Journal of Physical Chemistry. B

5,5',6,6',7,7',8,8'-Octahydro-1,1'-bi-2-naphthol (hbNaph) is an axially chiral molecule consisting of a smaller π-electronic system than that for 1,1'-bi-2-naphthol (BINOL). The absorption and circular dichroism (CD) bands of hbNaph appear in a shorter wavelength region below 310 nm, compared to those of BINOL, and its fluorescence is in the invisible UV region. However, increasing the concentration of hbNaph in solution up to 0.1 M results in its absorption edge gradually extending to longer wavelength, with a shoulder around 330 nm, and finally increasing to about 450 nm...

Human γD-crystallin belongs to a crucial family of proteins known as crystallins located in the fiber cells of the human lens. Since crystallins do not undergo any turnover after birth, they need to possess remarkable thermodynamic stability. However, their sporadic misfolding and aggregation, triggered by environmental perturbations or genetic mutations, constitute the molecular basis of cataracts, which is the primary cause of blindness in the globe according to the World Health Organization. Here, we investigate the impact of high pressure on the conformational landscape of wild-type HγD-crystallin using replica exchange molecular dynamics simulations augmented with principal component analysis...

Deep eutectic solvents (DESs) have emerged as promising tools for crafting polymeric materials across diverse domains. This study delves into the impact of a series of DESs on the phase behavior of poly( N -isopropylacrylamide) (PNIPAM) in aqueous environments, presenting compelling insights into their performance. Specifically, we explore the conformational phase behavior of PNIPAM in the presence of four distinct lactic acid (LA)-based DESs: LA-betaine (LA-BET), LA-proline (LA-PRO), LA-choline chloride (LA-CC), and LA-urea (LA-U)...

G protein-coupled receptors (GPCRs) are a major gateway to cellular signaling, which respond to ligands binding at extracellular sites through allosteric conformational changes that modulate their interactions with G proteins and arrestins at intracellular sites. High-resolution structures in different ligand states, together with spectroscopic studies and molecular dynamics simulations, have revealed a rich conformational landscape of GPCRs. However, their supramolecular structure and spatiotemporal distribution is also thought to play a significant role in receptor activation and signaling bias within the native cell membrane environment...

The anion-selective transport through subnanoporous liquid-crystalline (LC) water treatment membranes was quantitatively detected by the deposition and electrochemical analysis of the LC membrane on the GaN electrode. The time course of the capacitance and Warburg resistance of the LC membrane suggest that the interaction of the LC membrane with monovalent Cl- ions is distinctly different from that with SO4 2- ions. A continuous decay in capacitance suggests the condensation of Cl- ions in subnanopores, whereas the interaction between SO4 2- ions and the inner wall of subnanopores is much weaker...

Kidney-associated human lysozyme amyloidosis leads to renal impairments;thus, patients are often prescribed furosemide. Based on this fact, the effect of furosemide on induced human lysozyme fibrillation, in vitro , is evaluated by spectroscopic, calorimetric, computational, and cellular-based assays/methods. Results show that furosemide increases the lag phase and decreases the apparent rate of aggregation of human lysozyme, thereby decelerating the nucleation phase and amyloid fibril formation, as confirmed by the decrease in the level of Thioflavin-T fluorescence...

In electrolytes, the self- and interdiffusion coefficients, transport numbers, and electrical conductivity can be used to determine velocity cross-correlation coefficients (VCC) that are also accessible through molecular dynamics simulations. In an ionic liquid or molten salt, there are only three, corresponding to correlations between the velocities of distinct ion pairs (cation-anion, cation-cation, and anion-anion) averaged over both the ensemble and time, calculable from experimental ion self-diffusion coefficients and the electrolyte conductivity...

Deoxyribonucleic acid (DNA) stability is a prerequisite in many applications, ranging from DNA-based vaccines and data storage to gene therapy. However, the strategies to enhance DNA stability are limited, and the underlying mechanisms are poorly understood. Ionic liquids (ILs), molten salts of organic cations and organic/inorganic anions, are showing tremendous prospects in myriads of applications. With a judicious choice of constituent ions, the protic nature of ILs can be tuned. In this work, we investigate the relative stability of full-length genomic DNA in aqueous IL solutions of increasing protic nature...

Molecular simulations of water adsorption in porous materials often converge slowly due to sampling bottlenecks that follow from hydrogen bonding and, in many cases, the formation of water clusters. These effects may be exacerbated in metal-organic framework (MOF) adsorbents, due to the presence of pore spaces (cages) that promote the formation of discrete-size clusters and hydrophobic effects (if present), among other reasons. In Grand Canonical Monte Carlo (MC) simulations, these sampling challenges are typically manifested by low MC acceptance ratios, a tendency for the simulation to become stuck in a particular loading state (i...

