Keywords:
Crystals -- Structure.
;
Crystals -- Refining.
;
Crystals -- Data processing.
;
Electronic books.
Description / Table of Contents:
This book is a mixture of textbook and tutorial. As Guide to SHELXL it covers advanced aspects of practical crystal structure refinement, which have not been addressed by textbooks so far. In each of the chapters the book gives examples, describing every problem in detail. It comes with a CD-ROM with all files necessary to reproduce the refinements.
Type of Medium:
Online Resource
Pages:
1 online resource (232 pages)
Edition:
1st ed.
ISBN:
9780191524769
Series Statement:
International Union of Crystallography Texts on Crystallography Series ; v.8
URL:
https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=430346
DDC:
548.81
Language:
English
Note:
Intro -- Contents -- 1 SHELXL -- 1.1 The SHELX program suite -- 1.1.1 SHELXTL and other programs -- 1.2 SHELXL -- 1.2.1 Program organization -- 1.2.2 The instruction file name.ins -- 1.2.3 The reflection data file name.hkl -- 1.2.4 Merging data in SHELXL -- 1.2.5 The connectivity table -- 2 Crystal structure refinement -- 2.1 Least-squares refinement -- 2.1.1 Refinement against F or F[sup(2)]-is that a question? -- 2.2 Weak data and high-resolution cut-off -- 2.3 Residual factors -- 2.4 Parameters -- 2.5 Constraints -- 2.5.1 Site occupancy factors -- 2.5.2 Special position constraints -- 2.5.3 Rigid group constraints -- 2.5.4 Floating origin constraints -- 2.5.5 Hydrogen atoms -- 2.5.6 Constraints in SHELXL -- 2.6 Restraints -- 2.6.1 Geometrical restraints -- 2.6.2 Restraints on displacement parameters -- 2.6.3 Other restraints -- 2.7 Free variables in SHELXL -- 2.8 Results -- 2.8.1 Bond lengths and angles -- 2.8.2 Torsion angles -- 2.8.3 Atoms on common planes -- 2.8.4 Hydrogen bonds -- 2.8.5 The RTAB command -- 2.8.6 The MORE command -- 2.8.7 The .cif file -- 2.9 Refinement problems -- 3 Hydrogen atoms -- 3.1 X--H bond lengths and U[sub(eq)] values of H atoms -- 3.2 Hydrogen bound to different atom types -- 3.2.1 Hydrogen bound to carbon atoms -- 3.2.2 Hydrogen bound to nitrogen and oxygen -- 3.2.3 Hydrogen bound to metals -- 3.3 Placing hydrogen atoms in SHELXL -- 3.3.1 List of most common m and n values in HFIX commands -- 3.3.2 Semi-free refinement of acidic hydrogen atoms -- 3.4 Hydrogen bonds in SHELXL -- 3.5 Examples -- 3.5.1 Routine hydrogen atom placement: C[sub(31)]H[sub(54)]MoN[sub(2)]O[sub(2)] -- 3.5.2 Hydrogen atoms in a Zr-hydride -- 3.5.3 Acidic hydrogen atoms and hydrogen bonds -- 4 Atom type assignment -- 4.1 All electrons are blue -- 4.2 Chemical knowledge -- 4.3 Crystallographic knowledge -- 4.4 Examples.
