Crystallographic evidence for intramolecular C−H...O interactions in principal nucleosides. Refinement of the crystal structure of thymidine

An analysis of crystallographic data for the major nucleosides has shown that their molecules (except for guanosine) exhibit specific intramolecular C−H...O interactions, which are weak hydrogen bonds. In purine nucleosides these interactions are rare and rather weak. For pyrimidine nucleosides, in addition to the previously known intramolecular interaction C₆−H₆...O_5′, we have revealed the intramolecular interactions C_1′−H_1′...O₂ and C₆−H₆...O_1′. The three interactions make approximately equal contributions to the stabilization of the anti-conformation in pyrimidine nucleosides and make this conformation prevailing. To enhance the reliability of the results of studying the C−H...O interactions in thymidine, we performed an additional, more exact, X-ray diffraction analysis of the substance. Institute of Physiologically Active Substances, Russian Academy of Sciences, Chernogolovka. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 1, pp. 178–184, January–February, 1995. Translated by I. Izvekova     

A novel chromone-substituted trimeric dihydroflavonol from <Emphasis Type="Italic">Anogeissus pendula</Emphasis>

A new chromone-substituted dihydrotriflavonol, (2S,3S)[6-{(3S) 3″,5″-dihydroxy-6″-methoxydihydrochromone}5,3′,4′,5′-tetrahydroxy-7-methoxy-3-O-8-dihydroflavone]₂ 3-O-8[6-{(3S) 3″,5″-dihydroxy-6″methoxydihydrochromone}3,5,3′,4′,5′-pentahydroxy-7-methoxydihydroflavonol] was isolated from the leaves of Anogeissus pendula. The structure was determined by UV, ¹H NMR, ¹³C NMR, HMBC, and CD data.     

Synthesis and characterization of 2-phenylaniline cyclopalladated complexes

Reaction of the dinuclear complex [Pd{κ2-N2′,C1-2-(2′-NH₂C₆H₄)C₆H₄}Cl]₂ (1) with ligands (L = 4-picoline, sym-collidine) gave the six-membered palladacycles [Pd{κ2-N2′,C1-2-(2′-NH₂C₆H₄)C₆H₄}Cl(L)] (2). The complex 1 reacted with AgX (X = CF₃SO₃, BF₄) and bidentate ligands [L–L = phen (phenanthroline), dppe (bis(diphenylphosphino)ethane), bipy(2,2′-bipyridine) and dppp (bis(diphenylphosphino)propane)] giving the mononuclear orthopalladated complexes [Pd{κ2-N2′,C1-2-(2′-NH₂C₆H₄)C₆H₄}(L–L)] (3) [L–L = phen, dppe, bipy and dppp]. These compounds were characterized by physico-chemical methods, and the structure of [Pd{κ2-N2′,C1-2-(2′-NH₂C₆H₄)C₆H₄}Cl(L)] (L = sym-collidine) was determined by single-crystal X-ray analysis.     

ESR study of paramagnetic derivatives of sterically hindered di-<Emphasis Type="Italic">o</Emphasis>-quinone with the tetrathiafulvalene bridge

The paramagnetic derivatives of 4,4′,7,7′-tetra-tert-butyl-2,2′-bis-1,3-benzodithiol-5,5′,6,6′-tetraone (1), viz., radical anion salts of the alkali metals (Li, Na, K) and cobaltocenium cations, chelated mono-o-semiquinone complexes with different metal fragments (Tl, TlMe₂, SnPh₃, Mn(CO)₄, Mn(PPh₃)(CO)₃), a number of copper(I) complexes with sterically hindered phosphines as well as binuclear heterometallic derivatives of triphenylantimony(V) o-semiquinone-catecholate with the analogous paramagnetic centers, were studied by ESR spectroscopy. The reaction of di-o-quinone 1 with sodium amalgam resulted in the formation of all reduced forms including quinone-semiquinone, disemiquinone, semiquinone-catecholate, and dicatecholate. A radical cation with the unpaired electron localized on the tetrathiafulvalene (TTF) fragment, which resulted from the oxidation of di-o-quinone 1, was detected by ESR spectroscopy.     

