Three new amidophosphoric acid esters with a P(O)[OCH2C(CH3)2CH2O] segment: X-ray diffraction, DFT, AIM and Hirshfeld surface investigations of bi- and tri-furcated (three and four-center) hydrogen bond interactions

2020 ◽  
Vol 235 (3) ◽  
pp. 69-84 ◽  
Author(s):  
Marjan Sadat Bozorgvar ◽  
Atekeh Tarahhomi ◽  
Arie van der Lee
Keyword(s):  
Hydrogen Bond ◽  
Crystal Packing ◽  
Closed Shell ◽  
Hirshfeld Surface ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
Amidophosphoric Acid ◽  
Acid Esters

AbstractStructural and packing features of three new amidophosphoric acid esters having a common part XP(O)[OCH2C(CH3)2CH2O], with X = [(CH3)3CNH] (1), [(CH3)2HCNH] (2) and [C6H11(CH3)N] (3), are investigated by single crystal X-ray diffraction. The results illustrate that the compounds 1 and 3 crystallize with one independent molecule in the asymmetric unit; whereas, for 2, the compound crystallizes with three independent molecules in the asymmetric unit. The crystal structures are mostly stabilized via tri-furcated hydrogen bond interactions (C–H · · ·)2(N–H · · ·)O=P in 1 and (C–H · · ·)3O=P in 3, while the stability is given by bi-furcated hydrogen bond interactions (C–H · · ·)(N–H · · ·)O=P in 2. For a better understanding of the nature, strength and energetics associated with the formation of the quoted multi-center hydrogen bond interactions, the Natural Bond Order (NBO) method from Density Functional Theory (DFT) and a topological analysis by means of Atoms In Molecules (AIM) and Hirshfeld surface procedures were performed. These studies reveal that the studied multi-center hydrogen bond interactions of the type O · · · H are favoured in the crystal packing displaying enrichment ratios larger than unity. The detailed nature of the different interactions in these multi-center interactions is studied for the first time in such compounds. It is shown that the N–H · · · O interaction is rather non-covalent closed-shell whereas the C–H · · · O interaction is more van der Waals closed-shell. Stronger hydrogen bond interactions are observed for a lower multiple H-atom acceptor oxygen in three-center hydrogen bond interactions (C–H · · ·)(N–H · · ·)O=P of 2 than for four-center interactions in 1 [i.e. (C–H · · ·)2(N–H · · ·)O=P] and 3 [i.e. (C–H · · ·)3O=P]. The better H-atom acceptability of the O atom of P=O compared with the esteric O atom is explained by the richer s-character of the hybrid orbital of the O atom acceptor of P=O coupled with enhance of the polarization and charge. The obtained results are also confirmed by Molecular Electrostatic Potential (MEP).

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

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.

Influence of 3-{5-[4-(diethylamino)benzylidene]rhodanine}propionic acid on the conformation of 5-(4-chlorobenzylidene)-2-(4-methylpiperazin-1-yl)-3H-imidazol-4(5H)-one

2018 ◽  
Vol 74 (11) ◽  
pp. 1427-1433 ◽  
Author(s):  
Ewa Żesławska ◽  
Wojciech Nitek ◽  
Waldemar Tejchman ◽  
Jadwiga Handzlik
Keyword(s):  
Crystal Structures ◽  
Crystal Packing ◽  
Protonated Form ◽  
Acid Form ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Basic Form ◽  
Piperazine Ring ◽  
X Ray ◽  
Intermolecular Contacts

