organic compounds
1-(5-Carboxypentyl)-2,3,3-trimethyl-3H-indol-1-ium bromide monohydrate
aDepartment of Chemistry, Morgan State University, Baltimore, MD 21251, USA, bDepartment of Chemistry, Keene State College, 229 Main Street, Keene, NH 03435-2001, USA, and cDepartment of Chemistry, Howard University, 525 College Street NW, Washington, DC 20059, USA
*Correspondence e-mail: rbutcher99@yahoo.com
In the title compound, C17H24NO2+·Br−·H2O, the pentyl group chain in the cation extends nearly perpendicular [N—C—C—C = −64.4 (3)°] to the mean plane of the indole ring with the carboxyl end group twisted such that the dihedral angle between the mean planes of the indole and carboxy groups measures 43.2 (4)°. Both ions in the salt form intermolecular hydrogen bonds (O—H⋯Br and O—H⋯O) with the water molecule. As a result of the Br⋯H—O—H⋯Br interactions, a zigzag chain is formed in the c-axis direction. The crystal packing is influenced by the collective action of the O—H⋯O and O—H⋯Br intermolecular interactions as well as π–π stacking intermolecular interactions between adjacent benzyl rings of the indole group [centroid–centroid distance = 3.721 (13) Å] and intermolecular C—H⋯π interactions between a methyl hydrogen and the benzyl ring of the indole group. The O—H⋯Br interactions form a distorted tetrahedral array about the central Br atom. A MOPAC AM1 calculation provides support to these observations.
Related literature
For chemical and biological background, see: Zhu et al. (1994); Schwartz & Ulfelder (1992); Bengtsson et al. (2003); Hirons et al. (1994); Kurihara et al. (1977); Armitage & O'Brien (1992); Reers et al. (1991); Jung & Kim (2006); Menger & Pertusati (2008). A geometry optimized MOPAC AM1 computational calculation was performed using WebMO Pro (Schmidt & Polik, 2007).
Experimental
Crystal data
|
Refinement
|
Data collection: CrysAlis Pro (Oxford Diffraction, 2007); cell CrysAlis Pro; data reduction: CrysAlis Pro; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.
Supporting information
10.1107/S1600536809049204/fl2265sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809049204/fl2265Isup2.hkl
The title compound (I) has been previously synthesized by refluxing reagents with the solvent o-dichloro-benzene for 12–24 h followed by filtration (Jung et al., (2006); Menger et al. (2008)). For our study the title compound, (I), was synthesized as follows: 6-bromohexanoic acid (0.67 g, 0.0034 moles) and 2,3,3-trimethylindolenine (0.54 ml, 0.0034 moles) were added to a reaction vial via syringe and heated at 433 K for 1200 s and a ramp of 150 s in a Biotage Initiator microwave system (Scheme 2). The crystals were washed with acetone and dried under vacuum to yield (0.51 g, 42%). The sample was recrystallized by dissolving in dichloromethane then allowed to evaporate slowly at room temperature. 1H-NMR (DMSO-d6, 400 MHz): δ (p.p.m.): 7.87–8.01 (m, 1H), 7.78–7.87 (m, 1H), 7.26–7.64 (m, 2H) 4.45 (t, J = 7.6 Hz, 2H), 2.87 (s, 3H), 2.24 (t, J = 7.2 Hz, 2H), 1.85–1.81 (m, 2H), 1.6–1.5 (m, 8H), 1.44 (m, 3H); 13C-NMR (DMSO-d6, 100 MHz): δ (p.p.m.): 196.5 (C), 174.2 (C), 141.8 (C), 141.0 (C), 129.3 (CH), 128.9 (CH), 123.5 (CH), 115.4 (CH), 54.1 (C), 47.4 (CH2), 33.3 (CH2), 26.9 (CH2), 25.4 (CH2), 24.0 (CH2), 22.0 (CH3), 14.0 (CH3).
H1W1, H1W2 were obtained from a difference fourier map and refined with Uiso(H) = 1.5Ueq(O). The rest of the H atoms were placed in their calculated positions and then refined using a riding model with C(O)—H distances ranging from 0.84 to 0.99 Å, and with Uiso(H) = 1.2eq(C,O) [1.5Ueq for CH3].
