Combination of energy minimizations and rigid-body Rietveld refinement: the structure of 2,5-dihydroxybenzo[de]benzo[4,5]imidazo[2,1-a]isoquinolin-7-one

1999 ◽  
Vol 32 (2) ◽  
pp. 178-186 ◽  
Author(s):  
Martin U. Schmidt ◽  
Robert E. Dinnebier
Keyword(s):  
Crystal Structure ◽  
Rigid Body ◽  
Degrees Of Freedom ◽  
Three Dimensional ◽  
Rietveld Analysis ◽  
Hydrogen Bond Network ◽  
Intermolecular Energy ◽  
Planar Molecules ◽  
Bond Network ◽  
Random Packings

The crystal structure of the yellow pigment 2,5-dihydroxybenzo[de]benzo[4,5]imidazo[2,1-a]isoquinolin-7-one (C18H10N2O3) was determined from powder data. The crystal structure was solved by minimizing the intermolecular energy starting from random packings. Subsequently, the structure was refined by rigid-body Rietveld analysis, using synchrotron powder data. The refinement included several intramolecular degrees of freedom. The compound crystallizes inPna21,Z\,=\,4, with lattice parametersa\,=\,13.2759 (3),b\,=\,20.9561 (5),c\,=\,4.7798 (1) Å, andV\,=\,1329.79 (5) Å3. The crystal consists of planar molecules, connected by hydrogen bonds of the types O–H...OH and O–H...N, which form a three-dimensional hydrogen-bond network.

(NH4)[B3PO6(OH)3]·0.5H2O

2007 ◽  
Vol 63 (11) ◽  
pp. i185-i185 ◽  
Author(s):  
Wei Liu ◽  
Jingtai Zhao
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Ammonium Ions ◽  
One Dimensional ◽  
Bond Network ◽  
Solvothermal Conditions

The title compound, ammonium catena-[monoboro-monodihydrogendiborate-monohydrogenphosphate] hemihydrate, was obtained under solvothermal conditions using glycol as the solvent. The crystal structure is constructed of one-dimensional infinite borophosphate chains, which are interconnected by ammonium ions and water molecules via a complex hydrogen-bond network to form a three-dimensional structure. The water molecules of crystallization are disordered over inversion centres, and their H atoms were not located.

Crystal structure of rilpivirine, C22H18N6

2015 ◽  
Vol 30 (2) ◽  
pp. 170-174
Author(s):  
James A. Kaduk ◽  
Kai Zhong ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Three Dimensional ◽  
Hydrogen Bond Network ◽  
Powder Diffraction Data ◽  
Powder Diffraction File ◽  
X Ray ◽  
Bond Network

The crystal structure of rilpivirine has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Rilpivirine crystallizes in space group P21/c (#14) with a = 8.39049(3), b = 13.89687(4), c = 16.03960(6) Å, β = 90.9344(3)°, V = 1869.995(11) Å3, and Z = 4. The most prominent features of the structure are N–H···N hydrogen bonds. These form a R2,2(8) pattern which, along with C1,1(12) and longer chains, yield a three-dimensional hydrogen bond network. The powder pattern has been submitted to International Centre for Diffraction Data, ICDD, for inclusion in future releases of the Powder Diffraction File™.

Hydrogen-bond network and pH sensitivity in transthyretin: Neutron crystal structure of human transthyretin

2012 ◽  
Vol 177 (2) ◽  
pp. 283-290 ◽  
Author(s):  
Takeshi Yokoyama ◽  
Mineyuki Mizuguchi ◽  
Yuko Nabeshima ◽  
Katsuhiro Kusaka ◽  
Taro Yamada ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Ph Sensitivity ◽  
Hydrogen Bond Network ◽  
Bond Network

scholarly journals RbCa2Nb3O10from X-ray powder data

2009 ◽  
Vol 65 (6) ◽  
pp. i44-i44 ◽  
Author(s):  
Zhen-Hua Liang ◽  
Kai-Bin Tang ◽  
Qian-Wang Chen ◽  
Hua-Gui Zheng
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Solid State Reaction ◽  
Perovskite Structure ◽  
Three Dimensional ◽  
Rietveld Analysis ◽  
Powder Diffraction Data ◽  
X Ray

Rubidium dicalcium triniobate(V), RbCa2Nb3O10, has been synthesized by solid-state reaction and its crystal structure refined from X-ray powder diffraction data using Rietveld analysis. The compound is a three-layer perovskite Dion–Jacobson phase with the perovskite-like slabs derived by termination of the three-dimensional CaNbO3perovskite structure along theabplane. The rubidium ions (4/mmmsymmetry) are located in the interstitial space.

scholarly journals (Acetonitrile-κN)aqua[N,N′-bis(pyridin-2-ylmethyl)ethane-1,2-diamine-κ4N,N′,N′′,N′′′]zinc(II) perchlorate

