Reversible geminate recombination of hydrogen-bonded water molecule pair

Formation of Polyimide Membranes via Non-Solvent Induced Phase Separation: Insight from Molecular Dynamics Simulations

Molecular dynamics simulations were applied to investigate the formation of P84 polyimide membranes through the non-solvent induced phase separation (NIPS) process, considering two scenarios: one using a conventional organic solvent like n-methyl-2-pyrrolidone (NMP) and the other a greener alternative, γ-butyrolactone (GBL), with water serving as the non-solvent. Different compositions of polymer solutions were established along the binodal boundaries of the respective systems, derived from experimental cloud point data on the ternary phase diagram. The resulting polymer membranes were analyzed and compared in terms of their morphology. The wettability of their surfaces was notably affected by the polymer content in the initial casting solution and demonstrated a correlation with the Brunauer-Emmet-Teller (BET) specific surface area of the associated polymer nanostructures. The GBL solvent systems produced porous polymers qualitatively similar to those obtained with NMP, albeit with slightly narrower pore size distributions.

Graphene Exfoliation in Binary NMP/Water Mixtures by Molecular Dynamics Simulations

We investigate the molecular mechanism underlying the liquid-phase exfoliation of graphene in aqueous/N-methyl-2-pyrrolidone (NMP) solvent mixtures and calculate the associated free energies, considering different NMP concentrations and exfoliation temperatures. We employ steered molecular dynamics to establish a path for the exfoliation of a graphene sheet from graphite within each solvent environment. Then, we conduct umbrella sampling simulations throughout the created paths to compute the potential of mean force (PMF) of the graphene sheet. As the exfoliated nanosheet disperses into the liquid, it becomes fully covered by an adsorbed solvent monolayer. We analyze the composition of the monolayer by measuring the direct contacts of either NMP or water molecules with the carbon surface. The carbon surface exhibits a preference for adsorbing NMP over water. The NMP molecules form a hydrophobic compact monolayer structure, effectively protecting the carbon interface from unfavorable interactions with water. The creation of the hydrophobic monolayer is a key factor in the exfoliation process, as it effectively inhibits the restacking of exfoliated nanosheets. An adequate level of graphene solubility is achieved through the addition of 20 % to 30 % water by weight to the NMP solvent. This finding holds significant importance for improving production efficiency and reducing dependence on organic solvents in the industrial manufacturing of graphene.

An exact a posteriori correction for hydrogen bond population correlation functions and other reversible geminate recombinations obtained from simulations with periodic boundary conditions. Liquid water as a test case

The kinetics of breaking and re-formation of hydrogen bonds (HBs) in liquid water is a prototype of reversible geminate recombination. HB population correlation functions (HBPCFs) are a means to study the HB kinetics. The long-time limiting behavior of HBPCFs is controlled by translatoric diffusion and shows a t^-3/2 time-dependence, which can be described by analytical expressions based on the HB acceptor density and the donor-acceptor inter-diffusion coefficient. If the trajectories are not properly "unwrapped," the presence of periodic boundary conditions (PBCs) can perturb this long-time limiting behavior. Keeping the trajectories "wrapped," however, allows for a more efficient calculation of HBPCFs. We discuss the consequences of PBCs in combination with "wrapped" trajectories following from the approximations according to Luzar-Chandler and according to Starr, each deviating in a different fashion from the true long-time limiting behavior, but enveloping the unperturbed function. A simple expression is given for estimating the maximum time up to which the computed HBPCFs reliably describe the long-time limiting behavior. In addition, an exact a posteriori correction for systems with PBCs for "wrapped" trajectories is derived, which can be easily computed and which is able to fully recover the true t^-3/2 long-time behavior. For comparison, HBPCFs are computed from MD simulations of TIP4P/2005 model water for varying system sizes and temperatures of 273 and 298 K using this newly introduced correction. Implications for the computations of HB lifetimes and the effect of the system-size are discussed.

