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The topological features of the charge densities, ρ(
r), of three bioactive molecules, 2-thiouracil [2,3-dihydro-2-thioxopyrimidin-4(1
H)-one], cytosine [4-aminopyrimidin-2(1
H)-one] monohydrate and salicylic acid (2-hydroxybenzoic acid), have been determined from high-resolution X-ray diffraction data at 90 K. The corresponding results are compared with the periodic theoretical calculations, based on theoretical structure factors, performed using DFT (density-functional theory) at the B3LYP/6-31G** level. The molecules pack in the crystal lattices
via weak intermolecular interactions as well as strong hydrogen bonds. All the chemical bonds, including the intra- and intermolecular interactions in all three compounds, have been quantitatively described by topological analysis based on Bader's quantum theory of `
Atoms In Molecules'. The roles of interactions such as C—H
O, C—H
S, C—H
π and π
π have been investigated quantitatively in the presence of strong hydrogen bonds such as O—H
O, N—H
O and N—H
S, based on the criteria proposed by Koch and Popelier to characterize hydrogen bonds and van der Waals interactions. The features of weak intermolecular interactions, such as S
S in 2-thiouracil, the hydrogen bonds generated from the water molecule in cytosine monohydrate and the formation of the dimer
via strong hydrogen bonds in salicylic acid, are highlighted on a quantum basis. Three-dimensional electrostatic potentials over the molecular surfaces emphasize the preferable binding sites in the structure and the interaction features of the atoms in the molecules, which are crucial for drug–receptor recognition.
Supporting information
CCDC references: 276206; 276207; 276208
For all compounds, data collection: SMART (Bruker, 2004); cell refinement: SMART; data reduction: SAINT (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: Koritsanszky et al., (2003); molecular graphics: Koritsanszky et al., (2003); software used to prepare material for publication: Koritsanszky et al., (2003).
(2-thiouracil) 2-thioxo-2,3-dihydropyrimidin-4(1
H)-one
top
Crystal data top
C4H4N2OS | Z = 2 |
Mr = 128.16 | F(000) = 132 |
Triclinic, P1 | Dx = 1.661 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 4.2427 (4) Å | Cell parameters from 4983 reflections |
b = 5.9648 (5) Å | θ = 3.6–51.6° |
c = 10.5801 (10) Å | µ = 0.51 mm−1 |
α = 105.736 (5)° | T = 90 K |
β = 94.912 (5)° | Block, colorless |
γ = 91.927 (4)° | 0.39 × 0.19 × 0.12 mm |
V = 256.32 (4) Å3 | |
Data collection top
Bruker SMART APEX CCD area detector diffractometer | 4983 independent reflections |
Radiation source: fine-focus sealed tube | 4697 reflections with > 3σ(I) |
Graphite monochromator | Rint = 0.031 |
ϕ & ω scans | θmax = 51.6°, θmin = 3.6° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = 0→9 |
Tmin = 0.831, Tmax = 0.943 | k = −13→13 |
4983 measured reflections | l = −23→22 |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.014 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.017 | H-atom parameters not refined |
S = 1.93 | w2 = 1/[s2(Fo2)] |
4697 reflections | (Δ/σ)max < 0.001 |
229 parameters | Δρmax = 0.32 e Å−3 |
0 restraints | Δρmin = −0.20 e Å−3 |
Crystal data top
C4H4N2OS | γ = 91.927 (4)° |
Mr = 128.16 | V = 256.32 (4) Å3 |
Triclinic, P1 | Z = 2 |
