Bis­[N-(2-pyridyl­methyl)­glycinato]­zinc(II) dihydrate

In the mononuclear title complex, [Zn(PMG)₂]·2H₂O or [Zn(C₈H₉N₂O₂)₂]·2H₂O, the Zn^II center is surrounded by two N-(2-pyridyl­methyl)­glycinate (PMG) ligands, which impose a distorted octahedral environment on the metal. Two deprotonated mol­ecules of the new tridentate N,N',O-donor ligand HPMG are facially coordinated to the Zn^II center in such a way that the atoms of the same kind are mutually trans to each other, generating a centrosymmetric structure.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.025
• wR factor = 0.071
• Data-to-parameter ratio = 13.3

checkCIF results

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ADDSYM reports no extra symmetry

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S1. Comment

Zinc complexes are of great interest in organic synthesis and in bioinorganic chemistry. In the former, zinc complexes are used in stereospecific organic reactions (Lebel et al., 2003; Abufarag & Vahrenkamp, 1995a). In bioinorganic chemistry, it is well known that zinc plays an important role in many biological processes (Kimura, 1994; Valee & Auld, 1993; Uhlenbrock et al., 1996), so that Zn^II coordinated to a strategic ligand can lead to a structural and/or functional model for zinc metalloenzymes.

Modelling the metal binding site of zinc metalloenzymes is a goal that has been pursued by bioinorganic chemists over the past few years. Studies on the coordination chemistry of Zn^II with carboxylate ligands have aroused a growing interest during the last decade in view of the biological modelling applications (Chen & Tong, 1994; Sun et al., 2001; Vaira et al., 1998; Abufarag & Vahrenkamp, 1995b). Several zinc model complexes have been developed (Barbarin et al., 1994; Vaira et al., 1998; Abufarag & Vahrenkamp, 1995). However, one of the difficulties of the model approach is the synthesis of complexes with biologically relevant ligands. Thus, synthetic strategies employing pyridine and carboxylate groups to design new ligands have been focused on mimicking the histidine and aspartate amino acids, which are present in a large number of metalloenzymes (Chen & Tong, 1994; Neves et al., 1997; Riesen et al., 1991).

Some carboxylate derivatives, which have two N atoms of pyridine or amine moieties and one O atom of a carboxylate group have been previously reported e.g. N,N-bis(2-picolyl)-β-alanine (Hazell et al., 1993), N,N-bis(2-aminoethyl)glycine (Mao et al., 1992) and N,N-bis(2-picolyl)glycine (BPG; Cox et al., 1988). In attempts to model zinc enzymes, the octahedral complex [Zn(BPG)(H₂O)₂]NO₃·H₂O may be considered a structural model for the reactive center of the glyoxalase I enzyme, which according to spectroscopic data contains a hexacoordinate zinc ion bonded to an N,O-donor set (Abufarag & Vahrenkamp, 1995b).

In this report, we present the synthesis of the new ligand N-(2-pyridylmethyl)glycine (HPMG) and and the first crystal structure of its Zn^II mononuclear complex, [Zn(PMG)₂]·2H₂O, (I), as a further interesting model for mononuclear zinc-containing enzymes.

The molecular structure of the title complex consists of a neutral Zn(PMG)₂ unit and two water molecules of crystallization. In the crystal structure of (I), the Zn atom is located on a special position, lying at a center of symmetry, so that the two PMG⁻ ligands in the coordination sphere of the metal ion are related by symmetry. The deprotonated PMG⁻ ligands are facially coordinated to the Zn^II ion through the two N– (amine and pyridyne) and one O-atom (carboxylate) donors (Fig. 1). Since the molecule of Zn(PMG)₂ is centrosymmetric, the atoms of the same nature (two N_amine, two N_pyridyne and two O_carboxylate) are coordinated in trans positions with respect to each other. The cis angles O1—Zn1—N2 [81.99 (6)°] and N2—Zn1—N1 [78.54 (7)°] are significantly smaller than the ideal octahedral angle of 90° (Table 1). These angles reflect the restriction imposed by formation of the five-membered chelate rings and also reflect the distortion in the octahedral environment around of the metal center.

