UV resonance Raman spectroscopy of the supramolecular ligand guanidiniocarbonyl indole (GCI) with 244 nm laser excitation

• Tim Holtum,
• Vikas Kumar,
• Daniel Sebena,
• Jens Voskuhl and
• Sebastian Schlücker

Beilstein J. Org. Chem. 2020, 16, 2911–2919, doi:10.3762/bjoc.16.240

• strong dimerization based on zwitterion formation at neutral pH, as described for GCP (Kdim >102 in water) [29] as well as for a GCI derivative [30], which would interfere with the anion binding. Solid benzoic acid and RGD were purchased from Fluka Analytical and Sigma-Aldrich, respectively. Both

• chemicals were used without further purification. All liquid samples were prepared in 200 µM concentration in 6 mM BisTris buffer at pH 6. UV–vis absorption spectra of GCP ethyl amide [9] (in grey) and GCI ethyl amide (in green) at 200 µM concentration in 6 mM BisTris buffer solution at pH 6. The excitation

• solution of toluene in acetonitrile acquired with 240, 258, and 266 nm laser excitation, respectively. The UVRR spectra of a 200 µM solution of GCP ethyl amide in 6 mM BisTris buffer solution at pH 6 acquired with 266 nm (black curve) and 244 nm (magenta curve) laser excitation, respectively. The UVRR

Synthesis of imidazo[1,5-a]pyridines via cyclocondensation of 2-(aminomethyl)pyridines with electrophilically activated nitroalkanes

• Dmitrii A. Aksenov,
• Nikolai A. Arutiunov,
• Vladimir V. Maliuga,
• Alexander V. Aksenov and
• Michael Rubin

Beilstein J. Org. Chem. 2020, 16, 2903–2910, doi:10.3762/bjoc.16.239

• = 7.3 Hz, 2H, 2,6-H 3-Ph), 7.64 (d, J = 9.1 Hz, 1H, 8-H), 7.55 (dd, J = 9.1; 6.1 Hz, 3H, 3,4,5-H 3-Ph), 7.46 (t, J = 7.4 Hz, 1H, 1-H), 6.83 (dd, J = 9.0; 6.4 Hz, 1H, 7-H), 6.71 (t, J = 6.8 Hz, 1H, 6-H); 13C NMR (101 MHz, DMSO-d6) δ 137.3, 131.4, 130.2, 129.0 (2C), 128.4, 127.6 (2C), 121.8, 120.4, 119.3

Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

• Marius H. Heddinga and
• Jens Müller

Beilstein J. Org. Chem. 2020, 16, 2870–2879, doi:10.3762/bjoc.16.236

• system A via fluorescence spectroscopy. The measurements were conducted at pH 7.4 and 8.1. In both cases, similar results were obtained. Hence, the data for pH 7.4 will be presented and discussed in the following (Figure 6), whereas the data for pH 8.1 can be found in Supporting Information File 1

• ) at 65 °C for 15 min. They were purified using denaturing polyacrylamide gel electrophoresis (gel solution: 7 M urea, 1 TBE buffer, 14 or 18% (depending on the length of the oligonucleotide) polyacrylamide/bisacrylamide (29:1); loading buffer: 11.8 M urea, 42 mM Tris·HCl (pH 7.5), 0.83 mM EDTA (pH 8.0

• using an ATP-loaded agarose gel obtained from Sigma-Aldrich (cross-linked 4% beaded agarose, ATP is attached at its C8 position via a 9C linker, 1–5 μmol ATP per mL gel). For the binding assay, 5 nmol DNA in 200 μL column buffer (300 mM NaClO4, 5 mM Mg(ClO4)2, 20 mM MOPS (pH 7.4)) were loaded onto 500

Using multiple self-sorting for switching functions in discrete multicomponent systems

• Amit Ghosh and
• Michael Schmittel

Beilstein J. Org. Chem. 2020, 16, 2831–2853, doi:10.3762/bjoc.16.233

• ]. Over the years, a variety of chemical stimuli (pH [34], metal ions [35][36][37], ligands [38], solvents [39][40][41], and reagents [42]) have been successfully utilized in dual-state transformations. Multistate transformations with more than two well-defined states [43] should be beneficial for

• aggregates is converted to an n-fold completive mixture. Alike the material presented later we do not start from the ensemble of constituents, but already from aggregates. Basilio and Parola demonstrated the pH-triggered 2-fold completive self-sorting of four components comprising β-cyclodextrin (4

