Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines

• Vladimir Kubyshkin

Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151

• trifluoromethyl- or a difluoromethylene group. This orientation of the substituents explains the observed trends in the pKa values, lipophilicity, and the kinetics of the amide bond rotation. The study also provides a set of evidences that the transition state of the amide-bond rotation in peptidyl-prolyl favors

• the direction of the carbonyl bond (see Figure S1 in Supporting Information File 1 for the estimation of dipole size and orientation). A proline residue is surrounded by two such dipoles originated from the up- and downstream peptide bonds. The strength of the dipoles can be estimated as 4–5 D. A

• stereoelectronic (C–F) and steric (C–CF3) effects from the substituents. Acid–base transition The orientation of the substituents can also be inferred from the data on basicity of the ammonium group in free amino acids. It has been already mentioned that both, C–F and CF3 groups introduce dipoles of similar sizes

Synthesis of the tetrasaccharide repeating unit of the O-specific polysaccharide of Azospirillum doebereinerae type strain GSF71^T using linear and one-pot iterative glycosylations

• Arin Gucchait,
• Pradip Shit and
• Anup Kumar Misra

Beilstein J. Org. Chem. 2020, 16, 1700–1705, doi:10.3762/bjoc.16.141

• Azospirillum rely on capsular and O-specific polysaccharides present in the bacteria cell wall [12]. Due to their structural orientation, cell-wall polysaccharides play a pivotal role in the initial stage of the host–microbes interactions and colonization of rhizobacteria in the plant roots [13]. Therefore, it

Antibacterial scalarane from Doriprismatica stellata nudibranchs (Gastropoda, Nudibranchia), egg ribbons, and their dietary sponge Spongia cf. agaricina (Demospongiae, Dictyoceratida)

• Cora Hertzer,
• Stefan Kehraus,
• Nils Böhringer,
• Fontje Kaligis,
• Robert Bara,
• Dirk Erpenbeck,
• Gert Wörheide,
• Till F. Schäberle,
• Heike Wägele and
• Gabriele M. König

Beilstein J. Org. Chem. 2020, 16, 1596–1605, doi:10.3762/bjoc.16.132

• (δ 4.81 d, J = 12.9 Hz) and H3-25 (δ 0.98 s), and between H3-25 and H-19 (δ 5.24 d, J = 4.4 Hz), indicated that these protons share the same orientation on the molecular plane. The chemical shifts of the angular methyl groups CH3-23 (δ 14.0) and CH3-25 (δ 16.1) suggested that all ring junctions are

• trans [58][59][60]. This was supported by NOESY cross peaks between H-22b (δ −0.06 brt, J = 4.8 Hz) and H-5 (δ 0.92 m), angular methines H-5 and H-9 (δ 1.01 s), H-9 and H-14 (δ 1.40 brt, J = 8.5 Hz), and between H-14 and H-18 (δ 2.15 m), from which a shared α-orientation can be inferred. Moreover, the

One-step route to tricyclic fused 1,2,3,4-tetrahydroisoquinoline systems via the Castagnoli–Cushman protocol

• Aleksandar Pashev,
• Nikola Burdzhiev and
• Elena Stanoeva

Beilstein J. Org. Chem. 2020, 16, 1456–1464, doi:10.3762/bjoc.16.121

• C-1 acquired a spatial orientation with a smaller steric repulsion with H-11. Based on the data outlaid above the assignment of the preferred conformation of the acids trans- and cis- 21–24 posed significant challenge. Reactions of 1-alkyl-3,4-dihydroisoquinolines 19 and 20 with anhydrides 5–8 The

Disposable cartridge concept for the on-demand synthesis of turbo Grignards, Knochel–Hauser amides, and magnesium alkoxides

