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

• characteristics in the solid state. The crystal structures of the coupling products were also evaluated by single crystal X-ray analysis and the well-ordered intermolecular stacking arrangements appeared to be responsible for the enhanced CPL. Keywords: BINOL; C–H activation; circularly polarized luminescence

• and 4c were likely to assist the formation of well-ordered aggregates, being consistent with the observation of the red-shifted luminescence discussed above. Crystal structures of 4b and 4c The molecular structures of 4b and 4c were unambiguously determined by single crystal X-ray diffraction analysis

• stacking distance of around 3.45 Å. It is noteworthy that both 4b and 4c pile up while minimizing the steric repulsion between the tert-butyl groups which occupy “staggered” orientations in their crystal structures (Figure 5c and 5d). Unfortunately, the crystal structure of 4a was not determined after

Synthesis and herbicidal activities of aryloxyacetic acid derivatives as HPPD inhibitors

• Man-Man Wang,
• Hao Huang,
• Lei Shu,
• Jian-Min Liu,
• Jian-Qiu Zhang,
• Yi-Le Yan and
• Da-Yong Zhang

Beilstein J. Org. Chem. 2020, 16, 233–247, doi:10.3762/bjoc.16.25

• docking study was conducted with the method reported previously [10][19][32][33][34]. Crystal structures of Arabidopsis thaliana HPPD (PDB ID: 1TFZ) with the native ligand, named DAS869 were downloaded from the Protein Data Bank. The docking was carried out using Discovery Studio 4.0. During the docking

• binding modes of compound I39 and I40 in a target enzyme (AtHPPD). The key residues in the active site are shown in blue sticks, the FeII is shown as a dark blue sphere, and compound I39 and I40 is shown in gray sticks. Crystal structures of I18 and III4. Simulated binding mode of mesotrione (A), compound

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

• aldehydes [44]. Despite a variety of XB donors based on 1,2,3-triazole have been reported, no 4,5-diido-1,2,3-triazolium salts have been reported for an XB interaction. Herein, we report the synthesis and characterization of 4,5-diido-1,2,3-triazolium D with different anions. The crystal structures of these

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

• been reviewed elsewhere [3][10][11][12][13][14][15][16][17]. The first crystal structure of a monoterpene cyclase [18] was reported in 2002. Subsequently, the first crystal structures of a sesquiterpene [19][20] and a triterpene [21] cyclase were published in 1997. Less than a decade ago, the first

• reactivity of the isolated species and provided crucial mechanistic insights, the biorelevant mechanism cannot be fully understood without taking into account the enzyme–solvent environment. A common problem when studying these enzymes is the lack of high-resolution crystal structures that are biologically

Synthesis and optoelectronic properties of benzoquinone-based donor–acceptor compounds

• Daniel R. Sutherland,
• Nidhi Sharma,
• Georgina M. Rosair,
• Ifor D. W. Samuel,
• Ai-Lan Lee and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2019, 15, 2914–2921, doi:10.3762/bjoc.15.285

• (Scheme 3). Compounds 2–5 are novel and designed to contain a strong acceptor (BQ, in red) and a strong donor group (R, in blue): TPA in 2 and 5, 4-Cz-C4H4 in 3, and 3,5-diCz-C4H3 in 4. Crystal structures were successfully obtained for compounds 3 and 4, which show the expected twisting of the donor

• ), 121.5 ppm (CH); FTMS (+ p NSI, m/z): [M + H]+ calcd for C42H31N2O2, 595.2380; found, 595.2369; HRESIMS-TOF (m/z): [M + H]+ calcd for C42H30N2O2, 595.2385; found, 595.2383. Benzoquinone derivatives synthesized for this study, with the donor in red and the benzoquinone acceptor in blue. Crystal structures

Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering

• Eric J. N. Helfrich,
• Geng-Min Lin,
• Christopher A. Voigt and
• Jon Clardy

Beilstein J. Org. Chem. 2019, 15, 2889–2906, doi:10.3762/bjoc.15.283

• crystal structures, homology models, or mechanistic information to select the residues to be mutated. For example, P450BM3 (CYP102A1) was rationally evolved to catalyze the epoxidation of amorphadiene (21) by expanding the active site, minimizing competing reactions, and facilitating substrate access

Influence of the cis/trans configuration on the supramolecular aggregation of aryltriazoles

• Sara Tejera,
• Giada Caniglia,
• Rosa L. Dorta,
• Andrea Favero,
• Javier González-Platas and
• Jesús T. Vázquez

Beilstein J. Org. Chem. 2019, 15, 2881–2888, doi:10.3762/bjoc.15.282

• prone to forming thermoreversible gels than those with the trans configuration. In fact, compound 10, with an α-anomeric configuration (cis), showed the lowest gelation concentration at room temperature (G 0.5% w/w) in DMSO/H2O, 1:2, v/v. The crystal structures obtained for either the cis or trans

