Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807018764/bg2041sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807018764/bg2041IIIsup2.hkl |
CCDC reference: 646718
Key indicators
- Single-crystal X-ray study
- T = 296 K
- Mean (C-C) = 0.009 Å
- R factor = 0.033
- wR factor = 0.104
- Data-to-parameter ratio = 10.0
checkCIF/PLATON results
No syntax errors found
Alert level B PLAT029_ALERT_3_B _diffrn_measured_fraction_theta_full Low ....... 0.95
Alert level C PLAT022_ALERT_3_C Ratio Unique / Expected Reflections too Low .... 0.94 PLAT220_ALERT_2_C Large Non-Solvent C Ueq(max)/Ueq(min) ... 3.42 Ratio PLAT222_ALERT_3_C Large Non-Solvent H Ueq(max)/Ueq(min) ... 3.34 Ratio PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C4 PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ... 9 PLAT432_ALERT_2_C Short Inter X...Y Contact C2 .. C2 .. 3.17 Ang.
Alert level G REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 79.47 From the CIF: _reflns_number_total 834 Count of symmetry unique reflns 889 Completeness (_total/calc) 93.81% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 0 Fraction of Friedel pairs measured 0.000 Are heavy atom types Z>Si present no PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1 = . S
0 ALERT level A = In general: serious problem 1 ALERT level B = Potentially serious problem 6 ALERT level C = Check and explain 2 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 3 ALERT type 2 Indicator that the structure model may be wrong or deficient 4 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
checkCIF publication errors
Alert level A PUBL024_ALERT_1_A The number of authors is greater than 5. Please specify the role of each of the co-authors for your paper.
Author Response: Specially-designed pressure vessels were needed for high pressure crystallization. Sawamura and Kato designed the pressure vessels, and prepared the budget for this work. Yamashita, Inomata, and Matsuo took charge of building the high-pressure crystallization system, sample preparation, pressure control, density measurement and infrared spectra measurement. Ishikawa and Kashiwagi performed X-ray diffraction experiments and refinement. |
1 ALERT level A = Data missing that is essential or data in wrong format 0 ALERT level G = General alerts. Data that may be required is missing
Data collection: MSC/AFC Diffractometer Control Software (Molecular Structure Corporation, 1988); cell refinement: MSC/AFC Diffractometer Control Software; data reduction: TEXSAN (Molecular Structure Corporation, 2004); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: TEXSAN; molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: TEXSAN.
C6H13NO2 | F(000) = 288.00 |
Mr = 131.17 | Dx = 1.173 Mg m−3 Dm = 1.168 Mg m−3 Dm measured by not measured |
Monoclinic, C2 | Cu Kα radiation, λ = 1.5418 Å |
Hall symbol: C 2y | Cell parameters from 25 reflections |
a = 8.807 (3) Å | θ = 28.4–29.6° |
b = 5.975 (1) Å | µ = 0.72 mm−1 |
c = 14.193 (3) Å | T = 296 K |
β = 96.17 (2)° | Prism, colourless |
V = 742.5 (3) Å3 | 0.40 × 0.40 × 0.20 mm |
Z = 4 |
