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Vollmer C, Kepaptsoglou D, Leitner J, Mosberg AB, El Hajraoui K, King AJ, Bays CL, Schofield PF, Araki T, Ramasse QM. High-spatial resolution functional chemistry of nitrogen compounds in the observed UK meteorite fall Winchcombe. Nat Commun 2024; 15:778. [PMID: 38278803 PMCID: PMC10817942 DOI: 10.1038/s41467-024-45064-x] [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: 07/13/2023] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
Organic matter in extraterrestrial samples is a complex material that might have played an important role in the delivery of prebiotic molecules to the early Earth. We report here on the identification of nitrogen-containing compounds such as amino acids and N-heterocycles within the recent observed meteorite fall Winchcombe by high-spatial resolution spectroscopy techniques. Although nitrogen contents of Winchcombe organic matter are low (N/C ~ 1-3%), we were able to detect the presence of these compounds using a low-noise direct electron detector. These biologically relevant molecules have therefore been tentatively found within a fresh, minimally processed meteorite sample by high spatial resolution techniques conserving the overall petrographic context. Carbon functional chemistry investigations show that sizes of aromatic domains are small and that abundances of carboxylic functional groups are low. Our observations demonstrate that Winchcombe represents an important addition to the collection of carbonaceous chondrites and still preserves pristine extraterrestrial organic matter.
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Affiliation(s)
| | - Demie Kepaptsoglou
- SuperSTEM Laboratory, Keckwick Lane, Daresbury, UK
- School of Physics, Engineering and Technology, University of York, Heslington, UK
| | - Jan Leitner
- Institut für Geowissenschaften, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
- Max Planck Institute for Chemistry, Particle Chemistry Department, Mainz, Germany
| | | | - Khalil El Hajraoui
- SuperSTEM Laboratory, Keckwick Lane, Daresbury, UK
- School of Physics, Engineering and Technology, University of York, Heslington, UK
| | - Ashley J King
- Planetary Materials Group, Natural History Museum, London, UK
| | - Charlotte L Bays
- Planetary Materials Group, Natural History Museum, London, UK
- Department of Earth Sciences, Royal Holloway, University of London, Egham, UK
| | | | - Tohru Araki
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- National Institutes of Natural Sciences, Institute for Molecular Science, UVSOR Synchrotron Facility, Okazaki, Japan
| | - Quentin M Ramasse
- SuperSTEM Laboratory, Keckwick Lane, Daresbury, UK
- School of Chemical and Process Engineering and School of Physics and Astronomy, University of Leeds, Leeds, UK
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2
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Nuñez-Rios JD, Ulrich H, Díaz-Muñoz M, Lameu C, Vázquez-Cuevas FG. Purinergic system in cancer stem cells. Purinergic Signal 2023:10.1007/s11302-023-09976-5. [PMID: 37966629 DOI: 10.1007/s11302-023-09976-5] [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: 06/10/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
Accumulating evidence supports the idea that cancer stem cells (CSCs) are those with the capacity to initiate tumors, generate phenotypical diversity, sustain growth, confer drug resistance, and orchestrate the spread of tumor cells. It is still controversial whether CSCs originate from normal stem cells residing in the tissue or cancer cells from the tumor bulk that have dedifferentiated to acquire stem-like characteristics. Although CSCs have been pointed out as key drivers in cancer, knowledge regarding their physiology is still blurry; thus, research focusing on CSCs is essential to designing novel and more effective therapeutics. The purinergic system has emerged as an important autocrine-paracrine messenger system with a prominent role at multiple levels of the tumor microenvironment, where it regulates cellular aspects of the tumors themselves and the stromal and immune systems. Recent findings have shown that purinergic signaling also participates in regulating the CSC phenotype. Here, we discuss updated information regarding CSCs in the purinergic system and present evidence supporting the idea that elements of the purinergic system expressed by this subpopulation of the tumor represent attractive pharmacological targets for proposing innovative anti-cancer therapies.
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Affiliation(s)
- J D Nuñez-Rios
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Boulevard Juriquilla #3001, Juriquilla Querétaro, Querétaro, CP 76230, México
| | - H Ulrich
- Department of Biochemistry, Chemistry Institute, University of São Paulo (USP), São Paulo, Brazil
| | - M Díaz-Muñoz
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Boulevard Juriquilla #3001, Juriquilla Querétaro, Querétaro, CP 76230, México
| | - C Lameu
- Department of Biochemistry, Chemistry Institute, University of São Paulo (USP), São Paulo, Brazil
| | - F G Vázquez-Cuevas
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Boulevard Juriquilla #3001, Juriquilla Querétaro, Querétaro, CP 76230, México.
