An example of the refinement of positional disorder modeled as compositional disorder in [5-(2-formyl­phen­yl)-10,15,20-triphenyl­porphyrinato]nickel(II)

The title compound, [Ni(C₄₅H₂₈N₄O)], crystallizes in the space group I2d and resides on a crystallographic fourfold rotoinversion axis with only a quarter of the complex in the asymmetric unit. The complex displays positional disorder as the one aldehyde group on the ligand can be located at four different positions. It was necessary to model this as com­po­sitional disorder to obtain a correct model and refinement. The practical approach to the refinement is explained.

S1. Comment

Metalloporphyryin complexes and metalloporphyrin assemblies are of longstanding interest in biological systems, where they are widely used as active sites or cofactors in various enzymes to store redox equivalents, transport dioxygen, to collect solar energy and to activate small molecules (Behar et al., 1998; Morris et al., 2009; Naruta & Sasaki, 1994; Shimazaki et al., 2004; Collman et al., 2007). One of the recent advances in the field is the utilization of 1,2-phenylene-bridged bismanganese diporphyrin as a water oxidation catalyst (Shimazaki et al., 2004). The unsymmetrical free-base 5-(2-formylphenyl)-10,15,20-triphenylporphyrin (H₂TPP-CHO) is an important intermediate in the synthesis of this catalyst. Metallation of H₂TPP-CHO by nickel acetate (Yao et al., 2012) yielded [5-(2-formylphenyl)-10,15,20-triphenylporphyrinato] nickel(II), (I), a potentially useful precursor for the synthesis of heterobimetallic diporphyrins.

The structure of (I) based on the synthetic procedure and spectroscopic evidence is shown in the scheme. The Ni complex occupies the crystallographic fourfold rotoinversion axis (Wyckoff position a); thus only a fourth of the complex is symmetry independent (Fig.1). There must be disorder in this crystal structure because the complex lacks any symmetry except for the identity (theoretically C_S is possible). The aldehyde group is therefore required to be disordered over four positions in the structure. In the asymmetric unit this disorder manifests itself by having an occupancy of 25% for the aldehyde group, whereas the other 75% of the time a H atom must reside in its place.

A search of the IUCr journals for other similar examples of disorder modeling using the search terms `positional disorder' and `compositional disorder' yielded only one other relevant paper (Guzei et al., 2008). While this paper reports positional disorder modeled as compositional disorder similar to that in (I), it does not outline the procedure for such modeling. Therefore we will briefly describe the correct disorder handling procedure for (I) using the program SHELXL (Sheldrick, 2008).

The procedure is not difficult if one knows what needs to be done and what facilities SHELXL offers. First of all, the 3:1 ratio of the H:aldehyde group was known a priori. After the routine structure solution and straightforward refinement of atoms Ni1, N1, N2 and C1—C11, one must locate the partially occupied (occupancy of 1/4) aldehyde group and partially present (occupancy of 3/4) H atom on atom C11. When multiplied by 4, these occupancies produce the correct molecular composition. There were two peaks of electron density (circa 2 e Å^-3) near atom C11, and they were identified and labeled as C12 and O1. Option PART of program SHELXL was used to separate the partially occupied moieties and prevent them from binding to each other. The instruction file was manually edited as follows:

C11 1 0.68614 0.60979 0.58742 11.00000 0.04948

PART 1

AFIX 43

H11 2 0 0 0 10.75000 - 1.20000

AFIX 0

PART 2 10.25

HFIX 43 C12

C12 1 0.74510 0.61110 0.50400 11.00000 0.05000

O1 4 0.73520 0.63160 0.41710 11.00000 0.05000

PART 0

Atom H11 belongs to PART 1 whereas atoms C12 and O1 belong to PART 2. The use of two different PARTs was necessary in order to help the program place the H atoms at the correct positions at atoms C11 and C12. Atoms specified in PART 1 and PART 2 are not present simultaneously at any one location in the structure and cannot (and should not, vide infra) be chemically bonded. Atom H11 is input with dummy coordinates of 0,0,0, and command AFIX 43 which ensures the correct placement of the atom on C11 at an idealized position. The correct coordinates for H11 will be generated by the program. For all atoms in PART 2 the occupancy is assigned on the PART line with the second parameter. The first parameter designates the PART number, the second occupancy. In PART 2 the first command is HFIX 43 C12 which will generate the aldehyde H atom for C12 in an idealized position. These ten lines of instructions [as given] above completely address the disorder, but of course other approches are possible. After another cycle of least-squares the non-hydrogen atoms were refined anisotropically and a chemically reasonable and computationally stable refinement achieved.

