Mechanochemical synthesis of thioureas, ureas and guanidines

• Vjekoslav Štrukil

Beilstein J. Org. Chem. 2017, 13, 1828–1849, doi:10.3762/bjoc.13.178

• : corrugated chains of head-to-head or head-to-tail aligned molecules and discrete centrosymmetric dimers based on the R22(8) supramolecular synthon in the case of sterically hindered thioureas (Figure 2). The crystal structures of N,N'-diarylthioureas linked in chains via N–H···S hydrogen bonds can further be

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

• 1930, the first crystal structures of organic compounds to be investigated were carbohydrates of low molecular weight. Over the following years, only eight additional crystal structures were reported. The determination of the three dimensional structure of the dehydrated form of sucrose, in 1947, was

• few thousand entries for carbohydrate crystal structures, among which a limited number of molecules are relevant to glycobiology. With the exception of sucrose and cyclic compounds, such as cyclodextrins or cyclo-amyloses, carbohydrates are reluctant to crystallize in form and size suitable for X-ray

• molecular crystals of micrometric dimensions or in the form of polycrystalline materials. Small molecule crystals In the quest to solve the crystal structures of cello-oligosaccharides, as model compounds of cellulose, several attempts to grow crystals of β-D-cellotetraose of a size suitable for X-ray

G-Protein coupled receptors: answers from simulations

• Timothy Clark

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

• simulations often require a simulation induction period of several hundred nanoseconds to a microsecond before they undergo important conformational changes [26]. This is possibly because the starting structures are usually taken from X-ray crystal structures or homology model derived from them. As the force

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

• groups. Selected 1H, 13C, 15N NMR data for cations Ca and Cm generated by protonation of oxadiazoles 1a and 1m at the N4 nitrogen (FSO3H, −80 °C for Ca, and −60 °C for Cm, with CH2Cl2 as internal standard). X-ray crystal structures of compounds 2a (left) (CCDC 1526767) and 2m (right) (CCDC 1526105

Expression, purification and structural analysis of functional GABA transporter 1 using the baculovirus expression system

• Jing Hu,
• Chris Weise,
• Christoph Böttcher,
• Hua Fan and
• Jian Yin

Beilstein J. Org. Chem. 2017, 13, 874–882, doi:10.3762/bjoc.13.88

• dependence has also been elucidated by identifying crucial structural elements for chloride binding [15][16]. In addition, a similar core architecture was observed based on several crystal structures of sodium symporters from different families; this observation strongly supports an alternating access

Opportunities and challenges for the sustainable production of structurally complex diterpenoids in recombinant microbial systems

• Katarina Kemper,
• Max Hirte,
• Markus Reinbold,
• Monika Fuchs and
• Thomas Brück

Beilstein J. Org. Chem. 2017, 13, 845–854, doi:10.3762/bjoc.13.85

• in diterpene biosynthetic routes entail time-consuming genome-mining and high-throughput screening technologies [64][65]. Additionally, the number of currently available, even partly annotated plant genomes and crystal structures of diterpene synthases is still limited. Yet, in order to establish

Inclusion complexes of β-cyclodextrin with tricyclic drugs: an X-ray diffraction, NMR and molecular dynamics study

• Franca Castiglione,
• Fabio Ganazzoli,
• Luciana Malpezzi,
• Andrea Mele,
• Walter Panzeri and
• Giuseppina Raffaini

Beilstein J. Org. Chem. 2017, 13, 714–719, doi:10.3762/bjoc.13.70

• the crystal stability. In both cases the crystal structures are non-centrosymmetric, indicating that the crystal contains a single enantiomer of 1 and 2. The overall topology of inclusion matches that found in solution and through molecular simulations. In both cases the complex structures do not show

Derivatives of the triaminoguanidinium ion, 5. Acylation of triaminoguanidines leading to symmetrical tris(acylamino)guanidines and mesoionic 1,2,4-triazolium-3-aminides

