supplementary materials


xu5644 scheme

Acta Cryst. (2012). E68, m1538-m1539    [ doi:10.1107/S1600536812045783 ]

Bis{[mu]-2-[(pyrimidin-2-yl)aminomethyl]phenolato}-[kappa]2N1:O;[kappa]2O:N1-bis({2-[(pyrimidin-2-yl-[kappa]N)aminomethyl]phenol}silver(I)) dihydrate

S. Gao and S. W. Ng

Abstract top

The AgI atom in the title centrosymmetric dinuclear compound, [Ag2(C11H10N3O)2(C11H11N3O)2]·2H2O, shows a T-shaped coordination arising from bonding to the N atom of a neutral 2-[(pyrimidin-2-yl)aminomethyl]phenol ligand, the N atom of the 2-[(pyrimidin-2-yl)aminomethyl]phenolate anion [N-Ag-N = 171.8 (1)°] and the terminal O atom of the other anion [Ag-O = 2.606 (3) Å]. A pair of 2-[(pyrimidin-2-yl)aminomethyl]phenolate anions link the two AgI atoms to form the dinuclear compound. In the crystal, adjacent dinuclear molecules are linked to the lattice water molecules, generating an O-H...O- and N-H...O-connected three-dimensional network. In the crystal, the hydroxy H atom is disordered over two positions in a 1:1 ratio; one half-occupancy H atom is connected to one hydroxy group, whereas the other half-occupancy H atom is connected to another hydroxy group.

Comment top

A recent study reports 2-[(pyrimidin-2-yl)aminomethyl]phenol, a reduced Schiff-base that possesses an acidic phenolic group (Xu et al., 2011). The reaction with silver nitrate yields dinuclear [Ag(C11H10N3O)(C11H11N3O)]2.2H2O (Scheme I, Fig. 1). The asymmetric unit has one Ag atom; however, the hydroxy H-atom is disordered over two positions in a 1:1 ratio. One half-occupancy H-atom is connected to O1 whereas the other half-occupancy atom is connected to O2. The AgI atom shows T-shaped coordination. Adjacent molecules are linked to the lattice water molecules to generate a O–H···O and N–H···O connected three-dimensional network (Table 1).

Related literature top

For the structure of 2-{[(pyrimidin-2-yl)amino]methyl}phenol, see: Xu et al. (2011).

Experimental top

An acetonitrile solution (10 ml) of silver nitrate (1 mmol) was added to a methanol solution (5 ml) of 2-[(pyrimidin-2-yl)aminomethyl]phenol (1 mmol) and potassium hydroxide (0.5 mmol). The solution was filtered and then side aside, away from light, for the growth of crystals. Colorless crystals were obtained after several days.

Refinement top

Hydrogen atoms were placed in calculated positions (C–H 0.93–0.97 Å) and were included in the refinement in the riding model approximation, with U(H) set to 1.2U(C). The amino and hydroxy/water H atoms were located in a difference Fouier map, and were refined with distance restraints of N–H 0.88±0.01, O–H 0.84±0.01 and H···H 1.37±0.01 Å. Their temperature factors were refined.

The hydroxy H-atom is disordered over two positions in a 1:1 ratio; one half-occupancy H-atom is connected to O1 whereas the other half-occupancy atom is connected to O2.

The final difference Fouier map had a peak at 0.83 Å from Ag1 and a hole at 0.84 Å from this atom.

