Aromatic 19F–13C TROSY—[19F, 13C]‐Pyrimidine Labeling for NMR Spectroscopy of RNA

We present the access to [5‐¹⁹F, 5‐¹³C]‐uridine and ‐cytidine phosphoramidites for the production of site‐specifically modified RNAs up to 65 nucleotides (nts). The amidites were used to introduce [5‐¹⁹F, 5‐¹³C]‐pyrimidine labels into five RNAs—the 30 nt human immunodeficiency virus trans activation response (HIV TAR) 2 RNA, the 61 nt human hepatitis B virus ? (hHBV ?) RNA, the 49 nt SAM VI riboswitch aptamer domain from B. angulatum, the 29 nt apical stem loop of the pre‐microRNA (miRNA) 21 and the 59 nt full length pre‐miRNA 21. The main stimulus to introduce the aromatic ¹⁹F–¹³C‐spin topology into RNA comes from a work of Boeszoermenyi et al., in which the dipole‐dipole interaction and the chemical shift anisotropy relaxation mechanisms cancel each other leading to advantageous TROSY properties shown for aromatic protein sidechains. This aromatic ¹³C–¹⁹F labeling scheme is now transferred to RNA. We provide a protocol for the resonance assignment by solid phase synthesis based on diluted [5‐¹⁹F, 5‐¹³C]/[5‐¹⁹F] pyrimidine labeling. For the 61 nt hHBV ? we find a beneficial ¹⁹F–¹³C TROSY enhancement, which should be even more pronounced in larger RNAs and will facilitate the NMR studies of larger RNAs. The [¹⁹F, ¹³C]‐labeling of the SAM VI aptamer domain and the pre‐miRNA 21 further opens the possibility to use the biorthogonal stable isotope reporter nuclei in in vivo NMR to observe ligand binding and microRNA processing in a biological relevant setting.     

Regioselective deprotection of the monosaccharide‐bearing thiocyanomethyl group at the anomeric position monitored by reversed‐phase HPLC method

In the current work, the investigation and development of a chemo‐enzymatic approach for the synthesis of neo‐glycoproteins have been studied. This strategy is based on the regioselective enzymatic hydrolysis of peracetylated monosaccharide, functionalized at the anomeric position (C1) as 1‐thio‐(S‐cyanomethyl) group, a precursor of the 2‐ iminomethoxyethyl thioglycosides‐linker for protein glycosylation, catalyzed by immobilized enzymes to obtain selectively monodeprotected compounds. The use of this activation in C1 is the most frequently used strategy for glycoprotein preparation. The selected biocatalysts are the lipase from Candida rugosa and the acetyl xylan esterase from Bacillus pumilus. A reversed‐phase high‐performance liquid‐chromatographic (HPLC) method for monitoring the regioselective deprotection reaction has been developed. The developed HPLC method was used as a fingerprint to follow the hydrolysis of substrate 1 to substrate 1a and to determine its purity and yield. Moreover, the obtained compound was further purified by flash chromatography. The obtained compound 1a was further characterized using ¹H, ¹³C NMR, correlation spectroscopy (COSY) and heteronuclear multiple bond correlation. The resulting product can be used as an intermediate for the preparation of di‐ and more complex oligosaccharides aimed at protein conjugation. Copyright © 2016 John Wiley & Sons, Ltd.     

First Synthesis of 3‐O‐Functionalized Cellulose Ethers via 2,6‐Di‐O‐Protected Silyl Cellulose

The present paper describes the synthesis of 2,6‐di‐O‐thexyldimethylsilyl cellulose as a novel 2,6‐di‐O‐protected cellulose derivative. This material was obtained by reacting cellulose in N,N‐dimethylacetamide/LiCl solution with thexyldimethylchlorosilane and imidazole for 24 h at 100°C. In a typical subsequent reaction the residual OH‐group in position 3 could be completely etherified without loss of any protecting groups. Treatment with tetrabutylammonium fluoride leads to the novel compounds 3‐O‐allyl and 3‐O‐methyl cellulose. The structures of all polymers are revealed by means of one‐ (¹H and ¹³C) and two‐dimensional (COSY and HMQC) NMR techniques.     