2017 ◽  
Vol 73 (10) ◽  
pp. 1568-1571
Author(s):  
Ugochukwu Okeke ◽  
Yilma Gultneh ◽  
Ray J. Butcher
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Structural Features ◽  
Hydrogen Bond Network ◽  
Asymmetric Unit ◽  
Bond Network ◽  
Bifurcated Hydrogen Bond ◽  
Coordinated Water ◽  
Ionic Hydrogen Bonding

The structure of the title compound, [Zn(C14H18N4)(C2H3N)(H2O)](ClO4)2, contains a six-coordinate cation consisting of the tetradentate bispicen ligand, coordinated water, and coordinated acetonitrile, with the latter two ligands adopting acisconfiguration. There are two formula units in the asymmetric unit. Both cations show almost identical structural features with the bispicen ligand adopting the more commoncis-β conformation. One of the four perchlorate anions is disordered over two positions, with occupancies of 0.9090 (15) and 0.0910 (15). There is extensive inter-ionic hydrogen bonding between the perchlorate anions and O—H and N—H groups in the cations, including a bifurcated hydrogen bond between an N—H group and two O atoms of one perchlorate anion. As a result of this extended hydrogen-bond network, the ions are linked into a complex three-dimensional array.

Chemical accuracy and precision in Rietveld analysis: The crystal structure of cobalt(II) acetate tetrahydrate

1997 ◽  
Vol 12 (1) ◽  
pp. 27-39 ◽  
Author(s):  
James A. Kaduk ◽  
Walt Partenheimer
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Three Dimensional ◽  
Rietveld Analysis ◽  
Monoclinic Space Group ◽  
Acetate Tetrahydrate ◽  
Atomic Displacements ◽  
Synchrotron Powder Diffraction ◽  
Accuracy And Precision

The crystal structure of cobalt(II) acetate tetrahydrate, Co(C2H3O2)·4H2O, has been refined using single-crystal, laboratory powder, and synchrotron powder diffraction data, both individually and in various combinations. The compound crystallizes in the monoclinic space group P21/c, with a=4.80688(3), b=11.92012(7), c=8.45992(5) Å, β=94.3416(4)° at 27 °C, and Z=2. The crystal structure consists of discrete centrosymmetric trans-Co(C2H3O2)(H2O)4 complexes, linked by a three-dimensional network of hydrogen bonds. Each complex participates in 14 hydrogen bonds, 12 intermolecular, and 2 intramolecular. Compared to the single-crystal refinement, refinement of laboratory powder data yielded an average difference in bond distances of 0.02 Å, in bond angles of 3°, and in root mean square atomic displacements of 0.07 Å. The standard uncertainties of the bond distances were 0.01 Å, compared to the 0.001–0.002 Å in the single-crystal refinement. Refinement of the synchrotron powder data yielded improved accuracy and precision. It proved impossible to locate or refine hydrogen positions using a single-powder dataset, but the hydrogens could be refined using rigid groups in a joint refinement of the two powder datasets. Even from powder refinements, it is possible to obtain suitable accuracy and precision to distinguish C–O and C=O bonds, and to examine details of chemical bonding.

scholarly journals Reorientation-induced relaxation of free OH at the air/water interface revealed by ultrafast heterodyne-detected nonlinear spectroscopy

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Ken-ichi Inoue ◽  
Mohammed Ahmed ◽  
Satoshi Nihonyanagi ◽  
Tahei Tahara
Keyword(s):  
Hydrogen Bond ◽  
Vibrational Relaxation ◽  
Three Dimensional ◽  
Technical Difficulty ◽  
Nonlinear Spectroscopy ◽  
Water Interface ◽  
Hydrogen Bond Network ◽  
Relaxation Dynamics ◽  
Air Water Interface ◽  
Bond Network

Abstract The uniqueness of water originates from its three-dimensional hydrogen-bond network, but this hydrogen-bond network is suddenly truncated at the interface and non-hydrogen-bonded OH (free OH) appears. Although this free OH is the most characteristic feature of interfacial water, the molecular-level understanding of its dynamic property is still limited due to the technical difficulty. We study ultrafast vibrational relaxation dynamics of the free OH at the air/water interface using time-resolved heterodyne-detected vibrational sum frequency generation (TR-HD-VSFG) spectroscopy. With the use of singular value decomposition (SVD) analysis, the vibrational relaxation (T1) times of the free OH at the neat H2O and isotopically-diluted water interfaces are determined to be 0.87 ± 0.06 ps (neat H2O), 0.84 ± 0.09 ps (H2O/HOD/D2O = 1/2/1), and 0.88 ± 0.16 ps (H2O/HOD/D2O = 1/8/16). The absence of the isotope effect on the T1 time indicates that the main mechanism of the vibrational relaxation of the free OH is reorientation of the topmost water molecules. The determined sub-picosecond T1 time also suggests that the free OH reorients diffusively without the switching of the hydrogen-bond partner by the topmost water molecule.

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