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de la Puente S, Espinoza ML, Carrillo I, Rico C, Souto H, Acedo JA, Riñón C, Garcés C, Ramos P, Muñoz D, Zamora B, Espinosa R, Huertas AL, Rozas I, González M, Martín A, Alonso JL. Hemorrhagic cystitis following allogeneic hematopoietic stem cell transplantation: experience in a pediatric oncological institution. Cir Pediatr 2023; 36:128-134. [PMID: 37417217 DOI: 10.54847/cp.2023.03.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
OBJECTIVE To analyze the risk factors associated with hemorrhagic cystitis (HC) severity and the treatment strategies available in HC patients following allogeneic hematopoietic stem cell transplantation (AHSCT). MATERIALS AND METHODS A retrospective study of medical records was carried out. Patients with HC following AHSCT treated from 2017 to 2021 were divided into two groups according to severity -mild and severe. Demographic data, disease-specific characteristics, urological sequelae, and overall mortality were compared between both groups. The hospital's protocol was used for patient management. RESULTS 33 episodes of HC were collected in 27 patients, 72.7% of whom were male. HC incidence following AHSCT was 23.4% (33/141). 51.5% of HCs were severe (grades III-IV). Severe graft host disease (GHD) (grades III-IV) and thrombopenia at HC onset were associated with severe HC (p= 0.043 and p= 0.039, respectively). This group had longer hematuria times (p< 0.001) and required more platelet transfusions (p= 0.003). In addition, 70.6% required bladder catheterization, but only 1 case needed percutaneous cystostomy. None of the patients with mild HC required catheterization. No differences were found in terms of urological sequelae or overall mortality. CONCLUSIONS Severe HC could be predicted thanks to the presence of severe GHD or thrombopenia at HC onset. Severe HC can be managed with bladder catheterization in most of these patients. A standardized protocol may help reduce the need for invasive procedures in patients with mild HC.
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Affiliation(s)
- S de la Puente
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - M L Espinoza
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - I Carrillo
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - C Rico
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - H Souto
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - J A Acedo
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - C Riñón
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - C Garcés
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - P Ramos
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - D Muñoz
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - B Zamora
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - R Espinosa
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - A L Huertas
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - I Rozas
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - M González
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
| | - A Martín
- Hospital La Paz Reference coordination. Madrid (Spain)
| | - J L Alonso
- Pediatric Surgery Department. Hospital Infantil Universitario Niño Jesús. Madrid (Spain)
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Barone V, Fusè M, Aguado R, Potenti S, León I, Alonso ER, Mata S, Lazzari F, Mancini G, Spada L, Gualandi A, Cozzi PG, Puzzarini C, Alonso JL. Bringing Machine-Learning Enhanced Quantum Chemistry and Microwave Spectroscopy to Conformational Landscape Exploration: the Paradigmatic Case of 4-Fluoro-Threonine. Chemistry 2023; 29:e202203990. [PMID: 36734519 DOI: 10.1002/chem.202203990] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/04/2023]
Abstract
A combined experimental and theoretical study has been carried out on 4-fluoro-threonine, the only naturally occurring fluorinated amino acid. Fluorination of the methyl group significantly increases the conformational complexity with respect to the parent amino acid threonine. The conformational landscape has been characterized in great detail, with special attention given to the inter-conversion pathways between different conformers. This led to the identification of 13 stable low-energy minima. The equilibrium population of so many conformers produces a very complicated and congested rotational spectrum that could be assigned through a strategy that combines several levels of quantum chemical calculations with the principles of machine learning. Twelve conformers out of 13 could be experimentally characterized. The results obtained from the analysis of the intra-molecular interactions can be exploited to accurately model fluorine-substitution effects in biomolecules.
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Affiliation(s)
- V Barone
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - M Fusè
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - R Aguado
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - S Potenti
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - I León
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - E R Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - S Mata
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - F Lazzari
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - G Mancini
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - L Spada
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - A Gualandi
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - P G Cozzi
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - C Puzzarini
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - J L Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Aguado R, Sanz-Novo M, Mata S, León I, Alonso JL. Unveiling the Shape of N-Acetylgalactosamine: A Cancer-Associated Sugar Derivative. J Phys Chem A 2022; 126:7621-7626. [PMID: 36099577 DOI: 10.1021/acs.jpca.2c04595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the present work, we report the first rotational study of N-acetylgalactosamine, a cancer-associated sugar derivative, by means of high-resolution rotational spectroscopy. Two different conformers have been conclusively characterized using broadband Fourier transform microwave spectroscopy coupled with a laser ablation vaporization system. Additionally, we performed a comprehensive analysis of the intramolecular interactions that govern these structures, which allowed us to both characterize the existence of intramolecular hydrogen bond networks that drive the intrinsic conformation panorama of N-acetylgalactosamine and further rationalize the biological role of this aminosugar derivative as part of the Tn antigen.
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Affiliation(s)
- R 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, Valladolid 47011, Spain
| | - 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, Universidad de Valladolid, Valladolid 47011, Spain
| | - S 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, Valladolid 47011, Spain
| | - I 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, Valladolid 47011, Spain
| | - 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, Universidad de Valladolid, Valladolid 47011, Spain
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Moreno-Mesonero L, Amorós I, Moreno Y, Alonso JL. Simultaneous detection of less frequent waterborne parasitic protozoa in reused wastewater using amplicon sequencing and qPCR techniques. J Environ Manage 2022; 314:115029. [PMID: 35430514 DOI: 10.1016/j.jenvman.2022.115029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Waterborne parasitic protozoa (WPP) infections have a worldwide distribution and are a source for epidemic and endemic human diseases. Although a variety of protozoa are commonly detected in wastewater and cited as causative agents of outbreaks, effluents from wastewater treatment plants (WWTPs) used for irrigation can contain other pathogenic protozoa that are not currently being controlled. The lack of control on a routine basis using rapid and sensitive methods to detect these parasites in water may keep them under-recognized. This study focused on using molecular tools, 18 S rRNA amplicon-based sequencing and qPCR, to characterize WPP distribution in wastewater samples from urban WWTPs used for irrigation. A total of eight wastewater samples (from secondary and tertiary disinfection treatment effluents) were collected. Potentially pathogenic protozoa identified by 18 S rRNA sequencing and/or qPCR in the analyzed samples included Acanthamoeba spp., Blastocystis sp., Entamoeba coli, Entamoeba dispar, Entamoeba hartmanni, Giardia intestinalis assemblage A and Toxoplasma gondii Positive results by qPCR were in non-quantifiable levels. Blastocystis sp. was the most represented protozoa among the sequences retrieved from the amplicon sequencing. Blastocystis ST1 and ST2 were the most abundant subtypes among the obtained OTUs. Moreover, Blastocystis sp. ST3, ST4, ST6 and ST8 were also detected, although in lower abundances. Results of this study showed that WWTP effluents used for irrigation can provide a source of WPP.
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Affiliation(s)
- L Moreno-Mesonero
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, Camino de Vera S/n, 46022, Valencia, Spain.
| | - I Amorós
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, Camino de Vera S/n, 46022, Valencia, Spain.
| | - Y Moreno
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, Camino de Vera S/n, 46022, Valencia, Spain.
| | - J L Alonso
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, Camino de Vera S/n, 46022, Valencia, Spain.
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Alonso ER, Kolesniková L, Belloche A, Mata S, Garrod RT, Jabri A, León I, Guillemin JC, Müller HSP, Menten KM, Alonso JL. Rotational spectroscopic study and astronomical search for propiolamide in Sgr B2(N). Astron Astrophys 2021; 647:A55. [PMID: 34257461 PMCID: PMC7611197 DOI: 10.1051/0004-6361/202040211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
CONTEXT For all the amides detected in the interstellar medium (ISM), the corresponding nitriles or isonitriles have also been detected in the ISM, some of which have relatively high abundances. Among the abundant nitriles for which the corresponding amide has not yet been detected is cyanoacetylene (HCCCN), whose amide counterpart is propiolamide (HCCC(O)NH2). AIMS With the aim of supporting searches for this amide in the ISM, we provide a complete rotational study of propiolamide from 6 GHz to 440 GHz. METHODS Time-domain Fourier transform microwave (FTMW) spectroscopy under supersonic expansion conditions between 6 GHz and 18 GHz was used to accurately measure and analyze ground-state rotational transitions with resolved hyperfine structure arising from nuclear quadrupole coupling interactions of the 14N nucleus. We combined this technique with the frequency-domain room-temperature millimeter wave and submillimeter wave spectroscopies from 75 GHz to 440 GHz in order to record and assign the rotational spectra in the ground state and in the low-lying excited vibrational states. We used the ReMoCA spectral line survey performed with the Atacama Large Millimeter/submillimeter Array toward the star-forming region Sgr B2(N) to search for propiolamide. RESULTS We identified and measured more than 5500 distinct frequency lines of propiolamide in the laboratory. These lines were fitted using an effective semi-rigid rotor Hamiltonian with nuclear quadrupole coupling interactions taken into consideration. We obtained accurate sets of spectroscopic parameters for the ground state and the three low-lying excited vibrational states. We report the nondetection of propiolamide toward the hot cores Sgr B2(N1S) and Sgr B2(N2). We find that propiolamide is at least 50 and 13 times less abundant than acetamide in Sgr B2(N1S) and Sgr B2(N2), respectively, indicating that the abundance difference between both amides is more pronounced by at least a factor of 8 and 2, respectively, than for their corresponding nitriles. CONCLUSIONS Although propiolamide has yet to be included in astrochemical modeling networks, the observed upper limit to the ratio of propiolamide to acetamide seems consistent with the ratios of related species as determined from past simulations. The comprehensive spectroscopic data presented in this paper will aid future astronomical searches.
