1hJFH coupling in 2-fluorophenol revisited: is intramolecular hydrogen bond responsible for this long-range coupling?

The pitfalls of using JHF spin-spin coupling constants to infer hydrogen bond formation in organofluorine compounds

Theoretical decomposition of "through space" spin-spin coupling constants (SSCCs) in organofluorine compounds signal that intramolecular hydrogen bonds (H-bonds) are not the primary mechanism of transmission for SSCCs. Increasing solvent polarity may disrupt H-bonds, but not necessarily the JFH SSCC. Substituent effects may drastically alter the SSCC transmission pathway. Accurate SSCC analysis requires benchmarking theoretical calculations to support experimental data interpretation.

Stereoelectronic interactions: A booster for 4 JHF transmission

Long-range proton-fluorine coupling constants (ⁿ J_HF ) are helpful for the structure elucidation of fluorinated molecules. However, their magnitude and sign can change with the relative position of coupled nuclei and the presence of substituents. Here, trans-4-tert-butyl-2-fluorocyclohexanone was used as a model compound for the study of the transmission of ⁴ J_HF . In this compound, the ⁴ J_H6axF was measured to be +5.1 Hz, which is five times larger than the remaining ⁴ J_HF in the same molecule (⁴ J_H4F  = +1.0 Hz and ⁴ J_H6eqF  = +1.0 Hz). Through a combination of experimental data, natural bond orbital (NBO) and natural J-coupling (NJC) analyses, we observed that stereoelectronic interactions involving the π system of the carbonyl group are involved in the transmission pathway for the ⁴ J_H6axF . Interactions containing the π system as an electron acceptor (e.g., σ_C6H6ax  → π^*_C═O and σ_CF  → π^*_C═O ) increase the value of the ⁴ J_H6axF , while the interaction of the π system as an electron donor (e.g., π_C═O  → σ^*_CF ) decreases it. Additionally, the carbonyl group was shown not to be part of the transmission pathway of the diequatorial ⁴ J_H6eqF coupling in cis-4-tert-butyl-2-fluorocyclohexanone, revealing that there is a crucial symmetry requirement that must be fulfilled for the π system to influence the value of the ⁴ J_HF in these systems.

Through space JFH spin-spin coupling constant transmission pathways in 2-(trifluoromethyl)thiophenol: formation of unusual stabilizing bifurcated CFHS and CFSH interactions

Given its importance and the possibility of organic F to participate in hydrogen bonds (H-bonds), the understanding of its behavior as a H-bond acceptor with different donors is crucial. The interest in organofluorine compounds and the works related to the study of the participation of this atom in non-covalent interactions is constantly growing. Following recent studies in this subject, we evaluated the existence of two bifurcated intramolecular interactions, a bifurcated CFHS H-bond in the cis conformer of 2-trifluoromethylthiophenol and an unusual, bifurcated CFSH interaction in the trans conformer. The JFH spin-spin coupling constant (SSCC) was evaluated for 2-trifluoromethylthiophenol both experimentally by 1H and 19F NMR and theoretically using the natural bond orbitals (NBO), the quantum theory of atoms in molecules (QTAIM) and the non-covalent interactions (NCI) framework. Although both interactions are crucial for the stabilization of the conformer geometries, the observed positive JFH spin-spin coupling constant (SSCC) is mainly resultant from the trans conformer, which has a large calculated positive SSCC, and is transmitted through steric interactions involving the F lone pairs and the σSH bonding orbital.

