Regio- and stereochemical stability induced by anomeric and gauche effects in difluorinated pyrrolidines

• Ana Flávia Candida Silva,
• Francisco A. Martins and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2024, 20, 1572–1579, doi:10.3762/bjoc.20.140

• conformation. Consequently the introduction of a second fluorine atom with an appropriate relative configuration was thought to reinforce and establish a predominant conformation. Theoretical levels that closely approximated the CCSD outcome included B3LYP-D3BJ/6-311++G**, B3LYP-D3BJ/DGTZVP, and ωB97XD/DGTZVP

Primary amine-catalyzed enantioselective 1,4-Michael addition reaction of pyrazolin-5-ones to α,β-unsaturated ketones

• Pooja Goyal,
• Akhil K. Dubey,
• Raghunath Chowdhury and
• Amey Wadawale

Beilstein J. Org. Chem. 2024, 20, 1518–1526, doi:10.3762/bjoc.20.136

• on a 1 mmol scale under the optimized reaction conditions (Scheme 4). The product 3aa was isolated in slightly lower yield and similar enantioselectivity compared to the 0.2 mmol scale reaction. Subsequently, we turned our attention to determine the absolute configuration of the newly formed chiral

• crystallography data of ent-3ba (Figure 2) [37]. The stereochemistry of the products in this series was assigned by analogy. Based on the observed absolute configuration of product ent-3ba and preceding literature reports [38][40], a plausible mechanistic pathway is outlined in Scheme 5. Initially, in the

Towards an asymmetric β-selective addition of azlactones to allenoates

• Behzad Nasiri,
• Ghaffar Pasdar,
• Paul Zebrowski,
• Katharina Röser,
• David Naderer and
• Mario Waser

Beilstein J. Org. Chem. 2024, 20, 1504–1509, doi:10.3762/bjoc.20.134

• residual water during column chromatography. Unfortunately, attempts to assign the absolute configuration of products 5 failed, as we have not been able to obtain any crystals suited for single crystal X-ray diffraction analysis. Finally, we also tested the suitability of products 5 to access acyclic α-AA

Bioinformatic prediction of the stereoselectivity of modular polyketide synthase: an update of the sequence motifs in ketoreductase domain

• Changjun Xiang,
• Shunyu Yao,
• Ruoyu Wang and
• Lihan Zhang

Beilstein J. Org. Chem. 2024, 20, 1476–1485, doi:10.3762/bjoc.20.131

• substrate contains an α-substition. Subtype 1 (A1, B1, and C1) KRs retain the original α-ᴅ-configuration, while subtype 2 (A2, B2, and C2) KRs epimerize the α-carbon to yield α-ʟ-configured products (Figure 1b). The stereocontrol of KR has been found to correlate with several conserved sequence motifs

• ] PKS cannot be accurately predicted due to the absence of both the LDD and W motifs. Moreover, KR3 of neaumycin B [14], KR19 of caniferolide A [15], KR16 of epemicin B [16], and KR26 of gargantulide B [17] show discrepancies between bioinformatic prediction and the determined product configuration

• been investigated in several DH domains, which all follow the syn-elimination mechanism [5][21][33]. Based on the product configuration, we classified DHs into two types, E-type DHs (trans-double bond) and Z-type DHs (cis-double bond) and analyzed sequence logos of the DH-associated KRs. The sequence

Rapid construction of tricyclic tetrahydrocyclopenta[4,5]pyrrolo[2,3-b]pyridine via isocyanide-based multicomponent reaction

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

Beilstein J. Org. Chem. 2024, 20, 1436–1443, doi:10.3762/bjoc.20.126

• produced in the reaction, while the other diastereomers were not detected. In order to elucidate the relative configuration of the obtained compounds, the molecular structure of the compound 4a was determined by single crystal X-ray diffraction (Figure 1). From Figure 1, it can be seen that the fused

• that all tricyclic compounds have this kind of relative configuration on the basis of NMR spectra and single crystal structure. In order to develop the scope of the reaction, another kind of 5,6-unsubstituted 1,4-dihydropyridines 5 were also employed in the reaction, which were previously prepared from

• -position of the o-methoxyphenyl group. Therefore, compound 6g has the same relative configuration to that of the above mentioned product 3a, which also indicated that this reaction has same steric controlling effect. A plausible reaction mechanism is proposed in Scheme 1 to explain the formation of the

