Crystallographic computing system Jana2006: solution and refinement of twinned structures
Authors:Petricek, Vaclav; Dusek, Michal; Plasil, Jakub
Journal:Zeitschrift fur Kristallographie 231 583-599 (2016)
DOI:https://doi.org/10.1515/zkri-2016-1956
B-IncStrDB ID: EKtyCQwKHWX Entry date: 2021-12-16 Last revision: 2022-02-12
I
Chemical data
Structural Formula Sum: C10 H16 Cl1 N1 O1 [ Help ]
Formula weight: 201.7 Da [ Help ]
Crystallographic data and experimental details
Crystal system: orthorhombic [ Help ]
Superspace group name: P212121(00γ)000 [ Help ]
Symmetry operations of the superspace group: (Show/hide table) [ Help ]
| Operation code | Operation in algebraic form |
|---|---|
| 1 | x1,x2,x3,x4 |
| 2 | -x1+1/2,-x2,x3+1/2,x4 |
| 3 | -x1,x2+1/2,-x3+1/2,-x4 |
| 4 | x1+1/2,-x2+1/2,-x3,-x4 |
a: 6.8345(4) Å [ Help ]
b: 24.7743(13) Å [ Help ]
c: 6.4271(13) Å [ Help ]
α: 90 ° [ Help ]
β: 90 ° [ Help ]
γ: 90 ° [ Help ]
Volume: 1088.2(2) Å3 [ Help ]
Modulation dimension: 1 [ Help ]
Measured independent wave vectors: (Show/hide table) [ Help ]
| Wave vector id | q_x | q_y | q_z |
|---|---|---|---|
| 1 | 0.000000 | 0.000000 | 0.250000 |
Z: 4 [ Help ]
Cell measurement temperature: 293 K [ Help ]
μ: 0.314 mm-1 [ Help ]
Refinement details
Total nb. of reflections: 9621 [ Help ]
Nb. of observed reflections: 8699 [ Help ]
Intense reflections threshold: I>3σ(I) [ Help ]
Refinement based on: F [ Help ]
R(obs): 0.0376 [ Help ]
wR(obs): 0.0522 [ Help ]
R(all): 0.0419 [ Help ]
wR(all): 0.0525 [ Help ]
S(all): 2.8385 [ Help ]
S(obs): 2.9706 [ Help ]
Nb. of reflections: 9621 [ Help ]
Nb. of parameters: 206 [ Help ]
Number of restraints: 0 [ Help ]
Number of constraints: 151 [ Help ]
Weighting scheme: sigma [ Help ]
Weighting scheme remarks: w=1/(σ2(F)+0.0001F2) [ Help ]
Refinement of hydrogen atoms: mixed [ Help ]
Δ/σ(max): 0.0179 [ Help ]
Δ/σ(mean): 0.0015 [ Help ]
Δρ(max): 0.36 e_Å-3 [ Help ]
Δρ(min): -0.34 e_Å-3 [ Help ]
Extinction method: none [ Help ]
Absolute structure remarks: 4196 of Friedel pairs used in the refinement [ Help ]
Structural Information
Average Structure: (Show/hide table) [ Help ]
| Atom site label | Atom symbol | x | y | z | ADP type | Uiso/equiv | Symmetry multiplicity | Occupancy | Coords from (d)iffraction or (c)alculated | Coords restraints or constraints | Disordered cluster | Disordered group |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cl1 | Cl | 0.22262(4) | 0.823905(9) | 0.16306(4) | Uani | 0.02049(7) | 4 | 1 | d | . | . | . |
