5-Benzyl-1,3,5-trimethyl­pyrimidine-2,4,6(1H,3H,5H)-trithione

Takechi, H.; Kubo, K.; Takahashi, H.; Matsumoto, T.

doi:10.1107/S1600536807000888

5-Benzyl-1,3,5-trimethylpyrimidine-2,4,6(1H,3H,5H)-trithione

H. Takechi, K. Kubo, H. Takahashi and T. Matsumoto

The rings in the title compound, C₁₄H₁₆N₂S₃, adopt a syn conformation with respect to each other. The pyrimidinetrithione ring system exhibits conjugation involving the lone pairs on the N atoms and the three C=S bonds. Intermolecular C—H

S interactions and S

S contacts help stabilize the crystal packing.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807000888/fl2091sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536807000888/fl2091Isup2.hkl Contains datablock I

CCDC reference: 636632

checkCIF report

Key indicators

Single-crystal X-ray study
T = 123 K
Mean (C-C) = 0.002 Å
R factor = 0.028
wR factor = 0.089
Data-to-parameter ratio = 17.1

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......       0.96
PLAT128_ALERT_4_C Non-standard setting of Space group P21/c   ....    P21/a
PLAT230_ALERT_2_C Hirshfeld Test Diff for    S1     -   C1      ..       5.68 su
PLAT230_ALERT_2_C Hirshfeld Test Diff for    S3     -   C4      ..       5.76 su
PLAT480_ALERT_4_C Long H...A H-Bond Reported H6     ..  S3      ..       2.95 Ang.

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   5 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Computing details top

Data collection: CrystalClear (Rigaku, 1999); cell refinement: CrystalClear; data reduction: CrystalStructure (Rigaku/MSC, 2004); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: ORTEPIII (Burnett & Johnson, 1996) and Mercury (Version 1.3; Bruno et al., 2002); software used to prepare material for publication: CrystalStructure.

5-Benzyl-1,3,5-trimethylpyrimidine-2,4,6(1H,3H,5H)-trithione top

Crystal data top

C₁₄H₁₆N₂S₃	F(000) = 648.00
M_r = 308.47	D_x = 1.407 Mg m⁻³
Monoclinic, P2₁/a	Mo Kα radiation, λ = 0.71070 Å
Hall symbol: -P 2yab	Cell parameters from 4844 reflections
a = 13.112 (13) Å	θ = 3.1–27.5°
b = 8.350 (8) Å	µ = 0.50 mm⁻¹
c = 13.299 (13) Å	T = 123 K
β = 90.721 (7)°	Prism, red
V = 1456 (2) Å³	0.15 × 0.13 × 0.10 mm
Z = 4

Data collection top

Rigaku Saturn diffractometer	2731 reflections with F² > 2σ(F²)
Detector resolution: 7.31 pixels mm^-1	R_int = 0.035
ω scans	θ_max = 27.5°
Absorption correction: multi-scan (REQAB; Jacobson, 1998)	h = −16→16
T_min = 0.891, T_max = 0.952	k = −10→10
16694 measured reflections	l = −17→17
3216 independent reflections

Refinement top

Refinement on F²	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.028	w = 1/[0.0007F_o² + σ(F_o²)]/(4F_o²)
wR(F²) = 0.089	(Δ/σ)_max < 0.001
S = 1.06	Δρ_max = 0.40 e Å⁻³
3216 reflections	Δρ_min = −0.26 e Å⁻³
188 parameters