• Jan Szabo,
• Julian Greiner and
• Gerhard Maas

Beilstein J. Org. Chem. 2017, 13, 579–588, doi:10.3762/bjoc.13.57

• being very short (d(H···Cl) = 2.11(2) Å, d(N···Cl) = 3.060(1) Å) and linear and the other one much longer and non-linear. Short N–H···Cl hydrogen bonds have also been found in the crystal structures of related compounds, such as II·HCl·CH3OH (d(H···Cl) = 2.36 Å, d(N···Cl) = 3.15 Å [35]) and a 2

Adsorption of RNA on mineral surfaces and mineral precipitates

• Elisa Biondi,
• Yoshihiro Furukawa,
• Jun Kawai and
• Steven A. Benner

Beilstein J. Org. Chem. 2017, 13, 393–404, doi:10.3762/bjoc.13.42

• important in this trend. For example, like witherite and strontianite, aragonite adsorbs RNA better than calcite. Further, the crystal structures of witherite and strontianite belong in the same family as the crystal structure of aragonite. Likewise, vaterite resembles aragonite in its crystal structure

Polyketide stereocontrol: a study in chemical biology

• Kira J. Weissman

Beilstein J. Org. Chem. 2017, 13, 348–371, doi:10.3762/bjoc.13.39

• be borne out by the first crystal structures of epimerizing KRs in the presence of native substrate, and such data are eagerly anticipated. In the meantime, in the absence of a clear mechanistic basis for epimerization, it has been shown possible to rationally alter the methyl stereochemistry (both

• formation from a B-type alcohol precursor [110]. It may thus be the case that all PKS DHs produce trans double bonds. Consistent with this idea, comparative sequence analysis and the resolution of six DH crystal structures to date (1 from DEBS (trans-double bond producing module) [92], 4 from the curacin

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

• . These methods include molecular dynamics simulations [186], Monte Carlo simulations [187], enhanced sampling [177] or just simply experimental ensembles from NMR or multiple crystal structures, to generate an ensemble of conformations based on the starting target structure. By doing so, conformations of

Facile synthesis of a 3-deazaadenosine phosphoramidite for RNA solid-phase synthesis

• Elisabeth Mairhofer,
• Elisabeth Fuchs and
• Ronald Micura

Beilstein J. Org. Chem. 2016, 12, 2556–2562, doi:10.3762/bjoc.12.250

• -N3 is associated with the catalysis during ribosomal peptide bond formation, a proposal about its role in proton transfer has been disputed heavily since the first ribosome crystal structures up to very recent investigations [8][9][10]. The involvement of N3, and not N1, is surprising with respect to

Sydnone C-4 heteroarylation with an indolizine ring via Chichibabin indolizine synthesis

• Florin Albota,
• Mino R. Caira,
• Constantin Draghici,
• Florea Dumitrascu and
• Denisa E. Dumitrescu

Beilstein J. Org. Chem. 2016, 12, 2503–2510, doi:10.3762/bjoc.12.245

• 104 crystal structures that contain the sydnone moiety. Of these, eleven were found to display the same anti-parallel sydnone–sydnone motif as is occurring in 9d (Figure 2b), reflecting the dipolar alignment of these moieties consistent with the positive charge centered on the ring and the negative

Radical polymerization by a supramolecular catalyst: cyclodextrin with a RAFT reagent

• Kohei Koyanagi,
• Yoshinori Takashima,
• Takashi Nakamura,
• Hiroyasu Yamaguchi and
• Akira Harada

Beilstein J. Org. Chem. 2016, 12, 2495–2502, doi:10.3762/bjoc.12.244

• catalyst; Introduction The folding of proteins in biological systems, the replication of DNA, and specific substrate recognition by enzymes play important roles in forming supramolecular structures, achieving functions, and maintaining life [1][2][3][4][5][6]. The crystal structures of RNA polymerase, DNA

Experimental and theoretical investigations into the stability of cyclic aminals

• Edgar Sawatzky,
• Antonios Drakopoulos,
• Martin Rölz,
• Christoph Sotriffer,
• Bernd Engels and
• Michael Decker

