Synthesis, crystal structure and Hirshfeld surface analysis of (1H-benzimidazol-2-yl)(morpholin-4-yl)methane­thione

In the crystal of the title compound, mol­ecules are linked by N—H...N hydrogen bonds into chains running parallel to the c axis.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.004 Å
• Disorder in main residue
• R factor = 0.030
• wR factor = 0.079
• Data-to-parameter ratio = 9.1

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT915_ALERT_3_B No Flack x Check Done: Low Friedel Pair Coverage         48 %

Alert level C
PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax < 18) ........       6.15 Note
PLAT340_ALERT_3_C Low Bond Precision on  C-C Bonds ...............    0.00429 Ang.
PLAT715_ALERT_1_C D-H     Unknown or Inconsistent Label ..........         H9 Check
                    C9          H9
PLAT716_ALERT_1_C H...A   Unknown or Inconsistent Label ..........         H9 Check
                    H9          S1
PLAT718_ALERT_1_C D-H..A  Unknown or Inconsistent Label ..........         H9 Check
                    C9          H9          S1
PLAT978_ALERT_2_C Number C-C Bonds with Positive Residual Density.          0 Info

Alert level G
PLAT012_ALERT_1_G N.O.K.   _shelx_res_checksum Found in CIF ......     Please Check
PLAT171_ALERT_4_G The CIF-Embedded .res File Contains EADP Records          1 Report
PLAT199_ALERT_1_G Reported _cell_measurement_temperature ..... (K)        293 Check
PLAT200_ALERT_1_G Reported   _diffrn_ambient_temperature ..... (K)        293 Check
PLAT301_ALERT_3_G Main Residue  Disorder ..............(Resd  1  )        24% Note
PLAT398_ALERT_2_G Deviating  C-O-C   Angle From 120 for O1       .      109.4 Degree
PLAT432_ALERT_2_G Short Inter X...Y Contact  C7       ..C11B     .       3.15 Ang.
                                                   -1+x,y,z  =      1_455 Check
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600          7 Note

   0 ALERT level A = Most likely a serious problem - resolve or explain
   1 ALERT level B = A potentially serious problem, consider carefully
   6 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   8 ALERT level G = General information/check it is not something unexpected

   6 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   3 ALERT type 2 Indicator that the structure model may be wrong or deficient
   4 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


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.

   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

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Computing details

Data collection: CrysAlis PRO (Rigaku OD, 2020); cell refinement: CrysAlis PRO (Rigaku OD, 2020); data reduction: CrysAlis PRO (Rigaku OD, 2020); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: XP (Siemens, 1994), Mercury (Macrae et al. 2020); software used to prepare material for publication: PLATON (Spek, 2020).

(1H-Benzimidazol-2-yl)(morpholin-4-yl)methanethione

Crystal data

C12H13N3OS	Dx = 1.361 Mg m^−3
Mr = 247.31	Melting point: 513(2) K
Monoclinic, Ia	Cu Kα radiation, λ = 1.54184 Å
a = 8.1644 (2) Å	Cell parameters from 4375 reflections
b = 15.9237 (3) Å	θ = 5.5–71.1°
c = 9.6936 (2) Å	µ = 2.28 mm^−1
β = 106.661 (2)°	T = 293 K
V = 1207.33 (5) Å^3	Needle, colourless
Z = 4	0.30 × 0.25 × 0.14 mm
F(000) = 520

Data collection

XtaLAB Synergy, Single source at home/near, HyPix3000 diffractometer	1724 independent reflections
Radiation source: micro-focus sealed X-ray tube, PhotonJet (Cu) X-ray Source	1692 reflections with I > 2σ(I)
Mirror monochromator	Rint = 0.022
Detector resolution: 10.0000 pixels mm^-1	θmax = 71.3°, θmin = 5.5°
ω scans	h = −9→10
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2020)	k = −19→19
Tmin = 0.568, Tmax = 1.000	l = −9→11
5160 measured reflections

Refinement

Refinement on F^2	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.030	w = 1/[σ^2(Fo^2) + (0.0448P)^2 + 0.2955P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.079	(Δ/σ)max < 0.001
S = 1.10	Δρmax = 0.17 e Å^−3
1724 reflections	Δρmin = −0.19 e Å^−3
189 parameters	Absolute structure: Flack x determined using 531 quotients [(I^+)-(I^-)]/[(I^+)+(I^-)] (Parsons et al., 2013)
2 restraints	Absolute structure parameter: −0.001 (13)