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3
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Bechtel M, Ebeling M, Huber L, Trapp O. (Photoredox) Organocatalysis in the Emergence of Life: Discovery, Applications, and Molecular Evolution. Acc Chem Res 2023; 56:2801-2813. [PMID: 37752618 DOI: 10.1021/acs.accounts.3c00396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
ConspectusLife as we know it is built on complex and perfectly interlocking processes that have evolved over millions of years through evolutionary optimization processes. The emergence of life from nonliving matter and the evolution of such highly efficient systems therefore constitute an enormous synthetic and systems chemistry challenge. Advances in supramolecular and systems chemistry are opening new perspectives that provide insights into living and self-sustaining reaction networks as precursors for life. However, the ab initio synthesis of such a system requires the possibility of autonomous optimization of catalytic properties and, consequently, of an evolutionary system at the molecular level. In this Account, we present our discovery of the formation of substituted imidazolidine-4-thiones (photoredox) organocatalysts from simple prebiotic building blocks such as aldehydes and ketones under Strecker reaction conditions with ammonia and cyanides in the presence of hydrogen sulfide. The necessary aldehydes are formed from CO2 and hydrogen under prebiotically plausible meteoritic or volcanic iron-particle catalysis in the atmosphere of the early Earth. Remarkably, the investigated imidazolidine-4-thiones undergo spontaneous resolution by conglomerate crystallization, opening a pathway for symmetry breaking, chiral amplification, and enantioselective organocatalysis. These imidazolidine-4-thiones enable α-alkylations of aldehydes and ketones by photoredox organocatalysis. Therefore, these photoredox organocatalysts are able to modify their aldehyde building blocks, which leads in an evolutionary process to mutated second-generation and third-generation catalysts. In our experimental studies, we found that this mutation can occur not only by new formation of the imidazolidine core structure of the catalyst from modified aldehyde building blocks or by continuous supply from a pool of available building blocks but also by a dynamic exchange of the carbonyl moiety in ring position 2 of the imidazolidine moiety. Remarkably, it can be shown that by incorporating aldehyde building blocks from their environment, the imidazolidine-4-thiones are able to change and adapt to altering environmental conditions without undergoing the entire formation process. The selection of the mutated catalysts is then based on the different catalytic activities in the modification of the aldehyde building blocks and on the catalysis of subsequent processes that can lead to the formation of molecular reaction networks as progenitors for cellular processes. We were able to show that these imidazolidine-4-thiones not only enable α-alkylations but also facilitate other important transformations, such as the selective phosphorylation of nucleosides to nucleotides as a key step leading to the oligomerization to RNA and DNA. It can therefore be expected that evolutionary processes have already taken place on a small molecular level and have thus developed chemical tools that change over time, representing a hidden layer on the path to enzymatically catalyzed biochemical processes.
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Affiliation(s)
- Maximilian Bechtel
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Marian Ebeling
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Laura Huber
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Oliver Trapp
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
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4
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Rap DB, Simon A, Steenbakkers K, Schrauwen JGM, Redlich B, Brünken S. Fingerprinting fragments of fragile interstellar molecules: dissociation chemistry of pyridine and benzonitrile revealed by infrared spectroscopy and theory. Faraday Discuss 2023; 245:221-244. [PMID: 37404008 PMCID: PMC10510038 DOI: 10.1039/d3fd00015j] [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: 01/25/2023] [Accepted: 03/22/2023] [Indexed: 07/06/2023]
Abstract
The cationic fragmentation products in the dissociative ionization of pyridine and benzonitrile have been studied by infrared action spectroscopy in a cryogenic ion trap instrument at the Free-Electron Lasers for Infrared eXperiments (FELIX) Laboratory. A comparison of the experimental vibrational fingerprints of the dominant cationic fragments with those from quantum chemical calculations revealed a diversity of molecular fragment structures. The loss of HCN/HNC is shown to be the major fragmentation channel for both pyridine and benzonitrile. Using the determined structures of the cationic fragments, potential energy surfaces have been calculated to elucidate the nature of the neutral fragment partner. In the fragmentation chemistry of pyridine, multiple non-cyclic structures are formed, whereas the fragmentation of benzonitrile dominantly leads to the formation of cyclic structures. Among the fragments are linear cyano-(di)acetylene˙+, methylene-cyclopropene˙+ and o- and m-benzyne˙+ structures, the latter possible building blocks in interstellar polycyclic aromatic hydrocarbon (PAH) formation chemistry. Molecular dynamics simulations using density functional based tight binding (MD/DFTB) were performed and used to benchmark and elucidate the different fragmentation pathways based on the experimentally determined structures. The implications of the difference in fragments observed for pyridine and benzonitrile are discussed in an astrochemical context.
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Affiliation(s)
- Daniël B Rap
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Fédération FeRMI, CNRS & Université Toulouse III - Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France
| | - Kim Steenbakkers
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
| | - Johanna G M Schrauwen
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
| | - Britta Redlich
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
| | - Sandra Brünken
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
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5
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Perlin AL, Wolff W, Oliveira RR. Low Energy Isomers and Infrared Spectra Simulations of C 4H 3N, C 4H 4N, and C 4H 5N and Related Ions. J Phys Chem A 2023; 127:2481-2488. [PMID: 36913600 DOI: 10.1021/acs.jpca.2c09098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
The relative stability of pyrrole derivatives were investigated by applying a global minimum (GM) search for the low-lying energy structures of C4HnN (n = 3-5) clusters at neutral, anionic, and cationic states. Several low-energy structures, previously not reported, were identified. The present results reveal a preference for cyclic and conjugated systems for the C4H5N and C4H4N compounds. In particular, the structures of the cationic and neutral C4H3N species are different from the anionic ones. For the neutrals and cations, cumulenic carbon chains were found, while for the anions, conjugated open chains were obtained. Of particular relevance, the GM candidates C4H4N+ and C4H4N are different from those reported previously. For the most stable structures, infrared spectra were simulated and the main vibrational bands were assigned. Also, a comparison with available laboratory data was done aiming to corroborate with experimental detection.
