Nanoscale dynamics and protein adhesivity of alkylamine self-assembled monolayers on graphene.

Atomic-scale molecular dynamics computer simulations are used to probe the structure, dynamics, and energetics of alkylamine self-assembled monolayer (SAM) films on graphene and to model the formation of molecular bilayers and protein complexes on the films. Routes toward the development and exploitation of functionalized graphene structures are detailed here, and we show that the SAM architecture can be tailored for use in emerging applications (e.g., electrically stimulated nerve fiber growth via the targeted binding of specific cell surface peptide sequences on the functionalized graphene scaffold). The simulations quantify the changes in film physisorption on graphene and the alkyl chain packing efficiency as the film surface is made more polar by changing the terminal groups from methyl (-CH3) to amine (-NH2) to hydroxyl (-OH). The mode of molecule packing dictates the orientation and spacing between terminal groups on the surface of the SAM, which determines the way in which successive layers build up on the surface, whether via the formation of bilayers of the molecule or the immobilization of other (macro)molecules (e.g., proteins) on the SAM. The simulations show the formation of ordered, stable assemblies of monolayers and bilayers of decylamine-based molecules on graphene. These films can serve as protein adsorption platforms, with a hydrophobin protein showing strong and selective adsorption by binding via its hydrophobic patch to methyl-terminated films and binding to amine-terminated films using its more hydrophilic surface regions. Design rules obtained from modeling the atomic-scale structure of the films and interfaces may provide input into experiments for the rational design of assemblies in which the electronic, physicochemical, and mechanical properties of the substrate, film, and protein layer can be tuned to provide the desired functionality.

Quasiparticle energies and lifetimes in a metallic chain model of a tunnel junction.

As electronics devices scale to sub-10 nm lengths, the distinction between "device" and "electrodes" becomes blurred. Here, we study a simple model of a molecular tunnel junction, consisting of an atomic gold chain partitioned into left and right electrodes, and a central "molecule." Using a complex absorbing potential, we are able to reproduce the single-particle energy levels of the device region including a description of the effects of the semi-infinite electrodes. We then use the method of configuration interaction to explore the effect of correlations on the system's quasiparticle peaks. We find that when excitations on the leads are excluded, the device's highest occupied molecular orbital and lowest unoccupied molecular orbital quasiparticle states when including correlation are bracketed by their respective values in the Hartree-Fock (Koopmans) and ΔSCF approximations. In contrast, when excitations on the leads are included, the bracketing property no longer holds, and both the positions and the lifetimes of the quasiparticle levels change considerably, indicating that the combined effect of coupling and correlation is to alter the quasiparticle spectrum significantly relative to an isolated molecule.

Many-electron scattering applied to atomic point contacts.

Electron transport in a strong coupling regime is investigated by applying the many-electron correlated scattering (MECS) method to an atomic point contact model. Comparing the theoretical calculations to the quantum of conductance obtained experimentally for these systems allows for the error associated with the numerical implementation of the MECS method to be estimated and attributed to different components of the calculations. Errors associated with implementing the scattering boundary conditions and determination of the applied voltage in a finite explicit electrode model are assessed, and as well the impact on the basis set description on predicting the conductance is examined in this weakly correlated limit. The MECS calculation for the atomic point contact results in a conductance of 0.6G(0), in reasonable agreement with measurements for gold point contacts where approximately the conductance quantum G(0) is obtained. The analysis indicates the error attributable to numerical approximations and the explicit electrode model introduced in the calculations should not exceed 40% of the total conductance, whereas the effect of electron-electron correlations, even in this weakly correlated regime, can result in as much as a 30% change in the predicted conductance.

Molecular dynamics study of naturally occurring defects in self-assembled monolayer formation.

One of the major challenges for nanofabrication, in particular microcontact printing (mu-CP), is the control of molecular diffusion, or "ink spreading", for the creation of nanopatterns with minimized "smudging" at pattern boundaries. In this study, fully atomistic computer simulations were used to measure the impact of naturally occurring domain boundaries on the diffusion of excess alkanethiol ink molecules on printed alkanethiol self-assembled monolayers (SAM). A periodic unit cell containing approximately one million atoms and with a surface area of 56 nm x 55 nm was used to model a hexadecanethiol SAM on Au(111), featuring SAM domain boundaries and a range of concentrations of excess hexadecanethiol ink molecules diffusing on top. This model was simulated for a total of approximately 80 ns of molecular dynamics. The simulations reveal that domain boundaries impede the diffusion of excess ink molecules and can, in some cases, permanently trap excess inks. There is competition between ink spreading and ink trapping, with the ink/SAM interaction strongly dependent on both the ink concentration and the SAM orientation at domain boundaries. SAM defects thus provide potential diffusion barriers for the control of excess ink spreading, and simulations also illustrate atom-scale mechanisms for the repair of damaged areas of the SAM via self-healing. The ability of domain boundaries to trap excess ink molecules is accounted for using an accessible volume argument, and trapping is discussed in relation to experimental efforts to reduce molecular spreading on SAMs for the creation of ultrahigh resolution nanopatterns.

Deformation potentials and electron-phonon coupling in silicon nanowires.

