PERI–CC2: A Polarizable Embedded RI-CC2 Method

One- and two-photon absorption spectra of organoboron complexes: vibronic and environmental effects

We synthesized a series of four parent aza-β-ketoiminate organoboron complexes and performed spectroscopic studies using both experimental and computational techniques. We studied how benzannulation influences the vibronic structure of the UV/Vis absorption bands with a focus on the bright lowest-energy π → π* electronic excitation. Theoretical simulations, accounting for inhomogeneous broadening effects using different embedding schemes, allowed gaining in-depth insights into the observed differences in band shapes induced by structural modifications. We observed huge variations in the distributions of vibronic transitions depending on the position of benzannulation. By and large, the harmonic approximation combined with the adiabatic hessian model delivers qualitatively correct band shapes for the one-photon absorption spectra, except in one case. We also assessed the importance of non-Condon effects (accounted for by the linear term in Herzberg-Teller expansion of the dipole moment) for S0 → S1 band shapes. It turned out that non-Condon contributions have no effect on the band shape in one-photon absorption spectra. In contrast, these effects significantly change the Franck-Condon band shapes of the two-photon absorption spectra. For one of the studied organoboron complexes we also performed a preliminary exploration of mechanical anharmonicity, resulting in an increase of the intensity of the 0-0 transition, which improves the agreement with the experimental data compared to the harmonic model.

Role of Singles Amplitudes in ADC(2) and CC2 for Low-Lying Electronically Excited States

The closely related second-order methods CC2 and ADC(2) usually perform very similarly for single excitations of organic molecules. However, as rationalized in this work, significant deviations between these two methods can arise if the ground state and a low-lying singly excited state arise from a strong coupling between their leading configurations. Such a configuration mixing is partially accounted for in CC2 through the ground-state singles amplitudes but is omitted in ADC(2). This can cause unusual deviations between the results obtained with these methods. In this work, we study how severe this effect can become at the example of two solvatochromic dyes: the negatively solvatochromic betaine dye N1-tBu and the positively solvatochromic bithiophene P1. These two dyes allow one to study the limits of both small and somewhat larger excitation energies and configuration mixing by tuning the S0 → S1 transition energy through the polarity of the environment. Higher-level calculations at the CC3 level provide information on the accuracy of ADC(2) and CC2 in these cases. The most extreme deviation between ADC(2) and CC2 is found for N1-tBu in vacuum, where the ADC(2) result is 0.45 eV below that of CC2. In this case, the methodical error of CC2 with respect to CC3 is only 0.05 eV. With increasing excitation energy in polar solvents, the CC2-ADC(2) deviation decreases and reaches a value of only 0.15 eV. For P1, which has larger excitation energies, these effects are reversed due to the opposite solvatochromism but also smaller in magnitude: the deviation increases from 0.08 eV in vacuum to 0.16 eV in the so-called conductor limit of the continuum solvation model. Although for these two dyes larger deviations are observed for smaller excitation energies, the extent of configuration mixing does not generally correlate with only the size of excitation energy. For example, s-triazine (0.15 eV), formamide (0.19 eV), and formaldehyde (0.23 eV) also show large deviations between CC2 and ADC(2) despite their much higher excitation energies compared to those of N1-tBu and P1.

TURBOMOLE: Today and Tomorrow

TURBOMOLE is a highly optimized software suite for large-scale quantum-chemical and materials science simulations of molecules, clusters, extended systems, and periodic solids. TURBOMOLE uses Gaussian basis sets and has been designed with robust and fast quantum-chemical applications in mind, ranging from homogeneous and heterogeneous catalysis to inorganic and organic chemistry and various types of spectroscopy, light-matter interactions, and biochemistry. This Perspective briefly surveys TURBOMOLE's functionality and highlights recent developments that have taken place between 2020 and 2023, comprising new electronic structure methods for molecules and solids, previously unavailable molecular properties, embedding, and molecular dynamics approaches. Select features under development are reviewed to illustrate the continuous growth of the program suite, including nuclear electronic orbital methods, Hartree-Fock-based adiabatic connection models, simplified time-dependent density functional theory, relativistic effects and magnetic properties, and multiscale modeling of optical properties.

