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12 results on '"Khaoula Boukari"'

1. Nanovectorization of DNA Through Cells Using Protamine Complexation

Author

Régis Delage-Mourroux, Fabien Picaud, Tijani Gharbi, Khaoula Boukari, C. Caoduro, Marc Pudlo, Hatem Boulahdour, Nadia Skandrani, Eric Hervouet, Raoudha Kacem, Christophe Borg, Nanomédecine, imagerie, thérapeutique - UFC (EA 4662) (NIT / NANOMEDECINE), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Interactions hôte-greffon-tumeur, ingénierie cellulaire et génique - UFC (UMR INSERM 1098) (RIGHT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS [Bourgogne-Franche-Comté]), and Estrogènes, Expression génique et pathologies du Système Nerveux Central - UFC (E2SNC / ESTROGENES)

Subjects
Models, Molecular, Physiology, Molecular Conformation, Biophysics, Nanoparticle, Nanotechnology, 02 engineering and technology, Carbon nanotube, Molecular Dynamics Simulation, 010402 general chemistry, 01 natural sciences, law.invention, Molecular dynamics, chemistry.chemical_compound, Adsorption, law, Animals, Humans, [CHIM]Chemical Sciences, Molecule, Protamines, Particle Size, ComputingMilieux_MISCELLANEOUS, biology, Nanotubes, Carbon, Chemistry, Biological Transport, DNA, Cell Biology, 021001 nanoscience & nanotechnology, Protamine, 0104 chemical sciences, biology.protein, Nanoparticles, Nanocarriers, 0210 nano-technology
Abstract

Carbon nanotubes (CNT) are currently used as a promising family of nanovectors able to deliver different types of therapeutic molecules. Several applications dealing with CNT used as drug nanocarriers have been developed since their ability to penetrate into the cells has been proved. CNT can thus load several active molecules to various cells. In this paper, we will use molecular dynamic simulation to describe theoretically the potential of CNT to transport and deliver DNA through the formation of protamine-DNA-CNT complex.

Published
2016

2. Towards New Insights in the Sterol/Amphotericin Nanochannels Formation: A Molecular Dynamic Simulation Study

Author

Jean-Marc Janot, Khaoula Boukari, Sebastien Balme, Fabien Picaud, Laboratoire de physique et de spectroscopie électronique (LPSE), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS), Institut Européen des membranes (IEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM), Laboratoire de physique moléculaire, Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)

Subjects
Physiology, Molecular Conformation, Biophysics, 02 engineering and technology, Molecular Dynamics Simulation, Biology, 010402 general chemistry, 01 natural sciences, Cell membrane, chemistry.chemical_compound, Amphotericin B, medicine, [CHIM]Chemical Sciences, Lipid bilayer, ComputingMilieux_MISCELLANEOUS, Ergosterol, Cell Membrane, Hydrogen Bonding, Biological membrane, Cell Biology, 021001 nanoscience & nanotechnology, Polyene, Sterol, 0104 chemical sciences, Sterols, medicine.anatomical_structure, Membrane, Biochemistry, chemistry, lipids (amino acids, peptides, and proteins), 0210 nano-technology, medicine.drug
Abstract

Amphotericin B (AmB) is a well-known polyene which self-organizes into membrane cell in order to cause the cell death. Its specific action towards fungal cell is not fully understood but was proved to become from sterol composition. The mechanism was shown experimentally to require the formation of stable sterol/polyene couples which could then organize in a nanochannel. This would allow the leakage of ions responsible for the death of fungal cells, only. In this present study, we investigate the arrangement of AmB/sterols in biological membrane using molecular dynamic simulations in order to understand the role of the sterol structure on the antifungal action of the polyene. We show in particular that the nanochannels tend to close up when cell was composed with cholesterol (animal cell) due to strong interaction between amphotericin and sterol. On the other side, with ergosterol (fungal cell) the largest interactions between amphotericin and lipid membrane lead to the appearance of large hole that could favor the important leakage of ions and thus, the fungal cell death. This work appears as a good complement in the extensive studies linked to the understanding of the antifungal molecules in membrane cells.

