Comparison of Py*+/dU*- charge transfer state dynamics in 5-(1-pyrenyl)-2'-deoxyuridine nucleoside conjugates with amido-, ethylenyl-, and ethynyl linkers

Femtosecond, picosecond, and nanosecond transient absorbance (TA) and picosecond emission kinetics results are presented for three 5-(1-pyrenyl)-2'-deoxyuridine nucleosides each with a different two-atom linker joining pyrenyl C-1 to uracil C-5. The linkers are respectively -NHCO-, -(CH(2))(2)-, and -C[triple bond]C- for PAdU, PEdU, and PYdU. For all three nucleoside conjugates, most conformers undergo intramolecular charge transfer (CT) from their pyrenyl (1)(pi,pi) excited states to form Py(*+)/dU(*-) CT products in ultrashort times: 相似文献   

Barrier-free intermolecular proton transfer induced by excess electron attachment to the complex of alanine with uracil

The photoelectron spectrum of the uracil-alanine anionic complex (UA)(-) has been recorded with 2.540 eV photons. This spectrum reveals a broad feature with a maximum between 1.6 and 2.1 eV. The vertical electron detachment energy is too large to be attributed to an (UA)(-) anionic complex in which an intact uracil anion is solvated by alanine, or vice versa. The neutral and anionic complexes of uracil and alanine were studied at the B3LYP and second-order M?ller-Plesset level of theory with 6-31++G(*) (*) basis sets. The neutral complexes form cyclic hydrogen bonds and the three most stable neutral complexes are bound by 0.72, 0.61, and 0.57 eV. The electron hole in complexes of uracil with alanine is localized on uracil, but the formation of a complex with alanine strongly modulates the vertical ionization energy of uracil. The theoretical results indicate that the excess electron in (UA)(-) occupies a pi(*) orbital localized on uracil. The excess electron attachment to the complex can induce a barrier-free proton transfer (BFPT) from the carboxylic group of alanine to the O8 atom of uracil. As a result, the four most stable structures of the uracil-alanine anionic complex can be characterized as a neutral radical of hydrogenated uracil solvated by a deprotonated alanine. Our current results for the anionic complex of uracil with alanine are similar to our previous results for the anion of uracil with glycine, and together they indicate that the BFPT process is not very sensitive to the nature of the amino acid's hydrophobic residual group. The BFPT to the O8 atom of uracil may be relevant to the damage suffered by nucleic acid bases due to exposure to low energy electrons.     

Ultrafast proton-coupled electron-transfer dynamics in pyrene-modified pyrimidine nucleosides: model studies towards an understanding of reductive electron transport in DNA.

5-(Pyren-1-yl)-2'-deoxyuridine (PydU) and 5-(Pyren-1-yl)-2'-deoxycytidine (PydC) were used as model nucleosides for DNA-mediated reductive electron transport (ET) in steady-state fluorescence and femtosecond time-resolved transient absorption spectroscopy studies. Excitation of the pyrene moiety in PydU and PydC leads to an intramolecular electron transfer that yields the pyrenyl radical cation and the corresponding pyrimidine radical anion (dU.- and dC.-. By comparing the excited state dynamics of PydC and PydU, we derived information about the energy difference between the two pyrimidine radical anion states. To determine the influence of protonation on the rates of photoinduced intramolecular ET, the spectroscopic investigations were performed in acetonitrile, MeCN, and in water at different pH values. The results show a significant difference in the basicity of the generated pyrimidine radical anions and imply an involvement of proton transfer during electron hopping in DNA. Our studies revealed that the radical anion dC.- is being protonated even in basic aqueous solution on a picosecond time scale (or faster). These results suggest that protonation of dC.- may also occur in DNA. In contrast, efficient ET in PydU could only be observed at low pH values (< 5). In conclusion, we propose--based on the free energy differences and the different basicities--that only dT.- but not dC.- can participate as an intermediate charge carrier for excess electron migration in DNA.     

