Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807038962/hb2491sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807038962/hb2491Isup2.hkl |
CCDC reference: 660246
Key indicators
- Single-crystal X-ray study
- T = 120 K
- Mean (C-C) = 0.006 Å
- Disorder in main residue
- R factor = 0.043
- wR factor = 0.107
- Data-to-parameter ratio = 20.7
checkCIF/PLATON results
No syntax errors found
Alert level A PLAT222_ALERT_3_A Large Non-Solvent H Ueq(max)/Ueq(min) ... 7.10 Ratio
Author Response: see _publ_section_exptl_refinement |
Alert level B PLAT220_ALERT_2_B Large Non-Solvent C Ueq(max)/Ueq(min) ... 3.53 Ratio
Alert level C ABSTM02_ALERT_3_C The ratio of expected to reported Tmax/Tmin(RR') is < 0.90 Tmin and Tmax reported: 0.539 0.835 Tmin(prime) and Tmax expected: 0.604 0.829 RR(prime) = 0.887 Please check that your absorption correction is appropriate. PLAT061_ALERT_3_C Tmax/Tmin Range Test RR' too Large ............. 0.88 PLAT301_ALERT_3_C Main Residue Disorder ......................... 3.00 Perc. PLAT318_ALERT_2_C Check Hybridisation of N6 in Main Residue . ? PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ... 6 PLAT380_ALERT_4_C Check Incorrectly? Oriented X(sp2)-Methyl Moiety C7 PLAT380_ALERT_4_C Check Incorrectly? Oriented X(sp2)-Methyl Moiety C8 PLAT420_ALERT_2_C D-H Without Acceptor N6 - H6N ... ? PLAT431_ALERT_2_C Short Inter HL..A Contact Cl3 .. S1 .. 3.51 Ang. PLAT779_ALERT_2_C Suspect or Irrelevant (Bond) Angle in CIF ...... 39.50 Deg. C14' -C13 -C14 1.555 1.555 1.555 PLAT779_ALERT_2_C Suspect or Irrelevant (Bond) Angle in CIF ...... 40.80 Deg. C14 -C15 -C14' 1.555 1.555 1.555
Alert level G REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 27.48 From the CIF: _reflns_number_total 7560 Count of symmetry unique reflns 4349 Completeness (_total/calc) 173.83% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 3211 Fraction of Friedel pairs measured 0.738 Are heavy atom types Z>Si present yes
1 ALERT level A = In general: serious problem 1 ALERT level B = Potentially serious problem 11 ALERT level C = Check and explain 1 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 6 ALERT type 2 Indicator that the structure model may be wrong or deficient 5 ALERT type 3 Indicator that the structure quality may be low 3 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
checkCIF publication errors
Alert level A PUBL024_ALERT_1_A The number of authors is greater than 5. Please specify the role of each of the co-authors for your paper.
Author Response: This work is the product of a large ongoing international collaboration and involves intellectual input from three different institutions. |
Coles: Corresponding author responsible for manuscript preparation and crystal structure refinement, etc. Davies & Shaw: Co-coordinators of the international collaboration and intellectual founders/maintainers of the project. Hursthouse: Director of the x-ray crystallography laboratory. Ibisoglu: Research student responsible for synthesis. Kilic: Director of synthesis laboratory.
1 ALERT level A = Data missing that is essential or data in wrong format 0 ALERT level G = General alerts. Data that may be required is missing
A solution of (N3P3Cl5)spd(N3P3Cl4) (Labarre et al., 1984, Kılıç et al. 1991) (1 g, 1.367 mmol) in 10 ml dry THF was added dropwise to a stirred solution of triethylamine (1.38 g, 13.63 mmol) in 8 ml dry THF at 195 K. Then, 2,4-dimethylthiophenol (1.88 g, 13,6 mmol) in 10 ml dry THF was added and the reaction mixture was stirred under an atmosphere of argon at room temperature for 5 days. Triethylamine hydrochloride was filtered off and the solvent removed under reduced pressure at 303 K. One product,4,4,6,6-tetrachloro-2-[(2,4-dimethylphenyl)thio]-N-[4-(2,2,4,4-tetrachloro-1,3,5,7,11-pentaaza-2λ5,4λ5,6λ5-triphosphaspiro[5.5]undeca-1,3,5-trien-7-yl)butyl]-1,3,5,2λ5,4λ5,6λ5-triazatriphosphinin-2-amine, I, was detected by TLC using dichloromethane as mobile phase [Rf = 0.49] and was separated by column chromatography on silica gel using CHCl3 as eluant. Colourless rods of (I) were re-crystallized from dichloromethane-n-hexane (1:1 v/v) (m.p. 405–406 K, 0.74 g, yield 65%).