Computation-guided scaffold exploration of 2E,6E-1,10-trans/cis-eunicellanes

• Zining Li,
• Sana Jindani,
• Volga Kojasoy,
• Teresa Ortega,
• Erin M. Marshall,
• Khalil A. Abboud,
• Sandra Loesgen,
• Dean J. Tantillo and
• Jeffrey D. Rudolf

Beilstein J. Org. Chem. 2024, 20, 1320–1326, doi:10.3762/bjoc.20.115

• -eunicellane skeletons, respectively. Although the structures of these diterpenes only differed in their configuration at a single position, C1, they displayed distinct chemical and thermal reactivities. Here, we used a combination of quantum chemical calculations and chemical transformations to probe their

• family members in bacteria and plants [4], these diterpenoids have four main structural differences: the number and location of oxidized carbons, the absence or presence of transannular ether bridges, the configuration (cis or trans) of the bicyclic ring fusion, and the presence and configuration (E or Z

• (1) [6]. In 1, the C2–C3 and C6–C7 alkenes are E-configured, with the latter alkene configuration being conserved in all known eunicellane cyclization mechanisms. The first trans-eunicellane synthase, AlbS from the biosynthesis of albireticulone in Streptomyces albireticuli [10], was also identified

Enhancing structural diversity of terpenoids by multisubstrate terpene synthases

• Min Li and
• Hui Tao

Beilstein J. Org. Chem. 2024, 20, 959–972, doi:10.3762/bjoc.20.86

• analogues 80 and 81 with shifted double bonds were synthesized to study the stereochemistry and cyclization mechanism of casbene synthase (CS) from the castor bean (Ricinus communis), which indicated a stereochemical course in accordance with the reported absolute configuration of casbene [41] (Figure 6b

Enantioselective synthesis of β-aryl-γ-lactam derivatives via Heck–Matsuda desymmetrization of N-protected 2,5-dihydro-1H-pyrroles

• Arnaldo G. de Oliveira Jr.,
• Martí F. Wang,
• Rafaela C. Carmona,
• Danilo M. Lustosa,
• Sergei A. Gorbatov and
• Carlos R. D. Correia

Beilstein J. Org. Chem. 2024, 20, 940–949, doi:10.3762/bjoc.20.84

• upward, therefore creating an asymmetric center with absolute configuration (R), in accordance with experimental results. A rationalization for the transition state that would lead to the observed outcome is depicted in Figure 2. Conclusion The palladium-catalyzed Heck–Matsuda desymmetrization of N

Confirmation of the stereochemistry of spiroviolene

• Yao Kong,
• Yuanning Liu,
• Kaibiao Wang,
• Tao Wang,
• Chen Wang,
• Ben Ai,
• Hongli Jia,
• Guohui Pan,
• Min Yin and
• Zhengren Xu

Beilstein J. Org. Chem. 2024, 20, 852–858, doi:10.3762/bjoc.20.77

• the 9-organoborane intermediate IM-16 probably through borane–olefin complexes. The suprafacial nature of the boron migration allowed the boron to be α-oriented in intermediate IM-16, which would give 10 with retention of the configuration after NaOH/H2O2 oxidation. The formation of a significant

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 acetal in 3 and 6 to the neighbouring C4-position (Figure 1) [19][20]. A variety of products were reported resulting from fluorination as well as the skeletal rearrangement, with the reaction outcome highly substrate-dependent. A key finding in this work was that the configuration of the alcohol

• Diels–Alder adducts of 1, and similar results on the effect of configuration were observed [21]. During some recent attempts at the chlorination of the π-stacking chiral auxiliary 10a using SOCl2 [9], we observed the migration of O8 resulting in the formation of anomeric chlorides analogous to the

• the glycosidic bond using an organometallic purine or pyrimidine derivative and an electrophilic furanose derivative [23][25]. This process can result in anomeric mixtures, so 5 has potential applications in targeted synthesis, as the configuration of the pseudo-anomeric centre matches the common

Discovery and biosynthesis of bacterial drimane-type sesquiterpenoids from Streptomyces clavuligerus

• Dongxu Zhang,
• Wenyu Du,
• Xingming Pan,
• Xiaoxu Lin,
• Fang-Ru Li,
• Qingling Wang,
• Qian Yang,
• Hui-Min Xu and
• Liao-Bin Dong

