The effect of tip structure in atomic manipulation : a combined DFT and AFM study.

Non-contact atomic force microscopy allows us to directly probe the interactions between atoms and molecules. When operated in UHV and at low temperatures, a host of experiments, uniquely possible with the technique, can be carried out. The AFM allows us to characterise the forces present on a surface, resolve the atomic structure of molecules, measure the force required to move an atom, and even directly measure molecular pair potentials. Generally speaking, it is the interaction between the outermost tip and surface atoms that we measure. Therefore, in each of these experiments, understanding, or controlling, the tip termination is essential. As NC-AFM experiments become increasingly sophisticated, the combination of experiment and simulation has become critical to understand, and guide the processes at play. In this thesis, I focus on semiconductor surfaces and investigate the role of tip structure in a variety of situations with both DFT simulations and NC-AFM experiments. The clean Si(100) surface consists of rows of dimers, which can be manipulated between two different states using an NC-AFM. In order to understand the manipulation process, detailed DFT and NEB simulations were conducted to examine the energy balance of ideal and defective surfaces, with or without the presence of an AFM tip. We show that an explanation can only be reached when we consider both the AFM tip and variations in the PES caused by surface defects. NC-AFM experiments were also conducted on Si(100):H. We find that on this surface we regularly cultivate chemically passivated, hydrogen-terminated, tip apices which lead to distinct inverted image contrasts in our AFM images. Following a thorough characterisation of the tip apex, we conduct preliminary experiments designed to investigate surface defect structures, and to chemically modify the tip termination. Detailed DFT simulations show that this type of tip engineering, however, critically depends on the larger tip structure, significantly complicating the chances of success. Additionally, we investigate the structure and stability of silicon tip apices using DFT. Even with relatively simple tip structures, we observe complex behaviours, such as tip-dependent dissipation and structural development. These processes provide interesting information regarding tip stability, and commonly observed experimental behaviour. We also model an experiment in which we functionalise the tip apex with a C60 molecule, revealing for the first time that submolecular resolution is possible in the attractive regime

The effect of tip structure in atomic manipulation : a combined DFT and AFM study.

Non-contact atomic force microscopy allows us to directly probe the interactions between atoms and molecules. When operated in UHV and at low temperatures, a host of experiments, uniquely possible with the technique, can be carried out. The AFM allows us to characterise the forces present on a surface, resolve the atomic structure of molecules, measure the force required to move an atom, and even directly measure molecular pair potentials. Generally speaking, it is the interaction between the outermost tip and surface atoms that we measure. Therefore, in each of these experiments, understanding, or controlling, the tip termination is essential. As NC-AFM experiments become increasingly sophisticated, the combination of experiment and simulation has become critical to understand, and guide the processes at play. In this thesis, I focus on semiconductor surfaces and investigate the role of tip structure in a variety of situations with both DFT simulations and NC-AFM experiments. The clean Si(100) surface consists of rows of dimers, which can be manipulated between two different states using an NC-AFM. In order to understand the manipulation process, detailed DFT and NEB simulations were conducted to examine the energy balance of ideal and defective surfaces, with or without the presence of an AFM tip. We show that an explanation can only be reached when we consider both the AFM tip and variations in the PES caused by surface defects. NC-AFM experiments were also conducted on Si(100):H. We find that on this surface we regularly cultivate chemically passivated, hydrogen-terminated, tip apices which lead to distinct inverted image contrasts in our AFM images. Following a thorough characterisation of the tip apex, we conduct preliminary experiments designed to investigate surface defect structures, and to chemically modify the tip termination. Detailed DFT simulations show that this type of tip engineering, however, critically depends on the larger tip structure, significantly complicating the chances of success. Additionally, we investigate the structure and stability of silicon tip apices using DFT. Even with relatively simple tip structures, we observe complex behaviours, such as tip-dependent dissipation and structural development. These processes provide interesting information regarding tip stability, and commonly observed experimental behaviour. We also model an experiment in which we functionalise the tip apex with a C60 molecule, revealing for the first time that submolecular resolution is possible in the attractive regime

Measuring the reactivity of a silicon-terminated probe

It is generally accepted that the exposed surfaces of silicon crystals are highly reactive due to the dangling bonds which protrude into the vacuum. However, surface reconstruction can not only modify the reactivity of bulk silicon crystals, but plays a key role in determining the properties of silicon nanocrystals. In this study we probe the reactivity of silicon clusters at the end of a scanning probe tip by examining their interaction with closed shell fullerene molecules. Counter to intuitive expectations, many silicon clusters do not react strongly with the fullerene cage, and we find that only specific highly oriented clusters have sufficient reactivity to break open the existing carbon-carbon bonds

Measuring the mechanical properties of molecular conformers

Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules

Simulated structure and imaging of NTCDI on Si(1 1 1)-7 × 7 : a combined STM, NC-AFM and DFT study

