Semisynthesis of 3′(2′)‐O‐(Aminoacyl)‐tRNA Derivatives as Ribosomal Substrate

An efficient synthesis of (3′‐terminally) 3′(2′)‐O‐aminoacylated pCpA derivatives is described, which could lead to the production of (aminoacyl)‐tRNAs following T4 RNA ligase mediated ligation. The tetrahydrofuranyl (thf) group was used as a permanent protective group for the 2′‐OH of the cytidine moiety which can be removed during the purification of the 3′(2′)‐O‐aminoacylated‐pCpA. This approach allowed for a general synthesis of (3′‐terminally) 3′(2′)‐O‐aminoacylated oligonucleotides. The fully protected pCpA 14 was synthesized by phosphoramidite chemistry and treated with NH₃ solution to remove the 2‐cyanoethyl and benzoyl groups (→ 15 ; Schemes 1 and 2). The 2′‐O‐thf‐protected‐pCpA 15 was coupled with α‐amino acid cyanomethyl esters, and the products 20a – c were deprotected and purified with AcOH buffer to afford 3′(2′)‐O‐aminoacylated pCpA 21a – c in high yields. The 3′(2′)‐O‐aminoacylated pCpA were efficiently ligated with tRNA(? CA) to yield (aminoacyl)‐tRNA which was an active substrate for the ribosome.     

An Efficient Synthesis of 6′‐methyl‐1'H‐spiro[indoline‐3,4′‐pyrimidine]‐2,2′(3'H)‐dione Derivatives

The reactions of isatins, urea and 1‐(piperidin‐1‐yl)butane‐1,3‐dione or 1‐morpholinobutane‐1,3‐dione have been developed for the preparation of spiroheterocycles compounds. It was found these reactions could be given higher yields and required shorter time in our process. In this synthesis, some useful groups, such as pyridyl and morpholinyl were introduced into the structures of the products. The compounds were confirmed by IR, ¹H NMR, ¹³C NMR, and HRMS. Else, compounds 4i and 4r were additionally confirmed by X‐ray diffraction analysis. The other advantages of this procure were simple handling, high yields, and wide range substrates.     

The first structurally analysed nucleic acid building block containing the Reese protecting group: 2′‐O‐[1‐(2‐fluorophenyl)‐4‐methoxypiperidin‐4‐yl]‐β‐D‐(1′R,2′R,3′R,4′R)‐uridine

The title compound, C₂₁H₂₆FN₃O₇, is assembled by N—H...O and O—H...O hydrogen bonds into well‐separated two‐dimensional layers of about 15 Å thickness. The crescent conformation of the molecules is stabilized by weak intramolecular C—H...O and C—H...F hydrogen bonds. The uridine moiety adopts an anti conformation. The ribofuranose ring exists in an envelope conformation. All the endocyclic uracil bonds are shorter than normal single C—N and C—C bonds, and five of them have comparable lengths, which implies a considerable degree of delocalization of the electron density within this ring.     

Enzymatic Synthesis of Nucleoside‐5′‐O‐(1‐thiophosphates) and (SP)‐Adenosine‐5′‐O‐(1‐thiotriphosphate)

Treatment of adenosine with PSCl₃ in trimethyl phosphate gave, after ion‐exchange chromatography, adenosine‐5′‐O‐monophosphate (AMP; 28%) and adenosine‐5′‐O‐monothiophosphate (AMPS; 48%). AMPS was studied as a thiophosphate residue donor in an enzymatic transphosphorylation with nucleoside phosphotransferase (NPase) of the whole cells of Erwinia herbicola. As exemplified by a number of natural and sugar‐ and base‐modified nucleosides, it was demonstrated that NPase of the whole cells of Erwinia herbicola catalyzes the transfer of both thiophosphate and phosphate residues with a similar efficiency. An incubation of AMPS in a phosphorylating extract of Saccharomyces cerevisiae (K‐phosphate buffer (0.3 M , pH 7.0); 3% glucose; 15 mM MgCl₂; 28°, 8 h), followed by ion‐exchange column chromatography afforded AMP (8%), AMPS (recovered, 23%), ATP (11%), and (S_P)‐adenosine‐5′‐O‐(1‐thiotriphosphate) ((S_P)‐ATPαS); (total yield 37%; 48% based on the consumed AMPS). For comparison of physicochemical properties, adenosine was chemically transformed into ATPαS as a mixture of the (S_P) (53%) and (R_P) (44%) diastereoisomers.     

