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Pinillos P, Camiruaga A, Torres-Hernández F, Basterrechea FJ, Usabiaga I, Fernández JA. Exploring the interaction sites in glucose and galactose using phenol as a probe. Phys Chem Chem Phys 2023; 25:7205-7212. [PMID: 36846922 DOI: 10.1039/d2cp06036a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Sugars, together with amino acids and nucleobases, are the fundamental building blocks of a cell. They are involved in many fundamental processes and they especially play relevant roles as part of the immune system. The latter is connected to their ability to establish a collection of intermolecular interactions, depending on the position of their hydroxyl groups. Here we explore how the position of the OH in C4, the anomeric conformation and the nature substituent affect the interaction with phenol, which serves as a probe of the preferred site for the interaction. Using mass-resolved excitation spectroscopy and density functional calculations, we unravel the structure of the dimers and compare their conformation with those found for similar systems. The main conclusion is that the hydroxymethyl group has a very strong influence, guiding the whole aggregation process and that the position of the substituent in C4 has a stronger influence on the final structure of the dimer than the anomeric conformation.
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Affiliation(s)
- Paúl Pinillos
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Ander Camiruaga
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Fernando Torres-Hernández
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Francisco J Basterrechea
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - Imanol Usabiaga
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
| | - José A Fernández
- Department of Physical Chemistry, Fac. of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Spain.
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2
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Yeole SD. Quantum chemical study of molecular hydration of phenylxylopyranose sugar. J CHEM SCI 2022. [DOI: 10.1007/s12039-022-02100-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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3
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4
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Koli AR, Yeole SD. Understanding the interactions between hydrogen-bonded complexes of xylose and water: Quantum Chemical Investigation. J CHEM SCI 2020. [DOI: 10.1007/s12039-020-1741-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Koli AR, Yeole SD. Molecular hydration of carbohydrates: quantum chemical study of xylofuranose–(H2O)n clusters. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02634-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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6
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Matsuo K, Gekko K. Vacuum Ultraviolet Electronic Circular Dichroism Study of d-Glucose in Aqueous Solution. J Phys Chem A 2020; 124:642-651. [DOI: 10.1021/acs.jpca.9b09210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima 739-0046, Japan
| | - Kunihiko Gekko
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima 739-0046, Japan
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7
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López JC, Pérez C, Blanco S, Shubert VA, Temelso B, Shields GC, Schnell M. Water induces the same crown shapes as Li+ or Na+ in 15-crown-5 ether: a broadband rotational study. Phys Chem Chem Phys 2019; 21:2875-2881. [DOI: 10.1039/c8cp05552a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Complexation with water reduces the structural landscape of 15-crown-5 ether to the two forms observed for Li+ or Na+ complexes.
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Affiliation(s)
- Juan C. López
- Deutsches Elektronen-Synchrotron (DESY)
- Hamburg
- Germany
- Departamento de Química Física y Química Inorgánica
- Facultad de Ciencias
| | - Cristóbal Pérez
- Deutsches Elektronen-Synchrotron (DESY)
- Hamburg
- Germany
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV-EHU)
| | - Susana Blanco
- Departamento de Química Física y Química Inorgánica
- Facultad de Ciencias
- Universidad de Valladolid
- Valladolid
- Spain
| | | | - Berhane Temelso
- Provost's Office and Department of Chemistry
- Furman University
- Greenville
- USA
| | - George C. Shields
- Provost's Office and Department of Chemistry
- Furman University
- Greenville
- USA
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8
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Inakollu VSS, Yu H. A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function. J Comput Chem 2018; 39:2067-2078. [DOI: 10.1002/jcc.25390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/04/2018] [Accepted: 06/12/2018] [Indexed: 11/10/2022]
Affiliation(s)
- V. S. Sandeep Inakollu
