Salt formation, hydrogen-bonding patterns and supramolecular architectures of acridine with salicylic and hippuric acid molecules

Author(s):  
Suresh Suganya ◽  
Kandasamy Saravanan ◽  
Ramakrishnan Jaganathan ◽  
Poomani Kumaradhas

The intermolecular interactions and salt formation of acridine with 4-aminosalicylic acid, 5-chlorosalicylic acid and hippuric acid were investigated. The salts obtained were acridin-1-ium 4-aminosalicylate (4-amino-2-hydroxybenzoate), C13H10N+·C7H6NO3 − (I), acridin-1-ium 5-chlorosalicylate (5-chloro-2-hydroxybenzoate), C13H10N+·C7H4ClO3 − (II), and acridin-1-ium hippurate (2-benzamidoacetate) monohydrate, C13H10N+·C9H8NO3 −·H2O (III). Acridine is involved in strong intermolecular interactions with the hydroxy group of the three acids, enabling it to form supramolecular assemblies. Hirshfeld surfaces, fingerprint plots and enrichment ratios were generated and investigated, and the intermolecular interactions were analyzed, revealing their quantitative contributions in the crystal packing of salts I, II and III. A quantum theory of atoms in molecules (QTAIM) analysis shows the charge–density distribution of the intermolecular interactions. The isosurfaces of the noncovalent interactions were studied, which allows visualization of where the hydrogen-bonding and dispersion interactions contribute within the crystal.

CrystEngComm ◽  
2015 ◽  
Vol 17 (16) ◽  
pp. 3089-3102 ◽  
Author(s):  
J. L. Ferreira da Silva ◽  
Shrika G. Harjivan ◽  
André P. Ferreira ◽  
Karina Shimizu ◽  
M. Matilde Marques ◽  
...  

Relative positioning of substituents in a molecule is determinant in crystal packing of 1-ferrocenyl-2-(aryl)thioethanone derivatives displaying weak hydrogen bonding ability.


2020 ◽  
Vol 76 (8) ◽  
pp. 795-809
Author(s):  
Konstantin L'vovich Obydennov ◽  
Tatiana Andreevna Kalinina ◽  
Olga Alexandrovna Vysokova ◽  
Pavel Alexandrovich Slepukhin ◽  
Varvara Alexandrovna Pozdina ◽  
...  

The crystal structures of four new chiral [1,2,3]triazolo[5,1-b][1,3,4]thiadiazines are described, namely, ethyl 5′-benzoyl-5′H,7′H-spiro[cyclohexane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate, C19H22N4O3S, ethyl 5′-(4-methoxybenzoyl)-5′H,7′H-spiro[cyclohexane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate, C20H24N4O4S, ethyl 6,6-dimethyl-5-(4-methylbenzoyl)-6,7-dihydro-5H-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine-3-carboxylate, C17H20N4O3S, and ethyl 5-benzoyl-6-(4-methoxyphenyl)-6,7-dihydro-5H-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine-3-carboxylate, C21H20N4O4S. The crystallographic data and cell activities of these four compounds and of the structures of three previously reported similar compounds, namely, ethyl 5′-(4-methylbenzoyl)-5′H,7′H-spiro[cyclopentane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate, C19H22N4O3S, ethyl 5′-(4-methoxybenzoyl)-5′H,7′H-spiro[cyclopentane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate, C19H22N4O4S, and ethyl 6-methyl-5-(4-methylbenzoyl)-6-phenyl-6,7-dihydro-5H-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine-3-carboxylate, C22H22N4O3S, are contrasted and compared. For both crystallization and an MTT assay, racemic mixtures of the corresponding [1,2,3]triazolo[5,1-b][1,3,4]thiadiazines were used. The main manner of molecular packing in these compounds is the organization of either enantiomeric pairs or dimers. In both cases, the formation of two three-centre hydrogen bonds can be detected resulting from intramolecular N—H...O and intermolecular N—H...O or N—H...N interactions. Molecules of different enantiomeric forms can also form chains through N—H...O hydrogen bonds or form layers between which only weak hydrophobic contacts exist. Unlike other [1,2,3]triazolo[5,1-b][1,3,4]thiadiazines, ethyl 5′-benzoyl-5′H,7′H-spiro[cyclohexane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate contains molecules of only the (R)-enantiomer; moreover, the N—H group does not participate in any significant intermolecular interactions. Molecular mechanics methods (force field OPLS3e) and the DFT B3LYP/6-31G+(d,p) method show that the compound forming enantiomeric pairs via weak N—H...N hydrogen bonds is subject to greater distortion of the geometry under the influence of the intermolecular interactions in the crystal. For intramolecular N—H...O and S...O interactions, an analysis of the noncovalent interactions (NCIs) was carried out. The cellular activities of the compounds were tested by evaluating their antiproliferative effect against two normal human cell lines and two cancer cell lines in terms of half-maximum inhibitory concentration (IC50). Some derivatives have been found to be very effective in inhibiting the growth of Hela cells at nanomolar and submicromolar concentrations with minimal cytotoxicity in relation to normal cells.


