Stabilization of an excess electron on uracil by water. Ab initio study

Experiments performed on the uracil anion in the gaseous phase indicated that in this system the excess electron is dipole-bound.

The experiments, however, also indicated that water solvation changes the character of the anion from dipole-bound to covalent.

In this work we have used ab initio theoretical calculations to investigate the stabilization effect that the attachment of one or two water molecules has on the electron attached to uracil.

The calculations concern both dipole-bound and covalently-bound electrons and reveal rich configurational isomerism of the complex of the uracil anion with H2O molecules.

The systems differ in terms of the structure of the solvation cluster formed around the excess electron.


The existence of the dipole-bound anion of uracil was first predicted theoretically in our group1 and subsequently detected in gas phase experiments by the groups of Schermann2 and Bowen.3

Subsequent experiments concerning anion formation of hydrated molecules of nucleic acid bases4 showed that hydration changes the nature of the complex with an excess electron anion and converts the very weakly-dipole-bound uracil anion to a more stable conventional covalent anion.

The photoelectron spectroscopy (PES) showed very different spectral signatures of the two anions.

While for the former a sharp narrow peak at 93 ± 7 meV was observed, the latter produced a broad feature characteristic to a covalent anion.4

The broad feature did not show any vibrational structure and was noticeably shifted towards higher electron binding energies than the feature corresponding to the dipole-bound anion of the monomer.

The stabilization of an excess electron attached to a closed-shell system by solvating the anion with polar molecules is an effect that can be easily understood based on the analysis of the electrostatic interactions occurring between the excess electron and the solvating systems.

The transformation of a dipole-bound anion to a covalent anion upon solvation, however, may also involve, apart from the stabilization of the excess electron by the direct interaction with solvating systems, an additional effect resulting from the structural conformation of the solvated covalent anion being more stable than the conformation of the solvated dipole-bound anion.

Our previous calculations of the covalent electron attachment to uracil indicated that such an attachment causes a puckering distortion of the uracil ring.

If solvation stabilizes the puckered uracil structure more than the planar structure of the uracil dipole-bound anion, the covalent anion may become more stable.

The additional stabilization due to solvation may also result from a stronger interaction of the solvent with the more localized covalently-attached excess electron than with the much more diffused dipole-bound electron.

In this work, we study the solvation of the excess electron in uracil anion by one and two water molecules.

We only consider structures where at least one water molecule is in direct contact with the electron.

For the [uracil]·water complex, we have already studied one such configuration where the dipole-bound excess electron of uracil was localized between the uracil molecule and the water molecule.5

We showed that such a configuration is stable, the presence of water stabilizes the dipole-bound excess electron and makes it more localized.

In the present work, we study the stabilization of an excess electron covalently attached to a uracil molecule by a water molecule.

We also consider the stabilization effects on a dipole-bound and a covalently-bound excess electron in the uracil anion by two water molecules.

Trapping excess electrons in molecules and clusters either by fields of dipoles, higher multipoles or in covalent states, is a phenomenon with relevance to fundamental properties of molecular systems.

An electron trapped in a localized bound state of the system may significantly affect its chemical and physical properties.6

It is also interesting to investigate structures of possible molecular electron traps formed by molecular complexes.

For example, electron trapping is relevant to molecular charge conductivity and charge localization in such systems as DNA and other biopolymers.

In this work, we consider enhancement of the uracil ability to bind an excess electron resulting from direct interaction of the electron with water molecules.

In particular, the calculations performed here show a rich conformational topology of the uracil·(H2O)2·e system and describe the magnitude of the electron stabilization effects resulting from the solvation.

Calculations and discussion

All the calculations in this work have been performed using the Gaussian98 program package.7

The spin-restricted and spin-unrestricted Hartree–Fock (RHF and UHF) methods were used for neutral systems and anions, respectively.

For all systems, the structure optimizations have been performed using the second-order Møller–Plesset perturbation theory (MP2).

All structures reported in this work are available via e-mail from the corresponding author upon request.

In the first series of calculations we considered stabilization of a covalent uracil anion by a water molecule.

We only searched for a structure where water was directly interacting with its hydrogens with the excess electron.

Thus, the structure optimization of the system performed at the UMP2/aug-cc-pvdz level of theory was initiated with a puckered structure of uracil with a water molecule suspended above the uracil ring.

This calculation converged to a structure shown in Fig. 1.

