Explicit Solvent Model Research Articles

Targeted design of advanced electrocatalysts by machine learning

Exploring the production and application of clean energy has always been the core of sustainable development. As a clean and sustainable technology, electrocatalysis has been receiving widespread attention. It is crucial to achieve efficient, stable and cheap electrocatalysts. However, the traditional “trial and error” method is time-consuming, laborious and costly. In recent years, with the significant increase in computing power, computations have played an important role in electrocatalyst design. Nevertheless, it is still difficult to search for advanced electrocatalysts in the vast chemical space through traditional density functional theory (DFT) computations. Fortunately, the development of machine learning and interdisciplinary integration will inject new impetus into targeted design of electrocatalysts. Machine learning is able to predict electrochemical performances with an accuracy close to DFT. Here we provide an overview of the application of machine learning in electrocatalyst design, including the prediction of structure, thermodynamic properties and kinetic barriers. We also discuss the potential of explicit solvent model combined with machine learning molecular dynamics in this field. Finally, the favorable circumstances and challenges are outlined for the future development of machine learning in electrocatalysis. The studies on electrochemical processes by machine learning will further realize targeted design of high-efficiency electrocatalysts.

Beyond Continuum Solvent Models in Computational Homogeneous Catalysis

In homogeneous catalysis solvent is an inherent part of the catalytic system. As such, it must be considered in the computational modeling. The most common approach to include solvent effects in quantum mechanical calculations is by means of continuum solvent models. When they are properly used, average solvent effects are efficiently captured, mainly those related with solvent polarity. However, neglecting atomistic description of solvent molecules has its limitations, and continuum solvent models all alone cannot be applied to whatever situation. In many cases, inclusion of explicit solvent molecules in the quantum mechanical description of the system is mandatory. The purpose of this article is to highlight through selected examples what are the reasons that urge to go beyond the continuum models to the employment of micro-solvated (cluster-continuum) of fully explicit solvent models, in this way setting the limits of continuum solvent models in computational homogeneous catalysis. These examples showcase that inclusion of solvent molecules in the calculation not only can improve the description of already known mechanisms but can yield new mechanistic views of a reaction. With the aim of systematizing the use of explicit solvent models, after discussing the success and limitations of continuum solvent models, issues related with solvent coordination and solvent dynamics, solvent effects in reactions involving small, charged species, as well as reactions in protic solvents and the role of solvent as reagent itself are successively considered.

Hydration and Charge-Transfer Effects of Alkaline Earth Metal Ions Binding to a Carboxylate Anion, Phosphate Anion, and Guanine Nucleobase.

To investigate the ability of alkaline earth metal ions to tune ion-mediated DNA adsorption, hydrated Mg2+, Ca2+, Sr2+, and Ba2+ ions bound to a carboxylate anion, phosphate anion, and guanine nucleobase were modeled using density functional theory (DFT) and a combined explicit and continuum solvent model. The large first solvation shell of Ba2+ requires a larger solute cavity defined by a solvent-accessible surface, which is used to model all hydrated ions. Alkaline earth metal ions bind indirectly or directly to each binding site. DFT binding energies decrease with increasing ion size, which is likely due to ion size and hydration structure, rather than quantum effects such as charge transfer. However, charge transfer explains weaker ion binding to guanine compared to phosphate or carboxylate. Overall, carboxylate and phosphate anions are expected to compete equally for hydrated Mg2+, Ca2+, Sr2+, and Ba2+ ions and larger alkaline earth metal ions may induce weaker ion-mediated adsorption. The ion size and hydration structure of alkaline earth metal ions may effectively tune ion-mediated adsorption processes, such as DNA adsorption to functionalized surfaces.

