A tripodal tris­(thio­phene) derivative of hexa­hydro­pyrimidine and its ladder-like extended structure

In the title compound, 2-(2-thien­yl)-1,3-bis­(2-thienyl­methyl)­perhydro­pyrimidine, C₁₈H₂₀N₂S₃, a new hexa­hydro­pyrimidine derivative with no formal crystallographic symmetry (but approximate C_s mol­ecular symmetry), the thio­phene rings are approximately orthogonal to the mean plane of the saturated pyrimidine `core' of the mol­ecule, with the three S atoms positioned on one side of the six-atom mean plane. The S atom of the directly attached thio­phene ring is involved in an unconventional (alk­yl)C—H...S hydrogen bond (H...S = 2.87 Å) with a thio­phene CH group of the closest neighbouring mol­ecule, leading to a ladder-like one-dimensional chain as the extended structure. The crystal specimen used for data collection was an inversion twin [twin fraction x = 0.41 (4)].

Key indicators

• Single-crystal X-ray study
• T = 110 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.029
• wR factor = 0.082
• Data-to-parameter ratio = 27.2

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT230_ALERT_2_B Hirshfeld Test Diff for    C2     -   C3      ..      13.85 su
PLAT230_ALERT_2_B Hirshfeld Test Diff for    C3     -   C4      ..       9.27 su
PLAT230_ALERT_2_B Hirshfeld Test Diff for    C13    -   C14     ..      12.78 su

Alert level C
STRVA01_ALERT_4_C           Flack test results are ambiguous.
           From the CIF: _refine_ls_abs_structure_Flack    0.410
           From the CIF: _refine_ls_abs_structure_Flack_su    0.040
PLAT033_ALERT_2_C Flack Parameter Value Deviates from Zero .......       0.41
PLAT220_ALERT_2_C Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       3.25 Ratio
PLAT222_ALERT_3_C Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       3.23 Ratio
PLAT230_ALERT_2_C Hirshfeld Test Diff for    S1     -   C4      ..       6.62 su
PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.  #          1
              C18 H20 N2 S3

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           31.99
           From the CIF: _reflns_number_total               5679
           Count of symmetry unique reflns         3196
           Completeness (_total/calc)            177.69%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured      2483
           Fraction of Friedel pairs measured     0.777
           Are heavy atom types Z>Si present        yes

   0 ALERT level A = In general: serious problem
   3 ALERT level B = Potentially serious problem
   6 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
   1 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

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Computing details

Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell refinement: CrysAlis RED (Oxford Diffraction, 2006); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

2-(2-thienyl)-1,3-bis(2-thienylmethyl)perhydropyrimidine

Crystal data

C18H20N2S3	F(000) = 760
Mr = 360.54	Dx = 1.328 Mg m^−3
Orthorhombic, Pna21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2n	Cell parameters from 15496 reflections
a = 15.4391 (6) Å	θ = 3.6–31.9°
b = 5.9873 (2) Å	µ = 0.41 mm^−1
c = 19.5007 (7) Å	T = 110 K
V = 1802.62 (11) Å^3	Rectangular block, colourless
Z = 4	0.6 × 0.5 × 0.2 mm

Data collection

Oxford Xcalibur2 CCD area-detector diffractometer	5600 reflections with I > 2σ(I)
ω scans	Rint = 0.011
Absorption correction: multi-scan [CrysAlis RED (Oxford Diffraction, 2006; Blessing, 1995)]	θmax = 32.0°, θmin = 3.7°
Tmin = 0.790, Tmax = 0.92	h = −21→23
17289 measured reflections	k = −7→8
5679 independent reflections	l = −27→29

