二维NOESY核磁共振波谱结合全原子分子动力学模拟研究肌肽在水溶液中的构象变化

采用二维NOESY核磁共振波谱结合全原子分子动力学模拟研究了肌肽在水溶液中的构象变化和相互作用. 以分子内距离、回转半径、RMSD以及溶剂可接触表面积等性质进行表征. 分子动力学模拟显示肌肽分子在水溶液中表现出了较高的柔性,其构象在伸展、折叠之间互相转换,大部分情况下是以伸展的构象为主导的,而折叠构象较少. 二维NOESY核磁共振实验证实了模拟的结果,实验与理论得到很好的吻合.     

甘氨酸在纳米碳管中的吸附及性质的分子模拟

采用分子力学、分子动力学方法模拟研究了甘氨酸分子在单壁纳米碳管中的吸附和扩散行为 ,并对甘氨酸分子在纳米碳管中的构象和能量进行了优化 .模拟计算结果表明 ,甘氨酸在纳米碳管中的构象发生了伸缩和扭转 ,这种构象的改变将会导致氨基酸生物性能的改变 ;纳米碳管对氨基酸分子具有较强的吸附作用 ,其中纳米碳管和甘氨酸分子之间的π -π相互作用增加了纳米碳管对氨基酸的吸附能 .模拟过程中氨基酸分子和纳米碳管之间的运动会保持很强的协同效应 ,使模拟体系构型在能量上处于最稳定的状态     

粗粒化自由能模拟研究ABC输出蛋白质构象态转变

本文应用了粗粒化分子动力学方法模拟计算了ATP结合盒式输出蛋白沿其构象转变途径反应坐标的平均力势,这个反应坐标被定义为内门和外门质量中心距离之差. 计算得到的平均力势能很好地描述不同的向内构象态、向外构象态和阻塞构象状态,以及它们之间的转变. 粗粒化分子动力学自由能模拟显示,在向内构象态到向外构象态转变过程中,内门在外门打开之前先行关闭;反之,在向外构象态到向内构象态转变过程中,外门在内门大开之前先行关闭. 因此,在向内构象态和向外构象态两种转变过程中,都经过了阻塞构象状态. 模拟结果揭示了ATP结合盒式输出蛋白的传输单向性,这种特性在生命体系功能实现中具有十分重要的意义. 这些结果与先前晶体结构实验［Proc. Natl. Acad. Sci. USA 104,19005 (2007)］发现有根本的不同,这些实验结果显示了内外门同时打开的不合理结果. 本文通过计算模拟阐明了ABC输出蛋白构象态变化的分子机理.     

不同尺度的蛋白质在纯石墨烯及氧化石墨烯表面的吸附比较（英文）

本文运用分子动力学模拟的方法,系统地比较了不同大小的蛋白质在石墨烯及其氧化物表面的吸附稳定性和构象变化.结果表明在含氧官能团的静电作用的协助下,GO的吸附稳定性要强于PG:由少量残基组成的多肽在PG和GO表面其α螺旋结构都发生变化,蛋白片段在PG表面部分α螺旋被破坏,在GO表面保持完好,而完整的球状蛋白在PG和GO表面结构都没发生明显变化,尤其是GO,体现出良好的生物相容性.GO作为吸附底物在纳米生物技术领域显示出良好的应用前景.     

MDM2与抑制剂PDIQ作用机制的结合自由能计算研究

近年来p53-MDM2相互作用已成为抗癌药物设计的重要靶标.本工作采用分子动力学模拟和结合自由能计算研究抑制剂PDIQ与MDM2的结合模式.结果显示范德瓦尔斯作用是抑制剂结合的主体力量.基于残基的自由能分解计算结果表明CH-CH,CH-π和π-π相互作用驱动了抑制剂与MDM2的结合.这一研究可为抗癌药物的设计提供一定的理论指导.     

熵驱动下柱状高分子刷螺旋结构的研究

自然界中广泛存在螺旋结构,在特定情形下熵能驱动高分子链形成螺旋结构.本文采用分子动力学方法研究柱状高分子刷吸附在无限长圆柱表面时的构象行为.发现其构象与嫁接支链条数、柱状高分子刷与圆柱表面之间的吸附能密切相关.在较弱的吸附能下,具有较多支链条数的柱状高分子刷能形成完整的螺旋结构,其本质就是熵驱动下形成的螺旋结构.该研究有助于加深对生物大分子螺旋结构的理解.     

