Crystal structure of 1-propanethiol–Co2(dobdc) from laboratory X-ray powder diffraction data

2020 ◽  
Vol 35 (1) ◽  
pp. 3-6
Author(s):  
Jonathan B. Lefton ◽  
Kyle B. Pekar ◽  
Daniel Sethio ◽  
Elfi Kraka ◽  
Tomče Runčevski
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Density Functional ◽  
Weak Interactions ◽  
Geometry Optimization ◽  
Cobalt Metal ◽  
Guest Molecules ◽  
X Ray ◽  
Cell Parameters ◽  
Alkane Chain

Laboratory X-ray powder diffraction was used to solve and refine the crystal structures of appended guest molecules within the pores of metal–organic frameworks (MOFs). Herein, we report the crystal structure of 1-propanethiol adsorbed in the pores of Co2(dobdc) (dobdc4– = 2,5-dioxido-1,4-benzenedicarboxylate, MOF-74). Soaking the activated MOF in neat 1-propanethiol resulted in the formation of 1-propanethiol–Co2(dobdc). The thiol appendant MOF maintained the crystal symmetry, with a rhombohedral space group R-3 and unit-cell parameters a = 25.9597(9) Å, c = 6.8623(5) Å, and V = 4005.0(4) Å3. As expected, the thiol sulfur formed a bond with the open cobalt metal site. The alkane chain was directed toward the center of the pore, participating in numerous van der Waals weak interactions with neighboring molecules. For the final Rietveld refinement, soft restrains were applied using bond distances obtained by periodic density functional theory (DFT) geometry optimization.

scholarly journals Crystal structure determination of karibibite, an Fe3+ arsenite, using electron diffraction tomography

2017 ◽  
Vol 81 (5) ◽  
pp. 1191-1202 ◽  
Author(s):  
Fernando Colombo ◽  
Enrico Mugnaioli ◽  
Oriol Vallcorba ◽  
Alberto García ◽  
Alejandro R. Goñi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Electron Diffraction ◽  
Dft Calculations ◽  
Density Functional ◽  
Weak Interactions ◽  
Diffraction Tomography ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters

AbstractThe crystal structure of karibibite, Fe33+(As3+O2)4(As23+O5)(OH), from the Urucum mine (Minas Gerais, Brazil), was solved and refined from electron diffraction tomography data [R1 = 18.8% for F > 4σ(F)] and further confirmed by synchrotron X-ray diffraction and density functional theory (DFT) calculations. The mineral is orthorhombic, space group Pnma and unit-cell parameters (synchrotron X-ray diffraction) are a = 7.2558(3), b = 27.992(1), c = 6.5243 (3) Å, V = 1325.10(8) Å3, Z = 4. The crystal structure of karibibbite consists of bands of Fe3+O6 octahedra running along a framed by two chains of AsO3 trigonal pyramids at each side, and along c by As2O5 dimers above and below. Each band is composed of ribbons of three edge-sharing Fe3+O6 octahedra, apex-connected with other ribbons in order to form a kinked band running along a. The atoms As(2) and As(3), each showing trigonal pyramidal coordination by O, share the O(4) atom to form a dimer. In turn, dimers are connected by the O(3) atoms, defining a zig-zag chain of overall (As3+O2)n-n stoichiometry. Each ribbon of (Fe3+O6) octahedra is flanked on both edges by the (As3+O2)n-n chains. The simultaneous presence of arsenite chains and dimers is previously unknown in compounds with As3+. The lone-electron pairs (4s2) of the As(2) and As(3) atoms project into the interlayer located at y = 0 and y = ½, yielding probable weak interactions with the O atoms of the facing (AsO2) chain.The DFT calculations show that the Fe atoms have maximum spin polarization, consistent with the Fe3+ state.

scholarly journals Crystal structure of pimecrolimus Form B, C43H68ClNO11

2021 ◽  
Vol 36 (1) ◽  
pp. 35-42
Author(s):  
Shivang Bhaskar ◽  
Joseph T. Golab ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Density Functional ◽  
Van Der Waals Interactions ◽  
Powder Diffraction File ◽  
X Ray ◽  
Weak Intermolecular Interactions ◽  
Significant Difference ◽  
Atomic Coordinates ◽  
Solid State Conformation

The crystal structure of pimecrolimus Form B has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Pimecrolimus crystallizes in the space group P21 (#4) with a = 15.28864(7), b = 13.31111(4), c = 10.95529(5) Å, β = 96.1542(3)°, V = 2216.649(9) Å3, and Z = 2. Although there are an intramolecular six-ring hydrogen bond and some larger chain and ring patterns, the crystal structure is dominated by van der Waals interactions. There is a significant difference between the conformation of the Rietveld-refined and the DFT-optimized structures in one portion of the macrocyclic ring. Although weak, intermolecular interactions are apparently important in determining the solid-state conformation. The powder pattern is included in the Powder Diffraction File™ (PDF®) as entry 00-066-1619. This study provides the atomic coordinates to be added to the PDF entry.

