The 50 most-cited articles in The Journal of Physical Chemistry B, 2019

During the carbonization process of raw polymer precursors, graphitic structures can evolve. The presence of these graphitic structures affects mechanical properties of the carbonized carbon fibers. To gain a better understanding of the chemistry behind the evolution of these structures, we performed atomistic-scale simulations using the ReaxFF reactive force field. Three different polymers were considered as a precursor: idealized ladder PAN (polyacrylonitrile), a proposed oxidized PAN, and poly( p -phenylene-2,6-benzobisoxazole). We determined the underlying molecular details of polymer conversion into a carbon fiber structure. Because these are C/H/O/N-based polymers, we first developed an improved force field for C/H/O/N chemistry based on the density functional theory data with a particular focus on N 2 formation kinetics and its interactions with polymer-associated radicals formed during the carbonization process. Then, using this improved force field, we performed atomistic-scale simulations of the initial stage of the carbonization process for the considered polymers. On the…

Abstract Intrinsically disordered proteins (IDPs) lack well-defined three-dimensional structures, thus challenging the archetypal notion of structure-function relationships. Determining the ensemble of conformations that IDPs explore under physiological conditions is the first step towards understanding their diverse cellular functions. Here, we quantitatively characterize the structural features of IDPs as a function of sequence and length using coarse-grained simulations. For diverse IDP sequences, with the number of residues ( N T ) ranging from 24 to 441, our simulations not only reproduce the radii of gyration ( R g ) obtained from experiments, but also predict the full scattering intensity profiles in very good agreement with Small Angle X-ray Scattering experiments. The R g values are well-described by the standard Flory scaling law, , with v ≈ 0.588, making it tempting to assert that IDPs behave as polymers in a good solvent. However, clustering analysis reveals that the menagerie of structures explored by IDPs is diverse, with the extent of heterogeneity being highly…

Cross-linked polymers are used in many commercial products and are traditionally incapable of recycling via melt reprocessing. Recently, tough and reprocessable cross-linked polymers have been realized by incorporating cross-links that undergo associative exchange reactions, such as transesterification, at elevated temperatures. Here we investigate how cross-linked polymers containing urethane linkages relax stress under similar conditions, which enables their reprocessing. Materials based on hydroxyl-terminated star-shaped poly(ethylene oxide) and poly((±)-lactide) were cross-linked with methylene diphenyldiisocyanate in the presence of stannous octoate catalyst. Polymers with lower plateau moduli exhibit faster rates of relaxation. Reactions of model urethanes suggest that exchange occurs through the tin-mediated exchange of the urethanes that does not require free hydroxyl groups. Furthermore, samples were incapable of elevated-temperature dissolution in a low-polarity solvent (1,2,4-trichlorobenzene) but readily dissolved in a high-polarity aprotic solvent (DMSO, 24 to 48 h).…

Rosenfeld proposed two different scaling approaches to model the transport properties of fluids, separated by 22 years, one valid in the dilute gas, and another in the liquid phase. In this work, we demonstrate that these two limiting cases can be connected through the use of a novel approach to scaling transport properties and a bridging function. This approach, which is empirical and not derived from theory, is used to generate reference correlations for the transport properties of the Lennard-Jones 12-6 fluid of viscosity, thermal conductivity, and self-diffusion. This approach, with a very simple functional form, allows for the reproduction of the most accurate simulation data to within nearly their statistical uncertainty. The correlations are used to confirm that for the Lennard-Jones fluid the appropriately scaled transport properties are nearly monovariate functions of the excess entropy from low-density gases into the supercooled phase and up to extreme temperatures. This study represents the most comprehensive metastudy of the transport properties of the Lennard-Jones…

Halogen bonding has recently gained well deserved attention in present-day research for its importance in many fields of supramolecular science and crystal engineering. Although generally overlooked in comprehensive studies in the past, halogen bonding has become an important tool also in the field of materials science. An increased number of scientific reports are published every year where halogen bonding is exploited in soft materials rather than in crystal engineering. Here, we focus on a description of the most exciting contemporary developments in the field of halogen-bonded functional soft materials, assembled using the guiding principles of crystal engineering. We give a particular emphasis to those published in the past few years.

