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In the mononuclear title complex, [Zn(PMG)2]·2H2O or [Zn(C8H9N2O2)2]·2H2O, the ZnII 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 ZnII center in such a way that the atoms of the same kind are mutually trans to each other, generating a centrosymmetric structure.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536803012364/lh6069sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536803012364/lh6069Isup2.hkl
Contains datablock I

CCDC reference: 217371

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

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ADDSYM reports no extra symmetry








Comment top

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 ZnII 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 ZnII 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 ZnII 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 ZnII 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 Namine, two Npyridyne and two Ocarboxylate) 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—Npyridyne [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: [ZnII(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 ZnII is attached to the pyridine groups. The Zn—Namine distance of 2.1210 (17) Å in the title compound is somewhat shorter but also comparable to the corresponding bonds in the following hexacoordinated ZnII complexes: [Zn(BPA)2]·2H2O, Zn1—Namine = 2.148 (8) Å and Zn2—Namine = 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—Ocarboxylate 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 ZnII complex containing N,O-donor groups which are able to mimic bonded histidine and aspartate/glutamate amino acids in zinc metalloenzymes.

Experimental top

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, CHarom), 8.55 (s, 1H, CHarom). 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.

Refinement top

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 Uiso = 1.2Ueq of the carrier atom. H atoms bonded to N and O atoms were refined independently with isotropic displacement parameters

