organic compounds
(2RS)-3-Hydroxy-2-methyl-2-(2-pyridyl)imidazolidine-4-one
aKarakalpakian University, Department of Chemistry, Universitet Keshesi 1, 742012 Nukus, Uzbekistan, bKiev National Taras Shevchenko University, Department of Chemistry, Volodymyrska str. 64, 01601 Kiev, Ukraine, cFaculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie str., 50-383 Wrocław, Poland, and dKyiv National University of Construction and Architecture, Department of Chemistry, Povitroflotsky Ave., 31, 03680 Kiev, Ukraine
*Correspondence e-mail: eprisyazhnaya@ukr.net
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 ); Lipczynska-Kochany (1991); Kurzak et al. (1992); Whittaker et al. (1999). For reactions of α-amino with and resulting in 3-hydroxyimidazolidin-4-one derivatives, see: Vystorop et al. (2002, 2003); Marson & Pucci (2004). For related structures, see: Krämer & Fritsky (2000); Świątek-Kozłowska et al. (2000); Krämer et al. (2002); Kovbasyuk et al. (2004). For the synthesis, see: Cunningham et al. (1949). For hydrogen bonds, see: Desiraju & Steiner (1999).
in biological and coordination chemistry, see: Miller (1989Experimental
Crystal data
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Refinement
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Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell CrysAlis RED (Oxford Diffraction, 2006); data reduction: CrysAlis RED; 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, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).
Supporting information
10.1107/S1600536809030840/fb2163sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809030840/fb2163Isup2.hkl
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).
All the H-atoms were discernible in the difference
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.Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell
CrysAlis RED (Oxford Diffraction, 2006); data reduction: CrysAlis RED (Oxford Diffraction, 2006); 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, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).C9H11N3O2 | F(000) = 408 |
Mr = 193.21 | Dx = 1.445 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 505 reflections |
a = 8.207 (2) Å | θ = 4.5–27.0° |
b = 10.604 (2) Å | µ = 0.11 mm−1 |
c = 10.642 (2) Å | T = 100 K |
β = 106.43 (3)° | Block, colourless |
V = 888.3 (3) Å3 | 0.25 × 0.17 × 0.12 mm |
Z = 4 |
Kuma KM-4-CCD diffractometer | 2048 independent reflections |
Radiation source: fine-focus sealed tube | 1772 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.020 |
ω scans | θmax = 28.4°, θmin = 3.4° |
Absorption correction: multi-scan (CrysAlis RED, Oxford Diffraction, 2006) | h = −10→10 |
