Intra- and Intermolecular N–H•••O=C Hydrogen Bonds in 1-Acyl Urea Compounds: Synthesis, X-ray Structure, Conformational and Hirshfeld Surface Analyses of 1-(2,3-Dichlorophenyl)-3-pivaloylurea

Abstract: X-ray crystal and Hirshfeld surface analyses of 2-hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene and its 2-methoxylated homologue show quantitatively and visually distinct molecular contacts in crystals and minute differences in the weak intermolecular interactions. The title compound has a helical tubular packing, where molecules are piled in a two-folded head-to-tail fashion. The homologue has a tight zigzag molecular string lined up behind each other via nonclassical intermolecular hydrogen bonds between the carbonyl oxygen atom and the hydrogen atom of the naphthalene ring. The dnorm index obtained from the Hirshfeld surface analysis quantitatively demonstrates stronger molecular contacts in the homologue, an ethereal compound, than in the title compound, an alcohol, which is consistent with the higher melting temperature of the former than the latter. Stabilization through the significantly weak intermolecular nonclassical hydrogen bonding interactions in the homologue surpasses the stability imparted by the intramolecular C=O…H–O classical hydrogen bonds in the title compound. The classical hydrogen bond places the six-membered ring in the concave of the title molecule. The hydroxy group opposingly disturbs the molecular aggregation of the title compound, as demonstrated by the distorted H…H interactions covering the molecular surface, owing to the rigid molecular conformation. The position of effective interactions predominate over the strength of the classical/nonclassical hydrogen bonds in the two compounds.

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Crystal structure from X-ray powder diffraction data, DFT-D calculation, Hirshfeld surface analysis, and energy frameworks of (RS)-trichlormethiazide

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989021013633 ◽

2022 ◽

Vol 78 (2) ◽

Author(s):

Robert A. Toro ◽

Analio Dugarte-Dugarte ◽

Jacco van de Streek ◽

José Antonio Henao ◽

José Miguel Delgado ◽

...

Keyword(s):

Hydrogen Bonds ◽

Surface Analysis ◽

Powder Diffraction ◽

Diffraction Data ◽

Electrostatic Interactions ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis ◽

Powder Diffraction Data ◽

X Ray ◽

Π Interactions

The structure of racemic (RS)-trichlormethiazide [systematic name: (RS)-6-chloro-3-(dichloromethyl)-1,1-dioxo-3,4-dihydro-2H-1λ6,2,4-benzothiadiazine-7-sulfonamide], C8H8Cl3N3O4S2 (RS-TCMZ), a diuretic drug used in the treatment of oedema and hypertension, was determined from laboratory X-ray powder diffraction data using DASH [David et al. (2006). J. Appl. Cryst. 39, 910–915.], refined by the Rietveld method with TOPAS-Academic [Coelho (2018). J. Appl. Cryst. 51, 210–218], and optimized using DFT-D calculations. The extended structure consists of head-to-tail dimers connected by π–π interactions which, in turn, are connected by C—Cl...π interactions. They form chains propagating along [101], further connected by N—H...O hydrogen bonds to produce layers parallel to the ac plane that stack along the b-axis direction, connected by additional N—H...O hydrogen bonds. The Hirshfeld surface analysis indicates a major contribution of H...O and H...Cl interactions (32.2 and 21.7%, respectively). Energy framework calculations confirm the major contribution of electrostatic interactions (E elec) to the total energy (E tot). A comparison with the structure of S-TCMZ is also presented.

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Spectral, Thermal, Crystal Structure, Hirshfeld Surface Analyses and Biological Activities of New Hydrazinium Dipicolinato Copper(II) Tetrahydrate

Asian Journal of Chemistry ◽

10.14233/ajchem.2019.21958 ◽

2019 ◽

Vol 31 (8) ◽

pp. 1755-1761

Author(s):

