1
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Rap DB, Schrauwen JGM, Redlich B, Brünken S. Ionic fragmentation products of benzonitrile as important intermediates in the growth of polycyclic aromatic hydrocarbons. Phys Chem Chem Phys 2024; 26:7296-7307. [PMID: 38353151 PMCID: PMC10900304 DOI: 10.1039/d3cp05574d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
In various astronomical environments such as the interstellar medium or (exo)planetary atmospheres, an interplay of bottom-up growth and top-down destruction processes of (polycyclic) aromatic hydrocarbons (PAHs) takes place. To get more insight into the interplay of both processes, we disentangle the fragmentation and formation processes that take place upon dissociative ionization of benzonitrile. We build on previous spectroscopic detections of the ionic fragmentation products of benzonitrile and use these as reactants for low-temperature bottom-up ion-molecule reactions with acetylene. By combining kinetics and infrared action spectroscopy, we reveal exothermic pathways to various (polycyclic) aromatic molecules, including the pentalene and phenylacetylene radical cations. We determine the reaction rate coefficients and unambiguously assign the structures of the reaction products. The data is supplemented by potential energy surface calculations and the analysis of non-covalent interactions. This study shows the unexpected formation of a linked four- and six-membered ring structure (phenylcyclobutadiene radical cation) with molecular formula C10H8˙+, and not the commonly observed isomer naphthalene˙+. All observed reactions proceed via radiative association processes and are relevant for the chemistry in (cold) astrochemical environments.
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Affiliation(s)
- Daniël B Rap
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
| | - Johanna G M Schrauwen
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
| | - Britta Redlich
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
| | - Sandra Brünken
- Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
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2
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Fozouni Y, Larson EC, Gnade B. Towards automated molecular detection through simulated generation of CMOS-based rotational spectroscopy. Heliyon 2023; 9:e17055. [PMID: 37383210 PMCID: PMC10293684 DOI: 10.1016/j.heliyon.2023.e17055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/25/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023] Open
Abstract
The use of CMOS sensors for rotational spectroscopy is a promising, but challenging avenue for low-cost gas sensing and molecular identification. A main challenge in this approach is that practical CMOS spectroscopy samples contain various different noise sources that reduce the effectiveness of matching techniques for molecular identification with rotational spectroscopy. To help solve this challenge, we develop a software application tool that can demonstrate the feasibility and reliability of detection with CMOS sensor samples. Specifically, the tool characterizes the types of noise in CMOS sample collection and synthesizes spectroscopy files based upon existing databases of rotational spectroscopy samples gathered from other sensors. We use the software to create a large database of plausible CMOS-generated sample files of gases. This dataset is used to help evaluate spectral matching algorithms used in gas sensing and molecular identification applications. We evaluate these traditional methods on the synthesized dataset and discuss how peak finding and spectral matching algorithms can be altered to accommodate the noise sources present in CMOS sample collection.
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Affiliation(s)
- Yasamin Fozouni
- Computer Science, Southern Methodist University, Dallas, USA
| | - Eric C. Larson
- Computer Science, Southern Methodist University, Dallas, USA
| | - Bruce Gnade
- Engineering, University of Texas, Dallas, USA
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3
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Melli A, Melosso M, Bizzocchi L, Alessandrini S, Jiang N, Tonolo F, Boi S, Castellan G, Sapienza C, Guillemin JC, Dore L, Puzzarini C. Rotational Spectra of Unsaturated Carbon Chains Produced by Pyrolysis: The Case of Propadienone, Cyanovinylacetylene, and Allenylacetylene. J Phys Chem A 2022; 126:6210-6220. [PMID: 36044202 PMCID: PMC9483987 DOI: 10.1021/acs.jpca.2c05018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Several interstellar molecules are highly reactive unsaturated
carbon chains, which are unstable under terrestrial conditions. Laboratory
studies in support of their detection in space thus face the issue
of how to produce these species and how to correctly model their rotational
energy levels. In this work, we introduce a general approach for producing
and investigating unsaturated carbon chains by means of selected test
cases. We report a comprehensive theoretical/experimental spectroscopic
characterization of three species, namely, propadienone, cyanovinylacetylene,
and allenylacetylene, all of them being produced by means of flash
vacuum pyrolysis of a suitable precursor. For each species, quantum-chemical
calculations have been carried out with the aim of obtaining accurate
predictions of the missing spectroscopic information required to guide
spectral analysis and assignment. Rotational spectra of the title
molecules have been investigated up to 400 GHz by using a frequency-modulation
millimeter-/submillimeter-wave spectrometer, thus significantly extending
spectral predictions over a wide range of frequency and quantum numbers.
