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

Shennara, K.A.; Butcher, R.J.; Greenaway, F.T.

doi:10.1107/S2056989017004649

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Volume 73| Part 4| April 2017| Pages 620-622

https://doi.org/10.1107/S2056989017004649

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

Khaled A. Shennara,^a Ray J. Butcher ^b and Frederick T. Greenaway ^a ^*

^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 Mn^II 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.

Keywords: crystal structure; 4,6-dihydroxypyrimidine; manganese(II); octahedral coordination.

CCDC reference: 1539878

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 ). 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 ; Wang et al., 2006 ), 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 ).

2. Structural commentary

Crystallographic analysis reveals that the title compound consists of a centrosymmetric mononuclear [Mn(C₄H₃N₂O₂)₂(H₂O)₄] complex in which the Mn^II 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). 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). 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).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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⋯O2^iv	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
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). This gives rise to a complex three-dimensional network, which is best analyzed in terms of graph-set theory (Etter et al., 1990 ). There are four interpenetrating chains of hydrogen bonds. The first has a C(4)[R₂²(8)] motif and is shown in Fig. 1. The second has a C(6)[R₁¹(6)R₂²(8)] motif and is shown in Fig. 2. The chain depicted in Fig. 3 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.

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
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
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 ) 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). EPR spectra of aqueous solutions of the title complex had g = 2.006 and A_iso(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. All H atoms were positioned geometrically and refined as riding: C—H = 0.95 Å with U_iso(H) = 1.2U_eq(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]
M_r	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)
V (Å³)	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 )
T_min, T_max	0.614, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	2971, 1848, 1752
R_int	0.016
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.48, −0.32
Computer programs: APEX2 (Bruker, 2005 ), SAINT (Bruker, 2002 ), SHELXT (Sheldrick, 2015a ), SHELXL2014 (Sheldrick, 2015b ) and SHELXTL (Sheldrick, 2008 ).

Supporting information

CCDC reference: 1539878

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989017004649/wm5373sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017004649/wm5373Isup2.hkl

checkCIF report

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
M_r = 349.17	D_x = 1.766 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 5.2156 (5) Å	Cell parameters from 2512 reflections
b = 14.0812 (14) Å	θ = 2.7–31.2°
c = 9.0595 (9) Å	µ = 1.05 mm⁻¹
β = 99.366 (2)°	T = 120 K
V = 656.48 (11) Å³	Block, yellow
Z = 2	0.55 × 0.41 × 0.40 mm

Data collection top

Bruker APEXII CCD diffractometer	1752 reflections with I > 2σ(I)
ω scans	R_int = 0.016
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	θ_max = 31.2°, θ_min = 2.9°
T_min = 0.614, T_max = 0.746	h = −7→7
2971 measured reflections	k = −18→18
1848 independent reflections	l = −3→12

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.027	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.071	w = 1/[σ²(F_o²) + (0.033P)² + 0.3858P] where P = (F_o² + 2F_c²)/3
S = 1.10	(Δ/σ)_max < 0.001
1848 reflections	Δρ_max = 0.48 e Å⁻³
117 parameters	Δρ_min = −0.32 e Å⁻³

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

	x	y	z	U_iso*/U_eq
Mn	0.500000	0.500000	0.500000	0.00759 (9)
O1	0.25688 (17)	0.38379 (6)	0.56407 (10)	0.01144 (18)
O2	−0.08946 (18)	0.07807 (6)	0.62265 (10)	0.01204 (18)
O1W	0.17104 (18)	0.54921 (7)	0.33556 (11)	0.01243 (18)
H1W1	0.114 (5)	0.5129 (16)	0.271 (3)	0.029 (6)*
H1W2	0.045 (5)	0.5682 (17)	0.370 (3)	0.040 (7)*
O2W	0.6010 (2)	0.40720 (7)	0.32982 (11)	0.0164 (2)
H2W1	0.562 (5)	0.3534 (18)	0.353 (3)	0.037 (6)*
H2W2	0.702 (5)	0.4026 (17)	0.267 (3)	0.035 (6)*
N1	0.2263 (2)	0.10486 (8)	0.48187 (11)	0.0094 (2)
H1N	0.219 (5)	0.0429 (18)	0.453 (3)	0.033 (6)*
N2	0.4089 (2)	0.25411 (8)	0.45266 (11)	0.0102 (2)
C1	0.2421 (2)	0.29415 (9)	0.54070 (13)	0.0084 (2)
C2	0.0651 (2)	0.23594 (9)	0.60057 (13)	0.0101 (2)
H2A	−0.049639	0.263207	0.660180	0.012*
C3	0.0573 (2)	0.13885 (9)	0.57302 (13)	0.0090 (2)
C4	0.3920 (2)	0.16342 (9)	0.42645 (13)	0.0102 (2)
H4A	0.503298	0.136653	0.364320	0.012*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Mn	0.00731 (13)	0.00453 (14)	0.01196 (13)	−0.00112 (8)	0.00470 (9)	−0.00066 (8)
O1	0.0118 (4)	0.0049 (4)	0.0192 (4)	−0.0018 (3)	0.0074 (3)	−0.0011 (3)
O2	0.0165 (4)	0.0057 (4)	0.0163 (4)	−0.0030 (3)	0.0097 (3)	−0.0001 (3)
O1W	0.0105 (4)	0.0099 (5)	0.0173 (4)	0.0014 (3)	0.0032 (3)	−0.0025 (3)
O2W	0.0242 (5)	0.0076 (5)	0.0219 (5)	−0.0037 (4)	0.0172 (4)	−0.0024 (3)
N1	0.0123 (5)	0.0051 (5)	0.0121 (4)	−0.0013 (3)	0.0058 (4)	−0.0019 (3)
N2	0.0096 (5)	0.0085 (5)	0.0134 (4)	−0.0014 (3)	0.0050 (4)	−0.0002 (4)
C1	0.0073 (5)	0.0070 (5)	0.0110 (4)	−0.0006 (4)	0.0018 (4)	0.0000 (4)
C2	0.0101 (5)	0.0074 (6)	0.0143 (5)	−0.0010 (4)	0.0063 (4)	−0.0002 (4)
C3	0.0091 (5)	0.0082 (6)	0.0106 (4)	−0.0007 (4)	0.0040 (4)	0.0002 (4)
C4	0.0108 (5)	0.0090 (6)	0.0118 (5)	−0.0009 (4)	0.0049 (4)	0.0007 (4)

Geometric parameters (Å, º) top

Mn—O2W	2.1510 (10)	O2W—H2W2	0.84 (2)
Mn—O2Wⁱ	2.1510 (10)	N1—C4	1.3491 (15)
Mn—O1W	2.1934 (10)	N1—C3	1.3871 (14)
Mn—O1Wⁱ	2.1935 (10)	N1—H1N	0.91 (2)
Mn—O1	2.2050 (9)	N2—C4	1.2993 (16)
Mn—O1ⁱ	2.2050 (9)	N2—C1	1.3917 (15)
O1—C1	1.2801 (15)	C1—C2	1.4074 (16)
O2—C3	1.2778 (14)	C2—C3	1.3892 (17)
O1W—H1W1	0.80 (3)	C2—H2A	0.9500
O1W—H1W2	0.82 (3)	C4—H4A	0.9500
O2W—H2W1	0.82 (3)

O2W—Mn—O2Wⁱ	180.0	Mn—O2W—H2W1	106.3 (17)
O2W—Mn—O1W	87.76 (4)	Mn—O2W—H2W2	141.9 (16)
O2Wⁱ—Mn—O1W	92.24 (4)	H2W1—O2W—H2W2	108 (2)
O2W—Mn—O1Wⁱ	92.25 (4)	C4—N1—C3	121.20 (10)
O2Wⁱ—Mn—O1Wⁱ	87.75 (4)	C4—N1—H1N	118.5 (14)
O1W—Mn—O1Wⁱ	180.0	C3—N1—H1N	120.1 (15)
O2W—Mn—O1	87.49 (4)	C4—N2—C1	118.21 (10)
O2Wⁱ—Mn—O1	92.51 (4)	O1—C1—N2	117.88 (10)
O1W—Mn—O1	89.62 (4)	O1—C1—C2	122.43 (11)
O1Wⁱ—Mn—O1	90.38 (4)	N2—C1—C2	119.69 (11)
O2W—Mn—O1ⁱ	92.51 (4)	C3—C2—C1	120.38 (11)
O2Wⁱ—Mn—O1ⁱ	87.49 (4)	C3—C2—H2A	119.8
O1W—Mn—O1ⁱ	90.38 (4)	C1—C2—H2A	119.8
O1Wⁱ—Mn—O1ⁱ	89.62 (4)	O2—C3—N1	116.96 (11)
O1—Mn—O1ⁱ	180.0	O2—C3—C2	126.70 (11)
C1—O1—Mn	135.24 (8)	N1—C3—C2	116.34 (10)
Mn—O1W—H1W1	116.9 (17)	N2—C4—N1	124.15 (11)
Mn—O1W—H1W2	115.8 (18)	N2—C4—H4A	117.9
H1W1—O1W—H1W2	105 (2)	N1—C4—H4A	117.9

Mn—O1—C1—N2	−1.40 (18)	C4—N1—C3—O2	−178.77 (11)
Mn—O1—C1—C2	178.55 (9)	C4—N1—C3—C2	1.38 (17)
C4—N2—C1—O1	−178.88 (11)	C1—C2—C3—O2	178.56 (12)
C4—N2—C1—C2	1.17 (17)	C1—C2—C3—N1	−1.61 (17)
O1—C1—C2—C3	−179.55 (11)	C1—N2—C4—N1	−1.49 (18)
N2—C1—C2—C3	0.39 (18)	C3—N1—C4—N2	0.19 (19)

Symmetry code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1W—H1W1···O2ⁱⁱ	0.80 (3)	2.03 (3)	2.8152 (14)	170 (2)
O1W—H1W2···O1ⁱⁱⁱ	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···O2^iv	0.84 (2)	1.85 (2)	2.6754 (13)	167 (2)
N1—H1N···O2^v	0.91 (2)	1.92 (2)	2.7966 (14)	162 (2)

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

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