Pyridinium 2-thio­xo-2,3-di­hydro-1H-naphtho­[2,3-d]-1,3,2λ⁵-di­aza­phospho­le-2-thiol­ate

The reaction of chloro­di­thio­phoshoric acid pyridinium betaine, PyPS₂Cl, with 2,3-di­amino­naphthalene yields the title compound, (PyH)(C₁₀H₈N₂)PS₂ or C₅H₆N⁺·C₁₀H₈N₂PS₂⁻. The P atom is coordinated by both N atoms of 2,3-di­amino­naphthalene with the formation of a five-membered ring.

Key indicators

• Single-crystal X-ray study
• T = 183 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.028
• wR factor = 0.079
• Data-to-parameter ratio = 13.5

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level C:



ABSTM_02  Alert C The ratio of expected to reported Tmax/Tmin(RR') is < 0.90
          Tmin and Tmax reported:      0.646     0.862
          Tmin' and Tmax expected:      0.833     0.956
          RR' =      0.861
          Please check that your absorption correction is appropriate.

General Notes



ABSTM_02  When printed, the submitted absorption T values will be replaced
          by the scaled T values. Since the ratio of scaled T's is
          identical to the ratio of reported T values, the scaling does
          not imply a change to the absorption corrections used in the
          study.
          Ratio of Tmax expected/reported      1.109
          Tmax scaled      0.956 Tmin scaled      0.717


 0 Alert Level A = Potentially serious problem

 0 Alert Level B = Potential problem

 1 Alert Level C = Please check

---

Computing details

Data collection: SMART (Bruker, 1999); cell refinement: SMART; data reduction: SAINT (Bruker, 1999); program(s) used to solve structure: SHELXTL (Bruker, 1997); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

2-thioxo-1,3-dihydro-1H-2λ⁵-naphtho[2,3-d][1,3,2] diaza-phosphole-2-thiolate

Crystal data

C5H6N^+·C10H8N2PS2^−	F(000) = 688
Mr = 331.38	Dx = 1.437 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71069 Å
a = 11.6700 (18) Å	Cell parameters from 7150 reflections
b = 11.930 (3) Å	θ = 2.4–27.0°
c = 11.108 (3) Å	µ = 0.45 mm^−1
β = 98.005 (18)°	T = 183 K
V = 1531.4 (5) Å^3	Plate, yellow
Z = 4	0.40 × 0.30 × 0.10 mm

Data collection

Bruker SMART three-circle diffractometer [OK?]	3331 independent reflections
Radiation source: fine-focus sealed tube	2764 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.025
ω scans	θmax = 27.0°, θmin = 1.8°
Absorption correction: multi-scan (North et al., 1968)	h = −14→14
Tmin = 0.646, Tmax = 0.862	k = −15→15
24788 measured reflections	l = −14→14

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.028	Hydrogen site location: difference Fourier map
wR(F^2) = 0.079	All H-atom parameters refined
S = 1.05	w = 1/[σ^2(Fo^2) + (0.05P)^2 + 0.2P] where P = (Fo^2 + 2Fc^2)/3
3331 reflections	(Δ/σ)max < 0.001
246 parameters	Δρmax = 0.29 e Å^−3
0 restraints	Δρmin = −0.28 e Å^−3

Special details

Experimental. There is only one resonance in the ³¹P NMR spectrum of the title compound (98.0 p.p.m., 85% H₃PO₄ was used as a standard). Characteristic vibrations were identified in the IR spectrum of the reaction product: NH-bond (3174 cm^-1), CH bonds (3102, 3076, 3058, 3026, 2729, 2672 cm^-1) and P═S bond (650–750 cm^-1). These values are in agreement with the proposed structure.

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 I>2σ(I)(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 (Ų)

