Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP)

• Małgorzata Urbańczyk,
• Michał Jewgiński,
• Joanna Krzciuk-Gula,
• Jerzy Góra,
• Rafał Latajka and
• Norbert Sewald

Beilstein J. Org. Chem. 2019, 15, 1581–1591, doi:10.3762/bjoc.15.162

• conformation of the molecule as well an on the stereochemistry of amino acid residues. The desired monoglycosylated analogues with acetylated amino termini and the carboxy termini in form of N-methylamide have been synthesized. Conformational nuclear magnetic resonance (NMR) studies of the designed analogues

• antifreeze activity, as well as to clarify the influence of hydrogen bonds on the preferred conformation of the molecule. Model AFGP analogues were investigated by NMR in order to elucidate the stereochemical influence of the amino acid configuration on the three-dimensional structure of the glycopeptides. A

• (see Table 1) suggest that the conformation of each of the investigated pentapeptides is stabilized by one hydrogen bond, created by the amide proton of Ala4. In the case of peptide 4 we could observe the strongest hydrogen bond (Table 1). Previous studies pointed out the role of specific hydrogen

An azobenzene container showing a definite folding – synthesis and structural investigation

• Abdulselam Adam,
• Saber Mehrparvar and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2019, 15, 1534–1544, doi:10.3762/bjoc.15.156

• advantage of the use of azobenzene as switching unit is the fact that it is possible to control the conformation of the cis or the trans-isomers by chiral bridges [43][44][45][46][47][48]. Up to now two artificial Lissoclinum cyclopeptides, which feature an azobenzene moiety to change the distance between

• is dominated by only one transition (n→π*). Accordingly, the conformation (M or P) of the cis-azobenzene moiety can directly be identified from the sign of the Cotton effect at 450 nm. Previous studies have demonstrated that the cis-(M) isomer shows a positive and the cis-(P) isomer has a negative

• Cotton effect in this region [43][49]. If this is taken into account, it becomes obvious that the cis,cis-isomer adopts the M,M conformation. This is in line with the DFT calculations finding only the cis,cis-(M,M) isomer as minimum on the energy potential surface. The spectrum of cis,trans-10 allows the

Diazocine-functionalized TATA platforms

• Roland Löw,
• Talina Rusch,
• Fynn Röhricht,
• Olaf Magnussen and
• Rainer Herges

Beilstein J. Org. Chem. 2019, 15, 1485–1490, doi:10.3762/bjoc.15.150

• , the cis-configuration (boat conformation) is more stable than the trans-isomer (twist conformation). Upon irradiation with ≈400 nm the cis-form switches to the trans-isomer, and irradiation with ≈500 nm or heating leads back to the cis-form [22]. Hence, the diazocines are quasi reversed azobenzenes

• for both compounds as the thermodynamically most stable isomers. For the corresponding trans-configuration two different conformations were found: the twist and the chair structures. The twist conformation is about 2.5 kcal mol−1 more stable than the chair conformation. Our calculations predict

• energies Erel (M06-2X/def2-TZVP) of the twist and chair conformation of the trans-configuration of para-ethynyl-substituted diazocine 1b (para-diazocine), and meta-diazocine 2b, relative to the boat conformation of the cis-isomers 1a and 2a. ΔH≠ are the calculated reaction barriers (trans-twist→cis- boat

Cyclobutane dication, (CH₂)₄²⁺: a model for a two-electron four-center (2e-4c) Woodward–Hoffmann frozen transition state

• G. K. Surya Prakash and
• Golam Rasul

Beilstein J. Org. Chem. 2019, 15, 1475–1479, doi:10.3762/bjoc.15.148

• -PVTZ levels, the C2 symmetric form 1 (Figure 1) was found to be a minimum for (CH2)42+. This is confirmed by frequency calculations at the corresponding levels. The ring of the structure 1 embraces a puckered conformation with a puckering angle (the angle between the two three-membered rings) of 136

Synthesis and biological evaluation of truncated derivatives of abyssomicin C as antibacterial agents

• Leticia Monjas,
• Peter Fodran,
• Johanna Kollback,
• Carlo Cassani,
• Thomas Olsson,
• Maja Genheden,
• D. G. Joakim Larsson and
• Carl-Johan Wallentin

