Surface-site reactivity in small-molecule adsorption: A theoretical study of thiol binding on multi-coordinated gold clusters

• Elvis C. M. Ting,
• Tatiana Popa and
• Irina Paci

Beilstein J. Nanotechnol. 2016, 7, 53–61, doi:10.3762/bjnano.7.6

• cluster with a broad range of metal site coordination numbers, from 3 to 9, and examined the binding conditions of methylthiol at the various sites. Conclusion: We found that despite the small molecular size, the dispersive interactions of the backbone are a determining factor in the molecular affinity

• , we focus, in the current work, on the surface-binding groups. To this end, we replaced molecular backbones with methyl groups, in order to remove factors such as lone-pair or charge-group surface interactions, and the overall backbone–surface interaction. We designed a 20-atom Au cluster, with gold

• atom sites spanning an array of coordination numbers Ni, with i = 3–9, and investigated the binding behavior of single molecules of methylthiol in its non-dissociated and dissociated forms, as a model for the surface-binding group of physisorbed and chemisorbed thiols. The cluster itself was built to

Effects of electronic coupling and electrostatic potential on charge transport in carbon-based molecular electronic junctions

• Richard L. McCreery

Beilstein J. Nanotechnol. 2016, 7, 32–46, doi:10.3762/bjnano.7.4

• close to that of the free G9 HOMO (−4.75 eV). The system H−3 orbital resembles the original AB HOMO, and is localized on the AB molecule in the G9−AB system. It is important to note here that the system H−1 and H−2 orbitals are “hybrid” orbitals formed when the AB is bonded to the G9 cluster. G9–AB is a

• cluster (middle), all in eV relative to a vacuum reference. Selected orbitals and their energies (in eV) are surround the diagram. Molecules are in their optimized geometries, with a 37° dihedral between G9 and AB planes in G9–AB. HOMO and H−1 orbitals for G9–AB for a range of dihedral angles between the

• G9 plane and AB aromatic rings, indicated at left. Orbital energies for all orbitals are indicated in blue, while the sum of the Mulliken charges on the AB moiety is indicated in red. A negative Mulliken charge indicates partial electron transfer from G9 to AB upon forming the covalent G9–AB cluster

Large area scanning probe microscope in ultra-high vacuum demonstrated for electrostatic force measurements on high-voltage devices

• Urs Gysin,
• Thilo Glatzel,
• Thomas Schmölzer,
• Adolf Schöner,
• Sergey Reshanov,
• Holger Bartolf and
• Ernst Meyer

Beilstein J. Nanotechnol. 2015, 6, 2485–2497, doi:10.3762/bjnano.6.258

• . The grain seems to be covered by a residual layer partly smearing out the CPD contrast. The PtIr-coated tip is most probably contaminated by a metal oxide cluster (CuO or CrO) due to slight tip–sample contacts before the measurements, such that the work function is around Φtip = 5 eV [40]. Also in

Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials

• Andrew Williams and
• Sabina Halappanavar

Beilstein J. Nanotechnol. 2015, 6, 2438–2448, doi:10.3762/bjnano.6.252

• of biclustering is that genes in the same cluster do not have to behave similarly over all experimental conditions. Unlike classical clustering techniques, biclusters can overlap with each other. This is ideal for mining functionally related gene sets as genes can be associated with more than one

• inflammation to be the predominant response following exposure to a variety of NMs. Bicluster-7 was the other significant cluster that was enriched in most of the experiments related to CNTs and CB. This cluster consisted of gene symbols showing strong association with pulmonary fibrosis. CNTs are well known

• for the cluster analysis was 1-correlation estimated using Spearman correlation with average linkage. Gene set enrichment results of the NM datasets. Barplots of the −log10(p-value) from the GSEA are presented for each of the NM studies. The studies are ordered in the barplots as follows: TiO2: UV

Sub-monolayer film growth of a volatile lanthanide complex on metallic surfaces

• Hironari Isshiki,
• Jinjie Chen,
• Kevin Edelmann and
• Wulf Wulfhekel

Beilstein J. Nanotechnol. 2015, 6, 2412–2416, doi:10.3762/bjnano.6.248

• and small clusters at the elbow sites of the Au(111) herringbone reconstruction [16], but no large islands at this coverage (see Figure 2e). Figure 2f shows an isolated molecule in the center, and two clusters containing three molecules (i.e., molecular trimers). The cluster formation at the elbow

