1
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Jestilä JS, Wu N, Priante F, Foster AS. Accelerated Lignocellulosic Molecule Adsorption Structure Determination. J Chem Theory Comput 2024; 20:2297-2312. [PMID: 38408381 PMCID: PMC10939001 DOI: 10.1021/acs.jctc.3c01292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/28/2024]
Abstract
Here, we present a study combining Bayesian optimization structural inference with the machine learning interatomic potential Neural Equivariant Interatomic Potential (NequIP) to accelerate and enable the study of the adsorption of the conformationally flexible lignocellulosic molecules β-d-xylose and 1,4-β-d-xylotetraose on a copper surface. The number of structure evaluations needed to map out the relevant potential energy surfaces are reduced by Bayesian optimization, while NequIP minimizes the time spent on each evaluation, ultimately resulting in cost-efficient and reliable sampling of large systems and configurational spaces. Although the applicability of Bayesian optimization for the conformational analysis of the more flexible xylotetraose molecule is restricted by the sample complexity bottleneck, the latter can be effectively bypassed with external conformer search tools, such as the Conformer-Rotamer Ensemble Sampling Tool, facilitating the subsequent lower-dimensional global minimum adsorption structure determination. Finally, we demonstrate the applicability of the described approach to find adsorption structures practically equivalent to the density functional theory counterparts at a fraction of the computational cost.
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Affiliation(s)
- Joakim S. Jestilä
- Department
of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
| | - Nian Wu
- Department
of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
| | - Fabio Priante
- Department
of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
| | - Adam S. Foster
- Department
of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, 920-1192 Kanazawa, Japan
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2
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Juárez G, Sanz-Novo M, Aguado R, Alonso JL, León I, Alonso ER. The eight structures of caffeic acid: a jet-cooled laser ablated rotational study. RSC Adv 2022; 13:212-219. [PMID: 36605649 PMCID: PMC9768571 DOI: 10.1039/d2ra07124j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022] Open
Abstract
This work reports a complete conformational analysis of caffeic acid, an exceptionally versatile pharmacophore, using laser ablation chirped-pulse Fourier transform microwave spectroscopy. The whole conformational space consisting of eight distinct species has been fully deciphered based on the trend of the rotational constants supported by theoretical computations. We show how rotational spectroscopy can be confidently used to distinguish between conformers even when the structural differences are minimal, such as those involved in the conformational panorama of caffeic acid. Additionally, the structural information here provided, such as the planarity observed in all the conformers, could help to elucidate the mechanisms underlying the biological and pharmacological activity of hydroxycinnamic acids.
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Affiliation(s)
- G. Juárez
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad Asociada CSIC, Parque Científico Uva Universidad de ValladolidPaseo de Belén 547011 ValladolidSpain
| | - M. Sanz-Novo
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad Asociada CSIC, Parque Científico Uva Universidad de ValladolidPaseo de Belén 547011 ValladolidSpain
| | - R. Aguado
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad Asociada CSIC, Parque Científico Uva Universidad de ValladolidPaseo de Belén 547011 ValladolidSpain
| | - J. L. Alonso
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad Asociada CSIC, Parque Científico Uva Universidad de ValladolidPaseo de Belén 547011 ValladolidSpain
| | - I. León
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad Asociada CSIC, Parque Científico Uva Universidad de ValladolidPaseo de Belén 547011 ValladolidSpain
| | - E. R. Alonso
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad Asociada CSIC, Parque Científico Uva Universidad de ValladolidPaseo de Belén 547011 ValladolidSpain
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3
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Modak A, Gill D, Mankar AR, Pant KK, Bhasin V, Nayak C, Bhattacharya S. Controlled synthesis of Ru-single-atoms on ordered mesoporous phosphine polymers for microwave-assisted conversion of biomass-derived sugars to artificial sweeteners. NANOSCALE 2022; 14:15875-15888. [PMID: 36263781 DOI: 10.1039/d2nr03645b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Atomically dispersed metal-single-atoms have become a frontier in solid catalysis due to their characteristic electronic properties. However, for biomass conversion, employing metal-single-atoms as catalysts is rather challenging since they suffer from poor selectivity and yield due to inadequate metal-support interactions. We show here that Ru/triphenylphosphine (PPh)-based ordered mesoporous polymers afford high yields of reduced sugars, xylitol (yield ∼95%) and sorbitol (yield ∼65%) in a microwave reactor with formic acid as the only hydrogen donor. We have established a unique relationship within Ru/triphenylphosphine that shows an important ligand effect, in contrast to, Ru/triphenylamine and Ru/catechol. The tailored electronic properties in Ru/phosphine were thoroughly examined by using state-of-the-art experimental techniques viz. EXAFS, XANES, XPS, DRIFTS and HAADF-STEM. The resulting phosphine-modified catalysts show a promotion in activity and selectivity towards less vulnerable aldehydes for hydrogenation, further confirmed by DFT calculations. This finding reveals a new protocol to tailor the activity of metal-single-atoms utilizing functional porous polymers as nanoreactors.