• . Some selected self-sorting outcomes and their qualitative and quantitative assessment. Illustration of an integrative vs a non-integrative self-sorting. The pH-driven four-component 2-fold completive self-sorting based on host–guest chemistry. (a) The monomers 5 and 6 and their H-bonding array. (b) The

Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives

• Jonas Becher,
• Daria V. Berdnikova,
• Heiko Ihmels and
• Christopher Stremmel

Beilstein J. Org. Chem. 2020, 16, 2795–2806, doi:10.3762/bjoc.16.230

• (resistivity ≥ 18 MΩ cm) and filtered through a membrane filter (0.45 µm pore size). K-phosphate-buffer (22AG, a2): 25 mM K2HPO4, 70 mM KCl; pH 7.0; Na-cacodylate buffer (F21T, Fa2T, FmycT, FkitT, and FkrasT): 90 µM LiCl, 10 mM KCl, 10 mM Na(CH3)2AsO2 × 3H2O, pH 7.2–7.3. The K-phosphate buffer solutions and

• ; cDNA = 200 μM) in K+-phosphate buffer (pH 7.0) with 10% v/v DMSO). The arrows indicate the development of the absorption or emission bands with increasing DNA concentration. Insets: Plots of Abs./Abs.0 and I/I0, respectively, versus cDNA/c3c. Inset B1: Picture of the emission color and intensity of

• -cacodylate buffer (cK+ = 10 mM, pH 7.2); estimated error ±0.5 °C. F21T: fluo-d[(G3TTA)3G3]-tamra; Fa2T: fluo-d[(ACAG4TGTG4)2-tamra; FmycT: fluo-d(TGAG3TG3TAG3TG3TA2)-tamra; FkrasT: fluo-d(AG3CG2TGTG3A2GAG2A)-tamra]; FkitT: fluo-d(AG3AG3CGCTG3AG2AG3)-tamra], fluo = fluorescein, tamra = tetramethylrhodamine

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

• surfactants: amphiphilic molecules that can alter their properties upon an external stimulus [6]. The intelligent surfactants are not passive but designed to undergo a molecular change when it is triggered with either a change in the pH value [7][8], upon light irradiation [9] or in the presence of metal ions

• surfactants are triggered, thereby releasing the cargo [8]. Guo and co-workers have earlier succeeded with the use of pH-sensitive surfactants and even introduced the term “flipids” for such pH-responsive lipids [7][8]. This term could also describe compounds where the binding of a guest molecule is able to

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

• Rakesh Biswas,
• Surya Ghosh,
• Shubhra Kanti Bhaumik and
• Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

• buffer and also in buffer containing 150 mM NaCl at physiological pH value. Furthermore, the multivalent aggregates demonstrated a significant selectivity in ATP detection over ADP, AMP and pyrophosphate. Keywords: amphiphile; ATP; excimer; multivalency; self-assembly; Introduction Supramolecular anion

• derivatives in aqueous buffer (5 mM tris-HCl, 10 mM NaCl, water/DMSO 99.5:0.5, pH 7.4) were investigated using a combination of absorption and emission spectral studies, dynamic light scattering (DLS) and field emission scanning electron microscopy (FESEM). In a “good solvent” such as DMSO, in which all

• surprising to see a selectivity towards ATP (3 negative charges) over ADP and AMP (2 and 1 negative charge(s), respectively) at physiological pH. However, it was intriguing to note the selectivity over PPi which had four negative charges. It is likely that in the ATP induced co-assemblies, there is a more

Nocarimidazoles C and D, antimicrobial alkanoylimidazoles from a coral-derived actinomycete Kocuria sp.: application of ¹J_C,H coupling constants for the unequivocal determination of substituted imidazoles and stereochemical diversity of anteisoalkyl chains in microbial metabolites

• Md. Rokon Ul Karim,
• Enjuro Harunari,
• Amit Raj Sharma,
• Naoya Oku,
• Kazuaki Akasaka,
• Daisuke Urabe,
• Mada Triandala Sibero and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 2719–2727, doi:10.3762/bjoc.16.222

• -histidine, the 1JC,H values for H-2/C-2 (208 to ≈222 Hz) were found to be always larger by at least 15 Hz than those for H-4/C-4 (188 to ≈208 Hz) at any pH condition below 11 [24]. Because the sp2 methine group in 1 exhibited 1JC,H = 221 Hz in a coupled HSQC experiment, this was assignable to the imidazole

