Gas-phase interactions between lead(II) ions and thiouracil nucleobases: a combined experimental and theoretical study
Jean-Yves Salpin*, Sébastien Guillaumont and Jeanine Tortajada
Université d'Evry Val d’Essonne – Laboratoire d’Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE)
CNRS – UMR 8587 – Bâtiment Maupertuis, Boulevard François Mitterrand, 91025 Evry, France
Al Mokhtar Lamsabhi*
Departamento de Química C-9, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain.
Supporting information (a total of 10 pages)
Figure 1S.B3LYP/6-31G(d,p) optimized geometries of the [Pb(thiouracil)]2+ complexes.
Figure 2S. Potential energy surface corresponding to the loss of HNCS, PbS and the formation of [PbNCS]+ with origin in global minimum 24SU-1 and 24SU-3. Relative energies are in kJmol-1.
Table 1S. Calculated total energies (Hartree), relative energies and ZPE (kJ mol−1) of the various structures considered(ZPE values are obtained at the 6-31G(d,p) level)
Table 2S. Calculated B3LYP/6-311+G(3df,2p) total energies (Hartree), relative energies and ZPE (kJ mol−1) of the various fragments and transition states involvedin Figures 4, 5 and 2S (ZPE values are obtained at the B3LYP/6-31G(d,p) level).
Table 3S. Natural atomic charge obtained for Pb with the B3LYP functional
Table 4S. B3LYP/6-31G(d,p) values of the electron density (e.au-3), laplacian of the electron density () and ellipticity () at the bond critical point deduced from the AIM topological study of structures involving 2-thiouracil.
Table 5S. B3LYP/6-31G(d,p) values of the electron density (e.au-3), laplacian of the electron density () and ellipticity () at the bond critical point deduced from the AIM topological study of structures involving 4-thiouracil.
Table 6S. B3LYP/6-31G(d,p) values of the electron density (e.au-3), laplacian of the electron density () and ellipticity () at the bond critical point deduced from the AIM topological study of structures involving 2,4-dithiouracil.
Figure 1S. B3LYP/6-31G(d,p) optimized geometries of the [Pb(thiouracil)]2+ complexes.
Figure 2S. Potential energy surface corresponding to the loss of HNCS, PbS and the formation of [PbNCS]+ with origin in global minimum 24SU-1 and 24SU-3. Relative energies are in kJmol-1.
Table 1S: Calculated total energies (Hartree), relative energies and ZPE (kJ mol−1) of the various structures considered(ZPE values are obtained at the 6-31G(d,p) level)
Structure / B3LYP/6-311+G(3df.2p) / G96LYP/6-311+G(3df.2p)E / ZPEa / E+ZPE / E / ZPEa / E+ZPE
2-thiouracil
2SU-1 / -740.546788 / 193.36 / 49.3 / -740.445395 / 186.69 / 32.4
2SU-2 / -740.565576 / 193.39 / 0.0 / -740.457714 / 186.62 / 0.0
2SU-3 / -740.560653 / 192.86 / 12.4 / -740.453985 / 185.93 / 9.1
2SU-4t / -740.564929 / 193.56 / 1.9 / -740.457031 / 186.91 / 2.1
2SU-5t / -740.537435 / 183.38 / 63.9 / -740.430519 / 176.87 / 61.6
2SU-6t / -740.557559 / 192.94 / 20.6 / -740.449999 / 186.30 / 19.9
2SU-7t / -740.555990 / 192.39 / 24.2 / -740.448620 / 185.78 / 23.0
2SU-8t / -740.549652 / 191.79 / 40.2 / -740.442021 / 185.18 / 39.8
2SU-9t / -740.531848 / 183.13 / 78.3 / -740.425370 / 176.64 / 74.9
2SU-10t / -740.477280 / 188.40 / 226.8 / -740.379900 / 182.05 / 199.7
2SU-11t / -740.489165 / 180.81 / 188.0 / -740.387620 / 173.64 / 171.1
2SU-12 / -740.525845 / 195.24 / 106.2 / -740.420307 / 188.36 / 99.9
4-thiouracil