The correct assignment of the occupancies of PART 1 and PART 2 can also be checked by refining the occupancy of the aldehyde group independently; indeed, it refines to 0.237 (5). As mentioned above, the correct molecular composition was confirmed by other analyses.

The final structure is presented in Fig. 2. Only one of the four possible positions of the aldehyde group is shown to display the correct atomic composition. Aside from the disorder and its facile modeling, this structure is unexceptional with typical geometrical parameters as comfirmed by a Mogul structural check (Bruno et al., 2002). The porphyrinato ligand is saddle shaped, consistent with its 4 symmetry. The C5—Ni1—C5[2-X,1-Y,+Z] angle spans 162.59 (8)°, atom C5 and its symmetry mates alternatively reside 0.512 (2) Å below and above the best least-square plane defined by them. It should be noted that for this structure some visualization and data validation programs indicate the presence of conflicting close contacts between symmetry-related O atoms of the aldehyde groups. It is important to keep in mind that the observed structure is the average structure and that the fourfold symmetry of the average structure puts the minor aldehyde components at four different positions in the crystal. In each molecule, there is only one aldehyde group, thus any close `contact' between such symmetry-related aldehyde groups is not real because each group is occupied only 25% of the time. When the aldehyde group is present at one site in any particular molecule in the crystal, it is not present at a conflicting nearby site in the neighboring molecule. In general, such `false contacts' are not a concern if the total occupancy of the `conflicting' atoms does not exceed unity. Nonetheless, visualization and validation software are sometimes unable to appropriately recognize such situations and may produce false indications of close contacts or draw a spurious chemical bond between would-be conflicting atoms. The user should remain aware of the real situation at the local level of the structure.

Although the disorder in this structure is technically positional it was necessary to model it as compositional owing to the symmetry considerations: only one fourth of the Ni complex is symmetry independent, and two groups appear to share the same site.

Related literature

For related literature, see: Behar et al. (1998); Bruno et al. (2002); Collman et al. (2007); Guzei et al. (2008); Morris et al. (2009); Naruta & Sasaki (1994); Sheldrick (2008); Shimazaki et al. (2004); Yao et al. (2012); Ye & Naruta (2003).

S2. Experimental

All the solvents, chlorobenzene, chloroform, DMF [dimethylformamide?] and heptanes were purchased from Sigma–Aldrich. Nickel acetate and sodium acetate were also purchased from Sigma–Aldrich. The free-base porphyrin 5-(2-formylphenyl)-10,15,20-triphenylporphyrin was prepared according to a previously published procedure (Ye & Naruta, 2003).

The title nickel porphyrin complex, (I), was prepared in a similar manner to methods described previously (Yao et al., 2012). Under ambient atmospheric conditions, in a 100 ml distillation flask, 5-(2-formylphenyl)-10,15,20-triphenylporphyrin (170 mg, 0.26 mmol) and NaOAc (20 mg, 0.63 mmol) were stirred in a 3:1 (v/v) chlorobenzene–DMF solvent mixture (50 ml). After the addition of 8 equivalents of Ni(OAc)₂.4H₂O (440 mg, 1.28 mmol), a Soxhlet extractor with a cellulose filter thimble filled with ~3 g of K₂CO₃ was attached to the distillation flask. The assembly was completed with a condenser on the top of the extractor; and then the mixture was heated to reflux at 423.15 K overnight. The reaction progress was monitored by thin-layer chromatography until all the H₂TPP was consumed. After the reaction was complete, the solvent was removed under vacuum. The remaining solid was dissolved in chloroform (150 ml), and washed with water (5 × 20 ml). The organic layer was further washed with a saturated sodium bicarbonate solution (3 × 20 ml), and dried over K₂SO₄. After removal of the solvent in vacuo, bright orange solids were collected (yield: 76.5%, 123 mg, 0.18 mmol). MS (MALDI-anthracene) m/z (%): 699 (100) [M+H]⁺. ¹H NMR (300 MHz, CDCl₃): δ 9.34 [s, 1H, C(H)O], 8.74 (s, 6H, β-pyrrole), 8.54 (s, 1H, β-pyrrole), 8.55 (s, 1H, β-pyrrole), 8.35 (m, 1H, o-phenyl), 8.13 (m, 1H, p-phenyl), 7.69 (broad, 6H, o-phenyl), 7.85 (m, 2H, m-phenyl), 7.69 (broad, 9H, m- and p-phenyl). UV–vis (CH₂Cl₂) λ_max(nm): 415 (Soret), 530. About 10 mg of bright orange solid was dissolved in chloroform, which was layered with excess heptane. The recrystallization tube was stored at room temperature. Orange crystals suitable for single-crystal X-ray diffraction studies were isolated after two weeks.

