Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries

• Xiao Xie,
• Michela Zuffo,
• Marie-Paule Teulade-Fichou and
• Anton Granzhan

Beilstein J. Org. Chem. 2019, 15, 1872–1889, doi:10.3762/bjoc.15.183

• light-up data matrix for all dyes (ct DNA and cl RNA were excluded, as well as TBA and c-myb due to their low light-up factors). Color coding highlights the distribution of the dyes sharing similar structural motifs. Dual-dye conformational analysis of an extended panel of 33 DNA oligonucleotides. This

Strong hyperconjugative interactions limit solvent and substituent influence on conformational equilibrium: the case of cis-2-halocyclohexylamines

• Camila B. Francisco,
• Cleverton S. Fernandes,
• Ulisses Z. de Melo,
• Roberto Rittner,
• Gisele F. Gauze and
• Ernani A. Basso

Beilstein J. Org. Chem. 2019, 15, 818–829, doi:10.3762/bjoc.15.79

• interactions along the series. The strongly shifted and non-sensitive conformational equilibrium governed by a strong hyperconjugative interaction in cis-2-halocyclohexylamines shows that the conformational analysis of small molecules can still provide surprising results. Experimental Synthesis trans-2

Influence of per-O-sulfation upon the conformational behaviour of common furanosides

• Alexey G. Gerbst,
• Vadim B. Krylov,
• Dmitry A. Argunov,
• Maksim I. Petruk,
• Arsenii S. Solovev,
• Andrey S. Dmitrenok and
• Nikolay E. Nifantiev

Beilstein J. Org. Chem. 2019, 15, 685–694, doi:10.3762/bjoc.15.63

• of sulfates. Keywords: ab initio calculations; conformational analysis; furanosides; NMR; sulfation; Introduction Changes in the conformations of monosaccharides expectedly accompany their modification with different functional groups. Thus, spatial repulsion of silyl groups results in inversion or

• pyranosides [10][11] and thus the effects of substitution in them are more complex. The conformational effects underlay the striking stereoselectivity in the glycosylation reaction by furanosyl donors [12]. Conformational analysis of furanosides includes both conformation of the furanoside ring and

• , including fragments of a galactomannan from Aspergillus fumigatus [17][18][19], diheteroglycan from Enterococcus faecalis [20], galactan I from Klebsiella pneumoniae [21] and fucoidan from brown seaweed Chordaria flagelliformis [22]. In this communication the conformational analysis of three common per-O

Conformational signature of Ishikawa´s reagent using NMR information from diastereotopic fluorines

• Laize A. F. Andrade,
• Lucas A. Zeoly,
• Rodrigo A. Cormanich and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2019, 15, 506–512, doi:10.3762/bjoc.15.44

• polarity plays a significant role in the condensed phase. Thus, it is appropriate to study the conformations of Ishikawa´s reagent in different media, of low and high polarity. This is a challenging task, since the conformational analysis of flexible acyclic organic compounds using NMR SSCCs is more

Synthesis and fluorescent properties of N(9)-alkylated 2-amino-6-triazolylpurines and 7-deazapurines

• Andrejs Šišuļins,
• Jonas Bucevičius,
• Yu-Ting Tseng,
• Irina Novosjolova,
• Kaspars Traskovskis,
• Ērika Bizdēna,
• Huan-Tsung Chang,
• Sigitas Tumkevičius and
• Māris Turks

Beilstein J. Org. Chem. 2019, 15, 474–489, doi:10.3762/bjoc.15.41

• , steepest descent algorithm) and systematic conformational analysis as implemented in Avogadro 1.1.1 software. The minimum energy conformers found by molecular mechanics were further optimized with the Gaussian 09 program package [57] by the means of DFT using B3LYP exchange–correlation hybrid functional