4SU-1 / -740.574731 / 193.90 / 0.0 / -740.467312 / 187.23 / 0.0
4SU-3 / -740.542952 / 193.24 / 82.8 / -740.437265 / 186.47 / 78.1
4SU-4t / -740.542557 / 183.96 / 74.5 / -740.436361 / 177.36 / 71.4
4SU-5t / -740.564561 / 193.46 / 26.3 / -740.455514 / 186.83 / 30.6
4SU-6t / -740.540819 / 184.11 / 79.2 / -740.434645 / 177.47 / 76.0
4SU-7t / -740.536002 / 183.02 / 90.8 / -740.428969 / 176.53 / 90.0
4SU-8t / -740.532131 / 182.62 / 100.6 / -740.425516 / 176.19 / 98.7
4SU-9t / -740.548297 / 191.98 / 67.5 / -740.440262 / 185.34 / 69.1
4SU-10t / -740.517248 / 190.65 / 147.7 / -740.411620 / 183.33 / 142.3
4SU-11t / -740.486558 / 189.17 / 226.8 / - / - / -
4SU-12 / -740.547080 / 195.42 / 74.1 / -740.440890 / 188.57 / 70.7
2-4-dithiouracil
24SU-1 / -1063.529917 / 187.26 / 0.0 / -1063.434372 / 180.89 / 0.0
24SU-3 / -1063.517489 / 187.15 / 32.5 / -1063.423039 / 180.56 / 29.4
24SU-4t / -1063.521974 / 178.13 / 11.7 / -1063.427095 / 171.93 / 10.1
24SU-5t / -1063.517248 / 177.42 / 23.4 / -1063.421085 / 171.22 / 25.2
24SU-6t / -1063.520361 / 178.25 / 16.1 / -1063.425501 / 172.00 / 14.4
24SU-7t / -1063.515754 / 177.05 / 27.0 / -1063.420002 / 170.91 / 27.8
24SU-8t / -1063.511895 / 176.64 / 36.7 / -1063.416551 / 170.55 / 36.5
24SU-9t / -1063.511484 / 177.23 / 38.4 / -1063.415770 / 171.06 / 39.0
24SU-10t / -1063.470516 / 184.14 / 152.8 / -1063.423039 / 180.56 / 29.4
24SU-11t / -1063.448508 / 175.17 / 201.6 / -1063.427095 / 171.93 / 10.1
24SU-12 / -1063.500328 / 189.20 / 79.6 / -1063.421085 / 171.22 / 25.2
Table 2S: Calculated B3LYP/6-311+G(3df,2p) total energies (Hartree), relative energies and ZPE (kJ mol−1) of the various fragments and transition states involved in Figures 4, 5 and 2S (ZPE values are obtained at the B3LYP/6-31G(d,p) level).
Structure / 2-thiouracil / 4-thiouracil / 2,4-dithiouracilE / ZPE / E+ZPE / E / ZPE / E+ZPE / E / ZPE / E+ZPE
nSU-TS6 / -740.4271578 / 177.22 / 347.6 / -740.4224498 / 175.94 / 382.2 / -1063.381912 / 172.19 / 373.8
nSU-C / -1063.386162 / 172.34 / 362.8
nSU-TS7 / -740.4228628 / 174.70 / 379.9 / -1063.384959 / 167.20 / 360.9
nSU-TS4 / -740.4903821 / 185.24 / 189.5 / -740.4641861 / 183.77 / 280.3
nSU-TSA / -740.4517569 / 174.49 / 280.3 / -740.4488062 / 176.66 / 313.7 / -1063.409128 / 168.84 / 299.0
nSU-TS1 / -740.4509522 / 179.72 / 287.6 / -740.4250290 / 173.29 / 372.8 / -1063.416405 / 169.43 / 280.5
nSU-A / -740.4812859 / 191.18 / 219.2 / -740.4569847 / 181.58 / 297.1 / -1063.433618 / 175.61 / 241.4
nSU-TS2 / -740.4473698 / 182.07 / 299.3 / -740.4229366 / 172.21 / 377.3 / -1063.399326 / 165.75 / 321.7
nSU-B / -740.4692778 / 181.33 / 241.0 / -740.4465896 / 171.80 / 314.8 / -1063.427168 / 165.77 / 248.7
nSU-TS3 / -740.4267522 / 168.49 / 340.1 / -740.4143771 / 160.14 / 387.9 / -1063.384519 / 153.64 / 348.7
Fragments
HCNX / -491.7068245 / 49.24 / -168.7511796 / 55.98 / -491.7068245 / 49.24
PbNCHCHCY / -248.7508672 / 117.18 / -571.7086452 / 110.96 / -571.7086452 / 110.96
HCNX+PbNCHCHY / 256.8 / 275.2 / 273.9
NCXPb / -494.3160223 / 25.87 / -171.3514704 / 32.50 / -494.3160223 / 25.87
HNCHCHY / -246.1422507 / 145.78 / -569.0963885 / 139.67 / -569.0963885 / 139.67
NCXPb+ HNCHCHY / 260.4 / 311.8 / 287.2
PbNHCSCCH / -248.7214199 / 115.30 / -571.683925 / 109.65 / -571.683925 / 109.65
HNCX + PbNHCXCCH / 332.3 / 338.9 / 337.5
X and Y correspond to the heteroatom bonded to C(2) and C(4), respectively.