Fluorescent probe for Zn2+ with light-harvesting pyrenyl groups: sensitization via intramolecular energy transfer

Abstract  

Bis[N-(1-pyrenylmethyl)salicylideneaminato]zinc(II) emits intense fluorescence on excitation of the pyrenyl group. This fluorescence originates from the excited state of the salicylideneamine moiety, indicating that efficient intramolecular energy transfer takes place. The occurrence of such efficient energy transfer is accounted for by significant spectral overlap between the emission from the S₁ state of the pyrenyl group and the absorption of the salicylideneamine–zinc complex.     

'Remote' adiabatic photoinduced deprotonation and aggregate formation of amphiphilic N-alkyl-N-methyl-3-(pyren-1-yl)propan-1-ammonium chloride salts

The absorption and emission properties of a series of amphiphilic N-alkyl-N-methyl-3-(pyren-1-yl)propan-1-ammonium chloride salts were investigated in solvents of different polarities and over a wide concentration range. For example, at 10(-5) M concentrations in tetrahydrofuran (THF), salts with at least one N-H bond exhibited broad, structureless emissions even though time-correlated single photon counting (TCSPC) experiments indicated negligible static or dynamic intermolecular interactions. Salts with a butylene spacer or lacking an N-H bond showed no discernible structureless emission; their emission spectra were dominated by the normal monomeric fluorescence of a pyrenyl group and the TCSPC histograms could be interpreted on the basis of intramolecular photophysics. The broad, structureless emission is attributed to an unprecedented, rapid, adiabatic proton-transfer to the medium, followed by the formation of an intramolecular exciplex consisting of amine and pyrenyl groups. The proposed mechanism involves excitation of a ground-state conformer of the salts in which the ammonium group sits over the pyrenyl ring due to electrostatic stabilization. At higher concentrations, with longer N-alkyl groups, or in selected solvents, electronic excitation of the salts led to dynamic and static excimeric emissions. For example, whereas the emission spectrum of 10(-3) M N-hexyl-N-methyl-3-(pyren-1-yl)propan-1-ammonium chloride in THF consisted of comparable amounts of monomeric and excimeric emission, the emission from 10(-5) M N-dodecyl-N-methyl-3-(pyren-1-yl)propan-1-ammonium chloride in 1:9 (v:v) ethanol/water solutions was dominated by excimeric emission, and discrete particles near micrometer size were discernible from confocal microscopy and dynamic light scattering experiments. Comparison of the static and dynamic emission characteristics of the particles and of the neat solid of N-dodecyl-N-methyl-3-(pyren-1-yl)propan-1-ammonium chloride indicate that molecular packing in the microparticles and in the single crystal are very similar if not the same. It is suggested that other examples of the adiabatic proton transfer found in the dilute concentration regime with the pyrenyl salts may be occurring in very different systems, such as in proteins where conformational constraints hold ammonium groups over aromatic rings of peptide units.     

Do Photolyases Need To Provide Considerable Activation Energy for the Splitting of Cyclobutane Pyrimidine Dimer Radical Anions?

cis-syn Cyclobutane pyrimidine dimers, major UV-induced DNA lesions, are efficiently repaired by DNA photolyases. The key step of the repair reaction is a light-driven electron transfer from the FADH(-) cofactor to the dimer; the resulting radical anion splits spontaneously. Whether the splitting reaction requires considerable activation energy is still under dispute. Recent reports show that the splitting reaction of a dimer radical anion has a significant activation barrier (0.45 eV), and so photolyases have to provide considerable energy. However, these results contradict observations that cis-syn dimer radical anions split into monomers at -196 degrees C, and that the full process of DNA photoreactivation was fast (1.5-2 ns). To investigate the activation energies of dimer radical anions, three model compounds 1-3 were prepared. These include a covalently linked cyclobutane thymine dimer and a tryptophan residue (1) or a flavin unit (3), and the covalently linked uracil dimer and tryptophan (2). Their properties of photosensitised splitting of the dimer units by tryptophan or flavin unit were investigated over a large temperature range, -196 to 70 degrees C. The activation energies were obtained from the temperature dependency of splitting reactions for 1 and 2, 1.9 kJ mol(-1) and 0.9 kJ mol(-1) for the thymine and uracil dimer radical anions, respectively. These values are much lower than that obtained for E. coli photolyase (0.45 eV), and are surmountable at -196 degrees C. The activation energies provide support for previous observations that repair efficiencies for uracil dimers are higher than thymine dimers, both in enzymatic and model systems. The mechanisms of highly efficient enzymatic DNA repair are discussed.     

