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Crystal structure of tetra­aqua­bis­­(pyrimidin-1-ium-4,6-diolato-κO4)manganese(II)

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aCarlson School of Chemistry and Biochemistry, Clark University, 950 Main St, Worcester, MA 01610, USA, and bDepartment of Chemistry, Howard University, Washington, DC 20059, USA
*Correspondence e-mail: fgreenaway@clarku.edu

Edited by M. Weil, Vienna University of Technology, Austria (Received 3 March 2017; accepted 23 March 2017; online 31 March 2017)

The MnII ion in the structure of the mononuclear title compound, [Mn(C4H3N2O2)2(H2O)4], is situated on an inversion center and is coordinated by two O atoms from two deprotonated 4,6-di­hydroxy­pyrimidine ligands and by four O atoms from water mol­ecules giving rise to a slightly distorted octa­hedral coordination sphere. The complex includes an intra­molecular hydrogen bond between an aqua ligand and the non-protonated N ring atom. The extended structure is stabilized by inter­molecular hydrogen bonds between aqua ligands, by hydrogen bonds between N and O atoms of the ligands of adjacent mol­ecules, and by hydrogen bonds between aqua ligands and the non-coordinating O atom of an adjacent mol­ecule.

1. Chemical context

H-tautomeric forms of 4,6-di­hydroxy­pyrimidine (DHP) are known to exist and are associated with low disproportionation energies (Katrusiak & Katrusiak, 2003[Katrusiak, A. & Katrusiak, A. (2003). Org. Lett. 5, 1903-1905.]). Although crystal structures have been reported where cobalt(II) and nickel(II) are coordinated by the 4,6-di­hydroxy­pyrimidine ligand through a ring nitro­gen atom (Huang et al., 2005[Huang, Y.-G., Zhou, Y.-F., Yuan, D.-Q., Wu, B.-L. & Hong, M.-C. (2005). Acta Cryst. E61, m832-m834.]; Wang et al., 2006[Wang, Y.-T., Lou, X.-H., Wang, J.-G. & Fan, Y.-T. (2006). Acta Cryst. E62, m1924-m1926.]), prior to this report no complexes with ligation through a phenolate oxygen atom have been reported even though this mode of coordination does occur in complexes of 3,6-di­hydroxy­pyridizine (Shennara et al., 2015[Shennara, K. A., Butcher, R. J. & Greenaway, F. T. (2015). Inorg. Chim. Acta, 425, 247-254.]).

[Scheme 1]

2. Structural commentary

Crystallographic analysis reveals that the title compound consists of a centrosymmetric mononuclear [Mn(C4H3N2O2)2(H2O)4] complex in which the MnII ion is in an O6 environment that is close to octa­hedral. Two deprotonated 4,6-di­hydroxy­pyrimidine ligands coordinate through the phenolate oxygen atom (O1) at axial positions, while four water mol­ecules occupy the equatorial sites (Fig. 1[link]). The bond lengths in the pyrimidine ligand are very similar to those found for the Co and Ni complexes in which, however, ligation to the metal is through a nitro­gen atom. For all three complexes, the structures indicate a zwitterionic form of the ligand resulting from transfer of a proton from the hydroxyl group to a ring nitro­gen atom. Others have reported variability in the H-tautomeric forms of 4,6-di­hydroxy­pyrimidine associated with low disproportionation energies (Katrusiak & Katrusiak, 2003[Katrusiak, A. & Katrusiak, A. (2003). Org. Lett. 5, 1903-1905.]). The structure of the complex includes an intra­molecular hydrogen bond between an aqua ligand (O2W) and the non-protonated N3 ring atom (N2) (Table 1[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O1W—H1W1⋯O2i 0.80 (3) 2.03 (3) 2.8152 (14) 170 (2)
O1W—H1W2⋯O1ii 0.82 (3) 1.90 (3) 2.7127 (13) 176 (3)
O2W—H2W1⋯N2 0.82 (3) 1.91 (3) 2.6929 (14) 159 (2)
O2W—H2W2⋯O2iii 0.84 (2) 1.85 (2) 2.6754 (13) 167 (2)
N1—H1N⋯O2iv 0.91 (2) 1.92 (2) 2.7966 (14) 162 (2)
Symmetry codes: (i) [x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]; (ii) -x, -y+1, -z+1; (iii) [x+1, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]; (iv) -x, -y, -z+1.
[Figure 1]
Figure 1
Diagram showing the complex and atom labeling, as well as the formation of {C(4)[R22(8)]} chains in the a-axis direction linked by hydrogen bonds. Atomic displacement parameters are drawn at the 50% probability level. Hydrogen bonds are shown as dashed lines.

