Theoretical Study of the Interaction between Thymine and Water. Protonation and Deprotonation Enthalpies and Comparison with Uracil

Hydration and stability of nucleic acid bases and base pairs

Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.

Proton Transfers Induced by Lead(II) in a Uracil Nucleobase: A Study Based on Quantum Chemistry Calculations

Within the context of metal biotoxicity, electrospray ionization mass spectrometry experiments (ESIMS) have recently been performed by us on the pyrimidine nucleobases (B) uracil and thymine complexed with lead(II) [Int. J. Mass. Spectrom. 2005, 243, 279]. Among the ions detected, [Pb(B)-H]+ complexes, where the base has been deprotonated, have been identified as producing intense signals. In the same study, quantum calculations based on density functional theory (DFT) have assessed the complexation sites and energies of [Pb(B)-H]+ ions. The present DFT investigations aim at giving an understanding on the energetics and mechanisms associated with uracil's loss of a proton. We specifically assess and quantify the role of lead binding in this process. For that purpose, intra- and intermolecular proton transfers have been considered. We have found that uracil (U) 1,3-tautomerization can be exergonic when uracil is complexed with Pb2+, in opposition to the situation without lead. The corresponding intramolecular processes were nonetheless found to occur at geological time scales. In contrast, the addition of a second body to [Pb(U)]2+ complexes, namely OH- or H2O (as found in the initial water droplet of ESIMS experiments), gives exergonic and fast uracil 1,3-proton transfers. Finally, we have shown that intermolecular proton transfers in uracil-H2O, uracil-OH-, or uracil-uracil complexes are able to explain the experimentally detected [Pb(U)-H]+ ions.

On the Electron Donor and the Electrophilic Substitution Activating Abilities of Substituents in Uracil

QTAIM properties for uracil and 18 derivatives containing the substituents -NH(2), -OH, -OCH(3), -SH, -F, -Cl, -CH(3) -NO(2), and -Li in position 5 or 6 were computed on MP2/6-31++G//MP2/6-31G charge densities. The results indicate that -OH, -OCH(3), and -NH(2) groups are really retrieving charge from the ring. Also, the activating ability of the substituent groups, usually considered as the variation of electron population at the carbon where the electrophilic attack takes place, C, was studied. The study shows that the activating ability is reflected by the variation of pi charge or quadrupole moment at C, and also by the variation of the Laplacian of the charge density in the secondary charge concentration points around C (SCC-C). They indicate a similar, but not exactly equal, graduation of activating ability. The relative behavior of the substituents is basically the same as in benzene, though benzene has more tendency to concentrate charge in the SCC-C regions than uracil, where this tendency is larger for 6- than for 5-derivatives. sigma(+/-)(R) Taft parameters are found to display good correlations with the above indicated activating indexes. Finally, the resonance model predicts most of the main variations displayed by QTAIM atomic pi electron populations of derivatives with regard to uracil, but there are still some significant variations of the pi electron charge that it cannot predict.

Methyl and Phenyl Substitution Effects on the Proton Affinities of Hydrides of First and Second Row Elements and Substituent Effects on the Proton Affinities of Ring Carbons in Benzene: A DFT Study

Theoretical calculations using B3LYP density functional theory (DFT) with the 6-311++G(d,p) basis set have been performed to determine proton affinities (PAs) of a series of H-X compounds and the corresponding methyl- (H(3)C-X) and phenyl- (Ph-X) substituted derivatives with a variety of proton acceptor atoms, such as C, O, N, F, Si, P, S, Cl, etc. Our results illustrate an interesting substituent effect on PAs. The PAs of ring carbon atoms for a series of monosubstituted benzene molecules (Y-C(6)H(5); Y = F, Cl, CH(3), OCH(3), NH(2), PH(2), OH, SH, SiH(3), CN, CF(3), and NO(2)) have also been estimated. Correlations between proton affinities of H-X, H(3)C-X, and Ph-X and substituent effects on the PAs of the ring carbon atoms for a series of monosubstituted benzene molecules have been studied. It has been observed that substituent effects on the PAs of the ring carbon atoms follow a good Hammett-type correlation.

Valence- and Dipole-Bound Anions of the Thymine−Water Complex: Ab Initio Characterization of the Potential Energy Surfaces

The potential energy surfaces of the neutral and anionic thymine-water complexes are investigated using high-level ab initio calculations. Both dipole-bound (DB) and valence-bound (VB) anionic forms are considered. Four minima and three first-order stationary points are located, and binding energies are computed. All minima, for both anions, are found to be vertically and adiabatically stable. The binding energies are much higher for valence-bound than for dipole-bound anions. Adiabatic electron affinities are in the 66-287 meV range for VB anions and the 4-60 meV range for DB anions, and vertical detachment energies are in the 698-977 meV and 10-70 meV range for VB and DB anions, respectively. For cases where literature data are available, the computed values are in good agreement with previous experimental and theoretical studies. It is observed that electron attachment modifies the shape of the potential energy surfaces of the systems, especially for the valence-bound anions. Moreover, for both anions the size of the energy barrier between the two lowest energy minima is strongly reduced, rendering the coexistence of different structures more probable.

