scholarly journals HYDROGEN BONDS IN THE FORMATION OF COPPER(II) 1,10-PHENANTHROLINE HYDROXYCARBOXYLATOGERMANATE CRYSTALS USING HIRSHFELD SURFACE ANALYSIS

2021 ◽  
Vol 26 (1(77)) ◽  
pp. 85-96
Author(s):  
E. A. Chebanenko ◽  
O. V. Buchko ◽  
E. V. Afanasenko Afanasenko ◽  
I. I. Seifullina ◽  
E. E. Martsinko
Keyword(s):  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Complex Cation ◽  
Three Dimensional ◽  
Total Surface Area ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Complexing Agent ◽  
Water Molecules ◽  
Crystal Formation

This article is dedicated to the investigation of crystalline structure in the complex cation-anionic compounds Cu(Phen)2Cl]2[Ge(HCit)2]⋅6H2O (I), [Cu(Phen)3]2[Ge2(OH)(HTart)(μ-Tart)2]·11H2O (II), [CuCl(Phen)2]4[{Ge2(OH)2(μ-Tart)2}Cl2]·4Н2О (III), [Cu(Phen)3]2[(OH)2Ge2(μ-HXylar)4Ge2(μ-OH)2]·8H2O (IV), [CuCl(Phen)2]4[(OH)2Ge2(μ-HXylar)4Ge2(μ-OH)2]·8H2O (V) using Hirshfeld surface analysis. This method has showed itself as an effective tool for analysis of intermolecular interactions, such as hydrogen bonds or weaker C…H and С…Н…p connections. Three-dimensional picture of close interactions in the crystal was built for each of the compounds I–V, where short connections are red-colored, while others – weaker and shorter – are light areas and small spots. It was established that in the structures of all compounds different types of hydrogen bonds are presented: bifurcate connections, symmetrical О-Н…О, С-Н…С and asymmetrical ones with water molecules. Two-dimensional histograms – 2D-fingerprint plots, allowed to evaluate quantitively connections in the crystals and establish that H…O/O…H and H…H interactions make the biggest contribution to the total surface area. The presence of the big number of crystallization water molecules is determinant for the formation of complex system of hydrogen bonds and strengthening of the structure, that otherwise would be unstable because of the big size of cations and anions. Due to the fact, that all compounds have the same complexing agent Ge(IV), structure of the anion is determined by polydentate ligand. Obtained results are important for the further development of the water role in the processes of crystallization, crystal formation, electrical dissociation and, especially, dissolving of coordination compounds in biological systems.

scholarly journals Synthesis, crystal structure and Hirshfeld surface analysis of tetraaquabis(isonicotinamide-κN 1)cobalt(II) succinate

2018 ◽  
Vol 74 (7) ◽  
pp. 1026-1029 ◽  
Author(s):  
Sevgi Kansiz ◽  
Sergey Malinkin ◽  
Necmi Dege
Keyword(s):  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Complex Cation ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Title Complex ◽  
Hirshfeld Surface Analysis ◽  
Water Molecules ◽  
Basic Solution ◽  
Two Dimensional

The reaction of CoCl2 with succinic acid and isonicotinamide in basic solution produces the title complex [Co(C6H6N2O)2(H2O)4](C4H4O4). The cobalt(II) ion of the complex cation and the succinate anion are each located on an inversion centre. The CoII ion is octahedrally coordinated by four O atoms of water molecules and two N atoms of isonicotinamide molecules. The two ions are linked via Owater—H...Osuccinate hydrogen bonds, forming chains propagating along [001]. In the crystal, these hydrogen-bonded chains are linked into a three-dimensional framework by further O—H...O hydrogen bonds and N—H...O hydrogen bonds. The framework is reinforced by C—H...O hydrogen bonds. Hirshfeld surface analysis and two-dimensional fingerprint plots have been used to analyse the intermolecular interactions present in the crystal.

scholarly journals Crystal structure and Hirshfeld surface analysis of the 1:3 adduct of tetraaquatrinitratoneodymium(III) with 3-amino-1,2,4-triazine