Chemo‐ and Enzyme‐Catalyzed Reactions Revealing a Common Temperature‐Dependent Dynamic Solvent Effect on Enantioselectivity

The enantiomeric ratio E of enzyme‐catalyzed (Candida antarctica lipase and lipase PS) and chemo‐catalyzed (L ‐proline‐based diamines) acylation reactions of 1‐(naphthalen‐2‐yl)ethanol, 2‐phenylpropanol, and 2‐benzylpropane‐1,3‐diol is dependent on solvent and temperature. Plots of ln E vs. 1/T showed the presence of inversion temperatures (T_inv). The T_inv values for the bio‐catalyzed and the chemo‐catalyzed reactions are fairly in agreement, and correspond as well to the T_NMR values obtained by variable‐temperature ¹³C‐NMR experiments on the substrates in the same solvent of the resolution. This result demonstrates that clustering effects in the substrate solvation manage the chemical and the enzymatic enantioselectivity, and, moreover, that the solute? solvent cluster is always the real reacting species in solution for chemical as well as for enzymatic reactions.     

Synthesis of Chlorins Fused with Nitrogen‐Containing Heterocycle by the Modification along Their N21–N23 axis

Quinoxalinodeoxopyropheophorbide‐a and benzimidazolopurpurin‐18 imide were obtained from methyl pheophorbide‐a by one‐pot method. The synthesis of a series of chlorins fused with nitrogen‐containing heterocycle was fulfilled by chemical modifications along their N²¹–N²³ axis such as LiOH‐promoted allomerization of C12‐methyl group, electrophilic addition to C3‐vinyl group, substitution at 20‐meso‐position and 1, 3‐dipolar cycloaddition with diazomethane at 3‐position. The structures of new chlorins were characterized by UV–vis, MS, ¹H NMR spectra, and elemental analysis.     

The “Speedy” Synthesis of Atom‐Specific 15N Imino/Amido‐Labeled RNA

Although numerous reports on the synthesis of atom‐specific ¹⁵N‐labeled nucleosides exist, fast and facile access to the corresponding phosphoramidites for RNA solid‐phase synthesis is still lacking. This situation represents a severe bottleneck for NMR spectroscopic investigations on functional RNAs. Here, we present optimized procedures to speed up the synthesis of ¹⁵N(1) adenosine and ¹⁵N(1) guanosine amidites, which are the much needed counterparts of the more straightforward‐to‐achieve ¹⁵N(3) uridine and ¹⁵N(3) cytidine amidites in order to tap full potential of ¹H/¹⁵N/¹⁵N‐COSY experiments for directly monitoring individual Watson–Crick base pairs in RNA. Demonstrated for two preQ₁ riboswitch systems, we exemplify a versatile concept for individual base‐pair labeling in the analysis of conformationally flexible RNAs when competing structures and conformational dynamics are encountered.     

Ammonolysis of 1,2‐Bis[dichloro(methyl)silyl]ethane. On the Structure of 1,3,6,8‐Tetramethyl‐2,7,11,12‐tetraaza‐1,3,6,8‐tetrasila‐tricyclo[6.2.1.13,6]‐dodecane

Ammonolysis of 1,2‐bis[dichloro(methyl)silyl]ethane afforded a crystalline tricyclic silazane along with polymeric material. The crystalline material could be isolated in pure state. It was analyzed by ¹H, ¹³C, ¹⁵N and ²⁹Si NMR spectroscopy in solution, by ¹³C, ¹⁵N and ²⁹Si MAS NMR spectroscopy in the solid state, as well as by single‐crystal and powder X‐ray diffraction. The title compound exists as a single isomer in solution, whereas in the solid state the presence of several modifications is indicated, in particular by the solid‐state MAS NMR spectra.     

N,N′‐Dialkyl‐4‐Aryl‐3,4‐Dihydropyrimidinones and Thiones: Ceric Ammonium Nitrate Catalyzed Synthesis and Molecular Structure Determination by X‐ray Crystallography

This work presents a microwave assisted solvent‐free synthesis of N,N ′‐dialkyl‐4‐aryl‐3,4‐dihydropyrimidinones/thiones in the presence of Ceric Ammonium Nitrate (CAN) via direct condensation of aromatic aldehydes, β‐keto ester, and N,N ′‐dialkylurea/thiourea. The highlights of the methodology adopted are (i) facile condensation of the reactants into product without any side‐products, and (ii) short reaction time with high yield and good purity. All the compounds synthesized were characterized and established by spectroscopic techniques such as FTIR, ¹H NMR, ¹³C NMR, and Mass. The structure of the compound is further corroborated by single crystal X‐ray diffraction analysis.     

