cyclo-Tetra­kis[4-(amino­meth­yl)-5-(hydroxy­meth­yl)-2-methyl­pyridin-3-olato-κN¹:κ²N⁴,O³]tetra­kis[chloro­palladium(II)] nona­hydrate

The title compound, [Pd₄(C₈H₁₁N₂O₂)₄Cl₄]·9H₂O, is a cyclic tetra­mer. The Pd^II atom shows distorted square-planar coordination arising from chelation by the phenolate O atom and the pyridoxamine ligand; the metal atom is also linked to the pyridyl N atom from an adjacent ligand and a Cl atom. A twofold axis, which is parallel to the c axis, is located at the center of a tetramer. The crystal packing is stabilized by hydrogen bonding among neighboring complex mol­ecules via the solvent water mol­ecules.

Key indicators

• Single-crystal X-ray study
• T = 123 K
• Mean [sigma](C-C) = 0.031 Å
• R factor = 0.067
• wR factor = 0.226
• Data-to-parameter ratio = 17.8

checkCIF/PLATON results

No syntax errors found



Alert level A
ABSTM02_ALERT_3_A  The ratio of expected to reported Tmax/Tmin(RR') is < 0.50
            Tmin and Tmax reported:      0.206     0.670
            Tmin(prime) and Tmax expected:      0.692     0.765
            RR(prime) =      0.340
            Please check that your absorption correction is appropriate.

Author Response: We chose the best crystal and x-ray measurement proceeded at 123K, however the crystal condition might be not very suitable for experiment.

PLAT061_ALERT_3_A Tmax/Tmin Range Test RR' too Large .............       0.33

Author Response: We chose the best crystal and x-ray measurement proceeded at 123K, however the crystal condition might be not very suitable for experiment.

Alert level B
PLAT222_ALERT_3_B Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       4.08 Ratio
PLAT342_ALERT_3_B Low Bond Precision on C-C bonds (x 1000) Ang ...         31

Alert level C
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT062_ALERT_4_C Rescale T(min) & T(max) by .....................       1.14
PLAT220_ALERT_2_C Large Non-Solvent    O     Ueq(max)/Ueq(min) ...       3.45 Ratio
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for         C8
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        Pd1
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         C5

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      1.141
            Tmax scaled      0.765 Tmin scaled      0.235

Author Response: We chose the best crystal and x-ray measurement proceeded at 123K, however the crystal condition might be not very suitable for experiment.

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

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   4 ALERT type 2 Indicator that the structure model may be wrong or deficient
   5 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

---

Computing details

Data collection: RAPID-AUTO (Rigaku Corporation, 1998); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2005); 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.

cyclo-Tetrakis[4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-olato- κN¹:κ²N⁴,O³]tetrakis[chloropalladium(II)] nonahydrate

Crystal data

[Pd4(C8H11N2O2)4Cl4]·9H2O	Dx = 1.953 Mg m^−3
Mr = 1398.38	Mo Kα radiation, λ = 0.7107 Å
Tetragonal, I41/a	Cell parameters from 14154 reflections
Hall symbol: -I 4ad	θ = 3.3–27.4°
a = 12.26 (2) Å	µ = 1.79 mm^−1
c = 31.65 (4) Å	T = 123 K
V = 4757 (13) Å^3	Needle, red
Z = 4	0.20 × 0.20 × 0.15 mm
F(000) = 2792.0

Data collection

Rigaku R-AXIS RAPID diffractometer	1659 reflections with F^2 > 2σ(F^2)
Detector resolution: 10.00 pixels mm^-1	Rint = 0.048
ω scans	θmax = 27.5°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −15→15
Tmin = 0.206, Tmax = 0.670	k = −15→15
21727 measured reflections	l = −36→41
2736 independent reflections