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Affiliation(s)
- Amir L Perlin
- Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
| | - Wania Wolff
- Physics Institute, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
| | - Ricardo R Oliveira
- Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
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6
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Oba Y, Koga T, Takano Y, Ogawa NO, Ohkouchi N, Sasaki K, Sato H, Glavin DP, Dworkin JP, Naraoka H, Tachibana S, Yurimoto H, Nakamura T, Noguchi T, Okazaki R, Yabuta H, Sakamoto K, Yada T, Nishimura M, Nakato A, Miyazaki A, Yogata K, Abe M, Okada T, Usui T, Yoshikawa M, Saiki T, Tanaka S, Terui F, Nakazawa S, Watanabe SI, Tsuda Y. Uracil in the carbonaceous asteroid (162173) Ryugu. Nat Commun 2023; 14:1292. [PMID: 36944653 PMCID: PMC10030641 DOI: 10.1038/s41467-023-36904-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/15/2023] [Indexed: 03/23/2023] Open
Abstract
The pristine sample from the near-Earth carbonaceous asteroid (162173) Ryugu collected by the Hayabusa2 spacecraft enabled us to analyze the pristine extraterrestrial material without uncontrolled exposure to the Earth's atmosphere and biosphere. The initial analysis team for the soluble organic matter reported the detection of wide variety of organic molecules including racemic amino acids in the Ryugu samples. Here we report the detection of uracil, one of the four nucleobases in ribonucleic acid, in aqueous extracts from Ryugu samples. In addition, nicotinic acid (niacin, a B3 vitamer), its derivatives, and imidazoles were detected in search for nitrogen heterocyclic molecules. The observed difference in the concentration of uracil between A0106 and C0107 may be related to the possible differences in the degree of alteration induced by energetic particles such as ultraviolet photons and cosmic rays. The present study strongly suggests that such molecules of prebiotic interest commonly formed in carbonaceous asteroids including Ryugu and were delivered to the early Earth.
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Affiliation(s)
- Yasuhiro Oba
- Institute of Low Temperature Science (ILTS), Hokkaido University, N19W8, Kita-ku, Sapporo, 060-0819, Japan.
| | - Toshiki Koga
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan
| | - Yoshinori Takano
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan.
- Institute for Advanced Biosciences (IAB), Keio University, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.
| | - Nanako O Ogawa
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan
| | - Naohiko Ohkouchi
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan
| | - Kazunori Sasaki
- Institute for Advanced Biosciences (IAB), Keio University, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
- Human Metabolome Technologies Inc., Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Hajime Sato
- Human Metabolome Technologies Inc., Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Daniel P Glavin
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Jason P Dworkin
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Hiroshi Naraoka
- Department of Earth and Planetary Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Shogo Tachibana
- UTokyo Organization for Planetary and Space Science (UTOPS), University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033, Japan
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Hisayoshi Yurimoto
- Department of Earth and Planetary Sciences, Hokkaido University, Sapporo, 060-0810, Japan
| | - Tomoki Nakamura
- Department of Earth Material Science, Tohoku University, Sendai, 980-8578, Japan
| | - Takaaki Noguchi
- Department of Earth and Planetary Sciences, Kyoto University, Kyoto, 606-8502, Japan
| | - Ryuji Okazaki
- Department of Earth and Planetary Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hikaru Yabuta
- Department of Earth and Planetary Systems Science, Hiroshima University, 739-8526, Higashi-Hiroshima, Japan
| | - Kanako Sakamoto
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Toru Yada
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Masahiro Nishimura
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Aiko Nakato
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Akiko Miyazaki
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Kasumi Yogata
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Masanao Abe
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Tatsuaki Okada
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Tomohiro Usui
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Makoto Yoshikawa
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Takanao Saiki
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Satoshi Tanaka
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Fuyuto Terui
- Kanagawa Institute of Technology, Atsugi, 243-0292, Japan
| | - Satoru Nakazawa
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Sei-Ichiro Watanabe
- Graduate School of Environmental Studies, Nagoya University, Nagoya, 464-8601, Japan
| | - Yuichi Tsuda
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
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7
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Sources of Nitrogen-, Sulfur-, and Phosphorus-Containing Feedstocks for Prebiotic Chemistry in the Planetary Environment. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081268. [PMID: 36013447 PMCID: PMC9410288 DOI: 10.3390/life12081268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/13/2022] [Accepted: 08/17/2022] [Indexed: 11/21/2022]
Abstract
Biochemistry on Earth makes use of the key elements carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur (or CHONPS). Chemically accessible molecules containing these key elements would presumably have been necessary for prebiotic chemistry and the origins of life on Earth. For example, feedstock molecules including fixed nitrogen (e.g., ammonia, nitrite, nitrate), accessible forms of phosphorus (e.g., phosphate, phosphite, etc.), and sources of sulfur (e.g., sulfide, sulfite) may have been necessary for the origins of life, given the biochemistry seen in Earth life today. This review describes potential sources of nitrogen-, sulfur-, and phosphorus-containing molecules in the context of planetary environments. For the early Earth, such considerations may be able to aid in the understanding of our own origins. Additionally, as we learn more about potential environments on other planets (for example, with upcoming next-generation telescope observations or new missions to explore other bodies in our Solar System), evaluating potential sources for elements necessary for life (as we know it) can help constrain the potential habitability of these worlds.
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8
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Krishnamurthy R, Goldman AD, Liberles DA, Rogers KL, Tor Y. Nucleobases in Meteorites to Nucleobases in RNA and DNA? J Mol Evol 2022; 90:328-331. [PMID: 35960316 DOI: 10.1007/s00239-022-10069-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/29/2022] [Indexed: 10/16/2022]
Abstract
Nucleic acids likely played a foundational role in the origin of life. However, the prebiotic chemistry of nucleoside and nucleotide synthesis has proved challenging on a number of fronts. The recent discovery of both pyrimidine and purine nucleobases in carbonaceous chondrite meteorites has garnered much attention from both the popular press and the scientific community. Here, we discuss these findings in the context of nucleoside/nucleotide prebiotic chemistry. We consider that the main challenge of prebiotic nucleoside synthesis, that of nucleosidic bond formation, is not addressed by the identification nucleobases in meteorites. We further discuss issues of selection that arise from the observation that such meteorites contain both canonical and non-canonical nucleobases. In sum, we argue that, despite the major analytical achievement of identifying and characterizing nucleobases in meteorites, this observation does little to advance our understanding of the prebiotic chemistry that could have led to the first genetic molecules that gave rise to us.