The Influence of Microhydration on the Ionization Energy Thresholds of Uracil and Thymine

In the present study the ionization energy thresholds (IET's) of uracil and thymine have been calculated (with the B3LYP, PMP2, and P3 levels of theory using the standard 6-31++G(d,p) basis set) with one to three water molecules placed in the first hydration shell. Then (B3LYP) polarizable continuum model (PCM) calculations were performed with one to three waters of the hydration shell included. Calculations show there is a distinct effect of microhydration on uracil and thymine. For uracil, one added water results in a decrease in the IET of about 0.15 eV. The second and third water molecules cause a further decrease by about 0.07 eV each. For thymine, the first water molecule is seen to decrease the IET by about 0.1 eV, while the second and third water molecules cause a further decrease of less than 0.1 eV each. The changes in IET calculated here for thymine with one to three waters of hydration are smaller than the experimental values determined by Kim et al. (Kim, S. K.; Lee, W.; Herschbach, D. R. J. Phys. Chem. 1996, 100, 7933). Preliminary results presented here indicate that the experimental results may involve keto-enol tautomers of thymine. The results of placing the microhydrated structures of uracil and thymine in a PCM cavity was seen to make very little difference in the IET when compared to the IET of ordinary uracil or thymine in a PCM cavity. The implications are that accurate calculations of the IET's of uracil and thymine can be obtained by simply considering long-range solvation effects.

Potential Energy Surfaces of an Adenine−Thymine Base Pair and Its Methylated Analogue in the Presence of One and Two Water Molecules: Molecular Mechanics and Correlated Ab Initio Study

Potential energy surfaces of monohydrated and dihydrated adenine-thymine and 9-methyladenine-1-methylthymine base pairs were examined by the molecular dynamics/quenching technique using the Cornell et al. force field (J. Am. Chem. Soc. 1995, 117, 5179). Long runs of molecular dynamics/quenching calculations allowed us to evaluate the free energy surface. The most stable and populated structures found were fully reoptimized at the correlated ab initio level employing the resolution of identity Møller-Plesset method. A systematic study of the base pairs' microhydration using both the empirical and the high-level correlated ab initio approaches is presented for the first time. We show that the occurrence of water molecules and their gradually increasing number as well as the methylation of the bases favor stacked structures over the planar hydrogen-bonded ones. These results based on the correlated ab initio calculations are in the excellent agreement with data obtained from our previous empirical potential molecular dynamics study (Kabelác et al. Chem.-Eur. J. 2001, 7, 2067).

Vibrational and electronic excitations of H[sub 2]O on thymine films induced by low-energy electrons

We investigated vibrational and electronic excitations of 0.1-layer up to 2.4-layer film of H(2)O deposited on a 1.4-layer film of thymine condensed on Ar at a temperature of 18 K using high-resolution electron-energy loss (EEL) spectroscopy at the incident energy of 12 eV. The spectral contribution originating essentially from the H(2)O overlayer is obtained by separating the measured contribution from the underlying film of thymine, considering the electron beam attenuation in the H(2)O overlayer. The vibrational EEL spectrum of submonolayer amount of H(2)O on thymine, which excepts for small energy shift of the vibrational bands, is found to compare in intensity to that of the same amount of H(2)O deposited directly on the argon. The electronic energy-loss intensity near 8.6 eV, which is attributed to the excitation of (3,1)B(1) states of H(2)O in condensed phase, is observed to decrease by a factor of about 3 by the presence of the underlying film of thymine. This indicates that the corresponding cross section for excitation the (3,1)B(1) states of H(2)O by the electron impact is reduced significantly by the close proximity of the thymine molecules.

