Halides as versatile anions in asymmetric anion-binding organocatalysis

• Lukas Schifferer,
• Martin Stinglhamer,
• Kirandeep Kaur and
• Olga García Macheño

Beilstein J. Org. Chem. 2021, 17, 2270–2286, doi:10.3762/bjoc.17.145

• extended to other N- and O-heteroarenes and various nucleophiles (Scheme 18b) [87][88][89][90][91]. Computational studies on the helical tetrakistriazole catalyst were additionally carried out, aiming at gaining insight into its interactions with the anion and cationic counterpart of the ionic substrate

• -bonding to complex halide anion-binding catalyst designs has been outlined. Recent reports show that synthetic and computational research become more intertwined, and a trend towards multiple noncovalent interactions, as well as supramolecular chemistry, might be in-bound soon. Based on the tremendous

(Phenylamino)pyrimidine-1,2,3-triazole derivatives as analogs of imatinib: searching for novel compounds against chronic myeloid leukemia

• Luiz Claudio Ferreira Pimentel,
• Lucas Villas Boas Hoelz,
• Henayle Fernandes Canzian,
• Frederico Silva Castelo Branco,
• Andressa Paula de Oliveira,
• Vinicius Rangel Campos,
• Floriano Paes Silva Júnior,
• Rafael Ferreira Dantas,
• Jackson Antônio Lamounier Camargos Resende,
• Anna Claudia Cunha,
• Nubia Boechat and
• Mônica Macedo Bastos

Beilstein J. Org. Chem. 2021, 17, 2260–2269, doi:10.3762/bjoc.17.144

• a.u.) and steric interactions with Glu305, Met309, Ile312, Val318, Leu373, Phe378, His380, Val398, Ala399, and Asp400 (steric interaction energy = −149,932 a.u.) (Figure 4c). Therefore, the computational simulations suggest that the synthesized compounds interact at the same binding site as IMT

Photoredox catalysis in nickel-catalyzed C–H functionalization

• Lusina Mantry,
• Rajaram Maayuri,
• Vikash Kumar and
• Parthasarathy Gandeepan

Beilstein J. Org. Chem. 2021, 17, 2209–2259, doi:10.3762/bjoc.17.143

• high yields. Based on the detailed computational and experimental mechanistic studies, the authors proposed a catalytic cycle which involves the C–H cleavage prior to the oxidative addition of N-acylsuccinimide (Figure 19) [125]. The acylation of benzylic C‒H bonds with acid chlorides 45 by means of

• computational studies highlight the involvement of hydrogen bonding assistance during the radical addition to olefine. The proposed reaction mechanism has two synergistic catalytic cycles, namely a photocatalytic cycle and a nickel catalytic cycle (Figure 23). The photoexcitation of the ketone PC 96 results in

Nomimicins B–D, new tetronate-class polyketides from a marine-derived actinomycete of the genus Actinomadura

• Zhiwei Zhang,
• Tao Zhou,
• Taehui Yang,
• Keisuke Fukaya,
• Enjuro Harunari,
• Shun Saito,
• Katsuhisa Yamada,
• Chiaki Imada,
• Daisuke Urabe and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2194–2202, doi:10.3762/bjoc.17.141

• equipped with a diode array detector was used for analysis and purification. The computational study was performed using MacroModel implemented in the Maestro 12.3 software package [27] and the Gaussian16, Revision C.01 program [28]. A part of these computations was conducted using the SuperComputer System

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

Natural products in the predatory defence of the filamentous fungal pathogen Aspergillus fumigatus

• Jana M. Boysen,
• Nauman Saeed and
• Falk Hillmann

Beilstein J. Org. Chem. 2021, 17, 1814–1827, doi:10.3762/bjoc.17.124

• -melanin synthesis completely which leads to white spores [45]. DHN-melanin is a heterogeneous polymer, as such it does not have a unique structure. Its insolubility aggravates any structural analyses of the deciphering of repetitive motives. However, there were studies doing either computational

Development of N-F fluorinating agents and their fluorinations: Historical perspective