A comparison between our results and those available in the literature
points out the clear need of the reported laboratory measurements
at higher frequencies for setting up accurate line catalogs for astronomical
searches.
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Affiliation(s)
- Alessio Melli
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.,Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Naples, Italy
| | - Luca Bizzocchi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Silvia Alessandrini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Ningjing Jiang
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Francesca Tonolo
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Salvatore Boi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Giorgia Castellan
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Carlotta Sapienza
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Jean-Claude Guillemin
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR6226, F-35000 Rennes, France
| | - Luca Dore
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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4
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The Application Value and Influence of Integrated Nursing of Operating Room and Disinfection Supply Center Combined with 6Sigma Management in Operating Room Instruments. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:8490473. [PMID: 36017152 PMCID: PMC9398843 DOI: 10.1155/2022/8490473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/17/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022]
Abstract
In this study, 897 surgical instruments used for comprehensive management of hand supply from January to December 2019 were selected as the control group. Similarly, 1086 surgical instruments administered with 6Sigma from January to December 2020 were selected as the observation group. By observing and comparing the differences between the two groups of patients in the operating room equipment cleaning pass rate and general indicators, other related pass rate, operating room equipment defects, and doctors' satisfaction with equipment, to explore the application value and influence of comprehensive nursing in operating room and disinfection supply center combined with 6Sigma management in operating room equipment management. The results show that the application of hand-supply integration combined with 6Sigma management has a good effect on operating room equipment management, which significantly improves the qualified rate of operating room equipment cleaning and the satisfaction of doctors to the equipment, and reduces the defects of operating room equipment, which has a certain reference value for operating room equipment management.
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5
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Rap DB, van Boxtel TJHH, Redlich B, Brünken S. Spectroscopic Detection of Cyano-Cyclopentadiene Ions as Dissociation Products upon Ionization of Aniline. J Phys Chem A 2022; 126:2989-2997. [PMID: 35512055 PMCID: PMC9125686 DOI: 10.1021/acs.jpca.2c01429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The H-loss products
(C6H6N+) from
the dissociative ionization of aniline (C6H7N) have been studied by infrared predissociation spectroscopy in
a cryogenic ion trap instrument at the free electron laser for infrared
experiments (FELIX) laboratory. Broadband and narrow line width vibrational
spectra in the spectral fingerprint region of 550–1800 cm–1 have been recorded. The comparison to calculated
spectra of the potential isomeric structures of the fragment ions
reveals that the dominant fragments are five-membered cyano-cyclopentadiene
ions. Computed C6H7N•+ potential
energy surfaces suggest that the dissociation path leading to H loss
starts with an isomerization process, following a similar trajectory
as the one leading to HNC loss. The possible presence of cyano-cyclopentadiene
ions and related five-membered ring species in Titan’s atmosphere
and the interstellar medium are discussed.
