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

• robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known “S curve”, with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive

• methods and their potential impacts in chemistry, engineering, and medicine. Keywords: automated chemical synthesis; deep learning; evolutionary algorithms; in silico evolution; machine learning; materials design and development; neural networks; Introduction There is still not a clear understanding of

• pharmaceutical industry developed high-throughput chemical synthesis and screening technologies in the late 20th century. Materials scientists have recently begun adapting these technologies to the synthesis and characterization of materials. Figure 7 shows a new high-throughput-materials synthesis and

Strategies toward protecting group-free glycosylation through selective activation of the anomeric center

• A. Michael Downey and
• Michal Hocek

Beilstein J. Org. Chem. 2017, 13, 1239–1279, doi:10.3762/bjoc.13.123

• example of this powerful methodology has been reported from the Fairbanks group [16] recently. They synthesized a phosphorylated glycoprotein containing a mannose-6-phosphate (M6P)-terminated N-glycan (Scheme 3). Their work combined the chemical synthesis of a phosphotetrasaccharide with the enzymatic

• , as these enzymes can be utilized in drug design and hence has value to the medical community as well. These enzymes also are generally regioselective for the position 9 of purines and the position 1 of pyrimidines which is a persisting challenge in the chemical synthesis of biologically active

• field. It is driven by the appeal of waste reduction in chemical synthesis that the use of stoichiometric amounts of reagents, unfortunately cause. Typical transition metals employed for promoting the glycosylation of protected acceptors using protected donors include Pd, Ni, Au, Rh, Ru, and Ti [61]. In

Synthesis of alkynyl-substituted camphor derivatives and their use in the preparation of paclitaxel-related compounds

• M. Fernanda N. N. Carvalho,
• Rudolf Herrmann and
• Gabriele Wagner

Beilstein J. Org. Chem. 2017, 13, 1230–1238, doi:10.3762/bjoc.13.122

• ; platinum; Introduction Enantiomerically pure raw materials, available in a sustainable manner from the natural “chiral pool” [1], offer a convenient entrance for the chemical synthesis of other chiral compounds, e.g., rare natural products and their analogues [2], or chiral catalysts [3][4]. A prominent

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

• . The unpolymerized product shows AnGal as a C-threofuranose motif [7] (see agarobiose, 2, Scheme 1) and because C-glycosides are useful moieties for chemical synthesis and medicinal chemistry, agarose hydrolysis products can be considered interesting carbohydrate-based building blocks [8] to be

Automating multistep flow synthesis: approach and challenges in integrating chemistry, machines and logic

• Chinmay A. Shukla and
• Amol A. Kulkarni

Beilstein J. Org. Chem. 2017, 13, 960–987, doi:10.3762/bjoc.13.97

• reduce the reaction time scales significantly, complex work-up and offline analysis are some of the bottlenecks of easy implementation of multistep flow synthesis. It also brings the need for automation. Automation in chemical synthesis is not new for the chemical industry. However, for the multistep

• synthesis, viz. in terms of data, consistency, and reproducibility. Review Automation in flow synthesis Automation in target specific as well as routine chemical synthesis will be among the most likely happening things in the time to come [35][36]. The role of automation in the flow synthesis can be

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

• isoprenoid titers in plants may be low in dependence to seasonal [9] or circadian expression [10]. On the other hand for some members simply the number of available plants may be limited like the pacific yew Taxus brevifolia from which paclitaxel was first extracted [11]. The chemical synthesis can be an

• and sustainability akin to total chemical synthesis, which is often associated with toxic metal-organic chemistry, low product yields and/or insufficient purity [19][20]. A promising route for sufficient supply of industrially relevant products or their precursors is the heterologous production of

Contribution of microreactor technology and flow chemistry to the development of green and sustainable synthesis

• Flavio Fanelli,
• Giovanna Parisi,
• Leonardo Degennaro and
• Renzo Luisi

Beilstein J. Org. Chem. 2017, 13, 520–542, doi:10.3762/bjoc.13.51

• becoming a new technique for fulfilling several of the twelve green chemistry principles. The microreactor approach, could provide protection, preserves atom economy, guarantees less hazardous chemical synthesis and allows the use of safer solvents and auxiliaries. Furthermore, it pushes towards designing

• concept of flash chemistry as a "field of chemical synthesis using flow microreactors where extremely fast reactions are conducted in a highly controlled manner to produce desired compounds with high selectivity" was firstly introduced by Yoshida [10]. Flash chemistry can be considered a new concept in

