PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2009 November 1; 65(Pt 11): o2967.
Published online 2009 October 31. doi:  10.1107/S1600536809044729
PMCID: PMC2971350

(5R*,11R*)-5-Methyl-1,2-dihydro-5,11-methano-5H,11H-1,3-thia­zolo[2,3-d][1,3,5]benzoxadiazo­cine

Abstract

The title compound, C13H14N2OS, crystallizes as a racemate in a non-chiral space group. It represents a conformationally restricted analogue of so-called Biginelli compounds known to exhibit multiple pharmacological activities and was selected for a single-crystal X-ray analysis in order to probe the chemical and spatial requirements of some kinds of activity. It was found that the state of hybridization of the formally aminic nitro­gen of the heterocycle is between sp 2 and sp 3 with the lone-pair electrons partially delocalized through conjugation with the sulfur atom rather than the double bond of the pyrimidine nucleus. As a result, the thia­zolo ring adopts a flat-envelope conformation and the puckering of the central pyrimidine ring is close to a half-chair. The critical phenyl ring is fixed in a pseudo-axial and perpendicular [dihedral angle 84.6 (1)°] orientation with respect to the pyrimidine ring via an oxygen bridge.

Related literature

For typical bond lengths, see: Abrahams (1956 [triangle]); Burke-Laing & Laing (1976 [triangle]). For the pharmacological activity of Biginelli compounds, see: Deres et al. (2003 [triangle]); Kappe (2000 [triangle]). For the synthesis of rigid dihydro­pyrimidine derivatives, see: Světlík et al. (1991 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2967-scheme1.jpg

Experimental

Crystal data

  • C13H14N2OS
  • M r = 246.32
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2967-efi1.jpg
  • a = 14.307 (2) Å
  • b = 5.991 (1) Å
  • c = 15.203 (2) Å
  • β = 113.36 (1)°
  • V = 1196.3 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.26 mm−1
  • T = 296 K
  • 0.30 × 0.25 × 0.20 mm

Data collection

  • Siemens P4 diffractometer
  • Absorption correction: none
  • 4529 measured reflections
  • 3483 independent reflections
  • 2517 reflections with I > 2σ(I)
  • R int = 0.028
  • 3 standard reflections every 97 reflections intensity decay: none

Refinement

  • R[F 2 > 2σ(F 2)] = 0.053
  • wR(F 2) = 0.161
  • S = 1.05
  • 3483 reflections
  • 155 parameters
  • H-atom parameters constrained
  • Δρmax = 0.37 e Å−3
  • Δρmin = −0.24 e Å−3

Data collection: XSCANS (Siemens, 1991 [triangle]); cell refinement: XSCANS; data reduction: XSCANS; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: SHELXL97.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809044729/im2147sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809044729/im2147Isup2.hkl

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

Acknowledgments

This work was supported by the Grant Agency of the Slovak Republic, project Nos. 1/4298/07 and 1/4299/07.

supplementary crystallographic information

Comment

4-Aryl-3,4-dihydropyrimidine-2(1H)-ones and -thiones, known as Biginelli compounds, display a wide spectrum of significant pharmacological activities (Kappe, 2000). For example, these pyrimidine derivatives were assayed as antihypertensive agents, selective α1a-adrenergic receptor antagonists, neuropeptide Y antagonists and were used as a lead for development of anticancer drugs (Kappe, 2000). Recently, the Biginelli products have also been found to be potent hepatitis B replication inhibitors (Deres et al., 2003). As each of the above activities originates from stereo-selective binding of the drug molecule to its specific receptor, it is of interest to design a conformationally restricted probe molecule in order to examine geometric requirements of the given receptor binding site. Since we had previously synthesized such a rigid type of dihydropyrimidine, (I) (Světlík et al., 1991), we decided to examine the structure of this novel heterocyclic system by an X-ray analysis.

As mentioned above, from the pharmacological point of view the most important aspect of the molecular structure (Fig.1) concerns three-dimensional disposition of the key functional (pharmacophoric) elements (hydrophobic groups and heteroatoms able to form hydrogen bonds) which in turn depends on torsional (conformational) and bonding characteristics of the molecule. First, the central heterocycle assumes an unsymmetrical half-chair conformation in which atoms C6, N1, C2 and N3 are coplanar with r.m.s. deviation of 0.005 (1) Å, while atoms C4 and C5 are displaced from this plane by -0.281 (3) and 0.520 (3) Å, respectively. Next, the five-membered thiazolo ring adopts a flat-envelope conformation with atom C14 deviating by 0.423 (3) Å from the mean plane of the remaining four atoms [r.m.s. deviation 0.004 (1) Å]. Finally, the phenyl ring on C4 is, due to its pseudoaxial position and the O-atom bridge (Fig.1), fixed approximately in a perpendicular orientation with respect to the mean plane of the dihydropyrimidine ring [dihedral angle 84.6 (1)°]. All the above conformations arise from the rigidity of the polycyclic system as well as the bonding pattern within the π-electron portion of the fused heterocyclic substructure. Thus, the N1=C2 bond length of 1.287 (2) Å corresponds to pure double bond (Burke-Laing & Laing, 1976), while the formally single bonds S1—C2 and C2—N3 have partial double-bond character (Abrahams, 1956; Burke-Laing & Laing, 1976), obviously due to partial sp2-hybridization state of N3 and hence some degree of conjugation between N3 and S1.

