High-temperature induced dehydration, phase transition and exsolution in amicite: A single-crystal X-ray study

Temperature dependent single-crystal X-ray data were collected on amicite K4Na4(Al8Si8O32)·11H2O from Kola Peninsula (Russia) in steps of 25 °C from room temperature to 175 °C and of 50 °C up to 425 °C. At room temperature amicite has space group I2 with a = 10.2112(1), b = 10.4154(1), c = 9.8802(1) Å, β = 88.458(1)°, V = 1050.416(18) Å3. Its crystal structure is based on a Si–Al ordered tetrahedral framework of the GIS type with two systems of eight-membered channels running along the a and c axes. Extraframework K and Na cations are ordered at two fully occupied sites. Above 75 °C amicite was found to partly dehydrate into two separate but coherently intergrown phases, both of space group I2/a, one K-rich ∼K8(Al8Si8O32) ·4H2O (at 75 °C: a = 10.038(2), b = 9.6805(19), c = 9.843(2) Å, β = 89.93(3)°, V = 956.5(3) Å3) and the other Na-rich ∼Na8(Al8Si8O32)·2H2O (at 75 °C: a = 9.759(2), b = 8.9078(18), c = 9.5270(19) Å, β = 89.98(3)°, V = 828.2(3) Å3). Upon further heating above 75 °C the Na- and K-phases lost remaining H2O with only minor influence on the framework structure and became anhydrous at 175 °C and 375 °C, respectively. The two anhydrous phases persisted up to 425 °C. Backscattered electron images of a heated crystal displayed lamellar intergrowth of the K- and Na-rich phases. Exposed to ambient humid conditions K- and Na-rich phases rehydrated and conjoined to the original one phase I2 structure.

In situ dehydration behavior of veszelyite (Cu,Zn)2Zn(PO4)(OH)3·2H2O: A single-crystal X-ray study

The rare mixed copper-zinc phosphate mineral veszelyite (Cu,Zn)2Zn(PO4)(OH)3·2H2O space group P21/c, a = 7.5096(2), b = 10.2281(2), c = 9.8258(2) Å, β = 103.3040(10)°, V = 734.45(3) Å3 was investigated by in situ temperature-dependent single-crystal X-ray structure refinements. The atomic arrangement of veszelyite consists of an alternation of octahedral and tetrahedral sheets. The Jahn-Teller distorted CuO6 octahedra form sheets with eight-membered rings. The tetrahedral sheet composed of PO4 and ZnO3(OH) tetrahedra shows strong topological similarities to that of cavansite, gismondine, and kipushite.Diffraction data of a sample from Zdravo Vrelo, near Kreševo (Bosnia and Herzegovina) have been measured in steps of 25 up to 225 °C. Hydrogen positions and the hydrogen-bond system were determined experimentally from the structure refinements of data collected up to 125 °C. At 200 °C, the hydrogen-bonding scheme was inferred from bond-valence calculations and donor-acceptor distances. The hydrogen-bond system connects the tetrahedral sheet to the octahedral sheet and also braces the Cu sheet.At 150 °C, the H2O molecule at H2O2 was released and the Cu coordination (Cu1 and Cu2) decreased from originally six- to fivefold. Cu1 has a square planar coordination by four OH groups and an elongate distance to O3, whereas Cu2 has the Jahn-Teller characteristic elongate bond to H2O1. The unit-cell volume decreased 7% from originally 734.45(3) to 686.4(4) Å3 leading to a formula with 1 H2O pfu. The new phase observed above 150 °C is characterized by an increase of the c axis and a shortening of the b axis. The bending of T-O-T angles causes an increasing elliptical shape of the eight-membered rings in the tetrahedral and octahedral sheets. Moreover a rearrangement of the hydrogen-bond system was observed.At 225 °C, the structure degrades to an X-ray amorphous residual due to release of the last H2O molecule at H2O1. The stronger Jahn-Teller distortion of Cu1 relative to Cu2 suggests that Cu1 is fully occupied by Cu, whereas Cu2 bears significant Zn. H2O1 is the fifth ligand of Cu2. Zn at Cu2 is not favorable to adopt planar fourfold coordination. Thus, if the last water molecule is expelled the structure is destabilized.This study contributes to understanding the dehydration mechanism and thermal stability of supergene minerals characterized by Jahn-Teller distorted octahedra with mixed Cu, Zn occupancy.

