Effect of alkali metal cations interactions on the intramolecular proton transfers in [cytosine-X] + adduct ions,X = H,Li,Na,K

1 Introduction

Cytosine along with other primary nucleobases such as guanine, adenine, thymine and uracil are the building block of RNA or DNA. These nucleobases can exist in different tautomers due to their intramolecular proton transfers [1–5]. Hydration affects the stability of the nucleobase tautomers and catalyzes tautomerism by lowering the energy barriers of the intramolecular proton transfers [6–10]. Proton and cation transfers are involved in many biological functions of DNA. The proton transfers and intermolecular hydrogen bonds between the pair bases may be affected by the interaction of the nucleobases with ionic and neutral species. Interaction of the nucleobases with alkali and heavy metal cations, proton and other species such as carbon nanotube have been studied [11–15]. Tehrani et al. [16] studied interactions of alkali metal cations (Li⁺, Na⁺, K⁺) with cytidine and showed that the alkali metal cation coordination changes the acidity of the cytosine nucleoside. Also, interactions of the metal cations can stabilize the unstable isomers of the nucleobases and affect their tautomerisms [17]. Rincon et al. [18] studied effect of Ni⁺², Cu⁺² and Zn⁺² on the stability of thymine isomers and reported that the metal cation complexation lowers the energy barriers of the keto-enol tautomersim. Protonation and ionization also affect the energy barriers of single and double proton transfers in the base-pairs [19, 20]. Stabilizing effect of the metal cations has been attributed to oxidation of the nucleobases due to the cation-base interaction [21, 22]. The catalysis effect of metal cations on the proton transfer may be interpreted basis on Lowdin’s hypothesis: metal cations introduce positive charge facilitating the proton transfer from the more positively charged site to another site [19].

In this work, interactions of alkali metal cations (X⁺) with the most stable isomers of cytosine are studied and their effect on the energy barriers of intramolecular proton transfers in the cytosine-X⁺ complexes are investigated. The change in the energy barriers is interpreted basis on the change in the acidity and basicity of the proton donor and proton acceptor sites due to complexation.

2 Computational details

The structures of the molecules, adduct ions, and transition state (TS) complexes were fully optimized employing B3LYP and MP2 methods using 6-311++G(d,p) basis set. B97D, Grimme’s functional including dispersion was also used for calculations on the relative stability of the cytosine isomers [23]. The frequency calculations were performed on the optimized structures by the same method to obtain the thermodynamic parameters at 298.15 K. The structures were also optimized in water solvent with dielectric constant of 78.35 using Tomasi’s Polarized Continuum Model (PCM) [24]. The transition state structures were optimized using the keyword OPT = TS and calculation was carried out on an initial structure very close to the real structure of TS. An intrinsic reaction coordinate (IRC) [25] calculation was performed on the optimized TS geometry to confirm the accuracy of the TS structure. The vibrational frequencies of the TS structures were also checked to sure that they have only one imaginary frequency. The calculations were performed by Gaussian 09 software [26].

Cation affinity of a molecule (M) toward a cation (X⁺) is defined as a negative value of ΔH for the following reaction in gas phase M ( g ) + X + ( g ) → MX + ( g )(1)

The cation basicity of M is calculated as – ΔG value for the reaction (1).

Figure 1 shows the structures of 10 isomers of cytosine optimized in gas phase. Important geometry parameters (bond lengths and angles) of the cytosine isomers are shown in Fig. 1. The structures I, IV, and V are the keto-isomers and others are the enolic forms. The relative energies (ΔE) and Gibbs free energies (ΔG) of the cytosine isomers in gas phase and aqueous solution are compared in Table 1. The values in the parenthesis are the zero point vibrational energy (ZPE)-corrected values which show the same trend as the non-corrected ones do. The relative ΔHs were approximately equal to the corresponding ΔE values, therefore, they were not included in Table 1.

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Fig.1

The structures of 10 isomers of cytosine optimized by B3LYP/6-311++G(d,p) method in gas phase with bond lengths (ringA) and angles (deg).

The comparison of the relative energies calculated by B3LYP method shows that the isomer I (keto-form) is the most stable isomer of cytosine in both gas and aqueous phases and the isomers II (enol-form) has considerable stability. However, the results of MP2 calculations show that the isomer I is the most stable structure only in aqueous phase while the isomer II is the more stable in gas phase. The same discrepancy in the relative stability of the keto and enol isomers of cytosine has been reported previously [3–6]. However, the energy differences between the isomer I and II obtained by the different methods are small (about 6 kJ/mol). Independent calculations were performed by B97D functional which includes long-range dispersion correction. The B97D results show that the keto isomer, I, is more stable than the corresponding enol one, II, which is in agreement with the B3LYP results. The stability of the isomer II may be due to aromaticity and intramolecular hydrogen bonding interaction between hydrogen atom of O-H group and the adjacent nitrogen atom of the ring. Other than the isomers I and II, the data in Table 1 show that the isomers III, IV, and V have noticeable stability and consequently, considerable abundances. Therefore, the interactions of the alkali metal cations only with this five stable isomers, I-V, are considered.

