Complex Weblike Hydrogen Bonding in Large “Drain Pipe” Channels of Wightmanite Revealed by New X-Ray and Spectroscopic Measurements

2021 ◽  
Author(s):  
Bernard W. Liebich ◽  
Anthony R. Kampf ◽  
Edwin Gnos ◽  
Cédric Schnyder
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Molecular Hydrogen ◽  
Structure Refinement ◽  
Broad Band ◽  
Bound Water ◽  
Hydroxyl Groups ◽  
Hydrogen Atoms ◽  
Drain Pipe ◽  
Oh Groups

ABSTRACT The wallpaper-type crystal structure of wightmanite, Mg5(BO3)O(OH)5·1–2H2O, has been reanalyzed in order to better understand the position and bonding of hydrogen atoms. Single-crystal structure refinement yielded the monoclinic I2/m unit cell a = 13.5165(18), b = 3.0981(3), c = 18.170(3)Å, ß = 91.441(6)°, and V = 760.65(17)Å3, Z = 4. Hydrogen atoms of OH groups pointing to the inside of the elliptical channels oriented parallel to [010] are arranged in the form of two overlying, a–c parallel planar pentagons. The two pentagons point in opposite directions. Hydrogen-bond analysis shows that the hydroxyl groups are linked by complex polyfurcated, intra-molecular hydrogen bonds forming a web-like network coating the walls of the channels. The longest distance between hydrogens (7.226 Å) is observed in the pentagonal planes of the channel. The anisotropically refined oxygen atoms of the zeolitic water show their strongest vibration parallel to the b axis and in the direction of the largest diameter of the elliptical channel and similarly form a complex inter-molecular hydrogen-bond system to the hydroxyl groups coating the channel walls. This complex bonding is expressed in the Raman spectrum by a broad band between 3100 and 3300 cm–1 that is assigned to the OH / H2O stretching mode and one strong band at 3661 cm–1 attributable to an OH-stretching mode. Infrared spectra also show a pronounced broad band between 3200 and 3700 cm–1 attributed to H2O and OH-stretching modes. The weak bands around 1600 cm–1 observed in the Raman and IR spectra are probably due to relatively weakly bound water in the channels.

Crystal structure of atropine sulfate monohydrate, (C17H24NO3)2(SO4)·(H2O)

2019 ◽  
Vol 34 (4) ◽  
pp. 389-395 ◽  
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Water Molecule ◽  
Powder Diffraction ◽  
Density Functional ◽  
Atropine Sulfate ◽  
Strong Hydrogen Bond ◽  
Hydroxyl Groups ◽  
Hydrogen Atoms ◽  
Sulfate Anion

The crystal structure of atropine sulfate monohydrate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Atropine sulfate monohydrate crystallizes in space group P21/n (#14) with a = 19.2948(5), b = 6.9749(2), c = 26.9036(5) Å, β = 94.215(2)°, V = 3610.86(9) Å3, and Z = 4. Each of the two independent protonated nitrogen atoms participates in a strong hydrogen bond to the sulfate anion. Each of the two independent hydroxyl groups acts as a donor in a hydrogen bond to the sulfate anion, but only one of the water molecule hydrogen atoms acts as a hydrogen bond donor to the sulfate anion. The hydrogen bonds are all discrete but link the cations, anion, and water molecule along [101]. Although atropine and hyoscyamine (atropine is racemic hyoscyamine) crystal structures share some features, such as hydrogen bonding and phenyl–phenyl packing, the powder patterns show that the structures are very different. The powder pattern for atropine sulfate monohydrate has been submitted to ICDD for inclusion in the Powder Diffraction File™.

Cannonite [Bi2O(SO4)(OH)2] from Alfenza (Crodo, Italy): crystal structure and morphology

2013 ◽  
Vol 77 (8) ◽  
pp. 3067-3079 ◽  
Author(s):  
G. C. Capitani ◽  
T. Catelani ◽  
P. Gentile ◽  
A. Lucotti ◽  
M. Zema
Keyword(s):  
Crystal Structure ◽  
Cleavage Plane ◽  
Structure Refinement ◽  
Molecular Water ◽  
Hydrogen Atoms ◽  
Oh Groups ◽  
Cell Parameters ◽  
Difference Fourier ◽  
Raman And Ir Spectroscopy ◽  
The Ideal

