Tying a knot between crown ethers and porphyrins

• Maksym Matviyishyn and
• Bartosz Szyszko

Beilstein J. Org. Chem. 2023, 19, 1630–1650, doi:10.3762/bjoc.19.120

• with Zn(II) was crucial to achieving the final strapping reaction, affording 11. The presence of the diaza-crown-6 caps resulted in the meso-bridge carbon atoms being slightly pulled out of the porphyrin plane, causing 11 to adopt a ruffled conformation. The penta-coordinated Zn(II) contained an

• ligands. Compound 19-Co (structure not shown) retained the cobalt(II) oxidation state with a water molecule within the cleft. The XRD analysis of the structures of 19-Co and 18b-Co exhibited Pacman conformation. The X-ray molecular structure of 19-Co provided further insights, showing a square-planar

Complexes of resorcin[4]arene with secondary amines: synthesis, solvent influence on “in-out” structure, and theoretical calculations of non-covalent interactions

• Waldemar Iwanek

Beilstein J. Org. Chem. 2023, 19, 1525–1536, doi:10.3762/bjoc.19.109

• ; Introduction Resorcin[4]arenes are macrocyclic compounds with a cavity structure formed from resorcinol and aldehydes [1]. Of particular significance is their crown conformation, which stems from the presence of 8 hydroxy groups on the upper rim and a hydrophobic cavity [2]. This property plays an important

• a slight change in its conformation towards the boat conformation. The length of the hydrogen bond between the oxygen atom of the hydroxy group forming the hydrogen bond with pyrrolidine and the adjacent hydroxy group is 1.746 Å and is only slightly shorter than the other intramolecular hydrogen

Exploring the role of halogen bonding in iodonium ylides: insights into unexpected reactivity and reaction control

• Carlee A. Montgomery and
• Graham K. Murphy

Beilstein J. Org. Chem. 2023, 19, 1171–1190, doi:10.3762/bjoc.19.86

• 63a induced an energetically-disfavoured twist in the fluorine adduct’s conformation (INTA’), raising its energy over that of 63b and decreasing the energy barrier between it and the reductive elimination transition state TSA’. Additionally, the role of the halogen bond acceptor in 61d is also poorly

Five new sesquiterpenoids from agarwood of Aquilaria sinensis

• Hong Zhou,
• Xu-Yang Li,
• Hong-Bin Fang,
• He-Zhong Jiang and
• Yong-Xian Cheng

Beilstein J. Org. Chem. 2023, 19, 998–1007, doi:10.3762/bjoc.19.75

• conformation of the force field was optimized. DFT was used to calculate the gauge-independent atomic orbital [30] for 1H and 13C NMR chemical shifts using the PCM solvent model in Gaussian 09 software [29]. The NMR chemical shift was corrected by the isotope shift of TMS [31]. The calculated 13C NMR chemical

First synthesis of acylated nitrocyclopropanes

• Kento Iwai,
• Rikiya Kamidate,
• Khimiya Wada,
• Haruyasu Asahara and
• Nagatoshi Nishiwaki

Beilstein J. Org. Chem. 2023, 19, 892–900, doi:10.3762/bjoc.19.67

• the enol form, a C-attack (path a) furnishes cyclopropane 1, and an O-attack (path b) furnishes dihydrofuran 8. When the R1 group becomes bulkier, the hydroxy group may be far from the reaction site because of the steric repulsion in the stable conformation. Another possibility is that the bulky

Construction of hexabenzocoronene-based chiral nanographenes

• Ranran Li,
• Di Wang,
• Shengtao Li and
• Peng An

Beilstein J. Org. Chem. 2023, 19, 736–751, doi:10.3762/bjoc.19.54

• designed NGs with tailor-made sizes and structures not only show planar conformation as fragments of graphene, but also evolved with a diversity of other shapes, including bowls [10], saddles [11][12][13], helixes [14][15], belts [16], rings [17], and their hybrid conformations such as helical bilayers [18

• helical conformation was confirmed by the single-crystal X-ray crystallography of its methoxy-substituted analogue. Another method to obtain the incompletely cyclized seco-HBC is the introduction of a non-hexagonal ring into the precursors of HBC. Due to the large ring strain, the precursors are not prone

• . And the derivative 16 was also synthesized by allylic oxidation of compound 15 using selenium dioxide. As helical chiral NGs, helicene 14 and its derivatives 15 and 16 showed highly distorted helical conformation and also exhibited a relatively high isomerization barrier (over 28.9 kcal/mol determined

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• signalize complex formation (interaction with a biomolecule, cyclodextrine, metal cation, etc.) or change of receptor conformation [5][6]. Employment of pyrene as a biosensor is complicated due to its large aromatic surface's hydrophobicity and fluorescence sensitivity to oxygen. Therefore, modifications of

