On-surface chemical reactions characterised by ultra-high resolution scanning probe microscopy

In the last decade it has become possible to resolve the geometric structure of organic molecules with intramolecular resolution using high resolution scanning probe microscopy (SPM), and specifically using the subset of SPM known as noncontact atomic force microscopy (ncAFM). In world leading groups it has become routine not only to perform sub-molecular imaging of the chemical, electronic, and electrostatic properties of single molecules, but also to use this technique to track complex on-surface chemical reactions, investigate novel reaction products, and even synthesise new molecular structures one bond at a time. These developments represent the cutting edge of characterisation at the single chemical bond level, and have revolutionised our understanding of surface-based chemical processes

Physisorption controls the conformation and density of states of an adsorbed porphyrin

Conformational changes caused by adsorption can dramatically affect a molecule’s properties. Despite extensive study, however, the exact mechanisms underpinning conformational switching are often unclear. Here we show that the conformation of a prototypical flexible molecule, the freebase tetra(4-bromophenyl) porphyrin, adsorbed on Cu(111), depends critically on its precise adsorption site and that, remarkably, large conformational changes are dominated by van der Waals interactions between the molecule and the substrate surface. A combination of scanning probe microscopy, single-molecule manipulation, DFT with dispersion density functional theory, and molecular dynamics simulations show that van der Waals forces drive significant distortions of the molecular architecture so that the porphyrin can adopt one of two low-energy conformations. We find that adsorption driven by van der Waals forces alone is capable of causing large shifts in the molecular density of states, despite the apparent absence of chemical interactions. These findings highlight the essential role that van der Waals forces play in determining key molecular properties

Height dependent molecular trapping in stacked cyclic porphyrin nanorings

Stacked layers of cyclic porphyrin nanorings constitute nanoscale receptacles with variable height and diameter which preferentially adsorb sublimed molecules. Using scanning tunnelling microscopy we determine the filling capacity of these nanoring traps, and the dependence of adsorbate capture on stack height and diameter

Adsorption structure of iron phthalocyanine and titanyl phthalocyanine on Cu(1 1 1)

The adsorption structure of iron phthalocyanine (FePc) and titanyl phthalocyanine (TiOPc) was studied by a combination of near edge X-ray absorption fine structure (NEXAFS) spectroscopy and normal incidence X-ray standing waves (NIXSW) technique. The FePc results demonstrate that the molecule adsorbs with the Fe metal centre at an adsorption height of 2.44 ± 0.09 Å, its macrocycle plane mostly parallel with the underlying surface and a single adsorption configuration. However, a small distortion of the isoindole groups, with respect to one another, is required to rationalise the results. The TiOPc results similarly indicate that the macrocycle plane is mostly parallel with the underlying surface up to thick multilayer films, yet, in the monolayer regime, the molecule must adsorb in multiple configurations. These configurations are nominally assigned to a mixture of adsorption configurations with some Ti=O bonds pointing towards the surface, and some pointing away. We determine that, in both configurations, the Ti metal centre sits at a similar adsorption height above the surface of 3.00 ± 0.20 Å

Structural characterisation of molecular conformation and the incorporation of adatoms in an on-surface Ullmann-type reaction

© 2020, The Author(s). The on-surface synthesis of covalently bonded materials differs from solution-phase synthesis in several respects. The transition from a three-dimensional reaction volume to quasi-two-dimensional confinement, as is the case for on-surface synthesis, has the potential to facilitate alternative reaction pathways to those available in solution. Ullmann-type reactions, where the surface plays a role in the coupling of aryl-halide functionalised species, has been shown to facilitate extended one- and two-dimensional structures. Here we employ a combination of scanning tunnelling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and X-ray standing wave (XSW) analysis to perform a chemical and structural characterisation of the Ullmann-type coupling of two iodine functionalised species on a Ag(111) surface held under ultra-high vacuum (UHV) conditions. Our results allow characterisation of molecular conformations and adsorption geometries within an on-surface reaction and provide insight into the incorporation of metal adatoms within the intermediate structures of the reaction

