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Meléndez-López A, Cruz-Castañeda J, Negrón-Mendoza A, Ramos-Bernal S, Heredia A, Castro-Sanpedro L, Aguilar-Flores D. Gamma irradiation of adenine and guanine adsorbed into hectorite and attapulgite. Heliyon 2023; 9:e16071. [PMID: 37215897 PMCID: PMC10196509 DOI: 10.1016/j.heliyon.2023.e16071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
This study focuses on the radiolysis (up to 36 kGy) of guanine and adenine (nitrogenous bases) adsorbed in hectorite and attapulgite to highlight the potential role of clays as protective agents against ionizing radiation in prebiotic processes. In this framework, the study investigated the nitrogenous bases' behavior in two types of systems: a) aqueous suspension of adenine-clay systems and b) guanine-clay systems in the solid state. This research utilized spectroscopic and chromatographic techniques for its analytical purposes. Regardless of the reaction medium conditions, the results reveal that nitrogenous bases are stable under ionizing irradiation when adsorbed on both clays.
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Affiliation(s)
- A. Meléndez-López
- Instituto de Ciencias Nucleares, Circuito Exterior s/n, Ciudad Universitaria, Col. Universidad Nacional Autónoma de México, Deleg. Coyoacán, Apartado Postal 70-543, C.P. 04510, CDMX, Mexico
| | - J. Cruz-Castañeda
- Instituto de Ciencias Nucleares, Circuito Exterior s/n, Ciudad Universitaria, Col. Universidad Nacional Autónoma de México, Deleg. Coyoacán, Apartado Postal 70-543, C.P. 04510, CDMX, Mexico
| | - A. Negrón-Mendoza
- Instituto de Ciencias Nucleares, Circuito Exterior s/n, Ciudad Universitaria, Col. Universidad Nacional Autónoma de México, Deleg. Coyoacán, Apartado Postal 70-543, C.P. 04510, CDMX, Mexico
| | - S. Ramos-Bernal
- Instituto de Ciencias Nucleares, Circuito Exterior s/n, Ciudad Universitaria, Col. Universidad Nacional Autónoma de México, Deleg. Coyoacán, Apartado Postal 70-543, C.P. 04510, CDMX, Mexico
| | - A. Heredia
- Instituto de Ciencias Nucleares, Circuito Exterior s/n, Ciudad Universitaria, Col. Universidad Nacional Autónoma de México, Deleg. Coyoacán, Apartado Postal 70-543, C.P. 04510, CDMX, Mexico
| | - L.G. Castro-Sanpedro
- Facultad de Estudios Superiores Zaragoza Campus 2. Batalla 5 de Mayo s/n, Ejército de Oriente Zona Peñón, Iztapalapa, 09230, CDMX, Mexico
| | - D. Aguilar-Flores
- Facultad de Estudios Superiores Zaragoza Campus 2. Batalla 5 de Mayo s/n, Ejército de Oriente Zona Peñón, Iztapalapa, 09230, CDMX, Mexico
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Role of the Interchangeable Cations on the Sorption of Fumaric and Succinic Acids on Montmorillonite and its Relevance in Prebiotic Chemistry. ORIGINS LIFE EVOL B 2021; 51:87-116. [PMID: 34251577 DOI: 10.1007/s11084-021-09609-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/21/2021] [Indexed: 10/20/2022]
Abstract
It has been proposed that clays could have served as key factors in promoting the increase in complexity of organic matter in primitive terrestrial and extraterrestrial environments. The aim of this work is to study the adsorption-desorption of two dicarboxylic acids, fumaric and succinic acids, onto clay minerals (sodium and iron montmorillonite). These two acids may have played a role in prebiotic chemistry, and in extant biochemistry, they constitute an important redox couple (e.g. in Krebs cycle) in extant biochemistry. Smectite clays might have played a key role in the origins of life. The effect of pH on sorption has been tested; the analysis was performed by UV-vis and FTIR-ATR spectroscopy, X-ray diffraction and X-ray fluorescence. The results show that chemisorption is the main responsible of the adsorption processes among the dicarboxylic acids and clays. The role of the ion, present in the clay, is fundamental in the adsorption processes of dicarboxylic acids. These ions (sodium and iron) were selected due to their relevance on the geochemical environments that possibly existed into the primitive Earth. Different mechanisms are proposed to explain the sorption of dicarboxylic acids in the clay. In this work, we propose the formation of complexes among metal cations in the clays and dicarboxylic acids. The organic complexes were probably formed in the prebiotic environments enabling chemical processes, prior to the appearance of life. Thus, the data presented here are relevant to the origin of life studies.
