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

• useful catalysts that control the regiospecificity in an environmentally friendly manner. The information from their X-ray structures will contribute to future engineering of PTases. Furthermore, the structure of AmbP1 can serve as a model to alter the reaction through creating a metal binding site

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

• reasons why it is able to accommodate quite a disparity of encapsulated guests [45][46][47][48][49]. In Figure 3 is a collection of different [2]rotaxane X-ray structures with tetralactam A as the surrounding macrocycle. The collection has been divided into four groups according to the macrocyclic

• excellent guests [24]. Shown in Figure 5b are X-ray structures of AuBr4− inside organic-soluble versions of tetralactam B and C with 9,10-anthrylene or 2,3,5,6-tetramethyl-1,4-phenylene sidewalls, respectively. Solution-state binding studies in organic solvents showed that tetralactam C exhibited higher

• are omitted for clarity. Selected X-ray structures of [2]rotaxanes with tetralactam A as the surrounding macrocycle reported by groups led by Leigh, Smith, Cooke, and Berná [37][39][50][52][53][54][55][56]. (a) Chemical structures of squaraine, thiosquaraine, croconaine, and acene guests that can bind

Halogen bonding and host–guest chemistry between N-alkylammonium resorcinarene halides, diiodoperfluorobutane and neutral guests

• Fangfang Pan,
• Mohadeseh Dashti,
• Michael R. Reynolds,
• Kari Rissanen,
• John F. Trant and
• Ngong Kodiah Beyeh

Beilstein J. Org. Chem. 2019, 15, 947–954, doi:10.3762/bjoc.15.91

• , Finland Oakland University, Department of Chemistry, 146 Library Drive, Rochester, Michigan, 48309-4479, USA 10.3762/bjoc.15.91 Abstract Single crystal X-ray structures of halogen-bonded assemblies formed between host N-hexylammonium resorcinarene bromide (1) or N-cyclohexylammonium resorcinarene

Mechanochemistry of supramolecules

• Anima Bose and
• Prasenjit Mal

Beilstein J. Org. Chem. 2019, 15, 881–900, doi:10.3762/bjoc.15.86

• solvent-assisted grinding using ethanol (Figure 25). The single crystal X-ray structures of the obtained co-crystals 44–46 were reported to match with the solution-phase co-crystals. They have also studied energy levels, thermal properties and the stability of these structures through DFT calculations

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

• hydrogen bonds [74]. X-ray structures of BIFOXSi(OH)2 (9, Figure 16) and BIFOXSiCl(OH) (8, Figure 17) with co-crystallized acetone indicate the bonding behavior of the silanediols to carbonyl acceptors. Chlorosilanol 8 binds one acetone with a bonding length of 2.16(0) Å (H3···O4) and 2.89(4) Å (O3–H···O4

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

• to identify tricyclic intermediates on ThDP-dependent enzymes. Critically, even though they were treated dismissively, there are two X-ray structures which, at a minimum, provide unambiguous evidence for the formation of stable tricyclic intermediates on an enzyme [46][47]. Additional evidence

• evidence for the slow first step, i.e., formation of the mandelylThDP adduct [29]. In addition to BFDC, the X-ray structures of tricyclic intermediates suggest that an even greater stabilization is present on phosphoketolase and acetolactate synthase. It could well be argued that TC stabilization may prove

Reactions of 3-(p-substituted-phenyl)-5-chloromethyl-1,2,4-oxadiazoles with KCN leading to acetonitriles and alkanes via a non-reductive decyanation pathway

• Akın Sağırlı and
• Yaşar Dürüst

Beilstein J. Org. Chem. 2018, 14, 3011–3017, doi:10.3762/bjoc.14.280

• proton located between the methylene coupled with the C1 carbon and that the methylene protons H2 were incorporated in the C2 carbon signal. Fortunately, the exact structures of compounds 3a and 4e were also confirmed by X-ray structures (Figure 4). The CIF data of 3a and 4e have been deposited at

1,8-Bis(dimethylamino)naphthyl-2-ketimines: Inside vs outside protonation

• A. S. Antonov,
• A. F. Pozharskii,
• P. M. Tolstoy,
• A. Filarowski and
• O. V. Khoroshilova