Rigaku AFC-5S diffractometer | 756 reflections with F2 > 2σ(F2) |
Radiation source: sealed X-ray tube | Rint = 0.024 |
Graphite monochromator | θmax = 79.5° |
ω–2θ scans | h = −10→0 |
Absorption correction: ψ scan (North et al., 1968) | k = −7→7 |
Tmin = 0.738, Tmax = 0.868 | l = −17→18 |
1570 measured reflections | 3 standard reflections every 150 reflections |
834 independent reflections | intensity decay: 2.9% |
Refinement on F2 | 0 constraints |
Least-squares matrix: full | H-atom parameters not refined |
R[F2 > 2σ(F2)] = 0.033 | w = 1/[σ2(Fo2) + (0.05(Max(Fo2,0) + 2Fc2)/3)2] |
wR(F2) = 0.104 | (Δ/σ)max = 0.017 |
S = 1.50 | Δρmax = 0.17 e Å−3 |
834 reflections | Δρmin = −0.15 e Å−3 |
83 parameters | Extinction correction: Zachariasen (1967) type 2, Gaussian isotropic |
0 restraints | Extinction coefficient: 0.11 (2) |
Experimental. A value of '_diffrn_measured_fraction_theta_full' is slightly low. The reason is the blind region caused by the chi circle of the four-circle diffractometer. |
Geometry. Some bad geometries such as a relatively high Ueq value of C4 atom and a relatively short contact between C2 atoms were observed. The crystal was crystallized under a high pressure (400 MPa) and the data collection was carried out at a normal pressure condition. Actually, the peak profile of the diffraction was not so good. The stress brought by the change of the pressure may cause the bad effect to the crystal quality and the resulting structure. |
Refinement. Refinement was carried out using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F2. R-factor (gt) are based on F. The threshold expression of F2 > 2.0 σ(F2) is used only for calculating R-factor (gt). Because of the small anomalous dispersion effects, the Flack parameter resulted in the meaningless value (-0.31 (21)). Therefore, in order to improve data quality, the final cycles of refinement were performed using the reflection data in which Friedl pairs were merged and averaged, and the Flack parameter was not refined. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.4071 (1) | 0.592 (2) | 0.60053 (9) | 0.0373 (3) | |
O2 | 0.5502 (2) | 0.900 (2) | 0.6072 (1) | 0.0421 (4) | |
N1 | 0.7934 (2) | 0.640 (2) | 0.5727 (1) | 0.0308 (3) | |
C1 | 0.6790 (2) | 0.559 (2) | 0.6351 (1) | 0.0300 (4) | |
C2 | 0.5317 (2) | 0.693 (2) | 0.6121 (1) | 0.0300 (4) | |
C3 | 0.7453 (2) | 0.591 (2) | 0.7382 (1) | 0.0395 (5) | |
C4 | 0.6481 (3) | 0.493 (2) | 0.8107 (2) | 0.0534 (6) | |
C5 | 0.6636 (4) | 0.239 (2) | 0.8159 (2) | 0.0750 (9) | |
C6 | 0.6968 (6) | 0.595 (2) | 0.9079 (2) | 0.103 (1) | |
H1 | 0.6594 | 0.4026 | 0.6233 | 0.0365* | |
H2 | 0.7558 | 0.7455 | 0.7499 | 0.0486* | |
H3 | 0.8430 | 0.5206 | 0.7466 | 0.0486* | |
H4 | 0.5441 | 0.5268 | 0.7925 | 0.0657* | |
H5 | 0.7669 | 0.1987 | 0.8356 | 0.0911* | |
H6 | 0.6341 | 0.1747 | 0.7551 | 0.0911* | |
H7 | 0.5998 | 0.1798 | 0.8600 | 0.0911* | |
H8 | 0.8005 | 0.5607 | 0.9265 | 0.1220* | |
H9 | 0.6353 | 0.5318 | 0.9531 | 0.1220* | |
H10 | 0.6818 | 0.7507 | 0.9049 | 0.1220* | |
H11 | 0.8854 | 0.5561 | 0.5855 | 0.0376* | |