• , Japan). The pH value of the medium was adjusted to 7.0 before sterilization. The inoculated flasks were incubated at 30 °C for 5 days, with rotational shaking at 200 rpm. Extraction and isolation In a similar manner as described in [22], after fermentation, 100 mL of 1-butanol was added to each flask

Enzyme-instructed morphological transition of the supramolecular assemblies of branched peptides

• Dongsik Yang,
• Hongjian He and
• Bing Xu

Beilstein J. Org. Chem. 2020, 16, 2709–2718, doi:10.3762/bjoc.16.221

• solutions of 1 and 2 (5 mM, pH 7.0, in Tris-HCl buffer). Our results show that the branched peptide 1 undergoes proteolytic cleavage to form DEDDDLLIG and Nap-ffky after 24 h, while 2 proteolytically hydrolyzes into four parts, including DEDDDLLIG, DEDDDLL, DEDDDL, and Nap-ffky. These results indicate that

• the cleavage occurs depending on the acetylation of the N-terminal of the branch. Then, we conducted a time-dependent CD analysis to examine the change of the secondary structural conformations of 1 and 2 during the proteolysis catalyzed by proteinase K in Tris-HCl buffer at pH 7.0. As shown in Figure

• (CD) spectra of 1 incubated with proteinase K in Tris-HCl buffer at pH 7.0. C) CD simulation of the mixture from the spectra in B. D) LC–MS spectrum of the proteolytic products after 2 (5 mM) was incubated with proteinase K (5 U/mL) for 24 h. E) Time-dependent CD spectra of 2 incubated with proteinase

Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes

• Lena Reinke,
• Julia Bartl,
• Marcus Koch and
• Stefan Kubik

Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219

• the cyclopeptide-derived ligand used in our previous work had also failed, and we therefore had to use a two-step immobilization procedure to obtain the respective mixed monolayer-protected AuNPs [18]. Here, we tested whether performing the immobilization at a lower pH value at which 2 was partially

• prior to the addition of the ligand mixture caused the AuNPs to precipitate, likely because the protecting citrate molecules were protonated. Therefore, the reaction mixture was adjusted to pH 3 with 0.1 mol/L nitric acid shortly after adding the solution containing the ligands in methanol. A color

• another acid and tested citric acid, which was attractive because we expected this acid to produce a buffer together with the citrate present on the nanoparticles, which should reduce the influence of possible pH changes on the exchange reaction. In this case, adjusting the aqueous solution of NPcit to pH

Anion exchange resins in phosphate form as versatile carriers for the reactions catalyzed by nucleoside phosphorylases

• Julia N. Artsemyeva,
• Ekaterina A. Remeeva,
• Tatiana N. Buravskaya,
• Irina D. Konstantinova,
• Roman S. Esipov,
• Anatoly I. Miroshnikov,
• Natalia M. Litvinko and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2020, 16, 2607–2622, doi:10.3762/bjoc.16.212

• letter to the editor Kalckar reported for the first time that specific inosine nucleosidase from rat liver catalyzes the reversible reaction “inosine + phosphate ⇌ hypoxanthine + ribose-1-phosphate”: the equilibrium of this reaction in water at pH 6.5 is displaced to the nucleoside synthesis. Moreover

• amounts of inosine and phosphate as starting material it was found that only 10 per cent of the riboside undergoes phosphorolysis at pH 6.5” [16]. Presently, the observation made by Kalckar is one of the hot issues from a viewpoint of the development of efficient enzymatic synthesis of nucleosides

• -phosphate buffer, pH 7.4; 37 °C, 48 h; conversion >95%) and employed for the synthesis of adenosine (Ado; PNP, water, 3 days at 37 °C; conversion 95%), guanosine (Guo; PNP, water 90% and DMSO 10%, 9 days at 37 °C; conversion 40%), and uridine (Urd; UP, water, 20 h at 37 °C; conversion 85%). In the synthesis

Synthesis of 4-substituted azopyridine-functionalized Ni(II)-porphyrins as molecular spin switches

• Jannis Ludwig,
• Tobias Moje,
• Fynn Röhricht and
• Rainer Herges

Beilstein J. Org. Chem. 2020, 16, 2589–2597, doi:10.3762/bjoc.16.210

• are electron withdrawing (σ = 0.45), however, they are almost completely dissociated at neutral (physiological) pH. Carboxylate anion substituents are weakly electron donating and should improve both switching efficiency and water solubility. Results and Discussion Synthesis The record player

