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In the title compound, [Pd
II(C
3H
2O
4)(C
3H
10N
2)], the Pd
II atom adopts a distorted
cis-square-planar geometry. The ligands form two six-membered chelate rings, with propane-1,3-diamine adopting a chair conformation and the malonato ligand a boat conformation. The crystal packing is stabilized by a network of N—H
O and C—H
O hydrogen bonds.
Supporting information
CCDC reference: 636810
Key indicators
- Single-crystal X-ray study
- T = 123 K
- Mean (C-C) = 0.003 Å
- R factor = 0.016
- wR factor = 0.043
- Data-to-parameter ratio = 16.5
checkCIF/PLATON results
No syntax errors found
Alert level B
PLAT148_ALERT_3_B su on the a - Axis is Too Large (x 1000) . 5 Ang.
PLAT148_ALERT_3_B su on the b - Axis is Too Large (x 1000) . 10 Ang.
Alert level C
PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 = 3
0 ALERT level A = In general: serious problem
2 ALERT level B = Potentially serious problem
1 ALERT level C = Check and explain
0 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
3 ALERT type 3 Indicator that the structure quality may be low
0 ALERT type 4 Improvement, methodology, query or suggestion
0 ALERT type 5 Informative message, check
Data collection: RAPID-AUTO (Rigaku, 1998); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2005) and
CRYSTALS (Betteridge et al., 2003); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: CrystalStructure.
(Malonato-
κ2O:
O')(propane-1,3-diamine-
κ2N:
N')palladium(II)
top
Crystal data top
[Pd(C3H2O4)(C3H10N2)] | Z = 2 |
Mr = 282.60 | F(000) = 280.00 |
Triclinic, P1 | Dx = 2.183 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.7107 Å |
a = 4.430 (5) Å | Cell parameters from 4173 reflections |
b = 8.94 (1) Å | θ = 3.4–27.5° |
c = 11.40 (1) Å | µ = 2.14 mm−1 |
α = 106.93 (3)° | T = 123 K |
β = 90.83 (4)° | Needle, colorless |
γ = 95.03 (4)° | 0.50 × 0.05 × 0.05 mm |
V = 429.9 (8) Å3 | |
Data collection top
Rigaku R-AXIS RAPID diffractometer | 1889 reflections with F2 > 2σ(F2) |
Detector resolution: 10.00 pixels mm-1 | Rint = 0.018 |
ω scans | θmax = 27.5° |
Absorption correction: multi-scan (ABSCOR; Higashi, 1995) | h = −5→5 |
Tmin = 0.574, Tmax = 0.898 | k = −11→11 |
4252 measured reflections | l = −14→14 |
1958 independent reflections | |
Refinement top
Refinement on F2 | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.016 | w = 1/[σ2(Fo2) + (0.0242P)2 + 0.1199P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.043 | (Δ/σ)max < 0.001 |
S = 1.09 | Δρmax = 0.46 e Å−3 |
1958 reflections | Δρmin = −0.89 e Å−3 |
119 parameters | |
