scholarly journals 3,3-Bis(2-hydroxyethyl)-1-(4-nitrobenzoyl)thiourea: crystal structure, Hirshfeld surface analysis and computational study

2020 ◽  
Vol 76 (2) ◽  
pp. 155-161 ◽  
Author(s):  
Sang Loon Tan ◽  
Mukesh M. Jotani ◽  
Edward R. T. Tiekink
Keyword(s):  
Hydrogen Bonds ◽  
Gas Phase ◽  
Computational Study ◽  
Three Dimensional ◽  
Molecular Structures ◽  
Close Match ◽  
Covalent Interaction ◽  
Compound C ◽  
Hirshfeld Surfaces ◽  
Type C

In the title compound, C12H15N3O5S, a trisubstituted thiourea derivative, the central CN2S chromophore is almost planar (r.m.s. deviation = 0.018 Å) and the pendant hydroxyethyl groups lie to either side of this plane. While to a first approximation the thione-S and carbonyl-O atoms lie to the same side of the molecule, the S—C—N—C torsion angle of −47.8 (2)° indicates a considerable twist. As one of the hydroxyethyl groups is orientated towards the thioamide residue, an intramolecular N—H...O hydrogen bond is formed which leads to an S(7) loop. A further twist in the molecule is indicated by the dihedral angle of 65.87 (7)° between the planes through the CN2S chromophore and the 4-nitrobenzene ring. There is a close match between the experimental and gas-phase, geometry-optimized (DFT) molecular structures. In the crystal, O—H...O and O—H...S hydrogen bonds give rise to supramolecular layers propagating in the ab plane. The connections between layers to consolidate the three-dimensional architecture are of the type C—H...O, C—H...S and nitro-O...π. The nature of the supramolecular association has been further analysed by a study of the calculated Hirshfeld surfaces, non-covalent interaction plots and computational chemistry, all of which point to the significant influence and energy of stabilization provided by the conventional hydrogen bonds.

scholarly journals The 1:2 co-crystal formed between N,N′-bis(pyridin-4-ylmethyl)ethanediamide and benzoic acid: crystal structure, Hirshfeld surface analysis and computational study

2020 ◽  
Vol 76 (1) ◽  
pp. 102-110 ◽  
Author(s):  
Sang Loon Tan ◽  
Edward R. T. Tiekink
Keyword(s):  
Hydrogen Bonds ◽  
Benzoic Acid ◽  
Computational Study ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Molecular Structures ◽  
Amide Hydrogen ◽  
Title 1 ◽  
Crystal And Molecular Structures ◽  
Hirshfeld Surfaces

The crystal and molecular structures of the title 1:2 co-crystal, C14H14N4O2·2C7H6O2, are described. The oxalamide molecule has a (+)-antiperiplanar conformation with the 4-pyridyl residues lying to either side of the central, almost planar C2N2O2 chromophore (r.m.s. deviation = 0.0555 Å). The benzoic acid molecules have equivalent, close to planar conformations [C6/CO2 dihedral angle = 6.33 (14) and 3.43 (10)°]. The formation of hydroxy-O—H...N(pyridyl) hydrogen bonds between the benzoic acid molecules and the pyridyl residues of the diamide leads to a three-molecule aggregate. Centrosymmetrically related aggregates assemble into a six-molecule aggregate via amide-N—H...O(amide) hydrogen bonds through a 10-membered {...HNC2O}2 synthon. These are linked into a supramolecular tape via amide-N—H...O(carbonyl) hydrogen bonds and 22-membered {...HOCO...NC4NH}2 synthons. The contacts between tapes to consolidate the three-dimensional architecture are of the type methylene-C—H...O(amide) and pyridyl-C—H...O(carbonyl). These interactions are largely electrostatic in nature. Additional non-covalent contacts are identified from an analysis of the calculated Hirshfeld surfaces.

scholarly journals 3,3-Bis(2-hydroxyethyl)-1-(4-methylbenzoyl)thiourea: crystal structure, Hirshfeld surface analysis and computational study

