Mesoscopic dynamic Monte Carlo simulations of the adsorption of proteinlike HP chains within laterally constricted spaces

Two-dimensional dynamic Monte Carlo simulations are applied to the protein-like HP chain model to investigate the influence of lateral confinement of the adsorbed chain on adsorption thermodynamics and the ensemble of accessible chain conformations. The structure of the model makes it possible to enumerate all possible chain conformations and thereby define with precision the relation between adsorption thermodynamics and changes in accessible chain conformations resulting from the adsorption process. Lateral confinement of the adsorbed chain is shown to dramatically reduce the number of accessible energy states and unique chain conformations such that, under certain conditions, adsorption is predicted to actually stabilize the chain against denaturation. Lateral confinement preferentially eliminates expanded conformations of the adsorbed chain, shifting the equilibrium from the unfolded state toward the native state. As a result, the conformational entropy of the adsorbed chain is predicted to be lower than that of the chain free in solution. The protein-like HP chain responds to an increase in the hydrophobicity of the sorbent surface by strongly favoring those conformations that minimize the overall internal energy of the system. As a result, adsorption severely destabilizes the native-state conformation. The ability of our simulation results to provide insights into underlying mechanisms for nonspecific protein adsorption is illustrated through qualitative comparison with activity data for hen egg-white lysozyme adsorbed on silica at different surface concentrations.     

Energy landscapes for adsorption of a protein-like HP chain as a function of native-state stability

Dynamic Monte Carlo (DMC) simulations of the adsorption of simple protein-like chains are used to more clearly define the molecular basis for the dependence of adsorption thermodynamics on the stability of the unique lowest-energy "native state" conformation of the chain. Arai and Norde were among the first to show that proteins of low native-state stability strongly denature upon adsorption to weakly attractive sorbent surfaces, while relatively modest changes in conformation are observed in stable proteins under identical adsorption conditions. When the protein has a low native-state stability, favorable adsorption entropies are typically observed in such systems, leading to the general belief that the chain gains conformational entropy during adsorption through a net reduction in intramolecular interactions specific to the native-state structure. Analysis of energy landscapes generated from our DMC simulation results show that a net loss in specific intramolecular interactions can lead to a positive delta(ads)S under certain adsorption conditions. However, the influence of chain conformation on delta(ads)S is found to correlate more directly with the manner in which the unique states of the system are distributed among the energy levels available to the adsorbed chain. Delta(ads)S is found to tend toward a maximum for adsorption processes described by thermally averaged energy landscapes in which the energy levels carrying the highest Boltzmann weights have a high degree of conformational degeneracy. This condition is met when the average interaction energy between the chain and the sorbent equals that between two hydrophobic segments of the chain.     

Molecular dynamics simulation study on adsorption and diffusion processes of a hydrophilic chain on a hydrophobic surface

Molecular dynamics simulations are applied to investigate the adsorption and diffusion processes of a single hydrophilic poly(vinyl alcohol) (PVA) chain with different chain lengths on a hydrophobic graphite surface. It is expected that the chain and the surface "dislike" each other because one is hydrophilic and the other is hydrophobic. But surprisingly, a short PVA chain is well adsorbed on the surface, accompanied by large changes in the chain configuration. With increasing degree of polymerization (N), the chain turns gradually from two-dimensional adsorption to possessing certain height in the direction perpendicular to the surface. Moreover, the adsorption energy increases and the diffusion coefficient decreases with increasing N. In particular, for N = 20 in equilibrium, the hydroxyls of this short chain are close to the graphite surface in the stable adsorption configuration. In addition, we change the effective dielectric constant to 76.0 to mimic good solvent condition. The chain configurations and the diffusion coefficients both vary in contrast to the foregoing results.     

Fractions of thermodynamic functions for native lysozyme adsorption onto moderately hydrophobic surface

Calorimetric measurement of adsorption enthalpies of native lysozyme(Lyz) on a moderately hydrophobic surface at 25°C, pH 7.0 and various salt concentrations was performed. Based on the thermodynamics of stoichiometric displacement theory (SDT), we calculated the fractions of thermodynamic functions involving four subprocesses during a displacement adsorption process from the directly determined enthalpies in combination with adsorption isotherm measurements. The thermodynamic fractions reveal the relative degree of the four subprocesses for contributions to enthalpy, entropy and free energy. The results show that native Lyz adsorption on a moderately hydrophobic surface is an entropy driven process contributed mainly by conformational loss of adsorbed Lyz.     

