Machine learning-guided strategies for reaction conditions design and optimization

• Lung-Yi Chen and
• Yi-Pei Li

Beilstein J. Org. Chem. 2024, 20, 2476–2492, doi:10.3762/bjoc.20.212

• maximum common subgraph (MCS) problem and aligned reactants and products to identify non-overlapping segments, thereby generating the missing compounds. Another novel method is AutoTemplate [92], which extracts generic reaction templates from the reactions being preprocessed and recursively applies them

• of SMILES without affecting their molecular structures or modifying specific functional groups in coupling reactions with chemistry-informed reaction templates. Despite the need for large amounts of data to train base models, the main advantage of text-based reaction representation is that it can be

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• structure prediction with template-based modelling. It is known for its ability to predict both the structure and function of a protein. It is based on identifying structural templates from the PDB by several threading methodologies with full-length atomic models (https://zhanggroup.org/I-TASSER/). 3

• spatial constraints (https://salilab.org/modeller/). 4. Rosetta [91]: It was developed for de novo protein structure prediction in a free version. Homology modelling is also applied in this instance by using several protein templates that hybridise the most homologous sections of various templates into a

Cage-like microstructures via sequential Ugi reactions in aqueous emulsions

• Rita S. Alqubelat,
• Yaroslava A. Menzorova and
• Maxim A. Mironov

Beilstein J. Org. Chem. 2024, 20, 2078–2083, doi:10.3762/bjoc.20.179

• usually more complex than conventional colloidosomes and involves several stages. Pickering emulsions or polymer spheres coated with a monolayer of colloidal particles are used as initial templates for synthesis [11]. Thus, cage-like structures have been obtained using phase inversion in Pickering

Active-metal template clipping synthesis of novel [2]rotaxanes

• Cătălin C. Anghel,
• Teodor A. Cucuiet,
• Niculina D. Hădade and
• Ion Grosu

Beilstein J. Org. Chem. 2023, 19, 1776–1784, doi:10.3762/bjoc.19.130

• obtained by CuAAC in the presence of CuCl(SIMes)(4,7-diclorophenantroline) as catalyst, with very good yields. Next, we set to study the ability of compound 6 to form copper(I) complexes able to act as active-metal templates for [2]rotaxane synthesis. Therefore, complexation studies of 6 with CuCl(SIMes

Light-responsive rotaxane-based materials: inducing motion in the solid state

• Adrian Saura-Sanmartin

Beilstein J. Org. Chem. 2023, 19, 873–880, doi:10.3762/bjoc.19.64

• of different templates [64][65][66][67][68][69]. The use of pyridyl-acyl hydrazone rotaxanes in the construction of light-responsive interlocked materials is envisioned as a promising approach to circumvent both issues, since these interlocked molecules are obtained in high yields (over 80%) and show

• focused on the integration of new photoswitchable scaffolds which allow both the formation of the intertwined species and the arrangement of the solid materials. In this regard, the functionalization of different templates already tested in solution chemistry is envisioned as the main strategy

A new oxidatively stable ligand for the chiral functionalization of amino acids in Ni(II)–Schiff base complexes

• Alena V. Dmitrieva,
• Oleg A. Levitskiy,
• Yuri K. Grishin and
• Tatiana V. Magdesieva

Beilstein J. Org. Chem. 2023, 19, 566–574, doi:10.3762/bjoc.19.41

• )) and includes a chiral auxiliary, an amino acid, and a bifunctional linker capable to arrange the components in the Schiff base complex. Such templates provide a significant C–H acidity at the α-amino acid carbon and a possibility for recycling of the chiral auxiliaries (for reviews see [5][14][15][16

• oxidative stability. The reactivity of the glycine and dehydroalanine complexes in the nucleophilic functionalization of amino acids was compared to the corresponding derivatives of the parent ligand L1. The results clearly demonstrated the advantages of the new complexes as stereocontrolling templates

• be shown below, this is not necessary since the isomeric Schiff base template proved efficient in stereoselective modification of amino acids. The products of the oxidative dimerization via the phenylene ring were not detected for both isomeric templates. The subsequent reaction with (S

Combining the best of both worlds: radical-based divergent total synthesis

• Kyriaki Gennaiou,
• Antonios Kelesidis,
• Maria Kourgiantaki and
• Alexandros L. Zografos

