氧化石墨烯吸附亚甲基蓝的分子动力学模拟

采用分子动力学方法研究了亚甲基蓝在不同氧化度的氧化石墨烯表面的吸附行为及其动力学性质, 从微观角度讨论了亚甲基蓝由体相到氧化石墨烯表面的吸附过程及主要作用机制, 并通过亚甲基蓝分子动力学性质解释了氧化石墨烯的氧化度和含氧官能团类型对吸附行为的影响. 结果表明, 吸附过程中, 亚甲基蓝主要受氧化石墨烯表面含氧官能团的静电作用, 以近似垂直氧化石墨烯表面的方向进入, 并以平行的方式吸附于氧化石墨烯表面; 亚甲基蓝不易脱离高氧化度氧化石墨烯的吸附位点; 吸附平衡过程中, 相对于低氧化度的氧化石墨烯, 高氧化度氧化石墨烯对亚甲基蓝的束缚性更强, 同时与亚甲基蓝间相互作用更强; 含氧官能团中的环氧基与亚甲基蓝间的作用势能更强, 且羟基能够与亚甲基蓝间形成氢键结构, 共同保障了亚甲基蓝吸附层的稳定性.     

Coverage effects in the adsorption of H2 on Pd(100) studied by ab initio molecular dynamics simulations

The interaction of hydrogen with palladium surfaces represents one of the model systems for the study of the adsorption and absorption at metal surfaces. Theoretical gas-surface dynamics studies have usually concentrated on the adsorption dynamics on clean surfaces. Only recently it has become possible, based on advances in the electronic structure codes and improvements in the computer power, to address the much more complex problem of the adsorption dynamics on precovered surfaces. Here, I present ab initio molecular dynamics (AIMD) simulations based on periodic density functional theory (DFT) calculations of the adsorption of H(2) on hydrogen-precovered Pd(100) for a broad variety of different hydrogen coverage structures. The stability of the adsorbate structures and the adsorption dynamics are analyzed in detail. Calculated sticking probabilities are larger than expected for pure site-blocking consistent with experimental results. It turns out that the adsorption dynamics on the strongly corrugated surfaces depends sensitively on the dynamic response of the substrate atoms upon the impact of the impinging H(2) molecules. In addition, for some structures the adsorption probability was evaluated as a function of the kinetic energy. Adsorbate structures corresponding to the same coverage but with different arrangements of the adsorbed atoms can lead to a qualitatively different dependence of the adsorption probability on the kinetic energy changing also the order of the preferred structures, as far as the adsorption is concerned, as a function of the kinetic energy. This indicates that dynamical effects such as steering and dynamical trapping play an important role in the adsorption on these precovered substrates.     

A First-principles Study on the Gas Sensitivity of Metal-loaded Graphene with an Atomic Vacancy to O_2

In this work, adsorption energies, geometrical and electronic structures for adsorption systems of O_2 at metal-loaded graphene(M-Gra) and metal-loaded defective graphene(M-D-Gra)(M = Ni, Pd, Pt and Al) surfaces are studied using a GGA-PW91 method. Calculated results show that loaded M make the interaction between O_2 and the graphene surface change from physical to chemical adsorptions, band gaps of M-Gra systems after the O_2 adsorption change, and the Ni-loaded Gra has the highest sensitivity to O_2. For O_2-M-D-Gra systems, interactions between O_2 and the M-D-Gra surfaces are chemical, similar to the O_2-M-Gra systems, and loaded Pt and Al have the strongest effect on the sensitivity of D-Gra to O_2. The M loads at the perfect Gra and D-Gra surfaces make the interactions between O_2 and the surfaces have obvious charge transfer. This work would provide a valuable guidance on the gas sensitivity study of graphene to O_2.     

Comparison of Adsorption of Proteins at Di erent Sizes on Pristine Graphene and Graphene Oxide

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 α-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.     