a = 4.2427 (4) Å | Mo Kα radiation |
b = 5.9648 (5) Å | µ = 0.51 mm−1 |
c = 10.5801 (10) Å | T = 90 K |
α = 105.736 (5)° | 0.39 × 0.19 × 0.12 mm |
β = 94.912 (5)° | |
Data collection top
Bruker SMART APEX CCD area detector diffractometer | 4983 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 4697 reflections with > 3σ(I) |
Tmin = 0.831, Tmax = 0.943 | Rint = 0.031 |
4983 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.014 | 0 restraints |
wR(F2) = 0.017 | H-atom parameters not refined |
S = 1.93 | Δρmax = 0.32 e Å−3 |
4697 reflections | Δρmin = −0.20 e Å−3 |
229 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | Occ. (<1) |
S(2) | 0.45628 (1) | 0.64884 (1) | 0.37117 (1) | 0.012 | |
O(4) | −0.24292 (6) | 0.72104 (4) | −0.01050 (2) | 0.016 | |
N(1) | 0.14216 (4) | 1.02089 (3) | 0.35761 (2) | 0.011 | |
N(3) | 0.08327 (4) | 0.71272 (3) | 0.16998 (2) | 0.011 | |
C(2) | 0.21656 (4) | 0.80251 (3) | 0.29574 (2) | 0.010 | |
C(4) | −0.13325 (4) | 0.82225 (3) | 0.10352 (2) | 0.012 | |
C(6) | −0.06598 (4) | 1.14382 (3) | 0.30023 (2) | 0.012 | |
C(5) | −0.21041 (5) | 1.05168 (3) | 0.17684 (2) | 0.013 | |
H(6) | −0.08610 | 1.31703 | 0.36384 | 0.025 (2) | |
H(5) | −0.37972 | 1.15188 | 0.13684 | 0.030 (3) | |
H(1) | 0.25733 | 1.10703 | 0.44842 | 0.016 (2) | |
H(3) | 0.13712 | 0.54835 | 0.11787 | 0.019 (2) | |
DUM0 | 0.00000 | 0.00000 | 0.00000 | 0.000 | 0.0000 |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
S(2) | 0.01332 (2) | 0.01045 (2) | 0.01132 (2) | 0.00233 (1) | −0.00329 (1) | 0.00216 (1) |
O(4) | 0.01966 (9) | 0.01683 (8) | 0.00980 (7) | 0.00640 (6) | −0.00425 (6) | 0.00035 (6) |
N(1) | 0.01189 (6) | 0.00996 (5) | 0.00984 (5) | 0.00190 (4) | −0.00153 (4) | 0.00093 (4) |
N(3) | 0.01240 (6) | 0.01115 (5) | 0.00867 (5) | 0.00316 (4) | −0.00155 (4) | 0.00109 (4) |
C(2) | 0.01018 (6) | 0.01001 (5) | 0.00891 (5) | 0.00149 (4) | −0.00099 (4) | 0.00187 (4) |
C(4) | 0.01273 (6) | 0.01243 (6) | 0.00877 (5) | 0.00309 (4) | −0.00129 (4) | 0.00196 (5) |
C(6) | 0.01278 (6) | 0.01019 (5) | 0.01167 (6) | 0.00238 (4) | −0.00070 (4) | 0.00180 (5) |
C(5) | 0.01354 (7) | 0.01200 (6) | 0.01143 (6) | 0.00349 (4) | −0.00124 (4) | 0.00297 (5) |
Geometric parameters (Å, º) top
S(2)—C(2) | 1.6828 (2) | N(3)—C(4) | 1.3942 (2) |
O(4)—C(4) | 1.2354 (3) | N(3)—H(3) | 1.0300 (2) |
N(1)—C(2) | 1.3511 (2) | C(4)—C(5) | 1.4420 (3) |
N(1)—C(6) | 1.3709 (2) | C(6)—C(5) | 1.3538 (3) |
N(1)—H(1) | 1.0300 (2) | C(6)—H(6) | 1.0800 (2) |
N(3)—C(2) | 1.3570 (2) | C(5)—H(5) | 1.0800 (2) |
| | | |
C(2)—N(1)—C(6) | 122.692 (16) | O(4)—C(4)—N(3) | 119.512 (19) |
C(2)—N(1)—H(1) | 120.009 (16) | O(4)—C(4)—C(5) | 125.049 (18) |
C(6)—N(1)—H(1) | 117.100 (15) | N(3)—C(4)—C(5) | 115.439 (16) |
C(2)—N(3)—C(4) | 125.400 (16) | N(1)—C(6)—C(5) | 121.437 (16) |
C(2)—N(3)—H(3) | 119.129 (15) | N(1)—C(6)—H(6) | 111.386 (16) |
C(4)—N(3)—H(3) | 115.445 (15) | C(5)—C(6)—H(6) | 127.130 (17) |
S(2)—C(2)—N(1) | 121.904 (13) | C(4)—C(5)—C(6) | 118.709 (16) |
S(2)—C(2)—N(3) | 121.868 (13) | C(4)—C(5)—H(5) | 122.272 (17) |
N(1)—C(2)—N(3) | 116.222 (15) | C(6)—C(5)—H(5) | 119.018 (17) |
| | | |
C(6)—N(1)—C(2)—S(2) | −176.4 (1) | H(3)—N(3)—C(2)—S(2) | −2.5 (1) |
C(6)—N(1)—C(2)—N(3) | 2.7 (1) | H(3)—N(3)—C(2)—N(1) | 178.5 (1) |
C(2)—N(1)—C(6)—C(5) | 0.1 (1) | H(3)—N(3)—C(4)—O(4) | −0.6 (1) |
