Short hydrogen bonds enhance nonaromatic protein-related fluorescence.

Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, by employing a combined experimental and computational approach, we show that specific hydrogen bond networks can significantly affect fluorescence. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared with L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease nonradiative transition probabilities. Our findings open the door to the design of new photoactive materials with biophotonic applications.

Free energy decompositions illuminate synergistic effects in interfacial binding thermodynamics of mixed surfactant systems.

Recent vibrational sum frequency generation spectroscopic experiments [Sengupta et al., J. Phys. Chem. Lett. 13, 11391-11397 (2022)] demonstrated synergistic interfacial adsorption effects between the anionic dodecyl sulfate (DS-) and the polar, but charge-neutral hexaethylene glycol monododecyl ether (C12E6), surfactants. In this study, the interfacial adsorption thermodynamics underlying these synergistic effects are analyzed through free energy decompositions. A general decomposition method utilizing alchemical intermediate states is outlined. Combining free energy decompositions with the potential distribution theorem illuminates the statistical interpretations of correlated effects between different system components. This approach allows for the identification of the physical effects leading to synergistic adsorption thermodynamics of DS- binding to the air-C12E6-water interface. The binding properties are found to result from a combination of effects predominantly including energetic van der Waals stabilization between DS- and C12E6, as well as competing energetic and entropic effects due to changes in the interfacial water structure as a result of introducing a C12E6 monolayer into the bare air-water interface.

Lessons Learned from Multiobjective Automatic Optimizations of Classical Three-Site Rigid Water Models Using Microscopic and Macroscopic Target Experimental Observables.

The development of accurate water models is of primary importance for molecular simulations. Despite their intrinsic approximations, three-site rigid water models are still ubiquitously used to simulate a variety of molecular systems. Automatic optimization approaches have been recently used to iteratively refine three-site water models to fit macroscopic (average) thermodynamic properties, providing state-of-the-art three-site models that still present some deviations from the liquid water properties. Here, we show the results obtained by automatically optimizing three-site rigid water models to fit a combination of microscopic and macroscopic experimental observables. We use Swarm-CG, a multiobjective particle-swarm-optimization algorithm, for training the models to reproduce the experimental radial distribution functions of liquid water at various temperatures (rich in microscopic-level information on, e.g., the local orientation and interactions of the water molecules). We systematically analyze the agreement of these models with experimental observables and the effect of adding macroscopic information to the training set. Our results demonstrate how adding microscopic-rich information in the training of water models allows one to achieve state-of-the-art accuracy in an efficient way. Limitations in the approach and in the approximated description of water in these three-site models are also discussed, providing a demonstrative case useful for the optimization of approximated molecular models, in general.

Water Self-Dissociation is Insensitive to Nanoscale Environments.

Nanoconfinement effects on water dissociation and reactivity remain controversial, despite their importance to understand the aqueous chemistry at interfaces, pores, or aerosols. The pKw in confined environments has been assessed from experiments and simulations in a few specific cases, leading to dissimilar conclusions. Here, with the use of carefully designed ab initio simulations, we demonstrate that the energetics of bulk water dissociation is conserved intact to unexpectedly small length-scales, down to aggregates of only a dozen molecules or pores of widths below 2 nm. The reason is that most of the free-energy involved in water autoionization comes from breaking the O-H covalent bond, which has a comparable barrier in the bulk liquid, in a small droplet of nanometer size, or in a nanopore in the absence of strong interfacial interactions. Thus, dissociation free-energy profiles in nanoscopic aggregates or in 2D slabs of 1 nm width reproduce the behavior corresponding to the bulk liquid, regardless of whether the corresponding nanophase is delimited by a solid or a gas interface. The present work provides a definite and fundamental description of the mechanism and thermodynamics of water dissociation at different scales with broader implications on reactivity and self-ionization at the air-liquid interface.

Intracellular Aß42 Aggregation Leads to Cellular Thermogenesis.