The arylidene–imidazolone derivatives are a group of compounds of great interest in medicinal chemistry due to their various pharmacological actions. In order to study the possible conformations of an arylidene–imidazolone derivative, two new crystal structures were determined by X-ray diffraction, namely (Z)-5-(4-chlorobenzylidene)-2-(4-methylpiperazin-1-yl)-3H-imidazol-5(4H)-one, C15H17ClN4O, (6), and its salt 4-[5-(4-chlorobenzylidene)-5-oxo-4,5-dihydro-3H-imidazol-2-yl]-1-methylpiperazin-1-ium 3-{5-[4-(diethylamino)benzylidene]-4-oxo-2-thioxothiazolidin-3-yl}propionate, C15H18ClN4O+·C17H19N2O3S2 −, (7). Both compounds crystallize in the space group P\overline{1}. The basic form (6) crystallizes with two molecules in the asymmetric unit. In the acid form of (6), the N atom of the piperazine ring is protonated by proton transfer from the carboxyl group of the rhodanine acid derivative. The greatest difference in the conformations of (6) and its protonated form, (6c), is observed in the location of the arylidene–imidazolone substituent at the N atom. In the case of (6c), the position of this substituent is close to axial, while for (6), the corresponding position is intermediate between equatorial and axial. The crystal packing is dominated by a network of N—H...O hydrogen bonds. Furthermore, the crystal structures are stabilized by numerous intermolecular contacts of types C—H...N and C—H...Cl in (6), and C—H...O and C—H...S in (7). The geometry with respect to the location of the substituents at the N atoms of the piperazine ring was compared with other crystal structures possessing an N-methylpiperazine moiety.

Synthesis of ReItricarbonyl complexes with various sulfur- and oxygen-donating ligands: crystal structures of two ReIdinuclear structures bridged by S atoms

2018 ◽  
Vol 74 (10) ◽  
pp. 1116-1122
Author(s):  
Pheello I. Nkoe ◽  
Hendrik G. Visser ◽  
Chantel Swart ◽  
Alice Brink ◽  
Marietjie Schutte-Smith
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Synthesis And Characterization ◽  
X Ray Diffraction ◽  
Metal Centre ◽  
Pyridine Ligand ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
Mononuclear Complexes

The synthesis and characterization of two dinuclear complexes, namelyfac-hexacarbonyl-1κ3C,2κ3C-(pyridine-1κN)[μ-2,2′-sulfanediyldi(ethanethiolato)-1κ2S1,S3:2κ3S1,S2,S3]dirhenium(I), [Re2(C4H8S3)(C5H5N)(CO)6], (1), and tetraethylammoniumfac-tris(μ-2-methoxybenzenethiolato-κ2S:S)bis[tricarbonylrhenium(I)], (C8H20N)[Re2(C7H7OS)3(CO)6], (2), together with two mononuclear complexes, namely (2,2′-bithiophene-5-carboxylic acid-κ2S,S′)bromidotricarbonylrhenium(I), (3), and bromidotricarbonyl(methyl benzo[b]thiophene-2-carboxylate-κ2O,S)rhenium(I), (4), are reported. Crystals of (1) and (2) were characterized by X-ray diffraction. The crystal structure of (1) revealed two Re—S—Re bridges. The thioether S atom only bonds to one of the ReImetal centres, while the geometry of the second ReImetal centre is completed by a pyridine ligand. The structure of (2) is characterized by three S-atom bridges and an Re...Re nonbonding distance of 3.4879 (5) Å, which is shorter than the distance found for (1) [3.7996 (6)/3.7963 (6) Å], but still clearly a nonbonding distance. Complex (1) is stabilized by six intermolecular hydrogen-bond interactions and an O...O interaction, while (2) is stabilized by two intermolecular hydrogen-bond interactions and two O...π interactions.

scholarly journals A variable-temperature X-ray diffraction and theoretical study of conformational polymorphism in a complex organic molecule (DTC)

RSC Advances ◽  
2018 ◽  
Vol 8 (67) ◽  
pp. 38445-38454 ◽  
Author(s):  
Andrea Gionda ◽  
Giovanni Macetti ◽  
Laura Loconte ◽  
Silvia Rizzato ◽  
Ahmed M. Orlando ◽  
...  
Keyword(s):  
Theoretical Study ◽  
Crystal Packing ◽  
Variable Temperature ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Complex Organic Molecule ◽  
Non Covalent Interactions ◽  
Complex Organic ◽  
Covalent Interactions

A small conformational change in the asymmetric unit has a significant effect on how non-covalent interactions determine (i) the crystal packing and (ii) the effect of T on the relative balance of electrostatics and dispersion–repulsions.