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Affiliation(s)
- E R Alonso
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain
- Fundación Biofísica Bizkaia / Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, Spain
| | - L Kolesniková
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 166 28 Prague 6, Czech Republic
| | - A Belloche
- Max-Planck-Institut für Radioastronomie, Auf dem Hügel 69, 53121 Bonn, Germany
| | - S 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
| | - R T Garrod
- Departments of Chemistry and Astronomy, University of Virginia, Charlottesville, VA 22904, USA
| | - A Jabri
- 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
| | - I 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
| | - J-C Guillemin
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR - UMR 6226, F-35000 Rennes, France
| | - 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
| | - J L 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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Sanz-Novo M, León I, Alonso JL, Largo A, Barrientos C. Formation of interstellar cyanoacetamide: a rotational and computational study. Astron Astrophys 2020; 644:A3. [PMID: 33594291 PMCID: PMC7116755 DOI: 10.1051/0004-6361/202038766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
CONTEXT Cyanoacetamide is a -CN bearing molecule that is also an amide derivative target molecule in the interstellar medium. AIMS The aim of our investigation is to analyze the feasibility of a plausible formation process of protonated cyanoacetamide under interstellar conditions and to provide direct experimental frequencies of the ground vibrational state of the neutral form in the microwave region in order to enable its eventual identification in the interstellar medium. METHODS We used high-level theoretical computations to study the formation process of protonated cyanoacetamide. Furthermore, we employed a high-resolution laser-ablation molecular beam Fourier transform spectroscopic technique to measure the frequencies of the neutral form. RESULTS We report the first rotational characterization of cyanoacetamide, and a precise set of the relevant rotational spectroscopic constants have been determined as a first step to identifying the molecule in the interstellar medium. We fully explored the potential energy surface to study a gas-phase reaction on the formation process of protonated cyanoacetamide. We found that an exothermic process with no net activation barrier is initiated by the high-energy isomer of protonated hydroxylamine, which leads to protonated cyanoacetamide.
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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, 47011 Valladolid, Spain
- Computational Chemistry Group, Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47011 Valladolid, Spain
| | - I León
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopía y Bioespectroscopía, Parque Científico UVa, Unidad Asociada CSIC, 47011 Valladolid, Spain
| | - 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, 47011 Valladolid, Spain
| | - A Largo
- Computational Chemistry Group, Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47011 Valladolid, Spain
| | - C Barrientos
- Computational Chemistry Group, Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47011 Valladolid, Spain
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Lacaria L, Lange JR, Goldmann WH, Rico F, Alonso JL. Corrigendum to "alphavbeta3 integrin expression increases elasticity in human melanoma cells" [Biochem. Biophys. Res. Commun. 525 (2020)]. Biochem Biophys Res Commun 2020; 531:264. [PMID: 32800338 DOI: 10.1016/j.bbrc.2020.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- L Lacaria
- Aix Marseille Univ, CNRS, INSERM, LAI, Marseille, France
| | - J R Lange
- Dept. of Biophysics, Friedrich-Alexander-University, 91052, Erlangen, Germany
| | - W H Goldmann
- Dept. of Biophysics, Friedrich-Alexander-University, 91052, Erlangen, Germany.
| | - F Rico
- Aix Marseille Univ, CNRS, INSERM, LAI, Marseille, France
| | - J L Alonso
- Dept. of Medicine, Mass General Hospital/Harvard Medical School, Charlestown, MA, 02129, USA
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Alonso JL, Bouthelier C, Castro A, Clemente-Gallardo J, Jover-Galtier JA. Entropy and canonical ensemble of hybrid quantum classical systems. Phys Rev E 2020; 102:042118. [PMID: 33212583 DOI: 10.1103/physreve.102.042118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/16/2020] [Indexed: 11/07/2022]
Abstract
In this work we generalize and combine Gibbs and von Neumann approaches to build, for the first time, a rigorous definition of entropy for hybrid quantum-classical systems. The resulting function coincides with the two cases above when the suitable limits are considered. Then, we apply the MaxEnt principle for this hybrid entropy function and obtain the natural candidate for the hybrid canonical ensemble (HCE). We prove that the suitable classical and quantum limits of the HCE coincide with the usual classical and quantum canonical ensembles since the whole scheme admits both limits, thus showing that the MaxEnt principle is applicable and consistent for hybrid systems.
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Affiliation(s)
- J L Alonso
- Departamento de Física Teórica, Universidad de Zaragoza, Campus San Francisco, 50009 Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Edificio I+D, Mariano Esquillor s/n, 50018 Zaragoza, Spain.,Centro de Astropartículas y Física de Altas Energas (CAPA), Departamento de Física Teórica, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - C Bouthelier
- Departamento de Física Teórica, Universidad de Zaragoza, Campus San Francisco, 50009 Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Edificio I+D, Mariano Esquillor s/n, 50018 Zaragoza, Spain
| | - A Castro
- Departamento de Física Teórica, Universidad de Zaragoza, Campus San Francisco, 50009 Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Edificio I+D, Mariano Esquillor s/n, 50018 Zaragoza, Spain.,Fundación ARAID, Av. de Ranillas 1-D, planta 2, oficina B, 50018 Zaragoza, Spain
| | - J Clemente-Gallardo
- Departamento de Física Teórica, Universidad de Zaragoza, Campus San Francisco, 50009 Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Edificio I+D, Mariano Esquillor s/n, 50018 Zaragoza, Spain.,Centro de Astropartículas y Física de Altas Energas (CAPA), Departamento de Física Teórica, Universidad de Zaragoza, Zaragoza 50009, Spain
| | - J A Jover-Galtier
- Departamento de Física Teórica, Universidad de Zaragoza, Campus San Francisco, 50009 Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Edificio I+D, Mariano Esquillor s/n, 50018 Zaragoza, Spain.,Centro Universitario de la Defensa de Zaragoza, Academia General Militar, 50090 Zaragoza, Spain
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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.
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Affiliation(s)
- I León
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, 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.
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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). Astron Astrophys 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Neeman EM, León I, Alonso ER, Mata S, Alonso JL. Gas-Phase Conformational Map of the Amino Acid Isovaline. Chemphyschem 2020; 21:525-530. [PMID: 32012435 DOI: 10.1002/cphc.201901201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/28/2020] [Indexed: 11/11/2022]
Abstract
Four conformers of the non-proteinogenic α-amino acid isovaline, vaporized by laser ablation, are characterized by Fourier-transform microwave techniques in a supersonic expansion. The comparison between the experimental rotational and 14 N nuclear quadrupole coupling constants and the ab initio calculated ones provides conclusive evidence for the identification of the conformers. The most stable species is stabilized by an N-H⋅⋅⋅O =C intramolecular hydrogen bond and a cis-COOH interaction, whereas the higher-energy conformers exhibit an N⋅⋅⋅H-O intramolecular hydrogen bond and trans-COOH, as in other aliphatic amino acids. The spectroscopic data herein reported can be used for the astrophysical purpose in a possible detection of isovaline in space.
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Affiliation(s)
- E M Neeman
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico Universidad de Valladolid, 47011, Valladolid, Spain
| | - I León
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico Universidad de Valladolid, 47011, Valladolid, Spain
| | - E R Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico Universidad de Valladolid, 47011, Valladolid, Spain
| | - S Mata
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico Universidad de Valladolid, 47011, Valladolid, Spain
| | - J L Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico Universidad de Valladolid, 47011, Valladolid, Spain
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Sanz-Novo M, Alonso ER, León I, Alonso JL. The Shape of the Archetypical Oxocarbon Squaric Acid and Its Water Clusters. Chemistry 2019; 25:10748-10755. [PMID: 31283059 DOI: 10.1002/chem.201901916] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Indexed: 12/15/2022]
Abstract
Herein, a full structural description is presented for the archetypical supramolecular synthone squaric acid (3,4-dihydroxy-3-cyclobutene-1,2-dione), placed in the gas phase by laser ablation and characterized by chirped pulse Fourier transform microwave technique. Free from natural environmental disturbances, two different anti-anti and syn-anti planar forms and the corresponding water clusters have been revealed in a supersonic expansion. The substitution structure of the most stable anti-anti conformer has also been extracted from the analysis of the rotational spectra of the 13 C and 18 O isotopic species in their natural abundance. The interplay between inter- and intramolecular interactions involving hydroxy and carbonyl groups has been analyzed by QTAIM (quantum theory of atoms in molecules) methods for squaric acid and its water clusters to understand their chemical behavior and further rationalize their role in the stabilization of these molecular systems.
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Affiliation(s)
- Miguel Sanz-Novo
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de EspectroscopíayBioespectroscopía, Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Paseo de Belén 5, 47011, Valladolid, Spain
| | - Elena R Alonso
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de EspectroscopíayBioespectroscopía, Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Paseo de Belén 5, 47011, Valladolid, Spain
| | - Iker León
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de EspectroscopíayBioespectroscopía, Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Paseo de Belén 5, 47011, Valladolid, Spain
| | - J L Alonso
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de EspectroscopíayBioespectroscopía, Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, Paseo de Belén 5, 47011, Valladolid, Spain
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Neeman EM, León I, Alonso ER, Kolesniková L, Mata S, Alonso JL. The effect of N-methylation on the conformational landscape of alanine: the case of N-methyl-l-alanine. Phys Chem Chem Phys 2018; 20:29159-29165. [PMID: 30426989 DOI: 10.1039/c8cp06043f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The non-proteinogenic amino acid N-methyl-l-alanine has been brought into the gas phase using laser ablation techniques and studied by high resolution chirped pulse and molecular-beam Fourier transform microwave spectroscopies coupled to supersonic expansion. Four conformers showing the three types of hydrogen bond interactions I (NHO[double bond, length as m-dash]C), II (OHN) and III (N-HO-H) have been unambiguously identified, based on the comparison of the experimental rotational and 14N nuclear quadrupole constants with the calculated ab initio values. The observation of a type III conformer evidences the role of methyl groups in both sides to impose the steric hindrance, precluding the relaxation from type III to type I conformers and explains the responsibility for the unique conformational landscape observed in the case of NMA.
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Affiliation(s)
- E M Neeman
- 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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Kolesniková L, Peña I, Alonso ER, Tercero B, Cernicharo J, Mata S, Alonso JL. Laboratory rotational spectrum and astronomical search for methoxyacetaldehyde. Astron Astrophys 2018; 619:A67. [PMID: 30555173 PMCID: PMC6290985 DOI: 10.1051/0004-6361/201833773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
CONTEXT Methoxyacetaldehyde belongs to a group of structural isomers with the general formula C3H6O2, of which methyl acetate and ethyl formate are known interstellar molecules. Rotational data available for methoxyacetaldehyde are limited to 40 GHz, which makes predictions at higher frequencies rather uncertain. AIMS The aim of this work is to provide accurate experimental frequencies of methoxyacetaldehyde in the millimeter-wave region to support its detection in the interstellar medium. METHODS The rotational spectrum of methoxyacetaldehyde was recorded at room-temperature from 75 to 120 GHz and from 170 to 310 GHz using the millimeter-wave spectrometer in Valladolid. Additional measurements were also performed at conditions of supersonic expansion from 6 to 18 GHz. The assigned rotational transitions were analyzed using the S -reduced semirigid-rotor Hamiltonian. RESULTS We newly assigned over 1000 lines for the most stable conformer of methoxyacetaldehyde in its ground state and five lowest excited vibrational states, and precise sets of spectroscopic constants were obtained. We searched for spectral features of methoxyacetaldehyde in the high-mass star-forming regions Orion KL and Sagittarius B2, as well as in the cold dark cloud Barnard 1 (B1-b). No lines belonging to methoxyacetaldehyde were detected above the detection limit of our data. We provide upper limits to the methoxyacetaldehyde colum density in these sources.