Refinement

Refinement on F^2	H-atom parameters constrained
Least-squares matrix: full	w = 1/[σ^2(Fo^2) + (0.051P)^2 + 0.5189P] where P = (Fo^2 + 2Fc^2)/3
R[F^2 > 2σ(F^2)] = 0.029	(Δ/σ)max = 0.001
wR(F^2) = 0.082	Δρmax = 0.46 e Å^−3
S = 1.12	Δρmin = −0.37 e Å^−3
5679 reflections	Absolute structure: Flack (1983), 2483 Friedel pairs
209 parameters	Absolute structure parameter: 0.41 (4)
95 restraints

Special details

Experimental. IR (KBr, ν, cm^-1): 473 (m), 698 (str), 831 (str), 977 (m), 1095 (str), 1198 (str), 1220 (str), 1323 (str), 1365 (str), 1445 (m) 1545 (s), 2713 (str), 2805 (str), 2943 (str), 3084 (m) (w = weak, str = strong, m = moderate). ¹H NMR (500 MHz, CDCl₃, δ, p.p.m.): 7.36 (d, 1H), 7.20 (d, 2H), 7.16 (S, 1H), 6.96 (t, 1H), 6.92 (t, 2H), 6.86 (s, 2H), 4.35 (s, 1H), 3.95 (d, 2H), 3.60 (d, 2H), 3.12 (m, 2H), 2.38 (s, 2H), 1.70 (m, 2H). ¹³C NMR (125 MHz, CDCl₃, δ, p.p.m.): 22.9, 30,8, 49.0, 52.8, 76.7, 76.9, 77.2, 79.25, 124.7, 125.4, 125.65, 126.3, 126.4, 127.6, 142.8, 145.1, 185, 208.

