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

• traditional batch reactions by over a 500-fold and outperforming flow reactions with a five-fold improvement. A fully integrated automated multistep chemical synthesizer (AutoSyn) was reported to be able to autonomously synthesize milligram- to gram-scale amounts of any organic or drug-like molecule [49]. The

Synthesis of cyclic β-1,6-oligosaccharides from glucosamine monomers by electrochemical polyglycosylation

• Md Azadur Rahman,
• Hirofumi Endo,
• Takashi Yamamoto,
• Shoma Okushiba,
• Norihiko Sasaki and
• Toshiki Nokami

Beilstein J. Org. Chem. 2024, 20, 1421–1427, doi:10.3762/bjoc.20.124

• monomers and another synthetic approach using dimers for production of larger cyclic oligosaccharides are in progress in our laboratory. Experimental Electrochemical polyglycosylation (Scheme 3) was performed using our second-generation automated electrochemical synthesizer equipped with the H-type divided

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

• -polymerization (CBP) technique [19]. Using the method, long ODNs with 399 and 401 nt were directly synthesized on an automated synthesizer. The full-length sequences were extracted from the complex mixture generated from over a thousand reactions using CBP. The two ODNs were joined together to form the 800 nt

• 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

• . To ensure full coverage of CPG in the column by reagent solutions in each of the over one thousand reactions, the synthesizer manufacturer’s recommendation of 1 µmol instead of 0.2 µmol for standard synthetic cycle was used with several minor but critical modifications (see Supporting Information

Synthesis of protected precursors of chitin oligosaccharides by electrochemical polyglycosylation of thioglycosides

• Md Azadur Rahman,
• Kana Kuroda,
• Hirofumi Endo,
• Norihiko Sasaki,
• Tomoaki Hamada,
• Hiraku Sakai and
• Toshiki Nokami

Beilstein J. Org. Chem. 2022, 18, 1133–1139, doi:10.3762/bjoc.18.117

• oligosaccharides thus obtained are in progress in our laboratory. Experimental Electrochemical polyglycosylation (see Figure 4, T1 = −60 °C and T2 = −30 °C) was performed using our second-generation automated electrochemical synthesizer equipped with the H-type electrolysis cell. Thioglycoside 1a (0.20 mmol, 109

Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides

• Mathias B. Danielsen and
• Jesper Wengel

Beilstein J. Org. Chem. 2021, 17, 1828–1848, doi:10.3762/bjoc.17.125

• synthesis and coupling efficiency on the synthesizer, significant loss of the hydrocarbon-linked group was observed during the alkaline deprotection conditions [115]. After insertion into a 19-mer DNA-ON, modification 79 did not show any significant increase in Tm. This trend was changed when the

Synthesis and properties of oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing adenine, guanine, or 5-methylcytosine nucleobases

• Naohiro Horie,
• Takao Yamaguchi,
• Shinji Kumagai and
• Satoshi Obika

Beilstein J. Org. Chem. 2021, 17, 622–629, doi:10.3762/bjoc.17.54

• the middle position of 12-mer oligonucleotides (Table 1). The oligonucleotide synthesis was performed using an automated DNA synthesizer following the established synthetic method for GuNA[Me]-T-modified oligonucleotides [20]. 5-(Ethylthio)-1H-tetrazole (ETT) was used as an activator for the coupling

• modified with GuNA[Me]-A, -G, or -mC (0.2 µmol scale) was performed using the nS-8 oligonucleotide synthesizer (GeneDesign, Inc.) according to the standard phosphoramidite protocol with 0.5 M 5-ethylthiotetrazole as an activator. The protocol is similar to that described in reference [20]. A Custom Primer

Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

• Marius H. Heddinga and
• Jens Müller

Beilstein J. Org. Chem. 2020, 16, 2870–2879, doi:10.3762/bjoc.16.236

• phosphoramidite-protected imidazole nucleoside as required for automated DNA solid-phase synthesis was synthesized as previously reported [30]. The oligonucleotides were synthesized on a DNA/RNA synthesizer H-8 (K&A Laborgeräte) using standard protocols for automated solid-phase synthesis (coupling time: 1000 s