Tmin = 0.976, Tmax = 0.986 | k = −12→14 |
6025 measured reflections | l = −10→13 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.039 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.092 | w = 1/[σ2(Fo2) + (0.0423P)2 + 0.2114P] where P = (Fo2 + 2Fc2)/3 |
S = 1.12 | (Δ/σ)max < 0.001 |
2048 reflections | Δρmax = 0.31 e Å−3 |
137 parameters | Δρmin = −0.21 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
35 constraints | Extinction coefficient: 0.011 (3) |
Primary atom site location: structure-invariant direct methods |
C9H11N3O2 | V = 888.3 (3) Å3 |
Mr = 193.21 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 8.207 (2) Å | µ = 0.11 mm−1 |
b = 10.604 (2) Å | T = 100 K |
c = 10.642 (2) Å | 0.25 × 0.17 × 0.12 mm |
β = 106.43 (3)° |
Kuma KM-4-CCD diffractometer | 2048 independent reflections |
Absorption correction: multi-scan (CrysAlis RED, Oxford Diffraction, 2006) | 1772 reflections with I > 2σ(I) |
Tmin = 0.976, Tmax = 0.986 | Rint = 0.020 |
6025 measured reflections |
R[F2 > 2σ(F2)] = 0.039 | 0 restraints |
wR(F2) = 0.092 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.12 | Δρmax = 0.31 e Å−3 |
2048 reflections | Δρmin = −0.21 e Å−3 |
137 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.16520 (11) | 0.16310 (8) | 0.36523 (9) | 0.0161 (2) | |
O2 | 0.40231 (11) | 0.01414 (8) | 0.28974 (9) | 0.0197 (2) | |
N1 | 0.33317 (13) | 0.31162 (10) | 0.12474 (10) | 0.0143 (2) | |
N2 | 0.02391 (13) | 0.16898 (10) | 0.05476 (10) | 0.0162 (2) | |
N3 | 0.27351 (13) | 0.20590 (10) | 0.29470 (10) | 0.0135 (2) | |
C1 | 0.21832 (17) | 0.43456 (12) | 0.27885 (13) | 0.0175 (3) | |
H1A | 0.1455 | 0.4293 | 0.3351 | 0.026* | |
H1B | 0.1815 | 0.5026 | 0.2179 | 0.026* | |
H1C | 0.3330 | 0.4496 | 0.3307 | 0.026* | |
C2 | 0.21024 (15) | 0.31194 (11) | 0.20447 (11) | 0.0137 (3) | |
C3 | 0.03258 (15) | 0.27995 (11) | 0.11645 (11) | 0.0137 (3) | |
C4 | 0.36622 (15) | 0.12145 (12) | 0.24864 (12) | 0.0147 (3) | |
C5 | 0.41829 (16) | 0.18664 (12) | 0.14047 (12) | 0.0167 (3) | |
H5A | 0.5407 | 0.1966 | 0.1638 | 0.020* | |
H5B | 0.3818 | 0.1385 | 0.0598 | 0.020* | |
C6 | −0.10579 (17) | 0.36021 (12) | 0.09906 (13) | 0.0184 (3) | |
H6 | −0.0958 | 0.4360 | 0.1446 | 0.022* | |
C7 | −0.25965 (17) | 0.32455 (13) | 0.01199 (13) | 0.0206 (3) | |
H7 | −0.3546 | 0.3762 | −0.0018 | 0.025* | |
C8 | −0.26922 (16) | 0.21144 (13) | −0.05353 (13) | 0.0196 (3) | |
H8 | −0.3702 | 0.1859 | −0.1130 | 0.023* | |
C9 | −0.12508 (16) | 0.13664 (12) | −0.02886 (12) | 0.0177 (3) | |
H9 | −0.1323 | 0.0601 | −0.0727 | 0.021* | |
H1O | 0.229 (3) | 0.1711 (18) | 0.454 (2) | 0.049 (6)* | |
H1N | 0.409 (2) | 0.3703 (16) | 0.1556 (15) | 0.023 (4)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0174 (5) | 0.0199 (5) | 0.0126 (4) | −0.0039 (3) | 0.0067 (4) | 0.0010 (3) |
