A State-Specific PCM–DFT method to include dynamic solvent effects in the calculation of ionization energies: Application to DNA bases

Ultrafast Vibrational Wave Packet Dynamics of the Aqueous Guanine Radical Anion Induced by Photodetachment

Studying the ultrafast dynamics of ionized aqueous biomolecules is important for gaining an understanding of the interaction of ionizing radiation with biological matter. Guanine plays an essential role in biological systems as one of the four nucleobases that form the building blocks of deoxyribonucleic acid (DNA). Guanine radicals can induce oxidative damage to DNA, particularly due to the lower ionization potential of guanine compared to the other nucleobases, sugars, and phosphate groups that are constituents of DNA. This study utilizes femtosecond optical pump-probe spectroscopy to observe the ultrafast vibrational wave packet dynamics of the guanine radical anion launched by photodetachment of the aqueous guanine dianion. The vibrational wave packet motion is resolved into 11 vibrational modes along which structural reorganization occurs upon photodetachment. These vibrational modes are assigned with the aid of density functional theory (DFT) calculations. Our work sheds light on the ultrafast vibrational dynamics following the ionization of nucleobases in an aqueous medium.

BEP-Like Correction of Nonequilibrium Thermodynamic Parameters of the Solvent-Assisted Reactions: The DFT and Ab Initio Study of Hydration, Peroxidation, and Enolization of Acetone and 1,1,1-Trifluoroacetone in Aqueous Solutions

The mechanisms of enolization and reactions of nucleophilic addition to carbonyl compounds were analyzed by density functional theory (DFT) (PBE1PBE) and ab initio (DLPNO-CCSD(T)) level of theory using the interaction of water and hydrogen peroxide with acetone and 1,1,1-trifluoroacetone (TFA) as the reference reactions. The transition states of the studied reactions were localized within the integrated approach that includes both the dielectric continuum theory (polarizable continuum model (PCM)) and the cyclic or two-cluster explicit solvation models. The considered models provide proton transfer in the enolization, hydration, and peroxidation reactions by the Grotthuss mechanism. It is shown that the calculated activation parameters at a sufficiently high level of theory and a sufficiently flexible solvation model can be additionally refined using the Bell-Evans-Polanyi (BEP)-like correction (in a form of the Bell-Evans-Polanyi equation), which is linear scaling of the model potential energy surface according to the equilibrium parameters of the reference reaction (experiment or high-level calculation). Quite good correspondence of the corrected and reference activation parameters and the lower sensitivity of the calculation results to the choice of the solvation model indicate the high reliability of the proposed BEP-like correction technique.

Electronic relaxation of aqueous aminoazobenzenes studied by time-resolved photoelectron spectroscopy and surface hopping TDDFT dynamics calculations

Studies of ultrafast relaxation of molecular chromophores are complicated by the fact that most chromophores of biological and technological importance are rather large molecules and are strongly affected by their environment, either solvent or a protein cage. Here we present an approach which allows us to follow transient electronic structure of complex photoexcited molecules. We use the method of time-resolved photoelectron spectroscopy in solution to follow relaxation of two prototypical aqueous chromophores, Methyl Orange and Metanil Yellow, both of which are aminoazobenzene derivatives. Using excitation by 400 nm laser pulses and ionization by wavelength-selected 46.7 nm XUV pulses from high-order harmonic generation we follow relaxation of both molecules via the dark S1 state. The photoelectron spectra yield binding energies of both ground and excited states. We combine the experimental results with surface hopping time-dependent density functional theory (TDDFT) calculations employing B3LYP+D3 and ωB97X-D functionals. The results demonstrate that the method is generally suitable for description of ultrafast dynamics in these molecules and can recover absolute binding energies observed in the experiment. The B3LYP+D3 functional appears to be better suited for these systems, especially in the case of Metanil Yellow, where it indicates the importance of an intramolecular charge transfer state. Our results pave the way towards quantitative understanding of evolving electronic structure in photo-induced relaxation processes.

Redox Properties of Native and Damaged DNA from Mixed Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations

The redox properties of two large DNA fragments composed of 39 base pairs, differing only by an 8-oxoguanine (8oxoG) defect replacing a guanine (G), were investigated in physiological conditions using mixed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations. The quantum region of the native fragment comprised 3 G-C base pairs, while one G was replaced by an 8oxoG in the defect fragment. The calculated values for the redox free energy are 6.55 ± 0.28 eV and 5.62 ± 0.30 eV for the native and the 8oxoG-containing fragment, respectively. The respective estimates for the reorganization free energy are 1.25 ± 0.18 eV and 1.00 ± 0.18 eV. Both reactions follow the Marcus theory for electron transfer. The large difference in redox potential between the two fragments shows that replacement of a G by an 8oxoG renders the DNA more easily oxidizable. This finding is in agreement with the suggestion that DNA fragments containing an 8oxoG defect can act as sinks of oxidative damage that protect the rest of the genome from assault. In addition, the difference in redox potential between the native and the defect DNA fragment indicates that a charge transfer-based mechanism for the recognition of DNA defects might be feasible, in line with recent suggestions based on experimental observations.

