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In the title complex, [Pd(C3H2O4)(C12H8N2)], the PdII center has a distorted cis-square-planar geometry defined by an O,O′-bidentate malonate ligand and a chelating 1,10-phenanthroline ligand. The crystal structure is stabilized by inter­molecular π–π stacking inter­actions between pairs of 1,10-phenanthroline rings, as well as C—H...O hydrogen bonding.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536806020113/tk2041sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536806020113/tk2041Isup2.hkl
Contains datablock I

CCDC reference: 613828

Key indicators

  • Single-crystal X-ray study
  • T = 296 K
  • Mean [sigma](C-C) = 0.005 Å
  • R factor = 0.026
  • wR factor = 0.072
  • Data-to-parameter ratio = 14.7

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT062_ALERT_4_C Rescale T(min) & T(max) by ..................... 0.80 PLAT480_ALERT_4_C Long H...A H-Bond Reported H11 .. O2 .. 2.66 Ang.
Alert level G ABSTM02_ALERT_3_G When printed, the submitted absorption T values will be replaced by the scaled T values. Since the ratio of scaled T's is identical to the ratio of reported T values, the scaling does not imply a change to the absorption corrections used in the study. Ratio of Tmax expected/reported 0.802 Tmax scaled 0.802 Tmin scaled 0.774
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 2 ALERT level C = Check and explain 1 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 0 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 2 ALERT type 4 Improvement, methodology, query or suggestion

Computing details top

Data collection: RAPID-AUTO (Rigaku, 1998); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2005) and CRYSTALS (Watkin et al., 1996); program(s) used to solve structure: SHELXLS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: CrystalStructure.

(Malonato-κ2O,O')(1,10-phenanthroline-κ2N,N')palladium(II) top
Crystal data top
[Pd(C3H2O4)(C12H8N2)]F(000) = 768.0
Mr = 388.67Dx = 2.011 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.7107 Å
Hall symbol: -P 2ynCell parameters from 25 reflections
a = 7.825 (2) Åθ = 14.7–15.0°
b = 9.180 (3) ŵ = 1.47 mm1
c = 18.087 (2) ÅT = 296 K
β = 98.86 (2)°Prism, yellow
V = 1283.8 (6) Å30.20 × 0.15 × 0.15 mm
Z = 4
Data collection top
Rigaku AFC-5R
diffractometer
Rint = 0.025
ω–2θ scansθmax = 27.5°
Absorption correction: ψ scan
(North et al., 1968)
h = 010
Tmin = 0.964, Tmax = 1k = 011
3355 measured reflectionsl = 2323
2947 independent reflections3 standard reflections every 150 reflections
2419 reflections with I > 2σ(I) intensity decay: 1.1%
Refinement top
Refinement on F2H-atom parameters constrained
R[F2 > 2σ(F2)] = 0.026 w = 1/[σ2(Fo2) + (0.0347P)2 + 0.8246P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.072(Δ/σ)max = 0.001
S = 1.04Δρmax = 0.45 e Å3
2947 reflectionsΔρmin = 0.70 e Å3
200 parameters
Special details top

