1
|
Dong HC, Hsu PJ, Kuo JL. Searching low-energy conformers of neutral and protonated di-, tri-, and tetra-glycine using first-principles accuracy assisted by the use of neural network potentials. Phys Chem Chem Phys 2024; 26:11126-11139. [PMID: 38530660 DOI: 10.1039/d3cp05659g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
In the last ten years, combinations of state-of-the-art gas-phase spectroscopies and quantum chemistry calculations have suggested several intuitive trends in the structure of small polypeptides that may not hold true. For example, the preference for the cis form of the peptide bond and multiple protonated sites was proposed by comparing experimental spectra with low-energy minima obtained from limited structural sampling using various density functional theory methods. For understanding the structures of polypeptides, extensive sampling of their configurational space with high-accuracy computational methods is required. In this work, we demonstrated the use of deep-learning neural network potential (DL-NNP) to assist in exploring the structure and energy landscape of di-, tri-, and tetra-glycine with the accuracy of high-level quantum chemistry methods, and low-energy conformers of small polypeptides can be efficiently located. We hope that the structures of these polypeptides we found and our preliminary analysis will stimulate further experimental investigations.
Collapse
Affiliation(s)
- Hieu Cao Dong
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei 10617, Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan.
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei 10617, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Sanz‐Novo M, Mato M, León Í, Echavarren AM, Alonso JL. Shape‐Shifting Molecules: Unveiling the Valence Tautomerism Phenomena in Bare Barbaralones. Angew Chem Int Ed Engl 2022; 61:e202117045. [PMID: 35165988 PMCID: PMC9311078 DOI: 10.1002/anie.202117045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Indexed: 12/28/2022]
Abstract
We report a state‐of‐the‐art spectroscopic study of an archetypical barbaralone, conclusively revealing the valence tautomerism phenomena for this bistable molecular system. The two distinct 1‐ and 5‐substituted valence tautomers have been isolated in a supersonic expansion for the first time and successfully characterized by high‐resolution rotational spectroscopy. This work provides irrefutable experimental evidence of the [3,3]‐rearrangement in barbaralones and highlights the use of rotational spectroscopy to analyze shape‐shifting mixtures. Moreover, this observation opens the window toward the characterization of new fluxional systems in the isolation conditions of the gas phase and should serve as a reference point in the general understanding of valence tautomerism.
Collapse
Affiliation(s)
- Miguel Sanz‐Novo
- Grupo de Espectroscopía Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopía y Bioespectroscopía Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| | - Mauro Mato
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science and Technology Av. Països Catalans 16 43007 Tarragona Spain
- Departament de Química Analítica i Química Orgànica Universitat Rovira i Virgili C/Marcel⋅li Domingo s/n 43007 Tarragona Spain
| | - Íker León
- Grupo de Espectroscopía Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopía y Bioespectroscopía Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| | - Antonio M. Echavarren
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science and Technology Av. Països Catalans 16 43007 Tarragona Spain
- Departament de Química Analítica i Química Orgànica Universitat Rovira i Virgili C/Marcel⋅li Domingo s/n 43007 Tarragona Spain
| | - José L. Alonso
- Grupo de Espectroscopía Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopía y Bioespectroscopía Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| |
Collapse
|
4
|
Sanz‐Novo M, Mato M, León Í, Echavarren AM, Alonso JL. Shape‐Shifting Molecules: Unveiling the Valence Tautomerism Phenomena in Bare Barbaralones. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Miguel Sanz‐Novo
- Grupo de Espectroscopía Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopía y Bioespectroscopía Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| | - Mauro Mato
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science and Technology Av. Països Catalans 16 43007 Tarragona Spain
- Departament de Química Analítica i Química Orgànica Universitat Rovira i Virgili C/Marcel⋅li Domingo s/n 43007 Tarragona Spain
| | - Íker León
- Grupo de Espectroscopía Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopía y Bioespectroscopía Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| | - Antonio M. Echavarren
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science and Technology Av. Països Catalans 16 43007 Tarragona Spain
- Departament de Química Analítica i Química Orgànica Universitat Rovira i Virgili C/Marcel⋅li Domingo s/n 43007 Tarragona Spain
| | - José L. Alonso
- Grupo de Espectroscopía Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopía y Bioespectroscopía Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| |
Collapse
|
5
|
Juárez G, Sanz-Novo M, Alonso JL, Alonso ER, León I. Rotational Spectrum and Conformational Analysis of Perillartine: Insights into the Structure-Sweetness Relationship. Molecules 2022; 27:molecules27061924. [PMID: 35335289 PMCID: PMC8954681 DOI: 10.3390/molecules27061924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 11/29/2022] Open
Abstract
We used high-resolution rotational spectroscopy coupled to a laser ablation source to study the conformational panorama of perillartine, a solid synthetic sweetener. Four conformers were identified under the isolation conditions of the supersonic expansion, showing that all of them present an E configuration of the C=N group with respect to the double bond of the ring. The observed structures were verified against Shallenberger–Acree–Kier’s sweetness theory to shed light on the structure–sweetness relationship for this particular oxime, highlighting a deluge of possibilities to bind the receptor.
