Initiation Mechanism of Kinesin's Neck Linker Docking Process

The neck linker(NL) docking to the motor domain is the key force generation process of a kinesin motor. In the initiation step of NL docking the first three residues(LYS325, THR326 and ILE327 in 2 KIN) of the NL must form an 'extra turn', thus the other parts of the NL could dock to the motor domain. How the extra turn is formed remains elusive. We investigate the extra turn formation mechanism using structure-based mechanical analysis via molecular dynamics simulation. We find that the motor head rotation induced by ATP binding first drives ILE327 to move towards a hydrophobic pocket on the motor domain. The driving force, together with the hydrophobic interaction of ILE327 with the hydrophobic pocket, then causes a clockwise rotation of THR326,breaks the locking of LYS325, and finally drives the extra turn formation. This extra turn formation mechanism provides a clear pathway from ATP binding to NL docking of kinesin.     

X-ray spectroscopic study of the electronic structure and location of hydrogen atoms in HfTi2H x hydrides

The TiKβ₅ spectra and the electronic structure of HfTi₂H_x hydrides (x = 0, 0.5, 3.0, 4.0, 4.5, 5.95) are investigated. The location of hydrogen atoms in the structure of the HfTi₂H _x hydrides is determined, and the hydrogen occupancies of the positions e and g are calculated. The inference is made that the hydrogen atoms occupy only the e positions at a low hydrogen content up to x = 3.0 (this is confirmed by the experimental crystallographic data) and the positions e and g at a higher hydrogen content.     

界面氢键对受限水结构和动态特性的影响

应用反应力场分子动力学方法, 模拟了水限制在全羟基化二氧化硅晶体表面间的弛豫过程, 研究了基底表面与水形成的界面氢键, 及其对受限水结构和动态特性行为的影响. 当基底表面硅醇固定时, 靠近基底表面水分子中的氧原子与基底表面的氢原子形成强氢键, 这使得靠近表面水分子中的氧原子比对应的氢原子更靠近基底表面, 从而水分子的偶极矩远离表面. 当基底表面硅醇可动时, 靠近基底表面水分子与基底表面原子形成两种强氢键, 一种是水分子中的氧原子与表面的氢原子形成的强氢键, 数量较少, 另一种是水分子中的氢原子与表面的氧原子形成的强氢键, 数量较多, 这使得靠近表面水分子中的氢原子比对应的氧原子更靠近表面, 从而水分子的偶极矩指向表面. 在相同几何间距下, 当基底表面硅醇可动时, 表面的活动性使得几何限制作用减弱, 导致了受限水分层现象没有固定表面限制下的明显. 此外, 固定表面比可动表面与水形成的界面氢键作用较强, 数量较多, 导致了可动表面限制下水的运动更为剧烈.     

Symmetry analysis of the behavior of the family R<Subscript>6</Subscript>M<Subscript>23</Subscript> compounds upon hydrogenation

Symmetry analysis was applied in this work to discuss the behavior of the family R₆M₂₃ compounds upon hydrogenation (deuteration), where different structural transformations and magnetic properties, depending on the type of R and M atoms and hydrogen (deuterium) concentrations, have been found. The crystallographic structure of these compounds is described by the Fm3m space group and contain 116 atoms per unit cell occupying the positions 24e(R), 4b, 24d, 32f₁ and 32f₂(M). Additionally in the elementary cell, there could be up to 100 atoms of hydrogen (or deuterium) occupying the interstitial positions 4a, 32f₃, 96j₁ and 96k₁. The symmetry analysis in the frame of the theory of space groups and their representation gives the opportunity to find all possible transformations from high symmetry parent structure to the structures with symmetry belonging to one of its subgroups. For a given transformation it indicates possible displacements of atoms from initial positions in the parent structure, ordering of hydrogen over interstitial sites and also ordering of magnetic moments, described by the smallest possible number of free parameters. The analysis was carried out by means of the MODY computer program for vectors k = (0; 0; 0) and k = (0; 0; 1) describing the changes of translational symmetry and all positions occupied by the R, M and D atoms.     