Polyketide stereocontrol: a study in chemical biology

• Kira J. Weissman

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

• reduced product obtained by chemical synthesis, in which C-2 was deuterium labeled (i.e., [2-2H]-2-methyl-3-hydroxypentanoate); the substrate was tethered enzymatically to a model ACP domain sourced from the DEBS PKS. By incubating with NADP+, the redox reaction was run in reverse, establishing an

• economic importance of these compounds, there is significant interest in trying to generate new versions of polyketides for evaluation as drug leads. The significant bioactivity of these compounds derives from their complex structures (particularly when compared to the typical products of chemical

• synthesis [4]), which incorporate both high functional group density and rich stereochemistry. These features, coupled with the fact that the majority of reduced polyketides are macrocyclic, result in significant in-built conformational constraints. As a consequence, these molecules present their diverse

Diels–Alder reactions of myrcene using intensified continuous-flow reactors

• Christian H. Hornung,
• Miguel Á. Álvarez-Diéguez,
• Thomas M. Kohl and
• John Tsanaktsidis

Beilstein J. Org. Chem. 2017, 13, 120–126, doi:10.3762/bjoc.13.15

• of compact continuous-flow reactors has begun to transform the way chemical synthesis is conducted in research laboratories and small manufacturing over the past few years [14][15][16][17][18][19][20][21]. In several applications, where reaction times are short and heat management is important

3D printed fluidics with embedded analytic functionality for automated reaction optimisation

• Andrew J. Capel,
• Andrew Wright,
• Matthew J. Harding,
• George W. Weaver,
• Yuqi Li,
• Russell A. Harris,
• Steve Edmondson,
• Ruth D. Goodridge and
• Steven D. R. Christie

Beilstein J. Org. Chem. 2017, 13, 111–119, doi:10.3762/bjoc.13.14

• micro- and milliscale fluidic devices. When coupled with online monitoring and optimisation software, this offers an advanced, customised method for performing automated chemical synthesis. This paper reports the use of two additive manufacturing processes, stereolithography and selective laser melting

Extrusion – back to the future: Using an established technique to reform automated chemical synthesis

• Deborah E. Crawford

Beilstein J. Org. Chem. 2017, 13, 65–75, doi:10.3762/bjoc.13.9

• extensive amount of research into continuous organic transformations by extrusion and encourage them to consider the potential that extrusion holds for continuous chemical synthesis, particularly under solvent-free conditions. Reactive extrusion (REX) Extrusion is employed most frequently in the polymer

• ranging from room temperature to 250 °C [30]. Chemical synthesis by extrusion Extrusion is heavily relied upon within the pharmaceutical industry with regards to the formulation of drugs and their incorporation into drug delivery systems. However, extrusion has not been employed to carry out any organic

• technique in chemical synthesis, for example, reactions between two or more liquids have not been studied by extrusion and may be more difficult to carry out. In fact, there are still very few examples of this reported in ball mill reactions. Secondly, although it has been described that pyrophoric

O-Alkylated heavy atom carbohydrate probes for protein X-ray crystallography: Studies towards the synthesis of methyl 2-O-methyl-L-selenofucopyranoside

• Roman Sommer,
• Dirk Hauck,
• Annabelle Varrot,
• Anne Imberty,
• Markus Künzler and
• Alexander Titz

Beilstein J. Org. Chem. 2016, 12, 2828–2833, doi:10.3762/bjoc.12.282

• . Tested reaction conditions for the deprotection of benzylidene derivative 6. Supporting Information Supporting Information File 508: Chemical synthesis, 1H NMR and 13C NMR traces of synthesized compounds. Acknowledgements The authors thank Dr. Josef Zapp (Saarland University) for recording NMR spectra

The digital code driven autonomous synthesis of ibuprofen automated in a 3D-printer-based robot

• Philip J. Kitson,
• Stefan Glatzel and
• Leroy Cronin

Beilstein J. Org. Chem. 2016, 12, 2776–2783, doi:10.3762/bjoc.12.276

• by the method described, opening possibilities for the sharing of validated synthetic ‘programs’ which can run on similar low cost, user-constructed robotic platforms towards an ‘open-source’ regime in the area of chemical synthesis. Keywords: 3D printing; digitising chemistry; ibuprofen; laboratory

