Peculiar opportunities given by XPS spectroscopy for the clinician

X-ray Photoelectron Spectroscopy (XPS) constitutes an elegant way to describe the chemical characteristics of the surface of biological materials. It is thus a unique approach to decipher the interaction between biological materials and tissues. In the case of medical implants, it is thus possible to understand its biocompatibility as well as its integration in the body which can be wanted in the case of prothesis or avoided in the case of JJ-stents. More precisely, XPS can bring valuable information of the interaction between physiological calcification (here bone) and the prosthesis as well as the interaction between pathological calcifications (lithiasis) and the JJ-stent. This mini overview is dedicated to two communities, the physical chemists and the clinicians. In the first part of this overview, after an introduction on the basic principles of XPS, we focus on the theoretical techniques adopted for the computation of XPS spectra of materials.The second part, dedicated to clinicians, describes the use of XPS for the characterization of biological materials. We report which kind of chemical information can be gained by this surface-sensitive technique and how this information has a relevant impact on medical applications.Through different examples, we show that XPS is a strong and very useful tool, and thus receiving a crucial place in medical research

Peculiar opportunities given by XPS spectroscopy for the clinician

X-ray Photoelectron Spectroscopy (XPS) constitutes an elegant way to describe the chemical characteristics of the surface of biological materials. It is thus a unique approach to decipher the interaction between biological materials and tissues. In the case of medical implants, it is thus possible to understand its biocompatibility as well as its integration in the body which can be wanted in the case of prothesis or avoided in the case of JJ-stents. More precisely, XPS can bring valuable information of the interaction between physiological calcification (here bone) and the prosthesis as well as the interaction between pathological calcifications (lithiasis) and the JJ-stent. This mini overview is dedicated to two communities, the physical chemists and the clinicians. In the first part of this overview, after an introduction on the basic principles of XPS, we focus on the theoretical techniques adopted for the computation of XPS spectra of materials.The second part, dedicated to clinicians, describes the use of XPS for the characterization of biological materials. We report which kind of chemical information can be gained by this surface-sensitive technique and how this information has a relevant impact on medical applications.Through different examples, we show that XPS is a strong and very useful tool, and thus receiving a crucial place in medical research

