(Glycylglycinato-[kappa]³O,N,N')(2-methyl-1H-benzimidazole-[kappa]N³)copper(II) trihydrate

In the title compound, [Cu(C₄H₆N₂O₃)(C₈H₈N₂)]·3H₂O, the Cu^II atom is coordinated in a square-planar manner by one O atom and three N atoms from glycylglycinate and 2-methyl­benzimidazole ligands. The ternary complexes assemble into one-dimensional chains through C-H...[pi] inter­actions and direct N-H...O hydrogen bonding, as well as into hydrogen-bonded water helices with branches which also link the complex chains into a three-dimensional supra­molecular structure.

S1. Comment

Dipeptide metal complexes have attracted interest because they can act as model complexes to study metal–protein interactions (Tasiopoulos et al., 1998, 2000, 2002). Some ternary complexes of metal ions with peptides and other ligands can cleave DNA (García-Raso et al., 2003). To date, many crystal structures of peptide–metal complexes have been studied, with some of them investigated for their magnetic properties (García-Raso et al., 1998, 2002). As peptide–metal complexes can form abundant hydrogen bonds, by which the complexes possibly interact with proteins and further affect their structures and functions, the strutures and weak interactions of peptide–metal complexes have attracted our interest. During our experiment, the title compound, (I), [Cu(gg)(mbenz)]·3H₂O (H₂gg is glycylglycine and mbenz is 2-methylbenzimidazole), was synthesized and its crystal structure was determined.

Some features of the molecular geometry of (I) are listed in Table 1, and the molecular conformation is illustrated in Fig. 1. Compound (I) consists of a ternary complex and three water molecules. In the ternary complex, Cu is coordinated by one O atom and three N atoms, i.e. with the glycylglycinate ligand providing one O and two N atoms and the methylbenzimidazole ligand providing one N atom, forming a square-planar geometry. This square-planar coordination environment is in good agreement with that of compound (II), [Cu(gg)(bzim)]·3H₂O (bzim is benzimidazole; García-Raso et al., 1996). However, in (I), due to the steric effect of the methyl group of the 2-methylbenzimidazole ligand, the glycylglycinate (N1/N2/O1–O3/C1–C4) and 2-methylbenzimidazole (N3/N4/C5–C12) ligands are twisted with a dihedral angle of 53.8 (1)°, in contrast with (II), where the dihedral angle is 19.0 (1)°.

The supramolecular interactions in (I) are listed in Table 2 and illustrated in Fig. 2. The ternary complexes assemble in an antiparallel and alternating fashion into one-dimensional chains along the b axis through C—H···π interactions and N—H···O hydrogen bonds (N1—H1B···O2^v; see Table 2) between neighbouring complexes, as well as water chains (Fig. 2) which also link the one-dimensional complex chains into a three-dimensional supramolecular structure. The two C—H···π (C1—H···Cg1^v and C3—H···Cg1ⁱ) interactions are obviously different from what was seen in (II), where only the water chains take part in constructing one-dimensional chains of the [Cu(gg)(bzim)] complexes. Evidently, the C—H···π interactions and direct hydrogen bonding result from the conformational change, i.e. the larger twist between the peptide and benzimidazole groups in (I) than in (II), because of the steric effect of the methyl group of 2-methylbenzimidazole. This steric effect also changes the arrangement of the water molecules. In (I), the three water molecules are hydrogen bonded into a water helix with branches (Fig. 2), instead of the smooth helix in (II). Therefore, the steric effect of a methyl group can affect the molecular structure, which further changes the packing mode of the complexes in the crystal.

S2. Experimental

Aquaglyclyglycinatocopper(II) was synthesized according to the method of Sato et al. (1986). Compound (I) was synthesized by adding 2-methylbenzimidazole (0.53 mmol) to a hot aqueous solution (20 ml) of aquoglyclyglycinatocopper(II) (0.52 mmol), stirring the mixture at 353 K for 30 min, cooling to room temperature with stirring overnight, and filtering. Purple crystals of (I) were obtained from the filtrate at room temperature over a period of 10 d (yield 42.9%).

