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Julve M. A tribute to Professor Giovanni De Munno. J COORD CHEM 2022. [DOI: 10.1080/00958972.2022.2109151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Miguel Julve
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Universitat de València, Paterna, València, Spain
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Bruno R, Mastropietro TF. Cytosine as a root to a nonconventional layered hydroxide nanostructure. J COORD CHEM 2022. [DOI: 10.1080/00958972.2022.2092847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Rosaria Bruno
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Rende, Cosenza, Italy
| | - Teresa F. Mastropietro
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Rende, Cosenza, Italy
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Leonarski F, D'Ascenzo L, Auffinger P. Nucleobase carbonyl groups are poor Mg 2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey. RNA (NEW YORK, N.Y.) 2019; 25:173-192. [PMID: 30409785 PMCID: PMC6348993 DOI: 10.1261/rna.068437.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/16/2018] [Indexed: 05/04/2023]
Abstract
Precise knowledge of Mg2+ inner-sphere binding site properties is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, which represents the main source of Mg2+ binding sites, contains a substantial number of assignment issues that blur our understanding of the functions of these ions. Here, following a previous study devoted to Mg2+ binding to nucleobase nitrogens, we surveyed nucleic acid X-ray structures from the PDB with resolutions ≤2.9 Å to classify the Mg2+ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether, and phosphodiester oxygen atoms. From this classification, we derived a set of "prior-knowledge" nucleobase Mg2+ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg2+ binding sites are fewer than expected since many of those are associated with misidentified Na+ or K+ We also emphasize that binding of Na+ and K+ to nucleic acids is much more frequent than anticipated. Overall, we provide evidence derived from X-ray structures that nucleobases are poor inner-sphere binders for Mg2+ but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline Mg2+ stereochemistry is observed, alternative placement of Na+, K+, or Ca2+ must be considered. We also critically examine the use of lanthanides (Yb3+, Tb3+) as Mg2+ substitutes in crystallography experiments.
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Affiliation(s)
- Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
| | - Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
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Gryl M, Kozieł M, Stadnicka KM. A proposal for coherent nomenclature of multicomponent crystals. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:53-58. [PMID: 32830778 PMCID: PMC6457040 DOI: 10.1107/s2052520618015858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/08/2018] [Indexed: 11/13/2022]
Abstract
Here a new, systematic, unambiguous and unified nomenclature for multicomponent materials is presented. The approach simplifies naming schemes of extraordinary co-crystals containing multiple building blocks with different charges. Although the presented examples of cytosine compounds cannot cover all possibilities, they clearly show that the new nomenclature is flexible and can be easily extended to other multicomponent materials.
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Affiliation(s)
- Marlena Gryl
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Kraków, 30-387, Poland
| | - Marcin Kozieł
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Kraków, 30-387, Poland
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Karthikeyan A, Zeller M, Thomas Muthiah P. Supramolecular architectures in metal(II) (Cd/Zn) halide/nitrate complexes of cytosine/5-fluorocytosine. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2018; 74:789-796. [PMID: 29973418 DOI: 10.1107/s2053229618007672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/23/2018] [Indexed: 11/10/2022]
Abstract
Three new metal(II)-cytosine (Cy)/5-fluorocytosine (5FC) complexes, namely bis(4-amino-1,2-dihydropyrimidin-2-one-κN3)diiodidocadmium(II) or bis(cytosine)diiodidocadmium(II), [CdI2(C4H5N3O)2], (I), bis(4-amino-1,2-dihydropyrimidin-2-one-κN3)bis(nitrato-κ2O,O')cadmium(II) or bis(cytosine)bis(nitrato)cadmium(II), [Cd(NO3)2(C4H5N3O)2], (II), and (6-amino-5-fluoro-1,2-dihydropyrimidin-2-one-κN3)aquadibromidozinc(II)-6-amino-5-fluoro-1,2-dihydropyrimidin-2-one (1/1) or (6-amino-5-fluorocytosine)aquadibromidozinc(II)-4-amino-5-fluorocytosine (1/1), [ZnBr2(C4H5FN3O)(H2O)]·C4H5FN3O, (III), have been synthesized and characterized by single-crystal X-ray diffraction. In complex (I), the CdII ion is coordinated to two iodide ions and the endocyclic N atoms of the two cytosine molecules, leading to a distorted tetrahedral geometry. The structure is isotypic with [CdBr2(C4H5N3O)2] [Muthiah et al. (2001). Acta Cryst. E57, m558-m560]. In compound (II), each of the two cytosine molecules coordinates to the CdII ion in a bidentate chelating mode via the endocyclic N atom and the O atom. Each of the two nitrate ions also coordinates in a bidentate chelating mode, forming a bicapped distorted octahedral geometry around cadmium. The typical interligand N-H...O hydrogen bond involving two cytosine molecules is also present. In compound (III), one zinc-coordinated 5FC ligand is cocrystallized with another uncoordinated 5FC molecule. The ZnII atom coordinates to the N(1) atom (systematic numbering) of 5FC, displacing the proton to the N(3) position. This N(3)-H tautomer of 5FC mimics N(3)-protonated cytosine in forming a base pair (via three hydrogen bonds) with 5FC in the lattice, generating two fused R22(8) motifs. The distorted tetrahedral geometry around zinc is completed by two bromide ions and a water molecule. The coordinated and nonccordinated 5FCs are stacked over one another along the a-axis direction, forming the rungs of a ladder motif, whereas Zn-Br bonds and N-H...Br hydrogen bonds form the rails of the ladder. The coordinated water molecules bridge the two types of 5FC molecules via O-H...O hydrogen bonds. The cytosine molecules are coordinated directly to the metal ion in each of the complexes and are hydrogen bonded to the bromide, iodide or nitrate ions. In compound (III), the uncoordinated 5FC molecule pairs with the coordinated 5FC ligand through three hydrogen bonds. The crystal structures are further stabilized by N-H...O, N-H...N, O-H...O, N-H...I and N-H...Br hydrogen bonds, and stacking interactions.
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Affiliation(s)
- Ammasai Karthikeyan
- School of Chemistry, Bharathidasan University, Tiruchirappalli 620 024, Tamilnadu, India
| | - Matthias Zeller
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
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Marino N, Bruno R, Armentano D, De Munno G. Structural studies on Ba(II) adducts of the cytosine nucleobase and its derivative 1-Methylcytosine. J COORD CHEM 2018. [DOI: 10.1080/00958972.2018.1437912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Nadia Marino
- Dipartimento di Chimica e Tecnologie Chimiche (CTC), Università della Calabria, Rende, Italy
| | - Rosaria Bruno
- Dipartimento di Chimica e Tecnologie Chimiche (CTC), Università della Calabria, Rende, Italy
| | - Donatella Armentano
- Dipartimento di Chimica e Tecnologie Chimiche (CTC), Università della Calabria, Rende, Italy
| | - Giovanni De Munno
- Dipartimento di Chimica e Tecnologie Chimiche (CTC), Università della Calabria, Rende, Italy
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Lippert B, Sanz Miguel PJ. Merging Metal–Nucleobase Chemistry With Supramolecular Chemistry. ADVANCES IN INORGANIC CHEMISTRY 2018. [DOI: 10.1016/bs.adioch.2017.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Ključarić V, Kobetić R, Rinkovec J, Kazazić S, Gembarovski D, Saftić D, Matić J, Ban Ž, Žinić B. ESI-MS studies of the non-covalent interactions between biologically important metal ions and N-sulfonylcytosine derivatives. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:998-1005. [PMID: 27405069 DOI: 10.1002/jms.3810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 06/16/2016] [Accepted: 07/08/2016] [Indexed: 06/06/2023]
Abstract
The aim of this report is to present the electrospray ionization mass spectrometry results of the non-covalent interaction of two biologically active ligands, N-1-(p-toluenesulfonyl)cytosine, 1-TsC, 1 and N-1-methanesulfonylcytosine, 1-MsC, 2 and their Cu(II) complexes Cu(1-TsC-N3)2 Cl2 , 3 and Cu(1-MsC-N3)2 Cl2 and 4 with biologically important cations: Na+ , K+ , Ca2+ , Mg2+ and Zn2+ . The formation of various complex metal ions was observed. The alkali metals Na+ and K+ formed clusters because of electrostatic interactions. Ca2+ and Mg2+ salts produced the tris ligand and mixed ligand complexes. The interaction of Zn2+ with 1-4 produced monometal and dimetal Zn2+ complexes as a result of the affinity of Zn2+ ions toward both O and N atoms. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Valentina Ključarić
- Ministry of Defense of the Republic of Croatia, "Dr. Franjo Tuđman" Croatian Defense Academy, Ilica 256 b, Zagreb, Croatia
| | - Renata Kobetić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia.
| | - Jasmina Rinkovec
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, 10 000, Zagreb, Croatia
| | - Snježana Kazazić
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | | | - Dijana Saftić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | - Josipa Matić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | - Željka Ban
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | - Biserka Žinić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia.
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