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

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

	x	y	z	Uiso*/Ueq	Occ. (<1)
S1	0.43314 (11)	0.91597 (4)	0.55516 (11)	0.0555 (2)
O1	0.9333 (3)	0.79690 (17)	0.3720 (4)	0.0726 (8)
N1	0.3522 (3)	0.69924 (13)	0.3950 (2)	0.0334 (4)
N2	0.3362 (3)	0.72781 (14)	0.6169 (3)	0.0354 (5)
H2	0.350 (4)	0.754 (2)	0.695 (4)	0.038 (8)*
N3	0.6584 (3)	0.81395 (16)	0.4919 (4)	0.0555 (8)
C1	0.3992 (3)	0.74997 (16)	0.5073 (3)	0.0316 (5)
C2	0.1490 (4)	0.6052 (2)	0.6418 (4)	0.0490 (7)
H2B	0.1429	0.6168	0.7342	0.059*
C3	0.0676 (4)	0.5366 (2)	0.5648 (4)	0.0540 (8)
H3A	0.0048	0.5012	0.6066	0.065*
C4	0.0767 (4)	0.51882 (19)	0.4256 (4)	0.0498 (7)
H4A	0.0210	0.4716	0.3780	0.060*
C5	0.1663 (3)	0.56963 (17)	0.3576 (3)	0.0397 (6)
H5A	0.1708	0.5581	0.2647	0.048*
C6	0.2502 (3)	0.63938 (15)	0.4345 (3)	0.0320 (5)
C7	0.2407 (3)	0.65587 (16)	0.5736 (3)	0.0337 (5)
C8	0.5083 (3)	0.82515 (16)	0.5156 (3)	0.0377 (6)
C9	0.7777 (7)	0.8840 (3)	0.4960 (9)	0.0661 (16)	0.841 (11)
H9A	0.8705	0.8823	0.5848	0.079*	0.841 (11)
H9B	0.7187	0.9373	0.4916	0.079*	0.841 (11)
C10	0.8473 (9)	0.8753 (4)	0.3682 (10)	0.078 (2)	0.841 (11)
H10A	0.7541	0.8790	0.2799	0.093*	0.841 (11)
H10B	0.9263	0.9209	0.3686	0.093*	0.841 (11)
C11	0.8153 (7)	0.7297 (3)	0.3658 (7)	0.0530 (12)	0.841 (11)
H11A	0.8722	0.6764	0.3637	0.064*	0.841 (11)
H11B	0.7213	0.7343	0.2782	0.064*	0.841 (11)
C12	0.7468 (6)	0.7322 (2)	0.4947 (7)	0.0466 (11)	0.841 (11)
H12A	0.6675	0.6863	0.4903	0.056*	0.841 (11)
H12B	0.8397	0.7270	0.5828	0.056*	0.841 (11)
C9B	0.715 (5)	0.8869 (14)	0.398 (5)	0.067 (10)	0.159 (11)
H9C	0.6680	0.8780	0.2957	0.080*	0.159 (11)
H9D	0.6840	0.9425	0.4236	0.080*	0.159 (11)
C10B	0.901 (5)	0.873 (2)	0.447 (5)	0.078 (2)	0.159 (11)
H10C	0.9395	0.8654	0.5504	0.093*	0.159 (11)
H10D	0.9605	0.9211	0.4221	0.093*	0.159 (11)
C11B	0.872 (4)	0.7315 (17)	0.446 (4)	0.057 (7)	0.159 (11)
H11C	0.9141	0.7399	0.5495	0.069*	0.159 (11)
H11D	0.9110	0.6772	0.4231	0.069*	0.159 (11)
C12B	0.688 (4)	0.7353 (11)	0.400 (4)	0.047 (7)	0.159 (11)
H12C	0.6372	0.6845	0.4243	0.057*	0.159 (11)
H12D	0.6445	0.7455	0.2971	0.057*	0.159 (11)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0713 (5)	0.0311 (3)	0.0723 (5)	0.0025 (3)	0.0340 (4)	−0.0069 (4)
O1	0.0627 (14)	0.0675 (16)	0.104 (2)	−0.0080 (12)	0.0499 (15)	−0.0086 (15)
N1	0.0392 (10)	0.0334 (10)	0.0311 (11)	−0.0016 (8)	0.0157 (9)	−0.0017 (8)
N2	0.0419 (12)	0.0381 (11)	0.0294 (12)	−0.0055 (9)	0.0151 (9)	−0.0052 (10)
N3	0.0524 (15)	0.0346 (13)	0.092 (2)	−0.0092 (10)	0.0407 (16)	−0.0091 (13)
C1	0.0349 (13)	0.0307 (11)	0.0307 (12)	−0.0001 (9)	0.0121 (10)	−0.0004 (9)
C2	0.0532 (17)	0.0567 (16)	0.0425 (16)	−0.0104 (14)	0.0226 (14)	0.0030 (14)
C3	0.0517 (17)	0.0498 (16)	0.064 (2)	−0.0166 (14)	0.0231 (16)	0.0053 (15)
C4	0.0434 (15)	0.0411 (15)	0.065 (2)	−0.0097 (11)	0.0154 (14)	−0.0078 (14)
C5	0.0369 (12)	0.0408 (13)	0.0410 (15)	−0.0029 (10)	0.0105 (11)	−0.0085 (12)
C6	0.0314 (11)	0.0330 (11)	0.0325 (12)	0.0012 (9)	0.0107 (10)	−0.0017 (10)
C7	0.0351 (11)	0.0350 (11)	0.0329 (13)	−0.0020 (10)	0.0127 (10)	−0.0002 (10)
C8	0.0460 (14)	0.0318 (12)	0.0375 (14)	−0.0042 (10)	0.0153 (12)	−0.0009 (10)
C9	0.066 (3)	0.052 (2)	0.094 (5)	−0.027 (2)	0.045 (3)	−0.021 (3)
C10	0.093 (4)	0.057 (2)	0.108 (5)	−0.012 (3)	0.067 (5)	−0.003 (4)
C11	0.047 (3)	0.052 (2)	0.061 (3)	0.0026 (18)	0.017 (2)	−0.007 (2)
C12	0.0397 (19)	0.0437 (19)	0.059 (3)	0.0014 (16)	0.019 (2)	−0.0024 (19)
C9B	0.09 (2)	0.030 (9)	0.11 (3)	0.002 (11)	0.07 (2)	0.009 (14)
C10B	0.093 (4)	0.057 (2)	0.108 (5)	−0.012 (3)	0.067 (5)	−0.003 (4)
C11B	0.049 (14)	0.062 (14)	0.058 (17)	0.015 (10)	0.010 (12)	−0.002 (13)
C12B	0.050 (13)	0.029 (8)	0.08 (2)	−0.005 (8)	0.040 (14)	0.002 (10)

