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4-[(1RS,5RS,7SR)-5-Methyl-2,4-dioxo-3,6-di­aza­bi­cyclo­[3.2.1]octan-7-yl]benzo­nitrile

aDepartment of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow 119991, Russian Federation, bInstitute of Physiologically Active Compounds, Russian Academy of Sciences, Chernogolovka 142432, Moscow region, Russian Federation, and cInstitute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russian Federation
*Correspondence e-mail: kudr@org.chem.msu.ru

(Received 28 April 2012; accepted 4 May 2012; online 16 May 2012)

In the title compound, C14H13N3O2, the relative stereochemistry of the three stereogenic C atoms has been determined. In the crystal, N—H⋯O hydrogen bonds link the mol­ecules into chains of inversion dimers running along the b axis.

Related literature

For general background to chemistry affording a bridged 3,6-diaza­bicyclo­[3.2.1]octane scaffold, substituted at the 3, 5, 6, and 7 positions, and the biological activity of this class of compounds, see: Kudryavtsev (2010[Kudryavtsev, K. V. (2010). Russ. J. Org. Chem. 46, 372-379.]).

[Scheme 1]

Experimental

Crystal data
  • C14H13N3O2

  • Mr = 255.27

  • Monoclinic, P 21 /c

  • a = 14.8572 (13) Å

  • b = 6.2269 (6) Å

  • c = 13.1215 (12) Å

  • β = 95.568 (1)°

  • V = 1208.20 (19) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.10 mm−1

  • T = 150 K

  • 0.40 × 0.15 × 0.10 mm

Data collection
  • Bruker SMART APEXII diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2008[Bruker (2008). APEX2, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.962, Tmax = 0.990

  • 11909 measured reflections

  • 2924 independent reflections

  • 2601 reflections with I > 2σ(I)

  • Rint = 0.019

Refinement
  • R[F2 > 2σ(F2)] = 0.040

  • wR(F2) = 0.110

  • S = 1.06

  • 2924 reflections

  • 224 parameters

  • All H-atom parameters refined

  • Δρmax = 0.35 e Å−3

  • Δρmin = −0.21 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2⋯O2i 0.899 (18) 2.368 (19) 3.2377 (14) 162.8 (15)
N1—H1⋯O1ii 0.877 (17) 2.032 (17) 2.9019 (14) 171.3 (15)
Symmetry codes: (i) x, y+1, z; (ii) -x, -y+1, -z+1.

Data collection: APEX2 (Bruker, 2008[Bruker (2008). APEX2, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2008[Bruker (2008). APEX2, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

In the title compound, 4-cyanophenyl substituent occupies endo position (Fig. 1). The –C(=O)NHC(=O)- system is planar within 0.046 (3) Å. The adjacent molecules are combined into double centrosymmetric chains along b-axis by N—H···O=C hydrogen bonds (Fig. 2). These chains are linked by weak van der Waals interactions.

3,6-Diazabicyclo[3.2.1]octanes are of interest as a structural motif for enzymes inhibitors. Synthesis of substituted 3,6-diazabicyclo[3.2.1]octane is based on copper(I) catalyzed intramolecular imide formation (Kudryavtsev (2010), Fig. 3).

Related literature top

For general background to chemistry affording bridged a 3,6-diazabicyclo[3.2.1]octane scaffold, substituted at the 3, 5, 6, and 7 positions, and the biological activity of this class of compounds, see: Kudryavtsev (2010).

Experimental top

(2SR,4SR,5RS)-Methyl 4-carbamoyl-5-(4-cyanophenyl)-2-methylpyrrolidine-2-carboxylate (0.862 g, 3.0 mmol) was dissolved in 30 ml of DMF, 0.054 g (0.6 mmol) of CuCN were added, and the mixture was stirred under argon at 413 K during 6 h. The solvent was distilled off under reduced pressure, and the residue was dissolved in 20 ml of AcOEt, washed with saturated solution of NaHCO3 (2 x 7 ml). Organic phase was dried under Na2SO4, concentrated and recrystallized from hexane–ethyl acetate. 4-((1RS,5RS,7SR- 5-methyl-2,4-dioxo-3,6-diazabicyclo[3.2.1]octan-7-yl)benzonitrile. Yield 0.490 g (64%), colourless crystals, m.p. 497–499 K. 1H NMR (400 MHz, DMSO-d6): δ 1.38 (s, 3H, CH3), 2.00 (dd, J 11.8, 4.0, 1H, H-8a), 2.31 (d, J 11.8, 1H, H-8 b), 3.37 (br.s, 1H, H-1), 3.59 (d, J 7.8, 1H, N(6)H), 4.93 (dd, J 7.8, 5.8, 1H, H-7), 7.55 (d, J 8.3, 2H, Ar), 7.73 (d, J 8.3, 2H, Ar), 10.42(s, 1H, N(3)H). 13C NMR (100 MHz, DMSO-d6): δ 18.73, 40.82, 52.78, 62.73, 63.09, 109.99, 119.42, 128.01 (2 C), 132.33 (2 C), 147.52, 174.04, 176.39. Anal. Calcd. for C14H13N3O2: C, 65.87; H, 5.13; N, 16.46. Found: C, 65.92; H, 5.17; N,16.63. The crystals were obtained by slow evaporation of saturated solution in hexane–ethyl acetate (2:3) mixture at ambient temperature.