A two-dimensional copper(II) coordination polymer based on 2-propyl-1H-imidazole-4,5-dicarboxylic acid

2015 ◽  
Vol 71 (2) ◽  
pp. 152-154 ◽  
Author(s):  
Di-Chang Zhong ◽  
Hua-Bin Guo ◽  
Ji-Hua Deng ◽  
Ping Lian ◽  
Xu-Zhong Luo
Keyword(s):  
Hydrogen Bond ◽  
Carboxylic Acid ◽  
Dicarboxylic Acid ◽  
Three Dimensional ◽  
Acid Group ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Carboxylic Acid Group ◽  
X Ray ◽  
Hydrogen Bond Interactions

Single-crystal X-ray diffraction analysis of poly[bis(μ2-5-carboxy-2-propyl-1H-imidazole-4-carboxylato-κ3N3,O4:O5)copper(II)], [Cu(C8H9N2O4)2)]n, indicates that one carboxylic acid group of the 2-propyl-1H-imidazole-4,5-dicarboxylic acid (H3PDI) ligand is deprotonated. The resulting H2PDI−anion, acting as a bridge, connects the CuIIcations to form a two-dimensional (4,4)-connected layer. Adjacent layers are further linked through interlayer hydrogen-bond interactions, resulting in a three-dimensional supramolecular structure.

scholarly journals Substituent Effect on AIE Mechanism of Two Coumarin Derivatives: Uncommon TICT Fluorescence in Aggregation State

2022 ◽  
Author(s):  
Qiao Li ◽  
Yang Zhao ◽  
Zhigang Niu ◽  
Enju Wang
Keyword(s):  
Intramolecular Charge Transfer ◽  
Knoevenagel Condensation ◽  
Crystal Packing ◽  
Coumarin Derivatives ◽  
Dual Fluorescence ◽  
X Ray Diffraction ◽  
Aggregation State ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
Salicylaldehyde Derivatives

Abstract Two coumarin derivatives, 7-diethylamino-3-(4-nitrophenyl)coumarin (DNC) and 7-hydroxy-3-(4-nitrophenyl)coumarin (HNC), were synthesized via Knoevenagel condensation of salicylaldehyde derivatives with 4-nitrophenylacetonitrile and then cyclization reaction. Both of them were characterized by single-crystal X-ray diffraction. The molecules of DNC are stacked via π-π interaction, while the hydrogen bond interactions instead of π-π interaction were observed in the crystal packing of HNC. Both of DNC and HNC showed solvatochromic properties and aggregation-induced emission (AIE) activities, but the AIE characteristics of them were entirely different. HNC exhibited an AIE phenomenon as the result of the restriction of twisted intramolecular charge transfer (TICT), while DNC emited peculiar dual fluorescence which was assigned to the emission based on the inhibition of TICT state formation and the emission from the TICT state respectively.

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

2018 ◽  
Vol 74 (7) ◽  
pp. 847-855 ◽  
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.

A Study of Diastereomeric Mandelate Salts of Cinchonidine and the Relation to Their Quasidiastereomeric Analogues

1997 ◽  
Vol 53 (4) ◽  
pp. 708-718 ◽  
Author(s):  
A. Gjerløv ◽  
S. Larsen
Keyword(s):  
Hydrogen Bond ◽  
Solid State ◽  
Mandelic Acid ◽  
Crystal Packing ◽  
Steric Effects ◽  
Quinoline Ring ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diastereomeric Salts ◽  
Vinyl Group

