Conformational Landscape of α-Halopropiophenones Determined by nJC-H NMR Reveals Unexpected Patterns and Geometric Constraints.

The conformational features of α-halopropiophenones were investigated to understand the influence of α-halogens on conformation through hyperconjugative interactions, electrostatics, and steric factors. Using NMR, C-H scalar coupling constants were measured in different solvents, revealing a pattern in the conformational equilibria, which we validated by computational means. This behavior arises largely from hyperconjugative effects with the exception of the fluoro-derivatives, which are also influenced by steric and electrostatic interactions. In all cases, the contribution to hyperconjugation of the α-halo ketones is driven by the oxygen lone pair (rather than the C-X bond), which donates electron density to the adjacent C-C bonds. Additionally, C-Cα bond rotation generates distortions in the side chain, responsible for destabilization, thus affecting system conjugation. These structural features identified for the α-halo ketones are also reflected in their reactivity, which is distinct from that expected for nucleophilic addition.

Structural basis for the binding of the cancer targeting scorpion toxin, ClTx, to the vascular endothelia growth factor receptor neuropilin-1.

Chlorotoxin (ClTx) is a 36-residue disulfide-rich peptide isolated from the venom of the scorpion Leiurus quinquestriatus. This peptide has been shown to selectively bind to brain tumours (gliomas), however, with conflicting reports regarding its direct cellular target. Recently, the vascular endothelial growth factor receptor, neuropilin-1 (NRP1) has emerged as a potential target of the peptide. Here, we sought to characterize the details of the binding of ClTx to the b1-domain of NRP1 (NRP1-b1) using solution state nuclear magnetic resonance (NMR) spectroscopy. The 3D structure of the isotope labelled peptide was solved using multidimensional heteronuclear NMR spectroscopy to produce a well-resolved structural ensemble. The structure points to three putative protein-protein interaction interfaces, two basic patches (R14/K15/K23 and R25/K27/R36) and a hydrophobic patch (F6/T7/T8/H10). The NRP1-b1 binding interface of ClTx was elucidated using 15N chemical shift mapping and included the R25/K27/R36 region of the peptide. The thermodynamics of binding was determined using isothermal titration calorimetry (ITC). In both NMR and ITC measurements, the binding was shown to be competitive with a known NRP1-b1 inhibitor. Finally, combining all of this data we generate a model of the ClTx:NRP1-b1 complex. The data shows that the peptide binds to the same region of NRP1 that is used by the SARS-CoV-2 virus for cell entry, however, via a non-canonical binding mode. Our results provide evidence for a non-standard NRP1 binding motif, while also providing a basis for further engineering of ClTx to generate peptides with improved NRP1 binding for future biomedical applications.

Conformational Isomerism of 3-Chalcogenomethyl-N-Methyl-2-Pyrrolidinones: Insights from NMR Spectroscopy and Molecular Modeling.

A conformational analysis of N-methyl-2-pyrrolidinone 3-substituted by methoxyl, thiomethoxyl, and selenomethoxyl is reported by means of 1H nuclear magnetic resonance spectroscopy and electronic structure calculations. The five-membered ring has an envelope conformation with the α-carbonyl substituent being able to assume two positions: pseudo-axial and pseudo-equatorial. In vacuum, the calculations pointed to the pseudo-axial conformer as the most stable one, and this preference increases with the size of the substituent and a decrease in its electronegativity. Natural bond orbital analysis evidenced the importance of electron delocalization on the stability, and a principal component of analysis (PCA) plot of the hyperconjugative interactions revealed the main ones. Steric and electrostatic effects were also investigated by energy decomposition analysis.

Improving the Sensitivity of FESTA Methods for the Analysis of Fluorinated Mixtures.

The analysis of complex mixtures is an important but often intractable problem. When species contain sparse fluorine atoms, NMR spectra of fluorine-containing spin systems can be efficiently extracted from an intact mixture using the recently proposed FESTA (Fluorine-Edited Selective TOCSY Acquisition) methodology. Here an alternative approach to the existing selective reverse INEPT FESTA (SRI-FESTA) experiment is described, based on the use of a modulated spin echo for the initial excitation. MODO-FESTA (modulated echo FESTA) is simpler and has a significant sensitivity advantage over SRI-FESTA. Comparisons are presented of the relative sensitivity and spectral purity of the two types of methods.

Dealing with Hydrogen Bonding on the Conformational Preference of 1,3-Aminopropanols: Experimental and Molecular Dynamics Approaches.