• modification of a RepRap 3D printer to incorporate liquid handling components such that it can act as a unitary chemical synthesis robot which is capable of fabricating (3D printing) a reaction vessel and subsequently performing the complete synthesis of the common drug ibuprofen. Such low-cost, versatile

• include the development of further open source solutions to allow robotic platforms to perform more of the routine functions of chemical synthesis such as work-up and purification routines. The widespread use of such low-cost automation of chemical synthesis could allow the development of an ‘open source

Symmetry-based approach to oligostilbenoids: Rapid entry to viniferifuran, shoreaphenol, malibatol A, and diptoindonesin G

• Youngeun Jung,
• Dileep Kumar Singh and
• Ikyon Kim

Beilstein J. Org. Chem. 2016, 12, 2689–2693, doi:10.3762/bjoc.12.266

• structures [1][2][3]. Despite a long history of isolation and biological studies of these natural products, relatively little attention has been paid by the synthetic community to chemical synthesis of polyphenolic oligostilbenoids. Most synthetic works on these unique natural products have recently appeared

Interactions between cyclodextrins and cellular components: Towards greener medical applications?

• Loïc Leclercq

Beilstein J. Org. Chem. 2016, 12, 2644–2662, doi:10.3762/bjoc.12.261

• which substituents can easily be introduced. From a chemical synthesis point of view, the reactivity difference between the primary and secondary hydroxy groups allows selective functionalization on the narrow or the wider edge of the truncated cone (Table 1). Access to the gamut of functional groups

Enzymatic synthesis and phosphorolysis of 4(2)-thioxo- and 6(5)-azapyrimidine nucleosides by E. coli nucleoside phosphorylases

• Vladimir A. Stepchenko,
• Anatoly I. Miroshnikov,
• Frank Seela and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2016, 12, 2588–2601, doi:10.3762/bjoc.12.254

• chemical synthesis and investigation of their physicochemical and biological properties (early works are reviewed in [1][2]). Studies on thioxo- and azapyrimidine nucleosides are an inspiring subject of investigation due to their very special biochemical [3][4][5][6][7] and biophysical properties in

• antiviral activity in various experiments [15][16][17][18][19][20][21][22]. Regarding the chemical synthesis of this class of pyrimidine nucleosides various approaches were published (see, e.g., [8][9][10][11][14][15][16][23][24]; reviewed by Vorbrüggen and Ruh-Pohlenz [25]). On the contrary, only few

• differences of tautomeric structures of pyrimidines studied and their recognition by E. coli UP vs TP in the glycoside bond formation: Activation of uracil and thymine as well as their related analogues in the chemical synthesis of nucleosides consists in the trimethylsilylation giving rise to the formation

Scope and limitations of a DMF bio-alternative within Sonogashira cross-coupling and Cacchi-type annulation

• Kirsty L. Wilson,
• Alan R. Kennedy,
• Jane Murray,
• Ben Greatrex,
• Craig Jamieson and
• Allan J. B. Watson

Beilstein J. Org. Chem. 2016, 12, 2005–2011, doi:10.3762/bjoc.12.187

• solvents; however, despite their utility, these solvents are incompatible with the drive towards more sustainable chemical synthesis. Herein, we describe the scope and limitations of an alternative to DMF derived from renewable sources (CyreneTM) in Sonogashira cross-coupling and Cacchi-type annulations

The in situ generation and reactive quench of diazonium compounds in the synthesis of azo compounds in microreactors

• Faith M. Akwi and
• Paul Watts

Beilstein J. Org. Chem. 2016, 12, 1987–2004, doi:10.3762/bjoc.12.186

• principles of green chemistry [1][2] such as less hazardous chemical synthesis, efficient atom economy, reduction of waste produced, some alternative cleaner methods for the synthesis of azo dyes have been developed. These methods are however only representative of particular coupling agents and diazotized

• in a chemical synthesis, it is important to keep most factors constant especially those pertaining to the geometry of the reactor channel as this can affect the reaction output. Albeit comparable reaction conversions were attained from the two reactor systems investigated, it is worth determining the

Synthesis and NMR studies of malonyl-linked glycoconjugates of N-(2-aminoethyl)glycine. Building blocks for the construction of combinatorial glycopeptide libraries

• Markus Nörrlinger,
• Sven Hafner and
• Thomas Ziegler

Beilstein J. Org. Chem. 2016, 12, 1939–1948, doi:10.3762/bjoc.12.183

• saccharide synthesis makes it sometimes impossible to prepare a certain saccharide or glycoconjugate [9]. Therefore, gaining access to new glycoconjugates which are easily accessible by chemical synthesis and which are able to mimic the interaction between a specific protein and its natural oligosaccharide

