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Crystals, Volume 6, Issue 3 (March 2016) – 10 articles

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6633 KiB  
Article
Theoretical Studies on Hydrogen Bonds in Anions Encapsulated by an Azamacrocyclic Receptor
by Jing Wang, Jiande Gu, Md. Alamgir Hossain and Jerzy Leszczynski
Crystals 2016, 6(3), 31; https://doi.org/10.3390/cryst6030031 - 22 Mar 2016
Cited by 2 | Viewed by 4285
Abstract
Hydrogen bonds in two halides encapsulated by an azamacrocyclic receptor were studied in detail by the density functional theory (DFT) approaches at B3LYP/6-311++G(d,p) and M06-2X/6-311++G(d,p) levels. The atoms in molecules (AIM) theory and the electron density difference maps were applied for characterizing the [...] Read more.
Hydrogen bonds in two halides encapsulated by an azamacrocyclic receptor were studied in detail by the density functional theory (DFT) approaches at B3LYP/6-311++G(d,p) and M06-2X/6-311++G(d,p) levels. The atoms in molecules (AIM) theory and the electron density difference maps were applied for characterizing the hydrogen bond patterns. The results suggest that the fluoride complex has a unique binding pattern which shows a hydrogen bond augmented with ionic bond characteristics. Full article
(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)
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3035 KiB  
Article
Thermally Activated Paramagnets from Diamagnetic Polymers of Biphenyl-3,5-diyl Bis(tert-butyl Nitroxides) Carrying Methyl and Fluoro Groups at the 2’- and 5’-Positions
by Toru Yoshitake, Hiroki Kudo and Takayuki Ishida
Crystals 2016, 6(3), 30; https://doi.org/10.3390/cryst6030030 - 22 Mar 2016
Cited by 14 | Viewed by 4873
Abstract
Three new biradicals—2’,5’-dimethyl-, 2’-fluoro-5’-methyl-, and 5’-fluoro-2’-methyl- biphenyl-3,5-diyl bis(tert-butyl nitroxides)—were synthesized. The magnetic susceptibility measurements revealed their diamagnetism below and around room temperature. The nitroxide groups are located close to each other in an intermolecular fashion to form a weakly covalent head-to-tail [...] Read more.
Three new biradicals—2’,5’-dimethyl-, 2’-fluoro-5’-methyl-, and 5’-fluoro-2’-methyl- biphenyl-3,5-diyl bis(tert-butyl nitroxides)—were synthesized. The magnetic susceptibility measurements revealed their diamagnetism below and around room temperature. The nitroxide groups are located close to each other in an intermolecular fashion to form a weakly covalent head-to-tail (NO)2 ring. Biradical molecules are connected on both radical sites, constructing a diamagnetic chain. The dimethyl derivative underwent a structural phase transition at 83 °C, clarified via differential scanning calorimetry and powder X-ray diffraction, and a paramagnetic solid phase with S = 1 irreversibly appeared. The other analogues exhibited a similar irreversible upsurge of the magnetic susceptibility on heating, but the transition was characterized as the melting. Full article
(This article belongs to the Special Issue High Spin Molecules)
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4118 KiB  
Article
Effect of Intra- and Intermolecular Interactions on the Properties of para-Substituted Nitrobenzene Derivatives
by Halina Szatylowicz, Olga A. Stasyuk, Célia Fonseca Guerra and Tadeusz M. Krygowski
Crystals 2016, 6(3), 29; https://doi.org/10.3390/cryst6030029 - 18 Mar 2016
Cited by 21 | Viewed by 6599
Abstract
To study the influence of intra- and intermolecular interactions on properties of the nitro group in para-substituted nitrobenzene derivatives, two sources of data were used: (i) Cambridge Structural Database and (ii) quantum chemistry modeling. In the latter case, “pure” intramolecular interactions were [...] Read more.