Data collection: CrysAlis PRO (Oxford Diffraction, 2007); cell
CrysAlis PRO (Oxford Diffraction, 2007); data reduction: CrysAlis PRO (Oxford Diffraction, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).C17H24NO2+·Br−·H2O | F(000) = 776 |
Mr = 372.30 | Dx = 1.399 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54178 Å |
Hall symbol: -P 2ybc | Cell parameters from 8515 reflections |
a = 14.4528 (3) Å | θ = 5.6–73.5° |
b = 15.3367 (2) Å | µ = 3.27 mm−1 |
c = 8.0810 (2) Å | T = 200 K |
β = 99.437 (2)° | Needle, colorless |
V = 1766.98 (6) Å3 | 0.55 × 0.18 × 0.12 mm |
Z = 4 |
Oxford Diffraction Gemini R diffractometer | 3504 independent reflections |
Radiation source: fine-focus sealed tube | 3049 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.033 |
Detector resolution: 10.5081 pixels mm-1 | θmax = 73.7°, θmin = 5.8° |
ϕ and ω scans | h = −17→15 |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007) | k = −18→19 |
Tmin = 0.296, Tmax = 0.676 | l = −10→8 |
13155 measured reflections |
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)] = 0.037 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.098 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0518P)2 + 1.5238P] where P = (Fo2 + 2Fc2)/3 |
3504 reflections | (Δ/σ)max = 0.001 |
209 parameters | Δρmax = 0.52 e Å−3 |
3 restraints | Δρmin = −0.43 e Å−3 |
C17H24NO2+·Br−·H2O | V = 1766.98 (6) Å3 |
Mr = 372.30 | Z = 4 |
Monoclinic, P21/c | Cu Kα radiation |
a = 14.4528 (3) Å | µ = 3.27 mm−1 |
b = 15.3367 (2) Å | T = 200 K |
c = 8.0810 (2) Å | 0.55 × 0.18 × 0.12 mm |
β = 99.437 (2)° |
Oxford Diffraction Gemini R diffractometer | 3504 independent reflections |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007) | 3049 reflections with I > 2σ(I) |
Tmin = 0.296, Tmax = 0.676 | Rint = 0.033 |
13155 measured reflections |
R[F2 > 2σ(F2)] = 0.037 | 3 restraints |
wR(F2) = 0.098 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | Δρmax = 0.52 e Å−3 |
3504 reflections | Δρmin = −0.43 e Å−3 |
209 parameters |
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 | ||
Br | 0.168343 (18) | 0.871933 (16) | 0.50535 (3) | 0.03689 (11) | |
O1 | 0.5587 (2) | 0.7918 (2) | 0.1347 (5) | 0.0893 (10) | |
O2 | 0.42824 (18) | 0.81569 (14) | 0.2331 (4) | 0.0661 (7) | |
H2O | 0.3800 | 0.7873 | 0.2448 | 0.079* | |
O1W | 0.28626 (17) | 0.7310 (2) | 0.3254 (3) | 0.0707 (8) | |
H1W1 | 0.254 (3) | 0.764 (3) | 0.372 (5) | 0.106* | |
H1W2 | 0.251 (3) | 0.714 (3) | 0.242 (4) | 0.106* | |
