1
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Camiruaga A, Gouasmat A, Beau JM, Bourdreux Y, Causse M, Chapelle N, Doisneau G, Goldsztejn G, Urban D, Çarçabal P. Mixing water, sugar, and lipid: Conformations of isolated and micro-hydrated glycolipids in the gas phase. J Chem Phys 2024; 160:214313. [PMID: 38842492 DOI: 10.1063/5.0211435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
Both sugars and lipids are important biomolecular building blocks with exceptional conformational flexibility and adaptability to their environment. Glycolipids bring together these two molecular components in the same assembly and combine the complexity of their conformational landscapes. In the present study, we have used selective double resonance vibrational spectroscopy, in combination with a computational approach, to explore the conformational preferences of two glycolipid models (3-0-acyl catechol and guaiacol α-D-glucopyranosides), either fully isolated in the gas phase or controlled interaction with a single water molecule. We could identify the preferred conformation and structures of the isolated and micro-hydrated species and evidence of the presence of a strong water pocket, which may influence the conformational flexibility of such systems, even in less controlled environments.
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Affiliation(s)
- Ander Camiruaga
- Institute des Sciences Moléculaires d'Orsay, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Alexandra Gouasmat
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, Université Paris-Saclay, CNRS, UMR 8182, 91405 Orsay, France
| | - Jean-Marie Beau
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, Université Paris-Saclay, CNRS, UMR 8182, 91405 Orsay, France
| | - Yann Bourdreux
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, Université Paris-Saclay, CNRS, UMR 8182, 91405 Orsay, France
| | - Maélie Causse
- Institute des Sciences Moléculaires d'Orsay, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Nathan Chapelle
- Institute des Sciences Moléculaires d'Orsay, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Gilles Doisneau
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, Université Paris-Saclay, CNRS, UMR 8182, 91405 Orsay, France
| | - Gildas Goldsztejn
- Institute des Sciences Moléculaires d'Orsay, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Dominique Urban
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, Université Paris-Saclay, CNRS, UMR 8182, 91405 Orsay, France
| | - Pierre Çarçabal
- Institute des Sciences Moléculaires d'Orsay, Université Paris-Saclay, CNRS, 91405 Orsay, France
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2
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Ho JS, Gharbi A, Schindler B, Yeni O, Brédy R, Legentil L, Ferrières V, Kiessling LL, Compagnon I. Distinguishing Galactoside Isomers with Mass Spectrometry and Gas-Phase Infrared Spectroscopy. J Am Chem Soc 2021; 143:10509-10513. [PMID: 34236183 PMCID: PMC9867933 DOI: 10.1021/jacs.0c11919] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Sequencing glycans is demanding due to their structural diversity. Compared to mammalian glycans, bacterial glycans pose a steeper challenge because they are constructed from a larger pool of monosaccharide building blocks, including pyranose and furanose isomers. Though mammalian glycans incorporate only the pyranose form of galactose (Galp), many pathogens, including Mycobacterium tuberculosis and Klebsiella pneumoniae, contain galactofuranose (Galf) residues in their cell envelope. Thus, glycan sequencing would benefit from methods to distinguish between pyranose and furanose isomers of different anomeric configurations. We used infrared multiple photon dissociation (IRMPD) spectroscopy with mass spectrometry (MS-IR) to differentiate between pyranose- and furanose-linked galactose residues. These targets pose a challenge for MS-IR because the saccharides lack basic groups, and galactofuranose residues are highly flexible. We postulated cationic groups that could complex through hydrogen bonding would offer a solution. Here, we present the first MS-IR analysis of hexose ammonium adducts. We compared their IR fingerprints with those of lithium adducts. We determined the diagnostic MS-IR signatures of the α- and β-anomers of galactose in furanose and pyranose forms. We also showed these signatures could be applied to disaccharides to assign galactose ring size. Our findings highlight the utility of MS-IR for analyzing the unique substructures that occur in bacterial glycans.
