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 A 1:2 co-crystal of 2,2′-dithiodibenzoic acid and benzoic acid: crystal structure, Hirshfeld surface analysis and computational study

2019 ◽  
Vol 75 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Sang Loon Tan ◽  
Edward R. T. Tiekink
Keyword(s):  
Benzoic Acid ◽  
Dihedral Angle ◽  
Computational Study ◽  
Three Dimensional ◽  
Acid Group ◽  
Hirshfeld Surface ◽  
Carboxylic Acid Group ◽  
Title 1 ◽  
Axis Of Symmetry ◽  
Ring Centroid

The asymmetric unit of the title 1:2 co-crystal, C14H10O4S2·2C7H6O2, comprises half a molecule of dithiodibenzoic acid [systematic name: 2-[(2-carboxyphenyl)disulfanyl]benzoic acid, DTBA], as the molecule is located about a twofold axis of symmetry, and a molecule of benzoic acid (BA). The DTBA molecule is twisted about the disulfide bond [the C—S—S—C torsion angle is −83.19 (8)°] resulting in a near perpendicular relationship between the benzene rings [dihedral angle = 71.19 (4)°]. The carboxylic acid group is almost co-planar with the benzene ring to which it is bonded [dihedral angle = 4.82 (12)°]. A similar near co-planar relationship pertains for the BA molecule [dihedral angle = 3.65 (15)°]. Three-molecule aggregates are formed in the crystal whereby two BA molecules are connected to a DTBA molecule via hydroxy-O—H...O(hydroxy) hydrogen bonds and eight-membered {...HOC=O}2 synthons. These are connected into a supramolecular layer in the ab plane through C—H...O interactions. The interactions between layers to consolidate the three-dimensional architecture are π–π stacking interactions between DTBA and BA rings [inter-centroid separation = 3.8093 (10) Å] and parallel DTBA-hydroxy-O...π(BA) contacts [O...ring centroid separation = 3.9049 (14) Å]. The importance of the specified interactions as well as other weaker contacts, e.g. π–π and C—H...S, are indicated in the analysis of the calculated Hirshfeld surface and interaction energies.

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 2,2′-(Disulfanediyl)dibenzoic acid N,N-dimethylformamide monosolvate: crystal structure, Hirshfeld surface analysis and computational study

2020 ◽  
Vol 76 (7) ◽  
pp. 1150-1157
Author(s):  
Sang Loon Tan ◽  
Edward R. T. Tiekink
Keyword(s):  
Benzene Ring ◽  
Computational Study ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Title 1 ◽  
Torsion Angles ◽  
Carboxylic Acid Groups ◽  
Hirshfeld Surfaces ◽  
Intermolecular Contacts ◽  
Benzene Rings

The title 1:1 solvate, C14H10O4S2·C3H7NO, features a twisted molecule of 2,2′-dithiodibenzoic acid (DTBA), with the central C—S—S—C torsion angle being −88.57 (6)°, and a molecule of dimethylformamide (DMF). The carboxylic acid groups are, respectively, close to co-planar and twisted with respect to the benzene rings to which they are connected as seen in the CO2/C6 torsion angles of 1.03 (19) and 7.4 (2)°. Intramolecular, hypervalent S←O interactions are noted [S...O = 2.6140 (9) and 2.6827 (9) Å]. In the crystal, four-molecule aggregates are formed via DTBA-O—H...O(DMF) and DTBA-O—H...O(DTBA) hydrogen bonding, the latter via an eight-membered {...OHCO}2 homosynthon. These are linked into supramolecular layers parallel to (011) via benzene-C—H...O(DTBA) and DTBA-C=O...π(benzene) interactions, with the connections between these, giving rise to a three-dimensional architecture, being of the type benzene-C—H...π(benzene). An analysis of the calculated Hirshfeld surfaces indicates, in addition to the aforementioned intermolecular contacts, the presence of stabilizing interactions between a benzene ring and a quasi-π-system defined by O—H...O hydrogen bonds between a DTBA dimer, i.e. the eight-membered {...OCOH}2 ring system, and between a benzene ring and a quasi-π(OCOH...OCH) system arising from the DTBA-O—H...O(DMF) hydrogen bond. The inter-centroid separations are 3.65 and 3.49 Å, respectively.

