Nucleobases in Molecular Recognition: Molecular Adducts of Adenine and Cytosine with COOH Functional Groups

Perumalla, Sathyanarayana Reddy; Suresh, Eringathodi; Pedireddi, V. R.

doi:10.1002/ange.200502434

Cited by 12 publications

(6 citation statements)

References 78 publications

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“…By correlating the hydrogen-bonding pattern observed in the 2:1 structure of the present study with two of our previous structures (Sridhar & Ravikumar, 2008, 2010, as well as with structures reported in the literature (Perumalla et al, 2005), the existence of cytosine base-pair self-assembly with triple hydrogen-bonding patterns is predominant.…”

Section: Figuresupporting

confidence: 82%

“…Adjacent cytosinium-cytosine base pairs are held together by two N-HÁ Á ÁO hydrogen bonds between NH 2 and carbonyl groups, leading to one-dimensional supramolecular polymeric ribbons along the crystallographic b axis. Similar triple hydrogen-bonded Watson-Crick base pairs are observed in cytosinium 4-nitrobenzoate cytosine monohydrate (Sridhar & Ravikumar, 2008), cytosine salicylic acid hydrate (2/3/2) complex (Sridhar & Ravikumar, 2010) and cytosine complexes with benzoic and phthalic acids (Perumalla et al, 2005…”

Section: Figurementioning

confidence: 52%

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Supramolecular hydrogen-bonded networks in cytosinium nicotinate monohydrate and cytosinium isonicotinate cytosine dihydrate

Sridhar¹,

Ravikumar²

2010

Acta Crystallogr C

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The title compounds are proton-transfer compounds of cytosine with nicotinic acid [systematic name: 4-amino-2-oxo-2,3-dihydropyrimidin-1-ium nicotinate monohydrate (cytosinium nicotinate hydrate), C(4)H(6)N(3)O(+) x C(6)H(4)NO(2)(-) x H(2)O, (I)] and isonicotinic acid [systematic name: 4-amino-2-oxo-2,3-dihydropyrimidin-1-ium isonicotinate-4-aminopyrimidin-2(1H)-one-water (1/1/2) (cytosinium isonicotinate cytosine dihydrate), C(4)H(6)N(3)O(+) x C(6)H(4)NO(2)(-) x C(4)H(5)N(3)O x 2 H(2)O, (II)]. In (I), the cation and anion are interlinked by N-H...O hydrogen bonding to form a one-dimensional tape. These tapes are linked through water molecules to form discrete double sheets. In (II), the cytosinium-cytosine base pairs are connected by triple hydrogen bonds, leading to one-dimensional polymeric ribbons. These ribbons are further interconnected via nicotinate-water and water-water hydrogen bonding, resulting in an overall three-dimensional network.

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Section: Figuresupporting

confidence: 82%

Section: Figurementioning

confidence: 52%

Supramolecular hydrogen-bonded networks in cytosinium nicotinate monohydrate and cytosinium isonicotinate cytosine dihydrate

Sridhar¹,

Ravikumar²

2010

Acta Crystallogr C

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“…This cytosine-cytosine base pair (formed via three hydrogen bonds) is very similar to the protonated cytosine-neutral cytosine pair observed in many crystal structures (e.g. Das et al, 2010;Sridhar et al, 2010;Perumalla et al, 2005). Both these aspects are very interesting from a crystal engineering point of view .…”

Section: Structure Description Of [Znbr 2 (5fc)(h 2 O)]á(5fc) (Iii)supporting

confidence: 71%

Supramolecular architectures in metal(II) (Cd/Zn) halide/nitrate complexes of cytosine/5-fluorocytosine

2018

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Three new metal(II)-cytosine (Cy)/5-fluorocytosine (5FC) complexes, namely bis(4-amino-1,2-dihydropyrimidin-2-one-κN)diiodidocadmium(II) or bis(cytosine)diiodidocadmium(II), [CdI(CHNO)], (I), bis(4-amino-1,2-dihydropyrimidin-2-one-κN)bis(nitrato-κO,O')cadmium(II) or bis(cytosine)bis(nitrato)cadmium(II), [Cd(NO)(CHNO)], (II), and (6-amino-5-fluoro-1,2-dihydropyrimidin-2-one-κN)aquadibromidozinc(II)-6-amino-5-fluoro-1,2-dihydropyrimidin-2-one (1/1) or (6-amino-5-fluorocytosine)aquadibromidozinc(II)-4-amino-5-fluorocytosine (1/1), [ZnBr(CHFNO)(HO)]·CHFNO, (III), have been synthesized and characterized by single-crystal X-ray diffraction. In complex (I), the Cd ion is coordinated to two iodide ions and the endocyclic N atoms of the two cytosine molecules, leading to a distorted tetrahedral geometry. The structure is isotypic with [CdBr(CHNO)] [Muthiah et al. (2001). Acta Cryst. E57, m558-m560]. In compound (II), each of the two cytosine molecules coordinates to the Cd ion in a bidentate chelating mode via the endocyclic N atom and the O atom. Each of the two nitrate ions also coordinates in a bidentate chelating mode, forming a bicapped distorted octahedral geometry around cadmium. The typical interligand N-H...O hydrogen bond involving two cytosine molecules is also present. In compound (III), one zinc-coordinated 5FC ligand is cocrystallized with another uncoordinated 5FC molecule. The Zn atom coordinates to the N(1) atom (systematic numbering) of 5FC, displacing the proton to the N(3) position. This N(3)-H tautomer of 5FC mimics N(3)-protonated cytosine in forming a base pair (via three hydrogen bonds) with 5FC in the lattice, generating two fused R(8) motifs. The distorted tetrahedral geometry around zinc is completed by two bromide ions and a water molecule. The coordinated and nonccordinated 5FCs are stacked over one another along the a-axis direction, forming the rungs of a ladder motif, whereas Zn-Br bonds and N-H...Br hydrogen bonds form the rails of the ladder. The coordinated water molecules bridge the two types of 5FC molecules via O-H...O hydrogen bonds. The cytosine molecules are coordinated directly to the metal ion in each of the complexes and are hydrogen bonded to the bromide, iodide or nitrate ions. In compound (III), the uncoordinated 5FC molecule pairs with the coordinated 5FC ligand through three hydrogen bonds. The crystal structures are further stabilized by N-H...O, N-H...N, O-H...O, N-H...I and N-H...Br hydrogen bonds, and stacking interactions.