Elemental analysis calcd (%) for C15H25Cl8N9P6S;C, 21.63; H, 3.03; N, 15.13%; found: C, 21.36; H, 3.31; N, 15.22%; MS (M+H)+,833M+; 832.1H NMR at 298 K in CDCl3: δ 2.3 (s, 3H, CH3); δ 2.5 (s, 3H, CH3); δ 7.45 (q, 1H, CH-6); δ 7.07 (s, 1H, CH-3); δ 6.97 (d, 1H, CH-5); δ 3.3–2.8 p.p.m. (m, 8H)(4x N—CH2); δ 1.6–1.8 (m, 6H)(3x C—CH2); δ 3,0 (2H, 2x NH). The proton decoupled 31P NMR spectrum at 298 K in CDCl3 has two different spin A2X spin systems: >P(Nspiro) cyclophosphazene ring; (δP(Nspiro)(P1), 10.7 p.p.m. (triplet); δPCl2 (P2), 22.2 p.p.m. (doublet), 2J(P1P2) 40.3 Hz: >P(SC8H9) cyclophosphazene ring; δP(NHSC8H9)(P3), 30.7 p.p.m. (triplet); δPCl2 (P4), 20.3 p.p.m. (doublet), 2J(P3P4) 19.3 Hz.
The C-bound hydrogen atoms and H6N were fixed in idealized positions [0.88 (NH), 0.98 (CH3), 0.99 Å (CH2) & 0.95 Å (CH)] and refined using the riding model with Uiso(H) either set to 1.2Ueq(carrier) or 1.5Ueq(methyl C). Atom H4N was located in a difference map and freely refined. The C14 methylene group exhibits positional disorder within its ring system and has been modelled as two discrete sites with an occupancy ratio of 65:35. This disorder results in large anisotropic displacement parameters for this atom and those connected to it.
The reaction of biogenic spermidine with cyclophosphazene, N3P3Cl6, in aprotic solvents gives a spermidine-bridged cyclophosphazene compound, (N3P3Cl5)spd(N3P3Cl4), (spd = trifunctional spermidine residue), (Labarre et al., 1984; Guerch et al., 1984; Kılıç et al., 1991) and in protic solvents such as CHCl3 proceeds cleanly to yield a spiro-cis-ansa spermidine derivative, 2,2,6-trichloro-1,3,5,7,11,16-hexaaza-4,6-diphosphatricyclohexadeca-2,4,6-triene (Guerch & Labarre, 1989; Cameron et al.,1989). We have investigated previously the reactions of the spiro-cis-ansa compound with primary and secondary amines, mono- and difunctional alcohols (e.g. PhNH2, PrnNH2, HNC4H8, HNMe2, MeOH, and HOCH2(CF2)2CH2OH) (Beşli et al., 2004; İbişoğlu, 2007).
In this work reaction of the spermidine-bridged cyclophosphazene with 2,4-dimethylthiophenol gave a novel cyclophosphazene-thiolate derivative, (I), (Fig. 1), in which the bridgehead P—Cl bond was replaced with a thiolate group. Thus the SR reagent has attacked the PCl(NHR) group, rather than the more electrophilic PCl2 moiety, which is an attack not on the phosphorus centre, but on the hydrogen, giving the product via a proton abstraction/chloride elimination reaction.
In the cyclophosphazene rings of (I) the P—N bond lengths are in the range 1.554 (3)–1.632 (3) Å but separate into two distinct groups for each ring; the lengths of the four P—N bonds involving the >PCl2 moiety in both rings are in a narrow range [1.554 (3)–1.585 (3) Å] with averages of ca. 1.57(±0.01) Å compared to the two P—N bond lengths involving the >P(N)(X) moiety [X =SPh or NH(bridge)], which are in the range 1.610 (3)–1.632 (3)Å and average ca. 1.62(±0.01) Å. The increase in bond length involving the >P(N)(X) moiety depend on electron release from either the SPh or the NH(bridge) atoms to the phosphazene rings. The donation of electrons from the >P(N)(X) moiety to the phosphazene ring is also manifested by the decrease in endocyclic N—P(N)(X)—N bond angles for the two rings [X = SPh, 114.6 (2)°; X = NH(bridge), 110.7 (2)°] compared to those found for the N—P(Cl2)-N, 119.9(±0.3)°.
The effect of the electron-donating substituents is also reflected in differences in the P···P distances across the ring, even for rings that are nominally planar. It is found that the P···P distances involving the P(N)(X) moiety are 2.781 (6)/2.791 (6) Å (X = SPh) and 2.816 (5)/2.828 (6) Å (X = NH(bridge) are significantly greater than those involving the >PCl2 moiety, 2.71–2.72 Å.
An N—H···N hydrogen bond (Table 1) helps to establish the packing.
For background chemistry, see: Labarre et al. (1984); Beşli et al. (2004); Guerch et al. (1984); Kılıç et al. (1991); Cameron et al. (1989); İbişoğlu (2007); Guerch & Labarre (1989).
Data collection: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); cell refinement: DENZO and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: publCIF (Westrip, 2007).
