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Bergren A.J.,Canadian National Institute For Nanotechnology | McCreery R.L.,University of Alberta
Annual Review of Analytical Chemistry | Year: 2011

This review discusses the analytical characterization of molecular electronic devices and structures relevant thereto. In particular, we outline the methods for probing molecular junctions, which contain an ensemble of molecules between two contacts. We discuss the analytical methods that aid in the fabrication and characterization of molecular junctions, beginning with the confirmation of the placement of a molecular layer on a conductive or semiconductive substrate. We emphasize methods that provide information about the molecular layer in the junction and outline techniques to ensure molecular layer integrity after the complete fabrication of a device. In addition, we discuss the analytical information derived during the actual device operation. Copyright © 2011 by Annual Reviews. All rights reserved.

Buriak J.M.,University of Alberta | Buriak J.M.,Canadian National Institute For Nanotechnology
Chemistry of Materials | Year: 2014

Silicon is the cornerstone material of the semiconductor industry. As feature sizes on chips continue to decrease in size, the ratio of surface to bulk increases, and as a result, the role of surface defects, surface states and other subtle features play larger roles in the functioning of the device. Although silicon oxides have served the industry well as the passivation chemistry of choice, there is interest in expanding the repertoire of accessible and efficient chemical functional strategies available for use, and to fully understand the nature of these interfaces. For new applications such as molecular electronics on silicon and biochips, for example, there is a need to avoid the layer of intervening insulating oxide: A well-defined linkage of organic molecules through a silicon-carbon bond has great promise and appeal. Hydrosilylation, the insertion of an alkene or alkyne into a surface Si-H bond, is an ideal approach to producing these covalent Si-C bonds, and can be carried out in a number of ways. Light-promoted hydrosilylation is promising because it is clean and direct and can be patterned via masking; it requires no additional reagents such as catalysts or input of thermal energy and thus may have reduced surface contamination and numbers of defects. In this perspective, we start by making connections between the molecular silane literature, and the first reports of UV-mediated hydrosilylation of an alkene on a silicon surface, a reaction that was assumed to operate via a radical mechanism. We then describe the unexpected development of four new mechanisms that have no obvious parallels with the molecular silane literature, and take place as a result of the solid state electronics of the underlying silicon itself. From exciton involvement, to the influence of plasmonics, to the role of photoemission, the area of silicon surface hydrosilylation has become incredibly rich, and undoubtedly still contains new reactivity to be discovered. © 2013 American Chemical Society.

Xia J.,University of Alberta | Wishart D.S.,University of Alberta | Wishart D.S.,Canadian National Institute For Nanotechnology
Nature Protocols | Year: 2011

MetaboAnalyst is an integrated web-based platform for comprehensive analysis of quantitative metabolomic data. It is designed to be used by biologists (with little or no background in statistics) to perform a variety of complex metabolomic data analysis tasks. These include data processing, data normalization, statistical analysis and high-level functional interpretation. This protocol provides a step-wise description on how to format and upload data to MetaboAnalyst, how to process and normalize data, how to identify significant features and patterns through univariate and multivariate statistical methods and, finally, how to use metabolite set enrichment analysis and metabolic pathway analysis to help elucidate possible biological mechanisms. The complete protocol can be executed in ∼45 min. © 2011 Nature America, Inc. All rights reserved.

Woodside M.T.,University of Alberta | Woodside M.T.,Canadian National Institute For Nanotechnology | Block S.M.,Stanford University
Annual Review of Biophysics | Year: 2014

Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to controlled forces, has emerged as a powerful tool for probing energy landscapes. We summarize methods for reconstructing landscapes from force spectroscopy measurements under both equilibrium and nonequilibrium conditions. Other complementary, but technically less demanding, methods provide a model-dependent characterization of key features of the landscape. Once reconstructed, energy landscapes can be used to study critical folding parameters, such as the characteristic transition times required for structural changes and the effective diffusion coefficient setting the timescale for motions over the landscape. We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate. Copyright © 2014 by Annual Reviews. All rights reserved.

Bonifas A.P.,Ohio State University | Bonifas A.P.,Canadian National Institute For Nanotechnology | McCreery R.L.,Canadian National Institute For Nanotechnology | McCreery R.L.,University of Alberta
Nature Nanotechnology | Year: 2010

Virtually all types of molecular electronic devices depend on electronically addressing a molecule or molecular layer through the formation of a metallic contact. The introduction of molecular devices into integrated circuits will probably depend on the formation of contacts using a vapour deposition technique, but this approach frequently results in the metal atoms penetrating or damaging the molecular layer. Here, we report a method of forming soft metallic contacts on molecular layers through surface-diffusion-mediated deposition, in which the metal atoms are deposited remotely and then diffuse onto the molecular layer, thus eliminating the problems of penetration and damage. Molecular junctions fabricated by this method exhibit excellent yield (typically >90%) and reproducibility, and allow examination of the effects of molecular-layer structure, thickness and contact work function. © 2010 Macmillan Publishers Limited. All rights reserved.

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