石墨烯/聚乙烯复合材料及其拉伸性能的分子动力学模拟

利用分子动力学方法,模拟石墨烯/聚乙烯复合材料的微观结构和性能,并采用单轴拉伸模拟方法研究石墨烯/聚乙烯复合材料的拉伸性能.结果表明,在石墨烯/聚乙烯复合材料平衡构型中,聚乙烯基体分子在石墨烯表面处形成多层吸附层,吸附层处于动态稳定状态,层内分子可以发生扩散迁移.吸附层内聚乙烯分子发生"吸附固化"现象,分子弯曲程度减弱,发生有序排列,且在垂直于石墨烯方向的运动性能受到抑制.拉伸模拟结果表明,石墨烯能够提高聚乙烯材料的拉伸性能.在弹性区和屈服区,石墨烯阻碍了复合材料在垂直于拉伸方向的压缩变形,聚乙烯分子"吸附固化"结构保持稳定,引起体系整体应力的迅速升高.在软化区,由于石墨烯发生剧烈弯曲,"吸附固化"结构发生破坏,最终引起体系应力迅速减小.在弹性区和屈服区,体系应变主要引起了非键相互作用的改变.在软化区之后,应变主要导致了体系内分子成键相互作用的改变.应变速率能够提高复合材料的屈服应力,而不改变复合材料应力应变的整体趋势.     

Effects of electrolyte concentration and pH on the coalescence stability of beta-lactoglobulin emulsions: experiment and interpretation

Experimental results are presented about the effects of ionic strength and pH on the mean drop-size after emulsification and on the coalescence stability of emulsions, stabilized by a globular protein beta-lactoglobulin (BLG). The mean drop-size is determined by optical microscopy, whereas the coalescence stability is characterized by centrifugation. In parallel experiments, the zeta-potential and protein adsorption on drop surface are determined. The experiments are performed at two different BLG concentrations, 0.02 and 0.1 wt%. The electrolyte concentration in the aqueous phase, C(EL), is varied between 1.5 mM and 1 M, and pH is varied between 4.0 and 7.0. The experiments show that the mean drop-size after emulsification depends slightly on C(EL), at fixed protein concentration and natural pH = 6.2. When pH is varied, the mean drop-size passes through a maximum at fixed protein and electrolyte concentrations. A monolayer protein adsorption is registered in the studied ranges of C(EL) and pH at low BLG concentration of 0.02 wt%. In contrast, a protein multilayer is formed at higher BLG concentration, 0.1 wt%, above a certain electrolyte concentration (C(EL) > 100 mM, natural pH). The experimental results for the emulsion coalescence stability are analyzed by considering the surface forces acting between the emulsion drops. The electrostatic, van der Waals, and steric interactions are taken into account to calculate the barriers in the disjoining pressure isotherm at the various experimental conditions studied. The comparison of the theoretically calculated and the experimentally determined coalescence barriers shows that three qualitatively different cases can be distinguished. (1) Electrostatically stabilized emulsions, with monolayer protein adsorption, whose stability can be described by the DLVO theory. (2) Sterically stabilized emulsions, in which the drop-drop repulsion is created mainly by overlapping protein adsorption multilayers. A simple theoretical model is shown to describe emulsion stability in these systems. (3) Sterically stabilized emulsions with a monolayer adsorption on drop surface.     

Determining molecule-carbon surface adsorption energies using molecular mechanics and graphene nanostructures

Five model surfaces were developed using molecular mechanics with MM2 parameters. A smooth, flat model surface was constructed of three parallel graphene layers where each graphene layer contained 127 interconnected benzene rings. Four rough surfaces were constructed by varying the separation between a pair of graphene nanostructures placed on the topmost layer of graphene. Each nanostructure contained 17 benzene rings arranged in a linear strip. The parallel nanostructures were moved closer together to increase the surface roughness and to enhance the molecule-surface interaction. Experimental adsorption energy values from the temperature variation of second gas-solid virial coefficients values were available for 16 different alkanes, haloalkanes, and ether molecules adsorbed on Carbopack B (Supelco, 100 m(2)/g). For each of the five different surface models, sets of 16 calculated adsorption energies, E(cal)( *), were determined and compared to the available experimental adsorption energies, E( *). The best linear regression correlation between E( *) and E(cal)( *) was found for a 1.20 nm internuclei separation of the surface nanostructures, and for this surface model the calculated gas-solid interaction energies closely matched the experimental values (E( *)=1.018E(cal)( *), r(2)=0.964).     

Effect of carbon cathode morphology on the electrode/electrolyte interface structure

The study has focused on identifying possible factors that determine differences in electrocatalytic activity between carbon cathodes with different morphologies in Li–air batteries. The structure of the aprotic solvent dimethyl sulfoxide at carbon surfaces, such as nanotube, graphene plane, and single- and multilayer graphene edges, has been investigated using molecular dynamics simulation. It has been found that the solvent has a layered structure near the graphene plane, the graphene edge, and the nanotube. Moreover, the sharpness of the solvent layers decreases with the increasing surface curvature. The interface structure at the edge of the multilayer graphene has a qualitatively different, chessboard structure. It has been assumed that the observed differences in the interfacial solvent structure can influence the concentration distribution of the Li⁺ and O₂ reactants and in their adsorption rates, thereby affecting the kinetics of the oxygen reduction reaction.     

