Crystal structure of (2-amino-7-methyl-4-oxidopteridine-6-carboxyl-ato-κ(3) O (4),N (5),O (6))aqua-(1,10-phenanthroline-κ(2) N,N')zinc trihydrate.

In the title compound, [Zn(C8H5N5O3)(C12H8N2)(H2O)]·3H2O, a tridentate 2-amino-7-methyl-4-oxidopteridine-6-carboxyl-ate ligand, a bidentate ancillary 1,10-phenanthroline (phen) ligand and a water mol-ecule complete a distorted octa-hedral coordination geometry around the Zn(II) atom. The pterin ligand forms two chelate rings. The phen and pterin ring systems are nearly perpendicular [dihedral angle = 85.16 (5)°]. Classical N-H⋯O, O-H⋯N and O-H⋯O hydrogen bonds and weak C-H⋯O hydrogen bonds link the complex mol-ecules and lattice water mol-ecules into a three-dimensional network. π-π stacking contacts are observed as well, with centroid-to-centroid distances of 3.5679 (14), 3.7004 (14), 3.6641 (15), 3.6974 (13) and 3.3412 (12) Å.

Related literature

For the importance of pterin in metalloenzymes, see: Basu & Burgmayer (2011 ▸); Burgmayer (1998 ▸); Fitzpatrick (2003 ▸); Fukuzumi & Kojima (2008 ▸). For the biochemical importance of zinc–pterin inter­actions, see: Chreifi et al. (2014 ▸). For the structure of a related zinc complex, see: Mitsumi et al. (1995 ▸). For the electron-shuffling ability of the pterin unit, as well as its donor groups, and the effect on the geometric parameters of related complexes, see: Baisya & Roy (2014 ▸); Beddoes et al. (1993 ▸); Kohzuma et al. (1988 ▸); Miyazaki et al. (2008 ▸); Russell et al. (1992 ▸). For the synthesis of the pterin ligand, see: Wittle et al. (1947 ▸).

Experimental

Crystal data

[Zn(C8H5N5O3)(n class="CellLine">C12H8N2)(H2O)]·3H2O

M = 536.81

Triclinic,

a = 8.4819 (7) Å

b = 9.9573 (9) Å

c = 13.7257 (12) Å

α = 97.667 (1)°

β = 95.243 (1)°

γ = 110.716 (1)°

V = 1062.51 (16) Å3

Z = 2

Mo Kα radiation

μ = 1.22 mm−1

T = 293 K

0.24 × 0.19 × 0.04 mm

Data collection

Bruker Kappa APEXII diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2001 ▸) T min = 0.76, T max = 0.95

9149 measured reflections

4794 independent reflections

4456 reflections with I > 2.0σ(I)

R int = 0.018

Refinement

R[F 2 > 2σ(F 2)] = 0.039

wR(F 2) = 0.089

S = 0.94

4794 reflections

346 parameters

12 restraints

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.64 e Å−3

Δρmin = −0.33 e Å−3

Data collection: APEX2 (Bruker, 2007 ▸); cell refinement: SAINT (Bruker, 2007 ▸); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▸); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003 ▸); molecular graphics: CAMERON (Watkin et al., 1996 ▸); software used to prepare material for publication: CRYSTALS.

Crystal structure: contains datablock(s) global, New_Global_Publ_Block, I. DOI: 10.1107/S2056989015014619/xu5864sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015014619/xu5864Isup2.hkl

Click here for additional data file.

. DOI: 10.1107/S2056989015014619/xu5864fig1.tif

The mol­ecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level. Hydrogen atoms are shown as spheres of arbitrary radius.

Click here for additional data file.

b . DOI: 10.1107/S2056989015014619/xu5864fig2.tif

The crystal packing diagram of the title compound, viewed along the b axis. Dotted lines indicate hydrogen bonds.

Click here for additional data file.

. DOI: 10.1107/S2056989015014619/xu5864fig3.tif

A mol­ecular packing diagram highlighting π–π stacking inter­actions between two phen–phen and pterin–pterin rings, respectively.

