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prosECCo75 is an optimized force field effectively incorporating electronic polarization via charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular dynamics simulations for interactions in biologically relevant systems involving water, ions, proteins, lipids, and saccharides. Recognizing the inherent limitations of nonpolarizable force fields in precisely modeling electrostatic interactions essential for various biological processes, we mitigate these shortcomings by accounting for electronic polarizability in a physically rigorous mean-field way that does not add to computational costs. With this scaling of (both integer and partial) charges within the CHARMM36 framework, prosECCo75 addresses overbinding artifacts. This improves agreement with experimental ion binding data across a broad spectrum of systems─lipid membranes, proteins (including peptides and amino acids), and saccharides─without compromising their biomolecular structures. prosECCo75 thus emerges as a computationally efficient tool providing enhanced accuracy and broader applicability in simulating the complex interplay of interactions between ions and biomolecules, pivotal for improving our understanding of many biological processes.

The borohydride ion, BH 4 - , is an essential reducing agent in many technological processes, yet its full understanding has been elusive, because of at least two significant challenges. One challenge arises from its marginal stability in aqueous solutions outside of basic pH conditions, which considerably limits the experimental thermodynamic data. The other challenge comes from its unique and atypical hydration shell, stemming from the negative excess charge on its hydrogen atoms, which complicates the accurate modeling in classical atomistic simulations. In this study, we combine experimental and computer simulation techniques to devise a classical force field for NaBH 4 and deepen our understanding of its characteristics. We report the first measurement of the ion's activity coefficient and extrapolate it to neutral pH conditions. Given the difficulties in directly measuring its solvation free energies, owing to its instability, we resort to quantum chemistry calculations. This combined strategy allows us to derive a set of nonpolarizable force-field parameters for the borohydride ion for classical molecular dynamics simulations. The derived force field simultaneously captures the solvation free energy, the hydration structure, as well as the activity coefficient of NaBH 4 salt across a broad concentration range. The obtained insights into the hydration shell of the BH 4 - ion are crucial for accurately modeling and understanding its interactions with other molecules, ions, materials, and interfaces.

Electron transfer (ET) between neutral and cationic tryptophan residues in the azurin construct [Re I (H126)(CO) 3 (dmp)](W124)(W122)Cu I (dmp = 4,7-Me 2 -1,10-phenanthroline) was investigated by Born-Oppenheimer quantum-mechanics/molecular mechanics/molecular dynamics (QM/MM/MD) simulations. We focused on W124 •+ ← W122 ET, which is the middle step of the photochemical hole-hopping process *Re II (CO) 3 (dmp •- ) ← W124 ← W122 ← Cu I , where sequential hopping amounts to nearly 10,000-fold acceleration over single-step tunneling ( ACS Cent. Sci . 2019 , 5 , 192-200). In accordance with experiments, UKS-DFT QM/MM/MD simulations identified forward and reverse steps of W124 •+ ↔ W122 ET equilibrium, as well as back ET Re I (CO) 3 (dmp •- ) → W124 •+ that restores *Re II (CO) 3 (dmp •- ). Strong electronic coupling between the two indoles (≥40 meV in the crossing region) makes the productive W124 •+ ← W122 ET adiabatic. Energies of the two redox states are driven to degeneracy by fluctuations of the electrostatic potential at the two indoles, mainly caused by water solvation, with contributions from the protein dynamics in the W122 vicinity. ET probability depends on the orientation of Re(CO) 3 (dmp) relative to W124 and its rotation diminishes the hopping yield. Comparison with hole hopping in natural systems reveals structural and dynamics factors that are important for designing efficient hole-hopping processes.

Salts affect the solvation thermodynamics of molecules of all sizes; the Hofmeister series is a prime example in which different ions lead to salting-in or salting-out of aqueous proteins. Early work of Tanford led to the discovery that the solvation of molecular surface motifs is proportional to the solvent accessible surface area (SASA), and later studies have shown that the proportionality constant varies with the salt concentration and type . Using multiscale computer simulations combined with vapor-pressure osmometry on caffeine-salt solutions, we reveal that this SASA description captures a rich set of molecular driving forces in tertiary solutions at changing solute and osmolyte concentrations. Central to the theoretical work is a new potential energy function that depends on the instantaneous surface area, salt type, and concentration. Used in, e.g., Monte Carlo simulations, this allows for a highly efficient exploration of many-body interactions and the resulting thermodynamics at elevated solute and salt concentrations.

