A DFT study of uracil and 5-bromouracil in nanodroplets

Photo-ionization initiated differential ultrafast charge migration: impacts of molecular symmetries and tautomeric forms

Photo-ionization induced ultrafast electron dynamics is considered as a precursor for the slower nuclear dynamics associated with molecular dissociation. Here, using the ab initio multielectron wave-packet propagation method, we study the overall many-electron dynamics, triggered by ionizing the outer-valence orbitals of different tautomers for a prototype molecule with more than one symmetry element. From the time evolution of the initially created averaged hole density of each system, we identify distinctly different charge dynamics responses in the tautomers. We observe that the keto form shows a charge migration direction away from the nitrogen bonded with hydrogen, while in enol-U - away from oxygen bonded to hydrogen. Additionally, the dynamics following the ionization of molecular orbitals with different symmetries reveals that a' orbitals show a fast and highly delocalized charge density in comparison to a'' symmetry. These observations indicate why different tautomers respond differently to an XUV ionization, and might explain the subsequent different fragmentation pathways. An experimental schematics allowing the detection and reconstruction of such charge dynamics is also proposed. Although the present study uses a simple, prototypical bio-relevant molecule, it reveals the explicit role of molecular symmetry and tautomerism in the ionization-triggered charge migration that controls many ultrafast physical, chemical, and biological processes, making tautomeric forms a promising tool of molecular design for desired charge migration.

Isolating key reaction energetics and thermodynamic properties during hardwood model lignin pyrolysis

Computational studies on the pyrolysis of lignin using electronic structure methods have been largely limited to dimeric or trimeric models. In the current work we have modeled a lignin oligomer consisting of 10 syringyl units linked through 9 β-O-4' bonds. A lignin model of this size is potentially more representative of the polymer in angiosperms; therefore, we used this representative model to examine the behavior of hardwood lignin during the initial steps of pyrolysis. Using this oligomer, the present work aims to determine if and how the reaction enthalpies of bond cleavage vary with positions within the chain. To accomplish this, we utilized a composite method using molecular mechanics based conformational sampling and quantum mechanically based density functional theory (DFT) calculations. Our key results show marked differences in bond dissociation enthalpies (BDE) with the position. In addition, we calculated standard thermodynamic properties, including enthalpy of formation, heat capacity, entropy, and Gibbs free energy for a wide range of temperatures from 25 K to 1000 K. The prediction of these thermodynamic properties and the reaction enthalpies will benefit further computational studies and cross-validation with pyrolysis experiments. Overall, the results demonstrate the utility of a better understanding of lignin pyrolysis for its effective valorization.

Comparing the performances of various density functionals for modelling the mechanisms and kinetics of bimolecular free radical reactions in aqueous solution

We systematically tested the performances of 18 density functionals for the mechanisms and kinetics of reactions of the α-hydroxyisopropyl radical with 9 organic substrates.

Fragmentation of pure and hydrated clusters of 5Br-uracil by low energy carbon ions: observation of hydrated fragments

The fragmentation of the isolated 5-bromouracil (5BrU) molecule and pure and nano-hydrated 5BrU clusters induced by low energy ¹²C⁴⁺ ions has been studied.

Stacking of the mutagenic base analogue 5-bromouracil: energy landscapes of pyrimidine dimers in gas phase and water

