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Lefebvre C, Klein J, Khartabil H, Boisson JC, Hénon E. IGMPlot: A program to identify, characterize, and quantify molecular interactions. J Comput Chem 2023. [PMID: 37177853 DOI: 10.1002/jcc.27123] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023]
Abstract
We describe the development and features of a program called IGMPlot, which is based on the independent gradient model (IGM) and its local descriptor δ g $$ \delta g $$ . The IGM approach analyzes the gradient of the electron density (ED) in a molecular system to identify regions of space where chemical interactions take place. IGMPlot is intended for use by both experimental scientists and theoretical chemists. It is standalone software written in C++, with versions available for multiple platforms. Some key features are: probing and quantifying interactions between two given molecular fragments, determining bond strength (IBSI), estimating the atomic contributions to an intermolecular interaction and preparing data to build 2D and 3D representations of interaction regions. The software has been updated to include new features: critical point analysis of the ED, assessing ED asymmetry of a given bond (PDA) and a new descriptor called q g $$ qg $$ designed to enhance the IGM- δ g $$ \delta g $$ analysis. The program can be found at: http://igmplot.univ-reims.fr.
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Affiliation(s)
- C Lefebvre
- Laboratoire Lorrain de Chimie Moléculaire UMR CNRS 7053, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - J Klein
- Institut Charles Gerhardt Montpellier, UMR CNRS 5253, Université de Montpellier, Pôle Chimie Balard Recherche, Montpellier, France
| | - H Khartabil
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims, France
| | - J-C Boisson
- Laboratoire d'Informatique en Calcul Intensif et Image pour la Simulation (LICIIS), Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims, France
| | - E Hénon
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims, France
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Guérinot A, Cossy J, G.-Simonian N. SO2-Extrusive 1,4-(Het)Aryl Migration: Synthesis of α-Aryl Amides and Related Reactions. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/s-0040-1720035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Abstract(Het)aryl migration has emerged as a key synthetic tool and has particularly been exploited for the synthesis of α-aryl amides. This method overcomes the existing α-arylation methods, which are not always compatible with the introduction of (het)aryl groups possessing bulky or electrophilic substituents. This review focuses on SO2-extrusive (het)aryl migration in the frame of α-aryl amide synthesis. Anion- and radical-mediated transformations are reported, including the synthesis of polycyclic compounds through cascade reactions.1 Introduction2 Anionic Aryl Migration3 Radical Aryl Migration4 Conclusion
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Zhu G, You A, Song H, Li Z. A combined crystallography and DFT study on ring-shaped Cucurbit[ n]urils: structures, surface character, and host-guest recognition. RSC Adv 2022; 12:10014-10019. [PMID: 35424911 PMCID: PMC8965660 DOI: 10.1039/d2ra00797e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/24/2022] [Indexed: 12/12/2022] Open
Abstract
A combined crystallography and DFT study of cucurbit[n]urils (n = 5-8, 10) was carried out, and PBE0 was certified to be the most rational density functional method for optimization task. Steric hindrance and electronic effect of the hindered lone pair electrons in cucurbit[n]urils were qualitatively measured by bond order analysis, lone pair electron (LP) visualization and electrostatic potential (ESP) study. Together with energy decomposition analysis of some selected host-guest systems, we quantitatively verified the effect of size/cavity and noncovalent interaction in host-guest recognition. This solid study revealed that lone pairs electrons affect not only on host-guest identification mode but also on geometry stability, which pave the avenue for further sophisticated applications.