Herbal medications have an extensive history of use in treating various diseases, attributed to their perceived efficacy and safety. Traditional medicine practitioners and contemporary healthcare providers have shown particular interest in herbal syrups, especially for respiratory illnesses associated with the SARS-CoV-2 virus. However, the current understanding of the pharmacokinetic and toxicological properties of phytochemicals in these herbal mixtures is limited. This study presents a comprehensive computational analysis utilizing novel approach methodologies (NAMs) to investigate the pharmacokinetic and toxicological profiles of phytochemicals in herbal syrup, leveraging in-silico techniques and prediction tools such as PubChem, SwissADME, and Molsoft's database. Although molecular dynamics, docking, and broader system-wide analyses were not considered, future studies hold potential for further investigation in these areas. By combining drug-likeness with molecular simulation, researchers identify diverse phytochemicals suitable for complex medication development examining their pharmacokinetic-toxicological profiles in phytopharmaceutical syrup. The study focuses on herbal solutions for respiratory infections, with the goal of adding to the pool of all-natural treatments for such ailments. This research has the potential to revolutionize environmental and alternative medicine by leveraging in-silico models and innovative analytical techniques to identify novel phytochemicals with enhanced therapeutic benefits and explore network-based and systems biology approaches for a deeper understanding of their interactions with biological systems. Overall, our study offers valuable insights into the computational analysis of the pharmacokinetic and toxicological profiles of herbal concoction. This paves the way for advancements in environmental and alternative medicine. However, we acknowledge the need for future studies to address the aforementioned topics that were not adequately covered in this research., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Author(s).)

Severe acute respiratory syndrome coronavirus 2, abbreviated as SARS-CoV-2, has been associated with the transmission of infectious COVID-19 disease through breathing and speech droplets emitted by infected carriers including asymptomatic cases. As part of SARS-CoV-2 global pandemic preparedness, we studied the transmission of aerosolized air mimicking the infected person releasing speech aerosol with droplets containing CorNPs using a vibrating mesh nebulizer as human patient simulator. Generally speech produces nanoaerosols with droplets of <5 μm in diameter that can travel distances longer than 1 m after release. It is assumed that speech aerosol droplets are a main element of the current Corona virus pandemic, unlike droplets larger than 5 m, which settle down within a 1 m radius. There are no systemic studies, which take into account speech-generated aerosol/droplet experimental validation and their aerodynamics/particle kinetics analysis. In this study, we cover these topics and explore role of residual water in aerosol droplet stability by exploring drying dynamics. Furthermore, a candle experiment was designed to determine whether air pollution might influence respiratory virus like nanoparticle transmission and air stability., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

We present a study of excited-states relaxation of the complex ReCl(CO) 3 (bpy) (bpy = 2,2-bipyridine) using a nonadiabatic TD-DFT dynamics on spin-mixed potential energy surfaces in explicit acetonitrile (ACN) and dimethylsulfoxide (DMSO) solutions up to 800 fs. ReCl(CO) 3 (bpy) belongs to a group of important photosensitizers which show ultrafast biexponential subpicosecond fluorescence decay kinetics. The choice of solvents was motivated by the different excited-state relaxation dynamics observed in subpicosecond time-resolved IR (TRIR) experiments. Simulations of intersystem crossing (ISC) showed the development of spin-mixed states in both solvents. Transformation of time-dependent populations of spin-mixed states enabled to monitor the temporal evolution of individual singlet and triplet states, fitting of bi-exponential decay kinetics, and simulating the time-resolved fluorescence spectra that show only minor differences between the two solvents. Analysis of structural relaxation and solvent reorganization employing time-resolved proximal distribution functions pointed to the factors influencing the fluorescence decay time constants. Nonadiabatic dynamics simulations of time-evolution of electronic, molecular, and solvent structures emerge as a powerful technique to interpret time-resolved spectroscopic data and ultrafast photochemical reactivity.

