Small Molecule Crystallography Lab Department of Chemistry and Biochemistry University of Oklahoma 101 Stephenson Parkway Norman, OK
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1 Small Molecule Crystallography Lab Department of Chemistry and Biochemistry University of Oklahoma 101 Stephenson Parkway Norman, OK Sample: KP-XI-cinnamyl-chiral alcohol Lab ID: User: Kaushik Panigrahi Formula: C 14 H 19 F 2 O 4 P Date: May 11, 2012 For Prof. David Berkowitz
2 Table of Contents Figure 1. Thermal Ellipsoid Plot of Orientation A.. 3 Figure 2. Thermal Ellipsoid Plot of Orientation B.. 4 Figure 3. Packing Diagram 5 Comments.. 6 Experimental.. 6 Acknowledgements... 7 References. 7 Table 1. Crystal Data 8 Table 2. Atom Coordinates 9 Table 3. Bond Distances and Angles 10 Table 4. Anisotropic Displacement Parameters.. 12 Table 5. Hydrogen Atom Parameters 13 Table 6. Torsion Angles.. 14 Table 7. Hydrogen Bond Details 15 KP-XI-cinnamyl-chiral alcohol Page 2
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6 Comment The crystal structure exhibited disorder at atoms C4 and atoms C7 C14. The occupancies of C4 refined to 0.579(7) and 0.421(7) for the unprimed and primed atoms. The occupancies of C7 C14 refined to 0.504(3) and 0.496(3) for the unprimed and primed atoms. Restraints on the positional parameters of atoms C7 C14 were required. The displacement parameters of C4 and C4 were constrained to be equal. The displacement ellipsoids were drawn at the 50% probability level. Experimental A colorless block-shaped crystal of dimensions 0.40 x 0.38 x 0.32 mm was selected for structural analysis. Intensity data for this compound were collected using a diffractometer with a Bruker APEX ccd area detector (1) and graphite-monochromated Mo K radiation ( = Å). The sample was cooled to 100(2) K. Cell parameters were determined from a non-linear least squares fit of 5360 peaks in the range 2.48 < < A total of 7836 data were measured in the range 1.63 < < using and oscillation frames. The data were corrected for absorption by the empirical method (2) giving minimum and maximum transmission factors of and The data were merged to form a set of 3886 independent data with R(int) = and a coverage of 99.9 %. The monoclinic space group C2 was determined by systematic absences and statistical tests and verified by subsequent refinement. The structure was solved by direct methods and refined by full-matrix least-squares methods on F 2 (3). The positions of hydrogens bonded to carbons were initially determined by geometry and were refined with a riding model. The hydrogen bonded to O4 was located on a difference map, and its