1
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Li J, Li Y, Wu B, Xie M, Hu Y. Proton Transfer Processes in 2-Butenenitrile Dimer Cation Studied by Mass-Selective Infrared Spectroscopy. J Phys Chem A 2024; 128:4694-4700. [PMID: 38833155 DOI: 10.1021/acs.jpca.4c01989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
2-Butenenitrile (2-Bu) is a recently discovered crucial interstellar molecule. Herein, an abnormal NH band was observed in the infrared spectrum of the 2-Bu dimer cation, suggestive of a proton transfer reaction within the cluster. Through a comprehensive theoretical analysis of the IR spectrum of (2-Bu)2+, we discovered not only the formation of a new C-N bond through the attachment of one 2-Bu to another but also the occurrence of a proton transfer reaction in the cluster. This proton was identified as originating from the methyl group of the attaching 2-Bu in the cluster based on the analysis of IR spectra of (2-Bu)+ and [2-Bu-acrylonitrile (AN)]+. Furthermore, the detailed reaction process of this ion-molecule reaction is examined with theoretical calculation. This finding contributes significantly to our deeper understanding of ion-molecule reactions in the gas phase and the formation of nitrogen-containing prebiotic molecules in the interstellar medium.
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Affiliation(s)
- Jingyu Li
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yujian Li
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Bingbing Wu
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Min Xie
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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2
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Ohata J. Friedel-Crafts reactions for biomolecular chemistry. Org Biomol Chem 2024; 22:3544-3558. [PMID: 38624091 DOI: 10.1039/d4ob00406j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Chemical tools and principles have become central to biological and medical research/applications by leveraging a range of classical organic chemistry reactions. Friedel-Crafts alkylation and acylation are arguably some of the most well-known and used synthetic methods for the preparation of small molecules but their use in biological and medical fields is relatively less frequent than the other reactions, possibly owing to the notion of their plausible incompatibility with biological systems. This review demonstrates advances in Friedel-Crafts alkylation and acylation reactions in a variety of biomolecular chemistry fields. With the discoveries and applications of numerous biomolecule-catalyzed or -assisted processes, these reactions have garnered considerable interest in biochemistry, enzymology, and biocatalysis. Despite the challenges of reactivity and selectivity of biomolecular reactions, the alkylation and acylation reactions demonstrated their utility for the construction and functionalization of all the four major biomolecules (i.e., nucleosides, carbohydrates/saccharides, lipids/fatty acids, and amino acids/peptides/proteins), and their diverse applications in biological, medical, and material fields are discussed. As the alkylation and acylation reactions are often fundamental educational components of organic chemistry courses, this review is intended for both experts and nonexperts by discussing their basic reaction patterns (with the depiction of each reaction mechanism in the ESI) and relevant real-world impacts in order to enrich chemical research and education. The significant growth of biomolecular Friedel-Crafts reactions described here is a testament to their broad importance and utility, and further development and investigations of the reactions will surely be the focus in the organic biomolecular chemistry fields.
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Affiliation(s)
- Jun Ohata
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA.
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3
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van der Burgt PJM, Gradziel ML. Coincidence mass spectrometry study of double ionization of pyrene by 70 eV electron impact. Phys Chem Chem Phys 2024; 26:10688-10697. [PMID: 38511630 DOI: 10.1039/d4cp00443d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
We have performed coincidence mass spectrometry of fragmentation of pyrene molecules by 70 eV electron impact. Ionized fragments have been mass selected using a reflectron time-of-flight mass spectrometer, and a field programmable gate array has been used for the timing of the electron and ion extraction pulses and for the event-by-event detection of the ions. Double ionization results in a number of prominent fragmentations producing two singly-ionized fragments with kinetic energies of up to a few eV. A number of fragmentations produce ions with four or more carbon atoms, which can only be formed by the breaking of at least three C-C bonds.
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Affiliation(s)
- Peter J M van der Burgt
- Department of Experimental Physics, National University of Ireland Maynooth, Maynooth, Co, Kildare, Ireland.
| | - Marcin L Gradziel
- Department of Experimental Physics, National University of Ireland Maynooth, Maynooth, Co, Kildare, Ireland.
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4
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Iglesias-Groth S, Cataldo F, Marin-Dobrincic M. Infrared Spectroscopy of RNA Nucleosides in a Wide Range of Temperatures. Life (Basel) 2024; 14:436. [PMID: 38672708 PMCID: PMC11051033 DOI: 10.3390/life14040436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
The RNA world hypothesis suggests that early cellular ancestors relied solely on RNA molecules for both genetic information storage and cellular functions. RNA, composed of four nucleosides-adenosine, guanosine, cytidine, and uridine-forms the basis of this theory. These nucleosides consist of purine nucleobases, adenine and guanine, and pyrimidine nucleobases, cytosine and uracil, bonded to ribose sugar. Notably, carbonaceous chondrite meteorites have revealed the presence of these bases and sugar, hinting at the potential existence of nucleosides in space. This study aims to present the infrared spectra of four RNA nucleosides commonly found in terrestrial biochemistry, facilitating their detection in space, especially in astrobiological and astrochemical contexts. Laboratory measurements involved obtaining mid- and far-IR spectra at three temperatures (-180 °C, room temperature, and +180 °C), followed by calculating molar extinction coefficients (ε) and integrated molar absorptivities (ψ) for corresponding bands. These spectral data, along with ε and ψ values, serve to provide quantitative insights into the presence and relative abundance of nucleosides in space and aid in their detection.
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Affiliation(s)
| | - Franco Cataldo
- Actinium Chemical Research Institute, Via Casilina 1626A, 00133 Rome, Italy;
| | - Martina Marin-Dobrincic
- Applied Physics and Naval Technology Department, Universidad Politécnica de Cartagena, C/Doctor Fleming, s/n., 30202 Cartagena, Spain;
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5
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Nixon CA. The Composition and Chemistry of Titan's Atmosphere. ACS EARTH & SPACE CHEMISTRY 2024; 8:406-456. [PMID: 38533193 PMCID: PMC10961852 DOI: 10.1021/acsearthspacechem.2c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 11/02/2023] [Accepted: 02/02/2024] [Indexed: 03/28/2024]
Abstract
In this review I summarize the current state of knowledge about the composition of Titan's atmosphere and our current understanding of the suggested chemistry that leads to that observed composition. I begin with our present knowledge of the atmospheric composition, garnered from a variety of measurements including Cassini-Huygens, the Atacama Large Millimeter/submillimeter Array, and other ground- and space-based telescopes. This review focuses on the typical vertical profiles of gases at low latitudes rather than global and temporal variations. The main body of the review presents a chemical description of how complex molecules are believed to arise from simpler species, considering all known "stable" molecules-those that have been uniquely identified in the neutral atmosphere. The last section of the review is devoted to the gaps in our present knowledge of Titan's chemical composition and how further work may fill those gaps.
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Affiliation(s)
- Conor A. Nixon
- Planetary Systems Laboratory, NASA Goddard Space Flight Center, 8800 Greenbelt Road, Greenbelt, Maryland 20771, United
States
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6
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Wang J, Marks JH, Fortenberry RC, Kaiser RI. Interstellar formation of glyceric acid [HOCH 2CH(OH)COOH]-The simplest sugar acid. SCIENCE ADVANCES 2024; 10:eadl3236. [PMID: 38478624 PMCID: PMC10936953 DOI: 10.1126/sciadv.adl3236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024]
Abstract
Glyceric acid [HOCH2CH(OH)COOH]-the simplest sugar acid-represents a key molecule in biochemical processes vital for metabolism in living organisms such as glycolysis. Although critically linked to the origins of life and identified in carbonaceous meteorites with abundances comparable to amino acids, the underlying mechanisms of its formation have remained elusive. Here, we report the very first abiotic synthesis of racemic glyceric acid via the barrierless radical-radical reaction of the hydroxycarbonyl radical (HOĊO) with 1,2-dihydroxyethyl (HOĊHCH2OH) radical in low-temperature carbon dioxide (CO2) and ethylene glycol (HOCH2CH2OH) ices. Using isomer-selective vacuum ultraviolet photoionization reflectron time-of-flight mass spectrometry, glyceric acid was identified in the gas phase based on the adiabatic ionization energies and isotopic substitution studies. This work reveals the key reaction pathways for glyceric acid synthesis through nonequilibrium reactions from ubiquitous precursor molecules, advancing our fundamental knowledge of the formation pathways of key biorelevant organics-sugar acids-in deep space.
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Affiliation(s)
- Jia Wang
- W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Joshua H. Marks
- W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Ryan C. Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Ralf I. Kaiser
- W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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7
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Fortenberry RC. Quantum Chemistry and Astrochemistry: A Match Made in the Heavens. J Phys Chem A 2024; 128:1555-1565. [PMID: 38381079 DOI: 10.1021/acs.jpca.3c07601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Quantum chemistry can uniquely answer astrochemical questions that no other technique can provide. Computations can be parallelized, automated, and left to run continuously providing exceptional molecular throughput that cannot be done through experimentation. Additionally, the granularity of the individual computations that are required of potential energy surfaces, reaction mechanism pathways, or other quantum chemically derived observables produces a unique mosaic that make up the larger whole. These pieces can be dissected for their individual contributions or evaluated in an ad hoc fashion for each of their roles in generating the larger whole. No other scientific approach is capable of reporting such fine-grained insights. Quantum chemistry also works from a bottom-up approach in providing properties directly from the desired molecule instead of a top-down perspective as required of experiment where molecules have to be linked to observed phenomena. Furthermore, modern quantum chemistry is well within the range of "chemical accuracy" and is approaching "spectroscopic accuracy." As such, the seemingly difficult questions asked by astrochemistry that would not be asked initially for any other application require quantum chemical reference data. While the results of quantum chemical computations are needed to interpret astrochemical observation, modeling, or laboratory experimentation, such hard questions, regardless of the original need to answer them, produce unique solutions. While questions in astrochemistry often require novel developments in and implementations of quantum chemistry as outlined herein, the applications of these solutions will stretch beyond astrochemistry and may yet impact fields much closer to Earth.
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Affiliation(s)
- Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, Oxford, Mississippi 38677-1848, United States
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8
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Rodriguez LE, Altair T, Hermis NY, Jia TZ, Roche TP, Steller LH, Weber JM. Chapter 4: A Geological and Chemical Context for the Origins of Life on Early Earth. ASTROBIOLOGY 2024; 24:S76-S106. [PMID: 38498817 DOI: 10.1089/ast.2021.0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on Earth.
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Affiliation(s)
- Laura E Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA. (Current)
| | - Thiago Altair
- Institute of Chemistry of São Carlos, Universidade de São Paulo, São Carlos, Brazil
- Department of Chemistry, College of the Atlantic, Bar Harbor, Maine, USA. (Current)
| | - Ninos Y Hermis
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Physics and Space Sciences, University of Granada, Granada Spain. (Current)
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Luke H Steller
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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9
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Krohn OA, Lewandowski HJ. Cold Ion-Molecule Reactions in the Extreme Environment of a Coulomb Crystal. J Phys Chem A 2024. [PMID: 38359783 DOI: 10.1021/acs.jpca.3c07546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Coulomb crystals provide a unique environment in which to study ion-neutral gas-phase reactions. In these cold, trapped ensembles, we are able to study the kinetics and dynamics of small molecular systems. These measurements have connections to chemistry in the Interstellar Medium (ISM) and planetary atmospheres. This Feature Article will describe recent work in our laboratory that uses Coulomb crystals to study translationally cold, ion-neutral reactions. We provide a description of how the various affordances of our experimental system allow for detailed studies of the reaction mechanisms and the corresponding products. In particular, we will describe quantum-state resolved reactions, isomer-dependent reactions, and reactions with a rarely studied, astrophysically relevant ion, CCl+.