Beilstein J. Org. Chem. 2023, 19, 1–26, doi:10.3762/bjoc.19.1

• led to common scaffolds 47 and diene 48 after subsequent elimination. Those molecules serve as templates for Ni-based radical-based sp3–sp2 coupling and single-electron transfer (SET)-based [3 + 2] coupling, respectively (Scheme 4). Initial attempts to realize the [3 + 2] radical coupling with CAN led

BINOL as a chiral element in mechanically interlocked molecules

• Matthias Krajnc and
• Jochen Niemeyer

Beilstein J. Org. Chem. 2022, 18, 508–523, doi:10.3762/bjoc.18.53

• Incorporating BINOL into MIMs The introduction of axially chiral BINOL units into interlocked compounds can be achieved by different types of supramolecular template strategies that have been developed for MIM synthesis in the past decades, including passive metal templates [33][34], active metal templates [35

• ][36][37][38], anion templates [39][40], ammonium crown ether templates [41], and templates based on π–π interactions [42]. In 2004, Sauvage and co-workers have used a Cu(I)-based passive metal template approach to synthesize a [2]catenane containing an optically pure BINOL unit in each macrocycle [43

• supramolecular template strategies that have been developed in the past decades, including passive metal templates, active metal templates, anion templates, ammonium crown ether templates, and templates based on π–π interactions. This has opened the way for the application of the resulting chiral MIMs. The

Control over size, shape, and photonics of self-assembled organic nanocrystals

• Chen Shahar,
• Yaron Tidhar,
• Yunmin Jung,
• Haim Weissman,
• Sidney R. Cohen,
• Ronit Bitton,
• Iddo Pinkas,
• Gilad Haran and
• Boris Rybtchinski

Beilstein J. Org. Chem. 2021, 17, 42–51, doi:10.3762/bjoc.17.5

• mobility [20], but no control over the crystal size and morphology was demonstrated. Using self-assembled monolayers as templates for the seeding and growth of molecular crystals may offer control over structure and polymorphism [21]. However, in this method, the crystal formation is limited by the

Easy access to a carbohydrate-based template for stimuli-responsive surfactants

• Thomas Holmstrøm,
• Daniel Raydan and
• Christian Marcus Pedersen

Beilstein J. Org. Chem. 2020, 16, 2788–2794, doi:10.3762/bjoc.16.229

• metal-binding event. This study was carried out by having pyrene fluorophores attached to the two non-chelating positions, giving rise to excimer fluorescence when the distance between them was decreased due to the ring flip [12]. Carbohydrates with gluco stereochemistry have also been used as templates

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• models. These tools generally use 3D molecular templates of monosaccharides to reconstruct a 3D model. Energy minimisation methods can further refine the models. These models are essential for structure-based studies and complex calculations like Molecular Dynamics simulations. Therefore, the accurate

• model building requires the use of reliable databases to generate atomic coordinates and topology to provide an acceptable model. Some of the computational tools usually contain atom coordinates of generally used monosaccharides (as templates) and also use libraries of bond and angle parameters from

• list of pre-built core N- and O-linked carbohydrate moieties, which are usually present in glycoproteins structures, can be used as a template for further modification. A shortlist of glycan epitopes is also included providing templates for drawing more complex molecules. The software uses the Symbol

Hierarchically assembled helicates as reaction platform – from stoichiometric Diels–Alder reactions to enamine catalysis

• David Van Craen,
• Jenny Begall,
• Johannes Großkurth,
• Leonard Himmel,
• Oliver Linnenberg,
• Elisabeth Isaak and
• Markus Albrecht

Beilstein J. Org. Chem. 2020, 16, 2338–2345, doi:10.3762/bjoc.16.195

• Fujita et al. [9][10][11] or stereoselective nucleophilic substitutions by Raymond et al. [12] are important examples in this context. Recently, we described the use of hierarchically assembled helicates as templates for stereoselective Diels–Alder reactions via a post-functionalization process [13

A dynamic combinatorial library for biomimetic recognition of dipeptides in water

• Florian Klepel and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2020, 16, 1588–1595, doi:10.3762/bjoc.16.131

• exchange being one of the most prominent reactions [11][12][13][14]. Notably, while (pseudo)peptides are a common motif for DCL building blocks [7][11][15][16] very few DCLs use peptide templates. Still et al. showed early on that peptide receptors emerging from DCLs are possible. They screened for a

• , carboxyl groups, amides, amino acid side chains), our DCL should be applicable to a similar scope. In order to show that our system offers a general approach to find binders for biomolecules in water we choose to test our DCL against peptide templates. Results and Discussion We started from our established