C(2)—N(1)—C(6)—H(6) | −177.6 (1) | H(3)—N(3)—C(4)—C(5) | 179.6 (1) |
H(1)—N(1)—C(2)—S(2) | 8.9 (1) | O(4)—C(4)—C(5)—C(6) | −178.4 (1) |
H(1)—N(1)—C(2)—N(3) | −172.1 (1) | O(4)—C(4)—C(5)—H(5) | 1.8 (1) |
H(1)—N(1)—C(6)—C(5) | 174.9 (1) | N(3)—C(4)—C(5)—C(6) | 1.4 (1) |
H(1)—N(1)—C(6)—H(6) | −2.7 (1) | N(3)—C(4)—C(5)—H(5) | −178.3 (1) |
C(4)—N(3)—C(2)—S(2) | 175.6 (1) | N(1)—C(6)—C(5)—C(4) | −2.2 (1) |
C(2)—N(3)—C(4)—O(4) | −178.7 (1) | N(1)—C(6)—C(5)—H(5) | 177.6 (1) |
C(4)—N(3)—C(2)—N(1) | −3.4 (1) | H(6)—C(6)—C(5)—C(4) | 175.1 (1) |
C(2)—N(3)—C(4)—C(5) | 1.4 (1) | H(6)—C(6)—C(5)—H(5) | −5.1 (1) |
Crystal data top
C4H5N3O·H2O | F(000) = 272 |
Mr = 129.13 | Dx = 1.530 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 5948 reflections |
a = 7.7161 (8) Å | θ = 2.7–50.3° |
b = 9.8337 (10) Å | µ = 0.12 mm−1 |
c = 7.5131 (8) Å | T = 90 K |
β = 100.523 (5)° | Block, colorless |
V = 560.49 (10) Å3 | 0.32 × 0.22 × 0.03 mm |
Z = 4 | |
Data collection top
Bruker SMART APEX CCD area detector diffractometer | 5948 independent reflections |
Radiation source: fine-focus sealed tube | 4792 reflections with > 3σ(I) |
Graphite monochromator | Rint = 0.040 |
ϕ & ω scans | θmax = 50.3°, θmin = 2.7° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −16→16 |
Tmin = 0.961, Tmax = 0.996 | k = 0→21 |
5948 measured reflections | l = 0→16 |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.017 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.015 | H-atom parameters not refined |
S = 1.96 | w2 = 1/[s2(Fo2)] |
4792 reflections | (Δ/σ)max < 0.001 |
337 parameters | Δρmax = 0.27 e Å−3 |
0 restraints | Δρmin = −0.17 e Å−3 |
Crystal data top
C4H5N3O·H2O | V = 560.49 (10) Å3 |
Mr = 129.13 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 7.7161 (8) Å | µ = 0.12 mm−1 |
b = 9.8337 (10) Å | T = 90 K |
c = 7.5131 (8) Å | 0.32 × 0.22 × 0.03 mm |
β = 100.523 (5)° | |
Data collection top
Bruker SMART APEX CCD area detector diffractometer | 5948 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 4792 reflections with > 3σ(I) |
Tmin = 0.961, Tmax = 0.996 | Rint = 0.040 |
5948 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.017 | 0 restraints |
wR(F2) = 0.015 | H-atom parameters not refined |
S = 1.96 | Δρmax = 0.27 e Å−3 |
4792 reflections | Δρmin = −0.17 e Å−3 |
337 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | Occ. (<1) |
O(1) | 0.35423 (3) | 0.20877 (2) | 0.47471 (3) | 0.014 | |
O(2) | 0.14835 (3) | 0.12075 (2) | 0.71691 (3) | 0.012 | |
N(1) | −0.08534 (2) | 0.00432 (2) | 0.78140 (2) | 0.010 | |
N(3) | −0.07914 (2) | 0.24444 (2) | 0.78909 (3) | 0.010 | |
N(4) | −0.31101 (3) | 0.36205 (2) | 0.86904 (3) | 0.013 | |
C(2) | −0.00196 (2) | 0.12502 (2) | 0.76001 (2) | 0.009 | |
C(4) | −0.23597 (2) | 0.24325 (2) | 0.84319 (2) | 0.009 | |
C(5) | −0.32210 (2) | 0.11871 (2) | 0.87386 (3) | 0.011 | |
C(6) | −0.24197 (2) | 0.00145 (2) | 0.83951 (2) | 0.011 | |
H(1) | −0.01911 | −0.08184 | 0.75113 | 0.012 (2) | |
H(1A) | 0.27966 | 0.25771 | 0.37788 | 0.019 (2) | |
H(1B) | 0.27054 | 0.17438 | 0.54462 | 0.022 (2) | |
H(4A) | −0.25000 | 0.44671 | 0.83268 | 0.018 (2) | |
H(4B) | −0.43057 | 0.35719 | 0.90660 | 0.016 (2) | |
H(5) | −0.44472 | 0.12010 | 0.92387 | 0.025 (2) | |
H(6) | −0.29795 | −0.09781 | 0.85832 | 0.024 (2) | |