K. Naresh ◽

B.N. Sivasankar

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Single Crystal ◽

Water Clusters ◽

Hirshfeld Surface ◽

Water Molecules ◽

X Ray ◽

Biological Studies ◽

Calf Thymus ◽

Hydrazinium Cation

A new copper complex of pyridine-2,6-dicarboxylate containing hydrazinium cation, formulated as (N2H5)2[Cu(PDC)2]·4H2O (PDC = pyridine-2,6-dicarboxylate) has been synthesized from copper(II) nitrate, hydrazine hydrate and pyridine-2,6-dicarboxylic acid as a single crystal and characterized by elemental analysis and spectroscopic (IR and UV-visible), thermal (TG/DTG), single crystal X-ray diffraction and biological studies. A six-coordinate complex with a distorted octahedral geometry around Cu(II) ion is proposed and confirmed by X-ray single crystal method. The structure reveals that two pyridine-2,6-dicarboxylate species acting as tridentate ligands and hydrazinium cation present as a counter ion along with non-coordinated four water molecules. The structural units of copper(II) is mutually held by the hydrogen bonds and π···π and C–O···π interactions. The copper(II) complex is connected to one another via O–H···O hydrogen bonds, forming water clusters, which plays an important role in the stabilization of the crystal structure. In the water clusters, the water molecules are trapped by the cooperative association of coordination interactions as well as hydrogen bonds. Both cation and anion interactions and crystal from various types of intermolecular contacts and their importance were explored using Hirshfeld surface analysis. This indicates that O···H/H···O interactions are the superior interactions conforming excessive H-bond in the molecular structure. The interaction of copper(II) complex with calf thymus DNA (CT-DNA) was investigated by electronic absorption spectroscopic technique. The electronic evidence strongly shows that the compound interacts with calf thymus through intercalation with a binding constant of Kb = 5.7 × 104 M–1.

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The Importance of CH···X (X = O, π) Interaction of a New Mixed Ligand Cu(II) Coordination Polymer: Structure, Hirshfeld Surface and Theoretical Studies

Crystals ◽

10.3390/cryst8120455 ◽

2018 ◽

Vol 8 (12) ◽

pp. 455 ◽

Cited By ~ 16

Author(s):

Saikat Seth

Keyword(s):

Solid State ◽

Hydrogen Bonds ◽

Noncovalent Interactions ◽

Carbonyl Oxygen ◽

Hirshfeld Surface ◽

Mixed Ligand ◽

Binding Energies ◽

Zigzag Chain ◽

X Ray ◽

Π Interactions

In this study, a new equimolar (1:1:1) mixed ligand Cu(II) polymer, [Cu(IDA)(ImP)]n (1) with iminodiacetato (IDA) and imidazo[1,2-a]-pyridine (ImP) was synthesized and characterized by single crystal X-ray diffraction analysis. X-ray crystallography reveals that compound (1) consists of polymeric zigzag chain along [010] the carboxylate carbonyl oxygen atom by two-fold symmetry screw axis. The solid-state structure is stabilized through C–H···O hydrogen bonds and C–H···π interactions that lead the molecules to generate two-dimensional supramolecular assemblies. The intricate combinations of hydrogen bonds and C–H···π interactions are fully described along with computational studies. A thorough analysis of Hirshfeld surface and fingerprint plots elegantly quantify the interactions involved within the structure. The binding energies associated with the noncovalent interactions observed in the crystal structure and the interplay between them were calculated using theoretical DFT calculations. Weak noncovalent interactions were analyzed and characterized using Bader’s theory of ‘‘atoms-in-molecules’’ (AIM). Finally, the solid-state supramolecular assembly was characterized by the “Noncovalent Interaction” (NCI) plot index.

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Evaluation of N—H...S and N—H...π interactions inO,O′-diethylN-(2,4,6-trimethylphenyl)thiophosphate: a combination of X-ray crystallographic and theoretical studies

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229618007933 ◽

2018 ◽

Vol 74 (7) ◽

pp. 847-855 ◽

Cited By ~ 8

Author(s):

Elham Torabi Farkhani ◽

Mehrdad Pourayoubi ◽

Mohammad Izadyar ◽

Pavel V. Andreev ◽

Ekaterina S. Shchegravina

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonds ◽

Density Functional ◽

Natural Bond Orbital ◽

Crystal Packing ◽

Hirshfeld Surface ◽

Basis Set ◽

Theoretical Studies ◽

Functional Theory ◽

X Ray

In the crystal structure ofO,O′-diethylN-(2,4,6-trimethylphenyl)thiophosphate, C13H22NO2PS, two symmetrically independent thiophosphoramide molecules are linked through N—H...S and N—H...π hydrogen bonds to form a noncentrosymmetric dimer, withZ′ = 2. The strengths of the hydrogen bonds were evaluated using density functional theory (DFT) at the M06-2X level within the 6-311++G(d,p) basis set, and by considering the quantum theory of atoms in molecules (QTAIM). It was found that the N—H...S hydrogen bond is slightly stronger than the N—H...π hydrogen bond. This is reflected in differences between the calculated N—H stretching frequencies of the isolated molecules and the frequencies of the same N—H units involved in the different hydrogen bonds of the hydrogen-bonded dimer. For these hydrogen bonds, the corresponding charge transfers,i.e.lp (or π)→σ*, were studied, according to the second-order perturbation theory in natural bond orbital (NBO) methodology. Hirshfeld surface analysis was applied for a detailed investigation of all the contacts participating in the crystal packing.

