Solvatochromic Shifts in Uracil: A Combined MD-QM/MM Study

Computational Spectroscopy of Aqueous Solutions: The Underlying Role of Conformational Sampling

Fully atomistic multiscale polarizable quantum mechanics (QM)/molecular mechanics (MM) approaches, combined with techniques to sample the solute-solvent phase space, constitute the most accurate method to compute spectral signals in aqueous solution. Conventional sampling strategies, such as classical molecular dynamics (MD), may encounter drawbacks when the conformational space is particularly complex, and transition barriers between conformers are high. This can lead to inaccurate sampling, which can potentially impact the accuracy of spectral calculations. For this reason, in this work, we compare classical MD with enhanced sampling techniques, i.e., replica exchange MD and metadynamics. In particular, we show how the different sampling techniques affect computed UV, electronic circular dichroism, nuclear magnetic resonance shielding, and optical rotatory dispersion of N-acetylproline-amide in aqueous solution. Such a system is a model peptide characterized by complex conformational variability. Calculated values suggest that spectral properties are influenced by solute conformers, relative population, and solvent effects; therefore, particular care needs to be paid for when choosing the sampling technique.

Predicting Solvatochromism of Chromophores in Proteins through QM/MM and Machine Learning

Solvatochromism occurs in both homogeneous solvents and more complex biological environments, such as proteins. While in both cases the solvatochromic effects report on the surroundings of the chromophore, their interpretation in proteins becomes more complicated not only because of structural effects induced by the protein pocket but also because the protein environment is highly anisotropic. This is particularly evident for highly conjugated and flexible molecules such as carotenoids, whose excitation energy is strongly dependent on both the geometry and the electrostatics of the environment. Here, we introduce a machine learning (ML) strategy trained on quantum mechanics/molecular mechanics calculations of geometrical and electrochromic contributions to carotenoids' excitation energies. We employ this strategy to compare solvatochromism in protein and solvent environments. Despite the important specifities of the protein, ML models trained on solvents can faithfully predict excitation energies in the protein environment, demonstrating the robustness of the chosen descriptors.

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.

Reconciling TD-DFT and CASPT2 electronic structure methods for describing the photophysics of DNA

Time-dependent density functional theory (TD-DFT) and multiconfigurational second-order perturbation theory (CASPT2) are two of the most widely used methods to investigate photoinduced dynamics in DNA-based systems. These methods sometimes give diverse dynamics in physiological environments usually modeled by quantum mechanics/molecular mechanics (QM/MM) protocol. In this work, we demonstrate for the uridine test case that the underlying topology of the potential energy surfaces of electronic states involved in photoinduced relaxation is similar in both electronic structure methods. This is verified by analyzing surface-hopping dynamics performed at the QM/MM level on aqueous solvated uridine at TD-DFT and CASPT2 levels. By constraining the dynamics to remain onπ π * state we observe similar fluctuations in energy and relaxation lifetimes in surface-hopping dynamics in both TD-DFT and experimentally validated CASPT2 methods. This finding calls for a systematic comparison of the ES potential energy surfaces of DNA and RNA nucleosides at the single- and multi-reference levels of theory. The anomalous long excited state lifetime at the TD-DFT level is explained byn π * trapping due to the tendency of TD-DFT in QM/MM schemes with electrostatic embedding to underestimate the energy of theπ π * state leading to a wrongπ π * / n π * energetic order. A study of the FC energetics suggests that improving the description of the surrounding environment through polarizable embedding or by the expansion of QM layer with hydrogen-bonded waters helps restore the correct state order at TD-DFT level. Thus by combining TDDFT with an accurate modeling of the environment, TD-DFT is positioned as the standout protocol to model photoinduced dynamics in DNA-based aggregates and multimers.