In the figure we also show the UHF orbital occupied by the excess electron in this system.

One can notice that, as expected, the excess electron is covalently attached to uracil in a π-state and the water molecule directly interacts with the electron and does not form hydrogen bonds with the uracil molecule.

These features differentiate the structure found here from the structure of the uracil·H2O anion described by Dolgounitcheva et al.8

In their structure the water molecule had an in-plane hydrogen bond to one of the oxygens in uracil and its contact with the π excess electron was reduced.

Next, the electron binding energy in the anion was determined with respect to the neutral complex with the same geometry as the uracil·H2O anion (the vertical electron detachment energy, VDE) and with respect to the equilibrium geometry of the neutral complex obtained in the MP2/aug-cc-pvdz optimization (the adiabatic electron detachment energy, ADE).

This optimization was initiated with the geometry of the anion and the optimized H-bonded structure of the uracil·H2O complex is shown in Fig. 2.

The calculations of the VDE and ADE were performed at the MP2/aug-cc-pvdz//MP2/aug-cc-pvdz, MP2/aug-cc-pvtz//MP2/aug-cc-pvdz (except for VDE), and MP4/6-31++G**//MP2/aug-cc-pvdz levels of theory and the results are shown in Table 1.

This was performed to determine how these quantities change when the basis set is increased and when the level of theory is enhanced.

As one can see from the results, the VDE values are all positive and they increase slightly in going from the 6-31++G** basis to the aug-cc-pvdz basis.

Moving from the MP2 to the MP4 level of theory has very little effect on VDE and ADE.

The ADE values are all negative indicating that the covalent anion is a metastable system, less stable than the neutral complex.

Based on the MP2 energies obtained with the different basis sets, which seems to be converging to a value around −0.2 eV and based on the very small reduction of ADE due to inclusion of higher order effects of 0.04 eV, it is unlikely that the anion can become more stable than the neutral system.

There are a number of ways an excess electron attached to a uracil molecule can interact with two H2O molecules.

Both the dipole-bound σ excess electron and the covalently attached π-electron have to be considered as possible targets of hydration since in both cases the stabilization effect of hydration should render the excess electrons more strongly attached to the uracil moiety.

One can envision the following configurations of the two H2O molecules interacting with the dipole-bound excess electron of the uracil anion: a configuration where both waters point the positive ends of their dipoles at the electron; a configuration where an H2O dimer points its dipole at the excess electron; a configuration where the excess electron is dipole-bound to the complex of uracil with a water molecule and is solvated by the other water; and a configuration where an H2O dimer is H-bonded to uracil and at the same time solvates the dipole-bound electron of uracil.

An electron covalently attached to a uracil molecule in a π-state can be hydrated by two water molecules in the following ways: two waters can approach uracil perpendicularly to its ring, one on each side of the ring; two waters can independently approach the excess electron from one side of the ring; a water dimer can approach the electron perpendicularly to the uracil ring.

There are, perhaps, some other possibilities.

In the first series of calculations we have explored the topology of the uracil·(H2O)2·e anion by performing geometry optimizations of the system and initiating them with different initial geometries of the complex reflecting the structural isomerism described above.

The optimizations for the anions with two waters solvating the dipole-bound excess electron of uracil were performed at the UMP2 level of theory with the 6-31++G** basis set augmented with additional diffuse orbitals placed at the hydrogen of uracil located the closest to the positive pole of the uracil dipole.

The additional diffuse orbitals included six gaussian sp-shells with exponents 0.01, 0.002, 0.0004, 0.00008, 0.000016, and 0.0000032 and a p-subshell with the exponent 0.036.

In our previous studies we have determined that this set of additional orbitals should be sufficient to describe the ground states of the dipole-bound excess electron in systems with dipole moments similar to the dipole moments of the complexes considered in the present work.9

By including gaussians with very small exponents in the basis we allowed the excess electron to escape from the system, if such a process would lower the system's total energy.

Thus, the possibility that the excess electron stays confined to the system due to an overly confining orbital basis and not due to higher stability of the anion than the neutral cluster is eliminated.

The augmented 6-31++G** basis will be called 6-31++G**X in the discussion that follows.

The geometry optimizations of the hydrated covalent uracil anion with the excess electron occupying a π state was first performed at the UMP2/6-31++G** level of theory and then the structures were refined with the use of the UMP2/aug-cc-pvdz level.

