A Cyclophane Receptor for the Selective Complexation of Adenine Derivatives in Water

Rotger, Carmen; González, José Fernando; Ballester, Pablo; Deyà, Pere M.; Costa, Antoni

doi:10.1021/jo00095a027

Cited by 13 publications

(7 citation statements)

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“…The aminocalix[4]arenes AC4a and AC4c (Scheme 1), prepared according to literature procedures, 15 were used as tetrahydrochloride salts, as were the larger aminocalix [6]arene (AC6) and aminocalix [8]arene (AC8), synthesized from the known 15,16 calixarenes C6 and C8 by reaction with trimethylamine. It is known that in tetra-O-alkylcalix[4]arenes the methyl group is too small to suppress the oxygen-through-the annulus rotation.…”

Section: Nmr Characterization Of the Compoundsmentioning

confidence: 99%

“…Molecular recognition of nucleotides by synthetic receptors [1][2][3][4][5][6][7][8][9][10][11] and small ligand interactions with nucleic acids 12, 13 have recently received much attention. Macrocyclic polyamines, when protonated, bind strongly to nucleotides via electrostatic interactions and/or hydrogen bonding between the cationic ammonium groups of the receptor and the negatively charged nucleotide phosphate groups.…”

Section: Aims and Introductionmentioning

confidence: 99%

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Interactions between aminocalixarenes and nucleotides or nucleic acids †

Shi¹,

Schneider²

1999

J. Chem. Soc., Perkin Trans. 2

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Four calixarenes with (trimethylammonium)methyl groups at the phenyl rings in the upper rim were prepared. Association constants K with mononucleotides were determined in D 2 O by NMR shift titration, partially also by fluorescence competition titration using ANS as dye. The complexation free energies ∆G obtained with the derivatives of the calix[4]cone (AC4c) and the calix[4]-1,3-alternate (AC4a) conformation were similar, but increased from AMP (18 ± 1 kJ mol Ϫ1 ) to ADP (20 ± 1 kJ mol Ϫ1 ), to ATP (22 ± 1 kJ mol Ϫ1 ). With the calix[6] derivative (AC6) the corresponding values were 22, 24, 27 kJ mol Ϫ1 , with the calix[8] host (AC8) 24, 26, 28 kJ mol Ϫ1 , respectively. The large contribution of salt bridging to the complexation was obvious from the ∆G difference between adenosine and e.g. AMP (with the calix[4]cone derivative 5.6 and 17.7 kJ mol Ϫ1 , respectively). Affinity differences between different nucleobases increased moderately with the size of the macrocyclic host, e.g. ∆∆G between AMP and TMP was 1 kJ mol Ϫ1 with calix[4]cone, 2 kJ mol Ϫ1 with calix[6], and 3 kJ mol Ϫ1 with calix[8] compounds. The results are in line with computer simulated complex structures in which the nucleobase or sugar parts are only partially inserted into the calix cavity. This agrees with the observed complexation induced NMR shifts (CIS), which are small but increase with the ring size of the host. Noticeably the CIS values are substantially larger for much weaker bound nucleosides.Affinities of the four aminocalixarenes with double-stranded calf thymus (CT) DNA, with polydA*polydT and with polydG*polydC were characterized by ∆T m of the double-strand denaturation temperature and by fluorimetric assays using ethidium bromide (C 50 values). The calix[4]cone derivative AC4c shows, due to the four positive charges converging at one side, the strongest effects. They surpass spermine although this also bears four protonated ammonium groups, indicating additional binding contributions from the phenyl moieties. The larger, more flexible calix[6]-and calix[8]-derivatives AC6 and AC8 show only small affinity increases in spite of their 6 or 8 positive charges. Preliminary molecular modeling studies indicate that based on the distances between the ammonium centers only partial contact of all centers to the groove phosphates can materialize. The ligands AC4c, AC4a and AC6 exhibit a remarkable preference for DNA in comparison to RNA mimics.

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Section: Nmr Characterization Of the Compoundsmentioning

confidence: 99%

Section: Aims and Introductionmentioning

confidence: 99%

Interactions between aminocalixarenes and nucleotides or nucleic acids †

Shi¹,

Schneider²

1999

J. Chem. Soc., Perkin Trans. 2

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“…The lower squaramide Distances between minima, represented by stars, and hydrogen atoms are given in angstroms 4 The energies of complexed host and guest were calculated by performing a single-point calculation of the conformation presented by host or guest in the complex (frozen host and guest); thereby, they were not stationary points oxygen atoms of the host interact with both upper and lower hydrogen atoms of the guest. As a result, 12 short CAH Á Á Á O interactions are found (less than 2.90 A Ê ) for all complexes studied, except for two cases.…”

Section: Resultsmentioning

confidence: 99%

“…Intermolecular forces are in general weaker than in covalent bonds, so supramolecular species are thermodynamically less stable, kinetically more labile and dynamically morē exible than molecules. Our group has been using several receptors for the recognition of a variety of compounds, including carboxylic acids [2], carboxylates [3], adenine derivatives [4] and ammonium salts [5]. Recently, some of us have reported [6] the synthesis and applications of squaramidobased tripodal receptors to the recognition of quaternary ammonium compounds.…”

Section: Introductionmentioning

confidence: 99%

Squaramido-based receptors: applicability of molecular interaction potential to molecular recognition of polyalkylammonium compounds

Quiñonero

Frontera

Tomàs

et al. 2000

Theoretical Chemistry Accounts: Theory, Computation, and Modeli

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A computational study of the mechanism of host±guest complexation between quaternary ammonium compounds and squaramido-based tripodal receptors has been carried out. Semiempirical molecular orbital calculations, which are in qualitative agreement with experimental results have been performed using the PM3 Hamiltonian. Molecular interaction potential (MIP) maps were used to analyze the suitability of both host and guest binding units for a high-anity recognition process. MIP calculations were computed from PM3 wavefunctions of the corresponding ammonium cations and dimethyl squaramide as a model compound for the hydrogen-bond-acceptor unit of the receptors. MIP analyses are helpful for understanding the host± guest process from the point of view of the doublecomplementarity principle.

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“…The programmed switch between a neutral and a phosphorylated state poses the challenge to develop selective detection methods. Few examples are available for nucleotide-selective hosts in water, inter alia, based on cyclophane scaffolds [3]. High binding constants (micromolar K d values) were especially achieved with receptor molecules containing a central phenanthridinium system [4].…”

Section: Introductionmentioning

confidence: 99%

Nucleoside Sensing

Schräder

KlÃƒÂ¤rner

Fokkens

2006

Sensors

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A rigid molecular clip comprising bisphosphonate binding sites and aromatic sidewalls forming an electron-rich cavity is able to distinguish between nucleosides and nucleotides in aqueous solution. Neutral nucleosides as well as antibiotics derived thereof are drawn into the unpolar interior of the cleft and lead to substantial upfield-shifts in the 1 H NMR spectrum. Nucleoside drugs can therefore be detected with high selectivity in the presence of their phosphorylated pendants or nucleic acids.

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A Cyclophane Receptor for the Selective Complexation of Adenine Derivatives in Water

Cited by 13 publications

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Interactions between aminocalixarenes and nucleotides or nucleic acids †

Interactions between aminocalixarenes and nucleotides or nucleic acids †

Squaramido-based receptors: applicability of molecular interaction potential to molecular recognition of polyalkylammonium compounds

Nucleoside Sensing

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