Study of the chelating capacity of nucleobase analogs with biological interest: XRD structural study and ab initio molecular orbital calculations on 1-methyl and 1,6,7-trimethyllumazine

Acuña-Cueva, Esther R.; Faure, R.; Jiménez‐Pulido, Sonia B.; Moreno‐Carretero, Miguel N.; Peña-Ruiz, Tomás

doi:10.1016/j.molstruc.2004.03.022

Cited by 6 publications

(5 citation statements)

References 12 publications

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“…The second angle corresponds to the bite angle of the rigid chelating lumazine moiety. The Cu−O(4) bond distance of 2.449 Å is much longer than the usual values in lumazine derivatives complexes, ,, which allows us to define the geometry as tetrahedral with considerable trigonal planar distortion (“3 + 1”) with N(5), N(61), and S(63) in the basal plane and O(4) weakly coordinated in the apical position; in agreement with this, the sum of the angles S(63)−Cu−N(61), N(61)−Cu−N(5), and N(5)−Cu−S(63) (357.6°) is clearly closer to the expected value for a trigonal-planar configuration (360°) than the ideal value for a tetrahedron (328.5°). The Cu···Cu distance (2.876(2) Å) is almost equal to the sum of the van der Waals radius of copper (2.8 Å), indicating a minimum interaction between two copper atoms …”

Section: Resultssupporting

confidence: 64%

“…The ligand crystallized as hemihydrate. The lumazine skeleton displays a roughly planar geometry like related ligands, , so the pyrimidine and pyrazine rings exhibit a dihedral angle of 1.6(1)°. The bond lengths of the carbonyl groups are slightly different (C(2)O(2), 1.210(3) Å; C(4)O(4), 1.222(3) Å) 5,21 whereas bond lengths at the thiosemicarbazone moiety indicate an extensive delocalization as usual on the thiosemicarbazone derivatives which is clearly reflected in the C−S distance at 1.673(3) Å intermediate between a single and double bond character (1.82 and 1.56 Å, respectively) and the N−N (1.375(3) Å) distance, less than the 1.44 Å accepted as typical of single bonds .…”

Section: Resultsmentioning

confidence: 99%

“…5−10 cm -1 ) of the bands assignable to the carbonyl groups of the lumazine (1720 and 1685 cm -1 in the free TSCLMH) and the strong up-wavenumber shift (ca. 20−40 cm -1 ) of the CC and CN stretching vibrations indicate the N(5)−metal ligation, whereas carbonylic O(4) atoms are weak or null coordinated. ,,, In general, the greatest shifts take place in the bands related to the thiosemicarbazone moiety. Bands assigned to hydrazonic ν(N−H) do not appear in the NiL, ZnL, and CdL complexes indicating the deprotonation of the NH group and coordination via the thiolate sulfur.…”

Section: Resultsmentioning

confidence: 99%

“…A large number of complexes of different metals with the methylated lumazine derivatives (Chart ) ligands have been studied, and the biological activity of some of them has been explored . The structures and spectral properties of several metal complexes of lumazine derivatives, which usually coordinate to the metal ions in a bidentate pattern with N(5) and O(4) atoms (Chart ), have been already studied by our group 1 …”

Section: Introductionmentioning

confidence: 99%

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Versatile Coordinative Abilities of a New Hybrid Pteridine−Thiosemicarbazone Ligand: Crystal Structure, Spectroscopic Characterization, and Luminescent Properties

et al. 2008

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The synthesis and characterization of the first thiosemicarbazone-lumazine (TSCLMH=the thiosemicarbazone of 6-acetyl-1,3,7-trimethyllumazine) hybrid ligand is reported. The influence of the conformation of this compound on its energy and the atomic contribution to the molecular orbitals have been theoretically investigated. Ni(II), Cu(I), Zn(II), and Cd(II) complexes of this ligand have been synthesized and characterized by elemental analysis, thermogravimetric studies, IR, 1H, 13C, and 15N NMR, and UV-vis-NIR spectroscopy, magnetic measurements, and X-ray crystallography. Four types of coordination modes for the ligand may be predicted: (a) double bidentate; (b) tetradentate; (c) tridentate; (d) bidentate. Structures of representative complexes of types a, b, and d have been determined by X-ray crystallography. In the [Cu(TSCLMH)]2(ClO4)2 complex, TSCLMH acts as a doubly bidentate bridging ligand forming a dimer with a Cu...Cu distance of 2.876 A. The geometry around the metal ion is trigonally distorted tetrahedral with a relatively long (four-atom) bridge between the metal centers instead of the shorter, mainly single atom, bridges present in other thiosemicarbazone derivatives complexes. In the [Cd(NO3)2(TSCLMH)(EtOH)] complex, the metal ion displays eight-coordinated geometry with the TSCLMH ligand acting in a tetradentate planar fashion and two nitrate anions, one monodentate and the other bidentate. The coordination polyhedron in [Cd(TSCLM)2(H2O)].MeOH.2H2O is a square pyramid with two monoanionic ligands acting as bidentate NS donors and a water molecule completing the coordination sphere. Fluorescence spectroscopic properties of TSCLMH have been studied as well as the changes in position and intensity of fluorescence bands caused by the complexation with different metal ions (Ni2+, Cu+, Zn2+, Cd2+).

