The structure of the title compound, [Zn
4(C
40H
24N
8)
4]·8C
3H
7NO·3H
2O, has been redetermined at 100 K. The redetermination is of significantly higher precision and gives further insight into the disorder of pyridyl groups and solvent molecules. The molecules of (5,10,15,20-tetra-4-pyridylporphyrinato)zinc(II) (ZnTPyP) form homomolecular cyclic tetramers by coordination of a peripheral pyridyl group to the central Zn atom of an adjacent symmetry-related molecule. The tetramer so formed exhibits molecular
S4 symmetry and is located about a crystallographic fourfold rotoinversion axis. Severely disordered dimethylformamide and water molecules are present in the crystal, the contributions of which were omitted from refinement. Intermolecular C—H
N hydrogen bonding is observed.
Supporting information
CCDC reference: 811194
Key indicators
- Single-crystal X-ray study
- T = 100 K
- Mean (C-C) = 0.003 Å
Some non-H atoms missing
- R factor = 0.042
- wR factor = 0.108
- Data-to-parameter ratio = 17.5
checkCIF/PLATON results
No syntax errors found
Alert level A
CHEMW03_ALERT_2_A ALERT: The ratio of given/expected molecular weight as
calculated from the _atom_site* data lies outside
the range 0.90 <> 1.10
From the CIF: _cell_formula_units_Z 2
From the CIF: _chemical_formula_weight 3366.98
TEST: Calculate formula weight from _atom_site_*
atom mass num sum
C 12.01 160.00 1921.76
H 1.01 96.00 96.77
N 14.01 32.00 448.22
O 16.00 0.00 0.00
Zn 65.39 4.00 261.56
Calculated formula weight 2728.31
| Author Response: Contributions of disordered solvent molecules were removed from the
diffraction data with SQUEEZE. Details are discussed in the text.
|
PLAT602_ALERT_2_A VERY LARGE Solvent Accessible VOID(S) in Structure !
| Author Response: Contributions of disordered solvent molecules were removed from the
diffraction data with SQUEEZE. Details are discussed in the text.
|
PLAT043_ALERT_1_A Check Reported Molecular Weight ................ 3366.98
| Author Response: Contributions of disordered solvent molecules were removed from the
diffraction data with SQUEEZE. Details are discussed in the text.
|
PLAT044_ALERT_1_A Calculated and Reported Dx Differ .............. ?
| Author Response: Contributions of disordered solvent molecules were removed from the
diffraction data with SQUEEZE. Details are discussed in the text.
|
PLAT051_ALERT_1_A Mu(calc) and Mu(CIF) Ratio Differs from 1.0 by . 13.29 Perc.
| Author Response: Contributions of disordered solvent molecules were removed from the
diffraction data with SQUEEZE. Details are discussed in the text.
|
PLAT923_ALERT_1_A S values in the CIF and FCF Differ by ....... -0.06
| Author Response: This can also be attributed to the SQUEEZE procedure. The FCF file
was generated following the recommendations in the SQUEEZE manual.
|
PLAT926_ALERT_1_A Reported and Calculated R1 * 100.0 Differ by . -8.37
| Author Response: This can also be attributed to the SQUEEZE procedure. The FCF file
was generated following the recommendations in the SQUEEZE manual.
|
PLAT927_ALERT_1_A Reported and Calculated wR2 * 100.0 Differ by . -26.45
| Author Response: This can also be attributed to the SQUEEZE procedure. The FCF file
was generated following the recommendations in the SQUEEZE manual.
|
PLAT928_ALERT_1_A Reported and Calculated S value Differ by . -2.74
| Author Response: This can also be attributed to the SQUEEZE procedure. The FCF file
was generated following the recommendations in the SQUEEZE manual.
|
Alert level B
PLAT220_ALERT_2_B Large Non-Solvent C Ueq(max)/Ueq(min) ... 4.57 Ratio
PLAT971_ALERT_2_B Large Calcd. Non-Metal Positive Residual Density 2.56 eA-3
PLAT922_ALERT_1_B wR2 * 100.0 in the CIF and FCF Differ by ....... -0.53
Alert level C
PLAT220_ALERT_2_C Large Non-Solvent N Ueq(max)/Ueq(min) ... 3.66 Ratio
PLAT232_ALERT_2_C Hirshfeld Test Diff (M-X) Zn1 -- N101_b .. 9.87 su
PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for C152
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C54
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C154
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor .... 2.25
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L= 0.600 72
PLAT971_ALERT_2_C Large Calcd. Non-Metal Positive Residual Density 2.40 eA-3
PLAT971_ALERT_2_C Large Calcd. Non-Metal Positive Residual Density 2.36 eA-3
PLAT971_ALERT_2_C Large Calcd. Non-Metal Positive Residual Density 2.25 eA-3
PLAT971_ALERT_2_C Large Calcd. Non-Metal Positive Residual Density 2.18 eA-3
PLAT971_ALERT_2_C Large Calcd. Non-Metal Positive Residual Density 2.12 eA-3
PLAT971_ALERT_2_C Large Calcd. Non-Metal Positive Residual Density 2.10 eA-3
PLAT971_ALERT_2_C Large Calcd. Non-Metal Positive Residual Density 1.86 eA-3
PLAT971_ALERT_2_C Large Calcd. Non-Metal Positive Residual Density 1.74 eA-3
PLAT971_ALERT_2_C Large Calcd. Non-Metal Positive Residual Density 1.62 eA-3
PLAT971_ALERT_2_C Large Calcd. Non-Metal Positive Residual Density 1.60 eA-3
PLAT041_ALERT_1_C Calc. and Reported SumFormula Strings Differ ?
