Franck Jolibois - Academia.edu (original) (raw)
Papers by Franck Jolibois
Organic & Biomolecular Chemistry
The synthesis of β-peptoids with tert-butyl side chains up to 15 residues in length was achieved.... more The synthesis of β-peptoids with tert-butyl side chains up to 15 residues in length was achieved. Their backbone is characterized by cis-amide bonds, leading to helix and ribbon-like structures.
Theoretical Chemistry Accounts, 2021
Catalytic characteristics of metal nanoparticles heavily depend on their global shapes and sizes ... more Catalytic characteristics of metal nanoparticles heavily depend on their global shapes and sizes as well as on the structure and environment of catalytic sites. On the computational chemistry side, calculations of thermodynamic and kinetic data involve a high calculation cost which can be significantly lowered by the use of a trained machine learning model. This paper outlines a preliminary approach that aims at classifying the shape of the metal core of nanoparticles. Four different supervised artificial neural networks were trained, tested and submitted to a challenging dataset. They are based on two different structural descriptors, Coulomb matrices and radial distribution functions (RDFs). Each model is trained with hundreds of 3D models of nanoparticles that belong to eleven structural classes. The best model classifies a NP according to its discretized RDF profile and its first derivative. 100% accuracy is reached on the test stage, and up to 70% accuracy is obtained on the challenging dataset. It is mainly made of compounds that have global shapes significantly different from the training set. But some nonobvious structural patterns make then related to the eleven classes learned by the ANNs. Such strategy could easily be adapted to the recognition of NPs based on experimental neutron or X-ray diffraction data.
La mise en place d'un apprentissage de type par projet dans le cadre d'un enseignement pl... more La mise en place d'un apprentissage de type par projet dans le cadre d'un enseignement pluridisciplinaire au niveau Master 2 est presentee dans cette communication. Cet enseignement concerne un public heterogene de physiciens, mecaniciens et chimistes repartis sur 4 differentes filieres de Master. Apres une presentation de l'architecture du module, une critique de ce module est realisee en se basant sur les resultats de trois ans d'evaluations par les etudiants. Il apparait que, bien que ce type d'approche pedagogique soit plutot favorablement accepte et quelle favorise le developpement de competences plutot transversales, sa mise en pratique peut s'averer delicate si la collaboration ou la cooperation au sein de l'equipe pedagogique n'est pas correctement mise en place.
Differents facteurs tels les rayonnements uv ou ionisants, les agents oxydants, les radicaux libr... more Differents facteurs tels les rayonnements uv ou ionisants, les agents oxydants, les radicaux libres, peuvent engendrer des dommages au niveau des bases de l'adn. Ces modifications peuvent avoir une influence notable sur la structure et les proprietes du biopolymere. Afin de mieux comprendre la nature de ces lesions, leur mode de formation et les effets qu'elles peuvent avoir sur l'integrite de l'adn, l'etude de certains degradations de la thymine a ete realisee au moyen des outils de la chimie quantique. La premiere partie de ce travail est consacree a l'etude comparative des proprietes conformationnelles et electroniques de produits d'oxydation du groupement methyle de la thymidine par l'intermediaire d'une methode locale de la dft. Le chapitre suivant traite des intermediaires radicalaires formes par l'addition d'un atome d'hydrogene ou du radical hydroxyle sur la double liaison 5,6 de la thymine. Un protocole general d'etude de ...
