Search

A precise X-ray crystal structure determination of systems that exist in a polycrystalline form often poses a challenge due to several factors that limit the resolution of the diffraction measurement. The location of atoms is usually determined at significantly lower precision than the unit cell parameters, rendering the complete characterization of the structure difficult. This is particularly pronounced when precise location of hydrogen atoms is required, for instance in ionizable biomolecules or in hydrogen bonds. In such cases periodic quantum (DFT) calculations may crucially assist structure determination, because they can reliably predict the location of atoms, provided that the unit cell parameters, the space group and tentative atomic positions are known. In this work we present DFT-assisted structure determination of pentadecafluorooctanoic acid hydrate, a benchmark system featuring short hydrogen bonds (RO...O ≈ 2.5 Å) between acid and water molecules. While Rietveld refinement based solely on powder diffraction data cannot reliably resolve the location of crystal water molecules and even less so the position of hydrogen atoms in the network of hydrogen bonds, periodic DFT optimization yields several minimum energy structures suitable for further refinement. Due to the low experimental resolution and similarity, comparison between model and experimental powder diffraction pattern can barely distinguish between certain structure candidates provided by DFT calculations, but it can rule out those featuring larger misfits. The proposed structure solution is delivered from a tandem application of structure determination from powder diffraction data and DFT optimization, the former providing the unit cell parameters and estimated atomic positions that are finely tuned by DFT. The present strategy can in principle be generalized to other examples of structure determination at relatively low resolution, such as is often the case with biological macromolecules. Thi

A precise X-ray crystal structure determination of systems that exist in a polycrystalline form often poses a challenge due to several factors that limit the resolution of the diffraction measurement. The location of atoms is usually determined at significantly lower precision than the unit cell parameters, rendering the complete characterization of the structure difficult. This is particularly pronounced when precise location of hydrogen atoms is required, for instance in ionizable biomolecules or in hydrogen bonds. In such cases periodic quantum (DFT) calculations may crucially assist structure determination, because they can reliably predict the location of atoms, provided that the unit cell parameters, the space group and tentative atomic positions are known. In this work we present DFT-assisted structure determination of pentadecafluorooctanoic acid hydrate, a benchmark system featuring short hydrogen bonds (RO...O ≈ 2.5 Å) between acid and water molecules. While Rietveld refinement based solely on powder diffraction data cannot reliably resolve the location of crystal water molecules and even less so the position of hydrogen atoms in the network of hydrogen bonds, periodic DFT optimization yields several minimum energy structures suitable for further refinement. Due to the low experimental resolution and similarity, comparison between model and experimental powder diffraction pattern can barely distinguish between certain structure candidates provided by DFT calculations, but it can rule out those featuring larger misfits. The proposed structure solution is delivered from a tandem application of structure determination from powder diffraction data and DFT optimization, the former providing the unit cell parameters and estimated atomic positions that are finely tuned by DFT. The present strategy can in principle be generalized to other examples of structure determination at relatively low resolution, such as is often the case with biological macromolecules. Thi

ARKIVOC: vol. 2011, no. 6, (issn) 1551-7012, (dlps) 5550190.0012.610, This work is licensed under a Creative Commons Attribution-NonCommercial 3.0 License. Please contact mpub-help@umich.edu to use this work in a way not covered by the license.

ARKIVOC: vol. 2011, no. 6, (issn) 1551-7012, (dlps) 5550190.0012.610, This work is licensed under a Creative Commons Attribution-NonCommercial 3.0 License. Please contact mpub-help@umich.edu to use this work in a way not covered by the license.