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Affiliation(s)
- O A Krohn
- JILA and the Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
| | - H J Lewandowski
- JILA and the Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
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10
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Fortenberry RC. A Vision for the Future of Astrochemistry in the Interstellar Medium by 2050. ACS PHYSICAL CHEMISTRY AU 2024; 4:31-39. [PMID: 38283789 PMCID: PMC10811777 DOI: 10.1021/acsphyschemau.3c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 01/30/2024]
Abstract
By 2050, many, but not nearly all, unattributed astronomical spectral features will be conclusively linked to molecular carriers (as opposed to nearly none today in the visible and IR); amino acids will have been observed remotely beyond our solar system; the largest observatories ever constructed on the surface of the Earth or launched beyond it will be operational; high-throughput computation either from brute force or machine learning will provide unprecedented amounts of reference spectral and chemical reaction data; and the chemical fingerprints of the universe delivered by those of us who call ourselves astrochemists will provide astrophysicists with unprecedented resolution for determining how the stars evolve, planets form, and molecules that lead to life originate. Astrochemistry is a relatively young field, but with the entire universe as its playground, the discipline promises to persist as long as telescopic observations are made that require reference data and complementary chemical modeling. While the recent commissionings of the James Webb Space Telescope and Atacama Large Millimeter Array are ushering in the second "golden age" of astrochemistry (with the first being the radio telescopic boom period of the 1970s), this current period of discovery should facilitate unprecedented advances within the next 25 years. Astrochemistry forces the asking of hard questions beyond the physical conditions of our "pale blue dot", and such questions require creative solutions that are influential beyond astrophysics. By 2050, more creative solutions will have been provided, but even more will be needed to answer the continuing question of our astrochemical ignorance.
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Affiliation(s)
- Ryan C. Fortenberry
- Department of Chemistry &
Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United
States
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11
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Buckner DK, Anderson MJ, Wisnosky S, Alvarado W, Nuevo M, Williams AJ, Ricco AJ, Anamika, Debic S, Friend L, Hoac T, Jahnke L, Radosevich L, Williams R, Wilhelm MB. Quantifying Global Origin-Diagnostic Features and Patterns in Biotic and Abiotic Acyclic Lipids for Life Detection. ASTROBIOLOGY 2024; 24:1-35. [PMID: 38150549 DOI: 10.1089/ast.2023.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Lipids are a geologically robust class of organics ubiquitous to life as we know it. Lipid-like soluble organics are synthesized abiotically and have been identified in carbonaceous meteorites and on Mars. Ascertaining the origin of lipids on Mars would be a profound astrobiological achievement. We enumerate origin-diagnostic features and patterns in two acyclic lipid classes, fatty acids (i.e., carboxylic acids) and acyclic hydrocarbons, by collecting and analyzing molecular data reported in over 1500 samples from previously published studies of terrestrial and meteoritic organics. We identify 27 combined (15 for fatty acids, 12 for acyclic hydrocarbons) molecular patterns and structural features that can aid in distinguishing biotic from abiotic synthesis. Principal component analysis (PCA) demonstrates that multivariate analyses of molecular features (16 for fatty acids, 14 for acyclic hydrocarbons) can potentially indicate sample origin. Terrestrial lipids are dominated by longer straight-chain molecules (C4-C34 fatty acids, C14-C46 acyclic hydrocarbons), with predominance for specific branched and unsaturated isomers. Lipid-like meteoritic soluble organics are shorter, with random configurations. Organic solvent-extraction techniques are most commonly reported, motivating the design of our novel instrument, the Extractor for Chemical Analysis of Lipid Biomarkers in Regolith (ExCALiBR), which extracts lipids while preserving origin-diagnostic features that can indicate biogenicity.
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Affiliation(s)
- Denise K Buckner
- Department of Geological Sciences, University of Florida, Gainesville, Florida, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Morgan J Anderson
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Axient Corporation, Huntsville, Alabama, USA
| | - Sydney Wisnosky
- Axient Corporation, Huntsville, Alabama, USA
- Department of Biology, University of Miami, Coral Gables, Florida, USA
| | - Walter Alvarado
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Michel Nuevo
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Amy J Williams
- Department of Geological Sciences, University of Florida, Gainesville, Florida, USA
| | - Antonio J Ricco
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Electrical Engineering-Integrated Circuits Laboratory, Stanford University, Stanford, California, USA
| | - Anamika
- Department of Space Studies, University of North Dakota, Grand Forks, North Dakota, USA
| | - Sara Debic
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Trinh Hoac
- Axient Corporation, Huntsville, Alabama, USA
| | - Linda Jahnke
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | | | - Ross Williams
- Civil & Environmental Engineering & Earth Sciences, Notre Dame University, Notre Dame, Indiana, USA
| | - Mary Beth Wilhelm
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
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12
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Parker K, Bollis NE, Ryzhov V. Ion-molecule reactions of mass-selected ions. MASS SPECTROMETRY REVIEWS 2024; 43:47-89. [PMID: 36447431 DOI: 10.1002/mas.21819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Gas-phase reactions of mass-selected ions with neutrals covers a very broad area of fundamental and applied mass spectrometry (MS). Oftentimes, ion-molecule reactions (IMR) can serve as a viable alternative to collision-induced dissociation and other ion dissociation techniques when using tandem MS. This review focuses on the literature pertaining applications of IMR since 2013. During the past decade considerable efforts have been made in analytical applications of IMR, including advances in one of the major techniques for characterization of unsaturated fatty acids and lipids, ozone-induced dissociation, and the development of a new technique for sequencing of large ions, hydrogen atom attachment/abstraction dissociation. Many advances have also been made in identifying gas-phase chemistry specific to a functional group in organic and biological compounds, which are useful in structure elucidation of analytes and differentiation of isomers/isobars. With "soft" ionization techniques like electrospray ionization having become mainstream for quite some time now, the efforts in the area of metal ion catalysis have firmly moved into exploring chemistry of ligated metal complexes in their "natural" oxidation states allowing to model individual steps of mechanisms in homogeneous catalysis, especially in combination with high-level DFT calculations. Finally, IMR continue to contribute to the body of knowledge in the area of chemistry of interstellar processes.
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Affiliation(s)
- Kevin Parker
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois, USA
| | - Nicholas E Bollis
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois, USA
| | - Victor Ryzhov
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois, USA
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13
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Kowalski K. Synthesis and chemical transformations of glycol nucleic acid (GNA) nucleosides. Bioorg Chem 2023; 141:106921. [PMID: 37871392 DOI: 10.1016/j.bioorg.2023.106921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
Xeno nucleic acids (XNA) are an increasingly important class of hypermodified nucleic acids with great potential in bioorganic chemistry and synthetic biology. Glycol nucleic acid (GNA) is constructed from a three-carbon 1,2-propanediol (propylene glycol) backbone attached to a nucleobase entity, representing the simplest known XNA. This review is intended to present GNA nucleosides from a synthetic chemistry perspective-a perspective that serves as a starting point for biological studies. Therefore this account focuses on synthetic methods for GNA nucleoside synthesis, as well as their postsynthetic chemical transformations. The properties and biological activity of GNA constituents are also highlighted. A literature survey shows four major approaches toward GNA nucleoside scaffold synthesis. These approaches pertain to glycidol ring-opening, Mitsunobu, SN2, and dihydroxylation reactions. The general arsenal of reactions used in GNA chemistry is versatile and encompasses the Sonogashira reaction, Michael addition, silyl-Hilbert-Johnson reaction, halogenation, alkylation, cyclization, Rh-catalyzed N-allylation, Sharpless catalytic dihydroxylation, and Yb(OTf)3-catalyzed etherification. Additionally, various phosphorylation reactions have enabled the synthesis of diverse types of GNA nucleotides, dinucleoside phosphates, phosphordiamidites, and oligos. Furthermore, recent advances in GNA chemistry have resulted in the synthesis of previously unknown redox-active (ferrocenyl) and luminescent (pyrenyl and phenanthrenyl) GNA nucleosides, which are also covered in this review.
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Affiliation(s)
- Konrad Kowalski
- University of Lodz, Faculty of Chemistry, Department of Organic Chemistry, Tamka 12, PL-91403 Lodz, Poland.
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14
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Rosa CA, Bergantini A, Herczku P, Mifsud DV, Lakatos G, Kovács STS, Sulik B, Juhász Z, Ioppolo S, Quitián-Lara HM, Mason NJ, Lage C. Infrared Spectral Signatures of Nucleobases in Interstellar Ices I: Purines. Life (Basel) 2023; 13:2208. [PMID: 38004348 PMCID: PMC10672069 DOI: 10.3390/life13112208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/01/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
The purine nucleobases adenine and guanine are complex organic molecules that are essential for life. Despite their ubiquitous presence on Earth, purines have yet to be detected in observations of astronomical environments. This work therefore proposes to study the infrared spectra of purines linked to terrestrial biochemical processes under conditions analogous to those found in the interstellar medium. The infrared spectra of adenine and guanine, both in neat form and embedded within an ice made of H2O:NH3:CH4:CO:CH3OH (10:1:1:1:1), were analysed with the aim of determining which bands attributable to adenine and/or guanine can be observed in the infrared spectrum of an astrophysical ice analogue rich in other volatile species known to be abundant in dense molecular clouds. The spectrum of adenine and guanine mixed together was also analysed. This study has identified three purine nucleobase infrared absorption bands that do not overlap with bands attributable to the volatiles that are ubiquitous in the dense interstellar medium. Therefore, these three bands, which are located at 1255, 940, and 878 cm-1, are proposed as an infrared spectral signature for adenine, guanine, or a mixture of these molecules in astrophysical ices. All three bands have integrated molar absorptivity values (ψ) greater than 4 km mol-1, meaning that they should be readily observable in astronomical targets. Therefore, if these three bands were to be observed together in the same target, then it is possible to propose the presence of a purine molecule (i.e., adenine or guanine) there.