Beilstein J. Org. Chem. 2024, 20, 815–822, doi:10.3762/bjoc.20.73

• differences in 13C NMR (ΔδC = 3.3) (Figures S19–S25, Supporting Information File 1) [43]. Moreover, the key correlation observed between H5 and H7 in the ROESY spectrum provides additional support for the β-configuration of this hydroxy group (Figure S26 and Table S7 in Supporting Information File 1). These

• to note that CavA exhibits limited substrate promiscuity, predominantly targeting the drimenol skeleton with minor variations. This selectivity may be attributed to the structural configuration of the enzyme, which appears to be finely tuned to recognize and interact with specific features of the

Methodology for awakening the potential secondary metabolic capacity in actinomycetes

• Shun Saito and
• Midori A. Arai

Beilstein J. Org. Chem. 2024, 20, 753–766, doi:10.3762/bjoc.20.69

• culture conditions. Du et al. identified a new compound (designated ishigamide (10)) as 3-([2E,4E,6E,8E]-13-hydroxytetradeca-2,4,6,8-tetraenamido)propanoic acid and elucidated the biosynthetic machinery (Figure 2c) [43][44][45]. Seo et al. synthesized ishigamide and determined its absolute configuration

Substrate specificity of a ketosynthase domain involved in bacillaene biosynthesis

• Zhiyong Yin and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2024, 20, 734–740, doi:10.3762/bjoc.20.67

• structure of this intermediate as N-((S)-α-hydroxyisocaproyl)-γ-aminobutanoyl-S-ACP and also demonstrate that BaeJ-KS2 is not sensitive towards an inversion of the configuration in the α-hydroxyisocaproate moiety. This finding is in agreement with the phylogenetic analysis of KS domains from trans-AT PKSs

Genome mining of labdane-related diterpenoids: Discovery of the two-enzyme pathway leading to (−)-sandaracopimaradiene in the fungus Arthrinium sacchari

• Fumito Sato,
• Terutaka Sonohara,
• Shunta Fujiki,
• Akihiro Sugawara,
• Yohei Morishita,
• Taro Ozaki and
• Teigo Asai

Beilstein J. Org. Chem. 2024, 20, 714–720, doi:10.3762/bjoc.20.65

• and absolute configuration of 1, we assumed this compound could be a biosynthetic precursor of myrocins. In the flanking regions of AsPS and AsCPS, genes encoding oxidoreductases such as cytochrome P450 are present. These genes might be involved in the oxidation of 1 in the biosynthesis of myrocins. A

SOMOphilic alkyne vs radical-polar crossover approaches: The full story of the azido-alkynylation of alkenes

• Julien Borrel and
• Jerome Waser

Beilstein J. Org. Chem. 2024, 20, 701–713, doi:10.3762/bjoc.20.64

• azides substituted with heteroaryls such as thiophene (4i) or a bromofuran (4j) were obtained in 62% and 54% yield, respectively. When the azido-alkynylation was carried out on 1,2-dihydronaphthalene, 4k could be obtained in 71% yield and 3.8:1 dr. As expected, the configuration of the major

New variochelins from soil-isolated Variovorax sp. H002

• Jabal Rahmat Haedar,
• Aya Yoshimura and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2024, 20, 692–700, doi:10.3762/bjoc.20.63

• Na2SO4 and concentrated in vacuo. The samples were redissolved in acetone, and then injected into the aforementioned GC–MS system. Determination of amino acid configuration by Marfey’s method A 100 µg portion of each compound (3–5) was hydrolyzed with 6 M HCl at 110 °C overnight. The lyophilized

Evaluation of the enantioselectivity of new chiral ligands based on imidazolidin-4-one derivatives

• Jan Bartáček,
• Karel Chlumský,
• Jan Mrkvička,
• Lucie Paloušová,
• Miloš Sedlák and
• Pavel Drabina

Beilstein J. Org. Chem. 2024, 20, 684–691, doi:10.3762/bjoc.20.62

• depends on the relative configuration of the ligand used; cis-configuration of ligand affords the nitroaldols with major enantiomer S- (up to 97% ee), whereas the application of ligands with trans-configuration led to nitroaldols with major R-enantiomer (up to 96% ee). The “proline-type” ligand IV was

• group). The copper complex bearing a ligand with trans-trans configuration (Ia) is less enantioselective than those bearing a bidentate ligand analogue (87–96% ee, see [5]). Interestingly, the introduction of a methyl group at position 2 of the imidazolidin-4-one ring, i.e., ligand IIa, led to an

