Martini-Based Coarse-Grained Soil Organic Matter Model Derived from Atomistic Simulations.

The significance of soil organic matter (SOM) in environmental contexts, particularly its role in pollutant adsorption, has prompted an increased utilization of molecular simulations to understand microscopic interactions. This study introduces a coarse-grained SOM model, parametrized within the framework of the versatile Martini 3 force field. Utilizing models generated by the Vienna Soil Organic Matter Modeler 2, which constructs humic substance systems from a fragment database, we employed Swarm-CG to parametrize the fragments and subsequently assembled them into macromolecules. Direct Boltzmann inversion (DBI) facilitated the determination of bonded parameters between fragments. The parametrization yielded favorable agreement in the radius of gyration and solvent-accessible surface area. Transfer free energies exhibited a strong correlation with hexadecane-water and chloroform-water values, albeit deviations were noted for octanol-water values. Comparing densities of modeled Leonardite humic acid systems at coarse-grained and atomistic levels revealed promising agreement, particularly at higher water concentrations. The DBI approach effectively reproduced average values of bonded interactions between fragments. Radial distribution functions between carboxylate groups and calcium ions showed partial agreement, however, reproducing certain peaks was challenging due to fixed bead sizes. Detailed analysis of atomistic systems revealed different configurations between the groups, explaining discrepancies. The present contribution provides a comprehensive insight into the properties, strengths, and weaknesses of the coarse-grained SOM model, serving as a foundation for future investigations encompassing pollutant interactions and varied SOM compositions.

Deciphering competitive interactions: Phosphate and organic matter binding on goethite through experimental and theoretical insights.

The adsorption of phosphorus (P) onto active soil surfaces plays a pivotal role in immobilizing P, thereby influencing soil fertility and the filter function of soil to protect freshwater systems from eutrophication. Competitive anions, such as organic matter (OM), significantly affect the strength of this P-binding, eventually controlling P mobility and release, but surprisingly, these processes are insufficiently understood at the molecular level. In this study, we provide a molecular-level perspective on the influence of OM on P binding at the goethite-water interface using a combined experimental-theoretical approach. By examining the impact of citric acid (CIT) and histidine (HIS) on the adsorption of orthophosphate (OP), glycerol phosphate (GP), and inositol hexaphosphate (IHP) through adsorption experiments and molecular dynamics simulations, we address fundamental questions regarding P binding trends, OM interaction with the goethite surface, and the effect of OM on P adsorption. Our findings reveal the complex nature of P adsorption on goethite surfaces, where the specific OM, treatment conditions (covering the surface with OM or simultaneous co-adsorption), and initial concentrations collectively shape these interactions. P adsorption on goethite exhibits a binding strength increasing in the order of GP < OP < IHP. Crucially, this trend remains consistent across all adsorption experiments, regardless of the presence or absence of OM, CIT, or HIS, and irrespective of the specific treatment method. Notably, OP is particularly susceptible to inhibition by OM, while adsorption of GP depends on specific OM treatments. Despite being less sensitive to OM, IHP shows reduced adsorption, especially at higher initial P concentrations. Of significance is the strong inhibitory effect of CIT, particularly evident when the surface is pre-covered, resulting in a substantial 70 % reduction in OP adsorption compared to bare goethite. The sequence of goethite binding affinity to P and OM underscores a higher affinity of CIT and HIS compared to OP and GP, suggesting that OM can effectively compete with both OP and GP and replace them at the surface. In contrast, the impact of OM on IHP adsorption appears insignificant, as IHP exhibits a higher affinity than both CIT and HIS towards the goethite surface. The coverage of goethite surfaces with OM results in the blocking of active sites and the generation of an unfavorable electric potential and field, inhibiting anion adsorption and consequently reducing P binding. It is noteworthy that electrostatic interactions predominantly contribute more to the binding of P and OM to the surface compared to dispersion interactions.

