Molecular Dynamics Simulations of Particle Bombardment Induced Desorption Processes: Alkanethiolates on Au(111)

Heat conduction in polymer chains: Effect of substrate on the thermal conductance

In standard molecular junctions, a molecular structure is placed between and connected to metal leads. Understanding how mechanical tuning in such molecular junctions can change heat conductance has interesting applications in nanoscale energy transport. In this work, we use nonequilibrium molecular dynamics simulations to address the effect of stretching on the phononic contribution to the heat conduction of molecular junctions consisting of single long-chain alkanes and various metal leads, such as Ag, Au, Cu, Ni, and Pt. The thermal conductance of such junctions is found to be much smaller than the intrinsic thermal conductance of the polymer and significantly depends on the nature of metal leads as expressed by the metal–molecule coupling and metal vibrational density of states. This behavior is expected and reflects the mismatch of phonon spectra at the metal molecule interfaces. As a function of stretching, we find a behavior similar to what was observed earlier [M. Dinpajooh and A. Nitzan, J. Chem. Phys. 153, 164903 (2020)] for pure polymeric structures. At relatively short electrode distances, where the polyethylene chains are compressed, it is found that the thermal conductances of the molecular junctions remain almost constant as one stretches the polymer chains. At critical electrode distances, the thermal conductances start to increase, reaching the values of the fully extended molecular junctions. Similar behaviors are observed for junctions in which several long-chain alkanes are sandwiched between various metal leads. These findings indicate that this behavior under stretching is an intrinsic property of the polymer chain and not significantly associated with the interfacial structures.

Time-of-flight secondary ion mass spectrometry in the helium ion microscope

A helium ion microscope, known for high resolution imaging and modification with helium or neon ions, has been equipped with a time-of-flight spectrometer for compositional analysis. Here we report on its design, implementation and show first results of this powerful add-on. Our design considerations were based on the results of detailed ion collision cascade simulations that focus on the physically achievable resolution for various detection limits. Different secondary ion extraction geometries and spectrometer types are considered and compared with respect to the demands and limitations of the microscope. As a result the development and evaluation of a secondary ion extraction optics and time-of-flight spectrometer that allows the parallel measurement of all secondary ion masses is reported. First experimental results demonstrate an excellent mass resolution as well as high-resolution secondary ion imaging capabilities with sub-8 nm lateral resolution. The combination of high resolution secondary electron images and mass-separated sputtered ion distributions have a high potential to answer open questions in microbiology, cell biology, earth sciences and materials research.

Argon ion irradiation induced morphological instability of bare and thiol-functionalized Au(111) surfaces

Systematical investigation of Ar ion irradiation-induced changes in the surface morphology of bare and dodecanethiol self-assembled monolayer covered Au(111) surfaces.

Development of a semiempirical potential for simulations of thiol-gold interfaces. Application to thiol-protected gold nanoparticles

A new semiempirical potential, based on density functional calculations and a bond-order Morse-like potential, is developed to simulate the adsorption behavior of thiolate molecules on non-planar gold surfaces, including relaxing effects, in a more realistic way. The potential functions include as variables the metal-molecule separation, vibrational frequencies, bending and torsion angles between several pairs of atom types and the coordination number of both the metal (Au) and thiolate groups. The potential was parameterized based on a set of density functional calculations of molecular adsorption in several surface sites (i.e. hollow, bridge, top, on-top Au adatom and the novel staple motif) for different crystalline facets, i.e. Au(111) and (100). Langevin dynamics simulations have been performed to study the capping effects of alkanethiolates molecules on Au nanoparticles in the range 1-4 nm. The simulation results reveal an enhancement of the coverage degree whilst the nanoparticles diameter decreases. A high surface disorder due to the strong S-Au bond was found, in very good agreement with very recent experimental findings [M. M. Mariscal, J. A. Olmos-Asar, C. Gutierrez-Wing, A. Mayoral and M. J. Yacaman, Phys. Chem. Chem. Phys., 2010, 12, 11785].

