Molybdenum disulfide (MoS 2 ) is a layered material with outstanding electrical and optical properties. Numerous studies evaluate the performance in sensors, catalysts, batteries, and composites that can benefit from guidance by simulations in all-atom resolution. However, molecular simulations remain difficult due to lack of reliable models. We introduce an interpretable force field for MoS 2 with record performance that reproduces structural, interfacial, and mechanical properties in 0.1% to 5% agreement with experiments. The model overcomes structural instability, deviations in interfacial and mechanical properties by several 100%, and empirical fitting protocols in earlier models. It is compatible with several force fields for molecular dynamics simulation, including the interface force field (IFF), CVFF, DREIDING, PCFF, COMPASS, CHARMM, AMBER, and OPLS-AA. The parameters capture polar covalent bonding, X-ray structure, cleavage energy, infrared spectra, bending stability, bulk modulus, Young's modulus, and contact angles with polar and nonpolar solvents. We utilized the models to uncover the binding mechanism of peptides to the MoS 2 basal plane. The binding strength of several 7mer and 8mer peptides scales linearly with surface contact and replacement of surface-bound water molecules, and is tunable in a wide range from −86 to −6 kcal mol −1 . The binding selectivity is multifactorial, including major contributions by van-der-Waals coordination and charge matching of certain side groups, orientation of hydrophilic side chains towards water, and conformation flexibility. We explain the relative attraction and role of the 20 amino acids using computational and experimental data. The force field can be used to screen and interpret the assembly of MoS 2 -based nanomaterials and electrolyte interfaces up to a billion atoms with high accuracy, including multiscale simulations from the quantum scale to the microscale.
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Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials
The earlier integration of validated Lennard–Jones (LJ) potentials for 8 fcc metals into materials and biomolecular force fields has advanced multiple research fields, for example, metal–electrolyte interfaces, recognition of biomolecules, colloidal assembly of metal nanostructures, alloys, and catalysis. Here we introduce 12-6 and 9-6 LJ parameters for classical all-atom simulations of 10 further fcc metals (Ac, Ca (α), Ce (γ), Es (β), Fe (γ), Ir, Rh, Sr (α), Th (α), Yb (β)) and stainless steel. The parameters reproduce lattice constants, surface energies, water interfacial energies, and interactions with (bio)organic molecules in 0.1 to 5% agreement with experiment, as well as qualitative mechanical properties under standard conditions. Deviations are reduced up to a factor of one hundred in comparison to earlier Lennard–Jones parameters, embedded atom models, and density functional theory. We also explain a quantitative correlation between atomization energies from experiments and surface energies that supports parameter development. The models are computationally very efficient and applicable to an exponential space of alloys. Compatibility with a wide range of force fields such as the Interface force field (IFF), AMBER, CHARMM, COMPASS, CVFF, DREIDING, OPLS-AA, and PCFF enables reliable simulations of nanostructures up to millions of atoms and microsecond time scales. User-friendly model building and input generation are available in the CHARMM-GUI Nanomaterial Modeler. As a limitation, deviations in mechanical properties vary and are comparable to DFT methods. We discuss the incorporation of reactivity and features of the electronic structure to expand the range of applications and further increase the accuracy.
more » « less- NSF-PAR ID:
- 10211803
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- npj Computational Materials
- Volume:
- 7
- Issue:
- 1
- ISSN:
- 2057-3960
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Cation‐π interactions are noncovalent interactions between a π‐electron system and a positively charged ion that are regarded as a strong noncovalent interaction and are ubiquitous in biological systems. Similarly, though less studied, anion‐ring interactions are present in proteins along with in‐plane interactions of anions with aromatic rings. As these interactions are between a polarizing ion and a polarizable π system, the accuracy of the treatment of these interactions in molecular dynamics (MD) simulations using additive force fields (FFs) may be limited. In the present work, to allow for a better description of ion‐π interactions in proteins in the Drude‐2013 protein polarizable FF, we systematically optimized the parameters for these interactions targeting model compound quantum mechanical (QM) interaction energies with atom pair‐specific Lennard‐Jones parameters along with virtual particles as selected ring centroids introduced to target the QM interaction energies and geometries. Subsequently, MD simulations were performed on a series of protein structures where ion‐π pairs occur to evaluate the optimized parameters in the context of the Drude‐2013 FF. The resulting FF leads to a significant improvement in reproducing the ion‐π pair distances observed in experimental protein structures, as well as a smaller root‐mean‐square differences and fluctuations of the overall protein structures from experimental structures. Accordingly, the optimized Drude‐2013 protein polarizable FF is suggested for use in MD simulations of proteins where cation‐π and anion‐ring interactions are critical. © 2019 Wiley Periodicals, Inc.
