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

• absorption spectroscopy, viscosity measurement, cyclic voltammetry and molecular modeling (Figure 9) [93]. Docking results confirmed that these complexes have the ability to interact with the minor groove of the ct-DNA. In addition, the authors confirmed that in presence of ascorbic acid, these complexes

• characterized three mononuclear copper(II) complexes, [Cu(tpy)Cl2], [Cu(tpy)(NO3)2(H2O)] and [Cu(Ptpy)Cl2]·H2O·HCl and investigated their cytotoxicity and primary mode of DNA binding mechanism [94]. Molecular modeling as well as DNA cleavage studies have revealed that the first two complexes are DNA minor

• synthesized in order to investigate the molecular basis of carbohydrate–minor groove DNA interactions by Vicent et al. [95]. NMR spectroscopy and molecular modeling studies further confirmed the existence of directional intramolecular hydrogen bonds and CH–π interactions, which results in stabilizing these

Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies

• Elias Christoforides,
• Andreas Papaioannou and
• Kostas Bethanis

Beilstein J. Org. Chem. 2018, 14, 838–848, doi:10.3762/bjoc.14.69

• shown by molecular modeling, proposing a tail–tail dimer [37] and finally MD calculations concluded that efficient removal of cholesterol from membranes requires the presence of β-CD dimers [27]. In this work, the crystallographic analysis of CHL/β-CD complex conclusively clarifies the inclusion mode of

Enzyme-free genetic copying of DNA and RNA sequences

• Marilyne Sosson and
• Clemens Richert

Beilstein J. Org. Chem. 2018, 14, 603–617, doi:10.3762/bjoc.14.47

• , in extension buffer containing 80 mM MgCl2, were typically found to be in the range of 5–8 h at a pH of 8.9, both for ribonucleotides and for deoxynucleotides. Only OAt-dTMP was slower to hydrolyze, with a t1/2 of 16 h [28]. Molecular modeling suggested that this may be due to the steric effect of

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

The use of 4,4,4-trifluorothreonine to stabilize extended peptide structures and mimic β-strands

• Yaochun Xu,
• Isabelle Correia,
• Tap Ha-Duong,
• Nadjib Kihal,
• Jean-Louis Soulier,
• Julia Kaffy,
• Benoît Crousse,
• Olivier Lequin and
• Sandrine Ongeri

Beilstein J. Org. Chem. 2017, 13, 2842–2853, doi:10.3762/bjoc.13.276

• proteins aggregation characterized by ordered β-sheet structure assemblies [14][15]. In this context, we synthesized and analyzed, by NMR and molecular modeling, the conformational preferences of eight pentapeptides, containing a L-serine, a L-threonine, a (2S,3R)-L-allo-CF3-threonine or a (2S,3S)-L-CF3

A permutation approach to the assignment of the configuration to diastereomeric tetrads by comparison of experimental and ab initio calculated differences in NMR data

• Przemysław J. Boratyński

Beilstein J. Org. Chem. 2017, 13, 2478–2485, doi:10.3762/bjoc.13.245

• Cinchona alkaloids 1–4 obtained in our laboratory were analyzed (Figure 1, for references, see Supporting Information File 1). The configurations of these derivatives were established based on previous X-ray studies for compounds 2a and 3d, NOESY experiments combined with molecular modeling for compounds

p-tert-Butylthiacalix[4]arenes functionalized by N-(4’-nitrophenyl)acetamide and N,N-diethylacetamide fragments: synthesis and binding of anionic guests

• Alena A. Vavilova and
• Ivan I. Stoikov

Beilstein J. Org. Chem. 2017, 13, 1940–1949, doi:10.3762/bjoc.13.188

• thiacalix[4]arenes 2, 7–10 (Figure 1) [26][42] with N-(4’-nitrophenyl)acetamide and N,N-diethylacetamide fragments was of interest. Initially, molecular modeling of the host–guest complexes of the above-mentioned thiacalix[4]arenes 2, 3, 5–10 with a number of single-charged anions (F−, Cl−, Br−, I−, CH3CO2

• N-(4’-nitrophenyl)acetamide and N,N-diethylacetamide groups in cone and partial cone conformations were synthesized. The calculations of the proposed model for the anion binding by the synthesized thiacalix[4]arenes were carried out using molecular modeling (the quantum mechanical method PM3). Also

Molecular recognition of N-acetyltryptophan enantiomers by β-cyclodextrin

• Spyros D. Chatziefthimiou,
• Mario Inclán,
• Petros Giastas,
• Athanasios Papakyriakou,
• Konstantina Yannakopoulou and
• Irene M. Mavridis