Accelerated molecular dynamics simulation of the thermal desorption of n-alkanes from the basal plane of graphite

We utilize accelerated molecular dynamics to simulate alkane desorption from the basal plane of graphite. Eight different molecules, ranging from n-pentane to n-hexadecane, are studied in the low coverage limit. Acceleration of the molecular dynamics simulations is achieved using two different methods: temperature acceleration and a compensating potential scheme. We find that the activation energy for desorption increases with increasing chain length. The desorption prefactor increases with chain length for molecules ranging from pentane to decane. This increase subsides and the value of the preexponential factor fluctuates about an apparently constant value for decane, dodecane, tetradecane, and hexadecane. These trends are consistent with data obtained in experimental temperature-programed desorption (TPD) studies. We explain the dependence of the preexponential factor on alkane chain length by examining conformational changes within the alkane molecules. For the shorter molecules, torsional motion is not activated over experimental temperature ranges. These molecules can be treated as rigid rods and their partial loss in translational and rotational entropies upon adsorption increases as chain length increases, leading to an increasing preexponential factor. At their typical TPD peak temperatures, torsions are activated in the longer adsorbed chain molecules to a significant extent which increases with increasing chain length, increasing the entropy of the adsorbed molecule. This increase counteracts the decrease in entropy due to a loss of translation and rotation, leading to a virtually constant prefactor.     

Interactive adsorption behavior of NAD+ at a gold electrode surface

The adsorption of an oxidized form of nicotinamide adenine dinucleotide, NAD+, on a polycrystalline gold electrode surface and the subsequent surface conformation of the molecule were investigated over a wide temperature and potential range, using electrochemical differential capacitance and PM-IRRAS techniques. The adsorption process was described by the Langmuir adsorption isotherm. The corresponding thermodynamic parameters were determined: the Gibbs energy, enthalpy, and entropy of adsorption. The large negative Gibbs energy of adsorption (-43 +/- 4 kJ mol-1 and -39 +/- 2 kJ mol-1 on a positively and negatively charged surface, respectively) confirms that the NAD+ adsorption process is highly spontaneous, while the large entropy gain (285 J K-1 mol-1 and 127 J K-1 mol-1 on a positively and negatively charged surface, respectively) was found to represent the adsorption driving force. It was demonstrated that the energetics of the adsorption process is surface-charge controlled, while its kinetics is both mass-transport and surface-charge controlled. A surface-charge dependent conformation model for the adsorbed NAD+ molecule is proposed. These findings suggest that the origin of the NAD+ reduction overpotential is related to the surface conformation of the adsorbed NAD+ molecule, rather than to the electrode Fermi level position.     

Adsorption of organic molecules on a porous polymer surface modified with the supramolecular structure of melamine–cyanuric acid

The adsorption of organic molecules on the surface of a porous polymeric sorbent modified with a mixed cyanuric acid–melamine supramolecular structure is studied. The parameters of thermodynamic adsorption are considered and the contributions from intermolecular interactions to the Helmholtz energy of adsorption are assessed. Analysis of the molar changes in internal energy and adsorption entropy shows that the supramolecular structure formed on the surface could not exhibit dimension effects, indicating there were no cavities. The contributions from nonspecific interactions to the Helmholtz energy of adsorption generally fall, while those of specific interactions increase, indicating an increase in the polarity of the sorbent surface.

     

聚乙烯在羟基化β-石英(100)表面上的有序吸附

利用分子动力学模拟方法研究了聚乙烯链在羟基化β-石英(100)表面上的吸附. 结果表明, 吸附基底上的规则图案起到模板的作用, 无论是真空还是溶液环境, 都会引导聚乙烯链在表面形成二维沿着[110]方向取向的折叠构型. 为了与聚乙烯的吸附相比较, 进一步研究了聚氧化乙烯链在相同表面上的吸附情况. 结果表明, 极性链与非极性链在极性表面上的吸附情况完全不同.     

