Molecular dynamics simulations of sputtering of Langmuir-Blodgett multilayers by keV C(60) projectiles.

Coarse-grained molecular dynamics computer simulations are applied to investigate fundamental processes induced by an impact of keV C(60) projectile at an organic overlayer composed of long, well-organized linear molecules. The energy transfer pathways, sputtering yields, and the damage induced in the irradiated system, represented by a Langmuir-Blodgett (LB) multilayers composed from molecules of bariated arachidic acid, are investigated as a function of the kinetic energy and impact angle of the projectile and the thickness of the organic system. In particular, the unique challenges of depth profiling through a LB film vs. a more isotropic solid are discussed.The results indicate that the trajectories of projectile fragments and, consequently, the primary energy can be channeled by the geometrical structure of the overlayer. Although, a similar process is known from sputtering of single crystals by atomic projectiles, it has not been anticipated to occur during C(60) bombardment due to the large size of the projectile. An open and ordered molecular structure of LB films is responsible for such behavior. Both the extent of damage and the efficiency of sputtering depend on the kinetic energy, the impact angle, and the layer thickness. The results indicate that the best depth profiling conditions can be achieved with low-energy cluster projectiles irradiating the organic overlayer at large off-normal angles.

Dynamics of molecular impacts on soft materials: from fullerenes to organic nanodrops.

The present theoretical study explores the interaction of various energetic molecular projectiles and clusters with a model polymeric surface, with direct implications for surface analysis by mass spectrometry. The projectile sizes (up to 23 kDa) are intermediate between the polyatomic ions (SF(5), C(60)) used in secondary ion mass spectrometry and the large organic microdroplets generated, for example, in desorption electrospray ionization. The target is a model of amorphous polyethylene, already used in a previous study [Delcorte, A.; Garrison, B. J. J. Phys. Chem. C 2007, 111, 15312]. The chosen method relies on classical molecular dynamics (MD) simulations, using a coarse-grained description of polymeric samples for high energy or long time calculations (20-50 ps) and a full atomistic description for low energy or short time calculations (<1 ps). Two regions of sputtering or desorption are observed depending on the projectile energy per nucleon (i.e., effectively the velocity). The transition, occurring around 1 eV/nucleon, is identified by a change of slope in the curve of the sputtering yield per nucleon vs energy per nucleon. Beyond 1 eV/nucleon, the sputtering yield depends only on the total projectile energy and not on the projectile nuclearity. Below 1 eV/nucleon, i.e., around the sputtering threshold for small projectiles, yields are influenced by both the projectile energy and nuclearity. Deposition of intact molecular clusters is also observed at the lowest energies per nucleon. The transition in the sputtering curve is connected to a change of energy deposition mechanisms, from atomistic and mesoscopic processes to hydrodynamic flow. It also corresponds to a change in terms of fragmentation. Below 1 eV/nucleon, the projectiles are not able to induce bond scissions in the sample. This region of molecular emission with minimal fragmentation offers new analytical perspectives, out of reach of smaller molecular clusters such as fullerenes.

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.

Sputtering of water ice induced by C60 bombardment: onset of plume formation.

The interaction of a 5 keV C(60) projectile with amorphous water ice is studied using molecular dynamics computer simulations. The energetic C(60) molecule causes large-scale collisional events in the subsurface region, involving more than 10(4) water molecules in a time of less than 3 ps. The energy deposited in the sample is sufficiently large to turn the ice into a superheated and superdense gas. The gas is expelled into the vacuum, leading to the formation of a flow that manifests itself in the angular and velocity distributions of emitted water molecules.

Molecular dynamics simulation of the laser disintegration of aerosol particles.

The mechanisms of disintegration of submicrometer particles irradiated by short laser pulses are studied by a molecular dynamics simulation technique. Simulations at different laser fluences are performed for particles with homogeneous composition and particles with transparent inclusions. Spatially nonuniform deposition of laser energy is found to play a major role in defining the character and the extent of disintegration. The processes that contribute to the disintegration include overheating and explosive decomposition of the illuminated side of the particle, spallation of the backside of large particles, and disruption of the transparent inclusion caused by the relaxation of the laser-induced pressure. The observed mechanisms are related to the nature of the disintegration products and implications of the simulation results for aerosol time-of-flight mass spectrometry are discussed. Application of multiple laser pulses is predicted to be advantageous for efficient mass spectrometry sampling of aerosols with a large size to laser penetration depth ratio.

