The 50 most-cited articles in The Journal of Physical Chemistry B, 2020

Biomimetic nanosurfaces with distinct wettability and versatility have found special enthusiasm in both fundamental research and industrial applications. With the advent of nanotechnology, it is doable to acclimate surface architecture and surface chemistry to attain superhydrophobicity. The uniqueness of superhydrophobic surfaces arises from various phenomenal advances, and its progress is expected to continue for decades in the future. In this Review Article, we discuss recent progress made in defining physical aspects of numerical modeling, experimental practices adopted, and applications of superhydrophobic surfaces. First, we revisit various classical models of superhydrophobicity and recent theoretical advances achieved related to the wetting phenomena. Subsequently, we emphasize various precursors and advance fabrication strategies adopted to fabricate superhydrophobic surfaces. In the following section, we take up various potential applications and appropriate working principles to explain wettability phenomena. Finally, some general conclusions are drawn along with proposed…

This technical study describes all-atom modeling and simulation of a fully glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB: 6VSB and 6VXX, full-length S protein structures were modeled using template-based modeling, de-novo protein structure prediction, and loop modeling techniques in GALAXY modeling suite. Then, using the recently determined most occupied glycoforms, 22 N-glycans and 1 O-glycan of each monomer were modeled using Glycan Reader & Modeler in CHARMM-GUI. These fully glycosylated full-length S protein model structures were assessed and further refined against the low-resolution data in their respective experimental maps using ISOLDE. We then used CHARMM-GUI Membrane Builder to place the S proteins in a viral membrane and performed all-atom molecular dynamics simulations. All structures are available in CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19) so that researchers can use these models to carry out innovative and novel modeling and simulation research for the prevention and treatment of…

The formation of membraneless organelles in cells commonly occurs via liquid-liquid phase separation (LLPS) and is in many cases driven by multivalent interactions between intrinsically disordered proteins (IDPs). Investigating the nature of these interactions, and their effect on dynamics within the condensed phase, is therefore of critical importance but very challenging for either simulation or experiment. Here, we study these interactions and their dynamics by pairing a novel multiscale simulation strategy with microsecond all-atom MD simulations of a condensed, IDP-rich phase. We simulate two IDPs this way, the low complexity domain of FUS and the N-terminal disordered domain of LAF-1, and find good agreement with experimental information about average density, water content, and residue-residue contacts. We go significantly beyond what is known from experiments by showing that ion partitioning within the condensed phase is largely driven by the charge distribution of the proteins and-in the cases considered-shows little evidence of preferential interactions of the ions with…

In the last 5 years, the use of deep eutectic solvents (DESs) have been opening new perspectives toward the creation of novel ionic soft materials as alternatives to expensive ionic liquids. This Mini-Review Article highlights the progress and advances in soft ionic materials or gels, mostly composed by a DES immobilized within difference matrices, such as linear polymers, polymer networks, biopolymers, supramolecular compounds, or sol-gel derived silica networks. By taking advantage of the DESs characteristics and properties in the solid state, this building system delivers a variety of tailor-made materials showing different functionalities (ionic conductivity, self-healing, stretchability and pH-responsiveness) and offers a way to circumvent drawbacks related to shaping and risk of leakage in many technological applications. In this context, we provide a judicious analysis of these emerging ionic soft materials, their properties, and applications open in energy, (bio)electronics, drug delivery, analytical chemistry, and wastewater treatment. Perspectives and opportunities for…

molecular dynamics, and classical molecular dynamics simulations are used to probe the structural, thermodynamic, and transport properties of a deep eutectic solvent comprised of a 1:2 molar ratio of choline chloride and ethylene glycol. This mixture, known as Ethaline, has many desirable properties for use in a range of applications, and therefore, understanding its liquid structure and transport properties is of interest. Simulation results are able to capture experimental densities, diffusivities, viscosities, and structure factors extremely well. The solvation environment is dynamic and dominated by different hydrogen bonding interactions. Dynamic heterogeneities resulting from hydrogen bonding interactions are quantified. Rotational dynamics of molecular dipole moments of choline and ethylene glycol are computed and found to exhibit a fast and slow mode.

High Resolution Image Download MS PowerPoint Slide Starting from late 2019, the coronavirus disease 2019 (COVID-19) has emerged as a once-in-a-century pandemic with deadly consequences, which urgently calls for new treatments, cures, and supporting apparatuses. Recently, because of its positive results in clinical trials, remdesivir was approved by the Food and Drug Administration to treat COVID-19 through Emergency Use Authorization. Here, we used molecular dynamics simulations and free energy perturbation methods to study the inhibition mechanism of remdesivir to its target SARS-CoV-2 virus RNA-dependent RNA polymerase (RdRp). We first constructed the homology model of this polymerase based on a previously available structure of SARS-CoV NSP12 RdRp (with a sequence identity of 95.8%). We then built a putative preinsertion binding structure by aligning the remdesivir + RdRp complex to the ATP bound poliovirus RdRp without the RNA template. The putative binding structure was further optimized with molecular dynamics simulations. The resulting stable preinsertion state of remdesivir…