地黄梓醇和乙酰胆碱酯酶作用的分子动力学模拟

梓醇能有效的的改善阿茨海默尔症状,但与乙酰胆碱酯酶(Acetylcholinesterase,AchE)作用的分子机制尚不明晰.本文运用分子动力学模拟、结合自由能的计算和丙氨酸突变扫描的方法研究了两者的结合模式,结果表明:梓醇结合位点为乙酰胆碱酯酶的催化活性中心,并形成3个氢键,结合自由能为-60.59 k J/mol,结合的主要驱动力是范德华力和静电作用力,主要抑制力是极性溶剂化能,Tyr151和Gln176是两者结合的关键氨基酸.这些研究为开发高效的Ach E梓醇类似物抑制剂提供理论支持.     

过渡区内纳米颗粒的曳力特性模拟研究

在过渡区内,关于纳米颗粒曳力计算及输运特性的研究较为困难,通常会采用一些近似方法,将自由分子区或者连续介质区的理论计算式进行修正,以适用于过渡区,但是其准确性值得商榷.本文基于分子动力学模拟方法,研究了过渡区内纳米颗粒的曳力特性,并与相关理论进行对比.结果表明,气-固分子间相互作用对纳米颗粒的曳力具有显著影响.当气固结合强度较弱时,理论计算结果与分子动力学模拟值吻合较好;当气固结合强度较强时,分子动力学模拟结果明显大于理论值,这是由于气体分子在纳米颗粒表面的吸附所导致.基于气体分子在颗粒表面的吸附特性,提出引入有效颗粒半径修正,其过渡区内曳力的理论计算结果与分子动力学模拟结果吻合较好.     

MDM2与抑制剂PDIQ作用机制的结合自由能计算研究

p53-MDM2之间的相互作用是抗癌药物设计的重要靶标。采用分子动力学模拟和结合自由能计算研究抑制剂PDIQ与MDM2的结合模式,结果显示范德华作用是二者结合的主体力量。基于残基的自由能分解计算结果表明CH-CH、CH-π和π-π相互作用驱动了二者的结合。这一研究成果可为抗癌药物的设计提供理论上的指导。     

增强采样分子动力学模拟在生物分子研究中的进展

分子动力学模拟能够描述蛋白质分子在行使生物学功能过程中涉及的构象变化,已发展成为中物学研究中重要的计算工具.由于生物分子的构象分布存在崎岖的自由能面,在较为复杂的生物体系的模拟中,传统的分子动力学模拟的构象采样能力受到极大限制,模拟的时间尺度与真实的生物学过程之间仍存在差距.增强采样是解决这一问题的有效手段.本文综述了两类增强采样方法即约束型和无约束型增强采样算法的理论基础、最新进展及其在生物分子中的典型应用,同时也简要总结了组合型增强采样算法近些年的发展.     

Role of oxygen functional groups for structure and dynamics of interfacial water on low rank coal surface: a molecular dynamics simulation

Molecular dynamics simulations were employed to study the effects of oxygen functional groups for structure and dynamics properties of interfacial water molecules on the subbituminous coal surface. Because of complex composition and structure, the graphite surface modified by hydroxyl, carboxyl and carbonyl groups was used to represent the surface model of subbituminous coal according to XPS results, and the composing proportion for hydroxyl, carbonyl and carboxyl is 25:3:5. The hydration energy with ?386.28 kJ/mol means that the adsorption process between water and coal surface is spontaneous. Density profiles for oxygen atoms and hydrogen atoms indicate that the coal surface properties affect the structural and dynamic characteristics of the interfacial water molecules. The interfacial water exhibits much more ordering than bulk water. The results of radial distribution functions, mean square displacement and local self-diffusion coefficient for water molecule related to three oxygen moieties confirmed that the water molecules prefer to absorb with carboxylic groups, and adsorption of water molecules at the hydroxyl and carbonyl is similar.     

The adsorption of hydrogen on iron; A surface orbital modified occupancy — bond energy bond order calculation

