trans-Bis(1H-benzimidazol-2-yl­methyl-κN³ diethyl phosphate)­di­chloro­palladium(II) monohydrate

The title compound, trans-[PdCl₂(2-bimOpe)₂]·H₂O, where 2-bimOpe is 1H-benzimidazol-2-yl­methyl diethyl phosphate (C₁₂H₁₇N₂O₄P), crystallizes as a monohydrate. The most satisfactory structure refinement was obtained by eliminating the solvent contribution from the intensity data and the solvent-free model was employed for the final refinement. The Pd atom possesses a square-planar geometry in a centrosymmetric trans configuration.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.009 Å
Some non-H atoms missing
• R factor = 0.046
• wR factor = 0.120
• Data-to-parameter ratio = 17.5

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT242_ALERT_2_B Check Low    U(eq) as Compared to Neighbors  for         Pd

Alert level C
CHEMW03_ALERT_2_C The ratio of given/expected molecular weight as
            calculated from the _atom_site* data lies outside
            the range 0.99 <> 1.01
           From the CIF: _cell_formula_units_Z                    1
           From the CIF: _chemical_formula_weight           763.81
           TEST: Calculate formula weight from _atom_site_*
           atom     mass    num     sum
           C        12.01   24.00  288.26
           H         1.01   34.00   34.27
           Cl       35.45    2.00   70.91
           N        14.01    4.00   56.03
           O        16.00    8.00  127.99
           P        30.97    2.00   61.95
           Pd      106.42    1.00  106.42
           Calculated formula weight              745.83
PLAT026_ALERT_3_C Ratio Observed / Unique Reflections too Low ....         41 Perc.
PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings    Differ ....          ?
PLAT043_ALERT_1_C Check Reported Molecular Weight ................     763.81
PLAT044_ALERT_1_C Calculated and Reported Dx Differ ..............          ?
PLAT068_ALERT_1_C Reported F000 Differs from Calcd (or Missing)...          ?
PLAT220_ALERT_2_C Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       2.74 Ratio
PLAT241_ALERT_2_C Check High   U(eq) as Compared to Neighbors  for         C1
PLAT242_ALERT_2_C Check Low    U(eq) as Compared to Neighbors  for          P
PLAT301_ALERT_3_C Main Residue  Disorder .........................      16.00 Perc.
PLAT342_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          9
PLAT601_ALERT_2_C Structure Contains Solvent Accessible VOIDS of .      39.00 A   3  

Alert level G
FORMU01_ALERT_2_G  There is a discrepancy between the atom counts in the
            _chemical_formula_sum and the formula from the _atom_site* data.
            Atom count from _chemical_formula_sum:C24 H36 Cl2 N4 O9 P2 Pd1
            Atom count from the _atom_site data:  C24 H34 Cl2 N4 O8 P2 Pd1
CELLZ01_ALERT_1_G Difference between formula and atom_site contents detected.
CELLZ01_ALERT_1_G ALERT: Large difference may be due to a
            symmetry error - see SYMMG tests
           From the CIF: _cell_formula_units_Z    1
           From the CIF: _chemical_formula_sum  C24 H36 Cl2 N4 O9 P2 Pd
           TEST: Compare cell contents of formula and atom_site data

           atom    Z*formula  cif sites diff
           C         24.00     24.00    0.00
           H         36.00     34.00    2.00
           Cl         2.00      2.00    0.00
           N          4.00      4.00    0.00
           O          9.00      8.00    1.00
           P          2.00      2.00    0.00
           Pd         1.00      1.00    0.00

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
  12 ALERT level C = Check and explain
   3 ALERT level G = General alerts; check

   6 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   7 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

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Computing details

Data collection: MSC/AFC Diffractometer Control Software (Molecular Structure Corporation, 1989)'; cell refinement: MSC/AFC Diffractometer Control Software; data reduction: CrystalStructure (Rigaku/MSC, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2001); software used to prepare material for publication: PLATON.

trans-Bis(1H-benzimidazol-2-ylmethyl-κN³ diethyl phosphate)dichloropalladium(II) monohydrate

Crystal data

[PdCl2(C12H17N2O4P)2]·H2O	Z = 1
Mr = 763.81	F(000) = 390
Triclinic, P1	Dx = 1.496 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71070 Å
a = 9.463 (5) Å	Cell parameters from 25 reflections
b = 9.638 (2) Å	θ = 15.3–24.7°
c = 10.908 (3) Å	µ = 0.85 mm^−1
α = 100.31 (2)°	T = 293 K
β = 115.10 (3)°	Prism, yellow
γ = 100.64 (4)°	0.50 × 0.25 × 0.10 mm
V = 847.6 (6) Å^3

