organic compounds
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
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). 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
Crystal data
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Data collection
Refinement
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Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell CrysAlis CCD; 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).
Supporting information
10.1107/S1600536812011191/fj2523sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812011191/fj2523Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812011191/fj2523Isup3.cml
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
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).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)].
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
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).
Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell
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).C9H14F6N2O8P2 | F(000) = 920 |
Mr = 454.16 | Dx = 1.728 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 2504 reflections |
a = 19.7862 (13) Å | θ = 2.9–30° |
b = 5.2801 (4) Å | µ = 0.35 mm−1 |
c = 16.9943 (11) Å | T = 293 K |
β = 100.427 (6)° | Block, colourless |
V = 1746.1 (2) Å3 | 0.40 × 0.20 × 0.10 mm |
Z = 4 |
Oxford Diffraction Xcalibur3 diffractometer | 1669 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.023 |
Graphite monochromator | θmax = 30.0°, θmin = 2.9° |
ω scans | h = −27→27 |
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010) | k = −7→7 |
Tmin = 0.872, Tmax = 0.966 | l = −23→22 |
7084 measured reflections | 2 standard reflections every 50 reflections |
2504 independent reflections | intensity decay: 0.3% |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.037 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.106 | H-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 parameters | Δρmax = 0.29 e Å−3 |
0 restraints | Δρmin = −0.24 e Å−3 |
C9H14F6N2O8P2 | V = 1746.1 (2) Å3 |
Mr = 454.16 | Z = 4 |
Monoclinic, C2/c | Mo Kα radiation |
a = 19.7862 (13) Å | µ = 0.35 mm−1 |
b = 5.2801 (4) Å | T = 293 K |
c = 16.9943 (11) Å | 0.40 × 0.20 × 0.10 mm |
β = 100.427 (6)° |
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 = 0.966 | 2 standard reflections every 50 reflections |
7084 measured reflections | intensity decay: 0.3% |
2504 independent reflections |
R[F2 > 2σ(F2)] = 0.037 | 0 restraints |
wR(F2) = 0.106 | H-atom parameters constrained |
S = 0.93 | Δρmax = 0.29 e Å−3 |
2504 reflections | Δρmin = −0.24 e Å−3 |
125 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
F1 | 0.54045 (6) | −0.1156 (2) | 0.30276 (6) | 0.0559 (3) | |
F2 | 0.58399 (6) | −0.5823 (2) | 0.25478 (7) | 0.0568 (3) | |
