简介
Summary:
Publisher Summary 1
Crystal Structure Refinement is a mixture of textbook and tutorial. As A Crystallographers Guide to SHELXL it covers advanced aspects of practical crystal structure refinement, which have not been much addressed by textbooks so far. After an introduction to SHELXL in the first chapter, a brief survey of crystal structure refinement is provided. Chapters three and higher address the various aspects of structure refinement, from the treatment of hydrogen atoms to the assignment of atom types, to disorder, to non-crystallographic symmetry and twinning. One chapter is dedicated to the refinement of macromolecular structures and two short chapters deal with structure validation (one for small molecule structures and one for macromolecules). In each of the chapters the book gives refinement examples, based on the program SHELXL, describing every problem in detail. It comes with a CD-ROM with all files necessary to reproduce the refinements.
目录
Table Of Contents:
1 SHELXL 1(6)
Peter M眉ller
1.1 The SHELX program suite 1(2)
1.1.1 SHELXTL and other programs 1(2)
1.2 SHELXL 3(5)
1.2.1 Program organization 3(1)
1.2.2 The instruction file name.ins 4(1)
1.2.3 The reflection data file name.hkl 5(1)
1.2.4 Merging data in SHELXL 5(1)
1.2.5 The connectivity table 6(1)
2 Crystal structure refinement 7(19)
Peter M眉ller
2.1 Least-squares refinement 8(1)
2.1.1 Refinement against F or F虏鈥攊s that a question? 9(1)
2.2 Weak data and high-resolution cut-off 9(2)
2.3 Residual factors 11(1)
2.4 Parameters 12(1)
2.5 Constraints 13(3)
2.5.1 Site occupancy factors 13(1)
2.5.2 Special position constraints 13(1)
2.5.3 Rigid group constraints 14(1)
2.5.4 Floating origin constraints 15(1)
2.5.5 Hydrogen atoms 15(1)
2.5.6 Constraints in SHELXL 15(1)
2.6 Restraints 16(6)
2.6.1 Geometrical restraints 17(2)
2.6.2 Restraints on displacement parameters 19(2)
2.6.3 Other restraints 21(1)
2.7 Free variables in SHELXL 22(1)
2.8 Results 23(2)
2.8.1 Bond lengths and angles 23(1)
2.8.2 Torsion angles 23(1)
2.8.3 Atoms on common planes 24(1)
2.8.4 Hydrogen bonds 24(1)
2.8.5 The RTAB command 24(1)
2.8.6 The MORE command 25(1)
2.8.7 The .cif file 25(1)
2.9 Refinement problems 25(1)
3 Hydrogen atoms 26(16)
Peter M眉ller
3.1 X鈥擧 bond lengths and Ueq values of H atoms 26(1)
3.2 Hydrogen bound to different atom types 27(2)
3.2.1 Hydrogen bound to carbon atoms 27(1)
3.2.2 Hydrogen bound to nitrogen and oxygen 28(1)
3.2.3 Hydrogen bound to metals 29(1)
3.3 Placing hydrogen atoms in SHELXL 29(3)
3.3.1 List of most common m and n values in HFIX commands 30(1)
3.3.2 Semi free refinement of acidic hydrogen atoms 31(1)
3.4 Hydrogen bonds in SHELXL 32(1)
3.5 Examples 32(10)
3.5.1 Routine hydrogen atom placement: C31H54MON2O2 32(3)
3.5.2 Hydrogen atoms in a Zr-hydride 35(2)
3.5.3 Acidic hydrogen atoms and hydrogen bonds 37(5)
4 Atom type assignment 42(14)
Peter M眉ller
4.1 All electrons are blue 42(1)
4.2 Chemical knowledge 43(1)
4.3 Crystallographic knowledge 43(2)
4.4 Examples 45(12)
4.4.1 Tetrameric InCl3鈥攖he N or O question 45(3)
4.4.2 A cobalt salt 48(2)
4.4.3 Unclear central metal atom 50(6)
5 Disorder 56(41)
Peter M眉ller
5.1 Types of disorder 57(2)
5.1.1 Substitutional disorder 57(1)
5.1.2 Positional disorder 58(1)
5.1.3 Mess鈥攁 special case of disorder 59(1)
5.2 Refinement of disorder 59(8)
