Yongsheng Leng

Hydration structure of water confined between mica surfaces

We report further molecular dynamics simulations on the structure of bound hydration layers under extreme confinement between mica surfaces. We find that the liquid phase of water is maintained down to 2 monolayer (ML) thick, whereas the structure of the K(+) ion hydration shell is close to the bulk structure even under D = 0.92 nm confinement. Unexpectedly, the density of confined water remains approximately the bulk value or less, whereas the diffusion of water molecules decreases dramatically. Further increase in confinement leads to a transition to a bilayer ice, whose density is much less than that of ice Ih due to the formation of a specific hydrogen-bonding network.

Molecular dynamics simulations of stretched gold nanowires: The relative utility of different semiempirical potentials

The mechanical elongation of a finite gold nanowire has been studied by molecular dynamics simulations using different semiempirical potentials for transition metals. These potentials have been widely used to study the mechanical properties of finite metal clusters. Combining with density functional theory calculations along several atomic-configuration trajectories predicted by different semiempirical potentials, the authors conclude that the second-moment approximation of the tight-binding scheme (TB-SMA) potential is the most suitable one to describe the energetics of finite Au clusters. They find that for the selected geometries of Au wires studied in this work, the ductile elongation of Au nanowires along the [001] direction predicted by the TB-SMA potential is largely independent of temperature in the range of 0.01-298 K. The elongation leads to the formation of monatomic chains, as has been observed experimentally. The calculated force-versus-elongation curve is remarkably consistent with available experimental results.

Atomic indentation and friction of self-assembled monolayers by hybrid molecular simulations

This paper focuses on the atomic indentation and friction properties of self-assembled monolayers (SAMs) by a novel hybrid molecular simulation approach. By introducing a sliding dynamics for the tip-cantilever assembly in atomic force microscopy (AFM) and a fast molecular dynamics relaxation algorithm for SAMs, we simulate the scanning process of the assembly over SAMs in the time scale of AFM experiments. For the atomic indentation of SAM surfaces, we find that elastic modulus is chain-length independent, and has a value of 20±10 GPa. However, under shear, effective shear modulus is found to be chain-length dependent, which explains the SAM chain-length dependence of friction observed in AFM experiments. The calculated surface energy of methyl terminated SAMs is consistent with many experimental results.

Molecular Dynamics Simulations of Polyamide Membrane, Calcium Alginate Gel, and Their Interactions in Aqueous Solution

We perform molecular dynamics (MD) simulations to investigate the cross-linked polyamide (PA) membrane, the aggregation of alginate molecules in the presence of Ca(2+) ions, and their molecular binding mechanism in aqueous solution. We use a steered molecular dynamics (SMD) approach to simulate the unbinding process between a PA membrane and an alginate gel complex. Simulation results show that Ca(2+) ions are strongly associated with the carboxylate groups in alginate molecules, forming a web structure. The adhesion force between alginate gel and PA surface during unbinding originates from several important molecular interactions. These include the short-range hydrogen bonding and van der Waals attraction forces, and the ionic bridge binding that extends much longer pulling distances due to the significant chain deformations of alginate gel and PA membrane.

Hydrated Polyamide Membrane and Its Interaction with Alginate: A Molecular Dynamics Study

The properties of the hydrated amorphous polyamide (PA) membrane and its binding with alginate are investigated through molecular dynamics simulations. The density of the hydrated membrane, surface morphology, and water diffusion near and inside the membrane are compared to other studies. Particular focus is given to the steered molecular dynamics (SMD) simulation of the binding between the PA membrane and an alginate model. The PA surface composition is determined on the basis of experimental measurements of the oxygen/nitrogen (O/N) ratio. The surface model is built using a configurational-bias Monte Carlo technique. The consistent valence force field (CVFF) is used to describe the atomic interactions in the membrane-foulant system. Simulation results show that the carboxylate groups in both the PA surface and alginate exhibit strong binding with metal ions. This binding mechanism plays a major role in the PA-alginate fouling through the formation of an ionic binding bridge. Specifically, Ca(2+) ions have stronger binding with the carboxylate group than Na(+) ions, while the binding breakdown time is shorter for Ca(2+) than Na(+) because of the comparably higher hydration free energy of Ca(2+) ions with water molecules.

Unbinding of the streptavidin-biotin complex by atomic force microscopy: a hybrid simulation study.

A hybrid molecular simulation technique, which combines molecular dynamics and continuum mechanics, was used to study the single-molecule unbinding force of a streptavidin-biotin complex. The hybrid method enables atomistic simulations of unbinding events at the millisecond time scale of atomic force microscopy (AFM) experiments. The logarithmic relationship between the unbinding force of the streptavidin-biotin complex and the loading rate (the product of cantilever spring constant and pulling velocity) in AFM experiments was confirmed by hybrid simulations. The unbinding forces, cantilever and tip positions, locations of energy barriers, and unbinding pathway were analyzed. Hybrid simulation results from this work not only interpret unbinding AFM experiments but also provide detailed molecular information not available in AFM experiments.

Molecular simulations of stretching gold nanowires in solvents.

The effect of solvent on the elongation of gold nanowires has been further studied through molecular simulations. For a simple Lennard-Jones solvent (propane), which is a non-bonded solvent, extensive molecular dynamics (MD) runs demonstrated that below the melting point of gold nanowires, the solvent effect on the elongation properties of Au nanowires is minimal. In thiol organic liquid, such as in benzenedithiol (BDT), the situation is much more complicated due to the Au-BDT chemical bonding. Here, we present the initial adsorption structure of BDT on a stretched gold nanowire through grand canonical Monte Carlo (GCMC) simulations. A recently developed force field for the BDT-Au chemical bonding was implemented in the simulations. We found that the packing density of the bonded BDT on the surface of Au nanowire is larger than that on an extended Au(111) surface. The results from this work are helpful in understanding the underlying mechanism of the formation of Au-BDT-Au junctions implemented in molecular conductance measurements.

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Computational Chemistry for Molecular Electronics

We present a synergetic effort of a group of theorists to characterize a molecular electronics device through a multiscale modeling approach. We combine electronic-structure calculations with molecular dynamics and Monte Carlo simulations to predict the structure of self-assembled molecular monolayers on a metal surface. We also develop a novel insight into molecular conductance, with a particular resolution of its fundamental channels, which stresses the importance of a complete molecular structure description of all components of the system, including the leads, the molecule, and their contacts. Both molecular dynamics and electron transport simulations imply that knowledge of detailed molecular structure and system geometry are critical for successful comparison with carefully performed experiments. We illustrate our findings with benzenedithiolate molecules in contact with gold.

Hydration force and dynamic squeeze-out of hydration water under subnanometer confinement

We have performed molecular dynamics simulations to study the normal forces between two mica surfaces in water and the consequent dynamic squeeze-out process. A liquid–vapor molecular ensemble has been designed for this purpose. We find, however, that only the two-layer hydration water can support a repulsive hydration force, and beyond this thickness the overall forces are attractive. From the hydrodynamic pressure developed during a normal approach and dynamic squeeze-out, we estimate that the viscosity of confined hydration water in the thickness of 0.7–1.35 nm is about 5–16 times the bulk value. A steered diffusion model has been proposed, which directly predicts the critical velocity below which hydrodynamic effects can be eliminated in hydration force measurements.