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Section: Resultssupporting

confidence: 64%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Versatile Coordinative Abilities of a New Hybrid Pteridine−Thiosemicarbazone Ligand: Crystal Structure, Spectroscopic Characterization, and Luminescent Properties

et al. 2008

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“…Since then it has been reported in several studies on related lumazines. Characterization data for lumazine 3 is limited to a melting point, elemental analysis, and UV/vis peaks; no NMR, MS, or IR data have been reported to date. − Similarly, characterization data for lumazine 4 is limited to a melting point, elemental analysis, and UV/vis. − To date, no reports detailing the isolation of lumazines 3 or 4 from natural materials have been published.…”

Section: Resultsmentioning

confidence: 99%

Isolation, Structural Elucidation, and Synthesis of Lepteridine From Ma̅nuka (Leptospermum scoparium) Honey

Daniels

Prijic

Meidinger

et al. 2016

J. Agric. Food Chem.

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Ma̅nuka honey, made from the nectar of Leptospermum scoparium, has garnered scientific and economical interest due to its nonperoxide antibacterial activity. Biomarkers for genuine ma̅nuka honey are increasingly in demand due to the presence of counterfeit ma̅nuka honey. This work reports the identification of a compound previously unreported in ma̅nuka honey by HPLC, and determination of the structure of the as 3,6,7-trimethyllumazine using NMR, MS, IR, and UV/vis spectroscopy. This assignment was confirmed by total synthesis. The natural product, renamed lepteridine, was only observed in ma̅nuka honeys and could potentially serve as a biomarker for genuine ma̅nuka honey.

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XRD and DFT-modelized structures of a pteridine-2,4(1H,3H)-dithione/N,N′-dimethylformamide H-bonded cluster (2:2). MO study of the coordination ability

2011

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The title compound, C(6)H(4)N(4)S(2)·C(3)H(7)NO, crystallizes in the monoclinic space group C 2/c with a = 26.673(5), b = 5.397(1), c = 16.522(3) Å, β = 95.49(3)°, Z = 8, R = 0.0461 for 1891 reflections with I > 2σ(I) and 174 parameters (4 restraints). Single pteridine-2,4(1 H,3 H)-dithione and dimethylformamide molecules are packed via N-H···O and N-H···N hydrogen bonds into centrosymmetric clusters containing two molecules of each class; these are roughly planar and placed into two different sets of planes -both containing the [-1,0,2] direction- mutually angled by 77.8°. Despite the distance between two neighbor planes in each set is ca. 3.4 Å, the analysis of π,π-stacking interactions shows too large slippage distance between aromatic rings from contiguous planes. Additional σ-π interactions between S2, S4 and O1S atoms and pyrazine or pyrimidine rings from adjacent molecules are present. The structure for the cluster [DTLM-DMF](2) has been simulated by using the density functionals B1B95 (6-31 G(d) and 6-31+G(d) basis sets) and M06-2X (6-31 G(d) basis set). As a result, the M06-2X/6-31 G(d) approach provides the best agreement with the experimental XRD data. For a better evaluation of the intermolecular interactions, the superposition of two dimeric adducts [DTLM-DMF](2) has been modelized. The binding capability of DTLM ligand was simulated on systems containing two metal-binding modes to palladium (N5-S4 and N1-S2) with different chelate size. The analysis of the frontier orbitals points out that the link with the metallic centers will take place through the sulfur atoms.

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Study of the chelating capacity of nucleobase analogs with biological interest: XRD structural study and ab initio molecular orbital calculations on 1-methyl and 1,6,7-trimethyllumazine

Cited by 6 publications

References 12 publications

Versatile Coordinative Abilities of a New Hybrid Pteridine−Thiosemicarbazone Ligand: Crystal Structure, Spectroscopic Characterization, and Luminescent Properties

Versatile Coordinative Abilities of a New Hybrid Pteridine−Thiosemicarbazone Ligand: Crystal Structure, Spectroscopic Characterization, and Luminescent Properties

Isolation, Structural Elucidation, and Synthesis of Lepteridine From Ma̅nuka (Leptospermum scoparium) Honey

XRD and DFT-modelized structures of a pteridine-2,4(1H,3H)-dithione/N,N′-dimethylformamide H-bonded cluster (2:2). MO study of the coordination ability

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