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Affiliation(s)
- Daniël B Rap
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Tom J H H van Boxtel
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Britta Redlich
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Sandra Brünken
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
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6
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Barnum TJ, Siebert MA, Lee KLK, Loomis RA, Changala PB, Charnley SB, Sita ML, Xue C, Remijan AJ, Burkhardt AM, McGuire BA, Cooke IR. A Search for Heterocycles in GOTHAM Observations of TMC-1. J Phys Chem A 2022; 126:2716-2728. [PMID: 35442689 DOI: 10.1021/acs.jpca.2c01435] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have conducted an extensive search for nitrogen-, oxygen-, and sulfur-bearing heterocycles toward Taurus Molecular Cloud 1 (TMC-1) using the deep, broadband centimeter-wavelength spectral line survey of the region from the GOTHAM large project on the Green Bank Telescope. Despite their ubiquity in terrestrial chemistry, and the confirmed presence of a number of cyclic and polycyclic hydrocarbon species in the source, we find no evidence for the presence of any heterocyclic species. Here, we report the derived upper limits on the column densities of these molecules obtained by Markov Chain Monte Carlo (MCMC) analysis and compare this approach to traditional single-line upper limit measurements. We further hypothesize why these molecules are absent in our data, how they might form in interstellar space, and the nature of observations that would be needed to secure their detection.
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Affiliation(s)
- Timothy J Barnum
- Department of Chemistry, Union College, Schenectady, New York 12308, United States
| | - Mark A Siebert
- Department of Astronomy, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Kin Long Kelvin Lee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ryan A Loomis
- National Radio Astronomy Observatory, Charlottesville, Virginia 22903, United States
| | - P Bryan Changala
- Center for Astrophysics
- Harvard & Smithsonian, Cambridge, Massachusetts 02138, United States
| | - Steven B Charnley
- Astrochemistry Laboratory and the Goddard Center for Astrobiology, NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, United States
| | - Madelyn L Sita
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Ci Xue
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anthony J Remijan
- National Radio Astronomy Observatory, Charlottesville, Virginia 22903, United States
| | - Andrew M Burkhardt
- Department of Physics, Wellesley College, 106 Central Street, Wellesley, Massachusetts 02481, United States
| | - Brett A McGuire
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,National Radio Astronomy Observatory, Charlottesville, Virginia 22903, United States.,Center for Astrophysics
- Harvard & Smithsonian, Cambridge, Massachusetts 02138, United States
| | - Ilsa R Cooke
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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7
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Kolesniková L, León I, Alonso ER, Mata S, Alonso JL. An Innovative Approach for the Generation of Species of the Interstellar Medium. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Lucie Kolesniková
- Department of Analytical Chemistry University of Chemistry and Technology Technická 5 16628 Prague 6 Czech Republic
| | - Iker León
- Grupo de Espectroscopia Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopia y, Bioespectroscopia Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| | - Elena R. Alonso
- Instituto Biofisika (UPV/EHU, CSIC) University of the Basque Country 48940 Leioa Spain
- Departamento de Química Física Facultad de Ciencia y Tecnología Universidad del País Vasco Barrio Sarriena s/n 48940 Leioa Spain
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopia y, Bioespectroscopia Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| | - Jose Luis Alonso
- Grupo de Espectroscopia Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopia y, Bioespectroscopia Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
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8
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Kolesniková L, León I, Alonso ER, Mata S, Alonso JL. An Innovative Approach for the Generation of Species of the Interstellar Medium. Angew Chem Int Ed Engl 2021; 60:24461-24466. [PMID: 34496111 PMCID: PMC8597129 DOI: 10.1002/anie.202110325] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/02/2021] [Indexed: 11/16/2022]
Abstract
The large amount of unstable species in the realm of interstellar chemistry drives an urgent need to develop efficient methods for the in situ generations of molecules that enable their spectroscopic characterizations. Such laboratory experiments are fundamental to decode the molecular universe by matching the interstellar and terrestrial spectra. We propose an approach based on laser ablation of nonvolatile solid organic precursors. The generated chemical species are cooled in a supersonic expansion and probed by high‐resolution microwave spectroscopy. We present a proof of concept through a simultaneous formation of interstellar compounds and the first generation of aminocyanoacetylene using diaminomaleonitrile as a prototypical precursor. With this micro‐laboratory, we open the door to generation of unsuspected species using precursors not typically accessible to traditional techniques such as electric discharge and pyrolysis.