Monte Carlo simulation for the adsorption of symmetric triblock copolymers II. Adsorption layer information

By using Monte Carlo simulation, adsorption of both end-adsorbed and middle-adsorbed symmetric triblock copolymers from a non-selective solvent on an impenetrable surface has been studied. Influences of the adsorption energy, the bulk concentration, the chain composition and the chain length on the adsorption behavior including the surface coverage, the adsorption amount and the layer thickness are presented. It is shown that the total surface coverage for both end-adsorbed and middle-adsorbed copolymers increases monotonically as the bulk concentration increases. The higher the adsorption energy and the more the attractive segments, the higher the total surface coverage is exhibited. Surface coverage θ decreases with increasing the length of the non-attractive segments, but the product of θ and the proportion of the non-attractive segments in a triblock copolymer chain is nearly independent of the chain length. The adsorption amount increases almost monotonically with the bulk concentration. The logarithm of the adsorption amount is a linear function of the reciprocal of the reduced temperature. When the adsorption energy is large, the adsorption amount exhibits a maximum as the composition of the attractive segment increases. The adsorption isotherms of copolymers with different length of the non-attractive segments can be mapped onto a single curve under certain energy indicating that copolymers with different chain length have the same adsorption amount. The adsorption layer thickness for the end-adsorbed copolymers decreases as the energy and the number of adsorbing segments increases. The longer non-attractive segments, the larger adsorbed layer thickness is found. The tails mainly governs the adsorption layer thickness.     

Simulation of the sorption of cations on the surface of a selective sorbent with allowance for the possibility of their desorption

The process of sorption of several kinds of cations differing in affinity to adsorption groups on a plane sorbent surface from immobile dilute liquid solutions in the kinetic regime is simulated. Formulas are derived for estimating the time dependence of the surface concentration of adsorbed cations with allowance for the processes by which free and cation-containing adsorption groups are removed from the sorbent surface. The degree of inhibition of the adsorption of a cation in the presence of other cations is determined, which can occupy vacant sites on the sorbent surface. It is shown that the calculation results are in good agreement with experimental data.     

Temperature dependence of mucin adsorption

The kinetics of adsorption and desorption on a silica-like surface of the large glycoprotein mucin have been measured across a range of temperatures from 25 to 60 degrees C. The area occupied per molecule diminishes with increasing temperature both in the bulk and adsorbed states, implying that the glycoprotein belongs to the "natively open" conformational class. Due to the conformational rearrangement, the specific interaction energy governing desorption greatly increases with temperature, resulting in an impressively regulated temperature-invariant dynamic surface coating.     

Adsorption of trypsin on hydrophilic and hydrophobic surfaces

The adsorption of trypsin onto polystyrene and silica surfaces was investigated by reflectometry, spectroscopic methods, and atomic force microscopy (AFM). The affinity of trypsin for the hydrophobic polystyrene surface was higher than that for the hydrophilic silica surface, but steady-state adsorbed amounts were about the same at both surfaces. The conformational characteristics of trypsin immobilized on silica and polystyrene nanospheres were analyzed in situ by circular dichroism and fluorescence spectroscopy. Upon adsorption the trypsin molecules underwent structural changes at the secondary and tertiary level, although the nature of the structural alterations was different for silica and polystyrene surfaces. AFM imaging of trypsin adsorbed on silica showed clustering of enzyme molecules. Rinsing the silica surface resulted in 20% desorption of the originally adsorbed enzyme molecules. Adsorption of trypsin on the surface of polystyrene was almost irreversible with respect to dilution. After adsorption on silica the enzymatic activity of trypsin was 10 times lower, and adsorbed on polystyrene the activity was completely suppressed. The trypsin molecules that were desorbed from the sorbent surfaces by dilution with buffer regained full enzymatic activity.     

Effect of polymer architecture on the adsorption properties of a nonionic polymer

The adsorption of a linear- and bottle-brush poly(ethylene oxide (PEO))-based polymer, having comparable molecular weights, was studied by means of quartz crystal microbalance with dissipation monitoring ability (QCM-D) and AFM colloidal probe force measurements. The energy dissipation change monitored by QCM-D and the range of the steric forces obtained from force measurements demonstrated that linear PEO forms a more extended adsorption layer than the bottle-brush polymer, despite that the adsorbed mass is higher for the latter. Competitive adsorption studies revealed that linear PEO is readily displaced from the interface by the bottle-brush polymer. This was attributed to the higher surface affinity of the latter, which is governed by the number of contact points between the polymers and the interface, and the smaller loss of conformational entropy.     

Free energy of adsorption of water and calcium on the [10 1 4] calcite surface

Molecular dynamics simulations of the calcite-water interface have shown that the free energy of adsorption of water is relatively small compared to the previously calculated enthalpy of adsorption implying a large entropy change and that the free energy profile of a calcium adsorbing on the surface correlates with the solvent density; these calculations allow us to begin to address the rates of adsorption and desorption which are essential for studying growth and dissolution.     