Oxygen- versus carbon-coordination of the alpha-stabilized phosphorus ylide Ph<Subscript>3</Subscript>P=C(H)R in palladacycles bearing secondary amines

The ortho-metalated complex [Pd(x){κ ² (C,N)-[C₆H₄CH₂NRR′ (Y)}] (2a–4a and 2b–3b) was prepared by refluxing in benzene equimolecular amounts of Pd(OAc)₂ and secondary benzylamine [a, EtNHCH₂Ph; b, t-BuNHCH₂Ph followed by addition of excess NaCl. The reaction of the complexes [Pd(x){κ ² (C,N)-[C₆H₄CH₂NRR′ (Y)}] (2a–4a and 2b–3b) with a stoichiometric amount of Ph₃P=C(H)COC₆H₄-4-Z (Z = Br, Ph) (ZBPPY) (1:1 molar ratio), in THF at low temperature, gives the cationic derivatives [Pd(OC(Z-4-C₆H₄C=CHPPh₃){κ ² (C,N)-[C₆H₄CH₂NRR′(Y)}] (5a–9a, 4b–6b, and 4b′–6b′), in which the ylide ligand is O-coordinated to the Pd(II) center and trans to the ortho-metalated C(6)H(4) group, in an “end-on carbonyl”. Ortho-metallation, ylide O-coordination, and C-coordination in complexes (5a–9a, 4b–6b, and 4b′–6b′) were characterized by elemental analysis as well as various spectroscopic techniques.     

Iridoids from <Emphasis Type="Italic">Symphoricarpos albus</Emphasis>

Twelve compounds including secologanin, loganin, the aglycon of loganin, and a new iridoid called glucologanin were isolated from fruit of common snowberry Symphoricarpos albus (L.) Blake. The structure of glucologanin was confirmed using PMR and mass spectroscopy and chemical transformations. 2′,3′,4′,6′,7-Penta-O-acetylloganin and 2′,3′,4′,6′-tetra-O-acetylloganin were synthesized. Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 37–40, January–February, 2009.     

Epimerization,transacylation and bromination of dihydroquercetin acetates; synthesis of 8-bromodihydroquercetin

Dihydroquercetin (dhq) and its 3-acetate react with acetic anhydride in the absence of a base catalyst to yield mixtures of partially acetylated products. Three new esters were characterized by NMR spectroscopy as dhq 3,7,3′-triacetate, 3,7,4′-triacetate and 5,7,3′,4′-tetraacetate. At its melting point neat dhq 3,7,3′,4′-tetraacetate is partially converted to dhq 3,3′,4′-triacetate and dhq pentaacetate by intermolecular acetyl transfer. Dhq 7,3′,4′-triacetate yields exclusively dhq 3′,4′-di- and 3,7,3′,4′-tetraacetate under these conditions. The acetylation/deacetylation reactions are accompanied by partial epimerization: 3 new acetates with 2,3-cis stereochemistry (dhq 3-, 3,7,3′,4′-tetra- and penta-) were identified. Dhq and its 3,7,3′,4′-tetraacetate undergo regiospecific dibromination at C-6 and C-8 with excess N-bromosuccinimide in polar solvents, and 6,8-dibromo-dhq can be regioselectively debrominated to 8-bromo-dhq with sodium sulfite.     

An efficient method for the synthesis of 9-β-D-2′-deoxyribofuranosyl-6-methylpurine