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Affiliation(s)
- Arindam Modak
- Catalytic Reaction Engineering Lab, Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi-110016, India.
| | - Deepika Gill
- Department of Physics, Indian Institute of Technology Delhi, New Delhi-110016, India.
| | - Akshay R Mankar
- Catalytic Reaction Engineering Lab, Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi-110016, India.
| | - Kamal K Pant
- Catalytic Reaction Engineering Lab, Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi-110016, India.
| | - Vidha Bhasin
- Atomic and Molecular Physics Division, Bhabha Atomic Research Centre, Mumbai-400094, India
| | - Chandrani Nayak
- Atomic and Molecular Physics Division, Bhabha Atomic Research Centre, Mumbai-400094, India
| | - Saswata Bhattacharya
- Department of Physics, Indian Institute of Technology Delhi, New Delhi-110016, India.
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4
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Mato S, Aguado R, Mata S, Alonso JL, León I. A solvent-mediated conformational switch in sulfanilamide. Phys Chem Chem Phys 2022; 24:24032-24038. [PMID: 36106463 DOI: 10.1039/d2cp03367d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sulfanilamide, a widely used antibacterial drug, has been brought into the gas phase using laser ablation techniques, and its structure has been characterized in the isolated conditions of a supersonic expansion using Fourier transform microwave techniques. A single conformer stabilized by an N-H⋯OS intramolecular interaction in an equatorial disposition has been unequivocally characterized. To emulate the microsolvation process, we studied its hydrated cluster. The results show that a single water molecule alters the conformational preference and forces sulfanilamide to switch from its initial eclipsed configuration to a staggered disposition. The observed hydrated cluster adopts a structure in which water forms three hydrogen bonds with sulfanilamide stabilizing the molecule.
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Affiliation(s)
- Sergio Mato
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - Raúl Aguado
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - Santiago Mata
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - José Luis Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - Iker León
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
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5
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Juárez G, Alonso ER, Sanz-Novo M, Alonso JL, León I. Understanding the abundance of the rare sugar β-D-allose. Phys Chem Chem Phys 2022; 24:23076-23081. [DOI: 10.1039/d2cp03213a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformational landscape of β-D-allose, a rare sugar, has been investigated using laser ablation in combination with high-resolution rotational spectroscopy. Altogether, three species are identified, exhibiting a counter-clockwise intramolecular hydrogen...
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6
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Léon I, Tasinato N, Spada L, Alonso ER, Mata S, Balbi A, Puzzarini C, Alonso JL, Barone V. Looking for the Elusive Imine Tautomer of Creatinine: Different States of Aggregation Studied by Quantum Chemistry and Molecular Spectroscopy. Chempluschem 2021; 86:1374-1386. [PMID: 34255935 PMCID: PMC8519097 DOI: 10.1002/cplu.202100224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/22/2021] [Indexed: 01/06/2023]
Abstract
New spectroscopic experiments and state-of-the-art quantum-chemical computations of creatinine in different aggregation states unequivocally unveiled a significant tuning of tautomeric equilibrium by the environment: from the exclusive presence of the amine tautomer in the solid state and aqueous solution to a mixture of amine and imine tautomers in the gas phase. Quantum-chemical calculations predict the amine species as the most stable tautomer by about 30 kJ mol-1 in condensed phases. On the contrary, moving to the isolated forms, both Z and E imine isomers become more stable by about 7 kJ mol-1 . Since the imine isomers and one amine tautomer are separated by significant energy barriers, all of them should be present in the gas phase. This prediction has indeed been confirmed by high-resolution rotational spectroscopy, which provides the first experimental characterization of the elusive imine tautomer. The interpretation of the complicated hyperfine structure of the rotational spectrum, originated by three 14 N nuclei, makes it possible to use the spectral signatures as a sort of fingerprint for each individual tautomer in the complex sample.
