supplementary materials


HTML versionpdf versioncif file3d viewstructure factorssupplementary materialsCIF check reportsimilar papers Open access

hb2670 scheme

Acta Cryst. (2008). E64, m133    [ doi:10.1107/S1600536807065051 ]

catena-Poly[[bis(1H-benzimidazole-[kappa]N3)palladium(II)]-[mu]-benzene-1,4-dicarboxylato-[kappa]2O1:O4\]

Q. Meng, L. Wang, Y. Liu and Y. Pang

Abstract top

In the title compound, [Pd(C8H4O4)(C7H6N2)2]n, the Pd atom is tetracoordinated by two carboxylate O atoms from two benzene-1,4-dicarboxylate (bdc) dianions and two N atoms from two benzimidazole ligands, resulting in a slightly distorted tetrahedral PdO2N2 geometry. The bdc ligand acts as a bridge, linking the Pd atoms into a chain. Inter-chain N-H...O hydrogen bonds help to stabilize the crystal structure.

Comment top

Dicarboxylic acids are key components in the synthesis of coordination polymers (e.g. Okabe & Oya, 2000). In this paper, we report the structure of the title compound, (I).

In compound (I) the Pd atom is tetra-coordinated by two oxygen atoms from two benzene-1,4-dicarboxylate (bdc) dianions and two nitrogen atoms from two benzimidazole ligands, resulting in a slightly distorterd tetrahedral PdO4N2 geometry for the metal (Fig. 1, Table 1). Two short Pd···O contacts arise from this arrangement [Pd1···O2 = 2.7015 (15)Å and Pd1···O1i = 2.5324 (14) Å; i = x - 1/2,-y + 5/2,z - 1/2] The bdc acts as a bridge to link Pd atoms into a chain (Fig. 2).

Two N—H···O hydrogen bonds (Table 2) help to link the chains into a three-dimensional structure.

Related literature top

For background, see: Okabe & Oya (2000).

Experimental top

A mixture of palladium acetate (1 mmol), benzene-1,4-dicarboxylic acid (1 mmol), benzimidazole (2 mmol), and 8 ml H2O was sealed in a 25 ml autoclave and heated to 413 K for 2 days. On cooling to room temperature, colourless blocks of (I) were obtained with a yield of 12%. Anal. Calc. for C22H16N4O4Pd: C 60.77, H 3.16, N 11.05%; Found: C 60.71, H 3.22, N 47.01%.

Refinement top

All H atoms were placed in calculated positions with C—H = 0.93Å and N—H = 0.86Å and refined as riding with Uiso(H) = 1.2Ueq(carrier).