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Huang H, Yang S, Liu Y, Yang Y, Li H, McLeod JA, Ding G, Huang J, Kang Z. Photocatalytic Polymerization from Amino Acid to Protein by Carbon Dots at Room Temperature. ACS APPLIED BIO MATERIALS 2019; 2:5144-5153. [DOI: 10.1021/acsabm.9b00805] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Siwei Yang
- State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | | | - Yucheng Yang
- State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | | | | | - Guqiao Ding
- State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
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Campbell T, Febrian R, Kleinschmidt HE, Smith KA, Bracher PJ. Quantitative Analysis of Glycine Oligomerization by Ion-Pair Chromatography. ACS OMEGA 2019; 4:12745-12752. [PMID: 31460397 PMCID: PMC6681977 DOI: 10.1021/acsomega.9b01492] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
This paper describes a method for the quantitative analysis of mixtures of glycine and its oligomers by ion-pair high-performance liquid chromatography (IP-HPLC), with a particular focus on applications in origins-of-life research. We demonstrate the identification of glycine oligomers (Gly n ) up to 14 residues long-the approximate detectable limit of their solubility in water-and measurement of the concentration of these species in the product mixture of an oligomerization reaction. The molar response factors for higher oligomers of glycine-which are impractical to obtain as pure samples-are extrapolated from direct analysis of pure standards of n = 3-6, which established a clear linear trend. We compare and contrast our method to those in previous reports with respect to accuracy and practicality. While the data reported here are specific to the analysis of oligomers of glycine, the approach should be applicable to the design of methods for the analysis of oligomerization of other amino acids.
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Ligand substitution in chromium(III)-aqua complexes by l-histidine: kinetic resolution of two long-lived intermediates. REACTION KINETICS MECHANISMS AND CATALYSIS 2019. [DOI: 10.1007/s11144-019-01637-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Perez-Benito JF, Nicolas-Rivases J. Kinetics of the chromium(III)/l
-glutamic acid complexation reaction: Formation, decay, and UV-vis spectrum of a long-lived intermediate. INT J CHEM KINET 2018. [DOI: 10.1002/kin.21185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Joaquin F. Perez-Benito
- Departamento de Ciencia de Materiales y Quimica Fisica, Seccion de Quimica Fisica, Facultad de Quimica; Universidad de Barcelona; Barcelona Spain
| | - Joan Nicolas-Rivases
- Departamento de Ciencia de Materiales y Quimica Fisica, Seccion de Quimica Fisica, Facultad de Quimica; Universidad de Barcelona; Barcelona Spain
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Iqubal MA, Sharma R, Jheeta S, Kamaluddin. Thermal Condensation of Glycine and Alanine on Metal Ferrite Surface: Primitive Peptide Bond Formation Scenario. Life (Basel) 2017; 7:E15. [PMID: 28346388 PMCID: PMC5492137 DOI: 10.3390/life7020015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/13/2017] [Accepted: 03/24/2017] [Indexed: 11/17/2022] Open
Abstract