O2 | 0.0196 (5) | 0.0154 (5) | 0.0233 (5) | 0.0026 (3) | 0.0050 (4) | 0.0021 (4) |
N1 | 0.0146 (5) | 0.0152 (5) | 0.0135 (5) | −0.0028 (4) | 0.0049 (4) | −0.0007 (4) |
N2 | 0.0169 (5) | 0.0145 (5) | 0.0166 (5) | −0.0009 (4) | 0.0040 (4) | −0.0016 (4) |
N3 | 0.0147 (5) | 0.0148 (5) | 0.0117 (5) | −0.0010 (4) | 0.0052 (4) | 0.0016 (4) |
C1 | 0.0208 (7) | 0.0143 (6) | 0.0172 (6) | −0.0012 (5) | 0.0052 (5) | −0.0020 (5) |
C2 | 0.0165 (6) | 0.0132 (6) | 0.0118 (6) | 0.0003 (4) | 0.0046 (5) | 0.0010 (4) |
C3 | 0.0162 (6) | 0.0139 (6) | 0.0117 (6) | −0.0012 (4) | 0.0050 (5) | 0.0011 (4) |
C4 | 0.0111 (6) | 0.0170 (6) | 0.0139 (6) | −0.0022 (4) | −0.0001 (4) | −0.0033 (5) |
C5 | 0.0161 (6) | 0.0186 (6) | 0.0160 (6) | 0.0012 (5) | 0.0057 (5) | −0.0010 (5) |
C6 | 0.0211 (7) | 0.0155 (6) | 0.0187 (6) | 0.0025 (5) | 0.0060 (5) | −0.0019 (5) |
C7 | 0.0173 (7) | 0.0221 (7) | 0.0216 (7) | 0.0063 (5) | 0.0042 (5) | 0.0027 (5) |
C8 | 0.0156 (6) | 0.0236 (7) | 0.0171 (6) | −0.0009 (5) | 0.0008 (5) | 0.0017 (5) |
C9 | 0.0194 (7) | 0.0161 (6) | 0.0167 (6) | −0.0022 (5) | 0.0036 (5) | −0.0029 (5) |
O1—N3 | 1.3917 (13) | C1—H1C | 0.9600 |
O1—H1O | 0.95 (2) | C2—C3 | 1.5316 (18) |
O2—C4 | 1.2250 (16) | C3—C6 | 1.3891 (17) |
N1—C5 | 1.4854 (16) | C4—C5 | 1.5047 (17) |
N1—C2 | 1.4907 (16) | C5—H5A | 0.9700 |
N1—H1N | 0.874 (17) | C5—H5B | 0.9700 |
N2—C9 | 1.3376 (17) | C6—C7 | 1.3908 (19) |
N2—C3 | 1.3395 (16) | C6—H6 | 0.9300 |
N3—C4 | 1.3536 (16) | C7—C8 | 1.3783 (19) |
N3—C2 | 1.4744 (16) | C7—H7 | 0.9300 |
C1—C2 | 1.5139 (17) | C8—C9 | 1.3863 (19) |
C1—H1A | 0.9600 | C8—H8 | 0.9300 |
C1—H1B | 0.9600 | C9—H9 | 0.9300 |
N3—O1—H1O | 104.8 (12) | C6—C3—C2 | 123.14 (11) |
C5—N1—C2 | 108.08 (9) | O2—C4—N3 | 126.10 (12) |
C5—N1—H1N | 109.4 (11) | O2—C4—C5 | 127.42 (11) |
C2—N1—H1N | 107.8 (10) | N3—C4—C5 | 106.47 (11) |
C9—N2—C3 | 117.59 (11) | N1—C5—C4 | 105.65 (10) |
C4—N3—O1 | 119.32 (10) | N1—C5—H5A | 110.6 |
C4—N3—C2 | 113.53 (10) | C4—C5—H5A | 110.6 |
O1—N3—C2 | 116.04 (9) | N1—C5—H5B | 110.6 |
C2—C1—H1A | 109.5 | C4—C5—H5B | 110.6 |
C2—C1—H1B | 109.5 | H5A—C5—H5B | 108.7 |
H1A—C1—H1B | 109.5 | C3—C6—C7 | 118.43 (12) |
C2—C1—H1C | 109.5 | C3—C6—H6 | 120.8 |
H1A—C1—H1C | 109.5 | C7—C6—H6 | 120.8 |
H1B—C1—H1C | 109.5 | C8—C7—C6 | 119.00 (12) |
N3—C2—N1 | 101.45 (9) | C8—C7—H7 | 120.5 |
N3—C2—C1 | 111.05 (10) | C6—C7—H7 | 120.5 |
N1—C2—C1 | 111.28 (10) | C7—C8—C9 | 118.60 (12) |
N3—C2—C3 | 109.17 (10) | C7—C8—H8 | 120.7 |
N1—C2—C3 | 109.38 (9) | C9—C8—H8 | 120.7 |
C1—C2—C3 | 113.79 (10) | N2—C9—C8 | 123.35 (12) |
N2—C3—C6 | 123.02 (12) | N2—C9—H9 | 118.3 |
N2—C3—C2 | 113.82 (10) | C8—C9—H9 | 118.3 |