F3 | 0.50776 (6) | −0.5503 (2) | 0.14516 (6) | 0.0495 (3) | |
P1 | 0.61282 (2) | 0.06932 (8) | 0.04812 (2) | 0.03549 (13) | |
N1 | 0.57021 (7) | −0.1298 (3) | 0.09836 (8) | 0.0368 (3) | |
H1NA | 0.5280 | −0.1619 | 0.0784 | 0.044* | |
O1 | 0.65572 (7) | −0.2202 (3) | 0.20427 (8) | 0.0509 (3) | |
O2 | 0.67108 (6) | −0.0844 (2) | 0.01929 (7) | 0.0470 (3) | |
O3 | 0.65216 (6) | 0.2593 (2) | 0.10883 (7) | 0.0458 (3) | |
O4 | 0.56309 (6) | 0.1876 (3) | −0.01514 (7) | 0.0463 (3) | |
C1 | 0.5000 | −0.2656 (4) | 0.2500 | 0.0349 (5) | |
C2 | 0.54710 (9) | −0.4170 (3) | 0.20389 (9) | 0.0368 (3) | |
C3 | 0.59784 (8) | −0.2443 (3) | 0.16861 (9) | 0.0359 (3) | |
C4 | 0.65304 (12) | −0.2569 (4) | −0.04796 (13) | 0.0609 (6) | |
H4C | 0.6191 | −0.3749 | −0.0369 | 0.091* | |
H4B | 0.6933 | −0.3475 | −0.0561 | 0.091* | |
H4A | 0.6349 | −0.1621 | −0.0953 | 0.091* | |
C5 | 0.72440 (10) | 0.2612 (5) | 0.14340 (16) | 0.0672 (6) | |
H5C | 0.7340 | 0.4008 | 0.1799 | 0.101* | |
H5B | 0.7509 | 0.2787 | 0.1017 | 0.101* | |
H5A | 0.7363 | 0.1054 | 0.1716 | 0.101* |
U11 | U22 | U33 | U12 | U13 | U23 | |
F1 | 0.0650 (7) | 0.0573 (7) | 0.0483 (6) | −0.0249 (6) | 0.0182 (6) | −0.0188 (5) |
F2 | 0.0620 (7) | 0.0545 (7) | 0.0567 (7) | 0.0208 (6) | 0.0179 (6) | 0.0233 (5) |
F3 | 0.0586 (7) | 0.0482 (6) | 0.0447 (6) | −0.0125 (5) | 0.0172 (5) | −0.0133 (5) |
P1 | 0.0276 (2) | 0.0451 (2) | 0.0324 (2) | −0.00321 (17) | 0.00186 (15) | 0.00114 (16) |
N1 | 0.0276 (7) | 0.0485 (8) | 0.0325 (6) | −0.0032 (6) | 0.0008 (5) | 0.0049 (6) |
O1 | 0.0375 (7) | 0.0623 (8) | 0.0471 (7) | −0.0022 (6) | −0.0077 (6) | 0.0082 (6) |
O2 | 0.0322 (6) | 0.0634 (8) | 0.0463 (7) | −0.0026 (6) | 0.0093 (5) | −0.0114 (6) |
O3 | 0.0347 (6) | 0.0518 (7) | 0.0479 (7) | −0.0046 (5) | −0.0009 (5) | −0.0094 (5) |
O4 | 0.0367 (6) | 0.0573 (7) | 0.0413 (7) | −0.0064 (6) | −0.0026 (5) | 0.0145 (5) |
C1 | 0.0389 (12) | 0.0357 (11) | 0.0296 (10) | 0.000 | 0.0045 (9) | 0.000 |
C2 | 0.0420 (9) | 0.0365 (8) | 0.0311 (7) | 0.0032 (7) | 0.0042 (6) | 0.0042 (6) |
C3 | 0.0337 (8) | 0.0413 (8) | 0.0317 (7) | 0.0025 (7) | 0.0032 (6) | 0.0009 (6) |
C4 | 0.0603 (13) | 0.0614 (13) | 0.0622 (13) | −0.0049 (11) | 0.0143 (11) | −0.0208 (10) |
C5 | 0.0381 (10) | 0.0707 (14) | 0.0843 (15) | −0.0082 (10) | −0.0121 (10) | −0.0189 (12) |
F1—C1 | 1.3461 (16) | O3—C5 | 1.444 (2) |
F2—C2 | 1.3469 (18) | C1—F1i | 1.3461 (16) |
F3—C2 | 1.3475 (18) | C1—C2i | 1.545 (2) |
P1—O4 | 1.4598 (12) | C1—C2 | 1.545 (2) |
P1—O3 | 1.5444 (12) | C2—C3 | 1.555 (2) |
P1—O2 | 1.5595 (13) | C4—H4C | 0.9600 |
P1—N1 | 1.6751 (14) | C4—H4B | 0.9600 |
N1—C3 | 1.361 (2) | C4—H4A | 0.9600 |
N1—H1NA | 0.8600 | C5—H5C | 0.9600 |
O1—C3 | 1.202 (2) | C5—H5B | 0.9600 |
O2—C4 | 1.454 (2) | C5—H5A | 0.9600 |
O4—P1—O3 | 113.89 (8) | F3—C2—C1 | 108.98 (12) |
O4—P1—O2 | 115.43 (8) | F2—C2—C3 | 108.38 (13) |
