(Bio)isosteres of ortho- and meta-substituted benzenes

• H. Erik Diepers and
• Johannes C. L. Walker

Beilstein J. Org. Chem. 2024, 20, 859–890, doi:10.3762/bjoc.20.78

• proposed as ortho-benzene isosteres (Figure 14) [48]. Comparison of selected exit vector parameters obtained from reported crystal structures [48][49] indicates high geometric agreement between the stellane and benzene cores. Substituent distance d, scaffold carbon distance r, and the substituent scaffold

Skeletal rearrangement of 6,8-dioxabicyclo[3.2.1]octan-4-ols promoted by thionyl chloride or Appel conditions

• Martyn Jevric,
• Julian Klepp,
• Johannes Puschnig,
• Oscar Lamb,
• Christopher J. Sumby and
• Ben W. Greatrex

Beilstein J. Org. Chem. 2024, 20, 823–829, doi:10.3762/bjoc.20.74

• the X-ray crystal structures for 11a and 11b allowing for the unambiguous assignment of configuration. The chlorinated product 14 contaminating 11b exhibited a 1H NMR spectrum similar to the starting material 10b, except that the resonance for the H4 methine was shifted from δ 3.60 in 10b to δ 3.90

Production of non-natural 5-methylorsellinate-derived meroterpenoids in Aspergillus oryzae

• Jia Tang,
• Yixiang Zhang and
• Yudai Matsuda

Beilstein J. Org. Chem. 2024, 20, 638–644, doi:10.3762/bjoc.20.56

• conformational change after cyclization would afford the chair-chair conformation of 7 [19]. Supporting Information Supporting Information File 46: Experimental details, analytical data, tables of primer sequences, constructed plasmids, and A. oryzae transformants and figures showing the X-ray crystal

• structures, the biosynthetic pathway, and NMR data and spectra. Acknowledgements We thank Prof. Katsuya Gomi (Tohoku University), Prof. Katsuhiko Kitamoto (University of Tokyo), and Prof. Jun-ichi Maruyama (University of Tokyo) for providing the expression vectors and fungal strain. We are grateful to Dr

Substitution reactions in the acenaphthene analog of quino[7,8-h]quinoline and an unusual synthesis of the corresponding acenaphthylenes by tele-elimination

• Ekaterina V. Kolupaeva,
• Narek A. Dzhangiryan,
• Alexander F. Pozharskii,
• Oleg P. Demidov and
• Valery A. Ozeryanskii

Beilstein J. Org. Chem. 2024, 20, 243–253, doi:10.3762/bjoc.20.24

• , dipyridoacenaphthene chloride dihydrate, its 2:1 complex with 4,6-dichlororesorcinol, and neutral dipyridoacenaphthene as a self-associate were obtained and structurally characterized for the first time. The dominant feature of all crystal structures is the intramolecular NHN hydrogen bonding in combination with π

Using the phospha-Michael reaction for making phosphonium phenolate zwitterions

• Matthias R. Steiner,
• Max Schmallegger,
• Larissa Donner,
• Johann A. Hlina,
• Christoph Marschner,
• Judith Baumgartner and
• Christian Slugovc

Beilstein J. Org. Chem. 2024, 20, 41–51, doi:10.3762/bjoc.20.6

• in these cases (Supporting Information File 1, Figures S54 and S74). Crystal structures The solid-state structures of 2a and 2f were determined by single-crystal X-ray diffraction. The crystals were grown from concentrated solutions in toluene. A representation of the molecular structure of 2a is

Aldiminium and 1,2,3-triazolium dithiocarboxylate zwitterions derived from cyclic (alkyl)(amino) and mesoionic carbenes

• Nedra Touj,
• François Mazars,
• Guillermo Zaragoza and
• Lionel Delaude

Beilstein J. Org. Chem. 2023, 19, 1947–1956, doi:10.3762/bjoc.19.145

• compound 6e belonged to the P21/c space group. A comparison of the C1–S1 and C1–S2 distances recorded in the four crystal structures under scrutiny and those determined previously for 1,3-dimesitylimidazolium-2-dithiocarboxylate (IMes·CS2) and its more saturated analogue SIMes·CS2 showed that the negative

• trends observed on 13C NMR and IR spectroscopies for δ CS2 and ν̃ CS2 and support the hypothesis that the perpendicular arrangement between the CS2− and CCN+ units is retained in solution. Likewise, all the exocyclic C–C and C–N bond lengths in the crystal structures under examination were typical of

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• similar to the one of the initial pose despite the fact that much a smaller part of the GAG is located at the first binding site. Hence a comparison of the binding position of the ligand with both crystal structures (3C9E and 4N8W) were carried out to reveal which binding site is preferred upon the

