On the Relationship between Hydrogen Bond Strength and the Formation Energy in Resonance-Assisted Hydrogen Bonds

Effects of the aldehyde-derived ring substituent on the properties of two new bioinspired trimethoxybenzoylhydrazones: methyl vs nitro groups

N-Acylhydrazones are a versatile class of organic compounds with a diversity of potential applications. In this study, two new structure-related 3,4,5-trimethoxybenzoyl-containing N-acylhydrazones were synthesized and fully characterized, both in solution and in the solid state. The compounds differ with respect to the carbonyl precursors, i.e., 3-substituted salicylaldehydes with either a methyl or a nitro group. Single crystals of both compounds were isolated from the respective mother liquors and, in both cases, XRD confirmed the obtention of the (E)-isomer, in an anti-conformation. Computational calculations (gas and water phases) were performed in order to confirm some of the structural and vibrational aspects of the compounds. An important intramolecular H bond involving the phenolic hydroxy group and the azomethine nitrogen was identified in the solid state and seems to be maintained in solution. Moreover, the presence of the electron-withdrawing nitro substituent makes this interaction stronger. However, the contact should probably not subsist for the nitro compound under physiological conditions since the presence of this substituent significantly affects the pKa of the phenol: an apparent value of 5.68 ± 0.02 was obtained. This also impacts the basicity of the azomethine nitrogen and, as a consequence, increases the hydrazone's susceptibility to hydrolysis. Nevertheless, both compounds are stable at physiological-like conditions, especially the methyl-derived one, which qualifies them for further toxicological and activity studies, such as those involving trivalent metal ions sequestering in the context of neurodegenerative diseases.

Revealing the Reasons for Degeneration of Resonance-Assisted Hydrogen Bond on the Aromatic Platform: Calculations of Ortho-, Meta-, Para-Disubstituted Benzenes, and (Z)-(E)-Olefins

The energies of the O-H∙∙∙O=C intramolecular hydrogen bonds were compared quantitatively for the series of ortho-disubstituted benzenes and Z-isomers of olefins via a molecular tailoring approach. It was established that the hydrogen bond energy in the former series is significantly less than that in the latter one. The reason for lowering the hydrogen bond energy in the ortho-disubstituted benzenes compared to the Z-isomers of olefins is the decrease in the π-contribution to the total energy of the complex interaction, in which the hydrogen bond per se is enhanced by the resonance effect. By the example of the para- and meta-disubstituted benzenes, as well as E-isomers of olefins, it was explicitly shown that the aromatic ring is a much poorer conductor of the resonance effect compared to the double bond. The hydrogen bond in the ortho-disubstituted benzenes has a lower energy than a typical resonance-assisted hydrogen bond because the aromatic moiety cannot properly assist the hydrogen bond with a resonance effect. Thus, a hydrogen bond on an aromatic platform should fall into a special category, namely an aromaticity-assisted hydrogen bond, which is closer by nature to a simple hydrogen bond rather than to a resonance-assisted one.

Self Cycloaddition of o-Naphthoquinone Nitrosomethide to (±) Spiro{naphthalene(naphthopyranofurazan)}-one Oxide: An Insight into its Formation

2-Hydroxy-1-naphthaldehyde oxime was oxidized by AgO (or Ag2 O), in presence of N-methyl morpholine N-oxide (NMMO), to the title spiro adduct-dimer (±)-Spiro{naphthalene-1(2H),4'-(naphtho[2',1':2,3]pyrano[4,5-c]furazan)}-2-one-11'-oxide by a Diels-Alder(D-A) type self-cycloaddition, through the agency of an o-naphthoquinone nitrosomethide (o-NQM). Moreover, 2-hydroxy-8-methoxy-1-naphthaldehyde oxime was prepared and subjected to the same oxidation conditions. Its sterically guided result, 9-methoxynaphtho[1,2-d]isoxazole, was isolated, instead of the expected spiro adduct. The peri intramolecular H bonding in the oxime is considered to have a key contribution to the outcome. Geometry and energy features of the oxidant- and stereo-guided selectivity of both oxidation outcomes have been explored by DFT, perturbation theory and coupled cluster calculations. The reaction free energy of the D-A intermolecular cycloaddition is calculated at -82.0 kcal/mol, indicating its predominance over the intramolecular cyclization of ca. -37.6 kcal/mol. The cycloaddition is facilitated by NMMO through dipolar interactions and hydrogen bonding with both metal complexes and o-NQM. The 8(peri)-OMe substitution of the reactant oxime sterically impedes formation of the spiro adduct, instead it undergoes a more facile cyclodehydration to the isoxazole structure by ca. 4.9 kcal/mol.

A QCT View of the Interplay between Hydrogen Bonds and Aromaticity in Small CHON Derivatives

The somewhat elusive concept of aromaticity plays an undeniable role in the chemical narrative, often being considered the principal cause of the unusual properties and stability exhibited by certain π skeletons. More recently, the concept of aromaticity has also been utilised to explain the modulation of the strength of non-covalent interactions (NCIs), such as hydrogen bonding (HB), paving the way towards the in silico prediction and design of tailor-made interacting systems. In this work, we try to shed light on this area by exploiting real space techniques, such as the Quantum Theory of Atoms in Molecules (QTAIM), the Interacting Quantum Atoms (IQA) approaches along with the electron delocalisation indicators Aromatic Fluctuation (FLU) and Multicenter (MCI) indices. The QTAIM and IQA methods have been proven capable of providing an unbiased and rigorous picture of NCIs in a wide variety of scenarios, whereas the FLU and MCI descriptors have been successfully exploited in the study of diverse aromatic and antiaromatic systems. We used a collection of simple archetypal examples of aromatic, non-aromatic and antiaromatic moieties within organic molecules to examine the changes in π delocalisation and aromaticity induced by the Aromaticity and Antiaromaticity Modulated Hydrogen Bonds (AMHB). We observed fundamental differences in the behaviour of systems containing the HB acceptor within and outside the ring, e.g., a destabilisation of the rings in the former as opposed to a stabilisation of the latter upon the formation of the corresponding molecular clusters. The results of this work provide a physically sound basis to rationalise the strengthening and weakening of AMHBs with respect to suitable non-cyclic non-aromatic references. We also found significant differences in the chemical bonding scenarios of aromatic and antiaromatic systems in the formation of AMHB. Altogether, our investigation provide novel, valuable insights about the complex mutual influence between hydrogen bonds and π systems.