The crystal structures have been determined for the diastereomeric salts formed by cinchonidine and the two enantiomers of mandelic acid using low-temperature [122 (1) K] X-ray diffraction data. The less soluble salt is cinchonidinium (S)-mandelate, C19H23N20O+.C8H7O3 −, M r = 446.53, monoclinic, C2, a = 21.400 (2), b = 6.2777 (6), c = 17.853 (2) Å3, \beta = 109.304 (8)°, V = 2263.6 (4) Å3, Z = 4, D x = 1.310 g cm−3, \lambda(Cu K\alpha = 1.54184 Å, Z = 7.08 cm−1, F(000) = 952, R 1 = 0.0259 for 2684 observed reflections. The cinchonidine salt with (R)-mandelic acid, C19H23N2O+.C8H7O3, has M r = 446.53, monoclinic, P21, a = 6.410 (3), b = 32.808 (11), c = 11.222 (2) Å, \beta = 100.67 (2)°, V = 2319.2 (13) Å3, Z = 4, D x = 1.279 g cm−3, \lambda(Cu K\alpha) = 1.54184 Å, \mu = 6.91 cm−1, F(000) = 952, R 1 = 0.0380 for 8951 observed reflections. The two salts have virtually identical hydrogen-bond patterns and similar herringbone stacking of the quinoline ring systems. The crystal packing of the two salts differ only with respect to the packing of the phenyl groups. The packing of the cinchonidinium mandelates is significantly different from the crystal packing in the corresponding mandelates of cinchonine. The lack of a quasidiastereomeric relationship between the two sets of salts can be attributed to the steric effects of the vinyl group. The similarities between the two cinchonidinium mandelate structures is a possible explanation to the similar solubilities of the salts. DSC and NMR measurements showed that the cinchonidinium salts undergo a chemical opening reaction in the solid state. The arrangement of hydrogen-bonded chains of alternating cations and anions appear to be important for the solid-state reaction to take place.

scholarly journals Pressure-induced polymorphism in cyclopropylamine

2005 ◽  
Vol 61 (6) ◽  
pp. 717-723 ◽  
Author(s):  
Patricia Lozano-Casal ◽  
David R. Allan ◽  
Simon Parsons
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Hirshfeld Surface ◽  
Amino Group ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Dimensions ◽  
Graph Set ◽  
Unit Cell Dimensions

The crystal structure of cyclopropylamine at 1.2 GPa has been determined by X-ray diffraction methods. The structure of this phase is orthorhombic, space group Pbca and the unit-cell dimensions are a =  5.0741 (10), b  =  9.7594 (10) and c  =  13.305 (2) Å. Only one of the two H atoms of the amino group actively participates in the formation of the hydrogen-bonded chains, C(2) in graph-set notation, which lie parallel to the crystallographic a axis. Additionally, the topology of the crystal packing is studied using both Voronoi–Dirichlet polyhedra and Hirshfeld surface analyses for the low-temperature and the high-pressure structures of cyclopropylamine and the results are compared.

scholarly journals Synthesis and structure of (E)-N-(4-methoxyphenyl)-2-[4-(3-oxo-3-phenylprop-1-en-1-yl)phenoxy]acetamide

2021 ◽  
Vol 77 (2) ◽  
pp. 184-189
Author(s):  
Cong Nguyen Tien ◽  
Trung Vu Quoc ◽  
Dat Nguyen Dang ◽  
Giang Le Duc ◽  
Luc Van Meervelt
Keyword(s):  
Title Compound ◽  
Crystal Packing ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
H Nmr ◽  
Hydrogen Bonding Interactions ◽  
Hirshfeld Analysis ◽  
Phenyl Rings ◽  
C Nmr

The title compound N-(4-methoxyphenyl)-2-[4-(3-oxo-3-phenylprop-1-en-1-yl)phenoxy]acetamide, C24H21NO4, was prepared from reaction of N-(4-methoxyphenyl)-2-chloroacetamide and (E)-3-(4-hydroxyphenyl)-1-phenylprop-2-en-1-one, which was obtained from the reaction of 4-hydroxybenzaldehyde and acetophenone. The structure of the title compound was determined by IR, 1H-NMR, 13C-NMR and HR–MS spectroscopic data and further characterized by single-crystal X-ray diffraction. The asymmetric unit contains four molecules, each displaying an E-configuration of the C=C bond. The dihedral angle between the phenyl rings in each molecule varies between 14.9 (2) and 45.8 (2)°. In the crystal, C—H...O hydrogen-bonding interactions link the molecules into chains running along the [001] direction. In addition, C—H...π interactions further stabilize the crystal packing. A Hirshfeld analysis indicates that the most important contributions to the surface contacts are from H...H (43.6%), C...H/H...C (32.1%) and O...H/H...O (18.1%) interactions.

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