Re-investigation of the crystal structure of whewellite [Ca(C2O4)·H2O] and the dehydration mechanism of caoxite [Ca(C2O4)·3H2O]

2005 ◽  
Vol 69 (1) ◽  
pp. 77-88 ◽  
Author(s):  
T. Echigo ◽  
M. Kimata ◽  
A. Kyono ◽  
M. Shimizu ◽  
T. Hatta
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Structure Refinement ◽  
Structural Features ◽  
Infrared Analysis ◽  
Water Molecules ◽  
Hydrogen Atoms ◽  
Direct Transformation ◽  
Dehydration Mechanism ◽  
The Difference

AbstractThe crystal structure of whewellite [Ca(C2O4)·H2O] and the dehydration mechanism of caoxite [Ca(C2O4)·3H2O] have been studied by means of differential thermal analysis, X-ray diffraction (powder and single-crystal) analysis and infrared analysis. The first and second analyses confirmed the direct transformation of caoxite into whewellite without an intermediate weddellite [Ca(C2O4)·2H2O] stage. Infrared spectra obtained from caoxite, weddellite and whewellite emphasize the similarity of the O–H-stretching band and O–C–O-stretching band in whewellite and caoxite and the unique bands of weddellite. The structure refinement at low temperature (123 K) reveals that all the hydrogen atoms of whewellite form hydrogen bonds and the two water molecules prop up the crystal structure by the hydrogen bonds that cause a strong anisotropy of the displacement parameter.Comparing the structural features of whewellite with those of weddellite and caoxite suggests that caoxite and whewellite have a sheet structure consisting of Ca2+ ions and oxalate ions although weddellite does not. It is additionally confirmed that the sheets of caoxite are corrugated by hydrogen bonds but whewellite has flat sheets. The corrugated sheets of caoxite would be flattened by dehydration so the direct transformation of caoxite into whewellite would not occur via weddellite. Essential for this transformation is the dehydration of interlayered water molecules in caoxite leading to the building of the crystal structure of whewellite on its intralayered water molecules. The difference in conformation of water molecules between those two crystal structures may explain the more common occurrence of whewellite than of caoxite in nature.

Crystal Structure of Adeninium Trichloromercurate(II),

1975 ◽  
Vol 53 (15) ◽  
pp. 2345-2350 ◽  
Author(s):  
Monique Authier-Martin ◽  
André L. Beauchamp
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Least Squares ◽  
Title Compound ◽  
Heavy Atom ◽  
Chloride Ions ◽  
Water Molecules ◽  
Hydrogen Atoms ◽  
Space Group ◽  
Heavy Atom Method

The title compound belongs to space group P21/c with a = 23.99(1), b = 4.245(2), c = 25.98(1) Å, β = 117.58(7)°, and Z = 8. The structure was solved by the heavy-atom method and refined by block-diagonal least squares on 2589 independent observed reflections. All non-hydrogen atoms were refined anisotropically and some of the hydrogen atoms were located but their parameters were not refined. The final values of R and Rw were 0.042 and 0.047, respectively.The two nonequivalent mercury atoms have very similar environments. Two short Hg—Cl bonds (2.34–2.38 Å) at ∼ 165° define a quasi-molecular HgCl2 unit. Overall octahedral coordination is completed with two chloride ions at 2.76–2.84 Å and two chlorine atoms at 3.19–3.26 Å on neighboring HgCl2 quasi-molecules. HgCl6 octahedra share edges to form twofold ribbons in the b direction. This pattern of octahedra is identical with the onereported for β-NH4HgCl3. The cations are pairs of N(1)-protonated adenine molecules linked by two N(10)—H(10)… N(7) hydrogen bonds and stacked in the b direction. Water molecules act as acceptors in moderately strong hydrogen bonds with acidic protons H(1) and H(9) of adeninium ions. Other generally weaker hydrogen bonds exist between the various parts of the structure.

scholarly journals Crystal structure of bis(piperazin-1-ium-κN 4)bis(thiosulfato-κS)zinc(II) dihydrate

2018 ◽  
Vol 74 (2) ◽  
pp. 176-179
Author(s):  
Avijit Kumar Paul
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Water Molecules ◽  
Tetrahedral Coordination ◽  
Metal Centre ◽  
Hydrogen Atoms

