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The search for efficient inhibitors of the SARS-CoV-2 enzymes is ongoing due to the continuing COVID-19 pandemic. We report the results of computational modeling of the reactions of the SARS-CoV-2 main protease (MPro ) with four potential covalent inhibitors. Two of them, carmofur and nirmatrelvir, have been shown experimentally the ability to inhibit MPro . Two other compounds, X77A and X77C, were designed computationally in this work, derived from the structure of X77, a non-covalent inhibitor forming a tight surface complex with MPro . We modified the X77 structure by introducing warheads capable of efficient chemical reactions with the catalytic cysteine residue in the M Pro active site. The reaction mechanisms of the four molecules with M Pro were investigated by quantum mechanics/molecular mechanics (QM/MM) calculations using large quantum subsystems. First, at the QM/MM level, we optimized structures of stationary points on the potential energy surfaces corresponding to the reactants, products, intermediates, and transition states along the hypothesized reaction coordinates. Analysis of these structures has informed the selection of collective variables for the subsequent calculations of the Gibbs energy profiles using molecular dynamics simulations with QM/MM potentials (QM/MM MD). In these simulations, the QM part was treated by DFT with the PBE0 functional. The results show that all four compounds form covalent adducts with the catalytic cysteine Cys 145 of MPro . From the chemical perspective, the reactions of these four compounds with M Pro follow three distinct mechanisms. In all cases, the reaction is initiated by a nucleophilic attack of the thiolate group of the deprotonated cysteine residue from the catalytic dyad Cys145-His41 of MPro . In the case of carmofur and X77A, the covalent binding of the thiolate to the ligand is accompanied by the formation of the fluoro-uracil leaving group. The reaction with X77C follows the nucleophilic aromatic substitution SN Ar mechanism. The reaction of M Pro with nirmatrelvir, which has a reactive nitrile group, leads to the formation of the covalent thioimidate adduct with the thiolate of the Cys145 residue in the enzyme active site.

We report a combined experimental and theoretical investigation of electron–molecule interactions using pyrrole as a model system. Experimental two-dimensional electron energy loss spectra (EELS) encode information about the vibrational states of the molecule as well as the position and structure of electronic resonances. The calculations using complex-valued extensions of equation-of-motion coupled-cluster theory (based on non-Hermitian quantum mechanics) facilitate the assignment of all major EELS features. We confirm the two previously described π resonances at about 2.5 and 3.5 eV (the calculations place these two states at 2.92 and 3.53 eV vertically and 2.63 and 3.27 eV adiabatically). The calculations also predict a low-lying resonance at 0.46 eV, which has a mixed character—of a dipole-bound state and σ* type. This resonance becomes stabilized at one quanta of the NH excitation, giving rise to the sharp feature at 0.9 eV in the corresponding EELS. Calculations of Franck–Condon factors explain the observed variations in the vibrational excitation patterns. The ability of theory to describe EELS provides a concrete illustration of the utility of non-Hermitian quantum chemistry, which extends such important concepts as potential energy surfaces and molecular orbitals to states embedded in the continuum.

Table-top x-ray spectroscopy measurements at the carbon K-edge complemented by ab initio calculations are used to investigate the influence of the bromine atom on the carbon core-valence transitions in bromobenzene cation (BrBz+). The electronic ground state of the cation is prepared by resonance-enhanced two-photon ionization of neutral bromobenzene (BrBz) and probed by x-rays produced by high-harmonic generation (HHG). Replacing one of the hydrogen atoms in benzene with a bromine atom shifts the transition from the 1sC* orbital of the carbon atom (C*) bonded to bromine by ~1 eV to higher energy in the x-ray spectrum compared to the other carbon atoms (C). The x-ray absorption spectra of neutral BrBz reveals the influence of the bromine atom on the x-ray absorption spectrum due to the 1sC* orbital, while the influence of the bromine atom on the cation spectrum is even more prominent. The x-ray spectrum of the cation is dominated by two relatively intense transitions, the 1sC→ π* and the 1sC*→ σ*(C*-Br), where the second transition is enhanced relative to the neutral BrBz. In addition, a doublet peak shape for these two transitions is observed in the experiment. The 1sC→ π* doublet peak shape arises due to the spin coupling of the unpaired electron in the partially vacant π orbital (from ionization) with the two other unpaired electrons resulting from the transition from the 1sC core orbital to the fully vacant π* orbitals. The 1sC*→ σ* doublet peak shape results from several transitions involving σ* and vibrational C*-Br mode activation following the UV ionization, which demonstrates the impact of the C*-Br bond length on the core-valence transition as well as the relaxation geometry of BrBz+.