• reassociation of the ligand (Figure 6). It can be seen that the binding of the ligand to the protein at the end of the sliding in represents a combination of both the binding positions from the crystal structures and the RMSatd score obtained for the two different crystal structures are 4.1 Å and 8.3 Å for 3C9E

• sliding in process was done for the other complexes with their corresponding crystal structures and the one obtained after docking. The ligands’ RMSatd values (Tables S1 and S2 in Supporting Information File 1) show that in the majority of the complexes the final structure is more similar to the crystal

Selectivity control towards CO versus H₂ for photo-driven CO₂ reduction with a novel Co(II) catalyst

• Lisa-Lou Gracia,
• Philip Henkel,
• Olaf Fuhr and
• Claudia Bizzarri

Beilstein J. Org. Chem. 2023, 19, 1766–1775, doi:10.3762/bjoc.19.129

• concentrations of 1a. Photocatalytic CO2 reduction tests with different concentrations of HFIP.a Supporting Information Additional information regarding the instrumentation, structural analyses, and X-ray structures is provided. Crystal structures were deposited in the Cambridge Crystallographic Data Centre

Effects of the aldehyde-derived ring substituent on the properties of two new bioinspired trimethoxybenzoylhydrazones: methyl vs nitro groups

• Dayanne Martins,
• Roberta Lamosa,
• Talis Uelisson da Silva,
• Carolina B. P. Ligiero,
• Sérgio de Paula Machado,
• Daphne S. Cukierman and
• Nicolás A. Rey

Beilstein J. Org. Chem. 2023, 19, 1713–1727, doi:10.3762/bjoc.19.125

• Hirshfeld surfaces and evidence the strong flatness of the structures (Figures S2B and S3B in Supporting Information File 1). Important contributions of hydrogen bonds (O···H/H···O) can also be found, especially for hdz-NO2. Besides the interaction maps, crystal structures themselves may be used to

Benzoimidazolium-derived dimeric and hydride n-dopants for organic electron-transport materials: impact of substitution on structures, electrochemistry, and reactivity

• Swagat K. Mohapatra,
• Khaled Al Kurdi,
• Samik Jhulki,
• Georgii Bogdanov,
• John Bacsa,
• Maxwell Conte,
• Tatiana V. Timofeeva,
• Seth R. Marder and
• Stephen Barlow

Beilstein J. Org. Chem. 2023, 19, 1651–1663, doi:10.3762/bjoc.19.121

• , reacts more rapidly than any of the other dimers with VII via “electron-transfer-first”. Crystal structures show rather long central C–C bonds for 1b2 (1.5899(11) and 1.6194(8) Å) and 1h2 (1.6299(13) Å). Keywords: benzoimidazole; crystal structure; kinetics; n-dopant; reduction; Introduction Electrical

• donors (1gH, 1hH, 1iH). We also report crystal structures of several of these compounds and of several salts of the corresponding 1+ cations, and compare the electrochemistry and reactivity of these species. Results and Discussion Synthesis Although an unsymmetrical 12-like molecule, 2-diethoxyphosphoryl

• acquisition of a 1H NMR spectrum; however, handling under nitrogen is advisable as these species completely decompose to V (and perhaps 1+ species) on timescales of hours to days (see Supporting Information File 1, Figures S3–S5). Crystal structures We have determined the structures of two 12 dimers, four 1H

Synthesis and biological evaluation of Argemone mexicana-inspired antimicrobials

• Jessica Villegas,
• Bryce C. Ball,
• Katelyn M. Shouse,
• Caleb W. VanArragon,
• Ashley N. Wasserman,
• Hannah E. Bhakta,
• Allen G. Oliver,
• Danielle A. Orozco-Nunnelly and
• Jeffrey M. Pruet

Beilstein J. Org. Chem. 2023, 19, 1511–1524, doi:10.3762/bjoc.19.108

• (five Gram-positive and four Gram-negative bacteria, and three fungi). Additionally, the crystal structures of two berberine variants are described. Several berberine variants show enhanced antibacterial activity compared to the unaltered plant-derived molecule. We also report promising preliminary

• with associated standard error (n = 5). Vancomycin, streptomycin, and/or fluconazole were used as positive controls, and solvents were used as negative controls and showed no zones of inhibition. X-ray crystal structures of the oxidation byproducts a) B4 (CCDC 2271457) and b) B6 (CCDC 2271458; one

Functions of enzyme domains in 2-methylisoborneol biosynthesis and enzymatic synthesis of non-natural analogs

• Binbin Gu,
• Lin-Fu Liang and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 1452–1459, doi:10.3762/bjoc.19.104

