Mathematical simulation of interactions of protein molecules and prediction of their reactivity

A physical model of interactions of protein molecules has been developed. The regularities of their reactivity have been studied using electrostatics methods for two histone dimers H2A–H2B and H3–H4 assembled from monomers. The formation of histone dimers from different monomers has been simulated and their ability to the formation of stable compounds has been investigated by analyzing the potential energy matrix using the condition number. The results of a simulation of the electrostatic interaction in the formation of dimers from complete amino acid sequences of selected proteins and their truncated analogs have been considered. The calculations have been performed taking into account the screening of the electrostatic charge of charged amino acids for different concentrations of the monovalent salt using the Gouy–Chapman theory.     

Mathematical simulation of complex formation of protein molecules allowing for their domain structure

A physical model of the interactions between protein molecules has been presented and an analysis of their propensity to form complex biological complexes has been performed. The reactivities of proteins have been studied using electrostatics methods based on the example of the histone chaperone Nap1 and histones H2A and H2B. The capability of proteins to form stable biological complexes that allow for different segments of amino acid sequences has been analyzed. The ability of protein molecules to form compounds has been considered by calculating matrices of electrostatic potential energy of amino acid residues constituting the polypeptide chain. The method of block matrices has been used in the analysis of the ability of protein molecules to form complex biological compounds.     

Ab initio study of neutral (TiO2)n clusters and their interactions with water and transition metal atoms

We have systematically investigated the growth behavior and stability of small stoichiometric (TiO(2))(n) (n = 1-10) clusters as well as their structural, electronic and magnetic properties by using the first-principles plane wave pseudopotential method within density functional theory. In order to find out the ground state geometries, a large number of initial cluster structures for each n has been searched via total energy calculations. Generally, the ground state structures for the case of n = 1-9 clusters have at least one monovalent O atom, which only binds to a single Ti atom. However, the most stable structure of the n = 10 cluster does not have any monovalent O atom. On the other hand, Ti atoms are at least fourfold coordinated for the ground state structures for n ≥ 4 clusters. Our calculations have revealed that clusters prefer to form three-dimensional structures. Furthermore, all these stoichiometric clusters have nonmagnetic ground state. The formation energy and the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap for the most stable structure of (TiO(2))(n) clusters for each n have also been calculated. The formation energy and hence the stability increases as the cluster size grows. In addition, the interactions between the ground state structure of the (TiO(2))(n) cluster and a single water molecule have been studied. The binding energy (E(b)) of the H(2)O molecule exhibits an oscillatory behavior with the size of the clusters. A single water molecule preferably binds to the cluster Ti atom through its oxygen atom, resulting an average binding energy of 1.1 eV. We have also reported the interaction of the selected clusters (n = 3, 4, 10) with multiple water molecules. We have found that additional water molecules lead to a decrease in the binding energy of these molecules to the (TiO(2))(n) clusters. Finally, the adsorption of transition metal (TM) atoms (V, Co and Pt) on the n = 10 cluster has been investigated for possible functionalization. All these elements interact strongly with this cluster, and a permanent magnetic moment is induced upon adsorption of Co and V atoms. We have observed gap localized TM states leading to significant HOMO-LUMO gap narrowing, which is essential to achieve visible light response for the efficient use of TiO(2) based materials. In this way, electronic and optical as well as magnetic properties of TiO(2) materials can be modulated by using the appropriate adsorbate atoms.     

Structure and stability of self-assembled actin-lysozyme complexes in salty water

Interactions between actin, an anionic polyelectrolyte, and lysozyme, a cationic globular protein, have been examined using a combination of synchrotron small-angle x-ray scattering and molecular dynamics simulations. Lysozyme initially bridges pairs of actin filaments, which relax into hexagonally coordinated columnar complexes comprised of actin held together by incommensurate one-dimensional close-packed arrays of lysozyme macroions. These complexes are found to be stable even in the presence of significant concentrations of monovalent salt, which is quantitatively explained from a redistribution of salt between the condensed and the aqueous phases.     

