1,7-Di­hydro-1,4,7,10-tetra­aza­cyclo­­dodecane­phosphine oxide iodide

The title compound, C₈H₁₈N₄OP⁺·I⁻ or [H₂cyclenPO][I], contains a five-coordinate P atom arranged in a slightly distorted trigonal bipyramid. The asymmetric unit contains half the cyclen moiety of the H~2~cyclenPO unit and two distinct iodide positions. The full molecule can be symmetry generated around the P atom using the symmetry code  + x − y,  − y,  − z. The P—N bond length in the equatorial plane is 1.656 (5) Å and the apical P—N interaction is much longer, 1.891 (4) Å. The cyclen moieties are linked together via N—H...O hydrogen bonds and form a spiral chain along [001]. Crystallographically, there are two distinct anion sites, both in special positions, one of them with partial occupancy. One anion site may participate in an extremely weak hydrogen bond, linking the cyclen spiral chains into a pseudo-hexagonal three-dimensional array.

Key indicators

• Single-crystal X-ray study
• T = 213 K
• Mean [sigma](C-C) = 0.010 Å
• Disorder in solvent or counterion
• R factor = 0.047
• wR factor = 0.116
• Data-to-parameter ratio = 18.1

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level C:



PLAT_302  Alert C Anion/Solvent Disorder .......................      34.00 Perc.

PLAT_601  Alert C Structure Contains Solvent Accessible VOIDS of      94.00 A   3

General Notes



REFLT_03
         From the CIF: _diffrn_reflns_theta_max           25.36
         From the CIF: _reflns_number_total               1324
         Count of symmetry unique reflns          730
         Completeness (_total/calc)            181.37%
         TEST3: Check Friedels for noncentro structure
         Estimate of Friedel pairs measured       594
         Fraction of Friedel pairs measured     0.814
         Are heavy atom types Z>Si present          yes
          Please check that the estimate of the number of Friedel pairs is
          correct. If it is not, please give the correct count in the
          _publ_section_exptl_refinement section of the submitted CIF.


 0 Alert Level A = Potentially serious problem

 0 Alert Level B = Potential problem

 2 Alert Level C = Please check

---

S1. Comment

Cyclen chemistry is extensive with 431 hits in the November 2002 issue of the Cambridge Structural Database (CSD; Allen, 2002). However, only one cyclen phosphine oxide is described in the database, namely cyclenphosphine oxide dihydrate, (II) (Oget et al., 1999). Compound (II) was first described in a patent (Richman, 1976) and the solution structure elucidated by NMR methods (Richman & Kubale, 1983). Although other cyclen phosphine chalcogenide derivatives have been synthesized (Oget et al., 1998), no structural information has been reported.

Compound (I) is a hydrolytic by-product formed during reactions of cyclenphosphorane (Gupta et al., 1998). The title compound, (I), is similar to (II). (I) is protonated, cationic and charge balanced by an iodide anion (see Fig. 1). The P atom lies on a special position and the other half of the molecule is symmetry generated. The P atom is five-coordinate and forms a slightly distorted trigonal bipyramid (tbp). The equatorial plane [N2, O1, N2ⁱ and P1; symmtery code: (i) 1/3 + x-y, 2/3 − y, 5/3 − z] is planar, with the sum of the angles around P1 equal to 360°. The distortion from tbp can be seen in the axial and equatorial N—P—N angles [167.1 (3), 123.4 (4) and 118.3 (2)°]. The P—N distances show that the equatorial N atoms are bonded to the phosphorus [P1—N2 and P1—N2ⁱ = 1.656 (5) Å]. The apical P—N distances [P1—N1 and P1—Niⁱ = 1.891 (4) Å] are longer than a single P—N bond. They are considerably shorter than the sum of the van der Waals radii (3.35 Å) and indicate a strong coordination by these N atoms to the central phosphorus. The elongation of the apical P—N bond in a tbp is expected and this bond lengthening has been reported previously with a range of P—N_apical distances of 1.8 to 2.11 Å [e.g. CSD refcode YAFDUE (Khasnis et al., 1992), LOBYUW (Gupta et al., 1999) and GOCPUJ (Oget at al., 1999)]. Atoms N1 and N1ⁱ are both protonated and the H atom was located on the difference map. The I atom is site shared in the asymmetric unit in two distinct special positions, with occupancies of 1/6 for I1 and 1/3 for I1'. I1 is located at Wyckoff position b (multiplicity 3) at full occupancy. I1' is located at position d (multiplicity 9) at 0.6667 of full occupancy for charge balance, and in keeping with the refined occupancy (0.16666 for I1 and 0.3333 for I1').

The cyclen phosphine oxide moiety is twisted along the N1—P1—N1ⁱ plane. The amido H atoms are oriented to either side of this plane (0.41 and −0.41 Å). This produces a slight helical distortion of the cyclen moiety. This helical distortion can also be seen in bis(borane)cyclenphosphorane (Dupart et al., 1985). The absolute configuration of chiral (I) could not be determined reliably and (I) was refined as a racemic mixture.

