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Three new modes of adenine-copper(II) coordination: Interligand interactions controlling the selective N3-, N7- and bridging μ-N3,N7-metal-bonding of adenine to different N-substituted iminodiacetato-copper(II) chelates
Abstract
The reaction Of Cu2CO3(OH)(2), various N-substituted-iminodiacetic acids [R-N(CH2CO2H)(2))] and adenine (AdeH) in water yields crystalline samples of mixed-ligand copper(H) complexes of formulas [Cu(A)(N7 -AdeH)(H2O)] . H2O (A = N-methyl- or Nethyl-iminodiacetato(2-); compounds 1 and 2, respectively), [Cu(B)(N3-AdeH)(H2O)] . H2O (B = N-benzyl- or N-(p -methylbenzyl)-iminodiacetato(2-); compounds 3 and 4, respectively) as well as [Cu-4(pheida)(4)(mu-N3,N7 -AdeH)(2)(H2O)(4)] . 2H(2)O (pheida = N-phenethyl-iminodiacetato(2-)). Crystal structures of the acid H(2)pheida and compounds 1-5 are reported. H(2)pheida acid exhibits a typical zwitterionic structure. Copper(H) compounds were also studied by TG analysis (with FT-IR study of the evolved gasses), IR, electronic and ESR spectra and magnetic susceptibility data. The N-alkyl- or N-benzyl-like-iminodiacetato(2-) ligands (A or B) give complexes with Cu(II)/(A or B)/AdeH equimolar ratio, whereas pheida yields an unexpected tetranuclear compound with a 2:2:1 Cu(II)/pheida/AdeH molar ratio. In 1 and 2 AdeH binds to the metal by N7, whereas in 3 and 4 the N3 atom is used. An unexpected bridging mu-N3,N7-AdeH-dicopper(II) binding mode is found in the tetra-nuclear compound 5 (without interligand pi,pi-stacking interactions). These AdeH-Cu(II) binding modes have not been referred in the literature before. The difference in AdeH-Cu(II) binding modes in compounds I or 2 and 3 or 4 is rationalised on the basis of the absence or presence of a flexible N-benzyl-like substituent in the iminodiacetato(2-) ligand skeleton, which prevents or permits the interligand pi,pi-stacking interactions.
... The M-N7[H(N9)ade] coordination mode is known for a compound of Pt II and four compounds of Cu II . Two compounds have the general formula [Cu(N-alkyl-iminodiacetate)(Hade)(H 2 O)]·H 2 O (UHECUF [5,43], UHEDIU [5,43]). In these cases, the Cu-N7 coordination bond is reinforced by the intra-molecular inter-ligand H-bonding interaction N6-H· · ·O(coord. ...
... The M-N7[H(N9)ade] coordination mode is known for a compound of Pt II and four compounds of Cu II . Two compounds have the general formula [Cu(N-alkyl-iminodiacetate)(Hade)(H 2 O)]·H 2 O (UHECUF [5,43], UHEDIU [5,43]). In these cases, the Cu-N7 coordination bond is reinforced by the intra-molecular inter-ligand H-bonding interaction N6-H· · ·O(coord. ...
... The crystal packing of these compounds determine that the dinuclear core of TUMLET is reinforced by two intra-molecular (aqua)O-H· · ·O(non-coord. malonate) interactions (2.797Å, 170.00 • ) whereas in TUMLIX the aqua ligands are involved [43]), the Cu-N7 and Cu-N3 bonds are assisted by appropriate N-H· · ·O(coord. pheida) interactions. ...
... The M-N7[H(N9)ade] coordination mode is known for a compound of Pt II and four compounds of Cu II . Two compounds have the general formula [Cu(N-alkyl-iminodiacetate)(Hade)(H 2 O)]·H 2 O (UHECUF [5,43], UHEDIU [5,43]). In these cases, the Cu-N7 coordination bond is reinforced by the intra-molecular inter-ligand H-bonding interaction N6-H· · ·O(coord. ...
... The M-N7[H(N9)ade] coordination mode is known for a compound of Pt II and four compounds of Cu II . Two compounds have the general formula [Cu(N-alkyl-iminodiacetate)(Hade)(H 2 O)]·H 2 O (UHECUF [5,43], UHEDIU [5,43]). In these cases, the Cu-N7 coordination bond is reinforced by the intra-molecular inter-ligand H-bonding interaction N6-H· · ·O(coord. ...
... The crystal packing of these compounds determine that the dinuclear core of TUMLET is reinforced by two intra-molecular (aqua)O-H· · ·O(non-coord. malonate) interactions (2.797Å, 170.00 • ) whereas in TUMLIX the aqua ligands are involved [43]), the Cu-N7 and Cu-N3 bonds are assisted by appropriate N-H· · ·O(coord. pheida) interactions. ...
The metal coordination patterns of hypoxanthine, xanthine and related oxy-purines have been reviewed
on the basis of the structural information available in the Cambridge Structural Database (CSD), including
also the most recent reports founded in SciFinder. Attention is paid to the metal ion binding modes and
interligand interactions in mixed-ligand metal complexes, as well as the possibilities of metal binding of
the exocyclic-O atoms. The information in CSD is also reviewed for the complexes of adenine in cationic,
neutral and anionic forms with every metal ion. In contrast to the scarce structural information about
hypoxanthine and related complexes, large structural information is available for adenine complexes with
a variety of metals that reveals some correlations between the crystal–chemical properties of metal ions.
Three aspects are studied in deep: the coordination patterns, the interligand interactions influencing
the molecular recognition in mixed-ligand metal complexes and the connectivity between metals for
different adenine species, thus supporting its unique versatility as ligand. When possible, the overall
behaviour showed by adenine metal complexes is discussed according to the HSAB Pearson criteria and
the tautomeric behaviour observed for each protonated species of adenine. The differences between the
roles of adenine and the referred oxypurines ligands are underlined.
... Yield ~ 60%. Elemental analysis Calc. for C 19 2 ]·nH 2 O (3-H, 3-M and 3-L with n = 3, 1 or 0, for 'high', 'medium' and 'low' hydrates, respectively) These compounds were prepared by the reaction of equimolar amounts of Co 2 (CO 3 )(OH) 2 ·2H 2 O (62 mg, 0.25 mmol, 100% in excess) and H 2 pdc (42 mg, 0.25 mmol) in 50 mL of water, heating (50-60 °C) Scheme 1. Drawing of pdc ligand (top), adenine with purine conventional notation (middle) and a 4 + 1 metal surrounding with the pdc in mer-NO 2 conformation and neutral adenine coordinated in the basal plane via N7 (bottom). Dashed lines represent a possible intra-molecular interligand interaction with O(coord. ...
... The two ternary Cu(II)-pdc-Hade compounds (1-2) reported in this study have been prepared by reaction between the 'in situ' obtained Cu(pdc) chelate and Hade or the complementary base pair Hade:Hthy (see Experimental Sections 2.2.1 and 2.2.2). This strategy was also performed in previous works with closely related iminodiacetate-like ligands [19][20][21] Hthy, respectively. The role of Hthy in the synthesis was not fully understood at that time but further results revealed a marked influence of the temperature. ...
... carboxylate; 2.692 Å, 154.9°) interligand interaction. This pattern has also been found in [Cu(N-R-IDA)(H(N9)ade)(H 2 O)]·H 2 O [19] where non-rigid N-alkyl-iminodiacetates (R_Me or Et) adopt a mer-NO 2 conformation and the Hade ligands from pairs of symmetry related complex molecules with more (R_Me) or less (R_Et) pronounced π,π-stacking interactions. Such kind of pairs of complex molecules can also be considered in the crystal of 1, but the structural stacking parameters (inter-centroid distance d Cg-Cg = 3.77 Å, inter reveal the weakness of this interaction ( Fig. 1-b). ...
Mixed ligand M(II)-complexes (MCoZn) with pyridine-2,6-dicarboxylate(2-) chelator (pdc) and adenine (Hade) have been synthesized and studied by X-ray diffraction and other spectral and thermal methods: [Cu(pdc)(H(N9)ade)(H2O)] (1), [Cu2(pdc)2(H2O)2(μ2-N3,N7-H(N9)ade)]·3H2O (2), trans-[M(pdc)(H(N9)ade)(H2O)2]·nH2O for MCo (3-L, 3-M, 3-H) or Zn (4-L, 4-H), where n is 0, 1 or 3 for the 'lowest' (L), 'medium' (M) and 'highest' (H) hydrated forms, and the salt trans-[Ni(pdc)(H2(N1,N9)ade)(H2O)2]Cl·2H2O (5). In all the nine compounds, both neutral and cationic adenine exist as their most stable tautomer and the molecular recognition pattern between the metal-pdc chelates and the adenine or adeninium(1+) ligands involves the MN7 bond in cooperation with an intra-molecular N6H⋯O(coordinated carboxylate) interligand interaction. In addition the dinuclear copper(II) compound (2) has the CuN3 bond and the N9H⋯O(coord. carboxylate) interaction. The structures of mononuclear ternary complexes proved that the molecular recognition pattern is the same irrespective of (a) the coordination geometry of the complex molecule, (b) the different hydrated forms of crystals with Co or Zn, and (c) the neutral of cationic form of the adenine ligand. These features are related to the mer-NO2 chelating ligand conformation (imposed by the planar rigidity of pdc) as a driving force for the observed metal binding mode.
... The coordination polyhedron of metal centers are fullfilled by aqua ligands and/or a large variety of monodentate or bidentate auxiliary ligands [1][2][3][4][5] . Some recent studies have revealed that the type of non coordinating N-R-IDA substituent strongly influences the molecular recognition pattern between copper(II)-IDA-like chelates and the N-rich base adenine [6][7][8] . Interestingly, the Cu(II)-(pheida) chelate (where, pheida is N-phenethyliminodiacetate(2-) ion, Ph-CH 2 CH 2 N (CH 2 CO 2 -) 2 ion) binds the adenine (Hade) in the bridging mode μ 2 -N3,N7-H(N9)ade to give a tetranuclear molecule, as proved by its crystallographic results 1 . ...
... The acid form of tridentate chelating ligands (H 2 MOpheida and H 2 Fpheida), were obtained as previously reported for N-phenethyl-iminodiacetic acid (H 2 pheida) 6 , but using 4-Methoxyphenethylamine and 4-Fluoro-phenethylamine instead of N-phenethylamine. These amines were purchased from Aldrich and used without further purification. ...