We investigate the polariton-mediated electron transfer reaction in a model system with analytic rate constant theory and direct quantum dynamical simulations. We demonstrate that the photoinduced charge transfer reaction between a bright donor state and dark acceptor state can be significantly enhanced or suppressed by coupling the molecular system to the quantized radiation field inside an optical cavity. This is because the quantum light-matter interaction can influence the effective driving force and electronic couplings between the donor state, which is the hybrid light-matter excitation, and the molecular acceptor state. Under the resonance condition between the photonic and electronic excitations, the effective driving force can be tuned by changing the light-matter coupling strength; for an off-resonant condition, the same effect can be accomplished by changing the molecule-cavity detuning. We further demonstrate that using both the electronic coupling and light-matter coupling helps to extend the effective couplings across the entire system, even for the dark state that…

Ab initio molecular dynamics simulations at elevated temperature are carried out to investigate the microscopic structure of liquid mixtures (deep eutectic solvents) composed of 1:1 and 1:2 choline chloride:ethylene glycol ([Ch]Cl:EG) and 1:2:1 choline chloride:ethylene glycol:water ([Ch]Cl:EG:water). In the present study, we aim to understand the composition effect on the choline chloride:ethylene glycol deep eutectic solvent and whether there is a specific composition in these solvents with marked special behavior at the microscopic level. The role of hydrogen bonds between all components was investigated through distribution functions. The structures are governed by the balance of hydrogen bond networks and the different populations of the EG molecule conformations. In the water-containing system, water competes for association with the anion. Also, the charge distribution analysis, which is consistent with structural analysis, indicates that the results are not impacted by changing composition. In addition, the charge transfer observed between ions, EG, and water molecules…

Abstract Membraneless organelles are dynamical cellular condensates formed by the liquid-liquid phase separation of proteins and RNA molecules. Multiple evidence suggests that disordered proteins are structural scaffolds that drive the condensation by forming a dynamic network of inter- and intra-molecular contacts. Despite the blooming research activity in this field, the structural characterization of these condensates is very limited and we still do not understand how the phase behaviour is encoded in the amino-acid sequences of the scaffolding proteins. Here we exploited explicit-solvent atomistic simulations to disentangle the molecular interactions governing the phase behaviour of the N-terminal disordered region of DEAD-box helicase 4 (NDDX4), which is a well-established model for phase separation in vitro and in vivo . Single-molecule simulations clarified the interplay between the intramolecular interactions that shape NDDX4 conformational ensemble and the known determinants of its phase behaviour, such as the attraction between oppositely-charged regions and the presence…

In the past decade, researchers have put forth a lot of efforts to conceive a precise structural arrangement and properties of deep eutectic solvents (DESs) that provide designer pathways in order to broaden the application domain of these solvents. However, these contributions are limited to a few experimental and computational techniques. In this review, we have encompassed experimental techniques employed to establish the structure-property relationship of bulk DESs along with recent growth witnessed in this domain from a computational perspective. The nanostructuring plays an important role in various task specific applications of DESs. These solvents are found to exhibit unique heterogeneity at nanolength scales, the origin of which is unique and primarily depends on the constituent species involved. The hygroscopic nature of some DESs makes it crucial to explore the structural anatomy of hydrated DESs. Hence, this opens another subdomain to explore the impact of hydration on the bulk microscopic structure of DES and to know whether the nature is destructuring or structuring…

Abstract The 2019 novel coronavirus (SARS-CoV-2) epidemic, which was first reported in December 2019 in Wuhan, China, was declared a pandemic by the World Health Organization in March 2020. Genetically, SARS-CoV-2 is closely related to SARS-CoV, which caused a global epidemic with 8096 confirmed cases in more than 25 countries from 2002 to 2003. Given the significant morbidity and mortality rate, the current pandemic poses a danger to all of humanity, prompting us to understand the activity of SARS-CoV-2 at the atomic level. Experimental studies have revealed that spike proteins of both SARS-CoV-2 and SARS-CoV bind to angiotensin-converting enzyme 2 (ACE2) before entering the cell for replication. However, the binding affinities reported by different groups seem to contradict each other. Wrapp et al. (Science 2020, 367, 1260–1263) showed that the spike protein of SARS-CoV-2 binds to the ACE2 peptidase domain (ACE2-PD) more strongly than does SARS-CoV, and this fact may be associated with a greater severity of the new virus. However, Walls et al. (Cell 2020, 181, 281–292) reported…

Recently, it has been observed that choline chloride ([Ch][Cl]) based deep eutectic solvents (DESs) may possess nanostructures in which chloride ions play a major role by providing a backbone for the bridged hydrogen bond network. In this article, we present a fundamental study on the role of hydration on the nanostructure of a [Ch][Cl] based DES, ethaline. In this molecular dynamics investigation, we observe a nonlinear change in the structural morphology of ethaline on gradual addition of water. The initiation of disruption of the native structure of the DES at 40 mol % of water is clearly observed, after which the increasing dilution rapidly destructs the long-range as well as short-range intermolecular interactions existing between the constituent species of pure ethaline. Herein, we find that, at very high hydration level, chloride ion no longer acts as a bridge between the choline cation and ethylene glycol, as it forms strong hydrogen bond with water. Intriguingly, the strengthening of hydrogen bonding interactions among the ethylene glycol molecules is observed on increasing…

Abstract For estimating the infection risk from virus-containing airborne droplets, it is crucial to consider the interplay of all relevant physical-chemical effects that affect droplet evaporation and sedimentation times. For droplet radii in the range 70 nm < R < 60 μm, evaporation can be described in the stagnant-flow approximation and is diffusion-limited. Analytical equations are presented for the droplet evaporation rate, the time-dependent droplet size, and the sedimentation time, including evaporation cooling and solute osmotic-pressure effects. Evaporation makes the time for initially large droplets to sediment much longer and thus significantly increases the viral air load. Using recent estimates for SARS-CoV-2 concentrations in sputum and droplet production rates while speaking, a single infected person that constantly speaks without a mouth cover produces a total steady-state air load of more than 104 virions at a given time. In a midsize closed room, this leads to a viral inhalation frequency of at least 2.5 per minute. Low relative humidity, as encountered in airliners…

