In the title complex, [Pd(C
3H
2O
4)(C
12H
8N
2)], the Pd
II 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
CCDC reference: 613828
Key indicators
- Single-crystal X-ray study
- T = 296 K
- Mean (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
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 = 388.67 | Dx = 2.011 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.7107 Å |
Hall symbol: -P 2yn | Cell parameters from 25 reflections |
a = 7.825 (2) Å | θ = 14.7–15.0° |
b = 9.180 (3) Å | µ = 1.47 mm−1 |
c = 18.087 (2) Å | T = 296 K |
β = 98.86 (2)° | Prism, yellow |
V = 1283.8 (6) Å3 | 0.20 × 0.15 × 0.15 mm |
Z = 4 | |
Data collection top
Rigaku AFC-5R diffractometer | Rint = 0.025 |
ω–2θ scans | θmax = 27.5° |
Absorption correction: ψ scan (North et al., 1968) | h = 0→10 |
Tmin = 0.964, Tmax = 1 | k = 0→11 |
3355 measured reflections | l = −23→23 |
2947 independent reflections | 3 standard reflections every 150 reflections |
2419 reflections with I > 2σ(I) | intensity decay: 1.1% |
Refinement top
Refinement on F2 | H-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 = 1.04 | Δρmax = 0.45 e Å−3 |
2947 reflections | Δρmin = −0.70 e Å−3 |
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 | x | y | z | Uiso*/Ueq | |
Pd1 | 0.66289 (3) | 0.07358 (2) | 0.069568 (11) | 0.02864 (8) | |
O1 | 0.5834 (3) | 0.2740 (2) | 0.08805 (11) | 0.0415 (5) | |
O2 | 0.5069 (4) | 0.4379 (3) | 0.16532 (15) | 0.0596 (8) | |
O3 | 0.5975 (3) | −0.0068 (2) | 0.16347 (12) | 0.0400 (5) | |
O4 | 0.5402 (4) | 0.0269 (3) | 0.27774 (14) | 0.0576 (7) | |
N1 | 0.7237 (3) | 0.1318 (3) | −0.02997 (13) | 0.0301 (5) | |
N2 | 0.7379 (3) | −0.1232 (3) | 0.03756 (13) | 0.0306 (5) | |
C1 | 0.7034 (4) | 0.2601 (3) | −0.06389 (17) | 0.0370 (7) | |
H1 | 0.6579 | 0.3372 | −0.0398 | 0.044* | |
C2 | 0.7485 (4) | 0.2826 (4) | −0.13466 (18) | 0.0433 (7) | |
H2 | 0.7335 | 0.3739 | −0.1570 | 0.052* | |
C3 | 0.8143 (4) | 0.1709 (4) | −0.17095 (18) | 0.0405 (7) | |
H3 | 0.8451 | 0.1857 | −0.2180 | 0.049* | |
C4 | 0.8356 (4) | 0.0332 (4) | −0.13712 (16) | 0.0334 (6) | |
C5 | 0.7875 (4) | 0.0192 (3) | −0.06631 (15) | 0.0283 (6) | |
C6 | 0.7953 (4) | −0.1184 (3) | −0.03012 (16) | 0.0293 (6) | |
C7 | 0.8492 (4) | −0.2422 (3) | −0.06464 (16) | 0.0346 (7) | |