The amino acid condensation reaction on a heterogeneous mineral surface has been regarded as one of the important pathways for peptide bond formation. Keeping this in view, we have studied the oligomerization of the simple amino acids, glycine and alanine, on nickel ferrite (NiFe₂O₄), cobalt ferrite (CoFe₂O₄), copper ferrite (CuFe₂O₄), zinc ferrite (ZnFe₂O₄), and manganese ferrite (MnFe₂O₄) nanoparticles surfaces, in the temperature range from 50-120 °C for 1-35 days, without applying any wetting/drying cycles. Among the metal ferrites tested for their catalytic activity, NiFe₂O₄ produced the highest yield of products by oligomerizing glycine to the trimer level and alanine to the dimer level, whereas MnFe₂O₄ was the least efficient catalyst, producing the lowest yield of products, as well as shorter oligomers of amino acids under the same set of experimental conditions. It produced primarily diketopiperazine (Ala) with a trace amount of alanine dimer from alanine condensation, while glycine was oligomerized to the dimer level. The trend in product formation is in accordance with the surface area of the minerals used. A temperature as low as 50 °C can even favor peptide bond formation in the present study, which is important in the sense that the condensation process is highly feasible without any sort of localized heat that may originate from volcanoes or hydrothermal vents. However, at a high temperature of 120 °C, anhydrides of glycine and alanine formation are favored, while the optimum temperature for the highest yield of product formation was found to be 90 °C.
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Affiliation(s)
- Md Asif Iqubal
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247 667, Uttarakhand, India.
| | - Rachana Sharma
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247 667, Uttarakhand, India.
| | - Sohan Jheeta
- Network of Researchers on Horizontal Gene Transfer and Last Universal, Common Ancestor Leeds, Leeds LS7 3RB, UK.
| | - Kamaluddin
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247 667, Uttarakhand, India.
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Lambert JF. Adsorption and polymerization of amino acids on mineral surfaces: a review. ORIGINS LIFE EVOL B 2008; 38:211-42. [PMID: 18344011 DOI: 10.1007/s11084-008-9128-3] [Citation(s) in RCA: 224] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Accepted: 01/24/2008] [Indexed: 10/22/2022]
Abstract
The present paper offers a review of recent (post-1980) work on amino acid adsorption and thermal reactivity on oxide and sulfide minerals. This review is performed in the general frame of evaluating Bernal's hypothesis of prebiotic polymerization in the adsorbed state, but written from a surface scientist's point of view. After a general discussion of the thermodynamics of the problem and exactly what effects surfaces should have to make adsorbed-state polymerization a viable scenario, we examine some practical difficulties in experimental design and their bearing on the conclusions that can be drawn from extant works, including the relevance of the various available characterization techniques. We then present the state of the art concerning the mechanisms of the interactions of amino acids with mineral surfaces, including results from prebiotic chemistry-oriented studies, but also from several different fields of application, and discuss the likely consequences for adsorption selectivities. Finally, we briefly summarize the data concerning thermally activated amide bond formation of adsorbed amino acids without activating agents. The reality of the phenomenon is established beyond any doubt, but our understanding of its mechanism and therefore of its prebiotic potential is very fragmentary. The review concludes with a discussion of future work needed to fill the most conspicuous gaps in our knowledge of amino acids/mineral surfaces systems and their reactivity.
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Affiliation(s)
- Jean-François Lambert
- Laboratoire de Réactivité de Surface, UMR CNRS 7609, UPMC Univ Paris 06 and CNRS, Paris, France.