2019 ◽  
Vol 75 (10) ◽  
pp. 1472-1478 ◽  
Author(s):  
Sang Loon Tan ◽  
Ainnul Hamidah Syahadah Azizan ◽  
Mukesh M. Jotani ◽  
Edward R. T. Tiekink
Keyword(s):  
Hydrogen Bonds ◽  
Gas Phase ◽  
Computational Study ◽  
Supramolecular Interactions ◽  
Interaction Energies ◽  
Dft Methods ◽  
Covalent Interaction ◽  
Hirshfeld Surfaces ◽  
First Approximation ◽  
Hydroxyethyl Group

In the title tri-substituted thiourea derivative, C13H18N2O3S, the thione-S and carbonyl-O atoms lie, to a first approximation, to the same side of the molecule [the S—C—N—C torsion angle is −49.3 (2)°]. The CN2S plane is almost planar (r.m.s. deviation = 0.018 Å) with the hydroxyethyl groups lying to either side of this plane. One hydroxyethyl group is orientated towards the thioamide functionality enabling the formation of an intramolecular N—H...O hydrogen bond leading to an S(7) loop. The dihedral angle [72.12 (9)°] between the planes through the CN2S atoms and the 4-tolyl ring indicates the molecule is twisted. The experimental molecular structure is close to the gas-phase, geometry-optimized structure calculated by DFT methods. In the molecular packing, hydroxyl-O—H...O(hydroxyl) and hydroxyl-O—H...S(thione) hydrogen bonds lead to the formation of a supramolecular layer in the ab plane; no directional interactions are found between layers. The influence of the specified supramolecular interactions is apparent in the calculated Hirshfeld surfaces and these are shown to be attractive in non-covalent interaction plots; the interaction energies point to the important stabilization provided by directional O—H...O hydrogen bonds.

scholarly journals Steric control of supramolecular association in structures of Zn(S2COR)2 with N,N′-bis(pyridin-4-ylmethyl)oxalamide

2019 ◽  
Vol 234 (3) ◽  
pp. 165-175 ◽  
Author(s):  
Yee Seng Tan ◽  
Hao Zhe Chun ◽  
Mukesh M. Jotani ◽  
Edward R.T. Tiekink
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Molecular Structures ◽  
Coordination Geometry ◽  
Hirshfeld Surfaces ◽  
Binuclear Molecule ◽  
Supramolecular Chain ◽  
The One ◽  
Distorted Tetrahedral Coordination ◽  
Cyclohexyl Group

Abstract The crystal and molecular structures of the one-dimensional coordination polymer [Zn(S2COEt)2(4LH2)]n (1) and binuclear [Zn(S2COCy)2]2(4LH2) (2) are described, where 4LH2 is N,N′-bis(pyridin-4-ylmethyl)ethanediamide. In 1, the Zn(S2COEt)2 entities are linked by bidentate bridging 4LH2 ligands through the pyridyl-N atoms to generate a twisted supramolecular chain. As a result of monodentate xanthate ligands, the N2S4 donor set defines a distorted tetrahedral coordination geometry and, crucially, allows the participation of the non-coordinating sulfur atoms in supramolecular association. Thus, in the crystal amide-N–H···O(amide) and amide-N–H···S(thione) hydrogen bonds link chains into a three-dimensional architecture. The substitution of the ethyl group in the xanthate ligand with a cyclohexyl group results in very different structural outcomes. In 2, a binuclear molecule is observed with the coordination geometry for zinc being defined by chelating xanthate ligands and a pyridyl-N atom with the NS4 donor set defining a highly distorted geometry. In the molecular packing, amide-N–H···S(thione) hydrogen bonds stabilise a supramolecular chain along the a-axis and these are connected into a three-dimensional arrangement by methylene-C–H···O and methylene-C–H···π(pyridyl) interactions. The relative importance of the specified intermolecular interactions and weaker, contributing contacts has been revealed by an analysis of the calculated Hirshfeld surfaces of 1 and 2.

scholarly journals Bis(N-adamantyl-N′-ethylimidazolium) tetrabromidomanganate(II)

IUCrData ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Niels Ole Giltzau ◽  
Martin Köckerling
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Coulombic Interactions ◽  
Compound C ◽  
Dimensional Network ◽  
Weak Hydrogen Bonds ◽  
Type C