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Affiliation(s)
- Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA. .,NSF-NASA Center for Chemical Evolution, Atlanta, GA, USA.
| | - Aaron D Goldman
- Department of Biology, Oberlin College and Conservatory, Oberlin, OH, USA.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA
| | - Karyn L Rogers
- Department of Earth and Environmental Sciences and Rensselaer Astrobiology Research and Education Center, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
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9
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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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10
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Meyer KS, Westerfield JH, Johansen SL, Keane J, Wannenmacher AC, Crabtree KN. Rotational and Vibrational Spectra of the Pyridyl Radicals: A Coupled-Cluster Study. J Phys Chem A 2022; 126:3185-3197. [PMID: 35549287 DOI: 10.1021/acs.jpca.2c01761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyridyl is a prototypical nitrogen-containing aromatic radical that may be a key intermediate in the formation of nitrogen-containing aromatic molecules under astrophysical conditions. On meteorites, a variety of complex molecules with nitrogen-containing rings have been detected with nonterrestrial isotopic abundances, and larger nitrogen-containing polycyclic aromatic hydrocarbons (PANHs) have been proposed to be responsible for certain unidentified infrared emission bands in the interstellar medium. In this work, the three isomers of pyridyl (2-, 3-, and 4-pyridyl) have been investigated with coupled cluster methods. For each species, structures were optimized at the CCSD(T)/cc-pwCVTZ level of theory and force fields were calculated at the CCSD(T)/ANO0 level of theory. Second-order vibrational perturbation theory (VPT2) was used to derive anharmonic vibrational frequencies and vibrationally corrected rotational constants, and resonances among vibrational states below 3500 cm-1 were treated variationally with the VPT2+K method. The results yield a complete set of spectroscopic parameters needed to simulate the pure rotational spectrum of each isomer, including electron-spin, spin-spin, and nuclear hyperfine interactions, and the calculated hyperfine parameters agree well with the limited available data from electron paramagnetic resonance spectroscopy. For the handful of experimentally measured vibrational frequencies determined from photoelectron spectroscopy and matrix isolation spectroscopy, the typical agreement is comparable to experimental uncertainty. The predicted parameters for rotational spectroscopy reported here can guide new experimental investigations into the yet-unobserved rotational spectra of these radicals.
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Affiliation(s)
- Kelly S Meyer
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - John H Westerfield
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Sommer L Johansen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Jasmine Keane
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Anna C Wannenmacher
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Kyle N Crabtree
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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11
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Barnum TJ, Siebert MA, Lee KLK, Loomis RA, Changala PB, Charnley SB, Sita ML, Xue C, Remijan AJ, Burkhardt AM, McGuire BA, Cooke IR. A Search for Heterocycles in GOTHAM Observations of TMC-1. J Phys Chem A 2022; 126:2716-2728. [PMID: 35442689 DOI: 10.1021/acs.jpca.2c01435] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have conducted an extensive search for nitrogen-, oxygen-, and sulfur-bearing heterocycles toward Taurus Molecular Cloud 1 (TMC-1) using the deep, broadband centimeter-wavelength spectral line survey of the region from the GOTHAM large project on the Green Bank Telescope. Despite their ubiquity in terrestrial chemistry, and the confirmed presence of a number of cyclic and polycyclic hydrocarbon species in the source, we find no evidence for the presence of any heterocyclic species. Here, we report the derived upper limits on the column densities of these molecules obtained by Markov Chain Monte Carlo (MCMC) analysis and compare this approach to traditional single-line upper limit measurements. We further hypothesize why these molecules are absent in our data, how they might form in interstellar space, and the nature of observations that would be needed to secure their detection.
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Affiliation(s)
- Timothy J Barnum
- Department of Chemistry, Union College, Schenectady, New York 12308, United States
| | - Mark A Siebert
- Department of Astronomy, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Kin Long Kelvin Lee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ryan A Loomis
- National Radio Astronomy Observatory, Charlottesville, Virginia 22903, United States
| | - P Bryan Changala
- Center for Astrophysics
- Harvard & Smithsonian, Cambridge, Massachusetts 02138, United States
| | - Steven B Charnley
- Astrochemistry Laboratory and the Goddard Center for Astrobiology, NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, United States
| | - Madelyn L Sita
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Ci Xue
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anthony J Remijan
- National Radio Astronomy Observatory, Charlottesville, Virginia 22903, United States
| | - Andrew M Burkhardt
- Department of Physics, Wellesley College, 106 Central Street, Wellesley, Massachusetts 02481, United States
| | - Brett A McGuire
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,National Radio Astronomy Observatory, Charlottesville, Virginia 22903, United States.,Center for Astrophysics
- Harvard & Smithsonian, Cambridge, Massachusetts 02138, United States
| | - Ilsa R Cooke
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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12
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Oba Y, Takano Y, Furukawa Y, Koga T, Glavin DP, Dworkin JP, Naraoka H. Identifying the wide diversity of extraterrestrial purine and pyrimidine nucleobases in carbonaceous meteorites. Nat Commun 2022; 13:2008. [PMID: 35473908 PMCID: PMC9042847 DOI: 10.1038/s41467-022-29612-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/22/2022] [Indexed: 11/09/2022] Open
Abstract
The lack of pyrimidine diversity in meteorites remains a mystery since prebiotic chemical models and laboratory experiments have predicted that these compounds can also be produced from chemical precursors found in meteorites. Here we report the detection of nucleobases in three carbonaceous meteorites using state-of-the-art analytical techniques optimized for small-scale quantification of nucleobases down to the range of parts per trillion (ppt). In addition to previously detected purine nucleobases in meteorites such as guanine and adenine, we identify various pyrimidine nucleobases such as cytosine, uracil, and thymine, and their structural isomers such as isocytosine, imidazole-4-carboxylic acid, and 6-methyluracil, respectively. Given the similarity in the molecular distribution of pyrimidines in meteorites and those in photon-processed interstellar ice analogues, some of these derivatives could have been generated by photochemical reactions prevailing in the interstellar medium and later incorporated into asteroids during solar system formation. This study demonstrates that a diversity of meteoritic nucleobases could serve as building blocks of DNA and RNA on the early Earth.
