Hydrogen-bonded structures and interaction energies in two forms of the SGLT-2 inhibitor sotagliflozin

2017 ◽  
Vol 73 (9) ◽  
pp. 718-723
Author(s):  
Thomas Gelbrich ◽  
Verena Adamer ◽  
Marijan Stefinovic ◽  
Andrea Thaler ◽  
Ulrich J. Griesser
Keyword(s):  
Intermolecular Interactions ◽  
Crystallographic Axis ◽  
Interaction Energies ◽  
Molecular Conformations ◽  
Oh Groups ◽  
Molecule Interaction ◽  
Hydrogen Bonded

The sotagliflozin molecule exhibits two fundamentally different molecular conformations in form 1 {systematic name: (2S,3R,4R,5S,6R)-2-[4-chloro-3-(4-ethoxybenzyl)phenyl]-6-(methylsulfanyl)tetrahydro-2H-pyran-3,4,5-triol, C21H25ClO5S, (I)} and the monohydrate [C21H25ClO5S·H2O, (II)]. Both crystals display hydrogen-bonded layers formed by intermolecular interactions which involve the three –OH groups of the xyloside fragment of the molecule. The layer architectures of (I) and (II) contain a non-hydrogen-bonded molecule–molecule interaction along the short crystallographic axis (a axis) whose total PIXEL energy exceeds that of each hydrogen-bonded molecule–molecule pair. The hydrogen-bonded layer of (I) has the topology of the 4-connected sql net and that formed by the water and sotagliflozin molecules of (II) has the topology of a 3,7-connected net.

Intermolecular interactions and unexpected isostructurality in the crystal structures of the dichlorobenzaldehyde isomers

2011 ◽  
Vol 67 (5) ◽  
pp. 437-445 ◽  
Author(s):  
Katarzyna A. Solanko ◽  
Andrew D. Bond
Keyword(s):  
Crystal Structures ◽  
Intermolecular Interaction ◽  
Intermolecular Interactions ◽  
Crystallographic Axis ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Asymmetric Unit ◽  
Consistent Feature ◽  
Whole Molecule Disorder

The crystal structures of the six dichlorobenzaldehyde isomers, four of them newly determined, are analyzed in terms of the geometry and energies of their intermolecular interactions, quantified using the semi-classical density sums (SCDS-PIXEL) method. A consistent feature in all six structures is molecular stacks propagating along a short crystallographic axis of ca 3.8 Å. The stacks have a closely comparable geometry in each isomer, but the interaction energies between stacked molecules are variable on account of the differing relative positions of the Cl substituents. In the majority of the isomers the stacking interactions are the most stabilizing in the structure. Exceptions are the 2,4- and 3,5-isomers, where more stabilizing interactions are made between stacks. In general, the most stabilizing non-stacking intermolecular interactions in the structures are those involving C—H...O contacts. Observed motifs based on Cl...Cl interactions appear to be largely imposed by the constraints of other more stabilizing intermolecular interactions. The isomeric series displays the following noteworthy features: (i) the 2,3- and 2,6-isomers are isostructural despite having different orientations of the Cl and aldehyde functionalities; (ii) the 2,5-isomer exhibits whole-molecule disorder; (iii) the 2,5- and 3,5-isomers have more than one molecule in the crystallographic asymmetric unit (Z′ > 1). These features in particular are considered on the basis of the intermolecular interaction energies.

scholarly journals Crystal structure and Hirshfeld surface analysis of 2,4-diamino-6-phenyl-1,3,5-triazin-1-ium 4-methylbenzenesulfonate

2018 ◽  
Vol 74 (8) ◽  
pp. 1159-1162
Author(s):  
Ramalingam Sangeetha ◽  
Kasthuri Balasubramani ◽  
Kaliyaperumal Thanigaimani ◽  
Savaridasson Jose Kavitha
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Hirshfeld Surface ◽  
Amino Group ◽  
Asymmetric Unit ◽  
Graph Set ◽  
Molecular Salt ◽  
Sulfonate Anion ◽  
Hydrogen Bonded

In the title molecular salt, C9H10N5 +·C7H7O3S−, the asymmetric unit consists of a 2,4-diamino-6-phenyl-1,3,5-triazin-1-ium cation and a 4-methylbenzenesulfonate anion. The cation is protonated at the N atom lying between the amine and phenyl substituents. The protonated N and amino-group N atoms are involved in hydrogen bonding with the sulfonate O atoms through a pair of intermolecular N—H...O hydrogen bonds, giving rise to a hydrogen-bonded cyclic motif with R 2 2(8) graph-set notation. The inversion-related molecules are further linked by four N—H...O intermolecular interactions to produce a complementary DDAA (D = donor, A = acceptor) hydrogen-bonded array, forming R 2 2(8), R 4 2(8) and R 2 2(8) ring motifs. The centrosymmetrically paired cations form R 2 2(8) ring motifs through base-pairing via N—H...N hydrogen bonds. In addition, another R 3 3(10) motif is formed between centrosymetrically paired cations and a sulfonate anion via N—H...O hydrogen bonds. The crystal structure also features weak S=O...π and π–π interactions. Hirshfeld surface and fingerprint plots were employed in order to further study the intermolecular interactions.