Table 3S. Natural atomic charge obtained for Pb with the B3LYP functional
Structure / Net atomic charge [a.u.]B3LYP / G96LYP
2SU-1 (Pb-O) / +1.54 / +1.46
2SU-3 (Pb-S) / +1.37 / +1.31
4SU-1 (Pb-S) / +1.36 / +1.31
4SU-3 (Pb-O) / +1.51 / +1.42
24SU-1 (Pb-S) / +1.37 / +1.31
2,4SU-3 (Pb-S) / +1.35 / +1.29
U1 (Pb-O)[a] / +1.55 / +1.48
U3 (Pb-O)[a] / +1.55 / +1.48
[a] From ref. [5]
Table 4S: B3LYP/6-31G(d,p) values of the electron density (e.au-3), laplacian of the electron density () and ellipticity () at the bond critical point deduced from the AIM topological study of structures involving 2-thiouracil.
Complexes / Deprotonated forms / Neutral form2SU-2 / 2SU-3 / d2SU-1 / d2SU-2 / 2SU
N(1)-C(2) / 0.336 / -0.884 / 0.126 / 0.348 / -1.159 / 0.154 / 0.348 / -1.242 / 0.144 / 0.290 / -0.836 / 0.053 / 0.334 / -0.890 / 0.094
C(2)-N(3) / 0.352 / -1.139 / 0.145 / 0.345 / -0.913 / 0.152 / 0.303 / -0.900 / 0.076 / 0.362 / -1.267 / 0.173 / 0.271 / -0.694 / 0.122
C(2)-S(2) / 0.199 / -0.386 / 0.164 / 0.196 / -0.374 / 0.145 / 0.205 / -0.268 / 0.092 / 0.202 / -0.321 / 0.099 / 0.250 / +4.644 / 0.079
N(3)-C(4) / 0.284 / -0.871 / 0.040 / 0.262 / -0.733 / 0.042 / 0.296 / -0.924 / 0.089 / 0.315 / -1.035 / 0.083 / 0.272 / -0.760 / 0.092
C(4)-C(5) / 0.281 / -0.735 / 0.124 / 0.287 / -0.768 / 0.139 / 0.295 / -0.787 / 0.205 / 0.275 / -0.686 / 0.141 / 0.319 / -0.944 / 0.162
C(4)-O(4) / 0.409 / 0.247 / 0.120 / 0.417 / -0.316 / 0.131 / 0.392 / -0.149 / 0.087 / 0.391 / -0.075 / 0.094 / 0.380 / -0.315 / 0.111
C(5)-C(6) / 0.339 / -1.005 / 0.346 / 0.337 / -0.982 / 0.335 / 0.322 / -0.885 / 0.299 / 0.336 / -0.981 / 0.362 / 0.336 / -0.977 / 0.344
C(6)-N(1) / 0.291 / -0.679 / 0.022 / 0.301 / -0.838 / 0.030 / 0.339 / -1.163 / 0.101 / 0.316 / -0.882 / 0.109 / 0.329 / -0.745 / 0.045
Pb-S(2) / 0.032 / -0.025 / 2.626 / 0.031 / -0.021 / 2.850
Pb-(N1) / 0.030 / -0.069 / 22.142
Pb-N(3) / 0.029 / -0.070 / 27.109
Table 5S: B3LYP/6-31G(d,p) values of the electron density (e.au-3), laplacian of the electron density () and ellipticity () at the bond critical point deduced from the AIM topological study of structures involving 4-thiouracil.
