Dominique Costa

Glycine and lysine adsorption and reactivity on the surface of amorphous silica

In order to better control the adsorption of proteins on mineral surfaces, it is useful to gain a thorough understanding of the behaviour of their constituting monomers, namely, amino acids. We have therefore investigated the adsorption of glycine, lysine, and other small biomolecules on well-characterised surfaces of silica. While similar systems have been studied before, these studies usually concentrated on evidencing the effect of surfaces on peptide bond formation in a phenomenological, mostly macroscopic approach. In contrast, we have considered the adsorption process from the view-point of the surface, using knowledge previously gained on the molecular identification of surface functional groups to better characterise their interaction with amino acids, both from the aqueous phase and from the vapour phase. We combined macroscopic level information such as adsorbed amounts, pH dependence, or TGA, with molecular characterisation by vibrational spectroscopies and 13 C NMR of the adsorbed molecules. In parallel, we have carried out molecular modelling of candidate clusters containing the amino acid and the adsorption site by DFT. The structures of lowest energy were also those that best reproduced the observed spectroscopic properties. Different adsorption mechanisms can be postulated, corresponding to different spectroscopic signatures of the amino acid/adsorption site complexes. On silica surfaces, this implies cooperative hydrogen bonding in a kind of molecular recognition. The existence of molecular recognition is also evidenced by experiments on the coadsorption of different amino acids, where strong selectivity effects may be observed. Such phenomena may have much practical significance in the fields of biofilms and prebiotic chemistry.

Understanding small biomolecule‐biomaterial interactions: A review of fundamental theoretical and experimental approaches for biomolecule interactions with inorganic surfaces

Interactions between biomolecules and inorganic surfaces play an important role in natural environments and in industry, including a wide variety of conditions: marine environment, ship hulls (fouling), water treatment, heat exchange, membrane separation, soils, mineral particles at the earths surface, hospitals (hygiene), art and buildings (degradation and biocorrosion), paper industry (fouling) and more. To better control the first steps leading to adsorption of a biomolecule on an inorganic surface, it is mandatory to understand the adsorption mechanisms of biomolecules of several sizes at the atomic scale, that is, the nature of the chemical interaction between the biomolecule and the surface and the resulting biomolecule conformations once adsorbed at the surface. This remains a challenging and unsolved problem. Here, we review the state of art in experimental and theoretical approaches. We focus on metallic biomaterial surfaces such as TiO(2) and stainless steel, mentioning some remarkable results on hydroxyapatite. Experimental techniques include atomic force microscopy, surface plasmon resonance, quartz crystal microbalance, X-ray photoelectron spectroscopy, fluorescence microscopy, polarization modulation infrared reflection absorption spectroscopy, sum frequency generation and time of flight secondary ion mass spectroscopy. Theoretical models range from detailed quantum mechanical representations to classical forcefield-based approaches.

Water on extended and point defects at MgO surfaces

The interaction of water with extended defects such as mono- and diatomic steps at the MgO(100) surface is investigated through first-principles simulations, as a function of water coverage. At variance with flat MgO(100) terraces, water adsorption is always dissociative on mono- and diatomic steps, as well as on MgO(110) surfaces. In most of the equilibrium configurations, the oxygen of the hydroxyl groups is two- or fourfold coordinated, but single-coordinated OH groups can be stabilized at diatomic step edges. The structural properties of the hydroxyl groups are discussed as a function of their coordination numbers and mutual interactions, as well as the surface defect morphology. It is shown that characteristics of water adsorption are primarily driven by the coordination number of the surface acid-base pair where the dissociation occurs. However, the OH groups resulting from water dissociation are also considerably stabilized by the electrostatic interaction with coadsorbed protons. At low coverage such an interaction, considerably stronger than hydrogen bonding, practically hinders any proton diffusion away from its neighboring hydroxyl. The computed adsorption energies allow us to discuss the onset of water desorption from flat MgO(100) terraces, diatomic and monoatomic steps, and from Mg-O divacancy.

Biomolecule-biomaterial interaction: a DFT-D study of glycine adsorption and self-assembly on hydroxylated Cr2O3 surfaces.

The adsorption of glycine, the building block of amino acids, on hydroxylated (0001)-Cr2O3 model surfaces, representing the stainless steel passive film surface, was modeled by means of the GGA + U method. The roles of glycine coverage and surface termination (hydroxylated Cr- and O-terminated surfaces) on the adsorption mode and self-assembly properties were explored. The hydroxylated Cr-terminated Cr2O3 surface, which presents two types of (H)OH groups exhibiting different acidic character, is more reactive than the hydroxylated O-terminated surface, where one single type of OH group is present, for all adsorption modes and coverages considered. Outer sphere adsorption occurs in the zwitterion form, stabilized at low coverage through H-bond formation with coadsorbed water molecules, and at the monolayer coverage by glycine self-assembling. The OH substitution by glycinate is favored on the hydroxylated Cr-terminated surface and not on the O-terminated one. The inclusion of dispersion forces does not change the observed tendencies. An atomistic thermodynamics approach suggests that outer sphere adsorption is thermodynamically favored over inner sphere adsorption in the whole domain of glycine concentration. The obtained SAMs free energies of formation are rationalized in a model considering the balance between sublimation and solvation free energies, and extrapolated to other amino acids, to predict the SAMs formation above hydroxylated surfaces. It is found that hydrophobic AA tend to self-assemble at the surface, whereas hydrophilic ones do not.