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Affiliation(s)
- Lucie Kolesniková
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Iker León
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopia y, Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Elena R Alonso
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940, Leioa, Spain.,Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena s/n, 48940, Leioa, Spain
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopia y, Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Jose Luis Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopia y, Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, 47011, Valladolid, Spain
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9
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McCarthy MC, McGuire BA. Aromatics and Cyclic Molecules in Molecular Clouds: A New Dimension of Interstellar Organic Chemistry. J Phys Chem A 2021; 125:3231-3243. [DOI: 10.1021/acs.jpca.1c00129] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael C. McCarthy
- Center for Astrophysics
- Harvard & Smithsonian, 60 Garden Street, Cambridge Massachusetts 02138, United States
| | - Brett A. McGuire
- Center for Astrophysics
- Harvard & Smithsonian, 60 Garden Street, Cambridge Massachusetts 02138, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- National Radio Astronomy Observatory, Charlottesville, Virginia 22903, United States
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10
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Cernicharo J, Cabezas C, Agúndez M, Tercero B, Marcelino N, Pardo JR, Tercero F, Gallego J, López-Pérez J, deVicente P. Discovery of allenyl acetylene, H 2CCCHCCH, in TMC-1. A study of the isomers of C 5H 4. ASTRONOMY AND ASTROPHYSICS 2021; 647:L3. [PMID: 33850332 PMCID: PMC7610584 DOI: 10.1051/0004-6361/202140482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We present the discovery in TMC-1 of allenyl acetylene, H2CCCHCCH, through the observation of nineteen lines with a signal-to-noise ratio ~4-15. For this species, we derived a rotational temperature of 7±1K and a column density of 1.2±0.2×1013 cm-2. The other well known isomer of this molecule, methyl diacetylene (CH3C4H), has also been observed and we derived a similar rotational temperature, Tr=7.0±0.3 K, and a column density for its two states (A and E) of 6.5±0.3×1012 cm-2. Hence, allenyl acetylene and methyl diacetylene have a similar abundance. Remarkably, their abundances are close to that of vinyl acetylene (CH2CHCCH). We also searched for the other isomer of C5H4, HCCCH2CCH (1.4-Pentadiyne), but only a3σ upper limit of 2.5×1012 cm-2 to the column density can be established. These results have been compared to state-of-the-art chemical models for TMC-1, indicating the important role of these hydrocarbons in its chemistry. The rotational parameters of allenyl acetylene have been improved by fitting the existing laboratory data together with the frequencies of the transitions observed in TMC-1.
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Affiliation(s)
- J. Cernicharo
- Grupo de Astrofísica Molecular, Instituto de Física Fundamental (IFF-CSIC), C/ Serrano 121, 28006 Madrid, Spain
| | - C. Cabezas
- Grupo de Astrofísica Molecular, Instituto de Física Fundamental (IFF-CSIC), C/ Serrano 121, 28006 Madrid, Spain
| | - M. Agúndez
- Grupo de Astrofísica Molecular, Instituto de Física Fundamental (IFF-CSIC), C/ Serrano 121, 28006 Madrid, Spain
| | - B. Tercero
- Centro de Desarrollos Tecnológicos, Observatorio de Yebes (IGN), 19141 Yebes, Guadalajara, Spain
- Observatorio Astronómico Nacional (OAN, IGN), Madrid, Spain
| | - N. Marcelino
- Grupo de Astrofísica Molecular, Instituto de Física Fundamental (IFF-CSIC), C/ Serrano 121, 28006 Madrid, Spain
| | - J. R. Pardo
- Grupo de Astrofísica Molecular, Instituto de Física Fundamental (IFF-CSIC), C/ Serrano 121, 28006 Madrid, Spain
| | - F. Tercero
- Centro de Desarrollos Tecnológicos, Observatorio de Yebes (IGN), 19141 Yebes, Guadalajara, Spain
| | - J.D. Gallego
- Centro de Desarrollos Tecnológicos, Observatorio de Yebes (IGN), 19141 Yebes, Guadalajara, Spain
| | - J.A. López-Pérez
- Centro de Desarrollos Tecnológicos, Observatorio de Yebes (IGN), 19141 Yebes, Guadalajara, Spain
| | - P. deVicente
- Centro de Desarrollos Tecnológicos, Observatorio de Yebes (IGN), 19141 Yebes, Guadalajara, Spain
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11
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Joyce LA, Schultz DM, Sherer EC, Neill JL, Sonstrom RE, Pate BH. Direct regioisomer analysis of crude reaction mixtures via molecular rotational resonance (MRR) spectroscopy. Chem Sci 2020; 11:6332-6338. [PMID: 32953028 PMCID: PMC7472927 DOI: 10.1039/d0sc01853h] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/30/2020] [Indexed: 01/05/2023] Open