Theoretical study of the symmetry of the (OH...O)- hydrogen bonds in vinyl alcohol-vinyl alcoholate systems

The interactions between substituted vinyl alcohols and vinyl alcoholates (X = NH(2), H, F, Cl, CN) are studied at the B3LYP/6-311++G(d,p) level of theory. In a first step, the conformation of the monomers is investigated and the proton affinities (PA(A(-))) of the enolates are calculated. The enols and enolates are held together by strong (OH...O)(-) hydrogen bonds, the hydrogen bond energies ranging from 19.1 to 34.6 kcal mol(-1). The optimized O...O distances are between 2.414 and 2.549 A and the corresponding OH distances from 1.134 and 1.023 A. The other geometry parameters such as C[double bond]C or CO distances also indicate that, in the minimum energy configuration, the hydrogen bonds are characterized by a double well potential. The Mulliken charges on the different atoms of the proton donors and proton acceptors and the frequencies of the nu(OH) stretching vibrations agree with this statement. All the data indicate that the hydrogen bonds are the strongest in the homomolecular complexes. The transition state for hydrogen transfer is located with the transition barrier estimated to be about zero. Upon addition of the zero-point vibration energies to the total potential energy, the barrier vanishes. This is a characteristic feature of low-barrier hydrogen bonds (LBHBs). The hydrogen bond energies are correlated to the difference 1.5 PA(AH) - PA(A(-)). The correlation predicts different energies for homomolecular hydrogen bonds, in agreement with the theoretical calculations. Our results suggest that a PA (or pK(a)) match is not a necessary condition for forming LBHBs in agreement with recent data on the intramolecular hydrogen bond in the enol form of benzoylacetone (J. Am. Chem. Soc. 1998, 120, 12117).

Ab initio Hartree-Fock/6-31G** calculation on 9-beta-D-arabinofuranosyladenine-5'-monophosphate molecule: application to the analysis of its IR and Raman spectra

9-beta-D-arabinofuranosyaldenine-5'-monophosphate (5'-ara-AMP) is an arabinonucleotide that has antiviral and antitumor activity. The accurate knowledge of the nature of its vibrational modes is a valuable step for the forthcoming elucidation of drug-nucleotide and drug-enzyme interactions. The FTIR and FT Raman spectra (4000-30 cm(-1)) of 5'ara-AMP and two deuterated derivatives ara-AMP-d(C8) (deuteration in C8) and ara-AMP-d7 (deuteration in C8, amino and hydroxyl groups) are reported. Theoretical vibrational calculations were performed using the Hartree-Fock/6-31G** method. An assignment of the observed spectra is proposed considering the scaled potential energy distribution of the vibrational modes of the 5'ara-AMP molecule and the observed band shifts by deuteration. The scaled ab initio frequencies are in good agreement with the experimental data (<3 cm(-1) SD).

The acidity of uracil and uracil analogs in the gas phase: four surprisingly acidic sites and biological implications

The gas phase acidities of a series of uracil derivatives (1-methyluracil, 3-methyluracil, 6-methyluracil, 5,6-dimethyluracil, and 1,3-dimethyluracil) have been bracketed to provide an understanding of the intrinsic reactivity of uracil. The experiments indicate that in the gas phase, uracil has four sites more acidic than water. Among the uracil analogs, the N1-H sites have deltaH(acid) values of 331-333 kcal mol(-1); the acidity of the N3 sites fall between 347-352 kcal mol(-1). The vinylic C6 in 1-methyluracil and 3-methyluracil brackets to 363 kcal mol(-1), and 369 kcal mol(-1) in 1,3-dimethyluracil; the C5 of 1,3-dimethyluracil brackets to 384 kcal mol(-1). Calculations conducted at B3LYP/6-31+G* are in agreement with the experimental values. The bracketing of several of these sites involved utilization of an FTMS protocol to measure the less acidic site in a molecule that has more than one acidic site, establishing the generality of this method. In molecules with multiple acidic sites, only the two most acidic sites were bracketable, which is attributable to a kinetic effect. The measured acidities are in direct contrast to in solution, where the two most acidic sites of uracil (N1 and N3) are indifferentiable. The vinylic C6 site is also particularly acidic, compared to acrolein and pyridine. The biological implications of these results, particularly with respect to enzymes for which uracil is a substrate, are discussed.

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

This review summarizes results concerning molecular interactions of nucleic acid bases as revealed by advanced ab initio quantum chemical (QM) calculations published in last few years. We first explain advantages and limitations of modern QM calculations of nucleobases and provide a brief history of this still rather new field. Then we provide an overview of key electronic properties of standard and selected modified nucleobases, such as their charge distributions, dipole moments, polarizabilities, proton affinities, tautomeric equilibria, and amino group hybridization. Then we continue with hydrogen bonding of nucleobases, by analyzing energetics of standard base pairs, mismatched base pairs, thio-base pairs, and others. After this, the nature of aromatic stacking interactions is explained. Also, nonclassical interactions in nucleic acids such as interstrand bifurcated hydrogen bonds, interstrand close amino group contacts, C [bond] H...O interbase contacts, sugar-base stacking, intrinsically nonplanar base pairs, out-of-plane hydrogen bonds, and amino-acceptor interactions are commented on. Finally, we overview recent calculations on interactions between nucleic acid bases and metal cations. These studies deal with effects of cation binding on the strength of base pairs, analysis of specific differences among cations, such as the difference between zinc and magnesium, the influence of metalation on protonation and tautomeric equlibria of bases, and cation-pi interactions involving nucleobases. In this review, we do not provide methodological details, as these can be found in our preceding reviews. The interrelation between advanced QM approaches and classical molecular dynamics simulations is briefly discussed.

