1
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Dauletyarov Y, Wang S, Horke DA. Vaporization of Intact Neutral Biomolecules Using Laser-Based Thermal Desorption. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37319337 DOI: 10.1021/jasms.3c00194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The production of a clean neutral molecular sample is a crucial step in many gas-phase spectroscopy and reaction dynamics experiments investigating neutral species. Unfortunately, conventional methods based on heating cannot be used with most nonvolatile biomolecules due to their thermal instability. In this paper, we demonstrate the application of laser-based thermal desorption (LBTD) to produce neutral molecular plumes of biomolecules such as dipeptides and lipids. Specifically, we report mass spectra of glycylglycine, glycyl-l-alanine, and cholesterol obtained using LBTD vaporization, followed by soft femtosecond multiphoton ionization (fs-MPI) at 400 nm. For all molecules, the signal from the intact precursor ion was observed, highlighting the softness and applicability of the LBTD and fs-MPI approach. In more detail, cholesterol underwent hardly any fragmentation. Both dipeptides fragmented significantly, although mostly through only a single channel, which we attribute to the fs-MPI process.
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Affiliation(s)
- Yerbolat Dauletyarov
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Siwen Wang
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Daniel A Horke
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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2
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Sanz-Novo M, Kolesniková L, Insausti A, Alonso JL, León I, Alonso ER. A journey across dopamine Metabolism: A rotational study of DOPAC. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 290:122303. [PMID: 36608514 DOI: 10.1016/j.saa.2022.122303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
DOPAC, a relevant scaffold in dopamine metabolism, was probed in the gas phase and interrogated by high-resolution rotational spectroscopy. Herein, three distinct conformers were isolated in a supersonic jet and identified for the first time through an examination of the trend of the rotational constants and the dipole moment selection rules. Additionally, we examined the plausible relaxation pathways of the low-energy conformers of DOPAC, which helped us to claim the indirect detection of two additional conformers, providing conclusive experimental evidence of the flexible nature of this biomolecule. The current investigation sheds some light on the differences between jet-cooled rotational experiments and matrix-isolation infrared spectroscopy.
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Affiliation(s)
- Miguel Sanz-Novo
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Lucie Kolesniková
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 166 28 Prague 6, Czech Republic
| | - Aran Insausti
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/ EHU), 48940 Leioa, Spain
| | - José L Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Iker León
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Elena R Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
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3
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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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4
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Aguado R, Mata S, Sanz-Novo M, Alonso ER, León I, Alonso JL. The Nicotinic Agonist Cytisine: The Role of the NH···N Interaction. J Phys Chem Lett 2022; 13:9991-9996. [PMID: 36264108 PMCID: PMC9619914 DOI: 10.1021/acs.jpclett.2c02021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
We report a detailed structural study of cytisine, an alkaloid used to help with smoking cessation, looking forward to unveiling its role as a nicotinic agonist. High-resolution rotational spectroscopy has allowed us to characterize two different conformers exhibiting axial and equatorial arrangements of the piperidinic NH group. Unexpectedly, the axial form has been found as the predominant configuration, in contrast to that observed for related molecules, such as piperidine. This anomalous behavior has been justified in terms of an intramolecular NH···N hydrogen bond. Moreover, this interaction justifies the overstabilization of the axial conformer over the equatorial one and is crucial for the mechanism of action of cytisine over the nicotinic receptor, further rationalizing its behavior as a nicotinic agonist.
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Affiliation(s)
- Raúl Aguado
- 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
| | - Santiago Mata
- 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
| | - 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
| | - Elena R. 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
| | - Iker 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
| | - 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
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5
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León I, Fusè M, Alonso ER, Mata S, Mancini G, Puzzarini C, Alonso JL, Barone V. Unbiased disentanglement of conformational baths with the help of microwave spectroscopy, quantum chemistry and artificial intelligence: the puzzling case of homocysteine. J Chem Phys 2022; 157:074107. [DOI: 10.1063/5.0102841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An integrated experimental-computational strategy for the accurate characterization of the conformational landscape of flexible biomolecule building blocks is proposed. This is based on the combination of rotational spectroscopy with quantum-chemical computations guided by artificial intelligence tools. The first step of the strategy is the conformer search and relative stability evaluation performed by means of an evolutionary algorithm. In this step, last generation semiempirical methods are exploited together with hybrid and double-hybrid density functionals. Next, the barriers ruling the interconversion between the low-lying conformers are evaluated in order to unravel possible fast relaxation paths. The relative stabilities and spectroscopic parameters of the ``surviving' conformers are then refined using state-of-the-art composite schemes. The reliability of the computational procedure is further improved by the inclusion of vibrational and thermal effects. The final step of the strategy is the comparison between experiment and theory without any ad hoc adjustment, which allows an unbiased assignment of the spectroscopic features in terms of different conformers and their spectroscopic parameters. The proposed approach has been tested and validated for homocysteine, a highly flexible non-proteinogenic alpha-amino acid. The synergism of the integrated strategy allowed the characterization of five conformers stabilized by bifurcated N-H-O=C hydrogen bonds, together with an additional conformer involving a more conventional HNH-O hydrogen bond. The stability order estimated from the experimental intensities as well as the number and type of conformers observed in the gas phase are in full agreement with the theoretical predictions. Analogously, a good match has been found for the spectroscopic parameters.