Computing details top

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 top
[Figure 1] 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 top
Crystal data top
Zn(C8H9N2O2)2]·2H2OF(000) = 448
Mr = 431.75Dx = 1.538 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 25 reflections
a = 9.081 (2) Åθ = 8.3–18.2°
b = 9.480 (2) ŵ = 1.36 mm1
c = 10.834 (2) ÅT = 293 K
β = 91.99 (3)°Irregular block, colourless
V = 932.1 (3) Å30.30 × 0.23 × 0.17 mm
Z = 2
Data collection top
Enraf-Nonius CAD-4
diffractometer
1448 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.015
Graphite monochromatorθmax = 26.0°, θmin = 2.2°
ω–2θ scansh = 1111
Absorption correction: ψ scan
(PLATON; Spek, 1990)
k = 110
Tmin = 0.702, Tmax = 0.794l = 130
1930 measured reflections3 standard reflections every 200 reflections
1827 independent reflections intensity decay: 1%
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.025H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.071 w = 1/[σ2(Fo2) + (0.0342P)2 + 0.3276P]
where P = (Fo2 + 2Fc2)/3
S = 1.03(Δ/σ)max = 0.002
1827 reflectionsΔρmax = 0.26 e Å3
137 parametersΔρmin = 0.30 e Å3
0 restraintsExtinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0109 (13)
Crystal data top
Zn(C8H9N2O2)2]·2H2OV = 932.1 (3) Å3
Mr = 431.75Z = 2
Monoclinic, P21/cMo Kα radiation
a = 9.081 (2) ŵ = 1.36 mm1
b = 9.480 (2) ÅT = 293 K
c = 10.834 (2) Å0.30 × 0.23 × 0.17 mm
β = 91.99 (3)°
Data collection top
Enraf-Nonius CAD-4
diffractometer
1448 reflections with I > 2σ(I)
Absorption correction: ψ scan
(PLATON; Spek, 1990)
Rint = 0.015
Tmin = 0.702, Tmax = 0.7943 standard reflections every 200 reflections
1930 measured reflections intensity decay: 1%
1827 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0250 restraints
wR(F2) = 0.071H atoms treated by a mixture of independent and constrained refinement
S = 1.03Δρmax = 0.26 e Å3
1827 reflectionsΔρmin = 0.30 e Å3
137 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Zn10.50000.00000.00000.03153 (13)
O10.59052 (17)0.14294 (15)0.12405 (13)0.0413 (4)
O20.70146 (17)0.15519 (17)0.30198 (14)0.0466 (4)
N10.72095 (18)0.0702 (2)0.05839 (16)0.0385 (4)
N20.5482 (2)0.14548 (18)0.14175 (16)0.0332 (4)
H2N0.472 (2)0.186 (2)0.168 (2)0.039 (6)*
C10.8144 (3)0.0121 (3)0.1428 (2)0.0501 (6)
H10.78790.07170.18080.060*
C20.9475 (3)0.0725 (3)0.1748 (3)0.0632 (7)
H21.01000.03080.23400.076*
C30.9869 (3)0.1955 (3)0.1179 (3)0.0689 (8)
H31.07640.23850.13860.083*
C40.8933 (3)0.2551 (3)0.0299 (3)0.0581 (7)
H40.91920.33740.01060.070*
C50.7593 (2)0.1896 (2)0.0030 (2)0.0391 (5)
C60.6477 (2)0.2531 (2)0.0864 (2)0.0430 (5)
H6A0.58980.32270.04380.052*
H6B0.69860.30110.15150.052*
C70.6110 (3)0.0679 (2)0.2447 (2)0.0448 (5)
H7A0.70390.11160.26440.054*
H7B0.54500.07760.31660.054*
C80.6377 (2)0.0885 (2)0.22110 (19)0.0339 (4)
O1W0.7173 (3)0.5893 (2)0.0550 (2)0.0681 (6)
H1W0.731 (3)0.602 (3)0.015 (3)0.075 (11)*
H2W0.679 (4)0.667 (4)0.082 (3)0.083 (11)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Zn10.03191 (18)0.02775 (18)0.03502 (19)0.00197 (14)0.00247 (12)0.00329 (15)
O10.0509 (9)0.0288 (8)0.0446 (9)0.0022 (7)0.0088 (7)0.0010 (7)
O20.0492 (9)0.0463 (9)0.0447 (9)0.0008 (7)0.0066 (7)0.0108 (7)
N10.0338 (9)0.0407 (10)0.0406 (9)0.0037 (8)0.0021 (7)0.0020 (9)
N20.0353 (9)0.0262 (8)0.0379 (9)0.0011 (7)0.0015 (7)0.0034 (7)
C10.0406 (12)0.0592 (15)0.0500 (13)0.0001 (11)0.0052 (10)0.0088 (12)
C20.0393 (13)0.082 (2)0.0678 (17)0.0020 (14)0.0141 (12)0.0005 (16)
C30.0364 (13)0.084 (2)0.086 (2)0.0143 (13)0.0093 (13)0.0127 (17)
C40.0450 (13)0.0565 (16)0.0729 (17)0.0175 (12)0.0032 (12)0.0043 (14)
C50.0363 (11)0.0373 (11)0.0440 (11)0.0059 (9)0.0040 (9)0.0061 (10)
C60.0497 (12)0.0291 (11)0.0501 (12)0.0083 (10)0.0016 (10)0.0030 (10)
C70.0597 (15)0.0388 (13)0.0362 (11)0.0025 (11)0.0057 (10)0.0059 (10)
C80.0297 (9)0.0337 (11)0.0380 (11)0.0023 (8)0.0058 (8)0.0049 (9)
O1W0.1018 (17)0.0425 (12)0.0602 (13)0.0059 (11)0.0058 (12)0.0005 (10)
Geometric parameters (Å, º) top
Zn1—O12.0964 (15)C2—C31.373 (4)
Zn1—O1i2.0964 (15)C2—H20.9300
Zn1—N2i2.1210 (17)C3—C41.376 (4)
Zn1—N22.1210 (17)C3—H30.9300
Zn1—N1i2.1864 (17)C4—C51.388 (3)
Zn1—N12.1864 (17)C4—H40.9300
O1—C81.260 (2)C5—C61.504 (3)
O2—C81.240 (2)C6—H6A0.9700
N1—C51.333 (3)C6—H6B0.9700
N1—C11.344 (3)C7—C81.523 (3)
N2—C71.468 (3)C7—H7A0.9700
N2—C61.476 (3)C7—H7B0.9700
N2—H2N0.83 (2)O1W—H1W0.78 (3)
C1—C21.371 (3)O1W—H2W0.86 (4)
C1—H10.9300
O1—Zn1—O1i180.0C1—C2—C3118.8 (2)
O1—Zn1—N2i98.01 (6)C1—C2—H2120.6
O1i—Zn1—N2i81.99 (6)C3—C2—H2120.6
O1—Zn1—N281.99 (6)C2—C3—C4119.7 (2)
O1i—Zn1—N298.01 (6)C2—C3—H3120.1
N2i—Zn1—N2180.0C4—C3—H3120.1
O1—Zn1—N1i89.67 (7)C3—C4—C5118.5 (3)
O1i—Zn1—N1i90.33 (7)C3—C4—H4120.7
N2i—Zn1—N1i78.54 (7)C5—C4—H4120.7
N2—Zn1—N1i101.46 (7)N1—C5—C4121.7 (2)
O1—Zn1—N190.33 (7)N1—C5—C6116.73 (18)
O1i—Zn1—N189.67 (7)C4—C5—C6121.5 (2)
N2i—Zn1—N1101.46 (7)N2—C6—C5111.94 (17)
N2—Zn1—N178.54 (7)N2—C6—H6A109.2
N1i—Zn1—N1180.0C5—C6—H6A109.2
C8—O1—Zn1115.00 (13)N2—C6—H6B109.2
C5—N1—C1119.06 (19)C5—C6—H6B109.2
C5—N1—Zn1112.30 (13)H6A—C6—H6B107.9
C1—N1—Zn1128.59 (16)N2—C7—C8115.08 (17)
C7—N2—C6113.99 (18)N2—C7—H7A108.5
C7—N2—Zn1108.67 (13)C8—C7—H7A108.5
C6—N2—Zn1107.12 (13)N2—C7—H7B108.5
C7—N2—H2N108.4 (15)C8—C7—H7B108.5
C6—N2—H2N108.0 (16)H7A—C7—H7B107.5
Zn1—N2—H2N110.7 (15)O2—C8—O1124.2 (2)
N1—C1—C2122.1 (2)O2—C8—C7116.97 (19)
N1—C1—H1118.9O1—C8—C7118.83 (18)
C2—C1—H1118.9H1W—O1W—H2W104 (3)
Symmetry code: (i) x+1, y, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···O2ii0.83 (2)2.20 (2)2.998 (2)162 (2)
O1W—H1W···O2iii0.78 (3)2.07 (3)2.820 (3)163 (3)
O1W—H2W···O1iv0.86 (4)2.02 (4)2.876 (3)174 (3)
Symmetry codes: (ii) x+1, y+1/2, z1/2; (iii) x, y+1/2, z+1/2; (iv) x, y+1, z.