A combined experimental and molecular dynamics simulation study of an intrinsic self-healing polyurethane elastomer based on a dynamic non-covalent mechanism

An intrinsic self-healing polyurethane (PU) elastomer with excellent self-healing efficiency was prepared. The self-healing properties of this elastomer as well as the temperature dependence of self-healing can be tailored by regulating the molar ratio of hard to soft segments. The self-healing efficiency of 92.5% is the highest when the molar ratio of 4,4-methylenedicyclohexyl diisocyanate (HMDI) to polypropylene carbonate polyol (PPC) is 1.3 and the temperature is 25 °C. In situ temperature swing infrared spectra and low-field nuclear magnetic resonance reveal that the soft segment, PPC, endows PU with a dense dynamic hydrogen bond network, and the dissociation and reconstruction of the hydrogen bond network enable the PU to heal. To date, the exchange of hydrogen bonds has not been observed intuitively through experimental means. Therefore, the number, type, strength, lifetime, and the exchange of hydrogen bonds in the self-healing process at different temperatures were investigated by molecular dynamics (MD) simulation. The simulated results show that the type of hydrogen bond exchange between functional groups will be affected by temperature. The hydrogen bonds between urethane and urea groups play a leading role in the self-healing properties due to the high strength and a large number of hydrogen bonds at both 25 and 50 °C. The stronger strength, longer lifetime, and greater number of effective hydrogen bonds at 25 °C make the self-healing efficiency of PU higher than at 50 °C.

Molecular dynamics simulation insight into the temperature dependence and healing mechanism of an intrinsic self-healing polyurethane elastomer

An intrinsic self-healing polyurethane (PU) elastomer was synthesized in our previous work. In this work, three-dimensional (3D) micro-crack models based on experimental samples were further introduced to investigate their self-healing behavior, mechanism, and temperature dependence by molecular dynamics (MD) simulations. In particular, the number, type, strength, and lifetime of hydrogen bonds as well as the microscopic behavior of molecular diffusion in the self-healing process were investigated. It was found that the self-healing capacity of PU mainly results from intermolecular electrostatic interactions, and the hydrogen bond plays a key role in electrostatic interactions. There is an optimum ratio of soft and hard segments at which the number of hydrogen bonds is appropriate and the self-healing capacity is optimum. Besides, the temperature has an optimal value at which the self-healing rate of PU is the fastest. The exchanges of hydrogen bonds, which endowed PU with self-healing capacity, were further revealed intuitively. We found that the exchanges of hydrogen bonds are reversible and more likely to occur on the urethane groups. This study deepened the understanding of the self-healing character of PU at the molecular level.

Deciphering the Self-Cleavage Reaction Mechanism of Hairpin Ribozyme

Hairpin ribozyme catalyzes the reversible self-cleavage of phosphodiester bonds which plays prominent roles in key biological processes involving RNAs. Despite impressive advances on ribozymatic self-cleavage, critical aspects of its molecular reaction mechanism remain controversially debated. Here, we generate and analyze the multidimensional free energy landscape that underlies the reaction using extensive QM/MM metadynamics simulations to investigate in detail the full self-cleavage mechanism. This allows us to answer several pertinent yet controversial questions concerning activation of the 2'-OH group, the mechanistic role of water molecules present in the active site, and the full reaction pathway including the structures of transition states and intermediates. Importantly, we find that a sufficiently unrestricted reaction subspace must be mapped using accelerated sampling methods in order to compute the underlying free energy landscape. It is shown that lower-dimensional sampling where the bond formation and cleavage steps are coupled does not allow the system to sufficiently explore the landscape. On the basis of a three-dimensional free energy surface spanned by flexible generalized coordinates, we find that 2'-OH is indirectly activated by adjacent G8 nucleobase in conjunction with stabilizing H-bonding involving water. This allows the proton of the 2'-OH group to directly migrate toward the 5'-leaving group via a nonbridging oxygen of the phosphodiester link. At variance with similar enzymatic processes where water wires connected to protonable side chains of the protein matrix act as transient proton shuttles, no such de/reprotonation events of water molecules are found to be involved in this ribozymatic transesterification. Overall, our results support an acid-catalyzed reaction mechanism where A38 nucleobase directly acts as an acid whereas G8, in stark contrast, participates only indirectly via stabilizing the nascent nucleophile for subsequent attack. Moreover, we conclude that self-cleavage of hairpin ribozyme follows an A_N + D_N two-step associative pathway where the rate-determining step is the cleavage of the phosphodiester bond. These results provide a major advancement in our understanding of the unique catalytic mechanism of hairpin ribozyme which will fruitfully impact on the design of synthetic ribozymes.