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Affiliation(s)
| | | | - Baptiste Schindler
- Univ. Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Oznur Yeni
- Univ. Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Richard Brédy
- Univ. Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Laurent Legentil
- Univ. Rennes, Ecole Nationale Supérieure de Chimie de Rennes, F-35000 Rennes, France
| | - Vincent Ferrières
- Univ. Rennes, Ecole Nationale Supérieure de Chimie de Rennes, F-35000 Rennes, France
| | - Laura L. Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Isabelle Compagnon
- Univ. Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
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3
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Ab initio investigation of the first hydration shell of glucose. Carbohydr Res 2020; 496:108114. [DOI: 10.1016/j.carres.2020.108114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 06/15/2020] [Accepted: 08/03/2020] [Indexed: 11/23/2022]
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4
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5
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Gruet S, Pirali O, Steber AL, Schnell M. The structural determination and skeletal ring modes of tetrahydropyran. Phys Chem Chem Phys 2019; 21:3016-3023. [DOI: 10.1039/c8cp06204h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A high-resolution molecular spectroscopy study was carried out on the cyclic ether tetrahydropyran (THP), one of the smallest molecules composed of a pyranose ring.
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Affiliation(s)
- Sébastien Gruet
- Deutsches Elektronen-Synchrotron
- D-22607 Hamburg
- Germany
- The Hamburg Centre for Ultrafast Imaging
- D-22761 Hamburg
| | - Olivier Pirali
- AILES beamline, Synchrotron SOLEIL
- L'Orme des Merisiers
- F-91192 Gif sur Yvette Cedex
- France
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay
| | - Amanda L. Steber
- Deutsches Elektronen-Synchrotron
- D-22607 Hamburg
- Germany
- The Hamburg Centre for Ultrafast Imaging
- D-22761 Hamburg
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron
- D-22607 Hamburg
- Germany
- The Hamburg Centre for Ultrafast Imaging
- D-22761 Hamburg
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6
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Schindler B, Legentil L, Allouche AR, Ferrières V, Compagnon I. Spectroscopic diagnostic for the ring-size of carbohydrates in the gas phase: furanose and pyranose forms of GalNAc. Phys Chem Chem Phys 2019; 21:12460-12467. [DOI: 10.1039/c8cp04082f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Hexoses are sparingly found in nature in the furanose form (5-membered ring).
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Affiliation(s)
- Baptiste Schindler
- Univ. Lyon
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- F-69622 Villeurbanne
| | - Laurent Legentil
- Univ. Rennes
- Ecole Nationale Supérieure de Chimie de Rennes
- CNRS
- UMR 6226 – ISCR
- F-35 000 Rennes
| | - Abdul-Rhaman Allouche
- Univ. Lyon
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- F-69622 Villeurbanne
| | - Vincent Ferrières
- Univ. Rennes
- Ecole Nationale Supérieure de Chimie de Rennes
- CNRS
- UMR 6226 – ISCR
- F-35 000 Rennes
| | - Isabelle Compagnon
- Univ. Lyon
- Université Claude Bernard Lyon 1
- CNRS
- Institut Lumière Matière
- F-69622 Villeurbanne
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7
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Preferred conformational structures of disaccharides with β-1,4-linked N-acetylglucosamine and D-mannose in the gas phase: A tree-step computational approach study. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Chemical synthesis of 4-azido-β-galactosamine derivatives for inhibitors of N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase. Glycoconj J 2018; 35:477-491. [DOI: 10.1007/s10719-018-9839-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/27/2018] [Accepted: 08/15/2018] [Indexed: 12/15/2022]
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9
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Bermejo IA, Usabiaga I, Compañón I, Castro-López J, Insausti A, Fernández JA, Avenoza A, Busto JH, Jiménez-Barbero J, Asensio JL, Peregrina JM, Jiménez-Osés G, Hurtado-Guerrero R, Cocinero EJ, Corzana F. Water Sculpts the Distinctive Shapes and Dynamics of the Tumor-Associated Carbohydrate Tn Antigens: Implications for Their Molecular Recognition. J Am Chem Soc 2018; 140:9952-9960. [PMID: 30004703 DOI: 10.1021/jacs.8b04801] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The tumor-associated carbohydrate Tn antigens include two variants, αGalNAc- O-Thr and αGalNAc- O-Ser. In solution, they exhibit dissimilar shapes and dynamics and bind differently to the same protein receptor. Here, we demonstrate experimentally and theoretically that their conformational preferences in the gas phase are highly similar, revealing the essential role of water. We propose that water molecules prompt the rotation around the glycosidic linkage in the threonine derivative, shielding its hydrophobic methyl group and allowing an optimal solvation of the polar region of the antigen. The unusual arrangement of αGalNAc- O-Thr features a water molecule bound into a "pocket" between the sugar and the threonine. This mechanism is supported by trapping, for the first time, such localized water in the crystal structures of an antibody bound to two glycopeptides that comprise fluorinated Tn antigens in their structure. According to several reported X-ray structures, installing oxygenated amino acids in specific regions of the receptor capable of displacing the bridging water molecule to the bulk-solvent may facilitate the molecular recognition of the Tn antigen with threonine. Overall, our data also explain how water fine-tunes the 3D structure features of similar molecules, which in turn are behind their distinct biological activities.