S3. Refinement

H atoms attached to C atoms were placed in idealized locations and refined as riding with appropriate displacement parameters U_iso(H) = 1.2U_eq(parent atom). Default effective X—H distances for T = 100.0 K, Csp²—H = 0.95 Å.

Computing details

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT-Plus (Bruker, 2009); data reduction: SAINT-Plus (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008), OLEX2 (Dolomanov et al., 2009), FCF_filter (Guzei, 2007) and INSerter (Guzei, 2007); molecular graphics: SHELXTL (Sheldrick, 2008) and DIAMOND (Brandenburg, 1999); software used to prepare material for publication: SHELXTL (Sheldrick, 2008), publCIF (Westrip, 2010) and modiCIFer (Guzei, 2007).

Figures

	Fig. 1. The structure of the asymmetric unit of (I), with both parts of the disordered atoms shown (Pennington, 1999). The displacement ellipsoids are shown at 50% probability level.
	Fig. 2. Molecular structure of (I) (Pennington, 1999). The thermal ellipsoids are shown at 50% probability level. All hydrogen atoms were omitted for clarity. The aldehyde group is only shown in one of the four possible positions which are occupied 25% of the time each.

[5-(2-formylphenyl)-10,15,20-triphenylporphyrinato]nickel(II)

Crystal data

[Ni(C45H28N4O)]	Dx = 1.452 Mg m^−3
Mr = 699.42	Mo Kα radiation, λ = 0.71073 Å
Tetragonal, I42d	Cell parameters from 999 reflections
Hall symbol: I -4 2bw	θ = 3.3–28.3°
a = 15.6514 (5) Å	µ = 0.65 mm^−1
c = 13.0600 (4) Å	T = 100 K
V = 3199.26 (17) Å^3	Block, orange
Z = 4	0.09 × 0.08 × 0.07 mm
F(000) = 1448

Data collection

Bruker SMART APEXII area-detector diffractometer	1989 independent reflections
Radiation source: microfocus sealed X-ray tube, Incoatec Iµs	1865 reflections with I > 2σ(I)
Mirror optics monochromator	Rint = 0.047
0.60° ω and 0.6° ϕ scans	θmax = 28.3°, θmin = 3.3°
Absorption correction: analytical (SADABS; Bruker, 2009)	h = −20→20
Tmin = 0.944, Tmax = 0.958	k = −20→20
33791 measured reflections	l = −17→17

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.028	H-atom parameters constrained
wR(F^2) = 0.080	w = 1/[σ^2(Fo^2) + (0.0289P)^2 + 3.0244P] where P = (Fo^2 + 2Fc^2)/3
S = 1.16	(Δ/σ)max < 0.001
1989 reflections	Δρmax = 0.19 e Å^−3
130 parameters	Δρmin = −0.21 e Å^−3
0 restraints	Absolute structure: Flack (1983), 781 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.000 (19)