Beilstein J. Org. Chem. 2017, 13, 1572–1582, doi:10.3762/bjoc.13.157

• side of the cavity. Some were at bonding distances with each other, but by introducing the strongest of them as water molecules into the refinement did not result in a model of the guest (Table 2). Refinement details appear in CCDC 1531987. The structures were rendered in PyMOL [42]. Molecular modeling

• ” monomeric structure as indicated by molecular modeling studies (water molecules of the asymmetric unit are shown as spheres). L-NAcTrp and L-NAcPhe in β-CD dimers (the lines indicate the levels of the O2 and O3 secondary hydroxy groups. Numbering scheme of one glucopyranose residue (G) of β-CD and the

New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

• Pavel Nagorny and
• Zhankui Sun

Beilstein J. Org. Chem. 2016, 12, 2834–2848, doi:10.3762/bjoc.12.283

• L15 were proposed to form additional C–H hydrogen bonds between arene or α-halogenated acetyl groups and the carbonyl of lactide. X-ray crystallographic analysis and molecular modeling provided the evidence of such interactions in solid state, and the titration studies established weak binding (Ka ≈ 1

On the cause of low thermal stability of ethyl halodiazoacetates

• Magnus Mortén,
• Martin Hennum and
• Tore Bonge-Hansen

Beilstein J. Org. Chem. 2016, 12, 1590–1597, doi:10.3762/bjoc.12.155

• ) was included in the calculations even though the synthesis of this diazo compound has not been reported in the literature. We excluded 2c in our molecular modeling due to the need for a different basis set for iodine compared to the other halogens. We also included diethyl diazomalonate (2e, t1/2

• = 105 h at 100 °C [19]) having an electron-withdrawing α-substituent and allow comparison to literature t1/2 values. The trends obtained experimentally were confirmed by molecular modeling. EDA has the highest barrier towards loss of N2, while the halodiazoacetates follow the order Br > Cl > F. Even

Ring-whizzing in polyene-PtL₂ complexes revisited

• Oluwakemi A. Oloba-Whenu,
• Thomas A. Albright and
• Chirine Soubra-Ghaoui

Beilstein J. Org. Chem. 2016, 12, 1410–1420, doi:10.3762/bjoc.12.135

• Information Supporting Information File 212: The molecular geometry and total electronic energy for the molecules in this work are given in .xyz format. The file may be opened as a text file to read the coordinates, or opened directly by a molecular modeling program such as Mercury (http://www.ccdc.cam.ac.uk

Application of Cu(I)-catalyzed azide–alkyne cycloaddition for the design and synthesis of sequence specific probes targeting double-stranded DNA

• Svetlana V. Vasilyeva,
• Vyacheslav V. Filichev and
• Alexandre S. Boutorine

Beilstein J. Org. Chem. 2016, 12, 1348–1360, doi:10.3762/bjoc.12.128

• interaction or the non-optimal structure of linkers that connect two components. Additional studies aiming to optimize the structure of the linker using molecular modeling are necessary. A) Formation of nucleotide triplets in parallel and antiparallel (relatively to polypurine strand) complexes. The relative

Creating molecular macrocycles for anion recognition

• Amar H. Flood

Beilstein J. Org. Chem. 2016, 12, 611–627, doi:10.3762/bjoc.12.60

• ). The motivation for this new work was to generalize the idea of activating CH hydrogen bond donors using electron-withdrawing groups. In cyanostilbene, Lee recognized the cyano group could polarize the CH bond. Following some molecular modeling, he settled on a five-fold symmetric target that demanded

Interactions of cyclodextrins and their derivatives with toxic organophosphorus compounds

• Sophie Letort,
• Sébastien Balieu,
• William Erb,
• Géraldine Gouhier and
• François Estour

Beilstein J. Org. Chem. 2016, 12, 204–228, doi:10.3762/bjoc.12.23

• . However the inclusion complex formation was strengthen by molecular modeling studies with the aromatic group included into the cavity. Finally, DSC curves showed a first endothermic portion starting at 225 °C, typical of a melting process, and a second sharp exothermic decomposition peak, proving the

Determination of formation constants and structural characterization of cyclodextrin inclusion complexes with two phenolic isomers: carvacrol and thymol

• Miriana Kfoury,
• David Landy,
• Steven Ruellan,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2016, 12, 29–42, doi:10.3762/bjoc.12.5

