Modelling Photoionisation in Isocytosine: Potential Formation of Longer‐Lived Excited State Cations in its Keto Form

Abstract Studying the effects of UV and VUV radiation on non‐canonical DNA/RNA nucleobases allows us to compare how they release excess energy following absorption with respect to their canonical counterparts. This has attracted much research attention in recent years because of its likely influence on the origin of our genetic lexicon in prebiotic times. Here we present a CASSCF and XMS‐CASPT2 theoretical study of the photoionisation of non‐canonical pyrimidine nucleobase isocytosine in both its keto and enol tautomeric forms. We analyse their lowest energy cationic excited states including 2π+ , 2nO+ and 2nN+ and compare these to the corresponding electronic states in cytosine. Investigat…

First-principles characterization of the singlet excited state manifold in DNA/RNA nucleobases

An extensive theoretical characterization of the singlet excited state manifold of the five canonical DNA/RNA nucleobases (thymine, cytosine, uracil, adenine and guanine) in gas-phase is carried out with time-dependent density functional theory (TD-DFT) and restricted active space second-order perturbation theory (RASPT2) approaches. Both ground state and excited state absorptions are analyzed and compared between these different theoretical approaches, assessing the performance of the hybrid B3LYP and CAM-B3LYP (long-range corrected) functionals with respect to the RASPT2 reference. By comparing the TD-DFT estimates with our reference for high-lying excited states, we are able to narrow do…

Modelling Photoionisations in Tautomeric DNA Nucleobase Derivatives 7H-Adenine and 7H-Guanine: Ultrafast Decay and Photostability

The study of radiation effects in DNA is a multidisciplinary endeavour, connecting the physical, chemical and biological sciences. Despite being mostly filtered by the ozone layer, sunlight radiation is still expected to (photo)ionise DNA in sizeable yields, triggering an electron removal process and the formation of potentially reactive cationic species. In this manuscript, photoionisation decay channels of important DNA tautomeric derivatives, 7H-adenine and 7H-guanine, are characterised with accurate CASSCF/XMS-CASPT2 theoretical methods. These simulation techniques place the onset of ionisation for 7H-adenine and 7H-guanine on average at 8.98 and 8.43 eV, in line with recorded experimen…

Front Cover: Modelling Photoionisation in Isocytosine: Potential Formation of Longer‐Lived Excited State Cations in its Keto Form (ChemPhysChem 21/2021)

Modelling Photoionisation in Isocytosine: Potential Formation of Longer‐Lived Excited State Cations in its Keto Form

The front cover artwork is provided by Dr. Javier Segarra-Martí (University of Valencia, Spain) and Prof. Michael J. Bearpark (Imperial College London, UK). The image shows the ultrafast photoionisation of DNA canonical nucleobase cytosine and the slower ionization process in non-canonical base isocytosine embedded within a DNA backbone. Read the full text of the Article at 10.1002/cphc.202100402.

Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2

The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess t…

Towards the understanding at the molecular level of the structured-water absorption and fluorescence spectra: a fingerprint of π-stacked water

An intriguing absorption peak around ∼270 nm (4.59 eV) has been recurrently recorded in aqueous solutions of salts, sugars, amino acids, in the free-solute zone (exclusion zone) adjacent to various hydrophilic surfaces, as well as a transient in the conversion process of ice to water. The corresponding associated fluorescence has been observed in the interval 480–490 nm (2.58–2.53 eV). The spectroscopic features have been related to the presence of structured water but its nature remains incompletely understood. On the basis of high-level ab initio computations, the main absorption feature of structured water is assigned to the presence of two π-stacked ground-state water molecules, prefera…

Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate

The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D-UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine 1La state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine 1Lb and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter-base hydrogen transfer and decay to the ground state through a conical …

On the N1-H and N3-H Bond Dissociation in Uracil by Low Energy Electrons: A CASSCF/CASPT2 Study.

The dissociative electron-attachment (DEA) phenomena at the N1-H and N3-H bonds observed experimentally at low energies (<3 eV) in uracil are studied with the CASSCF/CASPT2 methodology. Two valence-bound π(-) and two dissociative σ(-) states of the uracil anionic species, together with the ground state of the neutral molecule, are proven to contribute to the shapes appearing in the experimental DEA cross sections. Conical intersections (CI) between the π(-) and σ(-) are established as the structures which activate the DEA processes. The N1-H and N3-H DEA mechanisms in uracil are described, and experimental observations are interpreted on the basis of two factors: (1) the relative energy of …

Ab initio determination of the ionization potentials of water clusters (H2O)n (n = 2-6).

High-level quantum-chemical ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute the vertical and adiabatic ionization potentials of several water clusters: dimer, trimer, tetramer, pentamer, hexamer book, hexamer ring, hexamer cage, and hexamer prism. The present results establish reference values at a level not reported before for these systems, calibrating different computational strategies and helping to discard less reliable theoretical and experimental data. The systematic study with the increasing size of the water cluster allows obtaining some clues on the structure and reductive properties of liquid water.