Beilstein J. Org. Chem. 2018, 14, 2940–2948, doi:10.3762/bjoc.14.273

• –7c) species were investigated by 1H NMR spectroscopy in DMSO-d6, CD3CN and acetone-d6 in a wide range of temperatures. Results obtained in solutions were compared to single crystal X-ray structures and calculated equilibrium geometries of isolated molecules in a vacuum. Results and Discussion

Diazirine-functionalized mannosides for photoaffinity labeling: trouble with FimH

• Femke Beiroth,
• Tomas Koudelka,
• Thorsten Overath,
• Stefan D. Knight,
• Andreas Tholey and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2018, 14, 1890–1900, doi:10.3762/bjoc.14.163

• force field and 30 different conformers of each ligand were docked into two different X-ray structures of FimH (for details see Supporting Information File 1). These two crystal structures differ in the conformation of the tyrosine gate, formed by Y48 and Y137 positioned at the entrance of the

• of FimH ligands using FlexX flexible docking and consensus scoring, both implemented in Sybyl 6.9, as described earlier [19]. Two published X-ray structures of FimH (PDB codes 1KLF and 1UWF) were considered. During docking, the receptor was held fixed whereas the ligand was allowed to change its

Water-soluble SNS cationic palladium(II) complexes and their Suzuki–Miyaura cross-coupling reactions in aqueous medium

• Alphonse Fiebor,
• Richard Tia,
• Banothile C. E. Makhubela and
• Henok H. Kinfe

Beilstein J. Org. Chem. 2018, 14, 1859–1870, doi:10.3762/bjoc.14.160

• ) (Figure 4). The Pd–Br distance is calculated to be 2.60 Å and is consistent with similar Pd–Br bond lengths found in the literature for single crystal X-ray structures [47][48]. This oxidative addition step involves a low activation energy barrier of −43.9 kcal/mol. This negative energy implies that there

Recent advances in phosphorescent platinum complexes for organic light-emitting diodes

• Cristina Cebrián and
• Matteo Mauro

Beilstein J. Org. Chem. 2018, 14, 1459–1481, doi:10.3762/bjoc.14.124

• , photophysical properties and OLED performances, Chi, Kim and co-workers analyzed the X-ray structures of Pt(fppz)2 (13) and other related platinum(II) complexes 14 and 15 in both single crystal and thin film samples (Figure 7) [13]. They observed different degrees of crystallinity as a function of the

Phosphodiester models for cleavage of nucleic acids

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

• protein nucleases and ribozymes a subject of intensive mechanistic studies. pH-Rate dependency, X-ray structures, amino acid/nucleotide substitution experiments and the effect of thiosubstitution of phosphate oxygens on the binding of metal ion cofactors have given invaluable information about the

What contributes to an effective mannose recognition domain?

• Christoph P. Sager,
• Deniz Eriş,
• Martin Smieško,
• Rachel Hevey and
• Beat Ernst

Beilstein J. Org. Chem. 2017, 13, 2584–2595, doi:10.3762/bjoc.13.255

• ]. Crystal structures of mannose–lectin complexes The X-ray structures of six mannose-binding receptors in complex with either α-D-mannose (1) or methyl α-D-mannopyranoside (2) were analyzed (Figure 1 and Table 1, A–C and G–I). Since for DC-SIGNR (Figure 1, D) and DC-SIGN (Figure 1, E) neither complexes with

¹⁵N-Labelling and structure determination of adamantylated azolo-azines in solution

• Sergey L. Deev,
• Alexander S. Paramonov,
• Tatyana S. Shestakova,
• Igor A. Khalymbadzha,
• Oleg N. Chupakhin,
• Julia O. Subbotina,
• Oleg S. Eltsov,
• Pavel A. Slepukhin,
• Vladimir L. Rusinov,
• Alexander S. Arseniev and
• Zakhar O. Shenkarev

Beilstein J. Org. Chem. 2017, 13, 2535–2548, doi:10.3762/bjoc.13.250

• slow evaporation from ethyl acetate solutions. The solved X-ray structures were in a full agreement with the results of the JCN and JHN analysis and confirmed the N2-substituted mesoionic form for compound 15a as well as the attachment of adamantane to the N1 atom in compound 15b. In accordance with