The stoichiometric reactions between Ni(II) hydroxy-carbonates and N-p-(R)-H 2 pheida derivatives (R = MeO or F for MOpheida or Fpheida, respectively) yield two binary compounds [Ni(MOpheida)(H 2 O) 3 ] (1) and [Ni(Fpheida)(H 2 O) 3 ] (2). The crystal of compounds 1 and 2 are iso-type; space group P2 1 /c. Our crystallographic results revealed that both studied metal-chelates have molecular structure and the used p-R substituents on the pheida skeleton yield the same structural features. The IDA moiety of pheida-like ligands exhibit the fac-NO 2 conformation (1 & 2). Crystal structure of H 2 Fpheida free acid have also been reported herein. Iminodiacetate(2-) and N-R substituted-iminodiacetate(2-) (IDA and IDA-like) are important tri-dentate chelating agents which are able to bind the metal from the three coordination sites. The coordination polyhedron of metal centers are fullfilled by aqua ligands and/or a large variety of monodentate or bidentate auxiliary ligands 1-5. Some recent studies have revealed that the type of non coordinating N-R-IDA substituent strongly influences the molecular recognition pattern between copper(II)-IDA-like chelates and the N-rich base adenine 6-8. Interestingly, the Cu(II)-(pheida) chelate (where, pheida is N-phenethyliminodiacetate(2-) ion, Ph-CH 2 CH 2 N (CH 2 CO 2-) 2 ion) binds the adenine (Hade) in the bridging mode μ 2-N3,N7-H(N9)ade to give a tetranuclear molecule, as proved by its crystallographic results 1. The crystal structure of the free ligand H 2 pheida is also known as well as a salt with the bis-chelate anion [Cu(pheida) 2 ] 2-and [Cu(phen) 3 ] 2+ as counter ion 9. Moreover, a ternary complex with hypoxanthine nucleo-base as auxiliary ligands also reported recently [Cu(pheida)(Hhyp) (H 2 O)]·2H 2 O 4. No other structural data concerning (N-pheida-like)-metal ion complexes are found in the CSD database. The mer-NO 2 or fac-NO 2 which is a conformation of IDA moiety, have been observed for most of the octahedral metal complexes irrespective of metal center. In contrast, the conformational behavior is versatile for copper(II) complexes where IDA arm adopted mer-NO 2 and/or fac-NO+O (apical/distal), fac-O 2 +N(apical/distal) 1. The molecular structure of the chelating ligand is depicted in Scheme 1. The aim of this work is to investigate the presence of IDA moiety and the crystal building in Ni(II) chelates with two p-R-substituted pheida-like ligands having methoxy or fluoro as R-group in order to see the effect of p-R-substitutive group on molecular and Scheme 1-Molecular structure of chelating ligand, N-(p-R-phenethyl)-iminodiacetic acid
... Evaporation of mother liquors gives many suitable single crystals for X-ray diffraction purposes. Crystal data were collected with a Bruker X8 Proteum (1 and 6) or a Bruker X8 Kappa APEXII diffractometer (2)(3)(4)(5). Data were processed with APEX2 suite and corrected for absorption using SADABS. The structures were solved by direct methods (SHELXS-97) and refined by full-matrix least-squares techniques (SHELXL-97). ...
... A priori, several tautomers of neutral Hhyp can be considered as potential ligands to binds Cu(IDA-like) chelate. On the basis of the knowledge from the structures of Cu(IDA-like)(Hade) ternary compounds [1,[4][5][6], the most relevant tautomers for the ligand Hhyp are showed in the Figure 6. ...
... Evaporation of mother liquors gives many suitable single crystals for X-ray diffraction purposes. Crystal data were collected with a Bruker X8 Proteum (1 and 6) or a Bruker X8 Kappa APEXII diffractometer (2)(3)(4)(5). Data were processed with APEX2 suite and corrected for absorption using SADABS. The structures were solved by direct methods (SHELXS-97) and refined by full-matrix least-squares techniques (SHELXL-97). ...
... A priori, several tautomers of neutral Hhyp can be considered as potential ligands to binds Cu(IDA-like) chelate. On the basis of the knowledge from the structures of Cu(IDA-like)(Hade) ternary compounds [1,[4][5][6], the most relevant tautomers for the ligand Hhyp are showed in the Figure 6. ...
... The available information strongly suggest that the non-coordinating moiety of the N-R-IDA ligand (R = H, alkyl, benzyl or phenyl) can influence the system towards a true mixed-ligand complex or to the corresponding salt. Under the same conditions, the behavior of these systems noticeably differs from that observed for the copper(II) analogues, for which salt formation has not been observed [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32]. In particular, it is known that N-methyliminodiacetate (MIDA) and N-benzyliminodiacetate (NBzIDA) ligands yield salts with Ni(II) and imidazole (Him), but not the corresponding ternary complexes [4]. ...
... The chelating ligands were synthesized in the acid form (H 2 MEBIDA or H 2 MOBIDA) as reported for N-benzyliminodiacetic acid (H 2 NBzIDA) [26], but using 4-methylbenzylamine or ...
In an attempt to prepare binary and ternary compounds, we have obtained two molecular complexes [Ni(MEBIDA or MOBIDA)(H 2 O) 3 ]ÁnH 2 O (n = 0 or 1) and two iso-type salts [Ni(Him) 6 ][Ni(MEBIDA or MOB-IDA) 2 ]Á4H 2 O [MEBIDA = N-(p-methylbenzyl)iminodiacetate(2À) and MOBIDA = N-(p-methoxybenzyl)-iminodiacetate(2À) ligands, Him = imidazole]. Our results are discussed with regard to related copper(II) and nickel(II) compounds. The reasons for which these chelating ligands produce nickel(II) salts instead of ternary compounds remain unclear since other iminodiacetate-like ligands give true ternary Ni(II) compounds with imidazole and other N-heterocyclic ligands.
... Surfactants containing amino acids or peptide head groups provided peculiar opportunities for association with mineral surfaces (Zaia 2004) by metal-ligand coordination. Adenine has also been found to make coordinate-covalent bonds through its secondary nitrogens with iron (Speca et al. 1981;Mikulski et al. 1985), copper (Bugella-Altamirano et al. 2002) and zinc (Morel et al. 2002) ions, transition metal (TM) elements found deposited around hydrothermal vents. This could have enabled a protocell to bond with metallic mineral surfaces (for example iron, zinc or copper sulfides) (Damer and Deamer 2015). ...
Scales of electronegativity values are used by chemists to describe numerous chemical features such as chemical mechanisms, bond polarity, band gap, atomic hardness, etc. While the many scales provide similar trends, all differ in their predictive quality. Confirmation of the quality of a new scale often uses a previous scale for comparison but does not use independent means to demonstrate the merits of the scale. Utilizing a table of binary compounds of known ionic, covalent, and metallic bonding characters, a means to evaluate electronegativity scales is developed here. By plotting the electronegativity values of the two bonded atoms in binary compounds of a known bonding character, a tripartite separation results that generally divides the three bond types. Using the results of graphs of this sort, the success of bonding separations of 14 different scales of electronegativity has been evaluated on the basis of three quantitative parameters that can provide a measure of the quality of the scales. Three scales, those of Allen, Martynov and Batsanov, and Nagle, have been shown to be superior in their ability to predict the expected separation of bond types. Since this scheme successfully demonstrates the ability to evaluate the quality of electronegativity scales, it can be applied to other scales to establish their effectiveness in predicting bond types in binary compounds and thus the quality of the scales. This scheme is applied to a recently published electronegativity scale to evaluate the ability to determine its quality.
... Above 560 °C a stable residue of 33.4% is formed. The calculated value to 2 CdO (24.59%) is too low, however, it is well known that the burning of this N-rich polymer can change it to a (not necessarily stoichiometric) cadmium oxy-nitrate [25]. Indeed, an estimation for CdO·Cd (NO3)2 as a final residue leads to a quite reasonable calculated value (35%); therefore, we tentatively assigned the residue to cadmium oxy-nitrate. ...
Three mixed-ligands of Cd(II) coordination polymers were unintentionally obtained: {[Cd(µ3-EDTA)(Him)·Cd(Him)(H2O)2]·H2O}n (1), {[Cd(µ4-CDTA)(Hade)·Cd(Hade)2]}n (2), and {[Cd(µ3-EDTA)(H2O)·Cd(H9heade)(H2O)]·2H2O}n (3), having imidazole (Him), adenine (Hade) or 9-(2-hydroxyethyl)adenine (9heade) as the N-heterocyclic coligands. Compounds 2 and 3 were obtained by working with an excess of corresponding N-heterocyclic coligands. The single-crystal X-ray diffraction structures and thermogravimetric analyses are reported. The chelate moieties in all three compounds exhibit hepta-coordinated Cd centers, whereas the non-chelated Cd center is five-coordinated in 1 and six-coordinated in 2 and 3. Him and Hade take part in the seven-coordinated chelate moieties in 1 and 2, respectively. In contrast, 9heade is unable to replace the aqua ligand of the chelate [Cd (EDTA) (H2O)] moiety in 3. The thermogravimetric analysis (TGA) behavior of [Cd (H2EDTA) (H2O)]·2H2O in 1 and 3 leads to a residue of CdO, whereas the N-rich compound 2 yields CdO·Cd(NO3)2 as a residue. Density functional theory (DFT) calculations along with molecular electrostatic potential (MEP) and quantum theory of atoms-in-molecules computations were performed in adenine (compound 2) and (2-hydroxyethyl)adenine (compound 3) to analyze how the strength of the H-bonding and π-stacking interactions, respectively, are affected by their coordination to the Cd-metal center.
... Nucleobase complexes with transition metals are continuously under investigation due to their applications as advanced functional materials, their biologic importance, structural diversity and use as molecular recognition models for nucleic acids [1][2][3][4][5][6]. The majority of structural information available in these systems is mainly dedicated to the adenine nucleobase [7][8][9][10][11][12][13][14][15][16] and a variety of N-alkylated derivatives as ligands [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31]. In contrast, available structural information in the Cambridge Structural Database (CSD) on metal complexes, co-crystals and salts with 2,6-diaminopurine (Hdap) nucleobase is much more limited, despite the fact that Hdap is an analog of adenine. ...
The proton transfer between equimolar amounts of [Cd(H2EDTA)(H2O)] and 2,6-diaminopurine (Hdap) yielded crystals of the out-of-sphere metal complex H2(N3,N7)dap [Cd(HEDTA)(H2O)]·H2O (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) (H2O)]·2H2O (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.
... Surfactants containing amino acids or peptide head groups provided peculiar opportunities for association with mineral surfaces (Zaia 2004) by metal-ligand coordination. Adenine has also been found to make coordinate-covalent bonds through its secondary nitrogens with iron (Speca et al. 1981;Mikulski et al. 1985), copper (Bugella-Altamirano et al. 2002) and zinc (Morel et al. 2002) ions, transition metal (TM) elements found deposited around hydrothermal vents. This could have enabled a protocell to bond with metallic mineral surfaces (for example iron, zinc or copper sulfides) (Damer and Deamer 2015). ...
Amino acids and peptides have been demonstrated to form lipoamino acids and lipopeptides under presumed prebiotic conditions, and readily form liposomes. Of the common nucleobases, adenine forms a liponucleobase even below 100 °C. Adenine as well as other nucleobases can also be derivatized with ethylene carbonate (and likely other similar compounds) onto which fatty acids can be attached. The fatty acid tails along with appropriately functionalized nucleobases provide some solubility of liponucleobases in membranes. Such membranes would provide a structure in which three of biology’s major components are closely associated and available for chemical interactions. Nucleobase-to-nucleobase interactions would ensure that the liponucleobases would have a uniquely different head-group relationship than other amphiphiles within a membrane, likely forming rafts due their π-π interactions and providing surface discontinuities that could serve as catalytic sites. The π-π bond distance in aromatic compounds is typically 0.34 nm, commensurate with that of the amine to carboxylate distance in alpha amino acids. This would have provided opportunity for hydrogen bonding between amino acids and the distal primary amines or tautomeric carbonyl/hydroxyl groups of two π-bonded nucleobases. Such bonding would weaken the covalent linkages within the amino acids, making them susceptible to forming peptide bonds with an adjacent amino acid, likely a lipoamino acid or lipopeptide. Were this second lipoamino acid bound to a third π-bonded nucleobase, it could result in orientation, destabilization and peptide formation. The stacked triplet of nucleobases might constitute the primordial codon triplet from which peptides were synthesized: primordial translation.
... In this case, the Cu-N7(Hade) bond is also reinforced by an N6-H⋯O(coordinated carboxylate) interligand interaction [21]. In contrast, neither Cu(BCBC) nor Cu(pheida) chelates have proved to be able to yield the corresponding mononuclear complexes with general formula Cu(chelator)(Hade) [20]. Note that both pheida and BCBC chelators have large and flexible N-aryl-alkyl (pheida) or N-aryl-pseudoaliphatic (BCBC) pendant arms linked to the iminodiacetate moiety. ...
