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

The stereochemical course of 2-methylisoborneol biosynthesis

• Binbin Gu,
• Anwei Hou and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 818–824, doi:10.3762/bjoc.18.82

• solved [32][33]. Notably, the structure of 2MIBS has been obtained in complex with the non-reactive substrate analog 2-fluoro-GPP (2FGPP), showing the substrate surrogate in a stretched conformation in the active site of 2MIBS (Figure 1A). The observed conformation of 2FGPP, if this is also relevant for

• this sample (<1%). A possible explanation is that (S)-2-Me-LPP can bind to the active site of 2MIBS in a non-productive conformation. Its enzyme assisted isomerization to 2-Me-GPP followed by a conformational change may allow for another isomerization to (R)-2-Me-LPP and thus lead to the observed minor

• isomerization to 2-Me-GPP and then to (R)-2-Me-LPP. Conclusively, these findings confirm Cane’s mechanistic proposal [23], while the observed conformation of 2FGPP in the crystal structure of 2MIBS may not represent the required conformation for 2-Me-GPP for the production of 1. A) Active site of 2MIBS with 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

• orbital-weighted Fukui function is not connected to conformation. In the orbital-weighted Fukui function, the larger the isosurface distribution, the higher the activity of reactions. Thus the 4 and 6-positions of benzene are the most likely sites for reaction (see Supporting Information File 1, Figure

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

• , which is quenched by reductants. The ternary complex structure of FtmOx1 with 2OG and fumitremorgin B was recently reported by Zhou and co-workers [71]. Fumitremorgin B binds in the active site with a planar conformation, through hydrophobic and hydrophilic interactions (Figure 3C). While Tyr68 is

• the substrate. The substrate asnovolin A binds in the closed conformation through a hydrogen bond network with active site residues (Figure 4D). In this binding mode, C7' of the substrate is 4.2 Å away from the iron center, which is shorter than the distance between the iron center and C13 (6.5 Å

• the partially closed conformation, the substrate binding mode in the crystal structure apparently shows a different stage of the reaction. The conformational changes of the loops, especially the flipping of Glu208, would contribute to alterations of the binding mode of the substrate and the long-lived

Synthesis of 3,4,5-trisubstituted isoxazoles in water via a [3 + 2]-cycloaddition of nitrile oxides and 1,3-diketones, β-ketoesters, or β-ketoamides

• Md Imran Hossain,
• Md Imdadul H. Khan,
• Seong Jong Kim and
• Hoang V. Le

Beilstein J. Org. Chem. 2022, 18, 446–458, doi:10.3762/bjoc.18.47

• carbanion I that is solvated by the polar solvent. The carbanion I then adds to the carbon (carbocation) of the nitrile oxide, to give the intermediate II. Due to steric effects, the intermediate II undergoes bond rotation to the lowest-energy conformation II-D in which the methyl group is at a close

Borylated norbornadiene derivatives: Synthesis and application in Pd-catalyzed Suzuki–Miyaura coupling reactions

• Robin Schulte and
• Heiko Ihmels

Beilstein J. Org. Chem. 2022, 18, 368–373, doi:10.3762/bjoc.18.41

• electron-donating or accepting properties of the substituent in this reaction because the methoxy substituent operates as +M donor in the para and ortho-position and as –I acceptor in the meta-position (as well as in the ortho position in a not conjugated conformation). Also, steric effects do not seem to

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

• organic compounds. Within the molecular container, guest molecules can be encapsulated with a certain orientation and conformation through various noncovalent interactions. In this mode, the molecular container can act as reaction template and give rise to selective products. For example, the molecular

• container can be used as anchoring template, which fix the substrate with a certain stable conformation, exposing one specific reactive site to the catalyst and producing site-selective product [25][26]. Moreover, molecular containers have more and more been applied to modulate site-selectivity of different

• the complex solution with three equivalents of PMe3 resulted in the reduction of one of the azide groups. At this stage, the monoamine guest showed a fixed unsymmetrical J-shaped conformation with the amine end exposed and the azide end deeply protected inside the cavitand. The addition of another 3

