organic compounds
Monoclinic modification of N-[(1,1-dimethylethoxy)carbonyl]-3-[(R)-prop-2-en-1-ylsulfinyl]-(R)-alanine ethyl ester at 200 (1) K
aDepartment of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2W1, and bDepartment of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
*Correspondence e-mail: alough@chem.utoronto.ca
In the monoclinic polymorph of the title compound, C13H23NO5S, intermolecular N—H⋯O hydrogen bonds link molecules into one-dimensional chains along [100]. The atoms of the terminal propenyl group are disordered over two sets of sites with refined occupancies of 0.69 (2) and 0.31 (2).
Related literature
For the et al. (2009). For background information on chiral see: Rose et al. (2005); Fernandez & Khiar, (2003); Olbe et al., 2003. For synthetic details, see: O'Donnell & Schwan (2003). For related crystal structures see: Allain et al. (1980); Nakamura et al. (1996). For temperature-dependent phase transition in cysteine, see: Paukov et al. (2007), Kolesov et al. (2008).
of the triclinic modification of the title compound at 120 (1) K see the paper which follows: SinghExperimental
Crystal data
|
Data collection: COLLECT (Nonius, 2002); cell DENZO-SMN (Otwinowski & Minor, 1997); data reduction: DENZO-SMN; program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXTL.
Supporting information
10.1107/S1600536809019023/hb2978sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809019023/hb2978Isup2.hkl
The N-protected amino acid derivative 1 (Fig. 3) was synthesized following a reported procedure. N-Boc-Alliin-OEt 2 was also synthesized by following the described procedure for its benzyl analog (O'Donnell and Schwan, 2003). Rerystallization from ethyl acetate and hexanes gave major diastereomer (RC, RS) of 2 as white solid, which was then dissolved in ethyl acetate and hexanes (9:1) and the solvent was allowed to evaporate slowly for several days to give white crystals of the major diastereomer (RC,RS) of 2.
Hydrogen atoms were placed in calculated positions with C—H = 0.95–0.99; N—H = 0.88 Å and refined as riding with Uiso(H) = 1.2Ueq(C, N) or 1.5Ueq(methyl C). The atoms of the terminal propenyl group are disordered over two sites with refined occupancies of 0.69 (2) and 0.31 (2); the bond lengths in the minor component were restrained to be equal to those of the major component.
Data collection: COLLECT (Nonius, 2002); cell
DENZO-SMN (Otwinowski & Minor, 1997); data reduction: DENZO-SMN (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).C13H23NO5S | F(000) = 328 |
Mr = 305.38 | Dx = 1.219 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 3908 reflections |
a = 5.1859 (6) Å | θ = 2.9–25.0° |
b = 11.5202 (18) Å | µ = 0.21 mm−1 |
c = 14.009 (2) Å | T = 200 K |
β = 96.396 (8)° | Needle, colourless |
V = 831.7 (2) Å3 | 0.38 × 0.12 × 0.12 mm |
Z = 2 |
Nonius KappaCCD diffractometer | 2397 independent reflections |
Radiation source: fine-focus sealed tube | 1844 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.070 |