Computing details top

Data collection: RAPID-AUTO (Rigaku, 1998); cell refinement: RAPID-AUTO (Rigaku, 1998); data reduction: CrystalClear (Rigaku/MSC, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. Thermal ellipsoid plot (Barbour, 2001) of [Ag2(C11H10N3O)2(C11H11N3O)]2.H2O at the 50% probability level; hydrogen atoms are drawn as spheres of arbitrary radius. The disorder in the phenolic –OH groups is not shown.
Bis{µ-2-[(pyrimidin-2-yl)aminomethyl]phenolato}- κ2N1:O;κ2O:N1-bis({2-[(pyrimidin-2- yl-κN)aminomethyl]phenol}silver(I)) dihydrate top
Crystal data top
[Ag2(C11H10N3O)2(C11H11N3O)2]·2H2OF(000) = 1072
Mr = 1054.67Dx = 1.631 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 13157 reflections
a = 9.2992 (4) Åθ = 3.1–27.5°
b = 24.808 (1) ŵ = 0.98 mm1
c = 9.8158 (5) ÅT = 293 K
β = 108.453 (1)°Prism, colorless
V = 2148.02 (17) Å30.23 × 0.20 × 0.17 mm
Z = 2
Data collection top
Rigaku R-AXIS RAPID IP
diffractometer
4910 independent reflections
Radiation source: fine-focus sealed tube3230 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.063
ω scanθmax = 27.5°, θmin = 3.1°
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
h = 1211
Tmin = 0.807, Tmax = 0.852k = 3232
20943 measured reflectionsl = 1212
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.044Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.133H atoms treated by a mixture of independent and constrained refinement
S = 1.11 w = 1/[σ2(Fo2) + (0.0382P)2 + 4.7243P]
where P = (Fo2 + 2Fc2)/3
4910 reflections(Δ/σ)max = 0.001
307 parametersΔρmax = 1.27 e Å3
7 restraintsΔρmin = 1.29 e Å3
Crystal data top
[Ag2(C11H10N3O)2(C11H11N3O)2]·2H2OV = 2148.02 (17) Å3
Mr = 1054.67Z = 2
Monoclinic, P21/cMo Kα radiation
a = 9.2992 (4) ŵ = 0.98 mm1
b = 24.808 (1) ÅT = 293 K
c = 9.8158 (5) Å0.23 × 0.20 × 0.17 mm
β = 108.453 (1)°
Data collection top
Rigaku R-AXIS RAPID IP
diffractometer
4910 independent reflections
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
3230 reflections with I > 2σ(I)
Tmin = 0.807, Tmax = 0.852Rint = 0.063
20943 measured reflectionsθmax = 27.5°
Refinement top
R[F2 > 2σ(F2)] = 0.044H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.133Δρmax = 1.27 e Å3
S = 1.11Δρmin = 1.29 e Å3
4910 reflectionsAbsolute structure: ?
307 parametersFlack parameter: ?
7 restraintsRogers parameter: ?
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
