Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT.

The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fittingfitted (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed accelerated deactivation decay pathways, which is consistent with the experimental decay time of ∼400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts.

Photoionization and core resonances from range-separated time-dependent density-functional theory for open-shell states: Example of the lithium atom.

We consider the calculations of photoionization spectra and core resonances of open-shell systems using range-separated time-dependent density-functional theory. Specifically, we use the time-dependent range-separated hybrid (TDRSH) scheme, combining a long-range Hartree-Fock exchange potential and kernel with a short-range potential and kernel from a local density-functional approximation, and the time-dependent locally range-separated hybrid (TDLRSH) scheme, which uses a local range-separation parameter. To efficiently perform the calculations, we formulate a spin-unrestricted linear-response Sternheimer approach in a non-orthogonal B-spline basis set using appropriate frequency-dependent boundary conditions. We illustrate this approach on the Li atom, which suggests that TDRSH and TDLRSH are adequate simple methods for estimating the single-electron photoionization spectra of open-shell systems.

Photoionization and core resonances from range-separated density-functional theory: General formalism and example of the beryllium atom.

We explore the merits of linear-response range-separated time-dependent density-functional theory (TDDFT) for the calculation of photoionization spectra. We consider two variants of range-separated TDDFT, namely, the time-dependent range-separated hybrid (TDRSH) scheme, which uses a global range-separation parameter, and the time-dependent locally range-separated hybrid (TDLRSH), which uses a local range-separation parameter, and compare with standard time-dependent local-density approximation (TDLDA) and time-dependent Hartree-Fock (TDHF). We show how to calculate photoionization spectra with these methods using the Sternheimer approach formulated in a non-orthogonal B-spline basis set with appropriate frequency-dependent boundary conditions. We illustrate these methods on the photoionization spectrum of the Be atom, focusing, in particular, on the core resonances. Both the TDRSH and TDLRSH photoionization spectra are found to constitute a large improvement over the TDLDA photoionization spectrum and a more modest improvement over the TDHF photoionization spectrum.

Infrared spectroscopy from electrostatic embedding QM/MM: local normal mode analysis of infrared spectra of arabidopsis thaliana plant cryptochrome.

Infrared (IR) spectroscopy is an undoubtedly valuable tool for analyzing vibrations, conformational changes, and chemical reactions of biological macromolecules. Currently, there is a lack of theoretical methods to create a model successfully and efficiently simulate and interpret the origin of the spectral signatures, which are often complex to analyze. Here, we develop a new method for IR vibrational spectroscopy based on analytic second derivatives of electrostatic embedding QM/MM energy, the computation of electric dipole moments with respect to nuclear perturbations and the localization of normal modes. In addition to the IR spectrum, the method can provide the origin of each peak from clearly identified molecular motions of constituent fragments. As a proof of concept, we analyze the IR spectra of flavin adenine dinucleotides in water and in Arabidopsis thaliana cryptochrome proteins for four redox forms, in addition to the difference IR spectra before and after illumination with blue light. We show that the main peaks in the difference spectrum are due to N-H hydrogen out-of-plane motions and hydrogen bendings.

UV-visible absorption spectrum of FAD and its reduced forms embedded in a cryptochrome protein.

Cryptochromes are a class of flavoproteins proposed as candidates to explain magnetoreception of animals, plants and bacteria. The main hypothesis is that a biradical is formed upon blue-light absorption by flavin adenine dinucleotide (FAD). In a protein milieu, the oxidized form of FAD can be reduced, leading to four redox derivative forms: anionic and neutral semi-reduced radicals, and anionic and neutral fully reduced forms. All these forms have a characteristic electronic absorption spectrum, with a strong vibrational resolution. Here, we carried out a normal mode analysis at the electrostatic embedding QM/MM level of theory to compute the vibrationally resolved absorption spectra of the five redox forms of FAD embedded in a plant cryptochrome. We show that explicitly accounting for vibrational broadening contributions to electronic transitions is essential to reproduce the experimental spectra. In the case of the neutral radical form of FAD, the absorption spectrum is reproduced only if the presence of a tryptophan radical is considered.

Efficient Analytic Second Derivative of Electrostatic Embedding QM/MM Energy: Normal Mode Analysis of Plant Cryptochrome.

Analytic second derivatives of electrostatic embedding (EE) quantum mechanics/molecular mechanics (QM/MM) energy are important for performing vibrational analysis and simulating vibrational spectra of quantum systems interacting with an environment represented as a classical electrostatic potential. The main bottleneck of EE-QM/MM second derivatives is the solution of coupled perturbed equations for each MM atom perturbation. Here, we exploit the Q-vector method [J. Chem. Phys., 2019, 151, 041102] to workaround this bottleneck. We derive the full analytic second derivative of the EE-QM/MM energy, which allows us to compute QM, MM, and QM-MM Hessian blocks in an efficient and easy to implement manner. To show the capabilities of our method, we compute the normal modes for the full Arabidopsis thaliana plant cryptochrome. We show that the flavin adenine dinucleotide vibrations (QM subsystem) strongly mix with protein modes. We compute approximate vibronic couplings for the lowest bright transition, from which we extract spectral densities and the homogeneous broadening of FAD absorption spectrum in protein using vibrationally resolved electronic spectrum simulations.

Analytic QM/MM atomic charge derivatives avoiding the scaling of coupled perturbed equations with the MM subsystem size.

In electrostatic embedding mixed quantum and molecular mechanics (QM/MM) approaches, the QM charge distribution is polarized by the electrostatic interaction with the MM environment. Analytic derivatives of expectation values of operators are required to extract properties such as vibrational spectra. These derivatives usually require solving a set of coupled perturbed equations for each nucleus/atom in the system, thus becoming prohibitive when the MM subsystem contains thousands of atoms. In the context of Electrostatic Potential Fitting (ESPF) QM/MM, we can easily overcome this bottleneck by defining a set of auxiliary coupled perturbed equations called the Q-vector equations. The Q-vector method scales only with the size of the QM subsystem, producing an effective charge tensor that leads to the atomic charge derivative after contraction with the MM electrostatic potential gradient. As an example, we use the charge derivatives as an analysis tool to identify the most important chromophore-polarizing amino-acids in plant cryptochrome. This finding opens up the route of defining polarizable force fields and simulating vibrational spectroscopy using ESPF QM/MM electrostatic embedding at an affordable computational cost.