Oligonucleotide analogues with cationic backbone linkages

• Melissa Meng and
• Christian Ducho

Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111

• fully cationic α-oligonucleotides bound to single-stranded DNA and RNA targets with high affinity, with duplex stabilization being proportional to the number of cationic modifications. It was also reported that these oligonucleotides showed retained base pairing fidelity, i.e., the Tm value was

London dispersion as important factor for the stabilization of (Z)-azobenzenes in the presence of hydrogen bonding

• Andreas H. Heindl,
• Raffael C. Wende and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2018, 14, 1238–1243, doi:10.3762/bjoc.14.106

• important classes of molecular switches is crucial for the design of light-responsive materials using this entity. Herein, we present the stabilization of metastable (Z)-azobenzenes by London dispersion interactions, even in the presence of comparably stronger hydrogen bonds in various solvents. The Z→E

• isomerization rates of several N-substituted 4,4′-bis(4-aminobenzyl)azobenzenes were measured. An intramolecular stabilization was observed and explained by the interplay of intramolecular amide and carbamate hydrogen bonds as well as London dispersion interactions. Whereas in toluene, 1,4-dioxane and tert

• -butyl methyl ether the hydrogen bonds dominate, the variation in stabilization of the different substituted azobenzenes in dimethyl sulfoxide can be rationalized by London dispersion interactions. These findings were supported by conformational analysis and DFT computations and reveal low-energy London

A selective removal of the secondary hydroxy group from ortho-dithioacetal-substituted diarylmethanols

• Anna Czarnecka,
• Emilia Kowalska,
• Agnieszka Bodzioch,
• Joanna Skalik,
• Marek Koprowski,
• Krzysztof Owsianik and
• Piotr Bałczewski

Beilstein J. Org. Chem. 2018, 14, 1229–1237, doi:10.3762/bjoc.14.105

• diarylmethanes. Most probably, electron-donating groups on aryls facilitate both Zn complexation and stabilization of the intermediate carbocationic species formed. Conclusion In summary, a new example of the selective functional group transformation of diarylmethanols (Ar1Ar2CH(OH)) to diarylmethanes (Ar1Ar2CH2

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

• could not bind into the minor groove due to change in their conformation, thereby showing negligible DNA binding. Thus, their antibacterial activity is not attributed to DNA binding affinity due to lack of DNA stabilization by these conjugates. 2.3. Bisamidines One of the oldest known clinically

2-Iodo-N-isopropyl-5-methoxybenzamide as a highly reactive and environmentally benign catalyst for alcohol oxidation

• Takayuki Yakura,
• Tomoya Fujiwara,
• Akihiro Yamada and
• Hisanori Nambu

Beilstein J. Org. Chem. 2018, 14, 971–978, doi:10.3762/bjoc.14.82

• in common organic solvents. To overcome these drawbacks, IBX analogs [12][13][14][15][16][17][18][19][20][21][22] and several iodoxyarene derivatives [23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38] have been developed, and the stabilization of IBX by combining it with benzoic and

Phosphodiester models for cleavage of nucleic acids

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

• transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme

• , for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering and departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on

Chlorination of phenylallene derivatives with 1-chloro-1,2-benziodoxol-3-one: synthesis of vicinal-dichlorides and chlorodienes

• Zhensheng Zhao and
• Graham K. Murphy

Beilstein J. Org. Chem. 2018, 14, 796–802, doi:10.3762/bjoc.14.67

• as resulting from the stabilization of radical intermediates gained upon methoxy substitution [51], which permitted further chlorination of either the methyl or arene groups. To gain insight into the reaction mechanism we carried out two key control experiments. First, to test for rearrangement

Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides

• Kartik Temburnikar and
• Katherine L. Seley-Radtke

Beilstein J. Org. Chem. 2018, 14, 772–785, doi:10.3762/bjoc.14.65

• cleavage proceeds either by activation of a nucleophile that attacks C1' or by stabilization of the leaving group, which could either be the nucleobase or an oxocarbenium ion [31][36]. As such, the oxocarbenium ion is a species formed during the glycosidic bond cleavage, which may be present as an

• ' pseudoaxial methoxy groups further stabilize the intermediate in E3 conformer, thereby favoring the E3 confomer over the 3E. In the case of an anomeric phenyl group (Ph, Figure 6C), stabilization of the positive charge (C=O+) through conjugation, via parallel alignment, helps to overcome the unfavorable

• acids. Shown is the monomeric building block of nucleic acids. Changes to the nucleotide structure can affect molecular recognition, as well as structure and function. Formation of oxocarbenium ion during glycosidic bond cleavage in nucleosides [31]. The extent of leaving group stabilization and

Nanoreactors for green catalysis

• M. Teresa De Martino,
• Loai K. E. A. Abdelmohsen,
• Floris P. J. T. Rutjes and
• Jan C. M. van Hest