• ) Fragment of the 2D 15N-HMBC spectrum of 15a-15N2. The 1H-15N cross-peaks between the adamantane protons and 15N-labelled atoms are shown. ORTEP diagrams of the X-ray structures of compounds 15a-15N2 (a) and 15b-15N2 (b). For clarity, the H atoms are omitted. The observed disorder of the adamantane fragment

A speedy route to sterically encumbered, benzene-fused derivatives of privileged, naturally occurring hexahydropyrrolo[1,2-b]isoquinoline

• Olga Bakulina,
• Alexander Ivanov,
• Vitalii Suslonov,
• Dmitry Dar’in and
• Mikhail Krasavin

Beilstein J. Org. Chem. 2017, 13, 1413–1424, doi:10.3762/bjoc.13.138

• (anti) and minor (syn) products obtained in the reactions discussed herein, we obtained single-crystal X-ray structures of sixteen CCR adducts synthesized in this work and correlated this structural information with the NMR behavior of these compounds. The range of the coupling constant J(H11-H11a

• ) display the J(H11-H11a) values of 3.0 Hz for both diastereomers, which is inconsistent with the regular values of corresponding dihedral angles (166.3° and 169.7° for anti-10d and anti-10e, respectively; 57.5° for syn-10e) measurable in the X-ray structures of these compounds. We reasoned that such a

• information on these compounds. Finally, the relative stereochemistry of compound 10o (for which neither X-ray structures nor reliable NMR criteria were available) was assigned on the basis of the through-space interactions observable in its NOESY spectrum and the value of a 3JCH coupling constant (Supporting

Strategies in megasynthase engineering – fatty acid synthases (FAS) as model proteins

• Manuel Fischer and
• Martin Grininger

Beilstein J. Org. Chem. 2017, 13, 1204–1211, doi:10.3762/bjoc.13.119

• picture of substrate shuttling being much more than just a mean to keep substrates recruited at the synthetic unit. Most of the understanding about the interaction of ACP with catalytic domains again originates from studies on FAS. Early information was received by S. cerevisiae FAS X-ray structures, in

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

G-Protein coupled receptors: answers from simulations

• Timothy Clark

Beilstein J. Org. Chem. 2017, 13, 1071–1078, doi:10.3762/bjoc.13.106

• fields have been optimized to reproduce X-ray structures, they likely have a kinetic bias that hinders rearrangement from typical starting structures. Nonetheless, the simulations were able to predict whether the receptor was induced (i.e., allows transcription) or not [26], in contrast to X-ray

• , react sensitively to perturbations. Given the reliability of protein force fields pointed out above, it should be clear that it is often possible to simulate systems that are closer to the biological situation than the crystals used to obtain X-ray structures. An early example of this is the fact that

• binding) and ligand bias. The simulations are predictive and can therefore be used in prospective computer-aided drug design. The cumulative number of different GPCRs for which X-ray structures were available in a given year. The data represent a total of 174 structures on 91 ligand–receptor complexes for

Metal-free hydroarylation of the side chain carbon–carbon double bond of 5-(2-arylethenyl)-3-aryl-1,2,4-oxadiazoles in triflic acid

• Anna S. Zalivatskaya,
• Dmitry S. Ryabukhin,
• Marina V. Tarasenko,
• Alexander Yu. Ivanov,
• Irina A. Boyarskaya,
• Elena V. Grinenko,
• Ludmila V. Osetrova,
• Eugeniy R. Kofanov and
• Aleksander V. Vasilyev

Beilstein J. Org. Chem. 2017, 13, 883–894, doi:10.3762/bjoc.13.89

• shown in Table 2 (see also X-ray structures of 2a and 2m in Figure 4). First, it should be emphasized that no reaction is observed under the conditions of generation of monoprotonated species C (see Table 1, and Figure 3). Thus, in FSO3H at low temperature (−80 to −60 °C) compounds 1e (Table 2, entries

Fluorinated cyclohexanes: Synthesis of amine building blocks of the all-cis 2,3,5,6-tetrafluorocyclohexylamine motif

