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

• a soft scoring function that assesses the complementarity between the surfaces of the ligand and the target. Thus, FlexAID has demonstrated superior performance compared to well-established software like AutoDock Vina, particularly when target flexibility plays a pivotal role, as is often the case

Chemo-enzymatic total synthesis: current approaches toward the integration of chemical and enzymatic transformations

• Ryo Tanifuji and
• Hiroki Oguri

Beilstein J. Org. Chem. 2024, 20, 1693–1712, doi:10.3762/bjoc.20.151

• considered a remarkable example of utilizing the complementarity between chemical and enzymatic transformations (Scheme 1 and Scheme 2). The cotylenin and fusicoccin families comprise structurally related diterpene glucosides with a 5/8/5 fused tricyclic aglycon and a sugar moiety linked through the C9

Photoredox catalysis harvesting multiple photon or electrochemical energies

• Mattia Lepori,
• Simon Schmid and
• Joshua P. Barham

Beilstein J. Org. Chem. 2023, 19, 1055–1145, doi:10.3762/bjoc.19.81

1,4-Dithianes: attractive C2-building blocks for the synthesis of complex molecular architectures

• Bram Ryckaert,
• Ellen Demeyere,
• Frederick Degroote,
• Hilde Janssens and
• Johan M. Winne

Beilstein J. Org. Chem. 2023, 19, 115–132, doi:10.3762/bjoc.19.12

• alkylations. Herein, the lithiated sulfur-heterocycles act as a cis-vinyl anion equivalent, a strategy that was developed by Palumbo and co-workers. The method shows some complementarity to the more classical acetylene alkylations, followed by partial hydrogenation to the cis-olefin (see Scheme 10 and Scheme

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

• disconnections. As radical disconnections are gaining ground, more sophisticated retrosyntheses of natural products are unlocked, enriching thus their synthetic scalability [6][7]. A direct comparison of a classic vs a radical approach highlights the complementarity and, more often than not, the superiority of

Complementarity of solution and solid state mechanochemical reaction conditions demonstrated by 1,2-debromination of tricyclic imides

• Petar Štrbac and
• Davor Margetić

Beilstein J. Org. Chem. 2022, 18, 746–753, doi:10.3762/bjoc.18.75

• ; cycloaddition; debromination; Diels−Alder reaction; mechanochemistry; Introduction The complementarity of reaction conditions [1][2][3] where the reaction takes place under some, but not under other conditions, or where a chemical reaction proceeds in a different way or mechanism is a useful feature in

• LAG, milling again gave 22, but it was accompanied with a larger amount of 40 and some side-product 12. A control LAG milling experiment without furan led to 40 and a significant amount of 12. These experiments emphasize the complementarity of ball milling conditions with solution chemistry (in

Heteroleptic metallosupramolecular aggregates/complexation for supramolecular catalysis

• Prodip Howlader and
• Michael Schmittel

Beilstein J. Org. Chem. 2022, 18, 597–630, doi:10.3762/bjoc.18.62

• complexes by Chan using complementary ligand binding [39], sometimes combined with conformational regulation [40], and of Newkome/Li [41] applying mainly geometric complementarity [42]. Clever utilized shape complementarity [21] for building heteroleptic palladium(II) cages whereas Crowley developed a

• the rotational speed [96]. Ligands 53 and 76 were conceived based on geometric complementarity at their coordination sites using the HETPYP interaction in both aggregates [Cu4(76)2]4+ and 77 = [Cu2(53)(76)]2+ (Figure 17). The structure of 76 suggested that the dimeric parallelogram-type double rotor

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

• complementarity as well. An elegant solution to this problem has been to use 2,6-diaminopurine (D) instead of adenosine and 2-thiouridine (s2U) instead of uridine as modified nucleobases in PNAs designed for double duplex invasion [129][130]. D and s2U form more stable Watson–Crick base pairs with T and A

Methodologies for the synthesis of quaternary carbon centers via hydroalkylation of unactivated olefins: twenty years of advances

• Thiago S. Silva and
• Fernando Coelho

Beilstein J. Org. Chem. 2021, 17, 1565–1590, doi:10.3762/bjoc.17.112

• (reductive ATR), in which carbon-centered radicals are added to the olefin double bond, followed by a hydrogen abstraction, are a complementary approach to the MHAT methodologies and allow the generation of anti-Markovnikov hydroalkylation products [112][113][114][115][116]. The polar complementarity

Co-crystallization of an organic solid and a tetraaryladamantane at room temperature