Special details top

Refinement. Refinement using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F². R-factor (gt) are based on F. The threshold expression of F² > 2.0 σ(F²) is used only for calculating R-factor (gt).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
S1	0.82751 (3)	1.01126 (4)	0.65760 (3)	0.02382 (10)
S2	0.90921 (3)	0.40050 (4)	0.60068 (3)	0.02236 (9)
S3	0.86167 (3)	0.64021 (5)	0.97563 (3)	0.02373 (10)
N1	0.85395 (8)	0.69707 (12)	0.64327 (8)	0.0138 (2)
N2	0.83463 (8)	0.80174 (12)	0.80762 (8)	0.0135 (2)
C1	0.83975 (10)	0.82990 (14)	0.70448 (10)	0.0136 (2)
C2	0.88931 (10)	0.55146 (14)	0.67729 (10)	0.0136 (2)
C3	0.91913 (10)	0.53998 (13)	0.78758 (10)	0.0130 (2)
C4	0.86716 (10)	0.66382 (14)	0.85298 (10)	0.0136 (2)
C5	0.83785 (12)	0.72041 (17)	0.53439 (10)	0.0225 (3)
C6	0.90158 (11)	0.36960 (16)	0.82784 (11)	0.0203 (3)
C7	0.79995 (12)	0.93419 (17)	0.87206 (11)	0.0229 (3)
C8	1.03780 (10)	0.57440 (16)	0.79624 (10)	0.0163 (3)
C9	1.07103 (9)	0.74045 (14)	0.76671 (10)	0.0147 (2)
C10	1.08275 (11)	0.86021 (17)	0.83933 (11)	0.0199 (3)
C11	1.10942 (11)	1.01518 (18)	0.81213 (12)	0.0248 (3)
C12	1.12483 (11)	1.05194 (18)	0.71204 (12)	0.0257 (3)
C13	1.11508 (11)	0.93387 (17)	0.63937 (12)	0.0240 (3)
C14	1.08883 (10)	0.77862 (16)	0.66676 (10)	0.0181 (3)
H1	0.8576	0.9934	0.8950	0.028*
H2	0.9167	0.3676	0.8979	0.025*
H3	0.7558	1.0025	0.8345	0.028*
H4	1.0583	0.5568	0.8641	0.020*
H5	1.0720	0.5008	0.7539	0.020*
H6	0.7646	0.8923	0.9281	0.028*
H7	0.8324	0.3402	0.8168	0.025*
H8	0.9447	0.2962	0.7941	0.025*
H9	1.1424	1.1581	0.6933	0.031*
H10	1.1167	1.0958	0.8621	0.030*
H11	1.0832	0.6977	0.6168	0.022*
H12	1.1262	0.9591	0.5707	0.029*
H13	1.0728	0.8353	0.9082	0.024*
H14	0.8988	0.7599	0.5055	0.027*
H15	0.7843	0.7954	0.5236	0.027*
H16	0.8200	0.6212	0.5039	0.028*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0383 (2)	0.01246 (18)	0.0207 (2)	0.00181 (13)	−0.00168 (16)	0.00411 (12)
S2	0.0322 (2)	0.01634 (18)	0.01851 (19)	0.00224 (13)	0.00108 (14)	−0.00522 (12)
S3	0.0330 (2)	0.0274 (2)	0.01088 (18)	0.00208 (14)	0.00303 (13)	0.00423 (12)
N1	0.0178 (5)	0.0133 (5)	0.0101 (5)	−0.0008 (4)	−0.0021 (4)	0.0012 (3)
N2	0.0148 (5)	0.0136 (5)	0.0120 (5)	0.0010 (4)	0.0011 (4)	−0.0011 (4)
C1	0.0120 (5)	0.0149 (5)	0.0137 (6)	−0.0006 (4)	−0.0018 (4)	0.0010 (4)
C2	0.0126 (5)	0.0135 (5)	0.0148 (6)	−0.0021 (4)	0.0014 (4)	0.0001 (4)
C3	0.0146 (6)	0.0112 (5)	0.0133 (5)	−0.0001 (4)	0.0003 (4)	0.0017 (4)
C4	0.0121 (5)	0.0150 (5)	0.0137 (6)	−0.0033 (4)	−0.0005 (4)	0.0017 (4)
C5	0.0344 (8)	0.0222 (7)	0.0109 (6)	0.0026 (5)	−0.0042 (5)	0.0010 (5)
C6	0.0259 (7)	0.0142 (6)	0.0209 (7)	−0.0016 (5)	−0.0005 (5)	0.0051 (5)
C7	0.0296 (7)	0.0201 (6)	0.0192 (7)	0.0064 (5)	0.0021 (5)	−0.0054 (5)
C8	0.0148 (6)	0.0178 (6)	0.0161 (6)	0.0027 (4)	−0.0015 (5)	0.0022 (5)
C9	0.0090 (5)	0.0180 (6)	0.0169 (6)	0.0012 (4)	−0.0016 (4)	0.0006 (5)
C10	0.0171 (6)	0.0255 (7)	0.0170 (6)	−0.0017 (5)	−0.0003 (5)	−0.0024 (5)
C11	0.0213 (7)	0.0213 (7)	0.0319 (8)	−0.0032 (5)	0.0009 (6)	−0.0078 (5)
C12	0.0220 (7)	0.0194 (6)	0.0358 (8)	−0.0034 (5)	0.0028 (6)	0.0044 (6)
C13	0.0212 (7)	0.0285 (7)	0.0225 (7)	−0.0029 (6)	0.0043 (5)	0.0077 (5)
C14	0.0148 (6)	0.0209 (6)	0.0187 (6)	−0.0010 (5)	0.0014 (5)	−0.0013 (5)