Molecular dynamics simulations of peptide-surface interactions

Proteins, which are bioactive molecules, adsorb on implants placed in the body through complex and poorly understood mechanisms and directly influence biocompatibility. Molecular dynamics modeling using empirical force fields provides one of the most direct methods of theoretically analyzing the behavior of complex molecular systems and is well-suited for the simulation of protein adsorption behavior. To accurately simulate protein adsorption behavior, a force field must correctly represent the thermodynamic driving forces that govern peptide residue-surface interactions. However, since existing force fields were developed without specific consideration of protein-surface interactions, they may not accurately represent this type of molecular behavior. To address this concern, we developed a host-guest peptide adsorption model in the form of a G(4)-X-G(4) peptide (G is glycine, X is a variable residue) to enable determination of the contributions to adsorption free energy of different X residues when adsorbed to functionalized Au-alkanethiol self-assembled monolayers (SAMs). We have previously reported experimental results using surface plasmon resonance (SPR) spectroscopy to measure the free energy of peptide adsorption for this peptide model with X = G and K (lysine) on OH and COOH functionalized SAMs. The objectives of the present research were the development and assessment of methods to calculate adsorption free energy using molecular dynamics simulations with the GROMACS force field for these same peptide adsorption systems, with an oligoethylene oxide (OEG) functionalized SAM surface also being considered. By comparing simulation results to the experimental results, the accuracy of the selected force field to represent the behavior of these molecular systems can be evaluated. From our simulations, the G(4)-G-G(4) and G(4)-K-G(4) peptides showed minimal to no adsorption to the OH SAM surfaces and the G(4)-K-G(4) showed strong adsorption to the COOH SAM surface, which is in agreement with our SPR experiments. Contrary to our experimental results, however, the simulations predicted a relatively strong adsorption of G(4)-G-G(4) peptide to the COOH SAM surface. In addition, both peptides were unexpectedly predicted to adsorb to the OEG surface. These findings demonstrate the need for GROMACS force field parameters to be rebalanced for the simulation of peptide adsorption behavior on SAM surfaces. The developed methods provide a direct means of assessing, modifying, and validating force field performance for the simulation of peptide and protein adsorption to surfaces, without which little confidence can be placed in the simulation results that are generated with these types of systems.     

Theory and experiment agree: single-walled carbon nanotube caps grow catalyst-free with chirality preference on a SiC surface

High-temperature quantum chemical molecular dynamics simulations have been performed on model systems of thin SiC crystal surfaces with two graphene sheets placed on top of either C or Si face. In agreement with experiment, we find that (a) the C-face-attached graphene layer warps readily to form small diameter, stable nanocaps, suitable for further perpendicular growth of nanotubes, (b) the Si-face-attached graphene sheet does not readily wrap and forms more volatile Si-graphene bonds, and (c) C face nanocaps appear to anneal to dome-shape structures with zigzag chirality.     

Removal of 4‐chlorophenol using graphene,graphene oxide,and a‐doped graphene (A = N,B): A computational study

Density functional theory (including van der Waals correction with the PBE‐D functional) is applied to the study of 4‐chlorophenol (4‐CP) adsorption on graphene oxide (GO), A‐doped graphene (A = N, B), and pristine graphene and test their possible application for 4‐CP removal. Results show that on GO adsorption is improved by the hydrogen bond interactions between the adsorbents and 4‐CP, suggesting that functionalized graphene is a preferable alternative than pristine graphene for 4‐CP removal. In addition, the stability of hydrogen bonds is confirmed by molecular dynamics calculations using the PM6 potential. Without hydrogen bonds, A‐doped graphene models show a comparable performance for 4‐CP removal than pristine graphene. Finally, even in a solvent medium, 4‐CP adsorption is strong. © 2013 Wiley Periodicals, Inc.     