Data collection

Rigaku AFC-5S diffractometer	1608 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.029
Graphite monochromator	θmax = 27.5°, θmin = 2.8°
ω scan	h = −12→12
Absorption correction: analytical (de Meulenaer & Tompa, 1965)	k = 0→12
Tmin = 0.723, Tmax = 0.905	l = −14→13
4131 measured reflections	3 standard reflections every 150 reflections
3898 independent reflections	intensity decay: none

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.046	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.120	H-atom parameters constrained
S = 0.90	[1.00000exp(3.00(sinθ/λ)^2)]/ [σ^2(Fo^2) + (0.0494P)^2] where P = 0.33333Fo^2 + 0.66667Fc^2
3898 reflections	(Δ/σ)max < 0.001
223 parameters	Δρmax = 0.51 e Å^−3
134 restraints	Δρmin = −0.41 e Å^−3

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)
Pd	0.5000	0.5000	0.5000	0.0606 (2)
Cl	0.2422 (2)	0.49982 (17)	0.3538 (2)	0.1264 (7)
N1	0.4414 (5)	0.2834 (4)	0.4120 (4)	0.0612 (10)
C2	0.4762 (6)	0.2185 (5)	0.3155 (5)	0.0652 (13)
N2	0.4210 (5)	0.0708 (4)	0.2785 (4)	0.0700 (11)
H2	0.4308	0.0098	0.2167	0.084*
C3	0.3463 (6)	0.0346 (5)	0.3569 (5)	0.0613 (13)
C4	0.2675 (7)	−0.1001 (6)	0.3611 (6)	0.0803 (16)
H4	0.2584	−0.1892	0.3044	0.096*
C5	0.2039 (8)	−0.0943 (7)	0.4531 (7)	0.1000 (19)
H5	0.1508	−0.1822	0.4591	0.120*
C6	0.2159 (8)	0.0385 (7)	0.5380 (7)	0.0992 (19)
H6	0.1701	0.0369	0.5984	0.119*
C7	0.2943 (7)	0.1722 (6)	0.5345 (6)	0.0857 (17)
H7	0.3040	0.2607	0.5925	0.103*
C8	0.3583 (6)	0.1693 (5)	0.4406 (5)	0.0618 (12)
C1	0.5744 (8)	0.3031 (6)	0.2618 (6)	0.097 (2)
H1A	0.5547	0.3983	0.2614	0.116*
H1B	0.6898	0.3191	0.3219	0.116*
P	0.6362 (2)	0.24676 (16)	0.04944 (18)	0.0864 (5)
O1	0.5254 (5)	0.2174 (4)	0.1196 (4)	0.0831 (11)
O2	0.5601 (6)	0.1485 (4)	−0.0918 (4)	0.1039 (14)
O3	0.6627 (7)	0.4140 (4)	0.0640 (5)	0.1316 (18)
O4	0.8084 (7)	0.2490 (7)	0.1514 (6)	0.1450 (19)
C31A	0.720 (2)	0.4956 (15)	−0.0196 (14)	0.130 (4)	0.50
H31A	0.6365	0.5279	−0.0866	0.156*	0.50
H31B	0.7704	0.4422	−0.0655	0.156*	0.50
C32A	0.843 (3)	0.6183 (18)	0.1133 (16)	0.151 (5)	0.50
H32A	0.8047	0.7039	0.1154	0.226*	0.50
H32B	0.9461	0.6420	0.1137	0.226*	0.50
H32C	0.8551	0.5865	0.1949	0.226*	0.50
C41A	0.809 (2)	0.0906 (14)	0.145 (2)	0.168 (5)	0.50
H41A	0.7968	0.0662	0.2230	0.202*	0.50
H41B	0.7175	0.0251	0.0575	0.202*	0.50
C42A	0.959 (2)	0.069 (2)	0.152 (2)	0.168 (5)	0.50
H42A	0.9543	0.0583	0.0611	0.252*	0.50
H42B	0.9740	−0.0189	0.1799	0.252*	0.50
H42C	1.0495	0.1521	0.2205	0.252*	0.50
C31B	0.8037 (17)	0.4860 (14)	0.042 (2)	0.135 (4)	0.50
H31C	0.9049	0.4791	0.1138	0.162*	0.50
H31D	0.7880	0.4346	−0.0497	0.162*	0.50
C32B	0.814 (3)	0.6436 (14)	0.0508 (19)	0.146 (5)	0.50
H32D	0.7190	0.6632	0.0526	0.219*	0.50
H32E	0.8200	0.6642	−0.0301	0.219*	0.50
H32F	0.9099	0.7051	0.1354	0.219*	0.50
C41B	0.894 (2)	0.1373 (19)	0.209 (2)	0.166 (5)	0.50
H41C	0.9868	0.1790	0.3032	0.199*	0.50
H41D	0.8213	0.0483	0.2032	0.199*	0.50
C42B	0.939 (3)	0.121 (2)	0.0960 (19)	0.163 (5)	0.50
H42D	0.8985	0.1839	0.0393	0.244*	0.50
H42E	0.8934	0.0201	0.0380	0.244*	0.50
H42F	1.0562	0.1474	0.1364	0.244*	0.50

