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2020 | OriginalPaper | Chapter

Recent Developments in the Refinement and Analysis of Crystal Structures

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Abstract

Crystal structure refinement and analysis is a powerful method for determination of crystal structures and finds widespread application in determination of structures of crystals of small molecules and frameworks at atomic resolution. The independent atom model is used to describe atomic scattering for routine use, while more accurate aspherical scattering factors are increasingly available. The structure factor is presented as the Fourier transform of convolutions of scattering and probability densities in the crystal structure to clarify how aspherical scattering factors and alternative displacement probabilities can be introduced into refinement methods. Non-linear least squares fitting of the crystal structure parameters in the structure factor equations is described using matrix algebra notation which enables simple derivation of the extensions required for discussion of crystallographic restraints and leverage analysis. Finally, combined analysis of multiple single-crystal experiments is discussed highlighting the potential of refinement tools to extract useful information from joint X-ray and neutron data and from mixed ground-state and excited-state X-ray data from pump-probe experiments.

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Literature
1.
go back to reference Brown PJ, Fox AG, Maslen EN, Keefe MA, Willis BTM (2006) Intensity of diffracted intensities. In: International tables for crystallography. International Union of Crystallography, pp 554–595 Brown PJ, Fox AG, Maslen EN, Keefe MA, Willis BTM (2006) Intensity of diffracted intensities. In: International tables for crystallography. International Union of Crystallography, pp 554–595
2.
go back to reference Sanjuan-Szklarz WF, Hoser AA, Gutmann M, Madsen AØ, Woźniak K (2016) Yes, one can obtain better quality structures from routine X-ray data collection. IUCrJ 3:61–70PubMedPubMedCentral Sanjuan-Szklarz WF, Hoser AA, Gutmann M, Madsen AØ, Woźniak K (2016) Yes, one can obtain better quality structures from routine X-ray data collection. IUCrJ 3:61–70PubMedPubMedCentral
3.
go back to reference Sheldrick GM (2015) Crystal structure refinement with SHELXL. Acta Crystallogr Sect C Struct Chem 71:3–8 Sheldrick GM (2015) Crystal structure refinement with SHELXL. Acta Crystallogr Sect C Struct Chem 71:3–8
4.
go back to reference Wilson AJC (1976) Statistical bias in least-squares refinement. Acta Crystallogr Sect A 32:994–996 Wilson AJC (1976) Statistical bias in least-squares refinement. Acta Crystallogr Sect A 32:994–996
5.
go back to reference Dominiak PM, Volkov A, Li X, Messerschmidt M, Coppens P (2007) A theoretical databank of transferable aspherical atoms and its application to electrostatic interaction energy calculations of macromolecules. J Chem Theory Comput 3:232–247PubMed Dominiak PM, Volkov A, Li X, Messerschmidt M, Coppens P (2007) A theoretical databank of transferable aspherical atoms and its application to electrostatic interaction energy calculations of macromolecules. J Chem Theory Comput 3:232–247PubMed
6.
go back to reference Fugel M et al (2017) Probing the accuracy and precision of hirshfeld atom refinement with HARt interfaced with Olex2. IUCrJ 5:32–44 Fugel M et al (2017) Probing the accuracy and precision of hirshfeld atom refinement with HARt interfaced with Olex2. IUCrJ 5:32–44
8.
go back to reference King MV, Lipscomb WN (1950) The X-ray scattering from a hindered rotator. Acta Crystallogr 3:155–158 King MV, Lipscomb WN (1950) The X-ray scattering from a hindered rotator. Acta Crystallogr 3:155–158
9.
go back to reference Reilly AM, Morrison CA, Rankin DWH, McLean KR (2011) Using molecular-dynamics simulations to understand and improve the treatment of anharmonic vibrations. II. Developing and assessing new Debye-Waller factors. Acta Crystallogr Sect A Found Crystallogr 67:346–356 Reilly AM, Morrison CA, Rankin DWH, McLean KR (2011) Using molecular-dynamics simulations to understand and improve the treatment of anharmonic vibrations. II. Developing and assessing new Debye-Waller factors. Acta Crystallogr Sect A Found Crystallogr 67:346–356
11.
