A gas phase ab initio excited state geometry optimization study of thymine, cytosine and uracil

Molecular geometries of the nucleic acid bases thymine, cytosine and uracil in the ground and the lowest two singlet excited states were optimized using the ab initio approach employing the 4-31G basis set for all the atoms except the amino group of cytosine for which the 6-311+G^* basis set was used. The excited state calculations were performed employing configuration interaction involving singly excited configurations (CIS). Vibrational frequencies were computed in order to examine the nature of the stationary points on the potential energy surfaces obtained by geometry optimization. While the ground state geometries of uracil and thymine (except the methyl group hydrogens) are planar, the corresponding excited state geometries were found to be significantly nonplanar. In the case of cytosine, the amino group is pyramidal and the rest of the molecule is only slightly nonplanar in the ground state, but the excited state geometries are appreciably nonplanar. In particular, consequent to the S₂(n–π^*) excitation of cytosine, the amino group plane is strongly rotated. While thymine is stable in the S₂(π–π^*) excited state, uracil appears to be dissociative in the corresponding excited state.     

Infrared spectra of protonated uracil, thymine and cytosine.

The gas-phase structures of protonated uracil, thymine, and cytosine are probed by using mid-infrared multiple-photon dissociation (IRMPD) spectroscopy performed at the Free Electron Laser facility of the Centre Laser Infrarouge d'Orsay (CLIO), France. Experimental infrared (IR) spectra are recorded for ions that were generated by electrospray ionization, isolated, and then irradiated in a quadrupole ion trap; the results are compared to the calculated infrared absorption spectra of the different low-lying isomers (computed at the B3LYP/6-31++G(d,p) level). For each protonated base, the global energy minimum corresponds to an enolic tautomer, whose infrared absorption spectrum matched very well with the experimental IRMPD spectrum, with the exception of a very weak IRMPD signal observed at about 1800 cm(-1) in the case of the three protonated bases. This signal is likely to be the signature of the second-energy-lying oxo tautomer. We thus conclude that within our experimental conditions, two tautomeric ions are formed which coexist in the quadrupole ion trap.     

Transition moment directions of some important in-plane vibrations of uracil,thymine and cytosine. A fixed partial charge model calculation

Transition moment directions for the double-bond region vibrations of uracil, thymine and cytosine are calculated using the fixed partial charge model approximation. The coupling between the two carbonyl bonds and the carbon—carbon double bond in uracil and thymine is sensitive to the choice of the corresponding stretching force constants. The transition moment directions are correspondingly changed, thus, in principle, enabling the quantitative determination of coupling between the vibrations from linear dichroism measurements.     

Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations

The energetics of the ion-molecule interactions and structures of the clusters formed between protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. For protonated cytosine, uracil, thymine, and adenine with ammonia, the measured enthalpies of association with ammonia are -21.7, -27.9, -22.1, and -17.5 kcal mol-1, respectively. Different isomers of the neutral and protonated nucleic acid bases as well as their clusters with ammonia have been investigated at the B3LYP/6-31+G(d,p) level of theory, and the corresponding binding energetics have also been obtained. The potential energy surfaces for proton transfer and interconversion of the clusters of protonated thymine and uracil with ammonia have been constructed. For cytosine, the experimental binding energy is in agreement with the computed binding energy for the most stable isomer, CN01-01, which is derived from the enol form of protonated cytosine, CH01, and ammonia. Although adenine has a proton affinity similar to that of cytosine, the binding energy of protonated adenine to ammonia is much lower than that for protonated cytosine. This is shown to be due to the differing types of hydrogen bonds being formed. Similarly, although uracil and thymine have similar structures and proton affinities, the binding energies between the protonated species and ammonia are different. Strikingly, the addition of a single methyl group, in going from uracil to thymine, results in a significant structural change for the most stable isomers, UN01-01 and TN03-01, respectively. This then leads to the difference in their measured binding energies with ammonia. Because thymine is found only in DNA while uracil is found in RNA, this provides some potential insight into the difference between uracil and thymine, especially their interactions with other molecules.     