In situ dehydration behavior of zeolite-like cavansite: A single-crystal X-ray study

To track dehydration behavior of cavansite, Ca(VO)(Si4O10)·4H2O space group Pnma, a = 9.6329(2), b = 13.6606(2), c = 9.7949(2) Å, V = 1288.92(4) Å3 single-crystal X-ray diffraction data on a crystal from Wagholi quarry, Poona district (India) were collected up to 400 °C in steps of 25 °C up to 250 °C and in steps of 50 °C between 250 and 400 °C. The structure of cavansite is characterized by layers of silicate tetrahedra connected by V4+O5 square pyramids. This way a porous framework structure is formed with Ca and H2O as extraframework occupants. At room temperature, the hydrogen bond system was analyzed. Ca is eightfold coordinated by four bonds to O of the framework structure and four bonds to H2O molecules. H2O linked to Ca is hydrogen bonded to the framework and also to adjacent H2O molecules. The dehydration in cavansite proceeds in four steps.At 75 °C, H2O at O9 was completely expelled leading to 3 H2O pfu with only minor impact on framework distortion and contraction V = 1282.73(3) Å3. The Ca coordination declined from originally eightfold to sevenfold and H2O at O7 displayed positional disorder.At 175 °C, the split O7 sites approached the former O9 position. In addition, the sum of the three split positions O7, O7a, and O7b decreased to 50% occupancy yielding 2 H2O pfu accompanied by a strong decrease in volume V = 1206.89(8) Å3. The Ca coordination was further reduced from sevenfold to sixfold.At 350 °C, H2O at O8 was released leading to a formula with 1 H2O pfu causing additional structural contraction (V = 1156(11) Å3). At this temperature, Ca adopted fivefold coordination and O7 rearranged to disordered positions closer to the original O9 H2O site.At 400 °C, cavansite lost crystallinity but the VO2+ characteristic blue color was preserved. Stepwise removal of water is discussed on the basis of literature data reporting differential thermal analyses, differential thermo-gravimetry experiments and temperature dependent IR spectra in the range of OH stretching vibrations.

A Pt(II) complex with both a phenanthroline and a tetrathiafulvalene-extended dithiolate ligand: Synthesis, crystal structure, electrochemical and spectroscopic properties

The reaction of 4,5-bis(2'-cyanoethylsulfanyl)-4',5'-dipropylthiotetrathiafulvalene with Pt(phen)Cl-2 (phen = 1,10-phenanthroline) with CsOH as base in CH3OH-THE affords the target complex I in 44% yield. This complex crystallizes in the monoclinic space group P2(1)/c, M = 790.01, a = 12.1732(12), b = 15.851(2), c = 14.5371(16) angstrom, beta = 107.693(12)degrees, V = 2672.4(5) angstrom(3) and Z = 4. It undergoes two reversible single-electron oxidation and two irreversible reduction processes. An intense electronic absorption band at 15200 cm(-1) (658 nm) in CH2Cl2 is assigned to the intramolecular mixed metal/ligand-to-ligand charge transfer (LLCT) from a tetrathiafulvalene-extended dithiolate-based HOMO to a phenanthroline-based LUMO. This band shifts hypsochromically with increasing solvent polarity. Systematic changes in the optical spectra upon oxidation allow precise tuning of the oxidation states of 1 and reversible control over its optical properties. Irradiation of 1 at 15625 cm(-1) (640 nm) in glassy solution below 150K results in emission from the (LLCT)-L-3 excited state. GRAPHICS (C) 2013 Elsevier Ltd. All rights reserved.

Crystal structure of the Anabaena sensory rhodopsin transducer.

We present crystal structures of the Anabaena sensory rhodopsin transducer (ASRT), a soluble cytoplasmic protein that interacts with the first structurally characterized eubacterial retinylidene photoreceptor Anabaena sensory rhodopsin (ASR). Four crystal structures of ASRT from three different spacegroups were obtained, in all of which ASRT is present as a planar (C4) tetramer, consistent with our characterization of ASRT as a tetramer in solution. The ASRT tetramer is tightly packed, with large interfaces where the well-structured beta-sandwich portion of the monomers provides the bulk of the tetramer-forming interactions, and forms a flat, stable surface on one side of the tetramer (the beta-face). Only one of our four different ASRT crystals reveals a C-terminal alpha-helix in the otherwise all-beta protein, together with a large loop from each monomer on the opposite face of the tetramer (the alpha-face), which is flexible and largely disordered in the other three crystal forms. Gel-filtration chromatography demonstrated that ASRT forms stable tetramers in solution and isothermal microcalorimetry showed that the ASRT tetramer binds to ASR with a stoichiometry of one ASRT tetramer per one ASR photoreceptor with a K(d) of 8 microM in the highest affinity measurements. Possible mechanisms for the interaction of this transducer tetramer with the ASR photoreceptor via its flexible alpha-face to mediate transduction of the light signal are discussed.