PLAT068_ALERT_1_C Reported F000 Differs from Calcd (or Missing)... ?
PLAT480_ALERT_4_C Long H...A H-Bond Reported H7 .. N151 .. 2.65 Ang.
PLAT480_ALERT_4_C Long H...A H-Bond Reported H17 .. N51 .. 2.66 Ang.
PLAT912_ALERT_4_C Missing # of FCF Reflections Above STh/L= 0.600 49
PLAT921_ALERT_1_C R1 * 100.0 in the CIF and FCF Differ by ....... -0.13
PLAT925_ALERT_1_C The Reported and Calculated Rho(max) Differ by . 1.97 eA-3
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:C184 H158 N40 O11 Zn4
Atom count from the _atom_site data: C160 H96 N32 Zn4
CELLZ01_ALERT_1_G Difference between formula and atom_site contents detected.
CELLZ01_ALERT_1_G ALERT: Large difference may be due to a
symmetry error - see SYMMG tests
From the CIF: _cell_formula_units_Z 2
From the CIF: _chemical_formula_sum C184 H158 N40 O11 Zn4
TEST: Compare cell contents of formula and atom_site data
atom Z*formula cif sites diff
C 368.00 320.00 48.00
H 316.00 192.00 124.00
N 80.00 64.00 16.00
O 22.00 0.00 22.00
Zn 8.00 8.00 0.00
PLAT083_ALERT_2_G SHELXL Second Parameter in WGHT Unusually Large. 5.05
PLAT794_ALERT_5_G Note: Tentative Bond Valency for Zn1 ....... 1.87
9 ALERT level A = In general: serious problem
3 ALERT level B = Potentially serious problem
24 ALERT level C = Check and explain
5 ALERT level G = General alerts; check
14 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
22 ALERT type 2 Indicator that the structure model may be wrong or deficient
1 ALERT type 3 Indicator that the structure quality may be low
3 ALERT type 4 Improvement, methodology, query or suggestion
1 ALERT type 5 Informative message, check
Small dark red plate-shaped crystals of the title compound were obtained
similarly as reported previously (Seidel et al., 2010); 12 mg of
ZnTPyP
(Aldrich) and 11 mg of [Pd(NO3)2(en)] (en = 1,2-diaminoethane) were placed
in an ampoule and 4 ml of DMF were added. The ampoule was sealed and placed in
a heater. The sample was heated to 150 °C in 24 h and held for five days at
this temperature. Subsequently, the sample was cooled down to room temperature
in 100 h. Noteworthy, the crystals of the title compound were accompanied by
crystals of the triclinic phase, containing a polymeric one-dimensional ladder
structure of ZnTPyP, as observed previously (Seidel et al.,
2010).
For the final refinement, the contributions of severely disordered DMF and water
molecules of crystallization were removed from the diffraction data with
PLATON / SQUEEZE (van der Sluis & Spek, 1990; Spek,
2009), see
comment. H atoms were placed at geometrically calculated positions and refined
with constrained C—H bond length of 0.95 Å and Uiso(H) = 1.2
Ueq(C) allowing them to ride on the parent C atom.
Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT (Bruker, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2010); software used to prepare material for publication: enCIFer (Allen et al., 2004).
cyclo-tetrakis(µ-5,10,15,20-tetra-4-pyridylporphyrinato)tetrazinc(II)
dimethylformamide octasolvate
top
Crystal data top
[Zn4(C40H24N8)4]·8C3H7NO·3H2O | Dx = 1.329 Mg m−3 |
Mr = 3366.98 | Cu Kα radiation, λ = 1.54178 Å |
Tetragonal, P42/n | Cell parameters from 130 reflections |
Hall symbol: -P 4bc | θ = 3.5–31.5° |
a = 23.6897 (5) Å | µ = 1.24 mm−1 |
c = 14.9876 (7) Å | T = 100 K |
V = 8411.1 (5) Å3 | Plate, dark red |
Z = 2 | 0.16 × 0.04 × 0.02 mm |
F(000) = 3500 | |
Data collection top
Bruker X8 PROSPECTOR goniometer diffractometer | 7723 independent reflections |
Radiation source: Incoatec IµS microfocus X-ray source | 6768 reflections with I > 2σ(I) |
Incoatec Quazar Multilayer Mirror monochromator | Rint = 0.018 |
