supplementary materials


hg5347 scheme

Acta Cryst. (2013). E69, o1577-o1578    [ doi:10.1107/S1600536813025774 ]

tert-Butyl 4-{[2-amino-4-(2-hydroxyphenyl)pyrimidin-5-yl]methyl}piperazine-1-carboxylate

N. N. Gajera, M. C. Patel, M. M. Jotani and E. R. T. Tiekink

Abstract top

In the title compound, C20H27N5O3, the central piperazine ring adopts a chair conformation, with the N-bound carboxylate and methylene substituents occupying bisectional and equatorial orientations, respectively. A twist is evident between the aromatic rings [dihedral angle = 25.61 (9)°] but an intramolecular O-H...N hydrogen bond persists between these. Supramolecular tapes along [1-10] are formed in the crystal packing through N(amino)-H...O(hydroxyl) and N(amino)-H...N(pyrimidinyl) hydrogen bonds, and these are linked into layers in the ab plane by [pi]-[pi] interactions [inter-centroid distance between pyrimidinyl rings = 3.5919 (9) Å].

Comment top

Pyrimidine-containing heterocyclic compounds show significant biological importance through various activities such as anti-viral, anti-tumour, anti-proliferative, anti-diabatic, anti-bacterial, etc. (Topalis et al., 2011; Sbardella et al., 2011; Zhang et al., 2011). It was the effectiveness of these derivatives against anti-microbial strains, such as S. aureus and P. aeruginosa, that motivated the present structural studies of a title compound, (I).

Despite there being a twist between the two aromatic rings in (I), Fig. 1, manifested in a dihedral angle of 25.61 (9)°, an intramolecular O—H···N hydrogen bond persists, Table 1. The piperazine ring adopts a chair conformation, and the N1- and N2-bound carboxylate and methylene substituents have bisectional and equatorial orientations, respectively.

In the crystal packing molecules assemble into supramolecular tapes along [1 - 1 0]. The amino-H atoms form hydrogen bonds (Table 1) to pyrimidinyl-N and hydroxyl-O atoms from different molecules, forming centrosymmetric eight-membered {···HNCN}2 and 16-membered {···HNCNC3O}2 synthons, respectively, Fig. 2. Layers in the ab plane are formed by ππ interactions occurring between centrosymmetrically related pyrimidinyl ring [inter-centroid distance = 3.5919 (9) Å for symmetry operation 2 - x, 1 - y, -z], with the layers being associated via hydrophobic interactions, Fig. 3.

Related literature top

For the biological activity of pyrimidine-containing heterocyclic compounds, see: Topalis et al. (2011); Sbardella et al. (2011); Zhang et al. (2011). For the synthesis, see: Patel et al. (2011).

Experimental top

The title compound, (I), was prepared according to the procedure reported in the literature (Patel et al., 2011). Crystals were obtained by were obtained by slow evaporation from an ethanol solution of (I).

Refinement top

The C-bound H atoms were geometrically placed (C—H = 0.93–0.97 Å) and refined as riding with Uiso(H) = 1.2–1.5Ueq(C). The O– and N-bound H-atoms were refined with the distance restraints O—H = 0.82±0.01 and N—H = 0.86±0.01 Å, and with Uiso(H) = 1.5Ueq(O) and 1.2Ueq(N).