The vibrational spectra of cold complexes of ethylenediaminetetraacetic acid (EDTA) with transition metal dications in vacuo show how the electronic structure of the metal provides a geometric template for interaction with the functional groups of the binding pocket. The OCO stretching modes of the carboxylate groups of EDTA serve as structural probes, informing on the spin state of the ion as well as the coordination number in the complex. The results highlight the flexibility of EDTA in accepting a large range of metal cations in its binding site.

This computational study characterizes charge-transfer-to-solvent (CTTS) states of aqueous thiocyanate anion using equation-of-motion coupled-cluster methods combined with electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) scheme. Equilibrium sampling was carried out using classical molecular dynamics (MD) with standard force-fields and QM/MM ab initio molecular dynamics (AIMD) using DFT. The two calculations yield significantly different local structure around solvated SCN−. Because of the diffuse character of CTTS states, they are very sensitive to the local structure of solvent around the solute and its dynamic fluctuations. Owing to this sensitivity, the spectra computed using MD and AIMD based snapshots differ considerably. This sensitivity suggests that the spectroscopy exploiting CTTS transitions can provide an experimental handle for assessing the quality of force-fields and density functionals.

A roadmap is developed that integrates simulation methodology and data science methods to target new theories that traverse the multiple length- and time-scale features of many-body phenomena.

Robustness of nickelocene’s (NiCp2, Cp = cyclopentadienyl) magnetic anisotropy and addressability of its spin states make this molecular magnet attractive as a spin sensor. However, microscopic understanding of its magnetic anisotropy is still lacking, especially when NiCp2 is deposited on a surface to make quantum sensing devices. Quantum chemical calculations of such molecule/solid-state systems are limited to density functional theory (DFT) or DFT+U (Hubbard correction to DFT). We investigate the magnetic behavior of NiCp2 using the equation-of-motion coupled-cluster (EOM-CC) framework. Our first-principle calculations agree well with experimentally derived magnetic anisotropy and susceptibility values. The calculations show that magnetic anisotropy in NiCp2 originates from a large spin-orbit coupling (SOC) between the triplet ground state and the third singlet state, whereas the coupling with lower singlet excited states is negligible. We also considered a set of six ring-substituted NiCp2 derivatives and a model system of the NiCp2/MgO(001) adsorption complex. To gain insight into the electronic structure of these systems, we analyze spinless transition density matrices and their natural transition orbitals (NTOs). The NTO analysis of SOCs explains how spin states and magnetic properties are retained upon modification of the NiCp2 coordination environment and upon its adsorption on a surface. Such resilience of the NiCp2 magnetic behavior supports using NiCp2 as a spin-probe molecule by functionalization of the tip of a scanning tunneling microscope.

The search for efficient inhibitors of the SARS-CoV-2 enzymes remains important due to the continuing COVID-19 pandemic. We report the results of computational modeling of the reactions of the SARS-CoV-2 main protease (MPro) with four potential covalent inhibitors. Two of them, carmofur and nirmatrelvir, have been shown experimentally the ability to inhibit MPro. Two other compounds, X77A and X77C, were designed computationally in this work, derived from the structure of X77, a non-covalent inhibitor forming a tight surface complex with MPro. We modified the X77 structure by introducing warheads capable of efficient chemical reactions with the catalytic cysteine residue in the MPro active site. The reactions of the four molecules with MPro were investigated by quantum mechanics/molecular mechanics (QM/MM) calculations. According to calculations, the reactions for all four compounds are exothermic, with sufficiently low barriers, suggesting efficient inhibition of the enzyme. From the chemical perspective, the four compounds react with MPro following three distinct mechanisms. In all cases, the reaction is initiated by a nucleophilic attack of the thiolate group of the deprotonated cysteine residue from the catalytic dyad Cys145-His41 of MPro. In the case of carmofur and X77A, the covalent binding of the thiolate to the ligand involves the formation of the fluoro-uracil leaving group. The reaction with X77C follows the nucleophilic aromatic substitution SNAr mechanism. The reaction of MPro with nirmatrelvir, which has a reactive nitrile group, leads to the formation of the covalent thioimidate adduct with the thiolate of the Cys145 residue in the enzyme active site.