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 using all reflections. 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 | 0.35023 (3) | 0.968883 (13) | 0.244399 (10) | 0.00850 (6) | |
O1 | 0.1297 (3) | 1.07758 (15) | 0.14101 (11) | 0.0123 (2) | |
O2 | −0.1441 (3) | 1.26866 (16) | 0.13242 (12) | 0.0194 (3) | |
O3 | 0.1240 (3) | 1.07096 (15) | 0.39429 (11) | 0.0124 (2) | |
O4 | −0.1469 (3) | 1.26194 (16) | 0.49075 (12) | 0.0188 (3) | |
N1 | 0.5509 (3) | 0.85836 (18) | 0.08874 (13) | 0.0114 (3) | |
H1A | 0.4403 | 0.8671 | 0.0247 | 0.014* | |
H1B | 0.7345 | 0.9101 | 0.0886 | 0.014* | |
N2 | 0.5457 (4) | 0.85110 (18) | 0.34821 (13) | 0.0114 (3) | |
H2A | 0.7290 | 0.9020 | 0.3759 | 0.014* | |
H2B | 0.4328 | 0.8572 | 0.4141 | 0.014* | |
C1 | 0.5925 (4) | 0.6901 (2) | 0.06755 (15) | 0.0128 (3) | |
H1C | 0.7029 | 0.6535 | −0.0066 | 0.015* | |
H1D | 0.3950 | 0.6304 | 0.0548 | 0.015* | |
C2 | 0.7629 (4) | 0.6588 (2) | 0.17344 (16) | 0.0132 (3) | |
H2C | 0.8158 | 0.5514 | 0.1476 | 0.016* | |
H2D | 0.9505 | 0.7273 | 0.1918 | 0.016* | |
C3 | 0.5878 (4) | 0.6832 (2) | 0.28991 (16) | 0.0133 (3) | |
H3A | 0.3907 | 0.6234 | 0.2706 | 0.016* | |
H3B | 0.6960 | 0.6438 | 0.3475 | 0.016* | |
C6 | 0.0247 (4) | 1.2072 (2) | 0.40964 (15) | 0.0114 (3) | |
C5 | 0.1312 (4) | 1.3001 (2) | 0.32211 (15) | 0.0130 (3) | |
H5A | 0.0503 | 1.4015 | 0.3460 | 0.016* | |
H5B | 0.3508 | 1.3181 | 0.3280 | 0.016* | |
C4 | 0.0279 (4) | 1.2125 (2) | 0.18947 (15) | 0.0119 (3) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Pd1 | 0.00930 (8) | 0.00899 (8) | 0.00757 (8) | 0.00094 (5) | 0.00011 (5) | 0.00297 (5) |
O1 | 0.0155 (6) | 0.0124 (6) | 0.0099 (6) | 0.0037 (5) | −0.0009 (5) | 0.0040 (5) |
O2 | 0.0255 (7) | 0.0190 (7) | 0.0161 (6) | 0.0079 (6) | −0.0028 (5) | 0.0073 (5) |
O3 | 0.0147 (6) | 0.0143 (6) | 0.0095 (6) | 0.0032 (5) | 0.0026 (5) | 0.0047 (5) |
O4 | 0.0221 (7) | 0.0193 (7) | 0.0163 (7) | 0.0067 (6) | 0.0077 (5) | 0.0055 (5) |
N1 | 0.0131 (7) | 0.0113 (7) | 0.0100 (7) | 0.0017 (6) | 0.0009 (5) | 0.0034 (5) |
N2 | 0.0132 (7) | 0.0125 (7) | 0.0096 (7) | 0.0024 (6) | −0.0003 (5) | 0.0043 (5) |
C1 | 0.0162 (9) | 0.0103 (8) | 0.0118 (8) | 0.0022 (7) | 0.0013 (6) | 0.0027 (6) |
C2 | 0.0122 (8) | 0.0106 (8) | 0.0164 (9) | 0.0028 (6) | −0.0001 (6) | 0.0027 (6) |
C3 | 0.0160 (9) | 0.0114 (8) | 0.0136 (8) | 0.0017 (7) | −0.0014 (7) | 0.0054 (6) |
C6 | 0.0120 (8) | 0.0129 (8) | 0.0088 (8) | −0.0004 (6) | −0.0022 (6) | 0.0031 (6) |
C5 | 0.0160 (8) | 0.0108 (8) | 0.0123 (8) | −0.0001 (7) | 0.0008 (6) | 0.0038 (6) |
C4 | 0.0129 (8) | 0.0116 (8) | 0.0119 (8) | −0.0002 (6) | 0.0026 (6) | 0.0049 (6) |
Geometric parameters (Å, º) top
