scholarly journals N,N′-Bis(pyridin-3-ylmethyl)ethanediamide monohydrate: crystal structure, Hirshfeld surface analysis and computational study

2020 ◽  
Vol 76 (1) ◽  
pp. 25-31 ◽  
Author(s):  
Sang Loon Tan ◽  
Edward R. T. Tiekink
Keyword(s):  
Hydrogen Bonds ◽  
Computational Study ◽  
Helical Chain ◽  
Central Plane ◽  
Orthogonal Relationship ◽  
Hydrogen Bonding Interactions ◽  
Hirshfeld Surfaces ◽  
Methylene Groups ◽  
Layer Region ◽  
The Stability

The molecular structure of the title bis-pyridyl substituted diamide hydrate, C14H14N4O2·H2O, features a central C2N2O2 residue (r.m.s. deviation = 0.0205 Å) linked at each end to 3-pyridyl rings through methylene groups. The pyridyl rings lie to the same side of the plane, i.e. have a syn-periplanar relationship, and form dihedral angles of 59.71 (6) and 68.42 (6)° with the central plane. An almost orthogonal relationship between the pyridyl rings is indicated by the dihedral angle between them [87.86 (5)°]. Owing to an anti disposition between the carbonyl-O atoms in the core, two intramolecular amide-N—H...O(carbonyl) hydrogen bonds are formed, each closing an S(5) loop. Supramolecular tapes are formed in the crystal via amide-N—H...O(carbonyl) hydrogen bonds and ten-membered {...HNC2O}2 synthons. Two symmetry-related tapes are linked by a helical chain of hydrogen-bonded water molecules via water-O—H...N(pyridyl) hydrogen bonds. The resulting aggregate is parallel to the b-axis direction. Links between these, via methylene-C—H...O(water) and methylene-C—H...π(pyridyl) interactions, give rise to a layer parallel to (10\overline{1}); the layers stack without directional interactions between them. The analysis of the Hirshfeld surfaces point to the importance of the specified hydrogen-bonding interactions, and to the significant influence of the water molecule of crystallization upon the molecular packing. The analysis also indicates the contribution of methylene-C—H...O(carbonyl) and pyridyl-C—H...C(carbonyl) contacts to the stability of the inter-layer region. The calculated interaction energies are consistent with importance of significant electrostatic attractions in the crystal.

scholarly journals 2-[(1E)-[(Z)-2-({[(1Z)-[(E)-2-[(2-Hydroxyphenyl)methylidene]hydrazin-1-ylidene]({[(4-methylphenyl)methyl]sulfanyl})methyl]disulfanyl}({[(4-methylphenyl)methyl]sulfanyl})methylidene)hydrazin-1-ylidene]methyl]phenol: crystal structure, Hirshfeld surface analysis and computational study

2020 ◽  
Vol 76 (8) ◽  
pp. 1245-1250
Author(s):  
Georgiana Paulus ◽  
Huey Chong Kwong ◽  
Karen A. Crouse ◽  
Edward R. T. Tiekink
Keyword(s):  
Crystal Structure ◽  
Torsion Angle ◽  
Computational Study ◽  
Hirshfeld Surface ◽  
Interaction Energies ◽  
Orthogonal Relationship ◽  
Hirshfeld Surfaces ◽  
Layer Region ◽  
Imine Bond ◽  
Dispersion Term

The complete molecule of the title hydrazine carbodithioate derivative, C32H30N4O2S4, is generated by a crystallographic twofold axis that bisects the disulfide bond. The molecule is twisted about this bond with the C—S—S—C torsion angle of 90.70 (8)° indicating an orthogonal relationship between the symmetry-related halves of the molecule. The conformation about the imine bond [1.282 (2) Å] is E and there is limited delocalization of π-electron density over the CN2C residue as there is a twist about the N—N bond [C—N—N—C torsion angle = −166.57 (15)°]. An intramolecular hydroxyl-O—H...N(imine) hydrogen bond closes an S(6) loop. In the crystal, methylene-C—H...π(tolyl) contacts assemble molecules into a supramolecular layer propagating in the ab plane: the layers stack without directional interactions between them. The analysis of the calculated Hirshfeld surfaces confirm the importance of H...H contacts, which contribute 46.7% of all contacts followed by H...C/C...H contacts [25.5%] reflecting, in part, the C—H...π(tolyl) contacts. The calculation of the interaction energies confirm the importance of the dispersion term and the influence of the stabilizing H...H contacts in the inter-layer region.

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 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-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 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 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 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 Effects of electron transfer on the stability of hydrogen bonds

2017 ◽  
Vol 8 (11) ◽  
pp. 7324-7329 ◽  
Author(s):  
Tyler M. Porter ◽  
Gavin P. Heim ◽  
Clifford P. Kubiak
Keyword(s):  
Electron Transfer ◽  
Hydrogen Bonds ◽  
Ruthenium Complexes ◽  
Complementary Pair ◽  
Redox States ◽  
The Stability ◽  
Hydrogen Bonded

The measurement of the dimerization constants of hydrogen-bonded ruthenium complexes (12, 22, 32) linked by a self-complementary pair of 4-pyridylcarboxylic acid ligands in different redox states is reported.

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.

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