Beilstein J. Org. Chem. 2019, 15, 1468–1474, doi:10.3762/bjoc.15.147

• resulting protein conformation was allowed to relax to ensure that the found conformation was an energy minimum. This protein structure was then used for docking of ligands using Glide [22][23][24]. Glide XP docking positioned both AbC and the analog atrop-O-benzyl-desmethyl-abyssomicin C with low energy

2,3-Dibutoxynaphthalene-based tetralactam macrocycles for recognizing precious metal chloride complexes

• Li-Li Wang,
• Yi-Kuan Tu,
• Huan Yao and
• Wei Jiang

Beilstein J. Org. Chem. 2019, 15, 1460–1467, doi:10.3762/bjoc.15.146

• orientations of the two 2,3-dibutoxynaphthalene moieties; but the same number of peaks in NMR spectra should be observed. Nevertheless, only one set of signals are observed, suggesting that either only one conformation is predominant in solution or the conformational interconversion is fast at the NMR

• butyl methylene group next to the oxygen atoms. A single crystal (Figure 2) of 1, which was suitable for X-ray crystallography, was obtained by slow evaporation of its solution in CH3CN. The crystal structure clearly shows that 1 adopts a flattened chair conformation with the two naphthalenes in

• of two conformations of 1, which is conformationally adaptive to the guests. That is, the guest can select the better conformation to maximize the binding affinities, as oxatub[4]arene and zorb[4]arene do [30][32]. In contrast, the addition of these precious metal chloride complexes does not induce

Anomeric sugar boronic acid analogues as potential agents for boron neutron capture therapy

• Daniela Imperio,
• Erika Del Grosso,
• Silvia Fallarini,
• Grazia Lombardi and
• Luigi Panza

Beilstein J. Org. Chem. 2019, 15, 1355–1359, doi:10.3762/bjoc.15.135

• expected for a 3-deoxy derivative. Moreover, compound 11 also proved to be stable towards oxidation of the C–B bond which could occur on boronic acids. Inspection of the NMR spectra can give some information on the conformation of cyclic boronic acids. Considering that the boron atom should be sp2

• hybridized it is not possible to assign any α/β configuration to the position 1 of the sugar analogue. Compound 7 showed the following coupling constants: J2a,3 = 4.6 Hz, J2b,3 = 5.7 Hz, J3,4 = 1.8 Hz and J4,5 = 7.2 Hz. From these values, a chair-like conformation could be inferred, with some flattening

• around the boron atom. Compound 8 shows two isochronal protons at C-2 with a J2,3 = 4.9 Hz, and superposition of protons H-3 and H-5 not allowing to hypothesize a clear picture of the 6-membered ring conformation. Concerning compound 10, the molecule is rigid around the benzylidene ring, while a

Efficient resolution of racemic crown-shaped cyclotriveratrylene derivatives and isolation and characterization of the intermediate saddle isomer

• Sven Götz,
• Andreas Schneider and
• Arne Lützen

Beilstein J. Org. Chem. 2019, 15, 1339–1346, doi:10.3762/bjoc.15.133

• [10][11] and cucurbiturils [12][13]. CTVs are cyclic trimers, originally formed from veratrole upon condensation with formaldehyde, which adopt a bowl-shaped form as the most stable conformation. Chiral derivatives result when the aromatic residues carry either one, three or two different additional

Host–guest interactions between p-sulfonatocalix[4]arene and p-sulfonatothiacalix[4]arene and group IA, IIA and f-block metal cations: a DFT/SMD study

• Valya K. Nikolova,
• Cristina V. Kirkova,
• Silvia E. Angelova and
• Todor M. Dudev

Beilstein J. Org. Chem. 2019, 15, 1321–1330, doi:10.3762/bjoc.15.131

• /thermodynamics of the binding event, complementarity of molecular shapes, etc., is useful for designing receptor molecules. Results and Discussion M062X/6-31G(d,p) optimized structures of the host systems in cone conformation are presented in Figure 1 in two projections: side view and view from the rim trimmed

• are oppositely placed. The other two sulfonate groups became more distant in the optimized structure of the complex (Figure 2). For the rest of the complexes, the starting conformation is built by locating the naked metal cation close to the sulfonate groups by using the optimized [C[4]A–Na]3

• the La3+ cation was approximately at the level of the SO3 groups. In the resultant complex (where C[4]A is a second-shell ligand) the cavity is not filled with water molecules, the four SO3 groups are attracted by the hydrated metal cation and the calixarene adopts a conformation with closer opposite

