Volatiles from the xylarialean fungus Hypoxylon invadens

• Jeroen S. Dickschat,
• Tao Wang and
• Marc Stadler

Beilstein J. Org. Chem. 2018, 14, 734–746, doi:10.3762/bjoc.14.62

• compounds (11, Figure 4A) suggested the structure of a dimethylphenol, but the mass spectra of several regioisomers in our database proved to be nearly identical. The measured retention index (I = 1152) matched with a published retention index for 2,5-dimethylphenol (I = 1151) [15], but retention indices

Latest development in the synthesis of ursodeoxycholic acid (UDCA): a critical review

• Fabio Tonin and
• Isabel W. C. E. Arends

Beilstein J. Org. Chem. 2018, 14, 470–483, doi:10.3762/bjoc.14.33

• Reference sequence (RefSeq) database at NCBI [73] typing “7-alpha-hydroxysteroid dehydrogenase”. 7β-Hydroxysteroid dehydrogenases (7β-HSDH) Unlike their homologues, only few examples of bioconversion with 7β-HSDH have been reported in literature (Table 3, [33][65][74][75][76][77], Figure 5): one NADP

Volatiles from the tropical ascomycete Daldinia clavata (Hypoxylaceae, Xylariales)

• Tao Wang,
• Kathrin I. Mohr,
• Marc Stadler and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2018, 14, 135–147, doi:10.3762/bjoc.14.9

• . clavata, showed a mass spectrum that was not included in our database (Figure 5A). However, the mass spectrum of 6-propyl-5,6-dihydro-2H-pyran-2-one (Figure 5B) is very similar, and the mass difference for the molecular ion of 28 Da suggested the structure of 6-methyl-5,6-dihydro-2H-pyran-2-one for

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

A permutation approach to the assignment of the configuration to diastereomeric tetrads by comparison of experimental and ab initio calculated differences in NMR data

• Przemysław J. Boratyński

Beilstein J. Org. Chem. 2017, 13, 2478–2485, doi:10.3762/bjoc.13.245

• computation has been applied for comparison of diastereomers against a universal database made of known compounds [11][12]. Results and Discussion The idea presented herein is to rank all possible permutations of experimental and computed data rather than focusing on individual pairs. The tetrads need to

Is the tungsten(IV) complex (NEt₄)₂[WO(mnt)₂] a functional analogue of acetylene hydratase?

• Matthias Schreyer and
• Lukas Hintermann

Beilstein J. Org. Chem. 2017, 13, 2332–2339, doi:10.3762/bjoc.13.230

• emphasized by the histogram in Figure 1 which was created from melting point data in the Reaxys database and shows scattering over 30 °C. Consequently, measuring a single or even a mixed melting point with a reference sample is not a reliable identification criterion for 9. An analysis of the compound by

• . Conclusively, the title question can be answered with "no". Frequency of reported melting points for acetaldehyde 2,4-dinitrophenylhydrazone (9) from the Reaxys database (June 2017). Where a melting-range had been reported, the upper limit was chosen for the analysis. Experimental setup for the study of

Enzymatic synthesis of glycosides: from natural O- and N-glycosides to rare C- and S-glycosides

• Jihen Ati,
• Pierre Lafite and
• Richard Daniellou

Beilstein J. Org. Chem. 2017, 13, 1857–1865, doi:10.3762/bjoc.13.180

• hydrolysis of the carbohydrate moieties in all the living organisms. They are actually classified in the CAZY database under 145 families, which contain more than 435,000 individual proteins [8]. Like the mechanisms described for the GTs, the catalysis of the hydrolytic reaction can occur with inversion or

• acceptors (Table 1). Still, as demonstrated by the CAZY database, the glycoscientists have nowadays access to a large (and increasing) library of GTs and GHs, and in a near future, they will be able to perform most reactions enzymatically. In addition, the access to large quantities of inexpensive

The chemistry and biology of mycolactones

• Matthias Gehringer and
• Karl-Heinz Altmann

Beilstein J. Org. Chem. 2017, 13, 1596–1660, doi:10.3762/bjoc.13.159

• established in 2001 by Kishi and co-workers [39][40], using a combination of model compound synthesis and exploitation of an NMR database [41][42]. The correctness of the assignment was subsequently verified by total synthesis (vide infra) [43]. After the discovery of mycolactones A/B (1a,b), eight congeners

Biomimetic molecular design tools that learn, evolve, and adapt

• David A Winkler

Beilstein J. Org. Chem. 2017, 13, 1288–1302, doi:10.3762/bjoc.13.125

• biological sciences. For example, they have recently been applied to predicting the feasibility of chemical reactions by learning relationships between the molecular properties of the reaction partners and the outcomes of the reactions in a large database [15]. Another recent example is the robot scientists

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

• considered a significant contribution to the field. A major breakthrough occurred in 1951, when Bijvoet confirmed, without ambiguity, the D-configuration of glucose, which had been assigned from indirect reasoning by Emil Fischer in 1891 [10]. At the present time, the Cambridge Structural Database contains a