A reverse crystal Engineering approach

The enormous impact of crystal engineering in modern solid state chemistry takes advantage from the connection between a typical basic science field and the word engineering. Regrettably, the engineering aspect of organic or metal organic crystalline materials are limited, so far, to descriptive structural features, sometime entangled with topological aspects, but only rarely with true material design. This should include not only the fabrication and structural description at micro- and nano-scopic level of the solids, but also a proper reverse engineering, a fundamental discipline for engineers. Translated into scientific language, the reverse crystal engineering refers to a dedicated and accurate analysis of how the building blocks contribute to generate a given material property. This would enable a more appropriate design of new crystalline material. We propose here the application of reverse crystal engineering to optical properties of organic and metal organic framework structures, applying the distributed atomic polarizability approach that we have extensively investigated in the past few years[1,2].

Calculation of crystal optical properties from molecular electron density

We have recently developed a method to obtain distributed atomic polarizabilities adopting a partitioning of the molecular electron density (for example, the Quantum Theory of Atoms in Molecules, [1]), calculated with or without an applied electric field. The procedure [2] allows to obtained atomic polarizability tensors, which are perfectly exportable, because quite representative of an atom in a given functional group. Among the many applications of this idea, the calculation of crystal susceptibility is easily available, either from a rough estimation (the polarizability of the isolated molecule is used) or from a more precise estimation (the polarizability of a molecule embedded in a cluster representing the first coordination sphere is used). Lorentz factor is applied to include the long range effect of packing, which is enhancing the molecular polarizability. Simple properties like linear refractive index or the gyration tensor can be calculated at relatively low costs and with good precision. This approach is particularly useful within the field of crystal engineering of organic/organometallic materials, because it would allow a relatively easy prediction of a property as a function of the packing, thus allowing "reverse crystal engineering". Examples of some amino acid crystals and salts of amino acids [3] will be illustrated, together with other crystallographic or non-crystallographic applications. For example, the induction and dispersion energies of intermolecular interactions could be calculated with superior precision (allowing anisotropic van der Waals interactions). This could allow revision of some commonly misunderstood intermolecular interactions, like the halogen bonding (see for example the recent remarks by Stone or Gilli [4]). Moreover, the chemical reactivity of coordination complexes could be reinvestigated, by coupling the conventional analysis of the electrostatic potential (useful only in the circumstances of hard nucleophilic/electrophilic interaction) with the distributed atomic polarizability. The enhanced reactivity of coordinated organic ligands would be better appreciated. [1] R. F. W. Bader, Atoms in Molecules: A Quantum Theory. Oxford Univ. Press, 1990. [2] A. Krawczuk-Pantula, D. Pérez, K. Stadnicka, P. Macchi, Trans. Amer. Cryst. Ass. 2011, 1-25 [3] A. S. Chimpri1, M. Gryl, L. H.R. Dos Santos1, A. Krawczuk, P. Macchi Crystal Growth & Design, in the press. [4] a) A. J. Stone, J. Am. Chem. Soc. 2013, 135, 7005−7009; b) V. Bertolasi, P. Gilli, G. Gilli Crystal Growth & Design, 2013, 12, 4758-4770.

Crystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme A carboxylase.

Propionyl-coenzyme A carboxylase (PCC), a mitochondrial biotin-dependent enzyme, is essential for the catabolism of the amino acids Thr, Val, Ile and Met, cholesterol and fatty acids with an odd number of carbon atoms. Deficiencies in PCC activity in humans are linked to the disease propionic acidaemia, an autosomal recessive disorder that can be fatal in infants. The holoenzyme of PCC is an alpha(6)beta(6) dodecamer, with a molecular mass of 750 kDa. The alpha-subunit contains the biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains, whereas the beta-subunit supplies the carboxyltransferase (CT) activity. Here we report the crystal structure at 3.2-A resolution of a bacterial PCC alpha(6)beta(6) holoenzyme as well as cryo-electron microscopy (cryo-EM) reconstruction at 15-A resolution demonstrating a similar structure for human PCC. The structure defines the overall architecture of PCC and reveals unexpectedly that the alpha-subunits are arranged as monomers in the holoenzyme, decorating a central beta(6) hexamer. A hitherto unrecognized domain in the alpha-subunit, formed by residues between the BC and BCCP domains, is crucial for interactions with the beta-subunit. We have named it the BT domain. The structure reveals for the first time the relative positions of the BC and CT active sites in the holoenzyme. They are separated by approximately 55 A, indicating that the entire BCCP domain must translocate during catalysis. The BCCP domain is located in the active site of the beta-subunit in the current structure, providing insight for its involvement in the CT reaction. The structural information establishes a molecular basis for understanding the large collection of disease-causing mutations in PCC and is relevant for the holoenzymes of other biotin-dependent carboxylases, including 3-methylcrotonyl-CoA carboxylase (MCC) and eukaryotic acetyl-CoA carboxylase (ACC).