Ultrastructural changes in methicillin-resistant Staphylococcus aureus induced by positively charged silver nanoparticles

• Dulce G. Romero-Urbina,
• Humberto H. Lara,
• J. Jesús Velázquez-Salazar,
• M. Josefina Arellano-Jiménez,
• Eduardo Larios,
• Anand Srinivasan,
• Jose L. Lopez-Ribot and
• Miguel José Yacamán

Beilstein J. Nanotechnol. 2015, 6, 2396–2405, doi:10.3762/bjnano.6.246

• to the MRSA cell wall, resulting in deformation and eventual cell bursting when AgNPs cluster around the cell wall (Figure 7a,b). SEM images were also obtained to compare MRSA and MSSA cells treated with AgNPs. In these images, we can see groups of whole cells and their sizes and morphologies, as

A simple and efficient quasi 3-dimensional viscoelastic model and software for simulation of tapping-mode atomic force microscopy

• Santiago D. Solares

Beilstein J. Nanotechnol. 2015, 6, 2233–2241, doi:10.3762/bjnano.6.229

• symmetric AFM tips and surfaces, including a defective tip that has a cluster protruding from its apex (this is described below). Similarly, the software tool provided assumes radial symmetry, but it can be easily modified to allow deviations from it. Figure 4a shows a typical force curve for the Q3D model

An adapted Coffey model for studying susceptibility losses in interacting magnetic nanoparticles

• Mihaela Osaci and
• Matteo Cacciola

Beilstein J. Nanotechnol. 2015, 6, 2173–2182, doi:10.3762/bjnano.6.223

• , and a clustered subsystem of nanoparticles. We considered the case of cluster forming because nanoparticles aggregate and form clusters in real-world specimens. Simulated clusters contain 50 nanoparticles with random local distribution. We defined the local volume fraction rV,loc, i.e., the volume

• fraction of nanoparticles in the cluster. The global volume fraction rV is the volume fraction in the simulated specimen. In case of uniformly and randomly distributed particles, or the clustered subsystem, the nanoparticles have been located within a body-centered cubic lattice. Considering each lattice

Distribution of Pd clusters on ultrathin, epitaxial TiO_x films on Pt₃Ti(111)

• Christian Breinlich,
• Maria Buchholz,
• Marco Moors,
• Tobias Pertram,
• Conrad Becker and
• Klaus Wandelt

Beilstein J. Nanotechnol. 2015, 6, 2007–2014, doi:10.3762/bjnano.6.204

• -type superstructure with fewer and shallower defects, making the template effect less discernible. Keywords: cluster growth; palladium; platinum–titanium alloy; scanning tunnelling microscopy (STM); template; titanium oxide; Introduction Catalysts often consist of metal nanoparticles dispersed on an

• we investigate the template effect of two different structures of the same type of oxide on the cluster growth of the same metal, namely Pd on z'-TiOx and w'-TiOx. Experimental setup The scanning tunnelling microscopy (STM) experiments were conducted on our custom-built LT-STM, which for the

• nucleation sites for cluster growth [15][16]. Pd cluster growth on the z'-TiOx phase Figure 2a shows an STM image of a z'-TiOx surface onto which Pd was deposited at room temperature for 90 s (≈0.1 ± 0.05 ML). The stripes and trenches of the z'-TiOx structure are visible in Figure 2a running from the upper

An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology

• Richard L. Marchese Robinson,
• Mark T. D. Cronin,
• Andrea-Nicole Richarz and
• Robert Rallo

Beilstein J. Nanotechnol. 2015, 6, 1978–1999, doi:10.3762/bjnano.6.202

• physicochemical characterisation data which the templates were designed to capture were based upon considering the well-known MINChar Initiative Parameters List [53], the provisional recommendations developed within the NanoSafety Cluster Databases Working Group [26], other resources developed within the context

• of the NanoSafety Cluster projects PreNanoTox [54] and MARINA [55] as well as discussions with nanotoxicology researchers and consideration of the published literature regarding toxicologically significant physicochemical characterisation parameters (for nanomaterials) and experimental variables