The bond length Zn—N_pyridyne [2.1864 (17) Å] is the longest in the coordination sphere in Zn(PMG)₂ and is similar to those observed in other octahedral zinc complexes: [Zn^II(BPA)₂]·2H₂O, average 2.163 Å (Neves et al., 1997), where BPA is bis[(2-hydroxybenzyl)(2-methylpyridyl)amine]; [Zn(BPG)(H₂O)₂]NO₃·H₂O, average 2.120 Å (Abufarag & Vahrenkamp, 1995b); Zn(TETAH₂)·4H₂O, average 2.181 Å (Riesen et al., 1991), where TETA is 1,4,8,11-tetraazacyclotetradecane-N,N',N'',N'''-tetraacetic acid; [ZnL]ClO₄·H₂O, average 2.077 Å (Vaira et al., 1998), where L is 1,4-bis-(1-methylimidazol-2-ylmethyl)-7-carboxymethyl-1,4,7-triazacyclononane); and [Zn(bipyridine)₃](ClO₄)₂, average 2.157 Å (Chen et al., 1995), in which the Zn^II is attached to the pyridine groups. The Zn—N_amine distance of 2.1210 (17) Å in the title compound is somewhat shorter but also comparable to the corresponding bonds in the following hexacoordinated Zn^II complexes: [Zn(BPA)₂]·2H₂O, Zn1—N_amine = 2.148 (8) Å and Zn2—N_amine = 2.186 (7) Å (Neves et al., 1997); and [Zn(BPG)(H₂O)₂]NO₃·H₂O, average 2.198 Å (Abufarag & Vahrenkamp, 1995b). The unique Zn—O_carboxylate bond length in Zn(PMG)₂ is 2.0964 (15) Å, which is shorter than those generally found in other octahedral complexes, such as 2.135 (2) Å (Abufarag & Vahrenkamp, 1995b) and 2.127 Å (Riesen et al., 1991).

An extensive hydrogen-bond network is observed in the three-dimensional packing of (I). The water molecules and amine groups are hydrogen bonded to neighboring molecules forming infinite two-dimensional aggregations that are parallel to the (100) plane. In this intricate arrangement the protonated groups (water and amine) only act as proton donors, while the O atoms from carboxylate moieties are the proton acceptors. Geometric parameters of the hydrogen-bond network are listed in Table 2.

In summary, we have synthesized and structurally characterized a new mononuclear Zn^II complex containing N,O-donor groups which are able to mimic bonded histidine and aspartate/glutamate amino acids in zinc metalloenzymes.

S2. Experimental

The HPMG ligand was prepared in high yield by a condensation reaction between a methanolic solution of glycine (1.27 g, 17 mmol), previously neutralized with LiOH (1.42 g, 17 mmol) and 2-pyridinecarboxaldehyde (1.82 g, 17 mmol). The reaction mixture was stirred for 2 h at 273 K. The solvent was evaporated and water (50 ml) was added, the pH was adjusted to 7.0 with 1 M HCl and the aqueous phase was extracted with three 50 ml portions of CH₂Cl₂ and the extracts were combined, dried over anhydrous MgSO₄, filtered off and evaporated. The oily residue was dissolved in methanolic solution and then reduced by catalytic hydrogenation (Pd/C 5%) for 24 h. The catalyst was filtered off and the resulting solution was evaporated under reduced pressure, yielding a clear oil that was used without further purification (yield 2.82 g, 100%). Spectroscopic analysis: ¹H NMR (CDCl₃ + D₂O, δ, p.p.m): 3.46 (s, 2H, CH₂), 3.94 (s, 2H, CH₂), 7.14–7.69 (m, 3H, CH_arom), 8.55 (s, 1H, CH_arom). The zinc complex was obtained by addition of one equivalent of [Zn(CH₃CO₂)₂]·2H₂O to a methanolic solution containing two equivalents of HPMG, affording a colourless solution. From slow evaporation of the solvent, crystals of Zn(PMG)₂·2H₂O suitable for X-ray analysis were obtained.

S3. Refinement

H atoms bonded to C atoms were placed in calculated positions with C—H distances ranging rom 0.93 to 0.97 Å and included in the refinement in riding-motion approximation with U_iso = 1.2U_eq of the carrier atom. H atoms bonded to N and O atoms were refined independently with isotropic displacement parameters

Computing details

Data collection: CAD-4 EXPRESS (Enraf-Nonius, 1994); cell refinement: SET4 in CAD-4 EXPRESS; data reduction: HELENA (Spek, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ZORTEP (Zsolnai et al., 1996); software used to prepare material for publication: SHELXL97.

Figures

Fig. 1. A view of the structure of (I) with the atom-labeling scheme. Ellipsoids are shown at the 40% probability level. H atoms have been omitted. [Symmetry code: (i) −x + 1, −y, −z.]