Réactivités aux interfaces aqueuses par simulations DFT-MD

The microscopic comprehension of chemical reactions that occur at the boundary between water and other media represents an essential step in chemical science for the development of high yield chemical reactions. However the experimental difficulty in discerning the specific catalytic effect originating from the specific interfacial water environment makes the role of the interface along the reaction pathways still far to be understood.The main objective of this PhD thesis has been to provide a molecular description of chemical reactions at aqueous interfaces by Density Functional Theory-based Molecular Dynamics simulation techniques (DFT-MD/AIMD) in order to rationalize the catalytic roles of interfaces, especially from the structural point of view.The first part of the manuscript is dedicated to the study of chemical reactions of relevance in prebiotic chemistry, where many routes at aqueous interfaces have been envisaged in the literature in order to rationalize the origin of the first biopolymers on the primordial Earth. In particular the first peptide bond condensation reaction is a highly debated topic. The condensation of amino acids into oligopeptides in absence of enzymes is known to be hindered by both thermodynamic and kinetic reasons in bulk water at ambient conditions. By contrast, Prof. Vaida group has experimentally observed the formation of polypeptides at room temperature in dilute conditions from amino acid esters and CuCl2 salt at the air-water interface, suggesting the surface of oceans as a suitable environment for the birth of life on the prebiotic Earth. However the specific role of the air-water interface during the peptide bond formation and the reasons for which this reaction occurs at the interface and not in bulk water are still unclear.We provide a microscopical insight into the peptide bond formation reaction at the air-water interface by DFT-MD simulations. The characterization of the interfacial water network, coupled with the comparison between energetics and reaction mechanisms observed at the air-water interface versus bulk water allows us to reveal the key factors that promote the polypeptides formation in such heterogeneous conditions. Our data point to novel catalytic roles of the air-water interface which are essential in making the reaction occur. We especially identify why the solvation properties of the reactive species and the presence of Cl- anions at the interface are of utmost importance in catalyzing the peptide bond condensation reaction.In the second part of this PhD, we have focused on the characterization of the structure and reactivity of aqueous amorphous silica interfaces by coupling DFT-MD and SFG (Sum Frequency Generation) spectroscopy. This is especially relevant for the development of new technologies in the field of materials design and heterogeneous catalysis. The main targets of our investigation is the comprehension of the silica surface reactivity in contact with liquid water as a function of pH conditions. We have followed the evolution of the silica surface structure and chemistry in response to the variation in the water pH conditions by coupling experimental SFG spectroscopy (in collaboration with Prof. Wei-Tao Liu, China) with DFT-MD simulations. Our work provides a deep insight into the controversial acid-base behaviour of the silica surface, showing that a molecular picture based only on the balance between silanol SiOH and silanolate SiO- species at the silica surface is not enough to rationalize the trends in the SFG bands as a function of pH. The emergence of a third molecular species, denoted ”Si5”, reveals a more complex acid-base surface chemistry, and strongly modulates the silica surface acidity. Our data provide a new microscopical rationalization of the acid-base bimodal behaviour of the silica surface groups observed experimentally and reveal the Si5 species as an essential key to understand the chemistry at aqueous silica surfaces.La compréhension microscopique des réactions chimiques qui se produisent à l’interface entre l'eau et d'autres milieux représente une étape essentielle de la chimie pour l'élaboration des réactions à haut rendement. Cependant, la difficulté expérimentale pour discerner l'effet catalytique provenant spécifiquement de l’environnement de l'eau interfaciale rend le rôle de l' interface au cours de la réaction encore incompris.L'objectif principal de cette thèse de doctorat a été de fournir une description moléculaire de réactions chimiques aux interfaces aqueuses par simulations de dynamique moléculaire basées sur la théorie de la fonctionnelle de la densité (DFT-MD / AIMD) afin de rationaliser les rôles catalytiques des interfaces.La première partie du manuscrit porte sur l'étude des réactions chimiques dans la chimie prébiotique, où de nombreuses réactions aux interfaces aqueuses ont été envisagées dans la littérature pour rationaliser l'origine des premiers biopolymères sur la Terre primordiale. En particulier, la première réaction de condensation d’une liaison peptidique est un sujet controversé. La condensation des acides aminés en oligopeptides en l'absence d'enzymes est connue pour être entravée par des raisons à la fois thermodynamiques et cinétiques dans l'eau liquide. Par contre, l’équipe de la Prof. Vaida a observé expérimentalement la formation de polypeptides à partir d'esters d'acides aminés et du sel CuCl2 à l’interface air-eau. Cela suggère que la surface des océans est un environnement approprié pour la naissance de la vie sur la Terre. Cependant, le rôle de l'interface air-eau lors de la formation des liaisons peptidiques et les raisons pour lesquelles cette réaction se produit à l'interface et non dans l'eau liquide n'est pas clair.Nous fournissons une compréhension à l'échelle microscopique de la réaction à l'interface air-eau par simulations DFT-MD. La caractérisation de la structure de l’eau interfaciale, couplée à la comparaison entre les mécanismes et les énergies de réactions observées à l'interface air-eau versus l'eau liquide nous permet de révéler les facteurs clés qui mènent à la formation de polypeptides. Nos données montrent de nouveaux rôles catalytiques de l'interface air-eau qui sont essentiels pour que la réaction se produise. Nous identifions notamment pourquoi les propriétés de solvatation des espèces réactives et la présence du Cl− à l'interface sont d’importance pour catalyser la réaction.Dans la deuxième partie de cette thèse de doctorat, nous nous sommes concentrés sur la caractérisation de la structure et de la réactivité d'interfaces de silices amorphes aqueuses en couplant des simulations DFT-MD et des calculs de spectroscopie SFG (Sum Frequency Génération). L'objectif principal de notre étude est la compréhension de la réactivité de la surface de la silice au contact de l'eau liquide en fonction des conditions du pH. Nous avons suivi l'évolution de la structure et de la surface de silice en réponse à la variation des conditions du pH de la solution en couplant simulations DFT-MD et spectroscopie SFG (en collaboration avec la Prof. Wei-Tao Liu, Chine). Nos travaux apportent une compréhension du comportement acido-basique controversé de la surface de silice, montrant qu'une image moléculaire basée uniquement sur l'équilibre entre Si-OH (silanol) et Si-O− (silanolate) à la surface de la silice n'est pas suffisante pour rationaliser les spectres SFG en fonction du pH. L'émergence d'une troisième espèce moléculaire, notée «Si5», révèle une chimie acide-base de la surface plus complexe. Nos données apportent une nouvelle rationalisation microscopique du comportement acido-basique bimodal des groupes de la surface de silice observés expérimentalement et révèlent l'espèce Si5 comme une clé pour comprendre la chimie des surfaces de silices aqueuses

