人类胞外信号调节激酶1的同源模建及其抑制剂的对接与结构改造

通过同源模建和分子动力学模拟构建了人类胞外信号调节激酶1(hERK1)的三维结构,并利用profile-3D和procheck方法评估了模型的合理性.对所得的结构使用分子对接程序Affinity和CDOCKER进行了两种抑制剂的对接.结果显示这两种抑制剂与酶的结合方式相似,它们均与残基K36,Q87之间存在氢键作用,二者取代基的不同导致了抑制能力的差别.基于对接结果分析,对已知抑制剂进行结构改造,得到了一个理论上结合能力更强的抑制剂.它在保持与K36和Q87之间氢键的同时,又与残基D93,K96,S135形成了四条氢键,显著提高了与酶的相互作用.对接相互作用能显著下降,MM-PBSA结合自由能降为负值,这些均体现了抑制能力的提高.本工作对于针对该酶的抑制剂设计和相关疾病的新药开发具有理论指导价值.     

The structure determination of two new acylphloroglucinols from Myrtus communis L.

Structures for two new acylpholorglucinols, myrtucommulone A (1) and myrtucommulone B (2) have been deduced from a detailed study of the NMR, IR and mass spectra of these substances, and their simple derivatives and degradation products. The compounds contain phloroglucinol and syncarpic acid (1,1,3,3, tetramethyl-cyclohexa-2,4,6-trione) residues, and are closely related chemically to fern constituents such as filixic acid, as well as to kosins and uliginosins isolated from higher plants. Compounds 1 and 2 are unique in having an isobutyl bridge connecting the rings. Compound 1 exhibits strong antibacterial activity against gram positive bacteria.     

A neutron diffraction study of room-temperature monoclinic Kd2PO4

The crystal structure of the room-temperature monoclinic phase of high-deuteration DKDP has been determined by neutron diffraction measurements on a single crystal. The arrangement of K, P and O atoms is essentially that determined previously by X-ray diffraction: the D atoms have been located. It is confirmed that the monoclinic-tetragonal transition is a reconstructive one involving large (> 1 Å) relative atomic displacements.     

Investigation on Thermal Decomposition of Pyrite Part I

Thermochemical decomposition of pyrite in air-gas medium has been studied by means of MOM-Q 1500D Derivatograph. The derivatograms have been obtained at a heating rate of 5 K min^-1 and air flowrate of 25 1 h^-1 to final temperatures of 833, 933 and 1273 K, chosen on the basis of the stepwise oxidation of pyrite. The solid product is analyzed using X-ray powder diffraction and Mössbauer spectrometer techniques. The formation of nonstoichiometric sulfides (pyrrhotines) as intermediates has been confirmed. The second stage of decomposition is the oxidation of these pyrrhotines to hematite. The recorded weight losses are lower than the theoretically possible because of the formed nonstoichiometric iron sulfides. The complicated structure of the intermediate products has been confirmed by means of other techniques.     

Large Mn25 single-molecule magnet with spin S = 51/2: magnetic and high-frequency electron paramagnetic resonance spectroscopic characterization of a giant spin state

