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Acta Crystallogr Sect E Struct Rep Online. 2008 July 1; 64(Pt 7): o1228.
Published online 2008 June 7. doi:  10.1107/S1600536808016851
PMCID: PMC2961807

2-(Tricyclo[3.3.1.13,7]dec-2-ylamino)ethanol hemihydrate

Abstract

The title adamantane derivative, C12H21NO·0.5H2O, was synthesized as part of an investigation into the biological activities of cage amino–alcohol compounds as potential anti-tuberculosis agents. The structure displays inter­molecular O—H(...)N, N—H(...)O, O—H(...)O hydrogen bonding and a layered packing structure with distinct hydro­philic and hydro­phobic regions. The water molecule lies on a twofold rotation axis.

Related literature

For related literature, see: Bogatcheva et al. (2006 [triangle]); du Pont de Nemours and Co. (1969 [triangle]); Lee et al. (2003 [triangle]); Tripathi et al. (2006 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-o1228-scheme1.jpg

Experimental

Crystal data

  • C12H21NO·0.5H2O
  • M r = 204.31
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1228-efi1.jpg
  • a = 11.6739 (3) Å
  • b = 6.5043 (2) Å
  • c = 28.6241 (7) Å
  • β = 99.8620 (10)°
  • V = 2141.33 (10) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 173 (2) K
  • 0.56 × 0.43 × 0.18 mm

Data collection

  • Bruker APEXII CCD area-detector diffractometer
  • Absorption correction: none
  • 13147 measured reflections
  • 2584 independent reflections
  • 2352 reflections with I > 2σ(I)
  • R int = 0.058

Refinement

  • R[F 2 > 2σ(F 2)] = 0.042
  • wR(F 2) = 0.112
  • S = 1.07
  • 2584 reflections
  • 141 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.39 e Å−3
  • Δρmin = −0.19 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT-Plus (Bruker, 1999 [triangle]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: Mercury (Macrae et al., 2006 [triangle]) and ORTEP-3 (Farrugia, 1997 [triangle]); software used to prepare material for publication: SHELXTL and PLATON (Spek, 2003 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808016851/hg2403sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808016851/hg2403Isup2.hkl

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

Acknowledgments

We thank Dr Manuel Fernandes of the Jan Boeyens Structural Chemistry Laboratory at the University of the Witwatersrand for his assistance in the acquisition of the crystallographic data. This work was supported by grants from the National Research Foundation (South Africa), GUN 2046819, the University of KwaZulu–Natal and Aspen Pharmacare.

supplementary crystallographic information

Comment

The title compound, an adamantane derivative, was synthesized as part of an ongoing study to evaluate the biological activity of such compounds as potential anti-tuberculosis agents (Bogatcheva et al. (2006), Lee et al. (2003), Tripathi et al. (2006)). Although the compound is known (du Pont de Nemours and Co.; 1969), its crystal structure has not been reported.

The compound contains a polycyclic (lipophilic) hydrocarbon region, polar amine and hydroxyl units, and crystallizes with half a water molecule in the asymmetric unit (Fig.1)- the water molecule being situated on a crystallographic 2-fold axis at (1, y, 3/4). The title molecule exhibits several C–C bond lengths in the adamantane skeleton that deviate from the expected value of 1.54 Å. This has been observed previously and is typical for these types of compounds.

The structure exhibits intermolecular hydrogen bonding between O1 and N1 of adjacent molecules as well as between O1 and O1W of the water molecule (Fig. 2). There is also a complex network of short contacts between the molecules in structure. These intermolecular interactions result in a layered structure with distinct hydrophilic and hydrophobic regions (Fig. 3). The adamantane skeleton forms the hydrophobic layer while the polar hydroxyl and amino moeties constitute the hydrophilic region.

Experimental

A mixture of 2-adamantanone (2 g, 13 mmol) and 2-aminoethanol (1 g, 16 mmol) in 20 ml of methanol was stirred under dinitrogen atmosphere at room temperature for 2 h. The mixture was cooled to zero degrees using an external ice bath after with NaBH4 (1 g, 26 mmol) was added slowly over a 30 minutes. The mixture was stirred for overnight at room temperature after which it was concentrated in vacuo and excess NaBH4 was quenched by adding 40 ml of 10% HCl and the product was also extracted as its HCl salt in the process. The aqueous solution was washed with 2x20ml of dichloromethane, after which the aqueous layer was basified (pH 12) with NH4OH and the product was extracted from the mixture with dichloromethane (2x30ml), the solvent was dried over Na2SO4 and concentrated in vacuo. The product was recrystallized from dichloromethane, thereby affording pure 2-aminoethanol adamantane (2 g, 77% yield).