N1 | 0.79026 (13) | 0.52889 (12) | 0.5047 (2) | 0.0254 (4) | |
C1 | 0.76946 (16) | 0.56100 (15) | 0.6432 (3) | 0.0279 (5) | |
C2 | 0.68861 (18) | 0.53476 (18) | 0.7221 (3) | 0.0379 (6) | |
H2A | 0.6566 | 0.4853 | 0.6607 | 0.057* | |
H2B | 0.6449 | 0.5838 | 0.7192 | 0.057* | |
H2C | 0.7106 | 0.5178 | 0.8389 | 0.057* | |
C3 | 0.84000 (16) | 0.63015 (14) | 0.7139 (3) | 0.0268 (5) | |
C4 | 0.78975 (19) | 0.71914 (16) | 0.7114 (3) | 0.0367 (6) | |
H4A | 0.7579 | 0.7317 | 0.5972 | 0.055* | |
H4B | 0.8359 | 0.7649 | 0.7478 | 0.055* | |
H4C | 0.7435 | 0.7173 | 0.7875 | 0.055* | |
C5 | 0.88798 (19) | 0.60805 (17) | 0.8929 (3) | 0.0348 (5) | |
H5A | 0.9155 | 0.5496 | 0.8944 | 0.052* | |
H5B | 0.8416 | 0.6097 | 0.9687 | 0.052* | |
H5C | 0.9375 | 0.6508 | 0.9297 | 0.052* | |
C6 | 0.90648 (16) | 0.62789 (13) | 0.5885 (3) | 0.0252 (4) | |
C7 | 0.98805 (16) | 0.67357 (15) | 0.5803 (3) | 0.0301 (5) | |
H7A | 1.0118 | 0.7148 | 0.6643 | 0.036* | |
C8 | 1.03446 (17) | 0.65748 (16) | 0.4452 (3) | 0.0327 (5) | |
H8A | 1.0904 | 0.6886 | 0.4369 | 0.039* | |
C9 | 1.00061 (17) | 0.59686 (16) | 0.3225 (3) | 0.0318 (5) | |
H9A | 1.0338 | 0.5873 | 0.2319 | 0.038* | |
C10 | 0.91882 (16) | 0.54979 (15) | 0.3296 (3) | 0.0281 (5) | |
H10A | 0.8952 | 0.5078 | 0.2470 | 0.034* | |
C11 | 0.87436 (15) | 0.56811 (14) | 0.4644 (3) | 0.0246 (4) | |
C12 | 0.73635 (17) | 0.46508 (15) | 0.3907 (3) | 0.0320 (5) | |
H12A | 0.6940 | 0.4319 | 0.4522 | 0.038* | |
H12B | 0.7800 | 0.4232 | 0.3508 | 0.038* | |
C13 | 0.67861 (17) | 0.51091 (16) | 0.2403 (3) | 0.0339 (5) | |
H13A | 0.7215 | 0.5454 | 0.1823 | 0.041* | |
H13B | 0.6488 | 0.4661 | 0.1607 | 0.041* | |
C14 | 0.60247 (18) | 0.57112 (19) | 0.2847 (3) | 0.0391 (6) | |
H14A | 0.5631 | 0.5384 | 0.3527 | 0.047* | |
H14B | 0.6323 | 0.6199 | 0.3540 | 0.047* | |
C15 | 0.5405 (2) | 0.6079 (2) | 0.1308 (4) | 0.0553 (8) | |
H15A | 0.5107 | 0.5590 | 0.0617 | 0.066* | |
H15B | 0.5800 | 0.6403 | 0.0628 | 0.066* | |
C16 | 0.46391 (19) | 0.66849 (18) | 0.1732 (4) | 0.0430 (6) | |
H16A | 0.4067 | 0.6601 | 0.0888 | 0.052* | |
H16B | 0.4486 | 0.6516 | 0.2838 | 0.052* | |
C17 | 0.4896 (2) | 0.7628 (2) | 0.1783 (4) | 0.0492 (7) |
U11 | U22 | U33 | U12 | U13 | U23 | |
Br | 0.04080 (17) | 0.03133 (16) | 0.03975 (18) | −0.00006 (10) | 0.01018 (12) | 0.00063 (10) |
O1 | 0.0628 (16) | 0.0726 (18) | 0.136 (3) | −0.0271 (14) | 0.0274 (17) | −0.0028 (18) |
O2 | 0.0607 (14) | 0.0372 (11) | 0.097 (2) | 0.0081 (10) | 0.0028 (13) | −0.0153 (12) |