Cost-Effective Simulations of Vibrationally-Resolved Absorption Spectra of Fluorophores with Machine-Learning-Based Inhomogeneous Broadening

The results of electronic and vibrational structure simulations are an invaluable support for interpreting experimental absorption/emission spectra, which stimulates the development of reliable and cost-effective computational protocols. In this work, we contribute to these efforts and propose an efficient first-principle protocol for simulating vibrationally-resolved absorption spectra, including nonempirical estimations of the inhomogeneous broadening. To this end, we analyze three key aspects: (i) a metric-based selection of density functional approximation (DFA) so to benefit from the computational efficiency of time-dependent density function theory (TD-DFT) while safeguarding the accuracy of the vibrationally-resolved spectra, (ii) an assessment of two vibrational structure schemes (vertical gradient and adiabatic Hessian) to compute the Franck-Condon factors, and (iii) the use of machine learning to speed up nonempirical estimations of the inhomogeneous broadening. In more detail, we predict the absorption band shapes for a set of 20 medium-sized fluorescent dyes, focusing on the bright ππ^★ S₀ → S₁ transition and using experimental results as references. We demonstrate that, for the studied 20-dye set which includes structures with large structural variability, the preselection of DFAs based on an easily accessible metric ensures accurate band shapes with respect to the reference approach and that range-separated functionals show the best performance when combined with the vertical gradient model. As far as band widths are concerned, we propose a new machine-learning-based approach for determining the inhomogeneous broadening induced by the solvent microenvironment. This approach is shown to be very robust offering inhomogeneous broadenings with errors as small as 2 cm^-1 with respect to genuine electronic-structure calculations, with a total CPU time reduced by 98%.

Structural Sampling and Solvation Models for the Simulation of Electronic Spectra: Pyrazine as a Case Study

The impact of sampling methods on spectral broadening in the gas phase and on the convergence of spectra in aqueous solution when using microsolvation, continuum solvation, and hybrid models is studied using pyrazine as a test case. For the sake of comparing classical Maxwell-Boltzmann and Wigner samplings in the gas phase, static and time-resolved X-ray absorption spectra after photoexcitation to the lowest ¹B_2u(ππ*) state, as well as the static UV-vis absorption spectrum, are considered. In addition, the UV-vis absorption spectrum of pyrazine in aqueous solution is also computed in order to systematically investigate its convergence with the number of explicitly included solvent shells with and without taking bulk solvation effects into account with the conductor-like screening model to represent implicit water beyond such explicit solute complexes. Concerning the static and time-resolved X-ray absorption spectra of pyrazine at the carbon K-edge as well as its UV-vis absorption spectrum in the gas phase, we find that these spectra obtained with Wigner and Maxwell-Boltzmann samplings substantially agree. For the UV-vis absorption spectrum in the aqueous solution, only the first two energetically low-lying bands converge quickly with the size of the explicitly included solvation shells, either with or without an additional continuum solvation taken into account. In stark contrast, calculations of the higher-lying excitations relying on finite microsolvated clusters without additional continuum solvation severely suffer from unphysical charge-transfer excitations into Rydberg-like orbitals at the cluster/vacuum interface. This finding indicates that computational UV-vis absorption spectra covering sufficiently high-lying states converge only if continuum solvation of the explicitly microsolvated solutes is included in the models.

Spatial Decay and Limits of Quantum Solute-Solvent Interactions

Molecular excitations in the liquid-phase environment are renormalized by the surrounding solvent molecules. Herein, we employ the GW approximation to investigate the solvation effects on the ionization energy of phenol in various solvent environments. The electronic effects differ by up to 0.4 eV among the five investigated solvents. This difference depends on both the macroscopic solvent polarizability and the spatial decay of the solvation effects. The latter is probed by separating the electronic subspace and the GW correlation self-energy into fragments. The fragment correlation energy decays with increasing intermolecular distance and vanishes at ∼9 Å, and this pattern is independent of the type of solvent environment. The 9 Å cutoff defines an effective interacting volume within which the ionization energy shift per solvent molecule is proportional to the macroscopic solvent polarizability. Finally, we propose a simple model for computing the ionization energies of molecules in an arbitrary solvent environment.

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.