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Affiliation(s)
- Caroline Antunes Rosa
- Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
| | - Alexandre Bergantini
- Celso Suckow da Fonseca Federal Centre for Technological Education, Rio de Janeiro 20271-110, Brazil
| | - Péter Herczku
- HUN-REN Institute for Nuclear Research (Atomki), H-4026 Debrecen, Hungary
| | - Duncan V. Mifsud
- HUN-REN Institute for Nuclear Research (Atomki), H-4026 Debrecen, Hungary
| | - Gergő Lakatos
- HUN-REN Institute for Nuclear Research (Atomki), H-4026 Debrecen, Hungary
- Institute of Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
| | | | - Béla Sulik
- HUN-REN Institute for Nuclear Research (Atomki), H-4026 Debrecen, Hungary
| | - Zoltán Juhász
- HUN-REN Institute for Nuclear Research (Atomki), H-4026 Debrecen, Hungary
| | - Sergio Ioppolo
- Centre for Interstellar Catalysis (InterCat), Department of Physics and Astronomy, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Heidy M. Quitián-Lara
- Centre for Astrophysics and Planetary Science, School of Physics and Astronomy, University of Kent, Canterbury CT2 7NH, UK
| | - Nigel J. Mason
- HUN-REN Institute for Nuclear Research (Atomki), H-4026 Debrecen, Hungary
- Centre for Astrophysics and Planetary Science, School of Physics and Astronomy, University of Kent, Canterbury CT2 7NH, UK
| | - Claudia Lage
- Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
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15
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Liao Q, Xie P, Wang Z. Enantiodetermining processes in the synthesis of alanine, serine, and isovaline. Phys Chem Chem Phys 2023; 25:28829-28834. [PMID: 37853775 DOI: 10.1039/d3cp03212d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
In this study, quantum chemical calculations were used to explore the synthesis of three chiral α-amino acids, specifically alanine, serine, and isovaline, from reactants found in interstellar space. Our focus is on the crucial step in the synthesis pathway that determines the chirality of the amino acids. The results indicate that in the case of alanine, the determination of enantiomer is primarily influenced by the direction of the collision of molecules or functional groups, which leads to the formation of a chirality center in a crucial intermediate. However, contrary to chemical expectations, the enantiodetermining/enantioselection step for serine and isovaline synthesis occurs prior to the creation of a chirality center.
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Affiliation(s)
- Qingli Liao
- School of Physical Science and Technology, Guangxi University, Nanning 530004, China.
| | - Peng Xie
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Zhao Wang
- School of Physical Science and Technology, Guangxi University, Nanning 530004, China.
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16
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Tino CJ, Stüeken EE, Arp G, Böttcher ME, Bates SM, Lyons TW. Are Large Sulfur Isotope Variations Biosignatures in an Ancient, Impact-Induced Hydrothermal Mars Analog? ASTROBIOLOGY 2023; 23:1027-1044. [PMID: 37498995 DOI: 10.1089/ast.2022.0114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Discrepancies have emerged concerning the application of sulfur stable isotope ratios as a biosignature in impact crater paleolakes. The first in situ δ34S data from Mars at Gale crater display a ∼75‰ range that has been attributed to an abiotic mechanism. Yet biogeochemical studies of ancient environments on Earth generally interpret δ34S fractionations >21‰ as indicative of a biological origin, and studies of δ34S at analog impact crater lakes on Earth have followed the same approach. We performed analyses (including δ34S, total organic carbon wt%, and scanning electron microscope imaging) on multiple lithologies from the Nördlinger Ries impact crater, focusing on hydrothermally altered impact breccias and associated sedimentary lake-fill sequences to determine whether the δ34S properties define a biosignature. The differences in δ34S between the host lithologies may have resulted from thermochemical sulfate reduction, microbial sulfate reduction, hydrothermal equilibrium fractionation, or any combination thereof. Despite abundant samples and instrumental precision currently exclusive to Earth-bound analyses, assertions of biogenicity from δ34S variations >21‰ at the Miocene Ries impact crater are tenuous. This discourages the use of δ34S as a biosignature in similar environments without independent checks that include the full geologic, biogeochemical, and textural context, as well as a comprehensive acknowledgment of alternative hypotheses.
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Affiliation(s)
- Christopher J Tino
- Department of Earth and Planetary Sciences, University of California, Riverside, California, USA
| | - Eva E Stüeken
- School of Earth and Environmental Sciences, University of St. Andrews, St. Andrews, Scotland, United Kingdom
- Virtual Planetary Laboratory, University of Washington, Seattle, Washington, USA
| | - Gernot Arp
- Geowissenschaftliches Zentrum, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Michael Ernst Böttcher
- Geochemistry & Isotope Biogeochemistry, Leibniz Institute for Baltic Sea Research (IOW), Warnemünde, Germany
- Marine Geochemistry, University of Greifswald, Greifswald, Germany
- Department of Maritime Systems, Interdisciplinary Faculty (INF), University of Rostock, Rostock, Germany
| | - Steven M Bates
- Department of Earth and Planetary Sciences, University of California, Riverside, California, USA
| | - Timothy W Lyons
- Department of Earth and Planetary Sciences, University of California, Riverside, California, USA
- Virtual Planetary Laboratory, University of Washington, Seattle, Washington, USA
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17
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Martin-Drumel MA, Spaniol JT, Hölzel H, Agúndez M, Cernicharo J, Moth-Poulsen K, Jacovella U. Searches for bridged bicyclic molecules in space-norbornadiene and its cyano derivatives. Faraday Discuss 2023; 245:284-297. [PMID: 37305958 PMCID: PMC10510035 DOI: 10.1039/d3fd00016h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 02/14/2023] [Indexed: 09/21/2023]
Abstract
The norbornadiene (NBD) molecule, C7H8, owes its fame to its remarkable photoswitching properties that are promising for molecular solar-thermal energy storage systems. Besides this photochemical interest, NBD is a rather unreactive species within astrophysical conditions and it should exhibit high photostability, properties that might also position this molecule as an important constituent of the interstellar medium (ISM)-especially in environments that are well shielded from short-wavelength radiation, such as dense molecular clouds. It is thus conceivable that, once formed, NBD can survive in dense molecular clouds and act as a carbon sink. Following the recent interstellar detections of large hydrocarbons, including several cyano-containing ones, in the dense molecular cloud TMC-1, it is thus logical to consider searching for NBD-which presents a shallow but non-zero permanent electric dipole moment (0.06 D)-as well as for its mono- and dicyano-substituted compounds, referred to as CN-NBD and DCN-NBD, respectively. The pure rotational spectra of NBD, CN-NBD, and DCN-NBD have been measured at 300 K in the 75-110 GHz range using a chirped-pulse Fourier-transform millimetre-wave spectrometer. Of the three species, only NBD was previously studied at high resolution in the microwave domain. From the present measurements, the derived spectroscopic constants enable prediction of the spectra of all three species at various rotational temperatures (up to 300 K) in the spectral range mapped at high resolution by current radio observatories. Unsuccessful searches for these molecules were conducted toward TMC-1 using the QUIJOTE survey, carried out at the Yebes telescope, allowing derivation of the upper limits to the column densities of 1.6 × 1014 cm-2, 4.9 × 1010 cm-2, and 2.9 × 1010 cm-2 for NBD, CN-NBD, and DCN-NBD, respectively. Using CN-NBD and cyano-indene as proxies for the corresponding bare hydrocarbons, this indicates that-if present in TMC-1-NBD would be at least four times less abundant than indene.
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Affiliation(s)
| | - Jean-Thibaut Spaniol
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France.
| | - Helen Hölzel
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Marcelino Agúndez
- Instituto de Física Fundamental, CSIC, Department of Molecular Astrophysics, Serrano 121, E-28006 Madrid, Spain
| | - Jose Cernicharo
- Instituto de Física Fundamental, CSIC, Department of Molecular Astrophysics, Serrano 121, E-28006 Madrid, Spain
| | - Kasper Moth-Poulsen
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
- The Institute of Materials Science of Barcelona, ICMAB-CSIC, Bellaterra, 08193 Barcelona, Spain
- Catalan Institution for Research & Advanced Studies, ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Department of Chemical Engineering, Universitat Politècnica de Catalunya, EEBE, Eduard Maristany 10-14, 08019 Barcelona, Spain
| | - Ugo Jacovella
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France.
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18
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Douglas KM, Li LHD, Walsh C, Lehman JH, Blitz MA, Heard DE. Experimental, theoretical, and astrochemical modelling investigation of the gas-phase reaction between the amidogen radical (NH 2) and acetaldehyde (CH 3CHO) at low temperatures. Faraday Discuss 2023; 245:261-283. [PMID: 37340790 DOI: 10.1039/d3fd00046j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
The first experimental study of the low-temperature kinetics of the gas-phase reaction of NH2 with acetaldehyde (CH3CHO) has been performed. Experiments were carried out using laser-flash photolysis and laser-induced fluorescence spectroscopy to create and monitor the temporal decay of NH2 in the presence of CH3CHO. Low temperatures relevant to the interstellar medium were achieved using a pulsed Laval nozzle expansion. Rate coefficients were measured over the temperature and pressure range of 29-107 K and 1.4-28.2 × 1016 molecules per cm3, with the reaction exhibiting a negative temperature dependence and a positive pressure dependence. The yield of CH3CO from the reaction has also been determined at 67.1 and 35.0 K, by observing OH produced from the reaction of CH3CO with added O2. Ab initio calculations of the potential energy surface (PES) were combined with Rice-Rampsberger-Kessel-Marcus (RRKM) calculations to predict rate coefficients and branching ratios over a broad range of temperatures and pressures. The calculated rate coefficients were shown to be sensitive to the calculated density of states of the stationary points, which in turn are sensitive to the inclusion of hindered rotor potentials for several of the vibrational frequencies. The experimentally determined rate coefficients and yields have been used to fit the calculated PES, from which low-pressure limiting rate coefficients relevant to the ISM were determined. These have been included in a single-point dark cloud astrochemical model, in which the reaction is shown to be a potential source of gas-phase CH3CO radicals under dark cloud conditions.
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Affiliation(s)
- Kevin M Douglas
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.
| | | | - Catherine Walsh
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
| | - Julia H Lehman
- School of Chemistry, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Mark A Blitz
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.
- National Centre for Atmospheric Science (NCAS), University of Leeds, Leeds, LS2 9JT, UK
| | - Dwayne E Heard
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.
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19
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Ballotta B, Martínez-Núñez E, Rampino S, Barone V. New prebiotic molecules in the interstellar medium from the reaction between vinyl alcohol and CN radicals: unsupervised reaction mechanism discovery, accurate electronic structure calculations and kinetic simulations. Phys Chem Chem Phys 2023; 25:22840-22850. [PMID: 37584420 DOI: 10.1039/d3cp02571c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Vinyl alcohol (VyA) and cyanide (CN) radicals are relatively abundant in the interstellar medium (ISM). VyA is the enolic tautomer of acetaldehyde and has two low-lying conformers, characterized by the syn or anti placement of hydroxyl hydrogen with respect to the double bond. In this paper, we present a gas-phase model of the barrierless reactions of both VyA's conformers with CN employing accurate quantum chemical computations in the framework of a master equation approach based on the transition state theory. Our results indicate that both VyA conformers feature a similar reactivity with CN, starting with a barrierless addition to the double bond and followed by different isomerization, dissociation, and/or hydrogen elimination steps. The rate constants computed for temperatures up to 600 K show that several reaction channels are open even under the harsh conditions of the ISM, with the favoured one providing the first feasible formation route of a prebiotic molecule not yet detected in the ISM, namely cyanoacetaldehyde. This finding suggests looking for cyanoacetaldehyde in regions where both VyA and CN have already been detected, like, e.g., Sagittarius B2N or G+0.693-0.027.