Efficient D-π-π-A-Type Dye Sensitizer Based on a Benzothiadiazole Moiety: A Computational Study.

The design of highly efficient sensitizers is one of the most significant areas in dye-sensitized solar cell (DSSC) research. We studied a series of benzothiadiazole-based D-π-π-A organic dyes, putting emphasis on the influence of the donor moiety on the DSSC's efficiency. Using (linear-response time-dependent) density functional theory ((TD)DFT)) with the CAM-B3LYP functional, different donor groups were characterized in terms of electronic absorption spectra and key photovoltaic parameters. As a reference, a dye was considered that had a benzothiadiazole fragment linked via thiophene rings to a diphenylamine donor and a cyanoacrylic-acid acceptor. The different systems were first studied in terms of individual performance parameters, which eventually aggregated into power conversion efficiency. Only the amino-substituted species showed a modest increase, whereas the dimethylamino case showed a decrease.

Advances in understanding the phosphate binding to soil constituents: A Computational Chemistry perspective.

Phosphorus (P) is an indispensable element to all forms of life and its efficient use in fertilizers is one of the conditions for food security. The efficiency of P fertilizers is affected by P mobilization and P fixation, both depending on the P binding strength to soil constituents. This review provides an overview of the P binding to soil constituents, especially to P-fixing mineral surfaces and its investigation using state-of-the-art Computational Chemistry (CC). A particular focus will be on goethite (α-FeOOH), which is highly significant in the context of P fixation in soils, given its prevalence, high susceptibility to P, and wide distribution across both oxic and anoxic environments. First, a brief overview will be given on experimental efforts related to the P adsorption at mineral surfaces and the factors affecting this process. Here, we will discuss the process of P adsorption, with a focus on important factors that influence this process, such as pH, surface crystallinity and morphology, competing anions, and electrolyte solutions. We will also explore the various techniques used to study this process and investigate the resulting binding motifs. Next, a brief introduction into common CC methods, techniques, and applications is presented, highlighting the advantages and limitations of each approach. Then, a comprehensive discussion of a wide range of the most relevant computational studies related to the phosphate binding issue will be provided. This will be followed by the main part of this review which is focusing on a possible strategy to cope with the soil heterogeneity by breaking down the complexity of P behavior in soil into well-defined models that can be discussed in terms of particular key factors. Hence, different molecular model systems and molecular simulations are introduced to reveal the P binding to soil organic matter (SOM), metal ions, and mineral surfaces. Simulation results provided an in-depth understanding of the P binding problem and explained at a molecular level the effects of surface plane, binding motif, kind and valency of metal ions, SOM composition, water, pH, and redox potential on the P binding in soil. On this basis, an overall molecular picture of P binding in soil can be then obtained by combining results for the different models. Eventually, challenges and further modifications of the existing molecular modeling approaches are discussed, such as steps necessary to bridge the molecular with the mesoscale.

A Multiconfigurational Wave Function Implementation of the Frenkel Exciton Model for Molecular Aggregates.

We present an implementation of the Frenkel exciton model into the OpenMolcas program package enabling calculations of collective electronic excited states of molecular aggregates based on a multiconfigurational wave function description of the individual monomers. The computational protocol avoids using diabatization schemes and, thus, supermolecule calculations. Additionally, the use of the Cholesky decomposition of the two-electron integrals entering pair interactions enhances the efficiency of the computational scheme. The application of the method is exemplified for two test systems, that is, a formaldehyde oxime and a bacteriochlorophyll-like dimer. For the sake of comparison with the dipole approximation, we restrict our considerations to situations where intermonomer exchange can be neglected. The protocol is expected to be beneficial for aggregates composed of molecules with extended π systems, unpaired electrons such as radicals or transition metal centers, where it should outperform widely used methods based on time-dependent density functional theory.

Formally Exact Simulations of Mesoscale Exciton Diffusion in a Light-Harvesting 2 Antenna Nanoarray.

