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While nanoporous graphene oxide (GO) is recognized as one of the most promising reverse osmosis desalination membranes, limited attention has been paid to controlling desalination performance through the large GO pores, primarily due to significant ion leakage resulting in the suboptimal performance of these pores. In this study, we employed a molecular dynamics simulation approach to demonstrate that Mg2+ ions, adhered to carboxylated GO nanopores, can function as gates, regulating the transport of ions (Na+ and Cl−) through the porous GO membrane. Specifically, the presence of divalent cations near a nanopore reduces the concentration of salt ions in the vicinity of the pore and prolongs their permeation time across the pore. This subsequently leads to a notable enhancement in salt rejection rates. Additionally, the ion rejection rate increases with more adsorbed Mg2+ ions. However, the presence of the adsorbed Mg2+ ions compromises water transport. Here, we also elucidate the impact of graphene oxidation degree on desalination. Furthermore, we design an optimal combination of adsorbed Mg2+ ion quantity and oxidation degree to achieve high water flux and salt rejection rates. This work provides valuable insights for developing new nanoporous graphene oxide membranes for controlled water desalination. [ABSTRACT FROM AUTHOR]

We theoretically and experimentally show that, with water being adsorbed, the graphene oxide (GO) is converted to a spontaneously dynamic covalent material under ambient conditions, where the dominated epoxy and hydroxyl groups are mediated by water molecules to spontaneously break/reform their C–O bonds to achieve dynamic oxygen migration. This dynamic material presents structural adaptivity for response to biomolecule adsorption. Both density functional theory calculations and ab initio molecular dynamics simulations demonstrate that this spontaneously dynamic characteristics is attributed to the adsorption of water molecules, which sharply reduces the barriers of these oxygen migration reactions on GO to the level less than or comparable to the hydrogen bonding energy in liquid water. [ABSTRACT FROM AUTHOR]

Identifying the oxidation structure of two-dimensional interfaces is crucial to improve surface chemistry and electronic properties. Beyond graphene with only phenyl rings, a novel carbon-nitrogen material, C3N, presents an intrinsic heterogeneous surface morphology where each phenyl ring is encircled by six nitrogen atoms, yet its atomistic oxidation structure remains unclear. Here, combining a series of density functional theory calculations and ab initio molecular dynamics simulations, we demonstrate that thermodynamically favorable oxidation loci are confined to the phenyl ring, and kinetic transformations of oxidation structures are feasible along the phenyl ring, whereas those toward nitrogen atoms are proven to be extremely difficult. These results are attributed to the lower barrier of oxygen atom migration along the phenyl ring, while the significantly high barriers toward nitrogen atoms are due to the heterogeneous potential energy surface for oxygen–C3N interaction. This work highlights the significance of surface morphology on the characteristics of oxidation structure, offering insights into tunable electronic properties via confined interfacial oxidation. [ABSTRACT FROM AUTHOR]

The evaporation of a tiny amount of water on the solidsurfacewith different wettabilities has been studied by molecular dynamicssimulations. From nonequilibrium MD simulations, we found that, asthe surface changed from hydrophobic to hydrophilic, the evaporationspeed did not show a monotonic decrease as intuitively expected, butincreased first, and then decreased after it reached a maximum value.The analysis of the simulation trajectory and calculation of the surfacewater interaction illustrate that the competition between the numberof water molecules on the water–gas surface from where thewater molecules can evaporate and the potential barrier to preventthose water molecules from evaporating results in the unexpected behaviorof the evaporation. This finding is helpful in understanding the evaporationon biological surfaces, designing artificial surfaces of ultrafastwater evaporating, or preserving water in soil. [ABSTRACT FROM AUTHOR]