The synthesis and structural, spectroscopic, and magnetic characterization of a Mn25 coordination cluster with a large ground-state spin of S = 51/2 are reported. Reaction of MnCl2 with pyridine-2,6-dimethanol (pdmH2) and NaN3 in MeCN/MeOH gives the mixed valence cluster [Mn25O18(OH)2(N3)12(pdm)6(pdmH)6]Cl2 (1; 6Mn(II), 18Mn(III), Mn(IV)), which has a barrel-like cage structure. Variable temperature direct current (dc) magnetic susceptibility data were collected in the 1.8-300 K temperature range in a 0.1 T field. Variable-temperature and -field magnetization (M) data were collected in the 1.8-4.0 K and 0.1-7 T ranges and fit by matrix diagonalization assuming only the ground state is occupied at these temperatures. The fit parameters were S = 51/2, D = -0.020(2) cm(-1), and g = 1.87(3), where D is the axial zero-field splitting parameter. Alternating current (ac) susceptibility measurements in the 1.8-8.0 K range and a 3.5 G ac field oscillating at frequencies in the 50-1500 Hz range revealed a frequency-dependent out-of-phase (chi(M)') signal below 3 K, suggesting 1 to be a single-molecule magnet (SMM). This was confirmed by magnetization vs dc field sweeps, which exhibited hysteresis loops but with no clear steps characteristic of resonant quantum tunneling of magnetization (QTM). However, magnetization decay data below 1 K were collected and used to construct an Arrhenius plot, and the fit of the thermally activated region above approximately 0.5 K gave U(eff)/k = 12 K, where U(eff) is the effective relaxation barrier. The g value and the magnitude and sign of the D value were independently confirmed by detailed high-frequency electron paramagnetic resonance (HFEPR) spectroscopy on polycrystalline samples. The combined studies confirm both the high ground-state spin S = 51/2 of complex 1 and that it is a SMM that, in addition, exhibits QTM.     

(Sr2N)H: Untersuchungen zur Redox‐Intercalation von Wasserstoff in Sr2N

(Sr₂N)H: On the Redox-Intercalation of Hydrogen into Sr₂N Strontium-nitride-hydride is obtained as brown-yellow single phase powder by reaction of strontium-subnitride (Sr₂N) with hydrogen (200 bar, 620 K) and subsequent treatment under vacuum (10⁻⁶ bar, 870 K). The structure determination was carried out by a combination of X-ray and neutron diffraction experiments on a deuterated sample. The elemental composition of the ternary compound was confirmed by means of chemical analyses. (Sr₂N)D crystallizes in the space group with a = 381.91(2) pm and c = 1887.61(2) pm. Strontium (Sr²⁺) in the crystal structure of (Sr₂N)D is arranged with an only slightly distorted ccp-motif. Nitrogen (N³⁻) and deuterium (D⁻) occupy the octahedral voids of the Sr²⁺-matrix in an ordered manner resulting in an alternating sequence of layers (anti-α-NaFeO₂-type structure).     

X-ray diffraction and inelastic neutron scattering study of 1:1 tetramethylpyrazine chloranilic acid complex: temperature, isotope, and pressure effects

The x-ray diffraction studies of the title complex were carried out at room temperature and 14 K for H/D (in hydrogen bridge) isotopomers. At 82 K a phase transition takes place leading to a doubling of unit cells and alternation of the hydrogen bond lengths linking tetramethylpyrazine (TMP) and chloranilic acid molecules. A marked H/D isotope effect on these lengths was found at room temperature. The elongation is much smaller at 14 K. The infrared isotopic ratio for O-H(D)...N bands equals to 1.33. The four tunnel splittings of methyl librational ground states of the protonated complex required by the structure are determined at a temperature T=4.2 K up to pressures P=4.7 kbars by high resolution neutron spectroscopy. The tunnel mode at 20.6 microeV at ambient pressure shifts smoothly to 12.2 microeV at P=3.4 kbars. This is attributed to an increase of the strength of the rotational potential proportional to r(-5.6). The three other tunnel peaks show no or weak shifts only. The increasing interaction with diminishing intermolecular distances is assumed to be compensated by a charge transfer between the constituents of deltae/e approximately 0.02 kbar(-1). The phase transition observed between 3.4 and 4.7 kbars leads to increased symmetry with only two more intense tunneling bands. In the isotopomer with deuterated hydrogen bonds and P=1 bar all tunnel intensities become equal in consistency with the low temperature crystal structure. The effect of charge transfer is confirmed by a weakening of rotational potentials for those methyl groups whose tunnel splittings were independent of pressure. Density functional theory calculations for the model TMP.(HF)2 complex and fully ionized molecule TMP+ point out that the intramolecular rotational potential of methyl groups is weaker in the charged species. They do not allow for the unequivocal conclusions about the role of the intermolecular charge transfer effect on the torsional frequencies.     