A Benzophenone‐Based Photocaging Strategy for the N7 Position of Guanosine

Selective modification of nucleobases with photolabile caging groups enables the study and control of processes and interactions of nucleic acids. Numerous positions on nucleobases have been targeted, but all involve formal substitution of a hydrogen atom with a photocaging group. Nature, however, also uses ring‐nitrogen methylation, such as m⁷G and m¹A, to change the electronic structure and properties of RNA and control biomolecular interactions essential for translation and turnover. We report that aryl ketones such as benzophenone and α‐hydroxyalkyl ketone are photolabile caging groups if installed at the N7 position of guanosine or the N1 position of adenosine. Common photocaging groups derived from the ortho‐nitrobenzyl moiety were not suitable. Both chemical and enzymatic methods for site‐specific modification of N7G in nucleosides, dinucleotides, and RNA were developed, thereby opening the door to studying the molecular interactions of m⁷G and m¹A with spatiotemporal control.     

{5′‐O‐[Bis(4‐methoxyphenyl)(phenyl)methyl]‐2′‐deoxy‐β‐D‐threopentofuranosyl}thymine ethyl acetate 0.25‐solvate

The title compound, C₃₁H₃₂N₂O₇·0.25C₄H₈O₂, is a key intermediate in the synthesis of [¹⁸F]fluorine‐labelled thymidine (¹⁸F‐FLT), which is the most widely used molecular imaging probe for positron emission tomography (PET). The crystallographic asymmetric unit contains two independent thymine molecules plus one partially occupied site for an ethyl acetate molecule. The two independent thymine molecules show similar geometrical features, except that the dimethoxytrityl groups adopt different orientations with respect to the remainder of the molecule. Each thymine base adopts an anti conformation with respect to the attached deoxyribose ring, and the deoxyribose rings show C3‐endo puckering. The conformation of the side chain at the C1 position of the deoxyribose ring is gauche+. Intermolecular N—H...O and O—H...O hydrogen bonds link the molecules into one‐dimensional chains.     

Automated Solid‐Phase Synthesis and Structural Investigation of β‐Peptidosulfonamides and β‐Peptidosulfonamide/β‐Peptide Hybrids: β‐Peptidosulfonamide and β‐Peptide Foldamers are Two of a Different Kind

Fmoc‐protected β‐aminoethane sulfonylchlorides can be employed for efficient automated solid phase synthesis of β‐peptidosulfonamides and β‐peptidosulfonamide/β‐peptide hybrids containing one or more β‐peptidosulfonamide residues. Thus, Fmoc‐protected β‐aminoethane sulfonylchlorides 5a – c led to the hexa‐β‐peptidosulfonamide 9 and the nona‐β‐peptidosulfonamide 10 . In addition, the β‐peptidosulfonamide/β‐peptide hybrids 13 and 16 , consisting of six and nine β‐residues, respectively, and containing a single β‐peptidosulfonamide unit in the middle, as well as the peptidosulfonamide/β‐peptide hybrid 15 with nine β‐residues, including an N‐terminal β‐peptidosulfonamide residue, were synthesized by automated solid‐phase synthesis. Both CD and NMR spectroscopic measurements did not indicate any helical secondary structure for 9 and 10 . As was shown by CD‐measurements, the β‐peptidosulfonamide residue in the hybrids 13, 15 , and 16 acts as a ‘helix breaker', especially when located in the middle of the hybrid chain ( 13 and 16 ), but, although to a lesser extent, also at the N‐terminus.     

1H{15N} GHMQC study of 5,7‐diphenyl‐1,2,4‐triazolo[1,5‐a]pyrimidine and 1H, 13C and 15N NMR coordination shifts in Au(III) chloride complexes of 1,2,4‐triazolo[1,5‐a]pyrimidines

