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Acta Crystallogr Sect E Struct Rep Online. 2009 August 1; 65(Pt 8): o1906–o1907.
Published online 2009 July 18. doi:  10.1107/S1600536809027238
PMCID: PMC2977230

2-{(E)-[1-(2-Hydroxy­ethyl)-3,3-dimethyl-3H-indol-1-ium-2-yl]vin­yl}-6-hydroxy­meth­yl-4-nitro­phenolate dihydrate

Abstract

The title merocyanine-type mol­ecule, C21H22N2O5·2H2O, crystallizes in a zwitterionic form and has an E configuration at the styryl C=C bond. The styryl part of the mol­ecule and the indolium ring are slightly twisted and form a dihedral angle of 13.4 (1)°. The 1.274 (3) Å C—O bond length in the phenolate fragment is the longest among similar mol­ecules. Hydrogen bonds between solvent water mol­ecules, two hydroxyl groups and the phenolate O atom dictate the packing arrangement of mol­ecules in the crystal and join the mol­ecules into a two-dimensional polymeric network which propagates parallel to (001). Four water mol­ecules and four hydr­oxy groups form a centrosymmetric homodromic cyclic motif of O—H(...)O hydrogen bonds. Another cyclic centrosymmetric motif is generated by four water mol­ecules and two phenolate O atoms.

Related literature

This structure is similar to the perviously reported trans-MEH compound, see: Raymo et al. (2003 [triangle]). For similar structures, see also: Aldoshin & Atovmyan (1985 [triangle]), Hobley et al. (1999 [triangle]), Zou et al. (2003 [triangle]). For the synthetic procedure, see: Raymo & Giordani (2001 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1906-scheme1.jpg

Experimental

Crystal data

  • C21H22N2O5·2H2O
  • M r = 418.44
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1906-efi1.jpg
  • a = 7.377 (2) Å
  • b = 8.868 (2) Å
  • c = 16.817 (5) Å
  • α = 94.603 (5)°
  • β = 101.639 (6)°
  • γ = 102.140 (7)°
  • V = 1044.8 (5) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 183 K
  • 0.10 × 0.10 × 0.10 mm

Data collection

  • Bruker APEX CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1999 [triangle]) T min = 0.981, T max = 0.990
  • 7525 measured reflections
  • 3651 independent reflections
  • 2472 reflections with I > 2σ(I)
  • R int = 0.039

Refinement

  • R[F 2 > 2σ(F 2)] = 0.054
  • wR(F 2) = 0.134
  • S = 1.02
  • 3651 reflections
  • 271 parameters
  • H-atom parameters constrained
  • Δρmax = 0.23 e Å−3
  • Δρmin = −0.20 e Å−3

Data collection: SMART (Bruker, 1998 [triangle]); cell refinement: SAINT-Plus (Bruker, 2001 [triangle]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: XSHELL (Bruker, 2000 [triangle]); molecular graphics: XSHELL and Mercury (Macrae et al., 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809027238/gk2221sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809027238/gk2221Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under contract DE—AC04–94 A L85000.

supplementary crystallographic information

Comment

Figure 1 shows an atomic displacement ellipsoid plot of the title compound. The zwitterionic molecule is nearly planar, with a 13.4 (1)o diheral angle tilt between the plane generated from the phenolate portions of the molecule as compared to the plane associated with the indole ring portion of the molecule. Thermal ellipsoids for most of the atoms are well defined. Only the O20 oxygen atom associated with one of two solvent water molecules shows some enlargement, and such enlargement is not unexpected. The title compound is similar to another merocyanine molecule (trans-MEH) as documented by Raymo & Giordani (2001) and Raymo et al. (2003), with the difference being that the title compound possesses an additional methanol group on the phenolate portion of the molecule. A review of similar structures which contain terminal alkoxy ligands (C—O-) shows C—O bond lengths in the range of 1.228 to 1.260 Angstroms; see Aldoshin & Atovmyan (1985), Hobley, et al. (1999), and Zou, et al. (2003). The C—O- bond for the title compound falls outside this range at 1.274 (3) Angstroms. This elongation is likely a result of H-bonding interactions as discussed below. Figure 2 shows the packing arrangement and intermolecular interactions for the title compound. One can see the nearly planar nature of the molecule from this perspective. There are two cyclic motifs assocated with the solvent water molecules in the structure. The ethanol group attached to the indole portion of the molecule is linked to the hydroxy O2 atom via hydrogen bonding interactions of the O10 solvent water. In addition, the intermolecular linkage of the molecules occurs via the O20 solvent water which connects the hydroxy O2 with the coordinated O10 solvent water. In addition, there is a second (Larger) cyclic motif generated by solvent water and OH groups from the hydroxymethyl and hydroxyethyl groups of the molecule. These H-bond interactions generate a two-dimensional polymeric network along the a-b plane of the structure. All O—H···O lengths and angles for these interactions are typical for hydrogen bonds as listed in Table 1.