As there is no classical hydrogen-bond donor site in the molecule, the crystal packing is governed by weak C–H···O and C–H···N contacts and van der Waals interactions.

Experimental

Synthesis of the title compound, (I), has been described (Světlík et al., 1991). In short, a solution of methyl 3,4,5,6-tetrahydro-2-methyl-2,6-methano-4-thioxo- 2H-1,3,5-benzoxadiazocine-11-carboxylate (1.0 g, 3.59 mmol) and 1,2-dibromoethane (0.35 ml, 4.0 mmol) in dimethylformamide was refluxed for 40 minutes. The resulting hydrobromide was treated with aqueous sodium carbonate to furnish the corresponding free base (42% yield; m.p. 513–514 K). Single crystals suitable for an X-ray analysis were obtained by recrystallization from acetonitrile.

Refinement

H atoms were visible in difference maps and were subsequently treated as riding atoms with distances C—H = 0.93 Å (CHarom), 0.97 (CH2) or 0.98 Å (CH) and 0.96 Å (CH3); Uiso of the H atoms were set to 1.2 (1.5 for the methyl H atoms) times Ueq of the parent atom.

Figures

Fig. 1.
Displacement ellipsoid plot of (I) with the labelling scheme for the non-H atoms, which are drawn as 35% probability ellipsoids.

Crystal data

C13H14N2OSF(000) = 520
Mr = 246.32Dx = 1.368 Mg m3
Monoclinic, P21/nMelting point: 513 K
Hall symbol: -P 2ynMo Kα radiation, λ = 0.71073 Å
a = 14.307 (2) ÅCell parameters from 20 reflections
b = 5.991 (1) Åθ = 7–18°
c = 15.203 (2) ŵ = 0.26 mm1
β = 113.36 (1)°T = 296 K
V = 1196.3 (3) Å3Prism, colourless
Z = 40.30 × 0.25 × 0.20 mm

Data collection

Siemens P4 diffractometerRint = 0.028
Radiation source: fine-focus sealed tubeθmax = 30.0°, θmin = 1.7°
graphiteh = −1→20
ω/2θ scansk = −1→8
4529 measured reflectionsl = −21→20
3483 independent reflections3 standard reflections every 97 reflections
2517 reflections with I > 2σ(I) intensity decay: none

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.053Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.161H-atom parameters constrained
S = 1.05w = 1/[σ2(Fo2) + (0.0855P)2 + 0.232P] where P = (Fo2 + 2Fc2)/3
3483 reflections(Δ/σ)max = 0.001
155 parametersΔρmax = 0.37 e Å3
0 restraintsΔρmin = −0.23 e Å3

