Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations

The free energy landscapes of peptide conformations were calibrated by ab initio quantum chemical calculations, after the enhanced conformational diversity search using the multicanonical molecular dynamics simulations. Three different potentials of mean force for an isolated dipeptide were individually obtained by the multicanonical molecular dynamics simulations using the conventional force fields, AMBER parm94, AMBER parm96, and CHARMm22. Each potential of mean force was then calibrated based upon the umbrella sampling algorithm from the adiabatic energy map that was calculated separately by the ab initio molecular orbital method, and all of the calibrated potentials of mean force coincided well. The calibration method was also applied to the simulations of a peptide dimer in explicit water models, and it was shown that the calibrated free energy landscapes did not depend on the force field used in the classical simulations, as far as the conformational space was sampled well. The current calibration method fuses the classical free energy calculation with the quantum chemical calculation, and it should generally make simulations for biomolecular systems much more reliable when combining with enhanced conformational sampling.     

Property control of new forms of carbon materials by fluorination

Multiwall carbon nanotubes (MWNTs) based on the template carbonization technique were fluorinated in a temperature range 323-473 K by elemental fluorine. The fluorination of the carbon nanotubes results in functionalization and modification of pristine nanotubes with respect to adsorption and electrochemical properties. Selective fluorination of the inner surface of the carbon nanotubes, brings about a decrease in the surface free energy of the inner surface of the tubes and an increase in colombic efficiency of Li/nanotubes rechargeable cells in an aprotic medium. Electrochemical fluoride-ion doping of fullerene C₆₀ thin films (250-450 nm) was carried out in a fluoride-ion conductive solution, MeCN solution of 1 M Et₄NF·4HF. Galvanostatic oxidation yielded C₆₀F_ca.1-3 where fluorine exists as a semi-ionic species in the cavity surrounded by C₆₀ molecules without forming covalent CF bonds     

beta-Hairpins,alpha-helices,and the intermediates among the secondary structures in the energy landscape of a peptide from a distal beta-hairpin of SH3 domain

Energy landscape of a peptide, extracted from a distal beta-hairpin of src SH3 domain, in explicit water was obtained with the multicanonical molecular dynamics. A variety of beta-hairpins with various strand-strand hydrogen bonds were found in the energy landscape at 300 K. There was no energy barrier between random-coil and hairpins. Thus, the peptide conformation can easily change from the random-coil to the hairpins in the thermal fluctuations at 300 K. The landscape also included two clusters of alpha-helices, among which an energy barrier existed, and besides, these helix clusters were separated from the other conformations. Thus, the free-energy barrier exists among the helices and the other conformations. Intermediate clusters were found between the helix and the hairpin clusters. The current study showed that the isolated state of this peptide in water fluctuates among random-coil, beta-hairpin, and alpha-helix. In SH3 domain, which has a topology of mainly beta-protein, the whole-protein folding may proceed when the segment is folded in the beta-hairpin and the other parts of the protein are coupled with the beta-hairpin in an energetically or kinetically favorite way.     

Homochiral column structure of rac- and lambda-tris(ethylenediamine)cobalt(III) cyclotriphosphate dihydrate in crystal structures and cation-anion association in aqueous solution

rac- and Lambda-tris(ethylenediamine)cobalt(III) cyclotriphosphate dihydrate with the chemical formulas rac-[Co(en)(3)]P(3)O(9).2H(2)O (1) and Lambda-[Co(en)(3)]P(3)O(9).2H(2)O (2) were synthesized, and their crystal structures were determined by single-crystal X-ray analyses. In 1, the cationic complex molecule [Co(en)(3)](3+) with the Delta or Lambda enantiomer and cyclotriphosphate anion are alternately arrayed and connected by multiple hydrogen bonds to form a homochiral column structure. Adjacent homochiral columns with different chirality for 1 are connected by intercolumn hydrogen bonds through P(3)O(9)(3)(-) anions, as the bridging groups, to form a tetrameric cyclic cylindrical structure, while the adjacent columns with the same chirality are connected for 2 to form the cyclic cylindrical structure. All 6 amino groups per [Co(en)(3)](3+) participate in the formation of 12 hydrogen bonds, in which 8 hydrogen bonds contribute to the construction of a homochiral column and the remaining 4 hydrogen bonds contribute to the intercolumn interactions. The circular dichroism spectrum of the aqueous solution of Lambda-[Co(en)(3)](3+) changes drastically when excess P(3)O(9)(3)(-) is added, and this change is explained by ion-pair formation. The thermodynamic association constant of [Co(en)(3)](3+) with P(3)O(9)(3)(-), calculated from the conductivity data, was log K = 4.26 at 25 degrees C.     

Liquid chromatographic determination of polyamines in human urine based on intramolecular excimer-forming fluorescence derivatization using 4-(1-pyrene)butanoyl chloride

A liquid chromatographic method for highly sensitive and selective fluorometric determination of polyamines (putrescine, cadaverine, spermidine and spermine) in human urine is described. This method is based on an intramolecular excimer-forming fluorescence derivatization with a pyrene reagent, 4-(1-pyrene)butanoyl chloride (PBC), followed by reversed-phase liquid chromatography. The method offers higher sensitivity for determination of spermidine and spermine than previously reported method utilizing 4-(1-pyrene)butyric acid N-hydroxysuccinimide ester as a derivatization reagent. Samples containing free polyamines in diluted human urine were directly derivatized with PBC and separated on an octyl column. The derivatives were detected at excitation 345 and emission 475 nm wavelengths. For determination of total polyamine content, the conjugated polyamines were first hydrolyzed in 4 M HCl. The detection limits (signal-to-noise ratio = 3) for polyamines in urine were 1.1-3.4 pmol/mL. At optimized derivatization and chromatographic conditions, interferences such as biogenic monoamines gave no peaks or the peaks did not interfere with the peaks of polyamine derivatives. In conclusion, the present derivatization method allows direct determination of polyamines in human urine samples without the need for sample clean-up procedures.     