5.2.1 Refinement of disorder with SHELXL 59(8)
5.3 Examples 67(31)
5.3.1 Gallium-iminosilicate鈥擠isorder of two ethyl groups 68(5)
5.3.2 Disorder of a Ti(III) compound 73(7)
5.3.3 A mixed crystal treated as occupancy disorder 80(1)
5.3.4 Disorder of solvent molecules 81(10)
5.3.5 Three types of disorder in one structure: cycloikositetraphenylene 91(6)
6 Pseudo-Symmetry 97(9)
Peter M眉ller
6.1 Global pseudo-symmetry 98(1)
6.2 True NCS 98(1)
6.3 Examples 99(7)
6.3.1 Pn or P21/n 99(4)
6.3.2 [Si(NH2)2CH(SiMe3)2]2: P1 with Z = 12 103(3)
7 Twinning 106(44)
Regine Herbst-Irmer
7.1 Definition of a Twin 106(3)
7.2 Classification of twins 109(9)
7.2.1 Twinning by merohedry 109(2)
7.2.2 Twinning by pseudo-merohedry 111(1)
7.2.3 Twinning by reticular merohedry 112(2)
7.2.4 Non-merohedral twins 114(4)
7.3 Tests for twinning 118(1)
7.4 Structure solution 119(1)
7.5 Twin refinement 120(1)
7.6 Determination of the absolute structure 121(1)
7.7 Warning signs of twinning 121(1)
7.8 Examples 122(27)
7.8.1 Twinning by merohedry 122(5)
7.8.2 An example of pseudo-merohedral twinning 127(3)
7.8.3 First example of twinning by reticular merohedry 130(3)
7.8.4 Second example of twinning by reticular merohedry 133(7)
7.8.5 First example of non-merohedral twinning 140(4)
7.8.6 Second example of non-merohedral twinning 144(5)
7.9 Conclusions 149(1)
8 Artefacts 150(9)
Peter M眉ller
8.1 What is an Artefact? 150(4)
8.1.1 Libration 151(1)
8.1.2 Shortened triple bonds 152(1)
8.1.3 Hydrogen positions 153(1)
8.1.4 Fourier truncation errors 153(1)
8.2 What is not an artefact? 154(1)
8.3 Example 154(6)
8.3.1 Fourier termination error in C3OH47N9Zr5 154(5)
9 Structure validation 159(7)
Anthony L. Spek
9.1 Validation 160(1)
9.2 Validation tests implemented in PLATON 161(3)
9.2.1 Missed symmetry 161(1)
9.2.2 Voids 161(1)
9.2.3 Displacement ellipsoids 162(1)
9.2.4 Bond lengths and angles 162(1)
9.2.5 Atom type assignment 162(1)
9.2.6 Intermolecular contacts 163(1)
9.2.7 Hydrogen bonds 163(1)
9.2.8 Connectivity 163(1)
9.2.9 Disorder 163(1)
9.2.10 Reflection data 164(1)
9.2.11 Refinement parameters 164(1)
9.3 When to validate 164(1)
9.4 Concluding remarks 164(2)
10 Protein refinement 166(21)
Thomas R. Schneider
10.1 Atomic resolution refinement vs. standard refinement 168(3)
10.1.1 Anisotropic displacement parameters 168(1)
10.1.2 Multiple discrete sites 169(1)
10.1.3 Hydrogens 169(1)
10.1.4 Solvent 170(1)
10.1.5 Standard uncertainties 170(1)
10.2 Stages of a typical refinement 171(13)
10.2.1 Getting started 171(1)
10.2.2 Rough adjustments of the model at 1.5 脜 172(1)
10.2.3 Including data to atomic resolution 173(1)
10.2.4 Going anisotropic 174(1)
10.2.5 Rebuilding the model at atomic resolution 174(4)
10.2.6 Inclusion of hydrogens鈥攚hen and how 178(1)
10.2.7 Solvent 179(1)
10.2.8 Finalizing the model 180(2)
10.2.9 Estimation of coordinate uncertainties 182(1)
10.2.10 Analysis and presentation of the structure 183(1)
10.3 Examples 184(4)
10.3.1 Course of a typical refinement of a protein 184(1)
10.3.2 Determination of standard uncertainties for protein-ligand contacts 185(2)
11 Protein structure (cross) validation 187(10)
Michael R. Sawaya
11.1 PROCHECK 188(3)
11.2 WHAT_CHECK 191(2)
11.2.1 List of close non-bonded contacts 191(1)
11.2.2 Unsatisfied hydrogen bond donors/acceptors 192(1)
