Quarternization of 3-azido-1-propyne oligomers obtained by copper(I)-catalyzed azide–alkyne cycloaddition polymerization

• Shun Nakano,
• Akihito Hashidzume and
• Takahiro Sato

Beilstein J. Org. Chem. 2015, 11, 1037–1042, doi:10.3762/bjoc.11.116

• chain model with d = 0.7 nm and the persistence length (q) = 2 nm, the theoretical RH [45][46] is in agreement with the experimental one (cf. Figure 3c). A more precise conformational analysis of oligoAP quarternized should be studied in future. Conclusion Quarternization of oligoAP was investigated

Preparation of neuroprotective condensed 1,4-benzoxazepines by regio- and diastereoselective domino Knoevenagel–[1,5]-hydride shift cyclization reaction

• László Tóth,
• Yan Fu,
• Hai Yan Zhang,
• Attila Mándi,
• Katalin E. Kövér,
• Tünde-Zita Illyés,
• Attila Kiss-Szikszai,
• Balázs Balogh,
• Tibor Kurtán,
• Sándor Antus and
• Péter Mátyus

Beilstein J. Org. Chem. 2014, 10, 2594–2602, doi:10.3762/bjoc.10.272

• Knoevenagel–[1,5]-hydride shift cyclization reaction of a 4-aryl-2-phenyl-1,4-benzoxazepine derivative obtained from flavanone. The relative configuration of products were determined by the correlation of 3JH,H coupling data with the geometry of major conformers accessed by DFT conformational analysis

• indicated that they were single diastereomers and the determination of the relative configuration was carried out by the correlation of NMR data and DFT conformational analysis of cis- and trans-7a,b (Figure 2 and Figure 3). Although the hydrogens 2-H and 15a-H of cis-7a,b are expected to point toward the

• ,15aS)-7d model compound of trans-7a used for the conformational analysis and ECD calculations. Protective effect of compound 7a on hydrogen peroxide-induced neurotoxicity in SH-SY5Y cells. ##P < 0.01 vs control group, **P< 0.01 vs hydrogen peroxide group. Protective effect of compound 7b on β-amyloid25

Pyrrolidine nucleotide analogs with a tunable conformation

• Lenka Poštová Slavětínská,
• Dominik Rejman and
• Radek Pohl

Beilstein J. Org. Chem. 2014, 10, 1967–1980, doi:10.3762/bjoc.10.205

• of a conformational analysis show that the alkylation/acylation can be effectively used for tuning the pyrrolidine conformation over the whole pseudorotation cycle. Keywords: conformation; NMR; nucleic acids; nucleotide analog; phosphonic acid; pseudorotation; pyrrolidine; Introduction Nucleotides

• -membered ring. Conformational analysis using vicinal proton–proton scalar couplings (3JHH) of ring protons obtained from 1H NMR spectra is a traditional and well-established experimental method. 3JHH encodes information on the exocyclic dihedral angle between coupled protons based on the Karplus

• interconverting conformer in solution, resulting in the observation of averaged experimental 3JHH. Nevertheless, even these averaged 3JHH can be used for conformational analysis by means of the program PSEUROT [10], which minimizes differences between experimental and calculated 3JHH, assuming a two-state

Sacrolide A, a new antimicrobial and cytotoxic oxylipin macrolide from the edible cyanobacterium Aphanothece sacrum

• Naoya Oku,
• Miyako Matsumoto,
• Kohsuke Yonejima,
• Keijiroh Tansei and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2014, 10, 1808–1816, doi:10.3762/bjoc.10.190

• in 1 was determined by a combination of chiral anisotropy analysis and conformational analysis of different ring-opened derivatives. Compound 1 inhibited the growth of some species of Gram-positive bacteria, yeast Saccharomyces cerevisiae and fungus Penicillium chrysogenum, and was also cytotoxic to

Why a diaminopyrrolic tripodal receptor binds mannosides in acetonitrile but not in water?

