Effect of hydration on the stability and tautomerisms of different isomers of uracil

Abstract

Thermodynamic and structural properties of isolated, hydrated and solvated forms of twelve isomers of uracil were studied theoretically. It was found that the di-keto tautomer is the most stable isomer in gas and aqueous phases and in hydrated forms. Internal proton transfers and O–H rotations in uracil were studied employing B3LYP and MP2 methods in a gas phase. Activation energies (E_a) and Gibbs free energies (ΔG^#) of the isomerization processes were calculated. The calculated activation energies of the proton transfer reactions were in the range of 110–180 kJ mol⁻¹ and the energy barriers of internal O–H rotations were generally smaller than 40 kJ mol⁻¹. The high energy barriers of the proton transfers indicate that proton transfers are hard to achieve. Therefore, the catalytic effects of one, two and three water molecules on the proton transfer processes in the hydrated isomers of uracil were investigated. The calculations showed that water molecules lower the energy barriers of the proton transfer reactions and catalyze the tautomerism processes in uracil.

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1 Introduction

Uracil is a naturally occurring pyrimidine derivative and one of the four nucleobases in the nucleic acids of RNA. Many researchers have studied the structures of different tautomers of uracil, as well as their stability in the gas and solution phases.^1–16 Furthermore, some studies have been performed on the reactions of uracil and its interaction with other molecules.^17,18

There are some experimental studies on the detection of different tautomers of uracil.^1,4,6 Tsuchiya et al.¹ studied uracil structure using fluorescence spectroscopy. They observed both di-keto and keto–enol tautomers of uracil. A photoemission spectroscopy study by Feyer et al.⁴ showed that only the di-keto tautomer of uracil has significant abundance at 405 K. Bakker et al.⁶ studied structures of protonated uracil using infrared (IR) photodissociation spectroscopy. The obtained IR spectrum confirmed the presence of two different types of protonated uracil that resulted from two tautomers of uracil.

The theoretical studies have mainly focused on the relative stability of different tautomers of uracil by comparison of the Gibbs free energies of the tautomers.^7–11 Tian et al.⁷ studied eight tautomers of uracil using a B3LYP method and reported that the di-keto tautomer is the most stable tautomer. Millefiori and Alparone⁸ studied the relative stability of six tautomers of uracil using CCSD(T) and DFT methods and obtained the same results. In addition, energy barriers of some tautomerism processes in uracil and its derivatives have been calculated theoretically.^12,13 Markova et al.¹² calculated the activation energies of the tautomerism of 5-fluorouracil in the absence and in the presence of three water molecules. They showed that water molecules decrease the activation energy of the tautomerism by 2.3 times. Li and Ai¹³ studied the catalytic effect of a water molecule on the tautomerism of uracil using a DFT method. They investigated only three tautomers of uracil and reported that the water molecule has a significant catalytic effect on the tautomerism in uracil.

In this work, the structures and stability of twelve different isomers of uracil are studied in gas and aqueous phases using MP2 and B3LYP methods. Activation energies (E_a) and Gibbs free energies (ΔG^#) of tautomerism processes in uracil are calculated. Then, the catalytic effects of one, two and three water molecules on the tautomerism processes are investigated.

2 Computational details

The structures of all the isomers, transition states, pre-reactive complexes and pre-product complexes were optimized at MP2 and B3LYP levels of theory. The 6-311++G(3df,3pd) and 6-311++G(d,p) basis sets were employed for the B3LYP and MP2 calculations, respectively. Also, the frequency calculations were performed at the same levels of theory and basis sets to obtain the thermodynamic properties of the structures. Zero-point vibrational energies and thermal corrections were considered in order to obtain the enthalpies (ΔH), Gibbs free energies (ΔG) and activation energies (E_a). The correctness of the transition state structures was verified by performing intrinsic reaction coordinate (IRC)¹⁹ calculations. Also, the structures of the uracil isomers were optimized in aqueous phase. For this reason, solvent (water) was modeled with Tomasi's Polarized Continuum Model (PCM).²⁰ The PCM uses the integral equation formalism variant (IEFPCM) as the default SCRF method in the Gaussian 09 package.²¹ This method creates the solute cavity via a set of overlapping spheres in which the radii of all the atoms in the molecule are obtained using the UFF method. The Gaussian 09 quantum chemistry package was used for all the calculations.²¹