• efficient chemical synthesis of a series of novel PNA-based glycopeptoids. We also studied the cis/trans rotamers of these glycopeptoids via temperature-dependent 1H NMR spectroscopy by determining the corresponding coalescence temperatures (Tc = 90–95 °C) and by calculating the specific rotation barrier

A flow reactor setup for photochemistry of biphasic gas/liquid reactions

• Josef Schachtner,
• Patrick Bayer and
• Axel Jacobi von Wangelin

Beilstein J. Org. Chem. 2016, 12, 1798–1811, doi:10.3762/bjoc.12.170

• to oxidation chemistry of utmost sustainability. Under irradiation in the presence of a sensitizer, singlet oxygen can easily be generated from the triplet ground state. Several applications of such photooxidations to chemical synthesis have been reported [71][72][73], in recent years most

Copper-catalyzed [3 + 2] cycloaddition of (phenylethynyl)di-p-tolylstibane with organic azides

• Mizuki Yamada,
• Mio Matsumura,
• Yuki Uchida,
• Masatoshi Kawahata,
• Yuki Murata,
• Naoki Kakusawa,
• Kentaro Yamaguchi and
• Shuji Yasuike

Beilstein J. Org. Chem. 2016, 12, 1309–1313, doi:10.3762/bjoc.12.123

• -triazoles (Bi), which could be employed as versatile building blocks in chemical synthesis [24]. One drawback of the Cu-catalyzed cycloaddition of alkynylbismuthanes is the requirement of alkyne derivatives based on the phenothiabismuthane 5,5-dioxide framework for stabilization. The utility of

Synthesis of a deuterated probe for the confocal Raman microscopy imaging of squalenoyl nanomedicines

• Eric Buchy,
• Branko Vukosavljevic,
• Maike Windbergs,
• Dunja Sobot,
• Camille Dejean,
• Simona Mura,
• Patrick Couvreur and
• Didier Desmaële

Beilstein J. Org. Chem. 2016, 12, 1127–1135, doi:10.3762/bjoc.12.109

• , its coupling with gemcitabine and the Raman spectra of the deuterated GemSQ nanoassemblies, opening the way to perform intracellular imaging of squalenoyl nanomedicine (Figure 1). Results and Discussion Chemical synthesis of squalenic acid-d6 and GemSQ-d6 conjugate In a first approach we decided to

Efficient syntheses of climate relevant isoprene nitrates and (1R,5S)-(−)-myrtenol nitrate

• Sean P. Bew,
• Glyn D. Hiatt-Gipson,
• Graham P. Mills and
• Claire E. Reeves

Beilstein J. Org. Chem. 2016, 12, 1081–1095, doi:10.3762/bjoc.12.103

• , reinforces the need for chemical synthesis studies on the formation of climate relevant organic nitrates [14]. Even though the atmospheric synthesis of structure diverse C5-IPNs, i.e., 4–10 is thought to be efficient, i.e., up to 15% yield [15] what is not currently fully understood is the mechanism or

Biosynthesis of α-pyrones

• Till F. Schäberle

Beilstein J. Org. Chem. 2016, 12, 571–588, doi:10.3762/bjoc.12.56

• isolated from Leptosphaeria maculans and named phomapyrone A, as well as from the mediterranean ascoglossan mollusc Ercolania funereal, described as cyercene [51]. Phomenin A displayed phytotoxicity at a concentration of 100 µg/mL. Chemical synthesis approaches enabled then to investigate many more α

• agronomically important pathogens, e.g., complete inhibition of Magnaporthe grisea and Phaeosphaeria nodorum at 67 µg/mL, and Botrytis cinerea was inhibited at 200 µg/mL. 2 Biosynthesis Even though the α-pyrones possessing interesting activities were in the focus of chemical synthesis approaches for a long time

A selective and mild glycosylation method of natural phenolic alcohols

• Mária Mastihubová and
• Monika Poláková

Beilstein J. Org. Chem. 2016, 12, 524–530, doi:10.3762/bjoc.12.51

• had to be optimized. The current paper deals with an efficient, safe and uniform chemical synthesis of various p-hydroxyarylalkyl glycosides, including compounds 1–3. Results and Discussion Preparation of aglycones The synthesis of the appropriate aglycones 6a–c was commenced from readily available