Published
2015

3. Production of H2 by water radiolysis in cement paste under electron irradiation: A joint experimental and theoretical study

Author

Khaoula Boukari, Thibault Charpentier, Conrad Johnston, Roland J.-M. Pellenq, Ryan M. Kavanagh, Jorge Kohanoff, Gareth A. Tribello, Konrad J. Krakowiak, Lucile Dezerald, Andrés Saúl, Sophie Le Caër, Eddy Foy, Franz J. Ulm, Maxime Lainé, Sébastien Taupin, Laboratoire Interdisciplinaire sur l'Organisation Nanométrique et Supramoléculaire (LIONS), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Institut Jean Lamour (IJL), Université de Lorraine (UL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Department of Civil and Environmental Engineering [Cambridge] (CEE), Massachusetts Institute of Technology (MIT), Multi-Scale Material Science for Energy and Environment ((MSC)2 UMI3466 CNRS-MIT), CNRS-MIT, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Queen's University [Belfast] (QUB), Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), Laboratoire Archéomatériaux et Prévision de l'Altération (LAPA - UMR 3685), IRAMAT - Laboratoire Métallurgies et Cultures (IRAMAT - LMC), Institut de Recherches sur les Archéomatériaux (IRAMAT), Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Montaigne-Université de Technologie de Belfort-Montbeliard (UTBM)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Montaigne-Université de Technologie de Belfort-Montbeliard (UTBM), Cullen college of Engineering, University of Houston, NEEDS MIPOR and NEEDS Déchets programs, Schlumberger-MIT cement research collaboration X-Cem, EPSRC grant EP-K013459/1, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Université de Technologie de Belfort-Montbeliard (UTBM)-Université d'Orléans (UO)-Université Bordeaux Montaigne (UBM)-Centre National de la Recherche Scientifique (CNRS)-Université de Technologie de Belfort-Montbeliard (UTBM)-Université d'Orléans (UO)-Université Bordeaux Montaigne (UBM)-Centre National de la Recherche Scientifique (CNRS), and Université de Technologie de Belfort-Montbeliard (UTBM)-Université d'Orléans (UO)-Université Bordeaux Montaigne-Centre National de la Recherche Scientifique (CNRS)-Université de Technologie de Belfort-Montbeliard (UTBM)-Université d'Orléans (UO)-Université Bordeaux Montaigne-Centre National de la Recherche Scientifique (CNRS)

Subjects
Materials science, Reaction mechanisms, Inorganic chemistry, 02 engineering and technology, Cement paste, 01 natural sciences, Ion, First-principles calculations, H 2 production, 0103 physical sciences, Radiolysis, Electron beam processing, General Materials Science, Relative humidity, Irradiation, H2 production, Cement, Fission products, 010304 chemical physics, Radiochemistry, Radioactive waste, Building and Construction, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, 13. Climate action, 0210 nano-technology
Abstract

Long-term confinement of nuclear waste is one of the main challenges faced by the nuclear industry. Fission products such as 90Sr and 137Cs, both β− emitters known to induce serious health hazards, represent the largest fraction of nuclear waste. Cement is a good candidate to store them, provided it can resist the effects of irradiation over time. Here, we have investigated the effects of β− decay on cement by performing electron irradiation experiments on different samples. We show that H2 production in cement, the main effect of water radiolysis, depends strongly on composition and relative humidity. First-principles calculations indicate that the water-rich interlayer regions with Ca2+ ions act as electron traps that promote the formation of H2. They also show that holes localize in water-rich regions in low Ca content samples and are then able to participate in H2 production. This work provides new understanding of radiolysis effects in cements.

