Literature DB >> 23476360

(2-Amino-7-methyl-4-oxido-pteridine-6-carboxyl-ato-κ(3) O (4),N (5),O (6))aqua(1,10-phen-an-thro-line-κ(2) N,N')cobalt(II) trihydrate.

Siddhartha S Baisya1, Samir Sen, Parag S Roy.   

Abstract

In the title compound, [Co(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 geometry around the Co(II) atom. The pterin ligand forms two chelate rings. The phen and pterin ring systems are nearly perpendicular [dihedral angle = 85.15 (8)°]. N-H⋯O, O-H⋯N and O-H⋯O hydrogen bonds link the complex mol-ecules and lattice water mol-ecules into a layer parallel to (001). π-π stacking contacts (involving phen-phen and pteridine-pteridine) are also observed [centroid-centroid distances = 3.670 (2), 3.547 (2), 3.698 (2) and 3.349 (2) Å].

Entities:  

Year:  2012        PMID： 23476360      PMCID： PMC3588366          DOI： 10.1107/S1600536812051185

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


Related literature

For background to the chemistry of pterins in metalloenzymes, see: Basu & Burgmayer (2011 ▶); Burgmayer (1998 ▶); Fitzpatrick (2003 ▶); Fukuzumi & Kojima (2008 ▶). For structures of related cobalt complexes, see: Acuña-Cueva et al. (2003 ▶); Beddoes et al. (1997 ▶); Burgmayer & Stiefel (1988 ▶); Funahashi et al. (1997 ▶). 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 ▶).

Experimental

Crystal data

[Co(C8H5N5O3)(C12H8N2)(H2O)]·3H2O M = 530.36 Triclinic, a = 8.454 (2) Å b = 9.934 (3) Å c = 13.778 (4) Å α = 97.534 (4)° β = 95.281 (4)° γ = 110.603 (4)° V = 1061.8 (5) Å3 Z = 2 Mo Kα radiation μ = 0.87 mm−1 T = 110 K 0.23 × 0.11 × 0.04 mm

Data collection

Bruker Kappa APEXII CCD diffractometer Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ▶) T min = 0.82, T max = 0.97 8945 measured reflections 4726 independent reflections 4360 reflections with I > 2σ(I) R int = 0.030