JACS Au, 2021
Ultrasmall gold nanoparticles (NPs) stabilized in networks by polymantane ligands (diamondoids) w... more Ultrasmall gold nanoparticles (NPs) stabilized in networks by polymantane ligands (diamondoids) were successfully used as precatalysts for highly selective heterogeneous gold-catalyzed dimethyl allyl(propargyl)malonate cyclization to 5-membered conjugated diene. Such reaction usually suffers from selectivity issues with homogeneous catalysts. This control over selectivity further opened the way to one-pot cascade reaction, as illustrated by the 1,6-enyne cycloisomerization−Diels−Alder reaction of dimethyl allyl propargyl malonate with maleic anhydride. The ability to assemble nanoparticles with controllable sizes and shapes within networks concerns research in sensors, medical diagnostics, information storage, and catalysis applications. Herein, the control of the synthesis of sub-2-nm gold NPs is achieved by the formation of dense networks, which are assembled in a single step reaction by employing ditopic polymantanethiols. By using 1,1′bisadamantane-3,3′-dithiol (BAd-SH) and diamantane-4,9-dithiol (DAd-SH), serving both as bulky surface stabilizers and short-sized linkers, we provide a simple method to form uniformly small gold NPs (1.3 ± 0.2 nm to 1.6 ± 0.3 nm) embedded in rigid frameworks. These NP arrays are organized alongside short interparticular distances ranging from 1.9 to 2.7 nm. The analysis of gold NP surfaces and their modification were achieved in joint experimental and theoretical studies, using notably XPS, NMR, and DFT modeling. Our experimental studies and DFT analyses highlighted the necessary oxidative surface reorganization of individual nanoparticles for an effective enyne cycloisomerization. The modifications at bulky stabilizing ligands allow surface steric decongestion for the alkyne moiety activation but also result in network alteration by overoxidation of sulfurs. Thus, sub-2-nm nanoparticles originating from networks building create convenient conditions for generating reactive Au(I) surface single-sitesin the absence of silver additivesuseful for heterogeneous gold-catalyzed enyne cyclization. These nanocatalysts, which as such ease organic products separation, also provide a convenient access for building further polycyclic complexity, owing to their high reactivity and selectivity.
The Journal of Physical Chemistry B, 2020
Classical molecular dynamics simulations have been combined to quantum (DFT) calculations of 13 C... more Classical molecular dynamics simulations have been combined to quantum (DFT) calculations of 13 C NMR parameters in order to relate the experimental spectrum of the double-helix form of the amylose B-polymorph in highly crystalline conditions not only to its 3D structure but also to the arrangement of atoms in the crystal lattice. Structures obtained from these simulations or from geometry optimizations procedure at the DFT level have shown the presence of hydrogen bond networks between sugars of the same helix or between residues of the two chains of the double helix. 13 C NMR parameter calculations have revealed the impact of such network on the chemical shifts of carbon atoms. In addition, DFT calculations using periodic boundary conditions were compulsory to highlight the presence of two types of sugar within the crystal sample. It allows us to confirm theoretically, the experimental hypothesis that the existence of two distinct sugar types in the NMR spectrum is a consequence of crystal packing. Introduction. Amylose, one of the major constituents of starch with amylopectin, is an essentially linear polymer composed of glucose residues linked in [α-1→4] and is often used to model the crystalline parts of starch. Most of the experimental structures are originated from X-ray diffraction studies 1-4 and it is well known that it can adopt different helical conformations, depending on its environment. The single helical structure called the V-polymorph, has been proven to encapsulate guest molecules of various sizes, such as Iodine 5 , flavor molecules 6,7 or even fatty acids 8-11. The double helical structures are called A or B-polymorphs (Figure 1) depending on the crystal packing conditions and are known to be present in highly crystalline material amongst starch. The method of choice used for the study of amylose structure is 13 C solid-state NMR spectroscopy 9,10,12-14 ,
Carbohydrate Polymers, 2020
We present, first, structural analysis of small sized amyloses complexed to palmitic acid studied... more We present, first, structural analysis of small sized amyloses complexed to palmitic acid studied using classical molecular dynamics. We show that even if amylose with a minimum of 11 residues exhibits transitional appearance of a V-type structure, 15 glucoses residues are necessary for the amylose to fold around the palmitic acid in a well-established helix conformation. Second, simulating 13C NMR spectrum using a strategy that combines molecular dynamics and quantum chemical DFT calculations, we demonstrate that part of the NMR spectrum is affected by the amylose size and by the presence of specific intramolecular hydrogen bonds. By mean of deconvolution procedure of NMR spectra of a 19-residues amylose calculated using a series of structures extracted from molecular dynamics, we have been able to precise the attribution of each characteristic resonances. In this context, we postulate that one chemical shift that is usually attributed to a specific carbon can, also, correspond to ...