Refinement

Non-hydrogen atoms were first refined isotropically followed by anisotropic refinement by full matrix least-squares calculations based on F2 using SHELXTL. With the exception to H1B and H1W, all hydrogen atoms were first located in the difference map then positioned geometrically, and allowed to ride on their respective parent atoms, with bond lengths of 0.99 Å (CH2), 1.00 Å (Methine CH) or 0.84 Å (OH). Isotropic displacement parameters for these atoms were set equal to 1.2 (CH2 and CH), or 1.5 OH) times Ueq of the parent atom. Atoms H1B and H1W were located in the difference map and refined freely.

Figures

Fig. 1.
The ORTEP (Farrugia, 1997) diagram of the title compound showing the displacement ellipsoids for non-hydrogen atoms at the 50% probability level.
Fig. 2.
Figure depicting the intermolecular hydrogen bonding.
Fig. 3.
Packing diagram depicting layered structure as seen down the b-axis.

Crystal data

C12H21NO·0.5H2OF(000) = 904
Mr = 204.31Dx = 1.267 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 7587 reflections
a = 11.6739 (3) Åθ = 2.9–28.3°
b = 6.5043 (2) ŵ = 0.08 mm1
c = 28.6241 (7) ÅT = 173 K
β = 99.862 (1)°Plate, colourless
V = 2141.33 (10) Å30.56 × 0.43 × 0.18 mm
Z = 8

Data collection

Bruker SMART CCD area-detector diffractometer2352 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.058
graphiteθmax = 28.0°, θmin = 1.4°
phi and ω scansh = −15→15
13147 measured reflectionsk = −8→8
2584 independent reflectionsl = −37→37

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)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.112H atoms treated by a mixture of independent and constrained refinement
S = 1.07w = 1/[σ2(Fo2) + (0.0507P)2 + 1.5961P] where P = (Fo2 + 2Fc2)/3
2584 reflections(Δ/σ)max = 0.001
141 parametersΔρmax = 0.39 e Å3
0 restraintsΔρmin = −0.19 e Å3

Special details

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.

