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The crystallization and characterization of a new polymorph of 2-thiouracil by single-crystal X-ray diffraction, Hirshfeld surface analysis and periodic density functional theory (DFT) calculations are described. The previously published polymorph (
A) crystallizes in the triclinic space group
P
, while that described herein (
B) crystallizes in the monoclinic space group
P2
1/
c. Periodic DFT calculations showed that the energies of polymorphs
A and
B, compared to the gas-phase geometry, were −108.8 and −29.4 kJ mol
−1, respectively. The two polymorphs have different intermolecular contacts that were analyzed and are discussed in detail. Significant differences in the molecular structure were found only in the bond lengths and angles involving heteroatoms that are involved in hydrogen bonds. Decomposition of the Hirshfeld fingerprint plots revealed that O
H and S
H contacts cover over 50% of the noncovalent contacts in both of the polymorphs; however, they are quite different in strength. Hydrogen bonds of the N—H
O and N—H
S types were found in polymorph
A, whereas in polymorph
B, only those of the N—H
O type are present, resulting in a different packing in the unit cell. QTAIM (quantum theory of atoms in molecules) computational analysis showed that the interaction energies for these weak-to-medium strength hydrogen bonds with a noncovalent or mixed interaction character were estimated to fall within the ranges 5.4–10.2 and 4.9–9.2 kJ mol
−1 for polymorphs
A and
B, respectively. Also, the NCI (noncovalent interaction) plots revealed weak stacking interactions. The interaction energies for these interactions were in the ranges 3.5–4.1 and 3.1–5.5 kJ mol
−1 for polymorphs
A and
B, respectively, as shown by QTAIM analysis.
Supporting information
CCDC reference: 1535305
Data collection: CrysAlis PRO (Agilent, 2014); cell refinement: CrysAlis PRO (Agilent, 2014); data reduction: CrysAlis PRO (Agilent, 2014); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: Mercury (Macrae at al., 2008) and
ORTEP-3 (Farrugia, 2012); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015).
Crystal data top
| C4H4N2OS | F(000) = 264 |
| Mr = 128.15 | Dx = 1.562 Mg m−3 |
| Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
| a = 4.1043 (2) Å | Cell parameters from 1185 reflections |
| b = 11.0458 (4) Å | θ = 5.4–32.0° |
| c = 12.0465 (4) Å | µ = 0.48 mm−1 |
| β = 93.740 (3)° | T = 298 K |
| V = 544.97 (4) Å3 | Prismatic, colourless |
| Z = 4 | 0.42 × 0.16 × 0.12 mm |
Data collection top
Agilent Xcalibur Sapphire3
diffractometer | 1367 independent reflections |
| Radiation source: Enhance (Mo) X-ray Source | 1169 reflections with I > 2σ(I) |
| Detector resolution: 16.3426 pixels mm-1 | Rint = 0.016 |
| ω scans | θmax = 28.5°, θmin = 5.0° |
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2014) | h = −4→5 |