• similarities and further consolidated by the availability of 3D dimensional structures [42]. The analysis of the GH structures present in the CAZy database helped not only to decipher the hydrolytic mechanism, but also reveal the evolutionary relationships between these enzymes. An extended classification

• to 900. In the CAZy database, CBMs are classified within 80 families based on amino acid sequence similarities, while a three-dimensional structural classification clusters CBM into seven fold families [43]. The most represented fold is the β-sandwich comprised of two β-sheets, each consisting of

Identification, synthesis and mass spectrometry of a macrolide from the African reed frog Hyperolius cinnamomeoventris

• Markus Menke,
• Pardha Saradhi Peram,
• Iris Starnberger,
• Walter Hödl,
• Gregory F.M. Jongsma,
• David C. Blackburn,
• Mark-Oliver Rödel,
• Miguel Vences and
• Stefan Schulz

Beilstein J. Org. Chem. 2016, 12, 2731–2738, doi:10.3762/bjoc.12.269

• chromatographic retention index are stored in our EIMS database, easing identification of similar compounds in the future. Using this approach, we could collect mass spectra of 5-dodecen-11-olide, 5- and 6-tridecen-12-olide, 5- to 9-tetradecen-13-olide, as well as 5- and 6-pentadec-14-olide (see Supporting

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

• interest, can assist in predicting the target structure, function and even possible binding and functional sites of the structure. In homology modeling, the first task is to find a homologous structure to the sequence of interest. To do that, the sequence is compared against a database of protein sequences

• structure is not known. The new “threaded” structure is then evaluated using various scoring methods [50][51]. This process is repeated for all experimentally determined 3D structures in a database and the best fit structure for the query sequence is obtained [35]. This process of identifying the best

• molecules and target proteins. PubChem, a small molecule repository is available through NIH which contains millions of biologically relevant small molecules [78]. ZINC is a virtual high-throughput screening compound library which is a free public resource [79][80]. This database contains over 35 million

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

• include C5–C4–C13–C14, −18.2(2)° and C4–N3–C7–C8, 111.2(2)°, defining the orientations of the indolizine and phenyl rings relative to the sydnone ring. Bond distances in the latter ring (see caption of Figure 2) compare favorably with previously published values in the Cambridge Structural Database (CSD

A new paradigm for designing ring construction strategies for green organic synthesis: implications for the discovery of multicomponent reactions to build molecules containing a single ring

• John Andraos

Beilstein J. Org. Chem. 2016, 12, 2420–2442, doi:10.3762/bjoc.12.236

• greenness” as a core principle based on reaction design was applied to a database of named organic reactions [10] and multicomponent reactions (MCRs) [11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49

• is essentially infinite [98][99][100][101][102] and that despite amassing a database of 1000 or more named reactions and functional group transformations over a period of almost three centuries, synthetic organic chemists have barely scratched the surface in exploring and eventually discovering what

• highlighting a particular 3- or other partition, rather than just inputting the structure itself. A similarity search would be conducted based on inputted target bond dissection maps already encoded in the database. Essentially each literature citation currently in any search engine, which reports syntheses of

TBHP-mediated highly efficient dehydrogenative cross-oxidative coupling of methylarenes with acetanilides

• Cui Chen,
• Weibing Liu and
• Peng Zhou

Beilstein J. Org. Chem. 2016, 12, 2250–2255, doi:10.3762/bjoc.12.217

• utilization in pharmaceutical and agrochemical applications [1][2][3], as well as for precursors in organic synthesis for the construction of natural products, polymers and organic materials [4][5][6]. The database of medicinal chemistry indicates that around 25% of synthetic drugs contain the amide moiety [7

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

• preferential cleavage with Lewis acids [31]. The Cambridge Structural Database (2015) [32] contains a single example of a five-membered 1,3-dioxolane orthoester [33]. Here, the ring adopts a distorted half-chair (C2) arrangement with a dihedral angle θ [O–C(4)–C(5)–O] = 32° [Figure 2a – ZICMED viewed C(4)→C(5

• located in the 2014 release of the Cambridge Structural Database (CSD v 5.35, which contains 658, 007 entries) using the Conquest software (v 1.16) and visualised using the Mercury software package (v 3.1). Conformational searching was conducted with Macromodel software, using a MonteCarlo search method

Ring-whizzing in polyene-PtL₂ complexes revisited

• Oluwakemi A. Oloba-Whenu,
• Thomas A. Albright and
• Chirine Soubra-Ghaoui

Beilstein J. Org. Chem. 2016, 12, 1410–1420, doi:10.3762/bjoc.12.135

• fragment orbital can interact with b2 to form an η3 complex as shown in 13. An η5 geometry, 14, will be favored using the empty e”1 orbital. The computed Gibbs free energy difference between the two is very small, namely 1.5 kcal/mol favoring η3. A recent search of the Cambridge crystallographic database

Towards the total synthesis of keramaphidin B

• Pavol Jakubec,
• Alistair J. M. Farley and
• Darren J. Dixon

Beilstein J. Org. Chem. 2016, 12, 1096–1100, doi:10.3762/bjoc.12.104

• the Oxford Chemical Crystallography Service for use of the instrumentation. X-ray crystallographic data have been deposited in the Cambridge Crystallographic Data Centre database (http://www.ccdc.cam.ac.uk/) under accession code 1481419.