Robust perfluorophenylboronic acid-catalyzed stereoselective synthesis of 2,3-unsaturated O-, C-, N- and S-linked glycosides

• Madhu Babu Tatina,
• Xia Mengxin,
• Rao Peilin and
• Zaher M. A. Judeh

Beilstein J. Org. Chem. 2019, 15, 1275–1280, doi:10.3762/bjoc.15.125

• perflurophenylboronic acid to the allylic acetate moiety of glucal 1a induces polarization (structure I) and leads to the formation of an allyloxycarbenium ion (structure II) in the preferred 4H3 conformation. Addition of the nucleophiles to C1 from the α-face gives the lower energy half-chair conformer and results in

Bambusuril analogs based on alternating glycoluril and xylylene units

• Tomáš Lízal and
• Vladimír Šindelář

Beilstein J. Org. Chem. 2019, 15, 1268–1274, doi:10.3762/bjoc.15.124

• of these protons because of its non-equivalent nature. The structures of conformers 1a-1 and 1a-2 were further confirmed by 2D NMR experiments. We performed 2D exchange spectrometry (EXSY) NMR experiments to confirm that there is a change of conformation on the NMR timescale [17]. This technique

Alkylation of lithiated dimethyl tartrate acetonide with unactivated alkyl halides and application to an asymmetric synthesis of the 2,8-dioxabicyclo[3.2.1]octane core of squalestatins/zaragozic acids

• Herman O. Sintim,
• Hamad H. Al Mamari,
• Hasanain A. A. Almohseni,
• Younes Fegheh-Hassanpour and
• David M. Hodgson

Beilstein J. Org. Chem. 2019, 15, 1194–1202, doi:10.3762/bjoc.15.116

• rationalised due to the enolate π-system and potentially cleavable beta σ-C–O bond lying mutually orthogonal, while the latter was subsequently ascribed to alkylation occurring from an envelope conformation wherein the unenolised ester resided pseudoequatorial to avoid 1,3-steric interactions with a

Design of a double-decker coordination cage revisited to make new cages and exemplify ligand isomerism

• Sagarika Samantray,
• Sreenivasulu Bandi and
• Dillip K. Chand

Beilstein J. Org. Chem. 2019, 15, 1129–1140, doi:10.3762/bjoc.15.109

• (regioisomer) of the known ligand L2 (Figure 1). Each of these ligands has three pyridine moieties separated by two spacer moieties (–CH2OC(=O)–). Both ligands are semi-rigid/semi-flexible due to the spacers’ conformational mobility. The “E-shaped” conformation of the ligand that is suitable for the formation

Molecular recognition using tetralactam macrocycles with parallel aromatic sidewalls

• Dong-Hao Li and
• Bradley D. Smith

Beilstein J. Org. Chem. 2019, 15, 1086–1095, doi:10.3762/bjoc.15.105

• conformation with one or more of its NH residues directed out of the macrocycle cavity which enables intermolecular hydrogen bonding [29]. This promotes macrocycle self-aggregation and insolubility in nonpolar solvents (<1 mg L−1 in chloroform). There are two ways to reduce the flexibility and preorganize the

• macrocyclic structure in a stable conformation with all NH residues directed into the cavity. One way is to use 2,6-pyridine dicarboxamides as the bridging units which permits intramolecular hydrogen bonding within the cavity (Figure 1) [30]. This internal hydrogen bonding stabilizes conformations that have

• association constants [32]. A second way to preorganize the macrocycle structure in a conformation with all NH residues directed into the macrocycle cavity was developed by the Smith group [33]. They substituted the 1,4-phenylene sidewalls with sterically encumbered aromatic units that reduced conformational

Mechanistic investigations on multiproduct β-himachalene synthase from Cryptosporangium arvum

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2019, 15, 1008–1019, doi:10.3762/bjoc.15.99

• similar binding conformation for the terminal C5-unit is reasonable for the three substrates. To complete the mechanistic picture of the initial 1,11-cyclisation, also the stereochemical course at C-1 was investigated. Unfortunately, this position is disturbed by the follow-up 1,3-hydride shift in 1 and

• vanished crosspeak. Combining the information deduced from the extensive incubation experiments stated above, a structural model for the reactive conformation of cation D is proposed (Figure S19, Supporting Information File 1). This intermediate, or structurally related transition states for the

