Theoretical study of resonance formation in microhydrated molecules. II. Thymine-(H2O)n, n = 1,2,3,5

Toward a numerically efficient description of bulk-solvated anionic states

We investigate the vertical electron attachment energy (VAE) of 1-methyl-4-nitroimidazole, a model radiosensitizer, employing quantum mechanics/molecular mechanics (QM/MM) and QM/polarized continuum (QM/PCM) solvation models. We considered the solvent-excluded surface (QM/PCM-SES) and Van der Waals (QM/PCM-VDW) cavities within the PCM framework, the electrostatic embedding QM/MM (EE-QM/MM) model, and the self-consistent sequential QM/MM polarizable electrostatic embedding (scPEE-S-QM/MM) model. Due to slow VAE convergence concerning the number of QM solvent molecules, full QM calculations prove inefficient. Ensemble averages in these calculations do not align with VAEs computed for the representative solute-solvent configuration. QM/MM and QM/PCM calculations show agreement with each other for sufficiently large QM regions, although the QM/PCM-VDW model exhibits artifacts linked to the cavity. QM/MM models demonstrate good agreement between ensemble averages and VAEs calculated with the representative configuration. Notably, the VAE computed with the scPEE-S-QM/MM model achieves faster convergence concerning the number of QM water molecules compared to the EE-QM/MM model, attributed to enhanced efficiency from MM charge polarization in the scPEE-S-QM/MM approach. This emphasizes the importance of QM/classical models with accurate solute-solvent and solvent-solvent mutual polarization for obtaining converged VAEs at a reasonable computational cost. The full-QM approach is very inefficient, while the microsolvation model is inaccurate. Computational savings in QM/MM models result from electrostatic embedding and the representative configuration, with the scPEE-S-QM/MM approach emerging as an efficient tool for describing bulk-solvated anions within the QM/MM framework. Its potential extends to improving transient anion state descriptions in biomolecules and radiosensitizers, especially given the frequent employment of microsolvation models.

Novel Approach for Predicting Vertical Electron Attachment Energies in Bulk-Solvated Molecules

When low-energy electrons interact with molecules, they can give rise to transient anion states commonly known as resonances. These states are formed through vertical electron attachment processes and have the potential to induce various forms of DNA lesions, including base damage, single- and double-strand breaks, cross-links, and clustered lesions that are challenging to repair. So far, most experimental and theoretical studies have investigated the formation of resonances of (bio)molecules in the gas phase or in microsolvated environments. Since cellular environments are mainly composed of water molecules, it is crucial to understand how bulk water affects the resonances of (bio)molecules. Given the existing gap in studies on resonances of bulk-solvated molecules, we propose a novel theoretical-computational approach to address this void. Our approach combines the multibasis-set (time-dependent-)density functional theory and self-consistent sequential quantum mechanics/molecular mechanics polarizable electrostatic embedding methods. We apply this combined methodology to predict the vertical electron attachment energies of 1-methyl-5-nitroimidazole (1M5NI), a well-known radiosensitizer model, in bulk water. In addition, we analyze the rapid mutual polarization between the resonances (both shape- and core-excited) of 1M5NI and the surrounding bulk water environment. For comparison, we also studied the isolated and microsolvated 1M5NI. Overall, while the polarization of the environment is clearly sensitive to the solute charge, causing a significant impact on the vertical electron affinity and consequently on the attachment electron energies, it does not have a significant impact on the excitation energies of the anion.

Shape resonance induced electron attachment to cytosine: The effect of aqueous media

We have investigated the impact of microsolvation on shape-type resonance states of nucleobases, taking cytosine as a case study. To characterize the resonance position and decay width of the metastable states, we employed the newly developed DLPNO-based EA-EOM-CCSD method in conjunction with the resonance via Padé (RVP) method. Our calculations show that the presence of water molecules causes a redshift in the resonance position and an increase in the lifetime for the three lowest-lying resonance states of cytosine. Furthermore, there are some indications that the lowest resonance state in isolated cytosine may get converted to a bound state in the presence of an aqueous environment. The obtained results are extremely sensitive to the basis set used for the calculations.