Published
2017

4. Confined Nystatin Polyenes in Nanopore Induce Biologic Ionic Selectivity

Author

Fabien Picaud, Guillaume Paris, Jean-Marc Janot, bastien Balme, Khaoula Boukari, Tijani Gharbi, Centre Interdisciplinaire de Nanoscience de Marseille ( CINaM ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Division of Geological and Planetary Sciences [Pasadena], California Institute of Technology ( CALTECH ), Nanomédecine, imagerie, thérapeutique - UFC ( NIT / NANOMEDECINE ), Université de Franche-Comté ( UFC ) -Université Bourgogne Franche-Comté ( UBFC ), Institut Européen des membranes ( IEM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Supérieure de Chimie de Montpellier ( ENSCM ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Université de Montpellier ( UM ), Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), California Institute of Technology (CALTECH), Nanomédecine, imagerie, thérapeutique - UFC (EA 4662) (NIT / NANOMEDECINE), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut Européen des membranes (IEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM), ANR-12-BS08-0023,TRANSION,TRANSport IONique au sein de canaux-ioniques biologiques confinés dans des nanopores: approche expérimentale et théorique(2012), Nanomédecine, imagerie, thérapeutique - UFC (UR 4662) (NIT / NANOMEDECINE), and Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Article Subject, Ionic bonding, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Divalent, Ion, Cell membrane, Molecular dynamics, lcsh:Technology (General), medicine, Organic chemistry, Molecule, General Materials Science, [PHYS]Physics [physics], chemistry.chemical_classification, [ PHYS ] Physics [physics], Chemistry, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Nanopore, Membrane, medicine.anatomical_structure, Biophysics, lcsh:T1-995, 0210 nano-technology
Abstract

International audience; Antifungal polyenes such as nystatin (or amphotericin B) molecules play an important role in regulating ions permeability through membrane cell. The creation of self-assembled nanopores into the fungal lipid membranes permits the leakage and the selectivity of ions (i.e., blockage of divalent cations) that cause the cell death. These abilities are thus of first interest to promote new biomimetic membranes with improved ionic properties. In the present work, we will use molecular dynamic simulations to interpret recent experimental data that showed the transfer of the nystatin action inside artificial nanopore in terms of ion permeability and selectivity. We will demonstrate that nystatin polyenes can be stabilized in a hydrophobic carbon nanotube, even at high concentration. The high potential interaction between the polyenes and the hydrophobic pore wall ensures the apparition of a hole inside the biomimetic nanopore that changes its intrinsic properties. The probability ratios of cation versus anion show interesting reproducibility of experimental measurements and, to a certain extent, opened the way for transferring biological properties in synthetic membranes.

Published
2016

5. Selectivity against proton in cation permeable hybrid solid state membrane

Author

Sebastien Balme, Khaoula Boukari, Jean-Marc Janot, Fabien Picaud, François Henn, Laboratoire de physique moléculaire, Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut de Science des Matériaux de Mulhouse (IS2M), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS), Institut Européen des membranes (IEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM), Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM ICMMM), and Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut de Chimie du CNRS (INC)

Subjects
010304 chemical physics, General Computer Science, Proton, General Physics and Astronomy, Nanotechnology, General Chemistry, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, Ion, Computational Mathematics, chemistry.chemical_compound, Molecular dynamics, Nanopore, Membrane, chemistry, Mechanics of Materials, Chemical physics, 0103 physical sciences, Gramicidin, Molecule, [CHIM]Chemical Sciences, General Materials Science, Selectivity, ComputingMilieux_MISCELLANEOUS
Abstract

Theoretical investigations based principally on Monte Carlo calculations were conducted to interpret the hindered mobility of protons which was experimentally observed in a hybrid biological/artificial nanopore constituted of the ion bio-channel gramicidin A confined inside an artificial solid-state nanopore. We show that this experimental outcome may result from the high concentration of gramicidin A that progressively diminishes the transfer of proton from one side to the other of the nanopore. More, using molecular dynamic simulations data we demonstrate that the water molecules are repelled from the gramicidin structure outside the nanopore, leading to a strong decrease of the proton transfer.

