Self-assembled H-bonded supramolecular interactions in monomeric complex [Mg(H2O)6].L2.2bipy.H2O; [LH = 2-amino-5-nitrobenzoic acid, bipy = 4,4′-bipyridine]]]]: Joint theoretical calculations and Hirshfeld surface analysis

The reaction of copper(II) sulfatepentahydrate with 2-nitrobenzoic acid and N,N,N′,N′-tetramethylethylenediamine (TMEDA) in basic solution produces the complex bis(2-nitrobenzoato-κO)(N,N,N′,N′-tetramethylethylenediamine-κ2 N,N′)copper(II), [Cu(C7H4NO4)2(C6H16N2)] or [Cu(2-nitrobenzoate)2(tmeda)]. Each carboxylate group of the 2-nitrobenzoate ligand is coordinated by CuII atom in a monodentate fashion and two TMEDA ligand nitrogen atoms are coordinate by the metal center, giving rise to a distorted square-planar coordination environment. In the crystal, metal complexes are linked by centrosymmetric C—H...O hydrogen bonds, forming ribbons via a R 2 2(10) ring motif. These ribbons are linked by further C—H...O hydrogen bonds, leading to two-dimensional hydrogen-bonded arrays parallel to the bc plane. Weak π–π stacking interactions provide additional stabilization of the crystal structure. Hirshfeld surface analysis, dnorm and two-dimensional fingerprint plots were examined to verify the contributions of the different intermolecular contacts within the supramolecular structure. The major interactions of the complex are O...H/H...O (44.9%), H...H (34%) and C...H (14.5%).

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Synthesis, crystal structure Hirshfeld surface analysis of the binuclear Cu(II) complex with 4-nitrobenzoic acid and triethanolamine

Chemical Data Collections ◽

10.1016/j.cdc.2021.100802 ◽

2021 ◽

pp. 100802

Author(s):

Oybek I. Khudoyberganov ◽

Abror Ruzmetov ◽

Aziz B. Ibragimov ◽

Jamshid M. Ashurov ◽

Shodlik B. Khasanov ◽

...

Keyword(s):

Crystal Structure ◽

Surface Analysis ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis ◽

Nitrobenzoic Acid

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Relevant π-hole tetrel bonding interactions in ethyl 2-triazolyl-2-oxoacetate derivatives: Hirshfeld surface analysis and DFT calculations

CrystEngComm ◽

10.1039/d0ce00335b ◽

2020 ◽

Vol 22 (21) ◽

pp. 3567-3578 ◽

Cited By ~ 5

Author(s):

Muhammad Naeem Ahmed ◽

Khawaja Ansar Yasin ◽

Shahid Aziz ◽

Saba Urooge Khan ◽

Muhammad Nawaz Tahir ◽

...

Keyword(s):

Solid State ◽

Dft Calculations ◽

Surface Analysis ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis ◽

X Ray ◽

Triazole Derivatives ◽

Self Assembled

We report the synthesis and X-ray characterization of four triazole derivatives that include an α-ketoester functionality and two phenyl substituents. The compounds form self-assembled dimers in the solid state establishing two symmetrically equivalent O⋯π-hole interactions.

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Crystal structure of 2-oxo-2H-chromen-3-yl 4-chlorobenzoate and Hirshfeld surface analysis

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989016019538 ◽

2017 ◽

Vol 73 (1) ◽

pp. 45-47 ◽

Cited By ~ 4

Author(s):

Eric Ziki ◽

Siaka Sosso ◽

Frédérica Mansilla-Koblavi ◽

Abdoulaye Djandé ◽

Rita Kakou-Yao

Keyword(s):

Dihedral Angle ◽

Surface Analysis ◽

Three Dimensional ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis ◽

Supramolecular Interactions ◽

Maximum Deviation ◽

Chemical Calculation ◽

Compound C ◽

Good Agreement

In the title compound, C16H9ClO4the dihedral angle between the coumarin ring system [maximum deviation = 0.023 (1) Å] and the benzene ring is 73.95 (8)°. In the crystal, π–π interactions link the dimers into a three-dimensional framework. A quantum chemical calculation is in generally good agreement with the observed structure, although the calculated dihedral angle between the ring systems (85.7%) is somewhat larger than the observed value [73.95 (8)°]. Hirshfeld surface analysis has been used to confirm and quantify the supramolecular interactions.

