High-Level Ab Initio Computations of the Absorption Spectra of Organic Iridium Complexes

The excited states of fac-tris­(phenylpyridinato)­iridium [Ir­(ppy)₃] and the smaller model complex Ir­(C₃H₄N)₃ are computed using a number of high-level ab initio methods, including the recently implemented algebraic diagrammatic construction method to third-order ADC(3). A detailed description of the states is provided through advanced analysis methods, which allow a quantification of different charge transfer and orbital relaxation effects and give extended insight into the many-body wave functions. Compared to the ADC(3) benchmark an unexpected striking difference of ADC(2) is found for Ir­(C₃H₄N)₃, which derives from an overstabilization of charge transfer effects. Time-dependent density functional theory (TDDFT) using the B3LYP functional shows an analogous but less severe error for charge transfer states, whereas the ωB97 results are in good agreement with ADC(3). Multireference configuration interaction computations, which are in reasonable agreement with ADC(3), reveal that static correlation does not play a significant role. In the case of the larger Ir­(ppy)₃ complex, results at the TDDFT/B3LYP and TDDFT/ωB97 levels of theory are presented. Strong discrepancies between the two functionals, which are found with respect to the energies, characters, as well as the density of the low lying states, are discussed in detail and compared to experiment

Predicting the Efficiency of Photoswitches Using Force Analysis

Photoswitches convert light into mechanical energy by exerting forces on their environment during photoisomerization. However, the mechanical efficiency of this conversion is limited because a plethora of internal modes of the photoswitch do not contribute to the desired switching function but are also changed during the photoisomerization. Here we present a computational approach to quantify the efficiency of a photoswitch during the initial motion on the excited-state potential energy surface. We demonstrate the gist of our method by looking at the excited-state relaxation of carbon monoxide. Subsequently, the photoswitching efficiency of <i>p</i>-coumaric acid is analyzed as one representative example of the approach

Proton-Transfer-Steered Mechanism of Photolesion Repair by (6–4)-Photolyases

DNA (6–4)-photolyases are enzymes initiating cleavage of mutagenic pyrimidine (6–4) pyrimidone photolesions by a photoinitiated electron transfer from flavin adenine dinucleotide to the lesion. Using state-of-the-art quantum chemical calculations, we present the first energetically feasible molecular repair mechanism. The initial step is electron transfer coupled to proton transfer from the protonated His345 to the N3′ nitrogen of the pyrimidone thymine of the lesion, which proceeds simultaneously with intramolecular OH transfer in a concerted reaction without formation of an oxetane or isolated water molecule intermediate. In contrast to previously suggested mechanisms, this newly identified pathway requires neither a two-photon process nor electronic excitation of the photolesion. Indeed, the recognition that the initial electron transfer is coupled to the proton transfer was critically important for clarification of the mechanism

Can Strained Hydrocarbons Be “Forced” To Be Stable?

Many strained hydrocarbons are prone to isomerization, dimerization, and trimerization under normal laboratory conditions. Here we investigate a method to stabilize angle-strained cycloalkynes by applying a mechanical pulling force to the carbon atoms adjacent to the triple bond, which partially linearizes the CC–C bond angles. We discuss various methods of applying such pulling forces, including photoswitches and incorporation into additional strained macrocycles. We use the computational JEDI (Judgement of Energy DIstribution) analysis to quantify the distribution of energy in strained cycloheptyne and judge the change in stability upon application of an external force via isodesmic and homodesmotic reactions. We find that cycloheptyne can indeed be stabilized by external forces. However, the force generated by photoswitches during isomerization is too low to lead to a significant stabilization of the molecule. Hence, stronger forces are needed, which can be achieved by incorporating cycloheptyne into a second strained macrocycle

Supplementary Information Files for: libwfa: Wavefunction analysis tools for excited and open‐shell electronic states

Supplementary Information Files for: libwfa: Wavefunction analysis tools for excited and open‐shell electronic statesAn open-source software library for wavefunction analysis, libwfa, provides a comprehensive and flexible toolbox for post-processing excited-state calculations, featuring a hierarchy of interconnected visual and quantitative analysis methods. These tools afford compact graphical representations of various excited-state processes, provide detailed insight into electronic structure, and are suitable for automated processing of large data sets. The analysis is based on reduced quantities, such as state and transition density matrices (DMs), and allows one to distill simple molecular orbital pictures of physical phenomena from intricate correlated wavefunctions. The implemented descriptors provide a rigorous link between many-body wavefunctions and intuitive physical and chemical models, for example, exciton binding, double excitations, orbital relaxation, and polyradical character. A broad range of quantum-chemical methods is interfaced with libwfa via a uniform interface layer in the form of DMs. This contribution reviews the structure of libwfa and highlights its capabilities by several representative use cases.<br

Universal Exciton Size in Organic Polymers is Determined by Nonlocal Orbital Exchange in Time-Dependent Density Functional Theory

