Crystal structure of trans-(1,8-dibutyl-1,3,6,8,10,13-hexa­aza­cyclo­tetra­decane-κ⁴N³,N⁶,N¹⁰,N¹³)bis­(perchlorato-κO)copper(II) from synchrotron data

The Cu^II ion in the title compound shows a slightly distorted octa­hedral coordination geometry with four N atoms of the aza­macrocyclic ligand and two perchlorate anions. In the crystal, mol­ecules are linked by N–H...O and C–H...O hydrogen bonds, forming a three-dimensional network.

Key indicators

• Single-crystal synchrotron study
• T = 100 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.034
• wR factor = 0.091
• Data-to-parameter ratio = 21.0

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT029_ALERT_3_B _diffrn_measured_fraction_theta_full Low .......      0.943 Note

Alert level C
PLAT430_ALERT_2_C Short Inter D...A Contact  O1     ..  O1      ..       2.89 Ang.
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600        125 Report

Alert level G
ABSMU01_ALERT_1_G  Calculation of _exptl_absorpt_correction_mu
                not performed for this radiation type.
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          2 Report
PLAT066_ALERT_1_G Predicted and Reported Tmin&Tmax Range Identical          ? Check
PLAT154_ALERT_1_G The su's on the Cell Angles are Equal ..........    0.03000 Degree
PLAT180_ALERT_4_G Check Cell Rounding: # of Values Ending with 0 =          3
PLAT232_ALERT_2_G Hirshfeld Test Diff (M-X)  Cu1    --  O2      ..        8.1 su
PLAT793_ALERT_4_G The Model has Chirality at N1      .............          S Verify
PLAT793_ALERT_4_G The Model has Chirality at N2      .............          R Verify
PLAT794_ALERT_5_G Tentative Bond Valency for Cu1     (II)    .....       2.17 Note
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600        120 Note
PLAT984_ALERT_1_G The Cu-f'=     0.355 Deviates from the B&C-Value      0.338 Check

   0 ALERT level A = Most likely a serious problem - resolve or explain
   1 ALERT level B = A potentially serious problem, consider carefully
   2 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  11 ALERT level G = General information/check it is not something unexpected

   4 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
   4 ALERT type 4 Improvement, methodology, query or suggestion
   2 ALERT type 5 Informative message, check

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S1. Chemical context

Coordination compounds with macrocyclic ligands have attracted considerable attention in chemistry, biological chemistry and materials science (Lehn, 1995). In particular, macrocyclic Cu^II complexes with vacant sites in the axial positions are good building blocks for assembling multi-dimensional frameworks (Ko et al., 2002), with potential applications as metal extra­cta­nts, radiotherapeutic materials and as medical imaging agents (Sowen et al., 2013). For example, Cu^II complexes with tetra-aza­macrocyclic ligands have been studied with various auxiliary anionic ligands such as ferricyanide and hexa­cyano­chromate and their biological redox-sensing and magnetic properties (Xiang et al., 2009) have been investigated. Moreover, the perchlorate ion is a versatile anion which can easily bridge two transition metal complexes, allowing the assembly of multi-dimensional compounds (Kwak et al., 2001). Here, we report the synthesis and crystal structure of a Cu^II aza­macrocyclic complex, trans-diperchlorato(1,8-di­butyl-1,3,6,8,10,13-hexa­aza­cyclo­tetra­decane)­copper(II), which has two perchlorate ions coordinated in the axial positions in the six-coordinate complex.

S2. Structural commentary

In the title compound, the coordination environment around the Cu^II ion, which lies on an inversion centre, is tetra­gonally distorted o­cta­hedral. The copper(II) ion binds to the four secondary N atoms of the aza­macrocyclic ligand in a square-planar fashion in the equatorial plane, with two O atoms from the perchlorate anions in axial positions as shown in Fig. 1. The bonds to the two axially located perchlorate anions are significantly longer than those to the donor N atoms in the equatorial plane. This can be attributed either to a rather large Jahn–Teller distortion of the Cu^II ion and/or to a considerable ring contraction of the aza­macrocyclic ligand (Halcrow, 2013). The six-membered chelate rings adopt chair conformations and the five-membered chelate rings assume gauche conformations (Min & Suh, 2001). Intra­molecular N—H···O hydrogen bonds between the secondary amine groups of the aza­macrocyclic ligand and an O atom of each perchlorate ion contribute to the molecular conformation (Fig. 1 and Table 1).

