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

• the two porphyrin units resulting in very strong electronic coupling, i.e., losing the characteristic of individual units due to delocalization of π-electrons. The Soret bands of the four different conformations of the porphyrins in the butadiyne-linked dimer 20 are barely distinguishable from one

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

• adopt conformations with low overall molecular polarities. A comparison of the Δε for 8 and 9 illustrates that incorporation of the third alpha-fluorine lowers the overall Δε value. This is presumably due to a resulting decrease in the overall molecular dipole moment () along the minor axis. When an

• conformational analysis of 11a (and 11b) was conducted computationally (ωB97X-D/6-311+G(2d,p)//ωB97X-D/6-31G(d) + ZPE level (see Supporting Information File 1)). There are many potential low energy conformations arising from alkyl side chain C–C bond rotations which would not be anticipated to change the overall

p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

• Panagiotis S. Gritzapis,
• Panayiotis C. Varras,
• Nikolaos-Panagiotis Andreou,
• Katerina R. Katsani,
• Konstantinos Dafnopoulos,
• George Psomas,
• Zisis V. Peitsinis,
• Alexandros E. Koumbis and
• Konstantina C. Fylaktakidou

Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33

• aspects of compounds 11 and 12 The ground state structures (S0) for both molecules 12 and 11 in their Z-conformations are similar (Figure S-8.1A and B, Supporting Information File 1) with the length of the N–O bond varying between r(N–O) = 1.423 (12) and 1.425 Å (11). (Table S-8.1, Supporting Information

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

• numerous attempts for obtaining crystals suitable for the X-ray analysis. Based on these observations, it is reasonable to conclude that the tert-butyl substituents effectively restricted the stacking structure to the specific conformations, thereby facilitating the assembly of well-ordered aggregates in

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

• crystal structure and solution-state NMR data of the coumarin 6 were studied to examine any C–F···H–C hydrogen bond interactions. DFT calculations were performed to determine the preferred conformations of the structure that might exhibit a C–F···H–C hydrogen bond. Results and Discussion Synthesis of 2

• these observations (Figure 1 and Figure 3) is that, in solution, rotation of the fluorophenyl ring (about C4–C1’) is permitted but that the average geometry of coumarin 6 has the fluorine atom closer to H5 than H3. The theoretical NMR data for twenty-four conformations of coumarin 6 were obtained from

• calculated 13C NMR chemical shifts for both the optimized and least-stable DFT-generated conformations, the RMSD values were found to be 8.84 ppm and 8.79 ppm, respectively. The RMSD value for the calculated 1H NMR chemical shifts of the optimized conformer was found to be substantially smaller (RMSD = 0.14

Synthesis, liquid crystalline behaviour and structure–property relationships of 1,3-bis(5-substituted-1,3,4-oxadiazol-2-yl)benzenes

• Afef Mabrouki,
• Malek Fouzai,
• Armand Soldera,
• Abdelkader Kriaa and
• Ahmed Hedhli

Beilstein J. Org. Chem. 2020, 16, 149–158, doi:10.3762/bjoc.16.17

• prepared compounds perform three kinds of conformations, A, B and C. The hydrocarbon derivatives exhibit conformation A (Figure 5a–a”), whereas the fluorocarbon analogues adopt, depending on whether they carry linking segment C2H4S or not, the conformation B (Figure 5b–b”) or C (Figure 5c–c”). In Figure 6

Understanding the role of active site residues in CotB2 catalysis using a cluster model

• Keren Raz,
• Ronja Driller,
• Thomas Brück,
• Bernhard Loll and
• Dan T. Major

Beilstein J. Org. Chem. 2020, 16, 50–59, doi:10.3762/bjoc.16.7

• distance between C4 and C13 was smaller by 0.5 Å in the gas phase. The net result of these differences was that intermediate E was more folded in the gas phase, although it was not as dramatically folded as D. The reason for greater folding in the gas phase could have been a tendency to adopt conformations

• plus signs note the location of the cations. Comparison between gas phase and active site model conformations. A) Intermediate D. B) Intermediate E. Mechanism for formation of cyclooctat-9-en-7-ol, published similarly in [42]. Interactions between intermediates and TS structures with active site

Synthesis and characterization of bis(4-amino-2-bromo-6-methoxy)azobenzene derivatives

• David Martínez-López,
• Amirhossein Babalhavaeji,
• Diego Sampedro and
• G. Andrew Woolley

