The surprising pairing of 2‐aminoimidazo[1,2‐a][1,3,5]triazin‐4‐one,a component of an expanded DNA alphabet

Synthetic biologists demonstrate their command over natural biology by reproducing the behaviors of natural living systems on synthetic biomolecular platforms. For nucleic acids, this is being done stepwise, first by adding replicable nucleotides to DNA, and then removing its standard nucleotides. This challenge has been met in vitro with `six‐letter' DNA and RNA, where the Watson–Crick pairing `concept' is recruited to increase the number of independently replicable nucleotides from four to six. The two nucleobases most successfully added so far are Z and P , which present a donor–donor–acceptor and an acceptor–acceptor–donor pattern, respectively. This pair of nucleobases are part of an `artificially expanded genetic information system' (AEGIS). The Z nucleobase has been already crystallized, characterized, and published in this journal [Matsuura et al. (2016). Acta Cryst. C 72 , 952–959]. More recently, variants of Taq polymerase have been crystallized with the pair P : Z trapped in the active site. Here we report the crystal structure of the nucleobase 2‐aminoimidazo[1,2‐a][1,3,5]triazin‐4‐one (trivially named P ) as the monohydrate, C₅H₅N₅O·H₂O. The nucleobase P was crystallized from water and characterized by X‐ray diffraction. Interestingly, the crystal structure shows two tautomers of P packed in a Watson–Crick fashion that cocrystallized in a 1:1 ratio.     

Crystal structures of deprotonated nucleobases from an expanded DNA alphabet

Reported here is the crystal structure of a heterocycle that implements a donor–donor–acceptor hydrogen‐bonding pattern, as found in the Z component [6‐amino‐5‐nitropyridin‐2(1H)‐one] of an artificially expanded genetic information system (AEGIS). AEGIS is a new form of DNA from synthetic biology that has six replicable nucleotides, rather than the four found in natural DNA. Remarkably, Z crystallizes from water as a 1:1 complex of its neutral and deprotonated forms, and forms a `skinny' pyrimidine–pyrimidine pair in this structure. The pair resembles the known intercalated cytosine pair. The formation of the same pair in two different salts, namely poly[[aqua(μ₆‐2‐amino‐6‐oxo‐3‐nitro‐1,6‐dihydropyridin‐1‐ido)sodium]–6‐amino‐5‐nitropyridin‐2(1H)‐one–water (1/1/1)], denoted Z‐Sod, {[Na(C₅H₄N₃O₃)(H₂O)]·C₅H₅N₃O₃·H₂O}_n, and ammonium 2‐amino‐6‐oxo‐3‐nitro‐1,6‐dihydropyridin‐1‐ide–6‐amino‐5‐nitropyridin‐2(1H)‐one–water (1/1/1), denoted Z‐Am, NH₄⁺·C₅H₄N₃O₃⁻·C₅H₅N₃O₃·H₂O, under two different crystallization conditions suggests that the pair is especially stable. Implications of this structure for the use of this heterocycle in artificial DNA are discussed.     

Structural basis of cooperative ligand binding by the glycine riboswitch

The glycine riboswitch regulates gene expression through the cooperative recognition of its amino acid ligand by a tandem pair of aptamers. A 3.6 ? crystal structure of the tandem riboswitch from the glycine permease operon of Fusobacterium nucleatum reveals the glycine binding sites and an extensive network of interactions, largely mediated by asymmetric A-minor contacts, that serve to communicate ligand binding status between the aptamers. These interactions provide a structural basis for how the glycine riboswitch cooperatively regulates gene expression.     

Polymorphs of the antiviral drug ganciclovir

Ganciclovir (GCV; systematic name: 2‐amino‐9‐{[(1,3‐dihydroxypropan‐2‐yl)oxy]methyl}‐6,9‐dihydro‐1H‐purin‐6‐one), C₉H₁₃N₅O₄, an antiviral drug for treating cytomegalovirus infections, has two known polymorphs (Forms I and II), but only the structure of the metastable Form II has been reported [Kawamura & Hirayama (2009). X‐ray Struct. Anal. Online , 25 , 51–52]. We describe a successful preparation of GCV Form I and its crystal structure. GCV is an achiral molecule in the sense that its individual conformers, which are generally chiral objects, undergo fast interconversion in the liquid state and cannot be isolated. In the crystalline state, GCV exists as two inversion‐related conformers in Form I and as a single chiral conformer in Form II. This situation is similar to that observed for glycine, also an achiral molecule, whose α‐polymorph contains two inversion‐related conformers, while the γ‐polymorph contains a single conformer that is chiral. The hydrogen bonds are exclusively intermolecular in Form I, but both inter‐ and intramolecular in Form II, which accounts for the different molecular conformations in the two polymorphs.     

