When Szent-Gyorgyi called water the “matrix of life”,1 he was echoing an old sentiment. Paracelsus in the 16th century said that “water was the matrix of the world and of all its creatures.”2 But Paracelsus’s notion of a matrixsan active substance imbued with fecund, life-giving propertiess was quite different from the picture that, until very recently, molecular biologists have tended to hold of water’s role in the chemistry of life. Although acknowledging that liquid water has some unusual and important physical and chemical propertiessits potency as a solvent, its ability to form hydrogen bonds, its amphoteric naturesbiologists have regarded it essentially as the backdrop on which life’s molecular components are arrayed. It used to be common practice, for example, to perform computer simulations of biomolecules in a vacuum. Partly this was because the computational intensity of simulating a polypeptide chain was challenging even without accounting for solvent molecules too, but it also reflected the prevailing notion that water does little more than temper or moderate the basic physicochemical interactions responsible for molecular biology. What Gerstein and Levitt said 9 years ago remains true today: “When scientists publish models of biological molecules in journals, they usually draw their models in bright colors and place them against a plain, black background”.3 Curiously, this neglect of water as an active component of the cell went hand in hand with the assumption that life could not exist without it. That was basically an empirical conclusion derived from our experience of life on Earth: environments without liquid water cannot sustain life, and special strategies are needed to cope with situations in which, because of extremes of either heat or cold, the liquid is scarce.4-6 The recent confirmation that there is at least one world rich in organic molecules on which rivers and perhaps shallow seas or bogs are filled with nonaqueous fluidsthe liquid hydrocarbons of Titan7smight now bring some focus, even urgency, to the question of whether water is indeed a * E-mail: p.ball@nature.com. Philip Ball is a science writer and a consultant editor for Nature, where he worked as an editor for physical sciences for more than 10 years. He holds a Ph.D. in physics from the University of Bristol, where he worked on the statistical mechanics of phase transitions in the liquid state. His book H2O: A Biography of Water (Weidenfeld & Nicolson, 1999) was a survey of the current state of knowledge about the behavior of water in situations ranging from planetary geomorphology to cell biology. He frequently writes about aspects of water science for both the popular and the technical media.

https://www.philipball.co.uk/images/stories/docs/pdf/ChemRev_final.pdf

Water as an Active Constituent in Cell Biology

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.

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Water in Nonpolar Confinement: From Nanotubes to Proteins and Beyond *

In this critical review we survey non-covalent interactions of carbon nanotubes with molecular species from a chemical perspective, particularly emphasising the relationship between the structure and dynamics of these structures and their functional properties. We demonstrate the synergistic character of the nanotube–molecule interactions, as molecules that affect nanotube properties are also altered by the presence of the nanotube. The diversity of mechanisms of molecule–nanotube interactions and the range of experimental techniques employed for their characterisation are illustrated by examples from recent reports. Some practical applications for carbon nanotubes involved in non-covalent interactions with molecules are discussed.

Noncovalent interactions of molecules with single walled carbon nanotubes

Large-scale storage of renewable energy in the form of hydrogen (H2) fuel via electrolytic water splitting requires the development of water oxidation catalysts that are efficient and abundant. Carbon-based nanomaterials such as carbon nanotubes have attracted significant applications for use as substrates for anchoring metal-based nanoparticles. We show that, upon mild surface oxidation, hydrothermal annealing and electrochemical activation, multiwall carbon nanotubes (MWCNTs) themselves are effective water oxidation catalysts, which can initiate the oxygen evolution reaction (OER) at overpotentials of 0.3 V in alkaline media. Oxygen-containing functional groups such as ketonic C═O generated on the outer wall of MWCNTs are found to play crucial roles in catalyzing OER by altering the electronic structures of the adjacent carbon atoms and facilitates the adsorption of OER intermediates. The well-preserved microscopic structures and highly conductive inner walls of MWCNTs enable efficient transport of the electrons generated during OER.

Electrocatalytic oxygen evolution at surface-oxidized multiwall carbon nanotubes

Experimental results have shown that CO2 electroreduction is sensitive to the surface morphology of Cu electrodes. We used density functional theory (DFT) to evaluate the thermodynamics and kinetics of CO2 reduction pathways on Cu(100) and Cu(111) with the aim of understanding the experimentally reported differences in CO2 reduction products. Results suggest that the hydrogenation of CO* to hydroxymethylidyne (COH*) or formyl (CHO*) is a key selective step. Cu(111) favors COH* formation, through which methane and ethylene are produced via a common CH2 species under high overpotential (<−0.8 V vs RHE). On Cu(100), formation of CHO* is preferred and ethylene formation goes through C–C coupling of two CHO* species followed by a series of reduction steps of the C2 intermediates, under relatively lower overpotential (−0.4 to −0.6 V vs RHE). Further reduction of these C2 intermediates, however, require larger potentials (∼−1.0 V vs RHE) and conflicts with the experimentally observed low potential pathway to C2 ...