This study expands the knowledge on the conformational preference of 1,3-amino alcohols in the gas phase and in solution. By employing Fourier transform infrared spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, density functional theory (DFT) calculations, quantum theory of atoms in molecules (QTAIM), natural bond orbital (NBO) analysis, and molecular dynamics (MD), the compounds 3-aminopropan-1-ol (1), 3-methylaminopropan-1-ol (2), and 3-dimethylaminopropan-1-ol (3) are evaluated. The results show that the most stable conformation of each compound in the gas phase and in nonpolar solvents exhibited an O-H···N intramolecular hydrogen bond (IHB). Based on the experimental and theoretical OH-stretching frequencies, the IHB becomes stronger from 1 to 3. In addition, from the experimental NMR J-couplings, the IHB conformers are predominant in nonbasic solvents, representing 70-80% of the conformational equilibrium, while in basic solvents, such conformers only represent 10%. DFT calculations and QTAIM analysis in the gas phase support the occurrence of IHBs in these compounds. The MD simulation indicates that the non-hydrogen-bonded conformers are the lowest energy conformations in the solution because of molecular interactions with the solvent, while they are absent in the implicit solvation model based on density. NBO analysis suggests that methyl groups attached on the nitrogen atom affect the charge transfer energy involved in the IHB. This effect occurs mostly because of a decrease in the s-character of the LPN orbital along with weakening of the charge transfer from LPN to σ*OH, which is caused by an increase in the C-C-N bond angle.

Strong hyperconjugative interactions limit solvent and substituent influence on conformational equilibrium: the case of cis-2-halocyclohexylamines.

The presence of strong stereoelectronic interactions involving the substituents in cis-2-substituted cyclohexanes may lead to results different from those expected. In this work, we studied the conformational behavior of cis-2-fluoro- (F), cis-2-chloro- (Cl), cis-2-bromo- (Br) and cis-2-iodocyclohexylamine (I) by dynamic NMR and theoretical calculations. The experimental data pointed to an equilibrium strongly shifted toward the ea conformer (equatorial amine group and axial halogen), with populations greater than 90% for F, Cl and Br in both dichloromethane-d 2 and methanol-d 4. Theoretical calculations (M06-2X/6-311++G(2df,2p)) were in agreement with the experimental, with no influence of the solvent or the halogen on the equilibrium. A principal component analysis of natural bond orbital energies pointed to the σ*C-X and σC-H orbitals and the halogen lone pairs (LPX) as the most significant for the hyperconjugative interactions that influenced the equilibrium. The σC-H → σ*C-X hyperconjugation and the interactions involving the LPX counterbalance each other, explaining the non-influence of the halogen on the conformational equilibrium. These interactions are responsible for the strong preference for the ea conformer in cis-2-halocyclohexylamines, being strong enough to restrain the shift in the equilibrium due to other factors such as steric repulsion or solvent effects.

Revealing the Conformational Preferences of Proteinogenic Glutamic Acid Derivatives in Solution by 1H NMR Spectroscopy and Theoretical Calculations.

The conformational preferences of proteinogenic glutamic acid esterified (GluOMe) and N-acetylated (AcGluOMe) derivatives have been determined in solution for the first time. Theoretical calculations at the ωB97X-D/aug-cc-pVTZ made possible the assignment of six and eight stable conformers for GluOMe and AcGluOMe, respectively. The conformational equilibrium of the studied compounds was evaluated in different organic solvents using a combination of the integral equation formalism polarizable continuum model (IEF-PCM) and 1H NMR spectroscopy data. The results showed that the conformational equilibrium of both derivatives change in the presence of solvent. According to the quantum theory of atoms in molecules (QTAIM), non-covalent interactions (NCI), and natural bond orbitals (NBO) analyses, the conformational preferences observed for GluOMe and AcGluOMe are not dictated by the presence of a specific interaction but are due to a combination of hyperconjugative and steric effects.

FESTA: An Efficient Nuclear Magnetic Resonance Approach for the Structural Analysis of Mixtures Containing Fluorinated Species.

In complex mixtures, proton nuclear magnetic resonance (NMR) spectra are often very crowded, making spectral analysis complicated or even impossible, particularly when detailed structural information about the mixture components is needed. A new 1D NMR method (fluorine-edited selective TOCSY acquisition, FESTA) is introduced that facilitates the structural analysis of mixtures of species that contain fluorine. It allows simplified 1H spectra to be obtained that show only those protons that are in a spin system coupled to fluorine of interest. The new method is illustrated by factorizing a complex 1H spectrum into subspectra for individual spin systems involving different 19F sites.

The Antagonist Effect of Nitrogen Lone Pair: 3 JHF versus 5 JHF.

