Grip on complexity in chemical reaction networks

• Albert S. Y. Wong and
• Wilhelm T. S. Huck

Beilstein J. Org. Chem. 2017, 13, 1486–1497, doi:10.3762/bjoc.13.147

• impossible, to solve without the reduction of variables [99]. To avoid loss in chemical information, we implemented the full set of rate equations in MATLAB and COPASI that could simulate the trajectory of the individual species by the stepwise numerical integration in time. Importantly, all rate constants

• perspective, however, urges an approach using a synthetic strategy based on the stepwise build-up of complex molecular systems. We envision the development of a toolbox that allows us to go beyond describing and understanding systems, extending to the rational design of function arising from a collection of

Synthesis of oligonucleotides on a soluble support

• Harri Lönnberg

Beilstein J. Org. Chem. 2017, 13, 1368–1387, doi:10.3762/bjoc.13.134

• strategy may be utilized, but the stepwise linear approach proceeding from the 3´- to the 5´-terminus of ON is nowadays almost exclusively exploited [1][2]. The coupling reaction may take place either at oxidation level III or V of phosphorus. Owing to higher reactivity of P(III) centers, appropriately

• DCM/Et2O. In spite of several precipitations and recrystallizations, one coupling cycle could be completed in 5 hours, the stepwise coupling yield ranging from 90% to 95% and the crude PEG-bound octamer was obtained in 79% yield. The coupling of dGibu proceeded, however, in more than 100% yield, which

• building blocks, and the coupling was carried out in a mixture of pyridine and dioxane in the presence of NMI (5 equiv). Otherwise, the protocol was similar to the previous one. The average stepwise coupling yield upon the assembly of octamer d(5´-TAGCGCTA-3´) was 93.5%, and 55% of the PEG-anchored

Aqueous semisynthesis of C-glycoside glycamines from agarose

• Juliana C. Cunico Dallagnol,
• Alexandre Orsato,
• Diogo R. B. Ducatti,
• Miguel D. Noseda,
• Maria Eugênia R. Duarte and
• Alan G. Gonçalves

Beilstein J. Org. Chem. 2017, 13, 1222–1229, doi:10.3762/bjoc.13.121

• , there is no available methodology to obtain this building block using chemical hydrolysis. We produced compound 9 by hydrolysis of the previously synthesized glycamine 7. In addition, we conducted a stepwise sequence of hydrolysis and reduction reactions, followed by periodate cleavage of the 1,2

From chemical metabolism to life: the origin of the genetic coding process

• Antoine Danchin

Beilstein J. Org. Chem. 2017, 13, 1119–1135, doi:10.3762/bjoc.13.111

• this intelligent way, but unfolded more slowly. The actual emergence of the genetic code required a succession of small steps involving progressive improvement of peptide-based metabolism. As expected from a stepwise development, this process created a fair number of anecdotal features that were

Aggregation behaviour of a single-chain, phenylene-modified bolalipid and its miscibility with classical phospholipids

• Simon Drescher,
• Vasil M. Garamus,
• Christopher J. Garvey,
• Annette Meister and
• Alfred Blume

Beilstein J. Org. Chem. 2017, 13, 995–1007, doi:10.3762/bjoc.13.99

• again several peaks: the most distinct ones at 52.1 °C, and three smaller ones at 53.9 °C, 47.8 °C, and 40.2 °C. In the DSC heating curve of some of our bolalipid/phospholipid mixtures, an additional exothermic peak as well as a continuous or stepwise decrease in the heat capacity is observed during

Pd- and Cu-catalyzed approaches in the syntheses of new cholane aminoanthraquinone pincer-like ligands

• Nikolay V. Lukashev,
• Gennadii A. Grabovyi,
• Dmitry A. Erzunov,
• Alexey V. Kazantsev,
• Gennadij V. Latyshev,
• Alexei D. Averin and
• Irina P. Beletskaya.