Pd1—N1 | 2.024 (2) | N2—H2B | 0.9000 |
Pd1—N2 | 2.029 (2) | C1—C2 | 1.521 (3) |
Pd1—O1 | 2.0225 (18) | C1—H1C | 0.9700 |
Pd1—O3 | 2.015 (2) | C1—H1D | 0.9700 |
O1—C4 | 1.296 (2) | C2—C3 | 1.518 (3) |
O2—C4 | 1.224 (2) | C2—H2C | 0.9700 |
O3—C6 | 1.296 (3) | C2—H2D | 0.9700 |
O4—C6 | 1.223 (2) | C3—H3A | 0.9700 |
N1—C1 | 1.481 (3) | C3—H3B | 0.9700 |
N1—H1A | 0.9000 | C6—C5 | 1.529 (3) |
N1—H1B | 0.9000 | C5—C4 | 1.529 (3) |
N2—C3 | 1.484 (3) | C5—H5A | 0.9700 |
N2—H2A | 0.9000 | C5—H5B | 0.9700 |
| | | |
O1—Pd1—N1 | 86.42 (9) | H1C—C1—H1D | 107.8 |
O1—Pd1—N2 | 176.25 (5) | C3—C2—C1 | 114.40 (16) |
O3—Pd1—N1 | 176.18 (5) | C3—C2—H2C | 108.7 |
O3—Pd1—N2 | 86.67 (9) | C1—C2—H2C | 108.7 |
O3—Pd1—O1 | 92.08 (9) | C3—C2—H2D | 108.7 |
N1—Pd1—N2 | 94.60 (9) | C1—C2—H2D | 108.7 |
C4—O1—Pd1 | 121.31 (12) | H2C—C2—H2D | 107.6 |
C6—O3—Pd1 | 121.25 (11) | N2—C3—C2 | 112.16 (15) |
C1—N1—Pd1 | 117.27 (11) | N2—C3—H3A | 109.2 |
C1—N1—H1A | 108.0 | C2—C3—H3A | 109.2 |
Pd1—N1—H1A | 108.0 | N2—C3—H3B | 109.2 |
C1—N1—H1B | 108.0 | C2—C3—H3B | 109.2 |
Pd1—N1—H1B | 108.0 | H3A—C3—H3B | 107.9 |
H1A—N1—H1B | 107.2 | O4—C6—O3 | 122.34 (16) |
C3—N2—Pd1 | 117.84 (12) | O4—C6—C5 | 120.12 (17) |
C3—N2—H2A | 107.8 | O3—C6—C5 | 117.54 (16) |
Pd1—N2—H2A | 107.8 | C4—C5—C6 | 111.33 (16) |
C3—N2—H2B | 107.8 | C4—C5—H5A | 109.4 |
Pd1—N2—H2B | 107.8 | C6—C5—H5A | 109.4 |
H2A—N2—H2B | 107.2 | C4—C5—H5B | 109.4 |
N1—C1—C2 | 113.04 (15) | C6—C5—H5B | 109.4 |
N1—C1—H1C | 109.0 | H5A—C5—H5B | 108.0 |
C2—C1—H1C | 109.0 | O2—C4—O1 | 121.97 (17) |
N1—C1—H1D | 109.0 | O2—C4—C5 | 120.81 (17) |
C2—C1—H1D | 109.0 | O1—C4—C5 | 117.22 (16) |
| | | |
Pd1—N1—C1—C2 | −54.76 (19) | O1—Pd1—N1—C1 | −140.02 (13) |
Pd1—N2—C3—C2 | 54.82 (19) | O3—Pd1—N2—C3 | 139.66 (14) |
N1—Pd1—N2—C3 | −36.73 (14) | Pd1—O3—C6—O4 | 169.98 (13) |
N1—C1—C2—C3 | 69.1 (2) | Pd1—O3—C6—C5 | −10.3 (2) |
N2—Pd1—N1—C1 | 36.36 (14) | O4—C6—C5—C4 | −118.12 (19) |
C1—C2—C3—N2 | −68.7 (2) | O3—C6—C5—C4 | 62.2 (2) |
O3—Pd1—O1—C4 | 28.41 (13) | Pd1—O1—C4—O2 | −168.81 (13) |
N1—Pd1—O1—C4 | −155.11 (14) | Pd1—O1—C4—C5 | 11.1 (2) |
O1—Pd1—O3—C6 | −28.80 (13) | C6—C5—C4—O2 | 117.4 (2) |
N2—Pd1—O3—C6 | 154.75 (14) | C6—C5—C4—O1 | −62.5 (2) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···O2i | 0.90 | 2.19 | 2.956 (3) | 143 |
N1—H1B···O1ii | 0.90 | 2.16 | 3.027 (4) | 163 |
N2—H2A···O3ii | 0.90 | 2.18 | 3.030 (4) | 158 |
N2—H2B···O4iii | 0.90 | 2.10 | 2.894 (3) | 147 |
C2—H2C···O2iv | 0.97 | 2.51 | 3.445 (4) | 163 |
Symmetry codes: (i) −x, −y+2, −z; (ii) x+1, y, z; (iii) −x, −y+2, −z+1; (iv) x+1, y−1, z. |
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