Bis[N-(2-pyridylmethyl)glycinato]zinc(II) dihydrate

Crystal data

Zn(C8H9N2O2)2]·2H2O	F(000) = 448
Mr = 431.75	Dx = 1.538 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 25 reflections
a = 9.081 (2) Å	θ = 8.3–18.2°
b = 9.480 (2) Å	µ = 1.36 mm^−1
c = 10.834 (2) Å	T = 293 K
β = 91.99 (3)°	Irregular block, colourless
V = 932.1 (3) Å^3	0.30 × 0.23 × 0.17 mm
Z = 2

Data collection

Enraf-Nonius CAD-4 diffractometer	1448 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.015
Graphite monochromator	θmax = 26.0°, θmin = 2.2°
ω–2θ scans	h = −11→11
Absorption correction: ψ scan (PLATON; Spek, 1990)	k = −11→0
Tmin = 0.702, Tmax = 0.794	l = −13→0
1930 measured reflections	3 standard reflections every 200 reflections
1827 independent reflections	intensity decay: 1%

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.025	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.071	w = 1/[σ^2(Fo^2) + (0.0342P)^2 + 0.3276P] where P = (Fo^2 + 2Fc^2)/3
S = 1.03	(Δ/σ)max = 0.002
1827 reflections	Δρmax = 0.26 e Å^−3
137 parameters	Δρmin = −0.30 e Å^−3
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0109 (13)

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
Zn1	0.5000	0.0000	0.0000	0.03153 (13)
O1	0.59052 (17)	−0.14294 (15)	−0.12405 (13)	0.0413 (4)
O2	0.70146 (17)	−0.15519 (17)	−0.30198 (14)	0.0466 (4)
N1	0.72095 (18)	0.0702 (2)	0.05839 (16)	0.0385 (4)
N2	0.5482 (2)	0.14548 (18)	−0.14175 (16)	0.0332 (4)
H2N	0.472 (2)	0.186 (2)	−0.168 (2)	0.039 (6)*
C1	0.8144 (3)	0.0121 (3)	0.1428 (2)	0.0501 (6)
H1	0.7879	−0.0717	0.1808	0.060*
C2	0.9475 (3)	0.0725 (3)	0.1748 (3)	0.0632 (7)
H2	1.0100	0.0308	0.2340	0.076*
C3	0.9869 (3)	0.1955 (3)	0.1179 (3)	0.0689 (8)
H3	1.0764	0.2385	0.1386	0.083*
C4	0.8933 (3)	0.2551 (3)	0.0299 (3)	0.0581 (7)
H4	0.9192	0.3374	−0.0106	0.070*
C5	0.7593 (2)	0.1896 (2)	0.0030 (2)	0.0391 (5)
C6	0.6477 (2)	0.2531 (2)	−0.0864 (2)	0.0430 (5)
H6A	0.5898	0.3227	−0.0438	0.052*
H6B	0.6986	0.3011	−0.1515	0.052*
C7	0.6110 (3)	0.0679 (2)	−0.2447 (2)	0.0448 (5)
H7A	0.7039	0.1116	−0.2644	0.054*
H7B	0.5450	0.0776	−0.3166	0.054*
C8	0.6377 (2)	−0.0885 (2)	−0.22110 (19)	0.0339 (4)
O1W	0.7173 (3)	0.5893 (2)	−0.0550 (2)	0.0681 (6)
H1W	0.731 (3)	0.602 (3)	0.015 (3)	0.075 (11)*
H2W	0.679 (4)	0.667 (4)	−0.082 (3)	0.083 (11)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Zn1	0.03191 (18)	0.02775 (18)	0.03502 (19)	−0.00197 (14)	0.00247 (12)	0.00329 (15)
O1	0.0509 (9)	0.0288 (8)	0.0446 (9)	0.0022 (7)	0.0088 (7)	0.0010 (7)
O2	0.0492 (9)	0.0463 (9)	0.0447 (9)	0.0008 (7)	0.0066 (7)	−0.0108 (7)
N1	0.0338 (9)	0.0407 (10)	0.0406 (9)	−0.0037 (8)	−0.0021 (7)	0.0020 (9)
N2	0.0353 (9)	0.0262 (8)	0.0379 (9)	0.0011 (7)	−0.0015 (7)	0.0034 (7)
C1	0.0406 (12)	0.0592 (15)	0.0500 (13)	−0.0001 (11)	−0.0052 (10)	0.0088 (12)
C2	0.0393 (13)	0.082 (2)	0.0678 (17)	0.0020 (14)	−0.0141 (12)	0.0005 (16)
C3	0.0364 (13)	0.084 (2)	0.086 (2)	−0.0143 (13)	−0.0093 (13)	−0.0127 (17)
C4	0.0450 (13)	0.0565 (16)	0.0729 (17)	−0.0175 (12)	0.0032 (12)	−0.0043 (14)
C5	0.0363 (11)	0.0373 (11)	0.0440 (11)	−0.0059 (9)	0.0040 (9)	−0.0061 (10)
C6	0.0497 (12)	0.0291 (11)	0.0501 (12)	−0.0083 (10)	0.0016 (10)	0.0030 (10)
C7	0.0597 (15)	0.0388 (13)	0.0362 (11)	0.0025 (11)	0.0057 (10)	0.0059 (10)
C8	0.0297 (9)	0.0337 (11)	0.0380 (11)	−0.0023 (8)	−0.0058 (8)	−0.0049 (9)
O1W	0.1018 (17)	0.0425 (12)	0.0602 (13)	0.0059 (11)	0.0058 (12)	−0.0005 (10)

