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Crystals
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Experimental and Theoretical Electron-Density Study of Crystalline Materials
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Experimental and Theoretical Electron-Density Study of Crystalline Materials

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Inorganic Crystalline Materials".

Deadline for manuscript submissions: closed (1 June 2020) | Viewed by 19234

Special Issue Editor

Dr. Lilianna Checinska

E-Mail Website
Guest Editor
Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163/165, 90-236 Lodz, Poland
Interests: electron-density analysis; experiment vs. theory; X-ray single-crystal diffraction; X-ray wavefunction refinement; chemical bonding; hydrogen bonding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It is a great honour to introduce the new Special Issue “Experimental and Theoretical Electron-Density Study of Crystalline Materials”. Electron density studies are still a challenging task, although the method of charge density determination has been known since 1960. Ideas for publications in this Special Issue may come from a variety of both experimental and/or theoretical of sources. We expect studies from many point of view and interest, from the electronic nature of chemical systems through chemical bonding analysis to hydrogen-bonding investigations. Any recent developments or innovations on methodological aspects are welcome, especially new ideas and solutions coming from X-ray wavefunction refinement, as one of the newest methods to obtain so-called experimental wave function. All topics, whether mentioned above or not, closely related to electron density studies of crystalline materials will be carefully considered.

We stress that the call for papers on “Experimental and Theoretical Electron-Density Study of Crystalline Materials” is open to everyone, so please make your colleagues aware of the forthcoming Special Issue. This is a great opportunity to show your outstanding results to a wider spectrum of readers using the open access form of the Crystals journal.

Dr. Lilianna Checinska
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 2600 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.

Published Papers (7 papers)

