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In the title compound {systematic name: N-[3-(5-aza-2,8,9-trioxa-1-silabicyclo­[3.3.3]undeca­n-1-yl)propyl]penta­fluorobenzamide}, C16H19F5N2O4Si, unexpected weak anion...π-type C=O...C(aromatic) inter­actions form a dimer [O...C distances of 3.096 (3) and 3.036 (3) Å]. These dimers are further connected by a normal N—H...O hydrogen bond [2.955 (2) Å], from the amide H atom to one of the silatrane O atoms. Also, four intermolecular contacts between CH groups and silatrane O and F atoms [3.101(3)–3.406 (3) Å] are observed.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807044777/bt2508sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807044777/bt2508Isup2.hkl
Contains datablock I

CCDC reference: 663805

Key indicators

  • Single-crystal X-ray study
  • T = 173 K
  • R factor = 0.039
  • wR factor = 0.092
  • Data-to-parameter ratio = 12.2

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Comment top

The title compound is a perfluorobenzamide derivative including a silatrane group (Fig. 1). A weak anion-π-type of interaction between the electron pair of the carbonyl oxygen O(8) and the two carbon atoms C(3) and C(4) of the perfluorobenzoic acid moiety creates a dimer. The interaction distances are 3.096 (3) and 3.036 (3) Å for the O(8)···C(3) and O(8)···C(4), respectively. Similar interaction but between the polarized iodine atoms in diiodotetrafluorobenzene and carbonyl oxygen has recently been observed in a study of halogen bonding (Russo et al., 2007). In addition a normal hydrogen bond, N···O = 2.954 (2) Å with angle of 172.45°, exists from the amide hydrogen to one of the silatrane O atoms, O(20). Also two short intermolecular contacts ranging from 3.027 to 3.406 Å between C—H and silatrane O atoms and three to the fluorine atoms, from 3.101 to 3.229 Å are observed.

Related literature top

For related literature, see: Russo et al. (2007); Semenov et al. (2002).

Experimental top

Analytical grade reagents were used. 1-(3'-Amino)propylsilatrane (Semenov et al., 2002) (400 mg, 1.72 mmol) was mixed in 30 ml dry dichloromethane under inert gas atmosphere. Triethylamine (470 µl, 3.44 mmol) was added. The reaction mixture was cooled (ice salt bath). Mixture of 2,3,4,5,6-pentafluorobenzoylchloride (240 µl, 1.72 mmol) and dry dichloromethane was added dropwise to the reaction flask. The reaction mixture was stirred at 0° C for 1 h and at the room temperature for 18 h. After that the mixture was washed with water, dried with MgSO4, filtered and evaporated. Yield 460 mg (63%). Colorless crystals were obtained from chloroform at room temperature via slow evaporation. (mp. 454.6–455.2 K). 1H-NMR (500 MHz, CDCl3)δ, p.p.m.: 0.509 (t. 2H), 1.736 (tt. 2H), 2.802 (t·6H), 3.454 (q. 2H), 3.718 (t. 6H), 6.923 (s. 1H). 13C NMR (126 MHz, CDCl3)δ, p.p.m.: -47.417, -38.863, -27.089, 12.856, 23.412, 43.013, 50.989, 57.550, 156.880. MS (ESI-TOF) 449 [M+Na].

Refinement top

All H atoms were visible in electron density maps, but were placed in idealized positions and allowed to ride on their parent atoms at C—H distances of 0.99 Å (methylene) and 0.88 Å for H—N with Uiso(H) of 1.2 times Ueq(C) and Ueq(N).

Structure description top

The title compound is a perfluorobenzamide derivative including a silatrane group (Fig. 1). A weak anion-π-type of interaction between the electron pair of the carbonyl oxygen O(8) and the two carbon atoms C(3) and C(4) of the perfluorobenzoic acid moiety creates a dimer. The interaction distances are 3.096 (3) and 3.036 (3) Å for the O(8)···C(3) and O(8)···C(4), respectively. Similar interaction but between the polarized iodine atoms in diiodotetrafluorobenzene and carbonyl oxygen has recently been observed in a study of halogen bonding (Russo et al., 2007). In addition a normal hydrogen bond, N···O = 2.954 (2) Å with angle of 172.45°, exists from the amide hydrogen to one of the silatrane O atoms, O(20). Also two short intermolecular contacts ranging from 3.027 to 3.406 Å between C—H and silatrane O atoms and three to the fluorine atoms, from 3.101 to 3.229 Å are observed.