• corresponding concerted reactions to avoid its secondary nature, are of central importance in understanding the initial HcS catalysed cyclisation towards cation B. The discussed conformation is imprinted by the structure of 7 with its relative conformation at the four-membered ring system allowing for a 2Si

Catalytic asymmetric oxo-Diels–Alder reactions with chiral atropisomeric biphenyl diols

• Chi-Tung Yeung,
• Wesley Ting Kwok Chan,
• Wai-Sum Lo,
• Ga-Lai Law and
• Wing-Tak Wong

Beilstein J. Org. Chem. 2019, 15, 955–962, doi:10.3762/bjoc.15.92

• )-(S,S) atropisomer (Figure 2). From the structure, no extensive intermolecular OH···O hydrogen bonds can be found for the formation of the supramolecular structure. Instead, intramolecular hydrogen bonds [D(O–H···O): 2.072(31) Å; (O–H∙∙∙O): 161.39(31)°] were found to keep the conformation of the

Halogen bonding and host–guest chemistry between N-alkylammonium resorcinarene halides, diiodoperfluorobutane and neutral guests

• Fangfang Pan,
• Mohadeseh Dashti,
• Michael R. Reynolds,
• Kari Rissanen,
• John F. Trant and
• Ngong Kodiah Beyeh

Beilstein J. Org. Chem. 2019, 15, 947–954, doi:10.3762/bjoc.15.91

• . employing substitutional disorder, achieved the co-crystallization of six components [28]. As for positional disorder, it generally indicates the same molecule or assembly can adopt more than one favourable conformation. From this perspective, disorder can be considered as a special case of a co-crystal or

• guests, and the length of the alkyl chain [30][31]. In our previous report, the basic conformation of the host N-hexylammonium resorcinarene bromide (Hex-NARBr) was driven by the incorporation of a 1,4-dioxane guest molecule [32], and the inter-cavitand bridging of DIOFB. The relatively long N

• tube, only creating isolated pores in the cavity of the resorcinarene. Note that the two modes are present simultaneously in the crystal lattice, thus, the structure formally contains around 75% halogen bonded dimer, and 25% halogen bonded capsule. Additionally, the conformation difference could reveal

Towards the preparation of synthetic outer membrane vesicle models with micromolar affinity to wheat germ agglutinin using a dialkyl thioglycoside

• Dimitri Fayolle,
• Nathalie Berthet,
• Bastien Doumeche,
• Olivier Renaudet,
• Peter Strazewski and
• Michele Fiore

Beilstein J. Org. Chem. 2019, 15, 937–946, doi:10.3762/bjoc.15.90

• , there is no obvious involvement of the ester bond in the binding of 8C2 or 8C4 at these secondary sites. The other main poses of 8C2 and 8C4 present the ligands adopting a linear conformation in a cleft between both monomers of WGA with similar energies (−5.3 to −6.2 kcal mol−1, pose C, Figure 6 and

An anomalous addition of chlorosulfonyl isocyanate to a carbonyl group: the synthesis of ((3aS,7aR,E)-2-ethyl-3-oxo-2,3,3a,4,7,7a-hexahydro-1H-isoindol-1-ylidene)sulfamoyl chloride

• Aytekin Köse,
• Aslı Ünal,
• Ertan Şahin,
• Uğur Bozkaya and
• Yunus Kara

Beilstein J. Org. Chem. 2019, 15, 931–936, doi:10.3762/bjoc.15.89

• ]. The C=C double bonds are in the cyclohexene units range between 1.307–1.316(3) Å and the S=O bonds are between 1.417–1.414(3) Å. The conformation is defined by steric effects, which force a fold of the cyclohexene rings relative to the mean plane through the pyrrolidine group. For both enantiomers

• , the cyclohexene ring has a twist-boat conformation and the pyrrolidine rings are in half-chair conformation. The structures contain four asymmetric carbon atoms and the stereogenic centers are as follows: C1(R), C6(S), C11(R), and C16(S), where the N-chlorosulfonyl group attached to the carbonyl atom

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

• the positions of both bonding and antibonding orbitals of the substituents change with the ring inversion, a conformation where a given substituent favors these interactions by performing them more effectively, may, in fact, govern the equilibrium. The C–X bonds have already been reported as excellent

• , the dominant conformation is ea. The higher values of J and W for H1 indicate the diaxial coupling of this hydrogen with the axial hydrogen of C6 (Figure 1). This behavior was observed for all compounds, in both solvents, as shown in Table 1. At −80 °C, two signals for H1 and H2 are observed, which