• Diogo Vila-Viçosa,
• Oscar Francesconi and
• Miguel Machuqueiro

Beilstein J. Org. Chem. 2014, 10, 1513–1523, doi:10.3762/bjoc.10.156

• : conformational analysis; constant-pH MD; mannose; multivalent glycosystems; pH; synthetic receptor; Introduction The recognition of specific carbohydrates is an important step in several biological processes [1]. To better understand these recognition processes, several synthetic receptors have been developed

• constant-pH MD methodologies and expose the strong limitations of classic MM/MD simulations to deal with such systems. Conformational analysis of the receptor As expected, both in ACN and in water at all simulated pH values, the receptor shows a large conformational variability. The radius of gyration (Rg

Human dendritic cell activation induced by a permannosylated dendron containing an antigenic GM₃-lactone mimetic

• Renato Ribeiro-Viana,
• Elena Bonechi,
• Javier Rojo,
• Clara Ballerini,
• Giuseppina Comito,
• Barbara Richichi and
• Cristina Nativi

Beilstein J. Org. Chem. 2014, 10, 1317–1324, doi:10.3762/bjoc.10.133

• conditions the available amount of lactone is below the recognition threshold and therefore scarcely effective as an immunostimulant. Several years ago [31], we reported on the conformational analysis and the synthesis of thioether 3 (Figure 1), a hydrolytically stable mimetic of the GM3-lactone 2

Conformational analysis of 2,2-difluoroethylamine hydrochloride: double gauche effect

• Josué M. Silla,
• Claudimar J. Duarte,
• Rodrigo A. Cormanich,
• Roberto Rittner and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2014, 10, 877–882, doi:10.3762/bjoc.10.84

• with both fluorine atoms) in 2 are the Lewis-type ones. Particularly, electrostatic interactions are operative even in water solution, where they should be significantly attenuated, whereas hyperconjugation and hydrogen bond have secondary importance. Keywords: conformational analysis; 2,2

Use of activated enol ethers in the synthesis of pyrazoles: reactions with hydrazine and a study of pyrazole tautomerism

• Denisa Tarabová,
• Stanislava Šoralová,
• Martin Breza,
• Marek Fronc,
• Wolfgang Holzer and
• Viktor Milata

Beilstein J. Org. Chem. 2014, 10, 752–760, doi:10.3762/bjoc.10.70

• S2–S5) ascribable to solid state effects. The accuracy of the calculated NMR data is insufficient to distinguish between possible conformers of individual tautomers and so we did not performed a full conformational analysis. Conclusion Activated enol ethers 3 derived from trialkyl orthoformate and

Chromatographically separable rotamers of an unhindered amide

• Mario Geffe,
• Lars Andernach,
• Oliver Trapp and
• Till Opatz

Beilstein J. Org. Chem. 2014, 10, 701–706, doi:10.3762/bjoc.10.63

• analysis. Computational studies The rotational barrier was also studied in silico. Therefore, a conformational analysis of 4 was performed using the systematic algorithm to search conformers as implemented in Spartan’10 with the semi-empirical PM6 level of theory [17][18]. All 2111 resulting conformers

Decandrinin, an unprecedented C₉-spiro-fused 7,8-seco-ent-abietane from the Godavari mangrove Ceriops decandra

• Hui Wang,
• Min-Yi Li,
• Félix Zongwe Katele,
• Tirumani Satyanandamurty,
• Jun Wu and
• Gerhard Bringmann

Beilstein J. Org. Chem. 2014, 10, 276–281, doi:10.3762/bjoc.10.23

• calculations. The conformational analysis of 1 by using RI-SCS-MP2/def2-TZVP//B97D/TZVP yielded six relevant conformers within the energetical range of 3 kcal/mol above the global minimum. For each of the six conformers thus identified, TDB2PLYP/def2-TZVP calculations were performed providing single UV and CD

• ; For 1H and 13C NMR spectroscopic data (see Table 1); HRMS (ESI) m/z: [M + H]+ calcd for C20H29O4, 333.2060; found 333.2053. Computational details The B97D/TZVP [28][29] method was used to perform the conformational analysis of 1 with Gaussian 09 [30]. Single-point energy calculations at the RI-SCS-MP2

Stereoselectively fluorinated N-heterocycles: a brief survey

• Xiang-Guo Hu and
• Luke Hunter

Beilstein J. Org. Chem. 2013, 9, 2696–2708, doi:10.3762/bjoc.9.306

• increased ridigity was credited with a dramatic improvement in the enantioselectivity. 3.3 Six-membered rings The conformational analysis of six-membered rings is a cornerstone in physical chemistry. Substituted saturated six-membered compounds usually adopt a chair conformation with substituents preferring

