Polarizable and Non-Polarizable Force Field Representations of Ferric Cation and Validations

Modeling solvation dynamics of transition metal redox ion through on-the-fly multi-objective Bayesian-optimized force field

Modeling solvation dynamics and properties is crucial for developing electrolytes for electrochemical energy storage and conversion devices. This work reports an on-the-fly multi-objective Bayesian optimization (OTF-MOBO) method to parameterize force fields for modeling ionic solvation structures, thermodynamics, and transport properties using molecular dynamics simulations. By leveraging solvation-free energy and solvation radii as training data, we employ the data-driven OTF-MOBO algorithm to actively optimize the force field parameters. The modeling accuracy was evaluated in molecular dynamics simulations until the Pareto front in the parameter space was reached through minimized prediction errors in both solvation-free energy and solvation radii. Using transition metal redox ions (Fe3+/Fe2+, Cr3+/Cr2+, and Cu2+/Cu+) in aqueous solution as examples, we demonstrate that simple force fields combining the Lenard-Jones potential and Coulombic potential can achieve relative error below 2% in both solvation free energy and solvation radii. The optimized force fields can be further extrapolated to predict solvation entropy and diffusivities with relative error below 10% compared with experiments.

BuRNN: Buffer Region Neural Network Approach for Polarizable-Embedding Neural Network/Molecular Mechanics Simulations

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have advanced the field of computational chemistry tremendously. However, they require the partitioning of a system into two different regions that are treated at different levels of theory, which can cause artifacts at the interface. Furthermore, they are still limited by high computational costs of quantum chemical calculations. In this work, we develop the buffer region neural network (BuRNN), an alternative approach to existing QM/MM schemes, which introduces a buffer region that experiences full electronic polarization by the inner QM region to minimize artifacts. The interactions between the QM and the buffer region are described by deep neural networks (NNs), which leads to the high computational efficiency of this hybrid NN/MM scheme while retaining quantum chemical accuracy. We demonstrate the BuRNN approach by performing NN/MM simulations of the hexa-aqua iron complex.

Iron coordination to pyochelin siderophore influences dynamics of FptA receptor from Pseudomonas aeruginosa: a molecular dynamics simulation study

FptA is a TonB-dependent transporter that permits the high affinity binding and transport of Fe(III)-pyochelin complex across the outer membrane of Pseudomonas aeruginosa. Molecular dynamics simulations were employed to FptA receptor and its complexes with pyochelin, and co-crystallized Fe(III)-pyochelin-ethanediol and Fe(III)-pyochelin-water embedded in dilauroyl phosphatidyl choline bilayer for the evaluation of their structural and dynamical properties. The evaluation of properties of the receptor bound to pyochelin molecule and Fe(III)-pyochelin complexes helped to figure out the iron coordination effect on the receptor properties. Moreover, comparison of these four simulation systems revealed further information on the dynamical changes occurred in extracellular loops, in particular loop-7 corresponding to the missing amino acid residues including the close-by loop-8 that was largely affected by the metal coordination to pyochelin. The binding of iron to pyochelin molecule affected the overall structure of the receptor therefore, evaluation fo the gyration radii and hydrogen bonding were evaluated as well as analysis of the pore size were also carried out to understand the effect of metal coordination on the dynamics of the helices which form a kind of translocation channel to transport the siderophore across the FptA protein into the periplasmic space. The properties of each component of the molecular systems were therefore observed to be perturbed by the incorporation of iron to the pyochelin molecule thus demonstrating that the bacteria use its receptor to abstract and transport iron from extracellular environment for its survival and that was made possible to understand at the molecular level through successful implementation of molecular dynamics simulations.

Evaluation of the AMOEBA force field for simulating metal halide perovskites in the solid state and in solution

In this work, we compare the existing nonpolarizable force fields developed to study the solid or solution phases of hybrid organic-inorganic halide perovskites with the AMOEBA polarizable force field. The aim is to test whether more computationally expensive polarizable force fields like AMOEBA offer better transferability between solution and solid phases, with the ultimate goal being the study of crystal nucleation, growth, and other interfacial phenomena involving these ionic compounds. In the context of hybrid perovskites, AMOEBA force field parameters already exist for several elements in solution, and we decided to leave them unchanged and to only parameterize the missing ones (Pb²⁺ and CH₃NH₃ ⁺ ions) in order to maximize transferability and avoid overfitting to the specific examples studied here. Overall, we find that AMOEBA yields accurate hydration free energies (within 5%) for typical ionic species while showing the correct ordering of stability for the different crystal polymorphs of CsPbI₃ and CH₃NH₃PbI₃. Although the existing parameters do not accurately reproduce all transition temperatures and lattice parameters, AMOEBA offers better transferability between solution and solid states than existing nonpolarizable force fields.

Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications

Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics, including electronic polarization. Due to recent advances in physical models, simulation algorithms, and computing hardware, biomolecular simulations with advanced force fields at biologically relevant timescales are becoming increasingly promising. These advancements have not only led to new biophysical insights but also afforded opportunities to advance our understanding of fundamental intermolecular forces. This article describes the recent advances and applications, as well as future directions, of polarizable force fields in biomolecular simulations.

The folding equilibria of enterobactin enantiomers and their interaction with actinides

The helicity preference of Ent enantiomers was enhanced when binding with Fe³⁺ while disrupted when binding with actinides.

Elucidating the Phosphate Binding Mode of Phosphate-Binding Protein: The Critical Effect of Buffer Solution

Phosphate is an essential component of cell functions, and the specific transport of phosphorus into a cell is mediated by phosphate-binding protein (PBP). The mechanism of PBP-phosphate recognition remains controversial: on the basis of similar binding affinities at acidic and basic pHs, it is believed that the hydrogen network in the binding site is flexible to adapt to different protonation states of phosphates. However, only hydrogen (1H) phosphate was observed in the sub-angstrom X-ray structures. To address this inconsistency, we performed molecular dynamics simulations using the AMOEBA polarizable force field. Structural and free energy data from simulations suggested that 1H phosphate was the preferred bound form at both pHs. The binding of dihydrogen (2H) phosphate disrupted the hydrogen-bond network in the PBP pocket, and the computed affinity was much weaker than that of 1H phosphate. Furthermore, we showed that the discrepancy in the studies described above is resolved if the interaction between phosphate and the buffer agent is taken into account. The calculated apparent binding affinities are in excellent agreement with experimental measurements. Our results suggest the high specificity of PBP for 1H phosphate and highlight the importance of the buffer solution for the binding of highly charged ligands.