Detangling Solvatochromic Effects by the Effective Fragment Potential Method

Understanding molecular interactions in complex systems opens avenues for the efficient design of new materials with target properties. Energy decomposition methods provide a means to obtain a detailed picture of intermolecular interactions. This work introduces a molecular modeling approach for decomposing the solvatochromic shifts of the electronic excited states into the contributions of the individual molecular fragments of the environment surrounding the chromophore. The developed approach is implemented for the QM/EFP (quantum mechanics/effective fragment potential) model that provides a rigorous first-principles-based description of the electronic states of the chromophores in complex polarizable environments. On the example of two model systems, water pentamer and hydrated uracil, we show how the decomposition of the solvatochromic shifts into the contributions of individual solvent water molecules provides a detailed picture of the intermolecular interactions in the ground and excited states of these systems. The analysis also demonstrates the nonadditivity of solute-solvent interactions and the significant contribution of solute polarization to the total values of solvatochromic shifts.

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.

Comparative Study of Uracil Excited-State Photophysics in Water and Acetonitrile via RMS-CASPT2-Driven Quantum-Classical Trajectories

We present a nonadiabatic molecular dynamics study of the ultrafast processes occurring in uracil upon UV light absorption, leading to electronic excitation and subsequent nonradiative decay. Previous studies have indicated that the mechanistic details of this process are drastically different depending on whether the process takes place in the gas phase, acetonitrile, or water. However, such results have been produced using quantum chemical methods that did not incorporate both static and dynamic electron correlation. In order to assess the previously proposed mechanisms, we simulate the photodynamics of uracil in the three environments mentioned above using quantum-classical trajectories and, for solvated uracil, hybrid quantum mechanics/molecular mechanics (QM/MM) models driven by the rotated multistate complete active space second-order perturbation (RMS-CASPT2) method. To do so, we exploit the gradient recently made available in OpenMolcas and compare the results to those obtained using the complete active space self-consistent field (CASSCF) method only accounting for static electron correlation. We show that RMS-CASPT2 produces, in general, a mechanistic picture different from the one obtained at the CASSCF level but confirms the hypothesis advanced on the basis of previous ROKS and TDDFT studies thus highlighting the importance of incorporating dynamic electron correlation in the investigation of ultrafast electronic deactivation processes.

Computational investigation of photoswitch conjugates for molecular solar energy storage

Solar energy conversion and storage are vital for combating climate change. Molecular solar thermal systems offer a promising solution, where energy is stored in molecular compounds. This study investigates dyad molecular photoswitches by combining bicyclooctadiene/tetracyclooctane and dihydroazulene/vinylheptafulvene systems with phenyl and cyano groups. Density functional theory calculations were employed to determine molecular properties and consider solvation effects in toluene and dichloromethane. The results show that the combined systems have a predicted storage energy of up to 206.14 kJ mol-1 and an absorption peak at 390.26 nm with appreciable intensity. These dyad photoswitches exhibit favorable properties for molecular solar thermal storage and other applications. A comparison with individual photoswitches reveals advantages and disadvantages. The most effective conjugate has a slightly lower storage density than an equal mixture of individual systems, but it demonstrates better absorption characteristics, with improved overlap with the solar spectrum and higher absorption intensity. These findings contribute to the understanding of dyad molecular photoswitches, showcasing their potential for advanced energy storage and conversion technologies.

Polarizable Embedding Complex Polarization Propagator in Four- and Two-Component Frameworks

Explicit embedding methods combined with the complex polarization propagator (CPP) enable the modeling of spectroscopy for increasingly complex systems with a high density of states. We present the first derivation and implementation of the CPP in four- and exact-two-component (X2C) polarizable embedding (PE) frameworks. We denote the developed methods PE-4c-CPP and PE-X2C-CPP, respectively. We illustrate the methods by estimating the solvent effect on ultraviolet-visible (UV-vis) and X-ray atomic absorption (XAS) spectra of [Rh(H₂O)₆]³⁺ and [Ir(H₂O)₆]³⁺ immersed in aqueous solution. We moreover estimate solvent effects on UV-vis spectra of a platinum complex that can be photochemically activated (in water) to kill cancer cells. Our results clearly show that the inclusion of the environment is required: UV-vis and (to a lesser degree) XAS spectra can become qualitatively different from vacuum calculations. Comparison of PE-4c-CPP and PE-X2C-CPP methods shows that X2C essentially reproduces the solvent effect obtained with the 4c methods.