The exciton size of the lowest singlet excited state in a diverse set of organic π-conjugated polymers is studied and found to be a universal, system-independent quantity of approximately 7 Å in the single-chain picture. With time-dependent density functional theory (TDDFT), its value as well as the overall description of the exciton is almost exclusively governed by the amount of nonlocal orbital exchange. This is traced back to the lack of the Coulomb attraction between the electron and hole quasiparticles in pure TDDFT, which is reintroduced only with the admixture of nonlocal orbital exchange

Combined QM/MM Investigation on the Light-Driven Electron-Induced Repair of the (6–4) Thymine Dimer Catalyzed by DNA Photolyase

The (6–4) photolyases are blue-light-activated enzymes that selectively bind to DNA and initiate splitting of mutagenic thymine (6–4) thymine photoproducts (T(6–4)­T-PP) via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH^–) to the lesion triggering repair. In the present work, the repair mechanism after the initial electron transfer and the effect of the protein/DNA environment are investigated theoretically by means of hybrid quantum mechanical/molecular mechanical (QM/MM) simulations using X-ray structure of the enzyme–DNA complex. By comparison of three previously proposed repair mechanisms, we found that the lowest activation free energy is required for the pathway in which the key step governing the repair photocycle is electron transfer coupled with the proton transfer from the protonated histidine, His365, to the N3′ nitrogen of the pyrimidone thymine. The transfer simultaneously occurs with concerted intramolecular OH transfer without formation of an oxetane or isolated water molecule intermediate. In contrast to previously suggested mechanisms, this newly identified pathway requires neither a subsequent two-photon process nor electronic excitation of the photolesion

Ultrafast C_Spiro–O Dissociation via a Conical Intersection Drives Spiropyran to Merocyanine Photoswitching

The mechanism of the photochemical conversion of spiropyran to merocyanine is investigated theoretically. Calculations were performed at TD-DFT/ωB97XD/cc-pVDZ level of theory, which shows good agreement with the reference RI-CC2 method. A two-dimensional scan of the potential energy surface has been performed along the C–O distance and the central torsion angle in the ground state and in the first excited state, where the reaction takes place. Starting at the Franck–Condon geometry, the energy of the first excited state decreases in the direction of the C–O dissociation while the ground-state energy increases. This leads to a barrierless C–O bond dissociation in the first excited state. While relaxing on the S₁ PES toward longer C–O distances, the torsion angle hardly changes, but other coordinates start to vary, leading to a conical intersection of the ground state and the first excited state at a C–O distance of about 3.4 Å. Passing the conical intersection, the reaction continues on the ground-state PES. At these large C–O distances, either barrierless C_spiro–O rebinding occurs that quenches spiropyran isomerization or rotation around the central torsion angle occurs that leads to merocyanine. For the latter an energy barrier of 0.1 eV must be overcome explaining the low quantum yield of spiropyran to merocyanine photoswitching

Molecular Mechanism of Flavin Photoprotection by Archaeal Dodecin: Photoinduced Electron Transfer and Mg²⁺-Promoted Proton Transfer

Photoinduced biochemical reactions are ubiquitously governed by derivatives of flavin, which is a key player in a manifold of cellular redox reactions. The photoreactivity of flavins is also one of their greatest disadvantages as the molecules are sensitive to photodegradation. To prevent this unfavorable reaction, UV-light-exposed archaea bacteria, such as <i>Halobacterium salinarum</i>, manage the task of protecting flavin derivatives by dodecin, a protein which stores flavins and efficiently photoprotects them. In this study, we shed light on the photoprotection mechanism, i.e., the excited state quenching mechanism by dodecin using computational methodology. Molecular dynamics (MD) simulations unraveled the hydrogen bond network in the flavin binding pocket as a starting point for proton transfer upon preceding electron transfer. Using high-level ab initio quantum chemical methods, different proton transfer channels have been investigated and an energetically feasible Mg²⁺-promoted channel has been identified fully explaining previous experimental observations. This is the first extensive theoretical study of archaeal dodecin, furthering the understanding of its photocycle and manipulation

libwfa: Wavefunction analysis tools for excited and open‐shell electronic states

An open-source software library for wavefunction analysis, libwfa, provides a comprehensive and flexible toolbox for post-processing excited-state calculations, featuring a hierarchy of interconnected visual and quantitative analysis methods. These tools afford compact graphical representations of various excited-state processes, provide detailed insight into electronic structure, and are suitable for automated processing of large data sets. The analysis is based on reduced quantities, such as state and transition density matrices (DMs), and allows one to distill simple molecular orbital pictures of physical phenomena from intricate correlated wavefunctions. The implemented descriptors provide a rigorous link between many-body wavefunctions and intuitive physical and chemical models, for example, exciton binding, double excitations, orbital relaxation, and polyradical character. A broad range of quantum-chemical methods is interfaced with libwfa via a uniform interface layer in the form of DMs. This contribution reviews the structure of libwfa and highlights its capabilities by several representative use cases