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Gilboa S, Panz L, Arbell N, Paz Y. Light-Assisted Formation of Nucleosides and Nucleotides from Formamide in the Presence of Cerium Phosphate. Life (Basel) 2024; 14:846. [PMID: 39063600 PMCID: PMC11277737 DOI: 10.3390/life14070846] [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: 05/16/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
The abiotic formation of nucleotides from small, simple molecules is of large interest in the context of elucidating the origin of life scenario. In what follows, it is shown that nucleosides and nucleotides can be formed from formamide in a one-pot reaction utilizing the mineral cerium phosphate (CePO4) as a photocatalyst, a catalyst and a reactant that supplies the necessary phosphate groups. While the most abundant RNA/DNA building blocks were thymidine and thymidine monophosphate, considerable yields of other building blocks such as cytidine, cytidine monophosphate, and adenosine cyclic monophosphate were found. Comparing the yield of nucleosides and nucleotides under light conditions to that in the dark suggests that in the presence of cerium phosphate, light promotes the formation of nucleobases, whereas the formation of nucleotides from nucleosides take place even in the absence of light. The scenario described herein is considerably simpler than other scenarios involving several steps and several reactants. Therefore, by virtue of the principle of Occam's razor, it should be of large interest for the community.
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Affiliation(s)
- Shoval Gilboa
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa 320003, Israel; (S.G.); (N.A.)
| | - Larisa Panz
- The Schulich Department of Chemistry, Technion-Israel Institute of Technology, Haifa 320003, Israel;
| | - Nitai Arbell
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa 320003, Israel; (S.G.); (N.A.)
| | - Yaron Paz
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa 320003, Israel; (S.G.); (N.A.)
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2
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Manna T, Maji S, Maity M, Debnath B, Panda S, Khan SA, Nath R, Akhtar MJ. Anticancer potential and structure activity studies of purine and pyrimidine derivatives: an updated review. Mol Divers 2024:10.1007/s11030-024-10870-4. [PMID: 38856835 DOI: 10.1007/s11030-024-10870-4] [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: 02/19/2024] [Accepted: 04/02/2024] [Indexed: 06/11/2024]
Abstract
Cancer is the world's leading cause of death impacting millions of lives globally. The increasing research over the past several decades has focused on the development of new anticancer drugs, but still cancer continues to be a global health challenge. Thus, several new alternative therapeutic strategies have been tried for the drug design and discovery. Purine and pyrimidine heterocyclic compounds have received attention recently due to their potential in targeting various cancers. It is evident from the recently published data over the last decade that incorporation of the purine and pyrimidine rings in the synthesized derivatives resulted in the development of potent anticancer molecules. This review presents synthetic strategies encompassing several examples of recently developed purine and pyrimidine-containing compounds as anticancer agents. In addition, their structure-activity relationships are represented in the schemes indicating the fragment or groups that are essential for the enhanced anticancer activities. Purine and pyrimidines combined with other heterocyclic compounds have resulted in many novel anticancer molecules that address the challenges of drug resistance. The purine and pyrimidine derivatives showed significantly enhanced anticancer activities against targeted receptor proteins with numerous compounds with an IC50 value in the nanomolar range. The review will support medicinal chemists and contribute in progression and development of synthesis of more potent chemotherapeutic drug candidates to mitigate the burden of this dreadful disease.
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Affiliation(s)
- Tanushree Manna
- Department of Pharmacy, Bharat Technology, Uluberia, 711316, Howrah, West Bengal, India
| | - Sumit Maji
- Department of Pharmacy, Bharat Technology, Uluberia, 711316, Howrah, West Bengal, India
| | - Mousumi Maity
- Department of Pharmacy, Bharat Technology, Uluberia, 711316, Howrah, West Bengal, India
| | - Biplab Debnath
- Department of Pharmacy, Bharat Technology, Uluberia, 711316, Howrah, West Bengal, India
| | - Shambo Panda
- Department of Pharmacy, Bharat Technology, Uluberia, 711316, Howrah, West Bengal, India
| | - Shah Alam Khan
- Department of Pharmaceutical Chemistry, National University of Science and Technology, PC 130, Azaiba, Bousher, PO 620, Muscat, Sultanate of Oman
| | - Rajarshi Nath
- Department of Pharmacy, Bharat Technology, Uluberia, 711316, Howrah, West Bengal, India.
- JIS University, Agarpara Campus, Kolkata-81, Nilgunj Road, Agarpara, Kolkata, 700109, India.
| | - Md Jawaid Akhtar
- Department of Pharmaceutical Chemistry, National University of Science and Technology, PC 130, Azaiba, Bousher, PO 620, Muscat, Sultanate of Oman.
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Ma X, He J, Liu Y, Bai X, Leng J, Zhao Y, Chen D, Wang J. Plant Photocatalysts: Photoinduced Oxidation and Reduction Abilities of Plant Leaf Ashes under Solar Light. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2260. [PMID: 37570577 PMCID: PMC10421452 DOI: 10.3390/nano13152260] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023]
Abstract
Plant leaf ashes were obtained via the high temperature calcination of the leaves of various plants, such as sugarcane, couchgrass, bracteata, garlic sprout, and the yellowish leek. Although the photosynthesis systems in plant leaves cannot exist after calcination, minerals in these ashes were found to exhibit photochemical activities. The samples showed solar light photocatalytic oxidation activities sufficient to degrade methylene blue dye. They were also shown to possess intrinsic dehydrogenase-like activities in reducing the colorless electron acceptor 2,3,5-triphenyltetrazolium chloride to a red formazan precipitate under solar light irradiation. The possible reasons behind these two unreported phenomena were also investigated. These ashes were characterized using a combination of physicochemical techniques. Moreover, our findings exemplify how the soluble and insoluble minerals in plant leaf ashes can be synergistically designed to yield next-generation photocatalysts. It may also lead to advances in artificial photosynthesis and photocatalytic dehydrogenase.
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Affiliation(s)
- Xiaoqian Ma
- School of Chemical Sciences & Technology, Yunnan University, Kunming 650091, China
| | - Jiao He
- School of Chemical Sciences & Technology, Yunnan University, Kunming 650091, China
| | - Yu Liu
- School of Materials and Energy, Yunnan University, Kunming 650091, China
| | - Xiaoli Bai
- School of Chemical Sciences & Technology, Yunnan University, Kunming 650091, China
| | - Junyang Leng
- School of Chemical Sciences & Technology, Yunnan University, Kunming 650091, China
| | - Yi Zhao
- School of Chemical Sciences & Technology, Yunnan University, Kunming 650091, China
| | - Daomei Chen
- School of Materials and Energy, Yunnan University, Kunming 650091, China
| | - Jiaqiang Wang
- School of Chemical Sciences & Technology, Yunnan University, Kunming 650091, China
- School of Materials and Energy, Yunnan University, Kunming 650091, China
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4
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Miodyńska M, Klimczuk T, Lisowski W, Zaleska-Medynska A. Bi-based halide perovskites: Stability and opportunities in the photocatalytic approach for hydrogen evolution. CATAL COMMUN 2023. [DOI: 10.1016/j.catcom.2023.106656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
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5
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Rimola A, Balucani N, Ceccarelli C, Ugliengo P. Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations. Int J Mol Sci 2022; 23:4252. [PMID: 35457069 PMCID: PMC9030215 DOI: 10.3390/ijms23084252] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 12/28/2022] Open
Abstract
Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembling those present in a primordial Earth has been demonstrated experimentally. Thus, Gly is a paradigmatic system for biomolecular building blocks to investigate how they can be synthesized in astrophysical environments, transported and delivered by fragments of asteroids (meteorites, once they land on Earth) and comets (interplanetary dust particles that land on Earth) to the primitive Earth, and there react to form biopolymers as a step towards the emergence of life. Quantum chemical investigations addressing these Gly-related events have been performed, providing fundamental atomic-scale information and quantitative energetic data. However, they are spread in the literature and difficult to harmonize in a consistent way due to different computational chemistry methodologies and model systems. This review aims to collect the work done so far to characterize, at a quantum mechanical level, the chemical life of Gly, i.e., from its synthesis in the interstellar medium up to its polymerization on Earth.