For related literature, see: Russo et al. (2007); Semenov et al. (2002).

Computing details top

Data collection: COLLECT (Nonius, 2004); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] Fig. 1. View of the molecule of (I) showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are represented by circles of arbitrary size.
N-[3-(5-aza-2,8,9-trioxa-1-silabicyclo[3.3.3]undecan-1-yl)propyl] pentafluorobenzamide top
Crystal data top
C16H19F5N2O4SiF(000) = 880
Mr = 426.42Dx = 1.608 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71069 Å
Hall symbol: -P 2ynCell parameters from 15147 reflections
a = 15.2027 (4) Åθ = 2.6–27.1°
b = 7.6207 (2) ŵ = 0.21 mm1
c = 16.2411 (4) ÅT = 173 K
β = 110.568 (1)°Prism, colourless
V = 1761.67 (8) Å30.3 × 0.2 × 0.1 mm
Z = 4
Data collection top
Nonius KappaCCD with APEXII detector
diffractometer
2456 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.031
Graphite monochromatorθmax = 25°, θmin = 2.7°
Detector resolution: 9 pixels mm-1h = 1718
φ and ω scansk = 98
5912 measured reflectionsl = 1919
3099 independent reflections
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.039 w = 1/[σ2(Fo2) + (0.0296P)2 + 1.504P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.092(Δ/σ)max = 0.001
S = 1.05Δρmax = 0.22 e Å3
3099 reflectionsΔρmin = 0.27 e Å3
253 parameters
Crystal data top
C16H19F5N2O4SiV = 1761.67 (8) Å3
Mr = 426.42Z = 4
Monoclinic, P21/nMo Kα radiation
a = 15.2027 (4) ŵ = 0.21 mm1
b = 7.6207 (2) ÅT = 173 K
c = 16.2411 (4) Å0.3 × 0.2 × 0.1 mm
β = 110.568 (1)°
Data collection top
Nonius KappaCCD with APEXII detector
diffractometer
2456 reflections with I > 2σ(I)
5912 measured reflectionsRint = 0.031
3099 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0390 restraints
wR(F2) = 0.092H-atom parameters constrained
S = 1.05Δρmax = 0.22 e Å3
3099 reflectionsΔρmin = 0.27 e Å3
253 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Si130.97532 (4)0.78594 (8)0.86902 (4)0.02310 (16)
F20.40578 (10)0.6889 (2)0.84279 (11)0.0522 (4)
F30.27692 (10)0.4350 (3)0.82441 (11)0.0594 (5)
F40.33118 (12)0.0976 (2)0.86283 (11)0.0614 (5)
F50.51698 (13)0.0127 (2)0.91677 (13)0.0692 (5)
F60.64535 (10)0.2641 (2)0.93287 (12)0.0594 (5)
O80.65323 (12)0.6813 (3)0.96762 (11)0.0464 (5)
O140.97348 (10)0.7809 (2)0.97124 (9)0.0269 (4)
O201.01580 (10)0.9657 (2)0.83334 (10)0.0269 (4)
O210.97836 (10)0.5987 (2)0.81759 (10)0.0312 (4)
N90.61017 (12)0.6639 (3)0.81880 (12)0.0278 (4)
H90.57080.61430.77120.033*
N171.12283 (12)0.7347 (3)0.93537 (12)0.0262 (4)
C10.52963 (15)0.4837 (3)0.88953 (14)0.0309 (6)
C20.43490 (16)0.5230 (4)0.86223 (15)0.0341 (6)
C30.36870 (16)0.3938 (4)0.85321 (16)0.0382 (6)
C40.39591 (18)0.2229 (4)0.87225 (17)0.0413 (7)
C50.48958 (19)0.1797 (4)0.89961 (18)0.0427 (7)
C60.55422 (16)0.3103 (4)0.90777 (16)0.0378 (6)
C70.60408 (16)0.6221 (3)0.89642 (15)0.0312 (6)
C100.67912 (15)0.7881 (3)0.80927 (15)0.0288 (5)
