Improved Large‐Scale Liquid‐Phase Synthesis and High‐Temperature NMR Characterization of Short ­(F‐)PNAs

We report on a large‐scale synthesis of F‐PNA trimer 10 and PNA trimer 11 . The key improvement is the facile two‐step synthesis of (2,4‐difluoro‐5‐methylphenyl)acetic acid ( 2 ). Water solubility of the corresponding F‐PNA oligomer 10 was achieved by synthesizing solubility enhancer 5a , which is twofold positively charged and only consists of inherent structural elements of PNA. Protected and unpaired PNA n‐mers exist in a mixture of 2ⁿ conformers undergoing slow exchange and leading to complicated NMR spectra. Structure analysis was improved by recording ¹H‐ and ¹³C‐NMR spectra at elevated temperatures above the coalescence point. Fully protected backbone derivatives show sharp resonances where expected, and spectra of protected PNAs are remarkably simplified, thereby allowing an interpretation for the first time. Both trimers 10 and 11 are considered as building blocks for a self‐replicating system based on PNA.     

Characterization of G‐Quadruplex/Hairpin Transitions of RNAs by 19F NMR Spectroscopy

2′‐O‐[(4‐Trifluoromethyl‐triazol‐1‐yl)methyl] reporter groups have been incorporated into guanosine‐rich RNA models (including a known bistable Qd/Hp RNA and two G‐rich regions of mRNA of human prion protein, PrP) and applied for the ¹⁹F NMR spectroscopic characterization of plausible G‐quadruplex/hairpin (Qd/Hp) transitions in these RNA structures. For the synthesis of the CF₃‐labeled RNAs, phosphoramidite building blocks of 2′‐O‐[(4‐CF₃‐triazol‐1‐yl)methyl] nucleosides (cytidine, adenosine, and guanosine) were prepared and used as an integral part of the standard solid‐phase RNA synthesis. The obtained ¹⁹F NMR spectra supported the usual characterization data (obtained by UV‐ and CD‐melting profiles and by ¹H NMR spectra of the imino regions) and additionally gave more detailed information on the Qd/Hp transitions. The molar fractions of the secondary structural species (Qd, Hp) upon thermal denaturation and under varying ionic conditions could be determined from the intensities and shifts of the ¹⁹F NMR signals. For a well‐behaved Qd/Hp transition, thermodynamic parameters could be extracted.     

Fluorinated Carbohydrates as Lectin Ligands: Versatile Sensors in 19F‐Detected Saturation Transfer Difference NMR Spectroscopy

As a novel approach for studying carbohydrate–lectin interactions spectroscopically, we combine the resolution and specificity of ¹⁹F‐detected NMR spectroscopy with the sensitivity of the saturation transfer difference (STD) technique. The resulting background‐free ¹⁹F‐STD spectra open a promising perspective for broad application with medical relevance, for example, in drug discovery.

     

Probing DNA Mismatched and Bulged Structures by Using 19F NMR Spectroscopy and Oligodeoxynucleotides with an 19F‐Labeled Nucleobase

In this study, DNA local structures with bulged bases and mismatched base pairs as well as ordinary full‐matched base pairs by using ¹⁹F NMR spectroscopy with ¹⁹F‐labeled oligodeoxynucleotides (ODNs) were monitored. The chemical shift change in the ¹⁹F NMR spectra allowed discrimination of the DNA structures. Two types of ODNs possessing the bis(trifluoromethyl)benzene unit (F‐unit) at specified uridines were prepared and hybridized with their complementary or noncomplementary strands to form matched, mismatched, or bulged duplexes. By using ODN F1, in which an F‐unit was connected directly to a propargyl amine‐substituted uridine, three local structures, that is, full‐matched, G–U mismatch, and A‐bulge could be analyzed, whereas other structures could not be discriminated. A molecular modeling study revealed that the F‐unit in ODN F1 interacted little with the nucleobases and sugar backbone of the opposite strand because the linker length between the F‐unit and the uridine base was too short. Therefore, the capacity of ODN F1 to discriminate the DNA local structures was limited. Thus, ODN F2 was designed to improve this system; aminobenzoic acid was inserted between the F‐unit and uridine base so the F‐unit could interact more closely with the opposite strand. Eventually, the G‐bulge and T–U mismatch and the three aforementioned local structures could be discriminated by using ODN F2. In addition, the dissociation processes of these duplexes could be monitored concurrently by ¹⁹F NMR spectroscopy.     

