Electrochemical and spectroscopic properties of twisted dibenzo[g,p]chrysene derivatives

• Tomoya Imai,
• Ryuhei Akasaka,
• Naruhiro Yoshida,
• Toru Amaya and
• Tetsuo Iwasawa

Beilstein J. Org. Chem. 2022, 18, 963–971, doi:10.3762/bjoc.18.96

• . Optimizations of DBC-H(56°)-1 and DBC-H(56°)-2 based on DFT calculations were performed by fixing the atoms, as described above [56]. The conformations of the MeO group in DBC-H(56°)-1 and DBC-H(56°)-2 are nearly perpendicular (98.3°) to and parallel (179.8°) to the benzene ring, respectively (Figure 3 and

First series of N-alkylamino peptoid homooligomers: solution phase synthesis and conformational investigation

• Maxime Pypec,
• Laurent Jouffret,
• Claude Taillefumier and
• Olivier Roy

Beilstein J. Org. Chem. 2022, 18, 845–854, doi:10.3762/bjoc.18.85

• observed for Xaa–Pro amide bonds and polyproline chains can adopt either the all-trans type II (PPII) or the all-cis type I (PPI) helical conformations, the latter being only observed in alcohol-type solvents [14]. In contrast to the prolyl-amide bond in acyclic peptides (≈5% of cis-Pro) [15], the cis

• form a unique sheet-like secondary structure, whereas molecular modeling showed that N-aryl peptoid oligomers composed of monomers in the same conformation (as observed in the crystal of dimer 2) might adopt right or left-handed helical conformations that resemble the polyproline type II helix. The χ1

• molecule are in the same conformation with either two positive values of the φ angle (conformation B) or two negative values for the mirror image conformation A. These two local conformations could exist at each monomer position, leading to a potential mixture of secondary structures. We therefore

Synthesis and HDAC inhibitory activity of pyrimidine-based hydroxamic acids

• Virginija Jakubkiene,
• Gabrielius Ernis Valiulis,
• Markus Schweipert,
• Asta Zubriene,
• Daumantas Matulis,
• Franz-Josef Meyer-Almes and
• Sigitas Tumkevicius

Beilstein J. Org. Chem. 2022, 18, 837–844, doi:10.3762/bjoc.18.84

• tend to adopt the more stable keto-E and keto-Z conformations [36]. In the 1H NMR spectra of the synthesized hydroxamic acids 12–18 and 25–31 two sets of proton signals from the NH and OH groups of the hydroxamic acid residue are observed. Following data [36], we assigned the more intense peaks to the

Thiophene/selenophene-based S-shaped double helicenes: regioselective synthesis and structures

• Mengjie Wang,
• Lanping Dang,
• Wan Xu,
• Zhiying Ma,
• Liuliu Shao,
• Guangxia Wang,
• Chunli Li and
• Hua Wang

Beilstein J. Org. Chem. 2022, 18, 809–817, doi:10.3762/bjoc.18.81

• photocyclization reaction sites of 5 were predicted by the orbital-weighted Fukui function in Multiwfn using Gaussian 09 [31][32] at the B3LYP/6-31G** [33] level of theory to verify the reaction-site selectivity of oxidative photocyclization further. Results showed that the conformations of 5a are varied, but the

Structural basis for endoperoxide-forming oxygenases

• Takahiro Mori and
• Ikuro Abe

Beilstein J. Org. Chem. 2022, 18, 707–721, doi:10.3762/bjoc.18.71

• . Structure of NvfI In the structural analysis of NvfI, three different active site conformations (open, partially closed, and closed) were observed (PDB IDs: 7DE2, 7EMZ, and 7ENB) (Figure 4A–C) [28]. The conformations of the loop regions between Ser122-Gly128 and Trp199-Pro209 were altered by soaking with

BINOL as a chiral element in mechanically interlocked molecules

• Matthias Krajnc and
• Jochen Niemeyer

Beilstein J. Org. Chem. 2022, 18, 508–523, doi:10.3762/bjoc.18.53

• polyacetylene, with a special focus on the different possible co-conformations of the rotaxane (see Figure 7) [54]. The synthesis of the acetylene monomers 31, containing a chiral rotaxane side-chain, was achieved by tributylphosphane-catalyzed esterification. Two different macrocycles having either one BINOL

Comparative study of thermally activated delayed fluorescent properties of donor–acceptor and donor–acceptor–donor architectures based on phenoxazine and dibenzo[a,j]phenazine

• Saika Izumi,
• Prasannamani Govindharaj,
• Anna Drewniak,
• Paola Zimmermann Crocomo,
• Satoshi Minakata,
• Leonardo Evaristo de Sousa,
• Piotr de Silva,
• Przemyslaw Data and
• Youhei Takeda

