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Dvores MP, Çarçabal P, Gerber RB. Selective reactivity of glycosyl cation stereoisomers: the role of intramolecular hydrogen bonding. Phys Chem Chem Phys 2023; 25:26737-26747. [PMID: 37779496 DOI: 10.1039/d3cp03326k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The impact of the stereochemistry of the glycosyl cation species upon its dynamic properties is examined together with their vibrational spectra in order to gain insight into the effects of configurational isomerism on conformer dynamics and proton mobility. Ab initio molecular dynamics (AIMD) simulations and infrared multiple photon dissociation (IRMPD) spectroscopy explore the conformational and reactive dynamics of two pairs of glycosyl cation isomers: (1) protonated α- and β- anomers of methyl-D-galactopyranoside and (2) the oxocarbenium ions of the D-aldohexose C2 epimers galactose and talose. Analysis of these simulations together with experimental spectroscopy, interpreted by anharmonic calculations, points to the key role played by the intramolecular hydrogen bonds which are present in a unique pattern and extent in each isomer. We find that the reactivity of galactoside stereoisomers toward acid-catalyzed nucleophilic substitution, as gauged by the ability to form free oxocarbenium ions, differs markedly in a way that agrees with experimental measurements in the condensed phase. Other properties such as conformer stability and vibrational transitions were also found to reflect the characteristic hydrogen bonding interactions present in each isomer. In both systems, the stereochemistry is shown to determine the strength of intramolecular hydrogen bonding as well as between which substituents proton transfer is possible. We expect that the critical impact of non-covalent interactions on stereoisomer selectivity may be a widely found phenomenon whose effects should be further investigated.
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Affiliation(s)
- M P Dvores
- Fritz Haber Centre for Molecular Dynamics, The Institute of Chemistry, The Hebrew University, Jerusalem 91904, Israel.
| | - P Çarçabal
- Insitut des Sciences Moléculaires d'Orsay, ISMO, Univ Paris-Sud, CNRS, bat 210, Univ Paris-Sud, 91405 Orsay Cedex, France
| | - R B Gerber
- Fritz Haber Centre for Molecular Dynamics, The Institute of Chemistry, The Hebrew University, Jerusalem 91904, Israel.
- Department of Chemistry, University of California Irvine, CA, 92697, USA
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2
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Gerber RB. My Trajectory in Molecular Reaction Dynamics and Spectroscopy. Annu Rev Phys Chem 2021; 72:1-34. [PMID: 33276702 DOI: 10.1146/annurev-physchem-090519-124238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This is the story of a career in theoretical chemistry during a time of dramatic changes in the field due to phenomenal growth in the availability of computational power. It is likewise the story of the highly gifted graduate students and postdoctoral fellows that I was fortunate to mentor throughout my career. It includes reminiscences of the great mentors that I had and of the exciting collaborations with both experimentalists and theorists on which I built much of my research. This is an account of the developments of exciting scientific disciplines in which I was involved: vibrational spectroscopy, molecular reaction mechanisms and dynamics, e.g., in atmospheric chemistry, and the prediction of new, exotic molecules, in particular noble gas molecules. From my very first project to my current work, my career in science has brought me the excitement and fascination of research. What a wonderful pursuit!
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Affiliation(s)
- Robert Benny Gerber
- The Fritz Haber Research Center and Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; .,Department of Chemistry, University of California, Irvine, California 92697, USA
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3
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Dvores MP, Çarçabal P, Maître P, Simons JP, Gerber RB. Gas phase dynamics, conformational transitions and spectroscopy of charged saccharides: the oxocarbenium ion, protonated anhydrogalactose and protonated methyl galactopyranoside. Phys Chem Chem Phys 2020; 22:4144-4157. [PMID: 32039431 DOI: 10.1039/c9cp06572e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protonated intermediates are postulated to be involved in the rate determining step of many sugar reactions. This paper presents a study of protonated sugar species, isolated in the gas phase, using a combination of infrared multiple photon dissociation (IRMPD) spectroscopy, classical ab initio molecular dynamics (AIMD) and quantum mechanical vibrational self-consistent field (VSCF) calculations. It provides a likely identification of the reactive intermediate oxocarbenium ion structure in a d-galactosyl system as well as the saccharide pyrolysis product anhydrogalactose (that suggests oxocarbenium ion stabilization), along with the spectrum of the protonated parent species: methyl d-galactopyranoside-H+. Its vibrational fingerprint indicates intramolecular proton sharing. Classical AIMD simulations for galactosyl oxocarbenium ions, conducted in the temperature range ∼300-350 K (using B3LYP potentials on-the-fly) reveal efficient transitions on the picosecond timescale. Multiple conformers are likely to exist under the experimental conditions and along with static VSCF calculations, they have facilitated the identification of the individual structural motifs of the galactosyl oxocarbenium ion and protonated anhydrogalactose ion conformers that contribute to the observed experimental spectra. These results demonstrate the power of experimental IRMPD spectroscopy combined with dynamics simulations and with computational spectroscopy at the anharmonic level to unravel conformer structures of protonated saccharides, and to provide information on their lifetimes.