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Affiliation(s)
- Iker Léon
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
| | - Lorenzo Spada
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy.,Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum -, Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Elena R Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Alice Balbi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum -, Università di Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Jose L Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy
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7
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Molecular modification, structural characterization, and biological activity of xylans. Carbohydr Polym 2021; 269:118248. [PMID: 34294285 DOI: 10.1016/j.carbpol.2021.118248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 12/17/2022]
Abstract
The differences in the source and structure of xylans make them have various biological activities. However, due to their inherent structural limitations, the various biological activities of xylans are far lower than those of commercial drugs. Currently, several types of molecular modification methods have been developed to address these limitations, and many derivatives with specific biological activity have been obtained. Further research on structural characteristics, structure-activity relationship and mechanism of action is of great significance for the development of xylan derivatives. Therefore, the major molecular modification methods of xylans are introduced in this paper, and the primary structure and conformation characteristics of xylans and their derivatives are summarized. In addition, the biological activity and structure-activity relationship of the modified xylans are also discussed.
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8
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Alonso ER, Fusè M, León I, Puzzarini C, Alonso JL, Barone V. Exploring the Maze of Cycloserine Conformers in the Gas Phase Guided by Microwave Spectroscopy and Quantum Chemistry. J Phys Chem A 2021; 125:2121-2129. [DOI: 10.1021/acs.jpca.1c00455] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elena R. Alonso
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, Spain
| | - Marco Fusè
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Iker León
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005 Valladolid, Spain
| | - Cristina Puzzarini
- Dipartimento di “Chimica Giacomo Ciamician”, University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - José L. Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005 Valladolid, Spain
| | - Vincenzo Barone
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
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9
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Goussougli M, Sirjean B, Glaude PA, Fournet R. Theoretical study of the pyrolysis of β-1,4-xylan: a detailed investigation on unimolecular concerted reactions. Phys Chem Chem Phys 2021; 23:2605-2621. [PMID: 33480926 DOI: 10.1039/d0cp06024k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A theoretical study of the thermal decomposition of β-1,4-xylan, a model polymer of hemicelluloses, is proposed for the first time. A mechanism based on unimolecular concerted reactions is elaborated in a comprehensive way. Elementary reactions, such as dehydrations, retro-aldol, retro Diels-Alder, retro-ene, glycosidic bond fissions, isomerizations, etc., are applied to β-1,4-xylan, as well as to the fragments formed. At each stage of the construction of the mechanism, the fragments previously retained are decomposed and the low energy paths are selected to define new fragments. Energy barriers are computed at the CBS-QB3 level of theory and rate coefficients of important reactions are calculated. It is shown that the main reaction pathways can be modelled by reactions involving two specific fragments, which react in closed sequences, similarly to chain-propagating reactions. The proposed reaction scheme allows to predict important species observed during the pyrolysis of xylan, such as aldehydes or CO. In addition, we show that dehydrations require high activation energy and cannot compete with the other reactions. Therefore, it seems difficult to explain, by means of unimolecular homogeneous gas phase reactions, the significant formation of specific species such as furfural as reported by several authors.
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Affiliation(s)
- M Goussougli
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, F-54000 Nancy, France.
| | - B Sirjean
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, F-54000 Nancy, France.
| | - P-A Glaude
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, F-54000 Nancy, France.
| | - R Fournet
- Laboratoire Réactions et Génie des Procédés, Université de Lorraine, CNRS, F-54000 Nancy, France.