CCDC reference: 1416736

Additional supporting information: crystallographic information; 3D view; checkCIF report

[Zn(C8H5N5O3)(C12H8N2(H2O)]·3H2O	Z = 2
Mr = 536.81	F(000) = 552
Triclinic, P1	Dx = 1.678 Mg m−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 8.4819 (7) Å	Cell parameters from 0 reflections
b = 9.9573 (9) Å	θ = 0–0°
c = 13.7257 (12) Å	µ = 1.22 mm−1
α = 97.667 (1)°	T = 293 K
β = 95.243 (1)°	Plate, orange brown
γ = 110.716 (1)°	0.24 × 0.19 × 0.04 mm
V = 1062.51 (16) Å3

Bruker Kappa APEXII diffractometer	4456 reflections with I > 2.0σ(I)
Graphite monochromator	Rint = 0.018
φ & ω scans	θmax = 28.3°, θmin = 1.5°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −11→11
Tmin = 0.76, Tmax = 0.95	k = −13→13
9149 measured reflections	l = −17→18
4794 independent reflections

Refinement on F2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.039	H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.089	Method, part 1, Chebychev polynomial, (Watkin, 1994, Prince, 1982) [weight] = 1.0/[A0*T0(x) + A1*T1(x) ··· + An-1]*Tn-1(x)] where Ai are the Chebychev coefficients listed below and x = F /Fmax Method = Robust Weighting (Prince, 1982) W = [weight] * [1-(deltaF/6*sigmaF)2]2 Ai are: 57.7 96.4 59.4 25.6 6.16
S = 0.94	(Δ/σ)max = 0.001
4794 reflections	Δρmax = 0.64 e Å−3
346 parameters	Δρmin = −0.33 e Å−3
12 restraints

	x	y	z	Uiso*/Ueq
Zn1	0.95623 (3)	0.21520 (3)	0.228578 (17)	0.0166
O2	0.70435 (19)	0.06939 (16)	0.23606 (11)	0.0206
C3	0.6217 (3)	0.1186 (2)	0.29541 (15)	0.0182
O4	0.47875 (19)	0.04655 (17)	0.31282 (12)	0.0231
C5	0.7109 (3)	0.2776 (2)	0.34528 (15)	0.0164
N6	0.8648 (2)	0.33756 (18)	0.32071 (12)	0.0149
C7	0.9604 (3)	0.4752 (2)	0.35603 (14)	0.0155
C8	0.9030 (3)	0.5640 (2)	0.41988 (15)	0.0169
N9	0.7480 (2)	0.5050 (2)	0.44879 (14)	0.0198
C10	0.6531 (3)	0.3650 (2)	0.41309 (16)	0.0191
C11	0.4848 (3)	0.3041 (3)	0.4490 (2)	0.0308
H111	0.3927	0.2783	0.3982	0.0483*
H113	0.4752	0.3721	0.4998	0.0481*
H112	0.4768	0.2178	0.4756	0.0485*
N12	0.9998 (2)	0.70678 (19)	0.45260 (13)	0.0182
C13	1.1515 (3)	0.7547 (2)	0.41752 (15)	0.0180
N14	1.2199 (2)	0.67528 (19)	0.35785 (13)	0.0175
C15	1.1294 (3)	0.5323 (2)	0.32689 (15)	0.0168
O16	1.17955 (19)	0.44769 (16)	0.27321 (11)	0.0198
N17	1.2464 (2)	0.8967 (2)	0.44431 (15)	0.0227
H172	1.213 (3)	0.954 (2)	0.481 (2)	0.0276*
H171	1.334 (3)	0.933 (2)	0.4174 (19)	0.0277*
O18	1.0532 (2)	0.14070 (18)	0.34889 (12)	0.0218
H181	0.989 (4)	0.061 (2)	0.355 (2)	0.0355*
H182	1.063 (4)	0.196 (3)	0.4008 (17)	0.0360*
N19	1.1061 (2)	0.15973 (19)	0.13227 (13)	0.0168
C20	1.2233 (3)	0.1030 (2)	0.15288 (16)	0.0204
C21	1.3255 (3)	0.0777 (3)	0.08353 (18)	0.0250
C22	1.3061 (3)	0.1119 (3)	−0.00880 (17)	0.0250
C23	1.1848 (3)	0.1743 (2)	−0.03259 (16)	0.0200
C24	1.0876 (3)	0.1965 (2)	0.04125 (15)	0.0171
C25	0.9617 (3)	0.2597 (2)	0.02089 (15)	0.0165
N26	0.8729 (2)	0.27983 (19)	0.09497 (13)	0.0174
C27	0.7551 (3)	0.3368 (2)	0.07879 (16)	0.0211
C28	0.7189 (3)	0.3760 (3)	−0.01264 (18)	0.0260
C29	0.8072 (3)	0.3552 (2)	−0.08843 (17)	0.0247
C30	0.9340 (3)	0.2960 (2)	−0.07305 (16)	0.0210
C31	1.0338 (3)	0.2694 (3)	−0.14734 (17)	0.0280
C32	1.1539 (3)	0.2124 (3)	−0.12796 (17)	0.0266
H321	1.2157	0.1968	−0.1756	0.0332*
H311	1.0138	0.2929	−0.2093	0.0332*
H291	0.7852	0.3813	−0.1476	0.0296*
H281	0.6360	0.4140	−0.0213	0.0316*
H271	0.6959	0.3519	0.1296	0.0262*
H221	1.3708	0.0958	−0.0549	0.0310*
H211	1.4043	0.0380	0.1006	0.0321*
H201	1.2367	0.0788	0.2153	0.0258*
O33	0.4935 (3)	0.4716 (2)	0.1913 (2)	0.0499
H331	0.407 (4)	0.454 (5)	0.216 (3)	0.0756*
H332	0.535 (6)	0.560 (2)	0.211 (4)	0.0757*
O34	0.5353 (2)	−0.23088 (17)	0.28297 (13)	0.0244
H341	0.452 (3)	−0.257 (4)	0.309 (2)	0.0388*
H342	0.547 (4)	−0.156 (3)	0.265 (2)	0.0388*
O35	0.8383 (2)	−0.09668 (17)	0.40775 (12)	0.0225
H351	0.747 (3)	−0.148 (3)	0.375 (2)	0.0346*
H352	0.874 (4)	−0.156 (3)	0.426 (2)	0.0349*