| O1 | O | 0.07436(11) | 0.68608(3) | 0.14719(13) | Uani | 0.0240(2) | 4 | 1 | d | . | . | . |
| N1 | N | 0.45581(12) | 0.71241(3) | 0.20254(13) | Uani | 0.0178(2) | 4 | 1 | d | . | . | . |
| C1 | C | 0.02317(15) | 0.59791(4) | 0.46538(16) | Uani | 0.0211(3) | 4 | 1 | d | . | . | . |
| C2 | C | 0.37556(15) | 0.66195(4) | 0.30208(16) | Uani | 0.0175(3) | 4 | 1 | d | . | . | . |
| C3 | C | 0.60756(15) | 0.74066(4) | 0.32854(18) | Uani | 0.0207(3) | 4 | 1 | d | . | . | . |
| C4 | C | 0.20550(14) | 0.64153(4) | 0.16832(17) | Uani | 0.0192(3) | 4 | 1 | d | . | . | . |
| C5 | C | 0.53663(15) | 0.62035(4) | 0.32956(18) | Uani | 0.0216(3) | 4 | 1 | d | . | . | . |
| C6 | C | 0.10799(15) | 0.59313(4) | 0.26899(16) | Uani | 0.0187(3) | 4 | 1 | d | . | . | . |
| C7 | C | -0.06888(16) | 0.50450(4) | 0.45776(18) | Uani | 0.0280(3) | 4 | 1 | d | . | . | . |
| C8 | C | -0.06448(16) | 0.55395(4) | 0.55919(18) | Uani | 0.0247(3) | 4 | 1 | d | . | . | . |
| C9 | C | 0.01577(17) | 0.49948(4) | 0.26458(18) | Uani | 0.0293(3) | 4 | 1 | d | . | . | . |
| C10 | C | 0.10340(16) | 0.54359(4) | 0.16934(18) | Uani | 0.0248(3) | 4 | 1 | d | . | . | . |
| H1c1 | H | 0.025704 | 0.631986 | 0.535918 | Uiso | 0.0253 | 4 | 1 | d | . | . | . |
| H1c2 | H | 0.326712 | 0.669306 | 0.439063 | Uiso | 0.0211 | 4 | 1 | d | . | . | . |
| H1c3 | H | 0.641048 | 0.774189 | 0.262824 | Uiso | 0.0248 | 4 | 1 | d | . | . | . |
| H2c3 | H | 0.557308 | 0.747615 | 0.46537 | Uiso | 0.0248 | 4 | 1 | d | . | . | . |
| H3c3 | H | 0.722031 | 0.718369 | 0.338555 | Uiso | 0.0248 | 4 | 1 | d | . | . | . |
| H1c4 | H | 0.248864 | 0.629376 | 0.034377 | Uiso | 0.0231 | 4 | 1 | d | . | . | . |
| H1c5 | H | 0.480352 | 0.586658 | 0.372641 | Uiso | 0.026 | 4 | 1 | d | . | . | . |
| H2c5 | H | 0.604124 | 0.615481 | 0.200085 | Uiso | 0.026 | 4 | 1 | d | . | . | . |
| H3c5 | H | 0.627146 | 0.632638 | 0.433315 | Uiso | 0.026 | 4 | 1 | d | . | . | . |
| H1c7 | H | -0.130629 | 0.474012 | 0.522092 | Uiso | 0.0336 | 4 | 1 | d | . | . | . |
| H1c8 | H | -0.122321 | 0.557567 | 0.694406 | Uiso | 0.0297 | 4 | 1 | d | . | . | . |
| H1c9 | H | 0.014237 | 0.465253 | 0.195118 | Uiso | 0.0352 | 4 | 1 | d | . | . | . |
| H1c10 | H | 0.16097 | 0.539742 | 0.034056 | Uiso | 0.0298 | 4 | 1 | d | . | . | . |