• ), differing only in the linker length between the aromatic units, have been prepared by condensation of two different pyrenecarboxylic acids with phenanthridine-labelled amino acid (Scheme 2). The influence of the linker length on the molecule flexibility, intramolecular conformation, spectroscopic properties

• electrostatic binding of the dye along the polynucleotide backbone. The reorganized intramolecular conformation of the ligand could explain the quenching of excimer fluorescence and/or redistribution of chromophore charges upon binding since fluorescence quenching is sensitive to factors that affect the rate

Synthesis, α-mannosidase inhibition studies and molecular modeling of 1,4-imino-ᴅ-lyxitols and their C-5-altered N-arylalkyl derivatives

• Martin Kalník,
• Sergej Šesták,
• Juraj Kóňa,
• Maroš Bella and
• Monika Poláková

Beilstein J. Org. Chem. 2023, 19, 282–293, doi:10.3762/bjoc.19.24

• inhibition of Golgi-type α-mannosidases [22]. It seems that the slightly bulkier (R)-1-hydroxyethyl group at C-5 of 29 compared to the hydroxymethyl at C-5 of 30 allows for a different conformation of the N-2-naphthylmethyl group in the active site of α-mannosidases (Figure 4). This would induce a shift in

• the N-2-naphthylmethyl group and the methyl component of (R)-1-hydroxyethyl group at C-5 of 28. In case of 31, the smaller hydroxymethyl group at C-5 allows for a different binding conformation of the N-2-naphthylmethyl group. FMO-PIEDA total pair interaction energies (ΔElinker-E) (in kcal mol−1

Strategies to access the [5-8] bicyclic core encountered in the sesquiterpene, diterpene and sesterterpene series

• Cécile Alleman,
• Charlène Gadais,
• Laurent Legentil and
• François-Hugues Porée

Beilstein J. Org. Chem. 2023, 19, 245–281, doi:10.3762/bjoc.19.23

Identification and determination of the absolute configuration of amorph-4-en-10β-ol, a cadinol-type sesquiterpene from the scent glands of the African reed frog Hyperolius cinnamomeoventris

• Angelique Ladwig,
• Markus Kroll and
• Stefan Schulz

Beilstein J. Org. Chem. 2023, 19, 167–175, doi:10.3762/bjoc.19.16

• synthesis by Taber that used dichromate as an oxidant [13] led to a less diastereoselective reaction furnishing the three ketones 9, 10, and 11 in a ratio of 36:2:5. The cis-conformation of the decalin backbone of 9 and 11 originates from the endo-selectivity of the Diels–Alder reaction and the boat

• conformation of the transition state. A chair transition state is less preferred because of inherent non-bonding interactions of some hydrogens. This has been discussed in detail in the original publication by Taber and Gunn, favoring 9 as the main diastereomer [13]. Our results confirm these data. To increase

• conformation was determined by calculation using force field methods (MMFF94 [16]) and is shown in Figure S2 of Supporting Information File 1. Key NOE couplings were observed between bridgehead H-8a, H-4a and H-4. The latter also couples with the methyl group at C-1, indicating a cis-decalin configuration with

1,4-Dithianes: attractive C2-building blocks for the synthesis of complex molecular architectures

• Bram Ryckaert,
• Ellen Demeyere,
• Frederick Degroote,
• Hilde Janssens and
• Johan M. Winne

Beilstein J. Org. Chem. 2023, 19, 115–132, doi:10.3762/bjoc.19.12

• , antiaromaticity is usually not a very relevant concept, as there will be no degeneration of the molecular orbitals. Nevertheless, 1,4-dithiin does adopt a non-planar boat-like conformation, which can rapidly interconvert through a planar, but nonaromatic geometry (with a shallow folding energy curve of less than

• single-cis conformation. Ando and co-workers prepared the symmetrical 1,4-dithiane 41 (Scheme 9a) [55], and amply illustrated the concept by reacting it in a [4 + 2] cycloaddition with a highly reactive diazo dienophile (Cookson’s reagent or 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD)) to afford the bis

• -adduct dithiin 42 in quantitative yield. Although 2,5-dimethylhexa-2,4-diene cannot possibly adopt a coplanar single-cis conformation, and is therefore completely unreactive in Diels–Alder reactions as a diene, its 1,4-dithiane-tethered version in 41 must show a sufficient proximity between the terminal

Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

Synthetic study toward the diterpenoid aberrarone

• Liang Shi,
• Zhiyu Gao,
• Yiqing Li,
• Yuanhao Dai,
• Yu Liu,
• Lili Shi and
• Hong-Dong Hao

