Special Issue "Characterisation and Study of Compounds by Single Crystal X-Ray Diffraction"

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Crystal Engineering".

Deadline for manuscript submissions: closed (31 March 2020).

Special Issue Editor

Dr. Josefina Perles
Website
Guest Editor
Laboratorio de Difracción de Rayos X de Monocristal, SIdI, Universidad Autónoma de Madrid, 28049 Madrid, Spain
Interests: single crystal X-ray diffraction; structure-properties relationship; supramolecular interactions; topological studies

Special Issue Information

Dear Colleagues,

X-ray diffraction has been widely regarded as the most powerful technique for the structural study of crystalline samples during the last century, as it provides detailed information about the atomic structure of ordered solids regardless of the chemical nature of the sample. Although in the early days it was mostly applied to mineral samples, the crystallisation of natural biological molecules and new synthetic compounds has extended the application of this technique to other disciplines such as chemistry, biology, materials science or pharmacology.

In particular, single crystal X-ray diffraction (SCXRD) has played a crucial role in the interpretation of the physicochemical properties of many substances, determining with high precision the location of the atoms in the crystal as well as the strength of interatomic bonds and supramolecular interactions. Advances in data collection and treatment have overcome many of the initial limitations such as small crystal size, twinning or poor crystallinity of the sample, and today SCXRD is a unique characterisation tool for many scientists.

In this Special Issue, on the topic “Characterisation and Study of Compounds by Single Crystal X-ray Diffraction”, we want to highlight the importance of this technique in scientific research, alone or in combination with other analytical methods. All contributions involving SCXRD are welcome, and especially those studies in which SCXRD has provided key information to solve experimental problems.

Kind regards,

Dr. Josefina Perles
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Crystals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • crystal structure
  • SCXRD
  • X-ray crystallography
  • structural study

Published Papers (12 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Editorial

Jump to: Research

Open AccessEditorial
Characterisation and Study of Compounds by Single Crystal X-ray Diffraction
Crystals 2020, 10(10), 934; https://doi.org/10.3390/cryst10100934 - 14 Oct 2020
Abstract
A few years after the discovery in 1895 of X-rays by Röntgen, the first successful experiment single crystal X-ray diffraction (SCXRD) was reported by Laue, Friedrich, and Knipping [...] Full article

Research

Jump to: Editorial

Open AccessArticle
Structural, Hirshfeld Surface Analysis, Morphological Approach, and Spectroscopic Study of New Hybrid Iodobismuthate Containing Tetranuclear 0D Cluster Bi4I16·4(C6H9N2) 2(H2O)
Crystals 2020, 10(5), 397; https://doi.org/10.3390/cryst10050397 - 15 May 2020
Cited by 1
Abstract
The Bi4I16·4(C6H9N2) 2(H2O) compound was synthesized by slow evaporation at room temperature. It exhibits a zero-dimensional (0D) tetrameric structure, comprising [Bi4I16]4− distorted octahedra, with strong I⋯I [...] Read more.
The Bi4I16·4(C6H9N2) 2(H2O) compound was synthesized by slow evaporation at room temperature. It exhibits a zero-dimensional (0D) tetrameric structure, comprising [Bi4I16]4− distorted octahedra, with strong I⋯I interactions among adjacent anionic clusters. We used Hirshfeld surface analysis to discuss the strength of hydrogen bonds and to quantify the inter-contacts (two-dimensional (2D) fingerprint plots). It revealed that the hydrogen bonding interactions H⋯I (56.3%), π–π stacking (11.7%), and I⋯I interactions (5.9%) play the major role in the stability of the crystal structure. The crystal morphology was simulated using Bravais–Friedel, Donnay–Harker (BFDH) and growth morphology (GM) methods. The experimental habit of the title compound was adequately reproduced by the two models. The calculated results show that the crystal morphology of the title compound in a vacuum is dominated by five facets: (020), (011), (110), (10−1), and (11−1). The (020) facet is the largest among all the facets calculated. Projection of the facet showed that there are a few polar groups on the (020) facet. In the 50–400 and 400–4000 cm−1 frequency regions, we measured the Raman and infrared spectra, respectively, of the title compound, and we assigned the observed vibration modes. Full article
Show Figures