The amorphous silica-liquid water interface studied by ab initio molecular dynamics (AIMD): local organization in global disorder

The structural organization of water at a model of amorphous silica-liquid water interface is investigated by ab initio molecular dynamics (AIMD) simulations at room temperature. The amorphous surface is constructed with isolated, H-bonded vicinal and geminal silanols. In the absence of water, the silanols have orientations that depend on the local surface topology (i.e. presence of concave and convex zones). However, in the presence of liquid water, only the strong inter-silanol H-bonds are maintained, whereas the weaker ones are replaced by H-bonds formed with interfacial water molecules. All silanols are found to act as H-bond donors to water. The vicinal silanols are simultaneously found to be H-bond acceptors from water. The geminal pairs are also characterized by the formation of water H-bonded rings, which could provide special pathways for proton transfer(s) at the interface. The first water layer above the surface is overall rather disordered, with three main domains of orientations of the water molecules. We discuss the similarities and differences in the structural organization of the interfacial water layer at the surface of the amorphous silica and at the surface of the crystalline (0 0 0 1) quartz surface.

Production of free radicals arising from the surface activity of minerals and oxygen. Part I. Iron mine ores.

The excess incidence of lung cancers observed in many metal mines probably is not only correlated with radioactivity but also with the inhaled dusts. In an attempt to determine a possible mechanism of carcinogenicity related to the surface activity of dusts, using the spin-trapping agent and ESR spectroscopy, one can demonstrate that some mineral dusts from iron ore mines are very active in an oxidative process in aqueous medium, implying the formation of radical oxygen species on reducing surface sites of the solid. This reducing surface activity of the dusts depends on the presence of Fe2+ ion in the lattice and on the process of activation and passivation of the surface sites. The more simple process of activation is the dissolution of the oxidized coating on the particle surface. Among the oxides, oxyhydroxides, carbonates, and silicates, the magnesium-iron phyllosilicates (chlorite, biotite, berthierine) appear the most active. The siderite FeCO3 is also active, but the iron oxides and oxyhydroxides are generally nonactive.

Self-assembly of (S)-glutamic acid on Ag(100): a combined LT-STM and ab initio investigation.

Self-assembly of organic molecules at metal surfaces is of greatest importance in nanoscience; in fact, it opens new perspectives in the field of molecular electronics and in the study of biocompatible materials. Combining an experimental low-temperature scanning tunneling microscopy investigation with ab initio calculations, we succeeded to describe in detail (S)-glutamic acid adsorption on Ag(100) at T = 350 K. We find that (S)-glutamic acid organizes in a squared structure and, at variance with the majority of cases reported in literature, it adsorbs in the neutral form, 4.6 A above the surface plane. The interaction with the poorly reactive Ag substrate is only due to weak van der Waals forces, while H-bonds between carboxyl groups and the formation of a OCOH-OCOH-OCOH-OCOH cycle at the vertex of the squares are the main responsible for the self-assembly.

First principles surface thermodynamics of industrial supported catalysts in working conditions

Ever stronger environmental concerns prompt the research in the area of heterogeneous catalysis to play an ever more crucial role to produce ever cleaner fuel from the refining of petroleum effluents. The catalytic active phase is often used in a dispersed state over a porous oxide material. This paper is a review of recent progress brought by periodic density functional theory (DFT) calculations in the area of two relevant industrial supported catalysts. We focus on two important supports used in the refining industry: anatase-TiO(2) and γ-alumina. According to the various reaction conditions, the presence of H(2)O, H(2) and H(2)S may change the surface states of the support. In particular, it is crucial to know and control the hydroxylation state depending on temperature and partial pressure of reactants (H(2)O, H(2), H(2)S). The support effects on the catalytic active phases are presented for MoS(2) particles, used in hydrodesulfurization catalysis, and for Pd particles, used in hydrogenation catalysis. It is shown how the wetting property and equilibrium morphology of the active phase depend on the support. A discussion on the impact for catalytic activities is provided.

CO adsorption on amorphous silica–alumina: electrostatic or Brønsted acidity probe?

The adsorption of CO on amorphous silica-alumina (ASA) was calculated by DFT. CO appears as a probe of the electrostatic field induced by the whole surface, at the origin of a so-called vibrational Stark effect responsible for the CO frequency shifts. Brønsted acidity of the ASA sites does not directly correlate CO frequency shifts.

Microsomal lipid peroxidation and oxy-radicals formation are induced by insoluble iron-containing minerals

Lipid peroxidation, measured by malondialdehyde formation is induced in rat liver microsomes by insoluble iron-containing minerals (pyrite, magnetite, nemalite and an iron ore, minette de Lorraine) which are generally found either in iron mines or as contaminants of asbestos fibers. In spin-trapping studies using DMPO as a spin trap those minerals are also found to catalyze the oxidation of formate to carboxylate radicals by oxygen, via the formation of hydroxyl radicals. The two processes are mainly due to the presence of redox active iron at the surface of the solid particles and thus are greatly inhibited by desferrioxamine, a strong iron chelator. However, these reactions are not correlated.