• diphosphate synthase (FPPS) and 2MIBS from Streptomyces coelicolor [26] (Scheme 1B). Crystal structures of both enzymes have been obtained [27][28] and allowed for a deep structure-based investigation of 2MIBS through site-directed mutagenesis [29]. The predicted amino acid sequences of 2MIBS homologs from

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

• calculations for enaminone synthesis from iodonium ylides and thioamides. Crystal structures of 76c (top) and 76e (bottom) [101], (CCDC# 2104180 & 2104181) [143][144]. Outline of possible reaction pathways between iodonium ylides and Lewis basic nucleophiles (top); and, reaction between 6 and HCl to give 7, as

• found were intermolecular interactions between the lone pairs of either the carbonyl or sulfonyl with the other I–C bond σ* orbital, at energies of 0.70 and 0.29 kcal/mol, respectively. These interactions were presumed to have contributed to the increased stability of such ylides. X-ray crystal

• structures of ylides 76c and 76e confirmed these interactions as intramolecular halogen bonds at lengths of 2.7 Å (Figure 17), and showed intermolecular halogen bonds with iodine’s remaining σ-hole, at bond lengths of 3.3 Å or 3.4 Å. Though the σ-hole syn to the arene was blocked, when these six ylides were

The unique reactivity of 5,6-unsubstituted 1,4-dihydropyridine in the Huisgen 1,4-diploar cycloaddition and formal [2 + 2] cycloaddition

• Xiu-Yu Chen,
• Hui Zheng,
• Ying Han,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2023, 19, 982–990, doi:10.3762/bjoc.19.73

• structures of both bicyclic compounds 5a–o and 6a–o were fully characterized by various spectroscopy methods. The single crystal structures of compounds 5a (Figure 2) and 6f (Figure 3) were successfully determined by X-ray diffraction analysis. From Figure 2 (compound 5a), it can be seen that the

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

• regioselectively at 0 °C, affording the desired π-extended [7]helicene 35 and [9]helicene 37 in 76 and 84% yields, respectively. Single-crystal structures of racemic 35 and 37 revealed the P/M enantiomers repectively, and the P/M racemization barriers of 35 and 37 were determined as 42.4 and 41.6 kcal/mol

Synthesis and reactivity of azole-based iodazinium salts

• Thomas J. Kuczmera,
• Annalena Dietz,
• Andreas Boelke and
• Boris J. Nachtsheim

Beilstein J. Org. Chem. 2023, 19, 317–324, doi:10.3762/bjoc.19.27

• indazole salt 5be was isolated in 30% yield and the benzyl-bridged, seven-membered salt 5bf could not be obtained under our optimized reaction conditions. Single crystal structures of selected salts were obtained to gain a better understanding of the bonding situation and the coordination states in these

• mixture was stirred for 14 d at 65 °C. a6.00 mmol scale, T = 50 °C, bT = 40 °C, cT = 80 °C, t = 6 d, dt = 7 d, e0.3 equiv of DCM were included in the product. Single crystal structures (ORTEP drawing with 50% probability) of the pyrazole-coordinated salt 5bb (dimer, a second structure was omitted for

Inclusion complexes of the steroid hormones 17β-estradiol and progesterone with β- and γ-cyclodextrin hosts: syntheses, X-ray structures, thermal analyses and API solubility enhancements

• Alexios I. Vicatos,
• Zakiena Hoossen and
• Mino R. Caira

Beilstein J. Org. Chem. 2022, 18, 1749–1762, doi:10.3762/bjoc.18.184

• diffraction (SCXRD) were employed for focused studies of the isostructurality of the CD complexes with known complexes and structural elucidation of the new complexes, respectively. SCXRD analyses of β-CD·BES, β-CD·PRO and γ-CD·PRO at 100(2) K yielded the first crystal structures of CD complexes containing

• composition from the residual electron density peaks in the respective crystal structures. We carried out analogous studies on the four CD complexes to establish whether they might also display enhanced aqueous solubilities of the included steroids relative to those of the pure drugs. We also present here

• and DSC results for each sample are available (Section 5, pp. S15 and S16 in Supporting Information File 1). Single crystal X-ray structural analysis The crystal structures of β-CD·BES, β-CD·PRO and γ-CD·PRO were solved by isomorphous replacement using as trial models the rigid host atom frameworks of

1,4,6,10-Tetraazaadamantanes (TAADs) with N-amino groups: synthesis and formation of boron chelates and host–guest complexes

• Artem N. Semakin,
• Ivan S. Golovanov,
• Yulia V. Nelyubina and
• Alexey Yu. Sukhorukov