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The potential energy curves (PECs) for the homonuclear He–He, Ar–Ar, Cu–Cu, and Si–Si dimers, as well as heteronuclear Cu–He, Cu–Ar, Cu–Xe, Si–He, Si–Ar, and Si–Xe dimers, are obtained in quantum Monte Carlo (QMC) calculations. It is shown that the QMC method provides the PECs with an accuracy comparable with that of the state-of-the-art coupled cluster singles and doubles with perturbative triples corrections [CCSD(T)] calculations. The QMC data are approximated by the Morse long range (MLR) and (12-6) Lennard-Jones (LJ) potentials. The MLR and LJ potentials are used to calculate the deflection angles in binary collisions of corresponding atom pairs and transport coefficients of Cu and Si vapors and their mixtures with He, Ar, and Xe gases in the range of temperature from 100 K to 10 000 K. It is shown that the use of the LJ potentials introduces significant errors in the transport coefficients of high-temperature vapors and gas mixtures. The mixtures with heavy noble gases demonstrate anomalous behavior when the viscosity and thermal conductivity can be larger than that of the corresponding pure substances. In the mixtures with helium, the thermal diffusion factor is found to be unusually large. The calculated viscosity and diffusivity are used to determine parameters of the variable hard sphere and variable soft sphere molecular models as well as parameters of the power-law approximations for the transport coefficients. The results obtained in the present work include all information required for kinetic or continuum simulations of dilute Cu and Si vapors and their mixtures with He, Ar, and Xe gases.more » « less
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The abundance and isotopic composition of noble gases dissolved in water have many applications in the geosciences. In recent years, new analytical techniques have opened the door to the use of high-precision measurements of noble gas isotopes as tracers for groundwater hydrology, oceanography, mantle geochemistry, and paleoclimatology. These analytical advances have brought about new measurements of solubility equilibrium isotope effects (SEIEs) in water (i.e., the relative solubilities of noble gas isotopes) and their sensitivities to the temperature and salinity. Here, we carry out a suite of classical molecular dynamics (MD) simulations and employ the theoretical method of quantum correction to estimate SEIEs for comparison with experimental observations. We find that classical MD simulations can accurately predict SEIEs for the isotopes of Ar, Kr, and Xe to order 0.01‰, on the scale of analytical uncertainty. However, MD simulations consistently overpredict the SEIEs of Ne and He by up to 40% of observed values. We carry out sensitivity tests at different temperatures, salinities, and pressures and employ different sets of interatomic potential parameters and water models. For all noble gas isotopes, the TIP4P water model is found to reproduce observed SEIEs more accurately than the SPC/E and TIP4P/ice models. Classical MD simulations also accurately capture the sign and approximate magnitude of temperature and salinity sensitivities of SEIEs for heavy noble gases. We find that experimental and modeled SEIEs generally follow an inverse-square mass dependence, which implies that the mean-square force experienced by a noble gas atom within a solvation shell is similar for all noble gases. This inverse-square mass proportionality is nearly exact for Ar, Kr, and Xe isotopes, but He and Ne exhibit a slightly weaker mass dependence. We hypothesize that the apparent dichotomy between He–Ne and Ar–Kr–Xe SEIEs may result from atomic size differences, whereby the smaller noble gases are more likely to spontaneously fit within cavities of water without breaking water–water H-bonds, thereby experiencing softer collisions during translation within a solvation shell. We further speculate that the overprediction of simulated He and Ne SEIEs may result from the neglection of higher-order quantum corrections or the overly stiff representation of van der Waals repulsion by the widely used Lennard-Jones 6–12 potential model. We suggest that new measurements of SEIEs of heavy and light noble gases may represent a novel set of constraints with which to refine hydrophobic solvation theories and optimize the set of interatomic potential models used in MD simulations of water and noble gases.more » « less
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null (Ed.)The Interface force field (IFF) enables accurate simulations of bulk and interfacial properties of compounds and multiphase materials. However, the simulation of reactions and mechanical properties up to failure remains challenging and expensive. Here we introduce the Reactive Interface Force Field (IFF-R) to analyze bond breaking and failure of complex materials using molecular dynamics simulations. IFF-R uses a Morse potential instead of a harmonic potential as typically employed in molecular dynamics force fields to describe the bond energy, which can render any desired bond reactive by specification of the curve shape of the potential energy and the bond dissociation energy. This facile extension of IFF and other force fields that utilize a harmonic bond energy term allows the description of bond breaking without loss in functionality, accuracy, and speed. The method enables quantitative, on-the-fly computations of bond breaking and stress-strain curves up to failure in any material. We illustrate accurate predictions of mechanical behavior for a variety of material systems, including metals (iron), ceramics (carbon nanotubes), polymers (polyacrylonitrile and cellulose I\b{eta}), and include sample parameters for common bonds based on using experimental and high-level (MP2) quantum mechanical reference data. Computed structures, surface energies, elastic moduli, and tensile strengths are in excellent agreement with available experimental data. Non-reactive properties are shown to be essentially identical to IFF values. Computations are approximately 50 times faster than using ReaxFF and require only a single set of parameters. Compatibility of IFF and IFF-R with biomolecular force fields allows the quantitative analysis of the mechanics of proteins, DNA, and other biological molecules.more » « less
