We studied for the first time 16 tautomers/rotamers of diphosphocytosine by four computational methods. Some of these tautomers/rotamers are isoenergetic although they have different structures. High-level electron correlation MP2 and MP4(SDQ)
DNA is a naturally occurring biological macromolecule, containing thousands of nucleic acid bases, and it is of prime importance in genetic determination [
Among cytosine tautomers, experimental investigations performed in gas phase, solid state, or in solution indicate that the canonic amino-oxo tautomer of cytosine is the most stable one [
All quantum chemical calculations were performed using the Gaussian 09 suite of programs [
Geometry of the 16 tautomers and rotamers was optimized at four different levels. Optimized structures of the 16 diphosphocytosine tautomers (at MP4(SDQ)/6-31+G(d)) are presented in Figure
Computed geometrical data of the 16 diphosphocytosine tautomers at MP4(SDQ)/6-31+G(d).
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R(1,2) | 1.469 | 1.403 | 1.409 | 1.472 | 1.475 | 1.476 | 1.479 | 1.478 | 1.487 | 1.364 | 1.403 | 1.409 | 1.477 | 1.481 | 1.477 | 1.481 |
R(1,6) | 1.350 | 1.39 | 1.385 | 1.351 | 1.351 | 1.351 | 1.351 | 1.349 | 1.348 | 1.443 | 1.390 | 1.385 | 1.345 | 1.345 | 1.346 | 1.346 |
R(1,9) | 1.093 | 1.093 | 1.094 | 1.091 | 1.094 | 1.091 | 1.093 | 1.091 | 1.093 | 1.093 | 1.094 | 1.094 | 1.091 | 1.094 | 1.091 | 1.094 |
R(2,3) | 1.741 | 1.658 | 1.766 | 1.863 | 1.854 | 1.858 | 1.847 | 1.868 | 1.855 | 1.834 | 1.766 | 1.766 | 1.859 | 1.854 | 1.858 | 1.851 |
R(2,7) | 1.377 | 1.399 | 1.397 | 1.290 | 1.290 | 1.290 | 1.289 | 1.290 | 1.287 | 1.393 | 1.399 | 1.397 | 1.294 | 1.294 | 1.293 | 1.293 |
R(3,4) | 1.856 | 1.752 | 1.755 | 1.844 | 1.848 | 1.834 | 1.836 | 1.875 | 1.877 | 1.876 | 1.752 | 1.756 | 1.701 | 1.701 | 1.705 | 1.705 |
R(4,5) | 1.867 | 1.759 | 1.754 | 1.426 | 1.427 | 1.422 | 1.418 | 1.420 | 1.417 | 1.420 | 1.759 | 1.754 | 1.836 | 1.836 | 1.832 | 1.833 |
R(4,8) | 1.229 | 1.382 | 1.383 | 1.701 | 1.702 | 1.704 | 1.707 | 1.871 | 1.882 | 1.868 | 1.382 | 1.383 | 1.382 | 1.387 | 1.373 | 1.373 |
R(5,6) | 1.813 | 1.744 | 1.746 | 1.382 | 1.381 | 1.374 | 1.372 | 1.223 | 1.224 | 1.227 | 1.744 | 1.746 | 1.818 | 1.818 | 1.821 | 1.821 |