Synthesis of eunicellane-type bicycles embedding a 1,3-cyclohexadiene moiety

• Alex Frichert,
• Peter G. Jones and
• Thomas Lindel

Beilstein J. Org. Chem. 2018, 14, 2461–2467, doi:10.3762/bjoc.14.222

• conversion to the diastereomer by oxidation and reduction. Conformational analysis of some of the resulting diols obtained under McMurry conditions was complicated by the presence of several conformers of similar energy. The pinacol coupling appears to start at the ketone, as indicated by the selective

• carbinols afforded novel allene systems. Our study may be of help towards the total synthesis of solenopodin or klysimplexin derivatives. Keywords: conformational analysis; low valent titanium; marine natural products; pinacol coupling; ten-membered rings; Introduction Eunicellane-type diterpenoids share

Nucleoside macrocycles formed by intramolecular click reaction: efficient cyclization of pyrimidine nucleosides decorated with 5'-azido residues and 5-octadiynyl side chains

• Jiang Liu,
• Peter Leonard,
• Sebastian L. Müller,
• Constantin Daniliuc and
• Frank Seela

Beilstein J. Org. Chem. 2018, 14, 2404–2410, doi:10.3762/bjoc.14.217

• Information File 402: Experimental procedures, analytical data, NMR spectra, conformational analysis and crystallographic data. Acknowledgements We would like to thank Dr. M. Letzel, Universität Münster, Germany, for the ESI–TOF spectra and Prof. Dr. B. Wünsch, Institut für Pharmazeutische und Medizinische

Recent applications of chiral calixarenes in asymmetric catalysis

• Mustafa Durmaz,
• Erkan Halay and
• Selahattin Bozkurt

Beilstein J. Org. Chem. 2018, 14, 1389–1412, doi:10.3762/bjoc.14.117

• in the presence of NaH or n-BuLi (Figure 5) [46]. Conformational analysis of calixarene-diphosphite ligands revealed that presence of sterically hindered groups led to the formation of the predominantly cone-conformer. In order to check whether calix[4]arene-diphosphite ligands may also serve as

London dispersion as important factor for the stabilization of (Z)-azobenzenes in the presence of hydrogen bonding

• Andreas H. Heindl,
• Raffael C. Wende and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2018, 14, 1238–1243, doi:10.3762/bjoc.14.106

• -butyl methyl ether the hydrogen bonds dominate, the variation in stabilization of the different substituted azobenzenes in dimethyl sulfoxide can be rationalized by London dispersion interactions. These findings were supported by conformational analysis and DFT computations and reveal low-energy London

• parentheses, see Figure S4 in Supporting Information File 1 for graphical representations of the compared conformers). Supporting Information Supporting Information File 338: NMR spectra of azobenzene 5, UV–vis data and detailed procedures, details for conformational analysis and DFT computations

Stereoselective nucleophilic addition reactions to cyclic N-acyliminium ions using the indirect cation pool method: Elucidation of stereoselectivity by spectroscopic conformational analysis and DFT calculations

• Koichi Mitsudo,
• Junya Yamamoto,
• Tomoya Akagi,
• Atsuhiro Yamashita,
• Masahiro Haisa,
• Kazuki Yoshioka,
• Hiroki Mandai,
• Koji Ueoka,
• Christian Hempel,
• Jun-ichi Yoshida and
• Seiji Suga

Beilstein J. Org. Chem. 2018, 14, 1192–1202, doi:10.3762/bjoc.14.100

Conformational preferences of α-fluoroketones may influence their reactivity

• Graham Pattison

Beilstein J. Org. Chem. 2017, 13, 2915–2921, doi:10.3762/bjoc.13.284

• , supported by computation, that this effect is due to reactive conformations in which the C–X bond is orthogonal to the carbonyl group for good orbital overlap being disfavoured in the case of fluoro ketones. Keywords: α-halogenated ketones; conformational analysis; reactivity; stereoelectronic effects

• taking NMR of the reaction mixture without isolation. This again showed the α-fluoroacetone to be slightly less reactive than the α-chloroacetone. A similar conformational analysis of the bond rotation of the O=C–C–X dihedral angle for the chloro and fluoro derivatives was performed (Figure 8). This

