Centre d’Élaboration de Matériaux et d’Etudes Structurales (UPR 8011)

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Interaction between an atom or a molecule and a nano-object or a surface.

Monday 17 October 2016, by Nathalie Tarrat

Selection of our most recent publications on this topic - The names of the team members are in blue

Carbohydrate self‐assembly at surfaces: STM imaging of sucrose conformation and ordering on Cu(100)

Sabine Abb, Nathalie Tarrat, Juan Cortés, Bohdan Andriyevsky, Ludger Harnau, J. Christian Schön, Stephan Rauschenbach, Klaus Kern

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Saccharides are ubiquitous biomolecules but little is known about their interaction with and assembly on surfaces. Combining preparative mass spectrometry with scanning tunneling microscopy, we have been able to address the conformation and self‐assembly of the disaccharide sucrose on the Cu(100) surface with subunit‐level imaging. By combining a multi‐stage modelling approach and experimental data, we can rationalize the conformation on the surface as well as the interactions between the sucrose molecules, yielding models of the observed self‐assembled patterns on the surface.

On the role of intermolecular interactions in stabilizing AuNP@Ampicillin nano-antibiotics

Xavier Fenouillet, Magali Benoit and Nathalie Tarrat

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 The fight against antibiotic resistance has become a major public health issue in recent years. In this context, nano-antibiotics composed of gold nanoparticles with antibiotics grafted on their surface often exhibit outstanding properties, sometimes even bypassing bacterial resistance mechanisms. Among these nano-antibiotics, gold nanoparticles/ampicillin hybrid systems (AuNPs@Ampicillin) are very effective. However, despite their very promising antibacterial properties, very little information concerning their atomic-scale structure is reported in the literature. In the present paper, the structure and energetics of AuNPs@Ampicillin nano-antibiotics have been investigated using first-principles numerical simulations through the study of the ampicillin adsorption on the three low Miller index facets Au(111), Au(100) and Au(110) of the AuNPs as a function of both the antibiotics coverage and its protonation state. Intermolecular interactions were found to be very stabilizing for coverages compatible with experimental data. An optimal coverage zone has been determined, in which the combination of a favorable gold surface-antibiotics interaction and of stabilizing intermolecular interactions can lead to an overall stabilization of the nano-antibiotics. As regards the mechanism of action of the nano-antibiotics, this study has confirmed that the active site of the free antibiotic is exposed to the solvent when the antibiotic is grafted onto the gold nanoparticle.

Self-organization of clusters by a standing surface acoustic wave

Christophe Taillan, Nicolas Combe, and Joseph Morillo

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 (a)–(d) Probability distributions P i (x) of the x coordinate of centers of mass of clusters composed of i atoms, i ∈ {1,2,3,4}. (e) Displacement z(x) of the top substrate atomic layer at 2 times corresponding to antinode maximum displacements.
(a)–(d) Probability distributions P i (x) of the x coordinate of centers of mass of clusters composed of i atoms, i ∈ {1,2,3,4}. (e) Displacement z(x) of the top substrate atomic layer at 2 times corresponding to antinode maximum displacements.

The diffusion of clusters on a crystalline substrate submitted to a standing surface acoustic wave (StSAW) is studied using molecular dynamics simulations. The distributions of positions of clusters with two, three, and four atoms are calculated and evidence that the wave encourages the presence of the clusters in the vicinity of the maximum transverse displacement field of the substrate. The physical mechanism leading to this self-organization is expected to be equivalent to the one operating for a single adatom, i.e., the displacement of the clusters induced by the longitudinal displacement field of the wave. The detailed shapes of the distributions of positions of clusters are related to the different clusters’ orientation and configurations. Finally, the possibility to use a StSAW to self-organize nanostructures during growth is addressed by simulating a deposition process on the substrate. We evidence that the use of a StSAW allows to especially control the spatial repartition of grown nanostructures.

Adsorption energy of small molecules on core-shell Fe@Au nanoparticles : tuning by shell thickness

Magali Benoit, Nathalie Tarrat and Joseph Morillo

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The adsorption of several small molecules on different gold surfaces, Au(001), strained Au(001) and Au(001) epitaxied on Fe(001), has been characterized using density functional theory. The surface strain leads to a less energetically favourable adsorption for all studied molecules. Moreover, the presence of the iron substrate induces an additional decrease of the binding energy, for 1 and 2 Au monolayers. For carbon monoxide CO, the structural and energetic variations with the number of Au monolayers deposited on Fe have been analyzed and correlated with the distance between the carbon atom and the gold surface. The effect of the subsurface layer has been evidenced for 1 and 2 monolayers. The other molecules show different quantitative behavior depending on the type of their interaction with the gold surface. However, the iron substrate weakens the interaction, either for the chemisorbed species or for the physisorbed ones. 2 Au monolayers seems like the best compromise to decrease the reactivity of the gold surface towards adsorption while preventing the Fe oxidation.