• combination of cyclic tripeptide dimer. Each peptide dimer has two peaks because of the two constitutional isomers. Note that intensities between different compounds are not directly comparable in mass spectrometry. Upon addition of certain templates, notable changes were found in the chromatograms of the CFC

Five-component, one-pot synthesis of an electroactive rotaxane comprising a bisferrocene macrocycle

• Natalie Lagesse,
• Luca Pisciottani,
• Maxime Douarre,
• Pascale Godard,
• Brice Kauffmann,
• Vicente Martí-Centelles and
• Nathan D. McClenaghan

Beilstein J. Org. Chem. 2020, 16, 1564–1571, doi:10.3762/bjoc.16.128

• -diaminomethylbenzene molecules, in the presence of a suitable hydrogen-bonding template. Among the different templates employed, 4a proved to be the most successful giving rise to rotaxane 1a in 41% yield. Meanwhile, 4b and 4c gave little or no rotaxane formation. Cyclic voltammetry showed that the electroactive

Activated carbon as catalyst support: precursors, preparation, modification and characterization

• Melanie Iwanow,
• Tobias Gärtner,
• Volker Sieber and
• Burkhard König

Beilstein J. Org. Chem. 2020, 16, 1188–1202, doi:10.3762/bjoc.16.104

• preparation of these carbon materials (preparation of the solid scaffolds, pyrolysis of the carbon precursors in these templates and finally, the selective removal of the silica template) and the risk of structure and morphology defects by the harsh carbonization and template removal processes, this method is

Synthesis of esters of diaminotruxillic bis-amino acids by Pd-mediated photocycloaddition of analogs of the Kaede protein chromophore

• Esteban P. Urriolabeitia,
• Pablo Sánchez,
• Alexandra Pop,
• Cristian Silvestru,
• Eduardo Laga,
• Ana I. Jiménez and
• Carlos Cativiela

Beilstein J. Org. Chem. 2020, 16, 1111–1123, doi:10.3762/bjoc.16.98

• of the free species [27] and on using Pd complexes as templates [28][29][30]. The latter approach has shown good potential as a synthetic tool because it allows 1,3-diaminotruxillic derivatives to be obtained in a fully regio- and stereoselective way (only the ε-isomer is obtained). The process

• ], did not produce the expected cyclobutanes or gave only very low conversions (<5%) after long reaction times (96 h). As this reactivity was poor, it was decided to attempt the reaction using Pd complexes as templates [28][29][30]. The first step in this process was to study the C–H bond activation in

Architecture and synthesis of P,N-heterocyclic phosphine ligands

• Wisdom A. Munzeiwa,
• Bernard Omondi and
• Vincent O. Nyamori

Beilstein J. Org. Chem. 2020, 16, 362–383, doi:10.3762/bjoc.16.35

• block for the assembly of homo and hetero-organometallic complexes. The 3- and 4-pyridylphosphine derivatives 5 have also been successfully used as templates for assembling supramolecular structures and coordination polymers [54][59]. Halogenated ring-fused pyridine reagents can also be used to generate

The use of isoxazoline and isoxazole scaffolding in the design of novel thiourea and amide liquid-crystalline compounds

• Itamar L. Gonçalves,
• Rafaela R. da Rosa,
• Vera L. Eifler-Lima and
• Aloir A. Merlo

Beilstein J. Org. Chem. 2020, 16, 175–184, doi:10.3762/bjoc.16.20

• study of gels derived from low molecular mass gelators [15][16], and consequently the investigation of gelators of low molar mass with liquid crystal proprieties remains active [17][18]. In addition, isoxazolines and isoxazoles have been identified as promising templates in liquid crystal development

Nanopatterns of arylene–alkynylene squares on graphite: self-sorting and intercalation

• Tristan J. Keller,
• Joshua Bahr,
• Kristin Gratzfeld,
• Nina Schönfelder,
• Marcin A. Majewski,
• Marcin Stępień,
• Sigurd Höger and
• Stefan-S. Jester

Beilstein J. Org. Chem. 2019, 15, 1848–1855, doi:10.3762/bjoc.15.180

• –alkynylene macrocycles 1a/b (Figure 1), and the intercalation of solvent molecules and polycyclic aromatic hydrocarbons (PAHs). Our way towards nanoporous quadratic templates containing long (OC16H33) alkoxy side chains on two opposite sides of the square and two shorter (OC10H21, OC6H13) side chains on the