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

• Jennifer Frommer and
• Sabine Müller

Beilstein J. Org. Chem. 2020, 16, 2854–2861, doi:10.3762/bjoc.16.234

• derivative 8 with free 3’-OH group, which then can be converted to the phosphoramidite prior to use at the RNA synthesizer. Protocols for selective 2’-O-silylation are available [29][30][31], however, the standard procedure using AgNO3, pyridine and TBDMS-Cl, in this case led to unexpected results. The

Disposable cartridge concept for the on-demand synthesis of turbo Grignards, Knochel–Hauser amides, and magnesium alkoxides

• Mateo Berton,
• Kevin Sheehan,
• Andrea Adamo and
• D. Tyler McQuade

Beilstein J. Org. Chem. 2020, 16, 1343–1356, doi:10.3762/bjoc.16.115

• Grignards is reported. A low-cost pod-style synthesizer prototype, which incorporates single-use prepacked perfluorinated cartridges and bags of reagents for the automated on-demand lab-scale synthesis of carbon, nitrogen, and oxygen turbo magnesium bases is presented. This concept will provide access to

• fresh organomagnesium reagents on a discovery scale and will do so independent from the operator’s experience in flow and/or organometallic chemistry. Keywords: Knochel–Hauser base; lithium chloride; magnesium; on-demand; packed-bed reactors; plug and flow reactor; synthesizer; turbo Grignard reagent

• reaction models are presented. In addition, a proof-of-concept, automated pod-type synthesizer prototype designed to generate up to 100 mmol of fresh reagents on demand is described. Our objective is to help others integrate this approach into their quotidian workflow to enable discovery-scale researchers

Microwave-assisted efficient and facile synthesis of tetramic acid derivatives via a one-pot post-Ugi cascade reaction

• Yong Li,
• Zheng Huang,
• Jia Xu,
• Yong Ding,
• Dian-Yong Tang,
• Jie Lei,
• Hong-yu Li,
• Zhong-Zhu Chen and
• Zhi-Gang Xu

Beilstein J. Org. Chem. 2020, 16, 663–669, doi:10.3762/bjoc.16.63

• then DBU (1.0 mmol) was added. The mixture was then placed in a microwave synthesizer and heated to 120 °C for 10 min. The mixture was then cooled to room temperature, and the residue was dissolved in EtOAc (15.0 mL). The solution was washed with brine, and the organic layer was dried with MgSO4 and

Efficient method for propargylation of aldehydes promoted by allenylboron compounds under microwave irradiation

• Jucleiton J. R. Freitas,
• Queila P. S. B. Freitas,
• Silvia R. C. P. Andrade,
• Juliano C. R. Freitas,
• Roberta A. Oliveira and
• Paulo H. Menezes

Beilstein J. Org. Chem. 2020, 16, 168–174, doi:10.3762/bjoc.16.19

• pinacol ester (1, 1.5 mmol) in a capped vial were irradiated in a MW synthesizer for 30 minutes under different temperatures. The results are depicted in Table 1. In all cases, the desired propargylic product 2a was obtained together with a small amount of the corresponding allenic product 3a. When the

Automated glycan assembly of arabinomannan oligosaccharides from Mycobacterium tuberculosis

• Alonso Pardo-Vargas,
• Priya Bharate,
• Martina Delbianco and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2019, 15, 2936–2940, doi:10.3762/bjoc.15.288

• required to access all six oligosaccharides, ranging from hexa- to dodecasaccharides. Results and Discussion The automated syntheses of oligomannosides 4–6 and oligoarabinomannosides 7–9 were performed on a self-built automated synthesizer using a Merrifield resin functionalized with a photocleavable

Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection

• Shahien Shahsavari,
• Dhananjani N. A. M. Eriyagama,
• Bhaskar Halami,
• Vagarshak Begoyan,
• Marina Tanasova,
• Jinsen Chen and
• Shiyue Fang