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	−0.00001 (11)	0.9888 (3)	−0.89257 (8)	0.0209 (3)
H1	0.0091	1.1214	−0.9183	0.025*
C2	−0.06152 (11)	0.8331 (3)	−0.90790 (8)	0.0241 (3)
H2	−0.0998	0.8472	−0.9458	0.029*
C3	−0.06329 (9)	0.6446 (2)	−0.86143 (7)	0.0180 (2)
H3	−0.1017	0.521	−0.8644	0.022*
C4	0.00179 (8)	0.6741 (2)	−0.81054 (6)	0.0136 (2)
C5	0.02754 (8)	0.5155 (2)	−0.75444 (7)	0.0137 (2)
H5A	−0.0224	0.4196	−0.7423	0.016*
H5B	0.075	0.4178	−0.7708	0.016*
C6	0.11383 (8)	0.5050 (2)	−0.64952 (6)	0.0109 (2)
H6	0.0808	0.3757	−0.6302	0.013*
C7	0.18942 (8)	0.4201 (2)	−0.69011 (6)	0.0108 (2)
C8	0.21565 (8)	0.2040 (2)	−0.69975 (7)	0.0132 (2)
H8	0.1864	0.0783	−0.6811	0.016*
C9	0.29187 (8)	0.1886 (2)	−0.74101 (8)	0.0163 (2)
H9	0.319	0.0513	−0.7527	0.02*
C10	0.32141 (9)	0.3920 (2)	−0.76182 (8)	0.0183 (3)
H10	0.3714	0.4137	−0.7894	0.022*
C11	0.20893 (10)	0.5386 (2)	−0.54955 (7)	0.0183 (3)
H11A	0.2525	0.4643	−0.579	0.022*
H11B	0.1804	0.4225	−0.5213	0.022*
C12	0.25324 (9)	0.7043 (3)	−0.50349 (7)	0.0181 (3)
C13	0.26842 (10)	0.6887 (3)	−0.43220 (7)	0.0213 (3)
H13	0.2493	0.5692	−0.404	0.026*
C14	0.31620 (12)	0.8766 (4)	−0.40854 (10)	0.0351 (4)
H14	0.3353	0.8928	−0.3625	0.042*
C15	0.33176 (12)	1.0293 (3)	−0.45774 (12)	0.0348 (4)
H15	0.3619	1.1653	−0.4501	0.042*
C16	0.07041 (9)	0.7217 (3)	−0.55082 (7)	0.0188 (3)
H16A	0.0914	0.8145	−0.5122	0.023*
H16B	0.0407	0.5894	−0.5315	0.023*
C17	0.00734 (9)	0.8557 (3)	−0.59415 (8)	0.0191 (3)
H17A	−0.0441	0.8959	−0.5664	0.023*
H17B	0.0353	0.9954	−0.6099	0.023*
C18	−0.02019 (8)	0.7176 (3)	−0.65545 (7)	0.0169 (2)
H18A	−0.0547	0.588	−0.6398	0.02*
H18B	−0.057	0.8092	−0.6861	0.02*
N2	0.14392 (7)	0.64972 (19)	−0.59294 (6)	0.01318 (19)
N1	0.05635 (7)	0.63855 (19)	−0.69341 (6)	0.01153 (18)
S1	0.05886 (2)	0.91768 (6)	−0.82157 (2)	0.02021 (8)
S2	0.25692 (2)	0.60454 (5)	−0.73185 (2)	0.01583 (7)
S3	0.29124 (3)	0.95067 (7)	−0.53518 (2)	0.02872 (9)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0262 (7)	0.0187 (6)	0.0177 (6)	0.0009 (5)	−0.0023 (5)	0.0028 (5)
C2	0.0275 (7)	0.0259 (7)	0.0190 (7)	−0.0010 (6)	−0.0084 (5)	0.0002 (6)
C3	0.0211 (6)	0.0180 (6)	0.0149 (6)	0.0028 (5)	0.0005 (5)	0.0063 (5)
C4	0.0126 (5)	0.0140 (5)	0.0143 (6)	−0.0002 (4)	−0.0005 (4)	−0.0013 (4)
C5	0.0138 (5)	0.0148 (5)	0.0126 (5)	0.0002 (4)	−0.0027 (4)	−0.0016 (4)
C6	0.0118 (5)	0.0096 (5)	0.0113 (5)	0.0004 (4)	−0.0005 (4)	−0.0012 (4)
C7	0.0105 (5)	0.0089 (5)	0.0130 (5)	−0.0010 (4)	0.0005 (4)	−0.0010 (4)
C8	0.0136 (5)	0.0093 (5)	0.0166 (6)	0.0002 (4)	0.0011 (4)	−0.0002 (4)
C9	0.0144 (5)	0.0117 (5)	0.0228 (6)	0.0018 (4)	0.0030 (4)	−0.0022 (5)
C10	0.0131 (5)	0.0151 (6)	0.0266 (7)	0.0004 (5)	0.0059 (5)	−0.0016 (5)
C11	0.0234 (6)	0.0178 (6)	0.0136 (6)	0.0040 (5)	−0.0067 (4)	−0.0025 (5)
C12	0.0175 (6)	0.0223 (7)	0.0144 (5)	0.0024 (5)	−0.0026 (4)	−0.0035 (5)
C13	0.0207 (6)	0.0281 (7)	0.0152 (6)	−0.0056 (6)	−0.0131 (5)	0.0063 (5)
C14	0.0243 (8)	0.0566 (12)	0.0244 (8)	0.0000 (8)	−0.0085 (6)	−0.0168 (8)
C15	0.0244 (8)	0.0316 (9)	0.0484 (11)	−0.0017 (7)	−0.0073 (7)	−0.0185 (8)
C16	0.0196 (6)	0.0224 (6)	0.0143 (6)	0.0034 (5)	0.0017 (4)	−0.0056 (5)
C17	0.0163 (6)	0.0198 (6)	0.0211 (6)	0.0044 (5)	0.0035 (5)	−0.0071 (5)
C18	0.0114 (5)	0.0228 (6)	0.0165 (6)	0.0036 (5)	0.0017 (4)	−0.0042 (5)
N2	0.0143 (4)	0.0138 (4)	0.0115 (5)	0.0031 (4)	−0.0023 (4)	−0.0042 (4)
N1	0.0102 (4)	0.0128 (4)	0.0115 (4)	0.0027 (3)	−0.0002 (3)	−0.0021 (4)
S1	0.02086 (16)	0.01746 (15)	0.02231 (16)	−0.00116 (12)	−0.00351 (12)	0.00044 (13)
S2	0.01320 (13)	0.00905 (12)	0.02523 (16)	−0.00133 (10)	0.00474 (12)	−0.00002 (12)
S3	0.0379 (2)	0.02175 (17)	0.02652 (19)	−0.00189 (16)	−0.00085 (16)	−0.00150 (15)