Monitoring Conformational Changes in the NDM‐1 Metallo‐β‐lactamase by 19F NMR Spectroscopy

The New Delhi metallo‐β‐lactamase (NDM‐1) is involved in the emerging antibiotic resistance problem. Development of metallo‐β‐lactamases (MBLs) inhibitors has proven challenging, due to their conformational flexibility. Here we report site‐selective labeling of NDM‐1 with 1,1,1‐trifluoro‐3‐bromo acetone (BFA), and its use to study binding events and conformational changes upon ligand–metal binding using ¹⁹F NMR spectroscopy. The results demonstrate different modes of binding of known NDM‐1 inhibitors, including L ‐ and D ‐captopril by monitoring the changing chemical environment of the active‐site loop of NDM‐1. The method described will be applicable to other MBLs and more generally to monitoring ligand‐induced conformational changes.     

Parahydrogen‐Induced Polarization Transfer to 19F in Perfluorocarbons for 19F NMR Spectroscopy and MRI

Fluorinated substances are important in chemistry, industry, and the life sciences. In a new approach, parahydrogen‐induced polarization (PHIP) is applied to enhance ¹⁹F MR signals of (perfluoro‐n‐hexyl)ethene and (perfluoro‐n‐hexyl)ethane. Unexpectedly, the end‐standing CF₃ group exhibits the highest amount of polarization despite the negligible coupling to the added protons. To clarify this non‐intuitive distribution of polarization, signal enhancements in deuterated chloroform and acetone were compared and ¹⁹F–¹⁹F NOESY spectra, as well as ¹⁹F T₁ values were measured by NMR spectroscopy. By using the well separated and enhanced signal of the CF₃ group, first ¹⁹F MR images of hyperpolarized linear semifluorinated alkenes were recorded.     

Characterization of 4,5‐Dihydro‐1H‐Pyrazole Derivatives by 13C NMR Spectroscopy

The ¹³ C NMR resonances of 19 1‐acyl‐3‐(2‐nitro‐5‐substitutedphenyl)‐4,5‐dihydro‐1H‐pyrazoles, and 19 1‐acyl‐3‐(2‐amino‐5‐substituted)‐4,5‐dihydro‐1H‐pyrazoles, were completely assigned using the concerted application of one‐ and two‐dimensional NMR experiments (DEPT, gs‐HSQC and gs‐HMBC). Copyright © 2012 John Wiley & Sons, Ltd.     

Solid‐state NMR Spectroscopy of Quadrupolar Nuclei in Inorganic Chemistry

We here review the principles and applications of solid‐state NMR spectroscopy of quadrupolar nuclei, with a special emphasis on structural studies of inorganic solids. Most NMR‐observable nuclei have spin I > 1/2, and possess a quadrupole moment. The resulting quadrupolar interaction severely broadens the resonances, but also encapsulates valuable information about the symmetry of the electronic surroundings of the observed nucleus. The effect of the quadrupolar interaction, as well as that of the chemical shift and dipolar interaction, on solid‐state NMR spectra is examined in this article. To regain good resolution, specifically designed NMR techniques exist to remove the quadrupolar broadening, i.e. overtone and MQMAS spectroscopy, the principles of which are outlined here. In addition, the possibility of distance measurements via the dipolar interaction using the REDOR technique is discussed. The combined information derived from distance measurements, quadrupolar and chemical shift parameters can be helpful for determination of the crystal structure, or for detection of impurity phases, as illustrated by surveying a number of case studies covering spin I = 1, 3/2, 5/2 and 7/2.     

Design,Synthesis, and Application of an Optimized Monofluorinated Aliphatic Label for Peptide Studies by Solid‐State 19F NMR Spectroscopy

A conformationally restricted monofluorinated α‐amino acid, (3‐fluorobicyclo[1.1.1]pentyl)glycine (F‐Bpg), was designed as a label for the structural analysis of membrane‐bound peptides by solid‐state ¹⁹F NMR spectroscopy. The compound was synthesized and validated as a ¹⁹F label for replacing natural aliphatic α‐amino acids. Calculations suggested that F‐Bpg is similar to Leu/Ile in terms of size and lipophilicity. The ¹⁹F NMR label was incorporated into the membrane‐active antimicrobial peptide PGLa and provided information on the structure of the peptide in a lipid bilayer.     

Chemical‐Shift‐Resolved 19F NMR Spectroscopy between 13.5 and 135 MHz: Overhauser–DNP‐Enhanced Diagonal Suppressed Correlation Spectroscopy

Overhauser–DNP‐enhanced homonuclear 2D ¹⁹F correlation spectroscopy with diagonal suppression is presented for small molecules in the solution state at moderate fields. Multi‐frequency, multi‐radical studies demonstrate that these relatively low‐field experiments may be operated with sensitivity rivalling that of standard 200–1000 MHz NMR spectroscopy. Structural information is accessible without a sensitivity penalty, and diagonal suppressed 2D NMR correlations emerge despite the general lack of multiplet resolution in the 1D ODNP spectra. This powerful general approach avoids the rather stiff excitation, detection, and other special requirements of high‐field ¹⁹F NMR spectroscopy.     