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: APEX2 and SAINT (Bruker, 2004); data reduction: SAINT (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) showing the atom-labelling scheme and displacement ellipsoids at the 35% probability level.
[Figure 2] Fig. 2. View of the supramolecular tape along [1 - 1 0] in (I) mediated by N—H···O, N hydrogen bonds, shown as orange and blue dashed lines, respectively.
[Figure 3] Fig. 3. A view in projection down the b axis of the unit-cell contents for (I). The N—H···O, N—H···N and ππ interactions are shown as orange, blue and purple dashed lines, respectively.
tert-Butyl 4-{[2-amino-4-(2-hydroxyphenyl)pyrimidin-5-yl]methyl}piperazine-1-carboxylate top
Crystal data top
C20H27N5O3F(000) = 824
Mr = 385.47Dx = 1.231 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 5662 reflections
a = 6.1925 (2) Åθ = 2.5–24.9°
b = 8.2636 (2) ŵ = 0.09 mm1
c = 40.7287 (11) ÅT = 293 K
β = 93.513 (2)°Block, yellow
V = 2080.27 (10) Å30.47 × 0.35 × 0.31 mm
Z = 4
Data collection top
Bruker APEXII CCD
diffractometer
4985 independent reflections
Radiation source: fine-focus sealed tube3339 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.026
Detector resolution: 10.0 pixels mm-1θmax = 28.1°, θmin = 1.0°
ω and φ scanh = 88
Absorption correction: multi-scan
(SADABS; Bruker, 2004)
k = 1010
Tmin = 0.980, Tmax = 0.997l = 5353
20251 measured reflections
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)] = 0.050Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.141H atoms treated by a mixture of independent and constrained refinement
S = 1.04 w = 1/[σ2(Fo2) + (0.0598P)2 + 0.4709P]
where P = (Fo2 + 2Fc2)/3
4984 reflections(Δ/σ)max < 0.001
265 parametersΔρmax = 0.19 e Å3
3 restraintsΔρmin = 0.17 e Å3
Crystal data top
C20H27N5O3V = 2080.27 (10) Å3
Mr = 385.47Z = 4
Monoclinic, P21/nMo Kα radiation
a = 6.1925 (2) ŵ = 0.09 mm1
b = 8.2636 (2) ÅT = 293 K
c = 40.7287 (11) Å0.47 × 0.35 × 0.31 mm
β = 93.513 (2)°
Data collection top
Bruker APEXII CCD
diffractometer
4985 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2004)
3339 reflections with I > 2σ(I)
Tmin = 0.980, Tmax = 0.997Rint = 0.026
20251 measured reflectionsθmax = 28.1°
Refinement top
R[F2 > 2σ(F2)] = 0.050H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.141Δρmax = 0.19 e Å3
S = 1.04Δρmin = 0.17 e Å3
4984 reflectionsAbsolute structure: ?
265 parametersAbsolute structure parameter: ?
3 restraintsRogers parameter: ?
Special details top