2018 ◽  
Vol 74 (9) ◽  
pp. 1309-1313
Author(s):  
Ramalingam Sangeetha ◽  
Kasthuri Balasubramani ◽  
Savaridasson Jose Kavitha ◽  
Madhukumar Hemamalini
Keyword(s):  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Water Molecules ◽  
Central Metal Atom ◽  
Central Metal ◽  
Nitrate Ions ◽  
Coordinated Water

In the title compound, [Nd(NO3)3(H2O)4]·3C3H4N4, neodymium is ten-coordinate with a distorted bicapped square-antiprismatic geometry formed from six O atoms from three nitrate ions and four O atoms from four coordinated water molecules. The structure also contains neutral 3-amino-1,2,4-triazine molecules which are not coordinated to the central metal atom. The coordinated water molecules and nitrate ions of adjacent complexes are linked by O—H...O hydrogen bonds to form cyclic R 2 2(8) ring motifs, which in turn are further connected via hydrogen bonds to generate a sheet-like structure. The triazine molecules are involved in a number of hydrogen-bonding interactions: N—H...N and O—H...N interactions to form R 3 3(9) motifs and N—H...N interactions to link the organic molecules into chains. Weak C—H...O hydrogen bonds also occur between triazine molecules and coordinated nitrate atoms. All these intermolecular contacts contribute to the stabilization of the three-dimensional supramolecular framework. Hirshfeld surface analysis shows that N...H/H...N and H...H interactions account for 42.9 and 20.6% of the surface, respectively.

scholarly journals Crystal structure and Hirshfeld surface analysis of tetraaquabis(isonicotinamide-κN 1)nickel(II) fumarate

2018 ◽  
Vol 74 (11) ◽  
pp. 1536-1539
Author(s):  
Sevgi Kansiz ◽  
Irina A. Golenya ◽  
Necmi Dege
Keyword(s):  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Crystal Packing ◽  
Complex Cation ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Title Complex ◽  
Hirshfeld Surface Analysis ◽  
Basic Solution ◽  
Supramolecular Architecture

The reaction of NiCl2 with fumaric acid and isonicotinamide in a basic solution produces the title complex, [Ni(C6H6N2O)2(H2O)4](C4H2O4). The nickel(II) ion of the complex cation and the fumarate anion are each located on an inversion centre. The NiII ion is coordinated octahedrally by four water O atoms and two N atoms of isonicotinamide molecules. The fumarate anion is linked to neighbouring complex cations via Owater—H...Ofumarate hydrogen bonds. In the crystal, the complex cations are further linked by O—H...O, N—H...O and C—H...O hydrogen bonds, forming a three-dimensional supramolecular architecture. Hirshfeld surface analysis and two-dimensional fingerprint plots were used to analyse the intermolecular interactions present in the crystal and indicate that the most important contributions for the crystal packing are from H...O/O...H (41.8%), H...H (35.3%) and H...C/C...H (10.2%) interactions.

scholarly journals Crystal structure, Hirshfeld surface analysis and contact enrichment ratios of 1-(2,7-dimethylimidazo[1,2-a]pyridin-3-yl)-2-(1,3-dithiolan-2-ylidene)ethanone monohydrate

2019 ◽  
Vol 75 (12) ◽  
pp. 1934-1939 ◽  
Author(s):  
Yvon Bibila Mayaya Bisseyou ◽  
Mahama Ouattara ◽  
Pénétjiligué Adama Soro ◽  
R. C. A. Yao-Kakou ◽  
Abodou Jules Tenon
Keyword(s):  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Crystal Packing ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Enrichment Ratio ◽  
Water Molecules ◽  
Hybrid Compound ◽  
Compound C ◽  
Hybrid Molecules

