Mid- and Far-Infrared Marker Bands of the Metal Coordination Sites of the Histidine Side Chains in the Protein Cu,Zn-Superoxide Dismutase

International audienceVibrational spectroscopy gives important information on the properties of ligand and metal–ligand bonds in metalloenzymes. Infrared spectroscopy is appealing for the study of metal active sites that are not amenable to Raman spectroscopy. We present a combined experimental and theoretical approach to analyze the mid- and far-IR spectra of Cu,Zn-superoxide dismutase (Cu,Zn-SOD) as a probe of the histidine ligands. This metalloenzyme provides a unique model to identify specific IR signatures of metal–histidine coordination and to study their alterations as a function of the metal (copper/zinc), the copper valence state (+I/+II), the histidine coordination mode (Nτ and Nπ) and the histidine protonation state. DFT calculations combined with normal mode descriptions from potential energy distribution calculations were performed on two slightly different cluster models. Differences in the constraints at the side chain of one histidine Cu ligand sensibly modify the geometric parameters and vibrational properties. Electrochemically induced FTIR difference spectroscopy provided mid- and far-IR fingerprint spectra of the Cu protein in aqueous media that are sensitive to the redox state of the Cu centre at the active site. Comparisons of the DFT predictions with the experimental IR modes of the histidine ligands at the Cu,Zn-SOD active site showed that useful mid-IR markers of histidine Nτ and Nπ coordination were predicted with good accuracy. The DFT analysis further demonstrated a link between the ν(C4–C5) mode frequency of His46 and the specific properties of the His46–Cu bond in Cu,Zn-SOD. A combined theoretical and experimental approach on samples in H2O and 2H2O or 15N-labelled samples identified the contributions from the histidine side chain modes in the 669–629 cm–1 region

Etude DFT de sites cationiques de la zéolithe CuIY (développement et méthodologie)

Les zéolithes Y de type Faujasite ayant un rapport Si/Al supérieur à 1 ne sont pas rigoureusement périodiques bien que globalement organisées. De ce fait et de par la grande taille de ces systèmes, pour étudier localement les sites actifs de cette zéolithe une approche cluster est utilisée. Les résultats de modélisation par des calculs quantiques (Density Functional Theory, DFT) des sites cationiques des zéolithes CuIY et NaY, montrent que seuls les sites I, I et II sont occupés. Dans cette approche, la taille du modèle ainsi que les atomes saturant les liaisons pendantes sont des facteurs primordiaux. Une amélioration possible de la description des bords des clusters est l utilisation de pseudo-atomes, OCECP (Capping Electron Core Potential), obtenus par un algorithme génétique. Les clusters saturés par les OCECP ont l avantage d introduire des charges plus proches du solide réel. Une deuxième méthode, SCC-DFTB (méthode semi-empirique), basée sur une stratégie de pré-optimisation de grands systèmes permet une économie de temps de calcul et apporte un outil supplémentaire pour l étude des matériaux. Le développement de ces deux méthodes, utiles pour des études par une approche cluster de systèmes de grandes tailles dans le domaine des zéolithes (ou d autres matériaux nanostructurés), s inscrit dans l évolution que suit la modélisation pour être utile à l expérience, notamment en constituant une perspective vers des calculs du type DFT/DFTBY Faujasite type zeolites with a Si/Al ratio higher than 1 are not rigorously periodic although they are globally organized. As a consequence and from the fact that these systems are very large, a cluster approach was used to model the local active sites of the zeolite. The results of modelling by quantum calculations (Density Functional Theory, DFT) of the cation sites of zeolites CuIY and NaY, show that only sites I, I' and II are occupied. In this approach, the sizes of the model as well as the atoms saturating the dangling bonds are paramount factors. A possible improvement of the description of the edges of the clusters is the use of pseudo-atoms, OCECP (Capping Electron Core Potential), obtained by a genetic algorithm. The clusters saturated by the OCECP have the advantage of introducing charges closer to the real solid. A second method, SCC-DFTB (semi-empirical method), based on a strategy of pre-optimization of big systems allows a saving in computing time and brings an additional tool for the study of materials. The development of these two methods, useful for studies by a cluster approach of big size systems in the field of zeolites (or other nanostructured materials), falls under the evolution that modelling follows to be useful for the experiment, in particular by constituting a perspective towards DFT/DFTB calculations typesMONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF

Multiple adsorption of CO on Na-exchanged Y faujasite: a DFT investigation

International audienceCarbon monoxide is involved in many chemical and industrial processes, and its removal is of great importance to reduce detrimental environmental and climate impacts. CO is also useful to characterise the metal exchanged in zeolites. Multiple adsorption of CO in zeolite faujasites containing Na cations is investigated through quantum chemical calculations. Density functional theory (DFT) calculations were chosen to investigate the structure of sodium-exchanged cations at site II in Y faujasite and to investigate multiple CO adsorption with Na to predict the structure and the infrared CO stretching signal. DFT analysis using B3LYP, B3LYP-D and M062X showed significant differences in the coordination of Na at site II when three CO are adsorbed. From these investigations, polyadsorption of CO in NaY could lead to threefold-coordinated Na at site II in six-membered rings (6MRs) containing two Al and twofold-coordinated Na at site II in 6MRs containing one Al. These results suggest that introduction of non-bonding interactions is necessary to study polyadsorption of CO in NaY

Recent Advances in CuI/IIY: Experiments and Modeling

International audienceAn overview of the CuI/IIY material is performed on the basis of the results obtained during the last 5 years on their structure (nature of the Cu species, siting, coordination ...), their use and reactivity, based on TPR, XRD and various ex situ and in situ spectroscopies such as XAS, IR and EPR. A brief summary of previous work is reported to position these recent advances in the context of three decades of studies devoted to the characterization of these materials. Quantum mechanics modeling of both the structure and reactivity of the material is also reported, providing complementary information. Insights related to the properties of the catalysts obtained recently using this molecular approach are presented to demonstrate that this material behaves as a supermolecule. In addition to its adsorption properties, the zeolite Y is one of the most popular zeolite used in catalysis. When it is exchanged with copper, in selective adsorption processes, it has been shown to be a promising adsorbent in the desulfurization of transportation fuels. In the area of environmental applications, a new catalyst based on CuY zeolite is now used for NOx removal from the tail gas of nitric acid plants. Some selected examples are given to illustrate some of the CuY zeolite properties such as adsorption, deNOx elimination and biomimetic behavior

Etude des propriétés vibrationnelles dans l'IR lointain d'une superoxyde dismutase à cuivre et zinc dans son état oxydé et réduit et d'analogues par des méthodes de la chimie quantique

MONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF

Recent Advances in CuI/IIY: Experiments and Modeling.

International audienceAn overview of the CuI/IIY material is performed on the basis of the results obtained during the last 5 years on their structure (nature of the Cu species, siting, coordination ...), their use and reactivity, based on TPR, XRD and various ex situ and in situ spectroscopies such as XAS, IR and EPR. A brief summary of previous work is reported to position these recent advances in the context of three decades of studies devoted to the characterization of these materials. Quantum mechanics modeling of both the structure and reactivity of the material is also reported, providing complementary information. Insights related to the properties of the catalysts obtained recently using this molecular approach are presented to demonstrate that this material behaves as a supermolecule. In addition to its adsorption properties, the zeolite Y is one of the most popular zeolite used in catalysis. When it is exchanged with copper, in selective adsorption processes, it has been shown to be a promising adsorbent in the desulfurization of transportation fuels. In the area of environmental applications, a new catalyst based on CuY zeolite is now used for NOx removal from the tail gas of nitric acid plants. Some selected examples are given to illustrate some of the CuY zeolite properties such as adsorption, deNOx elimination and biomimetic behavior

Modélisation de l'adsorption des molécules à fort impact sur l'environnement et la santé dans des matériaux nanoporeux en couplant des approches quantiques et classiques