The photosynthetic apparatus of plants and bacteria combine atomically precise pigment-protein complexes with dynamic membrane architectures to control energy transfer on the 10-100 nm length scales. Recently, synthetic materials have integrated photosynthetic antenna proteins to enhance exciton transport, though the influence of artificial packing on the excited-state dynamics in these biohybrid materials is not fully understood. Here, we use the adaptive hierarchy of pure states (adHOPS) to perform a formally exact simulation of excitation energy transfer within artificial aggregates of light-harvesting complex 2 (LH2) with a range of packing densities. We find that LH2 aggregates support a remarkable exciton diffusion length ranging from 100 nm at a biological packing density to 300 nm at the densest packing previously suggested in an artificial aggregate. The unprecedented scale of these formally exact calculations also underscores the efficiency with which adHOPS simulates excited-state processes in molecular materials.

Janus-type emission from a cyclometalated iron(III) complex.

Although iron is a dream candidate to substitute noble metals in photoactive complexes, realization of emissive and photoactive iron compounds is demanding due to the fast deactivation of their charge-transfer states. Emissive iron compounds are scarce and dual emission has not been observed before. Here we report the FeIII complex [Fe(ImP)2][PF6] (HImP = 1,1'-(1,3-phenylene)bis(3-methyl-1-imidazol-2-ylidene)), showing a Janus-type dual emission from ligand-to-metal charge transfer (LMCT)- and metal-to-ligand charge transfer (MLCT)-dominated states. This behaviour is achieved by a ligand design that combines four N-heterocyclic carbenes with two cyclometalating aryl units. The low-lying π* levels of the cyclometalating units lead to energetically accessible MLCT states that cannot evolve into LMCT states. With a lifetime of 4.6 ns, the strongly reducing and oxidizing MLCT-dominated state can initiate electron transfer reactions, which could constitute a basis for future applications of iron in photoredox catalysis.

Can range-separated functionals be optimally tuned to predict spectra and excited state dynamics in photoactive iron complexes?

Density functional theory is an efficient computational tool to investigate photophysical and photochemical processes in transition metal complexes, giving invaluable assistance in interpreting spectroscopic and catalytic experiments. Optimally tuned range-separated functionals are particularly promising, as they were created to address some of the fundamental deficiencies present in approximate exchange-correlation functionals. In this paper, we scrutinize the selection of optimally tuned parameters and its influence on the excited state dynamics, using the example of the iron complex [Fe(cpmp)2]2+ with push-pull ligands. Various tuning strategies are contemplated based on pure self-consistent DFT protocols, as well as on the comparison with experimental spectra and multireference CASPT2 results. The two most promising sets of optimal parameters are then employed to carry out nonadiabatic surface-hopping dynamics simulations. Intriguingly, we find that the two sets lead to very different relaxation pathways and timescales. While the set of optimal parameters from one of the self-consistent DFT protocols predicts the formation of long-lived metal-to-ligand charge transfer triplet states, the set in better agreement with CASPT2 calculations leads to deactivation in the manifold of metal-centered states, in better agreement with the experimental reference data. These results showcase the complexity of iron-complex excited state landscapes and the difficulty of obtaining an unambiguous parametrization of long-range corrected functionals without experimental input.

Correction: Distinct photodynamics of κ-N and κ-C pseudoisomeric iron(II) complexes.

Correction for 'Distinct photodynamics of κ-N and κ-C pseudoisomeric iron(II) complexes' by Philipp Dierks et al., Chem. Commun., 2021, 57, 6640-6643, https://doi.org/10.1039/D1CC01716K.

Stepwise redox changes alter the speciation and mobilization of phosphorus in hydromorphic soils.

