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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
CCDC reference: 217371
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (C-C) = 0.004 Å
- R factor = 0.025
- wR factor = 0.071
- Data-to-parameter ratio = 13.3
checkCIF results
No syntax errors found
ADDSYM reports no extra symmetry
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.
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
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.
Bis[
N-(2-pyridylmethyl)glycinato]zinc(II) dihydrate
top
Crystal data top
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) Å3 | 0.30 × 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 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 top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.025 | H 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 reflections | Δρmax = 0.26 e Å−3 |
137 parameters | Δρmin = −0.30 e Å−3 |
0 restraints | Extinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0109 (13) |
Crystal data top
Zn(C8H9N2O2)2]·2H2O | V = 932.1 (3) Å3 |
Mr = 431.75 | Z = 2 |
Monoclinic, P21/c | Mo Kα radiation |
a = 9.081 (2) Å | µ = 1.36 mm−1 |
b = 9.480 (2) Å | T = 293 K |
c = 10.834 (2) Å | 0.30 × 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 = 0.794 | 3 standard reflections every 200 reflections |
1930 measured reflections | intensity decay: 1% |
1827 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.025 | 0 restraints |
wR(F2) = 0.071 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | Δρmax = 0.26 e Å−3 |
1827 reflections | Δρmin = −0.30 e Å−3 |
137 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | 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 (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
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) top
Zn1—O1 | 2.0964 (15) | C2—C3 | 1.373 (4) |
Zn1—O1i | 2.0964 (15) | C2—H2 | 0.9300 |
Zn1—N2i | 2.1210 (17) | C3—C4 | 1.376 (4) |
Zn1—N2 | 2.1210 (17) | C3—H3 | 0.9300 |
Zn1—N1i | 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—O1i | 180.0 | C1—C2—C3 | 118.8 (2) |
O1—Zn1—N2i | 98.01 (6) | C1—C2—H2 | 120.6 |
O1i—Zn1—N2i | 81.99 (6) | C3—C2—H2 | 120.6 |
O1—Zn1—N2 | 81.99 (6) | C2—C3—C4 | 119.7 (2) |
O1i—Zn1—N2 | 98.01 (6) | C2—C3—H3 | 120.1 |
N2i—Zn1—N2 | 180.0 | C4—C3—H3 | 120.1 |
O1—Zn1—N1i | 89.67 (7) | C3—C4—C5 | 118.5 (3) |
O1i—Zn1—N1i | 90.33 (7) | C3—C4—H4 | 120.7 |
N2i—Zn1—N1i | 78.54 (7) | C5—C4—H4 | 120.7 |
N2—Zn1—N1i | 101.46 (7) | N1—C5—C4 | 121.7 (2) |
O1—Zn1—N1 | 90.33 (7) | N1—C5—C6 | 116.73 (18) |
O1i—Zn1—N1 | 89.67 (7) | C4—C5—C6 | 121.5 (2) |
N2i—Zn1—N1 | 101.46 (7) | N2—C6—C5 | 111.94 (17) |
N2—Zn1—N1 | 78.54 (7) | N2—C6—H6A | 109.2 |
N1i—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) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N···O2ii | 0.83 (2) | 2.20 (2) | 2.998 (2) | 162 (2) |
O1W—H1W···O2iii | 0.78 (3) | 2.07 (3) | 2.820 (3) | 163 (3) |
O1W—H2W···O1iv | 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. |
Experimental details
Crystal data |
Chemical formula | Zn(C8H9N2O2)2]·2H2O |
Mr | 431.75 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 9.081 (2), 9.480 (2), 10.834 (2) |
β (°) | 91.99 (3) |
V (Å3) | 932.1 (3) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 1.36 |
Crystal size (mm) | 0.30 × 0.23 × 0.17 |
|
Data collection |
Diffractometer | Enraf-Nonius CAD-4 diffractometer |
Absorption correction | ψ scan (PLATON; Spek, 1990) |
Tmin, Tmax | 0.702, 0.794 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 1930, 1827, 1448 |
Rint | 0.015 |
(sin θ/λ)max (Å−1) | 0.617 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.025, 0.071, 1.03 |
No. of reflections | 1827 |
No. of parameters | 137 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.26, −0.30 |
Selected geometric parameters (Å, º) topZn1—O1 | 2.0964 (15) | Zn1—N1 | 2.1864 (17) |
Zn1—N2 | 2.1210 (17) | | |
| | | |
O1—Zn1—N2i | 98.01 (6) | N2—Zn1—N1i | 101.46 (7) |
O1—Zn1—N2 | 81.99 (6) | O1—Zn1—N1 | 90.33 (7) |
O1—Zn1—N1i | 89.67 (7) | N2—Zn1—N1 | 78.54 (7) |
Symmetry code: (i) −x+1, −y, −z. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N···O2ii | 0.83 (2) | 2.20 (2) | 2.998 (2) | 162 (2) |
O1W—H1W···O2iii | 0.78 (3) | 2.07 (3) | 2.820 (3) | 163 (3) |
O1W—H2W···O1iv | 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. |
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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.