Published
2016

6. Carbon nanotube – Protamine hybrid: Evaluation of DNA cell penetration

Author

C. Caoduro, Marc Pudlo, Claire-Hélène Brachais, Tijani Gharbi, Fabien Picaud, Khaoula Boukari, Eric Hervouet, Raoudha Kacem, Hatem Boulahdour, Régis Delage-Mourroux, David Monchaud, Christophe Borg, Nanomédecine, imagerie, thérapeutique - UFC (EA 4662) (NIT / NANOMEDECINE), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] (ICMUB), Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Conception, synthèse et vectorisation de biomolécules. (CSVB), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris], Interactions hôte-greffon-tumeur, ingénierie cellulaire et génique - UFC (UMR INSERM 1098) (RIGHT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS [Bourgogne-Franche-Comté])-Université de Franche-Comté (UFC), Estrogènes, Expression génique et pathologies du Système Nerveux Central - UFC (E2SNC / ESTROGENES), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS [Bourgogne-Franche-Comté]), Laboratoire de physique et de spectroscopie électronique (LPSE), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Nanomédecine, imagerie, thérapeutique - UFC ( NIT / NANOMEDECINE ), Université Bourgogne Franche-Comté ( UBFC ) -Université de Franche-Comté ( UFC ), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] ( ICMUB ), Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Inserm UMR 1098, Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ), Estrogènes, Expression génique et pathologies du Système Nerveux Central - UFC ( E2SNC / ESTROGENES ), Université de Franche-Comté ( UFC ), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université de Franche-Comté (UFC), Institut Curie-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), Interactions hôte-greffon-tumeur, ingénierie cellulaire et génique - UFC (UMR INSERM 1098) (HOTE GREFFON), Université de Franche-Comté (UFC)-Etablissement français du sang [Bourgogne-France-Comté] (EFS [Bourgogne-France-Comté])-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Franche-Comté (UFC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Technologie de Belfort-Montbeliard (UTBM), and Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)

Subjects
Materials science, media_common.quotation_subject, mammalian-cells, Carbon nanotubes, noncovalent sidewall-functionalization, Protamine, Nanotechnology, 02 engineering and technology, Carbon nanotube, transporters, physicochemical properties, in-vitro, 010402 general chemistry, Endocytosis, 01 natural sciences, [ CHIM ] Chemical Sciences, law.invention, nonviral gene delivery, Cell membrane, chemistry.chemical_compound, law, Cellular internalization, medicine, endocytosis, [CHIM]Chemical Sciences, General Materials Science, Internalization, Functionalization, ComputingMilieux_MISCELLANEOUS, media_common, biology, Molecular dynamic simulation, General Chemistry, Transfection, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, proteins, 0104 chemical sciences, drug-delivery, medicine.anatomical_structure, plasmid dna, chemistry, Biophysics, Nucleic acid, biology.protein, 0210 nano-technology, Nanovectorization, DNA
Abstract

International audience; Carbon nanotubes (CNTs) represent a class of nanomaterials with important potential for biomedical and biotechnological applications. CNT based vectorization is an emerging approach to the transport of nucleic acid through cell membrane but limited by detachment of DNA and degradation process. To increase DNA internalization, it was proved that cationic functionalized CNT was essential. In such a way, protamine efficiently used in several transfection processes is a cationic protein which was never associated to CNT.We propose here a novel nanovector based on single-walled carbon nanotubes (SWCNT) functionalized by protamine. Our results based on qPCR methods clearly indicate that protamine-SWCNT/DNA hybrids were much more successful than ammonium-SWCNT/DNA hybrids to cross cell membrane and penetrate into cells. We also studied the cellular internalization mechanism of our complexes and showed that endocytosis was strongly involved. Finally, we proposed molecular dynamic simulations to understand the formation of the protamine-SWCNT/DNA complex and to extract the interaction responsible for its deliverance upon cell membrane. (C) 2015 Elsevier Ltd. All rights reserved.