Abstract The ability to accurately compute low-energy excited states of chlorophylls is critically important for understanding the vital roles they play in light harvesting, energy transfer, and photosynthetic charge separation. The challenge for quantum chemical methods arises both from the intrinsic complexity of the electronic structure problem and, in the case of biological models, from the need to account for protein–pigment interactions. In this work, we report electronic structure calculations of unprecedented accuracy for the low-energy excited states in the Q and B bands of chlorophyll a. This is achieved by using the newly developed domain-based local pair natural orbital (DLPNO) implementation of the similarity transformed equation of motion coupled cluster theory with single and double excitations (STEOM-CCSD) in combination with sufficiently large and flexible basis sets. The results of our DLPNO–STEOM-CCSD calculations are compared with more approximate approaches. The results demonstrate that, in contrast to time-dependent density functional theory, the…

Polyhexamethylene biguanide (PHMB) is a cationic polymer with antimicrobial and antiviral properties. It has been commonly accepted that the antimicrobial activity is due to the ability of PHMB to perforate the bacterial phospholipid membrane leading ultimately to its death. In this study, we show by the means of atomistic molecular dynamics (MD) simulations that, while the PHMB molecules attach to the surface of the phospholipid bilayer and partially penetrate it, they do not cause any pore formation at least within the microsecond simulation times. The polymers initially adsorb onto the membrane surface via the favorable electrostatic interactions between the phospholipid headgroups and the biguanide groups and then partially penetrate the membrane slightly disrupting its structure. This, however, does not lead to the formation of any pores. The microsecond-scale simulations reveal that it is unlikely for PHMB to spontaneously pass through the phospholipid membrane. Our findings suggest that PHMB translocation across the bilayer may take place through binding to the phospholipids.…

Abstract Electronically active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from π-conjugated oligopeptides composed of an aromatic core flanked by oligopeptide wings offer emergent optoelectronic properties within a water-soluble and biocompatible substrate. Nanoaggregate properties can be controlled by tuning core chemistry and peptide composition, but the sequence–structure–function relations remain poorly characterized. In this work, we employ coarse-grained molecular dynamics simulations within an active learning protocol employing deep representational learning and Bayesian optimization to efficiently identify molecules capable of assembling pseudo-1D nanoaggregates with good stacking of the electronically active π-cores. We consider the DXXX-OPV3-XXXD oligopeptide family, where D is an Asp residue and OPV3 is an oligophenylenevinylene oligomer (1,4-distyrylbenzene), to identify the top performing XXX tripeptides within all 203 = 8000 possible sequences. By direct simulation…

Abstract Hydrophobicity is a phenomenon of great importance in biology, chemistry, and biochemistry. It is defined as the interaction between nonpolar molecules or groups in water and their low solubility. Hydrophobic interactions affect many processes in water, for example, complexation, surfactant aggregation, and coagulation. These interactions play a pivotal role in the formation and stability of proteins or biological membranes. In the present study, we assessed the effect of ionic strength, solute size, and shape on hydrophobic interactions between pairs of nonpolar particles. Pairs of methane, neopentane, adamantane, fullerene, ethane, propane, butane, hexane, octane, and decane were simulated by molecular dynamics in AMBER 16.0 force field. As a solvent, TIP3P and TIP4PEW water models were used. Potential of mean force (PMF) plots of these dimers were determined at four values of ionic strength, 0, 0.04, 0.08, and 0.40 mol/dm3, to observe its impact on hydrophobic interactions. The characteristic shape of PMFs with three extrema (contact minimum, solvent-separated minimum,…

Over 50 peptides, which were known to inhibit SARS-CoV-1, were computationally screened against the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2. Based on the binding affinity and interaction, 15 peptides were selected, which showed higher affinity compared to the α-helix of the human ACE2 receptor. Molecular dynamics simulation demonstrated that two peptides, S2P25 and S2P26, were the most promising candidates, which could potentially block the entry of SARS-CoV-2. Tyr489 and Tyr505 residues present in the "finger-like" projections of the RBD were found to be critical for peptide interaction. Hydrogen bonding and hydrophobic interactions played important roles in prompting peptide-protein binding and interaction. Structure-activity relationship indicated that peptides containing aromatic (Tyr and Phe), nonpolar (Pro, Gly, Leu, and Ala), and polar (Asn, Gln, and Cys) residues were the most significant contributors. These findings can facilitate the rational design of selective peptide inhibitors targeting the spike protein of SARS-CoV-2.