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Affiliation(s)
- L Kolesniková
- 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
| | - I Peña
- 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
| | - E R 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
| | - B Tercero
- Observatorio Astronómico Nacional (OAN-IGN), Calle Alfonso XII 3, 28014 Madrid, Spain
| | - J Cernicharo
- Instituto de Física Fundamental (IFF-CSIC), Calle Serrano 123, 28006 Madrid, Spain
| | - S 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
| | - J L 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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18
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Kolesniková L, Alonso ER, Tercero B, Cernicharo J, Alonso JL. Millimeter wave spectra of ethyl isocyanate and searches for it in Orion KL and Sgr B2. Astron Astrophys 2018; 616:A173. [PMID: 30369619 PMCID: PMC6203308 DOI: 10.1051/0004-6361/201833223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
CONTEXT Relatively high abundances of methyl isocyanate (CH3NCO), a methyl derivative of isocyanic acid (HNCO), found in the Orion KL and Sgr B2 molecular clouds suggest that its ethyl derivative, ethyl isocyanate (CH3CH2NCO), may also be present. AIMS The aim of this work is to provide accurate experimental frequencies of ethyl isocyanate in its ground and excited vibrational states in the millimeter wave region to support searches for it in the interstellar medium. METHODS The rotational spectrum of ethyl isocyanate was recorded at room temperature from 80 to 340 GHz using the millimeter wave spectrometer in Valladolid. Assigned rotational transitions were analyzed using the S -reduced semirigid-rotor Hamiltonian. RESULTS More than 1100 distinct frequency lines were analyzed for the ground vibrational state of the cis conformer as well as for three vibrational satellites corresponding to successive excitation of the lowest-energy C-N torsional mode. Newly determined rotational and centrifugal distortion constants were used for searches of spectral features of ethyl isocyanate in Orion KL and Sgr B2 clouds. Upper limits to CH3CH2NCO in these high-mass star-forming regions were obtained.
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Affiliation(s)
- L Kolesniková
- 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, E-47011 Valladolid, Spain
| | - E R 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, E-47011 Valladolid, Spain
| | - B Tercero
- Observatorio Astronómico Nacional (OAN-IGN). Calle Alfonso XII, 3, E-28014 Madrid, Spain
| | - J Cernicharo
- Instituto de Ciencia de Materiales de Madrid, CSIC, C/ Sor Juana Inés de la Cruz 3,E-28049 Cantoblanco, Spain
| | - J L 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, E-47011 Valladolid, Spain
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Alonso JL, Bruscolini P, Castro A, Clemente-Gallardo J, Cuchí JC, Jover-Galtier JA. Ehrenfest Statistical Dynamics in Chemistry: Study of Decoherence Effects. J Chem Theory Comput 2018; 14:3975-3985. [DOI: 10.1021/acs.jctc.8b00511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. L. Alonso
- Departamento de Física Teórica, Universidad de Zaragoza, Pedro Cerbuna 12, ES 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor s/n, Edificio
I+D, ES 50018 Zaragoza, Spain
- Unidad asociada IQFR-BIFI, Universidad de Zaragoza, Edificio I+D-Campus Rı́o Ebro, Mariano Esquillor s/n, ES 50018 Zaragoza, Spain
| | - P. Bruscolini
- Departamento de Física Teórica, Universidad de Zaragoza, Pedro Cerbuna 12, ES 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor s/n, Edificio
I+D, ES 50018 Zaragoza, Spain
| | - A. Castro
- BIFI-Fundación ARAID, Universidad de Zaragoza, Edificio I+D-Campus Río Ebro, Mariano Esquillor s/n, ES 50018 Zaragoza, Spain
| | - J. Clemente-Gallardo
- Departamento de Física Teórica, Universidad de Zaragoza, Pedro Cerbuna 12, ES 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor s/n, Edificio
I+D, ES 50018 Zaragoza, Spain
| | - J. C. Cuchí
- Departament d’Enginyeria Agroforestal, ETSEA-Universitat de Lleida, Avenida Alcalde Rovira Roure 191, ES 25198 Lleida, Spain
| | - J. A. Jover-Galtier
- Departamento de Física Teórica, Universidad de Zaragoza, Pedro Cerbuna 12, ES 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor s/n, Edificio
I+D, ES 50018 Zaragoza, Spain
- Centro Universitario de la Defensa de Zaragoza, Academia General Militar, Carretera de Huesca s/n, ES 50090 Zaragoza, Spain
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Nieto Y, Alonso JL, Ayala F, Ortega L, Casado A, Martín M, Díaz-Rubio E. End-Stage Acute Hepatic Failure as Clinical Presentation of Liver Metastases from Breast Cancer. Tumori 2018; 84:616-7. [PMID: 9862530 DOI: 10.1177/030089169808400523] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A most unusual case of fatal acute hepatic failure as clinical presentation of liver metastases from breast cancer is described. The patient had a four-year history of indolent breast neoplasm and no previously known liver disease.
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Affiliation(s)
- Y Nieto
- Medical Oncology Department, Hospital Universitario San Carlos, Madrid, Spain.
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Tanarro I, Alemán B, de Vicente P, Gallego JD, Pardo JR, Santoro G, Lauwaet K, Tercero F, Díaz-Pulido A, Moreno E, Agúndez M, Goicoechea JR, Sobrado JM, López JA, Martínez L, Doménech JL, Herrero VJ, Hernández JM, Peláez RJ, López-Pérez JA, Gómez-González J, Alonso JL, Jiménez E, Teyssier D, Makasheva K, Castellanos M, Joblin C, Martín-Gago JA, Cernicharo J. Using radio astronomical receivers for molecular spectroscopic characterization in astrochemical laboratory simulations: A proof of concept. Astron Astrophys 2018; 609:A15. [PMID: 29277841 PMCID: PMC5741178 DOI: 10.1051/0004-6361/201730969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We present a proof of concept on the coupling of radio astronomical receivers and spectrometers with chemical reactors and the performances of the resulting setup for spectroscopy and chemical simulations in laboratory astrophysics. Several experiments including cold plasma generation and UV photochemistry were performed in a 40 cm long gas cell placed in the beam path of the Aries 40 m radio telescope receivers operating in the 41-49 GHz frequency range interfaced with fast Fourier transform spectrometers providing 2 GHz bandwidth and 38 kHz resolution. The impedance matching of the cell windows has been studied using different materials. The choice of the material and its thickness was critical to obtain a sensitivity identical to that of standard radio astronomical observations. Spectroscopic signals arising from very low partial pressures of CH3OH, CH3CH2OH, HCOOH, OCS, CS, SO2 (<10-3 mbar) were detected in a few seconds. Fast data acquisition was achieved allowing for kinetic measurements in fragmentation experiments using electron impact or UV irradiation. Time evolution of chemical reactions involving OCS, O2 and CS2 was also observed demonstrating that reactive species, such as CS, can be maintained with high abundance in the gas phase during these experiments.
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Affiliation(s)
- I Tanarro
- IEM. CSIC. Instituto de Estructura de la Materia. Molecular Physics Department. C/Serrano 123, 28006 Madrid, Spain
| | - B Alemán
- ICMM. CSIC. Molecular Astrophysics Group. C/ Sor Juana Inés de la Cruz 3. Cantoblanco, 28049 Madrid. Spain
| | - P de Vicente
- Centro Nacional de Tecnologías Radioastronómicas y Aplicaciones Geoespaciales (CNTRAG), Observatorio de Yebes (IGN), Spain
| | - J D Gallego
- Centro Nacional de Tecnologías Radioastronómicas y Aplicaciones Geoespaciales (CNTRAG), Observatorio de Yebes (IGN), Spain
| | - J R Pardo
- ICMM. CSIC. Molecular Astrophysics Group. C/ Sor Juana Inés de la Cruz 3. Cantoblanco, 28049 Madrid. Spain
| | - G Santoro
- ICMM. CSIC. Materials Science Factory. Structure of Nanoscopic Systems Group, ESISNA. C/ Sor Juana Inés de la Cruz 3. Cantoblanco, 28049 Madrid. Spain
| | - K Lauwaet
- ICMM. CSIC. Materials Science Factory. Structure of Nanoscopic Systems Group, ESISNA. C/ Sor Juana Inés de la Cruz 3. Cantoblanco, 28049 Madrid. Spain
| | - F Tercero
- Centro Nacional de Tecnologías Radioastronómicas y Aplicaciones Geoespaciales (CNTRAG), Observatorio de Yebes (IGN), Spain
| | - A Díaz-Pulido
- Centro Nacional de Tecnologías Radioastronómicas y Aplicaciones Geoespaciales (CNTRAG), Observatorio de Yebes (IGN), Spain
| | - E Moreno
- ICMM. CSIC. Molecular Astrophysics Group. C/ Sor Juana Inés de la Cruz 3. Cantoblanco, 28049 Madrid. Spain
| | - M Agúndez
- ICMM. CSIC. Molecular Astrophysics Group. C/ Sor Juana Inés de la Cruz 3. Cantoblanco, 28049 Madrid. Spain
| | - J R Goicoechea
- ICMM. CSIC. Molecular Astrophysics Group. C/ Sor Juana Inés de la Cruz 3. Cantoblanco, 28049 Madrid. Spain
| | - J M Sobrado
- Centro de Astrobiología, (CAB-CSIC/INTA). Carretera Torrejón a Ajalvir km 4, Torrejón de Ardoz 28850 (Madrid), Spain
| | - J A López
- Centro Nacional de Tecnologías Radioastronómicas y Aplicaciones Geoespaciales (CNTRAG), Observatorio de Yebes (IGN), Spain
| | - L Martínez
- ICMM. CSIC. Materials Science Factory. Structure of Nanoscopic Systems Group, ESISNA. C/ Sor Juana Inés de la Cruz 3. Cantoblanco, 28049 Madrid. Spain
| | - J L Doménech
- IEM. CSIC. Instituto de Estructura de la Materia. Molecular Physics Department. C/Serrano 123, 28006 Madrid, Spain
| | - V J Herrero
- IEM. CSIC. Instituto de Estructura de la Materia. Molecular Physics Department. C/Serrano 123, 28006 Madrid, Spain
| | - J M Hernández
- Centro Nacional de Tecnologías Radioastronómicas y Aplicaciones Geoespaciales (CNTRAG), Observatorio de Yebes (IGN), Spain
| | - R J Peláez
- IEM. CSIC. Instituto de Estructura de la Materia. Molecular Physics Department. C/Serrano 123, 28006 Madrid, Spain
| | - J A López-Pérez
- Centro Nacional de Tecnologías Radioastronómicas y Aplicaciones Geoespaciales (CNTRAG), Observatorio de Yebes (IGN), Spain
| | - J Gómez-González
- Centro Nacional de Tecnologías Radioastronómicas y Aplicaciones Geoespaciales (CNTRAG), Observatorio de Yebes (IGN), Spain
| | - 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, Universidad de Valladolid, 47011 Valladolid, Spain
| | - E Jiménez
- Departamento de Química Física, Facultad de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, Avda. Camilo José Cela 1B, E-13071, Ciudad Real, Spain
| | - D Teyssier
- European Space Astronomy Centre, ESA, PO Box 78, 28691 Villanueva de la Cañada, Madrid, Spain
| | - K Makasheva
- LAPLACE (Laboratoire Plasma et Conversion dÉnergie); Université de Toulouse; CNRS, UPS, INPT; 118 route de Narbonne, F-31062 Toulouse cedex 9, France
| | - M Castellanos
- ICMM. CSIC. Molecular Astrophysics Group. C/ Sor Juana Inés de la Cruz 3. Cantoblanco, 28049 Madrid. Spain
| | - C Joblin
- Université de Toulouse, UPS-OMS, IRAP, 31000 Toulouse, France
- CNRS, IRAP, 9 Av. Colonel Roche, BP 44346, 31028 Toulouse Cedex 4, France
| | - J A Martín-Gago
- ICMM. CSIC. Materials Science Factory. Structure of Nanoscopic Systems Group, ESISNA. C/ Sor Juana Inés de la Cruz 3. Cantoblanco, 28049 Madrid. Spain
| | - J Cernicharo
- ICMM. CSIC. Molecular Astrophysics Group. C/ Sor Juana Inés de la Cruz 3. Cantoblanco, 28049 Madrid. Spain
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León I, Peña I, Cabezas C, Alonso ER, Alonso JL. The last link of the x-aminobutyric acid series: the five conformers of β-aminobutyric acid. Phys Chem Chem Phys 2018; 20:15574-15580. [DOI: 10.1039/c8cp01734d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural characterization of β-aminobutyric acid by rotational spectroscopy.