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

• in protein data bank (PDB). For the prediction of the 3D homology prototype, the reported structure of mouse ENPP1 with PDB ID 4B56, was used as standard pattern [43]. Molecular Operating Environment (2014. 0901) was used for this purpose. The modeled crystal structures manifested 80% for ENPP1 and

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

• labeling [34]. Another important step towards a deeper understanding of the cyclization mechanism was the availability of crystal structures (Table 1) revealing structural snapshots along the reaction trajectory commencing with the open, inactive conformation completing with the closed, active conformation

• 3LGK; [51]), but not to the known plant structures of diterpene TPSs, such as the ent-copalyl diphosphate synthase (PDB-ID 3PYA; [52]) or taxadiene synthase (PDB-ID 3P5R; [53]). Two crystal structures of CotB2 resembling two distinct precatalytic states The structure of CotB2F107A was determined with

• (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

1,2,3,4-Tetrahydro-1,4,5,8-tetraazaanthracene revisited: properties and structural evidence of aromaticity loss

• Arnault Heynderickx,
• Sébastien Nénon,
• Olivier Siri,
• Vladimir Lokshin and
• Vladimir Khodorkovsky

Beilstein J. Org. Chem. 2019, 15, 2059–2068, doi:10.3762/bjoc.15.203

• of moisture. The photochemistry of both compounds is currently under investigation in our labs. Crystal structures Numerous short intermolecular contacts are revealed upon inspection the crystal lattice of 3, 6a and 7a. There are two independent molecules of 3 in the unit cell with slightly different

• sublimed at about 300 °C without decomposition. Sublimation is required for its complete purification. The crystal structures of 3 and its derivatives exhibit the formation of infinite chains binding molecules in the side-to-side manner even in the case when a substituent is present at one of the nitrogen

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

• affinity for the enzyme, and this might be relevant to substrate release. Few X-ray crystal structures of terpene cyclases are available [7][8], so we believe inherent mobility analysis will be useful to predict the mechanism of conformational preorganization of the substrate to achieve different

Complexation of 2,6-helic[6]arene and its derivatives with 1,1′-dimethyl-4,4′-bipyridinium salts and protonated 4,4'-bipyridinium salts: an acid–base controllable complexation

• Jing Li,
• Qiang Shi,
• Ying Han and
• Chuan-Feng Chen

Beilstein J. Org. Chem. 2019, 15, 1795–1804, doi:10.3762/bjoc.15.173

• derivatives for the additional multiple hydrogen bonding interactions between the hosts and the guests, which were evidenced by 1H NMR titrations, X-ray crystal structures and DFT calculations. Moreover, it was also found that the association constants (Ka) of the complexes could be significantly enhanced

• by the additional multiple hydrogen-bonding interactions between the hosts and the guests, which were evidenced by 1H NMR titration, X-ray crystal structures and DFT calculations. Moreover, we also found that the Ka values of the complexes could be significantly enhanced with larger counteranions of

• multiple intermolecular non-covalent interactions with distances ranging from 1.651 to 2.575 Å. Compared with hosts H2 and H3, helic[6]arene H1 and its derivatives H4 and H5 all show multiple hydrogen-bonding interactions with the examined guests, which were confirmed by not only X-ray crystal structures

Molecular basis for the plasticity of aromatic prenyltransferases in hapalindole biosynthesis

• Takayoshi Awakawa and
• Ikuro Abe

Beilstein J. Org. Chem. 2019, 15, 1545–1551, doi:10.3762/bjoc.15.157

• AmbP1 and AmbP3 functions, elucidated through their X-ray crystal structures. The knowledge presented here will contribute to the understanding of aromatic PTase reactions and will enhance their uses as biocatalysts. Keywords: crystal structure; cyanobacteria; Friedel–Crafts reaction; hapalindole

• the molecular bases and their functions, a number of PTases have been subjected to X-ray crystallographical analyses. It is important to compare the multiple X-ray crystal structures with each substrate for the various reactions, to understand their plasticity. Here, we summarize the molecular basis

• of the two ABBA type PTases, AmbP1 and AmbP3, which catalyze multiple reactions with different sets of substrates [13][14]. Their plasticities in the reactions were revealed by the X-ray crystal structures of their complexes with different substrates. Review Hapalindole/ambiguine biosynthesis

Molecular recognition using tetralactam macrocycles with parallel aromatic sidewalls