Beilstein J. Org. Chem. 2019, 15, 3000–3008, doi:10.3762/bjoc.15.296

• optimize geometry, and TD-DFT with a Solvation Model based on Density (SMD) to calculate absorption wavelength maxima. These computational methods have been used successfully with related compounds [16][17]. The relative stability of different conformations of the molecule was calculated, i.e., with the

Palladium-catalyzed synthesis and nucleotide pyrophosphatase inhibition of benzo[4,5]furo[3,2-b]indoles

• Hoang Huy Do,
• Saif Ullah,
• Alexander Villinger,
• Joanna Lecka,
• Jean Sévigny,
• Peter Ehlers,
• Jamshed Iqbal and
• Peter Langer

Beilstein J. Org. Chem. 2019, 15, 2830–2839, doi:10.3762/bjoc.15.276

• find docking calculations and scoring functions. Out of 40 conformations for each compound, the conformations with lowest free binding energies and S score were selected for visualization by using Discovery studio visualizer DS [47][48]. X-ray structure determination An X-ray quality crystal of 5d was

A combinatorial approach to improving the performance of azoarene photoswitches

• Joaquin Calbo,
• Aditya R. Thawani,
• Rosina S. L. Gibson,
• Andrew J. P. White and
• Matthew J. Fuchter

Beilstein J. Org. Chem. 2019, 15, 2753–2764, doi:10.3762/bjoc.15.266

• , 0.012 and 0.087 for 4pzMe-Cl2, 4pzMe-OMe2 and 4pzMe-Pyr2, respectively; see Figure 6 for 4pzH-F2 and 4pzH-Cl2). To experimentally compare the conformations of the E-isomers, we were able to characterize 4pzMe-F2, 4pzMe-Cl2 and 4pzH-F2 by X-ray crystallography (Figure 7). In agreement with the

Nanangenines: drimane sesquiterpenoids as the dominant metabolite cohort of a novel Australian fungus, Aspergillus nanangensis

• Heather J. Lacey,
• Cameron L. M. Gilchrist,
• Andrew Crombie,
• John A. Kalaitzis,
• Daniel Vuong,
• Peter J. Rutledge,
• Peter Turner,
• John I. Pitt,
• Ernest Lacey,
• Yit-Heng Chooi and
• Andrew M. Piggott

Beilstein J. Org. Chem. 2019, 15, 2631–2643, doi:10.3762/bjoc.15.256

• structures of 4 and 9 have one. The cyclohexane rings of all molecules have chair conformations, the cyclohexene rings of all molecules have half-chair conformations, and the furan rings of all molecules have flattened envelope conformations. See Supporting Information File 1 for detailed methods. Genomics

Self-assembled coordination thioether silver(I) macrocyclic complexes for homogeneous catalysis

• Zhen Cao,
• Aline Lacoudre,
• Cybille Rossy and
• Brigitte Bibal

Beilstein J. Org. Chem. 2019, 15, 2465–2472, doi:10.3762/bjoc.15.239

• different 1H NMR spectra may account for the existence of several conformations for these constrained coordinated architectures, which still have a certain degree of freedom, that is required for further catalytic properties. Diffusion-ordered spectroscopy (DOSY) 1H NMR was also used on complexes 1a–d (5 mM

Sugar-derived oxazolone pseudotetrapeptide as γ-turn inducer and anion-selective transporter

• Sachin S. Burade,
• Sushil V. Pawar,
• Tanmoy Saha,
• Navanath Kumbhar,
• Amol S. Kotmale,
• Manzoor Ahmad,
• Pinaki Talukdar and
• Dilip D. Dhavale

Beilstein J. Org. Chem. 2019, 15, 2419–2427, doi:10.3762/bjoc.15.234

• stereochemically stable quaternary carbon center [1]. For example, TAA-derived peptides containing a cyclopropane ring and ʟ/ᴅ-dimethyl tartrate showed an α-turn and form 310-helical conformations in higher oligomers [2][3][4]. While, TAA-derived peptides having a tetrahydrofuran ring demonstrated a β-turn type

• activity. Oxazolone pseudodipeptide 1 and tetrapeptide 2a. Characteristic NOEs of 2a. DMSO titration study of 2a. 1H NMR temperature study of 2a. Optimized helical conformations of (A) 2a, (B) 2b and (C) 9. Ion transport activity (A) for 1, (B) for 2a, across EYPC-LUVs HPTS. Cation (A) and anion (B

Effect of ring size on photoisomerization properties of stiff stilbene macrocycles