The molecular scale signal conversion, transmission, and amplification by a single external charge through a water-mediated Y-shaped nanotube have been studied using molecular dynamics simulations. Our results show that the signal converting capability is highly sensitive to the magnitude of the charge, while the signal transmitting capability is independent of the charge signal. There is a sharp two-state-like transition in the signal converting capacity for both positive and negative charges. When the charge magnitude is above a threshold (|q| ≥ ∼0.7 e), the water dipole orientations in the main tube can be effectively controlled by the signaling charge (i.e., signal conversion), and then be transmitted and amplified through the Y-junction, despite the thermal noises and interferences between branch signals. On the other hand, the signal transmitting capability, characterized by the correlation between the two water dipole orientations in the two branches, is found to be always larger than 0.6, independent of charge signals, indicating that the water-mediated Y-tube is an excellent signal transmitter. These findings may provide useful insights for the future design of molecular scale signal processing devices based on Y-shaped nanotubes. [ABSTRACT FROM AUTHOR]

G-quadruplexes (GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of linking loops, and the associated metal cations. However, our understanding on the basic physical properties of the formation process and the stability of GQs is rather limited. In this work, we employed ab initio, molecular dynamics (MD), and steered MD (SMD) simulations to study the interaction between loop bases and ions, and the effect on the stability of G-quadruplex DNA, the Drude oscillator model was used in MD and SMD simulations as a computationally efficient manner method for modeling electronic polarization in DNA ion solutions. We observed that the binding energy between DNA bases and ions (K+/Na+) is about the base stacking free energies indicates that there will be a competition among the binding of M+-base, H-bonds between bases, and the base-stacking while ions were bound in loop of GQs. Our SMD simulations indicated that the side loop inclined to form the base stacking while the loop sequence was Thy or Ade, and the cross-link loop upon the G-tetrads was not easy to form the base stacking. The base stacking side loop complex K+ was found to have a good stabilization synergy. Although a stronger interaction was observed to exist between Cyt and K+, such an interaction was unable to promote the stability of the loop with the sequence Cyt. [ABSTRACT FROM AUTHOR]

The scarcity of freshwater is of great challenge that the world is facing nowadays. The advances of nanomaterial based on the reverse osmosis (RO) technology provide new possibilities for desalination. In this study, using molecular dynamics simulation, we propose and design an excellent RO membrane composed of fluorinated graphene (F-GRA) nanochannels, by which the exceptionally high water permeation (reaching up to 61.1 L/cm2/day/MPa) and the almost complete ion rejection are achieved. Notably, F-GRA nanochannel membranes exhibit a desalination performance much more promising than many other nanomaterials in previously theoretical studies. This superior desalination performance of F-GRA channels is attributed to the negatively charged surface and hydrophobicity of F-GRA, where the electrostatic interactions (attraction or repulsion) between ions and F-GRA surface cause the ideal ion rejection and the ultralow water friction on F-GRA mediated by its hydrophobicity results in the excellent water penetration. Moreover, potential of mean force calculations further reveal that the water molecule reflects the lowest free energy barrier relative to ions when traversing through the F-GRA channel, indicating the energetical favorability of the successful water transport instead of ions. Our theoretical study offers a fascinating approach of molecular sieving design usable for future desalination. • Fluorinated graphene (F-GRA) nanochannel based membrane is constructed. • The F-GRA membrane presents an excellent desalination performance with the high water permeability and the high ion rejection. • The superior water permeability and ion rejection are resulted from the negatively charged surface and hydrophobicity of F-GRA. • The desalination performance of F-GRA nanochannel is investigated from the molecular level. [ABSTRACT FROM AUTHOR]

