Influence of Functional Groups on Charge Transport in Molecular Junctions

Using density functional theory (DFT), we analyze the influence of five classes of functional groups, as exemplified by NO2, OCH3, CH3, CCl3, and I, on the transport properties of a 1,4-benzenedithiolate (BDT) and 1,4-benzenediamine (BDA) molecular junction with gold electrodes. Our analysis demonstrates how ideas from functional group chemistry may be used to engineer a molecule's transport properties, as was shown experimentally and using a semiempirical model for BDA [Nano Lett. 7, 502 (2007)]. In particular, we show that the qualitative change in conductance due to a given functional group can be predicted from its known electronic effect (whether it is pi/sigma donating/withdrawing). However, the influence of functional groups on a molecule's conductance is very weak, as was also found in the BDA experiments. The calculated DFT conductances for the BDA species are five times larger than the experimental values, but good agreement is obtained after correcting for self-interaction and image charge effects.Comment: 6 pages, 3 figures, J. Chem. Phys (in press

Renormalization of Optical Excitations in Molecules near a Metal Surface

The lowest electronic excitations of benzene and a set of donor-acceptor molecular complexes are calculated for the gas phase and on the Al(111) surface using the many-body Bethe-Salpeter equation (BSE). The energy of the charge-transfer excitations obtained for the gas phase complexes are found to be around 10% lower than the experimental values. When the molecules are placed outside the surface, the enhanced screening from the metal reduces the exciton binding energies by several eVs and the transition energies by up to 1 eV depending on the size of the transition-generated dipole. As a striking consequence we find that close to the metal surface the optical gap of benzene can exceed its quasiparticle gap. A classical image charge model for the screened Coulomb interaction can account for all these effects which, on the other hand, are completely missed by standard time-dependent density functional theory.Comment: 4 pages, 3 figures; revised versio

Unraveling the acoustic electron-phonon interaction in graphene

Using a first-principles approach we calculate the acoustic electron-phonon couplings in graphene for the transverse (TA) and longitudinal (LA) acoustic phonons. Analytic forms of the coupling matrix elements valid in the long-wavelength limit are found to give an almost quantitative description of the first-principles based matrix elements even at shorter wavelengths. Using the analytic forms of the coupling matrix elements, we study the acoustic phonon-limited carrier mobility for temperatures 0-200 K and high carrier densities of 10^{12}-10^{13} cm^{-2}. We find that the intrinsic effective acoustic deformation potential of graphene is \Xi_eff = 6.8 eV and that the temperature dependence of the mobility \mu ~ T^{-\alpha} increases beyond an \alpha = 4 dependence even in the absence of screening when the full coupling matrix elements are considered. The large disagreement between our calculated deformation potential and those extracted from experimental measurements (18-29 eV) indicates that additional or modified acoustic phonon-scattering mechanisms are at play in experimental situations.Comment: 7 pages, 3 figure

Dispersive and Covalent Interactions Between Graphene and Metal Surfaces from the Random Phase Approximation

We calculate the potential energy surfaces for graphene adsorbed on Cu(111), Ni(111), and Co(0001) using density functional theory and the Random Phase Approximation (RPA). For these adsorption systems covalent and dispersive interactions are equally important and while commonly used approximations for exchange-correlation functionals give inadequate descriptions of either van der Waals or chemical bonds, RPA accounts accurately for both. It is found that the adsorption is a delicate competition between a weak chemisorption minimum close to the surface and a physisorption minimum further from the surface

An investigation of the formation and line properties of MgH in 3D hydrodynamical model stellar atmospheres