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“…Thus far, only two infinite arrangement patterns of CHC + have been reported, both of which have a ribbon‐like 1D structure in terms of double complementary NH⋅⋅⋅O hydrogen bonds as shown in Figure 5. In one arrangement pattern of CHC + , the hydrogen bonds are formed between the imino nitrogen atom (N11) and the ketone oxygen atom (O11), as found in 2 (Figure 5 a), whereas in the other pattern, the hydrogen bonds are formed between the amino nitrogen atom (N13) and the ketone oxygen atom (Figure 5 b), as observed for the salts with phthalate,5e [Ni(nitrilotriacetato)(H 2 O) 2 ] − ,6d TCNQ .− ,7c,d and TCNQ‐OMe − 7…”

Section: Resultsmentioning

confidence: 74%

Cover Picture: Oxidative Cyclization Reaction of 2‐Aryl‐Substituted Cinnamates To Form Phenanthrene Carboxylates by Using MoCl₅ (Chem. Eur. J. 39/2014)

Wehming

Schubert

Schnakenburg

et al. 2014

Chemistry A European J

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Protonated species of the nucleobase cytosine (C), namely the monoprotonated CH+ and the hemiprotonated CHC+, were used to obtain four charge‐transfer complexes of [Ni(dmit)2] (dmit: 1,3‐dithiole‐2‐thione‐4,5‐dithiolate). Diffusion methods afforded two semiconducting [Ni(dmit)2]− salts; (CH)[Ni(dmit)2](CH3CN) (1) and (CHC)[Ni(dmit)2] (2). In salt 1, the [Ni(dmit)2]− ions with a S=1/2 spin construct a uniform one‐dimensional array along the molecular long axis, and the significant intermolecular interaction along the face‐to‐face direction results in a spin‐singlet ground state. In contrast, salt 2 exhibits the Mott insulating behavior associated with uniform 1D arrays of [Ni(dmit)2]−, which assemble a two‐dimensional layer that is sandwiched between the layers of hydrogen‐bonded CHC+ ribbons. Multiple hydrogen bonds between CHC+ and [Ni(dmit)2]− seem to result in the absence of structural phase transition down to 0.5 K. Electrooxidation of [Ni(dmit)2]− afforded the polymorphs of the [Ni(dmit)2]0.5− salts, (CHC+)[{Ni(dmit)2}0.5−]2 (3 and 4), which are the first mixed‐valence salts of nucleobase cations with metal complex anions. Similar to 2, salt 3 contains CHC+ ribbons that are sandwiched between the 2D [Ni(dmit)2]0.5− layers. In the layer, the [Ni(dmit)2]0.5− ions form dimers with a S=1/2 spin and the narrow electronic bandwidth causes a semiconducting behavior. In salt 4, the CHC+ units form an unprecedented corrugated 2D sheet, which is sandwiched between the 2D [Ni(dmit)2]0.5− layers that involve ring‐over‐atom and spanning overlaps. In contrast to 3, salt 4 exhibits metallic behavior down to 1.8 K, associated with a wide bandwidth and a 2D Fermi surface. The ability of hydrogen‐bonded CHC+ sheets as a template for the anion radical arrangements is demonstrated.

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Nucleobases in Molecular Recognition: Molecular Adducts of Adenine and Cytosine with COOH Functional Groups

Cited by 12 publications

References 78 publications

Supramolecular hydrogen-bonded networks in cytosinium nicotinate monohydrate and cytosinium isonicotinate cytosine dihydrate

Supramolecular hydrogen-bonded networks in cytosinium nicotinate monohydrate and cytosinium isonicotinate cytosine dihydrate

Supramolecular architectures in metal(II) (Cd/Zn) halide/nitrate complexes of cytosine/5-fluorocytosine

Cover Picture: Oxidative Cyclization Reaction of 2‐Aryl‐Substituted Cinnamates To Form Phenanthrene Carboxylates by Using MoCl₅ (Chem. Eur. J. 39/2014)

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Nucleobases in Molecular Recognition: Molecular Adducts of Adenine and Cytosine with COOH Functional Groups

Cited by 12 publications

References 78 publications

Supramolecular hydrogen-bonded networks in cytosinium nicotinate monohydrate and cytosinium isonicotinate cytosine dihydrate

Supramolecular hydrogen-bonded networks in cytosinium nicotinate monohydrate and cytosinium isonicotinate cytosine dihydrate

Supramolecular architectures in metal(II) (Cd/Zn) halide/nitrate complexes of cytosine/5-fluorocytosine

Cover Picture: Oxidative Cyclization Reaction of 2‐Aryl‐Substituted Cinnamates To Form Phenanthrene Carboxylates by Using MoCl5 (Chem. Eur. J. 39/2014)

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Product

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Cover Picture: Oxidative Cyclization Reaction of 2‐Aryl‐Substituted Cinnamates To Form Phenanthrene Carboxylates by Using MoCl₅ (Chem. Eur. J. 39/2014)