skip to main content


The NSF Public Access Repository (NSF-PAR) system and access will be unavailable from 11:00 PM ET on Thursday, June 13 until 2:00 AM ET on Friday, June 14 due to maintenance. We apologize for the inconvenience.

Title: Organic contaminants and atmospheric nitrogen at the graphene–water interface: a simulation study
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 of 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.  more » « less
Award ID(s):
Author(s) / Creator(s):
; ;
Date Published:
Journal Name:
Nanoscale Advances
Page Range / eLocation ID:
1741 to 1757
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. This data set for the manuscript entitled "Design of Peptides that Fold and Self-Assemble on Graphite" 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.

    Version: 2.0

    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.

    Conventions Used in These Files

    Structure Files
    - graph_*.psf or sol_*.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.)

    - graph_*.pdb or sol_*.pdb (initial coordinates before equilibration)
    - repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl)
    - freeTop_*.pdb (same as the above pdb files, but the carbons of the lower graphene layer have been placed at a single z value and marked for restraints in NAMD)
    - amber_*.prmtop (combined topology and parameter files for Amber force field simulations)
    - repart_amber_*.prmtop (same as the above prmtop files, but the masses of non-water hydrogen atoms have been repartitioned by ParmEd)

    Force Field Parameters
    CHARMM format parameter files:
    - par_all36m_prot.prm (CHARMM36m FF for proteins)
    - par_all36_cgenff_no_nbfix.prm (CGenFF v4.4 for graphene) The NBFIX parameters are commented out since they are only needed for aromatic halogens and we use only the CG2R61 type for graphene.
    - toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out)

    Template NAMD Configuration Files
    These contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):
    - template_min.namd (minimization)
    - template_eq.namd (NPT equilibration with lower graphene fixed)
    - template_abf.namd (for adaptive biasing force)

    - namd/min_*.0.namd

    - namd/eq_*.0.namd

    Adaptive biasing force calculations
    - namd/eabfZRest7_graph_chp1404.0.namd
    - namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)

    Log Files
    For each NAMD configuration file given in the last two sections, there is a log file with the same prefix, which gives the text output of NAMD. For instance, the output of namd/eabfZRest7_graph_chp1404.0.namd is eabfZRest7_graph_chp1404.0.log.

    Simulation Output
    The simulation output files (which match the names of the NAMD configuration files) are in the output/ directory. Files with the extensions .coor, .vel, and .xsc are coordinates in NAMD binary format, velocities in NAMD binary format, and extended system information (including cell size) in text format. Files with the extension .dcd give the trajectory of the atomic coorinates over time (and also include system cell information). Due to storage limitations, large DCD files have been omitted or replaced with new DCD files having the prefix stride50_ including only every 50 frames. The time between frames in these files is 50 * 50000 steps/frame * 4 fs/step = 10 ns. The system cell trajectory is also included for the NPT runs are output/eq_*.xst.

    Files with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening. If there are scripts with step1_*.sh and step2_*.sh, they are intended to be run in order, with step1_*.sh first.


    The directory contents are as follows. The directories Sim_Figure-1 and Sim_Figure-8 include README.txt files that describe the files and naming conventions used throughout this data set.

    Sim_Figure-1: Simulations of N-acetylated C-amidated amino acids (Ac-X-NHMe) at the graphite–water interface.

    Sim_Figure-2: Simulations of different peptide designs (including acyclic, disulfide cyclized, and N-to-C cyclized) at the graphite–water interface.

    Sim_Figure-3: MM-GBSA calculations of different peptide sequences for a folded conformation and 5 misfolded/unfolded conformations.

    Sim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.

    Sim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 295 K.

    Sim_Figure-5_replica: Temperature replica exchange molecular dynamics simulations for the peptide cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) with 20 replicas for temperatures from 295 to 454 K.

    Sim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).

    Sim_Figure-7: Free energy calculations for folding, adsorption, and pairing for the peptide CHP1404 (sequence: cyc(GTGSGTG-GPGG-GCGTGTG-SGPG)). For folding, we calculate the PMF as function of RMSD by replica-exchange umbrella sampling (in the subdirectory Folding_CHP1404_Graphene/). We make the same calculation in solution, which required 3 seperate replica-exchange umbrella sampling calculations (in the subdirectory Folding_CHP1404_Solution/). Both PMF of RMSD calculations for the scrambled peptide are in Folding_scram1404/. For adsorption, calculation of the PMF for the orientational restraints and the calculation of the PMF along z (the distance between the graphene sheet and the center of mass of the peptide) are in Adsorption_CHP1404/ and Adsorption_scram1404/. The actual calculation of the free energy is done by a shell script ("") in the 1_free_energy/ subsubdirectory. Processing of the PMFs must be done first in the 0_pmf/ subsubdirectory. Finally, files for free energy calculations of pair formation for CHP1404 are found in the Pair/ subdirectory.

    Sim_Figure-8: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) where the peptides are far above the graphene–water interface in the initial configuration.

    Sim_Figure-9: Two replicates of a simulation of nine peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.

    Sim_Figure-9_scrambled: Two replicates of a simulation of nine peptide molecules with the control sequence cyc(GGTPTTGGGGGGSGGPSGTGGC) at the graphite–water interface at 370 K.

    Sim_Figure-10: Adaptive biasing for calculation of the free energy of the folded peptide as a function of the angle between its long axis and the zigzag directions of the underlying graphene sheet.