AbstractCanonite from Alfenza grows as crowded, radiating, acicular aggregates covering bismuthinite crystals. Individual crystals have a lozenge-shaped habit on {010}, the presumed cleavage plane of cannonite. Crystal structure refinements in the P21/c space group of two single crystals led to the following cell parameters: a = 7.7196(5) Å, b = 13.8856(9), c = 5.6980(4), b = 109.174(1)º (R1 = 0.0424); and a = 7.7100(8), b = 13.8717(14), c = 5.6939(6), b = 109.155(2)º (R1 = 0.0438). Hydrogen atoms were also localized in the density-difference Fourier map and refined with soft restraints on the bond distances. Raman and IR spectroscopy confirm the presence of OH groups and the absence of molecular water, and deliver OH···O geometry wholly comparable with the structure refinement. Electron microprobe analyses revealed no significant levels of elements other than those expected in the ideal formula except fluorine which was present up to 0.14 a.p.f.u. The crystal structure can be described in terms of anion-centred OBi4 edge-sharing tetrahedra forming chains running parallel to z and strongly cemented along x by isolated SO4 tetrahedra. Each OBi4 tetrahedron is further connected along y by OH groups, making walls of composition Bi4O2(SO4)2(OH)4 parallel to (010). These walls are tied to each other along y by fewer Bi–O–S bridges and weaker OH···O bonds.

Proton spin–spin coupling constants and intramolecular hydrogen bonding in bromine derivatives of 1,3-dihydroxybenzene

1976 ◽  
Vol 54 (14) ◽  
pp. 2228-2230 ◽  
Author(s):  
Ted Schaefer ◽  
J. Brian Rowbotham
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Proton Spin ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Hydroxyl Groups ◽  
Oh Groups ◽  
Spin Coupling Constants ◽  
Spin Spin Coupling ◽  
Derivatives Of

The conformational preferences in CCl4 solution at 32 °C of the hydroxyl groups in bromine derivatives of 1,3-dihydroxybenzene are deduced from the long-range spin–spin coupling constants between hydroxyl protons and ring protons over five bonds. Two hydroxyl groups hydrogen bond to the same bromine substituent in 2-bromo-1,3-dihydroxybenzene but prefer to hydrogen bond to different bromine substituents when available, as in 2,4-dibromo-1,3-dihydroxybenzene. When the OH groups can each choose between two ortho bromine atoms, as in 2,4,6-tribromoresorcinol, they apparently do so in a very nearly statistical manner except that they avoid hydrogen bonding to the common bromine atom.

Crystal structure of rivastigmine hydrogen tartrate Form I (Exelon®), C14H23N2O2(C4H5O6)

2016 ◽  
Vol 31 (2) ◽  
pp. 97-103 ◽  
Author(s):  
James A. Kaduk ◽  
Kai Zhong ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Carbonyl Oxygen ◽  
Strong Hydrogen Bond ◽  
Hydroxyl Groups ◽  
A Chain ◽  
Tartrate Anion

The crystal structure of rivastigmine hydrogen tartrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Rivastigmine hydrogen tartrate crystallizes in space group P21 (#4) with a = 17.538 34(5), b = 8.326 89(2), c = 7.261 11(2) Å, β = 98.7999(2)°, V = 1047.929(4) Å3, and Z = 2. The un-ionized end of the hydrogen tartrate anions forms a very strong hydrogen bond with the ionized end of another anion to form a chain. The ammonium group of the rivastigmine cation forms a strong discrete hydrogen bond with the carbonyl oxygen atom of the un-ionized end of the tartrate anion. These hydrogen bonds form a corrugated network in the bc-plane. Both hydroxyl groups of the tartrate anion form intramolecular O–H⋯O hydrogen bonds. Several C–H⋯O hydrogen bonds appear to contribute to the crystal energy. The powder pattern is included in the Powder Diffraction File™ as entry 00-064-1501.

Crystal structure of methylprednisolone acetate form II, C24H32O6

2018 ◽  
Vol 33 (1) ◽  
pp. 44-48
Author(s):  
Austin M. Wheatley ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Powder Diffraction ◽  
Density Functional ◽  
Hydroxyl Groups ◽  
Methylprednisolone Acetate ◽  
Powder Diffraction File ◽  
X Ray ◽  
Bond Network ◽  
Acetate Form

The crystal structure of methylprednisolone acetate form II, C24H32O6, has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Methylprednisolone acetate crystallizes in space group P212121 (#19) with a = 8.17608(2), b = 9.67944(3), c = 26.35176(6) Å, V = 2085.474(6) Å3, and Z = 4. Both hydroxyl groups act as hydrogen bond donors, resulting in a two-dimensional hydrogen bond network in the ab plane. C–H⋯O hydrogen bonds also contribute to the crystal energy. The powder pattern is included in the Powder Diffraction File™ as entry 00-065-1412.

