The Journal of Physical Chemistry B最新文献

Light-induced tissue damage is a crucial limitation for traditional microscopy of the living brain, underscoring the need for new techniques that minimize exposure of samples to light. Here, we tested the hypothesis that quantum light, i.e., entangled photons, could detect brain structures at a lower excitation energy. In a proof of principle, we show microscopic images of fixed brain tissue in the hippocampus area created by fluorescence selective excitation in the process of entangled two-photon absorption in a scanning microscope. Quantum-enhanced entangled two-photon microscopy (TPM) had brain imaging capabilities at an unprecedented low excitation intensity of ∼3.6 × 10⁷ photons/s, orders of magnitude lower than the excitation level for the classical two-photon fluorescence image obtained in the same microscope. The extremely low light probe intensity demonstrated in entangled TPM is of critical importance in the investigation of neural activity to minimize heating and photobleaching during repetitive imaging. It may have important functional implications in optogenetic technology, removing unintended heating and accumulated photodamage effects. This technology also opens avenues in spatially resolved brain tissue investigations with quantum light, providing new capabilities in local spectroscopy.

Recent years have witnessed drastic improvements in general-purpose explicit solvent protein force fields, partially driven by the need to study intrinsically disordered proteins (IDPs), and yet the state-of-the-art force fields such as CHARMM36m (c36m) and a99SB-disp still provide different performances in simulating disordered protein states, where c36m has a bias toward overcompaction for large IDPs. Here, we examine the performance of c36m and a99SB-disp in describing the stabilities of a set of 46 amino acid backbone and side chain pairs in various configurations. The free energy results show that c36m systematically predicts stronger interactions compared to a99SB-disp by an average of 0.2 kcal/mol for nonpolar pairs, 0.6 kcal/mol for polar pairs, and 0.8 kcal/mol for salt bridges. The most severe overstabilization in c36m is observed for charged pairs involving the Arg and Glu side chains by up to 2.9 kcal/mol. Importantly, the systematic overstabilization of c36m is only marginally alleviated by c36mw, an ad hoc patch to c36m that increases the dispersion interactions between TIP3P hydrogens and protein atoms. Guided by free energy decomposition, we evaluated if revising the charges alone could alleviate the severe overstabilization of salt bridges of c36m(w) vs a99SB-disp. The results suggested that the direct modification of protein-water interactions is also necessary. Toward this end, we proposed a tentative modification to c36m, referred to as c36mrb-disp, which combines modified Arg side chain charges, retuned backbone hydrogen bonding strength, and the a99SB-disp water model. The modified force field successfully reproduces the secondary structures of several intrinsically disordered peptides and proteins including (AAQAA)₃, GB1p, and p53 transactivation domain, while maintaining the stability of a set of folded proteins. This work provides a set of useful systems for benchmarking and optimizing protein force fields and highlights the importance of balancing protein-protein and protein-water electrostatic interactions for accurately describing both folded and disordered proteins.

This study introduces an implementation of multiple Gaussian filters within the Hamiltonian hybrid particle-field (HhPF) theory, aimed at capturing phase coexistence phenomena in mesoscopic molecular simulations. By employing a linear combination of two Gaussians, we demonstrate that HhPF can generate potentials with attractive and steric components analogous to Lennard-Jones (LJ) potentials, which are crucial for modeling phase coexistence. We compare the performance of this method with the multi-Gaussian core model (MGCM) in simulating liquid-gas coexistence for a single-component system across various densities and temperatures. Our results show that HhPF effectively captures detailed information on phase coexistence and interfacial phenomena, including microconfiguration transitions and increased interfacial fluctuations at higher temperatures. Notably, the phase boundaries obtained from HhPF simulations align more closely with those of LJ systems compared to the MGCM results. This work advances the hybrid particle-field methodology to address phase coexistence without requiring modifications to the equation of state or introducing additional interaction energy functional terms, offering a promising approach for mesoscale molecular simulations of complex systems.

Photodynamic therapy (PDT) represents a most attractive therapeutic strategy to reduce side-effects of chemotherapy and improve the global quality of life of patients. Yet, many PDT drugs suffer from poor bioavailability and cellular intake, and thus, drug-delivering strategies are mandatory. In this article, we rationalize the behavior of a temoporfin-based PDT drug, commercialized under the name of Foscan, complexed by two β-cyclodextrin units, acting as drug carriers, in the presence of a lipid bilayer. Our all-atom simulations have unequivocally shown the internalization of the drug-delivering complex and suggest its possible spontaneous dissociation in the lipid bilayer core. The factors favoring penetration and dissociation have also been analyzed, together with membrane perturbation due to the interaction with the drug carrier complex. Our results confirm the suitability of this encapsulation strategy for PDT and rationalize the experimental results concerning its efficacy.

The hydration properties of the Pb²⁺ ion in aqueous solution have been investigated by using a synergic approach based on Classical and Car-Parrinello molecular dynamics (CPMD) simulations and extended X-ray absorption fine structure (EXAFS) spectroscopy. A definite answer has been given to the main question on the Pb²⁺ hydration structure, which concerns the formation of either holodirected or hemidirected solvation geometries, such terms referring to the arrangements of the ligands that can be directed either throughout the surface of an encompassing globe around Pb²⁺ or throughout only part of the globe, respectively. Our CPMD results show that the Pb²⁺ ion in water forms a hemidirected 4-fold cluster with a well-defined distorted pyramidal geometry. This cluster is directed throughout one side of the first shell globe, while the other side contains either two or three very mobile water molecules that do not form a well-defined geometry around the Pb²⁺ ion. The Pb²⁺ first shell structural arrangement determined from the CPMD simulation was confirmed by the EXAFS experimental results. A homodirected Pb²⁺ first shell complex like the 8-fold SAP structure obtained from the classical MD simulations cannot be reconciled with the EXAFS experimental data. These findings represent a significant step forward in the understanding of the solvation chemistry of the Pb²⁺ ion, which is fundamental to improving the efficiency of lead removal procedures that are crucial to the safety of water resources.