	U11	U22	U33	U12	U13	U23
Zn1	0.01928 (13)	0.01775 (13)	0.01479 (12)	0.00892 (9)	0.00487 (8)	0.00239 (8)
O2	0.0205 (7)	0.0176 (7)	0.0217 (7)	0.0054 (6)	0.0039 (6)	0.0014 (6)
C3	0.0189 (10)	0.0180 (10)	0.0177 (9)	0.0069 (8)	−0.0001 (7)	0.0047 (8)
O4	0.0172 (7)	0.0204 (8)	0.0276 (8)	0.0015 (6)	0.0054 (6)	0.0043 (6)
C5	0.0157 (9)	0.0164 (9)	0.0174 (9)	0.0058 (7)	0.0024 (7)	0.0045 (7)
N6	0.0156 (8)	0.0158 (8)	0.0138 (7)	0.0060 (6)	0.0031 (6)	0.0033 (6)
C7	0.0172 (9)	0.0174 (9)	0.0122 (8)	0.0062 (7)	0.0025 (7)	0.0036 (7)
C8	0.0184 (9)	0.0176 (9)	0.0164 (9)	0.0082 (8)	0.0031 (7)	0.0039 (7)
N9	0.0184 (8)	0.0188 (8)	0.0239 (9)	0.0083 (7)	0.0070 (7)	0.0031 (7)
C10	0.0163 (9)	0.0209 (10)	0.0218 (10)	0.0078 (8)	0.0061 (8)	0.0043 (8)
C11	0.0196 (11)	0.0247 (11)	0.0435 (14)	0.0035 (9)	0.0146 (10)	−0.0026 (10)
N12	0.0199 (8)	0.0163 (8)	0.0188 (8)	0.0073 (7)	0.0040 (7)	0.0023 (7)
C13	0.0191 (9)	0.0185 (10)	0.0172 (9)	0.0079 (8)	0.0015 (7)	0.0041 (8)
N14	0.0180 (8)	0.0149 (8)	0.0188 (8)	0.0050 (7)	0.0048 (6)	0.0023 (6)
C15	0.0182 (9)	0.0177 (9)	0.0158 (9)	0.0071 (7)	0.0037 (7)	0.0057 (7)
O16	0.0197 (7)	0.0164 (7)	0.0229 (7)	0.0057 (6)	0.0088 (6)	0.0011 (6)
N17	0.0220 (9)	0.0152 (8)	0.0283 (10)	0.0036 (7)	0.0091 (8)	0.0000 (7)
O18	0.0228 (8)	0.0211 (8)	0.0204 (7)	0.0060 (6)	0.0029 (6)	0.0065 (6)
N19	0.0191 (8)	0.0142 (8)	0.0159 (8)	0.0062 (6)	0.0015 (6)	−0.0002 (6)
C20	0.0201 (10)	0.0187 (10)	0.0205 (10)	0.0071 (8)	−0.0013 (8)	−0.0001 (8)
C21	0.0200 (10)	0.0238 (11)	0.0308 (12)	0.0107 (9)	0.0013 (9)	−0.0026 (9)
C22	0.0207 (10)	0.0257 (11)	0.0259 (11)	0.0081 (9)	0.0079 (8)	−0.0065 (9)
C23	0.0189 (10)	0.0184 (9)	0.0187 (9)	0.0035 (8)	0.0047 (8)	−0.0012 (8)
C24	0.0170 (9)	0.0153 (9)	0.0155 (9)	0.0034 (7)	0.0017 (7)	−0.0010 (7)
C25	0.0162 (9)	0.0139 (9)	0.0173 (9)	0.0035 (7)	0.0025 (7)	0.0015 (7)
N26	0.0178 (8)	0.0183 (8)	0.0160 (8)	0.0063 (7)	0.0031 (6)	0.0032 (6)
C27	0.0190 (10)	0.0228 (10)	0.0230 (10)	0.0090 (8)	0.0055 (8)	0.0040 (8)
C28	0.0233 (11)	0.0261 (11)	0.0307 (12)	0.0107 (9)	0.0004 (9)	0.0100 (9)
C29	0.0262 (11)	0.0241 (11)	0.0216 (10)	0.0060 (9)	−0.0016 (9)	0.0099 (9)
C30	0.0225 (10)	0.0178 (10)	0.0188 (10)	0.0025 (8)	0.0015 (8)	0.0047 (8)
C31	0.0355 (13)	0.0291 (12)	0.0161 (10)	0.0069 (10)	0.0050 (9)	0.0058 (9)
C32	0.0296 (12)	0.0292 (12)	0.0187 (10)	0.0076 (9)	0.0098 (9)	0.0017 (9)
O33	0.0397 (12)	0.0342 (11)	0.0765 (16)	0.0141 (9)	0.0294 (11)	−0.0026 (11)
O34	0.0200 (8)	0.0188 (8)	0.0328 (9)	0.0042 (6)	0.0082 (6)	0.0043 (7)
O35	0.0222 (8)	0.0172 (7)	0.0278 (8)	0.0072 (6)	0.0017 (6)	0.0048 (6)

