Proton transport through water-filled carbon nanotubes

Single-Domain Ferroelectric Water and its Concerted Diffusion in Nanotubes

The term ‘ferroelectric water’ has so far stood for ‘ferroelectric ice.’ In molecular dynamics simulations, we find that, counter to intuition, single-domain ferroelectric water is possible inside carbon nanotubes open to a liquid water reservoir. Though this water is tube-shaped, it is strikingly different in structure and dynamics from ‘ice nanotubes.’ A series of step-wise changes in net polarization of water and mobile/immobile water transitions are observed to occur spontaneously. This study not only improves our general knowledge of water, but is also suggestive of potential multifunctional capabilities of simple hydrophobic nanotubes for future applications.

Energetics and dynamics of proton transfer reactions along short water wires

Proton transfer (pT) reactions in biochemical processes are often mediated by chains of hydrogen-bonded water molecules. We use hybrid density functional calculations to study pT along quasi one-dimensional water arrays that connect an imidazolium-imidazole proton donor-acceptor pair. We characterize the structures of intermediates and transition states, the energetics, and the dynamics of the pT reactions, including vibrational contributions to kinetic isotope effects. In molecular dynamics simulations of pT transition paths, we find that for short water chains with four water molecules, the pT reactions are semi-concerted. The formation of a high-energy hydronium intermediate next to the proton-donating group is avoided by a simultaneous transfer of a proton from the donor to the first water molecule, and from the first water molecule into the water chain. Lowering the dielectric constant of the environment and increasing the water chain length both reduce the barrier for pT. We study the effect of the driving force on the energetics of the pT reaction by changing the proton affinity of the donor and acceptor groups through halogen and methyl substitutions. We find that the barrier of the pT reaction depends linearly on the proton affinity of the donor but is nearly independent of the proton affinity of the acceptor, corresponding to Brønsted slopes of one and zero, respectively.

Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy

We propose a new method to determine the proton transfer (PT) rate in channel proteins by two-dimensional infrared (2DIR) spectroscopy. Proton transport processes in biological systems, such as proton channels, trigger numerous fundamental biochemical reactions. Due to the limitation in both spatial and time resolution of the traditional experimental approaches, describing the whole proton transport process and identifying the rate limiting steps at the molecular level is challenging. In the present paper, we focus on proton transport through the Gramicidin A channel. Using a kinetic PT model derived from all-atom molecular dynamics simulations, we model the amide I region of the 2DIR spectrum of the channel protein to examine its sensitivity to the proton transport process. We demonstrate that the 2DIR spectrum of the isotope-labeled channel contain information on the PT rate, which may be extracted by analyzing the antidiagonal linewidth of the spectral feature related to the labeled site. Such experiments in combination with detailed numerical simulations should allow the extraction of site dependent PT rates, providing a method for identifying possible rate limiting steps for proton channel transfer.

Structural inhomogeneity of interfacial water at lipid monolayers revealed by surface-specific vibrational pump-probe spectroscopy

We report vibrational lifetime measurements of the OH stretch vibration of interfacial water in contact with lipid monolayers, using time-resolved vibrational sum frequency (VSF) spectroscopy. The dynamics of water in contact with four different lipids are reported and are characterized by vibrational relaxation rates measured at 3200, 3300, 3400, and 3500 cm(-1). We observe that the water molecules with an OH frequency ranging from 3300 to 3500 cm(-1) all show vibrational relaxation with a time constant of T(1) = 180 ± 35 fs, similar to what is found for bulk water. Water molecules with OH groups near 3200 cm(-1) show distinctly faster relaxation dynamics, with T(1) < 80 fs. We successfully model the data by describing the interfacial water containing two distinct subensembles in which spectral diffusion is, respectively, rapid (3300-3500 cm(-1)) and absent (3200 cm(-1)). We discuss the potential biological implications of the presence of the strongly hydrogen-bonded, rapidly relaxing water molecules at 3200 cm(-1) that are decoupled from the bulk water system.

Anomalous ion transport in 2-nm hydrophilic nanochannels

Transmembrane proteins often contain nanoscale channels through which ions and molecules can pass either passively (by diffusion) or actively (by means of forced transport). These proteins play important roles in selective mass transport and electrical signalling in many biological processes. Fluidic nanochannels that are 1-2 nm in diameter act as functional mimics of protein channels, and have been used to explore the transport of ions and molecules in confined liquids. Here we report ion transport in 2-nm-deep nanochannels fabricated by standard semiconductor manufacturing processes. Ion transport in these nanochannels is dominated by surface charge until the ion concentration exceeds 100 mM. At low concentrations, proton mobility increases by a factor of four over the bulk value, possibly due to overlapping of the hydrogen-bonding network of the two hydration layers adjacent to the hydrophilic surfaces. The mobility of K+/Na+ ions also increases as the bulk concentration decreases, although the reasons for this are not completely understood.