S3. Supra­molecular features

Each complex molecule forms three N—H···O and two C—H···O hydrogen bonds (Steed & Atwood, 2009), as shown in Table 1, Fig. 2. Sheets of complex molecules form in the ab plane, Fig. 3, and additional C6—H6B···O3 contacts link these sheets into a three-dimensional network.

S4. Database survey

A search of the Cambridge Structural Database (Version 5.35, May 2014 with three updates; Groom & Allen 2014) indicated that 51 aza­macrocyclic Cu^II complexes with pendant alkyl groups had been reported previously. These complexes have been studied as good building blocks for supra­molecular chemistry and contain a variety of pendant alkyl groups (Cho et al., 2003). Their magnetic properties and guest-exchange effects with cyano groups and carb­oxy­lic acid groups as ligands have also been investigated (Ko et al., 2002; Zhou et al., 2014). No corresponding aza­macrocyclic Cu^II complex with pendant butyl groups has been reported and the title compound was newly synthesized for this research.

S5. Synthesis and crystallization

The title compound was prepared as follows. Ethyl­enedi­amine (3.4 ml, 0.05 mol), paraformaldehyde (3.0 g, 0.10 mol), and butyl­amine (3.7 g, 0.05 mol) were slowly added to a stirred solution of CuCl₂·2H₂O (4.26 g, 0.025 mol) in MeOH (50 ml). The mixture was heated to reflux for 1 day. The solution was filtered and cooled at room temperature. HClO₄ (70%, 15 ml) was added to the purple solution. A bright-purple precipitate formed and was filtered off, washed with H₂O, MeOH, and di­ethyl ether, and dried in air. Purple crystals of the title compound were obtained by diffusion of di­ethyl ether into the purple solution over several days. Yield: 2.38g (17%). FT–IR (ATR, cm^-1): 3240, 2936, 1443, 1053, 995, 962, 746. Safety note: Although we have experienced no problems with the compound reported in this study, perchlorate salts of metal complexes are often explosive and should be handled with great caution.

S6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3. All H atoms were placed in geometrically idealized positions and constrained to ride on their parent atoms, with C—H distances of 0.98–0.99 Å and an N—H distance of 1.0 Å with U_iso(H) values of 1.2 or 1.5 U_eq of the parent atoms.

Related literature

For related literature, see: Cho et al. (2003); Groom & Allen (2014); Halcrow (2013); Ko et al. (2002); Kwak et al. (2001); Lehn (1995); Min & Suh (2001); Sowen et al. (2013); Steed & Atwood (2009); Zhou et al. (2014).

Computing details

Data collection: PAL ADSC Quantum-210 ADX (Arvai & Nielsen, 1983); cell refinement: HKL3000sm (Otwinowski & Minor, 1997); data reduction: HKL3000sm (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures

	Fig. 1. View of the molecular structure of the title compound, showing the atom-labelling scheme, with displacement ellipsoids drawn at the 50% probability level. H atoms bonded to C atoms have been omitted for clarity. Intramolecular N—H···O hydrogen bonds are shown as black dashed lines. [Symmetry code: (i) -x + 1, -y + 1, -z + 1.]
	Fig. 2. View of the contacts made by an individual complex molecule with hydrogen bonds drawn as dashed lines.
	Fig. 3. Sheets of complex molecules in the ab plane.

trans-(1,8-Dibutyl-1,3,6,8,10,13-hexaazacyclotetradecane-κ⁴N³,N⁶,N¹⁰,N¹³)bis(perchlorato-κO)copper(II)