Phthiocerol dimycocerosate (DIM) is a major virulence factor of the pathogen Mycobacterium tuberc... more Phthiocerol dimycocerosate (DIM) is a major virulence factor of the pathogen Mycobacterium tuberculosis (Mtb). While this lipid promotes the entry of Mtb into macrophages, which occurs via phagocytosis, its molecular mechanism of action is unknown. Here, we combined biophysical, cell biology, and modelling approaches to reveal the molecular mechanism of DIM action on macrophage membranes leading to the first step of Mtb infection. MALDI-TOF mass spectrometry showed that DIM molecules are transferred from the Mtb envelope to macrophage membranes during infection. Multi-scale molecular modeling and 31P-NMR experiments revealed that DIM adopts a conical shape in membranes and aggregate in the stalks formed between two opposing lipid bilayers. Infection of macrophages pre-treated with lipids of various shapes uncovered a general role for conical lipids in promoting phagocytosis. Taken together, these results reveal how the molecular shape of a mycobacterial lipid can modulate the biolog...
The Journal of organic chemistry, Jan 15, 2018
The synthesis and conformational preferences of a set of new synthetic foldamers that combine bot... more The synthesis and conformational preferences of a set of new synthetic foldamers that combine both the α,β-peptoid backbone and side chains that alternately promote cis- and trans-amide bond geometries have been achieved and addressed jointly by experiment and molecular modeling. Four sequence patterns were thus designed and referred to as cis-β- trans-α, cis-α- trans-β, trans-β- cis-α, and trans-α- cis-β. α- and β NtBu monomers were used to enforce cis-amide bond geometries and α- and β NPh monomers to promote trans-amides. NOESY and molecular modeling reveal that the trans-α- cis-β and cis-β- trans-α tetramers show a similar pattern of intramolecular weak interactions. The same holds for the cis-α- trans-β and trans-β- cis-α tetramers, but the interactions are different in nature than those identified in the trans-α- cis-β-based oligomers. Interestingly, the trans-α- cis-β peptoid architecture allows establishment of a larger amount of structure-stabilizing intramolecular interact...
Journal of Chemical Theory and Computation, 2016
The determination of pKa values for molecules containing multiple acidic groups in solution is ch... more The determination of pKa values for molecules containing multiple acidic groups in solution is challenging both experimentally and theoretically. We propose a general method to obtain these values by combining a graphical analysis based on a predominance diagram, for amino acids and nicotianamine polyacid, with first principle DFT calculations. Implicit and semiexplicit water solvent models were included to account for solvation. This strategy enables the investigation of the protonation states of compounds containing acidic moieties in solution depending on the pH domain. The method was first validated on a set of amino acids with pKa values calculated with an accuracy within 0.5-1.0 pKa unit and then on the chalenging nicotianamine polyacid with six pKa values. This approach is particularly well suited for such a complex system including both zwitterionic structures and unknown experimental pKa values.
Chem. Commun., 2016
The authors regret their oversight in not representing appropriately the findings from previous w... more The authors regret their oversight in not representing appropriately the findings from previous work by F. S. Nandel et al., cited as ref. 15 on page 4576 of the original article. The authors therefore wish to change the sentence ''In contrast to the i/(i À 1) contact reported previously, 15 hydrogen bonds develop within the same residue and between CO(i) and tBu CH(i + 1) in (+) 8 .'' to ''In (+) 8 , hydrogen bonds develop within the same residue and, as previously reported in related systems, 15 between CO(i) and tBu CH(i + 1).'' The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers.
Http Www Theses Fr, 2005
Conclusion 197 Annexes 201 Systèmes à Échelles de Temps Multiples .
