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1. Advances and Challenges in the Molecular Characterization of Petroporphyrins

Author

Marianny Y. Combariza, Pierre Giusti, Carlos Afonso, Germain Vallverdu, Martha L. Chacón-Patiño, Amy M. McKenna, Brice Bouyssiere, Quan Shi, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), National High Magnetic Field Laboratory (NHMFL), and Florida State University [Tallahassee] (FSU)

Subjects
Chemistry, General Chemical Engineering, FT-ICR MS, Energy Engineering and Power Technology, Molecular evidence, petroporphyrins, 02 engineering and technology, Computational biology, geoporphyrins, 010402 general chemistry, 021001 nanoscience & nanotechnology, asphaltenes, 01 natural sciences, Petroleum biomarkers, 0104 chemical sciences, Fuel Technology, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, vanadyl porphyrins, nickel porphyrins, 0210 nano-technology, ComputingMilieux_MISCELLANEOUS, mass spectrometry
Abstract

International audience; Petroporphyrins, geoporphyrins, or metalloporphyrins are the original petroleum biomarkers, identified by Alfred Treibs more than a century ago and the first molecular evidence for the biogenic origins of petroleum. Since discovery, analytical strategies have been developed to identify porphyrins in petroleum and its fractions. This review focuses on the advances enabled by ultrahigh resolving power Fourier transform ion cyclotron resonance mass spectrometry in tribute to Professor Alan G. Marshall.

Published
2021
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2. Understanding the Vanadium–Asphaltene Nanoaggregate Link with Silver Triflate Complexation and GPC ICP-MS Analysis

Author

Brice Bouyssiere, Germain Vallverdu, Quan Shi, Fang Zheng, Pierre Giusti, Caroline Barrère-Mangote, and Remi Moulian

Subjects
Chemistry, General Chemical Engineering, Energy Engineering and Power Technology, Vanadium, chemistry.chemical_element, 02 engineering and technology, 021001 nanoscience & nanotechnology, Gel permeation chromatography, Fuel Technology, 020401 chemical engineering, 0204 chemical engineering, Inductively coupled plasma, 0210 nano-technology, Trifluoromethanesulfonate, Inductively coupled plasma mass spectrometry, Asphaltene, Nuclear chemistry
Abstract

The effect of silver triflate (AgOTf) on the interaction between vanadium and asphaltene nanoaggregates was investigated by gel permeation chromatography inductively coupled plasma high-resolution ...

Published
2020
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3. Role of the porphyrins and demulsifiers in the aggregation process of asphaltenes at water/oil interfaces under desalting conditions: a molecular dynamics study

Author

Germain Vallverdu, Didier Bégué, Brice Bouyssiere, Isabelle Baraille, A. Alfarra, and H. Santos Silva

Subjects
Molecular interactions, Chemistry, Energy Engineering and Power Technology, Ionic bonding, Geology, 02 engineering and technology, 021001 nanoscience & nanotechnology, Geotechnical Engineering and Engineering Geology, Demulsifier, Molecular dynamics, Geophysics, Fuel Technology, 020401 chemical engineering, Chemical engineering, Geochemistry and Petrology, Refining, Scientific method, Molecule, Economic Geology, 0204 chemical engineering, 0210 nano-technology, Asphaltene
Abstract

Breaking water-in-oil emulsions during the refining of crude oils is an important step before any upgrading process is started. Asphaltene molecules are incriminated as playing an important role in this phenomenon. Unraveling the mechanisms behind the affinity between them and water is a key step to understand how to break these emulsions more easily and require lower amounts of demulsifiers. Choosing which demulsifier molecule(s) to use is also primordial, but to do so rationally, one needs to know which are the molecular interactions in place between asphaltenes, porphyrins and water so that demulsifiers are chosen to destabilize a specific physical–chemical interaction. In this paper, we study the interactions arising between asphaltenes and porphyrins and six different molecules potentially displaying a demulsification action in the presence of water/oil interfaces. We demonstrate that the ionic demulsifier molecules present an interesting potential to either interact strongly with water, replacing asphaltenes in this interaction, or to interact with the active sites of asphaltenes, deactivating them and avoiding any asphaltenic interfacial activity. Finally, we also found that although asphaltenes do not migrate spontaneously toward the water/oil interfaces, porphyrins do so rather easily. This indicates that porphyrins do have an important activity at the water/oil interface.

Published
2020
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4. Volatile fingerprint of food products with untargeted SIFT-MS data coupled with mixomics methods for profile discrimination: application case on cheese

Author

Valérie Desauziers, Germain Vallverdu, Noëlle Bru, Mickael Le Bechec, Marine Reyrolle, Thierry Pigot, Mylène Ghislain, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Equipe RIME - Recherche sur les Interactions des Matériaux avec leur Environnement (RIME), IMT - MINES ALES (IMT - MINES ALES), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Laboratoire de Mathématiques et de leurs Applications [Pau] (LMAP), and Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
MixOmics, Scale-invariant feature transform, Mass spectrometry, 01 natural sciences, Mass Spectrometry, Analytical Chemistry, 0404 agricultural biotechnology, Fingerprint, Cheese, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Animals, Aroma, ewe cheeses, 2. Zero hunger, Typicality of agro-food products, Volatile Organic Compounds, Sheep, biology, 010401 analytical chemistry, Reproducibility of Results, 04 agricultural and veterinary sciences, General Medicine, biology.organism_classification, 040401 food science, 0104 chemical sciences, Volatile fingerprints, SIFT-M, Food products, Odorants, Environmental science, Female, Biochemical engineering, Food Science
Abstract

International audience; Volatile organic compounds (VOCs) emitted by food products are decisive for the perception of aroma and taste. The analysis of gaseous matrices is traditionally done by detection and quantification of few dozens of characteristic markers. Emerging direct injection mass spectrometry technologies offer rapid analysis based on a soft ionisation of VOCs without previous separation. The recent increase of selectivity offered by the use of several precursor ions coupled with untargeted analysis increases the potential power of these instruments. However, the analysis of complex gaseous matrix results in a large number of ion conflicts, making the quantification of markers difficult, and in a large volume of data. In this work, we present the exploitation of untargeted SIFT-MS volatile fingerprints of ewe PDO cheeses in a real farm model, using mixOmics methods allowing us to illustrate the typicality, the manufacturing processes reproducibility and the impact of the animals' diet on the final product.

