Hydrogen Bonding in Crystals of Pyrrol-2-yl Chloromethyl Ketone Derivatives and Methyl Pyrrole-2-Carboxylate

The crystal and molecular structure of three derivatives of carbonyl 2-substituted pyrroles was determined by the single crystal X-ray diffraction. There are 2,2-dichloro-1-(1-methyl-1H-pyrrol-2-yl)ethan-1-one (I), 2-chloro-1-(1H-pyrrol-2-yl)ethan-1-one (II) and methyl 1H-pyrrole-2-carboxylate (III). All compounds crystallize with one molecule in the asymmetric unit in P212121 for I and II, and P21/c group for III. Despite the similar structures of the investigated compounds, the hydrogen bonds formed in their crystal structures adopt different H-bond motifs. In structure I, the dimers R12(5) and R21(7) form a chain along the b-axis, while in structures II and III, chain C(5) structural motifs are formed. The single point calculations at a ωB97XD/6-311++G(d,p) level of theory indicate that systems with N-H⋯O bonds have greater interaction energies (are more stable) compared with systems featuring C-H⋯O/Cl bonds. A descriptive Hirshfeld analysis showed that the greatest differences are visible for the H⋯H interactions. These H⋯H interactions predominate in structure III, accounting for 45% of the intermolecular interactions, while in structures I and II, they account for only 25%. Although compounds I-II contain Cl-atoms, the percentage of Cl⋯Cl interactions is rather low. In structure with two Cl-atoms (I), the contribution of the Cl⋯Cl contacts is 8.7% and for II, the contribution accounts for only 0.4% of the interactions

Does the Intramolecular Hydrogen Bond Affect the Spectroscopic Properties of Bicyclic Diazole Heterocycles?

The formation of an intramolecular hydrogen bond in pyrrolo[1,2-a]pyrazin-1(2H)-one bicyclic diazoles was analyzed, and the influence of N-substitution on HB formation is discussed in this study. B3LYP/aug-cc-pVDZ calculations were performed for the diazole, and the quantum theory of atoms in molecules (QTAIM) approach as well as the natural bond orbital (NBO) method was applied to analyze the strength of this interaction. It was found that the intramolecular hydrogen bond that closes an extra ring between the C=O proton acceptor group and the CH proton donor, that is, C=O⋯H–C, influences the spectroscopic properties of pyrrolopyrazine bicyclic diazoles, particularly the carbonyl frequencies. The influence of N-substitution on the aromaticity of heterocyclic rings is also discussed in this report

Hydrogen Bonding in Crystals of Pyrrol-2-yl Chloromethyl Ketone Derivatives and Methyl Pyrrole-2-Carboxylate

The crystal and molecular structure of three derivatives of carbonyl 2-substituted pyrroles was determined by the single crystal X-ray diffraction. There are 2,2-dichloro-1-(1-methyl-1H-pyrrol-2-yl)ethan-1-one (I), 2-chloro-1-(1H-pyrrol-2-yl)ethan-1-one (II) and methyl 1H-pyrrole-2-carboxylate (III). All compounds crystallize with one molecule in the asymmetric unit in P212121 for I and II, and P21/c group for III. Despite the similar structures of the investigated compounds, the hydrogen bonds formed in their crystal structures adopt different H-bond motifs. In structure I, the dimers R12(5) and R21(7) form a chain along the b-axis, while in structures II and III, chain C(5) structural motifs are formed. The single point calculations at a ωB97XD/6-311++G(d,p) level of theory indicate that systems with N-H⋯O bonds have greater interaction energies (are more stable) compared with systems featuring C-H⋯O/Cl bonds. A descriptive Hirshfeld analysis showed that the greatest differences are visible for the H⋯H interactions. These H⋯H interactions predominate in structure III, accounting for 45% of the intermolecular interactions, while in structures I and II, they account for only 25%. Although compounds I-II contain Cl-atoms, the percentage of Cl⋯Cl interactions is rather low. In structure with two Cl-atoms (I), the contribution of the Cl⋯Cl contacts is 8.7% and for II, the contribution accounts for only 0.4% of the interactions