R(5,10) | 1.420 | 1.092 | 1.092 | 1.831 | 1.831 | 1.829 | 1.829 | 1.834 | 1.831 | 1.708 | 1.092 | 1.092 | 1.426 | 1.426 | 1.423 | 1.423 |
R(6,11) | 1.091 | 1.016 | 1.016 | 1.092 | 1.092 | 1.091 | 1.092 | 1.421 | 1.421 | 1.094 | 1.016 | 1.016 | 1.091 | 1.091 | 1.091 | 1.091 |
R(7,12) | 1.014 | 1.016 | 1.016 | 1.028 | 1.031 | 1.028 | 1.03 | 1.092 | 1.092 | 1.017 | 1.016 | 1.016 | 1.029 | 1.030 | 1.029 | 1.030 |
R(8,13) | 1.015 | 0.977 | 0.977 | 0.976 | 0.976 | 0.978 | 0.978 | 1.028 | 1.030 | 1.016 | 0.977 | 0.977 | 0.976 | 0.976 | 0.978 | 0.978 |
A(2,1,6) | 126.1 | 125.9 | 126.0 | 125.5 | 125.5 | 125.7 | 124.9 | 127.8 | 123.7 | 125.8 | 125.9 | 125.9 | 126.8 | 126.4 | 126.2 | 125.8 |
A(2,1,9) | 115.6 | 116.6 | 116.6 | 114.3 | 115.3 | 114.3 | 115.8 | 112.9 | 116.4 | 117.8 | 116.6 | 116.6 | 113.5 | 114.9 | 113.7 | 114.9 |
A(6,1,9) | 118.3 | 117.5 | 117.4 | 120.2 | 119.2 | 119.9 | 119.2 | 119.2 | 119.9 | 116.4 | 117.4 | 117.4 | 119.7 | 118.7 | 120.0 | 119.2 |
A(1,2,3) | 129.4 | 126.3 | 127.5 | 120.4 | 121.4 | 117.5 | 117.9 | 119.9 | 116.9 | 122.5 | 126.3 | 127.5 | 125.0 | 125.3 | 123.2 | 123.7 |
A(1,2,7) | 112.8 | 117.6 | 116.8 | 118.1 | 124.6 | 117.5 | 124.8 | 116.6 | 124.9 | 122.1 | 117.6 | 116.8 | 115.6 | 122.4 | 116.4 | 123.1 |
A(3,2,7) | 117.9 | 115.9 | 115.6 | 121.4 | 113.9 | 124.5 | 116.9 | 123.3 | 117.6 | 115.3 | 115.9 | 115.6 | 119.2 | 112.1 | 120.0 | 112.9 |
A(2,3,4) | 101.6 | 103.7 | 102.5 | 102.9 | 102.6 | 101.6 | 100.7 | 100.1 | 101.0 | 102.4 | 103.7 | 102.6 | 102.8 | 101.8 | 102.9 | 101.9 |
A(3,4,5) | 119.9 | 131.9 | 132.1 | 96.1 | 96.0 | 97.7 | 97.8 | 97.6 | 98.0 | 98.3 | 131.9 | 132.1 | 130.5 | 130.9 | 129.6 | 130.0 |
A(3,4,8) | 119.3 | 116.3 | 110.4 | 97.2 | 96.4 | 97.3 | 97.7 | 96.1 | 95.9 | 97.3 | 116.3 | 110.4 | 115.3 | 115.3 | 121.6 | 121.5 |
A(5,4,8) | 120.2 | 111.7 | 117.5 | 130.1 | 131.1 | 128.2 | 128.5 | 114.3 | 121.4 | 119.7 | 111.7 | 117.5 | 114.1 | 113.7 | 108.6 | 108.2 |
A(4,5,6) | 100.3 | 100.7 | 101.7 | 113.7 | 113.2 | 108.9 | 109.1 | 122.4 | 119.8 | 119.4 | 100.6 | 101.7 | 102.2 | 101.8 | 100.8 | 100.5 |
A(4,5,10) | 97.9 | 131.4 | 130.0 | 116.2 | 115.7 | 122.4 | 121.9 | 122.8 | 118.8 | 120.6 | 131.3 | 130.1 | 96.7 | 97.1 | 96.8 | 97.3 |