The formation of urea in space. I. Ion-molecule, neutral-neutral and radical gas phase reactions

International audienceContext. Many organic molecules have been observed in the interstellar medium thanks to advances in radioastronomy, and very recently the presence of urea was also suggested. While those molecules were observed, it is not clear what the mechanisms responsible to their formation are. In fact, if gas-phase reactions are responsible, they should occur through barrierless mechanisms (or with very low barriers). In the past, mechanisms for the formation of different organic molecules were studied, providing only in a few cases energetic conditions favorable to a synthesis at very low temperature. A particularly intriguing class of such molecules are those containing one N-CO peptide bond, which could be a building block for the formation of biological molecules. Urea is a particular case because two nitrogen atoms are linked to the CO moiety. Thus, motivated also by the recent tentative observation of urea, we have considered the synthetic pathways responsible to its formation. Aims. We have studied the possibility of forming urea in the gas phase via different kinds of bi-molecular reactions: ion-molecule, neutral, and radical. In particular we have focused on the activation energy of these reactions in order to find possible reactants that could be responsible for to barrierless (or very low energy) pathways. Methods. We have used very accurate, highly correlated quantum chemistry calculations to locate and characterize the reaction pathways in terms of minima and transition states connecting reactants to products. Results. Most of the reactions considered have an activation energy that is too high; but the ion-molecule reaction between NH 2 OH + 2 and formamide is not too high. These reactants could be responsible not only for the formation of urea but also of isocyanic acid, which is an organic molecule also observed in the interstellar medium

On the Chemistry at Oxide/Water Interfaces: the Role of Interfacial Water

Oxide-water interfaces host many chemical reactions in nature and industry. There, reaction free energies markedly differ from bulk. While we can experimentally and theoretically measure these changes, we are often unable to address the fundamental question: what catalyses these reactions? Recent studies suggest that surface and electrostatics contributions are insufficient to answer. The interface modulates chemistry in subtle ways. Revealing them is essential to understanding interfacial reactions, hence improving industrial processes. Here, we introduce a thermodynamic approach combined with cavitation free energy analysis to disentangle the driving forces at play. We find water dictates chemistry via large variations of cavitation free energies across the interface. The resulting driving forces are both large enough to determine reaction output and highly tunable by adjusting interface composition, as showcased for silica-water interfaces. These findings shift the focus from common interpretations based on surface and electrostatics, and open exciting perspectives for regulating interfacial chemistry

A Simplified Method for Theoretical Sum Frequency Generation Spectroscopy Calculation and Interpretation: the “pop model”