Fig. 1. View of (I) (50% probability displacement ellipsoids; H atoms omitted for clarity). |
C15H25Cl8N9P6S | F(000) = 1680 |
Mr = 832.92 | Dx = 1.636 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 18434 reflections |
a = 8.5829 (17) Å | θ = 2.9–27.5° |
b = 15.587 (3) Å | µ = 1.04 mm−1 |
c = 25.277 (5) Å | T = 120 K |
V = 3381.6 (12) Å3 | Rod, colourless |
Z = 4 | 0.48 × 0.20 × 0.18 mm |
Nonius KappaCCD diffractometer | 6007 reflections with I > 2σ(I) |
φ and ω scans | Rint = 0.082 |
Absorption correction: multi-scan (SORTAV; Blessing, 1997) | θmax = 27.5°, θmin = 3.1° |
Tmin = 0.539, Tmax = 0.835 | h = −11→11 |
20485 measured reflections | k = −20→20 |
7560 independent reflections | l = −31→32 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.043 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.107 | w = 1/[σ2(Fo2) + (0.0538P)2] where P = (Fo2 + 2Fc2)/3 |
S = 0.99 | (Δ/σ)max = 0.010 |
7560 reflections | Δρmax = 0.36 e Å−3 |
366 parameters | Δρmin = −0.38 e Å−3 |
0 restraints | Absolute structure: Flack (1983), 3211 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.10 (7) |
C15H25Cl8N9P6S | V = 3381.6 (12) Å3 |
Mr = 832.92 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 8.5829 (17) Å | µ = 1.04 mm−1 |
b = 15.587 (3) Å | T = 120 K |
c = 25.277 (5) Å | 0.48 × 0.20 × 0.18 mm |
Nonius KappaCCD diffractometer | 7560 independent reflections |
Absorption correction: multi-scan (SORTAV; Blessing, 1997) | 6007 reflections with I > 2σ(I) |
Tmin = 0.539, Tmax = 0.835 | Rint = 0.082 |
20485 measured reflections |
R[F2 > 2σ(F2)] = 0.043 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.107 | Δρmax = 0.36 e Å−3 |
S = 0.99 | Δρmin = −0.38 e Å−3 |
7560 reflections | Absolute structure: Flack (1983), 3211 Friedel pairs |
366 parameters | Absolute structure parameter: 0.10 (7) |
0 restraints |
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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
C1 | 0.7799 (5) | 0.2378 (2) | 0.17416 (15) | 0.0340 (9) | |
C2 | 0.6726 (5) | 0.2176 (3) | 0.13485 (16) | 0.0385 (10) | |
C3 | 0.7270 (6) | 0.2077 (3) | 0.08372 (18) | 0.0504 (12) | |
H3 | 0.6553 | 0.1926 | 0.0566 | 0.061* | |
C4 | 0.8822 (7) | 0.2192 (3) | 0.0706 (2) | 0.0563 (14) | |
C5 | 0.9872 (6) | 0.2373 (3) | 0.1105 (2) | 0.0579 (14) | |
H5 | 1.0947 | 0.2436 | 0.1024 | 0.069* | |
C6 | 0.9363 (5) | 0.2464 (3) | 0.1628 (2) | 0.0468 (11) | |
H6 | 1.0088 | 0.2584 | 0.1903 | 0.056* | |
C7 | 0.5021 (6) | 0.2092 (3) | 0.1452 (2) | 0.0607 (14) | |
H7A | 0.4483 | 0.1949 | 0.1122 | 0.091* | |
H7B | 0.4618 | 0.2636 | 0.1590 | 0.091* | |
H7C | 0.4844 | 0.1637 | 0.1713 | 0.091* | |
C8 | 0.9353 (9) | 0.2165 (3) | 0.0138 (2) | 0.095 (3) | |
H8A | 1.0482 | 0.2254 | 0.0122 | 0.142* | |
H8B | 0.8826 | 0.2619 | −0.0063 | 0.142* | |
H8C | 0.9094 | 0.1606 | −0.0016 | 0.142* | |
C9 | 0.5008 (4) | 0.1678 (3) | 0.33785 (15) | 0.0372 (9) | |
H9A | 0.4487 | 0.1147 | 0.3502 | 0.045* | |
H9B | 0.4545 | 0.1838 | 0.3034 | 0.045* | |