Advances in DNA Damage and Repair, 1999
Emphasis was placed in this short survey on recent chemical and biochemical aspects of oxidative ... more Emphasis was placed in this short survey on recent chemical and biochemical aspects of oxidative base damage to DNA. Significant progress has been accomplished in a better understanding of the oxidation reactions mediated by OH radical, singlet oxygen and one-electron oxidation of the guanine moiety of DNA and model compounds. As a second major topic, relevant information was recently gained on the origin of major artifacts in the measurement (gas chromatography-mass spectrometry, high performane liquid chromatography-[32P]-postlabeling and immunological assays) of oxidative base lesions in cellular DNA. Prepurification of the targeted base damage prior to derivatization and enzymatic phosphorylation is a requisite to prevent artifactual oxidation to occur in the two former assays. Finally insight is provided on the specificity of repair by DNA-glycosylases using site specific modified oligonucleotides
Theoretical Chemistry Accounts, 2009
A new multicentered effective group potential (EGP) is obtained for η 6-benzene. Applications on ... more A new multicentered effective group potential (EGP) is obtained for η 6-benzene. Applications on [Ru 4 (H) 4 (C 6 H 6) 4 ] n+ clusters (n=0 or 2) are in excellent agreement with reference DFT studies in terms of geometries, energies and electronic structures. In particular, the small singlet-triplet energy difference (3.8 kcal/mol) in [Ru 4 (H) 4 (C 6 H 6) 4 ] 2+ is very well reproduced. This new EGP is nevertheless not free from the limitations associated to this first generation of molecular pseudopotentials. A cautious analysis of the nature and exact role of this EGP is made, which provides new directions for the elaboration of the next generation of EGPs. In addition, the η 5-cyclopentadienyl EGP has been used to perform a constrained dynamical simulation for the reaction of Cp 2 LaH with H 2. The energy conservation during the simulation as well as the activation barrier extracted from the simulation clearly demonstrate the good behavior of this EGP in the context of molecular dynamics. Anharmonic effects on this reaction are underlined, further demonstrating the high accuracy of the potential energy surface obtained with EGPs. From a more general point of view, such EGPs are expected to provide accurate albeit low-cost ligand-field effects in organometallic clusters or nanoparticles and to allow dynamical studies at the surface of such compounds. Effective Group Potentials; ab initio molecular dynamics; organometallic clusters and nanoparticles; chemical reactivity
The Journal of Physical Chemistry A, 2005
Proton transfer is a very common and important chemical step in many systems. Despite its apparen... more Proton transfer is a very common and important chemical step in many systems. Despite its apparent simplicity, a correct description of this chemical process is difficult from a theoretical point of view. It requires a correct and simultaneous description of a bond breaking and a bond formation. The situation is even much more complicated when two protons are implied. This is the case for monothiooxalic acid, for which two different types (1,3- and 1,4-prototropy) of proton transfers can be invoked. A further problem is the type of the reaction (concerted or not). This paper reports a complete investigation of the potential energy surfaces: characterization of equilibrium points and transitions states. The main conclusion is: the 1,4-prototropic mechanism, mainly considered as a one step concerted exchange of protons, is the most favored from an energetic point of view.
The Journal of Physical Chemistry A, 2006
In this paper, a comparison between &... more In this paper, a comparison between "static" and "dynamic" determination of the thermodynamic (DeltarF degrees) and kinetic data (DeltarF#) for the reaction of Cl2LaR (R=H, CH3) and H2 is given. A difference is obtained in the case of the reaction between Cl2LaH and H2 and can be attributed to a failure of the "static" approach based on the harmonic approximation. The influence of the zero point energy correction is also analyzed but does not explain the 30% difference between the two calculated activation energies. The influence of the flatness of the potential energy surface around the transition state is proved as no such an effect is observed for the reaction of Cl2LaCH3 and H2.
The Journal of Physical Chemistry A, 2002
Phys. Chem. Chem. Phys., 2004
ABSTRACT
Organic & Biomolecular Chemistry, 2008
mixtures on the N 2 H proton resonances for VI.1 and V.1a.