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Affiliation(s)
- I. León
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - I. Peña
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - C. Cabezas
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - E. R. Alonso
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - J. L. Alonso
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
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23
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Kolesniková L, Tercero B, Alonso ER, Guillemin JC, Cernicharo J, Alonso JL. Rotational spectrum of methoxyamine up to 480 GHz: a laboratory study and astronomical search. Astron Astrophys 2018; 609:A24. [PMID: 29983447 PMCID: PMC6031297 DOI: 10.1051/0004-6361/201730744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
AIMS Methoxyamine is a potential interstellar amine that has been predicted by gas-grain chemical models for the formation of complex molecules. The aim of this work is to provide direct experimental frequencies of its ground-vibrational state in the millimeter- and submillimeter-wave regions to achieve its detection in the interstellar medium. METHODS Methoxyamine was chemically liberated from its hydrochloride salt, and its rotational spectrum was recorded at room temperature from 75 to 480 GHz using the millimeter-wave spectrometer in Valladolid. Many observed transitions revealed A-E splitting caused by the internal rotation of the methyl group, which had to be treated with specific internal rotation codes. RESULTS Over 400 lines were newly assigned for the most stable conformer of methoxyamine, and a precise set of spectroscopic constants was obtained. Spectral features of methoxyamine were then searched for in the Orion KL, Sgr B2, B1-b, and TMC-1 molecular clouds. Upper limits to the column density of methoxyamine were derived.
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Affiliation(s)
- L Kolesniková
- 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
| | - B Tercero
- Instituto de Ciencia de Materiales de Madrid, CSIC, C/ Sor Juana Inés de la Cruz 3, 28049 Cantoblanco, Spain
| | - E R 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
| | - J-C Guillemin
- Institut des Sciences Chimiques de Rennes, École Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, 11 Allée de Beaulieu, CS 50837, 35708 Rennes Cedex 7, France
| | - J Cernicharo
- Instituto de Ciencia de Materiales de Madrid, CSIC, C/ Sor Juana Inés de la Cruz 3, 28049 Cantoblanco, Spain
| | - J L 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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24
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Moreno Y, Moreno-Mesonero L, Amorós I, Pérez R, Morillo JA, Alonso JL. Multiple identification of most important waterborne protozoa in surface water used for irrigation purposes by 18S rRNA amplicon-based metagenomics. Int J Hyg Environ Health 2017; 221:102-111. [PMID: 29066287 DOI: 10.1016/j.ijheh.2017.10.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/04/2017] [Accepted: 10/18/2017] [Indexed: 10/18/2022]
Abstract
Understanding waterborne protozoan parasites (WPPs) diversity has important implications in public health. In this study, we evaluated a NGS-based method as a detection approach to identify simultaneously most important WPPs using 18S rRNA high-throughput sequencing. A set of primers to target the V4 18S rRNA region of WPPs such as Cryptosporidium spp., Giardia sp., Blastocystis sp., Entamoeba spp, Toxoplasma sp. and free-living amoebae (FLA) was designed. In order to optimize PCR conditions before sequencing, both a mock community with a defined composition of representative WPPs and a real water sample inoculated with specific WPPs DNA were prepared. Using the method proposed in this study, we have detected the presence of Giardia intestinalis, Acanthamoeba castellanii, Toxoplasma gondii, Entamoeba histolytica and Blastocystis sp. at species level in real irrigation water samples. Our results showed that untreated surface irrigation water in open fields can provide an important source of WPPs. Therefore, the methodology proposed in this study can establish a basis for an accurate and effective diagnostic of WPPs to provide a better understanding of the risk associated to irrigation water.
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Affiliation(s)
- Y Moreno
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - L Moreno-Mesonero
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - I Amorós
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - R Pérez
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - J A Morillo
- Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas (EEZA-CSIC), Carretera de Sacramento s/n, La Cañada, Almería, Spain
| | - J L Alonso
- Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
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25
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Cernicharo J, Agúndez M, Velilla Prieto L, Guélin M, Pardo JR, Kahane C, Marka C, Kramer C, Navarro S, Quintana-Lacaci G, Fonfría JP, Marcelino N, Tercero B, Moreno E, Massalkhi S, Santander-García M, McCarthy MC, Gottlieb CA, Alonso JL. Discovery of methyl silane and confirmation of silyl cyanide in IRC +10216. Astron Astrophys 2017; 606:L5. [PMID: 29142328 PMCID: PMC5683346 DOI: 10.1051/0004-6361/201731672] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report the discovery in space of methyl silane, CH3SiH3, from observations of ten rotational transitions between 80 and 350 GHz (Ju from 4 to 16) with the IRAM 30 m radio telescope. The molecule was observed in the envelope of the C-star IRC +10216. The observed profiles and our models for the expected emission of methyl silane suggest that the it is formed in the inner zones of the circumstellar envelope, 1-40 R*, with an abundance of (0.5-1) × 10-8 relative to H2. We also observed several rotational transitions of silyl cyanide (SiH3CN), confirming its presence in IRC +10216 in particular, and in space in general. Our models indicate that silyl cyanide is also formed in the inner regions of the envelope, around 20 R*, with an abundance relative to H2 of 6×10-10. The possible formation mechanisms of both species are discussed. We also searched for related chemical species but only upper limits could be obtained.
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Affiliation(s)
- J Cernicharo
- Group of Molecular Astrophysics, ICMM, CSIC, C/ Sor Juana Inés de La Cruz 3, 28049 Madrid, Spain
| | - M Agúndez
- Group of Molecular Astrophysics, ICMM, CSIC, C/ Sor Juana Inés de La Cruz 3, 28049 Madrid, Spain
| | - L Velilla Prieto
- Group of Molecular Astrophysics, ICMM, CSIC, C/ Sor Juana Inés de La Cruz 3, 28049 Madrid, Spain
| | - M Guélin
- Institut de Radioastronomie Millimétrique, 300 rue de la Piscine, 38406 St-Martin d'Hères, France
| | - J R Pardo
- Group of Molecular Astrophysics, ICMM, CSIC, C/ Sor Juana Inés de La Cruz 3, 28049 Madrid, Spain
| | - C Kahane
- Université Grenoble Alpes, CNRS, IPAG, 38000 Grenoble, France
| | - C Marka
- Instituto de Radioastronomía Milimétrica, Av. Divina Pastora 7, Local 20, 18012 Granada, Spain
| | - C Kramer
- Instituto de Radioastronomía Milimétrica, Av. Divina Pastora 7, Local 20, 18012 Granada, Spain
| | - S Navarro
- Instituto de Radioastronomía Milimétrica, Av. Divina Pastora 7, Local 20, 18012 Granada, Spain
| | - G Quintana-Lacaci
- Group of Molecular Astrophysics, ICMM, CSIC, C/ Sor Juana Inés de La Cruz 3, 28049 Madrid, Spain
| | - J P Fonfría
- Group of Molecular Astrophysics, ICMM, CSIC, C/ Sor Juana Inés de La Cruz 3, 28049 Madrid, Spain
| | - N Marcelino
- Group of Molecular Astrophysics, ICMM, CSIC, C/ Sor Juana Inés de La Cruz 3, 28049 Madrid, Spain
| | - B Tercero
- Group of Molecular Astrophysics, ICMM, CSIC, C/ Sor Juana Inés de La Cruz 3, 28049 Madrid, Spain
| | - E Moreno
- Group of Molecular Astrophysics, ICMM, CSIC, C/ Sor Juana Inés de La Cruz 3, 28049 Madrid, Spain
| | - S Massalkhi
- Group of Molecular Astrophysics, ICMM, CSIC, C/ Sor Juana Inés de La Cruz 3, 28049 Madrid, Spain
| | - M Santander-García
- Group of Molecular Astrophysics, ICMM, CSIC, C/ Sor Juana Inés de La Cruz 3, 28049 Madrid, Spain
| | - M C McCarthy
- Harvard-Smithsonian Center for Astrophysics, Cambridge, MA 02138, and School of Engineering & Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - C A Gottlieb
- Harvard-Smithsonian Center for Astrophysics, Cambridge, MA 02138, and School of Engineering & Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - 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, Universidad de Valladolid, 47011 Valladolid, Spain
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26
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León I, Alonso ER, Mata S, Cabezas C, Rodríguez MA, Grabow JU, Alonso JL. The role of amino acid side chains in stabilizing dipeptides: the laser ablation Fourier transform microwave spectrum of Ac-Val-NH2. Phys Chem Chem Phys 2017; 19:24985-24990. [DOI: 10.1039/c7cp03924g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The steric effects imposed by the isopropyl group of valine in the conformational stabilization of the capped dipeptide N-acetyl-l-valinamide (Ac-Val-NH2) have been studied by laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopy.