Theoretical sight into hydrogen bond interactions between arsenious acid and thiols in aqueous and HEPES solutions

Thiols compounds can be used as monomers of arsenious acid (H3AsO3) molecular-imprinted polymers to specifically recognize arsenic owing to the high affinity between arsenic and thiol. However, the recognition and binding interaction mechanisms between arsenious acid and thiol monomers remain unclear. Herein, the mechanisms of binding interaction between H3AsO3 and DTT/DTE in aqueous solution and HEPES solution were studied by quantum-chemistry calculations of density functional theory with dispersion correction (DFT-D). The most stable configurations of H3AsO3-DTT/DTE complex, connecting with O···H-O and S···H-O hydrogen bonds in the form of double-teeth were found out. In aqueous solution and HEPES solution, with polarizable continuum model, the calculated binding energies show that H3AsO3 has larger affinity towards DTT than DTE. However, in the explicit solvent model where HEPES molecule indeed participates in the hydrogen-bond binding, H3AsO3 combining with DTE (HEPES-H3AsO3-DTE) is more favorable than with DTT (HEPES-H3AsO3-DTT), which agrees well with experimental results. This finding suggests the effect of buffer solution cannot be ignored when selecting monomers for molecular-imprinted polymers. Reduced density gradient method reveals that the binding interactions are composed of hydrogen bonds, Van Der Waals force and repulsion force, while hydrogen bonds play a dominant role. Furthermore, the essence of those hydrogen bonds is identified to be electrostatic force in nature.

Unravelling Constant pH Molecular Dynamics in Oligopeptides with Explicit Solvation Model.

An accurate description of the protonation state of amino acids is essential to correctly simulate the conformational space and the mechanisms of action of proteins or other biochemical systems. The pH and the electrochemical environments are decisive factors to define the effective pKa of amino acids and, therefore, the protonation state. However, they are poorly considered in Molecular Dynamics (MD) simulations. To deal with this problem, constant pH Molecular Dynamics (cpHMD) methods have been developed in recent decades, demonstrating a great ability to consider the effective pKa of amino acids within complex structures. Nonetheless, there are very few studies that assess the effect of these approaches in the conformational sampling. In a previous work of our research group, we detected strengths and weaknesses of the discrete cpHMD method implemented in AMBER when simulating capped tripeptides in implicit solvent. Now, we progressed this assessment by including explicit solvation in these peptides. To analyze more in depth the scope of the reported limitations, we also carried out simulations of oligopeptides with distinct positions of the titratable amino acids. Our study showed that the explicit solvation model does not improve the previously noted weaknesses and, furthermore, the separation of the titratable amino acids in oligopeptides can minimize them, thus providing guidelines to improve the conformational sampling in the cpHMD simulations.

Machine learning implicit solvation for molecular dynamics.

Accurate modeling of the solvent environment for biological molecules is crucial for computational biology and drug design. A popular approach to achieve long simulation time scales for large system sizes is to incorporate the effect of the solvent in a mean-field fashion with implicit solvent models. However, a challenge with existing implicit solvent models is that they often lack accuracy or certain physical properties compared to explicit solvent models as the many-body effects of the neglected solvent molecules are difficult to model as a mean field. Here, we leverage machine learning (ML) and multi-scale coarse graining (CG) in order to learn implicit solvent models that can approximate the energetic and thermodynamic properties of a given explicit solvent model with arbitrary accuracy, given enough training data. Following the previous ML-CG models CGnet and CGSchnet, we introduce ISSNet, a graph neural network, to model the implicit solvent potential of mean force. ISSNet can learn from explicit solvent simulation data and be readily applied to molecular dynamics simulations. We compare the solute conformational distributions under different solvation treatments for two peptide systems. The results indicate that ISSNet models can outperform widely used generalized Born and surface area models in reproducing the thermodynamics of small protein systems with respect to explicit solvent. The success of this novel method demonstrates the potential benefit of applying machine learning methods in accurate modeling of solvent effects for in silico research and biomedical applications.

BEP-Like Correction of Nonequilibrium Thermodynamic Parameters of the Solvent-Assisted Reactions: The DFT and Ab Initio Study of Hydration, Peroxidation, and Enolization of Acetone and 1,1,1-Trifluoroacetone in Aqueous Solutions.