基于Rotaxane类分子的稳定、重复、可反复擦写的纳米信息存储

Rotaxane类分子在溶液中可以发生可逆的分子构型改变,并随之引起分子电导特性的转变,在纳米电子器件和分子存储器件中具有潜在的应用前景.但是还不能确定这类分子在固体薄膜中是否具有类似于在溶液中的结构与电导转变,需要对Rotaxane类分子固态薄膜进行深入的结构和特性研究.文章作者在一类Rotaxane分子H1和H2的固态薄膜上获得了纳米尺度的电导转变和稳定、重复的、近于单分子尺度的纳米级存储;同时,成功地在H2分子薄膜上实现了信息记录点的可反复擦写.另外,在单个分子和亚分子的水平上直接观察到了Rotax     

基于Rotaxane类分子的稳定、重复、可反复擦写的纳米信息存储

Rotaxane类分子在溶液中可以发生可逆的分子构型改变,并随之引起分子电导特性的转变,在纳米电子器件和分子存储器件中具有潜在的应用前景.但是还不能确定这类分子在固体薄膜中是否具有类似于在溶液中的结构与电导转变,需要对Rotaxane类分子固态薄膜进行深入的结构和特性研究.文章作者在一类Rotaxane分子H1和H2的固态薄膜上获得了纳米尺度的电导转变和稳定、重复的、近于单分子尺度的纳米级存储;同时,成功地在H2分子薄膜上实现了信息记录点的可反复擦写.另外,在单个分子和亚分子的水平上直接观察到了Rotaxane分子在外电场诱导下分子结构的可逆变化以及随之发生的相应电导特性的可逆转变, 证实了Rotaxane分子在固态薄膜中的可逆结构和电导转变.     

Scientific Review: Interactions of PEO with Monovalent Electrolytes in Solvents of Different Hydrogen Bonding Capacities

Small-Angle Neutron Scattering (SANS) has been used in order to investigate the ion binding capacities of PEO in different solvents. Aprotic (acetonitrile) as well as protic (methanol and water) solvents, have been studied where methanol and water form an average two and four tetrahedrally oriented hydrogen bonds per molecule, respectively [1]. Unusual behavior of PEO has been observed in aprotic solvents and solvents with moderate hydrogen bonding where monovalent ions associate to the polymer backbone leading to a polyelectrolyte-like (where a certain fraction of monomers are charged) behavior. This is in marked contrast to behavior in aqueous solutions where water molecules associate via hydrogen bonding to the polymer and the ions are more preferentially coordinated by the solvent than the polymer.     

Two salts and the salt cocrystal of ciprofloxacin with thiobarbituric and barbituric acids: The structure and properties

Ciprofloxacin (CfH, C₁₇H₁₈FN₃O₃) crystallizes with 2‐thiobarbituric (H₂tba) and barbituric acid (H₂ba) in the aqueous solution to yield salt CfH₂(Htba)·3H₂O ( 1 ), salt cocrystal CfH₂(Hba)(H₂ba)·3H₂O ( 2 ), and salt CfH₂(Hba)·H₂O ( 3 ). The compounds are structurally characterized by the X‐ray single‐crystal diffraction. The numerous intermolecular hydrogen bonds N–H?O and O–H?O formed by water molecules, Htba^?/Hba^? and CfH₂⁺ ions, and H₂ba molecules stabilize the crystal structures of 1 to 3 . Hydrogen bonds form a 2D plane network in the salts of 1 and 3 and a 3D network in the salt cocrystal of 2 . There are different π‐π interactions in 1 to 3 . The compounds have been characterized by powder X‐ray diffraction, thermogravimetry/differential scanning calorimetry, and Fourier transform infrared spectroscopy. The compounds dehydration ends at 130°C to 150°C, and their oxidative decomposition is observed in the range of 250°C to 275°C.     

Simulation of charge reversal in salty environments: Giant overcharging?

We have performed MD simulations of a highly charged colloid in a solution of 3:1 and additional 1:1 salt. The dependency of the colloid's inverted charge on the concentration of the additional 1:1 salt has been studied. Most theories predict, that the inverted charge increases when the concentration of monovalent salt grows, up to what is called giant overcharging, while experiments and simulational studies observe the opposite. Our simulations agree with the experimental findings and shed light onto the weaknesses of the theories.     

A Theoretical Study of a Single-Walled ZnO Nanotube as a Sensor for H_2 O Molecules

We have studied the property of single-walled ZnO nanotubes with adsorbed water molecules, and theoretically designed a new sensor for detecting water molecules using single-walled ZnO nanotubes using a combination of density functional theory and the non-equilibrium Green's function method. Details of the geometric structures and adsorption energies of the H 2 O molecules on the ZnO nanotube surface have been investigated. Our computational results demonstrate that the formation of hydrogen bonding between the H 2 O molecules and the ZnO nanotube, and adsorption energies of the H 2 O molecules on the ZnO nanotube are larger than the adsorption energies of other gas molecules present in the atmospheric environment. Moreover, the current-voltage curves of the ZnO nanotube with and without H 2 O molecules adsorbed on its surface are calculated, the results of which showed that the H 2 O molecules form stable adsorption configurations that could lead to the decrease in current. These results suggest that the single-walled ZnO nanotubes are able to detect and monitor the presence of H 2 O molecules by applying bias voltages.     