Alcohols are important products in chemical industry, but separating them from their aqueous solutions is very difficult due to the hydrophilic nature of alcohols. Based on molecular dynamics simulations, we observe a striking nanoscale drying phenomenon and suggest an energy-saving and efficient approach toward alcohol/water separation by using single-walled carbon nanotubes (SWNTs). We use various common linear alcohols including C1-C6 1-alcohols and glycerol for demonstration (the phenol is also used as comparison). Our simulations show that when SWNTs are immersed in aqueous alcohols solutions, although the alcohols concentration is low (1 M), all kinds of alcohols can induce dehydration (drying) of nanotubes and accumulate inside wide [(13, 13)] and narrow [(6, 6) or (7, 7)] SWNTs. In particular, most kinds of alcohols inside the narrow SWNTs form nearly uniform 1D molecular wires. Detailed energetic analyses reveal that the preferential adsorption of alcohols over water inside nanotubes is attributed to the stronger dispersion interactions of alcohols with SWNTs than water. Interestingly, we find that for the wide SWNT, the selectivity for 1-alcohols increases with the number of alcohol's carbon atoms (Ncarbon) and exhibits an exponential law with respect to Ncarbon for C1-C5 1-alcohols; for narrow SWNTs, the selectivity for 1-alcohols is very high for methanol, ethanol, and propanol, and reaches a maximum when Ncarbon = 3. The underlying physical mechanisms and the implications of these observations for alcohol/water separation are discussed. Our findings provide the possibility for efficient dehydration of aqueous alcohols (and other hydrophilic organic molecules) by using SWNT bundles/membranes. [ABSTRACT FROM AUTHOR]

Generally, the interface friction on solid surfaces is regarded as consistent with wetting behaviors, characterized by the contact angles. Here using molecular dynamics simulations, we find that even a small charge difference (≤0.36 e) causes a change in the friction coefficient of over an order of magnitude on two-dimensional material and lipid surfaces, despite similar contact angles. This large difference is confirmed by experimentally measuring interfacial friction of graphite and MoS2 contacting on water, using atomic force microscopy. The large variation in the friction coefficient is attributed to the different fluctuations of localized potential energy under inhomogeneous charge distribution. Our results help to understand the dynamics of two-dimensional materials and biomolecules, generally formed by atoms with small charge, including nanomaterials, such as nitrogen-doped graphene, hydrogen-terminated graphene, or MoS2, and molecular transport through cell membranes. The interface friction on solid surfaces is generally regarded as consistent with the wetting behaviour. Here the authors use molecular dynamics simulations and experiments to show that a small surface charge difference causes a change in the solid/water friction coefficient of over an order of magnitude, while the contact angles stay similar. [ABSTRACT FROM AUTHOR]

• Higher oxidization degree of GO membrane favors water permeation. • Optimal microstructures for highly separating water from ethanol were uncovered. • With low O/C ratio, diffusion effect governs water permeation behavior. • With high O/C ratio, preferential adsorption governs water permeation process. Molecular dynamics (MD) simulations were employed to investigate water-ethanol separation through monolayer graphene oxide (GO) membranes with different pore sizes and O/C ratios. The ultrahigh water flux and infinite water separation factors were achieved. The separation properties under 50/50 w/w water-ethanol mixtures reveal that higher O/C ratios favor water selectivity, and water flux is enhanced with O/C ratio and pore size. With the help of highest oxidization, water largely sorption amount governs permeation process. On the contrary, with low oxidization degree of GO membrane, water diffusion effect becomes dominant factor of permeation. We screen an optimal microstructure of GO membrane which equipped with an adequately sized pore (D = 2.4 Å) and a highest O/C ratio (R = 0.49). This optimal one D2.4Å_R0.49 achieves the highest water flux and fully ethanol rejection in the mimicked experimental system. This simulation study elucidates the role of O/C ratio and pore diameter in water-ethanol separation through porous GO membranes on the microscopic level and uncovers the governing effects for water permeation and also suggests a potential candidate as a water-ethanol separation membrane. [ABSTRACT FROM AUTHOR]