O1W | 0.0458 (12) | 0.102 (2) | 0.0635 (16) | 0.0124 (13) | 0.0056 (11) | −0.0374 (15) |
N1 | 0.0266 (9) | 0.0221 (8) | 0.0263 (10) | −0.0014 (7) | 0.0009 (7) | 0.0013 (7) |
C1 | 0.0300 (11) | 0.0264 (11) | 0.0259 (11) | 0.0015 (9) | 0.0005 (9) | 0.0053 (9) |
C2 | 0.0355 (13) | 0.0415 (14) | 0.0380 (14) | −0.0016 (10) | 0.0105 (11) | 0.0069 (11) |
C3 | 0.0325 (11) | 0.0237 (11) | 0.0238 (11) | −0.0012 (8) | 0.0033 (9) | −0.0004 (8) |
C4 | 0.0450 (14) | 0.0296 (12) | 0.0366 (14) | 0.0056 (10) | 0.0100 (11) | −0.0002 (10) |
C5 | 0.0439 (14) | 0.0343 (12) | 0.0244 (12) | −0.0008 (10) | 0.0004 (10) | 0.0014 (10) |
C6 | 0.0317 (11) | 0.0205 (10) | 0.0225 (11) | 0.0018 (8) | 0.0015 (9) | 0.0015 (8) |
C7 | 0.0334 (11) | 0.0232 (11) | 0.0319 (13) | −0.0025 (9) | 0.0003 (9) | 0.0005 (9) |
C8 | 0.0302 (11) | 0.0282 (11) | 0.0394 (14) | −0.0014 (9) | 0.0051 (10) | 0.0082 (10) |
C9 | 0.0348 (12) | 0.0313 (12) | 0.0306 (13) | 0.0075 (9) | 0.0089 (10) | 0.0065 (10) |
C10 | 0.0347 (12) | 0.0244 (11) | 0.0239 (11) | 0.0050 (9) | 0.0010 (9) | 0.0006 (9) |
C11 | 0.0275 (10) | 0.0210 (10) | 0.0243 (11) | 0.0008 (8) | 0.0015 (8) | 0.0045 (8) |
C12 | 0.0327 (11) | 0.0234 (11) | 0.0374 (13) | −0.0030 (9) | −0.0020 (10) | −0.0040 (10) |
C13 | 0.0330 (12) | 0.0330 (12) | 0.0332 (13) | 0.0007 (9) | −0.0018 (10) | −0.0069 (10) |
C14 | 0.0352 (13) | 0.0426 (14) | 0.0381 (14) | 0.0067 (11) | 0.0023 (11) | −0.0017 (11) |
C15 | 0.0538 (18) | 0.0570 (18) | 0.0493 (18) | 0.0244 (15) | −0.0087 (14) | −0.0133 (15) |
C16 | 0.0363 (13) | 0.0373 (14) | 0.0526 (17) | 0.0073 (11) | −0.0014 (12) | −0.0026 (12) |
C17 | 0.0405 (15) | 0.0418 (15) | 0.062 (2) | −0.0031 (12) | −0.0019 (13) | −0.0028 (14) |
O1—C17 | 1.198 (4) | C7—C8 | 1.394 (4) |
O2—C17 | 1.330 (4) | C7—H7A | 0.9500 |
O2—H2O | 0.8400 | C8—C9 | 1.389 (4) |
O1W—H1W1 | 0.812 (19) | C8—H8A | 0.9500 |
O1W—H1W2 | 0.817 (19) | C9—C10 | 1.394 (3) |
N1—C1 | 1.302 (3) | C9—H9A | 0.9500 |
N1—C11 | 1.440 (3) | C10—C11 | 1.381 (3) |
N1—C12 | 1.476 (3) | C10—H10A | 0.9500 |
C1—C2 | 1.476 (3) | C12—C13 | 1.528 (3) |
C1—C3 | 1.516 (3) | C12—H12A | 0.9900 |
C2—H2A | 0.9800 | C12—H12B | 0.9900 |
C2—H2B | 0.9800 | C13—C14 | 1.524 (3) |
C2—H2C | 0.9800 | C13—H13A | 0.9900 |
C3—C6 | 1.507 (3) | C13—H13B | 0.9900 |
C3—C5 | 1.536 (3) | C14—C15 | 1.518 (4) |
C3—C4 | 1.545 (3) | C14—H14A | 0.9900 |
C4—H4A | 0.9800 | C14—H14B | 0.9900 |
C4—H4B | 0.9800 | C15—C16 | 1.526 (4) |
C4—H4C | 0.9800 | C15—H15A | 0.9900 |
