Inclusion of trans-resveratrol in methylated cyclodextrins: synthesis and solid-state structures

• Lee Trollope,
• Dyanne L. Cruickshank,
• Terence Noonan,
• Susan A. Bourne,
• Milena Sorrenti,
• Laura Catenacci and
• Mino R. Caira

Beilstein J. Org. Chem. 2014, 10, 3136–3151, doi:10.3762/bjoc.10.331

• derivatised) to establish their effect on the aqueous solubility of trans-resveratrol and to estimate association constants for complex formation. Keywords: cyclodextrin; inclusion complexes; thermal analysis; trans-resveratrol; X-ray structures; Introduction The naturally occurring phytoalexin trans

Structure/affinity studies in the bicyclo-DNA series: Synthesis and properties of oligonucleotides containing bc^en-T and iso-tricyclo-T nucleosides

• Branislav Dugovic,
• Michael Wagner and
• Christian J. Leumann

Beilstein J. Org. Chem. 2014, 10, 1840–1847, doi:10.3762/bjoc.10.194

• of single modifications with nucleosides of the bicyclo-/tricyclo-DNA platform within deoxyoligonucleotides are not predictive for the stability of fully modified oligonucleotides. Keywords: DNA/RNA affinity; nucleic acids; nucleosides; oligonucleotides; oligonucleotide therapy; X-ray structures

• /tricyclo-nucleosides from X-ray structures. Sequence information and analytical data of ON1–7 as well as Tm data from UV-melting curves (260 nm) in 10 mM NaH2PO4/Na2HPO4, 150 mM NaCl, pH 7.0. Duplex concentration: 1.2 μM. ΔTm/modification data for four different bi/tricyclo modifications in one sequence

• . Acknowledgements A postdoctoral grant to B.D by ISIS Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA-92010 (USA) is gratefully acknowledged. We thank the group of Chemical Crystallography of the University of Bern (PD Dr. P. Macchi and Dr. J. Hauser) for the X-ray structures and the Swiss National Science

Rational design of cyclopropane-based chiral PHOX ligands for intermolecular asymmetric Heck reaction

• Marina Rubina,
• William M. Sherrill,
• Alexey Yu. Barkov and
• Michael Rubin

Beilstein J. Org. Chem. 2014, 10, 1536–1548, doi:10.3762/bjoc.10.158

• should be pointed out, that the resolved crystal structure of (L4)PdCl2 complex shows four sets of crystallographically independent molecules. However, all of them have nearly identical palladacycle conformations with the molecule shown in Figure 4 [64]. An overlay of X-ray structures obtained for (L1

• reaction. Chiral phosphanyl-oxazoline (PHOX) ligands used for intermolecular asymmetric Heck reaction. PHOX ligands with chiral cyclopropyl backbone employed in this study. X-ray structures of complexes (L1)PdCl2 (left) and (L4)PdCl2 (right). These structures were originally communicated in [64

The difluoromethylene (CF₂) group in aliphatic chains: Synthesis and conformational preference of palmitic acids and nonadecane containing CF₂ groups

• Yi Wang,
• Ricardo Callejo,
• Alexandra M. Z. Slawin and
• David O’Hagan

Beilstein J. Org. Chem. 2014, 10, 18–25, doi:10.3762/bjoc.10.4

• placement of two CF2 groups around the ring [6] (Figure 2). X-ray structures reveal that the CF2 groups only ever occupy corner locations. This is a result of several factors including C–CF2–C angle widening, which relaxes 1,4-torsional strain across corner positions, lengthening the contact distance

• group in 1c accelerates RCM reactions relative to CHF (1d) and CH2 (1e) and with a similar rate to classical or Thorpe–Ingold substituents such as the ketal 1a and dicarboxylate ester 1b [8]. X-ray structures of a) 1,1,4,4- (3) b) 1,1,7,7- (4) and c) 1,1,6,6- (5) tetrafluorocyclododecanes. The CF2

Synthesis, characterization and initial evaluation of 5-nitro-1-(trifluoromethyl)-3H-1λ³,2-benziodaoxol-3-one

• Nico Santschi,
• Roman C. Sarott,
• Elisabeth Otth,
• Reinhard Kissner and
• Antonio Togni