,
4.4.1 Tetrameric InCl[sub(3)]-the N or O question -- 4.4.2 A cobalt salt -- 4.4.3 Unclear central metal atom -- 5 Disorder -- 5.1 Types of disorder -- 5.1.1 Substitutional disorder -- 5.1.2 Positional disorder -- 5.1.3 Mess-a special case of disorder -- 5.2 Refinement of disorder -- 5.2.1 Refinement of disorder with SHELXL -- 5.3 Examples -- 5.3.1 Gallium-iminosilicate-Disorder of two ethyl groups -- 5.3.2 Disorder of a Ti(III) compound -- 5.3.3 A mixed crystal treated as occupancy disorder -- 5.3.4 Disorder of solvent molecules -- 5.3.5 Three types of disorder in one structure: cycloikositetraphenylene -- 6 Pseudo-Symmetry -- 6.1 Global pseudo-symmetry -- 6.2 True NCS -- 6.3 Examples -- 6.3.1 Pn or P2[sub(1)]/n -- 6.3.2 [Si(NH[sub(2)])[sub(2)]CH(SiMe[sub(3)])[sub(2)]][sub(2)]: P1 with Z = 12 -- 7 Twinning -- 7.1 Definition of a Twin -- 7.2 Classification of twins -- 7.2.1 Twinning by merohedry -- 7.2.2 Twinning by pseudo-merohedry -- 7.2.3 Twinning by reticular merohedry -- 7.2.4 Non-merohedral twins -- 7.3 Tests for twinning -- 7.4 Structure solution -- 7.5 Twin refinement -- 7.6 Determination of the absolute structure -- 7.7 Warning signs of twinning -- 7.8 Examples -- 7.8.1 Twinning by merohedry -- 7.8.2 An example of pseudo-merohedral twinning -- 7.8.3 First example of twinning by reticular merohedry -- 7.8.4 Second example of twinning by reticular merohedry -- 7.8.5 First example of non-merohedral twinning -- 7.8.6 Second example of non-merohedral twinning -- 7.9 Conclusions -- 8 Artefacts -- 8.1 What is an Artefact? -- 8.1.1 Libration -- 8.1.2 Shortened triple bonds -- 8.1.3 Hydrogen positions -- 8.1.4 Fourier truncation errors -- 8.2 What is not an artefact? -- 8.3 Example -- 8.3.1 Fourier termination error in C[sub(30)]H[sub(47)]N[sub(9)]Zr[sub(5)] -- 9 Structure validation -- 9.1 Validation -- 9.2 Validation tests implemented in PLATON.
,
9.2.1 Missed symmetry -- 9.2.2 Voids -- 9.2.3 Displacement ellipsoids -- 9.2.4 Bond lengths and angles -- 9.2.5 Atom type assignment -- 9.2.6 Intermolecular contacts -- 9.2.7 Hydrogen bonds -- 9.2.8 Connectivity -- 9.2.9 Disorder -- 9.2.10 Reflection data -- 9.2.11 Refinement parameters -- 9.3 When to validate -- 9.4 Concluding remarks -- 10 Protein refinement -- 10.1 Atomic resolution refinement vs. standard refinement -- 10.1.1 Anisotropic displacement parameters -- 10.1.2 Multiple discrete sites -- 10.1.3 Hydrogens -- 10.1.4 Solvent -- 10.1.5 Standard uncertainties -- 10.2 Stages of a typical refinement -- 10.2.1 Getting started -- 10.2.2 Rough adjustments of the model at 1.5 Å -- 10.2.3 Including data to atomic resolution -- 10.2.4 Going anisotropic -- 10.2.5 Rebuilding the model at atomic resolution -- 10.2.6 Inclusion of hydrogens-when and how -- 10.2.7 Solvent -- 10.2.8 Finalizing the model -- 10.2.9 Estimation of coordinate uncertainties -- 10.2.10 Analysis and presentation of the structure -- 10.3 Examples -- 10.3.1 Course of a typical refinement of a protein -- 10.3.2 Determination of standard uncertainties for protein-ligand contacts -- 11 Protein structure (cross) validation -- 11.1 PROCHECK -- 11.2 WHAT_CHECK -- 11.2.1 List of close non-bonded contacts -- 11.2.2 Unsatisfied hydrogen bond donors/acceptors -- 11.2.3 List of isolated water molecules -- 11.3 Verify3D -- 11.4 Errat -- 11.5 Prove -- 12 General remarks -- 12.1 How many refinement cycles do I need? -- 12.2 What to do with NPD atoms? -- 12.3 How many restraints may I use in a structure? -- 12.4 Coordination geometries of some cations -- 12.5 Some typical bond lengths -- 12.6 Resolution tables -- References -- Further Reading -- Index -- A -- B -- C -- D -- E -- F -- G -- H -- I -- K -- L -- M -- N -- O -- P -- R -- S -- T -- U -- V -- W -- X.
Permalink