Ag10.70167 (5)0.644035 (13)0.56817 (5)0.04905 (15)
O11.0721 (3)0.39077 (12)0.5102 (3)0.0383 (7)
H1O0.990 (7)0.376 (4)0.461 (10)0.057*0.50
O20.1768 (4)0.84419 (14)0.0994 (4)0.0458 (8)
H2O0.095 (7)0.858 (5)0.050 (11)0.069*0.50
O1W0.3708 (5)0.64557 (15)0.4170 (5)0.0650 (11)
H110.289 (4)0.659 (2)0.420 (8)0.097*
H120.353 (6)0.6145 (12)0.382 (7)0.097*
N10.8011 (4)0.51659 (14)0.5833 (4)0.0371 (9)
H10.838 (5)0.5460 (11)0.557 (5)0.045*
N20.6393 (4)0.56969 (14)0.6588 (4)0.0362 (8)
N30.6313 (4)0.47353 (14)0.6741 (4)0.0404 (9)
N40.7537 (4)0.72440 (15)0.5013 (5)0.0441 (10)
N50.7062 (5)0.80270 (15)0.3525 (5)0.0482 (10)
N60.5199 (4)0.73932 (15)0.3360 (5)0.0441 (10)
H60.487 (6)0.7108 (13)0.370 (5)0.053*
C10.5302 (5)0.57248 (19)0.7213 (6)0.0451 (11)
H1A0.49530.60620.73750.054*
C20.4682 (5)0.5276 (2)0.7621 (6)0.0472 (12)
H2A0.39400.53010.80690.057*
C30.5215 (6)0.4788 (2)0.7332 (6)0.0482 (12)
H30.47850.44770.75620.058*
C40.6884 (5)0.51959 (16)0.6398 (5)0.0328 (9)
C50.8671 (5)0.46637 (17)0.5550 (5)0.0350 (9)
H5A0.89790.47100.47010.042*
H5B0.78970.43860.53390.042*
C61.0024 (5)0.44711 (17)0.6770 (5)0.0350 (9)
C71.0368 (6)0.4667 (2)0.8155 (5)0.0443 (11)
H70.97290.49190.83650.053*
C81.1647 (6)0.4494 (2)0.9240 (6)0.0533 (13)
H81.18730.46351.01620.064*
C91.2577 (6)0.4113 (2)0.8933 (6)0.0499 (12)
H91.34350.39950.96530.060*
C101.2245 (5)0.39041 (18)0.7566 (5)0.0404 (10)
H101.28730.36410.73840.048*
C111.0981 (5)0.40809 (16)0.6445 (5)0.0347 (9)
C120.8956 (6)0.7416 (2)0.5634 (7)0.0660 (17)
H12A0.96080.72090.63600.079*
C130.9484 (7)0.7889 (2)0.5233 (9)0.078 (2)
H131.04750.80050.56690.094*
C140.8486 (6)0.8178 (2)0.4167 (7)0.0580 (14)
H140.88190.84980.38750.070*
C150.6627 (5)0.75617 (17)0.3970 (5)0.0392 (10)
C160.4023 (6)0.77407 (18)0.2440 (5)0.0446 (11)
H16A0.31970.75160.18690.054*
H16B0.44370.79300.17830.054*
C170.3390 (5)0.81517 (17)0.3238 (5)0.0355 (10)
C180.3894 (6)0.82048 (19)0.4713 (5)0.0447 (11)
H180.46710.79830.52550.054*
C190.3273 (6)0.8580 (2)0.5401 (6)0.0502 (12)
H190.36280.86090.63960.060*
C200.2126 (6)0.8911 (2)0.4609 (6)0.0503 (12)
H200.17010.91630.50690.060*
C210.1606 (6)0.88692 (19)0.3134 (6)0.0462 (12)
H210.08340.90950.26040.055*
C220.2225 (5)0.84915 (17)0.2430 (5)0.0361 (10)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Ag10.0552 (3)0.02896 (19)0.0589 (3)0.00169 (16)0.01237 (19)0.00829 (16)
O10.0365 (17)0.0369 (16)0.0407 (19)0.0016 (14)0.0111 (15)0.0062 (13)