Crystal data

[Cu(ClO4)2(C16H38N6)]	Z = 1
Mr = 576.96	F(000) = 303
Triclinic, P1	Dx = 1.571 Mg m^−3
a = 8.2230 (16) Å	Synchrotron radiation, λ = 0.62998 Å
b = 8.3600 (17) Å	Cell parameters from 16838 reflections
c = 10.039 (2) Å	θ = 0.4–33.6°
α = 92.87 (3)°	µ = 0.84 mm^−1
β = 96.12 (3)°	T = 100 K
γ = 116.60 (3)°	Plate, purple
V = 609.8 (3) Å^3	0.10 × 0.10 × 0.03 mm

Data collection

ADSC Q210 CCD area-detector diffractometer	2536 reflections with I > 2σ(I)
Radiation source: PLSII 2D bending magnet	Rint = 0.025
ω scans	θmax = 26.0°, θmin = 1.8°
Absorption correction: empirical (using intensity measurements) (HKL3000sm SCALEPACK; Otwinowski & Minor, 1997)	h = −11→11
Tmin = 0.921, Tmax = 0.975	k = −11→11
6292 measured reflections	l = −13→13
3195 independent reflections

Refinement

Refinement on F^2	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.034	H-atom parameters constrained
wR(F^2) = 0.091	w = 1/[σ^2(Fo^2) + (0.0574P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 1.02	(Δ/σ)max = 0.001
3195 reflections	Δρmax = 0.29 e Å^−3
152 parameters	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.

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

	x	y	z	Uiso*/Ueq
Cu1	0.5000	0.5000	0.5000	0.01063 (10)
N1	0.7678 (2)	0.6261 (2)	0.57656 (16)	0.0119 (3)
H1	0.8221	0.5443	0.5535	0.014*
N2	0.4291 (2)	0.3507 (2)	0.65492 (16)	0.0123 (3)
H2	0.4599	0.2490	0.6389	0.015*
N3	0.7247 (2)	0.5222 (2)	0.80108 (16)	0.0152 (3)
C1	0.8525 (2)	0.7860 (2)	0.5034 (2)	0.0155 (4)
H1A	0.9876	0.8328	0.5156	0.019*
H1B	0.8242	0.8821	0.5385	0.019*
C2	0.8084 (3)	0.6731 (3)	0.7267 (2)	0.0164 (4)
H2A	0.9432	0.7303	0.7541	0.020*
H2B	0.7654	0.7626	0.7508	0.020*
C3	0.5278 (3)	0.4466 (3)	0.7910 (2)	0.0158 (4)
H3A	0.4948	0.5445	0.8119	0.019*
H3B	0.4855	0.3612	0.8594	0.019*
C4	0.2256 (2)	0.2705 (3)	0.6448 (2)	0.0156 (4)
H4A	0.1894	0.3598	0.6819	0.019*
H4B	0.1786	0.1649	0.6964	0.019*
C5	0.8000 (3)	0.3919 (3)	0.7910 (2)	0.0169 (4)