Geometric parameters (Å, º)

C1—C2	1.364 (2)	C10—H10	0.95
C1—S1	1.7102 (16)	C11—N2	1.4719 (17)
C1—H1	0.95	C11—C12	1.503 (2)
C2—C3	1.448 (2)	C11—H11A	0.99
C2—H2	0.95	C11—H11B	0.99
C3—C4	1.4233 (19)	C12—C13	1.4128 (19)
C3—H3	0.95	C12—S3	1.7035 (16)
C4—C5	1.5021 (19)	C13—C14	1.422 (3)
C4—S1	1.7176 (14)	C13—H13	0.95
C5—N1	1.4687 (16)	C14—C15	1.347 (3)
C5—H5A	0.99	C14—H14	0.95
C5—H5B	0.99	C15—S3	1.701 (2)
C6—N1	1.4696 (16)	C15—H15	0.95
C6—N2	1.4779 (16)	C16—N2	1.4658 (17)
C6—C7	1.4989 (17)	C16—C17	1.518 (2)
C6—H6	1	C16—H16A	0.99
C7—C8	1.3687 (17)	C16—H16B	0.99
C7—S2	1.7228 (13)	C17—C18	1.514 (2)
C8—C9	1.4287 (18)	C17—H17A	0.99
C8—H8	0.95	C17—H17B	0.99
C9—C10	1.3625 (19)	C18—N1	1.4726 (16)
C9—H9	0.95	C18—H18A	0.99
C10—S2	1.7181 (14)	C18—H18B	0.99
C2—C1—S1	112.17 (12)	H11A—C11—H11B	108.1
C2—C1—H1	123.9	C13—C12—C11	128.30 (14)
S1—C1—H1	123.9	C13—C12—S3	110.92 (11)
C1—C2—C3	114.14 (14)	C11—C12—S3	120.77 (11)
C1—C2—H2	122.9	C12—C13—C14	110.67 (15)
C3—C2—H2	122.9	C12—C13—H13	124.7
C4—C3—C2	109.05 (13)	C14—C13—H13	124.7
C4—C3—H3	125.5	C15—C14—C13	113.48 (15)
C2—C3—H3	125.5	C15—C14—H14	123.3
C3—C4—C5	128.05 (12)	C13—C14—H14	123.3
C3—C4—S1	112.34 (10)	C14—C15—S3	112.27 (14)
C5—C4—S1	119.49 (9)	C14—C15—H15	123.9
N1—C5—C4	110.68 (11)	S3—C15—H15	123.9
N1—C5—H5A	109.5	N2—C16—C17	109.88 (11)
C4—C5—H5A	109.5	N2—C16—H16A	109.7
N1—C5—H5B	109.5	C17—C16—H16A	109.7
C4—C5—H5B	109.5	N2—C16—H16B	109.7
H5A—C5—H5B	108.1	C17—C16—H16B	109.7
N1—C6—N2	107.79 (10)	H16A—C16—H16B	108.2
N1—C6—C7	110.31 (10)	C18—C17—C16	109.33 (12)
N2—C6—C7	110.38 (10)	C18—C17—H17A	109.8
N1—C6—H6	109.4	C16—C17—H17A	109.8
N2—C6—H6	109.4	C18—C17—H17B	109.8
C7—C6—H6	109.4	C16—C17—H17B	109.8
C8—C7—C6	128.56 (11)	H17A—C17—H17B	108.3
C8—C7—S2	111.23 (9)	N1—C18—C17	110.31 (11)
C6—C7—S2	120.21 (9)	N1—C18—H18A	109.6
C7—C8—C9	112.47 (11)	C17—C18—H18A	109.6