Abstract
Direct analyses of crude reaction mixtures have been carried out using molecular rotational resonance (MRR) spectroscopy. Two examples are presented, a demonstration application in photocatalytic CH-arylation as well as generation of an intermediate in a natural product synthesis. In both cases, the reaction can proceed at more than one site, leading to a mixture of regioisomers that can be challenging to distinguish. MRR structural parameters were calculated for the low lying conformers for the desired compounds, and then compared to the experimental spectra of the crude mixtures to confirm the presence of these species. Next, quantitation was performed by comparing experimentally measured line intensities with simulations based on computed values for the magnitude and direction of the molecular dipole moment of each species. This identification and quantification was performed without sample purification and without isolated standards of the compounds of interest. The values obtained for MRR quantitation were in good agreement with the chromatographic values. Finally, previously unknown impurities were discovered within the photocatalytic CH-arylation work. This paper demonstrates the utility of MRR as a reaction characterization tool to simplify analytical workflows.
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Affiliation(s)
- Leo A Joyce
- Department of Process Research & Development , Merck & Co., Inc. , Rahway , NJ 07065 , USA .
| | - Danielle M Schultz
- Department of Process Research & Development , Merck & Co., Inc. , Rahway , NJ 07065 , USA .
| | - Edward C Sherer
- Department of Computational and Structural Chemistry , Merck & Co., Inc. , Rahway , NJ 07065 , USA
| | - Justin L Neill
- BrightSpec, Inc. , 770 Harris St., Suite 104b , Charlottesville , VA 22904 , USA .
| | - Reilly E Sonstrom
- Department of Chemistry , University of Virginia , McCormick Road , Charlottesville , VA 22904 , USA
| | - Brooks H Pate
- Department of Chemistry , University of Virginia , McCormick Road , Charlottesville , VA 22904 , USA
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12
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Quintas-Sánchez E, Dawes R, Lee K, McCarthy MC. Automated Construction of Potential Energy Surfaces Suitable to Describe van der Waals Complexes with Highly Excited Nascent Molecules: The Rotational Spectra of Ar-CS( v) and Ar-SiS( v). J Phys Chem A 2020; 124:4445-4454. [PMID: 32368913 DOI: 10.1021/acs.jpca.0c02685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Some reactions produce extremely hot nascent products which nevertheless can form sufficiently long-lived van der Waals (vdW) complexes-with atoms or molecules from a bath gas-as to be observed via microwave spectroscopy. Theoretical calculations of such unbound resonance states can be much more challenging than ordinary bound-state calculations depending on the approach employed. One encounters not just the floppy, and perhaps multiwelled potential energy surface (PES) characteristic of vdWs complexes, but in addition, one must contend with excitation of the intramolecular modes and its corresponding influence on the PES. Straightforward computation of the (resonance) rovibrational levels of interest, involves the added complication of the unbound nature of the wave function, often treated with techniques such as introducing a complex absorbing potential. Here, we have demonstrated that a simplified approach of making a series of vibrationally effective PESs for the intermolecular coordinates-one for each reaction product vibrational quantum number of interest-can produce vdW levels for the complex with spectroscopic accuracy. This requires constructing a series of appropriately weighted lower-dimensional PESs for which we use our freely available PES-fitting code AUTOSURF. The applications of this study are the Ar-CS and Ar-SiS complexes, which are isovalent to Ar-CO and Ar-SiO, the latter of which we considered in a previously reported study. Using a series of vibrationally effective PESs, rovibrational levels and predicted microwave transition frequencies for both complexes were computed variationally. A series of shifting rotational transition frequencies were also computed as a function of the diatom vibrational quantum number. The predicted transitions were used to guide and inform an experimental effort to make complementary observations. Comparisons are given for the transitions that are within the range of the spectrometer and were successfully recorded. Calculations of the rovibrational level pattern agree to within 0.2% with experimental measurements.
