Solvent-Induced Shifts in Electronic Spectra of Uracil

Reconciling TD-DFT and CASPT2 electronic structure methods for describing the photophysics of DNA

Time-dependent density functional theory (TD-DFT) and multiconfigurational second-order perturbation theory (CASPT2) are two of the most widely used methods to investigate photoinduced dynamics in DNA-based systems. These methods sometimes give diverse dynamics in physiological environments usually modeled by quantum mechanics/molecular mechanics (QM/MM) protocol. In this work, we demonstrate for the uridine test case that the underlying topology of the potential energy surfaces of electronic states involved in photoinduced relaxation is similar in both electronic structure methods. This is verified by analyzing surface-hopping dynamics performed at the QM/MM level on aqueous solvated uridine at TD-DFT and CASPT2 levels. By constraining the dynamics to remain onπ π * state we observe similar fluctuations in energy and relaxation lifetimes in surface-hopping dynamics in both TD-DFT and experimentally validated CASPT2 methods. This finding calls for a systematic comparison of the ES potential energy surfaces of DNA and RNA nucleosides at the single- and multi-reference levels of theory. The anomalous long excited state lifetime at the TD-DFT level is explained byn π * trapping due to the tendency of TD-DFT in QM/MM schemes with electrostatic embedding to underestimate the energy of theπ π * state leading to a wrongπ π * / n π * energetic order. A study of the FC energetics suggests that improving the description of the surrounding environment through polarizable embedding or by the expansion of QM layer with hydrogen-bonded waters helps restore the correct state order at TD-DFT level. Thus by combining TDDFT with an accurate modeling of the environment, TD-DFT is positioned as the standout protocol to model photoinduced dynamics in DNA-based aggregates and multimers.

Detangling Solvatochromic Effects by the Effective Fragment Potential Method

Understanding molecular interactions in complex systems opens avenues for the efficient design of new materials with target properties. Energy decomposition methods provide a means to obtain a detailed picture of intermolecular interactions. This work introduces a molecular modeling approach for decomposing the solvatochromic shifts of the electronic excited states into the contributions of the individual molecular fragments of the environment surrounding the chromophore. The developed approach is implemented for the QM/EFP (quantum mechanics/effective fragment potential) model that provides a rigorous first-principles-based description of the electronic states of the chromophores in complex polarizable environments. On the example of two model systems, water pentamer and hydrated uracil, we show how the decomposition of the solvatochromic shifts into the contributions of individual solvent water molecules provides a detailed picture of the intermolecular interactions in the ground and excited states of these systems. The analysis also demonstrates the nonadditivity of solute-solvent interactions and the significant contribution of solute polarization to the total values of solvatochromic shifts.

Comparative Study of Uracil Excited-State Photophysics in Water and Acetonitrile via RMS-CASPT2-Driven Quantum-Classical Trajectories

We present a nonadiabatic molecular dynamics study of the ultrafast processes occurring in uracil upon UV light absorption, leading to electronic excitation and subsequent nonradiative decay. Previous studies have indicated that the mechanistic details of this process are drastically different depending on whether the process takes place in the gas phase, acetonitrile, or water. However, such results have been produced using quantum chemical methods that did not incorporate both static and dynamic electron correlation. In order to assess the previously proposed mechanisms, we simulate the photodynamics of uracil in the three environments mentioned above using quantum-classical trajectories and, for solvated uracil, hybrid quantum mechanics/molecular mechanics (QM/MM) models driven by the rotated multistate complete active space second-order perturbation (RMS-CASPT2) method. To do so, we exploit the gradient recently made available in OpenMolcas and compare the results to those obtained using the complete active space self-consistent field (CASSCF) method only accounting for static electron correlation. We show that RMS-CASPT2 produces, in general, a mechanistic picture different from the one obtained at the CASSCF level but confirms the hypothesis advanced on the basis of previous ROKS and TDDFT studies thus highlighting the importance of incorporating dynamic electron correlation in the investigation of ultrafast electronic deactivation processes.

Molecular Identification of the Transient Species Mediating the Deactivation Dynamics of Solvated Guanosine and Deazaguanosine

Small structural alterations of the purine/pyrimidine core have been related to important photophysical changes, such as the loss of photostability. Similarly to canonical nucleobases, solute-solvent interactions can lead to a change in the excited state lifetimes and/or to the interplay of different states in the photophysics of these modified nucleobases. To shed light on both effects, we here report a complete picture of the absorption spectra and excited state deactivation of deoxyguanosine and its closely related derivative, deoxydeazaguanosine, in water and methanol through the mapping of the excited state potential energy surfaces and molecular dynamics simulations at the TD-DFT level of theory. We show that the N by CH exchange in the imidazole ring of deoxyguanosine translates into a small red-shift of the bright states and slightly faster dynamics. In contrast, changing solvent from water to methanol implies the opposite, i.e., that the deactivation of both systems to the ground state is significantly hindered.

