Rearrangements of organic peroxides and related processes

• Ivan A. Yaremenko,
• Vera A. Vil’,
• Dmitry V. Demchuk and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2016, 12, 1647–1748, doi:10.3762/bjoc.12.162

The EIMS fragmentation mechanisms of the sesquiterpenes corvol ethers A and B, epi-cubebol and isodauc-8-en-11-ol

• Patrick Rabe and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2016, 12, 1380–1394, doi:10.3762/bjoc.12.132

• , contain several methyl groups, and possibly one or more olefinic double bonds, an alcohol or ether function. Their much higher structural complexity compared to, e.g., FAMEs and monoterpenes renders a prediction of the fragmentation behaviour of unknown compounds in mass spectrometry and consequently the

Modular synthesis of the pyrimidine core of the manzacidins by divergent Tsuji–Trost coupling

• Sebastian Bretzke,
• Stephan Scheeff,
• Felicitas Vollmeyer,
• Friederike Eberhagen,
• Frank Rominger and
• Dirk Menche

Beilstein J. Org. Chem. 2016, 12, 1111–1121, doi:10.3762/bjoc.12.107

• dimer in the crystal lattice, which is stabilized by two hydrogen bonds between the urea oxygen atoms and the tosyl-protected nitrogens. This also unambiguously confirms the absolute configuration of 39 and corroborates our prediction of the asymmetric adduct 31. We then attempted the installation of

Is conformation a fundamental descriptor in QSAR? A case for halogenated anesthetics

• Maria C. Guimarães,
• Mariene H. Duarte,
• Josué M. Silla and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2016, 12, 760–768, doi:10.3762/bjoc.12.76

• stable minima (ruled by intramolecular interactions) do not necessarily coincide with the bioconformation (ruled by enzyme induced fit). Consequently, a QSAR model based on two-dimensional chemical structures was built and exhibited satisfactory modeling/prediction capability and interpretability, then

• structure indeed encodes biochemical properties and that MIA descriptors can be useful to anticipating pMAC of prospective congeneric drug-like candidates. MIA-QSAR and 3D-QSAR have already been compared to each other in a variety of studies and the prediction results are similar [10][24][25][26], but the

• available in the Dragon software. Thus, a major goal in QSAR is to determine and interpret the chemical motifs/properties responsible for the observed biological effects. We have checked that even the simple log P model yields good prediction ability upon selection of test set compounds using the Kennard

Strecker degradation of amino acids promoted by a camphor-derived sulfonamide

• M. Fernanda N. N. Carvalho,
• M. João Ferreira,
• Ana S. O. Knittel,
• Maria da Conceição Oliveira,
• João Costa Pessoa,
• Rudolf Herrmann and
• Gabriele Wagner

Beilstein J. Org. Chem. 2016, 12, 732–744, doi:10.3762/bjoc.12.73

• stable (10–16 kcal/mol) than the primary products, and once formed, they will probably not tautomerize back to 7 and 8. Interestingly, the primary products are of quite similar stability (16.4 to 18.2 kcal/mol, respectively), which does not allow a prediction of which path may dominate the

From steroids to aqueous supramolecular chemistry: an autobiographical career review

• Bruce C. Gibb

Beilstein J. Org. Chem. 2016, 12, 684–701, doi:10.3762/bjoc.12.69

• competition gives the computationalists a unique opportunity to try and hone their skills, which in return provides feedback to those interested in the a priori prediction of the thermodynamics of binding. For example, being able to predict ahead of time which ligands binds best to a protein binding-site has

Three new trixane glycosides obtained from the leaves of Jungia sellowii Less. using centrifugal partition chromatography

• Luíse Azevedo,
• Larissa Faqueti,
• Marina Kritsanida,
• Antonia Efstathiou,
• Despina Smirlis,
• Gilberto C. Franchi Jr,
• Grégory Genta-Jouve,
• Sylvie Michel,
• Louis P. Sandjo,
• Raphaël Grougnet and
• Maique W. Biavatti

Beilstein J. Org. Chem. 2016, 12, 674–683, doi:10.3762/bjoc.12.68

• . Similarly, H-13 unveiled the same interactions with H-1 and H-9 while H-14 correlated with H-8 (Figure 4). In order to determine the absolute configuration of the compounds 1–3, ECD spectra prediction was used [36][37]. The absolute configuration of 1 was assigned as 2R, 6S, 7R, 10R, and 11S by ECD analysis

Correction: Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 608–610, doi:10.3762/bjoc.12.59