• relevant in the case of haloacetones. This conformational analysis is supported by previous work by Abraham and Rittner who used NMR coupling constants and theory to demonstrate that a trans-conformation of fluoroacetone is always most favourable, but that the energy difference to the cis-conformation

The use of 4,4,4-trifluorothreonine to stabilize extended peptide structures and mimic β-strands

• Yaochun Xu,
• Isabelle Correia,
• Tap Ha-Duong,
• Nadjib Kihal,
• Jean-Louis Soulier,
• Julia Kaffy,
• Benoît Crousse,
• Olivier Lequin and
• Sandrine Ongeri

Beilstein J. Org. Chem. 2017, 13, 2842–2853, doi:10.3762/bjoc.13.276

• obtained through the aldol reaction of trifluoroacetaldehyde with the Ni(II) complex of the chiral Schiff base of glycine. The conformational analysis of these pentapeptides was conducted by the combined use of NMR spectroscopy and molecular dynamics simulations. NMR conformational studies showed that the

Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models

• Vladimir Kubyshkin and
• Nediljko Budisa

Beilstein J. Org. Chem. 2017, 13, 2442–2457, doi:10.3762/bjoc.13.241

• partitioning constants were identical within experimental error. Conformational analysis The amide rotational thermodynamic and kinetic measurements were performed by NMR as described in [50][68]. The equilibrium ratio between the rotameric states was obtained from the 1H, 19F and 19F{1H} (inverse-gated

• aqueous phosphate buffer (right, 50 mM buffer, pH 7.0) samples. Recorded at 298 K and 100 μM peptide. Conformational analysis of the peptides by 1H DOSY NMR (D2O, 298 K). The theoretical values were calculated according to Equation 5 assuming deuterium oxide viscosity and 298 K. Hydrolysis of the C

Homologated amino acids with three vicinal fluorines positioned along the backbone: development of a stereoselective synthesis

• Raju Cheerlavancha,
• Ahmed Ahmed,
• Yun Cheuk Leung,
• Aggie Lawer,
• Qing-Quan Liu,
• Marina Cagnes,
• Hee-Chan Jang,
• Xiang-Guo Hu and
• Luke Hunter

Beilstein J. Org. Chem. 2017, 13, 2316–2325, doi:10.3762/bjoc.13.228

• approach that was ultimately successful. We also present here, for the first time, a qualitative NMR J-based conformational analysis of the free amino acids including 6. Results and Discussion Early in our efforts to develop a successful synthesis of 6, we realized that it might be possible to construct

Conformational impact of structural modifications in 2-fluorocyclohexanone

• Francisco A. Martins,
• Josué M. Silla and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2017, 13, 1781–1787, doi:10.3762/bjoc.13.172

• compounds. Spectroscopic parameters (NMR chemical shifts and coupling constants), which can be useful to determine the stereochemistry and the interactions operating in the series of 2-fluorocyclohexanone derivatives, were also calculated. Keywords: classical effects; conformational analysis; 2

Cycloheximide congeners produced by Streptomyces sp. SC0581 and photoinduced interconversion between (E)- and (Z)-2,3-dehydroanhydrocycloheximides

• Li Yang,
• Ping Wu,
• Jinghua Xue,
• Huitong Tan,
• Zheng Zhang and
• Xiaoyi Wei

Beilstein J. Org. Chem. 2017, 13, 1039–1049, doi:10.3762/bjoc.13.103

• , anhydroisoheximide (4), cycloheximide (5), and isocycloheximide (6), were obtained from the cultures of Streptomyces sp. SC0581. Their structures were elucidated by extensive spectroscopic analysis in combination with theoretical conformational analysis and ECD computations. The photoinduced interconversion between

• important to the activities of cycloheximide congeners. Keywords: antifungal activity; cycloheximide derivatives; E/Z photoisomerization; Streptomyces sp; theoretical conformational analysis; Introduction The glutarimide-containing antibiotics represent a fascinating class of natural products that exhibit