Beilstein J. Org. Chem. 2017, 13, 564–570, doi:10.3762/bjoc.13.55

• +, Fe2+, Co2+, Ni2+, Zn2+, Cu2+, Ag+, Pb2+, Hg2+, Cr3+, Ga3+, Y3+, In3+) on the UV spectrum of 5c (Figure 2). The qualitative selectivity test by stepwise addition of 1, 2, 3, and 5 equiv of metal perchlorates in MeCN to the solution of 5c in MeCN revealed that the majority of cations did not influence

Fast and efficient synthesis of microporous polymer nanomembranes via light-induced click reaction

• Qi An,
• Youssef Hassan,
• Xiaotong Yan,
• Peter Krolla-Sidenstein,
• Tawheed Mohammed,
• Mathias Lang,
• Stefan Bräse and
• Manuel Tsotsalas

Beilstein J. Org. Chem. 2017, 13, 558–563, doi:10.3762/bjoc.13.54

• the substrates with an alkyne terminated self-assembled monolayer, which presents initial groups for the stepwise growing of the CMPs using the TYC reaction. In the first step, we immersed the functionalized surface in a solution of the tetra-topic thiol building block (tetrakis(4-sulfanylphenyl

Dimerization reactions of aryl selenophen-2-yl-substituted thiocarbonyl S-methanides as diradical processes: a computational study

• Michael L. McKee,
• Grzegorz Mlostoń,
• Katarzyna Urbaniak and
• Heinz Heimgartner

Beilstein J. Org. Chem. 2017, 13, 410–416, doi:10.3762/bjoc.13.44

• , Winterthurerstrasse 190, CH-8057 Zurich, Switzerland 10.3762/bjoc.13.44 Abstract An intriguing stepwise diradical mechanism of the dimerization of the reactive intermediate (thiocarbonyl S-methanide) appearing in the reaction of phenyl selenophen-2-yl thioketone with diazomethane was studied by means of

• processes have not been studied in detail yet. Whereas the formation of the 1,3-dithiolane 4 can be explained via a concerted [2 + 3] cycloaddition of 1 as a 1,3-dipole with the activated C=S bond of 1, the dimerization leading to 5 seems to occur stepwise via an intermediate stabilized 1,6-diradical 6. In

• isolated from the reaction mixture. Thus, the presence of the heteroatom is of crucial importance for this new type of dimerization of aryl/hetaryl thiocarbonyl S-methanides of type 1 and this fact reflects the importance of so called ‘heavy atom effect’ [15] in the studied system. Stepwise, diradical

Spectral and DFT studies of anion bound organic receptors: Time dependent studies and logic gate applications

• Srikala Pangannaya,
• Neethu Padinchare Purayil,
• Shweta Dabhi,
• Venu Mankad,
• Prafulla K. Jha,
• Satyam Shinde and
• Darshak R. Trivedi

Beilstein J. Org. Chem. 2017, 13, 222–238, doi:10.3762/bjoc.13.25

• the aforementioned color change. The stepwise addition of Hg2+ ions to a solution of R1 leads to an increased intensity and bathochromic shift by 8 units of the absorption band at 266 nm. On the other hand the intensities of the bands centered at 325 nm and 395 nm decreased due to the deprotonation of

Total synthesis of a Streptococcus pneumoniae serotype 12F CPS repeating unit hexasaccharide

• Peter H. Seeberger,
• Claney L. Pereira and
• Subramanian Govindan

Beilstein J. Org. Chem. 2017, 13, 164–173, doi:10.3762/bjoc.13.19

• + 3] total synthesis approach prompted us to retreat to the linear avenue (Scheme 1, route B) towards the target oligosaccharide in order to avoid the sterically demanding late-stage glycosylation. Differentially protected mannosazide 4 served as the starting point for stepwise assembly from the

Self-optimisation and model-based design of experiments for developing a C–H activation flow process

• Alexander Echtermeyer,
• Yehia Amar,
• Jacek Zakrzewski and
• Alexei Lapkin

Beilstein J. Org. Chem. 2017, 13, 150–163, doi:10.3762/bjoc.13.18

• algorithm to account for feasible and infeasible solutions in X, hence learning the promising regions of the design space and evolving some internal process knowledge stepwise with each new iteration. An infeasible solution could occur if an experiment fails in the laboratory. Thus, each point in the

New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

• Pavel Nagorny and
• Zhankui Sun

Beilstein J. Org. Chem. 2016, 12, 2834–2848, doi:10.3762/bjoc.12.283

• with significantly lower ee (11%) was observed. These results suggest that the reaction might proceed mainly in a stepwise SN1-like manner, via a benzylic carbocation intermediate. Despite the fact that several variants of chiral halogen bond-donor catalysts have been synthesized, to the best of our

cis-Diastereoselective synthesis of chroman-fused tetralins as B-ring-modified analogues of brazilin

• Dimpee Gogoi,
• Runjun Devi,
• Pallab Pahari,
• Bipul Sarma and
• Sajal Kumar Das