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Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Catalonia, Spain
| | - Nadia Balucani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy;
- Osservatorio Astrosico di Arcetri, Largo E. Fermi 5, 50125 Firenze, Italy
| | - Cecilia Ceccarelli
- CNRS, Institut de Planétologie et d’Astrophysique de Grenoble (IPAG), Université Grenoble Alpes, 38000 Grenoble, France;
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy;
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Enchev V, Slavova S. Self-catalytic mechanism of prebiotic reactions: from formamide to pterins and guanine. Phys Chem Chem Phys 2021; 23:19043-19053. [PMID: 34612442 DOI: 10.1039/d1cp02158c] [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
Reaction pathway of prebiotic reactions for formation of the pteridines: pterin, xanthopterine, isoxanthopterine and leucopterine, as well as the purine nucleobase guanine from pure formamide are presented. In these reactions, formamide or its tautomer, formimidic acid, play the role of proton-carrying catalyst. All required raw materials, such as hydrogen cyanide, ammonia, water, formic acid, urea, 2-aminomalononitrile, glyoxal, glyoxylic acid and oxalic acid needed in the self-catalyzed reactions are obtained by partial decomposition of formamide. We show that the prebiotic formation of nucleobases and pterins is closely linked and they probably coexisted at the beginning of chemical evolution.
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Affiliation(s)
- Venelin Enchev
- Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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Micellar electrokinetic chromatography as a powerful analytical tool for research on prebiotic chemistry. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bizzarri BM, Saladino R, Delfino I, García-Ruiz JM, Di Mauro E. Prebiotic Organic Chemistry of Formamide and the Origin of Life in Planetary Conditions: What We Know and What Is the Future. Int J Mol Sci 2021; 22:ijms22020917. [PMID: 33477625 PMCID: PMC7831497 DOI: 10.3390/ijms22020917] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/14/2021] [Accepted: 01/17/2021] [Indexed: 11/18/2022] Open
Abstract
The goal of prebiotic chemistry is the depiction of molecular evolution events preceding the emergence of life on Earth or elsewhere in the cosmos. Plausible experimental models require geochemical scenarios and robust chemistry. Today we know that the chemical and physical conditions for life to flourish on Earth were at work much earlier than thought, i.e., earlier than 4.4 billion years ago. In recent years, a geochemical model for the first five hundred million years of the history of our planet has been devised that would work as a cradle for life. Serpentinization processes in the Hadean eon affording self-assembled structures and vesicles provides the link between the catalytic properties of the inorganic environment and the impressive chemical potential of formamide to produce complete panels of organic molecules relevant in pre-genetic and pre-metabolic processes. Based on an interdisciplinary approach, we propose basic transformations connecting geochemistry to the chemistry of formamide, and we hint at the possible extension of this perspective to other worlds.
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Affiliation(s)
- Bruno Mattia Bizzarri
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (B.M.B.); (I.D.); (E.D.M.)
| | - Raffaele Saladino
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (B.M.B.); (I.D.); (E.D.M.)
- Correspondence: (R.S.); (J.M.G.-R.)
| | - Ines Delfino
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (B.M.B.); (I.D.); (E.D.M.)
| | - Juan Manuel García-Ruiz
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, Consejo Superior de Investigaciones Científicas–Universidad de Granada, Avenida de las Palmeras 4, Armilla, 18100 Granada, Spain
- Correspondence: (R.S.); (J.M.G.-R.)
| | - Ernesto Di Mauro
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (B.M.B.); (I.D.); (E.D.M.)
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Enchev V, Angelov I, Dincheva I, Stoyanova N, Slavova S, Rangelov M, Markova N. Chemical evolution: from formamide to nucleobases and amino acids without the presence of catalyst. J Biomol Struct Dyn 2020; 39:5563-5578. [PMID: 32677584 DOI: 10.1080/07391102.2020.1792986] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Abiotic synthesis of nucleobases and amino acids is of critical importance as it sheds light on potential prebiotic chemical reactions. During thermal decomposition of formamide in vacuum conditions, purine, cytosine, adenine, hypoxanthine, uracil, pterin, urea, urocanic acid, glycine, alanine and norvaline were detected. The compounds were obtained without catalyst by heating at 100-180 °C or microwave heating of formamide. Reaction network of self-catalyzed chemical reactions is suggested, showing how from only one parent molecule, nucleobases, urea and the amino acid glycine can be produced. The reaction pathways are theoretically determined using SCS-MP2 calculations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Venelin Enchev
- Bulgarian Academy of Sciences, Institute of General and Inorganic Chemistry, Sofia, Bulgaria
| | - Ivan Angelov
- Bulgarian Academy of Sciences, Institute of Organic Chemistry with Centre of Phytochemistry, Sofia, Bulgaria
| | | | - Nina Stoyanova
- Bulgarian Academy of Sciences, Institute of General and Inorganic Chemistry, Sofia, Bulgaria
| | - Sofia Slavova
- Bulgarian Academy of Sciences, Institute of General and Inorganic Chemistry, Sofia, Bulgaria
| | - Miroslav Rangelov
- Bulgarian Academy of Sciences, Institute of Organic Chemistry with Centre of Phytochemistry, Sofia, Bulgaria
| | - Nadezhda Markova
- Bulgarian Academy of Sciences, Institute of Organic Chemistry with Centre of Phytochemistry, Sofia, Bulgaria
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10
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Pantaleone S, Salvini C, Zamirri L, Signorile M, Bonino F, Ugliengo P. A quantum mechanical study of dehydration vs. decarbonylation of formamide catalysed by amorphous silica surfaces. Phys Chem Chem Phys 2020; 22:8353-8363. [PMID: 32266913 DOI: 10.1039/d0cp00572j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Formamide is abundant in the interstellar medium and was also present during the formation of the Solar system through the accretion process of interstellar dust. Under the physicochemical conditions of primordial Earth, formamide could have undergone decomposition, either via dehydration (HCN + H2O) or via decarbonylation (CO + NH3). The first reactive channel provides HCN, which is an essential molecular building block for the formation of RNA/DNA bases, crucial for the emergence of life on Earth. In this work, we studied, at the CCSD(T)/cc-pVTZ level, the two competitive routes of formamide decomposition, i.e. dehydration and decarbonylation, either in liquid formamide (by using the polarization continuum model technique) or at the interface between liquid formamide and amorphous silica. Amorphous silica was adopted as a convenient model of the crystalline silica phases ubiquitously present in the primordial (and actual) Earth's crust, and also due to its relevance in catalysis, adsorption and chromatography. Results show that: (i) silica surface sites catalyse both decomposition channels by reducing the activation barriers by about 100 kJ mol-1 with respect to the reactions in homogeneous medium, and (ii) the dehydration channel, giving rise to HCN, is strongly favoured from a kinetic standpoint over decarbonylation, the latter being, instead, slightly favoured from a thermodynamic point of view.
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Affiliation(s)
- Stefano Pantaleone
- Univ. Grenoble Alpes, CNRS, Institut de Planétologie et d'Astrophysique de Grenoble (IPAG), 38000 Grenoble, France.
| | - Clara Salvini
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, via P. Giuria 7, IT-10125, Torino, Italy.
| | - Lorenzo Zamirri
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, via P. Giuria 7, IT-10125, Torino, Italy.
| | - Matteo Signorile
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, via P. Giuria 7, IT-10125, Torino, Italy.
| | - Francesca Bonino
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, via P. Giuria 7, IT-10125, Torino, Italy.
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, via P. Giuria 7, IT-10125, Torino, Italy.