C10 | 0.4714 (4) | 0.2383 (3) | 0.37703 (14) | 0.0333 (9) | |
H10A | 0.3609 | 0.2560 | 0.3744 | 0.040* | |
H10B | 0.5363 | 0.2884 | 0.3673 | 0.040* | |
C11 | 0.5061 (4) | 0.2141 (2) | 0.43411 (14) | 0.0271 (8) | |
H11A | 0.4547 | 0.1589 | 0.4425 | 0.032* | |
H11B | 0.6198 | 0.2063 | 0.4385 | 0.032* | |
C12 | 0.4492 (4) | 0.2824 (2) | 0.47241 (14) | 0.0270 (8) | |
H12A | 0.4948 | 0.3384 | 0.4623 | 0.032* | |
H12B | 0.3345 | 0.2874 | 0.4695 | 0.032* | |
C13 | 0.4204 (4) | 0.1851 (2) | 0.54963 (15) | 0.0310 (8) | |
H13A | 0.3142 | 0.1804 | 0.5346 | 0.037* | |
H13B | 0.4809 | 0.1358 | 0.5360 | 0.037* | |
C14' | 0.4070 (17) | 0.1747 (8) | 0.6071 (5) | 0.034 (4) | 0.341 (13) |
H14A | 0.3043 | 0.1973 | 0.6182 | 0.041* | 0.341 (13) |
H14B | 0.4080 | 0.1125 | 0.6151 | 0.041* | 0.341 (13) |
C14 | 0.5145 (9) | 0.1547 (4) | 0.5968 (2) | 0.033 (2) | 0.659 (13) |
H14C | 0.4664 | 0.1016 | 0.6108 | 0.039* | 0.659 (13) |
H14D | 0.6209 | 0.1400 | 0.5846 | 0.039* | 0.659 (13) |
C15 | 0.5264 (5) | 0.2159 (3) | 0.63906 (18) | 0.0445 (10) | |
H15A | 0.6221 | 0.1805 | 0.6376 | 0.053* | |
H15B | 0.4908 | 0.2169 | 0.6763 | 0.053* | |
N1 | 0.9248 (3) | 0.11118 (19) | 0.28052 (12) | 0.0283 (7) | |
N2 | 0.9007 (4) | −0.0284 (2) | 0.21604 (15) | 0.0443 (9) | |
N3 | 0.6461 (3) | 0.0696 (2) | 0.23679 (12) | 0.0312 (7) | |
N4 | 0.6684 (4) | 0.1507 (2) | 0.33068 (12) | 0.0295 (7) | |
N5 | 0.4910 (3) | 0.26331 (18) | 0.52811 (11) | 0.0277 (7) | |
N6 | 0.5661 (4) | 0.3034 (2) | 0.62336 (12) | 0.0308 (7) | |
H6N | 0.6196 | 0.3349 | 0.6458 | 0.037* | |
N7 | 0.6552 (3) | 0.40436 (18) | 0.54310 (13) | 0.0315 (7) | |
N8 | 0.4825 (4) | 0.54976 (18) | 0.53518 (15) | 0.0393 (8) | |
N9 | 0.3597 (3) | 0.40272 (18) | 0.57517 (13) | 0.0291 (7) | |
P1 | 0.74388 (10) | 0.13582 (6) | 0.27261 (4) | 0.0250 (2) | |
P2 | 1.00284 (12) | 0.03262 (6) | 0.25224 (4) | 0.0326 (2) | |
P3 | 0.72065 (12) | −0.01195 (6) | 0.21149 (4) | 0.0334 (2) | |
P4 | 0.51752 (10) | 0.34622 (5) | 0.56690 (4) | 0.0243 (2) | |
P5 | 0.64364 (10) | 0.50149 (6) | 0.52941 (4) | 0.0304 (2) | |
P6 | 0.33674 (10) | 0.49668 (6) | 0.55497 (4) | 0.0271 (2) | |
S1 | 0.72088 (12) | 0.25711 (6) | 0.24069 (4) | 0.0352 (2) | |
Cl1 | 1.11015 (15) | −0.03697 (8) | 0.30779 (5) | 0.0569 (3) | |
Cl2 | 1.18636 (13) | 0.07085 (8) | 0.20992 (6) | 0.0611 (3) | |
Cl3 | 0.61143 (17) | −0.11661 (8) | 0.23825 (5) | 0.0639 (4) | |
Cl4 | 0.66310 (15) | −0.01667 (7) | 0.13493 (4) | 0.0517 (3) | |
Cl5 | 0.80436 (11) | 0.56671 (7) | 0.56962 (5) | 0.0464 (3) | |
Cl6 | 0.71814 (13) | 0.52044 (7) | 0.45493 (4) | 0.0490 (3) | |
Cl7 | 0.17627 (11) | 0.49868 (6) | 0.49709 (4) | 0.0395 (2) | |
Cl8 | 0.22764 (12) | 0.56464 (6) | 0.61084 (4) | 0.0415 (2) | |
H4N | 0.722 (4) | 0.129 (2) | 0.3513 (16) | 0.020 (10)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.051 (2) | 0.0225 (19) | 0.028 (2) | 0.0072 (16) | 0.0079 (18) | 0.0050 (16) |
C2 | 0.055 (3) | 0.032 (2) | 0.029 (2) | 0.0059 (18) | 0.0015 (19) | 0.0086 (17) |
