Computational Study of H2O Adsorption, Hydrolysis, and Water Splitting on (ZnO)3 Nanoclusters Deposited on Graphene and Graphene Oxides.

Graphene and graphene oxide (GO)-based metal oxides could play an important role in using metal oxide like zinc oxide (ZnO) as photocatalysts to split water. The π conjugation structure of GO shows greater electron mobility and could enhance the photocatalytic performance of the bare ZnO catalyst by increasing the electron-hole separation. In this work, we use density functional theory (DFT) with the B3LYP exchange functional and DGDZVP2 basis set to study the impact of adsorbing (ZnO)3 nanoparticles on graphene and four different GO models (GO1, GO2, GO4, and GO5) on the hydration and hydrolysis of water that precedes water splitting to produce H2 and O2 atoms in the gas phase and compare them with our previous studies on the bare catalyst in the absence of the substrate. The potential energy curves and activation energies are similar, but the triplet states are lower in energy than the singlet states in contrast to the bare (ZnO)3 catalyst. We extend our calculations to water splitting from the hydrolyzed (ZnO)3 on GO1 (GO1-(ZnO)3). The triplet state energy remains lower than the singlet state energy, and hydrogen production precedes the formation of oxygen, but there is no energy inter-crossing during the formation of O2 that occurs in the absence of a GO1 substrate. Although the hydrolysis reaction pathway follows similar steps in both the bare and GO1-(ZnO)3, water splitting with (ZnO)3 absorbed on the GO1 substrate skips two steps as it proceeds toward the production of the second H2. The production of two hydrogen molecules precedes oxygen formation during water splitting, and the first Zn-H bond formation step is the rate-determining step. The ZnO trimer deposited on GO systems could be potentially attractive nanocatalysts for water splitting.

Exchange Functionals and Basis Sets for Density Functional Theory Studies of Water Splitting on Selected ZnO Nanocluster Catalysts.

In this communication, we use density functional theory (DFT) to study the structural (geometry) and electronic properties (vertical detachment energy and electron affinity) of ZnO monomers and dimers that can be used to form ZnO clusters of different sizes, with a view to adapting one or more of them as catalysts or photocatalysts, standing alone or on suitable substrates like graphene, to split water. We also investigate different pairs of exchange functionals and basis sets to optimize their choice in our DFT calculations and to compare the singlet-triplet energy gaps of small ZnO clusters of different sizes to select an optimal cluster size for water splitting. We find that the B3LYP/DGDZVP2 exchange functional/basis set is a reliable combination for use with DFT to calculate the geometry and electronic properties of small ZnO nanoclusters from among several other combinations of exchange functionals and basis sets. Comparisons of the singlet-triplet energy gaps show that the trimer (ZnO)3 has an energy gap of 58.66 k cal/mol. which is approximately equal to the energy of a visible photon at a wavelength of 500 nm, and a HOMO-LUMO gap of 4.4 eV, making it a suitable choice of photocatalyst for the oxidation of water from among six (ZnO) n nanoclusters of monomers, with n ranging from 1 to 6. We used this exchange functional/basis set to study the structural and energetic details of hydration and hydrolysis of water absorbed on the (ZnO)3 nanocatalyst and calculated the corresponding potential energy profiles to identify three sets of singlet-triplet pathways for water splitting. Detailed study of a pathway showed that oxygen is produced after hydrogen, and the rate-determining step is the formation of hydrogen.

Theoretical study of the stability, structure, and optical spectra of small silver clusters and their formation using density functional theory.

An understanding of the mechanism of formation of small clusters would help to identify efficient routes to their synthesis. Here, we apply density functional theory (DFT) to study the free energies and structure of ultra-small silver clusters, and time-dependent density functional theory (TDDFT) to calculate their UV-Vis spectra and provide a better understanding of the intermediate steps in cluster formation in the gas phase and solution. Our calculations of the optical properties of neutral and cationic clusters confirm the presence of charged and uncharged intermediates observed in pulse radiolysis experiments during the early stages of the growth of silver clusters. The free energies of formation of hydrated clusters extracted from DFT calculations reveal the greater thermodynamic stability of cationic clusters compared to the corresponding neutral clusters of the same composition. This is consistent with the predominance of kinetically stable cationic clusters observed in pulse radiolysis experiments. Our DFT and TDDFT calculations clarify the effects of ligand, hydration, and oxidation states on the structure, stability, and optical properties of silver clusters that elucidate the mechanism of silver cluster formation in solution and the gas phase.

