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

• pentapeptide salts 1b–4b were obtained in quantitative yield. Conformational studies. The conformational properties of the eight pentapeptides (1a–4a and 1b–4b) were examined by NMR analyses in a protic solvent, which is more challenging than in aprotic organic solvents for maintaining intramolecular hydrogen

• bond network. Methanol was used because of the limited solubility of these compounds in aqueous solutions. The 1H and 13C chemical shifts of these pentapeptides were assigned using 1D 1H, 2D 1H,1H-TOCSY, 2D 1H,1H-ROESY, 2D 1H,13C-HSQC, and 2D 1H,13C-HMBC spectra. The 1H and 13C chemical shift

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• /C17/C18/O26 atoms and non-hydrogen atoms of the pyrenyl group are inclined by an angle of 17.26(5)°. The carbonyl oxygen atom O26 is involved in the intramolecular hydrogen bond with the hydrogen atom H3 of the pyrenyl group. The C3–H3···O26 hydrogen bond length is 2.879(2) Å. In the solid state, each

Dialkyl dicyanofumarates and dicyanomaleates as versatile building blocks for synthetic organic chemistry and mechanistic studies

• Grzegorz Mlostoń and
• Heinz Heimgartner

Beilstein J. Org. Chem. 2017, 13, 2235–2251, doi:10.3762/bjoc.13.221

• yields. The X-ray analysis showed that products 53 obtained with primary amines are Z-configured whereas those derived from secondary amines, 54, display E-configuration [58] (Scheme 18). The observed different configurations demonstrate the importance of the intramolecular hydrogen-bond between the NH

Complexation of molecular clips containing fragments of diphenylglycoluril and benzocrown ethers with paraquat and its derivatives

• Leonid S. Kikot',
• Catherine Yu. Kulygina,
• Alexander Yu. Lyapunov,
• Svetlana V. Shishkina,
• Roman I. Zubatyuk,
• Tatiana Yu. Bogaschenko and
• Tatiana I. Kirichenko

Beilstein J. Org. Chem. 2017, 13, 2056–2067, doi:10.3762/bjoc.13.203

• , the intramolecular hydrogen bonds with participation of the carbonyl oxygen atom which are typical for complexes 2@9 and 3@9 are not formed. In complex 2@10 one hydroxy group forms an intramolecular hydrogen bond with a polyether oxygen atom of the clip (О–H···O, O···O, О–H···O, 2.29, 2.99 Å, 141

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

• as Y, which exhibit intramolecular hydrogen bond with the equatorial fluorine) show axial prevalence. On the other hand, the equatorial conformer is preferred when X = S and NHeq (except for Y = NHE). While the axial preference for compounds with X = NHax can be determined by an electrostatic

• , dipolar relaxation F···HaxN (since an intramolecular hydrogen bond has not been clearly demonstrated in 3-fluoropiperidine [7][8][9][10][11][12][13]), such behavior for compounds with X = CH2 seems to be dependent on the C=Y bond, since X = CH2 is not a good proton donor. In this case, the axial

• hydrogen bond F···HN (e.g., dF···HN = 2.21 Å and F···H–N angle = 110.0°, when X/Y = CH2/NHZ), despite similar interactions hardly ever appear in organofluorine compounds when forming 5-membered rings [25][26]. In addition, it is also quite intuitive that fluorine tends to occupy the axial orientation in

Switchable highly regioselective synthesis of 3,4-dihydroquinoxalin-2(1H)ones from o-phenylenediamines and aroylpyruvates

• Juraj Dobiaš,
• Marek Ondruš,
• Gabriela Addová and
• Andrej Boháč

Beilstein J. Org. Chem. 2017, 13, 1350–1360, doi:10.3762/bjoc.13.132

• of the studied derivatives [4][5]. In this case, their tautomeric equilibrium is shifted to enamines 3 that have been stabilized by an intramolecular hydrogen bond (Scheme 1). A new pseudo-ring is formed via the hydrogen bond in 3, which further spreads the planarity of the 3,4-dihydroquinoxalin-2(1H

• crystallisation from DMSO, pure 16d (SYN) was isolated. We elucidated its structure in similar manner as for the 17d (ANTI) isomer (Figure 2) and confirmed that the 1H NMR (DMSO-d6) higher shifted signal for the H-N(4) group is the one that forms a intramolecular hydrogen bond with the carbonyl group from a side