Beilstein J. Org. Chem. 2014, 10, 1–6, doi:10.3762/bjoc.10.1

• X-ray structures 6 and 3. Thermal ellipsoids set to 30% probability. Hydrogen atoms omitted for clarity. DSC traces obtained for 2 (green) and 3 (blue). Cyclic voltammetry of 3 (1 mM, black) and of a mixture of 3 (1 mM) and methyl 2-iodo-5-nitrobenzoate (1 mM, green) in anhydrous MeCN + 0.1 M

Advancements in the mechanistic understanding of the copper-catalyzed azide–alkyne cycloaddition

• Regina Berg and
• Bernd F. Straub

Beilstein J. Org. Chem. 2013, 9, 2715–2750, doi:10.3762/bjoc.9.308

• for CuAAC reactions under Click conditions [144]. These copper(I) complexes can be handled under aerobic conditions and have been fully characterized including single crystal X-ray structures, which show a cubane-like [Cu4Br4] scaffold. Their main advantages are the ease of preparation, tolerance

Structure of 1,5-benzodiazepinones in the solid state and in solution: Effect of the fluorination in the six-membered ring

• Marta Pérez-Torralba,
• Rosa M. Claramunt,
• M. Ángeles García,
• Concepción López,
• M. Carmen Torralba,
• M. Rosario Torres,
• Ibon Alkorta and
• José Elguero

Beilstein J. Org. Chem. 2013, 9, 2156–2167, doi:10.3762/bjoc.9.253

• synthesized and their X-ray structures determined. 6,7,8,9-Tetrafluoro-4-methyl-1,3-dihydro-2H-1,5-benzodiazepin-2-one crystallizes in the monoclinic P21/c space group and 6,7,8,9-tetrafluoro-1,4-dimethyl-1,3-dihydro-2H-1,5-benzodiazepin-2-one in the triclinic P−1 space group. Density functional theory

• solid state. Keywords: benzodiazepinones; DFT; GIAO calculations; inversion barriers; multinuclear NMR; tautomerism; X-ray structures; Introduction In our previous paper [1] we already reported the relevance of 1,5-benzodiazepine derivatives in central nervous system pathologies as well as for other

• trifluoroacetate sample and then the chemical shifts were recalculated to the CFCl3 [δ (CF3COONH4+)] = –72.0 ppm) The six 1,5-benzodiazepinones discussed in this paper together with clobazam. The X-ray structures of 3a (TUPSAZ), 5a (EFARUA). In TUPSAZ there is a disordered water molecule. ORTEP plot (30

True and masked three-coordinate T-shaped platinum(II) intermediates

• Manuel A. Ortuño,
• Salvador Conejero and
• Agustí Lledós

Beilstein J. Org. Chem. 2013, 9, 1352–1382, doi:10.3762/bjoc.9.153

• the synthesis of cationic [Pt(norbornyl)(P–P)]+ complexes A1a–e (P–P = bidentate phosphine ligand) [34][35]. Further studies involved other alkyl ligands such as ethyl (A2b–c), 3,3-dimethylbutyl (A3b–c) and 2,3,3-trimethylbutyl (A4) [36][37][38]. NMR spectroscopic data and X-ray structures of A1a [34

• ’ = cyclometalated ligand) [44]. In sharp contrast with the analogous T5 and T6 (Figure 6) [28], δ- and ζ-agostic interactions at the fourth coordination site were detected by X-ray and NMR studies for complexes containing IPr (A11a) and It-Bu (A11b), respectively. Selected Pt···H–C parameters from the X-ray

• structures of agostic compounds are collected in Table 1. As it can be expected, short Pt–H and Pt–C distances are observed for the β-agostic interactions in A1a and A2b. In addition, Pt–H–C angles larger than 100° correlate with large Pt–C distances as shown in A7, A8 and A11a. Although a remote contact is

Host–guest complexes of mixed glycol-bipyridine cryptands: prediction of ion selectivity by quantum chemical calculations, part V