Chemical reactions in cracks of aluminum crystals: Generation of hydrogen from water

Pure hydrogen is generated from water molecules which are dissociated by specific aluminum particles called activated Al powder. Reaction mechanism of Al atoms with H₂O molecules is investigated in micro-cracks of Al crystals. It becomes obvious that hydrogen atoms exist in Al crystal mainly in states of AlH₃ hydrides. It is concluded that virgin walls of micro-cracks right after the creation provide virtually Al radical atoms of (Al−) or (Al=) with one or two free bonds, which react with H₂O molecules via surface diffusion resulting in producing AlH₃ and eventually in producing H₂. The production of H₂ seems to be a result of micro-tribochemical reactions in cracks, which are produced by mechanical crushing of Al crystals in water; tips of cracks as stress-focused points play a major role to create AlH_3. Peculiar environments of nano-spaces in micro-cracks surrounded by reactive atoms enable us to realize unusual chemical reactions at low temperatures as exemplified in the present paper.     

Monomer structures of water adsorbed on p(2 x 2)-Ni(111)-O surface at 25 and 140 K studied by surface X-ray diffraction

The structures of a monomeric water molecule adsorbed on p(2 x 2)-Ni(111)-O surface were determined by difference Fourier calculations. At temperatures of 25 K, water molecules chemisorb predominantly at 2 x 2 oxygen atom sites, forming an OH---O(ad) (2 x 2) hydrogen bond. A 2 x 2 oxygen atom (O(ad)) is surrounded by one to three monomeric water molecules, which take statistically disordered positions with threefold symmetry. At temperatures of 140 K, monomeric water molecules occupy a top site of Ni atoms via an oxygen lone pair and are stabilized as a singleton molecule on the surface.     

New phases of water ice predicted at megabar pressures

Based on density functional calculations we predict water ice to attain two new crystal structures with Pbca and Cmcm symmetry at 7.6 and 15.5?Mbar, respectively. The known high-pressure ice phases VII, VIII, X, and Pbcm as well as the Pbca phase are all insulating and composed of two interpenetrating hydrogen bonded networks, but the Cmcm structure is metallic and consists of corrugated sheets of H and O atoms. The H atoms are squeezed into octahedral positions between next-nearest O atoms while they occupy tetrahedral positions between nearest O atoms in the ice X, Pbcm, and Pbca phases.     

(1)H-(17)O nuclear-quadrupole double-resonance study of hydrogen disorder in 2-nitrobenzoic acid

Temperature dependence of (17)O nuclear quadrupole resonance frequencies was measured in solid 2-nitrobenzoic acid by a (1)H-(17)O nuclear quadrupole double resonance technique. The experimental results show the presence of a fast exchange of hydrogen atoms between two nonequivalent positions within the O-H ellipsis O hydrogen bonds. The hydrogen disorder is ascribed to concerted jumps of two hydrogen atoms within the hydrogen bonds connecting two molecules in a dimer. The energy difference DeltaE of the two hydrogen configurations is equal to DeltaE = 60 meV = 5.8 kJ/mol. The dipole structure of the (17)O NQR lines from the C-O-H oxygen positions was also measured at -100 degrees C and at room temperature. The orientation of the principal axes of the electric field gradient tensor with respect to the O-H bond and the sign of the quadrupole coupling constant were determined. The oxygen-hydrogen distance R(O-H), as determined from the dipole structure of the (17)O NQR lines is at -100 degrees C equal to 0.099 nm. At room temperature we observe a longer distance, R(O-H) = 0.101 nm, in agreement with the hydrogen intrabond exchange.     

用分子对接方法预测HIV-1整合酶与金精三羧酸抑制剂的相互作用

用分子对接方法 (Docking)研究了HIV 1整合酶与其抑制剂金精三羧酸的结合过程 .为弄清金属离子在结合中所起的作用 ,选择含有一个Mg+ 2 或不含Mg+ 2 的两种不同的整合酶受体分别与金精三羧酸对接 .结果表明 ,Mg+ 2 对稳定配体与受体的结合起了重要作用 .金精三羧酸配体与含有一个金属Mg+ 2 的整合酶受体对接 ,最优结合自由能为 - 4 5 .19kJ/mol.当Mg+ 2 失去后 ,整合酶的活性中心构象将发生变化 ,使金精三羧酸抑制剂与整合酶的结合自由能 (- 2 4 .35kJ/mol)明显增加 .预测了未知的HIV 1整合酶与其抑制剂金精三羧酸的复合物结构 ,并可对基于结构的抗HIV 1整合酶的药物设计提供重要信息     

Magnetic and structural instabilities in the hexagonal Laves hydride ErMn2H4.6 under high-pressure

The structural and magnetic properties of ErMn₂H_4.6 have been studied by X-ray and neutron diffraction up to the pressures of 15 and 6 GPa, respectively. In the pressure range 0<P<3 GPa we observe a first-order phase transition to new high-pressure (HP) phase. The HP phase has the same hexagonal unit cell as the ambient-pressure phase but smaller lattice parameters (ΔV/V=−5%). The structural transition results in suppression of the long-range antiferromagnetic order. Our results suggest that pressure changes positions of the hydrogen atoms in the metal host. We speculate that the new arrangement of hydrogen atoms induces spin frustration and, therefore, suppresses long-range magnetic order in the HP phase.     