A(6,5,10) | 98.9 | 115.5 | 116.2 | 101.8 | 101.4 | 101.7 | 101.6 | 99.5 | 102.3 | 99.9 | 115.5 | 116.2 | 98.5 | 97.9 | 98.9 | 98.4 |
A(1,6,5) | 124.8 | 113.1 | 113.7 | 131.5 | 131.5 | 130.9 | 130.7 | 95.9 | 95.6 | 134.6 | 113.1 | 113.7 | 126.9 | 126.4 | 126.5 | 126.0 |
A(1,6,11) | 118.4 | 115.3 | 115.7 | 116.6 | 116.5 | 116.8 | 116.9 | 98.4 | 98.8 | 113.3 | 115.2 | 115.7 | 118.7 | 118.8 | 118.5 | 118.7 |
A(5,6,11) | 116.5 | 116.2 | 116.3 | 111.8 | 111.9 | 112.0 | 112.2 | 130.1 | 126.2 | 112.0 | 116.1 | 116.3 | 114.1 | 114.6 | 114.5 | 114.9 |
A(2,7,12) | 118.8 | 111.6 | 111.9 | 111.4 | 110.4 | 112.0 | 110.7 | 116.9 | 118.4 | 115.2 | 111.6 | 111.8 | 111.4 | 110.6 | 111.5 | 110.7 |
A(4,8,13) | 118.5 | 110.6 | 109.9 | 110.3 | 110.2 | 110.2 | 110.4 | 112.9 | 114.8 | 116.5 | 110.5 | 109.9 | 110.9 | 110.8 | 110.4 | 110.2 |
D(6,1,2,3) | 114.4 | 0.1 | −0.1 | 24.8 | 23.7 | 28.9 | 31.9 | 112.3 | 110.7 | 111.5 | −0.1 | −0.1 | 17.9 | 22.2 | 24.9 | 27.4 |
D(6,1,2,7) | −18.9 | 176.7 | 176.7 | −159.5 | −160.2 | −158.8 | −155.1 | 14.6 | −45.5 | −7.8 | −176.7 | 176.7 | −165.5 | −161.3 | −160.6 | −157.9 |
D(9,1,2,3) | 162.8 | −179.2 | −179.3 | −158.3 | −158.5 | −154.7 | −151.5 | −169.5 | 142.2 | 174.7 | 179.2 | −179.3 | −163.1 | −158.7 | −156.6 | −153.7 |
D(9,1,2,7) | 161.9 | −2.7 | −2.6 | 17.5 | 17.5 | 17.7 | 21.5 | −167.7 | 135.2 | 172.3 | 2.7 | −2.6 | 13.4 | 17.7 | 17.9 | 21.0 |
D(2,1,6,5) | −16.9 | −0.4 | −0.5 | 3.2 | 1.8 | 3.8 | 2.4 | 8.1 | −37.1 | −5.2 | 0.4 | −0.5 | 4.4 | 3.4 | 5.9 | 4.9 |
D(2,1,6,11) | −5.4 | 179.9 | 179.9 | 177.5 | 177.5 | 177.9 | 177.4 | −4.5 | −7.9 | −11.7 | −179.9 | 179.9 | 178.3 | 177.8 | 177.7 | 177.5 |
D(9,1,6,5) | −179.2 | 178.9 | 178.8 | −173.6 | −175.9 | −172.4 | −174.1 | 178.8 | −178.4 | 171.8 | −178.9 | 178.7 | −174.4 | −175.6 | −172.5 | −173.9 |
D(9,1,6,11) | 174.4 | −0.8 | −0.8 | 0.8 | −0.1 | 1.6 | 0.8 | 177.9 | 171.4 | 168.2 | 0.8 | −0.8 | −0.6 | −1.2 | −0.7 | −1.4 |
D(1,2,3,4) | 0.5 | 0.2 | 0.5 | −29.8 | −26.7 | −41.3 | −43.4 | 1.3 | 0.9 | −8.3 | −0.2 | 0.5 | −15.7 | −18.9 | −22.2 | −23.6 |
D(7,2,3,4) | 3.9 | −176.3 | −176.3 | 69.1 | 71.2 | −140.4 | −142.9 | −39.2 | 52.8 | 32.2 | 176.4 | −176.3 | 167.9 | 164.3 | 163.5 | 161.2 |
