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Tetra­methyl N,N′-(2,2,3,3,4,4-hexa­fluoro-1,5-dioxo­pentane-1,5-di­yl)bis­­(phospho­ramidate)

aNational Taras Shevchenko University, Department of Chemistry, Volodymyrska str. 64, 01601 Kyiv, Ukraine, bNational University of Life and Environmental Sciences of Ukraine, Heroiv Oboroni str. 15, 03041 Kyiv, Ukraine, and cSTC "Institute for Single Crystals", 60 Lenina ave., Khar'kov 61001, Ukraine
*Correspondence e-mail: trush@univ.kiev.ua

(Received 20 February 2012; accepted 14 March 2012; online 21 March 2012)

The mol­ecule of the title compound, C9H14F6N2O8P2, lies on a twofold rotation axis that passes through the middle C atom of the three-atom fluoro­methyl­ene unit. The carbonyl and phosphoryl groups are in an antiperiplanar conformation. In the crystal, N—H⋯O=P hydrogen bonds link the mol­ecules into polymeric chains parallel to the c axis.

Related literature

For background to the chemistry of phospho­rus–organic compounds, see: Ly & Woollins (1998[Ly, T. Q. & Woollins, J. D. (1998). Coord. Chem. Rev. 176, 451-481.]). For the biological and pharmacological properties of carbacyl­amido­phosphate der­iv­atives, see: Adams et al. (2002[Adams, L. A., Cox, R. J., Gibson, J. S., Mayo-Martin, M. B., Walter, M. & Whittingham, W. (2002). Chem. Commun. pp. 2004-2005.]). For details of the synthesis and properties of phospho­ramide derivatives, see: Kirsanov & Levchenko (1957[Kirsanov, A. & Levchenko, E. (1957). Zh. Obshch. Khim. 27, 2585-2590.]); For structural analogues of phospho­rylated carbacyl­amides and their properties, see: Trush et al. (2005[Trush, V. A., Gubina, K. E., Amirkhanov, V. M., Swiatek-Kozlowska, J. & Domasevitch, K. V. (2005). Polyhedron, 24, 1007-1014.]); Gubina et al. (2000[Gubina, K. E., Ovchynnikov, V. A., Amirkhanov, V. M., Skopenko, V. V. & Shishkin, O. V. (2000). Z. Naturforsh. Teil B, 55, 495-498.]). For the synthesis and properties of fluorinated compounds, see: Leontieva et al. (2002[Leontieva, O. S., Chapurkin, V. V. & Baklanov, A. V. (2002). Russ. J. Org. Chem. 38, 1375-1376.]).

[Scheme 1]

Experimental

Crystal data
  • C9H14F6N2O8P2

  • Mr = 454.16

  • Monoclinic, C 2/c

  • a = 19.7862 (13) Å

  • b = 5.2801 (4) Å

  • c = 16.9943 (11) Å

  • β = 100.427 (6)°

  • V = 1746.1 (2) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.35 mm−1

  • T = 293 K

  • 0.40 × 0.20 × 0.10 mm

Data collection
  • Oxford Diffraction Xcalibur3 diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010[Oxford Diffraction (2010). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, England.]) Tmin = 0.872, Tmax = 0.966

  • 7084 measured reflections

  • 2504 independent reflections

  • 1669 reflections with I > 2σ(I)

  • Rint = 0.023

  • 2 standard reflections every 50 reflections intensity decay: 0.3%

Refinement
  • R[F2 > 2σ(F2)] = 0.037

  • wR(F2) = 0.106

  • S = 0.93

  • 2504 reflections

  • 125 parameters

  • H-atom parameters constrained

  • Δρmax = 0.29 e Å−3

  • Δρmin = −0.24 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1NA⋯O4i 0.86 1.93 2.7750 (17) 168
Symmetry code: (i) -x+1, -y, -z.

Data collection: CrysAlis CCD (Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction, Abingdon, England.]); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction, Abingdon, England.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: XP in SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Tetramethyl (2,2,3,3,4,4-hexafluoro-1,5-dioxopentane-1,5-diyl)bis(amidophosphate) is a representative of the carbacylamidophospates (CAPh), a family of compounds containing C(O)NHP(O) group. The presence of a peptide group in the carbacylamidophospates causes its diverse biological activity. (Adams et al., 2002). CAPh may be regarded as powerful chelating ligand systems. There has recently been a resurgence of interest in their coordination chemistry as a consequence of the steric control that this ligand system may impart compared to, for example, β-diketonates. The wide range of coordination compounds were synthesized and described in detailes (Ly & Woollins, 1998).