The outbreak of a new coronavirus SARS-CoV-2 (severe acute respiratory syndrome-coronavirus 2) has caused a global COVID-19 (coronavirus disease 2019) pandemic, resulting in millions of infections and thousands of deaths around the world. There is currently no drug or vaccine for COVID-19, but it has been revealed that some commercially available drugs are promising, at least for treating symptoms. Among them, remdesivir, which can block the activity of RNA-dependent RNA polymerase (RdRp) in old SARS-CoV and MERS-CoV viruses, has been prescribed to COVID-19 patients in many countries. A recent experiment showed that remdesivir binds to SARS-CoV-2 with an inhibition constant of μM, but the exact target has not been reported. In this work, combining molecular docking, steered molecular dynamics, and umbrella sampling, we examined its binding affinity to two targets including the main protease (Mpro), also known as 3C-like protease, and RdRp. We showed that remdesivir binds to Mpro slightly weaker than to RdRp, and the corresponding inhibition constants, consistent with the experiment,…

Machine learning has revolutionized the high-dimensional representations for molecular properties such as potential energy. However, there are scarce machine learning models targeting tensorial properties, which are rotationally covariant. Here, we propose tensorial neural network (NN) models to learn both tensorial response and transition properties in which atomic coordinate vectors are multiplied with scalar NN outputs or their derivatives to preserve the rotationally covariant symmetry. This strategy keeps structural descriptors symmetry invariant so that the resulting tensorial NN models are as efficient as their scalar counterparts. We validate the performance and universality of this approach by learning response properties of water oligomers and liquid water and transition dipole moment of a model structural unit of proteins. Machine-learned tensorial models have enabled efficient simulations of vibrational spectra of liquid water and ultraviolet spectra of realistic proteins, promising feasible and accurate spectroscopic simulations for biomolecules and materials.

-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. New vapor pressure osmometry and molecular dynamics simulation results on urea-TMAO solutions are presented, and a unified molecular mechanism of TMAO counteraction of urea-induced protein denaturation is introduced. In addition, a detailed technical assessment of molecular dynamics force fields for TMAO and for urea-TMAO solutions is presented. The force field analysis highlights how many of the commonly used force field models are in fact incompatible with solvation thermodynamics and can lead to misleading conclusions. A new optimized force field for TMAO (Shea(m)) is presented, and a recently optimized force field for TMAO-urea (Netz(m)) that best reproduces experimental data is highlighted.

Dielectric water properties, which significantly change in confinement, determine electrostatic interactions and thereby influence all molecular forces and chemical reactions. We present comparative simulations of water between graphene sheets, decanol monolayers, and phospholipid and glycolipid bilayers. Generally, dielectric profiles strongly differ in perpendicular and parallel surface directions and for large surface separation decay to the bulk value 1-2 nm away from the surface. Polar surface groups enhance the local interfacial dielectric response and for phospholipid bilayers induce a giant parallel contribution. A mapping on a box model with asymptotically determined effective water layer widths demonstrates that the perpendicular effective dielectric constant for all systems decreases for confinement below a nanometer, while the parallel one stays rather constant. The confinement-dependent perpendicular effective dielectric constant for graphene is in agreement with experimental data only if the effective water layer width is suitably adjusted. The interactions between two…

reduction, cationic surfactants promote carbon product formation and suppress hydrogen evolution. The interfacial field produced by the surfactants affects the energetics of electrochemical intermediates, mandating their detailed understanding. We have used two complementary tools-vibrational Stark shift spectroscopy which probes interfacial fields at molecular length scales and electrochemical impedance spectroscopy (EIS) which probes the entire double layer-to study the electric fields at metal-surfactant interfaces. Using a nitrile as a probe, we found that at open-circuit potentials, cationic surfactants produce larger effective interfacial fields (∼-1.25 V/nm) when compared to anionic surfactants (∼0.4 V/nm). At a high bulk surfactant concentration, the surface field reaches a terminal value, suggesting the formation of a full layer, which is also supported by EIS. We propose an electrostatic model that explains these observations. Our results help in designing tailored surfactants for influencing electrochemical reactions via the interfacial field effect.

, 2938-2948) generally provides a good description of various lipid bilayer systems. However, it was also found that order parameters of C-H bonds in the glycerol moiety of the phosphatidylcholine headgroup deviate significantly from NMR results. In this work, the dihedral force field parameters have been reparameterized in order to improve the agreement with experiment. For this purpose, we have computed energies for a large amount of lipid headgroup conformations using density functional theory on the B3P86/cc-pvqz level and optimized dihedral angle parameters simultaneously to provide the best fit to the quantum chemical energies. The new parameter set was validated for three lipid bilayer systems against a number of experimental properties including order parameters, area per lipid, scattering form factors, bilayer thickness, area compressibility and lateral diffusion coefficients. In addition, the order parameter dependence on cholesterol content in the POPC bilayer was investigated. It is shown that the new force field significantly improves agreement with the experimental…

Membrane-less organelles, the liquid droplets formed via liquid–liquid phase separation (LLPS) of biomolecules in cells, act to organize intracellular components into multiple compartments. As a model for this process, and as a potential vehicle for in vitro exploitation of its properties, we explore here a synthetic multiphase LLPS system consisting of a mixture of self-assembled DNA particles. The particles, termed “DNA nanostars” (NSs), consist of four double-stranded DNA arms that each terminate in a single-stranded overhang. NSs condense into droplets due to overhang hybridization. Using two types of NSs with orthogonal overhangs enables the creation of two types of immiscible DNA droplets. Adhesion between the droplets can be tuned by the addition of “cross-linker NSs” that have two overhang sequences of each type. We find that increasing the amount of the cross-linker NSs decreases the droplet/droplet surface tension until a microemulsion transition occurs. Controlled droplet adhesion can also be achieved, without cross-linkers, using overhangs that can weakly hybridize.…

