Matthew Watkins

Large variation of vacancy formation energies in the surface of crystalline ice

Resolving the atomic structure of the surface of ice particles within clouds, over the temperature range encountered in the atmosphere and relevant to understanding heterogeneous catalysis on ice, remains an experimental challenge. By using first-principles calculations, we show that the surface of crystalline ice exhibits a remarkable variance in vacancy formation energies, akin to an amorphous material. We find vacancy formation energies as low as ~0.1-0.2 eV, which leads to a higher than expected vacancy concentration. Because a vacancys reactivity correlates with its formation energy, ice particles may be more reactive than previously thought. We also show that vacancies significantly reduce the formation energy of neighbouring vacancies, thus facilitating pitting and contributing to pre-melting and quasi-liquid layer formation. These surface properties arise from proton disorder and the relaxation of geometric constraints, which suggests that other frustrated materials may possess unusual surface characteristics.

Role of water in atomic resolution AFM in solutions

We use computer modelling to investigate the mechanism of atomic-scale corrugation in frequency modulation atomic force microscopy imaging of inorganic surfaces in solution. Molecular dynamics simulations demonstrate that the forces acting on a model microscope tip result from the direct interaction between a tip and a surface, and forces entirely due to the water structure around both tip and surface. The observed force is a balance between largely repulsive potential energy changes as the tip approaches and the entropic gain when water is sterically prevented from occupying sites near the tip and surface. Only extremely sharp tips are likely to measure direct tip-surface interactions. An investigation into the dynamics of water confined between tip and surface shows that water diffusion can be slowed by at least two orders of magnitude compared to its rate in bulk solution.

Unambiguous Determination of the Adsorption Geometry of a Metal—Organic Complex on a Bulk Insulator

Individual molecules of Co-Salen, a small chiral paramagnetic metal--organic Schiff base complex, were deposited on NaCl(001) and subsequently imaged with noncontact atomic force microscopy employing Cr coated tips in a cryogenic ultrahigh vacuum environment. Images were obtained in which both the position and orientation of the adsorbed molecules and the atomic structure of the surface are resolved simultaneously, enabling the determination of the exact adsorption site. Density functional theory calculations were used to identify the ionic sublattice resolved with the Cr tip and also to confirm the adsorption site and orientation of the molecule on the surface. These calculations show that the central Co atom of the molecule physisorbs on top of a Cl ion and is aligned along 110-directions in its lowest energy configuration. In addition, a local energy minimum exists along 100-directions. Due to the chirality of the molecule, two mirror symmetric configurations rotated by approximately +/-5 degrees away from these directions are energetically equivalent. The resulting 16 low energy configurations are observed in the experimental images.

Point defects at the ice (0001) surface

Using density functional theory we investigate whether intrinsic defects in ice surface segregate. We predict that hydronium, hydroxide, and the Bjerrum L- and D-defects are all more stable at the surface. However, the energetic cost to create a D-defect at the surface and migrate it into the bulk crystal is smaller than its bulk formation energy. Absolute and relative segregation energies are sensitive to the surface structure of ice, especially the spatial distribution of protons associated with dangling hydrogen bonds. It is found that the basal plane surface of hexagonal ice increases the bulk concentration of Bjerrum defects, strongly favoring D-defects over L-defects. Dangling protons associated with undercoordinated water molecules are preferentially injected into the crystal bulk as Bjerrum D-defects, leading to a surface dipole that attracts hydronium ions. Aside from the disparity in segregation energies for the Bjerrum defects, we find the interactions between defect species to be very finely balanced; surface segregation energies for hydronium and hydroxide species and trapping energies of these ionic species with Bjerrum defects are equal within the accuracy of our calculations. The mobility of the ionic hydronium and hydroxide species is greatly reduced at the surface in comparison to the bulk due to surface sites with high trapping affinities. We suggest that, in pure ice samples, the surface of ice will have an acidic character due to the presence of hydronium ions. This may be important in understanding the reactivity of ice particulates in the upper atmosphere and at the boundary layer.

Using metallic noncontact atomic force microscope tips for imaging insulators and polar molecules: tip characterization and imaging mechanisms.

We demonstrate that using metallic tips for noncontact atomic force microscopy (NC-AFM) imaging at relatively large (>0.5 nm) tip-surface separations provides a reliable method for studying molecules on insulating surfaces with chemical resolution and greatly reduces the complexity of interpreting experimental data. The experimental NC-AFM imaging and theoretical simulations were carried out for the NiO(001) surface as well as adsorbed CO and Co-Salen molecules using Cr-coated Si tips. The experimental results and density functional theory calculations confirm that metallic tips possess a permanent electric dipole moment with its positive end oriented toward the sample. By analyzing the experimental data, we could directly determine the dipole moment of the Cr-coated tip. A model representing the metallic tip as a point dipole is described and shown to produce NC-AFM images of individual CO molecules adsorbed onto NiO(001) in good quantitative agreement with experimental results. Finally, we discuss methods for characterizing the structure of metal-coated tips and the application of these tips to imaging dipoles of large adsorbed molecules.