Intermolecular interactions in crystals of small unsubstituted cyclic ethers and substituted epoxides

2018 ◽  
Vol 233 (9-10) ◽  
pp. 641-648 ◽  
Author(s):  
Mark A. Spackman
Keyword(s):  
Intermolecular Interactions ◽  
Cyclic Ethers ◽  
Interaction Energies ◽  
X Ray Diffraction ◽  
Weakly Bound ◽  
X Ray ◽  
Experimental Interaction ◽  
Lattice Energies ◽  
Experimental Electron Density ◽  
Careful Investigation

Abstract CE-B3LYP model energies are used to investigate intermolecular interactions in crystals of the relatively weakly bound cyclic ethers, as well as a number of substituted epoxides that have been the focus of high-quality experimental electron density studies. This approach readily provides a complete picture of all intermolecular interactions in these molecular crystals, and CE-B3LYP lattice energies for the unsubstituted cyclic ethers are in excellent agreement with available thermodynamic data. When compared with the outcomes of multipole modelling of X-ray diffraction data, these results suggest that experimental interaction energies are typically underestimated and, contrarily, experimental lattice energies are typically overestimated. These observations deserve careful investigation.

The influence of intermolecular interactions and molecular packings on mechanochromism and mechanoluminescence – a tetraphenylethylene derivative case

2019 ◽  
Vol 7 (40) ◽  
pp. 12709-12716 ◽  
Author(s):  
Guangxi Huang ◽  
Yuqing Jiang ◽  
Jianguo Wang ◽  
Zhen Li ◽  
Bing Shi Li ◽  
...  
Keyword(s):  
Single Crystals ◽  
Intermolecular Interactions ◽  
Three Dimensional ◽  
Hydrogen Bonded

Compact packing and intact three-dimensional hydrogen-bonded networks in single crystals are favorable for ML properties.

A theoretical study of weak interactions in phenylenediamine homodimer clusters

2016 ◽  
Vol 18 (42) ◽  
pp. 29249-29257 ◽  
Author(s):  
Chengqian Yuan ◽  
Haiming Wu ◽  
Meiye Jia ◽  
Peifeng Su ◽  
Zhixun Luo ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Dft Calculations ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
Theoretical Study ◽  
Natural Bond Orbital ◽  
Weak Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Weak Intermolecular Interactions

Utilizing dispersion-corrected density functional theory (DFT) calculations, we demonstrate the weak intermolecular interactions of phenylenediamine dimer (pdd) clusters, emphasizing the local lowest energy structures and decomposition of interaction energies by natural bond orbital (NBO) and atoms in molecule (AIM) analyses.

Bases, solvates and salts: new benzimidazole- and pyridine-scaffolded ligands

2020 ◽  
Vol 76 (4) ◽  
pp. 367-374
Author(s):  
Aleksandra Bocian ◽  
Adam Gorczyński ◽  
Dawid Marcinkowski ◽  
Grzegorz Dutkiewicz ◽  
Violetta Patroniak ◽  
...  
Keyword(s):  
Schiff Base ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Stabilization Energy ◽  
Interaction Energies ◽  
Free Base ◽  
Schiff Base Ligands ◽  
Π Interactions ◽  
Charged Ligands

The intermolecular interactions in the structures of a series of Schiff base ligands have been thoroughly studied. These ligands can be obtained in different forms, namely, as the free base 2-[(2E)-2-(1H-imidazol-4-ylmethylidene)-1-methylhydrazinyl]pyridine, C10H11N5, 1, the hydrates 2-[(2E)-2-(1H-imidazol-2-ylmethylidene)-1-methylhydrazinyl]-1H-benzimidazole monohydrate, C12H12N6·H2O, 2, and 2-{(2E)-1-methyl-2-[(1-methyl-1H-imidazol-2-yl)methylidene]hydrazinyl}-1H-benzimidazole 1.25-hydrate, C13H14N6·1.25H2O, 3, the monocationic hydrate 5-{(1E)-[2-(1H-1,3-benzodiazol-2-yl)-2-methylhydrazinylidene]methyl}-1H-imidazol-3-ium trifluoromethanesulfonate monohydrate, C12H13N6 +·CF3O3S−·H2O, 5, and the dicationic 2-{(2E)-1-methyl-2-[(1H-imidazol-3-ium-2-yl)methylidene]hydrazinyl}pyridinium bis(trifluoromethanesulfonate), C10H13N5 2+·2CF3O3S−, 6. The connection between the forms and the preferred intermolecular interactions is described and further studied by means of the calculation of the interaction energies between the neutral and charged components of the crystal structures. These studies show that, in general, the most important contribution to the stabilization energy of the crystal is provided by π–π interactions, especially between charged ligands, while the details of the crystal architecture are influenced by directional interactions, especially relatively strong hydrogen bonds. In one of the structures, a very interesting example of the nontypical F...O interaction was found and its length, 2.859 (2) Å, is one of the shortest ever reported.

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