D(1,2,7,12) | −177.9 | 27.9 | 28.6 | 154.5 | 156.8 | 146.9 | 143.0 | −136.9 | 150.4 | 131.6 | −27.9 | 28.7 | −179.2 | 1.0 | −179.0 | 1.4 |
D(3,2,7,12) | 21.1 | 161.3 | 162.9 | −106.6 | −105.2 | 47.8 | 43.6 | 145.2 | −134.3 | −150.2 | −161.3 | 162.9 | −2.5 | 177.9 | −4.3 | 176.6 |
D(2,3,4,5) | 167.7 | −155.1 | −154.3 | 178.8 | −0.9 | 179.8 | −0.2 | 47.6 | −36.6 | −50.8 | 155.1 | −154.1 | −5.5 | −5.8 | −6.5 | −7.3 |
D(2,3,4,8) | −157.3 | −21.8 | −19.9 | −5.5 | 175.4 | −8.4 | 172.9 | −179.8 | −0.9 | 17.4 | 21.8 | −19.9 | 177.3 | 176.8 | 179.3 | 179.3 |
D(3,4,5,6) | −10.7 | −0.3 | −0.5 | 14.9 | 11.4 | 33.1 | 33.2 | −4.1 | −173.2 | 150.9 | 0.3 | −0.6 | 20.2 | 22.7 | 26.9 | 28.6 |
D(3,4,5,10) | 31.3 | −179.9 | 179.9 | −165.9 | −168.3 | −153.9 | −153.9 | 58.7 | −18.3 | −160.2 | 179.9 | 179.8 | 120.4 | 122.3 | 127.4 | 128.6 |
D(8,4,5,6) | −157.3 | 0.2 | 0.2 | −83.1 | −86.4 | 132.5 | 132.7 | −129.5 | 161.9 | −26.8 | −0.1 | 0.2 | −162.5 | −159.9 | −158.3 | −157.3 |
D(8,4,5,10) | −46.8 | 179.8 | 179.8 | 96.0 | 93.9 | −54.5 | −54.4 | 157.6 | −117.7 | −44.4 | −179.8 | 179.8 | −62.3 | −60.3 | −57.8 | −57.3 |
D(3,4,8,13) | −147.4 | −0.9 | 179.4 | 3.8 | 5.5 | −10.1 | −9.4 | −30.6 | 62.6 | 142.1 | 1.0 | 179.4 | 158.0 | 151.8 | 0.2 | 0.1 |
D(5,4,8,13) | 141.9 | 179.3 | −0.3 | −175.3 | −174.8 | 177.8 | 178.5 | −50.1 | −17.0 | −144.6 | −179.3 | −0.3 | −19.7 | −26.1 | −175.1 | −174.6 |
D(4,5,6,1) | 41.3 | 0.3 | 0.4 | 18.6 | 16.7 | −173.9 | −173.8 | −149.6 | −117.3 | 41.9 | −0.2 | 0.4 | −20.8 | −22.5 | −28.4 | −28.9 |
D(4,5,6,11) | 34.5 | 179.9 | 179.9 | −162.2 | −163.1 | −0.6 | −0.4 | 138.1 | 162.7 | 31.2 | −179.9 | 179.9 | 165.2 | 162.9 | 159.7 | 158.2 |
Optimized structures of the 16 PC isomers at MP4(SDQ)/6-31+G(d).
In the dienol form of diphosphocytosine, there are three double bonds giving it the six
Since our major objective of this study was to obtain information on the relative stabilities of diphosphocytosine tautomers and rotamers, we tried to go as high as possible, with the level of theory and use both DFT and high correlation
Thermodynamic parameters (kcal/mol)a for diphosphocytosine tautomers/rotamers at different levels in gas phase.