• % in aqueous environment (Figure 3). If it comes to medical applications, such as switchable contrast agents [3][4][5][6][7], the new carboxylate substituted system 1j has the distinct advantage of being deprotonated at neutral pH, whereas the previously synthesized hydroxylate system 1e exhibits its

• highest switching efficiency at unphysiological pH 10.5 [14]. Hence, further attempts to optimize our molecular spin switches will be based on pyridine-4-carboxylate-substituted systems. Conclusion Aiming at the optimization of molecular spin switches (record player molecules) towards higher switching

Water-soluble host–guest complexes between fullerenes and a sugar-functionalized tribenzotriquinacene assembling to microspheres

• Si-Yuan Liu,
• Xin-Rui Wang,
• Man-Ping Li,
• Wen-Rong Xu and
• Dietmar Kuck

Beilstein J. Org. Chem. 2020, 16, 2551–2561, doi:10.3762/bjoc.16.207

• heavier isotope (mainly 13C112C1241H15614N1823Na216O662+) [M + 6H2O + 2Na]2+, 1505.9611; found, 1505.9690 (Δ = +5.2 ppm). Synthesis of TBTQ-(OG)6. To a solution of TBTQ-(OAcG)6 (0.95 g, 0.33 mmol) in methanol (60 mL), sodium methoxide (about 1 mL) was added to adjust the pH value to 11. The mixture was

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• residues on the protein surface, are also sensitive to pH and in some cases ionic strength and type of counter ions. It is important to keep in mind that these factors can also affect the binding affinity of a ligand. The pH affects the protonation state, and thus charge, of both the protein and charged

Recent developments in enantioselective photocatalysis

• Callum Prentice,
• James Morrisson,
• Andrew D. Smith and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2020, 16, 2363–2441, doi:10.3762/bjoc.16.197

Host–guest interaction of cucurbit[8]uril with oroxin A and its effect on the properties of oroxin A

• Zhishu Zeng,
• Jun Xie,
• Guangyan Luo,
• Zhu Tao and
• Qianjun Zhang

Beilstein J. Org. Chem. 2020, 16, 2332–2337, doi:10.3762/bjoc.16.194

• and 4.80 × 10−6 mol·L−1, respectively, which indicates that Q[8] did not affect the antioxidant activity of OA. Drug release in vitro Figure 8 shows the cumulative release of the OA and the OA@Q[8] inclusion complex in artificial gastric juice (pH 1.2) and artificial intestinal juice (pH 6.8). It can

Design and synthesis of a bis-macrocyclic host and guests as building blocks for small molecular knots

• Elizabeth A. Margolis,
• Rebecca J. Keyes,
• Stephen D. Lockey IV and
• Edward E. Fenlon

Beilstein J. Org. Chem. 2020, 16, 2314–2321, doi:10.3762/bjoc.16.192

• mL/1 mL/0.1 mL) with [(CH3CN)4Cu]PF6 and ascorbic acid (see Scheme S2 in Supporting Information File 1). After removal of the solvent, the cutting step was performed by heating the crude product with KOH in a water/THF/ethanol mixture to saponify the esters. The pH of the mixture was adjusted to

Styryl-based new organic chromophores bearing free amino and azomethine groups: synthesis, photophysical, NLO, and thermal properties

• Anka Utama Putra,
• Deniz Çakmaz,
• Nurgül Seferoğlu,
• Alberto Barsella and
• Zeynel Seferoğlu

Beilstein J. Org. Chem. 2020, 16, 2282–2296, doi:10.3762/bjoc.16.189

• . The pH-sensitive properties of all prepared Schiff bases were examined against TBAOH in DMSO, via deprotonation of the OH group in the salicylidene moiety and their reverse protonation was also investigated using TFA. The Schiff bases exhibited a bathochromic shift upon the addition of TBAOH to their

• solutions in DMSO. Therefore, they showed potential to be utilized as colorimetric and luminescence pH sensors. The second-order nonlinear optical (NLO) responses of the dyes were measured by the electric field-induced second harmonic (EFISH) generation method. The highest μβ values were obtained for the

• all dyes were evaluated by thermogravimetric analysis (TGA). The TGA data showed that all dyes were thermally stable up to 250 °C. Keywords: DFT calculations; NLO; pH sensitive dyes; Schiff base; solvent effect; styryl dyes; Introduction Push-pull organic molecules are a class of organic dyes