Reactions of the ionized enol tautomer of acetanilide: elimination of HNCO via a novel rearrangement

The reactions of ionised acetanilide, C(6)H(5)NH(=O)CH(3)(.+), and its enol, C(6)H(5)NH(OH)=CH(2)(.+), have been studied by a combination of tandem mass spectrometric and computational methods. These two isomeric radical cations have distinct chemistries at low internal energies. The keto tautomer eliminates exclusively CH(2)=C=O to give ionised aniline. In contrast, the enol tautomer loses H-N=C=O, via an unusual skeletal rearrangement, to form predominantly ionised methylene cyclohexadiene. Hydrogen atom loss also occurs from the enol tautomer, with the formation of protonated oxindole. The mechanisms for H-N=C=O and hydrogen atom loss both involve cyclisation; the former proceeds via a spiro transition state formed by attachment of the methylene group to the ipso position, whereas the latter entails the formation of a five-membered ring by attachment to the ortho position. The behaviour of labelled analogues reveals that these two processes have different site selectivities. Hydrogen atom loss involves a reverse critical energy and is subject to an isotope effect. Surprisingly, attempts to promote the enolisation of ionised acetanilide by proton-transport catalysis were unsuccessful. In a reversal of the usual situation for ionised carbonyl compounds, ionised acetanilide is actually more stable than its enol tautomer. The enol tautomer was resistant to proton-transport catalysed ketonisation to ionised acetanilide, possibly because the favoured geometry of the encounter complex with the base molecule is inappropriate for facilitating tautomerisation.     

Protonation of thymine,cytosine, adenine,and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory

Gradient-corrected density functional computations with triple-zeta-type basis sets were performed to determine the preferred protonation site and the absolute gas-phase proton affinities of the most stable tautomer of the DNA bases thymine (T), cytosine (C), adenine (A), and guanine (G). Charge distribution, bond orders, and molecular electrostatic potentials were considered to rationalize the obtained results. The vibrational frequencies and the contribution of the zero-point energies were also computed. Significant geometrical changes in bond lengths and angles near the protonation sites were found. At 298 K, proton affinities values of 208.8 (T), 229.1 (C), 225.8 (A), and 230.3 (G) kcal/mol were obtained in agreement with experimental results. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 989–1000, 1998     

Probing the Watson-Crick, wobble, and sugar-edge hydrogen bond sites of uracil and thymine

The nucleobases uracil (U) and thymine (T) offer three hydrogen-bonding sites for double H-bond formation via neighboring N-H and C=O groups, giving rise to the Watson-Crick, wobble and sugar-edge hydrogen bond isomers. We probe the hydrogen bond properties of all three sites by forming hydrogen bonded dimers of U, 1-methyluracil (1MU), 3-methyluracil (3MU), and T with 2-pyridone (2PY). The mass- and isomer-specific S1 <-- S0 vibronic spectra of 2PY.U, 2PY.3MU, 2PY.1MU, and 2PY.T were measured using UV laser resonant two-photon ionization (R2PI). The spectra of the Watson-Crick and wobble isomers of 2PY.1MU were separated using UV-UV spectral hole-burning. We identify the different isomers by combining three different diagnostic tools: (1) Selective methylation of the uracil N3-H group, which allows formation of the sugar-edge isomer only, and methylation of the N1-H group, which leads to formation of the Watson-Crick and wobble isomers. (2) The experimental S1 <-- S0 origins exhibit large spectral blue shifts relative to the 2PY monomer. Ab initio CIS calculations of the spectral shifts of the different hydrogen-bonded dimers show a linear correlation with experiment. This correlation allows us to identify the R2PI spectra of the weakly populated Watson-Crick and wobble isomers of both 2PY.U and 2PY.T. (3) PW91 density functional calculation of the ground-state binding and dissociation energies De and D0 are in agreement with the assignment of the dominant hydrogen bond isomers of 2PY.U, 2PY.3MU and 2PY.T as the sugar-edge form. For 2PY.U, 2PY.T and 2PY.1MU the measured wobble:Watson-Crick:sugar-edge isomer ratios are in good agreement with the calculated ratios, based on the ab initio dissociation energies and gas-phase statistical mechanics. The Watson-Crick and wobble isomers are thereby determined to be several kcal/mol less strongly bound than the sugar-edge isomers. The 36 observed intermolecular frequencies of the nine different H-bonded isomers give detailed insight into the intermolecular force field.     

