In this work, the adsorptions of hydrophobin (HFBI) on four different self-assembled monolayers (SAMs) (i.e., CH3-SAM, OH-SAM, COOH-SAM, and NH2-SAM) were investigated by parallel tempering Monte Carlo and molecular dynamics simulations. Simulation results indicate that the orientation of HFBI adsorbed on neutral surfaces is dominated by a hydrophobic dipole. HFBI adsorbs on the hydrophobic CH3-SAM through its hydrophobic patch and adopts a nearly vertical hydrophobic dipole relative to the surface, while it is nearly horizontal when adsorbed on the hydrophilic OH-SAM. For charged SAM surfaces, HFBI adopts a nearly vertical electric dipole relative to the surface. HFBI has the narrowest orientation distribution on the CH3-SAM, and thus can form an ordered monolayer and reverse the wettability of the surface. For HFBI adsorption on charged SAMs, the adsorption strength weakens as the surface charge density increases. Compared with those on other SAMs, a larger area of the hydrophobic patch is exposed to the solution when HFBI adsorbs on the NH2-SAM. This leads to an increase of the hydrophobicity of the surface, which is consistent with the experimental results. The binding of HFBI to the CH3-SAM is mainly through hydrophobic interactions, while it is mediated through a hydration water layer near the surface for the OH-SAM. For the charged SAM surfaces, the adsorption is mainly induced by electrostatic interactions between the charged surfaces and the oppositely charged residues. The effect of a hydrophobic dipole on protein adsorption onto hydrophobic surfaces is similar to that of an electric dipole for charged surfaces. Therefore, the hydrophobic dipole may be applied to predict the probable orientations of protein adsorbed on hydrophobic surfaces.

The surrounding conditions, such as surface charge density and ionic strength, play an important role in enzyme adsorption. The adsorption of a nonmodular type-A feruloyl esterase from Aspergillus niger (AnFaeA) on charged surfaces was investigated by parallel tempering Monte Carlo (PTMC) and all-atom molecular dynamics (AAMD) simulations at different surface charge densities (±0.05 and ±0.16 C·m–2) and ionic strengths (0.007 and 0.154 M). The adsorption energy, orientation, and conformational changes were analyzed. Simulation results show that whether AnFaeA can adsorb onto a charged surface is mainly controlled by electrostatic interactions between AnFaeA and the charged surface. The electrostatic interactions between AnFaeA and charged surfaces are weakened when the ionic strength increases. The positively charged surface at low surface charge density and high ionic strength conditions can maximize the utilization of the immobilized AnFaeA. The counterion layer plays a key role in the adsorption of AnFaeA on the negatively charged COOH-SAM. The native conformation of AnFaeA is well preserved under all of these conditions. The results of this work can be used for the controlled immobilization of AnFaeA.

Controlling the orientation of laccase on electrodes is crucial for the achievement of fast direct electron transfer. It is important to find a short pathway between the T1 copper site of laccase and a substrate during the laccase immobilization. In this work, we studied the adsorption orientation and conformation of Trametes versicolor laccase (TvL) on two kinds of charged self-assembled monolayers (SAMs), including NH2–SAM and COOH–SAM, by parallel tempering Monte Carlo and all-atom molecular dynamics simulations. TvL adsorbs on positively and negatively charged surface with “end-on” and “lying” orientation, respectively. On the positively charged surface, T1 copper site of TvL is closer to the surface. The orientation of TvL on positively charged surface is narrower than that on negatively charged surface. Thus, the positively charged surface is more conducive to the immobilization of TvL. The conformational changes of TvL on the charged surfaces are analyzed by RMSD, superimposed structures, dipole moment, gyration radius, and eccentricity. Results show that native structures of TvL are well preserved when it adsorbs on the charged surfaces. This work provides atomistic insight into the mechanism of TvL adsorption on charged surface and is helpful for the design and development of laccase-based electrodes.

Nanoparticles’ phase transfer behaviors at the oil–water interface have many respects in common with lipid bilayer crossing behavior and the Pickering emulsion formation. Hence, the interfacial behavior and phase transfer behavior are intuitive indicators for the application potential of nanoparticle materials, e.g., on the emulsion formation and biomedical applications. Polymer brush modification enables nanoparticles to behave differently in hydrophilic solvent, hydrophobic solvent, and their interface region. In the present work, phase transfer behaviors of triblock polymer brush modified gold nanoparticles are explored by using coarse-grained simulations. The nanoparticles grafted with hydrophobic/weak hydrophilic/hydrophobic triblock brushes are found to have the best phase transfer performance, and the enhanced flexibility and mobility of head blocks are found to be the most vital factors. The inherent mechanism of interfacial behavior and phase transfer process are investigated and explained as perturbation effect and traction effect. According to our results, middle blocks dominate the brush morphology and decide whether NPs can be transferred into another phase. However, the inner blocks show higher dominance for the phase transfer behavior of nanoparticles restricted in the interface region, while the outer ones shows higher dominance for the nanoparticles departing from the interface region. Otherwise, interesting flat-Janus morphologies are found. Special applications in two-phase interface including emulsion stabilization could be expected. This work could provide some guidance for the molecular design and applications of polymer–nanoparticle composite materials.

