Highest Reported Denticity of a Synthetic Nucleoside in the Unprecedented Tetradentate Mode of Acyclovir

Pérez-Toro, Inmaculada; Domínguez‐Martín, Alicia; Choquesillo-Lazarte, Duane; González‐Pérez, Josefa María; Castiñeiras, Alfonso; Niclós‐Gutiérrez, Juan

doi:10.1021/acs.cgd.8b00893

Cited by 6 publications

(10 citation statements)

References 24 publications

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“…Along the past decades, mainly three research groups have contributed to enlighten the metal binding abilities of acyclovir [ 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 ]. According to this information, acv preferentially acts as monodentate ligand, involving the purine moiety, with the M-N7(acv) coordination bond acting in cooperation with an intramolecular interligand D-H···O6(acv) interaction (D = oxygen or nitrogen H-donor atoms) [ 8 , 10 , 11 , 13 , 16 , 18 , 19 , 20 , 21 , 22 ]. Besides this preferred molecular recognition pattern, further studies have reported more unconventional modes for acv such as the N7,O6-chelating mode or even the tetradentate μ 3 -N7,O6,O(e),O(ol) mode [ 12 , 14 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Deciphering the H-Bonding Preference on Nucleoside Molecular Recognition through Model Copper(II) Compounds

et al. 2021

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The synthetic nucleoside acyclovir is considered an outstanding model of the natural nucleoside guanosine. With the purpose of deepening on the influence and nature of non-covalent interactions regarding molecular recognition patterns, three novel Cu(II) complexes, involving acyclovir (acv) and the ligand receptor N-(2-hydroxyethyl)ethylenediamine (hen), have been synthesized and thoroughly characterized. The three novel compounds introduce none, one or two acyclovir molecules, respectively. Molecular recognition has been evaluated using single crystal X-ray diffraction. Furthermore, theoretical calculations and other physical methods such as thermogravimetric analysis, infrared and UV-Vis spectroscopy, electron paramagnetic resonance and magnetic measurements have been used. Theoretical calculations are in line with experimental results, supporting the relevance of the [metal-N7(acv) + H-bond] molecular recognition pattern. It was also shown that (hen)O-H group is used as preferred H-donor when it is found within the basal coordination plane, since the higher polarity of the terminal (hen)O-H versus the N-H group favours its implication. Otherwise, when (hen)O-H occupies the distal coordination site, (hen)N-H groups can take over.

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Section: Introductionmentioning

confidence: 99%

Deciphering the H-Bonding Preference on Nucleoside Molecular Recognition through Model Copper(II) Compounds

et al. 2021

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“…This review emphasizes the relevance of the N(heterocyclic)-H tautomeric possibilities in neutral and protonated forms of such kinds of natural or synthetic closely related N-heterocyclic ligands. Recent reports from our groups extend these points of view to the guanine-synthetic acyclovir as a ligand [52][53][54]. Now we have the opportunity to deep into the relevance of these factors on the basis of the available crystallographic results related to cationic forms of Hdap, its salts and inner-or out-sphere metal complexes.…”

Section: Structural Insides On N(heterocyclic)-proton Affinities H-tmentioning

confidence: 97%

Anion–Cation Recognition Pattern, Thermal Stability and DFT-Calculations in the Crystal Structure of H2dap[Cd(HEDTA)(H2O)] Salt (H2dap = H2(N3,N7)-2,6-Diaminopurinium Cation)

et al. 2020

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The proton transfer between equimolar amounts of [Cd(H 2 EDTA)(H 2 O)] and 2,6-diaminopurine (Hdap) yielded crystals of the out-of-sphere metal complex H 2 (N3,N7)dap [Cd(HEDTA)(H 2 O)]·H 2 O (1) that was studied by single-crystal X-ray diffraction, thermogravimetry, FT-IR spectroscopy, density functional theory (DFT) and quantum theory of "atoms-in-molecules" (QTAIM) methods. The crystal was mainly dominated by H-bonds, favored by the observed tautomer of the 2,6-diaminopurinium(1+) cation. Each chelate anion was H-bonded to three neighboring cations; two of them were also connected by a symmetry-related anti-parallel π,π-staking interaction. Our results are in clear contrast with that previously reported for H 2 (N1,N9)ade [Cu(HEDTA) (H 2 O)]·2H 2 O (EGOWIG in Cambridge Structural Database (CSD), Hade = adenine), in which H-bonds and π,π-stacking played relevant roles in the anion-cation interaction and the recognition between two pairs of ions, respectively. Factors contributing in such remarkable differences are discussed on the basis of the additional presence of the exocyclic 2-amino group in 2,6-diaminopurinium(1+) ion. Crystals 2020, 10, 304 2 of 15 reported analog of adenine, [Cu(HEDTA)(H 2 O)]·2H 2 O [5,32], was also performed. The H-bonding networks that are established at both faces of H 2 dap were also studied using DFT calculations and the relative strength of each H-bond was estimated using the QTAIM theory. The antiparallel π,π-stacking interactions that were formed between the cations were also studied, focusing on the effect of the counter-ions. Materials and Methods ReagentsH 4 EDTA acid (TCI), Hdap (Alfa Aesar) and CdCO 3 (Alfa Aesar) were used as received. CrystallographyA colorless needle crystal of H 2 dap[Cd(HEDTA)(H 2 O)]·H 2 O (1) was mounted on a glass fiber and used for data collection. Crystal data were collected at 100(2) K, using a Bruker D8 VENTURE PHOTON III-14 diffractometer. Graphite-monochromated MoK(α) radiation (λ = 0.71073 Å) was used throughout. The data were processed with APEX2 [33] and corrected for absorption using SADABS (transmissions factors: 1.000-0.962) [34]. The structure was solved by direct methods using the program SHELXS-2013 [35] and refined by full-matrix least-squares techniques against F 2 using SHELXL-2013 [35]. Positional and anisotropic atomic displacement parameters were refined for all non-hydrogen atoms. Hydrogen atoms were located in difference maps and included as fixed contributions riding on attached atoms with isotropic thermal parameters 1.2/1.5 times those of their carrier atoms. Criteria of a satisfactory complete analysis were the ratios of 'rms' shift to standard deviation less than 0.001 and no significant features in final difference maps. Atomic scattering factors were taken from the International Tables for Crystallography [36]. Molecular graphics were plotted with PLATON [37]. A summary of the crystal data, experimental details and refinement results are listed in Table 1. Crystallographic data for 1 has been deposited in the Cambridg...