Beilstein J. Org. Chem. 2016, 12, 2816–2822, doi:10.3762/bjoc.12.280

• that the [6,5]-ring system in brazilin and related natural products 1–4 remains cis-fused, its corresponding [6,6]-ring system in 5 can have cis or trans stereochemistry at the ring junction. In our previous work, we observed a cis relationship (both in concerted or/and stepwise-epoxide ring opening

• ) between the 4-aryl group and H atom at the C-3 position of 4-arylchroman-3-ols (thus giving rise to trans-4-arylchroman-3-ols) [22][23]. But it was not obvious how the planned IFCEA cyclization onto the pre-existing 6-membered ring, in case of stepwise-epoxide ring opening, would influence the product

A new protocol for the synthesis of 4,7,12,15-tetrachloro[2.2]paracyclophane

• Donghui Pan,
• Yanbin Wang and
• Guomin Xiao

Beilstein J. Org. Chem. 2016, 12, 2443–2449, doi:10.3762/bjoc.12.237

• generated in situ was reduced by stepwise addition of H2O2, which would improve the selectivity of 2a by preventing the side reactions. Next, the bromination of other para-xylene derivatives under optimized conditions (see Table 1, entry 11) were investigated to examine the versatility of the protocol. As

Combined experimental and theoretical studies of regio- and stereoselectivity in reactions of β-isoxazolyl- and β-imidazolyl enamines with nitrile oxides

• Ilya V. Efimov,
• Marsel Z. Shafikov,
• Nikolai A. Beliaev,
• Natalia N. Volkova,
• Tetyana V. Beryozkina,
• Wim Dehaen,
• Zhijin Fan,
• Viktoria V. Grishko,
• Gert Lubec,
• Pavel A. Slepukhin and
• Vasiliy A. Bakulev

Beilstein J. Org. Chem. 2016, 12, 2390–2401, doi:10.3762/bjoc.12.233

• yields. The intermediate 4,5-dihydroisoxazolines were isolated as trans isomers during the reaction of (E)-β-imidazol-4-yl enamines with aryl and cyclohexylhydroxamoyl chlorides. Stepwise and concerted pathways for the reaction of β-azolyl enamines with hydroxamoyl chlorides were considered and studied

• chlorides proceeds in a regio- and stereospecific manner. In contrast to the reactions of these β-azolyl enamines, similar reactions of β-alkyl enamines as reported by Bujak et al. [24] are regioselective and not stereospecific and therefore not concerted. We could propose stepwise (path 1) and concerted

• . Investigation of the stepwise mechanism’s pathway allowed locating the only transition state (1a_1−7), which is appropriate to the addition of nitrile oxide 2a onto the double bond of enamine 1a_1, and the respective product – oxime 7. However, the intermediate 7 was found to cyclize to isoxazoline 3a through

Highly chemo-, enantio-, and diastereoselective [4 + 2] cycloaddition of 5H-thiazol-4-ones with N-itaconimides

• Shuai Qiu,
• Choon-Hong Tan and
• Zhiyong Jiang

Beilstein J. Org. Chem. 2016, 12, 2293–2297, doi:10.3762/bjoc.12.222

• + 2] annulation between 5H-thiazol-4-ones and nitroalkenes [10]. In this stepwise process, the use of 3,5-dichlorophenyl as the substituent group of the urea in catalyst V would remarkably increase the free energy difference between R- and S-selection in the first Michael addition step, and also

Stereoselective synthesis of fused tetrahydroquinazolines through one-pot double [3 + 2] dipolar cycloadditions followed by [5 + 1] annulation

• Xiaofeng Zhang,
• Kenny Pham,
• Shuai Liu,
• Marc Legris,
• Alex Muthengi,
• Jerry P. Jasinski and
• Wei Zhang

Beilstein J. Org. Chem. 2016, 12, 2204–2210, doi:10.3762/bjoc.12.211

• ; tetrahydroquinazoline; Introduction The synthesis of new molecules with potential biological activity through pot, atom and step-economic (PASE) reactions is an attractive green organic technique [1][2][3][4][5]. By the combination of multicomponent reactions (MCR) [6][7][8][9][10][11] with stepwise one-pot reactions

Rapid regio- and multi-coupling reactivity of 2,3-dibromobenzofurans with atom-economic triarylbismuths under palladium catalysis