Sustainable engineering and management of hydromorphic arable soils need deep knowledge about the redox-mediated interactions between nutrients and soil colloids. Consequently, we examined the redox-mediated interactions of P with metal oxides and organic carbon (OC) in toe-, mid-, and upper-slope arable soils under dynamic redox changes using geochemical (biogeochemical microcosm), spectroscopic (XANES), and molecular (quantum chemical calculations (QCC)) approaches. We controlled the redox potential (EH) in two directions i.e., 1) slowly oxidizing direction (SOD; EH increased from -286 to +564 mV); and 2) slowly reducing direction (SRD; EH decreased from +564 to -148 mV). In the SOD of all soils, P, Fe2+ and OC mobilized at EH ≤ 200 mV, due to the pH decrease from 7.2 to 4.1 and dissolution of Fe-oxyhydroxides/carbonates, as indicated by the decrease of Fe-P and Ca-P determined by P-K-edge-XANES. At EH > 200 mV, P immobilized due to the strong P binding with Fe3+ as suggested by QCC. In the SRD of mid-slope-soil, P immobilized with decreasing EH, due to pH increase and P retention by aromatic carbon and/or precipitation by carbonates, as supported by increase of organic-P and Ca-P. These findings help for management of P in arable soils.

Strong Exciton-Vibrational Coupling in Molecular Assemblies. Dynamics Using the Polaron Transformation in HEOM Space.

In Frenkel exciton dynamics of aggregated molecules, the polaron transformation (PT) technique leads to decoupling of diagonal elements in the subspace of excited electronic states from vibrations. In this article we describe for the first time how PT becomes applicable in the framework of the "Hierarchical Equations of Motion" (HEOM) approach for treatment of open quantum systems. We extend the concept of formulating operators in HEOM space by deriving hierarchical equations of PT which lead to a shift in the excited state potential energy surface to compensate its displacement. While the assumption of thermal equilibration of the vibrational oscillators, introduced by PT, results in a stationary state in a monomer, in a dimer under the same assumption nonequilibrium dynamics appears because of the interplay of the transfer process and vibrational equilibration. Both vertical transitions generating a vibrationally hot state and initially equilibrated vibrational oscillators evolve toward the same stationary asymptotic state associated with polaron formation. The effect of PT on the dynamics of this process depends on initial excitation and basis representation of the electronic system. The developed approach facilitates a generic formulation of quantum master equations involving perturbative treatment of polaron dynamics.

Distinct photodynamics of κ-N and κ-C pseudoisomeric iron(II) complexes.

Two closely related FeII complexes with 2,6-bis(1-ethyl-1H-1,2,3-triazol-4yl)pyridine and 2,6-bis(1,2,3-triazol-5-ylidene)pyridine ligands are presented to gain new insights into the photophysics of bis(tridentate) iron(ii) complexes. The [Fe(N^N^N)2]2+ pseudoisomer sensitizes singlet oxygen through a MC state with nanosecond lifetime after MLCT excitation, while the bis(tridentate) [Fe(C^N^C)2]2+ pseudoisomer possesses a similar 3MLCT lifetime as the tris(bidentate) [Fe(C^C)2(N^N)]2+ complexes with four mesoionic carbenes.

Site-Selective Real-Time Observation of Bimolecular Electron Transfer in a Photocatalytic System Using L-Edge X-Ray Absorption Spectroscopy*.

Time-resolved X-ray absorption spectroscopy has been utilized to monitor the bimolecular electron transfer in a photocatalytic water splitting system. This has been possible by uniting the local probe and element specific character of X-ray transitions with insights from high-level ab initio calculations. The specific target has been a heteroleptic [IrIII (ppy)2 (bpy)]+ photosensitizer, in combination with triethylamine as a sacrificial reductant and Fe3(CO)12 as a water reduction catalyst. The relevant molecular transitions have been characterized via high-resolution Ir L-edge X-ray absorption spectroscopy on the picosecond time scale and restricted active space self-consistent field calculations. The presented methods and results will enhance our understanding of functionally relevant bimolecular electron transfer reactions and thus will pave the road to rational optimization of photocatalytic performance.