	x	y	z	Uiso*/Ueq
P	−0.00648 (3)	0.34204 (3)	0.10643 (3)	0.02226 (10)
S1	−0.10702 (3)	0.44896 (3)	0.18207 (4)	0.02998 (11)
S2	−0.08603 (3)	0.25960 (3)	−0.03473 (4)	0.02970 (11)
N1	0.11751 (10)	0.40119 (11)	0.07569 (12)	0.0267 (3)
H1N	0.1185 (16)	0.4429 (16)	0.0169 (19)	0.043 (5)*
N2	0.06916 (11)	0.26046 (10)	0.21474 (12)	0.0251 (3)
H2N	0.0395 (16)	0.2376 (14)	0.2697 (18)	0.030 (5)*
C1	0.21753 (12)	0.35782 (11)	0.14134 (13)	0.0219 (3)
C2	0.32980 (13)	0.38618 (12)	0.13501 (13)	0.0249 (3)
H2	0.3483 (15)	0.4425 (14)	0.0790 (16)	0.032 (4)*
C3	0.42046 (12)	0.33272 (12)	0.21349 (13)	0.0248 (3)
C4	0.53880 (13)	0.35772 (13)	0.21026 (15)	0.0302 (3)
H4	0.5591 (14)	0.4120 (14)	0.1515 (15)	0.030 (4)*
C5	0.62486 (14)	0.30543 (15)	0.28703 (15)	0.0336 (4)
H5	0.6987 (16)	0.3233 (14)	0.2824 (16)	0.034 (5)*
C6	0.59696 (14)	0.22550 (14)	0.37127 (16)	0.0343 (4)
H6	0.6574 (16)	0.1896 (14)	0.4230 (17)	0.036 (5)*
C7	0.48318 (13)	0.19927 (14)	0.37653 (15)	0.0309 (3)
H7	0.4632 (16)	0.1438 (15)	0.4319 (17)	0.038 (5)*
C8	0.39203 (13)	0.25143 (12)	0.29864 (13)	0.0250 (3)
C9	0.27364 (13)	0.22423 (12)	0.30422 (14)	0.0243 (3)
H9	0.2548 (13)	0.1716 (13)	0.3613 (15)	0.024 (4)*
C10	0.18925 (12)	0.27584 (11)	0.22662 (13)	0.0223 (3)
N3	0.12713 (16)	0.51061 (15)	0.35748 (18)	0.0513 (5)
H3N	0.068 (2)	0.510 (2)	0.312 (2)	0.072 (8)*
C11	0.1432 (2)	0.45051 (17)	0.4613 (3)	0.0606 (7)
H11	0.087 (2)	0.413 (2)	0.479 (3)	0.095 (9)*
C12	0.2477 (2)	0.45281 (17)	0.5322 (2)	0.0552 (6)
H12	0.268 (2)	0.415 (2)	0.604 (3)	0.085 (8)*
C13	0.33487 (18)	0.51536 (16)	0.49544 (17)	0.0448 (4)
H13	0.4124 (19)	0.5174 (17)	0.545 (2)	0.059 (6)*
C14	0.31582 (18)	0.57502 (16)	0.39022 (18)	0.0438 (4)
H14	0.3749 (19)	0.6195 (19)	0.361 (2)	0.064 (6)*
C15	0.21102 (19)	0.57213 (16)	0.32180 (18)	0.0463 (5)
H15	0.1928 (19)	0.6162 (19)	0.247 (2)	0.065 (6)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
P	0.02083 (19)	0.02580 (19)	0.02035 (19)	0.00149 (14)	0.00353 (14)	0.00430 (14)
S1	0.0315 (2)	0.0328 (2)	0.0274 (2)	0.00757 (16)	0.01034 (16)	0.00468 (15)
S2	0.0275 (2)	0.0357 (2)	0.0247 (2)	−0.00089 (15)	−0.00071 (15)	0.00002 (15)
N1	0.0230 (6)	0.0313 (7)	0.0262 (7)	0.0000 (5)	0.0042 (5)	0.0113 (5)
N2	0.0205 (6)	0.0318 (7)	0.0231 (7)	−0.0012 (5)	0.0037 (5)	0.0098 (5)
C1	0.0243 (7)	0.0233 (7)	0.0184 (7)	−0.0002 (5)	0.0037 (5)	−0.0006 (5)
C2	0.0276 (7)	0.0258 (7)	0.0221 (7)	−0.0023 (6)	0.0063 (6)	0.0011 (6)
C3	0.0241 (7)	0.0291 (7)	0.0214 (7)	−0.0024 (6)	0.0042 (6)	−0.0060 (6)
C4	0.0272 (8)	0.0360 (8)	0.0280 (8)	−0.0058 (6)	0.0061 (6)	−0.0039 (7)
C5	0.0215 (8)	0.0447 (9)	0.0345 (9)	−0.0044 (7)	0.0036 (6)	−0.0074 (7)
C6	0.0236 (8)	0.0441 (9)	0.0331 (9)	0.0035 (7)	−0.0033 (7)	−0.0031 (7)
C7	0.0273 (8)	0.0383 (8)	0.0262 (8)	0.0007 (7)	0.0011 (6)	0.0020 (7)
C8	0.0244 (7)	0.0295 (7)	0.0208 (7)	−0.0001 (6)	0.0017 (6)	−0.0034 (6)
C9	0.0253 (7)	0.0272 (7)	0.0205 (7)	−0.0003 (6)	0.0035 (6)	0.0033 (6)
C10	0.0221 (7)	0.0247 (7)	0.0204 (7)	−0.0021 (5)	0.0042 (6)	−0.0018 (5)
N3	0.0425 (10)	0.0530 (10)	0.0556 (11)	0.0052 (8)	−0.0034 (9)	−0.0315 (9)
C11	0.0657 (15)	0.0400 (11)	0.0846 (19)	−0.0197 (10)	0.0407 (14)	−0.0206 (11)
C12	0.0828 (17)	0.0448 (11)	0.0409 (11)	0.0025 (11)	0.0185 (11)	0.0081 (9)
C13	0.0497 (11)	0.0484 (10)	0.0353 (10)	0.0055 (9)	0.0021 (9)	−0.0064 (8)
C14	0.0494 (11)	0.0440 (10)	0.0400 (11)	−0.0038 (9)	0.0135 (9)	0.0002 (8)
C15	0.0609 (13)	0.0458 (10)	0.0318 (10)	0.0108 (9)	0.0056 (9)	−0.0026 (8)