Published
2016

7. Molecular chemisorption on passivated and defective boron doped silicon surfaces: a 'forced' dative bond

Author

Khaoula Boukari, Philippe Sonnet, Eric Duverger, Institut de Science des Matériaux de Mulhouse (IS2M), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SPI.ACOU]Engineering Sciences [physics]/Acoustics [physics.class-ph], Chemistry, Bond strength, Dangling bond, General Physics and Astronomy, Bond order, [SPI.MAT]Engineering Sciences [physics]/Materials, Bond length, Crystallography, symbols.namesake, Chemical bond, Computational chemistry, symbols, Single bond, Physical and Theoretical Chemistry, Bond energy, van der Waals force, [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics
Abstract

International audience; We investigate the adsorption mechanism of a single trans 4-pyridylazobenzene molecule (denoted by PAB) on a doped boron Si(111)√3×√3R30° surface (denoted by SiB) with or without boron-defects, by means of density functional theory calculations. The semiempirical approach proposed by Grimme allows us to take the dispersion correction into account. The role of the van der Waals correction in the adsorption geometries and energies is presented. In particular, two adsorption configurations are electronically studied. In the first one, the molecule is parallel to the surface and interacts with the SiB surface via the -N=N- bond. In the presence of a boron-defect, a Si-N chemical bond between the molecule and the surface is then formed, while electrostatic or/and van der Waals interactions are observed in the defectless surface. In the second adsorption configuration, the molecule presents different orientations with respect to the surface and interacts via the nitrogen atom of the pyridyl part of the PAB molecule. If the molecule is perpendicular to the perfect SiB surface, the lone-pair electrons associated with the heterocyclic nitrogen atom fill the empty dangling bond of a silicon adatom via a dative bond. Finally, in the presence of one boron-defect, the possibility of a "forced" dative bond, corresponding to a chemical bond formation between the PAB molecule and the silicon electron occupied dangling bond, is emphasized.

Published
2014

8. C60 molecules grown on a Si-supported nanoporous supramolecular network: a DFT study

Author

Eric Duverger, Marie-Christine Hanf, Khaoula Boukari, Philippe Sonnet, and Régis Stephan

Subjects
Silicon, Fullerene, Materials science, Macromolecular Substances, Surface Properties, Supramolecular chemistry, General Physics and Astronomy, Nanotechnology, 02 engineering and technology, Substrate (electronics), 010402 general chemistry, 01 natural sciences, Monolayer, Molecule, Physical and Theoretical Chemistry, Particle Size, Charge density, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Nanostructures, Covalent bond, Chemical physics, Quantum Theory, Density functional theory, Fullerenes, 0210 nano-technology, Porosity
Abstract

C60 fullerene assemblies on surfaces have attracted considerable attention because of their remarkable electronic properties. Now because of the competition between the molecules–substrate and the molecule–molecule interactions, an ordered C60 array is rather difficult to obtain on silicon surfaces. Here we present density functional theory simulations on C60 molecules deposited on a TBB (1,3,5-tri(1′-bromophenyl)benzene) monolayer lying on the Si(111)–boron surface (denoted SiB). The C60 molecules are located in the nanopores formed by the TBB network. Adsorption energy calculations show that the SiB surface governs the C60 vertical position, whereas the TBB network imposes the C60 lateral position, and stabilizes the molecule as well. The low charge density between the C60 and the SiB substrate on one hand, and on the other hand between the C60 and the TBB molecules, indicates that no covalent bond is formed between the C60 and its environment. However, according to charge density differences, a drastic charge reorganisation takes place between the Si adatoms and the C60 molecule, but also between the C60 and the surrounding TBB molecules. Finally, calculations show that a C60 array sandwiched between two TBB molecular layers is stable, which opens up the way to the growth of 3D supramolecular networks.