Author(s):  
Pradip Kumar Mondal ◽  
Rahul Shukla ◽  
Subha Biswas ◽  
Deepak Chopra

A total of 23 benzamides are obtained through a simple reaction between chloro-/bromo-/iodoaniline and trifluoromethylbenzoyl chloride and characterized using single-crystal X-ray diffraction. Crystal structures of three series of benzamides based on N-chlorophenyl–trifluoromethyl–benzamide (nine compounds), N-bromophenyl–trifluoromethyl–benzamide (six compounds), and N-iodophenyl–trifluoromethyl–benzamide (eight compounds) are prepared to analyse the halogen-mediated noncovalent interactions. The influences of Cl/Br/I and trifluoromethyl substituents on the respective interactions are examined in the presence of a strong N—H...O hydrogen bond. This exercise has resulted in the documentation of frequently occurring supramolecular synthons involving halogen atoms in the crystal packing of benzamide molecules in the solid state. In the present study, a detailed quantitative evaluation has been performed on the nature, energetics, electrostatic contributions, and topological properties of short and directional intermolecular interactions derived from the electron density on halogenated benzamides in the solid state. Besides these, the occurrence of three-, two- and one-dimensional isostructurality in halogen (Cl or Br or I) substituted benzamide analogues is also investigated. A `region of co-existence' involving halogen-based intermolecular interactions in the vicinity of the sum of the van der Waals radii has been identified. Thus, the nature of the halogen (effective size), type of interaction and the packing characteristics via presence of additional interactions establish the subtle, yet important, role of cooperativity in intermolecular interactions in crystal packing.


2001 ◽  
Vol 57 (1) ◽  
pp. 72-81 ◽  
Author(s):  
Yasuko In ◽  
Mayumi Fujii ◽  
Yasuhiro Sasada ◽  
Toshimasa Ishida

To elucidate the structural features of amino acids caused by the C-terminal α-amidation, the crystal structures of HCl salts of C-terminal amidated Ile, Val, Thr, Ser, Met, Trp, Gln and Arg were analysed and compared with those of their C-terminal free acids. The bonding parameter of the amide group was little affected by the different chemical properties of the side chains. As for the molecular packing patterns, some structural differences were observed by the C-amidation. The Cα—H...O hydrogen bonds and carbonyl–carbonyl interactions were more strengthened by the salt formation with HCl in C-amides than C-acids. Furthermore, there is a clear difference between the interaction patterns with Cl ions. In most C-amide crystals, Cl ions are bifurcately hydrogen-bonded to two neighbouring amide NH2 groups and the parallel layers of the C-amides and Cl ions are alternatively formed. In the case of the carboxyl OH in C-acid crystals, however, the direct hydrogen bond with the Cl ion is not always observed and is largely dependent on the crystal packing environment. This suggests the superior hydrogen-bonding ability of NH...Cl− compared with OH...Cl−. The difference in hydrogen-bonding ability between the amide and carboxyl groups is considered, based on the spatial dispositions of the hydrogen-bonding polar atoms/groups.


RSC Advances ◽  
2015 ◽  
Vol 5 (89) ◽  
pp. 72923-72936 ◽  
Author(s):  
Masoud Mirzaei ◽  
Hossein Eshtiagh-Hosseini ◽  
Mojtaba Shamsipur ◽  
Mahdi Saeedi ◽  
Mehdi Ardalani ◽  
...  

Five new coordination compounds derived from chelidamic acid and amines have been synthesized and X-ray characterized. The noncovalent interactions that govern the crystal packing have been rationalized by means of DFT calculations.