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
N10.24822 (12)0.3305 (3)−0.01176 (11)0.0354 (3)
C20.20695 (13)0.4743 (3)0.02460 (12)0.0316 (4)
N30.18468 (12)0.6936 (3)0.00041 (10)0.0345 (3)
C40.18874 (14)0.7633 (3)−0.09082 (13)0.0337 (4)
H40.19180.9264−0.09380.040*
C50.28506 (14)0.6602 (3)−0.09323 (14)0.0370 (4)
H5A0.34430.7084−0.03810.044*
H5B0.29360.7054−0.15090.044*
C60.27290 (14)0.4073 (3)−0.09162 (13)0.0338 (4)
C70.09818 (14)0.6755 (3)−0.17604 (12)0.0336 (4)
C80.10420 (13)0.4666 (3)−0.21460 (12)0.0337 (4)
O10.19045 (11)0.3365 (2)−0.18067 (9)0.0393 (3)
C90.02109 (17)0.3840 (4)−0.29390 (14)0.0450 (5)
H90.02490.2451−0.31950.054*
C10−0.06598 (17)0.5104 (5)−0.33332 (15)0.0552 (6)
H10−0.12100.4555−0.38570.066*
C11−0.07307 (17)0.7163 (5)−0.29657 (16)0.0565 (6)
H11−0.13240.8000−0.32410.068*
C120.00859 (16)0.7986 (4)−0.21826 (15)0.0447 (5)
H120.00360.9379−0.19350.054*
S10.17224 (4)0.40002 (11)0.12054 (4)0.04879 (19)
C130.1245 (2)0.6777 (5)0.12630 (16)0.0572 (6)
H13A0.06010.66940.13330.069*
H13B0.17270.75980.18020.069*
C140.11074 (18)0.7907 (4)0.03283 (16)0.0497 (5)
H14A0.04220.7665−0.01450.060*
H14B0.12200.95010.04250.060*
C150.36653 (17)0.2829 (4)−0.08909 (17)0.0490 (5)
H15A0.42350.3180−0.03080.074*
H15B0.38130.3269−0.14290.074*
H15C0.35390.1251−0.09190.074*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0407 (8)0.0327 (8)0.0351 (7)0.0028 (6)0.0173 (6)0.0016 (6)
C20.0295 (8)0.0363 (9)0.0270 (7)−0.0032 (7)0.0089 (6)−0.0013 (6)
N30.0366 (8)0.0346 (8)0.0323 (7)0.0010 (6)0.0137 (6)−0.0053 (6)
C40.0369 (9)0.0261 (8)0.0378 (9)−0.0025 (7)0.0144 (7)−0.0001 (7)
C50.0347 (9)0.0377 (10)0.0399 (9)−0.0056 (7)0.0161 (7)0.0001 (7)
C60.0347 (8)0.0339 (9)0.0346 (8)0.0010 (7)0.0156 (7)−0.0015 (7)
C70.0361 (9)0.0342 (9)0.0301 (8)−0.0007 (7)0.0127 (7)0.0052 (7)
C80.0368 (9)0.0386 (9)0.0273 (7)−0.0058 (7)0.0145 (7)0.0006 (7)
O10.0456 (7)0.0358 (7)0.0353 (6)−0.0002 (6)0.0148 (6)−0.0066 (5)
C90.0527 (12)0.0514 (12)0.0324 (9)−0.0127 (10)0.0185 (8)−0.0035 (8)
C100.0420 (11)0.0852 (18)0.0314 (9)−0.0130 (12)0.0073 (8)0.0010 (10)
C110.0391 (11)0.0803 (18)0.0417 (11)0.0066 (11)0.0072 (9)0.0170 (12)
C120.0451 (10)0.0470 (11)0.0416 (10)0.0078 (9)0.0168 (8)0.0104 (9)
S10.0577 (3)0.0566 (4)0.0390 (3)−0.0027 (3)0.0265 (2)0.0012 (2)
C130.0631 (14)0.0717 (16)0.0452 (11)0.0011 (12)0.0306 (11)−0.0175 (11)
C140.0528 (12)0.0471 (12)0.0556 (12)0.0061 (10)0.0283 (10)−0.0107 (10)
C150.0442 (11)0.0516 (13)0.0592 (13)0.0102 (10)0.0289 (10)0.0000 (10)

Geometric parameters (Å, °)