• Fabian Rami,
• Jan Nowak,
• Felix Krupp,
• Wolfgang Frey and
• Clemens Richert

Beilstein J. Org. Chem. 2021, 17, 1476–1480, doi:10.3762/bjoc.17.103

• -forming compound. The situation will be different, when there is shape complementarity between the two solids or when other specific interactions favor a co-crystal [20]. Thermodynamically, it is not unlikely that two separate sets of pure crystals, made up of only one organic compound each, represent the

• may be obtained from organic molecules chosen for their shape complementarity and ability to engage in specific molecular interactions [21][22]. Such co-crystals are a fascinating class of materials with applications very different from mere structure elucidation. Conclusion Taken together, the

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

Insight into functionalized-macrocycles-guided supramolecular photocatalysis

• Minzan Zuo,
• Krishnasamy Velmurugan,
• Kaiya Wang,
• Xueqi Tian and
• Xiao-Yu Hu

Beilstein J. Org. Chem. 2021, 17, 139–155, doi:10.3762/bjoc.17.15

• of the host and guest as well as the degree of geometric complementarity [21][22]. CDs can recognize guests in both aqueous and solid environments, so that they can be used as an excellent host for the construction of photocatalytic systems. CD-based host–guest systems can realize various types of

Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups

• Benjamin Jeffries,
• Zhong Wang,
• Robert I. Troup,
• Anaïs Goupille,
• Jean-Yves Le Questel,
• Charlene Fallan,
• James S. Scott,
• Elisabetta Chiarparin,
• Jérôme Graton and
• Bruno Linclau

Beilstein J. Org. Chem. 2020, 16, 2141–2150, doi:10.3762/bjoc.16.182

• groups is a common strategy in the drug optimization process. It is typically employed to ensure proper fitting of the part(s) of a ligand that interact with a receptor [1][2]. Apart from volume considerations, shape complementarity is regarded as important as well [3][4][5]. Hence, the modification of

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• structural and dynamic features of the glycans. This makes the 3D complementarity of the glycans architecture key towards the success of these processes and an essential piece of information for us to have in order to understand glycan recognition. Because of their chemical nature, glycans are intrinsically

• and complementarity to a receptor. However, these effects are rather complex to understand or to predict, if we think of the N-glycans 3D structure in terms of sequence of monosaccharides, a view that stems from the way we think about proteins. Our results show that the main effect of all

Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides

• Sabrina Müller,
• Jannik Paulus,
• Jochen Mattay,
• Heiko Ihmels,
• Veronica I. Dodero and
• Norbert Sewald

Beilstein J. Org. Chem. 2020, 16, 60–70, doi:10.3762/bjoc.16.8

• pyrrole/imidazole amide with DNA bases, helping to achieve proper shape complementarity only when the system is in the Z-configuration. Therefore, this azobenzene represents a promising approach to replace the γ-aminobutyric acid linker in the Im/Py polyamide systems. Design and synthesis of

Perspective isomorphs – a new classification of molecular structures based on artistic and chemical concepts

• Jannis Neumann,
• Ansgar Schnurr and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2019, 15, 2319–2326, doi:10.3762/bjoc.15.224

• complementarity of the different model concepts, it was necessary to look for new ways of representing atoms. Artists are experts in new, innovative image creations. They have the ability to process various aspects and complex information in images. In order to alternate the predominant omniscient view and in

Host–guest interactions between p-sulfonatocalix[4]arene and p-sulfonatothiacalix[4]arene and group IA, IIA and f-block metal cations: a DFT/SMD study

• Valya K. Nikolova,
• Cristina V. Kirkova,
• Silvia E. Angelova and
• Todor M. Dudev

Beilstein J. Org. Chem. 2019, 15, 1321–1330, doi:10.3762/bjoc.15.131

• /thermodynamics of the binding event, complementarity of molecular shapes, etc., is useful for designing receptor molecules. Results and Discussion M062X/6-31G(d,p) optimized structures of the host systems in cone conformation are presented in Figure 1 in two projections: side view and view from the rim trimmed

Stereo- and regioselective hydroboration of 1-exo-methylene pyranoses: discovery of aryltriazolylmethyl C-galactopyranosides as selective galectin-1 inhibitors

• Alexander Dahlqvist,
• Axel Furevi,
• Niklas Warlin,
• Hakon Leffler and
• Ulf J. Nilsson

Beilstein J. Org. Chem. 2019, 15, 1046–1060, doi:10.3762/bjoc.15.102

• -Glu71 groove may, in addition to a more favorable steric complementarity, benefit from the electron-poor triazole hydrogen sampling positions close to the Glu71 carboxylate and the electron-rich triazole nitrogens sampling positions close to the rim of Trp68 side chain. This hypothesis may also explain