Three dimensional structure prediction of panomycocin,a novel Exo-β-1,3-glucanase isolated from Wickerhamomyces anomalus NCYC 434 and the computational site-directed mutagenesis studies to enhance its thermal stability for therapeutic applications

Panomycocin is a naturally produced potent antimycotic/antifungal protein secreted by the yeast Wickerhamomyces anomalus NCYC 434 with an exo-β-1,3-glucanase activity. In this study the three dimensional structure of panomycocin was predicted and the computational site-directed mutagenesis was performed to enhance its thermal stability in liquid formulations over the body temperature for topical therapeutic applications. Homology modeling was performed with MODELLER and I-TASSER. Among the generated models, the model with the lowest energy and DOPE score was selected for further loop modeling. The loop model was optimized and the reliability of the model was confirmed with ERRAT, Verify 3D and Ramachandran plot values. Enhancement of the thermal stability of the model was done using contemporary servers and programs such as SPDBViewer, CNA, I-Mutant2.0, Eris, AUTO-MUTE and MUpro. In the region outside the binding site of the model Leu52 Arg, Phe223Arg and Gly254Arg were found to be the best thermostabilizing mutations with 6.26 K, 6.26 K and 8.27 K increases, respectively. In the binding site Glu186Arg was found to be the best thermostabilizer mutation with a 9.58 K temperature increase. The results obtained in this study led us to design a mutant panomycocin that can be used as a novel antimycotic/antifungal drug in a liquid formulation for topical applications over the normal body temperature.     

Structure, stability, thermodynamic properties, and infrared spectra of the protonated water octamer H(+)(H2O)8

We investigated various two-dimensional (2D) and three-dimensional (3D) structures of H (+)(H 2O) 8, using density functional theory (DFT), Moller-Plesset second-order perturbation theory (MP2), and coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)). The 3D structure is more stable than the 2D structure at all levels of theory on the Born-Oppenheimer surface. With the zero-point energy (ZPE) correction, the predicted structure varies depending on the level of theory. The DFT employing Becke's three parameters with Lee-Yang-Parr functionals (B3LYP) favors the 2D structure. At the complete basis set (CBS) limit, the MP2 calculation favors the 3D structure by 0.29 kcal/mol, and the CCSD(T) calculation favors the 3D structure by 0.27 kcal/mol. It is thus expected that both 2D and 3D structures are nearly isoenergetic near 0 K. At 100 K, all the calculations show that the 2D structure is much more stable in free binding energy than the 3D structure. The DFT and MP2 vibrational spectra of the 2D structure are consistent with the experimental spectra. First-principles Car-Parrinello molecular dynamics (CPMD) simulations show that the 2D Zundel-type vibrational spectra are in good agreement with the experiment.     

Quantum sieving effect of three-dimensional Cu-based organic framework for H2 and D2

The crystal structure of [Cu(4,4'-bipyridine) 2(CF 3SO 3) 2] n metal-organic framework (CuBOTf) of one-dimensional pore networks after pre-evacuation at 383 K was determined with synchrotron X-ray powder diffraction measurement. Effective nanoporosity of the pre-evacuated CuBOTf was determined with N 2 adsorption at 77 K. The experimental H 2 and D 2 adsorption isotherms of CuBOTf at 40 and 77 K were measured and then compared with GCMC-simulated isotherms using the effective nanoporosity. The quantum-simulated H 2 and D 2 isotherms at 77 K using the Feynman-Hibbs effective potential coincided with the experimental ones, giving a direct evidence on the quantum molecular sieving effect for adsorption of H 2 and D 2 on CuBOTf. However, the selectivity for the 1:1 mixed gas of H 2 and D 2 was 1.2. On the contrary, experimental H 2 and D 2 isotherms at 40 K had an explicit adsorption hysteresis, originating from the marked pore blocking effect on measuring the adsorption branch. The blocking effect for quantum H 2 is more prominent than that for quantum D 2; the selectivity for D 2 over H 2 at 40 K was in the range of 2.6 to 5.8. The possibility of the quantum molecular sieving effect for H 2 and D 2 adsorption on [Cu 3(benzene-1,3,5-tricarboxylate) 2(H 2O) 3] n of three-dimensional pore networks was also shown at 77 K.     

