Catalysis Effects of Water Molecules and of Charge on Intramolecular Proton Transfer of Uracil

A rotational spectroscopy study of microsolvation effects on intramolecular proton transfer in trifluoroacetylacetone-(H2O)1-3

Trifluoroacetylacetone (TFAA) has two enol forms, which can switch to each other via proton transfer. While much attention has been paid to their conformational preferences, the influence of microsolvation on regulating the proton position remains unexplored. Herein, we report the rotational spectra of trifluoroacetylacetone-(water)n (n = 1-3) investigated by chirped pulse Fourier transform microwave spectroscopy in the 2-8 GHz frequency range. Two conformers were identified for both TFAA-H2O and TFAA-(H2O)2, while only one conformer was characterized for TFAA-(H2O)3. The results indicate that water binding on the CH3 side stabilizes the enolF form, whereas water binding on the CF3 side stabilizes the enolH form. The enolF form predominates over the enolH form in these hydrated complexes, which contrasts with the fact that only enolH exists in isolated TFAA. EnolH becomes preferred only when water inserts itself into the intramolecular hydrogen bond. Instanton theory calculations reveal that the proton transfer reaction is dominated by quantum tunneling at low temperatures, leading to the stable existence of only one enol form in each configuration of the hydrated clusters.

Mechanistic insight into the tautomerization of histidine initiated by water-catalyzed N-H and C-H cleavages

The N-H and C-H activation is of great significance in organic chemistry and chemical industry fields, especially, in the utilization of petroleum raw materials. High NδH (tautomer of natural histidine) content would increase Alzheimer's disease risk. To inhibit this and improve the activation of N-H and C-H bonds, the isomerization mechanism from NδH to NεH of histidine-containing dipeptide catalyzed by water cluster was explored. The results discovered that water cluster assists this reaction by reducing the activation energies from 68.20 to 9.60 kcal mol^-1, and its size not only affects the reaction rate but also determines the reaction pathway in a degree. Moreover, water cluster, taken as a potential green catalyst, is more effective on the reactions involving N-H and C-H bond cleavages than reported common toxic organometallic compounds and has different catalytic mechanisms. This work also provides some theoretical guidance for the modulation of Alzheimer's disease induced by histidine isomerization.

The effect of water-mediated catalysis on the intramolecular proton-transfer reactions of the isomers of 5-chlorouracil: a theoretical study

The geometrical structures and thermal energies (E), enthalpies (H) and Gibbs free energies (G) of 13 isomers of 5-chlorouracil (5ClU) in the gas and water phases were investigated using the density functional theory (DFT) method at the M06-2X/6-311++g(3df,3pd) level. The isomers of 5ClU can be microhydrated at different molecular target sites. The mono- and dihydrated forms are the most stable in both the gas and water phases, and, because of the intermolecular interactions, the hydrations lead to a degree of change in the stability trend. Two types of isomerizations were considered: the internal H-O bond rotations in which the H atom rotates 180° around the C-O bond and the intramolecular proton-transfer reactions in which an H atom is transferred between an O atom and a neighbouring N atom. The forward and backward energy barriers for isomerizations of nonhydrated 5ClU were calculated. In addition, 16 optimized transition-state structures for water-mediated catalysis on isomerizations of 5ClU were investigated. The forward and backward proton-transfer energy barriers of water-mediated catalysis on isomerizations of 5ClU were obtained. The results indicate that the catalytic effect of two H₂O molecules is much greater than that of one H₂O molecule in isomerizations of 5ClU.

Ultrafast Excited-State Dynamics of Hydrogen-Bonded Cytosine Microsolvated Clusters with Protic and Aprotic Polar Solvents

Microsolvation effects on the ultrafast excited-state deactivation dynamics of cytosine (Cy) were studied in hydrogen-bonded Cy clusters with protic and aprotic solvents using mass-resolved femtosecond pump-probe ionization spectroscopy. Two protic solvents, water (H₂O) and methanol (MeOH), and one aprotic solvent, tetrahydrofuran (THF), were investigated, and transients of Cy·(H₂O)_1-6, Cy·(MeOH)_1-3, and Cy·THF microsolvated clusters produced in supersonic expansions were measured. With the aid of electronic structure calculations, we assigned the observed dynamics to the low-energy isomers of various Cy clusters and discussed the microsolvation effect on the excited-state deactivation dynamics. With the protic solvents only the microsolvated clusters of Cy keto tautomer were observed. The observed decay time constants of Cy·(H₂O) _n are 0.5 ps for n = 1 and ∼0.2-0.25 ps for n = 2-6. For Cy·(MeOH) _n clusters, the decay time constant for n = 1 cluster is similar to that of the Cy monohydrate, but for n = 2 and 3 the decays are about a factor of 2 slower than the corresponding microhydrates. With the aprotic solvent, THF, hydrogen-bonded complexes of both keto and enol tautomers are present in the beam. The keto-Cy·THF shows a decay similar to that of the keto-Cy monomer, whereas the enol-Cy·THF exhibits a 2-fold slower decay than the enol-Cy monomer, suggesting an increase in the barrier to excited-state deactivation upon binding of one THF molecule to the enol form of Cy.