N-Arylphenothiazines as strong donors for photoredox catalysis – pushing the frontiers of nucleophilic addition of alcohols to alkenes

• Fabienne Speck,
• David Rombach and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2019, 15, 52–59, doi:10.3762/bjoc.15.5

• applications. The access to electronically excited states of organic molecules allows unlocking new and sometimes complementary chemical reactivities that cannot be tackled by using thermally driven chemical reactions [1]. This complementarity allows for the development of so far unknown transformations [2

Coordination-driven self-assembly of discrete Ru₆–Pt₆ prismatic cages

• Aderonke Ajibola Adeyemo and
• Partha Sarathi Mukherjee

Beilstein J. Org. Chem. 2018, 14, 2242–2249, doi:10.3762/bjoc.14.199

• [47][48][49][50][51] and host–guest chemistry [52][53][54][55][56] among others. The cardinal prerequisites to obtain these self-assembled supramolecular architectures include stoichiometry and conformational complementarity on the binding sites of the building blocks [57][58][59][60][61]. However

Synthesis of new p-tert-butylcalix[4]arene-based polyammonium triazolyl amphiphiles and their binding with nucleoside phosphates

• Vladimir A. Burilov,
• Guzaliya A. Fatikhova,
• Mariya N. Dokuchaeva,
• Ramil I. Nugmanov,
• Diana A. Mironova,
• Pavel V. Dorovatovskii,
• Victor N. Khrustalev,
• Svetlana E. Solovieva and
• Igor S. Antipin

Beilstein J. Org. Chem. 2018, 14, 1980–1993, doi:10.3762/bjoc.14.173

• seen ADP more effectively embeds into the molecular cleft formed by two ammonium moieties due to a good host–guest geometric size and/or shape complementarity (Figure 4a and c). The three phosphate groups of ATP have a larger size and cannot realize a similar supramolecular motif in the complex. For

Host–guest complexes of conformationally flexible C-hexyl-2-bromoresorcinarene and aromatic N-oxides: solid-state, solution and computational studies

• Rakesh Puttreddy,
• Ngong Kodiah Beyeh,
• S. Maryamdokht Taimoory,
• Daniel Meister,
• John F. Trant and
• Kari Rissanen

Beilstein J. Org. Chem. 2018, 14, 1723–1733, doi:10.3762/bjoc.14.146

• encapsulation in the bowl-shaped upper rim (endo complexation) due to size complementarity between host cavity and guest shape, and are generally stabilised through multiple C–H···π interactions [26][27][28]. The cavity capacity to undergo induced conformational changes in response to the incorporation of

• , since 11 is able to undergo C–C bond rotation, BrC6 tends to maintain a nearly ideal crown geometry suggesting excellent conformational complementarity between 11 and BrC6. Comparison of ditopic H–G complexes In 3@BrC6, the asymmetric unit contains one host and four guest 3 molecules. Of the four guests

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• interactions are also augmented by a series of electrostatic and van der Waals interactions including salt bridge formation with the phosphate backbone [1]. Although, the majority of proteins recognize DNA in the major groove due, in large part, to the potential and shape complementarity, several others also

• successful class of synthetic DNA (minor groove) binders that can be designed to bind chosen DNA sequences via directed H-bonds, shape complementarity, and can compete with specific protein–DNA binding interactions in the minor or major grooves [67][68]. A variety of sequence-specific Py/Im polyamides were

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• investigation of DNA or RNA structure, as well as for DNA/RNA interactions with various ligands [2][6][9][10]. Figure 7 nicely summarizes the complementarity of the methods. As mentioned in the Introduction, the measurement of LD requires the sample to be oriented in a known way with respect to the polarization

Complexation of molecular clips containing fragments of diphenylglycoluril and benzocrown ethers with paraquat and its derivatives

• Leonid S. Kikot',
• Catherine Yu. Kulygina,
• Alexander Yu. Lyapunov,
• Svetlana V. Shishkina,
• Roman I. Zubatyuk,
• Tatiana Yu. Bogaschenko and
• Tatiana I. Kirichenko

Beilstein J. Org. Chem. 2017, 13, 2056–2067, doi:10.3762/bjoc.13.203

• . The stability constants with paraquat (7) rise with the increase of the polyether cycle size. The maximum complementarity of the pseudo cavity for binding of paraquat (7) was observed for clips based on benzo-21-crown-7 and benzo-24-crown-8. The introduction of substituents with terminal OH groups on