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Pd	0.0817 (5)	0.0422 (3)	0.0643 (4)	0.0179 (3)	0.0443 (4)	0.0050 (2)
Cl	0.0971 (13)	0.0655 (9)	0.1514 (16)	0.0268 (9)	0.0126 (12)	−0.0013 (10)
N1	0.078 (3)	0.045 (2)	0.062 (2)	0.014 (2)	0.040 (2)	0.0040 (18)
C2	0.074 (3)	0.049 (3)	0.070 (3)	0.010 (2)	0.041 (3)	0.001 (2)
N2	0.085 (3)	0.046 (2)	0.077 (3)	0.013 (2)	0.048 (3)	−0.0049 (19)
C3	0.066 (3)	0.048 (3)	0.069 (3)	0.023 (2)	0.030 (3)	0.014 (2)
C4	0.089 (4)	0.053 (3)	0.090 (4)	0.018 (3)	0.036 (4)	0.019 (3)
C5	0.114 (5)	0.077 (4)	0.116 (5)	0.016 (4)	0.061 (5)	0.039 (4)
C6	0.121 (5)	0.087 (4)	0.112 (5)	0.021 (4)	0.077 (4)	0.035 (4)
C7	0.113 (5)	0.069 (4)	0.093 (4)	0.020 (3)	0.069 (4)	0.020 (3)
C8	0.066 (3)	0.050 (3)	0.064 (3)	0.019 (2)	0.028 (3)	0.010 (2)
C1	0.137 (5)	0.060 (3)	0.094 (4)	0.000 (3)	0.080 (4)	−0.011 (3)
P	0.1124 (14)	0.0608 (9)	0.1017 (12)	0.0212 (9)	0.0731 (12)	0.0059 (8)
O1	0.111 (3)	0.058 (2)	0.083 (2)	0.0010 (19)	0.066 (2)	−0.0032 (17)
O2	0.157 (4)	0.070 (2)	0.098 (3)	0.025 (2)	0.083 (3)	0.002 (2)
O3	0.203 (5)	0.063 (3)	0.165 (4)	0.016 (3)	0.136 (4)	0.015 (3)
O4	0.138 (5)	0.152 (5)	0.152 (5)	0.066 (4)	0.074 (4)	0.022 (4)
C31A	0.144 (6)	0.111 (5)	0.138 (6)	0.031 (5)	0.061 (5)	0.062 (5)
C32A	0.156 (7)	0.119 (6)	0.151 (8)	0.009 (6)	0.049 (7)	0.072 (6)
C41A	0.168 (7)	0.168 (7)	0.158 (7)	0.036 (5)	0.064 (6)	0.069 (5)
C42A	0.166 (7)	0.165 (8)	0.160 (8)	0.050 (7)	0.060 (7)	0.060 (6)
C31B	0.149 (6)	0.113 (5)	0.140 (6)	0.027 (5)	0.061 (5)	0.061 (5)
C32B	0.154 (7)	0.112 (6)	0.150 (8)	0.013 (6)	0.050 (7)	0.071 (6)
C41B	0.164 (7)	0.169 (7)	0.159 (7)	0.037 (5)	0.067 (5)	0.066 (5)
C42B	0.163 (8)	0.168 (8)	0.153 (8)	0.039 (7)	0.066 (6)	0.070 (6)

Geometric parameters (Å, º)