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

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > 2σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.91283 (18)0.00416 (15)0.20530 (3)0.0595 (3)
O21.2654 (2)0.03360 (18)0.19456 (4)0.0730 (4)
O30.7761 (2)0.93303 (17)0.02308 (4)0.0754 (4)
H1O0.890 (3)0.881 (3)0.0213 (7)0.113*
N11.0148 (2)0.2184 (2)0.17776 (4)0.0570 (4)
N20.89391 (19)0.36533 (16)0.11658 (3)0.0439 (3)
N31.2749 (2)0.47841 (18)0.02609 (3)0.0547 (4)
N41.0670 (2)0.71577 (17)0.03355 (3)0.0485 (3)
N51.3458 (3)0.7126 (2)0.00122 (4)0.0586 (4)
H1N1.453 (2)0.660 (2)0.0085 (5)0.070*
H2N1.313 (3)0.8128 (13)0.0043 (5)0.070*
C10.9389 (3)0.1517 (2)0.22215 (5)0.0643 (5)
C20.7106 (4)0.1849 (3)0.23163 (7)0.0982 (8)
H2A0.61680.19580.21210.147*
H2B0.66190.09680.24460.147*
H2C0.70840.28330.24420.147*
C31.0205 (6)0.2767 (3)0.19926 (8)0.1142 (10)
H3A0.92650.28120.17960.171*
H3B1.02330.38050.20990.171*
H3C1.16400.24850.19360.171*
C41.0877 (4)0.1339 (3)0.25247 (6)0.0862 (7)
H4A1.23090.10870.24620.129*
H4B1.09090.23340.26470.129*
H4C1.03650.04830.26590.129*
C51.0795 (3)0.0788 (2)0.19248 (4)0.0502 (4)
C61.1675 (3)0.3157 (3)0.16089 (4)0.0583 (5)
H6A1.31260.27420.16560.070*
H6B1.16330.42630.16880.070*
C71.1151 (2)0.3135 (2)0.12434 (4)0.0505 (4)
H7A1.21350.38480.11360.061*
H7B1.13460.20480.11600.061*
C80.7452 (2)0.2609 (2)0.13308 (4)0.0539 (4)
H8A0.75850.15090.12510.065*
H8B0.59780.29650.12780.065*
C90.7909 (3)0.2634 (2)0.16981 (4)0.0571 (5)
H9A0.76410.37100.17820.069*
H9B0.69550.18830.18010.069*
C100.8377 (3)0.3662 (2)0.08106 (4)0.0501 (4)
H10A0.68810.39980.07740.060*
H10B0.84890.25660.07280.060*
C110.9763 (3)0.4747 (2)0.06151 (4)0.0461 (4)
C121.1442 (3)0.4048 (2)0.04594 (4)0.0523 (4)
H121.16840.29510.04970.063*
C131.2268 (3)0.6347 (2)0.02015 (4)0.0482 (4)
C140.9433 (2)0.6398 (2)0.05486 (4)0.0452 (4)
C150.7717 (3)0.7411 (2)0.06797 (4)0.0496 (4)
C160.6802 (3)0.7041 (3)0.09754 (5)0.0661 (5)
H160.73740.61900.11020.079*
C170.5086 (4)0.7892 (3)0.10848 (6)0.0808 (6)
H170.45080.76210.12830.097*
C180.4230 (4)0.9149 (3)0.08982 (6)0.0800 (6)
H180.30160.96940.09640.096*
C190.5151 (3)0.9602 (2)0.06172 (6)0.0712 (6)
H190.45821.04750.04970.085*
C200.6908 (3)0.8788 (2)0.05086 (5)0.0567 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0471 (6)0.0574 (7)0.0739 (8)0.0036 (5)0.0027 (6)0.0193 (6)
O20.0452 (7)0.0813 (9)0.0922 (10)0.0159 (7)0.0017 (6)0.0178 (8)
O30.0799 (10)0.0616 (9)0.0863 (10)0.0078 (7)0.0171 (8)0.0277 (7)
N10.0377 (7)0.0774 (10)0.0562 (8)0.0055 (7)0.0054 (6)0.0268 (7)
N20.0354 (6)0.0546 (8)0.0422 (7)0.0024 (6)0.0075 (5)0.0110 (6)
N30.0592 (8)0.0581 (9)0.0484 (8)0.0008 (7)0.0160 (7)0.0056 (7)
N40.0494 (7)0.0532 (8)0.0432 (7)0.0058 (6)0.0048 (6)0.0056 (6)
N50.0649 (10)0.0591 (9)0.0535 (9)0.0065 (8)0.0181 (7)0.0079 (7)
C10.0691 (12)0.0473 (10)0.0758 (13)0.0031 (9)0.0005 (10)0.0118 (9)
C20.0747 (15)0.0852 (16)0.134 (2)0.0138 (13)0.0032 (14)0.0445 (16)
C30.156 (3)0.0629 (15)0.124 (2)0.0019 (17)0.011 (2)0.0182 (15)