• improvement of enantioselectivity and the ee values obtained by its copper(II) complex were satisfactory (75–96%). This phenomenon was more distinct in the case of the application complexes of ligands with cis-trans configuration (Ib vs IIb). Whilst the complex of Ib exhibited only poor enantioselectivity

Isolation and structure determination of a new analog of polycavernosides from marine Okeania sp. cyanobacterium

• Kairi Umeda,
• Naoaki Kurisawa,
• Ghulam Jeelani,
• Tomoyoshi Nozaki,
• Kiyotake Suenaga and
• Arihiro Iwasaki

Beilstein J. Org. Chem. 2024, 20, 645–652, doi:10.3762/bjoc.20.57

• from a marine Okeania sp. cyanobacterium. The relative configuration was elucidated primarily by analyzing the two dimensional nuclear magnetism resonance (2D NMR) data. The absolute configuration was clarified by comparing the electronic circular dichroism (ECD) data of 1 with those of known analogs

• formula of 1 and the chemical shifts of known polycavernosides, we established the presence of a THP ring containing C-3 to C-7 and a THF ring containing C-10 to C-13 in the macrolide structure. Consequently, we established the planar structure of 1, as shown in Figure 2. The relative configuration of

• compound 1 was determined based on the NMR data obtained in CD3OD and CDCl3 (Table 1 and Table 2). The relative configuration of the THP ring and the disaccharide moiety of 1 was determined by analyzing the proton coupling constants and NOESY correlations (Figure 3). The two coupling constants in CD3OD

Chemical and biosynthetic potential of Penicillium shentong XL-F41

• Ran Zou,
• Xin Li,
• Xiaochen Chen,
• Yue-Wei Guo and
• Baofu Xu

Beilstein J. Org. Chem. 2024, 20, 597–606, doi:10.3762/bjoc.20.52

• unusual methyl modification at the oxygen atom of the typical succinimide ring, a feature not seen in the structurally similar brocaeloid D. Additionally, shentonin A (1) exhibits a cis relationship between H-3 and H-4, as opposed to the trans configuration in brocaeloid D, suggesting a divergent

• correlations linking three different fragments. Compound 1 features three stereogenic centers at C-2, C-3, and C-16. The relative configuration of C-2 and C-3 was determined as (2R*,3R*) by 1H-1H NOESY correlations (Figure 3), while the relative configuration of C-16 remains unresolved due to the

• inapplicability of the NOESY experiment. To establish the absolute configuration of compound 1, electron circular dichroism (ECD) calculations were conducted using the time-dependent density functional theory (TDDFT) approach at a B3LYP/6-311G (d,p) (IEFPCM) level (Figure 4). Considering the uncertainty of the

Possible bi-stable structures of pyrenebutanoic acid-linked protein molecules adsorbed on graphene: theoretical study

• Yasuhiro Oishi,
• Motoharu Kitatani and
• Koichi Kusakabe

Beilstein J. Org. Chem. 2024, 20, 570–577, doi:10.3762/bjoc.20.49

• stable configuration (conformation 1) in a straight form on graphene. There is at least one metastable bent configuration (conformation 2) on the potential energy surface. Besides, the reaction barrier of the conformational change of the PASE was determined. In this paper, we further examine a reaction

• PASE on graphene [3][4]. The protein and pyrene are connected via an alkyl chain. The atomic configuration of this alkyl chain is believed not to be largely affected by the substitution of the succinimidyl group with an amino group. On the other hand, proteins alone do not readily form adsorbed

Synthesis of photo- and ionochromic N-acylated 2-(aminomethylene)benzo[b]thiophene-3(2Н)-ones with a terminal phenanthroline group

• Vladimir P. Rybalkin,
• Sofiya Yu. Zmeeva,
• Lidiya L. Popova,
• Irina V. Dubonosova,
• Olga Yu. Karlutova,
• Oleg P. Demidov,
• Alexander D. Dubonosov and
• Vladimir A. Bren

Beilstein J. Org. Chem. 2024, 20, 552–560, doi:10.3762/bjoc.20.47

• vibrations of the thiophene and amide carbonyl groups were observed at 1663–1678 and 1705–1713 cm−1, respectively. The 1H NMR spectra contained signals of methine protons (=CH–) in the region 7.92–9.02 ppm, which corresponded to the Z-configuration of the C=C bond. According to data previously obtained [14

Switchable molecular tweezers: design and applications

• Pablo Msellem,
• Maksym Dekthiarenko,
• Nihal Hadj Seyd and
• Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

