Thermally activated conduction in molecular junctions

We report temperature dependence measurements on the conductance of individual molecular wires. The results show for the first time in a molecular junction the theoretically predicted transition from coherent superexchange tunneling conductance to an activated hopping mechanism as temperature is increased.     

Molecular optoelectronics: the interaction of molecular conduction junctions with light

The interaction of light with molecular conduction junctions is attracting growing interest as a challenging experimental and theoretical problem on one hand, and because of its potential application as a characterization and control tool on the other. It stands at the interface between two important fields, molecular electronics and molecular plasmonics and has attracted attention as a challenging scientific problem with potentially important technological consequences. Here we review the present state of the art of this field, focusing on several key phenomena and applications: using light as a switching device, using light to control junction transport in the adiabatic and non-adiabatic regimes, light generation in biased junctions and Raman scattering from such systems. This field has seen remarkable progress in the past decade, and the growing availability of scanning tip configurations that can combine optical and electrical probes suggests that further progress towards the goal of realizing molecular optoelectronics on the nanoscale is imminent.     

Mixing of generalized parity in molecular orbitals

The concept of generalized parity is introduced. It allows mixing of different symmetries in molecular orbitals in the framework of the Parity Mixing in Orbitals method. An extension of this SCF calculational scheme is also discussed and the relevant secular equations are reported.Alexander von Humboldt Fellow. On leave from the Institute Rudjer Bokovi, Zagreb, Croatia, Yugoslavia.     

Study of molecular orbitals in momentum space

Molecular orbitals are presented in configuration and momentum representations. We propose to minimize large oscillations present in calculated momentum wavefunctions by cancelling position factor phases. We illustrate the distortion introduced by different electron translation factors and show continuum states and dynamical wavefunctions in momentum coordinates. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Use of semifloating orbitals in molecular calculations

The use of semifloating orbitals of type A + cA', where A is an orbital centered on nucleus a and A' is a floating orbital, in quantum chemical calculations was proposed. The bonding wave function of diatomic molecule, which was constructed on the basis of semifloating orbitals by means of the electron pairs method, has a configuration of type A'(1)B(2) + B(1)A'(2) + A(1)B'(2) + B'(1)A(2); this configuration can be called semifloating two-electron function. In the example of a variation calculation of the hydrogen molecule it was shown that the use of semifloating functions together with the traditionally used functions fixed on the nuclei and pure floating functions decreases the calculated molecular energy and refines considerably the electron density distribution along the molecular axis.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 22, No. 6, pp. 712–715, November–December 1986.     

Description of interactions in molecular complexes by linear combination of educt orbitals

The Fock-matrix of a molecular system (F) composed of several fragments is transformed into the basis of the MO's of these subsystems (¯F). Interactions between the fragments during a chemical reaction or in molecular complexes like quinhydrone can be expressed as matrix elements of ¯F.     

Variability of conductance in molecular junctions

The conductance of molecular junctions, formed by breaking gold point contacts dressed with various thiol functionalized organic molecules, is measured at 293 K and at 30 K. In the presence of molecules, individual conductance traces measured as a function of increasing gold electrode displacement show clear steps below the quantum conductance steps of the gold contact. These steps are distributed over a wide range of molecule-dependent conductance values. Histograms constructed from all conductance traces therefore do not show clear peaks either at room or low temperatures. Filtering of the data sets by an objective automated procedure only marginally improves the visibility of such features. We conclude that the geometrical junction to junction variations dominate the conductance measurements.     

On-the-fly localization of electronic orbitals in Car-Parrinello molecular dynamics

The ab initio molecular-dynamics formalism of Car and Parrinello is extended to preserve the locality of the orbitals. The supplementary term in the Lagrangian does not affect the nuclear dynamics, but ensures "on the fly" localization of the electronic orbitals within a periodic supercell in the Gamma-point approximation. The relationship between the resulting equations of motion and the formation of a gauge-invariant Lagrangian combined with a gauge-fixing procedure is briefly discussed. The equations of motion can be used to generate a very stable and easy to implement numerical integration algorithm. It is demonstrated that this algorithm can be used to compute the trajectory of the maximally localized orbitals, known as Wannier orbitals, in ab initio molecular dynamics with only a modest increase in the overall computer time. In the present paper, the new method is implemented within the generalized gradient approximation to Kohn-Sham density-functional theory employing plane wave basis sets and atomic pseudopotentials. In the course of the presentation, we briefly discuss how the present approach can be combined with localized basis sets to design fast linear scaling ab initio molecular-dynamics methods.     

