Proton transport through water-filled carbon nanotubes

Ab initio molecular dynamics simulations of aqueous triflic acid confined in carbon nanotubes

Ab initio molecular dynamics simulations were performed to investigate the effects of nanoscale confinement on the structural and dynamical properties of aqueous triflic acid (CF3SO3H). Single-walled carbon nanotubes (CNTs) with diameters ranging from ∼11 to 14 Å were used as confinement vessels, and the inner surface of the CNT were either left bare or fluorinated to probe the influence of the confined environment on structural and dynamical properties of the water and triflic acidic. The systems were simulated at hydration levels of n = 1-3 H2O/CF3SO3H. Proton dissociation expectedly increased with increasing hydration. Along with the level of hydration, hydrogen bond connectivity between the triflic acid molecules, both directly and via a single water molecule, played a role on proton dissociation. Direct hydrogen bonding between the CF3SO3H molecules, most commonly found in the larger bare CNT, also promoted interactions between water molecules allowing for greater separation of the dissociated protons from the CF3SO3(-) as the hydration level was increased. However, this also resulted in a decrease in the overall proportion of dissociated protons. The confinement dimensions altered both the hydrogen bond network and the distribution of water molecules where the H2O in the fluorinated CNTs tended to form small clusters with less proton dissociation at n = 1 and 2 but the highest at n = 3. In the absence of nearby hydrogen bond accepting sites from H2O or triflic acid SO3H groups, the water molecules formed weak hydrogen bonds with the fluorine atoms. In the bare CNT systems, these involved the CF3 groups of triflic acid and were more frequently observed when direct hydrogen bonding between CF3SO3H hindered potential hydrogen bonding sites. In the fluorinated tubes, interactions with the covalently bound fluorine atoms of the CNT wall dominated which appear to stabilize the hydrogen bond network. Increasing the hydration level increased the frequency of the OH···F (CNT) hydrogen bonding which was highly pronounced in the smaller fluorinated CNT indicating an influence on the confinement dimensions on these interactions.

Vibrational excitation induced proton transfer in hydrated Nafion membranes

We study the energy relaxation and structural relaxation dynamics of hydrated protons in Nafion membranes at different hydration levels using femtosecond infrared transient absorption spectroscopy. At low hydration levels we observe that the excitation of the proton vibration of an Eigen-like proton hydration structure leads to a structural relaxation process in which the Eigen-like structure evolves to a Zundel-like proton hydration structure. This reorganization leads to a transfer of the proton charge and closely follows the mechanism of infrared-induced adiabatic proton transfer that has been proposed by S. Hammes-Schiffer, J. T. Hynes, and others. At high hydration levels, the spectral dynamics are dominated by vibrational energy relaxation and subsequent cooling of the proton hydration structures and the surrounding water molecules. Using a kinetic analysis of the transient spectral data, we determine the rates of proton transfer, vibrational energy relaxation, and cooling as a function of hydration level. We find that infrared-induced proton transfer occurs at all hydration levels but becomes less observable at high hydration levels due to the increasingly dominant influence of the vibrational energy relaxation.

The pathway for serial proton supply to the active site of nitrogenase: enhanced density functional modeling of the Grotthuss mechanism

Proton translocation along a chain of eight waters to the active site of nitrogenase is described in detail, using density functional simulations with a 269 atom system that includes surrounding amino acids.

Molecular dynamics simulations of proton-ordered water confined in low-diameter carbon nanotubes

Metastable ferroelectric, ferrielectric, and antiferroelectric structures of water confined in carbon nanotubes and their abrupt or continuous transitions are identified.

Biological wires, communication systems, and implications for disease

Microtubules, actin, and collagen are macromolecular structures that compose a large percentage of the proteins in the human body, helping form and maintain both intracellular and extracellular structure. They are biological wires and are structurally connected through various other proteins. Microtubules (MTs) have been theorized to be involved in classical and quantum information processing, and evidence continues to suggest possible semiconduction through MTs. The previous Dendritic Cytoskeleton Information Processing Model has hypothesized how MTs and actin form a communication network in neurons. Here, we review information transfer possibilities involving MTs, actin, and collagen, and the evidence of an organism-wide high-speed communication network that may regulate morphogenesis and cellular proliferation. The direct and indirect evidence in support of this hypothesis, and implications for chronic diseases such as cancer and neurodegenerative diseases are discussed.

