Ab initio Structure Determination of [Co(NH_3)_5Br]Br_2 Using Conventional X-ray Powder Diffraction

The crystal structure of [Co(NH3)5Br]Br2 has been determined ab initio from the conventional X-ray powder diffraction data. The approximate structure with all 7 indeyendent non-H atoms was solved by direct methods. The final orthorhombic unit-cell parameters after Rietveld refinement are: a=13.6927, b=10.7071, c=6.9400A, V=1017.47A3, F30=93(0.0075,43), M20=49, Z=4. Space group is Pnma. The structure agreement factors are: Rp=0.066,Rwp=0.090, RF=0.041, RB=0.042.

SYNTHESIS AND STRUCTURE DETERMINATION OF NEODYMIUM COMPLEXES WITH CYCLOHEXANECARBOXYLIC ACID

Two complexes,NdL_3·2C_2H_5OH and NdL_3·2H_2O where L=cyclohexane-carboxylate anion,were synthesized and the structure of the former was determined by the single-crystal X-ray diffration method. The crystal is triclinic,Pspace group with the cell parameters:a=1.2385(6),b=1.2385(6),c=0.9421(5) nm.α=91.69(4)°,β=98.49(4)°,γ=99.16(5)°,Z=2,V=1.436 nm^3.The structure was refined to R value of 0.0866.Each Nd atom is connected with other two Nd atoms by two bidentate and two tridentate carboxyl groups to form a linear polymer.The Nd atom is further coordinated by a chelating carboxyl and two ethanol molecules.So the central atom is nine-coordinated with a distorted monocapped square-antiprism geometry.The infrared spectra and the thermal analysis of the complexes were also studied.

ISOLATION AND STRUCTURE DETERMINATION OF XF-1,A NEW ANTHRACYCLINE ANTIBIOTIC

A new Mutactimycin group antibiotic(XF-1)was isolated from the mycelium of Streptomyces sp.80-115 and its structure has been determined on the basis of its spectroscopical and chemical properties. XF-1 showed active against some Gram positive bacteria.

The Structural Stability of Alpha-Helix Determined by the Preference of Amino Acids

To accomplish their functions, proteins have to achieve different conformations accompanied by conformational transitions. However, the relationship between the preference of amino acids and the stability of the secondary structure is still unclear. Here we perform molecular simulations on a series of helical structures. Our data show that the dissociation energy of the helical structure is related to the preference of amino acids, and the electrostatic repulsion of the residue i and i ＋ 3/4 with the same sign of charge destabilizes the alpha helix.

APPLICATION OF 2D-NMR TECHNIQUES IN THE STRUCTURE DETERMINATION OF HYPODEMATINE

An alkaloid with a novel structure,named Hypodematine,was isolated from Hypodematium sinense Iwatsuki(belonging to Thelypterdaceae).Its structure was elucidated by means of the ~1H-~1H COSY' ~1H-^(13)C COSY and long-range ~1H-^(13)C COSY spectroscopy to have the skeleton of benzo-aza-cyclooctatetraene with a phenyl substituent.Such basic structure has not been found in the na- tural product before.

ISOLATION AND STRUCTURE DETERMINATION OF LAMIOPHLOMICL C,A NEW HIGHLY OXYGENATED IRIDOID FROM LAMIOPHLOMIS ROTATA

A new highly oxygenated iridoid,lamiophlomiol C,was isolated from the roots of Lamiophlomis rotata and its structure was elucidated by spectrosoopic techniques and X-ray diffraction.

A Comparative Study of Dispersion Characteristics Determination of a Trapezoidally Corrugated Slow Wave Structure Using Different Techniques

The linear dispersion relation of a trapezoidally corrugated slow wave structure （TCSWS） is analyzed and presented. The size parameters of the TCSWS are chosen in such a way that they operate in the x-band frequency range. The dispersion relation is solved by utilizing the Rayleigh-Fourier method by expressing the radial function in terms of the Fourier series. A highly accurate synthetic technique is also applied to determine the complete dispersion characteristics from experimentally measured resonances （cold test）. Periodic structures resonate at specific frequencies when the terminals are shorted numerical calculation, synthetic technique and cold appropriately. The dispersion characteristics obtained from test are compared, and an excellent agreement is achieved.