Graphical abstract

Open AccessArticle
A Comprehensive Study of a New 1.75 Hydrate of Ciprofloxacin Salicylate: SCXRD Structure Determination, Solid Characterization, Water Stability, Solubility, and Dissolution Study
Crystals 2020, 10(5), 349; https://doi.org/10.3390/cryst10050349 - 28 Apr 2020
Abstract
One problem that often arises during the formulation of a dosage form is the solubility and dissolution of the active ingredients. This problem arises in ciprofloxacin, which is a BCS class IV fluoroquinolone antibiotic. A pseudopolymorph is a kind of polymorph in which [...] Read more.
One problem that often arises during the formulation of a dosage form is the solubility and dissolution of the active ingredients. This problem arises in ciprofloxacin, which is a BCS class IV fluoroquinolone antibiotic. A pseudopolymorph is a kind of polymorph in which the number of hydrates is different. In this study, a new pseudopolymorph comprised of ciprofloxacin and salicylic acid was found, namely the salt ciprofloxacin salicylate 1.75 hydrate form. This new solid phase was analyzed by Fourier-transform infrared spectroscope (FTIR), Raman spectroscopy, and thermal analysis and proven by Powder X-ray Diffractometry (PXRD) analysis. The crystal structure was successfully determined by Single Crystal X-ray Diffractometry (SCXRD) analysis. It was found that the piperazinyl group of ciprofloxacin is protonated by H+ from the carboxylic group of salicylic acid. In the unit cell, two ciprofloxacin and two salicylic acid molecules were independent with four water molecules, in which one water molecule had 0.5 occupancy due to inversion symmetry. Interestingly, this hydrate crystal dehydrated by grinding for 105 minutes forms an anhydrous crystalline phase, which was analyzed with FTIR, Raman spectroscopy, thermal analysis, and PXRD. The solubility and dissolution tests were carried out using UV-Visible spectrophotometry and a multiple linear regression method. This new hydrate solid phase has a better profile than the original ciprofloxacin crystal, according to the solubility and dissolution tests. Full article
Show Figures

Graphical abstract

Open AccessArticle
Novel Quaternary Ammonium Derivatives of 4-Pyrrolidino Pyridine: Synthesis, Structural, Thermal, and Antibacterial Studies
Crystals 2020, 10(5), 339; https://doi.org/10.3390/cryst10050339 - 25 Apr 2020
Abstract
Six novel quaternary ammonium derivatives of 4-pyrrolidino pyridine were prepared and isolated via a facile one-pot synthesis and a simple purification procedure. The purity and the molecular structure of the 4-pyrrolidino pyridine derivatives were confirmed with 1H and 13C NMR spectroscopy [...] Read more.
Six novel quaternary ammonium derivatives of 4-pyrrolidino pyridine were prepared and isolated via a facile one-pot synthesis and a simple purification procedure. The purity and the molecular structure of the 4-pyrrolidino pyridine derivatives were confirmed with 1H and 13C NMR spectroscopy and powder X-ray diffraction techniques. The crystal structures of the compounds were characterized by single crystal X-ray diffraction (SCXRD) and their thermal properties were studied by Differential Scanning Calorimetry (DSC) analyses. The antibacterial properties of the title compounds against five bacterial strains were evaluated using Kirby–Bauer disk diffusion susceptibility test. The compounds crystallize in the monoclinic or orthorhombic crystal systems (space groups: P21/c, P21/n, or P212121) and their crystal structures are stabilized by a combination of intra- and intermolecular halogen bonding interactions, short contacts and π-π interactions. Above interactions, they contribute to the thermal stability and lack of phase transition effects up to 350 °C. Two of the compounds possess antibacterial effect against E. coli or S. aureus bacterial strains—similar or better than the kanamycin reference. Full article
Show Figures