Solution NMR and X‐Ray Structural Studies on Phthalocyaninatoiron Complexes

The addition of primary amines as solubilizing reagents for phthalocyaninatoiron complexes is shown to afford six‐coordinate bis(amine)phthalocyaninato complexes, i.e., [Fe(amine)₂(pc)] 2 (amine = decan‐1‐amine) and 3 (amine = benzylamine), with the two new N‐donors occupying the trans‐axial positions. The new complexes were characterized by extensive NMR measurements in THF solution. For complex 3 with the benzylamine ligand, the solid‐state structure was determined by X‐ray diffraction methods. Complex 2 is sufficiently labile in THF solution to exchange one amine ligand against CO (gas) affording an equilibrium mixture containing [Fe(amine)(CO)(pc)] 4 .     

Synthesis and Solution Structure of 1H‐Benzo‐1,5‐diazepine Derivatives with a Perfluoroalkyl Side Chain

The reaction of perfluorinated 3,5‐dioxoesters with 1,2‐diaminobenzenes or 2,3‐diaminonaphthalenes afforded two types of 1H‐benzo‐1,5‐diazepine derivatives containing a perfluorinated side chain. 2,5‐Dihydro‐1H‐benzo‐1,5‐diazepin‐2‐ones were formed by cyclocondensation via the central keto and the ester group, whereas 1H‐benzo‐1,5‐diazepines resulted from cyclocondensation via the two keto groups. The tautomerism and isomerization of these compounds have been investigated by ¹H‐, ¹³C‐, and ¹⁹F‐NMR spectroscopy. The 1,5‐diazepines appear in CDCl₃ solution as mixtures of two tautomeric forms, the enaminoimine I and diaminodiene II . In DMSO solution, besides I and II , two further species, III and IV , are formed by (E/Z) isomerization on the exocyclic C=C bond.     

Complete NMR assignment of (+)‐10β,14‐dihydroxy‐allo‐aromadendrane

The assignment of ¹H and ¹³C NMR of the sesquiterpene (+)‐10β,14‐dihydroxy‐allo‐aromadendrane by means of two‐dimensional NMR is reported. Copyright © 2003 John Wiley & Sons, Ltd.     

Fluorinated Carbohydrates as Lectin Ligands: Dissecting Glycan–Cyanovirin Interactions by Using 19F NMR Spectroscopy

NMR spectroscopy and isothermal titration calorimetry (ITC) are powerful methods to investigate ligand–protein interactions. Here, we present a versatile and sensitive fluorine NMR spectroscopic approach that exploits the ¹⁹F nucleus of ¹⁹F‐labeled carbohydrates as a sensor to study glycan binding to lectins. Our approach is illustrated with the 11 kDa Cyanovirin‐N, a mannose binding anti‐HIV lectin. Two fluoro‐deoxy sugar derivatives, methyl 2‐deoxy‐2‐fluoro‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranoside and methyl 2‐deoxy‐2‐fluoro‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranosyl‐(1→2)‐α‐D ‐mannopyranoside were utilized. Binding was studied by ¹⁹F NMR spectroscopy of the ligand and ¹H–¹⁵N HSQC NMR spectroscopy of the protein. The NMR data agree well with those obtained from the equivalent reciprocal and direct ITC titrations. Our study shows that the strategic design of fluorinated ligands and fluorine NMR spectroscopy for ligand screening holds great promise for easy and fast identification of glycan binding, as well as for their use in reporting structural and/or electronic perturbations that ensue upon interaction with a cognate lectin.     

Direct Observation of Ca2+‐Induced Calmodulin Conformational Transitions in Intact Xenopus laevis Oocytes by 19F NMR Spectroscopy

The Ca²⁺‐mediated conformational transition of the protein calmodulin (CaM) is essential to a variety of signal transduction pathways. Whether the transition in living cells is similar to that observed in buffer is not known. Here, we report the direct observation by ¹⁹F NMR spectroscopy of the transition of the Ca²⁺‐free and ‐bound forms in Xenopus laevis oocytes at different Ca²⁺ levels. We find that the Ca²⁺‐bound CaM population increased greatly upon binding the target protein myosin light‐chain kinase (MLCK) at the same Ca²⁺ level. Paramagnetic NMR spectroscopy was also exploited for the first time to obtain long‐range structural constraints in cells. Our study shows that ¹⁹F NMR spectroscopy can be used to obtain long‐range structural constraints in living eukaryotic cells and paves the way for quantification of protein binding constants.