position was refined independently. Non-hydrogen atoms were refined with anisotropic displacement parameters. Hydrogen atom displacement parameters were set to 1.2 (1.5 for methyl) times the isotropic equivalent displacement parameters of the bonded atoms. A total of 268 parameters were refined against 144 restraints and 3886 data to give wr(f 2 ) = and S = for weights of w = 1/[ 2 (F 2 ) + ( P) P], where P = [F o 2 + 2F c 2 ] / 3. The final R(F) was for the 3623 observed, [F > 4 (F)], data. The largest shift/s.u. was in the final refinement cycle. The final difference map had maxima and minima of and e/å 3, respectively. The absolute structure was determined by refinement of the Flack parameter(4). KP-XI-cinnamyl-chiral alcohol Page 6
7 The polar axis restraint was taken from Flack and Schwarzenbach(5). Acknowledgment The authors thank the National Science Foundation (grant CHE ) and the University of Oklahoma for funds to purchase of the X-ray instrument and computers. This structure was determined by Douglas R. Powell. References (1) (a) Data Collection: SMART Software Reference Manual (2007). Bruker-AXS, 5465 E. Cheryl Parkway, Madison, WI USA. (b) Data Reduction: SAINT Software Reference Manual (2007). Bruker-AXS, 5465 E. Cheryl Parkway, Madison, WI USA. (2) G. M. Sheldrick (2001). SADABS. Program for Empirical Absorption Correction of Area Detector Data. University of Göttingen, Germany. (3) G. M. Sheldrick (2008). Acta Cryst., A64, (4) H. D. Flack (1983). Acta Cryst. A39, (5) H. D. Flack and D. Schwarzenbach (1988). Acta Cryst. A44, KP-XI-cinnamyl-chiral alcohol Page 7
8 Table 1. Crystal data and structure refinement for Empirical formula Formula weight Crystal system Space group C 14 H 19 F 2 O 4 P monoclinic Unit cell dimensions a = (3) Å = 90 C2 Volume (3) Å 3 Z, Z' 4, 1 Density (calculated) Mg/m 3 Wavelength Temperature F(000) 672 b = (7) Å = (2) c = (13) Å = Å 100(2) K Absorption coefficient mm -1 Absorption correction Semi-empirical from equivalents Max. and min. transmission and Theta range for data collection 1.63 to Reflections collected 7836 Independent reflections 3886 [R(int) = ] Data / restraints / parameters 3886 / 144 / 268 wr(f 2 all data) wr2 = R(F obsd data) R1 = Goodness-of-fit on F Observed data [I > 2 (I)] 3623 Absolute structure parameter 0.13(9) Largest and mean shift / s.u and Largest diff. peak and hole and e/å wr2 = { [w(f 2 o - F 2 c ) 2 ] / [w(f 2 o ) 2 ] } 1/2 R1 = F o - F c / F o KP-XI-cinnamyl-chiral alcohol Page 8