Detector resolution: 8.33 pixels mm-1 | θmax = 69.2°, θmin = 2.6° |
ω scans | h = −28→25 |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | k = −24→28 |
Tmin = 0.827, Tmax = 0.976 | l = −17→14 |
44415 measured reflections | |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.042 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.108 | H-atom parameters constrained |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0472P)2 + 5.0454P] where P = (Fo2 + 2Fc2)/3 |
7723 reflections | (Δ/σ)max < 0.001 |
442 parameters | Δρmax = 0.59 e Å−3 |
0 restraints | Δρmin = −0.42 e Å−3 |
Crystal data top
[Zn4(C40H24N8)4]·8C3H7NO·3H2O | Z = 2 |
Mr = 3366.98 | Cu Kα radiation |
Tetragonal, P42/n | µ = 1.24 mm−1 |
a = 23.6897 (5) Å | T = 100 K |
c = 14.9876 (7) Å | 0.16 × 0.04 × 0.02 mm |
V = 8411.1 (5) Å3 | |
Data collection top
Bruker X8 PROSPECTOR goniometer diffractometer | 7723 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | 6768 reflections with I > 2σ(I) |
Tmin = 0.827, Tmax = 0.976 | Rint = 0.018 |
44415 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.042 | 0 restraints |
wR(F2) = 0.108 | H-atom parameters constrained |
S = 1.04 | Δρmax = 0.59 e Å−3 |
7723 reflections | Δρmin = −0.42 e Å−3 |
442 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. |
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 (Å2) top | x | y | z | Uiso*/Ueq | |
Zn1 | 0.350673 (11) | 0.520064 (11) | 0.185590 (16) | 0.03823 (9) | |
N21 | 0.38601 (8) | 0.54998 (7) | 0.06850 (10) | 0.0433 (4) | |
N22 | 0.27781 (7) | 0.50134 (7) | 0.11541 (10) | 0.0404 (4) | |
N23 | 0.41242 (7) | 0.56428 (7) | 0.25451 (10) | 0.0404 (4) | |
N24 | 0.30440 (7) | 0.51392 (7) | 0.30222 (10) | 0.0377 (4) | |
C1 | 0.46288 (9) | 0.58336 (8) | 0.22081 (13) | 0.0420 (4) | |
C2 | 0.50033 (10) | 0.59793 (10) | 0.29314 (14) | 0.0532 (6) | |
H2 | 0.5379 | 0.6115 | 0.2880 | 0.064* | |
C3 | 0.47175 (10) | 0.58861 (10) | 0.36945 (15) | 0.0534 (6) | |
H3 | 0.4853 | 0.5949 | 0.4283 | 0.064* | |
C4 | 0.41675 (9) | 0.56739 (9) | 0.34544 (13) | 0.0428 (5) | |
C5 | 0.37497 (9) | 0.55138 (9) | 0.40720 (13) | 0.0442 (5) | |
C6 | 0.32280 (9) | 0.52641 (9) | 0.38657 (12) | 0.0411 (4) | |
C7 | 0.28126 (9) | 0.50864 (9) | 0.45108 (13) | 0.0451 (5) | |
H7 | 0.2835 | 0.5130 | 0.5140 | 0.054* | |
C8 | 0.23852 (9) | 0.48459 (9) | 0.40491 (13) | 0.0422 (4) | |
H8 | 0.2052 | 0.4684 | 0.4292 | 0.051* | |
C9 | 0.25323 (8) | 0.48825 (8) | 0.31165 (12) | 0.0362 (4) | |
C10 | 0.21846 (8) | 0.46994 (8) | 0.24113 (12) | 0.0360 (4) | |
C11 | 0.22974 (8) | 0.47834 (8) | 0.14991 (12) | 0.0376 (4) | |
C12 | 0.19052 (9) | 0.46543 (9) | 0.07858 (13) | 0.0460 (5) | |
H12 | 0.1543 | 0.4486 | 0.0845 | 0.055* | |
C13 | 0.21544 (10) | 0.48202 (10) | 0.00230 (14) | 0.0526 (6) | |
H13 | 0.1998 | 0.4794 | −0.0559 | 0.063* | |
C14 | 0.26979 (9) | 0.50435 (10) | 0.02480 (13) | 0.0477 (5) | |
C15 | 0.30923 (11) | 0.52569 (10) | −0.03612 (14) | 0.0545 (6) | |
C16 | 0.36281 (10) | 0.54737 (10) | −0.01508 (13) | 0.0515 (5) | |
C17 | 0.40164 (12) | 0.57099 (11) | −0.07905 (15) | 0.0636 (7) | |
H17 | 0.3959 | 0.5743 | −0.1416 | 0.076* | |
C18 | 0.44735 (11) | 0.58736 (10) | −0.03328 (15) | 0.0581 (6) | |
H18 | 0.4801 | 0.6046 | −0.0575 | 0.070* | |
C19 | 0.43790 (9) | 0.57411 (9) | 0.05937 (13) | 0.0455 (5) | |
C20 | 0.47569 (9) | 0.58754 (8) | 0.12914 (13) | 0.0429 (5) | |
N51 | 0.40921 (10) | 0.58630 (15) | 0.68340 (15) | 0.0812 (8) | |
C52 | 0.38597 (16) | 0.62318 (17) | 0.6300 (2) | 0.0945 (11) | |
H52 | 0.3762 | 0.6589 | 0.6542 | 0.113* | |
C53 | 0.37466 (15) | 0.61389 (13) | 0.54115 (18) | 0.0816 (9) | |