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“…This role will cooperate with other N or O donors of both nucleosides. The maximum expression of this is provided by the acv-H anion (which coexists with molecular acv) in the polymer DIDJUY [9]. It should also be noted that, while O6-acv is involved as H-acceptor in intramolecular interligand H-bonds, the H-atoms of the exocyclic -N(6)H 2 group of 9heade make it a hydrogen donor in such interactions.…”

Section: Introductionmentioning

confidence: 99%

The Copper(II)-Thiodiacetate (tda) Chelate as Efficient Receptor of N9-(2-Hydroxyethyl)Adenine (9heade): Synthesis, Molecular and Crystal Structures, Physical Properties and DFT Calculations of [Cu(tda)(9heade)(H2O)]·2H2O

Rosales-Martínez,

Matilla-Hernádez,

Choquesillo-Lazarte

et al. 2023

Molecules

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Considering that Cu(tda) chelate (tda: dithioacetate) is a receptor for adenine and related 6-aminopurines, this study reports on the synthesis, molecular and crystal structures, thermal stability, spectral properties and DFT calculations related to [Cu(tda)(9heade)(H2O)]·2H2O (1) [9heade: N9-(2-hydroxyethyl)adenine]. Concerning the molecular recognition of (metal chelate)-(adenine synthetic nucleoside), 1 represents an unprecedented metal binding pattern (MBP) for 9heade. However, unprecedentedly, the Cu(tda)-9heade molecular recognition in 1 is essentially featured in the Cu-N1(9heade) bond, without any N6-H⋯O(carboxyl tda) interligand interaction. Nevertheless, N1 being the most basic donor for N9-substituted adenines, this Cu-N1 bond is now assisted by an O2–water-mediated interaction (N6-H⋯O2 and O2⋯Cu weak contact). Also, in the crystal packing, the O-H(ol) of 9heade interacts with its own adenine moiety as a result of an O3–water-mediated interaction (O(ol)-H⋯O3 plus O3-H36⋯π(adenine moiety)). Both water-mediated interactions seem to be responsible for serious alterations in the physical properties of crystalline or grounded samples. Density functional theory calculations were used to evaluate the interactions energetically. Moreover, the quantum theory of atoms-in-molecules (QTAIM), in combination with the noncovalent interaction plot (NCIPlot), was used to analyze the interactions and rationalize the existence and relative importance of hydrogen bonding, chalcogen bonding and π-stacking interactions. The novelty of this work resides in the discovery of a novel binding mode for N9-(2-hydroxyethyl)adenine. Moreover, the investigation of the important role of water in the solid state of 1 is also relevant, along with the chalcogen bonding interactions demonstrated by the density functional theory (DFT) study.

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Highest Reported Denticity of a Synthetic Nucleoside in the Unprecedented Tetradentate Mode of Acyclovir

Cited by 6 publications

References 24 publications

Deciphering the H-Bonding Preference on Nucleoside Molecular Recognition through Model Copper(II) Compounds

Deciphering the H-Bonding Preference on Nucleoside Molecular Recognition through Model Copper(II) Compounds

Anion–Cation Recognition Pattern, Thermal Stability and DFT-Calculations in the Crystal Structure of H2dap[Cd(HEDTA)(H2O)] Salt (H2dap = H2(N3,N7)-2,6-Diaminopurinium Cation)

The Copper(II)-Thiodiacetate (tda) Chelate as Efficient Receptor of N9-(2-Hydroxyethyl)Adenine (9heade): Synthesis, Molecular and Crystal Structures, Physical Properties and DFT Calculations of [Cu(tda)(9heade)(H2O)]·2H2O

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