| Tmin = 0.985, Tmax = 1.000 | k = −14→13 |
| 2639 measured reflections | l = −16→12 |
Refinement top
| Refinement on F2 | 0 restraints |
| Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
| R[F2 > 2σ(F2)] = 0.030 | H-atom parameters constrained |
| wR(F2) = 0.081 | w = 1/[σ2(Fo2) + (0.0426P)2 + 0.0147P]
where P = (Fo2 + 2Fc2)/3 |
| S = 1.05 | (Δ/σ)max = 0.001 |
| 1367 reflections | Δρmax = 0.24 e Å−3 |
| 73 parameters | Δρmin = −0.24 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 | |
| C2 | 0.1455 (3) | 0.15324 (11) | 0.72131 (10) | 0.0273 (3) | |
| C4 | 0.2895 (3) | 0.15650 (11) | 0.52702 (10) | 0.0305 (3) | |
| C5 | 0.4587 (3) | 0.26792 (12) | 0.54972 (11) | 0.0345 (3) | |
| H5 | 0.5709 | 0.3058 | 0.4948 | 0.041* | |
| C6 | 0.4529 (3) | 0.31692 (12) | 0.65168 (10) | 0.0335 (3) | |
| H6 | 0.5600 | 0.3899 | 0.6664 | 0.040* | |
| N1 | 0.2937 (3) | 0.26216 (9) | 0.73413 (8) | 0.0317 (3) | |
| H1 | 0.2873 | 0.2986 | 0.7971 | 0.038* | |
| N3 | 0.1503 (3) | 0.10482 (9) | 0.61723 (8) | 0.0297 (2) | |
| H3 | 0.0578 | 0.0355 | 0.6067 | 0.036* | |
| O1 | 0.2582 (3) | 0.10499 (9) | 0.43524 (8) | 0.0415 (3) | |
| S1 | −0.03220 (9) | 0.08280 (3) | 0.82379 (3) | 0.03738 (14) | |
Atomic displacement parameters (Å2) top| | U11 | U22 | U33 | U12 | U13 | U23 |
| C2 | 0.0299 (6) | 0.0275 (6) | 0.0243 (6) | 0.0053 (5) | 0.0013 (4) | −0.0009 (4) |
| C4 | 0.0403 (7) | 0.0276 (6) | 0.0236 (6) | 0.0035 (6) | 0.0031 (5) | 0.0016 (4) |
| C5 | 0.0416 (8) | 0.0322 (7) | 0.0301 (6) | −0.0035 (6) | 0.0053 (5) | 0.0031 (5) |
| C6 | 0.0381 (7) | 0.0261 (6) | 0.0361 (7) | −0.0027 (6) | 0.0005 (5) | −0.0005 (5) |
| N1 | 0.0420 (6) | 0.0279 (5) | 0.0254 (5) | 0.0018 (5) | 0.0021 (4) | −0.0056 (4) |
| N3 | 0.0401 (6) | 0.0251 (5) | 0.0240 (5) | −0.0014 (5) | 0.0035 (4) | −0.0017 (4) |
| O1 | 0.0680 (7) | 0.0342 (5) | 0.0226 (5) | −0.0058 (5) | 0.0066 (4) | −0.0014 (3) |
| S1 | 0.0456 (2) | 0.0394 (2) | 0.0283 (2) | −0.00086 (15) | 0.01149 (15) | 0.00031 (12) |
Geometric parameters (Å, º) top
| C2—N1 | 1.3524 (16) | C5—C6 | 1.3439 (18) |
| C2—N3 | 1.3645 (15) | C5—H5 | 0.9300 |
| C2—S1 | 1.6670 (12) | C6—N1 | 1.3654 (16) |
| C4—O1 | 1.2427 (15) | C6—H6 | 0.9300 |
| C4—N3 | 1.3836 (16) | N1—H1 | 0.8600 |
| C4—C5 | 1.4307 (18) | N3—H3 | 0.8600 |
| | | |
| N1—C2—N3 | 114.86 (11) | C5—C6—N1 | 121.62 (12) |
| N1—C2—S1 | 123.09 (9) | C5—C6—H6 | 119.2 |
| N3—C2—S1 | 122.06 (10) | N1—C6—H6 | 119.2 |
| O1—C4—N3 | 119.06 (12) | C2—N1—C6 | 122.96 (11) |
| O1—C4—C5 | 125.78 (12) | C2—N1—H1 | 118.5 |
| N3—C4—C5 | 115.15 (11) | C6—N1—H1 | 118.5 |
| C6—C5—C4 | 118.93 (12) | C2—N3—C4 | 126.26 (11) |
| C6—C5—H5 | 120.5 | C2—N3—H3 | 116.9 |
| C4—C5—H5 | 120.5 | C4—N3—H3 | 116.9 |
| | | |
| O1—C4—C5—C6 | 175.47 (14) | C5—C6—N1—C2 | 3.3 (2) |
| N3—C4—C5—C6 | −4.11 (18) | N1—C2—N3—C4 | −0.03 (19) |
| C4—C5—C6—N1 | 0.9 (2) | S1—C2—N3—C4 | 179.64 (10) |
| N3—C2—N1—C6 | −3.66 (18) | O1—C4—N3—C2 | −175.79 (11) |