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

2020 ◽  
Vol 76 (2) ◽  
pp. 245-253 ◽  
Author(s):  
Sang Loon Tan ◽  
Edward R. T. Tiekink
Keyword(s):  
Hydrogen Bonding ◽  
Computational Study ◽  
Three Dimensional ◽  
Dihedral Angles ◽  
Interaction Energies ◽  
Carbonyl Groups ◽  
Amide Hydrogen ◽  
Title 1 ◽  
Chlorobenzoic Acid ◽  
Hirshfeld Surfaces

The asymmetric unit of the title 1:2 co-crystal, C14H14N4O2·2C7H5ClO2, comprises two half molecules of oxalamide (4 LH2), as each is disposed about a centre of inversion, and two molecules of 4-chlorobenzoic acid (CBA), each in general positions. Each 4 LH2 molecule has a (+)antiperiplanar conformation with the pyridin-4-yl residues lying to either side of the central, planar C2N2O2 chromophore with the dihedral angles between the respective central core and the pyridyl rings being 68.65 (3) and 86.25 (3)°, respectively, representing the major difference between the independent 4 LH2 molecules. The anti conformation of the carbonyl groups enables the formation of intramolecular amide-N—H...O(amide) hydrogen bonds, each completing an S(5) loop. The two independent CBA molecules are similar and exhibit C6/CO2 dihedral angles of 8.06 (10) and 17.24 (8)°, indicating twisted conformations. In the crystal, two independent, three-molecule aggregates are formed via carboxylic acid-O—H...N(pyridyl) hydrogen bonding. These are connected into a supramolecular tape propagating parallel to [100] through amide-N—H...O(amide) hydrogen bonding between the independent aggregates and ten-membered {...HNC2O}2 synthons. The tapes assemble into a three-dimensional architecture through pyridyl- and methylene-C—H...O(carbonyl) and CBA-C—H...O(amide) interactions. As revealed by a more detailed analysis of the molecular packing by calculating the Hirshfeld surfaces and computational chemistry, are the presence of attractive and dispersive Cl...C=O interactions which provide interaction energies approximately one-quarter of those provided by the amide-N—H...O(amide) hydrogen bonding sustaining the supramolecular tape.

scholarly journals N,N′-Bis(pyridin-4-ylmethyl)oxalamide benzene monosolvate: crystal structure, Hirshfeld surface analysis and computational study

2019 ◽  
Vol 75 (8) ◽  
pp. 1133-1139 ◽  
Author(s):  
Sang Loon Tan ◽  
Nathan R. Halcovitch ◽  
Edward R. T. Tiekink
Keyword(s):  
Computational Study ◽  
Hirshfeld Surface ◽  
Pyridyl Ring ◽  
Central Plane ◽  
Dispersion Forces ◽  
Amide Hydrogen ◽  
Asymmetric Unit ◽  
Title 1 ◽  
Orthogonal Relationship ◽  
Hirshfeld Surfaces

The asymmetric unit of the title 1:1 solvate, C14H14N4O2·C6H6 [systematic name of the oxalamide molecule: N,N′-bis(pyridin-4-ylmethyl)ethanediamide], comprises a half molecule of each constituent as each is disposed about a centre of inversion. In the oxalamide molecule, the central C2N2O2 atoms are planar (r.m.s. deviation = 0.0006 Å). An intramolecular amide-N—H...O(amide) hydrogen bond is evident, which gives rise to an S(5) loop. Overall, the molecule adopts an antiperiplanar disposition of the pyridyl rings, and an orthogonal relationship is evident between the central plane and each terminal pyridyl ring [dihedral angle = 86.89 (3)°]. In the crystal, supramolecular layers parallel to (10\overline{2}) are generated owing the formation of amide-N—H...N(pyridyl) hydrogen bonds. The layers stack encompassing benzene molecules which provide the links between layers via methylene-C—H...π(benzene) and benzene-C—H...π(pyridyl) interactions. The specified contacts are indicated in an analysis of the calculated Hirshfeld surfaces. The energy of stabilization provided by the conventional hydrogen bonding (approximately 40 kJ mol−1; electrostatic forces) is just over double that by the C—H...π contacts (dispersion forces).

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 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 A cinnamaldehyde Schiff base ofS-(4-methylbenzyl) dithiocarbazate: crystal structure, Hirshfeld surface analysis and computational study

2017 ◽  
Vol 73 (4) ◽  
pp. 543-549 ◽  
Author(s):  
Enis Nadia Md Yusof ◽  
Mohamed I. M. Tahir ◽  
Thahira B. S. A. Ravoof ◽  
Sang Loon Tan ◽  
Edward R. T. Tiekink
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Mirror Symmetry ◽  
Computational Study ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Hydrogen Atoms ◽  
Benzyl Substituent

The title dithiocarbazate ester (I), C18H18N2S2[systematic name: (E)-4-methylbenzyl 2-[(E)-3-phenylallylidene]hydrazinecarbodithioate, comprises an almost planar central CN2S2residue [r.m.s. deviation = 0.0131 Å]. The methylene(tolyl-4) group forms a dihedral angle of 72.25 (4)° with the best plane through the remaining non-hydrogen atoms [r.m.s. deviation = 0.0586 Å] so the molecule approximates mirror symmetry with the 4-tolyl group bisected by the plane. The configuration about both double bonds in the N—N=C—C=C chain isE; the chain has an alltransconformation. In the crystal, eight-membered centrosymmetric thioamide synthons, {...HNCS}2, are formedviaN—H...S(thione) hydrogen bonds. Connections between the dimersviaC—H...π interactions lead to a three-dimensional architecture. A Hirshfeld surface analysis shows that (I) possesses an interaction profile similar to that of a closely related analogue with anS-bound benzyl substituent, (II). Computational chemistry indicates the dimeric species of (II) connectedviaN—H...S hydrogen bonds is about 0.94 kcal mol−1more stable than that in (I).