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Affiliation(s)
- Bernardo Ballotta
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Emilio Martínez-Núñez
- Departamento de Química Física, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, Avenida das Ciencias s/n, 15782, Santiago de Compostela, Spain
| | - Sergio Rampino
- Università degli Studi di Padova, Dipartimento di Scienze Chimiche, Via Marzolo 1, 35131 Padova, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
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20
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Barik S, Behera NR, Dutta S, Kushawaha RK, Sajeev Y, Ramabhadran RO, Aravind G. Molecular growth of PANH via intermolecular Coulombic decay. SCIENCE ADVANCES 2023; 9:eadi0230. [PMID: 37494436 PMCID: PMC10371028 DOI: 10.1126/sciadv.adi0230] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/22/2023] [Indexed: 07/28/2023]
Abstract
Nitrogen-bearing polycyclic aromatic hydrocarbons (PANHs) are ubiquitous in space. They are considered precursors to advanced biomolecules identified in meteorites. However, their chemical evolution into biomolecules in photodestructive astrophysical mediums remains a paradox. Here, we show that light can efficiently initiate the molecular mass growth of PANHs. Ultraviolet-photoexcited quinoline monomers, the smallest PANH, were observed to associate and intermolecular Coulombic decay between the associating monomers formed the cations of quinoline-dimer. Molecular rearrangements in the dimer cation lead to a dominant formation of cations heavier than quinoline. The enrichment of these heavier cations over all the other cations reveals the efficiency of this route for the mass growth of PANHs in space. This mechanism also leads to a highly reactive unsaturated PANH-ring via CH loss, a hitherto unknown channel in any photon-driven process. The occurrence of this efficient pathway toward complex molecules points to a rich chemistry in dense interstellar clouds.
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Affiliation(s)
- Saroj Barik
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
| | - Nihar Ranjan Behera
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
| | - Saurav Dutta
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
| | | | - Y Sajeev
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, India
| | | | - G Aravind
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
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21
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García-Abenza A, Lozano AI, Álvarez L, Oller JC, Rosado J, Blanco F, Limão-Vieira P, García G. Evaluated electron scattering cross section dataset for gaseous benzene in the energy range 0.1-1000 eV. Phys Chem Chem Phys 2023. [PMID: 37470102 DOI: 10.1039/d3cp01908j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
In this study, a complete and self-consistent cross section dataset for electron transport simulations through gaseous benzene in the energy range 0.1-1000 eV has been critically compiled. Its reliability has been evaluated through a joint experimental and computational procedure. To accomplish this, the compiled dataset has been used as input for event-by-event Monte Carlo simulations of the magnetically confined electron transport through gaseous benzene, and the simulated transmitted intensity has been compared with the experimental one for different incident energies and benzene gas pressures.
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Affiliation(s)
- A García-Abenza
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain.
| | - A I Lozano
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain.
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
| | - L Álvarez
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain.
| | - J C Oller
- Centro de Investigaciones Energéticas Mediambientales y Tecnológicas - CIEMAT, 28040 Madrid, Spain
| | - J Rosado
- Departamento de Estructura de la Materia, Física Térmica y Electrónica e IPARCOS, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - F Blanco
- Departamento de Estructura de la Materia, Física Térmica y Electrónica e IPARCOS, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - P Limão-Vieira
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
| | - G García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain.
- Centre for Medical Radiation Physics, University of Wollongong, NSW, Australia
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22
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Potiszil C, Yamanaka M, Sakaguchi C, Ota T, Kitagawa H, Kunihiro T, Tanaka R, Kobayashi K, Nakamura E. Organic Matter in the Asteroid Ryugu: What We Know So Far. Life (Basel) 2023; 13:1448. [PMID: 37511823 PMCID: PMC10381145 DOI: 10.3390/life13071448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
The Hayabusa2 mission was tasked with returning samples from the C-complex asteroid Ryugu (1999 JU3), in order to shed light on the formation, evolution and composition of such asteroids. One of the main science objectives was to understand whether such bodies could have supplied the organic matter required for the origin of life on Earth. Here, a review of the studies concerning the organic matter within the Ryugu samples is presented. This review will inform the reader about the Hayabusa2 mission, the nature of the organic matter analyzed and the various interpretations concerning the analytical findings including those concerning the origin and evolution of organic matter from Ryugu. Finally, the review puts the findings and individual interpretations in the context of the current theories surrounding the formation and evolution of Ryugu. Overall, the summary provided here will help to inform those operating in a wide range of interdisciplinary fields, including planetary science, astrobiology, the origin of life and astronomy, about the most recent developments concerning the organic matter in the Ryugu return samples and their relevance to understanding our solar system and beyond. The review also outlines the issues that still remain to be solved and highlights potential areas for future work.
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Affiliation(s)
- Christian Potiszil
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Yamada 827, Misasa, Tottori 682-0193, Japan
| | - Masahiro Yamanaka
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Yamada 827, Misasa, Tottori 682-0193, Japan
| | - Chie Sakaguchi
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Yamada 827, Misasa, Tottori 682-0193, Japan
| | - Tsutomu Ota
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Yamada 827, Misasa, Tottori 682-0193, Japan
| | - Hiroshi Kitagawa
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Yamada 827, Misasa, Tottori 682-0193, Japan
| | - Tak Kunihiro
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Yamada 827, Misasa, Tottori 682-0193, Japan
| | - Ryoji Tanaka
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Yamada 827, Misasa, Tottori 682-0193, Japan
| | - Katsura Kobayashi
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Yamada 827, Misasa, Tottori 682-0193, Japan
| | - Eizo Nakamura
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Yamada 827, Misasa, Tottori 682-0193, Japan
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23
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Lipton-Duffin J, MacLeod J. Innovations in nanosynthesis: emerging techniques for precision, scalability, and spatial control in reactions of organic molecules on solid surfaces. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2023; 35:183001. [PMID: 36876935 DOI: 10.1088/1361-648x/acbc01] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The surface science-based approach to synthesising new organic materials on surfaces has gained considerable attention in recent years, owing to its success in facilitating the formation of novel 0D, 1D and 2D architectures. The primary mechanism used to date has been the catalytic transformation of small organic molecules through substrate-enabled reactions. In this Topical Review, we provide an overview of alternate approaches to controlling molecular reactions on surfaces. These approaches include light, electron and ion-initiated reactions, electrospray ionisation deposition-based techniques, collisions of neutral atoms and molecules, and superhydrogenation. We focus on the opportunities afforded by these alternative approaches, in particular where they may offer advantages in terms of selectivity, spatial control or scalability.
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Affiliation(s)
- Josh Lipton-Duffin
- School of Chemistry and Physics and Centre for Materials Science, Queensland University of Technology (QUT), Brisbane, Australia
- Central Analytical Research Facility, Queensland University of Technology (QUT), Brisbane, Australia
| | - Jennifer MacLeod
- School of Chemistry and Physics and Centre for Materials Science, Queensland University of Technology (QUT), Brisbane, Australia
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24
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Haney OG, Westbrook BR, Santaloci TJ, Fortenberry RC. Red-Shifting the Excitation Energy of Carbonic Acid Clusters Via Nonminimum Structures. J Phys Chem A 2023; 127:489-494. [PMID: 36622286 DOI: 10.1021/acs.jpca.2c07589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Nonminimum carbonic acid clusters provide excitation energies and oscillator strengths in line with observed ice-phase UV absorptions better than traditional optimized minima. This equation-of-motion coupled cluster quantum chemical analysis on carbonic acid monomers and dimers shows that shifts to the dihedral angle for the internal heavy atoms in the monomer produce UV electronic excitations close to 200 nm with oscillator strengths that would produce observable features. This τ(OCOO) dihedral is actually a relatively floppy motion unlike what is often expected for sp2 carbons and can be distorted by 30° away from equilibrium for an energy cost of only 11 kcal/mol. As this dihedral decreases beyond 30°, the excitation energies decrease further. The oscillator strengths do, as well, but only to a point. Hence, the lower-energy distortions of τ(OCOO) are sufficient to produce structures that exhibit excitation energies and oscillator strengths that would red-shift observed spectra of carbonic acid ices away from the highest UV absorption feature at 139 nm. Such data imply that colder temperatures (20 K) in the experimental treatment of carbonic acid ices are freezing these structures out after annealing, whereas the warmer temperature experiments (80 K) are not.
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Affiliation(s)
- Olivia G Haney
- Department of Chemistry & Biochemistry, Belhaven University, Jackson, Mississippi 39212, United States
| | - Brent R Westbrook
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Taylor J Santaloci
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
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25
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Roy D, Kovalenko A. Molecular Simulations of Liquid Aliphatic Carboxylic Acids (C1-C6) using the 3D-RISM-KH Molecular Solvation Theory. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Richardson V, Valença Ferreira de Aragão E, He X, Pirani F, Mancini L, Faginas-Lago N, Rosi M, Martini LM, Ascenzi D. Fragmentation of interstellar methanol by collisions with He˙ +: an experimental and computational study. Phys Chem Chem Phys 2022; 24:22437-22452. [PMID: 36102850 DOI: 10.1039/d2cp02458f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methanol is a key species in astrochemistry as its presence and reactivity provides a primary route to the synthesis of more complex interstellar organic molecules (iCOMs) that may eventually be incorporated in newly formed planetary systems. In the interstellar medium, methanol is formed by hydrogenation of CO ices on grains, and its fate upon collisions with interstellar ions should be accounted for to correctly model iCOM abundances in objects at various stages of stellar evolution. The absolute cross sections (CSs) and branching ratios (BRs) for the collisions of He˙+ ions with CH3OH are measured, as a function of the collision energy, using a Guided Ion Beam Mass Spectrometer (GIB-MS). Insights into the dissociative electron (charge) exchange mechanism have been obtained by computing the entrance and exit multidimensional Potential Energy Surfaces (PESs) and by modelling the non-adiabatic transitions using an improved Landau-Zener-Stückelberg approach. Notably, the dynamical treatment reproducing the experimental findings includes a strong orientation effect of the system formed by the small He˙+ ion and the highly polar CH3OH molecule, in the electric field gradient associated to the strongly anisotropic intermolecular interaction. This is a stereodynamical effect that plays a fundamental role in collision events occurring under a variety of conditions, with kinetic energy confined within intervals ranging from the sub-thermal to the hyper-thermal regime.