Beilstein J. Org. Chem. 2018, 14, 716–733, doi:10.3762/bjoc.14.61

• the diffusion through the membrane was not possible. Moreover, the crosslinking enabled stabilization of the enzymes, which remained active also after 10 days. Polymersome nanoreactors have also been used to perform many types of non-enzymatic catalytic reactions, such as the proline-catalyzed

Mannich base-connected syntheses mediated by ortho-quinone methides

• Petra Barta,
• Ferenc Fülöp and
• István Szatmári

Beilstein J. Org. Chem. 2018, 14, 560–575, doi:10.3762/bjoc.14.43

• –platinum(II) complexes [94]. Both DNA binding and topoisomerase I inhibition studies proved that the coordination and stabilization of the quinone methide structure can effect marked changes in DNA reactivity. In a recent publication, 3-(aminomethyl)naphthoquinones were investigated from the point of view

Electrochemical Corey–Winter reaction. Reduction of thiocarbonates in aqueous methanol media and application to the synthesis of a naturally occurring α-pyrone

• Ernesto Emmanuel López-López,
• José Alvano Pérez-Bautista,
• Fernando Sartillo-Piscil and
• Bernardo A. Frontana-Uribe

Beilstein J. Org. Chem. 2018, 14, 547–552, doi:10.3762/bjoc.14.41

• beneficial effect of β-oxygen substituents in radical deoxygenation [37], is dramatically favoured when the radical precursor group (or atom) is oriented antiperiplanar to the C−O bond via orbital interaction between the SOMO with the C−O σ* orbital [35]. Therefore, stabilization of intermediate E, which is

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

• intercalative binding, with the transition moment of the ligand oriented “parallel” to the long axis of adjacent base pairs (Figure 7, brown hue and bottom-right panel). It should be additionally supported by: i) a red-shift of the ligand absorption band; ii) at least moderate thermal stabilization of ds

Photocatalytic formation of carbon–sulfur bonds

• Alexander Wimmer and
• Burkhard König

Beilstein J. Org. Chem. 2018, 14, 54–83, doi:10.3762/bjoc.14.4

Aminosugar-based immunomodulator lipid A: synthetic approaches

• Alla Zamyatina

Beilstein J. Org. Chem. 2018, 14, 25–53, doi:10.3762/bjoc.14.3

Conformational preferences of α-fluoroketones may influence their reactivity

• Graham Pattison

Beilstein J. Org. Chem. 2017, 13, 2915–2921, doi:10.3762/bjoc.13.284

• stabilized in methanol, particularly for fluoroacetone, although in this case a trans-arrangement was still more stable. Neither cis- nor trans-arrangements of the C=O and C–X bonds can offer any stabilization by donation of halogen lone pairs into the C=O π* orbital, so this orbital interaction is not

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

• of Ile leads to almost complete proteolysis. However, substitution by TfIle slows down the degradation rate and results in a stabilization of around 37%. In P2’, fluorination shows in both cases a protective effect towards hydrolysis by elastase. Elastase preferably hydrolyses peptide bonds C

• result of steric occlusion of the peptide from the active site upon incorporation of sterically demanding fluorinated amino acids could not be verified based on the results of our current study. We found a significant stabilization towards proteolysis in 13 of a total of 24 peptides of the library

• introduction of fluorinated Leu and Ile analogues into P2 and P2’ position improved the proteolytic stability towards α-chymotrypsin. When introduced in the P1’ position a stabilization was still observed for TfIle, while incorporation of HfLeu made the peptide more prone to proteolytic digestion compared to

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• bridge. This so-called cap0 serves as quality control for correct mRNA processing and contributes to stabilization of eukaryotic mRNA [1][2], splicing [3][4], nuclear export [5], initiation of translation [6][7] and mRNA decay [8]. The most important direct interaction partners of the 5′-cap are the cap

Binding abilities of a chiral calix[4]resorcinarene: a polarimetric investigation on a complex case of study

• Marco Russo and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2698–2709, doi:10.3762/bjoc.13.268

• freedom for the arene–CH2–proline system. Subsequent proton loss simply results in further stabilization of the overall conformation assumed by the dianionic form. As a final remark, it is worth stressing that, irrespective of the amount of base added, the optical activity of a solution of CAP is lost

Ring-size-selective construction of fluorine-containing carbocycles via intramolecular iodoarylation of 1,1-difluoro-1-alkenes

• Takeshi Fujita,
• Ryo Kinoshita,
• Tsuyoshi Takanohashi,
• Naoto Suzuki and
• Junji Ichikawa

Beilstein J. Org. Chem. 2017, 13, 2682–2689, doi:10.3762/bjoc.13.266

• atom β to the fluorine substituents of the cyclic iodonium intermediate, which was derived from 1a and PyICl. This indicates that the cationic charge in the cyclic iodonium intermediate might be localized at the β-carbon atom because of stabilization by the proximal phenyl group [28]. Under the optimal