2022): Synthesis, characterization, and quantum chemical study of cobalt(II) chelates with N-phenethyl-iminodiacetate(2-)-like ligands. ABSTRACT From the reaction of Co(II) hydroxy-carbonates and N-p-(R)-phene-thyliminodiacetic acids (H 2 pheida, R ¼ H and H 2 MOpheida, R ¼ CH 3 O) two binary complexes have been obtained in aqueous media. The crystal pattern of [Co(pheida)(H 2 O) 3 ]Á1.5H 2 O (1) (monoclinic, space group C2/c) differs from the related non-hydrated crystal of [Co(MOpheida)(H 2 O) 3 ] (2) (monoclinic, space group P2 1 /c). Both Co(II) complexes display distorted octahedral geometry imposed by 3d 7 electronic configuration. Our crystallographic results reveal that the metal chelates have a molecular structure and the used methoxy-substituent on the pheida skeleton yield different structural features. The iminodiacetic acid-arms [IDA] of pheida-like ligands adopt fac-NO 2 conformation. For both chelators 1 and 2, single-point energy was calculated using restricted and/or unrestricted Hartree-Fock/BP/B3LYP functional. The analytical frequency, electronic absorption, and HOMO-LUMO energy gap were calculated using B3LYP functional with orbital basis set def2-SVP or def2-TZVP (for 2) along with the auxiliary basis set def2/J. The quantum chemical calculated geometry parameters are compared with their corresponding X-ray crystallographic data. The optical band gap (E g) arises due to the electronic transitions. The direct and indirect band gap energy measured 3.26, 3.19 eV for 1 and 3.39, 3.35 eV for 2, respectively, reflecting their semi-conducting nature. Crystal structure for H 2 MOpheida acid also reported herein. ARTICLE HISTORY Hardness g (in eV), softness r (in eV À1), and dipole moment m (in D) using Koopman's theorem.
The reactions of N-benzyliminodiacetic acid (BnidaH2) and its para-substituted derivatives, namely: N-(p-chlorobenzyl)iminodiacetic acid (p-ClBnidaH2), N-(p-nitrobenzyl)iminodiacetic acid (p-NO2BnidaH2) and N-(p-methoxybenzyl)iminodiacetic acid (p-MeOBnidaH2) with paladium(II) chloride and 2,2′-bipyridine, were performed in water-acetonitrile solutions. Four new prepared complexes [Pd(Bnida)(bipy)]∙2H2O (1), [Pd(p-ClBnida)(bipy)]∙4H2O (2), [Pd(p-NO2Bnida)(bipy)]∙2H2O (3) and [Pd(p-MeOBnida)(bipy)]∙3H2O (4) were identified by means of chemical analysis and mass spectrometry, and characterized by infrared spectroscopy and thermal analysis (TG/DTA). The molecular geometry and infrared spectra of these four complexes were modelled using DFT calculations at the BP86/def2-TZVP (Pd: ECP) level of theory. Extensive NMR studies have shown the presence of two isomers in solution (DMSO). The characterized palladium(II) complexes demonstrate valuable antiproliferative activity against Caco-2, SW620, NCI-H358 and MDCK I reducing cell growth from 71.7% to 79.9% (10⁻⁴ M) (1; 4). PANC-1 display mild sensitivity and slow reduction in cell growth (less than 50%) while BJ present higher viability range and proliferative status. BJ proliferation after exposure to palladium complexes at 10⁻⁴ M concentration ranged from 55.2% to 83.5% (1–4). In descending order, antiproliferative effect of tested palladium complexes is, as follows: 4 > 1 > 2 > 3.
This article describes the synthesis and spectroscopic characterization of several Pd(II), Pt(II), Ag(I) and Rh(III) complexes with multi-dentate adenine (Had) as primary ligand and 2,2’-bipyridyl (bpy), 1,10-phenanthroline (phen) as secondary ligand. In the complexes, adenine coordinates bidentately through cyclic N7 and NH2 {[M(L)(Had)]Cl2 (M(II) = Pd, Pt; L = bpy, phen)}; cyclic N3 and deprotonated N9 {[Pd(ad)2] and [M(ad)Cl(H2O)] (M(II) = Pd, Pt)} or N1 & N7 in {dimeric [Ag(Had)(NO3)]2}, and monodentate through cyclic N3 {[Rh(Had)3(H2O)3]Cl3}. The main goal of this study is to prepare new low toxic and effective anticancer metal-based molecules. The in vitro anticancer activity against the human breast cancer (MDA-MB231) and human ovarian cancer (OVCAR-8) cell lines was tested using selected Pt(II) and Pt(II) mixed ligand, Had-phen and Had-bpy, complexes, which are rich N-donors, in comparison to cisplatin as a reference. Moreover, CT-DNA-binding properties of some complexes were studied using circular dichroism (CD) spectroscopy. Moreover, intercalative CT-DNA binding capability was indicated.
Two Hade-based Cd(II) polymers, [Cd(Hade)(tp)]n (1) and {[Cd6(Hade)6(tp)6]·9H2O}n (2) (Hade = adenine, H2tp = benzene-1,4-dicarboxylic acid), were obtained from the same reaction system at different temperatures which have been characterized by single-crystal X-ray diffraction, elemental analysis, FT-IR spectroscopy, thermogravimetric analysis, and luminescence spectroscopy. Significantly resulting from the synergistic coordination of nucleobase and bicarboxylate groups, they are a 3-D pillared-layer structure for 1 and a 2-D grid structure where the dicadmium paddle-wheel motifs are double bridged by benzene-1,4-dicarboxylate anions for 2. The supramolecular architecture of 2 is essentially knitted by hydrogen bonding interactions produced by the exocyclic amino/endocyclic imino groups of the nucleobase and the carboxylate groups of the co-ligand to favorably stabilize the high-dimensional supramolecular architectures. At room temperature, 1 and 2 exhibit intense luminescent emissions originating from a Hade-based intraligand and/or photoinduced charge transfer upon adenine binding mode.
The synthesis, characterization, crystal structure and HSA-binding of a mixed ligand Cu-isothiosemicarbazonato complex with adenine nucleobase as an auxiliary ligand are reported. X-ray crystallography indicates that the cationic complex has a binuclear centrosymmetric structure in which the isothiosemicarbazone molecule coordinates to copper as a tridentate NNO ligand. Adenine participates in the structure of complex in neutral 7-H tautomer form in which N9 as its most basic nitrogen atom completes the square planar geometry. The planar complex entities are anti-parallel stacked and joined by means of long Cu–O bonds involving oxygen atoms from the other isothiosemicarbazone molecule, giving a [4 + 1] square pyramidal coordination around the copper ion. Adenine molecule plays a pivotal role in establishing intermolecular hydrogen bonding in the supramolecular structure. HSA interactions of the complex are investigated thorough spectroscopic and theoretical methods. Emission studies indicate that the complex quenches fluorescence emission of HSA by a static mechanism. They also show that hydrophobic forces are primary interactions between complex and protein. Circular dichroism studies illustrate that the complex induces unfolding of HSA through converting part of the α-helical content to β-structures and random coils. Finally, docking studies indicate that the complex places in the upper part of interdomain region of HSA.
The study of the metal binding pattern of N-methyladenines (1-, 3-, 7- or 9-Meade) towards CuII-iminodiacetate-like chelates is addressed on the basis of XRD crystal structures of sixteen novel ternary compounds. Except for three compounds, all others feature an square-based Cu(II) coordination, type 4 + 1, and the efficient cooperation of a CuN7 bond with an intra-molecular N6-H⋯O(coord. carboxylate) interligand interaction as the major metal-binding pattern. The three referred exceptions to this behavior are: (1) the compound [Cu(MIDA)(7Meade)(H2O)]·4H2O, which evidence the CuN3 binding pattern; the (2) [Cu(IDA)(1Meade)(H2O)2]·4H2O, which molecular recognition consist in the CuN9 bond and a (distal aqua)⋯⋯N3(1Meade) intra-molecular interaction, within an octahedral Cu(II) center; and (3) [Cu(IDA)(9Meade)(H2O)2]·3H2O, also with a 4 + 1 + 1 Cu(II) coordination, where the CuN7 bond exists along with an extremely weak N6-H⋯O(coord. carboxylate) interaction (3.33 Å, 140.2°). This former interaction is determined by packing forces that promote the participation of the N6H group in a 'trifurcated' H-bond. In conclusion, the cooperation between the CuN7 bond (not possible for 7Meade) and the intra-molecular N6-H⋯O interaction is clearly favored (a) by the H-accepting role of the O-coordinated carboxylate atoms from the iminodiacetate ligands in mer-NO2 conformation and (b) in compounds where the Cu(II) atom exhibits an elongated square-base pyramidal coordination, type 4 + 1.
Two Cd(II) coordination compounds, i.e. [Cd(HL)(phen)2(H2O)]·HL·3H2O (1) and {[Cd(HMeL)2(4,4′-bipy)(H2O)]·H2O}n (2) and (where HL = N-carboxymethyl-N-phenyliminoacetato, HMeL = N-carboxymethyl-N-(m-methylphenyl)iminoacetato, 4,4′-bipy = 4,4′-bipyridine and phen = phenanthroline) have been synthesized and characterized by elemental analysis, IR and single-crystal X-ray diffraction methods. The photoluminescence properties and mechanisms, studied by means of solid state absorption, excitation/emission spectra, time-resolved lifetime techniques, and density functional theory (DFT) calculations, indicate that the emissions of both compounds originate from a combination of exciplex and charge-transfer complex. Interestingly, both compounds exhibit excitation-dependent emissions, which can be used to fine-tune their emission wavelengths.
A comprehensive study of the protonation equilibria of a series of polyamine ligands along with their complex formation equilibria with Cu ²⁺ and Zn ²⁺ is reported in this work. The primary aim of this study has been the achievement of homogeneous thermodynamic data on these ligands, in order to evaluate their influence on the homeostatic equilibria of essential metal ions (Cu ²⁺ and Zn ²⁺ ) in biological fluids. These polyamines are largely used as linkers in the building of chelating agents for iron overload. Potentiometric and spectrophotometric techniques were used for the characterization of protonation and complex formation constants. In addition, the characterization of the formed complexes is discussed together with selected solid-state crystal structures, remarking the influence of the length of the chain and of the linear or tetradentate tripod nature of the polyamine ligands on the stability of the complexes.
The use of the cytosine nucleobase or its 1-Methylcytosine derivative as ligands toward barium(II) cations led to the formation of three compounds, {[Ba(1-Mecyt)(H2O)X2]}n [X = Cl (1), Br (2)], and {[Ba(cyt)2(H2O)(ClO4)2]}n (3). Depending on the ligand and the counterion employed, 1-3 exhibit different architectures, which serve as a playground to study how the methyl substitution, together with the nature of the counterion are both significant in the self-assembling process of such species. The effect of the nature and size of the alkaline-earth metal ion on the final structural motif is also evident when comparing these structures with parent complexes of the Ca(II) ion.