Geometric parameters (Å, º)

S1—C8	1.658 (3)	C5—C6	1.402 (3)
O1—C10	1.427 (7)	C5—H5A	0.9300
O1—C11	1.430 (5)	C6—C7	1.399 (4)
O1—C11B	1.43 (3)	C9—C10	1.511 (10)
O1—C10B	1.48 (4)	C9—H9A	0.9700
N1—C1	1.322 (3)	C9—H9B	0.9700
N1—C6	1.390 (3)	C10—H10A	0.9700
N2—C1	1.353 (3)	C10—H10B	0.9700
N2—C7	1.382 (3)	C11—C12	1.508 (8)
N2—H2	0.84 (4)	C11—H11A	0.9700
N3—C8	1.322 (3)	C11—H11B	0.9700
N3—C9	1.475 (5)	C12—H12A	0.9700
N3—C12	1.485 (5)	C12—H12B	0.9700
N3—C12B	1.60 (2)	C9B—C10B	1.47 (6)
N3—C9B	1.62 (2)	C9B—H9C	0.9700
C1—C8	1.480 (3)	C9B—H9D	0.9700
C2—C3	1.380 (5)	C10B—H10C	0.9700
C2—C7	1.390 (4)	C10B—H10D	0.9700
C2—H2B	0.9300	C11B—C12B	1.44 (4)
C3—C4	1.401 (5)	C11B—H11C	0.9700
C3—H3A	0.9300	C11B—H11D	0.9700
C4—C5	1.379 (4)	C12B—H12C	0.9700
C4—H4A	0.9300	C12B—H12D	0.9700
C10—O1—C11	109.5 (4)	O1—C10—C9	110.9 (6)
C11B—O1—C10B	102 (2)	O1—C10—H10A	109.5
C1—N1—C6	104.3 (2)	C9—C10—H10A	109.5
C1—N2—C7	106.6 (2)	O1—C10—H10B	109.5
C1—N2—H2	127 (2)	C9—C10—H10B	109.5
C7—N2—H2	127 (2)	H10A—C10—H10B	108.0
C8—N3—C9	122.1 (3)	O1—C11—C12	110.5 (4)
C8—N3—C12	125.8 (3)	O1—C11—H11A	109.5
C9—N3—C12	110.4 (3)	C12—C11—H11A	109.5
C8—N3—C12B	120.0 (9)	O1—C11—H11B	109.5
C8—N3—C9B	115.3 (10)	C12—C11—H11B	109.5
C12B—N3—C9B	97.8 (16)	H11A—C11—H11B	108.1
N1—C1—N2	113.7 (2)	N3—C12—C11	107.6 (4)
N1—C1—C8	124.5 (2)	N3—C12—H12A	110.2
N2—C1—C8	121.8 (2)	C11—C12—H12A	110.2
C3—C2—C7	116.4 (3)	N3—C12—H12B	110.2
C3—C2—H2B	121.8	C11—C12—H12B	110.2
C7—C2—H2B	121.8	H12A—C12—H12B	108.5
C2—C3—C4	122.0 (3)	C10B—C9B—N3	99 (3)
C2—C3—H3A	119.0	C10B—C9B—H9C	112.1
C4—C3—H3A	119.0	N3—C9B—H9C	112.1
C5—C4—C3	121.6 (3)	C10B—C9B—H9D	112.1
C5—C4—H4A	119.2	N3—C9B—H9D	112.1
C3—C4—H4A	119.2	H9C—C9B—H9D	109.7
C4—C5—C6	117.2 (3)	C9B—C10B—O1	106 (3)
C4—C5—H5A	121.4	C9B—C10B—H10C	110.5
C6—C5—H5A	121.4	O1—C10B—H10C	110.5
N1—C6—C7	109.9 (2)	C9B—C10B—H10D	110.5