Water Dynamics in Metal-Organic Frameworks: Effects of Heterogeneous Confinement Predicted by Computational Spectroscopy

The behavior of water confined in MIL-53(Cr), a flexible metal-organic framework (MOF), is investigated through computational infrared spectroscopy. As the number of molecules adsorbed inside of the pores increases, the water OH stretch band of the linear infrared spectrum grows in intensity and approaches that of bulk water. To assess whether the water confined in MIL-53(Cr) becomes liquid-like, two-dimensional infrared spectra (2DIR) are also calculated. Confinement effects result in distinct chemical environments that appear as specific features in the 2DIR spectra. The evolution of the 2DIR line shape as a function of waiting time is well described in terms of the orientational dynamics of the water molecules, with chemical exchange cross peaks appearing at a time scale similar to the hydrogen bond rearrangement lifetime. The confining environment considerably slows the hydrogen bond dynamics relative to bulk as a result of the competition between water-framework and water-water interactions.

Self-organized defect strings in two-dimensional crystals

Using experiments with single-particle resolution and computer simulations we study the collective behavior of multiple vacancies injected into two-dimensional crystals. We find that the defects assemble into linear strings, terminated by dislocations with antiparallel Burgers vectors. We show that these defect strings propagate through the crystal in a succession of rapid one-dimensional gliding and rare rotations. While the rotation rate decreases exponentially with the number of defects in the string, the diffusion constant is constant for large strings. By monitoring the separation of the dislocations at the end points, we measure their effective interactions with high precision beyond their spontaneous formation and annihilation, and we explain the double-well form of the dislocation interaction in terms of continuum elasticity theory.

Proton transfer through the water gossamer

The diffusion of protons through water is understood within the framework of the Grotthuss mechanism, which requires that they undergo structural diffusion in a stepwise manner throughout the water network. Despite long study, this picture oversimplifies and neglects the complexity of the supramolecular structure of water. We use first-principles simulations and demonstrate that the currently accepted picture of proton diffusion is in need of revision. We show that proton and hydroxide diffusion occurs through periods of intense activity involving concerted proton hopping followed by periods of rest. The picture that emerges is that proton transfer is a multiscale and multidynamical process involving a broader distribution of pathways and timescales than currently assumed. To rationalize these phenomena, we look at the 3D water network as a distribution of closed directed rings, which reveals the presence of medium-range directional correlations in the liquid. One of the natural consequences of this feature is that both the hydronium and hydroxide ion are decorated with proton wires. These wires serve as conduits for long proton jumps over several hydrogen bonds.

Direct observation of self-assembled chain-like water structures in a nanoscopic water meniscus

Sawtooth-like oscillatory forces generated by water molecules confined between two oxidized silicon surfaces were observed using a cantilever-based optical interfacial force microscope when the two surfaces approached each other in ambient environments. The humidity-dependent oscillatory amplitude and periodicity were 3-12 nN and 3-4 water diameters, respectively. Half of each period was matched with a freely jointed chain model, possibly suggesting that the confined water behaved like a bundle of water chains. The analysis also indicated that water molecules self-assembled to form chain-like structures in a nanoscopic meniscus between two hydrophilic surfaces in air. From the friction force data measured simultaneously, the viscosity of the chain-like water was estimated to be between 10(8) and 10(10) times greater than that of bulk water. The suggested chain-like structure resolves many unexplained properties of confined water at the nanometer scale, thus dramatically improving the understanding of a variety of water systems in nature.

Electrical-driven transport of endohedral fullerene encapsulating a single water molecule

Encapsulating a single water molecule inside an endohedral fullerene provides an opportunity for manipulating the H2O@C60 through the encapsulated polar H2O molecule. Using molecular dynamic simulations, we propose a strategy of electrical-driven transport of H2O@C60 inside a channel, underpinned by the unique behavior of a water molecule free from a hydrogen-bonding environment. When an external electrical field is applied along the channel's axial direction, steady-state transport of H2O@C60 can be reached. The transport direction and rate depend on the applied electrical intensity as well as the polar orientation of the encapsulated H2O molecule.