- School of Chemistry and Molecular Bioscience University of Wollongong Wollongong New South Wales 2522 Australia
- Molecular Horizons University of Wollongong New South Wales 2522 Australia
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience University of Wollongong Wollongong New South Wales 2522 Australia
- Molecular Horizons University of Wollongong New South Wales 2522 Australia
- Illawarra Health and Medical Research Institute Wollongong New South Wales 2522 Australia
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9
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Tan Y, Zhao N, Liu J, Li P, Stedwell CN, Yu L, Polfer NC. Vibrational Signatures of Isomeric Lithiated N-acetyl-D-hexosamines by Gas-Phase Infrared Multiple-Photon Dissociation (IRMPD) Spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:539-550. [PMID: 28050874 DOI: 10.1007/s13361-016-1575-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 05/14/2023]
Abstract
Three lithiated N-acetyl-D-hexosamine (HexNAc) isomers, N-acetyl-D-glucosamine (GlcNAc), N-acetyl-D-galactosamine (GalNAc), and N-acetyl-D-mannosamine (ManNAc) are investigated as model monosaccharide derivatives by gas-phase infrared multiple-photon dissociation (IRMPD) spectroscopy. The hydrogen stretching region, which is attributed to OH and NH stretching modes, reveals some distinguishing spectral features of the lithium-adducted complexes that are useful in terms of differentiating these isomers. In order to understand the effect of lithium coordination on saccharide structure, and therefore anomericity, chair configuration, and hydrogen bonding networks, the conformational preferences of lithiated GlcNAc, GalNAc, and ManNAc are studied by comparing the experimental measurements with density functional theory (DFT) calculations. The experimental results of lithiated GlcNAc and GalNAc show a good match to the theoretical spectra of low-energy structures adopting a 4 C 1 chair conformation, consistent with this motif being the dominant conformation in condensed-phase monosaccharides. The epimerization effect upon going to lithiated ManNAc is significant, as in this case the 1 C 4 chair conformers give a more compelling match with the experimental results, consistent with their lower calculated energies. A contrasting computational study of these monosaccharides in their neutral form suggests that the lithium cation coordination with Lewis base oxygens can play a key role in favoring particular structural motifs (e.g., a 4 C 1 versus 1 C 4 ) and disrupting hydrogen bond networks, thus exhibiting specific IR spectral features between these closely related lithium-chelated complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Yanglan Tan
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ning Zhao
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Jinfeng Liu
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China
| | - Pengfei Li
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Corey N Stedwell
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Long Yu
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Nicolas C Polfer
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.
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Szczepaniak M, Moc J. Anomerization reaction of bare and microhydrated d-erythrose via explicitly correlated coupled cluster approach. Two water molecules are optimal. J Comput Chem 2017; 38:288-303. [PMID: 27896831 DOI: 10.1002/jcc.24680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/27/2016] [Accepted: 11/02/2016] [Indexed: 01/23/2023]
Abstract
We present a comprehensive benchmark computational study which has explored a complete path of the anomerization reaction of bare d-erythrose involving a pair of the low-energy α- and β-furanose anomers, the former of which was observed spectroscopically (Cabezas et al., Chem. Commun. 2013, 49, 10826). We find that the ring opening of the α-anomer yields the most stable open-chain tautomer which step is followed by the rotational interconversion of the open-chain rotamers and final ring closing to form the β-anomer. Our results indicate the flatness of the reaction's potential energy surface (PES) corresponding to the rotational interconversion path and its sensitivity to the computational level. By using the explicitly correlated coupled cluster CCSD(T)-F12/cc-pVTZ-F12 energies, we determine the free energy barrier for the α-furanose ring-opening (rate-determining) step as 170.3 kJ/mol. The question of the number of water molecules (n) needed for optimal stabilization of the erythrose anomerization reaction rate-determining transition state is addressed by a systematic exploration of the PES of the ring opening in the α-anomer-(H2 O)n and various β-anomer-(H2 O)n (n = 1-3) clusters using density functional and CCSD(T)-F12 computations. These computations suggest the lowest free energy barrier of the ring opening for doubly hydrated α-anomer, achieved by a mechanism that involves water-mediated multiple proton transfer coupled with the furanose CO bond breakage. Among the methods used, the G4 performed best against the CCSD(T)-F12 reference at estimating the ring-opening barrier heights for both the hydrated and bare erythrose conformers. Our results for the hydrated species are most relevant to an experimental study of the anomerization reaction of d-erythrose to be carried out in microsolvation environment. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Marek Szczepaniak