Light-Nucleotide versus Ion-Nucleotide Interactions for Single-Nucleotide Resolution.

Several parallel reads of ionic currents through multiple CsgG nanopores provide information about ion-nucleotide interactions for sequencing single-stranded DNA (ss-DNA) using base-calling algorithms. However, the information in ion-nucleotide interactions seems insufficient for single-read nanopore DNA sequencing. Here we report discriminative light-nucleotide interactions calculated from density functional theory (DFT), which are compared with ionic currents obtained from molecular dynamics (MD) simulations. The MD simulations were performed on a system containing a transverse nanochannel and a longitudinal solid state nanopore. We show that both of the transverse and longitudinal ionic currents during the translocation of A16, G16, T16, and C16 through the nanopore, overlapped widely. On the other hand, the UV-vis and Raman spectra of different types of single nucleotides, nucleosides, and nucleobases show relatively higher resolution than the ionic currents. Light-nucleotide interactions provide better information for characterizing the nucleotides in comparison to ion-nucleotide interactions for nanopore DNA sequencing. This can be realized by using optical techniques including surface-enhanced Raman spectroscopy (SERS) or tip-enhanced Raman spectroscopy (TERS), while plasmon excitation can be used to localize light and control the rate of nucleotide flow.

Water-Mediated Interactions Determine Helix Formation of Peptides in Open Nanotubes.

Water-mediated interactions (WMIs) play diverse roles in molecular biology. They are particularly relevant in geometrically confined spaces such as the interior of the chaperonin, at the interface between ligands and their binding partners, and in the ribosome tunnel. Inspired in part by the geometry of the ribosome tunnel, we consider confinement effects on the stability of peptides. We describe results from replica exchange molecular dynamics simulations of a system containing a 23-alanine or 23-serine polypeptide confined to nonpolar and polar nanotubes in the gas phase and when open to a water reservoir. We quantify the effect of water in determining the preferred conformational states of these polypeptides by calculating the difference in the solvation free energy for the helix and coil states in the open nanotube in the two phases. Our simulations reveal several possibilities. We find that nanoscopic confinement preferentially stabilizes the helical state of polypeptides with hydrophobic side chains, which is explained by the entropic stabilization mechanism proposed on the basis of polymer physics. Polypeptide chains with hydrophilic side chains can adopt helical structures within nanotubes, but helix formation is sensitive to the nature of the nanotube due to WMIs. We elaborate on the potential implications of our findings to the stability of peptides in the ribosome tunnel.

Reverse Translocation of Nucleotides through a Carbon Nanotube.

We report molecular dynamics (MD) simulations of the reverse translocation of single nucleotides through a narrow carbon nanotube (CNT), with a diameter of 1.36 nm, immersed in a 1 M KCl electrolyte solution under an applied electric field along the tube axis. We observe ion selectivity by the narrow CNT, which leads to a high flow of K+ ions, in contrast to a negligible and opposing current of Cl- ions. The K+ ions, driven by the electric field, force a negatively charged single nucleotide into the narrow CNT where it is trapped by the incoming K+ ions and water molecules, and the nucleotide is driven in the same direction as the K+ ions. This illustrates a novel mechanism of nucleotide reverse translocation that is controlled by ion selectivity. An increase in the CNT diameter to 2.71 nm or an increase in nucleotide chain length both lead to translocation in the normal direction of the applied field. The reverse translocation rate of single nucleotides is correlated to the ionic current of K+ ions in the narrow tube, unlike translocation in the normal direction in the wider tube.

Thermodynamics of Helix-Coil Transitions of Polyalanine in Open Carbon Nanotubes.