Collapse
|
6
|
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...
Collapse
|
7
|
Kolesniková L, León I, Alonso ER, Mata S, Alonso JL. An Innovative Approach for the Generation of Species of the Interstellar Medium. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Lucie Kolesniková
- Department of Analytical Chemistry University of Chemistry and Technology Technická 5 16628 Prague 6 Czech Republic
| | - Iker León
- Grupo de Espectroscopia Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopia y, Bioespectroscopia Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| | - Elena R. Alonso
- Instituto Biofisika (UPV/EHU, CSIC) University of the Basque Country 48940 Leioa Spain
- Departamento de Química Física Facultad de Ciencia y Tecnología Universidad del País Vasco Barrio Sarriena s/n 48940 Leioa Spain
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopia y, Bioespectroscopia Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| | - Jose Luis Alonso
- Grupo de Espectroscopia Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopia y, Bioespectroscopia Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| |
Collapse
|
8
|
Kolesniková L, León I, Alonso ER, Mata S, Alonso JL. An Innovative Approach for the Generation of Species of the Interstellar Medium. Angew Chem Int Ed Engl 2021; 60:24461-24466. [PMID: 34496111 PMCID: PMC8597129 DOI: 10.1002/anie.202110325] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/02/2021] [Indexed: 11/16/2022]
Abstract
The large amount of unstable species in the realm of interstellar chemistry drives an urgent need to develop efficient methods for the in situ generations of molecules that enable their spectroscopic characterizations. Such laboratory experiments are fundamental to decode the molecular universe by matching the interstellar and terrestrial spectra. We propose an approach based on laser ablation of nonvolatile solid organic precursors. The generated chemical species are cooled in a supersonic expansion and probed by high‐resolution microwave spectroscopy. We present a proof of concept through a simultaneous formation of interstellar compounds and the first generation of aminocyanoacetylene using diaminomaleonitrile as a prototypical precursor. With this micro‐laboratory, we open the door to generation of unsuspected species using precursors not typically accessible to traditional techniques such as electric discharge and pyrolysis.
Collapse
Affiliation(s)
- Lucie Kolesniková
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Iker León
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopia y, Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Elena R Alonso
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940, Leioa, Spain.,Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena s/n, 48940, Leioa, Spain
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopia y, Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Jose Luis Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopia y, Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, 47011, Valladolid, Spain
| |
Collapse
|
9
|
León I, Alonso ER, Mata S, Alonso JL. Shape of Testosterone. J Phys Chem Lett 2021; 12:6983-6987. [PMID: 34283615 PMCID: PMC8327310 DOI: 10.1021/acs.jpclett.1c01743] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
We have successfully characterized the structure of testosterone, one of the essential steroids, through high-resolution rotational spectroscopy. A single conformer has been detected, and a total of 404 transitions have been fitted, allowing a precise determination of the rotational constants. It allowed us to unravel that the isolated structure of testosterone adopts an extended disposition. The results obtained in this work highlight how using laser ablation techniques in combination with Fourier transform microwave techniques allow the study of large biomolecules or common pharmaceuticals. It is an important step toward studying relevant biomolecules and developing new analytical techniques with unprecedented sensitivity and resolution.