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Affiliation(s)
- Iris A Bermejo
- Departamento de Química, Centro de Investigación en Síntesis Química , Universidad de La Rioja , 26006 Logroño , Spain
| | - Imanol Usabiaga
- Departamento de Química Física, Facultad de Ciencia y Tecnología , Universidad del País Vasco (UPV-EHU), 48080 Bilbao , Spain
| | - Ismael Compañón
- Departamento de Química, Centro de Investigación en Síntesis Química , Universidad de La Rioja , 26006 Logroño , Spain
| | - Jorge Castro-López
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza , BIFI-IQFR (CSIC), 50018 Zaragoza , Spain
| | - Aran Insausti
- Departamento de Química Física, Facultad de Ciencia y Tecnología , Universidad del País Vasco (UPV-EHU), 48080 Bilbao , Spain.,Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), 48940 Leioa , Spain
| | - José A Fernández
- Departamento de Química Física, Facultad de Ciencia y Tecnología , Universidad del País Vasco (UPV-EHU), 48080 Bilbao , Spain
| | - Alberto Avenoza
- Departamento de Química, Centro de Investigación en Síntesis Química , Universidad de La Rioja , 26006 Logroño , Spain
| | - Jesús H Busto
- Departamento de Química, Centro de Investigación en Síntesis Química , Universidad de La Rioja , 26006 Logroño , Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE , Bizkaia Technology Park, Building 801A , 48170 Derio , Spain.,Ikerbasque , Basque Foundation for Science , Maria Diaz de Haro 13 , 48009 Bilbao , Spain.,Department of Organic Chemistry II, Faculty of Science & Technology , University of the Basque Country , 48940 Leioa , Spain
| | - Juan L Asensio
- Instituto de Química Orgánica General , IQOG-CSIC. 28006 Madrid , Spain
| | - Jesús M Peregrina
- Departamento de Química, Centro de Investigación en Síntesis Química , Universidad de La Rioja , 26006 Logroño , Spain
| | - Gonzalo Jiménez-Osés
- Departamento de Química, Centro de Investigación en Síntesis Química , Universidad de La Rioja , 26006 Logroño , Spain
| | - Ramón Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza , BIFI-IQFR (CSIC), 50018 Zaragoza , Spain.,Fundación ARAID , 50018 Zaragoza , Spain
| | - Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología , Universidad del País Vasco (UPV-EHU), 48080 Bilbao , Spain.,Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), 48940 Leioa , Spain
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química , Universidad de La Rioja , 26006 Logroño , Spain
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10
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Saeui CT, Liu L, Urias E, Morrissette-McAlmon J, Bhattacharya R, Yarema KJ. Pharmacological, Physiochemical, and Drug-Relevant Biological Properties of Short Chain Fatty Acid Hexosamine Analogues Used in Metabolic Glycoengineering. Mol Pharm 2018; 15:705-720. [PMID: 28853901 PMCID: PMC6292510 DOI: 10.1021/acs.molpharmaceut.7b00525] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this study, we catalog structure activity relationships (SAR) of several short chain fatty acid (SCFA)-modified hexosamine analogues used in metabolic glycoengineering (MGE) by comparing in silico and experimental measurements of physiochemical properties important in drug design. We then describe the impact of these compounds on selected biological parameters that influence the pharmacological properties and safety of drug candidates by monitoring P-glycoprotein (Pgp) efflux, inhibition of cytochrome P450 3A4 (CYP3A4), hERG channel inhibition, and cardiomyocyte cytotoxicity. These parameters are influenced by length of the SCFAs (e.g., acetate vs n-butyrate), which are added to MGE analogues to increase the efficiency of cellular uptake, the regioisomeric arrangement of the SCFAs on the core sugar, the structure of the core sugar itself, and by the type of N-acyl modification (e.g., N-acetyl vs N-azido). By cataloging the influence of these SAR on pharmacological properties of MGE analogues, this study outlines design considerations for tuning the pharmacological, physiochemical, and the toxicological parameters of this emerging class of small molecule drug candidates.