Refinement top

All hydrogen atoms were located in a difference Fourier map and refined with isotropic thermal parameters.

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, showing the numbering scheme adopted. Displacement ellipsoids are shown at the 50% probability level.
[Figure 2] Fig. 2. Hydrogen-bonded chains along b-axis in the structure of the title compound. H-bonds are shown as dashed lines.
[Figure 3] Fig. 3. Synthetic scheme.
4-[(1RS,5RS,7SR)-5-Methyl-2,4-dioxo-3,6- diazabicyclo[3.2.1]octan-7-yl]benzonitrile top
Crystal data top
C14H13N3O2F(000) = 536
Mr = 255.27Dx = 1.403 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 5466 reflections
a = 14.8572 (13) Åθ = 2.3–31.0°
b = 6.2269 (6) ŵ = 0.10 mm1
c = 13.1215 (12) ÅT = 150 K
β = 95.568 (1)°Block, colourless
V = 1208.20 (19) Å30.40 × 0.15 × 0.10 mm
Z = 4
Data collection top
Bruker SMART APEXII
diffractometer
2924 independent reflections
Radiation source: fine-focus sealed tube2601 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.019
ω scansθmax = 28.0°, θmin = 2.8°
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
h = 1919
Tmin = 0.962, Tmax = 0.990k = 88
11909 measured reflectionsl = 1717
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)] = 0.040Hydrogen site location: difference Fourier map
wR(F2) = 0.110All H-atom parameters refined
S = 1.06 w = 1/[σ2(Fo2) + (0.0568P)2 + 0.4568P]
where P = (Fo2 + 2Fc2)/3
2924 reflections(Δ/σ)max < 0.001
224 parametersΔρmax = 0.35 e Å3
0 restraintsΔρmin = 0.21 e Å3
Crystal data top
C14H13N3O2V = 1208.20 (19) Å3
Mr = 255.27Z = 4
Monoclinic, P21/cMo Kα radiation
a = 14.8572 (13) ŵ = 0.10 mm1
b = 6.2269 (6) ÅT = 150 K
c = 13.1215 (12) Å0.40 × 0.15 × 0.10 mm
β = 95.568 (1)°
Data collection top
Bruker SMART APEXII
diffractometer
2924 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
2601 reflections with I > 2σ(I)
Tmin = 0.962, Tmax = 0.990Rint = 0.019
11909 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0400 restraints
wR(F2) = 0.110All H-atom parameters refined
S = 1.06Δρmax = 0.35 e Å3
2924 reflectionsΔρmin = 0.21 e Å3
224 parameters
Special details top