| H1n1 | H | 0.503487 | 0.704586 | 0.080811 | Uiso | 0.0214 | 4 | 1 | d | . | . | . |
| H2n1 | H | 0.36023 | 0.734525 | 0.175867 | Uiso | 0.0214 | 4 | 1 | d | . | . | . |
| H1o1 | H | -0.014(2) | 0.6771(5) | 0.065(2) | Uiso | 0.0288 | 4 | 1 | d | . | . | . |
ADP components: (Show/hide table) [ Help ]
| Atom site label | Atom site symbol | U11 | U22 | U33 | U12 | U13 | U23 |
|---|---|---|---|---|---|---|---|
| Cl1 | Cl | 0.02072(12) | 0.02465(12) | 0.01612(12) | 0.00100(9) | -0.00123(10) | -0.00104(9) |
| O1 | O | 0.0167(3) | 0.0249(4) | 0.0304(4) | -0.0002(3) | -0.0068(4) | 0.0055(3) |
| N1 | N | 0.0156(4) | 0.0220(4) | 0.0159(4) | 0.0010(3) | -0.0016(3) | 0.0006(3) |
| C1 | C | 0.0182(5) | 0.0211(5) | 0.0241(5) | 0.0010(4) | -0.0006(4) | -0.0010(4) |
| C2 | C | 0.0160(5) | 0.0210(5) | 0.0157(5) | -0.0013(4) | -0.0006(4) | 0.0009(4) |
| C3 | C | 0.0180(5) | 0.0247(5) | 0.0193(5) | -0.0021(4) | -0.0047(5) | -0.0004(4) |
| C4 | C | 0.0157(4) | 0.0243(5) | 0.0176(5) | 0.0000(4) | -0.0024(5) | -0.0004(4) |
| C5 | C | 0.0171(5) | 0.0231(5) | 0.0247(5) | -0.0003(4) | -0.0025(5) | 0.0010(4) |
| C6 | C | 0.0123(5) | 0.0209(5) | 0.0228(5) | 0.0019(4) | -0.0032(4) | 0.0007(4) |
| C7 | C | 0.0200(5) | 0.0231(5) | 0.0409(7) | -0.0017(4) | -0.0052(5) | 0.0082(5) |
| C8 | C | 0.0176(5) | 0.0295(5) | 0.0271(6) | 0.0005(4) | -0.0009(5) | 0.0053(5) |
| C9 | C | 0.0232(5) | 0.0208(5) | 0.0439(7) | -0.0001(4) | -0.0071(5) | -0.0074(5) |
| C10 | C | 0.0183(5) | 0.0295(5) | 0.0266(5) | 0.0009(4) | -0.0024(5) | -0.0071(5) |
Fourier Wave Vectors (explicit: q_x,q_y,q_z or coefficients: q_1,q_2,...): (Show/hide table) [ Help ]
| Wave vector code | q_1 |
|---|---|
| 1 | 1 |
Definition of the displacive (translational) Fourier series: (Show/hide table) [ Help ]
| Modulation code | Atom site label | Displacement axis | Wave vector code |
|---|---|---|---|
| Cl1x1 | Cl1 | x | 1 |
| Cl1y1 | Cl1 | y | 1 |
| Cl1z1 | Cl1 | z | 1 |
| O1x1 | O1 | x | 1 |
| O1y1 | O1 | y | 1 |
| O1z1 | O1 | z | 1 |
| N1x1 | N1 | x | 1 |
| N1y1 | N1 | y | 1 |
| N1z1 | N1 | z | 1 |
| C1x1 | C1 | x | 1 |
| C1y1 | C1 | y | 1 |
| C1z1 | C1 | z | 1 |
| C2x1 | C2 | x | 1 |
| C2y1 | C2 | y | 1 |
| C2z1 | C2 | z | 1 |
| C3x1 | C3 | x | 1 |
| C3y1 | C3 | y | 1 |
| C3z1 | C3 | z | 1 |
| C4x1 | C4 | x | 1 |
| C4y1 | C4 | y | 1 |