• Teruo Umemoto,
• Yuhao Yang and
• Gerald B. Hammond

Beilstein J. Org. Chem. 2021, 17, 1752–1813, doi:10.3762/bjoc.17.123

A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis

• Theodore Groth,
• Rudiyanto Gunawan and
• Sriram Neelamegham

Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119

• relate cell-signaling pathways to TFs and cellular glycosylation state. Whereas analysis results are presented for all 29 cancer types, specific focus is placed on human luminal and basal breast cancer disease progression. Overall, the article presents a computational approach to describe TF–glycogene

• α2-6 sialyltransferases ST6Gal-I/II by hypoxic nuclear factor 1-α (HNF1-α) in HepG2 cells [7], c-JUN-B3GNT8 regulatory relationships in gastric carcinoma cell lines [8], and SP1-B4GALT1 relations in lung cancer A549 cells [9]. A recent study also used computational predictions and wet-lab experiments

• to determine TFs that disproportionately regulate individual glycosylation pathways. It is important to note that the findings from this study represent computational inferences that are yet to be validated in the wet lab. Nevertheless, it provides a systems-based framework for the design and

Electron-rich triarylphosphines as nucleophilic catalysts for oxa-Michael reactions

• Susanne M. Fischer,
• Simon Renner,
• A. Daniel Boese and
• Christian Slugovc

Beilstein J. Org. Chem. 2021, 17, 1689–1697, doi:10.3762/bjoc.17.117

• from MZ-Gel SD plus, 500 A and 100 A, linear 5 µ; UV detector (SPD-20A) and RI detector (RID-20A)) using THF as eluent. Poly(styrene) standards in the range of 350 to 17800 g/mol purchased from Polymer Standard Service were used for calibration. Computational details All calculations were run with the

Fritsch–Buttenberg–Wiechell rearrangement of magnesium alkylidene carbenoids leading to the formation of alkynes

• Tsutomu Kimura,
• Koto Sekiguchi,
• Akane Ando and
• Aki Imafuji

Beilstein J. Org. Chem. 2021, 17, 1352–1359, doi:10.3762/bjoc.17.94

• -tolyl sulfoxide and ethylmagnesium bromide [16]. Reaction of sulfoxides 2a and 5–8 with organometallic reagents. Synthesis of alkynes 4b–g from sulfoxides 2b–g. Supporting Information Supporting Information File 30: Characterization data, copies of NMR spectra, and computational details. Funding This

Structural effects of meso-halogenation on porphyrins

• Keith J. Flanagan,
• Maximilian Paradiz Dominguez,
• Zoi Melissari,
• Hans-Georg Eckhardt,
• René M. Williams,
• Dáire Gibbons,
• Caroline Prior,
• Gemma M. Locke,
• Alina Meindl,
• Aoife A. Ryan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2021, 17, 1149–1170, doi:10.3762/bjoc.17.88

• present are a current limitation. To combat this, we decided to expand these series with ab-initio computational molecular modelling. We focused on the structural modelling of three series. The ground-state geometries of several members of these series were optimized at the wB97-XD/cc-pVDZ level of theory

N-tert-Butanesulfinyl imines in the asymmetric synthesis of nitrogen-containing heterocycles

• Joseane A. Mendes,
• Paulo R. R. Costa,
• Miguel Yus,
• Francisco Foubelo and
• Camilla D. Buarque

Beilstein J. Org. Chem. 2021, 17, 1096–1140, doi:10.3762/bjoc.17.86

• -tribromomethylamines 16. The structure and configuration of aziridines 15 were determined unambiguously by single crystal X-ray analysis [64]. In order to explain the experimental results, a nonchelation controlled transition state was proposed. Based on computational studies, it is known that a kind of s-cis

Metal-free glycosylation with glycosyl fluorides in liquid SO₂

• Krista Gulbe,
• Jevgeņija Lugiņina,
• Edijs Jansons,
• Artis Kinens and
• Māris Turks

Beilstein J. Org. Chem. 2021, 17, 964–976, doi:10.3762/bjoc.17.78

• can be performed in widely available glass pressure tubes. Detection of the FSO2− species by 19F NMR (471 MHz, D2O). Computational study of reaction mechanism α-11 + MeOH → α-13c in the presence of and in absence of SO2 (Gaussian 09, Revision D.01; Gaussian, Inc.; m052x method and the 6-31+g(d) basis