In the title compound, [Zn(C4H11N2)2(S2O3)2]·2H2O, two thiosulfate ions coordinate to the zinc(II) atom through the terminal S atoms. The tetrahedral coordination around the ZnII ion is completed by ligating to two N atoms of two piperazinium ions. The remaining two N atoms of the piperazinium ions are diprotonated and do not coordinate to the metal centre. In the crystal, however, they are involved in N—H...Owater and N—H...Osulfato hydrogen bonds. Together, a series of N—H...O and O—H...O hydrogen bonds, involving the O atoms of the thiosulfate ions and the water molecules as acceptors and the hydrogen atoms of the piperazinium ions and the water molecules as donors, form a three-dimensional supramolecuar structure. Within this framework there are a number of intra- and intermolecular C—H...O and C—H...S contacts present.

scholarly journals Crystal structure of pantoprazole sodium sesquihydrate Form I, C16H14F2N3O4SNa(H2O)1.5

2020 ◽  
Vol 35 (1) ◽  
pp. 53-60
Author(s):  
Diana Gonzalez ◽  
Joseph T. Golab ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Water Molecules ◽  
Hydrogen Atoms ◽  
Powder Diffraction File ◽  
Trigonal Bipyramidal ◽  
Pyridine Nitrogen ◽  
Coordination Spheres

The crystal structure of pantoprazole sodium sesquihydrate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Pantoprazole sodium sesquihydrate crystallizes in space group Pbca (#61) with a = 33.4862(6), b = 17.29311(10), c = 13.55953(10) Å, V = 7852.06(14) Å3, and Z = 16. The crystal structure is characterized by layers parallel to the bc-plane. One layer contains the Na coordination spheres. The two independent sodium ions are trigonal bipyramidal and octahedral. The NaO3N2 and NaO4N2 coordination spheres share an edge to form pairs. The sodium bond valence sums are 1.17 and 1.15. The difluoromethyl groups are probably disordered. Two water molecules act as hydrogen bond donors to pyridine nitrogen atoms and sulfoxide oxygen atoms. The third water molecule participates in bifurcated hydrogen bonds, but one of its hydrogen atoms does not participate in hydrogen bonds. The powder pattern is included in the Powder Diffraction File™ as entry 00-065-1424.

scholarly journals Tris(cis-2-hydroxycyclohexane-1,3,5-triaminium) hydrogen sulfate octachloride dihydrate

2012 ◽  
Vol 68 (6) ◽  
pp. o1899-o1900
Author(s):  
Christian Neis ◽  
Günter J. Merten ◽  
Kaspar Hegetschweiler
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Chloride Ions ◽  
Water Molecules ◽  
Hydrogen Sulfate ◽  
Sulfate Ion ◽  
Hydrogen Atoms ◽  
Threefold Axis ◽  
Sulfate Anion ◽  
Counter Ions

The 2-hydroxycyclohexane-1,3,5-triaminium (= H3 L 3+) cation of the title compound, 3C6H18N3O3+·8Cl−·HSO4 −·2H2O, exhibits a cyclohexane chair with three equatorial ammonium groups and one axial hydroxy group in an all-cis configuration. The hydrogen sulfate anion and two water molecules lie on or in proximity to a threefold axis and are disordered. The crystal structure features N—H...Cl and O—H...Cl hydrogen bonds. Three C 3-symmetric motifs can be identified in the structure: (i) Two chloride ions (on the C 3-axis) together with three H3 L 3+ cations constitute an [(H3 L)3Cl2]7+ cage. (ii) The lipophilic C6H6-sides of three H3 L 3+ cations, which are oriented directly towards the C 3-axis, generate a lipophilic void. The void is filled with the disordered water molecules and with the disordered part of the hydrogen sulfate ion. The hydrogen atoms of these disordered moieties were not located. (iii) Three H3 L 3+ cations together with one HSO4 − and three Cl− counter-ions form an [(HSO4)(H3 L)3Cl3]5+ cage. Looking along the C 3-axis, these three motifs are arranged in the order (cage 1)...(lipophilic void)...(cage 2). The crystal studied was found to be a racemic twin.

scholarly journals Low temperature crystal structure, experimental atomic charges and electrostatic potential of ammonium decavanadate hexahydrate (NH4)V10O28·6H2O

2007 ◽  
Vol 72 (6) ◽  
pp. 545-554 ◽  
Author(s):  
Goran Bogdanovic ◽  
Nada Bosnjakovic-Pavlovic ◽  
Bire Spasojevic-De ◽  
Eddine Ghermanic ◽  
Ubavka Mioc
Keyword(s):  
Crystal Structure ◽  
Low Temperature ◽  
Hydrogen Bonds ◽  
Electrostatic Potential ◽  
Water Molecules ◽  
Atomic Charges ◽  
Atomic Group ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Low Temperature Crystal Structure

The X-ray structure of ammonium decavanadate hexahydrate was redetermined at a low temperature (100 K) in order to locate the hydrogen sites and to study the hydrogen bonds. The hydrogen atoms were assigned to the appropriate atomic group, NH4 + cations, and water molecules, missing to the best of our knowledge in the literature. A kappa refinement was performed to estimate the experimental atomic charges. These charges were used to generale the electrostatic potential on the molecular surfaces of decavanadate polyanions isolated from the influence of the crystal lattice. Comparisons with previous theoretical (ab initio) calculations were made and are also discussed. .

