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Crystals
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Experimental and Theoretical Electron Density Analysis of Crystals
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Experimental and Theoretical Electron Density Analysis of Crystals

A special issue of Crystals (ISSN 2073-4352).

Deadline for manuscript submissions: closed (31 December 2017) | Viewed by 33254

Special Issue Editor

Dr. Jacob Overgaard

E-Mail Website
Guest Editor
Department of Chemistry, Aarhus Universitet, Aarhus, Denmark
Interests: electron density analysis; molecular magnetism; single-crystal diffraction; polarized neutron diffraction

Special Issue Information

Dear Colleagues,

The electron density of a given material, be that a molecular species of relevance to life science or an inorganic phase that physicists appreciate, is a determining factor for many of its essential and unique physical properties, and it is obviously of huge importance in any study of physical properties of solid matter. This year, we can all celebrate the half-century that has passed since the first experimental result that laid bare the potential that single crystal X-ray diffraction has for determination of the crystalline electron density distribution, namely the clear illustration of bonding electron density in s-triazine by Coppens (Science, 1967, 1577). Since these first steps, major improvements in instrumentation and analysis methods have taken the field extremely far, and the technique is continuously evolving. The chemical systems under scrutiny are increasingly complex, and for instance the first electron density determinations of excited states have surfaced in recent years. In parallel, the electron density may also be obtained by computational methods and this field is developing at an even higher pace thanks in large to the increasing speed of computers.

With this Special Issue, we aim to show the broad applicability of electron density analysis and its strength in addressing a large variety of chemical and physical problems.

Therefore, we invite you to contribute a research article to this Special Issue, featuring your particular scientific problem among others having in common the use of the electron density.

Dr. Jacob Overgaard
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 submissions that pass pre-check are 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 2100 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

  • X-ray diffraction

  • Electron density determination

  • Topological analysis

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Published Papers (6 papers)

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Research

12 pages, 18325 KiB  
Article
An Examination of the Electron Densities in a Series of Tripodal Cobalt Complexes Bridged by Magnesium, Calcium, Strontium, and Barium †
by John Bacsa, Lillian G. Ramírez-Palma, Fernando Cortés-Guzmán, Christian M. Wallen and Christopher C. Scarborough
Crystals 2018, 8(6), 234; https://doi.org/10.3390/cryst8060234 - 25 May 2018
Viewed by 4743
Abstract
X-ray crystallographic and theoretical charge-density data for a series of compounds—[(Co(Ts3tren))M(Co(Ts3tren))], (M = Mg, Ca, Sr and Ba)—were examined. The crystal structures were isostructural, and the alkaline-earth-metal ions had the same six-coordinate environment oxygen donor atoms which was octahedral [...] Read more.
X-ray crystallographic and theoretical charge-density data for a series of compounds—[(Co(Ts3tren))M(Co(Ts3tren))], (M = Mg, Ca, Sr and Ba)—were examined. The crystal structures were isostructural, and the alkaline-earth-metal ions had the same six-coordinate environment oxygen donor atoms which was octahedral despite the large variation in their ionic radii. The isomorphism of these molecules was surprising, and a theoretical examination of their electronic structures, with various metal ions along the series, provided detailed insight into their stabilities. The theoretical and experimental data were consistent and agreed well. The local properties of the Co(II) ion and its donor atoms were relatively independent of the alkaline earth metals. Full article
(This article belongs to the Special Issue Experimental and Theoretical Electron Density Analysis of Crystals)
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11 pages, 5250 KiB  
Article
New Polymorphs of the Phase-Change Material Sodium Acetate
by Birger Dittrich, Justin Bergmann, Peter Roloff and Guido J. Reiss
Crystals 2018, 8(5), 213; https://doi.org/10.3390/cryst8050213 - 15 May 2018
Cited by 6 | Viewed by 5191
Abstract
Two new polymorphs of the phase-change material sodium acetate were characterized by single-crystal X-ray diffraction. A tetragonal form was found first. It converted to a orthorhombic form after measurement of a single crystal of the tetragonal form at 100 K and subsequent warming [...] Read more.
Two new polymorphs of the phase-change material sodium acetate were characterized by single-crystal X-ray diffraction. A tetragonal form was found first. It converted to a orthorhombic form after measurement of a single crystal of the tetragonal form at 100 K and subsequent warming to ambient temperature. Hirshfeld surface fingerprint plots show the different packing environments of the two new compared to the two known orthorhombic polymorphs Forms I and II. The accuracy and precision of the structures were improved compared to conventional independent atom model refinement through the use of aspherical scattering factors of the invariom database. We think that the layered nature of all sodium acetate forms, and the thereby limited (“quantized”) availability of vibrational modes, is related to the phenomenon of supersaturation, which is connected to its phase-change properties. Full article
(This article belongs to the Special Issue Experimental and Theoretical Electron Density Analysis of Crystals)
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Graphical abstract

