Hybridized Molecule/metal interfaces are ubiquitous in molecular and organic devices. The energy level alignment (ELA) of frontier molecular levels relative to the metal Fermi level (E-F) is critical to the conductance and functionality of these devices. However, a clear understanding of the ELA that includes many-electron self-energy effects is lacking. Here, we investigate the many-electron effects on the ELA using state-of-the-art, benchmark GW calculations on prototypical chemisorbed molecules on Au(111), in eleven different geometries. The GW ELA is in good agreement with photoemission for monolayers of benzene diamine on Au(111). We find that in addition to static image charge screening, the frontier levels in most of these geometries are renormalized by additional screening from substrate-mediated intermolecular Coulomb interactions. For weakly chemisorbed systems, such as amines and pyridines on Au, this additional level renormalization (similar to 1.5 eV) comes solely from static screened exchange energy, allowing us to suggest computationally more tractable schemes to predict the ELA at such interfaces, However, for more strongly chemisorbed thiolate layers, dynamical effects are present. Our ab initio results constitute an important step toward the understanding and manipulation of functional molecular/organic systems for both,fundamental studies and applications.

}, keywords = {1st-principles, charge-transport, circuits, conductance, gw method, nanoscale, quasi-particle energies, self-assembled monolayers, single-molecule junctions}, issn = {1932-7447}, doi = {10.1021/acs.jpcc.7b00715}, author = {Chen, Yifeng and Tamblyn, Isaac and Quek, Su Ying} } @article {amara_dynamic_2016, title = {Dynamic {Structural} {Evolution} of {Metal}-{Metal} {Bonding} {Network} in {Monolayer} {WS}2}, journal = {Chem. Mat.}, volume = {28}, number = {7}, year = {2016}, note = {WOS:000374196000044}, month = {04/2016}, pages = {2308{\textendash}2314}, abstract = {Layered transition metal dichalcogenides (TMDs) exist in a range of crystal phases with distinct electronic character. Some crystal phases are known to exhibit unique in-plane anisotropy characterized by a periodic distortion of the lattice and a formation of metal metal bonding network. Here, we report in situ observation of dynamic structural evolution in the one-dimensional zigzag chains of single layer WS2 induced by electron beam irradiation. Metastable zigzag chains of tungsten atoms are found to undergo reorganization of metal-metal bonds, resulting in emergence of tetramer clusters and zigzag chains with a new orientation. Our first-principles calculations reveal a small (similar to 0.1 eV per formula unit) activation energy barrier for monolayer WS2 zigzag chain reorientation and a metastable transition state in the form of tetramer clusters. We further show that local tetramer clusters can be induced and stabilized by local electronic charging effects. The formation of local tetramer clusters indicate that this dynamic structural evolution is not a charge density wave phenomenon; we find instead that these lattice changes are a response to electronic instabilities that weaken the W-S bonds in the zigzag phase. Our findings shed light on the origin of structural instabilities and phases in two-dimensional materials, and constitute a step further toward their potential uses in phase change applications.

}, keywords = {atomic mechanism, dichalcogenides, hydrogen evolution, layer, mos2 nanosheets, mote2, phase-transition, state}, issn = {0897-4756}, doi = {10.1021/acs.chemmater.6b00379}, author = {Amara, Kiran Kumar and Chen, Yifeng and Lin, Yung-Chang and Kumar, Rajeev and Okunishi, Eiji and Suenaga, Kazu and Quek, Su Ying and Eda, Goki} } @article {khoo_length_2015, title = {Length dependence of electron transport through molecular wires - a first principles perspective}, journal = {Physical Chemistry Chemical Physics}, volume = {17}, number = {1}, year = {2015}, note = {{WOS}:000346235600005}, month = {01/2015}, pages = {77{\textendash}96}, abstract = {One-dimensional wires constitute a fundamental building block in nanoscale electronics. However, truly one-dimensional metallic wires do not exist due to Peierls distortion. Molecular wires come close to being stable one-dimensional wires, but are typically semiconductors, with charge transport occurring via tunneling or thermally-activated hopping. In this review, we discuss electron transport through molecular wires, from a theoretical, quantum mechanical perspective based on first principles. We focus specifically on the off-resonant tunneling regime, applicable to shorter molecular wires ({\textless}similar to 4-5 nm) where quantum mechanics dictates electron transport. Here, conductance decays exponentially with the wire length, with an exponential decay constant, beta, that is independent of temperature. Different levels of first principles theory are discussed, starting with the computational workhorse - density functional theory ({DFT}), and moving on to many-electron {GW} methods as well as {GW}-inspired {DFT} + Sigma calculations. These different levels of theory are applied in two major computational frameworks - complex band structure ({CBS}) calculations to estimate the tunneling decay constant, beta, and Landauer-Buttiker transport calculations that consider explicitly the effects of contact geometry, and compute the transmission spectra directly. In general, for the same level of theory, the Landauer-Buttiker calculations give more quantitative values of beta than the {CBS} calculations. However, the {CBS} calculations have a long history and are particularly useful for quick estimates of beta. Comparing different levels of theory, it is clear that {GW} and {DFT} + Sigma calculations give significantly improved agreement with experiment compared to {DFT}, especially for the conductance values. Quantitative agreement can also be obtained for the Seebeck coefficient -another independent probe of electron transport. This excellent agreement provides confirmative evidence of off-resonant tunneling in the systems under investigation. Calculations show that the tunneling decay constant beta is a robust quantity that does not depend on details of the contact geometry, provided that the same contact geometry is used for all molecular lengths considered. However, because conductance is sensitive to contact geometry, values of beta obtained by considering conductance values where the contact geometry is changing with the molecular junction length can be quite different. Experimentally measured values of beta in general compare well with beta obtained using {DFT} + Sigma and {GW} transport calculations, while discrepancies can be attributed to changes in the experimental contact geometries with molecular length. This review also summarizes experimental and theoretical efforts towards finding perfect molecular wires with high conductance and small beta values.

}, keywords = {ab-initio, atomic-force microscopy, Carbon nanotubes, charge-transport, current-voltage characteristics, energy-level alignment, graphene nanoribbons, junction conductance, metal work function, self-assembled monolayers}, issn = {1463-9076}, doi = {10.1039/c4cp05006a}, author = {Khoo, Khoong Hong and Chen, Yifeng and Li, Suchun and Quek, Su Ying} }