3 Results and discussion

3.1 Relative stability of uracil isomers

Twelve isomers of uracil were studied. Fig. 1 shows the structures of the uracil isomers optimized at the B3LYP level of theory. Isomer I is the di-keto form, isomers II–VII and XII are keto-imine tautomers and isomers VIII–XI are di-ol (di-imine) tautomers.

Fig. 1 Structures of uracil isomers optimized by B3LYP/6-311++G(3df,3pd).

Table 1 summarizes the energies (ΔE), enthalpies (ΔH) and Gibbs free energies (ΔG) of the twelve isomers of uracil in the gas phase relative to isomer I. A zero point energy (ZPE) correction was considered in the calculation of the energy values. Isomer I, the di-keto isomer, is the most stable isomer, while isomer VII is the most unstable one. The instability of isomer VII may be due to H–H repulsion between the hydrogen atoms of the NH and OH groups. Isomers IV and VIII are two stable isomers. Internal hydrogen bonds result in the stability of isomer IV, while isomer VIII is somewhat aromatic and has some hydrogen-bonding effect in its structure. Generally, isomers VIII–XI (di-ols) have the same stability. These di-ol isomers have some aromaticity properties and the small differences in their stability may be due to differences in the amount of the internal hydrogen-bonding effect in their structures. Li and Ai¹³ have studied the thermodynamic and structural properties of isomers I, II and IV and reported that isomer I is the most stable isomer and the ΔG values of isomers II and IV relative to isomer I are 51 and 47 kJ mol⁻¹, respectively. Their results are in good agreement with our data.

Table 1 Relative energies (ΔE), enthalpies (ΔH) and Gibbs free energies (ΔG) of the twelve isomers of uracil in the gas phase. All computed energies are ZPE corrected

Isomer	MP2/6-311++G(d,p)			B3LYP/6-311++G(3df,3pd)
	ΔE (kJ mol^−1)	ΔH (kJ mol^−1)	ΔG (kJ mol^−1)	ΔE (kJ mol^−1)	ΔH (kJ mol^−1)	ΔG (kJ mol^−1)
I	0.00	0.00	0.00	0.00	0.00	0.00
II	50.55	50.53	47.82	47.88	47.87	48.00
III	78.12	78.11	72.45	72.61	72.59	72.02
IV	45.20	45.19	43.67	46.03	46.01	46.30
V	73.94	73.93	72.74	74.16	74.14	73.05
VI	75.46	75.45	69.60	78.14	78.12	77.30
VII	111.28	111.27	110.33	113.79	113.77	108.58
VIII	45.86	45.85	46.13	53.08	53.07	54.10
IX	67.18	67.16	66.50	72.42	72.40	73.03
X	50.27	50.25	50.28	57.10	57.09	57.98
XI	67.37	67.35	66.75	72.66	72.65	73.25
XII	88.11	88.10	83.25	83.073	83.05	82.29

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The structures of uracil isomers were also optimized in the aqueous phase using a PCM model and a B3LYP method. Geometrical parameters of the optimized structures of the uracil isomers in gas and aqueous phases are compared in the ESI A.† Comparison of the geometrical parameters shows that the structures of the uracil isomers are almost the same in the gas and aqueous phases. The relative Gibbs free energies (ΔG) of the twelve isomers of uracil in the aqueous phase are summarized in Table A in the ESI.† Table A† shows that, similar to the gas phase, the isomer I is the most stable isomer in aqueous phase. Furthermore, the stabilities of all the isomers in the aqueous phase are more than those in the gas phase. The stability of the uracil isomers in the aqueous phase is due to the formation of hydrogen bonds between water molecules and uracil as well as to their dipole–dipole interactions.