• Svetlana Begel,
• Ralph Puchta and
• Rudi van Eldik

Beilstein J. Org. Chem. 2013, 9, 1252–1268, doi:10.3762/bjoc.9.142

• topic. Here we discuss two hybrid cryptands between [2.2.2] and [bpy.bpy.bpy]. They are abbreviated as [2.2.bpy] and [2.bpy.bpy] and are presented in Figure 2. Results and Discussion Although as of spring 2013 more than 650 X-ray structures are listed in the Cambridge Structural Database for [2.2.2] and

• supramolecular systems the applied method (RB3LYP/LANL2DZp) provided satisfactory results [1][2][3][4]. In all these cases the calculated bond length between the guest ions and the donor atoms was elongated compared to the analogous bonds in the X-ray structures. The same behavior is found when comparing [Na

Tandem dinucleophilic cyclization of cyclohexane-1,3-diones with pyridinium salts

• Mostafa Kiamehr,
• Firouz Matloubi Moghaddam,
• Satenik Mkrtchyan,
• Volodymyr Semeniuchenko,
• Linda Supe,
• Alexander Villinger,
• Peter Langer and
• Viktor O. Iaroshenko

Beilstein J. Org. Chem. 2013, 9, 1119–1126, doi:10.3762/bjoc.9.124

• -ray structures of compounds 6d, 7c and 8. Supporting Information File 166: Computational results, optimized structures (atomic coordinates as reported by Gaussian 09), charges and local softness indexes (nucleophilic attack) for cations 2a+, 2b+ and 2e+, additional discussions related to computations.

• base and the reaction time was 4 days. The influence of K+ on the product free energy. Optimization of the reaction conditions. Supporting Information Supporting Information File 165: Details on synthetic procedures, list of pyridinium salts, characterization of new compounds, copies of NMR spectra, X

Synthesis and structure of trans-bis(1,4-dimesityl-3-methyl-1,2,3-triazol-5-ylidene)palladium(II) dichloride and diacetate. Suzuki–Miyaura coupling of polybromoarenes with high catalytic turnover efficiencies

• Jeelani Basha Shaik,
• Venkatachalam Ramkumar,
• Babu Varghese and
• Sethuraman Sankararaman

Beilstein J. Org. Chem. 2013, 9, 698–704, doi:10.3762/bjoc.9.79

• with high turnover numbers. With 1,4-dibromobenzene the catalyst was found to be active for up to 13 consecutive cycles with a turnover number of 1260. The polyarylarenes were obtained in pure form after crystallization once without recourse to chromatographic purification. The single-crystal X-ray

• structures of the chloro (1) as well as the corresponding acetato (2) complexes are also reported and compared with the corresponding complexes of 1,4-diphenyl-3-methyl-1,2,3-triazol-5-ylidene as the ligand. Keywords: C–C coupling; N-heterocyclic carbene; palladium; Suzuki–Miyaura coupling; 1,2,3

Complete σ* intramolecular aromatic hydroxylation mechanism through O₂ activation by a Schiff base macrocyclic dicopper(I) complex

• Albert Poater and
• Miquel Solà

Beilstein J. Org. Chem. 2013, 9, 585–593, doi:10.3762/bjoc.9.63

• -ray structures [40][48][49][50][51][52][53][54][55][56]. Computational details All geometry optimizations, as described in [40], were performed with the Gaussian03 package [57], by using the B3LYP functional [58][59][60] and the standard 6-31G(d) basis set [61][62]. The geometries obtained at the

• ligand used (H3m) was more flexible [40]. Crystallographic data on related copper compounds by using the same ligand suggest that complex a may present many conformations of rather similar energy [47]; however, the optimized geometries of similar complexes was found to be in perfect agreement with the X

Synthesis and testing of the first azobenzene mannobioside as photoswitchable ligand for the bacterial lectin FimH

• Vijayanand Chandrasekaran,
• Katharina Kolbe,
• Femke Beiroth and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2013, 9, 223–233, doi:10.3762/bjoc.9.26

• of FimH FlexX [24][25][26], flexible docking and consensus scoring [27][28], as implemented in Sybyl 6.9 [29], was employed. Docking was based on two different X-ray structures of FimH. They differ in the conformation of the so-called tyrosine gate at the entrance of the CRD, formed by the side

Highly enantioselective access to cannabinoid-type tricyles by organocatalytic Diels–Alder reactions