H10A0.6790.89420.84440.035*
H10B0.65980.8240.74680.035*
C110.77909 (14)0.7152 (3)0.83832 (15)0.0295 (5)
H11A0.80260.69780.90280.035*
H11B0.77780.59910.81050.035*
C120.84674 (14)0.8355 (3)0.81418 (14)0.0257 (5)
H12A0.83550.95760.82890.031*
H12B0.83130.82980.74970.031*
C151.05262 (14)0.7340 (3)1.04586 (14)0.0282 (5)
H15A1.05160.60641.05710.034*
H15B1.05090.79761.09840.034*
C161.14112 (15)0.7814 (3)1.02816 (14)0.0307 (5)
H16A1.15460.90831.03780.037*
H16B1.19550.71461.06750.037*
C181.17155 (16)0.8512 (3)0.89244 (16)0.0329 (6)
H18A1.17620.79470.83920.04*
H18B1.23570.87880.93320.04*
C191.11278 (15)1.0158 (3)0.86826 (16)0.0305 (5)
H19A1.12451.09040.92090.037*
H19B1.12951.08350.82390.037*
C221.06325 (17)0.5059 (3)0.83005 (16)0.0354 (6)
H22A1.08980.54220.78510.042*
H22B1.05070.37820.82390.042*
C231.13256 (16)0.5461 (3)0.92118 (16)0.0330 (6)
H23A1.11790.4760.96610.04*
H23B1.19740.51860.92470.04*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Si130.0218 (3)0.0238 (3)0.0226 (3)0.0001 (3)0.0064 (2)0.0027 (3)
F20.0415 (9)0.0471 (10)0.0674 (11)0.0108 (7)0.0183 (8)0.0011 (8)
F30.0238 (7)0.0906 (14)0.0646 (11)0.0000 (8)0.0166 (7)0.0068 (10)
F40.0566 (10)0.0715 (12)0.0621 (11)0.0332 (9)0.0283 (9)0.0114 (9)
F50.0733 (12)0.0416 (11)0.0933 (14)0.0003 (9)0.0300 (11)0.0161 (10)
F60.0306 (8)0.0621 (11)0.0797 (12)0.0107 (8)0.0122 (8)0.0202 (10)
O80.0414 (10)0.0700 (14)0.0257 (9)0.0139 (10)0.0090 (8)0.0094 (9)
O140.0209 (7)0.0371 (9)0.0214 (8)0.0006 (7)0.0059 (6)0.0031 (7)
O200.0217 (8)0.0279 (9)0.0292 (8)0.0010 (7)0.0067 (6)0.0065 (7)
O210.0299 (8)0.0278 (9)0.0337 (9)0.0019 (7)0.0085 (7)0.0015 (7)
N90.0232 (9)0.0344 (11)0.0248 (10)0.0036 (8)0.0073 (8)0.0029 (9)
N170.0219 (9)0.0316 (11)0.0248 (10)0.0022 (8)0.0080 (8)0.0058 (8)
C10.0249 (11)0.0446 (16)0.0244 (12)0.0016 (11)0.0101 (10)0.0008 (11)
C20.0314 (13)0.0432 (16)0.0301 (13)0.0017 (12)0.0139 (11)0.0016 (11)
C30.0219 (12)0.0628 (19)0.0329 (13)0.0030 (12)0.0136 (10)0.0076 (13)
C40.0407 (14)0.0518 (18)0.0383 (14)0.0169 (13)0.0227 (12)0.0063 (13)
C50.0464 (15)0.0397 (17)0.0447 (15)0.0025 (13)0.0192 (13)0.0069 (13)
C60.0263 (12)0.0483 (17)0.0379 (14)0.0043 (12)0.0099 (11)0.0086 (12)
C70.0253 (11)0.0387 (15)0.0297 (13)0.0004 (11)0.0097 (10)0.0014 (11)
C100.0245 (11)0.0292 (13)0.0311 (12)0.0036 (10)0.0078 (9)0.0005 (10)
C110.0230 (11)0.0283 (13)0.0330 (13)0.0022 (10)0.0046 (10)0.0020 (11)
C120.0232 (11)0.0281 (13)0.0241 (11)0.0019 (10)0.0062 (9)0.0007 (10)
C150.0263 (11)0.0334 (14)0.0225 (11)0.0013 (10)0.0056 (9)0.0027 (10)
C160.0233 (11)0.0390 (14)0.0258 (12)0.0007 (10)0.0038 (9)0.0037 (11)
C180.0235 (11)0.0415 (15)0.0349 (13)0.0012 (11)0.0117 (10)0.0103 (12)
C190.0232 (11)0.0335 (14)0.0337 (12)0.0057 (10)0.0087 (10)0.0045 (11)
C220.0399 (13)0.0306 (14)0.0389 (14)0.0094 (11)0.0178 (11)0.0037 (11)
C230.0317 (12)0.0338 (14)0.0364 (13)0.0110 (11)0.0158 (11)0.0091 (11)
Geometric parameters (Å, º) top
