1,4,7 Tri­aza­cyclo­nonane hemihydrate

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Acta Crystallographica Section E Structure Reports

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ISSN 1600-5368

1,4,7-Triazacyclononane hemihydrate

Andrew R. Battle, Daniel L. Johnson and Lisandra L. Martin*

School of Chemistry, Monash University, Victoria 3800, Australia

Correspondence e-mail: [email protected]

Key indicators

Single-crystal X-ray study

T= 123 K

Mean(C±C) = 0.002 AÊ H-atom completeness 94%

Rfactor = 0.049

wRfactor = 0.140

Data-to-parameter ratio = 12.2

For details of how these key indicators were automatically derived from the article, see http://journals.iucr.org/e.

#2005 International Union of Crystallography Printed in Great Britain ± all rights reserved

The title compound, C6H15N30.5H2O, crystallizes in the

high-symmetry trigonal space groupP3c1. This is, after more than 30 years of effort on this compound, the ®rst reported structure of the free base of this macrocycle. Six NÐH O hydrogen bonds are formed between the water O atom occupying a special site at the origin and N atoms of six neighbouring 1,4,7-triazacyclononane molecules.

Comment

1,4,7-Triazacyclonone (tacn) and its derivatives form a very stable and diverse range of metal coordination compounds (Chaudhuri & Wieghardt, 1987; Daly & Martin, 2002) as a result of the propensity of tacn for facial coordination to metal ions. A survey of the Cambridge Structural Database (Version 5.25, update 3, July 2004; Allen, 2002) reveals around 1200 crystallographically characterized tacn compounds and complexes, the majority of these being metal coordination complexes. Although a recent publication (Warden et al., 2004) describes some aspects of the interesting hydrogen-bonding and electrostatic interactions formed between protonated tacn molecules and anions, it is surprising that, after 30 or more years of intense study on this compound, the crystal structure of the free (uncoordinated, unprotonated) compound has not been determined. There are only a few crystallographically characterized examples of free base derivatives of uncoordinated tacn compounds (Clegg et al., 1992; Blakeet al., 1994; Blake, Fallis, Gouldet al., 1996; Blake, Fallis, Heppeleret al., 1996; Adamet al., 1997; Pacchioniet al., 2002), but the title compound, (I), is the ®rst example of uncoordinated unprotonated tacn.

The compound crystallizes in the trigonal space groupP3c1, the asymmetric unit containing one-third of a tacn molecule and one-sixth of a water molecule. The tacn molecule contains the three N atoms oriented facially (Fig. 1), suitable for binding to metal ions. The water molecule occupies a special position at the origin. The H atoms on this molecule could not be located because of disorder. Six equivalent NÐH O hydrogen bonds are formed around the water molecule [N1Ð H1 = 1.00 (4) AÊ, N1 O1 = 3.0400 (13) AÊ and N1 O1 =

159 (9)_{; symmetry codes for N1 and H1: (i)x,y, z; (ii) ÿy,}

xÿy,z; (iii)ÿx+y,ÿx,z; (iv)ÿx,ÿy,ÿz; (v)y,ÿx+y,ÿz; (vi)xÿy,x,ÿz.] The packing diagram (Fig. 2) shows the NÐ H O hydrogen bonds and the alternating arrangement of hydrophobic and hydrophilic channels. The water molecules are located within the hydrophilic pockets.

Experimental

The compound was prepared using a modi®cation (Johnson, 2004) of a published procedure (Richman & Atkins, 1974). Tritosyltacn (104.1 g, 0.17 mol) was added slowly to concentrated sulfuric acid (350 ml) and the mixture was heated at 373 K with stirring for 3 d. The reaction mixture was poured slowly into a cooled mixture of absolute ethanol (1 l) and diethyl ether (250 ml). The resulting white solid was ®ltered under a nitrogen blanket, washed with an 80:20 ethanol/diethyl ether mixture (300 ml) and diethyl ether (200 ml), and dried at 343 K in vacuo. The white solid was dissolved in the minimum amount of warm water and cooled to room temperature, at which point 48% HBr (100 ml) was added with stirring and the solution was left at 278 K overnight. The precipitate was ®ltered, washed with ethanol (200 ml) and diethyl ether (200 ml), and driedin vacuo. The solid was added to a rapidly stirred mixture of toluene (400 ml) and water (80 ml), and cooled in an ice bath. Sodium hydroxide (20 g) dissolved in water (60 ml) was added slowly to the rapidly stirred mixture, and the water was azeotropically removed using a Dean±Stark apparatus. The toluene fraction was then decanted through a cotton wool column and the volume was reduced under vacuum, affording 1,4,7-triazacyclonone in high purity as a colourless viscous oil (yield 15.6 g, 71%). MS: M+ _129; 1_{H NMR} (CDCl3, p.p.m.): 2.75 (12H), 2.05 (3NH, 0.5H2O). Storage of this solid at 277 K afforded a crystalline solid, which melted at 318±323 K.