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A combined X-ray crystallography and theoretical study of N—H...OX (X is =P and —C) hydrogen bonds in two new structures with a (C—O)2(N)P(=Y) (Y is O and S) skeleton

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229618014006 ◽

2018 ◽

Vol 74 (12) ◽

pp. 1610-1621 ◽

Cited By ~ 4

Author(s):

Banafsheh Vahdani Alviri ◽

Mehrdad Pourayoubi ◽

Abolghasem Farhadipour ◽

Marek Nečas ◽

Valerio Bertolasi

Keyword(s):

Hydrogen Bonds ◽

Quantum Chemical ◽

Software Package ◽

Theoretical Study ◽

Natural Bond Orbital ◽

Crystal Packing ◽

Hirshfeld Surface ◽

X Ray ◽

X Ray Crystallography ◽

Hydrogen Bonding Interactions

The crystal structures of N,N′-(cyclohexane-1,4-diyl)bis(O,O′-diphenylphosphoramide), C30H32N2O6P2 or (C6H5O)2P(O)(1-NH)(C6H10)(4-NH)P(O)(OC6H5)2, (I), and N,N′-(1,4-phenylene)bis(O,O′-dimethylthiophosphoramide), C10H18N2O4P2S2 or (CH3O)2P(S)(1-NH)(C6H4)(4-NH)P(S)(OCH3)2, (II), have been investigated. In the structure of (I), with an (O)2(N)P(O) skeleton, two symmetry-independent phosphoramide molecules are linked through N—H...O=P hydrogen bonds. In the structure of (II), with an (O)2(N)P(S) skeleton, the ester O atoms take part in N—H...O—C hydrogen bonds as acceptors; the P=S groups do not participate in hydrogen-bonding interactions. The strengths of these hydrogen bonds were evaluated, using quantum chemical calculations with the GAUSSIAN09 software package at the B3LYP/6-311G(d,p) level of theory. For this, LP(O) to σ*(NH) charge transfers were studied, according to the second-order perturbation theory in natural bond orbital (NBO) methodology, for a three-component cluster of hydrogen-bonded molecules for both structures, including all of the independent N—H...O hydrogen bonds observed in the crystal packing. The details of the intermolecular interactions were studied by Hirshfeld surface maps and two-dimensional fingerprint plots.

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Hydrogen Bonds in Bis(1H-benzimidazole-κN3)cadmium(II) Dibenzoate: Hirshfeld Surface Analysis and AIM Perspective

Acta Chimica Slovenica ◽

10.17344/acsi.2020.6438 ◽

2021 ◽

Vol 68 (1) ◽

pp. 239-246

Author(s):

Jia-Jun Wang ◽

Li-Nan Dun ◽

Bao-Sheng Zhang ◽

Zhong-Hui Wang ◽

He Wang ◽

...

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonds ◽

Closed Shell ◽

Hirshfeld Surface ◽

X Ray Diffraction ◽

Single Crystal Diffraction ◽

Aim Analysis ◽

X Ray ◽

Hirshfeld Analysis ◽

Diffraction Structure

The coordination complex bis(1H-benzimidazole-κN3)cadmium(II) dibenzoate has been synthesized and characterized by single crystal diffraction analysis. Cadmium center is six coordinated and formed a distorted octahedron coordinated geometry. The Hirshfeld analysis shows that in the dnorm-surface of the compound, there are dark red spots near the hydrogen-bonds acceptor and donor atoms, while intermolecular interactions result in faint-red spots. The AIM analysis was performed, there exist a BCP in each N(C)–H∙∙∙O hydrogen bond, the bond paths also can be seen, the |V(b)|/G(b) < 1 and the H(b) > 0, the interaction is indicative of being a closed shell. The TG results are consistent with the X-ray diffraction structure.