Published
2022
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5. Asphaltene aggregation studied by molecular dynamics simulations: role of the molecular architecture and solvents on the supramolecular or colloidal behavior

Author

Germain Vallverdu, Isabelle Baraille, A. Alfarra, Brice Bouyssiere, H. Santos Silva, Didier Bégué, Instituto de Física, Universidade federal de uberlandia, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Isifor-Carnot Institute, and Total Refining & Chemicals

Subjects
Science, Heteroatom, Asphaltenes, 0211 other engineering and technologies, Supramolecular chemistry, Energy Engineering and Power Technology, 02 engineering and technology, Molecular dynamics, Conjugated system, Aggregation, Colloid, 020401 chemical engineering, Geochemistry and Petrology, 021105 building & construction, Molecule, 0204 chemical engineering, Petrology, Asphaltene, Chemistry, QE420-499, Asphaltenes Molecular dynamics Aggregation Heavy oil, Geology, Heavy oil, Geotechnical Engineering and Engineering Geology, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Geophysics, Fuel Technology, Chemical physics, Polar, Economic Geology
Abstract

Asphaltene aggregation is a subject under vivid discussion: There are several parameters one needs to determine before its behavior can be mastered and better target solutions can be tailored. The nature of asphaltene aggregation (colloidal or supramolecular) and the role of solvents and their mixtures are among the least understood parameters in asphaltene science. This paper addresses molecular dynamic simulations to correlate the aggregation properties of asphaltenes, their molecular structure and the concentration of these solvents. We show that the formation of the nanoaggregate depends, primarily, on the size of the conjugated core and on the eventual presence of polar groups capable of forming H-bonds. Heteroatoms on the conjugated core do not change their shape or type of aggregation but may induce stronger $$\uppi - \uppi$$ π-π interactions. The macroaggregation formation depends upon the length of the lateral chains of asphaltenes and also on the presence of polar groups at its end. Moreover, n-heptane and water may interact selectively with asphaltenes in function of their molecular architecture. Given this fact and the aggregation behavior observed, we advocate toward the assumption that a colloidal behavior of asphaltenes might be a particular case of a more general model, based on a supramolecular description.

Published
2019
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6. Surface reactivity and surface characterization of the layered β(III)-CoOOH material: an experimental and computational study

Author

Delphine Flahaut, Liliane Guerlou-Demourgues, Ronan Invernizzi, Jacob Olchowka, L. Madec, Alexia Lemoine, Germain Vallverdu, Isabelle Baraille, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Réseau sur le stockage électrochimique de l'énergie (RS2E), Université de Picardie Jules Verne (UPJV)-Institut de Chimie du CNRS (INC)-Aix Marseille Université (AMU)-Université de Pau et des Pays de l'Adour (UPPA)-Université de Nantes (UN)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Collège de France (CdF (institution))-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Université Grenoble Alpes (UGA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), Advanced Lithium Energy Storage Systems - ALISTORE-ERI (ALISTORE-ERI), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), The authors thank the financial support of Région Nouvelle Aquitaine. The theoretical calculations were performed using HPC resources from GENCI-CINES (grant A0080806920) and the Mesocentre de Calcul Intensif Aquitain (MCIA)., Université de Nantes (UN)-Aix Marseille Université (AMU)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Collège de France (CdF (institution))-Université de Picardie Jules Verne (UPJV)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), and Université Grenoble Alpes (UGA)-Université Grenoble Alpes (UGA)

Subjects
Reaction mechanism, Materials science, Photoemission spectroscopy, First-Principle Calculations, chemistry.chemical_element, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Redox, Adsorption, X-ray photoelectron spectroscopy, Supercapacitors, Molecule, Reactivity (chemistry), Physical and Theoretical Chemistry, Surface Reactivity, [CHIM.MATE]Chemical Sciences/Material chemistry, Energy Storage, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, General Energy, chemistry, Physical chemistry, 0210 nano-technology, Cobalt
Abstract

International audience; In this article, we focused on the comprehension of the surface reactivity of layered β(III)-cobalt oxyhydroxide, β(III)-CoOOH, by implementing a multiscale study associating both experimental, surface characterization by X-ray photoemission spectroscopy (XPS) and scanning electron microscopy and first-principles calculations. The surface reactivity and the chemical properties of the surface are key factors in the charge-storage mechanism, and β(III)-CoOOH presents interesting characteristics to be used as pseudo-capacitive electrode materials in supercapacitors thanks to its large surface specific area (∼100 m2/gs) and its high electronic conductivity (10–3 to 1 S cm–1). The surface reactivity (basic and redox character) of the synthesized compounds, which consists in aggregates of particles with 60–100 nm length, has been explored from the adsorption of SO2 molecules followed by XPS analyses. A kinetic study of the reactivity allowed us to identify three steps in the adsorption mechanism of our β(III)-CoOOH samples. The coupling of XPS and computational results allows us to establish a link between the surface reactivity in the identified domains, the formation of sulfate and sulfite species, and the cobalt Co3+ and Co4+ species of the active sites along with the underlying electronic processes.

Published
2021
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7. Surface reactivity of Li2MnO3: Structural and morphological impact

Author

Michel Ménétrier, Ambroise Quesne-Turin, Laurence Croguennec, Delphine Flahaut, Joachim Allouche, Germain Vallverdu, Isabelle Baraille, François Weill, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Réseau sur le stockage électrochimique de l'énergie (RS2E), Université de Picardie Jules Verne (UPJV)-Institut de Chimie du CNRS (INC)-Aix Marseille Université (AMU)-Université de Pau et des Pays de l'Adour (UPPA)-Université de Nantes (UN)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Collège de France (CdF (institution))-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Université Grenoble Alpes (UGA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Advanced Lithium Energy Storage Systems - ALISTORE-ERI (ALISTORE-ERI), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), The authors thank the Conseil Général des Pyrénées Atlantiques and the French Research Network on the Electrochemical Energy Storage (RS2E) for funding the AQT’s PhD fellowship, and Philippe Dagault (ICMCB-Pessac) for his technical support. This project received also funding from Région Nouvelle Aquitaine and the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). The theoretical calculations were performed using HPC resources from GENCI-CINES (Grant 2017 A0010806920) and the Mesocentre de Calcul Intensif Aquitain (MCIA)., ANR-10-LABX-0076,STORE-EX,Laboratory of excellency for electrochemical energy storage(2010), Université de Nantes (UN)-Aix Marseille Université (AMU)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Collège de France (CdF (institution))-Université de Picardie Jules Verne (UPJV)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), and Université Grenoble Alpes (UGA)-Université Grenoble Alpes (UGA)

Subjects
Materials science, Photoemission spectroscopy, Coprecipitation, Stacking, General Physics and Astronomy, Chemisorption, 02 engineering and technology, [CHIM.INOR]Chemical Sciences/Inorganic chemistry, 010402 general chemistry, 01 natural sciences, Adsorption, Surface reactivity, X-ray photoelectron spectroscopy, Li-ion battery, Lamellar structure, Stacking fault, Surfaces and Interfaces, General Chemistry, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Li2MnO3, 0104 chemical sciences, Surfaces, Coatings and Films, Chemical engineering, 0210 nano-technology
Abstract

