Chemical reasonableness in Rietveld analysis: Inorganics

2007 ◽  
Vol 22 (3) ◽  
pp. 268-278 ◽  
Author(s):  
James A. Kaduk
Keyword(s):  
Hydrogen Bonding ◽  
Rietveld Refinement ◽  
Rietveld Analysis ◽  
Structural Features ◽  
Rigid Bodies ◽  
Approximate Symmetry ◽  
Hydrogen Bonding Pattern ◽  
Normal Ranges ◽  
Chemical Knowledge

Besides statistical and graphical measures, many structural features can be used to assess the quality of a Rietveld refinement. These include the metric symmetry of the lattice (which can assist in determining the true symmetry and in identifying isostructural compounds), bond distances and angles (which should fall within normal ranges), displacement coefficients, refined stoichiometry, the absolute values of the standard uncertainties of the fractional coordinates, the hydrogen bonding pattern, the presence of approximate symmetry, the presence of unindexed peaks in the pattern, and whether the refinement converges at all. Chemical knowledge can be built into a Rietveld refinement though the use of restraints and rigid bodies. A knowledge of chemical reasonableness proved important in refining the correct structures of [Fe(H2O)6](BF4)2, (Ba1.5Sr0.5)TiO4, and (Ba1.25Sr0.75)TiO4.

Chemical reasonableness in Rietveld analysis; organics

2007 ◽  
Vol 22 (1) ◽  
pp. 74-82 ◽  
Author(s):  
James A. Kaduk
Keyword(s):  
Rietveld Refinement ◽  
Normal Values ◽  
Solution Process ◽  
Molecular Geometry ◽  
Rietveld Analysis ◽  
Rigid Bodies ◽  
Torsion Angles ◽  
Structure Solution ◽  
Calcium Tartrate

We know a lot about normal values of bond distances, bond angles, torsion angles, and other molecular parameters. This knowledge can be incorporated into the structure solution process and into Rietveld refinement through the use of restraints and rigid bodies. An important measure of the quality of the refined model is the chemical reasonableness of molecular geometry. Refinement of the structures of calcium tartrate tetrahydrate and guaifenesin is used to illustrate the importance of chemical reasonableness in determining the quality of a Rietveld refinement.

Five pseudopolymorphs of 6-amino-2-thiouracil: absence of N—H...S hydrogen bonds

2012 ◽  
Vol 69 (1) ◽  
pp. 93-100 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Cambridge Structural Database ◽  
Hydrogen Bonding Pattern ◽  
Crystallization Experiments ◽  
Structural Database ◽  
Thiouracil Derivatives

In order to study the preferred hydrogen-bonding pattern of 6-amino-2-thiouracil, C4H5N3OS, (I), crystallization experiments yielded five different pseudopolymorphs of (I), namely the dimethylformamide disolvate, C4H5N3OS·2C3H7NO, (Ia), the dimethylacetamide monosolvate, C4H5N3OS·C4H9NO, (Ib), the dimethylacetamide sesquisolvate, C4H5N3OS·1.5C4H9NO, (Ic), and two different 1-methylpyrrolidin-2-one sesquisolvates, C4H5N3OS·1.5C5H9NO, (Id) and (Ie). All structures containR21(6) N—H...O hydrogen-bond motifs. In the latter four structures, additionalR22(8) N—H...O hydrogen-bond motifs are present stabilizing homodimers of (I). No type of hydrogen bond other than N—H...O is observed. According to a search of the Cambridge Structural Database, most 2-thiouracil derivatives form homodimers stabilized by anR22(8) hydrogen-bonding pattern, with (i) only N—H...O, (ii) only N—H...S or (iii) alternating pairs of N—H...O and N—H...S hydrogen bonds.

scholarly journals Bis(3-carbamoylpyridin-1-ium) phosphite monohydrate

2018 ◽  
Vol 74 (9) ◽  
pp. 1295-1298
Author(s):  
Jan Fábry
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Secondary Amine ◽  
Symmetry Plane ◽  
Structural Features ◽  
Water Molecules ◽  
Amine Groups

Two of the constituent molecules in the title structure, 2C6H7N2O+·HPO3 2−·H2O, i.e. the phosphite anion and the water molecule, are situated on a symmetry plane. The molecules are held together by moderate N—H...O and O—H...N, and weak O—H...O and C—H...Ocarbonyl hydrogen bonds in which the amide and secondary amine groups, and the water molecules are involved. The structural features are usual, among them the H atom bonded to the P atom avoids hydrogen bonding.

scholarly journals Zoomqa: Residue-Level Single-Model QA Support Vector Machine Utilizing Sequential and 3D Structural Features

2021 ◽  
Author(s):  
Kyle Hippe ◽  
Cade Lilley ◽  
William Berkenpas ◽  
Kiyomi Kishaba ◽  
Renzhi Cao
Keyword(s):  
Protein Complex ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
State Of The Art ◽  
Chemical Properties ◽  
Structural Features ◽  
Residue Level ◽  
Support Vector ◽  
Single Model