Understanding structure formation in polypeptide chains and synthetic polymers encapsulated in pores is important in biology and nanotechnology. We present replica exchange molecular dynamics studies of the phase diagram for α-helix formation of capped polyalanine in nanotubes (NT) open to a water reservoir as a function of the NT diameter and hydrophobicity. A helix forms only in a narrow range of diameters, which surprisingly is comparable to the width of the ribosome tunnel. Increasing the hydrophobicity enhances helicity in the NT. Helix formation in polyalanine is driven by a small negative enthalpy and a positive entropy change at ≈300 K, in contrast to the large negative entropy change that destabilizes the helix and favors the coiled state in bulk water. There is an anticorrelation between water density inside the nanotube and structure formation. Confinement-induced helix formation depends on amino acid sequence. There is complete absence of helix in polyglutamine and polyserine confined to a open carbon nanotube.

Proton transfer and the diffusion of H+ and OH- ions along water wires.

Hydrogen and hydroxide ion transport in narrow carbon nanotubes (CNTs) of diameter 8.1 Å and lengths up to 582 Å are investigated by molecular dynamics simulations using a dissociating water model. The diffusion coefficients of the free ions in an open chain are significantly larger than in periodically replicated wires that necessarily contain D or L end defects, and both are higher than they are in bulk water. The free hydroxide ion diffuses faster than the free hydronium ion in short CNTs, unlike diffusion in liquid water, and both coefficients increase and converge to nearly the same value with increasing tube length. The diffusion coefficients of the two ions increase further when the tubes are immersed in a water reservoir and they move easily out of the tube, suggesting an additional pathway for proton transport via OH(-) ions in biological channels.

Entropy of single-file water in (6,6) carbon nanotubes.

We used molecular dynamics simulations to investigate the thermodynamics of filling of a (6,6) open carbon nanotube (diameter D = 0.806 nm) solvated in TIP3P water over a temperature range from 280 K to 320 K at atmospheric pressure. In simulations of tubes with slightly weakened carbon-water attractive interactions, we observed multiple filling and emptying events. From the water occupancy statistics, we directly obtained the free energy of filling, and from its temperature dependence the entropy of filling. We found a negative entropy of about -1.3 k(B) per molecule for filling the nanotube with a hydrogen-bonded single-file chain of water molecules. The entropy of filling is nearly independent of the strength of the attractive carbon-water interactions over the range studied. In contrast, the energy of transfer depends strongly on the carbon-water attraction strength. These results are in good agreement with entropies of about -0.5 k(B) per water molecule obtained from grand-canonical Monte Carlo calculations of water in quasi-infinite tubes in vacuum under periodic boundary conditions. Overall, for realistic carbon-water interactions we expect that at ambient conditions filling of a (6,6) carbon nanotube open to a water reservoir is driven by a favorable decrease in energy, and opposed by a small loss of water entropy.

Proton transfer and the mobilities of the H+ and OH- ions from studies of a dissociating model for water.

Hydrogen (H(+)) and hydroxide (OH(-)) ions in aqueous solution have anomalously large diffusion coefficients, and the mobility of the H(+) ion is nearly twice that of the OH(-) ion. We describe molecular dynamics simulations of a dissociating model for liquid water based on scaling the interatomic potential for water developed by Ojamäe-Shavitt-Singer from ab initio studies at the MP2 level. We use the scaled model to study proton transfer that occurs in the transport of hydrogen and hydroxide ions in acidic and basic solutions containing 215 water molecules. The model supports the Eigen-Zundel-Eigen mechanism of proton transfer in acidic solutions and the transient hyper-coordination of the hydroxide ion in weakly basic solutions at room temperature. The free energy barriers for proton transport are low indicating significant proton delocalization accompanying proton transfer in acidic and basic solutions. The reorientation dynamics of the hydroxide ion suggests changes in the proportions of hyper-coordinated species with temperature. The mobilities of the hydrogen and hydroxide ions and their temperature dependence between 0 and 50 °C are in excellent agreement with experiment and the reasons for the large difference in the mobilities of the two ions are discussed. The model and methods described provide a novel approach to studies of liquid water, proton transfer, and acid-base reactions in aqueous solutions, channels, and interfaces.

Water in the polar and nonpolar cavities of the protein interleukin-1ß.