Graphical abstract

Open AccessArticle
Extended π-Systems in Diimine Ligands in [Cu(P^P)(N^N)][PF6] Complexes: From 2,2′-Bipyridine to 2-(Pyridin-2-yl)Quinoline
Crystals 2020, 10(4), 255; https://doi.org/10.3390/cryst10040255 - 27 Mar 2020
Cited by 6
Abstract
We describe the synthesis and characterization of [Cu(POP)(1)][PF6], [Cu(POP)(2)][PF6], [Cu(xantphos)(1)][PF6], and [Cu(xantphos)(2)][PF6] in which ligands 1 and 2 are 2-(pyridin-2-yl)quinoline and 2-(6-methylpyridin-2-yl)quinoline, respectively. With 2,2'-bipyridine (bpy) as [...] Read more.
We describe the synthesis and characterization of [Cu(POP)(1)][PF6], [Cu(POP)(2)][PF6], [Cu(xantphos)(1)][PF6], and [Cu(xantphos)(2)][PF6] in which ligands 1 and 2 are 2-(pyridin-2-yl)quinoline and 2-(6-methylpyridin-2-yl)quinoline, respectively. With 2,2'-bipyridine (bpy) as a benchmark, we assess the impact of the extended π-system on structural and solid-state photophysical properties. The single crystal structures of [Cu(POP)(2)][PF6], [Cu(xantphos)(1)][PF6], and [Cu(xantphos)(2)][PF6] were determined and confirmed a distorted tetrahedral copper(I) coordination environment in each [Cu(P^P)(N^N)]+ cation. The xanthene unit in [Cu(xantphos)(1)][PF6] and [Cu(xantphos)(2)][PF6] hosts the quinoline unit of 1, and the 6-methylpyridine group of 2. 1H NMR spectroscopic data indicate that these different ligand orientations are also observed in acetone solution. In their crystal structures, the [Cu(POP)(2)]+, [Cu(xantphos)(1)]+, and [Cu(xantphos)(2)]+ cations exhibit different edge-to-face and face-to-face π-interactions, but in all cases, the copper(I) centre is effectively protected by a ligand sheath. In [Cu(POP)(2)][PF6], pairs of cations engage in an efficient face-to-face π-stacking embrace, and we suggest that this may contribute to this compound having the highest photoluminescence quantum yield (PLQY = 21%) of the series. With reference to data from the Cambridge Structural Database, we compare packing effects and PLQY data for the complexes incorporating 2-(pyridin-2-yl)quinoline and 2-(6-methylpyridin-2-yl)quinoline, with those of the benchmark bpy-containing compounds. We also assess the effect that Cu⋯O distances in the {Cu(POP)} and {Cu(xantphos)} domains of [Cu(P^P)(N^N)][X] compounds have on solid-state PLQY values. Full article
Show Figures

Graphical abstract

Open AccessArticle
Crystal Structure Dependence of the Energy Transfer from Tb(III) to Yb(III) in Metal–Organic Frameworks Based in Bispyrazolylpyridines
Crystals 2020, 10(2), 69; https://doi.org/10.3390/cryst10020069 - 27 Jan 2020
Cited by 1
Abstract
Luminescent mixed lanthanide metal−organic framwork (MOF) materials have been prepared from two polyheterocyclic diacid ligands, 2,6-bis(3-carboxy-1-pyrazolyl)pyridine and 2,6-bis(4-carboxy-1-pyrazolyl)pyridine. The crystal structures of the two organic molecules are presented together with the structures for the MOFs obtained by hydrothermal synthesis either with Yb(III) or [...] Read more.
Luminescent mixed lanthanide metal−organic framwork (MOF) materials have been prepared from two polyheterocyclic diacid ligands, 2,6-bis(3-carboxy-1-pyrazolyl)pyridine and 2,6-bis(4-carboxy-1-pyrazolyl)pyridine. The crystal structures of the two organic molecules are presented together with the structures for the MOFs obtained by hydrothermal synthesis either with Yb(III) or mixed Tb(III)/Yb(III) ions. Different coordination architectures result from each ligand, revealing also important differences between the lanthanides. The mixed lanthanide metal−organic frameworks also present diverse luminescent behavior; in the case of 2,6-bis(4-carboxy-1-pyrazolyl)pyridine, where no coordinated water is present in the metal environment, Tb(III) and Yb(III) characteristic emission is observed by excitation of the bispyrazolylpyridine chromophore. Full article
Show Figures