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Affiliation(s)
- Yasuhiro Oba
- Institute of Low Temperature Science (ILTS), Hokkaido University, N19W8, Kita-ku, Sapporo, Hokkaido, 060-0189, Japan.
| | - Yoshinori Takano
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Yoshihiro Furukawa
- Department of Earth Science, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Toshiki Koga
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Daniel P Glavin
- Solar System Exploration Division, National Aeronautics and Space Administration (NASA), Goddard Space Flight Center (GSFC), Greenbelt, MD, 20771, USA
| | - Jason P Dworkin
- Solar System Exploration Division, National Aeronautics and Space Administration (NASA), Goddard Space Flight Center (GSFC), Greenbelt, MD, 20771, USA
| | - Hiroshi Naraoka
- Department of Earth and Planetary Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan
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13
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Santalucia R, Pazzi M, Bonino F, Signorile M, Scarano D, Ugliengo P, Spoto G, Mino L. From gaseous HCN to nucleobases at the cosmic silicate dust surface: an experimental insight into the onset of prebiotic chemistry in space. Phys Chem Chem Phys 2022; 24:7224-7230. [PMID: 35274636 DOI: 10.1039/d1cp05407d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
HCN in the gas form is considered as a primary nitrogen source for the synthesis of prebiotic molecules in extraterrestrial environments. Nevertheless, the research mainly focused on the reactivity of HCN and its derivatives in aqueous systems, often using external high-energy supply in the form of cosmic rays or high energy photons. Very few studies have been devoted to the chemistry of HCN in the gas phase or at the gas/solid interphase, although they represent the more common scenarios in the outer space. In this paper we report about the reactivity of highly pure HCN in the 150-300 K range at the surface of amorphous and crystalline Mg2SiO4 (forsterite olivine), i.e. of solids among the constituents of the core of cosmic dust particles, comets, and meteorites. Amorphous silica and MgO were also studied as model representatives of Mg2SiO4 structural building blocks. IR spectroscopic results and the HR-MS analysis of the reaction products revealed Mg2+O2- acid/base pairs at the surface of Mg2SiO4 and MgO to be key in promoting the formation of HCN oligomers along with imidazole and purine compounds, already under very mild temperature and HCN pressure conditions, i.e. in the absence of external energetic triggers. Products include adenine nucleobase, a result which supports the hypothesis that prebiotic molecular building blocks can be easily formed through surface catalytic processes in the absence of high-energy supply.
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Affiliation(s)
- Rosangela Santalucia
- Department of Chemistry, University of Turin, 10125, Turin, Italy. .,Nanostructured Interfaces and Surfaces (NIS) Interdepartmental Centre, 10125, Turin, Italy
| | - Marco Pazzi
- Department of Chemistry, University of Turin, 10125, Turin, Italy.
| | - Francesca Bonino
- Department of Chemistry, University of Turin, 10125, Turin, Italy. .,Nanostructured Interfaces and Surfaces (NIS) Interdepartmental Centre, 10125, Turin, Italy
| | - Matteo Signorile
- Department of Chemistry, University of Turin, 10125, Turin, Italy. .,Nanostructured Interfaces and Surfaces (NIS) Interdepartmental Centre, 10125, Turin, Italy
| | - Domenica Scarano
- Department of Chemistry, University of Turin, 10125, Turin, Italy. .,Nanostructured Interfaces and Surfaces (NIS) Interdepartmental Centre, 10125, Turin, Italy
| | - Piero Ugliengo
- Department of Chemistry, University of Turin, 10125, Turin, Italy. .,Nanostructured Interfaces and Surfaces (NIS) Interdepartmental Centre, 10125, Turin, Italy
| | - Giuseppe Spoto
- Department of Chemistry, University of Turin, 10125, Turin, Italy. .,Nanostructured Interfaces and Surfaces (NIS) Interdepartmental Centre, 10125, Turin, Italy
| | - Lorenzo Mino
- Department of Chemistry, University of Turin, 10125, Turin, Italy. .,Nanostructured Interfaces and Surfaces (NIS) Interdepartmental Centre, 10125, Turin, Italy
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14
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Zhang YR, Yuan DF, Wang LS. Probing the Electronic Structure and Spectroscopy of the Pyrrolyl and Imidazolyl Radicals using High-Resolution Photoelectron Imaging of Cryogenically-Cooled Anions. Phys Chem Chem Phys 2022; 24:6505-6514. [DOI: 10.1039/d2cp00189f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High-resolution photoelectron imaging and photodetachment spectroscopy of cryogenically-cooled pyrrolide and imidazolide anions are used to probe the electronic structure and spectroscopy of the pyrrolyl and imidazolyl radicals. The high-resolution data...
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15
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Fialho DM, Karunakaran SC, Greeson KW, Martínez I, Schuster GB, Krishnamurthy R, Hud NV. Depsipeptide Nucleic Acids: Prebiotic Formation, Oligomerization, and Self-Assembly of a New Proto-Nucleic Acid Candidate. J Am Chem Soc 2021; 143:13525-13537. [PMID: 34398608 DOI: 10.1021/jacs.1c02287] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mechanism by which informational polymers first formed on the early earth is currently unknown. The RNA world hypothesis implies that RNA oligomers were produced prebiotically, before the emergence of enzymes, but the demonstration of such a process remains challenging. Alternatively, RNA may have been preceded by an earlier ancestral polymer, or proto-RNA, that had a greater propensity for self-assembly than RNA, with the eventual transition to functionally superior RNA being the result of chemical or biological evolution. We report a new class of nucleic acid analog, depsipeptide nucleic acid (DepsiPNA), which displays several properties that are attractive as a candidate for proto-RNA. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these DepsiPNA oligomers are capable of complementary self-assembly and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive, self-assembling, informational polymers on the early earth may have been relatively facile if the constraints of an RNA-first scenario are relaxed.
