Emerging trends in the optimization of organic synthesis through high-throughput tools and machine learning

• Pablo Quijano Velasco,
• Kedar Hippalgaonkar and
• Balamurugan Ramalingam

Beilstein J. Org. Chem. 2025, 21, 10–38, doi:10.3762/bjoc.21.3

• this robotic system promises remarkable applications in materials, polymers, and chemical synthesis. Most automated synthesis platforms are based on expensive scientific equipment, have a large equipment footprint, and need extensive reconfiguration to adapt to new synthetic protocols. To address this

• alternative that can be adapted to perform chemical reaction optimization. In addition to academia, industry is increasingly recognizing the value of investing in custom-built HTE setups to automate their synthesis workflows for enhanced productivity. A fully integrated, cloud-accessible, automated synthesis

Long oligodeoxynucleotides: chemical synthesis, isolation via catching-by-polymerization, verification via sequencing, and gene expression demonstration

• Yipeng Yin,
• Reed Arneson,
• Alexander Apostle,
• Adikari M. D. N. Eriyagama,
• Komal Chillar,
• Emma Burke,
• Martina Jahfetson,
• Yinan Yuan and
• Shiyue Fang

Beilstein J. Org. Chem. 2023, 19, 1957–1965, doi:10.3762/bjoc.19.146

• . Keywords: automated synthesis; catching-by-polymerization; gene assembly; long oligonucleotide; synthetic biology; Introduction Long oligodeoxynucleotides (ODNs) are segments of DNAs extending beyond one hundred nucleotides (nt). Emerging research areas such as synthetic biology [1][2], protein

• ODN sequences are provided in Supporting Information File 1) GFP gene construct was divided into a 399 and 401 nt ODNs for automated synthesis (step 1, Figure 1). The syntheses were carried out in commercial 0.2 µmol 2000 Å CPG columns on an ABI 394 DNA/RNA synthesizer using phosphoramidite chemistry

Progress and challenges in the synthesis of sequence controlled polysaccharides

• Giulio Fittolani,
• Theodore Tyrikos-Ergas,
• Denisa Vargová,
• Manishkumar A. Chaube and
• Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

On the application of 3d metals for C–H activation toward bioactive compounds: The key step for the synthesis of silver bullets

• Renato L. Carvalho,
• Amanda S. de Miranda,
• Mateus P. Nunes,
• Roberto S. Gomes,
• Guilherme A. M. Jardim and
• Eufrânio N. da Silva Júnior

Beilstein J. Org. Chem. 2021, 17, 1849–1938, doi:10.3762/bjoc.17.126

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• kinetics and higher solubility in organic solvents, useful for automated synthesis, such as the Beaucage reagent [86]. Conveniently, during deprotection of the support-bound oligonucleotide, aminolysis removes the β-thiobenzoylethyl group from the backbone to generate the free PS2-modified oligonucleotide

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

• monitored with in-line and on-line spectroscopies, such as UV–vis, FTIR, mass spectrometry, and NMR [63][64][65][66][67][68]. These systems can be automated to ensure consistency and to remove the need for laborious manual sampling. In-line and on-line monitoring is well aligned with automated synthesis and

Design and synthesis of multivalent α-1,2-trimannose-linked bioerodible microparticles for applications in immune response studies of Leishmania major infection

• Chelsea L. Rintelmann,
• Tara Grinnage-Pulley,
• Kathleen Ross,
• Daniel E. K. Kabotso,
• Angela Toepp,
• Anne Cowell,
• Christine Petersen,
• Balaji Narasimhan and
• Nicola Pohl

Beilstein J. Org. Chem. 2019, 15, 623–632, doi:10.3762/bjoc.15.58

• a handle for the incorporation of a fluorous-tag for ease of purification by fluorous solid phase-extraction (FSPE). The use of the fluorous tag enables solution-phase automated synthesis of α-1,2-trimannose in the future as shown previously with a related spacer and fluorous tag [47]. Incorporation