Figure 2 shows the different isomers of protonated and alkali metal cationized cytosine optimized by the B3LYP method in gas phase. Also, the main angles and bond lengths are shown in degree and ringA, respectively. Some of these isomers were not obtained by the MP2 method so that they converted to other isomers during optimization. Therefore, the MP2-energies of these isomers have not been reported in Tables 2, 3, and 4. Cytosine has different proton acceptor sites (N and O atom), therefore, protonation from these sites results in different protonated isomers. The alkali metal cation-cytosine interactions are almost ion-dipole electrostatic interactions [27, 28] so that Li⁺, Na⁺, and K⁺ can interact with two adjacent sites, simultaneously.

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Fig.2

The structures of different isomers of the protonated and alkali metal cationized cytosine, optimized by B3LYP/6-311++G(d,p) method in gas phase with bond lengths (ringA) and angles (deg).

Table 2 summarizes the relative energies of the cytosine adduct ions. In addition, the calculated cation affinities (CA) and cation basicities (CB) of different sites of cytosine have been tabulated in Table 3. The protonation and cation interactions change the stability trend of the cytosine isomers, however, the isomer I is still the most stable isomer in the cytosine-X⁺ complexes. The B3LYP calculations show that among the protonated forms of isomer I, the [I + H]⁺-a isomer, which is a keto tautomer, is the most stable structure. Its stability is due to higher proton affinity (PA) of the nitrogen site of the ring (956 kJ/mol) relative to the oxygen atom of the C = O group and nitrogen atom of the -NH₂. However, the MP2 calculations show that [I + H]⁺-b is slightly (0.04 kJ/mol) more stable than [I + H]⁺-a. Although PA of C = O group is usually smaller than that of the nitrogen sites [27, 28], the PA values of C = O group of the isomer I (954 kJ/mol) is larger than that for the -NH₂, 819 kJ/mol (protonated isomers [I + H]⁺-b and [I + H]⁺-d). These difference is attributed to the stabilization of the protonated isomers [I + H]⁺-b due to intramolecular hydrogen bonding interaction between the proton and neighboring nitrogen atom. For the neutral isomers, the energy difference between the most stable isomer I and other stable isomers (II, III, IV and V) is small (4–28 kJ/mol), while in the protonated structures, this energy gap increases up to 230 kJ/mol. Since the added proton and the hydrogen atoms of cytosine are not distinguishable, some of the protonated forms of isomers I-V are also protonated forms of the unstable isomers VI-X. For example, if an unstable isomer such as isomer VIII is protonated form the N atom of the ring, the obtained structure is the same as the [V-H]⁺-b.

Interactions of the Li⁺, Na⁺ and K⁺ cations with the cytosine isomers change the stability trend so that the interactions increase the stability of the isomer IV more than other isomers. In the neutral isomers, the isomer I is, about 28 kJ/mol, more stable than the isomer IV, while this energy difference decreases to 16–18 kJ/mol in the cytosine adduct ions with Li⁺, Na⁺ and K⁺. The cation affinities (CA) for the system in which the cation interact with the C = O are larger than those for systems with cation-hydroxyl and cation-amine interactions. Since the alkali cations-cytosine interaction is mainly electrostatic, the difference in the cation affinities of the different sites can be interpreted basis on the dipole moment magnitude. The dipole moments of aldehydes and ketones are larger than those of amines and alcohols [29], therefore, the observed CA values are expectable results.

Figure 3 shows the transition state (TS) structures for intramolecular proton transfers in isolated, protonated and alkali metal cationized cytosine optimized by the B3LYP/6-311++G(d,p) method. The important bond lengths and angles of the TS structures have been shown in angstrom (ringA) and degree, respectively. In the TS structures of the proton transfers I↔II and III↔IV, the distance between the transferred H and N is about 1.28ringA, while in the TS structures of the adduct ions, the corresponding distance is almost longer. On the other hand, the H...O bond length in the isolated TS and TS of adduct ions are almost comparable. The change in the bond lengths may be attributed to the change in the acidity and basicity of the proton donor and acceptor sites after cytosine-cation interaction.

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Fig.3

The transition state (TS) structures for intramolecular proton transfers in isolated, protonated and alkali metal cationized cytosine optimized by B3LYP/6-311++G(d,p) method with bond lengths (ringA) and angles (deg).

