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Acta Cryst. (2008). E64, m203    [ doi:10.1107/S1600536807047514 ]

[(1-Azulenyl)methanethiolato-[kappa]S](1,4,8,12-tetraazacyclopentadecane-[kappa]4N)zinc(II) perchlorate

H. Görls, J. Notni and E. Anders

Abstract top

In the title compound, [Zn(C11H26N4)(C11H9S)]ClO4, the ZnII atom is five-coordinated by four N atoms from a neutral 1,4,8,12-tetraazacyclopentadecane aza-macrocycle molecule, and one S atom from an azulenylmethanethiolate ligand. Only monomers are found in the crystal. The coordination geometry can be described as trigonal bipyramidal, with the thiolate group in an equatorial position. The Zn-N and Zn-S distances are in the usual ranges for this type of complex.

Comment top

The title compound belongs to a series of zinc thiolate complexes with azamacrocyclic ligands (Notni, Görls et al., 2006), which are potent model systems for a number of zinc enzymes (Schenk et al., 2006). These compounds possess nucleophilic p-methylthiolate or phenylmethylthiolate residues, the nucleophilicity of which is influenced by the nature of the macrocyclic ligand (Notni, Schenk et al., 2006; Notni et al., 2007). In order to gain insight into the electronic properties of the sulfur atom, azulenylmethyl derivatives were believed to allow a qualitative estimation of electron density at the thiolate sulfur employing VIS spectroscopy. However, the project failed since most of the desired complexes were elusive due to degradation processes during synthesis.

In crystalline form, the title compound is air-stable for several months. The crystal structure of the title compound contains a monovalent zinc(II) complex cation and a discrete perchlorate anion as shown in Fig. 1. Within the cation, the ZnII atom is coordinated by four N atoms and one S atom. Whether the coordination polyhedron can be assigned to tetragonal-pyramidal or trigonal-bipyramidal type is a question, which has been discussed in detail before (Notni, Görls et al., 2006). Following the argumentation given therein, we consider the title structure being trigonal-bipyramidal since pairs of opposing short Zn—N bond lengths [2.134 (4) and 2.139 (4) Å] as well as long Zn—N bond lengths [2.235 (3) and 2.272 (4) Å] are found. This is the largest difference between short and long Zn—N bond distances found for this type of zinc complexes (Notni, Görls et al., 2006; Salter et al., 2005). The pair of long N—Zn—N bonds is considered the axis of the trigonal bipyramid, the thiolate group thus being found in the equatorial position. The Zn—S bond length of 2.280 (1)Å is within the usual range for this kind of compounds (2.27–2.32 Å). The N atoms in these complexes are chiral in nature and the absolute configuration could be determined. In analogy to similar zinc–thiolate complexes of 1,4,8,12-tetraazacyclopentadecane, the N-bound H atoms are found in (+ – – –) positions ('+' denotes the H atom being positioned at the thiolate side of the macrocycle and '–' at the opposite side).

Related literature top

For related literature, see: Notni, Görls et al. (2006); Notni, Schenk et al. (2006); Notni et al. (2007); Salter et al. (2005); Schenk et al. (2006).

Experimental top

The title compound was prepared according to the published procedure (Notni, Görls et al., 2006). A solution of zinc perchlorate hexahydrate (0.750 g, 2 mmol) and 1,4,8,12,tetraazacyclopentadecane (0.430 g, 2 mmol) in methanol (20 ml) was heated for 15 min. Then a solution of potassium hydroxide (0.112 g, 2 mmol) and 1-azulenylmethylthiol (0.350 g, 2 mmol) in methanol (5 ml) was added dropwise, whereupon a fine-crystalline precipitate of potassium perchlorate was obtained. This was filtered off, and from the remaining deep-blue solution, blue needle crystals of the title compound precipitated after 5 min which were collected on a filter funnel and dried in vacuum. Yield 66% (0.731 g). m. p. 473.5–475.5 K. Analysis, calculated for C22H35ClN4O4SZn: C 47.83, H 6.39, N 10.14, S 5.80, Cl 6.42%; Found: C 47.81, H 6.42, N 9.94, S 5.70, Cl 6.49%.

