Literature DB >> 23424441

(2-Amino-7-methyl-4-oxidopteridine-6-carboxyl-ato-κ(3)O(4),N(5),O(6))aqua-(ethane-1,2-diamine-κ(2)N,N')nickel(II) dihydrate.

Siddhartha S Baisya1, Parag S Roy.   

Abstract

The Ni(II) atom in the title complex, [Ni(C(8)H(5)N(5)O(3))(C(2)H(8)N(2))(H(2)O)]·2H(2)O, is six-coordinated in a distorted octa-hedral geometry by a tridentate 2-amino-7-methyl-4-oxidopteridine-6-carboxyl-ate (pterin) ligand, a bidentate ancillary ethane-1,2-diamine (en) ligand and a water mol-ecule. The pterin ligand forms two chelate rings. The en and pterin ligands are arranged nearly orthogonally [dihedral angle between the mean plane of the en mol-ecule and the pterin ring = 77.1 (1)°]. N-H⋯O, O-H⋯N and O-H⋯O hydrogen bonds link the complex mol-ecules and lattice water mol-ecules into a three-dimensional network. π-π inter-actions are observed between the pyrazine and pyrimidine rings [centroid-centroid distance = 3.437 (2) Å].

Entities:  

Year:  2013        PMID： 23424441      PMCID： PMC3569197          DOI： 10.1107/S160053681300069X

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN： 1600-5368


Related literature

For the importance of pterin in metalloenzymes, see: Basu & Burgmayer (2011 ▶); Burgmayer (1998 ▶); Fitzpatrick (2003 ▶); Fukuzumi & Kojima (2008 ▶); Kaim et al. (1999 ▶). For the structure of a related nickel complex, see: Crispini et al. (2005 ▶). For structures of related copper complexes, see: Odani et al. (1992 ▶). 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: Beddoes et al. (1993 ▶); Kohzuma et al. (1988 ▶); Russell et al. (1992 ▶). For the synthesis of the pterin ligand, see: Wittle et al. (1947 ▶). For refinement of H atoms, see: Cooper et al. (2010 ▶).

Experimental

Crystal data

[Ni(C8H5N5O3)(C2H8N2)(H2O)]·2H2O M = 392.01 Monoclinic, a = 10.406 (4) Å b = 14.323 (5) Å c = 10.450 (4) Å β = 93.294 (6)° V = 1554.9 (10) Å3 Z = 4 Mo Kα radiation μ = 1.29 mm−1 T = 293 K 0.49 × 0.38 × 0.28 mm

Data collection

Bruker Kappa APEXII CCD diffractometer Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ▶) T min = 0.56, T max = 0.70 8393 measured reflections 3488 independent reflections 2760 reflections with I > 2σ(I) R int = 0.035

