Literature DB >> 21577537

(2RS)-3-Hydr-oxy-2-methyl-2-(2-pyrid-yl)imidazolidine-4-one.

Turganbay S Iskenderov, Irina A Golenya, Elźbieta Gumienna-Kontecka, Igor O Fritsky, Elena V Prisyazhnaya.   

Abstract

The title structure, C(9)H(11)N(3)O(2), is a racemate. The chiral centre is situated at the N-C-N C atom of the imidazolidine ring. The inter-planar 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 mol-ecules are arranged in zigzag layers parallel to the b axis. The mol-ecules within the layers are inter-connected 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 inter-actions are also present.

Entities:  

Year:  2009        PMID: 21577537      PMCID: PMC2970069          DOI: 10.1107/S1600536809030840

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For background to hydroxamic acids in biological and coord­ination chemistry, see: Miller (1989 ▶); Lipczynska-Kochany (1991 ▶); Kurzak et al. (1992 ▶); Whittaker et al. (1999 ▶). For reactions of α-amino hydroxamic acids with aldehydes and ketones 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 ▶).

Experimental

Crystal data

C9H11N3O2 M = 193.21 Monoclinic, 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 ▶) 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 ▶); cell refinement: 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 ▶). 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
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
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 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
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.
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)*
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)
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)
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
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—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) ; (ii) ; (iii) ; (iv) .

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