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Affiliation(s)
| | - Emília Valença Ferreira de Aragão
- Department of Chemistry, Biology and Biotechnology, Università degli studi di Perugia, Perugia, Italy.,Master-Tec s.r.l., Via Sicilia 41, Perugia, Italy
| | - Xiao He
- Department of Physics, University of Trento, Trento, Italy.
| | - Fernando Pirani
- Department of Chemistry, Biology and Biotechnology, Università degli studi di Perugia, Perugia, Italy.,Department of Civil and Environmental Engineering, Università degli studi di Perugia, Perugia, Italy
| | - Luca Mancini
- Department of Chemistry, Biology and Biotechnology, Università degli studi di Perugia, Perugia, Italy
| | - Noelia Faginas-Lago
- Department of Chemistry, Biology and Biotechnology, Università degli studi di Perugia, Perugia, Italy.,Master-Tec s.r.l., Via Sicilia 41, Perugia, Italy
| | - Marzio Rosi
- Department of Civil and Environmental Engineering, Università degli studi di Perugia, Perugia, Italy
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27
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Zhu C, Wang H, Medvedkov I, Marks J, Xu M, Yang J, Yang T, Pan Y, Kaiser RI. Exploitation of Synchrotron Radiation Photoionization Mass Spectrometry in the Analysis of Complex Organics in Interstellar Model Ices. J Phys Chem Lett 2022; 13:6875-6882. [PMID: 35861849 DOI: 10.1021/acs.jpclett.2c01628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Unravelling the generation of complex organic molecules (COMs) on interstellar nanoparticles (grains) is essential in establishing predictive astrochemical reaction networks and recognizing evolution stages of molecular clouds and star-forming regions. The formation of COMs has been associated with the irradiation of interstellar ices by ultraviolet photons and galactic cosmic rays. Herein, we pioneer the first incorporation of synchrotron vacuum ultraviolet photoionization reflectron time-of-flight mass spectrometry (SVUV-PI-ReTOF-MS) in laboratory astrophysics simulation experiments to afford an isomer-selective identification of key COMs (ketene (H2C═CO); acetaldehyde (CH3CHO); vinyl alcohol (H2C═CHOH)) based on photoionization efficiency (PIE) curves of molecules desorbing from exposed carbon monoxide-methane (CO-CH4) ices. Our results demonstrate that the SVUV-PI-ReTOF-MS approach represents a versatile, rapid methodology for a comprehensive identification and explicit understanding of the complex organics produced in space simulation experiments. This methodology is expected to significantly improve the predictive nature of astrochemical models of complex organic molecules formed abiotically in deep space, including biorelated species linked to the origins-of-life topic.
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Affiliation(s)
- Cheng Zhu
- Department of Chemistry, University of Hawai'i at Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Hailing Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, P.R. China
| | - Iakov Medvedkov
- Department of Chemistry, University of Hawai'i at Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Joshua Marks
- Department of Chemistry, University of Hawai'i at Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Minggao Xu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, P.R. China
| | - Jiuzhong Yang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, P.R. China
| | - Tao Yang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, P.R. China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, P.R. China
| | - Yang Pan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, P.R. China
| | - Ralf I Kaiser
- Department of Chemistry, University of Hawai'i at Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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28
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Barik S, Dutta S, Behera NR, Kushawaha RK, Sajeev Y, Aravind G. Ambient-light-induced intermolecular Coulombic decay in unbound pyridine monomers. Nat Chem 2022; 14:1098-1102. [PMID: 35909167 DOI: 10.1038/s41557-022-01002-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/16/2022] [Indexed: 11/09/2022]
Abstract
Intermolecular Coulombic decay (ICD) is a process whereby photoexcited molecules relax by ionizing their neighbouring molecules. ICD is efficient when intermolecular interactions are active and consequently it is observed only in weakly bound systems, such as clusters and hydrogen-bonded systems. Here we report an efficient ICD between unbound molecules excited at ambient-light intensities. On the photoexcitation of gas-phase pyridine monomers, well below the ionization threshold and at low laser intensities, we detected the parent and heavier-than-parent cations. The isotropic emission of slow electrons revealed ICD as the underlying process. π-π* excitation in unbounded pyridine monomers triggered an associative interaction between them, which leads to an efficient three-centre ICD. The cation resulting from the molecular association of the three pyridine centres relaxed through fragmentation. This below-threshold ionization under ambient light has implications for the understanding of radiation damage and astrochemistry.
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Affiliation(s)
- Saroj Barik
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
| | - Saurav Dutta
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
| | - Nihar Ranjan Behera
- Department of Physics, Indian Institute of Technology Madras, Chennai, India
| | | | - Y Sajeev
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, India.
| | - G Aravind
- Department of Physics, Indian Institute of Technology Madras, Chennai, India.
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29
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Perspectives of Gas Phase Ion Chemistry: Spectroscopy and Modeling. CONDENSED MATTER 2022. [DOI: 10.3390/condmat7030046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The study of ions in the gas phase has a long history and has involved both chemists and physicists. The interplay of their competences with the use of very sophisticated commercial and/or homemade instrumentations and theoretical models has improved the knowledge of thermodynamics and kinetics of many chemical reactions, even if still many stages of these processes need to be fully understood. The new technologies and the novel free-electron laser facilities based on plasma acceleration open new opportunities to investigate the chemical reactions in some unrevealed fundamental aspects. The synchrotron light source can be put beside the FELs, and by mass spectrometric techniques and spectroscopies coupled with versatile ion sources it is possible to really change the state of the art of the ion chemistry in different areas such as atmospheric and astro chemistry, plasma chemistry, biophysics, and interstellar medium (ISM). In this manuscript we review the works performed by a joint combination of the experimental studies of ion–molecule reactions with synchrotron radiation and theoretical models adapted and developed to the experimental evidence. The review concludes with the perspectives of ion–molecule reactions by using FEL instrumentations as well as pump probe measurements and the initial attempt in the development of more realistic theoretical models for the prospective improvement of our predictive capability.
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30
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Bera PP, Noneman KK, Lee TJ. Energy Landscape and Structural and Spectroscopic Characterization of Diazirine and Its Cyclic Isomers. J Phys Chem A 2022; 126:4700-4708. [PMID: 35853204 DOI: 10.1021/acs.jpca.2c01444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Identifying new nitrogenated hydrocarbon molecules in the interstellar medium (ISM) is challenging because of the lack of comprehensive spectroscopic data from experiments. In this computational work, we focus on investigating the structures, relative energies, spectroscopic constants, and energy landscape of the cyclic isomers of diazirine (c-CH2N2) using ab initio quantum chemical methods. Density functional theory (DFT) methods and coupled cluster theory with singles and doubles including perturbative triples [CCSD(T)] and CCSD(T) with the explicitly correlated F12b correction [CCSD(T)-F12b] were employed for this purpose along with large correlation consistent cc-pVTZ, cc-pVQZ, and cc-pV5Z basis sets. Harmonic vibrational frequencies, infrared vibrational intensities, rotational constants, and dipole moments are reported. Anharmonic vibrational fundamentals along with centrifugal distortion constants, and vibration-rotation interaction constants are also reported for all the cyclic isomers. The energies computed with the CCSD(T) and CCSD(T)-F12b methods were extrapolated to the one-particle complete basis set (CBS) limit following a three-point formula. At the CCSD(T)-F12b/CBS level of theory, the 3,3H-diazirine (c-CH2N2) is the lowest energy cyclic isomer followed by 1,3H-diazirine, (E)-1,2H-diazirine, and (Z)-1,2H-diazirine, which are 20.1, 47.8, and 51.3 kcal mol-1 above the 3,3H-diazirine, respectively. Accurate structures and spectroscopic constants that are reported here could be useful for future identification of these cyclic nitrogenated organic molecules in the interstellar medium or circumstellar disks.
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Affiliation(s)
- Partha P Bera
- Bay Area Environmental Research Institute, Moffett Field, California 94035, United States
- Space Science and Astrobiology Division, NASA Ames Research Center, Mountain View, California 94035, United States
| | - Kendra K Noneman
- Space Science and Astrobiology Division, NASA Ames Research Center, Mountain View, California 94035, United States
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Drive, Boise, Idaho 83725, United States
| | - Timothy J Lee
- Space Science and Astrobiology Division, NASA Ames Research Center, Mountain View, California 94035, United States
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31
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Ramanathan K, S. A, Bouwman J, Avaldi L, Vinitha MV, Bolognesi P, Richter R, Kadhane U. Photodissociation of Quinoline Cation: Mapping the Potential Energy Surface. J Chem Phys 2022; 157:064303. [DOI: 10.1063/5.0092161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A detailed exploration of the potential energy surface of quinoline cation (C9H7N ·+) is carried out to extend the present understanding of its fragmentation mechanisms. DFT calculations have been performed to explore new fragmentation mechanisms giving special attention to previously unexplored pathways such as isomerisation and elimination of HNC. The isomerization mechanisms producing 5-7 membered ring intermediates have been described and are found to be a dominant channel both energetically and kinetically. Energetically competing pathways have been established for the astrochemically important HNC-loss channel, which has hitherto never been considered in the context of the loss of a 27 amu fragment from the parent ions. Elimination of acetylene was also studied in great detail. Overall computational results are found to complement the experimental observations from the concurrently conducted PEPICO investigation. These could potentially open the doors for rich and interesting VUV radiation driven chemistry on the planetary atomospheres, meteorites and comets.
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Affiliation(s)
| | - Arun S.
- Physics, Indian Institute of Space Science and Technology, India
| | - Jordy Bouwman
- University of Colorado Boulder Laboratory for Atmospheric and Space Physics, United States of America
| | - Lorenzo Avaldi
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche Area della Ricerca di Roma 1, Italy
| | - M. V. Vinitha
- Indian Institute of Space Science and Technology, India
| | - Paola Bolognesi
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche Area della Ricerca di Roma 1, Italy
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32
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Martínez RF, Cuccia LA, Viedma C, Cintas P. On the Origin of Sugar Handedness: Facts, Hypotheses and Missing Links-A Review. ORIGINS LIFE EVOL B 2022; 52:21-56. [PMID: 35796896 DOI: 10.1007/s11084-022-09624-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022]
Abstract
By paraphrasing one of Kipling's most amazing short stories (How the Leopard Got His Spots), this article could be entitled "How Sugars Became Homochiral". Obviously, we have no answer to this still unsolved mystery, and this perspective simply brings recent models, experiments and hypotheses into the homochiral homogeneity of sugars on earth. We shall revisit the past and current understanding of sugar chirality in the context of prebiotic chemistry, with attention to recent developments and insights. Different scenarios and pathways will be discussed, from the widely known formose-type processes to less familiar ones, often viewed as unorthodox chemical routes. In particular, problems associated with the spontaneous generation of enantiomeric imbalances and the transfer of chirality will be tackled. As carbohydrates are essential components of all cellular systems, astrochemical and terrestrial observations suggest that saccharides originated from environmentally available feedstocks. Such substances would have been capable of sustaining autotrophic and heterotrophic mechanisms integrating nutrients, metabolism and the genome after compartmentalization. Recent findings likewise indicate that sugars' enantiomeric bias may have emerged by a transfer of chirality mechanisms, rather than by deracemization of sugar backbones, yet providing an evolutionary advantage that fueled the cellular machinery.
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Affiliation(s)
- R Fernando Martínez
- Departamento de Química Orgánica E Inorgánica, Facultad de Ciencias, and Instituto Universitario de Investigación del Agua, Cambio Climático Y Sostenibilidad, (IACYS), Universidad de Extremadura, Avenida de Elvas s/n, 06006, Badajoz, Spain.
| | - Louis A Cuccia
- Department of Chemistry and Biochemistry, Quebec Centre for Advanced Materials (QCAM/CQMF), FRQNT, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada
| | - Cristóbal Viedma
- Department of Crystallography and Mineralogy, University Complutense, 28040, Madrid, Spain
| | - Pedro Cintas
- Departamento de Química Orgánica E Inorgánica, Facultad de Ciencias, and Instituto Universitario de Investigación del Agua, Cambio Climático Y Sostenibilidad, (IACYS), Universidad de Extremadura, Avenida de Elvas s/n, 06006, Badajoz, Spain.