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT-Plus (Bruker, 2001); data reduction: SAINT-Plus (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2001); software used to prepare material for publication: SHELXTL (Bruker, 2001).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), drawn with 30% probability displacement ellipsoids for the non-hydrogen atoms. The unlabelled O3 atom is at the symmetry position (x - 1/2, -y + 5/2, z - 1/2).
[Figure 2] Fig. 2. Fragment of a one dimensional chain in (I).
catena-Poly[[bis(1H-benzimidazole-κN3)palladium(II)]- µ-benzene-1,4-dicarboxylato-κ2O1:O4] top
Crystal data top
[Pd(C8H4O4)(C7H6N2)2]F000 = 1016
Mr = 506.79Dx = 1.633 Mg m−3
Monoclinic, P21/nMo Kα radiation
λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 3823 reflections
a = 17.0627 (5) Åθ = 2.5–25.5º
b = 7.3612 (10) ŵ = 0.94 mm−1
c = 18.0210 (5) ÅT = 273 (2) K
β = 114.362 (3)ºBlock, colourless
V = 2061.9 (3) Å30.43 × 0.28 × 0.22 mm
Z = 4
Data collection top
Bruker APEXII CCD
diffractometer		3763 independent reflections
Radiation source: fine-focus sealed tube3136 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.021
T = 273(2) Kθmax = 25.5º
φ and ω scansθmin = 2.5º
Absorption correction: multi-scan
(SADABS; Bruker, 2001)		h = −20→18
Tmin = 0.689, Tmax = 0.820k = −8→8
10244 measured reflectionsl = −16→21
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.021H-atom parameters constrained
wR(F2) = 0.044  w = 1/[σ2(Fo2) + (0.0204P)2 + 0.1114P]
where P = (Fo2 + 2Fc2)/3
S = 1.00(Δ/σ)max = 0.007
3763 reflectionsΔρmax = 0.25 e Å−3
280 parametersΔρmin = −0.30 e Å−3
Primary atom site location: structure-invariant direct methodsExtinction correction: none
Crystal data top
[Pd(C8H4O4)(C7H6N2)2]V = 2061.9 (3) Å3
Mr = 506.79Z = 4
Monoclinic, P21/nMo Kα
a = 17.0627 (5) ŵ = 0.94 mm−1
b = 7.3612 (10) ÅT = 273 (2) K
c = 18.0210 (5) Å0.43 × 0.28 × 0.22 mm
β = 114.362 (3)º
Data collection top
Bruker APEXII CCD
diffractometer		3763 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2001)		3136 reflections with I > 2σ(I)
Tmin = 0.689, Tmax = 0.820Rint = 0.021
10244 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.021280 parameters
wR(F2) = 0.044H-atom parameters constrained
S = 1.00Δρmax = 0.25 e Å−3
3763 reflectionsΔρmin = −0.30 e Å−3
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
xyzUiso*/Ueq
Pd10.386453 (9)0.87505 (2)0.131047 (8)0.03602 (6)
C10.38692 (14)0.4922 (3)0.05522 (12)0.0501 (5)
H10.32730.50280.03200.060*
C20.51274 (14)0.3771 (3)0.08708 (12)0.0465 (5)
C30.51865 (12)0.5488 (3)0.12239 (11)0.0414 (5)
C40.58302 (16)0.2724 (3)0.09742 (14)0.0600 (6)
H40.57810.15950.07270.072*
C50.59695 (13)0.6213 (3)0.17173 (13)0.0514 (5)
H50.60210.73480.19590.062*
C60.66649 (15)0.5167 (4)0.18295 (14)0.0642 (6)
H60.72080.56010.21640.077*
C70.65997 (17)0.3453 (4)0.14617 (15)0.0677 (7)
H70.71000.28030.15560.081*
C80.23606 (14)0.7875 (3)0.18459 (14)0.0558 (6)
H80.19700.78110.13030.067*
C90.35186 (13)0.8107 (3)0.29148 (12)0.0442 (5)
C100.28633 (14)0.7875 (3)0.31634 (13)0.0498 (5)
C110.30073 (17)0.7824 (4)0.39652 (15)0.0698 (7)
H110.25590.76680.41260.084*
C120.43443 (14)0.8292 (3)0.34715 (13)0.0549 (6)
H120.47930.84570.33120.066*
C130.44869 (17)0.8227 (4)0.42700 (15)0.0749 (8)
H130.50470.83340.46650.090*
C140.3826 (2)0.8007 (4)0.45121 (16)0.0843 (8)