International audience; This paper investigates the role of the stacking fault (5%, 20% and 50%) and the morphology of Li2MnO3 lamellar materials, issued from coprecipitation method with three annealing temperatures, on the surface reactivity. The structure and the morphology have been characterized by XRD, SEM and TEM. We studied the surface reactivity of these materials by combining X-ray photoemission spectroscopy (XPS), gaseous adsorption and first-principle calculations. An evolution of the reactivity toward the SO2 acid gaseous probe has been observed for the three materials, from pure redox mechanism toward mixed acid-base/redox mechanisms, respectively for 5% and 50% of stacking faults. We demonstrated that the electronic structure of Li2MnO3 being not modified by stacking faulted. Thus, the surface reactivity of faulted Li2MnO3 is not linked to the SF rate but only governed by the accessible crystalline surfaces and the manganese environments at the surface atomic layer. The formation of (0 0 1)-Li surface according to the Li-overstoichiometry on the extreme surface and the random particles shape of the more faulted materials are responsible of the reactivity tuning.

Published
2021
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8. Tissue localization of selenium of parental or dietary origin in rainbow trout (Oncorhynchus mykiss) fry using LA-ICP MS bioimaging

Author

Pierre-André Geraert, Philip Antony Jesu Prabhu, Pauline Wischhusen, Stéphanie Fontagné-Dicharry, Benoit Fauconneau, Sadasivam Kaushik, Mickael Briens, Germain Vallverdu, Sandra Mounicou, Maïté Bueno, Carine Arnaudguilhem, Brice Bouyssiere, Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Adisseo France SAS, F-92160 Antony, Partenaires INRAE, Institute of Marine Research [Bergen] (IMR), University of Bergen (UiB), Aquitaine Region [AQUITRACES project n°20131206001-13010973], I-site E2S: Energy and Environmental Solutions from the University of Pau and Pays de l’Adour, and ANR-11-RSNR-0002,AMORAD,AMORAD1(2011)

Subjects
0301 basic medicine, Male, food.ingredient, Offspring, Biophysics, chemistry.chemical_element, Broodstock, Aquaculture, 010501 environmental sciences, Biology, 01 natural sciences, Biochemistry, Mass Spectrometry, Biomaterials, 03 medical and health sciences, Selenium, Animal science, food, Dietary Sodium, La icp ms, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Yolk, Animals, 14. Life underwater, Selenomethionine, 0105 earth and related environmental sciences, Metals and Alloys, Total body, Animal Feed, 030104 developmental biology, chemistry, Chemistry (miscellaneous), Oncorhynchus mykiss, Dietary Supplements, Rainbow trout, Female, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

In relation to the decrease of selenium (Se) content in aquafeeds, the impact of level and form of parental and dietary Se supplementation was investigated in rainbow trout fry using laser ablation-inductively coupled plasma mass spectrometry (LA-ICP MS) bioimaging. The offspring of rainbow trout broodstock, fed either a control diet without any Se supplementation (0.3 mg Se/kg diet) or a diet supplemented with Se (0.6 mg Se/kg diet) either as sodium selenite or hydroxy-selenomethionine, were sampled at swim-up fry stage or after 11 weeks of cross-feeding. Total body Se levels were influenced by parental Se nutrition in swim-up fry and by direct Se feeding in 11-week fry with higher levels in the Se-supplemented groups compared with the control and the highest levels in the hydroxy-selenomethionine treatment. The Se retention was lower for dietary sodium selenite. Selenomethionine levels increased when Se was provided as hydroxy-selenomethionine. LA-ICP MS maps revealed yolk in swim-up fry and intestine, liver, and kidney in 11-week fed fry as tissues with high Se abundance. In swim-up fry, muscle Se was the highest abundant when parents were fed hydroxy-selenomethionine. In 11-week fed fry, muscle Se abundance was higher in the head part of fry fed both Se-supplemented diets, but only in the tail part of fry fed hydroxy-selenomethionine. Liver Se abundance was higher in fry fed sodium selenite compared with the control diet supporting the hypothesis that tissue Se distribution can be influenced by parental and dietary Se forms and levels.

Published
2020
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9. Molecular Cartography of A1 and A2 Asphaltene Subfractions from Classical Molecular Dynamics Simulations

Author

Orlando Villegas, Sócrates Acevedo, Brice Bouyssiere, Germain Vallverdu, Isabelle Baraille, Jimmy Castillo, Faculté des sciences de Caracas, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Franco-Venezuelan Project RMR

Subjects
Aggregate (composite), Polymer science, Chemistry, General Chemical Engineering, Energy Engineering and Power Technology, Fraction (chemistry), 02 engineering and technology, 021001 nanoscience & nanotechnology, Crude oil, humanities, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Molecular dynamics, Fuel Technology, 020401 chemical engineering, [CHIM]Chemical Sciences, 0204 chemical engineering, 0210 nano-technology, Asphaltene
Abstract

International audience; The physical chemistry of the heavyweight fraction of crude oil is still a subject of vivid discussions due to the complications which arise from the tendency of this fraction to aggregate and finally hinder the refining processes. Asphaltene molecules, that compose the largest part of this fraction, can be separated into two subfractions, A1 and A2, through a treatment with p-nitrophenol. In this paper, starting from the molecule models suggested by Acevedo et al. (Acevedo et al. Energy Fuels 2018, 32, 6669−6677.), we screened the chemical structure and composition of the two subfractions and investigated their aggregation mechanism using classical molecular dynamics simulations. The results show that oxygen atoms, present as hydroxyl or carboxylic groups, are a key factor in the formation of large aggregate. From the analysis of the simulations, we estimated the size of the aggregates and showed how the flexibility of the molecules may affect the size of the aggregates. Finally we showed that in addition to the structural differences (such as the H/C ratio and DBE) that distinguish the A1 and A2 subfractions, the solubility of the subfractions is also strongly dependent on the ability of the molecules to bind through hydrogen bonds.