Enantiomerization mechanism of thalidomide and the role of water and hydroxide ions

The significance of the molecular chirality of drugs has been widely recognized due to the thalidomide tragedy. Most of the new drugs reaching the market today are single enantiomers, rather than racemic mixtures. However, many optically pure drugs, including thalidomide, undergo enantiomerization in vivo, thus negating the single enantiomers' benefits or inducing unexpected effects. A detailed atomic level understanding of chiral conversion, which is still largely lacking, is thus critical for drug development. Herein, we use first-principle density function theory (DFT) to explore the mechanism of enantiomerization of thalidomide. We have identified the two most plausible interconversion pathways for isolated thalidomide: 1) proton transfer from the chiral carbon center to an adjacent carbonyl oxygen atom, followed by isomerization and rotation of the glutarimide ring (before the proton hops back to the chiral carbon atom); and 2) a pathway that is the same as "1", but with the isomerization of the glutarimide ring occurring ahead of the initial proton transfer reaction. There are two remarkable energy barriers, 73.29 and 23.59 kcal mol(-1), corresponding to the proton transfer and the rotation of the glutarimide ring, respectively. Furthermore, we found that water effectively catalyzes the interconversion by facilitating the proton transfer with the highest energy barrier falling to approximately 30 kcal mol(-1), which, to our knowledge, is the first time that this important role of water in chiral conversion has been demonstrated. Finally, we show that the hydroxide ion can further lower the enantiomerization energy barrier to approximately 24 kcal mol(-1) by facilitating proton abstraction, which agrees well with recent experimental data under basic conditions. Our current findings highlight the importance of water and hydroxide ions in the enantiomerization of thalidomide and also provide new insights into the mechanism of enantiomerization at an atomic level.

Hydroxide ion can move faster than an excess proton through one-dimensional water chains in hydrophobic narrow pores

Carbon nanotubes (CNT) are known to provide a hydrophobic, confined environment for water where its structure and dynamics can be very different from those of bulk water. In particular, narrow CNTs of the type (6,6) allow only a single one-dimensional (1D) chain of water molecules inside them, thus providing an idealized scenario to study motion in 1D along water chains. In the present study, we have investigated structural and dynamic behavior of water and also of an excess proton and hydroxide ion in water-filled narrow CNTs by means of ab initio molecular dynamics and combined quantum-classical simulations. The main focus of the present work is on the molecular mechanism and kinetics of hydronium and hydroxide ion migration along 1D water chains of different lengths in confinement. It is found that the hydrogen-bonded structures of water and the excess proton and hydroxide ion in CNTs can be very different from those in bulk, and these altered solvation structures play critical roles in determining the proton-transfer (PT) rates along water chains. For the present 1D chain systems, the hydroxide ion is found to migrate at a slightly faster rate than the excess proton, unlike their relative mobilities in bulk water. This faster migration of the hydroxide ion is found not only in CNTs with periodicity along the tube axis but also in isolated CNTs where the excess proton and the hydroxide ion are allowed to move under the influence of an electric field of an oppositely charged ion. The roles of rotational jumps and hydrogen-bond fluctuations in the PT events are discussed. In addition, the significance of hydrogen-bonding defects on the dynamics of an excess proton and hydroxide ion is also discussed for varying chain lengths.

Phase transition and interpore correlations of water in nanopore membranes

Using computer simulations, we study a membrane of parallel narrow pores filled with one-dimensional wires of hydrogen-bonded water molecules. We show that such a membrane is equivalent to a system of effective charges located at opposite sides of the membrane offering a computationally efficient way to model correlation effects in water-filled nanopore membranes. Based on our simulations we predict that membranes with square pore lattices undergo a continuous order-disorder transition to an antiferroelectric low-temperature phase in which water wires in adjacent pores are oriented in opposite directions. Strong antiferroelectric correlations exist also in the disordered phase far above the critical temperature or in membranes with geometric frustration, leading to a dielectric constant that is reduced considerably with respect to the case of uncoupled water wires. These correlations are also expected to hinder proton translocation through the membrane.