S3. Refinement

H atoms attached to C and N atoms were placed in geometrically idealized positions, with Csp²—H = 0.93, Csp³(methyl)—H = 0.96, Csp³(methylene)—H = 0.97, Nsp²—H = 0.86 and Nsp³—H = 0.90 Å, and constrained to ride on their parent atoms, with U_iso(H) = 1.2U_eq(C,N), or 1.5U_eq(C) for methyl H. H atoms attached to O atoms were located in a difference Fourier map and refined with a global U_iso value = ?. The O—H distances are in the range 0.85(s.u.?)–0.87(s.u.?) Å.

Computing details

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL/PC (Sheldrick, 1999); software used to prepare material for publication: SHELXTL/PC.

Figures

	Fig. 1. The structure of (I), with displacement ellipsoids drawn at the 30% probability level. Dotted lines indicate hydrogen bonds.
	Fig. 2. The one-dimensional complex chain built from C—H···π interactions (dashed lines) and direct hydrogen bonding (dotted lines). The hydrogen-bonded water helix with branches is also shown. H atoms not involved in the hydrogen bonding have been omitted for clarity.

(Glycylglycinato-κ³O,N,N')(2-methyl-1H-benzimidazole-κN³)copper(II) trihydrate

Crystal data

[Cu(C4H6N2O3)(C8H8N2)]·3H2O	F(000) = 788
Mr = 379.86	Dx = 1.615 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2224 reflections
a = 13.094 (5) Å	θ = 2.2–26.4°
b = 7.840 (3) Å	µ = 1.44 mm^−1
c = 18.854 (5) Å	T = 298 K
β = 126.182 (18)°	Needle, purple
V = 1562.2 (9) Å^3	0.40 × 0.10 × 0.03 mm
Z = 4

Data collection

Bruker SMART 1K CCD area-detector diffractometer	2754 independent reflections
Radiation source: fine-focus sealed tube	2461 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.041
ω scans	θmax = 25.0°, θmin = 1.9°
Absorption correction: multi-scan (SADABS; Sheldrick, 2000)	h = −15→12
Tmin = 0.598, Tmax = 0.958	k = −7→9
6158 measured reflections	l = −22→22