• Mateo Berton,
• Kevin Sheehan,
• Andrea Adamo and
• D. Tyler McQuade

Beilstein J. Org. Chem. 2020, 16, 1343–1356, doi:10.3762/bjoc.16.115

• construction, pressure tolerance, heat conduction, and diameter/particle size matching; (3) the column orientation and setup–filters, etc.; (4) activation of the solid phase. The activation issue is one of the most important factors when considering the metal packing. Although our team had success with zinc

Highly selective Diels–Alder and Heck arylation reactions in a divergent synthesis of isoindolo- and pyrrolo-fused polycyclic indoles from 2-formylpyrrole

• Carlos H. Escalante,
• Eder I. Martínez-Mora,
• Carlos Espinoza-Hicks,
• Alejandro A. Camacho-Dávila,
• Fernando R. Ramos-Morales,
• Francisco Delgado and
• Joaquín Tamariz

Beilstein J. Org. Chem. 2020, 16, 1320–1334, doi:10.3762/bjoc.16.113

• . Accordingly, the R2 substituent in the diene would play an important role in directing the endo/exo orientation of the approach to the maleimide at the transition state (TS). Therefore, the endo diastereoselectivity is apparently not controlled by the presence or the absence of the substituent bonded to the

[3 + 2] Cycloaddition with photogenerated azomethine ylides in β-cyclodextrin

• Margareta Sohora,
• Leo Mandić and
• Nikola Basarić

Beilstein J. Org. Chem. 2020, 16, 1296–1304, doi:10.3762/bjoc.16.110

• @3@β-CD, compared to AN@2@β-CD. Namely, the adamantane is a bulky moiety that occupies most of the space in the inclusion complex 3@β-CD, making formation of the ternary complex less likely. Furthermore, if AN@3@β-CD was formed, photogenerated 3AMY@β-CD may not be in the right orientation for the

Ferrocenyl-substituted tetrahydrothiophenes via formal [3 + 2]-cycloaddition reactions of ferrocenyl thioketones with donor–acceptor cyclopropanes

• Grzegorz Mlostoń,
• Mateusz Kowalczyk,
• André U. Augustin,
• Peter G. Jones and
• Daniel B. Werz

Beilstein J. Org. Chem. 2020, 16, 1288–1295, doi:10.3762/bjoc.16.109

• molecular structures of cis-9c and trans-9d drawn using 50% probability displacement ellipsoids. The terminology cis and trans referred to the relative orientation of Ph and Fc groups. Synthesis of spirotetrahydrothiophenes 3 via non-concerted [3 + 2]-cycloadditions of thiocarbonyl ylide 1 with electron

Synthesis, antiinflammatory activity, and molecular docking studies of bisphosphonic esters as potential MMP-8 and MMP-9 inhibitors

• Abimelek Cortes-Pacheco,
• María Adelina Jiménez-Arellanes,
• Francisco José Palacios-Can,
• José Antonio Valcarcel-Gamiño,
• Rodrigo Said Razo-Hernández,
• María del Carmen Juárez-Vázquez,
• Adolfo López-Torres and
• Oscar Abelardo Ramírez-Marroquín

Beilstein J. Org. Chem. 2020, 16, 1277–1287, doi:10.3762/bjoc.16.108

• was pointing away from the zinc ion [39]. The calculated distances from the Zn2+ ion and the different sites at the ligand and the protein are summarized in Table 5. The zinc chelation in MMP-9 occurred in a different way. The predicted orientation of the histidine residues at the catalytic site were

• of the phosphonate moieties, while 5 and 6 had interactions through the C=O oxygen atom of the ester group. Because the interactions of the benzyl group of 5 and 6, respectively, with the Phe110 residue present at the catalytic site through π–π interactions are possible, the orientation of the

A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA

• Ekaterina A. Bryushkova,
• Erik R. Gandalipov and
• Julia V. Nuzhina

Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100

• ; lane 2: assembled SDFS; lanes 3–7: strands T1–T5, respectively. F) An initial 60-nt fragment of AR mRNA (60-AR_RNA); color lines indicate the possible orientation of the SDFS chains around the RNA structure; red arrows with dotted loops indicate the assumed cleavage sites. G) A short 27-nt fragment