Crystal data

C6H15N30.5H2O

Mr= 138.22

Trigonal,P3c1

a= 7.298 (1) AÊ

c= 16.560 (3) AÊ

V= 763.8 (2) AÊ3

Z= 4

Dx= 1.202 Mg mÿ3

MoKradiation Cell parameters from 7794

re¯ections = 4.1±27.9 = 0.08 mmÿ1

T= 123 (2) K Block, colourless 0.870.250.25 mm

Data collection

Nonius KappaCCD diffractometer 'and!scans

Absorption correction: none 7794 measured re¯ections 610 independent re¯ections 523 re¯ections withI> 2(I)

Rint= 0.037 max= 27.9

h=ÿ9!9

k=ÿ9!9

l=ÿ21!21

Refinement

Re®nement onF2

R[F2_{> 2(F}2_{)] = 0.049}

wR(F2_{) = 0.140}

S= 1.12 610 re¯ections 50 parameters

All H-atom parameters re®ned

w= 1/[2_(F

o2) + (0.0781P)2 + 0.2454P]

whereP= (Fo2+ 2Fc2)/3 (/)max< 0.001

max= 0.32 e AÊÿ3

min=ÿ0.19 e AÊÿ3

Table 1

Selected geometric parameters (AÊ,_).

C1ÐN1 1.4681 (18)

C1ÐC2 1.533 (2) N1ÐC2

vii _{1.4636 (19)}

N1ÐC1ÐC2 111.22 (11) C2vii_{ÐN1ÐC1 115.40 (11)} N1

viii_{ÐC2ÐC1 112.70 (11)}

Symmetry codes: (vii)ÿy‡1;xÿy‡1;z; (viii)ÿx‡y;ÿx‡1;z.

H-atom parameters of the tacn molecule were re®ned. H atoms of the water molecule were not located.

Data collection: COLLECT (Hooft, 2000); cell re®nement:

SCALEPACK (Otwinowski & Minor, 1997); data reduction:

DENZO (Otwinowski & Minor, 1997) and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to re®ne structure:SHELXL97(Sheldrick, 1997); molecular graphics:ORTEP-3 for Windows (Farrugia, 1997); soft-ware used to prepare material for publication: WinGX (Farrugia, 1999).

The award of the NHMRC Development Grant #284421 is acknowledged.

organic papers

Acta Cryst.(2005). E61, o330±o332 Battleet al. C6H15N30.5H2O

o331

Figure 2

View of the packing in (I) (50% probability displacement ellipsoids). Carbon-bound H atoms have been omitted.

Figure 1

References

Adam, B., Bill, E., Bothe, E., Goerdt, B., Haselhorst, G., Hildenbrand, K., Sokolowski, A., Steenken, S., Weyhermuller, T., & Wieghardt, K. (1997).

Chem. Eur. J.3, 308±319.

Allen, F. H. (2002).Acta Cryst.B58, 380±388.

Blake, A. J., Fallis, I. A., Gould, R. O., Parsons, S., Ross, S. A. & Schroder, M. (1994).Chem. Commun.2467±2469.

Blake, A. J., Fallis, I. A., Gould, R. O., Parsons, S., Ross, S. A. & Schroder, M. (1996).J. Chem. Soc. Dalton Trans.pp. 4379±4387.

Blake, A. J., Fallis, I. A., Heppeler, A., Parsons, S., Rose, S. A. & Schroder, M. (1996).J. Chem. Soc. Dalton Trans.pp. 31±43.

Chaudhuri, P. & Wieghardt, K. (1987).Prog. Inorg. Chem.35, 329±436. Clegg, W., Iveson, P. B. & Lockhart, J. C. (1992).J. Chem. Soc. Dalton Trans.

pp. 3291±3298.

Daly, R. I. & Martin, L. L. (2002).Inorg. Chem. Commun.5, 777±781. Farrugia, L. J. (1997).J. Appl. Cryst.30, 565.

Farrugia, L. J. (1999).J. Appl. Cryst.32, 837±838.

Hooft, R. R. W. (2000).COLLECT.Nonius BV, Delft, The Netherlands. Johnson, D. L. (2004). PhD thesis, Flinders University, Australia.

Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276,

Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307±326. New York: Academic Press.