• -dihydroquinoxaline-2(1H)-ones. Their ANTI (17) or SYN (16) structures were assigned by complex 2D NMR techniques (HSQC, NOESY and HMBC) or by a proposed simplified method (NOE interaction between higher 1H NMR (DMSO-d6) shifted H-N(4), bonded by intramolecular hydrogen bond, and H-C(5) or interaction of lower

Synthesis of tetrasubstituted pyrazoles containing pyridinyl substituents

• Josef Jansa,
• Ramona Schmidt,
• Ashenafi Damtew Mamuye,
• Laura Castoldi,
• Alexander Roller,
• Vittorio Pace and
• Wolfgang Holzer

Beilstein J. Org. Chem. 2017, 13, 895–902, doi:10.3762/bjoc.13.90

• 2a,b, 3a,b and 4a,b) strongly hints to the involvement of the former into an intramolecular hydrogen bond as indicated in Scheme 3. Cross-coupling reactions Initial attempts to react 4-bromopyrazole 5 – obtained from reaction of 2a with N-bromosuccinimide – with phenylboronic acid (or 3

Spectral and DFT studies of anion bound organic receptors: Time dependent studies and logic gate applications

• Srikala Pangannaya,
• Neethu Padinchare Purayil,
• Shweta Dabhi,
• Venu Mankad,
• Prafulla K. Jha,
• Satyam Shinde and
• Darshak R. Trivedi

Beilstein J. Org. Chem. 2017, 13, 222–238, doi:10.3762/bjoc.13.25

• gain insight into the binding mechanism, 1H NMR titration studies have been performed with the incremental addition of TBAOAc to a DMSO-d6 solution of receptor R1 and R2. The unbound receptor exhibited a OH proton signal at ~14 ppm due to the presence of an intramolecular hydrogen bond interaction with

The aminoindanol core as a key scaffold in bifunctional organocatalysts

• Isaac G. Sonsona,
• Eugenia Marqués-López and
• Raquel P. Herrera

Beilstein J. Org. Chem. 2016, 12, 505–523, doi:10.3762/bjoc.12.50

• catalyst, in its Z form, which is stabilized due to an intramolecular hydrogen bond (Scheme 14). In 2012, Dong and co-workers studied the catalytic activity of several β-amino alcohol-based squaramide organocatalysts involved in the Michael addition of acetylacetone (36a) to β-nitrostyrene (3a) in

Friedel–Crafts-type reaction of pyrene with diethyl 1-(isothiocyanato)alkylphosphonates. Efficient synthesis of highly fluorescent diethyl 1-(pyrene-1-carboxamido)alkylphosphonates and 1-(pyrene-1-carboxamido)methylphosphonic acid

• Anna Wrona-Piotrowicz,
• Janusz Zakrzewski,
• Anna Gajda,
• Tadeusz Gajda,
• Anna Makal,
• Arnaud Brosseau and
• Rémi Métivier

Beilstein J. Org. Chem. 2015, 11, 2451–2458, doi:10.3762/bjoc.11.266

• approximately two-fold increase in solution fluorescence quantum yield in comparison with that of a model N-alkyl pyrene-1-carboxamide. This effect was tentatively explained by stiffening of the amidophosphonate lateral chain which was caused by the interaction (intramolecular hydrogen bond) of phosphonate and

• of an intramolecular hydrogen bond between the N–H and P=O groups (Figure 4), which also leads to stiffening of the lateral chain and to blocking the non-radiative deactivation channel. The presence of such a bond was verified via variable concentration 1H NMR spectroscopy [33], which showed only

• emission (b) spectra of 3a in various solvents. Fluorescence decay curves for 3a and 5 in chloroform and for 4 in 0.01 M PBS (pH 7.35). λexcit = 360 nm; λem = 385, 390 and 383 nm, respectively. Intramolecular hydrogen bond in 3a–d. Normalized electronic absorption (violet) and emission (pink) spectrum of

2-Hetaryl-1,3-tropolones based on five-membered nitrogen heterocycles: synthesis, structure and properties