H5A	0.9359	0.4586	0.8041	0.020*
H5B	0.7593	0.3265	0.6992	0.020*
C6	0.7409 (3)	0.2567 (3)	0.8931 (2)	0.0177 (4)
H6A	0.6067	0.1782	0.8721	0.021*
H6B	0.7662	0.3217	0.9840	0.021*
C7	0.8401 (3)	0.1406 (3)	0.8937 (2)	0.0221 (4)
H7A	0.9723	0.2171	0.9266	0.026*
H7B	0.8289	0.0888	0.8003	0.026*
C8	0.7636 (3)	−0.0116 (3)	0.9822 (2)	0.0215 (4)
H8A	0.7749	0.0390	1.0749	0.032*
H8B	0.8328	−0.0812	0.9806	0.032*
H8C	0.6338	−0.0904	0.9481	0.032*
Cl1	0.32457 (6)	0.78356 (6)	0.65025 (4)	0.01406 (11)
O1	0.1610 (2)	0.6610 (2)	0.56090 (18)	0.0282 (4)
O2	0.48300 (19)	0.77847 (19)	0.60352 (16)	0.0221 (3)
O3	0.3102 (3)	0.7249 (2)	0.78200 (16)	0.0319 (4)
O4	0.3413 (2)	0.96148 (19)	0.65392 (18)	0.0285 (4)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cu1	0.00685 (15)	0.00798 (15)	0.01599 (17)	0.00179 (11)	0.00383 (11)	0.00327 (12)
N1	0.0092 (7)	0.0080 (6)	0.0180 (8)	0.0032 (5)	0.0030 (5)	0.0031 (6)
N2	0.0091 (6)	0.0114 (7)	0.0184 (8)	0.0053 (5)	0.0054 (6)	0.0044 (6)
N3	0.0152 (7)	0.0159 (8)	0.0170 (8)	0.0091 (6)	0.0028 (6)	0.0022 (6)
C1	0.0082 (8)	0.0091 (8)	0.0275 (10)	0.0015 (6)	0.0051 (7)	0.0069 (7)
C2	0.0143 (8)	0.0125 (8)	0.0208 (10)	0.0052 (7)	0.0009 (7)	0.0000 (7)
C3	0.0156 (9)	0.0176 (9)	0.0176 (9)	0.0100 (7)	0.0050 (7)	0.0034 (8)
C4	0.0094 (8)	0.0141 (8)	0.0253 (10)	0.0047 (7)	0.0096 (7)	0.0101 (8)
C5	0.0148 (8)	0.0199 (9)	0.0202 (9)	0.0112 (7)	0.0039 (7)	0.0046 (8)
C6	0.0197 (9)	0.0191 (9)	0.0194 (10)	0.0124 (8)	0.0057 (7)	0.0059 (8)
C7	0.0186 (9)	0.0242 (10)	0.0295 (11)	0.0133 (8)	0.0081 (8)	0.0100 (9)
C8	0.0242 (10)	0.0202 (10)	0.0244 (11)	0.0133 (8)	0.0050 (8)	0.0054 (8)
Cl1	0.0128 (2)	0.0121 (2)	0.0198 (2)	0.00762 (17)	0.00396 (16)	0.00067 (18)
O1	0.0152 (7)	0.0258 (8)	0.0420 (10)	0.0115 (6)	−0.0050 (6)	−0.0127 (7)
O2	0.0132 (6)	0.0216 (7)	0.0332 (8)	0.0088 (6)	0.0086 (6)	−0.0005 (6)
O3	0.0450 (10)	0.0412 (10)	0.0225 (8)	0.0280 (8)	0.0144 (7)	0.0124 (8)
O4	0.0297 (8)	0.0123 (7)	0.0490 (11)	0.0132 (6)	0.0101 (7)	0.0047 (7)