Crystal structure of ziprasidone hydrochloride monohydrate, C21H22Cl2N4OS(H2O)

2015 ◽  
Vol 30 (3) ◽  
pp. 192-198
Author(s):  
James A. Kaduk ◽  
Kai Zhong ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Powder Diffraction ◽  
Density Functional ◽  
Minimum Energy ◽  
Strong Hydrogen Bond ◽  
Powder Diffraction File ◽  
X Ray ◽  
Hydrochloride Monohydrate ◽  
Positively Charged

The crystal structure of ziprasidone hydrochloride monohydrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Ziprasidone hydrochloride monohydrate crystallizes in space group P-1 (#2) with a = 7.250 10(3), b = 10.986 66(8), c = 14.071 87(14) Å, α = 83.4310(4), β = 80.5931(6), γ = 87.1437(6)°, V = 1098.00(1) Å3, and Z = 2. The ziprasidone conformation in the solid state is very close to the minimum energy conformation. The positively-charged nitrogen in the ziprasidone makes a strong hydrogen bond with the chloride anion. The water molecule makes two weaker bonds to the chloride, and acts as an acceptor in an N–H⋯O hydrogen bond. The powder pattern is included in the Powder Diffraction File™ as entry 00-064-1492.

Crystal structure of oxybutynin hydrochloride hemihydrate, C22H32NO3Cl(H2O)0.5

2019 ◽  
Vol 34 (1) ◽  
pp. 50-58
Author(s):  
James A. Kaduk ◽  
Nicholas C. Boaz ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Hydroxyl Group ◽  
Layered Crystal ◽  
Powder Diffraction File ◽  
X Ray ◽  
Layered Crystal Structure ◽  
Oxybutynin Hydrochloride

The crystal structure of oxybutynin hydrochloride hemihydrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Oxybutynin hydrochloride hemihydrate crystallizes in space group I2/a (#15) with a = 14.57266(8), b = 8.18550(6), c = 37.16842(26) Å, β = 91.8708(4)°, V = 4421.25(7) Å3, and Z = 8. The compound exhibits X-ray-induced photoreduction of the triple bond. Prominent in the layered crystal structure is the N–H⋅⋅⋅Cl hydrogen bond between the cation and anion, as well as O–H⋅⋅⋅Cl hydrogen bonds from the water molecule and hydroxyl group of the oxybutynin cation. C–H⋅⋅⋅Cl hydrogen bonds also contribute to the crystal energy, and help determine the conformation of the cation. The powder pattern is included in the Powder Diffraction File™ as entry 00-068-1305.

Crystal structure of minocycline hydrochloride dihydrate form A, C23H28N3O7Cl (H2O)2

2018 ◽  
Vol 34 (1) ◽  
pp. 59-65
Author(s):  
Austin M. Wheatley ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Density Functional ◽  
Hydroxyl Group ◽  
Water Molecules ◽  
Powder Diffraction File ◽  
X Ray ◽  
Dimethyl Amine ◽  
Minocycline Hydrochloride ◽  
Amine Groups

The crystal structure of minocycline hydrochloride dihydrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Minocycline hydrochloride dihydrate crystallizes in space groupP212121(#19) witha= 7.40772(1),b= 14.44924(3),c= 22.33329(4) Å,V= 2390.465(12) Å3, andZ= 4. The minocycline cation is a zwitterion: both dimethylamino groups are protonated and one hydroxyl group is ionized. A potential ambiguity in the orientation of the amide group was resolved by considering Rietveld refinement residuals and displacement coefficients, as well as DFT energies. The crystal structure is dominated by hydrogen bonds. Both water molecules and a hydroxyl group act as donors to the chloride anion. Both protonated dimethyl amine groups act as donors to the ionized hydroxyl group. Several intramolecular O–H···O hydrogen groups help determine the conformation of the cation. The powder pattern is included in the Powder Diffraction File™ as entry 00-066-1606.

Crystal structure of potassium tetraperoxomolybdate (VI) K2[Mo(O2)4]

2005 ◽  
Vol 20 (3) ◽  
pp. 203-206 ◽  
Author(s):  
M. Grzywa ◽  
M. Różycka ◽  
W. Łasocha
Keyword(s):  
Crystal Structure ◽  
Low Temperature ◽  
Diffraction Pattern ◽  
Powder Diffraction ◽  
Rietveld Method ◽  
Structure Refinement ◽  
Crystal Structure Refinement ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters

Potassium tetraperoxomolybdate (VI) K2[Mo(O2)4] was prepared, and its X-ray powder diffraction pattern was recorded at low temperature (258 K). The unit cell parameters were refined to a=10.7891(2) Å, α=64.925(3)°, space group R−3c (167), Z=6. The compound is isostructural with potassium tetraperoxotungstate (VI) K2[W(O2)4] (Stomberg, 1988). The sample of K2[Mo(O2)4] was characterized by analytical investigations, and the results of crystal structure refinement by Rietveld method are presented; final RP and RWP are 9.79% and 12.37%, respectively.