The reactions of N-alkyl derivatives of iminodiacetic acid, RN(CH2COOH)2 (i-PridaH2 and t-BuidaH2; i-Pr = isopropyl, t-Bu = tert-butyl) with sodium tetrachloropalladate(II) in aqueous solutions were investigated. Four new palladium(II) complexes {[Na[PdCl(i-Prida)](H2O)2] ∙ ½H2O}n (1), [Na[PdCl(t-Buida)](H2O)2]n (2), [Pd(i-PridaH)2] ∙ 2H2O (3) and [Pd(t-BuidaH)2] (4) were obtained and characterized by X-ray crystallography, infrared spectroscopy, ¹H and ¹³C NMR spectroscopy, UV-Vis spectroscopy and thermal analysis (TG/DTA). In the solid state, the palladium(II) ion has square-planar coordination in all four complexes, composed of an O,N,O’-tridentate iminodiacetate ligand and a chloride ion in 1 and 2 and of two N,O-bidentate hidrogeniminodiacetate ligands in 3 and 4. Moreover, 1 is 2D coordination polymer composed of sodium ion clusters bridged by [PdCl(i-Prida)]‒ moieties, 2 is 1D coordination polymer composed of a zig-zag chain of sodium ions bridged by [PdCl(t-Buida)]‒ moieties and water molecules, while complexes 3 and 4 are monomeric species. Substitution of the chloride ligands in [PdCl(i-Prida)]‒ and [PdCl(t-Buida)]‒ by water molecules takes place after dissolution of the complexes 1 and 2, leading to formation of [Pd(i-Prida)(H2O)] (1') and [Pd(t-Buida)(H2O)] (2') species. Spectrophotometric potentiometric titration revealed that [PdCl(i-Prida)]‒ and [PdCl(t-Buida)]‒ are stable in acidic aqueous solution in the pH range 3-6 in the presence of chloride ions at [Cl–] > 0.1 M. Complexes 3 and 4 partially decompose upon dissolution in dimethyl sulfoxide, giving mixtures of the original complexes and by-products whose NMR spectra resemble those of 1' and 2'. Antibacterial and antitumor properties of the water-soluble complexes 1' and 2' were also investigated.
The reactions of N-benzyliminodiacetic acid (BnidaH2) and its para-substituted derivatives, namely N-(p-chlorobenzyl)iminodiacetic acid (p-ClBnidaH2), N-(p-nitrobenzyl)iminodiacetic acid (p-NO2BnidaH2), and N-(p-methoxybenzyl)iminodiacetic acid (p-MeOBnidaH2) with sodium tetrachloropalladate(II) were performed in aqueous solutions. Three new complexes [Pd(p-ClBnidaH)2]·2H2O (2), [Pd(p-NO2BnidaH)2]·2H2O (3), and [Pd(p-MeOBnidaH)2] (4) were prepared and characterized by infrared spectroscopy and thermogravimetric and differential thermal analyses. The molecular geometry and infrared spectra of these three complexes, together with the previously synthesized [Pd(BnidaH)2]·2H2O (1a) and [Pd(BnidaH)2] (1b) were also modelled using density functional theory calculations at the BP86/6-311+G(d,p) level of theory with SDD pseudopotentials.
To explore the interaction of nucleosides and nucleobases in the context of the Maillard reaction and to identify the selectivity of purine nitrogen atoms towards various electrophiles, model systems composed of adenine or adenosine, glycine, ribose and/or 2-furanmethanol (with and without copper) were studied in aqueous solutions heated at 110 °C for 2 hours and subsequently analyzed by ESI/qTOF/MS/MS in addition to isotope labeling techniques. The results indicated that ribose selectively formed mono-ribosylated N6 adenine, but in the presence of (Ade)2Cu complex the reaction mixture generated mono-, di- and tri- substituted sugar complexes and their hydrolysis products of mono-ribosylated N6 and N9 adenine adducts and di-ribosylated N6,9 adenine. Furthermore, the reaction of 2-furanmethanol with adenine in the presence of ribose generated kinetin and its isomer, while its reaction with adenosine generated kinetin riboside, as confirmed by comparing the MS/MS profiles of these adducts to those of commercial standards.
The reactions of N-benzyliminodiacetic acid (BnidaH2) and N-(para-nitrobenzyl)iminodiacetic acid (p-NO2BnidaH2) with cobalt(II) and nickel(II) acetate in aqueous solutions were performed. Three new complexes [Co(Bnida)(H2O)3] ⋅ H2O (1a ⋅ H2O), [Co(p-NO2Bnida)(H2O)3] ⋅ ½H2O (2a ⋅ ½H2O) and [Ni(p-NO2Bnida)(H2O)3] ⋅ ½H2O (2b ⋅ ½H2O) were prepared and characterized by infrared spectroscopy and thermal analysis (TG/DTA). The molecular and crystal structures of 1a ⋅ H2O and 2b ⋅ ½H2O were determined by X-ray crystallography. The octahedral coordination environments around the Co(II) ion in 1a and Ni(II) ion in 2b consist of an O,N,O’-tridentate N-arylalkyliminodiacetate ion and three water molecules, resulting in the formation of fac-isomers in both cases. The molecular geometry and infrared spectra of these three complexes, together with previously synthesized and characterized complex [Ni(Bnida)(H2O)3] ⋅ H2O (1b ⋅ H2O) are studied by DFT calculations using BP86/6-311G(d,p) and mPW1PW91/6-311G(d,p) computational model.
Two novel families of coordination polymers, [Ln(bzlida)(Hbzlida)]∙H2O (Ln = La, Nd) and [Ln2(bzlida)3]∙3H2O (Ln = Nd, Sm, Eu, Gd) were prepared by hydrothermal reaction of Ln2O3 with benzyliminodiacetic acid (H2bzlida). The conditions of synthesis, in particular pH value, were selected on the basis of previous speciation studies reported in this work. The first type of complexes consists of 1D chains built by fully deprotonated ligand bridging two lanthanide ions and protonated Hbzlida- ligands connecting three cations. The second type is formed by [Ln2(bzlida)3] bimetallic units in which the ligand has a tridentate NOO coordination mode. This is expanded to a 2D network through carboxylate linkers. Under similar synthetic conditions but including copper acetate in the reaction mixture, a new compound was also obtained and characterized: [Cu(bzlida)2{Er(AcO)(H2O)5}2][Cu(bzlida)2]6H2O (AcO = acetate). This salt is made by the [Cu(bzlida)2{Er(AcO)(H2O)5}2]2+ heterotrimetallic complex cation containing an acetato bridge, and the [Cu(bzlida)2]2- anion. The same reaction produces the monomeric [Cu(Hbzlida)2]∙4H2O whose structure was also elucidated. Magnetic properties of the Gd(III) derivative were studied and analyzed experimental and theoretically. The results are compared and discussed respect to those reported in the literature and a magnetostructural correlation is suggested.
The synthesis and crystal structure of the compounds [Mg(H2O)6(1-Mecyt)2]Br2 (1), [Mg(cyt)2(H2O)4]X2, [X = Br (2), Cl (3)], [Mg(cyt)4(H2O)2]X2 [X = Br (4), Cl (5)], and [Mn(cyt)4(H2O)2]Br2 (6) (where 1-Mecyt = 1-Methylcytosine and cyt = cytosine) are reported. Compounds 1 consist of hexa-aquo cations, 1-Mecyt molecules and bromide anions self-assembled through an extended network of hydrogen-bonding interactions. Compound 2, 3 and 4, 5 are made of [Mg(cyt)2(H2O)4]2+ or [Mg(cyt)4(H2O)2]2+ cations, with the cyt molecules directly coordinated to the metal centers through the O(2) atom. Compound 6 is isostructural to 4, containing Mn(II) instead of Mg(II) ions. In compounds 2-6 the electro-neutrality is achieved by means of bromide (2, 4, 6) or chloride ions (3, 5). When crystals of 2 and 3 were left in their mother solutions, they disappeared over time and crystals of different size and shape, corresponding to compounds 4 and 5, respectively, appeared in their place.
Introduction Metal-Oxalato-Nucleobase Extended Systems Other Metal-Nucleobase 1D Extended Systems Hybrid Systems Based on Metal-Oxalato and Protonated Nucleobases Conclusions References
Metal atoms and metal complexes can coordinate to electron donor groups of the nucleo bases and thereby influence the canonical DNA structures propagating the formation of mispairs of DNA. Guanine is an important nucleo base and its coordination behaviour with copper complexes [Cu(II)(Salgly)H2O] and [Cu (II)(Salhis)H2O] have been studied by various spectroscopic and electrochemical techniques. One guanine is found to bind to the complexes with high binding constant. Guanine binding makes the redox potential of Cu(II)/Cu(I) couple shifted towards negative direction. In cationic and anionic charged environment, provided by surfactant micelles, redox potential of the Cu(II)/Cu(I) couple was found to shift in positive (by 0.050 V) and in negative (by 0.025 V) direction.
A recent body of work highlights new applications of Immobilized metal ion affinity chromatography (IMAC) for the isolation of known drugs and for drug discovery, metabolome profiling, and for preparing metal-specific molecular probes for chemical proteomics-based drug discovery. IMAC is a method underpinned by the fundamental tenets of coordination chemistry. This chapter focuses on these aspects, and describes a number of recent innovations in IMAC. It aims at building interest in other research groups for expanding the use of IMAC across chemical biology. The chapter provides examples that illustrate the use of protein X-ray crystallography data to guide the selection of targets isolable using IMAC. In a recent development, the IMAC format has been extended beyond the affinity-based separation of non-protein based low molecular weight bacterial secondary metabolites. One of the major advantages of IMAC for metabolite capture is that the technique is water compatible.
Eight Cu(II) complexes with N-(p-, m- or o-trifluoromethylbenzyl)iminodiacetate chelators (x-3F ligands) have been synthesized to promote C–F/H interligand interactions involving the F3C-group: {[Cu(μ2-p-3F)(H2O)]·3H2O]}n (1), [Cu(m-3F)(H2O)2] (2), [Cu(p-3F)(Him)(H2O)] (3), [Cu(m-3F)(Him)(H2O)] (4), [Cu(o-3F)(Him)(H2O)] (5), [Cu2(p-3F)2(H5Meim)2(H2O)2] (6), [Cu(m-3F)(H5Meim)(H2O)] (7), and [Cu(o-3F)(H5Meim)(H2O)] (8) [Him and H5Meim = imidazole and the “remote” tautomer 5-methylimidazole, respectively]. The compounds were studied by single-crystal X-ray diffraction, FT-IR, electronic spectra and coupled thermogravimetric + FT-IR methods. The conformation of the iminodiacetate chelating moiety (IDA group) is fac-NO + O(apical) in 1 and mer-NO2 in 2–8. The fac-IDA conformation observed in 1 is related to its polymeric structure and the coordination of a O’-carboxylate donor, from an adjacent complex unit, trans to the Cu–N(IDA) bond. The mer-IDA conformation in 2 is in agreement with similar compounds with an aqua ligand trans to the corresponding Cu–N(IDA) bond. As expected, the ternary complexes 3–8 feature a mer-IDA conformation. Some of the studied complexes exhibit disorder in the –CF3 group and C–H…F interligand interactions along with conventional N–H…O and O–H…O interactions. The thermal decomposition of all studied compounds under air flow produces variable amounts of trifluorotoluene.
We report the synthesis of two new 3D coordination polymers (CPs) based on Co(II), adenine and aromatic tetracarboxylate linkers. Adenine exhibits bidentate binding modes in both CPs, coordinating through the N3 and N9 sites in a first compact CP and through the more rare N3 and N7 sites in a second open, flexible and H2O-responsive CP. These differences together with an analysis of the extended coordination structures made of adenine reported in Cambridge Structural Database illustrate the rich coordination versatility of adenine as a building block for CPs. Although the latter CP is non-porous to N2 or CO2, it shows a reversible and detectable colour change from pink to purple, and vice versa, upon hydration and dehydration, respectively.