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Research

8 pages, 1371 KiB  
Article
Synthesis, Structure and Bonding Analysis of the Zwitterionic PPP-Pincer Complex (6-Ph2P-Ace-5-)2P(O)AuCl2
by Daniel Duvinage, Enno Lork, Simon Grabowsky, Stefan Mebs and Jens Beckmann
Crystals 2020, 10(7), 564; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10070564 - 01 Jul 2020
Cited by 1 | Viewed by 1772
Abstract
The reaction of (6-Ph2P-Ace-5-)2P(O)H with (tht)AuCl3 proceeds via elimination of tetrahydrothiophene (tht) and HCl, providing the zwitterionic PPP-pincer complex (6-Ph2P-Ace-5-)2P(O)AuCl2 (1) as yellow crystals. The molecular structure of 1 was established [...] Read more.
The reaction of (6-Ph2P-Ace-5-)2P(O)H with (tht)AuCl3 proceeds via elimination of tetrahydrothiophene (tht) and HCl, providing the zwitterionic PPP-pincer complex (6-Ph2P-Ace-5-)2P(O)AuCl2 (1) as yellow crystals. The molecular structure of 1 was established and studied by X-ray crystallography. The electronic structure was computationally analyzed using a comprehensive set of real-space bonding indicators derived from electron and electron-pair densities, providing insight into the relative contributions of covalent and non-covalent forces to the polar-covalent Au–Cl, Au–P, and P–O− bonds; the latter being one of the textbook cases for strongly polarized covalent interactions. Partial spatial complementarity between both bonding aspects is suggested by the electronic properties of the distinctively different Au–Cl bonds. Full article
(This article belongs to the Special Issue Experimental and Theoretical Electron-Density Study of Crystalline Materials)
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13 pages, 3148 KiB  
Article
Structural Refinement and Density Functional Theory Study of Synthetic Ge-Akaganéite (β-FeOOH)
by Donghoon Chung, Changyun Park, Woohyun Choi and Yungoo Song
Crystals 2020, 10(4), 239; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10040239 - 25 Mar 2020
Cited by 2 | Viewed by 2815
Abstract
In this study, we propose a revised structural model for highly ordered synthetic Ge-akaganéite, a stable analogue of tunnel-type Fe-oxyhydroxide, based on the Rietveld refinement of synchrotron X-ray diffraction data and density functional theory with dispersion correction (DFT-D) calculations. In the proposed crystal [...] Read more.
In this study, we propose a revised structural model for highly ordered synthetic Ge-akaganéite, a stable analogue of tunnel-type Fe-oxyhydroxide, based on the Rietveld refinement of synchrotron X-ray diffraction data and density functional theory with dispersion correction (DFT-D) calculations. In the proposed crystal structure of Ge-akaganéite, Ge is found not only in the tunnel sites as GeO(OH)3− tetrahedra, but also 4/5 of total Ge atoms are in the octahedral sites substituting 1/10 of Fe. In addition, the tunnel structures are stabilized by the presence of hydrogen bonds between the framework OH and Cl− species, forming a twisted cube structure and the GeO(OH)3− tetrahedra corner oxygen, forming a conjugation bond. The chemical formula of the synthetic Ge-akaganéite was determined to be (Fe7.2Ge0.8)O8.8(OH)7.2Cl0.8(Ge(OH)4)0.2. Full article
(This article belongs to the Special Issue Experimental and Theoretical Electron-Density Study of Crystalline Materials)
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16 pages, 17827 KiB  
Article
Theoretical Study of the Electronic, Magnetic, Mechanical and Thermodynamic Properties of the Spin Gapless Semiconductor CoFeMnSi
by Xingwen Tan, Jiaxue You, Peng-Fei Liu and Yanfeng Wang
Crystals 2019, 9(12), 678; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9120678 - 17 Dec 2019
Cited by 13 | Viewed by 3145
Abstract
CoFeMnSi has been both experimentally and theoretically proven as a novel spin-gapless semiconductor and resulted in a new research direction in equiatomic full Heusler compounds. Using the first-principles calculation method, we investigated the electronic, magnetic and mechanical properties of CoFeMnSi material in this [...] Read more.
CoFeMnSi has been both experimentally and theoretically proven as a novel spin-gapless semiconductor and resulted in a new research direction in equiatomic full Heusler compounds. Using the first-principles calculation method, we investigated the electronic, magnetic and mechanical properties of CoFeMnSi material in this study. The obtained lattice constant under the LiMgPdSn-type Heusler structure is 5.611 Å and it is fairly consistent with previous experimental results and theoretical calculations. Furthermore, the achieved total magnetic moment of 4 μB follows the Slater–Pauling rule as Mtotal = Ztotal − 24, where Mtotal is the total magnetic moment per formula unit and Ztotal is the total valence electron number, i.e., 28 for CoFeMnSi material. We have also examined the mechanical properties of CoFeMnSi and computed its elastic constants and various moduli. Results show CoFeMnSi behaves in a ductile