H53 | 0.3581 | 0.6429 | 0.5060 | 0.098* | |
C54 | 0.38735 (9) | 0.56279 (11) | 0.50349 (14) | 0.0513 (5) | |
C55 | 0.41194 (13) | 0.52451 (15) | 0.55825 (18) | 0.0792 (8) | |
H55 | 0.4222 | 0.4884 | 0.5360 | 0.095* | |
C56 | 0.42214 (14) | 0.53814 (18) | 0.6469 (2) | 0.0885 (10) | |
H56 | 0.4397 | 0.5105 | 0.6834 | 0.106* | |
N101 | 0.06117 (6) | 0.38923 (7) | 0.30189 (10) | 0.0355 (3) | |
C102 | 0.06574 (8) | 0.44515 (8) | 0.29549 (13) | 0.0403 (4) | |
H102 | 0.0327 | 0.4673 | 0.3038 | 0.048* | |
C103 | 0.11567 (8) | 0.47254 (8) | 0.27747 (13) | 0.0406 (4) | |
H103 | 0.1167 | 0.5126 | 0.2740 | 0.049* | |
C104 | 0.16441 (8) | 0.44146 (8) | 0.26451 (11) | 0.0339 (4) | |
C105 | 0.16034 (9) | 0.38345 (9) | 0.27246 (17) | 0.0506 (5) | |
H105 | 0.1928 | 0.3604 | 0.2652 | 0.061* | |
C106 | 0.10845 (9) | 0.35925 (9) | 0.29112 (16) | 0.0490 (5) | |
H106 | 0.1064 | 0.3194 | 0.2965 | 0.059* | |
N151 | 0.2660 (2) | 0.5329 (2) | −0.3142 (2) | 0.1294 (17) | |
C152 | 0.2458 (3) | 0.5685 (2) | −0.2569 (3) | 0.155 (2) | |
H152 | 0.2211 | 0.5972 | −0.2780 | 0.185* | |
C153 | 0.2581 (2) | 0.56707 (18) | −0.1666 (2) | 0.1290 (18) | |
H153 | 0.2421 | 0.5945 | −0.1278 | 0.155* | |
C154 | 0.29319 (12) | 0.52625 (14) | −0.13291 (16) | 0.0729 (8) | |
C155 | 0.31337 (15) | 0.4886 (2) | −0.19209 (18) | 0.1009 (13) | |
H155 | 0.3375 | 0.4591 | −0.1726 | 0.121* | |
C156 | 0.29872 (18) | 0.4931 (2) | −0.2832 (2) | 0.1174 (17) | |
H156 | 0.3133 | 0.4659 | −0.3237 | 0.141* | |
N201 | 0.63736 (10) | 0.65387 (10) | 0.05085 (15) | 0.0695 (6) | |
C202 | 0.60235 (13) | 0.68222 (12) | 0.1038 (2) | 0.0742 (8) | |
H202 | 0.6140 | 0.7184 | 0.1241 | 0.089* | |
C203 | 0.55016 (12) | 0.66270 (10) | 0.13114 (18) | 0.0635 (7) | |
H203 | 0.5271 | 0.6852 | 0.1689 | 0.076* | |
C204 | 0.53176 (10) | 0.61002 (9) | 0.10312 (14) | 0.0474 (5) | |
C205 | 0.56798 (10) | 0.58046 (10) | 0.04725 (15) | 0.0548 (6) | |
H205 | 0.5577 | 0.5442 | 0.0255 | 0.066* | |
C206 | 0.61911 (11) | 0.60416 (12) | 0.02354 (17) | 0.0645 (7) | |
H206 | 0.6429 | 0.5831 | −0.0153 | 0.077* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Zn1 | 0.04778 (16) | 0.04374 (16) | 0.02318 (14) | −0.00756 (11) | 0.00168 (10) | −0.00080 (10) |
N21 | 0.0579 (10) | 0.0455 (9) | 0.0266 (8) | −0.0116 (8) | 0.0027 (7) | 0.0007 (7) |
N22 | 0.0485 (9) | 0.0476 (9) | 0.0251 (8) | −0.0020 (7) | −0.0005 (7) | 0.0025 (7) |
N23 | 0.0531 (10) | 0.0414 (9) | 0.0266 (8) | −0.0084 (7) | 0.0028 (7) | −0.0033 (6) |
N24 | 0.0438 (9) | 0.0446 (9) | 0.0247 (8) | −0.0010 (7) | 0.0004 (6) | −0.0035 (6) |
C1 | 0.0521 (12) | 0.0395 (10) | 0.0342 (10) | −0.0129 (9) | 0.0034 (8) | −0.0050 (8) |
C2 | 0.0581 (14) | 0.0608 (14) | 0.0408 (12) | −0.0204 (11) | 0.0039 (10) | −0.0108 (10) |
C3 | 0.0599 (14) | 0.0649 (14) | 0.0354 (11) | −0.0209 (11) | −0.0001 (10) | −0.0111 (10) |
C4 | 0.0522 (12) | 0.0473 (11) | 0.0290 (10) | −0.0094 (9) | 0.0010 (8) | −0.0072 (8) |
C5 | 0.0520 (12) | 0.0531 (12) | 0.0275 (10) | −0.0066 (9) | −0.0019 (8) | −0.0055 (8) |
C6 | 0.0479 (11) | 0.0494 (11) | 0.0259 (10) | 0.0000 (9) | 0.0024 (8) | −0.0038 (8) |
C7 | 0.0494 (12) | 0.0603 (13) | 0.0256 (10) | −0.0036 (10) | 0.0010 (8) | −0.0026 (9) |
C8 | 0.0458 (11) | 0.0528 (12) | 0.0279 (10) | 0.0012 (9) | 0.0035 (8) | −0.0002 (8) |
C9 | 0.0410 (10) | 0.0403 (10) | 0.0274 (9) | 0.0045 (8) | 0.0019 (7) | −0.0024 (7) |
C10 | 0.0421 (10) | 0.0373 (10) | 0.0286 (9) | 0.0047 (8) | 0.0014 (7) | −0.0020 (7) |
C11 | 0.0428 (10) | 0.0414 (10) | 0.0287 (10) | 0.0024 (8) | −0.0018 (8) | −0.0010 (8) |
C12 | 0.0457 (11) | 0.0623 (13) | 0.0300 (10) | −0.0037 (10) | −0.0036 (8) | −0.0017 (9) |