Secondary Electron Attachment-Induced Radiation Damage to Genetic Materials

Reactions of radiation-produced secondary electrons (SEs) with biomacromolecules (e.g., DNA) are considered one of the primary causes of radiation-induced cell death. In this Review, we summarize the latest developments in the modeling of SE attachment-induced radiation damage. The initial attachment of electrons to genetic materials has traditionally been attributed to the temporary bound or resonance states. Recent studies have, however, indicated an alternative possibility with two steps. First, the dipole-bound states act as a doorway for electron capture. Subsequently, the electron gets transferred to the valence-bound state, in which the electron is localized on the nucleobase. The transfer from the dipole-bound to valence-bound state happens through a mixing of electronic and nuclear degrees of freedom. In the presence of aqueous media, the water-bound states act as the doorway state, which is similar to that of the presolvated electron. Electron transfer from the initial doorway state to the nucleobase-bound state in the presence of bulk aqueous media happens on an ultrafast time scale, and it can account for the decrease in DNA strand breaks in aqueous environments. Analyses of the theoretically obtained results along with experimental data have also been discussed.

Electron Attachment to DNA: The Protective Role of Amino Acids

We have studied the effect of amino acids on the electron attachment properties of a DNA nucleobase, with cytosine as a model system. The equation of motion coupled cluster theory with an extended basis set has been used to simulate the electron-attached state of the DNA model system. Arginine, alanine, lysine, and glycine are the four amino acids considered to investigate their role in electron attachment to a DNA nucleobase. The electron attachment to cytosine in all the four cytosine-amino acid gas-phase dimer complexes follows a doorway mechanism, where the electron gets transferred from the initial dipole-bound doorway state to the final nucleobase-bound state through the mixing of electronic and nuclear degrees of freedom. When cytosine is bulk-solvated with glycine, the glycine-bound state acts as the doorway state, where the initial electron density is localized on the bulk amino acid and away from the nucleobase, thus leading to the physical shielding of the nucleobase from the incoming electron. At the same time, the presence of amino acids can increase the stability of the nucleobase-bound anionic state, which can suppress the sugar-phosphate bond rupture caused by dissociative electron attachment to DNA.

Low-Energy Shape Resonances of a Nucleobase in Water

When high-energy radiation passes through aqueous material, low-energy electrons are produced which cause DNA damage. Electronic states of anionic nucleobases have been suggested as an entrance channel to capture the electron. However, identifying these electronic resonances have been restricted to gas-phase electron-nucleobase studies and offer limited insight into the resonances available within the aqueous environment of DNA. Here, resonance and detachment energies of the micro-hydrated uracil pyrimidine nucleobase anion are determined by two-dimensional photoelectron spectroscopy and are shown to extrapolate linearly with cluster size. This extrapolation allows the corresponding resonance and detachment energies to be determined for uracil in aqueous solution as well as the reorganization energy associated with electron capture. Two shape resonances are clearly identified that can capture low-energy electrons and subsequently form the radical anion by solvent stabilization and internal conversion to the ground electronic state. The resonances and their dynamics probed here are the nucleobase-centered doorway states for low-energy electron capture and damage in DNA.

Density Functional Method Study on the Cooperativity of Intermolecular H-bonding and π-π+ Stacking Interactions in Thymine-[Cnmim]Br (n = 2, 4, 6, 8, 10) Microhydrates

The exploration of the ionic liquids’ mechanism of action on nucleobase’s structure and properties is still limited. In this work, the binding model of the 1-alkyl-3-methylimidazolium bromide ([Cnmim]Br, n = 2, 4, 6, 8, 10) ionic liquids to the thymine (T) was studied in a water environment (PCM) and a microhydrated surroundings (PCM + wH2O). Geometries of the mono-, di-, tri-, and tetra-ionic thymine (T-wH2O-y[Cnmim]+-xBr−, w = 5~1 and x + y = 0~4) complexes were optimized at the M06-2X/6-311++G(2d, p) level. The IR and UV-Vis spectra, QTAIM, and NBO analysis for the most stable T-4H2O-Br−-1, T-3H2O-[Cnmim]+-Br−-1, T-2H2O-[Cnmim]+-2Br−-1, and T-1H2O-2[Cnmim]+-2Br−-1 hydrates were presented in great detail. The results show that the order of the arrangement stability of thymine with the cations (T-[Cnmim]+) by PCM is stacking > perpendicular > coplanar, and with the anion (T-Br−) is front > top. The stability order for the different microhydrates is following T-5H2O-1 < T-4H2O-Br−-1 < T-3H2O-[Cnmim]+-Br−-1 < T-2H2O-[Cnmim]+-2Br−-1 < T-1H2O-2[Cnmim]+-2Br−-1. A good linear relationship between binding EB values and the increasing number (x + y) of ions has been found, which indicates that the cooperativity of interactions for the H-bonding and π-π+ stacking is varying incrementally in the growing ionic clusters. The stacking model between thymine and [Cnmim]+ cations is accompanied by weaker hydrogen bonds which are always much less favorable than those in T-xBr− complexes; the same trend holds when the clusters in size grow and the length of alkyl chains in the imidazolium cations increase. QTAIM and NBO analytical methods support the existence of mutually reinforcing hydrogen bonds and π-π cooperativity in the systems.