The crystal structure of tetramethyl (2,2,3,3,4,4-hexafluoro-1,5-dioxopentane-1,5-diyl)bis(amidophosphate) (1) reveals, that the molecule of phosphorylated amide consists of symmetric moiety lying on a twofold rotation axis that passes through the middle atom of the three-atom fluoromethylene unit (- x,y,-z + 1/2). CF2– groups are situated in the retarded conformation to each other with the values of dihedral FCCF angles in the range 57.76 - 68.62° (Fig.2). In the molecule, the carbonyl and phosphoryl groups are in antiperiplanar conformation. The frame O4—P1—N1—C3—O1 is almost flat (the values of dihedral O4—P1—N1—C3 and O1—C3—N1—P1 angles are -169.54 and -0.05°, respectively) as it has been observed for the most CAPh (Gubina et al., 2000; Trush et al. 2005). The crystal is composed from polymer chains which are built from molecules linked via intermolecular hydrogen N—H···O=P bonds (Fig.3). The parameters of the intermolecular hydrogen bond are listed in Table 1.

Related literature top

For background to the chemistry of phosphorus–organic compounds, see: Ly & Woollins (1998). For the biological and pharmacological properties of carbacylamidophosphate derivatives, see: Adams et al. (2002). For details of the synthesis and properties of phosphoramide derivatives, see: Kirsanov & Levchenko (1957); For structural analogues of phosphorylated carbacylamides and their properties, see: Trush et al. (2005); Gubina et al. (2000). For the synthesis and properties of fluorinated compounds, see: Leontieva et al. (2002).

Experimental top

The compound tetramethyl(2,2,3,3,4,4-hexafluoro-1,5-dioxopentane-1,5-diyl)bis(amidophosphate) (1) can be synthesized by multistep reaction (Fig.1) starting from dimethyl hexafluoropentanedioate (Leontieva et al. 2002). The solution of 26.81 g (0.1 mol) dimethyl hexafluoropentanedioate in 40 ml of methanol was added drop-wise to the well stirred saturated solution of ammonia in methanol (~ 200 ml) under cooling. The obtained mixture was allowed to stand for a weak. Then solvent was removed under reduced pressure to give the crude product. Recrystallization from water gave the white powder of 2,2,3,3,4,4-hexafluoropentanediamide (22.6 g, 95%). Subsequently, the meticulous dried diamide (11.91 g, 0.05 mol) was involved in phosphoroazo-reaction (Kirsanov & Levchenko, 1957) with 20.82 g (0.1 mol) of PCl5 in 10 ml CCl4. The treatment of crude hexachloroanhydride with NaOCH3 (0.3 mol) in methanol solution leads to obtain hexaester with good yield. Further alkaline hydrolysis and acidification gave the final product - tetramethyl(2,2,3,3,4,4-hexafluoro-1,5-dioxopentane-1,5-diyl)bis(amidophosphate) (yield 13.6 g, 60%). The single crystals of 1 suitable for X-ray analysis were grown from aqueous-methanol solution (1:1).

Refinement top

All H atoms were placed at calculated positions and treated as riding on their parent atoms [C—H = 0.96 Å, and Uiso(H) = 1.5Ueq(C), N—H = 0.86 Å and Uiso(H) = 1.2Ueq(N)].

Structure description top

Tetramethyl (2,2,3,3,4,4-hexafluoro-1,5-dioxopentane-1,5-diyl)bis(amidophosphate) is a representative of the carbacylamidophospates (CAPh), a family of compounds containing C(O)NHP(O) group. The presence of a peptide group in the carbacylamidophospates causes its diverse biological activity. (Adams et al., 2002). CAPh may be regarded as powerful chelating ligand systems. There has recently been a resurgence of interest in their coordination chemistry as a consequence of the steric control that this ligand system may impart compared to, for example, β-diketonates. The wide range of coordination compounds were synthesized and described in detailes (Ly & Woollins, 1998).