A new method for the preparation of 9-β-D-2′-deoxyribofuranosyl-6-methylpurine from inosine (1) is described. Inosine was converted to 6-chloropurinenucleoside (4) via acetylation, chlorination, and deacetylation. Compound 4 was transformed to the key intermediate 6-methylpurinenucleoside (7) via protection of the 2′,3′,5′-hydroxy groups of 4 with 3,4-dihydropyran to give compound 5, then methylation at the 6-position of 5 with dimethyl copper lithium gave compound 6; depyranylation of 6 led to the subsequent selective protection of the 3′,5′-hydroxy groups of 7 with O[Si(I-Pr)₂Cl]₂ followed by reaction with phenyl chlorothionoformate to give compound 9. Compound 9 was then converted to the target compound 11 via 2′-deoxidation and 3′, 5′-desilylation. The structures of these products were identified by Mass Spectrum (MS), ¹H-NMR (Nuclear Magnetic Resonance) spectra and elemental analysis. Translated from Chinese Journal of Organic Chemistry, 2006, 26(10): 1394–1397 (in Chinese)     

Fatty-acid composition and secondary metabolites from slightly polar extracts of the aerial part of <Emphasis Type="Italic">Primula macrocalyx</Emphasis>

Flavones 2′,5′-dimethoxyflavone, 3′-methoxy-4′,5′-methylenedioxyflavone, 3′,4′-dimethoxyflavone, 5,6,2′,3′,6′-pentamethoxyflavone, and 5,6,2′,3′,5′,6′-hexamethoxyflavone; salicylates, methyl-4-methoxysalicylate and peonol; and bisbibenzyl polyphenol riccardin C were isolated for the first time from the acetone extract of the aerial part of Primula macrocalyx Bge. The content of free and total fatty acids was determined by GC and GC—MS. Palmitic (16:0), octadecatetraenoic 18:4 (6,9,12,15), linoleic 18:2 (9,12), and α-linolenic 18:3 (9,12,15) were the principal acids from the aerial part of Primula macrocalyx. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 457–460, September-October, 2008.     

Two new isomeric lignans from <Emphasis Type="Italic">Eusideroxylon zwageri</Emphasis>

Two new lignans were isolated with two other known compounds, eusiderin A and eusiderin I, from Eusideroxylon zwageri (billian). The two new lignans have isomeric structure. The structures of the new lignans were determined to be (2R,3R,4S)-2,3-dimethyl-6,7-dimethoxy-4-ethoxy (3′,4′,5′-trimethoxybenzene)-1,5-dihydroxytetralin and (2R,3S,4S)-2,3-dimethyl-6,7-dimethoxy-4-ethoxy(3′,4′,5′-trimethoxybenzene)-1,5-dihydroxytetralin. Published in Khimiya Prirodnykh Soedinenii, No. 3, pp. 303–305, May–June, 2009.     

Synthesis, FT-Raman, FT-IR, NMR spectroscopic characterization and antimicrobial activity of new mixed aza-oxo-thia macrocyclic compounds

Series of new mixed aza-oxo-thia macrocyclic ligands {2,6,12,16-tetraaza-1,7,11,17-tetraoxo-9,19-dithia-[(4′-methyl-5′,4,3′)(14′-methyl-15′,14,13′)]ditriazine}cyclocosane (L ₁ ); {2,6,13,17-teraaza-1,7,12,18-tetraoxo-9,10,20,21-tetrathia-[(4′-methyl-5′,4,3′)(15′-methyl-14′,16′,15)]di-triazine}cyclodocosane (L ₂ ); {2,6,14,18-tetraaza-1,7,13,19-tetraoxo-10,22-dithia-[(4′-methyl-5′,3′,4)(16′-methyl-15′,17′,16)]ditriazine}cyclotetracosane (L ₃ ) and {2,6,15,19-tetraaza-1,7,14,12-tetraoxo-10,11,23,24-tetrathia-[(4′-methyl-5′,4,3′)(17′-methyl-8′,17,16′)]ditriazine}cyclohexa-cosane (L ₄ ) were synthesized. The structural features of the compounds have been studied by elemental analyses, Mass, FT-Raman, FT-IR, ¹H and ¹³C NMR spectroscopy. The antimicrobial activities of the ligands were evaluated using disk diffusion method in dimethyl sulfoxide as well as the minimal inhibitory concentration (MIC) dilution method, against 9 bacteria. The obtained results from disk diffusion method were assessed in side-by-side comparison with those of Penicillin-g, Ampicillin, Cefotaxime, Vancomycin, Oflaxacin, and Tetracyclin, well-known antibacterial agents. The results from dilution procedure were compared with Gentamycin as antibacterial and Nystatin as antifungal. The antifungal activities are reported on five yeast cultures namely Candida albicans, Kluyveromyces fragilis, Rhodotorula rubra, Debaryomyces hansenii, and Hanseniaspora guilliermondii, and the results are referenced with Nystatin, Ketaconazole, and Clotrimazole, commercial antifungal agents. In most cases, the compounds show strong antifungal activity in the comparison tests.     

