Enhanced nanochannel translocation and localization of genomic DNA molecules using three-dimensional nanofunnels.

The ability to precisely control the transport of single DNA molecules through a nanoscale channel is critical to DNA sequencing and mapping technologies that are currently under development. Here we show how the electrokinetically driven introduction of DNA molecules into a nanochannel is facilitated by incorporating a three-dimensional nanofunnel at the nanochannel entrance. Individual DNA molecules are imaged as they attempt to overcome the entropic barrier to nanochannel entry through nanofunnels with various shapes. Theoretical modeling of this behavior reveals the pushing and pulling forces that result in up to a 30-fold reduction in the threshold electric field needed to initiate nanochannel entry. In some cases, DNA molecules are stably trapped and axially positioned within a nanofunnel at sub-threshold electric field strengths, suggesting the utility of nanofunnels as force spectroscopy tools. These applications illustrate the benefit of finely tuning nanoscale conduit geometries, which can be designed using the theoretical model developed here.Forcing a DNA molecule into a nanoscale channel requires overcoming the free energy barrier associated with confinement. Here, the authors show that DNA injected through a funnel-shaped entrance more efficiently enters the nanochannel, thanks to facilitating forces generated by the nanofunnel geometry.

Polaronic transport and current blockades in epitaxial silicide nanowires and nanowire arrays.

Crystalline micrometer-long YSi2 nanowires with cross sections as small as 1 × 0.5 nm(2) can be grown on the Si(001) surface. Their extreme aspect ratios make electron conduction within these nanowires almost ideally one-dimensional, while their compatibility with the silicon platform suggests application as metallic interconnect in Si-based nanoelectronic devices. Here we combine bottom-up epitaxial wire synthesis in ultrahigh vacuum with top-down miniaturization of the electrical measurement probes to elucidate the electronic conduction mechanism of both individual wires and arrays of nanowires. Temperature-dependent transport through individual nanowires is indicative of thermally assisted tunneling of small polarons between atomic-scale defect centers. In-depth analysis of complex wire networks emphasize significant electronic crosstalk between the nanowires due to the long-range Coulomb fields associated with polaronic charge fluctuations. This work establishes a semiquantitative correlation between the density and distributions of atomic-scale defects and resulting current-voltage characteristics of nanoscale network devices.

Electrokinetically-driven transport of DNA through focused ion beam milled nanofluidic channels.

The electrophoretically driven transport of double-stranded λ-phage DNA through focused ion beam (FIB) milled nanochannels is described. Nanochannels were fabricated having critical dimensions (width and depth) corresponding to 0.5×, 1×, and 2× the DNA persistence length, or 25 nm, 50 nm, and 100 nm, respectively. The threshold field strength required to drive transport, the threading mobility, and the transport mobility were measured as a function of nanochannel size. As the nanochannel dimensions decreased, the entropic barrier to translocation increased and transport became more constrained. Equilibrium models of confinement provide a framework in which to understand the observed trends, although the dynamic nature of the experiments resulted in significant deviations from theory. It was also demonstrated that the use of dynamic wall coatings for the purpose of electroosmotic flow suppression can have a significant impact on transport dynamics that may obfuscate entropic contributions. The nonintermittent DNA transport through the FIB milled nanochannels demonstrates that they are well suited for use in nanofluidic devices. We expect that an understanding of the dynamic transport properties reported here will facilitate the incorporation of FIB-milled nanochannels in devices for single molecule and ensemble analyses.

A device for performing lateral conductance measurements on individual double-stranded DNA molecules.

A nanofluidic device is described that is capable of electrically monitoring the driven translocation of DNA molecules through a nanochannel. This is achieved by intersecting a long transport channel with a shorter orthogonal nanochannel. The ionic conductance of this transverse nanochannel is monitored while DNA is electrokinetically driven through the transport channel. When DNA passes the intersection, the transverse conductance is altered, resulting in a transient current response. In 1 M KCl solutions, this was found to be a current enhancement of 5-25%, relative to the baseline transverse ionic current. Two different device geometries were investigated. In one device, the DNA was detected after it was fully inserted into and translocating through the transport nanochannel. In the other device, the DNA was detected while it was in the process of entering the nanochannel. It was found that these two conditions are characterized by different transport dynamics. Simultaneous optical and electrical monitoring of DNA translocation confirmed that the transient events originated from DNA transport through the nanochannel intersection.