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Affiliation(s)
- David M Fialho
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Suneesh C Karunakaran
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Katherine W Greeson
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Isaac Martínez
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Gary B Schuster
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ramanarayanan Krishnamurthy
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
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16
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Johansen SL, Xu Z, Westerfield JH, Wannenmacher AC, Crabtree KN. Coupled Cluster Characterization of 1-, 2-, and 3-Pyrrolyl: Parameters for Vibrational and Rotational Spectroscopy. J Phys Chem A 2021; 125:1257-1268. [PMID: 33502858 DOI: 10.1021/acs.jpca.0c09833] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyrrolyl (C4H4N) is a nitrogen-containing aromatic radical that is a derivative of pyrrole (C4H5N) and is an important intermediate in the combustion of biomass. It is also relevant for chemistry in Titan's atmosphere and may be present in the interstellar medium. The lowest-energy isomer, 1-pyrrolyl, has been involved in many experimental and theoretical studies of the N-H photodissociation of pyrrole, yet it has only been directly spectroscopically detected via electron paramagnetic resonance and through the photoelectron spectrum of the pyrrolide anion, yielding three vibrational frequencies. No direct measurements of 2- or 3-pyrrolyl have been made, and little information is known from theoretical calculations beyond their relative energies. Here, we present an ab initio quantum chemical characterization of the three pyrrolyl isomers at the CCSD(T) level of theory in their ground electronic states, with an emphasis on spectroscopic parameters relevant for vibrational and rotational spectroscopy. Equilibrium geometries were optimized at the CCSD(T)/cc-pwCVTZ level of theory, and the quadratic, cubic, and partial quartic force constants were evaluated at CCSD(T)/ANO0 for analysis using second-order vibrational perturbation theory to obtain harmonic and anharmonic vibrational frequencies. In addition, zero-point-corrected rotational constants, electronic spin-rotation tensors, and nuclear hyperfine tensors are calculated for rotational spectroscopy. Our computed structures and energies agree well with earlier density functional theory calculations, and spectroscopic parameters for 1-pyrrolyl are compared with the limited existing experimental data. Finally, we discuss strategies for detecting these radicals using rotational and vibrational spectroscopy on the basis of the calculated spectroscopic constants.
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Affiliation(s)
- Sommer L Johansen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Zhongxing Xu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - J H Westerfield
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Anna C Wannenmacher
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Kyle N Crabtree
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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17
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Al-Ostoot FH, Salah S, Khanum SA. Recent investigations into synthesis and pharmacological activities of phenoxy acetamide and its derivatives (chalcone, indole and quinoline) as possible therapeutic candidates. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2021. [PMCID: PMC7849228 DOI: 10.1007/s13738-021-02172-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Medicinal chemistry can rightfully be regarded as a cornerstone in the public health of our modern society that combines chemistry and pharmacology with the aim of designing and developing new pharmaceutical compounds. For this purpose, many chemical techniques as well as new computational chemistry applications are used to study the utilization of drugs and their biological effects. In the biological interface, medicinal chemistry constitutes a group of interdisciplinary sciences, as well as controlling its organic, physical and computational pillars. Therefore, medicinal chemists working to design an integrated and developing system that portends an era of novel and safe tailored drugs either by synthesizing new pharmaceuticals or to improving the processes by which existing pharmaceuticals are made. It includes researching the effects of synthetic, semi-synthetic and natural biologically active substances based on molecular interactions in terms of molecular structure with triggered functional groups or the specific physicochemical properties. The present work focuses on the literature survey of chemical diversity of phenoxy acetamide and its derivatives (Chalcone, Indole and Quinoline) in the molecular framework in order to get complete information regarding pharmacologically interesting compounds of widely different composition. From a biological and industrial point of view, this literature review may provide an opportunity for the chemists to design new derivatives of phenoxy acetamide and its derivatives that proved to be the successful agent in view of safety and efficacy to enhance life quality.
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Affiliation(s)
- Fares Hezam Al-Ostoot
- Department of Chemistry, Yuvaraja’s College, University of Mysore, Mysuru, 570 006 India
- Department of Biochemistry, Faculty of Education and Science, Al-Baydha University, Al-Baydha, Yemen
| | - Salma Salah
- Faculty of Medicine and Health Sciences, Thamar University, Dhamar, Yemen
| | - Shaukath Ara Khanum
- Department of Chemistry, Yuvaraja’s College, University of Mysore, Mysuru, 570 006 India
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18
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Thermal unimolecular reactivity pathways in dehydro‐diazines radicals. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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Chandru K, Jia TZ, Mamajanov I, Bapat N, Cleaves HJ. Prebiotic oligomerization and self-assembly of structurally diverse xenobiological monomers. Sci Rep 2020; 10:17560. [PMID: 33067516 PMCID: PMC7567815 DOI: 10.1038/s41598-020-74223-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
Prebiotic chemists often study how modern biopolymers, e.g., peptides and nucleic acids, could have originated in the primitive environment, though most contemporary biomonomers don't spontaneously oligomerize under mild conditions without activation or catalysis. However, life may not have originated using the same monomeric components that it does presently. There may be numerous non-biological (or "xenobiological") monomer types that were prebiotically abundant and capable of facile oligomerization and self-assembly. Many modern biopolymers degrade abiotically preferentially via processes which produce thermodynamically stable ring structures, e.g. diketopiperazines in the case of proteins and 2', 3'-cyclic nucleotide monophosphates in the case of RNA. This weakness is overcome in modern biological systems by kinetic control, but this need not have been the case for primitive systems. We explored here the oligomerization of a structurally diverse set of prebiotically plausible xenobiological monomers, which can hydrolytically interconvert between cyclic and acyclic forms, alone or in the presence of glycine under moderate temperature drying conditions. These monomers included various lactones, lactams and a thiolactone, which varied markedly in their stability, propensity to oligomerize and apparent modes of initiation, and the oligomeric products of some of these formed self-organized microscopic structures which may be relevant to protocell formation.