The mechanisms of enolization and reactions of nucleophilic addition to carbonyl compounds were analyzed by density functional theory (DFT) (PBE1PBE) and ab initio (DLPNO-CCSD(T)) level of theory using the interaction of water and hydrogen peroxide with acetone and 1,1,1-trifluoroacetone (TFA) as the reference reactions. The transition states of the studied reactions were localized within the integrated approach that includes both the dielectric continuum theory (polarizable continuum model (PCM)) and the cyclic or two-cluster explicit solvation models. The considered models provide proton transfer in the enolization, hydration, and peroxidation reactions by the Grotthuss mechanism. It is shown that the calculated activation parameters at a sufficiently high level of theory and a sufficiently flexible solvation model can be additionally refined using the Bell-Evans-Polanyi (BEP)-like correction (in a form of the Bell-Evans-Polanyi equation), which is linear scaling of the model potential energy surface according to the equilibrium parameters of the reference reaction (experiment or high-level calculation). Quite good correspondence of the corrected and reference activation parameters and the lower sensitivity of the calculation results to the choice of the solvation model indicate the high reliability of the proposed BEP-like correction technique.

Theoretical insight into the conversion of glucose to 5-hydroxymethylfurfural in subcritical water

The reaction mechanism of the isomerization of glucose to fructose and further dehydration of fructose to 5-hydroxymethylfurfural (5-HMF) in subcritical water was investigated by the dispersion-corrected density functional theory (DFT-D) method with Dmol3 package in Materials Studio. The implicit solvent model was used to evaluate the bulk solvation under the conductor-like screening model (COSMO) approach, in which a dielectric constant (ɛ) of 27 was used to represent the subcritical water at 523.15 K. The explicit solvent model was adopted with a hybrid micro-solvation-continuum approach, to indicate the micro-solvation by explicit H2O molecules and the bulk solvation with ɛ = 27. The calculation results indicate that explicit H2O molecules participate in the reaction and catalytically promotes the proton transfer processes, suggesting that the explicit solvent model is preferable to the implicit solvent model to represent the conversion of 5-HMF in subcritical water. The isomerization of glucose to fructose is exothermic by 5.26 kcal/mol, where the isomerization of open-chain glucose to enol form is the rate-determining step, with the activation energy of 33.89 kcal/mol; the free energy of transition state configuration depends upon both the difficulty in α–H extraction of open-chain glucose and the stability of formed carbocation. In contrast, the hydration of fructose to 5-HMF is exothermic by 12.93 kcal/mol and the first hydration is the rate-determining step, with the activation energy of 50.59 kcal/mol; the free energy of transition state configuration is determined by the stability of carbocation formed by the dehydration of protonated OH group at C(2) site of fructose. This work discloses the promoting effect of Brønsted base on the isomerization of glucose to fructose and that of Brønsted acid on the dehydration of fructose to 5-HMF, which may provide certain clues to the modification of catalytic sites and the selection of solvent in the conversion of glucose to 5-HMF.

Forcefield evaluation and accelerated molecular dynamics simulation of Zn(II) binding to N-terminus of amyloid-β

We report conventional and accelerated molecular dynamics simulation of Zn(II) bound to the N-terminus of amyloid-β. By comparison against NMR data for the experimentally determined binding mode, we find that certain combinations of forcefield and solvent model perform acceptably in describing the size, shape and secondary structure, and that there is no appreciable difference between implicit and explicit solvent models. We therefore used the combination of ff14SB forcefield and GBSA solvent model to compare the result of different binding modes of Zn(II) to the same peptide, using accelerated MD to enhance sampling and comparing the free peptide simulated in the same way. We show that Zn(II) imparts significant rigidity to the peptide, disrupts the secondary structure and pattern of salt bridges seen in the free peptide, and induces closer contact between residues. Free energy surfaces in 1 or 2 dimensions further highlight the effect of metal coordination on peptide’s spatial extent. We also provide evidence that accelerated MD provides improved sampling over conventional MD by visiting as many or more configurations in much shorter simulation times.

Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles.

Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of forward models that relate measured SAXS intensities and structural features, and that are suitable to model either explicit-solvent effects or solute dynamics, have been proposed in the past years. Here, we introduce an approach that integrates atomistic molecular dynamics simulations and SAXS experiments to reconstruct RNA structural ensembles while simultaneously accounting for both RNA conformational dynamics and explicit-solvent effects. Our protocol exploits SAXS pure-solute forward models and enhanced sampling methods to sample an heterogenous ensemble of structures, with no information towards the experiments provided on-the-fly. The generated structural ensemble is then reweighted through the maximum entropy principle so as to match reference SAXS experimental data at multiple ionic conditions. Importantly, accurate explicit-solvent forward models are used at this reweighting stage. We apply this framework to the GTPase-associated center, a relevant RNA molecule involved in protein translation, in order to elucidate its ion-dependent conformational ensembles. We show that (a) both solvent and dynamics are crucial to reproduce experimental SAXS data and (b) the resulting dynamical ensembles contain an ion-dependent fraction of extended structures.

Theoretical estimates of equilibrium sulfur isotope effects among aqueous polysulfur and associated compounds with applications to authigenic pyrite formation and hydrothermal disproportionation reactions

Inorganic polysulfur compounds (polysulfides, Sx2-; polysulfur radical ions, Sx·-; thiosulfate, S2O32-; polythionate, SxO62-; elemental sulfur, e.g. S8) participate in numerous geochemical processes related to the sulfur cycle. These include authigenic pyrite formation in sediments undergoing early stages of diagenesis, reactions associated with magmatic-hydrothermal processes, and numerous other aquatic sulfur redox processes (e.g., pyrite and sulfide oxidation). Sulfur isotope fractionations among many of these and associated compounds (e.g., H2S, HSO4-) are either unknown or unconstrained over wide ranges of temperatures. We present theoretical estimates of equilibrium sulfur isotope fractionation factors among aqueous polysulfur compounds (including select polysulfides, polysulfur radical anions, and polythionates) and select aqueous sulfide and sulfate compounds that correspond to all three stable isotope ratios of sulfur (33S/32S, 34S/32S, 36S/32S). Our estimates are based on electronic structure calculations performed at the B3LYP/6–31+G(d,p) level of theory and basis set implemented in concert with an explicit solvation model whereby molecules are encapsulated in water clusters of varying size (30–52 H2O) to simulate the aqueous solvation environment. These calculations yield relatively small magnitude fractionation factors between aqueous polysulfides, polysulfur radicals, and reduced sulfur moieties in polythionates relative to the aqueous sulfide compounds but reveal numerous crossovers that result in non-intuitive temperature dependencies. Our predictions of 34S/32S-based fractionation factors among aqueous sulfur compounds generally agree with previous experimental constraints where available within estimated uncertainties (e.g., HSO4-/H2S(aq), H2S(aq)/HS-, HSO4-/S0, H2S(aq)/S0). We use our calculations to explore equilibrium isotope fractionations among polysulfur and sulfide compounds that are precursors to authigenic pyrite in the framework of established mechanisms (e.g., the polysulfide mechanism). We examine possible explanations for why pyrite formation may be associated with relatively small isotope fractionation with respect to precursor aqueous sulfur compounds. We additionally use our theoretical calculations to constrain multiple sulfur isotope (33S/32S, 34S/32S, 36S/32S) mass balance models associated with the abiotic hydrolytic disproportionation of intermediate sulfur compounds (SO2, S8, S3·-) relevant to hydrothermal-magmatic-volcanic systems in order to illustrate the potential for subtle but potentially resolvable effects expressed in values of Δ33S and Δ36S associated with these processes. We apply a SO2 disproportionation mass balance model based on previous work but newly constrained by our theoretical calculations to (hyper-) acid crater lakes associated with active volcanoes, and newly highlight the potential for the utility of multiple sulfur isotope analyses in volcanic gas monitoring and constraining sulfur cycling processes in such systems.

