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Acta Crystallogr Sect E Struct Rep Online. 2009 September 1; 65(Pt 9): o2123–o2124.
Published online 2009 August 8. doi:  10.1107/S1600536809030840
PMCID: PMC2970069

(2RS)-3-Hydr­oxy-2-methyl-2-(2-pyrid­yl)imidazolidine-4-one

Abstract

The title structure, C9H11N3O2, is a racemate. The chiral centre is situated at the N—C—N C atom of the imidazolidine ring. The inter­planar angle between the mean planes of the pyridine and imidazolidine rings is 89.41 (5)°. The methyl group is in a trans position with respect to the pyridine N atom. In the crystal, the mol­ecules are arranged in zigzag layers parallel to the b axis. The mol­ecules within the layers are inter­connected by strong O—H(...)N and weak N—H(...)O hydrogen bonds; the former take place between OH groups and amine N atoms and the latter between the amine N atom and the carbonyl O atom. In addition, C—H(...)O inter­actions are also present.

Related literature

For background to hydroxamic acids in biological and coord­ination chemistry, see: Miller (1989 [triangle]); Lipczynska-Kochany (1991 [triangle]); Kurzak et al. (1992 [triangle]); Whittaker et al. (1999 [triangle]). For reactions of α-amino hydroxamic acids with aldehydes and ketones resulting in 3-hydroxy­imidazolidin-4-one derivatives, see: Vystorop et al. (2002 [triangle], 2003 [triangle]); Marson & Pucci (2004 [triangle]). For related structures, see: Krämer & Fritsky (2000 [triangle]); Świątek-Kozłowska et al. (2000 [triangle]); Krämer et al. (2002 [triangle]); Kovbasyuk et al. (2004 [triangle]). For the synthesis, see: Cunningham et al. (1949 [triangle]). For hydrogen bonds, see: Desiraju & Steiner (1999 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2123-scheme1.jpg

Experimental

Crystal data

  • C9H11N3O2
  • M r = 193.21
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2123-efi1.jpg
  • a = 8.207 (2) Å
  • b = 10.604 (2) Å
  • c = 10.642 (2) Å
  • β = 106.43 (3)°
  • V = 888.3 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 100 K
  • 0.25 × 0.17 × 0.12 mm

Data collection

  • Kuma KM-4-CCD diffractometer
  • Absorption correction: multi-scan (CrysAlis RED, Oxford Diffraction, 2006 [triangle]) T min = 0.976, T max = 0.986
  • 6025 measured reflections
  • 2048 independent reflections
  • 1772 reflections with I > 2σ(I)
  • R int = 0.020

Refinement

  • R[F 2 > 2σ(F 2)] = 0.039
  • wR(F 2) = 0.092
  • S = 1.12
  • 2048 reflections
  • 137 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.31 e Å−3
  • Δρmin = −0.21 e Å−3

Data collection: CrysAlis CCD (Oxford Diffraction, 2006 [triangle]); cell refinement: CrysAlis RED (Oxford Diffraction, 2006 [triangle]); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809030840/fb2163sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809030840/fb2163Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors thank the Ministry of Education and Science of Ukraine for financial support (grant No. M/42–2008).

supplementary crystallographic information

Comment

Hydroxamic acids are important bioligands possessing a wide spectrum of biological activities (Lipczynska-Kochany, 1991). Notably, they have a high affinity to the transition metal ions (Kurzak et al., 1992). For example, naturally occurring hydroxamate siderophores are strong Fe(III) chelators (Miller, 1989). Hydroxamic acids are also efficient metalloenzyme inhibitors, e.g. urease and matrix metalloproteinase inhibitors (Whittaker et al., 1999).

These properties have provoked current interest in the development of novel synthetic routes for preparation of new selective hydroxamate chelating agents and siderophore mimics. Recently it was found that the reactions of α-amino hydroxamic acids with aldehydes and ketons do not result in the open-chain Schiff base hydroxamic acids but afford five-membered cyclic products containing residues of 3-hydroxyimidazolidine-4-one (Marson & Pucci, 2004; Vystorop et al., 2002; Vystorop et al., 2003). Here we describe a crystal structure of the title structure, 2-methyl-2-(pyridine-2-yl)-3-hydroxyimidazolidine-4-one, obtained as a result of the condensation of glycine hydroxamic acid and 2-acetylpyridine.