Surfaces with controlled oil wettability in water have great potential for numerous underwater applications. In this work, we proposed two schemes, alkyl chain length dependent and ionic strength dependent, to achieve controllable oelophobic surfaces. The underwater oil-resistant property of the obtained self-assembled monolayers (SAMs) was evaluated by using an oil droplet (1,2-dichloroethane) as a detecting probe. The oleophobicity of SAM surfaces could be modulated from superoleophilic (contact angle of ca. 0°) to superoleophobic (contact angle over 170°) by controlling the chain length difference between negatively charged HS(CH2)nCOO–-SAM (n = 17, 16, 14, 12, 10, 8, 6, 4) and positively charged HS(CH2)5N(CH3)3+-SAM. The observed phenomena could be explained by interchain interactions between charged −N(CH3)3+ and −COO–, in addition with the bending effect of the long chain in mixed-charged (pseudozwitterionic) SAMs. Furthermore, the effect of ionic strength on mixed-charged SAMs (negatively charged HS(CH2)mCOO–-SAM and positively charged HS(CH2)8N(CH3)3+-SAM, m = 8, 7, 6, 5, 4, 3) is also studied. Higher ionic strength could promote underwater superoleophobicity to an ideal oil contact angle of 180°. The additional ions markedly neutralized the effect of interchain interaction among charged head groups, which contributed to the formation of a more robust hydration network. This work provides two stratagies for preparation of hydrophilic mixed-charged surfaces with tunable underwater oleophobicity, which could not only help the fabrication of tunable underwater oil wetting surfaces, but also be potentially useful in numerous important applications, such as microfluidic devices, bioadhesion, chemical microreactors, and antifouling materials.

Molecular dynamics simulations are conducted to investigate the underwater oleophobicity of self-assembled monolayers (SAMs) with different head groups. Simulation results show that the order of underwater oleophobicity of SAMs is methyl < amide < oligo(ethylene glycol) (OEG) < ethanolamine (ETA) < hydroxyl < mixed-charged zwitterionic. The underwater–oil contact angles (OCAs) are <133° for all nonionic hydrophilic SAMs, while the mixed-charged zwitterionic SAMs are underwater superoleophobic (OCA can reach 180°). It appears that surfaces with stronger underwater oleophobicity have better antifouling performance. Further study on the effect of different alkyl ammonium ions on mixed-charged SAMs reveals that the underwater OCAs are >143.6° for all SAMs; mixed-charged SAMs containing primary alkyl ammonium ion are likely to possess the best underwater oleophobicity for its strong hydration capacity. It seems that alkyl sulfonate anion (SO3–) is more hydrophilic than alkyl trimethylammonium ion (NC3+) for the hydrophobic methyl groups on nitrogen atoms and that the hydration of SO3– in mixed-charged SAMs can be seriously blocked by NC3+. The monomer of SO3– should be slightly longer than that of NC3+ to obtain better underwater oleophobicity in NC3+–/SO3––SAMs. In addition, the underwater oleophobicity of SAMs might become worse at low grafting densities. This work systematically proves that a zwitterionic surface is more underwater oleophobic than a nonionic surface. These results will help for the design and development of superoleophobic surfaces.

In this work, the interactions between surface-functionalized gold nanoparticles (AuNPs) and asymmetric membranes and the associated cytotoxicity were explored by coarse-grained molecular dynamics simulations. Simulation results show that the surface chemistry of AuNPs and the asymmetry of lipid membranes play significant roles. AuNPs with different signs of charges spontaneously adhere to the membrane surface or penetrate the membrane core. Also, the asymmetric distribution of charged lipids in membranes can facilitate the penetration of cationic AuNPs. Increasing the surface charge density (SCD) of AuNPs can not only improve the penetration efficiency but also lead to more disruption of the membrane structure. Moreover, the flip-flop of charged lipids in the inner leaflet can be observed during the translocation of AuNPs with a high SCD. The breakdown of membrane asymmetry may hinder the cellular internalization of AuNPs in a direct penetration mechanism. More importantly, we demonstrate that the hydrophobic contact between protruding solvent-exposed lipid tails and the hydrophobic moieties of ligands can mediate the insertion of AuNPs with a low SCD into cell membranes, which will exhibit less cytotoxicity in most in vivo applications. This may open a new exciting avenue to developing nanocarriers with a higher translocation efficiency and a lower toxicity simultaneously for biomedical applications.

Understanding the interaction mechanism between catechol−cation and inorganic surfaces is vital for controlling the interfacial adhesion behavior. In this work, molecular dynamics simulations are employed to study the adhesion of siderophore analogues (Tren-Lys-Cam, Tren-Arg-Cam and Tren-His-Cam) on silica surfaces with different degrees of ionization and the effects of cationic amino acids and ionic strength on adhesion are discussed. Simulation results indicate that adhesion of catechol–cation onto the ionized silica surface is dominated by electrostatic interactions. At different degrees of ionization, the rank of the adhesions of three siderophore analogues on silica is different. Further analysis shows that the amino acid terminus has a large influence on the adhesion process, especially histidine adhesion on negatively charged surfaces. Tren-Lys-Cam (TLC) has a larger adhesion free energy than Tren-Arg-Cam (TAC) at a higher degree of ionization (18%); both the bulkier structure and delocalized charge of Arg decreased the cation's electrostatic interaction with the charged silica. In addition, the adhesion free energy on ionized silica surfaces decreased with increasing ionic strength of aqueous solutions. A linear correlation between the potential of mean force obtained from umbrella sampling and the rupture force via steered molecular dynamics simulations for siderophore analogue adhesion on silica surfaces is also found. This work may provide some guidance for developing the next generation underwater adhesives.