Intraband dynamics and exciton trapping in the LH2 complex of Rhodopseudomonas acidophila.

Over the last several decades, the light-harvesting protein complexes of purple bacteria have been among the most popular model systems for energy transport in excitonic systems in the weak and intermediate intermolecular coupling regime. Despite this extensive body of scientific work, significant questions regarding the excitonic states and the photo-induced dynamics remain. Here, we address the low-temperature electronic structure and excitation dynamics in the light-harvesting complex 2 of Rhodopseudomonas acidophila by two-dimensional electronic spectroscopy. We find that, although at cryogenic temperature energy relaxation is very rapid, exciton mobility is limited over a significant range of excitation energies. This points to the presence of a sub-200 fs, spatially local energy-relaxation mechanism and suggests that local trapping might contribute substantially more in cryogenic experiments than under physiological conditions where the thermal energy is comparable to or larger than the static disorder.

Coarse-grained molecular dynamics simulations of nanoplastics interacting with a hydrophobic environment in aqueous solution.

Nanoplastics (NPs) are emerging threats for marine and terrestrial ecosystems, but little is known about their fate in the environment at the molecular scale. In this work, coarse-grained molecular dynamics simulations were performed to investigate nature and strength of the interaction between NPs and hydrophobic environments. Specifically, NPs were simulated with different hydrophobic and hydrophilic polymers while carbon nanotubes (CNTs) were used to mimic surface and confinement effects of hydrophobic building blocks occurring in a soil environment. The hydrophobicity of CNTs was modified by introducing different hydrophobic and hydrophilic functional groups at their inner surfaces. The results show that hydrophobic polymers have a strong affinity to adsorb at the outer surface and to be captured inside the CNT. The accumulation within the CNT is even increased in presence of hydrophobic functional groups. This contribution is a first step towards a mechanistic understanding of a variety of processes connected to interaction of nanoscale material with environmental systems. Regarding the fate of NPs in soil, the results point to the critical role of the hydrophobicity of NPs and soil organic matter (SOM) as well as of the chemical nature of functionalized SOM cavities/voids in controlling the accumulation of NPs in soil. Moreover, the results can be related to water treatment technologies as it is shown that the hydrophobicity of CNTs and functionalization of their surfaces may play a crucial role in enhancing the adsorption capacity of CNTs with respect to organic compounds and thus their removal efficiency from wastewater.

The effect of N-heterocyclic carbene units on the absorption spectra of Fe(II) complexes: a challenge for theory.

The absorption spectra of five Fe(ii) homoleptic and heteroleptic complexes containing strong sigma-donating N-heterocyclic carbene (NHC) and polypyridyl ligands have been theoretically characterized using a tuned range-separation functional. From a benchmark comparison of the obtained results against other functionals and a multiconfigurational reference, it is concluded that none of the methods is completely satisfactory to describe the absorption spectra. As a compromise using 20% exact exchange, the electronic excited states underlying the absorption spectra are analyzed. The low-lying energy band of all the compounds shows predominant metal-to-ligand charge transfer (MLCT) character while the triplet excited states have metal-centered (MC) nature, which becomes more pronounced with increasing the number of NHC-donor groups. Excited MC states with partial charge transfer to the NHC-donor groups are higher in energy than comparable states without these contributions. The presence of the low-lying MC states prevents the formation of long-lived MLCT states.

Exciton transfer using rates extracted from the "hierarchical equations of motion".