Pulse radiolysis study on electron migration along polymer chain—ion radicals on poly(4-vinylbiphenyl-co-1-vinylpyrene)

Electron migration along polymer chain is shown by the pulse radiolysis study of poly(4-vinylbiphenyl-co-1-vinylpyrene) in 2-methyltetrahydrofuran solution. For the copolymer with small vinylpyrene contents (0.34–1.58%), excess electron is initially localized in a biphenylyl side-group to form anion radical, and then transfers to a pyrenyl side-group. The electron transfer is enhanced with the increase in the vinylpyrene content in the copolymer, whereas it is independent of the copolymer concentration in the solution. These results indicate that the electron migrates along the copolymer chain by hopping between neighboring biphenylyl side-groups until it is stably trapped on a pyrenyl side-group. Frequency of the electron hopping is estimated to be 5.2 x 10⁹ s^-1.Positive charge migration is suggested to occur similarly by the pulse radiolysis of the copolymer in 1,2-dichloroethane solution. It is about one-tenth slower than the electron migration.     

Pyrene-sensitized electron transport across vesicle bilayers: Dependence of transport efficiency on pyrene substituents

Endoergic electron transport across vesicle bilayers from ascorbate (Asc-) in the inner waterpool to methylviologen (MV2+) in the outer aqueous solution was driven by the irradiation of pyrene derivatives embedded in the vesicle bilayers. The initial rate of MV2+ reduction is dependent on the substituent group of the pyrenyl ring; a hydrophilic functional group linked with the pyrenyl ring by a short methylene chain acts as a sensitizer for the electron transport. Mechanistic studies using (1-pyrenyl)alkanoic acids (1a-c) as sensitizers suggest that the electron transport is mainly initiated by the reductive quenching of the singlet excited state of the pyrene by Asc- and proceeds by a mechanism involving electron exchange between the pyrenes located at the inner and outer interface across the vesicle bilayer. We designed and synthesized novel unsymmetrically substituted pyrenes having both a hydrophilic group linked by a short methylene chain and a hydrophobic long alkyl group (5a-c), which acted as excellent sensitizers for the electron transport across vesicle bilayers.     

Fluorescent probe for Zn<Superscript>2+</Superscript> with light-harvesting pyrenyl groups: sensitization via intramolecular energy transfer

Abstract  Bis[N-(1-pyrenylmethyl)salicylideneaminato]zinc(II) emits intense fluorescence on excitation of the pyrenyl group. This fluorescence originates from the excited state of the salicylideneamine moiety, indicating that efficient intramolecular energy transfer takes place. The occurrence of such efficient energy transfer is accounted for by significant spectral overlap between the emission from the S₁ state of the pyrenyl group and the absorption of the salicylideneamine–zinc complex. Graphical abstract        

Self-assembly of a diblock copolymer with pendant disulfide bonds and chromophore groups: a new platform for fast release

An amphiphilic block copolymer comprising poly(ethylene glycol) (PEG) and poly(2-(methacryloyl)oxyethyl-2'-hydroxyethyl disulfide) (PMAOHD) blocks was synthesized by atom transfer radical polymerization (ATRP). Pyrenebutyric acid was conjugated to the block copolymer by esterification, and a block copolymer with pendant disulfide bonds and pyrenyl groups (PEG-b-P(MAOHD-g-Py)) was obtained. (1)H NMR and gel permeation chromatography (GPC) results demonstrated the successful synthesis of the block copolymer. The cleavage of the disulfide bonds and the degrafting of the pyrenyl groups were investigated in THF and a THF/methanol mixture. Fluorescence spectroscopy, GPC, and (1)H NMR results demonstrated fast cleavage of the disulfide bonds by Bu(3)P in THF. Fluorescence results showed the ratio of the intensity of the excimer peak to the monomer peak decreased rapidly within 20 min. GPC traces of the block copolymer moved to a long retention time region after addition of Bu(3)P, indicating the cleavage of the disulfide bonds and the degrafting of the pyrenyl groups. PEG-b-P(MAOHD-g-Py) can self-assemble into micelles with poly(MAOHD-g-Py) cores and PEG coronae in a mixture of methanol and THF (9:1 by volume). The dissociation of the micelles in the presence of Bu(3)P was investigated. After cleavage of the disulfide bonds in the micellar cores, a pyrene-containing small molecular compound and a block copolymer with pendant thiol groups were produced. Transmission electron microscopy (TEM), dynamic light scattering (DLS), and (1)H NMR were employed to track the dissociation of the polymeric micelles. All the techniques demonstrated the dissociation of the micelles and the fast release of pyrenyl groups from the micelles.     