Geometric parameters (Å, º) top

S1—C1	1.6447 (13)	C12—C13	1.385 (2)
S2—C2	1.6436 (13)	C13—C14	1.3909 (19)
S3—C4	1.6455 (13)	C5—H14	0.950
N1—C1	1.3897 (16)	C5—H15	0.950
N1—C2	1.3757 (16)	C5—H16	0.950
N1—C5	1.4736 (17)	C6—H2	0.950
N2—C1	1.3941 (17)	C6—H7	0.950
N2—C4	1.3658 (16)	C6—H8	0.950
N2—C7	1.4745 (17)	C7—H1	0.950
C2—C3	1.5162 (18)	C7—H3	0.950
C3—C4	1.5182 (18)	C7—H6	0.950
C3—C6	1.5383 (18)	C8—H4	0.950
C3—C8	1.5851 (18)	C8—H5	0.950
C8—C9	1.5068 (18)	C10—H13	0.950
C9—C10	1.3973 (19)	C11—H10	0.950
C9—C14	1.3895 (18)	C12—H9	0.950
C10—C11	1.389 (2)	C13—H12	0.950
C11—C12	1.383 (2)	C14—H11	0.950

S1···S2ⁱ	3.508 (4)	H4···H3^vi	2.670
S2···S1ⁱⁱ	3.508 (4)	H4···H6^vi	2.857
S3···C7ⁱⁱⁱ	3.415 (4)	H5···C7^vi	3.403
N1···C13^iv	3.317 (4)	H5···H3^vi	2.626
N1···C14^iv	3.500 (4)	H5···H6^vi	3.521
N2···C9^iv	3.510 (4)	H5···H9ⁱⁱ	3.116
N2···C10^iv	3.599 (4)	H6···S3^v	2.952
C1···C14^iv	3.443 (4)	H6···C8^iv	3.444
C5···C13^iv	3.499 (2)	H6···C9^iv	3.484
C7···S3^v	3.415 (4)	H6···C10^iv	3.384
C7···C8^iv	3.571 (2)	H6···H2^v	3.344
C8···C7^vi	3.571 (2)	H6···H4^iv	2.857
C9···N2^vi	3.510 (4)	H6···H5^iv	3.521
C10···N2^vi	3.599 (4)	H6···H10^xii	3.179
C13···N1^vi	3.317 (4)	H6···H13^iv	3.160
C13···C5^vi	3.499 (2)	H7···S1ⁱⁱ	3.468
C14···N1^vi	3.500 (4)	H7···C7ⁱⁱ	3.495
C14···C1^vi	3.443 (4)	H7···C11^iv	3.163
S1···H7ⁱ	3.468	H7···C12^iv	3.172
S1···H8ⁱ	3.353	H7···H1ⁱⁱ	3.093
S1···H12^vii	3.114	H7···H3ⁱⁱ	3.003
S1···H16^viii	3.016	H7···H9^iv	2.966
S2···H11^ix	3.009	H7···H10^iv	2.947
S2···H14^ix	3.196	H8···S1ⁱⁱ	3.353
S2···H15^x	3.136	H8···C11ⁱⁱ	3.196
S3···H1ⁱⁱⁱ	3.585	H8···C12ⁱⁱ	3.316
S3···H2^xi	3.340	H8···H1ⁱⁱ	3.088
S3···H3ⁱⁱⁱ	3.189	H8···H3ⁱⁱ	3.530
S3···H4^xi	2.880	H8···H9ⁱⁱ	3.153
S3···H6ⁱⁱⁱ	2.952	H8···H10ⁱⁱ	2.942
S3···H10^xii	3.095	H9···C5^vii	3.207
N1···H12^iv	3.387	H9···H5ⁱ	3.116
C1···H11^iv	3.554	H9···H7^vi	2.966
C5···H9^vii	3.207	H9···H8ⁱ	3.153
C5···H(11)^iv	3.593	H9···H14^vii	2.777
C5···H12^vii	3.058	H9···H15^vii	3.076
C5···H12^iv	3.196	H9···H16^vii	3.248
C6···H1ⁱⁱ	3.319	H10···S3^xii	3.095
C7···H4^iv	3.169	H10···H1^xii	3.327
C7···H5^iv	3.403	H10···H2ⁱ	3.506
C7···H7ⁱ	3.495	H10···H6^xii	3.179
C8···H3^vi	2.968	H10···H7^vi	2.947
C8···H6^vi	3.444	H10···H8ⁱ	2.942
C9···H3^vi	3.278	H11···S2^ix	3.009
C9···H6^vi	3.484	H11···C1^vi	3.554
C10···H6^vi	3.384	H11···C5^vi	3.593
C11···H7^vi	3.163	H11···H15^vi	2.928
C11···H8ⁱ	3.196	H11···H16^ix	3.365