(Thio)urea-mediated synthesis of functionalized six-membered rings with multiple chiral centers

• Giorgos Koutoulogenis,
• Nikolaos Kaplaneris and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2016, 12, 462–495, doi:10.3762/bjoc.12.48

• mainly in the s-trans conformation, that factor is crucial since complete prediction of the stereochemical outcome of the reaction is possible. Generally, the enamines formed can interact with the substrates in two ways, via electronic or steric interactions (Scheme 2). The electronic interaction

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 415–428, doi:10.3762/bjoc.12.45

• experimentally known MIC values of eight linezolid analogues were used in order to crosscheck the robustness of our model. In a final step, this benchmarking led to the prediction of several new and promising lead compounds. Synthesis and biological evaluation of the new compounds are on the way. Keywords

• ) virtual screenings [28][29][30] of large molecular databases to B) sophisticated simulations of the state equations [31][32]. Nevertheless, both strategies have their own advantages and disadvantages when it comes to the reliable prediction of new drug candidates. While fast virtual screening methods

• calculated relative binding energy of −15.6 kJ/mol seems to be lower bound for the prediction of an effective binder. The experimental ineffectiveness of compound 3 (MIC value >50 mg/L) is mirrored by our computed decrease of the enthalpic contribution by more than 12 kJ/mol. Two earlier in silico approaches

Self and directed assembly: people and molecules

• Tony D. James

Beilstein J. Org. Chem. 2016, 12, 391–405, doi:10.3762/bjoc.12.42

• to bring together world leading researchers and junior scientists on an equal footing and to provide an environment where research ideas can be openly discussed in order to establish new collaborations and develop new ideas. The future “Prediction is very difficult, especially if it's about the

Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2016, 12, 377–390, doi:10.3762/bjoc.12.41

• rearranged product. In addition, the dynamics calculations indicated that the 1,2-methyl (C17) shift that forms the abietadiene precursor should occur specifically to one face of the carbocation carbon (C15), a prediction that could be tested through substrate labeling. If only trajectories that lead to the

• than others. Of particular note was the prediction that the TSS for conversion of the cedryl cation to the prezizyl cation (Figure 11, step 9) and for the conversion of the prezizyl cation to the zizyl cation (Figure 11, step 10) are bound more strongly than the carbocations that immediately precede

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

• gelators. To test this hypothesis, we used crystal morphology prediction tools to identify needle-shaped crystals in the CSD. Graduate student Kelsey (King) Carter and undergraduate student Sarah Cox predicted the morphologies of 186 Pb(II)-containing crystals. Focusing on the top 5% and selecting stable

• additional compounds were synthesized, all of which were gelators, with some exhibiting lower cgcs than the known gelators (Scheme 1b). Given the mixed results of this approach, we believe that our CSD-morpholgy prediction method represents a better strategy for identifying new gelators for specific

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

• experimental PXRD trace of the product with that of an isostructural inclusion complex, namely the β-CD complex of 4-tert-butylbenzyl alcohol (CSD refcode KOFJEU [16]), and finding a reasonable match [20]. This procedure also enabled correct prediction of the space group (C2221) of the complex and the

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

• The gas phase energy, ΔEMM, is a summation of bonded and non-bonded (electrostatic and van der Waals (vdW)) energies obtained from molecular mechanics calculation. The ΔGsolv is solvation free energy. In general, there are several methods for ΔGsolv prediction. Some methods calculate the ΔGsolv using

Mechanism, kinetics and selectivity of selenocyclization of 5-alkenylhydantoins: an experimental and computational study

• Biljana M. Šmit,
• Radoslav Z. Pavlović,
• Dejan A. Milenković and
• Zoran S. Marković

Beilstein J. Org. Chem. 2015, 11, 1865–1875, doi:10.3762/bjoc.11.200

• synthesis of fused bicyclic hydantoins. 1H NMR spectroscopy monitoring, as well as 1H NMR chemical shifts prediction [29][30][31][32][33][34] is used as a useful tool in the search of the most probable intermediates in the reaction. The theoretical results are discussed and compared with our experimental

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

Why base-catalyzed isomerization of N-propargyl amides yields mostly allenamides rather than ynamides

• Armando Navarro-Vázquez

Beilstein J. Org. Chem. 2015, 11, 1441–1446, doi:10.3762/bjoc.11.156

• for the corresponding isomers for a selected combination of starting amides or carbamates and a final urea example (Figure 1) were computed using ab initio and DFT methods. Results and Discussion Computational procedures It is known that ab initio prediction of cumulene–polyynes isomerization energies