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Affiliation(s)
- Ernesto Quintas-Sánchez
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Richard Dawes
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Kelvin Lee
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts 02138, United States
| | - Michael C McCarthy
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts 02138, United States.,School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Cambridge, Massachusetts 02138, United States
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13
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McCarthy MC, Lee KLK, Carroll PB, Porterfield JP, Changala PB, Thorpe JH, Stanton JF. Exhaustive Product Analysis of Three Benzene Discharges by Microwave Spectroscopy. J Phys Chem A 2020; 124:5170-5181. [DOI: 10.1021/acs.jpca.0c02919] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael C. McCarthy
- Center for Astrophysics, Harvard and Smithsonian, 60 Garden Street, Cambridge Massachusetts 02138, United States
| | - Kin Long Kelvin Lee
- Center for Astrophysics, Harvard and Smithsonian, 60 Garden Street, Cambridge Massachusetts 02138, United States
| | - P. Brandon Carroll
- Center for Astrophysics, Harvard and Smithsonian, 60 Garden Street, Cambridge Massachusetts 02138, United States
| | - Jessica P. Porterfield
- Center for Astrophysics, Harvard and Smithsonian, 60 Garden Street, Cambridge Massachusetts 02138, United States
| | - P. Bryan Changala
- JILA, University of Colorado, Boulder, Colorado 80309, United States
| | - James H. Thorpe
- Quantum Theory Project, Department of Chemistry and Physics, University of Florida, Gainesville, Florida 32611, United States
| | - John F. Stanton
- Quantum Theory Project, Department of Chemistry and Physics, University of Florida, Gainesville, Florida 32611, United States
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Reilly NJ, Kokkin DL, Ward ML, Flores J, Ross SD, McCaslin LM, Stanton JF. Gas-Phase Optical Detection of 3-Ethynylcyclopentenyl: A Resonance-Stabilized C7H7 Radical with an Embedded 1-Vinylpropargyl Chromophore. J Am Chem Soc 2020; 142:10400-10411. [DOI: 10.1021/jacs.0c01579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Neil J. Reilly
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston Massachusetts 02125, United States
| | - Damian L. Kokkin
- Department of Chemistry, Marquette University, P.O. Box 1881 Milwaukee, Wisconsin 53201, United States
| | - Meredith L. Ward
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston Massachusetts 02125, United States
| | - Jonathan Flores
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston Massachusetts 02125, United States
| | - Sederra D. Ross
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston Massachusetts 02125, United States
| | - Laura M. McCaslin
- Institute of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 9190401, Israel
| | - John F. Stanton
- Quantum Theory Project, Departments of Chemistry and Physics, The University of Florida, Gainesville Florida 32611, United States
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McCarthy M, Lee KLK. Molecule Identification with Rotational Spectroscopy and Probabilistic Deep Learning. J Phys Chem A 2020; 124:3002-3017. [PMID: 32212702 DOI: 10.1021/acs.jpca.0c01376] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A proof-of-concept framework for identifying molecules of unknown elemental composition and structure using experimental rotational data and probabilistic deep learning is presented. Using a minimal set of input data determined experimentally, we describe four neural network architectures that yield information to assist in the identification of an unknown molecule. The first architecture translates spectroscopic parameters into Coulomb matrix eigenspectra as a method of recovering chemical and structural information encoded in the rotational spectrum. The eigenspectrum is subsequently used by three deep learning networks to constrain the range of stoichiometries, generate SMILES strings, and predict the most likely functional groups present in the molecule. In each model, we utilize dropout layers as