The molecules of the title structure are interconnected by the H-bonds. The molecules contain a chiral centre at the C2 atom (Fig. 1) and the structure is a racemate. The molecule is not planar: the interplanar angle between the mean planes of the pyridine and imidazolidine rings equals to 89.41 (5)°. The imidazolidine ring exhibits the envelope conformation: the C2 atom is displaced by 0.320 (2) Å out of the mean plane defined by four other atoms of the ring. The methyl group is in the trans-position with respect to the pyridine nitrogen.

The bond lengths C—O, N—O and C—N in the hydroxamic function suggest the presence of the hydroxamic function in the hydroxamic form rather than in the oximic one (Świątek-Kozłowska et al., 2000). The C—N and C—C bond lengths within the pyridine ring are normal for 2-substituted pyridine derivatives (Krämer & Fritsky, 2000; Krämer et al., 2002; Kovbasyuk et al., 2004).

In the crystal packing, the molecules are arranged into zig-zagged layers by the O1—H···N2 and N2—H···O2 hydrogen bonds. These layers are parallel to the axis b. The former one takes place between NOH group and it is considered as a strong hydrogen bond (Desiraju & Steiner, 1999) while the latter one between the amine nitrogen and the carbonyl oxygen atom (Fig. 2) is considered as weak one (Desiraju & Steiner, 1999). Moreover, the mentioned layers are interconnected by C—H···O H-bonds (Tab. 1).

Experimental

A suspension of glycine hydroxamic acid (0.9 g, 10 mmol) and 2-acetylpyridine (12 mmol) in 30 ml of 96% aqueous ethanol was refluxed for at 78°C for 1-2 h. The hot reaction mixture was filtered, the filtrate produced a white precipitate on cooling. The precipitate was filtered, air-dried and recrystallized from absolute ethanol to yield the title structure as colourless prismatic crystals of average size 0.25 × 0.15 × 0.15 mm. The reagent, glycine hydroxamic acid, was prepared according to the procedure described by Cunningham et al. (1949).

Refinement

All the H-atoms were discernible in the difference electron density map. The coordinates and the isotropic displacement parameters of the hydroxyl and amine hydrogens that are involved in the strongest hydrogen bonds have been refined. The hydrogens with C atoms as their carriers were situated into the idealized positions and constrained: C—H = 0.93, 0.96 and 0.97 Å for aryl, methyl and methylene hydrogens; UisoHaryl/methylene=1.2UeqCaryl/methylene, UisoHmethyl=1.5UeqCmethyl. The methyl H atoms have been refined with AFIX 137 [SHELXL98 (Sheldrick, 2008] so their positions with regard to the electron density maps have been optimized.

Figures

Fig. 1.
A view of the (2R)-enantiomer of the title compound, with the displacement ellipsoids shown at the 50% probability level.
Fig. 2.
A packing diagram of the title compound. Oxygen and nitrogen atoms are depicted as larger (hatched) and smaller (dotted) circles, respectively. The O-H···N and N-H···O hydrogen bonds are indicated by the ...

Crystal data

C9H11N3O2F(000) = 408
Mr = 193.21Dx = 1.445 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 505 reflections
a = 8.207 (2) Åθ = 4.5–27.0°
b = 10.604 (2) ŵ = 0.11 mm1
c = 10.642 (2) ÅT = 100 K
β = 106.43 (3)°Block, colourless
V = 888.3 (3) Å30.25 × 0.17 × 0.12 mm
Z = 4

Data collection

Kuma KM-4-CCD diffractometer2048 independent reflections
Radiation source: fine-focus sealed tube1772 reflections with I > 2σ(I)
graphiteRint = 0.020
ω scansθmax = 28.4°, θmin = 3.4°
Absorption correction: multi-scan (CrysAlis RED, Oxford Diffraction, 2006)h = −10→10
Tmin = 0.976, Tmax = 0.986k = −12→14
6025 measured reflectionsl = −10→13