Zn1—O2	2.1373 (15)	N19—C20	1.332 (3)
Zn1—O16	2.3727 (15)	N19—C24	1.359 (3)
Zn1—O18	2.1128 (16)	C20—C21	1.401 (3)
Zn1—N6	2.0303 (17)	C20—H201	0.928
Zn1—N19	2.0684 (17)	C21—C22	1.366 (4)
Zn1—N26	2.1627 (18)	C21—H211	0.917
O2—C3	1.279 (3)	C22—C23	1.413 (3)
C3—O4	1.235 (3)	C22—H221	0.909
C3—C5	1.522 (3)	C23—C24	1.406 (3)
C5—N6	1.325 (3)	C23—C32	1.437 (3)
C5—C10	1.426 (3)	C24—C25	1.442 (3)
N6—C7	1.317 (3)	C25—N26	1.355 (3)
C7—C8	1.401 (3)	C25—C30	1.406 (3)
C7—C15	1.459 (3)	N26—C27	1.327 (3)
C8—N9	1.357 (3)	C27—C28	1.402 (3)
C8—N12	1.354 (3)	C27—H271	0.923
N9—C10	1.335 (3)	C28—C29	1.372 (3)
C10—C11	1.499 (3)	C28—H281	0.916
C11—H111	0.934	C29—C30	1.410 (3)
C11—H113	0.936	C29—H291	0.909
C11—H112	0.960	C30—C31	1.439 (3)
N12—C13	1.362 (3)	C31—C32	1.353 (4)
C13—N14	1.368 (3)	C31—H311	0.929
C13—N17	1.335 (3)	C32—H321	0.906
N14—C15	1.342 (3)	O33—H331	0.803 (19)
C15—O16	1.257 (3)	O33—H332	0.816 (19)
N17—H172	0.851 (17)	O34—H341	0.800 (18)
N17—H171	0.848 (17)	O34—H342	0.795 (18)
O18—H181	0.809 (17)	O35—H351	0.813 (17)
O18—H182	0.817 (17)	O35—H352	0.803 (17)
O2—Zn1—N6	76.37 (6)	C13—N17—H171	119.4 (14)
O2—Zn1—O16	150.97 (6)	H172—N17—H171	119 (2)
N6—Zn1—O16	74.60 (6)	Zn1—O18—H181	112 (2)
O2—Zn1—O18	90.05 (6)	Zn1—O18—H182	110 (2)
N6—Zn1—O18	91.77 (7)	H181—O18—H182	106 (3)
O16—Zn1—O18	91.21 (6)	Zn1—N19—C20	127.00 (15)
O2—Zn1—N19	121.85 (6)	Zn1—N19—C24	114.19 (14)
N6—Zn1—N19	160.68 (7)	C20—N19—C24	118.63 (18)
O16—Zn1—N19	86.96 (6)	N19—C20—C21	122.3 (2)
O18—Zn1—N19	94.39 (7)	N19—C20—H201	118.6
O2—Zn1—N26	92.53 (6)	C21—C20—H201	119.1
N6—Zn1—N26	94.76 (7)	C20—C21—C22	119.6 (2)
O16—Zn1—N26	89.49 (6)	C20—C21—H211	119.5
O18—Zn1—N26	173.38 (6)	C22—C21—H211	120.8
N19—Zn1—N26	79.07 (7)	C21—C22—C23	119.5 (2)
Zn1—O2—C3	115.97 (13)	C21—C22—H221	120.8
O2—C3—O4	124.45 (19)	C23—C22—H221	119.6
O2—C3—C5	115.38 (18)	C22—C23—C24	117.3 (2)
O4—C3—C5	120.17 (19)	C22—C23—C32	123.6 (2)
C3—C5—N6	112.43 (17)	C24—C23—C32	119.1 (2)
C3—C5—C10	129.33 (19)	C23—C24—N19	122.57 (19)
N6—C5—C10	118.23 (18)	C23—C24—C25	119.65 (19)
C5—N6—Zn1	119.65 (14)	N19—C24—C25	117.78 (18)
C5—N6—C7	120.98 (18)	C24—C25—N26	117.17 (18)
Zn1—N6—C7	119.37 (14)	C24—C25—C30	120.11 (19)
N6—C7—C8	121.49 (19)	N26—C25—C30	122.71 (19)
N6—C7—C15	117.67 (18)	Zn1—N26—C25	111.62 (13)
C8—C7—C15	120.84 (18)	Zn1—N26—C27	129.44 (14)
C7—C8—N9	119.03 (19)	C25—N26—C27	118.92 (18)
C7—C8—N12	120.91 (19)	N26—C27—C28	122.2 (2)
N9—C8—N12	120.06 (18)	N26—C27—H271	118.9
C8—N9—C10	118.80 (18)	C28—C27—H271	118.9
C5—C10—N9	121.40 (19)	C27—C28—C29	119.4 (2)
C5—C10—C11	121.82 (19)	C27—C28—H281	119.8
N9—C10—C11	116.77 (19)	C29—C28—H281	120.8
C10—C11—H111	112.4	C28—C29—C30	119.6 (2)
C10—C11—H113	110.0	C28—C29—H291	119.8
H111—C11—H113	109.1	C30—C29—H291	120.6
C10—C11—H112	109.7	C29—C30—C25	117.2 (2)
H111—C11—H112	107.5	C29—C30—C31	124.2 (2)
H113—C11—H112	107.9	C25—C30—C31	118.7 (2)
C8—N12—C13	114.98 (17)	C30—C31—C32	121.4 (2)
N12—C13—N14	128.05 (19)	C30—C31—H311	118.0
N12—C13—N17	116.57 (19)	C32—C31—H311	120.6
N14—C13—N17	115.38 (19)	C23—C32—C31	121.1 (2)
C13—N14—C15	118.29 (18)	C23—C32—H321	118.9
C7—C15—N14	116.72 (18)	C31—C32—H321	120.1
C7—C15—O16	119.05 (18)	H331—O33—H332	99 (5)
N14—C15—O16	124.20 (19)	H341—O34—H342	110 (3)
Zn1—O16—C15	109.18 (13)	H351—O35—H352	102 (3)
C13—N17—H172	121.5 (14)