To compare the relative stability of the isomers in the gas and aqueous phases, the following reaction was used

U_i (g) → U_i (aq) (1)

where U_i is a typical isomer of uracil. The enthalpies (ΔH) and Gibbs free energies (ΔG) of reaction (1) were calculated. In fact, these values are the enthalpies (H_aq − H_gas) and Gibbs free energies (G_aq − G_gas) of solvation of the uracil isomers in water. The ΔH and ΔG values of solvation of the uracil isomers are tabulated in Table 2. Solvation reactions of the uracil isomers in water are exothermic reactions. The enthalpies and Gibbs free energies of solvation are almost the same which indicates that their entropy values are negligible.

Table 2 Comparison of ΔH and ΔG values of mono- and di-hydrations and solvation of the uracil isomers. The data were calculated by the B3LYP method and ZPE corrected

Isomer	ΔH (kJ mol^−1)			ΔG (kJ mol^−1)
	Mono-hydration	Di-hydration	Solvation	Mono-hydration	Di-hydration	Solvation
I	−17.77	−42.35	−44.12	19.74	33.11	−44.03
II	−29.80	−59.92	−47.65	10.23	18.89	−47.23
III	−28.03	−57.32	−63.03	11.43	20.09	−62.18
IV	−29.50	−57.41	−34.65	10.86	21.76	−34.53
V	−29.78	−68.45	−48.68	10.20	9.81	−47.75
VI	−36.14	−70.62	−56.75	4.66	9.19	−56.12
VII	−26.17	−41.62	−76.92	11.55	25.47	−73.05
VIII	−22.66	−46.37	−25.70	17.06	31.89	−25.94
IX	−21.62	−45.07	−37.55	18.01	33.13	−37.41
X	−17.84	−42.08	−28.65	20.89	36.61	−28.80
XI	−22.56	−46.33	−37.57	16.59	29.74	−37.49
XII	−26.64	−53.74	−55.30	12.72	23.23	−54.36

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The uracil isomers were also optimized in the presence of one and two water molecules. Each isomer of uracil can be hydrated from different sites. Therefore, there are a few hydrated forms of each isomer. Fig. 2 shows the optimized structures of the mono- and di-hydrated forms of the twelve isomers of uracil. Fig. 2 shows only one of the mono- and one of the di-hydrated forms for each isomer. The geometrical parameters of the optimized structures of the complete mono- and di-hydrated forms of the uracil isomers are brought together in ESI B.†

Fig. 2 The optimized structures of the mono- and di-hydrated isomers of uracil.

The thermodynamic properties of mono- and di-hydration reactions of the uracil isomers were studied in the gas phase according to the following reactions

U_i (g) + H₂O (g) → U_i(H₂O) (g) (2)

U_i (g) + 2H₂O (g) → U_i(2H₂O) (g) (3)

The enthalpies and Gibbs free energies of mono- and di-hydrations of the uracil isomers were calculated at the B3LYP level of theory using the 6-311++G(3df,3pd) basis set. These thermodynamic quantities are summarized in Table 2. The calculated enthalpies of the mono-hydrations are negative values in the range of −17 to −35 kJ mol⁻¹. The ΔH values of the di-hydrations are about −45 to −70 kJ mol⁻¹. The mono- and di-hydrations of the uracil isomers are exothermic reactions. The hydrations of the uracil isomers proceed through the formation of hydrogen bonds. Since the hydrogen bond formations are exothermic reactions, the hydration reactions are also exothermic. The enthalpies of the mono- and di-hydrations of the di-keto isomer (isomer I) and di-enol isomers (isomers VIII–XI) are smaller than those for other isomers. Table 1 shows that the isolated isomers I and VIII–XI are more stable than others. Therefore, it seems that the tendency of these stable isomers for hydration is less than those of others. On the other hand, the Gibbs free energies of the both mono- and di-hydrations are positive values. The equation ΔG = ΔH − TΔS shows that, although the ΔH values of the hydrations are negative, the −TΔS is more positive which leads to positive values for Gibbs free energies of the hydrations. The effect of the hydration of the uracil isomers is different, so that the some of them become more stable than others. For example, the change in the stability of the isomers V and VI due to hydration is more than that of the other isomers (Table 2). However, since the changes in the stability due to hydrations are not as great, the hydrated forms of isomer I are the most stable hydrated forms. Although both isolated and hydrated forms of isomer I are the most stable isomers, the relative stability trends in the isolated isomers and their hydrated forms are not the same (Table A in ESI†). Generally, Table A† shows that isomer I is the most stable isomer in the isolated, hydrated and solvated forms.