Refinement. Refinement using reflections with F2 > -10.0 σ(F2). The weighted R-factor (wR) and goodness of fit (S) are based on F2. R-factor (gt) are based on F. The threshold expression of F2 > 2.0 σ(F2) is used only for calculating R-factor (gt).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Pd10.66289 (3)0.07358 (2)0.069568 (11)0.02864 (8)
O10.5834 (3)0.2740 (2)0.08805 (11)0.0415 (5)
O20.5069 (4)0.4379 (3)0.16532 (15)0.0596 (8)
O30.5975 (3)0.0068 (2)0.16347 (12)0.0400 (5)
O40.5402 (4)0.0269 (3)0.27774 (14)0.0576 (7)
N10.7237 (3)0.1318 (3)0.02997 (13)0.0301 (5)
N20.7379 (3)0.1232 (3)0.03756 (13)0.0306 (5)
C10.7034 (4)0.2601 (3)0.06389 (17)0.0370 (7)
H10.65790.33720.03980.044*
C20.7485 (4)0.2826 (4)0.13466 (18)0.0433 (7)
H20.73350.37390.15700.052*
C30.8143 (4)0.1709 (4)0.17095 (18)0.0405 (7)
H30.84510.18570.21800.049*
C40.8356 (4)0.0332 (4)0.13712 (16)0.0334 (6)
C50.7875 (4)0.0192 (3)0.06631 (15)0.0283 (6)
C60.7953 (4)0.1184 (3)0.03012 (16)0.0293 (6)
C70.8492 (4)0.2422 (3)0.06464 (16)0.0346 (7)
C80.8431 (4)0.3745 (4)0.0273 (2)0.0432 (8)
H80.87890.45960.04830.052*
C90.7845 (5)0.3795 (4)0.0403 (2)0.0469 (8)
H90.78030.46770.06520.056*
C100.7311 (4)0.2509 (3)0.07173 (17)0.0378 (7)
H100.69010.25500.11730.045*
C110.8991 (4)0.0936 (4)0.17050 (18)0.0412 (8)
H110.93700.08550.21660.049*
C120.9047 (4)0.2252 (4)0.13609 (18)0.0417 (7)
H120.94530.30580.15920.050*
C130.5752 (4)0.3228 (3)0.15465 (18)0.0369 (7)
C140.6556 (4)0.2297 (4)0.22053 (16)0.0379 (7)
H14A0.77970.22750.22090.045*
H14B0.63540.27760.26620.045*
C150.5921 (4)0.0738 (4)0.22244 (17)0.0373 (7)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.03576 (13)0.02754 (13)0.02379 (12)0.00085 (9)0.00826 (9)0.00235 (8)
O10.0623 (14)0.0350 (11)0.0297 (10)0.0111 (11)0.0150 (10)0.0016 (9)
O20.086 (2)0.0462 (15)0.0492 (15)0.0264 (14)0.0186 (14)0.0080 (12)
O30.0567 (13)0.0344 (12)0.0319 (11)0.0030 (10)0.0168 (10)0.0004 (10)
O40.0852 (19)0.0552 (16)0.0391 (13)0.0028 (15)0.0306 (13)0.0024 (12)
N10.0362 (13)0.0275 (12)0.0274 (12)0.0037 (10)0.0077 (10)0.0028 (10)
N20.0350 (12)0.0303 (12)0.0268 (12)0.0016 (10)0.0054 (10)0.0035 (10)
C10.0482 (18)0.0256 (15)0.0382 (16)0.0005 (13)0.0096 (13)0.0012 (12)
C20.058 (2)0.0332 (16)0.0395 (17)0.0021 (15)0.0099 (15)0.0087 (14)
C30.0462 (18)0.0461 (18)0.0316 (16)0.0050 (15)0.0135 (13)0.0020 (14)
C40.0317 (14)0.0389 (16)0.0303 (15)0.0001 (13)0.0072 (12)0.0040 (12)
C50.0294 (13)0.0298 (14)0.0265 (13)0.0015 (11)0.0071 (11)0.0034 (11)
C60.0300 (14)0.0307 (14)0.0266 (14)0.0021 (12)0.0027 (11)0.0036 (11)
C70.0362 (15)0.0325 (16)0.0344 (15)0.0052 (12)0.0033 (12)0.0056 (12)
C80.0477 (18)0.0326 (16)0.047 (2)0.0086 (14)0.0010 (15)0.0055 (15)
C90.058 (2)0.0296 (16)0.051 (2)0.0021 (15)0.0023 (17)0.0072 (15)
C100.0493 (17)0.0349 (17)0.0278 (14)0.0002 (14)0.0015 (12)0.0010 (12)
C110.0423 (17)0.051 (2)0.0323 (16)0.0047 (15)0.0132 (13)0.0056 (14)
C120.0467 (17)0.0417 (17)0.0377 (16)0.0108 (15)0.0102 (14)0.0104 (15)
C130.0415 (16)0.0352 (16)0.0362 (16)0.0017 (13)0.0126 (13)0.0046 (13)
C140.0437 (16)0.0435 (17)0.0275 (14)0.0001 (14)0.0088 (12)0.0066 (13)