A Surface Orbital Modified Occupancy — Bond Energy Bond Order (SOMO-BEBO) model calculation of hydrogen adsorption on iron is presented. This calculation represents a novel approach to the CFSO-BEBO method in that the calculation is correlated in a consistent way with the thermal desorption spectra of the hydrogen-iron system. Heats of molecular adsorption calculated are ?32.88, ?35.68 and ?49.57 kJ/mol for the iron (110), (100), and (111) surfaces, respectively. Heats of dissociative adsorption calculated are ?54.40, ?75.30 and ?87.90 kJ/mol for the three states on the iron (111) surface; ?51.21 and ? 73.62 kJ/mol for the two states on the iron (100) surface; and ?63.78 kJ/mol for the one state on the iron (110) surface. Activation energies for dissociative adsorption were found to be small or zero for the iron (111) surface while non-zero activation energies of 49.27 and 45.05 kJ/mol were calculated for the iron (100) and (110) surfaces, respectively. The FeH single-order bond energy has been calculated to be 298.2 kJ/mol. The radius of the hydrogen surface atom has been estimated to be 1.52 × 10^?10 m consistent with the expected size of an H^? ion. The elimination of certain surface sites for molecular adsorption as a result of the ferromagnetism of iron is suggested by the calculation. The reason for the absence of well defined LEED patterns for hydrogen adsorption on the iron (111) and (100) surfaces [Bozso et al., Appl. Surface Sci. 1 (1977) 103] is explained on the basis of the size of the H^? surface ion. The adsorption of hydrogen on the iron (110) surface is consistent with a relatively stable, small-sized H⁺₂ surface ion giving, therefore, a regular LEED pattern and a positive surface potential upon adsorption of hydrogen on this surface.     

Oxidation degree dependent adsorption of ssDNA onto graphene-based surface

DNA/GO composite plays a significant role in the research field of biotechnology and nanotechnology, and attracts a great deal of interest. However, it is still unclear how the oxidation degree of the graphene-based surface affects the adsorption process of single-strand DNA(ss DNA). In this paper, based on the molecular dynamics simulations, we find that ss DNA molecule is absorbed on the GO surface in the most stable state with the oxidation degree around 15%. The microscopic mechanism is attributed to the van Der Walls and the electrostatic interactions between the ss DNA molecule and the graphene-based surface, which is accompanied with the π–π stacking and hydrogen bond formation. The number of π–π stacking between ss DNA and GO reaches the maximum value when the oxidation degree is around 15% among all the GO surfaces. Our simulation results also reveal the coexistence of stretched and curved configurations as well as the adsorption orientation of ss DNA on the GO surface. Furthermore, it is found that the absorbed ss DNA molecules are more likely to move on the graphene-based surface of low oxidation degree, especially on pristine graphene. Our work provides the physics picture of ss DNA's physisorption dynamics onto graphene-based surface and it is helpful in designing DNA/GO nanomaterials.     

不同尺度的蛋白质在纯石墨烯及氧化石墨烯表面的吸附比较

Using all-atom molecular dynamics (MD) simulations, we have investigated the adsorption stability and conformation change of different proteins on the surface of pristine graphene (PG) and graphene oxide (GO). We find that: (i) with the cooperation of the electrostatic interactions between proteins and oxygen-containing groups, GO shows better adsorption stability than PG; (ii) the peptide loses its secondary structure on both PG and GO surface, and the a-helix structure of the protein fragment is partially broken on PG surface, but is well preserved on GO surface, while the secondary structure of globular protein has no distinct change on both PG and GO surface. In general, GO presents better biocompatibility than PG. Our results are of significant importance to understand the interactions between proteins and PG/GO and the applications of PG/GO in biotechnology and biomedicine.     

Adsorption dynamics of double-stranded DNA on a graphene oxide surface with both large unoxidized and oxidized regions

The adsorption dynamics of double-stranded DNA (dsDNA) molecules on a graphene oxide (GO) surface are important for applications of DNA/GO functional structures in biosensors, biomedicine and materials science. In this work, molecular dynamics simulations were used to examine the adsorption of different length dsDNA molecules (from 4 bp to 24 bp) on the GO surface. The dsDNA molecules could be adsorbed on the GO surface through the terminal bases and stand on the GO surface. For short dsDNA (4 bp) molecules, the double-helix structure was partially or totally broken and the adsorption dynamics was affected by the structural fluctuation of short dsDNA and the distribution of the oxidized groups on the GO surface. For long dsDNA molecules (from 8 bp to 24 bp) adsorption is stable. By nonlinear fitting of the contact angle between the axis of the dsDNA molecule and the GO surface, we found that a dsDNA molecule adsorbed on a GO surface has the chance of orienting parallel to the GO surface if the length of the dsDNA molecule is longer than 54 bp. We attributed this behavior to the flexibility of dsDNA molecules. With increasing length, the flexibility of dsDNA molecules also increases, and this increasing flexibility gives an adsorbed dsDNA molecule more chance of reaching the GO surface with the free terminal. This work provides a whole picture of adsorption of dsDNA molecules on the GO surface and should be of benefit for the design of DNA/GO based biosensors.     