The long-range scalar coupling constant between proton and fluorine nuclei, 5 JHF , is observed to be larger than 3 JHF in the pyrimidinyl moiety of voriconazole. A set of smaller molecules is chosen (fluorobenzene, N-methyl-2-fluoropyridine, N-methyl-3-fluoropyridine, 3-fluoropyridine, 5-pyrimidine, and 2-fluoropyridine) to evaluate the influence of the nitrogen atom in the experimental JHF values. Spectral aliased pure shift heteronuclear single quantum coherence spectroscopy (SAPS-HSQC) is applied to determine the relative sign between the JCF and JHF scalar couplings. Theoretical calculations show that the 3 JHF and 5 JHF coupling constants can be described mainly by a Fermi contact (FC) transmission mechanism. A decomposition analysis of JHF in terms of localized molecular orbital (LMO) contributions allows us to determine that the interaction involving the nitrogen lone pair (LPN) is the main reason for the larger 5 JHF compared to 3 JHF . Our analysis indicates that delocalization of LPN has a positive contribution to the long-range coupling, while a negative one is observed for 3 JHF .

Conformational study of L-methionine and L-cysteine derivatives through quantum chemical calculations and 3JHH coupling constant analyses.

The understanding of the conformational behavior of amino acids and their derivatives is a challenging task. Here, the conformational analysis of esterified and N-acetylated derivatives of L-methionine and L-cysteine using a combination of 1H NMR and electronic structure calculations is reported. The geometries and energies of the most stable conformers in isolated phase and taking into account the implicit solvent effects, according to the integral equation formalism polarizable continuum model (IEF-PCM), were obtained at the ωB97X-D/aug-cc-pVTZ level. The conformational preferences of the compounds in solution were also determined from experimental and theoretical 3JHH coupling constants analysis in different aprotic solvents. The results showed that the conformational stability of the esterified derivatives is not very sensitive to solvent effects, whereas the conformational equilibrium of the N-acetylated derivatives changes in the presence of solvent. According to the natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM) and noncovalent interactions (NCI) methodologies, the conformational preferences for the compounds are not dictated by intramolecular hydrogen bonding, but by a joint contribution of hyperconjugative and steric effects.

Trends of intramolecular hydrogen bonding in substituted alcohols: a deeper investigation.

Intramolecular hydrogen bonding (IAHB) is one of the most important intramolecular interactions and a critical element in adopted molecular arrangements. Moreover, slight substitution in a molecule can affect its strength to a great extent. It is well established that alkyl groups play a positive role in IAHB strength. However, the effects that drive it are specific to each system. To investigate the influence of IAHB and its strength dependency on different acyclic compounds, the conformational preferences of propane-1,3-diol, 3-methoxypropan-1-ol, 3-ethoxypropan-1-ol, 3-isopropoxypropan-1-ol, 3-(tert-butoxy)propan-1-ol, butane-1,3-diol, 3-methoxybutan-1-ol, 3-methylbutane-1-diol, and 3-methoxy-3-methylbutan-1-ol were evaluated experimentally using infrared spectroscopy theoretically supported by topological and natural bond orbital analyses. The most stable conformation of each compound exhibited IAHB and these conformers are more populated in the equilibrium for all studied compounds. Experimental infrared and topological data suggest that the strength of IAHB increases for each methyl group addition. NBO analyses indicate that methyl groups in different positions related to an OH moiety affect the charge transfer energy involved in intramolecular hydrogen bonding. This occurs mostly due to an increase in the spn-hybridized lone pair (LP1O) contribution to the charge transfer , which is a result of changes in s-character and orbital energy caused by geometrical rearrangements, rehybridization, and/or electronic effects.

Combined Utilization of 1H NMR, IR, and Theoretical Calculations To Elucidate the Conformational Preferences of Some l-Histidine Derivatives.

The conformational preferences of amino acids and their derivatives have been the subject of many investigations, because protein folding pathways that determine three-dimensional geometries are primarily restricted by the conformational space of each amino acid residue. Here we systematically describe the conformational behavior of l-histidine methyl ester (His-OMe) and its N-acetylated derivative (Ac-His-OMe) in the isolated phase and in solution. To this end, we employed spectroscopic techniques (1H NMR and IR), supported by quantum chemical calculations. Initially, the energetically favorable conformers, their energies, and structural properties obtained by density functional theory (DFT) and Møller-Plesset perturbation theory (MP2) calculations in the isolated phase and in solution via the implicit solvation model IEF-PCM were presented. Next, experimental 3JHH spin-spin coupling constants obtained in different aprotic nonpolar and polar solvents were compared with the theoretically predicted ones for each conformer at the IEF-PCM/ωB97X-D/EPR-III level. A joint analysis of these data allowed the elucidation of the conformational preferences of the compounds in solution. Infrared data were also employed as a complement to estimate the His-OMe conformer populations. Finally, the quantum theory of atoms in molecules (QTAIM), the noncovalent interactions (NCI), and the natural bond orbitals (NBO) analyses were used to determine the intramolecular interactions that govern the relative conformational stabilities.