Published
2014

9. Theoretical study of intermolecular interactions in nanoporous networks on boron doped silicon surface

Author

Khaoula Boukari, Philippe Sonnet, Eric Duverger, Régis Stephan, Marie-Christine Hanf, Institut de Science des Matériaux de Mulhouse (IS2M), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), and Femto-st, MN2S

Subjects
[SPI.ACOU]Engineering Sciences [physics]/Acoustics [physics.class-ph], [SPI.ACOU] Engineering Sciences [physics]/Acoustics [physics.class-ph], Materials science, Silicon, Hydrogen bond, Nanoporous, [SPI.NANO] Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, Intermolecular force, Inorganic chemistry, Supramolecular chemistry, General Physics and Astronomy, chemistry.chemical_element, [SPI.MAT] Engineering Sciences [physics]/Materials, [SPI.MAT]Engineering Sciences [physics]/Materials, symbols.namesake, chemistry, Halogen, symbols, Physical chemistry, Molecule, Physical and Theoretical Chemistry, van der Waals force, [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics
Abstract

International audience; Supramolecular networks on a doped boron silicon surface under ultra high vacuum (UHV) have been recently obtained (Makoudi et al., 2013). The used molecule contains different end-groups, bearing either bromine, iodine or hydrogen atoms denoted 1,3,5-tri(4′-bromophenyl)benzene (TBB), 1,3,5-tri(4-iodophenyl)benzene (TIB) and 1,3,5-triphenyl-benzene (THB). To explain the formation of the nanoporous structures, interactions of the type aryl-X⋯H hydrogen bonds (X being a halogen atom) have been proposed. In order to obtain a complete insight of the stabilizing interaction in these networks adsorbed on the Si(1 1 1)√3x√3R30°-boron surface, we present a full density-functional-theory study taking the van der Waals interactions into account. We investigated the energetic and structural properties of three different nanoporous networks constituted by TBB, TIB and THB molecules. The electronic studies allow us to identify hydrogen bond and dipole–dipole intermolecular interactions in the supramolecular halogen networks, whereas only dipole–dipole interactions are present in the 1,3,5-triphenyl-benzene nanoporous network.

Published
2014

10. DFT-D Studies of Single Porphyrin Molecule on Doped Boron Silicon Surfaces

Author

Khaoula Boukari, Philippe Sonnet, Eric Duverger, Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Laboratoire de physique et de spectroscopie électronique (LPSE), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS), Institut de Science des Matériaux de Mulhouse (IS2M), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Silicon, Porphyrins, Surface Properties, Molecular Conformation, chemistry.chemical_element, Electrons, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, law.invention, [SPI.MAT]Engineering Sciences [physics]/Materials, symbols.namesake, chemistry.chemical_compound, Physisorption, law, Computational chemistry, Microscopy, Scanning Tunneling, Molecule, Computer Simulation, Physical and Theoretical Chemistry, [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, ComputingMilieux_MISCELLANEOUS, Boron, [SPI.ACOU]Engineering Sciences [physics]/Acoustics [physics.class-ph], Doping, 021001 nanoscience & nanotechnology, Porphyrin, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Atomic and Molecular Physics, and Optics, 0104 chemical sciences, Crystallography, chemistry, Models, Chemical, symbols, van der Waals force, Scanning tunneling microscope, 0210 nano-technology, Ground state
Abstract

International audience; We present a theoretical study in the framework of density functional calculations, taking into account the van der Waals interactions (DFT-D) of isolated Cu-5,10,15,20-tetrakis(3,5-di-tert-butyl-phenyl) porphyrin (Cu-TBPP) molecules in a C2v conformation adsorbed on a Si(111)√3x√3R30°-boron surface [denoted Si(111)-B]. With this approach, we investigate interactions between perfect or boron-defect Si(111)-B substrates and the Cu-TBPP molecule as well as the consequences of demetallation of Cu-TBPP. For each model, we determine the structural equilibrium, the spatial charge-density distribution and the electronic properties of the ground state. We conclude that there is potential for Si adatom capture by a porphyrin without strong modification of the porphyrin response, as seen from simulated scanning tunneling microscopy (STM) images.

