Thermotropic and lyotropic behaviour of new liquid-crystalline materials with different hydrophilic groups: synthesis and mesomorphic properties

• Alexej Bubnov,
• Miroslav Kašpar,
• Věra Hamplová,
• Ute Dawin and
• Frank Giesselmann

Beilstein J. Org. Chem. 2013, 9, 425–436, doi:10.3762/bjoc.9.45

• scattering. As an example, the temperature dependence of the smectic layer spacing d, for TL1 is shown in Figure 4. The MOPAC/AM1 model has been used to calculate the length of TL1 in the energy-optimized conformation, which gives 41 Å for the most extended conformer. In X-ray data taken at small scattering

• conformer. This fact gives evidence for the bent-like conformation of the molecule, i.e., the molecule core is rigid but the flexible chains are bent and not extended at all. The increase of scattered X-ray signal intensity on cooling also confirms the increase of the order with temperature decrease (Figure

Caryolene-forming carbocation rearrangements

• Quynh Nhu N. Nguyen and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2013, 9, 323–331, doi:10.3762/bjoc.9.37

• -energy conformer found); see Experimental for details. Computed minima and transition-state structure involved in the single-step conversion of A to C. Relative energies shown (kcal/mol) were calculated at the mPW1PW91/6-31+G(d,p)//B3LYP/6-31+G(d,p) level. IRC from TS-AC toward C. Relative energies were

Synthesis of 5-(ethylsulfonyl)-2-methoxyaniline: An important pharmacological fragment of VEGFR2 and other inhibitors

• Miroslav Murár,
• Gabriela Addová and
• Andrej Boháč

Beilstein J. Org. Chem. 2013, 9, 173–179, doi:10.3762/bjoc.9.20

• ; S, 14.77%. The AAZ ligand conformer from PDB complex 1Y6A and its VEGFR2 intermolecular interaction map depicting three hydrogen bonds and two stacked (π,π) interactions. No lipophilic interactions are shown here. The part of the skeleton AAZ in bold represents the fragment originating from the

The diketopiperazine-fused tetrahydro-β-carboline scaffold as a model peptidomimetic with an unusual α-turn secondary structure

• Francesco Airaghi,
• Andrea Fiorati,
• Giordano Lesma,
• Manuele Musolino,
• Alessandro Sacchetti and
• Alessandra Silvani

Beilstein J. Org. Chem. 2013, 9, 147–154, doi:10.3762/bjoc.9.17

• molecular modeling and these experimental results, for 1a we can presume the presence in solution of conformers bearing a 13-membered intramolecular hydrogen bond involving the NHMe proton and the Cbz carbonyl group, as visualized in the perspective view of the low energy conformer of 1a. Conclusion In

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

• Jutta Erika Helga Köhler and
• Nicole Grczelschak-Mick

Beilstein J. Org. Chem. 2013, 9, 118–134, doi:10.3762/bjoc.9.15

• , 290, 280, and 273 K for 500 ps each, and their release of the guest was analysed from these trajectories. Results and Discussion AM1 Calculations The four conformers of empty β-CD The BCDO23rO6l structure turned out to be the lowest energy conformer, also having the lowest dipole moment of only 0.5618

• about 6 kcal mol−1 above, was conformer BCDO23rO6r. This oval structure has the highest dipole moment of 2.5639 D (x = +0.0268; y = +0.0236; z = −2.5637) and its O6 atomic charges display a range from −0.340 to −0.349 (average −0.344), but all O2 atoms still have the same charge of 0.325, and O3 and O4

• oxygen charges vary very little (−0.337 to −0.338 and −0.300 to −0.301, respectively). The third conformer BCDO23lO6l, lying about 7 kcal mol−1 above, was again total symmetric as shown by its dipole moment components of x = 0.0; y = 0.0; z = −1.0687 and also with respect to all its oxygen charge values

The chemistry of bisallenes

• Henning Hopf and
• Georgios Markopoulos

Beilstein J. Org. Chem. 2012, 8, 1936–1998, doi:10.3762/bjoc.8.225

• analysis of the transformation, including its study in the solid state [105], revealed that it begins with a rotation around the central single bond, thus converting the transoid structure into the cisoid conformer 140. Conrotatory ring closure subsequently leads to the bismethylenecyclobutene 141. The

Determination of the relative configuration of tropinone and granatanone aldols by using TBDMS ethers