Industrial Ziegler-type hydrogenation catalysts made from Co(neodecanoate)2 or Ni(2-ethylhexanoate)2 and AlEt3: evidence for nanoclusters and sub-nanocluster or larger Ziegler-nanocluster based catalysis.

Ziegler-type hydrogenation catalysts are important for industrial processes, namely, the large-scale selective hydrogenation of styrenic block copolymers. Ziegler-type hydrogenation catalysts are composed of a group 8-10 transition metal precatalyst plus an alkylaluminum cocatalyst (and they are not the same as Ziegler-Natta polymerization catalysts). However, for ∼50 years two unsettled issues central to Ziegler-type hydrogenation catalysis are the nature of the metal species present after catalyst synthesis, and whether the species primarily responsible for catalytic hydrogenation activity are homogeneous (e.g., monometallic complexes) or heterogeneous (e.g., Ziegler nanoclusters defined as metal nanoclusters made from combination of Ziegler-type hydrogenation catalyst precursors). A critical review of the existing literature (Alley et al. J. Mol. Catal. A: Chem. 2010, 315, 1-27) and a recently published study using an Ir model system (Alley et al. Inorg. Chem. 2010, 49, 8131-8147) help to guide the present investigation of Ziegler-type hydrogenation catalysts made from the industrially favored precursors Co(neodecanoate)(2) or Ni(2-ethylhexanoate)(2), plus AlEt(3). The approach and methods used herein parallel those used in the study of the Ir model system. Specifically, a combination of Z-contrast scanning transmission electron microscopy (STEM), matrix assisted laser desorption ionization mass spectrometry (MALDI MS), and X-ray absorption fine structure (XAFS) spectroscopy are used to characterize the transition metal species both before and after hydrogenation. Kinetic studies including Hg(0) poisoning experiments are utilized to test which species are the most active catalysts. The main findings are that, both before and after catalytic cyclohexene hydrogenation, the species present comprise a broad distribution of metal cluster sizes from subnanometer to nanometer scale particles, with estimated mean cluster diameters of about 1 nm for both Co and Ni. The XAFS results also imply that the catalyst solutions are a mixture of the metal clusters described above, plus unreduced metal ions. The kinetics-based Hg(0) poisoning evidence suggests that Co and Ni Ziegler nanoclusters (i.e., M(≥4)) are the most active Ziegler-type hydrogenation catalysts in these industrial systems. Overall, the novelty and primary conclusions of this study are as follows: (i) this study examines Co- and Ni-based catalysts made from the actual industrial precursor materials, catalysts that are notoriously problematic regarding their characterization; (ii) the Z-contrast STEM results reported herein represent, to our knowledge, the best microscopic analysis of the industrial Co and Ni Ziegler-type hydrogenation catalysts; (iii) this study is the first explicit application of an established method, using multiple analytical methods and kinetics-based studies, for distinguishing homogeneous from heterogeneous catalysis in these Ziegler-type systems; and (iv) this study parallels the successful study of an Ir model Ziegler catalyst system, thereby benefiting from a comparison to those previously unavailable findings, although the greater M-M bond energy, and tendency to agglomerate, of Ir versus Ni or Co are important differences to be noted. Overall, the main result of this work is that it provides the leading hypothesis going forward to try to refute in future work, namely, that sub, M(≥4) to larger, M(n) Ziegler nanoclusters are the dominant, industrial, Co- and Ni- plus AlR(3) catalysts in Ziegler-type hydrogenation systems.

The atomic structural dynamics of γ-Al2O3 supported Ir-Pt nanocluster catalysts prepared from a bimetallic molecular precursor: a study using aberration-corrected electron microscopy and X-ray absorption spectroscopy.