Beilstein J. Org. Chem. 2022, 18, 1625–1628, doi:10.3762/bjoc.18.173

• stereoselectivity is possible through the conformation of 14 where the OTBS group is in pseudoequatorial position (Scheme 2). Therefore, the Pauson–Khand reaction proceeded to afford 11 containing an α-H at C6. From this intermediate, to our delight, the stereoselective attachment of the requisite methyl group

Comparison of crystal structure and DFT calculations of triferrocenyl trithiophosphite’s conformance

• Ruslan P. Shekurov,
• Mikhail N. Khrizanforov,
• Ilya A. Bezkishko,
• Tatiana P. Gerasimova,
• Almaz A. Zagidullin,
• Daut R. Islamov and
• Vasili A. Miluykov

Beilstein J. Org. Chem. 2022, 18, 1499–1504, doi:10.3762/bjoc.18.157

• . Trithiophosphite has not been studied by X-ray diffraction analysis, although it is of great interest for the construction of complexes with multiferrocene systems. Herein we present for the first time X-ray diffraction data of (FcS)3P and compare it with DFT calculations to show which conformation are preferred

• trithiophosphite have been considered quantum-chemically (Figure 2, Table 1): trans-trans-trans (ttt), gauche-trans-trans (gtt), gauche-gauche-trans (ggt), and gauche-gauche-gauche (ggg). During optimization the ggt conformer adopted a cis-gauche-trans conformation with Fc(C)–S–P lone pair dihedral angles of 8

• °, −60°, and 173°, respectively (Table 1). The lowest energy has been predicted for the gtt conformer, nevertheless the energy differences between the gtt and cgt conformers are negligible (0.23 kcal/mol). Interestingly, the cgt conformation has been found previously for tricymantrenyl trithiophosphite

Supramolecular approaches to mediate chemical reactivity

• Pablo Ballester,
• Qi-Qiang Wang and
• Carmine Gaeta

Beilstein J. Org. Chem. 2022, 18, 1463–1465, doi:10.3762/bjoc.18.152

• whose geometry, in low-polarity solvents, is controlled by the 1,2,3-alternate conformation of the calix[6]arene skeleton. These catalysts can tune the selectivity of the catalytic cycloisomerization of 1,6-enynes in response to the relative orientation of the coordinated gold(I) atom with respect to

Naphthalimide-phenothiazine dyads: effect of conformational flexibility and matching of the energy of the charge-transfer state and the localized triplet excited state on the thermally activated delayed fluorescence

• Kaiyue Ye,
• Liyuan Cao,
• Davita M. E. van Raamsdonk,
• Zhijia Wang,
• Jianzhang Zhao,
• Daniel Escudero and
• Denis Jacquemin

Beilstein J. Org. Chem. 2022, 18, 1435–1453, doi:10.3762/bjoc.18.149

• investigate the joint influence of the conformation flexibility and the matching of the energies of the charge-transfer (CT) and the localized triplet excited (3LE) states on the thermally activated delayed fluorescence (TADF) in electron donor–acceptor molecules, a series of compact electron donor–acceptor

• . The tuning of the energy order of the CT and LE states is achieved by oxidation of the PTZ unit into the corresponding sulfoxide, whereas conformation restriction is imposed by introducing ortho-methyl substituents on the phenyl linker, so that the coupling magnitude between the CT and the 3LE states

• electron paramagnetic resonance (TREPR) spectra and theoretical methods also support that conformation fluctuations are beneficial to TADF [16]. This is in stark contrast with the SOCT-ISC mechanism. To further explore these contradictory requirements for SOCT-ISC and TADF, we designed herein a series of

Synthesis of C6-modified mannose 1-phosphates and evaluation of derived sugar nucleotides against GDP-mannose dehydrogenase

• Sanaz Ahmadipour,
• Alice J. C. Wahart,
• Jonathan P. Dolan,
• Laura Beswick,
• Chris S. Hawes,
• Robert A. Field and
• Gavin J. Miller

Beilstein J. Org. Chem. 2022, 18, 1379–1384, doi:10.3762/bjoc.18.142

• conformation has recently been shown to be an important factor contributing to anomeric reactivity of canonical pyranoses [12]). One phenyl ring of the phosphate ester group occupied a position folded underneath the pyranose ring and engaged in an intramolecular C–H···π interaction with the axial C5 proton

Synthesis and electrochemical properties of 3,4,5-tris(chlorophenyl)-1,2-diphosphaferrocenes

• Almaz A. Zagidullin,
• Farida F. Akhmatkhanova,
• Mikhail N. Khrizanforov,
• Robert R. Fayzullin,
• Tatiana P. Gerasimova,
• Ilya A. Bezkishko and
• Vasili A. Miluykov