• FSPE purification to rapidly afford appreciable and pure quantities in fewer steps than prior work enabled by the Cbz F-tag that allows for solution-phase automated synthesis in the future. In conclusion, these newly synthesized α-1,2-trimannose-linked bioerodible microparticles 2 are a feasible

1,3-Dibromo-5,5-dimethylhydantoin as promoter for glycosylations using thioglycosides

• Fei-Fei Xu,
• Claney L. Pereira and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2017, 13, 1994–1998, doi:10.3762/bjoc.13.195

• oligosaccharides [20][47]. Ideally, stable and non-toxic reagents should be used on such instruments. The automated synthesis of disaccharide 16 served to assess the suitability of the DBDMH/TMSOTf activation system using functionalized resin 15 [48] as solid support (Scheme 1). After two coupling cycles with

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 probes synthesized by automated synthesis by iterative coupling of different building blocks (colors). TBDPSE, tert-butyldiphenylsilylethyl; TMSE, trimethylsilylethyl. Adapted with permission from [37]; copyright 2015 American Association for the Advancement of Science. An example of a composition

• , and peptides and oligonucleotides can also be synthesized efficiently using automated methods, it is not yet possible to carry out chemical syntheses in a general sense using these technologies. However, several groups are making significant breakthroughs in generalizing and expanding the automated

• synthesis of organic compounds. Rzepa, and Murray-Rust among others, have begun systematizing chemistry using a type of chemical mark-up language (a machine-readable language designed to describe the central concepts in chemistry) and chemical ontologies (a formal naming and definition of the types

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

• need of repetitive work, which can be transformed to an automated synthesis platform (viz. vapourtec, H-cube, etc.). It is always possible to develop customized automation platforms that suit for specific synthesis and building such avenues using well-established programming tools like Lab View is

• diagram, helps to know the possible automated flow synthesis platform with better clarity (Figure 5B). For the said process the automated synthesis can be achieved as follows: The flow rate of aryl bromide can be fixed at a desired set point using a control valve or by setting the pump with feedback in

• scale. Developing an automated platform for such a synthesis is indeed a challenge. In the below, we describe this approach in a way that can help to build an automated synthesis platform. Figure 8A and 8B show the block diagram and possible P&ID for the cinnarizine/buclizine derivative manufacturing

Total synthesis of TMG-chitotriomycin based on an automated electrochemical assembly of a disaccharide building block

• Yuta Isoda,
• Norihiko Sasaki,
• Kei Kitamura,
• Shuji Takahashi,
• Sujit Manmode,
• Naoko Takeda-Okuda,
• Jun-ichi Tamura,
• Toshiki Nokami and
• Toshiyuki Itoh

Beilstein J. Org. Chem. 2017, 13, 919–924, doi:10.3762/bjoc.13.93

• electrochemical solution-phase synthesis developed by us. The synthesis of structurally well-defined TMG-chitotriomycin has been accomplished in 10-steps from a disaccharide building block. Keywords: automated synthesis; electrochemical oxidation; glycosylation; glucosamine; total synthesis; Introduction

• synthesis of oligosaccharides is a powerful tool for the rapid synthesis of complex oligosaccharides [11][12][13][14][15][16][17][18][19][20][21][22][23]. We are interested in the automated synthesis of oligosaccharides based on the concept of “reaction integration” [24] and developed an automated

• reactions were performed under an Ar atmosphere unless otherwise noted. Materials All materials including solvents were purchased and used without further purification. Carbohydrate building blocks 2a, 2b, and 4 were prepared according to an previous report [11]. Automated synthesis of TMG-chitotriomycin

Solution-phase automated synthesis of an α-amino aldehyde as a versatile intermediate