Using a combination of molecular dynamics simulation, dialysis experiments, and electronic circular dichroism measurements, we studied the solvation thermodynamics of proteins in two osmolyte solutions, trimethylamine N -oxide (TMAO) and betaine. We showed that existing force fields are unable to capture the solvation properties of the proteins lysozyme and ribonuclease T1 and that the inaccurate parametrization of protein-osmolyte interactions in these force fields promoted an unphysical strong thermal denaturation of the trpcage protein. We developed a novel force field for betaine (the KBB force field) which reproduces the experimental solution Kirkwood-Buff integrals and density. We further introduced appropriate scaling to protein-osmolyte interactions in both the betaine and TMAO force fields which led to successful reproduction of experimental protein-osmolyte preferential binding coefficients for lysozyme and ribonuclease T1 and prevention of the unphysical denaturation of trpcage in osmolyte solutions. Correct parametrization of protein-TMAO interactions also led to the stabilization of the collapsed conformations of a disordered elastin-like peptide, while the uncorrected parameters destabilized the collapsed structures. Our results establish that the thermodynamic stability of proteins in both betaine and TMAO solutions is governed by osmolyte exclusion from proteins.

The contributions from anions and cations from salt are inseparable in their perturbation of molecular systems by experimental and computational methods, rendering it difficult to dissect the effects exerted by the anions and cations individually. Here we investigate the solvation of a small molecule, caffeine, and its perturbation by monovalent salts from various parts of the Hofmeister series. Using molecular dynamics and the energy-representation theory of solvation, we estimate the solvation free energy of caffeine and decompose it into the contributions from anions, cations, and water. We also decompose the contributions arising from the solute-solvent and solute-ions interactions and that from excluded volume, enabling us to pin-point the mechanism of salt. Anions and cations revealed high contrast in their perturbation of caffeine solvation, with the cations salting-in caffeine via binding to the polar ketone groups, while the anions were found to be salting-out via perturbations of water. In agreement with previous findings, the perturbation by salt is mostly anion dependent, with the magnitude of the excluded-volume effect found to be the governing mechanism. The free-energy decomposition as conducted in the present work can be useful to understand ion-specific effects and the associated Hofmeister series.

In drug manufacturing, solvent-based methods are used for the crystallization of active pharmaceutical ingredients (APIs). Often, the solvent interacts with the API resulting in the formation of a new solid compound, the solvate. When desolvation occurs upon heating, it might result in the formation of new solid forms with significantly different physicochemical properties. Therefore, in this work, we study the desolvation kinetics by combining in situ powder X-ray diffraction (PXRD), all-atom molecular dynamics (MD) simulations, and macroscopic solid-state reaction kinetics modeling. The fluorobenzene (FB) solvate of Bruton's tyrosine kinase inhibitor Ibrutinib (IBR) was used as a model system. While the macroscopic solid-state modeling provides information about the desolvation kinetics, the MD simulations were used to trace individual FB molecules inside the crystal lattice. The activation energy of confined solvent diffusion, obtained by MD simulations, agrees well with results of the macroscopic solid-state reaction kinetics modeling. In addition, MD simulations provided detailed information about the IBR-FB interactions at the nanoscale. The mechanism revealed is that the solvent molecules diffusion, controlled by distinct open-close gating conformational changes of the drug, triggers the desolvation throughout the crystal lattice.

Weakly hydrated anions help to solubilize hydrophobic macromolecules in aqueous solutions, but small molecules comprising the same chemical constituents precipitate out when exposed to these ions. Here, this apparent contradiction is resolved by systematically investigating the interactions of NaSCN with polyethylene oxide oligomers and polymers of varying molecular weight. A combination of spectroscopic and computational results reveals that SCN - accumulates near the surface of polymers, but is excluded from monomers. This occurs because SCN - preferentially binds to the centre of macromolecular chains, where the local water hydrogen-bonding network is disrupted. These findings suggest a link between ion-specific effects and theories addressing how hydrophobic hydration is modulated by the size and shape of a hydrophobic entity., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