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Affiliation(s)
- M P Dvores
- Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel.
| | - P Çarçabal
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405, Orsay, France
| | - P Maître
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405, Orsay, France
| | - J P Simons
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ, UK
| | - R B Gerber
- Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel. and Department of Chemistry, University of California Irvine, CA 92697, USA
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4
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Teixeira F, Cordeiro MNDS. Improving Vibrational Mode Interpretation Using Bayesian Regression. J Chem Theory Comput 2019; 15:456-470. [PMID: 30525596 DOI: 10.1021/acs.jctc.8b00439] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
To streamline the interpretation of vibrational spectra, this work introduces the use of Bayesian linear regression with automatic relevance determination as a viable approach to decompose the atomic motions along any vibrational mode as a weighted combination of displacements along chemically meaningful internal coordinates. This novel approach denominated vibrational mode automatic relevance determination (VMARD) is presented and compared with the well-established potential energy decomposition (PED) scheme. Good agreement is generally attained between the two methods. VMARD returns a decomposition of the atomic displacement using only a small number of internal coordinates, thus aiding the interpretation of the vibrational spectra. Moreover, the results show that the VMARD descriptions are resilient toward the addition of additional internal coordinates, achieving a concise description of the vibrational modes despite the use of redundant internal coordinates. Potential applications of VMARD involving the gathering of physical insights on the atomic motions along the reaction coordinate at transition state structures, as well as the improvement of theoretically predicted vibrational frequencies, are also presented under a proof-of-concept perspective.
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Affiliation(s)
- Filipe Teixeira
- LAQV-REQUIMTE , Faculty of Sciences of the University of Porto , Rua do Campo Alegre , 4169-007 Porto , Portugal
| | - M Natália D S Cordeiro
- LAQV-REQUIMTE , Faculty of Sciences of the University of Porto , Rua do Campo Alegre , 4169-007 Porto , Portugal
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Wang P, Hu Y, Zhan H, Chen J. Gas-phase conformational preference of the smallest saccharide (glycolaldehyde) and its hydrated complexes with bridged hydrogen bonding. RSC Adv 2017. [DOI: 10.1039/c6ra26965f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Glycoaldehyde (GA, HOCH2CHO) is the simplest sugar unit of the carbohydrates and the only sugar to have been detected in interstellar space to date.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - Jiaxin Chen
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
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Chen W, Meng F, Cheng R, Deng C, Feijen J, Zhong Z. Biodegradable glycopolymer-b-poly(ε-caprolactone) block copolymer micelles: versatile construction, tailored lactose functionality, and hepatoma-targeted drug delivery. J Mater Chem B 2015; 3:2308-2317. [DOI: 10.1039/c4tb01962h] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An illustration of versatile construction of biodegradable glycopolymer-PCL micelles with tailored LBA-functionality for hepatoma-targeted drug delivery.
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Affiliation(s)
- Wei Chen
- Biomedical Polymers Laboratory
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Fenghua Meng
- Biomedical Polymers Laboratory
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Ru Cheng
- Biomedical Polymers Laboratory
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Chao Deng
- Biomedical Polymers Laboratory
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Jan Feijen
- Biomedical Polymers Laboratory
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- College of Chemistry
- Chemical Engineering and Materials Science
| | - Zhiyuan Zhong
- Biomedical Polymers Laboratory
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application
- Department of Polymer Science and Engineering
- College of Chemistry
- Chemical Engineering and Materials Science
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Thaunay F, Dognon JP, Ohanessian G, Clavaguéra C. Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field. Phys Chem Chem Phys 2015. [DOI: 10.1039/c5cp02270c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Driven Molecular Dynamics approach has been adapted and associated with the AMOEBA polarizable force field to assign and visualize vibrational modes in infrared spectra obtained by molecular dynamics simulations.