A significant fraction of the cell volume is occupied by various proteins, polysaccharides, nucleic acids, etc., which considerably reduces the mobility of macromolecules. Theoretical and experimental work so far have mainly focused on the dependence of the mobility on the occupied volume, while the effect of a macromolecular shape received less attention. Herein, using fluorescence correlation spectroscopy (FCS) and Brownian dynamics (BD) simulations, we report on a dramatic slowdown of tracer diffusion by cylindrically shaped double-stranded (ds) DNAs (16 nm in length). We find, for instance, that the translational diffusion coefficient of a streptavidin tracer is reduced by about 60% for a volume fraction of dsDNA as low as just 5%. For comparison, for a spherical crowder (Ficoll70) the slowdown is only 10% at the same volume fraction and 60% reduction occurs at a volume fraction as high as 35%. BD simulations reveal that this reduction can be attributed to a larger volume excluded to a tracer by dsDNA particles, as compared with spherical Ficoll70 at the same volume fraction,…

Abstract We herein report an all-atom molecular dynamics study on the role of solvent polarity for Li+ diffusion in polymer electrolytes using PEO–LiTFSI (poly(ethylene oxide)–lithium bis(trifluoromethane)sulfonimide) as a model system. By separating the effect of Tg and the effect of solvent polarity in our simulations, we show that the maximum in the diffusion coefficient of Li+ with respect to the dielectric constant of polymer solvent εp is due to transitions in the transport mechanism. In particular, it is found that the frequent interchain hopping involves the coordination of both PEO and TFSI. This optimal solvating ability of PEO at an intermediate value of εp leads to the fast ion conduction. These findings highlight the synergetic effect of solvent polarity and bond polarity on Li-ion diffusion in solid polymer electrolytes.

Water is arguably the most common and yet least understood material on Earth. The interface between water and a hydrophobic medium, such as air, oil, or lipids, plays a fundamental role in chemistry and biology. However, the behavior of molecules at interface of micron-sized water droplets (microdroplets) in such media is poorly characterized. Herein we employed two-photon fluorescence microscopy and Förster resonant energy transfer imaging to study the probe localization in water-oil microdroplets with high contrast and resolution. We found that there exists a general effect of surface enrichment and orientation alignment for water-soluble probes. Remarkably, probes are concentrated into a ∼10 nm thin layer at the microdroplet water-oil interface by up to 10 000-fold compared to the bulk counterpart. We suggest that the strong enrichment and alignment of water-soluble molecules, likely to be induced in part by a local electric field at the interface, could be a major factor accounting for orders of magnitude faster reaction rates observed in aqueous microdroplets compared to their…

The UV-to-IR transitions in p-doped poly(3-hexylthiophene) (P3HT) with alkyl side chains and polar polythiophene with tetraethylene glycol side chains are studied experimentally by means of the absorption spectroscopy and computationally using density functional theory (DFT) and tight-binding DFT. The evolution of electronic structure is calculated as the doping level is varied, while the roles of dopant ions, chain twisting, and π-π stacking are also considered, each of these having the effect of broadening the absorption peaks while not significantly changing their positions. The calculated spectra are found to be in good agreement with experimental spectra obtained for the polymers doped with a molybdenum dithiolene complex. As in other DFT studies of doped conjugated polymers, the electronic structure and assignment of optical transitions that emerge are qualitatively different from those obtained through earlier "traditional" approaches. In particular, the two prominent bands seen for the p-doped materials are present for both polarons and bipolarons/polaron pairs. The lowest…

Abstract The enzyme-catalyzed degradation of the biogenic amine serotonin is an essential regulatory mechanism of its level in the human organism. In particular, monoamine oxidase A (MAO A) is an important flavoenzyme involved in the metabolism of monoamine neurotransmitters. Despite extensive research efforts, neither the catalytic nor the inhibition mechanisms of MAO enzymes are currently fully understood. In this article, we present the quantum mechanics/molecular mechanics simulation of the rate-limiting step for the serotonin decomposition, which consists of hydride transfer from the serotonin methylene group to the N5 atom of the flavin moiety. Free-energy profiles of the reaction were computed by the empirical valence bond method. Apart from the enzymatic environment, the reference reaction in the gas phase was also simulated, facilitating the estimation of the catalytic effect of the enzyme. The calculated barrier for the enzyme-catalyzed reaction of 14.82 ± 0.81 kcal mol–1 is in good agreement with the experimental value of 16.0 kcal mol–1, which provides strong evidence…

High concentration lithium electrolytes have been found to be good candidates for high energy density and high voltage lithium batteries. Recent studies have shown that limiting the free solvent molecules in the electrolytes prevents the degradation of the battery electrodes. However, the molecular level knowledge of the structure and dynamics of such an electrolyte system is limited, especially for electrolytes based on typical organic carbonates. In this article, the interactions and motions involved in lithium bis(trifluoromethanesulfonyl)imide in carbonyl-containing solvents are investigated using linear and time-resolved vibrational spectroscopies and computational methods. Our results suggest that the overall structure and the speciation of the three high concentration electrolytes are similar. However, the cyclic carbonate-based electrolyte presents an additional interaction as a result of dimer formation. Time-resolved studies reveal similar and fast dynamics for the structural motions of solvent molecules in electrolytes composed of linear molecules, while the electrolyte…

