Structure determination of ylid with the Bruker SMART X2S benchtop crystallographic system


A yellow crystal of ylid with the dimensions of 0.79 mm x 0.81 mm x 0.82 mm mounted on a Mitegen Micromount was automatically centered on a Bruker SMART X2S benchtop crystallographic system. Intensity measurements were performed using a monochromated (Doubly Curved Silicon Crystal) Mo-Kα-radiation (0.71073 Å) from a sealed MicroFocus tube. Generator settings were 50 kV, 1 mA. Data collection temperature was 23°C.
Data were acquired using three sets of Omega scans at different Phi settings. The frame width was 0.5° with an exposure time of 5.0 s.

The detailed data collection strategy was as follows:
Detector distance: 40 mm
Detector swing angle (fixed 2 Theta): -20°.

Run

Omega (start)

Omega (end)

Phi

Frames

1

-20.0

-200.0

0.0

360

2

-20.0

-140.0

120.0

240

3

-20.0

-80.0

240.0

120


APEX2 software was used for preliminary determination of the unit cell. Determination of integral intensities and unit cell refinement were performed using SAINT. The integration of the data yielded a total of 6275 reflections to a maximum θ angle of 25.10° (0.84 Å resolution).
The constants for the orthorhombic unit cell are a = 5.9732(9) Å, b = 9.0529(13) Å, c = 18.431(3) Å, V = 996.7(3) Å3. They are based upon the refinement of the XYZ-centroids of 2872 reflections above 20.0 I/σ(I) with 2.21° ≤ θ ≤ 24.96°.
Data were corrected for absorption effects with SADABS using the multiscan technique. The ratio of minimum to maximum apparent transmission is 89.8:100. The average residual for symmetry equivalent reflections is Rint = 3.15% and Rσ = 2.83%. XPREP determined the space group to be P 21 21 21, with Z = 4 for the formula unit, C11H10O2S.
The structure was solved with XS and subsequent structure refinements were performed with XL. The final anisotropic full-matrix least-squares refinement on Fo2 with 130 variables converged at R1 = 2.80% for the observed data and wR2 = 9.24% for all data. The goodness-of-fit was 1.195. The largest peak on the final difference electron density synthesis was 0.22 e-/Å3 and the deepest hole was -0.16 e-/Å3 with an RMS deviation of 0.05 e-/Å3. On the basis of the final model, the calculated density is 1.375 g/cm3 and F(000) = 432.

APEX2 Version 2.2 (Bruker AXS Inc., 2007)
SAINT Version 7.34a (Bruker AXS Inc., 2007)
SADABS Version 2007/2 (Sheldrick, Bruker AXS Inc.)
XPREP Version 2005/2 (Sheldrick, Bruker AXS Inc.)
XS Version 2008/1 (George M. Sheldrick, Acta Cryst. (2008). A64, 112-122)
XL Version 2008/1 (George M. Sheldrick, Acta Cryst. (2008). A64, 112-122)

 

 

 

Table 1. Crystal data and structure refinement for ylid.

 

Identification code

ylid

Empirical formula

C11 H10 O2 S

Formula weight

206.25

Temperature

296(2) K

Wavelength

0.71073 Å

Crystal system

Orthorhombic

Space group

P 21 21 21

Unit cell dimensions

a = 5.9732(9) Å

α = 90°

 

b = 9.0529(13) Å

β = 90°

 

c = 18.431(3) Å

γ = 90°

Volume

996.7(3) Å3

 

Z

4

 

Density (calculated)

1.375 Mg/cm3

 

Absorption coefficient

0.293 mm-1

 

F(000)

432

 

Crystal size

0.79 x 0.81 x 0.82 mm3

 

Theta range for data collection

2.21 to 24.96°

 

Index ranges

-6<=h<=7, -10<=k<=10, -21<=l<=22

 

Reflections collected

6275

 

Independent reflections

1766 [R(int) = 0.0315]

 

Completeness to theta = 24.96°

99.7%

 

Absorption correction

Multiscan

 

Max. and min. transmission

0.8016 and 0.7197

 

Refinement method

Full-matrix least-squares on F2

 

Data / restraints / parameters

1766 / 0 / 130

 

Goodness-of-fit on F2

1.195

 

Final R indices [I>2sigma(I)]

R1 = 0.0280, wR2 = 0.0731

 

R indices (all data)

R1 = 0.0335, wR2 = 0.0924

 

Absolute structure parameter

0.02(9)

 

Extinction coefficient

0.035(5)

 

Largest diff. peak and hole

0.215 and -0.163

 


Rint = Σ|Fo2 - Fo2(mean)| / Σ[Fo2]
R1 = Σ||Fo| - |Fc|| / Σ|Fo|
GOOF = S = {Σ[w(Fo2 - Fc2)2] / (n - p)}1/2
wR2 = {Σ[w(Fo2 - Fc2)2] / Σ[w(Fo2)2]}1/2
w = 1 / [σ(Fo2) + (aP)2 + bP] where P is [2Fc2 + Max(Fo2, 0)] / 3



Table 2. Atomic coordinates (x104) and equivalent isotropic displacement parameters (Å2x103) for ylid.

