Comparing the strength of covalent bonds, intermolecular hydrogen bonds and other intermolecular interactions for organic molecules: X-ray diffraction data and quantum chemical calculations

2016 ◽  
Vol 40 (8) ◽  
pp. 6848-6853 ◽  
Author(s):  
Angelo Gavezzotti
Keyword(s):  
Hydrogen Bonds ◽  
Diffraction Data ◽  
Chemical Bonding ◽  
Quantum Chemical ◽  
Organic Molecules ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
Covalent Bonds ◽  
X Ray ◽  
Different Types

The chemical bonding landscape for organic molecules clearly demonstrates the different ranges of stability and predictability for the different types of interactions.

Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis

2022 ◽  
Vol 78 (2) ◽  
Author(s):  
Sehrish Akram ◽  
Arshad Mehmood ◽  
Sajida Noureen ◽  
Maqsood Ahmed
Keyword(s):  
Hydrogen Bonds ◽  
Glutamic Acid ◽  
Single Crystal ◽  
Diffraction Data ◽  
Density Functional ◽  
Quantitative Estimation ◽  
Topological Analysis ◽  
Pyroglutamic Acid ◽  
X Ray Diffraction ◽  
X Ray

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

The structures of benzimidazole derivatives and their potential as tuberculostatics

2018 ◽  
Vol 74 (12) ◽  
pp. 1684-1691
Author(s):  
Marek L. Główka ◽  
Sylwia Kałużyńska ◽  
Malwina Krause ◽  
Katarzyna Gobis ◽  
Henryk Foks ◽  
...  
Keyword(s):  
Multidrug Resistant ◽  
Benzimidazole Derivatives ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Resistant Varieties ◽  
Different Types ◽  
Mdr Tb ◽  
Aromatic Systems ◽  
Better Than

Tuberculosis still remains a very important problem, especially its multidrug resistant varieties (MDR-TB). Among the potential tuberculostatics, there are two benzimidazole derivatives, namely 5,6-dimethyl-2-phenylethylbenzo[d]imidazole (1) and (E)-5,6-dimethyl-2-styryl-1H-benzo[d]imidazole (2) which showed significant tuberculostatic activities, better than those of Pyrazinamide and Isoniazyd. Also, the cytotoxicity of 1 appeared promising. The compounds were studied (with the use of X-ray diffraction) in the form of the hemihydrate of 1, C17H18N2·0.5H2O (1a), the methanol hemisolvate of 2, C17H16N2·0.5CH3OH (2a), and the acid oxalate salt of 2, namely (E)-5,6-dimethyl-2-styryl-1H-benzo[d]imidazolium hydrogen oxalate, C17H17N2 +·C2HO4 − (2b). All three structures reveal a similar extended conformation, despite the flexible linker between the two aromatic systems and the different types of strong intermolecular hydrogen bonds. The molecules of 2a are practically planar due to the double bond in the linker, which enables conjugation along the whole molecule, while the molecules of 1a exhibit the possibility of parallel orientations of their aromatic systems, despite the aliphatic (ethyl) linker.

Evolution structurale de la nacrite en fonction de la nature des molécules organiques intercalees

2000 ◽  
Vol 33 (6) ◽  
pp. 1351-1359 ◽  
Author(s):  
A. Ben Haj Amara ◽  
H. Ben Rhaiem ◽  
A. Plançon
Keyword(s):  
Ir Spectroscopy ◽  
Hydrogen Bonds ◽  
Dimethyl Sulfoxide ◽  
Organic Molecules ◽  
Interlayer Space ◽  
X Ray Diffraction ◽  
X Ray ◽  
Intercalated Compounds ◽  
Xrd Study ◽  
Intercalation Process

Nacrite has been intercalated with two polar organic molecules: dimethyl sulfoxide (DMSO) andN-methylacetamide (NMA). The homogeneous nacrite complexes have been studied by X-ray diffraction (XRD) and infrared (IR) spectroscopy. The XRD study is based on a comparison between experimental and calculated patterns. The structures of the intercalated compounds have been determined, including the mutual positions of the layers after intercalation and the positions of the intercalated molecules in the interlayer space. It has been shown that the intercalation process causes not only a swelling of the interlayer space but also a shift in the mutual in-plane positions of the layers. This shift depends on the nature of the intercalated molecules and is related to their shape and the hydrogen bonds which are established with the surrounding surfaces. For a given molecule, the intercalation process is the same for the different polytypes of the kaolinite family. These XRD results are consistent with those of IR spectroscopy.