Polarizable embedding for simulating redox potentials of biomolecules

Redox reactions play a key role in various biological processes, including photosynthesis and respiration. Quantitative and predictive computational characterization of redox events is therefore highly desirable for enriching our knowledge on mechanistic features of biological redox-active macromolecules. Here, we present a computational protocol exploiting polarizable embedding hybrid quantum-classical approach and resulting in accurate estimates of redox potentials of biological macromolecules. A special attention is paid to fundamental aspects of the theoretical description such as the effects of environment polarization and of the long-range electrostatic interactions on the computed energetic parameters. Environment (protein and the solvent) polarization is shown to be crucial for accurate estimates of the redox potential: hybrid quantum-classical results with and without account for environment polarization differ by 1.4 V. Long-range electrostatic interactions are shown to contribute significantly to the computed redox potential value even at the distances far beyond the protein outer surface. The approach is tested on simulating reduction potential of cryptochrome 1 protein from Arabidopsis thaliana. The theoretical estimate (0.07 V) of the midpoint reduction potential is in good agreement with available experimental data (-0.15 V).

Combining the GW formalism with the polarizable continuum model: A state-specific non-equilibrium approach

We have implemented the polarizable continuum model within the framework of the many-body Green's function GW formalism for the calculation of electron addition and removal energies in solution. The present formalism includes both ground-state and non-equilibrium polarization effects. In addition, the polarization energies are state-specific, allowing to obtain the bath-induced renormalisation energy of all occupied and virtual energy levels. Our implementation is validated by comparisons with ΔSCF calculations performed at both the density functional theory and coupled-cluster single and double levels for solvated nucleobases. The present study opens the way to GW and Bethe-Salpeter calculations in disordered condensed phases of interest in organic optoelectronics, wet chemistry, and biology.

UV-Induced Adenine Radicals Induced in DNA A-Tracts: Spectral and Dynamical Characterization

Adenyl radicals generated in DNA single and double strands, (dA)₂₀ and (dA)₂₀·(dT)₂₀, by one- and two-photon ionization by 266 nm laser pulses decay at 600 nm with half-times of 1.0 ± 0.1 and 4 ± 1 ms, respectively. Though ionization initially forms the cation radical, the radicals detected for (dA)₂₀ are quantitatively identified as N6-deprotonated adenyl radicals by their absorption spectrum, which is computed quantum mechanically employing TD-DFT. Theoretical calculations show that deprotonation of the cation radical induces only weak spectral changes, in line with the spectra of the adenyl radical cation and the deprotonated radical trapped in low temperature glasses.

Free Energies of Redox Half-Reactions from First-Principles Calculations

Quantitative prediction of the energetics of redox half-reactions is still a challenge for modern computational chemistry. Here, we propose a simple scheme for reliable calculations of vertical ionization and attachment energies, as well as of redox potentials of solvated molecules. The approach exploits linear response approximation in the context of explicit solvent simulations with spherical boundary conditions. It is shown that both vertical ionization energies and vertical electron affinities, and, consequently redox potentials, exhibit linear dependence on the inverse radius of the solvation sphere. The explanation of the linear dependence is provided, and an extrapolation scheme is suggested. The proposed approach accounts for the specific short-range interactions within hybrid DFT and effective fragment potential approach as well as for the asymptotic system-size effects. The computed vertical ionization energies and redox potentials are in excellent agreement with the experimental values.

Organic Solvent Effects in Biomass Conversion Reactions

Transforming lignocellulosic biomass into fuels and chemicals has been intensely studied in recent years. A large amount of work has been dedicated to finding suitable solvent systems, which can improve the transformation of biomass into value-added chemicals. These efforts have been undertaken based on numerous research results that have shown that organic solvents can improve both conversion and selectivity of biomass to platform molecules. We present an overview of these organic solvent effects, which are harnessed in biomass conversion processes, including conversion of biomass to sugars, conversion of sugars to furanic compounds, and production of lignin monomers. A special emphasis is placed on comparing the solvent effects on conversion and product selectivity in water with those in organic solvents while discussing the origins of the differences that arise. We have categorized results as benefiting from two major types of effects: solvent effects on solubility of biomass components including cellulose and lignin and solvent effects on chemical thermodynamics including those affecting reactants, intermediates, products, and/or catalysts. Finally, the challenges of using organic solvents in industrial processes are discussed from the perspective of solvent cost, solvent stability, and solvent safety. We suggest that a holistic view of solvent effects, the mechanistic elucidation of these effects, and the careful consideration of the challenges associated with solvent use could assist researchers in choosing and designing improved solvent systems for targeted biomass conversion processes.