Published
2020
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10. Sensitivity of Asphaltene Aggregation toward the Molecular Architecture under Desalting Thermodynamic Conditions

Author

Isabelle Baraille, Germain Vallverdu, Brice Bouyssiere, H. Santos Silva, A. Alfarra, Didier Bégué, Instituto de Física, Universidade federal de uberlandia, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), and Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
General Chemical Engineering, Energy Engineering and Power Technology, 02 engineering and technology, Molecular dynamics, Shale oil, 020401 chemical engineering, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Phase (matter), Organic chemistry, Molecule, 0204 chemical engineering, Asphaltene, Refining (metallurgy), Aggregate (composite), Desalination, Chemistry, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [CHIM.POLY]Chemical Sciences/Polymers, Fuel Technology, Chemical engineering, 13. Climate action, 0210 nano-technology, Oil shale
Abstract

International audience; The challenges faced by the oil and shale industries include the comprehension of the physical-chemical behavior of heavy-weight phases. These phases have a high tendency to aggregate, mainly as a result of the presence of asphaltenes, the composition of which has been fairly unclear up to now. The chemical composition of this phase is one of the driving forces behind the physical-chemical behavior in oil, and the structure-property relations of these systems are key in the development of improved refining techniques, including the design of new catalysts. In this paper, the aggregation of asphaltene molecules is studied with regard to molecular architecture and variations in the size of the aromatic core and lateral chain length using classical molecular dynamics simulations. How these characteristics are impacted by the temperature and pressure is also examined. This analysis provides a general overview of the factors that have the strongest impact on the formation and stability of nanoaggregates and clusters of nanoaggregates.

Published
2017
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11. First principle study of the surface reactivity of layered lithium oxides LiMO2 (M = Ni, Mn, Co)

Author

Isabelle Baraille, Nathalie Andreu, Marie Minvielle, Germain Vallverdu, Danielle Gonbeau, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Advanced Lithium Energy Storage Systems - ALISTORE-ERI (ALISTORE-ERI), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Réseau sur le stockage électrochimique de l'énergie (RS2E), Université de Picardie Jules Verne (UPJV)-Institut de Chimie du CNRS (INC)-Aix Marseille Université (AMU)-Université de Pau et des Pays de l'Adour (UPPA)-Université de Nantes (UN)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Collège de France (CdF (institution))-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Université Grenoble Alpes (UGA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Pau et des Pays de l'Adour (UPPA), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Université de Nantes (UN)-Aix Marseille Université (AMU)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Collège de France (CdF (institution))-Université de Picardie Jules Verne (UPJV)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), and Université Grenoble Alpes (UGA)-Université Grenoble Alpes (UGA)

Subjects
Inorganic chemistry, chemistry.chemical_element, 02 engineering and technology, 010402 general chemistry, DFT, 01 natural sciences, Redox, chemistry.chemical_compound, Surface reactivity, Adsorption, Transition metal, Materials Chemistry, [CHIM]Chemical Sciences, Sulfate, NMC, Positive electrode materials, Surfaces and Interfaces, 021001 nanoscience & nanotechnology, Condensed Matter Physics, 0104 chemical sciences, Surfaces, Coatings and Films, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, chemistry, Chemisorption, Electrode, First principle, Lithium, 0210 nano-technology, First principle calculations
Abstract

International audience; LiNixMnyCo1 - x - yO2 compounds (NMC) are layered oxides widely used in commercial lithium-ion batteries at the positive electrode. Nevertheless surface reactivity of this material is still not well known. As a first step, based on first principle calculations, this study deals with the electronic properties and the surface reactivity of LiMO2 (M = Co, Ni, Mn) compounds, considering the behavior of each transition metal separately in the same R3m α-NaFeO2-type structure, the one of LiCoO2 and NMC. For each compound, after a brief description of the bare slab electronic properties, we explored the acido-basic and redox properties of the (110) and (104) surfaces by considering the adsorption of a gaseous probe. The chemisorption of SO2 produces both sulfite or sulfate species associated respectively to an acido-basic or a reduction process. These processes are localized on the transition metals of the first two layers of the surface. Although sulfate species are globally favored, a different behavior is obtained depending on both the surface and the transition metal considered. We conclude with a simple scheme which describes the reduction processes on the both surfaces in terms of formal oxidation degrees of transition metals

Published
2016
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12. Impact of H-Bonds and Porphyrins on Asphaltene Aggregation As Revealed by Molecular Dynamics Simulations

Author

Brice Bouyssiere, Isabelle Baraille, Didier Bégué, Germain Vallverdu, A. Alfarra, H. Santos Silva, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), and Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
General Chemical Engineering, Solvation, Energy Engineering and Power Technology, Vanadium, chemistry.chemical_element, 02 engineering and technology, 010402 general chemistry, Photochemistry, 01 natural sciences, Toluene, Porphyrin, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, chemistry.chemical_compound, Molecular dynamics, Nickel, Fuel Technology, 020401 chemical engineering, chemistry, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Molecule, [CHIM]Chemical Sciences, 0204 chemical engineering, Asphaltene
Abstract

International audience; The presence of metalloporphyrins alongside asphaltenes in heavy fractions of crude oil is a key issue in petroleum exploration and upgrading. These compounds are also expected to display interfacial activity in water/toluene mixtures, but the origin of this phenomenon remains uncertain. In this work, we use molecular dynamics simulations to investigate complex asphaltene mixtures constituted of 10 different molecules, under also multifaceted solvation conditions (toluene/n-heptane/water). We add nickel and vanadium (under the form of vanadyl) porphyrins with occasionally grafted polar lateral chains, in these mixtures. The aggregation behavior and interaction with water molecules (as a model to have insights from the interfacial activity of such molecules) are intimately linked to the type of porphyrin and to the molecular properties of the asphaltenes (mainly the presence of polar lateral chains). Vanadium porphyrins, even without polar lateral chains, can form H-bonds that might contribute to their presence within asphaltene nanoaggregates. Moreover, when polar lateral chains are present in asphaltene molecules, the systems display a supramolecular organization with several distinct interactions at the same time. The shapes of these systems do not totally agree with the traditional Yen–Mullins model. In the first part of this work, we finally propose that complex asphaltene systems in complex solvent mixtures seem to have a supramolecular behavior with non-negligent colloidal behavior as well. This should be indicative that Yen–Mullins and Gray’s models of asphaltene self-assembly are neither conflictual nor antagonistic. They are two facets of a scale- and molecular structure-dependent complex mechanism.

Published
2018
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13. Possible Existence of a Monovalent Coordination for Nitrogen Atoms in LixPOyNz Solid Electrolyte: Modeling of X-ray Photoelectron Spectroscopy and Raman Spectra

Author

Yann Tison, Émilie Guille, Isabelle Baraille, Germain Vallverdu, Didier Bégué, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), and Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Chemistry, Binding energy, Analytical chemistry, 02 engineering and technology, Electrolyte, lithium nitride phosphate electrolyte nitrogen atom monovalent coordination model, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, Spectral line, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, Amorphous solid, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Molecular dynamics, symbols.namesake, General Energy, X-ray photoelectron spectroscopy, Chemical physics, symbols, Ionic conductivity, Physical and Theoretical Chemistry, 0210 nano-technology, Raman spectroscopy
Abstract

International audience; LixPOyNz is an amorphous solid electrolyte widely used in microbattery devices. The present study, based on a confrontation between expt. and theory, aims at providing new knowledge regarding the ionic cond. model of such systems in correlation with its structure. The computational strategy involved mol. dynamic simulations and first-principle calcns. on mol. and periodic models. The exptl. target data involve electronic and vibrational properties and were considered through the simulation of Raman and X-ray photoemission spectra in order to identify characteristic patterns of LixPOyNz. In particular, the presence of short phosphate chains is suggested by mol. dynamics calcns., and the simulation of Raman spectra clearly evidenced a new coordination for nitrogen atoms in the amorphous state, not considered until now in the exptl. structural model of the electrolyte and initially hypothesized based on core level binding energy computations. Monovalent nitrogen atoms together with short phosphate chains were used to build a structural model of the electrolyte and appeared to lead to a better reprodn. of the target exptl. results, while it implies a necessary refinement of the diffusion schemes commonly considered for lithium ions.