Si13—O211.6625 (17)C4—C51.374 (4)
Si13—O141.6706 (15)C5—C61.372 (4)
Si13—O201.6860 (16)C10—C111.529 (3)
Si13—C121.880 (2)C10—H10A0.99
Si13—N172.1551 (18)C10—H10B0.99
F2—C21.341 (3)C11—C121.528 (3)
F3—C31.344 (3)C11—H11A0.99
F4—C41.341 (3)C11—H11B0.99
F5—C51.338 (3)C12—H12A0.99
F6—C61.346 (3)C12—H12B0.99
O8—C71.221 (3)C15—C161.515 (3)
O14—C151.421 (2)C15—H15A0.99
O20—C191.433 (2)C15—H15B0.99
O21—C221.422 (3)C16—H16A0.99
N9—C71.335 (3)C16—H16B0.99
N9—C101.460 (3)C18—C191.510 (3)
N9—H90.88C18—H18A0.99
N17—C231.472 (3)C18—H18B0.99
N17—C161.477 (3)C19—H19A0.99
N17—C181.478 (3)C19—H19B0.99
C1—C61.377 (4)C22—C231.516 (3)
C1—C21.383 (3)C22—H22A0.99
C1—C71.522 (3)C22—H22B0.99
C2—C31.378 (4)C23—H23A0.99
C3—C41.368 (4)C23—H23B0.99
O21—Si13—O14119.51 (9)C12—C11—C10112.86 (19)
O21—Si13—O20116.55 (8)C12—C11—H11A109
O14—Si13—O20119.73 (8)C10—C11—H11A109
O21—Si13—C1298.18 (9)C12—C11—H11B109
O14—Si13—C1295.62 (8)C10—C11—H11B109
O20—Si13—C1296.79 (9)H11A—C11—H11B107.8
O21—Si13—N1783.57 (8)C11—C12—Si13116.06 (15)
O14—Si13—N1782.92 (7)C11—C12—H12A108.3
O20—Si13—N1782.97 (7)Si13—C12—H12A108.3
C12—Si13—N17178.12 (9)C11—C12—H12B108.3
C15—O14—Si13123.26 (13)Si13—C12—H12B108.3
C19—O20—Si13121.96 (14)H12A—C12—H12B107.4
C22—O21—Si13122.63 (15)O14—C15—C16108.70 (17)
C7—N9—C10123.05 (19)O14—C15—H15A110
C7—N9—H9118.5C16—C15—H15A110
C10—N9—H9118.5O14—C15—H15B110
C23—N17—C16113.68 (18)C16—C15—H15B110
C23—N17—C18114.70 (18)H15A—C15—H15B108.3
C16—N17—C18113.02 (19)N17—C16—C15105.95 (17)
C23—N17—Si13104.05 (14)N17—C16—H16A110.5
C16—N17—Si13104.87 (13)C15—C16—H16A110.5
C18—N17—Si13105.15 (13)N17—C16—H16B110.5
C6—C1—C2116.7 (2)C15—C16—H16B110.5
C6—C1—C7120.7 (2)H16A—C16—H16B108.7
C2—C1—C7122.5 (2)N17—C18—C19105.81 (17)
F2—C2—C3118.7 (2)N17—C18—H18A110.6
F2—C2—C1120.0 (2)C19—C18—H18A110.6
C3—C2—C1121.3 (2)N17—C18—H18B110.6
F3—C3—C4119.7 (2)C19—C18—H18B110.6
F3—C3—C2120.0 (3)H18A—C18—H18B108.7
C4—C3—C2120.3 (2)O20—C19—C18108.34 (19)
F4—C4—C3120.0 (2)O20—C19—H19A110
F4—C4—C5120.1 (3)C18—C19—H19A110
C3—C4—C5119.8 (2)O20—C19—H19B110
F5—C5—C6120.7 (2)C18—C19—H19B110
F5—C5—C4120.4 (2)H19A—C19—H19B108.4
C6—C5—C4118.9 (3)O21—C22—C23108.86 (19)
F6—C6—C5117.7 (2)O21—C22—H22A109.9
F6—C6—C1119.3 (2)C23—C22—H22A109.9
C5—C6—C1123.0 (2)O21—C22—H22B109.9
O8—C7—N9125.7 (2)C23—C22—H22B109.9
O8—C7—C1121.2 (2)H22A—C22—H22B108.3
N9—C7—C1113.11 (19)N17—C23—C22106.05 (19)
N9—C10—C11113.86 (19)N17—C23—H23A110.5
N9—C10—H10A108.8C22—C23—H23A110.5
C11—C10—H10A108.8N17—C23—H23B110.5
N9—C10—H10B108.8C22—C23—H23B110.5
C11—C10—H10B108.8H23A—C23—H23B108.7
H10A—C10—H10B107.7
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N9—H9···O20i0.882.082.955 (2)172
C15—H15B···O20ii0.992.513.406 (3)150
C16—H16B···F6iii0.992.433.101 (3)125
C18—H18B···F6iii0.992.533.320 (3)136
C23—H23B···F3iv0.992.433.229 (3)137
Symmetry codes: (i) x+3/2, y1/2, z+3/2; (ii) x+2, y+2, z+2; (iii) x+2, y+1, z+2; (iv) x+1, y, z.