C40.0856 (15)0.0896 (16)0.0818 (15)0.0095 (13)0.0074 (12)0.0244 (13)
C50.0421 (9)0.0593 (10)0.0487 (9)0.0045 (8)0.0001 (7)0.0036 (8)
C60.0403 (8)0.0773 (12)0.0574 (10)0.0038 (8)0.0026 (7)0.0172 (9)
C70.0358 (8)0.0628 (10)0.0540 (9)0.0031 (7)0.0112 (7)0.0118 (8)
C80.0333 (8)0.0714 (11)0.0573 (10)0.0014 (8)0.0060 (7)0.0216 (8)
C90.0411 (8)0.0762 (12)0.0554 (10)0.0142 (8)0.0142 (7)0.0245 (9)
C100.0463 (9)0.0600 (10)0.0444 (9)0.0030 (8)0.0053 (7)0.0093 (7)
C110.0469 (8)0.0537 (9)0.0378 (8)0.0015 (7)0.0033 (6)0.0070 (7)
C120.0597 (10)0.0529 (10)0.0454 (9)0.0014 (8)0.0122 (7)0.0069 (7)
C130.0506 (9)0.0558 (10)0.0385 (8)0.0084 (8)0.0047 (7)0.0028 (7)
C140.0428 (8)0.0546 (9)0.0377 (8)0.0033 (7)0.0005 (6)0.0035 (7)
C150.0475 (9)0.0512 (9)0.0500 (9)0.0018 (7)0.0027 (7)0.0020 (7)
C160.0683 (12)0.0707 (12)0.0607 (11)0.0132 (10)0.0153 (9)0.0075 (9)
C170.0839 (15)0.0805 (15)0.0813 (15)0.0171 (12)0.0316 (12)0.0045 (12)
C180.0726 (13)0.0613 (13)0.1083 (18)0.0137 (11)0.0234 (13)0.0116 (12)
C190.0693 (12)0.0494 (11)0.0952 (16)0.0089 (9)0.0092 (11)0.0029 (10)
C200.0567 (10)0.0460 (9)0.0672 (11)0.0044 (8)0.0020 (8)0.0042 (8)
Geometric parameters (Å, º) top
O1—C51.336 (2)C4—H4C0.9600
O1—C11.464 (2)C6—C71.504 (2)
O2—C51.2080 (19)C6—H6A0.9700
O3—C201.354 (2)C6—H6B0.9700
O3—H1O0.832 (10)C7—H7A0.9700
N1—C51.350 (2)C7—H7B0.9700
N1—C61.447 (2)C8—C91.505 (2)
N1—C91.453 (2)C8—H8A0.9700
N2—C71.4513 (19)C8—H8B0.9700
N2—C81.4564 (19)C9—H9A0.9700
N2—C101.467 (2)C9—H9B0.9700
N3—C121.326 (2)C10—C111.503 (2)
N3—C131.345 (2)C10—H10A0.9700
N4—C131.338 (2)C10—H10B0.9700
N4—C141.3476 (19)C11—C121.378 (2)
N5—C131.339 (2)C11—C141.403 (2)
N5—H1N0.861 (9)C12—H120.9300
N5—H2N0.859 (9)C14—C151.477 (2)
C1—C41.502 (3)C15—C161.396 (2)
C1—C31.500 (3)C15—C201.411 (2)
C1—C21.513 (3)C16—C171.371 (3)
C2—H2A0.9600C16—H160.9300
C2—H2B0.9600C17—C181.375 (3)
C2—H2C0.9600C17—H170.9300
C3—H3A0.9600C18—C191.362 (3)
C3—H3B0.9600C18—H180.9300
C3—H3C0.9600C19—C201.375 (3)
C4—H4A0.9600C19—H190.9300
C4—H4B0.9600
C5—O1—C1121.59 (13)C6—C7—H7B109.5
C20—O3—H1O106 (2)H7A—C7—H7B108.1
C5—N1—C6120.09 (14)N2—C8—C9111.36 (14)
C5—N1—C9124.84 (14)N2—C8—H8A109.4
C6—N1—C9113.22 (13)C9—C8—H8A109.4
C7—N2—C8109.85 (12)N2—C8—H8B109.4
C7—N2—C10112.32 (12)C9—C8—H8B109.4
C8—N2—C10109.84 (12)H8A—C8—H8B108.0
C12—N3—C13114.41 (15)N1—C9—C8109.68 (13)
C13—N4—C14119.56 (14)N1—C9—H9A109.7
C13—N5—H1N116.6 (14)C8—C9—H9A109.7
C13—N5—H2N115.1 (14)N1—C9—H9B109.7
H1N—N5—H2N128 (2)C8—C9—H9B109.7
O1—C1—C4110.10 (16)H9A—C9—H9B108.2
O1—C1—C3110.25 (18)N2—C10—C11114.62 (13)
C4—C1—C3111.4 (2)N2—C10—H10A108.6
O1—C1—C2101.62 (15)C11—C10—H10A108.6
C4—C1—C2110.11 (19)N2—C10—H10B108.6
C3—C1—C2112.9 (2)C11—C10—H10B108.6
C1—C2—H2A109.5H10A—C10—H10B107.6
C1—C2—H2B109.5C12—C11—C14115.08 (14)
H2A—C2—H2B109.5C12—C11—C10117.72 (15)
C1—C2—H2C109.5C14—C11—C10126.96 (15)
H2A—C2—H2C109.5N3—C12—C11126.47 (17)
H2B—C2—H2C109.5N3—C12—H12116.8
C1—C3—H3A109.5C11—C12—H12116.8
C1—C3—H3B109.5N4—C13—N5118.34 (16)
H3A—C3—H3B109.5N4—C13—N3124.67 (14)