Graphical abstract

Open AccessArticle
Synthesis and Crystal Structure of Bis(2-phenylpyridine-C,N’)-bis(acetonitrile)iridium(III)hexafluorophosphate Showing Three Anion/Cation Couples in the Asymmetric Unit
Crystals 2019, 9(12), 617; https://doi.org/10.3390/cryst9120617 - 25 Nov 2019
Abstract
The title compound bis(2-phenylpyridine-C,N’)-bis(acetonitrile)iridium(III)hexafluorophosphate, a six-coordinate iridium(III) complex, crystallizes in the P-1 space group. Iridium is in a distorted octahedral (n = 6) coordination with the N,C’ atoms of two phenylpyridine and the N atoms of two acetonitrile ligands. The peculiarity of [...] Read more.
The title compound bis(2-phenylpyridine-C,N’)-bis(acetonitrile)iridium(III)hexafluorophosphate, a six-coordinate iridium(III) complex, crystallizes in the P-1 space group. Iridium is in a distorted octahedral (n = 6) coordination with the N,C’ atoms of two phenylpyridine and the N atoms of two acetonitrile ligands. The peculiarity of this structure is that three independent moieties of the title compound and three PF6 anions, to counterbalance the charge, are observed in the asymmetric unit and this is a rather uncommon fact among the Cambridge Crystallographic Database (CSD) entries. The three couples are almost identical conformers with very similar torsional angles. The packing, symmetry, and space group were accurately analyzed and described also by means of Hirshfeld surface analysis, which is able to underline subtle differences among the three anion/cation couples in the asymmetric unit. The driving force of the packing is the clustering of the aromatic rings and the maximization of acetonitrile:PF6 interactions. The asymmetry of the cluster is the cause of the unusual number of moieties in the asymmetric unit. Full article
Show Figures

Graphical abstract

Open AccessArticle
Linear One-Dimensional Coordination Polymers Constructed by Dirhodium Paddlewheel and Tetracyanido-Metallate Building Blocks
Crystals 2019, 9(12), 614; https://doi.org/10.3390/cryst9120614 - 23 Nov 2019
Cited by 1
Abstract
In this article, we describe the preparation of anionic heteronuclear one-dimensional coordination polymers made by dirhodium paddlewheels and tetracyanido-metallatate building blocks. A series of complexes of (PPh4)2n[{Rh2(µ-O2CCH3)4}{M(CN)4}]n (M [...] Read more.
In this article, we describe the preparation of anionic heteronuclear one-dimensional coordination polymers made by dirhodium paddlewheels and tetracyanido-metallatate building blocks. A series of complexes of (PPh4)2n[{Rh2(µ-O2CCH3)4}{M(CN)4}]n (M = Ni (1), Pd (2), Pt (3)) formulae were obtained by reaction of [Rh2(μ-O2CCH3)4] with (PPh4)2[M(CN)4] in a 1:1 or 2:1 ratio. Crystals of 1−3 suitable for single crystal X-ray diffraction were grown by slow diffusion of a dichloromethane solution of the dirhodium complex into a chloroform solution of the corresponding tetracyanido–metallatate salt. Compounds 1 and 2 are isostructural and crystallize in the triclinic P-1 space group, while compound 3 crystallizes in the monoclinic P21/n space group. A detailed description of the structures is presented, including the analysis of the packing of anionic chains and PPh4+ cations. Full article
Show Figures