L'adsorption de CO dans la faujasite échangée au CuI et au Na+ a été modélisée à l'aide des approches quantiques (DFT) et classiques (Monte Carlo). Grâce à l'approche DFT, la surface d'énergie potentielle de la faujasite a été explorée. Différents types d'interactions de CO avec les cations ont été identifiés, pour chacune les effets induits par l'adsorption de CO aux niveaux structural et énergétique ont été analysés, et le calcul de la fréquence de vibration de CO a été réalisé. Grâce aux valeurs obtenues, une nouvelle attribution des spectres d'adsorption de CO dans CuY et NaY a été établie. D'un autre côté, grâce aux simulations Monte Carlo dans l'ensemble Grand Canonique, les propriétés d'adsorption (isothermes et enthalpies) de la faujasite vis-à-vis de CO ont été modélisées, et le mécanisme microscopique d'adsorption de CO a été établi. La mise en œuvre de ces simulations a nécessité de paramétrer un nouveau champ de force destiné à décrire les interactions CO/faujasite et CO/CO.CO adsorption in CuI and Na+ exchanged faujasite has been modeled by mean of quantum (DFT) and classical (Monte Carlo) approaches. By mean of the DFT calculations, faujasite potential energy surface has been explored. Different types of CO interactions with the cations have been highlighted, for each one of them CO adsorption effects on the structural and energetic parameters have been analyzed, and calculations of the CO stretching frequency have been performed. Thanks to our calculated values, a new attribution of CO adsorption spectra in CuY and NaY has been established. On another side, by mean of Monte Carlo simulations in the Grand Canonical ensemble, faujasite adsorption properties regarding CO (isotherms and enthalpies) have been modeled, and the CO adsorption mechanism has been established at the microscopic level. The implementation of these simulations has required the derivation of a new force field describing the CO/faujasite and CO/CO interactions.MONTPELLIER-Ecole Nat.Chimie (341722204) / SudocSudocFranceF

Modeling Ammonia and Water Co-Adsorption in CuI-SSZ-13 Zeolite Using DFT Calculations

International audienceCu-SSZ-13 efficiently catalyzes the selective catalytic reduction (SCR) of NO by NH3 but the structure of the active site and, particularly, the redox state of the copper (+I or +II) is still debated. This paper focuses on the possible contribution of CuI species using quantum chemistry of adsorption and co-adsorption of NH3 and H2O on CuI species. The calculations show that CuI clearly migrates upon adsorption of NH3 and H2O. All the CuI complexes sit in the cage containing the 8 MR and interact with the zeolite framework through several H-bonds. In the experimental temperature and pressure domain of SCR conditions, calculated phase diagrams show that a coordination number of two is predicted for the co-adsorption of NH3 and H2O on CuI. Finally, the calculated phase diagrams of CuI-SSZ-13 are discussed together with those of CuII-SSZ-13 and recent experimental characterizations, providing a wider picture of the real catalyst in SCR conditions

Cooperative Cation Migrations upon CO Addition in CuI- and Alkali-Exchanged Faujasite: A DFT Study

International audienceCO adsorption in Al-rich faujasite zeolite containing copper and alkali cations has been investigated using DFT methods in order to determine how CO interacts and may modify the original position of the cations. Whether a cluster or a periodic model is used, addition of CO induces the formation of stable complexes labeled DI(CO) in which CO interacts by both its C-end and its O-end, resulting from a cooperative rearrangement of cations. In addition to a CuI migration from site II to the supercage, a migration of alkali from site III′ to site III may occur. DI(CO) also induces a downshift of the νCO mode in comparison with the complex containing CO interacting with a single cation, SI(CO). These results suggest a new assignment of the IR spectra of CO adsorbed in YCuI and YNa+: for YCuI, the upshifted signal at ca. 2160 cm-1 in comparison with νCOgas at 2143 cm-1 could be assigned to a SI(CO) structure, whereas the downshifted signal at ca. 2140 cm-1 could be assigned to a DI(CO) complex. For YNa+, the upshifted signal at ca. 2170 cm-1 could be assigned to SI(CO) NaSII · · ·CO and/or to DI(CO) NaSII · · ·OC· · · NaSIII′, whereas the downshifted signal at ca. 2122 cm-1 could be assigned to DI(CO) complex NaSII · · ·CO· · ·NaSIII′. This study shows that the DI(CO) interaction is a key ingredient for understanding the metal-exchanged zeolite properties