scholarly journals Water Structures and Packing Efficiency in Methylene Blue Cyanometallate Salts

Crystals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 558
Author(s):  
Stefano Canossa ◽  
Claudia Graiff ◽  
Domenico Crocco ◽  
Giovanni Predieri
Keyword(s):  
Crystal Structure ◽  
Methylene Blue ◽  
Crystal Engineering ◽  
Structure Prediction ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Leading Role ◽  
Solvent Molecules ◽  
Packing Efficiency

Crystal structure prediction is the holy grail of crystal engineering and is key to its ambition of driving the formation of solids based on the selection of their molecular constituents. However, this noble quest is hampered by the limited predictability of the incorporation of solvent molecules, first and foremost the ubiquitous water. In this context, we herein report the structure of four methylene blue cyanometallate phases, where anions with various shapes and charges influence the packing motif and lead to the formation of differently hydrated structures. Importantly, water molecules are observed to play various roles as isolated fillings, dimers, or an infinite network with up to 13 water molecules per repeating unit. Each crystal structure has been determined by single-crystal X-ray diffraction and evaluated with the aid of Hirshfeld surface analysis, focussing on the role of water molecules and the hierarchy of different classes of interactions in the overall supramolecular landscape of the crystals. Finally, the collected pieces of evidence are matched together to highlight the leading role of MB stacking and to derive an explanation for the observed hydration diversity based on the structural role of water molecules in the crystal architecture.

The Role of Sorptive Layers in the Formation And Change of the Crystal Structure of Montmorillonite

Clay Minerals ◽  
1970 ◽  
Vol 8 (3) ◽  
pp. 255-266 ◽  
Author(s):  
M. V. Eirish ◽  
L. I. Tret'Yakova
Keyword(s):  
Crystal Structure ◽  
Diffraction Analysis ◽  
Chemical Structure ◽  
Interaction Mechanism ◽  
Sorption Process ◽  
Water Molecules ◽  
Crystal Chemical ◽  
X Ray Diffraction ◽  
X Ray

AbstractThe influence of sorbed cations and hydration on the a and b dimensions of montmorillonite, has been established by the selected area diffraction technique (S.A.D.) and by X-ray diffraction analysis. Concepts on the bonds and interaction mechanism of aluminosilicate layers with sorbed cations and water molecules (which form hydrate-ionic layers) are discussed. These concepts also indicate the basic stages of the sorption process and the formation of the montmorillonite structure. Assuming that aluminosilicate and hydrate-ionic layers represent a single crystal-chemical structure, the change of configuration of the aluminosilicate layers and dimensions of the montmorillonite lattice are explained.

scholarly journals Contact map based crystal structure prediction using global optimization

CrystEngComm ◽  
2021 ◽  
Author(s):  
Jianjun Hu ◽  
Wenhui Yang ◽  
Rongzhi Dong ◽  
Yuxin Li ◽  
Xiang Li ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Global Optimization ◽  
Crystal Engineering ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
New Materials ◽  
Contact Map

Crystal structure prediction is now playing an increasingly important role in the discovery of new materials or crystal engineering.

Effects of dietary alteration of bicarbonate and magnesium on rat bone

1986 ◽  
Vol 250 (2) ◽  
pp. F302-F307 ◽  
Author(s):  
J. M. Burnell ◽  
C. Liu ◽  
A. G. Miller ◽  
E. Teubner
Keyword(s):  
Crystal Structure ◽  
Bone Formation ◽  
X Ray Diffraction ◽  
X Ray ◽  
Growing Rats ◽  
Final Composition ◽  
Rat Bone

To study the effects of bicarbonate and magnesium on bone, mild acidosis and/or hypermagnesemia were produced in growing rats by feeding ammonium chloride and/or magnesium sulfate. Bone composition, quantitative histomorphometry, and mineral x-ray diffraction (XRD) characteristics were measured after 6 wk of treatment. The results demonstrated that both acidosis (decreased HCO3) and hypermagnesemia inhibited periosteal bone formation, and, when combined, results were summative; and the previously observed in vitro role of HCO3- and Mg2+ as inhibitors of crystal growth were confirmed in vivo. XRD measurements demonstrated that decreased plasma HCO3 resulted in larger crystals and increased Mg resulted in smaller crystals. However, the combined XRD effects of acidosis and hypermagnesemia resembled acidosis alone. It is postulated that the final composition and crystal structure of bone are strongly influenced by HCO3- and Mg2+, and the effects are mediated by the combined influence on both osteoblastic bone formation and the growth of hydroxyapatite.

scholarly journals Synthesis and Complexation Properties of 2-Hydroxy-5-methoxyphenylphosphonic Acid (H3L1). Crystal Structure of the [Cu(H2L1)2(Н2О)2] Complex