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Affiliation(s)
- Iker León
- Universidad de Valladolid - Campus Miguel Delibes, Spain
| | | | - Elena R. Alonso
- Química Física y Química Inorgánica, Universidad de Valladolid, Spain
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM). Edificio Quifima. Laboratorios de Espectroscopia y Bioespectroscopia. Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Spain
| | | | | | - Jose L. Alonso
- Grupo de Espectroscopia Molecular (GEM). Edificio Quifima. Laboratorios de Espectroscopia y Bioespectroscopia, Universidad de Valladolid Departamento Química Física y Química Inorgánica, Spain
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6
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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.
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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
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7
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An MP2/Molecular Dynamics study of the solvent effects on the conformational equilibrium of the glycine dipeptide. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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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
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9
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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.
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10
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Buschmann P, Lengsfeld KG, Djahandideh J, Grabow JU. From rotational resolved spectra to an extended increment system of planar moments allowing ad-hoc conformational identification – Exemplification by the broadband microwave spectrum of α-hydroxyisobutyric acid. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131805] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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11
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Wang P, Shu C, Ye H, Biczysko M. Structural and Energetic Properties of Amino Acids and Peptides Benchmarked by Accurate Theoretical and Experimental Data. J Phys Chem A 2021; 125:9826-9837. [PMID: 34752094 DOI: 10.1021/acs.jpca.1c06504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Structural, energetic, and spectroscopic data derived in this work aim at the setup of an "experimentally validated" database for amino acids and polypeptides conformers. First, the "cheap" composite scheme (ChS, CCSD(T)/(CBS+CV)MP2) is tested for evaluation of conformational energies of all eight stable conformers of glycine, by comparing to the more accurate CCSD(T)/CBS+CV computations (Phys. Chem. Chem. Phys. 2013, 15, 10094-10111 and J Mol. Model. 2020, 26, 129). The recently proposed jun-ChS (J. Chem. Theory and Comput. 2020, 16, 988-1006), employing the jun-cc-pVnZ basis set family for CCSD(T) computations and CBS extrapolation, yields conformational energies accurate to 0.2 kJ·mol-1, at reduced computational cost with respect to aug-ChS employing aug-cc-pVnZ basis sets. The jun-ChS composite scheme is further applied to derive conformational energies for three dipeptide analogues Ac-Gly-NH2, Ac-Ala-NH2, and Gly-Gly. Finally, dipeptide conformational energies and semiexperimental equilibrium rotational constants along with the CCSD(T)/(CBS+CV)MP2 structural parameters (J. Phys. Chem. Lett. 2014, 5, 534-540) stand as the reference for benchmarking of selected density functional methodologies. The double-hybrid functionals B2-PLYP-D3(BJ) and DSD-PBEP86, perform best for structural and energetic characterization of all dipeptide analogues. From hybrid functionals CAM-B3LYP-D3(BJ) and ωB97X-D3(BJ) represent promising methods applicable for larger peptide-based systems for which computations with double-hybrid functionals are not feasible.
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Affiliation(s)
- Ping Wang
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Chong Shu
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Hexu Ye
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
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12
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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
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13
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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.
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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
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14
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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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15
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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: 0] [Impact Index Per Article: 0] [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.