Crystal structure of bretylium tosylate (Bretylol®), C18H24BrNO3S

2018 ◽  
Vol 33 (4) ◽  
pp. 298-302
Author(s):  
Austin M. Wheatley ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Double Layers ◽  
Powder Diffraction Data ◽  
Powder Diffraction File ◽  
X Ray ◽  
Polar Interactions ◽  
Normal Hydrogen

The crystal structure of bretylium tosylate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Bretylium tosylate crystallizes in space group C2/c (#15) with a = 32.6238(4), b = 12.40353(14), c = 9.93864(12) Å, β = 101.4676(10), V = 3941.39(5) Å3, and Z = 8. The sample exhibited visible decomposition in the X-ray beam. The unusual displacement ellipsoid of the Br atom probably indicates that the decomposition in the beam involves the Br atom. The crystal structure can be viewed as layered parallel to the bc plane. The layers are double, the center consisting of the cation/anion polar interactions and the outer surface of the double layers consists of hydrocarbon interactions. In the absence of normal hydrogen bond donors, the only hydrogen bonds in the bretylium tosylate structure are C–H…O hydrogen bonds. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.

scholarly journals Preparation, differential thermal analysis and crystal structure of the new quaternary compound CuVInSe3

2018 ◽  
Vol 64 (6) ◽  
pp. 548
Author(s):  
Gustavo Marroquin ◽  
Gerzon E. Delgado ◽  
Pedro Grima-Gallardo ◽  
Miguel Quintero
Keyword(s):  
Crystal Structure ◽  
Thermal Analysis ◽  
Differential Thermal Analysis ◽  
Powder Diffraction ◽  
Powder Diffraction Data ◽  
Unit Cell Parameters ◽  
Quaternary Compound ◽  
X Ray ◽  
Cell Parameters ◽  
Structural Variables

The crystal structure of the quaternary compound CuVInSe3 belonging to the system (CuInSe2)1-x(VSe)x with x= ½, was analyzed using X-ray powder diffraction data. This material was synthesized by the melt and anneal method and crystallizes in the tetragonal space group P2c (Nº 112), with unit cell parameters a = 5.7909(4) Å, c = 11.625(1) Å, V = 389.84(5) Å3. The Rietveld refinement of 25 instrumental and structural variables led to Rexp = 6.6 %, Rp = 8.7 %, Rwp = 8.8 % and S = 1.3 for 4501 step intensities and 153 independent reflections. This compound has a normal adamantane structure and is isostructural with CuFeInSe3. The DTA indicates that this compound melts at 1332 K.

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.

Powder X-ray diffraction of bendamustine hydrochloride monohydrate, C16H22Cl2N3O2Cl·H2O

2018 ◽  
Vol 34 (1) ◽  
pp. 74-75
Author(s):  
J. A. Kaduk ◽  
K. Zhong ◽  
T. N. Blanton ◽  
S. Gates-Rector ◽  
T. G. Fawcett
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Argonne National Laboratory ◽  
Lymphocytic Leukemia ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrochloride Monohydrate

Bendamustine hydrochloride monohydrate (marketed as Treanda®) is a nitrogen mustard purine analog alkylator used in the treatment of chronic lymphocytic leukemia (CLL) and non-Hodgkin lymphomas. Commercial bendamustine hydrochloride monohydrate crystallizes in the monoclinic space group P21/c (14), with a = 4.71348(4) Å, b = 47.5325(3) Å, c = 8.97458 (5) Å, β = 96.6515(8)°, V = 1997.161(23) Å3, and Z = 4. A reduced cell search in the Cambridge Structural Database yielded a previously reported crystal structure (Allen, 2002), which did not include hydrogens (Reck, 2006). In this work, the sample was ordered from Santa Cruz Biotechnology, and analyzed as received. The room-temperature crystal structure was refined using synchrotron (λ = 0.413896 Å) powder diffraction data, density functional theory (DFT), and Rietveld refinement techniques. Hydrogen positions were included as part of the structure, and recalculated during the refinement. The diffraction data were collected on beamline BM-11 at the Advanced Photon Source, Argonne National Laboratory. Figure 1 shows the powder X-ray diffraction pattern of the compound. The pattern is included in the Powder Diffraction File as entry 00-064-1508.

Sign in / Sign up

Export Citation Format

Share Document