Geometric parameters (Å, º)

P—N1	1.6870 (13)	C6—H6	0.947 (18)
P—N2	1.6966 (13)	C7—C8	1.418 (2)
P—S2	1.9703 (6)	C7—H7	0.954 (19)
P—S1	1.9960 (6)	C8—C9	1.429 (2)
N1—C1	1.3874 (19)	C9—C10	1.362 (2)
N1—H1N	0.82 (2)	C9—H9	0.940 (16)
N2—C10	1.4012 (18)	N3—C15	1.327 (3)
N2—H2N	0.79 (2)	N3—C11	1.348 (3)
C1—C2	1.364 (2)	N3—H3N	0.80 (3)
C1—C10	1.4317 (19)	C11—C12	1.357 (4)
C2—C3	1.424 (2)	C11—H11	0.84 (3)
C2—H2	0.960 (17)	C12—C13	1.369 (3)
C3—C4	1.418 (2)	C12—H12	0.92 (3)
C3—C8	1.426 (2)	C13—C14	1.360 (3)
C4—C5	1.373 (2)	C13—H13	0.99 (2)
C4—H4	0.972 (17)	C14—C15	1.347 (3)
C5—C6	1.406 (2)	C14—H14	0.96 (2)
C5—H5	0.896 (18)	C15—H15	0.98 (2)
C6—C7	1.373 (2)
N1—P—N2	90.41 (6)	C6—C7—C8	121.44 (16)
N1—P—S2	111.72 (5)	C6—C7—H7	120.7 (11)
N2—P—S2	114.77 (5)	C8—C7—H7	117.9 (11)
N1—P—S1	112.89 (5)	C7—C8—C3	118.63 (14)
N2—P—S1	110.27 (5)	C7—C8—C9	121.43 (14)
S2—P—S1	114.49 (3)	C3—C8—C9	119.93 (13)
C1—N1—P	114.85 (10)	C10—C9—C8	119.22 (14)
C1—N1—H1N	122.6 (14)	C10—C9—H9	120.8 (10)
P—N1—H1N	121.4 (14)	C8—C9—H9	120.0 (10)
C10—N2—P	113.98 (10)	C9—C10—N2	128.75 (14)
C10—N2—H2N	120.8 (13)	C9—C10—C1	120.96 (13)
P—N2—H2N	120.3 (13)	N2—C10—C1	110.29 (12)
C2—C1—N1	128.61 (13)	C15—N3—C11	121.93 (19)
C2—C1—C10	121.00 (13)	C15—N3—H3N	115.1 (19)
N1—C1—C10	110.36 (12)	C11—N3—H3N	122.9 (19)
C1—C2—C3	119.61 (14)	N3—C11—C12	119.5 (2)
C1—C2—H2	120.7 (10)	N3—C11—H11	118 (2)
C3—C2—H2	119.6 (10)	C12—C11—H11	123 (2)
C4—C3—C2	122.23 (14)	C11—C12—C13	118.9 (2)
C4—C3—C8	118.50 (14)	C11—C12—H12	126.3 (16)
C2—C3—C8	119.27 (13)	C13—C12—H12	114.8 (16)
C5—C4—C3	121.28 (15)	C14—C13—C12	120.1 (2)
C5—C4—H4	119.6 (10)	C14—C13—H13	119.5 (13)
C3—C4—H4	119.1 (10)	C12—C13—H13	120.3 (13)
C4—C5—C6	120.28 (15)	C15—C14—C13	119.88 (19)
C4—C5—H5	118.8 (11)	C15—C14—H14	117.3 (13)
C6—C5—H5	120.9 (11)	C13—C14—H14	122.8 (13)
C7—C6—C5	119.86 (15)	N3—C15—C14	119.66 (19)
C7—C6—H6	120.9 (11)	N3—C15—H15	117.8 (13)
C5—C6—H6	119.2 (11)	C14—C15—H15	122.5 (13)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···S1^i	0.82 (2)	2.55 (2)	3.3632 (15)	172.3 (18)
N3—H3N···S1	0.80 (3)	2.44 (3)	3.2127 (19)	163 (2)

Symmetry code: (i) −x, −y+1, −z.