This study describes a prototypical, bimetallic heterogeneous catalyst: compositionally well-defined Ir-Pt nanoclusters with sizes in the range of 1-2 nm supported on γ-Al(2)O(3). Deposition of the molecular bimetallic cluster [Ir(3)Pt(3)(µ-CO)(3)(CO)(3)(η-C(5)Me(5))(3)] on γ-Al(2)O(3), and its subsequent reduction with hydrogen, provides highly dispersed supported bimetallic Ir-Pt nanoparticles. Using spherical aberration-corrected scanning transmission electron microscopy (C(s)-STEM) and theoretical modeling of synchrotron-based X-ray absorption spectroscopy (XAS) measurements, our studies provide unambiguous structural assignments for this model catalytic system. The atomic resolution C(s)-STEM images reveal strong and specific lattice-directed strains in the clusters that follow local bonding configurations of the γ-Al(2)O(3) support. Combined nanobeam diffraction (NBD) and high-resolution transmission electron microscopy (HRTEM) data suggest the polycrystalline γ-Al(2)O(3) support material predominantly exposes (001) and (011) surface planes (ones commensurate with the zone axis orientations frequently exhibited by the bimetallic clusters). The data reveal that the supported bimetallic clusters exhibit complex patterns of structural dynamics, ones evidencing perturbations of an underlying oblate/hemispherical cuboctahedral cluster-core geometry with cores that are enriched in Ir (a result consistent with models based on surface energetics, which favor an ambient cluster termination by Pt) due to the dynamical responses of the M-M bonding to the specifics of the adsorbate and metal-support interactions. Taken together, the data demonstrate that strong temperature-dependent charge-transfer effects occur that are likely mediated variably by the cluster-support, cluster-adsorbate, and intermetallic bonding interactions.

Fabrication of sub-5 nm nanochannels in insulating substrates using focused ion beam milling.

The use of focused ion beam (FIB) milling to fabricate nanochannels with critical dimensions extending below 5 nm is described. FIB milled lines have narrowing widths as they are milled deeper into a substrate. This focusing characteristic is coupled with a two-layered architecture consisting of a relatively thick (>100 nm) metal film deposited onto a substrate. A channel is milled through the metal layer until it penetrates a prescribed depth into the substrate material. The metal is then removed, leaving a nanochannel with smooth surfaces and lateral dimensions as small as sub-5 nm. These open nanochannels can be sealed with a cover plate and the resulting devices are well-suited for single-molecule DNA transport studies. This methodology is used with quartz, single-crystal silicon, and polydimethylsiloxane substrates to demonstrate its general utility.

Iridium Ziegler-type hydrogenation catalysts made from [(1,5-COD)Ir(mu-O2C8H15)](2) and AlEt3: spectroscopic and kinetic evidence for the Ir(n) species present and for nanoparticles as the fastest catalyst.