9 Table 2. Atomic coordinates and equivalent isotropic displacement parameters for U(eq) is defined as one third of the trace of the orthogonalized U ij tensor. x y z U(eq) P(1) (15) (9) (4) (11) F(1) (5) (2) (10) (3) F(2) (4) (2) (12) (3) O(1) (6) (2) (13) (3) O(2) (5) (2) (12) (3) O(3) (5) (2) (12) (3) O(4) (6) (3) (14) (3) C(1) (9) (4) (2) (5) C(2) (13) (5) (3) (8) C(3) (8) (5) (18) (5) C(4) (19) (12) (5) (12) C(4') (3) (17) (7) (12) C(5) (7) (3) (16) (4) C(6) (7) (3) (17) (4) C(7) (12) (7) (3) (8) C(8) (12) (6) (3) (8) C(9) (12) (4) (2) (8) C(10) (12) (6) (4) (10) C(11) (13) (7) (4) (13) C(12) (19) (9) (6) (19) C(13) (16) (9) (5) (13) C(14) (10) (5) (3) (10) C(7') (10) (5) (3) (8) C(8') (12) (7) (3) (8) C(9') (12) (7) (2) (8) C(10') (13) (6) (3) (10) C(11') (14) (7) (4) (11) C(12') (2) (8) (6) (17) C(13') (17) (8) (5) (14) C(14') (14) (7) (3) (10) KP-XI-cinnamyl-chiral alcohol Page 9
10 Table 3. Bond lengths [Å] and angles [ ] for P(1)-O(1) (14) P(1)-O(3) (14) P(1)-O(2) (13) P(1)-C(5) (17) F(1)-C(5) 1.370(2) F(2)-C(5) 1.368(2) O(2)-C(1) 1.462(3) O(3)-C(3) 1.462(2) O(4)-C(6) 1.394(2) O(4)-H(4) 0.74(3) C(1)-C(2) 1.478(4) C(1)-H(1A) C(1)-H(1B) C(2)-H(2A) C(2)-H(2B) C(2)-H(2C) C(3)-C(4') 1.447(7) C(3)-C(4) 1.526(6) C(3)-H(3A) C(3)-H(3B) C(4)-H(4A) C(4)-H(4B) C(4)-H(4C) C(4')-H(4D) C(4')-H(4E) C(4')-H(4F) C(5)-C(6) 1.529(2) C(6)-C(7) 1.530(3) C(6)-C(7') 1.531(3) C(6)-H(6) C(6)-H(6') O(1)-P(1)-O(3) (8) O(1)-P(1)-O(2) (8) O(3)-P(1)-O(2) (7) O(1)-P(1)-C(5) (9) O(3)-P(1)-C(5) (8) O(2)-P(1)-C(5) (8) C(1)-O(2)-P(1) (13) C(3)-O(3)-P(1) (13) C(6)-O(4)-H(4) 109(2) O(2)-C(1)-C(2) 109.8(2) C(7)-C(8) 1.324(4) C(7)-H(7) C(8)-C(9) 1.484(4) C(8)-H(8) C(9)-C(10) 1.388(3) C(9)-C(14) 1.389(3) C(10)-C(11) 1.382(3) C(10)-H(10) C(11)-C(12) 1.382(4) C(11)-H(11) C(12)-C(13) 1.387(4) C(12)-H(12) C(13)-C(14) 1.387(3) C(13)-H(13) C(14)-H(14) C(7')-C(8') 1.319(4) C(7')-H(7') C(8')-C(9') 1.487(4) C(8')-H(8') C(9')-C(10') 1.387(3) C(9')-C(14') 1.388(4) C(10')-C(11') 1.393(3) C(10')-H(10') C(11')-C(12') 1.379(4) C(11')-H(11') C(12')-C(13') 1.388(4) C(12')-H(12') C(13')-C(14') 1.386(4) C(13')-H(13') C(14')-H(14') O(2)-C(1)-H(1A) C(2)-C(1)-H(1A) O(2)-C(1)-H(1B) C(2)-C(1)-H(1B) H(1A)-C(1)-H(1B) C(1)-C(2)-H(2A) C(1)-C(2)-H(2B) H(2A)-C(2)-H(2B) C(1)-C(2)-H(2C) H(2A)-C(2)-H(2C) KP-XI-cinnamyl-chiral alcohol Page 10
11 H(2B)-C(2)-H(2C) C(4')-C(3)-O(3) 107.6(3) O(3)-C(3)-C(4) 108.4(2) O(3)-C(3)-H(3A) C(4)-C(3)-H(3A) O(3)-C(3)-H(3B) C(4)-C(3)-H(3B) H(3A)-C(3)-H(3B) C(3)-C(4)-H(4A) C(3)-C(4)-H(4B) H(4A)-C(4)-H(4B) C(3)-C(4)-H(4C) H(4A)-C(4)-H(4C) H(4B)-C(4)-H(4C) C(3)-C(4')-H(4D) C(3)-C(4')-H(4E) H(4D)-C(4')-H(4E) C(3)-C(4')-H(4F) H(4D)-C(4')-H(4F) H(4E)-C(4')-H(4F) F(2)-C(5)-F(1) (14) F(2)-C(5)-C(6) (14) F(1)-C(5)-C(6) (16) F(2)-C(5)-P(1) (13) F(1)-C(5)-P(1) (11) C(6)-C(5)-P(1) (12) O(4)-C(6)-C(5) (15) O(4)-C(6)-C(7) 