Molecular dynamics and Monte Carlo simulations often rely on Lennard-Jones (LJ) potentials for nonbond interactions. We present 12-6 and 9-6 LJ parameters for several face-centered cubic metals (Ag, Al, Au, Cu, Ni, Pb, Pd, Pt) which reproduce densities, surface tensions, interface properties with water and (bio)organic molecules, as well as mechanical properties in quantitative (<0.1%) to good qualitative (25%) agreement with experiment under ambient conditions. Deviations associated with earlier LJ models have been reduced by 1 order of magnitude due to the precise fit of the new models to densities and surface tensions under standard conditions, which also leads to significantly improved results for surface energy anisotropies, interface tensions, and mechanical properties. The performance is comparable to tight-binding and embedded atom models at up to a million times lower computational cost. The models extend classical simulation methods to metals and a variety of interfaces with biopolymers, surfactants, and other nanostructured materials through compatibility with widely used force fields, including AMBER, CHARMM, COMPASS, CVFF, OPLS-AA, and PCFF. Limitations include the neglect of electronic structure effects and the restriction to noncovalent interactions with the metals.

We investigated molecular interactions involved in the selective binding of several short peptides derived from phage-display techniques (8−12 amino acids, excluding Cys) to surfaces of Au, Pd, and Pd−Au bimetal. The quantitative analysis of changes in energy and conformation upon adsorption on even {111} and {100} surfaces was carried out by molecular dynamics simulation using an efficient computational screening technique, including 1000 explicit water molecules and physically meaningful peptide concentrations at pH = 7. Changes in chain conformation from the solution to the adsorbed state over the course of multiple nanoseconds suggest that the peptides preferably interact with vacant sites of the face-centered cubic lattice above the metal surface. Residues that contribute to binding are in direct contact with the metal surfaces, and less-binding residues are separated from the surface by one or two water layers. The strength of adsorption ranges from 0 to −100 kcal/(mol peptide) and scales with the surface energy of the metal (Pd surfaces are more attractive than Au surfaces), the affinity of individual residues versus the affinity of water, and conformation aspects, as well as polarization and charge transfer at the metal interface (only qualitatively considered here). A hexagonal spacing of ∼1.6 Å between available lattice sites on the {111} surfaces accounts for the characteristic adsorption of aromatic side groups and various other residues (including Tyr, Phe, Asp, His, Arg, Asn, Ser), and a quadratic spacing of ∼2.8 Å between available lattice sites on the {100} surface accounts for a significantly lower affinity to all peptides in favor of mobile water molecules. The combination of these factors suggests a “soft epitaxy” mechanism of binding. On a bimetallic Pd−Au {111} surface, binding patterns are similar, and the polarity of the bimetal junction can modify the binding energy by ∼10 kcal/mol. The results are semiquantitatively supported by experimental measurements of the affinity of peptides and small molecules to metal surfaces as well as results from quantum-mechanical calculations on small peptide and surface fragments. Interfaces were modeled using the consistent valence force field extended for Lennard-Jones parameters for fcc metals which accurately reproduce surface and interface energies [Heinz, H.; Vaia, R. A.; Farmer, B. L.; Naik, R. R. J. Phys. Chem. C 2008, 112, 17281−17290].

Layered silicates are widely used in nanotechnology and composite materials. We describe a force field for phyllosilicates (mica, montmorillonite, and pyrophyllite) on the basis of physically justified atomic charges, van der Waals parameters, vibrational constants, and distributions of charge defects in agreement with solid state 29 Si NMR data. Unit cell parameters deviate only ∼0.5% relative to experimental X-ray measurements and surface (respectively cleavage) energies deviate less than 10% from experimental data, including the partition between Coulomb and van der Waals contributions. Reproduction of surface energies facilitates quantitative simulations of hybrid interfaces with water, organics, and biomolecules for which accurate force fields are available. Parameters are consistent with the force fields PCFF (polymer consistent force field), CVFF (consistent valence force field), CHARMM (chemistry at Harvard macromolecular mechanics), and GROMACS (Groningen machine for chemical simulations). As an example of interest, we investigate the structure and dynamics of octadecylammonium montmorillonite ("C 18 "-montmorillonite, cation exchange capacity ) 91 mmol/100 g) by molecular dynamics simulation. The surfactant chains assemble essentially as a bilayer with minimal interpenetration within the gallery while the ammonium headgroups are hydrogen-bonded to cavities in the montmorillonite surface. In contrast to quaternary ammonium ions, no rearrangements on the surface have been observed (cavity crossing barrier >5 kcal/mol). The alkyl chains are in a liquidlike state with approximately 30% gauche conformations, in agreement with previous Fourier-transform infrared and solid-state NMR measurements. Computed X-ray diffraction patterns of sodium and C 18 -montmorillonite agree very well with X-ray patterns from experiment, and the computational model can assist in the assignment of complex reflections.