Conformational preferences and intramolecular hydrogen bonding patterns of tetraflavaspidic acid BBBB – a tetrameric acylphloroglucinol

Tetraflavaspidic acid BBBB is a tetrameric acylphloroglucinol of natural origin isolated from Dryopteris aitoniana. Its molecule consists of four acylphloroglucinol units linked by methylene bridges and having the same R = propyl in their R−C=O groups. In one of the terminal monomers, one of the OHs ortho to R−C=O is replaced by a keto O. The paper reports the results of a conformational study performed at the HF/6-31G(d,p) and DFT/B3LYP/6-31+G(d,p) levels; two options are utilised for the latter, without and with the inclusion of the Grimme’s dispersion correction. Given the importance of intramolecular hydrogen bonds (IHBs) for the stabilisation of acylphloroglucinol conformers, only conformers containing the maximum IHBs’ number were calculated. The IHBs comprise an IHB between the sp2 O of R−C=O and a neighbouring OH in each monomeric unit and two inter-monomer IHBs between each pair of units. The single C−C bonds of the methylene bridges enable a variety of mutual orientations of the monomeric units, giving rise to a variety of conformations and IHB patterns. The results indicate greater stability for conformers in which individual monomers take lower energy conformations, and significant influence of the dispersion correction on the estimation of the energetics and of other molecular properties. The inclusion of the dispersion correction also strongly limits the number of low energy conformers. The influence of dispersion effects is consistent with the presence of four aromatic rings.

Malonaldehyde-like Systems: BeF2 Clusters—A Subtle Balance between Hydrogen Bonds, Beryllium Bonds, and Resonance

The stability of malonaldehyde is governed by intramolecular hydrogen bonds (IMHBs) as well as in malonaldehyde-like systems where oxygen is replaced by N or S at any of the basic sites. As beryllium bonds have been shown to strongly cooperate with hydrogen bonds, this work explores at the high level ab initio G4 level of theory the effect of including this non-covalent interaction in the system through its association with BeF2. Although malonaldehyde follows the expected trends, where the formation of a pseudocyclic form is favored also when IMHB and Be bonds are present, the subtle balance between both non-covalent interactions leads to some surprising results when other heteroatoms are involved, to the point that interaction energies can be much larger than expected or even cyclization is not favored. A complete analysis using different computational tools gives an answer to those cases escaping the predictable trends.

Proton leap: shuttling of protons onto benzonitrile

The detailed description of chemical transformations in the interstellar medium allows deciphering the origin of a number of small and medium - sized organic molecules. We present density functional theory analysis of proton transfer from the trihydrogen cation and the ethenium cation to benzonitrile, a recently discovered species in the Taurus Molecular Cloud 1. Detailed energy transformations along the reaction paths were analyzed using the interacting quantum atoms methodology, which elucidated how the proton carrier influences the lightness to deliver the proton to benzonitrile's nitrogen atom. The proton carriers' deformation energy represents the largest destabilizing effect, whereas a proton's promotion energy, the benzonitrile-proton Coulomb attraction, as well as non-classical benzonitrile-proton and carrier-proton interaction are the dominant stabilizing energy components. As two ion-molecule reactions proceed without energy barriers, rate constants were estimated using the classical capture theory and were found to be an order of magnitude larger for the reaction with the trihydrogen cation compared to that with the ethenium cation (∼10^-8 and 10^-9 cm³ s^-1, respectively). These results were obtained both with quantum chemical and ab initio molecular dynamics simulations (the latter performed at 10 K and 100 K), confirming that up to 100 K both systems choose energetically undemanding routes by tracking the corresponding minimum energy paths. A concept of a turning point is introduced, which is an equivalent to the transition state in barrierless reactions.

Correlation Effects in Trimeric Acylphloroglucinols

Trimeric acylphloroglucinols (T-ACPLs) are a subclass of the large class of acylphloroglucinols—derivatives of 1,3,5-trihydroxybenzene containing an R–C=O group. T-ACPL molecules contain three acylphloroglucinol moieties linked by methylene bridges. Many of them are present in natural sources and exhibit biological activities, often better than the corresponding activities of monomeric acylphloroglucinols. All the stable conformers of T-ACPLs contain seven intramolecular hydrogen bonds, which constitute the dominant stabilising factors. A total of 38 different T-ACPLs, including both naturally occurring and model molecules, have been calculated at the HF and DFT/B3LYP levels. The DFT/B3LYP calculations were carried out both without and with Grimme’s dispersion correction, to highlight the dispersion (and, therefore, also electron correlation) effects for these molecules. The roles of dispersion are evaluated considering the effects of Grimme’s correction on the estimation of the conformers’ energies, the description of the characteristics of the individual hydrogen bonds, the conformers’ geometries and other molecular properties. Overall, the results offer a comprehensive overview of the conformational preferences of T-ACPL molecules, their intramolecular hydrogen bond patterns, and the correlation effects on their properties.

Intramolecular Hydrogen Bonding 2021

Undoubtedly, hydrogen bonds occupy a leading place in the rich world of intermolecular interactions [...].