Predicting 19F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase–Inhibitor Complex

The absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor–protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable ¹⁹F chemical‐shift predictions to deduce ligand‐binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the ¹⁹F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleeping sickness. We include many protein–inhibitor conformations as well as monomeric and dimeric inhibitor–protein complexes, thus rendering it the largest computational study on chemical shifts of ¹⁹F nuclei in a biological context to date. Our predicted shifts agree well with those obtained experimentally and pave the way for future work in this area.     

13C and 19F chemical shifts of bridgehead halogenated adamantanes

The ¹³C chemical shifts of the sixteen bridgehead substituted mono-, di-, tri- and tetrahaloadamantanes (halo = F, Cl, Br, I) and four mixed 1,3-dihaloadamantanes are reported. The effect of bridgehead halogens on the shift values of carbons in β and δ positions is well correlated by the simple additivity relationship based on substituent shifts of 1-monohaloadamantanes. A substituted α-carbon is shifted upfield with an increase in the number of halogens at other bridgehead positions and this shift is relatively greater in the order F < Cl < Br < I. This observed upfield shift of α-carbons is opposite to the downfield shift expected from additivity. An unsubstituted bridgehead γ-carbon is moved to lower fields by one, two and three bromines (or iodines) at other bridge-heads while, in contrast, a third fluorine weakly shields the remaining unsubstituted γ-carbon. Some special noncumulative effects of halogens operating across the 1,3-bridgehead positions of adamantane are indicated by the data. The ¹⁹F chemical shifts of 1-fluoro-, 1,3-difluoro-, 1,3,5-trifluoro- and 1,3,5,7-tetrafluoroadamantanes are contrary to expectations based on inductive effects in that they move progressively upfield. Other 1-fluoroadamantanes with chloro, bromo, or methyl groups present also show substituent-induced chemical shifts which shield the fluorine.     

Predicting 19F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase–Inhibitor Complex

The absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor–protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable ¹⁹F chemical-shift predictions to deduce ligand-binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the ¹⁹F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleeping sickness. We include many protein–inhibitor conformations as well as monomeric and dimeric inhibitor–protein complexes, thus rendering it the largest computational study on chemical shifts of ¹⁹F nuclei in a biological context to date. Our predicted shifts agree well with those obtained experimentally and pave the way for future work in this area.     

19F chemical shifts of bridgehead fluorides

The ¹⁹F chemical shifts of a series of bridgehead fluorides are reported. It is found that, contrary to earlier conclusions based on a limited number of substrates, the fluorine shifts occur randomly.     

The 19F chemical shift in oxygen containing carbon fluorine products

We have examined the ¹⁹F NMR spectra of a number of oxygen-containing fluorocarbon products and obtained a comprehensive set of ¹⁹F chemical shift values, which enabled us to determine the influence of an oxygen atom bonded to a fluorocarbon group on the ¹⁹F chemical shift. The influence of neighbouring fluorocarbon groups, either directly connected or separated by an oxygen atom, was also considered. Our results may be summarized as follows. An oxygen atom bonded by a single bond (ether type bond) to a fluorine substituted carbon atom decreases the ¹⁹F chemical shift, as does the introduction of a further fluorine atom. Considering two adjacent fluorocarbon groups, a variation of x ppm in the ¹⁹F chemical shift of one of the two groups gives a variation of 0·12 x ppm in the opposite sense on the ¹⁹F chemical shift of the other group. If the two groups are connected by an ether oxygen atom, the effect is only about 0·06 x ppm.     

Bonding information in tungsten(VI) compounds from directly bonded fluorine and fluorophenoxy subtituents

The series of compounds (FC₆H₄O)_nWF_6-n, where n = 1-6 and F is meta or para to oxygen, has been prepared and all fluorine nmr chemical shifts determined. The W-$\text{F}$, para-$\text{F}$, and meta-$\text{F}$ resonances all shift upfield as a function of n with approximate relative sensitivities of 1, 1/20, and 1/30, respectively. All chemical shifts are also found to be sensitive to molecular stereochemistry, with subtituents trans to oxygen shifted to higher field than those trans to fluorine. ¹⁹F data is also reported for the complete series (C₆H₅O)_nWF_6-n     

