Synthesis of functionalized macrocyclic derivatives of trioxabicyclo[3.3.0]nonadiene

• Sabine Leber,
• Gert Kollenz and
• Curt Wentrup

Beilstein J. Org. Chem. 2012, 8, 738–743, doi:10.3762/bjoc.8.83

• principal structures). This will also be the case for the derivatives described below. The splitting of several signals in the NMR spectra may be ascribed to the presence of mixtures of diastereoisomers and conformers. Reduction Several methods were attempted for the reduction of the nitro groups in 8 and

An easy α-glycosylation methodology for the synthesis and stereochemistry of mycoplasma α-glycolipid antigens

• Yoshihiro Nishida,
• Yuko Shingu,
• Yuan Mengfei,
• Kazuo Fukuda,
• Hirofumi Dohi,
• Sachie Matsuda and
• Kazuhiro Matsuda

Beilstein J. Org. Chem. 2012, 8, 629–639, doi:10.3762/bjoc.8.70

• one-pot α-glycosylation method was effectively applied. The synthetic GGPL-I isomers were characterized with 1H NMR spectroscopy to determine the equilibrium among the three conformers (gg, gt, tg) at the acyclic glycerol moiety. The natural GGPL-I isomer was found to prefer gt (54%) and gg (39

• %) conformers around the lipid tail, while adopting all of the three conformers with equal probability around the sugar position. This property was very close to what we have observed with respect to the conformation of phosphatidylcholine (DPPC), suggesting that the Mycoplasma glycolipids GGPLs may constitute

• , each of them is allowed to have three staggered conformers of gg (gauche-gauche), gt (gauche-trans) and tg (trans-gauche) (Figure 3). In solution and also in self-contacting liquid-crystalline states, these conformers are thought to equilibrate with each other. In this study, we calculated time

Enantioselective supramolecular devices in the gas phase. Resorcin[4]arene as a model system

• Caterina Fraschetti,
• Matthias C. Letzel,
• Antonello Filippi,
• Maurizio Speranza and
• Jochen Mattay

Beilstein J. Org. Chem. 2012, 8, 539–550, doi:10.3762/bjoc.8.62

• ]+ complexes whose large enantioselectivity (ρ = 16.9 ± 2.8) must be essentially promoted by substantial differences in the relevant reaction pathway [49]. Indeed, from the computational analysis performed on catharanthine (T), two families of conformers resulted as stable from the study performed in vacuum as

• . Amidoresorcin[4]arene YS. Catharanthine and vindoline, monomers constituting the anticancer vinblastine and the analogous vincristine. Stable conformers of catharanthine. Global minima of (a) [VS∙H∙T]+ and (b) [VR∙H∙T]+ complexes. Guests studied in [47]. Selected nucleosides. Example of molecular logic gate

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

• bind such species. In common with other calix[n]arenes, oxacalix[3]arenes containing free OH groups are conformationally mobile, leading to cone and partial-cone conformers (Figure 6). Without lower-rim substituents there is free rotation of each phenolic unit through the macrocyclic annulus; however

• cone (8%) and partial-cone (68%) conformers, and the only isolated product with Cs2CO3 was the partial-cone conformer (75%) [28]. The X-ray structure of the partial-cone conformer (Figure 7), reported by Cragg, shows one pyridyl group to be included within the macrocyclic cavity and the remaining two

• analogue was, in both the cone (77% vs 24% E) and partial-cone (42% vs 6% E) conformers [29]. In a wider study, Yamato determined extraction data for 17a with n-BuNH3+ picrate (98% E cone vs 93% E partial-cone), iBuNH3+ picrate (48% E cone vs 37% E partial-cone) and t-BuNH3+ picrate (35% E cone vs 14% E

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

• ) calculations, and with the prediction of the twisting ability of conformers, by the surface chirality (SC) method [29]. Results and Discussion HTP measurement The propensity of a dopant to induce a helical organization in the liquid-crystalline matrix is measured by its helical twisting power, which is defined