3.2 Isomerization of uracil

Fig. 3 shows transition-state (TS) structures of the isomerizations of uracil optimized by an MP2 method. The geometric parameters of the TS structures are collected in ESI C.† The structures I ↔ II, I ↔ IV, I ↔ VI, II ↔ VIII, III ↔ IX, IV ↔ VIII, V ↔ X and XI ↔ XII are transition-state structures of keto ↔ enol or amine ↔ imine tautomerisms. In the amine ↔ imine tautomerisms of uracil, a hydrogen atom is transferred between a nitrogen atom and an oxygen atom. Other structures in Fig. 3 are transition-state structures of the internal O–H rotations.

Fig. 3 The transition-state structures of isomerization in uracil that have been optimized at the MP level of theory.

The calculated activation energies (E_a), Gibbs free energies (ΔG^#) and imaginary frequencies (ν) of TS structures of the tautomerisms of uracil are tabulated in Table 3. There is a good agreement between the MP2 and B3LYP calculated values. However, the B3LYP energies are a few kJ mol⁻¹ smaller than the MP2 energies, which is due to an underestimation of the energy barriers by the B3LYP method.²² As seen, the activation energies of the keto → enol and enol → keto tautomerisms are in the range of 140–180 and 110–135 kJ mol⁻¹, respectively, while the energy barriers of the internal O–H rotations are generally less than 40 kJ mol⁻¹. Since the di-keto tautomer (isomer I) is the most stable tautomer of uracil, the tautomerism processes I → II, I → IV and I → VI have the highest activation energies (160–180 kJ mol⁻¹), while the activation energies for the backward reactions (II → I, IV → I and VI → I) are about 110 kJ mol⁻¹. Furthermore, since the proton affinity of a nitrogen atom is more than that of an oxygen atom,²³ and in the I → II, I → IV and I → VI tautomerisms a proton is transferred from a nitrogen atom to an oxygen atom, it is expected that these tautomerisms have the largest activation energies. Li and Ai¹³ have calculated the activation energies of the tautomerism processes I → II and I → IV using B3LYP and MP2 methods. Their reported activation energies are about 174 to 179 kJ mol⁻¹, which are in agreement with our results. In some tautomerism processes, such as II → VIII, a di-ol tautomer is produced. The activation energies of these processes are in the range of 120–135 kJ mol⁻¹. The imaginary frequencies of the TS structures of the tautomerism processes are around 1870 cm⁻¹, which correspond to stretching vibrational modes. Also, the calculated imaginary frequencies of TS structures of the rotational processes are in the range of 350–550 cm⁻¹ (Table 3).

Table 3 The calculated activation energies (E_a), Gibbs free energies (ΔG^#) and imaginary frequencies (ν) of TS structures of tautomerisms of uracil in the gas phase. All computed energies are ZPE corrected