The potential energy surfaces of stacked base pairs consisting of cytosine (C), thymine (T), uracil (U) and the mutagenic thymine analogue 5-bromouracil (BrU) have been searched to obtain all possible minima. Minima and transition states were optimised at the counterpoise-corrected M06-2X/6-31+G(d) level, both in the gas phase and in water, modelled by the polarizable continuum model. The stacked dimers studied are BrU/BrU, C/BrU, C/C, C/T, C/U, T/BrU and T/U. Both face-to-back and face-to-face structures were considered. Free energies were calculated at 298.15 K. Together with U/U, T/T and BrU/U results from previous work, these results complete the family consisting of every stacked dimer combination consisting of C, T, U and BrU. The results were used to assess the hypothesis suggested in the literature that BrU stacks stronger than T, which could stabilise the mispair formed by BrU and guanine. In the gas phase, structures of C/BrU, T/BrU and U/BrU with greater zero-point-corrected binding energies than C/T, T/T and U/T, respectively, were found, with differences in favour of BrU of 3.1 kcal mol(-1), 1.7 kcal mol(-1) and 0.5 kcal mol(-1), respectively. However, the structure of these dimers differed considerably from anything encountered in DNA. When only the dimers with the most "DNA-like" twist (±36°) were considered, C/BrU and T/BrU were still more strongly bound than C/T and T/T, by 0.5 kcal mol(-1) and 1.7 kcal mol(-1), respectively. However, when enthalpic and/or solvent contributions were taken into account, the stacking advantage of BrU was reversed in the gas phase and mostly nullified in water. Enhanced stacking therefore does not seem a plausible mechanism for the considerably greater ability of BrU-G mispairs over T-G mispairs to escape enzymatic repair.

Competition between hydrogen and halogen bonding in halogenated 1-methyluracil: Water systems

The competition between hydrogen- and halogen-bonding interactions in complexes of 5-halogenated 1-methyluracil (XmU; X = F, Cl, Br, I, or At) with one or two water molecules in the binding region between C5-X and C4=O4 is investigated with M06-2X/6-31+G(d). In the singly-hydrated systems, the water molecule forms a hydrogen bond with C4=O4 for all halogens, whereas structures with a halogen bond between the water oxygen and C5-X exist only for X = Br, I, and At. Structures with two waters forming a bridge between C4=O and C5-X (through hydrogen- and halogen-bonding interactions) exist for all halogens except F. The absence of a halogen-bonded structure in singly-hydrated ClmU is therefore attributed to the competing hydrogen-bonding interaction with C4=O4. The halogen-bond angle in the doubly-hydrated structures (150-160°) is far from the expected linearity of halogen bonds, indicating that significantly non-linear halogen bonds may exist in complex environments with competing interactions.

A study of nucleic acid base-stacking by the Monte Carlo method: Extended cluster approach

The adenine-thymine (AT), adenine-uracil (AU) and guanine-cytosine (GC) base associates in clusters containing 400 water molecules were studied using a newly implemented Metropolis Monte Carlo algorithm based on the extended cluster approach. Starting from the hydrogen-bonded Watson-Crick geometries, all three base pairs are transformed into more favorable stacked configurations during the simulation. The obtained results show, for the first time, the transition from planar base pairs to stacked base associates in the Monte Carlo framework. Analysis of the interaction energies shows that, in the water cluster, the stacked dimers are energetically preferable compared to the corresponding Watson-Crick base pairs. This is due to the larger base-water interaction in the stacked structures. The water-water interaction is one of the main factors promoting the formation of stacked dimers, and the obtained data confirm the crucial role of the water-water interactions in base stacking.

Theoretical study on conformational preferences of ribose in 2-thiouridine--the role of the 2'OH group

Conformational changes in ribose are well-known to play a significant role in biomolecular identification. The mechanism of selectivity towards C3'-endo conformation (conformer b) in ribose of 2-thiouridine has been studied using DFT (B3LYP) and MP2 methodology, together with 6-31+G(d,p) basis set. The polarity of the C2S2 bond is enhanced due to the orientation of H2' towards the S2 atoms, which leads to a difference in the corresponding bond lengths, the atomic charges and the vO2'H2' stretch vibrations in all the conformers. NBO analysis shows that charge transfer mainly occurs in the C2N3 and C2S2 orbitals. The higher stability of conformer b is attributed to its larger orbital interaction energies within the 2-thiouracil base, and total orbital interaction energies of conformer b. Our conclusion is that the distant electrostatic rather than hydrogen bonding effects between 2'OH and the S2 atoms play the dominant role in the orbital interaction, and enhance the selectivity towards the C3'-endo conformation of ribose.