C13 | 0.0565 (13) | 0.0725 (15) | 0.0289 (11) | −0.0093 (11) | −0.0068 (9) | 0.0036 (10) |
C14 | 0.0566 (13) | 0.0600 (13) | 0.0264 (10) | −0.0071 (10) | −0.0044 (9) | 0.0036 (9) |
C15 | 0.0687 (15) | 0.0670 (15) | 0.0279 (11) | −0.0171 (12) | −0.0035 (10) | 0.0076 (9) |
C16 | 0.0697 (15) | 0.0574 (13) | 0.0273 (10) | −0.0158 (11) | 0.0024 (9) | 0.0052 (9) |
C17 | 0.0816 (18) | 0.0817 (17) | 0.0276 (11) | −0.0288 (14) | 0.0023 (11) | 0.0087 (11) |
C18 | 0.0723 (16) | 0.0672 (15) | 0.0347 (12) | −0.0260 (12) | 0.0053 (10) | 0.0071 (10) |
C19 | 0.0595 (13) | 0.0455 (11) | 0.0314 (10) | −0.0118 (9) | 0.0050 (9) | 0.0012 (8) |
C20 | 0.0570 (12) | 0.0366 (10) | 0.0351 (10) | −0.0118 (9) | 0.0066 (9) | −0.0009 (8) |
N51 | 0.0633 (14) | 0.145 (3) | 0.0359 (12) | −0.0305 (15) | −0.0006 (10) | −0.0144 (14) |
C52 | 0.126 (3) | 0.113 (3) | 0.0447 (17) | −0.011 (2) | −0.0056 (17) | −0.0286 (17) |
C53 | 0.126 (3) | 0.0787 (19) | 0.0403 (14) | −0.0017 (18) | −0.0102 (15) | −0.0181 (13) |
C54 | 0.0499 (12) | 0.0755 (16) | 0.0286 (11) | −0.0147 (11) | 0.0009 (9) | −0.0067 (10) |
C55 | 0.096 (2) | 0.100 (2) | 0.0419 (15) | 0.0139 (17) | −0.0143 (14) | −0.0037 (14) |
C56 | 0.082 (2) | 0.135 (3) | 0.0486 (17) | 0.002 (2) | −0.0152 (14) | 0.0081 (18) |
N101 | 0.0379 (8) | 0.0442 (9) | 0.0244 (8) | 0.0040 (7) | −0.0013 (6) | −0.0035 (6) |
C102 | 0.0418 (11) | 0.0434 (11) | 0.0358 (10) | 0.0092 (8) | 0.0059 (8) | −0.0024 (8) |
C103 | 0.0466 (11) | 0.0392 (10) | 0.0360 (10) | 0.0058 (8) | 0.0063 (8) | 0.0009 (8) |
C104 | 0.0386 (10) | 0.0412 (10) | 0.0218 (8) | 0.0052 (8) | −0.0005 (7) | −0.0033 (7) |
C105 | 0.0376 (11) | 0.0436 (12) | 0.0707 (15) | 0.0078 (9) | 0.0018 (10) | −0.0042 (10) |
C106 | 0.0422 (11) | 0.0384 (11) | 0.0665 (15) | 0.0038 (9) | −0.0002 (10) | −0.0022 (10) |
N151 | 0.157 (4) | 0.182 (4) | 0.0499 (18) | −0.092 (3) | −0.022 (2) | 0.029 (2) |
C152 | 0.267 (7) | 0.130 (4) | 0.067 (3) | −0.043 (4) | −0.074 (3) | 0.028 (3) |
C153 | 0.218 (5) | 0.105 (3) | 0.064 (2) | −0.016 (3) | −0.068 (3) | 0.026 (2) |
C154 | 0.0797 (18) | 0.108 (2) | 0.0312 (13) | −0.0441 (16) | −0.0058 (12) | 0.0136 (13) |
C155 | 0.088 (2) | 0.180 (4) | 0.0349 (15) | −0.029 (2) | 0.0018 (13) | −0.0193 (18) |
C156 | 0.098 (3) | 0.210 (5) | 0.0446 (19) | −0.059 (3) | 0.0097 (17) | −0.011 (2) |
N201 | 0.0714 (14) | 0.0754 (15) | 0.0616 (13) | −0.0299 (12) | 0.0153 (11) | −0.0022 (11) |
C202 | 0.0847 (19) | 0.0592 (15) | 0.0786 (19) | −0.0325 (14) | 0.0173 (16) | −0.0085 (14) |
C203 | 0.0751 (17) | 0.0495 (13) | 0.0658 (16) | −0.0190 (12) | 0.0165 (13) | −0.0104 (11) |
C204 | 0.0627 (13) | 0.0454 (11) | 0.0340 (11) | −0.0135 (10) | 0.0057 (9) | 0.0004 (8) |
C205 | 0.0693 (15) | 0.0540 (13) | 0.0410 (12) | −0.0153 (11) | 0.0148 (10) | −0.0076 (10) |
C206 | 0.0700 (16) | 0.0752 (17) | 0.0482 (14) | −0.0173 (13) | 0.0177 (12) | −0.0064 (12) |
Geometric parameters (Å, º) top
Zn1—N24 | 2.0684 (15) | C19—C20 | 1.413 (3) |
Zn1—N21 | 2.0695 (16) | C20—C204 | 1.483 (3) |
Zn1—N22 | 2.0695 (17) | N51—C56 | 1.302 (5) |
Zn1—N23 | 2.0747 (16) | N51—C52 | 1.306 (5) |
Zn1—N101i | 2.1385 (16) | C52—C53 | 1.376 (4) |
N21—C19 | 1.363 (3) | C52—H52 | 0.9500 |
N21—C16 | 1.369 (3) | C53—C54 | 1.369 (4) |
N22—C11 | 1.364 (3) | C53—H53 | 0.9500 |
N22—C14 | 1.373 (2) | C54—C55 | 1.355 (4) |
N23—C4 | 1.369 (3) | C55—C56 | 1.389 (4) |
N23—C1 | 1.374 (3) | C55—H55 | 0.9500 |
N24—C9 | 1.363 (3) | C56—H56 | 0.9500 |
N24—C6 | 1.370 (2) | N101—C102 | 1.333 (3) |
C1—C20 | 1.411 (3) | N101—C106 | 1.336 (3) |
C1—C2 | 1.443 (3) | N101—Zn1ii | 2.1385 (16) |
C2—C3 | 1.347 (3) | C102—C103 | 1.376 (3) |