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Affiliation(s)
- I. León
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - E. R. Alonso
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - S. Mata
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - C. Cabezas
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - M. A. Rodríguez
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
| | - J.-U. Grabow
- Institut für Physikalische Chemie und Elektrochemie
- Lehrgebiet A
- Gottfried-Wilhelm-Leibniz-Universität
- D-30167 Hannover
- Germany
| | - J. L. Alonso
- Grupo de Espectrocopía Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico UVa
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Cabezas C, Cernicharo J, Quintana-Lacaci G, Peña I, Agundez M, Prieto LV, Castro-Carrizo A, Zuñiga J, Bastida A, Alonso JL, Requena A. High-Resolution Rotational Spectrum, Dunham Coefficients, and Potential Energy Function of NaCl. Astrophys J 2016; 825:150. [PMID: 27733778 PMCID: PMC5056638 DOI: 10.3847/0004-637x/825/2/150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report laboratory spectroscopy for the first time of the J = 1-0 and J = 2-1 lines of Na35Cl and Na37Cl in several vibrational states. The hyperfine structure has been resolved in both transitions for all vibrational levels, which permit us to predict with high accuracy the hyperfine splitting of the rotational transitions of the two isotopologues at higher frequencies. The new data have been merged with all previous works at microwave, millimeter, and infrared wavelengths and fitted to a series of mass-independent Dunham parameters and to a potential energy function. The obtained parameters have been used to compute a new dipole moment function, from which the dipole moment for infrared transitions up to Δv = 8 has been derived. Frequency and intensity predictions are provided for all rovibrational transitions up to J = 150 and v = 8, from which the ALMA data of evolved stars can be modeled and interpreted.
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Affiliation(s)
- C Cabezas
- Grupo de Espectroscopía Molecular, Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad asociada CSIC, Parque científico Uva, Universidad de Valladolid, Paseo de Belén 5, E-47011, Valladolid, Spain
| | - J Cernicharo
- Group of Molecular Astrophysics, ICMM, CSIC. C/Sor Juana Inés de la Cruz 3, E-28049 Cantoblanco, Madrid, Spain
| | - G Quintana-Lacaci
- Group of Molecular Astrophysics, ICMM, CSIC. C/Sor Juana Inés de la Cruz 3, E-28049 Cantoblanco, Madrid, Spain
| | - I Peña
- Grupo de Espectroscopía Molecular, Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad asociada CSIC, Parque científico Uva, Universidad de Valladolid, Paseo de Belén 5, E-47011, Valladolid, Spain
| | - M Agundez
- Group of Molecular Astrophysics, ICMM, CSIC. C/Sor Juana Inés de la Cruz 3, E-28049 Cantoblanco, Madrid, Spain
| | - L Velilla Prieto
- Group of Molecular Astrophysics, ICMM, CSIC. C/Sor Juana Inés de la Cruz 3, E-28049 Cantoblanco, Madrid, Spain
| | - A Castro-Carrizo
- Institut de Radioastronomie Millimétrique, 300 rue de la la Piscine, F-38406, Saint Martin d'Hères, France
| | - J Zuñiga
- Universidad de Murcia. Faculdad de Química, Dpto. de Química-Física, Campus Espinardo E-30100, Murcia, Spain
| | - A Bastida
- Universidad de Murcia. Faculdad de Química, Dpto. de Química-Física, Campus Espinardo E-30100, Murcia, Spain
| | - J L Alonso
- Grupo de Espectroscopía Molecular, Edificio Quifima, Laboratorios de Espectroscopía y Bioespectroscopía, Unidad asociada CSIC, Parque científico Uva, Universidad de Valladolid, Paseo de Belén 5, E-47011, Valladolid, Spain
| | - A Requena
- Universidad de Murcia. Faculdad de Química, Dpto. de Química-Física, Campus Espinardo E-30100, Murcia, Spain
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28
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Kolesniková L, Alonso JL, Bermúdez C, Alonso ER, Tercero B, Cernicharo J, Guillemin JC. The millimeter wave spectrum of methyl cyanate: a laboratory study and astronomical search in space<sup/>. Astron Astrophys 2016; 591:A75. [PMID: 27721514 PMCID: PMC5055117 DOI: 10.1051/0004-6361/201628140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
AIMS The recent discovery of methyl isocyanate (CH3NCO) in Sgr B2(N) and Orion KL makes methyl cyanate (CH3OCN) a potential molecule in the interstellar medium. The aim of this work is to fulfill the first requirement for its unequivocal identification in space, i.e. the availability of transition frequencies with high accuracy. METHODS The room-temperature rotational spectrum of methyl cyanate was recorded in the millimeter wave domain from 130 to 350 GHz. All rotational transitions revealed A-E splitting owing to methyl internal rotation and were globally analyzed using the ERHAM program. RESULTS The data set for the ground torsional state of methyl cyanate exceeds 700 transitions within J″ = 10 - 35 and [Formula: see text] and newly derived spectroscopic constants reproduce the spectrum close to the experimental uncertainty. Spectral features of methyl cyanate were then searched for in Orion KL, Sgr B2(N), B1-b, and TMC-1 molecular clouds. Upper limits to the column density of methyl cyanate are provided.
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Affiliation(s)
- L Kolesniková
- Grupo de Espectroscopía 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
| | - J L Alonso
- Grupo de Espectroscopía 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
| | - C Bermúdez
- Grupo de Espectroscopía 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
| | - E R Alonso
- Grupo de Espectroscopía 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
| | - B Tercero
- Instituto de Ciencia de Materiales de Madrid, CSIC, C/ Sor Juana Inés de la Cruz 3, 28049 Cantoblanco, Spain
| | - J Cernicharo
- Instituto de Ciencia de Materiales de Madrid, CSIC, C/ Sor Juana Inés de la Cruz 3, 28049 Cantoblanco, Spain
| | - J-C Guillemin
- Institut des Sciences Chimiques de Rennes, École Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, 11 Allée de Beaulieu, CS 50837, 35708 Rennes Cedex 7, France
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29
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Cabezas C, Robben MAT, Rijs AM, Peña I, Alonso JL. Fourier transform microwave spectroscopy of Ac-Ser-NH2: the role of side chain interactions in peptide folding. Phys Chem Chem Phys 2016; 17:20274-80. [PMID: 26186259 DOI: 10.1039/c5cp02654g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Serine capped dipeptide N-acetyl-l-serinamide (Ac-Ser-NH2) has been investigated using Fourier transform microwave spectroscopic techniques combined with laser ablation sources. Spectral signatures originating from one dominant species have been detected in the supersonic expansion. Rotational and nuclear quadrupole coupling constants of the two (14)N nuclei have been used in the characterization of a C/γ-turn structure, which is stabilized by a CO∙∙∙HN intramolecular hydrogen bond closing a seven-membered ring. Two extra hydrogen bonds involving the polar side chain (-CH2OH) further stabilize the structure. The non-observation of C5 species, attributed to the presence of the polar side chain, is in contrast with the previous gas phase observation of the related dipeptides containing glycine or alanine residues. The A-E splitting pattern arising from the internal rotation of the methyl group has been analyzed and the internal rotation barrier has been determined.
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Affiliation(s)
- Carlos Cabezas
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, Paseo de Belén 5, 47011 Valladolid, Spain.
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Cernicharo J, Kisiel Z, Tercero B, Kolesniková L, Medvedev IR, López A, Fortman S, Winnewisser M, de Lucia FC, Alonso JL, Guillemin JC. A rigorous detection of interstellar CH 3NCO: An important missing species in astrochemical networks. Astron Astrophys 2016; 587:L4. [PMID: 27274565 PMCID: PMC4892348 DOI: 10.1051/0004-6361/201527531] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The recent analysis of the composition of the frozen surface of comet 67P/Churyumov-Gerasimenko has revealed a significant number of complex organic molecules. Methyl isocyanate (CH3NCO) is one of the more abundant species detected on the comet surface. In this work we report extensive characterization of its rotational spectrum resulting in a list of 1269 confidently assigned laboratory lines and its detection in space towards the Orion clouds where 399 lines of the molecule have been unambiguously identified. We find that the limited mm-wave laboratory data reported prior to our work require some revision. The abundance of CH3NCO in Orion is only a factor of ten below those of HNCO and CH3CN. Unlike the molecular abundances in the coma of comets, which correlate with those of warm molecular clouds, molecular abundances in the gas phase in Orion are only weakly correlated with those measured on the comet surface. We also compare our abundances with those derived recently for this molecule towards Sgr B2 (Halfen et al. 2015). A more accurate abundance of CH3NCO is provided for this cloud based on our extensive laboratory work.
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Affiliation(s)
- J Cernicharo
- Grupo de Astrofísica Molecular. Instituto de CC. de Materiales de Madrid (ICMM-CSIC). Sor Juana Inés de la Cruz 3, Cantoblanco, 28049 Madrid, Spain
| | - Z Kisiel
- Laboratory of Mm- and Submm- Spectroscopy. Institute of Physics, Polish Academy of Sciences. Al. Lotnikow 32/46, 02-668 Warszawa, Poland
| | - B Tercero
- Grupo de Astrofísica Molecular. Instituto de CC. de Materiales de Madrid (ICMM-CSIC). Sor Juana Inés de la Cruz 3, Cantoblanco, 28049 Madrid, 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, Universidad de Valladolid, 47011 Valladolid, Spain
| | - I R Medvedev
- Department of Physics, The Ohio State University, 191 W. Woodruff Ave, Columbus, OH 43210, USA; Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA
| | - A López
- Grupo de Astrofísica Molecular. Instituto de CC. de Materiales de Madrid (ICMM-CSIC). Sor Juana Inés de la Cruz 3, Cantoblanco, 28049 Madrid, Spain
| | - S Fortman
- Department of Physics, The Ohio State University, 191 W. Woodruff Ave, Columbus, OH 43210, USA
| | - M Winnewisser
- Department of Physics, The Ohio State University, 191 W. Woodruff Ave, Columbus, OH 43210, USA
| | - F C de Lucia
- Department of Physics, The Ohio State University, 191 W. Woodruff Ave, Columbus, OH 43210, USA
| | - 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, Universidad de Valladolid, 47011 Valladolid, Spain
| | - J-C Guillemin
- Institut des Sciences Chimiques de Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, 11 Allée de Beaulieu, CS 50837, 35708 Rennes Cedex 7, France
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Quintana-Lacaci G, Cernicharo J, Agúndez M, Prieto LV, Castro-Carrizo A, Marcelino N, Cabezas C, Peña I, Alonso JL, Zúñiga J, Requena A, Bastida A, Kalugina Y, Lique F, Guélin M. Hints of a rotating spiral structure in the innermost regions around IRC +10216. Astrophys J 2016; 818:192. [PMID: 26997665 PMCID: PMC4797422 DOI: 10.3847/0004-637x/818/2/192] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The Atacama Large Millimeter/submillimeter Array (ALMA) is allowing us to study the innermost regions of the circumstellar envelopes of evolved stars with un-precedented precision and sensitivity. Key processes in the ejection of matter and dust from these objects occur in their inner zones. In this work, we present sub-arcsecond interferometric maps of transitions of metal-bearing molecules towards the prototypical C-rich evolved star IRC +10216. While Al-bearing molecules seem to be present as a roughly spherical shell, the molecular emission from the salts NaCl and KCl presents an elongation in the inner regions, with a central minimum. In order to accurately analyze the emission from the NaCl rotational lines, we present new calculations of the collisional rates for this molecule based on new spectroscopic constants. The most plausible interpretation for the spatial distribution of the salts is a spiral with a NaCl mass of 0.08M☉. Alternatively, a torus of gas and dust would result in similar structures as those observed. From the torus scenario we derive a mass of ~ 1.1 × 10-4M☉. In both cases, the spiral and the torus, the NaCl structure presents an inner minimum of 27 AU. In the case of the torus, the outer radius is 73 AU. The kinematics of both the spiral and the torus suggests that they are slowly expanding and rotating. Alternative explanations for the presence of the elongation are explored. The presence of these features only in KCl and NaCl might be a result of their comparatively high dipole moment with respect to the Al-bearing species.