DUM0 | 0.00000 | 0.00000 | 0.00000 | 0.000 | 0.0000 |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O(1) | 0.01137 (6) | 0.01433 (7) | 0.01657 (8) | 0.00056 (5) | 0.00552 (6) | 0.00132 (5) |
O(2) | 0.01007 (6) | 0.01026 (7) | 0.01724 (8) | −0.00009 (5) | 0.00674 (6) | −0.00016 (5) |
N(1) | 0.01008 (6) | 0.00669 (6) | 0.01390 (7) | −0.00033 (4) | 0.00441 (5) | −0.00016 (4) |
N(3) | 0.00906 (6) | 0.00691 (6) | 0.01323 (7) | −0.00036 (4) | 0.00434 (5) | −0.00018 (4) |
N(4) | 0.01145 (6) | 0.00802 (6) | 0.01874 (8) | 0.00080 (5) | 0.00641 (5) | −0.00044 (5) |
C(2) | 0.00850 (6) | 0.00734 (6) | 0.01150 (7) | −0.00026 (4) | 0.00377 (4) | 0.00002 (4) |
C(4) | 0.00899 (6) | 0.00715 (6) | 0.01200 (7) | −0.00006 (4) | 0.00374 (5) | −0.00009 (4) |
C(5) | 0.01042 (6) | 0.00832 (6) | 0.01573 (7) | −0.00063 (5) | 0.00599 (5) | 0.00022 (5) |
C(6) | 0.01081 (7) | 0.00741 (6) | 0.01419 (8) | −0.00109 (5) | 0.00476 (5) | 0.00035 (4) |
Geometric parameters (Å, º) top
O(1)—H(1A) | 0.9690 (2) | N(4)—C(4) | 1.3337 (2) |
O(1)—H(1B) | 0.9650 (2) | N(4)—H(4A) | 1.0180 (2) |
O(2)—C(2) | 1.2605 (2) | N(4)—H(4B) | 1.0140 (2) |
N(1)—C(2) | 1.3734 (2) | C(4)—C(5) | 1.4320 (2) |
N(1)—C(6) | 1.3583 (2) | C(5)—C(6) | 1.3553 (2) |
N(1)—H(1) | 1.0360 (2) | C(5)—H(5) | 1.0800 (2) |
N(3)—C(2) | 1.3524 (2) | C(6)—H(6) | 1.0870 (2) |
N(3)—C(4) | 1.3451 (2) | | |
| | | |
H(1A)—O(1)—H(1B) | 102.595 (19) | N(1)—C(2)—N(3) | 120.129 (16) |
C(2)—N(1)—C(6) | 121.263 (16) | N(3)—C(4)—N(4) | 118.349 (17) |
C(2)—N(1)—H(1) | 114.880 (16) | N(3)—C(4)—C(5) | 121.711 (16) |
C(6)—N(1)—H(1) | 123.854 (16) | N(4)—C(4)—C(5) | 119.939 (17) |
C(2)—N(3)—C(4) | 119.229 (16) | C(4)—C(5)—C(6) | 117.113 (16) |
C(4)—N(4)—H(4A) | 116.292 (17) | C(4)—C(5)—H(5) | 120.463 (16) |
C(4)—N(4)—H(4B) | 116.138 (17) | C(6)—C(5)—H(5) | 122.420 (17) |
H(4A)—N(4)—H(4B) | 127.015 (18) | N(1)—C(6)—C(5) | 120.473 (17) |
O(2)—C(2)—N(1) | 118.290 (17) | N(1)—C(6)—H(6) | 117.292 (16) |
O(2)—C(2)—N(3) | 121.563 (17) | C(5)—C(6)—H(6) | 122.231 (17) |
| | | |
C(6)—N(1)—C(2)—O(2) | 175.5 (1) | H(4A)—N(4)—C(4)—N(3) | 6.4 (1) |
C(6)—N(1)—C(2)—N(3) | −3.0 (1) | H(4A)—N(4)—C(4)—C(5) | −173.9 (1) |
C(2)—N(1)—C(6)—C(5) | 1.6 (1) | H(4B)—N(4)—C(4)—N(3) | 178.5 (1) |
C(2)—N(1)—C(6)—H(6) | −177.7 (1) | H(4B)—N(4)—C(4)—C(5) | −1.8 (1) |
H(1)—N(1)—C(2)—O(2) | −4.0 (1) | N(3)—C(4)—C(5)—C(6) | −2.4 (1) |
H(1)—N(1)—C(2)—N(3) | 177.6 (1) | N(3)—C(4)—C(5)—H(5) | 176.8 (1) |
H(1)—N(1)—C(6)—C(5) | −179.0 (1) | N(4)—C(4)—C(5)—C(6) | 177.9 (1) |
H(1)—N(1)—C(6)—H(6) | 1.7 (1) | N(4)—C(4)—C(5)—H(5) | −2.9 (1) |
C(4)—N(3)—C(2)—O(2) | −176.9 (1) | C(4)—C(5)—C(6)—N(1) | 1.0 (1) |
C(4)—N(3)—C(2)—N(1) | 1.6 (1) | C(4)—C(5)—C(6)—H(6) | −179.7 (1) |
C(2)—N(3)—C(4)—N(4) | −179.2 (1) | H(5)—C(5)—C(6)—N(1) | −178.2 (1) |
C(2)—N(3)—C(4)—C(5) | 1.1 (1) | H(5)—C(5)—C(6)—H(6) | 1.0 (1) |
(salicylicacid) 2-hydroxybenzoic acid
top
Crystal data top
C7H6O3 | F(000) = 288 |
Mr = 138.12 | Dx = 1.495 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 31354 reflections |
a = 4.8818 (2) Å | θ = 2.6–50.3° |
b = 11.2009 (5) Å | µ = 0.12 mm−1 |
c = 11.2335 (5) Å | T = 90 K |
β = 92.621 (2)° | Prism, colorless |
V = 613.61 (5) Å3 | 0.25 × 0.22 × 0.2 mm |
Z = 4 | |
Data collection top
Bruker SMART APEX CCD area detector diffractometer | 6440 independent reflections |
Radiation source: fine-focus sealed tube | 5439 reflections with > 3σ(I) |
Graphite monochromator | Rint = 0.029 |