Studies of the isotopic composition of magnesium in cool stars have so far relied upon the use of one-dimensional (1D) model atmospheres. Since the isotopic ratios derived are based on asymmetries of optical MgH lines, it is important to test the impact from other effects affecting line asymmetries, like stellar convection. Here, we present a theoretical investigation of the effects of including self-consistent modeling of convection. Using spectral syntheses based on 3D hydrodynamical CO$^5$BOLD models of dwarfs (4000K$\lesssim T_\mathrm{eff}\lesssim5160K$, $4.0\leq$log(g)$\leq4.5$, $-3.0\leq[\mathrm{Fe/H}]\leq-1.0$) and giants ($T_\mathrm{eff}\sim4000$K, log(g)$=1.5$, $-3.0\leq[\mathrm{Fe/H}]\leq-1.0$), we perform a detailed analysis comparing 3D and 1D syntheses. We describe the impact on the formation and behavior of MgH lines from using 3D models, and perform a qualitative assessment of the systematics introduced by the use of 1D syntheses. Using 3D model atmospheres significantly affect the strength of the MgH lines, especially in dwarfs, with 1D syntheses requiring an abundance correction of up to +0.69 dex largest for our 5000K models. The corrections are correlated with $T_\mathrm{eff}$ and are also affected by the metallicity. The shape of the strong $^{24}$MgH component in the 3D syntheses is poorly reproduced in 1D. This results in 1D syntheses underestimating $^{25}$MgH by up to $\sim5$ percentage points and overestimating $^{24}$MgH by a similar amount for dwarfs. This discrepancy increases with decreasing metallicity. $^{26}$MgH is recovered relatively well, with the largest difference being $\sim2$ percentage points. The use of 3D for giants has less impact, due to smaller differences in the atmospheric structure and a better reproduction of the line shape in 1D.Comment: 20 pages, 15 figures, accepted for publication in Ap

Computational Design of Chemical Nanosensors: Metal Doped Carbon Nanotubes

We use computational screening to systematically investigate the use of transition metal doped carbon nanotubes for chemical gas sensing. For a set of relevant target molecules (CO, NH3, H2S) and the main components of air (N2, O2, H2O), we calculate the binding energy and change in conductance upon adsorption on a metal atom occupying a vacancy of a (6,6) carbon nanotube. Based on these descriptors, we identify the most promising dopant candidates for detection of a given target molecule. From the fractional coverage of the metal sites in thermal equilibrium with air, we estimate the change in the nanotube resistance per doping site as a function of the target molecule concentration assuming charge transport in the diffusive regime. Our analysis points to Ni-doped nanotubes as candidates for CO sensors working under typical atmospheric conditions

Correlating the ability of lignocellulosic polymers to constrain water with the potential to inhibit cellulose saccharification

BACKGROUND: Studies in bioconversions have continuously sought the development of processing strategies to overcome the “close physical association” between plant cell wall polymers thought to significantly contribute to biomass recalcitrance [Adv Space Res 18:251–265, 1996],[ Science 315:804–807, 2007]. To a lesser extent, studies have sought to understand biophysical factors responsible for the resistance of lignocelluloses to enzymatic degradation. Provided here are data supporting our hypothesis that the inhibitory potential of different cell wall polymers towards enzymatic cellulose hydrolysis is related to how much these polymers constrain the water surrounding them. We believe the entropy-reducing constraint imparted to polymer associated water plays a negative role by increasing the probability of detrimental interactions such as junction zone formation and the non-productive binding of enzymes. RESULTS: Selected commercial lignocellulose-derived polymers, including hemicelluloses, pectins, and lignin, showed varied potential to inhibit 24-h cellulose conversion by a mix of purified cellobiohydrolase I and β-glucosidase. At low dry matter loadings (0.5% w/w), insoluble hemicelluloses were most inhibitory (reducing conversion relative to cellulose-only controls by about 80%) followed by soluble xyloglucan and wheat arabinoxylan (reductions of about 70% and 55%, respectively), while the lignin and pectins tested were the least inhibitory (approximately 20% reduction). Low field nuclear magnetic resonance (LF-NMR) relaxometry used to observe water-related proton relaxation in saturated polymer suspensions (10% dry solids, w/w) showed spin-spin, T(2,) relaxation time curves generally approached zero faster for the most inhibitory polymer preparations. The manner of this decline varied between polymers, indicating different biophysical aspects may differentially contribute to overall water constraint in each case. To better compare the LF-NMR data to inhibitory potential, T(2) values from monocomponent exponential fits of relaxation curves were used as a measure of overall water constraint. These values generally correlated faster relaxation times (greater water constraint) with greater inhibition of the model cellulase system by the polymers. CONCLUSIONS: The presented correlation of cellulase inhibition and proton relaxation data provides support for our water constraint-biomass recalcitrance hypothesis. Deeper investigation into polymer-cellulose-cellulase interactions should help elucidate the types of interactions that may be propagating this correlation. If these observations can be verified to be more than correlative, the hypothesis and data presented suggest that a focus on water-polymer interactions and ways to alter them may help resolve key biological lignocellulose processing bottlenecks