Ab initio base-pairing energies of an oxidized thymine product, 5-formyluracil, with standard DNA bases at the BSSE-free DFT and MP2 theory levels

Oxidation of the thymine methyl group produces two stable products, non-mutagenic 5-hydroxymethyluracil and highly mutagenic 5-formyluracil. We have calculated the interaction energy of base-pair formation involving 5-formyluracil bound to the natural DNA bases adenine (A), cytosine (C), guanine (G), and thymine (T), and discuss the effects of the 5-formyl group with respect to similar base-pairs containing uracil, 5-hydroxyuracil, thymine (5-methyluracil), and 5-hydroxycytosine. The interaction geometries and energies were calculated four ways: (a) using density functional theory (DFT) without basis set super-position error (BSSE) corrections, (b) using DFT with BSSE correction of geometries and energies, (c) using M?ller-Plesset second order perturbation theory (MP2) without BSSE correction, and (d) using MP2 with BSSE geometry and energy correction. All calculations used the 6-311G(d,p) basis set. Notably, we find that the A:5-formyluracil base-pair is more stable than the precursor A:T base-pair. The relative order of base-pair stabilities is A:5-Fo-U > G:5-Fo-U > C:5-Fo-U > T:5-Fo-U.     

Na+, Mg2+, and Zn2+ binding to all tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine: a correlated ab initio quantum chemical study

Interactions of adenine, cytosine, guanine, and thymine with Na(+), Mg(2+), and Zn(2+) cations were studied using an approximate resolution of identity correlated second-order MP2 (RI-MP2) method with the TZVPP ([5s3p2d1f/3s2p1d]) basis set. All existing tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine were considered. Cations bind mostly in a bidentate manner, and stabilization energies of these complexes are larger than those in the case when cations bind in a unidentate manner. The cation...Y (Y equal to N or O) distances for divalent metals are shorter than those for Na(+) and for Zn(2+) are mostly shorter than the Mg(2+)...Y distance. The intermolecular distances between the cation and the base for complexes containing adenine and cytosine are systematically shorter than those for complexes containing guanine and thymine. Only for cytosine the canonical keto/amino tautomer structure with ions represents the global minimum. For guanine, the metalated canonical form is again the most stable, but its stabilization energy is within less than 5% of the stabilization energies of the two other rare tautomers, which indicates that the canonical form and these two rare tautomers could coexist. The canonical structures of adenine and thymine in the presence of ions are considerably less stable (by more than 10%) than the complexes of the rare tautomers. It can be concluded that the interaction of Na(+), Mg(2+), and Zn(2+) cations with cytosine in the gas phase will not induce the change of the canonical form to the rare tautomeric form. In the case of isolated guanine, the equilibrium of the canonical form with rare tautomers can be found. For isolated adenine and thymine the presence of rare tautomers is highly probable.     

DNA base stacking: The stacked uracil/uracil and thymine/thymine minima

The potential energy surfaces of stacked uracil dimer (U/U) and stacked thymine dimer (T/T) have been explored at the counterpoise (CP)‐corrected M06‐2X/6‐31+G(d) level of theory, in the gas phase and in solution (with water and, for U/U, 1,4‐dioxane as the solvents) modeled by a continuum solvent using the polarizable continuum model. Potential energy scans were created by rotation of one monomer around its center‐of‐mass, whereas the other monomer remained still. Both face‐to‐back (one molecule exactly on top of the other) and face‐to‐face (one base molecule flipped by 180°) structures were considered. Five or six (dependent on whether CP correction is included or not) stacked uracil dimer minima and six stacked thymine dimer minima were located. A number of transition states on the U/U and T/T potential energy surfaces were likewise identified. The general effect of the continuum solvent is a flattening of the potential energy surface. Comparison of the gas‐phase M06‐2X/6‐31+G(d) U/U interaction energies with estimated CCSD(T)/complete basis set values (where available) show the excellent performance of this functional for stacking energies. © 2012 Wiley Periodicals, Inc.     