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11
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Recent Results on Computational Molecular Modeling of The Origins of Life. FOUNDATIONS OF COMPUTING AND DECISION SCIENCES 2020. [DOI: 10.2478/fcds-2020-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
In the last decade of research in the origins of life, there has been an increase in the interest on theoretical molecular modeling methods aimed to improve the accuracy and speed of the algorithms that solve the molecular mechanics and chemical reactions of the matter. Research on the scenarios of prebiotic chemistry has also advanced. The presented work attempts to discuss the latest computational techniques and trends implemented so far. Although it is difficult to cover the full extent of the current publications, we tried to orient the reader into the modern tendencies and challenges faced by those who are in the origins of life field.
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12
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Wu L, Wang Z, Xiong F, Sun G, Chai P, Zhang Z, Xu H, Fu C, Huang W. Surface chemistry and photochemistry of small molecules on rutile TiO 2(001) and TiO 2(011)-(2 × 1) surfaces: The crucial roles of defects. J Chem Phys 2020; 152:044702. [PMID: 32007048 DOI: 10.1063/1.5135945] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Surface chemistry and photochemistry of small molecules on the rutile TiO2(001) and TiO2(011)-(2 × 1) surfaces were studied by low energy electron diffraction, thermal desorption spectroscopy, and x-ray photoelectron spectroscopy. It was found that the TiO2(001) surface mainly exhibits the defects of Ti interstitials in the near-surface region, while the TiO2(011)-(2 × 1) surface mainly exhibits the defects of double-oxygen vacancies. The defect structures of TiO2 surfaces strongly affect their adsorption and thermal/photodesorption behaviors. On the TiO2(001) surface, CH3OH and H2O dissociatively adsorb at the surface Ti sites near Ti interstitials; O2 molecularly adsorbs at the surface Ti sites adjacent to Ti interstitials, forming photoactive O2 species that undergoes a hole-mediated photodesorption process; CO adsorbs at the nearest surface Ti sites close to the Ti interstitials, but CO2 does not, and the resulting CO species is photoactive; and both CO and CO2 species adsorbed at the normal Ti4+ sites are photoinactive. On the TiO2(011)-(2 × 1) surface, O2 adsorbs only at the double-oxygen vacancy sites, and the resulting O2 species dissociates to form two oxygen atoms to refill in the oxygen vacancies upon heating; CO2 adsorbs at the double-oxygen vacancy sites, but CO does not, and the resulting CO2 species is photoactive; and both CO and CO2 species adsorbed at the surface Ti4+ sites are photoinactive. These results broaden the fundamental understandings of the chemistry and photochemistry of TiO2 surfaces, and the established structure-reactivity relation of small molecules on TiO2 surfaces is useful in probing complex structures of TiO2 powder catalysts.
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Affiliation(s)
- Longxia Wu
- Hefei National Laboratory for Physical Sciences at Microscale, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, CAS Key Laboratory of Materials for Energy Conversion, Department of Chemical Physics, University of Science and Technology of China, Jinzhai Road 96, Hefei 230026, China
| | - Zhengming Wang
- Hefei National Laboratory for Physical Sciences at Microscale, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, CAS Key Laboratory of Materials for Energy Conversion, Department of Chemical Physics, University of Science and Technology of China, Jinzhai Road 96, Hefei 230026, China
| | - Feng Xiong
- Hefei National Laboratory for Physical Sciences at Microscale, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, CAS Key Laboratory of Materials for Energy Conversion, Department of Chemical Physics, University of Science and Technology of China, Jinzhai Road 96, Hefei 230026, China
| | - Guanghui Sun
- Hefei National Laboratory for Physical Sciences at Microscale, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, CAS Key Laboratory of Materials for Energy Conversion, Department of Chemical Physics, University of Science and Technology of China, Jinzhai Road 96, Hefei 230026, China
| | - Peng Chai
- Hefei National Laboratory for Physical Sciences at Microscale, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, CAS Key Laboratory of Materials for Energy Conversion, Department of Chemical Physics, University of Science and Technology of China, Jinzhai Road 96, Hefei 230026, China
| | - Zhen Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, CAS Key Laboratory of Materials for Energy Conversion, Department of Chemical Physics, University of Science and Technology of China, Jinzhai Road 96, Hefei 230026, China
| | - Hong Xu
- Hefei National Laboratory for Physical Sciences at Microscale, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, CAS Key Laboratory of Materials for Energy Conversion, Department of Chemical Physics, University of Science and Technology of China, Jinzhai Road 96, Hefei 230026, China
| | - Cong Fu
- Hefei National Laboratory for Physical Sciences at Microscale, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, CAS Key Laboratory of Materials for Energy Conversion, Department of Chemical Physics, University of Science and Technology of China, Jinzhai Road 96, Hefei 230026, China
| | - Weixin Huang
- Hefei National Laboratory for Physical Sciences at Microscale, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, CAS Key Laboratory of Materials for Energy Conversion, Department of Chemical Physics, University of Science and Technology of China, Jinzhai Road 96, Hefei 230026, China
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Wang H, Zhao X, Huang C, Jin X, Wei D, Dai D, Ma Z, Li WX, Yang X. Adsorption Features of Formaldehyde on TiO 2(110) Surface Probed by High-Resolution Scanning Tunnelling Microscopy. J Phys Chem Lett 2019; 10:3352-3358. [PMID: 31181938 DOI: 10.1021/acs.jpclett.9b00522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We report a real-space imaging of formaldehyde (HCHO) adsorption on a TiO2(110) surface probed by high-resolution scanning tunnelling microscopy (STM). Density functional theory calculations (DFT) were carried out to assign the observed features. The adsorptions occur exclusively on 5-fold coordinated Ti (Ti5c) sites and oxygen vacancies (OVs). The well-resolved configurations on the Ti5c sites feature the overlapping of the two "dumbbell" structures which are originated from the empty orbitals of HCHO. The STM images for the physical adsorption of HCHO on the OV sites appear fuzzy because of the rapid switching of HCHO among the three stable orientations, while those for the chemical adsorption are much clearer, revealing a distinctive difference between chemical and physical adsorptions. This work presents a systematic characterization of the topological features of HCHO/TiO2(110) and provides useful information for mechanical understanding of the reaction mechanism of HCHO on the surfaces.
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Affiliation(s)
- Haochen Wang
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics, Chinese Academy of Science , Dalian , Liaoning 116023 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xiangyun Zhao
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics, Chinese Academy of Science , Dalian , Liaoning 116023 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Chuanqi Huang
- Hangzhou Institute of Advanced Studies , Zhejiang Normal University , Hangzhou , Zhejiang 311231 , China
| | - Xianchi Jin
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics, Chinese Academy of Science , Dalian , Liaoning 116023 , China
- Scienta Omicron GmbH , Limburger Strasse , 7565232 Taunusstein , Germany
| | - Dong Wei
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics, Chinese Academy of Science , Dalian , Liaoning 116023 , China
| | - Dongxu Dai
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics, Chinese Academy of Science , Dalian , Liaoning 116023 , China
| | - Zhibo Ma
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics, Chinese Academy of Science , Dalian , Liaoning 116023 , China
| | - Wei-Xue Li
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics , University of Science and Technology of China , Hefei 230026 , China
| | - Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics , Dalian Institute of Chemical Physics, Chinese Academy of Science , Dalian , Liaoning 116023 , China
- Department of Chemistry , Southern University of Science and Technology , Shenzhen 518055 , China
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Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations. Life (Basel) 2019; 9:life9020046. [PMID: 31167366 PMCID: PMC6617125 DOI: 10.3390/life9020046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/30/2019] [Accepted: 05/30/2019] [Indexed: 01/08/2023] Open
Abstract
The catalytic effects of complex minerals or meteorites are often mentioned as important factors for the origins of life. To assess the possible role of nanoconfinement within a catalyst consisting of montmorillonite (MMT) and the impact of local electric field on the formation efficiency of the simple hypothetical precursors of nucleic acid bases or amino acids, we performed ab initio Car–Parrinello molecular dynamics simulations. We prepared four condensed-phase systems corresponding to previously suggested prototypes of a primordial soup. We monitored possible chemical reactions occurring within gas-like bulk and MMT-confined four simulation boxes on a 20-ps time scale at 1 atm and 300 K, 400 K, and 600 K. Elevated temperatures did not affect the reactivity of the elementary components of the gas-like boxes considerably; however, the presence of the MMT nanoclay substantially increased the formation probability of new molecules. Approximately 20 different new compounds were found in boxes containing carbon monoxide or formaldehyde molecules. This observation and an analysis of the atom–atom radial distribution functions indicated that the presence of Ca2+ ions at the surface of the internal MMT cavities may be an important factor in the initial steps of the formation of complex molecules at the early stages of the Earth’s history.