Prototropic processes in benzaurins. <Superscript>19</Superscript>F and <Superscript>1</Superscript>H NMR spectra of fluoro- and methylsubstituted 4-hydroxyphenyl-diphenylcarbinols,related fuchsones and benzaurins

Tautomerism of benzaurins and hydration are studied. ¹H and ¹⁹F chemical shifts have been determined for a number of substituted 4-hydroxyphenyl-diphenyl carbinols containing fluorine in a 3-, 3*- or 4*-position, and for similar compounds containing additional methyl groups in a position of 3, 3** or 4**. The same data have been obtained for the fuchsones prepared by dehydration of the above carbinols. On this basis chemical shifts of fluorine in different positions have been evaluated as a monitor of the transformation of 4-hydroxyphenyl group to the semiquinone moiety. The ¹⁹F NMR can be used to monitor the transformation of 4**-fluorobenzaurin and the related 3,3*-disubstituted and 3,3*,5,5*-tetramethylsubstituted compounds to the corresponding carbinols due to the addition of a water molecule and to study the tautomerism of the two latter benzaurins as well as that of 3,3*,4**trifluorobenzaurin. Furthermore, fluorine and methyl group chemical shifts are sensitive to syn-anti-isomerism in substituted fuchsones.     

19F and 1H NMR of aldimines of fluoroamino acids with pyridoxal-5′-phosphate

¹H and ¹⁹F NMR spectra were obtained for six Schiff bases (aldimines) formed by pyridoxal-5′-phosphate (PLP) with four fluorinated or their two parent non-fluorinated α-amino acids (phenylalanine and α-aminobutyric acid). pK_A Values were derived from ¹H and ¹⁹F titration curves. The imine nitrogen of the aldimines is very basic (～13) and sensitive to the electron withdrawing effect of fluorine. The pyridine nitrogen is less basic in the aldimines (～7) than in PLP (8.12) and is less sensitive to the electron withdrawing effect of the fluorine than is the imine nitrogen. The phosphate group has a pK in the same range (～6) and the chemical shifts of some nuclei are sensitive to both pK values. Protonation of the aldimine causes the ¹H signal to shift downfield at the methyl protons of the pyridine ring and at the aldehydic proton of the aldimine for the high pK value (except for the aldimines prepared from the β-fluorophenylalanine), but upfield at the aromatic proton and at the aldehydic proton of the aldimine for the low pK. Protonation of the aldimine causes the ¹⁹F signal of an aryl fluorine to shift downfield but gives an upfield shift at a β-fluorine. These data are related to the highly conjugated electronic structure of the Schiff bases.     

Fluorine NMR spectra of pentafluorophenyl derivatives

The fluorine chemical shifts and spin-spin coupling constants of 65 pentafluorophenyl derivatives with widely varying organic substituents were examined. Useful correlations of the three meta coupling constants with the chemical shifts of the para fluorine were found. It is suggested that these relationships be extended to all compounds of the type considered in order to determine the signs and approximate values of meta coupling constants. Equations for correlation of the fluorine chemical shifts with the Taft constants are presented. The possibility of calculating the Taft constants from the ¹⁹F NMR spectra of pentafluorophenyl compounds is being discussed.     

Hydrogen Bond Acceptor Propensity of Different Fluorine Atom Types: An Analysis of Experimentally and Computationally Derived Parameters

The propensity of organic fluorine acting as a weak hydrogen bond acceptor (HBA) in intermolecular and intramolecular interactions has been the subject of many experimental and theoretical studies often reaching different conclusions. Over the last few years, new and stronger evidences have emerged for the direct involvement of fluorine in weak hydrogen bond (HB) formation. However, not all the fluorine atom types can act as weak HBA. In this work, the differential HBA propensity of various types of fluorine atoms was analyzed with a particular emphasis for the different types of alkyl fluorides. This was carried out by evaluating ab initio computed parameters, experimental ¹⁹F NMR chemical shifts and small molecule crystallographic structures (extracted from the CSD database). According to this analysis, shielded (with reference to the ¹⁹F NMR chemical shift) alkyl mono-fluorinated motifs display the highest HBA propensity in agreement with solution studies. Although much weaker than other well-characterized HB complexes, the fragile HBs formed by these fluorinated motifs have important implications for the chemical-physical and structural properties of the molecules, chemical reactions, and protein–ligand recognition.     