Water in the protein interior serves important structural and functional roles and is also increasingly recognized as a relevant factor in drug binding. The nonpolar cavity in the protein interleukin-1ß has been reported to be filled by water on the basis of some experiments and simulations and to be empty on the basis of others. Here we study the thermodynamics of filling the central nonpolar cavity and the four polar cavities of interleukin-1ß by molecular dynamics simulation. We use different water models (TIP3P and SPC/E) and protein force fields (amber94 and amber03) to calculate the semigrand partition functions term by term that quantify the hydration equilibria. We consistently find that water in the central nonpolar cavity is thermodynamically unstable, independent of force field and water model. The apparent reason is the relatively small size of the cavity, with a volume less than ∼80 Å(3). Our results are consistent with the most recent X-ray crystallographic and simulation studies but disagree with an earlier interpretation of nuclear magnetic resonance (NMR) experiments probing protein-water interactions. We show that, at least semiquantitatively, the measured nuclear Overhauser effects indicating the proximity of water to the methyl groups lining the nonpolar cavity can, in all likelihood, be attributed to interactions with buried and surface water molecules near the cavity. The same methods applied to determine the occupancy of the polar cavities show that they are filled by the same number of water molecules observed in crystallography, thereby validating the theoretical and simulation methods used to study the water occupancy in the nonpolar protein cavity.

Reaction coordinates for electron transfer reactions.

The polarization fluctuation and energy gap formulations of the reaction coordinate for outer sphere electron transfer are linearly related to the constant energy constraint Lagrangian multiplier m in Marcus' theory of electron transfer. The quadratic dependence of the free energies of the reactant and product intermediates on m and m+1, respectively, leads to similar dependence of the free energies on the reaction coordinates and to the same dependence of the activation energy on the reorganization energy and the standard reaction free energy. Within the approximations of a continuum model of the solvent and linear response of the longitudinal polarization to the electric field in Marcus' theory, both formulations of the reaction coordinate are expected to lead to the same results.

Water in nonpolar confinement: from nanotubes to proteins and beyond.

Water molecules confined to nonpolar pores and cavities of nanoscopic dimensions exhibit highly unusual properties. Water filling is strongly cooperative, with the possible coexistence of filled and empty states and sensitivity to small perturbations of the pore polarity and solvent conditions. Confined water molecules form tightly hydrogen-bonded wires or clusters. The weak attractions to the confining wall, combined with strong interactions between water molecules, permit exceptionally rapid water flow, exceeding expectations from macroscopic hydrodynamics by several orders of magnitude. The proton mobility along 1D water wires also substantially exceeds that in the bulk. Proteins appear to exploit these unusual properties of confined water in their biological function (e.g., to ensure rapid water flow in aquaporins or to gate proton flow in proton pumps and enzymes). The unusual properties of water in nonpolar confinement are also relevant to the design of novel nanofluidic and molecular separation devices or fuel cells.

Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion.

Water expulsion from the protein core is a key step in protein folding. Nevertheless, unusually large water clusters confined into the nonpolar cavities have been observed in the X-ray crystal structures of tetrabrachion, a bacterial protein that is thermostable up to at least 403 K (130 degrees C). Here, we use molecular dynamics (MD) simulations to investigate the structure and thermodynamics of water filling the largest cavity of the right-handed coiled-coil stalk of tetrabrachion at 365 K (92 degrees C), the temperature of optimal bacterial growth, and at room temperature (298 K). Hydrogen-bonded water clusters of seven to nine water molecules are found to be thermodynamically stable in this cavity at both temperatures, confirming the X-ray studies. Stability, as measured by the transfer free energy of the optimal size cluster, decreases with increasing temperature. Water filling is thus driven by the energy of transfer and opposed by the transfer entropy, both depending only weakly on temperature. Our calculations suggest that cluster formation becomes unfavorable at approximately 384 K (110 degrees C), signaling the onset of drying just slightly above the temperature of optimal growth. "Drying" thus precedes protein denaturation. At room temperature, the second largest cavity in tetrabrachion accommodates a five water molecule cluster, as reported in the X-ray studies. However, the simulations show that at 365 K the cluster is unstable and breaks up. We suggest that the large hydrophobic cavities may act as binding sites for two proteases, possibly explaining the unusual thermostability of the resulting protease-stalk complexes (up to approximately 393 K, 120 degrees C).