15 pages, 11610 KiB  
Article
Experimental Electron Density Distribution in Two Cocrystals of Betaines with p-Hydroxybenzoic Acid
by Agata Owczarzak and Maciej Kubicki
Crystals 2018, 8(3), 132; https://doi.org/10.3390/cryst8030132 - 10 Mar 2018
Cited by 5 | Viewed by 5321
Abstract
Experimental determination of electron density distribution in crystals by means of high-resolution X-ray diffraction allows, among others, for studying the details of intra- and inter-molecular interactions. In case of co-crystals, this method may help in finding the conditions of creating such species. The [...] Read more.
Experimental determination of electron density distribution in crystals by means of high-resolution X-ray diffraction allows, among others, for studying the details of intra- and inter-molecular interactions. In case of co-crystals, this method may help in finding the conditions of creating such species. The results of such analysis for two co-crystals containing betaines, namely trigonelline (TRG: nicotinic acid N-methylbetaine, IUPAC name: 1-methylpyridinium-3-carboxylate) and N-methylpiperidine betaine (MPB: 1-methylpiperidinium-1-yl-carboxylate) with p-hydroxybenzoic acid (HBA) are reported. TRG-HBA crystallizes as a hydrate. For both of the co-crystals, high-quality diffraction data were collected up to sinθ/λ = 1.13 Å−1. Hansen-Coppens multipolar model was then applied for modelling the electron density distribution and Atoms-In-Molecules approach was used for detailed analysis of interactions in crystals. A number of intermolecular interactions was identified, ranging from strong O-H···O hydrogen bonds through C-H···O to C-H···π and π···π interactions. Correlations between the geometrical characteristics of the contacts and the features of their critical points were analyzed in detail. Atomic charges show that in zwitterionic species there are regions of opposite charges, rather than charges that are localized on certain atoms. In case of MPB-HBA, a significant charge transfer between the components of co-crystal (0.5 e) was found, as opposed to TRG-HBA, where all of the components are almost neutral. Full article
(This article belongs to the Special Issue Experimental and Theoretical Electron Density Analysis of Crystals)
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11 pages, 3234 KiB  
Article
Atomic Charges and Chemical Bonding in Y-Ga Compounds
by Yuri Grin, Anatolij Fedorchuk, Rodolfo J. Faria and Frank R. Wagner
Crystals 2018, 8(2), 99; https://doi.org/10.3390/cryst8020099 - 16 Feb 2018
Cited by 14 | Viewed by 4494
Abstract
A negative deviation from Vegard rule for the average atomic volume versus yttrium content was found from experimental crystallographic information about the binary compounds of yttrium with gallium. Analysis of the electron density (DFT calculations) employing the quantum theory of atoms in molecules [...] Read more.
A negative deviation from Vegard rule for the average atomic volume versus yttrium content was found from experimental crystallographic information about the binary compounds of yttrium with gallium. Analysis of the electron density (DFT calculations) employing the quantum theory of atoms in molecules revealed an increase in the atomic volumes of both Y and Ga with the increase in yttrium content. The non-linear increase is caused by the strengthening of covalent Y-Ga interactions with stronger participation of genuine penultimate shell electrons (4d electrons of yttrium) in the valence region. Summing the calculated individual atomic volumes for a unit cell allows understanding of the experimental trend. With increasing yttrium content, the polarity of the Y-Ga bonding and, thus its ionicity, rises. The covalency of the atomic interactions in Y-Ga compounds is consistent with their delocalization from two-center to multi-center ones. Full article
(This article belongs to the Special Issue Experimental and Theoretical Electron Density Analysis of Crystals)
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17 pages, 6708 KiB  
Article
Monoclinic Paracetamol vs. Paracetamol-4,4′-Bipyridine Co-Crystal; What Is the Difference? A Charge Density Study
by Jonathan J. Du, Felcia Lai, Linda Váradi, Peter A. Williams, Paul W. Groundwater, James A. Platts, David E. Hibbs and Jacob Overgaard
Crystals 2018, 8(1), 46; https://doi.org/10.3390/cryst8010046 - 18 Jan 2018
Cited by 7 | Viewed by 8791
Abstract
Paracetamol (PCM) has two well-documented polymorphic forms at room temperature; monoclinic Form I is more stable than the other orthorhombic Form II. Form II exhibits improved tabletting properties compared to Form I due to low shearing forces; however, difficulties in its manufacture have [...] Read more.