In the title hydrated hybrid compound C14H14N2OS2·H2O, the planar imidazo[1,2-a]pyridine ring system is linked to the 1,3-dithiolane moiety by an enone bridge. The atoms of the C—C bond in the 1,3-dithiolane ring are disordered over two positions with occupancies of 0.579 (14) and 0.421 (14) and both disordered rings adopt a half-chair conformation. The oxygen atom of the enone bridge is involved in a weak intramolecular C—H...O hydrogen bond, which generates an S(6) graph-set motif. In the crystal, the hybrid molecules are associated in R 2 2(14) dimeric units by weak C—H...O interactions. O—H...O hydrogen bonds link the water molecules, forming infinite self-assembled chains along the b-axis direction to which the dimers are connected via O—H...N hydrogen bonding. Analysis of intermolecular contacts using Hirshfeld surface analysis and contact enrichment ratio descriptors indicate that hydrogen bonds induced by water molecules are the main driving force in the crystal packing formation.

scholarly journals Synthesis, Crystal Structure, Spectroscopic Properties, and Hirshfeld Surface Analysis of Diaqua [3,14-dimethyl-2,6,13,17 tetraazatricyclo(16.4.0.07,12)docosane]copper(II) Dibromide

Crystals ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 336 ◽  
Author(s):  
Jeon ◽  
Moncol ◽  
Mazúr ◽  
Valko ◽  
Choi
Keyword(s):  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Macrocyclic Ligand ◽  
Complex Salt ◽  
Spectroscopic Properties ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Axial Position ◽  
Tetragonal Symmetry ◽  
Water Molecules

A newly prepared Cu(II) complex salt, Cu(L1)(H2O)2Br2, where L1 is 3,14-dimethyl-2,6,13,17-tetraazatricyclo(16.4.0.07,12) docosane, is characterized by elemental and crystallographic analyses. The Cu(II) center is coordinated by four nitrogen atoms of macrocyclic ligand and the axial position by two water molecules. The macrocyclic ligand adopts an optimally stable trans-III conformation with normal Cu–N bond lengths of 2.018 (3) and 2.049 (3) Å and long axial Cu1–O1W length of 2.632 (3) Å due to the Jahn–Teller effect. The complex is stabilized by hydrogen bonds formed between the O atoms of water molecules and bromide anions. The bromide anion is connected to the neighboring complex cations and water molecules through N–H···Br and O–H···Br hydrogen bonds, respectively. The g-factors obtained from the electron spin resonance spectrum show the typical trend of g∥ > g⊥ > 2.0023, which is in a good accordance to the dx2-y2 ground state. It reveals a coordination sphere of tetragonal symmetry for the Cu(II) ion. The infrared and electronic absorption spectral properties of the complex are also discussed. Hirshfeld surface analysis represents that the H···H, H···Br/Br···H and H···O/O···H contacts are the major molecular interactions in the prepared complex.

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 Synthesis, crystal structure and spectroscopic and Hirshfeld surface analysis of 4-hydroxy-3-methoxy-5-nitrobenzaldehyde

2020 ◽  
Vol 76 (2) ◽  
pp. 239-244 ◽  
Author(s):  
Vitomir Vusak ◽  
Darko Vusak ◽  
Kresimir Molcanov ◽  
Mestrovic Ernest
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Hydrogen Atoms ◽  
Scanning Calorimetry ◽  
Bond Forming ◽  
Compound C

The title compound, C8H7NO5, is planar with an r.m.s. deviation for all non-hydrogen atoms of 0.018 Å. An intramolecular O—H...O hydrogen bond involving the adjacent hydroxy and nitro groups forms an S(6) ring motif. In the crystal, molecules are linked by O—H...O hydrogen bonds, forming chains propagating along the b-axis direction. The chains are linked by C—H...O hydrogen bonds, forming layers parallel to the bc plane. The layers are linked by a further C—H...O hydrogen bond, forming slabs, which are linked by C=O...π interactions, forming a three-dimensional supramolecular structure. Hirshfeld surface analysis was used to investigate intermolecular interactions in the solid state. The molecule was also characterized spectroscopically and its thermal stability investigated by differential scanning calorimetry and by thermogravimetric analysis.