C2—H2 | 0.9500 | C102—H102 | 0.9500 |
C3—C4 | 1.442 (3) | C103—C104 | 1.383 (3) |
C3—H3 | 0.9500 | C103—H103 | 0.9500 |
C4—C5 | 1.407 (3) | C104—C105 | 1.383 (3) |
C5—C6 | 1.404 (3) | C105—C106 | 1.385 (3) |
C5—C54 | 1.497 (3) | C105—H105 | 0.9500 |
C6—C7 | 1.442 (3) | C106—H106 | 0.9500 |
C7—C8 | 1.352 (3) | N151—C152 | 1.294 (7) |
C7—H7 | 0.9500 | N151—C156 | 1.307 (6) |
C8—C9 | 1.443 (3) | C152—C153 | 1.385 (5) |
C8—H8 | 0.9500 | C152—H152 | 0.9500 |
C9—C10 | 1.408 (3) | C153—C154 | 1.372 (5) |
C10—C11 | 1.407 (3) | C153—H153 | 0.9500 |
C10—C104 | 1.489 (3) | C154—C155 | 1.345 (5) |
C11—C12 | 1.449 (3) | C155—C156 | 1.413 (5) |
C12—C13 | 1.345 (3) | C155—H155 | 0.9500 |
C12—H12 | 0.9500 | C156—H156 | 0.9500 |
C13—C14 | 1.432 (3) | N201—C206 | 1.320 (3) |
C13—H13 | 0.9500 | N201—C202 | 1.330 (4) |
C14—C15 | 1.401 (3) | C202—C203 | 1.382 (4) |
C15—C16 | 1.405 (3) | C202—H202 | 0.9500 |
C15—C154 | 1.500 (3) | C203—C204 | 1.387 (3) |
C16—C17 | 1.442 (3) | C203—H203 | 0.9500 |
C17—C18 | 1.339 (3) | C204—C205 | 1.388 (3) |
C17—H17 | 0.9500 | C205—C206 | 1.382 (3) |
C18—C19 | 1.441 (3) | C205—H205 | 0.9500 |
C18—H18 | 0.9500 | C206—H206 | 0.9500 |
| | | |
N24—Zn1—N21 | 162.77 (7) | C17—C18—H18 | 126.1 |
N24—Zn1—N22 | 88.42 (6) | C19—C18—H18 | 126.1 |
N21—Zn1—N22 | 88.84 (7) | N21—C19—C20 | 126.29 (18) |
N24—Zn1—N23 | 89.34 (6) | N21—C19—C18 | 109.15 (18) |
N21—Zn1—N23 | 87.94 (6) | C20—C19—C18 | 124.46 (19) |
N22—Zn1—N23 | 161.70 (7) | C1—C20—C19 | 124.66 (19) |
N24—Zn1—N101i | 95.10 (6) | C1—C20—C204 | 118.30 (18) |
N21—Zn1—N101i | 102.11 (6) | C19—C20—C204 | 116.97 (18) |
N22—Zn1—N101i | 102.00 (6) | C56—N51—C52 | 115.3 (3) |
N23—Zn1—N101i | 96.29 (6) | N51—C52—C53 | 124.6 (3) |
C19—N21—C16 | 106.82 (16) | N51—C52—H52 | 117.7 |
C19—N21—Zn1 | 126.42 (13) | C53—C52—H52 | 117.7 |
C16—N21—Zn1 | 126.72 (14) | C54—C53—C52 | 119.8 (3) |
C11—N22—C14 | 106.27 (17) | C54—C53—H53 | 120.1 |
C11—N22—Zn1 | 126.10 (13) | C52—C53—H53 | 120.1 |
C14—N22—Zn1 | 127.37 (14) | C55—C54—C53 | 115.9 (2) |
C4—N23—C1 | 106.45 (16) | C55—C54—C5 | 123.2 (2) |
C4—N23—Zn1 | 125.15 (13) | C53—C54—C5 | 120.9 (2) |
C1—N23—Zn1 | 126.61 (13) | C54—C55—C56 | 119.9 (3) |
C9—N24—C6 | 106.48 (15) | C54—C55—H55 | 120.0 |
C9—N24—Zn1 | 126.17 (12) | C56—C55—H55 | 120.0 |
C6—N24—Zn1 | 126.59 (13) | N51—C56—C55 | 124.4 (3) |
N23—C1—C20 | 124.64 (18) | N51—C56—H56 | 117.8 |
N23—C1—C2 | 109.72 (17) | C55—C56—H56 | 117.8 |
C20—C1—C2 | 125.64 (19) | C102—N101—C106 | 116.85 (17) |
C3—C2—C1 | 106.8 (2) | C102—N101—Zn1ii | 120.26 (13) |
C3—C2—H2 | 126.6 | C106—N101—Zn1ii | 122.55 (14) |
C1—C2—H2 | 126.6 | N101—C102—C103 | 123.56 (18) |
C2—C3—C4 | 107.42 (19) | N101—C102—H102 | 118.2 |
C2—C3—H3 | 126.3 | C103—C102—H102 | 118.2 |
C4—C3—H3 | 126.3 | C102—C103—C104 | 119.61 (18) |
N23—C4—C5 | 126.00 (18) | C102—C103—H103 | 120.2 |
N23—C4—C3 | 109.56 (18) | C104—C103—H103 | 120.2 |
C5—C4—C3 | 124.42 (18) | C105—C104—C103 | 117.31 (18) |
C6—C5—C4 | 125.98 (18) | C105—C104—C10 | 122.03 (17) |
C6—C5—C54 | 117.43 (18) | C103—C104—C10 | 120.65 (17) |
C4—C5—C54 | 116.59 (18) | C104—C105—C106 | 119.38 (19) |
N24—C6—C5 | 125.05 (18) | C104—C105—H105 | 120.3 |
N24—C6—C7 | 109.78 (17) | C106—C105—H105 | 120.3 |
C5—C6—C7 | 125.15 (18) | N101—C106—C105 | 123.3 (2) |
C8—C7—C6 | 106.91 (17) | N101—C106—H106 | 118.4 |
C8—C7—H7 | 126.5 | C105—C106—H106 | 118.4 |
C6—C7—H7 | 126.5 | C152—N151—C156 | 117.0 (4) |
C7—C8—C9 | 106.83 (18) | N151—C152—C153 | 123.7 (5) |
C7—C8—H8 | 126.6 | N151—C152—H152 | 118.2 |
C9—C8—H8 | 126.6 | C153—C152—H152 | 118.2 |
N24—C9—C10 | 125.42 (17) | C154—C153—C152 | 120.3 (5) |