H140.39480.79850.50650.101*
C150.49046 (12)1.1428 (3)0.23451 (11)0.0402 (5)
C160.56002 (11)1.2527 (3)0.29649 (11)0.0381 (4)
C170.64130 (13)1.1842 (3)0.32852 (12)0.0508 (5)
H170.65281.07300.31070.061*
C180.54456 (13)1.4201 (3)0.32342 (12)0.0500 (5)
H180.48931.46830.30100.060*
C190.60938 (13)1.5157 (3)0.38254 (12)0.0517 (6)
H190.59801.62740.40010.062*
C200.70605 (13)1.2803 (3)0.38725 (12)0.0512 (5)
H200.76171.23380.40880.061*
C210.68998 (12)1.4463 (3)0.41515 (11)0.0392 (4)
C220.75824 (12)1.5416 (3)0.48470 (11)0.0423 (5)
N10.21398 (12)0.7742 (3)0.24689 (12)0.0596 (5)
H1A0.16270.75960.24360.072*
N20.31782 (11)0.8103 (2)0.20759 (10)0.0477 (4)
N30.42774 (12)0.3463 (2)0.04448 (10)0.0527 (5)
H3A0.40450.25140.01600.063*
N40.43772 (11)0.6190 (2)0.10114 (10)0.0456 (4)
O10.74180 (9)1.6814 (2)0.51415 (9)0.0616 (4)
O20.41604 (8)1.1972 (2)0.20972 (8)0.0517 (4)
O30.83114 (8)1.46812 (19)0.51434 (8)0.0510 (4)
O40.51057 (8)0.99635 (19)0.20976 (8)0.0516 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.02818 (8)0.04723 (9)0.02930 (9)−0.00258 (7)0.00849 (6)0.00106 (6)
C10.0435 (12)0.0563 (13)0.0459 (12)−0.0098 (10)0.0138 (10)−0.0010 (10)
C20.0561 (13)0.0490 (12)0.0371 (11)−0.0015 (11)0.0221 (10)0.0066 (10)
C30.0410 (12)0.0494 (12)0.0360 (11)−0.0018 (9)0.0180 (9)0.0026 (9)
C40.0762 (18)0.0561 (14)0.0552 (14)0.0118 (13)0.0348 (13)0.0061 (11)
C50.0415 (12)0.0627 (13)0.0506 (13)−0.0062 (11)0.0196 (10)−0.0052 (11)
C60.0425 (14)0.0929 (19)0.0581 (15)−0.0005 (13)0.0217 (11)0.0025 (14)
C70.0602 (17)0.090 (2)0.0626 (16)0.0250 (14)0.0351 (14)0.0149 (14)
C80.0415 (13)0.0714 (15)0.0541 (14)−0.0101 (11)0.0194 (11)0.0052 (12)
C90.0449 (12)0.0463 (11)0.0448 (12)0.0012 (9)0.0219 (10)0.0057 (9)
C100.0491 (13)0.0530 (12)0.0538 (14)−0.0008 (10)0.0277 (11)0.0044 (11)
C110.0730 (18)0.0872 (18)0.0654 (17)−0.0066 (15)0.0448 (15)0.0048 (14)
C120.0468 (13)0.0694 (15)0.0496 (13)0.0032 (11)0.0210 (11)0.0093 (11)
C130.0617 (16)0.108 (2)0.0487 (15)−0.0052 (14)0.0164 (13)0.0122 (14)
C140.094 (2)0.115 (2)0.0515 (16)−0.0136 (18)0.0375 (16)0.0058 (15)
C150.0316 (11)0.0570 (13)0.0334 (10)−0.0034 (9)0.0148 (8)0.0020 (9)
C160.0337 (10)0.0493 (12)0.0310 (10)−0.0023 (9)0.0128 (8)−0.0015 (8)
C170.0377 (12)0.0596 (13)0.0492 (13)0.0047 (10)0.0120 (10)−0.0170 (10)
C180.0344 (11)0.0571 (13)0.0470 (12)0.0087 (9)0.0053 (9)−0.0043 (10)
C190.0425 (12)0.0527 (13)0.0475 (13)0.0081 (10)0.0060 (10)−0.0107 (10)
C200.0320 (11)0.0648 (14)0.0487 (13)0.0076 (10)0.0084 (9)−0.0102 (11)
C210.0361 (11)0.0482 (11)0.0311 (10)0.0000 (9)0.0117 (8)−0.0008 (9)
C220.0386 (12)0.0510 (12)0.0335 (11)−0.0001 (10)0.0110 (9)0.0021 (9)
N10.0430 (11)0.0751 (13)0.0693 (13)−0.0076 (10)0.0317 (10)0.0075 (11)
N20.0404 (10)0.0595 (11)0.0452 (10)−0.0043 (8)0.0196 (8)0.0014 (8)
N30.0598 (12)0.0479 (11)0.0458 (10)−0.0114 (9)0.0171 (9)−0.0077 (8)
N40.0412 (10)0.0491 (10)0.0432 (10)−0.0059 (8)0.0141 (8)−0.0053 (8)
O10.0449 (9)0.0736 (10)0.0552 (10)0.0035 (7)0.0097 (7)−0.0251 (8)
O20.0290 (8)0.0759 (10)0.0461 (8)−0.0005 (7)0.0114 (6)−0.0057 (7)
O30.0378 (8)0.0546 (9)0.0441 (8)0.0077 (7)0.0002 (6)−0.0024 (7)
O40.0390 (8)0.0575 (9)0.0528 (9)−0.0046 (7)0.0134 (7)−0.0161 (7)
Geometric parameters (Å, °) top
Pd1—O42.1945 (13)C11—C141.343 (3)
Pd1—N22.1987 (17)C11—H110.9300
Pd1—N42.2355 (17)C12—C131.358 (3)
Pd1—O3i2.2382 (13)C12—H120.9300
Pd1—O1i2.5324 (14)C13—C141.377 (4)