Experimental

The title compound was synthesized by condensation of 3-chloromethyl-5-nitrosalicylaldehyde and 9,9,9a-trimethyl-2,3,9,9a-tetrahydrooxazolo[3,2-a]indole in refluxing ethanol and then recrystallized from an aqueous 70% acetonitrile solution. For synthesis procedures of related compounds see Raymo & Giordani (2001).

Refinement

H atoms present on the molecule were located in a straightforward manner using HFIX commands of SHELXL97 with attention to hybridization of the bound atom. The H atoms from water molecules were located in a difference Fourier map. They were refined using a riding-model approximation with C—H = 0.95-0.99 Å and O-H = 0.85-0.96 Å with Uiso(H)=1.2Ueq(C) except methyl group and water molecule, where Uiso(H)=1.5Ueq(C,O).

Figures

Fig. 1.
The molecular structure of the title compound, with labels and 50% probability displacement ellipsoids for non-H atoms.
Fig. 2.
Packing diagram for the title compound showing solvent water interactions. See text for details.

Crystal data

C21H22N2O5·2H2OZ = 2
Mr = 418.44F(000) = 444
Triclinic, P1Dx = 1.330 Mg m3Dm = 1.31 (8) Mg m3Dm measured by picnometer
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.377 (2) ÅCell parameters from 200 reflections
b = 8.868 (2) Åθ = 1–25°
c = 16.817 (5) ŵ = 0.10 mm1
α = 94.603 (5)°T = 183 K
β = 101.639 (6)°Block, dark red
γ = 102.140 (7)°0.10 × 0.10 × 0.10 mm
V = 1044.8 (5) Å3

Data collection

Bruker APEX CCD area-detector diffractometer3651 independent reflections
Radiation source: fine-focus sealed tube2472 reflections with I > 2σ(I)
graphiteRint = 0.039
[var phi] and ω scansθmax = 25.0°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Sheldrick, 1999)h = −8→8
Tmin = 0.981, Tmax = 0.990k = −10→10
7525 measured reflectionsl = −19→19

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.054Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.134H-atom parameters constrained
S = 1.02w = 1/[σ2(Fo2) + (0.0611P)2 + 0.0096P] where P = (Fo2 + 2Fc2)/3
3651 reflections(Δ/σ)max < 0.001
271 parametersΔρmax = 0.23 e Å3
0 restraintsΔρmin = −0.20 e Å3