The α-chymotrypsin (α-ChT) enzyme is extensively used for studying nanomaterial-induced enzymatic activity inhibition. A recent experimental study reported that carboxylized carbon nanotubes (CNTs) played an important role in regulating the α-ChT activity. In this study, parallel tempering Monte Carlo and molecular dynamics simulations were combined to elucidate the interactions between α-ChT and CNTs in relation to the CNT functional group density. The simulation results indicate that the adsorption and the driving force of α-ChT on different CNTs are contingent on the carboxyl density. Meanwhile, minor secondary structural changes are observed in adsorption processes. It is revealed that α-ChT interacts with pristine CNTs through hydrophobic forces and exhibits a non-competitive characteristic with the active site facing towards the solution; while it binds to carboxylized CNTs with the active pocket through a dominant electrostatic association, which causes enzymatic activity inhibition in a competitive-like mode. These findings are in line with experimental results, and well interpret the activity inhibition of α-ChT at the molecular level. Moreover, this study would shed light on the detailed mechanism of specific recognition and regulation of α-ChT by other functionalized nanomaterials.

In museums, libraries and archives, some of the paper relics, upon ageing, are very brittle and even cannot be handled without destroying the material. This is because of the depolymerization of cellulose and, consequently, the loss of mechanical strength. To prolong the life expectancy of paper relics, the poly(methyl methacrylate-co-butyl acrylate-co-styrene) (MMA-BA-ST) was used to strengthen the fragile paper fibers in this work. The relation between the mass concentration of MMA-BA-ST emulsion and the specific properties of papers (e.g., folding endurance, tensile strength, tearing strength, whiteness and glossiness) and the ageing resistance were investigated. In addition, the effect of MMA-BA-ST on different types of paper was also studied. Furthermore, the reinforcing mechanism of MMA-BA-ST on paper was also investigated by dissipative particle dynamics simulations. The results showed that MMA-BA-ST could significantly improve the mechanical properties and ageing resistance of papers.

A total of 41825 metal–organic frameworks (MOFs) were computationally screened toward the design of amine-functionalized MOFs for CO2 separation. Both the optimal species and number of amine functional groups were examined for eight MOFs with good performance in terms of CO2 uptake and selectivity. It was revealed that more amine functional groups grafted on the MOFs do not lead to a better CO2 separation capability, and the concept of saturation degree of functional groups was proposed. The ethylene-diamine-functionalized MOF-74 membrane was predicted to possess high CO2 permeation separation capability, which was confirmed by the parallel experimental test of gas permeation.

In this work, the structural properties of amphiphilic polymer-brush-grafted gold nanoparticles (AuNPs) at the oil–water interface were investigated by coarse-grained simulations. The effects of grafting architecture (diblock, mixed and Janus brush-grafted AuNPs) and hydrophilicity of polymer brushes are discussed. Simulation results indicate that functionalized AuNPs present abundant morphologies including typical core–shell, Janus-type, jellyfish-like, etc., in a water or oil–water solvent environment. It is found that hydrophobic/weak hydrophilic polymer-brush-grafted AuNPs have better phase transfer performance, especially for AuNPs modified with hydrophobic chains as outer blocks and weak hydrophilic chains as inner blocks. This kind of AuNP can cross the interface region and move into the oil phase completely. For hydrophobic/strong hydrophilic polymer-brush-grafted AuNPs, they are trapped in the interface region instead of moving into any phase. The mechanism of phase transfer is ascribed to the flexibility and mobility of outer blocks. Besides, we study the desorption energy by PMF analysis. The results demonstrate that Janus brush-grafted AuNPs show the highest interfacial stability and activity, which can be further strengthened by increasing the hydrophilicity of grafted polymer brushes. This work will promote the industrial applications of polymer-brush-grafted NPs such as phase transfer catalysis and Pickering emulsion catalysis.

Contradictory results have been reported regarding cytochrome c (Cyt-c) adsorption onto the positively charged SAMs, and the role of small anions in the adsorption is still unclear. In this work, the adsorption of Cyt-c on the amino-terminated SAM (NH2-SAM) and the effect of chloride and phosphate ions on the adsorption were studied using molecular dynamics simulations. The results reveal that Cyt-c could not stably adsorb onto the surface even at a relatively high ionic strength when chloride ions were added, while phosphate ions could promote its adsorption. At a low phosphate concentration, Cyt-c can adsorb on the NH2-SAM mainly with two opposite orientations. One is similar to that characterized in the experiments for Cyt-c adsorbed on the NH2-SAMs, in which the heme group points far away from the surface. The other orientation is similar to that for Cyt-c on the carboxyl-terminated SAMs. In the latter case, phosphate ions formed a distinct counterion layer near the surface and overcompensated the positive charge of the surface. Further analysis shows that chloride ions have no significant tendency to aggregate near the NH2-SAM surface and cannot shield the electrostatic repulsion between Cyt-c and the surface, while the phosphate ions can easily adsorb onto the surface and bind specifically to certain lysine residues of Cyt-c, which mediate its adsorption. At a high phosphate concentration, the phosphate and sodium ions will aggregate to form clusters, which results in random adsorption orientation. This work may provide some guidance for the design of Cyt-c-based bioelectronic devices and controlled enzyme immobilization.

We systematically investigated the self-assembly behavior of poly(1,2-butadiene)-b-poly(ethylene oxide) (PB-b-PEO) block copolymer in [Bmim][PF6] ionic liquid (IL) via dissipative particle dynamics simulations. An expanding scope of nanostructures, such as spherical micelles, rodlike micelles, entangled cylinders, sheets, branched lamellae, lamellae, platelets, tubes, and IL microphase structures, was observed under different polymer concentrations and polymer block ratios. When the polymer concentration was lower than 30 vol %, self-assembled morphologies transformed from spherical to rodlike or sheetlike micelles as the fraction of PEO block decreased. When the copolymer concentration was higher than 30 vol %, new morphologies such as wormlike micelles and branched lamellae emerged. Platelet and tube nanostructures were obtained when the concentration of PEO was lower than 10 vol %. In addition, lamellae structure was observed, represented as a triangular area in the phase diagram, and the IL microphase nanostructure appeared in the bottom right of the phase diagram. These various nanostructures observed in our study suggest a universal mechanism for the self-assembly of amphiphiles in given solvents.