Characterization of Thallium(I) Saccharinate: an unprecedented Coordination of the Saccharinate Ligand

The crystal structure of [Tl₂(sac)₂(H₂O)]_n (sac = saccharinate anion) has been solved using single crystal X‐ray diffraction. It crystallizes in the triclinic space group P 1 with Z = 2 and presents a polymeric structure formed by two saccharinate anions, one water molecule and two chemically different Tl^I cations, one 8‐coordinate and the other 5‐coordinate. Saccharinate shows an unprecedented coordination behavior as it acts as chelating ligand through its N and carbonyl O atoms with the N atom interacting simultaneously with both metal centers, and participation of sulphonyl oxygen atoms in bonding. The most important features of the IR spectrum of the complex are discussed on the basis of the structural peculiarities.     

Pyridine and 3‐methylpyridine solvates of the triple sulfa drug constitutent sulfamethazine

Sulfonamides display a wide variety of pharmacological activities. Sulfamethazine [abbreviated as SMZ; systematic name 4‐amino‐N‐(4,6‐dimethylpyrimidin‐2‐yl)benzenesulfonamide], one of the constitutents of the triple sulfa drugs, has wide clinical use. Pharmaceutical solvates are crystalline solids of active pharmaceutical ingredients (APIs) incorporating one or more solvent molecules in the crystal lattice, and these have received special attention, as the solvent molecule can impart characteristic physicochemical properties to APIs and solvates, therefore playing a significant role in drug development. The ability of SMZ to form solvates has been investigated. Both pyridine and 3‐methylpyridine form solvates with SMZ in 1:1 molar ratios. The pyridine monosolvate, C₁₂H₁₄N₄O₂S·C₅H₅N, crystallizes in the orthorhombic space group Pna 2₁, with Z = 8 and two molecules per assymetric unit, whereas the 3‐methylpyridine monosolvate, C₁₂H₁₄N₄O₂S·C₆H₇N, crystallizes in the orthorhombic space group P 2₁2₁2₁, with Z = 4. Crystal structure analysis reveals intramolecular N—H…N hydrogen bonds between the molecules of SMZ and the pyridine solvent molecules. The solvent molecules in both structures play an active part in strong intermolecular interactions, thereby contributing significantly to the stability of both structures. Three‐dimensional hydrogen‐bonding networks exist in both structures involving at least one sulfonyl O atom and the amine N atom. In the pyridine solvate, there is a short π–π interaction [centroid–centroid distance = 3.926 (3) Å] involving the centroids of the pyridine rings of two solvent molecules and a weak intermolecular C—H…π interaction also contributes to the stability of the crystal packing.     

The antitumour drug 7‐ethyl‐10‐hydroxycamptothecin monohydrate and its solid‐state hydrolysis mechanism on heating

7‐Ethyl‐10‐hydroxycamptothecin [systematic name: (4S)‐4,11‐diethyl‐4,9‐dihydroxy‐1H‐pyrano[3′,4′:6,7]indolizino[1,2‐b]quinoline‐3,14(4H,12H)‐dione, SN‐38] is an antitumour drug which exerts activity through the inhibition of topoisomerase I. The crystal structure of SN‐38 as the monohydrate, C₂₂H₂₀N₂O₅·H₂O, reveals that it is a monoclinic crystal, with one SN‐38 molecule and one water molecule in the asymmetric unit. When the crystal is heated to 473 K, approximately 30% of SN‐38 is hydrolyzed at its lactone ring, resulting in the formation of the inactive carboxylate form. The molecular arrangement around the water molecule and the lactone ring of SN‐38 in the crystal structure suggests that SN‐38 is hydrolyzed by the water molecule at (x, y, z) nucleophilically attacking the carbonyl C atom of the lactone ring at (x − 1, y, z − 1). Hydrogen bonding around the water molecules and the lactone ring appears to promote this hydrolysis reaction: two carbonyl O atoms, which are hydrogen bonded as hydrogen‐bond acceptors to the water molecule at (x, y, z), might enhance the nucleophilicity of this water molecule, while the water molecule at (−x, y + , −z), which is hydrogen bonded as a hydrogen‐bond donor to the carbonyl O atom at (x − 1, y, z − 1), might enhance the electrophilicity of the carbonyl C atom.     