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) top
xyzUiso*/Ueq
O10.01850 (6)0.66158 (14)0.61099 (7)0.0262 (2)
O20.17560 (6)0.06107 (15)0.54975 (7)0.0271 (2)
N10.10075 (7)0.36899 (17)0.57715 (8)0.0213 (2)
N20.23232 (7)0.66162 (17)0.70043 (8)0.0218 (2)
N30.47535 (9)0.5189 (2)0.21483 (9)0.0350 (3)
C10.08167 (7)0.54263 (19)0.63735 (9)0.0205 (2)
C20.16886 (8)0.22065 (19)0.60194 (9)0.0203 (2)
C30.23153 (8)0.27578 (19)0.69563 (9)0.0208 (2)
C40.28953 (8)0.47800 (19)0.67574 (8)0.0202 (2)
C50.14651 (8)0.5781 (2)0.73407 (9)0.0218 (2)
C60.17531 (8)0.3600 (2)0.77908 (9)0.0237 (3)
C70.10602 (9)0.7300 (2)0.80748 (11)0.0302 (3)
C80.44462 (9)0.5099 (2)0.29149 (9)0.0262 (3)
C100.32690 (7)0.48798 (19)0.57236 (8)0.0193 (2)
C110.32273 (10)0.6744 (2)0.51302 (11)0.0326 (3)
C120.36129 (10)0.6806 (2)0.42077 (11)0.0340 (3)
C130.40462 (8)0.5001 (2)0.38726 (9)0.0227 (3)
C140.41036 (9)0.3136 (2)0.44601 (10)0.0257 (3)
C150.37150 (9)0.3091 (2)0.53770 (10)0.0251 (3)
H40.3428 (10)0.470 (2)0.7280 (12)0.023 (4)*
H620.2141 (10)0.378 (3)0.8439 (12)0.027 (4)*
H30.2689 (11)0.147 (3)0.7158 (12)0.029 (4)*
H10.0636 (11)0.346 (3)0.5222 (13)0.027 (4)*
H610.1244 (10)0.265 (2)0.7877 (11)0.021 (3)*
H140.4399 (11)0.192 (3)0.4254 (13)0.031 (4)*
H730.0524 (12)0.658 (3)0.8305 (14)0.039 (5)*
H150.3758 (12)0.181 (3)0.5765 (13)0.038 (4)*
H20.2219 (11)0.755 (3)0.6484 (14)0.035 (4)*
H720.0885 (11)0.867 (3)0.7734 (13)0.035 (4)*
H710.1509 (12)0.751 (3)0.8687 (15)0.042 (5)*
H120.3569 (14)0.814 (3)0.3768 (16)0.055 (6)*
H110.2931 (13)0.803 (3)0.5349 (14)0.043 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0212 (4)0.0265 (5)0.0309 (5)0.0070 (3)0.0025 (3)0.0009 (4)
O20.0292 (5)0.0226 (4)0.0297 (5)0.0053 (4)0.0045 (4)0.0035 (4)
N10.0191 (5)0.0226 (5)0.0221 (5)0.0035 (4)0.0016 (4)0.0014 (4)
N20.0200 (5)0.0243 (5)0.0219 (5)0.0024 (4)0.0064 (4)0.0021 (4)
N30.0419 (7)0.0385 (7)0.0266 (6)0.0124 (5)0.0137 (5)0.0029 (5)
C10.0175 (5)0.0220 (5)0.0231 (5)0.0011 (4)0.0072 (4)0.0012 (4)
C20.0198 (5)0.0200 (5)0.0219 (5)0.0018 (4)0.0070 (4)0.0037 (4)
C30.0198 (5)0.0238 (6)0.0193 (5)0.0054 (4)0.0049 (4)0.0031 (4)
C40.0175 (5)0.0259 (6)0.0174 (5)0.0035 (4)0.0029 (4)0.0009 (4)
C50.0200 (5)0.0262 (6)0.0200 (5)0.0033 (4)0.0062 (4)0.0016 (4)
C60.0240 (6)0.0293 (6)0.0189 (5)0.0042 (5)0.0079 (4)0.0026 (5)
C70.0281 (6)0.0365 (7)0.0275 (6)0.0063 (6)0.0101 (5)0.0071 (6)
C80.0272 (6)0.0288 (6)0.0234 (6)0.0068 (5)0.0055 (5)0.0021 (5)
C100.0160 (5)0.0249 (6)0.0172 (5)0.0012 (4)0.0027 (4)0.0008 (4)
C110.0405 (7)0.0283 (7)0.0311 (7)0.0127 (6)0.0146 (6)0.0055 (5)
C120.0424 (8)0.0315 (7)0.0301 (7)0.0107 (6)0.0130 (6)0.0108 (6)
C130.0204 (5)0.0297 (6)0.0184 (5)0.0040 (5)0.0041 (4)0.0008 (5)
C140.0283 (6)0.0246 (6)0.0256 (6)0.0024 (5)0.0103 (5)0.0021 (5)
C150.0296 (6)0.0234 (6)0.0238 (6)0.0053 (5)0.0093 (5)0.0032 (5)
Geometric parameters (Å, º) top
O1—C11.2190 (14)C5—C61.5257 (17)
O2—C21.2164 (15)C6—H620.986 (16)
N1—C11.3845 (15)C6—H610.976 (15)
N1—C21.3853 (15)C7—H730.986 (19)
N1—H10.877 (17)C7—H720.988 (18)
N2—C41.4793 (15)C7—H711.002 (19)
N2—C51.4831 (15)C8—C131.4426 (16)
N2—H20.899 (18)C10—C151.3944 (16)
N3—C81.1457 (17)C10—C111.3960 (17)
C1—C51.5331 (16)C11—C121.3890 (18)
C2—C31.5080 (16)C11—H110.971 (19)
C3—C61.5327 (15)C12—C131.3879 (19)
C3—C41.5620 (17)C12—H121.01 (2)
C3—H30.998 (16)C13—C141.3919 (18)
C4—C101.5161 (15)C14—C151.3843 (17)
C4—H40.997 (15)C14—H140.931 (17)
C5—C71.5155 (16)C15—H150.944 (18)
C1—N1—C2124.90 (10)C5—C6—H62110.7 (9)
C1—N1—H1116.8 (11)C3—C6—H62109.9 (9)
C2—N1—H1118.0 (11)C5—C6—H61113.2 (9)
C4—N2—C5108.84 (9)C3—C6—H61110.9 (9)
C4—N2—H2113.2 (11)H62—C6—H61111.2 (12)
C5—N2—H2111.3 (11)C5—C7—H73107.1 (11)
O1—C1—N1120.48 (11)C5—C7—H72110.8 (10)
O1—C1—C5123.50 (11)H73—C7—H72110.3 (14)
N1—C1—C5115.97 (10)C5—C7—H71108.5 (11)
O2—C2—N1120.71 (11)H73—C7—H71107.9 (15)
O2—C2—C3124.53 (11)H72—C7—H71112.1 (15)
N1—C2—C3114.76 (10)N3—C8—C13179.09 (15)
C2—C3—C6108.91 (9)C15—C10—C11118.62 (11)
C2—C3—C4110.75 (9)C15—C10—C4119.08 (10)
C6—C3—C4101.02 (9)C11—C10—C4122.20 (11)
C2—C3—H3108.4 (9)C12—C11—C10120.64 (12)
C6—C3—H3114.4 (9)C12—C11—H11118.1 (11)
C4—C3—H3113.1 (9)C10—C11—H11121.3 (11)
N2—C4—C10115.62 (10)C13—C12—C11119.78 (12)
N2—C4—C3104.39 (9)C13—C12—H12119.5 (12)
C10—C4—C3116.00 (9)C11—C12—H12120.7 (12)
N2—C4—H4108.7 (9)C12—C13—C14120.37 (11)
C10—C4—H4106.4 (9)C12—C13—C8119.00 (12)
C3—C4—H4105.1 (9)C14—C13—C8120.62 (11)
N2—C5—C7112.09 (11)C15—C14—C13119.33 (11)
N2—C5—C6102.15 (9)C15—C14—H14119.0 (10)
C7—C5—C6115.05 (10)C13—C14—H14121.7 (10)
N2—C5—C1107.06 (9)C14—C15—C10121.25 (12)
C7—C5—C1111.09 (10)C14—C15—H15118.2 (11)
C6—C5—C1108.79 (10)C10—C15—H15120.5 (11)
C5—C6—C3100.36 (9)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···O2i0.899 (18)2.368 (19)3.2377 (14)162.8 (15)
N1—H1···O1ii0.877 (17)2.032 (17)2.9019 (14)171.3 (15)
Symmetry codes: (i) x, y+1, z; (ii) x, y+1, z+1.