• Hisashi Masui,
• Sae Yosugi,
• Shinichiro Fuse and
• Takashi Takahashi

Beilstein J. Org. Chem. 2017, 13, 106–110, doi:10.3762/bjoc.13.13

• -8503, Japan 10.3762/bjoc.13.13 Abstract A solution-phase automated synthesis of the versatile synthetic intermediate, Garner’s aldehyde, was demonstrated. tert-Butoxycarbonyl (Boc) protection, acetal formation, and reduction of the ester to the corresponding aldehyde were performed utilizing our

• originally developed automated synthesizer, ChemKonzert. The developed procedure was also useful for the synthesis of Garner’s aldehyde analogues possessing fluorenylmethyloxycarbonyl (Fmoc) or benzyloxycarbonyl (Cbz) protection. Keywords: acetal formation; amino acid; automated synthesis; Garner’s aldehyde

• ; reduction; Introduction Automated synthesis has attracted a great deal of attention in recent years because the automation of synthetic operations improves both the reproducibility and reliability of syntheses [1][2][3][4]. Synthetic chemists frequently perform repetitive processes such as the optimization

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

• Philip J. Kitson Stefan Glatzel Leroy Cronin WestCHEM, School of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, UK 10.3762/bjoc.12.276 Abstract An automated synthesis robot was constructed by modifying an open source 3D printing platform. The resulting automated system

• program needs to be tested in the bigger context of the rest of the source code. All working steps can simply be skipped without actually deactivating the responsible code. Automated ibuprofen synthesis The automated synthesis of ibuprofen is initiated with the running of the control software which then

• and made within autonomous chemical robots. Prusa i3 RepRap printer modified for the automated synthesis of ibuprofen. Left: Full view of robotic platform set-up with a 3D-printed reaction vessel. Left inset: Dispensing needle carriage for 3D printing/liquid deposition. Right: Front view of the 3D

Automated glycan assembly of a S. pneumoniae serotype 3 CPS antigen

• Markus W. Weishaupt,
• Stefan Matthies,
• Mattan Hurevich,
• Claney L. Pereira,
• Heung Sik Hahm and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2016, 12, 1440–1446, doi:10.3762/bjoc.12.139

• runs on the automated synthesis instrument illustrated regular washing steps following each deprotection failed to completely remove the deprotection solution. Therefore, an activator wash step was introduced between deprotection and glycosylation steps. In this step, the resin was washed with

• glucose building block. This monomer did not suffer from a loss of stereocontrol as was observed in the case of the similarly protected GlcA building block. The desired trisaccharide 5 was observed as the main product from the automated synthesis by HPLC analysis (Figure 5). The Lev protecting group had

• /AcOH (3:2 v/v), CH2Cl2, 30 min, n = 3; c) TMSOTf, CH2Cl2, −30 °C (1 min), n = 1; d) 1 (3 equiv), TMSOTf, CH2Cl2, −30 °C (30 min) to −15 °C (30 min), n = 3; e) hν. Automated synthesis of linker-bound glucuronic acid 10 using glycosyl phosphate building block 1. Reagents and conditions: a) 1 (3 equiv

Automated solid-phase synthesis of oligosaccharides containing sialic acids

• Chian-Hui Lai,
• Heung Sik Hahm,
• Chien-Fu Liang and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2015, 11, 617–621, doi:10.3762/bjoc.11.69

• 10.3762/bjoc.11.69 Abstract A sialic acid glycosyl phosphate building block was designed and synthesized. This building block was used to prepare α-sialylated oligosaccharides by automated solid-phase synthesis selectively. Keywords: α-sialylation; automated synthesis; glycosylation; sialic acid; solid

• the tumour-associated antigen sialyl Tn (sTn). (a) FmocCl, py, CH2Cl2, rt, 4 h, 77%, (b) 2-chloroacetyl chloride, py, CH2Cl2, 0 °C to rt, 3 h, 88%, (c) HOPO(OBu)2, NIS, TfOH, 4 Å MS, CH3CN/CH2Cl2, −78 °C to 0 °C, 2 h, 80%. Automated synthesis of oligosaccharides with α(2,3)-, α(2,6)-sialic acid

NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A–T phosphoramidite building blocks