Refinement

Refinement on F^2	All H-atom parameters refined
R[F^2 > 2σ(F^2)] = 0.067	w = 1/[σ^2(Fo^2) + (0.1218P)^2 + 4.0653P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.226	(Δ/σ)max < 0.001
S = 1.13	Δρmax = 1.53 e Å^−3
2736 reflections	Δρmin = −1.15 e Å^−3
154 parameters

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)
Pd1	0.50660 (13)	0.59240 (10)	0.42842 (4)	0.0804 (19)
Cl1	0.4041 (6)	0.6180 (4)	0.48825 (15)	0.113 (3)
O1	0.5953 (10)	0.5711 (10)	0.3761 (4)	0.084 (4)
O2	1.022 (2)	0.602 (4)	0.4285 (10)	0.26 (2)
H2	1.013 (2)	0.647 (4)	0.4122 (10)	0.388*	0.50
H3	1.068 (2)	0.606 (4)	0.4493 (10)	0.388*	0.50
O1W	1.0000	0.7500	0.3750	0.29 (4)
H1W	1.007273 (19)	0.69950 (13)	0.39318 (5)	0.441*	0.50
O2W	1.170 (3)	0.616 (3)	0.4947 (9)	0.29 (2)
H2W	1.242 (3)	0.616 (3)	0.4929 (9)	0.433*
H3W	1.153 (3)	0.667 (3)	0.5097 (9)	0.433*	0.50
H4W	1.125 (3)	0.612 (3)	0.4743 (9)	0.433*	0.50
O3W	1.114 (2)	0.7844 (19)	0.5434 (6)	0.158 (8)
H5W	1.134 (2)	0.8027 (19)	0.5685 (6)	0.238*
H6W	1.046 (2)	0.7634 (19)	0.5434 (6)	0.238*	0.50
H7W	1.131 (2)	0.7338 (19)	0.5285 (6)	0.238*	0.50
N1	0.8066 (11)	0.3748 (12)	0.3575 (4)	0.077 (4)
N2	0.6423 (19)	0.6277 (12)	0.4619 (5)	0.107 (7)
H2A	0.6286	0.6874	0.4775	0.128*
H2B	0.6550	0.5724	0.4799	0.128*
C2	0.7096 (13)	0.4273 (15)	0.3555 (5)	0.076 (5)
C3	0.6894 (15)	0.5187 (14)	0.3812 (5)	0.078 (5)
C4	0.7682 (17)	0.5514 (14)	0.4106 (7)	0.091 (6)
C5	0.8673 (18)	0.4947 (15)	0.4111 (7)	0.098 (7)
C6	0.8819 (16)	0.4088 (15)	0.3849 (6)	0.090 (6)
H6	0.9493	0.3707	0.3861	0.108*
C7	0.6224 (15)	0.386 (2)	0.3262 (6)	0.104 (7)
H7A	0.6073	0.4416	0.3046	0.155*
H7B	0.5558	0.3716	0.3424	0.155*
H7C	0.6472	0.3190	0.3126	0.155*
C8	0.743 (3)	0.6483 (17)	0.4376 (9)	0.125 (10)
H8A	0.8044	0.6620	0.4573	0.150*
H8B	0.7335	0.7136	0.4196	0.150*
C9	0.954 (3)	0.521 (2)	0.4452 (14)	0.175 (16)
H9A	0.9177	0.5481	0.4712	0.210*
H9B	0.9962	0.4552	0.4523	0.210*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Pd1	0.118 (2)	0.053 (2)	0.070 (2)	0.0088 (6)	−0.0148 (7)	−0.0031 (5)
Cl1	0.200 (6)	0.058 (3)	0.080 (3)	0.026 (3)	0.013 (3)	0.005 (2)
O1	0.082 (8)	0.091 (8)	0.078 (7)	0.009 (6)	−0.022 (6)	−0.001 (6)
O2	0.16 (2)	0.39 (6)	0.22 (3)	−0.09 (3)	−0.02 (2)	−0.13 (3)
O1W	0.23 (4)	0.23 (4)	0.42 (11)	0.000	0.000	0.000
O2W	0.30 (4)	0.37 (5)	0.20 (3)	−0.21 (4)	0.02 (3)	−0.05 (3)
O3W	0.180 (19)	0.18 (2)	0.114 (14)	−0.019 (16)	−0.003 (13)	0.010 (12)
N1	0.065 (8)	0.090 (10)	0.075 (8)	−0.016 (7)	−0.006 (6)	−0.005 (7)
N2	0.18 (2)	0.053 (8)	0.081 (10)	0.023 (10)	−0.051 (11)	−0.012 (7)
C2	0.061 (9)	0.095 (12)	0.071 (9)	−0.007 (8)	−0.007 (7)	−0.002 (9)
C3	0.085 (12)	0.072 (10)	0.078 (10)	0.000 (8)	−0.017 (9)	0.002 (8)
C4	0.100 (13)	0.066 (10)	0.107 (14)	−0.009 (9)	−0.045 (11)	−0.004 (9)
C5	0.103 (14)	0.070 (11)	0.122 (15)	0.003 (10)	−0.052 (12)	−0.011 (11)
C6	0.086 (12)	0.076 (11)	0.107 (13)	−0.011 (9)	−0.031 (10)	−0.001 (10)
C7	0.063 (11)	0.16 (2)	0.086 (12)	0.000 (11)	0.000 (9)	−0.033 (13)
C8	0.16 (2)	0.062 (11)	0.15 (2)	0.007 (13)	−0.080 (19)	−0.014 (13)
C9	0.13 (2)	0.093 (16)	0.30 (4)	0.006 (15)	−0.13 (3)	−0.04 (2)