    This material is based upon work supported by the US 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), which is supported by National Science Foundation grant number ACI-1548562, through allocation BIO200030. 
    more » « less
  2. Sum frequency generation (SFG) * Equal contributors. spectroscopy was used to deduce the orientation of the terminal methyl (CH 3 ) group of self-assembled monolayers (SAMs) at the air–solid and air–liquid interfaces at surface concentrations as low as 1% protonated molecules in the presence of 99% deuterated molecules. The SFG spectra of octadecanethiol (ODT) and deuterated octadecanethiol (d 37 ODT) SAMs on gold were used for analysis at the air–solid interface. However, the eicosanoic acid (EA) and deuterated EA (d 39 EA) SAMs on the water were analyzed at the air–liquid interface. The tilt angle of the terminal CH 3 group was estimated to be ∼39 ° for a SAM of 1% ODT : 99% d 37 ODT, whereas the tilt angle of the terminal CH 3 group of the 1% EA : 99% d 39 EA monolayer was estimated to be ∼32 °. The reliability of the orientational analysis at low concentrations was validated by testing the sensitivity of the SFG spectroscopy. A signal-to-noise (S/N) ratio of ∼60 and ∼45 was obtained for the CH 3 symmetric stretch (SS) of 1% ODT : 99% d 37 ODT and 1% EA : 99% d 39 EA, respectively. The estimated increase in S/N ratio values, as a measure of the sensitivity of the SFG spectroscopy, verified the capacity to acquire the SFG spectra at low concentrations of interfacial molecules under ambient conditions. Overall, the orientational analysis of CH 3 SS vibrational mode was feasible at low concentrations of protonated molecules due to increased S/N ratio. In support, the improved S/N ratio on varying incident power density of the visible beam was also experimentally demonstrated. 
    more » « less
  3. The impacts of wildfires along the wildland urban interface (WUI) on atmospheric particulate concentrations and composition are an understudied source of air pollution exposure. To assess the residual impacts of the 2021 Marshall Fire (Colorado), a wildfire that predominantly burned homes and other human-made materials, on homes within the fire perimeter that escaped the fire, we performed a combination of fine particulate matter (PM2.5) filter sampling and chemical analysis, indoor dust collection and chemical analysis, community scale PurpleAir PM2.5 analysis, and indoor particle number concentration measurements. Following the fire, the chemical speciation of dust collected in smoke-affected homes in the burned zone showed elevated concentrations of the biomass burning marker levoglucosan (medianlevo = 4147 ng g−1), EPA priority toxic polycyclic aromatic hydrocarbons (median Σ16PAH = 1859.3 ng g−1), and metals (median Σ20Metals = 34.6 mg g−1) when compared to samples collected in homes outside of the burn zone 6 months after the fire. As indoor dust particles are often resuspended and can become airborne, the enhanced concentration of hazardous metals and organics within dust samples may pose a threat to human health. Indoor airborne particulate organic carbon (median = 1.91 μg m−3), particulate elemental carbon (median = .02 μg m−3), and quantified semi-volatile organic species in PM2.5 were found in concentrations comparable to ambient air in urban areas across the USA. Particle number and size distribution analysis at a heavily instrumented supersite home located immediately next to the burned area showed indoor particulates in low concentrations (below 10 μg m−3) across various sizes of PM (12 nm–20 μm), but were elevated by resuspension from human activity, including cleaning. 
    more » « less
  4. Scented wax products, such as candles and wax warmers/melts, are popular fragranced consumer products that are commonly used in residential buildings. As scented wax products are intentionally fragranced to produce pleasant smellscapes for occupants, they may represent an important source of volatile organic compounds (VOCs) to indoor atmospheres. The aim of this study is to evaluate terpene emission factors (EFs) and inhalation intake fractions (iFs) for scented wax products to better understand their impact on indoor chemistry and chemical exposures. Full-scale emission experiments were conducted in the Purdue zEDGE Test House using a variety of scented candles (n = 5) and wax warmers/melts (n = 14) under different outdoor air exchange rates (AERs). Terpene concentrations were measured in real-time using a proton transfer reaction time-of-flight mass spectrometer (PTR-TOF-MS). PTR-TOF-MS measurements revealed that scented candle and wax warmer/melt products emit a variety of monoterpenes (C10H16) and oxygen-containing monoterpenoids (C10H14O, C10H16O, C10H18O, C10H20O), with peak concentrations in the range of 10^−1 to 10^2 ppb. Monoterpene EFs were much greater for scented wax warmers/melts (C10H16 EFs ~ 10^2 mg per g wax consumed) compared to scented candles (C10H16 EFs ~ 10^−1 to 100 mg per g wax consumed). Significant emissions of reactive terpenes from both products, along with nitrogen oxides (NO, NO2) from candles, depleted indoor ozone (O3) concentrations. Terpene iFs were similar between the two products (iFs ~ 10^3 ppm) and increased with decreasing outdoor AER. Terpene iFs during concentration decay periods were similar to, or greater than, iFs during active emission periods for outdoor AERs ≤ 3.0 h^−1. Overall, scented wax warmers/melts were found to release greater quantities of monoterpenes compared to other fragranced consumer products used in the home, including botanical disinfectants, hair care products, air fresheners, and scented sprays. 
    more » « less
    more » « less