Synthesis, crystal structure and molecular conformation of (±)-1-oxoferruginol and (±)-shonanol

2004 ◽  
Vol 219 (10) ◽  
Author(s):  
Swastik Mondal ◽  
Monika Mukherjee ◽  
Arnab Roy ◽  
Debabrata Mukherjee
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Diffraction Data ◽  
Molecular Conformation ◽  
Membered Ring ◽  
Methyl Groups ◽  
Single Bond ◽  
X Ray Diffraction ◽  
X Ray ◽  
Chemical Structures

Abstract(±)-1-oxoferruginol and (±)-shonanol, two potential intermediates in the synthesis of tricyclic diterpenoid ferruginol, have been prepared and crystal structures of the compounds have been investigated using single-crystal X-ray diffraction data. The methyl groups of the isopropyl moiety in (±)-shonanol are disordered over two positions with occupation factors 0.65(1) and 0.35(1), respectively. Although the chemical structures of two compounds are very similar, a C—C single bond in the terminal six-membered ring of (±)-1-oxoferruginol is replaced by a C=C bond in (±)-shonanol, the quantitative isostructurality index calculations indicate that the structures are not isostructural. Intermolecular O—H…O hydrogen bonds between pairs of molecules in the compounds related by center of inversion lead to characteristic dimers forming R

Analysis of chemical bonding in Zn3P2 crystals from X-ray diffraction data

2004 ◽  
Vol 49 (4) ◽  
pp. 579-584 ◽  
Author(s):  
I. E. Zanin ◽  
K. B. Aleinikova ◽  
M. Yu. Antipin ◽  
M. M. Afanas’ev
Keyword(s):  
Diffraction Data ◽  
Chemical Bonding ◽  
X Ray Diffraction ◽  
X Ray

The crystal and molecular structure of a 1:1 complex of 5-bromouridine and dimethylsulphoxide

1968 ◽  
Vol 302 (1469) ◽  
pp. 225-236 ◽  
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonds ◽  
Oxygen Atom ◽  
Diffraction Data ◽  
Crystal And Molecular Structure ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Anisotropic Temperature

A complex consisting of one molecule of 5-bromouridine ( BUR ) and one molecule of di­methylsulphoxide ( DMSO ) has been prepared in the form of monoclinic crystals. The unit cell parameters are as follows, a = 13⋅65 ± 0⋅01, b = 4.820 ± 0⋅005, c = 12⋅09 ± 0⋅01 Å, β = 91⋅8 ± 0.1°, space group P 2 1 . X-ray diffraction data ( ⋋ = 1⋅5418 Å) for 1389 independent reflexions were collected and the structure was determined from Patterson syntheses which gave the coordinates of the bromine and sulphur atoms. Fourier syntheses followed by least-squares refinement (including anisotropic temperature parameters) reduced the agreement index R to 0⋅067. The bond lengths and angles for each molecule are given, and it is shown that hydrogen bonds are formed between the oxygen atom of the DMSO molecule and the 03' and 05' of the BUR molecules. A comparison is made between the conformation of the BUR molecule in this complex and that of the same molecule in two other structures.

scholarly journals ISOLATION AND STRUCTURAL ELUCIDATION OF A NEW DEPSIDE OF LICHEN Everniopsis trulla

2021 ◽  
Vol 87 (2) ◽  
pp. 97-106
Author(s):  
Olivio Nino Castro ◽  
Jesús López Rodilla ◽  
Sofia Pombal ◽  
Francisca Sanz González ◽  
Julio Santiago Contreras
Keyword(s):  
Mass Spectrometry ◽  
Melting Point ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Spectroscopic Data ◽  
Intermolecular Forces ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Uv Visible

In this research, a new depside of the lichen Everniopsis trulla has been isolated. The extraction was carried out to 400 g of dry sample and ground with ethanol for 3 repetitions, then, it was fractionated by applying column chromatography with the CHCl3-MeOH system and purified by recrystallization with MeOH-Acetone (1: 1); Finally, white crystals in the form of needles (solid C) with a melting point of 198 ° C were obtained, whose structure was elucidated based on spectroscopic data (UV-Visible, IR, NMR-H1, NMR-C13, mass spectrometry and single crystal X-ray diffraction). According to the Science Finder databases, it is a new depside, called trullarin, and it is observed that molecular packing is influenced by both intramolecular and intermolecular forces. Intermolecular hydrogen bonds of O - H -O type binds neighboring molecules forming dimers.