Geometric parameters (Å, º)

Cu1—N1	2.0073 (17)	C4—C1^i	1.518 (3)
Cu1—N1^i	2.0073 (17)	C4—H4A	0.9900
Cu1—N2^i	2.0131 (17)	C4—H4B	0.9900
Cu1—N2	2.0131 (17)	C5—C6	1.515 (3)
N1—C1	1.478 (2)	C5—H5A	0.9900
N1—C2	1.501 (3)	C5—H5B	0.9900
N1—H1	1.0000	C6—C7	1.522 (3)
N2—C4	1.487 (2)	C6—H6A	0.9900
N2—C3	1.496 (3)	C6—H6B	0.9900
N2—H2	1.0000	C7—C8	1.523 (3)
N3—C2	1.432 (2)	C7—H7A	0.9900
N3—C3	1.440 (2)	C7—H7B	0.9900
N3—C5	1.478 (2)	C8—H8A	0.9800
C1—C4^i	1.518 (3)	C8—H8B	0.9800
C1—H1A	0.9900	C8—H8C	0.9800
C1—H1B	0.9900	Cl1—O4	1.4293 (15)
C2—H2A	0.9900	Cl1—O3	1.4318 (17)
C2—H2B	0.9900	Cl1—O1	1.4420 (17)
C3—H3A	0.9900	Cl1—O2	1.4481 (14)
C3—H3B	0.9900
N1—Cu1—N1^i	180.00 (9)	H3A—C3—H3B	107.7
N1—Cu1—N2^i	86.45 (7)	N2—C4—C1^i	107.28 (15)
N1^i—Cu1—N2^i	93.55 (7)	N2—C4—H4A	110.3
N1—Cu1—N2	93.55 (7)	C1^i—C4—H4A	110.3
N1^i—Cu1—N2	86.45 (7)	N2—C4—H4B	110.3
N2^i—Cu1—N2	180.0	C1^i—C4—H4B	110.3
C1—N1—C2	112.37 (15)	H4A—C4—H4B	108.5
C1—N1—Cu1	106.33 (11)	N3—C5—C6	113.14 (15)
C2—N1—Cu1	115.28 (12)	N3—C5—H5A	109.0
C1—N1—H1	107.5	C6—C5—H5A	109.0
C2—N1—H1	107.5	N3—C5—H5B	109.0
Cu1—N1—H1	107.5	C6—C5—H5B	109.0
C4—N2—C3	113.49 (15)	H5A—C5—H5B	107.8
C4—N2—Cu1	106.73 (11)	C5—C6—C7	112.19 (16)
C3—N2—Cu1	115.29 (12)	C5—C6—H6A	109.2
C4—N2—H2	107.0	C7—C6—H6A	109.2
C3—N2—H2	107.0	C5—C6—H6B	109.2
Cu1—N2—H2	107.0	C7—C6—H6B	109.2
C2—N3—C3	114.81 (15)	H6A—C6—H6B	107.9
C2—N3—C5	114.08 (15)	C6—C7—C8	112.45 (16)
C3—N3—C5	116.15 (16)	C6—C7—H7A	109.1
N1—C1—C4^i	107.87 (15)	C8—C7—H7A	109.1
N1—C1—H1A	110.1	C6—C7—H7B	109.1
C4^i—C1—H1A	110.1	C8—C7—H7B	109.1
N1—C1—H1B	110.1	H7A—C7—H7B	107.8
C4^i—C1—H1B	110.1	C7—C8—H8A	109.5
H1A—C1—H1B	108.4	C7—C8—H8B	109.5
N3—C2—N1	114.03 (15)	H8A—C8—H8B	109.5
N3—C2—H2A	108.7	C7—C8—H8C	109.5
N1—C2—H2A	108.7	H8A—C8—H8C	109.5
N3—C2—H2B	108.7	H8B—C8—H8C	109.5
N1—C2—H2B	108.7	O4—Cl1—O3	110.11 (11)
H2A—C2—H2B	107.6	O4—Cl1—O1	109.74 (10)
N3—C3—N2	113.39 (15)	O3—Cl1—O1	108.36 (11)
N3—C3—H3A	108.9	O4—Cl1—O2	110.65 (10)
N2—C3—H3A	108.9	O3—Cl1—O2	108.82 (10)
N3—C3—H3B	108.9	O1—Cl1—O2	109.12 (9)
N2—C3—H3B	108.9
C2—N1—C1—C4^i	−169.53 (14)	C4—N2—C3—N3	179.24 (14)
Cu1—N1—C1—C4^i	−42.53 (15)	Cu1—N2—C3—N3	−57.23 (18)
C3—N3—C2—N1	−69.8 (2)	C3—N2—C4—C1^i	168.24 (15)
C5—N3—C2—N1	67.8 (2)	Cu1—N2—C4—C1^i	40.14 (16)
C1—N1—C2—N3	178.48 (14)	C2—N3—C5—C6	167.34 (16)
Cu1—N1—C2—N3	56.43 (18)	C3—N3—C5—C6	−55.6 (2)
C2—N3—C3—N2	70.2 (2)	N3—C5—C6—C7	−172.24 (17)
C5—N3—C3—N2	−66.5 (2)	C5—C6—C7—C8	−172.38 (18)

Symmetry code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1^ii	1.00	2.50	3.136 (2)	121
N2—H2···O4^iii	1.00	2.17	3.000 (2)	139
C1—H1A···O1^ii	0.99	2.46	3.160 (2)	127
N1—H1···O1^i	1.00	2.08	3.018 (2)	155
C6—H6B···O3^iv	0.99	2.50	3.338 (3)	142

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