C1—C3—H3C109.5N5—C13—N3116.98 (15)
H3A—C3—H3C109.5N4—C14—C11119.68 (14)
H3B—C3—H3C109.5N4—C14—C15114.77 (14)
C1—C4—H4A109.5C11—C14—C15125.46 (14)
C1—C4—H4B109.5C16—C15—C20116.87 (16)
H4A—C4—H4B109.5C16—C15—C14121.81 (15)
C1—C4—H4C109.5C20—C15—C14121.32 (15)
H4A—C4—H4C109.5C17—C16—C15122.15 (19)
H4B—C4—H4C109.5C17—C16—H16118.9
O2—C5—O1125.84 (16)C15—C16—H16118.9
O2—C5—N1123.43 (16)C16—C17—C18119.2 (2)
O1—C5—N1110.66 (13)C16—C17—H17120.4
N1—C6—C7110.82 (14)C18—C17—H17120.4
N1—C6—H6A109.5C19—C18—C17120.32 (19)
C7—C6—H6A109.5C19—C18—H18119.8
N1—C6—H6B109.5C17—C18—H18119.8
C7—C6—H6B109.5C18—C19—C20121.1 (2)
H6A—C6—H6B108.1C18—C19—H19119.5
N2—C7—C6110.82 (13)C20—C19—H19119.4
N2—C7—H7A109.5O3—C20—C19117.65 (17)
C6—C7—H7A109.5O3—C20—C15122.34 (16)
N2—C7—H7B109.5C19—C20—C15119.98 (18)
C5—O1—C1—C463.7 (2)C14—N4—C13—N5179.31 (15)
C5—O1—C1—C359.6 (2)C14—N4—C13—N30.6 (2)
C5—O1—C1—C2179.57 (18)C12—N3—C13—N42.4 (2)
C1—O1—C5—O23.9 (3)C12—N3—C13—N5176.31 (16)
C1—O1—C5—N1178.86 (16)C13—N4—C14—C113.2 (2)
C6—N1—C5—O25.5 (3)C13—N4—C14—C15179.82 (14)
C9—N1—C5—O2168.93 (18)C12—C11—C14—N42.5 (2)
C6—N1—C5—O1177.24 (15)C10—C11—C14—N4171.82 (15)
C9—N1—C5—O113.8 (2)C12—C11—C14—C15178.75 (15)
C5—N1—C6—C7111.09 (18)C10—C11—C14—C154.5 (3)
C9—N1—C6—C754.2 (2)N4—C14—C15—C16157.67 (17)
C8—N2—C7—C658.01 (19)C11—C14—C15—C1625.9 (3)
C10—N2—C7—C6179.42 (14)N4—C14—C15—C2023.2 (2)
N1—C6—C7—N255.5 (2)C11—C14—C15—C20153.26 (16)
C7—N2—C8—C958.83 (18)C20—C15—C16—C174.9 (3)
C10—N2—C8—C9177.15 (14)C14—C15—C16—C17174.32 (19)
C5—N1—C9—C8110.40 (19)C15—C16—C17—C180.1 (4)
C6—N1—C9—C854.0 (2)C16—C17—C18—C193.6 (4)
N2—C8—C9—N156.0 (2)C17—C18—C19—C201.9 (4)
C7—N2—C10—C1159.36 (19)C18—C19—C20—O3178.7 (2)
C8—N2—C10—C11178.07 (14)C18—C19—C20—C153.3 (3)
N2—C10—C11—C1298.42 (18)C16—C15—C20—O3175.57 (18)
N2—C10—C11—C1487.4 (2)C14—C15—C20—O35.2 (3)
C13—N3—C12—C113.1 (3)C16—C15—C20—C196.5 (3)
C14—C11—C12—N30.8 (3)C14—C15—C20—C19172.72 (17)
C10—C11—C12—N3175.61 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H1O···N40.83 (1)1.80 (2)2.560 (2)151 (3)
N5—H1N···N3i0.86 (1)2.19 (1)3.054 (2)179 (2)
N5—H2N···O3ii0.86 (1)2.29 (1)3.139 (2)169 (2)
Symmetry codes: (i) x+3, y+1, z; (ii) x+2, y+2, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H1O···N40.832 (10)1.802 (17)2.560 (2)151 (3)
N5—H1N···N3i0.861 (9)2.193 (10)3.054 (2)179 (2)
N5—H2N···O3ii0.859 (9)2.292 (10)3.139 (2)168.9 (19)
Symmetry codes: (i) x+3, y+1, z; (ii) x+2, y+2, z.
Acknowledgements top

The authors are grateful to the Department of Science and Technology (DST), and SAIF, IIT Madras, Chennai, India, for the X-ray data collection. MCP is thankful to the University Grant Commission, New Delhi, India, for research funding under research project No. 39–715/2010(SR). The authors also thank the Ministry of Higher Education, Malaysia, for funding structural studies through the High-Impact Research scheme (UM·C/HIR-MOHE/SC/03).

references
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