The title compound, (C15H23N2)2[MnBr4], comprises two N-adamantyl-N′-ethylimidazolium cations and one tetrahedral [MnBr4]2− anion. Next to Coulombic interactions, weak hydrogen bonds of the type C—H...Br consolidate the crystal packing, building up a three-dimensional network.

scholarly journals A 1:2 co-crystal of 2,2′-thiodibenzoic acid and triphenylphosphane oxide: crystal structure, Hirshfeld surface analysis and computational study

2018 ◽  
Vol 74 (12) ◽  
pp. 1764-1771 ◽  
Author(s):  
Sang Loon Tan ◽  
Edward R. T. Tiekink
Keyword(s):  
Hydrogen Bonds ◽  
Conformational Changes ◽  
Disulfide Bonds ◽  
Computational Study ◽  
Three Dimensional ◽  
Dihedral Angles ◽  
Asymmetric Unit ◽  
Hirshfeld Surfaces ◽  
Oxide Crystal ◽  
Phenyl Rings

The asymmetric unit of the title co-crystal, 2,2′-thiodibenzoic acid–triphenylphosphane oxide (1/2), C14H10O4S·2C18H15OP, comprises two molecules of 2,2′-thiodibenzoic acid [TDBA; systematic name: 2-[(2-carboxyphenyl)sulfanyl]benzoic acid] and four molecules of triphenylphosphane oxide [TPPO; systematic name: (diphenylphosphoryl)benzene]. The two TDBA molecules are twisted about their disulfide bonds and exhibit dihedral angles of 74.40 (5) and 72.58 (5)° between the planes through the two SC6H4 residues. The carboxylic acid groups are tilted out of the planes of the rings to which they are attached forming a range of CO2/C6 dihedral angles of 19.87 (6)–60.43 (8)°. Minor conformational changes are exhibited in the TPPO molecules with the range of dihedral angles between phenyl rings being −2.1 (1) to −62.8 (1)°. In the molecular packing, each TDBA acid molecule bridges two TPPO molecules via hydroxy-O—H...O(oxide) hydrogen bonds to form two three-molecule aggregates. These are connected into a three-dimensional architecture by TPPO-C—H...O(oxide, carbonyl) and TDBA-C—H...(oxide, carbonyl) interactions. The importance of H...H, O...H/H...O and C...H/H...C contacts to the calculated Hirshfeld surfaces has been demonstrated. In terms of individual molecules, O...H/H...O contacts are more important for the TDBA (ca 28%) than for the TPPO molecules (ca 13%), as expected from the chemical composition of these species. Computational chemistry indicates the four independent hydroxy-O—H...O(oxide) hydrogen bonds in the crystal impart about the same energy (ca 52 kJ mol−1), with DTBA-phenyl-C—H...O(oxide) interactions being next most stabilizing (ca 40 kJ mol−1).

scholarly journals Crystal structure and Hirshfeld surface analysis of (Z)-3-methyl-4-(thiophen-2-ylmethylidene)isoxazol-5(4H)-one

2021 ◽  
Vol 77 (4) ◽  
pp. 378-382
Author(s):  
Rima Laroum ◽  
Assia Benouatas ◽  
Noudjoud Hamdouni ◽  
Wissame Zemamouche ◽  
Ali Boudjada ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
Title Compound ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Asymmetric Unit ◽  
Compound C ◽  
Hirshfeld Surfaces ◽  
Independent Molecules

The title compound, C9H7NO2S crystallizes with two independent molecules (A and B) in the asymmetric unit with Z = 8. Both molecules are almost planar with a dihedral angle between the isoxazole and thiophen rings of 3.67 (2)° in molecule A and 10.00 (1) ° in molecule B. The packing of molecules A and B is of an ABAB... type along the b-axis direction, the configuration about the C=C bond is Z. In the crystal, the presence of C—H...O, C—H... N and π–π interactions [centroid–centroid distances of 3.701 (2) and 3.766 (2) Å] link the molecules into a three-dimensional architecture. An analysis of Hirshfeld surfaces shows the importance of C—H...O and C—H...N hydrogen bonds in the packing mechanism of the crystalline structure.