• Stefan Bräse,
• Nicole Volz,
• Franziska Gläser and
• Martin Nieger

Beilstein J. Org. Chem. 2012, 8, 1385–1392, doi:10.3762/bjoc.8.160

• catalysts 15 could be confirmed by NOESY experiments and from their X-ray structures (Figure 5). Before testing the catalysts in the Diels–Alder reaction, we analyzed a few co-catalysts with the commercially available imidazolidinone catalyst 15h. A pentyl-substituted tricycle was used as a model system

The preferred conformation of erythro- and threo-1,2-difluorocyclododecanes

• Yi Wang,
• Peer Kirsch,
• Tomas Lebl,
• Alexandra M. Z. Slawin and
• David O'Hagan

Beilstein J. Org. Chem. 2012, 8, 1271–1278, doi:10.3762/bjoc.8.143

• over an edge location is very strong, and thus when the CF2 groups are spaced 1,4 to each other or 1,7 to each other within the ring, they occupy adjacent and opposite corners of the ring, respectively, and form stable ring systems. This is illustrated in the X-ray structures in Figure 2. However when

Synthesis and structure of tricarbonyl(η⁶-arene)chromium complexes of phenyl and benzyl D-glycopyranosides

• Thomas Ziegler and
• Ulrich Heber

Beilstein J. Org. Chem. 2012, 8, 1059–1070, doi:10.3762/bjoc.8.118

• argon on silica gel with n-hexane/ethyl acetate mixtures as eluent. Crystalline chromium complexes 2 were recrystallized from ethanol, and for suitable crystals X-ray structures were determined. Table 1 summarizes the results for the preparation of the complexes 2 from simple acetylated and methylated

• complexes. This is further confirmed by the X-ray structures obtained from crystalline chromium complexes. For the tricarbonylchromium complexes 2a–e,j,k,m which gave suitable crystals, structures were determined by X-ray diffraction [23]. Crystals were grown for all compounds by slow crystallization of the

• unusual intra- and intermolecular nonclassical hydrogen bonds [25], which will be discussed in more details for each individual X-ray structure in the following. For technical details of the X-ray structures see Supporting Information File 1. Figure 2 shows the asymmetric unit of compound 2a, which

Synthesis of fluorinated maltose derivatives for monitoring protein interaction by ¹⁹F NMR

• Michaela Braitsch,
• Hanspeter Kählig,
• Georg Kontaxis,
• Michael Fischer,
• Toshinari Kawada,
• Robert Konrat and
• Walther Schmid

Beilstein J. Org. Chem. 2012, 8, 448–455, doi:10.3762/bjoc.8.51

• , probably corresponding to the closed- and open-domain conformations of MBP; but only the α-anomer complex has been observed in X-ray structures of MBP with maltose [21]. Furthermore we used this technique for probing the interactions between 2-F-maltose and the MBP-V53 [43][44] fusion protein, which has

Perhydroazulene-based liquid-crystalline materials with smectic phases

• Zakir Hussain,
• Henning Hopf and
• S. Holger Eichhorn

Beilstein J. Org. Chem. 2012, 8, 403–410, doi:10.3762/bjoc.8.44

• orientation of the terminal groups and position of the double bonds in isomers similar to 4a and 4b was established by analysis of the X-ray structures of their corresponding acids [14]. Continuing the synthesis, the precursors 4a and 4b were hydrogenated in the presence of Pd/C, and ethyl acetate as solvent

Fifty years of oxacalix[3]arenes: A review

• Kevin Cottet,
• Paula M. Marcos and
• Peter J. Cragg

Beilstein J. Org. Chem. 2012, 8, 201–226, doi:10.3762/bjoc.8.22

• reported the crystal structure and dynamic behaviour of a scandium(III) complex of 3a [59]. Later, the X-ray structures of lanthanum, lutetium and yttrium complexes with the same macrocycle showed 2:2 complexes between the cations and macrocycles [60]. In these structures the lanthanides are either six

The interplay of configuration and conformation in helical perylenequinones: Insights from chirality induction in liquid crystals and calculations

• Elisa Frezza,
• Silvia Pieraccini,
• Stefania Mazzini,
• Alberta Ferrarini and
• Gian Piero Spada