D—H···A	D—H	H···A	D···A	D—H···A
N17—H171···O4i	0.85 (2)	2.15 (2)	2.942 (3)	156 (2)
N17—H172···O35ii	0.85 (3)	2.13 (3)	2.967 (3)	170 (2)
O18—H181···O35	0.81 (2)	1.92 (2)	2.700 (2)	163 (3)
O18—H182···N12ii	0.82 (2)	2.30 (3)	3.088 (2)	160 (3)
O33—H331···O16iii	0.81 (4)	2.13 (4)	2.929 (3)	169 (4)
O33—H332···O34iv	0.82 (3)	2.18 (4)	2.944 (3)	155 (5)
O34—H341···N14v	0.80 (3)	2.05 (3)	2.842 (3)	172 (3)
O34—H342···O2	0.79 (3)	2.28 (3)	3.010 (2)	154 (3)
O34—H342···O4	0.79 (3)	2.32 (3)	2.950 (2)	137 (3)
O35—H351···O34	0.81 (3)	1.94 (3)	2.735 (2)	167 (3)
O35—H352···N12vi	0.81 (3)	2.06 (3)	2.855 (3)	168 (3)
C20—H201···O4vii	0.93	2.49	3.186 (3)	132
C27—H271···O33	0.92	2.56	3.360 (4)	146
C29—H291···O16viii	0.91	2.55	3.394 (3)	156