The crystal structure of tetramethyl (2,2,3,3,4,4-hexafluoro-1,5-dioxopentane-1,5-diyl)bis(amidophosphate) (1) reveals, that the molecule of phosphorylated amide consists of symmetric moiety lying on a twofold rotation axis that passes through the middle atom of the three-atom fluoromethylene unit (- x,y,-z + 1/2). CF2– groups are situated in the retarded conformation to each other with the values of dihedral FCCF angles in the range 57.76 - 68.62° (Fig.2). In the molecule, the carbonyl and phosphoryl groups are in antiperiplanar conformation. The frame O4—P1—N1—C3—O1 is almost flat (the values of dihedral O4—P1—N1—C3 and O1—C3—N1—P1 angles are -169.54 and -0.05°, respectively) as it has been observed for the most CAPh (Gubina et al., 2000; Trush et al. 2005). The crystal is composed from polymer chains which are built from molecules linked via intermolecular hydrogen N—H···O=P bonds (Fig.3). The parameters of the intermolecular hydrogen bond are listed in Table 1.

For background to the chemistry of phosphorus–organic compounds, see: Ly & Woollins (1998). For the biological and pharmacological properties of carbacylamidophosphate derivatives, see: Adams et al. (2002). For details of the synthesis and properties of phosphoramide derivatives, see: Kirsanov & Levchenko (1957); For structural analogues of phosphorylated carbacylamides and their properties, see: Trush et al. (2005); Gubina et al. (2000). For the synthesis and properties of fluorinated compounds, see: Leontieva et al. (2002).

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell refinement: CrysAlis CCD (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: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. Scheme of synthesis of tetramethyl (2,2,3,3,4,4-hexafluoro-1,5-dioxopentane-1,5-diyl)bis(amidophosphate).
[Figure 2] Fig. 2. A view of tetramethyl(2,2,3,3,4,4-hexafluoro-1,5-dioxopentane-1,5-diyl)bis(amidophosphate). Symmetry transformation used to generate equivalent atoms: ix + 1,y,-z + 1/2.
[Figure 3] Fig. 3. A system of hydrogen bonds as a one-dimensional polymeric ladder chains.
Tetramethyl N,N'-(2,2,3,3,4,4-hexafluoro-1,5-dioxopentane- 1,5-diyl)bis(phosphoramidate) top
Crystal data top
C9H14F6N2O8P2F(000) = 920
Mr = 454.16Dx = 1.728 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 2504 reflections
a = 19.7862 (13) Åθ = 2.9–30°
b = 5.2801 (4) ŵ = 0.35 mm1
c = 16.9943 (11) ÅT = 293 K
β = 100.427 (6)°Block, colourless
V = 1746.1 (2) Å30.40 × 0.20 × 0.10 mm
Z = 4
Data collection top
Oxford Diffraction Xcalibur3
diffractometer
1669 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.023
Graphite monochromatorθmax = 30.0°, θmin = 2.9°
ω scansh = 2727
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2010)
k = 77
Tmin = 0.872, Tmax = 0.966l = 2322
7084 measured reflections2 standard reflections every 50 reflections
2504 independent reflections intensity decay: 0.3%
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)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.106H-atom parameters constrained
S = 0.93 w = 1/[σ2(Fo2) + (0.0667P)2]
where P = (Fo2 + 2Fc2)/3
2504 reflections(Δ/σ)max = 0.001
125 parametersΔρmax = 0.29 e Å3
0 restraintsΔρmin = 0.24 e Å3
Crystal data top
C9H14F6N2O8P2V = 1746.1 (2) Å3
Mr = 454.16Z = 4
Monoclinic, C2/cMo Kα radiation
a = 19.7862 (13) ŵ = 0.35 mm1
b = 5.2801 (4) ÅT = 293 K
c = 16.9943 (11) Å0.40 × 0.20 × 0.10 mm
β = 100.427 (6)°
Data collection top
Oxford Diffraction Xcalibur3
diffractometer
1669 reflections with I > 2σ(I)
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2010)
Rint = 0.023
Tmin = 0.872, Tmax = 0.9662 standard reflections every 50 reflections
7084 measured reflections intensity decay: 0.3%
2504 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0370 restraints
wR(F2) = 0.106H-atom parameters constrained
S = 0.93Δρmax = 0.29 e Å3
2504 reflectionsΔρmin = 0.24 e Å3
125 parameters
Special details top