To study the influence of intra- and intermolecular interactions on properties of the nitro group in para-substituted nitrobenzene derivatives, two sources of data were used: (i) Cambridge Structural Database and (ii) quantum chemistry modeling. In the latter case, “pure” intramolecular interactions were simulated by gradual rotation of the nitro group in para-nitroaniline, whereas H-bond formation at the amino group allowed the intermolecular interactions to be accounted for. BLYP functional with dispersion correction and TZ2P basis set (ADF program) were used to perform all calculations. It was found that properties of the nitro group dramatically depend on both its orientation with respect to the benzene ring as well as on the substituent in the para-position. The nitro group lies in the plane of the benzene ring for only a small number of molecules, whereas the mean value of the twist angle is 7.3 deg, mostly due to intermolecular interactions in the crystals. This distortion from planarity and the nature of para-substituent influence the aromaticity of the ring (described by HOMA index) and properties of the nitro group due to electronic effects. The results obtained by QM calculations fully coincide with observations found for the data set of crystal structures. Full article
(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)
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8164 KiB  
Article
Non-Covalent Interactions in Hydrogen Storage Materials LiN(CH3)2BH3 and KN(CH3)2BH3
by Filip Sagan, Radosław Filas and Mariusz P. Mitoraj
Crystals 2016, 6(3), 28; https://doi.org/10.3390/cryst6030028 - 18 Mar 2016
Cited by 28 | Viewed by 7976
Abstract
In the present work, an in-depth, qualitative and quantitative description of non-covalent interactions in the hydrogen storage materials LiN(CH3)2BH3 and KN(CH3)2BH3 was performed by means of the charge and energy decomposition method (ETS-NOCV) [...] Read more.
In the present work, an in-depth, qualitative and quantitative description of non-covalent interactions in the hydrogen storage materials LiN(CH3)2BH3 and KN(CH3)2BH3 was performed by means of the charge and energy decomposition method (ETS-NOCV) as well as the Interacting Quantum Atoms (IQA) approach. It was determined that both crystals are stabilized by electrostatically dominated intra- and intermolecular M∙∙∙H–B interactions (M = Li, K). For LiN(CH3)2BH3 the intramolecular charge transfer appeared (B–H→Li) to be more pronounced compared with the corresponding intermolecular contribution. We clarified for the first time, based on the ETS-NOCV and IQA methods, that homopolar BH∙∙∙HB interactions in LiN(CH3)2BH3 can be considered as destabilizing (due to the dominance of repulsion caused by negatively charged borane units), despite the fact that some charge delocalization within BH∙∙∙HB contacts is enforced (which explains H∙∙∙H bond critical points found from the QTAIM method). Interestingly, quite similar (to BH∙∙∙HB) intermolecular homopolar dihydrogen bonds CH∙∙∙HC appared to significantly stabilize both crystals—the ETS-NOCV scheme allowed us to conclude that CH∙∙∙HC interactions are dispersion dominated, however, the electrostatic and σ/σ*(C–H) charge transfer contributions are also important. These interactions appeared to be more pronounced in KN(CH3)2BH3 compared with LiN(CH3)2BH3. Full article
(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)
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3460 KiB  
Article
RCH3···O Interactions in Biological Systems: Are They Trifurcated H-Bonds or Noncovalent Carbon Bonds?
by Antonio Bauzá and Antonio Frontera
Crystals 2016, 6(3), 26; https://doi.org/10.3390/cryst6030026 - 17 Mar 2016
Cited by 66 | Viewed by 7377
Abstract
In this manuscript, we combine high-level ab initio calculations on some model systems (XCH3 σ-hole/H-bond donors) and a Protein Data Bank (PDB) survey to distinguish between trifurcated H-bonds and noncovalent carbon bonds in XCH3···O complexes (X = any atom or [...] Read more.
In this manuscript, we combine high-level ab initio calculations on some model systems (XCH3 σ-hole/H-bond donors) and a Protein Data Bank (PDB) survey to distinguish between trifurcated H-bonds and noncovalent carbon bonds in XCH3···O complexes (X = any atom or group). Recently, it has been demonstrated both experimentally and theoretically the importance of noncovalent carbon bonds in the solid state. When an electron-rich atom interacts with a methyl group, the role of the methyl group is commonly viewed as a weak H-bond donor. However, if the electron-rich atom is located equidistant from the three H atoms, the directionality of each individual H-bond in the trifurcated binding mode is poor. Therefore, the XCH3···O interaction could be also defined as a tetrel bond (C···O interaction). In this manuscript, we shed light into this matter and demonstrate the importance of XCH3···O noncovalent carbon bonding interactions in two relevant protein-substrate complexes retrieved from the PDB. Full article
(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)
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1325 KiB  
Article
Novel Charge Ordering in the Trimer Iridium Oxide BaIrO3
by Ichiro Terasaki, Shun Ito, Taichi Igarashi, Shinichiro Asai, Hiroki Taniguchi, Ryuji Okazaki, Yukio Yasui, Kensuke Kobayashi, Reiji Kumai, Hironori Nakao and Youichi Murakami
Crystals 2016, 6(3), 27; https://doi.org/10.3390/cryst6030027 - 16 Mar 2016
Cited by 10 | Viewed by 7052
Abstract
We have prepared polycrystalline samples of the trimer Ir oxide BaIrO3 with face-shared Ir3O12 trimers, and have investigated the origin of the phase transition at 182 K by measuring resistivity, thermopower, magnetization and synchrotron X-ray diffraction. We propose a [...] Read more.
