Influence of pump laser fluence on ultrafast myoglobin structural dynamics.

High-intensity femtosecond pulses from an X-ray free-electron laser enable pump-probe experiments for the investigation of electronic and nuclear changes during light-induced reactions. On timescales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer1,2. However, all ultrafast TR-SFX studies to date have employed such high pump laser energies that nominally several photons were absorbed per chromophore3-17. As multiphoton absorption may force the protein response into non-physiological pathways, it is of great concern18,19 whether this experimental approach20 allows valid conclusions to be drawn vis-à-vis biologically relevant single-photon-induced reactions18,19. Here we describe ultrafast pump-probe SFX experiments on the photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe-CO bond distance (predicted by recent quantum wavepacket dynamics21) are seen to depend strongly on pump laser energy, in line with quantum chemical analysis. Our results confirm both the feasibility and necessity of performing ultrafast TR-SFX pump-probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing both the design and the interpretation of ultrafast TR-SFX pump-probe experiments20 such that mechanistically relevant insight emerges.

Modeling pH-Dependent Biomolecular Photochemistry.

The tuning mechanism of pH can be extremely challenging to model computationally in complex biological systems, especially with respect to the photochemical properties. This article reports a protocol aimed at modeling pH-dependent photodynamics using a combination of constant-pH molecular dynamics and semiclassical nonadiabatic molecular dynamics simulations. With retinal photoisomerization in Anabaena sensory rhodopsin (ASR) as a testbed, we show that our protocol produces pH-dependent photochemical properties, such as the isomerization quantum yield or decay rates. We decompose our results into single-titrated residue contributions, identifying some key tuning amino acids. Additionally, we assess the validity of the single protonation state picture to represent the system at a given pH and propose the most populated protein charge state as a compromise between cost and accuracy.

Solvent Effects and pH Dependence of the X-ray Absorption Spectra of Proline from Electrostatic Embedding Quantum Mechanics/Molecular Mechanics and Mixed-Reference Spin-Flip Time-dependent Density-Functional Theory.

The accurate description of solvent effects on X-ray absorption spectra (XAS) is fundamental for comparing the simulated spectra with experiments in solution. Currently, few protocols exist that can efficiently reproduce the effects of the solute/solvent interactions on XAS. Here, we develop an efficient and accurate theoretical protocol for simulating the solvent effects on XAS. The protocol combines electrostatic embedding QM/MM based on electrostatic potential fitted operators for describing the solute/solvent interactions and mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) for simulating accurate XAS spectra. To demonstrate the capabilities of our protocol, we compute the X-ray absorption of neutral proline in the gas phase and ionic proline in water in all relevant K-edges, showing excellent agreement with experiments. We show that states represented by core to π* transitions are almost unaffected by the interaction with water, whereas the core to σ* transitions are more impacted by the fluctuation of proline structure and the electrostatic interaction with the solvent. Finally, we reconstruct the pH-dependent XAS of proline in solution, determining that the N K-edge can be used to distinguish its three protonation states.

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.

Doubly Tuned Exchange-Correlation Functionals for Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory.

It is demonstrated that significant accuracy improvements in MRSF-TDDFT can be achieved by introducing two different exchange-correlation (XC) functionals for the reference Kohn-Sham DFT and the response part of the calculations, respectively. Accordingly, two new XC functionals of doubly tuned Coulomb attenuated method-vertical excitation energy (DTCAM-VEE) and DTCAM-AEE were developed on the basis of the "adaptive exact exchange (AEE)" concept in the framework of the Coulomb-attenuating XC functionals. The values by DTCAM-VEE are in excellent agreement with those of Thiel's set [mean absolute errors (MAEs) and the interquartile range (IQR) values of 0.218 and 0.327 eV, respectively]. On the other hand, DTCAM-AEE faithfully reproduced the qualitative aspects of conical intersections (CIs) of trans-butadiene and thymine and the nonadiabatic molecular dynamics (NAMD) simulations on thymine. The latter functional also remarkably exhibited the exact 1/R asymptotic behavior of the charge-transfer state of an ethylene-tetrafluoroethylene dimer and the accurate potential energy surfaces (PESs) along the two torsional angles of retinal protonated Schiff base model with six double bonds (rPSB6). Overall, DTCAM-AEE generally performs well, as its MAE (0.237) and IQR (0.41 eV) are much improved as compared to BH&HLYP. The current idea can also be applied to other XC functionals as well as other variants of linear response theories, opening a new way of developing XC functionals.

Automatic Rhodopsin Modeling with Multiple Protonation Microstates.