• The anion plays a crucial function in controlling the GO interlayer spacing. • The ion bridge is chiefly responsible for the reducing of the GO interlayer spacing. • The ion bridge is composed of one anion sandwiched by two cations. • The effect of the number of ion bridges on the GO interlayer spacing is investigated. Interlayer spacing of graphene oxide (GO) membranes can be precisely controlled using cations, which has been extensively used in nanofiltration membrane. However, no report definitely discloses the specific performance of anion in treating GO membrane, although cations and anions naturally coexist in aqueous solution. Subjectively, anion might have weak/reverse effect in maintaining the interlayer of negatively charged GO, which is yet confirmed by no evidence. In this work, combining molecular dynamics simulations and density functional theory calculations, we have discovered a long-time unexplored effect that anion can also sustain the GO membrane interlayer — specifically, two types of ion bridges (confined within two neighboring GO sheets), one composed of one anion intercalated into two cations and the other composed of two anions sandwiched by two cations, can effectively and stably fix the interlayer spacing of GO membrane. Our calculations revealed that the ion bridges greatly enhance the interaction between two neighboring GO sheets, making them highly stabilize in aqueous solution. Moreover, free energy calculations and density functional theory calculations further confirm the critical role of ion bridge in controlling the interlayer spacing of GO membrane. Our findings highlight, for the first time, the undiscovered control of GO membrane interlayer with anions via forming an ingenious ion bridge, rather than the preconceived weak/reverse effect of anions, which could inspire the future application of anions (and ion bridge) in membrane design. [ABSTRACT FROM AUTHOR]

Highlights • Presence of salt influences the solute association behavior in nanoconfined solutions. • Dispersion, reversible and aggregation states are still observed. • Increase of salt concentration promotes the formation and growth of clusters. • Transformation of solute association states occurs due to ion polarization. • Tails are more in alignment along radius direction at higher salt concentrations. Abstract Using molecular dynamics simulations, we have studied the effects of salt on the association behavior of solute molecules in nanoconfined aqueous solutions. Three types of solute association states – dispersion, reversible and aggregation states – are still observed in nanoconfined aqueous solutions in the presence of salt. With the increase of ion concentration, the tendency toward the formation of larger clusters is enhanced and the solute critical aggregation number decreases. We even found the transformation of solute association state from the dispersion to the reversible state or from the reversible to the aggregation state within an intermediate range of solute number. This phenomenon is similar to the salting out process and is attributed to the decrease of free water molecules induced by the ion polarization. [ABSTRACT FROM AUTHOR]

Combining the molecular dynamics (MD) simulations and the free-energy-based thermodynamic analysis, we analyze the role of alkyl chain length on the nucleation of alcohol molecules with the mono-hydroxyl in nanoconfined solution. The free energy formulae and thermodynamic equilibrium equation are parameterized by fitting the theoretical equilibrium equation to MD simulation results. We find that alcohol molecules with the varied alkyl chain length show different nucleation states, i.e. , dispersion, reversible and aggregation states, corresponding to the total free energy G c o n f i n e (n , N) with a single minimum at n ∼ 1, two minima at n ∼ 1 and N separated by a maximum, and a local minimum at n ∼ N , respectively. The alcohol molecule with a longer alkyl chain tends to aggregate into a cluster at a lower solute number in nanoconfined solution. Besides, the free energy of cluster formation in nanoconfined solution G c l u s t e r (n) also depends on the alkyl chain length, and three regions can be identified: For the shorter alkyl chain, such as ethanol, there is no local maximum on G c l u s t e r (n), indicating that alcohol molecules tend to be dispersed in water; For the intermediate alkyl chain length, such as 1-propanol, 1-butanol, 1-pentanol, and 1-hexanol, the critical nucleation number n c and nucleation barrier G b monotonically decrease with the increase of alkyl chain length; For the longer alkyl chain, n c ∼ 1 and G b ∼ 0 k B T suggest that alcohol molecules, such as 1-heptanol, can aggregate into clusters easily. Our work deepens the understanding of the alkyl chain length effect on the nucleation behavior of alcohol molecules in nanoconfined solution. [ABSTRACT FROM AUTHOR]

Abstract: Using all-atom molecular dynamics (MD) simulation, we have investigated the adsorption of protein GA module (GA53) onto graphene oxide (GO), compared with similar adsorption onto pristine graphene (PG). We find that: (1) the protein GA53 can be easily and firmly adsorbed onto the surface of GO and PG, but the binding sites are not specific; the main difference is that the secondary structure of GA53 can be well preserved in protein–GO system, while GA53 will partially lose its secondary structure after adsorbed on PG. (2) in protein–GO system, hydroxyl and epoxy groups increase the distance between protein and GO, which weaken their vdW interactions, meanwhile, hydrogen bonds and electrostatic interactions enhance their binding affinity. In protein–PG system, strong vdW interactions between residues of GA53 and PG have destroyed its secondary structure. (3) π–π stacking interactions still exist between aromatic residues and both the basal plane of GO and PG. In comparison with PG, our results suggest that GO presents better biocompatibility to preserve protein secondary structure when simultaneously absorbing protein. [Copyright &y& Elsevier]