Geometric parameters (Å, º)

Pd1—O1	1.997 (13)	N2—C8	1.48 (4)
Pd1—N2	2.019 (19)	N2—H2A	0.8987
Pd1—N1^i	2.020 (15)	N2—H2B	0.8992
Pd1—Cl1	2.295 (6)	C2—C3	1.41 (3)
O1—C3	1.33 (2)	C2—C7	1.50 (2)
O2—C9	1.40 (5)	C3—C4	1.40 (2)
O2—H2	0.7649	C4—C5	1.40 (3)
O2—H3	0.8685	C4—C8	1.50 (3)
O1W—H1W	0.8500	C5—C6	1.35 (3)
O2W—H2W	0.8820	C5—C9	1.55 (3)
O2W—H3W	0.8119	C6—H6	0.9500
O2W—H4W	0.8531	C7—H7A	0.9800
O3W—H5W	0.8625	C7—H7B	0.9800
O3W—H6W	0.8764	C7—H7C	0.9800
O3W—H7W	0.8080	C8—H8A	0.9900
N1—C6	1.33 (2)	C8—H8B	0.9900
N1—C2	1.35 (2)	C9—H9A	0.9900
N1—Pd1^ii	2.020 (15)	C9—H9B	0.9900
O1—Pd1—N2	90.8 (7)	C5—C4—C3	117.6 (18)
O1—Pd1—N1^i	86.5 (5)	C5—C4—C8	124.6 (17)
N2—Pd1—N1^i	177.4 (7)	C3—C4—C8	117.7 (18)
O1—Pd1—Cl1	179.5 (4)	C6—C5—C4	119.7 (17)
N2—Pd1—Cl1	89.4 (6)	C6—C5—C9	120 (2)
N1^i—Pd1—Cl1	93.3 (4)	C4—C5—C9	120 (2)
C3—O1—Pd1	115.8 (11)	N1—C6—C5	123.4 (18)
C9—O2—H2	133.2	N1—C6—H6	118.3
C9—O2—H3	98.3	C5—C6—H6	118.3
H2W—O2W—H3W	107.3	C2—C7—H7A	109.5
H2W—O2W—H4W	126.7	C2—C7—H7B	109.5
H5W—O3W—H6W	110.5	H7A—C7—H7B	109.5
H5W—O3W—H7W	131.6	C2—C7—H7C	109.5
C6—N1—C2	119.3 (15)	H7A—C7—H7C	109.5
C6—N1—Pd1^ii	117.7 (13)	H7B—C7—H7C	109.5
C2—N1—Pd1^ii	123.0 (11)	N2—C8—C4	109.5 (18)
C8—N2—Pd1	116.9 (13)	N2—C8—H8A	109.8
C8—N2—H2A	107.7	C4—C8—H8A	109.8
Pd1—N2—H2A	108.0	N2—C8—H8B	109.8
C8—N2—H2B	108.2	C4—C8—H8B	109.8
Pd1—N2—H2B	108.3	H8A—C8—H8B	108.2
H2A—N2—H2B	107.4	O2—C9—C5	107 (3)
N1—C2—C3	120.5 (14)	O2—C9—H9A	110.3
N1—C2—C7	119.7 (16)	C5—C9—H9A	110.3
