Water conduction through the hydrophobic channel of a carbon nanotube
TL;DR: Observations suggest that carbon nanotubes, with their rigid nonpolar structures, might be exploited as unique molecular channels for water and protons, with the channel occupancy and conductivity tunable by changes in the local channel polarity and solvent conditions.
Abstract: Confinement of matter on the nanometre scale can induce phase transitions not seen in bulk systems1. In the case of water, so-called drying transitions occur on this scale2,3,4,5 as a result of strong hydrogen-bonding between water molecules, which can cause the liquid to recede from nonpolar surfaces to form a vapour layer separating the bulk phase from the surface6. Here we report molecular dynamics simulations showing spontaneous and continuous filling of a nonpolar carbon nanotube with a one-dimensionally ordered chain of water molecules. Although the molecules forming the chain are in chemical and thermal equilibrium with the surrounding bath, we observe pulse-like transmission of water through the nanotube. These transmission bursts result from the tight hydrogen-bonding network inside the tube, which ensures that density fluctuations in the surrounding bath lead to concerted and rapid motion along the tube axis7,8,9. We also find that a minute reduction in the attraction between the tube wall and water dramatically affects pore hydration, leading to sharp, two-state transitions between empty and filled states on a nanosecond timescale. These observations suggest that carbon nanotubes, with their rigid nonpolar structures10,11, might be exploited as unique molecular channels for water and protons, with the channel occupancy and conductivity tunable by changes in the local channel polarity and solvent conditions.
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TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.
14,558 citations
Cites background from "Water conduction through the hydrop..."
...Cumulant expansions [76,79,62,41] are an effective approximation for the exponential average; since the lower-order terms of the expansion are less influenced by statistical error, the systematic error introduced by truncating the higher order terms may be considerably smaller than the statistical error which would be introduced by including them....
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TL;DR: Some of the science and technology being developed to improve the disinfection and decontamination of water, as well as efforts to increase water supplies through the safe re-use of wastewater and efficient desalination of sea and brackish water are highlighted.
Abstract: One of the most pervasive problems afflicting people throughout the world is inadequate access to clean water and sanitation. Problems with water are expected to grow worse in the coming decades, with water scarcity occurring globally, even in regions currently considered water-rich. Addressing these problems calls out for a tremendous amount of research to be conducted to identify robust new methods of purifying water at lower cost and with less energy, while at the same time minimizing the use of chemicals and impact on the environment. Here we highlight some of the science and technology being developed to improve the disinfection and decontamination of water, as well as efforts to increase water supplies through the safe re-use of wastewater and efficient desalination of sea and brackish water.
6,967 citations
TL;DR: Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand to find the best docked pose using a model energy function that combines empirical and force-field-based terms.
Abstract: Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses The very best candidates are further refined via a Monte Carlo sampling of pose conformation; in some cases, this is crucial to obtaining an accurate docked pose Selection of the best docked pose uses a model energy function that combines empirical and force-field-based terms Docking accuracy is assessed by redocking ligands from 282 cocrystallized PDB complexes starting from conformationally optimized ligand geometries that bear no memory of the correctly docked pose Errors in geometry for the top-ranked pose are less than 1 A in nearly ha
6,828 citations
TL;DR: Enrichment results demonstrate the importance of the novel XP molecular recognition and water scoring in separating active and inactive ligands and avoiding false positives.
Abstract: A novel scoring function to estimate protein-ligand binding affinities has been developed and implemented as the Glide 4.0 XP scoring function and docking protocol. In addition to unique water desolvation energy terms, protein-ligand structural motifs leading to enhanced binding affinity are included: (1) hydrophobic enclosure where groups of lipophilic ligand atoms are enclosed on opposite faces by lipophilic protein atoms, (2) neutral-neutral single or correlated hydrogen bonds in a hydrophobically enclosed environment, and (3) five categories of charged-charged hydrogen bonds. The XP scoring function and docking protocol have been developed to reproduce experimental binding affinities for a set of 198 complexes (RMSDs of 2.26 and 1.73 kcal/mol over all and well-docked ligands, respectively) and to yield quality enrichments for a set of fifteen screens of pharmaceutical importance. Enrichment results demonstrate the importance of the novel XP molecular recognition and water scoring in separating active and inactive ligands and avoiding false positives.