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Limo MJ, Sola-Rabada A, Boix E, Thota V, Westcott ZC, Puddu V, Perry CC. Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications. Chem Rev 2018; 118:11118-11193. [PMID: 30362737 DOI: 10.1021/acs.chemrev.7b00660] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO2, SiO2, and GeO2 has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.
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Affiliation(s)
- Marion J Limo
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom.,Interface and Surface Analysis Centre, School of Pharmacy , University of Nottingham , University Park, Nottingham NG7 2RD , United Kingdom
| | - Anna Sola-Rabada
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Estefania Boix
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom.,Department of Bioproducts and Biosystems , Aalto University , P.O. Box 16100, FI-00076 Aalto , Finland
| | - Veeranjaneyulu Thota
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Zayd C Westcott
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Valeria Puddu
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
| | - Carole C Perry
- Interdisciplinary Biomedical Research Centre, School of Science and Technology , Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS , United Kingdom
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16
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Pantaleone S, Ugliengo P, Sodupe M, Rimola A. When the Surface Matters: Prebiotic Peptide-Bond Formation on the TiO 2 (101) Anatase Surface through Periodic DFT-D2 Simulations. Chemistry 2018; 24:16292-16301. [PMID: 30212609 DOI: 10.1002/chem.201803263] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Indexed: 12/13/2022]
Abstract
The mechanism of the peptide-bond formation between two glycine (Gly) molecules has been investigated by means of PBE-D2* and PBE0-D2* periodic simulations on the TiO2 (101) anatase surface. This is a process of great relevance both in fundamental prebiotic chemistry, as the reaction univocally belongs to one of the different organizational events that ultimately led to the emergence of life on Earth, as well as from an industrial perspective, since formation of amides is a key reaction for pharmaceutical companies. The efficiency of the surface catalytic sites is demonstrated by comparing the reactions in the gas phase and on the surface. At variance with the uncatalyzed gas-phase reaction, which involves a concerted nucleophilic attack and dehydration step, on the surface these two steps occur along a stepwise mechanism. The presence of surface Lewis and Brönsted sites exerts some catalytic effect by lowering the free energy barrier for the peptide-bond formation by about 6 kcal mol-1 compared to the gas-phase reaction. Moreover, the co-presence of molecules acting as proton-transfer assistants (i.e., H2 O and Gly) provide a more significant kinetic energy barrier decrease. The reaction on the surface is also favorable from a thermodynamic standpoint, involving very large and negative reaction energies. This is due to the fact that the anatase surface also acts as a dehydration agent during the condensation reaction, since the outermost coordinatively unsaturated Ti atoms strongly anchor the released water molecules. Our theoretical results provide a comprehensive atomistic interpretation of the experimental results of Martra et al. (Angew. Chem. Int. Ed. 2014, 53, 4671), in which polyglycine formation was obtained by successive feedings of Gly vapor on TiO2 surfaces in dry conditions and are, therefore, relevant in a prebiotic context envisaging dry and wet cycles occurring, at mineral surfaces, in a small pool.
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Affiliation(s)
- Stefano Pantaleone
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS), Inter-Departmental centre, Università degli Studi di Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
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Signorile M, Salvini C, Zamirri L, Bonino F, Martra G, Sodupe M, Ugliengo P. Formamide Adsorption at the Amorphous Silica Surface: A Combined Experimental and Computational Approach. Life (Basel) 2018; 8:life8040042. [PMID: 30249032 PMCID: PMC6316577 DOI: 10.3390/life8040042] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 09/19/2018] [Accepted: 09/20/2018] [Indexed: 11/16/2022] Open
Abstract
Mineral surfaces have been demonstrated to play a central role in prebiotic reactions, which are understood to be at the basis of the origin of life. Among the various molecules proposed as precursors for these reactions, one of the most interesting is formamide. Formamide has been shown to be a pluripotent molecule, generating a wide distribution of relevant prebiotic products. In particular, the outcomes of its reactivity are strongly related to the presence of mineral phases acting as catalysts toward specific reaction pathways. While the mineral–products relationship has been deeply studied for a large pool of materials, the fundamental description of formamide reactivity over mineral surfaces at a microscopic level is missing in the literature. In particular, a key step of formamide chemistry at surfaces is adsorption on available interaction sites. This report aims to investigate the adsorption of formamide over a well-defined amorphous silica, chosen as a model mineral surface. An experimental IR investigation of formamide adsorption was carried out and its outcomes were interpreted on the basis of first principles simulation of the process, adopting a realistic model of amorphous silica.
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Affiliation(s)
- Matteo Signorile
- Dipartimento di Chimica and NIS, Università di Torino, Via P. Giuria 7 - 10125 Torino and Via G. Quarello 15/A - 10135 Torino, Italy.
| | - Clara Salvini
- Dipartimento di Chimica and NIS, Università di Torino, Via P. Giuria 7 - 10125 Torino and Via G. Quarello 15/A - 10135 Torino, Italy.
| | - Lorenzo Zamirri
- Dipartimento di Chimica and NIS, Università di Torino, Via P. Giuria 7 - 10125 Torino and Via G. Quarello 15/A - 10135 Torino, Italy.
| | - Francesca Bonino
- Dipartimento di Chimica and NIS, Università di Torino, Via P. Giuria 7 - 10125 Torino and Via G. Quarello 15/A - 10135 Torino, Italy.
| | - Gianmario Martra
- Dipartimento di Chimica and NIS, Università di Torino, Via P. Giuria 7 - 10125 Torino and Via G. Quarello 15/A - 10135 Torino, Italy.
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalogna, Spain.
| | - Piero Ugliengo
- Dipartimento di Chimica and NIS, Università di Torino, Via P. Giuria 7 - 10125 Torino and Via G. Quarello 15/A - 10135 Torino, Italy.
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18
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Mattia Bizzarri B, Botta L, Pérez-Valverde MI, Saladino R, Di Mauro E, García-Ruiz JM. Silica Metal Oxide Vesicles Catalyze Comprehensive Prebiotic Chemistry. Chemistry 2018; 24:8126-8132. [PMID: 29603465 DOI: 10.1002/chem.201706162] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Indexed: 02/01/2023]
Abstract
It has recently been demonstrated that mineral self-assembled structures catalyzing prebiotic chemical reactions may form in natural waters derived from serpentinization, a geological process widespread in the early stages of Earth-like planets. We have synthesized self-assembled membranes by mixing microdrops of metal solutions with alkaline silicate solutions in the presence of formamide (NH2 CHO), a single-carbon molecule, at 80 °C. We found that these bilayer membranes, made of amorphous silica and metal oxide/hydroxide nanocrystals, catalyze the condensation of formamide, yielding the four nucleobases of RNA, three amino acids and, several carboxylic acids in a single-pot experiment. Besides manganese, iron and magnesium, two abundant elements in the earliest Earth crust that are key in serpentinization reactions, are enough to produce all these biochemical compounds. These results suggest that the transition from inorganic geochemistry to prebiotic organic chemistry is common on a universal scale and, most probably, occurred earlier than ever thought for our planet.