C3 | 0.090 (4) | 0.032 (2) | 0.029 (2) | 0.008 (2) | −0.001 (2) | 0.0071 (18) |
C4 | 0.103 (4) | 0.021 (2) | 0.045 (3) | −0.003 (2) | 0.029 (3) | 0.009 (2) |
C5 | 0.068 (3) | 0.034 (3) | 0.071 (4) | −0.005 (2) | 0.037 (3) | 0.005 (2) |
C6 | 0.053 (3) | 0.030 (2) | 0.057 (3) | −0.0063 (19) | 0.007 (2) | 0.003 (2) |
C7 | 0.054 (3) | 0.076 (4) | 0.051 (3) | 0.015 (3) | −0.010 (3) | 0.004 (3) |
C8 | 0.188 (7) | 0.038 (3) | 0.058 (4) | 0.003 (4) | 0.064 (5) | 0.004 (3) |
C9 | 0.027 (2) | 0.059 (3) | 0.026 (2) | −0.0028 (18) | 0.0038 (16) | −0.0086 (19) |
C10 | 0.032 (2) | 0.042 (2) | 0.025 (2) | 0.0060 (16) | 0.0009 (15) | −0.0065 (17) |
C11 | 0.0256 (17) | 0.0287 (19) | 0.027 (2) | −0.0005 (14) | 0.0036 (15) | 0.0010 (16) |
C12 | 0.0308 (18) | 0.029 (2) | 0.0209 (19) | 0.0035 (14) | −0.0021 (14) | 0.0002 (15) |
C13 | 0.036 (2) | 0.0249 (19) | 0.032 (2) | −0.0008 (15) | 0.0017 (16) | 0.0012 (16) |
C14' | 0.044 (10) | 0.034 (7) | 0.025 (6) | −0.002 (5) | 0.008 (5) | −0.003 (5) |
C14 | 0.039 (5) | 0.031 (3) | 0.028 (3) | 0.001 (3) | 0.008 (3) | 0.004 (3) |
C15 | 0.066 (3) | 0.034 (2) | 0.034 (2) | −0.006 (2) | −0.011 (2) | 0.0093 (19) |
N1 | 0.0297 (15) | 0.0263 (16) | 0.0288 (17) | 0.0001 (12) | −0.0021 (13) | −0.0043 (14) |
N2 | 0.050 (2) | 0.038 (2) | 0.045 (2) | 0.0053 (15) | −0.0034 (17) | −0.0168 (17) |
N3 | 0.0316 (15) | 0.0353 (18) | 0.0270 (17) | −0.0037 (13) | 0.0000 (13) | −0.0064 (14) |
N4 | 0.0309 (17) | 0.040 (2) | 0.0173 (17) | 0.0083 (14) | −0.0009 (13) | −0.0024 (14) |
N5 | 0.0423 (17) | 0.0206 (15) | 0.0203 (16) | 0.0012 (13) | 0.0018 (13) | 0.0011 (12) |
N6 | 0.0408 (18) | 0.0281 (17) | 0.0237 (17) | −0.0022 (13) | −0.0059 (14) | −0.0020 (13) |
N7 | 0.0306 (16) | 0.0215 (15) | 0.043 (2) | 0.0029 (12) | 0.0067 (14) | 0.0004 (14) |
N8 | 0.0343 (17) | 0.0204 (16) | 0.063 (2) | 0.0056 (13) | 0.0067 (16) | 0.0076 (16) |
N9 | 0.0302 (15) | 0.0226 (16) | 0.0347 (19) | 0.0032 (12) | 0.0022 (13) | 0.0042 (14) |
P1 | 0.0293 (5) | 0.0253 (5) | 0.0203 (5) | −0.0001 (3) | 0.0018 (3) | −0.0038 (4) |
P2 | 0.0363 (5) | 0.0306 (5) | 0.0308 (5) | 0.0054 (4) | 0.0038 (4) | −0.0049 (4) |
P3 | 0.0471 (6) | 0.0279 (5) | 0.0253 (5) | −0.0067 (4) | 0.0005 (4) | −0.0061 (4) |
P4 | 0.0282 (4) | 0.0207 (4) | 0.0238 (5) | 0.0015 (3) | 0.0015 (4) | −0.0011 (4) |
P5 | 0.0289 (5) | 0.0238 (5) | 0.0386 (6) | −0.0009 (4) | 0.0064 (4) | 0.0009 (4) |
P6 | 0.0277 (4) | 0.0225 (5) | 0.0310 (5) | 0.0028 (4) | 0.0011 (4) | −0.0005 (4) |
S1 | 0.0508 (5) | 0.0262 (5) | 0.0285 (5) | 0.0066 (4) | 0.0029 (4) | −0.0005 (4) |
Cl1 | 0.0682 (8) | 0.0498 (7) | 0.0527 (7) | 0.0245 (6) | −0.0079 (6) | 0.0022 (6) |
Cl2 | 0.0467 (6) | 0.0669 (8) | 0.0695 (9) | 0.0057 (6) | 0.0270 (6) | −0.0005 (7) |
Cl3 | 0.0988 (10) | 0.0427 (7) | 0.0501 (8) | −0.0335 (6) | 0.0029 (7) | −0.0012 (6) |
Cl4 | 0.0788 (8) | 0.0493 (7) | 0.0268 (5) | 0.0018 (6) | −0.0056 (5) | −0.0129 (5) |
Cl5 | 0.0415 (5) | 0.0398 (6) | 0.0578 (7) | −0.0148 (4) | 0.0028 (5) | −0.0044 (5) |