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Affiliation(s)
- Florian Thaunay
- Laboratoire de Chimie Moléculaire
- Ecole Polytechnique
- CNRS
- 91128 Palaiseau Cedex
- France
| | - Jean-Pierre Dognon
- CEA/Saclay
- DSM/IRAMIS/NIMBE
- CNRS
- UMR 3685
- Laboratoire de Chimie Moléculaire et de Catalyse pour l'Energie
| | - Gilles Ohanessian
- Laboratoire de Chimie Moléculaire
- Ecole Polytechnique
- CNRS
- 91128 Palaiseau Cedex
- France
| | - Carine Clavaguéra
- Laboratoire de Chimie Moléculaire
- Ecole Polytechnique
- CNRS
- 91128 Palaiseau Cedex
- France
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Lee W, Engels B. The Protonation State of Catalytic Residues in the Resting State of KasA Revisited: Detailed Mechanism for the Activation of KasA by Its Own Substrate. Biochemistry 2014; 53:919-31. [DOI: 10.1021/bi401308j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Wook Lee
- Institut für Physikalische
und Theoretische Chemie, Universität Würzburg, Emil-Fischer
Strasse 42, 97074 Würzburg, Germany
| | - Bernd Engels
- Institut für Physikalische
und Theoretische Chemie, Universität Würzburg, Emil-Fischer
Strasse 42, 97074 Würzburg, Germany
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Abstract
Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called "sugar code," just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).
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Affiliation(s)
- Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV - EHU), Apartado 644, 48940, Bilbao, Spain,
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Lignell H, Epstein SA, Marvin MR, Shemesh D, Gerber B, Nizkorodov S. Experimental and Theoretical Study of Aqueous cis-Pinonic Acid Photolysis. J Phys Chem A 2013; 117:12930-45. [DOI: 10.1021/jp4093018] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hanna Lignell
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
- Laboratory of Physical Chemistry, University of Helsinki, P.O. Box 55, FIN-00014 Helsinki, Finland
| | - Scott A. Epstein
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Margaret R. Marvin
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Dorit Shemesh
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Benny Gerber
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
- Laboratory of Physical Chemistry, University of Helsinki, P.O. Box 55, FIN-00014 Helsinki, Finland
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Sergey Nizkorodov
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
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Lee W, Engels B. Clarification on the Decarboxylation Mechanism in KasA Based on the Protonation State of Key Residues in the Acyl-Enzyme State. J Phys Chem B 2013; 117:8095-104. [DOI: 10.1021/jp403067m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wook Lee
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Emil-Fischer Strasse 42, 97074, Würzburg, Germany
| | - Bernd Engels
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Emil-Fischer Strasse 42, 97074, Würzburg, Germany
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12
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Pincu M, Brauer B, Gerber RB. When a proton attacks cellobiose in the gas phase: ab initio molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:15382-91. [DOI: 10.1039/c3cp52220b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Chutia S, Rossi M, Blum V. Water Adsorption at Two Unsolvated Peptides with a Protonated Lysine Residue: From Self-Solvation to Solvation. J Phys Chem B 2012; 116:14788-804. [DOI: 10.1021/jp3098268] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sucismita Chutia
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Theory
Department, D-14195 Berlin, Germany
| | - Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Theory
Department, D-14195 Berlin, Germany
| | - Volker Blum
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Theory
Department, D-14195 Berlin, Germany
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Xie HB, Gerber RB. Interaction and reaction of the hydroxyl ion with β-d-galactose and its hydrated complex: an ab initio molecular dynamics study. Phys Chem Chem Phys 2012; 14:12086-9. [DOI: 10.1039/c2cp41593c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Jin L, Gerber RB. Migration and chemical reaction of H+ in protonated β-galactose. Phys Chem Chem Phys 2012; 14:13522-6. [DOI: 10.1039/c2cp41766a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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