Condensed-phase relative Gibbs free energy and E/Z descriptors for 2-acetylthiophene and 2-acetylthiophene-N1-phenyl thiosemicarbazones.

Thiosemicarbazones (TSCs) encompasses a class of compounds relevant in the pharmacological context. Their specific applicability varies in function of the appropriated chemical modification and their binding to different transition metals. In the present work, we apply current standards functionals, B3LYP and B97D, with triple zeta basis set quality, 6-311++G(d,p), to investigate the relative stability of the various possible spatial arrangements for 2-acetylthiophene and 2-acetylthiophene-N1-phenyl thiosemicarbazones, denoted ATTSC and ATTSC-Ph, respectively.

The Role of Intramolecular Interactions on the Bioactive Conformation of Epinephrine.

The structure of bioactive compounds inside their biological target is mainly dictated by the intermolecular interactions present in the binding side, whereas intramolecular interactions are responsible for the structure of an isolated molecule. Accordingly, this work reports the relative significance of these interactions for the bioactive conformation of the N-protonated epinephrine. The crystallized structure of epinephrine has a gauche orientation of the O-C-C-N torsion angle.

Influence of stereoelectronic effects on the J spin-spin coupling constant in fluorinated heterocyclic compounds.

The Perlin effect and its analog for fluorinated compounds (the fluorine Perlin-like effect) manifest on one-bond C─H (C─F for the fluorine Perlin-like effect) spin-spin coupling constants (SSCCs) in six-membered rings. These effects can be useful to probe the stereochemistry (axial or equatorial) of the C─H and C─F bonds, respectively. The origin of these effects has been debatable in the literature as being due to hyperconjugative interactions, dipolar effects, and induced current density.

Infrared Fingerprints of n → σ* Hyperconjugation in Hydrazides.

An earlier study demonstrated that hyperconjugation operates in hydrazides by analyzing the N-H stretching mode in gas phase infrared (IR) spectroscopy, and then observing two very distinct bands corresponding to isolated isomers experiencing or not the n → σ* electron delocalization. The present work reports a chemical method to obtain insight on the hyperconjugation in hydrazide derivatives from solution IR spectroscopy. The analogous amides did not show a ν red-shifted band, as the electron donor orbital in the above hyperconjugative interaction does not exist.

Theoretical study on the anomeric effect in α-substituted tetrahydropyrans and piperidines.

Conformational effects, including some controversial examples, have been reported in this work for 2-substituted tetrahydropyrans and piperidines, and for the respective protonated compounds [substituent = F, OH, OCH, NH, NHCH and N(CH)]. Hyperconjugation plays a major role in most cases, either due to endo or exo-anomeric interactions, especially when nitrogen is the electron donor to an antiperiplanar σ* orbital. This interaction also seems to contribute for the Perlin and reverse fluorine Perlin-like effects, which are related to the relative magnitude of J and J coupling constants, respectively, in axial and equatorial conformers.

Conformational impact of structural modifications in 2-fluorocyclohexanone.

2-Haloketones are building blocks that combine physical, chemical and biological features of materials and bioactive compounds, while organic fluorine plays a fundamental role in the design of performance organic molecules. Since these features are dependent on the three-dimensional chemical structure of a molecule, simple structural modifications can affect its conformational stability and, consequently, the corresponding physicochemical/biological property of interest. In this work, structural changes in 2-fluorocyclohexanone were theoretically studied with the aim at finding intramolecular interactions that induce the conformational equilibrium towards the axial or equatorial conformer.

Theoretical Study on the Conformational Bioeffect of the Fluorination of Acetylcholine.

There has been an increasing interest in the study of fluorinated derivatives of gamma-aminobutyric acid (GABA), an acetylcholine (AC) analog. This work reports a theoretical study on the effect of an α-carbonyl fluorination in AC, aiming at understanding the role of a distant fluorine relative to the positively charged nitrogen on the conformational folding of the resulting fluorinated AC. In addition, the chemical and structural changes were evaluated on the basis of ligand-enzyme (acetylcholinesterase) interactions.

The mutual effect of a carbonyl polar bond and an endocyclic oxygen on the J coupling constant of fluorinated six-membered rings.

The J coupling constant can be useful to probe the conformational landscape of organofluorine compounds and the intramolecular interactions governing the stereochemistry of these compounds. Neighboring oxygen electron lone pairs and a carbonyl group relative to a C─F bond affect this coupling constant in an opposite way, and therefore, analysis of the interactions involving these entities simultaneously indicates which effect dominates J . Spin-spin coupling constant calculations for a series of fluorinated tetrahydropyrans, cyclohexanones, and dihydropyran-3-ones indicated that an electrostatic/dipolar interaction between the C─F and C═O bonds is more important than the steric interaction between the C─F bond and the oxygen electron lone pairs.

A halogen bond does not dictate the conformational preferences of cis-1,3-disubstituted cyclohexanes.

Halogen bonds are defined as interactions between halogens and a Lewis base in which the halogen (X) acts as the electrophilic species, and is typically explained by the presence of a σ-hole at the end of the C-X bond. Despite the important role of the halogen bond in intermolecularly interacting species, e.g.

Is conformation a fundamental descriptor in QSAR? A case for halogenated anesthetics.

An intriguing question in 3D-QSAR lies on which conformation(s) to use when generating molecular descriptors (MD) for correlation with bioactivity values. This is not a simple task because the bioactive conformation in molecule data sets is usually unknown and, therefore, optimized structures in a receptor-free environment are often used to generate the MD´s. In this case, a wrong conformational choice can cause misinterpretation of the QSAR model.

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.

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.

Endocyclic oxygen in 3-fluorodihydro-2H-pyran-4(3H)-one that does not induce the gauche effect.