scholarly journals Crystal structure and Hirshfeld surface analysis of tris(2,2′-bipyridine)nickel(II) bis(1,1,3,3-tetracyano-2-ethoxypropenide) dihydrate

2019 ◽  
Vol 75 (6) ◽  
pp. 867-871
Author(s):  
Ignacio Chi-Duran ◽  
Zouaoui Setifi ◽  
Fatima Setifi ◽  
Christian Jelsch ◽  
Bernd Morgenstern ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Title Compound ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Racemic Mixture ◽  
Water Molecules ◽  
Monoclinic Space Group ◽  
Two Dimensional

The title compound, [Ni(C10H8N2)3](C9H5N4O)2·2H2O, crystallizes as a racemic mixture in the monoclinic space group C2/c. In the crystal, the 1,1,3,3-tetracyano-2-ethoxypropenide anions and the water molecules are linked by O—H...N hydrogen bonds, forming chains running along the [010] direction. The bpy ligands of the cation are linked to the chain via C—H...π(cation) interactions involving the CH3 group. The intermolecular interactions were investigated by Hirshfeld surface analysis and two-dimensional fingerprint plots.

scholarly journals Crystal structure, Hirshfeld surface analysis and interaction energy calculation of 1-decyl-2,3-dihydro-1H-benzimidazol-2-one

2021 ◽  
Vol 77 (5) ◽  
pp. 559-563
Author(s):  
Younesse Ait Elmachkouri ◽  
Asmaa Saber ◽  
Ezaddine Irrou ◽  
Bushra Amer ◽  
Joel T. Mague ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Dimensional Structure ◽  
Energy Calculation ◽  
Model C ◽  
Hydrogen Bond Energies

The title molecule, C17H26N2O, adopts an L-shaped conformation, with the straight n-decyl chain positioned nearly perpendicular to the dihydrobenzimidazole moiety. The dihydrobenzimidazole portion is not quite planar as there is a dihedral angle of 1.20 (6)° between the constituent planes. In the crystal, N—H...O hydrogen bonds form inversion dimers, which are connected into the three-dimensional structure by C—H...O hydrogen bonds and C—H...π(ring) interactions. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H...H (75.9%), H...C/C...H (12.5%) and H...O/O...H (7.0%) interactions. Based on computational chemistry using the CE–B3LYP/6–31 G(d,p) energy model, C—H...O hydrogen bond energies are −74.9 (for N—H...O) and −42.7 (for C—H...O) kJ mol−1.

scholarly journals Crystal structure and Hirshfeld surface analysis of a new dithioglycoluril: 1,4-bis(4-methoxyphenyl)-3a-methyltetrahydroimidazo[4,5-d]imidazole-2,5(1H,3H)-dithione

2019 ◽  
Vol 75 (9) ◽  
pp. 1297-1300 ◽  
Author(s):  
Jonnie N. Asegbeloyin ◽  
Kenechukwu J. Ifeanyieze ◽  
Obinna C. Okpareke ◽  
Ebube E. Oyeka ◽  
Tatiana V. Groutso
Keyword(s):  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Steric Effect ◽  
Bond Angle ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Supramolecular Network ◽  
Torsion Angles ◽  
Methyl Group

In the title dithioglycoluril derivative, C19H20N4O3S2, there is a difference in the torsion angles between the thioimidazole moiety and the methoxyphenyl groups on either side of the molecule [C—N—Car—Car = 116.9 (2) and −86.1 (3)°, respectively]. The N—C—N bond angle on one side of the dithioglycoluril moiety is slightly smaller compared to that on the opposite side, [110.9 (2)° cf. 112.0 (2)°], probably as a result of the steric effect of the methyl group. In the crystal, N—H...S hydrogen bonds link adjacent molecules to form chains propagating along the c-axis direction. The chains are linked by C—H...S hydrogen bonds, forming layers parallel to the bc plane. The layers are then linked by C—H...π interactions, leading to the formation of a three-dimensional supramolecular network. Hirshfeld surface analysis and two-dimensional fingerprint plots were used to investigate the molecular interactions in the crystal.

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