Do the fragments from decomposed ZIF-8 greatly affect some of the intramolecular proton-transfer of thymine? A quantum chemical study

The intramolecular proton-transfer processes of thymine were investigated by the density functional theory method. It is shown that the mutation from keto (T) to enol (T′) form is affected by zeolitic imidazolate framework-8 (ZIF-8) fragments such as single 2-methylimidazole neutral crystals (M), and negatively charged 2-methylimidazole ligands (M⁻). Results show that with the number (n) of water (w) molecules that assist proton-transfer increasing from 1 to 4, the order of the tautomeric energy barriers (in kcal mol⁻¹) is T-2w (16.3) < T-1w (17.6) < T-3w (17.8) < T-4w (20.5). In the presence of M, the order of energy barrier is MT-2w (16.6) < MT-1w (17.7) < MT-3w (18.9) < MT-4w (20.8). M⁻ has a catalysis effect on the energy barrier and the order is M⁻T-2w (14.4) < M⁻T-3w (15.2) < M⁻T-1w (16.3) < M⁻T-4w (16.8). The attachment of the M⁻ fragment slightly promotes the proton-transfer processes in some instances. The characterization of the proton-transfer processes is helpful to understand the genotoxicity of ZIF-8 during drug delivery applications.

Investigations on whether fragments from decomposed ZIF-8 would affect the intramolecular proton-transfer of thymine by DFT modeling.

The influence of isolated and penta-hydrated Zn2+ on some of the intramolecular proton-transfer processes of thymine: a quantum chemical study

The influence of isolated and penta-hydrated Zn²⁺ on some of the intramolecular proton-transfer processes of thymine is investigated by DFT modeling.

Nanohydration of uracil: emergence of three-dimensional structures and proton-induced charge transfer

Stepwise hydration of uracil proceeds three dimensionally above three molecules and qualitatively changes the response to proton damage.

Effect of the methylation of uracil and/or glycine on their mutual interaction

In order to simulate the hydrogen bonding and proton transfer (PT) in protein-DNA/RNA interactions, a series of simplified models were employed and investigated in the gas phase. These models included various neutral, anionic and cationic glycine-uracil dimers, and their methylated derivatives generated by the mono- or dimethylation of glycine and/or uracil moieties of the dimer. The results reveal that the only process that can occur in the neutral complexes is a double-PT process leading to proton exchange between the two moieties (i.e., point mutation). The first methyl substitute can reduce the activation energy of the PT process and thus promote the isomerization of the two moieties; further methylation can reduce the isomerization in only some of the cases. In the anionic complexes, only the one-way PT (i.e., amino acid → nucleic acid base) process is energetically favorable, and this PT process is an interesting barrier-free one (BFPT), with the attached electron locating itself at the base moiety. Methylation will disfavor BFPT, but it cannot alter the nature of BFPT. In the cationic complexes, three different PT processes can occur. These processes can transform mutually by adjusting either or both of the methylated sites and methyl number, indicating that the methylation can regulate the dynamics of these PT processes.

Theoretical study of the tautomerism in the one-electron oxidized guanine-cytosine base pair

Ionizing radiation on DNA mainly generates one-electron oxidized guanine-cytosine base pair (G(+·):C), and in the present paper we study all possible tautomers of G(+·):C by using ab initio approaches. Our calculations reveal that the tautomeric equilibrium follows a peculiar path, characterized by a stepwise mechanism: first the proton in the central hydrogen bond N1(G)-H1-N3(C) migrates from guanine to cytosine, and then the cytosine cation releases one proton from its amino group. During this second step, water acts as a proton acceptor, localizing the positive charge on one of the water molecules interacting with the guanine radical. In agreement with experimental findings, the computed energy barriers show that the deprotonation of the cytosine cation is the speed-limiting step in the tautomeric equilibrium. The influence of the number of water molecules incorporated in the theoretical model is analyzed in detail. The evolution of electronic properties along the reaction path is also discussed on the basis of partial atomic charges and spin density distributions. This work demonstrates that water indeed plays a crucial role in the tautomeric equilibra of base pairs.