Table 4 compares the calculated activation energies (E_a), free energies (ΔG^#) and entropies (ΔS^#) of proton transfers in the isolated, protonated and cation adduct ions of cytosine. The MP2-calculated values of E_a and ΔG^# were also included in Table 4. Since there is a good agreement between the B3LYP and MP2 calculated activation energies, only the B3LYP results are discussed. The calculated E_a values of I⟶II and IV⟶III in isolated cytosine are about 140 kJ/mol and 130 kJ/mol, respectively, while in the presence of H⁺, Li⁺, Na⁺ and K⁺, the activation energies of the corresponding proton transfers increase. In other word, the cations do not catalyze proton transfers from N atom of the ring to the O atom of carbonyl group. For the reverse reactions, II⟶I and III⟶IV the alkali cations Li⁺, Na⁺ and K⁺ catalyze the proton transfer from O atom of carbonyl to the adjacent N atom of the ring, while H⁺ increases the activation energies except for [IV+H] ⁺ ⟶[III+H] ⁺ -b. In addition, catalysis effect of the alkali cations is as K⁺ >  Na⁺ >  Li⁺. For the proton transfers I⟶V and V⟶I a regular trend was not observed and in some cases the cations catalyze the proton transfer and in others they increase the energy barriers. The activation entropies are negative except for the [I + Li]⁺-c↔[II+Li]⁺-b proton transfer. In the [I + Li]⁺-c and [II+Li]⁺-b adduct ions, the Li atom is located in the molecule surface, however, in the transition state structure of [I + Li]⁺-c↔[II+Li]⁺-b reaction, the Li atom is out of the molecule surface. Therefore, the structures of the isomers [I + Li]⁺-c and [II+Li]⁺-b are more regular than the corresponding TS structure and their entropies are smaller than the entropy of the TS structure.

We assume that the change in the energy barriers of the proton transfers is due to the change in the acidities and basicities of the proton donor and acceptor sites of cytosine after their interactions with the cations. Therefore, the acidity of these sites were calculated in the absence and in the presence of the cations (X⁺) according to reaction (2) [ I + X ] + → [ I + X - H ] + H + , Δ H acid(2) where, [I + X]⁺ is a cytosine-cation complex and [I + X-H] is the corresponding conjugate base. ΔH_acid is the enthalpy of deprotonation of [I + X]⁺ in gas phase and its negative (–ΔH_acid) can be considered as the basicity or proton affinity of [I + X-H]. The ΔH_acid values calculated by the B3LYP/6-311++G(d,p) method are tabulated in Table 4. Comparison of the ΔH_acid values shows that the acidity of the cytosine increases in the presence of the cations which is an expectable result [16]. Increase in the acidity of a proton donor site (PDS) may decrease the energy barrier and catalyze the proton transfer, however, the energy barrier also depends on the acidity of the proton acceptor site (PAS). A proton acceptor site with higher basicity (–ΔH_acid) or weaker acidity facilitates the proton transfer. Therefore, the difference in the acidity of the PDS and PAS, Δ(ΔH_acid), was calculated according to equation 3, as a useful tool to interpret effect of cation-cytosine interaction on the intramolecular proton transfers Δ ( Δ H acid ) = Δ H acid ( PDS ) - Δ H acid ( PAS )(3)

The Δ(ΔH_acid) values calculated by the B3LYP method are summarized in Table 4. In the case of cation-catalyzed proton transfers, the Δ(ΔH_acid) values are more positive than the corresponding value of isolated cytosine. The large negative values of Δ(ΔH_acid) in the presence of the cations indicate the increase in the energy barriers. Figure 4 shows the correlation between the Δ(ΔH_acid) values and the E_a. For Δ(ΔH_acid)≈0.0, the E_a is about 160 kJ/mol, and as the Δ(ΔH_acid) increases the activation energy decreases.

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Fig.4

Linear relationship between the activation energies, E_a, of intramolecular proton transfers in cytosine and difference in the acidity of the proton donor and proton acceptor sites, Δ(ΔH_acid).

Cytosine has different isomers, however, in this work only five of the most stable isomers with considerable relative abundances were considered. Interactions of H⁺, Li⁺, Na⁺ and K⁺ with the cytosine isomers were studied using B3LYP and MP2 methods. The cation-cytosine interactions influenced the stability trend of the cytosine isomers, however, the keto structure (isomer I) was the most stable isomer in the all cytosine-X⁺ complexes. The energy barriers of the intramolecular proton transfers in isolated cytosine were about 130–160 kJ/mol. Effect of alkali metal cation interactions on the activation energies was different so that the cations catalyze some of the reactions and increase the energy barriers of other proton transfers. This different effect was attributed to change in the acidity and basicity of the proton donor and proton acceptor sites due to cation-cytosine interaction. A linear correlation was obtained between acidity difference of the proton donor and proton acceptor sites and the activation energy of the corresponding proton transfer.