Hole hopping through tryptophan/tyrosine chains enables rapid unidirectional charge transport over long distances. We have elucidated structural and dynamical factors controlling hopping speed and efficiency in two modified azurin constructs that include a rhenium(I) sensitizer, Re(His)(CO) 3 (dmp) + , and one or two tryptophans (W 1 , W 2 ). Experimental kinetics investigations showed that the two closely spaced (3 to 4 Å) intervening tryptophans dramatically accelerated long-range electron transfer (ET) from Cu I to the photoexcited sensitizer. In our theoretical work, we found that time-dependent density-functional theory (TDDFT) quantum mechanics/molecular mechanics/molecular dynamics (QM/MM/MD) trajectories of low-lying triplet excited states of Re I (His)(CO) 3 (dmp) + -W 1 (-W 2 ) exhibited crossings between sensitizer-localized (*Re) and charge-separated [Re I (His)(CO) 3 (dmp •- )/(W 1 •+ or W 2 •+ )] (CS1 or CS2) states. Our analysis revealed that the distances, angles, and mutual orientations of ET-active cofactors fluctuate in a relatively narrow range in which the cofactors are strongly coupled, enabling adiabatic ET. Water-dominated electrostatic field fluctuations bring *Re and CS1 states to a crossing where *Re(CO) 3 (dmp) + ←W 1 ET occurs, and CS1 becomes the lowest triplet state. ET is promoted by solvation dynamics around *Re(CO) 3 (dmp) + (W 1 ); and CS1 is stabilized by Re(dmp •- )/W 1 •+ electron/hole interaction and enhanced W 1 •+ solvation. The second hop, W 1 •+ ←W 2 , is facilitated by water fluctuations near the W 1 /W 2 unit, taking place when the electrostatic potential at W 2 drops well below that at W 1 •+ Insufficient solvation and reorganization around W 2 make W 1 •+ ←W 2 ET endergonic, shifting the equilibrium toward W 1 •+ and decreasing the charge-separation yield. We suggest that multiscale TDDFT/MM/MD is a suitable technique to model the simultaneous evolution of photogenerated excited-state manifolds., Competing Interests: The authors declare no competing interest.

The combination of computer assisted design and 3D printing has recently enabled fast and inexpensive manufacture of customized 'reactionware' for broad range of electrochemical applications. In this work bi-material fused deposition modeling 3D printing is utilized to construct an integrated platform based on a polyamide electrochemical cell and electrodes manufactured from a polylactic acid-carbon nanotube conductive composite. The cell contains separated compartments for the reference and counter electrode and enables reactants to be introduced and inspected under oxygen-free conditions. The developed platform was employed in a study investigating the electrochemical oxidation of aqueous hydrazine coupled to its bulk reaction with carbon dioxide. The analysis of cyclic voltammograms obtained in reaction mixtures with systematically varied composition confirmed that the reaction between hydrazine and carbon dioxide follows 1/1 stoichiometry and the corresponding equilibrium constant amounts to (2.8 ± 0.6) × 10 3 . Experimental characteristics were verified by results of numerical simulations based on the finite-element-method., Competing Interests: The authors declare no conflict of interests., (© 2020 Elsevier Ltd. All rights reserved.)