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Affiliation(s)
- Bruno Mattia Bizzarri
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100, Viterbo, Italy
| | - Lorenzo Botta
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100, Viterbo, Italy
| | - Maritza Iveth Pérez-Valverde
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la, Tierra, Consejo Superior de Investigaciones Científicas-Universidad de, Granada, Avenida de las Palmeras 4, Armilla, Granada, 18100, Spain
| | - Raffaele Saladino
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100, Viterbo, Italy
| | - Ernesto Di Mauro
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100, Viterbo, Italy
| | - Juan Manuel García-Ruiz
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la, Tierra, Consejo Superior de Investigaciones Científicas-Universidad de, Granada, Avenida de las Palmeras 4, Armilla, Granada, 18100, Spain
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19
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Šponer JE, Szabla R, Góra RW, Saitta AM, Pietrucci F, Saija F, Di Mauro E, Saladino R, Ferus M, Civiš S, Šponer J. Prebiotic synthesis of nucleic acids and their building blocks at the atomic level - merging models and mechanisms from advanced computations and experiments. Phys Chem Chem Phys 2018; 18:20047-66. [PMID: 27136968 DOI: 10.1039/c6cp00670a] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The origin of life on Earth is one of the most fascinating questions of contemporary science. Extensive research in the past decades furnished diverse experimental proposals for the emergence of first informational polymers that could form the basis of the early terrestrial life. Side by side with the experiments, the fast development of modern computational chemistry methods during the last 20 years facilitated the use of in silico modelling tools to complement the experiments. Modern computations can provide unique atomic-level insights into the structural and electronic aspects as well as the energetics of key prebiotic chemical reactions. Many of these insights are not directly obtainable from the experimental techniques and the computations are thus becoming indispensable for proper interpretation of many experiments and for qualified predictions. This review illustrates the synergy between experiment and theory in the origin of life research focusing on the prebiotic synthesis of various nucleic acid building blocks and on the self-assembly of nucleotides leading to the first functional oligonucleotides.
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Affiliation(s)
- Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic. and CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Rafał Szabla
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.
| | - Robert W Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - A Marco Saitta
- Sorbonne Universités, Université Pierre et Marie Curie Paris 6, CNRS, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d'Histoire Naturelle, Institut de Recherche pour le Développement, UMR 7590, F-75005 Paris, France
| | - Fabio Pietrucci
- Sorbonne Universités, Université Pierre et Marie Curie Paris 6, CNRS, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d'Histoire Naturelle, Institut de Recherche pour le Développement, UMR 7590, F-75005 Paris, France
| | - Franz Saija
- CNR-IPCF, Viale Ferdinando Stagno d'Alcontres 37, 98158 Messina, Italy
| | - Ernesto Di Mauro
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", "Sapienza" Università di Roma, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Raffaele Saladino
- Dipartimento di Scienze Ecologiche e Biologiche Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy
| | - Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic. and CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
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20
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Gahlaut A, Paranjothy M. Unimolecular decomposition of formamide via direct chemical dynamics simulations. Phys Chem Chem Phys 2018. [DOI: 10.1039/c8cp00541a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Classical chemical dynamics simulations show that formamide (NH2CHO) can dissociate via multiple pathways, either by direct dissociations or via intramolecular rearrangements to different isomers followed by dissociation.
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Affiliation(s)
- Anchal Gahlaut
- Department of Chemistry, Indian Institute of Technology Jodhpur
- Jodhpur
- India
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21
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The MUSCLES Treasury Survey. IV. Scaling Relations for Ultraviolet, Ca ii K, and Energetic Particle Fluxes from M Dwarfs. ACTA ACUST UNITED AC 2017. [DOI: 10.3847/1538-4357/aa76dd] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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22
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Novoselov AA, Silva D, Schneider J, Abrevaya XC, Chaffin MS, Serrano P, Navarro MS, Conti MJ, Souza Filho CRD. Geochemical constraints on the Hadean environment from mineral fingerprints of prokaryotes. Sci Rep 2017; 7:4008. [PMID: 28638074 PMCID: PMC5479841 DOI: 10.1038/s41598-017-04161-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/22/2017] [Indexed: 11/21/2022] Open
Abstract
The environmental conditions on the Earth before 4 billion years ago are highly uncertain, largely because of the lack of a substantial rock record from this period. During this time interval, known as the Hadean, the young planet transformed from an uninhabited world to the one capable of supporting, and inhabited by the first living cells. These cells formed in a fluid environment they could not at first control, with homeostatic mechanisms developing only later. It is therefore possible that present-day organisms retain some record of the primordial fluid in which the first cells formed. Here we present new data on the elemental compositions and mineral fingerprints of both Bacteria and Archaea, using these data to constrain the environment in which life formed. The cradle solution that produced this elemental signature was saturated in barite, sphene, chalcedony, apatite, and clay minerals. The presence of these minerals, as well as other chemical features, suggests that the cradle environment of life may have been a weathering fluid interacting with dry-land silicate rocks. The specific mineral assemblage provides evidence for a moderate Hadean climate with dry and wet seasons and a lower atmospheric abundance of CO2 than is present today.
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Affiliation(s)
- Alexey A Novoselov
- University of Campinas, Institute of Geosciences, Campinas, 13083-970, Brazil.
- University of Concepción, Institute of Applied Economic Geology, Concepción, Casilla 160-C, Chile.
| | - Dailto Silva
- University of Campinas, Institute of Geosciences, Campinas, 13083-970, Brazil
| | - Jerusa Schneider
- University of Campinas, School of Civil Engineering, Architecture and Urban Design, Campinas, 13083-889, Brazil
| | - Ximena Celeste Abrevaya
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, C1428EHA, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Astronomía y Física del Espacio (IAFE), Buenos Aires, C1428ZAA, Argentina
| | | | - Paloma Serrano
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, 14473, Germany
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23
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THE MUSCLES TREASURY SURVEY. III. X-RAY TO INFRARED SPECTRA OF 11 M AND K STARS HOSTING PLANETS. ACTA ACUST UNITED AC 2016. [DOI: 10.3847/0004-637x/824/2/102] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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24
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Khalili B, Rimaz M. Interaction of l-proline with group IIB (Zn2+, Cd2+, Hg2+) metal cations in the gas and aqueous phases: a quantum computational study. CAN J CHEM 2016. [DOI: 10.1139/cjc-2015-0616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The gas and aqueous phase complexation geometries, electronic interactions, and metal ion affinities of Zn2+, Cd2+, and Hg2+ metal cations with the two most stable conformations of l-proline complexes were studied. The complexes were optimized by density functional theory (B3LYP) using the 6-311++G(d,p) orbital basis set and relativistic pseudopotentials for the metal cations. The interactions of the metal cations at different nucleophilic sites of l-proline were considered as were three modes of interactions including salt bridged, charge solvated 1, and charge solvated 2, which are indicative of binding in a bidentate manner through the carboxylate group, carbonyl and hydroxyl oxygen, and carbonyl oxygen and the nitrogen atom of l-proline. All of the coordination patterns were characterized by both charge transfer and ionic interactions between l-proline and the metal cation. The metal ion affinity (MIA) and interaction energy were also computed for all of the complexes at both the gas and aqueous phases. Results showed that the order of MIA at the gas and aqueous phases are different. MIA order at the gas phase was in the order of Zn2+ > Hg2+ > Cd2+ whereas at the aqueous phase, the order of Zn2+ > Cd2+ > Hg2+ was obtained for MIA. The infrared stretching vibrational modes of the N–H and O–H groups of free l-proline were compared with l-proline–M2+ in both CS1 and CS2 coordination patterns at the gas phase and results showed a considerable shift to lower frequency during complexation process.