• the same system with a ΔH0 value of −1.1 kcal/mol (Table 1). The best performing DFT functional for the prediction of cumulene–polyynes isomerization energies was found by Zhao and Truhlar to be the hybrid meta-GGA M05 functional [9]. Since then, new functionals of the same family have been reported

• energies, providing a suitable computational methodology for the prediction of the result of the isomerization reaction in similar systems. Computational Procedures All reaction energies are reported as enthalpies at zero K (ΔH0 = ΔE + ZPVE). The structures were fully optimized at the reported levels of

Donor–acceptor type co-crystals of arylthio-substituted tetrathiafulvalenes and fullerenes

• Xiaofeng Lu,
• Jibin Sun,
• Shangxi Zhang,
• Longfei Ma,
• Lei Liu,
• Hui Qi,
• Yongliang Shao and
• Xiangfeng Shao

Beilstein J. Org. Chem. 2015, 11, 1043–1051, doi:10.3762/bjoc.11.117

• potentially accommodate the solvent molecules. In a previous report, we have proposed that C70 tends to form co-crystals with a larger acceptor ratio [63]. However, the present results suggest that this prediction would not hold because both C60 and C70 form the type I and type II co-crystals with Ar-S-TTFs

Cross-dehydrogenative coupling for the intermolecular C–O bond formation

• Igor B. Krylov,
• Vera A. Vil’ and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2015, 11, 92–146, doi:10.3762/bjoc.11.13

• also of fundamental interest because new aspects of the reactivity of organic compounds have to be found for the performance of these reactions. The prediction of the conditions necessary for the efficient cross-dehydrogenative coupling is an important problem that requires an understanding of the

Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

• Lidija-Marija Tumir,
• Marijana Radić Stojković and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

• mode, depending on the ratio r = [compound]/[polynucleotide]. Moreover, there is no set of rules which will accurately predict the dominant binding site of newly designed phenanthridine/phenanthridinium analogues. All aforementioned also hampers the prediction of the fluorimetric response, which is

Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes

• Bodee Nutho,
• Wasinee Khuntawee,
• Chompoonut Rungnim,
• Piamsook Pongsawasdi,
• Peter Wolschann,
• Alfred Karpfen,
• Nawee Kungwan and
• Thanyada Rungrotmongkol

Beilstein J. Org. Chem. 2014, 10, 2789–2799, doi:10.3762/bjoc.10.296

• radial distribution function (RDF). The calculations of MM-PBSA/GBSA binding free energies (∆GMM-PBSA and ∆GMM-GBSA) and their energy components were analyzed using the mm_pbsa module. Free energy prediction The MM-PBSA and MM-GBSA methods have been widely used to estimate the binding free energies of

• is worth to note that in comparison to the QM energy (∆EQM) the MM method was likely found to overestimate the binding interaction by ca. 10 kcal/mol for all snapshots in the three forms of complex (Figure 7). Our results also suggested that for binding free energy prediction, the entropy and

Self-assembled monolayers of shape-persistent macrocycles on graphite: interior design and conformational polymorphism

• Joscha Vollmeyer,
• Friederike Eberhagen,
• Sigurd Höger and
• Stefan-S. Jester

Beilstein J. Org. Chem. 2014, 10, 2774–2782, doi:10.3762/bjoc.10.294

• a prediction of the surface pattern at high concentrations. This should lead to a tailorable structure of both, the porous and dense polymorphs, or – in other words – an alteration between two discrete designable packings, here as an effect of the compound concentration in the supernatant solution

Building complex carbon skeletons with ethynyl[2.2]paracyclophanes

• Ina Dix,
• Lidija Bondarenko,
• Peter G. Jones,
• Thomas Oeser and
• Henning Hopf

Beilstein J. Org. Chem. 2014, 10, 2013–2020, doi:10.3762/bjoc.10.209

• ago we described the preparation of various ethynyl[2.2]paracyclophanes and suggested that these compounds could be developed into useful building blocks for the construction of larger, stereochemically complex carbon frameworks (scaffolds) [2]. This prediction is clearly becoming reality, as shown by

Pyrrolidine nucleotide analogs with a tunable conformation

• Lenka Poštová Slavětínská,
• Dominik Rejman and
• Radek Pohl

Beilstein J. Org. Chem. 2014, 10, 1967–1980, doi:10.3762/bjoc.10.205

• thereof to an active site of a particular enzyme. The knowledge of the conformation of nucleosides, nucleotides and their analogs is therefore essential for the understanding or even prediction of their biological properties. There are several approaches providing information on the conformation of a five