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Zolmitriptan, C
16H
21N
3O
2, a selective serotonin (5-HT) receptor agonist, is chemically designated as (
S)-4-{3-[2-(dimethylamino)ethyl]-1
H-indol-5-ylmethyl}oxazolidin-2-one. The molecular geometry is similar to that of sumatriptan, but the two differ in their side-chain orientations. Intermolecular N—H
O and N—H
N hydrogen bonds form a screw-symmetric helical chain along the
b axis.
Supporting information
CCDC reference: 642977
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (C-C) = 0.004 Å
- R factor = 0.040
- wR factor = 0.107
- Data-to-parameter ratio = 7.7
checkCIF/PLATON results
No syntax errors found
Alert level C
PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax .LT. 18) ..... 7.75
PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for O1
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for N2
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 25.00
From the CIF: _reflns_number_total 1549
Count of symmetry unique reflns 1550
Completeness (_total/calc) 99.94%
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
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature 293 K
PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature . 293 K
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C14 = . S
0 ALERT level A = In general: serious problem
0 ALERT level B = Potentially serious problem
3 ALERT level C = Check and explain
4 ALERT level G = General alerts; check
3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
2 ALERT type 2 Indicator that the structure model may be wrong or deficient
1 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
Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003) and DIAMOND (Brandenburg & Putz, 2005); software used to prepare material for publication: SHELXL97.
(
S)-4-{3-[2-(dimethylamino)ethyl]-1
H-indol-5-ylmethyl}oxazolidin-2-one
top
Crystal data top
C16H21N3O2 | F(000) = 616 |
Mr = 287.36 | Dx = 1.260 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 5206 reflections |
a = 9.0643 (7) Å | θ = 2.3–26.1° |
b = 11.4220 (9) Å | µ = 0.09 mm−1 |
c = 14.6320 (12) Å | T = 293 K |
V = 1514.9 (2) Å3 | Block, colourless |
Z = 4 | 0.19 × 0.17 × 0.12 mm |
Data collection top
Bruker SMART APEX CCD area-detector diffractometer | 1475 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.020 |
Graphite monochromator | θmax = 25.0°, θmin = 2.3° |
ω scans | h = −10→10 |
10937 measured reflections | k = −13→13 |
1549 independent reflections | l = −17→17 |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.040 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.107 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.12 | w = 1/[σ2(Fo2) + (0.0671P)2 + 0.1659P] where P = (Fo2 + 2Fc2)/3 |
1549 reflections | (Δ/σ)max < 0.001 |