Automatic Rhodopsin Modeling (ARM) is a simulation protocol providing QM/MM models of rhodopsins capable of reproducing experimental electronic absorption and emission trends. Currently, ARM is restricted to a single protonation microstate for each rhodopsin model. Herein, we incorporate an extension of the minimal electrostatic model (MEM) into the ARM protocol to account for all relevant protonation microstates at a given pH. The new ARM+MEM protocol determines the most important microstates contributing to the description of the absorption spectrum. As a test case, we have applied this methodology to simulate the pH-dependent absorption spectrum of a toy model, showing that the single-microstate picture breaks down at certain pH values. Subsequently, we applied ARM+MEM toAnabaenasensory rhodopsin, confirming an improved description of its absorption spectrum when the titration of several key residues is considered.

Ultrafast Spin Crossover Photochemical Mechanism in [FeII(2,2'-bipyridine)3]2+] Revealed by Quantum Dynamics.

Photoexcitation of [FeII(2,2'-bipyridine)3]2+ induces a subpicosecond spin crossover transformation from a low-spin singlet to a high-spin quintet state. The mechanism involves metal-centered (MC) and metal-ligand charge transfer (MLCT) triplet intermediates, but their individual contributions to this efficient intersystem crossing have been object of debate. Employing quantum wavepacket dynamics, we show that MC triplets are catalyzing the transfer to the high-spin state. This photochemical pathway is made possible thanks to bipyridine stretching vibrations, facilitating the conversion between the MLCT bands to such MC triplets. We show that the lifetime of the MLCT states can be increased to tens of picoseconds by breaking the conjugation between pyridine units, which increases the energetic gap between MLCT and MC states. This opens the route for the design of new chelating ligands inducing long-lived MLCT states in iron complexes.

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.

An efficient electrostatic embedding QM/MM method using periodic boundary conditions based on particle-mesh Ewald sums and electrostatic potential fitted charge operators.

Hybrid quantum mechanics/molecular mechanics (QM/MM) models are successful at describing the properties and reactivity of biological macromolecules. Combining ab initio QM/MM methods and periodic boundary conditions (PBC) is currently the optimal approach for modeling chemical processes in an infinite environment, but frequently, these models are too time-consuming for general applicability to biological systems in a solution. Here, we define a simple and efficient electrostatic embedding QM/MM model in PBC, combining the benefits of electrostatic potential fitted atomic charges and particle-mesh Ewald sums, which can efficiently treat systems of an arbitrary size at a reasonable computational cost. To illustrate this, we apply our scheme to extract the lowest singlet excitation energies from a model for Arabidopsis thaliana cryptochrome 1 containing circa 93 000 atoms, accurately reproducing the experimental absorption maximum.

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.

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.

Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory for Accurate X-ray Absorption Spectroscopy.

It is demonstrated that the challenging core-hole particle (CHP) orbital relaxation for core electron spectra can be readily achieved by the mixed-reference spin-flip (MRSF)-time-dependent density functional theory (TDDFT). With the additional scalar relativistic effects on K-edge excitation energies of 24 second- and 17 third-row molecules, the particular ΔCHP-MRSF(R) exhibited near perfect predictions with RMSE ∼0.5 eV, featuring a median value of 0.3 and an interquartile range of 0.4. Overall, the CHP effect is 2-4 times stronger than relativistic ones, contributing more than 20 eV in the cases of sulfur and chlorine third-row atoms. Such high precision allows to explain the splitting and spectral shapes of O, N, and C atom K-edges in the ground state of thymine with atom as well as orbital specific accuracy. The same protocol with a double hole particle relaxation also produced remarkably accurate K-edge spectra of core to valence hole excitation energies from the first (nO8π*) and second (ππ*) excited states of thymine, confirming the assignment of 1s → n excitation for the experimentally observed 526.4 eV peak. Regarding both accuracy and practicality, therefore, MRSF-TDDFT provides a promising protocol for core electron spectra of both ground and excited electronic states alike.

Stressing the differences in alizarin and purpurin dyes through UV-visible light absorption and 1H-NMR spectroscopies.

Three anthraquinone-based chromophores (9,10-anthraquinone, alizarin, purpurin) are compared from the point of view of their experimental and computed NMR and UV-visible light absorption spectra. Using a hybrid (explicit/implicit) solvent model, each proton chemical shift can be reproduced with an error of less than 7%, even when such protons are engaged in inter-molecular hydrogen bonds with the solvent or when the analyzed sample contains a significant amount of impurities, for instance, 9,10-anthraquinone in purpurin. All the steady-state UV-visible absorption spectra feature a significant vibrational progression in the first absorption band. The shape of the corresponding computed spectra, including vibronic couplings obtained with the adiabatic Hessian approach and the Franck-Condon and Herzberg-Teller approximation of the transition dipole, are in excellent agreement with the experimental ones. The importance and the nature of the vibronic couplings are different for the three molecules, even if they only differ by the number of hydroxyl groups.