Molecules with optical cycling centers (OCCs) are highly desirable in the context of fundamental studies as well as applications (e.g., quantum computing) because they can be effectively cooled to very low temperatures by repeated absorption and emission (hence, cycling). Charged species offer additional advantages for experimental control and manipulation. We present a systematic computational study of a series of diatomic radical-cations made of a d-block metal and a p-block ligand, that are isoelectronic (in their valence shell) to the successfully laser-cooled neutral molecules. Using high-level electronic structure methods, we characterize state and transition properties of low-lying electronic states and compute Franck-Condon factors. The computed branching ratios and radiative lifetimes reveal that the electronic transitions analogous to those successfully used in the laser cooling of neutral molecules are less than optimal in the cations. We propose alternative transitions suitable for optical cycling and highlight trends that could assist future designs of OCCs in charged or neutral molecules.

Photoelectron–photofragment coincidence spectroscopy was used to study the dissociation dynamics of the conjugate bases of benzoic acid and p-coumaric acid. Upon photodetachment at 266 nm (4.66 eV) both aromatic carboxylates undergo decarboxylation, as well as the formation of stable carboxyl radicals. The key energetics are computed using high-level electronic structure methods. The dissociation dynamics of benzoate were dominated by a two-body DPD channel resulting in CO2 + C6H5 + e−, with a very small amount of stable C6H5CO2 showing that the radical ground state is stable and the excited states are dissociative. For p-coumarate (p-CA−) the dominant channel is photodetachment resulting in a stable radical and a photoelectron with electron kinetic energy (eKE)

Low-energy spectra of single-molecule magnets (SMMs) are often described by Heisenberg Hamiltonians. Within this formalism, exchange interactions between magnetic centers determine the ground-state multiplicity and energy separation between the ground and excited states. In this contribution, we extract exchange coupling constants (J) for a set of iron (III) binuclear and tetranuclear complexes from all-electron calculations using non-collinear spin-flip time-dependent density functional theory (NC-SF-TDDFT). For 12 binuclear complexes with J-values ranging from -6 to -132 cm−1, our benchmark calculations using the short-range hybrid ωPBEh functional and 6-31G(d,p) basis set agree well with the experimentally derived values (mean absolute error of 4.7 cm−1). For the tetranuclear SMMs, the computed J constants are within 6 cm−1 from the experimentally derived values. We explore the range of applicability of the Heisenberg model by analyzing bonding patterns in these Fe(III) complexes using natural orbitals (NO), their occupations, and the number of effectively unpaired electrons. The results illustrate the efficiency of the spin-flip protocol for computing the exchange couplings and the utility of the NO analysis in assessing the validity of effective spin Hamiltonians.

This work explores the level of transparency in reporting the details of computational protocols that is required for practical reproducibility of quantum mechanics/molecular mechanics (QM/MM) simulations. Using the reaction of an essential SARS-CoV-2 enzyme (the main protease) with a covalent inhibitor (carmofur) as a test case of chemical reactions in biomolecules, we carried out QM/MM calculations to determine the structures and energies of the reactants, the product, and the transition state/intermediate using analogous QM/MM models implemented in two software packages, NWChem and Q-Chem. Our main benchmarking goal was to reproduce the key energetics computed with the two packages. Our results indicate that quantitative agreement (within the numerical thresholds used in calculations) is difficult to achieve. We show that rather minor details of QM/MM simulations must be reported in order to ensure the reproducibility of the results and offer suggestions toward developing practical guidelines for reporting the results of biosimulations.