环丙沙星的光谱性质、质子化作用与荧光量子产率

研究了环丙沙星(ciprofloxacin, CIP)在不同pH条件下的荧光光谱、紫外吸收光谱和质子化作用,测量了CIP在中性条件下的荧光量子产率。在H+浓度大于1 mol·L-1的HCl介质中,CIP分子(简写为HL)可以结合3个质子而以H₄L3+形式存在,有微弱的荧光,最大荧光发射波长(λ_ｍａｘ)为456 nm。在pH 0～2的酸性条件下,CIP主要以H₃L2+形式存在,λ_ｍａｘ为450 nm,荧光较弱,荧光强度随pH的升高而上升。在pH 2～4时,CIP主要以H₂L+形式存在,具有强荧光,λ_ｍａｘ仍为450 nm。当pH＞4时,λ_ｍａｘ逐步蓝移到414 nm,荧光强度随pH的升高而稍有降低,同时紫外吸收光谱也有明显变化,表明H₂L+随pH升高而失去质子,以双极离子HL形式存在。当pH＞8时,荧光强度随pH升高而减弱至消失,表明HL逐步失去质子,转化为无荧光的阴离子L-。在分子形态变化过程中,最大荧光激发波长始终在275 nm附近,但最大荧光发射波长有较大变化。在pH 7.0的缓冲溶液中,以硫酸奎宁为参比,测得CIP在最大荧光激发波长275 nm处的荧光量子产率为0.12。     

Flexible linear polyelectrolytes in multivalent salt solutions: Solubility conditions

Single- and double-stranded DNA and many biological and synthetic polyelectrolytes undergo two structural transitions upon increasing the concentration of multivalent salt or molecules. First, the expanded-stretched chains in low monovalent salt solutions collapse into nearly neutral compact structures when the density of multivalent salt approaches that of the monomers. With further addition of multivalent salt the chains redissolve acquiring expanded-coiled conformations. We study the redissolution transition using a two-state model (F.J. Solis, M. Olvera de la Cruz, J. Chem. Phys. 112, 2030 (2000)). The redissolution occurs when there is a high degree of screening of the electrostatic interactions between monomers, thus reducing the energy of the expanded state. The transition is determined by the chemical potential of the multivalent ions in the solution, μ and the inverse screening length, κ. The transition point also depends on the charge distribution along the chain but is nearly independent of the molecular weight and degree of flexibility of the polyelectrolytes. We generate a diagram of μversusκ² where we find two regions of expanded conformations, one with charged chains and the other with overcharged (inverted charge) chains, separated by a collapsed nearly neutral conformation region. The collapse and redissolution transitions occur when the trajectory of the properties of the salt crosses the boundaries between these regions. We find that in most cases the redissolution occurs within the same expanded branch from which the chain precipitates. Received 15 May 2000 and Received in final form 28 June 2000     

Protein hydration and location of water molecules in oxidized horse heart cytochrome c by (1)H NMR

The hydration properties of the oxidized form of horse heart cytochrome c have been studied by (1)H NMR spectroscopy. Two-dimensional, homonuclear ePHOGSY-NOESY experiments are used to map water-protein interactions. The detected NOEs reveal interactions between nonexchangeable protein protons and both water protons and labile protein protons which exchange with water protons. Among the many water molecules apparent in the X-ray structure, three have been identified with a residence time longer than 300 ps. One of them is located inside the distal heme cavity, in the deepest part of a hydration pathway extending toward the surface. The identification of hydrophilic regions and detection of three long-lived water molecules settles some ambiguities and provides a better representation of the water-protein interactions in oxidized cytochrome c.     

