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Syn Conformation (syn + conformation)
Selected AbstractsSynthesis and Preferred All- syn Conformation of C3 -Symmetrical N -(Hetero)arylmethyl TriindolesCHEMISTRY - A EUROPEAN JOURNAL, Issue 28 2008Abstract A new series of C3 -symmetrical N -(hetero)arylmethyl triindoles has been synthesized in a straightforward procedure. The structure and conformation in the solid state have been determined for three derivatives (3, 4, and 6) by X-ray crystallographic analysis. In all three cases, the molecules adopt a tripodal conformation with all of the flexible arms directed towards the same side, thereby delimiting an inner cavity. Compound 6 crystallizes and forms C3 -symmetric dimeric cagelike complexes. Guest molecules of chloroform and water are confined within the resulting cavities with stabilization by different intermolecular interactions; this highlights the potential of these compounds in the construction of supramolecular systems. A computational analysis has been performed to predict the most stable conformers. As a general trend, a preference for a conformation with all branches directed to the same side has been predicted. Comparison between theoretical and experimental results indicates that the computational level selected for the present study, B3LYP/6-31G*, is able to reproduce both the minimum energy conformations and the rotation barriers about the NCH2 bond. [source] Metal Ion Complementarity: Effect of Ring-Size Variation on the Conformation and Stability of Lead(II) and Cadmium(II) Complexes with Pendant-Armed CrownsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 15 2007Martín Regueiro-Figueroa Abstract The binding tendencies of the pendant-armed crown ethers L1,L3 [L1 = N,N, -bis(benzimidazol-2-ylmethyl)-1,7-diaza-12-crown-4, L2 = N,N, -bis(benzimidazol-2-ylmethyl)-1,10-diaza-15-crown-5) and L3 = N,N, -bis(benzimidazol-2-ylmethyl)-4,13-diaza-18-crown-6] towards PbII and CdII have been investigated. The X-ray crystal structure of [Cd(L3)](ClO4)2·EtOH shows that, in the solid state, the CdII ion is eight-coordinate and fits quite well into the crown hole, favouring an anti arrangement of the organic receptor. NMR measurements recorded in acetonitrile solution indicate that increasing the crown size induces a conformational change in the series of CdII complexes. The conformation goes from a syn arrangement for L1 to an anti arrangement for L3, passing through a syn [lrarr2] anti equilibrium in the complex derived from L2. On the contrary, no conformational change was observed for the corresponding PbII complexes, which have a syn conformation in all cases. These results have been confirmed by means of density functional theory (DFT) calculations performed by using the B3LYP model. The binding constants obtained from UV/Vis titration experiments in DMSO solution demonstrate that a decrease in the crown size provokes a 102 -fold enhancement of the stability for this series of CdII complexes, whereas for PbII a gradual decrease of the binding constants is observed. Receptor L1 shows a certain degree of selectivity for CdII over PbII, with a selectivity factor > 102. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] A Cyclic Fc,Histidine Conjugate: Synthesis and Properties , Interactions with Alkali Metal IonsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 5 2006Somenath Chowdhury Abstract The synthesis of the novel N,N, -(ferrocenophane-1,1,-diyldicarbonyl)-bridged histidine methyl ester 1 and of the acyclicbis(histidine methyl ester) derivative 3 are reported. The structure of 1 was studied in the solid state and in solution. The single-crystal structure of 1 shows that both proximal ferrocenyl (Fc) carbonyl groups are syn with respect to each other, which is a new structural motif for Fc,amino acid conjugates. This new syn conformation allows effective binding to alkali metal cations. Binding is evaluated by cyclic voltammetry monitoring the halfwave potential of the Fc group. Cation binding causes a shift to lower potential (Na+ > Li+ > K+, Cs+). Upon binding, compound 1 shows selectivity towards Na+ ions. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Syntheses, spectroscopic study and X-ray crystallography of some new phosphoramidates and lanthanide(III) complexes of N -(4-nitrobenzoyl)- N,,N,,-bis(morpholino)phosphoric triamideACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2010Khodayar Gholivand New phosphoramidates with the formula RC(O)N(H)P(O)X2, R = 2-NO2,C6H4, 3-NO2,C6H4 and 4-NO2,C6H4, X = N(CH2CH3) (1),(3), NC4H8 (4),(6), and NC4H8O (7),(9) were synthesized and characterized by 1H, 13C, 31P NMR and IR spectroscopy, and elemental analysis. The reaction of (9) with hydrated lanthanide(III) nitrate leads to ten- or nine-coordinated complexes, (10),(13). The crystal structure has been determined for (3), (5), (9), (10) and (13). In contrast to all of the previously reported similar phosphoramidate compounds, the ,C(O),N(H),P(O) skeleton in the free ligand (9) shows a cisoid conformation, with the C=O and P=O double bonds adopting a nearly syn conformation. Quantum chemical calculations were applied for clarifying this exceptional conformational behavior. The monodentate neutral ligand (9) is coordinated to the metal ions via the phosphoryl