The scanning two-dimensional ionization profile monitor (IPM) has been upgraded for the beam diagnostics in beam transport lines. The main parts of the monitor are an extractor, a scanner, and two analyzers with a slit at which residual-gas ionization products collected from a beam path as long as 50 mm arrive. The current amplifier based on microchannel plates and a current collector are placed in sequence behind the slit in order to increase the IPM sensitivity under high-vacuum conditions (n × 10−6 Pa). Two-dimensional beam profiles are obtained by scanning. A special electronic unit containing high-voltage supplies and collector-current meters has been created for the scanning and IPM control. Three upgraded IPMs have been placed between the accelerator and the physical facilities in each beamline of the DC-280 FLNR JINR cyclotron. Data processing and simultaneous display of experimental results from several IPMs are carried out by a program developed in the LabVIEW design environment. The minimum current of the 40Ar ion beam with the energy of 5 MeV/nucleon at which the monitor is still operable is estimated to be several tens of picoamperes. The reliability of the upgraded IPM has been demonstrated by its operation.

Ultracold organic chemistry enables studies of reaction dynamics and mechanisms in the quantum regime. Access to ultracold molecules hinges on the ability to efficiently scatter multiple photons via quasi-closed cycling transitions. Optical cycling in polyatomic molecules is challenging due to their complex electronic structure. Using equation-of-motion coupled-cluster calculations, we demonstrate that an alkaline earth metal attached to various aromatic ligands (such as benzene, phenol, cyclopentadienyl, and pyrrolide) offers nearly closed cycling transitions with only a few additional repump lasers. We also show that aromatic ligands such as benzene can accommodate multiple cycling centers in various geometrical arrangements, opening new avenues in quantum information science, precision measurements, and ultracold chemistry.

The equation-of-motion coupled-cluster singles and doubles method with double electron attachment (EOM-DEA-CCSD) is capable of computing reliable energies, wave functions, and first-order properties of excited states in diradicals and polyenes that have a significant doubly excited character with respect to the ground state, without the need for including the computationally expensive triple excitations. Here, we extend the capabilities of the EOM-DEA-CCSD method to the calculations of a multiphoton property, two-photon absorption (2PA) cross sections. Closed-form expressions for the 2PA cross sections are derived within the expectation-value approach using response wave functions. We analyze the performance of this new implementation by comparing the EOM-DEA-CCSD energies and 2PA cross sections with those computed using the CC3 quadratic response theory approach. As benchmark systems, we consider transitions to the states with doubly excited character in twisted ethene and in polyenes, for which EOM-EE-CCSD (EOM-CCSD for excitation energies) performs poorly. The EOM-DEA-CCSD 2PA cross sections are comparable with the CC3 results for twisted ethene; however, the discrepancies between the two methods are large for hexatriene. The observed trends are explained by configurational analysis of the 2PA channels.

Low-energy spectra of single-molecule magnets (SMMs) are often described by the Heisenberg Hamiltonian. Within this formalism, exchange interactions between magnetic centers determine the ground-state multiplicity and energy separation between the ground and excited states. In this contribution, we extract exchange coupling constants (J) for a set of iron (III) binuclear and tetranuclear complexes from all-electron calculations using non-collinear spin-flip time-dependent density functional theory (NC-SF-TDDFT). For the series of binuclear complexes with J-values ranging from -6 to -132 cm−1 , our benchmark calculations using the short-range hybrid LRC-ωPBEh functional and 6-31G(d,p) basis set agree well (mean absolute error of 4.7 cm−1) with the experimentally derived values. For the tetranuclear SMMs, the computed J constants are within 6 cm−1 from the values extracted from the experiment. We explore the range of applicability of the Heisenberg model by analyzing the radical character in the binuclear iron (III) complexes using natural orbitals (NO) and their occupations. On the basis of the number of effectively unpaired electrons and the NO occupancies, we attribute larger errors observed in strongly anti-ferromagnetic species to an increased ionic character. The results illustrate the efficiency of the spin-flip protocol for computing the exchange couplings and the utility of the NO analysis in assessing the validity of effective spin Hamiltonians.