Crystal structure of ammonium cis-Tetraamminedisulfitocobaltate(III) trihydrate (a redetermination)

1978 ◽  
Vol 31 (5) ◽  
pp. 999 ◽  
Author(s):  
CL Raston ◽  
AH White ◽  
JK Yandell
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Least Squares ◽  
Title Compound ◽  
Structural Data ◽  
Water Molecules ◽  
Hydrogen Atoms ◽  
Full Matrix ◽  
The Difference

The crystal structure of the title compound, NH4 [Co(NH3)4(SO3)2],3H2O, has been redetermined using diffractometer data at 295 K and refined by full-matrix least squares to a residual of 0.056 for 2068 'observed' reflections. Crystals are orthorhombic, P212121, a 10.978(4), b 17.552(7), c 6.828(3)Ǻ, Z 4. The redetermined structure provides accurate structural data for the cobalt environment; as well, it locates all hydrogen atoms and defines cations and water molecules un- ambiguously. Co-S are 2.224(2), 2.221(2) Ǻ. Co-N (trans to S) (1.993(6), 2.023(6) Ǻ) are longer than the mutually trans Co-N (1.970(7), 1.977(6) Ǻ); the difference in the former is a consequence of lattice hydrogen bonding.

Hydrogen Bonds in the Crystal Structure of Strontium Hydroxide Octahydrate Sr(OH)2 · 8H2O

2007 ◽  
Vol 62 (2) ◽  
pp. 215-219 ◽  
Author(s):  
Hans Reuter ◽  
Shouassi Kamaha ◽  
Otmane Zerzouf
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Water Molecules ◽  
Hydrogen Atoms ◽  
Coordination Polyhedra ◽  
Linear Chains ◽  
Weak Hydrogen Bonds ◽  
Strontium Hydroxide ◽  
First Time ◽  
Additional Hydrogen

Strontium hydroxide octahydrate Sr(OH)2 · 8 H2O crystallizes in the tetragonal space group P4/ncc with cell constants a = 9.017(1) and c = 11.603(1) Å . The crystal structure has been refined from 2656 diffractometer data up to 2ϑ = 60° to an R value of 0.0303. With the new diffraction data it was possible to localize the positions of all hydrogen atoms for the first time and to describe the hydrogen bonding scheme in detail. The Sr2+ ions are square antiprismatically coordinated by eight water molecules. These {Sr(H2O)8}2+ coordination polyhedra are linked with each other via hydrogen bonds in a way that linear columns parallel to the c axis result. The two hydroxyl anions of the asymmetric unit are linked by weak hydrogen bonds and are not coordinated to strontium atoms. Like the strontium atoms, they form linear chains parallel to the c axis. Both, {Sr(H2O)8}2+ columns and OH- chains, are interconnected through two types of additional hydrogen bonds.

Thomsenolite, NaCaAlF6•H2O: hydrogen bonding and comparison with pachnolite

1985 ◽  
Vol 63 (12) ◽  
pp. 3322-3327 ◽  
Author(s):  
D. Adhikesavalu ◽  
T. Stanley Cameron ◽  
Osvald Knop
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Detailed Comparison ◽  
Water Molecules ◽  
Two Dimensional ◽  
Hydrogen Atoms ◽  
Hydrogen Bonding Network ◽  
Bonding Scheme

The crystal structure of thomsenolite, NaCaAlF6•H2O, has been redetermined to establish the hydrogen-bonding scheme in this mineral. Both hydrogen atoms participate in branched [Formula: see text] bonds. The hydrogen bonds link the AlF6, octahedra to form infinite chains ||b, which in turn are cross-linked to form infinite double sheets {[AlF6] + Ca}—(H2O)—{[AlF6] + Ca}||(001). The Na atoms are located exclusively in layers ||(001) which separate the double sheets. A detailed comparison of thomsenolite with its dimorph, pachnolite, shows that the structure of pachnolite is obtained in essence by interchanging the positions of one half of the Na atoms and one half of the water molecules in thomsenolite. The two-dimensional, layerlike hydrogen-bonding network in thomsenolite is thereby changed to one of a three-dimensional character in pachnolite. Other features of the two structures, including the Al—F and [Formula: see text] distances, are compared and discussed in some detail.