scholarly journals 2-({[(Pyridin-1-ium-2-ylmethyl)carbamoyl]formamido}methyl)pyridin-1-ium bis(3,5-dicarboxybenzoate): crystal structure and Hirshfeld surface analysis

2016 ◽  
Vol 72 (2) ◽  
pp. 241-248 ◽  
Author(s):  
Mukesh M. Jotani ◽  
Sabrina Syed ◽  
Siti Nadiah Abdul Halim ◽  
Edward R. T. Tiekink
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Torsion Angle ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Carbonyl Groups ◽  
Amide Hydrogen ◽  
Asymmetric Unit ◽  
Torsion Angles ◽  
First Approximation

The asymmetric unit of the title salt, C14H16N4O22+·2C9H5O6−, comprises half a dication, being located about a centre of inversion, and one anion, in a general position. The central C4N2O2group of atoms in the dication are almost planar (r.m.s. deviation = 0.009 Å), and the carbonyl groups lie in anantidisposition to enable the formation of intramolecular amide-N—H...O(carbonyl) hydrogen bonds. To a first approximation, the pyridinium and amide N atoms lie to the same side of the molecule [Npy—C—C—Namidetorsion angle = 34.8 (2)°], and theantipyridinium rings are approximately perpendicular to the central part of the molecule [dihedral angle = 68.21 (8)°]. In the anion, one carboxylate group is almost coplanar with the ring to which it is connected [Cben—Cben—Cq—O torsion angle = 2.0 (3)°], whereas the other carboxylate and carboxylic acid groups are twisted out of the plane [torsion angles = 16.4 (3) and 15.3 (3)°, respectively]. In the crystal, anions assemble into layers parallel to (10-4)viahydroxy-O—H...O(carbonyl) and charge-assisted hydroxy-O—H...O(carboxylate) hydrogen bonds. The dications are linked into supramolecular tapes by amide-N—H...O(amide) hydrogen bonds, and thread through the voids in the anionic layers, being connected by charge-assisted pyridinium-N—O(carboxylate) hydrogen bonds, so that a three-dimensional architecture ensues. An analysis of the Hirshfeld surface points to the importance of O—H...O hydrogen bonding in the crystal structure.

scholarly journals Crystal structures of the 1:1 salts of 2-amino-4-nitrobenzoate with each of (2-hydroxyethyl)dimethylazanium, tert-butyl(2-hydroxyethyl)azanium and 1,3-dihydroxy-2-(hydroxymethyl)propan-2-aminium

2018 ◽  
Vol 74 (12) ◽  
pp. 1735-1740 ◽  
Author(s):  
James L. Wardell ◽  
Edward R. T. Tiekink
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Molecular Structures ◽  
Double Layers ◽  
Crystal And Molecular Structures ◽  
Ammonium N ◽  
Molecular Salts ◽  
Benzene Rings ◽  
The Common ◽  
Supramolecular Aggregation

The crystal and molecular structures of the title molecular salts, C4H12NO+·C7H5N2O4 −, (I), C6H16NO+·C7H5N2O4 −, (II), and C4H12NO3 +·C7H5N2O4 −, (III), are described. The common feature of these salts is the presence of the 2-amino-4-nitrobenzoate anion, which exhibit non-chemically significant variations in the conformational relationships between the carboxylate and nitro groups, and between these and the benzene rings they are connected to. The number of ammonium-N—H H atoms in the cations increases from one to three in (I) to (III), respectively, and this variation significantly influences the supramolecular aggregation patterns in the respective crystals. Thus, a linear supramolecular chain along [100] sustained by charge-assisted tertiary-ammonium-N—H...O(carboxylate), hydroxy-O—H...O(carboxylate) and amino-N—H...O(carboxylate) hydrogen-bonds is apparent in the crystal of (I). Chains are connected into a three-dimensional architecture by methyl-C—H...O(hydroxy) and π–π interactions, the latter between benzene rings [inter-centroid separation = 3.5796 (10) Å]. In the crystal of (II), a supramolecular tube propagating along [901] arises as a result of charge-assisted secondary-ammonium-N—H...O(carboxylate) and hydroxy-O—H...O(carboxylate) hydrogen-bonding. These are connected by methylene- and methyl-C—H...O(nitro) and π–π stacking between benzene rings [inter-centroid separation = 3.5226 (10) Å]. Finally, double-layers parallel to (100) sustained by charge-assisted ammonium-N—H...O(carboxylate), ammonium-N—H...O(hydroxy) and hydroxy-O—H...O(carboxylate) hydrogen-bonds are apparent in the crystal of (III). These are connected in a three-dimensional architecture by amine-N—H...O(nitro) hydrogen-bonds.

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