Regioselective N-Acetylation of 4-(2-Hydroxyphenyl)-2-phenyl-2,3- dihydro-1H-1,5-benzodiazepine Using Protection by an Intramolecular Hydrogen Bond

2009 ◽  
Vol 64 (8) ◽  
pp. 969-972 ◽  
Author(s):  
Carlos A. Escobar ◽  
Jorge Orellana-Vera ◽  
Andrés Vega ◽  
Dieter Sicker ◽  
Joachim Sieler
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Acetic Anhydride ◽  
Ambient Temperature ◽  
Intramolecular Hydrogen Bond ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
Hydroxyl Groups ◽  
Acetyl Group ◽  
Intramolecular Hydrogen

Since the amino and the hydroxyl groups of 4-(2-hydroxyphenyl)-2-phenyl-2,3-dihydro-1H-1,5- benzodiazepine can both act as nucleophiles, the introduction of both an N-acetyl and an O-acetyl group is expected when the compound is allowed to react with an excess of an electrophile such as acetic anhydride. An intramolecular hydrogen bond between OH and N-5 of the benzodiazepine has been used to obtain differentiation between the two possible sites of acetylation. Thus, this feature offers a preparatively utilizable protecting effect for the OH group and allows for a regioselective N-acetylation at ambient temperature. Both mono- and diacetylated compounds were prepared and characterized by crystal structure analysis

1-(4-Chlorophenyl)-4-(2-furoyl)-3-(2-furyl)-1H-pyrazol-5-ol

2007 ◽  
Vol 63 (3) ◽  
pp. o1289-o1290 ◽  
Author(s):  
Jin-Zhou Li ◽  
Heng-Qiang Zhang ◽  
Hong-Xin Li ◽  
Pi-Zhi Che ◽  
Tian-Chi Wang
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Intermolecular Hydrogen Bond ◽  
Hydroxyl Groups ◽  
Intermolecular Hydrogen Bonds ◽  
Compound C ◽  
Graph Set

The crystal structure of the title compound, C18H11ClN2O4, contains intra- and intermolecular hydrogen bonds that link the ketone and hydroxyl groups. The intermolecular hydrogen bond results in the formation of a dimer with an R 2 2(12) graph-set motif.

Redetermination of rifampicin pentahydrate revealing a zwitterionic form of the antibiotic

2012 ◽  
Vol 68 (5) ◽  
pp. o209-o212 ◽  
Author(s):  
Barbara Wicher ◽  
Krystian Pyta ◽  
Piotr Przybylski ◽  
Ewa Tykarska ◽  
Maria Gdaniec
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Amide Group ◽  
Water Molecules ◽  
Acta Cryst ◽  
Oh Groups ◽  
Zwitterionic Form ◽  
The Family

Rifampicin belongs to the family of naphthalenic ansamycin antibiotics. The first crystal structure of rifampicin in the form of the pentahydrate was reported in 1975 [Gadret, Goursolle, Leger & Colleter (1975).Acta Cryst.B31, 1454–1462] with the rifampicin molecule assumed to be neutral. Redetermination of this crystal structure now shows that one of the phenol –OH groups is deprotonated, with the proton transferred to a piperazine N atom, confirming earlier spectroscopic results that indicated a zwitterionic form for the molecule, namely (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-21-acetyloxy-6,9,17,19-tetrahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-8-[(E)-N-(4-methylpiperazin-4-ium-1-yl)formimidoyl]-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienimino)naphtho[2,1-b]furan-5-olate pentahydrate, C43H58N4O12·5H2O. The molecular structure of this antibiotic is stabilized by a system of four intramolecular O—H...O and N—H...N hydrogen bonds. Four of the symmetry-independent water molecules are arrangedviahydrogen bonds into helical chains extending along [100], whereas the fifth water molecule forms only one hydrogen bond, to the amide group O atom. The rifampicin molecules interactviaO—H...O hydrogen bonds, generating chains along [001]. Rifampicin pentahydrate is isostructural with recently reported rifampicin trihydrate methanol disolvate.

From structure topology to chemical composition. XIV. Titanium silicates: refinement of the crystal structure and revision of the chemical formula of mosandrite, (Ca3REE)[(H2O)2Ca0.5□0.5]Ti(Si2O7)2(OH)2(H2O)2, a Group-I mineral from the Saga mine, Morje, Porsgrunn, Norway

2013 ◽  
Vol 77 (6) ◽  
pp. 2753-2771 ◽  
Author(s):  
E. Sokolova ◽  
F. C. Hawthorne
Keyword(s):  
Crystal Structure ◽  
Long Range ◽  
Structure Refinement ◽  
Alkali Cations ◽  
Oh Groups ◽  
Structure Topology ◽  
Titanium Silicates ◽  
Group I ◽  
Ideal Composition ◽  
Cation Sites