Complexes / Deprotonated forms / Neutral form4SU-1 / 4SU-3 / d4SU-1 / d4SU-2 / 4SU
N(1)-C(2) / 0.294 / -0.939 / 0.113 / 0.341 / 0.160 / -1.242 / 0.323 / -1.131 / 0.131 / 0.280 / -0.829 / 0.098 / 0.308 / 0.146 / -1.020
C(2)-N(3) / 0.312 / -1.055 / 0.127 / 0.346 / 0.199 / -1.053 / 0.289 / -0.892 / 0.119 / 0.339 / -1.157 / 0.143 / 0.312 / 0.164 / -1.046
C(2)-O(2) / 0.417 / 0.196 / 0.159 / 0.354 / 0.075 / -0.441 / 0.398 / -0.143 / 0.132 / 0.397 / -0.171 / 0.137 / 0.415 / 0.146 / -0.379
N(3)-C(4) / 0.333 / -0.996 / 0.051 / 0.279 / 0.015 / -0.747 / 0.310 / -0.886 / 0.035 / 0.340 / -1.148 / 0.086 / 0.307 / 0.018 / -0.869
C(4)-C(5) / 0.308 / -0.859 / 0.196 / 0.290 / 0.138 / -0.772 / 0.306 / -0.918 / 0.229 / 0.280 / -0.705 / 0.127 / 0.290 / 0.147 / -0.762
C(4)-S(4) / 0.200 / -0.395 / 0.148 / 0.223 / 0.027 / 0.075 / 0.205 / -0.282 / 0.081 / 0.206 / -0.384 / 0.097 / 0.217 / 0.044 / -0.028
C(5)-C(6) / 0.323 / -0.930 / 0.267 / 0.334 / 0.327 / -0.970 / 0.313 / -0.847 / 0.267 / 0.336 / -0.979 / 0.363 / 0.335 / 0.349 / -0.973
C(6)-N(1) / 0.324 / -0.728 / 0.023 / 0.301 / 0.030 / -0.812 / 0.350 / -1.155 / 0.115 / 0.314 / -0.864 / 0.107 / 0.308 / 0.058 / -0.811
Pb-O(2) / 0.028 / 59.766 / -0.067
Pb-S(4) / 0.029 / -0.069 / 24.539
Pb-N(1) / 0.028 / 115.66 / -0.071
Pb-N(3) / 0.031 / -0.082 / 40.164
Table 6S: B3LYP/6-31G(d,p) values of the electron density (e.au-3), laplacian of the electron density () and ellipticity () at the bond critical point deduced from the AIM topological study of structures involving 2,4-dithiouracil.
Complexes / Deprotonated forms / Neutral form24SU-1 / 24SU-3 / d24SU-1 / d24SU-2 / 24SU
N(1)-C(2) / 0.303 / -0.913 / 0.080 / 0.347 / -1.168 / 0.150 / 0.345 / -1.228 / 0.132 / 0.294 / -0.835 / 0.057 / 0.314 / -0.946 / 0.113
C(2)-N(3) / 0.322 / -1.047 / 0.106 / 0.343 / -0.899 / 0.157 / 0.301 / -0.887 / 0.080 / 0.353 / -1.251 / 0.151 / 0.318 / -1.028 / 0.132
C(2)-S(2) / 0.216 / +0.022 / 0.093 / 0.197 / -0.381 / 0.150 / 0.207 / -0.209 / 0.084 / 0.205 / -0.253 / 0.092 / 0.213 / +0.067 / 0.039
N(3)-C(4) / 0.332 / -0.977 / 0.210 / 0.276 / -0.735 / 0.012 / 0.309 / -0.873 / 0.037 / 0.330 / -1.119 / 0.068 / 0.298 / -0.861 / 0.024
C(4)-C(5) / 0.306 / -0.846 / 0.178 / 0.291 / -0.776 / 0.132 / 0.304 / -0.826 / 0.204 / 0.284 / -0.722 / 0.130 / 0.290 / -0.765 / 0.142
C(4)-S(4) / 0.204 / -0.415 / 0.160 / 0.223 / +0.097 / 0.018 / 0.206 / -0.228 / 0.075 / 0.210 / -0.322 / 0.085 / 0.218 / -0.014 / 0.037
C(5)-C(6) / 0.324 / -0.935 / 0.272 / 0.335 / -0.975 / 0.322 / 0.318 / -0.875 / 0.267 / 0.335 / -0.979 / 0.346 / 0.336 / -0.976 / 0.340
C(6)-N(1) / 0.320 / -0.726 / 0.025 / 0.300 / -0.821 / 0.036 / 0.344 / -1.152 / 0.104 / 0.316 / -0.847 / 0.107 / 0.308 / -0.801 / 0.064
Pb-S(2) / 0.031 / -0.022 / 3.054
Pb-S(4) / 0.032
0.032 / -0.084
-0.028 / 30.985
2.659
Pb-N(1) / -0.030 / -0.069 / 25.228 / 9
Pb-N(3) / 0.029 / 21.005