Prediction of Co nanoparticle morphologies

stabilized by ligands: towards a kinetic model

Van Bac Nguyen, Magali Benoit, Nicolas Combe and Hao Tang

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Cobalt nanoparticles (NPs) synthesized in liquid environments present anisotropic shaped nanocrystals such as disks, plates, rods, wires or cubes. Though the synthesis parameters (precursor, reducing agent, stabilizing ligands, concentration, temperature or rate of precursor injection) controlling the final morphologies are experimentally well controlled, little is known concerning the growth mechanisms at the atomic scale. In this work, we intend to predict the morphology variation of hcp cobalt NPs as a function of the ligand concentration. To this aim, we consider two well-established thermodynamic models and develop a new kinetic one. These models require the knowledge of the adsorption behaviors of stabilizing molecules as a function of surface coverage on preferential facets of NPs. To this end, density functional theory (DFT) calculations were performed on the adsorption of a model carboxylate ligand CH3COO on different Co crystalline surfaces. The shapes of the Co NPs obtained by these models are compared to experimental morphologies and other theoretical results from the literature. While thermodynamic models are in poor agreement with experimental observations, the variety of shapes predicted by the kinetic model is much more promising. Our study confirms that the morphological control of NPs is mostly driven by kinetic effects.

Adsorption of iron tetraphenylporphyrin on (111) surfaces of coinage metals: a density functional theory study

Hao Tang, Nathalie Tarrat, Véronique Langlais and Yongfeng Wang

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The adsorption of the iron tetraphenylporphyrin (FeTPP) molecule in its deckchair conformation was investigated on Au(111), Ag(111) and Cu(111) surfaces by performing spin-polarized density functional theory (DFT) calculations taking into account both van der Waals (vdW) interaction and on-site Coulomb repulsion. The deckchair conformation of the molecule favours intermolecular π–π-type interactions in a less densely packed monolayer than the saddle conformation. The activation barrier between the two stable magnetic states (high spin, S = 2 and intermediate spin, S = 1) of the molecule in vacuum disappears upon adsorption on the metal surfaces. The high-spin state of physisorbed FeTPP is stable on all adsorption sites. This result reveals that an external permanent element such as a STM tip or an additional molecule is needed to use FeTPP or similar molecules as model system for molecular spin switches.

Robust Sierpinski triangle fractals on symmetry-mismatched Ag(100)

X. Zhang, N. Li, L. Liu, G. Gu, C. Li, H. Tang, L. Peng, S. Hou and Y. Wang

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Sierpinski triangle fractals were constructed on both Ag(111) andsymmetry-mismatched fourfold Ag(100) surfaces through chemical reaction between H3PH molecules and Fe atoms under vacuum. Density functional theory calculations revealed that the fractals were stabilized by the strong coordination interaction between Fe and O atoms. In comparison, pure H3PH molecules formed fractals via moderately strong hydrogen bonds only on Ag(111), not on Ag(100).

The gold/ampicillin interface at the atomic scale

N. Tarrat, M. Benoit, M. Giraud, A. Ponchet and M. J. Casanove

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In the fight against antibiotic resistance, gold nanoparticles (AuNP) with antibiotics grafted on their surfaces have been found to be potent agents. Ampicillin-conjugated AuNPs have been thus reported to overcome highly ampicillin-resistant bacteria. However, the structure at the atomic scale of these hybrid systems remains misunderstood. In this paper, the structure of the interface between an ampicillin molecule AMP and three flat gold facets Au(111), Au(110) and Au(100) has been investigated with numerical simulations (dispersion-corrected DFT). Adsorption energies, bond distances and electron densities indicate that the adsorption of AMP on these facets goes through multiple partially covalent bonding. The stability of the AuNP/AMP nanoconjugates is explained by large adsorption energies and their potential antibacterial activity is discussed on the basis of the constrained spatial orientation of the grafted antibiotic.