C5—H5A | 0.9800 | C15—H15B | 0.9900 |
C5—H5B | 0.9800 | C16—C17 | 1.493 (4) |
C5—H5C | 0.9800 | C16—H16A | 0.9900 |
C6—C11 | 1.382 (3) | C16—H16B | 0.9900 |
C6—C7 | 1.382 (3) | ||
C17—O2—H2O | 109.5 | C8—C9—H9A | 119.4 |
H1W1—O1W—H1W2 | 104 (3) | C10—C9—H9A | 119.4 |
C1—N1—C11 | 111.00 (19) | C11—C10—C9 | 115.8 (2) |
C1—N1—C12 | 127.9 (2) | C11—C10—H10A | 122.1 |
C11—N1—C12 | 120.96 (19) | C9—C10—H10A | 122.1 |
N1—C1—C2 | 125.4 (2) | C10—C11—C6 | 124.3 (2) |
N1—C1—C3 | 110.6 (2) | C10—C11—N1 | 127.7 (2) |
C2—C1—C3 | 124.0 (2) | C6—C11—N1 | 108.0 (2) |
C1—C2—H2A | 109.5 | N1—C12—C13 | 110.80 (19) |
C1—C2—H2B | 109.5 | N1—C12—H12A | 109.5 |
H2A—C2—H2B | 109.5 | C13—C12—H12A | 109.5 |
C1—C2—H2C | 109.5 | N1—C12—H12B | 109.5 |
H2A—C2—H2C | 109.5 | C13—C12—H12B | 109.5 |
H2B—C2—H2C | 109.5 | H12A—C12—H12B | 108.1 |
C6—C3—C1 | 101.18 (18) | C14—C13—C12 | 114.4 (2) |
C6—C3—C5 | 112.9 (2) | C14—C13—H13A | 108.7 |
C1—C3—C5 | 111.86 (19) | C12—C13—H13A | 108.7 |
C6—C3—C4 | 111.20 (19) | C14—C13—H13B | 108.7 |
C1—C3—C4 | 109.1 (2) | C12—C13—H13B | 108.7 |
C5—C3—C4 | 110.3 (2) | H13A—C13—H13B | 107.6 |
C3—C4—H4A | 109.5 | C15—C14—C13 | 112.6 (2) |
C3—C4—H4B | 109.5 | C15—C14—H14A | 109.1 |
H4A—C4—H4B | 109.5 | C13—C14—H14A | 109.1 |
C3—C4—H4C | 109.5 | C15—C14—H14B | 109.1 |
H4A—C4—H4C | 109.5 | C13—C14—H14B | 109.1 |
H4B—C4—H4C | 109.5 | H14A—C14—H14B | 107.8 |
C3—C5—H5A | 109.5 | C14—C15—C16 | 113.2 (3) |
C3—C5—H5B | 109.5 | C14—C15—H15A | 108.9 |
H5A—C5—H5B | 109.5 | C16—C15—H15A | 108.9 |
C3—C5—H5C | 109.5 | C14—C15—H15B | 108.9 |
H5A—C5—H5C | 109.5 | C16—C15—H15B | 108.9 |
H5B—C5—H5C | 109.5 | H15A—C15—H15B | 107.7 |
C11—C6—C7 | 119.3 (2) | C17—C16—C15 | 114.2 (3) |
C11—C6—C3 | 109.15 (19) | C17—C16—H16A | 108.7 |
C7—C6—C3 | 131.6 (2) | C15—C16—H16A | 108.7 |
C6—C7—C8 | 118.1 (2) | C17—C16—H16B | 108.7 |
C6—C7—H7A | 120.9 | C15—C16—H16B | 108.7 |
C8—C7—H7A | 120.9 | H16A—C16—H16B | 107.6 |
C9—C8—C7 | 121.3 (2) | O1—C17—O2 | 120.4 (3) |
C9—C8—H8A | 119.4 | O1—C17—C16 | 124.5 (3) |
C7—C8—H8A | 119.4 | O2—C17—C16 | 115.1 (3) |
C8—C9—C10 | 121.3 (2) | ||
C11—N1—C1—C2 | −179.2 (2) | C8—C9—C10—C11 | 0.5 (3) |
C12—N1—C1—C2 | 4.5 (4) | C9—C10—C11—C6 | −0.7 (3) |
C11—N1—C1—C3 | 1.0 (2) | C9—C10—C11—N1 | −179.0 (2) |
C12—N1—C1—C3 | −175.3 (2) | C7—C6—C11—C10 | 0.2 (3) |
N1—C1—C3—C6 | −1.7 (2) | C3—C6—C11—C10 | −180.0 (2) |
C2—C1—C3—C6 | 178.4 (2) | C7—C6—C11—N1 | 178.82 (19) |
N1—C1—C3—C5 | −122.2 (2) | C3—C6—C11—N1 | −1.4 (2) |