• Yury A. Sayapin,
• Inna O. Tupaeva,
• Alexandra A. Kolodina,
• Eugeny A. Gusakov,
• Vitaly N. Komissarov,
• Igor V. Dorogan,
• Nadezhda I. Makarova,
• Anatoly V. Metelitsa,
• Valery V. Tkachev,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2015, 11, 2179–2188, doi:10.3762/bjoc.11.236

• diffraction. 2-(2-Benzoxa(thia)zolyl)-6-alkoxycarbonylphenols display intense green fluorescence with anomalous Stokes shifts caused by the excited state intramolecular proton transfer (ESIPT) effects. Keywords: β-tropolones; fluorescence; intramolecular hydrogen bond; tautomerism; X-ray analysis

• )–С(2)–С(3) is equal to 1.5°. The intramolecular hydrogen bond in the cycle N(1)–С(8)–С(2)–С(3)–О(2)–Н(2) is characterized by the distances N(1)···О(2) = 2.599(4), N(1)···Н(2) = 1.830(6) Å and the angle N(1)–H(2)–O(2) of 150.4(9)°. The proton signals of the hydroxy groups of 11 (R1 = H) and 11 (R1

Conformational equilibrium in supramolecular chemistry: Dibutyltriuret case

• Karina Mroczyńska,
• Małgorzata Kaczorowska,
• Erkki Kolehmainen,
• Ireneusz Grubecki,
• Marek Pietrzak and
• Borys Ośmiałowski

Beilstein J. Org. Chem. 2015, 11, 2105–2116, doi:10.3762/bjoc.11.227

• polymerization needs properly prearranged monomers with intermolecular hydrogen bonding patterns fitting between molecules. In this sense the conformational freedom is a main limiting factor in molecular design. On the other hand in forms stabilized by an intramolecular hydrogen bond it is possible to break an

• to exist: a) breakage of the intramolecular hydrogen bond(s) and b) association of two (or more) molecules of 1a that are much less rigid structures than other ones locked by intramolecular HB. The probability of existence of form 1a is low at lowered temperatures. The signal broadening at room

• intramolecular hydrogen bond we opt for argument "a". Figure 9 shows the changes in the spectra upon cooling (top spectrum represents +20 °C, spectra were recorded in 5° steps; the last spectrum at bottom represents a temperature of −70 °C). The coalescence temperature for complex 1∙∙∙10 is −15 °C. At

An intramolecular C–N cross-coupling of β-enaminones: a simple and efficient way to precursors of some alkaloids of Galipea officinalis

• Hana Doušová,
• Radim Horák,
• Zdeňka Růžičková and
• Petr Šimůnek

Beilstein J. Org. Chem. 2015, 11, 884–892, doi:10.3762/bjoc.11.99

• ) indicates the presence of an intramolecular hydrogen bond N–H···O. The enaminones 3 therefore possess Z configuration on the C=C bond. The intramolecular C–N cross-coupling β-Enaminones and related polarized ethylenes (generally enamines substituted by EWG on β-carbon atom) belong among the rather neglected

• compounds 1 (δ > 12), it can be assumed that all of these compounds have Z configuration on the C=C double bond (increased chemical shifts due to the presence of an intramolecular hydrogen bond C=O···H–N). This assumption was confirmed by means of X-ray characterization of the compound 1a (Figure 4

Fluoride-driven ‘turn on’ ESPT in the binding with a novel benzimidazole-based sensor

• Kai Liu,
• Xiaojun Zhao,
• Qingxiang Liu,
• Jianzhong Huo,
• Bolin Zhu and
• Shihua Diao

Beilstein J. Org. Chem. 2015, 11, 563–567, doi:10.3762/bjoc.11.61

• studies, which were conducted in DMSO-d6. The characteristic peak of BIP at 12.85 ppm suggested the formation of an intramolecular hydrogen bond in BIP itself between the imine nitrogen and the phenolic OH proton [32][33][34], that progressively disappeared with the successive addition of F− (see Figure

• ][33][34], suggested the formation of the geometrically restricted six-membered intramolecular hydrogen bond ring in the BIP at transition state [32][33][34]. As displayed in Figure 3, with gradual addition of F− to the CH3CN solution of BIP, the fluorescence intensity at 411 nm increased slowly. This

The preparation of new functionalized [2.2]paracyclophane derivatives with N-containing functional groups