C8 | 0.8431 (4) | −0.3745 (4) | −0.0273 (2) | 0.0432 (8) | |
H8 | 0.8789 | −0.4596 | −0.0483 | 0.052* | |
C9 | 0.7845 (5) | −0.3795 (4) | 0.0403 (2) | 0.0469 (8) | |
H9 | 0.7803 | −0.4677 | 0.0652 | 0.056* | |
C10 | 0.7311 (4) | −0.2509 (3) | 0.07173 (17) | 0.0378 (7) | |
H10 | 0.6901 | −0.2550 | 0.1173 | 0.045* | |
C11 | 0.8991 (4) | −0.0936 (4) | −0.17050 (18) | 0.0412 (8) | |
H11 | 0.9370 | −0.0855 | −0.2166 | 0.049* | |
C12 | 0.9047 (4) | −0.2252 (4) | −0.13609 (18) | 0.0417 (7) | |
H12 | 0.9453 | −0.3058 | −0.1592 | 0.050* | |
C13 | 0.5752 (4) | 0.3228 (3) | 0.15465 (18) | 0.0369 (7) | |
C14 | 0.6556 (4) | 0.2297 (4) | 0.22053 (16) | 0.0379 (7) | |
H14A | 0.7797 | 0.2275 | 0.2209 | 0.045* | |
H14B | 0.6354 | 0.2776 | 0.2662 | 0.045* | |
C15 | 0.5921 (4) | 0.0738 (4) | 0.22244 (17) | 0.0373 (7) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Pd1 | 0.03576 (13) | 0.02754 (13) | 0.02379 (12) | 0.00085 (9) | 0.00826 (9) | −0.00235 (8) |
O1 | 0.0623 (14) | 0.0350 (11) | 0.0297 (10) | 0.0111 (11) | 0.0150 (10) | −0.0016 (9) |
O2 | 0.086 (2) | 0.0462 (15) | 0.0492 (15) | 0.0264 (14) | 0.0186 (14) | −0.0080 (12) |
O3 | 0.0567 (13) | 0.0344 (12) | 0.0319 (11) | −0.0030 (10) | 0.0168 (10) | −0.0004 (10) |
O4 | 0.0852 (19) | 0.0552 (16) | 0.0391 (13) | −0.0028 (15) | 0.0306 (13) | 0.0024 (12) |
N1 | 0.0362 (13) | 0.0275 (12) | 0.0274 (12) | −0.0037 (10) | 0.0077 (10) | −0.0028 (10) |
N2 | 0.0350 (12) | 0.0303 (12) | 0.0268 (12) | −0.0016 (10) | 0.0054 (10) | −0.0035 (10) |
C1 | 0.0482 (18) | 0.0256 (15) | 0.0382 (16) | −0.0005 (13) | 0.0096 (13) | −0.0012 (12) |
C2 | 0.058 (2) | 0.0332 (16) | 0.0395 (17) | −0.0021 (15) | 0.0099 (15) | 0.0087 (14) |
C3 | 0.0462 (18) | 0.0461 (18) | 0.0316 (16) | −0.0050 (15) | 0.0135 (13) | 0.0020 (14) |
C4 | 0.0317 (14) | 0.0389 (16) | 0.0303 (15) | −0.0001 (13) | 0.0072 (12) | −0.0040 (12) |
C5 | 0.0294 (13) | 0.0298 (14) | 0.0265 (13) | −0.0015 (11) | 0.0071 (11) | −0.0034 (11) |
C6 | 0.0300 (14) | 0.0307 (14) | 0.0266 (14) | 0.0021 (12) | 0.0027 (11) | −0.0036 (11) |
C7 | 0.0362 (15) | 0.0325 (16) | 0.0344 (15) | 0.0052 (12) | 0.0033 (12) | −0.0056 (12) |
C8 | 0.0477 (18) | 0.0326 (16) | 0.047 (2) | 0.0086 (14) | 0.0010 (15) | −0.0055 (15) |
C9 | 0.058 (2) | 0.0296 (16) | 0.051 (2) | 0.0021 (15) | 0.0023 (17) | 0.0072 (15) |
