Pseudosymmetry in pyridinium ­tetrachloro(oxo)pyridineniobate(V) pyridine solvate

The title compound, (C₅H₆N)[NbCl₄O(C₅H₅N)]·C₅H₅N, crystallizes as discrete ions, with a very strong linear N—H...N hydrogen-bonding interaction between the cation and the solvate pyridine molecule [N...N 2.755 (5) Å]. All chemical species occupy crystallographic twofold axes. The ligated and solvate pyridines form ABABAB stacks in the lattice. There is pseudosymmetry which emulates a centred unit cell in Amm2, but it is not supported by the diffraction pattern, which is consistent with the correct space group Pnc2. Three crystallographic software packages suggested space group Amm2 over Pnc2, while a fourth indicated Pnc2, a subgroup of Amm2.

S1. Comment

The title compound, (I), crystallizes in an orthorhombic space group, Pnc2 (Z = 2), and refines beautifully to an R factor of 0.020 [wR(F²) = 0.054] (Table 1), with expected interatomic bond distances, low s.u.s and normal atomic anisotropic displacement coefficients. \sch

Program XPREP of the SHELXTL software package (Sheldrick, 1997a) suggested two probable space groups, Pmna and Pnc2, but only the latter, non-centrosymmetric, space group yielded chemically reasonable and computationally stable results of refinement. All chemical moieties reside on crystallographic twofold axes.

Upon completion of the refinement, PLATON (Spek, 1991) was used to verify the correctness of the structure and a new space group, Amm2, was suggested. Refinement in this space group also proved to be reasonable, with all chemical entities possessing mm2 (C_2v) site symmetry. However, the R factor was slightly higher [R = 0.024 and wR(F²) = 0.063] and the displacement ellipsoids were elongated in the direction perpendicular to the crystallographic mirror planes. The bond distances differed slightly from the corresponding ones in the structure refined in Pnc2, but fell into the expected ranges with low s.u.s. Nonetheless, these s.u.s were twice as large as those determined in Pnc2.

The late Bob Sparks kindly analyzed the structure with the program FINDSYMM (not commercially available from Bruker AXS at the time) to discover that, again, space group Amm2 was chosen over Pnc2. Interestingly, the centred structure was never suggested by XPREP. Table 3 contains the XRPEP output of a statistical analysis of the current dataset. It is clear from the statistics that A-centring is not present.

The correct assignment of the space group came down to an analysis of the actual X-ray diffraction pattern by eye, which is rarely done nowadays, since fast computers and elaborate programs are readily available. Both space groups Pnc2 and Amm2 have the same reflection conditions for two sets of reflections 0kl and h0l. However, Amm2 has an extra reflection condition, hkl (k + l = even). While reflections with k + l = odd (hkl) were not very strong, their observed presence substantiated the correct assignment of the space group as Pnc2. This example illustrates that blindly relying upon modern software can lead to incorrect space group assignment, which in turn results in flawed structures.

A molecular packing diagram for (I) is shown in Fig. 1. The absence of C_2v symmetry in the structure is further evidenced by two structural parameters. Firstly, the orientation of the coordinated N1 pyridine ring relative to the Cl atoms is noteworthy. The Cl1—Nb—N1—C1 dihedral angle is 51.7 (2)°, rather than 45° which would correspond to the expected ideally staggered conformation. The observed deviation from the idealized geometry is attributed to packing forces. Secondly, the dihedral angle between the pyridine rings of the two solvate pyridine molecules participating in the hydrogen-bonding interaction is 82.16 (2)°. This value is consistent with the observed C₂ symmetry but contradicts C_2v symmetry, for which angles of 0 or 90° are required.

The [NbOCl₄(py)]^- anion (py is pyridine) exhibits a distorted octahedral geometry, with the pyridine ring trans to the oxo ligand. The Nb^V centre is displaced by -0.303 (2) Å toward the O atom and away from the equatorial plane defined by the four Cl^- ligands. Similar geometrical features have been observed in related compounds, such as PPh₃Me[NbOCl₄(CH₃CN)]^-, reported by Hiller et al. (1984), and compounds of the form [X]⁺[NbOCl₄(H₂O)]^-, where X is [(H₂dafone)Cl] (dafone is 4,5-diazafluoren-9-one; Balagopalakrishna et al., 1996), PPh₄ (Klingelhofer & Muller, 1984) or 1,2,3-tris(dimethylamino)cyclopropenylium (Schafer et al., 1991).