Modelling atomic scale manipulation with the non-contact atomic force microscope

We present the results of calculations performed to model the process of lateral manipulation of an oxygen vacancy in the MgO(001) surface using the non-contact atomic force microscope (NC-AFM). The potential energy surfaces for the manipulation as a function of tip position are determined from atomistic modelling of the MgO(001) surface interacting with a Mg terminated MgO tip. These energies are then used to model the dynamical evolution of the system as the tip oscillates and at a finite temperature using a kinetic Monte Carlo method. The manipulation process is strongly dependent on the lateral position of the tip and the system temperature. It is also found that the expectation value of the point at which the vacancy jumps depends on the trajectory of the oscillating cantilever as the surface is approached. The effect of the manipulation on the operation of the NC-AFM is modelled with a virtual dynamic AFM, which explicitly simulates the entire experimental instrumentation and control loops. We show how measurable experimental signals can result from a single controlled atomic scale event and suggest the most favourable conditions for achieving successful atomic scale manipulation experimentally.

Modelling of non-contact atomic force microscopy imaging of individual molecules on oxide surfaces

We have modelled NC-AFM imaging of organic molecules adsorbed on the MgO(100) and TiO2(110) surfaces, to study whether molecules adsorbed at well determined surface sites could serve as markers for chemical resolution of surface species and possible mechanisms of adsorption and manipulation of such molecules with NC-AFM tips. We calculated images of perfect MgO and TiO2 surfaces and considered the adsorption of the formate ion and 3-{4-[Tris-(3,5-di-tert-butyl-phenyl)-methyl]-phenoxy}-propionic acid (C52H72O3) at the MgO(100) and TiO2(110) surfaces, respectively, using several types of oxide tip models. The results demonstrate that using adsorption of even small molecules, such as formate, for identifying surface chemical species in NC-AFM images may not be practical. The interaction of hydrocarbon molecules with perfect oxide surfaces is weak and their adsorption should be aided by attaching special anchoring groups. Flat molecules can be identified by their shape, but simultaneous atomic resolution inside the molecule and on the substrate under the same imaging conditions is not feasible.

Models of the interaction of metal tips with insulating surfaces

Summary We present the results of atomistic simulations of metallic atomic-force-microscopy tips interacting with ionic substrates, with atomic resolution. Chromium and tungsten tips are used to image the NaCl(001) and MgO(001) surfaces. The interaction of the tips with the surface is simulated by using density-functional-theory calculations employing a mixed Gaussian and plane-wave basis and cluster-tip models. In each case, the apex of the metal cluster interacts more attractively with anions in the surfaces than with cations, over the range of typical imaging distances, which leads to these sites being imaged as raised features (bright) in constant-frequency-shift images. We compare the results of the interaction of a chromium tip with the NaCl surface, with calculations employing exclusively plane-wave basis sets and a fully periodic tip model, and demonstrate that the electronic structure of the tip model employed can have a significant quantitative effect on calculated forces when the tip and surface are clearly separated.

Efficient parametrization of complex molecule–surface force fields

We present an efficient scheme for parametrizing complex molecule–surface force fields from ab initio data. The cost of producing a sufficient fitting library is mitigated using a 2D periodic embedded slab model made possible by the quantum mechanics/molecular mechanics scheme in CP2K. These results were then used in conjunction with genetic algorithm (GA) methods to optimize the large parameter sets needed to describe such systems. The derived potentials are able to well reproduce adsorption geometries and adsorption energies calculated using density functional theory. Finally, we discuss the challenges in creating a sufficient fitting library, determining whether or not the GA optimization has completed, and the transferability of such force fields to similar molecules.

A comparison of dynamic atomic force microscope set-ups for performing atomic scale manipulation experiments

We present the results of calculations performed to investigate the process of single-atom manipulation with the non-contact atomic force microscope comparing the two most common experimental set-ups: a conventional large amplitude silicon cantilever and a small amplitude quartz tuning fork. The manipulation of a model system-an oxygen vacancy in the MgO(001) surface by a single vertical approach at a fixed lateral position-is simulated for each set-up using a detailed and realistic atomistic model that accounts for temperature and the tip trajectory, and it is found that both approaches produce the manipulation event in approximately the same way. The behaviour of the tip dynamics and the resulting response of the instrumentation to the manipulation event is studied using a virtual dynamic atomic force microscope that includes a realistic description of noise for each type of set-up. The results of these calculations indicate how a single-atom manipulation can be performed and recognized by each type of experiment.