- Faculty of Chemistry, Wroclaw University, F. Joliot-Curie 14, Wroclaw, 50-383, Poland
| | - Jerzy Moc
- Faculty of Chemistry, Wroclaw University, F. Joliot-Curie 14, Wroclaw, 50-383, Poland
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11
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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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12
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Lomas JS, Joubert L, Maurel F. Association of symmetrical alkane diols with pyridine: DFT/GIAO calculation of 1 H NMR chemical shifts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:805-814. [PMID: 27247256 DOI: 10.1002/mrc.4457] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/04/2016] [Accepted: 05/05/2016] [Indexed: 06/05/2023]
Abstract
Proton nuclear magnetic resonance (NMR) shifts of the free diol and of its 1 : 1 and 1 : 2 hydrogen-bonded complexes with pyridine have been computed for five symmetrical alkane diols on the basis of density functional theory, by applying the gauge-including atomic orbital method to geometry-optimized conformers. For certain conformers, intramolecular OH···OH interactions, evidenced by high NMR OH proton shifts, are further enhanced on going from the free diol to the corresponding 1 : 1 diol/pyridine complex. This is confirmed by atoms-in-molecules and non-covalent interaction plots. The computed OH and CH proton shifts for the diol and the two complexes correlate well with values obtained by analysing data from the NMR titration of the diols in benzene against pyridine. Shift values for the diols in neat pyridine are calculated by weighting the shifts of the various protons in the three forms (free diol, 1 : 1 and 1 : 2 diol/pyridine complexes) according to the experimentally determined association constants. The results are in good agreement with those observed, and after empirical scaling, the root mean square difference is 0.18 ppm. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- John S Lomas
- ITODYS (UMR 7086), Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Laurent Joubert
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, France
| | - François Maurel
- ITODYS (UMR 7086), Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
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13
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Lozada-Garcia R, Mu D, Plazanet M, Çarçabal P. Molecular gels in the gas phase? Gelator-gelator and gelator-solvent interactions probed by vibrational spectroscopy. Phys Chem Chem Phys 2016; 18:22100-7. [PMID: 27443393 DOI: 10.1039/c6cp02755e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Benzylidene glucose (BzGlc) is a member of the benzylidene glycoside family. These molecules have the ability to form molecular physical gels. These materials are formed when gelator molecules create a non-covalently bound frame where solvent molecules are trapped. Since the gel formation process and its properties are determined by the subtle balance between non-covalent forces, it is difficult to anticipate them. Quantitative and qualitative understanding of the gelator-gelator and gelator-solvent interactions is needed to better control these materials for important potential applications. We have used gas phase vibrational spectroscopy and theoretical chemistry to study the conformational choices of BzGlc, its dimer and the complexes it forms with water or toluene. To interpret the vibrational spectra we have used the dispersion corrected functional B97D which we have calibrated for the calculation of OH stretching frequencies. Even at the most basic molecular level, it is possible to interrogate a large range of non-covalent interactions ranging from OH → OH hydrogen bonding, to OH → π, and CH → π, all being at the center of gel properties at the macroscopic level.
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Affiliation(s)
- Rolando Lozada-Garcia
- Institut des Sciences Moléculaires d'Orsay, ISMO, UMR 8214, Univ Paris-Sud, CNRS, bat 210, Univ Paris-Sud, F-91405 Orsay cedex, France.
| | - Dan Mu
- Institute of Research on the Structure and Property of Matter, Zaozhuang University, Zaozhuang, 277160, China
| | - Marie Plazanet
- Laboratoire Interdisciplinaire de Physique, LiPhy, UMR 5588, Univ Grenoble Alpes and CNRS, F-38041 Grenoble, France
| | - Pierre Çarçabal
- Institut des Sciences Moléculaires d'Orsay, ISMO, UMR 8214, Univ Paris-Sud, CNRS, bat 210, Univ Paris-Sud, F-91405 Orsay cedex, France.