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A New Decavanadate with Organic Cation: Synthesis, Crystal Structure, and Hirshfeld Surface Analysis

Advances in Materials Science and Engineering ◽

10.1155/2021/5542315 ◽

2021 ◽

Vol 2021 ◽

pp. 1-8

Author(s):

Rawia Nasri ◽

Regaya Ksiksi ◽

Mohsen Graia ◽

Mohamed Faouzi Zid

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Room Temperature ◽

Organic Cation ◽

Three Dimensional ◽

Hirshfeld Surface ◽

Van Der Waals Interactions ◽

Water Molecules ◽

X Ray Diffraction ◽

X Ray

A new 2,6-bis aminomethyl piperidine decavanadate hydrate, (C7N3H20)2V10O28.4.21H2O, was synthesized by slow evaporation of a solution at room temperature. The molecular structure was investigated by single-crystal X-ray diffraction. In the crystal structure, the layers of decavanadate groups, organic cations, and water molecules are arranged parallel to the (010) plane. Also, the prepared compound has been analysed by FTIR spectroscopy and scanning electron microscopy (SEM). The crystal structure of the title compound is stabilized by hydrogen bonds and van der Waals interactions. The cohesion of the structure is ensured by O-H…O and N-H…O hydrogen bonds. The three-dimensional Hirshfeld surface (3D-HS) and the relative two-dimensional fingerprint plots (2D-FPs) of (C7N3H20)2V10O28.4.21H2O compound revealed that the structure is dominated by O…H/H…O (70.8%) and H…H (18.5%) contacts.

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Synthesis, structural elucidation, characterization and theoretical DFT study of 1-(o-tolyl)biguanidium chloride

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229620006336 ◽

2020 ◽

Vol 76 (6) ◽

pp. 572-578

Author(s):

Kamel Kaabi ◽

Kacem Klai ◽

Emmanuel Wenger ◽

Christian Jelsch ◽

Frédéric Lefebvre ◽

...

Keyword(s):

Hydrogen Bonds ◽

Hydrophobic Interactions ◽

Hirshfeld Surface ◽

Electrostatic Energy ◽

Monoclinic Space Group ◽

X Ray Diffraction ◽

Absorption Bands ◽

Methyl Group ◽

X Ray

The structure of the new salt 1-(o-tolyl)biguanidium chloride, C9H14N5 +·Cl−, has been determined by single-crystal X-ray diffraction. The salt crystallizes in the monoclinic space group C2/c. In this structure, the chloride and biguanidium hydrophilic ions are mostly connected to each other via N—H...N and N—H...Cl hydrogen bonds to form layers parallel to the ab plane around y = 1 \over 3 and y = 2 \over 3. The 2-methylbenzyl groups form layers between these layers around y = 0 and y = 1 \over 2, with the methyl group forming C—H...π interactions with the aromatic ring. Intermolecular interactions on the Hirshfeld surface were investigated in terms of contact enrichment and electrostatic energy, and confirm the role of strong hydrogen bonds along with hydrophobic interactions. A correlation between electrostatic energy and contact enrichment is found only for the strongly attractive (N—H...Cl−) and repulsive contacts. Electrostatic energies between ions reveal that the interacting biguanidium cation pairs are repulsive and that the crystal is maintained by attractive cation...Cl− dimers. The vibrational absorption bands were identified by IR spectroscopy.

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2,4-Dimethyl-1,3-thiazole-5-carboxylic acid: an X-ray structural study at 100 K and Hirshfeld surface analysis

Acta Crystallographica Section C Crystal Structure Communications ◽

10.1107/s010827011204142x ◽

2012 ◽

Vol 68 (11) ◽

pp. o452-o455

Author(s):

Dipak K. Hazra ◽

Monika Mukherjee ◽

Madeleine Helliwell ◽

Alok K. Mukherjee

Keyword(s):

Crystal Structure ◽

Carboxylic Acid ◽

Hydrogen Bonds ◽

Single Crystal ◽

Crystal Packing ◽

Hirshfeld Surface ◽

Two Dimensional ◽

Supramolecular Framework ◽

X Ray ◽

Polymeric Chains

The crystal structure of the title thiazolecarboxylic acid derivative, C6H7NO2S, (I), has been determined from single-crystal X-ray analysis at 100 K. In the crystal packing, an interplay of O—H...N and C—H...O hydrogen bonds connects the molecules to formC(6)R22(8) polymeric chains, which are further linkedviaweak C—H...O hydrogen bonds into a two-dimensional supramolecular framework. The relative contributions of different interactions to the Hirshfeld surface in (I) and a few related thiazolecarboxylic acid derivatives indicate that the H...H, N...H and O...H contacts can account for about 50–70% of the total Hirshfeld surface area in this class of compound.

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