Beilstein J. Org. Chem. 2022, 18, 459–468, doi:10.3762/bjoc.18.48

• internal conversion. In this sense, it is important to look into the energy gaps between triplet states of both molecules. Considering the average gaps taken from all the conformations sampled in the nuclear ensemble from the T1 state geometry, we obtain T1 to T2 gaps of approximately 0.4 eV for both

Site-selective reactions mediated by molecular containers

• Rui Wang and
• Yang Yu

Beilstein J. Org. Chem. 2022, 18, 309–324, doi:10.3762/bjoc.18.35

• cavitand hosts were also modified with imidazolium cationic or carboxylic anionic feet [29]. Before the reaction, NMR analysis of the host–guest complex indicated that the bound guest was in yo-yo motions time-averaged between unsymmetrical J-shaped conformations and symmetrical U-shaped ones. Treatment of

• -organize them with certain confined conformations. In this case, the linear diterpenoid substrate 29 possessed a folded U-shaped conformation within the cavity, with the terminal trisubstituted olefin exposed to the solution while the other three internal ones were protected by the cage host. The structure

• . Contemporaneously, the Rebek group illustrated another interesting site-selective monoepoxidation of α,ω-dienes mediated by the water-soluble cavitand host E (Figure 10) [71]. The α,ω-dienes were determined to adopt a yo-yo motion between two J-shaped conformations or the rapid tumbling of a coiled conformation

Peptide stapling by late-stage Suzuki–Miyaura cross-coupling

• Hendrik Gruß,
• Rebecca C. Feiner,
• Ridhiwan Mseya,
• David C. Schröder,
• Michał Jewgiński,
• Kristian M. Müller,
• Rafał Latajka,
• Antoine Marion and
• Norbert Sewald

Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1

• permeability [1][2][3]. Hence, peptide-based drugs became of high interest because of their high selectivity combined with low toxicity. Cross-linking of side chain residues results in constrained conformations and can be used to stabilise α-helical secondary structures. This technique is called peptide

• portion of the macrocycle and is similar to c1, with the Trp’s indole group pointing in the other direction. In the trans isomer, both conformations are also found, however, with different populations and order. Conformation c2 of P5 trans is helical and resembles c3 of P5 cis, yet with a significantly

• accurate values would be obtained with methods better adapted for kinetics, such as Markov models (for a general overview see reference [94]). Yet, such low barriers are not sufficient to trap the SMC peptide in conformations that can be separated experimentally at ambient conditions [95] and the analysis

Biological properties and conformational studies of amphiphilic Pd(II) and Ni(II) complexes bearing functionalized aroylaminocarbo-N-thioylpyrrolinate units

• Samet Poyraz,
• Samet Belveren,
• Sabriye Aydınoğlu,
• Mahmut Ulger,
• Abel de Cózar,
• Maria de Gracia Retamosa,
• Jose M. Sansano and
• H. Ali Döndaş

Beilstein J. Org. Chem. 2021, 17, 2812–2821, doi:10.3762/bjoc.17.192

• conformations analyzed by the 1H NMR spectra of nickel and palladium complexes, presumably correlated with their activity. According to the previous activities of derivatives of this nature [15][16] the cis-complex was identified as the therapeutic arrow. We initially tried to determine the driving force

• the metal atom considered, only one of the ligand conformations were energetically accessible (energetic difference of +14.6 and +5.7 kcal·mol−1, for nickel and palladium conformers, respectively, Figure 2). In these cases, the energetic difference between conformers A and B lies in the existence of

Progress and challenges in the synthesis of sequence controlled polysaccharides

• Giulio Fittolani,
• Theodore Tyrikos-Ergas,
• Denisa Vargová,
• Manishkumar A. Chaube and
• Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

• are ideal probes to study polysaccharides at the molecular level and identify structure–property correlations. Access to synthetic polysaccharides facilitated the correlation of chemical structure with molecular conformations [5][6], intermolecular interactions [7][8], and biological response [9

Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides

• Mathias B. Danielsen and
• Jesper Wengel

Beilstein J. Org. Chem. 2021, 17, 1828–1848, doi:10.3762/bjoc.17.125

• moieties attached to the sugar scaffold The sugar moiety of ONs has been extensively studied with respect to the significance of structure and configurations of substituents, and the resulting conformations of the furanose ring, on the properties of ONs (including ASOs). The great variation at which

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

• negative charge on PNA’s backbone. Electrostatic repulsion of the negatively charged phosphates dominates the conformational properties and structure of nucleic acids. In contrast to proteins that prefer to fold in compact structures, DNA and RNA inherently prefer extended conformations that minimize the