Gas‐phase hydration of Mg2+ complexes with deprotonated uracil,thymine, uridine,and thymidine

The gas‐phase hydration of Mg²⁺ complexes with deprotonated uracil ( U ), thymine ( T ), uridine ( U _r , uracil riboside), and thymidine ( T _dr , thymine deoxyriboside) was studied. The aim of the work was to analyze the hydration of product ions (eg, [2 U ‐H+Mg]⁺) formed as a result of the collision induced dissociation of the respective parent ion (eg, [3 U _r ‐H+Mg]⁺). The efficiency of gas‐phase hydration of the ions [2 U ‐H+Mg]⁺ and [2 T ‐H+Mg]⁺ was similar. However, the efficiency of gas‐phase hydration of the ion [ U + U _r ‐H+Mg]⁺ was much higher than that of gas‐phase hydration of the ion [ T + T _dr ‐H+Mg]⁺. On the basis of the mass spectra obtained and the performed molecular modelling, it was concluded that in the ion [ T + T _dr ‐H+Mg]⁺, we deal with a steric hindrance due to the presence of a sugar moiety, which affects water attachment. In the ion [ U + U _r ‐H+Mg]⁺, the position of the sugar moiety does not affect water attachment.     

Electron transfer-induced fragmentation of thymine and uracil in atom-molecule collisions

Ion-pair formation has been studied in hyperthermal (30-100 eV) neutral potassium collisions with gas phase thymine (C(5)H(6)N(2)O(2)) and uracil (C(4)H(4)N(2)O(2)). Negative ions formed by electron transfer from the alkali atom to the target molecule were analysed by time-of-flight (TOF) mass spectrometry. The most abundant product anions are assigned to CNO(-) and (U-H)(-)/(T-H)(-) and the associated electron transfer mechanisms are discussed. Special emphasis is given to the enhancement of ring breaking pathways in the present experiments, notably CNO(-) formation, compared with free electron attachment measurements.     

Quantum-chemical study on uracil and thymine nitrosonium complexes

Quantum-chemical calculations at the RI-MP2/L1 level of theory showed that the most energetically favorable complexes of uracil and thymine with nitrosonium cation are those of n-type with NO⁺ coordination at the nitrogen or oxygen atom. A correlation was found between the experimental and calculated affinities of the dioxo tautomer of thymine for nitrosonium ion ( $ A_{NO^ + } $ ). A linear relation was revealed between $ A_{NO^ + } $ values for structurally similar tautomers of uracil and thymine.     

(1‐Pyridinio)perfluorophenacylide: a new stable pyridinium ylide in the enol form

The title compound, C₁₃H₆F₅NO, exists in the enol form and adopts the E configuration about the enol double bond. It is the first example of an enol‐type pyridinium ylide. The enol structure was unambiguously determined on the basis of the significantly longer C—O bond and shorter C—C bond. Intramolecular C—H...O and C—H...F hydrogen bonds are responsible for promotion of the enol form and for the stability of this compound.     

Does Tautomerization of FapyG Influence Its Mutagenicity?

Oxidative degradation of guanine to 2,6‐diamino‐4‐oxo‐5‐formamidopyrimidine (FapyG) is believed to be mutagenic. It has been proposed recently that the enol tautomer of FapyG is mainly responsible for this effect leading to a guanine‐to‐thymine mutation (T. H. Gehrke, U. Lischke, K. L. Gasteiger, S. Schneider, S. Arnold, H. C. Muller, D. S. Stephenson, H. Zipse, T. Carell, Nat. Chem. Biol.­ 2013, 9, 455–461 ). Here, density functional methods suggest that the enol tautomer of FapyG might not be responsible for the proposed guanine‐to‐thymine mutation. Instead, it might result in a guanine‐to‐adenine mutation.     

