On the importance of excited state dynamic response electron correlation in polarizable embedding methods

Dynamical Effects of Solvation on Norbornadiene/Quadricyclane Systems

Molecules that can undergo reversible chemical transformations following the absorption of light, the so-called molecular photoswitches, have attracted increasing attention in technologies, such as solar energy storage. Here, the optical and thermochemical properties of the photoswitch are central to its applicability, and these properties are influenced significantly by solvation. We investigate the effects of solvation on two norbornadiene/quadricyclane photoswitches. Emphasis is put on the energy difference between the two isomers and the optical absorption as these are central to the application of the systems in solar energy storage. Using a combined classical molecular dynamics and quantum mechanical/molecular mechanical computational scheme, we showcase that the dynamic effects of solvation are important. In particular, it is found that standard implicit solvation models generally underestimate the energy difference between the two isomers and overestimate the strength of the absorption, while the explicit solvation spectra are also less red-shifted than those obtained using implicit solvation models. We also find that the absorption spectra of the two systems are strongly correlated with specific dihedral angles. Altogether, this highlights the importance of including the dynamic effects of solvation.

Artificial design of organic emitters via a genetic algorithm enhanced by a deep neural network

The design of molecules requires multi-objective optimizations in high-dimensional chemical space with often conflicting target properties. To navigate this space, classical workflows rely on the domain knowledge and creativity of human experts, which can be the bottleneck in high-throughput approaches. Herein, we present an artificial molecular design workflow relying on a genetic algorithm and a deep neural network to find a new family of organic emitters with inverted singlet-triplet gaps and appreciable fluorescence rates. We combine high-throughput virtual screening and inverse design infused with domain knowledge and artificial intelligence to accelerate molecular generation significantly. This enabled us to explore more than 800 000 potential emitter molecules and find more than 10 000 candidates estimated to have inverted singlet-triplet gaps (INVEST) and appreciable fluorescence rates, many of which likely emit blue light. This class of molecules has the potential to realize a new generation of organic light-emitting diodes.

Investigation of Solvent Effects on the Molecular Energy Storage and Optical Properties of Bicyclooctadiene/Tetracyclooctane Photoswitches

In this paper, we investigate the effects of solvation on the solar energy storage properties of bicyclooctadiene/tetracyclooctane (BOD/TCO) photoswitches. The solvent effects on the thermochemical and optical properties are studied in cyclohexane, toluene, dichloromethane, ethanol, acetonitrile, and a vacuum using density functional theory and coupled cluster theory. Our results show that the energy storage capacity of the BOD/TCO system increases as the solvent polarity increases, and the change is more significant with an unsubstituted system. The energy storage capacity of the substituted system is not dependent on the polarity of the solvent. As the solvent polarity increases, the absorption peaks shift away from each other and the absorption intensities increase. Overall, the solvents improve the performance of the optical properties and the energy storage capacities of the BOD/TCO molecular solar thermal systems.

Nuclear Magnetic Shielding Constants with the Polarizable Density Embedding Model

We extend the polarizable density embedding (PDE) model to support the calculation of nuclear magnetic resonance (NMR) shielding constants using gauge-including atomic orbitals (GIAOs) within a density functional theory (DFT) framework. The PDE model divides the total system into fragments, describing some by quantum mechanics (QM) and the others through an embedding model. The PDE model uses anisotropic polarizabilities, inter-fragment two-electron Coulomb integrals, and a non-local repulsion operator to emulate the QM effects. The terms involving Coulomb integrals are straightforwardly extended with GIAOs. In contrast, we consider two approaches to handle the gauge dependency of the non-local operator, employing either simple symmetrization or a gauge transformation. We find the latter approach to be most stable with respect to increasing the basis set size of the QM region. We examine the accuracy of the PDE model for calculating NMR shielding constants on several solutes in a water solution. The performance is compared with the classical polarizable embedding (PE) model in addition to supermolecular reference calculations. Based on these systems, we address the basis set convergence characteristics and the QM region size requirements. Furthermore, we investigate the performance of the PDE model for a system with significant electron spill-out. In many cases, we find that the PDE model outperforms the PE model, especially regarding the accuracy of nuclear shielding constants when using small QM region sizes and in systems with significant electron spill-out.

Combining multilevel Hartree–Fock and multilevel coupled cluster approaches with molecular mechanics: a study of electronic excitations in solutions

We present the coupling of different quantum-embedding approaches with a third molecular-mechanics layer, which can be either polarizable or non-polarizable.

Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems

The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.

Avoiding Electron Spill-Out in QM/MM Calculations on Excited States with Simple Pseudopotentials

QM/MM calculations of electronic excitations with diffuse basis sets often have large errors due to spill-out of electrons from the quantum subsystem. The Pauli repulsion of the electrons by the environment has to be included to avoid this. We propose transferable atomic all-electron pseudopotentials that can readily be combined with most MM force fields to avoid electron spill-out. QM/MM excitation energies computed with time-dependent Hartree-Fock and the algebraic diagrammatic construction through second-order are benchmarked against supermolecular calculations to validate these new pseudopotentials. The QM/MM calculations with pseudopotentials give accurate results that are stable with augmentation of the basis set with diffuse functions. We show that the largest contribution to residual deviations from full QM calculations is caused by the missing London dispersion interaction.