• this issue we performed a computational study at different levels: Single-molecule DFT calculations were carried out to evaluate energy and geometry of all the conformers of 1 and 2, and the SC method was used to estimate their twisting ability. Conformational analysis by DFT For each of the side

• chains in position 1 and 12 of cercosporin and phleichrome, three conformational states are possible, which are shown in Figure 2, where the same notation as in [31] is used. This makes a total of six conformers for each molecule, which are labeled according to the state of each side chain; thus, for

Laterally substituted symmetric and nonsymmetric salicylideneimine-based bent-core mesogens

• Sonja Findeisen-Tandel,
• Wolfgang Weissflog,
• Ute Baumeister,
• Gerhard Pelzl,
• H. N. Shreenivasa Murthy and
• Channabasaveshwar V. Yelamaggad

Beilstein J. Org. Chem. 2012, 8, 129–154, doi:10.3762/bjoc.8.15

• , which is significantly shorter than the molecular length Lcalc = 5.5 nm estimated by molecular models. The difference may be caused by a deviation of the molecular configuration from that assumed in the model calculations (e.g., by another bending angle or a high proportion of gauche conformers), or by

Computational evidence for intramolecular hydrogen bonding and nonbonding X···O interactions in 2'-haloflavonols

• Tânia A. O. Fonseca,
• Matheus P. Freitas,
• Rodrigo A. Cormanich,
• Teodorico C. Ramalho,
• Cláudio F. Tormena and
• Roberto Rittner

Beilstein J. Org. Chem. 2012, 8, 112–117, doi:10.3762/bjoc.8.12

• isomerization around the α [H–O–C–C(=O)] and β [C(X)–C–C–C(OH)] torsional angles (Figure 1), giving the energy minima obtained at the B3LYP/aug-cc-pVDZ level depicted in Table 1. Flavonol itself (X = H) exhibits two stable conformers, with the most stable one having the hydroxy hydrogen directed toward the

• conformers, in which those with the hydroxy hydrogen directed toward the carbonyl oxygen (A and B) are significantly more stable than the other two conformers (Table 1); clearly, the intramolecular HB O–H···O=C plays the determinant role for the conformational isomerism of 2'-fluoroflavonol, as confirmed by

• than in the remaining conformers (Table 1) provide evidence that fluorine lone pairs in C are involved in intramolecular HB O–H···F–C instead of contributing to the resonant structure with C=F+. HB involving fluorine as a proton acceptor when bonded to carbon is unusual [4], but it has been shown to be

On the mechanism of action of gated molecular baskets: The synchronicity of the revolving motion of gates and in/out trafficking of guests

• Keith Hermann,
• Stephen Rieth,
• Hashem A. Taha,
• Bao-Yu Wang,
• Christopher M. Hadad and
• Jovica D. Badjić

Beilstein J. Org. Chem. 2012, 8, 90–99, doi:10.3762/bjoc.8.9

• rise to two enantiomeric conformers 1A and 1B (Figure 7A). The interconversion kinetics of the 1A/B racemization can be followed by dynamic NMR spectroscopy in which a singlet corresponding to Ha/Hb nuclei at high temperatures is seen to split into two doublets at low temperatures. In particular, the

On the control of secondary carbanion structure utilising ligand effects during directed metallation

• Andrew E. H. Wheatley,
• Jonathan Clayden,
• Ian H. Hillier,
• Alison Campbell Smith,
• Mark A. Vincent,
• Laurence J. Taylor and
• Joanna Haywood

Beilstein J. Org. Chem. 2012, 8, 50–60, doi:10.3762/bjoc.8.5

• ). Computed minimum energy conformers (B3LYP density functional/6-311++G(2d,2p) basis set; H-atoms omitted for clarity) of trans-6-Lil·PMDTA with and without a Li–(α-C) interaction (a and b) and trans-6-Lil·DGME with and without a Li–(α-C) interaction (c and d). Molecular structures of 1/2-H and their

Binding of group 15 and group 16 oxides by a concave host containing an isophthalamide unit