Candida antarctica lipase B (CalB) is an efficient biocatalyst for hydrolysis and esterification, which plays an important role in the production of biodiesel in the bioenergy industries. The ordered immobilisation of lipases on different supports would be significant for its enzymatic catalysis in some biodiesel production processes; however, the underlying mechanisms and the preferred lipase orientation are not well understood yet. In this work, a fundamental understanding of the orientation and adsorption mechanism of lipase on four different nanomaterial surfaces with different surface chemistry are explored in detail by a combination of parallel tempering Monte Carlo (PTMC) and molecular dynamics (MD) simulations. Simulation results show that lipase is strongly adsorbed onto the hydrophobic graphite surface, as reflected by the large contact area and interaction energy; while the adsorption onto the hydrophilic TiO2 surface is weak due to two strongly adhered water layers; meanwhile lipase undergoes desorption and reorientation processes. For CalB adsorption on positively and negatively charged surfaces (NH2-SAM and COOH-SAM), the orientation distributions of lipase are narrow, and opposite orientations are obtained. CalB adsorbed on NH2-SAM has its catalytic centre oriented towards the surface, which is not conducive to the substrate binding; while the catalytic centre faces toward the solution when it is adsorbed on the COOH-SAM. Besides, the native structures of CalB adsorbed on different surfaces are preserved, which indicates lipase as a robust enzyme. The simulation results will promote our understanding on how surface properties of nanomaterials, such as charge or hydrophobicity, will affect lipase immobilisation, and help us in the rational design and development of immobilised lipase carriers.

Experimental studies have shown that the adsorption of horse heart cytochrome c (Cyt-c) on a bare gold surface leads to the hindrance of electron transfer (ET). The underlying mechanism remains controversial. In this work, the adsorption orientation and conformation of Cyt-c on Au(111) surface were investigated by performing Monte Carlo and molecular dynamics simulations. The results show that the most favorable binding mode of Cyt-c to gold agrees with the results characterized by SEIRA spectroscopy. The adsorption is mainly contributed by the strong van der Waals interactions between the surface and residues that have long side chains, which leads to the helix A and Ω1 loop of Cyt-c being in contact with the surface and most of the α-helixes being nearly parallel to the surface. The native structure of Cyt-c is well preserved during the adsorption, and only the flexible Ω1 loop and the N-terminal show a relatively larger mobility. The hindrance of ET is ascribed to the confined rotation of the heme prosthetic group and the farther positioning of the central iron to the surface (about 12.9 Å).

Control of mass transport through nanochannels is of critical importance in many nanoscale devices and nanofiltration membranes. The gates in biological channels, which control the transport of substances across cell membranes, can provide inspiration for this purpose. Gates in many biological channels are formed by a constriction ringed with hydrophobic residues which can prevent ion conduction even when they are not completely physically occluded. In this work, we use molecular dynamics simulations to design a nanogate inspired by this hydrophobic gating mechanism. Deforming a carbon nanotube (12,12) with an external force can form a hydrophobic constriction in the centre of the tube that controls ion conduction. The simulation results show that increasing the magnitude of the applied force narrows the constriction and lowers the fluxes of K+ and Cl− found under an electric field. With the exerted force larger than 5 nN, the constriction blocks the conduction of K+ and Cl− due to partial dehydration while allowing for a noticeable water flux. Ion conduction can revert back to the unperturbed level upon force retraction, suggesting the reversibility of the nanogate. The force can be exerted by available experimental facilities, such as atomic force microscope (AFM) tips. It is found that partial dehydration in a continuous water-filled hydrophobic constriction is enough to close the channel, while full dewetting is not necessarily required. This mechanically deformed nanogate has many potential applications, such as a valve in nanofluidic systems to reversibly control ion conduction and a high-performance nanomachine for desalination and water treatment.

The orientation and adsorption mechanism of the 10th and 7–10th type III modules of fibronectin (FN-III10, FN-III7–10) on hydroxyapatite surfaces were investigated by a combination of parallel tempering Monte Carlo (PTMC) and molecular dynamics (MD) methods. The PTMC results show a positively charged surface at low ionic strength is beneficial for FN-III10 and FN-III7–10 adsorption with RGD accessible in solution, i.e., FN-III10 adsorbs with “side-on” orientation while FN-III7–10 adsorbs with “lying” orientation. During the adsorption, FN-III10 adsorbs on the hydroxyapatite (HAP) surface first driven by Coulombic interactions at the pre-adsorption stage. At the post-adsorption stage, the driving force changes from Coulombic interactions to VDW interactions. Accordingly, slow translation of FN-III10 on the HAP surface was found due to the mismatching of charged groups of protein on the alternative charged surface. The conformational changes of adsorbed FN-III10 mainly take place at its coil/loop parts. FN-III7–10 experiences two stages from weak adsorption to strong adsorption when Coulombic interactions become the dominant driving force. The transition is determined by the anchoring of the basic residues in the Ca2+ vacancies by significant complementary electrostatic interactions and hydrogen bonds formed between the guanidine group and the surrounding phosphate groups. The module III10 of FN-III7–10 exhibits the largest conformational change and contributes to the adsorption most. The affinity of the guanidine group binding suggests that vacancies on biomaterials have the capacity to trap specific residues.

