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The title compound, C6H15N3·0.5H2O, crystallizes in the high-symmetry trigonal space group P\bar{3}c1. This is, after more than 30 years of effort on this compound, the first reported structure of the free base of this macrocycle. Six N—H...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.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805000814/is6022sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536805000814/is6022Isup2.hkl
Contains datablock I

CCDC reference: 263695

Key indicators

  • Single-crystal X-ray study
  • T = 123 K
  • Mean [sigma](C-C) = 0.002 Å
  • H-atom completeness 94%
  • R factor = 0.049
  • wR factor = 0.140
  • Data-to-parameter ratio = 12.2

checkCIF/PLATON results

No syntax errors found



Alert level A PLAT306_ALERT_2_A Isolated Oxygen Atom (H-atoms Missing ?) ....... O1
Author Response: The hydrogen atoms are missing due to the disordered oxygen atom being located at the origin, a special position.

Alert level B PLAT063_ALERT_3_B Crystal Probably too Large for Beam Size ....... 0.87 mm
Alert level C PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings Differ .... ? PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ .... ? PLAT045_ALERT_1_C Calculated and Reported Z Differ by ............ 0.50 Ratio PLAT068_ALERT_1_C Reported F000 Differs from Calcd (or Missing)... ? PLAT222_ALERT_3_C Large Non-Solvent H Ueq(max)/Ueq(min) ... 3.07 Ratio PLAT764_ALERT_4_C Overcomplete CIF Bond List Detected (Rep/Expd) . 1.33 Ratio
Alert level G FORMU01_ALERT_2_G There is a discrepancy between the atom counts in the _chemical_formula_sum and the formula from the _atom_site* data. Atom count from _chemical_formula_sum:C6 H16 N3 O0.5 Atom count from the _atom_site data: C6 H15 N3 O0.5 CELLZ01_ALERT_1_G Difference between formula and atom_site contents detected. CELLZ01_ALERT_1_G WARNING: H atoms missing from atom site list. Is this intentional? From the CIF: _cell_formula_units_Z 4 From the CIF: _chemical_formula_sum C6 H16 N3 O0.50 TEST: Compare cell contents of formula and atom_site data atom Z*formula cif sites diff C 24.00 24.00 0.00 H 64.00 60.00 4.00 N 12.00 12.00 0.00 O 2.00 2.00 0.00
1 ALERT level A = In general: serious problem 1 ALERT level B = Potentially serious problem 6 ALERT level C = Check and explain 3 ALERT level G = General alerts; check 6 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 2 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion

Computing details top

Data collection: COLLECT (Hooft, 2000); cell refinement: 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 refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

1,4,7-triazacyclononane hemihydrate top
Crystal data top
C6H15N3·0.5H2ODx = 1.202 Mg m3
Mr = 138.22Mo Kα radiation, λ = 0.71073 Å
Trigonal, P3c1Cell parameters from 7794 reflections
Hall symbol: -P 3 2"cθ = 4.1–27.9°
a = 7.298 (1) ŵ = 0.08 mm1
c = 16.560 (3) ÅT = 123 K
V = 763.8 (2) Å3Block, colourless
Z = 40.87 × 0.25 × 0.25 mm
F(000) = 308
Data collection top
Nonius KappaCCD
diffractometer
Rint = 0.037
φ and ω scansθmax = 27.9°, θmin = 4.1°
7794 measured reflectionsh = 99
610 independent reflectionsk = 99
523 reflections with I > 2σ(I)l = 2121
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullAll H-atom parameters refined
R[F2 > 2σ(F2)] = 0.049 w = 1/[σ2(Fo2) + (0.0781P)2 + 0.2454P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.140(Δ/σ)max < 0.001
S = 1.12Δρmax = 0.32 e Å3
610 reflectionsΔρmin = 0.19 e Å3
50 parameters
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
xyzUiso*/Ueq
C10.1191 (2)0.4022 (2)0.14760 (8)0.0280 (4)
N10.27316 (19)0.41635 (19)0.08734 (6)0.0254 (4)
C20.0008 (2)0.5138 (2)0.11820 (8)0.0273 (4)
H40.090 (3)0.517 (3)0.1643 (11)0.034 (4)*
H50.097 (3)0.431 (3)0.0739 (10)0.033 (4)*
H30.189 (3)0.463 (3)0.2011 (9)0.029 (4)*
H20.011 (3)0.249 (3)0.1587 (12)0.037 (5)*
H10.218 (5)0.282 (6)0.0559 (18)0.089 (9)*
O10000.0944 (16)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0268 (7)0.0289 (7)0.0257 (7)0.0120 (6)0.0054 (5)0.0044 (5)
N10.0260 (7)0.0272 (6)0.0231 (6)0.0134 (5)0.0015 (4)0.0003 (4)
C20.0230 (7)0.0297 (8)0.0275 (7)0.0119 (6)0.0014 (5)0.0012 (6)
O10.120 (3)0.120 (3)0.0433 (19)0.0600 (13)00
Geometric parameters (Å, º) top
C1—N11.4681 (18)N1—H11.00 (4)
C1—C21.533 (2)C2—N1ii1.4636 (19)
C1—H31.009 (16)C2—H41.021 (18)
C1—H21.01 (2)C2—H50.992 (17)
N1—C2i1.4636 (19)
N1—C1—C2111.22 (11)C1—N1—H1111.6 (18)
N1—C1—H3111.4 (10)N1ii—C2—C1112.70 (11)
C2—C1—H3109.9 (10)N1ii—C2—H4111.2 (10)
N1—C1—H2110.4 (11)C1—C2—H4108.8 (10)
C2—C1—H2107.9 (11)N1ii—C2—H5107.5 (11)
H3—C1—H2105.7 (14)C1—C2—H5109.8 (12)
C2i—N1—C1115.40 (11)H4—C2—H5106.7 (16)
C2i—N1—H1111.2 (19)
C2—C1—N1—C2i130.77 (12)N1—C1—C2—N1ii49.02 (15)
Symmetry codes: (i) y+1, xy+1, z; (ii) x+y, x+1, z.
 

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