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14
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Ueno-Noto K, Takano K. Water molecules inside protein structure affect binding of monosaccharides with HIV-1 antibody 2G12. J Comput Chem 2016; 37:2341-8. [DOI: 10.1002/jcc.24447] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/03/2016] [Accepted: 06/16/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Kaori Ueno-Noto
- Chemistry Section, Center for Natural Sciences, College of Liberal Arts and Sciences, Kitasato University; 1-15-1 Kitasato Minami-Ku, Sagamihara Kanagawa 252-0373 Japan
| | - Keiko Takano
- Department of Chemistry and Biochemistry; Graduate School of Humanities and Sciences, Ochanomizu University; 2-1-1 Otsuka, Bunkyo-Ku Tokyo 112-8610 Japan
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15
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Hsu CH, Park S, Mortenson DE, Foley BL, Wang X, Woods RJ, Case DA, Powers ET, Wong CH, Dyson HJ, Kelly JW. The Dependence of Carbohydrate-Aromatic Interaction Strengths on the Structure of the Carbohydrate. J Am Chem Soc 2016; 138:7636-48. [PMID: 27249581 DOI: 10.1021/jacs.6b02879] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Interactions between proteins and carbohydrates are ubiquitous in biology. Therefore, understanding the factors that determine their affinity and selectivity are correspondingly important. Herein, we have determined the relative strengths of intramolecular interactions between a series of monosaccharides and an aromatic ring close to the glycosylation site in an N-glycoprotein host. We employed the enhanced aromatic sequon, a structural motif found in the reverse turns of some N-glycoproteins, to facilitate face-to-face monosaccharide-aromatic interactions. A protein host was used because the dependence of the folding energetics on the identity of the monosaccharide can be accurately measured to assess the strength of the carbohydrate-aromatic interaction. Our data demonstrate that the carbohydrate-aromatic interaction strengths are moderately affected by changes in the stereochemistry and identity of the substituents on the pyranose rings of the sugars. Galactose seems to make the weakest and allose the strongest sugar-aromatic interactions, with glucose, N-acetylglucosamine (GlcNAc) and mannose in between. The NMR solution structures of several of the monosaccharide-containing N-glycoproteins were solved to further understand the origins of the similarities and differences between the monosaccharide-aromatic interaction energies. Peracetylation of the monosaccharides substantially increases the strength of the sugar-aromatic interaction in the context of our N-glycoprotein host. Finally, we discuss our results in light of recent literature regarding the contribution of electrostatics to CH-π interactions and speculate on what our observations imply about the absolute conservation of GlcNAc as the monosaccharide through which N-linked glycans are attached to glycoproteins in eukaryotes.
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Affiliation(s)
- Che-Hsiung Hsu
- Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States.,Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Sangho Park
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - David E Mortenson
- Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States
| | - B Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States
| | - Evan T Powers
- Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States.,Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.,The Skaggs Institute for Chemical Biology , La Jolla, California 92037, United States
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States.,Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States.,The Skaggs Institute for Chemical Biology , La Jolla, California 92037, United States
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16
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Calvo F, Bacchus-Montabonel MC, Clavaguéra C. Stepwise Hydration of 2-Aminooxazole: Theoretical Insight into the Structure, Finite Temperature Behavior and Proton-Induced Charge Transfer. J Phys Chem A 2016; 120:2380-9. [PMID: 27035034 DOI: 10.1021/acs.jpca.5b12392] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It was recently suggested that 2-aminooxazole (AO) could contribute to the formation of RNA nucleotides on primitive earth. In this article we have considered by means of computational modeling the influence of microhydration on the structural and spectral properties of this potential prebiotic molecule. The stable structures of AO(H2O)n were obtained first by sampling the potential energy landscapes of clusters containing up to n = 20 water molecules, using a simple but reasonably accurate force field and replica-exchange molecular dynamics simulations. Through reoptimization using an explicit description of electronic structure at the level of density functional theory with the M06-2X functional, the formation energies, ionization energies and electron affinities were determined in the vertical and adiabatic treatments, as well as vibrational and optical spectra covering the far-IR, mid-IR, and lower part of the UV ranges. The results generally show a clear segregation between the aminooxazole solute and the water molecules, a water cluster being formed near the nitrogen and amino group side leaving the hydrocarbon side dry even at temperatures corresponding to the liquid state. The spectral signatures generally concur and show distinct contributions of the solute and solvent, spectral shifts to lower energies being in agreement with earlier calculations in bulk solvent. We have also investigated the importance of microhydration on the charge transfer cross section upon collision with a proton, thereby extending an earlier investigation on the bare AO molecule. The presence of water molecules generally reduces the propensity for charge transfer at small sizes, but the influence of the solvent steadily decreases in larger droplets.