Diametric calix[6]arene-based phosphine gold(I) cavitands

• Gabriele Giovanardi,
• Andrea Secchi,
• Arturo Arduini and
• Gianpiero Cera

Beilstein J. Org. Chem. 2022, 18, 190–196, doi:10.3762/bjoc.18.21

• macrocyclic cavity. Keywords: 1,2,3-alternate conformation; calix[6]arenes; gold(I) catalysis; phosphines; Introduction One of the latest challenges in supramolecular chemistry is the design and development of novel macrocyclic-based entities able to influence the catalytic activities of the metal center [1

• dictate the position of the metal centers, we reasoned on the possibility to design a novel generation of diametric phosphine gold(I) cavitands exploiting a calix[6]arene scaffold characterized by a 1,2,3-alternate conformation. As working hypothesis, this geometry would segregate two catalytically active

• via conventional protocols using (Me2S)AuCl. Notably, the organometallic macrocycles A,B,C(AuCl)2 could be isolated via column chromatography separation. Gold(I) catalysts were subsequently fully characterized by NMR analysis and high-resolution mass spectrometry. The conformation of the catalysts, in

Synthesis and late stage modifications of Cyl derivatives

• Phil Servatius and
• Uli Kazmaier

Beilstein J. Org. Chem. 2022, 18, 174–181, doi:10.3762/bjoc.18.19

• digest and metabolic processes [3]. Furthermore, cyclization generally helps to fix the active conformation of a peptide needed to interact with the respective cellular target. Incorporation of non-proteinogenic and unusual amino acids often is related to their biological function. For example, trapoxin

Regioselective synthesis of methyl 5-(N-Boc-cycloaminyl)-1,2-oxazole-4-carboxylates as new amino acid-like building blocks

• Jolita Bruzgulienė,
• Greta Račkauskienė,
• Aurimas Bieliauskas,
• Vaida Milišiūnaitė,
• Miglė Dagilienė,
• Gita Matulevičiūtė,
• Vytas Martynaitis,
• Sonata Krikštolaitytė,
• Frank A. Sløk and
• Algirdas Šačkus

Beilstein J. Org. Chem. 2022, 18, 102–109, doi:10.3762/bjoc.18.11

• conformation. The 1,2-oxazole rings occupy equatorial positions at the 2nd atom of the piperidinium ring, and the dihedral angle H(10)–C(10)–C(5)–O(1) is 158°. The methoxycarbonyl group is in the same plane as the 1,2-oxazole ring. The bond lengths and angles of 1,2-oxazole rings are shown in Table 1 which

Efficient and regioselective synthesis of dihydroxy-substituted 2-aminocyclooctane-1-carboxylic acid and its bicyclic derivatives

• İlknur Polat,
• Selçuk Eşsiz,
• Uğur Bozkaya and
• Emine Salamci

Beilstein J. Org. Chem. 2022, 18, 77–85, doi:10.3762/bjoc.18.7

• seen that the conformation is quite appropriate for the formation of lactone 10. The hydrogen bond between the C=O group of methoxy ester and NH group of the carbamate in 7 provides an appropriate conformation for the formation of lactone 10. Additionally, according to the conformational analysis of

• . Our computations demonstrate that the formation of the five-membered lactone is kinetically more favourable, and the formation of six-membered lactone is not feasible under the experimental conditions. The conformation of epoxide 7 is quite appropriate for the formation of the five-membered lactone 10

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

• - instead of 7-bromotryptophan yielded the expected stapled peptide P1a. Next, the secondary structures of the two stapled peptides P1a and P1b were investigated by CD spectroscopy. Unfortunately, both peptides did not show enhanced helical conformation in water. To get more information about the structure

• additional ethylene unit in the linker suggested a conformation with the highest similarity to the linear reference peptide P6 (see Supporting Information File 1), thus representing a good compromise between rigidity and preservation of the target secondary structure. Serine in i-position and glutamic acid

• peptide (i.e., a cumulative total of 10.5 μs per peptide) performed with the ff14SB/GAFF [90][91] and TIP4Pew [91] force field parameters for the peptides and water, respectively, as well as specifically derived parameters for non-standard residues of the linker in stapled peptide P5. The conformation of