C7—C8—H8	123.8	N1—C18—H18B	109.6
C9—C8—H8	123.8	C17—C18—H18B	109.6
C10—C9—C8	112.67 (12)	H18A—C18—H18B	108.1
C10—C9—H9	123.7	C16—N2—C11	109.80 (11)
C8—C9—H9	123.7	C16—N2—C6	110.33 (10)
C9—C10—S2	111.53 (10)	C11—N2—C6	112.23 (10)
C9—C10—H10	124.2	C5—N1—C6	112.44 (10)
S2—C10—H10	124.2	C5—N1—C18	109.00 (10)
N2—C11—C12	110.81 (12)	C6—N1—C18	111.52 (10)
N2—C11—H11A	109.5	C1—S1—C4	92.31 (7)
C12—C11—H11A	109.5	C10—S2—C7	92.09 (6)
N2—C11—H11B	109.5	C15—S3—C12	92.53 (9)
C12—C11—H11B	109.5
S1—C1—C2—C3	−0.09 (19)	C12—C11—N2—C16	−70.25 (15)
C1—C2—C3—C4	0.1 (2)	C12—C11—N2—C6	166.64 (11)
C2—C3—C4—C5	−175.93 (13)	N1—C6—N2—C16	62.86 (13)
C2—C3—C4—S1	−0.06 (16)	C7—C6—N2—C16	−176.61 (11)
C3—C4—C5—N1	−147.79 (13)	N1—C6—N2—C11	−174.34 (11)
S1—C4—C5—N1	36.60 (14)	C7—C6—N2—C11	−53.80 (14)
N1—C6—C7—C8	−122.75 (14)	C4—C5—N1—C6	−156.52 (10)
N2—C6—C7—C8	118.23 (14)	C4—C5—N1—C18	79.28 (14)
N1—C6—C7—S2	57.68 (13)	N2—C6—N1—C5	175.78 (10)
N2—C6—C7—S2	−61.34 (13)	C7—C6—N1—C5	55.20 (13)
C6—C7—C8—C9	−179.08 (12)	N2—C6—N1—C18	−61.43 (13)
S2—C7—C8—C9	0.52 (15)	C7—C6—N1—C18	177.99 (10)
C7—C8—C9—C10	−0.21 (18)	C17—C18—N1—C5	−177.05 (12)
C8—C9—C10—S2	−0.21 (17)	C17—C18—N1—C6	58.21 (15)
N2—C11—C12—C13	131.74 (16)	C2—C1—S1—C4	0.05 (14)
N2—C11—C12—S3	−47.07 (16)	C3—C4—S1—C1	0.01 (11)
C11—C12—C13—C14	177.16 (15)	C5—C4—S1—C1	176.27 (11)
S3—C12—C13—C14	−3.94 (18)	C9—C10—S2—C7	0.43 (12)
C12—C13—C14—C15	3.3 (2)	C8—C7—S2—C10	−0.55 (11)
C13—C14—C15—S3	−1.2 (2)	C6—C7—S2—C10	179.09 (11)
N2—C16—C17—C18	55.84 (15)	C14—C15—S3—C12	−0.98 (16)
C16—C17—C18—N1	−54.04 (16)	C13—C12—S3—C15	2.86 (13)
C17—C16—N2—C11	174.63 (11)	C11—C12—S3—C15	−178.15 (13)
C17—C16—N2—C6	−61.15 (15)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C9—H9···S2^i	0.95	2.87	3.5423 (12)	129
C10—H10···Cg1^ii	0.95	2.78	3.643	151

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