Synthesis of esters of diaminotruxillic bis-amino acids by Pd-mediated photocycloaddition of analogs of the Kaede protein chromophore

• Esteban P. Urriolabeitia,
• Pablo Sánchez,
• Alexandra Pop,
• Cristian Silvestru,
• Eduardo Laga,
• Ana I. Jiménez and
• Carlos Cativiela

Beilstein J. Org. Chem. 2020, 16, 1111–1123, doi:10.3762/bjoc.16.98

• ) and the (E)-configuration of the styryl moiety (C11–C12) are clearly seen, thus confirming the results obtained in solution. It is worth noting the orientation of the chlorine atom Cl1, which is syn with respect to the benzylidene proton. This orientation minimizes steric repulsions in the molecule

• conclusions can be drawn from the analysis of the 13C NMR spectra, where the presence of the PdC6H3R–C(H)= group is clear. Therefore, the orientation of the C–H activation in these 4-aryliden-2-styryl-oxazolones is exactly the same as that observed for the 4-aryliden-2-aryloxazolones [28][29][30][56]. Signals

• mounted at the end of a quartz fiber in a random orientation, covered with perfluorinated oil (magic oil) (2c) or paratone oil (4a) on MiTeGen microMounts cryoloop and placed under a cold stream of nitrogen gas. Crystallographic measurements were carried out at 100 K on Bruker Smart APEX CCD (2c) or

Towards triptycene functionalization and triptycene-linked porphyrin arrays

• Gemma M. Locke,
• Keith J. Flanagan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2020, 16, 763–777, doi:10.3762/bjoc.16.70

• -linked porphyrin dimers as they exhibit high fluorescence emissions. Owing to the orthogonal orientation of the two porphyrins, distinct signals were also observed for the meso–meso-linked dimer 19. The effects of an orthogonal arrangement of the two subunits meso–meso-linked porphyrin dimers is well

Synthesis of organic liquid crystals containing selectively fluorinated cyclopropanes

• Zeguo Fang,
• Nawaf Al-Maharik,
• Peer Kirsch,
• Matthias Bremer,
• Alexandra M. Z. Slawin and
• David O’Hagan

Beilstein J. Org. Chem. 2020, 16, 674–680, doi:10.3762/bjoc.16.65

• . Notably for both the axial and equatorial conformers, the orientation of the CF2 group, and therefore its dipole, remains perpendicular to the long molecular axis (requirement for +ve dielectric). A similar result was obtained for stereoisomer 11b (see Supporting Information File 1) again with the first

• axial conformer at ΔG = +1.14 kcal/mol−1 above the ground state equatorial conformer. In this case the orientation of the CF2 group, and therefore the dipole, remains perpendicular to the long molecular axis (requirement for −ve dielectric) for both the axial and equatorial conformers. This analysis

Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition

• Sivaraman Balasubramaniam,
• Sajith Vijayan,
• Liam V. Goldman,
• Xavier A. May,
• Kyra Dodson,
• Sweta Adhikari,
• Fatima Rivas,
• Davita L. Watkins and
• Shana V. Stoddard

Beilstein J. Org. Chem. 2020, 16, 628–637, doi:10.3762/bjoc.16.59

• computationally was revealed via experiment to be a better inhibitor than TOI2 and TOI3-rev. The result was observed presumably due to a variation in the binding mode for TOI4 that differs from that of TOI1, TOI2, and TOI3-rev. TOI4 was shown to observe a slightly different orientation of the core heterocyclic

• ring as well as a change in the orientation of the terminal indole ring. It is not clear if this difference in binding mode affected the ability of TOI4 to maintain a higher potency at lower concentrations. However, this observation does raise an interesting question: “Are certain modes of binding more

Synthesis and circularly polarized luminescence properties of BINOL-derived bisbenzofuro[2,3-b:3’,2’-e]pyridines (BBZFPys)