• Dong-Hao Li and
• Bradley D. Smith

Beilstein J. Org. Chem. 2019, 15, 1086–1095, doi:10.3762/bjoc.15.105

• internally directed NH residues and it also contracts the macrocycle cavity. A measure of the cavity size is the centroid-to-centroid distance d between the two parallel aromatic sidewalls which can be obtained from X-ray crystal structures. As shown in Figure 1, d values for macrocycles with 2,6-pyridine

• flexibility. Two successful examples are macrocycles B and C with 9,10-anthrylene and 2,3,5,6-tetramethyl-1,4-phenylene sidewalls, respectively (Figure 2). X-ray crystal structures of these systems show all four NH residues directed into the cavity, even when the bridging unit is 1,3-benzene dicarboxamide (X

• crystal structures of acene and azaacene guests inside tetralactam B with the surrounding macrocycle in chair or boat conformations [25]. Recent work has shown that water-soluble versions of anthracene tetralactam B can be threaded by water soluble squaraine dyes with very high affinities (Ka ≈ 109 M−1

Catalytic asymmetric oxo-Diels–Alder reactions with chiral atropisomeric biphenyl diols

• Chi-Tung Yeung,
• Wesley Ting Kwok Chan,
• Wai-Sum Lo,
• Ga-Lai Law and
• Wing-Tak Wong

Beilstein J. Org. Chem. 2019, 15, 955–962, doi:10.3762/bjoc.15.92

• oxazaborate catalyst for 3, chiral resolution with (R)-menthyl chloroformate for 4 and chiral resolution with (1S)-camphanic chloride for 6. Crystal structures revealed that the presence and absence of additional CF3 substituents in 3 and 6 led to very different structures, as 3 forms helical supramolecular

Coordination chemistry and photoswitching of dinuclear macrocyclic cadmium-, nickel-, and zinc complexes containing azobenzene carboxylato co-ligands

• Jennifer Klose,
• Tobias Severin,
• Peter Hahn,
• Alexander Jeremies,
• Jens Bergmann,
• Daniel Fuhrmann,
• Jan Griebel,
• Bernd Abel and
• Berthold Kersting

Beilstein J. Org. Chem. 2019, 15, 840–851, doi:10.3762/bjoc.15.81

• = Zn (5), Cd (6), Ni (7); L' = azo-CO2Me, M = Cd (8), Ni (9)), and characterized by elemental analysis, electrospray ionization mass spectrometry (ESIMS), IR, UV–vis and NMR spectroscopy (for diamagnetic Zn and Cd complexes) and X-ray single crystal structure analysis. The crystal structures of 3' and

• bond lengths are given in Table S6, Supporting Information File 1. Description of the crystal structures [Zn2L(μ-azo-OH)][Zn2L(μ-azo-O)]·BPh4·4MeCN·3H2O (3'·4MeCN·3H2O): Suitable crystals of [Zn2L(μ-azo-OH)]ClO4 (3) could not be obtained. However, the addition of NaBPh4 to a solution of 3 in MeCN led

• were refined anisotropically. In the crystal structure of 3'·4MeCN·3H2O one MeCN molecule was found to be disordered over two positions (at half occupancy). It was not possible to locate H atoms for the H2O solvate molecules, and so no H2O hydrogen atoms were included in this structure. In the crystal

Azologization of serotonin 5-HT₃ receptor antagonists

• Karin Rustler,
• Galyna Maleeva,
• Piotr Bregestovski and
• Burkhard König

Beilstein J. Org. Chem. 2019, 15, 780–788, doi:10.3762/bjoc.15.74

• ]. Supporting Information Supporting Information File 98: Detailed photochromic characterization (UV–vis absorption spectra, cycle performances, thermal half-lives) and NMR spectra of all synthesized compounds are provided. The file contains crystal structures of compounds 12b and 16a and experimental

Application of olefin metathesis in the synthesis of functionalized polyhedral oligomeric silsesquioxanes (POSS) and POSS-containing polymeric materials

• Patrycja Żak and
• Cezary Pietraszuk

Beilstein J. Org. Chem. 2019, 15, 310–332, doi:10.3762/bjoc.15.28

• processes was tested. The X-ray crystal structures of the octaester showed an interpenetrated compact packing of the molecular building blocks without any specific supramolecular interaction. The structure of the octaacid was found to contain hydrogen-bonded ribbons, thanks to the two-dimensional character

Silanediol versus chlorosilanol: hydrolyses and hydrogen-bonding catalyses with fenchole-based silanes

• Falco Fox,
• Jörg M. Neudörfl and
• Bernd Goldfuss

Beilstein J. Org. Chem. 2019, 15, 167–186, doi:10.3762/bjoc.15.17

• reported silanediol derivatives 2a and 2b [43], an increase of acidity of one outward facing OH group is achieved by intermolecular hydrogen bonds [43]. Chloride binding The X-ray crystal structures of chlorosilanol 8 (Figure 17) and silanediol 9 (Figure 16) with co-crystallized acetone indicate the