go back to reference Binns J et al (2017) Phase transition sequences in tetramethylammonium tetrachlorometallates by X-ray diffraction and spectroscopic measurements. Acta Crystallogr Sect B Struct Sci Cryst Eng Mater 73:844–855 Binns J et al (2017) Phase transition sequences in tetramethylammonium tetrachlorometallates by X-ray diffraction and spectroscopic measurements. Acta Crystallogr Sect B Struct Sci Cryst Eng Mater 73:844–855
12.
go back to reference Bailey PJ et al (2010) A new synthesis of charge-neutral tris-pyrazolyl and -methimazolyl borate ligands. Chem Eur J 16:2819–2829PubMed Bailey PJ et al (2010) A new synthesis of charge-neutral tris-pyrazolyl and -methimazolyl borate ligands. Chem Eur J 16:2819–2829PubMed
13.
go back to reference Barrett ES, Irwin JL, Edwards AJ, Sherburn MS (2004) Superbowl container molecules. J Am Chem Soc 126:1 Barrett ES, Irwin JL, Edwards AJ, Sherburn MS (2004) Superbowl container molecules. J Am Chem Soc 126:1
14.
go back to reference Anderson E, Bai Z, Bischof J, Blackford S, Demmel J, Dongarra J, Du Croz J, Greenbaum A, Hammarling S, McKenney A, Sorensen D (1999) LAPACK users’ guide. Society for Industrial and Applied Mathematics, Philadelphia Anderson E, Bai Z, Bischof J, Blackford S, Demmel J, Dongarra J, Du Croz J, Greenbaum A, Hammarling S, McKenney A, Sorensen D (1999) LAPACK users’ guide. Society for Industrial and Applied Mathematics, Philadelphia
15.
go back to reference Wang Q, Zhang X, Zhang Y, Yi Q (2013) AUGEM: automatically generate high performance dense linear algebra kernels on x86 CPUs. In: International conference for high performance computing, networking, storage and analysis, SC, IEEE Computer Society. https://doi.org/10.1145/2503210.2503219 Wang Q, Zhang X, Zhang Y, Yi Q (2013) AUGEM: automatically generate high performance dense linear algebra kernels on x86 CPUs. In: International conference for high performance computing, networking, storage and analysis, SC, IEEE Computer Society. https://​doi.​org/​10.​1145/​2503210.​2503219
16.
go back to reference Wang E et al (2014) Intel math kernel library. In: High-performance computing on the Intel® Xeon PhiTM. Springer, Berlin, pp 167–188 Wang E et al (2014) Intel math kernel library. In: High-performance computing on the Intel® Xeon PhiTM. Springer, Berlin, pp 167–188
18.
go back to reference Spek AL (2015) Platon squeeze: a tool for the calculation of the disordered solvent contribution to the calculated structure factors. Acta Crystallogr Sect C Struct Chem 71:9–18 Spek AL (2015) Platon squeeze: a tool for the calculation of the disordered solvent contribution to the calculated structure factors. Acta Crystallogr Sect C Struct Chem 71:9–18
19.
go back to reference Frigo M, Johnson SG (2005) The design and implementation of FFTW3. In: Proceedings of the IEEE, pp 216–231 Frigo M, Johnson SG (2005) The design and implementation of FFTW3. In: Proceedings of the IEEE, pp 216–231
20.
go back to reference Coster D, Knol KS, Prins JA (1930) Unterschiede in der Intensität der Röntgenstrahlen-reflexion an den beiden 111-Flächen der Zinkblende. Z Phys 63:345–369 Coster D, Knol KS, Prins JA (1930) Unterschiede in der Intensität der Röntgenstrahlen-reflexion an den beiden 111-Flächen der Zinkblende. Z Phys 63:345–369
21.
go back to reference Hamilton WC (1965) Significance tests on the crystallographic R factor. Acta Crystallogr 18:502–510 Hamilton WC (1965) Significance tests on the crystallographic R factor. Acta Crystallogr 18:502–510
22.