Species | B3LYP | M06-2X | MP2 | MP4(SDQ)b | |||||||||
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3.70 | 7.01 | 5.78 | 4.66 | 6.84 | 10.26 | 8.99 | 7.83 | 9.90 | 13.27 | 11.61 | 11.38 | 7.19 |
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0.00 | 0.62 | 0.50 | 0.46 | 0.00 | 0.72 | 0.58 | 0.50 | 0.40 | 0.42 | 0.42 | 0.38 | 0.46 |
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0.47 | 0.00 | 0.00 | 0.00 | 0.40 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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24.73 | 28.43 | 26.96 | 25.99 | 25.98 | 29.52 | 28.11 | 27.05 | 27.46 | 31.80 | 30.46 | 30.01 | 24.82 |
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24.55 | 28.53 | 26.87 | 25.63 | 26.02 | 29.68 | 28.21 | 27.01 | 28.17 | 32.75 | 26.78 | 26.68 | 25.51 |
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22.28 | 25.73 | 24.30 | 23.46 | 23.58 | 26.75 | 25.49 | 24.67 | 24.72 | 28.90 | 26.94 | 26.91 | 22.23 |
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22.11 | 25.64 | 24.15 | 23.54 | 23.14 | 26.49 | 25.13 | 24.44 | 24.87 | 29.09 | 26.94 | 0.04 | 22.17 |
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9.97 | 16.68 | 13.65 | 12.64 | 12.76 | 19.53 | 16.50 | 15.40 | 15.91 | 23.12 | 19.50 | 0.03 | 13.96 |
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12.00 | 19.21 | 15.95 | 14.82 | 14.16 | 21.46 | 18.21 | 16.73 | 17.82 | 25.48 | 21.66 | 21.11 | 15.68 |
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5.37 | 8.90 | 7.56 | 6.44 | 8.83 | 12.65 | 11.21 | 9.95 | 11.78 | 15.27 | 13.56 | 13.24 | 9.63 |
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0.92 | 0.48 | 0.50 | 0.46 | 0.967 | 0.56 | 0.58 | 0.50 | 0.40 | 0.42 | 0.42 | 0.38 | 0.46 |
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0.47 | 0.00 | 0.00 | 0.00 | 0.400 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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23.47 | 27.01 | 25.57 | 24.70 | 24.31 | 27.87 | 26.48 | 25.13 | 26.13 | 30.61 | 28.41 | 27.86 | 23.42 |
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25.18 | 29.14 | 27.50 | 26.56 | 25.96 | 29.81 | 28.25 | 27.26 | 27.68 | 32.49 | 30.12 | 0.00 | 25.17 |
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20.56 | 23.71 | 22.39 | 21.86 | 21.26 | 24.50 | 23.17 | 22.55 | 22.98 | 26.92 | 24.90 | 0.00 | 20.05 |
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21.76 | 25.23 | 23.75 | 23.23 | 22.43 | 25.76 | 24.39 | 23.81 | 23.96 | 28.21 | 26.04 | 25.99 | 21.24 |
NPA atomic charges at MP2/6-31+G(d).
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C1 | −0.327 | −0.343 | −0.338 | −0.267 | −0.311 | −0.265 | −0.308 | −0.267 | −0.302 | −0.443 | −0.343 | −0.338 | −0.227 | −0.267 | −0.245 | −0.283 |
C2 | −0.041 | −0.068 | −0.077 | −0.025 | −0.024 | −0.017 | −0.016 | −0.015 | −0.033 | 0.017 | −0.068 | −0.077 | −0.061 | −0.064 | −0.041 | −0.045 |
P3 | 0.393 | 0.503 | 0.584 | 0.594 | 0.657 | 0.680 | 0.704 | 0.580 | 0.624 | 0.613 | 0.503 | 0.584 | 0.578 | 0.668 | 0.475 | 0.559 |
C4 | 0.029 | −0.336 | −0.338 | −0.352 | −0.326 | −0.293 | −0.268 | 0.061 | 0.057 | 0.033 | −0.335 | −0.338 | −0.322 | −0.361 | −0.280 | −0.314 |
P5 | 0.636 | 0.615 | 0.531 | 0.640 | 0.605 | 0.517 | 0.485 | 0.621 | 0.625 | 0.509 | 0.614 | 0.531 | 0.669 | 0.667 | 0.713 | 0.711 |
C6 | −0.468 | −0.533 | −0.523 | −0.555 | −0.521 | −0.545 | −0.514 | −0.535 | −0.525 | −0.515 | −0.533 | −0.523 | −0.559 | −0.530 | −0.553 | −0.525 |