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Affiliation(s)
- Behzad Khalili
- Department of Chemistry, Faculty of Sciences, University of Guilan, P.O. Box 41335-1914 Rasht, Iran
| | - Mehdi Rimaz
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran, Iran
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Rapf RJ, Vaida V. Sunlight as an energetic driver in the synthesis of molecules necessary for life. Phys Chem Chem Phys 2016; 18:20067-84. [DOI: 10.1039/c6cp00980h] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This review considers how photochemistry and sunlight-driven reactions can abiotically generate prebiotic molecules necessary for the evolution of life.
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Affiliation(s)
- Rebecca J. Rapf
- Department of Chemistry and Biochemistry
- CIRES
- University of Colorado at Boulder
- Boulder
- USA
| | - Veronica Vaida
- Department of Chemistry and Biochemistry
- CIRES
- University of Colorado at Boulder
- Boulder
- USA
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26
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Rugheimer S, Segura A, Kaltenegger L, Sasselov D. UV SURFACE ENVIRONMENT OF EARTH-LIKE PLANETS ORBITING FGKM STARS THROUGH GEOLOGICAL EVOLUTION. ACTA ACUST UNITED AC 2015. [DOI: 10.1088/0004-637x/806/1/137] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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27
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Saïagh K, Cottin H, Aleian A, Fray N. VUV and mid-UV photoabsorption cross sections of thin films of guanine and uracil: application on their photochemistry in the solar system. ASTROBIOLOGY 2015; 15:268-282. [PMID: 25836367 DOI: 10.1089/ast.2014.1196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a photostability study of two nucleobases, guanine and uracil. For the first time, the photoabsorption cross-section spectra of these molecules in the solid phase were measured in the VUV and mid-UV domain (115≤λ≤300 nm). They show a quite similar absorption level throughout this wavelength range, highlighting the importance of considering the whole VUV and UV domain during photolysis experiments in the laboratory. Their photolysis constant (J) can be estimated from those measurements as follows: 2.2×10(-2) s(-1)±11% for guanine and 5.3×10(-2) s(-1)±14% for uracil. This work shows that (i) measuring kinetic constants from a direct and "traditional" photolysis of a thin sample in the laboratory suffers strong limitations and (ii) achieving this measurement requires comprehensive modeling of the radiative transfer that occurs in any sample not optically thin (i.e.,≤2 nm). Moreover, this work has provided other data of interest: the refractive index of solid guanine and of uracil at 650 nm are 1.52 (±0.01) and 1.39 (±0.02), respectively, and the integrated IR band strengths (A) of solid guanine between 3700 and 2120 cm(-1) (3.4×10(-16) cm·molecule(-1)±13%) and of solid uracil between 3400 and 1890 cm(-1) (2.1×10(-16) cm·molecule(-1)±21%).
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Affiliation(s)
- Kafila Saïagh
- Laboratoire Interuniversitaire des Systèmes Atmosphériques, LISA, UMR CNRS 7583, Université Paris Est Créteil and Université Paris Diderot , Institut Pierre Simon Laplace, Créteil, France
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28
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Nguyen HT, Nguyen MT. Decomposition pathways of formamide in the presence of vanadium and titanium monoxides. Phys Chem Chem Phys 2015; 17:16927-36. [DOI: 10.1039/c5cp01456e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thermally feasible decomposition pathways of formamide (FM) in the presence of vanadium VO(X4Σ−) and titanium TiO(X3Δ) monoxides are determined using density functional theory (the BP86 functional) and coupled-cluster theory (CCSD(T)) computations with large basis sets.
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Affiliation(s)
| | - Minh Tho Nguyen
- Department of Chemistry
- University of Leuven
- B-3001 Leuven
- Belgium
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29
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High-energy chemistry of formamide: a unified mechanism of nucleobase formation. Proc Natl Acad Sci U S A 2014; 112:657-62. [PMID: 25489115 DOI: 10.1073/pnas.1412072111] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The coincidence of the Late Heavy Bombardment (LHB) period and the emergence of terrestrial life about 4 billion years ago suggest that extraterrestrial impacts could contribute to the synthesis of the building blocks of the first life-giving molecules. We simulated the high-energy synthesis of nucleobases from formamide during the impact of an extraterrestrial body. A high-power laser has been used to induce the dielectric breakdown of the plasma produced by the impact. The results demonstrate that the initial dissociation of the formamide molecule could produce a large amount of highly reactive CN and NH radicals, which could further react with formamide to produce adenine, guanine, cytosine, and uracil. Based on GC-MS, high-resolution FTIR spectroscopic results, as well as theoretical calculations, we present a comprehensive mechanistic model, which accounts for all steps taking place in the studied impact chemistry. Our findings thus demonstrate that extraterrestrial impacts, which were one order of magnitude more abundant during the LHB period than before and after, could not only destroy the existing ancient life forms, but could also contribute to the creation of biogenic molecules.
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30
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Artoshina OV, Vorob’eva MY, Dushanov EB, Kholmurodov KT. Molecular dynamics simulations of formamide interaction with hydrocyanic acid on a catalytic surface TiO2. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s0036024414060041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Ferus M, Michalčíková R, Shestivská V, Šponer J, Šponer JE, Civiš S. High-energy chemistry of formamide: a simpler way for nucleobase formation. J Phys Chem A 2014; 118:719-36. [PMID: 24437678 DOI: 10.1021/jp411415p] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The formation of nucleobases from formamide during a high-energy density event, i.e., the impact of an extraterrestrial body into the planetary atmosphere, was studied by irradiation of formamide ice and liquid samples with a high-power laser in the presence of potential catalysts. FTIR spectroscopy, time-resolved emission spectroscopy, and GC-MS were subsequently used to monitor the dissociation of this molecule into stable molecular fragments (HCN, H2O, HNCO, H2, CO, and NH3) and unstable species (HNC, •CN, and •NH). The kinetic and thermodynamic models of the high-energy density event molecular dynamics have been suggested together with the reaction routes leading from the dissociation products to the nucleobases. In addition, using theoretical calculations, we propose a simple new reaction pathway for the formation of both pyrimidine and purine nucleobases involving •CN radical chemistry.
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Affiliation(s)
- Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , Dolejškova 3, 18223 Prague 8, Czech Republic
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32
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Friedli P, Sigg H, Sá J. Dye-injected electron trapping in TiO2 determined by broadband transient infrared spectroscopy. Photochem Photobiol Sci 2014; 13:1393-6. [DOI: 10.1039/c4pp00152d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the dynamics of electrons injected into TiO2 due to the excitation of Ru-N719 dye at 532 nm.
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Affiliation(s)
- Peter Friedli
- Paul Scherrer Institut
- 5232 Villigen PSI, Switzerland
| | - Hans Sigg
- Paul Scherrer Institut
- 5232 Villigen PSI, Switzerland
| | - Jacinto Sá
- Paul Scherrer Institut
- 5232 Villigen PSI, Switzerland
- Institute of Physical Chemistry
- Polish Academy of Sciences
- Warsaw, Poland
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33
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Subrahmanyam A, Thangaraj PR, Kanuru C, Jayakumar A, Gopal J. Quantification of photocatalytic oxygenation of human blood. Med Eng Phys 2013; 36:530-3. [PMID: 24290134 DOI: 10.1016/j.medengphy.2013.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 10/29/2013] [Accepted: 11/06/2013] [Indexed: 01/21/2023]
Abstract
Photocatalytic oxygenation of human blood is an emerging concept based on the principle of photocatalytic splitting of water into oxygen and hydrogen. This communication reports: (i) a design of a photocatalytic cell (PC) that separates the blood from UV (incident) radiation source, (ii) a pH, temperature and flow controlled circuit designed for quantifying the oxygenation of human blood by photocatalysis and (iii) measuring the current efficacy of ITO/TiO2 nano thin films in oxygenating human blood in a dynamic circuit in real time. The average increase in oxygen saturation was around 5% above baseline compared to control (p<0.0005). We believe this is one of the first attempts to quantify photocatalytic oxygenation of human blood under controlled conditions.