The extended solid state structure generated by intermolecular interactions presents an interesting picture:

(i) N—H···O hydrogen bonding. There are two of these interactions per cyclen moiety. They link the cyclen PO units into a spiral chain that runs parallel to [001]. This is shown in Figs. 2(a) and 2(b). Distances and angles are given in Table 1.

(ii) C—H···I interactions. These `interactions' should be considered extremely weak or almost non-existant. They are at the furthest limit of reported weak C—H···X interactions (Desiraju & Steiner, 2001). However, they may have an influence on the supramolecular association by linking the spiral cyclen chains into a pseudo-hexagonal array (three H₂cyclenPO cations and three I⁻ anions) which is shown in Fig. 3. The space between these networked molecules are occupied by the symmetry related unassociated iodine position. This leaves large voids between the spiral chains, ca 94 ų in the asymmetric unit.

S2. Experimental

Compound (I) was synthesized as a hydrolytic byproduct from reactions of cyclenphosphorane (Gupta et al., 1998). Colorless crystals were obtained from a CHCl₃ solution, yield 95%. IR (cm⁻¹, KBr pellet): 3100 (w), 2935 (versus), 2856 (s), 1460 (s), 1392 (versus), 1232 (s), 1141 (versus), 1088 (versus), 746 (m), 627 (s).

S3. Refinement

H atoms were positioned geometrically and refined using a riding model, with U_iso values constrained to be 1.2U_eq of the carrier atom. Atom H1 was located in a difference map. The distance was restrained and the U_iso value constrained to be 1.2U_eq of carrier atom N1. The compound was refined as a racemic twin.

Computing details

Data collection: SMART (Bruker, 1997-1998); cell refinement: SAINT-Plus (Bruker, 1999); data reduction: SAINT-Plus; program(s) used to solve structure: XS in SHELXTL (Bruker, 1998); program(s) used to refine structure: XL in SHELXTL; molecular graphics: XP in SHELXTL; software used to prepare material for publication: XCIF in SHELXTL.

Figures

	Fig. 1. The molecular structure of (I). Displacement ellipsoids are shown at the 30% probability level. Only one of the iodide positions is shown.
	Fig. 2. (a) a head-on view of the hydrogen-bonded network between the cyclen units. Ellipsoids are shown at 30% probability. (b) A ball-and-stick side view of the hydrogen bonding between the cyclen units showning the spiral chain.
	Fig. 3. A ball-and-stick packing diagram of (I). The cell is shown. Very weak H···I interactions are indicated by dashed lines outlining the pseudo-hexagonal shape formed between the cyclen chains and one of anion positions.

1,7-Dihydro-1,4,7,10-tetraazacyclododecanephosphine oxide iodide

Crystal data

C8H18IN4OP	Melting point: 230°C (dec.) K
Mr = 344.13	Mo Kα radiation, λ = 0.71073 Å
Trigonal, R32	Cell parameters from 3934 reflections
a = 19.327 (3) Å	θ = 2.3–23.5°
c = 10.052 (2) Å	µ = 2.31 mm^−1
V = 3251.7 (10) Å^3	T = 213 K
Z = 9	Parallelepiped, colorless
F(000) = 1530	0.30 × 0.20 × 0.20 mm
Dx = 1.582 Mg m^−3

Data collection

Burker/Siemens SMART 1K diffractometer	1324 independent reflections
Radiation source: normal-focus sealed tube	1260 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.041
Detector resolution: 8.3 pixels mm^-1	θmax = 25.4°, θmin = 2.4°
ω scans	h = −23→16
Absorption correction: multi-scan (SADAB; Sheldrick, 1999)	k = −21→23
Tmin = 0.522, Tmax = 0.628	l = −12→11
14029 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.047	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.117	H-atom parameters constrained
S = 1.14	w = 1/[σ^2(Fo^2) + (0.0627P)^2 + 14.9452P] where P = (Fo^2 + 2Fc^2)/3
1324 reflections	(Δ/σ)max < 0.001
73 parameters	Δρmax = 0.86 e Å^−3
1 restraint	Δρmin = −0.86 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.