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10
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Calabrese C, Écija P, Compañón I, Vallejo-López M, Cimas Á, Parra M, Basterretxea FJ, Santos JI, Jiménez-Barbero J, Lesarri A, Corzana F, Cocinero EJ. Conformational Behavior of d-Lyxose in Gas and Solution Phases by Rotational and NMR Spectroscopies. J Phys Chem Lett 2019; 10:3339-3345. [PMID: 31141365 DOI: 10.1021/acs.jpclett.9b00978] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Understanding the conformational preferences of carbohydrates is crucial to explain the interactions with their biological targets and to improve their use as therapeutic agents. We present experimental data resolving the conformational landscape of the monosaccharide d-lyxose, for which quantum mechanical (QM) calculations offer model-dependent results. This study compares the structural preferences in the gas phase, determined by rotational spectroscopy, with those in solution, resolved by nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations. In contrast to QM calculations, d-lyxose adopts only pyranose forms in the gas phase, with the α-anomer exhibiting both the 4C1 and 1C4 chairs (60:40). The predominantly populated β-anomer shows the 4C1 form exclusively, as determined experimentally by isotopic substitution. In aqueous solution, the pyranose forms are also dominant. However, in contrast to the gas phase, the α-anomer as 1C4 chair is the most populated, and its solvation is more effective than for the β derivative. Markedly, the main conformers found in the gas phase and solution are characterized by the lack of the stabilizing anomeric effect. From a mechanistic perspective, both rotational spectroscopy and solid-state nuclear magnetic resonance (NMR) corroborate that α ↔ β or furanose ↔ pyranose interconversions are prevented in the gas phase. Combining microwave (MW) and NMR results provides a powerful method for unraveling the water role in the conformational preferences of challenging molecules, such as flexible monosaccharides.
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Affiliation(s)
- Camilla Calabrese
- Departamento de Química Física, Facultad de Ciencia y Tecnología , Universidad del País Vasco (UPV/EHU) , 48080 Bilbao , Spain
- Instituto Biofisika (CSIC, UPV/EHU) , 48080 Bilbao , Spain
| | - Patricia Écija
- 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
| | - Montserrat Vallejo-López
- Departamento de Química Física, Facultad de Ciencia y Tecnología , Universidad del País Vasco (UPV/EHU) , 48080 Bilbao , Spain
| | - Álvaro Cimas
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, LAMBE UMR8587 , Université d'Évry val d'Essonne , 91025 Évry , France
| | - Maider Parra
- Departamento de Química Física, Facultad de Ciencia y Tecnología , Universidad del País Vasco (UPV/EHU) , 48080 Bilbao , Spain
- Instituto Biofisika (CSIC, UPV/EHU) , 48080 Bilbao , Spain
| | - Francisco J Basterretxea
- Departamento de Química Física, Facultad de Ciencia y Tecnología , Universidad del País Vasco (UPV/EHU) , 48080 Bilbao , Spain
| | - José I Santos
- SGIker UPV/EHU , Centro Joxe Mari Korta , Tolosa Hiribidea 72 , 20018 Donostia , Spain
| | - Jesús Jiménez-Barbero
- Departamento de Química Orgánica II, Facultad de Ciencia y Tecnología , Universidad del País Vasco (UPV/EHU) , 48080 Bilbao , Spain
- IKERBASQUE, Basque Foundation for Science , 48009 Bilbao , Spain
- Chemical Glycobiology Laboratory, CIC bioGUNE , Bizkaia Technology Park , Building 800, 48160 Derio , Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica-IU CINQUIMA, Facultad de Ciencias , Universidad de Valladolid , 47011 Valladolid , Spain
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química , Universidad de La Rioja , 26006 Logroño , Spain
| | - Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología , Universidad del País Vasco (UPV/EHU) , 48080 Bilbao , Spain
- Instituto Biofisika (CSIC, UPV/EHU) , 48080 Bilbao , Spain
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11
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Švecová P, Petr J. Separation of cetirizine enantiomers by capillary electrophoresis with a dual selector system based on borate-glucose complexes and sulfated-β-cyclodextrin. Talanta 2019; 198:154-158. [DOI: 10.1016/j.talanta.2019.01.097] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 12/30/2022]
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12
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Alonso ER, León I, Kolesniková L, Alonso JL. Rotational Spectrum of Saccharin: Structure and Sweetness. J Phys Chem A 2019; 123:2756-2761. [PMID: 30844277 DOI: 10.1021/acs.jpca.8b12211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present the first high-resolution rotational study of the artificial sweetener saccharin. By combining laser ablation (LA), narrow- and broadband Fourier transform microwave techniques (FTMW), and supersonic expansions, we have transferred the solid of saccharin (mp 229 °C) to a supersonic jet and captured its rotational spectrum. The rotational constants were accurately determined by fitting more than 60 rotational transitions for the parent and 34S isotopic species in the 6.4-10.4 GHz frequency range. Experiment and complementary quantum-chemical calculations provide accurate geometrical parameters for saccharin, the first artificial sweetener investigated by high-resolution microwave spectroscopy. The detailed structural information extracted from the rotational and 14N nuclear quadrupole coupling constants provided useful data in the context of the old theories of sweetness.