Further studies of tetrakis(N,N′-dialkylbenzamidinato)diruthenium(III) chloro and alkynyl compounds: molecular engineering of metallayne monomers

Three diruthenium(III) compounds Ru₂(L)₄Cl₂, where L is mMeODMBA (N,N′-dimethyl-3-methoxybenzamidinate, 1a), DiMeODMBA (N,N′-dimethyl-3,5-dimethoxy benzamidinate, 1b), or DEBA (N,N′-diethylbenzamidinate, 1c), were prepared from the reactions between Ru₂(OAc)₄Cl and respective HL under reflux conditions. Metathesis reactions between 1 and LiC₂Y resulted in bis-alkynyl derivatives Ru₂(L)₄(C₂Y)₂ [Y=Ph (2), SiMe₃ (3), SiⁱPr₃ (4) and C₂SiMe₃ (5)]. The parent compounds 1 are paramagnetic (S=1), while bis-alkynyl derivatives 2-5 are diamagnetic and display well-solved ¹H- and ¹³C-NMR spectra. Molecular structures of compounds 1b, 1c, 2c, 3c and 4b were established through single crystal X-ray diffraction studies, which revealed RuRu bond lengths of ca. 2.32 Å for parent compounds 1 and 2.45 Å for bis-alkynyl derivatives. Cyclic voltammograms of all compounds feature three one-electron couples: an oxidation and two reductions, while the reversibility of observed couples depends on the nature of axial ligands.     

Thermoelectrics in an array of molecular junctions

The room temperature thermoelectric properties of a three-dimensional array of molecular junctions are calculated. The array is composed of n-doped silicon nanoparticles where the surfaces are partially covered with polar molecules and the nanoparticles are bridged by trans-polyacetylene molecules. The role of the polar molecules is to reduce the band bending in the n-doped silicon nanoparticles and to shift the electronic resonances of the bridging molecules to the nanoparticle conduction band edges where the molecular resonances act as electron energy filters. The transmission coefficients of the bridging molecules that appear in the formulas for the Seebeck coefficient, the electrical conductance, and the electronic thermal conductance, are calculated using the nonequilibrium Green's function technique. A simple tight-binding Hamiltonian is used to describe the bridging molecules, and the self-energy term is calculated using the parabolic conduction band approximation. The dependencies of the thermoelectric properties of the molecular junctions on the silicon doping concentration and on the molecule-nanoparticle coupling are discussed. The maximal achievable thermoelectric figure of merit ZT of the array is estimated as a function of the phononic thermal conductance of the bridging molecules and the doping of the nanoparticles. The power factor of the array is also calculated. For sufficiently small phononic thermal conductances of the bridging molecules, very high ZT values are predicted.     

E/Z isomerism in isoporphycene and its nickel complex. Strong influence of peripheral substituents on the molecular structure

We investigated the influence of peripheral ethyl substituents on the relative stability of the Z and E isomers of octaethylisoporphycene 1a using calculations at DFT level. Compared to the parent compound isoporphycene (1), for which the Z isomer is found to have a lower energy than the E isomer, the order of stability is reversed, if the ethyl groups are taken into consideration. The predicted preference of the E configuration in 1a agrees with experimental observations. An analysis of the molecular geometries reveals that the different behaviour of 1 and 1a results from steric interactions between the ethyl substituents and between these substituents and H atoms of the (CH)₃ bridge. For the nickel complex of isoporphycene (2) the calculated energy difference between Z and E isomer is larger and the effect of ethyl substitution is less pronounced than in the case of the free base. As a result, the Z-configured form remains the more stable isomer in the octaethyl derivative 2a.     

FTIR spectroscopy of buried interfaces in molecular junctions

We demonstrate that ATR-FTIR spectroscopy can be used to record high-quality vibrational spectra of molecules at buried interfaces in metal-molecule-silicon and metal-molecule-metal junctions. This provides quantitative information on the structure and conformation of molecules at buried interfaces, an issue of critical importance to molecular electronics. In the model systems of Au on octadecyltrichlorosilane self-assembled monolayer on Si or mecaptohexadecanoic acid multilayers on Au-covered Si, ATR-FTIR suggests that metal deposition leads to not only conformational disorder within the film but also the direct interaction of metal atoms/clusters with alkyl backbones.