Pd—N1^i	1.998 (3)	O3—C31B	1.518 (9)
Pd—N1	1.998 (3)	O4—C41A	1.517 (10)
Pd—Cl	2.278 (2)	O4—C41B	1.533 (10)
Pd—Cl^i	2.278 (2)	C31A—C32A	1.516 (9)
N1—C2	1.319 (5)	C31A—H31A	0.9700
N1—C8	1.392 (6)	C31A—H31B	0.9700
C2—N2	1.343 (5)	C32A—H32A	0.9600
C2—C1	1.492 (7)	C32A—H32B	0.9600
N2—C3	1.372 (6)	C32A—H32C	0.9600
N2—H2	0.8600	C41A—C42A	1.447 (10)
C3—C4	1.391 (7)	C41A—H41A	0.9700
C3—C8	1.402 (6)	C41A—H41B	0.9700
C4—C5	1.370 (8)	C42A—H42A	0.9600
C4—H4	0.9300	C42A—H42B	0.9600
C5—C6	1.394 (8)	C42A—H42C	0.9600
C5—H5	0.9300	C31B—C32B	1.487 (9)
C6—C7	1.379 (7)	C31B—H31C	0.9700
C6—H6	0.9300	C31B—H31D	0.9700
C7—C8	1.392 (7)	C32B—H32D	0.9600
C7—H7	0.9300	C32B—H32E	0.9600
C1—O1	1.446 (5)	C32B—H32F	0.9600
C1—H1A	0.9700	C41B—C42B	1.459 (10)
C1—H1B	0.9700	C41B—H41C	0.9700
P—O2	1.440 (4)	C41B—H41D	0.9700
P—O4	1.527 (6)	C42B—H42D	0.9600
P—O3	1.553 (4)	C42B—H42E	0.9600
P—O1	1.555 (4)	C42B—H42F	0.9600
O3—C31A	1.505 (9)
N1^i—Pd—N1	180.0	P—O4—C41B	137.1 (10)
N1^i—Pd—Cl	89.78 (13)	O3—C31A—C32A	91.4 (10)
N1—Pd—Cl	90.22 (13)	O3—C31A—H31A	113.4
N1^i—Pd—Cl^i	90.22 (13)	C32A—C31A—H31A	113.4
N1—Pd—Cl^i	89.78 (13)	O3—C31A—H31B	113.4
Cl—Pd—Cl^i	180.0	C32A—C31A—H31B	113.4
C2—N1—C8	105.5 (4)	H31A—C31A—H31B	110.7
C2—N1—Pd	126.9 (3)	C31A—C32A—H32A	109.5
C8—N1—Pd	127.6 (3)	C31A—C32A—H32B	109.5
N1—C2—N2	112.5 (4)	H32A—C32A—H32B	109.5
N1—C2—C1	122.5 (4)	C31A—C32A—H32C	109.5
N2—C2—C1	124.9 (4)	H32A—C32A—H32C	109.5
C2—N2—C3	107.8 (4)	H32B—C32A—H32C	109.5
C2—N2—H2	126.1	C42A—C41A—O4	111.1 (14)
C3—N2—H2	126.1	C42A—C41A—H41A	109.4
N2—C3—C4	132.4 (4)	O4—C41A—H41A	109.4
N2—C3—C8	105.5 (4)	C42A—C41A—H41B	109.4
C4—C3—C8	122.0 (5)	O4—C41A—H41B	109.4
C5—C4—C3	116.4 (5)	H41A—C41A—H41B	108.0
C5—C4—H4	121.8	C41A—C42A—H42A	109.5
C3—C4—H4	121.8	C41A—C42A—H42B	109.5
C4—C5—C6	122.4 (6)	H42A—C42A—H42B	109.5
C4—C5—H5	118.8	C41A—C42A—H42C	109.5
C6—C5—H5	118.8	H42A—C42A—H42C	109.5
C7—C6—C5	121.4 (6)	H42B—C42A—H42C	109.5
C7—C6—H6	119.3	C32B—C31B—O3	110.4 (12)
C5—C6—H6	119.3	C32B—C31B—H31C	109.6
C6—C7—C8	117.3 (5)	O3—C31B—H31C	109.6
C6—C7—H7	121.3	C32B—C31B—H31D	109.6
C8—C7—H7	121.3	O3—C31B—H31D	109.6