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
N10.4314 (3)0.7565 (2)0.27176 (12)0.0266 (5)
N2−0.7317 (3)0.3125 (2)0.07265 (13)0.0297 (5)
O10.3009 (3)0.8842 (2)0.40555 (12)0.0453 (5)
H10.31720.97300.39030.054*
O2−0.1195 (2)0.4576 (2)0.33751 (11)0.0348 (5)
O3−0.7048 (3)0.3290 (2)0.00334 (11)0.0399 (5)
O4−0.8914 (3)0.2639 (2)0.08513 (12)0.0439 (6)
O5−0.6302 (2)0.1775 (2)0.36144 (11)0.0376 (5)
H5−0.70150.22850.37870.045*
C10.5663 (3)0.8684 (3)0.24386 (15)0.0275 (6)
C20.7509 (4)0.9396 (3)0.28370 (17)0.0337 (7)
H2A0.80740.91500.33550.040*
C30.8489 (4)1.0488 (3)0.24380 (18)0.0392 (7)
H30.97551.10270.26940.047*
C40.7670 (4)1.0812 (3)0.16759 (18)0.0381 (7)
H40.83801.15640.14160.046*
C50.5822 (4)1.0052 (3)0.12871 (17)0.0331 (7)
H5A0.52671.02670.07600.040*
C60.4804 (3)0.8976 (3)0.16797 (15)0.0251 (6)
C70.2797 (3)0.8003 (3)0.14308 (14)0.0248 (6)
C80.2563 (4)0.6884 (3)0.06505 (15)0.0308 (6)
H8A0.26920.74820.01920.046*
H8B0.13020.61720.05290.046*
H8C0.35450.62850.07340.046*
C90.1368 (4)0.9048 (3)0.12986 (17)0.0355 (7)
H9A0.14980.97160.18100.053*
H9B0.00710.83980.11320.053*
H9C0.16250.96970.08710.053*
C100.2648 (3)0.7159 (3)0.21803 (15)0.0246 (6)
C110.4762 (4)0.7097 (3)0.35407 (15)0.0311 (6)
H11A0.60300.68510.36390.037*
H11B0.38130.61470.35750.037*
C120.4755 (4)0.8380 (3)0.41955 (16)0.0392 (7)
H12A0.49800.80060.47380.047*
H12B0.58040.92880.42030.047*
C130.1035 (3)0.6165 (3)0.23467 (15)0.0274 (6)
H130.11660.58110.28690.033*
C14−0.0685 (3)0.5680 (3)0.18168 (16)0.0275 (6)
H14−0.07600.59850.12840.033*
C15−0.2409 (3)0.4756 (3)0.19654 (15)0.0244 (6)
C16−0.3992 (3)0.4350 (3)0.13128 (15)0.0249 (6)
H16−0.38830.46510.07920.030*
C17−0.5708 (3)0.3522 (3)0.14124 (15)0.0249 (6)
C18−0.5931 (3)0.3052 (3)0.21741 (15)0.0252 (6)
H18−0.71420.25170.22370.030*
C19−0.4402 (4)0.3369 (3)0.28191 (15)0.0250 (6)
C20−0.2575 (4)0.4255 (3)0.27503 (15)0.0266 (6)
C21−0.4511 (4)0.2795 (3)0.36328 (16)0.0327 (7)
H21A−0.34870.22400.37910.039*
H21B−0.42920.36990.40540.039*
O100.9517 (3)0.7347 (2)0.43717 (12)0.0471 (6)
H10A1.07290.79790.43500.071*
H10B0.93190.63490.40700.071*
O200.1635 (3)0.3445 (3)0.42365 (13)0.0642 (7)
H20B0.10480.30710.46590.096*