The adsorption of myoglobin (Mb) on the surface of titanium dioxide is very important for the preparation of biosensors. Adsorption orientation and conformation of Mb on rutile (1 1 0) and (0 0 1) surfaces were investigated by combining Monte Carlo and molecular dynamics methods. The orientation, DSSP, superimposed structure, root-mean-square deviation and gyration radius of Mb were analyzed. Furthermore, the distribution of water molecules on rutile (1 1 0) and (0 0 1) surfaces and representative snapshots of water molecules at different rutile interfaces were also discussed in detail. Simulation results show that adsorbed Mb conformations are not influenced by surfaces obviously because of the strong hydrophilicity of both surfaces. Two layers of water molecules form on both rutile (1 1 0) and (0 0 1) surfaces. After 80 ns molecular dynamics simulation, the heme of Mb is close to the rutile (0 0 1) surface and far away from the rutile (1 1 0) surface; this infers that electron transfer pathway of Mb is closer to the rutile (0 0 1) surface, which is favorable for faster electron transfer.

Nanoparticles’ phase transfer behaviors at the oil–water interface have many respects in common with lipid bilayer crossing behavior and the Pickering emulsion formation. Hence, the interfacial behavior and phase transfer behavior are intuitive indicators for the application potential of nanoparticle materials, e.g., on the emulsion formation and biomedical applications. Polymer brush modification enables nanoparticles to behave differently in hydrophilic solvent, hydrophobic solvent, and their interface region. In the present work, phase transfer behaviors of triblock polymer brush modified gold nanoparticles are explored by using coarse-grained simulations. The nanoparticles grafted with hydrophobic/weak hydrophilic/hydrophobic triblock brushes are found to have the best phase transfer performance, and the enhanced flexibility and mobility of head blocks are found to be the most vital factors. The inherent mechanism of interfacial behavior and phase transfer process are investigated and explained as perturbation effect and traction effect. According to our results, middle blocks dominate the brush morphology and decide whether NPs can be transferred into another phase. However, the inner blocks show higher dominance for the phase transfer behavior of nanoparticles restricted in the interface region, while the outer ones shows higher dominance for the nanoparticles departing from the interface region. Otherwise, interesting flat-Janus morphologies are found. Special applications in two-phase interface including emulsion stabilization could be expected. This work could provide some guidance for the molecular design and applications of polymer–nanoparticle composite materials.

In this work, the adsorptions of hydrophobin (HFBI) on four different self-assembled monolayers (SAMs) (i.e., CH3-SAM, OH-SAM, COOH-SAM, and NH2-SAM) were investigated by parallel tempering Monte Carlo and molecular dynamics simulations. Simulation results indicate that the orientation of HFBI adsorbed on neutral surfaces is dominated by a hydrophobic dipole. HFBI adsorbs on the hydrophobic CH3-SAM through its hydrophobic patch and adopts a nearly vertical hydrophobic dipole relative to the surface, while it is nearly horizontal when adsorbed on the hydrophilic OH-SAM. For charged SAM surfaces, HFBI adopts a nearly vertical electric dipole relative to the surface. HFBI has the narrowest orientation distribution on the CH3-SAM, and thus can form an ordered monolayer and reverse the wettability of the surface. For HFBI adsorption on charged SAMs, the adsorption strength weakens as the surface charge density increases. Compared with those on other SAMs, a larger area of the hydrophobic patch is exposed to the solution when HFBI adsorbs on the NH2-SAM. This leads to an increase of the hydrophobicity of the surface, which is consistent with the experimental results. The binding of HFBI to the CH3-SAM is mainly through hydrophobic interactions, while it is mediated through a hydration water layer near the surface for the OH-SAM. For the charged SAM surfaces, the adsorption is mainly induced by electrostatic interactions between the charged surfaces and the oppositely charged residues. The effect of a hydrophobic dipole on protein adsorption onto hydrophobic surfaces is similar to that of an electric dipole for charged surfaces. Therefore, the hydrophobic dipole may be applied to predict the probable orientations of protein adsorbed on hydrophobic surfaces.

Coarse-grained simulations are adopted to study the adsorption behavior of lysozyme on different (hydrophobic, neutral hydrophilic, zwitterionic, negatively charged, and positively charged) surfaces at the mesoscopic microsecond time scale (1.2 μs). Simulation results indicate the following: (i) the conformation change of lysozyme on the hydrophobic surface is bigger than any other studied surfaces; (ii) the active sites of lysozyme are faced to the hydrophobic surface with a “top end-on” orientation, while they are exposed to the liquid phase on the hydrophilic surface with a “back-on” orientation; (iii) the neutral hydrophilic surface can induce the adsorption of lysozyme, while the nonspecific protein adsorption can be resisted by the zwitterionic surface; (iv) when the solution ionic strength is low, lysozyme can anchor on the negatively charged surface easily but cannot adsorb on the positively charged surface; (v) when the solution ionic strength is high, the positively charged lysozyme can also adsorb on the like-charged surface; (vi) the major positive potential center of lysozyme, especially the residue ARG128, plays a vital role in leading the adsorption of lysozyme on charged surfaces; (vii) when the ionic strength is high, a counterion layer is formed above the positively charged surface, which is the key factor why lysozyme can adsorb on a like-charged surface. The coarse-grained method based on the MARTINI force field for proteins and the BMW water model could provide an efficient way to understand protein interfacial adsorption behavior at a greater length scale and time scale.