Refinement top

H atoms were positioned geometrically and refined as riding, with C—H = 0.95Å (CH) and 0.99Å (CH2), and N—H = 0.93Å and Uiso(H) = 1.2Ueq(C, N). O atoms of the perchlorate group are disordered and they were refined isotropically.

Computing details top

Data collection: COLLECT (Nonius, 1998); cell refinement: DENZO (Otwinowski & Minor, 1997); data reduction: DENZO (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Siemens, 1990); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound. Displacement ellipsoids are drawn at the 40% probability level. The perchlorate anion was omitted for clarity. H atoms have been omitted except those attached to N atoms.
[(1-Azulenyl)methanethiolato-κS](1,4,8,12-tetraazacyclopentadecane-\ κ4N)zinc(II) perchlorate top
Crystal data top
[Zn(C11H26N4)(C11H9S)]ClO4F000 = 1160
Mr = 552.42Dx = 1.434 Mg m−3
Orthorhombic, P212121Mo Kα radiation
λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 18270 reflections
a = 8.0795 (1) Åθ = 2.3–27.5º
b = 13.7163 (3) ŵ = 1.18 mm−1
c = 23.0913 (5) ÅT = 183 (2) K
V = 2559.00 (8) Å3Prism, blue
Z = 40.06 × 0.06 × 0.05 mm
Data collection top
Nonius KappaCCD
diffractometer		4978 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.060
Monochromator: graphiteθmax = 27.5º
T = 183(2) Kθmin = 2.3º
φ and ω scansh = −10→9
Absorption correction: nonek = −17→17
18270 measured reflectionsl = −28→29
5858 independent reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.049  w = 1/[σ2(Fo2) + (0.0822P)2 + 1.0799P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.138(Δ/σ)max = 0.038
S = 1.04Δρmax = 0.73 e Å−3
5858 reflectionsΔρmin = −0.65 e Å−3
295 parametersExtinction correction: none
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack (1983), 2541 Friedel pairs
Secondary atom site location: difference Fourier mapFlack parameter: 0.002 (16)
Crystal data top
[Zn(C11H26N4)(C11H9S)]ClO4V = 2559.00 (8) Å3
Mr = 552.42Z = 4
Orthorhombic, P212121Mo Kα
a = 8.0795 (1) ŵ = 1.18 mm−1
b = 13.7163 (3) ÅT = 183 (2) K
c = 23.0913 (5) Å0.06 × 0.06 × 0.05 mm
Data collection top
Nonius KappaCCD
diffractometer		5858 independent reflections
Absorption correction: none4978 reflections with I > 2σ(I)
18270 measured reflectionsRint = 0.060
Refinement top
R[F2 > 2σ(F2)] = 0.049H-atom parameters constrained
wR(F2) = 0.138Δρmax = 0.73 e Å−3