The geometry optimizations produced five different uracil·(H2O)2·e structures (A, B, C, D, and E) corresponding to minima on the potential energy surface of the anion.

The structures are shown in Fig. 3.

In Fig. 4 we show the orbitals occupied by the excess electrons in these systems and in Table 2 we present their total UMP2 energies and their vertical electron detachment energies (VDE) calculated by subtracting the energy of the neutral cluster determined at the geometry of the anion (at the MP2/6-31++G**X level for A and B, and at the MP2/aug-cc-pvdz level for C, D, and E) from the anion energy.

The calculated VDEs of 0.45 eV for A and 0.43 eV for B indicate that the hydration stabilizes the excess electrons in these systems.

By examining the orbitals of the first two anions one can notice that for both systems we have the case of the two H-bonded water molecules solvating the uracil dipole-bound electron.

The difference in the systems, which is reflected in the total energy for A being slightly higher than for B, is a hydrogen bond between the uracil and the water dimer that exists in B, but is not present in A.

Anions C–E are different from anions A and B. Here the excess electron occupies a π-orbital of uracil and is solvated by waters approaching the uracil from axial directions.

As mentioned before,10 in the covalent anion of uracil its ring is noticeably puckered.

This puckering does not disappear upon hydration which is apparent in the structures of the C–E anions shown in Fig. 3.

In anion C, the two H2O molecules are positioned on opposite sides of the uracil ring and in anions D and E they are located on the same side.

In all three configurations the ring puckering is enforced and the stabilization of the excess electron in the π-state is enhanced.

For all three anions with a covalently attached excess electron, the VDE values are much larger than for anions A and B. They are 1.21 eV for anion C, 1.24 eV for anion D, and 1.18 eV for anion E. In this group anion E is slightly more stable than the other two.

There are some common structural features in anions C, D, and E. In all three systems, one of the water molecules is positioned exactly above the uracil ring with one of its hydrogens pointing at N3 and the other pointing at C6.

The position of the second water molecule is what differentiates the three structures; in C the second water is located on the other side of the ring with respect to the first water and in D and E the second water is H-bonded to the first one.

However, in all three anions, one of the hydrogens of the second water molecule always points at one of the uracil oxygen atoms and it is involved in a H-bond interaction with that atom.

Thus, in anions D and E, a cyclic structure is formed involving the water molecule linked with its hydrogens to the π-attached uracil excess electron, and the second water molecule which forms a bridge between the first water and an oxygen atom of uracil.

Finally, in the last series of calculations, geometry optimizations were performed for the neutral uracil·(H2O)2 cluster.

This system has been considered in a number of works including, for example, recent studies by van Mourik11 and Gadre et al.12

Since the optimizations of the uracil·(H2O)2 cluster in the present calculations were only initiated with the geometries of the A–E anions, the equilibrium structures found do not describe the complete topology of the uracil·(H2O)2 potential energy surface.

The “A,B”–initiated optimizations carried out at the MP2/6-31++G**X level converged to a single structure shown in Fig. 5 (structure A).

This appears to be the global minimum on the uracil·(H2O)2 potential energy surface.11

The optimizations initiated with the geometries of anions C, D and E and carried out at the MP2/aug-cc-pvdz level converged to structures B, C and D, respectively.

In A, the two H2O molecules and the uracil molecule form a cyclic hydrogen-bonded structure with three H-bonds.

In B, the two waters are separated and are H-bonded to uracil at opposite sides.

In C, the waters form a dimer which is H-bonded to uracil and only one water molecule is involved in this bond.

In D, the waters also form a dimer which is positioned above the uracil ring and interacts with π-electrons of the uracil.

The comparison of the total energy of the A uracil·(H2O)2 neutral cluster provided in Table 2 with the energies of anions A and B shows that the neutral system is more stable than any of the two anions by 0.49 and 0.30 eV, respectively.

Also, the energy of anion C is higher than the energy of the B uracil·(H2O)2 cluster by 0.10 eV.

However, the relative stability order is reversed for anions D and E. These systems are more stable than the neutral uracil·(H2O)2 clusters with the equilibrium geometries obtained in the optimizations initiated with the geometries of the two anions.

Since the structures of anions A and B and the structure of the neutral cluster are dissimilar, the relative stability determination as the difference of the total energies may be subject to the basis set superposition error (BSSE).