Effects of Ring Fluorination on the Ultraviolet Photodissociation Dynamics of Phenol

The dynamics of photoinduced O-H bond fission in five fluorinated phenols (2-fluorophenol, 3-fluorophenol, 2,6-difluorophenol, 3,4,5-trifluorophenol, and pentafluorophenol) have been investigated by H Rydberg atom photofragment translational spectroscopy following excitation at many wavelengths in the range 220 ≤ λ ≤ 275 nm. The presence of multiple fluorine substituents reduces the efficiency of O-H bond fission (by tunneling) from the first excited (1¹ππ*) electronic state, whereas all bar the perfluorinated species undergo O-H bond fission when excited at shorter wavelengths (to the 2¹ππ* state). As in bare phenol, O-H bond fission is deduced to occur by non-adiabatic coupling at conical intersections between the photoprepared "bright" ππ* states and the 1¹πσ* potential energy surface. In all cases, the fluorophenoxyl photoproducts are found to be formed in a range of vibrational levels, all of which include an odd number of quanta (typically one) in an out-of-plane (a″) vibrational mode; this product vibration is viewed as a legacy of the parent out-of-plane motions that promote non-adiabatic coupling to the dissociative 1¹πσ* potential. The radical products also show activity in in-plane vibrations involving coupled (both in- and out-of-phase) C-O and C-F wagging motions, which can be traced to the impulse between the recoiling O and H atoms and, in detail, are sensitive to the presence (or not) of an intramolecular F···H-O hydrogen bond. Upper limit values for the O-H bond dissociation energies are reported for all molecules studied apart from pentafluorophenol.

Approximating the Strength of the Intramolecular Hydrogen Bond in 2-Fluorophenol and Related Compounds: A New Application of a Classic Technique

Fluorinated organic compounds are ubiquitous in the pharmaceutical and agricultural industries. To better discern the mode of action of these compounds, it is critical to understand the strengths of hydrogen bonds involving fluorine. While established techniques can determine these strengths for intermolecular complexes, there is no analogous scheme for intramolecular hydrogen bonds. This work uses ¹H nuclear magnetic resonance spectroscopy to measure the strength of intramolecular hydrogen bonds in ortho-substituted phenols. Titration of each phenol with DMSO in CCl₄ yields a free energy of binding (ΔG). Subtraction of this value from the ΔG of binding of the standard, 4-fluorophenol, is shown to give the difference in ΔG for the cis and trans isomers of the ortho-substituted phenols. This difference is conventionally taken to be approximately equal to the ΔG of the intramolecular hydrogen bond. These data complement theoretical methods, which yield slightly larger ΔGs. Both theory and experiment point to a weak intramolecular hydrogen bond in 2-fluorophenol. The other 2-X-phenols have stronger hydrogen bonds, following the order F < Cl ≈ Br < OCH₃. The methodology developed here can be readily applied to other systems with intramolecular hydrogen bonds.

Intramolecular H-Bond Is Formed in 2-Fluorophenol and 2-Fluorothiophenol, but It May Not Be the Main Pathway of the JFH Coupling Constant Transmission

The intramolecular CF···HX (X = O or S) H-bond and J_FH spin-spin coupling constants (SSCCs) in 2-fluorophenol and 2-fluorothiophenol were investigated experimentally by ¹H and ¹⁹F NMR and theoretically in the framework of the natural bond orbital analysis. In contrast with recent findings from the literature, the results obtained in this work showed that an intramolecular H-bond is formed in the cis conformers and that it has an electrostatic origin. Such an intramolecular electrostatic H-bond is the interaction that rules the conformational preferences on these compounds. Moreover, the natural J-coupling analysis indicated that the J_HF SSCC in 2-fluorophenol has its origin on LP(F)/σ_OH steric interactions and should be labeled as ^4TSJ_HF. On the other hand, the analogue SSCC for 2-fluorothiophenol has its origin on the intramolecular H-bond LP(F) → σ_SH^* hyperconjugative interaction and should be described as a ^1hJ_FH SSCC.

Can 2-X-Ethanols Form Intramolecular Hydrogen Bonds?