an approximation to Bayesian sampling, which subsequently generates probabilistic predictions from otherwise deterministic models. These models are trained on a modestly sized theoretical dataset comprising ∼83 000 unique organic molecules (between 18 and 180 amu) optimized at the ωB97X-D/6-31+G(d) level of theory, where the theoretical uncertainties of the spectoscopic constants are well-understood and used to further augment training. Since chemical and structural properties depend strongly on molecular composition, we divided the dataset into four groups corresponding to pure hydrocarbons, oxygen-bearing species, nitrogen-bearing species, and both oxygen- and nitrogen-bearing species, training each type of network with one of these categories, thus creating "experts" within each domain of molecules. We demonstrate how these models can then be used for practical inference on four molecules and discuss both the strengths and shortcomings of our approach and the future directions these architectures can take.
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Affiliation(s)
- Michael McCarthy
- Center for Astrophysics
- Harvard & Smithsonian, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Kin Long Kelvin Lee
- Center for Astrophysics
- Harvard & Smithsonian, 60 Garden Street, Cambridge, Massachusetts 02138, United States
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16
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Lemmens AK, Rap DB, Thunnissen JMM, Willemsen B, Rijs AM. Polycyclic aromatic hydrocarbon formation chemistry in a plasma jet revealed by IR-UV action spectroscopy. Nat Commun 2020; 11:269. [PMID: 31937755 PMCID: PMC6959308 DOI: 10.1038/s41467-019-14092-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/16/2019] [Indexed: 11/09/2022] Open
Abstract
Large polycyclic aromatic hydrocarbons (PAHs) are the most abundant complex molecules in the interstellar medium; however, their possible formation pathways from small molecular species are still elusive. In the present work, we follow and characterize the formation of PAHs in an electrical discharge, specifically the PAH naphthalene in a molecular beam of argon. The fragments, products and reaction intermediates are unambiguously structurally identified by mass-selective IR-UV spectroscopy combined with quantum chemical calculations. This experiment provides evidence of the formation of larger PAHs containing up to four cyclic rings in the gas phase originating from a non-radical PAH molecule as a precursor. In addition to PAH formation, key resonance stabilized radical intermediates and intermediates containing di-acetylenic side groups are unambiguously identified in our experiment. We thereby not only reveal competing formation pathways to larger PAHs, but also identify intermediate species to PAH formation that are candidates for detection in radio-astronomy. Polycyclic aromatic hydrocarbons (PAHs) are present in the interstellar medium but their origin is unclear. Here the authors investigate large PAH formation from smaller PAHs in a plasma jet by mass-selective IR and UV laser spectroscopy, uncovering diacetylene radical addition as formation mechanism.
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Affiliation(s)
- Alexander K Lemmens
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands.,Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Daniël B Rap
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Johannes M M Thunnissen
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Bryan Willemsen
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - Anouk M Rijs
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands.
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Lee KLK, McCarthy M. Bayesian Analysis of Theoretical Rotational Constants from Low-Cost Electronic Structure Methods. J Phys Chem A 2020; 124:898-910. [DOI: 10.1021/acs.jpca.9b09982] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kin Long Kelvin Lee
- Harvard & Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Michael McCarthy
- Harvard & Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
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