Bonding character of lithium atoms adsorbed on a graphene layer

This work uses first-principles calculations to investigate the aspects of the bonding character of lithium atoms adsorbed on a graphene layer. The presented results are in contradiction to other results that have recently appeared in the specialized literature, although they confirm some previous claims. In particular, a discussion of the characteristics of the bonding between lithium and carbon atoms and whether they interact via an sp² or an sp³ hybridization is intended to clarify the problem. It is also found that the carbon-lithium bond is not purely covalent but instead presents a significant ionic character. The local geometry is governed by the π-acceptor character of lithium atoms which occupy reverse positions relative to the carbon atoms as compared to the positions of hydrogen in graphane.     

A molecular dynamics study of boron and nitrogen in diamond

Based upon molecular dynamics simulation via the Tersoff many-body potential, we proposed the co-doping method for fabricating n-type diamond. We calculated the optimal co-doping configurations of n-type (nitrogen) and p-type (boron) dopants, the stable structure of a boron atom in diamond is associated with four nitrogen atoms placed at the nearest neighbour positions, the total energy of the system with the stable structure is 136 MeV lower than that of the system with the nitrogen atoms placed in others positions. The results indicated that the co-dopants of nitrogen and boron were the perfect candidates to make n-type diamond, and additional boron would increase the solubility limit of nitrogen in diamond, reduce the lattice-relaxation energy of crystal and improve its doping efficiency in diamond.     

Effect of reduction on graphitization behavior of mesophase pitch-derived carbon fibers

Chemically reduced solid-state mesophase pitch carbon fibers below 1000 °C in a flow of hydrogen gas were treated up to 3000 °C in an argon atmosphere in order to evaluate the effect of hydrogen on the graphitization behavior. Major phenomena observed during the reduction process are chemical transformation from an ether to a hydroxyl group (corresponding to the rupture of the C-O-C bond) and their subsequent evolution as gases. Finally, oversupplied hydrogen might be utilized to satisfy the dangling bond. For the sample heat treated at 3000 °C, the low crystallinity indicates that hydrogen atoms covalently bonded to the end planes of graphitic layers act as an effective barrier to crystallite growth.     

Hydrogen-induced surface metallization of beta-SiC(100)-(3x2) revisited by density functional theory calculations

Recent experiments on the silicon terminated (3 x 2)-SiC(100) surface indicated an unexpected metallic character upon hydrogen adsorption. This effect was attributed to the bonding of hydrogen to a row of Si atoms and to the stabilization of a neighboring dangling bond row. Here, on the basis of density-functional calculations, we show that multiple-layer adsorption of H at the reconstructed surface is compatible with a different geometry: in addition to saturating the topmost Si dangling bonds, H atoms are adsorbed at rather unusual sites, i.e., stable bridge positions above third-layer Si dimers. The results thus suggest an alternative interpretation for the electronic structure of the metallic surface.     

A DFT study of H adsorption on Pt(111) and Pt-Ru(111) surfaces

In this work a comparative analysis between different Pt-Ru(111) surface models and pure Pt(111) surface is presented. Some aspects of the electronic structure of the surfaces and hydrogen adsorption are analysed based on density functional theory calculations. The hydrogen adsorption energy is significantly reduced when Ru is present on the surface. The substitution of Pt atoms by Ru atoms reinforce the Pt-H bond while the metal-metal bond is strongly modified, making the system less stable.     

基于第一性原理的含空位a-Fe和H原子相互作用研究

氢致裂纹是制约超高强度钢应用的关键问题,掌握扩散氢的分布行为有助于弄清氢致裂纹的形成机理.本文采用第一性原理方法计算了H原子占据α-Fe晶格间隙和空位时的情况,得到了晶体的稳定构型及能量,并据此分析了H原子在晶格间隙和空位中的溶解倾向;从Mulliken布居、电子密度分布、态密度分布等角度分析了H原子与α-Fe晶体间隙和空位之间的相互作用.结果表明:间隙H原子倾向占据α-Fe四面体间隙位,其1s轨道电子与Fe的4s轨道电子呈微弱共轭杂化;空位是强氢陷阱, H原子倾向占据空位内壁附近的等电荷面.在真空0 K条件下单空位最多稳定溶解3个H原子,且H原子之间未表现出自发形成H2的倾向;间隙和空位中的H原子溶入改变了Fe晶格内电子分布导致原子结合力弱化,并在局部区域形成反键.基于第一性原理能量计算结果开展热力学分析,分析结果表明大多数情况下间隙H原子都是H主要的固溶形式, H平衡溶解度计算结果与实际符合良好.     