Poly[aqua[μ3‐(pyridin‐1‐ium‐3,5‐diyl)diphosphonato‐κ3O:O′:O′′][μ2‐(pyridin‐1‐ium‐3,5‐diyl)diphosphonato‐κ2O:O′]calcium(II)]

The rigid organic ligand (pyridine‐3,5‐diyl)diphosphonic acid has been used to create the title novel three‐dimensional coordination polymer, [Ca(C₅H₆NO₆P₂)₂(H₂O)]_n. The six‐coordinate calcium ion is in a distorted octahedral environment, formed by five phosphonate O atoms from five different (pyridin‐1‐ium‐3,5‐diyl)diphosphonate ligands, two of which are unique, and one water O atom. Two crystallographically independent acid monoanions, L1 and L2, serve to link metal centres using two different coordination modes, viz.η²μ₂ and η³μ₃, respectively. The latter ligand, L2, forms a strongly undulated two‐dimensional framework parallel to the crystallographic bc plane, whereas the former ligand, L1, is utilized in the formation of one‐dimensional helical chains in the [010] direction. The two sublattices of L1 and L2 interweave at the Ca²⁺ ions to form a three‐dimensional framework. In addition, multiple O—H...O and N—H...O hydrogen bonds stabilize the three‐dimensional coordination network. Topologically, the three‐dimensional framework can be simplified as a very unusual (2,3,5)‐connected three‐nodal net represented by the Schläfli symbol (4·8²)(4·8⁸·10)(8).     

Bis(2,6‐diamino‐1H‐purin‐3‐ium) di‐μ‐croconato‐κ3O,O′:O′′;κ3O:O′,O′′‐bis[tetraaqua(croconato‐κ2O,O′)neodymium(III)]

The structure of the ionic title compound, (C₅H₇N₆)₂[Nd₂(C₅O₅)₄(H₂O)₈], consists of anionic dimers built around an inversion centre and is made up of an Nd^III cation, two croconate (croco) dianions and four water molecules (plus their inversion images), with two noncoordinated symmetry‐related 2,6‐diamino‐1H‐purin‐3‐ium (Hdap⁺) cations providing charge balance. Each Nd^III atom is bound to nine O atoms from four water and three croco units. The coordination polyhedron has the form of a rather regular monocapped square antiprism. The croconate anions are regular and the Hdap⁺ cation presents a unique, thus far unreported, protonation state. The abundance of hydrogen‐bonding donors and acceptors gives rise to a complex packing scheme consisting of dimers interlinked along the three crystallographic directions and defining anionic `cages' where the unbound Hdap⁺ cations lodge, linking to the mainframe via (N—H)_Hdap...O_water/croco and (O—H)_water...N_Hdap interactions.     

Energetic 4,4′‐Oxybis[3,3′‐(1‐hydroxytetrazolyl)]furazan and Its Salts

Energetic compounds that incorporate multiple nitrogen‐rich heterocycles are of great interest for high‐density energetic materials. A facile synthetic strategy to combine an oxy bridge and furazan groups, as well as tetrazole‐ols, into a molecule ( 5 ) was found. Some energetic salts based on 5 were prepared by neutralization. All of the compounds were fully characterized. Additionally, the structure of 7 has been elucidated by single‐crystal XRD analysis. Physicochemical and energetic properties were also studied; these show that these newly designed energetic salts exhibit good thermal stabilities. Hydroxylammonium salt ( 6 ) has a detonation performance and sensitivities comparable with those of 1,3,5‐trinitroperhydro‐1,3,5‐triazine (RDX).     

Chiral Space Formed by (+)‐(1S)‐1,1′‐Binaphthalene‐2,2′‐diyl Phosphate: Recognition of Aliphatic L‐α‐Amino Acids

(+)‐(1S)‐1,1′‐Binaphthalene‐2,2′‐diyl hydrogen phosphate (bnppa) is one of the useful optical selectors. To disclose the molecular mechanism by which bnppa recognizes aliphatic L ‐α‐amino acids and separates them by fractional crystallization, X‐ray analyses of bnppa and of its salts with L ‐alanine, L ‐valine, L ‐norvaline, and L ‐norleucine have been undertaken. All the amino acids adopt energetically favorable conformations in the crystal structures. The conformations and the packing patterns of bnppa in these crystal structures are very similar. The bnppa molecules are packed in a specific way to form hydrophobic and hydrophilic layers that are well separated. Between bnppa molecules, at the interface of these hydrophobic and hydrophilic layers, a space with chirality is formed. This space, designated as chiral space, recognizes the optically active amino acids. The packing of bnppa is mainly governed by intermolecular CH⋅⋅⋅π interactions between naphthalene moieties. The chiral space is responsible for the molecular recognition by bnppa allowing fractional crystallization of the L ‐α‐amino acids.     