C3—C2—C7	119.9 (17)	O2—C9—H9B	110.3
O1—C3—C4	122.7 (16)	C5—C9—H9B	110.3
O1—C3—C2	117.9 (15)	H9A—C9—H9B	108.6
C4—C3—C2	119.4 (17)
N2—Pd1—O1—C3	40.9 (12)	O1—C3—C4—C8	1 (3)
N1^i—Pd1—O1—C3	−139.3 (12)	C2—C3—C4—C8	−179 (2)
O1—Pd1—N2—C8	12.3 (13)	C3—C4—C5—C6	−3 (3)
Cl1—Pd1—N2—C8	−167.3 (13)	C8—C4—C5—C6	−179 (2)
C6—N1—C2—C3	2 (2)	C3—C4—C5—C9	−175 (3)
Pd1^ii—N1—C2—C3	−179.8 (12)	C8—C4—C5—C9	9 (4)
C6—N1—C2—C7	−177.1 (18)	C2—N1—C6—C5	−1 (3)
Pd1^ii—N1—C2—C7	1 (2)	Pd1^ii—N1—C6—C5	−179.1 (17)
Pd1—O1—C3—C4	−54 (2)	C4—C5—C6—N1	1 (3)
Pd1—O1—C3—C2	126.7 (14)	C9—C5—C6—N1	173 (3)
N1—C2—C3—O1	176.1 (16)	Pd1—N2—C8—C4	−57.4 (19)
C7—C2—C3—O1	−5 (3)	C5—C4—C8—N2	−125 (2)
N1—C2—C3—C4	−4 (3)	C3—C4—C8—N2	59 (3)
C7—C2—C3—C4	175.3 (19)	C6—C5—C9—O2	96 (3)
O1—C3—C4—C5	−175.6 (19)	C4—C5—C9—O2	−91 (4)
C2—C3—C4—C5	4 (3)

Symmetry codes: (i) −y+3/4, x−1/4, −z+3/4; (ii) y+1/4, −x+3/4, −z+3/4.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···Cl1^iii	0.90	2.44	3.276 (16)	155
O1W—H1W···O2	0.85	1.65	2.50 (5)	180
N2—H2B···Cl1^iv	0.90	2.64	3.448 (19)	149
O2W—H2W···Cl1^v	0.88	1.99	2.88 (4)	179
O2W—H3W···O3W	0.81	1.86	2.67 (4)	179
O3W—H5W···O1^vi	0.86	1.97	2.84 (2)	179
O3W—H6W···O3W^vii	0.88	2.04	2.92 (5)	180
O3W—H7W···O2W	0.81	1.86	2.67 (4)	179
O2—H2···O1W	0.76	1.74	2.50 (4)	177
O2—H3···O2W	0.87	1.91	2.78 (4)	179

Symmetry codes: (iii) −x+1, −y+3/2, z; (iv) −x+1, −y+1, −z+1; (v) x+1, y, z; (vi) −y+7/4, x+1/4, z+1/4; (vii) −x+2, −y+3/2, z.