Facet Dependence of CO2 Reduction Paths on Cu Electrodes

We present the first experimental vibrational spectroscopy study providing direct evidence of a water phase inside single-walled carbon nanotubes that exhibits an unusual form of hydrogen-bonding due to confinement. Water adopts a stacked-ring structure inside nanotubes, forming intra- and inter-ring hydrogen bonds. The intra-ring hydrogen bonds are bulk-like while the inter-ring hydrogen bonds are relatively weak, having a distorted geometry that gives rise to a distinct OH stretching mode. The experimentally observed infrared mode at 3507 cm-1 is assigned to vibrations of the inter-ring OH-groups based on detailed atomic-level modeling. The direct observation of unusual hydrogen bonding in nanotubes has potential implications for water in other highly confined systems, such as biological channels and nanoporous media.

Unusual Hydrogen Bonding in Water-Filled Carbon Nanotubes

We present theoretical and experimental evidence for CO(2) adsorption on different sites of single walled carbon nanotube (SWNT) bundles. We use local density approximation density functional theory (LDA-DFT) calculations to compute the adsorption energies and vibrational frequencies for CO(2) adsorbed on SWNT bundles. The LDA-DFT calculations give a range of shifts for the asymmetric stretching mode from about -6 to -20 cm(-1) for internally bound CO(2), and a range from -4 to -16 cm(-1) for externally bound CO(2) at low densities. The magnitude of the shift is larger for CO(2) adsorbed parallel to the SWNT surface; various perpendicular configurations yield much smaller theoretical shifts. The asymmetric stretching mode for CO(2) adsorbed in groove sites and interstitial sites exhibits calculated shifts of -22.2 and -23.8 cm(-1), respectively. The calculations show that vibrational mode softening is due to three effects: (1) dynamic image charges in the nanotube; (2) the confining effect of the adsorption potential; (3) dynamic dipole coupling with other adsorbate molecules. Infrared measurements indicate that two families of CO(2) adsorption sites are present. One family, exhibiting a shift of about -20 cm(-1) is assigned to internally bound CO(2) molecules in a parallel configuration. This type of CO(2) is readily displaced by Xe, a test for densely populated adsorbed species, which are expected to be present on the highest adsorption energy sites in the interior of the nanotubes. The second family exhibits a shift of about -7 cm(-1) and the site location and configuration for these species is ambiguous, based on comparison with the theoretical shifts. The population of the internally bound CO(2) may be enhanced by established etching procedures that open the entry ports for adsorption, namely, ozone oxidation followed by annealing in vacuum at 873 K. Xenon displacement experiments indicate that internally bound CO(2) is preferentially displaced relative to the -7 cm(-1) shifted species. The -7 cm(-1) shifted species is assigned to CO(2) adsorbed on the external surface based on results from etching and Xe displacement experiments.

Vibrational behavior of adsorbed CO2 on single-walled carbon nanotubes.

Ozone is known to react with single-walled nanotubes (SWNTs) to form oxide species on the nanotubes and, upon annealing, to etch the SWNTs. However, the mechanism of ozone attack is not known. We use gradient-corrected density functional theory to compute the potential energy surfaces for O3 dissociation on the sidewall of a pristine (8,8) SWNT. Two decomposition pathways were considered; the first involves the formation of a Criegee intermediate, with a barrier of 17 kcal/mol, followed by transformations leading to lactone, quinone, and carbonyl functional groups. The activation barriers for these transformations are below 23 kcal/mol. The cleavage of the lactone group, evolving CO and CO2, have barrier heights of 39.4 and 49.3 kcal/mol, respectively. This agrees well with experimental findings that the evolution of CO2 and CO occur at 600 K. The second decomposition pathway involves the direct cleavage of the ozonide, forming a singlet O2 and an ether or epoxide group on the SWNT. This pathway competes ...

Ozone Oxidation of Single Walled Carbon Nanotubes from Density Functional Theory

The development of longitudinal optical−transverse optical (LO−TO) modes in CF4 has been studied experimentally and theoretically as a function of dimensionality. Infrared absorption experiments for CF4 adsorbed on single-walled carbon nanotubes indicate a lack of LO−TO splitting at low coverage and a gradual appearance of LO−TO modes as the coverage of CF4 on the nanotubes is increased. We have performed density functional perturbation theory calculations for the vibrational frequencies, IR absorption spectra, and phonon density of states for CF4 in one, two, and three dimensions. The calculations demonstrate that LO−TO splitting in 1D is qualitatively different from that computed for 2D or the bulk. The magnitude of the splitting in 1D is about one-half that computed for the bulk, and the LO mode is very weakly blue-shifted in 1D. We predict that the phonon density of states changes dramatically as the dimensionality of the crystal is changed. This prediction can be tested experimentally via inelastic n...

Wai-Leung Yim

Papers

Unusual Hydrogen Bonding in Water-Filled Carbon Nanotubes

Vibrational behavior of adsorbed CO2 on single-walled carbon nanotubes.

Ozone Oxidation of Single Walled Carbon Nanotubes from Density Functional Theory

Dimensional effects on the LO-TO splitting in CF4: first-principles and infrared absorption studies