• , anhydroisoheximide (4) [6], together with cycloheximide (5) and isocycloheximide (6) [10]. Their structures were elucidated by spectroscopic analysis, theoretical conformational analysis, and ECD/TDDFT calculations. The photoinduced interconversion between 2 and 3 was observed and verified, and the possible reaction

Conformational study of L-methionine and L-cysteine derivatives through quantum chemical calculations and ³J_HH coupling constant analyses

• Weslley G. D. P. Silva,
• Carolyne B. Braga and
• Roberto Rittner

Beilstein J. Org. Chem. 2017, 13, 925–937, doi:10.3762/bjoc.13.94

• conformational analysis of esterified and N-acetylated derivatives of L-methionine and L-cysteine using a combination of 1H NMR and electronic structure calculations is reported. The geometries and energies of the most stable conformers in isolated phase and taking into account the implicit solvent effects

• atoms in molecules (QTAIM) and noncovalent interactions (NCI) methodologies, the conformational preferences for the compounds are not dictated by intramolecular hydrogen bonding, but by a joint contribution of hyperconjugative and steric effects. Keywords: amino acid derivatives; conformational

• analysis; cysteine; methionine; NMR spectroscopy; quantum chemical calculations; Introduction Amino acids constitute the building blocks of proteins and peptides, which play an important role in numerous biological processes [1][2]. However, their studies in both isolated and condensed phases have been

Synthesis and optical properties of new 5'-aryl-substituted 2,5-bis(3-decyl-2,2'-bithiophen-5-yl)-1,3,4-oxadiazoles

• Anastasia S. Kostyuchenko,
• Tatyana Yu. Zheleznova,
• Anton J. Stasyuk,
• Aleksandra Kurowska,
• Wojciech Domagala,
• Adam Pron and
• Alexander S. Fisyuk

Beilstein J. Org. Chem. 2017, 13, 313–322, doi:10.3762/bjoc.13.34

• applied. Figure 3 shows a general representation of the compounds studied in this work. At the initial stage, a systematic conformational analysis of the series of substituted 1,3,4-oxadiazoles was conducted with the goal to determine the lowest-energy conformer(s). It has been found that 15c and 15d can

Varioloid A, a new indolyl-6,10b-dihydro-5aH-[1]benzofuro[2,3-b]indole derivative from the marine alga-derived endophytic fungus Paecilomyces variotii EN-291

• Peng Zhang,
• Xiao-Ming Li,
• Xin-Xin Mao,
• Attila Mándi,
• Tibor Kurtán and
• Bin-Gui Wang

Beilstein J. Org. Chem. 2016, 12, 2012–2018, doi:10.3762/bjoc.12.188

• showed that there is no axial chirality in 1, and equilibrating conformers with M and P helicity are present in solution as obtained in the conformational analysis. The Boltzmann-weighted ECD spectra calculated for both the gas-phase and the solvent model conformers of (2R,3R)-1 at B3LYP/TZVP, BH&HLYP

• condensed heterocyclic system in compounds 1 and 2 is quite rare among natural products. The absolute configuration of 1 was confirmed to be (2S,3S) by conformational analysis and TDDFT-ECD calculations. In the cytotoxicity assay, both compounds exhibited remarkable cytotoxicity. Compound 1 showed potent

Synthesis of the C8’-epimeric thymine pyranosyl amino acid core of amipurimycin

• Pramod R. Markad,
• Navanath Kumbhar and
• Dilip D. Dhavale

Beilstein J. Org. Chem. 2016, 12, 1765–1771, doi:10.3762/bjoc.12.165

• this regard are in progress. Antifungal antibiotic amipurimycin (1). Conformational analysis of 13 and 14. Geometrically optimized conformation of 12 and 13 respectively by DFT study. Retrosynthesis of 2. Synthesis of 1,3-anhydrosugar 12 and 13. Formation of 2,7-dioxabicyclo[3.2.1]octane 12/13