Electronic transitions for a fully polarizable QM/MM approach based on fluctuating charges and fluctuating dipoles: Linear and corrected linear response regimes

The fully polarizable Quantum Mechanics/Molecular Mechanics (QM/MM) approach based on fluctuating charges and fluctuating dipoles, named QM/FQFμ [T. Giovannini et al., J. Chem. Theory Comput. 15, 2233 (2019)], is extended to the calculation of vertical excitation energies of solvated molecular systems. Excitation energies are defined within two different solvation regimes, i.e., linear response (LR), where the response of the MM portion is adjusted to the QM transition density, and corrected-Linear Response (cLR) in which the MM response is adjusted to the relaxed QM density, thus being able to account for charge equilibration in the excited state. The model, which is specified in terms of three physical parameters (electronegativity, chemical hardness, and polarizability) is applied to vacuo-to-water solvatochromic shifts of aqueous solutions of para-nitroaniline, pyridine, and pyrimidine. The results show a good agreement with their experimental counterparts, thus highlighting the potentialities of this approach.

CPPE: An Open-Source C++ and Python Library for Polarizable Embedding

We present a modular open-source library for polarizable embedding (PE) named CPPE. The library is implemented in C++, and it additionally provides a Python interface for rapid prototyping and experimentation in a high-level scripting language. Our library integrates seamlessly with existing quantum chemical program packages through an intuitive and minimal interface. Until now, CPPE has been interfaced to three packages, Q-Chem, Psi4, and PySCF. Furthermore, we show CPPE in action using all three program packages for a computational spectroscopy application. With CPPE, host program interfaces only require minor programming effort, paving the way for new combined methodologies and broader availability of the PE model.

An EOM-CCSD-PCM Benchmark for Electronic Excitation Energies of Solvated Molecules

In this work, we benchmark the equation of motion coupled cluster with single and double excitations (EOM-CCSD) method combined with the polarizable continuum model (PCM) for the calculation of electronic excitation energies of solvated molecules. EOM-CCSD is one of the most accurate methods for computing one-electron excitation energies, and accounting for the solvent effect on this property is a key challenge. PCM is one of the most widely employed solvation models due to its adaptability to virtually any solute and its efficient implementation with density functional theory methods (DFT). Our goal in this work is to evaluate the reliability of EOM-CCSD-PCM, especially compared to time-dependent DFT-PCM (TDDFT-PCM). Comparisons between calculated and experimental excitation energies show that EOM-CCSD-PCM consistently overestimates experimental results by 0.4-0.5 eV, which is larger than the expected EOM-CCSD error in vacuo. We attribute this decrease in accuracy to the approximated solvation model. Thus, we investigate a particularly important source of error: the lack of H-bonding interactions in PCM. We show that this issue can be addressed by computing an energy shift, Δ_HB, from bare-PCM to microsolvation + PCM at DFT level. Our results show that such a shift is independent of the functional used, contrary to the absolute value of the excitation energy. Hence, we suggest an efficient protocol where the EOM-CCSD-PCM transition energy is corrected by Δ_HB(DFT), which consistently improves the agreement with the experimental measurements.

Excited states in large molecular systems through polarizable embedding

Using the polarizable embedding model enables rational design of light-sensitive functional biological materials.

Assessing Molecular Dynamics Simulations with Solvatochromism Modeling

For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied.

Dye chemistry with time-dependent density functional theory

In this perspective, we present an overview of the determination of excited-state properties of "real-life" dyes, and notably of their optical absorption and emission spectra, performed during the last decade with time-dependent density functional theory (TD-DFT). We discuss the results obtained with both vertical and adiabatic (vibronic) approximations, choosing relevant examples for several series of dyes. These examples include reproducing absorption wavelengths of numerous families of coloured molecules, understanding the specific band shape of amino-anthraquinones, optimising the properties of dyes used in solar cells, mimicking the fluorescence wavelengths of fluorescent brighteners and BODIPY dyes, studying optically active biomolecules and photo-induced proton transfer, as well as improving the properties of photochromes.

Identification of ubiquinol binding motifs at the Qo-site of the cytochrome bc1 complex

Enzymes of the bc₁ complex family power the biosphere through their central role in respiration and photosynthesis. These enzymes couple the oxidation of quinol molecules by cytochrome c to the transfer of protons across the membrane, to generate a proton-motive force that drives ATP synthesis. Key for the function of the bc₁ complex is the initial redox process that involves a bifurcated electron transfer in which the two electrons from a quinol substrate are passed to different electron acceptors in the bc₁ complex. The electron transfer is coupled to proton transfer. The overall mechanism of quinol oxidation by the bc₁ complex is well enough characterized to allow exploration at the atomistic level, but details are still highly controversial. The controversy stems from the uncertain binding motifs of quinol at the so-called Q_o active site of the bc₁ complex. Here we employ a combination of classical all atom molecular dynamics and quantum chemical calculations to reveal the binding modes of quinol at the Q_o-site of the bc₁ complex from Rhodobacter capsulatus. The calculations suggest a novel configuration of amino acid residues responsible for quinol binding and support a mechanism for proton-coupled electron transfer from quinol to iron–sulfur cluster through a bridging hydrogen bond from histidine that stabilizes the reaction complex.

The Dalton quantum chemistry program system

Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, Møller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from http://www.daltonprogram.org for a number of UNIX platforms.