Conformational analysis and intramolecular interactions in monosubstituted phenylboranes and phenylboronic acids

• Josué M. Silla,
• Rodrigo A. Cormanich,
• Roberto Rittner and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2013, 9, 1127–1134, doi:10.3762/bjoc.9.125

• A 1TSJF,H(O) coupling pathway, dictated by a hydrogen bond, in some 2-fluorobenzoic acids has been observed, while such an interaction does not occur in 2-fluorophenol. Thus, this work reports the conformational analysis of 2-fluorophenylboronic acid (1), in order to evaluate a possible

• corresponding conformers appreciably populated, because of steric effects and the loss of πCC→pB resonance. Thus, the results found earlier for 2-fluorophenol about the lack of intramolecular hydrogen bonding are now corroborated. Keywords: conformational analysis; hydrogen bond; interactions with boron

Enantioselective reduction of ketoimines promoted by easily available (S)-proline derivatives

• Martina Bonsignore,
• Maurizio Benaglia,
• Laura Raimondi,
• Manuel Orlandi and
• Giuseppe Celentano

Beilstein J. Org. Chem. 2013, 9, 633–640, doi:10.3762/bjoc.9.71

• , and the two lowest energy transition states (TS) leading to the formation of R and S amine were located. In order to simplify the problem, we adopted a stepwise procedure for the location of the TS structures. First of all, a conformational analysis with Monte Carlo techniques was performed with MMFF

• below. Force field conformational analysis was performed with the Schroedinger suite MacroModel. Ab initio and DFT calculations were performed with Gaussian09 [33]. Frequency calculations allowed for characterization as such of the transition structures and for calculation of ZPE-corrected free energies

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

• that characterizes the α-turn structure is confirmed by 1H NMR conformational studies. To the best of our knowledge, this scaffold represents one of the rare examples of a designed constrained α-turn mimic. Keywords: α-turn; conformational analysis; diketopiperazine; peptidomimetics; tetrahydro-β

• Discussion In order to investigate the presence of a preferred conformation able to mimic an ordered protein secondary structure, a computer-aided conformational analysis was performed on 1a (6S,12aS-configuration, IUPAC atom numbering as in Figure 2) and diastereoisomeric 1b (6R, 12aS). Compounds 1a and 1b

• /EM conformational analysis for peptidomimetics 1a and 1b. The + symbol indicates the presence in the global minimum.

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

• conformational analysis. Inspection of molecular models indicates that the pseudoaxial substituent of the syn isomer should experience more steric congestion on the tropinone bicyclic skeleton with equatorial N-methyl [9], than the same group of the anti configuration. It was interesting to see if one could

Exploring chemical diversity via a modular reaction pairing strategy

• Joanna K. Loh,
• Sun Young Yoon,
• Thiwanka B. Samarakoon,
• Alan Rolfe,
• Patrick Porubsky,
• Benjamin Neuenswander,
• Gerald H. Lushington and
• Paul R. Hanson

Beilstein J. Org. Chem. 2012, 8, 1293–1302, doi:10.3762/bjoc.8.147

• of inertia (PMI) analysis [42] Conformational analysis Quantitative estimate of drug-like (QED) values [43] Cartesian grid-based chemical diversity analysis The grid-based diversity analysis protocol, described previously in the Library Design section, provides a simple measure of the relative

• , some of the compounds are located in the unpopulated region of chemical space, illustrating the novel nature of some of our compounds from the perspective of molecular shape. Conformational analysis While overlay and PMI analysis tend to focus on the shape diversity of libraries as a function of the

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

• edge CH2 groups. In this study erythro- and threo-1,2-difluorocyclododecanes were prepared to explore whether the two vicinal C–F bonds, with different relative configurations, preferably locate at corner/edge or edge/edge locations. Conformational analysis comparing the diastereoisomers was explored