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33
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Kadhane UR, Vinitha MV, Ramanathan K, S. A, Bouwman J, Avaldi L, Bolognesi P, Richter R. Comprehensive survey of dissociative photoionization of quinoline by PEPICO experiments. J Chem Phys 2022; 156:244304. [DOI: 10.1063/5.0092158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Dissociative photoionization of quinoline induced by vacuum ultraviolet radiation is investigated using photoelectron–photoion coincidence spectroscopy. Branching ratios of all the detectable fragment ions are measured as a function of internal energy ranging from 2 to 30 eV. A specific generation hierarchy is observed in the breakdown curves of a set of dissociation channels. Moreover, a careful comparison of the breakdown curves of fragments among the successive generations allowed to establish a decay sequence in the fragmentation of quinoline cation. This enabled us to revisit and refine the understanding of the first generation decay and reassign the origin of a few of the higher generation decay products of quinoline cation. With the help of the accompanying computational work (reported concurrently), we have demonstrated the dominance of two different HCN elimination pathways over previously interpreted mechanisms. For the first time, a specific pathway for acetylene elimination is identified in quinoline+ and the role of isomerization in both acetylene as well as hydrogen cyanide loss is also demonstrated. The experiment also established that the acetylene elimination exclusively occurs from the non-nitrogen containing rings of quinoline cation. The formation of a few astronomically important species is also discussed.
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Affiliation(s)
- Umesh R. Kadhane
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - M. V. Vinitha
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - Karthick Ramanathan
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - Arun S.
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - Jordy Bouwman
- Laboratory for Atmospheric and Space Physics, University of Colorado, Boulder, Colorado 80303, USA
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Monterotondo, Roma 00015, Italy
| | - Paola Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Monterotondo, Roma 00015, Italy
| | - Robert Richter
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163, 5 in AREA Science Park, Basovizza TS 34149, Italy
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34
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Field-Theodore TE, Taylor PR. Interstellar hide and go seek: C 3H 4O. There and back (again). Phys Chem Chem Phys 2022; 24:19184-19198. [PMID: 35730752 DOI: 10.1039/d2cp00995a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular species C3H4O represents a striking example of an astrochemical conundrum. With more than 60 structural isomers theoretically possible, to date only acrolein (CH2CHCHO) has been identified in the Sgr B2(N) region of the interstellar medium (ISM). The topography of the singlet potential energy surface is complicated, with three low-lying minima predicted to be almost isoenergetic: cis and trans-acrolein, and methylketene (CH3CHCO). Our CCSD(T)/cc-pVTZ calculations confirm that methylketene is energetically lower than cis-acrolein, lying only 1.9 kJ mol-1 above the trans-isomer, which is the global minimum. In this respect, methylketene is a promising candidate for interstellar observation. Unfortunately, however, despite several searches its astronomical detection has been unsuccessful. To this end, the key question is whether in fact methylketene exists as a discrete chemical entity in the ISM at all? In this paper, we present a detailed examination of the C3H4O potential energy surface, with specific focus on formation pathways. CCSD(T)/cc-pVTZ calculations enable a more elaborate interpretation of reaction mechanisms than was published hitherto. Our results show that gauche-propargyl alcohol and syn and anti-allenol emerge as interesting new targets for observational astronomers in TMC-1: given the recent discovery of the propargyl radical in this region, barrierless product channels involving OH˙ lend support to their candidacy as possible interstellar species. Finally, this work provides accurate spectral data of these three potential molecules, to be used for searches in interstellar space.
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Affiliation(s)
| | - Peter R Taylor
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.
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35
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DeVine JA, Choudhury A, Lau JA, Schwarzer D, Wodtke AM. Spin-Forbidden Carbon-Carbon Bond Formation in Vibrationally Excited α-CO. J Phys Chem A 2022; 126:2270-2277. [PMID: 35380441 PMCID: PMC9014413 DOI: 10.1021/acs.jpca.2c01168] [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
![]()
Fourier transform
infrared spectroscopy of laser-irradiated cryogenic
crystals shows that vibrational excitation of CO leads to the production
of equal amounts of CO2 and C3O2.
The reaction mechanism is explored using electronic structure calculations,
demonstrating that the lowest-energy pathway involves a spin-forbidden
reaction of (CO)2 yielding C(3P) + CO2. C(3P) then undergoes barrierless recombination with
two other CO molecules forming C3O2. Calculated
intersystem crossing rates support the spin-forbidden mechanism, showing
subpicosecond spin-flipping time scales for a (CO)2 geometry
that is energetically consistent with states accessed through vibrational
energy pooling. This spin-flip occurs with an estimated ∼4%
efficiency; on the singlet surface, (CO)2 reconverts back
to CO monomers, releasing heat which induces CO desorption. The discovery
that vibrational excitation of condensed-phase CO leads to spin-forbidden
C–C bond formation may be important to the development of accurate
models of interstellar chemistry.
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Affiliation(s)
- Jessalyn A DeVine
- Abteilung für Dynamik an Oberflächen, Max-Planck-Institut für Multidisziplinäre Naturwissenschaften, Am Faßberg 11, 37077 Göttingen, Germany
| | - Arnab Choudhury
- Abteilung für Dynamik an Oberflächen, Max-Planck-Institut für Multidisziplinäre Naturwissenschaften, Am Faßberg 11, 37077 Göttingen, Germany.,Institute for Physical Chemistry, Georg-August Universität Göttingen, Tammannstaße 6, 37077 Göttingen, Germany
| | - Jascha A Lau
- Abteilung für Dynamik an Oberflächen, Max-Planck-Institut für Multidisziplinäre Naturwissenschaften, Am Faßberg 11, 37077 Göttingen, Germany.,Institute for Physical Chemistry, Georg-August Universität Göttingen, Tammannstaße 6, 37077 Göttingen, Germany
| | - Dirk Schwarzer
- Abteilung für Dynamik an Oberflächen, Max-Planck-Institut für Multidisziplinäre Naturwissenschaften, Am Faßberg 11, 37077 Göttingen, Germany
| | - Alec M Wodtke
- Abteilung für Dynamik an Oberflächen, Max-Planck-Institut für Multidisziplinäre Naturwissenschaften, Am Faßberg 11, 37077 Göttingen, Germany.,Institute for Physical Chemistry, Georg-August Universität Göttingen, Tammannstaße 6, 37077 Göttingen, Germany
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36
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Sallembien Q, Bouteiller L, Crassous J, Raynal M. Possible chemical and physical scenarios towards biological homochirality. Chem Soc Rev 2022; 51:3436-3476. [PMID: 35377372 DOI: 10.1039/d1cs01179k] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The single chirality of biological molecules in terrestrial biology raises more questions than certitudes about its origin. The emergence of biological homochirality (BH) and its connection with the appearance of life have elicited a large number of theories related to the generation, amplification and preservation of a chiral bias in molecules of life under prebiotically relevant conditions. However, a global scenario is still lacking. Here, the possibility of inducing a significant chiral bias "from scratch", i.e. in the absence of pre-existing enantiomerically-enriched chemical species, will be considered first. It includes phenomena that are inherent to the nature of matter itself, such as the infinitesimal energy difference between enantiomers as a result of violation of parity in certain fundamental interactions, and physicochemical processes related to interactions between chiral organic molecules and physical fields, polarized particles, polarized spins and chiral surfaces. The spontaneous emergence of chirality in the absence of detectable chiral physical and chemical sources has recently undergone significant advances thanks to the deracemization of conglomerates through Viedma ripening and asymmetric auto-catalysis with the Soai reaction. All these phenomena are commonly discussed as plausible sources of asymmetry under prebiotic conditions and are potentially accountable for the primeval chiral bias in molecules of life. Then, several scenarios will be discussed that are aimed to reflect the different debates about the emergence of BH: extra-terrestrial or terrestrial origin (where?), nature of the mechanisms leading to the propagation and enhancement of the primeval chiral bias (how?) and temporal sequence between chemical homochirality, BH and life emergence (when?). Intense and ongoing theories regarding the emergence of optically pure molecules at different moments of the evolution process towards life, i.e. at the levels of building blocks of Life, of the instructed or functional polymers, or even later at the stage of more elaborated chemical systems, will be critically discussed. The underlying principles and the experimental evidence will be commented for each scenario with particular attention on those leading to the induction and enhancement of enantiomeric excesses in proteinogenic amino acids, natural sugars, and their intermediates or derivatives. The aim of this review is to propose an updated and timely synopsis in order to stimulate new efforts in this interdisciplinary field.
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Affiliation(s)
- Quentin Sallembien
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 Place Jussieu, 75005 Paris, France.
| | - Laurent Bouteiller
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 Place Jussieu, 75005 Paris, France.
| | - Jeanne Crassous
- Univ Rennes, CNRS, Institut des Sciences Chimiques de Rennes, ISCR-UMR 6226, F-35000 Rennes, France.
| | - Matthieu Raynal
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 Place Jussieu, 75005 Paris, France.
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37
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Kasai T, Muthiah B, Po X, Yan C, Lin K, Tanudji J, Diño WA. Pattern analysis of the impact‐parameter dependent trajectories for the H +
H
2
exchange reaction at
T
=
3
and
300 K
: A characteristic propensity for reactive versus nonreactive trajectories found in the time‐dependent interaction potential and a roaming‐like libration motion at cold temperature. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202100539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Toshio Kasai
- Department of Chemistry National Taiwan University Taipei Taiwan
- Department of Applied Physics Osaka University Suita Japan
| | | | - Xin‐Hui Po
- Department of Chemistry National Taiwan University Taipei Taiwan
- Department of Statistics National Chengchi University Taipei Taiwan
| | - Chu‐Chun Yan
- Department of Chemistry National Taiwan University Taipei Taiwan
| | - King‐Chuen Lin
- Department of Chemistry National Taiwan University Taipei Taiwan
- Department of Chemistry, Institute of Atomic and Molecular Sciences Academia Sinica Taipei Taiwan
| | | | - Wilson Agerico Diño
- Department of Applied Physics Osaka University Suita Japan
- Center for Atomic and Molecular Technologies Osaka University Suita Japan
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38
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Kaiser K, Schulz F, Maillard JF, Hermann F, Pozo I, Peña D, Cleaves HJ, Burton AS, Danger G, Afonso C, Sandford S, Gross L. Visualization and identification of single meteoritic organic molecules by atomic force microscopy. METEORITICS & PLANETARY SCIENCE 2022; 57:644-656. [PMID: 35912284 PMCID: PMC9305854 DOI: 10.1111/maps.13784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/16/2021] [Indexed: 06/15/2023]
Abstract
Using high-resolution atomic force microscopy (AFM) with CO-functionalized tips, we atomically resolved individual molecules from Murchison meteorite samples. We analyzed powdered Murchison meteorite material directly, as well as processed extracts that we prepared to facilitate characterization by AFM. From the untreated Murchison sample, we resolved very few molecules, as the sample contained mostly small molecules that could not be identified by AFM. By contrast, using a procedure based on several trituration and extraction steps with organic solvents, we isolated a fraction enriched in larger organic compounds. The treatment increased the fraction of molecules that could be resolved by AFM, allowing us to identify organic constituents and molecular moieties, such as polycyclic aromatic hydrocarbons and aliphatic chains. The AFM measurements are complemented by high-resolution mass spectrometry analysis of Murchison fractions. We provide a proof of principle that AFM can be used to image and identify individual organic molecules from meteorites and propose a method for extracting and preparing meteorite samples for their investigation by AFM. We discuss the challenges and prospects of this approach to study extraterrestrial samples based on single-molecule identification.