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Affiliation(s)
- Christopher T. Saeui
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Lingshu Liu
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Esteban Urias
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Justin Morrissette-McAlmon
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Rahul Bhattacharya
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Kevin J. Yarema
- Department of Biomedical Engineering and the Translational Tissue Engineering Center, The Johns Hopkins University, Baltimore, Maryland, USA
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11
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Jin S, Hu Y, Wang P, Zhan H, Lu Q, Liu F, Sheng L. Hydrogen bonding and dominant conformations of hydrated sugar analogue complexes using tetrahydrofurfuryl alcohol as the model sugar molecule. Phys Chem Chem Phys 2018; 20:7351-7360. [DOI: 10.1039/c7cp07935d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water molecules, which serve as both hydrogen bond donors and acceptors, have been found to influence the conformational landscape of gas-phase phenyl-β-d-glucopyranoside.
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Affiliation(s)
- Shan Jin
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Pengchao Wang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Huaqi Zhan
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Qiao Lu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Fuyi Liu
- National Synchrotron Radiation Laboratory
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Liusi Sheng
- National Synchrotron Radiation Laboratory
- University of Science and Technology of China
- Hefei
- P. R. China
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12
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Camiruaga A, Usabiaga I, Insausti A, León I, Fernández JA. Sugar-peptidic bond interactions: spectroscopic characterization of a model system. Phys Chem Chem Phys 2017; 19:12013-12021. [PMID: 28443888 DOI: 10.1039/c7cp00615b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Sugars are small carbohydrates which play numerous roles in living organisms such as storage of energy or as structural components. Modifications of specific sites within the glycan chain can modulate a carbohydrate's overall biological function as it happens with nucleic acids and proteins. Hence, identifying discrete carbohydrate modifications and understanding their biological effects is essential. A study of such processes requires of a deep knowledge of the interaction mechanism at the molecular level. Here, we use a combination of laser spectroscopy in jets and quantum mechanical calculations to characterize the interaction between phenyl-β-d-glucopyranoside and N-methylacetamide as a model to understand the interaction between a sugar and a peptide bond. The most stable structure of the molecular aggregate shows that the main interaction between the peptide fragment and the sugar proceeds via a C[double bond, length as m-dash]OH-O2 hydrogen bond. A second conformer was also found, in which the peptide establishes a C[double bond, length as m-dash]OH-O6 hydrogen bond with the hydroxymethyl substituent of the sugar unit. All the conformers present an additional interaction point with the aromatic ring. This particular preference of the peptide for the hydroxyl close to the aromatic ring could explain why glycogenin uses tyrosine in order to convert glucose into glycogen by exposing the O4H hydroxyl group for the other glucoses for the polymerization to take place.
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Affiliation(s)
- Ander Camiruaga
- Dpto. de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco-UPV/EHU, Bo Sarriena s/n, Leioa 48940, Spain.
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13
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Uriarte I, Écija P, Spada L, Zabalza E, Lesarri A, Basterretxea FJ, Fernández JA, Caminati W, Cocinero EJ. Potential energy surface of fluoroxene: experiment and theory. Phys Chem Chem Phys 2016; 18:3966-74. [DOI: 10.1039/c5cp06522d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The potential energy surface (PES) of the general anesthetic fluoroxene was probed in a supersonic jet expansion using broadband CP-FTMW spectroscopy and theoretical calculations.
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Affiliation(s)
- Iciar Uriarte
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- Bilbao
- Spain
| | - Patricia Écija
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- Bilbao
- Spain
| | - Lorenzo Spada
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- Bilbao
- Spain
| | - Eneko Zabalza
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- Bilbao
- Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica
- Facultad de Ciencias
- Universidad de Valladolid
- Valladolid
- Spain
| | - Francisco J. Basterretxea
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- Bilbao
- Spain
| | - José A. Fernández
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- Bilbao
- Spain
| | | | - Emilio J. Cocinero
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- Bilbao
- Spain
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14
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Baldauf C, Rossi M. Going clean: structure and dynamics of peptides in the gas phase and paths to solvation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:493002. [PMID: 26598600 DOI: 10.1088/0953-8984/27/49/493002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field.