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Affiliation(s)
- Elena R Alonso
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa , Universidad de Valladolid , 47011 Valladolid , Spain
| | - Iker León
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa , Universidad de Valladolid , 47011 Valladolid , Spain
| | - Lucie Kolesniková
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa , Universidad de Valladolid , 47011 Valladolid , Spain
| | - Jose L Alonso
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa , Universidad de Valladolid , 47011 Valladolid , Spain
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13
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Simão A, Cabezas C, León I, Alonso ER, Mata S, Alonso JL. Elucidating the multiple structures of pipecolic acid by rotational spectroscopy. Phys Chem Chem Phys 2019; 21:4155-4161. [PMID: 30520481 PMCID: PMC6478119 DOI: 10.1039/c8cp06120c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The complex conformational space of the non-proteinogenic cyclic amino acid pipecolic acid has been explored in the gas phase for the first time. Solid pipecolic acid samples were vaporized by laser ablation and expanded in a supersonic jet where the rotational spectral signatures owing to nine different conformers were observed by Fourier transform microwave spectroscopy. All species were identified by comparison of the experimental rotational and nuclear quadrupole coupling constants with those predicted theoretically. Observation of type-III conformers, leading to a difference when compared against the conformational behavior of the analog amino acid proline, has been interpreted by an increment in steric hindrance when increasing the number of carbons present in the ring.
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Affiliation(s)
- A Simão
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
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14
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Alonso JL, Peña I, López JC, Alonso ER, Vaquero V. The Shape of the Simplest Non-proteinogenic Amino Acid α-Aminoisobutyric Acid (Aib). Chemistry 2019; 25:2288-2294. [DOI: 10.1002/chem.201805038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/09/2018] [Indexed: 11/12/2022]
Affiliation(s)
- José L. Alonso
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorio de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
| | - Isabel Peña
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorio de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
| | - Juan C. López
- Departamento de Química Física e Inorgánica; Facultad de, Ciencias; Universidad de Valladolid; 47011 Valladolid Spain
| | - Elena R. Alonso
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorio de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
| | - Vanesa Vaquero
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorio de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
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15
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Alonso ER, León I, Kolesniková L, Alonso JL. The Structural Signs of Sweetness in Artificial Sweeteners: A Rotational Study of Sorbitol and Dulcitol. Chemphyschem 2018; 19:3334-3340. [DOI: 10.1002/cphc.201800977] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Elena R. Alonso
- Grupo de Espectroscopía Molecular (GEM) Edificio Quifima, Laboratorio de Espectroscopia y Bioespectroscopia Unidad Asociada CSIC, Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
| | - Iker León
- Grupo de Espectroscopía Molecular (GEM) Edificio Quifima, Laboratorio de Espectroscopia y Bioespectroscopia Unidad Asociada CSIC, Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
| | - Lucie Kolesniková
- Grupo de Espectroscopía Molecular (GEM) Edificio Quifima, Laboratorio de Espectroscopia y Bioespectroscopia Unidad Asociada CSIC, Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
| | - Jose L. Alonso
- Grupo de Espectroscopía Molecular (GEM) Edificio Quifima, Laboratorio de Espectroscopia y Bioespectroscopia Unidad Asociada CSIC, Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
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16
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Peña I, Sanz ME, Alonso ER, Alonso JL. The Multiple Hydrogen-Bonding Networks of Polyol Ribitol. Chemistry 2018; 24:13408-13412. [PMID: 30066382 DOI: 10.1002/chem.201803493] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 07/30/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Isabel Peña
- Department of Chemistry; King's College London; London SE1 1DB UK
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorio de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
| | | | - Elena R. Alonso
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorio de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
| | - José L. Alonso
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorio de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico Uva; Universidad de Valladolid; 47011 Valladolid Spain
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17
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León I, Peña I, Cabezas C, Alonso ER, Alonso JL. The last link of the x-aminobutyric acid series: the five conformers of β-aminobutyric acid. Phys Chem Chem Phys 2018; 20:15574-15580. [DOI: 10.1039/c8cp01734d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural characterization of β-aminobutyric acid by rotational spectroscopy.