• Ryszard Lazny,
• Aneta Nodzewska,
• Katarzyna Sidorowicz and
• Przemyslaw Kalicki

Beilstein J. Org. Chem. 2012, 8, 1877–1883, doi:10.3762/bjoc.8.216

• preliminary synthetic report the major isomeric products accessible under these conditions were assigned the exo,syn configuration. DFT calculations suggest that selectivity in the solventless reaction results from equilibration and the higher stability of the O–H…N-hydrogen-bond-stabilized conformer of the

Asymmetric desymmetrization of meso-diols by C₂-symmetric chiral 4-pyrrolidinopyridines

• Hartmut Schedel,
• Keizo Kan,
• Yoshihiro Ueda,
• Kenji Mishiro,
• Keisuke Yoshida,
• Takumi Furuta and
• Takeo Kawabata

Beilstein J. Org. Chem. 2012, 8, 1778–1787, doi:10.3762/bjoc.8.203

• responsible for the asymmetric acylation. The most stable conformer A of the acylpyridinium ion was generated by a molecular modeling search (AMBER* force field with the GB/SA solvation model for chloroform using MacroModel V 9.0 (50,000 steps MCMM)) and shown in Figure 2a and Figure 2b. Since the amide

Synthesis and evaluation of new guanidine-thiourea organocatalyst for the nitro-Michael reaction: Theoretical studies on mechanism and enantioselectivity

• Tatyana E. Shubina,
• Matthias Freund,
• Sebastian Schenker,
• Timothy Clark and
• Svetlana B. Tsogoeva

Beilstein J. Org. Chem. 2012, 8, 1485–1498, doi:10.3762/bjoc.8.168

• the further optimization at the B3PW91/6–31G(d) level. Conformer 7a is the only one with two hydrogen bonds between a nitrogen atom in the guanidine moiety and hydrogen atoms from the thiourea fragment. While inclusion of the solvent effect (DFT-PCM) gives a preference of 3.1 kcal·mol−1 for 7b over 7a

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

• a transition state. This may arise as a result of desolvation for this isomer. Computational study In order to explore conformer energies further, a theoretical study MP2/6-311+G(2d,p)//B3LYP/6-311+G(2d,p)+ZPE) [16] was carried out to assess relative ground-state energies of candidate conformers

• conformer III, the lowest in energy. For the threo stereoisomer 5b, four conformers, IV–VII were considered. Conformers IV and V, which have two and one endo fluorine, respectively, are highest in energy. In particular, conformer IV with two endo fluorines has a ground-state energy of 6.65 kcal·mol−1, the

• highest of all of those examined, illustrating the additive and negative impact of placing fluorines into endo orientations. Conformers VI and VII are lower in energy. It was anticipated at the outset that conformer VI may be the most favoured for the threo isomer; however, this does not appear to be the

Conformational analysis, stereoelectronic interactions and NMR properties of 2-fluorobicyclo[2.2.1]heptan-7-ols

• Fátima M. P. de Rezende,
• Marilua A. Moreira,
• Rodrigo A. Cormanich and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2012, 8, 1227–1232, doi:10.3762/bjoc.8.137

• ) in steps of 10° at the HF/6-31g(d,p) level, using the Gaussian09 package of programs [13]. Each minimum was subsequently optimized at the MP2/aug-cc-pVDZ level, and the respective energies are given in Table 1, which shows that the conformer of 5 with the hydroxy hydrogen directed toward the fluorine

• hydroxy group do not exhibit such an interaction and are highly stable [6][8]. This can be either due to other attractive interactions present in the referred conformer or prevalent repulsive interactions (e.g., between fluorine and oxygen lone pairs) in the other conformer(s). In the present study

• , comparison of 5 with three diastereoisomers (6–8) gives insight into the role of F∙∙∙HO intramolecular HB for the conformer stabilization, since the simple observation that the conformational energy in 5 is ca. 2.9 kcal mol−1 does not warrant that F∙∙∙HO intramolecular HB is the dominating, or even an

Synthesis of a library of tricyclic azepinoisoindolinones

• Bettina Miller,
• Shuli Mao,
• Kara M. George Rosenker,
• Joshua G. Pierce and
• Peter Wipf

