Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• . The orientation can be controlled by using, for example, an anti-affinity tag antibody [34] or an NTA surface [35]. Binding to the surface increases the density and the refractive index. Polarised light is irradiated on the surface at an angle around which SPR occurs (resonance angle). The binding

Chiral anion recognition using calix[4]arene-based ureido receptors in a 1,3-alternate conformation

• Tereza Horáčková,
• Jan Budka,
• Vaclav Eigner,
• Wen-Sheng Chung,
• Petra Cuřínová and
• Pavel Lhoták

Beilstein J. Org. Chem. 2020, 16, 2999–3007, doi:10.3762/bjoc.16.249

• same time, the carbonyl groups from the neighbouring receptor urea moieties interacted with the C–H bonds of the DMSO methyl group (the C=O···H–C distances were 2.486 and 2.452 Å), thus forming the calixarene dimer with a head-to-tail mutual orientation. The overall supramolecular binding motif was

Ultrasound-assisted Strecker synthesis of novel 2-(hetero)aryl-2-(arylamino)acetonitrile derivatives

• Emese Gal,
• Luiza Gaina,
• Hermina Petkes,
• Alexandra Pop,
• Castelia Cristea,
• Gabriel Barta,
• Dan Cristian Vodnar and
• Luminiţa Silaghi-Dumitrescu

Beilstein J. Org. Chem. 2020, 16, 2929–2936, doi:10.3762/bjoc.16.242

• enantiomers of the chiral molecular structure in an ordered 1:1 ratio in the elementary cell. The phenothiazine unit shows a quasi-equatorial orientation of the methyl group attached to the heterocyclic nitrogen atom and a folding angle of 143.3°, a value close to the typical folding angle for unsubstituted

Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives

• Jonas Becher,
• Daria V. Berdnikova,
• Heiko Ihmels and
• Christopher Stremmel

Beilstein J. Org. Chem. 2020, 16, 2795–2806, doi:10.3762/bjoc.16.230

• between the sign and pattern of the ICD signal of a quadruplex ligand in orientation relative to the binding site, as is well established for duplex binders [63], is not available for quadruplex ligands, yet. With most quadruplex-bound berberine and berberine derivatives, including compounds 1a–d, ICD

• CD bands with increasing LDR. Insets: Plots of intensity of the ICD signal of the ligand–DNA mixtures (LDR 1.0; 361 nm) for 22AG (A) and a2 (B) versus the alkyl chain lengths n of 4a–e. The simplified structure of the complex between 1e3 and quadruplex DNA (left; [38]) and the proposed orientation of

Easy access to a carbohydrate-based template for stimuli-responsive surfactants

• Thomas Holmstrøm,
• Daniel Raydan and
• Christian Marcus Pedersen

Beilstein J. Org. Chem. 2020, 16, 2788–2794, doi:10.3762/bjoc.16.229

• -responsive lipids [11]. The three compounds reluctance to adopt a 1C4 conformation may be due to a steric clash between the methylene group at C5 and the anomeric substituent when both of these groups are in axial orientation. To further study the scope and versatility of building block 5, we decided to

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

• Rakesh Biswas,
• Surya Ghosh,
• Shubhra Kanti Bhaumik and
• Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

• the nucleotides occurring through multivalent electrostatic interactions in the cavity/cleft created by the spatial orientation of the imidazolium groups. We herein consider a self-assembly based approach in which amphiphilic monomers with bisimidazolium moieties are utilized to create multivalent

Conformational preferences of fluorine-containing agrochemicals and their implications for lipophilicity prediction

• Daniela Rodrigues Silva,
• Joyce K. Daré and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2020, 16, 2469–2476, doi:10.3762/bjoc.16.200

• soil sorption and bioconcentration of organic compounds. Since the C–F bond is the most polar in organic chemistry, the orientation of fluorine substituents originating from the rotation around C–C(F) bonds should affect the polarity and, consequently, the physicochemical and biological properties of

• stereochemical effects of fluorination, responsible for specific interactions and conformational preferences of several groups of compounds, have become increasingly well understood [12], their direct implication on physicochemical properties has not been fully investigated yet. The orientation of fluorine