Published
2015
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14. Morphology and surface reactivity relationship in the Li1+xMn2–xO4 spinel with x = 0.05 and 0.10: a combined first-principle and experimental study

Author

Isabelle Baraille, Joachim Allouche, Ambroise Quesne-Turin, Delphine Flahaut, Germain Vallverdu, Laurence Croguennec, Michel Ménétrier, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Réseau sur le stockage électrochimique de l'énergie (RS2E), Université de Nantes (UN)-Aix Marseille Université (AMU)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Collège de France (CdF (institution))-Université de Picardie Jules Verne (UPJV)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Université Grenoble Alpes (UGA), Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), the Conseil Général des Pyrénées Atlantiques and the French Research Network on the Electrochemical Energy Storage (RS2E). This project also received funding from Région Nouvelle Aquitaine. The theoretical calculations were performed using HPC resources from GENCI-CINES (Grant 2017-A0010806920) and the Mesocentre de Calcul Intensif Aquitain (MCIA)., ANR-10-LABX-0076,STORE-EX,Laboratory of excellency for electrochemical energy storage(2010), Université de Picardie Jules Verne (UPJV)-Institut de Chimie du CNRS (INC)-Aix Marseille Université (AMU)-Université de Pau et des Pays de l'Adour (UPPA)-Université de Nantes (UN)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Collège de France (CdF (institution))-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Université Grenoble Alpes (UGA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), and Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Polytechnique de Bordeaux-Université de Bordeaux (UB)

Subjects
Materials science, Scanning electron microscope, spinel positive electrode materials, Spinel, 02 engineering and technology, [CHIM.MATE]Chemical Sciences/Material chemistry, engineering.material, first-principle calculations, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, Redox, 0104 chemical sciences, stoichiometry, Crystal, Adsorption, Surface reactivity, X-ray photoelectron spectroscopy, engineering, XPS, Physical chemistry, General Materials Science, Reactivity (chemistry), 0210 nano-technology, Stoichiometry
Abstract

International audience; This article focuses on the surface reactivity of two spinel samples with different stoichiometries and crystal morphologies, namely Li1+xMn2–xO4 with x = 0.05 and 0.10. LiMn2O4 compounds are good candidates as positive electrode of high-power lithium-ion batteries for portable devices. The samples were investigated using both experimental and theoretical approaches. On the experimental point of view, they were characterized in depth from X-ray diffraction, scanning electron microscopy, and X-ray photoelectron spectroscopy (XPS) analyses. Then, the reactivity was investigated through the adsorption of (SO2) gaseous probes, in controlled conditions, followed by XPS characterization. First-principle calculations were conducted simultaneously to investigate the electronic properties and the reactivity of relevant surfaces of an ideal LiMn2O4 material. The results allow us to conclude that the reactivity of the samples is dominated by an acido-basic reactivity and the formation of sulfite species. Nonetheless, on the x = 0.05 sample, both sulfite and sulfate species are obtained, the later, in lesser extent, corresponding to a redox reactivity. Combining experimental and theoretical results, this redox reactivity could be associated with the presence of a larger quantity of Mn4+ cations on the last surface layers of the material linked to a specific surface orientation.

Published
2017
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15. Morphology and Surface Reactivity Relationship in the Li

Author

Ambroise, Quesne-Turin, Germain, Vallverdu, Delphine, Flahaut, Joachim, Allouche, Laurence, Croguennec, Michel, Ménétrier, and Isabelle, Baraille

Abstract

This article focuses on the surface reactivity of two spinel samples with different stoichiometries and crystal morphologies, namely Li

Published
2017

16. Surface Reactivity of Li

Author

Ambroise, Quesne-Turin, Delphine, Flahaut, Laurence, Croguennec, Germain, Vallverdu, Joachim, Allouche, Youn, Charles-Blin, Jean-Noël, Chotard, Michel, Ménétrier, and Isabelle, Baraille

Abstract

This article deals with the surface reactivity of (001)-oriented Li

Published
2017

17. Surface reactivity of Li2MnO3: first-principles and experimental study

Author

Laurence Croguennec, Isabelle Baraille, Michel Ménétrier, Germain Vallverdu, Youn Charles-Blin, Jean-Noël Chotard, Joachim Allouche, Ambroise Quesne-Turin, Delphine Flahaut, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Polytechnique de Bordeaux-Université de Bordeaux (UB), Réseau sur le stockage électrochimique de l'énergie (RS2E), Université de Picardie Jules Verne (UPJV)-Institut de Chimie du CNRS (INC)-Aix Marseille Université (AMU)-Université de Pau et des Pays de l'Adour (UPPA)-Université de Nantes (UN)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Collège de France (CdF (institution))-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Université Grenoble Alpes (UGA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), Laboratoire réactivité et chimie des solides - UMR CNRS 7314 (LRCS), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), The authors thank the Conseil Général des Pyrénées Atlantiques and the French Research Network on the Electrochemical Energy Storage (RS2E) for funding the AQT’s PhD fellowship and Philippe Dagault (ICMCB-Pessac) for his technical support. This project also received funding from Région Nouvelle Aquitaine and the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). The theoretical calculations were performed using HPC resources from GENCI-CINES (Grant 2016—c2016086920) and the Mesocentre de Calcul Intensif Aquitain (MCIA). The acquisition of the RS2E single crystal diffractometer was also partially supported by the FEDER (European Fund for Regional Development) fund and the Picardie region., ANR-10-LABX-0076,STORE-EX,Laboratory of excellency for electrochemical energy storage(2010), Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Nantes (UN)-Aix Marseille Université (AMU)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Collège de France (CdF (institution))-Université de Picardie Jules Verne (UPJV)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Université Grenoble Alpes (UGA), and Université de Picardie Jules Verne (UPJV)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Auger electron spectroscopy, Materials science, AES, Photoemission spectroscopy, Scanning electron microscope, chemistry.chemical_element, 02 engineering and technology, [CHIM.MATE]Chemical Sciences/Material chemistry, first-principle calculations, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, 0104 chemical sciences, Characterization (materials science), Adsorption, Surface reactivity, X-ray photoelectron spectroscopy, chemistry, Chemical engineering, XPS, Molecule, General Materials Science, Lithium, 0210 nano-technology, single crystal
Abstract