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)] = 0.060	Hydrogen site location: water H atoms from ΔF, others placed geometrically
wR(F^2) = 0.127	H-atom parameters constrained
S = 1.23	w = 1/[σ^2(Fo^2) + (0.0372P)^2 + 2.2578P] where P = (Fo^2 + 2Fc^2)/3
2754 reflections	(Δ/σ)max = 0.002
209 parameters	Δρmax = 0.50 e Å^−3
0 restraints	Δρmin = −0.44 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
Cu1	0.08222 (5)	0.96255 (7)	0.79252 (3)	0.02617 (19)
N1	0.2370 (3)	1.0796 (5)	0.8176 (2)	0.0332 (9)
H1A	0.2738	1.0130	0.7997	0.040*
H1B	0.2146	1.1783	0.7875	0.040*
N2	0.1663 (4)	0.9875 (5)	0.9145 (2)	0.0295 (9)
N3	−0.0182 (3)	0.9284 (5)	0.6649 (2)	0.0283 (9)
N4	−0.0842 (3)	0.8626 (5)	0.5303 (2)	0.0306 (9)
H4	−0.0829	0.8233	0.4882	0.037*
C1	0.3278 (4)	1.1141 (6)	0.9125 (3)	0.0347 (11)
H1C	0.3398	1.2363	0.9219	0.042*
H1D	0.4089	1.0635	0.9339	0.042*
C2	0.2826 (4)	1.0430 (6)	0.9642 (3)	0.0320 (10)
C3	0.1083 (4)	0.9057 (6)	0.9514 (3)	0.0332 (11)
H3A	0.0986	0.9869	0.9859	0.040*
H3B	0.1609	0.8124	0.9895	0.040*
C4	−0.0198 (4)	0.8391 (6)	0.8762 (3)	0.0308 (10)
C5	0.1361 (4)	0.7816 (7)	0.6481 (3)	0.0416 (13)
H5A	0.1833	0.8596	0.6384	0.062*
H5B	0.1228	0.6773	0.6170	0.062*
H5C	0.1826	0.7582	0.7098	0.062*
C6	0.0125 (4)	0.8582 (6)	0.6157 (3)	0.0281 (10)
C7	−0.1860 (4)	0.9405 (5)	0.5206 (3)	0.0281 (10)
C8	−0.1437 (4)	0.9847 (5)	0.6059 (3)	0.0265 (10)
C9	−0.2236 (5)	1.0672 (6)	0.6206 (3)	0.0330 (11)
H9	−0.1973	1.0945	0.6771	0.040*
C10	−0.3431 (5)	1.1068 (6)	0.5481 (3)	0.0387 (12)
H10	−0.3980	1.1637	0.5560	0.046*
C11	−0.3848 (5)	1.0640 (7)	0.4628 (3)	0.0439 (13)
H11	−0.4665	1.0930	0.4155	0.053*
C12	−0.3074 (5)	0.9804 (6)	0.4477 (3)	0.0402 (12)
H12	−0.3349	0.9516	0.3911	0.048*
O1	0.3546 (3)	1.0411 (5)	1.0458 (2)	0.0483 (9)
O2	−0.0505 (3)	0.8550 (4)	0.79906 (19)	0.0340 (8)
O3	−0.0908 (3)	0.7732 (5)	0.8918 (2)	0.0433 (9)
O4	0.4209 (4)	0.6322 (5)	0.6971 (3)	0.0632 (11)
H41	0.3816	0.5922	0.6454	0.095*
H42	0.4995	0.6106	0.7256	0.095*
O5	0.4109 (3)	0.8257 (5)	0.8262 (2)	0.0598 (11)
H51	0.4882	0.8457	0.8672	0.090*
H52	0.4057	0.7806	0.7831	0.090*
O6	0.3595 (4)	0.3170 (6)	0.7410 (3)	0.0764 (14)
H61	0.2796	0.3109	0.7038	0.115*
H62	0.3851	0.4132	0.7339	0.115*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cu1	0.0256 (3)	0.0332 (3)	0.0188 (3)	−0.0024 (2)	0.0126 (2)	−0.0011 (2)
N1	0.031 (2)	0.037 (2)	0.033 (2)	−0.0042 (17)	0.0193 (19)	0.0051 (17)
N2	0.033 (2)	0.030 (2)	0.023 (2)	−0.0035 (17)	0.0154 (18)	−0.0033 (16)
N3	0.030 (2)	0.033 (2)	0.024 (2)	−0.0032 (16)	0.0176 (18)	−0.0001 (16)
N4	0.038 (2)	0.038 (2)	0.022 (2)	−0.0027 (18)	0.0213 (19)	−0.0060 (17)
C1	0.028 (2)	0.036 (3)	0.032 (3)	−0.003 (2)	0.014 (2)	−0.005 (2)
C2	0.034 (3)	0.026 (2)	0.025 (3)	0.002 (2)	0.011 (2)	−0.002 (2)
C3	0.037 (3)	0.039 (3)	0.024 (2)	0.000 (2)	0.018 (2)	−0.001 (2)
C4	0.036 (3)	0.031 (3)	0.025 (2)	0.004 (2)	0.018 (2)	0.007 (2)
C5	0.033 (3)	0.061 (4)	0.030 (3)	0.008 (2)	0.018 (2)	−0.001 (2)
C6	0.027 (2)	0.036 (3)	0.024 (2)	−0.004 (2)	0.016 (2)	−0.001 (2)
C7	0.034 (2)	0.026 (2)	0.027 (2)	−0.0035 (19)	0.019 (2)	−0.0019 (19)
C8	0.028 (2)	0.025 (2)	0.024 (2)	−0.0101 (18)	0.014 (2)	−0.0041 (18)
C9	0.040 (3)	0.030 (3)	0.033 (3)	−0.001 (2)	0.023 (2)	−0.003 (2)
C10	0.036 (3)	0.038 (3)	0.045 (3)	0.005 (2)	0.025 (3)	0.003 (2)
C11	0.029 (3)	0.054 (3)	0.035 (3)	−0.004 (2)	0.011 (2)	0.005 (2)
C12	0.036 (3)	0.048 (3)	0.023 (3)	−0.005 (2)	0.009 (2)	0.001 (2)
O1	0.044 (2)	0.059 (2)	0.0205 (19)	−0.0082 (18)	0.0067 (17)	−0.0001 (17)
O2	0.0309 (17)	0.050 (2)	0.0202 (16)	−0.0085 (15)	0.0144 (15)	0.0001 (15)
O3	0.0381 (19)	0.066 (3)	0.0300 (19)	−0.0058 (18)	0.0225 (17)	0.0100 (17)
O4	0.067 (3)	0.072 (3)	0.058 (3)	0.002 (2)	0.041 (2)	−0.006 (2)
O5	0.037 (2)	0.086 (3)	0.052 (3)	−0.003 (2)	0.024 (2)	−0.020 (2)
O6	0.052 (3)	0.092 (4)	0.066 (3)	0.001 (2)	0.024 (2)	0.027 (3)