Metal-mediated base pairs in parallel-stranded DNA

• Jens Müller

Beilstein J. Org. Chem. 2017, 13, 2671–2681, doi:10.3762/bjoc.13.265

• pyrrolocytosine as a derivative thereof, 6-furylpurine (FP) was reported as an artificial purine derivative for metal-mediated base pairing. When introduced into a regular antiparallel-stranded sequence context, the thermal stabilization upon incorporation of Ag(I) was rather low (ΔTm = 2 °C) and could not be

• unequivocally distinguished from unspecific binding to the canonical nucleobases [68]. However, when the FP–Ag(I)–FP base pair was incorporated into a parallel-stranded DNA duplex of the same sequence, a significant stabilization of almost 15 °C was observed [69]. In this study, a parallel-stranded orientation

• -mediated pyrrolocytosine:pyrrolocytosine base pairs [62]. These investigations not only included the 2PyrPC and 3PyrPC residues reported above, but also a PhPC nucleoside bearing a phenyl substituent. Accordingly, a possible additional stabilization due to the presence of the (potentially coordinating

Diastereoselective Mannich reactions of pseudo-C₂-symmetric glutarimide with activated imines

• Tatsuya Ishikawa,
• Tomoko Kawasaki-Takasuka,
• Toshio Kubota and
• Takashi Yamazaki

Beilstein J. Org. Chem. 2017, 13, 2473–2477, doi:10.3762/bjoc.13.244

• enolate conformation with the allylic hydrogen possessing the same plane for making the steric bias minimum (Int-b) [20][21]. The most important argument for this effect is the stabilization of the forming electron-deficient σ*≠ orbital in the transition state by the electron donation from the neighboring

Synthesis, effect of substituents on the regiochemistry and equilibrium studies of tetrazolo[1,5-a]pyrimidine/2-azidopyrimidines

• Elisandra Scapin,
• Paulo R. S. Salbego,
• Caroline R. Bender,
• Alexandre R. Meyer,
• Anderson B. Pagliari,
• Tainára Orlando,
• Geórgia C. Zimmer,
• Clarissa P. Frizzo,
• Helio G. Bonacorso,
• Nilo Zanatta and
• Marcos A. P. Martins

Beilstein J. Org. Chem. 2017, 13, 2396–2407, doi:10.3762/bjoc.13.237

• toluene due to the considerable difference in reaction time (IL (5 min) in comparison with toluene (16 h)). This can be attributed to the significant stabilization of charges in the activated complex of the reaction promoted by charged [HMIM][TsO]. Other advantages regarding special properties (such as

• energy data about the stabilization of the different forms, solvent effects, and shows that the azide–tetrazole transformation is initiated by a p–π atomic orbital overlap rather than an electrostatic attraction process [48]. To detect which form is more stable in the solid state, quantum mechanical

One-pot syntheses of blue-luminescent 4-aryl-1H-benzo[f]isoindole-1,3(2H)-diones by T3P^® activation of 3-arylpropiolic acids

• Melanie Denißen,
• Alexander Kraus,
• Guido J. Reiss and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2017, 13, 2340–2351, doi:10.3762/bjoc.13.231

• anhydrides as reactive intermediates blue-luminescent 4-aryl-1H-benzo[f]isoindole-1,3(2H)-diones are formed by consecutive pseudo three-component syntheses in a one-pot fashion. The Stokes shifts correlate excellently with the Hammett–Taft σR parameter indicating an extended degree of resonance stabilization

• substituent effects in the electronic ground and excited states (see Table S6 in Supporting Information File 1). Although the linear correlations of λmax,abs with all σ parameters are relatively poor, the correlations of λmax,em with σR and σp+ indicate a strong influence of resonance stabilization in the

• spectroscopy revealed that the Stokes shifts are excellently correlated with Hammett–Taft's σR parameters indicating an extended degree of resonance stabilization as a result of a charge transfer character in the vibrationally relaxed S1-state. The fluorescence can be redshifted by employing 1,2

Structural diversity in the host–guest complexes of the antifolate pemetrexed with native cyclodextrins: gas phase, solution and solid state studies

• Magdalena Ceborska,
• Magdalena Zimnicka,
• Aneta Aniela Kowalska,
• Kajetan Dąbrowa and
• Barbara Repeć

Beilstein J. Org. Chem. 2017, 13, 2252–2263, doi:10.3762/bjoc.13.222

• comparison of the data obtained from the gas phase (without the influence of the environment) with the data obtained for solution and solid state (strongly influenced by the molecule’s environment) for deeper understanding of the non-covalent interactions responsible for the formation and stabilization of

Dialkyl dicyanofumarates and dicyanomaleates as versatile building blocks for synthetic organic chemistry and mechanistic studies

• Grzegorz Mlostoń and
• Heinz Heimgartner

Beilstein J. Org. Chem. 2017, 13, 2235–2251, doi:10.3762/bjoc.13.221

• versatile building blocks for the synthesis of diverse carbo- and heterocycles through [2 + 2], [3 + 2] and [4 + 2]-cycloaddition reactions, functionalized with ester and cyano groups. The high ability for stabilization of radical and carbanionic centers leads, in many instances, to the violation of the