We analyze the influence of the asymmetry of the anion on coordination and transport processes in a Li salt/ionic liquid system. The relatively new asymmetric 2,2,2-trifluoromethylsulfonyl- N -cyanamide (TFSAM) anion was investigated in Pyr 14 TFSAM (1– x ) LiTFSAM x over a broad concentration range (up to x = 0.7 Li salt) and was compared to the well-known bis(trifluoromethanesulfonyl)amide (TFSA) anion. In contrast to the TFSA-based system, the system with TFSAM has no phase transition over the whole concentration range. Raman spectroscopy and NMR chemical shifts elucidate the Li coordination in detail. Up to x = 0.3, the asymmetric anion coordinates to Li + only via the cyano group. With increasing Li salt fraction, the contribution of Li–oxygen coordination increases. This coordination effects influence the transport properties of the system, as examined via pulsed-field-gradient NMR (PFG-NMR). Although the overall diffusivity of both systems is decreasing because of viscosity effects, the relative diffusivity of the Li cation is increasing with x . This suggests a change in the…

Cl were considered as the hydrogen bond acceptors (HBA). Molecular dynamics simulation (MD) was used as a tool to examine the distribution of molecules of DES and water in either phase. The intermolecular nonbonded interaction among the species of the systems was analyzed with radial distribution function, interaction energy, and hydrogen-bonding analysis to understand the stability of DESs in an aqueous medium. The results showed that the strong hydrogen bond plays a crucial role in the water stability of the DES. The degree of hydrogen bonding in HBD-water in terms of HBDs obtained by MD simulation can be presented in the order of acetic acid > levulinic acid > butanoic acid > pyruvic acid > hexanoic acid > octanoic acid > decanoic acid > dodecanoic acid. The strength of the hydrogen bond was attributed to the structure of solvents and the alkyl chain length of the HBD group. Overall, the order of stability of DES in water based on a "relative stability factor" was found as dl-menthol:acetic acid (1:1) < dl-menthol: levulinic acid (1:1) < dl-menthol:butanoic acid (1:1) <…

Abstract The mechanism and the nature of the species formed by molecular doping of the model polymer poly(3-hexylthiophene) (P3HT) in its regioregular (rre-) and regiorandom (rra-) forms in solution are investigated for three different dopants: the prototypical π-electron acceptor 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ), the strong Lewis acid tris(pentafluorophenyl)borane (BCF), and the strongly oxidizing complex molybdenum tris[1-(methoxycarbonyl)-2-(trifluoromethyl)ethane-1,2-dithiolene] (Mo(tfd-CO2Me)3). In a combined optical and electron paramagnetic resonance study, we show that the doping of rreP3HT in solution occurs by integer charge transfer, resulting in formation of P3HT radical cations (polarons) for all of the dopants considered here. Remarkably, despite the different chemical nature of the dopants and dopant–polymer interaction, the formed polarons exhibit essentially identical optical absorption spectra. The situation is very different for the doping of rraP3HT, where we observe formation of a charge-transfer complex with F4TCNQ and of a…

The two sugar molecules sucrose and trehalose are both considered as stabilizing molecules for the purpose of preserving biological materials during, for example, lyophilization or cryo-preservation. Although these molecules share a similar molecular structure, there are several important differences in their properties when they interact with water, such as differences in solubility, viscosity, and glass transition temperature. In general, trehalose has been shown to be more efficient than other sugar molecules in preserving different biological molecules against stress, and thus by investigating how these two disaccharides differ in their water interaction, it is possible to further understand what makes trehalose special in its stabilizing properties. For this purpose, the structure of aqueous solutions of these disaccharides was studied by using neutron and X-ray diffraction in combination with empirical potential structure refinement (EPSR) modeling. The results show that there are surprisingly few differences in the overall structure of the solutions, although there are…

The degree of crystallinity of a polymer is a critical parameter that controls a variety of polymer properties. A high degree of crystallinity is associated with excellent mechanical properties crucial for high-performing applications like composites. Low crystallinity promotes ion and gas mobility critical for battery and membrane applications. Experimental determination of the crystallinity for new polymers is time and cost intensive. A data-driven machine learning-based method capable of rapidly predicting the crystallinity could counter these disadvantages and be used to screen polymers for a myriad of applications in a fast, inexpensive fashion. In this work, we developed the first-of-its-kind, data-driven machine learning model to predict the most-likely polymer crystallinity trained on experimental data and theoretical group contribution methods. Since polymer data under consistent processing conditions are unavailable, we tackled process variability by using the "most-likely" polymer values which we refer to as the polymer's tendency to crystallize. Experimental data for…

Transformation of glasses into liquids is discussed in terms of configuron (broken chemical bond or transformation of an atom from one to another atomic shell) percolation theory with structural changes caused. The first sharp diffraction minimum (FSDM) in the pair distribution function (PDF) is shown to contain information on structural changes in amorphous materials at the glass transition temperature ( T g ). A method to determine the glass transition temperature is proposed based on allocating T g to the temperature when a sharp kink in FSDM occurs. The method proposed is more sensitive compared with empirical criterion of Wendt–Abraham; e.g., for amorphous Ni the kink that determines T g is almost twice sharper. Connection between the kink in fictive temperature behavior of PDF and Wendt–Abraham criterion is discussed.