To better understand the extreme versatility of adenine as a ligand, the metal binding patterns of some closely related N-ligands have been carefully analysed. All the selected ligands comply with the requirement of having at least one N-heterocyclic atom in each cycle of the purine skeleton. The N-ligands are: (a) deaza-adenines [7-azaindole (H7azain), 4-azabenzimidazole (H4abim), 5-azabenzimidazole (H5abim), 7-deaza-adenine (H7deaA), purine (Hpur)] (b) adenine isomers [2-aminopurine (H2AP), 4-aminopyrazolo[3,4-dlpyrimidine (H4app), 7-amino[1,2,4]triazolo[1,5-alpyrimidine (7atp)] and (c) aza-adenines [2,6-diaminopurine (Hdap), 8-aza-adenine (H8aA)]. The different molecular recognition patterns are reviewed on the basis of the available structural information in the Cambridge Structural Database, version 5.33 (updated Nov. 2012). No restraints have been placed concerning the neutral or charged species of these N-ligands or the metal ions involved in the coordination. Attention is paid to the proton tautomerism and its metal binding patterns, highlighting many examples where the molecular recognition pattern is carried out by the cooperation of a metal N bond and an intra-molecular inter-ligand H-bonding interaction.
The reactions of N-arylalkyl derivatives of iminodiacetamide (Bnimda, Peimda, Ppimda; Bn = benzyl, Pe = 2-phenylethyl; Pp = 3-phenylprop-1-yl) with nickel(II) and copper(II) salts in aqueous solutions were investigated. Four new nickel(II) complexes and three new copper(II) complexes [Ni(Bnimda)2](NO3)2·2H2O (1), [Ni(Peimda)2](NO3)2 (2), [Ni(Peimda)2]SO4·2H2O (3), [Ni(Ppimda)2](NO3)2·4H2O (4), [Cu(Bnimda)2](NO3)2·H2O (5), [Cu(Peimda)2](NO3)2·4H2O (6) and [Cu(Ppimda)2](NO3)2 (7) were prepared and characterized by infrared spectroscopy and thermal analysis (TG/DTA). The distorted octahedral coordination environments around the nickel(II) and copper(II) ions in complexes 1, 2, 3, 5 and 6 consist of two O,N,O′-tridentate N-arylalkyliminodiacetamide ligands, with imino N atoms in trans-position. Various hydrogen bond motifs were found in the crystal structures of these complexes – trimeric, tetrameric, pentameric and hexameric ring motifs. These motifs were formed by the amide moieties and by the oxoanions (nitrate or sulfate) and water molecules.
The reactions of N-aralkyl derivatives of iminodiacetic acid (H2Bnida, H2Peida, H2Ppida, o-H2Cbida, Bn = benzyl, Pe = 2-phenylethyl, Pp = 3-phenylprop-1-yl, o-Cb = o-chlorobenzyl) with nickel(II) chloride hexahydrate or nickel(II) acetate tetrahydrate in aqueous solutions were studied. Five new nickel(II) complexes [Ni(Bnida)(H2O)3]·H2O (1), [Ni(Peida)(H2O)3] (2), [Ni(Ppida)(H2O)3]·H2O (3a), [Ni(Ppida)(H2O)3] (3b) and [Ni(o-Cbida)(H2O)3] (4) were prepared and characterized by infrared spectroscopy and thermal analysis (TGA–DTA). The crystal structures of 1 and 3b were determined by single-crystal X-ray structural analysis. The octahedral coordination environment around the nickel(II) ion in 1 and 3b consists of an O,N,O′-tridentate N-aralkyliminodiacetate ion and three water molecules arranged in a fac-position. The molecules in the crystal structures of 1 and 3b are connected into a complicated hydrogen-bonded 2D network, dominated by the O–H⋯O hydrogen bonds. These 2D networks are in turn assembled into a 3D architecture only by weak van der Waals interactions.
The reactions of 1-(4-hydroxyphenyl)-1H-1,2,4-triazole (hptrz) and inorganic Cd(II) salts with different aromatic polycarboxylic acids in mixed-solvent led to the formation of three new crystalline coordination polymers, {[Cd(H2O)2(hptrz)(Hbtc)]n· CH3OH·H3O} 1, [Cd2(H2O) 2(hptrz)2(tp)2]n 2, and {[Cd(H nO)n(hptrz)-(OH-ip)]n·DMF·H 2O} 3 (H3btc = 1,3,5-benzenetricarboxylic acid, H 2tp = terephthalic acid, and OH-H2ip = 5-hydroxyisophthalic acid), which were fully characterized by elemental analysis, IR spectroscopy, single crystal X-ray crystallography, thermogravimertric analysis and luminescence spectra. Structure determination revealed that one-dimensional (1-D) polymeric chains for 1 and 3, and 2-D layered structure for 2 are significantly directed by the coordination mode of the carboxylate groups from aromatic coligands. In contrast, the terminal hptrz ligand affords its uncoordinated phenolic OH group to form classical H-bond interactions with coordinated water and/or carboxylate groups, which are responsible for the formation of 3-D supramolecular networks. In addition, the three solid coordination polymers with considerable thermal stability present strong hptrz-based fluorescence emissions at room temperature.
Six new Ca(II) adducts of formulae [Ca(cyt)2(H2O)4][ClO4]2·2cyt·2H2O (1), [Ca2(cyt)2(H2O)4(ClO4)4] (2), [Ca2(cyt)4(H2O)4Cl2]Cl2 (3), [Ca(H2cyd)2(H2O)4][ClO4]2·3H2O (4), [Ca(H2cyd)2(H2O)4]Cl2·3H2O (5) and [Ca2(CMP)2(H2O)11]·5H2O (6) [cyt = cytosine, H2cyd = cytidine, CMP = cytidine 5′-monophosphate] have been synthesized and structurally characterized. They reveal classical as well as uncommon structures, with H2cyd and CMP showing unprecedented binding sites for the calcium ion. The structure of compound 1 consists of monomeric [Ca(cyt)2(H2O)4]2+ cations and uncoordinated ClO4− anions as well as lattice nucleobase molecules. The structures of compounds 2 and 3 contain either neutral (2) or cationic (3) dinuclear entities. They have in common a bis-μ-carboxylate bridged [Ca2(cyt)2]4+ dinuclear core, where each cytosine molecule shows coordination simultaneously through O2–N3. The coordination sphere of each calcium ion in 2 is completed by two cis water molecules and two ClO4− groups, the latter either in a mono- or in a bis-monodentate fashion. In the structure of 3, the dinuclear entities are cationic due to the direct metal coordination of only two of four Cl− anions, the remaining two being engaged as counterions in hydrogen bonds with the metal complex. The coordination sphere of each calcium ion in 3 is completed by two trans water molecules and an additional cytosine molecule, coordinated this time via O2 only. Compounds 4 and 5 are, like 1 and 3, ionic salts. They share the same [Ca(H2cyd)2(H2O)4]2+ cationic unit and differ by the supramolecular packing motif generated with the aid of water molecules of crystallization and the specific counterions in each case [ClO4− in 4 and Cl− in 5]. The structure of compound 6 consists of neutral [Ca2(CMP)2(H2O)11] asymmetric moieties and crystallization water molecules. Each dimer contains two Ca(II) ions in a slightly different coordination environment and two CMP di-anions exhibiting the chelating coordination mode through the ribose O2′ and O3′ hydroxyl groups and each interacting with a calcium ion. One of them is further coordinated via the nucleobase O2 oxygen atom toward the exogenous calcium ion, thus building up the dinuclear unit. The lack of coordination of Ca2+ ions to phosphate groups observed in 6 is unusual.
The acidities of multiple sites in Cu+–guanine and Cu2+–guanine complexes have been investigated theoretically. To compare, the acidities of guanine (G) and guanine radical cation (G+) have also been included. The results clearly indicate that the acidities of CH or NH groups in Cu+/2+–guanine are significantly enhanced relative to the neutral guanine. The acidic order for guanine derivatives is as follows: Cu2+–guanine > G+ ⩾ Cu+–guanine > G. For Cu+/2+–guanine, N7-coordination exhibits N1–H acid, while for N3-coordination, Cu+–guanine and Cu2+–guanine behave as N2–H2b and N9–H acid, respectively. Moreover, for the given coordination site, N7-coordination greatly decreases the gap between the most acidic group and the least one with respect to that in the neutral guanine. Additionally, it is found that C8–H and N2–H2b groups are significantly acidified with respect to the other groups in the coordination complexes. Natural population analysis assumes the deprotonation process of Cu+/2+–guanine complexes and interprets the highest acidity of Cu2+–guanine of all the guanine derivatives studied. Consequent NBO analyses confirm this assumption. Also, electrostatic potential calculations of [G(–H)]− and [G(–H)] well reproduce the geometrical characters of the deprotonated structures.
Reaction of 1,4,7,10-tetraazacyclododecane (cyclen) and Cu(ClO4)2·6H2O with nucleobases (adenine, hypoxanthine, xanthine, theophylline, cytosine, or uracil) under alkaline conditions gave four ternary cyclen–metal–nucleobase complexes, [Cu(cyclen)(adeninato)]·ClO4·2H2O (1), [{Cu(cyclen)}2(hypoxanthinato)]·(ClO4)3 (2), [Cu(cyclen)(theophyllinato)]3·(ClO4)3·2H2O (3), and [Cu(cyclen)(xanthinato)]·(0.7ClO4)·(0.3ClO4)·3H2O·(0.5H2O)3 (4), whose crystal structures were determined by X-ray diffraction. In the adenine complex 1, a cyclen-capped square–pyramidal Cu2+ ion binds to an adeninato ligand through N(9) with the formation of an intramolecular interligand hydrogen bond between the secondary amino nitrogen of cyclen and N(3) of the base. In the hypoxanthine complex 2, two cyclen-capped Cu2+ ions bind to a hypoxanthinato ligand, one through N(7) with the formation of an intramolecular N(cyclen)–H···O(6) hydrogen bond and the other through N(9) to form an intramolecular N(cyclen)–H···N(3) hydrogen bond. Similarly, in both the theophylline complex 3 and the xanthine complex 4, each cyclen-capped Cu2+ ion binds to a theophyllinato or xanthinato ligand through N(7) with the formation of an intramolecular N(cyclen)–H···O(6) hydrogen bond. However, unlike in 2, steric constraints between amino group(s) of cyclen and the methyl group at N(3) of theophylline in 3 or the proton attached to N(9) of xanthine in 4 preclude the metal bonding to N(9) in 3 or N(3) in 4. The significance of intramolecular interligand interaction as a factor that affects metal-binding site(s) on nucleobases is emphasized.
Two new Cu(II) complexes with mixed ligands, [Cu(mal)(L)(H2O)]·H2O (1) and [Cu(phmal)(L)]2 (2) (mal=malonate dianion, phmal=phenylmalonate dianion, L=5,5′-dimethyl-2,2′-bipyridine) have been synthesized and characterized by elemental analyses, IR, UV–vis and X-ray single crystal diffraction. In both complexes the Cu(II) ions take five-coordinated square pyramidal geometry. 1 has a mononuclear structure, and assembles into a 2D supramolecular network by hydrogen bonding. 2 is a dinuclear complex, and also forms 2D framework via π–π interactions. The structural differences of the two complexes may be attributed to the variation of the substituted group of malonate dianion.
A series of novel copper(II) complexes with the composition of [Cu(H2O)2(L1–5)2(phen)]·2MeOH (1–5), where HL1 = 6-(2-fluorobenzylamino)purine, HL2 = 6-(3-fluorobenzylamino)purine, HL3 = 6-(4-fluorobenzylamino)purine, HL4 = 6-(2-chlorobenzylamino)purine, HL5 = 6-(3-chlorobenzylamino)purine, phen = 1,10-phenanthroline, was synthesized and characterized by elemental analysis, electronic and infrared spectroscopy, magnetic and conductivity measurements. Single-crystal X-ray analysis of complexes 1–4 showed the distorted octahedral geometry in the vicinity of the copper(II) atom, which is coordinated by four nitrogen atoms (two from the bidentate phen ligand and the other two from monodentate 6-(benzylamino)purine derivatives) and two oxygen atoms from the aqua ligands, which together form the N4O2 donor set. The antiradical activity of the prepared complexes was tested by an in vitro SOD-like assay. The IC50 values were found ranging between 104 and 146 μM, which represents ca. 0.5% of the native bovine Cu, Zn-SOD effect.