Refinement

R[F 2 > 2σ(F 2)] = 0.057 wR(F 2) = 0.129 S = 1.03 4726 reflections 316 parameters H-atom parameters constrained Δρmax = 0.99 e Å−3 Δρmin = −0.88 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/S1600536812051185/hy2609sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812051185/hy2609Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
[Co(C8H5N5O3)(C12H8N2)(H2O)]·3H2OZ = 2
Mr = 530.36F(000) = 546
Triclinic, P1Dx = 1.659 Mg m−3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.454 (2) ÅCell parameters from 8945 reflections
b = 9.934 (3) Åθ = 2–28°
c = 13.778 (4) ŵ = 0.87 mm−1
α = 97.534 (4)°T = 110 K
β = 95.281 (4)°Block, pink
γ = 110.603 (4)°0.23 × 0.11 × 0.04 mm
V = 1061.8 (5) Å3
Bruker Kappa APEXII CCD diffractometer4360 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.030
φ and ω scansθmax = 28.2°, θmin = 1.5°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −11→11
Tmin = 0.82, Tmax = 0.97k = −12→13
8945 measured reflectionsl = −18→18
4726 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)] = 0.057H-atom parameters constrained
wR(F2) = 0.129 Method = Modified Sheldrick w = 1/[σ2(F2) + ( 0.04P)2 + 3.34P], where P = (max(Fo2,0) + 2Fc2)/3
S = 1.03(Δ/σ)max = 0.0001859
4726 reflectionsΔρmax = 0.99 e Å−3
316 parametersΔρmin = −0.88 e Å−3
0 restraints
xyzUiso*/Ueq
Co10.45982 (5)0.22172 (4)0.22887 (3)0.0125
O10.2062 (3)0.0747 (2)0.23341 (17)0.0176
C130.1224 (4)0.1182 (3)0.2948 (2)0.0159
O2−0.0205 (3)0.0408 (2)0.31159 (18)0.0204
C140.2096 (4)0.2762 (3)0.3463 (2)0.0150
N30.3618 (3)0.3367 (3)0.32052 (19)0.0137
C190.4572 (4)0.4746 (3)0.3559 (2)0.0137
C160.4012 (4)0.5628 (3)0.4205 (2)0.0151
N50.4986 (3)0.7057 (3)0.4529 (2)0.0154
C170.6493 (4)0.7539 (3)0.4170 (2)0.0157
N40.7169 (3)0.6739 (3)0.3559 (2)0.0161
C180.6243 (4)0.5321 (3)0.3254 (2)0.0148
O30.6704 (3)0.4463 (2)0.26886 (17)0.0174
N70.7460 (4)0.8957 (3)0.4440 (2)0.0199
H1410.82930.93430.41350.0223*
H1420.70860.95220.47750.0228*
N60.2466 (3)0.5028 (3)0.4504 (2)0.0176
C150.1508 (4)0.3621 (3)0.4146 (2)0.0171
C20−0.0163 (4)0.2992 (4)0.4506 (3)0.0256
H172−0.03590.36960.49630.0378*
H173−0.01850.21880.48290.0383*
H171−0.10610.26800.39850.0380*
O40.5538 (3)0.1469 (2)0.35063 (17)0.0185
H1810.49640.06630.35970.0272*
H1820.54180.18940.40130.0271*
N20.3758 (3)0.2801 (3)0.0963 (2)0.0162
C120.2567 (4)0.3370 (4)0.0798 (3)0.0196
C110.2191 (4)0.3750 (4)−0.0116 (3)0.0230
C100.3071 (4)0.3548 (4)−0.0867 (3)0.0220
C80.4354 (4)0.2958 (4)−0.0719 (2)0.0183
C90.4634 (4)0.2593 (3)0.0218 (2)0.0138
C50.5897 (4)0.1963 (3)0.0422 (2)0.0147
N10.6075 (3)0.1592 (3)0.1330 (2)0.0152
C10.7247 (4)0.1018 (3)0.1537 (2)0.0178
C20.8260 (4)0.0749 (4)0.0839 (3)0.0225
C30.8069 (4)0.1096 (4)−0.0079 (3)0.0221
C40.6854 (4)0.1721 (3)−0.0323 (2)0.0179
C60.6545 (4)0.2115 (4)−0.1271 (3)0.0227
C70.5346 (5)0.2690 (4)−0.1461 (3)0.0241
H3210.51240.2898−0.20830.0280*
H3110.71360.1926−0.17710.0268*
H2910.87040.0898−0.05540.0258*
H2810.90860.03770.10200.0257*
H2710.74010.08140.21710.0208*
H2210.28150.3779−0.14770.0263*
H2110.13460.4115−0.02110.0270*
H2010.19760.35310.13040.0229*
O70.9931 (4)0.4695 (3)0.1919 (3)0.0445
H3311.03550.55680.19930.0644*
H3320.93090.48190.23050.0648*
O50.0341 (3)−0.2327 (3)0.28207 (18)0.0224