Geometric parameters (Å, º)

Cu1—N2	1.884 (4)	C4—O2	1.265 (5)
Cu1—N3	1.964 (4)	C5—C6	1.480 (6)
Cu1—O2	1.999 (3)	C5—H5A	0.9600
Cu1—N1	2.011 (4)	C5—H5B	0.9600
N1—C1	1.476 (6)	C5—H5C	0.9600
N1—H1A	0.9000	C7—C12	1.391 (7)
N1—H1B	0.9000	C7—C8	1.400 (6)
N2—C2	1.305 (6)	C8—C9	1.391 (6)
N2—C3	1.449 (6)	C9—C10	1.374 (7)
N3—C6	1.328 (5)	C9—H9	0.9300
N3—C8	1.404 (6)	C10—C11	1.401 (7)
N4—C6	1.338 (5)	C10—H10	0.9300
N4—C7	1.377 (6)	C11—C12	1.370 (7)
N4—H4	0.8600	C11—H11	0.9300
C1—C2	1.513 (6)	C12—H12	0.9300
C1—H1C	0.9700	O4—H41	0.8493
C1—H1D	0.9700	O4—H42	0.8511
C2—O1	1.243 (5)	O5—H51	0.8506
C3—C4	1.513 (6)	O5—H52	0.8505
C3—H3A	0.9700	O6—H61	0.8502
C3—H3B	0.9700	O6—H62	0.8672
C4—O3	1.241 (5)
N2—Cu1—N3	174.91 (15)	H3A—C3—H3B	108.4
N2—Cu1—O2	82.62 (14)	O3—C4—O2	122.7 (4)
N3—Cu1—O2	92.31 (13)	O3—C4—C3	119.5 (4)
N2—Cu1—N1	83.35 (16)	O2—C4—C3	117.9 (4)
N3—Cu1—N1	101.72 (15)	C6—C5—H5A	109.5
O2—Cu1—N1	165.96 (14)	C6—C5—H5B	109.5
C1—N1—Cu1	110.3 (3)	H5A—C5—H5B	109.5
C1—N1—H1A	109.6	C6—C5—H5C	109.5
Cu1—N1—H1A	109.6	H5A—C5—H5C	109.5
C1—N1—H1B	109.6	H5B—C5—H5C	109.5
Cu1—N1—H1B	109.6	N3—C6—N4	111.6 (4)
H1A—N1—H1B	108.1	N3—C6—C5	126.1 (4)
C2—N2—C3	121.6 (4)	N4—C6—C5	122.3 (4)
C2—N2—Cu1	120.3 (3)	N4—C7—C12	133.1 (4)
C3—N2—Cu1	116.5 (3)	N4—C7—C8	105.2 (4)
C6—N3—C8	105.8 (4)	C12—C7—C8	121.7 (4)
C6—N3—Cu1	130.7 (3)	C9—C8—C7	120.6 (4)
C8—N3—Cu1	123.5 (3)	C9—C8—N3	130.9 (4)
C6—N4—C7	108.9 (4)	C7—C8—N3	108.5 (4)
C6—N4—H4	125.5	C10—C9—C8	117.1 (4)
C7—N4—H4	125.5	C10—C9—H9	121.4
N1—C1—C2	111.9 (4)	C8—C9—H9	121.4
N1—C1—H1C	109.2	C9—C10—C11	122.1 (5)
C2—C1—H1C	109.2	C9—C10—H10	119.0
N1—C1—H1D	109.2	C11—C10—H10	119.0
C2—C1—H1D	109.2	C12—C11—C10	121.2 (5)
H1C—C1—H1D	107.9	C12—C11—H11	119.4
O1—C2—N2	126.5 (5)	C10—C11—H11	119.4
O1—C2—C1	120.2 (4)	C11—C12—C7	117.2 (5)
N2—C2—C1	113.3 (4)	C11—C12—H12	121.4
N2—C3—C4	107.9 (4)	C7—C12—H12	121.4