fashion and its strong elastic anisotropy is revealed with the help of the 3D-directional-dependent Young’s and shear moduli. Both mechanical and dynamic stabilities of CoFeMnSi are verified. In addition, strain effects on the electronic and magnetic properties of CoFeMnSi have been investigated, including both uniform and tetragonal strains, and we found that the spin-gapless feature is easily destroyed with both strain conditions, yet the total magnetic moment maintains a good stability. Furthermore, the specific behaviors under various temperatures and pressures have been accessed by the thermodynamic properties with a quasi-harmonic Debye model, including bulk modulus, thermal expansion coefficient, Grüneisen constant, heat capacity and Debye temperature. This comprehensive study can offer a very helpful and valuable reference for other relative research works. Full article
(This article belongs to the Special Issue Experimental and Theoretical Electron-Density Study of Crystalline Materials)
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17 pages, 1913 KiB  
Article
Intermolecular Interactions in Ionic Crystals of Nucleobase Chlorides—Combining Topological Analysis of Electron Densities with Energies of Electrostatic Interactions
by Prashant Kumar, Małgorzata Katarzyna Cabaj and Paulina Maria Dominiak
Crystals 2019, 9(12), 668; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9120668 - 11 Dec 2019
Cited by 12 | Viewed by 3041
Abstract
Understanding intermolecular interactions in crystals of molecular ions continues to be difficult. On the one hand, the analysis of interactions from the point of view of formal charges of molecules, similarly as it is commonly done for inorganic ionic crystals, should be performed. [...] Read more.
Understanding intermolecular interactions in crystals of molecular ions continues to be difficult. On the one hand, the analysis of interactions from the point of view of formal charges of molecules, similarly as it is commonly done for inorganic ionic crystals, should be performed. On the other hand, when various functional groups are present in the crystal, it becomes natural to look at the interactions from the point of view of hydrogen bonding, π…π stacking and many other kinds of non-covalent atom–atom bonding. Often, these two approaches seem to lead to conflicting conclusions. On the basis of experimental charge densities of cytosinium chloride, adeninium chloride hemihydrate, and guanine dichloride crystals, with the help of theoretical simulations, we have deeply analysed intermolecular interactions among protonated nucleobases, chloride anions and water molecules. Here, in the second paper of the series of the two (Kumar et al., 2018, IUCrJ 5, 449–469), we focus on applying the above two approaches to the large set of dimers identified in analysed crystals. To understand electrostatic interactions, we analysed electrostatic interaction energies (Ees) computed directly from molecular charge densities and contrasted them with energies computed only from net molecular charges, or from a sum of electric multipolar moments, to find the charge penetration contribution to Ees. To characterize non-covalent interactions we performed topological analyses of crystal electron densities and estimated their interaction energies (EEML) from properties of intermolecular bond critical points. We show that the overall crystal architecture of the studied compounds is governed by the tight packing principle and strong electrostatic attractions and repulsions between ions. Many ions are oriented to each other in a way to strengthen attractive electrostatic interactions or weaken strong repulsion, but not all of them. Numerous bond critical points and bond paths were found between ions, including nucleobase cations despite their overall repulsive interactions. It is clear there is no correlation between EEML and Ees. However, strong relation between EEML and the charge penetration component of Ees is observed. The relation holds regardless of interaction types or whether or not interacting molecules bear the same or opposite charges. Thus, a charge density-based approach for computing intermolecular interaction energies and the atom–atom approach to analyse non-covalent interactions do complement each other, even in ionic systems. Full article
(This article belongs to the Special Issue Experimental and Theoretical Electron-Density Study of Crystalline Materials)
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16 pages, 3701 KiB  
Article
Symmetric Fluoroborate and its Boron Modification: Crystal and Electronic Structures
by Błażej Dziuk, Borys Ośmiałowski, Bartosz Zarychta, Krzysztof Ejsmont and Lilianna Chęcińska
Crystals 2019, 9(12), 662; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9120662 - 09 Dec 2019
Cited by 6 | Viewed by 2991
Abstract
Four boron-carrying molecules were synthesized and purified. These were found to be (a) relatively neutral with respect to the parent BF derivative and (b) functionalized by donor–acceptor groups resulting in a charge transfer within the molecule. The study discusses the steric effect and [...] Read more.