Vectors for Glucose-Dependent Protein Expression in <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Based on the p426 series of expression vectors developed by Mumberg et al. (Gene 156, 119–122, 1995), we have generated a set of plasmids that allow the glucose-dependent expression of target genes in the yeast, Saccharomyces cerevisiae. The ADH1 promoter in plasmid p426-ADH1 was replaced by the 1-kb 5′-region from either of the following genes: HXK1, YGR243, HXT4 and HXT7. Expression mediated by the respective 5′-regions was monitored with EGFP, yEGFP3-CLN2pest and TurboGFP as marker genes. Fluorescence is induced 2.7-fold using the HXK1, 2.3-fold using the YGR243-, 5-fold using the HXT7- and 12.6-fold using the HXT4 5′-regions upon depletion of glucose to a concentration of <0.5 g/l.     

A Dehydrogenated Cycloadduct of N-Phenylmaleimide and the Azomethine Ylide Derived from Ninhydrine and Phenylalanine: Structure and Conformation

Summary.  The structure of the dehydrogenation product 1′,3a′-dihydro-3′-((1,3-dioxoindan-2-ylidene)-phenyl-methyl)-5′-phenyl-spiro-(indan-2,1′-pyrrolo[3,4-c]pyrrole)-1,3,4′,6′-(5′H, 6a′H)-tetrone derived from the cycloadducts (±)-(3a′S,6a′R)-1′,3a′-dihydro-3′-((R)-α-(1,3-dioxoindanyl)-benzyl)-5′-phenyl-spiro-(indan-2,1′-pyrrolo[3,4-c]pyrrole)-1,3,4′,6′(5H,6a′H)-tetrone and/or (±)-(3a′S,6a′R)-1′,3a′-dihydro-3′-((S)-α-(1,3-dioxoindanyl)-benzyl)-5′-phenyl-spiro-(indan-2,1′-pyrrolo[3,4-c]pyrrole)-1,3,4′,6′(5H,6a′H)-tetrone, which were synthesized by 1,3-dipolar cycloaddition of N-phenylmaleimide to 2-((2-(1,3-dioxoindan-2-yl)-2-phenyl-ethenyl)-imino)-indan-1,3-dione, was determined by X-ray analysis. Crystal data (CCD, 180 K): rhombohedral, R&3macr;;, a = 34.0871(7), c = 13.9358(5) ?, Z = 18; the structure was solved by direct methods and refined by full-matrix least-squares procedures to R(F, I ≥ 3σ(I)) = 0.053. The molecule contains a central folded ring system of two cis-fused 5-membered heterocyclic rings; each ring is nearly planar, and the angle between the rings amounts to 59.0°. Dynamic ¹H NMR spectroscopy of the product revealed an exchange process caused by restricted rotation of the double bonded 1,3-indandione moiety and the phenyl group about the C_sp2-C_sp2 single-bonds. Molecular modeling and complete lineshape analysis indicated a four site exchange process for which free energies of activation and free energies could be established. ΔG ^‡ values for the barriers of rotation are in the range of 57–59 kJ · mol^− 1 at 273 K, which is unusually high for an unsubstituted phenyl group. Received May 3, 2001. Accepted (revised) June 8, 2001     

Copolymerization of the poly(<Emphasis Type="Italic">N,N</Emphasis>-dimethyl-<Emphasis Type="Italic">N,N</Emphasis>-diallylammonium chloride) macromonomer with acrylamide