Photoelectron spectrum of valence anions of uracil and first-principles calculations of excess electron binding energies

The photoelectron spectrum (PES) of the uracil anion is reported and discussed from the perspective of quantum chemical calculations of the vertical detachment energies (VDEs) of the anions of various tautomers of uracil. The PES peak maximum is found at an electron binding energy of 2.4 eV, and the width of the main feature suggests that the parent anions are in a valence rather than a dipole-bound state. The canonical tautomer as well as four tautomers that result from proton transfer from an NH group to a C atom were investigated computationally. At the Hartree-Fock and second-order Moller-Plesset perturbation theory levels, the adiabatic electron affinity (AEA) and the VDE have been converged to the limit of a complete basis set to within +/-1 meV. Post-MP2 electron-correlation effects have been determined at the coupled-cluster level of theory including single, double, and noniterative triple excitations. The quantum chemical calculations suggest that the most stable valence anion of uracil is the anion of a tautomer that results from a proton transfer from N1H to C5. It is characterized by an AEA of 135 meV and a VDE of 1.38 eV. The peak maximum is as much as 1 eV larger, however, and the photoelectron intensity is only very weak at 1.38 eV. The PES does not lend support either to the valence anion of the canonical tautomer, which is the second most stable anion, and whose VDE is computed at about 0.60 eV. Agreement between the peak maximum and the computed VDE is only found for the third most stable tautomer, which shows an AEA of approximately -0.1 eV and a VDE of 2.58 eV. This tautomer results from a proton transfer from N3H to C5. The results illustrate that the characteristics of biomolecular anions are highly dependent on their tautomeric form. If indeed the third most stable anion is observed in the experiment, then it remains an open question why and how this species is formed under the given conditions.     

Structures and energetics of the deprotonated adenine-uracil base pair, including proton-transferred systems

The B3LYP/DZP++ level of theory has been employed to investigate the structures and energetics of the deprotonated adenine-uracil base pairs, (AU-H)-. Formation of the lowest-energy structure, [A(N9)-U]- (which corresponds to deprotonation at the N9 atom of adenine), through electron attachment to the corresponding neutral is accompanied by proton transfer from the uracil N3 atom to the adenine N1 atom. The driving force for this proton transfer is a significant stabilization from the base pairing in the proton transferred form. Such proton transfer upon electron attachment is also observed for the [A(N6b)-U]- and [A(C2)-U]- anions. Electron attachment to the A-U(N3) radical causes strong lone pair repulsion between the adenine N1 and the uracil N3 atoms, driving the two bases apart. Similarly, lone pair repulsion in the anion A(N6a)-U causes the loss of coplanarity of the two base units. The computed adiabatic electron attachment energies for nine AU-H radicals range from 1.86 to 3.75 eV, implying that the corresponding (AU-H)- anions are strongly bound. Because of the large AEAs of the (AU-H) radicals, the C-H and N-H bond dissociation in the AU- base pair anions requires less energy than the neutral AU base pair. The computed C-H and N-H bond dissociation energies for the AU- anion (i.e., the AU base pair plus one electron) are in the range 1.0-3.2 eV, while those for neutral AU are 4.08 eV or higher.     