C1—N41.310 (2)C13—H130.9300
C1—N31.337 (3)C14—H140.9300
C1—H10.9300C15—O21.227 (2)
C2—N31.351 (3)C15—O41.267 (2)
C2—C41.372 (3)C15—C161.489 (3)
C2—C31.400 (3)C16—C171.360 (3)
C3—C51.371 (3)C16—C181.389 (3)
C3—N41.373 (2)C17—C201.370 (3)
C4—C71.354 (3)C17—H170.9300
C4—H40.9300C18—C191.372 (3)
C5—C61.358 (3)C18—H180.9300
C5—H50.9300C19—C211.353 (3)
C6—C71.408 (3)C19—H190.9300
C6—H60.9300C20—C211.391 (3)
C7—H70.9300C20—H200.9300
C8—N21.292 (2)C21—C221.488 (3)
C8—N11.327 (3)C22—O11.242 (2)
C8—H80.9300C22—O31.256 (2)
C9—C121.358 (3)N1—H1A0.8600
C9—C101.376 (3)N3—H3A0.8600
C9—N21.378 (2)O1—Pd1ii2.5324 (14)
C10—N11.351 (3)O3—Pd1ii2.2382 (13)
C10—C111.363 (3)
O4—Pd1—N2107.72 (6)C14—C13—H13119.1
O4—Pd1—N497.45 (6)C11—C14—C13121.3 (2)
N2—Pd1—N4109.34 (6)C11—C14—H14119.4
O4—Pd1—O3i108.54 (5)C13—C14—H14119.4
N2—Pd1—O3i125.04 (6)O2—C15—O4122.67 (18)
N4—Pd1—O3i105.28 (6)O2—C15—C16118.73 (19)
N4—C1—N3114.5 (2)O4—C15—C16118.60 (17)
N4—C1—H1122.7C17—C16—C18119.19 (18)
N3—C1—H1122.7C17—C16—C15118.35 (18)
N3—C2—C4131.0 (2)C18—C16—C15122.46 (17)
N3—C2—C3105.61 (18)C16—C17—C20119.53 (19)
C4—C2—C3123.4 (2)C16—C17—H17120.2
C5—C3—N4129.27 (19)C20—C17—H17120.2
C5—C3—C2121.0 (2)C19—C18—C16121.20 (18)
N4—C3—C2109.73 (17)C19—C18—H18119.4
C7—C4—C2115.1 (2)C16—C18—H18119.4
C7—C4—H4122.4C21—C19—C18119.55 (19)
C2—C4—H4122.4C21—C19—H19120.2
C6—C5—C3115.7 (2)C18—C19—H19120.2
C6—C5—H5122.2C17—C20—C21121.10 (18)
C3—C5—H5122.2C17—C20—H20119.4
C5—C6—C7122.9 (2)C21—C20—H20119.4
C5—C6—H6118.5C19—C21—C20119.41 (18)
C7—C6—H6118.5C19—C21—C22119.34 (18)
C4—C7—C6121.9 (2)C20—C21—C22121.06 (17)
C4—C7—H7119.1O1—C22—O3122.26 (18)
C6—C7—H7119.1O1—C22—C21120.94 (18)
N2—C8—N1112.6 (2)O3—C22—C21116.68 (18)
N2—C8—H8123.7C8—N1—C10107.97 (19)
N1—C8—H8123.7C8—N1—H1A126.0
C12—C9—C10120.5 (2)C10—N1—H1A126.0
C12—C9—N2130.5 (2)C8—N2—C9105.25 (18)
C10—C9—N2109.00 (18)C8—N2—Pd1127.66 (15)
N1—C10—C11132.6 (2)C9—N2—Pd1126.54 (13)
N1—C10—C9105.20 (19)C1—N3—C2106.50 (17)
C11—C10—C9122.2 (2)C1—N3—H3A126.7
C14—C11—C10117.0 (2)C2—N3—H3A126.7
C14—C11—H11121.5C1—N4—C3103.61 (17)
C10—C11—H11121.5C1—N4—Pd1122.03 (15)
C9—C12—C13117.2 (2)C3—N4—Pd1134.34 (13)
C9—C12—H12121.4C22—O1—Pd1ii84.55 (11)
C13—C12—H12121.4C22—O3—Pd1ii97.89 (12)
C12—C13—C14121.9 (2)C15—O4—Pd1104.15 (12)
C12—C13—H13119.1
Symmetry codes: (i) x−1/2, −y+5/2, z−1/2; (ii) x+1/2, −y+5/2, z+1/2.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···O3iii0.862.042.762 (2)142
N1—H1A···O2iv0.861.912.699 (2)152
Symmetry codes: (iii) x−1/2, −y+3/2, z−1/2; (iv) −x+1/2, y−1/2, −z+1/2.
Table 1
Selected geometric parameters (Å) top
Pd1—O42.1945 (13)Pd1—N42.2355 (17)
Pd1—N22.1987 (17)Pd1—O3i2.2382 (13)
Symmetry codes: (i) x−1/2, −y+5/2, z−1/2.
Table 2
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···O3ii0.862.042.762 (2)142
N1—H1A···O2iii0.861.912.699 (2)152
Symmetry codes: (ii) x−1/2, −y+3/2, z−1/2; (iii) −x+1/2, y−1/2, −z+1/2.
Acknowledgements top

The authors thank the Education Department of Shandong Province for research and development projects (J06A55).

references
References top

Bruker (2001). SADABS, SAINT-Plus and SHELXTL. Bruker AXS Inc., Madison, Wisconsin, USA.

Bruker (2004). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.

Okabe, N. & Oya, N. (2000). Acta Cryst. C56, 1416–1417.

Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Gottingen, Germany.