Deep eutectic solvents (DESs) are a new generation of green solvents, which are considered an environmentally friendly alternative to ionic liquids and volatile organic compounds. The addition of controlled amounts of water to DESs has a significant effect on their microscopic structure and thus on their thermodynamic and transport properties. In this way, DESs can be modified, leading to solvents with improved characteristics. In this work, molecular dynamics (MD) simulations are performed to obtain a better understanding of the relation between the microscopic structure, molecular interactions, and thermophysical properties of aqueous reline and ethaline solutions at temperatures ranging from 303.15 to 363.15 K. For both reline and ethaline solutions, the hydrogen bond (HB) networks disappear with increasing mass fraction of water, and the intensity of radial distribution function (RDF) peaks decreases. For a mass fraction of water of 40%, most of the HBs between the compounds of reline and ethaline are broken, and DESs are fully dissolved in water. Consequently, a monotonic…

Atomistic molecular dynamics simulations have been performed to investigate the microscopic structure of ethaline deep eutectic solvent (DES), a mixture of choline chloride ([Ch][Cl]) and ethylene glycol (EG) in molar ratio of 1:2, respectively. As much as the structure of a DES is derived by the composition of the species present in it, the chemical nature of the hydrogen bond donor species involved also plays a crucial role in laying down the microscopic structure of DESs. By virtue of its inherent chemical structure, EG renders both intra- and intermolecular hydrogen bonds. Therefore, the molecular level structural landscape of DESs containing EG as hydrogen bond donor is reckoned to be a bit complex. In the present study, we aim to understand the structural morphology of ethaline using optimum force-field parameters for EG recently proposed by our group. After an initial assessment of the refined force-field parameters for ethaline DES, we have presented an in-depth analysis of the arrangement and ordering of its components at the molecular level. Simulated X-ray scattering…

Peptide-based hydrogels are highly promising for various biomedical applications owing to their precise self-assembly, biocompatibility, and sensitivity toward biologically relevant external stimuli. Herein, we report pH-responsive self-assembly and gelation of a highly biocompatible amphiphilic peptide PEP-1. This is an octa-peptide and double mutant of a naturally occurring β-strand peptide fragment of the protein Galectin-1, available in bovine spleen. PEP-1 was synthesized by using the Rink amide resin as the solid support in a homemade apparatus. At pH 7.4, it exhibits spontaneous gelation with very high yield stress of 88.0 Pa and gel-to-sol temperature of 84 °C at C = 2.0 wt %. Microscopy studies revealed entangled fibrillar morphology whereas circular dichroism, Fourier tranform IR, and Thioflavin T assay indicated formation of β-sheet rich secondary structure. The assembled state was found to be stable in neutral pH whereas either decrease or increase in the pH resulted in disassembly owing to the presence of the pH responsive Asp and Lys residues. The gel network showed…

The N-terminal fusion peptide (residues 770-788) of an S2 glycoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV), exposed upon receptor binding, is crucial for virus entry into the host cell. The fusion peptide alters the membrane organization and dynamics of the host membrane to facilitate membrane fusion. Generally, the effect of the fusion peptide on the membrane is sensitive to the lipid composition of target membranes. In the present work, we have utilized steady-state and time-resolved fluorescence spectroscopy in tandem with circular dichroism spectroscopy to elucidate the binding, oligomeric status, and secondary structure of the fusion peptide and its impact on the depth-dependent membrane organization and dynamics. We have used depth-dependent fluorescence probes, 1,6-diphenyl-1,3,5-hexatriene (DPH) and its trimethylammonium derivative (TMA-DPH), to evaluate the effect of the peptide binding along the bilayer normal. We have exploited the energy transfer efficiency of tryptophan between TMA-DPH and DPH to determine the relative location of the…