• –F bond endo into the ring, and appear to benefit from C–CHF–C angle widening, which relaxes 1,4-H,H transannular interactions. Keywords: alicyclic chemistry; conformational analysis; cyclododecane; 19F NMR; organo-fluorine chemistry; transannular interactions; Introduction The conformation of

• to conformational analysis by 19F NMR and X-ray structural analyses. A computational study was also carried out to explore the relative energies of the candidate edge/edge and edge/corner conformers. Results and Discussion Synthesis The synthetic route to erythro- (5a) and threo-1,2

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

• bond. Keywords: conformational analysis; 2-fluorobicyclo[2.2.1]heptan-7-ols; hydrogen bond; 1hJF,H(O) coupling constant; quantum-chemical calculations; Introduction Intra- and intermolecular hydrogen bonds (HB) play an important role in determining the molecular arrangements and properties, as well

Partial thioamide scan on the lipopeptaibiotic trichogin GA IV. Effects on folding and bioactivity

• Marta De Zotti,
• Barbara Biondi,
• Cristina Peggion,
• Matteo De Poli,
• Haleh Fathi,
• Simona Oancea,
• Claudio Toniolo and
• Fernando Formaggio

Beilstein J. Org. Chem. 2012, 8, 1161–1171, doi:10.3762/bjoc.8.129

• analogues. Conformational analysis A detailed analysis of the spectroscopic properties and conformational preferences of the three monothionated trichogin GA IV analogues synthesized in this work was performed by using CD, FT-IR absorption, and 2D NMR investigations in different solvents. The far- (250–195

The use of glycoinformatics in glycochemistry

• Thomas Lütteke

Beilstein J. Org. Chem. 2012, 8, 915–929, doi:10.3762/bjoc.8.104

• simulation trajectories [13]. MD software packages contain analysis tools [94][97][123], but these are tailored for analyzing simulations of proteins. Therefore, tools such as CAT (Conformational Analysis Tools) that serve the needs of glycoscientists are specifically developed [13]. Glycoinformatics in

An easily accessible sulfated saccharide mimetic inhibits in vitro human tumor cell adhesion and angiogenesis of vascular endothelial cells

• Grazia Marano,
• Claas Gronewold,
• Martin Frank,
• Anette Merling,
• Christian Kliem,
• Sandra Sauer,
• Manfred Wiessler,
• Eva Frei and
• Reinhard Schwartz-Albiez

Beilstein J. Org. Chem. 2012, 8, 787–803, doi:10.3762/bjoc.8.89

• parallel each performing 10 GA-LS runs, giving rise to 1000 individual GA-LS docking runs in total. For each GA-LS docking run 1,000,000 energy evaluations were performed. The Conformational Analysis Tools (CAT) program was used to merge the output data of the AUTODOCK runs, to perform the analysis of the

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

• that the simple method will allow us to prepare a variety of α-glycolipid antigens other than GGPLs and to prove their biological significance [43]. By the 1H NMR conformational analysis, which was based on our former studies on deuterium-labeled sn-glycerols and sugars, we have proven that GGPL-I and

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

• ) was investigated by integrating measurements of helical twisting power with a conformational analysis by DFT calculations and with the prediction of their twisting ability by the surface-chirality method. The two quasi-enantiomeric derivatives induce oppositely handed cholesteric phases when

• essentially determined by the axial chirality (helicity) of the core of the perylenequinones. Keywords: chirality; conformational analysis; DFT calculations; helical twisting power; nematic liquid crystals; Introduction The phenomenon of chiral induction in nematic mesophases has been known for a long time

• give 1 and 2 a limited, though non-negligible conformational freedom. To understand the relation between molecular structure and chiral induction in liquid crystals, we integrated measurements of helical twisting power (HTP) with a conformational analysis, performed by density functional theory (DFT

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

• found to be dictated mainly by a C=O···H–O intramolecular hydrogen bond, but an unusual C–F···H–O hydrogen-bond and intramolecular C–X···O nonbonding interactions are also present in such compounds. Keywords: conformational analysis; 2'-haloflavonols; intramolecular hydrogen bond; nonbonding

(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

• repeating these calculations at the HF/6-31G* level of theory (Table 4). This method, although simple by modern standards, is suitable for conformational analysis and allowed us to calculate the relatively large systems (below) in a short time. Seven conformations including the lowest four conformations