Experimental details

Crystal data
Chemical formulaC14H13N3O2
Mr255.27
Crystal system, space groupMonoclinic, P21/c
Temperature (K)150
a, b, c (Å)14.8572 (13), 6.2269 (6), 13.1215 (12)
β (°) 95.568 (1)
V3)1208.20 (19)
Z4
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.40 × 0.15 × 0.10
Data collection
DiffractometerBruker SMART APEXII
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2008)
Tmin, Tmax0.962, 0.990
No. of measured, independent and
observed [I > 2σ(I)] reflections
11909, 2924, 2601
Rint0.019
(sin θ/λ)max1)0.661
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.040, 0.110, 1.06
No. of reflections2924
No. of parameters224
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)0.35, 0.21

Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···O2i0.899 (18)2.368 (19)3.2377 (14)162.8 (15)
N1—H1···O1ii0.877 (17)2.032 (17)2.9019 (14)171.3 (15)
Symmetry codes: (i) x, y+1, z; (ii) x, y+1, z+1.
 

Acknowledgements

This study was partially supported by the Russian Foundation for Basic Research (project Nos. 11–03–00630_ a and 11–03–91375-ST_a) and State Contract No. 11.519.11.2032.

References

First citationBruker (2008). APEX2, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationKudryavtsev, K. V. (2010). Russ. J. Org. Chem. 46, 372–379.  Web of Science CrossRef CAS Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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