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Affiliation(s)
| | - Fabian Schulz
- IBM Research—ZurichRüschlikon8003Switzerland
- Present address:
Fritz Haber Institute of the Max Planck SocietyBerlin14195Germany
| | - Julien F. Maillard
- Normandie UnivCOBRAUMR 6014 et FR 3038 Univ RouenINSA RouenCNRS IRCOF1 Rue TesnièreMont‐Saint‐Aignan Cedex76821France
| | | | - Iago Pozo
- Departamento de Química OrgánicaCentro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)Universidade de Santiago de CompostelaSantiago de Compostela15782Spain
| | - Diego Peña
- Departamento de Química OrgánicaCentro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)Universidade de Santiago de CompostelaSantiago de Compostela15782Spain
| | - H. James Cleaves
- Earth‐Life Science InstituteTokyo Institute of Technology2‑12‑1‑IE‑1 Ookayama, Meguro‑kuTokyo152‑8550Japan
- Blue Marble Space Institute for Science1001 4th Ave, Suite 3201SeattleWashington98154USA
| | - Aaron S. Burton
- Astromaterials Research and Exploration Science DivisionNASA Johnson Space CenterMS XI‐3HoustonTexas77058USA
| | - Gregoire Danger
- Laboratoire de Physique des Interactions Ioniques et Moléculaires (PIIM)CNRSAix‐Marseille UniversitéMarseilleFrance
- CNRSCNESLAMAix‐Marseille UniversitéMarseilleFrance
- Institut Universitaire de FranceParisFrance
| | - Carlos Afonso
- Normandie UnivCOBRAUMR 6014 et FR 3038 Univ RouenINSA RouenCNRS IRCOF1 Rue TesnièreMont‐Saint‐Aignan Cedex76821France
| | - Scott Sandford
- Space Science DivisionNASA Ames Research CenterMS 245‐6Moffett FieldCalifornia94035USA
| | - Leo Gross
- IBM Research—ZurichRüschlikon8003Switzerland
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39
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Webster IJ, Beckham JL, Johnson ND, Duncan MA. Photochemical Synthesis and Spectroscopy of Covalent PAH Dimers. J Phys Chem A 2022; 126:1144-1157. [PMID: 35152698 DOI: 10.1021/acs.jpca.1c10606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Laser photochemistry of pressed-pellet samples of polycyclic aromatic hydrocarbons (PAHs) produces covalently bonded dimers and some higher polymers. This chemistry was discovered initially via laser desorption time-of-flight mass spectrometry experiments, which produced masses (m/z) of 2M-2 and 2M-4 (where M is the monomer parent mass). Dimers are believed to be formed from photochemical dehydrogenation and radical polymerization chemistry in the desorption plume. Replication of these ablation conditions at higher throughput allowed PAH dimers of pyrene, perylene, and coronene to be produced and collected in milligram quantities. Differential sublimation provided purification of the dimers and elimination of residual monomers. The purified dimers were investigated with UV-visible, IR, and Raman spectroscopy, complemented by computational studies using density functional theory at the CAM-B3LYP/def2-TZV level. Calculations and predicted spectra were calibrated by comparison with the corresponding monomers and used to determine the lowest energy dimer structures. Infrared and Raman spectroscopy provided few distinctive signatures, but UV-visible spectra detected new transitions for each dimer. The comparison of simulated and experimental spectra allows determination of the most prevalent structures for the PAH dimers. The work presented here provides interesting insights into the spectroscopy of extended aromatic systems and a new strategy for the photochemical synthesis of large PAH dimers.
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Affiliation(s)
- Ian J Webster
- Department of Chemistry, University of Georgia, Athens 30602-2556, Georgia
| | - Jacob L Beckham
- Department of Chemistry, University of Georgia, Athens 30602-2556, Georgia
| | - Natalie D Johnson
- Department of Chemistry, University of Georgia, Athens 30602-2556, Georgia
| | - Michael A Duncan
- Department of Chemistry, University of Georgia, Athens 30602-2556, Georgia
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40
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Lozano AI, Kumar S, Kerkeni B, García G, Limão-Vieira P. Methanol Negative Ion Fragmentation Probed in Electron Transfer Experiments. J Phys Chem A 2022; 126:1076-1084. [PMID: 35143199 DOI: 10.1021/acs.jpca.1c07588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this contribution, we report a novel comprehensive investigation on negative ion formation from electron transfer processes mediated by neutral potassium atom collisions with neutral methanol molecules employing experimental and theoretical methodologies. Methanol collision-induced fragmentation yielding anion formation has been obtained by time-of-flight mass spectrometry in the wide energy range of 19 to 275 eV in the lab frame. The negative ions formed in such a collision process have been assigned to CH3O-, OH-, and O-, with a strong energy dependence especially at lower collision energies. The most intense fragment anions in the whole energy range investigated have been assigned to OH- and CH3O-. Additionally, the potassium cation energy loss spectrum in the forward scattering direction at 205 eV impact energy has revealed several features, where the two main electronic states accessible during the collision events have vertical electron affinities of -8.26 ± 0.20 and -10.36 ± 0.2 eV. Quantum chemical calculations have been performed for the lowest-lying unoccupied molecular orbitals of methanol in the presence of a potassium atom, lending strong support to the experimental findings.
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Affiliation(s)
- Ana Isabel Lozano
- Atomic and Molecular Collisions Laboratory, Centro de Física e Investigação Tecnológica, Department of Physics, Universidade NOVA de Lisboa, Caparica 2829-516, Portugal.,Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, Madrid 28006, Spain
| | - Sarvesh Kumar
- Atomic and Molecular Collisions Laboratory, Centro de Física e Investigação Tecnológica, Department of Physics, Universidade NOVA de Lisboa, Caparica 2829-516, Portugal
| | - Boutheïna Kerkeni
- Institut Supérieur des Arts Multimédia de la Manouba, Université de la Manouba, La Manouba 2010, Tunisia.,Département de Physique, Laboratoire de recherche: Physique de la matière condensée, Faculté des Sciences de Tunis, Université de Tunis el Manar, Tunis 2092, Tunisia
| | - Gustavo García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, Madrid 28006, Spain
| | - Paulo Limão-Vieira
- Atomic and Molecular Collisions Laboratory, Centro de Física e Investigação Tecnológica, Department of Physics, Universidade NOVA de Lisboa, Caparica 2829-516, Portugal
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41
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Simmie JM. C 2H 5NO Isomers: From Acetamide to 1,2-Oxazetidine and Beyond. J Phys Chem A 2022; 126:924-939. [PMID: 35113546 PMCID: PMC8859852 DOI: 10.1021/acs.jpca.1c09984] [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: 11/30/2022]
Abstract
![]()
This work documents
the properties of a number of isomers of molecular
formula C2H5NO from the most stable, acetamide,
through 1,2-oxazetidine and including even higher energy species largely
of a dipolar nature. Only two of the isomers have been detected in
emissions from the interstellar medium (ISM); possible further candidates
are identified, and the likelihood of their being detectable is considered.
In general, hardly any of these compounds have been discussed in the
existing chemical literature, so this work represents an important
contribution extending the canon of chemical bonding which can contribute
to machine learning, providing a more exacting test of AI applications.
The presence in the ISM of acetamide, CH3C(O)NH2, is the subject of current debate with no clear and obvious paths
to its formation; it is shown that a 1,3-[H]-transfer from (E,Z)-ethanimidic acid, CH3C(OH)=NH, is
feasible in spite of an energy barrier of 130 kJ mol–1. It is speculated that imidic acid can itself be formed from abundant
precursors, H2O and CH3C≡N, in an acid-induced,
water addition, autocatalytic reaction on water–ice grains.
H3CC≡NH3CC≡NH+ +
H2OH3CC(O+H2)=NHH3CC(OH)=NH
+ H3O+
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Affiliation(s)
- John M Simmie
- School of Chemistry, National University of Ireland, Galway H91 TK33, Ireland
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42
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Lavado N, de la Concepción JG, Cintas P, Babiano R. Synthesis of C xN y-rich polycyclic oligomers from primeval monomers in aqueous media. Phys Chem Chem Phys 2022; 24:3632-3646. [PMID: 35103738 DOI: 10.1039/d1cp05204g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A multichannel, non-thermolytic and efficient pathway is described toward the formation of functionalized carbon nitride-like oligomers, starting from readily available cyanamide and glyoxal (in ratios >2), in aqueous media under mild conditions. Such oligomers can be isolated as stable solids that result from structures involving cyanamide self-additions along with structures formally derived from the condensation of cyanamide, dicyandiamide or melamine with glyoxal, leading occasionally to oxygen-containing units. The oligomeric aggregates have masses up to 500 u, as inferred from mass spectra analyses, and their formation can be rationalized in terms of polyadditions of cyanamide (up to 10-mer) and glyoxal. The latter is not only a willing reaction partner, but also promotes facile condensation by enhancing the reactivity of nitrile fragments and inducing a significant lowering of the energy barriers. This mechanistic surmise is also supported by DFT calculations of the early condensation steps. As a result, melamine/triazine-type structures are obtained in aquatic environments under much milder conditions than those usually required by other synthetic procedures. Moreover, our results also help unveil the abiotic processes affording complex organic matter on celestial bodies and early earth.
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Affiliation(s)
- Nieves Lavado
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias, and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain.
| | - Juan García de la Concepción
- Departamento de Astrofísica, Centro de Astrobiología (INTA-CSIC), 28850 Torrejón de Ardoz, Madrid, Spain.,Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias, and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain.
| | - Pedro Cintas
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias, and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain.
| | - Reyes Babiano
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencias, and IACYS-Unidad de Química Verde y Desarrollo Sostenible, Universidad de Extremadura, E-06006 Badajoz, Spain.
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43
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Baú JPT, Carneiro CEA, da Costa ACS, Valezi DF, di Mauro E, Pilau E, Zaia DAM. The Effect of Goethites on the Polymerization of Glycine and Alanine Under Prebiotic Chemistry Conditions. ORIGINS LIFE EVOL B 2022; 51:299-320. [PMID: 35064872 DOI: 10.1007/s11084-021-09618-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022]
Abstract
After pre concentration of monomers, polymerization is the second most important step for molecular evolution. The formation of peptides is an important issue for prebiotic chemistry and consequently for the origin of life. In this work, goethite was synthesized by two different routes, named goethite-I and goethite-II. Although both samples are goethite, Far-FT-IR spectroscopy and EPR spectroscopy showed differences between them, and these differences had an effect on the polymerization of glycine and alanine. For the amino acid polymerization, three protocols were used, that resembled prebiotic Earth conditions: a) amino acid plus goethite were mixed and heated at 90 °C for 10 days in solid state, b) a wet impregnation of the amino acid in the goethite, with subsequent heating at 90 °C for 10 days in solid state, and c) 10 wet/dry cycles each one for 24 h at 90 °C. Experiments with glycine plus goethite-II, using protocols B and C, produced only Gly-Gly. In addition, for the C protocol the amount of Gly-Gly synthesized was 3 times higher than the amount of Ala-Ala. Goethite-I presented a decrease in the EPR signal, when it was submitted to the protocols with and without amino acids. It is probable the decrease in the intensity of the EPR signal was due to a decrease in the imperfections of the mineral. For all protocols the mixture of alanine plus goethite-I or goethite-II produced c(Ala-Ala). However, for wet/dry cycles, protocol C presented higher yields (p < 0.05). In addition, Ala-Ala was produced using protocols A and C. The c(Ala-Ala) formation fitted a zero-order kinetic equation model. The surface areas of goethite-I and goethite-II were 35 m2 g-1 and 37 m2 g-1, respectively. Thermal analysis indicated that the mineral changes the thermal behavior of the amino acids. The main reactions for the thermal decomposition of glycine were deamination and dehydration and for alanine was deamination.