C10 | 0.0493 (17) | 0.0349 (17) | 0.0278 (14) | 0.0002 (14) | 0.0015 (12) | 0.0010 (12) |
C11 | 0.0423 (17) | 0.051 (2) | 0.0323 (16) | 0.0047 (15) | 0.0132 (13) | −0.0056 (14) |
C12 | 0.0467 (17) | 0.0417 (17) | 0.0377 (16) | 0.0108 (15) | 0.0102 (14) | −0.0104 (15) |
C13 | 0.0415 (16) | 0.0352 (16) | 0.0362 (16) | 0.0017 (13) | 0.0126 (13) | −0.0046 (13) |
C14 | 0.0437 (16) | 0.0435 (17) | 0.0275 (14) | 0.0001 (14) | 0.0088 (12) | −0.0066 (13) |
C15 | 0.0397 (16) | 0.0453 (18) | 0.0286 (15) | 0.0052 (14) | 0.0103 (12) | 0.0017 (13) |
Geometric parameters (Å, º) top
Pd1—O1 | 1.987 (2) | C4—C5 | 1.395 (4) |
Pd1—O3 | 1.990 (2) | C4—C11 | 1.435 (4) |
Pd1—N1 | 2.004 (2) | C5—C6 | 1.420 (4) |
Pd1—N2 | 2.012 (3) | C6—C7 | 1.393 (4) |
O1—C13 | 1.296 (4) | C7—C8 | 1.394 (5) |
O2—C13 | 1.213 (4) | C7—C12 | 1.434 (4) |
O3—C15 | 1.304 (4) | C8—C9 | 1.372 (5) |
O4—C15 | 1.215 (4) | C8—H8 | 0.9300 |
N1—C1 | 1.326 (4) | C9—C10 | 1.401 (5) |
N1—C5 | 1.360 (4) | C9—H9 | 0.9300 |
N2—C10 | 1.330 (4) | C10—H10 | 0.9300 |
N2—C6 | 1.368 (4) | C11—C12 | 1.356 (5) |
C1—C2 | 1.394 (4) | C11—H11 | 0.9300 |
C1—H1 | 0.9300 | C12—H12 | 0.9300 |
C2—C3 | 1.361 (5) | C13—C14 | 1.521 (5) |
C2—H2 | 0.9300 | C14—C15 | 1.517 (5) |
C3—C4 | 1.402 (5) | C14—H14A | 0.9700 |
C3—H3 | 0.9300 | C14—H14B | 0.9700 |
| | | |
O1—Pd1—O3 | 94.08 (9) | C7—C6—C5 | 120.9 (3) |
O1—Pd1—N1 | 91.60 (9) | C6—C7—C8 | 117.3 (3) |
O1—Pd1—N2 | 173.04 (9) | C6—C7—C12 | 118.0 (3) |
O3—Pd1—N1 | 173.48 (9) | C8—C7—C12 | 124.7 (3) |
O3—Pd1—N2 | 92.15 (9) | C9—C8—C7 | 120.1 (3) |
N1—Pd1—N2 | 82.01 (10) | C9—C8—H8 | 119.9 |
C13—O1—Pd1 | 122.6 (2) | C7—C8—H8 | 119.9 |
C15—O3—Pd1 | 122.2 (2) | C8—C9—C10 | 119.7 (3) |
C1—N1—C5 | 118.5 (3) | C8—C9—H9 | 120.1 |
C1—N1—Pd1 | 128.6 (2) | C10—C9—H9 | 120.1 |
C5—N1—Pd1 | 112.76 (19) | N2—C10—C9 | 121.2 (3) |
C10—N2—C6 | 119.1 (3) | N2—C10—H10 | 119.4 |
C10—N2—Pd1 | 128.5 (2) | C9—C10—H10 | 119.4 |
C6—N2—Pd1 | 112.3 (2) | C12—C11—C4 | 121.2 (3) |
N1—C1—C2 | 121.8 (3) | C12—C11—H11 | 119.4 |
N1—C1—H1 | 119.1 | C4—C11—H11 | 119.4 |
C2—C1—H1 | 119.1 | C11—C12—C7 | 121.2 (3) |
C3—C2—C1 | 119.9 (3) | C11—C12—H12 | 119.4 |
C3—C2—H2 | 120.0 | C7—C12—H12 | 119.4 |
C1—C2—H2 | 120.0 | O2—C13—O1 | 122.4 (3) |