Helix-coil transition and conformational deformity in Aβ 42-monomer: a case study using the Zn2+ cation

The metal ions (like Fe Zn2+, Cu) are known to influence the amyloid beta (Aβ) aggregation. In this study, we have examined the conformational and dynamical changes during the coordination of Aβ-monomer with the Zn ion using all-atom molecular dynamics (MD) simulations using explicit solvent models. We have probed the unfolding of the full-length Aβ 42 monomer both inclusive and exclusive of the Zn cation, with 1:1 ratio of the peptide and the Zn cation. The inclusion of the Zn cation shows differential intra-peptide interactions which has been probed using various analyses. The Helix – Coil transition of the wild type A monomer is studied using the steered molecular dynamics simulations by taking the end-to-end C-α distance across the peptide. This gives an idea of the unequal intra – peptide and peptide – water interactions being found across the length of the Aβ monomer. The transition of an α-helix dominated wild-type (WT) Aβ structure to the unfolded coil structure gives significant evidence of the intra-peptide hydrogen bonding shifts in the presence of the Zn cation. This accounts for the structural and the dynamical variations that take place in the Aβ monomer in the presence of the Zn cation to mimic the conditions/environment at the onset of fibrillation. Communicated by Ramaswamy H. Sarma

SN1 reaction mechanisms of tert-butyl chloride in aqueous solution: What can be learned from reaction path search calculations and trajectory calculations for small hydrated clusters?

The SN1 reaction mechanisms of tert-butyl chloride (t-BuCl) in aqueous solution were studied using a small hydrated cluster model, t-BuCl·(H2O)n (n = 1–3), and density functional theory calculations. Our explicit solvation model is combined with a polarizable continuum model. Reaction path search calculations yielded various transition state structures associated with configurations to form retained and inverted t-BuOH (t-BuOH2+) products, respectively. Intrinsic reaction coordinate (IRC) analyses revealed that the retention process occurs via a three-step mechanism comprising initial CCl elongation, subsequent translational motion of the Cl−·(H2O)n moiety, and finally CO bond formation, while the inversion process essentially occurs via a concerted mechanism. To further elucidate the differences in the reaction mechanism between retention and inversion, on-the-fly trajectories were integrated starting from the identified transition state structures. The calculated trajectories exhibited non-IRC dynamic behavior.

Quantum chemical study of the mechanisms, kinetics, and ecotoxicity assessment of OH radical-initiated reactions of 2,2′,4,4′,5,5′ -hexabrominated diphenyl ether (BDE-153) in atmosphere and wastewater

2,2′,4,4′,5,5′-hexabrominated diphenyl ether (BDE-153) and its OH radical addition products are considered potentially harmful to ecological systems. Therefore, the oxidation reactions mechanisms of BDE-153 initiated by OH radical, the reaction kinetics and the ecotoxicity of BDE-153 assessment in the gas and the aqueous phase were investigated using quantum chemical methods. It is more feasible for the OH radical to add at the nonbromine substituted carbon atoms of the aromatic ring in the BDE-153 molecule to create OH addition intermediates. The secondary reactions involving OH addition intermediates in the presence of O2/NO would generate preferred tribromophenol and OH-addition products. Most of the transformation products are still toxic to aquatic organisms. The total and individual rate constants were evaluated by using the KiSThelP program in a suitable temperature range (198–338 K) and a pressure of 1 atm. At 298 K and 1 atm, the total rate constants in atmosphere and wastewater are 2.90 × 10-13 cm3 molecule-1 s−1 and 9.61 × 106 M−1 s−1, and the half-lives are 39.9 days and 72.1–7.21 × 1010 s, respectively. The implicit and explicit solvent models were used to examine the solvent effect on the total reaction. These results clarify the transformation mechanism, atmospheric fate, and ecotoxicity of BDE-153 in advanced oxidation processes. The calculations provided a basis for designing experimental and industrial applications of BDE-153.