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Affiliation(s)
- Kuhan Chandru
- Space Science Center (ANGKASA), Institute of Climate Change, Level 3, Research Complex, National University of Malaysia, UKM, 43600, Bangi, Selangor, Malaysia.
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628, Prague 6-Dejvice, Czech Republic.
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
- Blue Marble Space Institute for Science, 1001 4th Ave, Suite 3201, Seattle, WA, 98154, USA
| | - Irena Mamajanov
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Niraja Bapat
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, 411 008, India
| | - H James Cleaves
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
- Blue Marble Space Institute for Science, 1001 4th Ave, Suite 3201, Seattle, WA, 98154, USA
- Institute for Advanced Study, 1 Einstein Drive, Princeton, NJ, 08540, USA
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20
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Closs AC, Fuks E, Bechtel M, Trapp O. Prebiotically Plausible Organocatalysts Enabling a Selective Photoredox α-Alkylation of Aldehydes on the Early Earth. Chemistry 2020; 26:10702-10706. [PMID: 32233051 PMCID: PMC7496864 DOI: 10.1002/chem.202001514] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Indexed: 12/03/2022]
Abstract
Organocatalysis is a powerful approach to extend and (enantio-) selectively modify molecular structures. Adapting this concept to the Early Earth scenario offers a promising solution to explain their evolution into a complex homochiral world. Herein, we present a class of imidazolidine-4-thione organocatalysts, easily accessible from simple molecules available on an Early Earth under highly plausible prebiotic reaction conditions. These imidazolidine-4-thiones are readily formed from mixtures of aldehydes or ketones in presence of ammonia, cyanides and hydrogen sulfide in high selectivity and distinct preference for individual compounds of the resulting catalyst library. These organocatalysts enable the enantioselective α-alkylation of aldehydes under prebiotic conditions and show activities that correlate with the selectivity of their formation. Furthermore, the crystallization of single catalysts as conglomerates opens the pathway for symmetry breaking.
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Affiliation(s)
- Anna C. Closs
- Department of ChemistryLudwig Maximilian University MunichButenandtstrasse 5–1381377MunichGermany
- Max-Planck-Institute for AstronomyKönigstuhl 1769117HeidelbergGermany
| | - Elina Fuks
- Department of ChemistryLudwig Maximilian University MunichButenandtstrasse 5–1381377MunichGermany
| | - Maximilian Bechtel
- Department of ChemistryLudwig Maximilian University MunichButenandtstrasse 5–1381377MunichGermany
| | - Oliver Trapp
- Department of ChemistryLudwig Maximilian University MunichButenandtstrasse 5–1381377MunichGermany
- Max-Planck-Institute for AstronomyKönigstuhl 1769117HeidelbergGermany
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21
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Chan QHS, Stroud R, Martins Z, Yabuta H. Concerns of Organic Contamination for Sample Return Space Missions. SPACE SCIENCE REVIEWS 2020; 216:56. [PMID: 32624626 PMCID: PMC7319412 DOI: 10.1007/s11214-020-00678-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Analysis of organic matter has been one of the major motivations behind solar system exploration missions. It addresses questions related to the organic inventory of our solar system and its implication for the origin of life on Earth. Sample return missions aim at returning scientifically valuable samples from target celestial bodies to Earth. By analysing the samples with the use of state-of-the-art analytical techniques in laboratories here on Earth, researchers can address extremely complicated aspects of extra-terrestrial organic matter. This level of detailed sample characterisation provides the range and depth in organic analysis that are restricted in spacecraft-based exploration missions, due to the limitations of the on-board in-situ instrumentation capabilities. So far, there are four completed and in-process sample return missions with an explicit mandate to collect organic matter: Stardust and OSIRIS-REx missions of NASA, and Hayabusa and Hayabusa2 missions of JAXA. Regardless of the target body, all sample return missions dedicate to minimise terrestrial organic contamination of the returned samples, by applying various degrees or strategies of organic contamination mitigation methods. Despite the dedicated efforts in the design and execution of contamination control, it is impossible to completely eliminate sources of organic contamination. This paper aims at providing an overview of the successes and lessons learned with regards to the identification of indigenous organic matter of the returned samples vs terrestrial contamination.