The Nb—Cl distances in (I) [mean 2.400 (4) Å] compare well with the average Nb—Cl bond length of 2.35 (5) Å obtained by averaging 261 N b—Cl distances found in 57 complexes reported in the Cambridge Strcutural Database (CSD, Release?; Allen & Kennard, 1993). The Nb═O formal double bond in (I) [1.708 (3) Å] is in good agreement with the average Nb═O separation of 1.72 (3) Å calculated by averaging 20 relevant distances in 15 complexes in the CSD. The Nb—N(py) coordinative bond is generally observed to vary in length depending on the ligand trans to the pyridine. In cases where the pyridine is opposite to a doubly bound ligand, the bond is considerably longer than in the instances when the pyridine is trans to a singly bound group, a typical manifestation of the trans influence. Thus, the Nb—N(py) distances in (ⁱPrN)NbCl₃py₂, (II) (Chiu et al., 1998), (ⁱPrN)NbCl₃py₂, (III) NB This looks identical to (II) - please state the point of difference (Chiu et al., 1998), and cis-mer-[NbCl₃(OC₆H₃ⁱPr-2,6)₂(py)] (Clark et al., 1997) are, respectively, 2.307 (3), 2.313 (4) and 2.331 (4) Å to the pyridines trans to single M-ligand bonds, while the Nb—N(py) distances to the pyridines trans to the imido ligands in (II), (III) and [Ph₃PCH₂Ph][Nb(N^tBu)Cl₄(py)]·CH₂Cl₂ (Clegg et al., 1991) are 2.463 (3), 2.480 (4) and 2.479 (4) Å, respectively. The Nb—N1 bond length in (I) [2.488 (4) Å] compares well with the latter three values, which is in accord with the slight concomitant compression of the Nb═O double bond.

The negative charge on the Nb complex is balanced by an H atom located between the N atoms of the two solvate pyridine molecules residing on a crystallographic twofold axis. The N···N separation of 2.756 (5) Å corresponds to a very strong intermolecular N—H···N hydrogen bonding interaction. For the initial structural refinement, the H atom was arbitrarily placed in an idealized position on atom N2, but it can be refined equally well on the other nitrogen, N3. Thus for the final refinement, the H atom was refined as being equally disordered between the two positions. The resulting N—H.·N hydrogen bonds are equivalent. The N—H.·N angle is linear due to symmetry considerations. A CSD search on intermolecular N—H···N interactions returned 4200 hits, with an N···N separation range of 2.634–3.754 Å. The hydrogen-bonding interaction observed in (I) is among the 30 shortest reported to date.

The spatial arrangement of the molecules and ions in the lattice of (I) is such that the ligated pyridine and the N2 pyridine form stacks in an ABABAB fashion, with an interplanar distance of 3.56 (3) Å. While the aromatic rings are not quite parallel, these π-stacking interactions are significant, as they fall within the sum of the van der Waals radii of the delocalized π-systems of aromatic rings, approximated to be 3.70 Å (Cotton & Wilkinson, 1972).

S2. Experimental

Adventitious hydrolysis of Nb(═O)Cl₃ in the presence of pyridine yields (I). Crystals of (I) were obtained from a pyridine/hexane system (Saulys, 2001).

S3. Refinement

H atoms were treated as riding in idealized positions, with C—H = 0.95 and N—H = 0.88 Å. Displacement parameters for H were assigned as U_iso(H) = 1.2U_eq of the attached atom. H atoms on N were treated as half populated.

Computing details

Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997b); program(s) used to refine structure: SHELXTL (Sheldrick, 1997a); molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Figures

Fig. 1. The spatial arrangement of ions and solvate molecules in the structure of (I). Only one of the disordered H-atom sites between N2 and N3 is shown.

pyridinium tetrachloro(oxo)pyridineniobate(V) pyridine solvate

Crystal data

(C5H6N)[NbCl4O(C5H5N)]·C5H5N	Dx = 1.661 Mg m^−3
Mr = 489.02	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pnc2	Cell parameters from 5722 reflections
a = 7.3355 (3) Å	θ = 2–25°
b = 9.4033 (4) Å	µ = 1.17 mm^−1
c = 14.1728 (7) Å	T = 173 K
V = 977.61 (8) Å^3	Block, yellow
Z = 2	0.41 × 0.32 × 0.30 mm
F(000) = 488

Data collection

Bruker SMART 1000 CCD area-detector diffractometer	2000 independent reflections
Radiation source: fine-focus sealed tube	1975 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.030
ω scans	θmax = 26.4°, θmin = 2.6°
Absorption correction: empirical (using intensity measurements) (SADABS; Blessing, 1995)	h = −9→8
Tmin = 0.646, Tmax = 0.721	k = −11→11
7522 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)] = 0.020	H-atom parameters constrained
wR(F^2) = 0.054	w = 1/[σ^2(Fo^2) + (0.0357P)^2 + 0.0707P] where P = (Fo^2 + 2Fc^2)/3
S = 1.04	(Δ/σ)max < 0.001
2000 reflections	Δρmax = 0.57 e Å^−3
115 parameters	Δρmin = −0.29 e Å^−3
1 restraint	Absolute structure: Flack (1983); 952 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: −0.03 (4)