H20A0.06280.37210.38720.096*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0212 (12)0.0303 (12)0.0277 (12)0.0033 (10)0.0063 (10)0.0044 (10)
N20.0267 (13)0.0250 (12)0.0348 (14)−0.0003 (10)0.0046 (11)0.0106 (10)
O10.0443 (13)0.0374 (12)0.0578 (14)0.0064 (10)0.0235 (11)0.0051 (10)
O20.0280 (11)0.0442 (12)0.0284 (10)0.0022 (9)0.0019 (9)0.0099 (9)
O30.0369 (12)0.0498 (13)0.0275 (11)−0.0016 (10)0.0049 (9)0.0094 (9)
O40.0216 (11)0.0570 (13)0.0477 (13)−0.0046 (10)0.0038 (9)0.0221 (10)
O50.0340 (11)0.0422 (12)0.0401 (11)0.0048 (9)0.0168 (9)0.0148 (9)
C10.0214 (14)0.0312 (15)0.0306 (15)0.0028 (12)0.0119 (12)0.0014 (12)
C20.0203 (15)0.0408 (17)0.0372 (16)0.0033 (13)0.0063 (12)−0.0003 (13)
C30.0215 (15)0.0390 (17)0.054 (2)−0.0017 (13)0.0140 (14)−0.0045 (15)
C40.0347 (17)0.0322 (16)0.053 (2)0.0054 (14)0.0255 (15)0.0068 (14)
C50.0342 (17)0.0317 (16)0.0372 (17)0.0073 (13)0.0163 (14)0.0070 (13)
C60.0252 (14)0.0232 (14)0.0272 (14)0.0053 (11)0.0081 (12)−0.0006 (11)
C70.0238 (14)0.0268 (14)0.0245 (14)0.0064 (12)0.0065 (11)0.0030 (11)
C80.0326 (16)0.0335 (16)0.0275 (15)0.0082 (13)0.0086 (12)0.0054 (12)
C90.0275 (16)0.0291 (15)0.0486 (18)0.0047 (13)0.0075 (13)0.0042 (13)
C100.0209 (14)0.0281 (14)0.0245 (14)0.0061 (12)0.0054 (11)−0.0003 (11)
C110.0268 (15)0.0379 (16)0.0270 (15)0.0074 (13)0.0009 (12)0.0085 (13)
C120.0405 (18)0.0474 (19)0.0272 (15)0.0073 (15)0.0049 (14)0.0047 (13)
C130.0238 (15)0.0321 (15)0.0242 (14)0.0016 (12)0.0041 (12)0.0066 (11)
C140.0284 (15)0.0276 (14)0.0267 (14)0.0038 (12)0.0090 (12)0.0035 (11)
C150.0225 (14)0.0223 (13)0.0293 (14)0.0054 (11)0.0073 (12)0.0043 (11)
C160.0265 (15)0.0230 (13)0.0256 (14)0.0028 (11)0.0085 (12)0.0074 (11)
C170.0214 (14)0.0227 (13)0.0284 (14)0.0023 (11)0.0031 (11)0.0041 (11)
C180.0223 (14)0.0221 (13)0.0320 (15)0.0027 (11)0.0090 (12)0.0065 (11)
C190.0271 (15)0.0211 (13)0.0286 (14)0.0056 (11)0.0091 (12)0.0063 (11)
C200.0273 (15)0.0247 (14)0.0269 (15)0.0056 (12)0.0037 (12)0.0036 (11)
C210.0298 (16)0.0367 (16)0.0316 (15)0.0037 (13)0.0090 (13)0.0085 (13)
O100.0411 (12)0.0499 (13)0.0513 (13)0.0091 (10)0.0144 (10)0.0054 (10)
O200.0526 (15)0.104 (2)0.0522 (14)0.0420 (14)0.0186 (12)0.0250 (14)

