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The title compound, C
6H
15N
3·0.5H
2O, crystallizes in the high-symmetry trigonal space group
Pc1. 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
CCDC reference: 263695
Key indicators
- Single-crystal X-ray study
- T = 123 K
- Mean (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
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
C6H15N3·0.5H2O | Dx = 1.202 Mg m−3 |
Mr = 138.22 | Mo Kα radiation, λ = 0.71073 Å |
Trigonal, P3c1 | Cell parameters from 7794 reflections |
Hall symbol: -P 3 2"c | θ = 4.1–27.9° |
a = 7.298 (1) Å | µ = 0.08 mm−1 |
c = 16.560 (3) Å | T = 123 K |
V = 763.8 (2) Å3 | Block, colourless |
Z = 4 | 0.87 × 0.25 × 0.25 mm |
F(000) = 308 | |
Data collection top
Nonius KappaCCD diffractometer | Rint = 0.037 |
φ and ω scans | θmax = 27.9°, θmin = 4.1° |
7794 measured reflections | h = −9→9 |
610 independent reflections | k = −9→9 |
523 reflections with I > 2σ(I) | l = −21→21 |
Refinement top
Refinement on F2 | 0 restraints |
Least-squares matrix: full | All 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 = 1.12 | Δρmax = 0.32 e Å−3 |
610 reflections | Δρmin = −0.19 e Å−3 |
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 | x | y | z | Uiso*/Ueq | |
C1 | 0.1191 (2) | 0.4022 (2) | 0.14760 (8) | 0.0280 (4) | |
N1 | 0.27316 (19) | 0.41635 (19) | 0.08734 (6) | 0.0254 (4) | |
C2 | 0.0008 (2) | 0.5138 (2) | 0.11820 (8) | 0.0273 (4) | |
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) top | 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) top
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—N1ii | −49.02 (15) |
Symmetry codes: (i) −y+1, x−y+1, z; (ii) −x+y, −x+1, z. |
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