125.2(2) C(5)-C(6)-C(7) (18) O(4)-C(6)-C(7') (17) C(5)-C(6)-C(7') (17) O(4)-C(6)-H(6) C(5)-C(6)-H(6) C(7)-C(6)-H(6) O(4)-C(6)-H(6') C(5)-C(6)-H(6') C(7')-C(6)-H(6') C(8)-C(7)-C(6) 119.6(3) C(8)-C(7)-H(7) C(6)-C(7)-H(7) C(7)-C(8)-C(9) 125.1(3) C(7)-C(8)-H(8) C(9)-C(8)-H(8) C(10)-C(9)-C(14) 118.3(3) C(10)-C(9)-C(8) 119.1(3) C(14)-C(9)-C(8) 122.6(3) C(11)-C(10)-C(9) 121.1(3) C(11)-C(10)-H(10) C(9)-C(10)-H(10) C(12)-C(11)-C(10) 120.1(3) C(12)-C(11)-H(11) C(10)-C(11)-H(11) C(11)-C(12)-C(13) 119.7(4) C(11)-C(12)-H(12) C(13)-C(12)-H(12) C(12)-C(13)-C(14) 119.9(4) C(12)-C(13)-H(13) C(14)-C(13)-H(13) C(13)-C(14)-C(9) 120.9(3) C(13)-C(14)-H(14) C(9)-C(14)-H(14) C(8')-C(7')-C(6) 119.9(3) C(8')-C(7')-H(7') C(6)-C(7')-H(7') C(7')-C(8')-C(9') 126.4(3) C(7')-C(8')-H(8') C(9')-C(8')-H(8') C(10')-C(9')-C(14') 118.6(3) C(10')-C(9')-C(8') 122.7(3) C(14')-C(9')-C(8') 118.7(3) C(9')-C(10')-C(11') 120.5(3) C(9')-C(10')-H(10') C(11')-C(10')-H(10') C(12')-C(11')-C(10') 120.4(3) C(12')-C(11')-H(11') C(10')-C(11')-H(11') C(11')-C(12')-C(13') 119.5(4) C(11')-C(12')-H(12') C(13')-C(12')-H(12') C(14')-C(13')-C(12') 119.8(4) C(14')-C(13')-H(13') C(12')-C(13')-H(13') C(13')-C(14')-C(9') 121.1(3) C(13')-C(14')-H(14') C(9')-C(14')-H(14') KP-XI-cinnamyl-chiral alcohol Page 11
12 Table 4. Anisotropic displacement parameters (Å 2 x 10 3 ) for The anisotropic displacement factor exponent takes the form: -2 2 [ h 2 a* 2 U h k a* b* U 12 ] U 11 U 22 U 33 U 23 U 13 U 12 P(1) 19(1) 23(1) 22(1) 1(1) 4(1) 3(1) F(1) 39(1) 51(1) 21(1) 2(1) -4(1) 16(1) F(2) 24(1) 55(1) 48(1) -28(1) 4(1) -11(1) O(1) 43(1) 28(1) 31(1) 7(1) 11(1) 8(1) O(2) 25(1) 32(1) 24(1) -4(1) 5(1) 1(1) O(3) 23(1) 36(1) 22(1) -1(1) -4(1) -2(1) O(4) 51(1) 29(1) 29(1) -2(1) 17(1) 6(1) C(1) 47(1) 44(1) 38(1) -17(1) 10(1) -5(1) C(2) 76(2) 43(1) 70(2) -11(1) 34(2) 11(1) C(3) 31(1) 62(1) 22(1) -5(1) -4(1) -6(1) C(4) 27(2) 77(4) 35(1) -16(3) -6(1) -5(2) C(4') 27(2) 77(4) 35(1) -16(3) -6(1) -5(2) C(5) 18(1) 32(1) 24(1) -6(1) -2(1) 1(1) C(6) 20(1) 33(1) 26(1) -6(1) -5(1) 6(1) C(7) 18(2) 19(2) 26(2) 2(1) 0(1) 1(2) C(8) 21(2) 21(2) 25(2) 3(1) 1(1) 2(1) C(9) 17(2) 18(2) 25(2) 2(2) 0(2) 0(1) C(10) 21(2) 33(2) 53(3) 18(2) 6(2) 4(2) C(11) 21(2) 45(3) 66(3) 22(2) 7(2) 3(2) C(12) 20(3) 47(4) 39(3) 3(2) -3(2) 2(3) C(13) 28(2) 35(3) 35(3) 11(2) -2(2) 5(2) C(14) 17(2) 34(3) 38(3) 17(2) 1(2) -1(2) C(7') 21(2) 26(2) 24(2) -2(2) 0(1) 0(2) C(8') 21(2) 29(2) 24(2) -5(2) -1(1) 1(2) C(9') 20(2) 29(2) 19(2) 1(2) 2(2) 1(2) C(10') 29(2) 32(2) 37(2) 2(2) -2(2) 7(2) C(11') 23(2) 51(3) 42(3) 4(2) -5(2) -4(2) C(12') 22(3) 41(4) 31(3) 6(2) 1(2) 11(3) C(13') 29(2) 43(3) 32(3) 6(2) -3(2) 12(2) C(14') 30(2) 32(2) 25(2) 7(2) -1(2) 8(2) KP-XI-cinnamyl-chiral alcohol Page 12