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Affiliation(s)
- Guoxun Zhu
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou) Guangzhou 510070 P. R. China
| | - Ao You
- School of Eco-Environmental Technology, Guangdong Industry Polytechnic Guangzhou 510300 P. R. China
| | - Huacan Song
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou) Guangzhou 510070 P. R. China
- School of Chemical Engineering and Technology, Sun Yat-sen University Tangjia Zhuhai City 519082 P. R. China
| | - Zhengquan Li
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou) Guangzhou 510070 P. R. China
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Mamane V, Weiss R, Cornaton Y, Khartabil H, Groslambert L, Hénon E, Pale P, Djukic JP. Deciphering the Role of Noncovalent Interactions in the Conformations of Dibenzo‐1,5‐dichalcogenocines. Chempluschem 2022; 87:e202100518. [DOI: 10.1002/cplu.202100518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/03/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Victor Mamane
- University of Strasbourg: Universite de Strasbourg Institut of Chemistry 1 Rue Blaise Pascal 67008 Strasbourg FRANCE
| | - Robin Weiss
- Université de Strasbourg: Universite de Strasbourg Institut de Chimie de Strasbourg FRANCE
| | - Yann Cornaton
- Université de Strasbourg: Universite de Strasbourg Institut de Chimie de Strasbroug FRANCE
| | - Hassan Khartabil
- Université de Reims Champagne-Ardenne: Universite de Reims Champagne-Ardenne Institut de Chimie Moléculaire FRANCE
| | - Loïc Groslambert
- Universite de Strasbourg Institut de Chimie de Strasbourg FRANCE
| | - Eric Hénon
- Universite de Reims Champagne-Ardenne Institut de Chimie Moléculaire FRANCE
| | - Patrick Pale
- Universite de Strasbourg Institut de Cimie de Strasbourg FRANCE
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Radical and Ionic Mechanisms in Rearrangements of o-Tolyl Aryl Ethers and Amines Initiated by the Grubbs-Stoltz Reagent, Et 3SiH/KO tBu. Molecules 2021; 26:molecules26226879. [PMID: 34833971 PMCID: PMC8619283 DOI: 10.3390/molecules26226879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Rearrangements of o-tolyl aryl ethers, amines, and sulfides with the Grubbs–Stoltz reagent (Et3SiH + KOtBu) were recently announced, in which the ethers were converted to o-hydroxydiarylmethanes, while the (o-tol)(Ar)NH amines were transformed into dihydroacridines. Radical mechanisms were proposed, based on prior evidence for triethylsilyl radicals in this reagent system. A detailed computational investigation of the rearrangements of the aryl tolyl ethers now instead supports an anionic Truce–Smiles rearrangement, where the initial benzyl anion can be formed by either of two pathways: (i) direct deprotonation of the tolyl methyl group under basic conditions or (ii) electron transfer to an initially formed benzyl radical. By contrast, the rearrangements of o-tolyl aryl amines depend on the nature of the amine. Secondary amines undergo deprotonation of the N-H followed by a radical rearrangement, to form dihydroacridines, while tertiary amines form both dihydroacridines and diarylmethanes through radical and/or anionic pathways. Overall, this study highlights the competition between the reactive intermediates formed by the Et3SiH/KOtBu system.
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Charpentier E, Doudet L, Allart-Simon I, Colin M, Gangloff SC, Gérard S, Reffuveille F. Synergy between Indoloquinolines and Ciprofloxacin: An Antibiofilm Strategy against Pseudomonas aeruginosa. Antibiotics (Basel) 2021; 10:antibiotics10101205. [PMID: 34680786 PMCID: PMC8532862 DOI: 10.3390/antibiotics10101205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 01/01/2023] Open
Abstract
Antibiotic treatments can participate in the formation of bacterial biofilm in case of under dosage. The interest of indoloquinoline scaffold for drug discovery incited us to study the preparation of new indolo [2,3-b]quinoline derivatives by a domino radical process. We tested the effect of two different “indoloquinoline” molecules (Indol-1 and Indol-2) without antimicrobial activity, in addition to ciprofloxacin, on biofilm formation thanks to crystal violet staining and enumeration of adhered bacteria. This association of ciprofloxacin and Indol-1 or Indol-2 attenuated the formation of biofilm up to almost 80% compared to ciprofloxacin alone, or even prevented the presence of adhered bacteria. In conclusion, these data prove that the association of non-antimicrobial molecules with an antibiotic can be a solution to fight against biofilm and antibiotic resistance emergence.
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Affiliation(s)
- Emilie Charpentier
- EA 4691 Biomatériaux et Inflammation en Site Osseux (BIOS), UFR Pharmacie, Université de Reims Champagne-Ardenne, SFR Cap Santé (FED 4231), 51097 Reims, France; (E.C.); (M.C.); (S.C.G.)
| | - Ludovic Doudet
- Institut de Chimie Moléculaire de Reims (ICMR-UMR CNRS 7312), UFR Pharmacie, Université de Reims Champagne-Ardenne, 51097 Reims, France; (L.D.); (I.A.-S.); (S.G.)