We have prepared polycrystalline samples of the trimer Ir oxide BaIrO3 with face-shared Ir3O12 trimers, and have investigated the origin of the phase transition at 182 K by measuring resistivity, thermopower, magnetization and synchrotron X-ray diffraction. We propose a possible electronic model and transition mechanism, starting from a localized electron picture on the basis of the Rietveld refinement. Within this model, BaIrO3 can be basically regarded as a Mott insulator, when the Ir3O12 trimer is identified to one pseudo-atom or one lattice site. The transition can be viewed as a transition from the Mott insulator phase to a kind of charge ordered insulator phase. Full article
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9668 KiB  
Article
Theoretical Analysis of SAW Propagation in 3C-SiC/c-AlN
by Cinzia Caliendo
Crystals 2016, 6(3), 25; https://doi.org/10.3390/cryst6030025 - 15 Mar 2016
Cited by 7 | Viewed by 4973
Abstract
The anisotropic materials as the acoustic wave propagating medium introduce the dependence of the phase velocity on the wave propagation direction, as opposed to the isotropic counterparts; in addition, the profile of the particle displacement components can be quite different, depending on the [...] Read more.
The anisotropic materials as the acoustic wave propagating medium introduce the dependence of the phase velocity on the wave propagation direction, as opposed to the isotropic counterparts; in addition, the profile of the particle displacement components can be quite different, depending on the crystal type and propagation direction. The propagation of surface and bulk acoustic waves (SAWs and BAWs) along the (001), (111) and (110) planes of cubic SiC crystals have been studied. For specific propagation directions in these planes, slight variations in the velocity of the elastic surface waves are found. It was observed that Rayleigh-type, generalized and pseudo-surface waves can propagate at specific directions, thus confirming how the anisotropic behavior of the bare SiC substrate modifies the existence and the field profile of the SAW that propagates at its free surface. Finally, the SAW propagation along AlN/SiC-based multilayered structures is studied for the three SiC planes, different AlN piezoelectric layer thicknesses and electrical boundary conditions. Full article
(This article belongs to the Section Crystalline Materials)
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13539 KiB  
Review
Inorganic–Organic Hybrid Surfactant Crystals: Structural Aspects and Functions
by Takeru Ito
Crystals 2016, 6(3), 24; https://doi.org/10.3390/cryst6030024 - 10 Mar 2016
Cited by 25 | Viewed by 9930
Abstract
Hybrid single crystals consisting of an organic surfactant and an inorganic moiety are promising functional materials. Layered crystals composed from alternate inorganic and surfactant layers are obtained by the template effect of long alkyl chain moiety. The composition, crystal packing, and molecular arrangement [...] Read more.