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Affiliation(s)
- F Calvo
- LiPhy, Université Grenoble Alpes and CNRS UMR 5588 , 140 Avenue de la Physique, 38402 St Martin d'Hères, France
| | - M-C Bacchus-Montabonel
- ILM, Université Lyon I and CNRS UMR 5306, Université de Lyon , 43 Bd du 11 Novembre 1918, F69622 Villeurbanne Cedex, France
| | - C Clavaguéra
- LCM, CNRS, Ecole Polytechnique, Université Paris Saclay , 91128 Palaiseau, France
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17
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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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18
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Zrelov OY, Syroeshkin AV, Uspenskaya EV, Titorovich OV, Pleteneva TV. Effect of Water Isotopic Composition on Galactose Mutarotation Kinetics. Pharm Chem J 2015. [DOI: 10.1007/s11094-015-1296-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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19
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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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20
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Szczepaniak M, Moc J. Cyclic and Acyclic Fructose Conformers in the Gas Phase: A Large-Scale Second-Order Perturbation Theory Study. J Phys Chem A 2014; 118:7925-38. [DOI: 10.1021/jp505719m] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Marek Szczepaniak
- Faculty of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Jerzy Moc
- Faculty of Chemistry, Wroclaw University, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
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Conformational studies of gas-phase ribose and 2-deoxyribose by density functional, second order PT and multi-level method calculations: the pyranoses, furanoses, and open-chain structures. Carbohydr Res 2014; 384:20-36. [DOI: 10.1016/j.carres.2013.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 09/09/2013] [Accepted: 10/18/2013] [Indexed: 11/21/2022]
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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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Stanca-Kaposta EC, Carçabal P, Cocinero EJ, Hurtado P, Simons JP. Carbohydrate-aromatic interactions: vibrational spectroscopy and structural assignment of isolated monosaccharide complexes with p-hydroxy toluene and N-acetyl l-tyrosine methylamide. J Phys Chem B 2013; 117:8135-42. [PMID: 23773008 DOI: 10.1021/jp404527s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The nature of carbohydrate binding first to p-hydroxy toluene and then the capped amino acid, N-acetyl l-tyrosine methyl amide (AcTyrNHMe), has been investigated in a solvent-free environment under molecular beam conditions. A combination of double resonance IR-UV spectroscopy and quantum chemical calculations has established the structures of complexes with the α and β anomers of methyl d-gluco- and d-galacto- and l-fucopyranosides (α/βMeGlc, MeGal, MeFuc). The new results, when combined with dispersion-corrected DFT calculations, reveal gas phase structures which are dominated by hydrogen bonding but also with evidence of CH-π bonded interactions in complexes with α/βMeGal. These adopt stacked intermolecular structures in marked contrast to those with α/βMeGlc; p-OH → O bonds linking AcTyrNHMe, or p-hydroxy toluene, to the carbohydrate provide an anchor that facilitates further binding, both through OH → O and NH → O hydrogen bonds to the peptide backbone and through CH-π dispersion interactions with the aromatic side group. "Stacked" structures associated with dispersion interactions with the aromatic ring are not detected in the corresponding complexes of capped phenylalanine, despite their common occurrence in bound carbohydrate-protein structures.
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Affiliation(s)
- E Cristina Stanca-Kaposta
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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24
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Çarçabal P, Cocinero EJ, Simons JP. Binding energies of micro-hydrated carbohydrates: measurements and interpretation. Chem Sci 2013. [DOI: 10.1039/c3sc50135c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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25
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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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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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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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