Water-in-salts are a new family of electrolytes that may allow the development of aqueous Li-ion batteries. They have a structure that is reminiscent of ionic liquids, and they are characterized by a high concentration of ionic species. In this work, we study their transport properties and how they evolve with concentration by using molecular dynamic simulations. We first focus on the choice of the force field. By comparing the simulated viscosities and self-diffusion coefficients with experimental measurements, we select a set of parameters that reproduces well the transport properties. We then use the selected force field to study in detail the variations of the self and collective diffusivities of all the species as well as the transport number of the lithium ion. We show that correlations between ions and water play an important role over the whole concentration range. In the water-in-salt regime, the anions form a percolating network that reduces the cation-anion correlations and leads to rather large values for the transport number compared to other standard electrolytes.

Autoxidation of dopamine to polydopamine by dissolved oxygen is a slow process that requires highly alkaline conditions. Polydopamine can be formed rapidly also in mildly acidic and neutral solutions by using redox-active transition-metal ions. We present a comparative study of polydopamine nanoparticles formed by autoxidation and aerobic or anaerobic oxidation in the presence of Ce(IV), Fe(III), Cu(II), and Mn(VII). The UV-vis spectra of the purified nanoparticles are similar, and dopaminechrome is an early intermediate species. At low pH, Cu(II) requires the presence of oxygen and chloride ions to produce polydopamine at a reasonable rate. The changes in dispersibility and surface charge take place at around pH 4, which indicates the presence of ionizable groups, especially carboxylic acids, on their surface. X-ray photoelectron spectroscopy shows the presence of three different classes of carbons, and the carbonyl/carboxylate carbons amount to 5-15 atom %. The N 1s spectra show the presence of protonated free amino groups, suggesting that these groups may interact with the…

Deep eutectic solvents (DESs) have potential as designer media whose physical, chemical, electrochemical, and spectroscopic properties are easily and broadly tuned. Due to the ubiquity of water and the hygroscopic nature of many DES components, it is important to understand how water affects DESs both on the nanoscale and in the bulk. Here, we present a study of the physical properties of DES/water mixtures. We found that water appears to form a ternary DES when mixed with 2:1 urea/ChCl.

Ensemble docking in drug discovery or chemical biology uses dynamical simulations of target proteins to generate binding site conformations for docking campaigns. We show that 600 ns molecular dynamics simulations of four G-protein-coupled receptors in their membrane environments generate ensembles of protein configurations that, collectively, are selected by 70?99% of the known ligands of these proteins. Therefore, the process of ligand recognition by conformational selection can be reproduced by combining molecular dynamics and docking calculations. Clustering of the molecular dynamics trajectories, however, does not necessarily identify the protein conformations that are most often selected by the ligands.

In this work, the Angell analysis of Walden plots of the conductivity of ionic liquids and other electrolytes against viscosity is used to examine simple molten salts at high temperatures, a test that does not appear to have been made previously. It is found that many simple salts such as alkali metal fluorides and chlorides are predicted to be "superionic" as their Walden plots fall above the arbitrary reference line introduced by Angell, which passes through the datum point for 1 M aqueous KCl at 25 °C. This contradicts long-standing molecular dynamics evidence in the literature showing that these salts conduct simply by ion migration in an electric field. Zinc chloride is also predicted to be "ideal", whereas one would expect it to be "subionic" in Angell's terminology given that it is an associated salt. Results for certain protic ionic liquids are also contradictory. Therefore, Angell-Walden analyses of this type do not convey any useful information other than a qualitative ranking of the conductivity of similar ionic liquids at a given viscosity and their use for estimating…