Detector resolution: 9 pixels mm-1 | θmax = 25.0°, θmin = 2.9° |
ϕ scans and ω scans with κ offsets | h = −6→6 |
Absorption correction: multi-scan (SORTAV; Blessing, 1995) | k = −12→13 |
Tmin = 0.711, Tmax = 0.974 | l = −14→16 |
3908 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.059 | H-atom parameters constrained |
wR(F2) = 0.164 | w = 1/[σ2(Fo2) + (0.0816P)2 + 0.1385P] where P = (Fo2 + 2Fc2)/3 |
S = 1.05 | (Δ/σ)max = 0.002 |
2397 reflections | Δρmax = 0.30 e Å−3 |
196 parameters | Δρmin = −0.22 e Å−3 |
4 restraints | Absolute structure: Flack (1983), 898 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: −0.08 (15) |
C13H23NO5S | V = 831.7 (2) Å3 |
Mr = 305.38 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 5.1859 (6) Å | µ = 0.21 mm−1 |
b = 11.5202 (18) Å | T = 200 K |
c = 14.009 (2) Å | 0.38 × 0.12 × 0.12 mm |
β = 96.396 (8)° |
Nonius KappaCCD diffractometer | 2397 independent reflections |
Absorption correction: multi-scan (SORTAV; Blessing, 1995) | 1844 reflections with I > 2σ(I) |
Tmin = 0.711, Tmax = 0.974 | Rint = 0.070 |
3908 measured reflections |
R[F2 > 2σ(F2)] = 0.059 | H-atom parameters constrained |
wR(F2) = 0.164 | Δρmax = 0.30 e Å−3 |
S = 1.05 | Δρmin = −0.22 e Å−3 |
2397 reflections | Absolute structure: Flack (1983), 898 Friedel pairs |
196 parameters | Absolute structure parameter: −0.08 (15) |
4 restraints |
Experimental. Absorption correction: multi-scan from symmetry-related measurements (SORTAV; Blessing, 1995) |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
S1 | 0.4365 (2) | 0.46507 (13) | 0.25026 (8) | 0.0632 (4) | |
O1 | 0.1763 (5) | 0.4581 (4) | 0.2851 (3) | 0.0810 (10) | |
O2 | 0.6209 (19) | 0.7332 (5) | 0.4815 (4) | 0.175 (3) | |
O3 | 0.6089 (8) | 0.8717 (4) | 0.3748 (3) | 0.0850 (11) | |
O4 | 0.0034 (6) | 0.7655 (3) | 0.2141 (2) | 0.0667 (9) | |
O5 | 0.2554 (5) | 0.8446 (3) | 0.1080 (2) | 0.0656 (9) | |
N1 | 0.4391 (7) | 0.7397 (4) | 0.2270 (3) | 0.0576 (10) | |
H1 | 0.5784 | 0.7447 | 0.1966 | 0.069* | |
C1 | 0.6118 (9) | 0.5732 (4) | 0.3246 (4) | 0.0578 (12) | |
H1A | 0.6416 | 0.5449 | 0.3916 | 0.069* | |
H1B | 0.7828 | 0.5871 | 0.3015 | 0.069* | |
C2 | 0.4583 (9) | 0.6867 (4) | 0.3214 (3) | 0.0594 (12) | |
H2A | 0.2780 | 0.6674 | 0.3351 | 0.071* | |
C3 | 0.5757 (12) | 0.7652 (5) | 0.4014 (4) | 0.0775 (16) | |
C4 | 0.7307 (14) | 0.9553 (8) | 0.4454 (5) | 0.1019 (19) | |
H4A | 0.6164 | 1.0237 | 0.4490 | 0.122* | |
H4B | 0.7574 | 0.9189 | 0.5097 | 0.122* | |
C5 | 0.9780 (13) | 0.9914 (8) | 0.4162 (6) | 0.116 (3) | |
H5A | 1.0601 | 1.0474 | 0.4627 | 0.174* | |
H5B | 0.9502 | 1.0276 | 0.3526 | 0.174* | |
H5C | 1.0909 | 0.9235 | 0.4135 | 0.174* | |
C6 | 0.628 (4) | 0.3423 (8) | 0.2976 (17) | 0.067 (5) | 0.694 (18) |
H6A | 0.8146 | 0.3592 | 0.2950 | 0.080* | 0.694 (18) |
H6B | 0.6012 | 0.3302 | 0.3657 | 0.080* | 0.694 (18) |
C7 | 0.557 (2) | 0.2340 (8) | 0.2422 (9) | 0.082 (3) | 0.694 (18) |
H7 | 0.6299 | 0.2247 | 0.1833 | 0.098* | 0.694 (18) |
C8 | 0.406 (2) | 0.1516 (9) | 0.2657 (9) | 0.100 (4) | 0.694 (18) |