A Simple Explicit-Solvent Model of Polyampholyte Phase Behaviors and Its Ramifications for Dielectric Effects in Biomolecular Condensates.

Biomolecular condensates such as membraneless organelles, underpinned by liquid-liquid phase separation (LLPS), are important for physiological function, with electrostatics, among other interaction types, being a prominent force in their assembly. Charge interactions of intrinsically disordered proteins (IDPs) and other biomolecules are sensitive to the aqueous dielectric environment. Because the relative permittivity of protein is significantly lower than that of water, the interior of an IDP condensate is expected to be a relatively low-dielectric regime, which aside from its possible functional effects on client molecules should facilitate stronger electrostatic interactions among the scaffold IDPs. To gain insight into this LLPS-induced dielectric heterogeneity, addressing in particular whether a low-dielectric condensed phase entails more favorable LLPS than that posited by assuming IDP electrostatic interactions are uniformly modulated by the higher dielectric constant of the pure solvent, we consider a simplified multiple-chain model of polyampholytes immersed in explicit solvents that are either polarizable or possess a permanent dipole. Notably, simulated phase behaviors of these systems exhibit only minor to moderate differences from those obtained using implicit-solvent models with a uniform relative permittivity equals to that of pure solvent. Buttressed by theoretical treatments developed here using random phase approximation and polymer field-theoretic simulations, these observations indicate a partial compensation of effects between favorable solvent-mediated interactions among the polyampholytes in the condensed phase and favorable polyampholyte-solvent interactions in the dilute phase, often netting only a minor enhancement of overall LLPS propensity from the very dielectric heterogeneity that arises from the LLPS itself. Further ramifications of this principle are discussed.

A theoretical study on structures of an epigallocatechin-3-O-gallate/caffeine complex in aqueous solution

Complexations between aromatic compounds often affect food quality. For example, it is well-known that catechins form complexes with caffeine. Both are major compounds in green tea but the structures of their complexes in aqueous solution have not been clarified. In this study, we elucidated the structure of the epigallocatechin-3-O-gallate (EGCg)/caffeine complex in aqueous solution by DFT calculations and NMR experiments. A detailed analysis of 1H NMR titration data revealed that EGCg forms a 1:1 complex with caffeine, and our combination of the DFT calculations and NOESY experiments showed that EGCg binds with caffeine in the space surrounded by the axial galloyloxy group and the A-ring. Aromatic/aromatic and CH/π interactions are the major intermolecular forces in the complex. Furthermore, calculations using an explicit solvent model suggested that water molecules stabilize the EGCg/caffeine complex by hydration and intermolecular cross-linking.

Solvent effects on Stokes shifts, and NLO response of thieno[3,4-b]pyrazine: A comprehensive QM/MM investigation

The analysis of solvent effects on the fluorescence and nonlinear optical (NLO) response of thieno[3,4-b]pyrazine was performed using the sequential Monte Carlo/Quantum Mechanics (s-MC/QM) approach. For this, the theoretical analysis was based on time-dependent density functional methods considering several implicit and explicit solvent models. Explicit solvent models include either electrostatic or non-electrostatic intermolecular forces like Keeson, London, and Debye interactions. The first absorption transition occurs with a charge transfer from the pyrazine to the thieno ring leading to a decrease in the molecular dipole moment by changing the average number of hydrogen-bonds on nitrogen and sulfur atoms. Including the solvent effects, this leads to a strong Stokes shift (~110 nm), showing that the title compound and its derivatives are promising for solar cells or even as a biological marker. Regarding the NLO response of the chromophore, the results indicate that the electronic-correlation (EC) plays a fundamental role for the first hyperpolarizability (β) but the solvent effect is negligible. The second-order Møller-Plesset perturbation theory and the long-range and dispersion corrected DFT-based methods show that EC corrections can improve the description of β by ca. 150% when compared with the Hartree–Fock approximation.