Molecular simulations of phenol and ibuprofen removal from water using multilayered graphene oxide membranes

We present here non-equilibrium molecular dynamic simulations concerning the separation of phenol and ibuprofen as impurities compounds (ICs) in water by novel graphene oxide (GO) membranes. The coupling between water permeability and impurity rejection is studied as a function of membrane thickness and concentration, focusing on the underlying molecular phenomena. Results show that water permeability decreases as the number of layers increases. Moreover, molecular sieving can be achieved by tuning the number of GO layers and the surface chemistry of the sheet: water flow through layers is up to 20% faster than that in graphene layers, because of strong hydrogen bonded interactions with the oxygenated groups. Analysis of the simulation results suggests that upon adsorbing on the GO surface, the translational motion of ICs in water would be supressed. Nevertheless, hydrophilicity affects the permeability for membranes with high O/C ratio, owing to these strong hydrogen bonds. Furthermore, 100% rejection for the ICs can be obtained for most of the GO membranes with four layers. This study elucidates the important role of hydrophilic interactions in GO membranes to become ideal candidates for removal of organic pollutants from water, showing the applicability of molecular simulations to obtain molecular insights into this problem.     

Luminescent properties of thermally activated delayed fluorescence molecule with intramolecular π-π interaction between donor and acceptor

Influence of intramolecular π-π interaction on the luminescent properties of thermally activated delayed fluorescence(TADF) molecule(3, 5-bis(3,6-di-tert-butyl-9 H-carbazol-9-yl)-phenyl)(pyridin-4-yl) methanone(DTCBPY) is theoretically studied by using the density functional theory(DFT) and time-dependent density functional theory(TD-DFT).Four conformations(named as A, B, C, and D) of the DTCBPY can be found by relax scanning, and the configuration C corresponds to the luminescent molecule detected experimentally. Besides, we calculate the proportion of each conformation by Boltzmann distribution, high configuration ratios(44% and 52%) can be found for C and D. Moreover, C and D are found to exist with an intramolecular π-π interaction between one donor and the acceptor; the intramolecular interaction brings a smaller Huang-Rhys factor and reduced reorganization energy. Our work presents a rational explanation for the experimental results and demonstrates the importance of the intramolecular π-π interaction to the photophysical properties of TADF molecules.     

Study of the Binding Energy of Relativistic Nuclear Matter in the Relativistic σ-ω-π Model

A relativistic σ-ω-π model is proposed to calculate the binding energy of relativistic nuclear matter. We put emphasis on the relativistic particle-hole, delta-hole excitation of pion propagator in nuclear matter. The renormalization of the nucleon self-energy in nuclear matter is made for the pseudo-vector πNN and πNΔ couplings by introducing corresponding form factor and by dispersion relation. We find that the density dependence correction to meson-NN coupling constants is very important to saturate the binding energy of nuclear matter. The density dependence correction to πNN and πNΔ coupling constants has the effect of softening the EOS of nuclear matter.     

DFT study of graphene oxide reduction by a dopamine species

Recently a large interest has arisen for using less active reducers of graphene oxide, GO, that are friendly with the environment. In the present work, a DFT theoretical study on the reduction process of GO model surfaces is performed taking into account zwitterionic dopamine, ZDA, as reducing agent. Several periodic models representing epoxy and hydroxyl patches on GO basal plane are proposed. As the number of oxide groups in a patch of epoxies or hydroxyls on the surface of graphene increases from 1 to 5, these systems become more stable. Whereas the adsorption of ZDA on patches of GO with 5 epoxy groups is non-dissociative, that of ZDA on patches of GO with 5 hydroxyl groups is fundamentally dissociative, reducing the surface of graphene oxide. The H₂O molecule produced in the GO reduction becomes trapped to ZDA through a hydrogen bond. The ZDA binding to GO was analysed by considering electrostatic effects and attractive non-covalent contributions due to vdW interactions.     

Adsorption of water molecules on yttrium barium cuprate superconductors

Gravimetry and thermogravimetric analysis were used to study the adsorption of water molecules on the high temperature superconductor YBa₂Cu₃O₇ at room temperature. It was found that water adsorption subdivides into surface adsorption and bulk adsorption, which starts after the formation at the surface of a physically bound water layer no less than 65–100 Å thick. During bulk adsorption, H₂O molecules diffuse from this surface layer to the lattice, where they form four bound states with desorption temperatures of ～208, 330, 370, and 775°C and heats of formation of 38, 99, 72, and 68 kJ/mol, respectively, and mainly occupy interstitial sites of the intermediate layers. The presence of molecules in the lattice does not affect either the superconducting transition temperature or resistance to direct current; however, it results in an increase in the surface resistance. The resistance to direct current increases due to the formation of dielectric inclusions of other phases.