O20.047 (2)0.0487 (19)0.0391 (19)0.0124 (16)0.0096 (16)0.0051 (15)
O1W0.076 (3)0.048 (2)0.081 (3)0.020 (2)0.040 (3)0.005 (2)
N10.036 (2)0.0258 (17)0.054 (2)0.0002 (15)0.0206 (19)0.0032 (16)
N20.0352 (19)0.0296 (17)0.042 (2)0.0038 (16)0.0092 (17)0.0002 (15)
N30.040 (2)0.0309 (18)0.055 (3)0.0011 (16)0.0223 (19)0.0027 (17)
N40.036 (2)0.0319 (19)0.061 (3)0.0074 (17)0.011 (2)0.0106 (18)
N50.054 (3)0.036 (2)0.055 (3)0.0006 (19)0.018 (2)0.0101 (18)
N60.042 (2)0.0288 (19)0.058 (3)0.0006 (17)0.010 (2)0.0057 (18)
C10.043 (3)0.040 (2)0.053 (3)0.009 (2)0.018 (2)0.003 (2)
C20.035 (2)0.060 (3)0.050 (3)0.006 (2)0.019 (2)0.000 (2)
C30.044 (3)0.043 (3)0.062 (3)0.002 (2)0.023 (3)0.007 (2)
C40.029 (2)0.028 (2)0.039 (2)0.0002 (17)0.0069 (19)0.0012 (17)
C50.030 (2)0.031 (2)0.046 (3)0.0026 (18)0.014 (2)0.0020 (18)
C60.035 (2)0.032 (2)0.040 (2)0.0017 (18)0.016 (2)0.0007 (18)
C70.047 (3)0.045 (3)0.044 (3)0.007 (2)0.020 (2)0.000 (2)
C80.056 (3)0.062 (3)0.040 (3)0.004 (3)0.014 (3)0.001 (2)
C90.044 (3)0.059 (3)0.045 (3)0.005 (2)0.011 (2)0.009 (2)
C100.035 (2)0.038 (2)0.048 (3)0.007 (2)0.012 (2)0.003 (2)
C110.036 (2)0.030 (2)0.041 (3)0.0045 (18)0.015 (2)0.0016 (18)
C120.042 (3)0.052 (3)0.095 (5)0.010 (3)0.008 (3)0.022 (3)
C130.040 (3)0.058 (4)0.131 (6)0.005 (3)0.017 (4)0.022 (4)
C140.053 (3)0.044 (3)0.079 (4)0.004 (3)0.024 (3)0.010 (3)
C150.042 (3)0.028 (2)0.050 (3)0.0072 (19)0.019 (2)0.0009 (19)
C160.044 (3)0.033 (2)0.053 (3)0.005 (2)0.010 (2)0.002 (2)
C170.036 (2)0.030 (2)0.039 (2)0.0042 (18)0.009 (2)0.0043 (18)
C180.045 (3)0.041 (2)0.047 (3)0.004 (2)0.013 (2)0.004 (2)
C190.060 (3)0.054 (3)0.036 (3)0.007 (3)0.013 (2)0.003 (2)
C200.055 (3)0.051 (3)0.051 (3)0.002 (2)0.025 (3)0.007 (2)
C210.045 (3)0.040 (3)0.057 (3)0.007 (2)0.021 (3)0.004 (2)
C220.033 (2)0.035 (2)0.041 (2)0.0045 (18)0.013 (2)0.0049 (18)
Geometric parameters (Å, º) top
Ag1—N42.200 (4)C5—H5A0.9700
Ag1—N22.204 (4)C5—H5B0.9700
Ag1—O1i2.606 (3)C6—C71.382 (6)
Ag1—O1W2.963 (5)C6—C111.419 (6)
O1—C111.333 (5)C7—C81.389 (7)
O1—H1O0.840 (10)C7—H70.9300
O2—C221.343 (5)C8—C91.379 (7)
O2—H2O0.839 (10)C8—H80.9300
O1W—H110.842 (10)C9—C101.379 (7)
O1W—H120.840 (10)C9—H90.9300
N1—C41.334 (5)C10—C111.402 (6)
N1—C51.454 (5)C10—H100.9300
N1—H10.877 (10)C12—C131.376 (8)
N2—C11.343 (6)C12—H12A0.9300
N2—C41.357 (5)C13—C141.363 (8)
N3—C31.331 (6)C13—H130.9300
N3—C41.347 (5)C14—H140.9300
N4—C121.336 (7)C16—C171.514 (6)
N4—C151.356 (6)C16—H16A0.9700