N24—C9—C8 | 110.00 (16) | C154—C153—H153 | 119.9 |
C10—C9—C8 | 124.54 (18) | C152—C153—H153 | 119.9 |
C11—C10—C9 | 125.06 (18) | C155—C154—C153 | 116.1 (3) |
C11—C10—C104 | 117.12 (16) | C155—C154—C15 | 122.8 (3) |
C9—C10—C104 | 117.77 (16) | C153—C154—C15 | 121.1 (3) |
N22—C11—C10 | 125.68 (17) | C154—C155—C156 | 120.0 (4) |
N22—C11—C12 | 109.87 (17) | C154—C155—H155 | 120.0 |
C10—C11—C12 | 124.42 (18) | C156—C155—H155 | 120.0 |
C13—C12—C11 | 106.50 (19) | N151—C156—C155 | 122.9 (5) |
C13—C12—H12 | 126.7 | N151—C156—H156 | 118.6 |
C11—C12—H12 | 126.7 | C155—C156—H156 | 118.6 |
C12—C13—C14 | 107.59 (19) | C206—N201—C202 | 115.6 (2) |
C12—C13—H13 | 126.2 | N201—C202—C203 | 124.5 (2) |
C14—C13—H13 | 126.2 | N201—C202—H202 | 117.8 |
N22—C14—C15 | 124.8 (2) | C203—C202—H202 | 117.8 |
N22—C14—C13 | 109.76 (18) | C202—C203—C204 | 119.5 (2) |
C15—C14—C13 | 125.41 (19) | C202—C203—H203 | 120.3 |
C14—C15—C16 | 126.03 (19) | C204—C203—H203 | 120.3 |
C14—C15—C154 | 117.7 (2) | C203—C204—C205 | 116.2 (2) |
C16—C15—C154 | 116.28 (19) | C203—C204—C20 | 121.7 (2) |
N21—C16—C15 | 125.76 (19) | C205—C204—C20 | 122.07 (19) |
N21—C16—C17 | 109.5 (2) | C206—C205—C204 | 119.5 (2) |
C15—C16—C17 | 124.7 (2) | C206—C205—H205 | 120.3 |
C18—C17—C16 | 106.7 (2) | C204—C205—H205 | 120.3 |
C18—C17—H17 | 126.6 | N201—C206—C205 | 124.8 (2) |
C16—C17—H17 | 126.6 | N201—C206—H206 | 117.6 |
C17—C18—C19 | 107.8 (2) | C205—C206—H206 | 117.6 |
Symmetry codes: (i) y, −x+1/2, −z+1/2; (ii) −y+1/2, x, −z+1/2. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
C7—H7···N151iii | 0.95 | 2.65 | 3.583 (4) | 167 |
C17—H17···N51iv | 0.95 | 2.66 | 3.583 (3) | 165 |
Symmetry codes: (iii) x, y, z+1; (iv) x, y, z−1. |
Experimental details
Crystal data |
Chemical formula | [Zn4(C40H24N8)4]·8C3H7NO·3H2O |
Mr | 3366.98 |
Crystal system, space group | Tetragonal, P42/n |
Temperature (K) | 100 |
a, c (Å) | 23.6897 (5), 14.9876 (7) |
V (Å3) | 8411.1 (5) |
Z | 2 |
Radiation type | Cu Kα |
µ (mm−1) | 1.24 |
Crystal size (mm) | 0.16 × 0.04 × 0.02 |
|
Data collection |
Diffractometer | Bruker X8 PROSPECTOR goniometer diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2008) |
Tmin, Tmax | 0.827, 0.976 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 44415, 7723, 6768 |
Rint | 0.018 |
(sin θ/λ)max (Å−1) | 0.606 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.042, 0.108, 1.04 |
No. of reflections | 7723 |
No. of parameters | 442 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.59, −0.42 |
Selected geometric parameters (Å, º) topZn1—N24 | 2.0684 (15) | Zn1—N23 | 2.0747 (16) |
Zn1—N21 | 2.0695 (16) | Zn1—N101i | 2.1385 (16) |
Zn1—N22 | 2.0695 (17) | | |
| | | |
N24—Zn1—N21 | 162.77 (7) | N22—Zn1—N23 | 161.70 (7) |
N24—Zn1—N22 | 88.42 (6) | N24—Zn1—N101i | 95.10 (6) |
N21—Zn1—N22 | 88.84 (7) | N21—Zn1—N101i | 102.11 (6) |
N24—Zn1—N23 | 89.34 (6) | N22—Zn1—N101i | 102.00 (6) |
N21—Zn1—N23 | 87.94 (6) | N23—Zn1—N101i | 96.29 (6) |
Symmetry code: (i) y, −x+1/2, −z+1/2. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
C7—H7···N151ii | 0.95 | 2.65 | 3.583 (4) | 167.1 |
C17—H17···N51iii | 0.95 | 2.66 | 3.583 (3) | 164.9 |
Symmetry codes: (ii) x, y, z+1; (iii) x, y, z−1. |
5,10,15,20-Tetra(4-pyridyl)porphyrin has been widely used as ligand for the construction of coordination polymers (DeVries & Choe, 2009). We and others have reported on the solid-state supramolecular chemistry of the self-complementary [5,10,15,20-tetra(4-pyridyl)porphyrinato]zinc(II) (ZnTPyP) building block (Lipstman & Goldberg, 2010; Seidel et al., 2010 and references cited therein). Recently, we reported the title structure of [ZnTPyP]4.