C12···H7^vi	3.172	H12···S1^vii	3.114
C12···H8ⁱ	3.316	H12···N1^vi	3.387
C12···H14^vii	3.303	H12···C5^vii	3.058
C12···H15^vii	3.600	H12···C5^vi	3.196
C13···H14^vii	3.205	H12···H14^vii	2.575
C13···H15^vii	3.409	H12···H15^vii	2.681
C13···H15^vi	3.324	H12···H15^vi	3.039
C13···H16^vi	3.287	H12···H16^vi	2.785
C14···H15^vi	3.271	H13···H1^xii	3.109
H1···S3^v	3.585	H13···H2^xi	3.087
H1···C6ⁱ	3.319	H13···H6^vi	3.160
H1···H2ⁱ	3.220	H14···S2^ix	3.196
H1···H7ⁱ	3.093	H14···C12^vii	3.303
H1···H8ⁱ	3.088	H14···C13^vii	3.205
H1···H10^xii	3.327	H14···H9^vii	2.777
H1···H13^xii	3.109	H14···H12^vii	2.575
H2···S3^xi	3.340	H15···S2^viii	3.136
H2···H1ⁱⁱ	3.220	H15···C12^vii	3.600
H2···H4^xi	3.240	H15···C13^vii	3.409
H2···H6ⁱⁱⁱ	3.344	H15···C13^iv	3.324
H2···H10ⁱⁱ	3.506	H15···C14^iv	3.271
H2···H13^xi	3.087	H15···H9^vii	3.076
H3···S3^v	3.189	H15···H11^iv	2.928
H3···C8^iv	2.968	H15···H12^vii	2.681
H3···C9^iv	3.278	H15···H12^iv	3.039
H3···H4^iv	2.670	H15···H16^viii	3.065
H3···H5^iv	2.626	H16···S1^x	3.016
H3···H7ⁱ	3.003	H16···C13^iv	3.287
H3···H8ⁱ	3.530	H16···H9^vii	3.248
H4···S3^xi	2.880	H16···H11^ix	3.365
H4···C7^vi	3.169	H16···H12^iv	2.785
H4···H2^xi	3.240	H16···H15^x	3.065

C1—N1—C2	124.04 (10)	N1—C5—H16	109.6
C1—N1—C5	116.84 (10)	H14—C5—H15	109.5
C2—N1—C5	118.92 (10)	H14—C5—H16	109.5
C1—N2—C4	123.93 (10)	H15—C5—H16	109.5
C1—N2—C7	117.67 (10)	C3—C6—H2	109.1
C4—N2—C7	118.20 (10)	C3—C6—H7	109.4
S1—C1—N1	121.73 (9)	C3—C6—H8	109.9
S1—C1—N2	121.51 (9)	H2—C6—H7	109.5
N1—C1—N2	116.76 (10)	H2—C6—H8	109.5
S2—C2—N1	121.96 (9)	H7—C6—H8	109.5
S2—C2—C3	120.67 (9)	N2—C7—H1	109.1
N1—C2—C3	117.11 (10)	N2—C7—H3	109.6
C2—C3—C4	113.52 (10)	N2—C7—H6	109.7
C2—C3—C6	110.93 (10)	H1—C7—H3	109.5
C2—C3—C8	107.44 (10)	H1—C7—H6	109.5
C4—C3—C6	111.12 (10)	H3—C7—H6	109.5
C4—C3—C8	106.39 (10)	C3—C8—H4	107.9
C6—C3—C8	107.06 (10)	C3—C8—H5	108.0
S3—C4—N2	121.43 (9)	C9—C8—H4	108.1
S3—C4—C3	120.79 (9)	C9—C8—H5	107.5
N2—C4—C3	117.46 (11)	H4—C8—H5	109.5
C3—C8—C9	115.77 (10)	C9—C10—H13	119.6
C8—C9—C10	120.53 (11)	C11—C10—H13	119.5
C8—C9—C14	120.86 (11)	C10—C11—H10	120.1
C10—C9—C14	118.60 (12)	C12—C11—H10	120.1
C9—C10—C11	120.82 (13)	C11—C12—H9	119.9
C10—C11—C12	119.83 (14)	C13—C12—H9	120.1
C11—C12—C13	120.01 (14)	C12—C13—H12	119.9
C12—C13—C14	120.10 (14)	C14—C13—H12	120.0
C9—C14—C13	120.62 (12)	C9—C14—H11	119.6
N1—C5—H14	109.4	C13—C14—H11	119.8
N1—C5—H15	109.4