H3410.0418−0.15590.26370.0322*
H342−0.0472−0.25710.31240.0321*
O60.3374 (3)−0.0951 (2)0.40693 (18)0.0204
H3510.2468−0.14200.36960.0287*
H3520.3795−0.15520.41820.0294*
U11U22U33U12U13U23
Co10.0135 (2)0.0131 (2)0.0129 (2)0.00622 (16)0.00458 (15)0.00324 (15)
O10.0164 (11)0.0142 (11)0.0210 (12)0.0040 (9)0.0048 (9)0.0026 (9)
C130.0156 (15)0.0157 (15)0.0168 (15)0.0064 (12)−0.0002 (12)0.0050 (12)
O20.0143 (11)0.0173 (11)0.0269 (13)0.0015 (9)0.0059 (9)0.0056 (10)
C140.0134 (14)0.0150 (15)0.0185 (15)0.0062 (12)0.0048 (12)0.0053 (12)
N30.0134 (12)0.0130 (12)0.0153 (13)0.0049 (10)0.0035 (10)0.0038 (10)
C190.0139 (14)0.0141 (14)0.0156 (15)0.0062 (12)0.0053 (12)0.0057 (12)
C160.0158 (15)0.0172 (15)0.0152 (15)0.0085 (12)0.0029 (12)0.0050 (12)
N50.0149 (13)0.0129 (12)0.0196 (14)0.0060 (10)0.0040 (10)0.0030 (10)
C170.0157 (15)0.0175 (15)0.0167 (15)0.0083 (12)0.0030 (12)0.0063 (12)
N40.0150 (13)0.0148 (13)0.0202 (14)0.0057 (10)0.0078 (11)0.0047 (11)
C180.0144 (15)0.0169 (15)0.0150 (15)0.0065 (12)0.0036 (12)0.0063 (12)
O30.0173 (11)0.0170 (11)0.0193 (12)0.0073 (9)0.0065 (9)0.0028 (9)
N70.0188 (14)0.0136 (13)0.0264 (15)0.0044 (11)0.0081 (12)0.0020 (11)
N60.0164 (13)0.0169 (13)0.0224 (14)0.0083 (11)0.0071 (11)0.0041 (11)
C150.0148 (15)0.0171 (15)0.0226 (16)0.0075 (12)0.0065 (12)0.0079 (13)
C200.0163 (16)0.0207 (17)0.040 (2)0.0056 (14)0.0126 (15)0.0024 (15)
O40.0198 (12)0.0193 (11)0.0174 (11)0.0069 (9)0.0052 (9)0.0063 (9)
N20.0151 (13)0.0150 (13)0.0203 (14)0.0061 (10)0.0063 (11)0.0055 (11)
C120.0169 (16)0.0171 (15)0.0263 (18)0.0064 (13)0.0075 (13)0.0055 (13)
C110.0193 (17)0.0195 (16)0.0319 (19)0.0082 (14)0.0003 (14)0.0098 (14)
C100.0202 (17)0.0232 (17)0.0224 (17)0.0061 (14)−0.0007 (13)0.0107 (14)
C80.0177 (16)0.0168 (15)0.0178 (16)0.0030 (12)0.0007 (12)0.0044 (13)
C90.0133 (14)0.0114 (14)0.0153 (15)0.0026 (11)0.0032 (11)0.0022 (11)
C50.0129 (14)0.0113 (14)0.0176 (15)0.0020 (11)0.0022 (12)0.0015 (12)
N10.0152 (13)0.0133 (12)0.0158 (13)0.0040 (10)0.0034 (10)0.0013 (10)
C10.0171 (15)0.0150 (15)0.0199 (16)0.0058 (12)0.0002 (12)0.0005 (12)
C20.0169 (16)0.0214 (17)0.0312 (19)0.0103 (14)0.0035 (14)0.0025 (14)
C30.0162 (16)0.0190 (16)0.0298 (19)0.0059 (13)0.0079 (14)−0.0016 (14)
C40.0152 (15)0.0162 (15)0.0200 (16)0.0032 (12)0.0055 (13)0.0009 (13)
C60.0241 (17)0.0251 (17)0.0181 (17)0.0072 (14)0.0093 (14)0.0026 (14)
C70.0299 (19)0.0254 (18)0.0169 (16)0.0070 (15)0.0085 (14)0.0086 (14)
O70.0352 (16)0.0272 (15)0.074 (2)0.0127 (13)0.0292 (16)−0.0010 (15)
O50.0178 (11)0.0184 (12)0.0318 (14)0.0057 (9)0.0095 (10)0.0059 (10)
O60.0192 (12)0.0166 (11)0.0266 (13)0.0077 (9)0.0020 (10)0.0060 (10)
Co1—O12.140 (2)N2—C121.333 (4)
Co1—N32.016 (3)N2—C91.355 (4)
Co1—O32.270 (2)C12—C111.402 (5)
Co1—O42.120 (2)C12—H2010.923
Co1—N22.123 (3)C11—C101.363 (5)
Co1—N12.079 (3)C11—H2110.914
O1—C131.279 (4)C10—C81.414 (5)
C13—O21.244 (4)C10—H2210.926
C13—C141.519 (4)C8—C91.408 (4)
C14—N31.319 (4)C8—C71.435 (5)
C14—C151.426 (4)C9—C51.439 (4)
N3—C191.319 (4)C5—N11.359 (4)
C19—C161.397 (4)C5—C41.411 (4)
C19—C181.450 (4)N1—C11.333 (4)
C16—N51.354 (4)C1—C21.406 (5)
C16—N61.360 (4)C1—H2710.930
N5—C171.360 (4)C2—C31.363 (5)
C17—N41.378 (4)C2—H2810.928
C17—N71.337 (4)C3—C41.412 (5)
N4—C181.335 (4)C3—H2910.928