Copolymers of the poly(N,N-dimethyl-N,N-diallylammonium chloride) macromonomer (1′) with acrylamide (2) with a high content of cationic groups (up to 50%) were synthesized. The relative activities r _1′ and r ₂ were calculated. The relative activities calculated by the Kelen—Tudos (r _1′ = 0.057±0.009, r ₂ = 1.57±0.12) and Feynman—Ross (r _1′ = 0.055±0.011, r ₂ = 1.58±0.14) methods are in accordance. The intrinsic viscosity and the yield of copolymers were found to decrease with an increase in the molar fraction of macromonomer 1′ in the monomer mixture. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 515–518, March, 2007.     

Si-Containing Amides of Phosphoric Acid

The first representative of the N-silylmethylamides of phosphoric acid O=P[NMe(CH₂SiMe _n (OEt)_3-n ]₃ have been synthesized by interaction of MeNHCH₂SiMe _n (OEt)_3-n (n = 2, 3) with POCl₃. The interaction of the N,N′,N″-trimethyl-N,N′,N″-tris[(ethoxydimethyl- silyl)methyl]triamide phosphoric acid with BF₃·Et₂O or BCl₃ results in the formation of the N,N′,N″-trimethyl-N,N′,N″-tris[(fluorodimethyl-silyl)methyl]triamide phosphoric acid or N,N′,N″-trimethyl-N,N′,N″-tris[(chlorodimethylsilyl)methyl]triamide phosphoric acid. NMR data show on the tetracoordinate state of silicon in these products.     

Studies on the Synthesis and Potentiometric Properties of Three Novel Tripodal Ligands and their Complexes

Three novel tripodal ligands, N,N′,N′′-tri-(3′-phenylpropionic acid-2′-yl-)-1,3,5-triaminomethylbenzene (Ll), N,N′,N′′-tri-(4′-methylvaleric acid-2′-y1-)-1,3,5-triaminomethylbenzene (L2) and N,N′,N′′-tri-(3′methylvaleric acid-2′-yl-)-1,3,5-triaminomethylbenzene (L3), have been synthesized and fully characterized. The stabilizing ability of complexes of the three ligands with transition metal ions Cu(II), Ni(II), Zn(II) and Co(II) and rare earth metal ions La(III), Nd(III), Sm(III), Eu(III) and Gd(III) has been investigated by the pontentiometric method in water and in aqueous KNO₃ (0.1 mol dm⁻³) at 25.0±0.1 °C, respectively. The results show that there is a great deal of difference between two series of complexes’ stabilities. An explanation of the difference has been given.     

Synthesis,Spectra and Electrochemistry of Dinitro-bis-{1-alkyl-2-(arylazo) imidazole} Ruthenium(II). Nitro-nitroso Derivatives and Reactivity of the Electrophilic {Ru-NO}<Superscript>6</Superscript>System

Ag⁺ assisted aquation of blue cis-trans-cis-RuCl₂(RaaiR′)₂ (4–6) leads to the synthesis of solvento species, blue-violet cis-trans-cis-[Ru(OH₂)₂(RaaiR′)₂](ClO₄)₂ [Raai R′=p-R-C₆H₄ N=N–C₃H₂–NN–1–R′, (1–3), abbreviated as N,N′-chelator, where N(imidazole) and N(azo) represent N and N′, respectively; R = H (a), OMe (b), NO₂ (c) and R′ = Me (1/4/7/10), CH₂CH₃ (2/5/8/11), CH₂Ph (3/6/9/12)] that have been reacted with NO₂⁻in warm EtOH resulting in violet dinitro complexes of the type, Ru(NO₂)₂(RaaiR′)₂ (7–9). The nitrite complexes are useful synthons of electrophilic nitrosyls, and on triturating the compounds, (7b–9b) with conc. HClO₄ nitro-nitrosyl derivatives, [Ru(NO₂)(NO)(OMeaaiR′)₂](ClO₄)₂ (10b–12b) are isolated. The solution structure and stereoretentive transformation in each step have been established from ¹H n.m.r. results. All the complexes exhibit strong MLCT transitions in the visible region. They are redox active and display one metal-centred oxidation and successive ligand-based reductions. The redox potentials of Ru(III)/Ru(II) (E_1/2^M) of (10b–12b) are anodically shifted by ∼ ∼0.2 V as compared to those of dinitro precursors, (7b–9b). The ν(NO) >1900 cm⁻¹ strongly suggests the presence of linear Ru–NO bonding. The electrophilic behaviour of metal bound nitrosyl has been proved in one case (12b) by reacting with a bicyclic ketone, camphor, containing an active methylene group and an arylhydrazone with an active methine group, and the heteroleptic tris chelates thus formed have been characterised.     