N1—C6—C5	129.6 (2)	O1—C10B—H10D	110.5
C7—C6—C5	120.5 (2)	H10C—C10B—H10D	108.7
N2—C7—C2	132.2 (3)	O1—C11B—C12B	107 (2)
N2—C7—C6	105.4 (2)	O1—C11B—H11C	110.3
C2—C7—C6	122.4 (2)	C12B—C11B—H11C	110.3
N3—C8—C1	117.1 (2)	O1—C11B—H11D	110.3
N3—C8—S1	125.5 (2)	C12B—C11B—H11D	110.3
C1—C8—S1	117.5 (2)	H11C—C11B—H11D	108.5
N3—C9—C10	108.0 (5)	C11B—C12B—N3	100 (3)
N3—C9—H9A	110.1	C11B—C12B—H12C	111.8
C10—C9—H9A	110.1	N3—C12B—H12C	111.8
N3—C9—H9B	110.1	C11B—C12B—H12D	111.8
C10—C9—H9B	110.1	N3—C12B—H12D	111.8
H9A—C9—H9B	108.4	H12C—C12B—H12D	109.5
C6—N1—C1—N2	0.1 (3)	C12—N3—C8—S1	162.8 (4)
C6—N1—C1—C8	−179.1 (2)	C12B—N3—C8—S1	−156.9 (15)
C7—N2—C1—N1	0.6 (3)	C9B—N3—C8—S1	−40.3 (19)
C7—N2—C1—C8	179.8 (2)	N1—C1—C8—N3	−55.2 (4)
C7—C2—C3—C4	0.1 (5)	N2—C1—C8—N3	125.7 (3)
C2—C3—C4—C5	−0.7 (5)	N1—C1—C8—S1	125.4 (2)
C3—C4—C5—C6	0.9 (4)	N2—C1—C8—S1	−53.7 (3)
C1—N1—C6—C7	−0.7 (3)	C8—N3—C9—C10	−135.7 (5)
C1—N1—C6—C5	−179.5 (3)	C12—N3—C9—C10	58.2 (9)
C4—C5—C6—N1	178.1 (3)	C11—O1—C10—C9	61.3 (8)
C4—C5—C6—C7	−0.5 (4)	N3—C9—C10—O1	−59.2 (9)
C1—N2—C7—C2	179.1 (3)	C10—O1—C11—C12	−62.0 (8)
C1—N2—C7—C6	−1.0 (3)	C8—N3—C12—C11	135.6 (4)
C3—C2—C7—N2	−179.8 (3)	C9—N3—C12—C11	−58.9 (7)
C3—C2—C7—C6	0.3 (5)	O1—C11—C12—N3	60.2 (6)
N1—C6—C7—N2	1.1 (3)	C8—N3—C9B—C10B	157 (2)
C5—C6—C7—N2	180.0 (2)	C12B—N3—C9B—C10B	−74 (3)
N1—C6—C7—C2	−179.0 (3)	N3—C9B—C10B—O1	76 (3)
C5—C6—C7—C2	−0.1 (4)	C11B—O1—C10B—C9B	−73 (4)
C9—N3—C8—C1	179.5 (5)	C10B—O1—C11B—C12B	74 (4)
C12—N3—C8—C1	−16.6 (5)	O1—C11B—C12B—N3	−77 (3)
C12B—N3—C8—C1	23.7 (15)	C8—N3—C12B—C11B	−160.0 (16)
C9B—N3—C8—C1	140.3 (19)	C9B—N3—C12B—C11B	75 (3)
C9—N3—C8—S1	−1.1 (6)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···N1^i	0.84 (4)	2.07 (4)	2.903 (3)	169 (3)
C9—H9B···S1	0.97	2.60	3.070 (5)	110
C12—H12A···N1	0.97	2.48	3.131 (5)	124

Symmetry code: (i) x, −y+3/2, z+1/2.