One-pot synthesis of 4′-alkyl-4-cyanobiaryls on the basis of the terephthalonitrile dianion and neutral aromatic nitrile cross-coupling

• Roman Yu. Peshkov,
• Elena V. Panteleeva,
• Wang Chunyan,
• Evgeny V. Tretyakov and
• Vitalij D. Shteingarts

Beilstein J. Org. Chem. 2016, 12, 1577–1584, doi:10.3762/bjoc.12.153

• being used as components of liquid crystal mixtures [3][4][5][6][7][8], lubricants [9], media for conformational analysis using NMR [10][11][12] and EPR [13] techniques, and nanoparticles-doped liquid crystals [14]. The classic multistage approaches to these compounds, including successive biphenyl

Is conformation a fundamental descriptor in QSAR? A case for halogenated anesthetics

• Maria C. Guimarães,
• Mariene H. Duarte,
• Josué M. Silla and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2016, 12, 760–768, doi:10.3762/bjoc.12.76

• can cause misinterpretation of the QSAR model. The present computational work reports the conformational analysis of the volatile anesthetic isoflurane (2-chloro-2-(difluoromethoxy)-1,1,1-trifluoroethane) in the gas phase and also in polar and nonpolar implicit and explicit solvents to show that

• suggesting that these 2D MD´s can be advantageous over some three-dimensional descriptors. Keywords: conformational analysis; isoflurane; QSAR; theoretical calculations; volatile anesthetics; Introduction Quantitative structure–activity relationship (QSAR) studies try to find a correlation between chemical

• ]. Results and Discussion Conformational analysis 2-Chloro-2-(difluoromethoxy)-1,1,1-trifluoroethane (isoflurane) undergoes rotational isomerization around two dihedral angles (Cl–C–O–C and C–O–C–H) and, considering three limit orientations for each of them (gauche, gauche' and anti), nine conformations are

Coupling of α,α-difluoro-substituted organozinc reagents with 1-bromoalkynes

• Artem A. Zemtsov,
• Alexander D. Volodin,
• Vitalij V. Levin,
• Marina I. Struchkova and
• Alexander D. Dilman

Beilstein J. Org. Chem. 2015, 11, 2145–2149, doi:10.3762/bjoc.11.231

• , unique stereoelectronic properties of the CF2-unit may be exploited in conformational analysis [3][4][5], carbohydrate and peptide research [6][7], and reaction engineering [8][9]. Typically, the difluoromethylene fragment is created by deoxyfluorination, which requires harsh or hazardous conditions [10

Investigation of the role of stereoelectronic effects in the conformation of piperidones by NMR spectroscopy and X-ray diffraction

• Cesar Garcias-Morales,
• David Ortegón-Reyna and
• Armando Ariza-Castolo

Beilstein J. Org. Chem. 2015, 11, 1973–1984, doi:10.3762/bjoc.11.213

• of aldehyde to form a second aldimine. Finally, 6-endo-enol-endo intramolecular cyclization leads to piperidone formation (Scheme 2) [58][59]. Structural and conformational analysis of piperidones 1–8 by NMR and X-ray diffraction Solution characterization of 1–8 was performed by 1H and 13C NMR, and

Structure and conformational analysis of spiroketals from 6-O-methyl-9(E)-hydroxyiminoerythronolide A

• Ana Čikoš,
• Irena Ćaleta,
• Dinko Žiher,
• Mark B. Vine,
• Ivaylo J. Elenkov,
• Marko Dukši,
• Dubravka Gembarovski,
• Marina Ilijaš,
• Snježana Dragojević,
• Ivica Malnar and
• Sulejman Alihodžić

Beilstein J. Org. Chem. 2015, 11, 1447–1457, doi:10.3762/bjoc.11.157

• a 400 ms mixing time. NMR analysis of compound 2 was performed in both DMSO-d6 and CDCl3. Initial full assignment and conformational analysis of compound 3 was performed at the point of maximum concentration of compound 3. The final kinetics reaction mixture was evaporated to dryness and re