| S1—C2—N1—C6 | 176.68 (10) | C5—C4—N3—C2 | 3.8 (2) |
Hydrogen-bond geometry (Å, º) top
| D—H···A | D—H | H···A | D···A | D—H···A |
| N1—H1···O1i | 0.86 | 1.99 | 2.8443 (14) | 175 |
| N3—H3···O1ii | 0.86 | 2.06 | 2.9057 (15) | 166 |
| C5—H5···S1iii | 0.86 | 2.97 | 3.9031 (14) | 176 |
| C6—H6···S1iv | 0.86 | 2.88 | 3.7780 (14) | 163 |
| Symmetry codes: (i) x, −y+1/2, z+1/2; (ii) −x, −y+1, −z; (iii) x+1, −y+1/2, z−1/2; (iv) −x, y−1/2, −z+1/2. |
2 Bond lengths (Å) and angles (°) in the crystal structures of
2-thiouracil polymorphs A and B
ALT are data at 100 K (Jarzembska et al., 2012) and
were
obtained after transferable aspherical atom model (TAAM) refinement,
ART are room-temperature data (Tiekink, 1989) using standard
independent atom model (IAM) refinement and B is IAM refinement. top| Bond lengths | Bond angles | | | | | | |
| ALT | ART | B | | ALT | ART | B |
| C2—N1 | 1.3521 (4) | 1.338 (4) | 1.3524 (16) | N1—C2—N3 | 116.29 (3) | 116.0 (3) | 114.85 (11) |
| C2—N3 | 1.3558 (4) | 1.357 (4) | 1.3644 (15) | N1—C2—S | 121.93 (3) | 122.2 (2) | 123.09 (9) |
| C2—S | 1.6839 (4) | 1.683 (3) | 1.6670 (13) | N3—C2—S | 121.78 (2) | 121.8 (2) | 122.06 (9) |
| C4—O | 1.2318 (4) | 1.227 (4) | 1.2426 (15) | O—C4—N3 | 119.44 (4) | 119.2 (3) | 119.06 (11) |
| C4—N3 | 1.3951 (4) | 1.389 (4) | 1.3837 (16) | O—C4—C5 | 125.05 (4) | 125.4 (3) | 125.79 (12) |
| C4—C5 | 1.4443 (5) | 1.432 (5) | 1.4305 (18) | N3—C4—C5 | 115.51 (3) | 115.4 (3) | 115.15 (11) |
| C5—C6 | 1.3523 (5) | 1.338 (5) | 1.3439 (18) | C6—C5—C4 | 118.58 (4) | 119.2 (3) | 118.94 (12) |
| C6—N1 | 1.3707 (4) | 1.373 (4) | 1.3653 (16) | C5—C6—N1 | 121.57 (3) | 121.2 (3) | 121.62 (12) |
| | | | C2—N1—C6 | 122.64 (3) | 122.9 (3) | 122.96 (10) |
| | | | C2—N3—C4 | 125.32 (3) | 125.2 (3) | 126.26 (11) |
Hydrogen-bond geometry (Å, °) for N—H···O, N—H···S and C—H···O
interactions for polymorphs A and B (first row, at 100 K;
Jarzembska et al., 2012) (the data were obtained after TAAM
refinement);
second row (at
room temperature) (Tiekink, 1989).
Contact geometry is given for C—H···S interactions. top | D—H | H···A | D···A | D–H···A |
| Polymorph A | | | | |
| N1—H1···S1i | 1.029 (1) 0.90 | 2.292 (2) 2.44 | 3.2991 (3) 3.315 (3) | 165.7 (2) 164 |
| N3—H3···O1ii | 1.029 (1) 0.90 | 1.795 (1) 1.94 | 2.8202 (4) 2.835 (4) | 173.6 (2) 175 |
| C5—H5···O1iii | 1.083 (1) 0.83 | 2.263 (2) 2.54 | 3.3377 (4) 3.362 (4) | 171.4 (1) 164 |
| C6—H6···S1iv | 1.082 (1) 0.94 | 2.771 (4) 2.91 | 3.6363 (3) 3.663 (3) | 136.8 (3) 138 |
| | | | |
| Polymorph B | | | | |
| N1—H1···O1v | 0.86 | 1.99 | 2.8443 (14) | 175 |
| N3—H3···O1vi | 0.86 | 2.06 | 2.9057 (15) | 166 |
| C5—H5···S1vii | 0.86 | 2.97b | 3.9031 (14) | 176 |
| C6—H6···S1viii | 0.86 | 2.88a | 3.7780 (14) | 163 |
Symmetry codes: (i) -x, -y, -z;
(ii) -x+1, -y+1, -z+1;
(iii) -x+2, -y, -z+1;
(iv) x+1, y-1, z;
(v) x, -y+1/2, z+1/2;
(vi) -x, -y+1, -z;
(vii) x+1, -y+1/2, z-1/2;
(viii) -x, y-1/2, -z+1/2.