Published
2012

11. A new assisted molecular cycloaddition on boron doped silicon surfaces: a predictive DFT-D study

Author

Khaoula Boukari, Philippe Sonnet, Eric Duverger, Louise Stauffer, Institut de Science des Matériaux de Mulhouse (IS2M), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), and Femto-st, MN2S

Subjects
Silicon, [SPI.NANO] Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, Inorganic chemistry, General Physics and Astronomy, chemistry.chemical_element, 02 engineering and technology, Substrate (electronics), [SPI.MAT] Engineering Sciences [physics]/Materials, 010402 general chemistry, 01 natural sciences, [SPI.MAT]Engineering Sciences [physics]/Materials, chemistry.chemical_compound, Molecule, [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, Physical and Theoretical Chemistry, Boron, [SPI.ACOU]Engineering Sciences [physics]/Acoustics [physics.class-ph], [SPI.ACOU] Engineering Sciences [physics]/Acoustics [physics.class-ph], social sciences, 021001 nanoscience & nanotechnology, Cycloaddition, 0104 chemical sciences, Crystallography, chemistry, Chemical bond, Phthalocyanine, Density functional theory, 0210 nano-technology
Abstract

International audience; In the framework of the Density Functional Theory (DFT-D), we investigate the phthalocyanine (H2Pc) molecule adsorption on SiC(0001)3 × 3 and Si(111)√3 × √3R30°-B (SiB) surfaces, and particularly compare the involved molecular adsorptions. In the H2Pc–SiC(0001)3 × 3 system, the molecular adsorption can be ascribed to a [10+2] cycloaddition. The H2Pc–SiB system is considered in three cases: defectless SiB surface (denoted SiB-0D) and SiB surfaces presenting one or two boron defects (denoted SiB-1D and SiB-2D respectively). The SiB-0D surface is passivated by a charge transfer from the Si adatoms to the boron atoms and therefore no chemical bond between the molecule and the substrate is observed. A similar molecular adsorption as already evidenced in the H2Pc–SiC(0001)3 × 3 system is involved in the SiB-2D case. In the case of the SiB-1D surface, two Si–N bonds (Si1–N1 and Si2–N2) are observed. One of them, Si1–N1, is nearly similar to that found in the H2Pc–SiB-2D system, but the Si2–N2 bond is unexpected. The Bader charge analysis suggests that, in the presence of the H2Pc molecule, the boron atoms behave like an electron reservoir whose availability varies following the involved molecular adsorption process. In the SiB-1D case, charges are transferred from the substrate to the molecule, allowing the Si2–N2 bond formation. Such a kind of molecular adsorption, not yet observed, could be designed by “assisted pseudo cycloaddition”.

Published
2014

12. Full DFT-D description of a nanoporous supramolecular network on a silicon surface

Author

Eric Duverger, Khaoula Boukari, Philippe Sonnet, Institut de Science des Matériaux de Mulhouse (IS2M), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Silicon, Nanoporous, Supramolecular chemistry, General Physics and Astronomy, chemistry.chemical_element, 02 engineering and technology, Substrate (electronics), Tungsten, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, Molecular physics, 0104 chemical sciences, symbols.namesake, chemistry, Computational chemistry, Covalent bond, symbols, Density functional theory, [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, Physical and Theoretical Chemistry, van der Waals force, 0210 nano-technology
Abstract

International audience; We present a full density-functional-theory study taking into account the van der Waals interactions of a 2D supramolecular network adsorbed on the Si(111)root 3x root 3R30 degrees-boron surface denoted SiB. We show that, contrarily to the previous calculations [B. Baris, V. Luzet, E. Duverger, Ph. Sonnet, F. Palmino, and F. Cherioux, Angew. Chem., Int. Ed. 50, 4094 (2011)] molecule-molecule interactions are attractive, thanks to van der Waals corrections which are essential to describe such systems. We confirm the importance of the substrate effect to achieve the molecular network on the boron doped silicon surface without covalent bond. Our simulated STM images, calculated in the framework of the bSKAN code, give better agreement with the experimental STM images than those obtained by the integrated LDOS calculations within the Tersoff-Hamann approximation. The tungsten tip presence is essential to retrieve three paired lobes as observed experimentally. The observed protrusions arise from the phenyl arms located above silicon adatoms. (C) 2013 American Institute of Physics. [http://dx.doi.org.gate6.inist.fr/10.1063/1.4792442]

Published
2013

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