Quaternized Amphiphilic Block Copolymers as Antimicrobial Agents

In this study, a novel polystyrene-block-quaternized polyisoprene amphipathic block copolymer (PS-b-PIN) is derived from anionic polymerization. Quaternized polymers are prepared through post-quaternization on a functionalized polymer side chain. Moreover, the antibacterial activity of quaternized polymers without red blood cell (RBCs) hemolysis can be controlled by block composition, side chain length, and polymer morphology. The solvent environment is highly related to the polymer morphology, forming micelles or other structures. The polymersome formation would decrease the hemolysis and increase the electron density or quaternized groups density as previous research and our experiment revealed. Herein, the PS-b-PIN with N,N-dimethyldodecylamine as side chain would form a polymersome structure in the aqueous solution to display the best inhibiting bacterial growth efficiency without hemolytic effect. Therefore, the different single-chain quaternized groups play an important role in the antibacterial action, and act as a controllable factor.

Towards a quantitative description of excitonic couplings in photosynthetic pigment-protein complexes: quantum chemistry driven multiscale approaches

A structure-based quantitative calculation of excitonic couplings between photosynthetic pigments has to describe the dynamical polarization of the protein/solvent environment of the pigments, giving rise to reaction field and screening...

The solvent influenced coordination variation of flexible ligands to Y(iii) towards MOF structural diversity

Coordination variation by solvent environment change leading to various yttrium-based MOFs with flexible ligands.

A Conserved Allosteric Site on Drug-Metabolizing CYPs: A Systematic Computational Assessment

Cytochrome P450 enzymes (CYPs) are the largest group of enzymes involved in human drug metabolism. Ligand tunnels connect their active site buried at the core of the membrane-anchored protein to the surrounding solvent environment. Recently, evidence of a superficial allosteric site, here denoted as hotspot 1 (H1), involved in the regulation of ligand access in a soluble prokaryotic CYP emerged. Here, we applied multi-scale computational modeling techniques to study the conservation and functionality of this allosteric site in the nine most relevant mammalian CYPs responsible for approximately 70% of drug metabolism. In total, we systematically analyzed over 44 μs of trajectories from conventional MD, cosolvent MD, and metadynamics simulations. Our bioinformatic analysis and simulations with organic probe molecules revealed the site to be well conserved in the CYP2 family with the exception of CYP2E1. In the presence of a ligand bound to the H1 site, we could observe an enlargement of a ligand tunnel in several members of the CYP2 family. Further, we could detect the facilitation of ligand translocation by H1 interactions with statistical significance in CYP2C8 and CYP2D6, even though all other enzymes except for CYP2C19, CYP2E1, and CYP3A4 presented a similar trend. As the detailed comprehension of ligand access and egress phenomena remains one of the most relevant challenges in the field, this work contributes to its elucidation and ultimately helps in estimating the selectivity of metabolic transformations using computational techniques.

Quantifying Fluctuations of Average Environments for Embedding Calculations

In the context of employing embedding methods to study spectroscopic properties, the viability and effectiveness of replacing an ensemble of calculations by a single calculation using an average description of the system of study are evaluated. This work aims to provide a baseline of the expected fluctuations in the average description of the system obtained in the two cases: from calculations of an ensemble of geometries, and from an average environment constructed with the same ensemble. To this end, the classical molecular dynamics simulation of a very simple system was used: a rigid molecule of acetone in a solution of rigid water. We perform a careful numerical analysis of the fluctuations of the electrostatic potential felt by the solute, as well as the fluctuations in the effect on its electronic density, measure through the dipole moment and the atomic charges derived from the corresponding potential. At the same time, we inspect the accuracy of the methods used to construct average environments. Finally, the proposed approach to generate the embedding potential from an average environment density is applied to estimate the solvatochromic shift of the first excitation of acetone. In order to account for quantum-confinement effects that may be important in certain cases, the fluctuations on the shift due to the interaction with the solvent are evaluated using Frozen-Density Embedding Theory. Our results demonstrate that, for normally-behaved environments, the constructed average environment is a reasonably good representation of a discrete solvent environment.