By a selective exchange of ligand Br by Cl, a series of nonstoichiometric bromo-chloro-pyridine- molybdenum(III) octahedral compounds of the type (cat)[MoBraCl(4-a)py2] (cat = pyH, a = 3–1 (1, 4, 7)); cat = [(C2H5)3NH], a = 2.744 (2); cat = Rb, a = 2.278 (5); cat =[(C6H5)4)As], a = 1.258 (8) and [MoBraCl(3–a)py3] (a = 2–1 (3, 6)) have been prepared and characterized. Owing to great similarity of the powder diffraction patterns and IR spectra of compounds mer- [MoBraCl(3-a)py3] (a = 3–0) with the known monoclinic modification in the space group P21/c and compounds [MoBraCl(3-a)py3] (a = 2-1 (3, 6)), the same type of crystal lattice was confirmed. Isostructurality was observed also for the orthorhombic trans-(pyH)[MoBr4py2]](Pnma) and compounds 1 and 4, while compound 7 is isostructural to trans-(pyH)[MoCl4py2]. X-ray crystallographic analyses of 2, 5 and 8, obtained by recrystallization of (pyH)[MoBraCl(4-a)py2] (a = 3–1) with different cations, were performed. In these compounds, MoIII is octahedrally coordinated with four halogenido ions at distances 2.4953(6)–2.5920(10) Å and two pyridine molecules at distances 2.195(4)-2.220(4) Å. Trans oriented pyridine rings in compounds 5 and 8 are co-planar, while deviation from co-planarity was noticed for compound 2 (8.9(3)°). The stoichiometry of four coordinated Br and Cl atoms in these compounds is not ideal, since the structure analysis results for 2, 5 and 8 show a mixed occupancy of crystallographic sites; thus, refined population parameters for both atoms (Br and Cl) were calculated., Selektivnom zamjenom bromovoga liganda klorovim dobijena je i karakterizirana serija nestehiometrijskih bromo-kloro-piridin-MoIII kompleksa tipa (cat)[MoBraCl(4–a)py2] (cat = pyH, a = 3–1 (1, 4, 7); cat = [(C2H5)3NH], a = 2.744 (2); cat = Rb, a = 2.278 (5); cat = [(C6H5)4As], a = 1.258 (8)) i [MoBraCl(3–a)py3] (a = 2–1 (3, 6)). Uslijed velike sličnosti difraktograma praha i IR spektara spojeva mer-[MoBraCl(3–a)py3] (a = 3–0) poznate monoklinske modifikacije u prostornoj grupi P21/c i spojeva [MoBraCl(3–a)py3] (a = 2–1 (3, 6)), potvr|en je isti tip kristalne re{etke. Opa`ena je izostrukturnost rompskoga trans-(pyH)[MoBr4py2] (Pnma) i spojeva 1 i 4, dok je spoj 7 izostrukturiran s trans-(pyH)[MoCl4py2]. Načinjena je rentgenska strukturna analiza spojeva 2, 5 i 8 dobijenih prekristalizacijom (pyH)[MoBraCl(4–a)py2] (a = 3–1) s različitim kationima. U tim je spojevima MoIII oktaedarski koordiniran s četiri halogenidna iona na udaljenostima 2.4953(6)–2.5920(10) Å i dvije molekule piridina na udaljenostima 2.195(4)–2.220(4) Å. Trans orijentirani piridinski prstenovi u spojevima 5 i 8 su koplanarni dok je kod spoja 2 ustanovljena devijacija od koplanarnosti (8.9(3)°). Strukturnom analizom utočnjeni su faktori zauzetosti četiri koordinirana atoma (Br, Cl) u spojevima 2, 5 i 8. Na|eno je da su navedeni kristalografski položaji zauzeti atomima Cl i Br u nestehiometrijskome omjeru.

Methods for the crystal structure determination from powder diffraction data are reviewed with special emphasis on the application to technical ceramics. Experimental techniques using other than laboratory X-ray, such as synchrotron radiation, neutron and electron beams, are also described. As an illustrative example, the crystal structure determinations of compounds LaNbTiO6, La0.462Nb0.614Ti0.386O3 and La0.37Nb0.889Ti0.111O3 in the ternary system of La2O3–Nb2O5–TiO2 are reported.

ARKIVOC: vol. 2003, no. 5, (issn) 1551-7012, (dlps) 5550190.0004.508, This work is licensed under a Creative Commons Attribution-NonCommercial 3.0 License. Please contact mpub-help@umich.edu to use this work in a way not covered by the license.

ARKIVOC: vol. 2003, no. 5, (issn) 1551-7012, (dlps) 5550190.0004.508, This work is licensed under a Creative Commons Attribution-NonCommercial 3.0 License. Please contact mpub-help@umich.edu to use this work in a way not covered by the license.

An overview of contemporary methods of crystal structure solution from powder diffraction data is given. Methods are compared with respect to their advantages and disadvantages. A choice of an appropriate method is discussed in the light of understanding the structural problem to be solved. The need of the variety of methods for the variety of problems is illustrated by examples. Some directions of possible future development are discussed.

An overview of contemporary methods of crystal structure solution from powder diffraction data is given. Methods are compared with respect to their advantages and disadvantages. A choice of an appropriate method is discussed in the light of understanding the structural problem to be solved. The need of the variety of methods for the variety of problems is illustrated by examples. Some directions of possible future development are discussed.