Experimental. Analysis found: IR (KBr pellet, cm-1): 3095(s, NH), 2925(ns, CH), 1190(s), 1746(s, C=O), 1478(s CN); 1291 (as, CF), 1212 (s, PO), 1141 (s, CF). NMR - 1H (DMSO-d6): C—H 3.74 (d) 12H, 3JPH = 11.6 Hz; NH 11.38 (d) 2H; 31P (DMSO-d6): -0.28 (hept) 3JHP = 11.6 Hz; 13C (DMSO-d6): C(O) 159.68, CF 108.6 - 105.9, CH3 54.74.

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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
F10.54045 (6)0.1156 (2)0.30276 (6)0.0559 (3)
F20.58399 (6)0.5823 (2)0.25478 (7)0.0568 (3)
F30.50776 (6)0.5503 (2)0.14516 (6)0.0495 (3)
P10.61282 (2)0.06932 (8)0.04812 (2)0.03549 (13)
N10.57021 (7)0.1298 (3)0.09836 (8)0.0368 (3)
H1NA0.52800.16190.07840.044*
O10.65572 (7)0.2202 (3)0.20427 (8)0.0509 (3)
O20.67108 (6)0.0844 (2)0.01929 (7)0.0470 (3)
O30.65216 (6)0.2593 (2)0.10883 (7)0.0458 (3)
O40.56309 (6)0.1876 (3)0.01514 (7)0.0463 (3)
C10.50000.2656 (4)0.25000.0349 (5)
C20.54710 (9)0.4170 (3)0.20389 (9)0.0368 (3)
C30.59784 (8)0.2443 (3)0.16861 (9)0.0359 (3)
C40.65304 (12)0.2569 (4)0.04796 (13)0.0609 (6)
H4C0.61910.37490.03690.091*
H4B0.69330.34750.05610.091*
H4A0.63490.16210.09530.091*
C50.72440 (10)0.2612 (5)0.14340 (16)0.0672 (6)
H5C0.73400.40080.17990.101*
H5B0.75090.27870.10170.101*
H5A0.73630.10540.17160.101*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
F10.0650 (7)0.0573 (7)0.0483 (6)0.0249 (6)0.0182 (6)0.0188 (5)
F20.0620 (7)0.0545 (7)0.0567 (7)0.0208 (6)0.0179 (6)0.0233 (5)
F30.0586 (7)0.0482 (6)0.0447 (6)0.0125 (5)0.0172 (5)0.0133 (5)
P10.0276 (2)0.0451 (2)0.0324 (2)0.00321 (17)0.00186 (15)0.00114 (16)
N10.0276 (7)0.0485 (8)0.0325 (6)0.0032 (6)0.0008 (5)0.0049 (6)
O10.0375 (7)0.0623 (8)0.0471 (7)0.0022 (6)0.0077 (6)0.0082 (6)
O20.0322 (6)0.0634 (8)0.0463 (7)0.0026 (6)0.0093 (5)0.0114 (6)
O30.0347 (6)0.0518 (7)0.0479 (7)0.0046 (5)0.0009 (5)0.0094 (5)
O40.0367 (6)0.0573 (7)0.0413 (7)0.0064 (6)0.0026 (5)0.0145 (5)
C10.0389 (12)0.0357 (11)0.0296 (10)0.0000.0045 (9)0.000
C20.0420 (9)0.0365 (8)0.0311 (7)0.0032 (7)0.0042 (6)0.0042 (6)
C30.0337 (8)0.0413 (8)0.0317 (7)0.0025 (7)0.0032 (6)0.0009 (6)
C40.0603 (13)0.0614 (13)0.0622 (13)0.0049 (11)0.0143 (11)0.0208 (10)
C50.0381 (10)0.0707 (14)0.0843 (15)0.0082 (10)0.0121 (10)0.0189 (12)
Geometric parameters (Å, º) top
F1—C11.3461 (16)O3—C51.444 (2)
F2—C21.3469 (18)C1—F1i1.3461 (16)
F3—C21.3475 (18)C1—C2i1.545 (2)
P1—O41.4598 (12)C1—C21.545 (2)
P1—O31.5444 (12)C2—C31.555 (2)
P1—O21.5595 (13)C4—H4C0.9600
P1—N11.6751 (14)C4—H4B0.9600
N1—C31.361 (2)C4—H4A0.9600
N1—H1NA0.8600C5—H5C0.9600
O1—C31.202 (2)C5—H5B0.9600