Nuclear quantum effects on autoionization of water isotopologs studied by ab initio path integral molecular dynamics.

In this study, we investigate the nuclear quantum effects (NQEs) on the acidity constant (pKA) of liquid water isotopologs under the ambient condition by path integral molecular dynamics (PIMD) simulations. We compared simulations using a fully explicit solvent model with a classical polarizable force field, density functional tight binding, and ab initio density functional theory, which correspond to empirical, semiempirical, and ab initio PIMD simulations, respectively. The centroid variable with respect to the proton coordination number of a water molecule was restrained to compute the gradient of the free energy, which measures the reversible work of the proton abstraction for the quantum mechanical system. The free energy curve obtained by thermodynamic integration was used to compute the pKA value based on probabilistic determination. This technique not only reproduces the pKA value of liquid D2O experimentally measured (14.86) but also allows for a theoretical prediction of the pKA values of liquid T2O and aqueous HDO and HTO, which are unknown due to their scarcity. It is also shown that the NQEs on the free energy curve can result in a downshift of 4.5 ± 0.9 pKA units in the case of liquid water, which indicates that the NQEs plays an indispensable role in the absolute determination of pKA. The results of this study can help inform further extensions into the calculation of the acidity constants of isotope substituted species with high accuracy.

Quantum Chemical Simulation of the Qy Absorption Spectrum of Zn Chlorin Aggregates for Artificial Photosynthesis.

Zn chlorin (Znchl) is easy to synthesize and has similar optical properties to those of bacteriochlorophyll c in the nature, which is expected to be used as a light-harvesting antenna system in artificial photosynthesis. In order to further explore the optical characteristics of Znchl, various sizes of a parallel layered Znchl-aggregate model and the THF-Znchl explicit solvent monomer model were constructed in this study, and their excited state properties were simulated by using time-dependent density functional theory (TDDFT) and exciton theory. For the Znchl monomer, with a combination of the explicit solvent model and the implicit solvation model based on density (SMD), the calculated excitation energy agreed very well with the experimental one. The Znchl aggregates may be simplified to a Zn36 model to reproduce the experimental absorption spectrum by the Förster coupling theory. The proposed Znchl aggregate model provides a good foundation for the future exploration of other properties of Znchl and simulations of artificial light-harvesting antennas. The results also indicate that J-aggregrates along z-direction, due to intermolecular coordination bonds, are the dominant factor in extending the band of Znchl into the near infrared region.

Modeling solvation effects on absorption and fluorescence spectra of indole in aqueous solution.

Modeling the optical spectra of molecules in solution presents a challenge, so it is important to understand which of the solvation effects (i.e., electrostatics, mutual polarization, and hydrogen bonding interactions between solute and solvent molecules) are crucial in reproducing the various features of the absorption and fluorescence spectra and to identify a sufficient theoretical model that accurately captures these effects with minimal computational cost. In this study, we use various implicit and explicit solvation models, such as molecular dynamics coupled with non-polarizable and polarizable force fields, as well as Car-Parrinello molecular dynamics, to model the absorption and fluorescence spectra of indole in aqueous solution. The excited states are computed using the equation of motion coupled cluster with single and double excitations combined with the effective fragment potential to represent water molecules, which we found to be a computationally efficient approach for modeling large solute-solvent clusters at a high level of quantum theory. We find that modeling mutual polarization, compared to other solvation effects, is a dominating factor for accurately reproducing the position of the peaks and spectral line shape of the absorption spectrum of indole in solution. We present an in-depth analysis of the influence that different solvation models have on the electronic excited states responsible for the features of the absorption spectra. Modeling fluorescence is more challenging since it is hard to reproduce even the correct emitting state, and force field parameters need to be re-evaluated.