go back to reference Rogers D (1981) On the application of Hamilton’s ratio test to the assignment of absolute configuration and an alternative test. Acta Crystallogr Sect A 37:734–741 Rogers D (1981) On the application of Hamilton’s ratio test to the assignment of absolute configuration and an alternative test. Acta Crystallogr Sect A 37:734–741
23.
go back to reference Flack HD (1983) On enantiomorph-polarity estimation. Acta Crystallogr Sect A 39:876–881 Flack HD (1983) On enantiomorph-polarity estimation. Acta Crystallogr Sect A 39:876–881
24.
go back to reference Flack HD, Bernardinelli G (2000) Reporting and evaluating absolute-structure and absolute-configuration determinations. J Appl Crystallogr 33:1143–1148 Flack HD, Bernardinelli G (2000) Reporting and evaluating absolute-structure and absolute-configuration determinations. J Appl Crystallogr 33:1143–1148
25.
go back to reference Cooper RI, Watkin DJ, Flack HD (2016) Absolute structure determination using CRYSTALS. Acta Crystallogr Sect C Struct Chem 72:261–267 Cooper RI, Watkin DJ, Flack HD (2016) Absolute structure determination using CRYSTALS. Acta Crystallogr Sect C Struct Chem 72:261–267
26.
go back to reference Parsons S, Flack HD, Wagner T (2013) Use of intensity quotients and differences in absolute structure refinement. Acta Crystallogr Sect B Struct Sci Cryst Eng Mater 69:249–259 Parsons S, Flack HD, Wagner T (2013) Use of intensity quotients and differences in absolute structure refinement. Acta Crystallogr Sect B Struct Sci Cryst Eng Mater 69:249–259
27.
go back to reference Cooper RI, Flack HD, Watkin DJ (2017) HUG and SQUEEZE: using CRYSTALS to incorporate resonant scattering in the SQUEEZE structure-factor contributions to determine absolute structure. Acta Crystallogr Sect C Struct Chem 73:845–853 Cooper RI, Flack HD, Watkin DJ (2017) HUG and SQUEEZE: using CRYSTALS to incorporate resonant scattering in the SQUEEZE structure-factor contributions to determine absolute structure. Acta Crystallogr Sect C Struct Chem 73:845–853
28.
go back to reference Brázda P, Palatinus L, Babor M (2019) Electron diffraction determines molecular absolute configuration in a pharmaceutical nanocrystal. Science (80-.) 364:667–669 Brázda P, Palatinus L, Babor M (2019) Electron diffraction determines molecular absolute configuration in a pharmaceutical nanocrystal. Science (80-.) 364:667–669
29.
go back to reference Waser J (1963) Least-squares refinement with subsidiary conditions. Acta Crystallogr 16:1091–1094 Waser J (1963) Least-squares refinement with subsidiary conditions. Acta Crystallogr 16:1091–1094
30.
go back to reference Hirshfeld FL (1976) Can X-ray data distinguish bonding effects from vibrational smearing? Acta Crystallogr Sect A 32:239–244 Hirshfeld FL (1976) Can X-ray data distinguish bonding effects from vibrational smearing? Acta Crystallogr Sect A 32:239–244
31.
go back to reference Thorn A, Dittrich B, Sheldrick GM (2012) Enhanced rigid-bond restraints. Acta Crystallogr Sect A Found Crystallogr 68:448–451 Thorn A, Dittrich B, Sheldrick GM (2012) Enhanced rigid-bond restraints. Acta Crystallogr Sect A Found Crystallogr 68:448–451
32.
go back to reference Parois P, Arnold J, Cooper R (2018) An enhanced set of displacement parameter restraints in CRYSTALS. J Appl Crystallogr 51:1059–1068 Parois P, Arnold J, Cooper R (2018) An enhanced set of displacement parameter restraints in CRYSTALS. J Appl Crystallogr 51:1059–1068
33.