Magnetic reversal dynamics of a quantum system on a picosecond timescale

• Nikolay V. Klenov,
• Alexey V. Kuznetsov,
• Igor I. Soloviev,
• Sergey V. Bakurskiy and
• Olga V. Tikhonova

Beilstein J. Nanotechnol. 2015, 6, 1946–1956, doi:10.3762/bjnano.6.199

• ][27]. However, in our case, the problem is solved for a simple two-level system suitable for modeling the behavior of not only the superconducting flux qubits, but the atomic systems, including promising molecular magnetic memory cells, atom-like spins in semiconductors, magnetic cluster inclusion in

NanoE-Tox: New and in-depth database concerning ecotoxicity of nanomaterials

• Katre Juganson,
• Angela Ivask,
• Irina Blinova,
• Monika Mortimer and
• Anne Kahru

Beilstein J. Nanotechnol. 2015, 6, 1788–1804, doi:10.3762/bjnano.6.183

• that the available data on nanomaterials in environmental, health and safety databases and online chemical databases were very scarce [14]. Recently, a databases working group was established in the framework of European Union NanoSafety Cluster [15] which highlights the importance of development of in

The Nanomaterial Data Curation Initiative: A collaborative approach to assessing, evaluating, and advancing the state of the field

• Christine Ogilvie Hendren,
• Christina M. Powers,
• Mark D. Hoover and
• Stacey L. Harper

Beilstein J. Nanotechnol. 2015, 6, 1752–1762, doi:10.3762/bjnano.6.179

• called for in various ways by the NRC, the NNI and the EU Nanosafety Cluster. Multiple focal areas and driving goals must be considered across the data life cycle; multiple roles exist as well, with different orientations toward the data including creators, customers, curators, and analysts. At this

Radiation losses in the microwave K_u band in magneto-electric nanocomposites

• Talwinder Kaur,
• Sachin Kumar,
• Jyoti Sharma and
• A. K. Srivastava

Beilstein J. Nanotechnol. 2015, 6, 1700–1707, doi:10.3762/bjnano.6.173

• hexaferrite and (b) composite COP at room temperature in the X band. Hysteresis loops of composites. Transmission electron micrographs of magneto-electric composites (a) cluster of composites (b and c) particles of hexaferrite enclosed by polyaniline (CL6P). Reflection loss for composites. Real (µ′) and

In situ SU-8 silver nanocomposites

• Søren V. Fischer,
• Basil Uthuppu and
• Mogens H. Jakobsen

Beilstein J. Nanotechnol. 2015, 6, 1661–1665, doi:10.3762/bjnano.6.168

• . Acknowledgements This work is supported by the Copenhagen Cleantech Cluster and the DTU – KAIST IWT project.

Analysis of soil bacteria susceptibility to manufactured nanoparticles via data visualization

• Rong Liu,
• Yuan Ge,
• Patricia A. Holden and
• Yoram Cohen

Beilstein J. Nanotechnol. 2015, 6, 1635–1651, doi:10.3762/bjnano.6.166

• identify treatments that induced similar impacts on the soil bacterial communities (i.e., the main underlying structure of the MNP soil bacterial community data). Hierarchical clustering successively merges together similar treatments or treatment groups until a single cluster is attained [38][39

• ], providing a dendrogram of hierarchical similarity among the treatments. In the hierarchical clustering, average-link (defined as for two clusters Ci and Cj) was used as inter-cluster distance measure since it is robust to outliers [38][39]. An advantage of the hierarchical clustering based on the L1

• ] established using average-link [32][38][39]. According to the recommended threshold of L1 < 0.5 [32], three meta-clusters were identified from the heatmap with Cluster II and III mainly comprised of MNPs exposed for 15 and 60 days and Cluster I formed by the remainder (Figure 11). Characterization of Cluster

The eNanoMapper database for nanomaterial safety information

• Nina Jeliazkova,
• Charalampos Chomenidis,
• Philip Doganis,
• Bengt Fadeel,
• Roland Grafström,
• Barry Hardy,
• Janna Hastings,
• Markus Hegi,
• Vedrin Jeliazkov,
• Nikolay Kochev,
• Pekka Kohonen,
• Cristian R. Munteanu,
• Haralambos Sarimveis,
• Bart Smeets,
• Pantelis Sopasakis,
• Georgia Tsiliki,
• David Vorgrimmler and
• Egon Willighagen