The importance of including long-range electron-molecule interactions in treatments of photodetachment and/or photoionization is demonstrated. A combined experimental and computational study of CN- detachment is presented in which near threshold anisotropy parameters (β) are measured via photoelectron imaging. Calculated β values, based on an EOM-IP-CCSD/aug-cc-pVTZ Dyson orbital, are obtained using free-particle and point dipole models. The results demonstrate the influence of the molecular dipole moment in the detachment process and provide an explanation of the recently reported near threshold behavior of the overall photodetachment cross section in CN- detachment.

Investigation of microwave-activated CH4/H2 plasma used in chemical vapour deposition of diamond revealed the presence of electronically excited C2−∗ (B2Σu+). Using high-level electronic structure ...

We present several strategies for computing electronic circular dichroism (CD) spectra across different frequency ranges at the equation-of-motion coupled-cluster singles and doubles level of theory. CD spectra of both ground and electronically excited states are discussed. For selected cases, the approach is compared with coupled-cluster linear response results as well as time-dependent density functional theory. The extension of the theory to include the effect of spin-orbit coupling is presented and illustrated by calculations of X-ray CD spectra at the L edge.

The importance of including long-range electron-molecule interactions in treatments of photodetachment/photoionization is demonstrated. A combined experimental and computational study of CN− detachment is presented in which near threshold anisotropy parameters (β) are measured via photoelectron imaging. Calculated β values, based on an EOM-IP-CCSD/aug-cc-pVTZ Dyson orbital, are obtained using free particle and point dipole models. The results demonstrate the influence of the molecular dipole moment in the detachment process, and provide an explanation of the near threshold behavior of the overall photodetachment cross section in CN− detachment [J. Chem. Phys. 2020, 153, 184309]

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design. This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.

We present an approach for obtaining a molecular orbital picture of the first dipole hyperpolarizability (β) from correlated many-body electronic structure methods. Ab initio calculations of β rely on quadratic response theory, which recasts the sum-over-all-states expression of β into a closed-form expression by calculating a handful of first- and second-order response states; for resonantly enhanced β, damped response theory is used. These response states are then used to construct second-order response reduced one-particle density matrices (1PDMs), which, upon visualization in terms of natural orbitals (NOs), facilitate a rigorous and black-box mapping of the underlying electronic structure with β. We explain the interpretation of different components of the response 1PDMs and the corresponding NOs within both the undamped and damped response theory framework. We illustrate the utility of this new tool by deconstructing β for cis-difluoroethene, para-nitroaniline, and hemibonded OH· + H2O complex, computed within the framework of coupled-cluster singles and doubles response theory, in terms of the underlying response 1PDMs and NOs for a range of frequencies.

The unique properties of the photoswitchable protein Dreiklang are attributed to a reversible hydration/dehydration reaction at the imidazolinone ring of the chromophore. Recovery of the fluorescent state, which is associated with a chemical reaction of the chromophore's dehydration, is an important part of the photocycle of this protein. Here we characterize the fluorescent (ON) and nonfluorescent (OFF) states of Dreiklang and simulate the thermal recovery reaction OFF → ON using computational approaches. By using molecular modeling methods including the quantum mechanics/molecular mechanics (QM/MM) technique, we characterize the structures and spectra of the ON- and OFF-states. The results are consistent with available experimental data. The computed reaction profile explains the observed recovery reaction and clarifies the mechanism of chemical transformations in the chromophore-containing pocket in Dreiklang.

One-particle transition density matrices and natural transition orbitals enable quantitative description of electronic transitions and interstate properties involving correlated many-body wave functions within the molecular orbital framework. Here we extend the formalism to the analysis of tensor properties, such as spin-orbit couplings (SOCs), which involve states of different spin projection. By using spinless density matrices and Wigner-Eckart's theorem, the approach allows one to treat the transitions between states with arbitrary spin projections in a uniform way. In addition to a pictorial representation of the transition, the analysis also yields quantitative contributions of hole-particle pairs into the overall many-body matrix elements. In particular, it helps to rationalize the magnitude of computed SOCs in terms of El-Sayed's rules. The capabilities of the new tool are illustrated by the analysis of the equation-of-motion coupled-cluster calculations of two transition metal complexes.