| C4z1 | C4 | z | 1 |
| C5x1 | C5 | x | 1 |
| C5y1 | C5 | y | 1 |
| C5z1 | C5 | z | 1 |
| C6x1 | C6 | x | 1 |
| C6y1 | C6 | y | 1 |
| C6z1 | C6 | z | 1 |
| C7x1 | C7 | x | 1 |
| C7y1 | C7 | y | 1 |
| C7z1 | C7 | z | 1 |
| C8x1 | C8 | x | 1 |
| C8y1 | C8 | y | 1 |
| C8z1 | C8 | z | 1 |
| C9x1 | C9 | x | 1 |
| C9y1 | C9 | y | 1 |
| C9z1 | C9 | z | 1 |
| C10x1 | C10 | x | 1 |
| C10y1 | C10 | y | 1 |
| C10z1 | C10 | z | 1 |
| H1c1x1 | H1c1 | x | 1 |
| H1c1y1 | H1c1 | y | 1 |
| H1c1z1 | H1c1 | z | 1 |
| H1c2x1 | H1c2 | x | 1 |
| H1c2y1 | H1c2 | y | 1 |
| H1c2z1 | H1c2 | z | 1 |
| H1c3x1 | H1c3 | x | 1 |
| H1c3y1 | H1c3 | y | 1 |
| H1c3z1 | H1c3 | z | 1 |
| H2c3x1 | H2c3 | x | 1 |
| H2c3y1 | H2c3 | y | 1 |
| H2c3z1 | H2c3 | z | 1 |
| H3c3x1 | H3c3 | x | 1 |
| H3c3y1 | H3c3 | y | 1 |
| H3c3z1 | H3c3 | z | 1 |
| H1c4x1 | H1c4 | x | 1 |
| H1c4y1 | H1c4 | y | 1 |
| H1c4z1 | H1c4 | z | 1 |
| H1c5x1 | H1c5 | x | 1 |
| H1c5y1 | H1c5 | y | 1 |
| H1c5z1 | H1c5 | z | 1 |
| H2c5x1 | H2c5 | x | 1 |
| H2c5y1 | H2c5 | y | 1 |
| H2c5z1 | H2c5 | z | 1 |
| H3c5x1 | H3c5 | x | 1 |
| H3c5y1 | H3c5 | y | 1 |
| H3c5z1 | H3c5 | z | 1 |
| H1c7x1 | H1c7 | x | 1 |
| H1c7y1 | H1c7 | y | 1 |
| H1c7z1 | H1c7 | z | 1 |
| H1c8x1 | H1c8 | x | 1 |
| H1c8y1 | H1c8 | y | 1 |
| H1c8z1 | H1c8 | z | 1 |
| H1c9x1 | H1c9 | x | 1 |
| H1c9y1 | H1c9 | y | 1 |
| H1c9z1 | H1c9 | z | 1 |
| H1c10x1 | H1c10 | x | 1 |
| H1c10y1 | H1c10 | y | 1 |
| H1c10z1 | H1c10 | z | 1 |
| H1n1x1 | H1n1 | x | 1 |
| H1n1y1 | H1n1 | y | 1 |
| H1n1z1 | H1n1 | z | 1 |
| H2n1x1 | H2n1 | x | 1 |
| H2n1y1 | H2n1 | y | 1 |
| H2n1z1 | H2n1 | z | 1 |
| H1o1x1 | H1o1 | x | 1 |
| H1o1y1 | H1o1 | y | 1 |
| H1o1z1 | H1o1 | z | 1 |
Displacive (translational) Fourier coefficients: (Show/hide table) [ Help ]
| Modulation code | Cosine coefficient | Sine coefficient |
|---|---|---|
| Cl1x1 | -0.00946(5) | -0.00227(4) |
| Cl1y1 | -0.000481(13) | 0.010399(12) |
| Cl1z1 | -0.01082(4) | -0.00134(4) |
| O1x1 | -0.00866(13) | -0.00617(12) |
| O1y1 | -0.00072(4) | 0.00956(4) |
| O1z1 | 0.00686(13) | 0.00834(14) |
| N1x1 | -0.00873(14) | -0.00452(13) |
| N1y1 | -0.00029(4) | 0.00917(4) |
| N1z1 | 0.00451(14) | 0.00226(14) |
| C1x1 | -0.00894(17) | -0.00760(17) |
| C1y1 | 0.00034(5) | 0.00687(5) |
| C1z1 | 0.02323(19) | 0.00239(19) |
| C2x1 | -0.00879(17) | -0.00466(16) |
| C2y1 | -0.00026(6) | 0.00857(5) |
