The application of Aj, BAC, I6, HOMA indexes for quantitative determination of aromaticity of metal complexes with benzoic, salicylic, nicotinic acids and benzene derivatives

Structure, bonding and adaptive aromaticity in rhenium-oxo complexes: a DFT study

The concept of adaptive aromaticity has been extended to a rhenium-oxo complex, introducing a new member into this novel family.

Plant-Derived and Dietary Hydroxybenzoic Acids-A Comprehensive Study of Structural, Anti-/Pro-Oxidant, Lipophilic, Antimicrobial, and Cytotoxic Activity in MDA-MB-231 and MCF-7 Cell Lines

Seven derivatives of plant-derived hydroxybenzoic acid (HBA)—including 2,3-dihydroxybenzoic (2,3-DHB, pyrocatechuic), 2,4-dihydroxybenzoic (2,4-DHB, β-resorcylic), 2,5-dihydroxybenzoic (2,5-DHB, gentisic), 2,6-dihydroxybenzoic (2,6-DHB, γ-resorcylic acid), 3,4-dihydroxybenzoic (3,4-DHB, protocatechuic), 3,5-dihydroxybenzoic (3,5-DHB, α-resorcylic), and 3,4,5-trihydroxybenzoic (3,4,5-THB, gallic) acids—were studied for their structural and biological properties. Anti-/pro-oxidant properties were evaluated by using DPPH^• (2,2-diphenyl-1-picrylhydrazyl), ABTS^•+ (2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), FRAP (ferric-reducing antioxidant power), CUPRAC (cupric-reducing antioxidant power), and Trolox oxidation assays. Lipophilicity was estimated by means of experimental (HPLC) and theoretical methods. The antimicrobial activity against Escherichia coli (E. coli), Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus), Bacillus subtilis (B. subtilis), Salmonella enteritidis (S. enteritidis), and Candida albicans (C. albicans) was studied. The cytotoxicity of HBAs in MCF-7 and MDA-MB-231 cell lines was estimated. Moreover, the structure of HBAs was studied by means of experimental (FTIR, ¹H, and ¹³C NMR) and quantum chemical DFT methods (the NBO and CHelpG charges, electrostatic potential maps, and electronic parameters based on the energy of HOMO and LUMO orbitals). The aromaticity of HBA was studied based on the calculated geometric and magnetic aromaticity indices (HOMA, Aj, BAC, I6, NICS). The biological activity of hydroxybenzoic acids was discussed in relation to their geometry, the electronic charge distribution in their molecules, their lipophilicity, and their acidity. Principal component analysis (PCA) was used in the statistical analysis of the obtained data and the discussion of the dependency between the structure and activity (SAR: structure–activity relationship) of HBAs. This work provides valuable information on the potential application of hydroxybenzoic acids as bioactive components in dietary supplements, functional foods, or even drugs.

Spectroscopic (FT-IR, FT-Raman, 1H- and 13C-NMR), theoretical and microbiological study of trans o-coumaric acid and alkali metal o-coumarates

This work is a continuation of research on a correlation between the molecular structure and electronic charge distribution of phenolic compounds and their biological activity. The influence of lithium, sodium, potassium, rubidium and cesium cations on the electronic system of trans o-coumaric (2-hydroxy-cinnamic) acid was studied. We investigated the relationship between the molecular structure of the tested compounds and their antimicrobial activity. Complementary molecular spectroscopic techniques such as infrared (FT-IR), Raman (FT-Raman), ultraviolet-visible (UV-VIS) and nuclear magnetic resonance (¹H- and ¹³C-NMR) were applied. Structures of the molecules were optimized and their structural characteristics were calculated by the density functional theory (DFT) using the B3LYP method with 6-311++G** as a basis set. Geometric and magnetic aromaticity indices, atomic charges, dipole moments and energies were also calculated. Theoretical parameters were compared to the experimental characteristics of investigated compounds. Correlations between certain vibrational bands and some metal parameters, such as electronegativity, ionization energy, atomic and ionic radius, were found. The microbial activity of studied compounds was tested against Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, Staphylococcus aureus, Proteus vulgaris and Candida albicans.

1H/2H and azide/tetrazole isomerizations and their effects on the aromaticity and stability of azido triazoles

DFT studies on NAzTA, AAzTA, and AzTA show –NH₂ facilitates but –NO₂ impedes 1H/2H tautomerization. AZ/TZ isomerization of molecules with –N₃ only is the easiest. 1H/2H tautomerization decreases while AZ/TZ isomerization increases the stability.

Theoretical (in B3LYP/6-3111++G** level), spectroscopic (FT-IR, FT-Raman) and thermogravimetric studies of gentisic acid and sodium, copper(II) and cadmium(II) gentisates

The DFT calculations (B3LYP method with 6-311++G(d,p) mixed with LanL2DZ for transition metals basis sets) for different conformers of 2,5-dihydroxybenzoic acid (gentisic acid), sodium 2,5-dihydroxybenzoate (gentisate) and copper(II) and cadmium(II) gentisates were done. The proposed hydrated structures of transition metal complexes were based on the results of experimental findings. The theoretical geometrical parameters and atomic charge distribution were discussed. Moreover Na, Cu(II) and Cd(II) gentisates were synthesized and the composition of obtained compounds was revealed by means of elemental and thermogravimetric analyses. The FT-IR and FT-Raman spectra of gentisic acid and gentisates were registered and the effect of metals on the electronic charge distribution of ligand was discussed.