Beilstein J. Nanotechnol. 2015, 6, 1609–1634, doi:10.3762/bjnano.6.165

• , Lucca, Italy in silico toxicology Gmbh (IST), Basel, Switzerland 10.3762/bjnano.6.165 Abstract Background: The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials

• originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. Results: The eNanoMapper database

• interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure–activity relationships for nanomaterials (NanoQSAR). Keywords: database; EU NanoSafety Cluster; nanoinformatics; nanomaterials; nanomaterials ontology; NanoQSAR; safety

Experiences in supporting the structured collection of cancer nanotechnology data using caNanoLab

• Stephanie A. Morris,
• Sharon Gaheen,
• Michal Lijowski,
• Mervi Heiskanen and
• Juli Klemm

Beilstein J. Nanotechnol. 2015, 6, 1580–1593, doi:10.3762/bjnano.6.161

• area have included development and enhancement of the NPO and ISA-TAB-Nano. ISA-TAB-Nano is currently used by NCI, the NBI Knowledgebase (http://nbi.oregonstate.edu/), and the EU NanoSafety Cluster (http://www.nanosafetycluster.eu/) to enable interoperability between databases. Most recently, the Nano

Influence of surface chemical properties on the toxicity of engineered zinc oxide nanoparticles to embryonic zebrafish

• Zitao Zhou,
• Jino Son,
• Bryan Harper,
• Zheng Zhou and
• Stacey Harper

Beilstein J. Nanotechnol. 2015, 6, 1568–1579, doi:10.3762/bjnano.6.160

• using either four or five clusters shows minor differences compared to the use of three clusters, namely the coated 26 nm NPs (except octanoic acid) separated out of Group 3 in the four cluster calculation and the blank control point separated out of Group 1 in the five clusters calculation in addition

• between clusters might happen making determination of the cluster number the first concern. Although there are several algorithms to decide the cluster number, the lack of robust data sets such as this preclude a current understanding of which algorithm may be appropriate [48]. Kriging estimation Based on

• each concentration (Figure 6, Supporting Information File 4). Kriging estimation further elucidated the impacts of NP size. Based on Figure 6, we can see that the largest bare particle (NGZ) also has the highest mortality (Figure 3B) and the cluster 2 surface modified 26 nm particles were predicted to

Peptide-equipped tobacco mosaic virus templates for selective and controllable biomineral deposition

• Klara Altintoprak,
• Axel Seidenstücker,
• Alexander Welle,
• Sabine Eiben,
• Petia Atanasova,
• Nina Stitz,
• Alfred Plettl,
• Joachim Bill,
• Hartmut Gliemann,
• Holger Jeske,
• Dirk Rothenstein,
• Fania Geiger and
• Christina Wege

Beilstein J. Nanotechnol. 2015, 6, 1399–1412, doi:10.3762/bjnano.6.145

• residues arranged blockwise to expose a cluster of imidazole side chains; and (iii) 44C (HSSHHQPKGTNPC) and 31C (HHGHSPTSPQVRC), two ZnO-binding peptides isolated by phage display [60]. The distinct peptide-fashioned TMVLys templates were incubated in TEOS precursor solution in parallel with linker-coated

• mineralized TMV or control preparations in ultrapure water (see TMV particle mineralization) were pipetted on a gold-covered n-Si wafer and air dried. ToF-SIMS was performed on a TOF.SIMS5 instrument (ION-TOF GmbH, Münster, Germany). The spectrometer was equipped with a Bi cluster primary ion source and a

Scalable, high performance, enzymatic cathodes based on nanoimprint lithography

• Dmitry Pankratov,
• Richard Sundberg,
• Javier Sotres,
• Dmitry B. Suyatin,
• Ivan Maximov,
• Sergey Shleev and
• Lars Montelius

Beilstein J. Nanotechnol. 2015, 6, 1377–1384, doi:10.3762/bjnano.6.142

• concomitant reduction of O2 directly to H2O in a trinuclear Cu cluster (T2/T3 Cu cluster) positioned 12–13 Å away [5][6][7], without releasing reactive O2 species, such as hydrogen peroxide or superoxide radicals [8][9]. Three-dimensional electrodes for enzyme-based cathodes are usually used to design high