AbstractThe crystal structure of mosandrite, ideally (Ca3REE)[(H2O)2Ca0.5☐0.5]Ti(Si2O7)2(OH)2(H2O)2, from the Saga mine, Morje, Porsgrunn, Norway, has been refined as two components related by the TWIN matrix ( 0 0, 0 0, 1 0 1): a 7.4222(3), b 5.6178(2), c 18.7232(7) Å, β 101.4226(6)°, V = 765.23(9) Å3, space group P21/c, Dcalc. = 3.361 g.cm–3, R1 = 3.69% using 1347 observed (Fo > 4σF) reflections. The empirical formula of mosandrite (EMPA) was calculated on the basis of 4 Si a.p.f.u., with H2O determined from structure refinement: [(Ca2.89Ba0.01)Σ2.90(Ce0.39La0.18Nd0.14Sm0.02Gd0.03Y0.16Th0.03)Σ1.01Zr0.09]Σ4 [(H2O)2.00Ca0.32Na0.17Al0.10Mn0.04Fe2+0.02☐0.35]Σ3(Ti0.87Nb0.09Zr0.04)Σ1(Si2O7)2[(OH)1.54F0.46]Σ2[(H2O)1.50F0.50]Σ2, Z = 2. The crystal structure of mosandrite is a framework of TS (titanium silicate) blocks; each TS block consists of HOH sheets (H-heteropolyhedral, O-octahedral). In the TS block, there are five fully occupied cation sites, two [4]-coordinated Si sites with <Si–O> 1.623 Å , [7]-coordinated MH and AP sites occupied by Ca and REE in the ratio ∼3:1, and one [6]-coordinated Ti-dominant MO(1) site. There are two H2O-dominant H2O-alkali-cation sites. The partly occupied MO(2) site has composition [(H2O)0.5☐0.33Na0.17], ideally [(H2O)0.5☐0.5] p.f.u. The MO(3) site has ideal composition [(H2O)1.5Ca0.5] p.f.u. In the O sheet, the XOM and XOA anion sites have compositions [(OH)1.54F0.46] (XOM) and [(H2O)1.50F0.50] (XOA), ideally (OH)2 and (H2O)2 p.f.u. The MH and AP polyhedra and Si2O7 groups constitute the H sheet that is completely ordered. In the O sheet, MO(1) octahedra are long-range ordered whereas H2O and OH groups and alkali cations Na and Ca are long-range disordered. Two SRO (short-range ordered) arrangements have been proposed for the O sheet: (1) Na [MO(2)], Ca2 [MO(3)] and F4[XOM and XOA anion sites]; (2) 2 H2O [MO(2)] and MO(3)] and (OH)2 and (H2O)2 [XOM and XOA]. Linkage of H and O sheets occurs mainly via common vertices of MH polyhedra and Si2O7 groups and MO(1) octahedra. Two adjacent TS blocks are related by the glide plane cy. Mosandrite is an H2O- and OH-bearing Na- and Ca-depleted analogue of rinkite, ideally (Ca3REE)Na(NaCa) Ti(Si2O7)2(OF)F2. Mosandrite and rinkite are related by the following substitution at the MO(2,3) and XO(M,A) sites in the O sheet: M[(H2O)2 + ☐0.5] + X[(OH)–2 + (H2O)2] ↔ M[Na+2 + Ca2+0.5] + X[(OF)3– + (F2)2–].

scholarly journals Crystal structure of 6-azido-6-deoxy-1,2-O-isopropylidene-α-D-glucofuranose

2020 ◽  
Vol 76 (10) ◽  
pp. 1653-1656
Author(s):  
Adam Wood ◽  
Paul V. Bernhardt ◽  
Ian van Altena ◽  
Michela I. Simone
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Biological Activities ◽  
Membered Ring ◽  
Protecting Groups ◽  
Hydroxyl Groups ◽  
Synthetic Strategy ◽  
Compound C ◽  
Hydrogen Bonding Interactions ◽  
Cross Links

Short syntheses to high Fsp 3 index natural-product analogues such as iminosugars are of paramount importance in the investigation of their biological activities and reducing the use of protecting groups is an advantageous synthetic strategy. An isopropylidene group was employed towards the synthesis of seven-membered ring iminosugars and the title compound, C9H15N3O5, was crystallized as an intermediate, in which the THF ring is twisted and the dioxolane ring adopts an envelope conformation: the dihedral angle between the rings is 67.50 (13)°. In the crystal, the hydroxyl groups participate in O—H...(O,O) and O—H...N hydrogen-bonding interactions, which generate chains of molecules propagating parallel to the a-axis direction. There is a notable non-classical C—H...O hydrogen bond, which cross-links the [100] chains into (001) sheets.

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