Poly­[[bis­(pyridine‐κN)copper(II)]‐μ3‐5‐hydroxy­isophthalato‐κ3O:O′:O′′]

In the title compound, [Cu(C₈H₄O₅)(C₅H₅N)₂]_n or [Cu(OH‐BDC)(py)₂]_n (where OH‐H₂BDC is 5‐hydroxy­isophthalic acid and py is pyridine), the Cu atoms are coordinated by two N atoms from the pyridine ligands and by three O atoms from hydroxy­isophthalate ligands in a highly distorted triangular bipyramidal environment, with Cu—O distances in the range 1.941 (4)–2.225 (5) Å and Cu—N distances of 2.014 (6) and 2.046 (6) Å. The [Cu(OH‐BDC)]_n two‐dimensional network is built up from interlocking 22‐, 15‐ and eight‐membered rings via sharing of Cu atoms and O—H⋯O hydrogen bonds. Consolidation of the packing structure is achieved by edge‐ or point‐to‐face C—H⋯π interactions and offset or slipped π–π stacking interactions.     

Aqua­(2,2′‐diamino‐4,4′‐bi‐1,3‐thia­zole‐κ2N,N′)(oxydiacetato‐κ3O,O′,O′′)cobalt(II) trihydrate

The title compound, [Co(C₄H₄O₅)(C₆H₆N₄S₂)(H₂O)]·3H₂O, displays a distorted octa­hedral coordination geometry. The tridentate oxydiacetate dianion chelates the Cu^II atom in the meridional mode. In the crystal packing, hydro­philic and hydro­phobic layers are arranged in an alternating manner. In addition, a three‐dimensional hydrogen‐bonding framework and π–π stacking are present.     

N‐tert‐Butyl‐N′‐(5,7‐di­methyl‐1,8‐naphthyridin‐2‐yl)­urea

The title compound, C₁₅H₂₀N₄O, has been synthesized as an AADD recognition unit for quadruple hydrogen bonds. All non‐H atoms of the mol­ecule apart from two methyl groups of the tert‐butyl group lie in a common plane. An intramolecular hydrogen bond is formed connecting two N atoms. In the solid state, the title compound crystallizes as a centrosymmetric dimer connected by N—H?O=C interactions with an N?O distance of 2.824 (2) Å.     

Di‐μ‐acetato‐O:O′‐di‐μ‐acetato‐O,O′:O′‐bis­{[(cyclo­penta­dienyl)tris­(di­methyl­phosphito‐P)­cobalt‐O,O′,O′′]neodymium(III)}

In the title compound, [{η⁵‐CpCo[P(O)(OMe)₂]₃}Nd(O₂CCH₃)₂]₂, with a centrosymmetric mol­ecule, each Nd atom has an eight‐coordination environment, surrounded by a tripodal {L_OMe = CpCo[P(O)(OMe)₂]₃} and four bridging acetato ligands. The coordination geometry around each Nd centre is described as a distorted square‐antiprism and the two different types of acetato ligands have μ‐O:O′‐ and μ‐O,O′:O′‐acetato coordination modes. The Nd—O distances are in the range 2.378 (4)–2.594 (5) Å and the Nd?Nd distance is 3.9913 (6) Å.     

Aqua­(5,6‐di­methyl‐1,10‐phenanthroline‐N,N′)­(glycolato‐O,O′)­copper(II) nitrate

The title compound, [Cu(C₂H₃O₃)(C₁₄H₁₂N₂)(H₂O)]NO₃, is the first example of a mixed copper glycolate compound with a di­imine ligand. The copper(II) compound lies in a slightly distorted square‐pyramidal coordination environment with one water mol­ecule coordinated in the apical position. The glycolate ligand binds to the Cu atom as a chelate through a carboxyl­ate and the α‐OH O atom which, together with the N atoms of the substituted phenanthroline, constitute the base of the pyramid.     

Poly[[[aqua­(2,2′‐bipyridine‐κ2N,N′)manganese(II)]‐μ3‐acetyl­enedicarboxylato‐κ3O:O′:O′′] monohydrate]

In the title complex, {[Mn(C₄O₄)(C₁₀H₈N₂)(H₂O)]·H₂O}_n, each Mn^II ion has a distorted octa­hedral coordination formed by two N atoms of a 2,2′‐bipyridine ligand, three carboxyl O atoms of three different acetyl­ene­dicarboxyl­ate ligands and one coordinated water mol­ecule. The acetyl­ene­dicarboxyl­ate ligands act in a tridentate mode connecting adjacent Mn^II ions and constructing a two‐dimensional structure which can be regarded as an unusual plywood‐like stacked network.     