Perturbation of the UV transitions of formaldehyde by TiO2 photocatalysts and Aun nanoclusters

In the gas phase, formaldehyde has an electric-dipole forbidden transition that becomes allowed by vibronic coupling. In this paper we explore whether perturbation by surfaces could also enhance light absorption by CH₂O. We investigate the electronic transitions of formaldehyde in the gas phase and interacting with rutile (110) TiO₂, Au_n nanoclusters, and Au_n on (110)-TiO₂. These surfaces are chosen as being representative of metals and metal-oxide minerals, and also because of specific interest in photocatalysts and noble metal nanocluster catalysts. The oscillator strength of the forbidden n → π* transition of formaldehyde in vacuum is investigated by modelling vibrational coupling to the electronic transition with equation-of-motion coupled cluster theory. The excitation energies and oscillator strengths of formaldehyde are calculated for different orientations and distances to the surfaces using the coupled cluster singles and doubles linear response method within the Quantum Mechanical and Molecular Mechanical (QM/MM) model using the aug-cc-pVTZ basis set and compared with the values calculated in vacuo. The electronic transitions of formaldehyde vary very little when placed near a pure TiO₂-surface with only minor variations depending on the orientation of formaldehyde. Introducing a gold nanoparticle (by itself or supported by TiO₂) induces dramatic changes in the absorption properties. This is due to vibronic interactions and the effect of the broken symmetry on the n → π* transition. We see a large redshift in the transition of 90 nm and oscillator strengths larger than 1.0 × 10^-4 for CH₂O interacting with Au_n.

Optimization of the thermochemical properties of the norbornadiene/quadricyclane photochromic couple for solar energy storage using nanoparticles

In this paper, we present an investigation concerning the prospects of using nanoparticles to improve solar energy storage properties of three different norbornadiene/quadricyclane derivatives. Computationally, we study how different nanoparticles influence the properties of the systems that relate to the storage of solar energy, namely, the storage energy and the back reaction barrier. Our approach employs hybrid quantum mechanical/molecular mechanical calculations in which the molecular systems are described using density functional theory while the nanoparticles are described using molecular mechanics. The interactions between the two subsystems are determined using polarization dynamics. The results show that the influence of the nanoparticles on the thermochemical properties largely depends on the type of nanoparticle used, the relative orientation with respect to the nanoparticle, and the distance between the the nanoparticle and the molecular system. Additionally, we find indications that copper and/or titanium dioxide nanoparticles can lower the energy barrier of the back reaction for all of the studied systems without significantly lowering the storage capability of the systems. Consequently, the study shows that nanoparticles can potentially be employed in the optimization of molecular photoswitches towards solar energy storage.

The riddle of the forbidden UV absorption of aqueous nitrate: the oscillator strength of the n → π* transition in NO3− including second order vibronic coupling

The environmentally relevant n → π* transition in the nitrate anion is doubly forbidden by symmetry. A simple scheme for including second order vibronic coupling is presented.

Computational construction of the electronic Hamiltonian for photoinduced electron transfer and Redfield propagation

The construction of open-system diabatic Hamiltonians relevant for the investigation of electron transfer processes is a computational challenge. Here all relevant parameters for Redfield propagations are extracted fromab initiocomputations.

How intermolecular interactions influence electronic absorption spectra: insights from the molecular packing of uracil in condensed phases

Intermolecular interactions in terms of molecular packing are crucial for the investigation of the absorption spectra of uracil in different environments.