• by the weighted averages of both conformers, considering the rotational populations in each. The negative values, both in gas phase and in solution, indicate that ea is the more stable conformation. A trend in energy values was observed at all the theory levels employed in this study, there being a

Stereochemical investigations on the biosynthesis of achiral (Z)-γ-bisabolene in Cryptosporangium arvum

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2019, 15, 789–794, doi:10.3762/bjoc.15.75

• of the C-2,C-3-double bond by the enzyme’s active site (e.g., on top of it, Figure 4A). This migration of OPP to C-3 results in a reorganisation of the resulting structure to a cisoid conformation for the follow up 1,6-ring closure. To explain the astonishing selectivity between the two NPP

• productive conformation that exhibits a close proximity between C-6 and C-1 for ring closure to (S)-A initiated by OPP abstraction, (S)-NPP cannot occupy this conformation for its different stereocentre. Instead, abstraction of the OPP moiety leads to an allylic cation with an unproductive conformation for

Hoveyda–Grubbs catalysts with an N→Ru coordinate bond in a six-membered ring. Synthesis of stable, industrially scalable, highly efficient ruthenium metathesis catalysts and 2-vinylbenzylamine ligands as their precursors

• Kirill B. Polyanskii,
• Kseniia A. Alekseeva,
• Pavel V. Raspertov,
• Pavel A. Kumandin,
• Eugeniya V. Nikitina,
• Atash V. Gurbanov and
• Fedor I. Zubkov

Beilstein J. Org. Chem. 2019, 15, 769–779, doi:10.3762/bjoc.15.73

• ruthenium atom. The ruthenium-containing six-membered ring has a slightly distorted envelope conformation with a ca. 51° to 54° deviation of the nitrogen atom from the mean plane of other five atoms. The most important feature of the catalyst structure is the length of the ruthenium–nitrogen bond, which

Synthesis of functionalized diazocines for application as building blocks in photo- and mechanoresponsive materials

• Widukind Moormann,
• Daniel Langbehn and
• Rainer Herges

Beilstein J. Org. Chem. 2019, 15, 727–732, doi:10.3762/bjoc.15.68

• to 3,3’- and 4,4’-diaminodiazocine, which have been implemented in macromolecules for conformation switching, our compounds exhibit improved photophysical properties (photostationary states, separation of absorption bands in the cis and trans configuration). Hence they are promising candidates as

Homo- and hetero-difunctionalized β-cyclodextrins: Short direct synthesis in gram scale and analysis of regiochemistry

• Gábor Benkovics,
• Mihály Bálint,
• Éva Fenyvesi,
• Erzsébet Varga,
• Szabolcs Béni,
• Konstantina Yannakopoulou and
• Milo Malanga

Beilstein J. Org. Chem. 2019, 15, 710–720, doi:10.3762/bjoc.15.66

• for H6 and an apparent doublet of doublets for H6’. The tg conformation is the least populated in solution and is considered as unfavorable (≈0% population) [30], especially if the substituent is bulky as in the present case. In the spectrum of 6A,6D-ditosyl-β-CD (Figure 3b, lower spectrum) the tosyl

• -substituted unit A presumably adopts a gg conformation as both H6,6’ protons give rise to one doublet (yellow labelled, 4.28 ppm), whereas in unit D (orange labelled) gt is the preferred conformation because a doublet of doublets (H6’D, 4.16 ppm) and a doublet (H6D, 4.05 ppm) are observed. The gt seems also

• to be the predominant conformation in solution for both tosyl substituents in 6A,6C-ditosyl-β-CD (Figure 3b, middle spectrum) and 6A,6B-ditosyl-β-CD (Figure 3b, upper spectrum) as revealed by the patterns of the signals due to H6,6’. In summary, the orientations of the tosyl groups as defined by the

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

• drastic changes of the ring conformation occurred while sometimes only the conformation of the exocyclic C4–C5 linkage changed. Herein we describe a combined quantum chemical and NMR conformational investigation of three common monosaccharide furanosides as their propyl glycosides: α-mannose, β-glucose

• 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

• conformation of the side chain at C(4). The conformation of the furanoside ring can be one of ten envelope (E) or ten twist (T) forms and it is convenient to describe it using the pseudo-rotation diagram [13]. The conformation of the exocyclic chain (i.e., rotation of C4−C5 and C5−C6 bonds) is described by two