Anionic effects on the structure and dynamics of water in superconcentrated aqueous electrolytes

Dissolved ions in aqueous solutions are ubiquitous in a variety of systems and the addition of ions to water gives rise to dramatic effects on the properties of water. Due to a significant role of ions in the structure and dynamics of water, the ionic conditions, such as the ion type and concentration, have been considered as critical factors. Here we study the effects of anions on the structure and dynamics of water in aqueous electrolytes for various lithium salt concentrations via extensive molecular dynamics simulations. Our results demonstrate that a certain amount of salt is needed to show the different properties of water caused by the presence of different types of anion. Below the cutoff concentration, most features of water show the same characteristics in spite of the presence of different anions. In the superconcentrated limit, we find that full disruption of the hydrogen bond network between water molecules occurs for most anions investigated, indicating that the effect of the water–water interaction becomes negligible. However, a certain type of anion could enhance an ion-pairing of cations and anions and the water–water interaction remains considerable even in the superconcentrated limit. We further investigate the cationic and anionic hydration shell structures and dynamics, revealing their dependence on the anion type and the salt concentration. Finally, we observe that the anionic effects on water extend to the dynamics of water molecules, such as an anionic dependence of the onset of subdiffusive translation and anisotropic rotation.

The effects of anions on the properties of water are examined for various salt concentrations.

Dynamic features of water molecules in superconcentrated aqueous electrolytes

An existence of ions dissolved in water has significant effects on bulk properties of water. Superconcentrated conditions have been recently proposed to provide a new concept of lithium ion batteries in order to overcome limitations for practical applications. In those conditions, water would undergo significant changes in structure and dynamics compared to its bulk properties. However, little is known about water in superconcentrated aqueous electrolytes. Here we study the properties of water in aqueous electrolytes with various salt concentrations via molecular dynamics simulations. We find that new dynamic features of water arise in the limit of an extremely high salt concentration. In particular, we observe a decoupled temporal character of water molecules exhibiting a subdiffusive translation and a diffusive rotation in the superconcentrated condition. Furthermore, we find that the rotational dynamics for each principal axis of a water molecule differently responds to the salt concentration, resulting in an occurrence of anisotropy in the rotation as the salt concentration increases. The superconcentrated environments also invoke new features in the hydrogen-bonding characteristics of water such as an emergence of two time scales in the hydrogen bond dynamics of water with respect to the salt concentration.

Curvature dependence of hydrophobic hydration dynamics

We investigate the solute curvature dependence of water dynamics in the vicinity of hydrophobic spherical solutes using molecular dynamics simulations. For both the lateral and perpendicular diffusivity, as well as for H-bond kinetics of water in the first hydration shell, we find a nonmonotonic solute-size dependence, exhibiting extrema close to the well-known structural crossover length scale for hydrophobic hydration. Additionally, we find an apparent anomalous diffusion for water moving parallel to the surface of small solutes, which, however, can be explained by topology effects. Our findings regarding the intimate connection between solute curvature and water dynamics has implications for our understanding of hydration dynamics at heterogeneous biomolecular surfaces.

Green's function for reversible geminate reaction with volume reactivity

The kinetics of a diffusing particle near a reversible trap may be described by an extension of the Feynman-Kac equation to the case of reversible binding, which can occur within a finite reaction sphere. We obtain the Green's function solution for the Laplace transform of this equation when the particle is initially either bound or unbound. We study the solution in the time-domain by either inverting the Laplace transform numerically or propagating the partial differential equation in the time-domain. We show that integrals of this solution over the reaction sphere agree with previously obtained solutions.