Depressive symptoms and the associations with individual, psychosocial, and structural determinants in Swedish adolescents

Depressive symptoms in adolescents are an increasing public health issue in Sweden and in most Western countries. Aim: To explore how individual, psychosocial, and structural determinants are associated with depressive symptoms in Swedish adolescents. Methods: A web-based questionnaire was answered by 1193 13- to 16-year-old boys (n = 566) and girls (n = 627). Stepwise logistic regressions were employed to analyse the association between depressive symptoms and various determinants at the individual level (self-efficacy), the psychosocial level (parental, peer, and teacher support, school demands, sexual harassment, and bullying) and the structural level (family affluence, having less money than friends, and parental foreign background). Results: Determinants at the individual, psychosocial, and structural levels were independently associated with high levels of depressive symptoms in both boys and girls. The full model explained a high proportion of the variance in depressive symptoms in both genders;34.1% in boys and 36.8% in girls. The psychosocial level contributed the most to explaining the variance in depressive symptoms in boys. In girls, when harassment variables were separated from psychosocial variables, the harassment variables contributed as much to the full model as the rest of the psychosocial variables combined. Conclusions: Addressing psychosocial determinants provides the greatest benefits for preventing depressive symptoms in adolescents. Acknowledging the association between sexual harassment and depressive symptoms for girls and having less money than their friends for boys and girls are particularly important.

Modified RNA with a Phosphate-Methylated Backbone. A Serious Omission in Our (Retracted) Study at HIV-1 RNA Loops and Integrated DNA. Specific Properties of the (Modified) RNA and DNA Dimers

After the recent publication in the Journal of Biophysical Chemistry entitled “Retracted HIV Study Provides New Information about the Status of the in Vitro Inhibition of DNA Replication by Back-bone Methylation”, it is of importance to review the results of Buck’s group on the synthesis and conformation analyses of phosphate-methylated RNAs in order to afford information on the absence of a further investigation with regard to this de facto acceptable approach. In fact these compounds belong to the very first group of RNAs with a modified neutral backbone by phosphatemethylation. In contrast to the corresponding phosphate-methylated DNAs with a frozen B-conformation, the phosphate-methylated RNAs show an A-conformation. The latter is a prerequisite for duplex formation with (complementary) (natural) RNA. A number of experiments support this fundamental statement. After the HIV study was retracted, the overall results concerning the phosphate-methylated RNAs were published without mentioning Buck’s initial proof of concept and his contributions. Generally, the (modified) dimer RNAs and DNAs possess a number of specific biophysical properties. A novel explanation is given for conflicting structural determinations.

Tetra-,penta-,and hexa-nor-lanostane triterpenes from the medicinal fungus Ganoderma australe

Chemical investigation on the medicinal fungus Ganoderma australe led to the identification of ten new nor-lanostane triterpenes,namely two hexa-nor ones,ganoaustratetraenones A(1)and B(2),five penta-nor ones,ganoaustraldehydes A-E(3-7),and three tetra-nor ones ganoaustrenoic acids A-C(8-10).The chemical structures along with the absolute configurations were determined by extensive spectroscopic analysis of 1D&2D NMR and HRESIMS data.The postulated biosynthesis pathways of these compounds were proposed.Ganoaustraldehydes A(3)and B(4)showed moderate inhibition against nitric oxide production in RAW264.7 macrophage cells with the respec-tive IC_(50) values of 32.5,34.2μM(the IC_(50) of positive control pyrrolidine dithiocarbamate was 20.0μM).

