The role of OH and H2O in oxide and oxysalt minerals

Author(s):  
Frank C. Hawthorne

AbstractHydrogen plays an extremely important role in the structure and chemistry of the oxide and oxysalt minerals. The characteristics of this role can be profitably analyzed in a simple and intuitive fashion using bond-valence theory. For any crystal structure, theAs components of the structural unit, (OH)

2019 ◽  
Vol 57 (4) ◽  
pp. 519-528 ◽  
Author(s):  
Frank C. Hawthorne ◽  
Elena Sokolova ◽  
Atali A. Agakhanov ◽  
Leonid A. Pautov ◽  
Vladimir Yu. Karpenko

Abstract The crystal structure of polylithionite-1M from Darai-Pioz, (K0.97Na0.03Rb0.01)Σ1.01(Li2.04Al0.84 Ti4+0.09Fe3+0.03)Σ3.00(Si3.98Al0.02)O10[F1.68(OH)0.33]Σ2, a 5.1974(4), b 8.9753(6), c 10.0556(7) Å, β 100.454(1)°, V 461.30(6) Å3, space group C2, Z = 2, was refined to R1 = 1.99% using MoKα X-radiation. In the space group C2, there are three octahedrally coordinated M sites in the 1M mica structure: the M(1) site is occupied by Li+ and minor vacancy that is likely locally associated with Ti4+ at the M(2) site; the M(2) site is occupied dominantly by Al3+, with other minor divalent to tetravalent cations; the M(3) site is completely occupied by Li+. In the space group C2, the structure is completely ordered. Each non-bridging O2– ion is surrounded by an ordered arrangement of 2Li+ + Al3+ + Si4+ with an incident bond-valence sum of 1.95 vu (valence units). The F– ion is coordinated by Li+ + Li+ + Al3+ with an incident bond-valence sum of 0.84 vu (values around F– generally tend to be lower than ideal). Thus, the valence-sum rule is satisfied, both long range and short range. In the space group C2/m, there is long-range order but not short-range order. There are three different short-range arrangements, one of which has bond-valence deficiencies of 0.38 and 0.49 vu around the non-bridging O2– ion and the F– ion, destabilizing the structure relative to the more ordered arrangement of the C2 structure, which conforms more closely to the valence-sum rule. The drive to lower the symmetry in polylithionite-1M from C2/m to C2 comes from the short-range bond-valence requirements of the structure.


1998 ◽  
Vol 62 (2) ◽  
pp. 141-164 ◽  
Author(s):  
Frank C. Hawthorne

AbstractFor complex rocks in which the structure of minerals, rather than their chemical composition, changes with progressive evolution of the system, it makes sense to try and monitor such an evolving system through the progressive change in the crystal structures of the constituent phases. In effect, the paragenetic sequences of minerals in such complex environments should be related to the crystal structures of the constituent minerals. In order to consider variations in structure topology, we need to organize crystal structures into hierarchical schemes, using the hypothesis that structures may be hierarchically ordered according to the polymerization of the coordination polyhedra with higher bondstrengths. Structural units are organized according to the mode of polymerization: unconnected polyhedra, clusters, chains, sheets and frameworks.The bond-valence structure of (OH) and (H2O) shows that on one side, (OH) and H2O are strong Lewis bases; on the other side, they are weak Lewis acids. As a result, a very important role of both (OH) and (H2O) is to prevent polymerization of the structural unit in specific directions. Thus, the dimensionality of the structural unit is controlled primarily by the amount and role of hydrogen in the structure. The way in which we have formulated these ideas also allows development of a predictive framework within which specific aspects of the chemistry and structure of phosphates can be considered.This approach to mineral structure, applied via the idea of a structural unit, can play a major role in developing structural hierarchies in order to bring about some sort of order to the plethora of hydroxyhydrated-phosphate structures. Furthermore, by combining the idea of binary structural representation with bond-valence theory, we see the eventual possibility of predicting stoichiometry and structural characteristics of these minerals, particularly those in complex low-temperature hydrothermal environments


