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1. Ten-Fold Solvent Kinetic Isotope Effect for the Nonradiative Relaxation of the Aqueous Ferrate(VI) Ion

   https://doi.org/10.1021/acs.jpca.3c06042  

   Antolini, Cali; Jacoby, Danielle J.; Tiano, Sophia M.; Otolski, Christopher J.; Doumy, Gilles; March, Anne Marie; Walko, Donald A.; Goodwill, Joseph E.; Hayes, Dugan (December 2023, The Journal of Physical Chemistry A)

   Hypervalent iron intermediates have been invoked in the catalytic cycles of many metalloproteins, and thus, it is crucial to understand how the coupling between such species and their environment can impact their chemical and physical properties in such contexts. In this work, we take advantage of the solvent kinetic isotope effect (SKIE) to gain insight into the nonradiative deactivation of electronic excited states of the aqueous ferrate(VI) ion. We observe an exceptionally large SKIE of 9.7 for the nanosecond-scale relaxation of the lowest energy triplet ligand field state to the ground state. Proton inventory studies demonstrate that a single solvent O–H bond is coupled to the ion during deactivation, likely due to the sparse vibrational structure of ferrate(VI). Such a mechanism is consistent with that reported for the deactivation of f–f excited states of aqueous trivalent lanthanides, which exhibit comparably large SKIE values. This phenomenon is ascribed entirely to dissipation of energy into a higher overtone of a solvent acceptor mode, as any impact on the apparent relaxation rate due to a change in solvent viscosity is negligible. 

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2. A Mixed‐Pure Planar Heterojunction Structure of Active Layers for Efficient Sequential Blade‐Coating Organic Solar Cells

   https://doi.org/10.1002/smll.202407435  

   Wang, Yilin; Tang, Yabing; Ouyang, Yanni; Wu, Weiwei; Patterson, Acacia; Alqahtani, Obaid; Melody, Tanner; Zhou, Ke; Lu, Guanghao; Min, Jie; et al (January 2025, Small)

   Abstract Precise modulating the vertical structure of active layers to boost charge transfer is an effective way to achieve high power conversion efficiencies (PCEs) in organic solar cells (OSCs). Herein, efficient OSCs with a well‐controlled vertical structure are realized by a rapid film‐forming method combining low boiling point solvent and the sequential blade‐coating (SBC) technology. The results of grazing incident wide‐angle X‐ray scattering measurement show that the vertical component distribution is varied by changing the processing solvent. Novel characterization technique such as tilt resonant soft X‐ray scattering is used to test the vertical structure of the films, demonstrating the dichloromethane (DCM)‐processed film is truly planar heterojunction. The devices with chloroform (CF) processed upper layer show an increased mixed phase region compared to these devices with toluene (TL) or ‐DCM‐, which is beneficial for improving charge generation and achieving a superior PCE of 17.36%. Despite significant morphological varies, the DCM‐processed devices perform slightly lower PCE of 16.66%, which is the highest value in truly planar heterojunction devices, demonstrating higher morphological tolerance. This work proposes a solvent‐regulating method to optimize the vertical structure of active layers through SBC technology, and provides a practical guidance for the optimization of the active‐layer microstructure. 

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3. Integral equation models for solvent in macromolecular crystals

   https://doi.org/10.1063/5.0070869  

   Gray, Jonathon_G; Giambaşu, George_M; Case, David_A; Luchko, Tyler (January 2022, The Journal of Chemical Physics)

   The solvent can occupy up to ∼70% of macromolecular crystals, and hence, having models that predict solvent distributions in periodic systems could improve the interpretation of crystallographic data. Yet, there are few implicit solvent models applicable to periodic solutes, and crystallographic structures are commonly solved assuming a flat solvent model. Here, we present a newly developed periodic version of the 3D-reference interaction site model (RISM) integral equation method that is able to solve efficiently and describe accurately water and ion distributions in periodic systems; the code can compute accurate gradients that can be used in minimizations or molecular dynamics simulations. The new method includes an extension of the Ornstein–Zernike equation needed to yield charge neutrality for charged solutes, which requires an additional contribution to the excess chemical potential that has not been previously identified; this is an important consideration for nucleic acids or any other charged system where most or all the counter- and co-ions are part of the “disordered” solvent. We present several calculations of proteins, RNAs, and small molecule crystals to show that x-ray scattering intensities and the solvent structure predicted by the periodic 3D-RISM solvent model are in closer agreement with the experiment than are intensities computed using the default flat solvent model in the refmac5 or phenix refinement programs, with the greatest improvement in the 2 to 4 Å range. Prospects for incorporating integral equation models into crystallographic refinement are discussed. 

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4. Crowding alters F-actin secondary structure and hydration

   https://doi.org/10.1038/s42003-023-05274-3  

   Chen, Xiaobing; Roeters, Steven J.; Cavanna, Francis; Alvarado, José; Baiz, Carlos R. (December 2023, Communications Biology)

   Abstract Actin, an important component of eukaryotic cell cytoskeleton, regulates cell shape and transport. The morphology and biochemical properties of actin filaments are determined by their structure and protein-protein contacts. Crowded environments can organize filaments into bundles, but less is known about how they affect F-actin structure. This study used 2D IR spectroscopy and spectral calculations to examine how crowding and bundling impact the secondary structure and local environments in filaments and weakly or strongly bundled networks. The results reveal that bundling induces changes in actin’s secondary structure, leading to a decrease inβ-sheet and an increase in loop conformations. Strongly bundled networks exhibit a decrease in backbone solvent exposure, with less perturbedα-helices and nearly “locked”β-sheets. Similarly, the loops become less hydrated but maintain a dynamic environment. These findings highlight the role of loop structure in actin network morphology and stability under morphology control by PEG. 

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5. MLIMC: Machine learning-based implicit-solvent Monte Carlo

   https://doi.org/10.1063/1674-0068/cjcp2109150  

   Chen, Jiahui; Geng, Weihua; Wei, Guo-Wei (December 2021, Chinese Journal of Chemical Physics)

   Monte Carlo (MC) methods are important computational tools for molecular structure optimizations and predictions. When solvent effects are explicitly considered, MC methods become very expensive due to the large degree of freedom associated with the water molecules and mobile ions. Alternatively implicit-solvent MC can largely reduce the computational cost by applying a mean field approximation to solvent effects and meanwhile maintains the atomic detail of the target molecule. The two most popular implicit-solvent models are the Poisson-Boltzmann (PB) model and the Generalized Born (GB) model in a way such that the GB model is an approximation to the PB model but is much faster in simulation time. In this work, we develop a machine learning-based implicit-solvent Monte Carlo (MLIMC) method by combining the advantages of both implicit solvent models in accuracy and efficiency. Specifically, the MLIMC method uses a fast and accurate PB-based machine learning (PBML) scheme to compute the electrostatic solvation free energy at each step. We validate our MLIMC method by using a benzene-water system and a protein-water system. We show that the proposed MLIMC method has great advantages in speed and accuracy for molecular structure optimization and prediction. 

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