Cl6 | 0.0599 (6) | 0.0455 (6) | 0.0416 (6) | 0.0046 (5) | 0.0146 (5) | 0.0103 (5) |
Cl7 | 0.0442 (5) | 0.0385 (6) | 0.0358 (5) | 0.0040 (4) | −0.0094 (4) | 0.0021 (5) |
Cl8 | 0.0455 (6) | 0.0374 (5) | 0.0415 (6) | 0.0103 (4) | 0.0030 (4) | −0.0115 (5) |
C1—C2 | 1.391 (6) | C14'—C15 | 1.456 (13) |
C1—C6 | 1.379 (6) | C14'—H14A | 0.9900 |
C1—S1 | 1.782 (4) | C14'—H14B | 0.9900 |
C2—C3 | 1.383 (6) | C14—C15 | 1.436 (7) |
C2—C7 | 1.493 (7) | C14—H14C | 0.9900 |
C3—C4 | 1.385 (8) | C14—H14D | 0.9900 |
C3—H3 | 0.9500 | C15—N6 | 1.460 (5) |
C4—C5 | 1.381 (8) | C15—H15A | 0.9900 |
C4—C8 | 1.508 (7) | C15—H15B | 0.9900 |
C5—C6 | 1.401 (7) | N1—P2 | 1.568 (3) |
C5—H5 | 0.9500 | N1—P1 | 1.612 (3) |
C6—H6 | 0.9500 | N2—P3 | 1.571 (4) |
C7—H7A | 0.9800 | N2—P2 | 1.585 (4) |
C7—H7B | 0.9800 | N3—P3 | 1.561 (3) |
C7—H7C | 0.9800 | N3—P1 | 1.609 (3) |
C8—H8A | 0.9800 | N4—P1 | 1.621 (3) |
C8—H8B | 0.9800 | N4—H4N | 0.78 (4) |
C8—H8C | 0.9800 | N5—P4 | 1.638 (3) |
C9—N4 | 1.475 (5) | N6—P4 | 1.630 (3) |
C9—C10 | 1.501 (5) | N6—H6N | 0.8800 |
C9—H9A | 0.9900 | N7—P5 | 1.556 (3) |
C9—H9B | 0.9900 | N7—P4 | 1.606 (3) |
C10—C11 | 1.521 (5) | N8—P5 | 1.581 (3) |
C10—H10A | 0.9900 | N8—P6 | 1.581 (3) |
C10—H10B | 0.9900 | N9—P6 | 1.564 (3) |
C11—C12 | 1.520 (5) | N9—P4 | 1.629 (3) |
C11—H11A | 0.9900 | P1—S1 | 2.0651 (13) |
C11—H11B | 0.9900 | P2—Cl2 | 1.9950 (15) |
C12—N5 | 1.483 (4) | P2—Cl1 | 1.9991 (16) |
C12—H12A | 0.9900 | P3—Cl4 | 1.9986 (15) |
C12—H12B | 0.9900 | P3—Cl3 | 1.9995 (15) |
C13—N5 | 1.466 (5) | P5—Cl5 | 1.9924 (14) |
C13—C14' | 1.466 (12) | P5—Cl6 | 2.0100 (15) |
C13—C14 | 1.516 (7) | P6—Cl8 | 1.9984 (13) |
C13—H13A | 0.9900 | P6—Cl7 | 2.0097 (13) |
C13—H13B | 0.9900 | ||
C2—C1—C6 | 121.2 (4) | H14A—C14'—H14B | 107.3 |
C2—C1—S1 | 121.6 (3) | C15—C14—C13 | 114.6 (5) |
C6—C1—S1 | 117.1 (4) | C15—C14—H14C | 108.6 |
C3—C2—C1 | 118.1 (4) | C13—C14—H14C | 108.6 |
C3—C2—C7 | 119.0 (5) | C15—C14—H14D | 108.6 |
C1—C2—C7 | 122.9 (4) | C13—C14—H14D | 108.6 |
C2—C3—C4 | 122.3 (5) | H14C—C14—H14D | 107.6 |
C2—C3—H3 | 118.9 | C14—C15—N6 | 115.7 (4) |
C4—C3—H3 | 118.9 | C14—C15—C14' | 40.8 (5) |
C5—C4—C3 | 118.6 (5) | N6—C15—C14' | 115.2 (6) |
C5—C4—C8 | 120.3 (6) | C14—C15—H15A | 70.0 |
C3—C4—C8 | 121.0 (6) | N6—C15—H15A | 108.5 |
C4—C5—C6 | 120.5 (5) | C14'—C15—H15A | 108.5 |
C4—C5—H5 | 119.8 | C14—C15—H15B | 134.0 |
C6—C5—H5 | 119.8 | N6—C15—H15B | 108.5 |
C1—C6—C5 | 119.3 (5) | C14'—C15—H15B | 108.5 |
C1—C6—H6 | 120.3 | H15A—C15—H15B | 107.5 |
C5—C6—H6 | 120.3 | P2—N1—P1 | 122.7 (2) |
C2—C7—H7A | 109.5 | P3—N2—P2 | 119.2 (2) |
C2—C7—H7B | 109.5 | P3—N3—P1 | 122.6 (2) |
H7A—C7—H7B | 109.5 | C9—N4—P1 | 121.8 (3) |
C2—C7—H7C | 109.5 | C9—N4—H4N | 125 (3) |
H7A—C7—H7C | 109.5 | P1—N4—H4N | 108 (3) |
H7B—C7—H7C | 109.5 | C13—N5—C12 | 114.8 (3) |
C4—C8—H8A | 109.5 | C13—N5—P4 | 119.4 (2) |
C4—C8—H8B | 109.5 | C12—N5—P4 | 116.3 (2) |
H8A—C8—H8B | 109.5 | C15—N6—P4 | 124.2 (3) |