• resembled the B- and A-form conformations of natural nucleic acids. The PNA–RNA duplex adopted a conformation very close to the standard A-form helix [40]. In contrast, the PNA–DNA duplex adopted an intermediate structure where positioning of the base pairs was A-like, while the backbone curvature, sugar

• -form helix" by the study authors [41]. Despite the much larger displacement of the bases from the helix axis, the base stacking in the P-form helix resembles that of an A-form DNA duplex. The sugars of a DNA strand adopt C3′-endo conformations with an average interphosphate distance of ≈6 Å, which is

Breaking paracyclophane: the unexpected formation of non-symmetric disubstituted nitro[2.2]metaparacyclophanes

• Suraj Patel,
• Tyson N. Dais,
• Paul G. Plieger and
• Gareth J. Rowlands

Beilstein J. Org. Chem. 2021, 17, 1518–1526, doi:10.3762/bjoc.17.109

• chains at non-adjacent carbon positions. Their constrained three-dimensional shapes enforce unusual conformations and interactions between the aromatic decks, all of which results in their unique properties [2][3][4][5]. The most studied cyclophane is [2.2]paracyclophane (1, Figure 1). Not only is it the

Structural effects of meso-halogenation on porphyrins

• Keith J. Flanagan,
• Maximilian Paradiz Dominguez,
• Zoi Melissari,
• Hans-Georg Eckhardt,
• René M. Williams,
• Dáire Gibbons,
• Caroline Prior,
• Gemma M. Locke,
• Alina Meindl,
• Aoife A. Ryan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2021, 17, 1149–1170, doi:10.3762/bjoc.17.88

• data in the supporting information for completion. However, we were able to extract atom coordinates and NSD data which can be compared to the existing crystal structures (Supporting Information File 1, Figures S72–S74 and S75–S129) [28][45]. Series 1 In series 1 (Figure 22) the conformations of the

Synthesis of multiply fluorinated N-acetyl-D-glucosamine and D-galactosamine analogs via the corresponding deoxyfluorinated glucosazide and galactosazide phenyl thioglycosides

• Vojtěch Hamala,
• Lucie Červenková Šťastná,
• Martin Kurfiřt,
• Petra Cuřínová,
• Martin Dračínský and
• Jindřich Karban

Beilstein J. Org. Chem. 2021, 17, 1086–1095, doi:10.3762/bjoc.17.85

• exocyclic C5‒C6 bond in solution (3JH5-F6 = 24.6–27.1 Hz), whereas the corresponding ᴅ-galacto-configured analogs 60, 67, 69, and 72 adopted gauche,trans (gt) or trans,gauche (tg) conformations to a significant degree (3JH5-F6 = 12.7–14.6 Hz). These findings were in accordance with the previous reports by

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• ][105][106][107]. GNA duplexes possess only one large groove which corresponds to the canonical minor groove, the canonical major groove is a convex surface. Furthermore, the glycol backbone adopts two conformations alternating between gauche and anti conformations such that each base pair contains one

Menthyl esterification allows chiral resolution for the synthesis of artificial glutamate analogs

• Kenji Morokuma,
• Shuntaro Tsukamoto,
• Kyosuke Mori,
• Kei Miyako,
• Ryuichi Sakai,
• Raku Irie and
• Masato Oikawa

Beilstein J. Org. Chem. 2021, 17, 540–550, doi:10.3762/bjoc.17.48

• supported by taking into account the steric interactions between the heterotricycle and the menthyl ring, as follows. There are no major differences in the conformations of the heterotricycle and the menthyl rings in 10, 10*, 21, and 21*. It is reasonably speculated that 1) the four bonds between the rings

• Corporation), employing initial conformations generated by MM2 (ChemBio3D Ultra, Version 14.0.0.117). The calculations were basically independent from the initial conformations. A same set of conformers was obtained after CONFLEX calculations, starting with different conformers employed as initial conformers

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

• residue that appear altered in fluoroprolines. The first one to mention is the conformation of the pyrrolidine ring, which exhibits a dynamic transition between several distinct states in a relatively fast kinetic mode (roughly on a GHz scale) [48][49]. For simplicity, two conformations are considered

• the conformations. However, R-Flp stabilizes the C4-exo-pucker, while S-Flp stabilizes the C4-endo system [51]. It is believed that Dfp has no conformational preference akin to proline [52]. The stabilization of the puckers is one of the most prominent features of fluoroprolines that justifies their

• use in protein engineering. The "freezing" of certain proline pucker conformations due to stereospecific fluorination has an effect on the packing within a protein structure as well as the backbone folding parameters (vide infra). 2.5 Thermodynamics of the amide rotation Another special feature of