Beilstein J. Org. Chem. 2012, 8, 155–163, doi:10.3762/bjoc.8.16

• found in one of the available X-ray structures of cercosporin [26], whereas the other structure has the methoxy groups in the (m,p) state [28]. Our calculations confirm that the “propeller” form, found in X-ray structures of 1 [26][28], is significantly more stable than the other, called “double

• decrease of the energy differences between conformers, which points to an important role of diffuse functions. Although the conformer population is not directly accessible, we can try to analyze our results in the light of experimental data. Of the two X-ray structures of cercosporin reported in the

• trend reported in Figure 5 (middle). We have also shown in Figure 5 (left) the Q values calculated for the available X-ray structures of cercosporin [26][28]. The differences from the results reported for structures obtained by DFT, with the same conformation of the side chains, derive from relatively

Thermodynamic and kinetic stabilization of divanadate in the monovanadate/divanadate equilibrium using a Zn-cyclene derivative: Towards a simple ATP synthase model

• Hanno Sell,
• Anika Gehl,
• Frank D. Sönnichsen and
• Rainer Herges

Beilstein J. Org. Chem. 2012, 8, 81–89, doi:10.3762/bjoc.8.8

• coordination bond to the Zn2+ ion and two hydrogen bonds to the NH groups of the cyclene ring (Figure 2). The formation of a bidentate complex (two vanadate oxygens coordinating with Zn2+) is considerably less favorable. This is also in agreement with X-ray structures of Zn-cyclene phosphate complexes [15

Development of the titanium–TADDOLate-catalyzed asymmetric fluorination of β-ketoesters

• Lukas Hintermann,
• Mauro Perseghini and
• Antonio Togni

Beilstein J. Org. Chem. 2011, 7, 1421–1435, doi:10.3762/bjoc.7.166

• the ligand (R,R)-phenyl-TADDOL (L1)) (Table 2). Consistent catalysis results were obtained when the crystalline Lewis acid complexes K1 and K2 were applied instead of the complexes generated in situ. The synthesis, characterization and X-ray structures of these complexes, which are now commercially

Lithium phosphonate umpolung catalysts: Do fluoro substituents increase the catalytic activity?

• Anca Gliga,
• Bernd Goldfuss and
• Jörg M. Neudörfl

Beilstein J. Org. Chem. 2011, 7, 1189–1197, doi:10.3762/bjoc.7.138

• (racemate); 7: tR = 22.1 min; X-ray structures shown in Figure 1 and Figure 2, respectively) and an additional meso product for diol 8 (HPLC: tR2 = 22.4 min; tR3 = 30.6 min (racemate); tR1 = 9.1 min). A dimer associated by a hydrogen bond is apparent for the enantiomeric pair (6: intermolecular O1–O2

Single enantiomer synthesis of α-(trifluoromethyl)-β-lactam

• Václav Jurčík,
• Alexandra M. Z. Slawin and
• David O'Hagan

Beilstein J. Org. Chem. 2011, 7, 759–766, doi:10.3762/bjoc.7.86

• Centre as supplementary publication (CCDC 821177). Enantiomers of α-(trifluoromethyl)-β-lactam (1). X-ray structures of (a) β-lactam (S)-1 and (b) (αR,3R)-5c. (a) Determination of the absolute stereochemistry of (αR,3R)-5c by X-ray crystallography allowed an absolute assignment of β-lactam 1. Synthetic

SbCl₃-catalyzed one-pot synthesis of 4,4′-diaminotriarylmethanes under solvent-free conditions: Synthesis, characterization, and DFT studies

• Ghasem Rezanejade Bardajee

Beilstein J. Org. Chem. 2011, 7, 135–144, doi:10.3762/bjoc.7.19

• compound 11, calculated by HF and DFT levels with the HF/6-31G*, 6-31G*/B3LYP, and B3LYP/cc-pVDZ methods, are listed in Table 2. The optimized configuration is shown in Figure 2. Because of unavailability of X-ray crystal structures for these compounds, the optimized structure is compared with X-ray

• structures of similar compounds. This comparison shows good agreement between optimized and actual molecular structures. Here, we compare the bond lengths of the C–C, C–O, and C–N bonds of similar structures with the results of HF/6-31G*, 6-31G*/B3LYP, and B3LYP/cc-pVDZ calculations. The optimized C–C bond