| | - Ingrid Allart-Simon
- Institut de Chimie Moléculaire de Reims (ICMR-UMR CNRS 7312), UFR Pharmacie, Université de Reims Champagne-Ardenne, 51097 Reims, France; (L.D.); (I.A.-S.); (S.G.)
| | - Marius Colin
- EA 4691 Biomatériaux et Inflammation en Site Osseux (BIOS), UFR Pharmacie, Université de Reims Champagne-Ardenne, SFR Cap Santé (FED 4231), 51097 Reims, France; (E.C.); (M.C.); (S.C.G.)
| | - Sophie C. Gangloff
- EA 4691 Biomatériaux et Inflammation en Site Osseux (BIOS), UFR Pharmacie, Université de Reims Champagne-Ardenne, SFR Cap Santé (FED 4231), 51097 Reims, France; (E.C.); (M.C.); (S.C.G.)
| | - Stéphane Gérard
- Institut de Chimie Moléculaire de Reims (ICMR-UMR CNRS 7312), UFR Pharmacie, Université de Reims Champagne-Ardenne, 51097 Reims, France; (L.D.); (I.A.-S.); (S.G.)
| | - Fany Reffuveille
- EA 4691 Biomatériaux et Inflammation en Site Osseux (BIOS), UFR Pharmacie, Université de Reims Champagne-Ardenne, SFR Cap Santé (FED 4231), 51097 Reims, France; (E.C.); (M.C.); (S.C.G.)
- Correspondence:
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Wu F, Deraedt C, Cornaton Y, Ruhlmann L, Karmazin L, Bailly C, Kyritsakas N, Le Breton N, Choua S, Djukic JP. Fate of Cobaltacycles in Cp*Co-Mediated C–H Bond Functionalization Catalysis: Cobaltacycles May Collapse upon Oxidation via Co(IV) Species. Organometallics 2021. [DOI: 10.1021/acs.organomet.1c00301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fule Wu
- Laboratoire de Chimie et Systémique Organométalliques, Institut de Chimie de Strasbourg (UMR 7177) CNRS/Université de Strasbourg, 4 rue Blaise Pascal, F-67000 Strasbourg, France
| | - Christophe Deraedt
- Laboratoire de Chimie et Systémique Organométalliques, Institut de Chimie de Strasbourg (UMR 7177) CNRS/Université de Strasbourg, 4 rue Blaise Pascal, F-67000 Strasbourg, France
| | - Yann Cornaton
- Laboratoire de Chimie et Systémique Organométalliques, Institut de Chimie de Strasbourg (UMR 7177) CNRS/Université de Strasbourg, 4 rue Blaise Pascal, F-67000 Strasbourg, France
| | - Laurent Ruhlmann
- Laboratoire d’Electrochimie et Chimie Physique du Corps Solide, Institut de Chimie de Strasbourg (UMR 7177) CNRS/Université de Strasbourg, 4 rue Blaise Pascal, F-67000 Strasbourg, France
| | - Lydia Karmazin
- Service de Radiocristallographie Fédération de Chimie Le Bel−FR2010 BP 296R8, 1 rue Blaise Pascal, F-67008 Strasbourg Cedex, France
| | - Corinne Bailly
- Service de Radiocristallographie Fédération de Chimie Le Bel−FR2010 BP 296R8, 1 rue Blaise Pascal, F-67008 Strasbourg Cedex, France
| | - Nathalie Kyritsakas
- Service de Radiocristallographie Fédération de Chimie Le Bel−FR2010 BP 296R8, 1 rue Blaise Pascal, F-67008 Strasbourg Cedex, France
| | - Nolwenn Le Breton
- Laboratoire Propriétés Optiques et Magnétiques des Architectures Moléculaires, Institut de Chimie de Strasbourg (UMR 7177) CNRS/Université de Strasbourg, 4 rue Blaise Pascal, F-67000 Strasbourg, France
| | - Sylvie Choua
- Laboratoire Propriétés Optiques et Magnétiques des Architectures Moléculaires, Institut de Chimie de Strasbourg (UMR 7177) CNRS/Université de Strasbourg, 4 rue Blaise Pascal, F-67000 Strasbourg, France
| | - Jean-Pierre Djukic
- Laboratoire de Chimie et Systémique Organométalliques, Institut de Chimie de Strasbourg (UMR 7177) CNRS/Université de Strasbourg, 4 rue Blaise Pascal, F-67000 Strasbourg, France
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