Hybrid single crystals consisting of an organic surfactant and an inorganic moiety are promising functional materials. Layered crystals composed from alternate inorganic and surfactant layers are obtained by the template effect of long alkyl chain moiety. The composition, crystal packing, and molecular arrangement of the hybrid single crystals are controllable by changing the inorganic constituent and the surfactant molecular structure. The types of hybrid surfactant single crystals are twofold: (i) crystals consisting of discrete inorganic cation coordinated by ligands having amphiphilic moiety; and (ii) crystals comprising a surfactant cation and a discrete inorganic anion including polyoxometalate (POM) oxide clusters. The POM-surfactant hybrid single crystals are rather rare, and therefore promising as unprecedented functional materials. Their structural variation and functional properties are discussed. Full article
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1520 KiB  
Communication
A Cadmium Anionic 1-D Coordination Polymer {[Cd(H2O)6][Cd2(atr)22-btc)2(H2O)4] 2H2O}n within a 3-D Supramolecular Charge-Assisted Hydrogen-Bonded and π-Stacking Network
by Anas Tahli, Ümit Köc, Reda F. M. Elshaarawy, Anna Christin Kautz and Christoph Janiak
Crystals 2016, 6(3), 23; https://doi.org/10.3390/cryst6030023 - 2 Mar 2016
Cited by 13 | Viewed by 5975
Abstract
The hydrothermal reaction of 4,4′-bis(1,2,4-triazol-4-yl) (btr) and benzene-1,3,5-tricarboxylic acid (H3btc) with Cd(OAc)2·2H2O at 125 °C in situ forms 4-amino-1,2,4-triazole (atr) from btr, which crystallizes to a mixed-ligand, poly-anionic chain of [Cd2(atr)22-btc) [...] Read more.
The hydrothermal reaction of 4,4′-bis(1,2,4-triazol-4-yl) (btr) and benzene-1,3,5-tricarboxylic acid (H3btc) with Cd(OAc)2·2H2O at 125 °C in situ forms 4-amino-1,2,4-triazole (atr) from btr, which crystallizes to a mixed-ligand, poly-anionic chain of [Cd2(atr)22-btc)2(H2O)4]2–. Together with a hexaaquacadmium(II) cation and water molecules the anionic coordination-polymeric forms a 3-D supramolecular network of hexaaquacadmium(II)-catena-[bis(4-amino-1,2,4-triazole)tetraaquabis(benzene-1,3,5-tricarboxylato)dicadmate(II)] dihydrate, 1-D-{[Cd(H2O)6][Cd2(atr)22-btc)2(H2O)4] 2H2O}n which is based on hydrogen bonds (in part charge-assisted) and π–π interactions. Full article
(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)
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1980 KiB  
Article
Charge-Assisted Hydrogen-Bonded Networks of NH4+ and [Co(NH3)6]3+ with the New Linker Anion of 4-Phosphono-Biphenyl-4′-Carboxylic Acid
by Christian Heering, Bahareh Nateghi and Christoph Janiak
Crystals 2016, 6(3), 22; https://doi.org/10.3390/cryst6030022 - 24 Feb 2016
Cited by 11 | Viewed by 9270
Abstract
The new linker molecule 4-phosphono-biphenyl-4′-carboxylic acid (H2O3P-(C6H4)2-COOH, H3BPPA) has been structurally elucidated in hydrogen-bonded networks with the ammonium cation NH4(H2BPPA)(H3BPPA) (1) and the [...] Read more.
The new linker molecule 4-phosphono-biphenyl-4′-carboxylic acid (H2O3P-(C6H4)2-COOH, H3BPPA) has been structurally elucidated in hydrogen-bonded networks with the ammonium cation NH4(H2BPPA)(H3BPPA) (1) and the hexaamminecobalt(III) cation [Co(NH3)6](BPPA)·4H2O (2). The protic O-H and N-H hydrogen atoms were found and refined in the low-temperature single-crystal X-ray structures. The hydrogen bonds in both structures are so-called charge-assisted; that is, the H-bond donor and/or acceptor carry positive and/or negative ionic charges, respectively. The H-bonded network in 1 consists of one formally mono-deprotonated 4-phosphonato-biphenyl-4′-carboxylic acid group; that is, a H2BPPA anion and a neutral H3BPPA molecule, which together form a 3D hydrogen-bonded network. However, an almost symmetric resonance-assisted hydrogen bond (RAHB) bond [O···H = 1.17 (3) and 1.26 (3) Å, O···H···O = 180 (3)°] signals charge delocalization between the formal H2BPPA anion and the formally neutral H3BPPA molecule. Hence, the anion in 1 is better formulated as [H2BPPA···H···H2BPPA]. In the H-bonded network of 2 the 4-phosphonato-biphenyl-4′-carboxylic acid is triply deprotonated, BPPA3−. The [Co(NH3)6]3+ cation is embedded between H-bond acceptor groups, –COO and –PO3 and H2O molecules. The incorporation of sixteen H2O molecules per unit cell makes 2 an analogue of the well-studied guanidinium sulfonate frameworks. Full article
(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)
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