scholarly journals Crystal structure and Hirshfeld surface analysis of (Z)-4-(4-hydroxybenzylidene)-3-methylisoxazol-5(4H)-one

2018 ◽  
Vol 74 (7) ◽  
pp. 926-930
Author(s):  
Wissem Zemamouche ◽  
Rima Laroun ◽  
Noudjoud Hamdouni ◽  
Ouarda Brihi ◽  
Ali Boudjada ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Title Compound ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Π Interactions ◽  
Compound C ◽  
Hirshfeld Surfaces

The title compound, C11H9NO3, contains an isoxazole and a hydroxybenzylidene ring, which are inclined to each another by 3.18 (8)°. There is an intramolecular C—H...O contact forming an S(7) ring. In the crystal, molecules stack head-to-tail in columns along the b-axis direction, linked by offset π–π interactions [intercentroid distances of 3.676 (1) and 3.723 (1) Å]. The columns are linked by O—H...O and O—H...N hydrogen bonds, forming layers parallel to the ab plane. The layers are linked by C—H...O hydrogen bonds, forming a supramolecular three-dimensional framework. An analysis of the Hirshfeld surfaces points to the importance of the O—H...O and O—H...N hydrogen bonding in the packing mechanism of the crystal structure.

scholarly journals 3-{(E)-[4-(4-Hydroxy-3-methoxyphenyl)butan-2-ylidene]amino}-1-phenylurea: crystal structure and Hirshfeld surface analysis

2018 ◽  
Vol 74 (1) ◽  
pp. 21-27 ◽  
Author(s):  
Ming Yueh Tan ◽  
Karen A. Crouse ◽  
Thahira B. S. A. Ravoof ◽  
Mukesh M. Jotani ◽  
Edward R. T. Tiekink
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Dihedral Angles ◽  
Amide Hydrogen ◽  
Asymmetric Unit ◽  
Compound C ◽  
Hirshfeld Surfaces ◽  
Disubstituted Benzene ◽  
Independent Molecules

Two independent molecules (AandB) comprise the asymmetric unit of the title compound, C18H21N3O3. The urea moiety is disubstituted with one amine being linked to a phenyl ring, which is twisted out of the plane of the CN2O urea core [dihedral angles = 25.57 (11) (A) and 29.13 (10)° (B)]. The second amine is connected to an imine (Econformation), which is linked in turn to an ethane bridge that links a disubstituted benzene ring. Intramolecular amine-N—H...N(imine) and hydroxyl-O—H...O(methoxy) hydrogen bonds closeS(5) loops in each case. The molecules have twisted conformations with the dihedral angles between the outer rings being 38.64 (81) (A) and 48.55 (7)° (B). In the crystal, amide-N—H...O(amide) hydrogen bonds link the moleculesAandB viaan eight-membered {...HNCO}2synthon. Further associations between molecules, leading to supramolecular layers in theacplane, are hydrogen bonds of the type hydroxyl-O—H...N(imine) and phenylamine-N—H...O(methoxy). Connections between layers, leading to a three-dimensional architecture, comprise benzene-C—H...O(hydroxy) interactions. A detailed analysis of the calculated Hirshfeld surfaces shows moleculesAandBparticipate in very similar intermolecular interactions and that any variations relate to conformational differences between the molecules.

scholarly journals 4-[(1E)-({[(Benzylsulfanyl)methanethioyl]amino}imino)methyl]benzene-1,3-diol chloroform hemisolvate: crystal structure, Hirshfeld surface analysis and computational study

2020 ◽  
Vol 76 (7) ◽  
pp. 990-997
Author(s):  
Nadia Liyana Khairuanuar ◽  
Karen A. Crouse ◽  
Huey Chong Kwong ◽  
Sang Loon Tan ◽  
Edward R. T. Tiekink
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Phenyl Ring ◽  
Computational Study ◽  
Three Dimensional ◽  
Central Plane ◽  
Threefold Axis ◽  
Covalent Interaction ◽  
Imine Bond ◽  
Gas Phase Structure