Ferroelectric mobile water

In molecular dynamics simulations single-domain ferroelectric water is produced under ordinary ambient conditions utilizing carbon nanotubes open to a water reservoir. This ferroelectric water diffuses while keeping its proton-ordered network intact. The mobile/immobile water transitions and the step-wise changes in net polarization of water are observed to occur spontaneously. The immobile water becomes mobile by transforming into the single-domain ferroelectric water. Our general notion of relating a more highly ordered structure with a lower temperature has so far restricted researchers' attention to very low temperatures when experimenting on proton-ordered phases of water. The present study improves our general understanding of water, considering that the term 'ferroelectric water' has so far practically stood for 'ferroelectric ice,' and that single-domain ferroelectric water has not been reported even for the ice nanotubes.

Microscopic properties of nanopore water from its time-dependent dielectric response

We present a simple kinetic model for the orientational dynamics of a chain of hydrogen-bonded molecules due to the diffusion of orientational defects. We derive an event-driven algorithm which allows us to do kinetic simulations for chains from nanoscopic to macroscopic lengths, spanning huge orders of magnitude in time. Our simulations and analytical calculations show that nanopore water exhibits Debye behavior arising from the diffusive dynamics of orientational defects. For the limits of short and long chains we derive analytical expressions for the relaxation times which allow to extract the diffusion constant, the effective interaction, and the excitation energy of these defects from dielectric spectroscopy experiments. We also discuss the possibility to use such experiments to detect if the two possible kinds of orientational defects differ in excitation energy and diffusion constant.

Single-file water as a one-dimensional Ising model

We show that single-file water in nanopores can be viewed as a one-dimensional Ising model and investigate, on this basis, the static dielectric response of a chain of hydrogen-bonded water molecules to an external field. To this end, we use a recently developed dipole lattice model which accurately captures the free energetics of nanopore water. In this model, the total energy of the system can be expressed as a sum of effective interactions of chain ends and orientational defects. Neglecting these interactions, we essentially obtain the one-dimensional Ising model which allows us to derive analytical expressions for the free energy as a function of the total dipole moment and for the dielectric susceptibility. Our expressions, which agree very well with simulation results, provide the basis for the interpretation of future dielectric spectroscopy experiments on water-filled nanopore membranes.

Coherence Resonance in a Single-Walled Carbon Nanotube Ion Channel

Biological ion channels are able to generate coherent and oscillatory signals from intrinsically noisy and stochastic components for ultrasensitive discrimination with the use of stochastic resonance, a concept not yet demonstrated in human-made analogs. We show that a single-walled carbon nanotube demonstrates oscillations in electroosmotic current through its interior at specific ranges of electric field that are the signatures of coherence resonance. Stochastic pore blocking is observed when individual cations partition into the nanotube obstructing an otherwise stable proton current. The observed oscillations occur because of coupling between pore blocking and a proton-diffusion limitation at the pore mouth. The result illustrates how simple ionic transport can generate coherent waveforms within an inherently noisy environment and points to new types of nanoreactors, sensors, and nanofluidic channels based on this platform.

Simulating proton transport through a simplified model for trans-membrane proteins

Ab initio MD simulations on a polyglycine helix and water-wire expressed under periodic boundary conditions have created a channel that supports proton transfer up to distances of 10.5 A. The effect of varying the density of water molecules in the channel has been investigated. A range of cationic states are identified with widely varying lifetimes. The mechanism of proton transport in this model shares some features with the simulations reported for bulk water, with, e.g., the hydrogen bond distance shortening in the time period leading up to successful proton transfer. However, there are also some important differences such as the observation of a heightened number of proton rattling events. We also observe that the helix plays an important role in directing the behavior of the water wire: the most active proton transport regions of the water-wire are found in areas where the helix is most tightly coiled. Finally, we report on the effects of different DFT functionals to model a water-wire and on the importance of including dispersion corrections to stabilize the alpha-helical structure.