On the atomic structure of thiol-protected gold nanoparticles: a combined experimental and theoretical study

In the present work new findings on the structure of the S-Au interface are presented. Theoretical calculations using a new semiempirical potential, based on density functional theory and a bond-order Morse potential, are employed to simulate the adsorption process in a more realistic way. The simulation results reveal the formation of gold adatoms on the nanoparticle surface and high surface disorder due to the strong S-Au bond. Experimental data were acquired by aberration (Cs) corrected scanning transmission electron microscopy (STEM) using a high angle annular dark field detector (HAADF) that showed a great similarity with the theory predicted.

Simulation of atmospheric transport and droplet–thin film collisions in desorption electrospray ionization

Computational fluid dynamics is used to model atmospheric transport and droplet-thin film (surface) collisions in desorption electrospray ionization; experimentally obtained droplet properties are replicated in the simulations while a "droplet pick-up" mechanism of analyte transport is confirmed.

Diffusion on a Self-Assembled Monolayer: Molecular Modeling of a Bound + Mobile Lubricant

The diffusion of tricresyl phosphate molecules on an octadecyltrichlorosilane self-assembled monolayer (SAM) was characterized using molecular dynamics simulations. The simulations predict that when placed on the top of a close-packed SAM, the molecules remain mobile on the surface with an isotropic diffusion activation energy of approximately 9 kJ/mol. In contrast, an anisotropic barrier that results from chain tilt within the SAM is predicted for diffusion into a defect created by reducing the alkane chain length within a cylinderical region of the surface. Once in the defect, the molecules become trapped by embedding part of the molecule into the side of the SAM.

Understanding Gold−Thiolate Cluster Emission from Self-assembled Monolayers upon Kiloelectronvolt Ion Bombardment

This article focuses on the emission of organometallic clusters upon kiloelectronvolt ion bombardment of self-assembled monolayers. It is particularly relevant for the elucidation of the physical processes underlying secondary ion mass spectrometry (SIMS). The experimental system, an overlayer of octanethiols on gold, was modeled by classical molecular dynamics, using a hydrocarbon potential involving bonding and nonbonding interactions (AIREBO). To validate the model, the calculated mass and energy distributions of sputtered atoms and molecules were compared to experimental data. Our key finding concerns the emission mechanism of large clusters of the form MxAuy up to M6Au5 (where M is the thiolate molecule), which were not observed under sub-kiloelectronvolt projectile bombardment. Statistically, they are predominantly formed in high-yield events, where many atoms, fragments, and (supra)molecular species are desorbed from the surface. From the microscopic viewpoint, these high-yield events mostly stem from the confinement of the projectile and recoil atom energies in a finite microvolume of the sample surface. As a result of the high local energy density, molecular aggregates desorb from an overheated liquidlike region surrounding the impact point of the projectile.

Metal Salts for Molecular Ion Yield Enhancement in Organic Secondary Ion Mass Spectrometry: A Critical Assessment

In a search for molecular ion signal enhancement in organic SIMS, the efficiency of a series of organic and inorganic salts for molecular cationization has been tested using a panel of nonvolatile molecules with very different chemical characteristics (leucine enkephalin, Irganox 1010, tetraphenylnaphthalene, polystyrene). The compounds used for cationization include alkali bromide and group Ib metal salts (XBr with X = Li, Na, K; CF3CO2Ag; AgNO3; [CH3COCH=C(O-)CH3]2Cu; AuCl3). Alkali ions, very good for polar molecule cationization, prove to be of limited interest for nonpolar molecules such as polystyrene. Silver trifluoroacetate displays excellent results for all the considered molecules, except for leucine enkephalin (which might be due to the use of different solvents for the analyte and the salt). Instead, silver nitrate mixed with leucine enkephalin in an ethanol solution provides intense molecular signals. The influence of the respective concentrations of analyte and salt in solution, of the silver trifluoroacetate solution stability, and of the sample microstructure on the secondary ion intensities are also investigated. The results of other combinations of analyte and salts are reported. Finally, the use of salts is critically compared to other sample preparation procedures previously proposed for SIMS analysis of large organic molecules.