Heterometal nanoparticles from Ru-based molecular clusters covalently anchored onto functionalized carbon nanotubes and nanofibers

• Deborah Vidick,
• Xiaoxing Ke,
• Michel Devillers,
• Claude Poleunis,
• Arnaud Delcorte,
• Pietro Moggi,
• Gustaaf Van Tendeloo and
• Sophie Hermans

Beilstein J. Nanotechnol. 2015, 6, 1287–1297, doi:10.3762/bjnano.6.133

• Scienze 17/A, 43124 Parma, Italy 10.3762/bjnano.6.133 Abstract Heterometal clusters containing Ru and Au, Co and/or Pt are anchored onto carbon nanotubes and nanofibers functionalized with chelating phosphine groups. The cluster anchoring yield is related to the amount of phosphine groups available on

• and atmospheric pressure with very low Ru loading. Keywords: ammonia synthesis; cluster; nanofibers; nanoparticles; nanotubes; Introduction Metal nanoparticles (NPs) supported on nanoscopic forms of carbon (nanotubes, nanofibers) are an important class of nanostructured materials that find

• associations can be synthesized with a large degree of freedom. This ensures the intimate mixing of the metals when nucleating heterometal nanoparticles by thermal treatment. Because this treatment only requires removing the ligand sheath, ultrasmall, mixed-metal entities directly derived from the cluster

Tattoo ink nanoparticles in skin tissue and fibroblasts

• Colin A. Grant,
• Peter C. Twigg,
• Richard Baker and
• Desmond J. Tobin

Beilstein J. Nanotechnol. 2015, 6, 1183–1191, doi:10.3762/bjnano.6.120

• (Figure 4b and Figure 4d), the periodic banding that is associated with collagen fibrils can clearly be resolved [26][27]. The inset of Figure 4e is a detailed view of the area surrounding a small cluster of particles from Figure 4d, with the corresponding line profile shown in Figure 4e. The pigment

• tattoo ink particles in the collagen network. Height (a & c) and amplitude (b & d) images of disperse ink particles in the dermal collagen network. (Inset of (e)) 500 nm image of small cluster of ink particles from the solid red square (e) Line profile showing a particle of 37.5 nm width at half height

Magnetic properties of iron cluster/chromium matrix nanocomposites

• Arne Fischer,
• Robert Kruk,
• Di Wang and
• Horst Hahn

Beilstein J. Nanotechnol. 2015, 6, 1158–1163, doi:10.3762/bjnano.6.117

• A custom-designed apparatus was used for the fine-tuned co-deposition of preformed Fe clusters into antiferromagnetic Cr matrices. Three series of samples with precisely defined cluster sizes, with accuracy to a few atoms, and controlled concentrations were fabricated, followed by a complete

• characterization of structure and magnetic performance. Relevant magnetic characteristics, reflecting the ferromagnetic/antiferromagnetic coupling between Fe clusters and the Cr matrix, i.e., blocking temperature, coercivity field, and exchange bias were measured and their dependence on cluster size and cluster

• concentration in the matrix was analyzed. It is evident that the blocking temperatures are clearly affected by both the cluster size and their concentration in the Cr matrix. In contrast the coercivity shows hardly any dependence on size or inter-cluster distance. The exchange bias was found to be strongly

High sensitivity and high resolution element 3D analysis by a combined SIMS–SPM instrument

• Yves Fleming and
• Tom Wirtz

Beilstein J. Nanotechnol. 2015, 6, 1091–1099, doi:10.3762/bjnano.6.110

• of the TiCN cermet. Keywords: alloy; atomic force microscopy (AFM); correlative microscopy; differential sputtering; in situ; multimodal imaging; nano-cluster; polymer blend; secondary ion mass spectrometry (SIMS); scanning probe microscopy (SPM); SIMS artefacts; sputter-induced effects; sputter

• CN− signal. The secondary ion signal corresponding to the CN− cluster is much more intense than the signal of monatomic nitrogen. The obtained 3D map shows that the two polymer phases are well separated and that the sample under investigation is far from being flat. Prior to Cs+ bombardment, the