Frenkel exciton population dynamics of an excitonic dimer is studied by comparing the results from a quantum master equation involving rates from second-order perturbative treatment with respect to the excitonic coupling with the non-perturbative results from "Hierarchical Equations of Motion" (HEOM). By formulating generic Liouville-space expressions for the rates, we can choose to evaluate them either via HEOM propagations or by applying the cumulant expansion. The coupling of electronic transitions to bath modes is modeled either as overdamped oscillators for the description of thermal bath components or as underdamped oscillators to account for intramolecular vibrations. Cases of initial nonequilibrium and equilibrium vibrations are discussed. In the case of HEOM, initial equilibration enters via a polaron transformation. Pointing out the differences between the nonequilibrium and equilibrium approach in the context of the projection operator formalism, we identify a further description, where the transfer dynamics is driven only by fluctuations without involvement of dissipation. Despite this approximation, this approach can also yield meaningful results in certain parameter regimes. While for the chosen model, HEOM has no technical advantage for evaluation of the rate expressions compared to cumulant expansion, there are situations where only evaluation with HEOM is applicable. For instance, a separation of reference and interaction Hamiltonian via a polaron transformation to account for the interplay between Coulomb coupling and vibrational oscillations of the bath at the level of a second-order treatment can be adjusted for a treatment with HEOM.

Molecular level picture of the interplay between pH and phosphate binding at the goethite-water interface.

The soil pH plays a substantial role in controlling phosphorus (P) adsorption and mobilization. These processes are strongly affected by the phosphate interaction strength with P-fixing soil minerals such as goethite. The target of the current contribution is to draw a molecular level picture of the interplay between pH and phosphate binding at the goethite-water interface via a joint experimental-theoretical approach. Periodic density functional theory (DFT) calculations were carried out to provide a molecular level understanding of the pH dependence of P adsorption. To validate the modeling approach, adsorption experiments of phosphate at goethite were performed in the pH range of 4-12. There was agreement between experiments and simulations in the description of the adsorption behavior by two pH-dependent successive stages. The adsorption increases along the pH change from 4 to 8. A further increase of pH leads to a decrease of adsorption. By comparing with literature data it is concluded that the first stage will be observed only if there is no significant change of the surface charge at low pH. Moreover, the molecular modeling results point to the abundance of the monodentate (M) binding motif at both extremely low and high pH ranges. Otherwise, the bidentate (B) one is predominant along the intermediate pH range. These observations could resolve the existing debate about the assignment of phosphate-goethite binding motifs. Furthermore, the results point to a decrease of pH upon phosphate sorption due to an induced acidification of soil solution. The present joint experimental-theoretical approach provides a better understanding and description of the existing phosphate sorption experiments and highlights new findings at the atomistic/molecular scale.

Ground- and Excited-State Properties of Iron(II) Complexes Linked to Organic Chromophores.

Two new bichromophoric complexes, [Fe(bim-ant)2]2+ and [Fe(bim-pyr)2]2+ ([H2-bim]2+ = 1,1'-(pyridine-2,6-diyl)bis(3-methyl-1H-imidazol-3-ium); ant = 9-anthracenyl; pyr = 1-pyrenyl), are investigated to explore the possibility of tuning the excited-state behavior in photoactive iron(II) complexes to design substitutes for noble-metal compounds. The ground-state properties of both complexes are characterized thoroughly by electrochemical methods and optical absorption spectroscopy, complemented by time-dependent density functional theory calculations. The excited states are investigated by static and time-resolved luminescence and femtosecond transient absorption spectroscopy. Both complexes exhibit room temperature luminescence, which originates from singlet states dominated by the chromophore (1Chrom). In the cationic pro-ligands and in the iron(II) complexes, the emission is shifted to red by up to 110 nm (5780 cm-1). This offers the possibility of tuning the organic chromophore emission by metal-ion coordination. The fluorescence lifetimes of the complexes are in the nanosecond range, while triplet metal-to-ligand charge-transfer (3MLCT) lifetimes are around 14 ps. An antenna effect as in ruthenium(II) polypyridine complexes connected to an organic chromophore is found in the form of an internal conversion within 3.4 ns from the 1Chrom to the 1MLCT states. Because no singlet oxygen forms from triplet oxygen in the presence of the iron(II) complexes and light, efficient intersystem crossing to the triplet state of the organic chromophore (3Chrom) is not promoted in the iron(II) complexes.