Organic & Biomolecular Chemistry
The synthesis of β-peptoids with tert-butyl side chains up to 15 residues in length was achieved.... more The synthesis of β-peptoids with tert-butyl side chains up to 15 residues in length was achieved. Their backbone is characterized by cis-amide bonds, leading to helix and ribbon-like structures.
Theoretical Chemistry Accounts, 2021
Catalytic characteristics of metal nanoparticles heavily depend on their global shapes and sizes ... more Catalytic characteristics of metal nanoparticles heavily depend on their global shapes and sizes as well as on the structure and environment of catalytic sites. On the computational chemistry side, calculations of thermodynamic and kinetic data involve a high calculation cost which can be significantly lowered by the use of a trained machine learning model. This paper outlines a preliminary approach that aims at classifying the shape of the metal core of nanoparticles. Four different supervised artificial neural networks were trained, tested and submitted to a challenging dataset. They are based on two different structural descriptors, Coulomb matrices and radial distribution functions (RDFs). Each model is trained with hundreds of 3D models of nanoparticles that belong to eleven structural classes. The best model classifies a NP according to its discretized RDF profile and its first derivative. 100% accuracy is reached on the test stage, and up to 70% accuracy is obtained on the challenging dataset. It is mainly made of compounds that have global shapes significantly different from the training set. But some nonobvious structural patterns make then related to the eleven classes learned by the ANNs. Such strategy could easily be adapted to the recognition of NPs based on experimental neutron or X-ray diffraction data.
La mise en place d'un apprentissage de type par projet dans le cadre d'un enseignement pl... more La mise en place d'un apprentissage de type par projet dans le cadre d'un enseignement pluridisciplinaire au niveau Master 2 est presentee dans cette communication. Cet enseignement concerne un public heterogene de physiciens, mecaniciens et chimistes repartis sur 4 differentes filieres de Master. Apres une presentation de l'architecture du module, une critique de ce module est realisee en se basant sur les resultats de trois ans d'evaluations par les etudiants. Il apparait que, bien que ce type d'approche pedagogique soit plutot favorablement accepte et quelle favorise le developpement de competences plutot transversales, sa mise en pratique peut s'averer delicate si la collaboration ou la cooperation au sein de l'equipe pedagogique n'est pas correctement mise en place.
Differents facteurs tels les rayonnements uv ou ionisants, les agents oxydants, les radicaux libr... more Differents facteurs tels les rayonnements uv ou ionisants, les agents oxydants, les radicaux libres, peuvent engendrer des dommages au niveau des bases de l'adn. Ces modifications peuvent avoir une influence notable sur la structure et les proprietes du biopolymere. Afin de mieux comprendre la nature de ces lesions, leur mode de formation et les effets qu'elles peuvent avoir sur l'integrite de l'adn, l'etude de certains degradations de la thymine a ete realisee au moyen des outils de la chimie quantique. La premiere partie de ce travail est consacree a l'etude comparative des proprietes conformationnelles et electroniques de produits d'oxydation du groupement methyle de la thymidine par l'intermediaire d'une methode locale de la dft. Le chapitre suivant traite des intermediaires radicalaires formes par l'addition d'un atome d'hydrogene ou du radical hydroxyle sur la double liaison 5,6 de la thymine. Un protocole general d'etude de ...