ϕ & ω scans | θmax = 50.3°, θmin = 2.6° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −10→10 |
Tmin = 0.886, Tmax = 0.977 | k = −23→24 |
31354 measured reflections | l = −24→24 |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.020 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.020 | H-atom parameters not refined |
S = 1.96 | w2 = q/[s2(Fo2) + (0.00 P)2 + 0.00 P + 0.00 + 0.00 sin(th)]
where P = (0.3333 Fo2 + 0.6667 Fc2)
q = 1.0 |
5439 reflections | (Δ/σ)max < 0.001 |
276 parameters | Δρmax = 0.27 e Å−3 |
0 restraints | Δρmin = −0.26 e Å−3 |
Crystal data top
C7H6O3 | V = 613.61 (5) Å3 |
Mr = 138.12 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 4.8818 (2) Å | µ = 0.12 mm−1 |
b = 11.2009 (5) Å | T = 90 K |
c = 11.2335 (5) Å | 0.25 × 0.22 × 0.2 mm |
β = 92.621 (2)° | |
Data collection top
Bruker SMART APEX CCD area detector diffractometer | 6440 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 5439 reflections with > 3σ(I) |
Tmin = 0.886, Tmax = 0.977 | Rint = 0.029 |
31354 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.020 | 0 restraints |
wR(F2) = 0.020 | H-atom parameters not refined |
S = 1.96 | Δρmax = 0.27 e Å−3 |
5439 reflections | Δρmin = −0.26 e Å−3 |
276 parameters | |
Special details top
Experimental. Crystal to Detector distance was 6.03 cm, ω range is 0.3 ° and exposure time was 20 s, 40 s and 80 s in three batches respectively. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | Occ. (<1) |
O(1) | 0.83999 (4) | 0.13928 (2) | −0.05215 (2) | 0.014 | |
O(3) | 0.39275 (5) | 0.06756 (2) | 0.24999 (2) | 0.016 | |
O(2) | 0.76762 (4) | 0.01483 (2) | 0.09897 (2) | 0.013 | |
C(1) | 0.50516 (3) | 0.19284 (2) | 0.08238 (2) | 0.010 | |
C(3) | 0.15873 (4) | 0.24924 (2) | 0.22021 (2) | 0.014 | |
C(6) | 0.45370 (4) | 0.29928 (2) | 0.01908 (2) | 0.013 | |
C(2) | 0.35609 (4) | 0.16777 (2) | 0.18410 (2) | 0.012 | |
C(5) | 0.25886 (4) | 0.37961 (2) | 0.05541 (2) | 0.015 | |
C(4) | 0.11104 (4) | 0.35399 (2) | 0.15648 (2) | 0.015 | |
C(7) | 0.71398 (3) | 0.10908 (2) | 0.04397 (2) | 0.010 | |
H(6) | 0.57311 | 0.31697 | −0.05713 | 0.027 (2) | |
H(3) | 0.04064 | 0.22880 | 0.29617 | 0.030 (2) | |
H(5) | 0.21541 | 0.45737 | 0.00156 | 0.036 (2) | |
H(4) | −0.04312 | 0.41534 | 0.18430 | 0.036 (2) | |
H(2) | 0.54071 | 0.02176 | 0.21898 | 0.017 (2) | |
H(1) | 0.98372 | 0.07598 | −0.07049 | 0.013 (2) | |
DUM0 | 0.00000 | 0.00000 | 0.00000 | 0.000 | 0.0000 |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O(1) | 0.01430 (7) | 0.01378 (6) | 0.01421 (6) | 0.00347 (6) | 0.00571 (5) | 0.00264 (6) |
O(3) | 0.01832 (8) | 0.01545 (7) | 0.01425 (7) | 0.00385 (6) | 0.00600 (6) | 0.00245 (6) |
O(2) | 0.01341 (6) | 0.01152 (5) | 0.01396 (6) | 0.00309 (5) | 0.00397 (5) | 0.00218 (5) |
C(1) | 0.00986 (5) | 0.01006 (5) | 0.01145 (6) | 0.00119 (5) | 0.00128 (4) | −0.00038 (5) |
C(3) | 0.01351 (7) | 0.01583 (7) | 0.01403 (6) | 0.00326 (6) | 0.00273 (5) | −0.00293 (6) |
C(6) | 0.01237 (6) | 0.01147 (6) | 0.01546 (6) | 0.00205 (5) | 0.00152 (5) | 0.00136 (5) |
C(2) | 0.01145 (6) | 0.01200 (6) | 0.01141 (6) | 0.00152 (5) | 0.00202 (5) | −0.00112 (5) |
C(5) | 0.01407 (7) | 0.01204 (6) | 0.01979 (8) | 0.00347 (5) | 0.00050 (6) | −0.00003 (6) |
C(4) | 0.01348 (7) | 0.01417 (7) | 0.01786 (7) | 0.00388 (6) | 0.00044 (6) | −0.00383 (6) |