High-Pressure 19F NMR Measurements of a Series of Fluorinated Benzenes in Supercritical Carbon Dioxide

The high-pressure and high-resolution NMR cell method has been developed for precise measurements of supercritical carbon dioxide solutions. ¹⁹F NMR chemical shifts of a series of fluorinated benzenes, C₆H _n F _m (n = 6 ? m and m = 1 ～ 6) in CO₂ at dilute concentrations were measured over a wide pressure range up to 35 MPa at 314.3 K. The density dependence of the corrected chemical shift, where the bulk magnetic susceptibility contribution was subtracted, was well represented by a cubic function of CO₂ density for any fluorinated benzene. The linear coefficients, arising from pairwise intermolecular interactions, were found to be dependent on the numbers and positions of fluorine atoms in the fluorinated benzenes. The solute–solvent interaction between fluorine and CO₂ was discussed.     

A study by 19F NMR of the structure of 1,2-dithiole derivatives and correlation with the S4p electron energy determined by ESCA

A correlation is established between the ¹⁹F NMR chemical shifts and the S₂p electron energies measured by ESCA in the 1,2-dithiole derivatives. This correlation shows that the fluorine chemical shifts depends on the positive charge taken by the 1,2-dithiole ring and then constitutes a convenient evaluation of this charge.     

The effect of the structure of substituted phenylphosphonic difluorides on their 19F and 31P NMR spectral parameters

The ¹⁹F and ³¹P NMR spectral parameters of a series of meta and para substituted phenylphosphonic difluorides were found to be linearly related to the substituent parameters: the phosphorus chemical shifts correlated with Hammett's σ constant, the fluorine chemical shifts with Taft's σ_R parameter and the phosphorus–fluorine coupling constants with σ⁺.     

Carbon-13 nuclear magnetic resonance spectroscopy—VII:para-substituted fluorobenzenes

C-13 and F-19 NMR spectra of seventeen para-substituted fluorobenzenes were measured and the chemical shifts as well as coupling constants with respect to substituents were analysed. The chemical shifts of the fluorine, the C₁ and the C₂ atoms were found to depend on the total electron densities. In the case of the C₃ atom, the chemical shifts seem to depend on π-electron densities rather than the total electron densities. The present calculations also indicate that the chemical shift of the C₄ atom depends mainly on σ-electron densities due to the inductive effects of substituents. The strongest factor influencing the coupling constant, ⁿJ(C? F), is also considered to be the π-electron densities on the carbon atoms. In the case of the direct couplings, ¹J(C? F), the π-bond orders are important.     

Exposing the Origins of Irreproducibility in Fluorine NMR Spectroscopy

Fluorine chemistry has taken a pivotal role in chemical reaction discovery, drug development, and chemical biology. NMR spectroscopy, arguably the most important technique for the characterization of fluorinated compounds, is rife with highly inconsistent referencing of fluorine NMR chemical shifts, producing deviations larger than 1 ppm. Herein, we provide unprecedented evidence that both spectrometer design and the current unified scale system underpinning the calibration of heteronuclear NMR spectra have unintentionally led to widespread variation in the standardization of ¹⁹F NMR spectral data. We demonstrate that internal referencing provides the most robust, practical, and reproducible method whereby chemical shifts can be consistently measured and confirmed between institutions to less than 30 ppb deviation. Finally, we provide a comprehensive table of appropriately calibrated chemical shifts of reference compounds that will serve to calibrate ¹⁹F spectra correctly.     

Computation and analysis of 19F substituent chemical shifts of some bridgehead‐substituted polycyclic alkyl fluorides

The ¹⁹F NMR shieldings for several remotely substituted rigid polycyclic alkyl fluorides with common sets of substituents covering a wide range of electronic effects were calculated using the DFT‐GIAO theoretical model. The level of theory, B3LYP/6–311+G(2d,p), was chosen based on trial calculations which gave good agreement with experimental values where known. The optimized geometries were used to obtain various molecular parameters (fluorine natural charges, electron occupancies on fluorine of lone pairs and of the C? F bond, and hybridization states) by means of natural bond orbital (NBO) analysis which could help in understanding electronic transmission mechanisms underlying ¹⁹F substituent chemical shifts (SCS) in these systems. Linear regression analysis was employed to explore the relationship between the calculated ¹⁹F SCS and polar substituent constants and also the NBO derived molecular parameters. The ¹⁹F SCS are best described by an electronegativity parameter. The most pertinent molecular parameters appear to be the occupation number of the NBO p‐type fluorine lone pair and the occupation number of the C? F antibonding orbital. This trend suggests that in these types of rigid saturated systems hyperconjugative interactions play a key role in determining the ¹⁹F SCS. Electrostatic field effects appear to be relatively unimportant. Copyright © 2003 John Wiley & Sons, Ltd.     