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

xyzUiso*/Ueq
C10.76341 (9)−0.06132 (17)0.61221 (4)0.0189 (2)
H10.6899−0.09460.62410.023*
C20.81420 (9)0.13986 (16)0.63482 (3)0.0156 (2)
H20.75820.25200.62290.019*
C30.92859 (10)0.18681 (17)0.61700 (4)0.0181 (2)
H30.96350.31620.63210.022*
C41.01487 (10)0.00885 (18)0.62888 (4)0.0205 (2)
H4A1.08800.04110.61730.025*
H4B1.0334−0.00960.66370.025*
C50.96251 (10)−0.18982 (17)0.60569 (4)0.0208 (2)
H51.0189−0.30540.61370.025*
C60.93562 (11)−0.16124 (19)0.55178 (4)0.0243 (3)
H6A1.0082−0.13010.53960.029*
H6B0.9023−0.28960.53660.029*
C70.84905 (11)0.01531 (19)0.53962 (4)0.0240 (3)
H70.83130.03380.50440.029*
C80.73704 (10)−0.0346 (2)0.55821 (4)0.0250 (3)
H8A0.7025−0.16270.54330.030*
H8B0.68020.07810.54990.030*
C90.85024 (10)−0.23740 (17)0.62443 (4)0.0208 (2)
H9A0.8159−0.36680.61010.025*
H9B0.8677−0.25610.65930.025*
C100.90159 (11)0.21388 (18)0.56282 (4)0.0241 (3)
H10A0.84620.32880.55460.029*
H10B0.97390.24750.55070.029*
C110.83975 (9)0.33596 (16)0.70953 (4)0.0170 (2)
H11A0.77280.42580.69730.020*
H11B0.91090.40070.70180.020*
C120.85067 (10)0.31373 (16)0.76292 (4)0.0186 (2)
H12A0.77700.25870.77060.022*
H12B0.91320.21410.77450.022*
N10.82297 (8)0.13298 (14)0.68680 (3)0.0156 (2)
O10.87618 (7)0.50454 (12)0.78653 (3)0.01947 (19)
H1C0.81670.54770.79630.029*
O1W1.00000.82045 (19)0.75000.0240 (3)
H1B0.8774 (13)0.053 (2)0.6990 (5)0.024 (4)*
H1W1.0445 (14)0.737 (3)0.7380 (6)0.037 (4)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0192 (5)0.0197 (5)0.0178 (5)−0.0041 (4)0.0030 (4)−0.0029 (4)
C20.0175 (5)0.0146 (5)0.0146 (5)0.0007 (4)0.0027 (4)0.0003 (4)
C30.0224 (5)0.0155 (5)0.0172 (5)−0.0032 (4)0.0059 (4)−0.0004 (4)
C40.0178 (5)0.0236 (6)0.0200 (5)0.0000 (4)0.0033 (4)−0.0024 (4)
C50.0247 (6)0.0180 (5)0.0198 (5)0.0045 (4)0.0038 (4)−0.0010 (4)
C60.0310 (6)0.0236 (6)0.0193 (5)0.0008 (5)0.0072 (4)−0.0046 (4)
C70.0313 (6)0.0265 (6)0.0138 (5)0.0015 (5)0.0030 (4)0.0010 (4)
C80.0245 (6)0.0296 (6)0.0188 (5)−0.0003 (5)−0.0023 (4)−0.0036 (4)
C90.0300 (6)0.0137 (5)0.0189 (5)−0.0029 (4)0.0048 (4)−0.0006 (4)
C100.0339 (6)0.0206 (6)0.0195 (5)0.0004 (5)0.0092 (4)0.0040 (4)
C110.0207 (5)0.0133 (5)0.0170 (5)0.0003 (4)0.0033 (4)−0.0009 (4)
C120.0239 (5)0.0151 (5)0.0172 (5)−0.0006 (4)0.0049 (4)−0.0010 (4)
N10.0189 (4)0.0131 (4)0.0149 (4)0.0008 (3)0.0033 (3)−0.0003 (3)
O10.0195 (4)0.0188 (4)0.0208 (4)−0.0012 (3)0.0054 (3)−0.0058 (3)
O1W0.0293 (6)0.0175 (6)0.0259 (6)0.0000.0064 (5)0.000

Geometric parameters (Å, °)