• Tetiana Bykova,
• Nawaf Al-Maharik,
• Alexandra M. Z. Slawin and
• David O'Hagan

Beilstein J. Org. Chem. 2017, 13, 728–733, doi:10.3762/bjoc.13.72

• . However suitable crystals were obtained from acetone/acetonitrile for X-ray structure analysis. The X-ray structures of 13, 14 and 15 are illustrated in Figure 2. It was assumed that the facial polarity of the tetrafluorocyclohexane rings would be apparent in the molecular ordering in the solid state

• of the cyclohexane rings. These polarized cyclohexyl derivatives should prove valuable as potential building blocks in drug discovery and agrochemistry research programs [3][25]. The derivatives of all-cis-2,3,5,6-tetrafluorocyclohexane. X-ray structures and crystal packing of compounds 13, 14 and 15

Diastereoselective anodic hetero- and homo-coupling of menthol-, 8-methylmenthol- and 8-phenylmenthol-2-alkylmalonates

• Matthias C. Letzel,
• Hans J. Schäfer and
• Roland Fröhlich

Beilstein J. Org. Chem. 2017, 13, 33–42, doi:10.3762/bjoc.13.5

• current-controlled with a cheap power supply and an up-scale of the reaction is mostly easy. Experimental General remarks Optical rotations: Perkin-Elmer polarimeter 241, specific rotations in grad·cm3·dm−1·g−1, c in g/100 mL. FTIR: Bruker IFS 28. 1H, 13C NMR: Bruker WM 300. X-ray structures: Data sets

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

• various docking algorithms has been evaluated and they are able to generate docked ligand conformations that are similar to experimental complexes [146]. Compared to co-crystallized X-ray structures of target–ligand complexes docking results can sometimes even predict poses with RMSDs of less than 1 Å

Synthesis and properties of fluorescent 4′-azulenyl-functionalized 2,2′:6′,2″-terpyridines

• Adrian E. Ion,
• Liliana Cristian,
• Mariana Voicescu,
• Masroor Bangesh,
• Augustin M. Madalan,
• Daniela Bala,
• Constantin Mihailciuc and
• Simona Nica

Beilstein J. Org. Chem. 2016, 12, 1812–1825, doi:10.3762/bjoc.12.171

• 4a and 4b respectively in Figure 6) is localized only over azulene moiety, while the LUMO+1 (orbitals 96, 108 for 4a and 4b, respectively) is an orbital delocalized over the azulene moiety and the central pyridine ring. On the other hand both DFT calculated (vide infra) and X-ray structures show that

Photoinduced 1,2,3,4-tetrahydropyridine ring conversions

• Baiba Turovska,
• Henning Lund,
• Viesturs Lūsis,
• Anna Lielpētere,
• Edvards Liepiņš,
• Sergejs Beljakovs,
• Inguna Goba and
• Jānis Stradiņš

Beilstein J. Org. Chem. 2015, 11, 2166–2170, doi:10.3762/bjoc.11.234

• oxidation of 1 in deareated (blue) and O2 saturated (red) solutions of CH2Cl2/0.1 M TBAPF6, c = 5 × 10−4 M. The X-ray structures of compounds 1 and 2. Decrease of the UV absorption band of compound 1 under irradiation (254 nm) in air-saturated CHCl3, c = 5 × 10−5 M. The X-ray structures of compounds 4 and 5

The simple production of nonsymmetric quaterpyridines through Kröhnke pyridine synthesis

• Isabelle Sasaki,
• Jean-Claude Daran and
• Gérard Commenges

Beilstein J. Org. Chem. 2015, 11, 1781–1785, doi:10.3762/bjoc.11.193

• -ray structures are described (for compound 5, see Supporting Information File 1 for a description of the structure). The X-ray structures for the chiral quaterpyridine 8 and its Pt complex 9 are presented in Figure 1 and Figure 2 (for details, see Supporting Information File 1). Compound 8 is

• on C5 and C4, belonging to the aromatic ring substituted by the pinene moieties. These may impose some strain in the Pt complex, resulting in a slightly different electronic environment as compared to the other nonsubstituted aromatic rings. Crystals of compounds 5, 8 and 9 were obtained and their X