200 parameters | Δρmax = 0.21 e Å−3 |
0 restraints | Δρmin = −0.11 e Å−3 |
Special details top
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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
C1 | 0.2900 (3) | 1.0570 (2) | 1.00847 (16) | 0.0541 (6) | |
H1 | 0.2342 | 1.1163 | 1.0349 | 0.065* | |
C2 | 0.2334 (3) | 0.9655 (2) | 0.96041 (16) | 0.0474 (6) | |
C3 | 0.3572 (2) | 0.8950 (2) | 0.93382 (14) | 0.0405 (5) | |
C4 | 0.3732 (3) | 0.7919 (2) | 0.88279 (15) | 0.0427 (5) | |
H4 | 0.2900 | 0.7534 | 0.8609 | 0.051* | |
C5 | 0.5119 (3) | 0.74708 (19) | 0.86478 (15) | 0.0435 (5) | |
C6 | 0.6368 (3) | 0.8041 (2) | 0.90192 (16) | 0.0479 (6) | |
H6 | 0.7299 | 0.7728 | 0.8910 | 0.057* | |
C7 | 0.6255 (3) | 0.9042 (2) | 0.95350 (16) | 0.0478 (6) | |
H7 | 0.7087 | 0.9401 | 0.9779 | 0.057* | |
C8 | 0.4851 (3) | 0.9500 (2) | 0.96800 (14) | 0.0430 (5) | |
C9 | 0.0744 (3) | 0.9408 (3) | 0.9392 (2) | 0.0574 (7) | |
H9A | 0.0132 | 0.9911 | 0.9768 | 0.069* | |
H9B | 0.0527 | 0.8604 | 0.9558 | 0.069* | |
C10 | 0.0321 (3) | 0.9592 (2) | 0.8388 (2) | 0.0572 (7) | |
H10A | 0.1005 | 0.9156 | 0.8009 | 0.069* | |
H10B | −0.0654 | 0.9267 | 0.8289 | 0.069* | |
C11 | −0.0846 (4) | 1.1466 (3) | 0.8544 (3) | 0.0810 (10) | |
H11A | −0.1775 | 1.1077 | 0.8460 | 0.122* | |
H11B | −0.0898 | 1.2238 | 0.8286 | 0.122* | |
H11C | −0.0630 | 1.1521 | 0.9184 | 0.122* | |
C12 | 0.0067 (4) | 1.0878 (3) | 0.7103 (2) | 0.0825 (10) | |
H12A | 0.0800 | 1.0425 | 0.6788 | 0.124* | |
H12B | 0.0134 | 1.1681 | 0.6913 | 0.124* | |
H12C | −0.0896 | 1.0580 | 0.6960 | 0.124* | |
C13 | 0.5292 (3) | 0.6397 (2) | 0.80671 (17) | 0.0501 (6) | |
H13A | 0.4395 | 0.5937 | 0.8113 | 0.060* | |
H13B | 0.6089 | 0.5929 | 0.8316 | 0.060* | |
C14 | 0.5611 (3) | 0.6623 (2) | 0.70485 (16) | 0.0472 (6) | |
H14 | 0.5568 | 0.5878 | 0.6718 | 0.057* | |
C15 | 0.4589 (3) | 0.7498 (3) | 0.65801 (18) | 0.0592 (7) | |
H15A | 0.3929 | 0.7097 | 0.6162 | 0.071* | |
H15B | 0.4001 | 0.7912 | 0.7030 | 0.071* | |
C16 | 0.6936 (3) | 0.8032 (2) | 0.62663 (19) | 0.0591 (7) | |
N1 | 0.4406 (3) | 1.0495 (2) | 1.01252 (15) | 0.0525 (5) | |
H1N | 0.496 (3) | 1.091 (2) | 1.037 (2) | 0.056 (9)* | |
N2 | 0.0317 (2) | 1.08013 (18) | 0.80867 (14) | 0.0492 (5) | |
N3 | 0.7028 (2) | 0.7173 (2) | 0.68729 (14) | 0.0501 (5) | |
H3N | 0.779 (4) | 0.676 (3) | 0.687 (2) | 0.059 (8)* | |
O1 | 0.5508 (2) | 0.8291 (2) | 0.60966 (17) | 0.0764 (6) | |
O2 | 0.7915 (3) | 0.8552 (2) | 0.58831 (19) | 0.0956 (8) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
C1 | 0.0599 (15) | 0.0570 (14) | 0.0453 (12) | 0.0132 (12) | 0.0087 (12) | −0.0006 (11) |
C2 | 0.0467 (12) | 0.0540 (14) | 0.0417 (11) | 0.0076 (11) | 0.0048 (10) | 0.0067 (11) |
C3 | 0.0351 (11) | 0.0471 (12) | 0.0392 (10) | −0.0002 (9) | 0.0018 (9) | 0.0072 (9) |
C4 | 0.0368 (11) | 0.0471 (12) | 0.0443 (11) | −0.0053 (10) | −0.0004 (10) | 0.0055 (10) |