• rate-determining. In the X-ray crystal structures of BIFOXSiCl(OH) (8, Figure 13) and BIFOXSi(OH)2 (9, Figures 14–16), intermolecular hydrogen bonds are apparent. The lengths of these hydrogen bonds vary from 1.88(3) to 2.16(2) Å (Table 5). The longest bond appears between BIFOXSiCl(OH) (8) and acetone

• )2SiCl(OH), Si(OH)4, methanol and [CH2O]2C(OH)2. Bond lengths and angles of hydrogen bonds in X-ray crystal structures of BIFOXSiCl(OH) (8) and BIFOXSi(OH)2 (9). Chloride binding constants (K [M−1], error (%)) to BIFOXSiCl(OH) (8), BIFOXSi(OH)2 (9) and di(1-naphthyl)silanediol (1) in HCCl3 at 22 °C [75

Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

• Ferran Planas,
• Michael J. McLeish and
• Fahmi Himo

Beilstein J. Org. Chem. 2019, 15, 145–159, doi:10.3762/bjoc.15.15

• , serves as the prototypical ThDP-dependent enzyme. A model of the active site was constructed on the basis of available crystal structures, and the cofactor states were characterized in the presence of three different ligands (crystallographic water, benzoylformate as substrate, and (R)-mandelate as

• each model is indicated in bold face. Supporting Information Supporting Information File 16: Lowest-energy conformation of model A, superpositions of the AP state/model C and APH+ state/model E with crystal structures, superposition of the AP state/models B and C, superposition of the AP states/models

Adhesion, forces and the stability of interfaces

• Robin Guttmann,
• Johannes Hoja,
• Christoph Lechner,
• Reinhard J. Maurer and
• Alexander F. Sax

Beilstein J. Org. Chem. 2019, 15, 106–129, doi:10.3762/bjoc.15.12

Generation of 1,2-oxathiolium ions from (arysulfonyl)- and (arylsulfinyl)allenes in Brønsted acids. NMR and DFT study of these cations and their reactions

• Stanislav V. Lozovskiy,
• Alexander Yu. Ivanov,
• Olesya V. Khoroshilova and
• Aleksander V. Vasilyev

Beilstein J. Org. Chem. 2018, 14, 2897–2906, doi:10.3762/bjoc.14.268

• reaction products: conjugated dienes, allyl alcohols, or thiochromene 1,1-dioxides. These reactions open new opportunities for organic synthesis based on electrophilic activation of sulfur containing allenes. X-ray crystal structures of compounds 2h (CCDC 1843276), 3e (CCDC 1843277), 5c (CCDC 1580895), 7b

Protein–protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics

• Laura Carro

Beilstein J. Org. Chem. 2018, 14, 2881–2896, doi:10.3762/bjoc.14.267

• clamp, and, hence, exhibiting an excellent selectivity profile. Crystal structures revealed that GM (21) and CGM (23) bind to a hydrophobic pocket between domains II and III, the protein–protein interaction site responsible for the recruitment of DNA enzymes by the sliding clamp, and therefore

• values ranging from 8–80 μM. Afterwards, the scientists were able to successfully obtain the crystal structures of the complexes of ExoI with both CFAM (24) and BCBP (25). From the crystallography studies it was revealed that, even though both compounds bind to the B site of ExoI, only CFAM (24) is able

The influence of the cationic carbenes on the initiation kinetics of ruthenium-based metathesis catalysts; a DFT study

• Magdalena Jawiczuk,
• Angelika Janaszkiewicz and
• Bartosz Trzaskowski

Beilstein J. Org. Chem. 2018, 14, 2872–2880, doi:10.3762/bjoc.14.266

• previous studies. We have used all-atom models for all studied catalysts. Starting models for carbenes and precatalyst were prepared on the basis of available CSD crystal structures of a Grubbs and Hoveyda–Grubbs precatalysts (refcodes: ABEJUM01, GUBQUP, ZETLOZ and LOVPAP) [58][59][64][66]. In the geometry

Non-native autoinducer analogs capable of modulating the SdiA quorum sensing receptor in Salmonella enterica serovar Typhimurium

• Matthew J. Styles and
• Helen E. Blackwell

Beilstein J. Org. Chem. 2018, 14, 2651–2664, doi:10.3762/bjoc.14.243

• [37]. Recently, two groups reported X-ray crystal structures of full-length EHEC SdiA as a homodimer in the presence of four naturally occurring AHLs (shown in Figure 1B) [21][22]. These studies reveal a structure for the SdiA dimer that incorporates LBD and DBD domains comparable to those of the