The title hydrazine carbodithioate chloroform hemisolvate, 2C15H14N2O2S2·CHCl3, comprises two independent hydrazine carbodithioate molecules, A and B, and a chloroform molecule; the latter is statistically disordered about its molecular threefold axis. The common features of the organic molecules include an almost planar, central CN2S2 chromophore [r.m.s. deviation = 0.0203 Å (A) and 0.0080 Å (B)], an E configuration about the imine bond and an intramolecular hydroxyl-O—H...N(imine) hydrogen bond. The major conformational difference between the molecules is seen in the relative dispositions of the phenyl rings as indicated by the values of the dihedral angles between the central plane and phenyl ring of 71.21 (6)° (A) and 54.73 (7)° (B). Finally, a difference is seen in the disposition of the outer hydroxyl-H atoms, having opposite relative orientations. In the calculated gas-phase structure, the entire molecule is planar with the exception of the perpendicular phenyl ring. In the molecular packing, the A and B molecules assemble into a two-molecule aggregate via N—H...S hydrogen bonds and eight-membered {...HNCS}2 synthons. The dimeric assemblies are connected into supramolecular chains via hydroxyl-O—H...O(hydroxyl) hydrogen bonds and these are linked into a double-chain through hydroxy-O—H...π(phenyl) interactions. The double-chains are connected into a three-dimensional architecture through phenyl-C—H...O(hydroxyl) and phenyl-C—H...π(phenyl) interactions. The overall assembly defines columns along the a-axis direction in which reside the chloroform molecules, which are stabilized by chloroform–methine-C—H...S(thione) and phenyl-C—H...Cl contacts. The analysis of the calculated Hirshfeld surfaces, non-covalent interaction plots and interaction energies confirm the importance of the above-mentioned interactions, but also of cooperative, non-standard interactions such as π(benzene)...π(hydrogen-bond-mediated-ring) contacts.

scholarly journals Bis(N,N-diethyldithiocarbamato-κ2S,S′)(3-hydroxypyridine-κN)zinc and bis[N-(2-hydroxyethyl)-N-methyldithiocarbamato-κ2S,S′](3-hydroxypyridine-κN)zinc: crystal structures and Hirshfeld surface analysis

2016 ◽  
Vol 72 (12) ◽  
pp. 1700-1709 ◽  
Author(s):  
Mukesh M. Jotani ◽  
Hadi D. Arman ◽  
Pavel Poplaukhin ◽  
Edward R. T. Tiekink
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Molecular Structures ◽  
Trigonal Bipyramidal ◽  
Hirshfeld Surfaces ◽  
The Common ◽  
Independent Molecules ◽  
Dimeric Aggregates ◽  
Supramolecular Chains ◽  
Hydrogen Bonding Potential

The common feature of the molecular structures of the title compounds, [Zn(C5H10NS2)2(C5H5NO)], (I), and [Zn(C4H8NOS2)2(C5H5NO)], (II), are NS4donor sets derived fromN-bound hydroxypyridyl ligands and asymmetrically chelating dithiocarbamate ligands. The resulting coordination geometries are highly distorted, being intermediate between square pyramidal and trigonal bipyramidal for both independent molecules comprising the asymmetric unit of (I), and significantly closer towards square pyramidal in (II). The key feature of the molecular packing in (I) is the formation of centrosymmetric, dimeric aggregates sustained by pairs of hydroxy-O—H...S(dithiocarbamate) hydrogen bonds. The aggregates are connected into a three-dimensional architecture by methylene-C—H...O(hydroxy) and methyl-C—H...π(chelate) interactions. With greater hydrogen-bonding potential, supramolecular chains along thecaxis are formed in the crystal of (II), sustained by hydroxy-O—H...O(hydroxy) hydrogen bonds, with ethylhydroxy and pyridylhydroxy groups as the donors, along with ethylhydroxy-O—H...S(dithiocarbamate) hydrogen bonds. Chains are connected into layers in theacplane by methylene-C—H...π(chelate) interactions and these stack along thebaxis, with no directional interactions between them. An analysis of the Hirshfeld surfaces clearly distinguished the independent molecules of (I) and reveals the importance of the C—H...π(chelate) interactions in the packing of both (I) and (II).

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