The osmolyte trimethylamine- N -oxide (TMAO) is able to increase the thermodynamic stability of folded proteins, counteracting pressure denaturation. Herein, we report experimental solubility data on penta-alanine (pAla) in aqueous TMAO solutions (at pH = 7 and pH = 13) together with molecular simulation data for pAla, penta-serine (pSer), and an elastin-like peptide (ELP) sequence (VPGVG) under varying pH and pressure conditions. The effect of the peptide end groups on TMAO-peptide interactions is investigated by comparing the solvation of zwitterionic and negatively charged pentamers with the solvation of pentamers with charge-neutral C- and N-termini and linear, virtually infinite, peptide chains stretched across the periodic boundaries of the simulation cell. The experiments and simulations consistently show that TMAO is net-depleted from the pAla-water interface, but local accumulation of TMAO is observed just outside the first hydration shell of the peptide. While the same observations are also made in the simulations of the zwitterionic pentamers (Ala, Ser, and ELP) and virtually infinite peptide chains (Ala and ELP), weak preferential binding of TMAO is instead observed for pAla with neutral end groups at a 1 M TMAO concentration and for an ELP pentamer with capped neutral end groups at a 0.55 M TMAO concentration studied in previous work (Y.-T. Liao et al. Proc. Natl. Acad. Sci. USA , 2017, 114 , 2479-2484). The above observations made at 1 bar ambient pressure remain qualitatively unchanged at 500 bar and 2 kbar. Local accumulation of TMAO correlates with a reduction in the total number of peptide-solvent hydrogen bonds, independent of the peptide's primary sequence and the applied pressure. By weakening water hydrogen bonds with the protein backbone, TMAO indirectly contributes to stabilizing internal hydrogen bonds in proteins, thus providing a protein stabilization mechanism beyond net depletion.

Osmolytes are essential for cellular function under ubiquitous osmotic stress. Trimethylamine N -oxide (TMAO) is one such osmolyte that has gained remarkable attention due to its protein-protective ability against urea. This Review aims at providing a detailed account of recent theoretical and experimental developments in characterizing the structural changes and thermodynamic stability of proteins in the presence of TMAO and urea. New vapor pressure osmometry and molecular dynamics simulation results on urea-TMAO solutions are presented, and a unified molecular mechanism of TMAO counteraction of urea-induced protein denaturation is introduced. In addition, a detailed technical assessment of molecular dynamics force fields for TMAO and for urea-TMAO solutions is presented. The force field analysis highlights how many of the commonly used force field models are in fact incompatible with solvation thermodynamics and can lead to misleading conclusions. A new optimized force field for TMAO (Shea(m)) is presented, and a recently optimized force field for TMAO-urea (Netz(m)) that best reproduces experimental data is highlighted.

The behavior of thermoresponsive polymer poly( N -isopropylacrylamide) (PNiPAM), an essential building block in the design of smart soft materials, in aqueous solutions has attracted much interest, which contrasts with our knowledge of N -isopropylacrylamide (NiPAM) monomer. Strikingly, the physicochemical properties of aqueous NiPAM are similarly rich, and their understanding is far from being complete. This stems from the lack of accurate thermodynamic data and quantitative model for atomistic simulations. In this joint study, we have probed the thermodynamic behavior of aqueous NiPAM by experimental methods, molecular dynamics (MD) simulations, and Kirkwood-Buff (KB) analysis at ambient conditions. From the partial molar volumes and simultaneously correlated osmotic coefficients, with excess partial molar enthalpies of NiPAM in water, the concentration and temperature dependence of KB integrals was determined. For the purpose of this work, we have developed and employed a novel NiPAM force field, which not only reproduces KB integrals ( G ij ) and adequately captures macroscopic thermodynamic quantities but also provides more accurate structural insight than the original force fields. We revealed in the vicinity of NiPAM the competing effect of amide hydration with interaction between nonpolar regions. This microscopic picture is reflected in the experimentally observed NiPAM-NiPAM association, which is present from highly dilute conditions up to the solubility limit and is evidenced by G 22 . From intermediate concentrations, it is accompanied by the existence of apparent dense-water regions, as indicated by positive G 11 values. The here-employed KB-based framework provided a mutually consistent thermodynamic and microscopic insight into the NiPAM solution and may be further extended for ion-specific effects. Moreover, our findings contribute to the understanding of thermodynamic grounds behind PNiPAM collapse transition.