H8A | 0.3285 | 0.1565 | 0.3238 | 0.120* | 0.694 (18) |
H8B | 0.3740 | 0.0861 | 0.2249 | 0.120* | 0.694 (18) |
C6A | 0.600 (8) | 0.3431 (15) | 0.312 (3) | 0.057 (13)* | 0.306 (18) |
H6A1 | 0.7852 | 0.3428 | 0.3015 | 0.069* | 0.306 (18) |
H6A2 | 0.5896 | 0.3502 | 0.3824 | 0.069* | 0.306 (18) |
C7A | 0.474 (5) | 0.233 (2) | 0.2760 (18) | 0.076 (9)* | 0.306 (18) |
H7A | 0.3078 | 0.2138 | 0.2940 | 0.091* | 0.306 (18) |
C8A | 0.582 (6) | 0.161 (3) | 0.2209 (17) | 0.100 (9)* | 0.306 (18) |
H8A1 | 0.7483 | 0.1786 | 0.2021 | 0.120* | 0.306 (18) |
H8A2 | 0.4950 | 0.0921 | 0.1994 | 0.120* | 0.306 (18) |
C9 | 0.2142 (8) | 0.7809 (4) | 0.1855 (3) | 0.0542 (11) | |
C10 | 0.0367 (8) | 0.8905 (5) | 0.0423 (4) | 0.0668 (14) | |
C11 | 0.1753 (10) | 0.9514 (7) | −0.0349 (4) | 0.0905 (18) | |
H11A | 0.2817 | 1.0150 | −0.0056 | 0.136* | |
H11C | 0.0462 | 0.9825 | −0.0848 | 0.136* | |
H11D | 0.2866 | 0.8956 | −0.0637 | 0.136* | |
C12 | −0.1300 (11) | 0.7915 (5) | −0.0014 (4) | 0.0801 (16) | |
H12C | −0.2007 | 0.7478 | 0.0497 | 0.120* | |
H12D | −0.0241 | 0.7399 | −0.0367 | 0.120* | |
H12A | −0.2729 | 0.8229 | −0.0456 | 0.120* | |
C13 | −0.1142 (9) | 0.9761 (5) | 0.0933 (4) | 0.0732 (13) | |
H13C | −0.2131 | 0.9352 | 0.1386 | 0.110* | |
H13D | −0.2339 | 1.0182 | 0.0465 | 0.110* | |
H13A | 0.0053 | 1.0312 | 0.1284 | 0.110* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0581 (6) | 0.0632 (7) | 0.0675 (7) | −0.0011 (7) | 0.0036 (5) | 0.0038 (7) |
O1 | 0.0487 (16) | 0.079 (2) | 0.114 (3) | −0.005 (2) | 0.0032 (16) | 0.000 (3) |
O2 | 0.370 (10) | 0.077 (3) | 0.064 (3) | 0.004 (5) | −0.035 (4) | −0.003 (3) |
O3 | 0.108 (3) | 0.077 (3) | 0.070 (2) | −0.019 (2) | 0.0107 (19) | −0.002 (2) |
O4 | 0.0447 (16) | 0.076 (2) | 0.080 (2) | 0.0025 (17) | 0.0113 (15) | 0.0132 (17) |
O5 | 0.0517 (17) | 0.083 (2) | 0.062 (2) | 0.0055 (17) | 0.0057 (13) | 0.0213 (18) |
N1 | 0.044 (2) | 0.065 (3) | 0.064 (2) | 0.0082 (19) | 0.0095 (16) | 0.006 (2) |
C1 | 0.052 (2) | 0.059 (3) | 0.062 (3) | −0.004 (2) | 0.004 (2) | 0.004 (2) |
C2 | 0.057 (3) | 0.066 (3) | 0.056 (3) | 0.006 (2) | 0.014 (2) | 0.008 (2) |
C3 | 0.102 (4) | 0.067 (4) | 0.063 (4) | 0.022 (3) | 0.003 (3) | 0.004 (3) |
C4 | 0.116 (5) | 0.100 (5) | 0.090 (4) | −0.014 (5) | 0.011 (3) | −0.023 (4) |
C5 | 0.089 (4) | 0.140 (8) | 0.115 (5) | −0.022 (5) | −0.005 (4) | −0.028 (5) |
C6 | 0.056 (6) | 0.058 (7) | 0.085 (9) | −0.004 (4) | 0.005 (8) | 0.005 (4) |
C7 | 0.100 (8) | 0.062 (7) | 0.084 (7) | 0.010 (6) | 0.015 (6) | 0.005 (6) |
C8 | 0.117 (9) | 0.071 (7) | 0.105 (8) | −0.017 (6) | −0.021 (6) | 0.007 (6) |
C9 | 0.047 (3) | 0.054 (3) | 0.061 (3) | 0.001 (2) | 0.004 (2) | −0.002 (2) |
C10 | 0.049 (2) | 0.078 (4) | 0.072 (3) | 0.008 (3) | 0.001 (2) | 0.014 (3) |
C11 | 0.075 (3) | 0.123 (5) | 0.073 (3) | 0.005 (4) | 0.002 (2) | 0.033 (4) |
C12 | 0.079 (3) | 0.078 (4) | 0.081 (4) | 0.012 (3) | −0.003 (3) | −0.004 (3) |
C13 | 0.064 (3) | 0.061 (3) | 0.092 (3) | −0.001 (3) | −0.002 (2) | 0.003 (3) |