Geometric parameters (Å, º)

Zn1—O1	2.0964 (15)	C2—C3	1.373 (4)
Zn1—O1^i	2.0964 (15)	C2—H2	0.9300
Zn1—N2^i	2.1210 (17)	C3—C4	1.376 (4)
Zn1—N2	2.1210 (17)	C3—H3	0.9300
Zn1—N1^i	2.1864 (17)	C4—C5	1.388 (3)
Zn1—N1	2.1864 (17)	C4—H4	0.9300
O1—C8	1.260 (2)	C5—C6	1.504 (3)
O2—C8	1.240 (2)	C6—H6A	0.9700
N1—C5	1.333 (3)	C6—H6B	0.9700
N1—C1	1.344 (3)	C7—C8	1.523 (3)
N2—C7	1.468 (3)	C7—H7A	0.9700
N2—C6	1.476 (3)	C7—H7B	0.9700
N2—H2N	0.83 (2)	O1W—H1W	0.78 (3)
C1—C2	1.371 (3)	O1W—H2W	0.86 (4)
C1—H1	0.9300
O1—Zn1—O1^i	180.0	C1—C2—C3	118.8 (2)
O1—Zn1—N2^i	98.01 (6)	C1—C2—H2	120.6
O1^i—Zn1—N2^i	81.99 (6)	C3—C2—H2	120.6
O1—Zn1—N2	81.99 (6)	C2—C3—C4	119.7 (2)
O1^i—Zn1—N2	98.01 (6)	C2—C3—H3	120.1
N2^i—Zn1—N2	180.0	C4—C3—H3	120.1
O1—Zn1—N1^i	89.67 (7)	C3—C4—C5	118.5 (3)
O1^i—Zn1—N1^i	90.33 (7)	C3—C4—H4	120.7
N2^i—Zn1—N1^i	78.54 (7)	C5—C4—H4	120.7
N2—Zn1—N1^i	101.46 (7)	N1—C5—C4	121.7 (2)
O1—Zn1—N1	90.33 (7)	N1—C5—C6	116.73 (18)
O1^i—Zn1—N1	89.67 (7)	C4—C5—C6	121.5 (2)
N2^i—Zn1—N1	101.46 (7)	N2—C6—C5	111.94 (17)
N2—Zn1—N1	78.54 (7)	N2—C6—H6A	109.2
N1^i—Zn1—N1	180.0	C5—C6—H6A	109.2
C8—O1—Zn1	115.00 (13)	N2—C6—H6B	109.2
C5—N1—C1	119.06 (19)	C5—C6—H6B	109.2
C5—N1—Zn1	112.30 (13)	H6A—C6—H6B	107.9
C1—N1—Zn1	128.59 (16)	N2—C7—C8	115.08 (17)
C7—N2—C6	113.99 (18)	N2—C7—H7A	108.5
C7—N2—Zn1	108.67 (13)	C8—C7—H7A	108.5
C6—N2—Zn1	107.12 (13)	N2—C7—H7B	108.5
C7—N2—H2N	108.4 (15)	C8—C7—H7B	108.5
C6—N2—H2N	108.0 (16)	H7A—C7—H7B	107.5
Zn1—N2—H2N	110.7 (15)	O2—C8—O1	124.2 (2)
N1—C1—C2	122.1 (2)	O2—C8—C7	116.97 (19)
N1—C1—H1	118.9	O1—C8—C7	118.83 (18)
C2—C1—H1	118.9	H1W—O1W—H2W	104 (3)

Symmetry code: (i) −x+1, −y, −z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2N···O2^ii	0.83 (2)	2.20 (2)	2.998 (2)	162 (2)
O1W—H1W···O2^iii	0.78 (3)	2.07 (3)	2.820 (3)	163 (3)
O1W—H2W···O1^iv	0.86 (4)	2.02 (4)	2.876 (3)	174 (3)

Symmetry codes: (ii) −x+1, y+1/2, −z−1/2; (iii) x, −y+1/2, z+1/2; (iv) x, y+1, z.