• Ryo Takishima,
• Yuji Nishii,
• Tomoaki Hinoue,
• Yoshitane Imai and
• Masahiro Miura

Beilstein J. Org. Chem. 2020, 16, 325–336, doi:10.3762/bjoc.16.32

• × 10−5 M) and in solid states (dispersed in Fomblin®). ORTEP drawings of 4b and 4c with 50% thermal probability. Hydrogen atoms and solvent molecules are omitted for clarity. Only major orientation of the disordered structure is displayed. The CCDC numbers are 1971471 for (R)-4b and 1971470 for (R)-4c

Formal preparation of regioregular and alternating thiophene–thiophene copolymers bearing different substituents

• Atsunori Mori,
• Keisuke Fujita,
• Chihiro Kubota,
• Toyoko Suzuki,
• Kentaro Okano,
• Takuya Matsumoto,
• Takashi Nishino and
• Masaki Horie

Beilstein J. Org. Chem. 2020, 16, 317–324, doi:10.3762/bjoc.16.31

• head-to-tail (HT) orientation with respect to the substituent at the 3-position are extensively studied to date since they generally show superior performances as materials [1][2][3][4][5][6]. Cross-coupling polymerization catalyzed by a transition metal complex has been recognized as an effective tool

Synthesis of 4-(2-fluorophenyl)-7-methoxycoumarin: experimental and computational evidence for intramolecular and intermolecular C–F···H–C bonds

• Vuyisa Mzozoyana,
• Fanie R. van Heerden and
• Craig Grimmer

Beilstein J. Org. Chem. 2020, 16, 190–199, doi:10.3762/bjoc.16.22

• this F···H interaction. The single crystal X-ray structure and the DFT-optimized structure showed that the fluorinated phenyl ring favors the orientation with the fluorine atom closer to H5 than H3. The X-ray structure also showed the existence of the intermolecular C–F···H–C interaction. Keywords

• a manner that brings the fluorine atom closer to H5 than H3. The same orientation was observed in the DFT-optimized (B3LYP/6-311G) structure. The X-ray data also showed the intermolecular C–F···H–C interactions which, together with other interactions, are resposible for the crystal packing

The use of isoxazoline and isoxazole scaffolding in the design of novel thiourea and amide liquid-crystalline compounds

• Itamar L. Gonçalves,
• Rafaela R. da Rosa,
• Vera L. Eifler-Lima and
• Aloir A. Merlo

Beilstein J. Org. Chem. 2020, 16, 175–184, doi:10.3762/bjoc.16.20

• behavior displayed SmA mesophase. A similar liquid crystal behavior can be seen in amides 19 and 21 where the isomers differ only in the relative orientation of the isoxazoline ring to the amide group, while the amide group in 19 can resonate to the nitrogen atom in the isoxazoline ring, 21 does not. All

Potent hemithioindigo-based antimitotics photocontrol the microtubule cytoskeleton in cellulo

• Alexander Sailer,
• Franziska Ermer,
• Yvonne Kraus,
• Rebekkah Bingham,
• Ferdinand H. Lutter,
• Julia Ahlfeld and
• Oliver Thorn-Seshold

Beilstein J. Org. Chem. 2020, 16, 125–134, doi:10.3762/bjoc.16.14

• match. Mainly, we assumed that re-orientation of the substituent pattern on one or both rings (e.g., re-orientation of the archetypal 3,4,5-trimethoxyphenyl south ring pattern to a 4,5,6-trimethoxyaryl pattern) might be needed to occupy a similar space. A wealth of CDIs have been reported, including

Reversible photoswitching of the DNA-binding properties of styrylquinolizinium derivatives through photochromic [2 + 2] cycloaddition and cycloreversion

• Sarah Kölsch,
• Heiko Ihmels,
• Jochen Mattay,
• Norbert Sewald and
• Brian O. Patrick