13 Table 5. Hydrogen coordinates and isotropic displacement parameters for x y z U(eq) H(4) (10) 0.632(5) 0.511(3) H(1A) H(1B) H(2A) H(2B) H(2C) H(3A) H(3B) H(4A) H(4B) H(4C) H(4D) H(4E) H(4F) H(6) H(6') H(7) H(8) H(10) H(11) H(12) H(13) H(14) H(7') H(8') H(10') H(11') H(12') H(13') H(14') KP-XI-cinnamyl-chiral alcohol Page 13
14 Table 6. Torsion angles [ ] for O(1)-P(1)-O(2)-C(1) (17) O(3)-P(1)-O(2)-C(1) (15) C(5)-P(1)-O(2)-C(1) 76.15(16) O(1)-P(1)-O(3)-C(3) 19.99(17) O(2)-P(1)-O(3)-C(3) (15) C(5)-P(1)-O(3)-C(3) (15) P(1)-O(2)-C(1)-C(2) (19) P(1)-O(3)-C(3)-C(4') (4) P(1)-O(3)-C(3)-C(4) (3) O(1)-P(1)-C(5)-F(2) 47.88(14) O(3)-P(1)-C(5)-F(2) (11) O(2)-P(1)-C(5)-F(2) (13) O(1)-P(1)-C(5)-F(1) (12) O(3)-P(1)-C(5)-F(1) (13) O(2)-P(1)-C(5)-F(1) 34.96(14) O(1)-P(1)-C(5)-C(6) (16) O(3)-P(1)-C(5)-C(6) 52.84(16) O(2)-P(1)-C(5)-C(6) (14) F(2)-C(5)-C(6)-O(4) (18) F(1)-C(5)-C(6)-O(4) (14) P(1)-C(5)-C(6)-O(4) 49.60(18) F(2)-C(5)-C(6)-C(7) 65.3(2) F(1)-C(5)-C(6)-C(7) -49.6(2) P(1)-C(5)-C(6)-C(7) (19) F(2)-C(5)-C(6)-C(7') 35.3(2) F(1)-C(5)-C(6)-C(7') -79.6(2) P(1)-C(5)-C(6)-C(7') (16) O(4)-C(6)-C(7)-C(8) 16.8(4) C(5)-C(6)-C(7)-C(8) (3) C(6)-C(7)-C(8)-C(9) 178.4(2) C(7)-C(8)-C(9)-C(10) (4) C(7)-C(8)-C(9)-C(14) 3.8(4) C(14)-C(9)-C(10)-C(11) -1.2(4) C(8)-C(9)-C(10)-C(11) 179.6(3) C(9)-C(10)-C(11)-C(12) 0.1(6) C(10)-C(11)-C(12)-C(13) 0.7(8) C(11)-C(12)-C(13)-C(14) -0.4(8) C(12)-C(13)-C(14)-C(9) -0.7(6) C(10)-C(9)-C(14)-C(13) 1.5(4) C(8)-C(9)-C(14)-C(13) (3) O(4)-C(6)-C(7')-C(8') (3) C(5)-C(6)-C(7')-C(8') 110.7(3) C(6)-C(7')-C(8')-C(9') (19) C(7')-C(8')-C(9')-C(10') 1.3(3) C(7')-C(8')-C(9')-C(14') (3) C(14')-C(9')-C(10')-C(11') -0.4(4) C(8')-C(9')-C(10')-C(11') 179.8(2) C(9')-C(10')-C(11')-C(12') -0.1(6) C(10')-C(11')-C(12')-C(13') 0.4(8) C(11')-C(12')-C(13')-C(14') -0.3(8) C(12')-C(13')-C(14')-C(9') -0.2(6) C(10')-C(9')-C(14')-C(13') 0.6(5) C(8')-C(9')-C(14')-C(13') (3) KP-XI-cinnamyl-chiral alcohol Page 14
15 Table 7. Hydrogen bonds for 12040[Å and ]. D-H...A d(d-h) d(h...a) d(d...a) <(DHA) O(4)-H(4)...O(1)#1 0.74(3) 2.06(3) 2.768(2) 161(3) Symmetry transformations used to generate equivalent atoms: #1 -x+1/2, y-1/2, -z+1 KP-XI-cinnamyl-chiral alcohol Page 15
Small Molecule Crystallography Lab Department of Chemistry and Biochemistry University of Oklahoma 101 Stephenson Parkway Norman, OK
Small Molecule Crystallography Lab Department of Chemistry and Biochemistry University of Oklahoma 101 Stephenson Parkway Norman, OK 73019-5251 Sample: KP-XI-furan-enzymatic alcohol Lab ID: 12042 User:
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