4,666 citations
References
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NEC1
TL;DR: Iijima et al. as mentioned in this paper reported the preparation of a new type of finite carbon structure consisting of needle-like tubes, which were produced using an arc-discharge evaporation method similar to that used for fullerene synthesis.
Abstract: THE synthesis of molecular carbon structures in the form of C60 and other fullerenes1 has stimulated intense interest in the structures accessible to graphitic carbon sheets. Here I report the preparation of a new type of finite carbon structure consisting of needle-like tubes. Produced using an arc-discharge evaporation method similar to that used for fullerene synthesis, the needles grow at the negative end of the electrode used for the arc discharge. Electron microscopy reveals that each needle comprises coaxial tubes of graphitic sheets, ranging in number from 2 up to about 50. On each tube the carbon-atom hexagons are arranged in a helical fashion about the needle axis. The helical pitch varies from needle to needle and from tube to tube within a single needle. It appears that this helical structure may aid the growth process. The formation of these needles, ranging from a few to a few tens of nanometres in diameter, suggests that engineering of carbon structures should be possible on scales considerably greater than those relevant to the fullerenes. On 7 November 1991, Sumio Iijima announced in Nature the preparation of nanometre-size, needle-like tubes of carbon — now familiar as 'nanotubes'. Used in microelectronic circuitry and microscopy, and as a tool to test quantum mechanics and model biological systems, nanotubes seem to have unlimited potential.
39,086 citations
"Water conduction through the hydrop..." refers background in this paper
...These observations suggest that carbon nanotubes, with their rigid nonpolar structure...
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TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
Abstract: Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P. Comparisons are made with experimental thermodynamic and structural data including the recent neutron diffraction results of Thiessen and Narten. The computed densities and potential energies are in reasonable accord with experiment except for the original BF model, which yields an 18% overestimate of the density and poor structural results. The TIPS2 and TIP4P potentials yield oxygen–oxygen partial structure functions in good agreement with the neutron diffraction results. The accord with the experimental OH and HH partial structure functions is poorer; however, the computed results for these functions are similar for all the potential functions. Consequently, the discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons are also made for self‐diffusion coefficients obtained from molecular dynamics simulations. Overall, the SPC, ST2, TIPS2, and TIP4P models give reasonable structural and thermodynamic descriptions of liquid water and they should be useful in simulations of aqueous solutions. The simplicity of the SPC, TIPS2, and TIP4P functions is also attractive from a computational standpoint.
33,683 citations
"Water conduction through the hydrop..." refers background in this paper
...Solvated in a cubic box with 1,034 TIP3P water molecule...
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TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
Abstract: In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints The influence of coupling time constants on dynamical variables is evaluated A leap‐frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath
25,256 citations
"Water conduction through the hydrop..." refers methods in this paper
...Molecular dynamics simulations were performed at constant pressur...
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TL;DR: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms.
Abstract: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms. Timings and accuracies are presented for three large crystalline ionic systems.
24,332 citations
"Water conduction through the hydrop..." refers background in this paper
...0 (University of California at San Francisco), with particle-mesh Ewald electrostatic...
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TL;DR: Weiner et al. as mentioned in this paper derived a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases.
Abstract: We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body force field is the successor to the Weiner et al. force field and was developed with some of the same philosophies, such as the use of a simple diagonal potential function and electrostatic potential fit atom centered charges. The need for a 10-12 function for representing hydrogen bonds is no longer necessary due to the improved performance of the new charge model and new van der Waals parameters. These new charges are determined using a 6-31G* basis set and restrained electrostatic potential (RESP) fitting and have been shown to reproduce interaction energies, free energies of solvation, and conformational energies of simple small molecules to a good degree of accuracy. Furthermore, the new RESP charges exhibit less variability as a function of the molecular conformation used in the charge determination. The new van der Waals parameters have been derived from liquid simulations and include hydrogen parameters which take into account the effects of any geminal electronegative atoms. The bonded parameters developed by Weiner et al. were modified as necessary to reproduce experimental vibrational frequencies and structures. Most of the simple dihedral parameters have been retained from Weiner et al., but a complex set of 4 and yj parameters which do a good job of reproducing the energies of the low-energy conformations of glycyl and alanyl dipeptides has been developed for the peptide backbone.
12,660 citations
"Water conduction through the hydrop..." refers background in this paper
...086 kcal mol -1 , corresponding to sp 2 carbons in the AMBER96 force fiel...
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