N1—C8—C7	130.9 (4)	H31C—C31B—H31D	108.1
N1—C8—C3	108.6 (4)	C31B—C32B—H32D	109.5
C7—C8—C3	120.5 (5)	C31B—C32B—H32E	109.5
O1—C1—C2	107.6 (4)	H32D—C32B—H32E	109.5
O1—C1—H1A	110.2	C31B—C32B—H32F	109.5
C2—C1—H1A	110.2	H32D—C32B—H32F	109.5
O1—C1—H1B	110.2	H32E—C32B—H32F	109.5
C2—C1—H1B	110.2	C42B—C41B—O4	88.5 (12)
H1A—C1—H1B	108.5	C42B—C41B—H41C	113.9
O2—P—O4	117.7 (3)	O4—C41B—H41C	113.9
O2—P—O3	116.8 (3)	C42B—C41B—H41D	113.9
O4—P—O3	100.1 (3)	O4—C41B—H41D	113.9
O2—P—O1	110.3 (2)	H41C—C41B—H41D	111.1
O4—P—O1	108.6 (3)	C41B—C42B—H42D	109.5
O3—P—O1	101.9 (2)	C41B—C42B—H42E	109.5
C1—O1—P	120.9 (3)	H42D—C42B—H42E	109.5
C31A—O3—P	125.7 (7)	C41B—C42B—H42F	109.5
C31B—O3—P	114.3 (6)	H42D—C42B—H42F	109.5
C41A—O4—P	107.8 (9)	H42E—C42B—H42F	109.5
Cl—Pd—N1—C2	100.6 (4)	N1—C2—C1—O1	−152.6 (5)
Cl^i—Pd—N1—C2	−79.4 (4)	N2—C2—C1—O1	31.0 (8)
Cl—Pd—N1—C8	−80.6 (4)	C2—C1—O1—P	−160.9 (4)
Cl^i—Pd—N1—C8	99.4 (4)	O2—P—O1—C1	−179.5 (4)
C8—N1—C2—N2	0.4 (6)	O4—P—O1—C1	50.2 (5)
Pd—N1—C2—N2	179.4 (3)	O3—P—O1—C1	−54.8 (5)
C8—N1—C2—C1	−176.4 (5)	O2—P—O3—C31A	−41.5 (10)
Pd—N1—C2—C1	2.6 (7)	O4—P—O3—C31A	86.7 (9)
N1—C2—N2—C3	−0.8 (6)	O1—P—O3—C31A	−161.8 (9)
C1—C2—N2—C3	175.9 (5)	O2—P—O3—C31B	−76.0 (9)
C2—N2—C3—C4	179.3 (5)	O4—P—O3—C31B	52.2 (9)
C2—N2—C3—C8	0.9 (5)	O1—P—O3—C31B	163.8 (9)
N2—C3—C4—C5	−179.1 (5)	O2—P—O4—C41A	−49.0 (10)
C8—C3—C4—C5	−0.9 (8)	O3—P—O4—C41A	−176.7 (9)
C3—C4—C5—C6	0.3 (9)	O1—P—O4—C41A	77.0 (9)
C4—C5—C6—C7	−0.5 (10)	O2—P—O4—C41B	−55.8 (11)
C5—C6—C7—C8	1.2 (10)	O3—P—O4—C41B	176.5 (11)
C2—N1—C8—C7	179.1 (5)	O1—P—O4—C41B	70.3 (11)
Pd—N1—C8—C7	0.1 (8)	C31B—O3—C31A—C32A	−54.5 (16)
C2—N1—C8—C3	0.1 (5)	P—O3—C31A—C32A	−133.2 (11)
Pd—N1—C8—C3	−178.9 (3)	P—O4—C41A—C42A	141.3 (16)
C6—C7—C8—N1	179.4 (5)	C41B—O4—C41A—C42A	−48.0 (19)
C6—C7—C8—C3	−1.7 (8)	C31A—O3—C31B—C32B	58.1 (16)
N2—C3—C8—N1	−0.6 (5)	P—O3—C31B—C32B	177.1 (11)
C4—C3—C8—N1	−179.3 (4)	C41A—O4—C41B—C42B	81 (2)
N2—C3—C8—C7	−179.7 (5)	P—O4—C41B—C42B	93.6 (14)
C4—C3—C8—C7	1.7 (8)

Symmetry code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···O2^ii	0.86	1.90	2.749 (6)	171

Symmetry code: (ii) −x+1, −y, −z.