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Affiliation(s)
- G Quintana-Lacaci
- Group of Molecular Astrophysics. ICMM, CSIC. C/ Sor Juana Inés de la Cruz 3, 28049 Cantoblanco, Madrid, Spain
| | - J Cernicharo
- Group of Molecular Astrophysics. ICMM, CSIC. C/ Sor Juana Inés de la Cruz 3, 28049 Cantoblanco, Madrid, Spain
| | - M Agúndez
- Group of Molecular Astrophysics. ICMM, CSIC. C/ Sor Juana Inés de la Cruz 3, 28049 Cantoblanco, Madrid, Spain
| | - L Velilla Prieto
- Group of Molecular Astrophysics. ICMM, CSIC. C/ Sor Juana Inés de la Cruz 3, 28049 Cantoblanco, Madrid, Spain ; Centro de Astrobiología, INTA-CSIC. E-28691 Villanueva de la Cañada, Madrid, Spain
| | - A Castro-Carrizo
- Institut de Radioastronomie Millimétrique. 300 rue de la la Piscine, F-38406, Saint Martin d'Hères, France
| | - N Marcelino
- INAF, Istituto di Radioastronomia, via P. Gobetti 101, 40129, Bologna, Italy
| | - C Cabezas
- Grupo de Espectroscopía Molecular, Edificio Quifima, Laboratorios de Espectroscopía y Bioe-spectroscopía. Unidad asociada CSIC, Parque científico Uva, Universidad de Valladolid, Paseo de Belén 5, E-47011, Valladolid, Spain
| | - I Peña
- Grupo de Espectroscopía Molecular, Edificio Quifima, Laboratorios de Espectroscopía y Bioe-spectroscopía. Unidad asociada CSIC, Parque científico Uva, Universidad de Valladolid, Paseo de Belén 5, E-47011, Valladolid, Spain
| | - J L Alonso
- Grupo de Espectroscopía Molecular, Edificio Quifima, Laboratorios de Espectroscopía y Bioe-spectroscopía. Unidad asociada CSIC, Parque científico Uva, Universidad de Valladolid, Paseo de Belén 5, E-47011, Valladolid, Spain
| | - J Zúñiga
- Universidad de Murcia. Faculdad de Química. Dpto. de Química-Física. Campus Espinardo E-30100, Murcia, Spain
| | - A Requena
- Universidad de Murcia. Faculdad de Química. Dpto. de Química-Física. Campus Espinardo E-30100, Murcia, Spain
| | - A Bastida
- Universidad de Murcia. Faculdad de Química. Dpto. de Química-Física. Campus Espinardo E-30100, Murcia, Spain
| | - Y Kalugina
- LOMC-UMR 6294, CNRS-Université du Havre, 25 rue Philippe Lebon, BP. 1123, 76063 Le Havre cedex, France ; Department of Optics and Spectroscopy, Tomsk State University, 36 Lenin av., Tomsk 634050, Russia
| | - F Lique
- LOMC-UMR 6294, CNRS-Université du Havre, 25 rue Philippe Lebon, BP. 1123, 76063 Le Havre cedex, France
| | - M Guélin
- Institut de Radioastronomie Millimétrique. 300 rue de la la Piscine, F-38406, Saint Martin d'Hères, France ; LERMA, Observatoire de Paris, PSL Research University, CNRS, UMR 8112, F-75014, Paris, France
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Cabezas C, Barrientos C, Largo A, Guillemin JC, Alonso JL. Metallic cyanoacetylides of copper, silver and gold: generation and structural characterization. Phys Chem Chem Phys 2016; 18:28538-28547. [DOI: 10.1039/c6cp04474c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Copper, silver and gold cyanoacetylides have been synthesized and characterized in the laboratory using a combination of a laser ablation technique and Fourier transform microwave spectroscopy. A study of the chemical bonding helps to understand the preference for metal–C bonding over metal–N bonding.
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Affiliation(s)
- Carlos Cabezas
- Grupo de Espectroscopia Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico Uva
| | - Carmen Barrientos
- Departamento de Química Física y Química Inorgánica
- Facultad de Ciencias
- Universidad de Valladolid
- Campus Miguel Delibes
- 47011 Valladolid
| | - Antonio Largo
- Departamento de Química Física y Química Inorgánica
- Facultad de Ciencias
- Universidad de Valladolid
- Campus Miguel Delibes
- 47011 Valladolid
| | - Jean-Claude Guillemin
- Institut des Sciences Chimiques de Rennes
- École Nationale Supérieure de Chimie de Rennes
- CNRS
- UMR 6226
- 35708 Rennes Cedex 7
| | - J. L. Alonso
- Grupo de Espectroscopia Molecular (GEM)
- Edificio Quifima
- Laboratorios de Espectroscopia y Bioespectroscopia
- Unidad Asociada CSIC
- Parque Científico Uva
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Tercero B, Cernicharo J, López A, Brouillet N, Kolesniková L, Motiyenko RA, Margulès L, Alonso JL, Guillemin JC. Searching for trans ethyl methyl ether in Orion KL . Astron Astrophys 2015; 582:L1. [PMID: 26869726 PMCID: PMC4747151 DOI: 10.1051/0004-6361/201526255] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We report on the tentative detection of trans ethyl methyl ether (tEME), t-CH3CH2OCH3, through the identification of a large number of rotational lines from each one of the spin states of the molecule towards Orion KL. We also search for gauche-trans-n-propanol, Gt-n-CH3CH2CH2OH, an isomer of tEME in the same source. We have identified lines of both species in the IRAM 30 m line survey and in the ALMA Science Verification data. We have obtained ALMA maps to establish the spatial distribution of these species. Whereas tEME mainly arises from the compact ridge component of Orion, Gt-n-propanol appears at the emission peak of ethanol (south hot core). The derived column densities of these species at the location of their emission peaks are ≤(4.0 ± 0.8) × 1015 cm-2 and ≤(1.0 ± 0.2)× 1015 cm-2 for tEME and Gt-n-propanol, respectively. The rotational temperature is ~100 K for both molecules. We also provide maps of CH3OCOH, CH3CH2OCOH, CH3OCH3, CH3OH, and CH3CH2OH to compare the distribution of these organic saturated O-bearing species containing methyl and ethyl groups in this region. Abundance ratios of related species and upper limits to the abundances of non-detected ethers are provided. We derive an abundance ratio N(CH3OCH3)/N(tEME) ≥ 150 in the compact ridge of Orion.
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Affiliation(s)
- B Tercero
- Grupo de Astrofísica Molecular. Instituto de CC. de Materiales de Madrid (ICMM-CSIC). Sor Juana Inés de la Cruz, 3, Cantoblanco, 28049 Madrid, Spain
| | - J Cernicharo
- Grupo de Astrofísica Molecular. Instituto de CC. de Materiales de Madrid (ICMM-CSIC). Sor Juana Inés de la Cruz, 3, Cantoblanco, 28049 Madrid, Spain
| | - A López
- Grupo de Astrofísica Molecular. Instituto de CC. de Materiales de Madrid (ICMM-CSIC). Sor Juana Inés de la Cruz, 3, Cantoblanco, 28049 Madrid, Spain ; Dpto. de Astrofísica, CAB, INTA-CSIC, Crta Torrejón-Ajalvir, km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - N Brouillet
- Université Bordeaux, LAB, UMR 5804, 33270 Floirac, France ; CNRS, LAB, UMR 5804, 33270 Floirac, France
| | - L Kolesniková
- 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
| | - R A Motiyenko
- Laboratoire de Physique des Lasers, Atomes, et Molécules, UMR CNRS 8523, Université de Lille I, 59655 Villeneuve d'Ascq Cédex, France
| | - L Margulès
- Laboratoire de Physique des Lasers, Atomes, et Molécules, UMR CNRS 8523, Université de Lille I, 59655 Villeneuve d'Ascq Cédex, France
| | - 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, Universidad de Valladolid, 47011 Valladolid, Spain
| | - J-C Guillemin
- Institut des Sciences Chimiques de Rennes, École Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, 11 Allée de Beaulieu, CS 50837, 35708 Rennes Cedex 7, France
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Kuş N, Sharma A, Peña I, Bermúdez MC, Cabezas C, Alonso JL, Fausto R. Conformers of β-aminoisobutyric acid probed by jet-cooled microwave and matrix isolation infrared spectroscopic techniques. J Chem Phys 2015; 138:144305. [PMID: 24981533 DOI: 10.1063/1.4799456] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
β-aminoisobutyric acid (BAIBA) has been studied in isolation conditions: in the gas phase and trapped into a cryogenic N2 matrix. A solid sample of the compound was vaporized by laser ablation and investigated through their rotational spectra in a supersonic expansion using two different spectroscopic techniques: broadband chirped pulse Fourier transform microwave spectroscopy and conventional molecular beam Fourier transform microwave spectroscopy. Four conformers with structures of two types could be successfully identified by comparison of the experimental rotational and (14)N nuclear quadruple coupling constants with those predicted theoretically: type A, bearing an OH⋯N intramolecular hydrogen bond and its carboxylic group in the trans geometry (H-O-C=O dihedral ∼180°), and type B, having an NH⋯O bond and the cis arrangement of the carboxylic group. These two types of conformers could also be trapped from the gas phase into a cryogenic N2 matrix and probed by Fourier transform infrared (IR) spectroscopy. In situ irradiation of BAIBA isolated in N2 matrix of type B conformers using near-IR radiation tuned at the frequency of the O-H stretching 1st overtone (∼6930 cm(-1)) of these forms allowed to selectively convert them into type A conformers and into a new type of conformers of higher energy (type D) bearing an NH⋯O=C bond and a O-H "free" trans carboxylic group.