Experimental Electrochemical Potentials of Nickel Complexes

Nickel-catalyzed cross-coupling and photoredox catalytic reactions has found widespread utilities in organic synthesis. Redox processes are key intermediate steps in many catalytic cycles. As a result, it is pertinent to measure and document the redox potentials of various nickel species as precatalysts, catalysts, and intermediates. The redox potentials of a transition-metal complex are governed by its oxidation state, ligand, and the solvent environment. This article tabulates experimentally measured redox potentials of nickel complexes supported on common ligands under various conditions. This review article serves as a versatile tool to help synthetic organic and organometallic chemists evaluate the feasibility and kinetics of redox events occurring at the nickel center, when designing catalytic reactions and preparing nickel complexes.1 Introduction1.1 Scope1.2 Measurement of Formal Redox Potentials1.3 Redox Potentials in Nonaqueous Solution2 Redox Potentials of Nickel Complexes2.1 Redox Potentials of (Phosphine)Ni Complexes2.2 Redox Potentials of (Nitrogen)Ni Complexes2.3 Redox Potentials of (NHC)Ni Complexes

Molecular Dynamics Simulation of Solvation NanoStructure in Carbonate-Based Electrolyte of Lithium–Sulfur Battery

Lithium–sulfur (Li–S) batteries are widely regarded as the most promising batteries for the future due to their higher specific capacity and lower prices. Various strategies are utilized to alleviate the shortcomings of Li–S batteries failing to reach theoretical capacity. However, basic research at the molecular level continues to be lacking. Therefore, we use molecular dynamics to study the details of the solvated structure of Li–S batteries electrolyte and the nature of the transport process, revealing the relationship between the solvated structure of the electrolyte of LiPF6 and the organic solvent ethylene carbonate/dimethyl carbonate (EC/DMC). The electrolyte of Li2S4 was first simulated in a pure solvent environment. Then the LiPF6 salt was added to the model to simulate a typical electrolyte for a working Li–S battery. Regarding the rationality of the solvent system, various reference systems such as density, dielectric constant, viscosity and diffusion coefficient of the solvent were used for verification. And the detailed composition of the first solvation shell of the polysulfate ion and the coordination number of the ions are discussed. These results provide new insights into the use of EC/DMC electrolytes in Li–S batteries, while at the same time providing a basis for efficient future predictions of electrolyte structure and transport in complex electrode confinements.

Molecular Mechanisms on the Selectivity Enhancement of Ascorbic Acid, Dopamine, and Uric Acid by Serine Oligomers Decoration on Graphene Oxide: A Molecular Dynamics Study

The selectivity in the simultaneous detection of ascorbic acid (AA), dopamine (DA), and uric acid (UA) has been an open problem in the biosensing field. Many surface modification methods were carried out for glassy carbon electrodes (GCE), including the use of graphene oxide and amino acids as a selective layer. In this work, molecular dynamics (MD) simulations were performed to investigate the role of serine oligomers on the selectivity of the AA, DA, UA analytes. Our models consisted of a graphene oxide (GO) sheet under a solvent environment. Serine tetramers were added into the simulation box and were adsorbed on the GO surface. Then, the adsorption of each analyte on the mixed surface was monitored from MD trajectories. It was found that the adsorption of AA was preferred by serine oligomers due to the largest number of hydrogen-bond forming functional groups of AA, while UA was the least preferred due to its highest aromaticity. Finally, the role of hydrogen bonds on the electron transfer selectivity of biosensors was discussed with some previous studies.

Membrane transporter dimerization driven by differential lipid solvation energetics of dissociated and associated states

Over two-thirds of integral membrane proteins of known structure assemble into oligomers. Yet, the forces that drive the association of these proteins remain to be delineated, as the lipid bilayer is a solvent environment that is both structurally and chemically complex. In this study we reveal how the lipid solvent defines the dimerization equilibrium of the CLC-ec1 Cl-/H+ antiporter. Integrating experimental and computational approaches, we show that monomers associate to avoid a thinned-membrane defect formed by hydrophobic mismatch at their exposed dimerization interfaces. In this defect, lipids are strongly tilted and less densely packed than in the bulk, with a larger degree of entanglement between opposing leaflets and greater water penetration into the bilayer interior. Dimerization restores the membrane to a near-native state and therefore, appears to be driven by the larger free-energy cost of lipid solvation of the dissociated protomers. Supporting this theory, we demonstrate that addition of short-chain lipids strongly shifts the dimerization equilibrium towards the monomeric state, and show that the cause of this effect is that these lipids preferentially solvate the defect. Importantly, we show that this shift requires only minimal quantities of short-chain lipids, with no measurable impact on either the macroscopic physical state of the membrane or the protein's biological function. Based on these observations, we posit that free-energy differentials for local lipid solvation define membrane-protein association equilibria. With this, we argue that preferential lipid solvation is a plausible cellular mechanism for lipid regulation of oligomerization processes, as it can occur at low concentrations and does not require global changes in membrane properties.