The first 2D aggregate, {[Cd3(μ3-ade)2(ap)2(H2O)2]·1.5H2O}n (1) (where adeH = adenine; H2ap = adipic acid), with trinuclear Cd(II) as secondary building units, has been successfully synthesized, the compound shows scarce coordination modes (tridentate μ3-N3,N7,N9 for ade and hexadentate η1:η2:η2:η1 for flexible ap) and a novel crystal packing arrangement, exhibiting strong fluorescent emission properties.
A novel Cu(II) mixed-ligand complex, {[Cu(sq)(L)(H2O)]· 0.9H2O}n (1) (sq = squarate dianion, L = 5,5′-dimethyl-2,2′-bipyridine), has been synthesized and characterized by elemental analyses, infrared (IR), and X-ray single-crystal diffraction. In 1, each copper(II) ion has a five-coordinated environment with square pyramidal geometry. A one-dimensional (1D) chain structure of the complex is constructed by squarate in μ-1,2-bis(monodentate) coordination mode and further forms a two-dimensional (2D) framework via “metal chelate–metal chelate ring” π–π stacking interactions between the adjacent chains. This unexpected π–π stacking interaction provides structural evidence for the metalloaromaticity of the Cu(II)-(aromatic α,α′-diimines) chelate rings.
The stability constants of the 1 : 1 complexes formed between Cu(Arm), where Arm = 2,2′-bipyridine or 1,10-phenanthroline, and guanosine 5′-diphosphate (GDP) or its monoprotonated form H(GDP) were determined by potentiometric pH titrations in water and in water containing 30 or 50% (v/v) 1,4-dioxane (25°C; I = 0.1 M, NaNO3). The stability of the binary Cu(GDP) complex is enhanced due to macrochelate formation of the diphosphate-coordinated Cu with N7 of the guanine residue as previously shown. In Cu(Arm)(GDP) the N7 is released from Cu and the stability enhancement of more than one log unit in aqueous solution is clearly attributable to intramolecular stack formation between the aromatic rings of Arm and the guanine moiety. Indeed, stacked isomers occur to more than 90% in equilibrium with open unstacked forms. Surprisingly, the same formation degrees of the stacks are observed for Cu(Arm)(dGMP) complexes, where dGMP = 2′-deoxyguanosine 5′-monophosphate, despite the fact that the overall stability of the latter species is by about 2.7 log units lower. In 1,4-dioxane–water mixtures stack formation is drastically reduced, probably due to hydrophobic solvation of the aromatic rings by the ethylene bridges of 1,4-dioxane. The relevance of these results regarding biological systems is indicated. †This study is dedicated to Professor Dr Alfredo Mederos on the occasion of his retirement from the University of La Laguna (Spain) with the very best wishes for all of his future endeavors.‡This is part 70 of the series Ternary Complexes in Solution; for parts 69 and 68 see 14 and 15, respectively.
The reaction in water of the N-benzyliminodiacetate-copper(II) chelate ([Cu(NBzIDA)]) and the adenine:thymine base pair complex (AdeH:ThyH) with a Cu/NBzIDA/AdeH/ThyH molar ratio of 2:21:1 yields [Cu-2(NBzIDA)(2)(H2O)(2)(mu-N7,Ng-Ade(N3)H)].3H(2)O and free ThyH. The compound has been studied by thermal, spectral, and X-ray diffraction methods. In the asymmetric dinuclear complex units both Cu(II) atoms exhibit a square pyramidal coordination, where the four closest donors are supplied by NBzIDA in a mertridentate conformation and the N7 or N9 donors of AdeH, which is protonated at N3. The mu-N7,N9 bridge represents a new coordination mode for nonsubstituted AdeH, except for some adeninate(1-)-[methylmercury(II)] derivatives studied earlier. The dinuclear complex is stabilized by the Cu-N7 and Cu-N9 bonds and N6-H(exocyclic)...O(carboxyl) and N3-H(heterocyclic)...O(carboxyl) interligand interactions, respectively. The structure of the new compound differs from that of the mononuclear compound [Cu(NBzIDA)(Ade(N9)H)(H2O)].H2O, in which the unusual Cu-N3-(AdeH) bond is stabilized by a N9-H...O(carboxyl) interligand interaction and where alternating benzyl-AdeH intermolecular pi,pi-stacking interactions produce infinite stacked chains. The possibility for ThyH to be involved in the molecular recognition between [Cu(NBzIDA)] and the AdeH:ThyH base pair is proposed.
Two novel Cd(II) coordination polymers, [(CH3)2NH2]2[Cd(cma)2](H2O) (1) and [Cd3(bcma)2(H2O)](H2O) (2) (H2cma=N-(carboxymethyl)-anthranilic acid, H3bcma=N,N′-bis-(carboxymethyl)-anthranilic acid), have been synthesized under hydrothermal conditions and characterized by X-ray single crystal analysis, IR spectra and TGA. Compound 1 possesses 1D double-stranded chain, which further packs into square channels. Compound 2 consists of a novel 3D framework, which not only possesses unique meniscus-like channels but also contains infinite helical chains. Compound 2 is the first example of Cd(II)–aminopolycarboxylate coordination polymers containing three crystallographically independent Cd(II) centres, in which Cd(1), Cd(2), and Cd(3) present distorted pentagonal bipyramidal, tetragonal antiprismatic, and trigonal bipyramidal coordination geometry, respectively. Both compounds display intense room temperature photoluminescence in the solid state.
Treatment of Ni(OAc)2 and nitrilotriacetic acid (H3nta) with nucleobases, adenine, 9-ethylguanine, cytosine, or uracil, provides a complex, [Ni(nta)(adeninium)(H2O)]2·5H2O (1), and two salts, [Ni(nta)(H2O)2]·(cytosinium)·2H2O (2) and [Ni(nta)(H2O)2]·(cytosinium)·(cytosine)·2H2O (3), crystal structures of which were determined by X-ray diffraction, but no adduct for 9-ethylguanine and uracil. In 1, the adeninium moiety binds to the octahedral Ni2+ atom, which is capped with a tripodal nta ligand to form the [Ni(nta)(H2O)]− fragment, at the axial position through the N(7) atom with the formation of an interligand hydrogen bond or hydrogen bonds between the amino substituent N(6) of the base and a carboxylato oxygen or carboxylato oxygens of nta. In 2, the cytosinium molecule does not bind directly to the Ni2+ atom but attaches to the [Ni(nta)(H2O)2]− fragment through triple hydrogen bonds. Complex 3 includes neutral and cationic cytosine molecules, neither of which bind to the Ni2+ atom and to the [Ni(nta)(H2O)2]− fragment either, and, instead, there forms a cytosinium–cytosine complementary base-pair through triple hydrogen bonds. The observed base-specific binding property of the nta-capped octahedral Ni2+ species, that is, adenine≫9-ethylguanine, cytosine, and uracil, is discussed in terms of interligand interactions.
The crystal and molecular structure of the title compound has been determined from three-dimensional X-ray data. The structure was solved by the standard heavy-atom method and refined by least-squares procedures to a conventional R of 0.046 for 2420 observed reflections. The purple complex crystallizes in the monoclinic space group P21/c and the cell dimensions are a = 12.212 (6), b = 12.240 (6), c = 17.635 (9) Å, β = 130.27 (3)°, and V = 2011.3 Å3. The four Cu(C5H5-N5)2 units in the cell pair up to form two centrosymmetric dimeric ions, in which adenine acts as a bridging bidentate ligand. Each copper atom is surrounded by four nitrogen atoms (at 2.00-2.04 Å) from four different adenine molecules and by the oxygen atom (at 2.166 Å) of a water molecule. The geometry around copper may be described as a tetragonal pyramid. The four basal nitrogen atoms are coplanar, but the copper atom is displaced from that plane by 0.269 Å toward the apical water molecule. The large Cu-Cu separation (2.951 Å) is not considered to be consistent with significant metal-metal bonding.
The crystal structure of fac-[bis-(adeninato)(dien) copper (II)] monohydrate has been determined from three-dimensional X-ray diffractometer data by heavy atom Fourier methods. Crystals of fac-[Cu (Ade)2 (dien)]·H2O are monoclinic with unit cell dimensions a=16.015 (2), b=14.577 (2), c=7.959 (1) A, β=90.11 (1)°, space group P21/n, and Z=4. Block-diagonal least-squares refinement using 2695 independent reflexions yielded the R value of 0.068. The copper ion assumes a distorted square pyramidal coordination with five coordination sites of which four square planar sites are occupied by the nitrogen N (9) atoms of two unidentate adenine monoanions and the two (terminal and central) nitrogen atoms of tridentate dien, and the axial site (apical position) is occupied by another terminal nitrogen atom of dien. Therefore, the present dien-copper (II) complex takes a bent form (facial coordination). The propensity of adenine to occupy the cis position in equatorial plane of the copper (II) coordination is much stronger than that of dien to take a planar coordination form.
The structure of dichlorotetra-µ-adenine-dicopper(II) chloride hexahydrate, [Cu2(ade)4Cl2]Cl2,6H2O, has been determined by three-dimensional X-ray crystal structure analysis. The crystals are orthorhombic with unit-cell dimensions a= 23·92, b= 13·844, c= 11·262 Å, Z= 4, space group Cmca. Full-matrix least-squares refinement, using 870 visually estimated reflections, has reached R 0·098.The structure contains the complex ion [Cu2(ade)4Cl2]2+, chloride ions and molecules of water of solvation. The complex ion, which has 2/m crystallographic symmetry, is dimeric with pairs of copper atoms held together by four bridging adenine ligans, co-ordinated via N(3) and N(9). The copper atoms have a square pyramidal co-ordination, with chlorine in the apical position at a distance of 2·429 Å. The metal is 0·33 Å above the plane of four nitrogen atoms, with Cu–N distances of 2·008 and 2·041 Å. The Cu Cu non-bonded separation is 3·066 Å.The chloride ions together with the water molecules and all non-donor nitrogen atoms of adenine form an intricate network of hydrogen bonds in which linkages of the type O–H N, N–H O, and O–H Cl– are involved.
Two zinc complexes—trichloroadeninium zinc(II)(Form 11), C5H6N5Cl3Zn [structure(I)] and a similar complex of Arprinocid, (6-amino-9-(2-chloro-6-fluorobenzyl)purine], C12H10N5FCl4Zn [structure(II)]—have been prepared Structure(I) crystallizes in the space group P21/c with a = 8.223(1)Å, b = 6.755(1) Å, c = 18.698(3) Å, β = 96.10(2)°,and Z = 4. Structure(II) crystallizes in the space group P21/c with a = 8.209(2) Å, b = 6.421(8) Å, c = 31.794(8) Å, β = 90.76(2)°, and Z = 4. Both of these structures were solved by the heavy atom method using diffractometric data and refined to R = 0.028 [structure(I)] and 0.038 [structure(II)]. Zinc with a distorted tetrahedral coordination having three chlorines and N(7) as ligators, protonation of the adenine moiety at N(1), dissymmetry of exocyclic angles at N(7), and an interligand hydrogen bond (“indirect chelation”) involving one of the three chlorines, coordinated to zinc and a proton of the exocylic amino group are the striking features common to both structures. Similar types of indirect chelation as observed in the different complexes of purines have been discussed. The zinc ion deviates from the imidazole plane by 0.412 Å in structure(I) and 0.524 Å in Structure(II). The imidazol and pyrimidine planes fold about the C(4)-C(5) bond by 2.4° in strctur(I) and 3.8° in structure(II). In structure(I), inversion related molecules are paired through N(9)-H…N(3) hydrogen bonds. N-H…Cl hydrogen bonds and C(8)-H…Cl interactions have been observed in both structures.