Exploring the possibility of using fluorine-involved non-conjugated electron-withdrawing groups for thermally activated delayed fluorescence emitters by TD-DFT calculation

• Dongyang Chen and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2021, 17, 210–223, doi:10.3762/bjoc.17.21

• the increased bulkiness of the SF5 group, the corresponding twist angle increased to 78.5o and 78.7o. These highly twisted conformations contribute to the spatial separation of the HOMO and LUMO. Figure 3 shows the energies of the HOMOs and LUMOs and the S1 and T1 states for the fluorinated acceptor

• intermediate excited triplet states to S1 thereby improving the rISC rate [22][24]. The presence of multiple donors, each possessing slightly different conformations, and thereby presenting slightly different electronic coupling with the central acceptor guarantees a dense population of excited states [22][24

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• containers [90]. CCMV was the first icosahedral viral capsid to be disassembled and reassembled in vitro [91]. The CCMV capsid can be reassembled into empty capsids as well as into different conformations, such as disks, rods, tubes, and multiwalled capsids by using different scaffolds [92]. In these cases

Chiral anion recognition using calix[4]arene-based ureido receptors in a 1,3-alternate conformation

• Tereza Horáčková,
• Jan Budka,
• Vaclav Eigner,
• Wen-Sheng Chung,
• Petra Cuřínová and
• Pavel Lhoták

Beilstein J. Org. Chem. 2020, 16, 2999–3007, doi:10.3762/bjoc.16.249

• basic conformations (cone, partial cone, 1,3-alternate, and 1,2-alternate) offers the combination of a precisely defined 3D structure, with functional groups being introduced at exactly defined mutual positions. This makes calix[4]arenes an ideal molecular scaffold [25][26] for the construction of

• different conformations. Although the overwhelming majority of calixarene-based receptors makes use of the cone conformer A (Figure 1), the corresponding diureidocalix[4]arenes in the 1,3-alternate conformation B showed [42][43] surprisingly good complexation abilities towards selected anions. Especially

Naphthalonitriles featuring efficient emission in solution and in the solid state

• Sidharth Thulaseedharan Nair Sailaja,
• Iván Maisuls,
• Jutta Kösters,
• Alexander Hepp,
• Andreas Faust,
• Jens Voskuhl and
• Cristian A. Strassert

Beilstein J. Org. Chem. 2020, 16, 2960–2970, doi:10.3762/bjoc.16.246

• (AIE) [23][24][25][26][27]. They mentioned a series of silole derivatives with propeller-like conformations that show no emission in dilute solutions, but are highly luminescent when aggregated in the solid state. Their work has attracted major attention and quickly became one of the most sought-after

Ring-closing metathesis of prochiral oxaenediynes to racemic 4-alkenyl-2-alkynyl-3,6-dihydro-2H-pyrans

• Viola Kolaříková,
• Markéta Rybáčková,
• Martin Svoboda and
• Jaroslav Kvíčala

Beilstein J. Org. Chem. 2020, 16, 2757–2768, doi:10.3762/bjoc.16.226

• obtained two diastereoisomers, we decided to perform a short DFT study of the Diels–Alder reaction between dihydropyran 12b and maleimide 13. We started the study with the optimization of the starting compound. While the optimization of the rigid maleimide 13 was straightforward, 18 conformations had to be

• considered for the dihydropyran 12b, namely all combinations of equatorial or axial positions of the but-2-ynyl substituent, three staggered conformations of the prop-1-ynyl group with respect to the C–O bond of the ring, and three conformations of the dienyl system (s-trans and two tilted s-cis

• conformations) (Figure 5). Among the 18 conformations, the structure with an equatorial conformation of the but-2-ynyl group, an anti-arrangement of the O–C bond and the prop-1-ynyl group, and an s-trans conformation of the diene system proved to be the most stable by more than 7 kJ/mol (Figure 6). Of course

Enzyme-instructed morphological transition of the supramolecular assemblies of branched peptides

• Dongsik Yang,
• Hongjian He and
• Bing Xu

Beilstein J. Org. Chem. 2020, 16, 2709–2718, doi:10.3762/bjoc.16.221

• the cleavage occurs depending on the acetylation of the N-terminal of the branch. Then, we conducted a time-dependent CD analysis to examine the change of the secondary structural conformations of 1 and 2 during the proteolysis catalyzed by proteinase K in Tris-HCl buffer at pH 7.0. As shown in Figure

• conformations than that of peptide 2. With increasing proteolysis time, the CD spectra indicate that the cleavage of 1 or 2 results in more assemblies that favor β-strand conformations (Figure 2D and Figure 2E). In addition, the ratio of the β-strand conformation resulted from the cleavage of 1 being slightly