S = 1.04Δρmin = −0.65 e Å−3
5858 reflectionsAbsolute structure: Flack (1983), 2541 Friedel pairs
295 parametersFlack parameter: 0.002 (16)
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
Zn0.54052 (5)0.85174 (3)0.645222 (17)0.03886 (13)
S0.38553 (14)0.73185 (7)0.60351 (5)0.0489 (2)
N10.5011 (5)0.8137 (3)0.74001 (15)0.0618 (11)
H1C0.41440.76910.74000.074*
N20.3875 (5)0.9714 (3)0.67100 (19)0.0631 (10)
H2C0.45801.02370.67790.076*
N30.5965 (5)0.9402 (3)0.56637 (15)0.0554 (9)
H3C0.65220.99650.57760.067*
N40.8012 (4)0.8308 (3)0.65356 (15)0.0541 (9)
H4C0.84610.89260.65890.065*
C10.4320 (9)0.9025 (4)0.7666 (2)0.084 (2)
H1A0.52230.94920.77510.100*
H1B0.37670.88580.80350.100*
C20.3087 (8)0.9488 (5)0.7257 (3)0.0865 (19)
H2A0.21520.90350.71910.104*
H2B0.26431.00930.74320.104*
C30.2676 (7)1.0040 (6)0.6259 (3)0.095 (2)
H3A0.19841.05670.64230.113*
H3B0.19340.94880.61640.113*
C40.3464 (8)1.0407 (5)0.5699 (3)0.0880 (19)
H4A0.25741.06560.54440.106*
H4B0.41931.09640.57950.106*
C50.4450 (8)0.9681 (4)0.5367 (2)0.0724 (14)
H5A0.37670.90920.53010.087*
H5B0.47340.99590.49840.087*
C60.7047 (7)0.8838 (4)0.5260 (2)0.0691 (14)
H6A0.71890.92140.48970.083*
H6B0.64950.82160.51610.083*
C70.8750 (7)0.8621 (5)0.5518 (2)0.0780 (16)
H7A0.94700.83630.52060.094*
H7B0.92420.92410.56520.094*
C80.8765 (7)0.7925 (4)0.6002 (2)0.0718 (14)
H8A0.99250.77380.60840.086*
H8B0.81630.73290.58840.086*
C90.8607 (6)0.7707 (5)0.7035 (2)0.0704 (14)
H9A0.98310.77220.70430.084*
H9B0.82590.70230.69760.084*
C100.7948 (7)0.8062 (5)0.7619 (2)0.0766 (16)
H10A0.87120.78470.79290.092*
H10B0.79290.87840.76200.092*
C110.6270 (9)0.7697 (5)0.7749 (2)0.0811 (17)
H11A0.62470.69820.76880.097*
H11B0.60200.78210.81620.097*
C120.4652 (7)0.6230 (3)0.6411 (2)0.0608 (11)
H12A0.58630.62940.64650.073*
H12B0.41350.61820.67990.073*
C130.4289 (5)0.5323 (3)0.60742 (18)0.0495 (10)
C140.2793 (5)0.4818 (3)0.60754 (16)0.0422 (8)
C150.1353 (6)0.5078 (3)0.63574 (18)0.0547 (10)
H15A0.14180.56570.65820.066*
C16−0.0175 (7)0.4616 (4)0.6360 (2)0.0653 (12)
H16A−0.10210.49420.65710.078*
C17−0.0651 (7)0.3740 (4)0.6098 (2)0.0698 (13)
H17A−0.17560.35370.61690.084*
C180.0282 (8)0.3127 (4)0.5746 (2)0.0692 (13)
H18A−0.02730.25580.56140.083*
C190.1875 (7)0.3225 (4)0.5565 (2)0.0665 (13)
H19A0.22660.27230.53170.080*
C200.2998 (6)0.3947 (3)0.5689 (2)0.0546 (10)
C210.4628 (8)0.4009 (4)0.5486 (3)0.0780 (16)