利用选择性激发核磁共振对混合物中的两种化合物进行结构解析

利用现代NMR的1D、2D技术对一个混合物进行了分析。结果表明：混合物由两种化合物组成。为了同时准确确定两种化合物的结构，本工作应用了1D-TOCSY技术，利用该技术选择性强的特点来补充常规的1D、2DHMR实验所提供的分子结构的信息。在没有进行预分离的条件下，顺利地完成了样品中两种化合物的核磁信号归属，并最终确定了它们的结构。     

考拉维酸对人血清白蛋白结构的影响

利用多种荧光光谱法、紫外光谱法并结合分子模拟等方法, 表征了模拟生理条件下一种植物药活性组分考拉维酸(KA)影响人血清白蛋白(HSA)的结构信息. 同步荧光及紫外光谱证实考拉维酸的存在影响了HSA的微环境; 二维及三维荧光光谱表明考拉维酸可以猝灭HSA的内源荧光, 使其构象发生变化. 荧光偏振的测定提供了考拉维酸与HSA作用后生成的配合物弛豫时间与聚集特性的信息, 揭示KA的存在使HSA的流动性和微粘度发生变化. 定量求得不同温度下(298、308 和318 K)考拉维酸与HSA作用的键合参数和热力学参数. 分子模拟表明考拉维酸键合位点于HSA分子的疏水腔内, 并与赖氨酸Lys195 和天冬氨酸Asp451 形成三个氢键, 与HSA的键合模式主要是疏水作用; 位点竞争实验证明考拉维酸在HSA亚结构域的位点Ⅱ位发生作用. 另外, 获得的相关物理化学参数从分子水平上揭示了考拉维酸与HSA相互作用的机制. 结果表明, HSA对考拉维酸有较强的结合能力, 提示人血清白蛋白对考拉维酸可起到储存和转运的作用.     

考拉维酸对人血清白蛋白结构的影响

利用多种荧光光谱法、紫外光谱法并结合分子模拟等方法,表征了模拟生理条件下一种植物药活性组分考拉维酸(KA)影响人血清白蛋白(HSA)的结构信息.同步荧光及紫外光谱证实考拉维酸的存在影响了HSA的微环境;二维及三维荧光光谱表明考拉维酸可以猝灭HSA的内源荧光,使其构象发生变化.荧光偏振的测定提供了考拉维酸与HSA作用后生成的配合物弛豫时间与聚集特性的信息,揭示KA的存在使HSA的流动性和微粘度发生变化.定量求得不同温度下(298、308和318 K)考拉维酸与HSA作用的键合参数和热力学参数.分子模拟表明考拉维酸键合位点于HSA分子的疏水腔内,并与赖氨酸Lys195和天冬氨酸Asp451形成三个氢键,与HSA的键合模式主要是疏水作用;位点竞争实验证明考拉维酸在HSA亚结构域的位点II位发生作用.另外,获得的相关物理化学参数从分子水平上揭示了考拉维酸与HSA相互作用的机制.结果表明,HSA对考拉维酸有较强的结合能力,提示人血清白蛋白对考拉维酸可起到储存和转运的作用.     

Nitrous oxide tetramer has two highly symmetric isomers

Infrared spectra of the nitrous oxide tetramer, (N(2)O)(4), are studied in the region of the N(2)O ν(1) fundamental band (～2200 cm(-1)). The spectra are observed using a tunable diode laser to probe a pulsed supersonic jet expansion. Parallel (ΔK = 0) bands are observed for the previously observed isomer of (N(2)O)(4), which is confirmed by isotopic substitution to have an oblate symmetric rotor structure with D(2d) symmetry. A distinct new isomer of (N(2)O)(4) is observed by means of a perpendicular (ΔK = ±1) band. It has a prolate symmetric rotor structure with S(4) symmetry. These isomers represent two distinct, but almost equally favorable, ways of bringing together a pair of nonpolar N(2)O dimers to form a tetramer. It is not clear at present which one represents the true ground state.     