Graphical abstract

Open AccessArticle
Site Selectivity of Halogen Oxygen Bonding in 5- and 6-Haloderivatives of Uracil
Crystals 2019, 9(9), 467; https://doi.org/10.3390/cryst9090467 - 06 Sep 2019
Abstract
Seven 5-and 6-halogenated derivatives of uracil or 1-methyluracil (halogen = Cl, Br, I) were studied by single crystal X-ray diffraction. In contrast with pure 5-halouracils, where the presence of N-H⋯O and C-H⋯O hydrogen bonds prevents the formation of other intermolecular interactions, the general [...] Read more.
Seven 5-and 6-halogenated derivatives of uracil or 1-methyluracil (halogen = Cl, Br, I) were studied by single crystal X-ray diffraction. In contrast with pure 5-halouracils, where the presence of N-H⋯O and C-H⋯O hydrogen bonds prevents the formation of other intermolecular interactions, the general ability of pyrimidine nucleobases to provide electron donating groups to halogen bonding was confirmed in three crystals and cocrystals containing uracil with the halogen atom at the C6 position. In the latter compounds, among the two nucleophilic oxygen atoms in the C=O moiety, only the urea carbonyl oxygen O1 can act as halogen bond acceptor, being not saturated by conventional hydrogen bonds. The halogen bonds in pure 6-halouracils are all rather weak, as supported by Hirshfeld surface analysis. The strongest interaction was found in the structure of 6-iodouracil, which displayed the largest (13%) reduction of the sum of van der Waals (vdW) radii for the contact atoms. Despite this, halogen bonding plays a role in determining the crystal packing of 6-halouracils, acting alongside conventional hydrogen bonds. Full article
Show Figures

Graphical abstract

Open AccessArticle
Preparation and Single Crystal Structure Determination of the First Biobased Furan-Polydiacetylene Using Topochemical Polymerization
Crystals 2019, 9(9), 448; https://doi.org/10.3390/cryst9090448 - 29 Aug 2019
Cited by 2
Abstract
Crystal structure elucidations of bio-based polymers provide invaluable data regarding structure–property relationships. In this work, we achieved synthesis and Single Crystal X-ray Diffraction (SCXRD) structural determination of a new furan-based polydiacetylene (PDA) derivative with carbamate (urethane) functionality. Firstly, diacetylene (DA) monomers were found [...] Read more.
Crystal structure elucidations of bio-based polymers provide invaluable data regarding structure–property relationships. In this work, we achieved synthesis and Single Crystal X-ray Diffraction (SCXRD) structural determination of a new furan-based polydiacetylene (PDA) derivative with carbamate (urethane) functionality. Firstly, diacetylene (DA) monomers were found to self-assemble in the crystalline state in such a way that the polymerization theoretically occurred in two different directions. Indeed, for both directions, geometrical parameters for the reactive alignment of DA are satisfied and closely related with the optimal geometrical parameters for DA topochemical polymerization (d(1) = 4.7–5.2 Å, d(2) ≤ 3.8 Å, θ ≈ 45°). However, within the axis of hydrogen bonds (HB), the self-assembling monomers display distances and angles (d(1) = 4.816 Å, d(2) = 3.822 Å, θ = 51°) that deviate more from the ideal values than those in the perpendicular direction (d(1) = 4.915Å, d(2) = 3.499Å, θ ≈ 45°). As expected from these observations, the thermal topochemical polymerization occurs in the direction perpendicular to the HB and the resulting PDA was characterized by SCXRD. Full article
Show Figures

