-ethyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)pyrrolidin-3-yl]-methyl}-2,4-difluoro-benzamide) is an important contributor to its PKBα selectivity due to its hydrophobic interaction with the side chain of Thr291 in PKBα. The substituted groups on the pyrrolidine ring of Lig1 also show a strong tendency to mediate protein-ligand interactions through the hydrogen bonds formed between the amino or amide groups of Lig1 and the carboxyl O atoms of Glu234, Glu278, and Asp292 of PKBα. It was reported that there are only three key amino acid differences between PKBα (Thr211, Ala230, Met281) and PKA (Val104, Val123, Leu173) within the clefts of ATP-binding sites. These differences propel a drastic conformational change in PKA, weakening its binding interactions with inhibitor. The impact was also confirmed by MD simulated interaction modes of inhibitor binding to PKBα mutants with the in silico mutations of the three key amino acids, respectively. We expect that the results obtained here could be useful for future rational design of specific ATP-competitive inhibitors of PKBα.     

Sodium Storage and Transport Properties in Layered Na2Ti3O7 for Room‐Temperature Sodium‐Ion Batteries

Layered sodium titanium oxide, Na₂Ti₃O₇, is synthesized by a solid‐state reaction method as a potential anode for sodium‐ion batteries. Through optimization of the electrolyte and binder, the microsized Na₂Ti₃O₇ electrode delivers a reversible capacity of 188 mA h g^?1 in 1 M NaFSI/PC electrolyte at a current rate of 0.1C in a voltage range of 0.0–3.0 V, with sodium alginate as binder. The average Na storage voltage plateau is found at ca. 0.3 V vs. Na⁺/Na, in good agreement with a first‐principles prediction of 0.35 V. The Na storage properties in Na₂Ti₃O₇ are investigated from thermodynamic and kinetic aspects. By reducing particle size, the nanosized Na₂Ti₃O₇ exhibits much higher capacity, but still with unsatisfied cyclic properties. The solid‐state interphase layer on Na₂Ti₃O₇ electrode is analyzed. A zero‐current overpotential related to thermodynamic factors is observed for both nano‐ and microsized Na₂Ti₃O₇. The electronic structure, Na⁺ ion transport and conductivity are investigated by the combination of first‐principles calculation and electrochemical characterizations. On the basis of the vacancy‐hopping mechanism, a quasi‐3D energy favorable trajectory is proposed for Na₂Ti₃O₇. The Na⁺ ions diffuse between the TiO₆ octahedron layers with pretty low activation energy of 0.186 eV.     

Fused Heteroaromatic Organic Compounds for High‐Power Electrodes of Rechargeable Lithium Batteries

Organic redox compounds are emerging electrode materials for rechargeable lithium batteries. However, their electrically insulating nature plagues efficient charge transport within the electroactive bulk. Alternative to the popular solution of elaborating nanocomposite materials, herein we report on a molecular‐level engineering strategy towards high‐power organic electrode materials with multi‐electron reactions. Systematic comparisons of anthraquinone analogues incorporating fused heteroaromatic structures as cathode materials in rechargeable lithium batteries reveal that the judicious incorporation of heteroaromatics improves the cell performance in terms of specific gravimetric capacity, working potential, rate capability, and cyclability. Combination studies with morphological observation, electrochemical impedance characterization, and theoretical modeling provide insight into the advantage of heteroaromatic building blocks. In particular, benzofuro[5,6‐b]furan‐4,8‐dione ( BFFD ) bearing furan moeities shows a reversible capacity of 181 mAh g^?1 when charged/discharged at 100C, corresponding to a power density of 29.8 kW kg^?1. These results have pointed to a general design route of high‐rate organic electrode materials by rational functionalization of redox compounds with appropriate heteroaromatic units as versatile structural tools.