The structure elucidation of isomalyngamide K from the marine cyanobacterium Lyngbya majuscula by experimental and DFT computational methods

The 2Z-isomer of malyngamide K has been isolated along with the known compounds malyngamide C, deoxy-C and K, and characterized from a Papua New Guinea field collection of the cyanobacterium Lyngbya majuscula. The planar structure was deduced by 1D and 2D NMR spectroscopic and mass spectral data interpretation. The absolute configurations were determined on the basis of spectroscopic techniques, chemical degradation and DFT theoretical calculations.     

Structural-electronic correlation in the first-order phase transition of [FeH2L2-Me](ClO4)2 (H2L2-Me = bis[((2-methylimidazol-4-yl)methylidene)-3- aminopropyl]ethylenediamine)

The synthesis and detailed study of the new mononuclear spin crossover complex [Fe(II)H2L(2-Me)](ClO4)2 (where H2L(2-Me) = bis[((2-methylimidazol-4-yl)methylidene)-3-aminopropyl]ethylenediamine) are reported. Variable-temperature magnetic susceptibility measurements show the occurrence of a steep spin crossover centered at 171.5 K with a hysteresis loop of ca. 5 K width (T(/2)(increasing) = 174 K and T(1/2)(decreasing) = 169 K, for increasing and decreasing temperatures, respectively). The crystal structure has been resolved for the high-spin (HS) and low-spin (LS) states at 200 and 123 K, respectively, revealing a crystallographic phase transition that occurs concomitantly to the spin crossover: at 200 K, the complex crystallizes in the monoclinic system, space group P2(1)/n, while the space group is P2(1) at 123 K. The mean Fe-N distances are shortened by 0.2 A, but the thermal spin crossover is accompanied by significant structural changes: the rearrangement of the central atom C12 of a six-membered chelate ring of [Fe(II)H2L(2-Me)]2+ to two positions (C12A and C12B) and, consequently, the lack of an inversion center at 123 K (P2(1) space group). Both HS and LS supramolecular structures involve all possible hydrogen bonds between imidazole and amine NH functions, and perchlorate anions; however, the HS supramolecular structure is a one-dimensional (1D) network, and the LS phase may better be described as a two-dimensional (2D) extended structure of A and B molecules. The structural phase transition of [FeH2L(2-Me)](ClO4)2 seems to trigger the steep and hysteretic spin crossover. Discontinuities in the temperature dependence of the M?ssbauer parameters (isomer shift and quadrupole splitting) at the spin crossover temperature confirmed the occurrence of a structural phase transition. The experimental enthalpy and entropy variations were determined by differential scanning calorimetry (DSC) as 7.5 +/- 0.4 kJ/mol and 45 +/- 3 J K(-1) mol(-1), respectively. The regular solution theory was applied to the experimental data, yielding an interaction parameter of Gamma = 3.36 kJ/mol, which is larger than 2RT(1/2), which fulfills the condition for observing hysteresis.     

The first solid enols of anhydrides. Structure, properties, and enol/anhydride equilibria(1)