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Crystal structure and Hirshfeld surface analysis of 1-(2,4-dichlorobenzyl)-5-methyl-N-(thiophene-2-sulfonyl)-1H-pyrazole-3-carboxamide

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989018006242 ◽

2018 ◽

Vol 74 (5) ◽

pp. 747-751

Author(s):

Abdullah Aydin ◽

Mehmet Akkurt ◽

Zehra Tugce Gur ◽

Erden Banoğlu

Keyword(s):

Hydrogen Bonds ◽

Surface Analysis ◽

Molecular Conformation ◽

Thiophene Ring ◽

Three Dimensional ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis ◽

Supramolecular Interactions ◽

Compound C ◽

Graph Set

In the title compound, C16H13Cl2N3O3S2, the thiophene ring is disordered in a 0.762 (3):0.238 (3) ratio by an approximate 180° rotation of the ring around the S—C bond linking the ring to the sulfonyl unit. The dichlorobenzene group is also disordered over two sets of sites with the same occupancy ratio. The molecular conformation is stabilized by intramolecular C—H...Cl and C—H...N hydrogen bonds, forming rings with graph-set notation S(5). In the crystal, pairs of molecules are linked by N—H...O and C—H...O hydrogen bonds, forming inversion dimers with graph-set notation R 2 2(8) and R 1 2(11), which are connected by C—H...O hydrogen-bonding interactions into ribbons parallel to (100). The ribbons are further connected into a three-dimensional network by C—H...π interactions and π–π stacking interactions between benzene and thiophene rings, with centroid-to-centroid distances of 3.865 (2), 3.867 (7) and 3.853 (2) Å. Hirshfeld surface analysis has been used to confirm and quantify the supramolecular interactions.

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Weak hydrogen and dihydrogen bonds instead of strong N–H⋯O bonds of a tricyclic [1,2,4,5]-tetrazine derivative. Single-crystal X-ray diffraction, theoretical calculations and Hirshfeld surface analysis

CrystEngComm ◽

10.1039/c4ce00571f ◽

2014 ◽

Vol 16 (33) ◽

pp. 7638-7648 ◽

Cited By ~ 12

Author(s):

Magdalena Owczarek ◽

Irena Majerz ◽

Ryszard Jakubas

Keyword(s):

Single Crystal ◽

Surface Analysis ◽

Intermolecular Interactions ◽

Theoretical Calculations ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis ◽

X Ray Diffraction ◽

Surface Studies ◽

X Ray ◽

Dihydrogen Bonds

Experimental (single-crystal X-ray diffraction) and theoretical (AIM, DFT, NBO, Hirshfeld surface) studies have been performed to elucidate intermolecular interactions of anhydrous C8H16N4O2 and its monohydrated analog.

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Synthesis, characterization, crystal structures, Hirshfeld surface analysis and theoretical calculations of some new bisphosphoramidate derivatives and novel binuclear triorganotin(IV) complexes with diphosphoryl ligand

Journal of Organometallic Chemistry ◽

10.1016/j.jorganchem.2018.10.012 ◽

2019 ◽

Vol 879 ◽

pp. 27-39 ◽

Cited By ~ 1

Author(s):

Khodayar Gholivand ◽

Masoumeh Azadbakht ◽

Yazdan Maghsoud ◽

Mahdieh Hosseini ◽

Canan Kazak

Keyword(s):

Crystal Structures ◽

Surface Analysis ◽

Theoretical Calculations ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis

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A Supramolecular Approach to Structure-Based Design with A Focus on Synthons Hierarchy in Ornithine-Derived Ligands: Review, Synthesis, Experimental and in Silico Studies

Molecules ◽

10.3390/molecules25051135 ◽

2020 ◽

Vol 25 (5) ◽

pp. 1135 ◽

Cited By ~ 2

Author(s):

Joanna Bojarska ◽

Milan Remko ◽

Martin Breza ◽

Izabela D. Madura ◽

Krzysztof Kaczmarek ◽

...

Keyword(s):

