We present an efficient implementation of a surface Green's-function method for atomistic modeling of surfaces within the framework of density functional theory using a pseudopotential localized basis set approach. In this method, the system is described as a truly semi-infinite solid with a surface region coupled to an electron reservoir, thereby overcoming several fundamental drawbacks of the traditional slab approach. The versatility of the method is demonstrated with several applications to surface physics and chemistry problems that are inherently difficult to address properly with the slab method, including metal work function calculations, band alignment in thin-film semiconductor heterostructures, surface states in metals and topological insulators, and surfaces in external electrical fields. Results obtained with the surface Green's-function method are compared to experimental measurements and slab calculations to demonstrate the accuracy of the approach.PACS numbers: 68.47.Fg

By using a newly implemented QM/MM multiscale MD method to simulate the excited state dynamics of the Ir 2 (dimen) 4 2+ (dimen = 1,8-diisocyano-pmenthane) complex, we not only report on results that support the two experimentally observed coherent dynamical modes in the molecule but also reveal a third mode, not distinguishable by spectroscopic methods. We directly follow the channels of energy dissipation to the solvent and report that the main cause for coherence decay is the initial wide range of configurations in the excited state population. We observe that the solvent can actually extend the coherence lifetime by blocking channels for intramolecular vibrational energy redistribution (IVR).

The cocaine aptamer is a DNA molecule that binds cocaine at the junction of three helices. The bifunctional spectroscopic probe Ç was incorporated independently into three different positions of the aptamer and changes in structure and dynamics upon addition of the cocaine ligand were studied. Nucleoside Ç contains a rigid nitroxide spin label and can be studied directly by electron paramagnetic resonance (EPR) spectroscopy and fluorescence spectroscopy after reduction of the nitroxide to yield the fluoroside Çf. Both the EPR and the fluorescence data for aptamer 2 indicate that helix III is formed before cocaine binding. Upon addition of cocaine, increased fluorescence of a fully base-paired Çf, placed at the three-way junction in helix III, was observed and is consistent with a helical tilt from a coaxial stack of helices II and III. EPR and fluorescence data clearly show that helix I is formed upon addition of cocaine, concomitant with the formation of the Y-shaped three-way helical junction. The EPR data indicate that nucleotides in helix I are more mobile than nucleotides in regular duplex regions and may reflect increased dynamics due to the short length of helix I.

Density functional theory (DFT) is widely applied in calculations of molecules and materials. Yet, it suffers from a well-known over-emphasis on charge delocalization arising from self-interaction error that destabilizes localized states. Here, using the symmetric diamine N,N′-dimethylpiperazine as a model, we have experimentally determined the relative energy of a state with positive charge localized on one of the two nitrogen atoms, and a state with positive charge delocalized over both nitrogen atoms. The charge-localized state was found to be 0.33 (0.04) eV higher in energy than the charge-delocalized state. This provides an important test of theoretical approaches to electronic structure calculations. Calculations with all DFT functionals commonly used today, including hybrid functionals with exact exchange, fail to predict a stable charge-localized state. However, the application of an explicit self-interaction correction to a semi-local functional identifies both states and gives relative energy in excellent agreement with both experiment and CCSD(T) calculations.