Ziegler-type hydrogenation catalysts, those made from a group 8-10 transition metal precatalyst and an AlR(3) cocatalyst, are often used for large scale industrial polymer hydrogenation; note that Ziegler-type hydrogenation catalysts are not the same as Ziegler-Natta polymerization catalysts. A review of prior studies of Ziegler-type hydrogenation catalysts (Alley et al. J. Mol. Catal. A: Chem. 2010, 315, 1-27) reveals that a approximately 50 year old problem is identifying the metal species present before, during, and after Ziegler-type hydrogenation catalysis, and which species are the kinetically best, fastest catalysts--that is, which species are the true hydrogenation catalysts. Also of significant interest is whether what we have termed "Ziegler nanoclusters" are present and what their relative catalytic activity is. Reported herein is the characterization of an Ir Ziegler-type hydrogenation catalyst, a valuable model (vide infra) for the Co-based industrial Ziegler-type hydrogenation catalyst, made from the crystallographically characterized [(1,5-COD)Ir(mu-O(2)C(8)H(15))](2) precatalyst plus AlEt(3). Characterization of this Ir model system is accomplished before and after catalysis using a battery of physical methods including Z-contrast scanning transmission electron microscopy (STEM), high resolution (HR)TEM, and X-ray absorption fine structure (XAFS) spectroscopy. Kinetic studies plus Hg(0) poisoning experiments are then employed to probe which species are the fastest catalysts. The main findings herein are that (i) a combination of the catalyst precursors [(1,5-COD)Ir(mu-O(2)C(8)H(15))](2) and AlEt(3) gives catalytically active solutions containing a broad distribution of Ir(n) species ranging from monometallic Ir complexes to nanometer scale, noncrystalline Ir(n) nanoclusters (up to Ir(approximately 100) by Z-contrast STEM) with the estimated mean Ir species being 0.5-0.7 nm, Ir(approximately 4-15) clusters considering the similar, but not identical results from the different analytical methods; furthermore, (ii) the mean Ir(n) species are practically the same regardless of the Al/Ir ratio employed, suggesting that the observed changes in catalytic activity at different Al/Ir ratios are primarily the result of changes in the form or function of the Al-derived component (and not due to significant AlEt(3)-induced changes in initial Ir(n) nuclearity). However (iii), during hydrogenation, a shift in the population of Ir species toward roughly 1.0-1.6 nm, fcc Ir(0)(approximately 40-150), Ziegler nanoclusters occurs with, significantly, (iv) a concomitant increase in catalytic activity. Importantly, and although catalysis by discrete subnanometer Ir species is not ruled out by this study, (v) the increases in activity with increased nanocluster size, plus Hg(0) poisoning studies, provide the best evidence to date that the approximately 1.0-1.6 nm, fcc Ir(0)(approximately 40-150), heterogeneous Ziegler nanoclusters are the fastest catalysts in this industrially related catalytic hydrogenation system (and in the simplest, Ockham's Razor interpretation of the data). In addition, (vi) Ziegler nanoclusters are confirmed to be an unusual, hydrocarbon-soluble, highly coordinatively unsaturated, Lewis-acid containing, and highly catalytically active type of nanocluster for use in other catalytic applications and other areas.

The emergence of nonbulk properties in supported metal clusters: negative thermal expansion and atomic disorder in Pt nanoclusters supported on gamma-Al2O3.

The structural dynamics-cluster size and adsorbate-dependent thermal behaviors of the metal-metal (M-M) bond distances and interatomic order-of Pt nanoclusters supported on a gamma-Al(2)O(3) are described. Data from scanning transmission electron microscopy (STEM) and X-ray absorption spectroscopy (XAS) studies reveal that these materials possess a dramatically nonbulklike nature. Under an inert atmosphere small, subnanometer Pt/gamma-Al(2)O(3) clusters exhibit marked relaxations of the M-M bond distances, negative thermal expansion (NTE) with an average linear thermal expansion coefficient alpha = (-2.4 +/- 0.4) x 10(-5) K(-1), large static disorder and dynamical bond (interatomic) disorder that is poorly modeled within the constraints of classical theory. The data further demonstrate a significant temperature-dependence to the electronic structure of the Pt clusters, thereby suggesting the necessity of an active model to describe the cluster/support interactions mediating the cluster's dynamical structure. The quantitative dependences of these nonbulklike behaviors on cluster size (0.9 to 2.9 nm), ambient atmosphere (He, 4% H(2) in He or 20% O(2) in He) and support identity (gamma-Al(2)O(3) or carbon black) are systematically investigated. We show that the nonbulk structural, electronic and dynamical perturbations are most dramatically evidenced for the smallest clusters. The adsorption of hydrogen on the clusters leads to an increase of the Pt-Pt bondlengths (due to a lifting of the surface relaxation) and significant attenuation of the disorder present in the system. Oxidation of these same clusters has the opposite effect, leading to an increase in Pt-Pt bond strain and subsequent enhancement in nonbulklike thermal properties. The structural and electronic properties of Pt nanoclusters supported on carbon black contrast markedly with those of the Pt/gamma-Al(2)O(3) samples in that neither NTE nor comparable levels of atomic disorder are observed. The Pt/C nanoclusters do exhibit, however, both size- and adsorbate-induced trends in bond strain that are similar to those of their Pt/gamma-Al(2)O(3) analogues. Taken together, the data highlight the significant role that electronic effects--specifically charge exchange due to both metal-support and metal-adsorbate interactions--play in mediating the structural dynamics of supported nanoscale metal clusters that are broadly used as heterogeneous catalysts.