Effects of dipole moment, linkers, and chromophores at side chains on long-range electron transfer through helical peptides

Octadecapeptides carrying a ferrocene moiety at the molecular terminal were self-assembled on gold, and long-range electron transfer from the ferrocene moiety to gold was investigated by electrochemical methods. Effects on electron transfer of dipole moment of helical peptides, linkers connecting the peptide to gold, and chromophores introduced into the side chains were discussed. Cyclic voltammetry of the monolayers in an aqueous solution revealed that long-range electron transfer over 40 A occurred along the peptide molecule. Chronoamperometry showed that the long-range electron transfer should be ascribed to a hopping mechanism with use of amide groups as hopping sites. Electron transfer through the long peptide was not significantly accelerated by the dipole moment. However, the linker remarkably affected electron transfer depending on whether it was a methylene chain or a phenylene group, suggesting that local electron transfer between gold and the peptides should be the slowest step to determine the overall rate. Pyrenyl groups introduced into the side chains in the middle of the peptide molecule did not noticeably change electron transfer, probably because pyrenyl groups were too distant to allow direct electron transfer between them. Electrostatic potential profiles across the peptide monolayers were also calculated to explain reasonably the several interesting features in the present peptide systems.     

Explicit and implicit solvation of radical ions: the cycloreversion of CPD dimers

The electron transfer catalyzed cycloreversion of cyclobutane pyrimidine dimers is the key step in repair of light-induced DNA lesions catalyzed by the enzyme CPD photolyase. The formation of the CPD radical anion was found to be strongly solvent dependent due to a specific hydrogen bond that stabilizes the valence bound state over the dipole bound state of the additional electron. The effect of solvation on the vertical and adiabatic electron affinity of uracil and uracil dimers as well as on the mechanism of the cycloreversion of the uracil dimer radical anion is explored for three model systems that include explicit solvent molecules at the B3LYP/6-311++G^∗∗/B3LYP/6-31+G^∗ level of theory. The second solvation shell is described using the implicit C-PCM solvation model. These calculations indicate an effectively barrierless mechanism. These results are in agreement with the available experimental data for the reaction energies and isotope effects. It is also shown that a single hydrogen bond donor is a sufficient minimal model for the first solvation shell by adequately describing the stabilization of the valence bound state of the radical anion through hydrogen bonding. The relationship of these model systems with the enzymatic reaction catalyzed by DNA photolyase is also discussed.     

PHOTOSENSITIZED OXIDATION OF BIOMATERIALS and RELATED MODEL COMPOUNDS

Aluminium trisulfonatophthalocyanine (A1PCS), a dye being widely advocated for use in photodynamic therapy, produces singlet oxygen with a quantum yield of 0.34 in oxygenated water at pH 7. Triplet A1PCS abstracts an electron from a variety of amines and phenols, the rate of electron transfer depending upon the thermodynamic driving force, forming the A1PCS radical anion. This latter species reduces molecular oxygen to superoxide ions with high efficiency. The triplet state also abstracts an electron from biological components, including NADH, vitamin C, cysteine, methionine, tyrosine, tryptophan, uracil, and guanine, but not from DNA. These results suggest that photoinduced electron abstraction from appropriate biomaterials could compete with singlet oxygen production under in vivo conditions.     

Direct measurement of the dynamics of excess electron transfer through consecutive thymine sequence in DNA

Charge transfer in DNA is an essential process in biological systems because of its close relation to DNA damage and repair. DNA is also an important material used in nanotechnology for wiring and constructing various nanomaterials. Although hole transfer in DNA has been investigated by various researchers and the dynamic properties of this process have been well established, the dynamics of a negative charge, that is, excess electron, in DNA have not been revealed until now. In the present paper, we directly measured the rate of excess electron transfer (EET) through a consecutive thymine (T) sequence in nicked-dumbbell DNAs conjugated with a tetrathiophene derivative (4T) as an electron donor and diphenylacetylene (DPA) as an electron acceptor at both ends. The selective excitation of 4T by a femtosecond laser pulse caused the excess electron injection into DNA, and led to EET in DNA by a consecutive T-hopping mechanism, which eventually formed the DPA radical anion (DPA(?-)). The rate constant for the process of EET through consecutive T was determined to be (4.4 ± 0.3) × 10(10) s(-1) from an analysis of the kinetic traces of the ΔO.D. during the laser flash photolysis. It should be emphasized that the EET rate constant for T-hopping is faster than the rate constants for oxidative hole transfers in DNA (10(4) to 10(10) s(-1) for A- and G-hopping).     