Expanding the view of proton pumping in cytochrome c oxidase through computer simulation

In cytochrome c oxidase (CcO), a redox-driven proton pump, protons are transported by the Grotthuss shuttling via hydrogen-bonded water molecules and protonatable residues. Proton transport through the D-pathway is a complicated process that is highly sensitive to alterations in the amino acids or the solvation structure in the channel, both of which can inhibit proton pumping and enzymatic activity. Simulations of proton transport in the hydrophobic cavity showed a clear redox state dependence. To study the mechanism of proton pumping in CcO, multi-state empirical valence bond (MS-EVB) simulations have been conducted, focusing on the proton transport through the D-pathway and the hydrophobic cavity next to the binuclear center. The hydration structures, transport pathways, effects of residues, and free energy surfaces of proton transport were revealed in these MS-EVB simulations. The mechanistic insight gained from them is herein reviewed and placed in context for future studies.

Ion transport in mesoporous silica SBA-16 thin films with 3D cubic structures

Mesoporous silica SBA-16 thin films with highly ordered 3D cubic structures were synthesized on a Si substrate via the dip-coating method. After these films were filled with KCl aqueous solutions, the ionic current passing through the mesopores was measured by applying dc electric fields. At low ion concentrations, the measured I-V curves were nonlinear and the current increased exponentially with respect to voltage. As the ion concentration increased, the I-V curve approached linear behavior. The nonlinear behavior of I-V curves can be reasonably attributed to the electric potential barrier created in nanopores.

Proton-pumping mechanism of cytochrome c oxidase: a kinetic master-equation approach

Cytochrome c oxidase is an efficient energy transducer that reduces oxygen to water and converts the released chemical energy into an electrochemical membrane potential. As a true proton pump, cytochrome c oxidase translocates protons across the membrane against this potential. Based on a wealth of experiments and calculations, an increasingly detailed picture of the reaction intermediates in the redox cycle has emerged. However, the fundamental mechanism of proton pumping coupled to redox chemistry remains largely unresolved. Here we examine and extend a kinetic master-equation approach to gain insight into redox-coupled proton pumping in cytochrome c oxidase. Basic principles of the cytochrome c oxidase proton pump emerge from an analysis of the simplest kinetic models that retain essential elements of the experimentally determined structure, energetics, and kinetics, and that satisfy fundamental physical principles. The master-equation models allow us to address the question of how pumping can be achieved in a system in which all reaction steps are reversible. Whereas proton pumping does not require the direct modulation of microscopic reaction barriers, such kinetic gating greatly increases the pumping efficiency. Further efficiency gains can be achieved by partially decoupling the proton uptake pathway from the active-site region. Such a mechanism is consistent with the proposed Glu valve, in which the side chain of a key glutamic acid shuttles between the D channel and the active-site region. We also show that the models predict only small proton leaks even in the absence of turnover. The design principles identified here for cytochrome c oxidase provide a blueprint for novel biology-inspired fuel cells, and the master-equation formulation should prove useful also for other molecular machines. .

Single-file water in nanopores

Water molecules confined to pores with sub-nanometre diameters form single-file hydrogen-bonded chains. In such nanoscale confinement, water has unusual physical properties that are exploited in biology and hold promise for a wide range of biomimetic and nanotechnological applications. The latter can be realized by carbon and boron nitride nanotubes which confine water in a relatively non-specific way and lend themselves to the study of intrinsic properties of single-file water. As a consequence of strong water-water hydrogen bonds, many characteristics of single-file water are conserved in biological and synthetic pores despite differences in their atomistic structures. Charge transport and orientational order in water chains depend sensitively on and are mainly determined by electrostatic effects. Thus, mimicking functions of biological pores with apolar pores and corresponding external fields gives insight into the structure-function relation of biological pores and allows the development of technical applications beyond the molecular devices found in living systems. In this Perspective, we revisit results for single-file water in apolar pores, and examine the similarities and the differences between these simple systems and water in more complex pores.