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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
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16
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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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17
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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18
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Thomas DA, Chang R, Mucha E, Lettow M, Greis K, Gewinner S, Schöllkopf W, Meijer G, von Helden G. Probing the conformational landscape and thermochemistry of DNA dinucleotide anions via helium nanodroplet infrared action spectroscopy. Phys Chem Chem Phys 2020; 22:18400-18413. [PMID: 32797142 DOI: 10.1039/d0cp02482a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Isolation of biomolecules in vacuum facilitates characterization of the intramolecular interactions that determine three-dimensional structure, but experimental quantification of conformer thermochemistry remains challenging. Infrared spectroscopy of molecules trapped in helium nanodroplets is a promising methodology for the measurement of thermochemical parameters. When molecules are captured in a helium nanodroplet, the rate of cooling to an equilibrium temperature of ca. 0.4 K is generally faster than the rate of isomerization, resulting in "shock-freezing" that kinetically traps molecules in local conformational minima. This unique property enables the study of temperature-dependent conformational equilibria via infrared spectroscopy at 0.4 K, thereby avoiding the deleterious effects of spectral broadening at higher temperatures. Herein, we demonstrate the first application of this approach to ionic species by coupling electrospray ionization mass spectrometry (ESI-MS) with helium nanodroplet infrared action spectroscopy to probe the structure and thermochemistry of deprotonated DNA dinucleotides. Dinucleotide anions were generated by ESI, confined in an ion trap at temperatures between 90 and 350 K, and entrained in traversing helium nanodroplets. The infrared action spectra of the entrained ions show a strong dependence on pre-pickup ion temperature, consistent with the preservation of conformer population upon cooling to 0.4 K. Non-negative matrix factorization was utilized to identify component conformer infrared spectra and determine temperature-dependent conformer populations. Relative enthalpies and entropies of conformers were subsequently obtained from a van't Hoff analysis. IR spectra and conformer thermochemistry are compared to results from ion mobility spectrometry (IMS) and electronic structure methods. The implementation of ESI-MS as a source of dopant molecules expands the diversity of molecules accessible for thermochemical measurements, enabling the study of larger, non-volatile species.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
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19
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Sanz-Novo M, Belloche A, Alonso JL, Kolesniková L, Garrod RT, Mata S, Müller HSP, Menten KM, Gong Y. Interstellar glycolamide: A comprehensive rotational study and an astronomical search in Sgr B2(N). ASTRONOMY AND ASTROPHYSICS 2020; 639:A135. [PMID: 33154598 PMCID: PMC7116316 DOI: 10.1051/0004-6361/202038149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
CONTEXT Glycolamide is a glycine isomer and also one of the simplest derivatives of acetamide (e.g., one hydrogen atom is replaced with a hydroxyl group), which is a known interstellar molecule. AIMS In this context, the aim of our work is to provide direct experimental frequencies of the ground vibrational state of glycolamide in the centimeter-, millimeter- and submillimeter-wavelength regions in order to enable its identification in the interstellar medium. METHODS We employed a battery of state-of-the-art rotational spectroscopic techniques in the frequency and time domain to measure the frequencies of glycolamide. We used the spectral line survey named Exploring Molecular Complexity with ALMA (EMoCA), which was performed toward the star forming region Sgr B2(N) with ALMA to search for glycolamide in space. We also searched for glycolamide toward Sgr B2(N) with the Effelsberg radio telescope. The astronomical spectra were analyzed under the local thermodynamic equilibrium approximation. We used the gas-grain chemical kinetics model MAGICKAL to interpret the results of the astronomical observations. RESULTS About 1500 transitions have been newly assigned up to 460 GHz to the most stable conformer, and a precise set of spectroscopic constants was determined. Spectral features of glycolamide were then searched for in the prominent hot molecular core Sgr B2(N2). We report the nondetection of glycolamide toward this source with an abundance at least six and five times lower than that of acetamide and glycolaldehyde, respectively. Our astrochemical model suggests that glycolamide may be present in this source at a level just below the upper limit, which was derived from the EMoCA survey. We could also not detect the molecule in the region's extended molecular envelope, which was probed with the Effelsberg telescope. We find an upper limit to its column density that is similar to the column densities obtained earlier for acetamide and glycolaldehyde with the Green Bank Telescope.