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Affiliation(s)
- I. León
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - I. Peña
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - C. Cabezas
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - E. R. Alonso
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - J. L. Alonso
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
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18
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19
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Bermúdez C, Peña I, Mata S, Alonso JL. Sweet Structural Signatures Unveiled in Ketohexoses. Chemistry 2016; 22:16829-16837. [DOI: 10.1002/chem.201603223] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Celina Bermúdez
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorios de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; Paseo de Belén 5 47011 Valladolid Spain
| | - Isabel Peña
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorios de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; Paseo de Belén 5 47011 Valladolid Spain
| | - Santiago Mata
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorios de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; Paseo de Belén 5 47011 Valladolid Spain
| | - José L. Alonso
- Grupo de Espectroscopía Molecular (GEM); Edificio Quifima; Laboratorios de Espectroscopia y Bioespectroscopia; Unidad Asociada CSIC; Parque Científico Uva; Universidad de Valladolid; Paseo de Belén 5 47011 Valladolid Spain
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20
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Cabezas C, Robben MAT, Rijs AM, Peña I, Alonso JL. Fourier transform microwave spectroscopy of Ac-Ser-NH2: the role of side chain interactions in peptide folding. Phys Chem Chem Phys 2016; 17:20274-80. [PMID: 26186259 DOI: 10.1039/c5cp02654g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Serine capped dipeptide N-acetyl-l-serinamide (Ac-Ser-NH2) has been investigated using Fourier transform microwave spectroscopic techniques combined with laser ablation sources. Spectral signatures originating from one dominant species have been detected in the supersonic expansion. Rotational and nuclear quadrupole coupling constants of the two (14)N nuclei have been used in the characterization of a C/γ-turn structure, which is stabilized by a CO∙∙∙HN intramolecular hydrogen bond closing a seven-membered ring. Two extra hydrogen bonds involving the polar side chain (-CH2OH) further stabilize the structure. The non-observation of C5 species, attributed to the presence of the polar side chain, is in contrast with the previous gas phase observation of the related dipeptides containing glycine or alanine residues. The A-E splitting pattern arising from the internal rotation of the methyl group has been analyzed and the internal rotation barrier has been determined.
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Affiliation(s)
- Carlos Cabezas
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, Paseo de Belén 5, 47011 Valladolid, Spain.
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21
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Loru D, Peña I, Alonso JL, Sanz ME. Intramolecular interactions in the polar headgroup of sphingosine: serinol. Chem Commun (Camb) 2016; 52:3615-8. [PMID: 26727395 PMCID: PMC4766959 DOI: 10.1039/c5cc09423b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 12/15/2015] [Indexed: 01/04/2023]
Abstract
The intramolecular interactions in the lipid sphingosine have been elucidated through the investigation of the amino alcohol serinol which mimics its polar headgroup. Intricate networks of intramolecular hydrogen bonds involving the hydroxyl groups and the amino group contribute to the stabilisation of five different conformations observed in the broadband rotational spectrum.