International audience; The present paper deals with the surface reactivity of (001) oriented Li2MnO3 crystals investigated from a multi-techniques approach combining, material synthesis, X-ray photoemission spectroscopy (XPS), Scanning Electron Microscopy (SEM), Auger Electron Spectroscopy (AES) and first-principle calculations. Li2MnO3 is considered as a model compound suitable to go further in the understanding of the role of tetravalent manganese atoms in the surface reactivity of layered lithium oxides. The knowledge of the surface properties of such materials is essential in order to understand the mechanisms involved in parasitic phenomena responsible for early aging or poor storage performances of lithium-ion batteries. The surface reactivity was probed through the adsorption of SO2 gas molecules on large Li2MnO3 crystals in order to be able to focus the XPS beam on the top of the (001) surface. A chemical mapping and XPS characterization of the material before and after the SO2 adsorption show in particular that the adsorption is homogeneous at the micro and nanoscale and involves Mn reduction, while first-principle calculations on a slab model of the surface allow us to conclude that the most energetically favorable species formed is a sulfate with charge transfer implying reduction of Mn.

Published
2017
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18. The role of metalloporphyrins on the physical-chemical properties of petroleum fluids

Author

Isabelle Baraille, Didier Bégué, Germain Vallverdu, Hugo Santos Silva, Pierre Giusti, Jean-Pierre Korb, A. Alfarra, Brice Bouyssiere, Ana Carolina Rennó Sodero, Laboratoire de Physique de la Matière Condensée - UR UPJV 2081 (LPMC), Université de Picardie Jules Verne (UPJV), TOTAL Refining and Chemical, Institut pluridisciplinaire de recherche sur l'environnement et les matériaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physique de la matière condensée (LPMC), and École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Chemical substance, Molecular model, Chemistry, General Chemical Engineering, Organic Chemistry, Energy Engineering and Power Technology, 02 engineering and technology, Electronic structure, [CHIM.MATE]Chemical Sciences/Material chemistry, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Molecular dynamics, Fuel Technology, Chemical engineering, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Nano, Molecule, Density functional theory, metalloporphyrin phys chem property petroleum fluid, 0210 nano-technology, Asphaltene
Abstract

International audience; The presence of metalloporphyrins in crude oil has been known by many years now but their role on the physical-chemical properties of petroleum fluids, such as the aggregation of the high-molecular weight phases, remains unknown. In this paper, these properties are studied using different molecular modeling techniques (Molecular Dynamics, Semi-empirical PM7 and Density Functional Theory). This combined methodology allowed us characterizing the nature of these interactions, how it dominates the electronic structure of the stacked molecules and what is their participation on the formation of the nano-, microand macro-aggregates.

Published
2016
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19. Molecular Dynamics Study of Nanoaggregation in Asphaltene Mixtures: Effects of the N, O, and S Heteroatoms

Author

Isabelle Baraille, Germain Vallverdu, Jean-Pierre Korb, Hervé Carrier, Ana Carolina Rennó Sodero, Brice Bouyssiere, Didier Bégué, A. Alfarra, Hugo Santos Silva, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), and Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Work (thermodynamics), General Chemical Engineering, Heteroatom, Asphaltenes, Energy Engineering and Power Technology, 02 engineering and technology, Chemical characteristic, Molecular dynamics, 010402 general chemistry, Lateral chains, 01 natural sciences, Chain-ends, 020401 chemical engineering, Computational chemistry, Interaction energies, Molecule, [CHIM]Chemical Sciences, 0204 chemical engineering, Asphaltene, Chemistry, Molecular dynamics simulations, Chains, Molecules, Relative concentration, 0104 chemical sciences, Fuel Technology, Nanoaggregation, Heteroatoms, Physical chemistry
Abstract

International audience; In this paper the aggregation of asphaltenes is studied for two asphaltene molecule families, namely, PA3 and CA22 analogues, on the basis of the work of Schuler et al. (J. Am. Chem. Soc., 2015, 137, 9870). The chemical characteristics of these molecules were screened by changing the heteroatoms on the backbone and the lateral chain-ends. These molecules were mixed together with different relative concentrations, and for the first time, the aggregation of different asphaltenes was determined using molecular dynamics simulations (MDS). The results show that the interaction energies vary for different heteroatom arrangement within a given structure and depend on the type of asphaltene. Moreover, we showed that the chain-ends have a crucial role on this phenomenon.

Published
2016
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20. First-principle calculation of core level binding energies of LixPOyNz solid electrolyte

Author

Émilie Guille, Germain Vallverdu, Isabelle Baraille, Institut pluridisciplinaire de recherche sur l'environnement et les matériaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), and Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Photoemission spectroscopy, Chemistry, Binding energy, General Physics and Astronomy, Thermodynamics, 02 engineering and technology, Electronic structure, [CHIM.MATE]Chemical Sciences/Material chemistry, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, 0104 chemical sciences, Amorphous solid, core level energy XPS lithium nitride phosphate electrolyte DFT, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Ab initio quantum chemistry methods, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Molecular vibration, Phase (matter), First principle, Physical and Theoretical Chemistry, Atomic physics, 0210 nano-technology
Abstract

International audience; We present first-principle PAW-DFT-PBE calcns. of core-level binding energies for the study of insulating, bulk phase, compds., based on the Slater-Janak transition state model. Those calcns. were performed in order to find a reliable model of the amorphous LixPOyNz solid electrolyte which is able to reproduce its electronic properties gathered from X-ray photoemission spectroscopy (XPS) expts. As a starting point, Li2PO2N models were investigated. These models, proposed by Du et al. on the basis of thermodn. and vibrational properties, were the first structural models of LixPOyNz. Thanks to chem. and structural modifications applied to Li2PO2N structures, which allow to demonstrate the relevance of our computational approach, we raise an issue concerning the possibility of encountering a non-bridging kind of nitrogen atoms ( = N-) in LixPOyNz compds.