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.039H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.092w = 1/[σ2(Fo2) + (0.0423P)2 + 0.2114P] where P = (Fo2 + 2Fc2)/3
S = 1.12(Δ/σ)max < 0.001
2048 reflectionsΔρmax = 0.31 e Å3
137 parametersΔρmin = −0.21 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
35 constraintsExtinction coefficient: 0.011 (3)
Primary atom site location: structure-invariant direct methods

Special details

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

xyzUiso*/Ueq
O10.16520 (11)0.16310 (8)0.36523 (9)0.0161 (2)
O20.40231 (11)0.01414 (8)0.28974 (9)0.0197 (2)
N10.33317 (13)0.31162 (10)0.12474 (10)0.0143 (2)
N20.02391 (13)0.16898 (10)0.05476 (10)0.0162 (2)
N30.27351 (13)0.20590 (10)0.29470 (10)0.0135 (2)
C10.21832 (17)0.43456 (12)0.27885 (13)0.0175 (3)
H1A0.14550.42930.33510.026*
H1B0.18150.50260.21790.026*
H1C0.33300.44960.33070.026*
C20.21024 (15)0.31194 (11)0.20447 (11)0.0137 (3)
C30.03258 (15)0.27995 (11)0.11645 (11)0.0137 (3)
C40.36622 (15)0.12145 (12)0.24864 (12)0.0147 (3)
C50.41829 (16)0.18664 (12)0.14047 (12)0.0167 (3)
H5A0.54070.19660.16380.020*
H5B0.38180.13850.05980.020*
C6−0.10579 (17)0.36021 (12)0.09906 (13)0.0184 (3)
H6−0.09580.43600.14460.022*
C7−0.25965 (17)0.32455 (13)0.01199 (13)0.0206 (3)
H7−0.35460.3762−0.00180.025*
C8−0.26922 (16)0.21144 (13)−0.05353 (13)0.0196 (3)
H8−0.37020.1859−0.11300.023*
C9−0.12508 (16)0.13664 (12)−0.02886 (12)0.0177 (3)
H9−0.13230.0601−0.07270.021*
H1O0.229 (3)0.1711 (18)0.454 (2)0.049 (6)*
H1N0.409 (2)0.3703 (16)0.1556 (15)0.023 (4)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0174 (5)0.0199 (5)0.0126 (4)−0.0039 (3)0.0067 (4)0.0010 (3)
O20.0196 (5)0.0154 (5)0.0233 (5)0.0026 (3)0.0050 (4)0.0021 (4)
N10.0146 (5)0.0152 (5)0.0135 (5)−0.0028 (4)0.0049 (4)−0.0007 (4)
N20.0169 (5)0.0145 (5)0.0166 (5)−0.0009 (4)0.0040 (4)−0.0016 (4)
N30.0147 (5)0.0148 (5)0.0117 (5)−0.0010 (4)0.0052 (4)0.0016 (4)
C10.0208 (7)0.0143 (6)0.0172 (6)−0.0012 (5)0.0052 (5)−0.0020 (5)
C20.0165 (6)0.0132 (6)0.0118 (6)0.0003 (4)0.0046 (5)0.0010 (4)
C30.0162 (6)0.0139 (6)0.0117 (6)−0.0012 (4)0.0050 (5)0.0011 (4)
C40.0111 (6)0.0170 (6)0.0139 (6)−0.0022 (4)−0.0001 (4)−0.0033 (5)
C50.0161 (6)0.0186 (6)0.0160 (6)0.0012 (5)0.0057 (5)−0.0010 (5)
C60.0211 (7)0.0155 (6)0.0187 (6)0.0025 (5)0.0060 (5)−0.0019 (5)
C70.0173 (7)0.0221 (7)0.0216 (7)0.0063 (5)0.0042 (5)0.0027 (5)
C80.0156 (6)0.0236 (7)0.0171 (6)−0.0009 (5)0.0008 (5)0.0017 (5)
C90.0194 (7)0.0161 (6)0.0167 (6)−0.0022 (5)0.0036 (5)−0.0029 (5)

Geometric parameters (Å, °)