Author(s):  
А. Я. Штейфан ◽  
В. І. Сідей ◽  
І. І. Небола ◽  
І. П. Студеняк

Materials ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 1032
Author(s):  
Anirban Naskar ◽  
Rabi Khanal ◽  
Samrat Choudhury

The electronic structure of a series perovskites ABX3 (A = Cs; B = Ca, Sr, and Ba; X = F, Cl, Br, and I) in the presence and absence of antisite defect XB were systematically investigated based on density-functional-theory calculations. Both cubic and orthorhombic perovskites were considered. It was observed that for certain perovskite compositions and crystal structure, presence of antisite point defect leads to the formation of electronic defect state(s) within the band gap. We showed that both the type of electronic defect states and their individual energy level location within the bandgap can be predicted based on easily available intrinsic properties of the constituent elements, such as the bond-dissociation energy of the B–X and X–X bond, the X–X covalent bond length, and the atomic size of halide (X) as well as structural characteristic such as B–X–B bond angle. Overall, this work provides a science-based generic principle to design the electronic states within the band structure in Cs-based perovskites in presence of point defects such as antisite defect.


2019 ◽  
Vol 116 (22) ◽  
pp. 10763-10772 ◽  
Author(s):  
Bernd R. Gardill ◽  
Ricardo E. Rivera-Acevedo ◽  
Ching-Chieh Tung ◽  
Filip Van Petegem

Voltage-gated sodium (NaV) and calcium channels (CaV) form targets for calmodulin (CaM), which affects channel inactivation properties. A major interaction site for CaM resides in the C-terminal (CT) region, consisting of an IQ domain downstream of an EF-hand domain. We present a crystal structure of fully Ca2+-occupied CaM, bound to the CT of NaV1.5. The structure shows that the C-terminal lobe binds to a site ∼90° rotated relative to a previous site reported for an apoCaM complex with the NaV1.5 CT and for ternary complexes containing fibroblast growth factor homologous factors (FHF). We show that the binding of FHFs forces the EF-hand domain in a conformation that does not allow binding of the Ca2+-occupied C-lobe of CaM. These observations highlight the central role of the EF-hand domain in modulating the binding mode of CaM. The binding sites for Ca2+-free and Ca2+-occupied CaM contain targets for mutations linked to long-QT syndrome, a type of inherited arrhythmia. The related NaV1.4 channel has been shown to undergo Ca2+-dependent inactivation (CDI) akin to CaVs. We present a crystal structure of Ca2+/CaM bound to the NaV1.4 IQ domain, which shows a binding mode that would clash with the EF-hand domain. We postulate the relative reorientation of the EF-hand domain and the IQ domain as a possible conformational switch that underlies CDI.


Crystals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1013
Author(s):  
Stefanie Gärtner

Alkali metal thallides go back to the investigative works of Eduard Zintl about base metals in negative oxidation states. In 1932, he described the crystal structure of NaTl as the first representative for this class of compounds. Since then, a bunch of versatile crystal structures has been reported for thallium as electronegative element in intermetallic solid state compounds. For combinations of thallium with alkali metals as electropositive counterparts, a broad range of different unique structure types has been observed. Interestingly, various thallium substructures at the same or very similar valence electron concentration (VEC) are obtained. This in return emphasizes that the role of the alkali metals on structure formation goes far beyond ancillary filling atoms, which are present only due to charge balancing reasons. In this review, the alkali metals are in focus and the local surroundings of the latter are discussed in terms of their crystallographic sites in the corresponding crystal structures.


Polyhedron ◽  
2006 ◽  
Vol 25 (3) ◽  
pp. 747-752
Author(s):  
Ashok K.S. Chauhan ◽  
Arun Kumar ◽  
Shobhit Charan ◽  
Ramesh C. Srivastava ◽  
Ray J. Butcher

Biochemistry ◽  
2007 ◽  
Vol 46 (41) ◽  
pp. 11494-11503 ◽  
Author(s):  
Dong-Ju You ◽  
Hyongi Chon ◽  
Yuichi Koga ◽  
Kazufumi Takano ◽  
Shigenori Kanaya

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