O atom, adopting the usual anti conformation between the C=O and P=O groups. [source] A toyocamycin analogue with the sugar moiety in a syn conformationACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2009Frank Seela The title compound [systematic name: 4-amino-5-cyano-1-(,- d -ribofuranosyl)-7H -pyrrolo[2,3- d]pyrimidine hemihydrate], C12H13N5O4·0.5H2O, is a regioisomer of toyocamycin with the ribofuranosyl residue attached to the pyrimidine moiety of the heterocycle. This analogue exhibits a syn glycosylic bond conformation with a , torsion angle of 57.51,(17)°. The ribofuranose moiety shows an envelope C2,- endo (2E) sugar conformation (S -type), with P = 161.6,(2)° and ,m = 41.3,(1)°. The conformation at the exocyclic C4,,C5, bond is +sc (gauche, gauche), with a , torsion angle of 54.4,(2)°. The crystal packing is stabilized by intermolecular O,H...O, N,H...N and O,H...N hydrogen bonds; water molecules, located on crystallographic twofold axes, participate in interactions. An intramolecular O,H...N hydrogen bond stabilizes the syn conformation of the nucleoside. [source] An unusual syn conformation of 5-formyluracil stabilized by supramolecular interactionsACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2007Gustavo Portalone 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. [source] Application of NMR, molecular simulation, and hydrodynamics to conformational analysis of trisaccharides,BIOPOLYMERS, Issue 4 2003Ann M. Dixon Abstract The preferred conformations and conformational flexibilities of the trisaccharides ,-D-Glcp -(1,2)-,-D-Glcp -(1,3)-,-D-Glcp -OMe (I) and ,-D-Glcp -(1,3)[,-D-Glcp -(1,4)]-,-D-Glcp -OMe (II) in aqueous solution were determined using nuclear magnetic resonance (NMR) spectroscopy, molecular dynamics (MD) and Langevin dynamics (LD) simulations, and hydrodynamics calculations. Both trisaccharides have a vicinal substitution pattern in which long range (nonsequential) interactions may play an important role. LD simulation at 600 K indicated that the all- syn conformation predominated, though other conformations were apparent. NOE data and MD and LD simulations at 298 K all indicated that trisaccharide I is a single all- syn conformer in solution. Given that previous studies showed evidence of anti -conformers in ,-D-Glcp -(1,2)-,-D-Glcp -(1,3)-,-D-Glcp -OMe, this result provides an example of how changing the anomeric configuration of one residue from , to , can make an oligosaccharide more rigid. Discrepancies in inter-ring distances obtained by experiment and by simulation of the all- syn conformer suggest the presence of an anti -, conformation at the ,-(1,4)-linkage for II. A combined analysis of measured and calculated translational diffusion constants and 13C T1 relaxation times yield order parameters of 0.9 for each trisaccharide. This implies that any interconversion among conformations is significantly slower than tumbling. Anisotropies of approximately 1.6 and 1.3 calculated for I and II, respectively, are consistent with the observed relatively flat T1 profiles because the tumbling is not in the motional narrowing regime. Published 2003 Wiley Periodicals, Inc. Biopolymers 69: 448,460, 2003 [source] Structures and Stabilities of Small DNA Dumbbells with Watson,Crick and Hoogsteen Base PairsCHEMBIOCHEM, Issue 7 2003Nuria Escaja Dr. Abstract The structures and stabilities of cyclic DNA octamers of different sequences have been studied by NMR and CD spectroscopy and by restrained molecular dynamics. At low oligonucleotide concentrations, some of these molecules form stable monomeric structures consisting of a short stem of two base pairs connected by two mini-loops of two residues. To our knowledge, these dumbbell-like structures are the smallest observed to date. The relative stabilities of these cyclic dumbbells have been established by studying their melting transitions. Dumbbells made up purely of GC stems are more stable than those consisting purely of AT base pairs. The order of the base pairs closing the loops also has an important effect on the stabilities of these structures. The NMR data indicate that there are significant differences between the solution structures of dumbbells with G,C base pairs in the stem compared to those with A,T base pairs. In the case of dumbbells with G,C base pairs, the residues in the stem form a short segment of a BDNA helix stabilized by two Watson,Crick base pairs. In contrast, in the case of d,pCATTCATT,, the stem is formed by two A,T base pairs with the glycosidic angles of the adenine bases in a syn conformation, most probably forming Hoogsteen base pairs. Although the conformations of the loop residues are not very well defined, the thymine residues at the first position of the loop are observed to fold back into the minor groove of the stem. [source] Bisamides Derived from Azulene-1,3- and -5,7-dicarboxylic Acids as New Building Blocks for Anion ReceptorsCHEMISTRY - A EUROPEAN JOURNAL, Issue 3 2008Tomasz Zieli, ski Dr. Abstract Bisamides based on the azulene moiety were investigated as building blocks for anion receptors. In the course of these studies, derivatives of azulene-1,3- and -5,7-dicarboxylic acid were synthesized and thoroughly characterized. The anion affinities of the derivatives based on functionalization in the