The small dark red plate-shaped crystals of the title compound were subjected to diffraction experiments using a Bruker AXS X8 PROSPECTOR diffractometer equipped with an INCOATEC microfocus X-ray source (IµS) for Cu radiation (Graf, 2008). Such microfocus X-ray sources use multilayer mirrors to focus the X-ray beam onto the crystal and, therefore, lead to a significant reduction of the background and an increase in diffracted intensities. It has already been demonstrated that the Mo IµS gives data of significantly higher quality than a 2 kW Mo fine focus sealed tube, when small crystals are examined (Schulz et al., 2009). The data collection presented here, using the Cu IµS, resulted in intensity data of surprisingly good quality and, hence, indicated a re-refinement of the crystal structure. The crystals investigated in the original work were significantly larger than those examined in the present study and split on cooling to 100 K. For this reason, the data were collected at 200 K with a Cu rotating anode system at that time. Using small crystals has the advantage that these are less likely to split on flash cooling.
The molecular structure of [ZnTPyP]4 is depicted in Fig. 1. The asymmetric unit contains one ZnTPyP unit (Fig 2.) and the S4 symmetric tetramer is generated by crystallographic fourfold rotoinversion symmetry. One peripheral pyridyl group binds to the central Zn atom of an adjacent symmetry related ZnTPyP unit. Zn1 is pentacoordinated and is displaced from the N4 mean plane by 0.3196 (9) Å. The coordination geometry parameters about Zn1 are given in Table 1. The three remaining pyridyl groups are non-coordinating. Even at 100 K, the pyridyl groups attached to C5 and C15 show elongated ellipsoids, which cause a checkCIF B level alert (Spek, 2009) due to large Ueq(max)/Ueq(min) ratio. This reveals that the disorder is rather of static than dynamic nature. Attempts were made to describe the electron density of the pyridyl ring attached to C15 (Fig. 3) by a split model. However, the refinement results could not be improved thereby. Thus, both pyridyl rings were finally described with large displacement parameters.
In the crystal, the [ZnTPyP]4 entities are stacked into columns located at x = 1/4, y = 1/4 and x = 3/4, y = 3/4 (Fig 4). The stacking propagates via Cβ—H···Npy interactions (see Table 2) by translational symmetry in the c axis direction. Within a column, the distance between the centroids of the pyridyl rings attached to C5 and C15iii is 4.0714 (1) Å. Adjacent columns of [ZnTPyP]4 are arranged with an offset of c/2 (ca 7.49 Å). Interstitial channels are formed parallel to the c axis direction centred at x = 1/4, y = 3/4 and x = 3/4, y = 1/4 (Fig 5). The potential solvent accessible void estimated with PLATON / SOLV (Spek, 2009) is 33.2% of the unit cell volume. On cooling to 100 K, the a lattice vector is shortened by approximately 0.27 Å in comparison to the tetragonal unit cell at 200 K (a = 23.958 (2) Å), whereas the length of c lattice vector remains relatively unaffected (c = 15.0646 (16) Å at 200 K; Seidel et al., 2010).
Despite intensive efforts, the disordered solvent molecules filling the voids within the columns of [ZnTPyP]4 and the interstitial channels could not be modeled reasonably with the data collected at 100 K. Nevertheless, residual electron density was visible in a difference Fourier synthesis calculated for the solvent regions (Fig. 6) with phases based on the model using COOT (Emsley et al., 2010). For the visualization of the surface of the (difference) electron density using a three-dimensional mesh, the electron densities should be read into COOT in terms of structure factors. To obtain a structure factor (.fcf) file containg the informations necessary for the calculation of electron density maps and suitable for COOT, the LIST 6 instruction of SHELXL-97 was used. The atomic model of the framework was read into COOT by means of the SHELXL-97. res file. The visual inspection of the difference electron density map indicates that four molecules of dimethylformamide (DMF) plus one water molecule are located within the voids in the columns approximately centred at (1/4,1/4,0), whereas another four molecules of DMF and two water molecules are clustered around the 42 screw axes running through the interstitial channels parallel to the c axis direction. The compound can, therefore, probably best be described as [ZnTPyP]4. 8 DMF. 3 H2O. The compound was originally formulated as being a pure DMF solvate (Seidel et al., 2010). To improve the fit of the model to the data and, hence, the precision of the main part of the structure, the contributions of the disordered solvent molecules were removed from the diffraction data with PLATON / SQUEEZE (van der Sluis & Spek, 1990; Spek, 2009). SQUEEZE estimated the electron counts in the voids within the columns and interstitial channels of [ZnTPyP]4 to be 182 and 207, respectively. These values are relatively close to those based on the proposed chemical formula (178 and 196).