Reaction	MP2/6-311++G(d,p)			B3LYP/6-311++G(3df,3pd)
	Ea (kJ mol^−1)	ΔG^# (kJ mol^−1)	ν (cm^−1)	Ea (kJ mol^−1)	ΔG^# (kJ mol^−1)	ν (cm^−1)
I → II	161.68	159.82	−1877.31	157.07	157.91	−1889.34
II → I	111.14	112.01	−1877.31	109.18	109.89	−1889.34
I → IV	164.58	161.32	−1874.80	161.87	162.67	−1884.68
IV → I	119.38	117.65	−1874.80	115.84	116.36	−1884.68
I→VI	183.38	181.32	−1869.55	183.07	183.48	−1889.99
VI → I	107.92	111.73	−1869.55	104.93	106.17	−1889.99
II → III	43.24	44.62	−549.24	41.34	41.69	−523.70
III → II	15.67	19.98	−549.24	16.62	17.67	−523.70
II → VIII	130.41	133.10	−1867.22	132.54	133.90	−1874.14
VIII → II	135.09	134.78	−1867.22	127.35	127.81	−1874.14
III → IX	126.52	130.83	−1862.79	129.24	130.81	−1871.85
IX → III	137.47	136.79	−1862.79	126.95	129.80	−1871.85
IV → V	34.41	36.09	−395.12	32.72	33.51	−395.81
V → IV	5.67	7.02	−395.12	4.59	6.75	−395.81
IV → VIII	135.05	136.58	−1867.64	135.36	136.63	−1872.34
VIII → IV	134.39	134.12	−1867.64	128.30	128.83	−1872.34
V → X	120.94	121.58	−1851.56	120.21	122.52	−1858.76
X → V	144.62	144.10	−1851.56	137.26	137.59	−1858.76
VI → VII	41.98	46.36	−335.69	36.79	37.48	−353.34
VII → VI	6.16	5.63	−335.69	1.14	6.21	−353.34
VIII → IX	34.92	35.86	−516.95	34.90	35.49	−495.24
IX → VIII	13.61	15.49	−516.95	15.56	16.56	−495.24
VIII → X	30.45	31.38	−558.57	31.26	31.87	−523.44
X → VIII	26.04	27.24	−558.57	27.24	27.99	−523.44
IX → XI	29.95	30.98	−571.39	30.83	31.44	−535.16
XI → IX	29.76	30.72	−571.39	30.59	31.22	−535.16
XI → XII	143.62	141.34	−1868.72	136.37	136.56	−1873.97
XII → XI	122.87	124.84	−1868.72	125.96	127.51	−1873.97

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3.3 Water-assisted tautomerism in uracil

The large values of the activation energies of the tautomerism processes imply that these processes cannot occur easily. In the presence of a catalyst, the activation energies are decreased and the tautomerism processes may occur. Protic molecules such as water can act as a bridge to transfer a proton from one site of uracil to another site.²⁴ Therefore, the water molecule facilitates the proton transfer and catalyzes the tautomerisms in uracil.

Fig. 4 shows the optimized TS structures of water-assisted tautomerisms in uracil. Geometric parameters of the TS structures of the water-assisted tautomerisms are collected in ESI C.† The effect of one and two water molecules on the tautomerisms in uracil was investigated. The TS structures in Fig. 4 are mono- and di-hydrated TS in which water molecules catalyze proton transfers between neighboring groups. The tautomerism process II ↔ VI is a proton transfer reaction involving distant groups. This intra-molecule proton transfer cannot occur in the absence of water molecules. Three water molecules were employed to catalyze the II ↔ VI tautomerism.

Fig. 4 The transition-state structures of water-assisted tautomerism in uracil optimized at the MP2 level of theory.

During the water-assisted tautomerisms, water molecules and uracil (U) form a pre-reactive complex before passing through the transition state (TS). The following path was used for calculating the activation energies of the water-assisted proton transfers in uracil:

nH₂O + U_i ↔ pre-reactive complex ↔ TS ↔ pre-product complex ↔ nH₂O + U_j

where U_i and U_j are two different tautomers of uracil and n = 1, 2 or 3. Fig. 5 shows a typical reaction path for the water-assisted I ↔ II tautomerism which starts from a pre-reactive complex (I + 2H₂O) and, after passing from the TS structure, becomes a pre-product complex (II + 2H₂O). The energy differences between the TS structures and pre-reactive complexes were reported as the activation energies for the forward reactions. The same method was used for calculating the activation energies of the backward reactions. In fact, the pre-reactive and pre-product complexes are the mono- and di-hydrated isomers studied in Section 3.1. The optimized structures of all the pre-reactive and pre-product complexes, as well as their geometric parameters are collected in ESI B.†

Fig. 5 A typical reaction path for the water-assisted I ↔ II tautomerism.