The aggregation of Aß42 is a hallmark of Alzheimer's disease. It is still not known what the biochemical changes are inside a cell which will eventually lead to Aß42 aggregation. Thermogenesis has been associated with cellular stress, the latter of which may promote aggregation. We perform intracellular thermometry measurements using fluorescent polymeric thermometers to show that Aß42 aggregation in live cells leads to an increase in cell-averaged temperatures. This rise in temperature is mitigated upon treatment with an aggregation inhibitor of Aß42 and is independent of mitochondrial damage that can otherwise lead to thermogenesis. With this, we present a diagnostic assay which could be used to screen small-molecule inhibitors to amyloid proteins in physiologically relevant settings. To interpret our experimental observations and motivate the development of future models, we perform classical molecular dynamics of model Aß peptides to examine the factors that hinder thermal dissipation. We observe that this is controlled by the presence of ions in its surrounding environment, the morphology of the amyloid peptides, and the extent of its hydrogen-bonding interactions with water. We show that aggregation and heat retention by Aß peptides are favored under intracellular-mimicking ionic conditions, which could potentially promote thermogenesis. The latter will, in turn, trigger further nucleation events that accelerate disease progression.

The behavior of methane-water mixtures under elevated pressures from simulations using many-body potentials.

Non-polarizable empirical potentials have been proven to be incapable of capturing the mixing of methane-water mixtures at elevated pressures. Although density functional theory-based ab initio simulations may circumvent this discrepancy, they are limited in terms of the relevant time and length scales associated with mixing phenomena. Here, we show that the many-body MB-nrg potential, designed to reproduce methane-water interactions with coupled cluster accuracy, successfully captures this phenomenon up to 3 GPa and 500 K with varying methane concentrations. Two-phase simulations and long time scales that are required to fully capture the mixing, affordable due to the speed and accuracy of the MBX software, are assessed. Constructing the methane-water equation of state across the phase diagram shows that the stable mixtures are denser than the sum of their parts at a given pressure and temperature. We find that many-body polarization plays a central role, enhancing the induced dipole moments of methane by 0.20 D during mixing under pressure. Overall, the mixed system adopts a denser state, which involves a significant enthalpic driving force as elucidated by a systematic many-body energy decomposition analysis.

How to determine solubility in binary mixtures from neutron scattering data: The case of methane and water.

It has recently been discovered that, when subjected to moderate amounts of pressure, methane dissolves in water to form binary mixtures of up to 40% molar methane. No significant solubility of water in methane is known. In these mixtures, the water hydrogen-bond network is largely complete and surrounds the methane molecules. The discovery of this dense mixture has once again highlighted the technical difficulties involved in accurately describing and sampling mixing phenomena both computationally and experimentally. Here, we present a systematic and critical study of the methods employed to characterize binary mixtures and their robustness. This study highlights the requirements needed to develop a quantitative understanding, and it proposes new and more accessible measures of miscibility to investigators, particularly for in silico analysis.

Emergence of Electric Fields at the Water-C12E6 Surfactant Interface.

We study the properties of the interface of water and the surfactant hexaethylene glycol monododecyl ether (C12E6) with a combination of heterodyne-detected vibrational sum frequency generation (HD-VSFG), Kelvin-probe measurements, and molecular dynamics (MD) simulations. We observe that the addition of the hydrogen-bonding surfactant C12E6, close to the critical micelle concentration (CMC), induces a drastic enhancement in the hydrogen bond strength of the water molecules close to the interface, as well as a flip in their net orientation. The mutual orientation of the water and C12E6 molecules leads to the emergence of a broad (∼3 nm) interface with a large electric field of ∼1 V/nm, as evidenced by the Kelvin-probe measurements and MD simulations. Our findings may open the door for the design of novel electric-field-tuned catalytic and light-harvesting systems anchored at the water-surfactant-air interface.

Phospholipids dock SARS-CoV-2 spike protein via hydrophobic interactions: a minimal in-silico study of lecithin nasal spray therapy.