Synthesis and Properties of O‐β‐D‐ribofuranosyl‐(1″→2′)‐guanosine‐5″‐ O‐phosphate and Its Derivatives

The efficient synthesis of O‐β‐D ‐ribofuranosyl‐(1″→2′)‐guanosine‐5″‐O‐phosphate and O‐β‐D ‐ribofuranosyl‐(1″→2′)‐adenosine‐5″‐O‐phosphate, minor tRNA components, have been developed, and their conformational properties were examined by NMR spectroscopy.     

Stereoselective Synthesis of (−)‐(1R,1′R,5′R,7′R)‐1‐Hydroxy‐exo‐brevicomin and (+)‐exo‐Brevicomin from 3,4,6‐Tri‐O‐acetyl‐D‐glucal

Stereoselective syntheses of (?)‐(1R,1′R,5′R,7′R)‐1‐hydroxy‐exo‐brevicomin ( 1 ) and (+)‐exo‐brevicomin ( 2 ) were accomplished from 3,4,6‐tri‐O‐acetyl‐D ‐glucal ( 5 ; Schemes 2 and 3). Chemoselective reduction, Grignard reaction, Barton? McCombie deoxygenation, and ketalization were used as key steps.     

Aqua(oxydiacetato‐κ3O,O′,O′′)(pyridine‐3‐carboxamide‐κN1)copper(II) sesquihydrate

In the monomeric title compound, [Cu(C₄H₄O₅)(C₆H₆N₂O)(H₂O)]·1.5H₂O, the Cu^II cation is bound in a square‐pyramidal coordination to a tridentate oxydiacetate (ODA) ligand, a monodentate pyridine‐3‐carboxamide (p3ca) ligand and one aqua ligand, where the two organic ligands form the basal plane and the water O atom occupies the unique apical site. The ODA ligand presents a slight out‐of‐plane puckering in its central ether O atom, while the p3ca ligand is essentially planar. The availability of efficient donors and acceptors for hydrogen bonding results in the formation of strongly linked hydrogen‐bonded bilayers parallel to (101), with an interplanar distance of 3.18 (1) Å and a stacking separation between the bilayers of 3.10 (1) Å, both of them governed by extended π–π interactions. The disordered nature of the solvent water molecules around inversion centres is discussed. The monoaqua compound is compared with the octahedral diaqua analogue, [Cu(C₄H₄O₅)(C₆H₆N₂O)(H₂O)₂], reported recently [Perec & Baggio (2009). Acta Cryst. C 65 , m296–m298].     

Diaqua(oxydiacetato‐κ3O,O′,O′′)(pyridine‐3‐carboxamide‐κN1)copper(II)

In the mononuclear title compound, [Cu(C₄H₄O₅)(C₆H₆N₂O)(H₂O)₂], the Cu^II centre is bound to a chelating oxydiacetate ligand, a monodentate pyridine‐3‐carboxamide unit and two water molecules, defining an octahedral coordination where the first two ligands form the equatorial plane and the last two occupy the apical sites. The planar oxydiacetate ligand is slightly disordered at its central ether O atom. The availability of efficient donors and acceptors for hydrogen bonding results in a complex interaction scheme where each monomer links to six similar units to define a well connected three‐dimensional structure. A comparison is made with related structures in the literature, and the reasons for their differences are discussed.     

Synthesis of benzyl O-(2,3,3'-tri-O-acetyl-β-D-apiofuranosyl)-(1→3)-2,4-di-O-benzoyl-α-D-xylopyranoside and its X-ray structure

The protected apiose-containing disaccharide, benzyl O-(2,3, 3'-tri-O-acetyl-β-D-apiofuranosyl)-( 1→3)-2, 4-di-O-benzoyl-α-D-xylopyranoside, was synthesized and its X-ray structure provided.     

A Facile and Simple Synthesis of Novel 2‐(substituted)‐5‐(1‐methyl‐1H‐indazol‐3‐yl)‐Oxazole Derivatives

Novel 2‐(substituted)‐5‐(1‐methyl‐1H‐indazol‐3‐yl)‐oxazoles ( 13 ) were synthesized in moderate yields, from 1‐methyl‐1H‐Indazole 3‐carboxylic acid ( 1 ), by converting it into a variety of amides ( 12 ) and further its heterocyclization. The structures of all the compounds have been elucidated on the basis of IR, ¹H‐NMR, and HRMS.