five-membered ring and in the seven-membered ring were determined by 1H,NMR titration. The structural analysis of these building blocks was performed by X-ray diffractometry, molecular modelling and 2D NMR spectroscopy. The five-membered ring derivatives are easy to obtain, offer a binding site preorganized in the syn,syn conformation and bind anions with a strength similar to those of pyrrole-based analogues. There is also strong evidence for aromatic CH,,,anion interactions. The ligands substituted at the 5- and 7-positions offer a binding cleft with an uncommon geometry that originates from the seven-membered ring and seems to be complementary to the chloride anion. [source] Multifunctional "Clickates" as Versatile Extended Heteroaromatic Building Blocks: Efficient Synthesis via Click Chemistry, Conformational Preferences, and Metal CoordinationCHEMISTRY - A EUROPEAN JOURNAL, Issue 35 2007Robert Abstract Click chemistry has been utilized to access 2,6-bis(1-aryl-1,2,3-triazol-4-yl)pyridines (BTPs) as versatile extended heteroaromatic building blocks for their exploitation in supramolecular chemistry, in particular foldamer and ligand design. In addition to their high-yielding synthesis using CuI -catalyzed Huisgen-type 1,3-dipolar cycloaddition reactions the formed triazole moieties constitute an integral part of the BTP framework and encode both its pronounced conformational preferences as well as its chelating ability. A diverse set of symmetrical and non-symmetrical BTPs carrying electron-donating and -withdrawing substituents at both terminal aryl and the central pyridine moieties has efficiently been synthesized and could furthermore readily be postfunctionalized with amphiphilic side chains and porphyrin chromophores. In both solution and solid state, the BTP scaffold adopts a highly conserved horseshoe-like anti,anti conformation. Upon protonation or metal coordination, the BTP scaffold switches to the chelating syn,syn conformation. Iron and europium complexes have been prepared, successfully characterized by single-crystal X-ray diffraction analysis, and investigated with regard to their spin state and luminescent properties. The extended heteroaromatic BTP scaffold should prove useful for the design of responsive foldamer backbones and the preparation of new magnetic and emissive materials. [source] The existence of secondary orbital interactionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2007Chaitanya S. Wannere Abstract B3LYP/6-311+G** (and MP2/6-311+G**) computations, performed for a series of Diels-Alder (DA) reactions, confirm that the endo transition states (TS) and the related Cope-TSs are favored energetically over the respective exo -TSs. Likewise, the computed magnetic properties (nucleus-independent chemical shifts and magnetic susceptibililties) of the endo - (as well as the Cope) TS's reveal their greater electron delocalization and greater aromaticity than the exo -TS's. However, Woodward and Hoffmann's original example is an exception: their endo -TS model, involving the DA reaction of a syn - with an anti -butadiene (BD), actually is disfavored energetically over the corresponding exo -TS; magnetic criteria also do not indicate the existence of SOI delocalization in either case. Instead, a strong energetic preference for endo -TSs due to SOI is found when both BDs are in the syn conformations. This is in accord with Alder and Stein's rule of "maximum accumulation of double bonds:" both the dienophile and the diene should have syn conformations. Plots along the IRC's show that the magnetic properties typically are most strongly exalted close to the energetic TS. Because of SOI, all the points along the endo reaction coordinates are more diatropic than along the corresponding exo pathways. We find weak SOI effects to be operative in the endo -TSs involved in the cycloadditions of cyclic alkenes, cyclopropene, aziridine, cyclobutene, and cyclopentene, with cyclopentadiene. While the endo -TSs are only slightly lower in energy than the respective exo -TSs, the magnetic properties of the endo -TS's are significantly exalted over those for the exo -TS's and the Natural Bond Orbitals indicate small stabilizing interactions between the methylene cycloalkene hydrogen orbitals (and lone pairs in case of aziridine) with ,-character and the diene , MOs. © 2006 Wiley Periodicals, Inc. J Comput Chem 2007 [source] The cocrystal nicotinamide,succinic acid (2/1)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2010Laura J. Thompson In the asymmetric unit of the crystal structure of nicotinamide,succinic acid (2/1), 2C6H6N2O·C4H6O4, there are two independent nicotinamide molecules in general positions and two half succinic acid molecules which lie about inversion centres. The structure contains acid,pyridine and amide,amide synthons with nicotinamide molecules forming ladders of alternating R22(8) and R42(8) rings linked through succinic acid to generate a corrugated hydrogen-bonded sheet. This sheet is a common supramolecular unit found in other 2:1 nicotinamide,dicarboxylic acid cocrystals, but the presence of two crystallographically distinct nicotinamides with anti and syn conformations, forming two distinct sheets within the same structure, is a novel packing feature in this type of material. [source] | ||||||||||