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 (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
P1	0.90744 (10)	0.3333	0.8333	0.0208 (5)
O1	0.9861 (3)	0.3333	0.8333	0.0205 (11)
I1	0.6667	0.3333	0.8333	0.0380 (3)
I1'	0.49062 (10)	0.3333	0.3333	0.0771 (5)	0.67
N1	0.8791 (3)	0.2988 (3)	1.0111 (4)	0.0225 (10)
H1	0.9201	0.3149	1.0620	0.027*
N2	0.9082 (3)	0.4160 (3)	0.8791 (5)	0.0259 (10)
C2	0.8380 (4)	0.3400 (4)	1.0694 (6)	0.0314 (13)
H2A	0.8412	0.3410	1.1667	0.038*
H2B	0.7816	0.3130	1.0430	0.038*
C3	0.8830 (4)	0.4243 (4)	1.0126 (6)	0.0348 (16)
H3A	0.8481	0.4476	1.0082	0.042*
H3B	0.9294	0.4587	1.0679	0.042*
C4	0.9185 (4)	0.4756 (4)	0.7788 (6)	0.0343 (15)
H4A	0.9555	0.5298	0.8106	0.041*
H4B	0.8672	0.4718	0.7576	0.041*
C1	0.8298 (3)	0.2109 (4)	1.0083 (6)	0.0317 (14)
H1A	0.7978	0.1912	1.0897	0.038*
H1B	0.8636	0.1866	1.0006	0.038*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
P1	0.0196 (7)	0.0259 (11)	0.0190 (9)	0.0130 (5)	−0.0004 (4)	−0.0008 (7)
O1	0.0173 (19)	0.024 (3)	0.023 (3)	0.0118 (13)	−0.0009 (10)	−0.002 (2)
I1	0.0285 (3)	0.0285 (3)	0.0570 (7)	0.01423 (17)	0.000	0.000
I1'	0.1195 (11)	0.0398 (6)	0.0453 (7)	0.0199 (3)	0.0013 (2)	0.0026 (5)
N1	0.018 (2)	0.029 (3)	0.020 (2)	0.012 (2)	−0.0017 (17)	0.0021 (19)
N2	0.033 (3)	0.028 (3)	0.023 (2)	0.020 (2)	0.010 (2)	0.004 (2)
C2	0.034 (3)	0.043 (4)	0.024 (3)	0.024 (3)	0.009 (3)	0.001 (3)
C3	0.037 (3)	0.045 (4)	0.026 (3)	0.023 (3)	0.008 (3)	−0.002 (3)
C4	0.043 (4)	0.037 (4)	0.034 (3)	0.029 (3)	0.008 (3)	0.009 (3)
C1	0.027 (3)	0.036 (4)	0.030 (3)	0.013 (3)	0.005 (2)	0.010 (2)

Geometric parameters (Å, º)

P1—O1	1.520 (5)	C2—H2A	0.9800
P1—N2^i	1.656 (5)	C2—H2B	0.9800
P1—N2	1.656 (5)	C3—H3A	0.9800
P1—N1^i	1.891 (4)	C3—H3B	0.9800
P1—N1	1.891 (4)	C4—C1^i	1.513 (8)
N1—C1	1.475 (8)	C4—H4A	0.9800
N1—C2	1.498 (7)	C4—H4B	0.9800
N1—H1	0.8595	C1—C4^i	1.513 (8)
N2—C3	1.464 (7)	C1—H1A	0.9800
N2—C4	1.468 (7)	C1—H1B	0.9800
C2—C3	1.524 (9)
O1—P1—N2^i	118.3 (2)	N1—C2—H2B	110.8
O1—P1—N2	118.3 (2)	C3—C2—H2B	110.8
N2^i—P1—N2	123.4 (4)	H2A—C2—H2B	108.9
O1—P1—N1^i	96.47 (14)	N2—C3—C2	105.6 (5)
N2^i—P1—N1^i	86.5 (2)	N2—C3—H3A	110.6
N2—P1—N1^i	87.3 (2)	C2—C3—H3A	110.6
O1—P1—N1	96.47 (14)	N2—C3—H3B	110.6
N2^i—P1—N1	87.3 (2)	C2—C3—H3B	110.6
N2—P1—N1	86.5 (2)	H3A—C3—H3B	108.7
N1^i—P1—N1	167.1 (3)	N2—C4—C1^i	104.9 (5)
C1—N1—C2	114.2 (4)	N2—C4—H4A	110.8
C1—N1—P1	107.2 (3)	C1^i—C4—H4A	110.8
C2—N1—P1	108.6 (4)	N2—C4—H4B	110.8
C1—N1—H1	112.2	C1^i—C4—H4B	110.8
C2—N1—H1	102.3	H4A—C4—H4B	108.8
P1—N1—H1	112.5	N1—C1—C4^i	105.9 (5)
C3—N2—C4	117.7 (5)	N1—C1—H1A	110.6
C3—N2—P1	121.2 (4)	C4^i—C1—H1A	110.6
C4—N2—P1	120.0 (4)	N1—C1—H1B	110.6
N1—C2—C3	104.6 (4)	C4^i—C1—H1B	110.6
N1—C2—H2A	110.8	H1A—C1—H1B	108.7
C3—C2—H2A	110.8

Symmetry code: (i) x−y+1/3, −y+2/3, −z+5/3.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2B···I1	0.98	3.23	4.023 (6)	140
N1—H1···O1^ii	0.86	1.91	2.769 (5)	176

Symmetry code: (ii) −x+y+5/3, −x+4/3, z+1/3.