Graphical abstract

Open AccessArticle
Elucidation of the Structure of the 2-amino-3,5-Dibromochalcone Epoxides in Solution and Solid State
Crystals 2019, 9(6), 277; https://doi.org/10.3390/cryst9060277 - 28 May 2019
Cited by 3
Abstract
The conformation of the title compounds was determined in solution by 1H-NMR spectroscopy and in solid state by single-crystal X-ray diffraction (XRD) complemented with density functional theory. The compounds were found to exist exclusively in solution and solid state as trans-2-aminochalcone [...] Read more.
The conformation of the title compounds was determined in solution by 1H-NMR spectroscopy and in solid state by single-crystal X-ray diffraction (XRD) complemented with density functional theory. The compounds were found to exist exclusively in solution and solid state as trans-2-aminochalcone epoxides with strong intramolecular hydrogen bonding interaction between the amino and carbonyl groups. These 2-aminochalcone epoxides experienced a solvent effect in DMSO-d6, which resulted in an anomalous chemical shift for the α-hydrogen signal, presumably due to complexation of solute molecules with DMSO. The solute–solvent interaction would probably fix the trans conformation of epoxyketone such that α-H is more accessible to both aryl rings, and in turn, experience their combined anisotropic effect. Intermolecular interactions in the crystal structures were confirmed and quantified using the Hirshfeld surface analysis. Moreover, the trans stereochemistry of the α-epoxyketones facilitated direct one-pot sequential sulfuric acid-mediated ring opening and aryl migration to afford the corresponding 3-arylquinolin-4(1H)-ones (azaisoflavones). Full article
Show Figures

Figure 1

Open AccessArticle
Substituent Effects in the Crystal Packing of Derivatives of 4′-Phenyl-2,2′:6′,2″-Terpyridine
Crystals 2019, 9(2), 110; https://doi.org/10.3390/cryst9020110 - 20 Feb 2019
Cited by 1
Abstract
We report the preparation of a series of new 4′-substituted 2,2′:6′,2″-terpyridines: 4′-(3,5-dimethylphenyl)-2,2′:6′,2″-terpyridine (2), 4′-(3-fluoro-5-methylphenyl)-2,2′:6′,2″-terpyridine (3), 4′-(3,5-difluorophenyl)-2,2′:6′,2″-terpyridine (4), and 4′-(3,5- bis(trifluoromethyl)phenyl)-2,2′:6′,2″-terpyridine (5). The compounds have been characterized by mass spectrometry, solid-state IR spectroscopy and solution NMR [...] Read more.
We report the preparation of a series of new 4′-substituted 2,2′:6′,2″-terpyridines: 4′-(3,5-dimethylphenyl)-2,2′:6′,2″-terpyridine (2), 4′-(3-fluoro-5-methylphenyl)-2,2′:6′,2″-terpyridine (3), 4′-(3,5-difluorophenyl)-2,2′:6′,2″-terpyridine (4), and 4′-(3,5- bis(trifluoromethyl)phenyl)-2,2′:6′,2″-terpyridine (5). The compounds have been characterized by mass spectrometry, solid-state IR spectroscopy and solution NMR and absorption spectroscopies. The single-crystal X-ray diffraction structures of 3, 5 and 6·EtOH (6 = 4′-(3,5-bis(tert-butyl)phenyl)-2,2′:6′,2″-terpyridine) have been elucidated. The molecular structures of the compounds are unexceptional. Since 3 and 5 crystallize without lattice solvent, we are able to understand the influence of introducing substituents in the 4′-phenyl ring and compare the packing in the structures with that of the previously reported 4′-phenyl-2,2′:6′,2″-terpyridine (1). On going from 1 to 3, face-to-face π-stacking of pairs of 3-fluoro-5-methylphenyl rings contributes to a change in packing from a herringbone assembly in 1 with no ring π-stacking to a layer-like packing. The latter arises through a combination of π-stacking of aromatic rings and N…H–C hydrogen bonding. On going from 3 to 5, N…H–C and F…H–C hydrogen-bonding is dominant, supplemented by π-stacking interactions between pairs of pyridine rings. A comparison of the packing of molecules of 6 with that in 1, 3 and 5 is difficult because of the incorporation of solvent in 6·EtOH. Full article
Show Figures

Graphical abstract

Back to TopTop