Structure and thermodynamics of protein-polymer solutions: effects of spatially distributed hydrophobic surface residues

Protein-polymer association in solution driven by a short-range attraction has been investigated using a simple coarse-grain model solved by Monte Carlo simulations. The effect of the spatial distribution of the hydrophobic surface residues of the protein on the adsorption of weakly hydrophobic polymers at variable polymer concentration, polymer length, and polymer stiffness has been considered. Structural data on the adsorbed polymer layer and thermodynamic properties, such as the free energy, energy, and entropy, related to the protein-polymer interaction were calculated. It was found that a more heterogeneous distribution of the surface residues promotes adsorption and that this also applies for different polymer concentrations, polymer chain lengths, and polymer flexibilities. Furthermore, the polymer adsorption onto proteins with more homogeneous surface distributions displayed larger sensitivity to polymer properties such as chain length and flexibility. Finally, a simple relation between the adsorption probability and the change in the free energy was found and rationalized by a simple two-state adsorption model.     

Free energy of adsorption of water and metal ions on the [1014] calcite surface

We calculated the free energy profiles of water and three metal ions (magnesium, calcium, and strontium) adsorbing on the [1014] calcite surface in aqueous solution. The approach uses molecular dynamics with parametrized equations to describe the interatomic forces. The potential model is able to reproduce the interactions between water and the metal ions regardless of whether they are at the mineral surface or in bulk water. The simulations predict that the free energy of adsorption of water is relatively small compared to the enthalpy of adsorption calculated in previous papers. This suggests a large change in entropy associated with the water adsorption on the surface. We also demonstrate that the free energy profile of a metal ion adsorbing on the surface correlates with the solvent density and that the rate of formation of an innersphere complex depends on overcoming a large free energy barrier, which is mainly electrostatic in nature. Furthermore, comparison among the rates of desorption of magnesium, calcium, and strontium from the calcite surface suggests that magnesium has a much lower rate of desorption due to its strong interactions with both water and the surface.     

十二烷基苯磺酸钠在SiO2表面聚集的分子动力学模拟

采用分子动力学方法研究了阴离子表面活性剂十二烷基苯磺酸钠(SDBS)在无定形SiO2固体表面的吸附. 设置不同的水层厚度, 观察固液界面和气液界面吸附的差异. 模拟发现表面活性剂分子能够在短时间内吸附到SiO2表面, 受碳链和固体表面之间相互作用的影响形成表面活性剂分子层, 并依据吸附量的大小形成不同的聚集结构; 在水层足够厚的情况下, 由于有较多的表面活性剂分子吸附在固体表面,从而形成带有疏水核心的半胶束结构; 计算得到的成对势表明极性头与钠离子或水分子之间的结合或解离与二者之间的能垒有关, 解离能垒远大于结合能垒, 引起更多Na+聚集在极性头周围而只有少数Na+存在于溶液中; 无论气液还是固液界面, 极性头均伸向水相, 与水分子形成不同类型的氢键. 模拟表明, 分子动力学方法可以作为实验的一种补充, 为实验提供必要的微观结构信息.     

Effect of chain length of self-assembled monolayers in dip-pen nanolithography using molecular dynamics simulations

The pattern transfer mechanism of an alkanethiol self-assembled monolayer (SAM) with different chain lengths during the dip-pen nanolithography (DPN) process and pattern characterizations are studied using molecular dynamics (MD) simulations. The mechanisms of molecular transference, alkanethiol meniscus characteristics, surface adsorbed energy, transfer number, and pattern formation are evaluated during the DPN process at room temperature. The simulation results clearly show that the molecular transfer ability in DPN is strongly dependent on the chain length. Shorter molecules have significantly better transport and diffusion abilities between the meniscus and substrate surface, and the transport period can be maintained longer. The magnitude of adsorbed energy increases with chain length, so many more molecules can be transferred to the surface when shorter molecules are used. After deposition, the magnitude of the adsorbed area and pattern height decrease with increasing chain length.     

聚苯乙烯在石墨表面吸附的分子动力学模拟

采用分子动力学(MD)模拟方法研究了单链聚苯乙烯(PS)在石墨表面的吸附. 模拟结果表明, 吸附后PS在平行于石墨表面的方向可视为准二维椭圆结构, 并且在此方向上的均方回转半径值(R2∥)与其所含单体数目(N)具有指数关系R2∥-N2v, 指数2v约等于1.04; 最后指出PS吸附过程的主要驱动力为PS链段与表面之间的范德华作用力.