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Affiliation(s)
- Carsten Baldauf
- Fritz Haber Institute, Faradayweg 4-6, 14195 Berlin, Germany
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15
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Mezei PD, Csonka GI. Unified picture for the conformation and stabilization of the O-glycosidic linkage in glycopeptide model structures. Struct Chem 2015. [DOI: 10.1007/s11224-015-0666-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Deshmukh MM, Gadre SR, Cocinero EJ. Stability of conformationally locked free fructose: theoretical and computational insights. NEW J CHEM 2015. [DOI: 10.1039/c5nj02106e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Total stabilization is governed by three predominant factors viz. the sum of energy of all H-bonds, ring strain and anomeric stabilization.
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Affiliation(s)
- Milind M. Deshmukh
- Department of Chemistry
- Dr. Harisingh Gour Central University
- Sagar, 470003
- India
| | - Shridhar R. Gadre
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur 208 016
- India
| | - Emilio J. Cocinero
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV-EHU)
- 48080 Bilbao
- Spain
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17
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Peyret A, Trant JF, Bonduelle CV, Ferji K, Jain N, Lecommandoux S, Gillies ER. Synthetic glycopolypeptides: synthesis and self-assembly of poly(γ-benzyl-l-glutamate)-glycosylated dendron hybrids. Polym Chem 2015. [DOI: 10.1039/c5py01060h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polyester dendrons with peripheral α-galactose moieties were synthesized and coupled to poly(γ-benzyl-l-glutamate) to afford amphiphilic linear-dendron hybrid glycopolypeptides that self-assembled in water.
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Affiliation(s)
- Ariane Peyret
- Université de Bordeaux/INP
- ENSCBP
- CNRS
- Laboratoire de Chimie des Polymères Organiques (LCPO)
- UMR 5629
| | - John F. Trant
- Department of Chemistry
- The University of Western Ontario
- London
- Canada
| | - Colin V. Bonduelle
- Université de Bordeaux/INP
- ENSCBP
- CNRS
- Laboratoire de Chimie des Polymères Organiques (LCPO)
- UMR 5629
| | - Khalid Ferji
- Université de Bordeaux/INP
- ENSCBP
- CNRS
- Laboratoire de Chimie des Polymères Organiques (LCPO)
- UMR 5629
| | - Namrata Jain
- Department of Chemistry
- The University of Western Ontario
- London
- Canada
| | - Sebastien Lecommandoux
- Université de Bordeaux/INP
- ENSCBP
- CNRS
- Laboratoire de Chimie des Polymères Organiques (LCPO)
- UMR 5629
| | - Elizabeth R. Gillies
- Department of Chemistry
- The University of Western Ontario
- London
- Canada
- Department of Chemical and Biochemical Engineering
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18
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Gadre SR, Yeole SD, Sahu N. Quantum chemical investigations on molecular clusters. Chem Rev 2014; 114:12132-73. [PMID: 25341561 DOI: 10.1021/cr4006632] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208 016, India
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19
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Aguado E, León I, Millán J, Cocinero EJ, Jaeqx S, Rijs AM, Lesarri A, Fernández JA. Unraveling the Benzocaine–Receptor Interaction at Molecular Level Using Mass-Resolved Spectroscopy. J Phys Chem B 2013; 117:13472-80. [DOI: 10.1021/jp4068944] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Edurne Aguado
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
| | - Iker León
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
| | - Judith Millán
- Departamento
de Química, Facultad de
Ciencias, Estudios Agroalimentarios
e Informática, Universidad de La Rioja, Madre de Dios,
51, 26006 Logroño, Spain
| | - Emilio J. Cocinero
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
| | - Sander Jaeqx
- Radboud
University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Anouk M. Rijs
- Radboud
University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Alberto Lesarri
- Departamento de Química Física y Química
Inorgánica, Facultad de
Ciencias, Universidad de Valladolid, E-47011 Valladolid, Spain
| | - José A. Fernández
- Departamento de Química
Física, Facultad de Ciencia
y Tecnología, Universidad del País Vasco (UPV/EHU), B°
Sarriena s/n, 48940 Leioa, Spain
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20
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Han C, Zhao J, Yang F, Wang J. Structural Dynamics of N-Propionyl-d-glucosamine Probed by Infrared Spectroscopies and Ab Initio Computations. J Phys Chem A 2013; 117:6105-15. [DOI: 10.1021/jp400096a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Chen Han
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