For 2-X-ethanols, where X = F, OH, or NH₂, the gauche conformer is favored over the trans conformer by at least 2 kcal/mol. Initially, this preference, ΔE, was attributed to an intramolecular hydrogen bond, IMHB, between the OH and X groups. Over the years, this conclusion has been challenged by two major arguments. One claim is that the entirety of ΔE can be accounted for by the gauche effect. Against this, calculations using five different methods show that the maximum contribution of the gauche effect to ΔE is less than 1 kcal/mol. A second argument employs the quantum theory of atoms in molecules to contend that the absence of a bond critical point (BCP) between the OH and X groups in 2-X-ethanols denotes the lack of an IMHB. By looking at the 2-X-ethanols at fixed XCCO torsional angles ranging from 0° to 60°, it is shown that the BCP criterion is inconsistent with other properties such as energy, bond lengths, and stretching frequencies. These inconsistencies are removed when the theory of noncovalent interactions is used. The IMHBs in 2-X-ethanols are found to be similar in form but smaller in magnitude than their intermolecular counterparts. This work concludes that 2-X-ethanols form IMHBs.

1 J CH Coupling in Benzaldehyde Derivatives: Ortho Substitution Effect

The natural J-coupling (NJC) method is applied to analyze the Fermi contact contribution of the NMR spin-spin coupling constant decomposing this contribution in terms of natural localized molecular orbitals. We investigated the influence of the basis set on the NJC analysis for the formyl group coupling constant (¹ J _CHf) of benzaldehyde derivatives. NJC and other NBO analyses, like steric and natural Coulombic energy, were chosen to explain the influence of electron-donating and electron-withdrawing groups on ¹ J _CHf for some substituted benzaldehydes (Me, OH, OMe, F, Cl, Br, I, and NO₂). For the ortho derivatives, electronegative substituents near the C-Hf bond increase the ¹ J _CHf coupling. This effect could be related to an increase in formyl carbon s character and changes in the carbon and hydrogen natural charges. This indicates that the substituents in ortho have a proximity effect on ¹ J _CHf coupling mainly of electrostatic origin instead of the expected hyperconjugative interactions.

Retention of strong intramolecular hydrogen bonds in high polarity solvents in binaphthalene–benzamide derivatives: extensive NMR studies

Advanced multidimensional NMR techniques have been employed to investigate the intramolecular hydrogen bonds (HBs) in a series of N,N′-([1,1′-binaphthalene]-2,2′-diyl)bis(benzamide) derivatives, with the site-specific substitution of different functional groups. The existence of intramolecular HBs and the elimination of any molecular aggregation and possible intermolecular HBs are ascertained by various experimental NMR techniques, including solvent polarity dependent modifications of HB strengths. In the fluorine substituted derivative, direct evidence for the engagement of organic fluorine in HB is obtained by the detection of heteronuclear through-space correlation and the coupling between two NMR active nuclei where the transmission of spin polarization is mediated through HBs (^1hJ_FH). The extent of reduction in the strength of ^1hJ_FH on dilution with high polarity solvents directly provided the qualitative measure of HB strength. The HB, although becoming weakened, does not get nullified even in pure high polarity solvent, which is attributed to the structural constraints. The rate of exchange of a labile hydrogen atom with the deuterium of the solvent permitted the measurement of their half-lives, that are correlated to the relative strengths of HBs. The experimental NMR findings are further validated by XRD and DFT-based theoretical computations, such as, NCI and QTAIM.

NMR studies reveal very strong hydrogen bond unbreakable even in high polarity solvents.

QSAR Study of N-Myristoyltransferase Inhibitors of Antimalarial Agents

Malaria is a disease caused by protozoan parasites of the genus Plasmodium that affects millions of people worldwide. In recent years there have been parasite resistances to several drugs, including the first-line antimalarial treatment. With the aim of proposing new drugs candidates for the treatment of disease, Quantitative Structure–Activity Relationship (QSAR) methodology was applied to 83 N-myristoyltransferase inhibitors, synthesized by Leatherbarrow et al. The QSAR models were developed using 63 compounds, the training set, and externally validated using 20 compounds, the test set. Ten different alignments for the two test sets were tested and the models were generated by the technique that combines genetic algorithms and partial least squares. The best model shows r² = 0.757, q²_adjusted = 0.634, R²_pred = 0.746, R²_m = 0.716, ∆R²_m = 0.133, R²_p = 0.609, and R²_r = 0.110. This work suggested a good correlation with the experimental results and allows the design of new potent N-myristoyltransferase inhibitors.