H21A0.51430.35560.52320.094*
C220.5374 (7)0.4838 (4)0.5715 (3)0.0699 (13)
H22A0.64740.50420.56350.084*
Cl0.79877 (18)0.11964 (9)0.68485 (6)0.0683 (3)
O410.8208 (14)0.2153 (8)0.7006 (5)0.091 (3)*0.575 (13)
O420.6918 (15)0.0533 (10)0.7147 (5)0.114 (4)*0.575 (13)
O430.918 (3)0.0559 (17)0.6803 (12)0.221 (9)*0.575 (13)
O440.8335 (15)0.0986 (8)0.6292 (5)0.122 (4)*0.575 (13)
O41A0.823 (3)0.2011 (15)0.7194 (9)0.126 (7)*0.425 (13)
O42A0.6508 (15)0.0964 (10)0.7185 (5)0.082 (3)*0.425 (13)
O43A0.961 (2)0.0861 (11)0.7227 (7)0.120 (5)*0.425 (13)
O44A0.7107 (19)0.1457 (11)0.6300 (6)0.116 (5)*0.425 (13)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Zn0.0422 (2)0.0405 (2)0.0338 (2)−0.00398 (19)−0.00309 (18)−0.00221 (17)
S0.0618 (6)0.0410 (5)0.0440 (5)−0.0080 (4)−0.0168 (5)−0.0002 (4)
N10.079 (3)0.069 (2)0.0373 (17)−0.025 (2)0.0085 (17)−0.0057 (17)
N20.054 (2)0.056 (2)0.079 (3)−0.0016 (19)0.008 (2)−0.015 (2)
N30.071 (2)0.059 (2)0.0365 (17)−0.0173 (19)−0.0119 (16)0.0113 (15)
N40.0449 (16)0.069 (2)0.0479 (19)−0.0047 (17)0.0017 (15)−0.0041 (17)
C10.114 (5)0.085 (4)0.052 (3)−0.037 (4)0.032 (3)−0.025 (3)
C20.070 (3)0.094 (4)0.096 (5)−0.003 (3)0.027 (3)−0.033 (4)
C30.055 (3)0.107 (5)0.121 (5)0.022 (3)−0.019 (3)−0.033 (4)
C40.089 (4)0.080 (4)0.095 (5)0.007 (3)−0.035 (4)0.015 (3)
C50.085 (4)0.073 (3)0.059 (3)0.001 (3)−0.017 (3)0.018 (2)
C60.083 (3)0.088 (4)0.037 (2)−0.004 (3)0.014 (2)0.003 (2)
C70.066 (3)0.117 (5)0.051 (3)−0.017 (3)0.015 (2)−0.014 (3)
C80.062 (3)0.089 (4)0.064 (3)−0.005 (3)0.012 (2)−0.008 (3)
C90.054 (3)0.082 (3)0.075 (3)0.003 (3)−0.024 (2)0.008 (3)
C100.083 (4)0.092 (4)0.055 (3)0.003 (3)−0.032 (3)0.001 (3)
C110.111 (5)0.086 (4)0.047 (3)−0.019 (4)−0.007 (3)0.014 (3)
C120.086 (3)0.044 (2)0.053 (2)−0.009 (2)−0.025 (3)0.0027 (18)
C130.057 (2)0.0449 (19)0.046 (2)−0.0006 (18)−0.0149 (18)0.0022 (17)
C140.055 (2)0.0375 (18)0.0337 (17)0.0030 (17)−0.0042 (16)0.0017 (15)
C150.075 (3)0.050 (2)0.038 (2)0.008 (2)0.002 (2)0.0029 (18)
C160.067 (3)0.075 (3)0.054 (3)0.004 (3)0.012 (2)0.005 (2)
C170.065 (3)0.077 (3)0.067 (3)−0.011 (3)0.007 (2)0.017 (3)
C180.083 (3)0.059 (3)0.066 (3)−0.022 (3)−0.007 (3)−0.002 (2)
C190.075 (3)0.052 (2)0.073 (3)−0.007 (2)−0.004 (3)−0.012 (2)
C200.068 (3)0.044 (2)0.052 (2)0.001 (2)0.001 (2)−0.0080 (18)
C210.064 (3)0.067 (3)0.103 (4)−0.006 (3)0.016 (3)−0.032 (3)
C220.056 (2)0.068 (3)0.086 (3)−0.005 (3)−0.003 (3)−0.005 (3)