Collapse
Affiliation(s)
- 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
| | - Elena R. Alonso
- Instituto
Biofisika (UPV/EHU, CSIC), University of
the Basque Country, 48940 Leioa, Spain
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena s/n, 48940 Leioa, 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 L. 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
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Chakraborty D, Banerjee A, Wales DJ. Side-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides. J Phys Chem B 2021; 125:5809-5822. [PMID: 34037392 PMCID: PMC8279551 DOI: 10.1021/acs.jpcb.1c02412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
intrinsic conformational preferences of small peptides may
provide additional insight into the thermodynamics and kinetics of
protein folding. In this study, we explore the underlying energy landscapes
of two model peptides, namely, Ac-Ala-NH2 and Ac-Ser-NH2, using geometry-optimization-based tools developed within
the context of energy landscape theory. We analyze not only how side-chain
polarity influences the structural preferences of the dipeptides,
but also other emergent properties of the landscape, including heat
capacity profiles, and kinetics of conformational rearrangements.
The contrasting topographies of the free energy landscape agree with
recent results from Fourier transform microwave spectroscopy experiments,
where Ac-Ala-NH2 was found to exist as a mixture of two
conformers, while Ac-Ser-NH2 remained structurally locked,
despite exhibiting an apparently rich conformational landscape.
Collapse
Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Atreyee Banerjee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
12
|
León I, Alonso ER, Mata S, Alonso JL. A rotational study of the AlaAla dipeptide. Phys Chem Chem Phys 2020; 22:13867-13871. [PMID: 32368774 DOI: 10.1039/d0cp01043j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we present the first rotational study of the AlaAla dipeptide, brought into the gas phase by laser ablation. Two different structures have been unveiled in the isolated environment of a supersonic expansion by Fourier transform microwave spectroscopy. These structures have been identified through their rotational and 14N quadrupole coupling constants. The flexibility of the -NH2 and -COOH ends allows the formation of strong intramolecular interactions giving rise to five- and seven-membered ring configurations.
Collapse
Affiliation(s)
- I 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.
| | - E R 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. and Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, E-48940, Spain and Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, E-48940, Spain
| | - S 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.
| | - J L 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.
| |
Collapse
|
13
|
León I, Alonso ER, Mata S, Cabezas C, Alonso JL. Unveiling the Neutral Forms of Glutamine. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Iker León
- Grupo de Espectrocopía Molecular (GEM)Edificio QuifimaLaboratorios de Espectroscopia y BioespectroscopiaUnidad Asociada CSICParque Científico UVaUniversidad de Valladolid 47011 Valladolid Spain
| | - Elena R. Alonso
- Grupo de Espectrocopía Molecular (GEM)Edificio QuifimaLaboratorios de Espectroscopia y BioespectroscopiaUnidad Asociada CSICParque Científico UVaUniversidad de Valladolid 47011 Valladolid Spain
| | - Santiago Mata
- Grupo de Espectrocopía Molecular (GEM)Edificio QuifimaLaboratorios de Espectroscopia y BioespectroscopiaUnidad Asociada CSICParque Científico UVaUniversidad de Valladolid 47011 Valladolid Spain
| | - Carlos Cabezas
- Grupo de Espectrocopía Molecular (GEM)Edificio QuifimaLaboratorios de Espectroscopia y BioespectroscopiaUnidad Asociada CSICParque Científico UVaUniversidad de Valladolid 47011 Valladolid Spain
| | - Jose Luis Alonso
- Grupo de Espectrocopía Molecular (GEM)Edificio QuifimaLaboratorios de Espectroscopia y BioespectroscopiaUnidad Asociada CSICParque Científico UVaUniversidad de Valladolid 47011 Valladolid Spain
| |
Collapse
|
14
|
León I, Alonso ER, Mata S, Cabezas C, Alonso JL. Unveiling the Neutral Forms of Glutamine. Angew Chem Int Ed Engl 2019; 58:16002-16007. [DOI: 10.1002/anie.201907222] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/21/2019] [Indexed: 11/08/2022]