C(7) | 0.01001 (5) | 0.01005 (5) | 0.01117 (5) | 0.00092 (5) | 0.00191 (4) | 0.00023 (5) |
Geometric parameters (Å, º) top
O(1)—C(7) | 1.3113 (2) | C(3)—C(2) | 1.4005 (3) |
O(1)—H(1) | 1.0250 (2) | C(3)—C(4) | 1.3886 (3) |
O(3)—C(2) | 1.3519 (3) | C(3)—H(3) | 1.0760 (2) |
O(3)—H(2) | 0.9640 (2) | C(6)—C(5) | 1.3843 (3) |
O(2)—C(7) | 1.2450 (2) | C(6)—H(6) | 1.0760 (2) |
C(1)—C(6) | 1.4049 (3) | C(5)—C(4) | 1.4025 (3) |
C(1)—C(2) | 1.4107 (2) | C(5)—H(5) | 1.0760 (2) |
C(1)—C(7) | 1.4648 (2) | C(4)—H(4) | 1.0760 (2) |
| | | |
C(7)—O(1)—H(1) | 109.777 (18) | O(3)—C(2)—C(3) | 117.254 (18) |
C(2)—O(3)—H(2) | 109.061 (18) | C(1)—C(2)—C(3) | 119.484 (18) |
C(6)—C(1)—C(2) | 119.465 (16) | C(6)—C(5)—C(4) | 119.444 (19) |
C(6)—C(1)—C(7) | 120.344 (16) | C(6)—C(5)—H(5) | 118.74 (2) |
C(2)—C(1)—C(7) | 120.187 (16) | C(4)—C(5)—H(5) | 121.682 (19) |
C(2)—C(3)—C(4) | 120.166 (18) | C(3)—C(4)—C(5) | 120.659 (18) |
C(2)—C(3)—H(3) | 119.45 (2) | C(3)—C(4)—H(4) | 119.52 (2) |
C(4)—C(3)—H(3) | 120.356 (18) | C(5)—C(4)—H(4) | 119.81 (2) |
C(1)—C(6)—C(5) | 120.781 (18) | O(1)—C(7)—O(2) | 122.100 (17) |
C(1)—C(6)—H(6) | 117.917 (17) | O(1)—C(7)—C(1) | 115.871 (17) |
C(5)—C(6)—H(6) | 121.291 (18) | O(2)—C(7)—C(1) | 122.028 (16) |
O(3)—C(2)—C(1) | 123.262 (17) | | |
| | | |
H(1)—O(1)—C(7)—O(2) | −1.3 (1) | C(4)—C(3)—C(2)—O(3) | 180.0 (1) |
H(1)—O(1)—C(7)—C(1) | 178.9 (1) | C(4)—C(3)—C(2)—C(1) | −0.2 (1) |
H(2)—O(3)—C(2)—C(1) | 3.7 (1) | C(2)—C(3)—C(4)—C(5) | 0.1 (1) |
H(2)—O(3)—C(2)—C(3) | −176.5 (1) | C(2)—C(3)—C(4)—H(4) | 179.1 (1) |
C(6)—C(1)—C(2)—O(3) | 180.0 (1) | H(3)—C(3)—C(2)—O(3) | −1.8 (1) |
C(6)—C(1)—C(2)—C(3) | 0.1 (1) | H(3)—C(3)—C(2)—C(1) | 178.1 (1) |
C(2)—C(1)—C(6)—C(5) | 0.0 (1) | H(3)—C(3)—C(4)—C(5) | −178.2 (1) |
C(2)—C(1)—C(6)—H(6) | 178.8 (1) | H(3)—C(3)—C(4)—H(4) | 0.9 (1) |
C(6)—C(1)—C(7)—O(1) | −1.3 (1) | C(1)—C(6)—C(5)—C(4) | −0.2 (1) |
C(6)—C(1)—C(7)—O(2) | 178.9 (1) | C(1)—C(6)—C(5)—H(5) | −176.0 (1) |
C(7)—C(1)—C(6)—C(5) | −179.3 (1) | H(6)—C(6)—C(5)—C(4) | −178.9 (1) |
C(7)—C(1)—C(6)—H(6) | −0.5 (1) | H(6)—C(6)—C(5)—H(5) | 5.2 (1) |
C(2)—C(1)—C(7)—O(1) | 179.3 (1) | C(6)—C(5)—C(4)—C(3) | 0.1 (1) |
C(7)—C(1)—C(2)—O(3) | −0.7 (1) | C(6)—C(5)—C(4)—H(4) | −178.9 (1) |
C(2)—C(1)—C(7)—O(2) | −0.4 (1) | H(5)—C(5)—C(4)—C(3) | 175.8 (1) |
C(7)—C(1)—C(2)—C(3) | 179.5 (1) | H(5)—C(5)—C(4)—H(4) | −3.2 (1) |
Experimental details
| (2-thiouracil) | (cytosine) | (salicylicacid) |
Crystal data |
Chemical formula | C4H4N2OS | C4H5N3O·H2O | C7H6O3 |
Mr | 128.16 | 129.13 | 138.12 |
Crystal system, space group | Triclinic, P1 | Monoclinic, P21/c | Monoclinic, P21/c |
Temperature (K) | 90 | 90 | 90 |
a, b, c (Å) | 4.2427 (4), 5.9648 (5), 10.5801 (10) | 7.7161 (8), 9.8337 (10), 7.5131 (8) | 4.8818 (2), 11.2009 (5), 11.2335 (5) |
α, β, γ (°) | 105.736 (5), 94.912 (5), 91.927 (4) | 90, 100.523 (5), 90 | 90, 92.621 (2), 90 |
V (Å3) | 256.32 (4) | 560.49 (10) | 613.61 (5) |
Z | 2 | 4 | 4 |
Radiation type | Mo Kα | Mo Kα | Mo Kα |
µ (mm−1) | 0.51 | 0.12 | 0.12 |
Crystal size (mm) | 0.39 × 0.19 × 0.12 | 0.32 × 0.22 × 0.03 | 0.25 × 0.22 × 0.2 |
|
Data collection |
Diffractometer | Bruker SMART APEX CCD area detector diffractometer | Bruker SMART APEX CCD area detector diffractometer | Bruker SMART APEX CCD area detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996) | Multi-scan (SADABS; Sheldrick, 1996) | Multi-scan (SADABS; Sheldrick, 1996) |