The calculated activation energies (E_a) and Gibbs free energies (ΔG^#) of simple and water-assisted tautomerisms in uracil are tabulated in Table 4. The data in Table 4 are easily comparable, so that Table 4 represents the catalytic effects of water molecules on the proton transfer in uracil. In the absence of water molecules, the energy barriers for the internal proton transfers are very high, and therefore the probability of the occurrence of the reactions is low. Table 4 shows that one water molecule lowers the energy barriers by about 100 kJ mol⁻¹ and that in the presence of two water molecules a further decrease in the activation energies is observed.

Table 4 The calculated activation energies (E_a) and Gibbs free energies (ΔG^#) of simple and water-assisted tautomerisms in uracil. All computed energies are ZPE corrected

Energies	MP2/6-311++G(d,p)			B3LYP/6-311++G(3df,3pd)
	No water	1 water	2 water	No water	1 water	2 water
Ea (I → II)	161.68	48.92	41.29	157.07	45.76	35.02
ΔG^# (I → II)	159.82	57.84	54.41	157.91	55.91	49.01
Ea (II → I)	111.14	17.07	14.70	109.18	9.96	4.70
ΔG^# (II → I)	112.01	25.40	23.55	109.89	17.41	15.21
Ea (I → IV)	164.58	47.76	42.06	161.87	46.56	35.46
ΔG^# (I → IV)	161.32	56.47	54.59	162.67	56.27	48.63
Ea (IV → I)	119.38	14.35	5.93	115.84	7.15	−4.13
ΔG^# (IV → I)	117.65	21.48	15.48	116.36	14.24	5.44
Ea (I → VI)	183.38	60.16	49.71	183.07	60.03	44.16
ΔG^# (I → VI)	181.32	69.21	64.51	183.48	70.41	58.17
Ea (VI → I)	107.92	9.41	8.17	104.93	2.71	−2.73
ΔG^# (VI → I)	111.72	17.60	19.62	106.17	9.95	7.31
Ea (II → VIII)	130.41	30.53	27.45	132.54	28.96	19.97
ΔG^# (II → VIII)	133.10	40.79	41.14	133.90	37.96	32.59
Ea (VIII → II)	135.09	30.06	20.18	127.35	19.34	2.27
ΔG^# (VIII → II)	134.78	38.24	31.34	127.81	26.77	15.52
Ea (III → IX)	126.52	28.30	25.63	129.24	27.04	18.54
ΔG^# (III → IX)	130.83	39.06	39.57	130.81	36.08	31.14
Ea (IX → III)	137.47	32.31	22.15	126.95	20.77	6.59
ΔG^# (IX → III)	136.79	40.43	33.19	129.80	28.43	17.20
Ea (IV → VIII)	135.05	31.22	26.89	135.36	28.58	21.08
ΔG^# (IV → VIII)	136.58	41.32	40.83	136.63	37.83	33.80
Ea (VIII → IV)	134.39	32.37	27.46	128.30	22.15	13.71
ΔG^# (VIII → IV)	134.12	40.44	37.96	128.83	29.98	25.09
Ea (V → X)	120.94	23.36	27.89	120.21	21.94	24.44
ΔG^# (V → X)	121.58	33.40	39.83	122.52	30.94	37.36
Ea (X → V)	144.62	38.12	25.21	137.26	27.05	15.22
ΔG^# (X → V)	144.10	46.88	36.22	137.59	35.31	25.72
Ea (XI → XII)	143.62	41.14	36.09	136.37	28.58	19.56
ΔG^# (XI → XII)	141.34	49.56	46.03	136.56	36.64	31.62
Ea (XII → XI)	122.87	23.60	22.14	125.96	22.34	16.69
ΔG^# (XII → XI)	124.84	34.03	35.09	127.51	31.54	29.16
Ea (II → VI-3H2O)		26.47			16.05
ΔG^# (II → VI-3H2O)		34.94			28.07
Ea (VI → II-3H2O)		10.86			6.46
ΔG^# (VI → II-3H2O)		26.97			18.65

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Water molecules and the uracil isomer form stable complexes via the formation of some hydrogen bonds. In some cases, a covalence bond is replaced with a hydrogen bond. This bond rearrangement is, in fact, a proton-transfer reaction. During the bond rearrangement in the water–uracil complexes, the bonds are not completely broken and so the energy barriers of the proton transfers in the presence of water molecules are smaller than those in the absence of water molecules.

