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  1. Ordered nanoscale patterns have been observed by atomic force microscopy at graphene–water and graphite–water interfaces. The two dominant explanations for these patterns are that (i) they consist of self-assembled organic contaminants or (ii) they are dense layers formed from atmospheric gases (especially nitrogen). Here we apply molecular dynamics simulations to study the behavior of dinitrogen and possible organic contaminants at the graphene–water interface. Despite the high concentration of N 2 in ambient air, we find that its expected occupancy at the graphene–water interface is quite low. Although dense (disordered) aggregates of dinitrogen have been observed in previous simulations, our results suggest that they are stable only in the presence of supersaturated aqueous N 2 solutions and dissipate rapidly when they coexist with nitrogen gas near atmospheric pressure. On the other hand, although heavy alkanes are present at only trace concentrations (micrograms per cubic meter) in typical indoor air, we predict that such concentrations can be sufficient to form ordered monolayers that cover the graphene–water interface. For octadecane, grand canonical Monte Carlo suggests nucleation and growth of monolayers above an ambient concentration near 6 μg m −3 , which is less than some literature values for indoor air. The thermodynamics ofmore »the formation of these alkane monolayers includes contributions from the hydration free-energy (unfavorable), the free-energy of adsorption to the graphene–water interface (highly favorable), and integration into the alkane monolayer phase (highly favorable). Furthermore, the peak-to-peak distances in AFM force profiles perpendicular to the interface (0.43–0.53 nm), agree with the distances calculated in simulations for overlayers of alkane-like molecules, but not for molecules such as N 2 , water, or aromatics. Taken together, these results suggest that ordered domains observed on graphene, graphite, and other hydrophobic materials in water are consistent with alkane-like molecules occupying the interface.« less
    Free, publicly-accessible full text available March 29, 2023
  2. Abstract
    <p>This data set provides files needed to run the simulations described in the manuscript entitled &#34;Organic contaminants and atmospheric nitrogen at the graphene–water interface: A simulation study&#34; using the molecular dynamics software NAMD and LAMMPS. The output of the simulations, as well as scripts used to analyze this output, are also included. The files are organized into directories corresponding to the figures of the main text and supplementary information. They include molecular model structure files (NAMD psf), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD or LAMMPS configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and some trajectories in dcd format (downsampled). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts. A modified LAMMPS C&#43;&#43; source file is also included.</p>
    Other
    This material is based upon work supported by the National Science Foundation under Grant No. DMR-1945589. A majority of the computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CHE-1726332, CNS-1006860, EPS-1006860, and EPS-0919443. This work used the Extreme Science and Engineering Discovery Environment (XSEDE) andMore>>
  3. Abstract
    <p>This data set for the manuscript entitled &#34;Design of Peptides that Fold and Self-Assemble on Graphite&#34; includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software NAMD, as well as the output of the simulations. The files are organized into directories corresponding to the figures of the main text and supporting information. They include molecular model structure files (NAMD psf or Amber prmtop format), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled to 10 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included.</p> <p>Version: 2.0</p> <p>Changes versus version 1.0 are the addition of the free energy of folding, adsorption, and pairing calculations (Sim_Figure-7) and shifting of the figure numbers to accommodate this addition.</p> <p><br /> Conventions Used in These Files<br /> &#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;</p> <p>Structure Files<br /> ----------------<br /> - graph_*.psf or sol_*.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass),More>>
  4. Free, publicly-accessible full text available February 1, 2023
  5. Hydration layers are formed on hydrophilic crystalline surfaces immersed in water. Their existence has also been predicted for hydrophobic surfaces, yet the experimental evidence is controversial. Using 3D-AFM imaging, we probed the interfacial water structure of hydrophobic and hydrophilic surfaces with atomic-scale spatial resolution. We demonstrate that the atomic-scale structure of interfacial water on crystalline surfaces presents two antagonistic arrangements. On mica, a common hydrophilic crystalline surface, the interface is characterized by the formation of 2 to 3 hydration layers separated by approximately 0.3 nm. On hydrophobic surfaces such as graphite or hexagonal boron nitride (h-BN), the interface is characterized by the formation of 2 to 4 layers separated by about 0.5 nm. The latter interlayer distance indicates that water molecules are expelled from the vicinity of the surface and replaced by hydrocarbon molecules. This creates a new 1.5–2 nm thick interface between the hydrophobic surface and the bulk water. Molecular dynamics simulations reproduced the experimental data and confirmed the above interfacial water structures.