go back to reference Schomaker V, Trueblood KN (1968) On the rigid-body motion of molecules in crystals. Acta Crystallogr Sect B Struct Crystallogr Cryst Chem 24:63–76 Schomaker V, Trueblood KN (1968) On the rigid-body motion of molecules in crystals. Acta Crystallogr Sect B Struct Crystallogr Cryst Chem 24:63–76
34.
go back to reference Madsen AØ (2006) SHADE web server for estimation of hydrogen anisotropic displacement parameters. J Appl Crystallogr 39:757–758 Madsen AØ (2006) SHADE web server for estimation of hydrogen anisotropic displacement parameters. J Appl Crystallogr 39:757–758
35.
go back to reference Marsh RE, Bernal I (1995) More space-group changes. Acta Crystallogr Sect B Struct Sci 51:300–307 Marsh RE, Bernal I (1995) More space-group changes. Acta Crystallogr Sect B Struct Sci 51:300–307
36.
go back to reference Marsh RE (2005) Space group P1: an update. Acta Crystallogr Sect B Struct Sci 61:359 Marsh RE (2005) Space group P1: an update. Acta Crystallogr Sect B Struct Sci 61:359
37.
go back to reference Harlow RL (1996) Troublesome crystal structures. Prevention, detection, and resolution. J Res Natl Inst Stand Technol 101:327PubMedPubMedCentral Harlow RL (1996) Troublesome crystal structures. Prevention, detection, and resolution. J Res Natl Inst Stand Technol 101:327PubMedPubMedCentral
38.
go back to reference Schwalbe CH (2018) Should we remediate small molecule structures? If so, who should do it? Crystallogr Rev 24:217–235 Schwalbe CH (2018) Should we remediate small molecule structures? If so, who should do it? Crystallogr Rev 24:217–235
39.
go back to reference Spek AL (2020) CheckCIF validation ALERTS: what they mean and how to respond. Acta Crystallogr Sect E Crystallogr Commun 76:1–11 Spek AL (2020) CheckCIF validation ALERTS: what they mean and how to respond. Acta Crystallogr Sect E Crystallogr Commun 76:1–11
40.
go back to reference Harrison WTA, Simpson J, Weil M (2010) Acta Crystallographica section E: structure reports online: editorial. Acta Crystallogr Sect E Struct Rep 66:1–2 Harrison WTA, Simpson J, Weil M (2010) Acta Crystallographica section E: structure reports online: editorial. Acta Crystallogr Sect E Struct Rep 66:1–2
41.
go back to reference Henn J, Meindl K (2015) Statistical tests against systematic errors in data sets based on the equality of residual means and variances from control samples: theory and applications. Acta Crystallogr Sect A Found Adv 71:203–211 Henn J, Meindl K (2015) Statistical tests against systematic errors in data sets based on the equality of residual means and variances from control samples: theory and applications. Acta Crystallogr Sect A Found Adv 71:203–211
42.
go back to reference Henn J, Meindl K (2014) About systematic errors in charge-density studies. Acta Crystallogr Sect A Found Adv 70:248–256 Henn J, Meindl K (2014) About systematic errors in charge-density studies. Acta Crystallogr Sect A Found Adv 70:248–256
43.
go back to reference Meindl K, Henn J (2008) Foundations of residual-density analysis. Acta Crystallogr Sect A Found Crystallogr 64:404–418 Meindl K, Henn J (2008) Foundations of residual-density analysis. Acta Crystallogr Sect A Found Crystallogr 64:404–418
44.
go back to reference Prince E (2004) Mathematical techniques in crystallography and materials science. Springer, Berlin Prince E (2004) Mathematical techniques in crystallography and materials science. Springer, Berlin
45.
go back to reference Prince E, Nicholson WL (1985) In: Wilson AJC (ed) Structure & statistics in crystallography: proceedings of the Symposium on Crystallographic Statistics, held in Hamburg, West Germany in August, 1984 in the course of the Thirteenth International Congress of the International Union of Crystallography, A. J. C. Adenine Press Prince E, Nicholson WL (1985) In: Wilson AJC (ed) Structure & statistics in crystallography: proceedings of the Symposium on Crystallographic Statistics, held in Hamburg, West Germany in August, 1984 in the course of the Thirteenth International Congress of the International Union of Crystallography, A. J. C. Adenine Press
46.