Reaction of beta-methylglutaconic anhydride with NaOMe followed by reaction with methyl or phenyl chloroformate gave the corresponding O-methoxy (and O-phenoxy) carbonylation derivatives. Reaction of the anhydride with MgCl2/pyridine, followed by methyl chloroformate gave C-methoxycarbonylation at C3 of the anhydride. The product (4) was previously suggested by calculation to be the enol of the anhydride 5 and this is confirmed by X-ray crystallography (bond lengths: C-OH, 1.297 A; C1C2 1.388 A; HO...O=C(OMe) distance 2.479 A) making it the first solid enol of an anhydride. In CDCl3, CD3CN, or C6D6 solution it displays the OH as a broad signal at ca. 15 ppm, suggesting a hydrogen bond with the CO2Me group. NICS calculations indicate that 4 is nonaromatic. With D2O in CDCl3 both the OH and the C5H protons exchange rapidly the H for D. An isomeric anhydride 5a of 5 is formed in equilibrium with 4 in polar solvents. In solution, anhydride(s)/enol equilibria are rapidly established with Kenol of 6.40 (C6D6, 298 K), 0.52 (CD3CN, 298 K), 9.8 (CDCl3, 298 K), 22.8 (CDCl3, 240 K), and decreasing Kenol in CDCl3:CD3CN mixtures with the increase in percent of CD3CN. The percentage of the rearranged anhydride in CDCl3:(CD3)2CO increases with the increased percent of (CD3)2CO. In DMSO-d6 and DMF-d7 the observed species are mainly the conjugated base 4- and 5a. Deuterium effects on the delta(13C) values were determined. An analogous C2-OH enol of anhydride 15 substituted by 3-CO2Me and 4-OCO2Me groups was prepared. Its structure was confirmed by X-ray crystallography (CO bond length 1.298 A, O...O distance 2.513 A); delta(OH) = 12.04-13.22 ppm in CDCl3, THF-d8, and CD3CN, and Kenol = > or = 100, 7.7, and 3.4 respectively. In DMSO-d6 enol 15 ionizes to its conjugate base. Substantial upfield shifts of the apparent delta("OH") proton on diluting the enol solutions are ascribed to the interaction of the H+ formed with the traces of water in the solvent to give H3O+, which gives the alleged "OH proton" signal.     

Identification and determination of fat-soluble vitamins and metabolites in human serum by liquid chromatography/triple quadrupole mass spectrometry with multiple reaction monitoring

A method for determination of fat-soluble vitamins K(1), K(3), A, D(2), D(3) and E (as alpha- and delta-tocopherol) and metabolites 25-hydroxyvitamin D(2) and D(3) and 1,25-dihydroxyvitamin D(3) in human serum by liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) in positive mode is proposed. Highly selective identification of the target compounds in serum was confirmed by the most representative transitions from precursor ion to product ion. Quantitative MS/MS analysis was carried out by multiple reaction monitoring optimizing the most sensitive transition for each analyte in order to achieve low detection limits (from 0.012 to 0.3 ng/mL estimated with serum). The analysis was performed with 1 mL of serum, which was subjected to protein precipitation, liquid-liquid extraction to an organic phase, evaporation to dryness and reconstitution with methanol. The precision of the overall method ranged from 3.17-6.76% as intra-day variability and from 5.07-11.53% as inter-day variability. The method, validated by the standard addition method, provides complete information on the fat-soluble vitamins profile, which is of interest in clinical and metabolomics studies.     

Thermodynamic, structural, and dynamic properties of supercooled water confined in mesoporous MCM-41 studied with calorimetric, neutron diffraction, and neutron spin echo measurements

Thermodynamic, structural, and dynamic properties of heavy water (D(2)O) confined in mesoporous silica glass MCM-41 C10, C12, and C14 were investigated by differential scanning calorimetry, neutron diffraction, and neutron spin echo (NSE) measurements, respectively. The DSC data showed that no crystallization of D(2)O confined in C10 occurs in a temperature range between 298 and 180 K, and that crystalline ice is formed at 204 and 221 K for C12 and C14, respectively. For C10, the neutron radial distribution functions of confined D(2)O suggested a structural change in the supercooled state between 223 and 173 K. For C10 sample, it has been found that the tetrahedral-like water structure is partially enhanced in the central part of pores at 173 K. For all the samples, the intermediate scattering functions from the NSE measurements are fitted by the Kohlrausch-Williams-Watts stretched exponential function which implies that confined supercooled D(2)O exhibits a wide distribution of relaxation times. For C10, C12, and C14 samples, between 298 and 240 K, the relaxation times of supercooled D(2)O follow remarkably well the Vogel-Fulcher-Tamman equation; for C10 sample, below 240 K, the relaxation times of nonfreezing D(2)O show an Arrhenius type behavior. From the present experimental results on calorimetric, structural, and dynamic properties, it has been concluded that supercooled D(2)O confined in MCM-41 C10 experiences a transition from high-density to low-density hydrogen-bonded structure at around 229 K.