O3—P1—O2 | 103.65 (7) | F3—C2—C3 | 110.33 (12) |
O4—P1—N1 | 108.04 (7) | C1—C2—C3 | 112.52 (14) |
O3—P1—N1 | 107.84 (7) | O1—C3—N1 | 126.17 (16) |
O2—P1—N1 | 107.59 (7) | O1—C3—C2 | 119.38 (14) |
C3—N1—P1 | 124.51 (11) | N1—C3—C2 | 114.45 (13) |
C3—N1—H1NA | 117.7 | O2—C4—H4C | 109.5 |
P1—N1—H1NA | 117.7 | O2—C4—H4B | 109.5 |
C4—O2—P1 | 118.85 (13) | H4C—C4—H4B | 109.5 |
C5—O3—P1 | 128.21 (14) | O2—C4—H4A | 109.5 |
F1—C1—F1i | 107.92 (19) | H4C—C4—H4A | 109.5 |
F1—C1—C2i | 107.89 (7) | H4B—C4—H4A | 109.5 |
F1i—C1—C2i | 107.56 (8) | O3—C5—H5C | 109.5 |
F1—C1—C2 | 107.56 (8) | O3—C5—H5B | 109.5 |
F1i—C1—C2 | 107.89 (7) | H5C—C5—H5B | 109.5 |
C2i—C1—C2 | 117.67 (19) | O3—C5—H5A | 109.5 |
F2—C2—F3 | 108.08 (13) | H5C—C5—H5A | 109.5 |
F2—C2—C1 | 108.44 (12) | H5B—C5—H5A | 109.5 |
O4—P1—N1—C3 | −169.53 (14) | F1i—C1—C2—F3 | −57.75 (17) |
O3—P1—N1—C3 | −46.00 (15) | C2i—C1—C2—F3 | 64.07 (10) |
O2—P1—N1—C3 | 65.23 (15) | F1—C1—C2—C3 | −51.23 (15) |
O4—P1—O2—C4 | −45.46 (17) | F1i—C1—C2—C3 | 64.95 (15) |
O3—P1—O2—C4 | −170.70 (14) | C2i—C1—C2—C3 | −173.22 (13) |
N1—P1—O2—C4 | 75.24 (15) | P1—N1—C3—O1 | −0.1 (3) |
O4—P1—O3—C5 | −137.75 (19) | P1—N1—C3—C2 | 178.97 (11) |
O2—P1—O3—C5 | −11.5 (2) | F2—C2—C3—O1 | −22.1 (2) |
N1—P1—O3—C5 | 102.4 (2) | F3—C2—C3—O1 | −140.28 (16) |
F1—C1—C2—F2 | 68.63 (17) | C1—C2—C3—O1 | 97.78 (17) |
F1i—C1—C2—F2 | −175.18 (13) | F2—C2—C3—N1 | 158.77 (14) |
C2i—C1—C2—F2 | −53.36 (10) | F3—C2—C3—N1 | 40.62 (19) |
F1—C1—C2—F3 | −173.94 (12) | C1—C2—C3—N1 | −81.33 (15) |
Symmetry code: (i) −x+1, y, −z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1NA···O4ii | 0.86 | 1.93 | 2.7750 (17) | 168 |
Symmetry code: (ii) −x+1, −y, −z. |
Experimental details
Crystal data | |
Chemical formula | C9H14F6N2O8P2 |
Mr | 454.16 |
Crystal system, space group | Monoclinic, C2/c |
Temperature (K) | 293 |
a, b, c (Å) | 19.7862 (13), 5.2801 (4), 16.9943 (11) |
β (°) | 100.427 (6) |
V (Å3) | 1746.1 (2) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.35 |
Crystal size (mm) | 0.40 × 0.20 × 0.10 |
Data collection | |
Diffractometer | Oxford Diffraction Xcalibur3 |
Absorption correction | Multi-scan (CrysAlis PRO; Oxford Diffraction, 2010) |
Tmin, Tmax | 0.872, 0.966 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7084, 2504, 1669 |
Rint | 0.023 |
(sin θ/λ)max (Å−1) | 0.703 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.106, 0.93 |
No. of reflections | 2504 |
No. of parameters | 125 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 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).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1NA···O4i | 0.86 | 1.93 | 2.7750 (17) | 168 |
Symmetry code: (i) −x+1, −y, −z. |
References
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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.