Beilstein J. Org. Chem. 2016, 12, 2280–2292, doi:10.3762/bjoc.12.221

• minimal energy where the residues are in equatorial position (exemplarily shown for compound 9b in Figure 7b). Both conformations of minimum energy found in this study are in agreement with crystal structures reported in the literature [46][49][50][51][52] (CCDC reference numbers for anti-axial motif

• findings, minimum conformational energy calculations were conducted. We found that all compounds adhere to two groups of conformers in accordance with crystal structures reported in literature. Changing the minimum energy conformers of 9b and 13b,c into the reference structure 8a revealed an increase in

Practical synthetic strategies towards lipophilic 6-iodotetrahydroquinolines and -dihydroquinolines

• David R. Chisholm,
• Garr-Layy Zhou,
• Ehmke Pohl,
• Roy Valentine and
• Andrew Whiting

Beilstein J. Org. Chem. 2016, 12, 1851–1862, doi:10.3762/bjoc.12.174

• 21 and 22 using typical Miyaura borylation conditions (Scheme 10) [32]. Both were highly crystalline compounds, and comparison of the two crystal structures (Figure 4) highlighted the more planar structure of 30 as a result of the enamine function, as predicted by ab initio methods in Figure 2

• conducted using Spartan’10, and visualised using UCSF Chimera 1.11 [28][29]. Combined, normalised absorption and emission spectra of 28 in chloroform. Absorption spectrum was recorded at 10 μM. Emission spectrum was recorded at 100 nM, with excitation at 360 nm. Comparison of the crystal structures of 29

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

• when methyl groups are grafted on the azulenyl seven-membered ring. According to the crystal structures and TDDFT calculations, different twisting of the aromatic constituents is responsible for the observed fluorescent behavior. The electrochemical profile contains one-electron oxidation/reduction

• /dichloromethane/acetonitrile solutions upon slow evaporation of the solvents at room temperature. The crystal structures confirm the solution assignment for both compounds. The 4′-azulenyl-substituted terpyridine 4a crystallized in the orthorhombic P21cn space group, whereas 4b crystallized in the monoclinic C2/n

• fluorescence emission upon excitation at the corresponding absorption maximum. The fluorescence quantum yield is influenced by the azulenyl substitution from 0.14 in the case of the parent 4′-azulenyl-2,2′:6′,2″-terpyridine to 0.64 for the trimethyl substituted azulenylterpyridine. According to the crystal

The hydrolysis of geminal ethers: a kinetic appraisal of orthoesters and ketals

• Sonia L. Repetto,
• James F. Costello,
• Craig P. Butts,
• Joseph K. W. Lam and
• Norman M. Ratcliffe

Beilstein J. Org. Chem. 2016, 12, 1467–1475, doi:10.3762/bjoc.12.143

• -, respectively by 1H NMR [48]) also affords the same product ratio with 65% conversion. Performing the procedure at −10 and +20 °C does not change the product distribution; we conclude then, that the exchange reaction proceeds via equilibrium control. Computational techniques. X-ray crystal structures were

Discovery of an inhibitor of the production of the Pseudomonas aeruginosa virulence factor pyocyanin in wild-type cells

• Bernardas Morkunas,
• Balint Gal,
• Warren R. J. D. Galloway,
• James T. Hodgkinson,
• Brett M. Ibbeson,
• Yaw Sing Tan,
• Martin Welch and
• David R. Spring

Beilstein J. Org. Chem. 2016, 12, 1428–1433, doi:10.3762/bjoc.12.137

• conformations in various crystal structures of LasR LBD complexes and hence, they were made flexible in the flexible receptor docking runs. The best score for OdDHL (−9.1 kcal/mol) was obtained from the rigid receptor docking run with water. The docked and crystallographic conformations of OdDHL agree closely

Synergistic chiral iminium and palladium catalysis: Highly regio- and enantioselective [3 + 2] annulation reaction of 2-vinylcyclopropanes with enals

• Haipan Zhu,
• Peile Du,
• Jianjun Li,
• Ziyang Liao,
• Guohua Liu,
• Hao Li and
• Wei Wang