We have investigated photoinduced hole hopping in a Pseudomonas aeruginosa azurin mutant Re126WWCu I , where two adjacent tryptophan residues (W124 and W122) are inserted between the Cu I center and a Re photosensitizer coordinated to a H126 imidazole (Re = Re I (H126)(CO) 3 (dmp) + , dmp = 4,7-dimethyl-1,10-phenanthroline). Optical excitation of this mutant in aqueous media (≤40 μM) triggers 70 ns electron transport over 23 Å, yielding a long-lived (120 μs) Re I (H126)(CO) 3 (dmp •- )WWCu II product. The Re126FWCu I mutant (F124, W122) is not redox-active under these conditions. Upon increasing the concentration to 0.2-2 mM, {Re126WWCu I } 2 and {Re126FWCu I } 2 are formed with the dmp ligand of the Re photooxidant of one molecule in close contact (3.8 Å) with the W122' indole on the neighboring chain. In addition, {Re126WWCu I } 2 contains an interfacial tryptophan quadruplex of four indoles (3.3-3.7 Å apart). In both mutants, dimerization opens an intermolecular W122' → //*Re ET channel (// denotes the protein interface, *Re is the optically excited sensitizer). Excited-state relaxation and ET occur together in two steps (time constants of ∼600 ps and ∼8 ns) that lead to a charge-separated state containing a Re(H126)(CO) 3 (dmp •- )//(W122 •+ )' unit; then (Cu I )' is oxidized intramolecularly (60-90 ns) by (W122 •+ )', forming Re I (H126)(CO) 3 (dmp •- )WWCu I //(Cu II )'. The photocycle is closed by ∼1.6 μs Re I (H126)(CO) 3 (dmp •- ) → //(Cu II )' back ET that occurs over 12 Å, in contrast to the 23 Å, 120 μs step in Re126WWCu I . Importantly, dimerization makes Re126FWCu I photoreactive and, as in the case of {Re126WWCu I } 2 , channels the photoproduced "hole" to the molecule that was not initially photoexcited, thereby shortening the lifetime of Re I (H126)(CO) 3 (dmp •- )//Cu II . Although two adjacent W124 and W122 indoles dramatically enhance Cu I → *Re intramolecular multistep ET, the tryptophan quadruplex in {Re126WWCu I } 2 does not accelerate intermolecular electron transport; instead, it acts as a hole storage and crossover unit between inter- and intramolecular ET pathways. Irradiation of {Re126WWCu II } 2 or {Re126FWCu II } 2 also triggers intermolecular W122' → //*Re ET, and the Re(H126)(CO) 3 (dmp •- )//(W122 •+ )' charge-separated state decays to the ground state by ∼50 ns Re I (H126)(CO) 3 (dmp •- ) + → //(W122 •+ )' intermolecular charge recombination. Our findings shed light on the factors that control interfacial hole/electron hopping in protein complexes and on the role of aromatic amino acids in accelerating long-range electron transport.

We have constructed and structurally characterized a Pseudomonas aeruginosa azurin mutant Re126WWCu I , where two adjacent tryptophan residues (W124 and W122, indole separation 3.6-4.1 Å) are inserted between the Cu I center and a Re photosensitizer coordinated to the imidazole of H126 (Re I (H126)(CO) 3 (4,7-dimethyl-1,10-phenanthroline) + ). Cu I oxidation by the photoexcited Re label (*Re) 22.9 Å away proceeds with a ∼70 ns time constant, similar to that of a single-tryptophan mutant (∼40 ns) with a 19.4 Å Re-Cu distance. Time-resolved spectroscopy (luminescence, visible and IR absorption) revealed two rapid reversible electron transfer steps, W124 → *Re (400-475 ps, K 1 ≅ 3.5-4) and W122 → W124 •+ (7-9 ns, K 2 ≅ 0.55-0.75), followed by a rate-determining (70-90 ns) Cu I oxidation by W122 •+ ca. 11 Å away. The photocycle is completed by 120 μs recombination. No photochemical Cu I oxidation was observed in Re126FWCu I , whereas in Re126WFCu I , the photocycle is restricted to the ReH126W124 unit and Cu I remains isolated. QM/MM/MD simulations of Re126WWCu I indicate that indole solvation changes through the hopping process and W124 → *Re electron transfer is accompanied by water fluctuations that tighten W124 solvation. Our finding that multistep tunneling (hopping) confers a ∼9000-fold advantage over single-step tunneling in the double-tryptophan protein supports the proposal that hole-hopping through tryptophan/tyrosine chains protects enzymes from oxidative damage., Competing Interests: The authors declare no competing financial interest.