Synthesis and characterization of a new water-soluble sodium 5,7,4'-trihydroxyflavone-6,3'-disulfonate

Aim To synthesize a new water-soluble Na 2(C15H8O5)(SO3) 2 and determine its structure.Method The new water-soluble apigenin sulfonated derivative was synthesized by sulfonation with concentrated sulfuric acid at 40℃for half an hour and the products were obtained in ethanol-water(V∶V =1∶1).The structure of the product was identified by IR,NMR spectrum and elemental analysis.Results and Conclusion After highly selective introduced two - SO 3 groups at C3′and C6of the substrate,the new water-soluble apigenin sulfonated derivative,sodium 5,7,4 '-trihydroxyflavone-6,3′-sulfonate was obtained in good yield(78%) at moderate conditions.This method is an ideal synthesis way because of its simple operation,mild reaction conditions,high selectivity,easy separation of the product and higher yield.

Structure and magnetic properties of new compounds CdYFeWO_7

The solid solutions of CdYFeWO7,which are cubic pyrochlores of the type A2B2O7,have been prepared and their structures were determined using Ab initio method.Rietveld refinement of the powder XRD data showed that CdYFeWO7 adopted cubic(Fd-3m) structure,while oxides crystallized in a defect-pyrochlore structure where both O(48f) and O (8b) sites were partially occupied,and the frustrated cations sublattice precluded long range ordering of Fe/W in the pyrochlore structure.Charge distribution analysis also sug...

Synthesis, Crystal and Molecular Structure and Biological Activity of Dimethyl Trans-3-(2-bromophenyl)-2-methylisoxazolidine-4,5-dicarboxylate

The compound of dimethyl trans-3-（2-bromophenyl）-2-methylisoxazolidine-4,5-dicarboxylate has been synthesized and characterized by IR, 1H-NMR, 13C-NMR, 2D-NMR （COSY, NOESY, HMQC, HMBC） and UV-vis. spectroscopy techniques and single-crystal X-ray diffraction （XRD）. The biological activities of the title compound have been investigated in detail. The new compound crystallizes in monoclinic, space group C2/c with a = 26.9263（10）, b = 7.0970（2）, c = 19.8554（7） ？, and β = 126.630（2）. In addition to the single crystal structure, the molecular geometry, vibrational frequencies, chemical shifts, molecular electrostatic potential and frontier molecular orbital analysis of the title compound in the ground state have been calculated by Density Functional Theory （DFT） method.

Observation of lateral long range order in superconducting FeTe thin films

We find that the superconductivity in the thin films of the formerly believed non-superconducting parent compound FeTe is accompanied by an emergence of second order with a correlation length of 742 nm and 258 nm at 10 K and 300 K, respectively. The structural phase transition found in iron pnictide superconductors, in non-superconducting FeTe bulk samples, and in FeSe superconducting thin films is not observed in the superconducting FeTe thin films. The interplay between superconductivity and long range order may suggest the crucial role of competition between electronic localization and itinerancy which leads to strong quantum fluctuations in the FeTe system.

A Novel Synthesis of Methyl 4, 6-O-Benzylidene-α-D-Glucopyranoside 2, 3-Cyclic Phosphite Ethyl Ester

A new compound. methyl 4. 6-O-benzylidene-a-D-glucopyranoside 2. 3-cyclicphosphite ethyl ester was synthesized via the reaction of methyl 4. 6-O-benzylidene-a-D-glucopyranoside and ethyl dichlorophosphite. Its structure was confirmed by NMR and MSspectral methods.

A New Anthraquinone from Clinopodium polycephalum Glyceroyl-1,6,8-trihydroxy-3-methyl-9,10-dioxo-2-anthracene Carboxylate

A new anthraquinone, Glyceroyl-1,6,8-trihydroxy-3-methyl-9, 10-dioxo-2-anthracene carboxylate I, was isolated from Clinopodium polycephalum. The chemical structure was determined by spectroscopic methods.