C4—C8—H8C | 109.5 | C15—N6—H6N | 117.9 |
H8A—C8—H8C | 109.5 | P4—N6—H6N | 117.9 |
H8B—C8—H8C | 109.5 | P5—N7—P4 | 125.84 (18) |
N4—C9—C10 | 112.1 (3) | P5—N8—P6 | 118.17 (19) |
N4—C9—H9A | 109.2 | P6—N9—P4 | 124.70 (19) |
C10—C9—H9A | 109.2 | N3—P1—N1 | 114.83 (16) |
N4—C9—H9B | 109.2 | N3—P1—N4 | 113.10 (17) |
C10—C9—H9B | 109.2 | N1—P1—N4 | 107.87 (18) |
H9A—C9—H9B | 107.9 | N3—P1—S1 | 108.49 (13) |
C9—C10—C11 | 114.3 (3) | N1—P1—S1 | 111.01 (12) |
C9—C10—H10A | 108.7 | N4—P1—S1 | 100.64 (13) |
C11—C10—H10A | 108.7 | N1—P2—N2 | 119.74 (18) |
C9—C10—H10B | 108.7 | N1—P2—Cl2 | 110.37 (13) |
C11—C10—H10B | 108.7 | N2—P2—Cl2 | 107.86 (16) |
H10A—C10—H10B | 107.6 | N1—P2—Cl1 | 107.48 (13) |
C12—C11—C10 | 111.6 (3) | N2—P2—Cl1 | 109.54 (15) |
C12—C11—H11A | 109.3 | Cl2—P2—Cl1 | 100.08 (7) |
C10—C11—H11A | 109.3 | N3—P3—N2 | 120.47 (18) |
C12—C11—H11B | 109.3 | N3—P3—Cl4 | 108.99 (13) |
C10—C11—H11B | 109.3 | N2—P3—Cl4 | 107.95 (15) |
H11A—C11—H11B | 108.0 | N3—P3—Cl3 | 109.50 (13) |
N5—C12—C11 | 112.7 (3) | N2—P3—Cl3 | 107.62 (16) |
N5—C12—H12A | 109.0 | Cl4—P3—Cl3 | 100.47 (7) |
C11—C12—H12A | 109.0 | N7—P4—N9 | 110.77 (15) |
N5—C12—H12B | 109.0 | N7—P4—N6 | 111.80 (17) |
C11—C12—H12B | 109.0 | N9—P4—N6 | 108.77 (17) |
H12A—C12—H12B | 107.8 | N7—P4—N5 | 108.85 (16) |
N5—C13—C14' | 119.5 (6) | N9—P4—N5 | 112.82 (16) |
N5—C13—C14 | 109.3 (4) | N6—P4—N5 | 103.67 (15) |
C14'—C13—C14 | 39.5 (5) | N7—P5—N8 | 119.88 (16) |
N5—C13—H13A | 107.4 | N7—P5—Cl5 | 109.82 (13) |
C14'—C13—H13A | 107.4 | N8—P5—Cl5 | 108.40 (14) |
C14—C13—H13A | 140.0 | N7—P5—Cl6 | 109.32 (13) |
N5—C13—H13B | 107.4 | N8—P5—Cl6 | 107.14 (15) |
C14'—C13—H13B | 107.4 | Cl5—P5—Cl6 | 100.52 (6) |
C14—C13—H13B | 76.0 | N9—P6—N8 | 119.59 (15) |
H13A—C13—H13B | 107.0 | N9—P6—Cl8 | 108.95 (13) |
C15—C14'—C13 | 116.5 (9) | N8—P6—Cl8 | 108.47 (14) |
C15—C14'—H14A | 108.2 | N9—P6—Cl7 | 109.80 (13) |
C13—C14'—H14A | 108.2 | N8—P6—Cl7 | 107.69 (15) |
C15—C14'—H14B | 108.2 | Cl8—P6—Cl7 | 100.67 (6) |
C13—C14'—H14B | 108.2 | C1—S1—P1 | 100.74 (12) |
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4N···N9i | 0.77 (4) | 2.26 (4) | 3.009 (4) | 164 (3) |
Symmetry code: (i) x+1/2, −y+1/2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C15H25Cl8N9P6S |
Mr | 832.92 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 120 |
a, b, c (Å) | 8.5829 (17), 15.587 (3), 25.277 (5) |
V (Å3) | 3381.6 (12) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 1.04 |
Crystal size (mm) | 0.48 × 0.20 × 0.18 |
Data collection | |
Diffractometer | Nonius KappaCCD |
Absorption correction | Multi-scan (SORTAV; Blessing, 1997) |
Tmin, Tmax | 0.539, 0.835 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 20485, 7560, 6007 |
Rint | 0.082 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.043, 0.107, 0.99 |
No. of reflections | 7560 |
No. of parameters | 366 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.36, −0.38 |
Absolute structure | Flack (1983), 3211 Friedel pairs |