NMR and DFT study of chemical bonding of the titanyl ion in pentafluoro complexes (NH4)3TiOF5 and Rb2KTiOF5

19F NMR and DFT methods are used to study the electronic structure and chemical bonding of titanyl ions in pentafluoro titanyl complexes (NH₄)₃TiOF₅ and Rb₂KTiOF₅. The experimental values of the anisotropy of ¹⁹F NMR chemical shifts (CSs) are shown to be consistent with the calculated parameters within the DFT method. At normal temperatures orientational disordering of octahedral [TiOF₅]^3- anions occurs, fluorine atoms steadily occupying cis- and trans-positions with respect to the O^2- ion. In both complexes, trans-position is not fully occupied; the occupation ratio does not exceed ~4:0.9. When the temperature is decreased to 150 K, the value of the CS anisotropy of the fluorine atom resonance line in trans-position is found to be smaller than the dipole-dipole broadening, whereas the line from fluorine atoms in cis-positions transforms into an asymmetric broad line characterized by the triaxial anisotropy of the CS tensor. It is shown that the found anisotropy corresponds to violation of the axial symmetry of Ti—F cis bonds because of strong delocalization of the electron density of Ti—O bonds in the titanyl ion.     

Crystalline aluminium hydroxy fluorides—Suitable reference compounds for F chemical shift trend analysis of related amorphous solids

On the basis of MAS NMR-data for crystalline AlF_x(OH)_3−x·H₂O samples in the pyrochlore structure, ¹⁹F chemical shifts correlate with the average chemical composition of the octahedral environment, given by AlF_xO_6−x in these compounds.The attribution of local structures in sol-gel derived amorphous AlF_x(OX)_3−x·XOH (X = H, R (alkyl)) compounds is of special interest as these or consecutively prepared solids exhibit remarkable features, for example, a high surface (HS) area accompanied by a high Lewis acidity.By transferring this scale of a ¹⁹F chemical shift trend analysis to such compounds a prediction of the chemical nature of the average Al coordination becomes possible.A new synthetic approach to crystalline aluminium hydroxy fluorides involving a sol gel fluorination as the first reaction step and an aluminium alkoxide as precursor compound is presented. Varying the amount of HF leads to different F-OH-ratios in the AlF_x(OH)_3−x compounds.     

19F n.m.r spectra of polyfluoroquinolines. Long range inter-ring 19F?19F coupling constants and 19F chemical shifts

The signs and magnitudes of every fluorine–fluorine coupling constant in perfluoroquinoline ( 1 ), 2,4-dichloropentafluoroquinoline ( 2 ) and 2-bromohexafluoroquinoline ( 3 ) have been determined by ¹⁹F n.m.r. These provide an unambiguous assignment of the spectrum of the first compound and its derivatives. Inter-ring fluorine–fluorine coupling constants were found to be positive over an odd number of bonds and negative over an even number of bonds, similar to that observed in proton–proton coupling constants in multicyclic systems. The ¹⁹F chemical shifts of perfluoroquinoline and its protonated salt are reported and directly correlated with SCF MO calculated π-electron densities at both fluorine and bonded carbon atoms.     

Low-temperature F NMR spectroscopy of 1-fluoro-1-lithioethenes : Stability, shifts and unexpected coupling constants

Half-lives and fluorine atom shifts of stabilized 1-fluoro-1-lithioethenes bearing hydrogen, fluorine, phenyl, and/or dimethylphenylsilyl groups in the β-positions have been determined by a low-temperature ¹⁹F NMR spectroscopy. Some 1-fluoro-1-lithioethenes displayed an exceptionally low value of the trans-³J_FF coupling constant. Stereoselectivity of carbenoid formation, as well as an effect of configuration on the stability is discussed.