The role of reduced dimensionality and of the surface on electron-phonon (e-ph) coupling in silicon nanowires is determined from first principles. Surface termination and chemistry is found to have a relatively small influence, whereas reduced dimensionality fundamentally alters the behavior of deformation potentials. As a consequence, electron coupling to "breathing modes" emerges that cannot be described by conventional treatments of e-ph coupling. The consequences for physical properties such as scattering lengths and mobilities are significant: the mobilities for [110] grown wires are 6 times larger than those for [100] wires, an effect that cannot be predicted without the form we find for Si nanowire deformation potentials.

Quantification of ink diffusion in microcontact printing with self-assembled monolayers.

Spreading of ink outside the desired printed area is one of the major limitations of microcontact printing (micro-CP) with alkanethiol self-assembled monolayers (SAMs) on gold. We use molecular dynamics (MD) computer simulations to quantify the temperature and concentration dependence of hexadecanethiol (HDT) ink spreading on HDT SAMs, modeling 18 distinct printing conditions using periodic simulation cells of approximately 7 nm edge length and printing conditions ranging from 7 ink molecules per cell at 270 K to 42 ink molecules per cell at 371K. The computed alkanethiol ink diffusion rates on the SAM are of the same order of magnitude as bulk liquid alkanethiol diffusion rates at all but the lowest ink concentrations and highest temperatures, with up to 20-30 times increases in diffusion rates at the lowest concentration-highest temperature conditions. We show that although alkanethiol surfaces are autophobic, autophobicity is not enough to pin the ink solutions on the SAM, and so any overinking of the SAM will lead to spreading of the printed pattern. Comparison of experimental and calculated diffusion data supports an interpretation of pattern broadening as a mixture of spreading on fully and partially formed SAMs, and the calculated spreading rates establish some of the fundamental limitations of mu-CP in terms of stamp contact time and desired pattern width.

Monte Carlo configuration interaction predictions for the electronic spectra of Ne, CH2, C2, N2, and H2O compared to full configuration interaction calculations.

Singlet and triplet electronic excitation energies have been calculated for Ne, CH(2), C(2), N(2), and H(2)O using the Monte Carlo configuration interaction (CI) method. We find that excitation energies can be predicted to within a few tens of meV of full CI (FCI) results using expansions consisting of only a few thousand configuration state functions as compared to the O(10(8)) configurations occurring in the corresponding FCI expansions. The method provides a consistently accurate and balanced description of electronic excitations with accuracy for small molecular systems comparable to the equation-of-motion coupled cluster method with full triples.

Guanidinium chloride molecular diffusion in aqueous and mixed water-ethanol solutions.

Solutions containing guanidinium chloride (GdmCl), or equivalently guanidine hydrochloride (GdnHCl), are commonly used to denature macromolecules such as proteins and DNA in, for example, microfluidics studies of protein unfolding. To design and study such applications, it is necessary to know the diffusion coefficients for GdmCl in the solution. To this end, we use molecular dynamics simulations to calculate the diffusion coefficients of GdmCl in water and in water-ethanol solutions, for which no direct experimental measurements exist. The fully atomistic simulations show that the guandinium cation Gdm (+) diffusion decreases as the concentration of both Gdm (+) and ethanol in the solution increases. The simulations are validated against available literature data, both transformed measured viscosity values and computed diffusion coefficients, and we show that a prudent choice of water model, namely TIP4P-Ew, gives calculated diffusion coefficients in good agreement with the transformed measured viscosity values. The calculated Gdm (+) diffusion behavior is explained as a dynamic mixture of free cation, stacked cation, and ion-paired species in solution, with weighted contributions to Gdm (+) diffusion from the stacked and paired states helping explain measured viscosity data in terms of atom-scale dynamics.

Statistical estimates of electron correlations.

While arbitrarily accurate solutions to the many-body Schrodinger equation are possible through a brute force expansion of the wave function, the length of the expansions required renders the approach intractable except for few-electron problems. By considering the form of the energy resulting from truncation of the many-particle expansion space, it is shown that accurate determination of electron correlations may be extracted from estimates of average or effective energy contributions while maintaining a reduced dimension for the expansion space. An energy formula expressed as a rational function of the expansion vector length is determined, allowing for estimates of asymptotic limits of many-body correlations.

Symmetry, delocalization, and molecular conductance.

Molecules bonded between two metal contacts form the simplest possible molecular devices. Coupled by the molecule, the left and right contact-based states form symmetric and antisymmetric pairs near the Fermi level. We relate the size of the resulting energy splitting DeltaE to the symmetry and degree of delocalization of the coupling molecular orbital. Qualitative trends in molecular conductances are then estimated from the variations in DeltaE. We examine benzenedithiol and other molecules of interest in transport.

Correlated electron transport in molecular electronics.

Theoretical and experimental values to date for the resistances of single molecules commonly disagree by orders of magnitude. By reformulating the transport problem using boundary conditions suitable for correlated many-electron systems, we approach electron transport across molecules from a new standpoint. Application of our correlated formalism to benzene-dithiol gives current-voltage characteristics close to experimental observations. The method can solve the open system quantum many-body problem accurately, treats spin exactly, and is valid beyond the linear response regime.