Beilstein J. Org. Chem. 2022, 18, 1424–1434, doi:10.3762/bjoc.18.148

• 2190361, 2190362, 2190363, 2182991, 2182992, 2182993, 2182994, 2182995, 2183048. Acknowledgements The authors thank Dr. M. E. Minyaev, E. I. Tuzharov, and D. I. Nasyrova from the Department of Structural Studies of N. D. Zelinsky Institute of Organic Chemistry for determination of crystal structures for

Make or break: the thermodynamic equilibrium of polyphosphate kinase-catalysed reactions

• Michael Keppler,
• Sandra Moser,
• Henning J. Jessen,
• Christoph Held and
• Jennifer N. Andexer

Beilstein J. Org. Chem. 2022, 18, 1278–1288, doi:10.3762/bjoc.18.134

• fractions [5][10][15][16]. Based on the crystal structures of three PPK2-III, the coordination of polyP and ADP by positively charged amino acids (lysine and arginine) has been suggested [16][17]. Two magnesium ions are held in place by two conserved aspartate residues that further coordinate the polyP and

Molecular diversity of the base-promoted reaction of phenacylmalononitriles with dialkyl but-2-ynedioates

• Hui Zheng,
• Ying Han,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2022, 18, 991–998, doi:10.3762/bjoc.18.99

• clearly indicated that only one diastereoisomer was actually produced in the reaction. The chemical structures of the compounds 4a–k were established by various spectroscopy methods. Additionally, the single crystal structures of compounds 4a and 4c were successfully determined (Figure 2 and Figure 3

• cyclopent-1-ene ring, the aryl group and the cyano group are in cis-orientation, while the hydroxy group and carboxamide group exist on the other side of the ring. On the basis of the NMR spectra and the single crystal structures, it can be concluded that all the obtained products 4a–k have this kind of

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

• ]. Table 1 summarizes the first and second oxidation potentials based on Fc/Fc+ (Eox1 and Eox2) determined from the SWVs, together with the torsion angles determined from the X-ray crystal structures [52], the HOMO and LUMO levels determined from DFT calculations [52][54] and estimated based on Eox1. The

• (upper graphs) in CH2Cl2 and simulations of absorption based on TD-DFT calculations [lower graphs, TD-B3LYP-D3/6-31G(d,p)//B3LYP/6-31G(d,p)] for DBC derivatives. Electrochemical data, torsion angles determined from the X-ray crystal structures, and HOMO and LUMO levels for DBC derivativesa. Dihedral

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

• by GC/MS analysis and synthesis of reference compounds [29], several of which also occur in Escherichia coli or yeast strains that were engineered for the biosynthesis of methylated monoterpenes derived from 2-Me-GPP [30][31]. About one decade ago, the crystal structures of GPPMT and 2MIBS have been

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

• , regioselective double oxidative photocyclization was observed during the construction of three S-shaped double helicenes DH-1–3 based on thiophene/selenophene. From DH-1 to DH-3, sulfur atoms in the molecular framework were gradually replaced by selenium atoms. The crystal structures of DH-1 and DH-2 and

• corrected for Lorentz and polarization effects, and absorption corrections were performed using the SADABS program [43]. The crystal structures were solved using the SHELXTL program and refined using full-matrix least-squares [44]. Further details are in the deposited CIF files. Slow evaporation of

Copper-catalyzed multicomponent reactions for the efficient synthesis of diverse spirotetrahydrocarbazoles

• Shao-Cong Zhan,
• Ren-Jie Fang,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2022, 18, 796–808, doi:10.3762/bjoc.18.80

• aldehydes that bore different substituents at the ortho- (4c), meta- (4e, 4g) and para-position (4b, 4d, 4f and 4h) of the phenyl ring reacted smoothly to give the corresponding products 4a–h in moderate to good yields with excellent diastereoselectivity (dr > 20:1). The single crystal structures of the

• developed the practical synthetic values of the well-known Levy reaction by using inactivated indole derivatives. The outcome of diastereoselectivity of the reaction was clearly elucidated by determination of the several single crystal structures and the analysis of the reaction mechanism. The experimental

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

• [41][42][43]. Crystal structures of COXs The structural basis for the di-peroxide formation reaction by COXs has been substantially elucidated by electron paramagnetic resonance (EPR), kinetic analysis, X-ray crystallography, and mutagenesis experiments [24][44][45]. The structural analyses of

• debated. COX-like mechanism of FtmOx1 The first crystal structures of FtmOx1 in the apo form and in complex with 2OG were reported in 2015 [68] (this article got retracted [69] in 2021). The overall structure of FtmOx1 exists as a functional homodimer and possesses the double-stranded β-helix (DSBH) fold