3. Supra­molecular features

Inter­molecular hydrogen bonds between the aqua ligands of adjacent mol­ecules are present. Hydrogen bonds also occur between the non-coordinating NH+ and O atoms of two DHP ligands in adjacent mol­ecules and between an aqua ligand and the non-coordinating oxygen atom of an adjacent mol­ecule (Table 1[link]). This gives rise to a complex three-dimensional network, which is best analyzed in terms of graph-set theory (Etter et al., 1990[Etter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256-262.]). There are four inter­penetrating chains of hydrogen bonds. The first has a C(4)[R22(8)] motif and is shown in Fig. 1[link]. The second has a C(6)[R11(6)R22(8)] motif and is shown in Fig. 2[link]. The chain depicted in Fig. 3[link] has a C(6)[R32(8)] motif and is duplicated in two mutually perpendicular directions, thus making up four chains altogether. The overall packing is shown in Fig. 4[link].

[Figure 2]
Figure 2
Diagram showing how the mol­ecules link up into chains through the formation of C(6)[R(6)R22(8)] hydrogen bonds. Atomic displacement parameters are drawn at the 50% probability level. Hydrogen bonds are shown as dashed lines.
[Figure 3]
Figure 3
Diagram showing one of the two mutually perpendicular chains linked through the formation of C(6)[R32(8)] hydrogen bonds. Atomic displacement parameters are drawn at the 50% probability level. Hydrogen bonds are shown as dashed lines.
[Figure 4]
Figure 4
Diagram showing how the four sets of chains linked by hydrogen bonds gives rise to the overall packing. Hydrogen bonds are shown as dashed lines.

4. Database survey

A search in the Cambridge Structural Database (CSD version 5.37; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) for structures of manganese of 4,6-di­hydroxy­pyrimidines revealed that no such structures exist, although there are twelve examples of manganese complexes of 2,4-di­hydroxy­pyrimidine derivatives (CSD codes AMPTMN, AQAPAK, ICESEQ, IMEGAJ, JIRNUU, NOPSER, OFUDAU, QOSDOT, QOSNOD, RAGLAO, TAGVOM, and ZOGFOQ).

5. Synthesis and crystallization

0.5 mM aqueous solutions of the ligand and anhydrous MnCl2, both purchased from Aldrich, were adjusted to pH 5.5 with NaOH/HCl and then mixed together in a 1:2 stoichiometry. The solutions were left to crystallize slowly at room temperature. Light-yellow crystals formed over two weeks. Room-temperature X-band EPR spectra of powdered crystals exhibited a single broad line centered at a g-value of near to 2.0 with a peak-to-peak line width of 660 G, the breadth of which indicates Mn⋯Mn magnetic inter­actions, although not as strong as in the related maleic hydrazide (MH), Mn(MH)2(H2O)4, complex, for which a line width of 920 G was found (Shennara et al., 2015[Shennara, K. A., Butcher, R. J. & Greenaway, F. T. (2015). Inorg. Chim. Acta, 425, 247-254.]). EPR spectra of aqueous solutions of the title complex had g = 2.006 and Aiso(Mn) = 95.2 G, similar to that of the Mn(MH)2 complex

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. All H atoms were positioned geometrically and refined as riding: C—H = 0.95 Å with Uiso(H) = 1.2Ueq(C). N—H and O—H hydrogen atoms were refined isotropically without restrictions on the bond lengths. Four reflections which were obvious outliers were omitted from the refinement (132, 163, 100, 011).