11.2.3 List of isolated water molecules 193(1)
11.3 Verify3D 193(1)
11.4 Errat 194(1)
11.5 Prove 195(2)
12 General remarks 197(7)
Peter M眉ller
12.1 How many refinement cycles do I need? 197(1)
12.2 What to do with NPD atoms? 197(1)
12.3 How many restraints may I use in a structure? 198(1)
12.4 Coordination geometries of some cations 199(2)
12.5 Some typical bond lengths 201(1)
12.6 Resolution tables 202(2)
References 204(5)
Further Reading 209(2)
Index 211
1 SHELXL 1(6)
Peter M眉ller
1.1 The SHELX program suite 1(2)
1.1.1 SHELXTL and other programs 1(2)
1.2 SHELXL 3(5)
1.2.1 Program organization 3(1)
1.2.2 The instruction file name.ins 4(1)
1.2.3 The reflection data file name.hkl 5(1)
1.2.4 Merging data in SHELXL 5(1)
1.2.5 The connectivity table 6(1)
2 Crystal structure refinement 7(19)
Peter M眉ller
2.1 Least-squares refinement 8(1)
2.1.1 Refinement against F or F虏鈥攊s that a question? 9(1)
2.2 Weak data and high-resolution cut-off 9(2)
2.3 Residual factors 11(1)
2.4 Parameters 12(1)
2.5 Constraints 13(3)
2.5.1 Site occupancy factors 13(1)
2.5.2 Special position constraints 13(1)
2.5.3 Rigid group constraints 14(1)
2.5.4 Floating origin constraints 15(1)
2.5.5 Hydrogen atoms 15(1)
2.5.6 Constraints in SHELXL 15(1)
2.6 Restraints 16(6)
2.6.1 Geometrical restraints 17(2)
2.6.2 Restraints on displacement parameters 19(2)
2.6.3 Other restraints 21(1)
2.7 Free variables in SHELXL 22(1)
2.8 Results 23(2)
2.8.1 Bond lengths and angles 23(1)
2.8.2 Torsion angles 23(1)
2.8.3 Atoms on common planes 24(1)
2.8.4 Hydrogen bonds 24(1)
2.8.5 The RTAB command 24(1)
2.8.6 The MORE command 25(1)
2.8.7 The .cif file 25(1)
2.9 Refinement problems 25(1)
3 Hydrogen atoms 26(16)
Peter M眉ller
3.1 X鈥擧 bond lengths and Ueq values of H atoms 26(1)
3.2 Hydrogen bound to different atom types 27(2)
3.2.1 Hydrogen bound to carbon atoms 27(1)
3.2.2 Hydrogen bound to nitrogen and oxygen 28(1)
3.2.3 Hydrogen bound to metals 29(1)
3.3 Placing hydrogen atoms in SHELXL 29(3)
3.3.1 List of most common m and n values in HFIX commands 30(1)
3.3.2 Semi free refinement of acidic hydrogen atoms 31(1)
3.4 Hydrogen bonds in SHELXL 32(1)
3.5 Examples 32(10)
3.5.1 Routine hydrogen atom placement: C31H54MON2O2 32(3)
3.5.2 Hydrogen atoms in a Zr-hydride 35(2)
3.5.3 Acidic hydrogen atoms and hydrogen bonds 37(5)
4 Atom type assignment 42(14)
Peter M眉ller
4.1 All electrons are blue 42(1)
4.2 Chemical knowledge 43(1)
4.3 Crystallographic knowledge 43(2)
4.4 Examples 45(12)
4.4.1 Tetrameric InCl3鈥攖he N or O question 45(3)
4.4.2 A cobalt salt 48(2)
4.4.3 Unclear central metal atom 50(6)
5 Disorder 56(41)
Peter M眉ller
5.1 Types of disorder 57(2)
5.1.1 Substitutional disorder 57(1)
5.1.2 Positional disorder 58(1)
5.1.3 Mess鈥攁 special case of disorder 59(1)
5.2 Refinement of disorder 59(8)
5.2.1 Refinement of disorder with SHELXL 59(8)
5.3 Examples 67(31)
5.3.1 Gallium-iminosilicate鈥擠isorder of two ethyl groups 68(5)
5.3.2 Disorder of a Ti(III) compound 73(7)
5.3.3 A mixed crystal treated as occupancy disorder 80(1)
5.3.4 Disorder of solvent molecules 81(10)
5.3.5 Three types of disorder in one structure: cycloikositetraphenylene 91(6)
6 Pseudo-Symmetry 97(9)
Peter M眉ller
6.1 Global pseudo-symmetry 98(1)
6.2 True NCS 98(1)
6.3 Examples 99(7)
6.3.1 Pn or P21/n 99(4)
6.3.2 [Si(NH2)2CH(SiMe3)2]2: P1 with Z = 12 103(3)