Cl0.0732 (7)0.0494 (6)0.0825 (8)−0.0190 (5)0.0227 (7)−0.0145 (6)
Geometric parameters (Å, °) top
Zn—N42.134 (4)C9—C101.530 (8)
Zn—N22.139 (4)C9—H9A0.9900
Zn—N32.235 (3)C9—H9B0.9900
Zn—N12.272 (4)C10—C111.476 (9)
Zn—S2.2804 (10)C10—H10A0.9900
S—C121.843 (4)C10—H10B0.9900
N1—C111.431 (8)C11—H11A0.9900
N1—C11.474 (7)C11—H11B0.9900
N1—H1C0.9300C12—C131.496 (6)
N2—C21.448 (8)C12—H12A0.9900
N2—C31.491 (8)C12—H12B0.9900
N2—H2C0.9300C13—C221.379 (7)
N3—C51.454 (7)C13—C141.393 (6)
N3—C61.494 (7)C14—C151.380 (6)
N3—H3C0.9300C14—C201.500 (6)
N4—C81.472 (6)C15—C161.388 (7)
N4—C91.496 (6)C15—H15A0.9500
N4—H4C0.9300C16—C171.400 (8)
C1—C21.512 (10)C16—H16A0.9500
C1—H1A0.9900C17—C181.390 (8)
C1—H1B0.9900C17—H17A0.9500
C2—H2A0.9900C18—C191.360 (8)
C2—H2B0.9900C18—H18A0.9500
C3—C41.527 (10)C19—C201.374 (7)
C3—H3A0.9900C19—H19A0.9500
C3—H3B0.9900C20—C211.401 (8)
C4—C51.488 (10)C21—C221.392 (7)
C4—H4A0.9900C21—H21A0.9500
C4—H4B0.9900C22—H22A0.9500
C5—H5A0.9900Cl—O431.31 (2)
C5—H5B0.9900Cl—O441.345 (12)
C6—C71.529 (8)Cl—O411.373 (11)
C6—H6A0.9900Cl—O41A1.39 (2)
C6—H6B0.9900Cl—O421.432 (12)
C7—C81.469 (8)Cl—O42A1.461 (11)
C7—H7A0.9900Cl—O44A1.496 (15)
C7—H7B0.9900Cl—O43A1.640 (16)
C8—H8A0.9900O43—O441.48 (3)
C8—H8B0.9900
N4—Zn—N2130.42 (16)N4—C9—H9A109.0
N4—Zn—N386.95 (15)C10—C9—H9A109.0
N2—Zn—N385.81 (17)N4—C9—H9B109.0
N4—Zn—N191.17 (15)C10—C9—H9B109.0
N2—Zn—N180.05 (17)H9A—C9—H9B107.8
N3—Zn—N1159.70 (15)C11—C10—C9113.0 (5)
N4—Zn—S118.88 (11)C11—C10—H10A109.0
N2—Zn—S110.70 (12)C9—C10—H10A109.0
N3—Zn—S99.13 (10)C11—C10—H10B109.0
N1—Zn—S99.46 (11)C9—C10—H10B109.0
C12—S—Zn101.15 (14)H10A—C10—H10B107.8
C11—N1—C1112.6 (5)N1—C11—C10113.3 (4)
C11—N1—Zn122.7 (3)N1—C11—H11A108.9
C1—N1—Zn105.3 (3)C10—C11—H11A108.9
C11—N1—H1C104.9N1—C11—H11B108.9
C1—N1—H1C104.9C10—C11—H11B108.9
Zn—N1—H1C104.9H11A—C11—H11B107.7
C2—N2—C3112.8 (5)C13—C12—S111.1 (3)
C2—N2—Zn109.4 (4)C13—C12—H12A109.4
C3—N2—Zn114.3 (4)S—C12—H12A109.4
C2—N2—H2C106.6C13—C12—H12B109.4
C3—N2—H2C106.6S—C12—H12B109.4
Zn—N2—H2C106.6H12A—C12—H12B108.0
C5—N3—C6109.5 (4)C22—C13—C14108.2 (4)
C5—N3—Zn110.9 (3)C22—C13—C12126.1 (4)
C6—N3—Zn110.2 (3)C14—C13—C12125.7 (4)
C5—N3—H3C108.7C15—C14—C13127.1 (4)
C6—N3—H3C108.7C15—C14—C20125.4 (4)
Zn—N3—H3C108.7C13—C14—C20107.4 (4)
C8—N4—C9108.4 (4)C14—C15—C16129.4 (4)
C8—N4—Zn112.4 (3)C14—C15—H15A115.3
C9—N4—Zn117.4 (3)C16—C15—H15A115.3