A 2:1 sulfamethazine–theophylline cocrystal exhibiting two tautomers of sulfamethazine

In the title cocrystal, 4‐amino‐N‐(4,6‐dimethylpyrimidin‐2‐yl)benzenesulfonamide–4‐amino‐N‐(4,6‐dimethyl‐1,2‐dihydropyrimidin‐2‐ylidene)benzenesulfonamide–1,3‐dimethyl‐7H‐purine‐2,6‐dione (1/1/1), C₇H₈N₄O₂·2C₁₂H₁₄N₄O₂S, two sulfamethazine molecules cocrystallize with a single molecule of theophylline. Each molecule of sulfamethazine forms a hydrogen‐bonded ribbon along the b axis crosslinked by further hydrogen bonding. The two sulfamethazine molecules exhibit a hydrogen‐shift isomerization so that the crystal structure contains both tautomeric forms. Calculation of their relative energies showed that the tautomer protonated at the chain N atom is considerably more stable than the one where an N atom in the aromatic ring is protonated. The latter, here observed for the first time, is stabilized through strong intermolecular interactions with the theophylline molecules.     

Supramolecular hydrogen‐bonding patterns in the organic–inorganic hybrid compound bis(4‐amino‐5‐chloro‐2,6‐dimethylpyrimidinium) tetrathiocyanatozinc(II)–4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–water (1/2/2)

Zinc thiocyanate complexes have been found to be biologically active compounds. Zinc is also an essential element for the normal function of most organisms and is the main constituent in a number of metalloenzyme proteins. Pyrimidine and aminopyrimidine derivatives are biologically very important as they are components of nucleic acids. Thiocyanate ions can bridge metal ions by employing both their N and S atoms for coordination. They can play an important role in assembling different coordination structures and yield an interesting variety of one‐, two‐ and three‐dimensional polymeric metal–thiocyanate supramolecular frameworks. The structure of a new zinc thiocyanate–aminopyrimidine organic–inorganic compound, (C₆H₉ClN₃)₂[Zn(NCS)₄]·2C₆H₈ClN₃·2H₂O, is reported. The asymmetric unit consist of half a tetrathiocyanatozinc(II) dianion, an uncoordinated 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidinium cation, a 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine molecule and a water molecule. The Zn^II atom adopts a distorted tetrahedral coordination geometry and is coordinated by four N atoms from the thiocyanate anions. The Zn^II atom is located on a special position (twofold axis of symmetry). The pyrimidinium cation and the pyrimidine molecule are not coordinated to the Zn^II atom, but are hydrogen bonded to the uncoordinated water molecules and the metal‐coordinated thiocyanate ligands. The pyrimidine molecules and pyrimidinium cations also form base‐pair‐like structures with an R₂²(8) ring motif via N—H…N hydrogen bonds. The crystal structure is further stabilized by intermolecular N—H…O, O—H…S, N—H…S and O—H…N hydrogen bonds, by intramolecular N—H…Cl and C—H…Cl hydrogen bonds, and also by π–π stacking interactions.     

2‐Amino‐5‐(3,4‐dimethoxybenzylidene)‐1‐methylimidazol‐4(5H)‐one N,N‐dimethylformamide monosolvate

The crystal structure of the title compound, C₁₃H₁₅N₃O₃·C₃H₇NO, was determined as part of a larger project focusing on creatinine derivatives as potential pharmaceuticals. The molecule is essentially planar, in part because of intramolecular hydrogen bonding. Inversion‐related pairs of molecules result from intermolecular hydrogen bonding. The π systems of 2‐amino‐5‐(3,4‐dimethoxybenzylidene)‐1‐methylimidazol‐4(5H)‐one and an inversion‐related molecule overlap slightly, indicating a small amount of π–π stacking. Bond lengths, angles and torsion angles are consistent with similar structures, except in the imidazolone ring near the doubly bonded C atom, where significant differences occur.     

Adiponitrile at 100 K

Adiponitrile, C₆H₈N₂, is a key intermediate in the synthesis of the polyamide Nylon 66 and is produced industrially on a large scale. We have determined the crystal and molecular structure of adiponitrile by single‐crystal X‐ray analysis at 100 K, a suitable crystal (m.p. 275 K) having been grown from the melt at low temperature. The compound crystallizes in the monoclinic space group P 2₁/c with Z = 2. In the crystal structure, the molecule adopts an exact C_i‐symmetric gauche –anti –gauche conformation of the C—C—C—C skeleton about an inversion centre. The molecules are densely packed, with short intermolecular contacts between the α‐H and nitrile N atoms.     