Probing long-range spin-spin coupling constants in 2-halo-substituted cyclohexanones and cyclohexanethiones: The role of solvent and stereoelectronic effects

Earlier studies with 2-bromocyclohexanone demonstrated a measurable long-range coupling constant (⁴ J_H2,H6 ) for the equatorial conformer, although ⁴ J_H2,H4 and ⁴ J_H4,H6 were not observed; as a consequence, it is inferred that the carbonyl group plays an important role particularly due to hyperconjugative interactions σ_C2H2 →π*_C═O and σ_C6H6 →π*_C═O. In the present study, NBO analysis and coupling constant calculations were performed to cyclohexanone and cyclohexanethione alpha substituted with F, Cl, and Br, aiming to evaluate the halogen effect and acceptor character of the π* orbital on the long-range coupling pathway. The σ_C2H2 →π*_C1═Y and σ_C6H6 →π*_C1═Y (Y═O and S) hyperconjugative interactions for the equatorial conformer indeed contribute for the ⁴ J_H2,H6 transmission mechanism_. Surprisingly, the ⁴ J_H2,H6 value is higher for the carbonyl compounds, although the interactions σ_C2H2 →π*_C═Y and σ_C6H6 →π*_C═Y are more efficient for the thiocarbonyl compounds. Accordingly, the Fermi contact (FC) contribution for the thiocarbonyl compounds decays deeper than in ketones, thus reducing more the ⁴ J_H2,H6 values. Moreover, both π_C═S →σ*_C─X and π_C═S →σ*_C─H interactions seem to be stronger in thiocarbonyl than in carbonylic compounds. The implicit solvent effect (DMSO and water) on the coupling constant values was negligible when compared with the gas phase. On the other hand, an explicit solvent effect was found and ⁴ J_H2,H6 for the thiocarbonyl compounds appeared to be more sensitive than for the cyclohexanones.

NMR spin-spin coupling constants: bond angle dependence of the sign and magnitude of the vicinal (3)JHF coupling

The dependence of the magnitude and sign of (3)JHFF on the bond angle in fluoro-cycloalkene compounds is evaluated by electronic structure calculations using different levels of theory, viz. DFT, SOPPA(CCSD) and SOPPA(CC2). Localized molecular orbital contributions to (3)JHFF are analyzed to assess which orbitals are responsible for (3)JHFF and which are the most important coupling transmission mechanisms for each compound. Fluoro-ethylene is used as a model system to evaluate the dependence of the (3)JHFF coupling constant on the angle between the σCα-F and σCα'-HF vectors. Through-space and hyperconjugative transmission pathways and ring strain are identified as responsible for the opposite trend between (3)JHFF and bond angle, and for the negative signs obtained for the two molecules, respectively. One of the fluorine lone pairs, σCα'-HF, σCα-F, σCα'-Cβ' bonding orbitals and the σ*Cα-F antibonding orbital are involved in the J-coupling pathways, according to analyses of pairwise-steric and hyperconjugative energies.

Conformational analysis of small molecules: NMR and quantum mechanics calculations

This review deals with conformational analysis in small organic molecules, and describes the stereoelectronic interactions responsible for conformational stability. Conformational analysis is usually performed using NMR spectroscopy through measurement of coupling constants at room or low temperature in different solvents to determine the populations of conformers in solution. Quantum mechanical calculations are used to address the interactions responsible for conformer stability. The conformational analysis of a large number of small molecules is described, using coupling constant measurements in different solvents and at low temperature, as well as recent applications of through-space and through-hydrogen bond coupling constants JFH as tools for the conformational analysis of fluorinated molecules. Besides NMR parameters, stereoelectronic interactions such as conjugative, hyperconjugative, steric and intramolecular hydrogen bond interactions involved in conformational preferences are discussed.