Sum Frequency Generation (SFG) spectroscopy is a powerful tool to probe molecular environments of oth- erwise nearly inaccessible buried interfaces. Theoretical spectroscopy is required to reveal the structure- spectroscopy relationship. Existing methods to compute theoretical spectra are restricted to the use of time- correlation functions evaluated from accurate atomistic molecular dynamics simulations, often at the ab-initio level. The interpretation of the computed spectra requires additional steps to deconvolve the spectroscopic contributions from local water and surface structural populations at the interface. The lack of a standard procedure to do this often hampers rationalization. To overcome these challenges, we rewrite the equations for spectra calculation into a sum of partial contributions from interfacial populations, weighted by their abundance at the interface. We show that SFG signatures from each population can be parameterized into a minimum dataset of reference partial spectra. Accurate spectra can then be predicted by just evaluating the statistics of interfacial populations, which can be done even with force field simulations as well as with analytic models. This approach broadens the range of simulation techniques from which theoretical spectra can be calculated, opening toward non-atomistic and Monte Carlo simulation approaches. Most notably, it allows constructing accurate theoretical spectra for interfacial conditions that can not even be simulated, as we demonstrate for the pH-dependent SFG spectra of silica/water interfaces

Ions Tune Interfacial Water Structure and Modulate Hydrophobic Interactions at Silica Surfaces

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Influence of argon and D₂ tagging on the hydrogen bond network in Cs⁺(H₂O)₃; kinetic trapping below 40 K

International audienceThe influence of enthalpic and entropic effects as well as of kinetic trapping processes on the structure of Ar/D2-tagged Cs+(H2O)3 clusters is studied by temperature-dependent infrared photodissociation spectroscopy combined with harmonic vibrational spectra calculations and anharmonic free energy profiles from finite temperature metadynamics molecular dynamics simulations. Each tag favors a different hydrogen bond network of water molecules, with Ar-tagging (vs. D2-tagging) of Cs+(H2O)3 leading to the lower energy conformation. The relative population of these conformers can be tuned over a temperature range of 12 to 21 K. The formation mechanisms of these tagged clusters can be deduced from the free energy profiles. This investigation demonstrates that a variety of factors, both thermodynamic and kinetic, play a role in the structure of flexible molecular species, even at cryogenic temperatures

On the trail of molecular hydrophilicity and hydrophobicity at aqueous interfaces

Uncovering microscopic hydrophilicity and hydrophobicity at heterogeneous aqueous interfaces is essential as it dictates physical and chemical properties such as wetting, electrical double layer, reactivity. Here, we combine density functional theory-based MD simulations (DFT-MD) and both theoretical and experimental SFG spectroscopy to explore how the interfacial water responds in contact with self-assembled monolayers (SAM) of tunable hydrophilicity. We introduce a microscopic metric to track the transition from hydrophobic to hydrophilic interfaces, which combines a structural descriptor based on the preferential orientation within the water network in the topmost binding interfacial layer (BIL) and spectroscopic fingerprints of H-bonded and dangling OH groups of water pointing towards the surface carried by BIL-resolved SFG spectra. This metric builds a bridge between molecular descriptors of hydrophilicity/hydrophobicity and spectroscopically measured quantities, and provides a recipe to quantitatively or qualitatively interpret experimental SFG signals

A molecular understanding of citrate adsorption on calcium oxalate polyhydrates

Calcium oxalate precipitation is a common pathological calcification in the human body, whereby crystallite morphology is influenced by the chelating properties of biological ions such as citrate. It has been suggested that citrate could steer oxalate formation towards its dihydrated form and away from the monohydrated form, which was identified as a major cause for disease. To assess the influence of the citrate ion on the resulting calcium oxalate, surface energies were calculated at the dispersion-corrected density functional level of theory for both monohydrated and dihydrated calcium oxalate. Different adsorption geometries were considered by varying the attacking angle of citrate as well as by considering the citrate ion on top of an adsorbed water layer or penetrating the water layer. The obtained results were compared to ab initio molecular dynamics simulations and experimental scanning electron microscope images. A strong preference for citrate adsorption on calcium oxalate dihydrate was observed, suggesting medical applications for the treatment of such pathological calcifications