• Maddali L. N. Rao,
• Jalindar B. Talode and
• Venneti N. Murty

Beilstein J. Org. Chem. 2016, 12, 2065–2076, doi:10.3762/bjoc.12.195

• performed in a stepwise manner (step 1 and step 2) in a one-pot operation without any intermediate isolation. These results are given in Table 6. To elaborate, firstly we carried out the preparation of 2-aryl-3-bromobenzofuran in step 1 and it was followed by a second arylation at the 3-position as part of

Varioloid A, a new indolyl-6,10b-dihydro-5aH-[1]benzofuro[2,3-b]indole derivative from the marine alga-derived endophytic fungus Paecilomyces variotii EN-291

• Peng Zhang,
• Xiao-Ming Li,
• Xin-Xin Mao,
• Attila Mándi,
• Tibor Kurtán and
• Bin-Gui Wang

Beilstein J. Org. Chem. 2016, 12, 2012–2018, doi:10.3762/bjoc.12.188

• extracted repeatedly with EtOAc (3 × 15 L) to afford a residue (4.3 g), which was subjected to silica gel chromatography using a VLC column with a stepwise gradient of a mixture of petroleum ether (PE)−ethyl acetate (EtOAc) (from 5:1 to 1:1), and then by CHCl3−MeOH (20:1 and 10:1) to provide 7 fractions (1

Synthesis and characterization of fluorinated azadipyrromethene complexes as acceptors for organic photovoltaics

• Forrest S. Etheridge,
• Roshan J. Fernando,
• Sandra Pejić,
• Matthias Zeller and
• Geneviève Sauvé

Beilstein J. Org. Chem. 2016, 12, 1925–1938, doi:10.3762/bjoc.12.182

• cleaned stepwise in each of the following under ultra-sonication for 15 minutes: detergent, deionized water, acetone, and isopropanol. From a 0.25 M ZnO precursor solution, the ZnO layer was spun coat. For all of the devices fabricated, the total concentration of the active layer was 20 mg/mL with varying

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

• alternative stepwise process involves the C–OR bond spontaneously cleaving at a rate similar to that of RO− protonation by H3O+. The latter describes a spontaneous uncatalysed hydrolysis. In the case of 1,3-dioxolanes, the concerted mechanism is believed to dominate [25]; however Guthrie [9] asserts that

• orthoesters are in fact delicately poised between stepwise and concerted processes; depending upon the substituent, both mechanisms are operational for aryl dimethyl orthoformates [21]. Stage 2 sees reaction of B with H2O to afford 2-hydroxy-1,3-dioxolane C (i.e., k2) with the overall equilibrium constant K2

Synthesis of ferrocenyl-substituted 1,3-dithiolanes via [3 + 2]-cycloadditions of ferrocenyl hetaryl thioketones with thiocarbonyl S-methanides

• Grzegorz Mlostoń,
• Róża Hamera-Fałdyga,
• Anthony Linden and
• Heinz Heimgartner

Beilstein J. Org. Chem. 2016, 12, 1421–1427, doi:10.3762/bjoc.12.136

• -methanides led to mixtures of 2-CH2 and 5-CH2 isomers with the major component being the sterically more crowded 2-CH2 isomers. The preferred formation of the latter products is explained by the assumption that the formal [3 + 2]-cycloadducts were formed via a stepwise reaction mechanism with a stabilized

• -dithiolanes, supports the proposed stepwise radical reaction mechanism via a stabilized 1,5-diradical as an intermediate. Finally, in the case of ferrocenyl methyl thioketone used as a dipolarophile, the concerted [3 + 2]-cycloaddition dominated due to the reduced stabilizing effect of the methyl group

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

• avoided by the assumption of a concerted process from A1+ to H1+, but it will be very difficult, if not impossible, to distinguish experimentally between a stepwise and the alternative concerted mechanism. Both PMA119 and PMA119(179) point to a formation of the ion m/z = 119 from the C1–C6 + C15 portion

Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides

• Andrew W. Truman

Beilstein J. Org. Chem. 2016, 12, 1250–1268, doi:10.3762/bjoc.12.120

• , dehydropiperidine or piperidine is consistent with a [4 + 2] cycloaddition across two dehydrated serine residues [79][80]. Genetic disruption of tclM from the thiocillin pathway showed that TclM was responsible for this transformation [81], although the precise cyclisation mechanism (concerted or stepwise) could

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

• . Therefore, a stepwise approach towards 19 was pursued instead. This involved either a coupling of 12 first with isocyanate to give 16 followed by a cross-metathesis or starting with the cross-metathesis to 18 and subsequent installment of the urea motif. As shown in the table inserted in Scheme 3 for