The effect of interstitial hydrogen on the electronic structure of Fe-Pd alloys

The electronic structure and bonding in Fe-Pd alloys were computed using a tight binding method. Two phases have been identified for these alloys, a high temperature fcc and a low temperature fct structure. The hydrogen absorption turns out to be a favorable process in both structures. The hydrogen at tetrahedral interstitial site for the fct structure is 2.2 eV more stable than that impurity atom located at an octahedral interstitial site in the fcc structure.The density of states curves show a peak below the d metal band which is made up mostly of hydrogen based states (>50% H_1s) while the metal contribution includes mainly s and p orbitals.In the fcc structure, both Fe-H and Pd-H bonds are developed while the Fe-Pd interface shows antibonding filled states near the Fermi level. When the fct phase is considered, the Fe-H overlap population (OP) decreases, while the Pd-H remains similar to the previous case. The Fe-Fe OP decreases and the Pd-Pd bonds are almost unaltered. The interfacial Fe-Pd bonds are almost unaffected by hydrogen. The band structure of the hydrogenated alloys in the fcc and fct phases were also computed.     

LCAO studies of hydrogen chemisorption on nickel: II. Cluster models for adsorption sites

The adsorption of single hydrogen atoms, investigated by means of cluster calculations, has been compared with the adsorption of hydrogen monolayers on periodic crystals (paper I). From the similarity of the adsorption energy curves we conclude that the (direct and indirect) interactions between adsorbed hydrogen atoms are relatively small up to monolayer coverage. For adsorption on different sites of ideal low index surfaces the stability decreases in the order Atop > Bridge > Centred. For Atop adsorption it increases with a decreasing number of nearest neighbours to the nickel atom in the NiH “surface molecule”, thus leading to especially strong adsorption sites at the edges of a stepped surface and to low stability in the notches. In general, we find that the Ni_nH “surface molecule” with n = 1, 2, 3 or 4 determines the equilibrium positions for H adsorption; the inclusion of one shell of neighbours to the nickel atoms is sufficient to explain the differences in adsorption energy. The Extended Hückel method is not well suited to study dissociative chemisorption of H₂, although some qualitative trends are correct.     

Abnormally deep penetration of hydrogen into niobium under the influence of the pulse high-temperature plasma

The process of storing and redistributing hydrogen atoms under the action of pulse high-temperature hydrogen plasma obtained on the PF-4 plasma focus (PF) plant in an assembly of three high-purity niobium foils is studied by the elastic recoil detection (ERD) method. It is determined that, as the number of hydrogen plasma pulses increases, the implanted hydrogen atoms are redistributed at larger depths in an assembly of niobium foils which significantly exceed the projected range of hydrogen ions (when their maximal velocity reaches ??10⁸ cm/s). A maximum hydrogen concentration of up to 60 at % is reached in the nearest (to PF-4) surface of the third Nb foil under the action of 20 hydrogen plasma pulses. The observed phenomenon can be attributed to the ejections of implanted hydrogen atoms under the action of high-power shock waves created in niobium foils by the pulse hydrogen plasma and/or by the accelerating diffusion of hydrogen atoms under the action of compression-straining waves at the front of the shock wave with redistributions of hydrogen atoms at larger depths. Similar behavior is found in assemblies of two or three and more nickel, vanadium, niobium, and tantalum foils of different thicknesses, including foil assemblies made of heterogeneous materials, which were also studied.     

Li原子修饰笼型Si6团簇的结构和储氢性能

利用杂化密度泛函B3LYP方法, 在6-311+G(d, p)基组水平上对Si6和Li修饰的Si6团簇的几何结构和电子性质及储氢性能进行模拟计算和理论研究. 结果表明, Si6团簇最低能量构型为笼型结构, 纯Si6团簇不能有效吸附氢分子. Li原子的引入显著改善了Si6团簇的储氢能力. 以两个Li原子端位修饰Si6团簇为载体, 其氢分子的平均吸附能为1.692~2.755 kcal/mol, 每个Li原子周围可以有效吸附五个氢分子, 储氢密度可达9.952wt%. 合适的吸附能和较高储氢密度表明Li修饰Si6团簇有望成为理想的储氢材料.