Plasma membranes (PMs) contain hundreds of different lipid species that contribute differently to overall bilayer properties. By modulation of these properties, membrane protein function can be affected. Furthermore, inhomogeneous lipid mixing and domains of lipid enrichment/depletion can sort proteins and provide optimal local environments. Recent coarse-grained (CG) Martini molecular dynamics efforts have provided glimpses into lipid organization of different PMs: an "Average" and a "Brain" PM. Their high complexity and large size require long simulations (∼80 μs) for proper sampling. Thus, these simulations are computationally taxing. This level of complexity is beyond the possibilities of all-atom simulations, raising the question-what complexity is needed for "realistic" bilayer properties? We constructed CG Martini PM models of varying complexity (63 down to 8 different lipids). Lipid tail saturations and headgroup combinations were kept as consistent as possible for the "tissues'" (Average/Brain) at three levels of compositional complexity. For each system, we analyzed…

In this article, we propose a new excited state dynamics mechanism for quinoline–pyrazole isomers (QP-1 and QP-2) in the liquid phase based on the time-dependent density functional theory (TD-DFT) method. The calculated potential energy curve shows that QP-2 is more likely to occur as an excited state intramolecular proton-transfer (ESIPT) process than QP-1, whereas QP-2 will occur as a twisted intramolecular charge transfer (TICT) process, which is also the main decay pathway of QP-2 fluorescence quenching. The TICT process is not involved in QP-1 due to the high energy barrier. Based on excited state energy decomposition and charge decomposition analysis, it is determined that the energy gap and hole–electron interaction are the main driving forces that can cause the TICT process to occur. These results are inconsistent with the conclusions of recent theoretical reports [ J. Phys. Chem. A 2015, 119, 6269–6247], in which the authors proposed that QP-2 will not twist after proton transfer (PT-2) in the lowest singlet excited state, and its fluorescence quenching pathway is the rapid…

Deep-eutectic solvents (DESs) are a new class of green solvents. Here, we report the hydrogen bonding and structural properties of the archetypal DES ethaline, a mixture of choline chloride (ChCl) and ethylene glycol (EG) of a 1:2 molar ratio, and its pseudo-binary mixtures with acetonitrile. The investigations were carried out employing Fourier-transform infrared (FTIR) spectroscopy combined with quantum chemical calculations. Excess and two-dimensional (2D)-correlation spectroscopies were used to identify favorable species in the solutions and to explore the heterogeneity. The results show that the mixing process is the transformation from ethaline and CH 3 CN dimer to the complexes of ethaline–1CH 3 CN and ethaline–2CH 3 CN, together with the increased percentages of the EG dimer, EG trimer, and CH 3 CN monomer with respect to their total amounts in the mixtures. Theoretical calculations show that, for ChCl, the positive charge is located at the methyl groups and methylenes, rendering their ability to form hydrogen bonds. Adding CH 3 CN to ethaline can hardly break apart the…

We address the problem of efficient phase diagram sampling by adopting active learning techniques from machine learning and achieve drastic reduction in the sample size (number of sampled state points) needed to establish the phase boundary up to a given precision. Although advanced sampling techniques such as Gibbs ensemble and Gibbs-Duhem integration can sample phase equilibria efficiently, they may fail to generalize to many nonequilbrium systems. This forces researchers to resort to grid search simulations when studying many important active matter systems. Grid search suffers from low efficiency by sampling predetermined state points that provide little information about the phase boundaries. We propose an active learning framework to overcome this deficiency by adaptively choosing the next most informative state point(s) every round. This is done by interpolating the sampled state points' phases by Gaussian process regression and then using an acquisition function to quantify the informativeness of possible next state points. We generalize our approach with asynchronous…

Thin polymer films have found many important applications in organic electronics, such as active layers, protective layers, or antistatic layers. Among the various experimental methods suitable for studying the thermo-optical properties of thin polymer films, temperature-dependent spectroscopic ellipsometry plays a special role as a nondestructive and very sensitive optical technique. In this Review Article, issues related to the physical origin of the dependence of ellipsometric angles on temperature are surveyed. In addition, the Review Article discusses the use of temperature-dependent spectroscopic ellipsometry for studying phase transitions in thin polymer films. The benefits of studying thermal transitions using different cooling/heating speeds are also discussed. Furthermore, it is shown how the analysis and modeling of raw ellipsometric data can be used to determine the thermal properties of thin polymer films.

The design and engineering of composite materials is one strategy to satisfy the materials needs of systems with multiple orthogonal property requirements. In the case of rechargeable batteries with lithium metal anodes, the system requires a separator with fast lithium ion transport and good mechanical strength. In this work, we focus on the system polystyrene- block -poly(ethylene oxide) (SEO) with bis(trifluoromethane)sulfonimide lithium salt (LiTFSI). Ion transport occurs in the salt-containing poly(ethylene oxide)-rich domains. Mechanical rigidity arises due to the glassy nature of polystyrene (PS). If we assume that the salt does not interact with the PS-rich domains, we can describe ion transport in the electrolyte by three transport parameters (ionic conductivity, κ, salt diffusion coefficient, D, and cation transference number, t + 0 ) and a thermodynamic factor, T f . By systematically varying the volume fraction of the conducting phase, ϕ c between 0.29 and 1.0, and chain length, N between 80 and 8000, we elucidate the role of morphology on ion transport. We find that κ…

The present work follows the trend to develop non-aqueous electrolytes for the deposition of corrosion resistant ZnNi alloys. It investigates the use of the choline chloride/ethylene glycol (1:2 molar ratio) eutectic mixture and of pure ethylene glycol as solvents for ZnNi electroplating. The electrochemical behavior of Zn and Ni is investigated via cyclic voltammetry, and potentiostatic ZnNi deposition is performed. Ni content is found to be precisely tunable in the 10-20% wt range, which presents the highest industrial interest for corrosion protection. ZnNi coatings obtained are characterized from the morphological and phase composition point of view. Evidence of the formation of a metastable γ ZnNi phase is observed for both choline chloride/ethylene glycol and pure ethylene glycol. Finally, potentiodynamic corrosion tests are performed to assess their corrosion properties.