Notes: (a) the value is shorter than the sum of the van der Waals radii
by only 0.12 Å; (b) the value is shorter than the sum of the van der
Waals radii by only 0.03 Å. Contact radii are those given in Bondi
(1964). |
4 QTAIM descriptorsa of the selected bond path (3, -1) critical points
(BCP) for intermolecular interactions in the crystal structures of polymorphs
Ab and Bc. All values are in atomic units (a.u.) top| BCP | | ρ(r) | \nabla2ρ(r) | G(r) | V(r) | H(r) | |V(r)|/G(r) | Symmetry code |
| Polymorph A | | | | | | | | |
| A1 | H1···S1 | 0.0256 | 0.0493 | 0.0064 | -0.0005 | 0.0059 | 0.0781 | -x, -y, -z |
| A2 | H3···O1 | 0.0368 | 0.1109 | 0.0117 | 0.0043 | 0.0160 | 0.3675 | -x+1, -y+1, -z+1 |
| A3 | H5···O1 | 0.0130 | 0.0476 | 0.0021 | 0.0078 | 0.0098 | 3.7143 | -x+2, -y, -z+1 |
| A4 | H6···S1 | 0.0090 | 0.0254 | 0.0011 | 0.0041 | 0.0052 | 3.7273 | x+1, y-1, z |
| A5 | N1···S1 | 0.0055 | 0.0164 | 0.0005 | 0.0031 | 0.0036 | 6.2000 | x+1, y, z |
| A6 | N3···S1 | 0.0060 | 0.0159 | 0.0006 | 0.0028 | 0.0034 | 4.6667 | x+1, y, z |
| A7[ | C5···C2 | 0.0070 | 0.0168 | 0.0007 | 0.0027 | 0.0035 | 3.8571 | x+1, y, z |
| Polymorph B | | | | | | | | |
| B1 | H1···O1 | 0.0352 | 0.1055 | 0.0109 | 0.0047 | 0.0155 | 0.3133 | x, -y+1/2, z+1/2 |
| B2 | H3···O1 | 0.0302 | 0.0952 | 0.0084 | 0.0070 | 0.0154 | 0.8333 | -x, -y+1, -z |
| B3 | H5···S1 | 0.0080 | 0.0222 | 0.0009 | 0.0037 | 0.0046 | 4.1111 | x+1, -y+1/2, z-1/2 |
| B4 | H6···S1 | 0.0097 | 0.0266 | 0.0013 | 0.0041 | 0.0054 | 3.1538 | -x, y-1/2, -z+1/2 |
| B5 | S1···C5 | 0.0055 | 0.0152 | 0.0005 | 0.0028 | 0.0033 | 5.6000 | x-1, -y+1/2, z+1/2 |
| B6 | S1···C6 | 0.0074 | 0.0232 | 0.0008 | 0.0042 | 0.0050 | 5.2500 | x-1, y, z |
| B7 | N1···S1 | 0.0070 | 0.0172 | 0.0007 | 0.0028 | 0.0035 | 4.0000 | x-1, y, z |
| B8 | C6···N3 | 0.0054 | 0.0136 | 0.0005 | 0.0024 | 0.0029 | 4.8000 | x-1, y, z |
| Notes: (a) ρ(r) is the electron density,
\nabla2ρ(r) is the Laplacian of the electron density,
G(r) is the kinetic energy density,
V(r) is the potential energy density,
H(r) is the energy density and
|V(r)|/G(r) is the ratio of the potential energy
to the kinetic energy density. (b)
BCP A1–A4 in Fig. 7(a and BCP A5–A7 in
Fig. 8(a). (c) BCP B1–B4 in Fig. 7(b) and
BCP B5–B8 in Fig. 8(b). All values are in atomic units
(a.u.). |
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, while that described herein (B) crystallizes in the monoclinic space group P21/c. Periodic DFT calculations showed that the energies of polymorphs A and B, compared to the gas-phase geometry, were −108.8 and −29.4 kJ mol−1, respectively. The two polymorphs have different intermolecular contacts that were analyzed and are discussed in detail. Significant differences in the molecular structure were found only in the bond lengths and angles involving heteroatoms that are involved in hydrogen bonds. Decomposition of the Hirshfeld fingerprint plots revealed that O