• Henning Hopf,
• Swaminathan Vijay Narayanan and
• Peter G. Jones

Beilstein J. Org. Chem. 2015, 11, 437–445, doi:10.3762/bjoc.11.50

• ): The molecule of compound 18 in the crystal; ellipsoids represent 50% probability levels. The intramolecular hydrogen bond is indicated by a dashed line. (b, below): Packing diagram of 18 viewed parallel to the c axis in the region z ≈ 0. Intermolecular hydrogen bonds (one classical, one "weak") are

Molecular cleft or tweezer compounds derived from trioxabicyclo[3.3.1]nonadiene diisocyanate and diacid dichloride

• Gert Kollenz,
• Ralf Smounig,
• Ferdinand Belaj,
• David Kvaskoff and
• Curt Wentrup

Beilstein J. Org. Chem. 2015, 11, 1–8, doi:10.3762/bjoc.11.1

• with arbitrary radii; the other H atoms as well as the disordered atoms with site occupation factors less than 0.5 were omitted for the sake of clarity. The intramolecular hydrogen bond is indicated by a dashed line (H(N32)–O40 = 1.970 Å). Stereoscopic ORTEP plot of molecule B of 4 with atomic

• numbering scheme. The ellipsoids are drawn at the 50% probability level. The H atoms bonded to N are drawn with arbitrary radii; the other H atoms as well as the disordered atoms with site occupation factors less than 0.5 were omitted for reasons of clarity. The intramolecular hydrogen bond is indicated by

Synthesis and immunological evaluation of protein conjugates of Neisseria meningitidis X capsular polysaccharide fragments

• Laura Morelli,
• Damiano Cancogni,
• Marta Tontini,
• Alberto Nilo,
• Sara Filippini,
• Paolo Costantino,
• Maria Rosaria Romano,
• Francesco Berti,
• Roberto Adamo and
• Luigi Lay

Beilstein J. Org. Chem. 2014, 10, 2367–2376, doi:10.3762/bjoc.10.247

• , when the hemiacetal 6 was treated with salicylchlorophosphite in pyridine at room temperature the α-H-phosphonate 7 was obtained as a single anomer in only 2 h in 62% yield. We reasoned that the occurrence of an intramolecular hydrogen bond involving the acetamido group could be the main responsible

De novo macrolide–glycolipid macrolactone hybrids: Synthesis, structure and antibiotic activity of carbohydrate-fused macrocycles

• Richard T. Desmond,
• Anniefer N. Magpusao,
• Chris Lorenc,
• Jeremy B. Alverson,
• Nigel Priestley and
• Mark W. Peczuh

Beilstein J. Org. Chem. 2014, 10, 2215–2221, doi:10.3762/bjoc.10.229

• (defined as the torsional angle about the C5’–C6’ bond) is in the gt conformation for each structure [27]. An intramolecular hydrogen bond between the C4’ hydroxy group and the C3’ oxygen is also apparent in 5 whereas in 6 the same hydroxy group is hydrogen-bonded to a bound water molecule. Observations

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

• 10.3762/bjoc.10.84 Abstract The gauche effect in fluorinated alkylammonium salts is well known and attributed either to an intramolecular hydrogen bond or to an electrostatic attraction between the positively charged nitrogen and the vicinal electronegative fluorine atom. This work reports the effect of

• participation of intramolecular hydrogen bond and hyperconjugation. These findings can be useful to predict the structure and stereochemistry of multifluorinated organic compounds with, e.g., pharmaceutical and/or agrochemical interest. Experimental 2,2-Difluoroethylamine hydrochloride (2) was purchased from

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

• 15.9(3)°, 11.1(3)°, 0.6(3)° for the first three ester groups (C6–C7–C8–O5, C6–C7–C12–O7, C3–C2–C10–O3) and 152.28(17)° for the last one (O1–C1–C2–C3) (Supporting Information File 1, Table S5). N5–H5A forms an intramolecular hydrogen bond with O3 and an intermolecular hydrogen bond with O4. N6–H6A forms

• an intramolecular hydrogen bond with O5, while both also form an intermolecular hydrogen bond with O5 from the next molecule as shown in Table S2. These two hydrogen bonds are in a rhomboid arrangement with angles H6A–O5–H6A 86.10(5)° and O5–H6A–O5 93.90(5)°. Selected interatomic distances, bond and

