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.

Correction: The solution structures and relative stability constants of lanthanide-EDTA complexes predicted from computation.

Correction for 'The solution structures and relative stability constants of lanthanide-EDTA complexes predicted from computation' by Ravi D. O'Brien et al., Phys. Chem. Chem. Phys., 2022, 24, 10263-10271, https://doi.org/10.1039/D2CP01081J.

Assessment of the Electron Correlation Treatment on the Quantum-Classical Dynamics of Retinal Protonated Schiff Base Models: XMS-CASPT2, RMS-CASPT2, and REKS Methods.

We compare the performance of three different multiconfigurational wave function-based electronic structure methods and two implementations of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method. The study is characterized by three features: (i) it uses a small set of quantum-classical trajectories rather than potential energy surface mapping, (ii) it focuses, exclusively, on the photoisomerization of retinal protonated Schiff base models, and (iii) it probes the effect of both methyl substitution and the increase in length of the conjugate π-system. For each tested method, the corresponding analytical gradients are used to drive the quantum-classical (Tully's FSSH method) trajectory propagation, including the recent multistate XMS-CASPT2 and RMS-CASPT2 gradients. It is shown that while CASSCF, XMS-CASPT2, and RMS-CASPT2 yield consistent photoisomerization dynamics descriptions, REKS produces, in some of these systems, qualitatively different behavior that is attributed to a flatter and topographically different excited state potential energy surface. The origin of this behavior can be traced back to the effect of the employed density functional approximation. The above studies are further expanded by benchmarking, at the CASSCF and REKS levels, the electronic structure methods using a QM/MM model of the visual pigment rhodopsin.

The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry.

The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.

On the fluorescence enhancement of arch neuronal optogenetic reporters.

The lack of a theory capable of connecting the amino acid sequence of a light-absorbing protein with its fluorescence brightness is hampering the development of tools for understanding neuronal communications. Here we demonstrate that a theory can be established by constructing quantum chemical models of a set of Archaerhodopsin reporters in their electronically excited state. We found that the experimentally observed increase in fluorescence quantum yield is proportional to the computed decrease in energy difference between the fluorescent state and a nearby photoisomerization channel leading to an exotic diradical of the protein chromophore. This finding will ultimately support the development of technologies for searching novel fluorescent rhodopsin variants and unveil electrostatic changes that make light emission brighter and brighter.

Towards the engineering of a photon-only two-stroke rotary molecular motor.

The rational engineering of photoresponsive materials, e.g., light-driven molecular motors, is a challenging task. Here, we use structure-related design rules to prepare a prototype molecular rotary motor capable of completing an entire revolution using, exclusively, the sequential absorption of two photons; i.e., a photon-only two-stroke motor. The mechanism of rotation is then characterised using a combination of non-adiabatic dynamics simulations and transient absorption spectroscopy measurements. The results show that the rotor moiety rotates axially relative to the stator and produces, within a few picoseconds at ambient T, an intermediate with the same helicity as the starting structure. We discuss how such properties, that include a 0.25 quantum efficiency, can help overcome the operational limitations of the classical overcrowded alkene designs.

The solution structures and relative stability constants of lanthanide-EDTA complexes predicted from computation.

Ligand selectivity to specific lanthanide (Ln) ions is key to the separation of rare earth elements from each other. Ligand selectivity can be quantified with relative stability constants (measured experimentally) or relative binding energies (calculated computationally). The relative stability constants of EDTA (ethylenediaminetetraacetic acid) with La3+, Eu3+, Gd3+, and Lu3+ were predicted from relative binding energies, which were quantified using electronic structure calculations with relativistic effects and based on the molecular structures of Ln-EDTA complexes in solution from density functional theory molecular dynamics simulations. The protonation state of an EDTA amine group was varied to study pH ∼7 and ∼11 conditions. Further, simulations at 25 °C and 90 °C were performed to elucidate how structures of Ln-EDTA complexes varying with temperature are related to complex stabilities at different pH conditions. Relative stability trends are predicted from computation for varying Ln3+ ions (La, Eu, Gd, Lu) with a single ligand (EDTA at pH ∼11), as well as for a single Ln3+ ion (La) with varying ligands (EDTA at pH ∼7 and ∼11). Changing the protonation state of an EDTA amine site significantly changes the solution structure of the Ln-EDTA complex resulting in a reduction of the complex stability. Increased Ln-ligand complex stability is correlated to reduced structural variations in solution upon an increase in temperature.