Using polycyclic aromatic hydrocarbons for graphene growth on Cu(111) under ultra-high vacuum

Ultra-high vacuum deposition of the polycyclic aromatic hydrocarbons azupyrene and pyrene onto a Cu(111) surface held at a temperature of 1000 K is herein shown to result in the formation of graphene. The presence of graphene was proven using scanning tunneling microscopy, x-ray photoelectron spectroscopy, angle-resolved photoemission spectroscopy, Raman spectroscopy, and low energy electron diffraction. The precursors, azupyrene and pyrene, are comparatively large aromatic molecules in contrast to more commonly employed precursors like methane or ethylene. While the formation of the hexagonal graphene lattice could naively be expected when pyrene is used as a precursor, the situation is more complex for azupyrene. In this case, the non-alternant topology of azupyrene with only 5- and 7-membered rings must be altered to form the observed hexagonal graphene lattice. Such a rearrangement, converting a non-alternant topology into an alternant one, is in line with previous reports describing similar topological alterations, including the isomerization of molecular azupyrene to pyrene. The thermal synthesis route to graphene, presented here, is achievable at comparatively low temperatures and under ultra-high vacuum conditions, which may enable further investigations of the growth process in a strictly controlled and clean environment that is not accessible with traditional precursors

Self-Assembled Monolayer of Cr7Ni Molecular Nanomagnets by Sublimation

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Southeast Asia and the Politics of Vulnerability

The economic and political crises that have recently engulfed the countries of Southeast Asia provide a stark reminder of just how difficult the challenge of sustained regional development remains. In retrospect, the hyperbole that surrounded the 'East Asian miracle' looks overblown, and testimony to the manner in which rhetoric can outstrip reality, especially in the minds of international investors. Certainly, some observers had questioned the depth and resilience of capitalist development in Southeast Asia, but in the years immediately prior to 1997 such analyses tended to be in the minority. Now, of course, it is painfully obvious that much of Southeast Asia's economic and political development was extremely fragile. When seen in historical context, this outcome should not have been surprising since the countries of modern Southeast Asia, both as independent nations and as colonies of various imperial powers, have been highly vulnerable to the actions of powerful external political and economic forces. This paper will examine the economic bases and the political consequences of this vulnerablity, both domestically and at a regional level. I argue that the recent crisis has served as an unwelcome reminder of just how constrained, dependent and vulnerable the Southeast Asia region's development prospects remain, a situation that is exacerbated by, and which contributes to, domestic political crises

An Analysis on the Detection of Biological Contaminants Aboard Aircraft

The spread of infectious disease via commercial airliner travel is a significant and realistic threat. To shed some light on the feasibility of detecting airborne pathogens, a sensor integration study has been conducted and computational investigations of contaminant transport in an aircraft cabin have been performed. Our study took into consideration sensor sensitivity as well as the time-to-answer, size, weight and the power of best available commercial off-the-shelf (COTS) devices. We conducted computational fluid dynamics simulations to investigate three types of scenarios: (1) nominal breathing (up to 20 breaths per minute) and coughing (20 times per hour); (2) nominal breathing and sneezing (4 times per hour); and (3) nominal breathing only. Each scenario was implemented with one or seven infectious passengers expelling air and sneezes or coughs at the stated frequencies. Scenario 2 was implemented with two additional cases in which one infectious passenger expelled 20 and 50 sneezes per hour, respectively. All computations were based on 90 minutes of sampling using specifications from a COTS aerosol collector and biosensor. Only biosensors that could provide an answer in under 20 minutes without any manual preparation steps were included. The principal finding was that the steady-state bacteria concentrations in aircraft would be high enough to be detected in the case where seven infectious passengers are exhaling under scenarios 1 and 2 and where one infectious passenger is actively exhaling in scenario 2. Breathing alone failed to generate sufficient bacterial particles for detection, and none of the scenarios generated sufficient viral particles for detection to be feasible. These results suggest that more sensitive sensors than the COTS devices currently available and/or sampling of individual passengers would be needed for the detection of bacteria and viruses in aircraft