Pacchioni, M., Bega, A., Fabretti, A. C., Rovai, D. & Cornia, A. (2002).

Tetrahedron Lett.43, 771±774.

Richman, J. E. & Atkins, T. J. (1974). J Am. Chem. Soc. 96, 2268± 2270.

Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of GoÈttingen, Germany.

Warden, A. W., Warren, M., Battle, A. R., Hearn, M. T. W. & Spiccia, L. (2004).

CrystEngComm,6, 522±530.

organic papers

supporting information

sup-1 Acta Cryst. (2005). E61, o330–o332

supporting information

Acta Cryst. (2005). E61, o330–o332 [https://doi.org/10.1107/S1600536805000814]

1,4,7-Triazacyclononane hemihydrate

Andrew R. Battle, Daniel L. Johnson and Lisandra L. Martin

1,4,7-triazacyclononane hemihydrate

Crystal data

C6H15N3·0.5H2O

Mr = 138.22 Trigonal, P3c1 Hall symbol: -P 3 2"c

a = 7.298 (1) Å

c = 16.560 (3) Å

V = 763.8 (2) Å3

Z = 4

F(000) = 308

Dx = 1.202 Mg m−3

Mo Kα radiation, λ = 0.71073 Å Cell parameters from 7794 reflections

θ = 4.1–27.9°

µ = 0.08 mm−1

T = 123 K Block, colourless 0.87 × 0.25 × 0.25 mm

Data collection

Nonius KappaCCD diffractometer

φ and ω scans

7794 measured reflections 610 independent reflections 523 reflections with I > 2σ(I)

Rint = 0.037

θmax = 27.9°, θmin = 4.1°

h = −9→9

k = −9→9

l = −21→21

Refinement

Refinement on F2 Least-squares matrix: full

R[F2 _{> 2σ(F}2_{)] = 0.049}

wR(F2_{) = 0.140}

S = 1.12 610 reflections 50 parameters

0 restraints

All H-atom parameters refined

w = 1/[σ2_(F

o2) + (0.0781P)2 + 0.2454P] where P = (Fo2 + 2Fc2)/3

(Δ/σ)max < 0.001 Δρmax = 0.32 e Å−3 Δρmin = −0.19 e Å−3

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.

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

x y z Uiso*/Ueq

supporting information

sup-2 Acta Cryst. (2005). E61, o330–o332

H4 −0.090 (3) 0.517 (3) 0.1643 (11) 0.034 (4)* H5 −0.097 (3) 0.431 (3) 0.0739 (10) 0.033 (4)* H3 0.189 (3) 0.463 (3) 0.2011 (9) 0.029 (4)* H2 0.011 (3) 0.249 (3) 0.1587 (12) 0.037 (5)* H1 0.218 (5) 0.282 (6) 0.0559 (18) 0.089 (9)* O1 0 0 0 0.0944 (16)

Atomic displacement parameters (Å2₎

U11 _U22 _U33 _U12 _U13 _U23

C1 0.0268 (7) 0.0289 (7) 0.0257 (7) 0.0120 (6) 0.0054 (5) 0.0044 (5) N1 0.0260 (7) 0.0272 (6) 0.0231 (6) 0.0134 (5) 0.0015 (4) −0.0003 (4) C2 0.0230 (7) 0.0297 (8) 0.0275 (7) 0.0119 (6) 0.0014 (5) −0.0012 (6) O1 0.120 (3) 0.120 (3) 0.0433 (19) 0.0600 (13) 0 0

Geometric parameters (Å, º)

C1—N1 1.4681 (18) N1—H1 1.00 (4) C1—C2 1.533 (2) C2—N1ii _{1.4636 (19)} C1—H3 1.009 (16) C2—H4 1.021 (18) C1—H2 1.01 (2) C2—H5 0.992 (17) N1—C2i _{1.4636 (19)}

N1—C1—C2 111.22 (11) C1—N1—H1 111.6 (18) N1—C1—H3 111.4 (10) N1ii_{—C2—C1 112.70 (11)} C2—C1—H3 109.9 (10) N1ii_{—C2—H4 111.2 (10)} N1—C1—H2 110.4 (11) C1—C2—H4 108.8 (10) C2—C1—H2 107.9 (11) N1ii_{—C2—H5 107.5 (11)} H3—C1—H2 105.7 (14) C1—C2—H5 109.8 (12) C2i_{—N1—C1 115.40 (11) H4—C2—H5 106.7 (16)} C2i_{—N1—H1 111.2 (19)}

C2—C1—N1—C2i _{130.77 (12) N1—C1—C2—N1}ii _{−49.02 (15)}