Remarkable success in engineering novel efficient biomarkers based on fluorescent and photoactive proteins provokes a question of whether computational modeling of their properties can contribute to this important field. In this Feature Article, we analyze selected papers devoted to computer simulations of three types of photoactive systems: the green fluorescent protein and its derivatives, the flavin-binding proteins, and the phytochrome domains. The main emphasis is on structures, optical spectra, and chemical reactions in the chromophore-containing pockets. Quantum chemistry, quantum mechanics/molecular mechanics, and molecular dynamics methods are effective tools in these simulations. We highlight both the success stories and the persisting challenges, discussing the ways of elevating theoretical approaches to the level of testable predictions.

Despite their small size, C2 species pose big challenges to electronic structure methods, owing to extensive electronic degeneracies and multi-configurational wave functions, which lead to a dense manifold of electronic states. We present detailed electronic structure calculations of C2, C2−, and C22−, emphasizing spectroscopically relevant properties. We employ the double ionization potential (DIP) and ionization potential (IP) variants of the equation-of-motion coupled-cluster method with single and double substitutions (EOM-CCSD) and a dianionic reference state. We show that EOM-CCSD is capable of describing multiple interacting states in C2 and C2− in an accurate, robust, and effective way. We also characterize the electronic structure of C22−, which is metastable with respect to electron detachment.

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The electronic structure of four prototypical Cvetanović diradicals, species derived by addition of O( 3 P) to unsaturated compounds, is investigated by high-level electronic structure calculations and kinetics modeling. The main focus of this study is on the electronic factors controlling the rate of intersystem crossing (ISC): minimal energy crossing points (MECPs) and spin-orbit couplings (SOCs). The calculations illuminate significant differences in the electronic structure of ethene- and ethyne-derived compounds and explain the effect of methylation. The computed MECP heights and SOCs reveal different mechanisms of ISC in ethene- and ethyne-derived species, thus explaining variations in the observed branching ratios between singlet and triplet products and a puzzling effect of methyl substitution. In the ethene- and propene-derived species, the MECP is very low and the rate is controlled by variations of SOC, whereas in the ethyne- and propyne-derived species the MECP is high and the changes in the ISC rate due to methyl substitutions are driven by the variations of MECP heights.

We report a production-level implementation of equation-of-motion coupled-cluster method with double electron- attaching EOM operators of 2p and 3p1h types, EOM-DEA-CCSD. This ansatz, suitable for treating electronic structure patterns that can be described as two-electrons-in-many orbitals, represents a useful addition to EOM-CC family of methods. We analyze the performance of EOM-DEA-CCSD for energy differences and molecular properties. By considering reduced quantities, such as state and transition one-particle density matrices, we can compare EOM-DEA- CCSD wave-functions with wave-functions computed by other EOM-CCSD methods. The benchmarks illustrate that EOM-DEA-CCSD capable of treating diradicals, bond-breaking, and some types of conical intersection.

This themed collection includes a selection of articles on quantum computing and quantum information storage.

This is the peer reviewed version of the following article: Mroginski, Adam, Amoyal, Barnoy, Bondar, ... Schapiro. (2020). Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochemistry and Photobiology, 97(2):243-269, which has been published in final form at https://doi.org/10.1111/php.13372. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited. This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.

We present the results of high-level electronic structure and dynamics simulations of the photoactive protein Dreiklang. With the goal of understanding the details of the Dreiklang photocycle, we carefully characterize the excited states of the ON- and OFF-forms of Dreiklang. The key finding of our study is the existence of a low-lying excited state of a charge-transfer character in the neutral ON form and that population of this state, which is nearly isoenergetic with the locally excited bright state, initiates a series of steps that ultimately lead to the formation of the hydrated dark chromophore (OFF state). These results allow us to refine the mechanistic picture of Dreiklang's photocycle and photoactivation.