C2—C1—C3—C5 | 58.0 (3) | C1—N1—C11—C10 | 178.8 (2) |
N1—C1—C3—C4 | 115.6 (2) | C12—N1—C11—C10 | −4.6 (3) |
C2—C1—C3—C4 | −64.3 (3) | C1—N1—C11—C6 | 0.3 (2) |
C1—C3—C6—C11 | 1.9 (2) | C12—N1—C11—C6 | 176.90 (19) |
C5—C3—C6—C11 | 121.6 (2) | C1—N1—C12—C13 | 99.2 (3) |
C4—C3—C6—C11 | −113.9 (2) | C11—N1—C12—C13 | −76.8 (3) |
C1—C3—C6—C7 | −178.4 (2) | N1—C12—C13—C14 | −64.4 (3) |
C5—C3—C6—C7 | −58.7 (3) | C12—C13—C14—C15 | −174.0 (2) |
C4—C3—C6—C7 | 65.8 (3) | C13—C14—C15—C16 | −179.9 (3) |
C11—C6—C7—C8 | 0.4 (3) | C14—C15—C16—C17 | 94.4 (4) |
C3—C6—C7—C8 | −179.3 (2) | C15—C16—C17—O1 | 8.5 (5) |
C6—C7—C8—C9 | −0.5 (4) | C15—C16—C17—O2 | −172.8 (3) |
C7—C8—C9—C10 | 0.0 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2O···O1W | 0.84 | 1.82 | 2.637 (4) | 166 |
O1W—H1W1···Br | 0.81 (2) | 2.43 (2) | 3.240 (2) | 175 (5) |
O1W—H1W2···Bri | 0.82 (2) | 2.47 (2) | 3.262 (3) | 165 (5) |
C4—H4B···Cg2ii | 0.99 | 2.88 | 3.828 (3) | 162 |
Symmetry codes: (i) x, −y+3/2, z−1/2; (ii) x, −y+3/2, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C17H24NO2+·Br−·H2O |
Mr | 372.30 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 200 |
a, b, c (Å) | 14.4528 (3), 15.3367 (2), 8.0810 (2) |
β (°) | 99.437 (2) |
V (Å3) | 1766.98 (6) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 3.27 |
Crystal size (mm) | 0.55 × 0.18 × 0.12 |
Data collection | |
Diffractometer | Oxford Diffraction Gemini R diffractometer |
Absorption correction | Multi-scan (CrysAlis RED; Oxford Diffraction, 2007) |
Tmin, Tmax | 0.296, 0.676 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 13155, 3504, 3049 |
Rint | 0.033 |
(sin θ/λ)max (Å−1) | 0.623 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.098, 1.06 |
No. of reflections | 3504 |
No. of parameters | 209 |
No. of restraints | 3 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.52, −0.43 |
Computer programs: CrysAlis PRO (Oxford Diffraction, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2O···O1W | 0.84 | 1.82 | 2.637 (4) | 165.6 |
O1W—H1W1···Br | 0.812 (19) | 2.431 (19) | 3.240 (2) | 175 (5) |
O1W—H1W2···Bri | 0.817 (19) | 2.47 (2) | 3.262 (3) | 165 (5) |
C4—H4B···Cg2ii | 0.99 | 2.88 | 3.828 (3) | 162 |
Symmetry codes: (i) x, −y+3/2, z−1/2; (ii) x, −y+3/2, z+1/2. |
Acknowledgements
AW and YH acknowledges support from by DOE-CETBR grant No. DE-FG02-03ER63580 and NSF–RISE Award No. HRD-0627276. RJB acknowledges the NSF MRI program (grant No. CHE-0619278) for funds to purchase an X-ray diffractometer.