Surface Analysis ◽

In Silico ◽

Supramolecular Structure ◽

Active Sites ◽

Crystal Packing ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis ◽

Supramolecular Interactions ◽

Advanced Therapies ◽

In Silico Studies

The success of innovative drugs depends on an interdisciplinary and holistic approach to their design and development. The supramolecular architecture of living systems is controlled by non-covalent interactions to a very large extent. The latter are prone to extensive cooperation and like a virtuoso play a symphony of life. Thus, the design of effective ligands should be based on thorough knowledge on the interactions at either a molecular or high topological level. In this work, we emphasize the importance of supramolecular structure and ligand-based design keeping the potential of supramolecular H-bonding synthons in focus. In this respect, the relevance of supramolecular chemistry for advanced therapies is appreciated and undisputable. It has developed tools, such as Hirshfeld surface analysis, using a huge data on supramolecular interactions in over one million structures which are deposited in the Cambridge Structure Database (CSD). In particular, molecular interaction surfaces are useful for identification of macromolecular active sites followed by in silico docking experiments. Ornithine-derived compounds are a new, promising class of multi-targeting ligands for innovative therapeutics and cosmeceuticals. In this work, we present the synthesis together with the molecular and supramolecular structure of a novel ornithine derivative, namely N-α,N-δ)-dibenzoyl-(α)-hydroxymethylornithine, 1. It was investigated by modern experimental and in silico methods in detail. The incorporation of an aromatic system into the ornithine core induces stacking interactions, which are vital in biological processes. In particular, rare C=O…π intercontacts have been identified in 1. Supramolecular interactions were analyzed in all structures of ornithine derivatives deposited in the CSD. The influence of substituent was assessed by the Hirshfeld surface analysis. It revealed that the crystal packing is stabilized mainly by H…O, O…H, C…H, Cl (Br, F)…H and O…O interactions. Additionally, π…π, C-H…π and N-O…π interactions were also observed. All relevant H-bond energies were calculated using the Lippincott and Schroeder H-bond model. A library of synthons is provided. In addition, the large synthons (Long-Range Synthon Aufbau Module) were considered. The DFT optimization either in vacuo or in solutio yields very similar molecular species. The major difference with the relevant crystal structure was related to the conformation of terminal benzoyl C15-C20 ring. Furthermore, in silico prediction of the extensive physicochemical ADME profile (absorption, distribution, metabolism and excretion) related to the drug-likeness and medicinal chemistry friendliness revealed that a novel ornithine derivative 1 has the potential to be a new drug candidate. It has shown good in silico absorption and very low toxicity.

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Two dialkylammonium salts of 2-amino-4-nitrobenzoic acid: crystal structures and Hirshfeld surface analysis

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989016017266 ◽

2016 ◽

Vol 72 (12) ◽

pp. 1691-1699 ◽

Cited By ~ 2

Author(s):

James L. Wardell ◽

Mukesh M. Jotani ◽

Edward R. T. Tiekink

Keyword(s):

Hydrogen Bonding ◽

Hydrogen Bonds ◽

Crystal Structures ◽

Surface Analysis ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis ◽

Dihedral Angles ◽

Asymmetric Unit ◽

Nitrobenzoic Acid ◽

Ammonium N

The crystal structures of two ammonium salts of 2-amino-4-nitrobenzoic acid are described, namely dimethylazanium 2-amino-4-nitrobenzoate, C2H8N+·C7H5N2O4−, (I), and dibutylazanium 2-amino-4-nitrobenzoate, C8H20N+·C7H5N2O4−, (II). The asymmetric unit of (I) comprises a single cation and a single anion. In the anion, small twists are noted for the carboxylate and nitro groups from the ring to which they are connected, as indicated by the dihedral angles of 11.45 (13) and 3.71 (15)°, respectively; the dihedral angle between the substituents is 7.9 (2)°. The asymmetric unit of (II) comprises two independent pairs of cations and anions. In the cations, different conformations are noted in the side chains in that three chains have an all-trans[(+)-antiperiplanar] conformation, while one has a distinctive kink resulting in a (+)-synclinal conformation. The anions, again, exhibit twists with the dihedral angles between the carboxylate and nitro groups and the ring being 12.73 (6) and 4.30 (10)°, respectively, for the first anion and 8.1 (4) and 12.6 (3)°, respectively, for the second. The difference between anions in (I) and (II) is that in the anions of (II), the terminal groups are conrotatory, forming dihedral angles of 17.02 (8) and 19.0 (5)°, respectively. In each independent anion of (I) and (II), an intramolecular amino-N—H...O(carboxylate) hydrogen bond is formed. In the crystal of (I), anions are linked into a jagged supramolecular chain by charge-assisted amine-N—H...O(carboxylate) hydrogen bonds and these are connected into layersviacharge-assisted ammonium-N—H...O(carboxylate) hydrogen bonds. The resulting layers stack along theaaxis, being connected by nitro-N—O...π(arene) and methyl-C—H...O(nitro) interactions. In the crystal of (II), the anions are connected into four-ion aggregates by charge-assisted amino-N—H...O(carboxylate) hydrogen bonding. The formation of ammonium-N—H...O(carboxylate) hydrogen bonds, involving all ammonium-N—H and carboxylate O atoms leads to a three-dimensional architecture; additional C—H...O(nitro) interactions contribute to the packing. The Hirshfeld surface analysis confirms the importance of the hydrogen bonding in both crystal structures. Indeed, O...H/H...O interactions contribute nearly 50% to the entire Hirshfeld surface in (I).

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