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Affiliation(s)
| | - Paul R Thangaraj
- Department of Physics, Indian Institute of Technology - Madras, Chennai, India; Department of Cardiothoracic Surgery, Apollo Hospital, Chennai, India.
| | | | | | - Jayashree Gopal
- Department of Endocrinology, Apollo Hospital, Chennai, India
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34
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Wang J, Gu J, Nguyen MT, Springsteen G, Leszczynski J. From Formamide to Adenine: A Self-Catalytic Mechanism for an Abiotic Approach. J Phys Chem B 2013; 117:14039-45. [DOI: 10.1021/jp409296k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Wang
- Interdisciplinary
Nanotoxicity Center, Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
| | - Jiande Gu
- Interdisciplinary
Nanotoxicity Center, Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
- Drug
Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, CAS, Shanghai 201203, People’s Republic of China
| | - Minh Tho Nguyen
- Department
of Chemistry, University of Leuven, B-3001 Leuven, Belgium
| | - Greg Springsteen
- Department
of Chemistry, Furman University, 3300 Poinsett Hwy, Greenville, South Carolina 29613, United States
| | - Jerzy Leszczynski
- Interdisciplinary
Nanotoxicity Center, Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
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35
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Gupta D, Naghma R, Antony B. Electron impact total ionisation cross sections for simple bio-molecules: a theoretical approach. Mol Phys 2013. [DOI: 10.1080/00268976.2013.839841] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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36
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Dushanov E, Kholmurodov K, Yasuoka K. Structural and diffusion properties of formamide/water mixture interacting with TiO2 surface. Bioorg Chem 2013; 50:11-6. [PMID: 23933355 DOI: 10.1016/j.bioorg.2013.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 07/13/2013] [Accepted: 07/15/2013] [Indexed: 11/30/2022]
Abstract
The photoreaction and adsorption properties on surfaces, thermal decomposition, chemical transformation, and other properties of the formamide molecule are widely used to understand the origins of the formation of biological molecules (nucleosides, amino acids, DNA, monolayers, etc.) needed for life. The titanium oxide (TiO2) surface can act both as a template on which the accumulation of adsorbed molecules like formamide occurs through the concentration effect, and as a catalytic material that lowers the activation energy needed for the formation of intermediate products. In this paper, a formamide-water solution interacting with TiO2 (anatase) surface is simulated using the molecular dynamics method. The structural, diffusion and density properties of formamide-water mixture on TiO2 are established for a wide temperature range from T=250 K up to T=400 K.
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Affiliation(s)
- E Dushanov
- Laboratory of Radiation Biology, JINR, 141980 Dubna, Moscow Region, Russia; Institute of Nuclear Physics, 702132 Ulugbek, Tashkent, Uzbekistan
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37
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Dushanov E, Kholmurodov K, Yasuoka K. Activation Energy Calculations for Formamide-TiO2 and Formamide-Pt Interactions in the Presence of Water. Open Biochem J 2013; 7:33-43. [PMID: 23802018 PMCID: PMC3680988 DOI: 10.2174/1874091x01307010033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 10/12/2012] [Accepted: 10/23/2012] [Indexed: 11/22/2022] Open
Abstract
Formamide contains the four elements (C, H, O, and N) most required for life and it is attractive as a potential prebiotic starting material for nucleobase synthesis. In the presence of catalysts (for example, TiO2) and with moderate heating, formamide can pass surface energy barriers, yielding a complete set of nucleic bases and acyclonucleosides, and favoring both phosphorylations and transphosphorylations necessary for life. In the reaction mechanism, interaction with water seems to be an essential factor for the formamide molecule to function. In this paper, a formamide–water solution on a TiO$_2$ (anatase) surface is simulated using the molecular dynamics method, and activation energy calculations are performed for the temperature range of T = 250 K to T = 400 K. A correlation is established between the diffusion and density profiles for the formamide and water molecules on an anatase surface. Also, the calculated activation energies of the formamide–water–anatase and formamide–water–platinum systems are compared. A comparative analysis is performed of the behavior of formamide–water and ethanol–water interaction on the same (anatase and platinum) surfaces.
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Affiliation(s)
- E Dushanov
- Laboratory of Radiation Biology, JINR, 141980, Dubna, Moscow Region, Russia ; Institute of Nuclear Physics, 702132, Ulugbek, Tashkent, Uzbekistan
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38
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M. R. Muir J, Idriss H. Formaldehyde adsorption geometry and energies over TiO2(110) rutile surface. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.03.070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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39
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Di Mauro E, Saladino R, Trifonov EN. The path to life's origins. Remaining hurdles. J Biomol Struct Dyn 2013; 32:512-22. [PMID: 23582097 DOI: 10.1080/07391102.2013.783509] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Recent progress in abiotic syntheses, especially self-catalytic syntheses, as well as theoretical breakthroughs such as reconstruction of events of early molecular evolution and tracing repeat expansions in contemporary genomes, converge to a rather simple possible scenario of origin of life, notwithstanding the enormity of the problem. The scenario includes self-replicating RNA duplexes, supplemented by monomers and high-energy compounds that, as demonstrated or assumed, can all be synthesized abiotically. The self-replication would proceed with occasional mutational changes, propagated in later cycles. This audacious, as it may seem, walk toward the life origin already involves many laboratories, each exploring its own scenario. The one suggested in this outline seems to the authors well justified to engage in, while bypassing few steps to deal with later.
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Affiliation(s)
- Ernesto Di Mauro
- a Dipartimento di, Biologia e Biotecnologie "Charles Darwin" , Istituto Pasteur "Fondazione Cenci-Bolognetti", "Sapienza" Universita' , di Roma, P.leAldo Moro, 5, Rome , 00185 , Italy
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40
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Godlewski S, Szymonski M. Adsorption and Self-Assembly of Large Polycyclic Molecules on the Surfaces of TiO2 Single Crystals. Int J Mol Sci 2013; 14:2946-66. [PMID: 23364615 PMCID: PMC3588024 DOI: 10.3390/ijms14022946] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/14/2013] [Accepted: 01/16/2013] [Indexed: 11/20/2022] Open
Abstract
Titanium dioxide is one of the most frequently studied metal oxides, and its (110) rutile surface serves as a prototypical model for the surface science of such materials. Recent studies have also shown that the (011) surface is relatively easy for preparation in ultra-high vacuum (UHV) and that both the (110) and (011) surfaces could be precisely characterized using scanning tunneling microscopy (STM). The supramolecular self-assembly of organic molecules on the surfaces of titanium dioxide plays an important role in nanofabrication, and it can control the formation and properties of nanostructures, leading to wide range of applications covering the fields of catalysis, coatings and fabrication of sensors and extends to the optoelectronic industry and medical usage. Although the majority of experiments and theoretical calculations are focused on the adsorption of relatively small organic species, in recent years, there has been increasing interest in the properties of larger molecules that have several aromatic rings in which functional units could also be observed. The purpose of this review is to summarize the achievements in the study of single polycyclic molecules and thin layers adsorbed onto the surfaces of single crystalline titanium dioxide over the past decade.
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Affiliation(s)
- Szymon Godlewski
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Reymonta 4, 30-059 Krakow, Poland.