Ferutinin as a Ca²⁺ complexone: Lipid bilayers, conductometry, FT-IR, NMR studies and DFT-B3LYP calculations

Calcium ionophoretic properties of ferutinin were re-evaluated in solvent-containing bilayer lipid membranes. The slopes of conductance-concentration curves suggest that in the presence of a solvent in the membrane the majority of complexes appear to consist of a single terpenoid molecule bound to one Ca ion. By contrast, the stoichiometry of ferutinin-Ca2+ complexes in acetone determined using the conductometric method was 2 :1. While the cation-cation selectivity of ferutinin did not change, the cation-anion selectivity slightly decreased in solvent containing membranes. FT-IR and NMR data together with DFT calculations at the B3LYP/6-31G(d) level of theory indicate that in the absence of Ca ions ferutinin molecules are hydrogen-bonded at the phenol hydroxyl groups. The variations of absorption assigned to -OH and -C-O stretching mode suggest that ferutinin interacts strongly with Ca ions via the hydroxyl group of ferutinol and carboxyl oxygen of the complex ether bond. The coordination through the carbonyl group of ferutinin was demonstrated by theoretical calculations. Taken together, ferutinin molecules form H-bonded dimers, while complexation of Ca2+ by ferutinin ruptures this hydrogen bond due to spatial re-orientation of the ferutinin molecules from parallel to antiparallel alignment.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Testing of Exchange-Correlation Functionals of DFT for a Reliable Description of the Electron Density Distribution in Organic Molecules

Researchers carrying out calculations using the DFT method face the problem of the correct choice of the exchange-correlation functional to describe the quantities they are interested in. This article deals with benchmark calculations aimed at testing various exchange-correlation functionals in terms of a reliable description of the electron density distribution in molecules. For this purpose, 30 functionals representing all rungs of Jacob’s Ladder are selected and then the values of some QTAIM-based parameters are compared with their reference equivalents obtained at the CCSD/aug-cc-pVTZ level of theory. The presented results show that the DFT method undoubtedly has the greatest problems with a reliable description of the electron density distribution in multiple strongly polar bonds, such as C=O, and bonds associated with large electron charge delocalization. The performance of the tested functionals turned out to be unsystematic. Nevertheless, in terms of a reliable general description of QTAIM-based parameters, the M11, SVWN, BHHLYP, M06-HF, and, to a slightly lesser extent, also BLYP, B3LYP, and X3LYP functionals turned out to be the worst. It is alarming to find the most popular B3LYP functional in this group. On the other hand, in the case of the electron density at the bond critical point, being the most important QTAIM-based parameter, the M06-HF functional is especially discouraged due to the very poor description of the C=O bond. On the contrary, the VSXC, M06-L, SOGGA11-X, M06-2X, MN12-SX, and, to a slightly lesser extent, also TPSS, TPSSh, and B1B95 perform well in this respect. Particularly noteworthy is the overwhelming performance of double hybrids in terms of reliable values of bond delocalization indices. The results show that there is no clear improvement in the reliability of describing the electron density distribution with climbing Jacob’s Ladder, as top-ranked double hybrids are also, in some cases, able to produce poor values compared to CCSD

Helical model of compression and thermal expansion

Abstract A negative linear temperature expansion and a negative linear compressibility were observed for imidazolium benzoate salt. Its strongly anisotropic strain induced by the temperature and pressure changes has been explained by the mechanism of H-bonded helices deformed in the structure. X-ray diffraction and vibrational spectroscopy were used to analyze interactions in the crystal. The Quantum Theory of Atoms in Molecules (QTAiM) approach was applied to analyze the hydrogen bonds and other interactions. In the salt under study, the interactions within the helix are substantially higher in energy than between helices. With decreasing temperature and increasing pressure, the value of the helix pitch increases while the value of the semi-major axis decreases, which results in the negative linear expansion and negative linear compression, respectively