Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field.

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.

Unveiling the Borohydride Ion through Force-Field Development.

The borohydride ion, BH, 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.

Tryptophan to Tryptophan Hole Hopping in an Azurin Construct.

Electron transfer (ET) between neutral and cationic tryptophan residues in the azurin construct [Re(H126)(CO)(dmp)](W124)(W122)Cu (dmp = 4,7-Me-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(CO)(dmp) ← W124 ← W122 ← Cu, where sequential hopping amounts to nearly 10,000-fold acceleration over single-step tunneling (. , , 192-200).

Salt Effects on Caffeine across Concentration Regimes.

Salts affect the solvation thermodynamics of molecules of all sizes; the Hofmeister series is a prime example in which different ions lead to or 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 and . 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 and concentrations.

Herbal concoction Unveiled: A computational analysis of phytochemicals' pharmacokinetic and toxicological profiles using novel approach methodologies (NAMs).

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.

Coronavirus-mimicking nanoparticles (CorNPs) in artificial saliva droplets and nanoaerosols: Influence of shape and environmental factors on particokinetics/particle aerodynamics.

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.

Nonadiabatic excited-state dynamics of ReCl(CO)(bpy) in two different solvents.

We present a study of excited-states relaxation of the complex ReCl(CO)(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)(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.

Cosolvent Exclusion Drives Protein Stability in Trimethylamine -Oxide and Betaine Solutions.

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 -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.

Anion-cation contrast of small molecule solvation in salt solutions.

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.

Impact of Solvent-Drug Interactions on the Desolvation of a Pharmaceutical Solvate.

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.

Weakly hydrated anions bind to polymers but not monomers in aqueous solutions.

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.

Photoinduced hole hopping through tryptophans in proteins.

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)(dmp), and one or two tryptophans (W, W). Experimental kinetics investigations showed that the two closely spaced (3 to 4 Å) intervening tryptophans dramatically accelerated long-range electron transfer (ET) from Cu to the photoexcited sensitizer.

Pressure, Peptides, and a Piezolyte: Structural Analysis of the Effects of Pressure and Trimethylamine--oxide on the Peptide Solvation Shell.

The osmolyte trimethylamine--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.

Protein Stability in TMAO and Mixed Urea-TMAO Solutions.

Osmolytes are essential for cellular function under ubiquitous osmotic stress. Trimethylamine -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.

Thermodynamics of -Isopropylacrylamide in Water: Insight from Experiments, Simulations, and Kirkwood-Buff Analysis Teamwork.

The behavior of thermoresponsive polymer poly(-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 -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.

Two Tryptophans Are Better Than One in Accelerating Electron Flow through a Protein.

We have constructed and structurally characterized a azurin mutant , where two adjacent tryptophan residues (W124 and W122, indole separation 3.6-4.1 Å) are inserted between the Cu center and a Re photosensitizer coordinated to the imidazole of H126 (Re(H126)(CO)(4,7-dimethyl-1,10-phenanthroline)).

Hole Hopping Across a Protein-Protein Interface.

We have investigated photoinduced hole hopping in a Pseudomonas aeruginosa azurin mutant Re126WWCu, where two adjacent tryptophan residues (W124 and W122) are inserted between the Cu center and a Re photosensitizer coordinated to a H126 imidazole (Re = Re(H126)(CO)(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(H126)(CO)(dmp)WWCu product. The Re126FWCu mutant (F124, W122) is not redox-active under these conditions.

Tuning the collapse transition of weakly charged polymers by ion-specific screening and adsorption.

The experimentally observed swelling and collapse response of weakly charged polymers to the addition of specific salts displays quite convoluted behavior that is not easy to categorize. Here we use a minimalistic implicit-solvent/explicit-salt simulation model with a focus on ion-specific interactions between ions and a single weakly charged polyelectrolyte to qualitatively explain the observed effects. In particular, we demonstrate ion-specific screening and bridging effects cause collapse at low salt concentrations whereas the same strong ion-specific direct interactions drive re-entrant swelling at high concentrations.

Arginine "Magic": Guanidinium Like-Charge Ion Pairing from Aqueous Salts to Cell Penetrating Peptides.

It is a textbook knowledge that charges of the same polarity repel each other. For two monovalent ions in the gas phase at a close contact this repulsive interaction amounts to hundreds of kilojoules per mole. In aqueous solutions, however, this Coulomb repulsion is strongly attenuated by a factor equal to the dielectric constant of the medium.

Self-association of a highly charged arginine-rich cell-penetrating peptide.

Small-angle X-ray scattering (SAXS) measurements reveal a striking difference in intermolecular interactions between two short highly charged peptides-deca-arginine (R10) and deca-lysine (K10). Comparison of SAXS curves at high and low salt concentration shows that R10 self-associates, while interactions between K10 chains are purely repulsive. The self-association of R10 is stronger at lower ionic strengths, indicating that the attraction between R10 molecules has an important electrostatic component.

Temperature-Dependent Implicit-Solvent Model of Polyethylene Glycol in Aqueous Solution.

A temperature (T)-dependent coarse-grained (CG) Hamiltonian of polyethylene glycol/oxide (PEG/PEO) in aqueous solution is reported to be used in implicit-solvent material models in a wide temperature (i.e., solvent quality) range.

Beyond the Hofmeister Series: Ion-Specific Effects on Proteins and Their Biological Functions.

Ions differ in their ability to salt out proteins from solution as expressed in the lyotropic or Hofmeister series of cations and anions. Since its first formulation in 1888, this series has been invoked in a plethora of effects, going beyond the original salting out/salting in idea to include enzyme activities and the crystallization of proteins, as well as to processes not involving proteins like ion exchange, the surface tension of electrolytes, or bubble coalescence. Although it has been clear that the Hofmeister series is intimately connected to ion hydration in homogeneous and heterogeneous environments and to ion pairing, its molecular origin has not been fully understood.

Guanidinium can both Cause and Prevent the Hydrophobic Collapse of Biomacromolecules.

A combination of Fourier transform infrared and phase transition measurements as well as molecular computer simulations, and thermodynamic modeling were performed to probe the mechanisms by which guanidinium (Gnd) salts influence the stability of the collapsed versus uncollapsed state of an elastin-like polypeptide (ELP), an uncharged thermoresponsive polymer. We found that the cation's action was highly dependent upon the counteranion with which it was paired. Specifically, Gnd was depleted from the ELP/water interface and was found to stabilize the collapsed state of the macromolecule when paired with well-hydrated anions such as SO.

Lower critical solution temperature (LCST) phase behaviour of an ionic liquid and its control by supramolecular host-guest interactions.

Lower critical solution temperature (LCST) phase behaviour of an imidazolium-based ionic liquid is reported, which can be controlled by concentration, the choice of cation, anion and solvent, and by supramolecular host-guest complex formation. Molecular dynamics simulations provide insight into the molecular basis of this LCST phenomenon. This thermo-responsive system has potential applications in cloud point extraction processes.