• Jens Eckelmann,
• Vittorio Saggiomo,
• Svenja Fischmann and
• Ulrich Lüning

Beilstein J. Org. Chem. 2012, 8, 11–17, doi:10.3762/bjoc.8.2

• anion transport. Rotation along the amide–aryl bonds leads to syn/anti, syn/syn and anti/anti conformers (syn and anti defined with respect to the relative orientation of the NH atoms), and only the syn/syn conformer of an isophthalamide is capable of simultaneously binding an anion by both NH groups

(How) does 1,3,5-triethylbenzene scaffolding work? Analyzing the abilities of 1,3,5-triethylbenzene- and 1,3,5-trimethylbenzene-based scaffolds to preorganize the binding elements of supramolecular hosts and to improve binding of targets

• Xing Wang and
• Fraser Hof

Beilstein J. Org. Chem. 2012, 8, 1–10, doi:10.3762/bjoc.8.1

• calculations. The conformers ududud and uddudd, are almost of the same energy and the next two most stable conformers, ududdd and udduud, lie only 0.3 and 0.4 kcal/mol above the ududud conformer. When the solvent condition is changed to water the trend of the results is much closer to those of hexaethylbenzene

• positively charged substituents. This difference disappears when the calculation is carried out in water, in which the alike charges are more effectively screened from each other, and the uuu conformers are favored by 1.0 kcal/mol (for 5H) and 0.5 kcal/mol (for 5Me). The uuu conformers that are best suited

• period. Faced with evidence that the barriers to exchange of “up” and “down” conformers in the sterically congested 1,3,5-triethylbenzene and 1,3,5-trimethylbenzene systems are too high to examine conveniently by MD simulations, we turned instead to a calculation of the barriers to bond rotation for a

Structural conditions required for the bridge lithiation and substitution of a basic calix[4]arene

• Conrad Fischer,
• Wilhelm Seichter and
• Edwin Weber

Beilstein J. Org. Chem. 2011, 7, 1602–1608, doi:10.3762/bjoc.7.188

• 1,2-alternate conformation (Supporting Information File 1, Figure S9). In both conformers, the lateral substituent is located at the equatorial position, assuming a rotation of both methoxy groups before the substitution step. Thus, a subsequent rotation of both methoxy groups through the annulus

• by the presence of two nonconvertible conformers of the calixarene acid 14. Experimental General remarks Melting points were determined on a microscope heating stage PHMK Rapido (VEB Dresden Analytik) and are uncorrected. IR spectra were measured on a Nicolet FT-IR 510 as KBr pellets. NMR spectra

NMR studies of anion-induced conformational changes in diindolylureas and diindolylthioureas

• Damjan Makuc,
• Jennifer R. Hiscock,
• Mark E. Light,
• Philip A. Gale and
• Janez Plavec

Beilstein J. Org. Chem. 2011, 7, 1205–1214, doi:10.3762/bjoc.7.140

• major, energetically preferred, conformers are likely to be observed (Figure 3). The syn–syn conformer, where NH protons form a convergent hydrogen-bonding array, is expected to be adopted in the presence of bound anionic guests, based on the previous solid-state studies. On the other hand, this

• cases were restrained along the [C6–C7–N7α–C7β] torsion angle, while other degrees of freedom were freely optimized. The relative energies for the three representative conformers are reported in Table 4. The anti–anti conformer of 1 was found to be the lowest in energy, while the syn–syn conformer

• showed considerably higher energy (11.6 kcal·mol−1). The angle between the two indolyl rings in the freely optimized anti–anti conformer was 53.9° (Figure 6a). The relative energies of the three representative conformers were also computed for complexes of 1 with chloride, acetate and bicarbonate anions

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

• ) [31][32]. The energy differences of the terpene-based conformers are between 5.1 and 5.8 kcal/mol [32][33] (B3LYP/6-31++G**:AM1). The conversion of diols 1–5, 7, and 8 to the desired phosphonates can be achieved by twofold addition to phosphorus trichloride and subsequent hydrolysis. Diol 6 could not