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Affiliation(s)
- N Kuş
- Department of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal
| | - A Sharma
- Department of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal
| | - I Peña
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Universidad de Valladolid, 47005 Valladolid, Spain
| | - M C Bermúdez
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Universidad de Valladolid, 47005 Valladolid, Spain
| | - C Cabezas
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Universidad de Valladolid, 47005 Valladolid, Spain
| | - J L Alonso
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Universidad de Valladolid, 47005 Valladolid, Spain
| | - R Fausto
- Department of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal
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Corzo N, Alonso JL, Azpiroz F, Calvo MA, Cirici M, Leis R, Lombó F, Mateos-Aparicio I, Plou FJ, Ruas-Madiedo P, Rúperez P, Redondo-Cuenca A, Sanz ML, Clemente A. [Prebiotics: concept, properties and beneficial effects]. NUTR HOSP 2015; 31 Suppl 1:99-118. [PMID: 25659062 DOI: 10.3305/nh.2015.31.sup1.8715] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Prebiotics are non-digestible food ingredients (oligosaccharides) that reach the colon and are used as substrate by microorganisms producing energy, metabolites and micronutrients used for the host; in addition they also stimulate the selective growth of certain beneficial species (mainly bifidobacteria and lactobacilli) in the intestinal microbiota. In this article, a multidisciplinary approach to understand the concept of prebiotic carbohydrates, their properties and beneficial effects in humans has been carried out. Definitions of prebiotics, reported by relevant international organizations and researchers, are described. A comprehensive description of accepted prebiotics having strong scientific evidence of their beneficial properties in humans (inulin-type fructans, FOS, GOS, lactulose and human milk oligosaccharides) is reported. Emerging prebiotics and those which are in the early stages of study have also included in this study. Taken into account that the chemical structure greatly influences carbohydrates prebiotic properties, the analytical techniques used for their analysis and characterization are discussed. In vitro and in vivo models used to evaluate the gastrointestinal digestion, absorption resistance and fermentability in the colon of prebiotics as well as major criteria to design robust intervention trials in humans are described. Finally, a comprehensive summary of the beneficial effects of prebiotics for health at systemic and intestinal levels is reported. The research effort on prebiotics has been intensive in last decades and has demonstrated that a multidisciplinary approach is necessary in order to claim their health benefits.
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Affiliation(s)
- N Corzo
- Departamento de Bioactividad y Análisis de Alimentos, Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM) Madrid..
| | - J L Alonso
- Departamento de Ingeniería Química, Universidad de Vigo. Facultad de Ciencias, Campus de Ourense, Ourense
| | - F Azpiroz
- Servicio de Aparato Digestivo, Hospital Vall d'Hebron, Universidad Autónoma de Barcelona, Barcelona
| | - M A Calvo
- Grupo de investigación en Microbiología aplicada y medio-ambiental, Facultad de Veterinaria, Universidad Autónoma de Barcelona, Campus de Bellaterra, Barcelona
| | - M Cirici
- BENEO. Connecting nutrition and health, BENEO-Ibérica Barcelona
| | - R Leis
- Unidad de Gastroenterología, Hepatología y Nutrición Pediátrica, Dpto. Pediatría, Hospital Clínico Universitario de Santiago, Área de Gestión Integrada de Santiago, Universidad de Santiago de Compostela
| | - F Lombó
- Grupo de Investigación de Biotecnología y Terapia Experimental basada en Nutraceúticos (BITTEN), Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, Facultad de Medicina, Oviedo
| | - I Mateos-Aparicio
- Departamento de Nutrición y Bromatología II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid
| | - F J Plou
- Grupo de Biocatálisis Aplicada, Instituto de Catálisis y Petroleoquímica, CSIC, Madrid
| | - P Ruas-Madiedo
- Departamento de Microbiología y Bioquímica de Productos Lácteos, Instituto de Productos Lácteos de Asturias - (IPLA-CSIC) Asturias
| | - P Rúperez
- Departamento de Metabolismo y Nutrición, Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN-CSIC) Madrid
| | - A Redondo-Cuenca
- Departamento de Nutrición y Bromatología II, Bromatología, Facultad de Farmacia, Universidad Complutense de Madrid
| | - M L Sanz
- Departamento de Análisis Instrumental y Química Ambiental, Instituto de Química Orgánica General (CSIC), Madrid
| | - A Clemente
- Departamento de Fisiología y Bioquímica de la Nutrición Animal, Estación Experimental del Zaidin (CSIC), Granada. España
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Alonso JL, Castro A, Clemente-Gallardo J, Cuchí JC, Echenique P, Esteve JG, Falceto F. Nonextensive thermodynamic functions in the Schrödinger-Gibbs ensemble. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 91:022137. [PMID: 25768488 DOI: 10.1103/physreve.91.022137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Indexed: 06/04/2023]
Abstract
Schrödinger suggested that thermodynamical functions cannot be based on the gratuitous allegation that quantum-mechanical levels (typically the orthogonal eigenstates of the Hamiltonian operator) are the only allowed states for a quantum system [E. Schrödinger, Statistical Thermodynamics (Courier Dover, Mineola, 1967)]. Different authors have interpreted this statement by introducing density distributions on the space of quantum pure states with weights obtained as functions of the expectation value of the Hamiltonian of the system. In this work we focus on one of the best known of these distributions and prove that, when considered in composite quantum systems, it defines partition functions that do not factorize as products of partition functions of the noninteracting subsystems, even in the thermodynamical regime. This implies that it is not possible to define extensive thermodynamical magnitudes such as the free energy, the internal energy, or the thermodynamic entropy by using these models. Therefore, we conclude that this distribution inspired by Schrödinger's idea cannot be used to construct an appropriate quantum equilibrium thermodynamics.
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Affiliation(s)
- J L Alonso
- Departamento de Física Teórica, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Mariano Esquillor s/n, 50018 Zaragoza, Spain
- Unidad Asociada IQFR-BIFI, Universidad de Zaragoza, Mariano Esquillor s/n, 50018 Zaragoza, Spain
| | - A Castro
- Fundación ARAID, Universidad de Zaragoza, Mariano Esquillor s/n, 50018 Zaragoza, Spain
| | - J Clemente-Gallardo
- Departamento de Física Teórica, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Mariano Esquillor s/n, 50018 Zaragoza, Spain
- Unidad Asociada IQFR-BIFI, Universidad de Zaragoza, Mariano Esquillor s/n, 50018 Zaragoza, Spain
| | - J C Cuchí
- Departament d'Enginyeria Agroforestal, Escola Tècnica Superior d'Enginyeria Agrària, Universitat de Lleida, Alcalde Rovira Roure 191, 25198 Lleida, Spain
| | - P Echenique
- Departamento de Física Teórica, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Mariano Esquillor s/n, 50018 Zaragoza, Spain
- Unidad Asociada IQFR-BIFI, Universidad de Zaragoza, Mariano Esquillor s/n, 50018 Zaragoza, Spain
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - J G Esteve
- Departamento de Física Teórica, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Mariano Esquillor s/n, 50018 Zaragoza, Spain
| | - F Falceto
- Departamento de Física Teórica, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Mariano Esquillor s/n, 50018 Zaragoza, Spain
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Anniccherico FJ, Alonso JL, Urbieta M, Pérez Ricarte S. [Dabigatran as a therapeutic possibility in heparin-induced thrombocytopenia type II]. An Sist Sanit Navar 2013; 35:521-4. [PMID: 23296239 DOI: 10.23938/assn.0109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The syndrome of heparin-induced thrombocytopenia (HIT), with an incidence of 0.2-0.5% in patients exposed to heparin for more than 4 days, is produced by an immune alteration with the formation of antibodies against the heparin platelet factor 4 complex. It presents a wide spectrum of clinical manifestations, the most frequent of which are thrombocytopenia, thrombotic arterial-venous phenomena, and cutaneous necrosis. Up to the present, lepiridin, recently suspended, and argatroban (direct thrombin inhibitors) have been the approved medicines normally used in treatment, administered in parenteral form. Dabigatran, a new anticoagulant medicine that is a direct and reversible thrombin inhibitor, could theoretically be a medicine employed in treating HIT. According to the bibliography consulted we are presenting the first case of HIT treated with dabigatran in the medical literature.
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Affiliation(s)
- F J Anniccherico
- Servicio de Medicina Interna, Complejo Hospitalario de Navarra, Pamplona, 31008, Spain.
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Alonso JL, Clemente-Gallardo J, Echenique-Robba P, Jover-Galtier JA. Comment on “Correlated electron-nuclear dynamics: Exact factorization of the molecular wavefunction” [J. Chem. Phys. 137, 22A530 (2012)]. J Chem Phys 2013; 139:087101. [DOI: 10.1063/1.4818521] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Alonso JL, Castro A, Clemente-Gallardo J, Echenique P, Mazo JJ, Polo V, Rubio A, Zueco D. Non-adiabatic effects within a single thermally averaged potential energy surface: Thermal expansion and reaction rates of small molecules. J Chem Phys 2012; 137:22A533. [DOI: 10.1063/1.4747699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Cuesta G, Soler A, Alonso JL, Ruvira MA, Lucena T, Arahal DR, Goodfellow M. Pseudonocardia hispaniensis sp. nov., a novel actinomycete isolated from industrial wastewater activated sludge. Antonie Van Leeuwenhoek 2012; 103:135-42. [PMID: 22899021 DOI: 10.1007/s10482-012-9792-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/06/2012] [Indexed: 10/28/2022]
Abstract
A novel actinomycete, designated PA3(T), was isolated from an oil refinery wastewater treatment plant, located in Palos de la Frontera, Huelva, Spain, and characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a distinct subclade in the Pseudonocardia tree together with Pseudonocardia asaccharolytica DSM 44247(T). The chemotaxonomic properties of the isolate, for example, the presence of MK-8 (H(4)) as the predominant menaquinone and iso-C(16:0) as the major fatty acid, are consistent with its classification in the genus Pseudonocardia. DNA:DNA pairing experiments between the isolate and the type strain of P. asaccharolytica DSM 44247(T) showed that they belonged to separate genomic species. The two strains were readily distinguished using a combination of phenotypic properties. Consequently, it is proposed that isolate PA3(T) represents a novel species for which the name Pseudonocardia hispaniensis sp. nov. is proposed. The type strain is PA3(T) (= CCM 8391(T) = CECT 8030(T)).