Affiliation(s)
- 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
| | - Elena R. 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
| | - 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
| | - Carlos Cabezas
- Grupo de Espectrocopía Molecular (GEM) Edificio Quifima Laboratorios de Espectroscopia y Bioespectroscopia Unidad Asociada CSIC Parque Científico UVa Universidad de Valladolid 47011 Valladolid Spain
| | - Jose 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
| |
Collapse
|
15
|
Uriarte I, Reviriego F, Calabrese C, Elguero J, Kisiel Z, Alkorta I, Cocinero EJ. Bond Length Alternation Observed Experimentally: The Case of 1H‐Indazole. Chemistry 2019; 25:10172-10178. [DOI: 10.1002/chem.201901666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Iciar Uriarte
- Departamento de Química Física, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Apartado 644 48080 Bilbao Spain
- Biofisika InstituteCSICUPV/EHU Apartado 644 48080 Bilbao Spain
| | - Felipe Reviriego
- Instituto de Ciencia y Tecnología de Polímeros (ICTP)CSIC c/Juan de la Cierva, 3 28006 Madrid Spain
| | - Camilla Calabrese
- Departamento de Química Física, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Apartado 644 48080 Bilbao Spain
- Biofisika InstituteCSICUPV/EHU Apartado 644 48080 Bilbao Spain
| | - José Elguero
- Instituto de Química MédicaCSIC C/Juan de la Cierva, 3 28006 Madrid Spain
| | - Zbigniew Kisiel
- Institute of PhysicsPolish Academy of Sciences Al. Lotnikow 32/46 02-668 Warszawa Poland
| | - Ibon Alkorta
- Instituto de Química MédicaCSIC C/Juan de la Cierva, 3 28006 Madrid Spain
| | - Emilio J. Cocinero
- Departamento de Química Física, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Apartado 644 48080 Bilbao Spain
- Biofisika InstituteCSICUPV/EHU Apartado 644 48080 Bilbao Spain
| |
Collapse
|
16
|
Kolesniková L, León I, Alonso ER, Mata S, Alonso JL. Laser Ablation Assists Cyclization Reactions of Hydantoic Acid: A Proof for the Near-Attack Conformation Theory? J Phys Chem Lett 2019; 10:1325-1330. [PMID: 30807178 PMCID: PMC6534498 DOI: 10.1021/acs.jpclett.9b00208] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In the course of the investigation of the rotational spectrum of prebiotic hydantoic acid by Fourier transform microwave spectroscopy coupled to a laser ablation source in a supersonic expansion, rotational signatures of two cyclic molecules, hydantoin and 2,5-oxazolidinedione, have been unexpectedly observed along with the four most stable conformers of hydantoic acid. Interestingly, two of them presented folded geometric arrangements that might act as precursors in the cyclization reactions assisted by laser ablation. They could play the role of near-attack conformations (NACs) in the framework of the NAC theory for intramolecular reactions. A detailed analysis of the spectrum further revealed the simultaneous formation of other species in the jet, showing that the laser ablation of solid organic precursors constitutes an alternative tool in the generation of new chemical species.
Collapse
Affiliation(s)
- Lucie Kolesniková
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Laboratorios de Espectroscopia y Bioespectroscopia, Edificio Quifima, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Iker León
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Laboratorios de Espectroscopia y Bioespectroscopia, Edificio Quifima, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Elena R. Alonso
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Laboratorios de Espectroscopia y Bioespectroscopia, Edificio Quifima, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Laboratorios de Espectroscopia y Bioespectroscopia, Edificio Quifima, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Jose L. Alonso
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Laboratorios de Espectroscopia y Bioespectroscopia, Edificio Quifima, Universidad de Valladolid, 47011 Valladolid, Spain
| |
Collapse
|
17
|
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
| |
Collapse
|
18
|
León I, Alonso ER, Cabezas C, Mata S, Alonso JL. Unveiling the n→π* interactions in dipeptides. Commun Chem 2019. [DOI: 10.1038/s42004-018-0103-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
|