A convenient synthesis of tricyclic purine derivatives

A convenient synthesis of new heterocycles such as 7,8-dihydro-1H-imidazo[2,1-i]purin-5(4H)-ones ( 2 , n = 0) and 5,6-dihydro-1H-imidazo[2,1-b]purin-9(8H)-ones ( 3 ) was described. The syntheses of 2 and 3 were accomplished by treatment of 6-methylthio-7H-purin-2(3-H)-ones 7 or 2-benzylthio-1-methyl-9-triphenylmethyl-9H-purin-6(1H)-one ( 15 ) with appropriate aminoalcohol followed by dehydrative cyclization using thionyl chloride. Compound 15 was efficiently prepared by benzylation of 6-hydroxy-2-mercaptopurine ( 12 ) followed by tritylation and N-methylation.     

相对论重离子碰撞中Λ粒子产生和Λ/p比率

利用强子输运–弦碎裂模型研究了200A GeV重离子碰撞中Λ多重产生和Λ/p比率.研究了它们随反应系统大小和碰撞中心度的变化.研究表明Λ和p多重数都随反应系统增大和随碰撞中心度提高而增大,但它们的比率基本保持不变.Λ的湮没截面大小变化对Λ的多重数产生有一定影响,但对Λ/p比率影响不大.结果很好地再现了pp反应中Λ/p比率.并获得这一比率在AA反应中是pp反应中的3—5倍.     

Microscopic magnetic property of perpendicular magnetic films of DyxCo100−x measured using soft X-ray magnetic circular dichroism

We have carried out X-ray absorption measurements with its magnetic circular dichroism (MCD) of perpendicular magnetic films of Dy_xCo_100−x (15?x?33) at Dy M_4,5 and Co L_2,3 absorption edges to investigate electronic and spin states of the Dy 4f and Co 3d states, respectively. The replacement of major spin between Dy 4f and Co3d is clearly observed in the spectra between 20?x?25. The expected values of the orbital angular moment ∣〈L_z〉∣ of Dy 4f were estimated to be 1.4-0.8 μ_B while that of Co 3d was estimated to be around 0.2 μ_B.     

Key role of chemical hardness to compare 2,2-diphenyl-1-picrylhydrazyl radical scavenging power of flavone and flavonol O-glycoside and C-glycoside derivatives

The antioxidant activities of flavonoids and their glycosides were measured with the 2,2-diphenyl-1-picrylhydrazyl radical (DPPH radical, DPPH(·)) scavenging method. The results show that free hydroxyl flavonoids are not necessarily more active than O-glycoside. Quercetin and kaempferol showed higher activity than apigenin. The C- and O-glycosides of flavonoids generally showed higher radical scavenging activity than aglycones; however, kaempferol C3-O-glycoside (astragalin) showed higher activity than kaempferol. In the radical scavenging activity of flavonoids, it was expected that OH substitutions at C3 and C5 and catechol substitution at C2 of B ring and intramolecular hydrogen bonding between OH at C5 and ketone at C3 would increase the activity; however, the reasons have yet to be clarified. We here show that the radical scavenging activities of flavonoids are controlled by their absolute hardness (η) and absolute electronegativity (χ) as a electronic state. Kaempferol and quercetin provide high radical scavenging activity since (i) OH substitutions at C3 and C5 strikingly decrease η of flavones, (ii) OH substitutions at C3 and C7 decrease χ and η of flavones, and (iii) phenol or o-catechol substitution at C2 of B ring decrease χ of flavones. The coordinate r(χ,?η) as the electron state must be small to increase the radical scavenging activity of flavonoids. The results show that chemically soft kaempferol and quercetin have higher DPPH radical scavenging activity than chemically hard genistein and daidzein.     

Facile Preparation of Organometallic Nanorods from Various Ethynyl-Substituted Molecules

A facile method to prepare one-dimensional (1D) organometallic nanomaterials from various ethynyl-substituted molecules is reported. The reactions of 3-chloro-1-ethynylbenzene, p-tBu-phenylacetylene and 4-ethynylbiphenyl with Cu⁺ ions in acetonitrile yield nanorod-shaped copper acetylides (Cu−C≡C−R) crystals. In the case of linear alkynes, namely, propyne, 1-pentyne and 1-hexyne, it was found that using an aqueous ammonia/ethanol mixed solvent instead of acetonitrile is a better approach to obtain 1D nanostructures. This procedure also enables us to prepare functional 1D nanomaterials. We demonstrate the preparation of a paramagnetic nanorod from the organic radical p-ethynylphenyl nitronyl nitroxide, and fluorescent nanorods from 9-ethynylphenanthrene and 2-ethynyl-9,9′-spirobifluorene.