We report a theoretical investigation and elucidation of the X-ray absorption spectra of neutral benzene and of the benzene cation. The generation of the cation by multiphoton ultraviolet (UV) ionization and the measurement of the carbon K-edge spectra of both species using a table-top high-harmonic generation source are described in the companion experimental paper [Epshtein, M.; et al. J. Phys. Chem. Ahttp://dx.doi.org/10.1021/acs.jpca.0c08736]. We show that the 1sC → π transition serves as a sensitive signature of the transient cation formation, as it occurs outside of the spectral window of the parent neutral species. Moreover, the presence of the unpaired (spectator) electron in the π-subshell of the cation and the high symmetry of the system result in significant differences relative to neutral benzene in the spectral features associated with the 1sC → π* transitions. High-level calculations using equation-of-motion coupled-cluster theory provide the interpretation of the experimental spectra and insight into the electronic structure of benzene and its cation. The prominent split structure of the 1sC → π* band of the cation is attributed to the interplay between the coupling of the core → π* excitation with the unpaired electron in the π-subshell and the Jahn–Teller distortion. The calculations attribute most of the splitting (∼1–1.2 eV) to the spin coupling, which is visible already at the Franck–Condon structure, and we estimate the additional splitting due to structural relaxation to be around ∼0.1–0.2 eV. These results suggest that X-ray absorption with increased resolution might be able to disentangle electronic and structural aspects of the Jahn–Teller effect in the benzene cation.

Damped linear response calculations within the equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) framework usually diverge in the x-ray regime. This divergent behavior stems from the valence ionization continuum in which the x-ray response states are embedded. Here, we introduce a general strategy for removing the continuum from the response manifold while preserving important spectral properties of the model Hamiltonian. The strategy is based on decoupling the core and valence Fock spaces using the core–valence separation (CVS) scheme combined with separate (approximate) treatment of the core and valence resolvents. We illustrate this approach with the calculations of resonant inelastic x-ray scattering (RIXS) spectra of benzene and para-nitroaniline using EOM-CCSD wave functions and several choices of resolvents, which differ in their treatment of the valence manifold. The method shows robust convergence and extends the previously introduced CVS-EOM-CCSD RIXS scheme to systems for which valence contributions to the total cross section are important, such as the push–pull chromophores with charge-transfer states.

We present the results of high-level electronic structure and dynamics simulationsof the photoactive protein Dreiklang. With the goal to understand the details ofDreiklang's photocycle, we carefully characterize the excited states of the ON- andOFF-forms of Dreiklang. The key ?nding of our study is the existence of a lowlyingexcited state of a charge-transfer (CT) character in the neutral ON form andthat population of this state, which is nearly isoenergetic with the locally excited(LE) bright state, initiates series of steps ultimately leading to the formation ofthe hydrated dark chromophore (OFF state). These results allow us to re?ne themechanistic picture of the Dreiklang's photocycle and photoactivation.

We report a theoretical investigation and elucidation of the x-ray absorption spectra of neutral benzene and of the benzene cation. The generation of the cation by multiphoton ultraviolet (UV) ionization as well as the experimental measurement ofthe carbon K-edge spectra of both species using a table-top high-harmonic generation (HHG) source have been described in a companion paper [M. Epshtein et al., J. Am.Chem. Soc., submitted. Available on ChemRxiv]. We show that the 1sC -> pi transition serves as a sensitive signature of the transient cation formation, as it occurs outside of the spectral window of the parent neutral species. Moreover, the presenceof the unpaired (spectator) electron in the pi-subshell of the cation and the high symmetry of the system result in significant differences relative to neutral benzene in the spectral features associated with the 1sC ->pi* transitions. High-level calculations using equation-of-motion coupled-cluster theory provide the interpretation of the experimental spectra and insight into the electronic structure of benzene and its cation.The prominent split structure of the 1sC -> pi* band of the cation is attributed to the interplay between the coupling of the core -> pi* excitation with the unpaired electronin the pi-subshell and the Jahn-Teller distortion. The calculations attribute most ofthe splitting (~1-1.2 eV) to the spin coupling, which is visible already at the Franck-Condon structure, and estimate the additional splitting due to structural relaxation tobe around ~0.1-0.2 eV. These results suggest that x-ray absorption with increased resolution might be able to disentangle electronic and structural aspects of the Jahn-Tellereffect in benzene cation.