The adsorption of basic fibroblast growth factor (bFGF) on the hydroxyapatite (001) surface was investigated by a combination of replica-exchange molecular dynamics (REMD) and conventional molecular dynamics (CMD) methods. In CMD, the protein cannot readily cross the surface water layer, whereas in REMD, the protein can cross the adsorption barrier from the surface water layer and go through weak, medium, then strong adsorption states with three energetically preferred configurations: heparin-binding-up (HP-up), heparin-binding-middle (HP-middle), and heparin-binding-down (HP-down). The HP-middle orientation, with the strongest adsorption energy (−1149 ± 40 kJ·mol–1), has the largest adsorption population (52.1–52.6%) and exhibits the largest conformational charge (RMSD of 0.26 ± 0.01 nm) among the three orientations. The HP-down and HP-up orientations, with smaller adsorption energies of −1022 ± 55 and −894 ± 70 kJ·mol–1, respectively, have smaller adsorption populations of 27.4–27.7% and 19.7–20.5% and present smaller RMSD values of 0.21 ± 0.01 and 0.19 ± 0.01 nm, respectively. The convergent distribution indicates that nearly half of the population (in the HP-middle orientation) will support both FGF/FGFR and DGR–integrin signaling and another half (in the HP-up and HP-down orientations) will support DGR–integrin signaling. The major population (∼80%) has the protein dipole directed outward. In the strong adsorption state, there are usually 2 to 3 basic residues that form the anchoring interactions of 210–332 kJ·mol–1 per residue or that are accompanied by an acidic residue with an adsorption energy of ∼207 kJ·mol–1. Together, the major bound residues form a triangle or a quadrilateral on the surface and stabilize the adsorption geometrically, which indicates topologic matching between the protein and HAP surfaces.

•Protein adsorption could generally be promoted by positive electric fields and retarded by negative electric fields.•Migration of counterions onto surfaces plays a role in lysozyme adsorption under external electric fields.•An applied electric field may narrow the protein orientation distribution.•Structural deformation of lysozyme does not increase monotonically with the increasing electric field strength.Lysozyme adsorption on carboxyl-terminated self-assembled monolayers under external electric fields has been studied by all-atom molecular dynamics simulations. Lysozyme adsorption on negatively charged surfaces could generally be enhanced by positive electric fields and retarded by negative ones. Under positive electric fields, electrostatic interactions between protein and surface are strengthened; however, the interaction energy descends with field strength increases probably due to the co-adsorption of counterions onto the surface to neutralize surface charge. Comparison of orientation distributions of lysozyme adsorption on the surface in the presence and in the absence of electric fields reveals that an applied electric field could narrow the distribution and therefore helps to immobilize protein on surface with uniform orientation. Orientation angle analysis shows that lysozyme is adsorbed on the surface with “bottom end-on”, “side-on”, “back-on” or “top end-on” orientation under different field strengths, suggesting the possibility of controlling the preferred orientation of lysozyme on surface by applying electric fields. Conformation analysis of protein implies that the structure deformation of adsorbed lysozyme does not increase monotonically with the rising field strength. Under some field strengths, there is no additional structure deformation caused by the electric fields compared with that in the absence of electric fields; while under some other field strengths, there are larger conformational change occurrences. We propose that due to the rearrangement of positions of the local atomic charges of protein to couple its dipole with an external electric field, large position alterations of atoms might be avoided and thus conformational changes be restricted. This work may provide guidance for controlling protein adsorption behaviors via external electric fields for applications of protein immobilization and anti-fouling surfaces.

The orientation of an antibody plays an important role in the development of immunosensors. Protein G is an antibody binding protein, which specifically targets the Fc fragment of an antibody. In this work, the orientation of prototypical and mutated protein G B1 adsorbed on positively and negatively charged self-assembled monolayers was studied by parallel tempering Monte Carlo and all-atom molecular dynamics simulations. Both methods present generally similar orientation distributions of protein G B1 for each kind of surface. The root-mean-square deviation, DSSP, gyration radius, eccentricity, dipole moment, and superimposed structures of protein G B1 were analyzed. Moreover, the orientation of binding antibody was also predicted in this work. Simulation results show that with the same orientation trends, the mutant exhibits narrower orientation distributions than does the prototype, which was mainly caused by the stronger dipole of the mutant. Both kinds of proteins adsorbed on charged surfaces were induced by the competition of electrostatic interaction and vdW interaction; the electrostatic interaction energy dominated the adsorption behavior. The protein adsorption was also largely affected by the distribution of charged residues within the proteins. Thus, the prototype could adsorb on a negatively charged surface, although it keeps a net charge of −4 e. The mutant has imperfect opposite orientation when it adsorbed on oppositely charged surfaces. For the mutant on a carboxyl-functionalized self-assembled monolayer (COOH-SAM), the orientation was the same as that inferred by experiments. While for the mutant on amine-functionalized self-assembled monolayer (NH2-SAM), the orientation was induced by the competition between attractive interactions (led by ASP40 and GLU56) and repulsive interactions (led by LYS10); thus, the perfect opposite orientation could not be obtained. On both surfaces, the adsorbed protein could retain its native conformation. The desired orientation of protein G B1, which would increase the efficiency of binding antibodies, could be obtained on a negatively charged surface adsorbed with the prototype. Further, we deduced that with the packing density of 12 076 protein G B1 domain per μm2, the efficiency of the binding IgG would be maximized. The simulation results could be applied to control the orientation of protein G B1 in experiments and to provide a better understanding to maximize the efficiency of antibody binding.