Four boron-carrying molecules were synthesized and purified. These were found to be (a) relatively neutral with respect to the parent BF derivative and (b) functionalized by donor–acceptor groups resulting in a charge transfer within the molecule. The study discusses the steric effect and the influence of the substitution of the side rings on the surroundings of the boron atom. Electronic structures were characterized by real-space bonding indicators. Hirshfeld surface and energy frameworks tools were applied to examine the crystal packing features. Full article
(This article belongs to the Special Issue Experimental and Theoretical Electron-Density Study of Crystalline Materials)
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12 pages, 3042 KiB  
Article
Solid-State Photoinitiated Cycloaddition Reaction of 4,4′-(Ethene-1,2-diyl)bis(pyridinium) Dinitrate: Charge-Density Perspective on Initial Stage of the Reaction
by Anna V. Vologzhanina, Dmitry Yu. Aleshin, Alexander D. Volodin, Anton V. Savchenkov, Ivan E. Ushakov and Alexander A. Korlyukov
Crystals 2019, 9(12), 613; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9120613 - 23 Nov 2019
Cited by 3 | Viewed by 2113
Abstract
Solid-state photoinitiated [2 + 2] cycloaddition reaction 2(H2bpe)(NO3)2 → (H4tpcb)(NO3)4 (bpe = 1,2-bis(pyrid-4-yl)ethylene; tpcb = 1,2,3,4-tetrakis(pyrid-4-yl)cyclobutane) was carried out in a single-crystal-to-single-crystal manner. The reaction product was characterized by means of X-ray diffraction [...] Read more.
Solid-state photoinitiated [2 + 2] cycloaddition reaction 2(H2bpe)(NO3)2 → (H4tpcb)(NO3)4 (bpe = 1,2-bis(pyrid-4-yl)ethylene; tpcb = 1,2,3,4-tetrakis(pyrid-4-yl)cyclobutane) was carried out in a single-crystal-to-single-crystal manner. The reaction product was characterized by means of X-ray diffraction and 1H NMR spectroscopy. Only the rctt-isomer of tpcb was found as the reaction product. Intermolecular interactions in a single crystal of (H2bpe)(NO3)2 were studied within the QTAIM approach. Although sum energy of strong and weak hydrogen bonds dominates in total packing energy, contribution of π…π stacking interactions to the packing energy is also prominent. At solid (H2bpe)(NO3)2, stacking of photoreactive H2bpe2+ cations is realized via N…C, C…C and C–H…C bonding, although no four-membered cycles formed by these bond paths was found in molecular graph representation. Reduced density gradient (RDG) surfaces and molecular Voronoi surfaces clearly demonstrate accumulation of charge density between olefin groups prone to take part in photoinitiated cycloaddition reactions. Good correlation between description of hydrogen bonding in terms of QTAIM and Voronoi approaches was demonstrated. The Voronoi approach confirmed that during the photoreaction the system of hydrogen bonds remained almost unchanged. Full article
(This article belongs to the Special Issue Experimental and Theoretical Electron-Density Study of Crystalline Materials)
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14 pages, 2631 KiB  
Article
Bifurcated Triel Bonds—Hydrides and Halides of 1,2-Bis(Dichloroboryl)Benzene and 1,8-Bis(Dichloroboryl)Naphthalene
by Sławomir J. Grabowski
Crystals 2019, 9(10), 503; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst9100503 - 27 Sep 2019
Cited by 17 | Viewed by 2791
Abstract
MP2/aug-cc-pVTZ calculations were performed on hydrides, fluorides, and chlorides of 1,8-bis(dichloroboryl)naphthalene and 1,2-bis(dichloroboryl)benzene. The theoretical analysis of BHB−, BFB−, and BClB− arrangements occurring in these complexes and classified as bifurcated triel bonds was partly based on decomposition of [...] Read more.
MP2/aug-cc-pVTZ calculations were performed on hydrides, fluorides, and chlorides of 1,8-bis(dichloroboryl)naphthalene and 1,2-bis(dichloroboryl)benzene. The theoretical analysis of BHB−, BFB−, and BClB− arrangements occurring in these complexes and classified as bifurcated triel bonds was partly based on decomposition of the energy of interaction. The latter was carried out for structures optimized using the DFT method. The complexes analyzed were characterized by a partly covalent character of the links to the hydride and halide anions; these anions strongly influenced the geometry of the complexes. The boron centers’ links for the neutral 1,8-bis(dichloroboryl)naphthalene and 1,2-bis(dichloroboryl)benzene molecules were characterized by approximately trigonal and planar configurations, while for anionic complexes, tetrahedral configurations were observed. The crystal structures of compounds related to species calculated here were found in the Cambridge Structural Database (CSD). Full article
(This article belongs to the Special Issue Experimental and Theoretical Electron-Density Study of Crystalline Materials)
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