Ni（Ⅱ）,Cu（Ⅱ）,Zn（Ⅱ）的硝酸盐与氟哌酸的固态配合物的 …

由氟哌酸与Ｎｉ（Ⅱ）、Ｃｕ（Ⅱ）、Ｚｎ（Ⅱ）的硝酸盐合成了三个未见报道的固态配合物,并用元素分析、摩尔电导、红外光谱、热重分析表征了它们的组成和性质。     

<Emphasis Type="Italic">X</Emphasis><Subscript>α</Subscript> discrete variational analysis and <Superscript>1</Superscript>H nuclear magnetic resonance study of the dissociation of water molecules on the surface of TiO and TiO<Subscript>2</Subscript> oxides

The disordered state of hydrogen in titanium oxyhydrate has been investigated by ¹H nuclear magnetic resonance. The protonation of TiO and TiO₂ oxides has been simulated by the X _α discrete variational method. It is established that an increase in the number of protons decreases the stability of coordination polyhedra of titanium atoms, while an increase in the O-H bond length enhances the ability of water molecules to dissociate.     

Spin density distribution of the conduction electrons in diperylene hexafluorophosphate analysed by high-resolution NMR

High-resolution ¹³C nuclear magnetic resonance with ¹H cross polarization and ¹H decoupling under magic angle spinning is measured for the quasi-one dimensional organic conductor diperylene hexafluorophosphate (including tetrahydrofurane solvent molecules) at temperatures between 160 K and 270 K. Ab initio molecular orbital calculations are used for chemical shift analysis and for assignment of Knight shifted lines and individual carbon positions. The coexistence of neutral perylene molecules and perylene radicals in the same radical cation salt is revealed. From Knight and chemical shifts we were able to distinguish two inequivalent perylene radicals within the conducting stack. The spin density distribution of the molecular electronic wave function is determined quantitatively for these radicals. Received 29 June 1999 and Received in final form 4 November 1999     

Probing the evolution of water clusters during hydration of the solid acid catalyst H-ZSM-5

A technique developed recently for in situ solid-state ¹H NMR studies of adsorption processes has been used to probe hydration of the solid acid catalyst H-ZSM-5, yielding information on the interaction between the adsorbed water molecules and Brønsted acid sites on the H-ZSM-5 host material. Quantitative analysis of the results from the in situ experiment allows the average size of water clusters associated with the Brønsted acid sites to be determined directly, and suggests that there is a preference to form clusters comprising five–six water molecules. The in situ ¹H NMR data also provide insights into kinetic aspects of the adsorption process.     

紫外光谱法研究β-环糊精与卵磷脂的包结作用

不同摩尔配比的β-环糊精／卵磷脂的甲醇－水溶液的紫外吸收光谱和固体包结化合物的元素分析结果表明,约2分子的β-环糊精和1分子的卵磷脂依据范德华作用力和疏水作用力等发生包结作用,生成了稳定的包结化合物。     

Role of adsorption complexes in catalytic acceleration of heterogeneous reactions

The universal equation that imposes restrictions on the kinetics of heterogeneous chemical reactions has been derived. A method of studying the participation of chemisorbed or physisorbed gas molecules in heterogeneous chemical reactions has been proposed. It has been shown that the heterogeneous reaction rate is independent of the degree of occupation of the catalyst surface by the reactants as long as the product is formed by chemisorbed complexes and physisorbed molecules. It has been found that the formation of CO₂ in the heterogeneous chemical reactions CO+ O → CO₂ and 2CO + O₂ → 2CO₂ is participated by physisorbed particles and chemisorbed complexes of oxygen atoms and CO molecules.     

碱金属修饰的多孔石墨烯的储氢性能

基于第一性原理深入研究了碱金属原子(Li,Na,K)修饰的多孔石墨烯(PG)体系的储氢性能,并且通过从头算分子动力学模拟了温度对Li-PG吸附的H2分子稳定性的影响.研究结果表明,PG结构的碳环中心是碱金属原子最稳定的吸附位置,PG单胞最多可以吸附4个碱金属原子,Li原子被束缚最强,金属原子间无团聚的倾向;H2分子通过极化机制吸附在碱金属修饰的PG结构上,每个金属原子周围最多可以稳定地吸附3个H2分子;Li-PG对H2分子的吸附最强(平均吸附能为-0.246 eV/H2),Na-PG对H2分子的吸附较弱(平均吸附能为-0.129 eV/H2),K-PG对H2分子的吸附最弱(平均吸附能为-0.056 eV/H2),不适合用做储氢材料;在不考虑外界压强且温度为300 K的情况下,Li-PG结构可稳定地吸附9个H2分子,储氢量为9.25 wt.%;在400 K时,有7个吸附H2分子脱离Li-PG的束缚,在600-700 K的范围内,吸附H2分子全部脱离了Li-PG体系的束缚.