Beilstein J. Org. Chem. 2016, 12, 1340–1347, doi:10.3762/bjoc.12.127

• product 3a in 83% yield as a colorless oil. Catalytic regio- and enantioselective [3 + 2] annulation reactions of 2-vinylcyclopropanes with enals. Single X-ray crystal structures of 7h’ and 7h’’. The proposed transition states. Screening of lewis acids.a The optimization of reaction conditions.a Scope of

Reactivity studies of pincer bis-protic N-heterocyclic carbene complexes of platinum and palladium under basic conditions

• David C. Marelius,
• Curtis E. Moore,
• Arnold L. Rheingold and
• Douglas B. Grotjahn

Beilstein J. Org. Chem. 2016, 12, 1334–1339, doi:10.3762/bjoc.12.126

• -PtCl, the NH proton resonance is typically downfield shifted with a chemical shift of ca. 11 ppm, whereas this signal is strongly shifted upfield to 8.03 (6-Pd) or 8.19 ppm (6-Pt). The crystal structures for both 6-Pd and 6-Pt show that the NH is located above the pi system of one imidazole ring of the

NeoPHOX – a structurally tunable ligand system for asymmetric catalysis

• Jaroslav Padevět,
• Marcus G. Schrems,
• Robin Scheil and
• Andreas Pfaltz

Beilstein J. Org. Chem. 2016, 12, 1185–1195, doi:10.3762/bjoc.12.114

• -TBDMS gave somewhat lower enantioselectivities. In the hydrogenation of imine S4 none of the catalysts shown in Table 2 induced high enantioselectivity. Crystal structures of iridium NeoPHOX complexes The three dimensional structures of several threonine and serine-derived NeoPHOX iridium complexes were

• phospinooxazoline ligands. Asymmetric hydrogenation with iridium-NeoPHOX catalysts [19]. Employing L-valine as a starting material for C5 substituted oxazoline. Retrosynthetic analysis for NeoPHOX ligands derived from serine and threonine. Crystal structures of selected Ir-complexes. Hydrogen atoms, COD and BArF

• determined by X-ray diffraction and compared with known phosphinooxazoline complexes. We were interested to see whether the differences in steric shielding of the coordination sphere by the protecting groups on the tertiary alcohol function correlated with the hydrogenation results. From the obtained crystal

Antibacterial structure–activity relationship studies of several tricyclic sulfur-containing flavonoids

• Lucian G. Bahrin,
• Henning Hopf,
• Peter G. Jones,
• Laura G. Sarbu,
• Cornelia Babii,
• Alina C. Mihai,
• Marius Stefan and
• Lucian M. Birsa

Beilstein J. Org. Chem. 2016, 12, 1065–1071, doi:10.3762/bjoc.12.100

• the X-ray section below. X-ray analyses The crystal structures of flavanones 4d and 4f are presented in Figure 3. We found that compounds of general structure 4, despite their close chemical similarity, display conformational differences, especially regarding the ethyl groups. Relevant torsion angles

• constants (the structure was not determined), whereas 4k proved to be seriously disordered. The crystal structures of tricyclic flavonoids 5a and 5b are displayed in Figure 4. Both compounds crystallize with two independent molecules in the asymmetric unit. The main possible degrees of freedom involve the

A robust synthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin

• Matthias Bender,
• Henrik Mouritsen and
• Jens Christoffers

Beilstein J. Org. Chem. 2016, 12, 912–917, doi:10.3762/bjoc.12.89

• ) or a FAD and a 5,10-methenyltetrahydrofolate (MTHF) still attached [4][12][13]). Consequently, no crystal structures of a functional avian cryptochrome are known at present. While FAD and MTHF are commercially available, FO (1) is not. However, this compound is potentially needed in order to

Creating molecular macrocycles for anion recognition

• Amar H. Flood

Beilstein J. Org. Chem. 2016, 12, 611–627, doi:10.3762/bjoc.12.60

• plot of anion affinities (40:60 methanol/dichloromethane). (a) Representation and (b) crystal structure of cyanostar-based [3]rotaxane. Crystal structures of cyanostar sandwich around (a) perchlorate and (b) diglyme (molecules shown with stick models and representative electron-density contours). Part