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Affiliation(s)
- João Paulo T Baú
- Laboratório de Química Prebiótica, Departamento de Química-CCE, Universidade Estadual de Londrina, 86051-990, Londrina, PR, Brasil
| | - Cristine E A Carneiro
- Centro das Ciências Exatas E Tecnologia, Universidade Federal Do Oeste da Bahia, 47810-059, Barreiras, BA, Brasil
| | | | - Daniel F Valezi
- Departamento de Física-CCE, Universidade Estadual de Londrina, 86051-990, Londrina, PR, Brasil
| | - Eduardo di Mauro
- Departamento de Física-CCE, Universidade Estadual de Londrina, 86051-990, Londrina, PR, Brasil
| | - Eduardo Pilau
- Departamento de Química-CCE, Universidade Estadual de Maringá, 87020-900, Maringá, PR, Brasil
| | - Dimas A M Zaia
- Laboratório de Química Prebiótica, Departamento de Química-CCE, Universidade Estadual de Londrina, 86051-990, Londrina, PR, Brasil.
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44
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Kovalenko SP. On the Origin of Genetically Coded Protein Synthesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021060121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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45
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Rocha CMR, Linnartz H. High-level ab initio quartic force fields and spectroscopic characterization of C 2N . Phys Chem Chem Phys 2021; 23:26227-26240. [PMID: 34787132 DOI: 10.1039/d1cp03505c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While it is now well established that large carbon chain species and radiative electron attachment (REA) are key ingredients triggering interstellar anion chemistry, the role played by smaller molecular anions, for which REA appears to be an unlikely formation pathway, is as yet elusive. Advancing this research undoubtedly requires the knowledge (and modeling) of their astronomical abundances which, for the case of C2N-, is largely hindered by a lack of accurate spectroscopic signatures. In this work, we provide such data for both ground -CCN-(3Σ-) and low-lying c-CNC-(1A1) isomers and their singly-substituted isotopologues by means of state-of-the-art rovibrational quantum chemical techniques. Their quartic force fields are herein calibrated using a high-level composite energy scheme that accounts for extrapolations to both one-particle and (approximate) -particle basis set limits, in addition to relativistic effects, with the final forms being subsequently subject to nuclear motion calculations. Besides standard spectroscopic attributes, the full set of computed properties includes fine and hyperfine interaction constants and can be readily introduced as guesses in conventional experimental data reduction analyses through effective Hamiltonians. On the basis of benchmark calculations performed anew for a minimal test set of prototypical triatomics and limited (low-resolution) experimental data for -CCN-(3Σ-), the target accuracies are determined to be better than 0.1% of experiment for rotational constants and 0.3% for vibrational fundamentals. Apart from laboratory investigations, the results here presented are expected to also prompt future astronomical surveys on C2N-. To this end and using the theoretically-predicted spectroscopic constants, the rotational spectra of both -CCN-(3Σ-) and c-CNC-(1A1) are derived and their likely detectability in the interstellar medium is further explored in connection with working frequency ranges of powerful astronomical facilities. Our best theoretical estimate places c-CNC-(1A1) at about 15.3 kcal mol-1 above the ground-state -CCN-(3Σ-) species.
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Affiliation(s)
- C M R Rocha
- Laboratory for Astrophysics, Leiden Observatory, Leiden University, P.O. Box 9513, NL-2300 RA Leiden, The Netherlands.
| | - H Linnartz
- Laboratory for Astrophysics, Leiden Observatory, Leiden University, P.O. Box 9513, NL-2300 RA Leiden, The Netherlands.
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46
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Sheng M, Silvestrini F, Biczysko M, Puzzarini C. Structural and Vibrational Properties of Amino Acids from Composite Schemes and Double-Hybrid DFT: Hydrogen Bonding in Serine as a Test Case. J Phys Chem A 2021; 125:9099-9114. [PMID: 34623165 DOI: 10.1021/acs.jpca.1c06993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap" composite approach (CCSD(T)/(CBS+CV)MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm-1, has been obtained by combining CCSD(T)/(CBS+CV)MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included.
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Affiliation(s)
- Mingzhu Sheng
- International Centre for Quantum and Molecular Structures, Physics Department, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Filippo Silvestrini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Physics Department, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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47
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Timón V, Maté B, Herrero VJ, Tanarro I. Infrared spectra of amorphous and crystalline urea ices. Phys Chem Chem Phys 2021; 23:22344-22351. [PMID: 34604879 DOI: 10.1039/d1cp03503g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Urea is a molecule of great interest in chemistry and biology. In particular, it is considered a key building block in prebiotic chemistry on Earth. The hypothesis of its possible exogenous origin has been reinforced after the recent detection of this molecule in the interstellar medium, where it is believed to form in the ice mantles of dust grains. In this work the infrared spectra of urea ices and urea:H2O ice mixtures have been studied both experimentally and theoretically. Urea ices were generated by vapour deposition at temperatures between 10 K and 270 K. It was found that an amorphous phase is formed at temperatures below 200 K. A theoretical modelling of crystalline urea and of a tentative amorphous urea solid phase, as well as of amorphous urea:H2O ice mixtures, has been performed. The corresponding infrared spectra were simulated with density functional theory. The main spectral features observed in the various solid samples are interpreted with the help of the theoretical results. Infrared band strengths are also provided for amorphous and crystalline urea. The infrared spectroscopic information given in this work is expected to be useful for the detection and quantification of urea in astrophysical ices.
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Affiliation(s)
- Vicente Timón
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Belén Maté
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Victor J Herrero
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Isabel Tanarro
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
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48
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Freindorf M, Beiranvand N, Delgado AAA, Tao Y, Kraka E. On the formation of CN bonds in Titan's atmosphere-a unified reaction valley approach study. J Mol Model 2021; 27:320. [PMID: 34633543 DOI: 10.1007/s00894-021-04917-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/15/2021] [Indexed: 08/30/2023]
Abstract
In this work, we investigated the formation of protonated hydrogen cyanide HCNH+ and methylene amine cation CH[Formula: see text] (both identified in Titan's upper atmosphere) from three different pathways which stem from the interaction between CH4 and N+(3P). As a mechanistic tool, we used the Unified Reaction Valley Approach (URVA) complemented with the Local Mode Analysis (LMA) assessing the strength of the CN bonds formed in these reactions. Our URVA studies could provide a comprehensive overview on bond formation/cleavage processes relevant to the specific mechanism of eight reactions R1- R8 that occur across the three pathways. In addition, we could explain the formation of CH[Formula: see text] and the appearance of HCNH+ and CHNH[Formula: see text] along these paths. Although only smaller molecules are involved in these reactions including isomerization, hydrogen atom abstraction, and hydrogen molecule capture, we found a number of interesting features, such as roaming in reaction R3 or the primary interaction of H2 with the carbon atom in HCNH+ in reaction R8 followed by migration of one of the H2 hydrogen atoms to the nitrogen which is more cost effective than breaking the HH bond first; a feature often found in catalysis. In all cases, charge transfer between carbon and nitrogen could be identified as a driving force for the CN bond formation. As revealed by LMA, the CN bonds formed in reactions R1-R8 cover a broad bond strength range from very weak to very strong, with the CN bond in protonated hydrogen cyanide HCNH+ identified as the strongest of all molecules investigated in this work. Our study demonstrates the large potential of both URVA and LMA to shed new light into these extraterrestrial reactions to help better understand prebiotic processes as well as develop guidelines for future investigations involving areas of complex interstellar chemistry. In particular, the formation of CN bonds as a precursor to the extraterrestrial formation of amino acids will be the focus of future investigations. Formation of CN bonds in Titan's atmosphere visualized via the reaction path curvature.
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Affiliation(s)
- Marek Freindorf
- Chemistry Department, SMU, Fondren Science Building, Dallas, 75275-0314, TX, USA
| | - Nassim Beiranvand
- Chemistry Department, SMU, Fondren Science Building, Dallas, 75275-0314, TX, USA
| | - Alexis A A Delgado
- Chemistry Department, SMU, Fondren Science Building, Dallas, 75275-0314, TX, USA
| | - Yunwen Tao
- Chemistry Department, SMU, Fondren Science Building, Dallas, 75275-0314, TX, USA
| | - Elfi Kraka
- Chemistry Department, SMU, Fondren Science Building, Dallas, 75275-0314, TX, USA.
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49
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Liu Y, Mathis C, Bajczyk MD, Marshall SM, Wilbraham L, Cronin L. Exploring and mapping chemical space with molecular assembly trees. SCIENCE ADVANCES 2021; 7:eabj2465. [PMID: 34559562 PMCID: PMC8462901 DOI: 10.1126/sciadv.abj2465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/03/2021] [Indexed: 06/01/2023]
Abstract
The rule-based search of chemical space can generate an almost infinite number of molecules, but exploration of known molecules as a function of the minimum number of steps needed to build up the target graphs promises to uncover new motifs and transformations. Assembly theory is an approach to compare the intrinsic complexity and properties of molecules by the minimum number of steps needed to build up the target graphs. Here, we apply this approach to prebiotic chemistry, gene sequences, plasticizers, and opiates. This allows us to explore molecules connected to the assembly tree, rather than the entire space of molecules possible. Last, by developing a reassembly method, based on assembly trees, we found that in the case of the opiates, a new set of drug candidates could be generated that would not be accessible via conventional fragment-based drug design, thereby demonstrating how this approach might find application in drug discovery.
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Affiliation(s)
- Yu Liu
- School of Chemistry, University of Glasgow, University Avenue,
Glasgow G12 8QQ, UK
| | - Cole Mathis
- School of Chemistry, University of Glasgow, University Avenue,
Glasgow G12 8QQ, UK
| | | | - Stuart M. Marshall
- School of Chemistry, University of Glasgow, University Avenue,
Glasgow G12 8QQ, UK
| | - Liam Wilbraham
- School of Chemistry, University of Glasgow, University Avenue,
Glasgow G12 8QQ, UK
| | - Leroy Cronin
- School of Chemistry, University of Glasgow, University Avenue,
Glasgow G12 8QQ, UK
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50
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Field-Theodore TE, Taylor PR. Conjugation trumps cumulation: the global minimum on the C3H4O surface. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1979263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Terri E. Field-Theodore
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Peter R. Taylor
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, People's Republic of China
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