Refinement

R[F 2 > 2σ(F 2)] = 0.050 wR(F 2) = 0.135 S = 0.92 3488 reflections 217 parameters H-atom parameters constrained Δρmax = 1.12 e Å−3 Δρmin = −0.84 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. Click here for additional data file. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S160053681300069X/hy2612sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681300069X/hy2612Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
[Ni(C8H5N5O3)(C2H8N2)(H2O)]·2H2OF(000) = 816
Mr = 392.01Dx = 1.675 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 8393 reflections
a = 10.406 (4) Åθ = 2.0–28.2°
b = 14.323 (5) ŵ = 1.29 mm−1
c = 10.450 (4) ÅT = 293 K
β = 93.294 (6)°Plate, brown
V = 1554.9 (10) Å30.49 × 0.38 × 0.28 mm
Z = 4
Bruker Kappa APEXII CCD diffractometer2760 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.035
φ & ω scansθmax = 28.2°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −13→13
Tmin = 0.56, Tmax = 0.70k = −18→15
8393 measured reflectionsl = −11→13
3488 independent reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.050H-atom parameters constrained
wR(F2) = 0.135 Method = Modified Sheldrick w = 1/[σ2(F2) + (0.09P)2 + 1.95P], where P = (max(Fo2,0) + 2Fc2)/3
S = 0.92(Δ/σ)max = 0.001
3488 reflectionsΔρmax = 1.12 e Å−3
217 parametersΔρmin = −0.84 e Å−3
0 restraints
Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems open-flow nitrogen cryostat (Cosier, J. & Glazer, A.M., 1986. J. Appl. Cryst. 105–107) with a nominal stability of 0.1 K.
xyzUiso*/Ueq
Ni10.33168 (3)0.37414 (3)0.40998 (3)0.0270
O10.2677 (2)0.35342 (17)0.2158 (2)0.0355
C90.1450 (3)0.3461 (2)0.1944 (3)0.0297
O20.0914 (2)0.3290 (2)0.0880 (2)0.0430
C30.0659 (3)0.3591 (2)0.3117 (3)0.0255
N30.1423 (2)0.37361 (17)0.4173 (2)0.0245
C80.0909 (3)0.3850 (2)0.5295 (3)0.0236
C5−0.0427 (3)0.3859 (2)0.5402 (3)0.0248
N4−0.1228 (2)0.37363 (19)0.4340 (2)0.0282
C4−0.0692 (3)0.3588 (2)0.3213 (3)0.0279
C10−0.1616 (3)0.3442 (3)0.2074 (3)0.0400
H111−0.16530.28100.18530.0637*
H113−0.13530.37680.13260.0631*
H112−0.24770.36440.22570.0629*
N5−0.0930 (2)0.39909 (19)0.6560 (2)0.0285
C6−0.0042 (3)0.4045 (2)0.7565 (3)0.0290
N60.1283 (2)0.4046 (2)0.7564 (2)0.0310
C70.1792 (3)0.3970 (2)0.6422 (3)0.0268
O30.2995 (2)0.39847 (18)0.6257 (2)0.0369
N7−0.0522 (3)0.4136 (3)0.8732 (3)0.0489
O60.3383 (2)0.51989 (16)0.3730 (2)0.0341
H1820.28330.56260.37350.0551*
H1810.38890.52300.31560.0554*
N10.3513 (3)0.2334 (2)0.4537 (3)0.0343
C10.4854 (4)0.2201 (3)0.5050 (4)0.0463
C20.5735 (3)0.2713 (3)0.4201 (4)0.0475
N20.5298 (3)0.36927 (19)0.4057 (3)0.0343
H2210.55590.38880.33260.0516*
H2220.56300.39940.46910.0520*
H2110.66260.27050.45600.0603*
H2120.57060.23940.33830.0606*
H2020.50960.15460.51230.0585*
H2010.49100.24820.59080.0590*
H1920.29660.21950.51350.0560*
H1910.33710.20060.38170.0561*
O40.5313 (3)0.5259 (3)0.2007 (3)0.0699
H2310.59470.54990.23950.1050*
H2320.57490.51890.13840.1048*
O50.2936 (3)0.4894 (2)−0.0008 (3)0.0646
H2410.31130.53700.04130.1023*
H2420.30590.45420.06220.1021*
H1710.00410.42060.94330.0500*
H172−0.13060.44160.89770.0500*
U11U22U33U12U13U23
Ni10.0198 (2)0.0344 (2)0.0270 (2)−0.00059 (15)0.00148 (14)−0.00027 (15)
O10.0291 (12)0.0516 (15)0.0262 (11)−0.0017 (10)0.0057 (9)−0.0032 (10)
C90.0317 (16)0.0329 (16)0.0248 (14)0.0026 (12)0.0035 (12)0.0003 (12)
O20.0388 (13)0.0651 (17)0.0246 (11)0.0035 (12)−0.0024 (9)−0.0070 (11)
C30.0270 (15)0.0261 (15)0.0230 (13)0.0008 (11)−0.0010 (11)−0.0025 (11)
N30.0232 (12)0.0270 (12)0.0234 (12)−0.0004 (9)0.0012 (9)−0.0012 (9)
C80.0213 (13)0.0270 (15)0.0225 (13)0.0001 (11)0.0002 (10)0.0002 (11)
C50.0243 (14)0.0264 (15)0.0236 (13)0.0007 (11)0.0010 (11)0.0007 (11)
N40.0210 (12)0.0360 (14)0.0273 (12)−0.0003 (10)−0.0011 (9)0.0011 (10)
C40.0254 (14)0.0316 (16)0.0261 (14)−0.0005 (11)−0.0026 (11)0.0014 (12)
C100.0275 (16)0.062 (2)0.0293 (16)0.0013 (15)−0.0087 (13)−0.0057 (15)