Equimolar (1:1:1) mixed-ligand Cu(II) complexes with iminodiacetato (IDA) or N-methyl-IDA (MIDA) and N-methyl-imidazole (1MeImH) or ImH, respectively, have been prepared and characterized by thermal, spectral, magnetic and X-ray diffraction methods. [Cu(MIDA) (ImH)] (I) crystallizes in the monoclinic system ). The Cu(II) atom exhibits a flattened square base byramidal coordination (type 4 + 1). The N and two O atoms of the tridentate MIDA and one N of ImH form the square base; one longer CuO bond with the next MIDA ligand in the chain complex completes the Cu(II) five-coordination. [Cu(IDA) (1MeImH) (H2O)2]·H2O (II) crystallizes in the orthorhombic system ). The N and two O atoms from IDA and one N from 1 MeImH define a square coordination; two longer CuOH2 bonds complete the unsymmetrical elongated octahedral coordnation of Cu(II) (type 4 + 1 + 1). The polar NH bonds of ImH in I and of IDA in II as well as the OH bonds of the water molecules of the latter compound are involved in hydrogen bonds. The stepwise water loss in II is explained on the basis of its structural role in the Cu(II) coordination and/or in the crystal packing.
The five-co-ordinate complexes [CuII(tren)(H2O)]Cl21, [CuII(tren)(HAde)]Cl22, [CuII(tren)(HAde)]-[NO3]23 and [CuII(tren)(Ade)]Cl·2H2O 4[tren = tris(2-aminoethyl)amine and HAde = neutral adenine] have been synthesized and characterized. The geometry and structures of the complexes were studied by electronic and IR spectra and, in addition, the structure of complex 4 has been determined by X-ray crystallography. The physicochemical data for complexes 2 and 3 support the presence of neutral adenine co-ordinated to CuII, whereas in complex 4 the adenine molecule is bound in its monoanionic form, as confirmed by the X-ray analysis [monoclinic, space group P21/a, a= 15.001(2), b= 8.422(1), c= 15.039(2)Å, β= 105.90(6)°, Z= 4; R= 0.065 for 2596 unique diffraction data]. The co-ordination polyhedron around the Cu2+ ion is approximately trigonal bipyramidal, with the equatorial sites occupied by the three primary amino nitrogen atoms and the axial positions occupied by the tertiary amino nitrogen and the imidazole N9 nitrogen from the adenine monoanion. The Cu–N(9) distance is rather short at 1.965(9)Å. Such selective metal bonding in adenine is very probably promoted by the trigonal-bipyramidal geometry around CuII and by the relatively low steric hindrance of the CuII(tren) moiety.
The crystal structure of the title compound has been determined from three-dimensional X-ray diffractometer data by Patterson and Fourier methods. Crystals are monoclinic with unit-cell dimensions a = 18.649. b = 8.731, c = 12.028 Å, β = 113.14°, space group C2/c, and Z = 4. Full-matrix least-squares refinement by use of 1657 independent reflections has reached R 0.056. The structure contains complex cations [Cu(adenineH) 2Br 2] 2+ and bromide ions. In the complex cation the central copper atom lies on a diad and is co-ordinated to two N(9) atoms of unidentate adeninium ligands and to two terminal bromide atoms. The copper atom has a co-ordination intermediate between tetrahedral and square planar, with Cu-N 2.013 and Cu-Br 2.361 Å. The adenine molecule is protonated at N(1), and atoms N(1) and N(7) are involved in hydrogen bonding of the type N-H ⋯ Br -.
The structure of the title compound has been determined from three-dimensional X-ray diffractometer data. The crystals are monoclinic, with a = 11.134, b = 12.726, c = 10.404 Å, β = 119° 30′, Z = 2, space group p2 1/c. Full-matrix least-squares refinement, using 1187 independent reflections, has reached R 0.051. The complex, which has 1 crystallographic symmetry, is trinuclear with two adenine molecules bridging three copper atoms via N(3) and N(9). Each adenine molecule spans a Cu ⋯ Cu separation of 3.479 Å. The central copper atom is six-co-ordinate, with two N(3) atoms at 2.027 Å, and four chlorine bridging atoms forming two strong (2.313 Å) and two weak bonds (2.766 Å). The two terminal copper atoms are five-co-ordinate: Cu-N(9) 2.028 Å, Cu-Cl(terminal) 2.272 and 2.291 Å, and Cu-Cl(bridge) 2.324 and 2.743 Å. The co-ordination geometry is based on a square pyramid. A chlorine atom from an adjacent trinuclear unit occupies the sixth pseudo-octahedral position at 3.274 Å. Molecules of water of solvation, all non-donor nitrogen atoms of adenine and the chlorine atoms take part in a network of hydrogen bonds in which linkages of the type N-H ⋯ O, N-H ⋯ Cl, and probably O-H ⋯ Cl are involved. The adenine molecule is protonated at N(1).
Under acidic aqueous conditions, reaction of adenine with copper(II) yields monomeric (AdH22+)2CuCl6, dimeric (Ad)CuCl2, and linear chain polymeric (AdH+)2CuCl4, as well as the previously reported trimeric (AdH+)2Cu3Cl8·4H 2O. The crystal structure of (AdH+)2CuCl4 is analogous to that of (AdH+)2CuBr4. The chloro analogue crystallizes in the space group C2/c of the monoclinic system with the cell dimensions being a = 18.117 (4), b = 8.576 (1), c = 11.814 (4) Å and β = 114.29 (1)° with Z = 4. The structure has been refined by least-squares techniques to a final value of the R factor (on F) of 0.042 based on 2156 independent data. The copper atom is roughly tetrahedrally coordinated and lies on a crystallographic twofold axis with the four coordination sites being occupied by two chloride ligands with a Cu-Cl distance of 2.228 (1) A and by the N(9) atoms of two adeninium cations with a Cu-N(9) distance of 2.012 (2) Å. The cationic purine is protonated at N(1) and N(7). There are weak Cl⋯Cl interactions of length 3.755 (2) Å which link the monomeric units into zigzag polymeric chains with a Cu-Cl⋯Cl angle of 169.23 (7)°. The corresponding Br⋯Br contacts are calculated to be 3.791 Å. These ligand-ligand contacts support Heisenberg linear chain antiferromagnetism with JCl = -7.6 cm-1 and JBr = -36.5 cm-1. The exchange coupling constant observed for dimeric (Ad)CuCl2 is -32 cm-1.
The stoichiometric reaction of Cu2CO3(OH)(2), ethylenediaminetetraacetic acid (H(4)EDTA=C2H4(N(CH2CO2H)(2))(2)) and adenine (AdeH) in water yields crystalline samples of adeninium aqua-(ethylenediamine-N,N,N'-triacetato-N'-acetic)copper(II) dihydrate. The compound (AdeH(2))[Cu(HEDTA)(H2O)].2H(2)O Was studied by TG analysis (with FT-IR study of the evolved gasses), IR, electronic and ESR spectra, magnetic susceptibility data, and single crystal X-ray diffraction methods (monoclinic system, space group P2(1)/c (a=7.053(1), b=42.540(5), c=7.798(1) Angstrom, beta=104.24(1)degrees, Z=4, and final R-1=0.042 for 5113 independent reflections). The asymmetric unit consists of a salt of adeninium(1+) and the aqua-copper(II) complex of HEDTA(3-) as chelating agent, and two crystallisation water molecules. The Cu(II) atom exhibits an elongated octahedral coordination (type 4+1+1). The pentadentate HEDTA(3-) ligand has a typical E,G/R configuration and a free N-carboxymethyl arm. The uncoordinated AdeH(2)(+) ion recognises the anion [Cu(HEDTA)(H2O)](-) through two rather linear N-H...O hydrogen bonds involving the protonated N1 heterocyclic atom and one H atom of the exocyclic-N6 amino group with two 0 atoms of the same HEDTA(3-) carboxylate group (173(3) or 175(3)degrees, and 2.64(1) or 2.80(1) Angstrom, respectively). This ion pair recognises itself by a pi,pi-stacking between the six-membered aromatic rings of adjacent AdeH(2)(+) ions which lay out slightly slipped (beta=gamma=10.1degrees) and anti-parallel at 3.34 Angstrom, thus forming aggregates {(AdeH(2))[Cu(HEDTA)(H2O)]}(2). The remaining O-H (carboxy or water) and N-H (heterocyclic or exocyclic) polar bonds interact with O carboxylate or water atoms or N3 and N7 adeninium atoms building the crystal in an extensive 3D-hydrogen bonded network.
A number of extensions to the multisolution approach to the crystallographic phase problem are discussed in which the negative quartet relations play an important role. A phase annealing method, related to the simulated annealing approach in other optimization problems, is proposed and it is shown that it can result in an improvement of up to an order of magnitude in the chances of solving large structures at atomic resolution. The ideas presented here are incorporated in the program system SHELX-90; the philosophical and mathematical background to the direct-methods part (SHELXS) of this system is described.
Thiacyclophane ligands 1 and 2, containing a meta-xylyldithiaether unit, an aromatic spacing unit and a polyether chain, were prepared in good yield in a three-step synthesis, The macrocyclic organopalladium complexes [Pd(L)(MeCN)][BF4] (3: L = 1, 4: L = 2) were prepared through palladation of the respective thiacyclophane ligand by reaction with [Pd(MeCN)(4)]I[BF4](2). These complexes act as metalloreceptors to aromatic amines such as p-aminopyridine (pap), m-aminopyridine (map) and the DNA nucleobases adenine and guanine. second-sphere coordination. This involves three separate interactions: first-sphere a donation from an aromatic N atom to the Pd centre, second-sphere hydrogen bonds between the NH2 group and polyether O atoms, and pi stacking between the electron-poor aromatic rings of the substrate and the electron-rich aromatic spacing units of the receptor, H-1 NMR spectra exhibit chemical shift changes indicative of the H-bonding and pi-stacking interactions in solution. X-ray structures for thiacyclophane 1, metalloreceptor [Pd(1)(MeCN)][BF4] (3), metalloreceptor/model substrate complexes [Pd(1)(pap)][BF4] (5) and [Pd(2)(pap)][BF4] (7), and metalloreceptor/nucleobase complexes [Pd(1)(adenine)][BF4] (13), [Pd(2)(adenine)][BF4] (14) and [Pd(1)(guanine-BF3)][BF4] (15b) show details of these interactions in the solid state.
The stoichiometric reaction of copper(II) hydroxycarbonate with iminodiacetic acid (H2IDA) in water under reduced pressure yields good crystalline samples of [Cu(IDA)(H2O)2] (compound I). Using equimolar amounts of benzimidazole (HBzIm) the above reaction produces crystals of [Cu(IDA)(HBzIm)(H2O)] (compound II). Both compounds were characterised by TG analysis (with IR study of the evolved gasses in the pyrolysis), spectral and/or magnetic properties (IR, electronic, ESR spectrum, magnetic susceptibility in the 1.8–300 K range) and single crystal X-ray diffraction. The structure of I was re-determined (final R1=0.022) and it confirms the earlier reported distorted octahedral Cu(II) coordination (type 4+1+1), the fac-terdentate chelating and bridging roles for IDA ligand, as well as the ‘polymeric’ chain structure, but with a rather different hydrogen bonding network. In compound II (final R1=0.035) the Cu(II) exhibits a square base pyramidal coordination (type 4+1) and the IDA exhibits the mer-terdentate chelating configuration observed earlier for complexes having equimolar Cu(II)/IDA/HIm or HIm-like ratio, but now with a large dihedral angle (31.3°) between basal Cu(II) coordination and HBzIm mean planes.