JACS Au, 2021
Ultrasmall gold nanoparticles (NPs) stabilized in networks by polymantane ligands (diamondoids) w... more Ultrasmall gold nanoparticles (NPs) stabilized in networks by polymantane ligands (diamondoids) were successfully used as precatalysts for highly selective heterogeneous gold-catalyzed dimethyl allyl(propargyl)malonate cyclization to 5-membered conjugated diene. Such reaction usually suffers from selectivity issues with homogeneous catalysts. This control over selectivity further opened the way to one-pot cascade reaction, as illustrated by the 1,6-enyne cycloisomerization−Diels−Alder reaction of dimethyl allyl propargyl malonate with maleic anhydride. The ability to assemble nanoparticles with controllable sizes and shapes within networks concerns research in sensors, medical diagnostics, information storage, and catalysis applications. Herein, the control of the synthesis of sub-2-nm gold NPs is achieved by the formation of dense networks, which are assembled in a single step reaction by employing ditopic polymantanethiols. By using 1,1′bisadamantane-3,3′-dithiol (BAd-SH) and diamantane-4,9-dithiol (DAd-SH), serving both as bulky surface stabilizers and short-sized linkers, we provide a simple method to form uniformly small gold NPs (1.3 ± 0.2 nm to 1.6 ± 0.3 nm) embedded in rigid frameworks. These NP arrays are organized alongside short interparticular distances ranging from 1.9 to 2.7 nm. The analysis of gold NP surfaces and their modification were achieved in joint experimental and theoretical studies, using notably XPS, NMR, and DFT modeling. Our experimental studies and DFT analyses highlighted the necessary oxidative surface reorganization of individual nanoparticles for an effective enyne cycloisomerization. The modifications at bulky stabilizing ligands allow surface steric decongestion for the alkyne moiety activation but also result in network alteration by overoxidation of sulfurs. Thus, sub-2-nm nanoparticles originating from networks building create convenient conditions for generating reactive Au(I) surface single-sitesin the absence of silver additivesuseful for heterogeneous gold-catalyzed enyne cyclization. These nanocatalysts, which as such ease organic products separation, also provide a convenient access for building further polycyclic complexity, owing to their high reactivity and selectivity.
The Journal of Physical Chemistry B, 2020
Classical molecular dynamics simulations have been combined to quantum (DFT) calculations of 13 C... more Classical molecular dynamics simulations have been combined to quantum (DFT) calculations of 13 C NMR parameters in order to relate the experimental spectrum of the double-helix form of the amylose B-polymorph in highly crystalline conditions not only to its 3D structure but also to the arrangement of atoms in the crystal lattice. Structures obtained from these simulations or from geometry optimizations procedure at the DFT level have shown the presence of hydrogen bond networks between sugars of the same helix or between residues of the two chains of the double helix. 13 C NMR parameter calculations have revealed the impact of such network on the chemical shifts of carbon atoms. In addition, DFT calculations using periodic boundary conditions were compulsory to highlight the presence of two types of sugar within the crystal sample. It allows us to confirm theoretically, the experimental hypothesis that the existence of two distinct sugar types in the NMR spectrum is a consequence of crystal packing. Introduction. Amylose, one of the major constituents of starch with amylopectin, is an essentially linear polymer composed of glucose residues linked in [α-1→4] and is often used to model the crystalline parts of starch. Most of the experimental structures are originated from X-ray diffraction studies 1-4 and it is well known that it can adopt different helical conformations, depending on its environment. The single helical structure called the V-polymorph, has been proven to encapsulate guest molecules of various sizes, such as Iodine 5 , flavor molecules 6,7 or even fatty acids 8-11. The double helical structures are called A or B-polymorphs (Figure 1) depending on the crystal packing conditions and are known to be present in highly crystalline material amongst starch. The method of choice used for the study of amylose structure is 13 C solid-state NMR spectroscopy 9,10,12-14 ,
Carbohydrate Polymers, 2020
We present, first, structural analysis of small sized amyloses complexed to palmitic acid studied... more We present, first, structural analysis of small sized amyloses complexed to palmitic acid studied using classical molecular dynamics. We show that even if amylose with a minimum of 11 residues exhibits transitional appearance of a V-type structure, 15 glucoses residues are necessary for the amylose to fold around the palmitic acid in a well-established helix conformation. Second, simulating 13C NMR spectrum using a strategy that combines molecular dynamics and quantum chemical DFT calculations, we demonstrate that part of the NMR spectrum is affected by the amylose size and by the presence of specific intramolecular hydrogen bonds. By mean of deconvolution procedure of NMR spectra of a 19-residues amylose calculated using a series of structures extracted from molecular dynamics, we have been able to precise the attribution of each characteristic resonances. In this context, we postulate that one chemical shift that is usually attributed to a specific carbon can, also, correspond to ...