Coupling between G-protein-coupled receptors (GPCRs) and the G proteins is a key step in cellular signaling. Despite extensive experimental and computational studies, the mechanism of specific GPCR–G protein coupling remains poorly understood. This has greatly hindered effective drug design of GPCRs that are primary targets of ∼ 1 / 3 of currently marketed drugs. Here, we have employed all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method to decipher the mechanism of the GPCR–G protein interactions. Adenosine receptors (ARs) were used as model systems based on very recently determined cryo-EM structures of the A 1 AR and A 2A AR coupled with the G i and G s proteins, respectively. Changing the G i protein to the G s led to increased fluctuations in the A 1 AR and agonist adenosine (ADO), while agonist 5′- N -ethylcarboxamidoadenosine (NECA) binding in the A 2A AR could be still stabilized upon changing the G s protein to the G i . Free energy calculations identified one stable low-energy conformation for each of the A 1 AR-G i and A 2A AR-G s…

Broadband dielectric relaxation spectroscopy (DRS) has been used to investigate aqueous solutions of MgCl 2 and CaCl 2 up to concentrations of about 1.8 mol L –1 at 25 °C over the frequency range 0.07 ≤ ν/GHz ≤ 89. Detailed analysis of the dominant solvent mode centered at ∼20 GHz showed that both Mg 2+ and Ca 2+ are strongly solvated, each immobilizing ∼20 water molecules on the DRS timescale. This is consistent with the formation of two well-defined hydration layers around both cations. The hydration shell of Ca 2+ (aq) was found to be slightly more labile compared with Mg 2+ (aq). Two or three low-intensity solute-related modes were observed at frequencies ≲10 GHz for MgCl 2 (aq) and CaCl 2, respectively. Two of these modes were attributed to the formation of double-solvent-separated and solvent-shared 1:1 ion pairs. The third mode (observed at very low frequencies and only for some CaCl 2 solutions) was thought to be due to an ion-cloud relaxation. No evidence was found for “slow” water or, consistent with the strong cation hydration, for contact ion pairs. The overall…

Molecularly imprinted polymers (MIPs) have potential as alternatives to antibodies in the diagnosis and treatment of disease. However, atomistic level knowledge of the prepolymerization process is limited that would facilitate rational design of more efficient MIPs. Accordingly, we have investigated using computation and experiment the protein-monomer binding interactions that may influence the desired specificity. Myoglobin was used as the target protein and five different acrylamide-based monomers were considered. Protein binding sites were predicted using SiteMap and binding free energies of monomers at each site were calculated using MM-GBSA. Statistical thermodynamic analysis and study of atomistic interactions facilitated rationalization of monomer performance in MIP rebinding studies (% rebind; imprinting factors). CD spectroscopy was used to determine monomer effects on myoglobin secondary structure, with all monomers except the smallest monomer (acrylamide) causing significant changes. A complex interplay between different protein-monomer binding effects and MIP efficacy…

Room-temperature ionic liquids (RTILs) are a class of organic salts that are liquid at room temperature. Their physiochemical properties, including low vapor pressure and wide electrochemical stability window, have driven their use as electrolytes in many electrochemical applications; however, the slow transport properties of many RTILs have limited their utility in some applications. This issue is often mitigated by solvating ionic liquids in neutral organic solvents. To date, however, solvent interactions have only been explored for a small number of solvents, particularly acetonitrile and propylene carbonate, at only a few compositions. In this work, we use molecular dynamics simulations in the context of a computational screening approach to study mixtures of ionic liquids in many different solvents at a range of concentrations. Building on prior work, we again find that ionic liquid diffusivity increases monotonically with greater solvent concentration. In contrast to prior work, we find that pure solvent diffusivity, not polarity, is the most influential solvent property on…

-isopropylacrylamide) (PNIPAM) undergo a phase transition in aqueous solution from a random-coil structural ensemble to a globule structural ensemble at the lower critical solution temperature (LCST). Above this temperature, PNIPAM agglomerates and becomes insoluble, whereas it is soluble below the temperature. Thus, thermosensitive polymers represent essential targets for several applications, e.g., in drug delivery. Although their ability to change structure in response to a temperature alteration is highly relevant for industrial processes, their thermodynamic properties are mostly qualitatively understood, and the quantitative thermodynamic picture is still elusive. In this study, we used a combined atomistic molecular dynamics and well-tempered metadynamics simulation approach to estimate coil-globule transition thermodynamics. An isotactic 30-mer of PNIPAM was investigated over a broad temperature range between 200 and 360 K. The transition from the globule to the random-coil structure was observed with well-tempered metadynamics. For the first time, the free energy surface of…