N5—C141.328 (7)C16—H16B0.9700
N5—C151.341 (6)C17—C181.379 (6)
N6—C151.340 (6)C17—C221.403 (6)
N6—C161.459 (6)C18—C191.379 (7)
N6—H60.877 (10)C18—H180.9300
C1—C21.371 (7)C19—C201.375 (7)
C1—H1A0.9300C19—H190.9300
C2—C31.371 (7)C20—C211.377 (7)
C2—H2A0.9300C20—H200.9300
C3—H30.9300C21—C221.393 (6)
C5—C61.514 (6)C21—H210.9300
N4—Ag1—N2171.75 (14)C9—C8—C7119.2 (5)
N4—Ag1—O1i86.43 (12)C9—C8—H8120.4
N2—Ag1—O1i100.50 (11)C7—C8—H8120.4
N4—Ag1—O1W97.51 (13)C10—C9—C8120.5 (5)
N2—Ag1—O1W81.30 (12)C10—C9—H9119.7
O1i—Ag1—O1W131.60 (11)C8—C9—H9119.7
C11—O1—H1O124 (8)C9—C10—C11121.4 (4)
C22—O2—H2O120 (9)C9—C10—H10119.3
Ag1—O1W—H11142 (4)C11—C10—H10119.3
Ag1—O1W—H12103 (4)O1—C11—C10121.3 (4)
H11—O1W—H12109 (2)O1—C11—C6120.8 (4)
C4—N1—C5124.2 (3)C10—C11—C6117.8 (4)
C4—N1—H1120 (3)N4—C12—C13122.1 (5)
C5—N1—H1115 (3)N4—C12—H12A118.9
C1—N2—C4116.5 (4)C13—C12—H12A118.9
C1—N2—Ag1118.3 (3)C14—C13—C12116.8 (5)
C4—N2—Ag1124.6 (3)C14—C13—H13121.6
C3—N3—C4116.3 (4)C12—C13—H13121.6
C12—N4—C15116.7 (4)N5—C14—C13123.3 (5)
C12—N4—Ag1115.6 (3)N5—C14—H14118.3
C15—N4—Ag1127.5 (3)C13—C14—H14118.3
C14—N5—C15116.5 (4)N6—C15—N5118.8 (4)
C15—N6—C16122.4 (4)N6—C15—N4116.8 (4)
C15—N6—H6120 (4)N5—C15—N4124.5 (4)
C16—N6—H6115 (4)N6—C16—C17114.6 (4)
N2—C1—C2122.7 (4)N6—C16—H16A108.6
N2—C1—H1A118.7C17—C16—H16A108.6
C2—C1—H1A118.7N6—C16—H16B108.6
C3—C2—C1116.3 (4)C17—C16—H16B108.6
C3—C2—H2A121.8H16A—C16—H16B107.6
C1—C2—H2A121.8C18—C17—C22118.8 (4)
N3—C3—C2123.7 (4)C18—C17—C16123.3 (4)
N3—C3—H3118.2C22—C17—C16118.0 (4)
C2—C3—H3118.2C19—C18—C17121.5 (5)
N1—C4—N3118.7 (4)C19—C18—H18119.3
N1—C4—N2116.8 (4)C17—C18—H18119.3
N3—C4—N2124.4 (4)C20—C19—C18119.7 (5)
N1—C5—C6114.5 (4)C20—C19—H19120.1
N1—C5—H5A108.6C18—C19—H19120.1
C6—C5—H5A108.6C19—C20—C21120.1 (5)
N1—C5—H5B108.6C19—C20—H20120.0
C6—C5—H5B108.6C21—C20—H20120.0
H5A—C5—H5B107.6C20—C21—C22120.6 (5)
C7—C6—C11119.6 (4)C20—C21—H21119.7
C7—C6—C5122.9 (4)C22—C21—H21119.7
C11—C6—C5117.4 (4)O2—C22—C21122.6 (4)
C6—C7—C8121.5 (4)O2—C22—C17118.0 (4)
C6—C7—H7119.3C21—C22—C17119.3 (4)
C8—C7—H7119.3
O1i—Ag1—N2—C1175.4 (3)C7—C6—C11—O1176.3 (4)
O1W—Ag1—N2—C153.7 (3)C5—C6—C11—O12.4 (6)
O1i—Ag1—N2—C413.9 (4)C7—C6—C11—C100.7 (6)
O1W—Ag1—N2—C4117.0 (4)C5—C6—C11—C10179.4 (4)
O1i—Ag1—N4—C1255.8 (4)C15—N4—C12—C130.6 (9)
O1W—Ag1—N4—C12172.7 (4)Ag1—N4—C12—C13174.3 (5)
O1i—Ag1—N4—C15118.4 (4)N4—C12—C13—C140.2 (11)
O1W—Ag1—N4—C1513.1 (4)C15—N5—C14—C130.4 (9)