A new analog of dihydroxybenzoic acid from Saccharopolyspora sp. KR21-0001

• Rattiya Janthanom,
• Yuta Kikuchi,
• Hiroki Kanto,
• Tomoyasu Hirose,
• Arisu Tahara,
• Takahiro Ishii,
• Arinthip Thamchaipenet and
• Yuki Inahashi

Beilstein J. Org. Chem. 2024, 20, 497–503, doi:10.3762/bjoc.20.44

• 129.4) and C-10 through a sulfur atom. Based on these results, the structure of 1 was elucidated as 4-((2-acetamido-2-carboxyethyl)thio)-2,3-dihydroxybenzoic acid. The absolute configuration of 1 was determined by advanced Marfey’s analysis. 1 was de-sulfurized with skeletal Ni and then hydrolyzed with

• HCl. The obtained amino acid (alanine) and authentic amino acids were modified using Nα-(5-fluoro-2,4-dinitrophenyl)-ᴅ-leucinamide (ᴅ-FDLA). The LC–MS analysis of ᴅ-FDLA derivatives revealed that the chiral center of the amino acid in 1 had ʟ configuration (Figure S7, Supporting Information File 1

• Saccharopolyspora. Only bootstrap values above 50% (percentages of 1000 replications) are shown. Structure of KR21-0001A (1). (a) 1H,1H COSY and HMBC correlations and (b) absolute configuration. Fermentation of Saccharopolyspora sp. KR21-0001 and isolation procedure of KR21-0001A (1). NMR spectroscopic data of KR21

Pseudallenes A and B, new sulfur-containing ovalicin sesquiterpenoid derivatives with antimicrobial activity from the deep-sea cold seep sediment-derived fungus Pseudallescheria boydii CS-793

• Zhen Ying,
• Xiao-Ming Li,
• Sui-Qun Yang,
• Hong-Lei Li,
• Xin Li,
• Bin-Gui Wang and
• Ling-Hong Meng

Beilstein J. Org. Chem. 2024, 20, 470–478, doi:10.3762/bjoc.20.42

• the HMBC correlation from H-14 to C-8, as well as the molecular formula combined with chemical shifts (δC 35.9, CH2-14, and δC 45.8, CH-8) [12]. Furthermore, HMBC correlations from the protons of methoxy to C-2 attached the methoxy group to C-2. The relative configuration of compound 1 was determined

• verified by the COSY and HMBC correlations (Figure 2). The structure and relative configuration of compound 2 were deduced the same as for 1 by NOE correlations (Figure 3). Moreover, the absolute configurations of compound 2 were unambiguous determined by X-ray diffraction with the refined Flack parameter

• should be mentioned that compound 3 was the first sulfur-containing ovalicin sesquiterpenoid, which was previously isolated from Sporothrix sp. FO-4649, but its absolute configuration was not explicitly represented, and their 1H and 13C NMR data were incomplete [10]. Thus, a full assignment of the NMR

(E,Z)-1,1,1,4,4,4-Hexafluorobut-2-enes: hydrofluoroolefins halogenation/dehydrohalogenation cascade to reach new fluorinated allene

• Nataliia V. Kirij,
• Andrey A. Filatov,
• Yurii L. Yagupolskii,
• Sheng Peng and
• Lee Sprague

Beilstein J. Org. Chem. 2024, 20, 452–459, doi:10.3762/bjoc.20.40

• all cases, except the reaction in diglyme (Table 1, entry 5), a mixture of (E)- and (Z)-2-bromo-1,1,1,4,4,4-hexafluorobut-2-enes (3a,b) in a ratio of 2:1 was formed. The configuration of the isomers was determined by the 5JFFcis coupling constant in the 19F{H} NMR spectrum (ca. 0 Hz for (Z)-isomer and

• distillation in 52% yield for 6a,b and 34% yield for 7a,b. NMR analysis showed the mixtures of (E)- and (Z)-isomers in both cases with the ratio E/Z = ≈4:5 for 6a,b and E/Z = ≈1:2 for 7a,b. The configuration of the isomers was determined by the 5JFFcis coupling constant in the 19F{H} NMR spectrum (ca. 0 Hz for

• column 7a was isolated in 67% yield. The 19F{1H} NMR spectra of 7a, showed the coupling constant of CF3 and CF3 to be 11.3 Hz, suggesting strongly that product 7a like the original silane 8 has (E)-configuration. Although some olefins presented above were obtained several decades ago, there was almost no