N1—C21.287 (2)C8—C91.405 (3)
N1—C61.466 (2)C9—C101.375 (3)
C2—N31.368 (2)C9—H90.9300
C2—S11.7738 (18)C10—C111.375 (4)
N3—C141.454 (2)C10—H100.9300
N3—C41.471 (2)C11—C121.387 (3)
C4—C71.518 (2)C11—H110.9300
C4—C51.524 (3)C12—H120.9300
C4—H40.9800S1—C131.814 (3)
C5—C61.527 (3)C13—C141.515 (3)
C5—H5A0.9700C13—H13A0.9700
C5—H5B0.9700C13—H13B0.9700
C6—O11.462 (2)C14—H14A0.9700
C6—C151.520 (3)C14—H14B0.9700
C7—C121.395 (3)C15—H15A0.9600
C7—C81.399 (3)C15—H15B0.9600
C8—O11.375 (2)C15—H15C0.9600
C2—N1—C6116.60 (16)C10—C9—C8119.5 (2)
N1—C2—N3128.72 (17)C10—C9—H9120.3
N1—C2—S1120.73 (15)C8—C9—H9120.3
N3—C2—S1110.54 (13)C11—C10—C9121.1 (2)
C2—N3—C14114.61 (17)C11—C10—H10119.4
C2—N3—C4115.73 (14)C9—C10—H10119.4
C14—N3—C4120.80 (16)C10—C11—C12119.7 (2)
N3—C4—C7111.52 (14)C10—C11—H11120.2
N3—C4—C5106.36 (14)C12—C11—H11120.2
C7—C4—C5108.24 (15)C11—C12—C7121.0 (2)
N3—C4—H4110.2C11—C12—H12119.5
C7—C4—H4110.2C7—C12—H12119.5
C5—C4—H4110.2C2—S1—C1392.48 (10)
C4—C5—C6106.99 (15)C14—C13—S1106.02 (14)
C4—C5—H5A110.3C14—C13—H13A110.5
C6—C5—H5A110.3S1—C13—H13A110.5
C4—C5—H5B110.3C14—C13—H13B110.5
C6—C5—H5B110.3S1—C13—H13B110.5
H5A—C5—H5B108.6H13A—C13—H13B108.7
O1—C6—N1107.76 (14)N3—C14—C13107.34 (18)
O1—C6—C15105.11 (15)N3—C14—H14A110.2
N1—C6—C15108.93 (16)C13—C14—H14A110.2
O1—C6—C5109.15 (15)N3—C14—H14B110.2
N1—C6—C5113.02 (15)C13—C14—H14B110.2
C15—C6—C5112.47 (17)H14A—C14—H14B108.5
C12—C7—C8118.55 (18)C6—C15—H15A109.5
C12—C7—C4121.83 (18)C6—C15—H15B109.5
C8—C7—C4119.62 (16)H15A—C15—H15B109.5
O1—C8—C7123.01 (16)C6—C15—H15C109.5
O1—C8—C9116.78 (18)H15A—C15—H15C109.5
C7—C8—C9120.17 (18)H15B—C15—H15C109.5
C8—O1—C6117.24 (14)
C6—N1—C2—N3−1.7 (3)C12—C7—C8—O1177.30 (17)
C6—N1—C2—S1179.22 (12)C4—C7—C8—O1−2.0 (3)
N1—C2—N3—C14161.48 (18)C12—C7—C8—C9−0.3 (3)
S1—C2—N3—C14−19.39 (19)C4—C7—C8—C9−179.59 (17)
N1—C2—N3—C413.7 (3)C7—C8—O1—C69.4 (2)
S1—C2—N3—C4−167.15 (12)C9—C8—O1—C6−172.92 (16)
C2—N3—C4—C773.81 (19)N1—C6—O1—C881.42 (18)
C14—N3—C4—C7−71.8 (2)C15—C6—O1—C8−162.51 (16)
C2—N3—C4—C5−44.00 (19)C5—C6—O1—C8−41.7 (2)
C14—N3—C4—C5170.38 (16)O1—C8—C9—C10−177.58 (18)
N3—C4—C5—C662.31 (18)C7—C8—C9—C100.1 (3)
C7—C4—C5—C6−57.65 (19)C8—C9—C10—C110.1 (3)
C2—N1—C6—O1−97.83 (18)C9—C10—C11—C12−0.2 (4)
C2—N1—C6—C15148.63 (17)C10—C11—C12—C70.1 (3)
C2—N1—C6—C522.9 (2)C8—C7—C12—C110.2 (3)
C4—C5—C6—O166.42 (18)C4—C7—C12—C11179.48 (19)
C4—C5—C6—N1−53.5 (2)N1—C2—S1—C13179.86 (16)
C4—C5—C6—C15−177.33 (16)N3—C2—S1—C130.65 (14)
N3—C4—C7—C1291.3 (2)C2—S1—C13—C1416.47 (17)
C5—C4—C7—C12−152.05 (17)C2—N3—C14—C1332.1 (2)
N3—C4—C7—C8−89.41 (19)C4—N3—C14—C13178.03 (17)
C5—C4—C7—C827.3 (2)S1—C13—C14—N3−28.8 (2)

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IM2147).

References

  • Abrahams, S. C. (1956). Q. Rev. Chem. Soc.10, 407–436.
  • Burke-Laing, M. & Laing, M. (1976). Acta Cryst. B32, 3216–3224.
  • Deres, K., Schröder, C. H., Paessens, A., Goldmann, S., Hacker, H. J., Weber, O., Krämer, T., Niewöhner, U., Pleiss, U., Stoltefuss, J., Graef, E., Koletzki, D., Masantschek, R. N. A., Reimann, A., Jaeger, R., Grob, R., Beckermann, B., Schlemmer, K. H., Haebich, D. & Rübsamen-Weigmann, H. (2003). Science, 299, 893–896. [PubMed]
  • Kappe, C. O. (2000). Eur. J. Med. Chem.35, 1043–1052. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Siemens (1991). XSCANS. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]
  • Světlík, J., Hanus, V. & Bella, J. (1991). J. Chem. Res. (S), pp. 4–5.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography