Cocrystals of thiourea with 4-nitropyridine
N-oxide, C
5H
4N
2O
3·2CH
4N
2S, (
I), and 3-bromopyridine
N-oxide, C
5H
4BrNO·CH
4N
2S, (
II), crystallize in the monoclinic space group
P2
1/
c. In the crystals, molecules of both components are linked by N—H
O hydrogen bonds, creating
R21(6) synthons. The bromine substituent of the
N-oxide component in (
II) is a centre for C—Br
S halogen bonding to the thiourea molecule. Computations based on quantum chemistry methods (quantum theory of atoms in molecules, QTAIM) and atoms in molecules (AIM) theory were performed for a more detailed description of the observed type of halogen-bonding interaction.
Supporting information
CCDC references: 1979836; 1979835
For both structures, data collection: CrysAlis PRO (Rigaku OD, 2015); cell refinement: CrysAlis PRO (Rigaku OD, 2015); data reduction: CrysAlis PRO (Rigaku OD, 2015); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018 (Sheldrick, 2015b); software used to prepare material for publication: SHELXL2018 (Sheldrick, 2015b).
4-Nitropyridine
N-oxide–thiourea (1/2) (structure_I)
top
Crystal data top
C5H4N2O3·2CH4N2S | F(000) = 608 |
Mr = 292.35 | Dx = 1.532 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54184 Å |
a = 9.1446 (2) Å | Cell parameters from 6151 reflections |
b = 13.8603 (3) Å | θ = 3.2–76.3° |
c = 10.6447 (2) Å | µ = 3.95 mm−1 |
β = 109.989 (3)° | T = 100 K |
V = 1267.91 (5) Å3 | Plate, yellow |
Z = 4 | 0.15 × 0.09 × 0.05 mm |
Data collection top
Rigaku SuperNova (Cu) X-ray Source diffractometer | 2331 independent reflections |
Radiation source: micro-focus sealed X-ray tube | 2168 reflections with I > 2σ(I) |
Detector resolution: 10.4052 pixels mm-1 | Rint = 0.042 |
ω scans | θmax = 68.5°, θmin = 5.2° |
Absorption correction: analytical (CrysAlis PRO; Rigaku OD, 2015; Clark & Reid, 1995) | h = −11→10 |
Tmin = 0.956, Tmax = 0.982 | k = −16→16 |
12163 measured reflections | l = −12→12 |
Refinement top
Refinement on F2 | 1 restraint |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.058 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.142 | w = 1/[σ2(Fo2) + (0.0577P)2 + 4.4349P] where P = (Fo2 + 2Fc2)/3 |
S = 1.08 | (Δ/σ)max < 0.001 |
2331 reflections | Δρmax = 1.21 e Å−3 |
195 parameters | Δρmin = −0.50 e Å−3 |
Special details top
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 (Å2) top | x | y | z | Uiso*/Ueq | |
S12A | 0.29723 (10) | 0.60095 (6) | −0.06020 (8) | 0.0207 (2) | |
S12B | 1.10630 (10) | 0.64116 (6) | 1.55686 (8) | 0.0211 (2) | |
N13A | 0.3011 (3) | 0.6508 (2) | 0.1815 (3) | 0.0163 (6) | |
N11B | 1.0279 (4) | 0.7262 (2) | 1.3202 (3) | 0.0176 (6) | |
N11A | 0.4971 (3) | 0.5509 (2) | 0.1772 (3) | 0.0192 (6) | |
O1 | 0.5215 (3) | 0.6035 (2) | 0.4396 (2) | 0.0296 (6) | |
O41 | 0.7607 (3) | 0.6965 (2) | 1.0409 (3) | 0.0366 (7) | |
O42 | 0.9447 (3) | 0.6057 (2) | 1.0290 (3) | 0.0303 (6) | |
N13B | 0.9161 (4) | 0.5793 (2) | 1.3225 (3) | 0.0207 (6) | |
N1 | 0.5949 (4) | 0.6121 (2) | 0.5647 (3) | 0.0242 (7) | |
N4 | 0.8178 (4) | 0.6477 (2) | 0.9743 (3) | 0.0251 (7) | |
C12B | 1.0103 (4) | 0.6491 (2) | 1.3884 (3) | 0.0145 (6) | |
C12A | 0.3697 (4) | 0.6008 (2) | 0.1108 (3) | 0.0145 (6) | |
C5 | 0.8071 (4) | 0.5761 (2) | 0.7616 (3) | 0.0165 (7) | |
H5 | 0.902137 | 0.543050 | 0.804661 | 0.020* | |
C3 | 0.6021 (4) | 0.6828 (3) | 0.7703 (4) | 0.0273 (8) | |
H3 | 0.557338 | 0.723134 | 0.819602 | 0.033* | |
C6 | 0.7306 (4) | 0.5664 (3) | 0.6266 (4) | 0.0255 (8) | |
H6 | 0.774232 | 0.526734 | 0.575771 | 0.031* | |
C2 | 0.5309 (4) | 0.6706 (3) | 0.6379 (4) | 0.0268 (8) | |
H2 | 0.435135 | 0.702610 | 0.593875 | 0.032* | |
C4 | 0.7421 (4) | 0.6356 (3) | 0.8338 (4) | 0.0230 (7) | |
H14A | 0.234 (5) | 0.687 (3) | 0.138 (5) | 0.029 (12)* | |
H13A | 0.333 (5) | 0.648 (3) | 0.264 (5) | 0.026 (11)* | |
H13B | 0.877 (5) | 0.582 (3) | 1.246 (5) | 0.031 (13)* | |
H11B | 0.981 (5) | 0.731 (3) | 1.246 (5) | 0.024 (12)* | |
H12B | 1.087 (5) | 0.765 (3) | 1.359 (5) | 0.024 (11)* | |
H14B | 0.911 (6) | 0.529 (4) | 1.359 (5) | 0.039 (14)* | |
H12A | 0.532 (5) | 0.551 (3) | 0.261 (5) | 0.023 (11)* | |
H11A | 0.552 (6) | 0.520 (4) | 0.134 (5) | 0.043 (14)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
S12A | 0.0235 (4) | 0.0237 (5) | 0.0123 (4) | 0.0087 (3) | 0.0026 (3) | −0.0021 (3) |
S12B | 0.0312 (5) | 0.0165 (4) | 0.0109 (4) | −0.0083 (3) | 0.0011 (3) | 0.0005 (3) |
N13A | 0.0202 (14) | 0.0149 (14) | 0.0122 (14) | 0.0046 (11) | 0.0035 (12) | 0.0012 (11) |
N11B | 0.0222 (15) | 0.0156 (14) | 0.0112 (14) | −0.0038 (12) | 0.0008 (12) | −0.0005 (12) |
N11A | 0.0208 (14) | 0.0214 (15) | 0.0136 (14) | 0.0067 (12) | 0.0036 (12) | −0.0006 (11) |
O1 | 0.0328 (14) | 0.0372 (15) | 0.0125 (12) | 0.0016 (12) | −0.0005 (11) | 0.0010 (11) |
O41 | 0.0386 (16) | 0.0484 (18) | 0.0231 (14) | 0.0013 (14) | 0.0111 (12) | −0.0149 (13) |
O42 | 0.0266 (14) | 0.0360 (16) | 0.0225 (13) | 0.0064 (12) | 0.0011 (11) | 0.0033 (11) |
N13B | 0.0297 (16) | 0.0165 (15) | 0.0118 (15) | −0.0062 (12) | 0.0019 (13) | 0.0018 (12) |
N1 | 0.0250 (15) | 0.0233 (15) | 0.0200 (15) | −0.0015 (12) | 0.0020 (13) | 0.0056 (12) |
N4 | 0.0349 (17) | 0.0190 (15) | 0.0258 (16) | −0.0037 (13) | 0.0160 (14) | −0.0025 (12) |
C12B | 0.0168 (15) | 0.0136 (15) | 0.0144 (15) | 0.0007 (12) | 0.0069 (12) | 0.0006 (12) |
C12A | 0.0152 (15) | 0.0121 (15) | 0.0153 (15) | −0.0015 (12) | 0.0041 (12) | −0.0003 (12) |
C5 | 0.0161 (15) | 0.0140 (15) | 0.0194 (16) | 0.0011 (12) | 0.0059 (13) | −0.0006 (12) |
C3 | 0.0222 (18) | 0.0190 (17) | 0.044 (2) | 0.0067 (14) | 0.0150 (17) | 0.0041 (16) |
C6 | 0.0269 (18) | 0.0243 (18) | 0.0272 (19) | 0.0040 (15) | 0.0116 (15) | −0.0020 (15) |
C2 | 0.0281 (19) | 0.0250 (19) | 0.028 (2) | 0.0095 (15) | 0.0098 (16) | 0.0021 (15) |
C4 | 0.0261 (18) | 0.0214 (18) | 0.0208 (18) | −0.0030 (14) | 0.0070 (15) | 0.0001 (14) |
Geometric parameters (Å, º) top
S12A—C12A | 1.711 (3) | N13B—C12B | 1.326 (4) |
S12B—C12B | 1.709 (3) | N1—C6 | 1.347 (5) |
N13A—C12A | 1.328 (4) | N1—C2 | 1.385 (5) |
N11B—C12B | 1.331 (4) | N4—C4 | 1.427 (5) |
N11A—C12A | 1.331 (4) | C5—C6 | 1.373 (5) |
O1—N1 | 1.275 (4) | C5—C4 | 1.391 (5) |
O41—N4 | 1.218 (4) | C3—C2 | 1.346 (6) |
O42—N4 | 1.250 (4) | C3—C4 | 1.391 (5) |
| | | |
O1—N1—C6 | 122.3 (3) | N13A—C12A—S12A | 121.0 (3) |
O1—N1—C2 | 118.0 (3) | N11A—C12A—S12A | 121.0 (3) |
C6—N1—C2 | 119.7 (3) | C6—C5—C4 | 118.3 (3) |
O41—N4—O42 | 120.1 (3) | C2—C3—C4 | 119.0 (3) |
O41—N4—C4 | 121.6 (3) | N1—C6—C5 | 121.4 (3) |
O42—N4—C4 | 118.2 (3) | C3—C2—N1 | 121.1 (3) |
N13B—C12B—N11B | 118.3 (3) | C3—C4—C5 | 120.4 (3) |
N13B—C12B—S12B | 121.1 (3) | C3—C4—N4 | 119.3 (3) |
N11B—C12B—S12B | 120.6 (3) | C5—C4—N4 | 120.2 (3) |
N13A—C12A—N11A | 117.9 (3) | | |
| | | |
O1—N1—C6—C5 | −179.5 (3) | C2—C3—C4—N4 | −179.6 (3) |
C2—N1—C6—C5 | 0.4 (5) | C6—C5—C4—C3 | 0.8 (5) |
C4—C5—C6—N1 | −0.8 (5) | C6—C5—C4—N4 | −180.0 (3) |
C4—C3—C2—N1 | −0.1 (6) | O41—N4—C4—C3 | 2.1 (5) |
O1—N1—C2—C3 | 179.9 (3) | O42—N4—C4—C3 | −179.0 (3) |
C6—N1—C2—C3 | 0.1 (6) | O41—N4—C4—C5 | −177.2 (3) |
C2—C3—C4—C5 | −0.3 (5) | O42—N4—C4—C5 | 1.7 (5) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N11B—H12B···O1 | 0.88 (5) | 2.10 (5) | 2.867 (4) | 145 (4) |
N13B—H14B···O1 | 0.86 (5) | 2.04 (5) | 2.819 (4) | 151 (4) |
N13A—H13A···O41 | 0.81 (5) | 2.58 (5) | 3.242 (4) | 140 (4) |
N11A—H12A···O42 | 0.79 (5) | 2.43 (5) | 3.165 (4) | 157 (5) |
N11B—H11B···S12Ai | 0.82 (5) | 2.66 (4) | 3.413 (3) | 154 (4) |
N11A—H11A···S12Bii | 0.81 (5) | 2.58 (5) | 3.359 (3) | 167 (4) |
N13A—H14A···S12Aiii | 0.84 (5) | 2.52 (5) | 3.345 (3) | 172 (5) |
N13B—H13B···S12Biv | 0.89 (5) | 2.48 (5) | 3.334 (3) | 164 (4) |
Symmetry codes: (i) x−1, −y+3/2, z−3/2; (ii) x+1, −y+3/2, z+3/2; (iii) −x+2, −y+1, −z+3; (iv) −x+1, −y+1, −z. |
3-Bromopyridine
N-oxide–thiourea (1/1) (structure_II)
top
Crystal data top
C5H4BrNO·CH4N2S | F(000) = 496 |
Mr = 250.12 | Dx = 1.845 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
a = 8.9440 (3) Å | Cell parameters from 8749 reflections |
b = 12.4204 (2) Å | θ = 2.8–32.5° |
c = 8.3042 (2) Å | µ = 4.75 mm−1 |
β = 102.506 (3)° | T = 100 K |
V = 900.61 (4) Å3 | Plate, colorless |
Z = 4 | 0.33 × 0.12 × 0.03 mm |
Data collection top
Rigaku SuperNova Dual Source diffractometer with an Atlas detector | 2065 independent reflections |
Radiation source: micro-focus sealed X-ray tube | 1891 reflections with I > 2σ(I) |
Detector resolution: 10.4052 pixels mm-1 | Rint = 0.045 |
ω scans | θmax = 27.5°, θmin = 2.9° |
Absorption correction: analytical (CrysAlis PRO; Rigaku OD, 2019) | h = −11→11 |
Tmin = 0.393, Tmax = 0.886 | k = −16→16 |
18912 measured reflections | l = −10→10 |
Refinement top
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.020 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.050 | w = 1/[σ2(Fo2) + (0.0212P)2 + 0.774P] where P = (Fo2 + 2Fc2)/3 |
S = 1.05 | (Δ/σ)max = 0.001 |
2065 reflections | Δρmax = 0.39 e Å−3 |
125 parameters | Δρmin = −0.30 e Å−3 |
Special details top
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 (Å2) top | x | y | z | Uiso*/Ueq | |
Br3 | 0.23177 (2) | 0.52622 (2) | 0.09504 (2) | 0.01826 (7) | |
S12 | 0.46557 (5) | 1.29005 (3) | 0.12455 (6) | 0.01538 (10) | |
O1 | 0.19740 (17) | 0.93678 (11) | 0.04294 (18) | 0.0222 (3) | |
N1 | 0.13610 (18) | 0.84827 (12) | 0.08721 (19) | 0.0155 (3) | |
C3 | 0.1368 (2) | 0.65962 (14) | 0.1202 (2) | 0.0143 (3) | |
N11 | 0.3612 (2) | 1.10976 (14) | 0.2350 (2) | 0.0174 (3) | |
C12 | 0.4014 (2) | 1.15944 (14) | 0.1089 (2) | 0.0135 (3) | |