C5 | 0.0451 (12) | 0.0445 (12) | 0.0409 (11) | −0.0005 (10) | 0.0048 (10) | 0.0080 (9) |
C6 | 0.0355 (11) | 0.0575 (14) | 0.0507 (12) | 0.0049 (11) | 0.0046 (11) | 0.0073 (11) |
C7 | 0.0373 (11) | 0.0574 (14) | 0.0485 (12) | −0.0072 (11) | −0.0048 (11) | 0.0044 (11) |
C8 | 0.0452 (12) | 0.0490 (11) | 0.0349 (10) | −0.0010 (11) | −0.0007 (9) | 0.0034 (9) |
C9 | 0.0419 (13) | 0.0641 (16) | 0.0663 (16) | 0.0081 (12) | 0.0119 (12) | 0.0111 (13) |
C10 | 0.0400 (13) | 0.0591 (15) | 0.0726 (16) | −0.0019 (12) | −0.0019 (12) | −0.0073 (13) |
C11 | 0.0647 (19) | 0.074 (2) | 0.104 (2) | 0.0211 (17) | 0.0151 (18) | 0.0026 (19) |
C12 | 0.078 (2) | 0.106 (2) | 0.0630 (17) | −0.016 (2) | −0.0151 (16) | 0.0047 (18) |
C13 | 0.0507 (13) | 0.0442 (12) | 0.0554 (13) | 0.0004 (11) | 0.0063 (12) | 0.0065 (10) |
C14 | 0.0459 (13) | 0.0477 (12) | 0.0480 (12) | 0.0035 (10) | 0.0026 (11) | −0.0045 (10) |
C15 | 0.0453 (14) | 0.0804 (19) | 0.0518 (13) | 0.0064 (13) | −0.0007 (11) | 0.0049 (13) |
C16 | 0.0539 (15) | 0.0577 (15) | 0.0659 (16) | −0.0037 (13) | −0.0004 (13) | 0.0094 (13) |
N1 | 0.0578 (12) | 0.0539 (12) | 0.0457 (11) | −0.0020 (11) | −0.0032 (10) | −0.0094 (10) |
N2 | 0.0408 (10) | 0.0568 (12) | 0.0499 (10) | −0.0011 (9) | −0.0024 (9) | −0.0035 (9) |
N3 | 0.0396 (10) | 0.0584 (12) | 0.0524 (11) | 0.0087 (10) | 0.0048 (10) | 0.0029 (10) |
O1 | 0.0597 (12) | 0.0765 (13) | 0.0929 (14) | 0.0059 (10) | −0.0084 (11) | 0.0356 (12) |
O2 | 0.0720 (14) | 0.0914 (16) | 0.123 (2) | −0.0205 (13) | 0.0075 (14) | 0.0423 (15) |
Geometric parameters (Å, º) top
C1—C2 | 1.360 (4) | C11—N2 | 1.461 (4) |
C1—N1 | 1.369 (4) | C11—H11A | 0.9600 |
C1—H1 | 0.9300 | C11—H11B | 0.9600 |
C2—C3 | 1.435 (3) | C11—H11C | 0.9600 |
C2—C9 | 1.501 (4) | C12—N2 | 1.460 (4) |
C3—C4 | 1.402 (3) | C12—H12A | 0.9600 |
C3—C8 | 1.411 (3) | C12—H12B | 0.9600 |
C4—C5 | 1.383 (3) | C12—H12C | 0.9600 |
C4—H4 | 0.9300 | C13—C14 | 1.540 (3) |
C5—C6 | 1.415 (3) | C13—H13A | 0.9700 |
C5—C13 | 1.500 (3) | C13—H13B | 0.9700 |
C6—C7 | 1.374 (3) | C14—N3 | 1.453 (3) |
C6—H6 | 0.9300 | C14—C15 | 1.525 (4) |
C7—C8 | 1.392 (3) | C14—H14 | 0.9800 |
C7—H7 | 0.9300 | C15—O1 | 1.419 (3) |
C8—N1 | 1.370 (3) | C15—H15A | 0.9700 |
C9—C10 | 1.532 (4) | C15—H15B | 0.9700 |
C9—H9A | 0.9700 | C16—O2 | 1.207 (3) |
C9—H9B | 0.9700 | C16—N3 | 1.325 (3) |
C10—N2 | 1.450 (3) | C16—O1 | 1.351 (3) |
C10—H10A | 0.9700 | N1—H1N | 0.78 (3) |
C10—H10B | 0.9700 | N3—H3N | 0.83 (3) |
| | | |
C2—C1—N1 | 110.5 (2) | H11A—C11—H11C | 109.5 |
C2—C1—H1 | 124.7 | H11B—C11—H11C | 109.5 |
N1—C1—H1 | 124.7 | N2—C12—H12A | 109.5 |
C1—C2—C3 | 106.0 (2) | N2—C12—H12B | 109.5 |
C1—C2—C9 | 127.9 (2) | H12A—C12—H12B | 109.5 |
C3—C2—C9 | 126.1 (2) | N2—C12—H12C | 109.5 |
C4—C3—C8 | 118.5 (2) | H12A—C12—H12C | 109.5 |
C4—C3—C2 | 134.2 (2) | H12B—C12—H12C | 109.5 |