Anion photoelectron imaging of deprotonated thymine and cytosine

We report the anion photoelectron spectra of deprotonated thymine and cytosine at 3.496 eV photodetachment energy using velocity-mapped imaging. The photoelectron spectra of both species exhibit bands resulting from detachment transitions between the anion ground state and the ground state of the neutral radical. Franck-Condon simulations identify the anion isomers that contribute to the observed photoelectron spectrum. For both thymine and cytosine, the photoelectron spectra are consistent with anions formed by removal of a proton from the N atom that normally attaches to the sugar in the nucleotide (N1). For deprotonated thymine, the photoelectron spectrum shows a band due to a ring breathing vibration excited during the photodetachment transition. The electron affinity for the dehydrogenated thymine radical is determined as 3.250 +/- 0.015 eV. For deprotonated cytosine, the photoelectron spectrum lacks any resolved structure and the electron affinity of the dehydrogenated cytosine radical is determined to be 3.037 +/- 0.015 eV. By combining the electron affinity with previously measured gas phase acidities of thymine and cytosine, we determine the bond dissociation energy for the N-H bond that is broken.     

Interaction with glycine increases stability of a mutagenic tautomer of uracil. A density functional theory study

The most stable structures for the gas-phase complexes of minor tautomers of uracil (U) with glycine (G) were characterized at the density functional B3LYP/6-31++G level of theory. These are cyclic structures stabilized by two hydrogen bonds. The relative stability of isolated tautomers of uracil was rationalized by using thermodynamic and structural arguments. The stabilization energies for complexes between the tautomers of U and G result from interplay between the stabilizing two-body interaction energies and destabilizing one-body terms. The latter are related to the energies of (i) tautomerization of the unperturbed moieties and (ii) distortions of the resulting rare tautomers in the complex. The two-body term describes the interaction energy between distorted tautomers. The two-body interaction energy term correlates with perturbations of length of the proton-donor bonds as well as with deprotonation enthalpies and proton affinities of the appropriate monomer sites. It was demonstrated that the relative instability of rare tautomers of uracil is diminished due to their interactions with glycine. In particular, the instability of the third most stable tautomer (U(III)) is decreased from 11.9 kcal/mol for non-interacting uracil to 6.7 kcal/mol for uracil in a complex with the zwitterionic tautomer of glycine. A decrease of instability by 5.2 kcal/mol could result in an increase of concentration of U(III) by almost 5 orders of magnitude. This is the tautomer with proton donor and acceptor sites matching guanine rather than adenine. Moreover, kinetic characteristics obtained for the glycine-assisted conversion of the most stable tautomer of uracil (U(I)) to U(III) indicate that the U(I)<-->U(III) thermodynamic equilibrium could be easily attained at room temperature. The resulting concentration of this tautomer falls in a mutationally significant range.     

Uracil and the tautomer 4-hydroxyuracil: An ab initio study with geometry optimization

Ab initio STO -3G geometries and relative energies for uracil (U) and the tautomer 4-hydroxyuracil (U*) were obtained with the HONDO program utilizing the rapidly convergent method of Murtaugh and Sargent for geometry optimization. ΔE for U?U* is 6.61 kcal/mole. The reaction field continuum model for solvent effect indicates a preferential stabilization of U* by 1.0 kcal/mole. The calculated gas phase K_t and solution K_t for U?U* are 1.44×10^?5 and 1.3×10^?4, respectively.     

Ferrocene-bis(thymine/uracil) conjugates: base pairing directed, spacer dependent self-assembly and supramolecular packing

X-ray crystallographic studies of methylene linked Ferrocene-bis(thymine/uracil) conjugates Fc(T:T)(M) and Fc(U:U)(M) reveal base dependent 2-D supramolecular assemblies generated via wobble self-pairing for bis-thymine and reverse wobble self-pairing for bis-uracil conjugates, differing in architecture from the corresponding butylene spacer linked conjugates.