• to a different binding stability with CDs. 2D ROESY NMR experiments were also performed to prove the encapsulation and illustrate the stable 3D conformation of the inclusion complexes. The structural investigation was accomplished with molecular modeling studies. Finally, the radical scavenging

• : cyclodextrins; DOSY-NMR; formation constant; molecular modeling; solubility; Introduction Carvacrol (2-methyl-5-(1-methylethyl)phenol, 1) and thymol (5-methyl-2-(1-methylethyl)phenol, 2) are monoterpenic phenol isomers (Figure 1) produced by several aromatic plants (oregano, thyme, savory, marjoram, etc.) [1

• entities of the guest molecule (different guest protons) simultaneously to calculate one Kf value. Then, 2D ROESY NMR was carried out to prove the encapsulation as well as to investigate the geometry of inclusion complexes. NMR studies were completed by molecular modeling investigations to illustrate the

Synthesis and characterization of a new photoinduced switchable β-cyclodextrin dimer

• Florian Hamon,
• Claire Blaszkiewicz,
• Marie Buchotte,
• Estelle Banaszak-Léonard,
• Hervé Bricout,
• Sébastien Tilloy,
• Eric Monflier,
• Christine Cézard,
• Laurent Bouteiller,
• Christophe Len and
• Florence Djedaini-Pilard

Beilstein J. Org. Chem. 2014, 10, 2874–2885, doi:10.3762/bjoc.10.304

• . The photoinduced, switchable binding behavior of AZO-CDim 1 was evaluated by ITC, NMR and molecular modeling in the presence of a ditopic adamantyl guest. The results indicate that AZO-CDim 1 can form two different inclusion complexes with an adamantyl dimer depending on its photoinduced isomers. Both

• times without causing side effects, as shown in Figure 3. Ab initio calculations were also performed but the cis/trans transition was not observed since molecular modeling methods are unable to break bonds. In order to collect data on this phenomenon, the two configurations of the system had to be taken

• software with the one set or two sets of sites models. During this fitting, enthalpy (ΔH), stoichiometry (n) and association constants (Ka) were adjustable parameters. Molecular modeling Initial geometries of the β-cyclodextrin dimers studied in this work were built using the LEaP program from the

Encapsulation of biocides by cyclodextrins: toward synergistic effects against pathogens

• Véronique Nardello-Rataj and
• Loïc Leclercq

Beilstein J. Org. Chem. 2014, 10, 2603–2622, doi:10.3762/bjoc.10.273

• -, β-, γ-, HP-α-, HP-β- and CM-β-CD) was investigated by Leclercq et al. [73]. The binding constants and stoichiometries were determined by combining the use of ammonium and chloride selective electrodes, NMR spectroscopy and molecular modeling. The biocidal activity of the inclusion complexes against

Versatile synthesis of amino acid functionalized nucleosides via a domino carboxamidation reaction

• Vicky Gheerardijn,
• Jos Van den Begin and
• Annemieke Madder

Beilstein J. Org. Chem. 2014, 10, 2566–2572, doi:10.3762/bjoc.10.268

• have a stable and predictable structure allowing the design of engineered active sites through the carefully planned introduction of extra catalytic functionalities via solid phase DNA synthesis. We have further recently shown that the combination of solid phase synthesis and molecular modeling

Effect of cyclodextrin complexation on phenylpropanoids’ solubility and antioxidant activity

• Miriana Kfoury,
• David Landy,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2014, 10, 2322–2331, doi:10.3762/bjoc.10.241

• , France ULCO, UCEIV, F-59140 Dunkerque, France 10.3762/bjoc.10.241 Abstract The complexation abilities of five cyclodextrins (CDs) with seven phenylpropanoids (PPs) were evaluated by UV–visible spectroscopy, phase solubility studies and molecular modeling. Formation constants (Kf), complexation

• ) and the solubilizing potential of CD was proposed. Molecular modeling was used to investigate the complementarities between host and guest. Finally, the antioxidant activity of encapsulated PPs was evaluated by scavenging of the stable DPPH radical. Keywords: antioxidant activity; complexation

• UV–visible spectroscopy and phase solubility studies. The solubilizing effects of CDs was investigated by determining their complexation efficiency (CE) [18][19]. A theoretical molecular modeling study has been realized to estimate the complexation energies and illustrate the most favorable inclusion