C1—N1—C2—S2	−177.39 (10)	N1—C2—C3—C8	−93.61 (12)
C1—N1—C2—C3	−3.13 (18)	C2—C3—C4—S3	161.80 (9)
C2—N1—C1—S1	163.24 (10)	C2—C3—C4—N2	−24.59 (16)
C2—N1—C1—N2	−17.82 (17)	C2—C3—C8—C9	64.59 (13)
C5—N1—C1—S1	−11.48 (16)	C6—C3—C4—S3	35.94 (14)
C5—N1—C1—N2	167.47 (11)	C6—C3—C4—N2	−150.44 (11)
C5—N1—C2—S2	−2.78 (16)	C4—C3—C8—C9	−57.31 (14)
C5—N1—C2—C3	171.48 (11)	C8—C3—C4—S3	−80.25 (12)
C1—N2—C4—S3	178.38 (9)	C8—C3—C4—N2	93.36 (13)
C1—N2—C4—C3	4.81 (17)	C6—C3—C8—C9	−176.19 (11)
C4—N2—C1—S1	−164.13 (10)	C3—C8—C9—C10	94.32 (14)
C4—N2—C1—N1	16.92 (17)	C3—C8—C9—C14	−84.48 (14)
C7—N2—C1—S1	10.58 (16)	C8—C9—C10—C11	−177.42 (12)
C7—N2—C1—N1	−168.37 (11)	C8—C9—C14—C13	177.12 (12)
C7—N2—C4—S3	3.69 (16)	C10—C9—C14—C13	−1.71 (19)
C7—N2—C4—C3	−169.88 (11)	C14—C9—C10—C11	1.42 (19)
S2—C2—C3—C4	−161.93 (9)	C9—C10—C11—C12	−0.12 (19)
S2—C2—C3—C6	−35.98 (15)	C10—C11—C12—C13	−0.9 (2)
S2—C2—C3—C8	80.73 (12)	C11—C12—C13—C14	0.6 (2)
N1—C2—C3—C4	23.73 (16)	C12—C13—C14—C9	0.7 (2)
N1—C2—C3—C6	149.68 (11)

Symmetry codes: (i) x, y+1, z; (ii) x, y−1, z; (iii) −x+3/2, y−1/2, −z+2; (iv) x−1/2, −y+3/2, z; (v) −x+3/2, y+1/2, −z+2; (vi) x+1/2, −y+3/2, z; (vii) −x+2, −y+2, −z+1; (viii) −x+3/2, y+1/2, −z+1; (ix) −x+2, −y+1, −z+1; (x) −x+3/2, y−1/2, −z+1; (xi) −x+2, −y+1, −z+2; (xii) −x+2, −y+2, −z+2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C7—H6···S3^v	0.95	2.95	3.415 (2)	111
C8—H4···S3^xi	0.95	2.88	3.749 (4)	153

Symmetry codes: (v) −x+3/2, y+1/2, −z+2; (xi) −x+2, −y+1, −z+2.

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5-Benzyl-1,3,5-trimethyl­pyrimidine-2,4,6(1H,3H,5H)-trithione

Supporting information

Key indicators

checkCIF/PLATON results

5-Benzyl-1,3,5-trimethylpyrimidine-2,4,6(1H,3H,5H)-trithione