C1—C91.5297 (16)C7—C81.5287 (17)
C1—C81.5334 (15)C7—C101.5316 (17)
C1—C21.5334 (14)C7—H71.0000
C1—H11.0000C8—H8A0.9900
C2—N11.4745 (12)C8—H8B0.9900
C2—C31.5395 (15)C9—H9A0.9900
C2—H21.0000C9—H9B0.9900
C3—C41.5339 (15)C10—H10A0.9900
C3—C101.5388 (15)C10—H10B0.9900
C3—H31.0000C11—N11.4700 (13)
C4—C51.5314 (16)C11—C121.5187 (14)
C4—H4A0.9900C11—H11A0.9900
C4—H4B0.9900C11—H11B0.9900
C5—C91.5305 (16)C12—O11.4200 (13)
C5—C61.5324 (15)C12—H12A0.9900
C5—H51.0000C12—H12B0.9900
C6—C71.5299 (17)N1—H1B0.849 (16)
C6—H6A0.9900O1—H1C0.8400
C6—H6B0.9900O1W—H1W0.863 (16)
C9—C1—C8109.03 (9)C6—C7—C10109.54 (10)
C9—C1—C2110.44 (9)C8—C7—H7109.5
C8—C1—C2108.97 (9)C6—C7—H7109.5
C9—C1—H1109.5C10—C7—H7109.5
C8—C1—H1109.5C7—C8—C1109.82 (9)
C2—C1—H1109.5C7—C8—H8A109.7
N1—C2—C1110.79 (8)C1—C8—H8A109.7
N1—C2—C3115.22 (8)C7—C8—H8B109.7
C1—C2—C3108.91 (8)C1—C8—H8B109.7
N1—C2—H2107.2H8A—C8—H8B108.2
C1—C2—H2107.2C1—C9—C5110.01 (9)
C3—C2—H2107.2C1—C9—H9A109.7
C4—C3—C10108.86 (9)C5—C9—H9A109.7
C4—C3—C2110.53 (9)C1—C9—H9B109.7
C10—C3—C2108.48 (9)C5—C9—H9B109.7
C4—C3—H3109.6H9A—C9—H9B108.2
C10—C3—H3109.6C7—C10—C3109.77 (9)
C2—C3—H3109.6C7—C10—H10A109.7
C5—C4—C3110.03 (9)C3—C10—H10A109.7
C5—C4—H4A109.7C7—C10—H10B109.7
C3—C4—H4A109.7C3—C10—H10B109.7
C5—C4—H4B109.7H10A—C10—H10B108.2
C3—C4—H4B109.7N1—C11—C12109.98 (8)
H4A—C4—H4B108.2N1—C11—H11A109.7
C9—C5—C4108.72 (9)C12—C11—H11A109.7
C9—C5—C6109.72 (9)N1—C11—H11B109.7
C4—C5—C6109.38 (9)C12—C11—H11B109.7
C9—C5—H5109.7H11A—C11—H11B108.2
C4—C5—H5109.7O1—C12—C11111.73 (8)
C6—C5—H5109.7O1—C12—H12A109.3
C7—C6—C5109.49 (9)C11—C12—H12A109.3
C7—C6—H6A109.8O1—C12—H12B109.3
C5—C6—H6A109.8C11—C12—H12B109.3
C7—C6—H6B109.8H12A—C12—H12B107.9
C5—C6—H6B109.8C11—N1—C2113.60 (8)
H6A—C6—H6B108.2C11—N1—H1B109.6 (10)
C8—C7—C6109.42 (10)C2—N1—H1B110.6 (10)
C8—C7—C10109.34 (10)C12—O1—H1C109.5
C9—C1—C2—N1−69.54 (11)C6—C7—C8—C160.43 (12)
C8—C1—C2—N1170.72 (9)C10—C7—C8—C1−59.53 (12)
C9—C1—C2—C358.18 (11)C9—C1—C8—C7−60.00 (12)
C8—C1—C2—C3−61.56 (11)C2—C1—C8—C760.61 (12)
N1—C2—C3—C467.40 (11)C8—C1—C9—C559.43 (11)
C1—C2—C3—C4−57.78 (11)C2—C1—C9—C5−60.27 (11)
N1—C2—C3—C10−173.32 (9)C4—C5—C9—C160.16 (11)
C1—C2—C3—C1061.50 (11)C6—C5—C9—C1−59.42 (11)
C10—C3—C4—C5−59.70 (12)C8—C7—C10—C359.75 (12)
C2—C3—C4—C559.36 (11)C6—C7—C10—C3−60.14 (12)
C3—C4—C5—C9−59.71 (11)C4—C3—C10—C759.61 (12)
C3—C4—C5—C660.09 (12)C2—C3—C10—C7−60.72 (12)
C9—C5—C6—C759.30 (12)N1—C11—C12—O1175.36 (9)
C4—C5—C6—C7−59.87 (12)C12—C11—N1—C2−178.67 (8)
C5—C6—C7—C8−59.80 (12)C1—C2—N1—C11−164.04 (9)
C5—C6—C7—C1060.05 (12)C3—C2—N1—C1171.76 (11)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1C···N1i0.841.862.7007 (12)175
N1—H1B···O1Wii0.849 (16)2.398 (16)3.2241 (12)164.6 (14)
O1W—H1W···O1iii0.863 (16)1.963 (17)2.8147 (12)168.7 (16)

Symmetry codes: (i) −x+3/2, y+1/2, −z+3/2; (ii) x, y−1, z; (iii) −x+2, y, −z+3/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HG2403).

References

  • Bogatcheva, E., Hanrahan, C., Nikonenko, B., Samala, R., Chen, P., Gearhart, J., Barbosa, F., Einck, L., Nacy, C. A. & Protopopova, M. (2006). J. Med. Chem.49, 3045–3048. [PubMed]
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  • Bruker (2005). APEX2 Bruker AXS Inc., Madison,Wisconsin, USA.
  • du Pont de Nemours, E. I., and Co. (1969). Patent No. GB 1 157 143 19 690 702.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Lee, R. E., Protopopova, M., Crooks, E., Slayden, R. A., Terrot, M. & Barry, C. E. (2003). J. Comb. Chem.5, 172–187. [PubMed]
  • Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst.39, 453–457.
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  • Tripathi, R. P., Saxena, N., Tiwari, V. K., Verma, S. S., Chaturvedi, V., Manju, Y. K., Srivastva, A. K., Gaikwad, A. & Sinha, S. (2006). Bioorg. Med. Chem.14, 8186–8196. [PubMed]

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