C18—O31.265 (4)C4—C61.439 (5)
N7—H1410.852C6—C71.349 (5)
N7—H1420.843C6—H3110.925
N6—C151.342 (4)C7—H3210.926
C15—C201.491 (4)O7—H3310.800
C20—H1720.947O7—H3320.810
C20—H1730.960O5—H3410.811
C20—H1710.930O5—H3420.820
O4—H1810.810O6—H3510.830
O4—H1820.801O6—H3520.820
O1—Co1—N375.10 (10)H172—C20—H171106.6
O1—Co1—O3151.22 (8)H173—C20—H171109.7
N3—Co1—O376.26 (9)Co1—O4—H181116.6
O1—Co1—O490.13 (9)Co1—O4—H182109.7
N3—Co1—O490.23 (10)H181—O4—H18295.0
O3—Co1—O492.74 (9)Co1—N2—C12128.8 (2)
O1—Co1—N290.99 (10)Co1—N2—C9112.7 (2)
N3—Co1—N296.45 (10)C12—N2—C9118.5 (3)
O3—Co1—N289.46 (9)N2—C12—C11122.3 (3)
O4—Co1—N2173.29 (10)N2—C12—H201119.1
O1—Co1—N1119.55 (10)C11—C12—H201118.6
N3—Co1—N1164.48 (10)C12—C11—C10119.6 (3)
O3—Co1—N188.76 (9)C12—C11—H211120.2
O4—Co1—N194.58 (10)C10—C11—H211120.2
N2—Co1—N179.12 (10)C11—C10—C8119.9 (3)
Co1—O1—C13116.8 (2)C11—C10—H221120.1
O1—C13—O2124.1 (3)C8—C10—H221120.0
O1—C13—C14114.6 (3)C10—C8—C9116.7 (3)
O2—C13—C14121.2 (3)C10—C8—C7124.4 (3)
C13—C14—N3111.4 (3)C9—C8—C7118.9 (3)
C13—C14—C15129.9 (3)C8—C9—N2123.1 (3)
N3—C14—C15118.8 (3)C8—C9—C5120.1 (3)
Co1—N3—C14121.6 (2)N2—C9—C5116.8 (3)
Co1—N3—C19117.6 (2)C9—C5—N1117.5 (3)
C14—N3—C19120.8 (3)C9—C5—C4119.5 (3)
N3—C19—C16121.8 (3)N1—C5—C4123.0 (3)
N3—C19—C18117.4 (3)Co1—N1—C5113.6 (2)
C16—C19—C18120.7 (3)Co1—N1—C1127.6 (2)
C19—C16—N5120.8 (3)C5—N1—C1118.5 (3)
C19—C16—N6118.7 (3)N1—C1—C2122.0 (3)
N5—C16—N6120.4 (3)N1—C1—H271118.0
C16—N5—C17115.1 (3)C2—C1—H271120.0
N5—C17—N4127.9 (3)C1—C2—C3119.8 (3)
N5—C17—N7117.0 (3)C1—C2—H281119.3
N4—C17—N7115.1 (3)C3—C2—H281120.9
C17—N4—C18117.6 (3)C2—C3—C4119.9 (3)
C19—C18—N4117.7 (3)C2—C3—H291120.7
C19—C18—O3118.1 (3)C4—C3—H291119.4
N4—C18—O3124.2 (3)C3—C4—C5116.8 (3)
Co1—O3—C18110.63 (19)C3—C4—C6124.2 (3)
C17—N7—H141119.8C5—C4—C6119.0 (3)
C17—N7—H142119.9C4—C6—C7121.2 (3)
H141—N7—H142117.6C4—C6—H311119.5
C16—N6—C15119.0 (3)C7—C6—H311119.2
C14—C15—N6120.8 (3)C8—C7—C6121.3 (3)
C14—C15—C20121.7 (3)C8—C7—H321118.4
N6—C15—C20117.4 (3)C6—C7—H321120.3
C15—C20—H172111.5H331—O7—H33286.2
C15—C20—H173110.1H341—O5—H342108.7
H172—C20—H173108.2H351—O6—H352105.5
C15—C20—H171110.7
D—H···AD—HH···AD···AD—H···A
N7—H141···O2i0.852.122.942 (4)163
N7—H142···O6ii0.842.152.970 (4)165
O4—H181···O60.811.932.717 (3)164
O4—H182···N5ii0.802.253.051 (4)176
O5—H341···O10.822.343.079 (4)151
O5—H341···O20.822.232.896 (4)139
O5—H342···N4iii0.822.042.844 (4)166
O6—H351···O50.831.922.740 (4)174
O6—H352···N5iv0.822.052.871 (4)176
O7—H331···O5i0.802.252.941 (4)145
O7—H332···O30.812.232.962 (5)151
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A D⋯A D—H⋯A
N7—H141⋯O2i 0.852.122.942 (4)163
N7—H142⋯O6ii 0.842.152.970 (4)165
O4—H181⋯O60.811.932.717 (3)164
O4—H182⋯N5ii 0.802.253.051 (4)176
O5—H341⋯O10.822.343.079 (4)151
O5—H341⋯O20.822.232.896 (4)139
O5—H342⋯N4iii 0.822.042.844 (4)166
O6—H351⋯O50.831.922.740 (4)174
O6—H352⋯N5iv 0.822.052.871 (4)176
O7—H331⋯O5i 0.802.252.941 (4)145
O7—H332⋯O30.812.232.962 (5)151

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

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

Authors:  Siddhartha S Baisya; Parag S Roy
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2014-10-18
  1 in total

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