Ab initio vibrational calculations on ara-T molecule: application to analysis of IR and Raman spectra

The FTIR and FT-Raman spectra are reported for the arabinonucleoside ara-T (1-beta-D-arabinofuranosylthymine), which shows antiviral activity. The accurate knowledge of the vibrational modes is a prerequisite for the elucidation of drug-nucleotide and drug-enzyme interactions. The FTIR and FT-Raman spectra of ara-T were recorded from 4000 to 30 cm(-1). A tetradeuterated derivative (deuteration at N3, and hydroxyl groups O'2, O'3, and O'5) was synthesized and the observed isotopic shifts in its spectra were used for the vibrational analysis of ara-T. The theoretical frequencies and the potential energy distribution (PED) of the vibrational modes of ara-T were calculated using the ab initio Hartree-Fock/3-21G method. An assignment of the vibrational spectra of ara-T is proposed considering the scaled PED and the observed band shifts under deuteration. The scaled ab initio frequencies were in reasonable agreement with the experimental data.

Protonation of platinated adenine nucleobases. Gas phase vs condensed phase picture

Protonation of adenine carrying a Pt(II) moiety either at N7, N3, or N1 is possible in solution, but the site of protonation is influenced by the location of the Pt(II) electrophile and to some extent also by the overall charge of the metal entity (+2, +1, 0, -1), hence the other ligands (NH(3), Cl(-), OH(-)) bound to Pt(II). Quantum chemical calculations based on density functional theory (DFT) have been carried out for intrinsic protonation energies of adenine complexes carrying the following Pt(II) species at either of the three ring N atoms: [Pt(NH(3))(3)](2+) (1), trans- [Pt(NH(3))(2)Cl](+) (2a), cis-[Pt(NH(3))(2)Cl](+) (2b), trans-[Pt(NH(3))(2)Cl(2)] (3a), cis-[Pt(NH(3))Cl(2)] (3b), [PtCl(3)](-) (4), trans-[Pt(NH(3))(2)OH](+) (5a), cis-[Pt(NH(3))(2)(OH)](+) (5b), trans-[Pt(NH(3))(OH)(2)] (6a), cis-[Pt(NH(3))(OH)(2)] (6b), and [Pt(OH)(3)](-) (7). The data have been compared with results derived from solution studies (water) and X-ray crystallography, whenever available. The electrostatic effects associated with the charge of the metal entity have the major influence on the calculated intrinsic (gas phase) proton affinities, unlike the condensed phase data. Nevertheless, the relative gas phase trends correlate surprisingly well with condensed phase data; i.e., variation of the pK(a) values measured in solution is consistent with the calculated gas phase protonation energies. In addition to a systematic study of the ring proton affinities, proton transfer processes within the platinated adenine species were often observed when investigating Pt adducts with OH(-) ligands, and they are discussed in more detail. To the best of our knowledge, this is the first study attempting to find a systematic correlation between gas phase and condensed phase data on protonation of metalated nucleobases. The gas phase data provide a very useful complement to the condensed phase and X-ray experiments, showing that the gas phase studies are capable of valuable predictions and contribute to our understanding of the solvent and counterion effects on metal-assisted proton shift processes.

Proton affinity of uracil. A computational study of protonation sites

Relative stabilities of uracil tautomers and cations formed by gas-phase protonation were studied computationally with the B3LYP, MP2, QCISD, and QCISD(T) methods and with basis sets expanding from 6-31G(d,p) to 6-311+G(3df,2p). In accordance with a previous density functional theory study, the dioxo tautomer 1a was the most stable uracil isomer in the gas phase. Gibbs free energy calculations using effective QCISD(T)/6-311+G(3df,2p) energies suggested >99.9% of 1a at equilibrium at 523 K. The most stable ion isomer corresponded to N-1 protonated 2,4-dihydroxypyrimidine, which however is not formed by direct protonation of 1a. The topical proton affinities in 1a followed the order O-8 > O-7 > C-5 > N-3 > N-1. The thermodynamic proton affinity of 1a was calculated as 858 kJ mol(-1) at 298 K. A revision is suggested for the current estimate included in the ion thermochemistry database.