Recent developments in the general atomic and molecular electronic structure system

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized.

Discrete Solvent Reaction Field Calculations for One- and Two-Photon Absorptions of Solution-Phase Dimethylaminonitrostilbene Molecule

Based on the configurations generated by molecular dynamics (MD) simulations using the on-the-fly density-functional tight-bonding (DFTB) force field, we investigated performance of the discrete solvent reaction field (DRF) model coupled to time-dependent density functional theory (TD-DFT) for solvatochromic effect of one- and two-photon absorption phenomena. Dimethylaminonitrostilbene (DANS) molecule solvated in chloroform, dichloromethane, and dimethyl sulfoxide solvents was selected as a model system for our research purpose. For every selected MD/DFTB configuration, within the context of the DRF, solute molecule is represented by TD-DFT and solvent molecules are described by atomic charges and polarizabilities. The calculated one-photon absorption energies reproduce well the positive solvatochromic behavior of solvated DANS and are in good agreement with available experimental data. For the two-photon absorption cross section, even though our approach overshot the experimental data by about 20% in absolute magnitude, experimentally observed solvatochromic change was captured qualitatively in this work. At last, we examined the contributions of atomic charges and polarizabilities of solvent molecules to the solvatochromic shifts of properties of interest.

How intermolecular interactions influence electronic absorption spectra: insights from the molecular packing of uracil in condensed phases

Intermolecular interactions in terms of molecular packing are crucial for the investigation of the absorption spectra of uracil in different environments.

Exchange-repulsion energy in QM/EFP

The effective fragment potential (EFP) is a quantum mechanics (QM)-based model designed to accurately describe intermolecular interactions. Hybrid QM/EFP calculations combine quantum mechanical methods with an EFP embedding to study complex systems in which many-body effects are relevant. As in EFP-only calculations, non-bonded interactions between the QM region and EFP fragments are computed as a sum of electrostatic, polarization, dispersion, and exchange-repulsion energies. The exchange-repulsion term is a computational bottleneck of the EFP calculations. Here, we present a general procedure for computing the QM/EFP exchange-repulsion interactions based on one-electron contributions to the QM Hamiltonian, by using Gaussian functions to represent localized molecular orbitals of the effective fragments. The accuracy of the exchange-repulsion and total QM/EFP interaction energies is evaluated on a diverse set of dimers, including complexes from the S22 dataset of non-covalent interactions. In most cases, the QM/EFP energies are at least as accurate as corresponding EFP energies. A simple and computationally efficient form of the introduced QM/EFP exchange-repulsion term will facilitate further developments and applications of QM/EFP methods.

Characterization of the Photochemical Properties of 5-Benzyluracil via Time-Dependent Density Functional Theory

We present a detailed study of the excited state properties of 5-benzyluracil (5BU) in the gas phase and in implicit solvent using different electronic structure approaches ranging from time-dependent density functional theory in the linear response regime (LR-TDDFT) to a set of different wave-function-based methods for excited states, namely perturbed coupled cluster (CC2), algebraic diagrammatic construction method to second order (ADC(2)), and perturbed configuration interaction (CIS(D)). 5BU has been used to investigate DNA base-amino acid interactions. In particular, it served as a model of protein-DNA photoinduced cross-linking. While LR-TDDFT is computationally the most efficient first-principles approach for static and dynamic simulations of this bichromophoric system, its accuracy is difficult to assess due to the presence of excited states with charge transfer character. In this work, the performance of different exchange correlation functionals is compared against accurate benchmarks obtained either from high level wave-function-based methods or directly from experimental absorption spectra. Our investigation shows that accurate results for the excitation energies can be obtained using the hybrid meta-GGA functional M06. In view of dynamical studies of the relaxation of 5BU after photoexcitation, we also show that the PBE functional, while failing in the Franck-Condon region, provides qualitatively good results for the characterisation of a possible photocyclization path.

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.

UV laser photoactivation of hexachloroplatinate bound to individual nucleobases in vacuo as molecular level probes of a model photopharmaceutical

UV excitation of mass-selected hexachloroplatinate–nucleobase clusters provides detailed insight into the photophysics and photochemistry of a model DNA photopharmaceutical.

Assessing Molecular Dynamics Simulations with Solvatochromism Modeling

For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied.