N2—C3—H3A	110.1	C4—O2—Cu1	114.5 (3)
C4—C3—H3A	110.1	H41—O4—H42	109.7
N2—C3—H3B	110.1	H51—O5—H52	109.2
C4—C3—H3B	110.1	H61—O6—H62	108.7
N2—Cu1—N1—C1	1.6 (3)	Cu1—N3—C6—C5	1.5 (7)
N3—Cu1—N1—C1	−178.9 (3)	C7—N4—C6—N3	0.2 (5)
O2—Cu1—N1—C1	3.8 (8)	C7—N4—C6—C5	179.7 (4)
O2—Cu1—N2—C2	172.9 (4)	C6—N4—C7—C12	178.8 (5)
N1—Cu1—N2—C2	−7.6 (4)	C6—N4—C7—C8	0.8 (5)
O2—Cu1—N2—C3	7.2 (3)	N4—C7—C8—C9	179.8 (4)
N1—Cu1—N2—C3	−173.4 (3)	C12—C7—C8—C9	1.5 (7)
O2—Cu1—N3—C6	−128.7 (4)	N4—C7—C8—N3	−1.4 (5)
N1—Cu1—N3—C6	51.9 (4)	C12—C7—C8—N3	−179.7 (4)
O2—Cu1—N3—C8	53.7 (3)	C6—N3—C8—C9	−179.9 (5)
N1—Cu1—N3—C8	−125.7 (3)	Cu1—N3—C8—C9	−1.8 (6)
Cu1—N1—C1—C2	3.4 (5)	C6—N3—C8—C7	1.5 (5)
C3—N2—C2—O1	−3.4 (7)	Cu1—N3—C8—C7	179.6 (3)
Cu1—N2—C2—O1	−168.4 (4)	C7—C8—C9—C10	−1.7 (6)
C3—N2—C2—C1	176.3 (4)	N3—C8—C9—C10	179.8 (4)
Cu1—N2—C2—C1	11.3 (5)	C8—C9—C10—C11	1.1 (7)
N1—C1—C2—O1	170.6 (4)	C9—C10—C11—C12	−0.1 (8)
N1—C1—C2—N2	−9.1 (6)	C10—C11—C12—C7	−0.2 (7)
C2—N2—C3—C4	−173.4 (4)	N4—C7—C12—C11	−178.3 (5)
Cu1—N2—C3—C4	−7.9 (5)	C8—C7—C12—C11	−0.5 (7)
N2—C3—C4—O3	−175.4 (4)	O3—C4—O2—Cu1	−179.2 (4)
N2—C3—C4—O2	3.9 (6)	C3—C4—O2—Cu1	1.6 (5)
C8—N3—C6—N4	−1.1 (5)	N2—Cu1—O2—C4	−4.8 (3)
Cu1—N3—C6—N4	−179.0 (3)	N3—Cu1—O2—C4	175.6 (3)
C8—N3—C6—C5	179.4 (4)	N1—Cu1—O2—C4	−7.1 (8)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O6—H62···O4	0.87	2.01	2.867 (6)	171
O6—H61···O3^i	0.85	2.05	2.892 (5)	174
O5—H52···O4	0.85	2.10	2.934 (5)	168
O5—H51···O1^ii	0.85	1.93	2.756 (5)	163
O4—H42···O6^iii	0.85	2.25	2.787 (6)	121
O4—H41···O1^iv	0.85	1.99	2.796 (5)	158
N4—H4···O3^iv	0.86	1.91	2.773 (5)	176
N1—H1B···O2^v	0.90	2.25	3.021 (5)	144
N1—H1A···O5	0.90	2.14	2.956 (5)	151
C1—H1C···Cg1^v	0.97	2.77	3.604 (6)	144
C3—H3B···Cg1^i	0.97	2.81	3.547 (6)	133

Symmetry codes: (i) −x, y−1/2, −z+3/2; (ii) −x+1, −y+2, −z+2; (iii) −x+1, y+1/2, −z+3/2; (iv) x, −y+3/2, z−1/2; (v) −x, y+1/2, −z+3/2.