C8—N4—H4C105.9C15—C16—C17129.3 (5)
C9—N4—H4C105.9C15—C16—H16A115.3
Zn—N4—H4C105.9C17—C16—H16A115.3
N1—C1—C2109.7 (4)C18—C17—C16128.6 (5)
N1—C1—H1A109.7C18—C17—H17A115.7
C2—C1—H1A109.7C16—C17—H17A115.7
N1—C1—H1B109.7C19—C18—C17129.3 (5)
C2—C1—H1B109.7C19—C18—H18A115.4
H1A—C1—H1B108.2C17—C18—H18A115.4
N2—C2—C1110.2 (5)C18—C19—C20129.2 (5)
N2—C2—H2A109.6C18—C19—H19A115.4
C1—C2—H2A109.6C20—C19—H19A115.4
N2—C2—H2B109.6C19—C20—C21126.5 (5)
C1—C2—H2B109.6C19—C20—C14128.7 (5)
H2A—C2—H2B108.1C21—C20—C14104.8 (4)
N2—C3—C4114.8 (5)C22—C21—C20109.2 (5)
N2—C3—H3A108.6C22—C21—H21A125.4
C4—C3—H3A108.6C20—C21—H21A125.4
N2—C3—H3B108.6C13—C22—C21110.4 (5)
C4—C3—H3B108.6C13—C22—H22A124.8
H3A—C3—H3B107.5C21—C22—H22A124.8
C5—C4—C3116.0 (5)O43—Cl—O4468.0 (13)
C5—C4—H4A108.3O43—Cl—O41124.5 (12)
C3—C4—H4A108.3O44—Cl—O41115.5 (7)
C5—C4—H4B108.3O43—Cl—O41A119.0 (15)
C3—C4—H4B108.3O44—Cl—O41A133.9 (10)
H4A—C4—H4B107.4O41—Cl—O41A19.9 (9)
N3—C5—C4112.5 (5)O43—Cl—O4293.4 (11)
N3—C5—H5A109.1O44—Cl—O42116.7 (7)
C4—C5—H5A109.1O41—Cl—O42123.9 (8)
N3—C5—H5B109.1O41A—Cl—O42108.6 (11)
C4—C5—H5B109.1O43—Cl—O42A120.1 (11)
H5A—C5—H5B107.8O44—Cl—O42A129.2 (7)
N3—C6—C7112.6 (4)O41—Cl—O42A100.0 (8)
N3—C6—H6A109.1O41A—Cl—O42A89.0 (11)
C7—C6—H6A109.1O42—Cl—O42A27.3 (6)
N3—C6—H6B109.1O43—Cl—O44A116.3 (14)
C7—C6—H6B109.1O44—Cl—O44A48.9 (6)
H6A—C6—H6B107.8O41—Cl—O44A93.2 (8)
C8—C7—C6115.5 (5)O41A—Cl—O44A111.1 (11)
C8—C7—H7A108.4O42—Cl—O44A105.8 (7)
C6—C7—H7A108.4O42A—Cl—O44A96.5 (7)
C8—C7—H7B108.4O43—Cl—O43A42.8 (11)
C6—C7—H7B108.4O44—Cl—O43A106.4 (8)
H7A—C7—H7B107.5O41—Cl—O43A91.3 (8)
C7—C8—N4113.7 (5)O41A—Cl—O43A78.9 (11)
C7—C8—H8A108.8O42—Cl—O43A92.7 (7)
N4—C8—H8A108.8O42A—Cl—O43A107.9 (7)
C7—C8—H8B108.8O44A—Cl—O43A154.0 (8)
N4—C8—H8B108.8Cl—O43—O4457.3 (11)
H8A—C8—H8B107.7Cl—O44—O4354.7 (10)
N4—C9—C10113.1 (5)
Table 1
Selected geometric parameters (Å, °) top
Zn—N42.134 (4)Zn—N12.272 (4)
Zn—N22.139 (4)Zn—S2.2804 (10)
Zn—N32.235 (3)
N4—Zn—N2130.42 (16)N3—Zn—N1159.70 (15)
N4—Zn—N386.95 (15)N4—Zn—S118.88 (11)
N2—Zn—N385.81 (17)N2—Zn—S110.70 (12)
N4—Zn—N191.17 (15)N3—Zn—S99.13 (10)
N2—Zn—N180.05 (17)N1—Zn—S99.46 (11)
Acknowledgements top

The authors gratefully acknowledge financial support from the Deutsche Forschungsgemeinschaft, SFB 436 'Metal Mediated Reactions Modelled after Nature'.

references
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