Calix[4]arene-based, Hg2+ -induced intramolecular fluorescence resonance energy transfer chemosensor

A novel calix[4]arene-based chemosensor 1 based on Hg2+-induced fluorescence resonance energy transfer (FRET) was synthesized, and its sensing behavior toward metal ions was investigated by UV/vis and fluorescence spectroscopies. Addition of Hg2+ to a CH3CN solution of 1 gave a significantly enhanced fluorescence at approximately 575 nm via energy transfer (FRET-ON) from the pyrenyl excimer to a ring-opened rhodamine moiety. In contrast, addition of Al3+ induced a distinct increase of pyrenyl excimer emission ( approximately 475 nm), while no obvious FRET-ON phenomenon was observed. Different binding behaviors of 1 toward Hg2+ and Al3+ were also proposed for the interesting observation.     

Reactions of OH* and eaq − with uracil and thymine in the presence of Cu(II) ions in dilute aqueous solutions: A pulse radiolysis study

The reactions of OH^* and e_aq ^? adducts of uracil and thymine with Cu(II) ions in aqueous solutions were followed by pulse radiolysis. The transient absorption spectra of the OH^* adducts of uracil when followed in the presence of Cu(II) ions show growth in absorption at wavelengths 420 and 350 nm at 15 μs and 65 μs after the pulse respectively. Similar transient absorption spectra of thymine showed growth in absorption at wavelengths 390 and 320 nm at 38 μs and 65 μs after the pulse respectively. The rates of electron transfer from the OH^* adducts of uracil and thymine to various Cu(II) compounds when monitored at 360 nm lie between 10⁶ and 10⁸ mol^?1 dm³ s^?1 this implies that the electron transfer process is not an efficient process. Low rate constants coupled with the spectral changes suggest formation of a radical copper adduct which decays by water insertion to give cis-glycols as the major product. The electron transfer from the electron adducts of uracil and thymine to various copper(II) compounds takes place more efficiently (rate constants of the order of 10⁸ and 10⁹ mol^?1 dm³ s^?1) compared with that from the OH^* adducts. The t-butanol radicals formed on scavenging the OH^* radicals also produce adducts with Cu(I) ions which are formed on oxidation of the electron adducts by Cu(II) ions. This adduct has absorption around 400 nm both in the case of uracil and thymine.     

Design of photoactivated DNA oxidizing agents: synthesis and study of photophysical properties and DNA interactions of novel viologen-linked acridines

A new series of photoactivated DNA oxidizing agents in which an acridine moiety is covalently linked to viologen by an alkylidene spacer was synthesized, and their photophysical properties and interactions with DNA, including DNA cleaving properties, were investigated. The fluorescence quantum yields of the viologen-linked acridines were found to be lower than that of the model compound 9-methylacridine (MA). The changes in free energy for the electron transfer reactions were found to be favorable, and the fluorescence quenching observed in these systems is explained by an electron transfer mechanism. Intramolecular electron transfer rate constants were calculated from the observed fluorescence quantum yields and singlet lifetime of MA and are in the range from 1.06x10(10) s(-1) for 1 a (n=1) to 6x10(8) s(-1) for 1 c (n=11), that is, the rate decreases with increasing spacer length. Nanosecond laser flash photolysis of these systems in aqueous solutions showed no transient absorption, but in the presence of guanosine or calf thymus DNA, transient absorption due to the reduced viologen radical cation was observed. Studies on DNA binding demonstrated that the viologen-linked acridines bind effectively to DNA in both intercalative and electrostatic modes. Results of PM2 DNA cleavage studies indicate that, on photoexcitation, these molecules induce DNA damage that is sensitive to formamidopyrimidine DNA glycosylase. These viologen-linked acridines are quite stable in aqueous solutions and oxidize DNA efficiently and hence can be useful as photoactivated DNA-cleaving agents which function purely by the co-sensitization mechanism.     

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.