C2—C3—C4 | 119.8 (3) | O2—C13—C14 | 120.3 (3) |
C2—C3—H3 | 120.1 | O1—C13—C14 | 117.4 (3) |
C4—C3—H3 | 120.1 | C15—C14—C13 | 116.8 (3) |
C5—C4—C3 | 116.9 (3) | C15—C14—H14A | 108.1 |
C5—C4—C11 | 118.1 (3) | C13—C14—H14A | 108.1 |
C3—C4—C11 | 125.0 (3) | C15—C14—H14B | 108.1 |
N1—C5—C4 | 123.0 (3) | C13—C14—H14B | 108.1 |
N1—C5—C6 | 116.5 (3) | H14A—C14—H14B | 107.3 |
C4—C5—C6 | 120.4 (3) | O4—C15—O3 | 121.9 (3) |
N2—C6—C7 | 122.6 (3) | O4—C15—C14 | 120.4 (3) |
N2—C6—C5 | 116.4 (3) | O3—C15—C14 | 117.7 (3) |
| | | |
O3—Pd1—O1—C13 | 25.4 (3) | Pd1—N2—C6—C5 | −1.8 (3) |
N1—Pd1—O1—C13 | −157.8 (2) | N1—C5—C6—N2 | −0.1 (4) |
O1—Pd1—O3—C15 | −27.1 (3) | C4—C5—C6—N2 | −177.0 (3) |
N2—Pd1—O3—C15 | 155.9 (2) | N1—C5—C6—C7 | 176.3 (3) |
O1—Pd1—N1—C1 | −2.2 (3) | C4—C5—C6—C7 | −0.7 (4) |
N2—Pd1—N1—C1 | 175.0 (3) | N2—C6—C7—C8 | −0.1 (4) |
O1—Pd1—N1—C5 | −179.5 (2) | C5—C6—C7—C8 | −176.2 (3) |
N2—Pd1—N1—C5 | −2.25 (19) | N2—C6—C7—C12 | 179.2 (3) |
O3—Pd1—N2—C10 | 2.3 (3) | C5—C6—C7—C12 | 3.1 (4) |
N1—Pd1—N2—C10 | −174.8 (3) | C6—C7—C8—C9 | 0.5 (5) |
O3—Pd1—N2—C6 | 179.31 (19) | C12—C7—C8—C9 | −178.7 (3) |
N1—Pd1—N2—C6 | 2.21 (19) | C7—C8—C9—C10 | −0.1 (5) |
C5—N1—C1—C2 | −1.2 (5) | C6—N2—C10—C9 | 1.2 (5) |
Pd1—N1—C1—C2 | −178.3 (2) | Pd1—N2—C10—C9 | 178.1 (2) |
N1—C1—C2—C3 | 0.4 (5) | C8—C9—C10—N2 | −0.8 (5) |
C1—C2—C3—C4 | 0.4 (5) | C5—C4—C11—C12 | 3.1 (5) |
C2—C3—C4—C5 | −0.3 (5) | C3—C4—C11—C12 | −175.5 (3) |
C2—C3—C4—C11 | 178.2 (3) | C4—C11—C12—C7 | −0.7 (5) |
C1—N1—C5—C4 | 1.2 (4) | C6—C7—C12—C11 | −2.4 (5) |
Pd1—N1—C5—C4 | 178.8 (2) | C8—C7—C12—C11 | 176.8 (3) |
C1—N1—C5—C6 | −175.6 (3) | Pd1—O1—C13—O2 | −170.6 (3) |
Pd1—N1—C5—C6 | 1.9 (3) | Pd1—O1—C13—C14 | 9.4 (4) |
C3—C4—C5—N1 | −0.5 (4) | O2—C13—C14—C15 | 124.5 (3) |
C11—C4—C5—N1 | −179.1 (3) | O1—C13—C14—C15 | −55.5 (4) |
C3—C4—C5—C6 | 176.3 (3) | Pd1—O3—C15—O4 | 174.6 (3) |
C11—C4—C5—C6 | −2.4 (4) | Pd1—O3—C15—C14 | −6.2 (4) |
C10—N2—C6—C7 | −0.8 (4) | C13—C14—C15—O4 | −127.2 (3) |
Pd1—N2—C6—C7 | −178.1 (2) | C13—C14—C15—O3 | 53.6 (4) |
C10—N2—C6—C5 | 175.5 (3) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
C11—H11···O2i | 0.93 | 2.66 | 3.514 (4) | 154 |
C12—H12···O4ii | 0.93 | 2.50 | 3.426 (4) | 177 |
Symmetry codes: (i) x+1/2, −y+1/2, z−1/2; (ii) x+1/2, −y−1/2, z−1/2. |