• Sandra Olsson,
• Óscar Benito Pérez,
• Magnus Blom and
• Adolf Gogoll

Beilstein J. Org. Chem. 2019, 15, 2408–2418, doi:10.3762/bjoc.15.233

• stiff stilbene segment with decreasing ring size is indicated by the substantial deviation of the dihedral angle from 180°. Furthermore, the alkyl chains adopt more similar conformations in the E-isomers with stretched alkyl chains. In the Z-isomers, the alkyl chains adopt a larger variety of

• conformations. This will add an entropy penalty for the E-isomers. Interatomic distances from NOE buildup rates Interatomic distances, derived from NOE buildup rates, are summarized in Figure 7. Signal overlap prevented an analysis accounting for the presence of an ensemble of conformers such as NAMFIS [39][40

• calculated in MacroModel 9.9 with the OPLS3e force field, CHCl3 as solvent and dielectric constant 9.1 [48][49]. Redundant conformer elimination in MacroModel was used to reduce the number of conformations to 10–20 structures [50]. Synthesis Synthesis of 6-methoxyindan-1-one (3) Compound 2 (2.523 g, 14.0

Reversible switching of arylazopyrazole within a metal–organic cage

• Anton I. Hanopolskyi,
• Soumen De,
• Michał J. Białek,
• Yael Diskin-Posner,
• Liat Avram,
• Moran Feller and
• Rafal Klajn

Beilstein J. Org. Chem. 2019, 15, 2398–2407, doi:10.3762/bjoc.15.232

• release of "high-energy" water molecules from the cavity of 2 [50][51]. Determining the X-ray structure was challenging; the difficulty lies in the fact that both the cage and the encapsulated guest dimer exist in the form of two different conformations. Figure 3 shows (E-1)22 that features the main

• conformations of both (E-1)2 and 2, amounting to 59% and 93% of the total population of the guest and the host component, respectively. The remaining 41% of (E-1)2 features the same separation distance between the two guest molecules (d = 3.503 Å vs 3.497 Å in the major isomer; a distance typical of π–π-stacked

• , Supporting Information File 1). Front view (a) and side view (b) of the X-ray crystal structure of (E-1)22 (major conformations of 1 and 2; see also Supporting Information File 1, Figures S15 and S16). The horizontal plane (pink) denotes the positions of eight equatorial imidazole groups; four axial

Current understanding and biotechnological application of the bacterial diterpene synthase CotB2

• Ronja Driller,
• Daniel Garbe,
• Norbert Mehlmer,
• Monika Fuchs,
• Keren Raz,
• Dan Thomas Major,
• Thomas Brück and
• Bernhard Loll

Beilstein J. Org. Chem. 2019, 15, 2355–2368, doi:10.3762/bjoc.15.228

• (Table 2 and Scheme 1). Notably, in the crystal structures of CotB2 (Table 1) [36][37][38], we perceive that the amino acid side chains with an aromatic character in the active site (Figure 7) frequently adopt energetically unfavorable side chain conformations. Moreover, the crystal structures of the

• CotB2F107A [37] and CotB2F149L [38] variants revealed that other aromatic amino acid side chains adopt different side chain conformations compared to the structure of CotB2wt. This hints to long-range effects of the introduced mutation on other amino acid side chains in the active cavity. We are convinced

Perspective isomorphs – a new classification of molecular structures based on artistic and chemical concepts

• Jannis Neumann,
• Ansgar Schnurr and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2019, 15, 2319–2326, doi:10.3762/bjoc.15.224

• to van der Waals contacts) All conformations possible at room temperature are considered To translate the atomic dimensions to a viewing process the van der Waals radii and the following scale has been applied: 1 pm 1 mm The hypothetical viewing distance for the mathematic calculation as well as for

Harnessing enzyme plasticity for the synthesis of oxygenated sesquiterpenoids

• Melodi Demiray,
• David J. Miller and
• Rudolf K. Allemann

Beilstein J. Org. Chem. 2019, 15, 2184–2190, doi:10.3762/bjoc.15.215

• bisabolyl cation and the amorphane skeleton. Rather the active site conformations of 11 and cation 22 appear to enable a 1,11-cyclisation to 23. A subsequent [1,3]-hydride shift to cation 24 and deprotonation from C15 lead to 8-methoxy-γ-humulene (20, Scheme 3A). Alternatively, the nucleophilic 8-methoxy