2021 ◽  
Vol 91 (11) ◽  
pp. 2176-2186
Author(s):  
G. S. Tsebrikova ◽  
Yu. I. Rogacheva ◽  
I. S. Ivanova ◽  
A. B. Ilyukhin ◽  
V. P. Soloviev ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Methoxy Group ◽  
Protonation Constants ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
The Stability ◽  
Intramolecular Hydrogen ◽  
Oxygen Atoms

Abstract 2-Hydroxy-5-methoxyphenylphosphonic acid (H3L1) and the complex [Cu(H2L1)2(H2O)2] were synthesized and characterized by IR spectroscopy, thermogravimetry, and X-ray diffraction analysis. The polyhedron of the copper atom is an axially elongated square bipyramid with oxygen atoms of phenolic and of monodeprotonated phosphonic groups at the base and oxygen atoms of water molecules at the vertices. The protonation constants of the H3L1 acid and the stability constants of its Cu2+ complexes in water were determined by potentiometric titration. The protonation constants of the acid in water are significantly influenced by the intramolecular hydrogen bond and the methoxy group. The H3L1 acid forms complexes CuL‒ and CuL24‒ with Cu2+ in water.

Crystal Structure of Calcium Picrate Pentahydrate: A New Eight-Coordinate Stereochemistry for [M(bidentate)2(unidentate)4]

1979 ◽  
Vol 32 (2) ◽  
pp. 301 ◽  
Author(s):  
V Diakiw ◽  
TW Hambley ◽  
DL Kepert ◽  
CL Raston ◽  
AH White
Keyword(s):  
Crystal Structure ◽  
Water Molecule ◽  
Single Crystal ◽  
Title Compound ◽  
Lattice Site ◽  
The Other ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Triangular Face ◽  
X Ray

The crystal structure of the title compound, Ca(C6H2N307)2,5H2O, has been determined by single-crystal X-ray diffraction at 295(1) K and refined by least squares to a residual of 0.049 for 1513 'observed' reflections. Crystals are orthorhombic, Pmab, a 24.169(6), b l0.292(7), c 8.554(2) �, Z 4. The stereochemistry about the calcium has not been observed previously for the system [M(bidentate)2- (unidentate)4]; in the present structure, the calcium is coordinated by a pair of bidentate picrate ligands and the four water molecules in an array in which three of the water molecules occupy a triangular face of a square antiprism, the overall array having m symmetry. The remaining water molecule occupies a lattice site with no close interaction with the other species.

Synthesis, crystal structure, and vibrational spectra of the complex maleic acid•2H2O•18-crown-6

1990 ◽  
Vol 68 (12) ◽  
pp. 2183-2189 ◽  
Author(s):  
Pierre Audet ◽  
Rodrigue Savoie ◽  
Michel Simard
Keyword(s):  
Crystal Structure ◽  
Water Molecule ◽  
Maleic Acid ◽  
Water Molecules ◽  
Infrared And Raman Spectra ◽  
X Ray Diffraction ◽  
Monoclinic System ◽  
X Ray ◽  
O 18 ◽  
Stoichiometric Complex

A stoichiometric complex of formula maleic acid•2H2O•18-crown-6 has been obtained from maleic acid and the macrocyclic polyether 18-crown-6. Crystals of this complex have been shown by X-ray diffraction crystallography to belong to the Cc space group of the monoclinic system. The acid molecules in the adduct are linked to each other through a water molecule, giving infinite [-acid-H2O-]n chains. They are also linked to the crown ether via water molecules. The infrared and Raman spectra of the complex are presented and compared to those of crystalline maleic acid. Keywords: maleic acid/18-crown-6, structure, X-ray, spectra.

The crystal-structure determination and redefinition of eztlite, Pb22+ Fe33+(Te4+O3)3(SO4)O2Cl

2018 ◽  
Vol 82 (6) ◽  
pp. 1355-1367 ◽  
Author(s):  
Owen P. Missen ◽  
Stuart J. Mills ◽  
John Spratt ◽  
Mark D. Welch ◽  
William D. Birch ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Mixed Valence ◽  
Lone Pair ◽  
Water Molecules ◽  
Monoclinic Space Group ◽  
Charge Balance ◽  
X Ray Diffraction ◽  
International Mineralogical Association ◽  
Bond Valence Analysis