[Display omitted] • A prior exploration of the potential biological effect of a carbon nitride (C 3 N 3). • The moderate adsorption of C 3 N 3 nanosheet to membrane. • The molecular insights and mechanism of the interaction between C 3 N 3 and membrane. • The specific attraction between C 3 N 3 pores and lipid heads. Recently, the novel hole-containing carbon nitride C 3 N 3 nanomaterial was successfully synthesized, featuring outstanding and unique mechanical and electrical properties. However, to fully exploit this nanomaterial in biomedical applications, information regarding its biocompatibility is necessary. Herein, by using all-atom molecular dynamics simulations, we evaluate the interactions between a C 3 N 3 nanosheet and a critical cellular component, that is, a lipid membrane bilayer. Our results indicate that the C 3 N 3 nanosheet is able to interact with the lipid bilayer surface without affecting the membrane's structural integrity. Moreover, our results showed that the C 3 N 3 nanosheet is adsorbed on the surface of the lipid bilayer without inflicting any structural damage to the membrane, regardless of the conditions of the system (that is, with and without restrains in the C 3 N 3 nanosheet). Also, we found that both energy contributions, namely vdW and Coulomb energies, conjointly mediated the C 3 N 3 adsorption process. In comparison and as expected, pristine graphene significantly disturbed the membrane structure. Perpendicularly-oriented-sheet simulations described the significance of the surface charges of the C 3 N 3 nanosheet in prohibiting its insertion into the membrane. Detailed analysis indicated that the electrostatic attraction between the pores in the C 3 N 3 structure and the lipid head amino groups stabilized the interaction restricting the insertion of the C 3 N 3 structure deeper into the membrane. Our results suggested the importance of the negatively charged C 3 N 3 pores when interacting with lipid membranes. Our findings shed light on the potential compatibility of C 3 N 3 with biomembranes and its underlying molecular mechanism, which might provide a useful foundation for the future exploration of this 2D nanomaterial in biomedical applications. [ABSTRACT FROM AUTHOR]

We develop a new Gibbs free energy-based association model and perform series of molecular dynamics (MD) simulations to study the association behavior of Lennard-Jones (LJ) particles in nanoconfined aqueous solution. In the association model, the total Gibbs free energy is the sum of free energy cost in the nucleation of a densely packed cluster with an isotropic shape and a radius dependent interfacial tension coefficient, and the translation entropy of dispersed particles outside the cluster. Two key theoretical expressions – total Gibbs free energy formula and the thermodynamic equilibrium equation – are obtained to estimate the cluster aggregation number for a given LJ particle number and the corresponding total Gibbs free energy. Using MD simulations, we observe that the association state transforms from the stable dispersion state, through the reversible state, finally to the stable aggregation state as the LJ particle number increases. In the reversible state, the system reversibly switch in between the dispersion and aggregation states. The existence of three types of association states is also found for LJ particles with the varied well depth. According to our model, the Gibbs free energy curve shows from a single minimum, through two minima, finally to a single minimum, leading to the transformation of association states. The occurrence of reversible state transition is attributed to the free energy barrier of the order of thermal fluctuation in water between the dispersion and aggregation states. These findings deepen the understanding of nucleation/aggregation of hydrophobic gas molecules or particles in solution under nanoconfinement. • LJ particles show dispersion, reversible, aggregation states in nanoconfined solution. • Three association states still exist even if the well depth changes. • A Gibbs free energy-based association model is developed. • The Gibbs free energy profile shows two minima in the reversible state. • The free energy barrier is the order of thermal fluctuation. [ABSTRACT FROM AUTHOR]