Curvature effect in the longitudinal unzipping carbon nanotubes

Density functional theory (DFT) calculations are performed to analyze curvature effects in the oxidative longitudinal unzipping of carbon nanotubes (CNTs) of different diameters. The reactions considered involve the adsorption of permanganate, followed by the oxidation of the nanotube, which results in dione and hole formation. The study was performed with armchair CNTs of different diameters and with corrugated graphene layers, which emulate the curvature of CNT of larger radii, with the finding that the curvature and the pyramidalization angle of the these structures strongly affects the stability of the intermediate dione structure formed during the unzipping process. Permanganate adsorption energies increase for more curved surfaces promoting the oxidation reaction in surfaces of small radius, making this reaction spontaneous for small radius. The second permanganate adsorbs on the parallel carbon–carbon bond to first diona formation resulting the longitudinal unzipping of the CNT.     

First-principles studies on doped graphene as anode materials in lithium-ion batteries

Using density functional theory computations, we investigated Li adsorption, diffusion, and desorption in pristine, B- or N-doped graphene. Compared with pristine graphene, B-doping significantly enhances Li adsorption, whereas Li adsorption is slightly weakened on N-doped graphene, which should be attributed to the different electronic structures due to doping. Li diffusion on various graphene systems was also computed through nudged elastic band method, and the results revealed that Li diffusion on N-doped graphene is faster than on pristine and B-doped graphene. Moreover, for Li desorption from the graphene substrate, N-doped graphene showed the lowest desorption barrier. Our results are in agreement with recent experimental reports and also demonstrate that N-doped graphene is a promising anode material with high-rate charge/discharge ability for Li-ion batteries.     

Effects of surface heterogeneity of carbon nanotubes in adsorption of colloid nanoparticles studied by means of computer simulations

This work deals with a construction of an implicit solvent model which can be used in molecular dynamics simulations of systems comprising colloid nanoparticles and carbon nanotubes. Such systems, due to finite sizes of both components, cannot be accurately approximated by a smaller slab geometry and thus represent a particularly difficult case in terms of computer simulations. Adsorption of large colloid nanoparticles on the surfaces of carbon nanotubes were studied and we determined the adsorption energy profiles of the nanoparticles on the carbon nanotubes surfaces. We also determined the adsorption isotherms which help to understand a preferred location of the nanoparticles on the nanotubes surfaces.     

DFT Study on the Effect of Hydrogen-bond Formation on the Adsorption of Aminotriazines on Graphene

DFT calculations have been performed to explore the aminotriazine adsorption on graphene surfaces.Relative energies,equilibrium geometries and electronic structures of monomer and dimer of aminotriazine molecules adsorbed at the surface were investigated and analyzed in details.It was found that the hydrogen atoms in the NH2 group of aminotriazine molecules are directed toward the graphene surface,and the adsorption energy increases as the NH2 group is added.The adsorbed aminotriazine molecules facilely form a dimer through the hydrogen bonding interactions,and the two aromatic rings of optimized structure of 2-amino-1,3,5-triazine(B) dimmer(denoted by B2) and melamine(D) dimmer(denoted by D2) are parallel to the graphene sheet.The large deviation of the averaged adsorption energy of B2 and D2 compared to monor adsorption may reflect the increase of π-π repulsion and the effect of hydrogen bond formation.The electronic structure analyses reveal that the formation of hydrogen bonds in melamine dimer has great influence on the adsorption mode at the graphene surface.     

Molecular dynamics simulation study on controlling the adsorption behavior of polyethylene by fine tuning the surface nanodecoration of graphite

Molecular dynamics simulations are applied to study the adsorption of polyethylene with different chain lengths on patterned graphite surfaces that contain nanoscale protrusions. The influence of the nanostructure on the strong attractive interaction inherently in the hydrophobic polyethylene and hydrophobic graphite system is investigated by modifying the top surface area and the height and the shape of the protrusions. The results are analyzed in terms of the chain configuration, the adsorption energy, the global orientational order parameter, and the normalized surface-chain contacting pair number in the first adsorption layer. When the size of the protrusion increases, the adsorption energy, the order parameter, and the normalized surface-chain contacting pair number decrease at a fixed chain length. When the size of the protrusion is fixed, the average adsorption energy per monomer and the order parameter decrease with increasing chain length because of the stronger intramolecular interactions between the monomers. Changing the protrusion shape in a suitable way will effectively reduce the strong surface-chain interaction.     