N13 | 0.38890 (19) | 1.10512 (13) | −0.0308 (2) | 0.0158 (3) | |
C2 | 0.2021 (2) | 0.75165 (15) | 0.0720 (2) | 0.0155 (4) | |
H2 | 0.292036 | 0.747273 | 0.028939 | 0.019* | |
C4 | 0.0075 (2) | 0.66377 (15) | 0.1860 (2) | 0.0166 (4) | |
H4 | −0.034988 | 0.600378 | 0.221891 | 0.020* | |
C5 | −0.0579 (2) | 0.76412 (15) | 0.1975 (2) | 0.0178 (4) | |
H5 | −0.147509 | 0.769920 | 0.240985 | 0.021* | |
C6 | 0.0063 (2) | 0.85540 (15) | 0.1463 (2) | 0.0174 (4) | |
H6 | −0.040396 | 0.923526 | 0.152376 | 0.021* | |
H11A | 0.321 (3) | 1.0463 (19) | 0.220 (3) | 0.016 (5)* | |
H11B | 0.384 (3) | 1.135 (2) | 0.331 (3) | 0.029 (7)* | |
H13A | 0.358 (3) | 1.041 (2) | −0.035 (3) | 0.024 (6)* | |
H13B | 0.413 (3) | 1.1351 (19) | −0.111 (3) | 0.022 (6)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Br3 | 0.02166 (11) | 0.01115 (10) | 0.02216 (11) | 0.00290 (7) | 0.00513 (8) | 0.00010 (7) |
S12 | 0.0212 (2) | 0.0113 (2) | 0.0145 (2) | −0.00159 (17) | 0.00583 (17) | −0.00075 (16) |
O1 | 0.0263 (8) | 0.0113 (6) | 0.0305 (8) | −0.0057 (6) | 0.0090 (6) | 0.0042 (6) |
N1 | 0.0182 (8) | 0.0105 (7) | 0.0168 (8) | −0.0027 (6) | 0.0019 (6) | 0.0005 (6) |
C3 | 0.0167 (9) | 0.0096 (8) | 0.0147 (9) | 0.0022 (7) | −0.0006 (7) | −0.0007 (6) |
N11 | 0.0238 (9) | 0.0140 (8) | 0.0154 (8) | −0.0029 (7) | 0.0064 (7) | −0.0005 (6) |
C12 | 0.0116 (8) | 0.0126 (8) | 0.0161 (9) | 0.0025 (6) | 0.0022 (7) | 0.0009 (6) |
N13 | 0.0209 (8) | 0.0114 (8) | 0.0166 (8) | −0.0012 (6) | 0.0074 (7) | −0.0006 (6) |
C2 | 0.0156 (9) | 0.0146 (8) | 0.0161 (9) | 0.0007 (7) | 0.0028 (7) | −0.0007 (7) |
C4 | 0.0192 (9) | 0.0124 (8) | 0.0172 (9) | −0.0016 (7) | 0.0017 (7) | 0.0021 (7) |
C5 | 0.0162 (9) | 0.0171 (9) | 0.0200 (9) | 0.0003 (7) | 0.0041 (7) | −0.0001 (7) |
C6 | 0.0190 (9) | 0.0130 (8) | 0.0202 (9) | 0.0012 (7) | 0.0043 (7) | −0.0008 (7) |
Geometric parameters (Å, º) top
Br3—C3 | 1.8940 (18) | C12—N13 | 1.326 (2) |
S12—C12 | 1.7163 (18) | N13—H13A | 0.85 (3) |
O1—N1 | 1.3159 (19) | N13—H13B | 0.83 (3) |
N1—C2 | 1.355 (2) | C2—H2 | 0.9500 |
N1—C6 | 1.357 (2) | C4—C5 | 1.389 (3) |
C3—C2 | 1.382 (3) | C4—H4 | 0.9500 |
C3—C4 | 1.383 (3) | C5—C6 | 1.379 (3) |
N11—C12 | 1.330 (2) | C5—H5 | 0.9500 |
N11—H11A | 0.86 (2) | C6—H6 | 0.9500 |
N11—H11B | 0.84 (3) | | |
| | | |
O1—N1—C2 | 119.83 (15) | H13A—N13—H13B | 122 (2) |
O1—N1—C6 | 119.15 (15) | N1—C2—C3 | 119.05 (16) |