N50.0222 (12)0.0391 (15)0.0242 (12)0.0033 (10)0.0026 (9)−0.0006 (10)
C60.0281 (15)0.0344 (16)0.0245 (14)0.0061 (12)0.0006 (11)0.0019 (12)
N60.0258 (13)0.0416 (15)0.0252 (12)0.0018 (11)−0.0016 (10)−0.0017 (11)
C70.0233 (14)0.0311 (16)0.0255 (14)0.0000 (11)−0.0018 (11)−0.0014 (12)
O30.0213 (11)0.0557 (15)0.0332 (12)−0.0005 (10)−0.0013 (9)−0.0076 (10)
N70.0346 (16)0.090 (3)0.0223 (13)0.0139 (16)0.0031 (11)−0.0031 (15)
O60.0233 (10)0.0379 (13)0.0413 (12)0.0031 (9)0.0028 (9)0.0008 (10)
N10.0297 (14)0.0376 (15)0.0361 (14)−0.0018 (11)0.0058 (11)0.0034 (12)
C10.042 (2)0.047 (2)0.049 (2)0.0061 (16)−0.0049 (16)0.0111 (17)
C20.0299 (18)0.047 (2)0.065 (2)0.0032 (15)−0.0009 (17)0.0042 (19)
N20.0263 (13)0.0369 (15)0.0396 (15)−0.0014 (11)0.0009 (11)0.0022 (12)
O40.0535 (18)0.117 (3)0.0386 (15)−0.0370 (18)−0.0034 (13)0.0002 (16)
O50.065 (2)0.0592 (19)0.071 (2)0.0075 (15)0.0150 (16)0.0168 (16)
Ni1—O12.120 (2)C6—N71.350 (4)
Ni1—N31.977 (3)N6—C71.338 (4)
Ni1—O32.324 (2)C7—O31.273 (4)
Ni1—O62.125 (2)N7—H1710.917
Ni1—N12.075 (3)N7—H1720.958
Ni1—N22.066 (3)O6—H1820.838
O1—C91.288 (4)O6—H1810.821
C9—O21.239 (4)N1—C11.478 (5)
C9—C31.527 (4)N1—H1920.892
C3—N31.339 (4)N1—H1910.892
C3—C41.416 (4)C1—C21.503 (5)
N3—C81.326 (4)C1—H2020.974
C8—C51.401 (4)C1—H2010.981
C8—C71.461 (4)C2—N21.479 (5)
C5—N41.361 (4)C2—H2110.980
C5—N51.359 (4)C2—H2120.969
N4—C41.349 (4)N2—H2210.872
C4—C101.501 (4)N2—H2220.847
C10—H1110.934O4—H2310.828
C10—H1130.965O4—H2320.821
C10—H1120.970O5—H2410.827
N5—C61.361 (4)O5—H2420.833
C6—N61.378 (4)
O1—Ni1—N377.16 (10)C5—N5—C6114.6 (2)
O1—Ni1—O3153.46 (8)N5—C6—N6129.4 (3)
N3—Ni1—O376.30 (9)N5—C6—N7115.6 (3)
O1—Ni1—O688.57 (10)N6—C6—N7115.0 (3)
N3—Ni1—O693.08 (9)C6—N6—C7116.6 (2)
O3—Ni1—O692.13 (9)C8—C7—N6117.7 (3)
O1—Ni1—N195.53 (11)C8—C7—O3118.1 (3)
N3—Ni1—N194.21 (11)N6—C7—O3124.2 (3)
O3—Ni1—N187.12 (10)Ni1—O3—C7109.05 (19)
O6—Ni1—N1172.28 (9)C6—N7—H171118.7
O1—Ni1—N2103.50 (11)C6—N7—H172130.3
N3—Ni1—N2177.63 (11)H171—N7—H172104.8
O3—Ni1—N2103.04 (10)Ni1—O6—H182133.3
O6—Ni1—N289.22 (10)Ni1—O6—H181102.4
N1—Ni1—N283.47 (11)H182—O6—H181115.6
Ni1—O1—C9115.57 (18)Ni1—N1—C1106.5 (2)
O1—C9—O2124.2 (3)Ni1—N1—H192108.2
O1—C9—C3115.1 (3)C1—N1—H192110.2
O2—C9—C3120.6 (3)Ni1—N1—H191108.4
C9—C3—N3111.1 (3)C1—N1—H191110.2
C9—C3—C4129.8 (3)H192—N1—H191113.2
N3—C3—C4119.1 (3)N1—C1—C2108.6 (3)
C3—N3—Ni1120.9 (2)N1—C1—H202112.7
C3—N3—C8119.9 (3)C2—C1—H202110.7
Ni1—N3—C8119.15 (19)N1—C1—H201106.5
N3—C8—C5121.6 (3)C2—C1—H201109.5
N3—C8—C7117.4 (3)H202—C1—H201108.8
C5—C8—C7121.0 (3)C1—C2—N2109.2 (3)
C8—C5—N4119.9 (3)C1—C2—H211111.3
C8—C5—N5120.5 (3)N2—C2—H211109.2
N4—C5—N5119.6 (3)C1—C2—H212107.6
C5—N4—C4117.9 (3)N2—C2—H212111.4
C3—C4—N4121.6 (3)H211—C2—H212108.2
C3—C4—C10122.6 (3)C2—N2—Ni1109.3 (2)
N4—C4—C10115.9 (3)C2—N2—H221106.5
C4—C10—H111110.4Ni1—N2—H221111.7
C4—C10—H113112.1C2—N2—H222107.1
H111—C10—H113106.2Ni1—N2—H222109.2
C4—C10—H112111.0H221—N2—H222112.9
H111—C10—H112108.2H231—O4—H23288.8
H113—C10—H112108.8H241—O5—H24293.4
D—H···AD—HH···AD···AD—H···A
N1—H192···O1i0.892.393.175 (4)147
N1—H192···O2i0.892.423.243 (4)154
N2—H221···O40.872.403.103 (5)137
N2—H222···O6ii0.852.223.064 (4)176
N7—H171···O2iii0.922.162.890 (4)136
N7—H172···O5iv0.962.293.225 (5)167
O4—H231···O3ii0.831.892.683 (4)160
O4—H232···O5v0.822.042.858 (5)171
O5—H242···O10.832.213.010 (4)160
O6—H181···O40.821.962.774 (4)171
O6—H182···N5iv0.842.062.805 (3)148
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A D⋯A D—H⋯A
N1—H192⋯O1i 0.892.393.175 (4)147
N1—H192⋯O2i 0.892.423.243 (4)154
N2—H221⋯O40.872.403.103 (5)137
N2—H222⋯O6ii 0.852.223.064 (4)176
N7—H171⋯O2iii 0.922.162.890 (4)136
N7—H172⋯O5iv 0.962.293.225 (5)167
O4—H231⋯O3ii 0.831.892.683 (4)160
O4—H232⋯O5v 0.822.042.858 (5)171
O5—H242⋯O10.832.213.010 (4)160
O6—H181⋯O40.821.962.774 (4)171
O6—H182⋯N5iv 0.842.062.805 (3)148