Quantum dynamics simulations of the thermal and light-induced high-spin to low-spin relaxation in Fe(bpy)3 and Fe(mtz)6.

First row transition metal complexes with d4 to d7 electronic configurations exhibit spin-crossover (SCO), which can be induced by external stimuli, such as temperature, pressure and light. The low-spin to high-spin transition has been widely studied, but very little is known about the reverse process. Here, we present a theoretical study of thermal and light-induced high-to-low spin crossover in prototypical Fe(II) complexes. The lifetime of the high-spin state in the thermal process is determined using Fermi's golden rule. With this methodology, we have accurately computed the transfer rate of the HS state thermal relaxation at several time scales (from sub-nanosecond to a few seconds) in two different iron complexes. The use of quasi-degenerate perturbation theory (QDPT2) in the analysis of the LS-HS spin-orbit coupling has allowed us to identify 3T1 as the main intermediate state coupling the LS and HS states. The light-induced process has been studied using wavepacket quantum dynamics along the main vibrational coordinates (one symmetric and two asymmetric Fe-N stretchings). The study suggests that after the initial excitation from the 5T2g to the 5Eg state, the population is transferred back to a vibrationally hot 5T2g state, from which a small amount of the population is transferred to the 1A1g state via the intermediate 3T1g. Most of the population remains trapped in the HS state at the time scale of the simulation.

Ultrafast Intersystem Crossing in Xanthone from Wavepacket Dynamics.

Most aromatic ketones containing first-row elements undergo unexpectedly fast intersystem crossing in a few tens of picoseconds and a quantum yield close to unity. Among them, xanthone (9H-xanthen-9-one) possesses one of the fastest singlet-triplet rates of only ∼1.5 ps. The exact mechanism of this unusually fast transition is still under debate. Here, we perform wavepacket dynamics of the photochemistry of xanthone in the gas phase and in polar solvents. We show that xanthone follows El-Sayed's rule for intersystem crossing. From the second singlet excited state, the mechanism is sequential: (i) an internal conversion between singlets 1ππ* → 1nπ* (85 fs), (ii) an intersystem crossing 1nπ* → 3ππ* (2.0 ps), and (iii) an internal conversion between triplets 3ππ* → 3nπ* (602 fs). Each transfer finds its origin in a barrierless access to electronic state intersections. These intersections are close to minimum energy structures, allowing for efficient transitions from the initial singlet state to the triplets.

Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM.

Thymine photochemistry is important for understanding DNA photodamage. In the gas phase, thymine undergoes a fast non-radiative decay from S2 to S1. In the S1 state, it gets trapped for several picoseconds until returning to the ground-state S0. Here, we explore the electrostatic effects of nanomeric droplets of methanol and water on the excited states of thymine. For this purpose, we develop and implement an electrostatic embedding TD-DFT/MM method based on a QM/MM coupling defined through electrostatic potential fitting charges. We show that both in methanol and water, the mechanism is similar to the gas phase. The solvent molecules participate in defining the branching plane of S0/S1 intersection and have a negligible effect on the S1/S2 intersection. Despite the wrong topology of the ground/excited state intersections, electrostatic embedding TD-DFT/MM allows for a fast exploration of the potential energy surfaces and a qualitative picture of the photophysics of thymine in solvent droplets.

Impact of the Dynamic Electron Correlation on the Unusually Long Excited-State Lifetime of Thymine.

Non-radiative relaxation of the photoexcited thymine in the gas phase shows an unusually long excited-state lifetime, and, over the years, a number of models, i.e., S1-trapping, S2-trapping, and S1&S2-trapping, have been put forward to explain its mechanism. Here, we investigate this mechanism using non-adiabatic molecular dynamics (NAMD) simulations in connection with the recently developed mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) method. We show that the previously predicted S2-trapping model was due to an artifact caused by an insufficient account of the dynamic electron correlation. The current work supports the S1-trapping mechanism with two lifetimes, τ1 = 30 ± 1 fs and τ2 = 6.1 ± 0.035 ps, quantitatively consistent with the recent time-resolved experiments. Upon excitation to the S2 (ππ*) state, thymine undergoes an ultrafast (ca. 30 fs) S2→S1 internal conversion and resides around the minimum on the S1 (nOπ*) surface, slowly decaying to the ground state (ca. 6.1 ps). While the S2→S1 internal conversion is mediated by fast bond length alternation distortion, the subsequent S1→S0 occurs through several conical intersections, involving a slow puckering motion.

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.