| C2z1 | 0.01473(18) | 0.00046(17) |
| C3x1 | -0.00748(18) | -0.00646(16) |
| C3y1 | -0.00054(6) | 0.00878(5) |
| C3z1 | -0.00127(17) | 0.00391(18) |
| C4x1 | -0.00802(17) | -0.00551(16) |
| C4y1 | -0.00048(6) | 0.00965(5) |
| C4z1 | 0.01632(18) | -0.00144(19) |
| C5x1 | -0.00832(17) | -0.00514(16) |
| C5y1 | 0.00003(5) | 0.00804(5) |
| C5z1 | 0.02756(18) | -0.00487(19) |
| C6x1 | -0.00694(17) | -0.00288(17) |
| C6y1 | -0.00089(5) | 0.00820(5) |
| C6z1 | 0.02627(20) | -0.00432(19) |
| C7x1 | -0.00648(20) | 0.00677(19) |
| C7y1 | -0.00025(6) | 0.00582(5) |
| C7z1 | 0.0463(2) | 0.0020(2) |
| C8x1 | -0.00873(19) | -0.00387(17) |
| C8y1 | 0.00069(6) | 0.00612(6) |
| C8z1 | 0.0327(2) | 0.0064(2) |
| C9x1 | -0.0006(2) | 0.00950(19) |
| C9y1 | -0.00134(6) | 0.00730(5) |
| C9z1 | 0.0473(2) | -0.0111(2) |
| C10x1 | -0.00203(19) | 0.00403(17) |
| C10y1 | -0.00118(6) | 0.00888(6) |
| C10z1 | 0.0363(2) | -0.0137(2) |
| H1c1x1 | -0.0097 | -0.0143 |
| H1c1y1 | 0.0009 | 0.0071 |
| H1c1z1 | 0.0135 | 0.0035 |
| H1c2x1 | -0.0103 | -0.0043 |
| H1c2y1 | 0 | 0.0082 |
| H1c2z1 | 0.0115 | 0.0045 |
| H1c3x1 | -0.0109 | -0.0075 |
| H1c3y1 | 0.0001 | 0.0093 |
| H1c3z1 | -0.0048 | 0.0069 |
| H2c3x1 | -0.0048 | -0.0068 |
| H2c3y1 | -0.0014 | 0.0077 |
| H2c3z1 | -0.0023 | 0.0046 |
| H3c3x1 | -0.0061 | -0.0054 |
| H3c3y1 | -0.0002 | 0.0091 |
| H3c3z1 | -0.0005 | 0.001 |
| H1c4x1 | -0.0087 | -0.0065 |
| H1c4y1 | 0.0003 | 0.0114 |
| H1c4z1 | 0.0174 | -0.0083 |
| H1c5x1 | -0.0085 | -0.0055 |
| H1c5y1 | -0.0002 | 0.0082 |
| H1c5z1 | 0.0301 | -0.0012 |
| H2c5x1 | -0.0051 | -0.0085 |
| H2c5y1 | 0.0006 | 0.008 |
| H2c5z1 | 0.029 | -0.0134 |
| H3c5x1 | -0.0122 | -0.0035 |
| H3c5y1 | 0 | 0.0079 |
| H3c5z1 | 0.0306 | -0.003 |
| H1c7x1 | -0.0076 | 0.0105 |
| H1c7y1 | 0.0002 | 0.0052 |
| H1c7z1 | 0.0529 | 0.0073 |
| H1c8x1 | -0.0085 | -0.009 |
| H1c8y1 | 0.0017 | 0.0065 |
| H1c8z1 | 0.0293 | 0.0114 |
| H1c9x1 | 0.0047 | 0.0142 |
| H1c9y1 | -0.0017 | 0.0078 |
| H1c9z1 | 0.0542 | -0.0191 |
| H1c10x1 | 0.0006 | 0.0042 |
| H1c10y1 | -0.0006 | 0.0107 |
| H1c10z1 | 0.0339 | -0.0219 |
| H1n1x1 | -0.0092 | -0.003 |
| H1n1y1 | -0.0001 | 0.0101 |
| H1n1z1 | 0.0064 | 0.0002 |
| H2n1x1 | -0.0087 | -0.0047 |
| H2n1y1 | -0.0002 | 0.0092 |
| H2n1z1 | 0.0003 | 0.0043 |
| H1o1x1 | -0.0059(19) | -0.0064(18) |
| H1o1y1 | 0.0002(5) | 0.0108(5) |
| H1o1z1 | 0.0112(18) | 0.0025(19) |