Benchmarking of Density Functionals for Z-Azoarene Half-Lives via Automated Transition State Search.

Molecular photoswitches use light to interconvert from a thermodynamically stable isomer into a metastable isomer. Photoswitches have been used in photopharmacology, catalysis, and molecular solar thermal (MOST) materials because of their spatiotemporal activation. Visible-light-absorbing photoswitches are especially attractive because low-energy light minimizes undesired photochemical reactions and enables biological applications. Ideal photoswitches require well-separated absorption spectra for both isomers and long-lived metastable states. However, predicting thermal half-lives with density functional theory is difficult because it requires locating transition structures and chosing an accurate model chemistry. We now report EZ-TS; by automatically calculating activation energies for the thermal Z → E isomerization. We used 28 density functionals [local spin density approximation, generalized gradient approximation, meta-GGA, hybrid GGA, and hybrid meta-GGA] and five basis sets [6-31G(d), 6-31+G(d,p), 6-311+G(d,p), cc-pVDZ, and aug-cc-pVDZ]. The hybrid GGA functionals performed the best among all tested functionals. We demonstrate that the mean absolute errors of 14 model chemistries approach chemical accuracy.

Solution structure of a europium-nicotianamine complex supports that phytosiderophores bind lanthanides.

We report the solution structure of a europium-nicotianamine complex predicted from ab initio molecular dynamics simulations with density functional theory. Emission and excitation spectroscopy show that the Eu3+ coordination environment changes in the presence of nicotianamine, suggesting complex formation, such as what is seen for the Eu3+-nicotianamine complex structure predicted from computation. We modeled Eu3+-ligand complexes with explicit water molecules in periodic boxes, effectively simulating the solution phase. Our simulations consider possible chemical events (e.g. coordination bond formation, protonation state changes, charge transfers), as well as ligand flexibility and solvent rearrangements. Our computational approach correctly predicts the solution structure of a Eu3+-ethylenediaminetetraacetic acid complex within 0.05 Å of experimentally measured values, backing the fidelity of the predicted solution structure of the Eu3+-nicotianamine complex. Emission and excitation spectroscopy measurements were also performed on the well-known Eu3+-ethylenediaminetetraacetic acid complex to validate our experimental methods. The electronic structure of the Eu3+-nicotianamine complex is analyzed to describe the complexes in greater detail. Nicotianamine is a metabolic precursor of, and structurally very similar to, phytosiderophores, which are responsible for the uptake of metals in plants. Although knowledge that nicotianamine binds europium does not determine how plants uptake rare earths from the environment, it strongly supports that phytosiderophores bind lanthanides.

Spin controlled surface chemistry: alkyl desorption from Si(100)-2×1 by nonadiabatic hydrogen elimination.

An understanding of the role that spin states play in semiconductor surface chemical reactions is currently limited. Herein, we provide evidence of a nonadiabatic reaction involving a localized singlet to triplet thermal excitation of the Si(100) surface dimer dangling bond. By comparing the ß-hydrogen elimination kinetics of ethyl adsorbates probed by thermal desorption experiments to electronic structure calculation results, we determined that a coverage-dependent change in mechanism occurs. At low coverage, a nonadiabatic, inter-dimer mechanism is dominant, while adiabatic mechanisms become dominant at higher coverage. Computational results indicate that the spin crossover is rapid near room temperature and the nonadiabatic path is accelerated by a barrier that is 40 kJ mol-1 less than the adiabatic path. Simulated thermal desorption reactions using nonadiabatic transition state theory (NA-TST) for the surface dimer intersystem crossing are in close agreement with experimental observations.

FMOxFMO: Elucidating Excitonic Interactions in the Fenna-Matthews-Olson Complex with the Fragment Molecular Orbital Method.