Understanding the physical and chemical properties of viral infections at molecular scales is a major challenge for the scientific community more so with the outbreak of global pandemics. There is currently a lot of effort being placed in identifying molecules that could act as putative drugs or blockers of viral molecules. In this work, we computationally explore the importance in antiviral activity of a less studied class of molecules, namely surfactants. We employ all-atoms molecular dynamics simulations to study the interaction between the receptor-binding domain of the SARS-CoV-2 spike protein and the phospholipid lecithin (POPC), in water. Our microsecond simulations show a preferential binding of lecithin to the receptor-binding motif of SARS-CoV-2 with binding free energies significantly larger than [Formula: see text]. Furthermore, hydrophobic interactions involving lecithin non-polar tails dominate these binding events, which are also accompanied by dewetting of the receptor binding motif. Through an analysis of fluctuations in the radius of gyration of the receptor-binding domain, its contact maps with lecithin molecules, and distributions of water molecules near the binding region, we elucidate molecular interactions that may play an important role in interactions involving surfactant-type molecules and viruses. We discuss our minimal computational model in the context of lecithin-based liposomal nasal sprays as putative mitigating therapies for COVID-19.

Structure and dynamics of nanoconfined water and aqueous solutions.

This review is devoted to discussing recent progress on the structure, thermodynamic, reactivity, and dynamics of water and aqueous systems confined within different types of nanopores, synthetic and biological. Currently, this is a branch of water science that has attracted enormous attention of researchers from different fields interested to extend the understanding of the anomalous properties of bulk water to the nanoscopic domain. From a fundamental perspective, the interactions of water and solutes with a confining surface dramatically modify the liquid's structure and, consequently, both its thermodynamical and dynamical behaviors, breaking the validity of the classical thermodynamic and phenomenological description of the transport properties of aqueous systems. Additionally, man-made nanopores and porous materials have emerged as promising solutions to challenging problems such as water purification, biosensing, nanofluidic logic and gating, and energy storage and conversion, while aquaporin, ion channels, and nuclear pore complex nanopores regulate many biological functions such as the conduction of water, the generation of action potentials, and the storage of genetic material. In this work, the more recent experimental and molecular simulations advances in this exciting and rapidly evolving field will be reported and critically discussed.

Toward Understanding Optical Properties of Amyloids: A Reaction Path and Nonadiabatic Dynamics Study.

Amyloids have unique structural, chemical, and optical properties. Although much theoretical effort has been directed toward understanding amyloid nucleation, the understanding of their optical properties has remained rather limited. In particular, the photophysical mechanisms leading to near-UV excitation and characteristic blue-green luminescence in amyloid systems devoid of aromatic amino acids have not been resolved. We use ab initio static calculations and nonadiabatic dynamics simulations to study the excited electronic states of model amyloid-like peptides. We show that their photophysics is essentially governed by the multitude of nπ* states with excitation localized on the amide groups. The strong stabilization of the nπ* states with respect to the amide group deplanarization and the concomitant increase of the oscillator strength make excitation in the near-UV possible. With respect to emission, our dynamics simulations revealed that the amyloid cross ß arrangement effectively hinders the nonradiative relaxation channels usually operative in proteins. Finally, we show that after relaxation of the photoexcited peptides toward the minimum of the different nπ* states, fluorescence takes place in the visible (green) part of the electromagnetic spectrum.

First-passage fingerprints of water diffusion near glutamine surfaces.

The extent to which biological interfaces affect the dynamics of water plays a key role in the exchange of matter and chemical interactions that are essential for life. The density and the mobility of water molecules depend on their proximity to biological interfaces and can play an important role in processes such as protein folding and aggregation. In this work, we study the dynamics of water near glutamine surfaces-a system of interest in studies of neurodegenerative diseases. Combining molecular-dynamics simulations and stochastic modelling, we study how the mean first-passage time and related statistics of water molecules escaping subnanometer-sized regions vary from the interface to the bulk. Our analysis reveals a dynamical complexity that reflects underlying chemical and geometrical properties of the glutamine surfaces. From the first-passage time statistics of water molecules, we infer their space-dependent diffusion coefficient in directions normal to the surfaces. Interestingly, our results suggest that the mobility of water varies over a longer length scale than the chemical potential associated with the water-protein interactions. The synergy of molecular dynamics and first-passage techniques opens the possibility for extracting space-dependent diffusion coefficients in more complex, inhomogeneous environments that are commonplace in living matter.