U(eq) is defined as one third of the trace of the orthogonalized Uij tensor.

 

 

 

x

y

z

U(eq)

S1

-1903(1)

-8186(1)

-7405(1)

38(1)

O1

-1587(3)

-10890(2)

-6292(1)

52(1)

O2

-6644(3)

-6979(2)

-6769(1)

49(1)

C1

-3506(6)

-8239(3)

-8227(1)

60(1)

C6

-7000(6)

-10611(3)

-4628(1)

59(1)

C10

-8499(5)

-9509(3)

-4777(1)

56(1)

C5

-5136(5)

-10876(2)

-5075(1)

50(1)

C7

-1646(5)

-6233(2)

-7292(1)

49(1)

C9

-8225(5)

-8598(3)

-5381(1)

48(1)

C4

-4896(4)

-9978(2)

-5681(1)

38(1)

C8

-6426(4)

-8856(2)

-5823(1)

37(1)

C3

-3105(4)

-9989(2)

-6253(1)

36(1)

C2

-3645(4)

-8758(2)

-6720(1)

35(1)

C11

-5657(4)

-8053(3)

-6498(1)

36(1)





Table 3. Bond lengths (Å) and angles (°) for ylid.

 

S1-C2

1.716(2)

S1-C7

1.787(2)

S1-C1

1.794(3)

O1-C3

1.222(3)

O2-C11

1.242(3)

C6-C10

1.368(4)

C6-C5

1.406(4)

C10-C9

1.395(3)

C5-C4

1.389(3)

C9-C8

1.368(3)

C4-C8

1.391(3)

C4-C3

1.502(3)

C8-C11

1.513(3)

C3-C2

1.444(3)

C2-C11

1.421(3)

 

 

C2-S1-C7

105.36(11)

C2-S1-C1

106.86(13)

C7-S1-C1

99.82(13)

C10-C6-C5

121.7(2)

C6-C10-C9

121.0(3)

C4-C5-C6

116.9(2)

C8-C9-C10

117.8(3)

C5-C4-C8

120.7(2)

C5-C4-C3

129.4(2)

C8-C4-C3

109.96(18)

C9-C8-C4

122.0(2)

C9-C8-C11

130.2(2)

C4-C8-C11

107.8(2)

O1-C3-C2

130.2(2)

O1-C3-C4

125.0(2)

C2-C3-C4

104.7(2)

C11-C2-C3

111.4(2)

C11-C2-S1

126.08(17)

C3-C2-S1

122.38(17)

O2-C11-C2

129.6(2)

O2-C11-C8

124.2(2)

C2-C11-C8

106.1(2)





Table 4. Anisotropic displacement parameters (Å2x103) for ylid.

The anisotropic displacement factor exponent takes the form: -2π2[ h2 a*2 U11 + ... + 2 h k a* b* U12 ]

 

 

U11

U22

U33

U23

U13

U12

S1

40(1)

34(1)

40(1)

4(1)

9(1)

5(1)

O1

59(1)

44(1)

52(1)

10(1)

9(1)

17(1)

O2

42(1)

48(1)

57(1)

12(1)

1(1)

11(1)

C1

87(2)

55(2)

37(1)

2(1)

-2(1)

-3(2)

C6

92(2)

47(1)

38(1)

-1(1)

19(2)

-15(2)

C10

65(2)

56(2)

47(1)

-8(1)

24(1)

-12(2)

C5

73(2)

37(1)

38(1)

3(1)

7(1)

-1(1)

C7

49(2)

37(1)

61(1)

2(1)

12(1)

-10(1)

C9

44(1)

51(1)

48(1)

-5(1)

9(1)

-6(1)

C4

50(2)

31(1)

32(1)

-4(1)

3(1)

-5(1)

C8

40(1)

36(1)

34(1)

-4(1)

1(1)

-8(1)

C3

44(1)

31(1)

35(1)

-0(1)

0(1)

1(1)

C2

39(1)

34(1)

34(1)

3(1)

3(1)

-1(1)

C11

34(1)

34(1)

39(1)

0(1)

-3(1)

-3(1)





Table 5. Hydrogen coordinates (x104) and isotropic displacement parameters (Å2x103) for ylid.

 

 

x

y

z

U(eq)

H1A

-3695

-9247

-8378

90

H1B

-2734

-7699

-8599

90

H1C

-4947

-7801

-8145

90

H6

-7220

-11199

-4220

71

H10

-9718

-9365

-4471

67

H5

-4111

-11619

-4970

59

H7A

-3108

-5793

-7286

73

H7B

-793

-5830

-7686

73

H7C

-899

-6026

-6842

73

H9

-9232

-7841

-5480

57