1,2,3-Triazolium macrocycles in supramolecular chemistry

• Mastaneh Safarnejad Shad,
• Pulikkal Veettil Santhini and
• Wim Dehaen

Beilstein J. Org. Chem. 2019, 15, 2142–2155, doi:10.3762/bjoc.15.211

• -derived tris(crown ether) host (eTC) via a dynamic covalent chemistry approach involving triple threading and a Grubbs-catalyzed ring-closing metathesis [68]. 1H NMR titration experiments have been used for the identification of co-conformations of the four related stable states of 19. The authors have

• mechanism has been proposed for the MIM macrocycle 19 involving a stepwise co-conformational progression. After the deprotonation of dibenzylammonium (DBA) sites, the rings prefer to move toward the adjacent N-methyl-1,2,3-triazolium (MTA) sites to the thermodynamically stable co-conformations rather than

Synthesis of 1-azaspiro[4.4]nonan-1-oxyls via intramolecular 1,3-dipolar cycloaddition

• Yulia V. Khoroshunova,
• Denis A. Morozov,
• Andrey I. Taratayko,
• Polina D. Gladkikh,
• Yuri I. Glazachev and
• Igor A. Kirilyuk

Beilstein J. Org. Chem. 2019, 15, 2036–2042, doi:10.3762/bjoc.15.200

• conformations of neighbouring geminal ethyl groups, thereby preventing averaging. In agreement with this conclusion, there are no large splittings in the EPR spectrum of 12c, and the line width is a bit greater than that in the spectra of similar nonspirocyclic 3,4-unsubstituted 2,2-diethylpyrrolidine

Synthesis and anion binding properties of phthalimide-containing corona[6]arenes

• Meng-Di Gu,
• Yao Lu and
• Mei-Xiang Wang

Beilstein J. Org. Chem. 2019, 15, 1976–1983, doi:10.3762/bjoc.15.193

• editing or varying the meta-substitution of arylenes within heteracalixaromatics into the para-substitution. In contrast to heteracalixaromatics which adopt generally 1,3-alternate conformations giving V-shaped cleft structures [17][18][19][20][21], the resulting coronarenes form, however, cylindroid

Inherent atomic mobility changes in carbocation intermediates during the sesterterpene cyclization cascade

• Hajime Sato,
• Takaaki Mitsuhashi,
• Mami Yamazaki,
• Ikuro Abe and
• Masanobu Uchiyama

Beilstein J. Org. Chem. 2019, 15, 1890–1897, doi:10.3762/bjoc.15.184

• 351-0198, Japan Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan 10.3762/bjoc.15.184 Abstract We previously showed that the regio- and stereoselectivity in terpene-forming reactions are determined by the conformations of the carbocation

• . Based on this analysis, it appears that the destination of the cyclization cascade is determined by the conformations of the carbocation intermediates, but not by enzymatic constraints. This insight is consistent with our previous findings [1]. Conclusion In order to clarify the influence of the

Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries

• Xiao Xie,
• Michela Zuffo,
• Marie-Paule Teulade-Fichou and
• Anton Granzhan

Beilstein J. Org. Chem. 2019, 15, 1872–1889, doi:10.3762/bjoc.15.183

• mirroring their conformations. Specifically, parallel G4s cluster in the upper left part of the plot (red dots), as a result of high fluorescence response with 18a and moderate-to-low response with 1p. Hybrid G4s (green dots) produce moderate light-up values for 18a and high ones for 1p, thus clustering on

• the existence of an equilibrium between a monomolecular antiparallel form and a bimolecular parallel one, affected by K+ and oligonucleotide concentration [86]. As already suggested, this oligonucleotide is probably present as a mixture of conformations in our working conditions [14]. It is thus

The cyclopropylcarbinyl route to γ-silyl carbocations

• Xavier Creary

Beilstein J. Org. Chem. 2019, 15, 1769–1780, doi:10.3762/bjoc.15.170

• of cation 37. This study at the B3LYP/6-31G* level suggested that migration of bond a in 43 is not viable since the resultant cation 47 is not an energy minimum at this level, but a transition state. However, a current study at the M062X/6-311+G** level finds that both conformations 47a and 47b are

Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP)

• Małgorzata Urbańczyk,
• Michał Jewgiński,
• Joanna Krzciuk-Gula,
• Jerzy Góra,
• Rafał Latajka and
• Norbert Sewald

Beilstein J. Org. Chem. 2019, 15, 1581–1591, doi:10.3762/bjoc.15.162

• calculated with the usage of the XPLOR-NIH program [34]. The obtained conformations were clustered based on the main chain backbone dihedral angles (φ and ψ) using the AmberTools package [35]. The first analysis of the number of obtained distance constrains clearly suggested that peptides containing ʟ-amino