Tautomerism in 8-Nitroguanosine Studied by NMR and Theoretical Calculations.

The guanine base in DNA, due to its low oxidation potential, is particularly sensitive to chemical modifications. A large number of guanine lesions have been characterized and studied in some detail due to their relationship with tissue inflammations. Nevertheless, one example of these lesions is the formation of 8-nitro-guanosine, but the NMR data of this compound was only partially interpreted. A comprehensive study of the two possible tautomeric forms, through a detailed characterization of this compound, has implications for its base pairing properties. The target compound was obtained through a synthetic sequence of five steps, where all intermediates were fully characterized using spectral data. The analysis of the two tautomers was then evaluated through NMR spectroscopy and theoretical calculations of the chemical shifts and NH coupling constants, which were also compared with the data from guanosine.

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.

Particularly strong C-H···π interactions between benzene and all-cis 1,2,3,4,5,6-hexafluorocyclohexane.

We present the first high-level ab initio benchmark study of the interaction energy between fluorocyclohexanes and benzene. These compounds form CH···π interactions with aromatic solvents which causes notable shielding of the axial cyclohexane protons. For the recently synthesised all-cis 1,2,3,4,5,6-hexafluorocyclohexane the interaction energy with benzene amounts to -7.9 kcal mol(-1) and -6.4 kcal mol(-1) at the MP2 and SCS-MP2 levels, respectively (extrapolated to the complete basis set limit), which according to dispersion-corrected density functional calculations, is largely due to dispersion.

Understanding the conformational behaviour of Ac-Ala-NHMe in different media. A joint NMR and DFT study.

The conformational behaviour of Ac-Ala-NHMe was studied in the gas-phase and in solution by theoretical calculations (B3LYP-D3/aug-cc-pVDZ level) and experimental (1)H NMR. The conformational preferences of this compound were shown to result from a complex interplay between the strengths of possible intramolecular hydrogen bonds, steric interactions, hyperconjugation, entropy effects and the overall dipole moments. The Ac-Ala-N(Me)2 derivative was studied in addition, to design a system akin to Ac-Ala-NHMe, but with disrupted intramolecular hydrogen bonds involving the -NHMe group, mimicking the effect of polar protic solvents.

NMR spectroscopy and theoretical calculations in the conformational analysis of 1-methylpyrrolidin-2-one 3-halo-derivatives.

This study reports the results of ab initio and density functional theory (DFT) electronic structure calculations as well as (3)J(HH) experimental and calculated coupling constant data obtained in the investigation of the conformational equilibrium of 3-halo-derivatives of 1-methylpyrrolidin-2-one. The five-membered ring assumes an envelope conformation owing to the plane of formation of the O═C-N-R bond, with C4 forming the "envelope lid". When the conformation changes, the "lid" alternates between positions above and below the amide plane. The α-carbonyl halogen assumes two positions: a pseudo-axial and a pseudo-equatorial. In the gaseous phase, the calculations indicate that the pseudo-axial conformer is more stable and preferable going down the halogen family. Natural bond orbital analysis showed that electronic delocalization is significant only for the iodo derivative. In the other derivatives, the electrostatic repulsion between oxygen and the halogen determines the conformational equilibrium. When the solvated molecule was taken into account, the pseudo-equatorial conformer population increased with the relative permittivity of the solvent. This variation was strong in the fluoro derivative, and the preference was inverted. In the chlorine derivative, the two populations became closer in methanol and acetonitrile. In the bromine and iodine derivatives, the percentage of pseudo-equatorial conformer increased only slightly owing to the dipole moment of the conformation: the pseudo-equatorial conformation has a greater dipole moment and thus is stable in media with high relative permittivity.

The conformational analysis of 2-halocyclooctanones.

The establishment of the most stable structures of eight membered rings is a challenging task to the field of conformational analysis. In this work, a series of 2-halocyclooctanones were synthesized (including fluorine, chlorine, bromine and iodine derivatives) and submitted to conformational studies using a combination of theoretical calculation and infrared spectroscopy. For each compound, four conformations were identified as the most important ones. These conformations are derived from the chair-boat conformation of cyclooctanone. The pseudo-equatorial (with respect to the halogen) conformer is preferred in vacuum and in low polarity solvents for chlorine, bromine and iodine derivatives. For 2-fluorocyclooctanone, the preferred conformation in vacuum is pseudo-axial. In acetonitrile, the pseudo-axial conformer becomes the most stable for the chlorine derivative. According to NBO calculations, the conformational preference is not dictated by electron delocalization, but by classical electrostatic repulsions.