A heteroditopic macrocycle as organocatalytic nanoreactor for pyrroloacridinone synthesis in water

• Piyali Sarkar,
• Sayan Sarkar and
• Pradyut Ghosh

Beilstein J. Org. Chem. 2019, 15, 1505–1514, doi:10.3762/bjoc.15.152

• of macrocycles with multiple functional groups has been employed as alternative templates to induce the organic environment for catalysis via multiple weak interactions viz. π–π stacking, hydrogen bonding, etc. [25][26][27][28][29]. At the same time, several efforts have been made to develop

Design of a double-decker coordination cage revisited to make new cages and exemplify ligand isomerism

• Sagarika Samantray,
• Sreenivasulu Bandi and
• Dillip K. Chand

Beilstein J. Org. Chem. 2019, 15, 1129–1140, doi:10.3762/bjoc.15.109

• as BF4−, ClO4− and OTf− are not accommodated in the cavities and not helpful as templates. The Pd(NO3)2 sample prepared from PdCl2 and AgNO3, contained chloride as impurity and resulted in a mixture of products along with the targeted 4a (Supporting Information File 1, Figure S35b). The products in

Molecular recognition using tetralactam macrocycles with parallel aromatic sidewalls

• Dong-Hao Li and
• Bradley D. Smith

Beilstein J. Org. Chem. 2019, 15, 1086–1095, doi:10.3762/bjoc.15.105

• -based templates [35][36][37][38][39][40][41][42][43]. These reactions are remarkable examples of templated syntheses since they form four covalent bonds and bring together five molecules in a single reaction. The key step is the final amide-bond formation that clips the tetralactam around the template

• internal cavity of the tetralactam precursor that is undergoing cyclization. Inspection of the yields in Scheme 2 shows that higher rotaxane yields are obtained when the template has: (a) preorganized shape (compare rigid fumaryl templates 7, 8, 9, 10 and 11 with corresponding flexible succinyl analogues 3

• , 4, and 6), (b) increased hydrogen-bonding-acceptor basicity which is obtained by replacing ester carbonyls with amide carbonyls (compare guest templates 7, 8 and 9), and (c) complementary distance between the two carbonyls (compare template 3 with 16). 3.2. Squaraine, thiosquaraine, croconaine, and

Novel (2-amino-4-arylimidazolyl)propanoic acids and pyrrolo[1,2-c]imidazoles via the domino reactions of 2-amino-4-arylimidazoles with carbonyl and methylene active compounds

• Victoria V. Lipson,
• Tetiana L. Pavlovska,
• Nataliya V. Svetlichnaya,
• Anna A. Poryvai,
• Nikolay Yu. Gorobets,
• Erik V. Van der Eycken,
• Irina S. Konovalova,
• Svetlana V. Shiskina,
• Alexander V. Borisov,
• Vladimir I. Musatov and
• Alexander V. Mazepa

Beilstein J. Org. Chem. 2019, 15, 1032–1045, doi:10.3762/bjoc.15.101

• the formation of both unexplored heterocyclic systems containing a free amino group open for chemical modifications and the corresponding hetarylpropanoic acids providing useful templates for the synthesis of some marine alkaloids or their analogues. In domino reactions of the 2-amino-4-arylimidazoles

Back to the future: Why we need enzymology to build a synthetic metabolism of the future

• Tobias J. Erb

Beilstein J. Org. Chem. 2019, 15, 551–557, doi:10.3762/bjoc.15.49

• essential to identify suitable candidate templates to engineer or evolve a new activity within the backbone of a given enzyme. For example, although the BRENDA database is probably one of the best resources to learn about the detailed catalytic properties of enzymes, it only provides in selected cases

Regioselective addition of Grignard reagents to N-acylpyrazinium salts: synthesis of substituted 1,2-dihydropyrazines and Δ⁵-2-oxopiperazines

• Valentine R. St. Hilaire,
• William E. Hopkins,
• Yenteeo S. Miller,
• Srinivasa R. Dandepally and
• Alfred L. Williams

Beilstein J. Org. Chem. 2019, 15, 72–78, doi:10.3762/bjoc.15.8

• -oxopiperazines. These compounds can potentially serve as templates for making substituted 2-oxopiperazines. The investigation into the synthetic utility of this reaction is currently underway and will be reported in due course. Regioselective addition of Grignard reagents to mono- and disubstituted pyrazinium