Table 2
Experimental details

Crystal data
Chemical formula [Mn(C4H3N2O2)2(H2O)4]
Mr 349.17
Crystal system, space group Monoclinic, P21/c
Temperature (K) 120
a, b, c (Å) 5.2156 (5), 14.0812 (14), 9.0595 (9)
β (°) 99.366 (2)
V3) 656.48 (11)
Z 2
Radiation type Mo Kα
μ (mm−1) 1.05
Crystal size (mm) 0.55 × 0.41 × 0.40
 
Data collection
Diffractometer Bruker APEXII CCD
Absorption correction Multi-scan (SADABS; Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.])
Tmin, Tmax 0.614, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections 2971, 1848, 1752
Rint 0.016
(sin θ/λ)max−1) 0.730
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.027, 0.071, 1.10
No. of reflections 1848
No. of parameters 117
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.48, −0.32
Computer programs: APEX2 (Bruker, 2005[Bruker (2005). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.]), SAINT (Bruker, 2002[Bruker (2002). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2014 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]) and SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Supporting information


Computing details top

Data collection: APEX2 (Bruker, 2005); cell refinement: APEX2 (Bruker, 2005); data reduction: SAINT (Bruker, 2002); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Tetraaquabis(pyrimidin-1-ium-4,6-diolato-κO4)manganese(II) top
Crystal data top
[Mn(C4H3N2O2)2(H2O)4]F(000) = 358
Mr = 349.17Dx = 1.766 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 5.2156 (5) ÅCell parameters from 2512 reflections
b = 14.0812 (14) Åθ = 2.7–31.2°
c = 9.0595 (9) ŵ = 1.05 mm1
β = 99.366 (2)°T = 120 K
V = 656.48 (11) Å3Block, yellow
Z = 20.55 × 0.41 × 0.40 mm
Data collection top
Bruker APEXII CCD
diffractometer
1752 reflections with I > 2σ(I)
ω scansRint = 0.016
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
θmax = 31.2°, θmin = 2.9°
Tmin = 0.614, Tmax = 0.746h = 77
2971 measured reflectionsk = 1818
1848 independent reflectionsl = 312
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.027H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.071 w = 1/[σ2(Fo2) + (0.033P)2 + 0.3858P]
where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max < 0.001
1848 reflectionsΔρmax = 0.48 e Å3
117 parametersΔρmin = 0.32 e Å3
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Mn0.5000000.5000000.5000000.00759 (9)
O10.25688 (17)0.38379 (6)0.56407 (10)0.01144 (18)
O20.08946 (18)0.07807 (6)0.62265 (10)0.01204 (18)
O1W0.17104 (18)0.54921 (7)0.33556 (11)0.01243 (18)
H1W10.114 (5)0.5129 (16)0.271 (3)0.029 (6)*
H1W20.045 (5)0.5682 (17)0.370 (3)0.040 (7)*
O2W0.6010 (2)0.40720 (7)0.32982 (11)0.0164 (2)
H2W10.562 (5)0.3534 (18)0.353 (3)0.037 (6)*
H2W20.702 (5)0.4026 (17)0.267 (3)0.035 (6)*
N10.2263 (2)0.10486 (8)0.48187 (11)0.0094 (2)
H1N0.219 (5)0.0429 (18)0.453 (3)0.033 (6)*
N20.4089 (2)0.25411 (8)0.45266 (11)0.0102 (2)
C10.2421 (2)0.29415 (9)0.54070 (13)0.0084 (2)
C20.0651 (2)0.23594 (9)0.60057 (13)0.0101 (2)
H2A0.0496390.2632070.6601800.012*
C30.0573 (2)0.13885 (9)0.57302 (13)0.0090 (2)
C40.3920 (2)0.16342 (9)0.42645 (13)0.0102 (2)