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

  5 in total

Review 1.  Mechanism of aromatic amino acid hydroxylation.

Authors:  Paul F Fitzpatrick
Journal:  Biochemistry       Date:  2003-12-09       Impact factor: 3.162

Review 2.  Control of redox reactivity of flavin and pterin coenzymes by metal ion coordination and hydrogen bonding.

Authors:  Shunichi Fukuzumi; Takahiko Kojima
Journal:  J Biol Inorg Chem       Date:  2008-02-13       Impact factor: 3.358

3.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

4.  Pterin chemistry and its relationship to the molybdenum cofactor.

Authors:  Partha Basu; Sharon J N Burgmayer
Journal:  Coord Chem Rev       Date:  2011-05       Impact factor: 22.315

5.  Oxidative degradation of vitamin Bc (pteroylglutamic acid).

Authors:  E L WITTLE; B L O'DELL
Journal:  J Am Chem Soc       Date:  1947-07       Impact factor: 15.419
  5 in total
  1 in total

1.  (2-Amino-7-methyl-4-oxidopteridine-6-carboxyl-ato-κ(3) O (4),N (5),O (6))(ethane-1,2-diamine-κ(2) N,N')(1H-imidazole-κN (3))nickel(II) dihydrate.

Authors:  Siddhartha S Baisya; Parag S Roy
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2013-03-09
  1 in total

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