Ab initio study of charge transport through single oxygen molecules in atomic aluminum contacts

We present ab initio calculations of transport properties of atomic-sized aluminum contacts in the presence of oxygen. The experimental situation is modeled by considering a single oxygen atom (O) or one of the molecules O2 and O3 bridging the gap between electrodes forming ideal, atomically sharp pyramids. The transport characteristics are computed for these geometries with increasing distances between the leads, simulating the opening of a break junction. To facilitate comparison with experiments further, the vibrational modes of the oxygen connected to the electrodes are studied. It is found that in the contact regime the change of transport properties due to the presence of oxygen is strong and should be detectable in experiments. All three types of oxygen exhibit a comparable behavior in their vibrational frequencies and conductances, which are well below the conductance of pure aluminum atomic contacts. The conductance decreases for an increasing number of oxygen atoms. In the tunneling regime the conductance decays exponentially with distance and the decay length depends on whether or not oxygen is present in the junction. This fact may provide a way to identify the presence of a gas molecule in metallic atomic contacts.Comment: 8 pages, 9 figures; added appendi

Accurate molecular energies by extrapolation of atomic energies using an analytic quantum mechanical model

Using a new analytic quantum mechanical method based on Slater's Xalpha method, we show that a fairly accurate estimate of the total energy of a molecule can be obtained from the exact energies of its constituent atoms. The mean absolute error in the total energies thus determined for the G2 set of 56 molecules is about 16 kcal/mol, comparable to or better than some popular pure and hybrid density functional models.Comment: 5 pages, REVTE

Tilt-angle landscapes and temperature dependence of the conductance in biphenyl-dithiol single-molecule junctions

Using a density-functional-based transport method we study the conduction properties of several biphenyl-derived dithiol (BPDDT) molecules wired to gold electrodes. The BPDDT molecules differ in their side groups, which control the degree of conjugation of the pi-electron system. We have analyzed the dependence of the low-bias zero-temperature conductance on the tilt angle phi between the two phenyl ring units, and find that it follows closely a cos^2(phi) law, as expected from an effective pi-orbital coupling model. We show that the tilting of the phenyl rings results in a decrease of the zero-temperature conductance by roughly two orders of magnitude, when going from a planar conformation to a configuration in which the rings are perpendicular. In addition we demonstrate that the side groups, apart from determining phi, have no influence on the conductance. All this is in agreement with the recent experiment by Venkataraman et al. [Nature 442, 904 (2006)]. Finally, we study the temperature dependence of both the conductance and its fluctuations and find qualitative differences between the examined molecules. In this analysis we consider two contributions to the temperature behavior, one coming from the Fermi functions and the other one from a thermal average over different contact configurations. We illustrate that the fluctuations of the conductance due to temperature-induced changes in the geometric structure of the molecule can be reduced by an appropriate design.Comment: 9 pages, 6 figures; submitted to Phys. Rev.

Accurate Treatment of Large Supramolecular Complexes by Double-Hybrid Density Functionals Coupled with Nonlocal van der Waals Corrections

In this work, we present a thorough assessment of the performance of some representative double-hybrid density functionals (revPBE0-DH-NL and B2PLYP-NL) as well as their parent hybrid and GGA counterparts, in combination with the most modern version of the nonlocal (NL) van der Waals correction to describe very large weakly interacting molecular systems dominated by noncovalent interactions. Prior to the assessment, an accurate and homogeneous set of reference interaction energies was computed for the supramolecular complexes constituting the L7 and S12L data sets by using the novel, precise, and efficient DLPNO-CCSD(T) method at the complete basis set limit (CBS). The correction of the basis set superposition error and the inclusion of the deformation energies (for the S12L set) have been crucial for obtaining precise DLPNO-CCSD(T)/CBS interaction energies. Among the density functionals evaluated, the double-hybrid revPBE0-DH-NL and B2PLYP-NL with the three-body dispersion correction provide remarkably accurate association energies very close to the chemical accuracy. Overall, the NL van der Waals approach combined with proper density functionals can be seen as an accurate and affordable computational tool for the modeling of large weakly bonded supramolecular systems.Financial support by the “Ministerio de Economía y Competitividad” (MINECO) of Spain and European FEDER funds through projects CTQ2011-27253 and CTQ2012-31914 is acknowledged. The support of the Generalitat Valenciana (Prometeo/2012/053) is also acknowledged. J.A. thanks the EU for the FP7-PEOPLE-2012-IEF-329513 grant. J.C. acknowledges the “Ministerio de Educación, Cultura y Deporte” (MECD) of Spain for a predoctoral FPU grant