S1—O1 | 1.487 (3) | C6—H6A | 0.9900 |
S1—C1 | 1.803 (5) | C6—H6B | 0.9900 |
S1—C6 | 1.813 (6) | C7—C8 | 1.296 (12) |
S1—C6A | 1.813 (7) | C7—H7 | 0.9500 |
O2—C3 | 1.179 (7) | C8—H8A | 0.9500 |
O3—C3 | 1.300 (7) | C8—H8B | 0.9500 |
O3—C4 | 1.471 (8) | C6A—C7A | 1.493 (14) |
O4—C9 | 1.218 (5) | C6A—H6A1 | 0.9900 |
O5—C9 | 1.347 (6) | C6A—H6A2 | 0.9900 |
O5—C10 | 1.477 (5) | C7A—C8A | 1.296 (13) |
N1—C9 | 1.331 (6) | C7A—H7A | 0.9500 |
N1—C2 | 1.450 (6) | C8A—H8A1 | 0.9500 |
N1—H1 | 0.8800 | C8A—H8A2 | 0.9500 |
C1—C2 | 1.529 (7) | C10—C13 | 1.491 (8) |
C1—H1A | 0.9900 | C10—C12 | 1.518 (8) |
C1—H1B | 0.9900 | C10—C11 | 1.534 (8) |
C2—C3 | 1.514 (8) | C11—H11A | 0.9800 |
C2—H2A | 1.0000 | C11—H11C | 0.9800 |
C4—C5 | 1.450 (10) | C11—H11D | 0.9800 |
C4—H4A | 0.9900 | C12—H12C | 0.9800 |
C4—H4B | 0.9900 | C12—H12D | 0.9800 |
C5—H5A | 0.9800 | C12—H12A | 0.9800 |
C5—H5B | 0.9800 | C13—H13C | 0.9800 |
C5—H5C | 0.9800 | C13—H13D | 0.9800 |
C6—C7 | 1.494 (13) | C13—H13A | 0.9800 |
O1—S1—C1 | 105.4 (2) | C8—C7—H7 | 116.5 |
O1—S1—C6 | 108.6 (9) | C6—C7—H7 | 116.5 |
C1—S1—C6 | 96.2 (4) | C7—C8—H8A | 120.0 |
O1—S1—C6A | 101.1 (18) | C7—C8—H8B | 120.0 |
C1—S1—C6A | 94.6 (9) | H8A—C8—H8B | 120.0 |
C3—O3—C4 | 119.1 (5) | C7A—C6A—S1 | 109.5 (16) |
C9—O5—C10 | 121.2 (3) | C7A—C6A—H6A1 | 109.8 |
C9—N1—C2 | 121.1 (4) | S1—C6A—H6A1 | 109.8 |
C9—N1—H1 | 119.5 | C7A—C6A—H6A2 | 109.8 |
C2—N1—H1 | 119.5 | S1—C6A—H6A2 | 109.8 |
C2—C1—S1 | 110.3 (3) | H6A1—C6A—H6A2 | 108.2 |
C2—C1—H1A | 109.6 | C8A—C7A—C6A | 123 (4) |
S1—C1—H1A | 109.6 | C8A—C7A—H7A | 118.6 |
C2—C1—H1B | 109.6 | C6A—C7A—H7A | 118.6 |
S1—C1—H1B | 109.6 | C7A—C8A—H8A1 | 120.0 |
H1A—C1—H1B | 108.1 | C7A—C8A—H8A2 | 120.0 |
N1—C2—C3 | 113.9 (4) | H8A1—C8A—H8A2 | 120.0 |
N1—C2—C1 | 111.7 (4) | O4—C9—N1 | 125.4 (4) |
C3—C2—C1 | 108.9 (4) | O4—C9—O5 | 125.0 (4) |
N1—C2—H2A | 107.4 | N1—C9—O5 | 109.6 (4) |
C3—C2—H2A | 107.4 | O5—C10—C13 | 110.2 (4) |
C1—C2—H2A | 107.4 | O5—C10—C12 | 110.3 (4) |
O2—C3—O3 | 123.3 (6) | C13—C10—C12 | 112.6 (4) |
O2—C3—C2 | 122.6 (6) | O5—C10—C11 | 102.5 (3) |
O3—C3—C2 | 114.0 (5) | C13—C10—C11 | 110.3 (5) |
C5—C4—O3 | 109.0 (5) | C12—C10—C11 | 110.5 (5) |
C5—C4—H4A | 109.9 | C10—C11—H11A | 109.5 |
O3—C4—H4A | 109.9 | C10—C11—H11C | 109.5 |
C5—C4—H4B | 109.9 | H11A—C11—H11C | 109.5 |
O3—C4—H4B | 109.9 | C10—C11—H11D | 109.5 |
H4A—C4—H4B | 108.3 | H11A—C11—H11D | 109.5 |
C4—C5—H5A | 109.5 | H11C—C11—H11D | 109.5 |
C4—C5—H5B | 109.5 | C10—C12—H12C | 109.5 |
H5A—C5—H5B | 109.5 | C10—C12—H12D | 109.5 |
C4—C5—H5C | 109.5 | H12C—C12—H12D | 109.5 |
H5A—C5—H5C | 109.5 | C10—C12—H12A | 109.5 |
H5B—C5—H5C | 109.5 | H12C—C12—H12A | 109.5 |
C7—C6—S1 | 111.5 (7) | H12D—C12—H12A | 109.5 |
C7—C6—H6A | 109.3 | C10—C13—H13C | 109.5 |
S1—C6—H6A | 109.3 | C10—C13—H13D | 109.5 |
C7—C6—H6B | 109.3 | H13C—C13—H13D | 109.5 |
S1—C6—H6B | 109.3 | C10—C13—H13A | 109.5 |
H6A—C6—H6B | 108.0 | H13C—C13—H13A | 109.5 |
C8—C7—C6 | 126.9 (18) | H13D—C13—H13A | 109.5 |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O4i | 0.88 | 2.20 | 2.967 (5) | 145 |