Table 1

Selected bond lengths ()

Zn1O2	2.1373(15)
Zn1O16	2.3727(15)
Zn1O18	2.1128(16)
Zn1N6	2.0303(17)
Zn1N19	2.0684(17)
Zn1N26	2.1627(18)

Table 2

Hydrogen-bond geometry (, )

DHA	DH	HA	D A	DHA
N17H171O4i	0.85(2)	2.15(2)	2.942(3)	156(2)
N17H172O35ii	0.85(3)	2.13(3)	2.967(3)	170(2)
O18H181O35	0.81(2)	1.92(2)	2.700(2)	163(3)
O18H182N12ii	0.82(2)	2.30(3)	3.088(2)	160(3)
O33H331O16iii	0.81(4)	2.13(4)	2.929(3)	169(4)
O33H332O34iv	0.82(3)	2.18(4)	2.944(3)	155(5)
O34H341N14v	0.80(3)	2.05(3)	2.842(3)	172(3)
O34H342O2	0.79(3)	2.28(3)	3.010(2)	154(3)
O34H342O4	0.79(3)	2.32(3)	2.950(2)	137(3)
O35H351O34	0.81(3)	1.94(3)	2.735(2)	167(3)
O35H352N12vi	0.81(3)	2.06(3)	2.855(3)	168(3)
C20H201O4vii	0.93	2.49	3.186(3)	132
C27H271O33	0.92	2.56	3.360(4)	146
C29H291O16viii	0.91	2.55	3.394(3)	156

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) ; (vi) ; (vii) ; (viii) .