The ¹H{¹⁵N} NMR spectrum of 5,7‐diphenyl‐1,2,4‐triazolo[1,5‐a]‐pyrimidine ( 3 ) was measured by GHMQC, unambiguously assigned and compared with the spectra of 1,2,4‐triazolo[1,5‐a]pyrimidine ( 1 ) and 5,7‐dimethyl‐1,2,4‐triazolo[1,5‐a]pyrimidine ( 2 ). A series of Au(III) chloride complexes of general formula AuLCl₃, where L = 1 , 2 , 3 , was synthesized and studied by ¹HH{¹⁵N} GHMQC and ¹H{¹³C} GHMBC. Low‐frequency shifts of 72–74 ppm (¹⁵N) and 5–6 ppm (¹³C) were observed upon complexation by Au(III) ions for the coordination site N‐3 and adjacent C‐2, C‐3a atoms, respectively. The ¹³C signals of C‐5, C‐6, C‐7 and the ¹H resonances of H‐2, H‐6 were shifted to higher frequency. Comparison with analogous Pd(II), Pt(II) and Pt(IV) complexes revealed that in the case of Au(III) coordination the ¹⁵N shifts were relatively smaller, whereas those for ¹³C and ¹H were larger. Copyright © 2002 John Wiley & Sons, Ltd.     

New Pyrazole‐ and Benzimidazole‐derived Ligand Systems

A series of N‐containing heterocyclic compounds have been synthesized using approaches such as the well‐known Knorr synthesis, and a facile N‐alkylation method. This series of compounds includes pyrazole derivatives, tris(2‐benzimidazolylmethyl)amine derivatives, and “pincer” ligands. Characterization methods include ¹H NMR, FT‐IR, CHN analyses, UV‐vis spectroscopy, and fluorimetry, while X‐ray crystal structures are reported for most of the compounds. The crystallographic results affirm a ¹³C NMR method for isomer assignment of substituted pyrazoles.     

Nicotine,acetanilide and urea multi‐level 2H‐, 13C‐ and 15N‐abundance reference materials for continuous‐flow isotope ratio mass spectrometry

Accurate determinations of stable isotope ratios require a calibration using at least two reference materials with different isotopic compositions to anchor the isotopic scale and compensate for differences in machine slope. Ideally, the δ values of these reference materials should bracket the isotopic range of samples with unknown δ values. While the practice of analyzing two isotopically distinct reference materials is common for water (VSMOW‐SLAP) and carbonates (NBS 19 and L‐SVEC), the lack of widely available organic reference materials with distinct isotopic composition has hindered the practice when analyzing organic materials by elemental analysis/isotope ratio mass spectrometry (EA‐IRMS). At present only L‐glutamic acids USGS40 and USGS41 satisfy these requirements for δ¹³C and δ¹⁵N, with the limitation that L‐glutamic acid is not suitable for analysis by gas chromatography (GC). We describe the development and quality testing of (i) four nicotine laboratory reference materials for on‐line (i.e. continuous flow) hydrogen reductive gas chromatography‐isotope ratio mass‐spectrometry (GC‐IRMS), (ii) five nicotines for oxidative C, N gas chromatography‐combustion‐isotope ratio mass‐spectrometry (GC‐C‐IRMS, or GC‐IRMS), and (iii) also three acetanilide and three urea reference materials for on‐line oxidative EA‐IRMS for C and N. Isotopic off‐line calibration against international stable isotope measurement standards at Indiana University adhered to the ‘principle of identical treatment’. The new reference materials cover the following isotopic ranges: δ²H_nicotine ?162 to ?45‰, δ¹³C_nicotine ?30.05 to +7.72‰, δ¹⁵N_nicotine ?6.03 to +33.62‰; δ¹⁵N_acetanilide +1.18 to +40.57‰; δ¹³C_urea ?34.13 to +11.71‰, δ¹⁵N_urea +0.26 to +40.61‰ (recommended δ values refer to calibration with NBS 19, L‐SVEC, IAEA‐N‐1, and IAEA‐N‐2). Nicotines fill a gap as the first organic nitrogen stable isotope reference materials for GC‐IRMS that are available with different δ¹⁵N values. Comparative δ¹³C and δ¹⁵N on‐line EA‐IRMS data from 14 volunteering laboratories document the usefulness and reliability of acetanilides and ureas as EA‐IRMS reference materials. Published in 2009 by John Wiley & Sons, Ltd.     