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)
Ni1	1.0000	0.5000	0.7500	0.02707 (13)
N1	0.89460 (11)	0.43652 (11)	0.75058 (15)	0.0292 (3)
C1	0.88407 (14)	0.35050 (14)	0.76797 (16)	0.0316 (5)
C2	0.79656 (13)	0.32558 (14)	0.7520 (2)	0.0357 (5)
H2	0.7731	0.2701	0.7610	0.043*
C3	0.75421 (16)	0.39660 (16)	0.72153 (18)	0.0367 (5)
H3	0.6958	0.3998	0.7023	0.044*
C4	0.81370 (14)	0.46595 (15)	0.72372 (17)	0.0307 (5)
C5	0.79242 (15)	0.55143 (14)	0.71077 (17)	0.0306 (5)
C6	0.70306 (14)	0.57520 (14)	0.68364 (17)	0.0309 (4)
C7	0.63700 (15)	0.56675 (16)	0.7547 (2)	0.0397 (5)
H7	0.6484	0.5426	0.8200	0.048*
C8	0.55496 (17)	0.59336 (18)	0.7307 (2)	0.0443 (6)
H8	0.5104	0.5883	0.7798	0.053*
C9	0.53822 (16)	0.62729 (17)	0.6350 (2)	0.0420 (6)
H9	0.4819	0.6453	0.6184	0.050*
C10	0.60174 (17)	0.63518 (17)	0.56425 (19)	0.0417 (6)
H10	0.5894	0.6583	0.4986	0.050*
C11	0.68477 (16)	0.60945 (15)	0.58783 (18)	0.0355 (5)
H11	0.7289	0.6153	0.5384	0.043*	0.75
C12	0.7462 (6)	0.6094 (5)	0.5054 (7)	0.0317 (16)	0.25
H12	0.8020	0.5896	0.5212	0.038*	0.25
O1	0.7336 (4)	0.6323 (4)	0.4178 (5)	0.0364 (14)	0.25

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Ni1	0.02970 (16)	0.02970 (16)	0.0218 (2)	0.000	0.000	0.000
N1	0.0331 (8)	0.0318 (8)	0.0226 (7)	0.0008 (6)	−0.0020 (8)	0.0008 (8)
C1	0.0345 (11)	0.0349 (10)	0.0253 (11)	−0.0027 (8)	0.0000 (8)	0.0009 (8)
C2	0.0362 (10)	0.0385 (11)	0.0325 (10)	−0.0030 (9)	−0.0045 (12)	0.0011 (12)
C3	0.0357 (11)	0.0397 (12)	0.0347 (12)	−0.0027 (9)	−0.0072 (9)	0.0002 (9)
C4	0.0332 (11)	0.0355 (11)	0.0235 (10)	−0.0011 (9)	−0.0017 (8)	−0.0003 (8)
C5	0.0337 (11)	0.0329 (11)	0.0252 (10)	0.0004 (9)	−0.0014 (9)	−0.0006 (8)
C6	0.0346 (11)	0.0297 (10)	0.0283 (10)	−0.0006 (9)	−0.0051 (9)	−0.0030 (8)
C7	0.0401 (11)	0.0512 (13)	0.0277 (10)	0.0020 (10)	−0.0036 (10)	0.0033 (11)
C8	0.0380 (12)	0.0541 (15)	0.0407 (14)	0.0008 (10)	−0.0007 (10)	−0.0028 (11)
C9	0.0379 (12)	0.0442 (13)	0.0438 (13)	0.0070 (10)	−0.0115 (10)	−0.0060 (11)
C10	0.0514 (14)	0.0396 (13)	0.0340 (12)	0.0110 (11)	−0.0083 (10)	0.0013 (10)
C11	0.0419 (13)	0.0327 (11)	0.0318 (11)	0.0022 (10)	−0.0011 (9)	−0.0005 (9)
C12	0.040 (4)	0.027 (4)	0.028 (4)	0.004 (3)	0.000 (4)	0.003 (4)
O1	0.051 (4)	0.028 (3)	0.030 (3)	0.002 (3)	−0.006 (3)	0.005 (3)

Geometric parameters (Å, º)