It is well recognized that ice-like water can be formed in carbon nanotubes (CNTs). Here, we perform molecular dynamics simulations of the hydration of Na+, K+ and Cl– in armchair CNT(n,n) (n = 6, 7, 8, 9 and 10) at 300 K to elucidate the effect of such water structures on ionic hydration. It is found that the interaction of Na+ and K+ with the water molecules is enhanced in CNT(8,8), but is similar or weaker than in bulk in the other CNTs. In bulk, water molecules orient in specific directions around ions due to the electrostatic interaction between them. Under the confinement of CNTs, the hydrogen bonds formed in the first hydration shell of Na+ and K+ disturb this orientation greatly. An exception is in CNT(8,8), where the dipole orientation is even more favorable for cations than in bulk due to the formation of a unique ice-like water structure that aligns the water molecules in specific directions. In contrast, the coordination number is more important than hydration shell orientation in determining the Cl––water interaction. Additionally, the preference for ions to adopt specific radial positions in the CNTs also affects ionic hydration.

Biological protein channels have many remarkable properties such as gating, high permeability, and selectivity, which have motivated researchers to mimic their functions for practical applications. Herein, using molecular dynamics simulations, we design bioinspired nanopores in graphene sheets that can discriminate between Na+ and K+, two ions with very similar properties. The simulation results show that, under transmembrane voltage bias, a nanopore containing four carbonyl groups to mimic the selectivity filter of the KcsA K+ channel preferentially conducts K+ over Na+. A nanopore functionalized by four negatively charged carboxylate groups to mimic the selectivity filter of the NavAb Na+ channel selectively binds Na+ but transports K+ over Na+. Surprisingly, the ion selectivity of the smaller diameter pore containing three carboxylate groups can be tuned by changing the magnitude of the applied voltage bias. Under lower voltage bias, it transports ions in a single-file manner and exhibits Na+ selectivity, dictated by the knock-on ion conduction and selective blockage by Na+. Under higher voltage bias, the nanopore is K+-selective, as the blockage by Na+ is destabilized and the stronger affinity for carboxylate groups slows the passage of Na+ compared with K+. The computational design of biomimetic ion-selective nanopores helps to understand the mechanisms of selectivity in biological ion channels and may also lead to a wide range of potential applications such as sensitive ion sensors, nanofiltration membranes for Na+/K+ separation, and voltage-tunable nanofluidic devices.Keywords: graphene; ion channel; ion selectivity; molecular dynamics; nanofluidics; nanopores

The use of THB molecules as a guest template tunes the formation of a two-dimensional honeycomb network in preference to alternative close packed structures of TECDB self-assembled on HOPG surface at the solid–liquid interface.

Grand canonical Monte Carlo and molecular dynamics simulation methods are used to simulate oxygen sorption and diffusion in amorphous poly(lactic acid) (PLA). The simulated solubility coefficient of oxygen is close to experimental data obtained from the quartz crystal microbalance but much higher than those from the time-lag method. This discrepancy is explained by using the dual-mode sorption model. It is found that oxygen sorption in PLA is predominantly Langmuir type controlled, i.e., through the process of filling holes. The time-lag method only takes into account oxygen molecules that participate the diffusion process whereas a large proportion of oxygen molecules trapped in the void have little chance to execute hopping due to the glassy nature of PLA at room temperature. The simulated diffusion coefficient of oxygen is reasonably close to the data obtained from the time-lag method. The solubility coefficient of oxygen decreases linearly with increasing relative humidity while its diffusion coefficient firstly decreases and then increases as a function of relative humidity.

•The DOX loaded microstructures of pH-sensitive amphiphilic triblock copolymer are studied by DPD simulations.•When increasing copolymer concentration, spherical, cylindrical and lamellar micelles are observed for drug loaded system.•The stability of the system contains zwitterionic sulfobetaine is superior to that of PEGMA system for drug delivery.•Upon reducing pH, DOX is released from the micelles and follows the swelling-demicellization-release mechanism.In this work, dissipative particle dynamics (DPD) simulations were performed to study the self-assembled microstructures and doxorubicin (DOX) loading/release properties of pH-sensitive amphiphilic triblock copolymer: poly(ε-caprolactone)-b-poly(diethylaminoethyl methacrylate)-b-poly(sulfobetaine methacrylate) or poly (ethylene glycol methacrylate) (PCL-PDEA-PSBMA/PEGMA). Our results show that both copolymers can self-assemble into core-shell-corona micelles in aqueous environment. However, the corona structures are quite different for the two copolymer micelles. The shell layers formed by PEGMA have heterogeneous sizes while the shell layers in PCL-PDEA-PSBMA micelles are homogenous. This is mainly attributed to the stronger hydrophilicity of PSBMA than PEGMA. As the mole concentration of copolymer is increased from 10% to 50%, the microstructures formed by PCL-PDEA-PSBMA and DOX remains spherical micelles whereas PCL-PDEA-PEGMA undergoes structural transition from spherical to cylindrical and finally to lamellar micelles. Interestingly, the studied micelles have a pH-responsive drug release property, owing to the protonation of the PDEA block. The drug release process follows a “swelling-demicellization-release” mode. The multi-scale simulations demonstrate an avenue to the optimal design of nanomaterials for drug delivery with desired properties.

The use of THB molecules as a guest template tunes the formation of a two-dimensional honeycomb network in preference to alternative close packed structures of TECDB self-assembled on HOPG surface at the solid–liquid interface.