Toward an integrated route to the vernonia allenes and related sesquiterpenoids

• Da Xu,
• Michael A. Drahl and
• Lawrence J. Williams

Beilstein J. Org. Chem. 2011, 7, 937–943, doi:10.3762/bjoc.7.104

• -decalin system. Low energy conformers were identified for these species [59]. The lowest energy conformer gave the greatest torsion angles (~175°) for both the alcohol V and the alkoxide VI, and these approach 180°. For comparison purposes, the cis-hydrindane derivative in entry 3 was also studied [38

• alkoxide (R = O−) [62]. In light of the above data, we targeted compound 24 (c.f. 14, Scheme 1) to extend the C–C fragmentation to cis-decalins and to provide an important model for our synthetic studies. This substrate should be able to adopt conformers with the proper orientation for fragmentation and

Anion–π interactions influence pK_a values

• Christopher J. Cadman and
• Anna K. Croft

Beilstein J. Org. Chem. 2011, 7, 320–328, doi:10.3762/bjoc.7.42

• minimum energy conformers of all molecules examined have C1 symmetry. Vibrational frequencies and zero point energies were calculated by the M06-2X method, and scaled by 0.9670 [36]. AIM analyses were performed using XAim on Gaussian wfn output to examine densities and laplacians [47], and AIM2000 to

Accuracy in determining interproton distances using Nuclear Overhauser Effect data from a flexible molecule

• Catharine R. Jones,
• Craig P. Butts and
• Jeremy N. Harvey

Beilstein J. Org. Chem. 2011, 7, 145–150, doi:10.3762/bjoc.7.20

• NMR spectroscopy is widely employed in the determination of stereochemical and conformational details [1]. It is traditionally used in a qualitative or semi-quantitative manner to establish gross differences between conformers. However, the quantitative use of NOEs is often discounted or at least

• -averaged NOE-determined distances can thus be used, along with computations of conformer geometries, to confirm the structures and energies/populations of contributing conformers. An excellent description of the advantages and disadvantages of such an approach was made by Kozerski et al., using

• molecules when compared to their time-averaged computationally-derived distances in the alkyl chain of a small molecule – 4-propylaniline. These NOE-derived distances can thus be applied to modelling the populations (and hence energy differences) of the conformers, again with good accuracy when compared to

Heavy atom effects in the Paternò–Büchi reaction of pyrimidine derivatives with 4,4’-disubstituted benzophenones

• Feng-Feng Kong,
• Jian-Bo Wang and
• Qin-Hua Song

Beilstein J. Org. Chem. 2011, 7, 113–118, doi:10.3762/bjoc.7.16

• regioselectivity by changing the populations of two regioisomeric diradicals as a result of differences in the potential energies of two stable conformers, the productive conformation of the triplet diradical and the unproductive conformation of the triplet diradical, for each regioisomeric diradical [9][11]. To

• productive conformers of singlet diradicals C5-1DR1 and C6-1DR1 are determined not only by the populations of C5-3DR1 and C6-3DR1 but also by the relative rate constants of ISC processes, the k2I/k2I’ and k3I/k3I’. The former is determined by the equilibrium constants, K2 and K3, whilst the latter processes

• (k2I, k2I’, k3I and k3I’) would be accelerated by heavy atoms. Thus, the equilibrium between the productive conformers and the unproductive conformers, of the triplet 1,4-diradicals, would be achieved at a higher temperature for the system with heavy atoms than that without heavy atoms. Due to the

Anthracene appended pyridinium amide–urea conjugate in selective fluorometric sensing of L-N-acetylvaline salt

• Kumaresh Ghosh,
• Tanmay Sarkar and
• Asoke P. Chattopadhyay

Beilstein J. Org. Chem. 2010, 6, 1211–1218, doi:10.3762/bjoc.6.139

• more stable than 1A by 2.82 kcal/mol. Therefore, we may reasonably expect that in solution both conformers may remain in equilibrium. However, conformation 1A may form a more stable hydrogen-bonded complex with guests, owing to formation of a greater number of hydrogen bonds with the guests. For