7 Twinning 106(44)
Regine Herbst-Irmer
7.1 Definition of a Twin 106(3)
7.2 Classification of twins 109(9)
7.2.1 Twinning by merohedry 109(2)
7.2.2 Twinning by pseudo-merohedry 111(1)
7.2.3 Twinning by reticular merohedry 112(2)
7.2.4 Non-merohedral twins 114(4)
7.3 Tests for twinning 118(1)
7.4 Structure solution 119(1)
7.5 Twin refinement 120(1)
7.6 Determination of the absolute structure 121(1)
7.7 Warning signs of twinning 121(1)
7.8 Examples 122(27)
7.8.1 Twinning by merohedry 122(5)
7.8.2 An example of pseudo-merohedral twinning 127(3)
7.8.3 First example of twinning by reticular merohedry 130(3)
7.8.4 Second example of twinning by reticular merohedry 133(7)
7.8.5 First example of non-merohedral twinning 140(4)
7.8.6 Second example of non-merohedral twinning 144(5)
7.9 Conclusions 149(1)
8 Artefacts 150(9)
Peter M眉ller
8.1 What is an Artefact? 150(4)
8.1.1 Libration 151(1)
8.1.2 Shortened triple bonds 152(1)
8.1.3 Hydrogen positions 153(1)
8.1.4 Fourier truncation errors 153(1)
8.2 What is not an artefact? 154(1)
8.3 Example 154(6)
8.3.1 Fourier termination error in C3OH47N9Zr5 154(5)
9 Structure validation 159(7)
Anthony L. Spek
9.1 Validation 160(1)
9.2 Validation tests implemented in PLATON 161(3)
9.2.1 Missed symmetry 161(1)
9.2.2 Voids 161(1)
9.2.3 Displacement ellipsoids 162(1)
9.2.4 Bond lengths and angles 162(1)
9.2.5 Atom type assignment 162(1)
9.2.6 Intermolecular contacts 163(1)
9.2.7 Hydrogen bonds 163(1)
9.2.8 Connectivity 163(1)
9.2.9 Disorder 163(1)
9.2.10 Reflection data 164(1)
9.2.11 Refinement parameters 164(1)
9.3 When to validate 164(1)
9.4 Concluding remarks 164(2)
10 Protein refinement 166(21)
Thomas R. Schneider
10.1 Atomic resolution refinement vs. standard refinement 168(3)
10.1.1 Anisotropic displacement parameters 168(1)
10.1.2 Multiple discrete sites 169(1)
10.1.3 Hydrogens 169(1)
10.1.4 Solvent 170(1)
10.1.5 Standard uncertainties 170(1)
10.2 Stages of a typical refinement 171(13)
10.2.1 Getting started 171(1)
10.2.2 Rough adjustments of the model at 1.5 脜 172(1)
10.2.3 Including data to atomic resolution 173(1)
10.2.4 Going anisotropic 174(1)
10.2.5 Rebuilding the model at atomic resolution 174(4)
10.2.6 Inclusion of hydrogens鈥攚hen and how 178(1)
10.2.7 Solvent 179(1)
10.2.8 Finalizing the model 180(2)
10.2.9 Estimation of coordinate uncertainties 182(1)
10.2.10 Analysis and presentation of the structure 183(1)
10.3 Examples 184(4)
10.3.1 Course of a typical refinement of a protein 184(1)
10.3.2 Determination of standard uncertainties for protein-ligand contacts 185(2)
11 Protein structure (cross) validation 187(10)
Michael R. Sawaya
11.1 PROCHECK 188(3)
11.2 WHAT_CHECK 191(2)
11.2.1 List of close non-bonded contacts 191(1)
11.2.2 Unsatisfied hydrogen bond donors/acceptors 192(1)
11.2.3 List of isolated water molecules 193(1)
11.3 Verify3D 193(1)
11.4 Errat 194(1)
11.5 Prove 195(2)
12 General remarks 197(7)
Peter M眉ller
12.1 How many refinement cycles do I need? 197(1)
12.2 What to do with NPD atoms? 197(1)
12.3 How many restraints may I use in a structure? 198(1)
12.4 Coordination geometries of some cations 199(2)
12.5 Some typical bond lengths 201(1)
12.6 Resolution tables 202(2)
References 204(5)
Further Reading 209(2)
Index 211
- 名称
- 类型
- 大小
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