Paracetamol (PCM) has two well-documented polymorphic forms at room temperature; monoclinic Form I is more stable than the other orthorhombic Form II. Form II exhibits improved tabletting properties compared to Form I due to low shearing forces; however, difficulties in its manufacture have limited its use in industrial manufacture. Previous studies have found that the introduction of a co-former to form co-crystals would allow the PCM molecule to exist in a conformation similar to that of the orthorhombic form while being more stable at room temperature. Experimental charge density analysis of the paracetamol-4,4′-bipyridine (PCM-44BP) co-crystal system, and its constituent molecules, has been carried out to examine the forces that drive the formation and stabilisation of the co-crystal, while allowing PCM to maintain a packing motif similar to that found in Form II. It is hoped studies on this well-known compound will help apply the knowledge gained to other drug molecules that are less successful. The PCM molecules in the co-crystal were found to exhibit similar packing motifs to that found in Form I, however, intercalation of the 44BP molecule between the PCM layers resulted in a shallower angle between molecular planes, which could result in the required lateral shear. Topological analysis identified more weak interactions in the co-crystal compared to the individual molecules, thus allowing for greater stability as evidenced by the lattice energies. Weak interactions in the PCM-44BP co-crystal were found to range in strength from 4.08–84.33 kJ mol−1, and this variety allowed the PCM-44BP planes to be held together, while a weak π–π interaction (15.14 kJ mol−1) allowed lateral shear to occur, thus mimicking the planes found in Form II PCM and offering the possibility of improved tabletting properties. A comparison of integrated atomic charges between partitions of the PCM molecules in the single and co-crystal found that the hydroxyl and amide groups were involved in greater hydrogen bonding in the co-crystal, resulting in a charge redistribution across the molecule evidenced by a larger molecular dipole moment (µ = 12.34D). These findings, in addition to the co-crystal having the largest lattice energy, form a potential basis with which to predict that the co-crystal exhibits improved solubility and stability profiles. It is anticipated that these findings will contribute to improvements in the formulation and other physical properties of PCM and other pharmaceutical compounds. Full article
(This article belongs to the Special Issue Experimental and Theoretical Electron Density Analysis of Crystals)
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3299 KiB  
Article
Synthesis, Characterization and DFT Calculations of 4,5,12- and 1,8,12-trichloro-9,10-dihydro-9,10-ethanoanthracene-12-carbonitriles
by Mujeeb A. Sultan, Usama Karama, Abdulrahman I. Almansour, Saied M. Soliman, Hazem A. Ghabbour and Yahia N. Mabkhot
Crystals 2017, 7(9), 259; https://doi.org/10.3390/cryst7090259 - 25 Aug 2017
Cited by 3 | Viewed by 3656
Abstract
The chlorinated ethanoanthracenes: 4,5,12- and 1,8,12-(trichloro-9,10-dihydro-9,10-ethanoanthracene-12-carbonitriles) (1 and 2), which are regioisomers, were synthesized and characterized using nuclear magnetic resonance (1H- and 13C-NMR) and infrared (IR) spectroscopic techniques. The structure of isomer 1 was further confirmed using a [...] Read more.
The chlorinated ethanoanthracenes: 4,5,12- and 1,8,12-(trichloro-9,10-dihydro-9,10-ethanoanthracene-12-carbonitriles) (1 and 2), which are regioisomers, were synthesized and characterized using nuclear magnetic resonance (1H- and 13C-NMR) and infrared (IR) spectroscopic techniques. The structure of isomer 1 was further confirmed using a single-crystal X-ray technique. The relative stabilities of the title compounds were calculated using the density functional theory (DFT) method on the basis of their total energies and thermodynamic parameters. Isomer 1 is thermodynamically more stable than isomer 2 in the gas phase and in solution. The calculated molecular geometry of isomer 1 agreed well with the experimental X-ray structure. The atomic charge distribution at the different atomic sites was calculated using natural bond orbital analysis. Isomer 2 was predicted to be more polar than isomer 1. Full article
(This article belongs to the Special Issue Experimental and Theoretical Electron Density Analysis of Crystals)
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