Symmetry code: (i) x+1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C13H23NO5S |
Mr | 305.38 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 200 |
a, b, c (Å) | 5.1859 (6), 11.5202 (18), 14.009 (2) |
β (°) | 96.396 (8) |
V (Å3) | 831.7 (2) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.21 |
Crystal size (mm) | 0.38 × 0.12 × 0.12 |
Data collection | |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (SORTAV; Blessing, 1995) |
Tmin, Tmax | 0.711, 0.974 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3908, 2397, 1844 |
Rint | 0.070 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.059, 0.164, 1.05 |
No. of reflections | 2397 |
No. of parameters | 196 |
No. of restraints | 4 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.30, −0.22 |
Absolute structure | Flack (1983), 898 Friedel pairs |
Absolute structure parameter | −0.08 (15) |
Computer programs: COLLECT (Nonius, 2002), DENZO-SMN (Otwinowski & Minor, 1997), SIR92 (Altomare et al., 1994), SHELXTL (Sheldrick, 2008), PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O4i | 0.88 | 2.20 | 2.967 (5) | 145 |
Symmetry code: (i) x+1, y, z. |
Acknowledgements
The authors wish to acknowledge NSERC Canada and the University of Toronto for funding and the donors of the American Chemical Society Petroleum Research Fund for partial support of this research
References
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A number of biologically significant molecules have a chiral sulfoxide functionality in their structure which is important for stereochemically dependent biological actions like metabolism and enzyme inhibition (Rose et al., 2005). Owing to the existence of pharmacological and toxicological differences between stereoisomers, chiral recognition has now become an integral part of drug research and development. Therefore, there has been a great interest in the synthesis of optically pure sulfoxides in recent years (Fernandez & Khiar, 2003). For example, the chiral switch drug esomeprazole [(S) isomer of omeprazole], the first single-optical-isomer gastric proton pump inhibitor (PPI), generally provides better acid control than current racemic PPIs and has a favourable pharmacokinetic profile relative to omeprazole (Olbe et al., 2003). However, only few examples of crystal structures of chirally pure cysteinyl sulfoxides have been reported in the literature (Nakamura et al., 1996). Moreover, temperature dependent phase trasitions in the crystal structures of cysteinyl sulfoxides are unknown till date (Paukov et al., 2007 and Kolesov et al., 2008).
The molecular structure of the title compound, (I), is shown in Fig. 1. In the crystal structure, intermolecular N—H···O hydrogen bonds link molecules into one-dimensional chains along [100] (Table 1, Fig. 2). Data for the title compound (using the same crystal) were also collected at 120 (1) K and the crystal structure solves and refines in the triclinic space group P1 (Singh et al., 2009).