Structural and dynamic properties of concentrated alkali halide solutions: a molecular dynamics simulation study.

The physicochemical properties of alkali halide solutions have long been attributed to the collective interactions between ions and water molecules in the solution, yet the structure of water in these systems and its effect on the equilibrium and dynamic properties of these systems are not clearly understood. Here, we present a systematic view of water structure in concentrated alkali halide solutions using molecular dynamics simulations. The results of the simulations show that the size of univalent ions in the solution has a significant effect on the dynamics of ions and other transport properties such as the viscosity that are correlated with the structural properties of water in aqueous ionic solution. Small cations (e.g., Li+) form electrostatically stabilized hydrophilic hydration shells that are different from the hydration shells of large ions (e.g., Cs+) which behave more like neutral hydrophobic particles, encapsulated by hydrogen-bonded hydration cages. The properties of solutions with different types of ion solvation change in different ways as the ion concentration increases. Examples of this are the diffusion coefficients of the ions and the viscosities of solutions. In this paper we use molecular dynamics (MD) simulations to study the changes in the equilibrium and transport properties of LiCl, RbCl, and CsI solutions at concentrations from 0.22 to 3.97 M.

Water between plates in the presence of an electric field in an open system.

Molecular dynamics simulations of water at 298 K and 1 atm of pressure are used to investigate the electric-field dependence of the density and polarization density of water between two graphite-like plates of different sizes (9.8 x 9.2 and 17.7 x 17.2 A) in an open system for plate separations of 8.0, 9.5, and 16.4 A. The interactions with water were tuned to "hard-wall-like" and "normal" C-O hydrophobic potentials. Water between the larger plates at 16.4 A separation is layered but is metastable with respect to capillary evaporation at zero field (Bratko, D.; Curtis, R. A.; Blanch, H. W.; Prausnitz, J. M. J. Chem. Phys. 2001, 115, 3873). Applying a field decreases the density of the water between the plates, in apparent contradiction to thermodynamic and integral equation theories of bulk fluid electrostriction that ignore surface effects, rendering them inapplicable to finite-sized films of water between hydrophobic plates. This suggests that the free energy barrier for evaporation is lowered by the applied field. Water, between "hard-wall-like" plates at narrower separations of 9.5 A and less, shows a spontaneous but incomplete evaporation at zero field within the time scale of our simulation. Evaporation is further enhanced by an electric field. No such evaporation occurs, on these time scales, for the smaller plates with the "hard-wall-like" potential at a separation of 8.0 A at zero field, signaling a crossover in behavior as the plate dimension decreases, but the water density still diminishes with increasing field strength. These observations could have implications for the behavior of thin films of water between surfaces in real physical and biological systems.

Water clusters in nonpolar cavities.

We explore the structure and thermodynamics of water clusters confined in nonpolar cavities. By calculating the grand-canonical partition function term by term, we show that small nonpolar cavities can be filled at equilibrium with highly structured water clusters. The structural and thermodynamic properties of these encapsulated water clusters are similar to those observed experimentally in the gas phase. Water filling is highly sensitive to the size of the cavity and the strength of the interactions with the cavity wall. Water penetration into pores can thus be modulated by small changes in the polarity and structure of the cavity. Implications on water penetration into proteins are discussed.

Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes.

Water molecules in the narrow cylindrical pore of a (6,6) carbon nanotube form single-file chains with their dipoles collectively oriented either up or down along the tube axis. We study the interaction of such water chains with homogeneous electric fields for finite closed and infinite periodically replicated tubes. By evaluating the grand-canonical partition function term-by-term, we show that homogeneous electric fields favor the filling of previously empty nanotubes with water from the bulk phase. A two-state description of the collective water dipole orientation in the nanotube provides an excellent approximation for the dependence of the water-chain polarization and the filling equilibrium on the electric field. The energy and entropy contributions to the free energy of filling the nanotube were determined from the temperature dependence of the occupancy probabilities. We find that the energy of transfer depends sensitively on the water-tube interaction potential, and that the entropy of one-dimensionally ordered water chains is comparable to that of bulk water. We also discuss implications for proton transfer reactions in biology.