CdTe Quantum Dot/Dye Hybrid System as Photosensitizer for Photodynamic Therapy

We have studied the photodynamic properties of novel CdTe quantum dots—methylene blue hybrid photosensitizer. Absorption spectroscopy, photoluminescence spectroscopy, and fluorescence lifetime imaging of this system reveal efficient charge transfer between nanocrystals and the methylene blue dye. Near-infrared photoluminescence measurements provide evidence for an increased efficiency of singlet oxygen production by the methylene blue dye. In vitro studies on the growth of HepG2 and HeLa cancerous cells were also performed, they point toward an improvement in the cell kill efficiency for the methylene blue-semiconductor nanocrystals hybrid system

Interfacial Chemistry in Al/CuO Reactive Nanomaterial and Its Role in Exothermic Reaction.

Interface layers between reactive and energetic materials in nanolaminates or nanoenergetic materials are believed to play a crucial role in the properties of nanoenergetic systems. Typically, in the case of Metastable Interstitial Composite nanolaminates, the interface layer between the metal and oxide controls the onset reaction temperature, reaction kinetics, and stability at low temperature. So far, the formation of these interfacial layers is not well understood for lack of in situ characterization, leading to a poor control of important properties. We have combined in situ infrared spectroscopy and ex situ X-ray photoelectron spectroscopy, differential scanning calorimetry, and high resolution transmission electron microscopy, in conjunction with firstprinciples calculations to identify the stable configurations that can occur at the interface and determine the kinetic barriers for their formation. We find that (i) an interface layer formed during physical deposition of aluminum is composed of a mixture of Cu, O, and Al through Al penetration into CuO and constitutes a poor diffusion barrier (i.e., with spurious exothermic reactions at lower temperature), and in contrast, (ii) atomic layer deposition (ALD) of alumina layers using trimethylaluminum (TMA)produces a conformal coating that effectively prevents Al diffusion even for ultrathin layer thicknesses (∼0.5 nm), resulting in better stability at low temperature and reduced reactivity. Importantly, the initial reaction of TMA with CuO leads to the extraction of oxygen from CuO to form an amorphous interfacial layer that is an important component for superior protection properties of the interface and is responsible for the high system stability. Thus, while Al e-beam evaporation and ALD growth of an alumina layer on CuO both lead to CuO reduction, the mechanism for oxygen removal is different, directly affecting the resistance to Al diffusion. This work reveals that it is the nature of the monolayer interface between CuO and alumina/Al rather than the thickness of the alumina layer that controls the kinetics of Al diffusion, underscoring the importance of the chemical bonding at the interface in these energetic materials

Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods

We have used combined quantum mechanical and molecular mechanical free-energy perturbation methods in combination with explicit solvent simulations to study the reaction mechanism of the multicopper oxidases, in particular the regeneration of the reduced state from the native intermediate. For 52 putative states of the trinuclear copper cluster, differing in the oxidation states of the copper ions and the protonation states of water- and O2-derived ligands, we have studied redox potentials, acidity constants, isomerisation reactions, as well as water- and O2 binding reactions. Thereby, we can propose a full reaction mechanism of the multicopper oxidases with atomic detail. We also show that the two copper sites in the protein communicate so that redox potentials and acidity constants of one site are affected by up to 0.2 V or 3 pKa units by a change in the oxidation state of the other site

Integrated Ugi-Based Assembly of Functionally, Skeletally, and Stereochemically Diverse 1,4-Benzodiazepin-2-ones

A practical, integrated and versatile U-4CR-based assembly of 1,4-benzodiazepin-2-ones exhibiting functionally, skeletally, and stereochemically diverse substitution patterns is described. By virtue of its convergence, atom economy, and bond-forming efficiency, the methodology documented herein exemplifies the reconciliation of structural complexity and experimental simplicity in the context of medicinal chemistry projects.This work was financially supported by the Galician Government (Spain), Projects: 09CSA016234PR and GPC-2014-PG037. J.A. thanks FUNDAYACUCHO (Venezuela) for a predoctoral grant and Deputación da Coruña (Spain) for a postdoctoral research grant. A.N.-V. thanks the Spanish government for a Ramón y Cajal research contract