Mapping the UV Photophysics of Platinum Metal Complexes Bound to Nucleobases: Laser Spectroscopy of Isolated Uracil·Pt(CN)4(2-) and Uracil·Pt(CN)6(2-) Complexes

We report the first UV laser spectroscopic study of isolated gas-phase complexes of platinum metal complex anions bound to a nucleobase as model systems for exploring at the molecular level the key photophysical processes involved in photodynamic therapy. Spectra of the Pt(IV)(CN)6(2-)·Ur and Pt(II)(CN)4(2-)·Ur complexes were acquired across the 220-320 nm range using mass-selective photodepletion and photofragment action spectroscopy. The spectra of both complexes reveal prominent UV absorption bands (λmax = 4.90 and 4.70 eV) that we assign primarily to excitation of the Ur π-π* localized chromophore. Distinctive UV photofragmentation products are observed for the complexes, with Pt(IV)(CN)6(2-)·Ur photoexcitation resulting in complex fission, while Pt(II)(CN)4(2-)·Ur photoexcitation initiates a nucleobase proton-transfer reaction across 4.4-5.2 eV and electron detachment above 5.2 eV. The observed photofragments are consistent with ultrafast decay of a Ur localized excited state back to the electronic ground state followed by intramolecular vibrational relaxation and ergodic complex fragmentation.

Solvent effects on the ultrafast nonradiative deactivation mechanisms of thymine in aqueous solution: excited-state QM/MM molecular dynamics simulations

On-the-fly excited-state quantum mechanics/molecular mechanics molecular dynamics (QM/MM-MD) simulations of thymine in aqueous solution are performed to investigate the role of solvent water molecules on the nonradiative deactivation process. The complete active space second-order perturbation theory (CASPT2) method is employed for a thymine molecule as the QM part in order to provide a reliable description of the excited-state potential energies. It is found that, in addition to the previously reported deactivation pathway involving the twisting of the C-C double bond in the pyrimidine ring, another efficient deactivation pathway leading to conical intersections that accompanies the out-of-plane displacement of the carbonyl group is observed in aqueous solution. Decay through this pathway is not observed in the gas phase simulations, and our analysis indicates that the hydrogen bonds with solvent water molecules play a key role in stabilizing the potential energies of thymine in this additional decay pathway.

Photophysics and photochemistry of a DNA-protein cross-linking model: a synergistic approach combining experiments and theory

The photophysical and photochemical properties of 5-benzyluracil and 5,6-benzyluracil, the latter produced by photocyclization of the former through irradiation with femtosecond UV laser pulses, are investigated both experimentally and theoretically. The absorption spectra of the two molecules are compared, and the principal electronic transitions involved are discussed, with particular emphasis on the perturbation induced on the two chromophore species (uracil and benzene) by their proximity. The photoproduct formation for different irradiation times was verified with high-performance liquid chromatography and nuclear magnetic resonance measurements. The steady-state fluorescence demonstrates that the fluorescence is a distinctive physical observable for detection and selective identification of 5- and 5,6-benzyluracil. The principal electronic decay paths of the two molecules, obtained through TDDFT calculations, explain the features observed in the emission spectra and the photoreactivity of 5-benzyluracil. The order of magnitude of the lifetime of the excited states is derived with steady-state fluorescence anisotropy measurements and rationalized with the help of the computational findings. Finally, the spectroscopic data collected are used to derive the photocyclization and fluorescence quantum yields. In obtaining a global picture of the photophysical and photochemical properties of the two molecules, our findings demonstrates that the use of 5-benzyluracil as a model system to study the proximity relations of a DNA base with a close-lying aromatic amino acid is valid at a local level since the main characteristics of the decay processes from the excited states of the uracil/thymine molecules remain almost unchanged in 5-benzyluracil, the main perturbation arising from the presence of the close-lying aromatic group.

Accurate first principles model potentials for intermolecular interactions

The general effective fragment potential (EFP) method provides model potentials for any molecule that is derived from first principles, with no empirically fitted parameters. The EFP method has been interfaced with most currently used ab initio single-reference and multireference quantum mechanics (QM) methods, ranging from Hartree-Fock and coupled cluster theory to multireference perturbation theory. The most recent innovations in the EFP model have been to make the computationally expensive charge transfer term much more efficient and to interface the general EFP dispersion and exchange repulsion interactions with QM methods. Following a summary of the method and its implementation in generally available computer programs, these most recent new developments are discussed.

Solvent induced shifts in the UV spectrum of amides

Solvent effects on the electronic spectra of formamide and trans-N-methylacetamide are studied using four different levels of theory: singly excited configuration interaction (CIS), equations of motion coupled-cluster theory with singles and doubles (EOM-CCSD), completely renormalized coupled-cluster theory with singles and doubles with perturbative triple excitations (CR-EOM-CCSD(T)), and time-dependent density functional theory (TDDFT), employing small clusters of water molecules. The simulated electronic spectrum is obtained via molecular dynamics simulations with 100 waters modeled with the effective fragment potential method and exhibits a blue-shift and red-shift, respectively, for the n → π* and πnb → π* vertical excitation energies, in good agreement with the experimental electronic spectra of amides.