Beilstein J. Org. Chem. 2012, 8, 1091–1097, doi:10.3762/bjoc.8.120

• steric bulk of the adamantyl group: molecular mechanics calculations indicate that the aminolysis of 5 to regioisomer 10 proceeds with minimal isomerization of the seven-membered ring geometry in the lowest-energy product conformer, whereas the formation of 9 requires a substantial ring flip [41

Toward unidirectional switches: 2-(2-Hydroxyphenyl)pyridine and 2-(2-methoxyphenyl)pyridine derivatives as pH-triggered pivots

• Christina Tepper and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2012, 8, 977–985, doi:10.3762/bjoc.8.110

• repulsive interaction between the free electron pairs of the nitrogen and the oxygen atoms, should be the more stable one (Scheme 1). A protonation of the nitrogen inverts the relative energies of the two conformers. Due to the internal hydrogen bridge the conformer of 4 having a dihedral angle of 0° is the

• . Unfortunately, there is no hint toward a preference for the M conformer of 13 in solution: For example, in the 1H NMR spectrum of 13 signals for only one conformer were found, even at lower temperatures, which means that the diastereomers are rapidly interconverting and the ratio between them cannot be

On the bromination of the dihydroazulene/vinylheptafulvene photo-/thermoswitch

• Virginia Mazzanti,
• Martina Cacciarini,
• Søren L. Broman,
• Christian R. Parker,
• Magnus Schau-Magnussen,
• Andrew D. Bond and
• Mogens B. Nielsen

Beilstein J. Org. Chem. 2012, 8, 958–966, doi:10.3762/bjoc.8.108

• ; photoswitch; vinylheptafulvene; Introduction 1,8a-Dihydroazulene-1,1-dicarbonitrile (DHA, 1) is a yellow photochromic compound, which undergoes a light-induced 10-electron retro-electrocyclization to a red-colored vinylheptafulvene (VHF) (Scheme 1) [1][2][3]. The VHF compound is formed as the s-cis conformer

• , which, however, is in equilibrium with the more stable s-trans conformer. The s-cis VHF undergoes a thermally induced cyclization to regenerate the original DHA. The significant structural difference between the DHA and VHF forms, as reflected in their different colors and hence electronic properties

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

• + gt + tg = 1. In this equation, a perfect staggering (Φ1 and Φ2 = +60, −60 or 180 degree) is assumed for every conformer. Figure 3 summarizes the results for a series of 3-substituted 1,2-di-O-palmitoyl-sn-glycerols, which involve tripalmitin (Figure 3, entry 1), DPPC (1,2-di-O

• symmetric lipid, the asymmetric phospholipid (DPPC) favors the gt-conformer more strongly around the tail lipid moiety along the sn-1,2 position, while disfavoring the tg-conformer, in the ratio of gt (59%), gg (34%) and tg (7%). The head phosphate moiety along the sn-2,3 position adopts the three

• conformation. Here, it should be mentioned that the conformer distribution coincides between I-a (Figure 3, entry 5) and DPPC (Figure 3, entry 2) at the head moiety [gt (33%), gg (34%) and tg (33%)]. The above analysis was carried out also for the stereoisomer I-b and the related glycolipids (Figure 4, entries

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

• , the presence of a hydrogen-bond motif in the cone conformer makes it the more stable form. In 1985, Gutsche investigated the conformational flexibility of parent calix[n]arenes (n = 4–8) and oxacalixarenes by temperature-dependent 1H NMR [5]. The through-the-annulus rotation barrier for oxacalix[3

• inversion in CDCl3 was <38 kJ mol−1, in contrast with 66 kJ mol−1 for the calix[4]arene analogue. To freeze the oxacalix[3]arene conformer, through-the-annulus rotation must be prevented. This can be achieved by the introduction of sufficiently large groups on the lower rim of the macrocycle. Upper-rim

• conformation only. When the reaction was performed in the presence of t-BuOK a 1:4 mixture of cone and partial-cone was obtained and even with Cs2CO3 the cone conformer could be detected. It seems that K+ and Cs+ favourably interact with the three phenolic oxygen atoms placed on the same side, whereas Na

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

• instance, g+ t is a conformer with one chain in the gauche+ and the other in the trans state. The conformers with side chains in different states are two-fold degenerate: g+ t (= t g+), g+ g− (= g− g+) and g− t (= t g−). For the conformational study, we used DFT calculations in vacuum as implemented in the