H12 | 0.7542 | 0.6195 | 0.5083 | 0.0376* | |
H13 | 0.8133 | 0.7930 | 0.5849 | 0.0376* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0243 (6) | 0.0374 (7) | 0.0493 (7) | −0.0031 (5) | −0.0006 (5) | 0.0008 (6) |
O2 | 0.0252 (7) | 0.0277 (6) | 0.0723 (10) | 0.0064 (5) | 0.0009 (6) | −0.0016 (6) |
N1 | 0.0237 (7) | 0.0275 (7) | 0.0408 (7) | 0.0045 (6) | 0.0018 (5) | −0.0002 (5) |
C1 | 0.0248 (8) | 0.0271 (8) | 0.0377 (7) | 0.0034 (6) | 0.0014 (6) | −0.0002 (6) |
C2 | 0.0251 (8) | 0.0283 (7) | 0.0360 (8) | 0.0038 (6) | 0.0006 (6) | −0.0023 (6) |
C3 | 0.037 (1) | 0.040 (1) | 0.0393 (8) | 0.0054 (8) | −0.0062 (6) | −0.0007 (7) |
C4 | 0.051 (1) | 0.067 (1) | 0.043 (1) | 0.014 (1) | 0.0085 (9) | 0.0078 (9) |
C5 | 0.093 (2) | 0.065 (1) | 0.066 (2) | −0.019 (2) | 0.000 (2) | 0.012 (1) |
C6 | 0.184 (4) | 0.083 (2) | 0.041 (1) | 0.007 (3) | 0.012 (2) | −0.004 (1) |
O1—C2 | 1.248 (8) | C3—H3 | 0.954 |
O2—C2 | 1.250 (17) | C4—C5 | 1.525 (17) |
N1—C1 | 1.493 (3) | C4—C6 | 1.526 (5) |
N1—H11 | 0.955 | C4—H4 | 0.947 |
N1—H12 | 0.951 | C5—H5 | 0.954 |
N1—H13 | 0.941 | C5—H6 | 0.954 |
C1—C2 | 1.530 (9) | C5—H7 | 0.954 |
C1—C3 | 1.528 (3) | C6—H8 | 0.946 |
C1—H1 | 0.960 | C6—H9 | 0.960 |
C3—C4 | 1.526 (4) | C6—H10 | 0.941 |
C3—H2 | 0.942 | ||
O1···N1i | 2.884 (2) | O1···O2i | 3.530 (9) |
O1···N1ii | 2.893 (16) | O2···N1iii | 2.678 (9) |
O1···C2i | 3.179 (3) | O2···O2i | 3.078 (4) |
O1···C1i | 3.355 (2) | O2···N1iv | 3.351 (8) |
O1···O2ii | 3.357 (6) | O2···C2i | 3.355 (7) |
O1···N1iii | 3.434 (16) | O2···C1iii | 3.467 (3) |
O1···O1i | 3.439 (3) | N1···C2v | 3.406 (13) |
O1···C1iii | 3.503 (14) | C2···C2i | 3.170 (4) |
C1—N1—H11 | 109.1 | H2—C3—H3 | 109.9 |
C1—N1—H12 | 109.2 | C3—C4—C5 | 111.2 (3) |
C1—N1—H13 | 109.4 | C3—C4—C6 | 109.4 (3) |
H11—N1—H12 | 109.0 | C3—C4—H4 | 109.2 |
H11—N1—H13 | 109.9 | C5—C4—C6 | 109.9 (3) |
H12—N1—H13 | 110.3 | C5—C4—H4 | 107.9 |
N1—C1—C2 | 108.4 (7) | C6—C4—H4 | 109.2 |
N1—C1—C3 | 108.3 (2) | C4—C5—H5 | 110.1 |
N1—C1—H1 | 109.6 | C4—C5—H6 | 110.1 |
C2—C1—C3 | 111.5 (5) | C4—C5—H7 | 110.2 |
C2—C1—H1 | 109.9 | H5—C5—H6 | 108.8 |
C3—C1—H1 | 109.4 | H5—C5—H7 | 108.9 |
O1—C2—O2 | 126.1 (7) | H6—C5—H7 | 108.8 |
O1—C2—C1 | 119.3 (11) | C4—C6—H8 | 109.6 |
O2—C2—C1 | 114.7 (5) | C4—C6—H9 | 108.9 |
C1—C3—C4 | 114.5 (5) | C4—C6—H10 | 109.3 |
C1—C3—H2 | 108.2 | H8—C6—H9 | 108.9 |
C1—C3—H3 | 108.1 | H8—C6—H10 | 110.6 |
C4—C3—H2 | 108.1 | H9—C6—H10 | 109.4 |
C4—C3—H3 | 108.1 | ||
O1—C2—C1—N1 | 133.1 (5) | N1—C1—C3—C4 | −173.9 (9) |
O1—C2—C1—C3 | −107.8 (7) | C1—C3—C4—C5 | 76.1 (8) |
O2—C2—C1—N1 | −47.3 (6) | C1—C3—C4—C6 | −162.5 (8) |
O2—C2—C1—C3 | 71.9 (7) | C2—C1—C3—C4 | 67.0 (12) |
Symmetry codes: (i) −x+1, y, −z+1; (ii) x−1/2, y−1/2, z; (iii) x−1/2, y+1/2, z; (iv) −x+3/2, y+1/2, −z+1; (v) x+1/2, y−1/2, z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H13···O1vi | 0.940 | 1.972 | 2.890 (10) | 165.100 |
N1—H12···O1i | 0.951 | 1.990 | 2.884 (2) | 155.910 |
N1—H11···O2v | 0.955 | 1.725 | 2.680 (8) | 178.977 |
Symmetry codes: (i) −x+1, y, −z+1; (v) x+1/2, y−1/2, z; (vi) x+1/2, y+1/2, z. |
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