Benchmarking sampling methodology for calculations of Rayleigh light scattering properties of atmospheric molecular clusters

We present four different computational methods for benchmarking the sampling and Rayleigh light scattering of hydrogen bonded atmospheric molecular clusters.

The influence of gold nanoparticles on the two photon absorption of photochromic molecular systems

In this study, we investigate the influence of gold nanoparticles on the nonlinear optical properties of the dihydroazulene/vinylheptafulvene photo- and thermochromic system.

Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA

The intrinsic photostability of nucleic acids is intimately related to evolution of life, while its understanding at the molecular and electronic levels remains a challenge for modern science. Among the different decay pathways proposed in the last two decades, the excited-state hydrogen transfer between guanine-cytosine base pairs has been identified as an efficient non-reactive channel to dissipate the excess of energy provided by light absorption. The present work studies the dynamics of such phenomena taking place in a (dG)·(dC) B-DNA homopolymer in water solution using state-of-the-art molecular modelling and simulation methods. A dynamic effect that boosts the photostability of the inter-strand hydrogen atom transfers, inherent to the Watson-Crick base pairing, is unveiled and ascribed to the energy released during the proton transfer step. Our results also reveal a novel mechanism of DNA decay named four proton transfer (FPT), in which two protons of two adjacent G-C base pairs are transferred to form a biradical zwitterionic intermediate. Decay of the latter intermediate to the ground state triggers the transfer of the protons back to the guanine molecules recovering the Watson-Crick structure of the tetramer. This FPT process is activated by the close interaction of a nearby Na+ counterion with the oxygen atoms of the guanine nucleobases and hence represents a photostable channel operative in natural nucleic acids.

Sampling the protonation states: the pH-dependent UV absorption spectrum of a polypeptide dyad

When a chromophore interacts with several titratable molecular sites, the modeling of its photophysical properties requires to take into account all their probable protonation states.

Polarizable Embedding Density Matrix Renormalization Group

The polarizable embedding (PE) approach is a flexible embedding model where a preselected region out of a larger system is described quantum mechanically, while the interaction with the surrounding environment is modeled through an effective operator. This effective operator represents the environment by atom-centered multipoles and polarizabilities derived from quantum mechanical calculations on (fragments of) the environment. Thereby, the polarization of the environment is explicitly accounted for. Here, we present the coupling of the PE approach with the density matrix renormalization group (DMRG). This PE-DMRG method is particularly suitable for embedded subsystems that feature a dense manifold of frontier orbitals which requires large active spaces. Recovering such static electron-correlation effects in multiconfigurational electronic structure problems, while accounting for both electrostatics and polarization of a surrounding environment, allows us to describe strongly correlated electronic structures in complex molecular environments. We investigate various embedding potentials for the well-studied first excited state of water with active spaces that correspond to a full configuration-interaction treatment. Moreover, we study the environment effect on the first excited state of a retinylidene Schiff base within a channelrhodopsin protein. For this system, we also investigate the effect of dynamical correlation included through short-range density functional theory.

Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes

Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells.

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.

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.

Studies of pH-Sensitive Optical Properties of the deGFP1 Green Fluorescent Protein Using a Unique Polarizable Force Field

The aim of this study is to identify the responsible molecular forms for the pH dependent optical properties of the deGFP1 green fluorescent protein mutant. We have carried out static and dynamic type calculations for all four protonation states of the chromophore to unravel the contributions due to finite temperature and the flexible protein backbone on the pH dependent optical properties. In particular, we have used a combined molecular dynamics and density functional-molecular mechanics linear response approach by means of which the optical property calculations were carried out for the chromophore in the explicitly treated solvent and bioenvironment. Two different models were used to describe the environment-electronic embedding and polarizable electronic embedding-accounting for the polarization of the chromophore and the mutual polarization between the chromophore and the environment, respectively. For this purpose a polarizable force field was derived quantum mechanically for the protein environment by use of analytical response theory. While the gas-phase calculations for the chromophore predict that the induced red shift going from low to high pH is attributed to the change of molecular forms from neutral to zwitterionic, the two more advanced models that explicitly account for the protein backbone attribute the pH shift to a neutral to anionic conversion. Some ramifications of the results for the use of GFPs as pH sensors are discussed.