Ab initio molecular dynamics simulations investigating proton transfer in perfluorosulfonic acid functionalized carbon nanotubes

Proton dissociation and transfer were examined with ab initio molecular dynamics (AIMD) simulations of carbon nanotubes (CNT) functionalized with perfluorosulfonic acid (-CF(2)SO(3)H) groups with 1-3 H(2)O/SO(3)H. The CNT systems were constructed both with and without fluorine atoms covalently bound to the walls to elucidate the effects of the presence of a strongly hydrophobic environment, the fluorine, on proton dissociation, hydration, and stabilization. The simulations revealed that the dissociated proton was preferentially stabilized as a hydrated hydronium cation (i.e., Eigen like) in the fluorinated CNTs but as a Zundel (H(5)O(2)(+)) cation in the nonfluorinated CNTs. This feature is attributed to the fluorine atoms forming hydrogen bonds with the water molecules coordinated to the central hydronium ion.

H(aq)+ structures in proton wires inside nanotubes

The hydrated carborane acid H(CHB(11)I(11)).8H(2)O crystallizes in nanometer-diameter tubes of H(aq)(+) enclosed by walls of carborane anions. Three different types of H(aq)(+) clusters are found in these tubes: a symmetrical H(13)O(6)(+) ion with an unusually elongated Zundel-type H(5)O(2)(+) core, two hydrated H(7)O(3)(+) ions, and an unprecedented H(17)O(8)(+) ion having a nearly square core. All of the H(aq)(+) cations show unexpectedly longer O...O separations than in discrete H(aq)(+) ions, indicating greater delocalization of positive charge. The centrosymmetric H(aq)(+) ions are linked via short H bonds, forming a true one-dimensional proton wire.

Orientational dynamics and dielectric response of nanopore water

We present numerical calculations, simulation results, and analytical considerations for the frequency-dependent dielectric constant of single-file water in narrow nanopores, described by a recently developed dipole lattice model. We find Debye relaxation over all length scales with relaxation times that strongly depend on pore length. This behavior is analyzed in terms of the dynamics of orientational defects leading to simple quantitative expressions for the static dielectric susceptibility and the relaxation time in the limits of short and long pores. Based on these formulas, we suggest how the predicted macroscopic order of nanopore water can be probed via dielectric spectroscopy and explain how the excitation energy, diffusion constant, and effective interaction of the defects that destroy the order can be extracted from such measurements.

Kinetic gating of the proton pump in cytochrome c oxidase

Cytochrome c oxidase (CcO), the terminal enzyme of the respiratory chain, reduces oxygen to water and uses the released energy to pump protons across a membrane. Here, we use kinetic master equations to explore the energetic and kinetic control of proton pumping in CcO. We construct models consistent with thermodynamic principles, the structure of CcO, experimentally known proton affinities, and equilibrium constants of intermediate reactions. The resulting models are found to capture key properties of CcO, including the midpoint redox potentials of the metal centers and the electron transfer rates. We find that coarse-grained models with two proton sites and one electron site can pump one proton per electron against membrane potentials exceeding 100 mV. The high pumping efficiency of these models requires strong electrostatic couplings between the proton loading (pump) site and the electron site (heme a), and kinetic gating of the internal proton transfer. Gating is achieved by enhancing the rate of proton transfer from the conserved Glu-242 to the pump site on reduction of heme a, consistent with the predictions of the water-gated model of proton pumping. The model also accounts for the phenotype of D-channel mutations associated with loss of pumping but retained turnover. The fundamental mechanism identified here for the efficient conversion of chemical energy into an electrochemical potential should prove relevant also for other molecular machines and novel fuel-cell designs.

A one-dimensional dipole lattice model for water in narrow nanopores

We present a recently developed one-dimensional dipole lattice model that accurately captures the key properties of water in narrow nanopores. For this model, we derive three equivalent representations of the Hamiltonian that together yield a transparent physical picture of the energetics of the water chain and permit efficient computer simulations. In the charge representation, the Hamiltonian consists of nearest-neighbor interactions and Coulomb-like interactions of effective charges at the ends of dipole ordered segments. Approximations based on the charge picture shed light on the influence of the Coulomb-like interactions on the structure of nanopore water. We use Monte Carlo simulations to study the system behavior of the full Hamiltonian and its approximations as a function of chemical potential and system size and investigate the bimodal character of the density distribution occurring at small system sizes.