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Rimola A, Rodríguez-Santiago L, Ugliengo P, Sodupe M. Is the Peptide Bond Formation Activated by Cu2+ Interactions? Insights from Density Functional Calculations. J Phys Chem B 2007; 111:5740-7. [PMID: 17469869 DOI: 10.1021/jp071071o] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The catalytic role that Cu(2+) cations play in the peptide bond formation has been addressed by means of density functional calculations. First, the Cu(2+)-(glycine)2 --> Cu(2+)-(glycylglycine) + H2O reaction was investigated since mass spectrometry low collision activated dissociation (CAD) spectra of Cu(2+)-(glycine)2 led to the elimination of a water molecule, which suggested that an intracomplex peptide bond formation might have occurred. Results show that this intracomplex condensation is associated to a very high free energy barrier (97 kcal mol(-1)) and reaction free energy (66 kcal mol(-1)) because of the loss of metal coordination during the reaction. Second, on the basis of the salt-induced peptide formation theory, the condensation reaction between two glycines was studied in aqueous solution using discrete water molecules and the conductor polarized continuum model (CPCM) continuous method. It is found that the synergy between the interaction of glycines with Cu(2+) and the presence of water molecules acting as proton-transfer helpers significantly lower the activation barrier (from 55 kcal/mol for the uncatalyzed system to 20 kcal/mol for the Cu(2+) solvated system) which largely favors the formation of the peptide bond.
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Affiliation(s)
- A Rimola
- Departament de Química, Universitat Autonoma de Barcelona, Bellaterra 08193, Spain
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Greenwell HC, Coveney PV. Layered double hydroxide minerals as possible prebiotic information storage and transfer compounds. ORIGINS LIFE EVOL B 2006; 36:13-37. [PMID: 16372196 DOI: 10.1007/s11084-005-2068-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Accepted: 06/17/2005] [Indexed: 10/25/2022]
Abstract
One of the fundamental difficulties when considering the origin of life on Earth is the identification of an emergent system that not only replicated, but also had the capacity to undergo discrete mutation in such a way that following generations might inherit and pass on the mutation. We speculate that the layered double hydroxide (LDH) minerals are plausible candidates for a proto-RNA molecule. We describe a hypothetical LDH-like system which, when intercalated with certain anions, forms crystals with a high degree of internal order giving rise to novel information storage structures in which replication fidelity is maintained, a concept we use to propose an explanation for interstratification in terephthalate LDHs. The external surfaces of these hypothetical crystals provide active sites whose structure and chemistry is dictated by the internal information content of the LDH. Depending on the LDH polytype, the opposing external surfaces of a crystal may give rise to reactive sites that are either complementary or mirror images of each other, and so may be chiral. We also examine similarities between these proposed "proto-RNA" structures and the DNA that encodes the hereditary information in life today, concluding with a hypothetical scenario wherein these proto-RNA molecules predated the putative RNA-world.
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Affiliation(s)
- H Chris Greenwell
- Centre for Computational Science, Christopher Ingold Laboratory, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
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Bujdák J, Rode BM. Preferential amino acid sequences in alumina-catalyzed peptide bond formation. J Inorg Biochem 2002; 90:1-7. [PMID: 12009249 DOI: 10.1016/s0162-0134(02)00395-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The catalytic effect of activated alumina on amino acid condensation was investigated. The readiness of amino acids to form peptide sequences was estimated on the basis of the yield of dipeptides and was found to decrease in the order glycine (Gly), alanine (Ala), leucine (Leu), valine (Val), proline (Pro). For example, approximately 15% Gly was converted to the dipeptide (Gly(2)), 5% to cyclic anhydride (cyc(Gly(2))) and small amounts of tri- (Gly(3)) and tetrapeptide (Gly(4)) were formed after 28 days. On the other hand, only trace amounts of Pro(2) were formed from proline under the same conditions. Preferential formation of certain sequences was observed in the mixed reaction systems containing two amino acids. For example, almost ten times more Gly-Val than Val-Gly was formed in the Gly+Val reaction system. The preferred sequences can be explained on the basis of an inductive effect that side groups have on the nucleophilicity and electrophilicity, respectively, of the amino and carboxyl groups. A comparison with published data of amino acid reactions in other reaction systems revealed that the main trends of preferential sequence formation were the same as those described for the salt-induced peptide formation (SIPF) reaction. The results of this work and other previously published papers show that alumina and related mineral surfaces might have played a crucial role in the prebiotic formation of the first peptides on the primitive earth.
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Affiliation(s)
- J Bujdák
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, 842 36 Bratislava, Slovak Republic.
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