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Molecular modeling of thermosetting polymers has been presented with special emphasis on building atomistic models. Different approaches to build highly cross-linked polymer networks are discussed. A multistep relaxation procedure for relaxing the molecular topology during cross-linking is proposed. This methodology is then applied to an epoxy-based thermoset (EPON-862/DETDA). Several materials properties such as density, glass transition temperature, thermal expansion coefficient, and volume shrinkage during curing are calculated and found to be in good agreement with experimental results. Along with the material's properties, the simulations also highlight the distribution of molecular weight buildup and inception of gel point during the network formation.

The structure and dynamics of alkylammonium-modified montmorillonites with different cation exchange capacity (CEC), ammonium head groups, and chain length is investigated by molecular dynamics simulation for a large set of structures and compared to a wide array of experimental data. In the 44 systems, the relationship between computational (molecular dynamics) and experimental data (X-ray, IR, NMR, and DSC) was found to be very complementary. Much of the properties appear to be dictated through the inorganic-organic interface, which in addition to electrostatic interactions involves hydrogen bonds between primary ammonium head groups (NH 3 + -R) and oxygen on the silicate surface (O•••H distance ∼150 pm) or flexibly attached quaternary ammonium head groups (NMe 3 + -R) of higher lateral mobility (O•••H distance ∼290 pm). The gauche content is a function of the packing density of the head groups on the surface, the preferred orientation of the head groups, and the interlayer density of the alkyl chains. These effects cause up to 45% gauche conformations as compared to only 5% gauche conformations in chains with crystalline order. A low CEC leads to stepwise increases of the basal plane spacing with increasing chain length, corresponding to the subsequent formation of alkyl monolayers, bilayers, trilayers, etc., while a high CEC leads to a continuous increase in basal plane spacing with increasing chain length. The density of the organic interlayer space between two silicate layers shows minima for emerging new layers of alkyl chains and maxima for densely packed layers. These fluctuations decrease as the number of layers increases. On an isolated clay mineral surface, layer formation of the surfactants is also found and lateral 2D diffusion constants range from 5 × 10 -6 cm 2 /s to <10 -9 cm 2 /s depending on the structure of the surfactant.

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Carbon nanotubes (CNT) and graphene are considered as potential future candidates for many nano/microscale integrated devices due to their superior thermal properties. Both systems, however, exhibit significant anisotropy in their thermal conduction, limiting their performance as three-dimensional thermal transport materials. From thermal management perspective, one way to tailor this anisotropy is to consider designing alternative carbon-based architectures. This paper investigates the thermal transport in one such novel architecture-a pillared-graphene (PG) network nanostructure which combines graphene sheets and carbon nanotubes to create a three-dimensional network. Nonequilibrium molecular dynamics simulations have been carried out using the AIREBO potential to calculate the thermal conductivity of pillared-graphene structures along parallel (in-plane) as well as perpendicular (out-of-plane) directions with respect to the graphene plane. The resulting thermal conductivity values for PG systems are discussed and compared with simulated values for pure CNT and graphite. Our results show that in these PG structures, the thermal transport is governed by the minimum interpillar distance and the CNT-pillar length. This is primarily attributed to scattering of phonons occurring at the CNT-graphene junctions in these nanostructures. We foresee that such architecture could potentially be used as a template for designing future structurally stable microscale systems with tailorable in-plane and out-of-plane thermal transport.