Formation of Hybrid Ring Structure of Cyanurate/Isocyanurate in the Reaction be-tween 2,4,6-Tris(4-Phenyl-Phenoxy)-1, 3,5-Triazine and Phenyl Glycidyl Ether

Reaction products of 2,4,6-tris(4-phenyl-phenoxy)-1,3,5-triazine derived from 4-phenylphenol cyanate ester and phenyl glycidyl ether were analyzed. In addition to an isocyanurate compound and an oxazolidone compound which were well known as reaction products of cyanate esters and epoxy resins, compounds with hybrid ring structure of cyanurate/isocyanurate were determined. Gibbs free energies of the compound having hybrid ring structure of cyanurate/isocyanurate with two isocyanurate moiety were found to be lower than that of the compound with cyanurate ring structure through calculations. Calculation data supported the existence of hybrid ring structure of cy-anurate/isocyanurate. It was revealed that isomerization from cyanurate to isocyanurate occurs via hybrid ring structure of cyanurate/isocyanurate in the reaction of aryl cyanurate and epoxy.

Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information

Proteases are enzymes that cleave and hydrolyse the peptide bonds between two specific amino acid residues of target substrate proteins.Protease-controlled proteolysis plays a key role in the degradation and recycling of proteins,which is essential for various physiological processes.Thus,solving the substrate identification problem will have important implications for the precise understanding of functions and physiological roles of proteases,as well as for therapeutic target identification and pharmaceutical applicability.Consequently,there is a great demand for bioinformatics methods that can predict novel substrate cleavage events with high accuracy by utilizing both sequence and structural information.In this study,we present Procleave,a novel bioinformatics approach for predicting protease-specific substrates and specific cleavage sites by taking into account both their sequence and 3D structural information.Structural features of known cleavage sites were represented by discrete values using a LOWESS data-smoothing optimization method,which turned out to be critical for the performance of Procleave.The optimal approximations of all structural parameter values were encoded in a conditional random field(CRF)computational framework,alongside sequence and chemical group-based features.Here,we demonstrate the outstanding performance of Procleave through extensive benchmarking and independent tests.Procleave is capable of correctly identifying most cleavage sites in the case study.Importantly,when applied to the human structural proteome encompassing 17,628 protein structures,Procleave suggests a number of potential novel target substrates and their corresponding cleavage sites of different proteases.Procleave is implemented as a webserver and is freely accessible at http://procleave.erc.monash.edu/.

An Ultrastable π-π Stacked Porous Organic Molecular Framework as a Crystalline Sponge for Rapid Molecular Structure Determination

The crystalline sponge method is a pragmatic and promising strategy for molecular structure determination.However,the dominant metal-organic framework crystal sponge platforms always face poor chemical stability,especially solvent instability,hampering their application in a vaster domain.Herein,we report an ultrastable π-π stacked porous organic molecular framework which exhibits permanent porosity,high thermal stability,and good chemical resistance.It can efficiently implement an approach to molecular structure determination via a single-crystal-to-single-crystal transformation.This is the first example utilizing π-π stacked porous organic molecular framework as“crystalline sponge”to determine a wide variety of guests,ranging from hydrophilic to hydrophobic,and from aliphatic to aromatic,which complements the crystalline sponges based on the famous metal-organic frameworks.More importantly,it can achieve rapid structure determination of small molecules within 3 h.

Accelerating the cryo-EM structure determination in RELION on GPU cluster

The cryo-electron microscopy(cryo-EM)is one of the most powerful technologies available today for structural biology.The RELION(Regularized Likelihood Optimization)implements a Bayesian algorithm for cryo-EM structure determination,which is one of the most widely used software in this field.Many researchers have devoted effort to improve the performance of RELION to satisfy the analysis for the ever-increasing volume of datasets.In this paper,we focus on performance analysis of the most time-consuming computation steps in RELION and identify their performance bottlenecks for specific optimizations.We propose several performance optimization strategies to improve the overall performance of RELION,including optimization of expectation step,parallelization of maximization step,accelerating the computation of symmetries,and memory affinity optimization.The experiment results show that our proposed optimizations achieve significant speedups of RELION across representative datasets.In addition,we perform roofline model analysis to understand the effectiveness of our optimizations.