N-(Carbamoylmethyl)iminodiacetic [H2ADA=H2NCOCH2N(CH2CO2H)2)] has been crystallised from water and characterised by X-ray crystallography (final value R1=0.051). This compound exhibits a zwitterionic structure (H2ADA±) whose conformation is stabilised by an intra-molecular hydrogen bond interaction between the ‘ammonium’ hydrogen atom and the O-amide atom as acceptor one. All the other polar bonds give hydrogen bonds, which link adjacent zwitterions, one of them is a rather symmetrical and linear link (170(2)°). The appropriate stoichiometric reaction of nickel(II) hydroxycarbonate, NiCO3·2Ni(OH)2·4H2O, and H2ADA in water yields crystalline, green samples of cis-diaqua(N-carbamoylmethyl-iminodiacetato)nickel(II), [Ni(ADA)(H2O)2] (I). Its single crystal X-ray diffraction study was also carried out (final R1=0.031). The crystal of complex I consists of slightly asymmetrical, octahedral coordination units linked in a three-dimensional network stabilised by hydrogen bonds where the water molecules play the most relevant role. Coordination bond distances in I (Å): Ni(1)–N(1)=2.072(2), Ni(1)–O(11)=2.051(2), Ni(1)–O(21)=2.045(2) and Ni(1)–O(31, amide)=2.065(2) with ADA, and Ni(1)–O(1)=2.000(2) and Ni(1)–O(2)=2.106(2) with aqua ligands. ADA acts as tetradentate chelating ligand, which is in contrast with chelating and bridging functions for such ligand in the polymeric Cu(II) derivative, where the metal exhibits a square base pyramidal coordination (type 4+1).
Reaction of tris(2-aminoethyl)amine (tren) and Cu(ClO4)2 or Ni(ClO4)2 with nucleobases (adenine, 9-methyladenine, 9-ethylguanine, hypoxanthine, cytosine, or uracil) has yielded ternary metal complexes of adenine (complex 1 for Cu2+), 9-ethylguanine (2 for Cu2+ and 3 for Ni2+), and hypoxanthine (4 for Cu2+ and 5 for Ni2+) but no adduct for 9-methyladenine, cytosine, and uracil. Crystal structures of [Cu(tren)(adeninato)]·ClO4 (1), [Ni(tren)(9-ethylguanine–0.5H)(H2O)]2·(ClO4)2.5·(ClO3)0.5 (3), and [{Cu(tren)}2(hypoxanthinato)]·(ClO4)3 (4) were determined by X-ray diffraction. In 1, the trigonal-bipyramidal Cu2+ ion capped with a tripodal tetradentate tren ligand, [Cu(tren)]2+, binds to an adeninate anion through N(9) with the formation of an intramolecular hydrogen bond between the amino group of tren and N(3) of the base. The complex 3 involves two crystallographically independent but chemically equivalent [Ni(tren)(9-ethylguanine–0.5H)(H2O)]1.5+ structural units, in each of which the tren-capped octahedral Ni2+ ion, [Ni(tren)(H2O)]2+, binds to the guanine moiety, its N(1) site being hemideprotonated, through N(7) with the formation of two intramolecular hydrogen bonds involving the keto substituent O(6) of the base, one with the amino group of tren and the other with the water ligand. In 4, a hypoxanthinate anion is bound to two [Cu(tren)]2+ fragments, one through N(7) with the formation of an intramolecular hydrogen bond between O(6) of the base and the amino group of tren and the other through N9 with the formation of an intramolecular hydrogen bond between the ring nitrogen N(3) of the base and the amino group of tren. The observed guanine-specific binding property of the tren-capped 5-coordinated Cu2+ or 6-coordinated Ni2+ species, that is, 9-ethylguanine≫9-methyladenine, cytosine, and uracil, is rationalized by interligand interactions.
The systematic study of interactions between metal ions and nucleobases, the constituents of nucleic acids, as well as nucleic acids in general started some 50 years ago, around 1950. This review is an attempt to recall the developments in this field, to list metal binding patterns as established today, and to examine prospects for the future. The focus of this survey will be on the coordination chemistry of metal species with the heterocyclic parts of nucleobases.
SHELXL-93 was originally written as a replacement for the refinement part of the small-molecule program SHELX-76. The program is designed to be easy to use and general for all space groups and uses a conventional structure-factor calculation rather than a fast Fourier transform (FFT) summation. The latter would be faster but in practice involves some small approximations and is not suitable for the treatment of anomalous dispersion or anisotropic thermal motion. The price to pay for the extra precision and generality is that SHELXL is much slower than programs written specifically for macromolecules. This is compensated for, to some extent, by the better convergence properties, reducing the amount of manual intervention required. A new version, SHELXL-97, was released in May 1997; this is the version described in the chapter. The changes are primarily designed to make the program easier to use for macromolecules. Advances in cryogenic techniques, area detectors, and the use of synchrotron radiation enable macromolecular data to be collected to higher resolution than was previously possible. In practice, this tends to complicate the refinement because it is possible to resolve finer details of the structure. It is often necessary to model alternative conformations, and in a few cases, even anisotropic refinement is justified.
Nicló s-Gutiérrez, XI Spanish-Italian Congress on Thermodynamics of Metal Complexes
- E Bugella-Altamirano
- J M González-Pérez
- A G Sicilia-Zafra
- A Castiñ Eiras-Campos
E. Bugella-Altamirano, J.M. González-Pérez, A.G. Sicilia-Zafra,
A. Castiñ eiras-Campos, J. Nicló s-Gutiérrez, XI Spanish-Italian
Congress on Thermodynamics of Metal Complexes, Valencia,
Spain, 2000, Report P-18.
- J E Kickman
- S J Loeb
- S L Murphy
J.E. Kickman, S.J. Loeb, S.L. Murphy, Chem. Eur. J. 3 (1997)
1203.
[15] Md. Abdus Salam, K. Aoki, Inorg. Chim. Acta 311 (2000) 15
(and references therein).
- K Tomita
- T Izuno
- T Fujiwara
K. Tomita, T. Izuno, T. Fujiwara, Biochem. Biophys. Res.
Commun. (1973) 54.
sadabs: Program for Empirical Absorption Correction of Area Detector Data
- G M Sheldrick
G.M. Sheldrick, SADABS: Program for Empirical Absorption
Correction of Area Detector Data, University of Gö ttingen,
Gö ttingen, Germany, 1997.
- M A Salam
- K Aoki
M.A. Salam, K. Aoki, Inorg. Chim. Acta 314 (2001) 71 (and
references therein).
- A Marzotto
- D A Clemente
- A Ciccarese
- G Valle
A. Marzotto, D.A. Clemente, A. Ciccarese, G. Valle, J. Crystallogr. Spectrosc. Res. (1993) 23.
- H Sigel
H. Sigel, Met. Ions Biol. Syst. 2 (1973) 64.
[20] (a) Ch. Janiak, J. Chem. Soc., Dalton Trans. (2000) 3885 (and
references therein);
- H Sakaguchi
- H Anzai
- K Furuhata
- H Ogura
- Y Iitaka
- T Fujita
- T Sakaguchi
H. Sakaguchi, H. Anzai, K. Furuhata, H. Ogura, Y. Iitaka, T.
Fujita, T. Sakaguchi, Chem. Pharm. Bull. 26 (1978) 2465.
- A Marzotto
- D Ciccarese
- A Clemente
- G Valle
A. Marzotto, D. Ciccarese, A. Clemente, G. Valle, J. Chem. Soc.,
Dalton Trans. (1995) 1461.
Area Detector Control and Integration Software , Bruker Analytical X-ray Instruments Inc
- Saint Smart
SMART and SAINT, Area Detector Control and Integration Software, Bruker Analytical X-ray Instruments Inc., Madison, WI,
1997.
SHELXTL: Integrated System for the Determination of Crystal Structures
SHELXTL: Integrated System for the Determination of Crystal
Structures, Bruker AXS Inc., Madison, WI, 2000.
Castiñ eiras, J. Nicló s-Gutiérrez
- D Choquesillo-Lazarte
- B Covelo
- J M González-Pérez
D. Choquesillo-Lazarte, B. Covelo, J.M. González-Pérez, A.
Castiñ eiras, J. Nicló s-Gutiérrez, Polyhedron (2002) in press.
- B Lippert
B. Lippert, Coord. Chem. Rev. 487 (2000) 200.
- E Sletten
E. Sletten, Acta Crystallogr., B 25 (1969) 1480.
- P De Meester
- A C Skapski
P. de Meester, A.C. Skapski, J. Chem. Soc., A (1971) 2167.
- P De Meester
- A C Skapski
P. de Meester, A.C. Skapski, J. Chem. Soc., Dalton Trans. (1972)
2400.
- P De Meester
- A C Skapski
P. de Meester, A.C. Skapski, J. Chem. Soc., Dalton Trans. (1973)
424.
- D B Brown
- J W Hall
- H M Helis
- E G Walton
- D J Hodgson
- W E Hatfield
D.B. Brown, J.W. Hall, H.M. Helis, E.G. Walton, D.J. Hodgson,
W.E. Hatfield, Inorg. Chem. 16 (1977) 2675.
- E Serrano-Padial
- D Choquesillo-Lazarte
- E Bugella-Altamirano
- A Castiñ Eiras
- R Carballo
- J Nicló S-Gutiérrez
E. Serrano-Padial, D. Choquesillo-Lazarte, E. Bugella-Altamirano, A. Castiñ eiras, R. Carballo, J. Nicló s-Gutiérrez, Polyhedron
21 (2002) 1451.
- J E Kickman
- S J Loeb
- S L Murphy
J.E. Kickman, S.J. Loeb, S.L. Murphy, Chem. Eur. J. 3 (1997)
1203.
- Md
- K Salam
- Aoki
Md. Abdus Salam, K. Aoki, Inorg. Chim. Acta 311 (2000) 15
(and references therein).
- M R Taylor
M.R. Taylor, Acta Crystallogr., B 29 (1973) 884;
- P T Muthiah
- S K Mazumdar
- S Chaudhuri
P.T. Muthiah, S.K. Mazumdar, S. Chaudhuri, J. Inorg.
Biochem. 19 (1983) 237;
- M R Taylor
- J A Westphalen
M.R. Taylor, J.A. Westphalen, Acta Crystallogr., A 37 (1981)
C63.
- M J Román-Alpiste
- J D Martín-Ramos
- A Castiñ Eiras-Campos
- E Bugella-Altamirano
- A G Sicilia-Zafra
- J M González-Pérez
M.J. Román-Alpiste, J.D. Martín-Ramos, A. Castiñ eiras-Campos, E. Bugella-Altamirano, A.G. Sicilia-Zafra, J.M. González-Pérez, J. Nicló s-Gutiérrez, Polyhedron 18 (1999) 3341.
- H Sigel
H. Sigel, Met. Ions Biol. Syst. 2 (1973) 64.
- A Castiñ Eiras Campos
- A G Sicilia Zafra
- J M González Pérez
- J Nicló S Gutiérrez
- E Chinea
- A Mederos
A. Castiñ eiras Campos, A.G. Sicilia Zafra, J.M. González Pérez,
J. Nicló s Gutiérrez, E. Chinea, A. Mederos, Inorg. Chim. Acta
241 (1996) 39.
- Saint Smart
SMART and SAINT, Area Detector Control and Integration Software, Bruker Analytical X-ray Instruments Inc., Madison, WI,
1997.