N7 | −0.893 | −0.903 | −0.904 | −0.646 | −0.655 | −0.683 | −0.690 | −0.675 | −0.663 | −0.896 | −0.903 | −0.904 | −0.676 | −0.671 | −0.677 | −0.677 |
O8 | −0.661 | −0.774 | −0.776 | −0.771 | −0.771 | −0.773 | −0.770 | −0.628 | −0.635 | −0.645 | −0.774 | −0.776 | −0.771 | −0.775 | −0.772 | −0.778 |
H9 | 0.234 | 0.232 | 0.232 | 0.256 | 0.237 | 0.257 | 0.239 | 0.262 | 0.248 | 0.233 | 0.232 | 0.232 | 0.259 | 0.239 | 0.258 | 0.240 |
H10 | −0.021 | 0.259 | 0.261 | 0.254 | 0.254 | 0.257 | 0.256 | −0.019 | −0.022 | −0.013 | 0.259 | 0.261 | −0.037 | −0.036 | −0.029 | −0.030 |
H11 | 0.261 | 0.414 | 0.413 | 0.373 | 0.517 | 0.367 | 0.522 | 0.261 | 0.261 | 0.262 | 0.414 | 0.413 | 0.261 | 0.260 | 0.259 | 0.258 |
H12 | 0.421 | 0.419 | 0.421 | 0.515 | −0.025 | 0.523 | −0.006 | 0.371 | −0.003 | 0.423 | 0.419 | 0.421 | 0.371 | 0.359 | 0.370 | 0.361 |
H13 | 0.436 | 0.513 | 0.515 | −0.016 | 0.365 | −0.026 | 0.365 | −0.017 | 0.367 | 0.423 | 0.513 | 0.515 | 0.514 | 0.511 | 0.522 | 0.521 |
Relative energy of different diphosphocytosine tautomers at different levels.
MP2 corrected for zero-point and thermal energy versus uncorrected one for all the 16 diphosphocytosine tautomers.
Tautomers’ order by DFT and MP2 methods.
The amino N accommodates the highest negative charge (up to −0.904); then the O atom comes in the second place (up to −0.778). Positive charges are accommodated on the P and H atoms. Very little negative charge on H bonded to P atoms as appeared in
One of the most crucial factors determining the tautomer distribution in the biological media is the environment. Solvent preferentially stabilizes structures with localized charges. Solvation effect has been explored in water (
Thermodynamic parameters for different tautomers (kcal/mol) at B3LYP/6-31+G(d) in water.
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3.531 | 0.658 | 2.021 | 22.773 |
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0.177 | 0.122 | 0.137 | 0.275 |
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0.000 | 0.000 | 0.000 | 0.000 |
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27.936 | 23.999 | 25.904 | 25.843 |
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28.035 | 23.887 | 25.919 | 25.612 |
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26.048 | 22.526 | 24.159 | 24.496 |
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26.193 | 22.510 | 24.229 | 24.550 |
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16.902 | 10.067 | 13.404 | 13.409 |
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19.178 | 11.994 | 15.528 | 15.411 |
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5.515 | 2.203 | 3.824 | 3.970 |
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0.177 | 0.126 | 0.137 | 0.287 |
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0.000 | 0.000 | 0.000 | 0.000 |
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25.953 | 22.167 | 23.990 | 24.103 |
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26.648 | 22.727 | 24.617 | 24.804 |
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24.025 | 20.722 | 22.223 | 22.721 |
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24.613 | 21.245 | 22.773 | 23.353 |
The NPA charges computed for tautomers/rotamers geometry optimized in water are given in Table
NPA atomic charges at B3lyp/6-31+G(d)//B3lyp/6-31+G(d) PCM.