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Affiliation(s)
- Donatella Loru
- Department of Chemistry, King's College London, London, SE1 1DB, UK.
| | - Isabel Peña
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia. Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Paseo de Belén 5, 47011 Valladolid, Spain
| | - José L Alonso
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia. Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Paseo de Belén 5, 47011 Valladolid, Spain
| | - M Eugenia Sanz
- Department of Chemistry, King's College London, London, SE1 1DB, UK.
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22
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Alonso ER, Peña I, Cabezas C, Alonso JL. Structural Expression of Exo-Anomeric Effect. J Phys Chem Lett 2016; 7:845-850. [PMID: 26889578 DOI: 10.1021/acs.jpclett.6b00028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Structural signatures for exo-anomeric effect have been extracted from the archetypal methyl-β-D-xyloside using broadband Fourier transform microwave spectroscopy combined with laser ablation. Spectrum analysis allows the determination of a set of rotational constants, which has been unequivocally attributed to conformer cc-β-(4)C1 g-, corresponding to the global minimum of the potential energy surface, where the aglycon residue (CH3) orientation contributes to maximization of the exo-anomeric effect. Further analysis allowed the determination of the rs structure, based on the detection of 11 isotopologues--derived from the presence of six (13)C and five (18)O atoms--observed in their natural abundances. The observed glycosidic C1-O1 bond length decrease (1.38 Å) can be interpreted in terms of the exo-anomeric effect. As such, the exo-anomeric effect presents itself as one of the main driving forces controlling the shape of many biologically important oligosaccharides.
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Affiliation(s)
- Elena R Alonso
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid , 47011 Valladolid, Spain
| | - Isabel Peña
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid , 47011 Valladolid, Spain
| | - Carlos Cabezas
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid , 47011 Valladolid, Spain
| | - José L Alonso
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid , 47011 Valladolid, Spain
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23
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Thorsheim K, Siegbahn A, Johnsson RE, Stålbrand H, Manner S, Widmalm G, Ellervik U. Chemistry of xylopyranosides. Carbohydr Res 2015; 418:65-88. [PMID: 26580709 DOI: 10.1016/j.carres.2015.10.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/09/2015] [Accepted: 10/10/2015] [Indexed: 12/22/2022]
Abstract
Xylose is one of the few monosaccharidic building blocks that are used by mammalian cells. In comparison with other monosaccharides, xylose is rather unusual and, so far, only found in two different mammalian structures, i.e. in the Notch receptor and as the linker between protein and glycosaminoglycan (GAG) chains in proteoglycans. Interestingly, simple soluble xylopyranosides can not only initiate the biosynthesis of soluble GAG chains but also function as inhibitors of important enzymes in the biosynthesis of proteoglycans. Furthermore, xylose is a major constituent of hemicellulosic xylans and thus one of the most abundant carbohydrates on Earth. Altogether, this has spurred a strong interest in xylose chemistry. The scope of this review is to describe synthesis of xylopyranosyl donors, as well as protective group chemistry, modifications, and conformational analysis of xylose.
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Affiliation(s)
- Karin Thorsheim
- Centre for Analysis and Synthesis, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Anna Siegbahn
- Centre for Analysis and Synthesis, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Richard E Johnsson
- Centre for Analysis and Synthesis, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Henrik Stålbrand
- Centre for Molecular Protein Science, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Sophie Manner
- Centre for Analysis and Synthesis, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ulf Ellervik
- Centre for Analysis and Synthesis, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
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Peña I, Cabezas C, Alonso JL. Unveiling epimerization effects: a rotational study of α-d-galactose. Chem Commun (Camb) 2015; 51:10115-8. [DOI: 10.1039/c5cc01783a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four conformers of α-d-galactose have been detected in the gas phase by laser ablation coupled with broadband Fourier transform microwave spectroscopy.