An unusual syn conformation of 5‐formyluracil stabilized by supramolecular interactions

The asymmetric unit of the amino–oxo tautomer of 5‐formyluracil (systematic name: 2,4‐dioxo‐1,2,3,4‐tetrahydropyrimidine‐5‐carbaldehyde), C₅H₄N₂O₃, comprises one planar amino–oxo tautomer, as every atom in the structure lies on a crystallographic mirror plane. At variance with all the previously reported small‐molecule crystal structures containing the 5‐formyluracil residue, the formyl substituent in the title compound exhibits an unusual syn conformation. The molecules are linked into planar sheets parallel to the bc plane by a combination of six N—H...O and C—H...O hydrogen bonds. Four of the hydrogen bonds are utilized to stabilize the formyl group in the syn conformation.     

Conformational study of the 3,6‐dihydro‐2H‐1,4‐oxazin‐2‐one fragment in 8‐tert‐butyl‐7‐methoxy‐8‐methyl‐9‐oxa‐6‐azaspiro[4.5]decane‐2,10‐dione stereoisomers

Unnatural cyclic α‐amino acids play an important role in the search for biologically active compounds and macromolecules. Enantiomers of natural amino acids with a d configuration are not naturally encoded, but can be chemically synthesized. The crystal structures of two enantiomers obtained by a method of stereoselective synthesis, namely (5R ,8S )‐8‐tert‐butyl‐7‐methoxy‐8‐methyl‐9‐oxa‐6‐azaspiro[4.5]decane‐2,10‐dione, (1), and (5S ,8R )‐8‐tert‐butyl‐7‐methoxy‐8‐methyl‐9‐oxa‐6‐azaspiro[4.5]decane‐2,10‐dione, (2), both C₁₄H₂₁NO₄, were determined by X‐ray diffraction. Both enantiomers crystallize isostructurally in the space group P 2₁, with one molecule in the asymmetric unit and with the same packing motif. The crystal structures are stabilized by C—H…O hydrogen bonds, resulting in the formation of chains along the [100] and [010] directions. The conformation of the 3,6‐dihydro‐2H‐1,4‐oxazin‐2‐one fragment was compared with other crystal structures possessing this heterocyclic moiety. The comparison showed that the title compounds are not exceptional among structures containing the 3,6‐dihydro‐2H‐1,4‐oxazin‐2‐one fragment. The planar moiety was more frequently observed in derivatives in which this fragment was not condensed with other rings.     

Supramolecular architectures in CoII and CuII complexes with thiophene‐2‐carboxylate and 2‐amino‐4,6‐dimethoxypyrimidine ligands

The coordination chemistry of mixed‐ligand complexes continues to be an active area of research since these compounds have a wide range of applications. Many coordination polymers and metal–organic framworks are emerging as novel functional materials. Aminopyrimidine and its derivatives are flexible ligands with versatile binding and coordination modes which have been proven to be useful in the construction of organic–inorganic hybrid materials and coordination polymers. Thiophenecarboxylic acid, its derivatives and their complexes exhibit pharmacological properties. Cobalt(II) and copper(II) complexes of thiophenecarboxylate have many biological applications, for example, as antifungal and antitumor agents. Two new cobalt(II) and copper(II) complexes incorporating thiophene‐2‐carboxylate (2‐TPC) and 2‐amino‐4,6‐dimethoxypyrimidine (OMP) ligands have been synthesized and characterized by X‐ray diffraction studies, namely (2‐amino‐4,6‐dimethoxypyrimidine‐κN)aquachlorido(thiophene‐2‐carboxylato‐κO)cobalt(II) monohydrate, [Co(C₅H₃O₂S)Cl(C₆H₉N₃O₂)(H₂O)]·H₂O, (I), and catena‐poly[copper(II)‐tetrakis(μ‐thiophene‐2‐carboxylato‐κ²O:O′)‐copper(II)‐(μ‐2‐amino‐4,6‐dimethoxypyrimidine‐κ²N¹:N³)], [Cu₂(C₅H₃O₂S)₄(C₆H₉N₃O₂)]_n, (II). In (I), the Co^II ion has a distorted tetrahedral coordination environment involving one O atom from a monodentate 2‐TPC ligand, one N atom from an OMP ligand, one chloride ligand and one O atom of a water molecule. An additional water molecule is present in the asymmetric unit. The amino group of the coordinated OMP molecule and the coordinated carboxylate O atom of the 2‐TPC ligand form an interligand N—H…O hydrogen bond, generating an S(6) ring motif. The pyrimidine molecules also form a base pair [R₂²(8) motif] via a pair of N—H…N hydrogen bonds. These interactions, together with O—H…O and O—H…Cl hydrogen bonds and π–π stacking interactions, generate a three‐dimensional supramolecular architecture. The one‐dimensional coordination polymer (II) contains the classical paddle‐wheel [Cu₂(CH₃COO)₄(H₂O)₂] unit, where each carboxylate group of four 2‐TPC ligands bridges two square‐pyramidally coordinated Cu^II ions and the apically coordinated OMP ligands bridge the dinuclear copper units. Each dinuclear copper unit has a crystallographic inversion centre, whereas the bridging OMP ligand has crystallographic twofold symmetry. The one‐dimensional polymeric chains self‐assemble via N—H…O, π–π and C—H…π interactions, generating a three‐dimensional supramolecular architecture.     