Published
2015
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21. Mesoscopic simulations of shock-to-detonation transition in reactive liquid high explosive

Author

Emeric Bourasseau, Nicolas Desbiens, Jean-Bernard Maillet, Germain Vallverdu, Gabriel Stoltz, DAM Île-de-France (DAM/DIF), Direction des Applications Militaires (DAM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut Pluridisciplinaire de Recherche sur l'Environnement et les Matériaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS), École des Ponts ParisTech (ENPC), and Institut pluridisciplinaire de recherche sur l'environnement et les matériaux (IPREM)

Subjects
Materials science, Explosive material, Astrophysics::High Energy Astrophysical Phenomena, Detonation, General Physics and Astronomy, Non-equilibrium thermodynamics, Thermodynamics, 02 engineering and technology, 01 natural sciences, law.invention, [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], chemistry.chemical_compound, law, 0103 physical sciences, 010306 general physics, 05.10.-a,82.40.Fp,05.70.Ln, Mesoscopic physics, Nitromethane, Dissipative particle dynamics, Mechanics, 021001 nanoscience & nanotechnology, Shock (mechanics), Ignition system, chemistry, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], 0210 nano-technology
Abstract

International audience; An extension of the model described in a previous work (see Maillet J. B. et al., EPL, 78 (2007) 68001) based on Dissipative Particle Dynamics is presented and applied to a liquid high explosive (HE), with thermodynamic properties mimicking those of liquid nitromethane. Large scale nonequilibrium simulations of reacting liquid HE with model kinetic under sustained shock conditions allow a better understanding of the shock-to-detonation transition in homogeneous explosives. Moreover, the propagation of the reactive wave appears discontinuous since ignition points in the shocked material can be activated by the compressive waves emitted from the onset of chemical reactions.

Published
2011
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22. Excited state dynamics of the green fluorescent protein on the nanosecond time scale

Author

Gabriella Jonasson, Fabienne Merola, Jean-Marie Teuler, Germain Vallverdu, Isabelle Demachy, Bernard I. Levy, Jacqueline Ridard, Laboratoire de Chimie Physique D'Orsay (LCPO), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Pau et des Pays de l'Adour (UPPA), Hôpital Lariboisière, Université Paris Diderot - Paris 7 (UPD7)-Hôpital Lariboisière-Fernand-Widal [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), and Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Lariboisière-Université Paris Diderot - Paris 7 (UPD7)

Subjects
010304 chemical physics, Scale (ratio), Chemistry, Dynamics (mechanics), Nanotechnology, [CHIM.MATE]Chemical Sciences/Material chemistry, Chromophore, Nanosecond, 010402 general chemistry, 01 natural sciences, Fluorescence, Molecular physics, 0104 chemical sciences, Computer Science Applications, Green fluorescent protein, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Parallel processing (DSP implementation), Excited state, 0103 physical sciences, [CHIM]Chemical Sciences, Physical and Theoretical Chemistry
Abstract

cited By 18; International audience; We have introduced a new algorithm in the parallel processing PMEMD module of the AMBER suite that allows MD simulations with a potential involving two coupled torsions. We have used this modified module to study the green fluorescent protein. A coupled torsional potential was adjusted on high accuracy quantum chemical calculations of the anionic chromophore in the first excited state, and several 15-ns-long MD simulations were performed. We have obtained an estimate of the fluorescence lifetime (2.2 ns) to be compared to the experimental value (3 ns), which is, to the best of our knowledge, the first theoretical estimate of that lifetime.

Published
2011
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23. Relation between pH, structure, and absorption spectrum of Cerulean: a study by molecular dynamics and TD DFT calculations

Author

Bernard I. Levy, Isabelle Demachy, Hélène Pasquier, Germain Vallverdu, Jacqueline Ridard, Fabienne Merola, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Pau et des Pays de l'Adour (UPPA), Laboratoire de Chimie Physique D'Orsay (LCPO), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Hôpital Lariboisière, Université Paris Diderot - Paris 7 (UPD7)-Hôpital Lariboisière-Fernand-Widal [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), and Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Lariboisière-Université Paris Diderot - Paris 7 (UPD7)

Subjects
Models, Molecular, crystal structure, Absorption spectroscopy, Cerulean, Green Fluorescent Proteins, Molecular Dynamics Simulation, 010402 general chemistry, Photochemistry, chemistry, 01 natural sciences, Biochemistry, Protein Structure, Secondary, 03 medical and health sciences, Molecular dynamics, chemistry.chemical_compound, fluorescence analysis, Protein structure, Structural Biology, protein conformation, Single bond, [CHIM]Chemical Sciences, Carboxylate, crystallography, Molecular Biology, 030304 developmental biology, calculation, 0303 health sciences, hydrogen bond, chromatophore, Chemistry, Hydrogen bond, pH measurement, [CHIM.MATE]Chemical Sciences/Material chemistry, Chromophore, Hydrogen-Ion Concentration, simulation, molecular dynamics, structure analysis, 0104 chemical sciences, unclassified drug, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Crystallography, chemical structure, proton transport, protein secondary structure, absorption
Abstract

cited By 6; International audience; Molecular dynamics (MD) and quantum mechanical calculations of the Cerulean green fluorescent protein (a variant of enhanced cyan fluorescent protein ECFP) at pH 5.0 and 8.0 are presented, addressing two questions arising from experimental results (Malo et al., Biochemistry 2007;46:9865 - 9873): the origin of the blue shift of absorption spectrum when the pH is decreased from 8.0 to 5.0, and the lateral chain orientation of the key residue Asp 148. We demonstrate that the blue shift is reproduced assuming that a rotation around the single bond of the exocydie ring of the chromophore takes place when the pH changes from 5.0 to 8.0. We find that Asp 148 is protonated and inside the barrel at pH 5.0 in agreement with crystallographic data. However, the hydrogen bond pattern of Asp 148 is different in simulations of the solvated protein and in the crystal structure. This difference is explained by a partial closing of the cleft between strands 6 and 7 in MD simulations. This study provides also a structure at pH 8.0: the Asp 148 carboxylate group is exposed to the solvent and the chromophore is stabilized in the trans conformation by a tighter hydrogen bond network. This work gives some insight into the relationship between the pH and the chromophore conformation and suggests an interpretation of the very similar fluorescent properties of ECFP and ECFP/ H148D.

Published
2009
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24. Using biased molecular dynamics and Brownian dynamics in the study of fluorescent proteins

Author

Bernard I. Levy, Germain Vallverdu, Jacqueline Ridard, Isabelle Demachy, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Pau et des Pays de l'Adour (UPPA), Laboratoire de Chimie Physique D'Orsay (LCPO), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Hôpital Lariboisière, Université Paris Diderot - Paris 7 (UPD7)-Hôpital Lariboisière-Fernand-Widal [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), and Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Lariboisière-Université Paris Diderot - Paris 7 (UPD7)