Structural Study of the Disordered RECd6 Quasicrystal Approximants (RE = Tb, Ho, Er, Tm and Lu)

2006 ◽  
Vol 61 (6) ◽  
pp. 644-649 ◽  
Author(s):  
Shu Ying Piao ◽  
Cesar P. Gömez ◽  
Sven Lidin
Keyword(s):  
Single Crystal ◽  
Crystal Structures ◽  
Structural Study ◽  
Diffraction Data ◽  
Unit Cell Dimension ◽  
Unit Cell ◽  
Cell Dimension ◽  
X Ray Diffraction ◽  
X Ray ◽  
Different Types

The crystal structures of approximants RECd6 (RE = Tb, Ho, Er, Tm and Lu) have been refined from single crystal X-ray diffraction data. This work is a continuation of a previous study of MCd6 approximants [1] in which the different types of disorder of the central Cd4 tetrahedra located in the dodecahedral cavities were examined. The structures of the title compounds are all similar to GdCd6 and disorder was observed in all these compounds. There is a correlation between the anisotropic displacement parameter and the unit cell dimension

scholarly journals New superprotonic crystals with dynamically disordered hydrogen bonds: cation replacements as the alternative to temperature increase

2017 ◽  
Vol 73 (6) ◽  
pp. 1105-1113 ◽  
Author(s):  
Elena V. Selezneva ◽  
Irina P. Makarova ◽  
Inna A. Malyshkina ◽  
Nadezhda D. Gavrilova ◽  
Vadim V. Grebenev ◽  
...  
Keyword(s):  
High Temperature ◽  
Dielectric Properties ◽  
Hydrogen Bonds ◽  
Single Crystals ◽  
Diffraction Data ◽  
Room Temperature ◽  
Ambient Conditions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Superprotonic Phase

Investigations of new single crystals grown in the K3H(SO4)2–(NH4)3H(SO4)2–H2O system from solutions with different K:NH4 concentration ratios have been carried out. Based on the X-ray diffraction data, the atomic structure of the crystals was determined at room temperature taking H atoms into account. It has been determined that [K0.43(NH4)0.57]3H(SO4)2 crystals are trigonal at ambient conditions such as the superprotonic phase of (NH4)3H(SO4)2 at high temperature. A distribution of the K and N atoms in the crystal was modelled on the basis of the refined occupancies of K/N positions. Studies of dielectric properties over the temperature range 223–353 K revealed high values of conductivity of the crystals comparable with the conductivity of known superprotonic compounds at high temperatures, and an anomaly corresponding to a transition to the phase with low conductivity upon cooling.

scholarly journals Synthese und Umsetzungen von 4-Acyl/Carbamoyl-N-aryl-3-chloropyrrol-2,5-dionen: Kristallstruktur eines auf Wasserstoffbrückenbindungen basierenden supramolekularen Bandes [1] / Synthesis and Reactions of 4-Acyl/Carbamoyl-N-aryl-3-chloro-pyrrol-2,5-diones: Crystal Structure of a Supramolecular Ribbon Based on Hydrogen Bonds [ 1]

1996 ◽  
Vol 51 (8) ◽  
pp. 1084-1098 ◽  
Author(s):  
Rolf W. Saalfrank ◽  
Bernd Hörner ◽  
Stephan Reck ◽  
Jochen Nachtrab ◽  
Eva-Maria Peters ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Diffraction Analysis ◽  
Thionyl Chloride ◽  
Oxalyl Chloride ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray

Reaction of malondiamides 1 with oxalyl chloride (2) leads to the formation of 2,3-dioxo-2,3- dihydrofuran hydrochlorides 3 and 2,3-dioxo-2,3-dihydro-furanes 4, respectively. The structure of 3a was established by X-ray diffraction. The β-oxo-dibenzylamides 5 react with 2 regiospecifically to give the 2,3-dioxo-2,3-dihydrofuranes 6. Addition of water in 1,4-position to 6a yields hydroxy-enol 7, which forms bimolecular aggregates via intermolecular hydrogen bonds as shown by X-ray analysis. Intramolecular C,N-bisacylation of β-oxoamides 8 and malondiamides 11 with 2 leads to the pyrrol-2,5-diones 9 and 12. Reaction of the enols 9 and 12 with thionyl chloride leads to 3-chloro-pyrrol-2,5-diones 13. 3-Amino-pyrrol-2,5-diones 15 are obtained from 13 and amines 14, while 1, ω-diamines 16 yield the bispyrrol systems 17. X-ray diffraction analysis of 17g reveals a supramolecular ribbon based on intermolecular hydrogen bonds between two different conformeres of 17g and in addition establishes unequivocally the imid-structures of 9 and 12. Intermolecular cyclisation of 13 with amino-tetrazol 18 gives the azido-pyrrolo-pyrimidine-diones 20, which reacts with triphenylphosphane to give phosphinimines 22. The structure of 22a was established by X-ray diffraction.

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