On the stability of the polymer brushes formed by adsorption of ionomer complexes on hydrophilic and hydrophobic surfaces

We have studied the effect of normal forces and shear forces on the stability and functionality of a polymer brush layer formed upon adsorption of polymeric micelles on hydrophilic and hydrophobic surfaces. The micelles consist of oppositely charged polyelectrolyte blocks (poly(acrylic acid) and poly(N-methyl 2-vinyl pyridinium iodide), and a neutral block (poly(vinyl alcohol)) or neutral grafts (poly(ethylene oxide)). The strength of the attachment of the micellar layers to various substrates was evaluated with Atomic Force Microscopy. Flow cell experiments allowed for the evaluation of long-term stability of coatings in lateral flow. Fixed angle optical reflectometry was used to quantify protein (BSA) adsorption on the micellar layers after their exposure to flow. The results show that adsorbed micellar layers are relatively weakly attached to hydrophobic surfaces and much stronger to hydrophilic surfaces, which has a significant impact on their stability. Adsorbed layers maintain their ability to suppress protein adsorption on hydrophilic surfaces but not on hydrophobic surfaces. Due to the relatively weak attachment to hydrophobic surfaces the structure of adsorbed layers may easily be disrupted by lateral forces, such that the complex coacervate-brush structure no longer exists.     

Nonrandom adsorption of polyelectrolyte chains on finite regularly charged surfaces

Adsorption phenomena are relevant in a wide variety of subjects, from biophysics to technological applications. Different aspects, such as molecular recognition, multilayer deposition, and dynamics of polymer adsorption have been addressed. The methodologies used range from analytical and numerical methods to molecular dynamics or Monte Carlo simulations. In this work, a coarse‐grained model is used to explore the adsorption of charged backbones to oppositely charged regions of a surface. These regions encompass those small enough to prevent complete adsorption, but extend to surfaces sufficiently large to promote adsorption with minimal effect on the three‐dimensional conformation in bulk. Apart from the different surface areas explored, variations on the surface charge density, polyelectrolyte chain length, and chain stiffness were also considered. The degree of compaction of the polyelectrolyte, on adsorption, is different from that found in the bulk. Also, results indicate an nonuniform adsorption pattern on regularly charged surfaces. © 2013 Wiley Periodicals, Inc.     

Molecular dynamics simulations of the adsorption of bone morphogenetic protein-2 on surfaces with medical relevance

Bone morphogenetic protein-2 (BMP-2) plays a crucial role in osteoblast differentiation and proliferation. Its effective therapeutic use for ectopic bone and cartilage regeneration depends, among other factors, on the interaction with the carrier at the implant site. In this study, we used classical molecular dynamics (MD) and a hybrid approach of steered molecular dynamics (SMD) combined with MD simulations to investigate the initial stages of the adsorption of BMP-2 when approaching two implant surfaces, hydrophobic graphite and hydrophilic titanium dioxide rutile. Surface adsorption was evaluated for six different orientations of the protein, two end-on and four side-on, in explicit water environment. On graphite, we observed a weak but stable adsorption. Depending on the initial orientation, hydrophobic patches as well as flexible loops of the protein were involved in the interaction with graphite. On the contrary, BMP-2 adsorbed only loosely to hydrophilic titanium dioxide. Despite a favorable interaction energy between protein and the TiO(2) surface, the rapid formation of a two-layer water structure prevented the direct interaction between protein and titanium dioxide. The first water adlayer had a strong repulsive effect on the protein, while the second attracted the protein toward the surface. For both surfaces, hydrophobic graphite and hydrophilic titanium dioxide, denaturation of BMP-2 induced by adsorption was not observed on the nanosecond time scale.     

Effect of surface composition on the adsorption of photosystem I onto alkanethiolate self-assembled monolayers on gold

We have used self-assembled monolayers (SAMs) prepared from omega-terminated alkanethiols on gold to generate model surfaces and examine the effect of surface composition on the adsorption of Photosystem I (PSI), stabilized in aqueous solution by Triton X-100. Triton-stabilized PSI adsorbs to high-energy surfaces prepared from HO- and HO2C-terminated alkanethiols but does not adsorb to low-energy surfaces. The inhibition of PSI adsorption at low-energy surfaces is consistent with the presence of a layer of Triton X-100 that adsorbs atop the hydrophobic SAM and presents a protein-resistant poly(ethylene glycol) (PEG) surface. While the presence of the PEG surface prevents the adsorption of PSI, the displacement of the inhibiting layer of Triton X-100 by dodecanol, a more active surfactant, greatly enhances the adsorption of PSI. This inhibiting effect by Triton X-100 can be extended to other protein systems such as bovine serum albumin.