Lifetimes of excess protons in water using a dissociative water potential

Molecular dynamics simulations using a dissociative water potential were applied to study transport of excess protons in water and determine the applicability of this potential to describe such behavior. While originally developed for gas-phase molecules and bulk liquid water, the potential is transferrable to nanoconfinement and interface scenarios. Applied here, it shows proton behavior consistent with ab initio calculations and empirical models specifically designed to describe proton transport. Both Eigen and Zundel complexes are observed in the simulations showing the Eigen-Zundel-Eigen-type mechanism. In addition to reproducing the short-time rattling of the excess proton between the two oxygens of Zundel complexes, a picosecond-scale lifetime was also found. These longer-lived H3O(+) ions are caused by the rapid conversion of the local solvation structure around the transferring proton from a Zundel-like form to an Eigen-like form following the transfer, effectively severing the path along which the proton can rattle. The migration of H(+) over long times (>100 ps) deviates from the conventional short-time multiexponentially decaying lifetime autocorrelation model and follows the t(-3/2) power-law behavior. The potential function employed here matches many of the features of proton transport observed in ab initio molecular dynamics simulations as well as the highly developed empirical valence bond models, yet is computationally very efficient, enabling longer time and larger systems to be studied.

Liquid water: from symmetry distortions to diffusive motion

Water deviates from tetrahedral symmetry on different scales, creating "defects" that are important for its dynamics. In this Account, I trace the manifestations of these distortions from the isolated molecule through gas-phase clusters to the liquid phase. Unlike the common depiction, an isolated water molecule has a nonsymmetric charge distribution: although its positive charge is localized at the hydrogens, the negative charge is smeared between the lone-pair sites. This creates a "negativity track" along which a positive charge may slide. Consequently, the most facile motion within the water dimer is a reorientation of the hydrogen-bond (HB) accepting molecule (known as an "acceptor switch"), such that the donor hydrogen switches from one lone pair to the other. Liquid water exhibits asymmetry between donor and acceptor HBs. Molecular dynamics simulations show that the water oxygens accepting HBs from the central molecule are spatially localized, whereas water hydrogens donating HBs to it are distributed along the negativity track. This asymmetry is manifested in a wider acceptor- versus donor-HB distribution. There is a higher probability for a water molecule to accept one (trigonal symmetry) or three HBs than to donate one or three HBs. A simple model can explain semiquantitatively how these distributions evolve by distorting perfectly tetrahedral water. Just two reactions are required: the dissociation of a HB between a double-donor donating to a double-acceptor, D(2)···A(2), followed by a switching reaction in which a HB donor rotates its hydrogen between two double-acceptor molecules. The preponderance of D(2)···A(2) dissociation events is in line with HB "anticooperativity", whereas positive cooperativity is exhibited by conditional HB distributions: a molecule with more acceptor bonds tends to have more donor bonds and vice versa. Quantum mechanically, such an effect arises from intermolecular charge transfer, but it is observed even for fixed-charge water models. Possibly, in the liquid state this is partly a collective effect, for example, a more ordered hydration shell that enhances the probability for both acceptor and donor HBs. The activation energy for liquid water self-diffusion is considerably larger than its HB strength, pointing to the involvement of collective dynamics. The remarkable agreement between the temperature dependence of the water self-diffusion coefficient and its Debye relaxation time suggests that both share the same mechanism, likely consisting of coupled rotation and translation with collective rearrangement of the environment. The auto-correlation function of a hydrogen-bonded water molecule pair is depicted quantitatively by the solution of the diffusion equation for reversible geminate recombination, up to long times where the ubiquitous t(-3/2) power law prevails. From the model, one obtains the HB dissociation and formation rate coefficients and their temperature dependence. Both have a similar activation enthalpy, suggesting rapid formation of HBs with alternate partners, perhaps by the HB switching reaction involving the trigonal site. A detailed picture of how small fluctuations evolve into large-scale molecular motions in water remains elusive. Nonetheless, our results demonstrate how the plasticity of water can be traced to its asymmetric charge distribution, with duality between tetrahedral and trigonal ligation states.