Solvent effects on the ultrafast nonradiative deactivation mechanisms of thymine in aqueous solution: excited-state QM/MM molecular dynamics simulations

On-the-fly excited-state quantum mechanics/molecular mechanics molecular dynamics (QM/MM-MD) simulations of thymine in aqueous solution are performed to investigate the role of solvent water molecules on the nonradiative deactivation process. The complete active space second-order perturbation theory (CASPT2) method is employed for a thymine molecule as the QM part in order to provide a reliable description of the excited-state potential energies. It is found that, in addition to the previously reported deactivation pathway involving the twisting of the C-C double bond in the pyrimidine ring, another efficient deactivation pathway leading to conical intersections that accompanies the out-of-plane displacement of the carbonyl group is observed in aqueous solution. Decay through this pathway is not observed in the gas phase simulations, and our analysis indicates that the hydrogen bonds with solvent water molecules play a key role in stabilizing the potential energies of thymine in this additional decay pathway.

QM/MM investigations of organic chemistry oriented questions

About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.

ABSORPTION SPECTRA OF NUCLEIC ACID BASES IN WATER ENVIRONMENT: INSIGHTS INTO FROM COMBINED QM/MM AND CLUSTER-CONTINUUM MODEL CALCULATIONS

Electronic spectra of uracil, thymine, adenine, guanine, and cytosine in the gas phase and aqueous solution have been studied by extensive time-dependent density functional calculations. Calculations show that the Quantum mechanics/molecular mechanics (QM/MM) geometry optimization based on the molecular dynamics (MD) equilibrated configuration can locate an optimal solvated cluster for the base solvation, and the combined QM/MM and cluster-continuum computational protocol is capable of handling the solvent effect on the excited states of nucleic acid bases and providing realistic absorption spectra in water environment with relatively low computational costs. Generally, the vertical excitation energies in aqueous solution by PCM/TD-X3LYP calculations show excellent agreement with the experimental observations and the maximum deviation is less than 0.2 eV. The present results reveal that the hydrogen bond network around the excited-state base and its dipole moment change may remarkably modify the absorption spectra of nucleic acid bases in aqueous solution.

The role of molecular conformation and polarizable embedding for one- and two-photon absorption of disperse orange 3 in solution

Solvent effects on the one- and two-photon absorption (1PA and 2PA) of disperse orange 3 (DO3) in dimethyl sulfoxide (DMSO) are studied using a discrete polarizable embedding (PE) response theory. The scheme comprises a quantum region containing the chromophore and an atomically granulated classical region for the solvent accounting for full interactions within and between the two regions. Either classical molecular dynamics (MD) or hybrid Car-Parrinello (CP) quantum/classical (QM/MM) molecular dynamics simulations are employed to describe the solvation of DO3 in DMSO, allowing for an analysis of the effect of the intermolecular short-range repulsion, long-range attraction, and electrostatic interactions on the conformational changes of the chromophore and also the effect of the solute-solvent polarization. PE linear response calculations are performed to verify the character, solvatochromic shift, and overlap of the two lowest energy transitions responsible for the linear absorption spectrum of DO3 in DMSO in the visible spectral region. Results of the PE linear and quadratic response calculations, performed using uncorrelated solute-solvent configurations sampled from either the classical or hybrid CP QM/MM MD simulations, are used to estimate the width of the line shape function of the two electronic lowest energy excited states, which allow a prediction of the 2PA cross-sections without the use of empirical parameters. Appropriate exchange-correlation functionals have been employed in order to describe the charge-transfer process following the electronic transitions of the chromophore in solution.