• Boris Schmidtgall,
• Claudia Höbartner and
• Christian Ducho

Beilstein J. Org. Chem. 2015, 11, 50–60, doi:10.3762/bjoc.11.8

• synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step

• ' phosphoramidites (S)-7 and (R)-7 were employed for the automated synthesis of two DNA oligonucleotides 30 and 31, each bearing two NAA-modifications with defined stereochemistry at the NAA-linkage ((6'S) or (6'R)) and therefore displaying partially zwitterionic backbone structures. After assembly on the

• employed 'dimeric' T–T phosphoramidites 6 [38] for the automated synthesis of NAA-modified oligonucleotides; new 'dimeric' A–T phosphoramidites 7 as target structures of this study (DMTr = 4,4'-dimethoxytrityl). Retrosynthetic analysis of target phosphoramidites (S)-7 and (R)-7 (BOM = benzyloxymethyl

Autonomous assembly of synthetic oligonucleotides built from an expanded DNA alphabet. Total synthesis of a gene encoding kanamycin resistance

• Kristen K. Merritt,
• Kevin M. Bradley,
• Daniel Hutter,
• Mariko F. Matsuura,
• Diane J. Rowold and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 2348–2360, doi:10.3762/bjoc.10.245

• facilitate subsequent manipulation, add 'watermarks' to track the gene’s provenance, and choose codons to improve the expression of the gene [10]. This combination of automated synthesis of DNA fragments followed by their manual assembly, with PCR used to recover manually assembled partial constructs, began

• non-standard nucleotides to the repertoire introduced into DNA strands by automated synthesis. These additional non-standard nucleotides come from components of an artificially expanded genetic information system (AEGIS) [18][19]. AEGIS adds nucleotides to the DNA alphabet by rearranging the hydrogen

Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid

• Keunsoo Kim,
• Venkateshwarlu Punna,
• Phaneendrasai Karri and
• Ramanarayanan Krishnamurthy

Beilstein J. Org. Chem. 2014, 10, 2131–2138, doi:10.3762/bjoc.10.220

• were achieved with N4-isobutyrylcytosine as the nucleophile [19][20][21]. In the guanine series, the N2-isobutyryl, O6-diphenylcarbamoyl protected guanine worked well (Scheme 3) [22]. With all the four phosphoramidites in hand we proceeded to the automated synthesis of the oligomers, which proceeded

OligArch: A software tool to allow artificially expanded genetic information systems (AEGIS) to guide the autonomous self-assembly of long DNA constructs from multiple DNA single strands

• Kevin M. Bradley and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 1826–1833, doi:10.3762/bjoc.10.192

• 17, Alachua, FL 32615, USA 10.3762/bjoc.10.192 Abstract Synthetic biologists wishing to self-assemble large DNA (L-DNA) constructs from small DNA fragments made by automated synthesis need fragments that hybridize predictably. Such predictability is difficult to obtain with nucleotides built from

• a scalable and integrated infrastructure for the rapid and designed engineering of biology. Keywords: AEGIS; bioinformatics; DNA self-assembly; long DNA constructs; software; Introduction Automated synthesis of single stranded DNA fragments has, perhaps more than any other technology, enabled the

• development of "synthetic biology“ as a modern field over the past 30 years [1][2][3][4][5]. While oligonucleotides can be reliably prepared by automated synthesis up to ca. 100 nucleotides in length and (even today) are most often used as primers, many seek to create large DNA (L-DNA) constructs by assembly

Pyrene-modified PNAs: Stacking interactions and selective excimer emission in PNA₂DNA triplexes

• Alex Manicardi,
• Lucia Guidi,
• Alice Ghidini and
• Roberto Corradini

Beilstein J. Org. Chem. 2014, 10, 1495–1503, doi:10.3762/bjoc.10.154

• -azidomethyluracil precursor, as described previously [35], whereas a pyrene-containing modified monomer 1 (Scheme 1), more suitable for automated synthesis, was designed for the realization of all the other oligomers (PNA2–6, Figure 1c). For the synthesis of the modified monomer bearing the pyrene moiety, we