Apparent stoichiometry of water in proton hydration and proton dehydration reactions in CH3CN/H2O solutions

Gradual solvation of protons by water is observed in liquids by mixing strong mineral acids with various amounts of water in acetonitrile solutions, a process which promotes rapid dissociation of the acids in these solutions. The stoichiometry of the reaction XH(+) + n(H(2)O) = X + (H(2)O)(n)H(+) was studied for strong mineral acids (negatively charged X, X = ClO(4)¯, Cl¯, Br¯, I¯, CF(3)SO(3)¯) and for strong cationic acids (uncharged X, X = R*NH(2), H(2)O). We have found by direct quantitative analysis preference of n = 2 over n = 1 for both groups of proton transfer reactions at relatively low water concentrations in acetonitrile. At high water concentrations, we have found that larger water solvates must also be involved in the solvation of the proton while the spectral features already observed for n = 2, H(+)(H(2)O)(2), remain almost unchanged at large n values up to at least 10 M of water.

A statistical mechanical theory of proton transport kinetics in hydrogen-bonded networks based on population correlation functions with applications to acids and bases

Extraction of relaxation times, lifetimes, and rates associated with the transport of topological charge defects in hydrogen-bonded networks from molecular dynamics simulations is a challenge because proton transfer reactions continually change the identity of the defect core. In this paper, we present a statistical mechanical theory that allows these quantities to be computed in an unbiased manner. The theory employs a set of suitably defined indicator or population functions for locating a defect structure and their associated correlation functions. These functions are then used to develop a chemical master equation framework from which the rates and lifetimes can be determined. Furthermore, we develop an integral equation formalism for connecting various types of population correlation functions and derive an iterative solution to the equation, which is given a graphical interpretation. The chemical master equation framework is applied to the problems of both hydronium and hydroxide transport in bulk water. For each case it is shown that the theory establishes direct links between the defect's dominant solvation structures, the kinetics of charge transfer, and the mechanism of structural diffusion. A detailed analysis is presented for aqueous hydroxide, examining both reorientational time scales and relaxation of the rotational anisotropy, which is correlated with recent experimental results for these quantities. Finally, for OH(-)(aq) it is demonstrated that the "dynamical hypercoordination mechanism" is consistent with available experimental data while other mechanistic proposals are shown to fail. As a means of going beyond the linear rate theory valid from short up to intermediate time scales, a fractional kinetic model is introduced in the Appendix in order to describe the nonexponential long-time behavior of time-correlation functions. Within the mathematical framework of fractional calculus the power law decay ∼t(-σ), where σ is a parameter of the model and depends on the dimensionality of the system, is obtained from Mittag-Leffler functions due to their long-time asymptotics, whereas (stretched) exponential behavior is found for short times.

Hydrogen-bond dynamics of water in a quasi-two-dimensional hydrophobic nanopore slit

We perform molecular dynamics simulations to investigate hydrogen-bond dynamics of the TIP5P (transferable intermolecular potential with five points) model of water confined in a quasi-two-dimensional hydrophobic nanopore slit. We find that even if the average number and the lifetime of hydrogen bonds are affected by nanoconfinement, the characteristics of hydrogen-bond dynamics in hydrophobic confined water are the same as in bulk water-such as an Arrhenius temperature dependence of average hydrogen-bond lifetime and a nonexponential behavior of lifetime distributions at short time scales. The different physical properties of water in hydrophobic confinement compared to bulk water-such as approximately 40 K temperature shift-may be primarily due to the reduction of the lifetime of hydrogen bonds in confined environments. We also find that the hydrogen-bond autocorrelation function exhibits a power-law tail following a stretched exponential behavior. The relaxation time of hydrogen bonds in confined water is smaller than in bulk water. Further, we find that the temperature dependence of the relaxation time follows a power-law behavior, and the exponents for bulk and confined water are similar to each other.