The Microtubule-binding repeat region (MTBR) of Tau has been studied extensively due to its pathological implications in neurodegenerative diseases like Alzheimer's disease. The pathological property of MTBR is mainly due to the R3 repeat's high propensity for self-aggregation, highlighting the critical molecular grammar of the repeat. Utilizing the R1R3 construct (WT) and its G326E mutant (EE), we determine the distinct characteristics of various peptide segments that modulate the aggregation propensity of the R3 repeat using NMR spectroscopy...

pH-sensitive peptides bind and traverse lipid membranes in response to changes in pH. They can be used to target tumors and other acidic tissues. We investigate the influence of acidic lipids on the pH-driven adsorption of recently synthesized peptides. Using a statistical-thermodynamic theory that takes into account the acid-base chemistry of peptides and lipids, we find that the presence of acidic lipids amplifies changes in peptide surface concentration when transitioning from high to low pH. We study cyclic and linear peptides, containing tryptophan, glutamic acid, and arginine residues, examining their behavior in both neutral and acidic membranes...

Owing to structural defects, stress concentration frequently occurs in polymer network materials (PEMs), significantly altering their overall mechanical properties. Here, we investigate the impact of dangling chain defects on the stress concentration in PEMs using coarse-grained molecular dynamics simulation. Stress distributions on the network structure are calculated by using graph theory, with considering the effects of defect ratio (ϕ) and the distance from defects. It is found that the existence of dangling chains can alleviate stress by dissipating more internal energy...

Ionic liquids (ILs) as polar components in nonaqueous microemulsions are complex formulations that have interesting transport and structural properties, and offer broader applicability of ILs in areas such as drug delivery and cleaning technology. The phase behavior, electrical conductivity, and nanostructures of these formulations have been investigated for quite some time, but the characteristics of the diffusion of nanodroplets were rarely explored─ and hence little understood. This work investigates the droplet diffusion processes in a series of IL-microemulsions containing 1-butyl-3-methylimidazolium tetrafluoroborate ([C4 mim]BF4 ) by means of viscosity and depolarized dynamic light scattering (DDLS) measurements...

5-( tert -Butyl)-2-hydroxy-1,3-isophthalaldehyde (5- t BHI) is a photochromic material susceptible to either excited state proton transfer or excited state intramolecular proton transfer, depending upon the solvent. However, it has also been found to aggregate in the presence of sodium dodecyl sulfate. In this current study, based on the steady-state and time-resolved spectroscopy, supported by crystallography, quantum chemical density functional theory calculation, and molecular dynamics (MD) simulation, we report on the aggregation of this potential single benzene-based emitter (SBBE) in neat solvents as well as solid phase to modulate its photophysics...

Deep eutectic solvents (DESs) are low-melting mixtures, often prepared from a salt and a molecular hydrogen bond donor. Like ionic liquids, DESs that contain at least one sufficiently amphiphilic component can form bicontinuous nanostructures consisting of polar and nonpolar domains, although this has not been widely explored for many DES combinations. Here, the bulk nanostructures of DESs comprising tetraalkylammonium bromide salts (tetrabutylammonium bromide, tetraoctylammonium bromide, and methyltrioctylammonium bromide) with alkanols and alkanoic acids of systematically varied chain lengths (C2 , C6 , C8 , and C10 ) as hydrogen bond donors have been studied...

To understand the behavior of ionic liquids (ILs) at carbon material, i.e., carbon nanotube (CNT)-containing pores, we simulated different systems and analyzed their structural─in particular their coordination─behavior as well as their velocity distribution. The extension of our analysis tool CONAN presented here allowed us to study the coordination behavior as a function of the distance to the carbon material. Our systems were composed of three different CNTs combined with either the neat IL 1-ethyl-3-methylimidazolium tetrafluoroborate or with their NaBF4 salt mixtures...

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel coronavirus, is the causative agent responsible for the spread of the COVID19 pandemic across the globe. The global impact of the COVID19 pandemic, the successful approval of vaccines for controlling the pandemic, and the further resurgence of COVID19 necessitate the exploration and validation of alternative therapeutic avenues targeting SARS-CoV-2. The initial entry and further invasion by SARS-CoV-2 require strong protein-protein interactions (PPIs) between the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptors expressed on the cell surfaces of various tissues...

Riboswitches are widely distributed, conserved RNAs which regulate metabolite levels in bacterial cells through direct, noncovalent binding of their cognate metabolite. Various riboswitch families are highly enriched in gut bacteria, suggestive of a symbiotic relationship between the host and bacteria. Previous studies of the distribution of riboswitches have examined bacterial taxa broadly. Thus, the distribution of riboswitches associated with bacteria inhabiting the intestines of healthy individuals is not well understood...

We have studied the excited states and structural properties for the complexes of cytosine (dC)10 chains with silver ions (Ag+ ) in a wide range of the Ag+ to DNA ratio ( r ) and pH conditions using circular dichroism, steady-state absorption, and fluorescence spectroscopy along with the ultrafast fluorescence upconversion technique. We also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in some models of the cytosine-Ag+ complexes. We show that (dC)10 chains in the presence of silver ions form a duplex stabilized by C-Ag+ -C bonds...

Gas-liquid interfaces have a unique structure different from the bulk phase due to the complex intermolecular interactions within them and are regarded as barriers that prevent gases from entering solution or as channels that affect gas reactions. In this study, the adsorption and mass-transfer mechanisms of sulfur dioxide and nitric oxide at the gas-liquid interface of a H2 O2 solution were comprehensively analyzed using molecular dynamics (MD) simulations. The analysis on molecule angle showed that H2 O molecules tended to align parallel to the solution surface on the surface of the H2 O2 solution...