• employed to describe lipophilicity. It has been previously established that the lipophilicity of a compound depends greatly on the overall molecular polarity [15], which is often expressed as the molecular dipole moment (μ). In turn, the orientation of polar bonds also influences the overall polarity of an

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• adaptability. By allowing to modify colours, sizes, lengths/widths and turn some features on/off, a “sketcher” would allow maximum flexibility to depict carbohydrates in any desired or necessary form, size, orientation. However, this adaptability should become available without hampering the sketching effort

• file or as GlycoCT text. The interface also provides additional options to add, replace or delete each monosaccharide, modify the sizes of symbols and text fonts, and turn off the linkage annotations or change their orientation; all of which increases the usability of the software. The input structure

• monosaccharide by adding substituents and alterations. Free movement of the monosaccharides is allowed through movement and orientation buttons. GlycanBuilder offers multiple options for glycan notation which include CFG, CFG colour, UOXF, UOXF colour and text only. GlycanBuilder can also calculate the masses of

Chan–Evans–Lam N1-(het)arylation and N1-alkеnylation of 4-fluoroalkylpyrimidin-2(1H)-ones

• Viktor M. Tkachuk,
• Oleh O. Lukianov,
• Mykhailo V. Vovk,
• Isabelle Gillaizeau and
• Volodymyr A. Sukach

Beilstein J. Org. Chem. 2020, 16, 2304–2313, doi:10.3762/bjoc.16.191

• analogous enamides [57], the facile [2 + 2] photocycloaddition process likely occurred due to favorable orientation of the interacting molecules and close contacts between alkene carbon atoms in the crystal structure. Consequently, the synthesis of product 5c was performed in darkness. N1-Styryl-substituted

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• binding constants (Table 2) support an intercalative binding of the naphthalene diimide unit in AT-DNAs [26][27], whereby the positive sign of the ICD band (380 nm) supports a perpendicular orientation of the longer axis of the naphthalene diimide in respect to the longer axes of DNA base pairs [13][14

Reactions of 3-aryl-1-(trifluoromethyl)prop-2-yn-1-iminium salts with 1,3-dienes and styrenes

• Thomas Schneider,
• Michael Keim,
• Bianca Seitz and
• Gerhard Maas

Beilstein J. Org. Chem. 2020, 16, 2064–2072, doi:10.3762/bjoc.16.173

• with the expected orientation of the cycloaddition. Cis-annelated cyclobutene 18 (1H NMR: 3JH,H = 3.8 Hz for the angular protons) and the iminium-substituted primary cycloadduct are not expected to undergo a fast ring opening under moderate thermal conditions, because the orbital-symmetry-allowed

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• systems, which recovers a conformational propensity similar to the non-fucosylated, xylosylated A2G2, see Figure 5 and Tables S8 and S10 in Supporting Information File 1. α(1-3)-fucosylated mammalian N-glycans. Because of its orientation tucked “behind” the chitobiose core defined in the context of plants

• specific branching and spatial orientation of the motif allowed for a stable interaction between the arms, which is not observed in complex N-glycans with a linear functionalization of the arms [24]. Notably, the same hydrogen bonding network between the arms cannot be established when the same N-glycan

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

• Annike Weißenstein,
• Myroslav O. Vysotsky,
• Ivo Piantanida and
• Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

• )-polynucleotides. The DNA/RNA binding-induced circular dichroism (ICD) response of NDI at 450–550 nm strongly depended on the length and rigidity of the linker to the amino acid unit, which controls the orientation of the NDI unit inside within the intercalative binding site. The ICD selectivity also depends on

• uniform orientation related to the DNA/RNA chiral axis [49][50]. Furthermore, differences in the ICD response in the wavelength range from 400 to 540 nm were observed between our NDI compounds which were most pronounced upon binding to poly(dG-dC)2 (Figure 7). These simple and rather weak ICD signals

• predominantly a parallel orientation for all dyes as shown in Figure 8 for the DNA–3b complex. The absence of any measurable ICD signal for poly(A)-poly(U) (ds-RNA) (Supporting Information File 1, Figure S26) supports the intercalation of all NDI chromophores at approximately 45° with respect to the base pair

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