Syntheses and properties of thienyl-substituted dithienophenazines

• Annemarie Meyer,
• Eva Sigmund,
• Friedhelm Luppertz,
• Gregor Schnakenburg,
• Immanuel Gadaczek,
• Thomas Bredow,
• Stefan-S. Jester and
• Sigurd Höger

Beilstein J. Org. Chem. 2010, 6, 1180–1187, doi:10.3762/bjoc.6.135

• of the molecules in CH2Cl2 [32][33]. The calculated spectra of the most stable conformers and the Sn–S0 difference electron densities of selected compounds are shown in Figure 2. In general, the calculated excitation energies are in reasonable agreement with the experimental results (see also Table 3

Catalysis: transition-state molecular recognition?

• Ian H. Williams

Beilstein J. Org. Chem. 2010, 6, 1026–1034, doi:10.3762/bjoc.6.117

• exhibits no detectable enzyme activity [22], and so it is an intriguing question to investigate the nature of this OYHY…Oring interaction. MD simulations with the hybrid AM1/OPLS-AA/TIP3P method showed that both 4C1 chair and 2,5B boat conformers of phenyl β-xyloside remained stable in water during the

Synthesis and crystallographic analysis of meso-2,3-difluoro-1,4-butanediol and meso-1,4-dibenzyloxy-2,3-difluorobutane

• Bruno Linclau,
• Leo Leung,
• Jean Nonnenmacher and
• Graham Tizzard

Beilstein J. Org. Chem. 2010, 6, No. 62, doi:10.3762/bjoc.6.62

• ether 7 crystallises in the monoclinic P21/c space group with half a molecule of 7 in the asymmetric unit. The molecule possesses crystallographic inversion symmetry. Two conformers are present in the crystal (55:45) which differ only in the sign of the torsion angle of the rings (Figure 2). The

• ); HRMS (EI+) for C6H12O79BrSi (M-tBu)+: Calcd 206.9835; Measured 206.9841. Vicinal difluoride containing building blocks. Molecular overlay of both conformers of 7. Crystal packing of 7 viewed along the b axis. Short contacts (see text) are shown in light blue. Crystal structure of 3. Crystal packing of

The C–F bond as a conformational tool in organic and biological chemistry

• Luke Hunter

Beilstein J. Org. Chem. 2010, 6, No. 38, doi:10.3762/bjoc.6.38

• [8]. For example, in the 2-fluoroethylammonium ion (8) and protonated 2-fluoroethanol (9) (Figure 1b), the gauche conformers are strongly preferred because these bring the (partially negative) fluorine atoms close to the formally positively-charged oxygen or nitrogen [9]. It is possible to envisage

• an intramolecular hydrogen bond helping to stabilise the gauche conformers of 8 and 9, but the gauche preference is also maintained in systems such as 10 (Figure 1b) which cannot accommodate a hydrogen bond [10], confirming that the charge–dipole interaction is more important than any weak H-bonding

• in these systems. Hyperconjugation effects Consider the well-studied molecule 1,2-difluoroethane (11, Figure 1c). There are two possible staggered conformers, with the fluorine atoms either gauche or anti. NMR and molecular modelling studies have shown that the gauche conformer is lower in energy

Molecular recognition of organic ammonium ions in solution using synthetic receptors

• Andreas Späth and
• Burkhard König

Beilstein J. Org. Chem. 2010, 6, No. 32, doi:10.3762/bjoc.6.32

Bis(oxazolines) based on glycopyranosides – steric, configurational and conformational influences on stereoselectivity

• Tobias Minuth and
• Mike M. K. Boysen

Beilstein J. Org. Chem. 2010, 6, No. 23, doi:10.3762/bjoc.6.23

• presence of a 4,6-O-benzylidene group has a pronounced influence on the conformation adopted by the pyranose scaffold in gluco-configured ligands (Scheme 1, conformers A and B), which in turn has a direct influence on the stereoselectivity in the model reaction. In order to ascertain if a similar