Geometric parameters (Å, °)

N1—C101.331 (3)C9—H9A0.9797
N1—C11.429 (3)C9—H9B0.9799
N1—C111.471 (3)C9—H9C0.9803
N2—O41.232 (3)C10—C131.416 (3)
N2—O31.236 (3)C11—C121.520 (4)
N2—C171.439 (3)C11—H11A0.9895
O1—C121.414 (3)C11—H11B0.9895
O1—H10.8400C12—H12A0.9904
O2—C201.273 (3)C12—H12B0.9898
O5—C211.429 (3)C13—C141.357 (3)
O5—H50.8405C13—H130.9492
C1—C61.376 (3)C14—C151.440 (3)
C1—C21.380 (3)C14—H140.9503
C2—C31.385 (4)C15—C161.393 (3)
C2—H2A0.9507C15—C201.446 (3)
C3—C41.382 (4)C16—C171.373 (3)
C3—H30.9503C16—H160.9504
C4—C51.387 (4)C17—C181.408 (3)
C4—H40.9500C18—C191.361 (3)
C5—C61.382 (3)C18—H180.9499
C5—H5A0.9502C19—C201.442 (3)
C6—C71.506 (3)C19—C211.509 (3)
C7—C101.527 (3)C21—H21A0.9901
C7—C81.538 (3)C21—H21B0.9898
C7—C91.539 (3)O10—H10A0.9594
C8—H8A0.9795O10—H10B0.9515
C8—H8B0.9805O20—H20B0.9502
C8—H8C0.9795O20—H20A0.9513
C10—N1—C1111.6 (2)C13—C10—C7128.7 (2)
C10—N1—C11127.0 (2)N1—C11—C12111.2 (2)
C1—N1—C11121.1 (2)N1—C11—H11A109.4
O4—N2—O3122.4 (2)C12—C11—H11A109.4
O4—N2—C17118.9 (2)N1—C11—H11B109.4
O3—N2—C17118.8 (2)C12—C11—H11B109.4
C12—O1—H1109.4H11A—C11—H11B108.0
C21—O5—H5109.4O1—C12—C11111.7 (2)
C6—C1—C2123.8 (2)O1—C12—H12A109.2
C6—C1—N1108.1 (2)C11—C12—H12A109.3
C2—C1—N1128.0 (2)O1—C12—H12B109.3
C1—C2—C3116.1 (3)C11—C12—H12B109.3
C1—C2—H2A121.9H12A—C12—H12B108.0
C3—C2—H2A122.0C14—C13—C10125.0 (2)
C4—C3—C2121.5 (3)C14—C13—H13117.5
C4—C3—H3119.2C10—C13—H13117.5
C2—C3—H3119.2C13—C14—C15127.7 (2)
C3—C4—C5120.7 (3)C13—C14—H14116.1
C3—C4—H4119.6C15—C14—H14116.2
C5—C4—H4119.7C16—C15—C14117.3 (2)
C6—C5—C4118.8 (3)C16—C15—C20119.2 (2)
C6—C5—H5A120.6C14—C15—C20123.5 (2)
C4—C5—H5A120.6C17—C16—C15120.9 (2)
C1—C6—C5119.0 (2)C17—C16—H16119.5
C1—C6—C7109.7 (2)C15—C16—H16119.6
C5—C6—C7131.3 (2)C16—C17—C18121.4 (2)
C6—C7—C10101.47 (19)C16—C17—N2119.5 (2)
C6—C7—C8110.0 (2)C18—C17—N2119.1 (2)
C10—C7—C8112.7 (2)C19—C18—C17119.7 (2)
C6—C7—C9110.5 (2)C19—C18—H18120.2
C10—C7—C9111.1 (2)C17—C18—H18120.2
C8—C7—C9110.8 (2)C18—C19—C20121.1 (2)
C7—C8—H8A109.4C18—C19—C21122.3 (2)
C7—C8—H8B109.5C20—C19—C21116.6 (2)
H8A—C8—H8B109.5O2—C20—C19119.4 (2)
C7—C8—H8C109.5O2—C20—C15122.9 (2)
H8A—C8—H8C109.5C19—C20—C15117.7 (2)
H8B—C8—H8C109.5O5—C21—C19112.6 (2)
C7—C9—H9A109.5O5—C21—H21A109.0
C7—C9—H9B109.5C19—C21—H21A109.1
H9A—C9—H9B109.4O5—C21—H21B109.1
C7—C9—H9C109.5C19—C21—H21B109.1
H9A—C9—H9C109.4H21A—C21—H21B107.8
H9B—C9—H9C109.5H10A—O10—H10B110.1
N1—C10—C13122.2 (2)H20B—O20—H20A102.9
N1—C10—C7109.0 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O20—H20B···O10i0.961.802.739 (4)166
O10—H10B···O2ii0.951.812.750 (3)172
O20—H20A···O20.951.782.714 (3)167
O10—H10A···O1ii0.951.872.811 (3)165
O5—H5···O20iii0.841.802.633 (3)175
O1—H1···O5iv0.841.902.734 (3)176

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x+1, y, z; (iii) x−1, y, z; (iv) x+1, y+1, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: GK2221).

References

  • Aldoshin, S. M. & Atovmyan, L. O. (1985). Bull. Acad. Sci. USSR Div. Chem. Sci.34, 180–182.
  • Bruker (1998). SMART Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bruker (2000). XSHELL Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bruker (2001). SAINT-Plus Bruker AXS Inc., Madison, Wisconsin, USA.
  • Hobley, J., Malatesta, V., Millini, R., Montanari, L. & Parker Junior, W. O. N. (1999). Phys. Chem. Chem. Phys.1, 3259–3267.
  • Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst.41, 466–470.
  • Raymo, F. M. & Giordani, S. (2001). J. Am. Chem. Soc.123, 4651–4652. [PubMed]
  • Raymo, F. M., Giordani, S., White, A. J. P. & Williams, D. J. (2003). J. Org. Chem.68, 4158–4169. [PubMed]
  • Sheldrick, G. M. (1999). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst A64, 112–122. [PubMed]
  • Zou, W., Chen, P., Gao, Y. & Meng, J. (2003). Acta Cryst. E59, o337–o339.

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