Absolute structure parameter | 0.10 (7) |
Computer programs: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998), DENZO and COLLECT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003), publCIF (Westrip, 2007).
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4N···N9i | 0.77 (4) | 2.26 (4) | 3.009 (4) | 164 (3) |
Symmetry code: (i) x+1/2, −y+1/2, −z+1. |
The reaction of biogenic spermidine with cyclophosphazene, N3P3Cl6, in aprotic solvents gives a spermidine-bridged cyclophosphazene compound, (N3P3Cl5)spd(N3P3Cl4), (spd = trifunctional spermidine residue), (Labarre et al., 1984; Guerch et al., 1984; Kılıç et al., 1991) and in protic solvents such as CHCl3 proceeds cleanly to yield a spiro-cis-ansa spermidine derivative, 2,2,6-trichloro-1,3,5,7,11,16-hexaaza-4,6-diphosphatricyclohexadeca-2,4,6-triene (Guerch & Labarre, 1989; Cameron et al.,1989). We have investigated previously the reactions of the spiro-cis-ansa compound with primary and secondary amines, mono- and difunctional alcohols (e.g. PhNH2, PrnNH2, HNC4H8, HNMe2, MeOH, and HOCH2(CF2)2CH2OH) (Beşli et al., 2004; İbişoğlu, 2007).
In this work reaction of the spermidine-bridged cyclophosphazene with 2,4-dimethylthiophenol gave a novel cyclophosphazene-thiolate derivative, (I), (Fig. 1), in which the bridgehead P—Cl bond was replaced with a thiolate group. Thus the SR reagent has attacked the PCl(NHR) group, rather than the more electrophilic PCl2 moiety, which is an attack not on the phosphorus centre, but on the hydrogen, giving the product via a proton abstraction/chloride elimination reaction.
In the cyclophosphazene rings of (I) the P—N bond lengths are in the range 1.554 (3)–1.632 (3) Å but separate into two distinct groups for each ring; the lengths of the four P—N bonds involving the >PCl2 moiety in both rings are in a narrow range [1.554 (3)–1.585 (3) Å] with averages of ca. 1.57(±0.01) Å compared to the two P—N bond lengths involving the >P(N)(X) moiety [X =SPh or NH(bridge)], which are in the range 1.610 (3)–1.632 (3)Å and average ca. 1.62(±0.01) Å. The increase in bond length involving the >P(N)(X) moiety depend on electron release from either the SPh or the NH(bridge) atoms to the phosphazene rings. The donation of electrons from the >P(N)(X) moiety to the phosphazene ring is also manifested by the decrease in endocyclic N—P(N)(X)—N bond angles for the two rings [X = SPh, 114.6 (2)°; X = NH(bridge), 110.7 (2)°] compared to those found for the N—P(Cl2)-N, 119.9(±0.3)°.
The effect of the electron-donating substituents is also reflected in differences in the P···P distances across the ring, even for rings that are nominally planar. It is found that the P···P distances involving the P(N)(X) moiety are 2.781 (6)/2.791 (6) Å (X = SPh) and 2.816 (5)/2.828 (6) Å (X = NH(bridge) are significantly greater than those involving the >PCl2 moiety, 2.71–2.72 Å.
An N—H···N hydrogen bond (Table 1) helps to establish the packing.