C2—N1—C6 | 121.02 (16) | N1—C2—H2 | 120.5 |
C2—C3—C4 | 121.71 (17) | C3—C2—H2 | 120.5 |
C2—C3—Br3 | 117.64 (14) | C3—C4—C5 | 117.50 (17) |
C4—C3—Br3 | 120.64 (14) | C3—C4—H4 | 121.3 |
C12—N11—H11A | 119.1 (15) | C5—C4—H4 | 121.3 |
C12—N11—H11B | 121.5 (17) | C6—C5—C4 | 120.41 (17) |
H11A—N11—H11B | 119 (2) | C6—C5—H5 | 119.8 |
N13—C12—N11 | 117.84 (17) | C4—C5—H5 | 119.8 |
N13—C12—S12 | 120.69 (14) | N1—C6—C5 | 120.26 (17) |
N11—C12—S12 | 121.46 (14) | N1—C6—H6 | 119.9 |
C12—N13—H13A | 118.9 (17) | C5—C6—H6 | 119.9 |
C12—N13—H13B | 119.0 (16) | | |
| | | |
O1—N1—C2—C3 | 179.56 (16) | Br3—C3—C4—C5 | −178.67 (14) |
C6—N1—C2—C3 | −1.0 (3) | C3—C4—C5—C6 | −0.7 (3) |
C4—C3—C2—N1 | −1.1 (3) | O1—N1—C6—C5 | −178.31 (17) |
Br3—C3—C2—N1 | 179.45 (13) | C2—N1—C6—C5 | 2.2 (3) |
C2—C3—C4—C5 | 1.9 (3) | C4—C5—C6—N1 | −1.4 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N13—H13A···O1i | 0.88 | 2.11 | 2.852 (2) | 142 |
N11—H11A···O1i | 0.88 | 2.15 | 2.881 (2) | 141 |
N13—H13B···S12ii | 0.88 | 2.47 | 3.347 (2) | 174 |
N11—H11B···S12iii | 0.88 | 2.55 | 3.401 (2) | 162 |
Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) x, −y+1/2, z−1/2; (iii) x, −y+1/2, z+1/2. |
Selected geometrical, energetic and topological parameters of complexes
investigated theoretically
The charge transfer (CT) always acts in the direction from thiourea towards
an adjacent molecule as in the crystals. (II)sp and (OQITUF)sp
indicate complexes with geometries known from the crystal state (single-point
calculations), and (II)opt and (OQITUF)optindicate complexes
with optimized geometries. topComplex | (II)sp | (II)opt | (OQITUF)sp | (OQITUF)opt |
C—Br (Å) | 1.89 (2) | 1.89 | 1.88 (4) | 1.87 |
Br···S (Å) | 3.58 (2) | 3.49 | 3.21 (2) | 3.40 |
C—Br···S (°) | 168 (2) | 172 | 177 (1) | 166 |
N—H (Å) | - | 1.00 | - | 1.00 |
H···Br (Å) | - | 2.79 | - | 2.71 |
N—H···Br (°) | - | 150 | - | 148 |
Eint (kcal mol-1) (corrected) | -1.67 | -3.34 | -3.32 | -4.44 |
Eint (kcal mol-1) (raw) | -1.71 | -3.45 | -3.43 | -4.60 |
ρ (au) S···Br | 0.0070 | 0.0156 | 0.0101 | 0.0121 |
∇2ρ (au) S···Br | 0.0219 | 0.0422 | 0.0274 | 0.0317 |
H (au) S···Br | 0.0011 | 0.0008 | 0.0010 | 0.0009 |
ρ (au) N—H···Br | - | - | 0.0084 | 0.0101 |
∇2ρ (au) N—H···Br | - | - | 0.0253 | 0.0303 |
H (au) N—H···Br | - | - | 0.0009 | 0.0010 |
CT (au) | 0.0158 | 0.0190 | 0.0273 | 0.0446 |