Experimental details

Crystal data
Chemical formulaC16H19F5N2O4Si
Mr426.42
Crystal system, space groupMonoclinic, P21/n
Temperature (K)173
a, b, c (Å)15.2027 (4), 7.6207 (2), 16.2411 (4)
β (°) 110.568 (1)
V3)1761.67 (8)
Z4
Radiation typeMo Kα
µ (mm1)0.21
Crystal size (mm)0.3 × 0.2 × 0.1
Data collection
DiffractometerNonius KappaCCD with APEXII detector
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
5912, 3099, 2456
Rint0.031
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.039, 0.092, 1.05
No. of reflections3099
No. of parameters253
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.22, 0.27

Computer programs: COLLECT (Nonius, 2004), DENZO and SCALEPACK (Otwinowski & Minor, 1997), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 1997), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N9—H9···O20i0.882.082.955 (2)172
C15—H15B···O20ii0.992.513.406 (3)150
C16—H16B···F6iii0.992.433.101 (3)125
C18—H18B···F6iii0.992.533.320 (3)136
C23—H23B···F3iv0.992.433.229 (3)137
Symmetry codes: (i) x+3/2, y1/2, z+3/2; (ii) x+2, y+2, z+2; (iii) x+2, y+1, z+2; (iv) x+1, y, z.
 

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