C4—N2—C1—C21.1 (7)C12—C13—C14—N50.4 (10)
Ag1—N2—C1—C2170.3 (4)C16—N6—C15—N512.2 (7)
N2—C1—C2—C31.2 (8)C16—N6—C15—N4167.5 (4)
C4—N3—C3—C21.3 (8)C14—N5—C15—N6179.7 (5)
C1—C2—C3—N32.6 (8)C14—N5—C15—N40.1 (7)
C5—N1—C4—N30.4 (7)C12—N4—C15—N6179.2 (5)
C5—N1—C4—N2179.7 (4)Ag1—N4—C15—N66.6 (6)
C3—N3—C4—N1178.5 (4)C12—N4—C15—N50.6 (7)
C3—N3—C4—N21.4 (7)Ag1—N4—C15—N5173.6 (3)
C1—N2—C4—N1177.3 (4)C15—N6—C16—C1777.1 (6)
Ag1—N2—C4—N111.8 (6)N6—C16—C17—C181.2 (6)
C1—N2—C4—N32.6 (7)N6—C16—C17—C22178.3 (4)
Ag1—N2—C4—N3168.3 (3)C22—C17—C18—C190.5 (7)
C4—N1—C5—C691.6 (5)C16—C17—C18—C19179.1 (4)
N1—C5—C6—C716.3 (6)C17—C18—C19—C200.1 (7)
N1—C5—C6—C11162.4 (4)C18—C19—C20—C210.3 (8)
C11—C6—C7—C80.8 (7)C19—C20—C21—C220.4 (7)
C5—C6—C7—C8177.8 (4)C20—C21—C22—O2179.1 (4)
C6—C7—C8—C91.2 (8)C20—C21—C22—C170.0 (7)
C7—C8—C9—C100.1 (8)C18—C17—C22—O2178.7 (4)
C8—C9—C10—C111.5 (7)C16—C17—C22—O21.7 (6)
C9—C10—C11—O1175.2 (4)C18—C17—C22—C210.4 (6)
C9—C10—C11—C61.9 (6)C16—C17—C22—C21179.2 (4)
Symmetry code: (i) x+2, y+1, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1o···O2ii0.84 (1)1.68 (3)2.504 (4)166 (12)
O2—H2o···O1iii0.84 (1)1.68 (3)2.504 (4)166 (13)
O1w—H11···O2iv0.84 (1)2.31 (6)2.927 (5)130 (6)
O1w—H12···N3v0.84 (1)2.27 (2)3.085 (5)165 (6)
N1—H1···O1i0.88 (1)1.99 (1)2.863 (5)176 (4)
N6—H6···O1w0.88 (1)2.08 (2)2.943 (5)169 (5)
Symmetry codes: (i) x+2, y+1, z+1; (ii) x+1, y1/2, z+1/2; (iii) x+1, y+1/2, z+1/2; (iv) x, y+3/2, z+1/2; (v) x+1, y+1, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1o···O2i0.84 (1)1.68 (3)2.504 (4)166 (12)
O2—H2o···O1ii0.84 (1)1.68 (3)2.504 (4)166 (13)
O1w—H11···O2iii0.84 (1)2.31 (6)2.927 (5)130 (6)
O1w—H12···N3iv0.84 (1)2.27 (2)3.085 (5)165 (6)
N1—H1···O1v0.88 (1)1.99 (1)2.863 (5)176 (4)
N6—H6···O1w0.88 (1)2.08 (2)2.943 (5)169 (5)
Symmetry codes: (i) x+1, y1/2, z+1/2; (ii) x+1, y+1/2, z+1/2; (iii) x, y+3/2, z+1/2; (iv) x+1, y+1, z+1; (v) x+2, y+1, z+1.
Acknowledgements top

We thank the Key Project of the Natural Science Foundation of Heilongjiang Province (No. ZD200903), the Key Project of the Education Bureau of Heilongjiang Province (No. 12511z023, No. 2011CJHB006), the Innovation team of the Education Bureau of Heilongjiang Province (No. 2010 t d03), Heilongjiang University (Hdtd2010–04) and the Ministry of Higher Education of Malaysia (grant No. UM.C/HIR/MOHE/SC/12) for supporting this study.

references
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