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• the reaction conditions (i.e., high temperatures, inert atmosphere, control of pH of the media), and the continuous removal of water (i.e., Soxhlet extractor, Dean-Stark trap, molecular sieves) to drive the reaction to completion [22][23]. Finally, depending on the substrates, these reactions often

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• naphthalene diimde analogue (NDI) equipped at the imide positions with two guanidinio-carbonyl-pyrrole (GCP) pendant arms interacted significantly stronger with ds-DNA at pH 5 than at pH 7, due to reversible protonation of the GCP arms. This was consequence of a pH-switchable threading intercalation into ds

• -DNAs only at pH 5, while at neutral conditions (pH 7) NDI-GCP2 switched to the DNA minor groove binding. Intriguingly, NDI-GCP2 was at both pH values studied bound to the ds-RNA major groove, still showing a higher affinity and thermal denaturation effect at pH 5 due to GCP protonation. At excess over

• recognition of various DNA/RNA sequences could be reversibly changed by adjusting the pH of the solution. The fine structural tuning of such aryl-GCP conjugates allowed us to prepare a wide variety of small molecules with different DNA or RNA sequence selectivity, many of them acting as multipurpose probes

Regioselective cobalt(II)-catalyzed [2 + 3] cycloaddition reaction of fluoroalkylated alkynes with 2-formylphenylboronic acids: easy access to 2-fluoroalkylated indenols

• Tatsuya Kumon,
• Miroku Shimada,
• Jianyan Wu,
• Shigeyuki Yamada and
• Tsutomu Konno

Beilstein J. Org. Chem. 2020, 16, 2193–2200, doi:10.3762/bjoc.16.184

• corresponding trimer of the fluoroalkylated alkyne, as reported by our group [27]. Finally, only 2-iodoaryl ketones (R3 = Me, Cy, Ph) were applicable in this catalytic reaction, whereas the cycloaddition using 2-iodobenzaldehyde (R3 = H) did not work at all. Therefore, the development of practical protocols for

Photosensitized direct C–H fluorination and trifluoromethylation in organic synthesis

• Shahboz Yakubov and
• Joshua P. Barham

Beilstein J. Org. Chem. 2020, 16, 2151–2192, doi:10.3762/bjoc.16.183

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

• ]. In this case, the expected lipophilicity reducing effect is offset by the electron-withdrawing effect on the nitrogen (ΔlogP +0.34). The reduction in amine basicity also shifts the distribution of free base and protonated species, resulting in a higher proportion of free base in solution at pH 7.4

Access to highly substituted oxazoles by the reaction of α-azidochalcone with potassium thiocyanate

• Mysore Bhyrappa Harisha,
• Pandi Dhanalakshmi,
• Rajendran Suresh,
• Raju Ranjith Kumar and
• Shanmugam Muthusubramanian

Beilstein J. Org. Chem. 2020, 16, 2108–2118, doi:10.3762/bjoc.16.178

• synthesis of 2,4,5-trisubstituted oxazole from azirine. a) I2, PPh3; b) NaH, 1H-pyrazole; c) 2-bromoacetyl bromide, NaN3; d) heating; e) t-BuOK; f) Ph-CHO, visible light; g) KSCN, K2S2O8. Scope of the α-azidochalcones. The reactions were carried out at reflux temperature, using 1 (1 mmol), 2 (3 mmol

Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations

• Ian Walsh,
• Matthew S. F. Choo,
• Sim Lyn Chiin,
• Amelia Mak,
• Shi Jie Tay,
• Pauline M. Rudd,
• Yang Yuansheng,
• Andre Choo,
• Ho Ying Swan and
• Terry Nguyen-Khuong

Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176

• of heterogeneity and is influenced by several factors including the host expression system and process parameters such as temperature shifts, pH, and the type of basal/feed media [7]. To understand how these environmental factors impact the glycosylation of a biologic, analytical methods are needed

• . This can be caused by a combination of sample complexity, temperature, pH, day of analysis, and other physicochemical fluctuations during the operation of the analysis. Although GU calculation can help solve this for the qualitative analysis, there is still difficulty automating peak picking due to

• , GE Healthcare, USA). The columns were equilibrated and washed via centrifugation (100g, 30 s) with 20 mM sodium phosphate (pH 7.0). The sample was loaded to each column (maximum volume of 600 µL) and incubated end-over-end for 10 min. The column was washed with 20 mM sodium phosphate (pH 7.0) via