Tmin, Tmax | 0.831, 0.943 | 0.961, 0.996 | 0.886, 0.977 |
No. of measured, independent and observed [ > 3σ(I)] reflections | 4983, 4983, 4697 | 5948, 5948, 4792 | 31354, 6440, 5439 |
Rint | 0.031 | 0.040 | 0.029 |
(sin θ/λ)max (Å−1) | 1.103 | 1.082 | 1.083 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.014, 0.017, 1.93 | 0.017, 0.015, 1.96 | 0.020, 0.020, 1.96 |
No. of reflections | 4697 | 4792 | 5439 |
No. of parameters | 229 | 337 | 276 |
H-atom treatment | H-atom parameters not refined | H-atom parameters not refined | H-atom parameters not refined |
Δρmax, Δρmin (e Å−3) | 0.32, −0.20 | 0.27, −0.17 | 0.27, −0.26 |
Selected geometric parameters (Å, º) for (2-thiouracil) topS(2)—C(2) | 1.6828 (2) | N(3)—C(4) | 1.3942 (2) |
O(4)—C(4) | 1.2354 (3) | N(3)—H(3) | 1.0300 (2) |
N(1)—C(2) | 1.3511 (2) | C(4)—C(5) | 1.4420 (3) |
N(1)—C(6) | 1.3709 (2) | C(6)—C(5) | 1.3538 (3) |
N(1)—H(1) | 1.0300 (2) | C(6)—H(6) | 1.0800 (2) |
N(3)—C(2) | 1.3570 (2) | C(5)—H(5) | 1.0800 (2) |
| | | |
C(2)—N(1)—C(6) | 122.692 (16) | O(4)—C(4)—N(3) | 119.512 (19) |
C(2)—N(1)—H(1) | 120.009 (16) | O(4)—C(4)—C(5) | 125.049 (18) |
C(6)—N(1)—H(1) | 117.100 (15) | N(3)—C(4)—C(5) | 115.439 (16) |
C(2)—N(3)—C(4) | 125.400 (16) | N(1)—C(6)—C(5) | 121.437 (16) |
C(2)—N(3)—H(3) | 119.129 (15) | N(1)—C(6)—H(6) | 111.386 (16) |
C(4)—N(3)—H(3) | 115.445 (15) | C(5)—C(6)—H(6) | 127.130 (17) |
S(2)—C(2)—N(1) | 121.904 (13) | C(4)—C(5)—C(6) | 118.709 (16) |
S(2)—C(2)—N(3) | 121.868 (13) | C(4)—C(5)—H(5) | 122.272 (17) |
N(1)—C(2)—N(3) | 116.222 (15) | C(6)—C(5)—H(5) | 119.018 (17) |
| | | |
C(6)—N(1)—C(2)—S(2) | −176.4 (1) | H(3)—N(3)—C(2)—S(2) | −2.5 (1) |
C(6)—N(1)—C(2)—N(3) | 2.7 (1) | H(3)—N(3)—C(2)—N(1) | 178.5 (1) |
C(2)—N(1)—C(6)—C(5) | 0.1 (1) | H(3)—N(3)—C(4)—O(4) | −0.6 (1) |
C(2)—N(1)—C(6)—H(6) | −177.6 (1) | H(3)—N(3)—C(4)—C(5) | 179.6 (1) |
H(1)—N(1)—C(2)—S(2) | 8.9 (1) | O(4)—C(4)—C(5)—C(6) | −178.4 (1) |
H(1)—N(1)—C(2)—N(3) | −172.1 (1) | O(4)—C(4)—C(5)—H(5) | 1.8 (1) |
H(1)—N(1)—C(6)—C(5) | 174.9 (1) | N(3)—C(4)—C(5)—C(6) | 1.4 (1) |
H(1)—N(1)—C(6)—H(6) | −2.7 (1) | N(3)—C(4)—C(5)—H(5) | −178.3 (1) |
C(4)—N(3)—C(2)—S(2) | 175.6 (1) | N(1)—C(6)—C(5)—C(4) | −2.2 (1) |
C(2)—N(3)—C(4)—O(4) | −178.7 (1) | N(1)—C(6)—C(5)—H(5) | 177.6 (1) |
C(4)—N(3)—C(2)—N(1) | −3.4 (1) | H(6)—C(6)—C(5)—C(4) | 175.1 (1) |
C(2)—N(3)—C(4)—C(5) | 1.4 (1) | H(6)—C(6)—C(5)—H(5) | −5.1 (1) |
Selected geometric parameters (Å, º) for (cytosine) topO(1)—H(1A) | 0.9690 (2) | N(4)—C(4) | 1.3337 (2) |
O(1)—H(1B) | 0.9650 (2) | N(4)—H(4A) | 1.0180 (2) |
O(2)—C(2) | 1.2605 (2) | N(4)—H(4B) | 1.0140 (2) |
N(1)—C(2) | 1.3734 (2) | C(4)—C(5) | 1.4320 (2) |
N(1)—C(6) | 1.3583 (2) | C(5)—C(6) | 1.3553 (2) |
N(1)—H(1) | 1.0360 (2) | C(5)—H(5) | 1.0800 (2) |
N(3)—C(2) | 1.3524 (2) | C(6)—H(6) | 1.0870 (2) |
N(3)—C(4) | 1.3451 (2) | | |
| | | |
H(1A)—O(1)—H(1B) | 102.595 (19) | N(1)—C(2)—N(3) | 120.129 (16) |
C(2)—N(1)—C(6) | 121.263 (16) | N(3)—C(4)—N(4) | 118.349 (17) |
C(2)—N(1)—H(1) | 114.880 (16) | N(3)—C(4)—C(5) | 121.711 (16) |
C(6)—N(1)—H(1) | 123.854 (16) | N(4)—C(4)—C(5) | 119.939 (17) |
C(2)—N(3)—C(4) | 119.229 (16) | C(4)—C(5)—C(6) | 117.113 (16) |
C(4)—N(4)—H(4A) | 116.292 (17) | C(4)—C(5)—H(5) | 120.463 (16) |
C(4)—N(4)—H(4B) | 116.138 (17) | C(6)—C(5)—H(5) | 122.420 (17) |