Pushing the limits: Efficient wavefunction methods for excited states in complex systems using frozen-density embedding

Frozen density embedding (FDE) is an embedding method for complex environments that is simple for users to set up. It reduces the computation time by dividing the total system into small subsystems and approximating the interaction by a functional of their densities. Its combination with wavefunction methods is, however, limited to small- or medium-sized molecules because of the steep scaling in computation time of these methods. To mitigate this limitation, we present a combination of the FDE approach with pair natural orbitals (PNOs) in the TURBOMOLE software package. It combines the uncoupled FDE (FDEu) approach for excitation energy calculations with efficient implementations of second-order correlation methods in the ricc2 and pnoccsd programs. The performance of this combination is tested for tetraazaperopyrene (TAPP) molecular crystals. It is shown that the PNO truncation error on environment-induced shifts is significantly smaller than the shifts themselves and, thus, that the local approximations of PNO-based wavefunction methods can without the loss of relevant digits be combined with the FDE method. Computational wall times are presented for two TAPP systems. The scaling of the wall times is compared to conventional supermolecular calculations and demonstrates large computational savings for the combination of FDE- and PNO-based methods. Additionally, the behavior of excitation energies with the system size is investigated. It is found that the excitation energies converge quickly with the size of the embedding environment for the TAPPs investigated in the current study.

Theoretical Study on the Photoacidity of Hydroxypyrene Derivatives in DMSO Using ADC(2) and CC2

This work applies the thermodynamic Förster cycle to theoretically investigate the pK_a^*, i.e., excited-state pK_a values of pyranine-derived superphotoacids developed by Jung and co-workers. The latter photoacids are strong enough to transfer a proton to the aprotic solvent dimethyl sulfoxide (DMSO). The Förster cycle provides access to pK_a^* via the ground-state pK_a and the electronic excitation energies. We use the conductor-like screening model for real solvents (COSMO-RS) to compute the ground-state pK_a and the correlated wavefunction-based methods ADC(2) and CC2 with the continuum solvation model COSMO to calculate the pK_a change upon excitation. A comparison of the calculated UV/Vis absorption and fluorescence emission energies to the experimental results leads us to infer that this approach allows for a proper description of the electronic excitations. In particular, implicit solvation by means of the COSMO model appears to be sufficient for the treatment of these photoacids in DMSO. The calculations confirm the presumption that a charge redistribution from the hydroxy group to the aromatic ring and the electron-withdrawing substituents is the origin of photoacidity for these photoacids. Moreover, the calculations with the continuum solvation model predict that the pK_a jump upon excitation decreases with increasing solvent polarity, as rationalized based on the Förster cycle.

Solvent Effects in the Ultraviolet and X-ray Absorption Spectra of Pyridazine in Aqueous Solution

Electrostatic interaction of the solvent with the solute and fluctuations of the solvent configurations may make excitation energies of the solute different from those in the gas phase. These effects may dominate photoinduced or chemical reaction dynamics in solution systems and can be observed as shifts or broadening of peaks in absorption spectra. In this work, the nitrogen K-edge X-ray absorption spectra were measured for pyridazine in the gas phase and in aqueous solution. The ultraviolet and X-ray absorption spectra of pyridazine in aqueous solution, as well as those in the gas phase, were then calculated with models based on the algebraic-diagrammatic construction through second order [ADC(2)] with the resolution-of-identity (RI) approximation and compared with the spectra obtained in experiments. For aqueous solution, explicit local solvation structures were extracted from an ab initio molecular dynamics (AIMD) trajectory of pyridazine in bulk water, and RI-ADC(2) was combined with the conductor-like screening model (COSMO). The experimental absorption spectra of pyridazine in aqueous solution were reproduced with good accuracy by theoretical treatment of an ensemble containing the explicit local solvation structures of pyridazine with relevant water molecules combined with the COSMO solvation model of water for long-range solvation.

TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations

TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy-cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe-Salpeter methods, second-order Møller-Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE's functionality, including excited-state methods, RPA and Green's function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE's current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE's development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted.

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.

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.