Lenalidomide,an antineoplastic drug,and its hemihydrate

The crystal structures of lenalidomide [systematic name: (RS)‐3‐(4‐amino‐1‐oxoisoindolin‐2‐yl)piperidine‐2,6‐dione], C₁₃H₁₃N₃O₃, (I), an antineoplastic drug, and its hemihydrate, C₁₃H₁₃N₃O₃·0.5H₂O, (II), have been determined by single‐crystal X‐ray diffraction analysis. The overall conformation of the molecule defined by the orientation of the two ring portions, viz. pyridinedione and isoindolinone, is twisted in both structures. The influence of the self‐complementary pyridinedione ring is seen in the crystal packing of both structures through its involvement in forming hydrogen‐bonded dimers, although alternate dione O atoms are utilized. An extensive series of N—H...O hydrogen bonds link the dimers into two‐dimensional supramolecular arrays built up from infinite chains. The water molecule in (II) has a cohesive function, connecting three lenalidomide molecules by hydrogen bonds. The significance of this study lies in the analysis of the interactions in these structures and the aggregations occurring via hydrogen bonds in the hydrated and dehydrated crystalline forms of the title compound.     

Structural and Spectroscopic Characterization of Ammonium Thiosaccharinate Monohydrate

The crystal structure of NH₄[tsac]·H₂O (tsac = anion of the thiosaccharin molecule) has been determined by single crystal X‐ray diffractometry. It crystallizes in the orthorhombic space group Pbca with Z = 8. The infrared spectrum of the compound was also recorded and its most important features discussed on the basis of its structural peculiarities.     

Conformational study of (Z)‐5‐(4‐chlorobenzylidene)‐2‐[4‐(2‐hydroxyethyl)piperazin‐1‐yl]‐3H‐imidazol‐4(5H)‐one in different environments: insight into the structural properties of bacterial efflux pump inhibitors

The 2‐amine derivatives of 5‐arylidene‐3H‐imidazol‐4(5H )‐one are a new class of bacterial efflux pump inhibitors, the chemical compounds that are able to restore antibiotic efficacy against multidrug resistant bacteria. 5‐Arylidene‐3H‐imidazol‐4(5H )‐ones with a piperazine ring at position 2 reverse the mechanisms of multidrug resistance (MDR) of the particularly dangerous Gram‐negative bacteria E. coli by inhibition of the efflux pump AcrA/AcrB/TolC (a main multidrug resistance mechanism in Gram‐negative bacteria, consisting of a membrane fusion protein, AcrA, a Resistant‐Nodulation‐Division protein, AcrB, and an outer membrane factor, TolC). In order to study the influence of the environment on the conformation of (Z )‐5‐(4‐chlorobenzylidene)‐2‐[4‐(2‐hydroxyethyl)piperazin‐1‐yl]‐3H‐imidazol‐4(5H )‐one, ( 3 ), two different salts were prepared, namely with picolinic acid {systematic name: 4‐[(Z )‐4‐(4‐chlorobenzylidene)‐5‐oxo‐3,4‐dihydro‐1H‐imidazol‐2‐yl]‐1‐(2‐hydroxyethyl)piperazin‐1‐ium pyridine‐2‐carboxylate, C₁₆H₂₀ClN₄O₂⁺·C₆H₄NO₂⁻, ( 3 a )} and 4‐nitrophenylacetic acid {systematic name: 4‐[(Z )‐4‐(4‐chlorobenzylidene)‐5‐oxo‐3,4‐dihydro‐1H‐imidazol‐2‐yl]‐1‐(2‐hydroxyethyl)piperazin‐1‐ium 2‐(4‐nitrophenyl)acetate, C₁₆H₂₀ClN₄O₂⁺·C₈H₆NO₄⁻, ( 3 b )}. The crystal structures of the new salts were determined by X‐ray diffraction. In both crystal structures, the molecule of ( 3 ) is protonated at an N atom of the piperazine ring by proton transfer from the corresponding acid. The carboxylate group of picolinate engages in hydrogen bonds with three molecules of the cation of ( 3 ), whereas the carboxylate group of 4‐nitrophenylacetate engages in hydrogen bonds with only two molecules of ( 3 ). As a consequence of these interactions, different orientations of the hydroxyethyl group of ( 3 ) are observed. The crystal structures are additionally stabilized by both C—H…N [in ( 3 a )] and C—H…O [in ( 3 a ) and ( 3 b )] intermolecular interactions. The geometry of the imidazolone fragment was compared with other crystal structures possessing this moiety. The tautomer observed in the crystal structures presented here, namely 3H‐imidazol‐4(5H )‐one [systematic name: 1H‐imidazol‐5(4H )‐one], is also that most frequently observed in other structures containing this heterocycle.     