H(4A)—N(4)—H(4B) | 127.015 (18) | N(1)—C(6)—C(5) | 120.473 (17) |
O(2)—C(2)—N(1) | 118.290 (17) | N(1)—C(6)—H(6) | 117.292 (16) |
O(2)—C(2)—N(3) | 121.563 (17) | C(5)—C(6)—H(6) | 122.231 (17) |
| | | |
C(6)—N(1)—C(2)—O(2) | 175.5 (1) | H(4A)—N(4)—C(4)—N(3) | 6.4 (1) |
C(6)—N(1)—C(2)—N(3) | −3.0 (1) | H(4A)—N(4)—C(4)—C(5) | −173.9 (1) |
C(2)—N(1)—C(6)—C(5) | 1.6 (1) | H(4B)—N(4)—C(4)—N(3) | 178.5 (1) |
C(2)—N(1)—C(6)—H(6) | −177.7 (1) | H(4B)—N(4)—C(4)—C(5) | −1.8 (1) |
H(1)—N(1)—C(2)—O(2) | −4.0 (1) | N(3)—C(4)—C(5)—C(6) | −2.4 (1) |
H(1)—N(1)—C(2)—N(3) | 177.6 (1) | N(3)—C(4)—C(5)—H(5) | 176.8 (1) |
H(1)—N(1)—C(6)—C(5) | −179.0 (1) | N(4)—C(4)—C(5)—C(6) | 177.9 (1) |
H(1)—N(1)—C(6)—H(6) | 1.7 (1) | N(4)—C(4)—C(5)—H(5) | −2.9 (1) |
C(4)—N(3)—C(2)—O(2) | −176.9 (1) | C(4)—C(5)—C(6)—N(1) | 1.0 (1) |
C(4)—N(3)—C(2)—N(1) | 1.6 (1) | C(4)—C(5)—C(6)—H(6) | −179.7 (1) |
C(2)—N(3)—C(4)—N(4) | −179.2 (1) | H(5)—C(5)—C(6)—N(1) | −178.2 (1) |
C(2)—N(3)—C(4)—C(5) | 1.1 (1) | H(5)—C(5)—C(6)—H(6) | 1.0 (1) |
Selected geometric parameters (Å, º) for (salicylicacid) topO(1)—C(7) | 1.3113 (2) | C(3)—C(2) | 1.4005 (3) |
O(1)—H(1) | 1.0250 (2) | C(3)—C(4) | 1.3886 (3) |
O(3)—C(2) | 1.3519 (3) | C(3)—H(3) | 1.0760 (2) |
O(3)—H(2) | 0.9640 (2) | C(6)—C(5) | 1.3843 (3) |
O(2)—C(7) | 1.2450 (2) | C(6)—H(6) | 1.0760 (2) |
C(1)—C(6) | 1.4049 (3) | C(5)—C(4) | 1.4025 (3) |
C(1)—C(2) | 1.4107 (2) | C(5)—H(5) | 1.0760 (2) |
C(1)—C(7) | 1.4648 (2) | C(4)—H(4) | 1.0760 (2) |
| | | |
C(7)—O(1)—H(1) | 109.777 (18) | O(3)—C(2)—C(3) | 117.254 (18) |
C(2)—O(3)—H(2) | 109.061 (18) | C(1)—C(2)—C(3) | 119.484 (18) |
C(6)—C(1)—C(2) | 119.465 (16) | C(6)—C(5)—C(4) | 119.444 (19) |
C(6)—C(1)—C(7) | 120.344 (16) | C(6)—C(5)—H(5) | 118.74 (2) |
C(2)—C(1)—C(7) | 120.187 (16) | C(4)—C(5)—H(5) | 121.682 (19) |
C(2)—C(3)—C(4) | 120.166 (18) | C(3)—C(4)—C(5) | 120.659 (18) |
C(2)—C(3)—H(3) | 119.45 (2) | C(3)—C(4)—H(4) | 119.52 (2) |
C(4)—C(3)—H(3) | 120.356 (18) | C(5)—C(4)—H(4) | 119.81 (2) |
C(1)—C(6)—C(5) | 120.781 (18) | O(1)—C(7)—O(2) | 122.100 (17) |
C(1)—C(6)—H(6) | 117.917 (17) | O(1)—C(7)—C(1) | 115.871 (17) |
C(5)—C(6)—H(6) | 121.291 (18) | O(2)—C(7)—C(1) | 122.028 (16) |
O(3)—C(2)—C(1) | 123.262 (17) | | |
| | | |
H(1)—O(1)—C(7)—O(2) | −1.3 (1) | C(4)—C(3)—C(2)—O(3) | 180.0 (1) |
H(1)—O(1)—C(7)—C(1) | 178.9 (1) | C(4)—C(3)—C(2)—C(1) | −0.2 (1) |
H(2)—O(3)—C(2)—C(1) | 3.7 (1) | C(2)—C(3)—C(4)—C(5) | 0.1 (1) |
H(2)—O(3)—C(2)—C(3) | −176.5 (1) | C(2)—C(3)—C(4)—H(4) | 179.1 (1) |
C(6)—C(1)—C(2)—O(3) | 180.0 (1) | H(3)—C(3)—C(2)—O(3) | −1.8 (1) |
C(6)—C(1)—C(2)—C(3) | 0.1 (1) | H(3)—C(3)—C(2)—C(1) | 178.1 (1) |
C(2)—C(1)—C(6)—C(5) | 0.0 (1) | H(3)—C(3)—C(4)—C(5) | −178.2 (1) |
C(2)—C(1)—C(6)—H(6) | 178.8 (1) | H(3)—C(3)—C(4)—H(4) | 0.9 (1) |
C(6)—C(1)—C(7)—O(1) | −1.3 (1) | C(1)—C(6)—C(5)—C(4) | −0.2 (1) |
C(6)—C(1)—C(7)—O(2) | 178.9 (1) | C(1)—C(6)—C(5)—H(5) | −176.0 (1) |
C(7)—C(1)—C(6)—C(5) | −179.3 (1) | H(6)—C(6)—C(5)—C(4) | −178.9 (1) |
C(7)—C(1)—C(6)—H(6) | −0.5 (1) | H(6)—C(6)—C(5)—H(5) | 5.2 (1) |
C(2)—C(1)—C(7)—O(1) | 179.3 (1) | C(6)—C(5)—C(4)—C(3) | 0.1 (1) |
C(7)—C(1)—C(2)—O(3) | −0.7 (1) | C(6)—C(5)—C(4)—H(4) | −178.9 (1) |
C(2)—C(1)—C(7)—O(2) | −0.4 (1) | H(5)—C(5)—C(4)—C(3) | 175.8 (1) |
C(7)—C(1)—C(2)—C(3) | 179.5 (1) | H(5)—C(5)—C(4)—H(4) | −3.2 (1) |
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