C8—C3—C2 | 107.3 (2) | C5—C13—C14 | 115.49 (19) |
C5—C4—C3 | 120.5 (2) | C5—C13—H13A | 108.4 |
C5—C4—H4 | 119.8 | C14—C13—H13A | 108.4 |
C3—C4—H4 | 119.8 | C5—C13—H13B | 108.4 |
C4—C5—C6 | 118.9 (2) | C14—C13—H13B | 108.4 |
C4—C5—C13 | 120.3 (2) | H13A—C13—H13B | 107.5 |
C6—C5—C13 | 120.7 (2) | N3—C14—C15 | 100.0 (2) |
C7—C6—C5 | 122.3 (2) | N3—C14—C13 | 114.2 (2) |
C7—C6—H6 | 118.8 | C15—C14—C13 | 115.5 (2) |
C5—C6—H6 | 118.8 | N3—C14—H14 | 108.9 |
C6—C7—C8 | 117.7 (2) | C15—C14—H14 | 108.9 |
C6—C7—H7 | 121.2 | C13—C14—H14 | 108.9 |
C8—C7—H7 | 121.2 | O1—C15—C14 | 106.6 (2) |
N1—C8—C7 | 130.8 (2) | O1—C15—H15A | 110.4 |
N1—C8—C3 | 107.2 (2) | C14—C15—H15A | 110.4 |
C7—C8—C3 | 122.0 (2) | O1—C15—H15B | 110.4 |
C2—C9—C10 | 114.4 (2) | C14—C15—H15B | 110.4 |
C2—C9—H9A | 108.7 | H15A—C15—H15B | 108.6 |
C10—C9—H9A | 108.7 | O2—C16—N3 | 129.0 (3) |
C2—C9—H9B | 108.7 | O2—C16—O1 | 120.8 (3) |
C10—C9—H9B | 108.7 | N3—C16—O1 | 110.2 (2) |
H9A—C9—H9B | 107.6 | C1—N1—C8 | 109.0 (2) |
N2—C10—C9 | 115.0 (2) | C1—N1—H1N | 129 (2) |
N2—C10—H10A | 108.5 | C8—N1—H1N | 122 (2) |
C9—C10—H10A | 108.5 | C10—N2—C12 | 110.9 (2) |
N2—C10—H10B | 108.5 | C10—N2—C11 | 111.0 (2) |
C9—C10—H10B | 108.5 | C12—N2—C11 | 108.0 (3) |
H10A—C10—H10B | 107.5 | C16—N3—C14 | 112.5 (2) |
N2—C11—H11A | 109.5 | C16—N3—H3N | 118 (2) |
N2—C11—H11B | 109.5 | C14—N3—H3N | 119 (2) |
H11A—C11—H11B | 109.5 | C16—O1—C15 | 109.3 (2) |
N2—C11—H11C | 109.5 | | |
| | | |
N1—C1—C2—C3 | 0.9 (3) | C3—C2—C9—C10 | −71.7 (4) |
N1—C1—C2—C9 | −179.5 (3) | C2—C9—C10—N2 | −69.6 (3) |
C1—C2—C3—C4 | −178.7 (2) | C4—C5—C13—C14 | 95.6 (3) |
C9—C2—C3—C4 | 1.7 (4) | C6—C5—C13—C14 | −84.4 (3) |
C1—C2—C3—C8 | −0.3 (2) | C5—C13—C14—N3 | 65.8 (3) |
C9—C2—C3—C8 | −179.9 (2) | C5—C13—C14—C15 | −49.5 (3) |
C8—C3—C4—C5 | −1.5 (3) | N3—C14—C15—O1 | 8.7 (2) |
C2—C3—C4—C5 | 176.8 (2) | C13—C14—C15—O1 | 131.8 (2) |
C3—C4—C5—C6 | 2.7 (3) | C2—C1—N1—C8 | −1.2 (3) |
C3—C4—C5—C13 | −177.31 (19) | C7—C8—N1—C1 | 180.0 (2) |
C4—C5—C6—C7 | −1.6 (3) | C3—C8—N1—C1 | 1.0 (3) |
C13—C5—C6—C7 | 178.4 (2) | C9—C10—N2—C12 | 173.5 (2) |
C5—C6—C7—C8 | −0.6 (3) | C9—C10—N2—C11 | −66.4 (3) |
C6—C7—C8—N1 | −177.0 (2) | O2—C16—N3—C14 | −169.1 (3) |
C6—C7—C8—C3 | 1.9 (3) | O1—C16—N3—C14 | 10.6 (3) |
C4—C3—C8—N1 | 178.27 (18) | C15—C14—N3—C16 | −11.8 (3) |
C2—C3—C8—N1 | −0.4 (2) | C13—C14—N3—C16 | −135.8 (2) |
C4—C3—C8—C7 | −0.8 (3) | O2—C16—O1—C15 | 175.7 (3) |
C2—C3—C8—C7 | −179.5 (2) | N3—C16—O1—C15 | −4.0 (3) |
C1—C2—C9—C10 | 108.8 (3) | C14—C15—O1—C16 | −3.5 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···O2i | 0.78 (3) | 2.16 (3) | 2.883 (3) | 155 (3) |
N3—H3N···N2ii | 0.83 (3) | 2.04 (3) | 2.873 (3) | 177 (3) |
Symmetry codes: (i) −x+3/2, −y+2, z+1/2; (ii) −x+1, y−1/2, −z+3/2. |
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