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Affiliation(s)
- Isabel Peña
- Grupo de Espectroscopía Molecular (GEM)
- Edificio Quifima, Área de Química-Física
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - Carlos Cabezas
- Grupo de Espectroscopía Molecular (GEM)
- Edificio Quifima, Área de Química-Física
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - José L. Alonso
- Grupo de Espectroscopía Molecular (GEM)
- Edificio Quifima, Área de Química-Física
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
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25
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Ring- and side-group conformational properties of di-O-acylated xylopyranosides: A computational study. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Peña I, Kolesniková L, Cabezas C, Bermúdez C, Berdakin M, Simão A, Alonso JL. The shape ofd-glucosamine. Phys Chem Chem Phys 2014; 16:23244-50. [DOI: 10.1039/c4cp03593c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Écija P, Evangelisti L, Vallejo M, Basterretxea FJ, Lesarri A, Castaño F, Caminati W, Cocinero EJ. Conformational flexibility of mephenesin. J Phys Chem B 2014; 118:5357-64. [PMID: 24754523 DOI: 10.1021/jp5014785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mephenesin molecule (3-(2-methylphenoxy)propane-1,2-diol) serves as a test bank to explore several structural and dynamical issues, such as conformational flexibility, the orientation of the carbon linear chain relative to the benzene plane, or the effect of substituent position on the rotational barrier of a methyl group. The molecule has been studied by rotational spectroscopy in the 4-18 GHz frequency range by Fourier-transform methods in a supersonic expansion. The experiment has been backed by a previous conformational search plus optimization of the lowest energy structures by ab initio and density functional quantum calculations. The three lowest-lying conformers that can interconvert to each other by simple bond rotations have been detected in the jet. Rotational parameters for all structures have been obtained, and methyl torsional barriers have been determined for the two lowest-lying rotamers. The lowest-lying structure of mephenesin is highly planar, with all carbon atoms lying nearly in the benzene ring plane, and is stabilized by the formation of cooperative intramolecular hydrogen bonding. An estimation of the relative abundance of the detected conformers indicates that the energetically most stable conformer will have an abundance near 80% at temperatures relevant for biological activity.
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Affiliation(s)
- Patricia Écija
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU) , Campus de Leioa, Ap. 644, E-48080 Bilbao, Spain
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Puzzarini C, Biczysko M, Barone V, Largo L, Peña I, Cabezas C, Alonso JL. Accurate Characterization of the Peptide Linkage in the Gas Phase: A Joint Quantum-Chemical and Rotational Spectroscopy Study of the Glycine Dipeptide Analogue. J Phys Chem Lett 2014; 5:534-540. [PMID: 26276605 DOI: 10.1021/jz402744a] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Accurate structures of aminoacids in the gas phase have been obtained by joint microwave and quantum-chemical investigations. However, the structure and conformational behavior of α-aminoacids once incorporated into peptide chains are completely different and have not yet been characterized with the same accuracy. To fill this gap, we present here an accurate characterization of the simplest dipeptide analogue (N-acetyl-glycinamide) involving peptidic bonds. State-of-the-art quantum-chemical computations are complemented by a comprehensive study of the rotational spectrum using a combination of Fourier transform microwave spectroscopy with laser ablation. The coexistence of the C7 and C5 conformers has been proved and energetically as well as spectroscopically characterized. This joint theoretical-experimental investigation demonstrated the feasibility of obtaining accurate structures for flexible small biomolecules, thus paving the route to the elucidation of the inherent behavior of peptides.
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Affiliation(s)
- Cristina Puzzarini
- †Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | | | - Vincenzo Barone
- ‡Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Laura Largo
- §Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, S-47005 Valladolid, Spain
| | - Isabel Peña
- §Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, S-47005 Valladolid, Spain
| | - Carlos Cabezas
- §Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, S-47005 Valladolid, Spain
| | - José Luis Alonso
- §Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, S-47005 Valladolid, Spain
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30
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Alonso JL, Lozoya MA, Peña I, López JC, Cabezas C, Mata S, Blanco S. The conformational behaviour of freed-glucose—at last. Chem Sci 2014. [DOI: 10.1039/c3sc52559g] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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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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Cabezas C, Peña I, Daly AM, Alonso JL. Erythrose revealed as furanose forms. Chem Commun (Camb) 2013; 49:10826-8. [DOI: 10.1039/c3cc46405a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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