Beilstein J. Org. Chem. 2020, 16, 111–124, doi:10.3762/bjoc.16.13

• the differential absorption of linearly polarized light, which was polarized parallel and perpendicular to a reference axis, respectively, thus indicating the orientation of the transition moment of the chromophores relative to the electric field vector of the light [75]. The LD spectrum of DNA-bound

• an aggregation of the molecules along the DNA backbone at very high ligand concentrations. Nevertheless, the CD and LD spectroscopic data revealed at least some specific binding interactions of 4b with DNA that caused a distinct orientation of the aromatic units relative to the host DNA. In

Halogen-bonding-induced diverse aggregation of 4,5-diiodo-1,2,3-triazolium salts with different anions

• Xingyu Xu,
• Shiqing Huang,
• Zengyu Zhang,
• Lei Cao and
• Xiaoyu Yan

Beilstein J. Org. Chem. 2020, 16, 78–87, doi:10.3762/bjoc.16.10

• ], diiodoacetylene [15] and iodo/bromoethynyl moieties [16] have revealed that the XB-donors interacting with XB-acceptors (a nucleophilic region) are in approximately linear orientation. Besides, linearity, tunability and hydrophobicity (features of the XB ) are widely applied in crystal engineering, supramolecular

Synthesis of C-glycosyl phosphonate derivatives of 4-amino-4-deoxy-α-ʟ-arabinose

• Lukáš Kerner and
• Paul Kosma

Beilstein J. Org. Chem. 2020, 16, 9–14, doi:10.3762/bjoc.16.2

• orientation of the anomeric hydroxy group was proven by NOESY correlations between the H-2 proton and both geminal protons of the CH2P unit. A strong NOE was also observed for the upfield-shifted doublet of doublets at 1.71 ppm of the methylene group, which had an additional NOE correlation with the broad

• purification (Scheme 2). The equatorial arrangement of the C-glycosyl linkage was supported from the large value of the coupling constant J1,2 (9.5 Hz), indicating a 1,2-trans orientation of the respective protons. The monomethyl phosphonate ester 9 was then subjected to alkylation reactions in order to allow

Regioselectivity of glycosylation reactions of galactose acceptors: an experimental and theoretical study

• Enrique A. Del Vigo,
• Carlos A. Stortz and
• Carla Marino

Beilstein J. Org. Chem. 2019, 15, 2982–2989, doi:10.3762/bjoc.15.294

• regioselectivities were achieved in favor of the 1→3 products due to the equatorial orientation of the OH-3 group. A molecular modeling approach endorsed this general trend of favoring O-3 substitution, although it showed some failures to explain subtler factors governing the difference in regioselectivity between

Chemical tuning of photoswitchable azobenzenes: a photopharmacological case study using nicotinic transmission

• Lorenzo Sansalone,
• Jun Zhao,
• Matthew T. Richers and
• Graham C. R. Ellis-Davies

Beilstein J. Org. Chem. 2019, 15, 2812–2821, doi:10.3762/bjoc.15.274

• maintains the near-ideal chemical properties of Hecht’s 4FAB chromophores [12][13] (see below). The final synthetic challenge was the installation of a maleimide onto chromophore 2. The original AB photoswitchable probes which were cross-linked to cysteine mutants had amides with a reverse orientation [19

Emission solvatochromic, solid-state and aggregation-induced emissive α-pyrones and emission-tuneable 1H-pyridines by Michael addition–cyclocondensation sequences

• Natascha Breuer,
• Irina Gruber,
• Christoph Janiak and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2019, 15, 2684–2703, doi:10.3762/bjoc.15.262

• excited state [59]. Plotting Stokes shifts Δν̃ against the orientation polarizabilities Δƒ of the respective solvents (Lippert plot) [60] gives a reasonable linear correlation with a moderate fit of r2 = 0.970 (Figure 13). The orientation polarizabilities Δƒ were calculated according to Equation 1 where