| | - Fan Yang
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
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21
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Cocinero EJ, Lesarri A, Écija P, Cimas Á, Davis BG, Basterretxea FJ, Fernández JA, Castaño F. Free Fructose Is Conformationally Locked. J Am Chem Soc 2013; 135:2845-52. [DOI: 10.1021/ja312393m] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Emilio J. Cocinero
- Departamento de Química
Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV-EHU), Apartado
644, 48080 Bilbao, Spain
| | - Alberto Lesarri
- Departamento de Química
Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Patricia Écija
- Departamento de Química
Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV-EHU), Apartado
644, 48080 Bilbao, Spain
| | - Álvaro Cimas
- Centro de Investigação
em Química, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Benjamin G. Davis
- Chemistry Department, Oxford University, Chemistry Research Laboratory, 12
Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Francisco J. Basterretxea
- Departamento de Química
Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV-EHU), Apartado
644, 48080 Bilbao, Spain
| | - José A. Fernández
- Departamento de Química
Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV-EHU), Apartado
644, 48080 Bilbao, Spain
| | - Fernando Castaño
- Departamento de Química
Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV-EHU), Apartado
644, 48080 Bilbao, Spain
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22
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León I, Cocinero EJ, Lesarri A, Castaño F, Fernández JA. A Spectroscopic Approach to the Solvation of Anesthetics in Jets: Propofol(H2O)n, n = 4–6. J Phys Chem A 2012; 116:8934-41. [DOI: 10.1021/jp305795u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Iker León
- Departamento de Química
Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco—UPV/EHU, Barrio
de Sarriena, s/n, 48940, Leioa, Spain
| | - Emilio J. Cocinero
- Departamento de Química
Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco—UPV/EHU, Barrio
de Sarriena, s/n, 48940, Leioa, Spain
| | - Alberto Lesarri
- Departamento de Química
Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, E-47011 Valladolid, Spain
| | - Fernando Castaño
- Departamento de Química
Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco—UPV/EHU, Barrio
de Sarriena, s/n, 48940, Leioa, Spain
| | - José A. Fernández
- Departamento de Química
Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco—UPV/EHU, Barrio
de Sarriena, s/n, 48940, Leioa, Spain
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23
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Jin L, Simons JP, Gerber RB. Monosaccharide-Water Complexes: Vibrational Spectroscopy and Anharmonic Potentials. J Phys Chem A 2012; 116:11088-94. [DOI: 10.1021/jp303080k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lin Jin
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
| | - John P. Simons
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ,
U.K
| | - R. Benny Gerber
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
- Institute of Chemistry
and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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24
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León I, Millán J, Cocinero EJ, Lesarri A, Castaño F, Fernández JA. Mimicking anaesthetic-receptor interaction: a combined spectroscopic and computational study of propofol···phenol. Phys Chem Chem Phys 2012; 14:8956-63. [PMID: 22516915 DOI: 10.1039/c2cp40656j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Propofol is a general anaesthetic that exerts its action by interaction with the GABA(A) receptor. Crystallographic studies suggest that there is a direct interaction between propofol and the phenolic residue of a tyrosine in the channel. In this study we create propofol···phenol clusters by their co-expansion in jets. The complex is probed using a set of mass-resolved spectroscopic strategies: 2-color REMPI, UV/UV hole-burning, IR/UV double resonance and the novel technique IR/IR/UV triple resonance. The existence of at least six different isomers in the expansion is demonstrated. All the isomers are stabilized by interactions between their aromatic rings. Additionally, in some conformers the OH moieties form hydrogen bonds in some of the isomers, with propofol and phenol alternating their donor-acceptor roles, while in others the -OH···OH angle points to a dipole-dipole interaction. Interpretation of the data in the light of dispersion-corrected DFT calculations shows that shallow barriers separate all the isomers, both in the ground and excited electronic states. Comparison of the structures of the complex with the X-ray diffraction data is also offered.