Is obesity associated with impaired reaction time in youth?

BACKGROUND AND PURPOSE: Recent research demonstrates a significant relationship between weight status and impaired reaction time in young, adult, and elderly individuals. However, most such studies were performed on small samples, used only body mass index as the body obesity index, used simple reaction time, and oftentimes did not consider some potential confounders such as age, socioeconomic status, or physical activity in their studies. The present study explored the relationship between various reaction time tasks and various obesity indices in a sample of youth. METHODS: Two hundred and thirty-four young males (19-24 years) underwent standard anthropometry, various information processing tasks (e.g., clinical reaction time, simple audio and visual reaction time, and choice reaction time), as well as an inhibitory control task (congruent and incongruent Simon reaction time). RESULTS: Results revealed no significant relationship between any of the information processing tests and body mass index, nor for fat percentage, waist circumference, and waist-to-height ratio after adjustment for potential confounders. A weak positive association was observed only between congruent Simon reaction time (but not incongruent Simon reaction time) and waist circumference in participants (t value = 0.199; Std error = 0.0014; p = 0.047; Cohen's f2 = 0.09). CONCLUSION: Inhibitory control, but not information processing speed, was associated only with waist circumference in apparently healthy young men. LEVEL OF EVIDENCE: Level I, experimental study.

Structural and dynamical heterogeneities at glutamine-water interfaces.

The behavior of water at the surfaces of solid amino acid crystals has received little attention despite its importance in nucleation processes. In this work, we take a first step to fill this gap by using molecular dynamics simulations to study the structural and dynamical properties of water near the (100), (010) and (001) surfaces of l-glutamine crystals. These highly hydrophilic surfaces serve as excellent model systems for interrogating the behavior of water. Despite having the same molecular composition, water at each surface displays characteristic structural, orientational and dynamical correlations. This behavior is tuned by how the different chemical groups of amino acids make contact with the liquid phase. All three surfaces yield a glassy layer of interfacial water which is reflected in different ways such as the presence of a rotationally arrested layer of water molecules and substantial slow down of the diffusion of water near the interface. By increasing the concentration of molecules in solution, we show that the binding of glutamine molecules to the crystal surface creates a crowded environment involving pockets of trapped water molecules altering the water dynamics in a highly non-trivial manner suggesting that the solvent dynamics may have important implications on crystal nucleation.

Low energy optical excitations as an indicator of structural changes initiated at the termini of amyloid proteins.

There is a growing body of experimental work showing that protein aggregates associated with amyloid fibrils feature intrinsic fluorescence. In order to understand the microscopic origin of this behavior observed in non-aromatic aggregates of peptides and proteins, we conducted a combined experimental and computational study on the optical properties of amyloid-derived oligopeptides in the near-UV region. We have focused on a few model systems having charged termini (zwitterionic) or acetylated termini. For the zwitterionic system, we were able to simulate the longer tail absorption in the near UV (250-350 nm), supporting the experimental results in terms of excitation spectra. We analyzed the optical excitations responsible for the low-energy absorption and found a large role played by charge-transfer states around the termini. These charge-transfer excitations are very sensitive to the conformation of the peptide and in realistic fibrils may involve inter and intra chain charge reorganization.

Thermal transport at a nanoparticle-water interface: A molecular dynamics and continuum modeling study.