Exploration of the theobromine-water dimer: comparison with DNA microhydration

Understanding the molecular basis of the appearance of life on Earth is an exciting research field. Many factors may have influenced the election of the molecules used by living beings and evolution may have modified those original compounds. In an attempt to understand the role played by intermolecular interactions in the election of CGAT as the alphabet of life, we present here a thorough experimental and computational study on the interaction of theobromine with water. Theobromine is a xanthine derivative, structurally related to the nucleobases, and also present in many living beings. The experimental results demonstrate that the most stable isomer of theobromine-water was formed and detected in supersonic expansions. This isomer very well resembles the structure of the dimers between nucleobases and water, offering similar values of binding energy. A comparison between the results obtained for theobromine-water with those reported in the literature for monohydrates of nucleobases is also offered.

Enhancement of electron accepting ability of para-benzoquinone by a single water molecule

Electron acceptors built upon the para-benzoquinone (pBQ) electrophore are ubiquitous in nature. Here, we present a frequency-resolved photoelectron spectroscopic study of the cold pBQ radical anion, pBQ-, solvated by a single water molecule, as commonly encountered in nature. Our results show that the electron accepting ability is enhanced by the single water molecule and by elevated temperatures.

Solvation Effects on Dissociative Electron Attachment to Thymine

Ionizing radiation can excite the cellular medium to produce secondary electrons that can subsequently cause damage to DNA. The damage is believed to occur via dissociative electron attachment (DEA). In DEA, the electron is captured by a molecule in a resonant antibonding state and a transient negative ion is formed. If this ion survives against electron autodetachment, then bonds within the molecule may dissociate as energy is transferred from the electronic degrees of freedom into vibrational modes of the molecule. We present a model for studying the effect that transferring kinetic energy into the vibrational modes of a molecule in this way has on a DNA nucleobase. We show that when the base is in an aqueous environment, dissociation is affected by interactions with the surrounding water molecules. In particular, hydrogen bonding between the nucleobase and the solvent can suppress the dissociative channel.

Electron Attachment to Microhydrated Deoxycytidine Monophosphate

DNA constituents are effectively decomposed via dissociative electron attachment (DEA). However, the DEA contribution to radiation damage in living tissues is a subject of ongoing discussion. We address an essential question, how aqueous environment influences the DEA to DNA. In particular, we report experimental fragmentation patterns for DEA to microhydrated 2-deoxycytidine 5-monophosphate (dCMP). Isolated dCMP was previously set as a model to describe mechanisms of DNA-strand breaks induced by secondary electrons and decomposes primarily by dissociation of the C-O phosphoester bond. We show that hydrated molecules decompose via dissociation of the C-N glycosidic bond followed by dissociation of the P-O bond. This significant change of the proposed mechanism can be interpreted by a reactive role of water in the postattachment dynamics. Comparison of the fragmentation with previous macroscopic irradiation studies suggests that the actual contribution of DEA to DNA radiation damage in living tissue is rather small.

Temporary Anion States of Ethene Interacting with Single Molecules of Methane, Ethane, and Water

When an excess electron is added into the π* orbital of ethene, the resulting anion decays by electron autodetachment; that is, it represents an electronic state referred to as a temporary anion or resonance state. Here, the influence of a cluster environment on the energy and lifetime of this state is investigated. The clusters considered are ethene···CH₄, ethene···C₂H₆, and ethene···H₂O. Most of these clusters are systematically constructed so that the solvent interacts with the π system in a specific way, and are thus by construction not minima with respect to all intermolecular degrees of freedom. However, for water, in addition, a minimal energy structure is examined. Systematic variation of the solvent and solvation geometry allows us to identify trends regarding effects due to polarizability, excluded volume, and polarity of the solvent molecules. The resonance parameters of ethene and all temporary cluster anions are computed with the symmetry-adapted cluster-configuration interaction electronic structure method in combination with a complex absorbing potential. This method is well-established for small to intermediate sized molecules. In addition to the study of the solvation effects themselves, the question of how many basis functions are needed on the closed-shell solvating unit is examined.