Unusual non-bulk properties in nanoscale materials: thermal metal-metal bond contraction of gamma-alumina-supported Pt catalysts.

Variable-temperature X-ray absorption spectroscopy measurements of sub-nanometer Pt nanoparticles on a high-surface-area gamma-alumina support reveal that the Pt-Pt bonds exhibit contraction upon heating [i.e., negative thermal expansion (NTE)]. Bare clusters under a He environment show an average linear expansion coefficient of -2.5 x 10-5 K-1 over the temperature range studied. Adsorption of hydrogen results in an overall bond relaxation and less dramatic Pt-Pt thermal bond-length contraction. From the temperature effect on bond length, disorder parameters, and the X-ray absorption near edge structure (XANES) spectra, temperature-dependent charge transfer between the support and the Pt clusters was concluded to be responsible for the observed behavior.

Metal core bonding motifs of monodisperse icosahedral Au13 and larger Au monolayer-protected clusters as revealed by X-ray absorption spectroscopy and transmission electron microscopy.

The atomic metal core structures of the subnanometer clusters Au13[PPh3]4[S(CH2)11CH3]2Cl2 (1) and Au13[PPh3]4[S(CH2)11CH3]4 (2) were characterized using advanced methods of electron microscopy and X-ray absorption spectroscopy. The number of gold atoms in the cores of these two clusters was determined quantitatively using high-angle annular dark field scanning transmission electron microscopy. Multiple-scattering-path analyses of extended X-ray absorption fine structure (EXAFS) spectra suggest that the Au metal cores of each of these complexes adopt an icosahedral structure with a relaxation of the icosahedral strain. Data from microscopy and spectroscopy studies extended to larger thiolate-protected gold clusters showing a broader distribution in nanoparticle core sizes (183 +/- 116 Au atoms) reveal a bulklike fcc structure. These results further support a model for the monolayer-protected clusters (MPCs) in which the thiolate ligands bond preferentially at 3-fold atomic sites on the nanoparticle surface, establishing an average composition for the MPC of Au180[S(CH2)11CH3]40. Results from EXAFS measurements of a gold(I) dodecanethiolate polymer are presented that offer an alternative explanation for observations in previous reports that were interpreted as indicating Au MPC structures consisting of a Au core, Au2S shell, and thiolate monolayer.

Sub-nanometer Au monolayer-protected clusters exhibiting molecule-like electronic behavior: quantitative high-angle annular dark-field scanning transmission electron microscopy and electrochemical characterization of clusters with precise atomic stoichiometry.

The synthesis and characterization of the clusters Au13[PPh3]4[S(CH2)11CH3]2Cl2 (1) and Au13[PPh3]4[S(CH2)11CH3]4 (2) are described. These mixed-ligand, sub-nanometer clusters, prepared via exchange of dodecanethiol onto phosphine-halide gold clusters, show enhanced stability relative to the parent. The characterization of these clusters features the precise determination of the number of gold atoms in the cluster cores using high-angle annular dark-field scanning transmission electron microscopy, allowing the assignment of 13 gold atoms (+/-3 atoms) to the composition of both cluster molecules. Electrochemical and optical measurements reveal discrete molecular orbital levels and apparent energy gaps of 1.6-1.7 eV for the two cluster molecules. The electrochemical measurements further indicate that the Au13[PPh3]4[S(CH2)11CH3]2Cl2 cluster undergoes an overall two-electron reduction. The electrochemical and spectroscopic properties of the two Au13 cluster molecules are compared with those of a secondary synthetic product, which proved to be larger Au thiolate-derivatized monolayer-protected clusters with an average core of Au180. The latter shows behavior fully consistent with the adoption of metallic-like properties.