Phthiocerol dimycocerosate (DIM) is a major virulence factor of the pathogen Mycobacterium tuberc... more Phthiocerol dimycocerosate (DIM) is a major virulence factor of the pathogen Mycobacterium tuberculosis (Mtb). While this lipid promotes the entry of Mtb into macrophages, which occurs via phagocytosis, its molecular mechanism of action is unknown. Here, we combined biophysical, cell biology, and modelling approaches to reveal the molecular mechanism of DIM action on macrophage membranes leading to the first step of Mtb infection. MALDI-TOF mass spectrometry showed that DIM molecules are transferred from the Mtb envelope to macrophage membranes during infection. Multi-scale molecular modeling and 31P-NMR experiments revealed that DIM adopts a conical shape in membranes and aggregate in the stalks formed between two opposing lipid bilayers. Infection of macrophages pre-treated with lipids of various shapes uncovered a general role for conical lipids in promoting phagocytosis. Taken together, these results reveal how the molecular shape of a mycobacterial lipid can modulate the biolog...
The Journal of organic chemistry, Jan 15, 2018
The synthesis and conformational preferences of a set of new synthetic foldamers that combine bot... more The synthesis and conformational preferences of a set of new synthetic foldamers that combine both the α,β-peptoid backbone and side chains that alternately promote cis- and trans-amide bond geometries have been achieved and addressed jointly by experiment and molecular modeling. Four sequence patterns were thus designed and referred to as cis-β- trans-α, cis-α- trans-β, trans-β- cis-α, and trans-α- cis-β. α- and β NtBu monomers were used to enforce cis-amide bond geometries and α- and β NPh monomers to promote trans-amides. NOESY and molecular modeling reveal that the trans-α- cis-β and cis-β- trans-α tetramers show a similar pattern of intramolecular weak interactions. The same holds for the cis-α- trans-β and trans-β- cis-α tetramers, but the interactions are different in nature than those identified in the trans-α- cis-β-based oligomers. Interestingly, the trans-α- cis-β peptoid architecture allows establishment of a larger amount of structure-stabilizing intramolecular interact...
Journal of Chemical Theory and Computation, 2016
The determination of pKa values for molecules containing multiple acidic groups in solution is ch... more The determination of pKa values for molecules containing multiple acidic groups in solution is challenging both experimentally and theoretically. We propose a general method to obtain these values by combining a graphical analysis based on a predominance diagram, for amino acids and nicotianamine polyacid, with first principle DFT calculations. Implicit and semiexplicit water solvent models were included to account for solvation. This strategy enables the investigation of the protonation states of compounds containing acidic moieties in solution depending on the pH domain. The method was first validated on a set of amino acids with pKa values calculated with an accuracy within 0.5-1.0 pKa unit and then on the chalenging nicotianamine polyacid with six pKa values. This approach is particularly well suited for such a complex system including both zwitterionic structures and unknown experimental pKa values.
Chem. Commun., 2016
The authors regret their oversight in not representing appropriately the findings from previous w... more The authors regret their oversight in not representing appropriately the findings from previous work by F. S. Nandel et al., cited as ref. 15 on page 4576 of the original article. The authors therefore wish to change the sentence ''In contrast to the i/(i À 1) contact reported previously, 15 hydrogen bonds develop within the same residue and between CO(i) and tBu CH(i + 1) in (+) 8 .'' to ''In (+) 8 , hydrogen bonds develop within the same residue and, as previously reported in related systems, 15 between CO(i) and tBu CH(i + 1).'' The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers.
Http Www Theses Fr, 2005
Conclusion 197 Annexes 201 Systèmes à Échelles de Temps Multiples .