C4—N3—C2—N1 | −23.00 (12) | N1—C2—C3—C6 | −120.73 (13) |
O1—N3—C2—N1 | −166.82 (9) | C1—C2—C3—C6 | 4.41 (17) |
C4—N3—C2—C1 | −141.35 (11) | O1—N3—C4—O2 | −21.10 (17) |
O1—N3—C2—C1 | 74.84 (13) | C2—N3—C4—O2 | −163.63 (11) |
C4—N3—C2—C3 | 92.40 (12) | O1—N3—C4—C5 | 160.17 (9) |
O1—N3—C2—C3 | −51.42 (13) | C2—N3—C4—C5 | 17.65 (13) |
C5—N1—C2—N3 | 18.56 (12) | C2—N1—C5—C4 | −9.58 (12) |
C5—N1—C2—C1 | 136.75 (10) | O2—C4—C5—N1 | 176.85 (11) |
C5—N1—C2—C3 | −96.68 (11) | N3—C4—C5—N1 | −4.45 (13) |
C9—N2—C3—C6 | 1.26 (18) | N2—C3—C6—C7 | −1.06 (19) |
C9—N2—C3—C2 | −176.93 (11) | C2—C3—C6—C7 | 176.96 (11) |
N3—C2—C3—N2 | −52.74 (13) | C3—C6—C7—C8 | 0.01 (19) |
N1—C2—C3—N2 | 57.46 (13) | C6—C7—C8—C9 | 0.7 (2) |
C1—C2—C3—N2 | −177.41 (10) | C3—N2—C9—C8 | −0.43 (19) |
N3—C2—C3—C6 | 129.08 (12) | C7—C8—C9—N2 | −0.6 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1O···N1i | 0.95 (2) | 1.78 (2) | 2.7287 (16) | 175.5 (18) |
N1—H1N···O2ii | 0.874 (17) | 2.135 (18) | 3.0058 (15) | 173.7 (15) |
C6—H6···O1iii | 0.93 | 2.47 | 3.2867 (17) | 147 |
C7—H7···O2iii | 0.93 | 2.81 | 3.3559 (17) | 119 |
C8—H8···O2iv | 0.93 | 2.80 | 3.4177 (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. |
Experimental details
Crystal data | |
Chemical formula | C9H11N3O2 |
Mr | 193.21 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 8.207 (2), 10.604 (2), 10.642 (2) |
β (°) | 106.43 (3) |
V (Å3) | 888.3 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.25 × 0.17 × 0.12 |
Data collection | |
Diffractometer | Kuma KM-4-CCD diffractometer |
Absorption correction | Multi-scan (CrysAlis RED, Oxford Diffraction, 2006) |
Tmin, Tmax | 0.976, 0.986 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6025, 2048, 1772 |
Rint | 0.020 |
(sin θ/λ)max (Å−1) | 0.669 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.039, 0.092, 1.12 |
No. of reflections | 2048 |
No. of parameters | 137 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.31, −0.21 |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2006), CrysAlis RED (Oxford Diffraction, 2006), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1O···N1i | 0.95 (2) | 1.78 (2) | 2.7287 (16) | 175.5 (18) |
N1—H1N···O2ii | 0.874 (17) | 2.135 (18) | 3.0058 (15) | 173.7 (15) |
C6—H6···O1iii | 0.93 | 2.47 | 3.2867 (17) | 146.6 |
C7—H7···O2iii | 0.93 | 2.81 | 3.3559 (17) | 118.8 |
C8—H8···O2iv | 0.93 | 2.80 | 3.4177 (17) | 125.1 |
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. |
Acknowledgements
The authors thank the Ministry of Education and Science of Ukraine for financial support (grant No. M/42–2008).
References
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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).