In nanobiotechnology applications, curvature of nanoparticles has a significant effect on protein activities. In this work, lysozyme adsorption on different-sized silica nanoparticles (SNPs) was simulated at the microsecond timescale by using mesoscopic coarse-grained molecular dynamics simulations. It is found that, with the increase of nanoparticle size, which indicates a decrease of surface curvature, adsorbed lysozyme shows a narrower orientation distribution and a greater conformation change, as the electrostatic attraction dominates lysozyme adsorption, and this trend is more pronounced on larger SNPs. Interestingly, the effect induced by different SNP surface curvatures is not related to the direct contact area between lysozyme and SNPs, but to the interfacial hydration layer above the silica surface, since a smaller curvature can lead to a stronger interfacial hydration and make the distribution of interfacial water molecules more ordered. Besides, at higher ionic strength, lysozyme conformation is less affected by strongly negatively charged SNPs, especially for larger nanoparticles. This work might shed some light on how to prepare protein coronas with higher bioactivities in nanobiotechnology.

The α-chymotrypsin (α-ChT) enzyme is extensively used for studying nanomaterial-induced enzymatic activity inhibition. A recent experimental study reported that carboxylized carbon nanotubes (CNTs) played an important role in regulating the α-ChT activity. In this study, parallel tempering Monte Carlo and molecular dynamics simulations were combined to elucidate the interactions between α-ChT and CNTs in relation to the CNT functional group density. The simulation results indicate that the adsorption and the driving force of α-ChT on different CNTs are contingent on the carboxyl density. Meanwhile, minor secondary structural changes are observed in adsorption processes. It is revealed that α-ChT interacts with pristine CNTs through hydrophobic forces and exhibits a non-competitive characteristic with the active site facing towards the solution; while it binds to carboxylized CNTs with the active pocket through a dominant electrostatic association, which causes enzymatic activity inhibition in a competitive-like mode. These findings are in line with experimental results, and well interpret the activity inhibition of α-ChT at the molecular level. Moreover, this study would shed light on the detailed mechanism of specific recognition and regulation of α-ChT by other functionalized nanomaterials.

Contradictory results have been reported regarding cytochrome c (Cyt-c) adsorption onto the positively charged SAMs, and the role of small anions in the adsorption is still unclear. In this work, the adsorption of Cyt-c on the amino-terminated SAM (NH2-SAM) and the effect of chloride and phosphate ions on the adsorption were studied using molecular dynamics simulations. The results reveal that Cyt-c could not stably adsorb onto the surface even at a relatively high ionic strength when chloride ions were added, while phosphate ions could promote its adsorption. At a low phosphate concentration, Cyt-c can adsorb on the NH2-SAM mainly with two opposite orientations. One is similar to that characterized in the experiments for Cyt-c adsorbed on the NH2-SAMs, in which the heme group points far away from the surface. The other orientation is similar to that for Cyt-c on the carboxyl-terminated SAMs. In the latter case, phosphate ions formed a distinct counterion layer near the surface and overcompensated the positive charge of the surface. Further analysis shows that chloride ions have no significant tendency to aggregate near the NH2-SAM surface and cannot shield the electrostatic repulsion between Cyt-c and the surface, while the phosphate ions can easily adsorb onto the surface and bind specifically to certain lysine residues of Cyt-c, which mediate its adsorption. At a high phosphate concentration, the phosphate and sodium ions will aggregate to form clusters, which results in random adsorption orientation. This work may provide some guidance for the design of Cyt-c-based bioelectronic devices and controlled enzyme immobilization.

Candida antarctica lipase B (CalB) is an efficient biocatalyst for hydrolysis and esterification, which plays an important role in the production of biodiesel in the bioenergy industries. The ordered immobilisation of lipases on different supports would be significant for its enzymatic catalysis in some biodiesel production processes; however, the underlying mechanisms and the preferred lipase orientation are not well understood yet. In this work, a fundamental understanding of the orientation and adsorption mechanism of lipase on four different nanomaterial surfaces with different surface chemistry are explored in detail by a combination of parallel tempering Monte Carlo (PTMC) and molecular dynamics (MD) simulations. Simulation results show that lipase is strongly adsorbed onto the hydrophobic graphite surface, as reflected by the large contact area and interaction energy; while the adsorption onto the hydrophilic TiO2 surface is weak due to two strongly adhered water layers; meanwhile lipase undergoes desorption and reorientation processes. For CalB adsorption on positively and negatively charged surfaces (NH2-SAM and COOH-SAM), the orientation distributions of lipase are narrow, and opposite orientations are obtained. CalB adsorbed on NH2-SAM has its catalytic centre oriented towards the surface, which is not conducive to the substrate binding; while the catalytic centre faces toward the solution when it is adsorbed on the COOH-SAM. Besides, the native structures of CalB adsorbed on different surfaces are preserved, which indicates lipase as a robust enzyme. The simulation results will promote our understanding on how surface properties of nanomaterials, such as charge or hydrophobicity, will affect lipase immobilisation, and help us in the rational design and development of immobilised lipase carriers.

A total of 41825 metal–organic frameworks (MOFs) were computationally screened toward the design of amine-functionalized MOFs for CO2 separation. Both the optimal species and number of amine functional groups were examined for eight MOFs with good performance in terms of CO2 uptake and selectivity. It was revealed that more amine functional groups grafted on the MOFs do not lead to a better CO2 separation capability, and the concept of saturation degree of functional groups was proposed. The ethylene-diamine-functionalized MOF-74 membrane was predicted to possess high CO2 permeation separation capability, which was confirmed by the parallel experimental test of gas permeation.