O2—C41.454 (2)C5—H5A0.9600
O4—P1—O3113.89 (8)F3—C2—C1108.98 (12)
O4—P1—O2115.43 (8)F2—C2—C3108.38 (13)
O3—P1—O2103.65 (7)F3—C2—C3110.33 (12)
O4—P1—N1108.04 (7)C1—C2—C3112.52 (14)
O3—P1—N1107.84 (7)O1—C3—N1126.17 (16)
O2—P1—N1107.59 (7)O1—C3—C2119.38 (14)
C3—N1—P1124.51 (11)N1—C3—C2114.45 (13)
C3—N1—H1NA117.7O2—C4—H4C109.5
P1—N1—H1NA117.7O2—C4—H4B109.5
C4—O2—P1118.85 (13)H4C—C4—H4B109.5
C5—O3—P1128.21 (14)O2—C4—H4A109.5
F1—C1—F1i107.92 (19)H4C—C4—H4A109.5
F1—C1—C2i107.89 (7)H4B—C4—H4A109.5
F1i—C1—C2i107.56 (8)O3—C5—H5C109.5
F1—C1—C2107.56 (8)O3—C5—H5B109.5
F1i—C1—C2107.89 (7)H5C—C5—H5B109.5
C2i—C1—C2117.67 (19)O3—C5—H5A109.5
F2—C2—F3108.08 (13)H5C—C5—H5A109.5
F2—C2—C1108.44 (12)H5B—C5—H5A109.5
O4—P1—N1—C3169.53 (14)F1i—C1—C2—F357.75 (17)
O3—P1—N1—C346.00 (15)C2i—C1—C2—F364.07 (10)
O2—P1—N1—C365.23 (15)F1—C1—C2—C351.23 (15)
O4—P1—O2—C445.46 (17)F1i—C1—C2—C364.95 (15)
O3—P1—O2—C4170.70 (14)C2i—C1—C2—C3173.22 (13)
N1—P1—O2—C475.24 (15)P1—N1—C3—O10.1 (3)
O4—P1—O3—C5137.75 (19)P1—N1—C3—C2178.97 (11)
O2—P1—O3—C511.5 (2)F2—C2—C3—O122.1 (2)
N1—P1—O3—C5102.4 (2)F3—C2—C3—O1140.28 (16)
F1—C1—C2—F268.63 (17)C1—C2—C3—O197.78 (17)
F1i—C1—C2—F2175.18 (13)F2—C2—C3—N1158.77 (14)
C2i—C1—C2—F253.36 (10)F3—C2—C3—N140.62 (19)
F1—C1—C2—F3173.94 (12)C1—C2—C3—N181.33 (15)
Symmetry code: (i) x+1, y, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1NA···O4ii0.861.932.7750 (17)168
Symmetry code: (ii) x+1, y, z.

Experimental details

Crystal data
Chemical formulaC9H14F6N2O8P2
Mr454.16
Crystal system, space groupMonoclinic, C2/c
Temperature (K)293
a, b, c (Å)19.7862 (13), 5.2801 (4), 16.9943 (11)
β (°) 100.427 (6)
V3)1746.1 (2)
Z4
Radiation typeMo Kα
µ (mm1)0.35
Crystal size (mm)0.40 × 0.20 × 0.10
Data collection
DiffractometerOxford Diffraction Xcalibur3
Absorption correctionMulti-scan
(CrysAlis PRO; Oxford Diffraction, 2010)
Tmin, Tmax0.872, 0.966
No. of measured, independent and
observed [I > 2σ(I)] reflections
7084, 2504, 1669
Rint0.023
(sin θ/λ)max1)0.703
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.106, 0.93
No. of reflections2504
No. of parameters125
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.29, 0.24

Computer programs: CrysAlis CCD (Oxford Diffraction, 2006), CrysAlis RED (Oxford Diffraction, 2006), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), XP in SHELXTL (Sheldrick, 2008), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1NA···O4i0.861.932.7750 (17)168
Symmetry code: (i) x+1, y, z.
 

References

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