We have used molecular dynamics simulations to determine the transport properties of liquid pentaerythritol tetranitrate (PETN), an important energetic material. The density, ρ, self-diffusion coefficient, D, thermal conductivity, κ, and shear viscosity, μ, have been computed over pressures and temperatures relevant to the subshock regime (up to 1000 K and a few GPa), where PETN is known to melt prior to initiation. We find that the thermal conductivity κ(P, T) can be represented by a simple analytical function that fits the data points with very good accuracy, even beyond the subshock regime, up to 2000 K and 20 GPa. The self-diffusion coefficient, D, exhibits nonmonotonic behavior, with notably the temperature-independent prefactor decreasing by several orders of magnitude between 0 and 2 GPa before remaining nearly constant after, and the activation energy varying little in the subshock regime before increasing linearly beyond. Lastly, the viscosity, μ, is well described by Nahme's law, which is fitted to the MD results and allows us to predict μ(P, T) for temperatures and pressures corresponding to the subshock regime. These results can be used to model the response of PETN to low-velocity impacts, where the material melts prior to the first reactions, and thermal conduction and viscosity play a crucial role.

β-Lactamases are one of the primary enzymes responsible for antibiotic resistance and have existed for billions of years. The structural differences between a modern class A TEM-1 β-lactamase compared to a sequentially reconstructed Gram-negative bacteria β-lactamase are minor. Despite the similar structures and mechanisms, there are different functions between the two enzymes. We recently identified differences in dynamics effects that result from evolutionary changes that could potentially account for the increase in substrate specificity and catalytic rate. In this study, we used transition path sampling-based calculations of free energies to identify how evolutionary changes found between an ancestral β-lactamase, and its extant counterpart TEM-1 β-lactamase affect rate.

Hepatitis B virus (HBV) is a double-stranded DNA virus, but its life cycle involves an intermediate stage, during which pregenomic RNA (pgRNA) is encapsulated in the capsid and then reverse-transcribed into the minus DNA strand. These immature HBV virions are the key target for antiviral drug discovery. In this study, we investigate the flexibility and mechanical stability of the HBV capsid containing pgRNA by employing residue-resolved coarse-grained molecular dynamics simulations. The results showed that the presence of pgRNA tends to decrease the overall flexibility of the capsid. In addition, the symmetrically arranged subunits of the capsid show asymmetry in the dominant modes of the conformational fluctuations with or without the presence of pgRNA. Furthermore, the simulations revealed that the presence of pgRNA enhances the overall mechanical stability of the virion particle. Electrostatic interactions between the disordered CTD of capsid and pgRNA were found to play a crucial role in modulating viral mechanical stability. Decreasing the electrostatic interactions by CTD phosphorylation or high salt concentration significantly reduces the mechanical stability of the HBV capsid containing pgRNA. Finally, the 2-fold symmetric sites have been proposed to be the most vulnerable to rupture during the initial stages of capsid disassembly. These findings could enhance our understanding of the physical basis of viral invasion and provide valuable insights into the development of antiviral drugs.

All-atom constant pH molecular dynamics simulations offer a powerful tool for understanding pH-mediated and proton-coupled biological processes. As the protonation equilibria of protein side chains are shifted by electrostatic interactions and desolvation energies, pK_a values calculated from the constant pH simulations may be sensitive to the underlying protein force field and water model. Here we investigated the force field dependence of the all-atom particle mesh Ewald (PME) continuous constant pH (PME-CpHMD) simulations of a mini-protein BBL. The replica-exchange titration simulations based on the Amber ff19sb and ff14sb force fields with the respective water models showed significantly overestimated pK_a downshifts for a buried histidine (His166) and for two glutamic acids (Glu141 and Glu161) that are involved in salt-bridge interactions. These errors (due to undersolvation of neutral histidines and overstabilization of salt bridges) are consistent with the previously reported pK_a's based on the CHARMM c22/CMAP force field, albeit in larger magnitudes. The pK_a calculations also demonstrated that ff19sb with OPC water is significantly more accurate than ff14sb with TIP3P water, and the salt-bridge related pK_a downshifts can be partially alleviated by the atom-pair specific Lennard-Jones corrections (NBFIX). Together, these data suggest that the accuracies of the protonation equilibria of proteins from constant pH simulations can significantly benefit from improvements of force fields.

In this article, the nonadiabatic excited-state Molecular dynamics (NEXMD) package is linked with the SANDER package, provided by AMBERTOOLS. The combination of these software packages enables the simulation of photoinduced dynamics of large multichromophoric conjugated molecules involving several coupled electronic excited states embedded in an explicit solvent by using the quantum/mechanics/molecular mechanics (QM/MM) methodology. The fewest switches surface hopping algorithm, as implemented in NEXMD, is used to account for quantum transitions among the adiabatic excited-state simulations of the photoexcitation and subsequent nonadiabatic electronic transitions, and vibrational energy relaxation of a substituted polyphenylenevinylene oligomer (PPV3-NO2) in vacuum and methanol as an explicit solvent has been used as a test case. The impact of including specific solvent molecules in the QM region is also analyzed. Our NEXMD-SANDER QM/MM implementation provides a useful computational tool to simulate qualitatively solvent-dependent effects, like electron transfer, stabilization of charge-separated excited states, and the role of solvent reorganization in the molecular optical properties, observed in solution-based spectroscopic experiments.