Interaction Site Preference between Carbon Nanotube and Nifedipine: A Combined Density Functional Theory and Classical Molecular Dynamics Study

A novel hybrid density functional theory, MPWB1K, was firstly employed to investigate static adsorptions of a nifedipine on a (10,10) type of single-walled carbon nanotube (SWCNT), which was modeled by C(200)H(40) and C(280) respectively. For both SWCNT models the internal adsorption is more stable than the external adsorption in a range of 5.3-7.8 kcal/mol, which indicates that a nifedipine has a preference to internally adsorb on the (10,10) SWCNT. Molecular dynamic simulations were then used to predict the dynamic behaviors of a nifedipine and the (10, 10) SWCNT system in both gas phase and aqueous solution. The classical MD simulations show that for both cases a nifedipine could spontaneously encapsulate into the SWCNT and migrate in a surprising oscillation behavior inside the SWCNT, however, both phenomena are significantly delayed in the presence of water molecules. The present study suggests that the nanotube network may be used as an efficient tool for transporting this kind of calcium channel antagonists.

Carbon nanotube based artificial water channel protein: membrane perturbation and water transportation

We functionalized double-walled carbon nanotubes (DWCNTs) as artificial water channel proteins. For the first time, molecular dynamics simulations show that the bilayer structure of DWCNTs is advantageous for carbon nanotube based transmembrane channels. The shielding of the amphiphilic outer layer could guarantee biocompatibility of the synthetic channel and protect the inner tube (functional part) from disturbance of the membrane environment. This novel design could promote more sophisticated nanobiodevices which could function in a bioenvironment with high biocompatibility.

Fluorescent single walled carbon nanotube/silica composite materials

We present a new approach for the preparation of single walled carbon nanotube silica composite materials that retain the intrinsic fluorescence characteristics of the encapsulated nanotubes. Incorporation of isolated nanotubes into optically transparent matrices, such as sol-gel prepared silica, to take advantage of their near-infrared emission properties for applications like sensing has been a challenging task. In general, the alcohol solvents and acidic conditions required for typical sol-gel preparations disrupt the nanotube/surfactant assembly and cause the isolated nanotubes to aggregate leading to degradation of their fluorescence properties. To overcome these issues, we have used a sugar alcohol modified silica precursor molecule, diglycerylsilane, for encapsulation of nanotubes in silica under aqueous conditions and at neutral pH. The silica/nanotube composite materials have been prepared as monoliths, at least 5 mm thick, or as films (<1 mm) and were characterized using fluorescence and Raman spectroscopy. In the present work we have investigated the fluorescence characteristics of the silica encapsulated carbon nanotubes by means of redox doping studies as well as demonstrated their potential for biosensing applications. Such nanotube/silica composite systems may allow for new sensing and imaging applications that are not currently achievable.

Macroscopically ordered water in nanopores

Water confined into the interior channels of narrow carbon nanotubes or transmembrane proteins forms collectively oriented molecular wires held together by tight hydrogen bonds. Here, we explore the thermodynamic stability and dipolar orientation of such 1D water chains from nanoscopic to macroscopic dimensions. We show that a dipole lattice model accurately recovers key properties of 1D confined water when compared to atomically detailed simulations. In a major reduction in computational complexity, we represent the dipole model in terms of effective Coulombic charges, which allows us to study pores of macroscopic lengths in equilibrium with a water bath (or vapor). We find that at ambient conditions, the water chains filling the tube are essentially continuous up to macroscopic dimensions. At reduced water vapor pressure, we observe a 1D Ising-like filling/emptying transition without a true phase transition in the thermodynamic limit. In the filled state, the chains of water molecules in the tube remain dipole-ordered up to macroscopic lengths of approximately 0.1 mm, and the dipolar order is estimated to persist for times up to approximately 0.1 s. The observed dipolar order in continuous water chains is a precondition for the use of nanoconfined 1D water as mediator of fast long-range proton transport, e.g., in fuel cells. For water-filled nanotube bundles and membranes, we expect anti-ferroelectric behavior, resulting in a rich phase diagram similar to that of a 2D Coulomb gas.

Strongly anisotropic orientational relaxation of water molecules in narrow carbon nanotubes and nanorings

Molecular dynamics simulations of the orientational dynamics of water molecules confined in narrow carbon nanotubes and nanorings reveal that confinement leads to strong anisotropy in the orientational relaxation. The relaxation of the aligned dipole moments, occurring on a time scale of nanoseconds, is 3 orders of magnitude slower than that of bulk water. In contrast, the relaxation of the vector joining the two hydrogens is ten times faster compared to bulk, with a time scale of about 150 fs. The slow dipolar relaxation is mediated by the hopping of orientational defects, which are nucleated by the water molecules outside the tube, across the linear water chain.