Marine-derived myxobacteria of the suborder Nannocystineae: An underexplored source of structurally intriguing and biologically active metabolites

• Antonio Dávila-Céspedes,
• Peter Hufendiek,
• Max Crüsemann,
• Till F. Schäberle and
• Gabriele M. König

Beilstein J. Org. Chem. 2016, 12, 969–984, doi:10.3762/bjoc.12.96

• metabolites and for the biosynthesis of antimicrobials [59]. In these studies, PKS genes could be amplified, sequenced and compared with known sequences in the BLAST database. The potential of producing active molecules was established by using disc diffusion antibiotic activity testing of the bacterial

• synthesis of NRPS, PKS and hybrid NRPS-PKS products (see Table 1). Apart from the geosmin biosynthesis genes, no gene cluster or fragment thereof shares an identity higher than 33% to any known gene cluster in the MiBIG database [64]. It should be noted that since this is a draft genome sequence, the actual

cis–trans-Amide isomerism of the 3,4-dehydroproline residue, the ‘unpuckered’ proline

• Vladimir Kubyshkin and
• Nediljko Budisa

Beilstein J. Org. Chem. 2016, 12, 589–593, doi:10.3762/bjoc.12.57

• Cambridge Structural Database under the following IDs: 5- CCDC1443104, 6- CCDC1443105, 8- CCDC1443103, 9- CCDC1443102. The crystal structure of 7 have already been discussed in [35] and the deposit number was CCDC1042476. The structure files can be retrieved free of charge at http://www.ccdc.cam.ac.uk

My maize and blue brick road to physical organic chemistry in materials

• Anne J. McNeil

Beilstein J. Org. Chem. 2016, 12, 229–238, doi:10.3762/bjoc.12.24

• gelator design. We hypothesized that the Cambridge Structural Database (CSD), which contains over 700,000 organic and inorganic crystal structures, could be used to identify molecules that exhibit 1D interactions in the solid state. The rationale was that these molecules, or closely related derivatives

Inclusion complexes of 2-methoxyestradiol with dimethylated and permethylated β-cyclodextrins: models for cyclodextrin–steroid interaction

• Mino R. Caira,
• Susan A. Bourne,
• Halima Samsodien and
• Vincent J. Smith

Beilstein J. Org. Chem. 2015, 11, 2616–2630, doi:10.3762/bjoc.11.281

• parameters [15], from which the authors inferred a ‘channel cyclindrical structure’ as a possible arrangement in the crystalline state. However, no definitive structural studies were subsequently published. Our search in the Cambridge Structural Database [16] for CD complex structures revealed two reported

• Crystallographic Database [16], structure solution by isomorphous replacement was not possible. Both crystal structures were therefore solved ab initio by direct methods using the program SHELXD [22]. Model development involved successive difference Fourier syntheses and iterative refinement by the full-matrix

Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex

• Chompoonut Rungnim,
• Sarunya Phunpee,
• Manaschai Kunaseth,
• Supawadee Namuangruk,
• Kanin Rungsardthong,
• Thanyada Rungrotmongkol and
• Uracha Ruktanonchai

Beilstein J. Org. Chem. 2015, 11, 2306–2317, doi:10.3762/bjoc.11.251

• databank (3C6G), while the α-MGS structure was extracted from the International Union of Crystallography (KP2293) database, see Figure 1. According to the ChemAxon method [25][26][27], the calculated pKa of three hydroxy groups are 7.4 (O6), 7.8 (O3), and 8.2 (O5). For that reason, the α-mangostin was

The Beilstein Journal of Organic Chemistry and the changing face of scientific publishing

• Martin G. Hicks and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2015, 11, 2242–2244, doi:10.3762/bjoc.11.242

• made available to experts working directly in a particular field. Further processing will allow it to be stored in structured databases for searching, and with further annotation, it can be linked or added to publications. The Protein Data Bank [15] and the Cambridge Structural Database [16] are two

• , to which most scientific publishers (including the Beilstein-Institut), belong. CrossCheck is a database maintained by CrossRef [20] containing all publications of all of its members where new submissions can be checked using the iThenticate system. The use of CrossCheck requires manual control to

Pyridinoacridine alkaloids of marine origin: NMR and MS spectral data, synthesis, biosynthesis and biological activity

• Louis P. Sandjo,
• Victor Kuete and
• Maique W. Biavatti

Beilstein J. Org. Chem. 2015, 11, 1667–1699, doi:10.3762/bjoc.11.183

• of the A ring when the B ring is not aromatic. The compilation of this NMR data could be used as a library for a database prediction and could also save time with respect to structure elucidation of related natural congeners. Earlier, successful synthetic figures have also been presented as well as