Conformational Exploration of Enflurane in Solution and in a Biological Environment

Enflurane is a fluorinated volatile anesthetic, whose bioactive conformation is not known. Actually, a few studies have reported on the conformations of enflurane in nonpolar solution and gas phase. The present computational and spectroscopic (infrared and NMR) work shows that three pairs of isoenergetic conformers take place in the gas phase, neat liquid, polar, and nonpolar solutions. According to docking studies, a single conformation is largely preferred over its isoenergetic isomers to complex with the active site of Integrin LFA-1 enzyme (PDB code: 3F78 ), where the widely used anesthetic isoflurane (a constitutional isomer of enflurane) is known to bind. Weak hydrogen bonding from an electrostatic interaction between the CHF2 hydrogen and the central CF2 fluorines was not found to rule the conformational isomerism of enflurane. Moreover, intramolecular interactions based on steric, electrostatic, and hyperconjugative effects usually invoked to describe the anomeric effect are not responsible for the possible bioactive conformation of enflurane, which is rather governed by the enzyme induced fit.

Applications of Fluorine in Medicinal Chemistry

The role of fluorine in drug design and development is expanding rapidly as we learn more about the unique properties associated with this unusual element and how to deploy it with greater sophistication. The judicious introduction of fluorine into a molecule can productively influence conformation, pKa, intrinsic potency, membrane permeability, metabolic pathways, and pharmacokinetic properties. In addition, (18)F has been established as a useful positron emitting isotope for use with in vivo imaging technology that potentially has extensive application in drug discovery and development, often limited only by convenient synthetic accessibility to labeled compounds. The wide ranging applications of fluorine in drug design are providing a strong stimulus for the development of new synthetic methodologies that allow more facile access to a wide range of fluorinated compounds. In this review, we provide an update on the effects of the strategic incorporation of fluorine in drug molecules and applications in positron emission tomography.

Inter- and intramolecular CF···C=O interactions on aliphatic and cyclohexane carbonyl derivatives

Weak inter- and intra- molecular C(δ+)F(δ-)···C(δ+)=O(δ-) interactions were theoretically evaluated in 4 different sets of compounds at different theoretical levels. Intermolecular CH3F···C=O interactions were stabilizing by about 1 kcal mol(-1) for various carbonyl containing functional groups. Intramolecular CF···C=O interactions were also detected in aliphatic and fluorinated cyclohexane carbonyl derivatives. However, the stabilization provided by intramolecular CF···C=O interactions was not enough to govern the conformational preferences of compounds 2-4.

Does intramolecular hydrogen bond play a key role in the stereochemistry of α- and β-D-glucose?

Four α- and three β-isomers of the d-glucose were optimized in gas phase using ab initio (MP2) and DFT (ωB97X-D) methods, both using the aug-cc-pVDZ basis set. While earlier works suggest that the orientation of the hydroxyl groups is due to intramolecular hydrogen bonds (H-bonds), the present study reveals that most H-bonds forming five-membered rings are either weak or even do not exist. The quantum theory of atoms in molecules (QTAIM) analysis showed only a few cases of H-bond in d-glucose, particularly for those H-bonds forming six-membered rings, while the non-covalent interactions (NCI) analysis indicated that most intramolecular H-bonds are not strong enough to justify the counter-clockwise arrangement of the OH⋯O chains. Natural bond orbital analysis supported the findings obtained from QTAIM and NCI analyses and indicated that the anomeric effect for d-glucose in the gas phase is governed by a balance of steric, electrostatic, and hyperconjugative interactions.

Significant evidence of C⋯O and C⋯C long-range contacts in several heterodimeric complexes of CO with CH3–X, should one refer to them as carbon and dicarbon bonds!

An illustrated example of a ‘dicarbon bond’ formed between a pair of two carbon atoms of the OC⋯CH₃–Cl₃intermolecular complex, one corresponding to the methylated carbon in 1,1,1-trichloro-ethane (CH₃–Cl₃) and one to the carbon in the carbon dioxide (CO) molecule.