2-Fluorocyclohexanone undergoes chair inversion, giving rise to axial and equatorial conformers, with the equatorial form being highly preferred in solution, for example, 87% in chloroform and 93% in methylene chloride. Modifications in the conformational preferences can modify macroscopic properties of 2-fluoro ketones. The introduction of an endocyclic oxygen in 2-fluorocyclohexanone to give 3-fluorodihydro-2H-pyran-4(3H)-one would be expected to create a gauche effect in the axial conformer along with the O-C-C-F moiety, inducing an increase of its population.

The reverse fluorine Perlin-like effect and related stereoelectronic interactions.

A similar effect to the well-known reverse Perlin effect was observed on the (1)JC-F coupling constants of α- and β-d-glucopyranosyl fluoride tetracetate, both in nonpolar and polar solution. This can be called "reverse fluorine Perlin-like effect", and it is shown to be ruled by dipolar interactions rather than by hyperconjugation. The reverse fluorine Perlin-like effect does not have a general relationship with the anomeric effect, and it can be useful to determine the structure and stereochemistry of organofluorine compounds.

Conformational analysis of 2,2-difluoroethylamine hydrochloride: double gauche effect.

The gauche effect in fluorinated alkylammonium salts is well known and attributed either to an intramolecular hydrogen bond or to an electrostatic attraction between the positively charged nitrogen and the vicinal electronegative fluorine atom. This work reports the effect of adding a fluorine atom in 2-fluoroethylamine hydrochloride on the conformational isomerism of the resulting 2,2-difluoroethylamine chloride (2). The analysis was carried out using NMR coupling constants in D2O solution, in order to mimic the equilibrium conditions in a physiological medium, in the gas phase and in implicit water through theoretical calculations.

Gauche preference of β-fluoroalkyl ammonium salts.

The strong gauche preference along with the F-C-C-N(+) fragment in 3-fluoropiperidinium cation and analogues, in the gas phase, is dictated by electrostatic interactions, which can be both hydrogen bond F···H(N(+)) and F/N(+) attraction. In aqueous solution, where most biochemical processes take place, electrostatic effects are strongly attenuated and hyperconjugation is calculated to be at least competitive with Lewis-type interactions.

The preferred all-gauche conformations in 3-fluoro-1,2-propanediol.

A competition between the terminal fluorine and hydroxyl groups by the central hydroxyl group as hydrogen bond donor in 3-fluoro-1,2-propanediol would be expected to dictate the conformational isomerism of this compound, but also the repulsion between the electronegative and bulky vicinal substituents. Indeed, an intramolecular hydrogen bond has been verified only for a local minimum using QTAIM calculations, while the most stable conformer exhibits an all-gauche conformation with a small stabilizing contribution from the nF→σ interaction. The preferred orientation of the OH and F substituents was confirmed from the chemical shifts and coupling constants of the diastereotopic hydrogens.

Conformational analysis and intramolecular interactions in monosubstituted phenylboranes and phenylboronic acids.

A (1) (TS) J 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 nF→pB interaction, which mimics the quantum nF→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 nF→pB interaction governs the conformational equilibrium in 1 due to a predominant OH∙∙∙F hydrogen bond or to other effects.

Conformational analysis and intramolecular interactions in aminofluorobenzoic acids.

Some aminofluorobenzoic acids were studied to evaluate the power of the F···HO hydrogen bond and other interactions as driving forces of the conformational isomerism of these compounds. Despite the occurrence of this hydrogen bond in the 2-fluorinated derivatives, as well as attractive O/F nonbonding interactions and NH···O═C hydrogen bond, the O/O repulsion dictates the orientation of the carboxyl group. Unlike 2-fluorophenol, which is reported to not experience a F···HO hydrogen bond, 2-fluorobenzoic acid derivatives were calculated to exhibit such interaction, but it could not be monitored experimentally by means of F/H(O) coupling constant, because of the low solubility of these compounds in nonpolar solvents, the acidity of the carboxyl hydrogen, the small population of some conformers capable of exhibiting hydrogen bond, and the solute self-association in solution, which make their conformational equilibrium different from that in gas phase.

Alkyl group effect on the conformational isomerism of trans-2-bromoalkoxycyclohexanes analyzed by nmr spectroscopy and theoretical calculations.

Suitable (3)J(H,H) coupling constants and theoretical calculations were used to define the conformational preferences of trans-2-bromoalkoxycyclohexanes (alkoxy = OMe, OEt, O(i)Pr, and O(t)Bu) for the isolated molecule and as a function of the medium. The diaxial conformer was preponderant, or at least similarly populated to the diequatorial form, for the tert-butoxy derivative only, while the diequatorial conformer was prevalent for the remaining alkoxy derivatives (except for the OMe derivative in CCl(4) solution). The conformational behavior of these compounds was analyzed on the basis of classical steric effects and attractive electron delocalizations, by means of natural bond orbital analysis.

Theoretical and infrared studies on the conformational isomerism of trans-2-bromo-alkoxycyclohexanes.

The infrared spectra of trans-2-bromo-alkoxycyclohexanes (alcoxy = OMe, OEt, O(i)Pr and O(t)Bu) were obtained for the neat liquid, and the C-Br stretching mode was quantitatively analyzed to give insight about the conformational isomerism of these compounds. Frequency calculations supported the band assignments, and the relative band intensities suggest that the diaxial conformer is prevalent for the methoxy and tert-butoxy derivatives (51 and 56%, respectively), while the diequatorial form is preponderant for the ethoxy and isopropoxy derivatives (76 and 77%, respectively). Therefore, the size of the alkoxy group plays a determinant role in determining the conformational preferences of the title compounds.