• into a doublet (3J = 11.0 Hz) due to the coupling with the alkene-H (δ 8.05 ppm). The ester moiety involved in the intramolecular hydrogen bond exhibits a marked downfield shift for C=O (δ 168.5 ppm) in comparison to the other ester carbonyl C-atom (δ 164.7 ppm), which is typical for such a situation

Conformation of dehydropentapeptides containing four achiral amino acid residues – controlling the role of L-valine

• Michał Jewgiński,
• Joanna Krzciuk-Gula,
• Maciej Makowski,
• Rafał Latajka and
• Paweł Kafarski

Beilstein J. Org. Chem. 2014, 10, 660–666, doi:10.3762/bjoc.10.58

• that it is involved in an intramolecular hydrogen bond. In the case of peptide 3, the temperature factor of the amide proton of ΔAla(2) is slightly higher than the threshold indicating the presence of hydrogen bonding. Such a value could suggest that the amide proton of ΔAla(2) is at least partially

New hydrogen-bonding organocatalysts: Chiral cyclophosphazanes and phosphorus amides as catalysts for asymmetric Michael additions

• Helge Klare,
• Jörg M. Neudörfl and
• Bernd Goldfuss

Beilstein J. Org. Chem. 2014, 10, 224–236, doi:10.3762/bjoc.10.18

• were obtained from catalysts 6 and 7a. Both catalysts form dimers with short intermolecular hydrogen bonds between P1O1–H3 and P2O2–H2 (1.843/1.810 Å and 2.148/2.103 Å respectively, Figure 3 and Figure 4). In each case the second acidic NH proton H1 forms an intramolecular hydrogen bond to quinuclidin

• nitrogen N1, which is significantly shorter in 7a (2.194/2.110 Å respectively). The intramolecular hydrogen bond is probably also the cause for the occurrence of conformational isomers when inverting the configuration at C9. While catalyst (S)-4 solely exists as one conformer on the NMR timescale, its

• , which was confirmed by DOSY and temperature-dependent NMR (Supporting Information File 1). The cause is probably the hindered rotation by the intramolecular hydrogen bond N1–H1. Synthesis of chiral PV-cyclodiphosphazane amides In order to synthesize chiral cyclodiphosphazanes 14a/14b, PCl5 was reacted

New developments in gold-catalyzed manipulation of inactivated alkenes

• Michel Chiarucci and
• Marco Bandini

Beilstein J. Org. Chem. 2013, 9, 2586–2614, doi:10.3762/bjoc.9.294

• the key role of intramolecular hydrogen bond (H-bond) interactions for both reactivity and stereoselectivity [65]. Theoretical calculations and experimental evidences ruled out the SN1 reaction mechanism via allylic carbocation. Experiments with stereodefined hydroxy allylic alcohols revealed that the

Synthesis and characterization of novel bioactive 1,2,4-oxadiazole natural product analogs bearing the N-phenylmaleimide and N-phenylsuccinimide moieties

• Catalin V. Maftei,
• Elena Fodor,
• Peter G. Jones,
• M. Heiko Franz,
• Gerhard Kelter,
• Heiner Fiebig and
• Ion Neda

Beilstein J. Org. Chem. 2013, 9, 2202–2215, doi:10.3762/bjoc.9.259

• compound 6 was also confirmed by X-ray structure analysis (Figure 10 and Figure 11). In compound 6 the interplanar angle is 11°; the intramolecular hydrogen bond is almost symmetrical (O4–H04 1.03(3), H04···O2 1.47(3)) Å. The molecules are linked to form layers perpendicular to the hexagonal c axis by one

A simple, enaminone-based approach to some bicyclic pyridazinium tetrafluoroborates

• František Josefík,
• Markéta Svobodová,
• Valerio Bertolasi and
• Petr Šimůnek

Beilstein J. Org. Chem. 2013, 9, 1463–1471, doi:10.3762/bjoc.9.166

•  1 (Table S1). A selection of bond distances and angles and the intramolecular hydrogen bond parameters are also reported in Supporting Information File 1 (Table S2 and Table S3). Conclusion We have developed an improved simple methodology for the construction of bicyclic pyridazinium