• butterfly” by Falk and co-workers [37]. The two geometries, as obtained for the g+ g+ conformer of 1, are shown in Figure 3. Table 1 reports the twist angles χ1 [C(1)–C(12b)–C(12a)–C(12)] and χ2 [C(6)–C(6a)–C(6b)–C(7)], which characterize the helical shape of the core of 1 and 2. Not surprisingly, in view

• considered in our systematic analysis of the effects of side-chain conformations. Very similar structures were obtained by geometry optimization at the B3LYP/6-31g(d,p) and at the M06-2X/6-31+g(d,p) level; the latter are shown in Figure 4. On the contrary, the conformer energies were found to depend strongly

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

• 10.3762/bjoc.8.12 Abstract The conformational isomerism and stereoelectronic interactions present in 2'-haloflavonols were computationally analyzed. On the basis of the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis, the conformer stabilities of 2'-haloflavonols were

• carbonyl oxygen (conformer A), establishing an intramolecular HB as the stabilizing interaction of this conformation, in agreement with the crystal structure of 2'-methoxyflavonol [19] and with the bioactive conformation of fisetin [20] and quercetin [21]. Moreover, a weak (H)O···H–C HB also takes place in

• and a nonbonding F…O interaction. The formation of the nonbonding F…O interaction in conformer A, having fluorine as electron acceptor, is supposed to be due to the partial negative atomic charge on the ether oxygen and a less negative atomic charge on the fluorine atom (the QTAIM atomic charges are

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

• were studied and reported here. The results of the calculation in the gas phase were in good agreement with the values reported by Mislow (Table 4). The ududud conformer adopted the most stable conformation and the energy level of this conformation was 4.3 kcal/mol lower than the second most stable

• conformer, namely uddudd. One can expect a significant effect of the nature of the recognition elements on conformational energies. Many recognition elements that vary in shape, functionality, charge, and chirality have been reported. We picked pyrazole-derived hosts 4 (used for cation binding) [17] and

• 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

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

• methine proton. In contrast, after addition of the fixatives to a CDCl3 solution of 14, a more complex signal pattern indicates the presence of at least two fixed conformations. One can be related to the expected resonances of the cone conformer, while the resonances of the second species fit best to a

• , transferring the 1,2-alternate to the cone conformer, is impossible, since it would ultimately lead to an axial orientation of the COOH group, which is strictly avoided for steric reasons [4][10]. Crystal structure of compound 12 Crystallization of the mixed calixarene ether 12 from ethanol yielded colourless

Synthesis of enantiomerically enriched (R)-¹³C-labelled 2-aminoisobutyric acid (Aib) by conformational memory in the alkylation of a derivative of L-alanine

• Stephen P. Fletcher,
• Jordi Solà,
• Dean Holt,
• Robert A. Brown and
• Jonathan Clayden

Beilstein J. Org. Chem. 2011, 7, 1304–1309, doi:10.3762/bjoc.7.152

• less hindered conformer of 3. Alkylated 5 was freed from its protecting group and the naphthamide “aide-mémoire” by heating to reflux in 47% hydrobromic acid, followed by esterification with methanol and thionyl chloride, which returned the labelled Aib as its methyl ester hydrochloride salt 6* in 93

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

• mechanics calculations. NOE experiments showed that the anti–anti conformer along the C7–N7α bonds was predominant in DMSO-d6 solution in the absence of anions. Anion-induced changes in the 1H and 15N chemical shifts confirm the weak binding of chloride anions with negligible conformational changes. Strong

• along the C7–N7α bonds and the syn–syn conformer was preferred for anion–receptor complexes. The conformational changes upon anion binding are in good agreement with energetic preferences established by ab initio calculations. Keywords: anion recognition; conformation analysis; host–guest systems; NMR

• 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

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

Intraannular photoreactions in pseudo-geminally substituted [2.2]paracyclophanes

• Henning Hopf,
• Vitaly Raev and
• Peter G. Jones

Beilstein J. Org. Chem. 2011, 7, 658–667, doi:10.3762/bjoc.7.78

• -conformation, which has been shown to be present as a conformer in the solid state by X-ray structural analysis does not photocyclize to 8. Moreover, syn,syn-7 is evidently too sterically hindered (by repulsion of the relevant hydrogen atoms as shown in Scheme 3) to be part of the conformational equilibrium