ABSTRACTMotivationThe Estimation of Model Accuracy problem is a cornerstone problem in the field of Bioinformatics. When predictions are made for proteins of which we do not know the native structure, we run into an issue to tell how good a tertiary structure prediction is, especially the protein binding regions, which are useful for drug discovery. Currently, most methods only evaluate the overall quality of a protein decoy, and few can work on residue level and protein complex. Here we introduce ZoomQA, a novel, single-model method for assessing the accuracy of a tertiary protein structure / complex prediction at residue level. ZoomQA differs from others by considering the change in chemical and physical features of a fragment structure (a portion of a protein within a radius r of the target amino acid) as the radius of contact increases. Fourteen physical and chemical properties of amino acids are used to build a comprehensive representation of every residue within a protein and grades their placement within the protein as a whole. Moreover, ZoomQA can evaluate the quality of protein complex, which is unique.ResultsWe benchmark ZoomQA on CASP14, it outperforms other state of the art local QA methods and rivals state of the art QA methods in global prediction metrics. Our experiment shows the efficacy of these new features, and shows our method is able to match the performance of other state-of-the-art methods without the use of homology searching against database or PSSM matrix.Availabilityhttp://[email protected]

scholarly journals Crystal structures of butyl 2-amino-5-hydroxy-4-(4-nitrophenyl)benzofuran-3-carboxylate and 2-methoxyethyl 2-amino-5-hydroxy-4-(4-nitrophenyl)benzofuran-3-carboxylate

2019 ◽  
Vol 75 (6) ◽  
pp. 880-887 ◽  
Author(s):  
Rosita Diana ◽  
Angela Tuzi ◽  
Barbara Panunzi ◽  
Antonio Carella ◽  
Ugo Caruso
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Molecular Structures ◽  
Antitumoral Activity ◽  
Space Group ◽  
One Dimensional ◽  
Axis Direction ◽  
Hydrogen Bonding Pattern ◽  
Butyl Group

The title benzofuran derivatives 2-amino-5-hydroxy-4-(4-nitrophenyl)benzofuran-3-carboxylate (BF1), C19H18N2O6, and 2-methoxyethyl 2-amino-5-hydroxy-4-(4-nitrophenyl)benzofuran-3-carboxylate (BF2), C18H16N2O7, recently attracted attention because of their promising antitumoral activity. BF1 crystallizes in the space group P\overline{1}. BF2 in the space group P21/c. The nitrophenyl group is inclined to benzofuran moiety with a dihedral angle between their mean planes of 69.2 (2)° in BF1 and 60.20 (6)° in BF2. A common feature in the molecular structures of BF1 and BF2 is the intramolecular N—H...Ocarbonyl hydrogen bond. In the crystal of BF1, the molecules are linked head-to-tail into a one-dimensional hydrogen-bonding pattern along the a-axis direction. In BF2, pairs of head-to-tail hydrogen-bonded chains of molecules along the b-axis direction are linked by O—H...Omethoxy hydrogen bonds. In BF1, the butyl group is disordered over two orientations with occupancies of 0.557 (13) and 0.443 (13).

Ultrafine Cellulose Acetate Fibers with Nanoscale Structural Features

2008 ◽  
Vol 8 (9) ◽  
pp. 4461-4469 ◽  
Author(s):  
Lifeng Zhang ◽  
You-Lo Hsieh
Keyword(s):  
Hydrogen Bonding ◽  
Cellulose Acetate ◽  
Pore Volume ◽  
Structural Features ◽  
Fiber Formation ◽  
Vinyl Pyrrolidone ◽  
Chain Entanglement ◽  
Bicomponent Fibers ◽  
Micron Size ◽  
Poly Vinyl Pyrrolidone

Nano-structural features were introduced to ultrafine cellulose acetate (CA) fibers by electrospinning of its mixtures with either poly(vinyl pyrrolidone) PVP or β-cyclodextrin (β-CD) in DMF, followed by dissolution of the added PVP or β-CD. The presence of the charge-holding PVP enabled fiber formation from CA below its entanglement chain length and improved the electrospinning efficiency to produce bicomponent fibers with wide ranging diameters from 30 to 650 nm. At up to 50% contents, the PVP in the bicomponent fibers was phase-separated from CA and, upon removal, resulting in highly angulated fiber surfaces with nanometer-size spherulites and sub-micron size ridges and grooves. Adding β-CD to CA enabled fiber formation at concentrations below the chain entanglement concentration Ce (16.5%). Hydrogen bonding between β-CD and CA, as evident by FTIR, helped to distribute β-CD as individual molecules in the CA matrix and producing more uniform and finer (130–150 nm in diameters) fibers, irrespective of their β-CD contents. Removal of β-CD from the fibers originally containing 40% β-CD, generated nanoporous fibers with 2-nm nanopores and 70% increase in specific surface and doubled pore volume.

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