Molecular electronics and molecules on surfaces

Investigation of the thiol bond to gold (Au) for molecular electronics application from first principles methods.

In our study of the thiol bond to Au for molecular electronics, we have been able to demonstrate significant changes in the Au-Au bonds in the metal, and thus the importance of not preventing the metal surface from relaxing when equilibrium geometries are to be obtained. The calculated molecules now represent a standard reference system in molecular electronics, the thiol-terminated molecules bonded to gold contacts. Our cluster models of these systems, with full geometrical degrees of freedom, paved the way for a very tractable protocol to describe possible molecular devices, i.e. by not only looking at the properties of the molecule, but also including parts of the metal conductor as clusters, which has since been widely used. Our results show how thiol molecules bind as thiolates on gold, which is the basis for modern self-organized monolayers (SOMs).

We also study phthalocyanines, porphyrins and fullerenes, their doping and binding to metal surfaces. We simulate scanning tunneling microscopy (STM) images and curves when these molecules are bound on surfaces. We also make calculations of single-molecule spectroscopy performed with STM tip, e.g. scanning tunneling spectroscopy (STS) and inelastic tunneling spectroscopy (IETS) for the study of single molecule vibrations excited by electron-vibration interactions. We study how doping affects the molecular conductivity and how molecular structure changes can be used to switch on and off a potential molecular device for molecular electronics. For these simulations we use density functional theory (DFT), for which standard functionals have difficulty describing the weak van der Waals interactions in general, and the dispersion contribution in particular. Then we use special functionals designed for the purpose, or we correct for this by including dispersion in a similar way as is done in the force fields in Molecular Mechanics based Molecular Dynamics (MD), in DFT with dispersion (so called DFT-D). These effects are important for molecules that are physisorbed on a substrate surface, and are also needed for quantitative results for large molecules that are chemisorbed but also have large contributions from physisorption.

Publications

• Two-Dimensional Nitrogenated Holey Graphene (C2N) Monolayer Based Glucose Sensor for Diabetes Mellitus
• Sensing of Volatile Organic Compounds on Two-Dimensional Nitrogenated Holey Graphene, Graphdiyne, and Their Heterostructure
• Physisorption Controls the Conformation and Density of States of an Adsorbed Porphyrin
• Measuring the mechanical properties of molecular conformers
• Theoretical insights into adsorption of cobalt phthalocyanine on Ag (111: A combination of chemical and van der waals bonding
• Endohedral Fullerene Ce@C82 on Cu (111: Orientation, Electronic Structure, and Electron-Vibration Coupling
• Structure and energetics of shuttlecock-shaped tin-phthalocyanine on Ag (111: A density functional study employing dispersion correction
• Electron-induced excitation of vibrations of Ce atoms inside a C 80 cage
• Inversion of the shuttlecock shaped metal phthalocyanines MPc (M = Ge, Sn, Pb): A density functional study
• Theoretical and experimental comparison of SnPc, PbPc, and CoPc adsorption on Ag (111)
• Modification of the conductance of single fullerene molecules by endohedral doping
• The role of ellipticity on the preferential binding site of Ce and la in C78-D3h: A density functional theory study
• A density functional study of Ce@C82: Explanation of the Ce preferential bonding site
• Explanation of the different preferential binding sites for Ce and la in M2@C80 (M = Ce, La)
• Orientation of individual C60 molecules adsorbed on Cu (111): Low-temperature scanning tunneling microscopy and density functional calculations
• Electrostatic ordering of the lanthanum endoatom in La@C 82 adsorbed on metal surfaces
• A physical compact model for electron transport across single molecules
• Band structure engineering of a molecular wire system composed of dimercaptoacetoamidobenzene, its derivatives, and gold clusters
• Interactions between thiol molecular linkers and the Au13 nanoparticle