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Affiliation(s)
- G Cuesta
- Área de Microbiología, Departamento de Biotecnología, E.T.S.I. Agronómica y Medio Natural, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain.
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Alonso JL, Clemente-Gallardo J, Cuchí JC, Echenique P, Falceto F. Ehrenfest dynamics is purity non-preserving: A necessary ingredient for decoherence. J Chem Phys 2012; 137:054106. [DOI: 10.1063/1.4737861] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
The conformational landscape of crown ethers has constituted a central topic in the development of host-guest supramolecular chemistry. We report a high-resolution rotational study of a crown ether, 1,4,7,10,13-pentaoxacyclopentadecane (15-crown-5), by means of molecular beam Fourier transform microwave spectroscopy. The considerable size and the broad range of conformations allowed by the flexibility of the cyclic backbone of this ether pose important challenges to spectroscopy approaches. In this investigation, three stable rotamers of the 15-crown-5 ether have been identified and characterized through their rotational constants and centrifugal distortion coefficients. Ab initio quantum calculations at the MP2 level predict these conformers as the most stable ones for the title system and reproduce accurately their distinct structural features. The results pave the ground for an extensive survey of the conformational landscape of the 15-crown-5 and related cyclic ethers in the near term.
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Affiliation(s)
- F Gámez
- †Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013 Seville, Spain
| | - B Martínez-Haya
- †Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013 Seville, Spain
| | - S Blanco
- ‡Grupo de Espectroscopía Molecular, Edificio Quifima, Área de Química Física, Campus Miguel Delibes, Universidad de Valladolid, 47011 Valladolid, Spain
| | - J C López
- ‡Grupo de Espectroscopía Molecular, Edificio Quifima, Área de Química Física, Campus Miguel Delibes, Universidad de Valladolid, 47011 Valladolid, Spain
| | - J L Alonso
- ‡Grupo de Espectroscopía Molecular, Edificio Quifima, Área de Química Física, Campus Miguel Delibes, Universidad de Valladolid, 47011 Valladolid, Spain
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Rodriguez-Manzano J, Alonso JL, Ferrús MA, Moreno Y, Amorós I, Calgua B, Hundesa A, Guerrero-Latorre L, Carratala A, Rusiñol M, Girones R. Standard and new faecal indicators and pathogens in sewage treatment plants, microbiological parameters for improving the control of reclaimed water. Water Sci Technol 2012; 66:2517-23. [PMID: 23109565 DOI: 10.2166/wst.2012.233] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
This study involved collaboration between three centres with expertise in viruses, bacteria and protozoa. The focus of the research was the study of the dissemination and removal of pathogens and faecal indicators in two sewage treatment plants (STP1 and STP2) using tertiary treatments. Samples were collected over a period of five months through the sewage treatment processes. Analysis of the samples revealed that the plants were not efficient at removing the faecal indicators and pathogens tested during the study. From entry point (raw sewage) to effluent level (tertiary treatment effluent water), the experimental results showed that the reduction ratios of human adenoviruses were 1.2 log₁₀ in STP1 and 1.9 log₁₀ in STP2. Whereas for Giardia spp. and Cryptosporidium spp. the reduction ratios were 2.3 log₁₀ for both pathogens in STP1, and 3.0 and 1.7 log₁₀ in STP2, respectively. Furthermore, the presence of faecal indicators and pathogens at different sampling points was evaluated revealing that the tested pathogens were present in reclaimed water. Human adenovirus and Arcobacter spp. showed positive results in infectivity assays for most of the tertiary effluent water samples that comply with current legislation in Spain. The pathogens detected must be evaluated using a risk assessment model, which will be essential for the development of improved guidelines for the re-use of reclaimed water.
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Affiliation(s)
- J Rodriguez-Manzano
- Department of Microbiology, Faculty of Biology, University of Barcelona, Spain.
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Gámez F, Martínez-Haya B, Blanco S, López JC, Alonso JL. Microwave spectroscopy and quantum chemical investigation of nine low energy conformers of the 15-crown-5 ether. Phys Chem Chem Phys 2012; 14:12912-8. [PMID: 22898803 DOI: 10.1039/c2cp41635b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- F Gámez
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013 Seville, Spain
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Alonso JL, Domínguez H, Garrote G, González-Muñoz M, Gullón B, Moure A, Santos V, Vila C, Yáñez R. Biorefinery processes for the integral valorization of agroindustrial and forestal wastes Procesos de biorrefinería para la valorización integral de residuos agroindustriales y forestales. CyTA - Journal of Food 2011. [DOI: 10.1080/19476337.2011.598949] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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García-Risueño P, Echenique P, Alonso JL. Exact and efficient calculation of Lagrange multipliers in biological polymers with constrained bond lengths and bond angles: proteins and nucleic acids as example cases. J Comput Chem 2011; 32:3039-46. [PMID: 21823135 DOI: 10.1002/jcc.21885] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 06/21/2011] [Indexed: 11/05/2022]
Abstract
To accelerate molecular dynamics simulations, it is common to impose holonomic constraints on the hardest degrees of freedom. In this way, the time step used to integrate the equations of motion can be increased, thereby allowing longer total simulation times. The imposition of such constraints results in an aditional set of N(c) equations (the equations of constraint) and unknowns (their associated Lagrange multipliers), whose solution is closely related to any algorithm implementing the constraints in Euclidean coordinates. In this work, it is shown that, due to the essentially linear structure of typical biological polymers the algebraic equations that need to be solved involve a matrix which is not only sparse, but also banded if the constraints are indexed in a skilful way. This allows the Lagrange multipliers to be obtained through a noniterative procedure, which can be considered exact up to machine precision, and which takes O(N(c)) operations, instead of the usual O(N c3) for generic molecular systems. We develop the formalism, and describe the appropriate indexing for a number of model molecules. Finally, we provide a numerical example of the technique in a series of polyalanine peptides of different lengths. Although a use of the Lagrange multipliers without any modification in the solution of the underlying ordinary differential equations yields unstable integration algorithms, the central role of these quantities makes their efficient calculation useful for the improvement of methods that correctly enforce the exact satisfaction of the constraints at each time step. We provide several examples of this.
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Affiliation(s)
- Pablo García-Risueño
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, E-28006 Madrid, Spain.
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Echenique P, Cavasotto CN, De Marco M, Garca-Risueño P, Alonso JL. An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints. PLoS One 2011; 6:e24563. [PMID: 21931757 PMCID: PMC3171457 DOI: 10.1371/journal.pone.0024563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 08/15/2011] [Indexed: 11/18/2022] Open
Abstract
In this work, we introduce an algorithm to compute the derivatives of physical observables along the constrained subspace when flexible constraints are imposed on the system (i.e., constraints in which the constrained coordinates are fixed to configuration-dependent values). The presented scheme is exact, it does not contain any tunable parameter, and it only requires the calculation and inversion of a sub-block of the Hessian matrix of second derivatives of the function through which the constraints are defined. We also present a practical application to the case in which the sought observables are the Euclidean coordinates of complex molecular systems, and the function whose minimization defines the flexible constraints is the potential energy. Finally, and in order to validate the method, which, as far as we are aware, is the first of its kind in the literature, we compare it to the natural and straightforward finite-differences approach in a toy system and in three molecules of biological relevance: methanol, N-methyl-acetamide and a tri-glycine peptide.
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Affiliation(s)
- Pablo Echenique
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
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Gullón B, Yáñez R, Alonso JL, Parajó JC. Production of oligosaccharides and sugars from rye straw: a kinetic approach. Bioresour Technol 2010; 101:6676-84. [PMID: 20400295 DOI: 10.1016/j.biortech.2010.03.080] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 03/15/2010] [Accepted: 03/19/2010] [Indexed: 05/03/2023]
Abstract
Following the biorefinery philosophy, the non-isothermal autohydrolysis of rye straw (an agroindustrial byproduct) was carried out to obtain liquors containing substituted xylooligosaccharides and solids enriched in cellulose (suitable as substrates for further enzymatic hydrolysis). The effects of temperature (in the range 185-220 degrees C) on the composition of solids and liquid phases were evaluated, and kinetic models were developed. When operation was carried out at 208 degrees C, 69.2% of the initial xylan was converted into xylooligosaccharides, leading to reaction liquors containing up to 22.4 g oligosaccharides/L. The effects of treatments on the DP of the target products and on their substituents were also measured. At 208 degrees C, the percentages of XOS having DP2-4, DP5-6 and DP>6 were 24.8%, 22.4% and 54.8%, respectively. Under selected conditions, the molar ratio Xyl:Ac:UA of the oligomers was 10:1.54:0.50. Finally, when the solid was subjected to enzymatic hydrolysis, 70.6% of cellulose and 63.8% of xylan were saccharified after 48 h.
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Affiliation(s)
- B Gullón
- Department of Chemical Engineering, Faculty of Science, University of Vigo (Campus Ourense), As Lagoas, 32004 Ourense, Spain
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Yañez R, Alonso JL, Díaz MJ. Influence of bulking agent on sewage sludge composting process. Bioresour Technol 2009; 100:5827-5833. [PMID: 19560348 DOI: 10.1016/j.biortech.2009.05.073] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 05/27/2009] [Accepted: 05/28/2009] [Indexed: 05/28/2023]
Abstract
Four types of compost, consisting of mixtures of Acacia dealbata (A) with sewage sludge (SS) were studied in a laboratory reactor. Composting time was 80 days and parameters monitored over this period included temperature, organic matter, pH, CO(2), O(2), C/N ratio, Kjeldahl-N, as well as maturity indexes. All the studied parameters were influenced by the bulking amount used. The highest profile temperature measured was for the A/SS 1/2 (w/w) mixture that reached a maxima temperature of 67 degrees C and lower maximum temperatures of 52, 48 and 46 degrees C were observed for A/SS 1/3, 1/1 and 1/0 composts, respectively. The kinetic model used showed that a descent of sewage sludge in the composting mixtures favored the enzyme-substrate affinity. However, an increase in depending on the parameters of the process factors was observed when the sewage sludge ratio was increased in mixtures. The optimal amounts of sewage sludge for co-composting with Acacia indicate that moderate amounts of sludge (1/1) would be the best compromise.
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Affiliation(s)
- R Yañez
- Chemical Engineering Department, Facultad de Ciencias, Campus de Oruense, Universidad de Vigo, Ourense, Spain
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