O1—N31.3917 (13)C1—H1C0.9600
O1—H1O0.95 (2)C2—C31.5316 (18)
O2—C41.2250 (16)C3—C61.3891 (17)
N1—C51.4854 (16)C4—C51.5047 (17)
N1—C21.4907 (16)C5—H5A0.9700
N1—H1N0.874 (17)C5—H5B0.9700
N2—C91.3376 (17)C6—C71.3908 (19)
N2—C31.3395 (16)C6—H60.9300
N3—C41.3536 (16)C7—C81.3783 (19)
N3—C21.4744 (16)C7—H70.9300
C1—C21.5139 (17)C8—C91.3863 (19)
C1—H1A0.9600C8—H80.9300
C1—H1B0.9600C9—H90.9300
N3—O1—H1O104.8 (12)C6—C3—C2123.14 (11)
C5—N1—C2108.08 (9)O2—C4—N3126.10 (12)
C5—N1—H1N109.4 (11)O2—C4—C5127.42 (11)
C2—N1—H1N107.8 (10)N3—C4—C5106.47 (11)
C9—N2—C3117.59 (11)N1—C5—C4105.65 (10)
C4—N3—O1119.32 (10)N1—C5—H5A110.6
C4—N3—C2113.53 (10)C4—C5—H5A110.6
O1—N3—C2116.04 (9)N1—C5—H5B110.6
C2—C1—H1A109.5C4—C5—H5B110.6
C2—C1—H1B109.5H5A—C5—H5B108.7
H1A—C1—H1B109.5C3—C6—C7118.43 (12)
C2—C1—H1C109.5C3—C6—H6120.8
H1A—C1—H1C109.5C7—C6—H6120.8
H1B—C1—H1C109.5C8—C7—C6119.00 (12)
N3—C2—N1101.45 (9)C8—C7—H7120.5
N3—C2—C1111.05 (10)C6—C7—H7120.5
N1—C2—C1111.28 (10)C7—C8—C9118.60 (12)
N3—C2—C3109.17 (10)C7—C8—H8120.7
N1—C2—C3109.38 (9)C9—C8—H8120.7
C1—C2—C3113.79 (10)N2—C9—C8123.35 (12)
N2—C3—C6123.02 (12)N2—C9—H9118.3
N2—C3—C2113.82 (10)C8—C9—H9118.3
C4—N3—C2—N1−23.00 (12)N1—C2—C3—C6−120.73 (13)
O1—N3—C2—N1−166.82 (9)C1—C2—C3—C64.41 (17)
C4—N3—C2—C1−141.35 (11)O1—N3—C4—O2−21.10 (17)
O1—N3—C2—C174.84 (13)C2—N3—C4—O2−163.63 (11)
C4—N3—C2—C392.40 (12)O1—N3—C4—C5160.17 (9)
O1—N3—C2—C3−51.42 (13)C2—N3—C4—C517.65 (13)
C5—N1—C2—N318.56 (12)C2—N1—C5—C4−9.58 (12)
C5—N1—C2—C1136.75 (10)O2—C4—C5—N1176.85 (11)
C5—N1—C2—C3−96.68 (11)N3—C4—C5—N1−4.45 (13)
C9—N2—C3—C61.26 (18)N2—C3—C6—C7−1.06 (19)
C9—N2—C3—C2−176.93 (11)C2—C3—C6—C7176.96 (11)
N3—C2—C3—N2−52.74 (13)C3—C6—C7—C80.01 (19)
N1—C2—C3—N257.46 (13)C6—C7—C8—C90.7 (2)
C1—C2—C3—N2−177.41 (10)C3—N2—C9—C8−0.43 (19)
N3—C2—C3—C6129.08 (12)C7—C8—C9—N2−0.6 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1O···N1i0.95 (2)1.78 (2)2.7287 (16)175.5 (18)
N1—H1N···O2ii0.874 (17)2.135 (18)3.0058 (15)173.7 (15)
C6—H6···O1iii0.932.473.2867 (17)147
C7—H7···O2iii0.932.813.3559 (17)119
C8—H8···O2iv0.932.803.4177 (17)125

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FB2163).

References

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