scholarly journals Synthesis and absolute structure of (R)-2-(benzylselanyl)-1-phenylethanaminium hydrogen sulfate monohydrate: crystal structure and Hirshfeld surface analyses

2021 ◽  
Vol 77 (11) ◽  
Author(s):  
H. R. Rajegowda ◽  
P. A. Suchetan ◽  
R. J. Butcher ◽  
P. Raghavendra Kumar
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Solvent Molecule ◽  
Shape Index ◽  
Hirshfeld Surface ◽  
Water Molecules ◽  
Hydrogen Sulfate ◽  
Hydrogen Atoms ◽  
Amine Nitrogen Atom ◽  
Amine Nitrogen

A hydrogen sulfate salt, C15H18NSe+·HSO4 −·H2O or [BnSeCH2CH(Ph)NH3 +](HSO4 −), of a chiral selenated amine (R)-2-(benzylselanyl)-1-phenylethanamine (BnSeCH2CH(Ph)NH2) has been synthesized and characterized by elemental analysis,1H and 13C{1H} NMR, FT–IR analysis, and single-crystal X-ray diffraction studies. The title salt crystallizes in the monohydrate form in the non-centrosymmetric monoclinic P21 space group. The cation is somewhat W shaped with the dihedral angle between the two aromatic rings being 60.9 (4)°. The carbon atom attached to the amine nitrogen atom is chiral and in the R configuration, and, the –C—C– bond of the –CH2—CH– fragment has a staggered conformation. In the crystal structure, two HSO4 − anions and two water molecules form an R 4 4(12) tetrameric type of assembly comprised of alternating HSO4 − anions and water molecules via discrete D(2) O—H...O hydrogen bonds. This tetrameric assembly aggregates along the b-axis direction as an infinite one-dimensional tape. Adjacent tapes are interconnected via discrete D(2) N—H...O hydrogen bonds between the three amino hydrogen atoms of the cation sandwiched between the two tapes and the three HSO4 − anions of the nearest asymmetric units, resulting in a complex two-dimensional sheet along the ab plane. The pendant arrangement of the cations is stabilized by C—H...π interactions between adjacent cations running as chains down the [010] axis. Secondary Se...O [3.1474 (4) Å] interactions are also observed in the crystal structure. A Hirshfeld surface analysis, including d norm, shape-index and fingerprint plots of the cation, anion and solvent molecule, was carried out to confirm the presence of various interactions in the crystal structure.

scholarly journals Crystal structure of the sesquihydrate of dehydroepiandrosterone propan-2-ylidene hydrazone: Participation of the hydrazonyl nitrogen atoms as acceptors in the elaborate hydrogen bond scheme

2021 ◽  
Vol 12 (1) ◽  
pp. 81-85
Author(s):  
James Lewis Wardell ◽  
John Nicholson Low
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Room Temperature ◽  
Water Molecules ◽  
Torsional Angle ◽  
Orthorhombic Space Group ◽  
The Difference ◽  
Torsional Angles ◽  
Water Hydrogen

The crystal structure of the sesquihydrate of dehydroepiandrosterone propan-2-ylidene hydrazone, [(7)2·(H2O)3], isolated from a solution of dehydroepiandrosterone propan-2-ylidene hydrazone, (7), in moist ethanol at room temperature, has been determined from data collected at 100 K. The sesquihydrate recrystallizes in the orthorhombic space group, P212121 with Z = 8. The asymmetric unit of [(7)2·(H2O)3] consists of two independent molecules of the steroid, Mol A and Mol B, and three moles of water. The six membered saturated rings, A and C, in both molecules have ideal or near ideal chair shapes, the unsaturated rings, B, have the expected half-chair shapes, while the five-membered rings, D, have envelope shapes with flaps at C114 and C214 for Mol A and Mol B, respectively. Differences in the conformations of the two molecules reside essentially completely within the hydrazonyl fragments with significantly different torsional angles, C117-N120-N121-C122 (in Mol A) and C217-N220-N221-C222 (in Mol B), of 149.19(14) and -93.08(17)°, respectively. The difference in this torsional angle is reflected in the hydrogen bonds involving the nitrogen atoms in the hydrazonyl units: it is of interest that the hydrazonyl nitrogen atoms partake as acceptors in hydrogen bonding with water molecules. The only intermolecular interactions in these molecules are hydrogen bonds -all classical O-H-O and OH···N hydrogen bonds with just one exception, a C-H···O(water) hydrogen bond. Of interest, there are no direct steroid-steroid links: molecules are linked solely by hydrogen bonds involving the hydrate molecules. All three hydrate molecules take part in the indirect linking of the steroid molecules, but each has its own set of contacts.

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