Ni1—N1^i	1.9259 (17)	C6—C11	1.391 (3)
Ni1—N1^ii	1.9259 (17)	C6—C7	1.396 (3)
Ni1—N1	1.9259 (17)	C7—C8	1.386 (3)
Ni1—N1^iii	1.9259 (17)	C7—H7	0.9500
N1—C1	1.375 (3)	C8—C9	1.384 (4)
N1—C4	1.392 (3)	C8—H8	0.9500
C1—C5^i	1.387 (3)	C9—C10	1.363 (4)
C1—C2	1.439 (3)	C9—H9	0.9500
C2—C3	1.354 (3)	C10—C11	1.395 (3)
C2—H2	0.9500	C10—H10	0.9500
C3—C4	1.430 (3)	C11—C12	1.443 (9)
C3—H3	0.9500	C11—H11	0.9500
C4—C5	1.389 (3)	C12—O1	1.215 (11)
C5—C1^iii	1.387 (3)	C12—H12	0.9500
C5—C6	1.490 (3)
N1^i—Ni1—N1^ii	90.001 (1)	C11—C6—C7	118.8 (2)
N1^i—Ni1—N1	90.001 (1)	C11—C6—C5	120.2 (2)
N1^ii—Ni1—N1	179.55 (12)	C7—C6—C5	120.9 (2)
N1^i—Ni1—N1^iii	179.55 (12)	C8—C7—C6	120.5 (2)
N1^ii—Ni1—N1^iii	90.001 (1)	C8—C7—H7	119.7
N1—Ni1—N1^iii	90.001 (1)	C6—C7—H7	119.7
C1—N1—C4	104.87 (17)	C9—C8—C7	119.7 (2)
C1—N1—Ni1	127.47 (14)	C9—C8—H8	120.2
C4—N1—Ni1	127.39 (14)	C7—C8—H8	120.2
N1—C1—C5^i	126.0 (2)	C10—C9—C8	120.6 (2)
N1—C1—C2	110.82 (18)	C10—C9—H9	119.7
C5^i—C1—C2	123.0 (2)	C8—C9—H9	119.7
C3—C2—C1	106.6 (2)	C9—C10—C11	120.3 (2)
C3—C2—H2	126.7	C9—C10—H10	119.9
C1—C2—H2	126.7	C11—C10—H10	119.9
C2—C3—C4	107.4 (2)	C6—C11—C10	120.1 (2)
C2—C3—H3	126.3	C6—C11—C12	122.3 (4)
C4—C3—H3	126.3	C10—C11—C12	117.1 (4)
C5—C4—N1	124.57 (19)	C6—C11—H11	120.0
C5—C4—C3	124.9 (2)	C10—C11—H11	120.0
N1—C4—C3	110.24 (19)	O1—C12—C11	126.5 (8)
C1^iii—C5—C4	121.3 (2)	O1—C12—H12	116.8
C1^iii—C5—C6	118.8 (2)	C11—C12—H12	116.8
C4—C5—C6	119.6 (2)
N1^i—Ni1—N1—C1	12.06 (14)	N1—C4—C5—C6	−178.94 (19)
N1^iii—Ni1—N1—C1	−168.4 (2)	C3—C4—C5—C6	−5.5 (4)
N1^i—Ni1—N1—C4	−161.1 (2)	C1^iii—C5—C6—C11	74.1 (3)
N1^iii—Ni1—N1—C4	18.45 (15)	C4—C5—C6—C11	−112.0 (3)
C4—N1—C1—C5^i	174.7 (2)	C1^iii—C5—C6—C7	−103.4 (3)
Ni1—N1—C1—C5^i	0.4 (3)	C4—C5—C6—C7	70.5 (3)
C4—N1—C1—C2	0.1 (3)	C11—C6—C7—C8	−1.1 (4)
Ni1—N1—C1—C2	−174.31 (17)	C5—C6—C7—C8	176.5 (2)
N1—C1—C2—C3	1.9 (3)	C6—C7—C8—C9	1.0 (4)
C5^i—C1—C2—C3	−173.0 (2)	C7—C8—C9—C10	−0.3 (4)
C1—C2—C3—C4	−3.0 (3)	C8—C9—C10—C11	−0.3 (4)
C1—N1—C4—C5	172.3 (2)	C7—C6—C11—C10	0.4 (3)
Ni1—N1—C4—C5	−13.3 (3)	C5—C6—C11—C10	−177.1 (2)
C1—N1—C4—C3	−1.9 (3)	C7—C6—C11—C12	−171.2 (5)
Ni1—N1—C4—C3	172.46 (16)	C5—C6—C11—C12	11.3 (5)
C2—C3—C4—C5	−171.0 (3)	C9—C10—C11—C6	0.3 (4)
C2—C3—C4—N1	3.2 (3)	C9—C10—C11—C12	172.3 (4)
N1—C4—C5—C1^iii	−5.2 (4)	C6—C11—C12—O1	174.4 (7)
C3—C4—C5—C1^iii	168.2 (2)	C10—C11—C12—O1	2.5 (10)

Symmetry codes: (i) −y+3/2, x−1/2, −z+3/2; (ii) −x+2, −y+1, z; (iii) y+1/2, −x+3/2, −z+3/2.