Beilstein J. Org. Chem. 2019, 15, 1116–1128, doi:10.3762/bjoc.15.108

• MerMade 6 DNA/RNA synthesizer. The dT-Dmoc-CPG (4) was used as the solid support. Detritylation was carried out under standard conditions suggested by the synthesizer manufacturer for 1 µmol synthesis. The 0.1 M acetonitrile solutions of phosphoramidite monomers 3a–c and the commercially available 5'-DMTr

• useful tool for the synthesis of sensitive ODN analogs. Experimental ODN synthesis, deprotection, cleavage and characterization: All ODNs were synthesized on dT-Dmoc-CPG [40] (4, 26 µmol/g loading, 20 mg, 0.52 µmol) using a MerMade 6 Synthesizer. dM-Dmoc phosphoramidites 3a–c and the commercial 5'-DMTr-2

• -cyanoethyl-dT phosphoramidite were used as monomers. The conditions suggested by synthesizer manufacturer for 1 μmol synthesis were used except that coupling was optionally increased from 2 to 3 times and capping was achieved using 25 instead of acetic anhydride. Briefly, detritylation, DCA (3%, DCM), 90 s

Defining the hydrophobic interactions that drive competence stimulating peptide (CSP)-ComD binding in Streptococcus pneumoniae

• Bimal Koirala,
• Robert A. Hillman,
• Erin K. Tiwold,
• Michael A. Bertucci and
• Yftah Tal-Gan

Beilstein J. Org. Chem. 2018, 14, 1769–1777, doi:10.3762/bjoc.14.151

• ) procedures [34]. Phenylglycine and norvaline derivatives were prepared on a CEM Discover microwave synthesizer, with diisopropyl carbodiimide (DIC) as the coupling reagent along with Oxyma Pure. The ratio of DIC:Oxyma Pure:AA was 3.6:3:3 dissolved in N,N-dimethylformamide (DMF) for a final DIC concentration

Natural and redesigned wasp venom peptides with selective antitumoral activity

• Marcelo D. T. Torres,
• Gislaine P. Andrade,
• Roseli H. Sato,
• Cibele N. Pedron,
• Tania M. Manieri,
• Giselle Cerchiaro,
• Anderson O. Ribeiro,
• Cesar de la Fuente-Nunez and
• Vani X. Oliveira Jr.

Beilstein J. Org. Chem. 2018, 14, 1693–1703, doi:10.3762/bjoc.14.144

• , purification and analysis Peptides were synthesized by solid-phase peptide synthesis on Rink Amide resin, with a substitution degree of 0.52 mmol g−1 on a 0.1 mmol scale, using the Fmoc strategy on a peptide synthesizer (PS3 – Protein Technologies) as described by Torres et al. [9][10]. Dry-protected peptidyl

Design and biological characterization of novel cell-penetrating peptides preferentially targeting cell nuclei and subnuclear regions

• Anja Gronewold,
• Mareike Horn and
• Ines Neundorf

Beilstein J. Org. Chem. 2018, 14, 1378–1388, doi:10.3762/bjoc.14.116

• synthesized using a combination of standard Fmoc/t-Bu solid-phase peptide synthesis (SPPS) on a Syro I peptide synthesizer (MultiSynTech, Bochum, Germany) and manual coupling protocols according to previous works [17][19][20]. Peptides were generated on a Rink amide resin (loading 0.48 mmol/g) yielding C

Microfluidic radiosynthesis of [¹⁸F]FEMPT, a high affinity PET radiotracer for imaging serotonin receptors

• Thomas Lee Collier,
• Steven H. Liang,
• J. John Mann,
• Neil Vasdev and
• J. S. Dileep Kumar

Beilstein J. Org. Chem. 2017, 13, 2922–2927, doi:10.3762/bjoc.13.285

• individual steps, using the Discovery mode of the Advion NanoTek® microfluidic synthesizer [16]. The first step is the preparation of the labeling reagent [18F]fluoroethyltosylate (10) via tetraethylammonium fluoride ([18F]TEAF). The second step is the reaction of the [18F]fluoroethyltosylate (10), with the

Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

• Susanne Huhmann,
• Anne-Katrin Stegemann,
• Kristin Folmert,
• Damian Klemczak,
• Johann Moschner,
• Michelle Kube and
• Beate Koksch

Beilstein J. Org. Chem. 2017, 13, 2869–2882, doi:10.3762/bjoc.13.279

• support by means of an Fmoc/tert-butyl protecting group strategy on a preloaded Fmoc-Lys(Boc)Wang resin (0.57 mmol/g loading) using 10 mL polypropylene reactors. HfLeu containing peptides were synthesized with an Activo-P11 automated peptide synthesizer (Activotec, Cambridge, United Kingdom). Couplings of

Peptide synthesis: ball-milling, in solution, or on solid support, what is the best strategy?

• Ophélie Maurin,
• Pascal Verdié,
• Gilles Subra,
• Frédéric Lamaty,
• Jean Martinez and
• Thomas-Xavier Métro

Beilstein J. Org. Chem. 2017, 13, 2087–2093, doi:10.3762/bjoc.13.206

• Fmoc chemistry commonly utilized in laboratories was employed [25][26]. It has to be noted that in this case the fully deprotected TFA·H-VVIA-OH peptide was obtained. Practically, the peptide chain was elongated by means of a peptide synthesizer employing the standard Fmoc chemistry (Scheme 3). The

Synthesis of oligonucleotides on a soluble support

• Harri Lönnberg

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

• Harri Lonnberg Department of Chemistry, University of Turku, FIN-20014 Turku, Finland 10.3762/bjoc.13.134 Abstract Oligonucleotides are usually prepared in lab scale on a solid support with the aid of a fully automated synthesizer. Scaling up of the equipment has allowed industrial synthesis up

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

• purity of a chemical synthesis. Reprinted with permission from [36]; copyright 2016 Macmillan Publishers Ltd. (Top) Photograph of a small-molecule synthesizer comprised of three modules for deprotection, coupling, and purification steps. (Bottom) Natural products, materials, pharmaceuticals, and

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

• its instructions as they appear –in fact, if we can make a DNA synthesizer– then I think we can start building live tissue”. Today, it is not difficult to find statements of this kind in connection with the study of the genome of living organisms, and, naturally in scenarios of the origin of life

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

• -chitotriomycin using an automated electrochemical synthesizer for the assembly of carbohydrate building blocks is demonstrated. We have successfully prepared a precursor of TMG-chitotriomycin, which is a structurally-pure tetrasaccharide with typical protecting groups, through the methodology of automated

• synthesizer for the automated electrochemical assembly of carbohydrate building blocks [25]. During the course of our study, we have achieved the synthesis of a potential precursor of TMG-chitotriomycin (1); however, we obtained the tetrasaccharide as a mixture of α- and β-isomers in the terminal glycosidic

A postsynthetically 2’-“clickable” uridine with arabino configuration and its application for fluorescent labeling and imaging of DNA

• Heidi-Kristin Walter,
• Bettina Olshausen,
• Ute Schepers and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2017, 13, 127–137, doi:10.3762/bjoc.13.16

• obtained as a colorless foam. Rf 0.56 (CH2Cl2/acetone 5:1); APCI–MS m/z (%): 785.6 (70) [M + H]+. Preparation, purification and characterization of DNA. All oligonucleotides were synthesized on an Expedite 8909 Synthesizer from Applied Biosystems (ABI) using standard phosphoramidite chemistry. Reagents and

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

• 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

• developed solution-phase automated synthesizer, ChemKonzert [9]. Protected α-amino aldehydes are versatile intermediates for the synthesis of vicinal amino alcohols and important building blocks for various bioactive natural products [10][11][12]. In particular, Garner’s aldehyde (4a) is very useful as a

• synthesis of Garner’s aldehyde (4a) and its analogues. Results and Discussion Our synthetic route is shown in Scheme 1. We planned to synthesize 4a with various protecting groups from a commercially available amino ester through a three-step procedure utilizing the automated synthesizer, ChemKonzert (Figure