Advances in DNA Damage and Repair, 1999
Emphasis was placed in this short survey on recent chemical and biochemical aspects of oxidative ... more Emphasis was placed in this short survey on recent chemical and biochemical aspects of oxidative base damage to DNA. Significant progress has been accomplished in a better understanding of the oxidation reactions mediated by OH radical, singlet oxygen and one-electron oxidation of the guanine moiety of DNA and model compounds. As a second major topic, relevant information was recently gained on the origin of major artifacts in the measurement (gas chromatography-mass spectrometry, high performane liquid chromatography-[32P]-postlabeling and immunological assays) of oxidative base lesions in cellular DNA. Prepurification of the targeted base damage prior to derivatization and enzymatic phosphorylation is a requisite to prevent artifactual oxidation to occur in the two former assays. Finally insight is provided on the specificity of repair by DNA-glycosylases using site specific modified oligonucleotides
Theoretical Chemistry Accounts, 2009
A new multicentered effective group potential (EGP) is obtained for η 6-benzene. Applications on ... more A new multicentered effective group potential (EGP) is obtained for η 6-benzene. Applications on [Ru 4 (H) 4 (C 6 H 6) 4 ] n+ clusters (n=0 or 2) are in excellent agreement with reference DFT studies in terms of geometries, energies and electronic structures. In particular, the small singlet-triplet energy difference (3.8 kcal/mol) in [Ru 4 (H) 4 (C 6 H 6) 4 ] 2+ is very well reproduced. This new EGP is nevertheless not free from the limitations associated to this first generation of molecular pseudopotentials. A cautious analysis of the nature and exact role of this EGP is made, which provides new directions for the elaboration of the next generation of EGPs. In addition, the η 5-cyclopentadienyl EGP has been used to perform a constrained dynamical simulation for the reaction of Cp 2 LaH with H 2. The energy conservation during the simulation as well as the activation barrier extracted from the simulation clearly demonstrate the good behavior of this EGP in the context of molecular dynamics. Anharmonic effects on this reaction are underlined, further demonstrating the high accuracy of the potential energy surface obtained with EGPs. From a more general point of view, such EGPs are expected to provide accurate albeit low-cost ligand-field effects in organometallic clusters or nanoparticles and to allow dynamical studies at the surface of such compounds. Effective Group Potentials; ab initio molecular dynamics; organometallic clusters and nanoparticles; chemical reactivity
The Journal of Physical Chemistry A, 2005
Proton transfer is a very common and important chemical step in many systems. Despite its apparen... more Proton transfer is a very common and important chemical step in many systems. Despite its apparent simplicity, a correct description of this chemical process is difficult from a theoretical point of view. It requires a correct and simultaneous description of a bond breaking and a bond formation. The situation is even much more complicated when two protons are implied. This is the case for monothiooxalic acid, for which two different types (1,3- and 1,4-prototropy) of proton transfers can be invoked. A further problem is the type of the reaction (concerted or not). This paper reports a complete investigation of the potential energy surfaces: characterization of equilibrium points and transitions states. The main conclusion is: the 1,4-prototropic mechanism, mainly considered as a one step concerted exchange of protons, is the most favored from an energetic point of view.
The Journal of Physical Chemistry A, 2006
In this paper, a comparison between &... more In this paper, a comparison between "static" and "dynamic" determination of the thermodynamic (DeltarF degrees) and kinetic data (DeltarF#) for the reaction of Cl2LaR (R=H, CH3) and H2 is given. A difference is obtained in the case of the reaction between Cl2LaH and H2 and can be attributed to a failure of the "static" approach based on the harmonic approximation. The influence of the zero point energy correction is also analyzed but does not explain the 30% difference between the two calculated activation energies. The influence of the flatness of the potential energy surface around the transition state is proved as no such an effect is observed for the reaction of Cl2LaCH3 and H2.
The Journal of Physical Chemistry A, 2002
Phys. Chem. Chem. Phys., 2004
ABSTRACT
Organic & Biomolecular Chemistry, 2008
mixtures on the N 2 H proton resonances for VI.1 and V.1a.