We study the correlations length of the charge-charge pair correlations in concentrated electrolyte solutions by means of all-atom, explicit-solvent molecular dynamics simulations. We investigate LiCl and NaI in water, which constitute highly soluble, prototypical salts for experiments, as well as two more complex, molecular electrolyte systems of lithium bis(trifluoromethane)sulfonimide (LiTFSI), commonly employed in electrochemical storage systems, in water and in an organic solvent mixture of dimethoxyethane (DME) and dioxolane (DOL). Our simulations support the recent experimental observations as well as theoretical predictions of a non-monotonic behavior of the correlation length with increasing salt concentration. We observe a Debye-Hückel like regime at low concentration, followed by a minimum reached when d/λD = 1, where λD is the Debye correlation length and d the effective ionic diameter, and an increasing correlation length with salt concentration in very concentrated electrolytes. As in the experiments, we find that the screening length in the concentrated regime follows…

In view of the vital role of water, exact knowledge of its dielectric function over a large frequency range is important. We report on currently available measurements of the dielectric function of water at room temperature (25 °C) across the full spectrum: microwave, IR, UV, and X-ray (up to 100 eV). We parameterize the complex dielectric function of water with two Debye (microwave) oscillators and high resolution of IR and UV/X-ray oscillators. We also report dielectric parameters for ice-cold water with a microwave/IR spectrum measured at 0.4 °C, while taking the UV spectrum at 25 °C (assuming negligible temperature dependence in UV). We employ van der Waals dispersion interactions to contrast our model of ice-cold water with earlier models. Air bubbles in water and dissolved gas molecules show attraction toward interfaces rather than repulsion. The van der Waals interaction promotes complete freezing rather than supporting a thin layer of water on ice. We infer that premelting is driven by charge and ion adsorption. Density-based extrapolation from warm to cold water of the…

The research on the design of efficient, reliable, and cost-effective biosensors is expanding given its high demand in various fields such as health care, environmental surveillance, agriculture, diagnostics, industries, and so forth. In the last decade, various fascinating and interesting 2D materials with extraordinary properties have been experimentally synthesized and theoretically predicted. 2D materials have been explored for the sensing of different biomolecules because of their large surface area and strong interaction with different biomolecules. Theoretical simulations can bring important insight on the interaction of biomolecules on 2D materials, charge transfer, orbital interactions, and so forth and may play an important role in the development of efficient biosensors. Quantum simulation techniques, such as density functional theory (DFT), are very powerful and are gaining popularity especially with the advent of high-speed computing facilities. This review article provides theoretical insight regarding the interaction of various biomolecules on different 2D materials…

The novel coronavirus (nCOV-2019) outbreak has put the world on edge, causing millions of cases and hundreds of thousands of deaths all around the world, as of June 2020, let alone the societal and economic impacts of the crisis. The spike protein of nCOV-2019 resides on the virion's surface mediating coronavirus entry into host cells by binding its receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2). Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier severe acute respiratory syndrome coronavirus (SARS-COV) in 2002 via extensive molecular dynamics (MD) simulations. Numerous mutations have been identified in the RBD of nCOV-2019 strains isolated from humans in different parts of the world. In this study, we investigated the effect of these mutations as well as other Ala-scanning mutations on the stability of the RBD/ACE2 complex. It is found that most of the naturally occurring mutations to the RBD either slightly strengthen or…

One of the main differences in the intercellular environment compared to the laboratory condition is the presence of macromolecular crowders of various compositions, sizes, and shapes. In this article, we have contemplated a systematic shape dependency of macromolecular crowders on the thermodynamics and microsecond conformational fluctuation dynamics of protein unfolding by taking human serum albumin (HSA) as the model protein and similar-sized crowders, namely, dextran-40, ficoll-70, and PEG-35 as macromolecular crowders of different shapes, to mimic the cell environment. We observed that dextran-40 and ficoll-70 counteract the thermal denaturation and PEG-35 assists it. A complete thermodynamic analysis suggests that the stabilization by dextran-40 and ficoll-70 occurs mainly through stabilizing entropic effect, which is somewhat counteracted by the destabilizing enthalpic effect, in line with what is expected from the traditional interpretation of excluded volume and soft interaction. Surprisingly, the destabilizing effect of PEG-35 is not through unfavorable interaction but…

The speciation of calcium carbonate in water is important to the geochemistry of the world's oceans and has ignited significant debate regarding the mechanism by which nucleation occurs. Here, it is vital to be able to quantify the thermodynamics of ion pairing versus higher order association processes in order to distinguish between possible pathways. Given that it is experimentally challenging to quantify such species, here we determine the thermodynamics for ion pairing and multiple binding of calcium carbonate species using bias-enhanced molecular dynamics. In order to examine the uncertainties underlying these results, we derived a new polarizable force field for both calcium carbonate and bicarbonate in water based on the AMOEBA model to compare against our earlier rigid ion model, both of which are further benchmarked against ab initio molecular dynamics for the ion pair. Both force fields consistently indicate that the association of calcium carbonate ion pairs to form larger species is stable, though with an equilibrium constant that is lower than for ion pairing itself.