H4A0.5032980.1366530.3643200.012*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Mn0.00731 (13)0.00453 (14)0.01196 (13)0.00112 (8)0.00470 (9)0.00066 (8)
O10.0118 (4)0.0049 (4)0.0192 (4)0.0018 (3)0.0074 (3)0.0011 (3)
O20.0165 (4)0.0057 (4)0.0163 (4)0.0030 (3)0.0097 (3)0.0001 (3)
O1W0.0105 (4)0.0099 (5)0.0173 (4)0.0014 (3)0.0032 (3)0.0025 (3)
O2W0.0242 (5)0.0076 (5)0.0219 (5)0.0037 (4)0.0172 (4)0.0024 (3)
N10.0123 (5)0.0051 (5)0.0121 (4)0.0013 (3)0.0058 (4)0.0019 (3)
N20.0096 (5)0.0085 (5)0.0134 (4)0.0014 (3)0.0050 (4)0.0002 (4)
C10.0073 (5)0.0070 (5)0.0110 (4)0.0006 (4)0.0018 (4)0.0000 (4)
C20.0101 (5)0.0074 (6)0.0143 (5)0.0010 (4)0.0063 (4)0.0002 (4)
C30.0091 (5)0.0082 (6)0.0106 (4)0.0007 (4)0.0040 (4)0.0002 (4)
C40.0108 (5)0.0090 (6)0.0118 (5)0.0009 (4)0.0049 (4)0.0007 (4)
Geometric parameters (Å, º) top
Mn—O2W2.1510 (10)O2W—H2W20.84 (2)
Mn—O2Wi2.1510 (10)N1—C41.3491 (15)
Mn—O1W2.1934 (10)N1—C31.3871 (14)
Mn—O1Wi2.1935 (10)N1—H1N0.91 (2)
Mn—O12.2050 (9)N2—C41.2993 (16)
Mn—O1i2.2050 (9)N2—C11.3917 (15)
O1—C11.2801 (15)C1—C21.4074 (16)
O2—C31.2778 (14)C2—C31.3892 (17)
O1W—H1W10.80 (3)C2—H2A0.9500
O1W—H1W20.82 (3)C4—H4A0.9500
O2W—H2W10.82 (3)
O2W—Mn—O2Wi180.0Mn—O2W—H2W1106.3 (17)
O2W—Mn—O1W87.76 (4)Mn—O2W—H2W2141.9 (16)
O2Wi—Mn—O1W92.24 (4)H2W1—O2W—H2W2108 (2)
O2W—Mn—O1Wi92.25 (4)C4—N1—C3121.20 (10)
O2Wi—Mn—O1Wi87.75 (4)C4—N1—H1N118.5 (14)
O1W—Mn—O1Wi180.0C3—N1—H1N120.1 (15)
O2W—Mn—O187.49 (4)C4—N2—C1118.21 (10)
O2Wi—Mn—O192.51 (4)O1—C1—N2117.88 (10)
O1W—Mn—O189.62 (4)O1—C1—C2122.43 (11)
O1Wi—Mn—O190.38 (4)N2—C1—C2119.69 (11)
O2W—Mn—O1i92.51 (4)C3—C2—C1120.38 (11)
O2Wi—Mn—O1i87.49 (4)C3—C2—H2A119.8
O1W—Mn—O1i90.38 (4)C1—C2—H2A119.8
O1Wi—Mn—O1i89.62 (4)O2—C3—N1116.96 (11)
O1—Mn—O1i180.0O2—C3—C2126.70 (11)
C1—O1—Mn135.24 (8)N1—C3—C2116.34 (10)
Mn—O1W—H1W1116.9 (17)N2—C4—N1124.15 (11)
Mn—O1W—H1W2115.8 (18)N2—C4—H4A117.9
H1W1—O1W—H1W2105 (2)N1—C4—H4A117.9
Mn—O1—C1—N21.40 (18)C4—N1—C3—O2178.77 (11)
Mn—O1—C1—C2178.55 (9)C4—N1—C3—C21.38 (17)
C4—N2—C1—O1178.88 (11)C1—C2—C3—O2178.56 (12)
C4—N2—C1—C21.17 (17)C1—C2—C3—N11.61 (17)
O1—C1—C2—C3179.55 (11)C1—N2—C4—N11.49 (18)
N2—C1—C2—C30.39 (18)C3—N1—C4—N20.19 (19)
Symmetry code: (i) x+1, y+1, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1W—H1W1···O2ii0.80 (3)2.03 (3)2.8152 (14)170 (2)
O1W—H1W2···O1iii0.82 (3)1.90 (3)2.7127 (13)176 (3)
O2W—H2W1···N20.82 (3)1.91 (3)2.6929 (14)159 (2)
O2W—H2W2···O2iv0.84 (2)1.85 (2)2.6754 (13)167 (2)
N1—H1N···O2v0.91 (2)1.92 (2)2.7966 (14)162 (2)
Symmetry codes: (ii) x, y+1/2, z1/2; (iii) x, y+1, z+1; (iv) x+1, y+1/2, z1/2; (v) x, y, z+1.
 

Acknowledgements

Data were collected by Matthias Zeller of Youngstown State University, Youngstown, Ohio, USA, on an X-ray diffractometer funded by NSF grant 0087210, Ohio Board of Regents Grant CAP-491, and by Youngstown State University. RJB is grateful to NSF award 1205608, Partnership for Reduced Dimensional Materials for partial funding of this research.

Funding information

Funding for this research was provided by: National Science Foundation, Division of Chemistry (award Nos. 0087210, 1205608); Ohio Board of Regents (award No. CAP-491).

References

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