The adsorption of naphthalene tetracarboxylic diimide (NTCDI) on Si(1 1 1)-7 × 7 is investigated through a combination of scanning tunnelling microscopy (STM), noncontact atomic force microscopy (NC-AFM) and density functional theory (DFT) calculations. We show that NTCDI adopts multiple planar adsorption geometries on the Si(1 1 1)-7 × 7 surface which can be imaged with intramolecular bond resolution using NC-AFM. DFT calculations reveal adsorption is dominated by covalent bond formation between the molecular oxygen atoms and the surface silicon adatoms. The chemisorption of the molecule is found to induce subtle distortions to the molecular structure, which are observed in NC-AFM images

Intermolecular artifacts in probe microscope images of C60 assemblies

Claims that dynamic force microscopy has the capability to resolve intermolecular bonds in real space continue to be vigorously debated. To date, studies have been restricted to planar molecular assemblies with small separations between neighboring molecules. Here we report the observation of intermolecular artifacts over much larger distances in 2D assemblies of C60 molecules, with compelling evidence that in our case the tip apex is terminated by a C60 molecule (rather than the CO termination typically exploited in ultrahigh resolution force microscopy). The complete absence of directional interactions such as hydrogen or halogen bonding, the nonplanar structure of C60, and the fullerene termination of the tip apex in our case highlight that intermolecular artifacts are ubiquitous in dynamic force microscopy

Mapping the force field of a hydrogen-bonded assembly

Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism

Mapping the force field of a hydrogen-bonded assembly

Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism. © 2014 Macmillan Publishers Limited. All rights reserved

AIDS-related mycoses: the way forward.

The contribution of fungal infections to the morbidity and mortality of HIV-infected individuals is largely unrecognized. A recent meeting highlighted several priorities that need to be urgently addressed, including improved epidemiological surveillance, increased availability of existing diagnostics and drugs, more training in the field of medical mycology, and better funding for research and provision of treatment, particularly in developing countries

Effects of a high-dose 24-h infusion of tranexamic acid on death and thromboembolic events in patients with acute gastrointestinal bleeding (HALT-IT): an international randomised, double-blind, placebo-controlled trial

Background: Tranexamic acid reduces surgical bleeding and reduces death due to bleeding in patients with trauma. Meta-analyses of small trials show that tranexamic acid might decrease deaths from gastrointestinal bleeding. We aimed to assess the effects of tranexamic acid in patients with gastrointestinal bleeding. Methods: We did an international, multicentre, randomised, placebo-controlled trial in 164 hospitals in 15 countries. Patients were enrolled if the responsible clinician was uncertain whether to use tranexamic acid, were aged above the minimum age considered an adult in their country (either aged 16 years and older or aged 18 years and older), and had significant (defined as at risk of bleeding to death) upper or lower gastrointestinal bleeding. Patients were randomly assigned by selection of a numbered treatment pack from a box containing eight packs that were identical apart from the pack number. Patients received either a loading dose of 1 g tranexamic acid, which was added to 100 mL infusion bag of 0·9% sodium chloride and infused by slow intravenous injection over 10 min, followed by a maintenance dose of 3 g tranexamic acid added to 1 L of any isotonic intravenous solution and infused at 125 mg/h for 24 h, or placebo (sodium chloride 0·9%). Patients, caregivers, and those assessing outcomes were masked to allocation. The primary outcome was death due to bleeding within 5 days of randomisation; analysis excluded patients who received neither dose of the allocated treatment and those for whom outcome data on death were unavailable. This trial was registered with Current Controlled Trials, ISRCTN11225767, and ClinicalTrials.gov, NCT01658124. Findings: Between July 4, 2013, and June 21, 2019, we randomly allocated 12 009 patients to receive tranexamic acid (5994, 49·9%) or matching placebo (6015, 50·1%), of whom 11 952 (99·5%) received the first dose of the allocated treatment. Death due to bleeding within 5 days of randomisation occurred in 222 (4%) of 5956 patients in the tranexamic acid group and in 226 (4%) of 5981 patients in the placebo group (risk ratio [RR] 0·99, 95% CI 0·82–1·18). Arterial thromboembolic events (myocardial infarction or stroke) were similar in the tranexamic acid group and placebo group (42 [0·7%] of 5952 vs 46 [0·8%] of 5977; 0·92; 0·60 to 1·39). Venous thromboembolic events (deep vein thrombosis or pulmonary embolism) were higher in tranexamic acid group than in the placebo group (48 [0·8%] of 5952 vs 26 [0·4%] of 5977; RR 1·85; 95% CI 1·15 to 2·98). Interpretation: We found that tranexamic acid did not reduce death from gastrointestinal bleeding. On the basis of our results, tranexamic acid should not be used for the treatment of gastrointestinal bleeding outside the context of a randomised trial