go back to reference Wilson CC, Morrison CA (2002) Structural and theoretical investigations of short hydrogen bonds: neutron diffraction and plane-wave DFT calculations of urea-phosphoric acid. Chem Phys Lett 362:85–89 Wilson CC, Morrison CA (2002) Structural and theoretical investigations of short hydrogen bonds: neutron diffraction and plane-wave DFT calculations of urea-phosphoric acid. Chem Phys Lett 362:85–89
48.
go back to reference Deringer VL et al (2014) Ab initio ORTEP drawings: a case study of N-based molecular crystals with different chemical nature. CrystEngComm 16:10907–10915 Deringer VL et al (2014) Ab initio ORTEP drawings: a case study of N-based molecular crystals with different chemical nature. CrystEngComm 16:10907–10915
49.
go back to reference Van De Streek J, Neumann MA (2010) Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations. Acta Crystallogr Sect B Struct Sci 66:544–558 Van De Streek J, Neumann MA (2010) Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations. Acta Crystallogr Sect B Struct Sci 66:544–558
50.
go back to reference Kyriacou A et al (2013) Combined X-ray and neutron diffraction Rietveld refinement in iron-substituted nano-hydroxyapatite. J Mater Sci 48:3535–3545 Kyriacou A et al (2013) Combined X-ray and neutron diffraction Rietveld refinement in iron-substituted nano-hydroxyapatite. J Mater Sci 48:3535–3545
51.
go back to reference Liu H et al (2017) Sensitivity and limitations of structures from X-ray and neutron-based diffraction analyses of transition metal oxide lithium-battery electrodes. J Electrochem Soc 164:A1802–A1811 Liu H et al (2017) Sensitivity and limitations of structures from X-ray and neutron-based diffraction analyses of transition metal oxide lithium-battery electrodes. J Electrochem Soc 164:A1802–A1811
52.
go back to reference Il Kim Y, Jeon MK (2004) Combined structural refinement of Bi4Ti3O 12 using X-ray and neutron powder diffraction data. Mater Lett 58:1889–1893 Il Kim Y, Jeon MK (2004) Combined structural refinement of Bi4Ti3O 12 using X-ray and neutron powder diffraction data. Mater Lett 58:1889–1893
53.
go back to reference Petrícek V, Dušek M, Palatinus L (2014) Crystallographic computing system JANA2006: general features. Zeitschrift fur Krist 229:345–352 Petrícek V, Dušek M, Palatinus L (2014) Crystallographic computing system JANA2006: general features. Zeitschrift fur Krist 229:345–352
54.
go back to reference Coelho AA (2018) TOPAS and TOPAS-academic: an optimization program integrating computer algebra and crystallographic objects written in C++: an. J Appl Crystallogr 51:210–218 Coelho AA (2018) TOPAS and TOPAS-academic: an optimization program integrating computer algebra and crystallographic objects written in C++: an. J Appl Crystallogr 51:210–218
55.
go back to reference Toby BH, Von Dreele RB (2013) GSAS-II: the genesis of a modern open-source all purpose crystallography software package. J Appl Crystallogr 46:544–549 Toby BH, Von Dreele RB (2013) GSAS-II: the genesis of a modern open-source all purpose crystallography software package. J Appl Crystallogr 46:544–549
56.
go back to reference Grzechnik A, Meven M, Paulmann C, Friese K (2020) Combined X-ray and neutron single-crystal diffraction in diamond anvil cells. J Appl Crystallogr 53:9–14PubMedPubMedCentral Grzechnik A, Meven M, Paulmann C, Friese K (2020) Combined X-ray and neutron single-crystal diffraction in diamond anvil cells. J Appl Crystallogr 53:9–14PubMedPubMedCentral
Metadata
Title
Recent Developments in the Refinement and Analysis of Crystal Structures
Author
Richard I. Cooper
Copyright Year
2020
DOI
https://doi.org/10.1007/430_2020_76

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