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Affiliation(s)
- M Sanz-Novo
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopía y Bioespectroscopía, Parque Científico UVa, Unidad Asociada CSIC, E-47011 Valladolid, Spain
| | - A Belloche
- Max-Planck-Institut für Radioastronomie, Auf dem Hügel 69, 53121 Bonn, Germany
| | - J L Alonso
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopía y Bioespectroscopía, Parque Científico UVa, Unidad Asociada CSIC, E-47011 Valladolid, Spain
| | - L Kolesniková
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopía y Bioespectroscopía, Parque Científico UVa, Unidad Asociada CSIC, E-47011 Valladolid, Spain
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 166 28 Prague 6, Czech Republic
| | - R T Garrod
- Departments of Chemistry and Astronomy, University of Virginia, Charlottesville, VA 22904, USA
| | - S Mata
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopía y Bioespectroscopía, Parque Científico UVa, Unidad Asociada CSIC, E-47011 Valladolid, Spain
| | - H S P Müller
- I. Physikalisches Institut, Universität zu Köln, Zülpicher Str. 77, 50937 Köln, Germany
| | - K M Menten
- Max-Planck-Institut für Radioastronomie, Auf dem Hügel 69, 53121 Bonn, Germany
| | - Y Gong
- Max-Planck-Institut für Radioastronomie, Auf dem Hügel 69, 53121 Bonn, Germany
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20
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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
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21
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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
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22
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Kumar S, Mishra KK, Singh SK, Borish K, Dey S, Sarkar B, Das A. Observation of a weak intra-residue C5 hydrogen-bond in a dipeptide containing Gly-Pro sequence. J Chem Phys 2019; 151:104309. [DOI: 10.1063/1.5115040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Satish Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Kamal K. Mishra
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Santosh K. Singh
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Sanjit Dey
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Biplab Sarkar
- Department of Chemistry, North Eastern Hill University, Shillong, Meghalaya 793022, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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23
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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
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24
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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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25
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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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26
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Yatsyna V, Mallat R, Gorn T, Schmitt M, Feifel R, Rijs AM, Zhaunerchyk V. Conformational Preferences of Isolated Glycylglycine (Gly-Gly) Investigated with IRMPD-VUV Action Spectroscopy and Advanced Computational Approaches. J Phys Chem A 2019; 123:862-872. [DOI: 10.1021/acs.jpca.8b10881] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Vasyl Yatsyna
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Ranim Mallat
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Tim Gorn
- Institut für Physikalische Chemie I, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Michael Schmitt
- Institut für Physikalische Chemie I, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Raimund Feifel
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Anouk M. Rijs
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Vitali Zhaunerchyk
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
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27
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Chandramouli B, Del Galdo S, Mancini G, Tasinato N, Barone V. Tailor-made computational protocols for precise characterization of small biological building blocks using QM and MM approaches. Biopolymers 2018. [DOI: 10.1002/bip.23109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Balasubramanian Chandramouli
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Compunet, Istituto Italiano di Tecnologia, via Morego 30; Genova Italy
| | - Sara Del Galdo
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
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Abstract
The benefits of vaporization by laser ablation and the high resolution and sensitivity attained by the chirped pulse Fourier transform microwave spectroscopy CP-FTMW have provided the first conformational map of the simplest phenolic acids of trans-cinnamic and p-coumaric. Two conformers of trans-cinnamic acid and four conformers of trans-p-coumaric acid have been characterized under the isolation conditions of a supersonic expansion. The spectroscopic constants derived from the analysis of the rotational spectra compared with those predicted theoretically provide an unmatched means to achieve an unambiguous identification of the observed species.
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Affiliation(s)
- Vanessa Cortijo
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Cientı́fico UVa, Unidad Asociada CSIC, Universidad de Valladolid , 47011, Valladolid, Spain
| | - Elena R Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Cientı́fico UVa, Unidad Asociada CSIC, Universidad de Valladolid , 47011, Valladolid, Spain
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Cientı́fico UVa, Unidad Asociada CSIC, Universidad de Valladolid , 47011, Valladolid, Spain
| | - José L Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Cientı́fico UVa, Unidad Asociada CSIC, Universidad de Valladolid , 47011, Valladolid, Spain
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29
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Yang B, Liu S, Lin Z. Computational study on single molecular spectroscopy of tyrosin-glycine, tryptophane-glycine and glycine-tryptophane. Sci Rep 2017; 7:15869. [PMID: 29158576 PMCID: PMC5696477 DOI: 10.1038/s41598-017-16234-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/09/2017] [Indexed: 12/29/2022] Open
Abstract
Quantum chemistry calculations play a fundamental role in revealing the molecular structures observed in gas-phase spectroscopic measurements. The supersonic jet cooling widely used in single molecular spectroscopy experiment is a non-equilibrium process and often causes confusion on the theoretical and experimental comparison. A computational approach is proposed here to account for the effect of the non-equilibrium cooling on the experimental spectra and applied to the cases of tyrosin-glycine (YG), tryptophane-glycine (WG) and glycine-tryptophane (GW). The low energy conformers of YG, WG and GW are obtained through thorough conformational searches. The structural features and equilibrium distributions of conformations and the energy barriers for conformer conversions are then determined. Three classes of transition energy barriers, high, medium and low, are found for the conversions among conformers with distinctly different, similar and the same structural types, respectively. The final conformation populations are determined by assuming an initial temperature of about 450 K and allowing for only the conformation conversion with a low energy barrier to occur during the rapid cooling process. The results provide a natural explanation for the numbers of YG, WG and GW conformations observed experimentally. The theoretical conformation assignments are also in good agreement with the experimental IR data.
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Affiliation(s)
- Bing Yang
- Hefei National Laboratory for Physical Sciences at Microscale & CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Department of Physics, University of Science and Technology of China, Hefei, 230026, China
| | - Shixue Liu
- Department of Nanotechnology for Sustainable Energy, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo, 669-1337, Japan
| | - Zijing Lin
- Hefei National Laboratory for Physical Sciences at Microscale & CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Department of Physics, University of Science and Technology of China, Hefei, 230026, China.
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