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Affiliation(s)
- Iker León
- Dpto. Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Bo Sarriena s/n, Leioa 48940, Spain
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25
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Cocinero EJ, Lesarri A, Écija P, Basterretxea FJ, Grabow JU, Fernández JA, Castaño F. Ribose Found in the Gas Phase. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201107973] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Cocinero EJ, Lesarri A, Écija P, Basterretxea FJ, Grabow JU, Fernández JA, Castaño F. Ribose Found in the Gas Phase. Angew Chem Int Ed Engl 2011; 51:3119-24. [DOI: 10.1002/anie.201107973] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Indexed: 11/11/2022]
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27
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Chen P, Nishiyama Y, Mazeau K. Torsional Entropy at the Origin of the Reversible Temperature-Induced Phase Transition of Cellulose. Macromolecules 2011. [DOI: 10.1021/ma201954s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pan Chen
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS), BP 53, F-38041
Grenoble cedex 9, France
| | - Yoshiharu Nishiyama
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS), BP 53, F-38041
Grenoble cedex 9, France
| | - Karim Mazeau
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS), BP 53, F-38041
Grenoble cedex 9, France
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28
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Jin L, Simons JP, Gerber RB. Structures of the xylose–water complex: Energetics, transitions between conformers and spectroscopy. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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29
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Wincel H. Thermochemistry of microhydration of sodiated and potassiated monosaccharides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1570-1576. [PMID: 21953260 PMCID: PMC3158851 DOI: 10.1007/s13361-011-0175-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/13/2011] [Accepted: 05/19/2011] [Indexed: 05/31/2023]
Abstract
The thermochemical properties ΔH(o)(n), ΔS(o)(n), and ΔG(o)(n) for the hydration of sodiated and potassiated monosaccharides (Ara = arabinose, Xyl = xylose, Rib = ribose, Glc = glucose, and Gal = galactose) have been experimentally studied in the gas phase at 10 mbar by equilibria measurements using an electrospray high-pressure mass spectrometer equipped with a pulsed ion beam reaction chamber. The hydration enthalpies for sodiated complexes were found to be between -46.4 and -57.7 kJ/mol for the first, and -42.7 and -52.3 kJ/mol for the second water molecule. For potassiated complexes, the water binding enthalpies were similar for all studied systems and varied between -48.5 and -52.7 kJ/mol. The thermochemical values for each system correspond to a mixture of the α and β anomeric forms of monosaccharide structures involved in their cationized complexes.
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Affiliation(s)
- Henryk Wincel
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Poland.
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30
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Pincu M, Cocinero EJ, Mayorkas N, Brauer B, Davis BG, Gerber RB, Simons JP. Isotopic Hydration of Cellobiose: Vibrational Spectroscopy and Dynamical Simulations. J Phys Chem A 2011; 115:9498-509. [DOI: 10.1021/jp112109p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Madeleine Pincu
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Emilio J. Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, (UPV − EHU), Apartado 644, E-48940, Bilbao, Spain
| | - Nitzan Mayorkas
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Brina Brauer
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Benjamin G. Davis
- Department of Chemistry, University of Oxford, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, U.K
| | - R. Benny Gerber
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - John P. Simons
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, U.K
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31
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Cocinero EJ, Çarçabal P, Vaden TD, Davis BG, Simons JP. Exploring Carbohydrate−Peptide Interactions in the Gas Phase: Structure and Selectivity in Complexes of Pyranosides with N-Acetylphenylalanine Methylamide. J Am Chem Soc 2011; 133:4548-57. [DOI: 10.1021/ja109664k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emilio J. Cocinero
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Pierre Çarçabal
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Timothy D. Vaden
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Benjamin G. Davis
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - John P. Simons
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
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32
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Mayorkas N, Rudić S, Cocinero EJ, Davis BG, Simons JP. Carbohydrate hydration: heavy water complexes of α and β anomers of glucose, galactose, fucose and xylose. Phys Chem Chem Phys 2011; 13:18671-8. [DOI: 10.1039/c1cp22348h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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33
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Mayorkas N, Rudić S, Davis BG, Simons JP. Heavy water hydration of mannose: the anomeric effect in solvation, laid bare. Chem Sci 2011. [DOI: 10.1039/c1sc00002k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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34
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Buchanan EG, James III WH, Gutberlet A, Dean JC, Guo L, Gellman SH, Zwier TS. Single-conformation spectroscopy and population analysis of model γ-peptides: New tests of amide stacking. Faraday Discuss 2011; 150:209-26; discussion 257-92. [DOI: 10.1039/c1fd00001b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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35
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Cocinero EJ, Lesarri A, Écija P, Grabow JU, Fernández JA, Castaño F. Conformational equilibria in vanillin and ethylvanillin. Phys Chem Chem Phys 2010; 12:12486-93. [DOI: 10.1039/c0cp00585a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Simons J. Good vibrations: probing biomolecular structure and interactions through spectroscopy in the gas phase. Mol Phys 2009. [DOI: 10.1080/00268970903409812] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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