A novel oxazolidinone antibiotic: RWJ‐416457

The crystal structure of the antibiotic drug candidate RWJ‐416457 (systematic name: N‐{(5S)‐3‐[4‐(5,6‐dihydro‐2H,4H‐2‐methylpyrrolo[3,4‐c]pyrazol‐5‐yl)‐3‐fluorophenyl]‐2‐oxo‐1,3‐oxazolidin‐5‐yl}acetamide), C₁₈H₂₀FN₅O₃, which belongs to the first new class of antibiotics discovered in the past 30 years, has been determined at 150 K. Each molecule of this drug donates one hydrogen bond to a neighboring molecule and accepts one hydrogen bond to give (O=C—R—N—H...O=C—R—N—H...)_n linkages along the b‐axis direction. The compound contains a pyrrolopyrazole ring, which, owing to its uncommon structure, has been shown to have particular effectiveness against multi‐drug‐resistant bacteria.     

Shape‐Assisted Self‐Organization in Highly Disordered Liquid Crystal Phases

In achiral rod‐like molecules, a nematic phase is the most disordered liquid crystal phase, which only has one‐directional order in the direction of the molecular long axis. A dumbbell‐shaped molecule (compound 3 : R−C₆H₁₀−CH=CH−C₆H₄−CH=CH−C₆H₁₀−R, (R=n C₅H₁₁)), and its liquid crystal phase (X phase) are reported, which exhibit high scattering without thermal fluctuation between two nematic phases under a polarized light optical microscope. The X phase was investigated by X‐ray diffraction, scanning electron microscopy, atomic force microscopy, and molecular dynamics simulation. A layered structure was ascertained for which a molecular self‐organization mechanism was postulated in which the super‐structure is based on lateral intermolecular interlocking. A second nematic phase above the X phase consisted of “rice grain”‐shaped particles.     

Expanding the Genetic Alphabet: Pyrazine Nucleosides That Support a Donor?Donor?Acceptor Hydrogen‐Bonding Pattern

The 6‐aminopyrazin‐2(1H)‐one, when incorporated as a pyrimidine‐base analog into an oligonucleotide chain, presents a H‐bond donor? donor? acceptor pattern to a complementary DNA or RNA strand. When paired with the corresponding acceptor? acceptor? donor purine in oligonucleotides, the heterocycle selectively contributes to the stability of the duplex, presumably by forming a base pair of Watson? Crick geometry joined by a nonstandard H‐bonding pattern, expanding the genetic alphabet. Reported here is a short, high yielding, β‐D ‐selective synthesis of a 6‐aminopyrazin‐2(1H)‐one nucleoside via the glycine riboside derivative 28 . The key steps include a Wittig? Horner reaction of an appropriately protected ribose derivative (Scheme 10, 19 → 21 ) followed by a Michael‐like ring closure (Scheme 12, 30 → 1a and 32 → 1b ). Thus, a variety of pyrazine nucleosides (Scheme 13) including the target 6‐aminopyrazin‐2(1H)‐one riboside 1a , and its 5‐methyl derivative 1b , 6‐amino‐5‐methylpyrazin‐2(1H)‐one riboside, are obtained.