Pyrrolidine nucleotide analogs with a tunable conformation

• Lenka Poštová Slavětínská,
• Dominik Rejman and
• Radek Pohl

Beilstein J. Org. Chem. 2014, 10, 1967–1980, doi:10.3762/bjoc.10.205

• 7–14 were investigated by means of NMR and molecular modeling. The effect of the relative configuration of hydroxy and nucleobase substituents as well as the effect of the alkylation or acylation of the pyrrolidine nitrogen atom on the conformation of the pyrrolidine ring were studied. The results

• . The parameters A and B for the five-membered ribose and deoxyribose ring had been traditionally obtained from X-ray data [18]. In the case of a five-membered ring for which X-ray data are not available, DFT-optimized geometries of a number of conformations are used [19]. This molecular modeling

• by B3LYP/6-31++G* in water (the CPCM model). The optimized conformations were compared with those obtained by conformational analysis using 3JHH and the results showed a good agreement of the molecular modeling and the experiment (cf. Table 3 and Figure 14). Conclusion In summary, we presented an NMR

Photoswitchable precision glycooligomers and their lectin binding

• Daniela Ponader,
• Sinaida Igde,
• Marko Wehle,
• Katharina Märker,
• Mark Santer,
• David Bléger and
• Laura Hartmann

Beilstein J. Org. Chem. 2014, 10, 1603–1612, doi:10.3762/bjoc.10.166

• glycooligomer Azo-Gal(1,3,5)-5 binds with the same affinity before and after switching (entry 2 Table 2). In order to gain a first insight into the possible conformations of the glycooligomers and thus their potential binding modes, we performed molecular modeling as outlined in the caption of Figure 3. This

Substitution effect and effect of axle’s flexibility at (pseudo-)rotaxanes

• Friedrich Malberg,
• Jan Gerit Brandenburg,
• Werner Reckien,
• Oldamur Hollóczki,
• Stefan Grimme and
• Barbara Kirchner

Beilstein J. Org. Chem. 2014, 10, 1299–1307, doi:10.3762/bjoc.10.131

• based molecular shuttles was investigated by means of molecular modeling [19]. The Peyerimhoff group has carried out an in depth study of the rotaxane formation [20]. A later study investigated the shuttling motion of the wheel as a one-dimensional translation, together with the influence of the Kohn

Conformation of dehydropentapeptides containing four achiral amino acid residues – controlling the role of L-valine

• Michał Jewgiński,
• Joanna Krzciuk-Gula,
• Maciej Makowski,
• Rafał Latajka and
• Paweł Kafarski

Beilstein J. Org. Chem. 2014, 10, 660–666, doi:10.3762/bjoc.10.58

• molecular modeling was carried out using hardware and software resources of The Supercomputing and Networking Centre in Wroclaw. Paweł Kafarski and Maciej Makowski were supported by the Wroclaw Research Center EIT+ („Biotechnologies and advanced medical technologies – BioMed”; POIG 01.01.02-02-003/08-00

Topochemical control of the photodimerization of aromatic compounds by γ-cyclodextrin thioethers in aqueous solution

• Hai Ming Wang and
• Gerhard Wenz

Beilstein J. Org. Chem. 2013, 9, 1858–1866, doi:10.3762/bjoc.9.217

• aqueous solution of the inclusion complex of ACE with γ-CD thioether. Molecular modeling: A previously described procedure was used [25]. The geometries of the orientational isomers of the COU gas-phase dimer were fully optimized without any symmetry restriction at the MP2/6-31G* level of theory by using

Self-assembly of 2,3-dihydroxycholestane steroids into supramolecular organogels as a soft template for the in-situ generation of silicate nanomaterials

• Valeria C. Edelsztein,
• Andrea S. Mac Cormack,
• Matías Ciarlantini and
• Pablo H. Di Chenna

Beilstein J. Org. Chem. 2013, 9, 1826–1836, doi:10.3762/bjoc.9.213

• -assembly to promote gelation. To get an insight of the necessary molecular spatial requirements for the 2,3-dihydroxy moiety to reach an optimal hydrogen bonding, we studied the possible mode of self-assembly of the four isomers by a molecular modeling simulation in vacuum (semiempirical AM1). A

• zone, but a qualitative analysis showed that predictions are still possible for this complex system. The FTIR, XRPD, and semiempirical molecular modeling studies allowed us to propose a packing mode in which the amphiphilic steroid self-assembles in a head-to-head mode through two hydrogen bonds

• observed and then left at room temperature for 6 days. Subsequently, the sample was diluted in dichloromethane, the solid was centrifuged, and washed once with dichloromethane. The silica was heated at 200 °C for 2 h and 600 °C for 4 h in air. Molecular modeling experiment: These experiments were conducted