Experimental details

Crystal data
Chemical formulaZn(C8H9N2O2)2]·2H2O
Mr431.75
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)9.081 (2), 9.480 (2), 10.834 (2)
β (°) 91.99 (3)
V3)932.1 (3)
Z2
Radiation typeMo Kα
µ (mm1)1.36
Crystal size (mm)0.30 × 0.23 × 0.17
Data collection
DiffractometerEnraf-Nonius CAD-4
diffractometer
Absorption correctionψ scan
(PLATON; Spek, 1990)
Tmin, Tmax0.702, 0.794
No. of measured, independent and
observed [I > 2σ(I)] reflections
1930, 1827, 1448
Rint0.015
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.025, 0.071, 1.03
No. of reflections1827
No. of parameters137
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.26, 0.30

Computer programs: CAD-4 EXPRESS (Enraf-Nonius, 1994), SET4 in CAD-4 EXPRESS, HELENA (Spek, 1996), SHELXS97 (Sheldrick, 1990), SHELXL97 (Sheldrick, 1997), ZORTEP (Zsolnai et al., 1996), SHELXL97.

Selected geometric parameters (Å, º) top
Zn1—O12.0964 (15)Zn1—N12.1864 (17)
Zn1—N22.1210 (17)
O1—Zn1—N2i98.01 (6)N2—Zn1—N1i101.46 (7)
O1—Zn1—N281.99 (6)O1—Zn1—N190.33 (7)
O1—Zn1—N1i89.67 (7)N2—Zn1—N178.54 (7)
Symmetry code: (i) x+1, y, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···O2ii0.83 (2)2.20 (2)2.998 (2)162 (2)
O1W—H1W···O2iii0.78 (3)2.07 (3)2.820 (3)163 (3)
O1W—H2W···O1iv0.86 (4)2.02 (4)2.876 (3)174 (3)
Symmetry codes: (ii) x+1, y+1/2, z1/2; (iii) x, y+1/2, z+1/2; (iv) x, y+1, z.
 

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