Beilstein J. Org. Chem. 2022, 18, 1338–1345, doi:10.3762/bjoc.18.139

• chemically, two possible conformations of 8b were considered, 8b-I and 8b-II (Figure 2). Similar to a previous report on 8c [37], both 8b-I and 8b-II adopted an almost eclipsed conformation during optimization. Computations predicted slightly lower energy (1 kcal⋅mol−1) for conformation 8b-I, with Cl

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• that in the absence of C-Raf peptides, the minimum energy conformation of 1 lies below the ω, under the central pore of 14-3-3ζ (Figure 6a and b). With this conformation, one of the GCP groups falls into the energy minimum of the GCP affinity grid. The same happens to the Lys groups. As Figure 6 shows

• be minimized). What matters is to find the minimum energy conformation of the ligand with regard to the affinity maps of lysine and GCP. Simulated annealing schedule To identify the energy minima of the coarse-grained ligand model around 14-3-3ζ, we used simulated annealing. This computational method

• simulations are then analyzed to find the minimum energy conformation which is the most probable binding position of the ligand. Log-scaled histogram of total energies at the final steps of all simulations. (a) Simulated annealing (SA) runs with 1 around 14-3-3ζ protein, (b) 1 around 14-3-3ζ/C-Raf complex

Ionic multiresonant thermally activated delayed fluorescence emitters for light emitting electrochemical cells

• Merve Karaman,
• Abhishek Kumar Gupta,
• Subeesh Madayanad Suresh,
• Tomas Matulaitis,
• Lorenzo Mardegan,
• Daniel Tordera,
• Henk J. Bolink,
• Sen Wu,
• Stuart Warriner,
• Ifor D. Samuel and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2022, 18, 1311–1321, doi:10.3762/bjoc.18.136

• suggests that the conformation of the emitter in the solid state is slightly more conjugated than that in solution or that there are specific host–guest interactions with the DPA unit that perturbs the energy of the excited state. The emission is broader than that of a structurally similar emitter, QAD

Polymer and small molecule mechanochemistry: closer than ever

• José G. Hernández

Beilstein J. Org. Chem. 2022, 18, 1225–1235, doi:10.3762/bjoc.18.128

• cellulose and chitin and approximation to the structure of lignin. Tensile forces by ball milling change the conformation of a chitin model compound. This deformation facilitates the subsequent cleavage of glycosidic bonds to produce oxocarbenium ion intermediates for hydrolysis [45]. (a) Representation of

Understanding the competing pathways leading to hydropyrene and isoelisabethatriene

• Shani Zev,
• Marion Ringel,
• Ronja Driller,
• Bernhard Loll,
• Thomas Brück and
• Dan T. Major

Beilstein J. Org. Chem. 2022, 18, 972–978, doi:10.3762/bjoc.18.97

• ’) occurs immediately due to the cis conformation and the short distance between the cation and the double bond (≈2 Å), which could be due to the active site substrate fold. In intermediate C, the trans conformation and possibly slightly different substrate fold, results in an alternative reaction route

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

• conformation of the MeO groups, making the conjugation of the MeO groups ineffective, thus resulting in the lowering of both HOMO and LUMO energy levels. Concerning the twisting, the effect to the HOMO and LUMO energy levels was found to be small. We anticipate that the impact of diverse substituents and

• on DFT calculations. Theoretical calculations DFT calculations were performed to clarify the reasons for the oxidation potentials [52][54][56]. To investigate the effects of the torsion of the naphthalene moiety and the conformation of the MeO group on the oxidation potential of these materials

• , hypothetical compounds DBC-H(56°)-1 and DBC-H(56°)-2 were created, respectively. In DBC-H(56°)-1, the atoms are fixed except for the Me group of DBC-Me (torsion angle = 56.5°), and the Me group is changed to H. DBC-H(56°)-2 is the same structure as DBC-H(56°)-1 except for the MeO group conformation

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

• conformation of peptoid amide bonds is generally much more populated, leading to substantial conformational heterogeneity [16]. Thus, adoption of well-defined secondary structures requires fine control of backbone amide isomerism. Considerable efforts have been made to regulate the conformation of peptoids

• crystal structure of dimer 2 confirms the trans geometry of the two amide bonds (Figure 3A). The unit cell contains eight molecules, including two groups of four identical molecules (Figure 3B), the conformation of the first group (conformation A, Table 2) being the mirror image of that observed for the

• second group of molecules (conformation B). In the crystal lattice, each molecule establishes four intermolecular CO···HN hydrogen bonds. Only the inter-residue carbonyl (oxygen atom labeled O2, Figure 3C) participates in this network, making two hydrogen bonds with two different molecules and different

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

• °C (Scheme 2). It is known that there are two possible tautomeric forms of each hydroxamic acid: the keto and enol tautomer. Furthemore, each tautomer can adopt an E or Z conformation (Figure 2) [32][33][34][35][36]. The results of NMR spectra and theoretical calculations showed that hydroxamic acids