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)
Nb	0.0000	0.0000	0.02797 (3)	0.02526 (9)
Cl1	0.20434 (7)	0.19501 (6)	0.05364 (3)	0.04146 (15)
Cl2	−0.25238 (7)	0.16099 (5)	0.04506 (3)	0.03758 (13)
O	0.0000	0.0000	−0.0924 (2)	0.0428 (7)
N1	0.0000	0.0000	0.2034 (3)	0.0251 (6)
N2	0.5000	0.0000	0.4232 (3)	0.0390 (9)
H2A	0.5000	0.0000	0.4853	0.047*	0.50
N3	0.5000	0.0000	0.6177 (3)	0.0338 (8)
H3A	0.5000	0.0000	0.5556	0.041*	0.50
C1	−0.0335 (3)	0.1185 (2)	0.25262 (17)	0.0331 (4)
H1	−0.0568	0.2040	0.2190	0.040*
C2	−0.0359 (3)	0.1224 (3)	0.3501 (2)	0.0445 (6)
H2	−0.0620	0.2083	0.3827	0.053*
C3	0.0000	0.0000	0.3984 (3)	0.0503 (12)
H3	0.0000	0.0000	0.4654	0.060*
C4	0.4598 (3)	0.1197 (3)	0.37807 (18)	0.0403 (5)
H4	0.4325	0.2036	0.4127	0.048*
C5	0.4577 (3)	0.1220 (2)	0.28134 (18)	0.0383 (5)
H5	0.4275	0.2070	0.2487	0.046*
C6	0.5000	0.0000	0.2317 (3)	0.0317 (9)
H6	0.5000	0.0000	0.1646	0.038*
C7	0.3472 (4)	−0.0147 (2)	0.6669 (2)	0.0435 (6)
H7	0.2362	−0.0253	0.6331	0.052*
C8	0.3403 (6)	−0.0155 (2)	0.7633 (3)	0.0626 (11)
H8	0.2279	−0.0264	0.7958	0.075*
C9	0.5000	0.0000	0.8110 (5)	0.071 (2)
H9	0.5000	0.0000	0.8781	0.085*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Nb	0.02706 (12)	0.03326 (13)	0.01544 (14)	0.00004 (7)	0.000	0.000
Cl1	0.0431 (3)	0.0417 (2)	0.0396 (3)	−0.0145 (2)	−0.0024 (3)	0.0132 (3)
Cl2	0.0373 (2)	0.0443 (3)	0.0312 (3)	0.01137 (19)	0.0023 (3)	0.0090 (2)
O	0.0417 (15)	0.073 (2)	0.0140 (15)	0.0058 (10)	0.000	0.000
N1	0.0274 (13)	0.0304 (13)	0.0175 (16)	−0.0006 (8)	0.000	0.000
N2	0.040 (2)	0.058 (2)	0.0188 (18)	−0.0063 (10)	0.000	0.000
N3	0.045 (2)	0.0347 (17)	0.0218 (19)	0.0009 (8)	0.000	0.000
C1	0.0357 (10)	0.0354 (11)	0.0283 (12)	0.0014 (8)	−0.0013 (8)	−0.0075 (9)
C2	0.0434 (11)	0.0594 (15)	0.0308 (13)	−0.0019 (11)	0.0009 (10)	−0.0185 (11)
C3	0.039 (2)	0.091 (4)	0.021 (2)	−0.0095 (14)	0.000	0.000
C4	0.0432 (11)	0.0402 (13)	0.0374 (13)	0.0017 (10)	0.0055 (10)	−0.0107 (10)
C5	0.0435 (10)	0.0331 (11)	0.0381 (13)	0.0000 (9)	−0.0046 (10)	0.0043 (9)
C6	0.040 (2)	0.042 (2)	0.0132 (19)	−0.0105 (10)	0.000	0.000
C7	0.0414 (15)	0.0376 (12)	0.0516 (18)	−0.0010 (8)	0.0030 (13)	−0.0017 (9)
C8	0.091 (3)	0.0374 (13)	0.059 (2)	−0.0003 (12)	0.043 (2)	−0.0009 (11)
C9	0.154 (8)	0.032 (3)	0.027 (3)	0.0013 (19)	0.000	0.000

Geometric parameters (Å, º)