Solid‐State and Solution Structural Studies of 4‐{[C(E)]‐1H‐Azol‐1‐ylimino)methyl}pyridin‐3‐ols

The new N‐salicylideneheteroarenamines 1 – 4 were prepared by reacting the biologically relevant 3‐hydroxy‐4‐pyridinecarboxaldehyde ( 5 ) with 1H‐imidazol‐1‐amine ( 6 ), 1H‐pyrazol‐1‐amine ( 7 ), 1H‐1,2,4‐triazol‐1‐amine ( 8 ), and 1H‐1,3,4‐triazol‐1‐amine ( 9 ). Solution ¹H‐, ¹³C‐, and ¹⁵N‐NMR were used to establish that the hydroxyimino form A is the predominant tautomer. A combination of ¹³C‐ and ¹⁵N‐CPMAS‐NMR with X‐ray crystallographic studies confirms that the same form is present in the solid state. The stabilities and H‐bond geometries of the different forms, tautomers and rotamers, are discussed by using B3LYP/6‐31G** calculations.     

Synthesis and Anti‐tumor Evaluation of B‐ring Modified Caged Xanthone Analogues of Gambogic Acid

Gambogic acid (GA, 1 ), the most prominent member of Garcinia natural products, has been reported to be a promising anti‐tumor agent. Previous studies have suggested that the planar B ring and the unique 4‐oxa‐tricyclo[4.3.1.0^3,7]dec‐2‐one caged motif were essential for anti‐tumor activity. To further explore the structure‐activity relationship (SAR) of caged Garcinia xanthones, two new series of B‐ring modified caged GA analogues 13a – 13e and 15a – 15e were synthesized utilizing a Claisen/Diel‐Alder cascade reaction. Subsequently, these compounds were evaluated for their in vitro anti‐tumor activities against A549, MCF‐7, SMMC‐7721 and BGC‐823 cancer cell lines by MTT assay. Among them, 13b – 13e exhibited micromolar inhibition against several cancer cell lines, being approximately 2–4 fold less potent in comparison to GA. SAR analysis revealed that the peripheral gem‐dimethyl groups are essential for maintaining anti‐tumor activity and substituent group on C1 position of B‐ring has a significant effect on potency, while modifications at C‐2, C‐3 and C‐4 positions are relatively tolerated. These findings will enhance our understanding of the SAR of Garcinia xanthones and lead to the development of simplified analogues as potential anti‐tumor agents.     

Intrinsic Acid–Base Properties of a Hexa‐2′‐deoxynucleoside Pentaphosphate,d(ApGpGpCpCpT): Neighboring Effects and Isomeric Equilibria

The intrinsic acid‐base properties of the hexa‐2′‐deoxynucleoside pentaphosphate, d(ApGpGpCpCpT) [=(A1?G2?G3?C4?C5?T6)=(HNPP)^5?] have been determined by ¹H NMR shift experiments. The pK_a values of the individual sites of the adenosine (A), guanosine (G), cytidine (C), and thymidine (T) residues were measured in water under single‐strand conditions (i.e., 10 % D₂O, 47 °C, I=0.1 M , NaClO₄). These results quantify the release of H⁺ from the two (N7)H⁺ (G?G), the two (N3)H⁺ (C?C), and the (N1)H⁺ (A) units, as well as from the two (N1)H (G?G) and the (N3)H (T) sites. Based on measurements with 2′‐deoxynucleosides at 25 °C and 47 °C, they were transferred to pK_a values valid in water at 25 °C and I=0.1 M . Intramolecular stacks between the nucleobases A1 and G2 as well as most likely also between G2 and G3 are formed. For HNPP three pK_a clusters occur, that is those encompassing the pK_a values of 2.44, 2.97, and 3.71 of G2(N7)H⁺, G3(N7)H⁺, and A1(N1)H⁺, respectively, with overlapping buffer regions. The tautomer populations were estimated, giving for the release of a single proton from five‐fold protonated H₅(HNPP)^±, the tautomers (G2)N7, (G3)N7, and (A1)N1 with formation degrees of about 74, 22, and 4 %, respectively. Tautomer distributions reveal pathways for proton‐donating as well as for proton‐accepting reactions both being expected to be fast and to occur practically at no “cost”. The eight pK_a values for H₅(HNPP)^± are compared with data for nucleosides and nucleotides, revealing that the nucleoside residues are in part affected very differently by their neighbors. In addition, the intrinsic acidity constants for the RNA derivative r(A1?G2?G3? C4?C5?U6), where U=uridine, were calculated. Finally, the effect of metal ions on the pK_a values of nucleobase sites is briefly discussed because in this way deprotonation reactions can easily be shifted to the physiological pH range.