Crystal structures of progressive Ca2+ binding states of the Ca2+ sensor Ca2+ binding domain 1 (CBD1) from the CALX Na+/Ca2+ exchanger reveal incremental conformational transitions.

Na(+)/Ca(2+) exchangers (NCX) constitute a major Ca(2+) export system that facilitates the re-establishment of cytosolic Ca(2+) levels in many tissues. Ca(2+) interactions at its Ca(2+) binding domains (CBD1 and CBD2) are essential for the allosteric regulation of Na(+)/Ca(2+) exchange activity. The structure of the Ca(2+)-bound form of CBD1, the primary Ca(2+) sensor from canine NCX1, but not the Ca(2+)-free form, has been reported, although the molecular mechanism of Ca(2+) regulation remains unclear. Here, we report crystal structures for three distinct Ca(2+) binding states of CBD1 from CALX, a Na(+)/Ca(2+) exchanger found in Drosophila sensory neurons. The fully Ca(2+)-bound CALX-CBD1 structure shows that four Ca(2+) atoms bind at identical Ca(2+) binding sites as those found in NCX1 and that the partial Ca(2+) occupancy and apoform structures exhibit progressive conformational transitions, indicating incremental regulation of CALX exchange by successive Ca(2+) binding at CBD1. The structures also predict that the primary Ca(2+) pair plays the main role in triggering functional conformational changes. Confirming this prediction, mutagenesis of Glu(455), which coordinates the primary Ca(2+) pair, produces dramatic reductions of the regulatory Ca(2+) affinity for exchange current, whereas mutagenesis of Glu(520), which coordinates the secondary Ca(2+) pair, has much smaller effects. Furthermore, our structures indicate that Ca(2+) binding only enhances the stability of the Ca(2+) binding site of CBD1 near the hinge region while the overall structure of CBD1 remains largely unaffected, implying that the Ca(2+) regulatory function of CBD1, and possibly that for the entire NCX family, is mediated through domain interactions between CBD1 and the adjacent CBD2 at this hinge.

The Crystal Chemistry of Holtite

Holtite, approximately (Al,Ta,square)Al(6)(BO(3))(Si,Sb(3+),As(3+))(Sigma 3)O(12)(O,OH,square)(Sigma 3), is a member of the dumortierite group that has been found in pegmatite, or alluvial deposits derived from pegmatite, at three localities: Greenbushes, Western Australia; Voron'i Tundry, Kola Peninsula, Russia; and Szklary, Lower Silesia, Poland. Holtite can contain >30 wt.% Sb(2)O(3), As(2)O(3), Ta(2)O(5), Nb(2)O(5), and TiO(2) (taken together), but none of these constituents is dominant at a crystallographic site, which raises the question whether this mineral is distinct from dumortierite. The crystal structures of four samples from the three localities have been refined to R(1) = 0.02-0.05. The results show dominantly: Al, Ta, and vacancies at the Al(1) position; Al and vacancies at the Al(2), (3) and (4) sites; Si and vacancies at the Si positions; and Sb, As and vacancies at the Sb sites for both Sb-poor (holtite I) and Sb-rich (holtite II) specimens. Although charge-balance calculations based on our single-crystal structure refinements suggest that essentially no water is present, Fourier transform infrared spectra confirm that some OH is present in the three samples that could be measured. By analogy with dumortierite, the largest peak at 3505-3490 cm(-1) is identified with OH at the O(2) and O(7) positions. The single-crystal X-ray refinements and FTIR results suggest the following general formula for holtite: Al(7-[5x+y+z]/3)(Ta,Nb)(x)square([2x+y+z]/3)BSi(3-y)(Sb,As)(y)O(18-y-z)(OH)(z), where x is the total number of pentavalent cations, y is the total amount of Sb + As, and z <= y is the total amount of OH. Comparison with the electron microprobe compositions suggests the following approximate general formulae Al(5.83)(Ta,Nb)(0.50)square(0.67)BSi(2.50)(Sb,As)(0.50)O(17.00)(OH)(0.50) and Al(5.92)(Ta,Nb)(0.25)square(0.83)BSi(2.00)(Sb,As)(1.00) O(16.00)(OH)(1.00) for holtite I and holtite II respectively. However, the crystal structure refinements do not indicate a fundamental difference in cation ordering that might serve as a criterion for recognizing the two holtites as distinct species, and anion compositions are also not sufficiently different. Moreover, available analyses suggest the possibility of a continuum in the Si/(Sb + As) ratio between holtite I and dumortierite, and at least a partial continuum between holtite I and holtite II. We recommend that use of the terms holtite I and holtite II be discontinued.