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41
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McGill PR, Muir JMR, Idriss H, Söhnel T. Formamide adsorption over the TiO2 (110) surface: a theoretical study. RSC Adv 2013. [DOI: 10.1039/c3ra41286e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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42
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Saladino R, Botta G, Pino S, Costanzo G, Di Mauro E. Genetics first or metabolism first? The formamide clue. Chem Soc Rev 2012; 41:5526-65. [PMID: 22684046 DOI: 10.1039/c2cs35066a] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Life is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, and carbon). The transmissible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information, of living and non-living. The origin-of-life quest has long been split into several attitudes exemplified by the aphorisms "genetics-first" or "metabolism-first". Recently, the opposition between these approaches has been solved by more unitary theoretical and experimental frames taking into account energetic, evolutionary, proto-metabolic and environmental aspects. Nevertheless, a unitary and simple chemical frame is still needed that could afford both the precursors of the synthetic pathways eventually leading to RNA and to the key components of the central metabolic cycles, possibly connected with the synthesis of fatty acids. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, and were embedded under physical-chemical conditions favourable for the onset of both. The singleness of such a prebiotically productive chemical process would partake of Darwinian advantages over more complex fragmentary chemical systems. The prebiotic chemistry of formamide affords in a single and simple physical-chemical frame nucleic bases, acyclonucleosides, nucleotides, biogenic carboxylic acids, sugars, amino sugars, amino acids and condensing agents. Thus, we suggest the possibility that formamide could have jointly provided the main components for the onset of both (pre)genetic and (pre)metabolic processes. As a note of caution, we discuss the fact that these observations only indicate possible solutions at the level of organic substrates, not at the systemic chemical level.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy.
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43
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Shankar R, Kolandaivel P, Senthil kumar L. Coordination and binding properties of zwitterionic glutathione with transition metal cations. Inorganica Chim Acta 2012. [DOI: 10.1016/j.ica.2012.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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44
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Mulkidjanian AY, Bychkov AY, Dibrova DV, Galperin MY, Koonin EV. Origin of first cells at terrestrial, anoxic geothermal fields. Proc Natl Acad Sci U S A 2012; 109:E821-30. [PMID: 22331915 PMCID: PMC3325685 DOI: 10.1073/pnas.1117774109] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
All cells contain much more potassium, phosphate, and transition metals than modern (or reconstructed primeval) oceans, lakes, or rivers. Cells maintain ion gradients by using sophisticated, energy-dependent membrane enzymes (membrane pumps) that are embedded in elaborate ion-tight membranes. The first cells could possess neither ion-tight membranes nor membrane pumps, so the concentrations of small inorganic molecules and ions within protocells and in their environment would equilibrate. Hence, the ion composition of modern cells might reflect the inorganic ion composition of the habitats of protocells. We attempted to reconstruct the "hatcheries" of the first cells by combining geochemical analysis with phylogenomic scrutiny of the inorganic ion requirements of universal components of modern cells. These ubiquitous, and by inference primordial, proteins and functional systems show affinity to and functional requirement for K(+), Zn(2+), Mn(2+), and phosphate. Thus, protocells must have evolved in habitats with a high K(+)/Na(+) ratio and relatively high concentrations of Zn, Mn, and phosphorous compounds. Geochemical reconstruction shows that the ionic composition conducive to the origin of cells could not have existed in marine settings but is compatible with emissions of vapor-dominated zones of inland geothermal systems. Under the anoxic, CO(2)-dominated primordial atmosphere, the chemistry of basins at geothermal fields would resemble the internal milieu of modern cells. The precellular stages of evolution might have transpired in shallow ponds of condensed and cooled geothermal vapor that were lined with porous silicate minerals mixed with metal sulfides and enriched in K(+), Zn(2+), and phosphorous compounds.
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Affiliation(s)
- Armen Y. Mulkidjanian
- School of Physics, University of Osnabrück, D-49069 Osnabrück, Germany
- A. N. Belozersky Institute of Physico-Chemical Biology and Schools of
| | | | - Daria V. Dibrova
- School of Physics, University of Osnabrück, D-49069 Osnabrück, Germany
- Bioengineering and Bioinformatics, Moscow State University, Moscow 119992, Russia; and
| | - Michael Y. Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
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45
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Saladino R, Crestini C, Pino S, Costanzo G, Di Mauro E. Formamide and the origin of life. Phys Life Rev 2012; 9:84-104. [DOI: 10.1016/j.plrev.2011.12.002] [Citation(s) in RCA: 194] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 12/06/2011] [Indexed: 11/16/2022]
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46
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Saladino R, Botta G, Pino S, Costanzo G, Di Mauro E. From the one-carbon amide formamide to RNA all the steps are prebiotically possible. Biochimie 2012; 94:1451-6. [PMID: 22738728 DOI: 10.1016/j.biochi.2012.02.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 02/16/2012] [Indexed: 01/07/2023]
Abstract
Formamide provides the raw material and the reaction leads connecting hydrogen cyanide HCN chemistry with higher complexity molecular structures. Formamide is liquid between 4 and 210 °C and, upon heating in the presence of one of several catalysts, affords nucleic bases, acyclonucleosides, carboxylic acids and aminoacids. In formamide in the presence of a source of phosphate, nucleosides are non-fastidiously phosphorylated in every position of the sugar residue, also yielding cyclic nucleotides. Guanine 3',5' cyclic nucleotide monophosphates polymerize to oligonucleotides, up to 30 nucleotides long. Adenine 3',5' cyclic nucleotide monophosphate reacts similarly but less efficiently. Preformed oligonucleotides may undergo terminal ligation in the absence of enzymes, thus allowing the formation of abiotically obtained long RNA chains.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy
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47
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Costanzo G, Pino S, Botta G, Saladino R, Di Mauro E. May cyclic nucleotides be a source for abiotic RNA synthesis? ORIGINS LIFE EVOL B 2011; 41:559-62. [PMID: 22139510 DOI: 10.1007/s11084-011-9249-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Accepted: 07/24/2011] [Indexed: 11/24/2022]
Abstract
Nucleic bases are obtained by heating formamide in the presence of various catalysts. Formamide chemistry also allows the formation of acyclonucleosides and the phosphorylation of nucleosides in every possible position, also affording 2',3' and 3',5' cyclic forms. We have reported that 3',5' cyclic GMP and 3',5' cyclic AMP polymerize in abiotic conditions yielding short oligonucleotides. The characterization of this reaction is being pursued, several of its parameters have been determined and experimental caveats are reported. The yield of non-enzymatic polymerization of cyclic purine nucleotides is very low. Polymerization is strongly enhanced by the presence of base-complementary RNA sequences.
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Affiliation(s)
- Giovanna Costanzo
- Istituto di Biologia e Patologia Molecolari CNR, P.le Aldo Moro, 5, 00185, Rome, Italy
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Affiliation(s)
- Katherine M. Buettner
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Ann M. Valentine
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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49
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Ferus M, Kubelík P, Civiš S. Laser Spark Formamide Decomposition Studied by FT-IR Spectroscopy. J Phys Chem A 2011; 115:12132-41. [DOI: 10.1021/jp205413d] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Ferus
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 18223 Prague 8, Czech Republic
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 182 21 Prague 8, Czech Republic
| | - P. Kubelík
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 18223 Prague 8, Czech Republic
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 182 21 Prague 8, Czech Republic
| | - S. Civiš
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 18223 Prague 8, Czech Republic
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50
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Saladino R, Brucato JR, De Sio A, Botta G, Pace E, Gambicorti L. Photochemical synthesis of citric acid cycle intermediates based on titanium dioxide. ASTROBIOLOGY 2011; 11:815-824. [PMID: 22007741 DOI: 10.1089/ast.2011.0652] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The emergence of the citric acid cycle is one of the most remarkable occurrences with regard to understanding the origin and evolution of metabolic pathways. Although the chemical steps of the cycle are preserved intact throughout nature, diverse organisms make wide use of its chemistry, and in some cases organisms use only a selected portion of the cycle. However, the origins of this cycle would have arisen in the more primitive anaerobic organism or even back in the proto-metabolism, which likely arose spontaneously under favorable prebiotic chemical conditions. In this context, we report that UV irradiation of formamide in the presence of titanium dioxide afforded 6 of the 11 carboxylic acid intermediates of the reductive version of the citric acid cycle. Since this cycle is the central metabolic pathway of contemporary biology, this report highlights the role of photochemical processes in the origin of the metabolic apparatus.
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Affiliation(s)
- Raffaele Saladino
- Department of Agrobiology and Agrochemistry, University of Tuscia, Viterbo, Italy
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