References
Armitage, B. & O'Brien, D. F. (1992). J. Am. Chem. Soc. 114, 7396–7403. CrossRef CAS Web of Science Google Scholar
Bengtsson, M., Karlsson, H. J., Westman, G. & Kubista, M. (2003). Nucleic Acids Res. 31, e45/1. Web of Science CrossRef Google Scholar
Hirons, G. T., Fawcett, J. J. & Crissman, H. A. (1994). Cytometry, 15, 129–140. CrossRef CAS PubMed Web of Science Google Scholar
Jung, M. E. & Kim, W. (2006). Bio. Med. Chem. 14, 92–97. Web of Science CrossRef CAS Google Scholar
Kurihara, K., Toyoshima, Y. & Sukigara, M. (1977). J. Phys. Chem. 81, 1833–1837. CrossRef CAS Web of Science Google Scholar
Menger, F. M. & Pertusati, P. (2008). J. Org. Chem. 73, 2939–2942. Web of Science PubMed Google Scholar
Oxford Diffraction (2007). CrysAlis Pro and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, England. Google Scholar
Reers, M., Smith, T. W. & Chen, L. B. (1991). Biochemistry, 30, 4480–4486. CrossRef CAS PubMed Web of Science Google Scholar
Schmidt, J. R. & Polik, W. F. (2007). WebMO Pro, Version 8.0.010e; WebMO, LLC: Holland, MI, USA, available from http://www.webmo.net. Google Scholar
Schwartz, H. E. & Ulfelder, K. J. (1992). Anal. Chem. 64, 1737–1740. CrossRef CAS Web of Science Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Zhu, H., Clark, S. M., Benson, S. C., Rye, H. S., Glazer, A. N. & Mathies, R. A. (1994). Anal. Chem. 66, 1941–1948. CrossRef CAS PubMed Web of Science Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
The title compound,C17H24NO2+, Br-, H2O, (I), a salt with a crystallized water molecule, was synthesized under microwave conditions (Scheme 1). It has been used as a precursor for cyanine dyes which have widespread application as fluorescent probes. They have been used in DNA sequencing, immunoassays, agarose gel and capillary electrophoresis staining (Zhu et al., (1994)), DNA analysis in polymerization chain reactions (Schwartz et al., (1992); Bengtsson et al., (2003)), in flow cytometry (Hirons et al., (1994)), or as fluorescent probes for membrane fluidity (Kurihara et al., 1977); Armitage et al., 1992)) as well as in membrane potential studies (Reers et al., (1991)). This precursor is of particular importance due to the presence of the carboxylic acid group, which when converted to the NHS ester, allows the attachment of these dyes to proteins.
In the cation, the mean plane of indole ring bisects the angle between the two attached 3,3 dimethyl groups (angles C1–C3–C4 = 109.1 (2)°; C1–C3–C5 = 111.86 (19)°; C5–C3–C4 = 110.3 (2)°) whereas the third methyl group is nearly in the plane of the indole ring (torsion angle C2–C1–C3–C6 = 178.4 (2)°), Fig. 1. The pentyl group chain extends nearly perpendicular to the mean plane of the indole ring (torsion angle N1–C12–C13–C14 = -64.4 (3)°) with the carboxyl end group twisted such that the dihedral angle between the mean planes of the indole and carboxy groups measures 43.2 (4)° (torsion angle C14–C15–C16–C17 = 94.4 (4)°).
Both ions from the salt form intermolecular hydrogen bonds (O–H···Br & O–H···O) with the water molecule. As a result of the Br···H–O–H···Br interactions a zigzag one-dimensional chain is formed in the c direction.(Fig. 2). Crystal packing is influenced by the collective action of intermolecular O—H···O and O—H···Br hydrogen bond interactions as well as π-π stacking intermolecular interactions between the center of gravity of nearby benzyl rings of the indole group (Cg2···Cg2: 3.721 (13) Å; slippage = 1.514 Å; 2 - x, 1 - y, 1 - z) and π-ring C4–H4B···Cg2 intermolecular interactions between a methyl hydrogen and the benzene ring of the indole group [H···Cg = 2.88 Å; X—H···Cg = 162°; X···CgX-H = 3.828 (3) Å; Cg2 = C6–C11; x, 3/2 - y, 1/2 + z] in the unit cell (Fig. 3). In addition there are weak C—H···Br interactions between the phenyl H atoms of two adjoining cations which, together with the O–H···Br interactions, form a distorted tetrahedral array about the central Br.
A geometry optimized MOPAC AM1 computational calculation was performed on the cation in the absence of the bromide ion and water molecule using WebMO Pro (Schmidt & Polik, 2007). The Hartree-Fock closed-shell (restricted) wavefunction along with [AM1 (Austin Model 1)] was used and minimizations were terminated at an r.m.s. gradient of less than 0.01 kJ mol-1 Å-1]. As a result of this calculation the dihedral angle between the mean planes of the indole and carboxy groups changes from 43.2 (4)° to 34.5 (2) Å. From this it is apparent that the collective influence of O–H···O and O–H···Br hydrogen bonds, weaker C–H···Br intermolecular interactions, π-π stacking intermolecular interactions, and π-ring C–H···Cg2 intermolecular interactions significantly influence crystal packing for this molecule.