Subjects
010304 chemical physics, Chemistry, Fluorescence correlation spectroscopy, [CHIM.MATE]Chemical Sciences/Material chemistry, Chromophore, 010402 general chemistry, Condensed Matter Physics, 01 natural sciences, Biochemistry, Molecular physics, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Molecular dynamics, 0103 physical sciences, Brownian dynamics, [CHIM]Chemical Sciences, Physical and Theoretical Chemistry, Umbrella sampling, First-hitting-time model, Atomic physics, Potential of mean force, Ground state
Abstract

cited By 7; International audience; The present article presents a theoretical study of the dynamics of the chromophore of the Green Fluorescent Protein in its excited state on a long time scale (a few ten nanoseconds) in order to help the interpretation of time resolved experiments. The starting hypothesis is that the quenching of fluorescence is related to the internal motion of the chromophore, usually called 'φ torsion'. In fact, that motion is hindered by the protein and cannot be studied by standard molecular dynamics. Therefore we have developed a different approach involving three steps. First the potential of mean force (PMF) along the considered torsion is obtained by biased molecular dynamics (umbrella sampling). Then, a long time scale, single particle Brownian dynamics is performed using that PMF and an appropriate diffusion constant. Finally we determine the nth passage time (NPT) distribution functions at geometries or regions where nonradiative ground state recovery may occur. The NPT distributions generalize the more usual 'mean first passage time' and allow determining different quantities like fluorescence decay profiles, mean fluorescence lifetime, quantum yield etc. These quantities are used here in a qualitative discussion of the fluorescence decay in Green Fluorescent Protein.

Published
2009
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25. Complex fluorescence of the cyan fluorescent protein: comparisons with the H148D variant and consequences for quantitative cell imaging

Author

Bertrand Cinquin, Myriam Ridhoir, Régis Grailhe, Fabienne Merola, Pascal Pernot, Marie Erard, Hélène Pasquier, Aude Villoing, Luis Alvarez, Germain Vallverdu, Institut de pharmacologie et de biologie structurale (IPBS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire des colloïdes, verres et nanomatériaux (LCVN), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Centre National de la Recherche Scientifique (CNRS)-Université de Pau et des Pays de l'Adour (UPPA), Laboratoire de Chimie Physique, Centre Universitaire Paris-Sud-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur Korea - Institut Pasteur de Corée, Réseau International des Instituts Pasteur (RIIP), Laboratoire de Chimie Physique D'Orsay (LCPO), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur de Corée

Subjects
Models, Molecular, Luminescence, Cell imaging, Cerulean, Protein Conformation, Mutant, Green Fluorescent Proteins, 010402 general chemistry, 01 natural sciences, Biochemistry, Fluorescence, Nuclear magnetic resonance, Cell Line, 03 medical and health sciences, Mole, Molecule, [CHIM]Chemical Sciences, Animals, Humans, Thermodynamic analysis, 030304 developmental biology, Cyan fluorescent proteins, 0303 health sciences, Chemistry, PH dependences, Temperature, Conformational exchanges, Proteins, Thermoanalysis, [CHIM.MATE]Chemical Sciences/Material chemistry, Chromophore, Hydrogen-Ion Concentration, Crystallographic studies, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Cytosol, Crystallography, Kinetics, Spectrometry, Fluorescence, Mutation, Thermodynamics, Mutant Proteins
Abstract

cited By 37; International audience; We have studied the fluorescence decays of the purified enhanced cyan fluorescent protein (ECFP, with chromophore sequence Thr-Trp-Gly) and of its variant carrying the single H148D mutation characteristic of the brighter form Cerulean. Both proteins exhibit highly complex fluorescence decays showing strong temperature and pH dependences. At neutral pH, the H148D mutation leads (i) to a general increase in all fluorescence lifetimes and (ii) to the disappearance of a subpopulation, estimated to be more than 25% of the total ECFP molecules, characterized by a quenched and red-shifted fluorescence. The fluorescence lifetime distributions of ECFP and its H148D mutant remain otherwise very similar, indicating a high degree of structural and dynamic similarity of the two proteins in their major form. From thermodynamic analysis, we conclude that the multiexponential decay of ECFP cannot be simply ascribed, as is generally admitted, to the slow conformational exchange characterized by NMR and X-ray crystallographic studies [Seifert, M. H., et al. (2002) J. Am. Chem. Soc. 124, 7932-7942; Bae, J. H., et al. (2003) J. Mol. Biol. 328, 1071-1081]. Parallel measurements in living cells show that these fluorescence properties in neutral solution are very similar to those of cytosolic ECFP.

Published
2008
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26. Cyan fluorescent protein : molecular dynamics, simulations, and electronic absorption spectrum

Author

Germain Vallverdu, Isabelle Demachy, Bernard I. Levy, Helene Laguitton-Pasquier, Pierre Archirel, Jacqueline Ridard, Elodie Durnerin, Laboratoire de Chimie Physique D'Orsay (LCPO), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), and Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Pau et des Pays de l'Adour (UPPA)

Subjects
Absorption spectroscopy, Protein Conformation, Charge cloud, Green Fluorescent Proteins, Molecular Conformation, Molecular dynamics, 010402 general chemistry, Photochemistry, Crystallography, X-Ray, 01 natural sciences, Sensitivity and Specificity, Molecular electronic transition, Fluorescence, Green fluorescent protein, Absorption, Hydrogen bonds, Protein structure, 0103 physical sciences, Materials Chemistry, Electronic transition, [CHIM]Chemical Sciences, Computer Simulation, Physical and Theoretical Chemistry, 010304 chemical physics, Chemistry, Hydrogen bond, Proteins, Hydrogen Bonding, Time-dependent density functional theory, [CHIM.MATE]Chemical Sciences/Material chemistry, Chromophore, X-ray conformations, 0104 chemical sciences, Surfaces, Coatings and Films, Conformations, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Models, Chemical, Chemical physics, Spectrophotometry, Quantum theory, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Electronic absorption
Abstract

cited By 30; International audience; The dynamics and electronic absorption spectrum of enhanced cyan fluorescent protein (ECFP), a mutant of green fluorescent protein (GFP), have been studied by means of a 1 ns molecular dynamics (MD) simulation. The two X-ray conformations A′ and B′ of ECFP were considered. The chromophore was assumed to be neutral, and all titratable residues were taken in their standard protonation state at neutral pH. The protein was embedded in a box of water molecules (and counterions). The first result is that the two conformations A′ and B′ are found to be stable all along the simulation. Then, an analysis of the hydrogen-bond networks shows strong differences between the two conformations in the surroundings of the nitrogen atom of the indolic part of the chromophore. This is partly due to the imperfection in the β barrel near the His148 residue, which allows the access of one solvent molecule inside the protein in conformation A′. Finally, quantum mechanical calculations of the electronic transition energies of the chromophore in the charge cloud of the protein and solvent water molecules were performed using the TDDFT method on 160 snapshots extracted every 5 ps of the MD trajectories. It is found that conformations A′ and B′ exhibit very similar spectra despite different H-bond networks involving the chromophore. This similarity is related to the weak charge transfer involved in the electronic transition and the weak electrostatic field created by ECFP near the chromophore, within the hypotheses made in the present simulation.

Published
2005
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