Chiral isothiourea-catalyzed kinetic resolution of 4-hydroxy[2.2]paracyclophane

• David Weinzierl and
• Mario Waser

Beilstein J. Org. Chem. 2021, 17, 800–804, doi:10.3762/bjoc.17.68

• anhydride 4a [33][34][35][36][37], which then allows for the resolution of the enantiomers of alcohol 2. Unfortunately, however, the true nature of this enantiodiscriminating step has not yet been elucidated and will require detailed computational studies. Conclusion In conclusion, we identified conditions

Synthesis, structural characterization, and optical properties of benzo[f]naphtho[2,3-b]phosphoindoles

• Mio Matsumura,
• Takahiro Teramoto,
• Masato Kawakubo,
• Masatoshi Kawahata,
• Yuki Murata,
• Kentaro Yamaguchi,
• Masanobu Uchiyama and
• Shuji Yasuike

Beilstein J. Org. Chem. 2021, 17, 671–677, doi:10.3762/bjoc.17.56

• ]. Unfortunately, the electrochemistry of some compounds could not be determined under the conditions available to us. Therefore, computational investigations are particularly useful for understanding the trends of the electrochemical and photophysical properties of molecular materials. Density functional theory

• research was supported by a research grant from Institute of Pharmaceutical Life Sciences, Aichi Gakuin University. Allotment of computational resources from HOKUSAI BigWaterfall (Project G19012, RIKEN) is also gratefully acknowledged.

Amino- and polyaminophthalazin-1(2H)-ones: synthesis, coordination properties, and biological activity

• Zbigniew Malinowski,
• Emilia Fornal,
• Agata Sumara,
• Renata Kontek,
• Karol Bukowski,
• Beata Pasternak,
• Dariusz Sroczyński,
• Joachim Kusz,
• Magdalena Małecka and
• Monika Nowak

Beilstein J. Org. Chem. 2021, 17, 558–568, doi:10.3762/bjoc.17.50

• Information File 65: Experimental details, synthetic procedures, and characterization data of new compounds including copies of spectra. Supporting Information File 66: Experimental details, computational details, X-ray crystallographic data, FTIR and vis–NIR spectra, and cyclic voltammetry for compounds 7

The synthesis of chiral β-naphthyl-β-sulfanyl ketones via enantioselective sulfa-Michael reaction in the presence of a bifunctional cinchona/sulfonamide organocatalyst

• Deniz Tözendemir and
• Cihangir Tanyeli

Beilstein J. Org. Chem. 2021, 17, 494–503, doi:10.3762/bjoc.17.43

• transition state model to explain the origin of the stereoinduction was proposed (Scheme 2), according to the Houk’s Brønsted acid hydrogen bonding model. Guo’s computational work in 2017 on the sulfa-Michael addition of thiols to enones in the presence of cinchona alkaloid-type organocatalysts showed that

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

• fluoroprolines in peptide and protein degradation is lacking though. 8 The potency of computational modeling in the design of proteins containing fluoroprolines The conformational consequences of the fluorination of the 4-position of proline have been well studied using computational methods. The latter provided

CF₃-substituted carbocations: underexploited intermediates with great potential in modern synthetic chemistry

• Anthony J. Fernandes,
• Armen Panossian,
• Bastien Michelet,
• Agnès Martin-Mingot,
• Frédéric R. Leroux and
• Sébastien Thibaudeau

Beilstein J. Org. Chem. 2021, 17, 343–378, doi:10.3762/bjoc.17.32

• benzylic alcohols 61 did not undergo further arylation and were stable under the reaction conditions. In agreement with computational studies [97], this behavior was assigned to the presence of the CF3 group, which induces a shortening of the C–O bond in the product (dC–O = 1.426 Å) compared to the CH3

Diels–Alder reaction of β-fluoro-β-nitrostyrenes with cyclic dienes

• Savva A. Ponomarev,
• Roman V. Larkovich,
• Alexander S. Aldoshin,
• Andrey A. Tabolin,
• Sema L. Ioffe,
• Jonathan Groß,
• Till Opatz and
• Valentine G. Nenajdenko