In order to study Förster resonance energy transfer (FRET), the fragment molecular orbital (FMO) method is extended to compute electronic couplings between local excitations via the excited state transition density model, enabling efficient calculations of nonlocal excitations in a large molecular system and overcoming the previous limitation of being able to compute only local excitations. The results of these simple but accurate models are validated against full quantum calculations without fragmentation. The developed method is applied to a very important photosynthetic pigment-protein complex, the Fenna-Matthews-Olson complex (FMOc), that is responsible for the energy transfer from a chlorosome to the reaction center in the green sulfur bacteria. Absorption and circular dichroism spectra of FMOc are simulated, and the role of the molecular environment on the excitations is revealed.

Locating Minimum Energy Crossings of Different Spin States Using the Fragment Molecular Orbital Method.

Spin-dependent processes involving nonadiabatic transitions between electronic states with different spin multiplicities play important roles in the chemistry of complex systems. The rates of these processes can be predicted based on the molecular properties at the minimum energy crossing point (MECP) between electronic states. We present the development of the MECP search technique within the fragment molecular orbital (FMO) method applicable to large complex systems. The accuracy and scalability of the new method is demonstrated on several models of the metal-sulfur protein rubredoxin. The effect of the model size on the MECP geometry and relative energy is discussed. The fragment energy decomposition and spin density delocalization analyses reveal how different protein residues and solvent molecules contribute to stabilization of the spin states. The developed FMO-MECP method can help to clarify the role of nonadiabatic spin-dependent processes in complex systems and can be used for designing mutations aimed at controlling these processes in metalloproteins, including spin-dependent catalysis and electron transfer.

Spin-Forbidden Transitions between Electronic States in the Active Site of Rubredoxin.

Rubredoxin is a small iron-sulfur protein involved in biological electron transfer, which is accomplished by changing the oxidation state of the iron atom in the active site. We investigate the possibility of spin-forbidden transitions between the lowest energy electronic states with different spin multiplicities in the rubredoxin active site models [Fe(SCH3)4]n (n = 2-, 1-, 0) using nonadiabatic transition state theory (NA-TST). The equilibrium structures, minimum energy crossing point structures and Hessians were obtained with density functional theory. The spin-orbit coupling (SOC) was calculated with the complete active space configuration interaction method using the two-electron spin-orbit Breit-Pauli Hamiltonian. We found several crossings between the lowest energy spin states associated with the changes in Fe coordination. However, only triplet/quintet crossings in [Fe(SCH3)4]2- and [Fe(SCH3)4]0, as well as a quartet/sextet crossing in [Fe(SCH3)4]- are characterized by nonzero first-order SOC responsible for transitions between these spin states. The rates of spin-forbidden transitions in the [Fe(SCH3)4]2- complex are 1 and 2 orders of magnitude higher than the rates in the [Fe(SCH3)4]- and [Fe(SCH3)4]0 complexes, respectively. These rate differences are related to a large variation of the SOC between the complexes with different charges, which in turn comes from different molecular orbitals involved in the spin-flip transitions. Finally, we demonstrate that the differences between the NA-TST rates and the rates calculated under the assumption of completely spin-allowed transitions could be as large as 4 orders of magnitude. This means that even in qualitative discussions of the reaction mechanisms involving changes in spin states the partially spin-forbidden nature of the transitions between these states must be taken into account.

Effect of H2 binding on the nonadiabatic transition probability between singlet and triplet states of the [NiFe]-hydrogenase active site.

We investigate the effect of H2 binding on the spin-forbidden nonadiabatic transition probability between the lowest energy singlet and triplet electronic states of [NiFe]-hydrogenase active site model, using a velocity averaged Landau-Zener theory. Density functional and multireference perturbation theories were used to provide parameters for the Landau-Zener calculations. It was found that variation of the torsion angle between the terminal thiolate ligands around the Ni center induces an intersystem crossing between the lowest energy singlet and triplet electronic states in the bare active site and in the active site with bound H2. Potential energy curves between the singlet and triplet minima along the torsion angle and H2 binding energies to the two spin states were calculated. Upon H2 binding to the active site, there is a decrease in the torsion angle at the minimum energy crossing point between the singlet and triplet states. The probability of nonadiabatic transitions at temperatures between 270 and 370 K ranges from 35% to 32% for the active site with bound H2 and from 42% to 38% for the bare active site, thus indicating the importance of spin-forbidden nonadiabatic pathways for H2 binding on the [NiFe]-hydrogenase active site.