C150.0397 (16)0.0453 (18)0.0286 (15)0.0052 (14)0.0103 (12)0.0017 (13)
Geometric parameters (Å, º) top
Pd1—O11.987 (2)C4—C51.395 (4)
Pd1—O31.990 (2)C4—C111.435 (4)
Pd1—N12.004 (2)C5—C61.420 (4)
Pd1—N22.012 (3)C6—C71.393 (4)
O1—C131.296 (4)C7—C81.394 (5)
O2—C131.213 (4)C7—C121.434 (4)
O3—C151.304 (4)C8—C91.372 (5)
O4—C151.215 (4)C8—H80.9300
N1—C11.326 (4)C9—C101.401 (5)
N1—C51.360 (4)C9—H90.9300
N2—C101.330 (4)C10—H100.9300
N2—C61.368 (4)C11—C121.356 (5)
C1—C21.394 (4)C11—H110.9300
C1—H10.9300C12—H120.9300
C2—C31.361 (5)C13—C141.521 (5)
C2—H20.9300C14—C151.517 (5)
C3—C41.402 (5)C14—H14A0.9700
C3—H30.9300C14—H14B0.9700
O1—Pd1—O394.08 (9)C7—C6—C5120.9 (3)
O1—Pd1—N191.60 (9)C6—C7—C8117.3 (3)
O1—Pd1—N2173.04 (9)C6—C7—C12118.0 (3)
O3—Pd1—N1173.48 (9)C8—C7—C12124.7 (3)
O3—Pd1—N292.15 (9)C9—C8—C7120.1 (3)
N1—Pd1—N282.01 (10)C9—C8—H8119.9
C13—O1—Pd1122.6 (2)C7—C8—H8119.9
C15—O3—Pd1122.2 (2)C8—C9—C10119.7 (3)
C1—N1—C5118.5 (3)C8—C9—H9120.1
C1—N1—Pd1128.6 (2)C10—C9—H9120.1
C5—N1—Pd1112.76 (19)N2—C10—C9121.2 (3)
C10—N2—C6119.1 (3)N2—C10—H10119.4
C10—N2—Pd1128.5 (2)C9—C10—H10119.4
C6—N2—Pd1112.3 (2)C12—C11—C4121.2 (3)
N1—C1—C2121.8 (3)C12—C11—H11119.4
N1—C1—H1119.1C4—C11—H11119.4
C2—C1—H1119.1C11—C12—C7121.2 (3)
C3—C2—C1119.9 (3)C11—C12—H12119.4
C3—C2—H2120.0C7—C12—H12119.4
C1—C2—H2120.0O2—C13—O1122.4 (3)
C2—C3—C4119.8 (3)O2—C13—C14120.3 (3)
C2—C3—H3120.1O1—C13—C14117.4 (3)
C4—C3—H3120.1C15—C14—C13116.8 (3)
C5—C4—C3116.9 (3)C15—C14—H14A108.1
C5—C4—C11118.1 (3)C13—C14—H14A108.1
C3—C4—C11125.0 (3)C15—C14—H14B108.1
N1—C5—C4123.0 (3)C13—C14—H14B108.1
N1—C5—C6116.5 (3)H14A—C14—H14B107.3
C4—C5—C6120.4 (3)O4—C15—O3121.9 (3)
N2—C6—C7122.6 (3)O4—C15—C14120.4 (3)
N2—C6—C5116.4 (3)O3—C15—C14117.7 (3)
O3—Pd1—O1—C1325.4 (3)Pd1—N2—C6—C51.8 (3)
N1—Pd1—O1—C13157.8 (2)N1—C5—C6—N20.1 (4)
O1—Pd1—O3—C1527.1 (3)C4—C5—C6—N2177.0 (3)
N2—Pd1—O3—C15155.9 (2)N1—C5—C6—C7176.3 (3)
O1—Pd1—N1—C12.2 (3)C4—C5—C6—C70.7 (4)
N2—Pd1—N1—C1175.0 (3)N2—C6—C7—C80.1 (4)
O1—Pd1—N1—C5179.5 (2)C5—C6—C7—C8176.2 (3)
N2—Pd1—N1—C52.25 (19)N2—C6—C7—C12179.2 (3)
O3—Pd1—N2—C102.3 (3)C5—C6—C7—C123.1 (4)
N1—Pd1—N2—C10174.8 (3)C6—C7—C8—C90.5 (5)
O3—Pd1—N2—C6179.31 (19)C12—C7—C8—C9178.7 (3)
N1—Pd1—N2—C62.21 (19)C7—C8—C9—C100.1 (5)
C5—N1—C1—C21.2 (5)C6—N2—C10—C91.2 (5)
Pd1—N1—C1—C2178.3 (2)Pd1—N2—C10—C9178.1 (2)
N1—C1—C2—C30.4 (5)C8—C9—C10—N20.8 (5)
C1—C2—C3—C40.4 (5)C5—C4—C11—C123.1 (5)
C2—C3—C4—C50.3 (5)C3—C4—C11—C12175.5 (3)
C2—C3—C4—C11178.2 (3)C4—C11—C12—C70.7 (5)
C1—N1—C5—C41.2 (4)C6—C7—C12—C112.4 (5)
Pd1—N1—C5—C4178.8 (2)C8—C7—C12—C11176.8 (3)
C1—N1—C5—C6175.6 (3)Pd1—O1—C13—O2170.6 (3)
Pd1—N1—C5—C61.9 (3)Pd1—O1—C13—C149.4 (4)
C3—C4—C5—N10.5 (4)O2—C13—C14—C15124.5 (3)
C11—C4—C5—N1179.1 (3)O1—C13—C14—C1555.5 (4)
C3—C4—C5—C6176.3 (3)Pd1—O3—C15—O4174.6 (3)
C11—C4—C5—C62.4 (4)Pd1—O3—C15—C146.2 (4)
C10—N2—C6—C70.8 (4)C13—C14—C15—O4127.2 (3)
Pd1—N2—C6—C7178.1 (2)C13—C14—C15—O353.6 (4)
C10—N2—C6—C5175.5 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C11—H11···O2i0.932.663.514 (4)154
C12—H12···O4ii0.932.503.426 (4)177
Symmetry codes: (i) x+1/2, y+1/2, z1/2; (ii) x+1/2, y1/2, z1/2.
 

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