Structure, aromaticity, stability, and energetic performance of the analogues and derivatives of s-heptazine

s-heptazine is one of the most attractive polycyclic C-N precursors for graphitic carbon nitride materials (CNx). In this paper in order to find the relationships between the structure, aromaticity, and stability for this novel compound, its analogues with three conjoint six-membered rings (I∼V) and derivatives with different substituents (VI-1∼VI-5) were investigated using the density functional theory method. Aromaticity was predicted using the magnetic criterion iso-chemical shielding surface in the Z direction (ICSSzz) obtained with the gauge-independent atomic orbital (GIAO) method. Stability was estimated by the band gap and the topological properties obtained from the atoms in molecules theory. Results show that replacement of the CH groups with the nitrogen atoms in the tricyclic core enhances both the aromaticity and the stability. s-heptazine (VI) that has the maximum number of N atoms among analogues I∼VI possesses the largest aromaticity and the best stability. Substitutions of -NH2, -NHNH2, and -N3 groups increase not only the aromaticity but also the stability; -NO2 increases the aromaticity while decreases the stability; -CN decreases both the aromaticity and the stability. Furthermore, the energetic performance of VI-1∼VI-5 was evaluated according to the estimated specific impulse (Is). The obtained Is has the order of VI-5>VI-4>VI-3>VI>VI-1>VI-2. The Is of VI-5 is higher than that of HMX (1, 3, 5, 7-tetranitro-1, 3, 5, 7-tetraazacyclooctane).

Molecular structure and spectroscopic analysis of homovanillic acid and its sodium salt--NMR, FT-IR and DFT studies

The estimation of the electronic charge distribution in metal complex or salt allows to predict what kind of deformation of the electronic system of ligand would undergo during complexation. It also permits to make more precise interpretation of mechanism by which metals affect the biochemical properties of ligands. Theinfluence ofsodium cation on the electronic system of homovanillic acid was studied in this paper. Optimized geometrical structures of studied compounds were calculated by B3LYP/6-311++G(**) method. Mulliken, MK and ChelpG atomic charges were analyzed. The theoretical NMR and IR spectra were obtained. (1)H and (13)C NMR as well as FT-IR and FT-Raman spectra of studied compounds were also recorded and analyzed. The calculated parameters are compared with experimental characteristics of these molecules.

Experimental and theoretical study of molecular structure of beryllium, magnesium, calcium, strontium and barium 4-nitrobenzoates

The influence of alkaline earth metal ions on the electronic system of 4-nitrobenzoic acid was studied in this paper. The vibrational (FT-IR) and NMR ((1)H and (13)C) spectra were recorded for 4-nitrobenzoic acid (4-nba) and its salts (4-nb). The assignment of vibrational spectra was done. Some shifts of band wavenumbers in alkaline earth metal 4-nitrobenzoates spectra were observed in the series from magnesium to barium salts. Good correlations between wavenumbers of the vibrational bands in the IR spectra of studied salts and ionic potential, electronegativity, inverse of atomic mass, ionic radius and ionization energy of studied metals were found. The regular changes in the chemical shifts of protons ((1)H NMR) and carbons ((13)C NMR) in the series of studied salts were also observed. Optimized geometrical structures of studied compounds were calculated by B3LYP method using 6-311++G(**) as well as LANL2DZ basis sets. Theoretical wavenumbers and intensities in IR and chemical shifts in NMR spectra were also obtained. The calculated parameters were compared with experimental data of studied compounds.

Environment influences on the aromatic character of nucleobases and amino acids

Geometric (HOMA) and magnetic (NICS) indices of aromaticity were estimated for aromatic rings of amino acids and nucleobases. Cartesian coordinates were taken directly either from PDB files deposited in public databases at the finest resolution available (≤ 1.5 Å), or from structures resulting from full gradient geometry optimization in a hybrid QM/MM approach. Significant environmental effects imposing alterations of HOMA values were noted for all aromatic rings analysed. Furthermore, even extra fine resolution (≤ 1.0 Å) is not sufficient for direct estimation of HOMA values based on Cartesian coordinates provided by PDB files. The values of mean bond errors seem to be much higher than the 0.05 Å often reported for PDB files. The use of quantum chemistry geometry optimization is strongly advised; even a simple QM/MM model comprising only the aromatic substructure within the QM region and the rest of biomolecule treated classically within the MM framework proved to be a promising means of describing aromaticity inside native environments. According to the results presented, three consequences of the interaction with the environment can be observed that induce changes in structural and magnetic indices of aromaticity. First, broad ranges of HOMA or NICS values are usually obtained for different conformations of nearest neighborhood. Next, these values and their means can differ significantly from those characterising isolated monomers. The most significant increase in aromaticities is expected for the six-membered rings of guanine, thymine and cytosine. The same trend was also noticed for all amino acids inside proteins but this effect was much smaller, reaching the highest value for the five-membered ring of tryptophan. Explicit water solutions impose similar changes on HOMA and NICS distributions. Thus, environment effects of protein, DNA and even explicit water molecules are non-negligible sources of aromaticity changes appearing in the rings of nucleobases and aromatic amino acids residues.