Design, automated synthesis and immunological evaluation of NOD2-ligand–antigen conjugates

• Marian M. J. H. P. Willems,
• Gijs G. Zom,
• Nico Meeuwenoord,
• Ferry A. Ossendorp,
• Herman S. Overkleeft,
• Gijsbert A. van der Marel,
• Jeroen D. C. Codée and
• Dmitri V. Filippov

Beilstein J. Org. Chem. 2014, 10, 1445–1453, doi:10.3762/bjoc.10.148

• incorporated antigen. Here we describe the design, automated synthesis and immunological evaluation of a set of four muramyl dipeptide–peptide antigen conjugates. Muramyl dipeptide (MDP) represents a well-known ligand for the intracellular NOD2 receptor and our study shows that covalently linking an MDP-moiety

• incorporated SIINFEKL epitope on MHC-I molecules. However, stimulation of the NOD2 receptor in DCs was not sufficient to provide a strong immunostimulatory signal. Keywords: automated synthesis; glycopeptide; innate immunity; muramyl dipeptide; NOD2 receptor; solid phase synthesis; Introduction In recent

Molecular recognition of surface-immobilized carbohydrates by a synthetic lectin

• Melanie Rauschenberg,
• Eva-Corrina Fritz,
• Christian Schulz,
• Tobias Kaufmann and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2014, 10, 1354–1364, doi:10.3762/bjoc.10.138

• sequencing, automated synthesis and high-throughput microarray screening are lacking in glycobiology [5]. However, during the last decade, these methods have also been adapted to carbohydrates [6][7][8]. Carbohydrate microarrays on chips proved to be a particularly useful tool in glycomics [9][10][11] since

Automated solid-phase peptide synthesis to obtain therapeutic peptides

• Veronika Mäde,
• Sylvia Els-Heindl and
• Annette G. Beck-Sickinger

Beilstein J. Org. Chem. 2014, 10, 1197–1212, doi:10.3762/bjoc.10.118

• application of SPPS is described for neuropeptide Y receptor analogs as an example for bioactive hormones. The applied strategies represent innovative and potent methods for the development of novel peptide drug candidates that can be manufactured with optimized automated synthesis technologies. Keywords

• : automated synthesis; automation; lipidation; PEGylation; peptide drugs; solid-phase peptide synthesis; therapeutic peptides; Introduction Peptides and proteins are involved in a large variety of biochemical processes and physiological functions. Peptides can consist of up to 50 amino acids and have

• strategies are used for the synthesis of peptides and both methods can be applied for automated synthesis. Nevertheless, the Fmoc/t-Bu protecting-group approach offers the great advantage of orthogonality. This concept [36] enables the selective removal of the protecting groups using completely different

Integration of enabling methods for the automated flow preparation of piperazine-2-carboxamide

• Richard J. Ingham,
• Claudio Battilocchio,
• Joel M. Hawkins and
• Steven V. Ley

Beilstein J. Org. Chem. 2014, 10, 641–652, doi:10.3762/bjoc.10.56

• explored the possibility of developing a machine-automated synthesis of this compound which might later be extended to analogous structures. For the facile machine-assisted synthesis of 1 we devised and optimised the fully continuous sequential hydration of nitrile 3 to amide 2 and hydrogenation of

Isocyanide-based multicomponent reactions towards cyclic constrained peptidomimetics

• Gijs Koopmanschap,
• Eelco Ruijter and
• Romano V.A. Orru

Beilstein J. Org. Chem. 2014, 10, 544–598, doi:10.3762/bjoc.10.50

• ideally suited for automated synthesis [14][15][16][17][18]. Among the MCRs, the isocyanide-based multicomponent reactions (IMCRs), such as the Ugi and the Passerini reaction, are the most relevant reactions for constructing peptidomimetics since they give access to (depsi)peptide-like structures. However