ABSTRACTThe crystal structure of eztlite has been determined using single-crystal synchrotron X-ray diffraction and supported using electron microprobe analysis and powder diffraction. Eztlite, a secondary tellurium mineral from the Moctezuma mine, Mexico, is monoclinic, space group Cm, with a = 11.466(2) Å, b = 19.775(4) Å, c = 10.497(2) Å, β = 102.62(3)° and V = 2322.6(9) Å3. The chemical formula of eztlite has been revised to ${\rm Pb}_{\rm 2}^{2 +} {\rm Fe}_3^{3 +} $(Te4+O3)3(SO4)O2Cl from that stated previously as ${\rm Fe}_6^{3 +} {\rm Pb}_{\rm 2}^{2 +} $(Te4+O3)3(Te6+O6)(OH)10·nH2O. This change has been accepted by the Commission on New Minerals, Nomenclature and Classification of the International Mineralogical Association, Proposal 18-A. Eztlite was reported originally to be a mixed-valence Te oxysalt; however the crystal structure, bond-valence analysis and charge balance considerations clearly show that all Te is tetravalent. Eztlite contains a unique combination of elements and is only the second Te oxysalt to contain both sulfate and chloride. The crystal structure of eztlite contains mitridatite-like layers, with a repeating triangular nonameric [${\rm Fe}_9^{3 +} $O36]45– arrangement formed by nine edge-sharing Fe3+O6 octahedra, decorated by four trigonal pyramidal Te4+O3 groups, compared to PO4 or AsO4 tetrahedra in mitridatite-type minerals. In eztlite, all four tellurite groups associated with one nonamer are orientated with the lone pair of the Te atoms pointing in the same direction, whereas in mitridatite the central tetrahedron is orientated in the opposite direction to the others. In mitridatite-type structures, interlayer connections are formed exclusively via Ca2+ and water molecules, whereas the eztlite interlayer contains Pb2+, sulfate tetrahedra and Cl–. Interlayer connectivity in eztlite is achieved primarily by connections via the long bonds of Pbφ8 and Pbφ9 groups to sulfate tetrahedra and to Cl–. Secondary connectivity is via Te–O and Te–Cl bonds.

scholarly journals The three-dimensional structure of a class-Pi glutathione S-transferase complexed with glutathione: the active-site hydration provides insights into the reaction mechanism

1998 ◽  
Vol 333 (3) ◽  
pp. 811-816 ◽  
Author(s):  
Antonio PÁRRAGA ◽  
Isabel GARCÍA-SÁEZ ◽  
Sinead B. WALSH ◽  
Timothy J. MANTLE ◽  
Miquel COLL
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Glutathione S Transferase ◽  
X Ray ◽  
The Right

The structure of mouse liver glutathione S-transferase P1-1 complexed with its substrate glutathione (GSH) has been determined by X-ray diffraction analysis. No conformational changes in the glutathione moiety or in the protein, other than small adjustments of some side chains, are observed when compared with glutathione adduct complexes. Our structure confirms that the role of Tyr-7 is to stabilize the thiolate by hydrogen bonding and to position it in the right orientation. A comparison of the enzyme–GSH structure reported here with previously described structures reveals rearrangements in a well-defined network of water molecules in the active site. One of these water molecules (W0), identified in the unliganded enzyme (carboxymethylated at Cys-47), is displaced by the binding of GSH, and a further water molecule (W4) is displaced following the binding of the electrophilic substrate and the formation of the glutathione conjugate. The possibility that one of these water molecules participates in the proton abstraction from the glutathione thiol is discussed.

scholarly journals Towards computer-guided tuning of the crystal packing of porous organic cages

2014 ◽  
Vol 70 (a1) ◽  
pp. C667-C667
Author(s):  
Angeles Pulido ◽  
Ming Liu ◽  
Paul Reiss ◽  
Anna Slater ◽  
Sam Chong ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Engineering ◽  
Molecular Sieves ◽  
Structure Prediction ◽  
Crystal Packing ◽  
Aromatic Aldehydes ◽  
Lattice Energy ◽  
Building Blocks ◽  
Molecular Assembly ◽  
Computational Techniques

Among microporous materials, there has been an increasing recent interest in porous organic cage (POC) crystals, which can display permanent intrinsic (molecular) and extrinsic (crystal network) porosity. These materials can be used as molecular sieves for gas separation and potential applications as enzyme mimics have been suggested since they exhibit structural response toward guest molecules[1]. Small structural modifications of the initial building blocks of the porous organic molecules can lead to quite different molecular assembly[1]. Moreover, the crystal packing of POCs is based on weak molecular interactions and is less predictable that other porous materials such as MOFs or zeolites.[2] In this contribution, we show that computational techniques -molecular conformational searches and crystal structure prediction- can be successfully used to understand POC crystal packing preferences. Computational results will be presented for a series of closely related tetrahedral imine- and amine-linked porous molecules, formed by [4+6] condensation of aromatic aldehydes and cyclohexyl linked diamines. While the basic cage is known to have one strongly preferred crystal structure, the presence of small alkyl groups on the POC modifies its crystal packing preferences, leading to extensive polymorphism. Calculations were able to successfully identify these trends as well as to predict the structures obtained experimentally, demonstrating the potential for computational pre-screening in the design of POCs within targeted crystal structures. Moreover, the need of accurate molecular (ab initio calculations) and crystal (based on atom-atom potential lattice energy minimization) modelling for computer-guided crystal engineering will be discussed.

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