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Affiliation(s)
- Queenie Hoi Shan Chan
- Planetary and Space Sciences, School of Physical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA UK
- Present Address: Department of Earth Sciences, Royal Holloway University of London, Egham Surrey, TW20 0EX UK
| | - Rhonda Stroud
- Code 6360, Naval Research Laboratory, Washington, DC 20375 USA
| | - Zita Martins
- Centro de Química Estrutural, Departamento de Engenharia Química, Instituto Superior Técnico (IST), Universidade de Lisboa, Avenida Rovisco Pais 1, 1049-001 Lisbon, Portugal
| | - Hikaru Yabuta
- Department of Earth and Planetary Systems Science, Hiroshima University, 1-3-1 Kagamiyama, Hiroshima, 739-8526 Japan
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22
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Sandford SA, Nuevo M, Bera PP, Lee TJ. Prebiotic Astrochemistry and the Formation of Molecules of Astrobiological Interest in Interstellar Clouds and Protostellar Disks. Chem Rev 2020; 120:4616-4659. [DOI: 10.1021/acs.chemrev.9b00560] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Scott A. Sandford
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035, United States
| | - Michel Nuevo
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035, United States
- BAER Institute, NASA Research Park, MS 18-4, Moffett Field, California 94035, United States
| | - Partha P. Bera
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035, United States
- BAER Institute, NASA Research Park, MS 18-4, Moffett Field, California 94035, United States
| | - Timothy J. Lee
- NASA Ames Research Center, MS 245-3, Moffett Field, California 94035, United States
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23
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Polyesters as a Model System for Building Primitive Biologies from Non-Biological Prebiotic Chemistry. Life (Basel) 2020; 10:life10010006. [PMID: 31963928 PMCID: PMC7175156 DOI: 10.3390/life10010006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/22/2019] [Accepted: 01/10/2020] [Indexed: 12/14/2022] Open
Abstract
A variety of organic chemicals were likely available on prebiotic Earth. These derived from diverse processes including atmospheric and geochemical synthesis and extraterrestrial input, and were delivered to environments including oceans, lakes, and subaerial hot springs. Prebiotic chemistry generates both molecules used by modern organisms, such as proteinaceous amino acids, as well as many molecule types not used in biochemistry. As prebiotic chemical diversity was likely high, and the core of biochemistry uses a rather small set of common building blocks, the majority of prebiotically available organic compounds may not have been those used in modern biochemistry. Chemical evolution was unlikely to have been able to discriminate which molecules would eventually be used in biology, and instead, interactions among compounds were governed simply by abundance and chemical reactivity. Previous work has shown that likely prebiotically available α-hydroxy acids can combinatorially polymerize into polyesters that self-assemble to create new phases which are able to compartmentalize other molecule types. The unexpectedly rich complexity of hydroxy acid chemistry and the likely enormous structural diversity of prebiotic organic chemistry suggests chemical evolution could have been heavily influenced by molecules not used in contemporary biochemistry, and that there is a considerable amount of prebiotic chemistry which remains unexplored.
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Oba Y, Takano Y, Naraoka H, Watanabe N, Kouchi A. Nucleobase synthesis in interstellar ices. Nat Commun 2019; 10:4413. [PMID: 31562325 PMCID: PMC6764953 DOI: 10.1038/s41467-019-12404-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/03/2019] [Indexed: 11/09/2022] Open
Abstract
The synthesis of nucleobases in natural environments, especially in interstellar molecular clouds, is the focus of a long-standing debate regarding prebiotic chemical evolution. Here we report the simultaneous detection of all three pyrimidine (cytosine, uracil and thymine) and three purine nucleobases (adenine, xanthine and hypoxanthine) in interstellar ice analogues composed of simple molecules including H2O, CO, NH3 and CH3OH after exposure to ultraviolet photons followed by thermal processes, that is, in conditions that simulate the chemical processes accompanying star formation from molecular clouds. Photolysis of primitive gas molecules at 10 K might be one of the key steps in the production of nucleobases. The present results strongly suggest that the evolution from molecular clouds to stars and planets provides a suitable environment for nucleobase synthesis in space.
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Affiliation(s)
- Yasuhiro Oba
- Institute of Low Temperature Science (ILTS), Hokkaido University, N19W8, Kita-ku, Sapporo, Hokkaido, 060-0819, Japan.
| | - Yoshinori Takano
- Department of Biogeochemistry, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan.,Biogeochemistry Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Hiroshi Naraoka
- Department of Earth and Planetary Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan.,Research Center for Planetary Trace Organic Compounds, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan
| | - Naoki Watanabe
- Institute of Low Temperature Science (ILTS), Hokkaido University, N19W8, Kita-ku, Sapporo, Hokkaido, 060-0819, Japan
| | - Akira Kouchi
- Institute of Low Temperature Science (ILTS), Hokkaido University, N19W8, Kita-ku, Sapporo, Hokkaido, 060-0819, Japan
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25
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Sousa JN, Ribeiro LC, Arruda MS, Homem MGP, Tanaka HK, Credidio BC, Marinho RRT, Medina A, Prazeres I, Santos ACF, Prudente FV. Photoabsorption and Photoionization Cross Sections of Pyridine in the Vacuum-Ultraviolet Energy Range. J Phys Chem A 2019; 123:5164-5170. [DOI: 10.1021/acs.jpca.9b03778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. N. Sousa
- Instituto de Física, Universidade Federal da Bahia, Salvador 40170-115, BA, Brazil
- Instituto Federal Baiano, Campus Guanambi, Guanambi 46430-000, BA, Brazil
| | - L. C. Ribeiro
- Instituto de Física, Universidade Federal da Bahia, Salvador 40170-115, BA, Brazil
| | - Manuela S. Arruda
- Instituto de Física, Universidade Federal da Bahia, Salvador 40170-115, BA, Brazil
| | - M. G. P. Homem
- Departamento de Química, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil
| | - H. K. Tanaka
- Instituto Federal da Bahia, Campus Porto Seguro, Porto Seguro 45810-000, BA, Brazil
| | - B. C. Credidio
- Instituto de Física, Universidade Federal da Bahia, Salvador 40170-115, BA, Brazil
| | - R. R. T. Marinho
- Instituto de Física, Universidade Federal da Bahia, Salvador 40170-115, BA, Brazil
- Instituto de Física, Universidade de Brasilia, Box 4455, Brasília 70910-970, Brazil
| | - Aline Medina
- Instituto de Física, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, RJ, Brazil
| | - I. Prazeres
- Instituto de Física, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, RJ, Brazil
| | - A. C. F. Santos
- Instituto de Física, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, RJ, Brazil
| | - F. V. Prudente
- Instituto de Física, Universidade Federal da Bahia, Salvador 40170-115, BA, Brazil
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