Electronic Excitations in Complex Molecular Environments: Many-Body Green's Functions Theory in VOTCA-XTP

Many-body Green's functions theory within the GW approximation and the Bethe-Salpeter Equation (BSE) is implemented in the open-source VOTCA-XTP software, aiming at the calculation of electronically excited states in complex molecular environments. Based on Gaussian-type atomic orbitals and making use of resolution of identity techniques, the code is designed specifically for nonperiodic systems. Application to a small molecule reference set successfully validates the methodology and its implementation for a variety of excitation types covering an energy range from 2 to 8 eV in single molecules. Further, embedding each GW-BSE calculation into an atomistically resolved surrounding, typically obtained from Molecular Dynamics, accounts for effects originating from local fields and polarization. Using aqueous DNA as a prototypical system, different levels of electrostatic coupling between the regions in this GW-BSE/MM setup are demonstrated. Particular attention is paid to charge-transfer (CT) excitations in adenine base pairs. It is found that their energy is extremely sensitive to the specific environment and to polarization effects. The calculated redshift of the CT excitation energy compared to a nucelobase dimer treated in vacuum is of the order of 1 eV, which matches expectations from experimental data. Predicted lowest CT energies are below that of a single nucleobase excitation, indicating the possibility of an initial (fast) decay of such an UV excited state into a binucleobase CT exciton. The results show that VOTCA-XTP's GW-BSE/MM is a powerful tool to study a wide range of types of electronic excitations in complex molecular environments.

Analytic Excited State Gradients for the QM/MM Polarizable Embedded Second-Order Algebraic Diagrammatic Construction for the Polarization Propagator PE-ADC(2)

An implementation of a QM/MM embedding in a polarizable environment is presented for second-order Møller-Plesset perturbation theory, MP2, for ground state energies and molecular gradients and for the second-order Algebraic Diagrammatic Construction, ADC(2), for excitation energies and excited state molecular gradients. In this implementation of PE-MP2 and PE-ADC(2), the polarizable embedded Hartree-Fock wave function is used as uncorrelated reference state. The polarization-correlation cross terms for the ground and excited states are included in this model via an approximate coupling density. A Lagrangian formulation is used to derive the relaxed electron densities and molecular gradients. The resolution-of-the-identity approximation speeds up the calculation of four-index electron repulsion integrals in the molecular orbital basis. As a first application, the method is used to study the photophysical properties of host-guest complexes where the accuracy and weaknesses of the model are also critically examined. It is demonstrated that the ground state geometries of the full quantum mechanical calculation for the supermolecule can be well reproduced. For excited state geometries, the deviations from the supermolecular calculation are slightly larger, but still the environment effects are captured qualitatively correctly, and energy gaps between the ground and excited states are obtained with sufficient accuracy.

COSMO-RI-ADC(2) excitation energies and excited state gradients

Evaluating vertical excitation energies and excited state analytic gradients in solution at COSMO-ADC(2).

Rationalisation of the optical signatures of nor-dihydroxanthene-hemicyanine fused near-infrared fluorophores by first-principle tools

The perfect pair towards more effective nor-DXH-hemicyanine fused NIR fluoroohores.

Nonempirical Simulations of Inhomogeneous Broadening of Electronic Transitions in Solution: Predicting Band Shapes in One- and Two-Photon Absorption Spectra of Chalcones

We have examined several approaches relying on the Polarizable Embedding (PE) scheme to predict optical band shapes for two chalcone molecules in methanol solution. The PE-TDDFT and PERI-CC2 methods were combined with molecular dynamics simulations, where the solute geometry was kept either as rigid, flexible or partly-flexible (restrained) body. The first approach, termed RBMD-PE-TDDFT, was employed to estimate the inhomogeneous broadening for subsequent convolution with the vibrationally-resolved spectra of the molecule in solution determined quantum-mechanically (QM). As demonstrated, the RBMD-PE-TDDFT/QM-PCM approach delivers accurate band widths, also reproducing their correct asymmetric shapes. Further refinement can be obtained by the estimation of the inhomogeneous broadening using the RBMD-PERI-CC2 method. On the other hand, the remaining two approaches (FBMD-PE-TDDFT and ResBMD-PE-TDDFT), which lack quantum-mechanical treatment of molecular vibrations, lead to underestimated band widths. In this study, we also proposed a simple strategy regarding the rapid selection of the exchange-correlation functional for the simulations of vibrationally-resolved one- and two-photon absorption spectra based on two easy-to-compute metrics.