Molecular excited state calculations with adaptive wavefunctions on a quantum eigensolver emulation: reducing circuit depth and separating spin states

Ab initio electronic excited state calculations are necessary for the quantitative study of photochemical reactions, but their accurate computation on classical computers is plagued by prohibitive resource scaling. The Variational Quantum Deflation (VQD) is an extension of the quantum-classical Variational Quantum Eigensolver (VQE) algorithm for calculating electronic excited state energies, and has the potential to address some of these scaling challenges using quantum computers. However, quantum computers available in the near term can only support a limited number of quantum circuit operations, so reducing the quantum computational cost in VQD methods is critical to their realisation. In…

On the hexagonal ice-like model of structured water: Theoretical analysis of the low-lying excited states

Abstract The basic molecular unit ( BMU ) of the hexameric ice-like model has been identified as the negatively charged radical species [H 19 O 10 ] − . On the basis of high-level ab initio computations, by means of using the CASPT2 methodology, the low-lying excited states of BMU and its π-stacked dimer are analysed. It is concluded that the BMU constitutes certainly a versatile unit having two spectroscopic features in the near infrared region, two in the visible range and two in the near ultraviolet zone. The main absorption feature is found however for the π-stacked dimer formed by two BMUs , the H 38 O 20 system, which has a pronounced stabilization in the ground state with respect to …

Excitation of Nucleobases from a Computational Perspective I: Reaction Paths

The main intrinsic photochemical events in nucleobases can be described on theoretical grounds within the realm of non-adiabatic computational photochemistry. From a static standpoint, the photochemical reaction path approach (PRPA), through the computation of the respective minimum energy path (MEP), can be regarded as the most suitable strategy in order to explore the electronically excited isolated nucleobases. Unfortunately, the PRPA does not appear widely in the studies reported in the last decade. The main ultrafast decay observed experimentally for the gas-phase excited nucleobases is related to the computed barrierless MEPs from the bright excited state connecting the initial Franck…

3-Methylation alters excited state decay in photoionised uracil.

UV and VUV-induced processes in DNA/RNA nucleobases are central to understand photo-damaging and photo-protecting mechanisms in our genetic material. Here we model the events following photoionisation and electronic excitation in uracil, methylated in the 1′ and 3′ positions, using the correlated XMS-CASPT2 method. We compare our results against those for uracil and 5-methyl-uracil (thymine) previously published. We find 3-methylation, an epigenetic modification in non-negligible amounts, shows the largest differences in photoionised decay of all three derivatives studied compared to uracil itself. At the S0 minimum, 3-methyl-uracil (3mUra) shows almost degenerate excited cation states. Upo…

On the photophysics and photochemistry of the water dimer

The photochemistry of the water dimer irradiated by UV light is studied by means of the complete active space perturbation theory//complete active space self-consistent field (CASPT2//CASSCF) method and accurate computational approaches like as minimum energy paths. Both electronic structure computations and ab initio molecular dynamics simulations are carried out. The results obtained show small shifts relative to a single water molecule on the vertical excitation energies of the dimer due to the hydrogen bond placed between the water donor (W(D)) and the water acceptor (W(A)). A red-shift and a blue-shift are predicted for the W(D) and W(A), respectively, supporting previous theoretical a…

Complete-active-space second-order perturbation theory (CASPT2//CASSCF) study of the dissociative electron attachment in canonical DNA nucleobases caused by low-energy electrons (0-3 eV).

Low-energy (0-3 eV) ballistic electrons originated during the irradiation of biological material can interact with DNA/RNA nucleobases yielding transient-anion species which undergo decompositions. Since the discovery that these reactions can eventually lead to strand breaking of the DNA chains, great efforts have been dedicated to their study. The main fragmentation at the 0-3 eV energy range is the ejection of a hydrogen atom from the specific nitrogen positions. In the present study, the methodological approach introduced in a previous work on uracil [I. González-Ramírez et al., J. Chem. Theory Comput. 8, 2769-2776 (2012)] is employed to study the DNA canonical nucleobases fragmentations…

A theoretical study of the intramolecular charge transfer in 4-(dimethylamino)benzethyne

We have investigated the non-adiabatic relaxation processes occurring in the singlet manifold of 4-(dimethylamino)benzethyne (DMABE){,} a molecule isoelectronic with 4-(dimethylamino)benzonitrile (DMABN) but lacking its characteristic dual fluorescence{,} using multireference perturbation theory methods. The results obtained point out to the existence of a two-fold decay mechanism in which the population of the initially accessed La state bifurcates towards a locally excited (LE) and a [small pi][sigma]* state. Further relaxation to an emitting intramolecular charge transfer (ICT) state is impeded due to the presence of pronounced energy barriers along their associated potential energy surf…