Conformational analysis and intramolecular interactions in monosubstituted phenylboranes and phenylboronic acids

A ^1TSJ_F,H(O) coupling pathway, dictated by a hydrogen bond, in some 2-fluorobenzoic acids has been observed, while such an interaction does not occur in 2-fluorophenol. Thus, this work reports the conformational analysis of 2-fluorophenylboronic acid (1), in order to evaluate a possible intramolecular OH∙∙∙F hydrogen bond in comparison to an n_F→p_B interaction, which mimics the quantum n_F→σ*_OH hydrogen bond that would be expected in 2-fluorophenol. 2-Fluorophenylborane (3), which does not experience hydrogen bonding, was used to verify whether n_F→p_B interaction governs the conformational equilibrium in 1 due to a predominant OH∙∙∙F hydrogen bond or to other effects. A series of 2-X-phenylboranes (X = Cl, Br, NH₂, PH₂, OH and SH) were further computationally analyzed to search for electron donors to boron, capable of influencing the conformational equilibrium. Overall, the intramolecular OH∙∙∙F hydrogen bond in 1 is quite stabilizing and dictates the ^1hJ_F,H(O) coupling constant. Moreover, electron donation to the empty p orbital of boron (for noncoplanar BH₂ moiety relative to the phenyl ring) is also significantly stabilizing for the NH₂ and PH₂ derivatives, but not enough to make the corresponding conformers appreciably populated, because of steric effects and the loss of π_CC→p_B resonance. Thus, the results found earlier for 2-fluorophenol about the lack of intramolecular hydrogen bonding are now corroborated.

The electronic origin of unusually large (n)J(FN) coupling constants in some fluoroximes

SOPPA(CCSD) calculations show that the FC term is the most important contribution to the through-space transmission of JFN coupling constants for the fluoroximes studied in this work. Because of the well-known behavior of FC term, a new rationalization for the experimental (TS)JFN SSCC is presented. It is mainly based on the overlap matrix (Sij) between fluorine and nitrogen lone pairs obtained from NBO analyses. An expression is proposed to take into account the influence of the electronic density (Dij) between coupled nuclei as well as the s% character at the site of the coupling nuclei of bonds and non-bonding electron pairs involved in Dij. In using this approach, a linear correlation between (TS)JFN versus Dij is obtained. The most important aspect of this rationalization is related to the facility for understanding the behavior of some unusual experimental coupling constants. It is shown that, at least in this case, the electronic origin of the so-called through-space coupling is transmitted through to the overlap of orbitals on the coupled atoms, suggesting that, at least for these compounds, instead of through-space coupling, it should better be dubbed as 'through overlapping orbital coupling'.

Conformational analysis, stereoelectronic interactions and NMR properties of 2-fluorobicyclo[2.2.1]heptan-7-ols

Four diastereoisomers of 2-fluorobicyclo[2.2.1]heptan-7-ols were computationally investigated by using quantum-chemical calculations, and their relative energies were analyzed on the basis of stereoelectronic interactions, particularly the presence or otherwise of the F∙∙∙HO intramolecular hydrogen bond in the syn-exo isomer. It was found through NBO and AIM analyses that such an interaction contributes to structural stabilization and that the ^1hJ_F,H(O) coupling constant in the syn-exo isomer is modulated by the n_F→σ*_OH interaction, i.e., the quantum nature of the F∙∙∙HO hydrogen bond.

F···HO intramolecular hydrogen bond as the main transmission mechanism for (1h)J(F,H(O)) coupling constant in 2'-fluoroflavonol

Flavonoids are useful compounds in medicinal chemistry and exhibit conformational isomerism, which is ruled by intramolecular interactions. One of the main intramolecular forces governing the stability of conformations is the hydrogen bond. Hydrogen bond involving fluorine covalently bonded to carbon has been found to be rare, but it appears in 2'-fluoroflavonol, although the F···HO hydrogen bond cannot be considered the main effect governing the conformational stability of this compound. Because (19)F is magnetically active and suitable for NMR studies, the (1h)J(F,H(O)) coupling constant can be used as a probe for such an interaction in 2'-fluoroflavonol. In fact, the (1h)J(F,H(O)) coupling was computationally analyzed in this work, and the F···HO hydrogen bond was found to be its main transmission mechanism, which modulates this coupling in 2'-fluoroflavonol, rather than overlap of proximate electronic clouds, such as in 2-fluorophenol.