2019 ◽  
Vol 75 (3) ◽  
pp. 329-335 ◽  
Author(s):  
Kyle A. Powers ◽  
David K. Geiger

The isostructural salts benzene-1,2-diaminium bis(pyridine-2-carboxylate), 0.5C6H10N2 2+·C6H4NO2 −, (1), and 4,5-dimethylbenzene-1,2-diaminium bis(pyridine-2-carboxylate), 0.5C8H14N2 2+·C6H4NO2 −, (2), and the 1:2 benzene-1,2-diamine–benzoic acid cocrystal, 0.5C6H8N2·C7H6O2, (3), are reported. All of the compounds exhibit extensive N—H...O hydrogen bonding that results in interconnected rings. O—H...N hydrogen bonding is observed in (3). Additional π–π and C—H...π interactions are found in each compound. Hirshfeld and fingerprint plot analyses reveal the primary intermolecular interactions and density functional theory was used to calculate their strengths. Salt formation by (1) and (2), and cocrystallization by (3) are rationalized by examining pK a differences. The R 2 2(9) hydrogen-bonding motif is common to each of these structures.


CrystEngComm ◽  
2014 ◽  
Vol 16 (19) ◽  
pp. 3867-3882 ◽  
Author(s):  
Andrew G. P. Maloney ◽  
Peter A. Wood ◽  
Simon Parsons

In the short chain amines H-bonding dominates crystal packing, but dispersion wins-out for the long chain compounds. The cross-over point occurs between butyl and pentylamine, where interactions are finely balanced.


2019 ◽  
Vol 75 (3) ◽  
pp. 231-247 ◽  
Author(s):  
Fatemeh Taghipour ◽  
Masoud Mirzaei

The important role of pyrazine (pz) and its derivatives in fields such as biochemistry and pharmacology, as well as in the study of magnetic properties, is surveyed. Recognition of these properties without extensive investigations into their structural properties is not possible. This review summarizes interactions that exist between these organic compounds by themselves in the solid state, as well as those in coordination polymers with metal ions and in polyoxometalate-based hybrids. Complexes based on pyrazine ligands can generate metal–organic framework (MOF) structures that bind polyoxometalates (POMs) through covalent and noncovalent interactions. Some biological and magnetic properties involving these compounds are considered and the effect of hydrogen bonding on their supramolecular architectures is highlighted.


2018 ◽  
Vol 233 (9-10) ◽  
pp. 675-687 ◽  
Author(s):  
Lilianna Chęcińska ◽  
Andrzej Jóźwiak ◽  
Magdalena Ciechańska ◽  
Carsten Paulmann ◽  
Julian J. Holstein ◽  
...  

Abstract The aim of the study was to examine noncovalent interactions in considerably different crystal packings of three isoindole compounds. Their structures were compared to three other closely-related derivatives described earlier in the literature. Here we discuss the crystal structures in the context of the hydrogen-bonded motifs and other weak interactions. The hierarchy of investigated intermolecular interactions was examined in a quantitative manner through pairwise interaction energies and energy framework analysis.


2020 ◽  
Vol 07 ◽  
Author(s):  
Neslihan Demirbas ◽  
Ahmet Demirbas

Background: Since the discovery of metal-free catalysts or organocatalysts about twenty years ago, a number of small molecules with different structures have been using to accelerate organic transformations. With the development of environmental awareness, in order to obtain highly privileged scaffolds, scientists have directed their studies towards the synthetic methodologies which minimize or preferably eliminate the formation of waste, avoid from toxic solvents and reagents and use renewable starting materials as far as possible. Methods: In this connection, the organocatalytic reactions providing efficiency and selectivity for most of case have become an endless topic in organic chemistry since several advantages from both practical and environmental standpoints. Organocatalysts supplying transformation of reactants into products with the least possible waste production have been serving to the concept of green chemistry. Results and Conclusion: Organocatalysts have been classified on the basis of their binding capacity to the substrate with covalently or noncovalent interactions involving hydrogen bonding and electrostatic interaction. Diverse types of small organic compounds including proline and its derivatives, phase-transfer catalysts, (thio)urease, phosphoric acids, sulfones, N-oxides, guanidines, cinchona derivatives, aminoindanol and amino acids have been utilized as hydrogen bonding organocatalysts in different chemical transformations.


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