The same effect, however, probably smaller, may also occur for anions C, D, and E. To verify this point a series of calculations were carried out to estimate the magnitude of this error in the determination of the ADE energy for anion A where dipole-bound uracil electron is solvated and for anion C where a covalently-attached excess electron of uracil is subject to solvation.

Two series of three calculations were undertaken for each of the two systems.

In the first series we considered an isolated uracil molecule and each of the two waters and the calculations were undertaken in the basis set of the whole anion and in the second series the calculations for the three systems were repeated in the basis set of each individual molecule.

For calculations pertaining to anion A we used the MP2/6-31++G**X level of theory and for those pertaining to anion C we used the MP2/aug-cc-pvdz level.

The difference of the energies obtained in this way for each of the three systems (i.e. uracil and two waters) provided an estimation of how much each system is stabilized by calculating it in the basis set of the cluster vs. calculating it in its own basis.

The total stabilization effect was obtained by summing up the contributions obtained for the three systems.

A similar series of calculations was also performed for the equilibrium geometries of the A and B neutral uracil·(H2O)2 clusters and the basis-set stabilization effect determined for these systems was subtracted from the corresponding stabilization energies obtained for anions A and C. In this way, the corrections that need to be added to the ADE values of anions A and C to approximately compensate for the BSSEs were determined.

In the above approach we assumed that the basis set effect does not change much in moving from the anion to the neutral system and, thus all the above calculations could be performed for the neutral forms of the molecules forming anions A and C.

Since in the neutral equilibrium uracil·(H2O)2A cluster the three molecules are closer together than in anion A, we anticipated a larger basis-set related stabilization effect for the former than for the latter system.

This was indeed confirmed by the calculations which yielded a value of 0.14 eV for the difference of the two basis-set stabilization effects in favour of the neutral cluster (i.e. the neutral cluster was more stabilized than the anion by the molecules forming the cluster using the basis functions of the partner molecules to lower their energies).

Thus, in order to correct the ADE for anion A the value 0.14 eV should be added to the value −0.49 eV obtained without the BSSE correction.

Although this changes the ADE somewhat, it still remains negative indicating metastability of the anion with respect to the neutral cluster.

For anion C one can expect that the basis set effect should also reduce the magnitude of the ADE but to a much lesser degree than for anion A because the intermolecular distances in C and its corresponding neutral cluster (B) are not as different as they are in A and its neutral counterpart (A).

Again the calculations confirmed the anticipated trend and gave the value of only 0.02 eV for the basis-set related stabilization effect in this case.

This value should be added to the value −0.10 eV obtained without the BSSE correction.

Again in this case the correction does not reverse the stability order of the anion and the neutral cluster.


The calculations performed in this work describe an interesting topology of the configurational space of the anion consisting of a uracil molecule and one and two H2O molecules.

We have only considered structures where either one or both waters are in direct contact with the excess electron attached to the uracil, and for the anion involving a single water molecule we only considered a structure with a covalently attached electron in a π-state because the other isomers of this system had been studied before.5

In all the considered systems the interaction of the H2O molecules with the dipole-bound or covalently-bound excess electron significantly enhances the bonding of the electron.

Also, the state of the excess electron becomes more localized.

The uracil·(H2O)2 system is an interesting model of an electron trap formed by clusters of polar molecules.

It is evident that an excess electron attached to a molecule can be solvated through direct contact with polar molecules of the solvent.

The solvation cluster formed around the electron can accommodate more than one molecule and may have different configurations which, in addition to the direct links of the systems forming the cluster to the electron, may also involve inter-system links.

Most of the anions studied in in this work, though quite stable with respect to removal of the excess electron without geometry relaxation, are metastable with respect to the neutral clusters at their equilibrium geometries.

Only two uracil·(H2O)2 anions (anions D and E) are both “vertically” and “adiabatically” stable.

Here the adiabatic stability corresponds to the energy of the anion being lower than the energy of the neutral complex with the equilibrium structure obtained in the geometry optimization initiated with the geometry of the anion (not with regard to the lowest energy structure).

This is the first time such anions have been predicted for the uracil·(H2O)2 system using ab initio calculations.

The hydrated uracil·H2O·e and uracil·(H2O)2·e systems described in the calculations performed in this work may be the covalent anions of uracil·water clusters observed in the experiments.4

We hope the present calculations will inspire further experimental attempts to study the configurational isomerism of anions of hydrated uracil in the gas phase.