Heat transfer between a silver nanoparticle and surrounding water has been studied using molecular dynamics (MD) simulations. The thermal conductance (Kapitza conductance) at the interface between a nanoparticle and surrounding water has been calculated using four different approaches: transient with/without temperature gradient (internal thermal resistance) in the nanoparticle, steady-state non-equilibrium, and finally equilibrium simulations. The results of steady-state non-equilibrium and equilibrium are in agreement but differ from the transient approach results. MD simulation results also reveal that in the quenching process of a hot silver nanoparticle, heat dissipates into the solvent over a length-scale of ∼2 nm and over a time scale of less than 5 ps. By introducing a continuum solid-like model and considering a heat conduction mechanism in water, it is observed that the results of the temperature distribution for water shells around the nanoparticle agree well with the MD results. It is also found that the local water thermal conductivity around the nanoparticle is greater by about 50% than that of bulk water. These results have important implications for understanding heat transfer mechanisms in nanofluid systems and also for cancer photothermal therapy, wherein an accurate local description of heat transfer in an aqueous environment is crucial.

Protons and Hydroxide Ions in Aqueous Systems.

Understanding the structure and dynamics of water's constituent ions, proton and hydroxide, has been a subject of numerous experimental and theoretical studies over the last century. Besides their obvious importance in acid-base chemistry, these ions play an important role in numerous applications ranging from enzyme catalysis to environmental chemistry. Despite a long history of research, many fundamental issues regarding their properties continue to be an active area of research. Here, we provide a review of the experimental and theoretical advances made in the last several decades in understanding the structure, dynamics, and transport of the proton and hydroxide ions in different aqueous environments, ranging from water clusters to the bulk liquid and its interfaces with hydrophobic surfaces. The propensity of these ions to accumulate at hydrophobic surfaces has been a subject of intense debate, and we highlight the open issues and challenges in this area. Biological applications reviewed include proton transport along the hydration layer of various membranes and through channel proteins, problems that are at the core of cellular bioenergetics.

Water Determines the Structure and Dynamics of Proteins.

Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.

Quantum mechanical effects in zwitterionic amino acids: The case of proline, hydroxyproline, and alanine in water.

In this work, we use ab initio molecular dynamics simulations to elucidate the electronic properties of three hydrated zwitterionic amino acids, namely proline, hydroxyproline, and alanine, the former two forming an important constituent of collagen. In all three systems, we find a substantial amount of charge transfer between the amino acids and surrounding solvent, which, rather surprisingly, also involves the reorganization of electron density near the hydrophobic non-polar groups. Water around proline appears to be slightly more polarized, as reflected by the enhanced water dipole moment in its hydration shell. This observation is also complemented by an examination of the IR spectra of the three systems where there is a subtle red and blue shift in the O-H stretch and bend regions, respectively, for proline. We show that polarizability of these amino acids as revealed by a dipole moment analysis involves a significant enhancement from the solvent and that this also involves non-polar groups. Our results suggest that quantum mechanical effects are likely to be important in understanding the coupling between biomolecules and water in general and in hydrophobic interactions.

Central or overall obesity: which one is a better predictor of depressive symptoms in children, adolescents, and youths?

BACKGROUND AND PURPOSE: Despite the strong effect of central obesity on individuals' physical health outcomes, there is little evidence underlying the relationship between central obesity and mental disorders such as depression, especially in children, adolescents, and youths of the developing countries. This study explores the relationship between depressive symptoms (DS) with central and overall obesity in a sample of Iranian children, adolescents, and youths. METHODS: One thousand and fifty-two male participants ranging from 7 to 24 years old underwent standard anthropometry, and filled the DS questionnaire. RESULTS: Having controlled the potential confounders (e.g., age, socioeconomic status, pubertal maturation status, and physical activity), we found waist circumference (WC) significantly related to DS in the children (standardized ß = 0.14; P < 0.05) and adolescents (standardized ß = 0.13; P < 0.05). No significant relationship was observed between WC and DS in the youths (standardized ß = 0.09; P = 0.22). In addition, no significant relationship was observed between DS and the percentage of fat in the sampled children (standardized ß = 0.085; P = 0.13), adolescents (standardized ß = 0.10; P = 0.10), and youths (standardized ß = -0.02; P = 0.75). CONCLUSION: Central obesity (but not overall obesity) was a significant predictor of DS in the children and adolescents (7-18 years). However, DS in the youths (19-24 years) were not significantly associated with both the central and overall body obesity indices.