The NCO angle of isomer I, which is involved in the proton transfer, is about 120°, whereas it becomes about 106° in the TS structure in the absence of water (see ESI†). When the proton transfer is catalyzed by water molecules, the change in the NCO angle is very small during the tautomerism, whereas the change in the angle of the TS structure in the absence of water molecule makes it more unstable. Therefore, the activation energies in the absence of water molecules are larger than those when water molecules catalyze the tautomerism.

All of the TS structures of internal proton transfers form a ring to transfer a proton between the acceptor and donor atoms. The formed ring in the absence of water molecules is tetragonal (Fig. 3). The small tetragonal ring has sharp angles, and therefore the TS structure with this tetragonal ring is unstable. When water molecules catalyze the proton transfers, rings with larger sizes are formed (Fig. 4). These larger rings are more stable than the tetragonal rings, and therefore they transfer the proton more easily through themselves.

Water-assisted proton-transfer reactions have been well studied.^12,13,24,25 These studies showed that water molecules decrease the activation energies of the proton transfers. In addition, the catalytic effects of water molecules vary with the number of them. One and two water molecules usually have a considerable catalytic effect on proton-transfer reactions, whereas a further increase in the number of water molecules (n ≥ 3) does not guarantee a decrease in the activation energies.^13,25 In some cases, the catalytic effects of two and three water molecules are the same, and sometimes three water molecules have a lesser catalytic effect than one and two water molecules.^13,25 In these cases, since there is not enough space around the isomers to accommodate extra water molecules, an unstable TS structure is formed. For this reason, we investigated only the effect of one and two water molecules on all the tautomerism processes in uracil except the II ↔ VI process, in which the proton is transferred between two distant groups and needs three water molecules to occur. The activation energies of II → VI and VI → II reactions, catalyzed by three water molecules, are about 25 and 10 kJ mol⁻¹, respectively. These values indicate that, although the II ↔ VI proton transfer does not take place spontaneously, it is easily achievable when catalyzed by three water molecules. In the TS structure of II ↔ VI, four simultaneous hydrogen transfers occur along the bridge skeleton. In other words, during this process four bonds are formed and four other bonds are ruptured.

4 Conclusion

Twelve isomers of uracil were studied using B3LYP and MP2 methods. The di-keto isomer (isomer I) was the most stable isomers in both gas and aqueous phases. The di-enol tautomers had moderate stability, which was attributed to the aromaticity property of these tautomers. Generally, the stability of the isomer in the aqueous phase was more than that in the gas phase. The effect of mono- and di-hydration on the relative stability of the uracil was investigated. The hydrated forms of isomer I were more stable than those of other hydrated isomers. However, the relative stability trends in the bare isomers and their hydrated forms are not the same. Inter-conversion between the twelve tautomers was investigated and the energy barriers of the tautomerisms in uracil were calculated. The calculated activation energies of the internal proton-transfer reaction were about 110–180 kJ mol⁻¹, indicating that the tautomerisms are hard to achieve. If there are some water molecules in the medium, they can hydrate uracil. These water molecules can catalyze the internal proton transfer in uracil to make it achievable. The calculations show that water molecules lower the energy barriers of the proton-transfer reaction, and hence they can catalyze the tautomerisms in uracil. The catalytic effects of one and two water molecules on the proton transfer were compared and it was observed that the catalysis effect of two water molecules is more than that of one water molecule.

Acknowledgements

The authors wish to express their thanks to the Center of Excellency in Chemistry at Isfahan University of Technology.

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Footnote

† Electronic supplementary information (ESI) available. See DOI: 10.1039/c4ra09733e

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