Synthesis,crystal structure and magnetic properties of the complex Co[Me<Subscript>2</Subscript>NC(S)NP(S)(OPr-<Emphasis Type="Italic">i</Emphasis>)<Subscript>2</Subscript>]<Subscript>2</Subscript>

The reaction of N-(diisopropoxyphosphorothioyl)-N′,N′-dimethylthiourea [Me₂NC(S)NHP(S)(OPr-i)₂, HL) potassium salt with Co(II) cation in aqueous ethanol gave the chelate complex Co(L-S,S′)₂(CoL₂). The structure of the resulting compound was studied by means of IR spectroscopy, microanalysis, and X-ray analysis. The metal center was found to occur in a tetrahedral S₄ environment formed by the C=S and P=S sulfur atoms of two deprotonated ligands L. Magnetic properties of the complex CoL₂ were also studied.     

Synthesis and crystal structures of silver(I) and copper(II) complexes with <Emphasis Type="Italic">p</Emphasis>-xylylene-bridged bipyrazolyl ligands

Two semi-rigid bipyrazolyl ligands, namely 2,3,5,6-tetramethyl-1,4-bis[(3′,5′-dimethyl-1H -pyrazol-4′-yl)methylene]benzene (H₂L) and 2,3,5,6-tetramethyl-1,4-bis[(3′,5′-diphenyl-1H -pyrazol-4′-yl)methylene]benzene (H₂L′), and their Ag(I) and Cu(II) complexes have been prepared and structurally characterized by means of X-ray analysis. In the structures of the metal complexes, namely [Ag₂(H₂L)₂](BF₄)₂·2H₂O (1), [Ag(H₂L)(NO₃)]_n (2), [Cu₂(H₂L)₄(SO₄)₂]·11H₂O (3), and {[Ag(H₂L′)]BF₄}_n (4), the bipyrazoles act as bridging ligands to connect two metal atoms. Complexes 2 and 4 exhibit 1-D polymeric structures, while 1 and 3 are discrete molecules with a rectangular dimer or tetragonal prismatic shapes, respectively. Two different conformations, namely cis and trans, have been observed for these bipyrazolyl ligands.     

A bicyclo[3.2.1]octanoid neolignan and toxicity of the ethanol extract from the fruit of <Emphasis Type="Italic">Ocotea heterochroma</Emphasis>

A new bicyclo[3.2.1]octanoid neolignan rel-(7S,8R,1′S,2′R,3′S)-Δ8′-2′-hydroxy-5,1′,3′-trimethoxy-3,4methylenedioxy-7,3′,8,1′-neolignan (1) was isolated from ethanol extract from the fruit of Ocotea heterochroma Mez & Sodiro ex Mez as well as the known compounds β-friedelanol (2), meso-dehydroguaiaretic acid (3), and yangambin (4), whose structures were elucidated on the basis of their comprehensive spectroscopic analysis including 2D NMR data. Lethality bioassay using brine shrimp (Artemia salina Leach) was evaluated with the ethanol extract from the Ocotea heterochroma’s fruit. The toxicity of this extract was greater than the toxicity of those fractions obtained in a first solvent partition (benzene, ethyl acetate, and butanol subfractions) and that of a mixture of acetylated 2′-epimers from the new neolignan 1. Published in Khimiya Prirodnykh Soedinenii, No. 2, pp. 158–160, March–April, 2009.