Bethe-Salpeter study of cationic dyes: Comparisons with ADC(2) and TD-DFT

We present a theoretical investigation of the excited-state properties of a large series of structurally diverse arylcarbonium derivatives that are known to be challenging for theoretical models. More specifically, we compare the pros and cons of TD-DFT (TD-M06-2X), ADC(2), and BSE/GW approaches for a large panel of compounds, using two different solvent models. Both 0-0 and vertical transition energies are considered and compared to the experimental values. All approaches reasonably reproduce the auxochromic and acidochromic shifts, although in most cases both TD-DFT and BSE/GW return larger correlation with experimental values than ADC(2) for these shifts. In contrast, the absolute transition energies obtained with ADC(2) tend to be closer to the measurements, TD-DFT using the M06-2X functional largely overestimating the experimental references (by ca. 0.5 eV), and BSE/GW providing intermediate values. In addition, we show that the selected solvent model has a significant impact on the results, the corrected linear-response approach providing larger transition energies than its linear-response counterpart.

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.

Efficient determination of accurate atomic polarizabilities for polarizeable embedding calculations

We evaluate embedding potentials, obtained via various methods, used for polarizable embedding computations of excitation energies of para-nitroaniline in water and organic solvents as well as of the green fluorescent protein. We found that isotropic polarizabilities derived from DFTD3 dispersion coefficients correlate well with those obtained via the LoProp method. We show that these polarizabilities in conjunction with appropriately derived point charges are in good agreement with calculations employing static multipole moments up to quadrupoles and anisotropic polarizabilities for both computed systems. The (partial) use of these easily-accessible parameters drastically reduces the computational effort to obtain accurate embedding potentials especially for proteins. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Communication: A simplified coupled-cluster Lagrangian for polarizable embedding

A simplified coupled-cluster Lagrangian, which is linear in the Lagrangian multipliers, is proposed for the coupled-cluster treatment of a quantum mechanical system in a polarizable environment. In the simplified approach, the amplitude equations are decoupled from the Lagrangian multipliers and the energy obtained from the projected coupled-cluster equation corresponds to a stationary point of the Lagrangian.

Approaching Phosphorescence Lifetimes in Solution: The Two-Component Polarizable-Embedding Approximate Coupled-Cluster Method

Theoretical description of phosphorescence lifetimes in the condensed phase requires a method that takes into account both spin-orbit coupling and solvent-solute interactions. To obtain such a method, we have coupled our recently developed two-component coupled-cluster method with singles and approximated doubles to a polarizable environment. With this new method, we investigate how different solvents effect the electronic phosphorescence energies and lifetimes of 4H-pyran-4-thione.

Excited states in large molecular systems through polarizable embedding

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

Quantifying electron transfer reactions in biological systems: what interactions play the major role?

Various biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve light absorption, excited electronic states formation, excitation energy transfer, electrons and protons tunnelling which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between quantum physics and biology. In this paper we consider electron transfer in biological processes, from a theoretical view-point; namely in terms of quantum mechanical and semi-classical models. We systematically characterize the interactions between the moving electron and its biological environment to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe specifically the electron transfer reactions in Arabidopsis thaliana cryptochrome-a signaling photoreceptor protein that became attractive recently due to its possible function as a biological magnetoreceptor.

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.

Polarizable Embedded RI-CC2 Method for Two-Photon Absorption Calculations

We present a novel polarizable embedded resolution-of-identity coupled cluster singles and approximate doubles (PERI-CC2) method for calculation of two-photon absorption (TPA) spectra of large molecular systems. The method was benchmarked for three types of systems: a water-solvated molecule of formamide, a uracil molecule in aqueous solution, and a set of mutants of the channelrhodopsin (ChR) protein. The first test case shows that the PERI-CC2 method is in excellent agreement with the PE-CC2 method and in good agreement with the PE-CCSD method. The uracil test case indicates that the effects of hydrogen bonding on the TPA of a chromophore with the nearest environment is well-described with the PERI-CC2 method. Finally, the ChR calculation shows that the PERI-CC2 method is well-suited and efficient for calculations on proteins with medium-sized chromophores.

Analysis of computational models for an accurate study of electronic excitations in GFP

The accuracy of PERI-CC2 is successfully assessed against RVS-CC2 for GFP model clusters and subsequently applied to a whole protein model.

Frequency-dependent force fields for QMMM calculations

The frequency-dependent localized polarizabilities are calculated for the first time using analytical response theory and benchmarked for different water clusters and the tryptophan residue embedded in a protein.

Experimental and computational study of solvent effects on one- and two-photon absorption spectra of chlorinated harmines

We present a combined experimental and computational study of one- and two-photon absorption spectra of protonated chloroharmines in aqueous and acetonitrile solutions.