Molecule liftoff from surfaces.

Molecular dynamics simulations have been used to model the kiloelectronvolt particle bombardment of organic layers on metal substrates such as occurs in the analytical techniques of secondary ion mass spectrometry and fast atom bombardment mass spectrometry. Vignettes of insights gained from the simulations along with comparisons to experimental data are presented in this Account. Topics include intact molecular ejection vs fragmentation, prediction of reaction pathways, influence of the substrate, and quantitative predictions of energy and angular distributions.

Consideration of the pH-dependent inhibition of dihydrofolate reductase by methotrexate.

Poisson-Boltzmann calculations were used to determine the pKa of protein functional groups in the unliganded dihydrofolate reductase enzyme, and the pKa of protein and ligand groups in methotrexate-enzyme complexes. The results reported here are in conflict with two fundamental tenets of dihydrofolate reductase inhibition by methotrexate: (1) Asp27 is not expected to be protonated near pH 6.5 in the apoenzyme as previously proposed based on fitting of empirical equations to binding data, and (2) the calculated pKa for the pteridine N1 of the inhibitor while bound to the protein is significantly lower than that estimated for this group from interpretation of NMR data (>10). In fact, the electrostatic calculations and complementary quantum chemical calculations indicate that Asp27 is likely protonated when methotrexate is bound, resulting in a neutral dipole-dipole interaction rather than a salt-bridge between the enzyme and the inhibitor. Reasons for this discrepancy with the experimental data are discussed. Furthermore, His45 and Glu17 in the Escherichia coli enzyme are proposed to be in part responsible for the pH dependence of the conformational degeneracy in the inhibitor-enzyme complex.

Potential energy surfaces for chemical reactions at solid surfaces.

Many-body potential energy surfaces (PESs) for describing atomic interactions in gas-solid and surface reaction dynamics are reviewed in this work. Initial PESs from the 1960s-1970s were restricted to a diatomic molecule interacting with a solid surface. Since the 1980s, a multitude of many-body reactive PESs, their parameterization, and their applications have been reported in the literature. Although we mention most of the PESs in general, we have chosen to describe only those that either have had general utility or have had staying power, i.e. they have been used widely by other research groups. The potentials discussed in the most detail are the Stillinger-Weber and Tersoff Si PESs, the Brenner hydrocarbon PES, and the embedded-atom method (EAM) style potentials for metals. We conclude that although these PESs have been used successfully in large-scale computer simulations, further development is needed in many-body PESs. In particular, the development of new functional forms for multicomponent reactive systems is required.

Molecular dynamics simulations of dimer opening on a diamond {001}(2x1) surface.

Computer simulations of hydrocarbon and related molecules using empirical force fields have become important tools for studying a number of biological and related processes at the atomic scale. Traditional force fields, however, cannot be used to simulate dynamic chemical reactivity that involves changes in atomic hybridization. Application of a many-body potential function allows such reactivity to occur in a computer simulation. Simulations of the reaction of small hydrocarbon molecules adsorbed on a reconstructed diamond {001}(2x1) surface suggest that these hydrocarbons are highly reactive species and that initial stages of diamond growth proceed through a dimer-opening mechanism. Rates estimated from transition state theory of two interconversions between states where the dimer is open and closed are given.

Ion beam spectroscopy of solids and surfaces.

Ion beams are important new probes for characterizing the chemistry and structure of a wide variety of materials. When beams of particles with energies of approximately 1000 electron volts are used, as in secondary ion mass spectrometry, it is possible to detect ions ejected from the top layer of the material with sensitivities we below the picogram level. A number of theoretical developments now permit analysis of the geometry of adsorbed atoms and molecules on surfaces from the angular distributions of the ejected particles. Much surface chemical information can also be deduced from ejected molecular cluster ions. In addition, the observation of clusters with weights up to nearly 20,000 atomic mass units promises to expand applications of mass spectrometry to the analysis of biomolecules and the sequencing of proteins.