Beilstein J. Org. Chem. 2021, 17, 283–292, doi:10.3762/bjoc.17.27

• [67] level of theory in combination with a Pople basis set and the IEFPCM [68] solvation model for o-xylene. Both functionals are already known in the literature for the investigation of cycloadditions [69][70][71][72]. For the computational details the reader is referred to Supporting Information

• File 206: Copies of spectra, experimental section, and computational details of DFT calculations. Acknowledgements The authors acknowledge the partial support in measuring of NMR spectra from the M. V. Lomonosov Moscow State University Program of Development. We thank Jan Brauer and Paul Eckhardt for

• their assistance with the computational calculations and evaluations. Parts of this research were conducted using the supercomputer MOGON and/or advisory services offered by the Johannes Gutenberg University Mainz (hpc.uni-mainz.de), which is a member of the AHRP (Alliance for High Performance Computing

The preparation and properties of 1,1-difluorocyclopropane derivatives

• Kymbat S. Adekenova,
• Peter B. Wyatt and
• Sergazy M. Adekenov

Beilstein J. Org. Chem. 2021, 17, 245–272, doi:10.3762/bjoc.17.25

• the activation energies for both cis–trans-isomerization and for the transformation of vinylcyclopropanes into cyclopentenes. Both processes could occur by a C–C-bond homolysis to form a diradical. Computational studies by Gety, Hrovat, and Borden indicated that there would be a preference for

Exploring the possibility of using fluorine-involved non-conjugated electron-withdrawing groups for thermally activated delayed fluorescence emitters by TD-DFT calculation

• Dongyang Chen and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2021, 17, 210–223, doi:10.3762/bjoc.17.21

• assist in the rISC process, and improve the TADF characteristics, mitigating the somewhat larger ΔEST values in these compounds. Conclusion This computational study demonstrates the high potential of fluorinated acceptors in TADF emitter design. In particular, we showed that OCF3, SCF3 and SF5 groups

Tuning the solid-state emission of liquid crystalline nitro-cyanostilbene by halogen bonding

• Subrata Nath,
• Alexander Kappelt,
• Matthias Spengler,
• Bibhisan Roy,
• Jens Voskuhl and
• Michael Giese

Beilstein J. Org. Chem. 2021, 17, 124–131, doi:10.3762/bjoc.17.13

• weakens the halogen bond. In a first step, we calculated the interaction energies of the assemblies of the azobenzene halogen bond donors F4St, F4Az, F3Az, F2Az or F2’Az with NO2-C1. For computational efficiency reasons the terminal alkoxy chains were substituted by methoxy groups. The interaction

• interaction energies in kJ/mol of the XB-acceptor NO2-C1 with F4St, F4Az, F3Az, F2Az, and F2’Az. For computational efficiency, the octyl chains have been replaced by methoxy groups. Summary of the thermal behaviour of the azo complexes with decreasing fluorination degree as observed by DSC upon cooling from

Direct synthesis of anomeric tetrazolyl iminosugars from sugar-derived lactams

• Michał M. Więcław and
• Bartłomiej Furman

Beilstein J. Org. Chem. 2021, 17, 115–123, doi:10.3762/bjoc.17.12

• an attempt at resolving this problem by means of the electronic circular dichroism (ECD) technique. We recorded an ECD spectrum of both compounds and compared it with simulated spectra, generated for both possible diastereomers (2-(R) and 2-(S)) using computational chemistry software. Unfortunately

• azide addition to nitriles [45]. It is important to note that the computational investigation of this reaction mechanism was not a primary goal of this work. That said, we consider this simple, crude DFT research to support our model of the transformation described herein. Conclusion During the course

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• proteins and other biological molecules, all of which have their own biological role and chemical interactions. Characterisation methods that can be employed to study PPIs can be divided into four categories: atomic resolution methods, mass spectrometry methods, biophysical methods, and computational

• characterisation of the binding reaction. Computational methods are used to predict PPIs and interfaces. The advantage of performing in silico experiments includes narrowing down the number of the binding partners to be tested in vitro or in vivo. Computational methods include supervised machine learning, where

• models are predicted from positive and negative training datasets [37], and statistical methods using genome-based data to predict interactions [38]. However, some PPIs can be difficult to predict using computational programmes, and thus resulting in absent or wrong PPIs. It is important to note that a