Nb—O	1.706 (3)	C2—C3	1.365 (4)
Nb—Cl1	2.3962 (5)	C2—H2	0.9500
Nb—Cl1^i	2.3962 (5)	C3—C2^i	1.365 (4)
Nb—Cl2	2.4037 (5)	C3—H3	0.9500
Nb—Cl2^i	2.4037 (5)	C4—C5	1.371 (4)
Nb—N1	2.486 (4)	C4—H4	0.9500
N1—C1	1.338 (3)	C5—C6	1.381 (3)
N1—C1^i	1.338 (3)	C5—H5	0.9500
N2—C4^ii	1.328 (3)	C6—C5^ii	1.381 (3)
N2—C4	1.328 (3)	C6—H6	0.9500
N2—H2A	0.8800	C7—C8	1.368 (5)
N3—C7	1.327 (4)	C7—H7	0.9500
N3—C7^ii	1.327 (4)	C8—C9	1.361 (6)
N3—H3A	0.8800	C8—H8	0.9500
C1—C2	1.382 (4)	C9—C8^ii	1.361 (6)
C1—H1	0.9500	C9—H9	0.9500
O—Nb—Cl1	98.733 (18)	C2—C1—H1	118.5
O—Nb—Cl1^i	98.733 (18)	C3—C2—C1	118.4 (3)
Cl1—Nb—Cl1^i	162.53 (4)	C3—C2—H2	120.8
O—Nb—Cl2	95.782 (17)	C1—C2—H2	120.8
Cl1—Nb—Cl2	89.113 (18)	C2^i—C3—C2	119.8 (4)
Cl1^i—Nb—Cl2	89.134 (17)	C2^i—C3—H3	120.1
O—Nb—Cl2^i	95.782 (17)	C2—C3—H3	120.1
Cl1—Nb—Cl2^i	89.134 (17)	N2—C4—C5	119.8 (3)
Cl1^i—Nb—Cl2^i	89.113 (18)	N2—C4—H4	120.1
Cl2—Nb—Cl2^i	168.44 (3)	C5—C4—H4	120.1
O—Nb—N1	180.0	C4—C5—C6	119.6 (3)
Cl1—Nb—N1	81.267 (18)	C4—C5—H5	120.2
Cl1^i—Nb—N1	81.267 (18)	C6—C5—H5	120.2
Cl2—Nb—N1	84.218 (17)	C5—C6—C5^ii	118.7 (4)
Cl2^i—Nb—N1	84.218 (17)	C5—C6—H6	120.6
C1—N1—C1^i	117.1 (3)	C5^ii—C6—H6	120.6
C1—N1—Nb	121.45 (17)	N3—C7—C8	123.8 (4)
C1^i—N1—Nb	121.45 (17)	N3—C7—H7	118.1
C4^ii—N2—C4	122.4 (4)	C8—C7—H7	118.1
C4^ii—N2—H2A	118.8	C9—C8—C7	117.7 (4)
C4—N2—H2A	118.8	C9—C8—H8	121.2
C7—N3—C7^ii	116.7 (4)	C7—C8—H8	121.2
C7—N3—H3A	121.7	C8—C9—C8^ii	120.4 (6)
C7^ii—N3—H3A	121.7	C8—C9—H9	119.8
N1—C1—C2	123.1 (3)	C8^ii—C9—H9	119.8
N1—C1—H1	118.5
Cl1—Nb—N1—C1	51.70 (10)	N1—C1—C2—C3	0.9 (3)
Cl1^i—Nb—N1—C1	−128.30 (10)	C1—C2—C3—C2^i	−0.43 (15)
Cl2—Nb—N1—C1	−38.29 (10)	C4^ii—N2—C4—C5	0.43 (16)
Cl2^i—Nb—N1—C1	141.71 (10)	N2—C4—C5—C6	−0.9 (3)
Cl1—Nb—N1—C1^i	−128.30 (10)	C4—C5—C6—C5^ii	0.42 (16)
Cl1^i—Nb—N1—C1^i	51.70 (10)	C7^ii—N3—C7—C8	−0.06 (16)
Cl2—Nb—N1—C1^i	141.71 (10)	N3—C7—C8—C9	0.1 (3)
Cl2^i—Nb—N1—C1^i	−38.29 (10)	C7—C8—C9—C8^ii	−0.05 (14)
C1^i—N1—C1—C2	−0.46 (16)	Cl1—Nb—N1—C1	51.70 (10)
Nb—N1—C1—C2	179.54 (16)	Cl1—Nb—N1—C6	−50.738 (14)

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

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···N3	0.88	1.88	2.756 (5)	180
N3—H3A···N2	0.88	1.88	2.756 (5)	180