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C1 | −0.298 | −0.316 | −0.297 | −0.385 | −0.302 | −0.263 | −0.297 | −0.269 | −0.303 | −0.367 | −0.308 | −0.296 | −0.238 | −0.271 | −0.251 | −0.282 |
C2 | −0.147 | −0.106 | −0.152 | −0.057 | −0.052 | −0.056 | −0.057 | −0.049 | −0.061 | −0.061 | −0.126 | −0.151 | −0.096 | −0.088 | −0.067 | −0.073 |
P3 | 0.441 | 0.462 | 0.591 | 0.530 | 0.577 | 0.614 | 0.648 | 0.516 | 0.563 | 0.539 | 0.484 | 0.591 | 0.571 | 0.655 | 0.474 | 0.556 |
C4 | −0.066 | −0.375 | −0.403 | −0.361 | −0.369 | −0.348 | −0.338 | −0.007 | −0.011 | −0.033 | −0.383 | −0.403 | −0.374 | −0.402 | −0.347 | −0.369 |
P5 | 0.591 | 0.585 | 0.545 | 0.627 | 0.597 | 0.513 | 0.498 | 0.561 | 0.564 | 0.534 | 0.605 | 0.544 | 0.603 | 0.589 | 0.647 | 0.645 |
C6 | −0.495 | −0.559 | −0.568 | −0.158 | −0.526 | −0.536 | −0.521 | −0.515 | −0.517 | −0.587 | −0.567 | −0.568 | −0.535 | −0.515 | −0.530 | −0.516 |
N7 | −0.819 | −0.835 | −0.846 | −0.585 | −0.616 | −0.636 | −0.645 | −0.629 | −0.620 | −0.836 | −0.840 | −0.845 | −0.631 | −0.630 | −0.633 | −0.635 |
O8 | −0.562 | −0.702 | −0.706 | −0.662 | −0.692 | −0.697 | −0.693 | −0.535 | −0.539 | −0.545 | −0.698 | −0.705 | −0.698 | −0.707 | −0.699 | −0.704 |
H9 | 0.237 | 0.232 | 0.236 | 0.293 | 0.243 | 0.262 | 0.245 | 0.268 | 0.253 | 0.238 | 0.232 | 0.235 | 0.265 | 0.244 | 0.263 | 0.245 |
H10 | 0.010 | 0.263 | 0.267 | −0.157 | 0.261 | 0.264 | 0.263 | 0.013 | 0.011 | 0.018 | 0.262 | 0.2665 | −0.003 | 0.001 | 0.004 | 0.003 |
H11 | 0.266 | 0.420 | 0.412 | 0.379 | 0.508 | 0.363 | 0.511 | 0.267 | 0.266 | 0.266 | 0.415 | 0.411 | 0.266 | 0.264 | 0.264 | 0.263 |
H12 | 0.415 | 0.428 | 0.417 | 0.507 | 0.011 | 0.512 | 0.025 | 0.366 | 0.029 | 0.415 | 0.421 | 0.417 | 0.365 | 0.355 | 0.365 | 0.357 |
H13 | 0.427 | 0.504 | 0.506 | 0.029 | 0.361 | 0.006 | 0.361 | 0.012 | 0.363 | 0.418 | 0.502 | 0.506 | 0.506 | 0.504 | 0.510 | 0.511 |
The NPA charges computed for tautomers/rotamers geometry optimized in water are generally smaller than those computed for tautomers/rotamers optimized in gas phase. This is understandable as a role of the high dielectric constant solvent, water. The amino N accommodates the highest negative charge (up to −0.846), then the O atom comes in the second place (up to −0.707). Positive charges are accommodated on the P and H atoms. Very little negative charge on H bonded to P atoms as appeared in
On the basis of the present theoretical study, we may confirm the following conclusions. We studied for the first time 16 tautomers/rotamers of diphosphocytosine by four computational methods. Some of these tautomers/rotamers are isoenergetic although they have different structure. From the total energy point of view, the 16 tautomers/rotamers are categorized into three main groups. These are low-energy difference group, moderate-energy difference group, and high-energy difference group. Our systematic calculations show that the energy difference between components of a rotamer pair is very stable, independent of the level of theory. This leads to the important conclusion that besides the dominant Benzene-like structures are the most stable tautomers/rotamers. Charge is distributed on the ring atoms; −ve charges are on N and O, while +ve charges on P and H. Solvation does not affect the order significantly;
This work was done at the Vienna Supercomputer Centre of the University of Vienna, Austria.