Currently, a theoretical understanding of thermodynamics and kinetics of the oxidative polymerization of poly(3,4-ethylenedioxythiophene) (best known as PEDOT) is missing. In the present study, step-by-step density functional theory calculations of the radical polymerization of PEDOT with tosylate counterions (PEDOT:TOS) using Fe 3+ (TOS – ) 3 as oxidant and dopant are performed. We calculate the Gibbs free energy for the conventional mechanism that consists of the polymerization of neutral PEDOT oligomers first, followed by their oxidation (doping). We also propose an alternative mechanism of polymerization, in which the already oxidized oligomers are used as reactants, leading to doped (oxidized) oligomers as products during polymerization. Our calculations indicate that the alternative mechanism is more efficient for longer PEDOT oligomers (chain length N > 6). We find that the oxidation of the EDOT monomer is the rate-limiting step for both mechanisms. Another focus of our study is the understanding of the maximum oxidation level that can be achieved during polymerization. Our…

UBQLN2 450-624 oligomerizes and undergoes temperature-responsive liquid-liquid phase transitions following a closed-loop temperature-concentration phase diagram. We recently showed that disease-linked mutations to UBQLN2 450-624 impart highly varying effects to its phase behavior, ranging from little change to significant decrease of saturation concentration and formation of gels and aggregates. However, how single mutations lead to these properties is unknown. Here, we use UBQLN2 450-624 as a model system to study the sequence determinants of phase separation. We hypothesized that UBQLN2 450-624 regions previously identified to promote its oligomerization are the "stickers" that drive interchain interactions and phase separation. We systematically investigated how phase behavior is affected by all 19 possible single amino acid substitutions at three sticker and two "spacer" (sequences separating stickers) positions. Overall, substitutions to stickers, but not spacers, substantially altered the shape of the phase diagram. Within the sticker regions, increasing hydrophobicity…

Next generation lithium ion batteries require higher energy and power density, which can be achieved by tailoring the cathode particle morphology, such as particle size, size distribution, and internal porosity. All these morphological features are determined during the cathode synthesis process, which consists of two steps, (i) coprecipitation and (ii) calcination. Transition metal hydroxide precursors are synthesized during the coprecipitation process, whereas their oxidation and lithiation occur during calcination. The size and size distribution of crystalline primary and aggregated secondary particles and their internal porosity are determined during coprecipitation. Operating conditions of the chemical reactor, such as solution pH, ammonia concentration, and stirring speed control the final morphological features. Here, a multiscale computational model has been developed to capture the nucleation and growth of crystalline primary particles and their aggregation into secondary transition metal hydroxide precursor particles. The simulations indicate that increasing solution pH…

Traditionally, ion selectivity in nanopores and nanoporous membranes is understood to be a consequence of Debye overlap, in which the Debye screening length is comparable to the nanopore radius somewhere along the length of the nanopore(s). This criterion sets a significant limitation on the size of ion-selective nanopores, as the Debye length is on the order of 1-10 nm for typical ionic concentrations. However, the analytical results we present here demonstrate that surface conductance generates a dynamical selectivity in ion transport, and this selectivity is controlled by so-called Dukhin, rather than Debye, overlap. The Dukhin length, defined as the ratio of surface to bulk conductance, reaches values of hundreds of nanometers for typical surface charge densities and ionic concentrations, suggesting the possibility of designing large-nanopore (10-100 nm), high-conductance membranes exhibiting significant ion selectivity. Such membranes would have potentially dramatic implications for the efficiency of osmotic energy conversion and separation techniques. Furthermore, we…

The concept of eutectic molecular liquids (EMLs) was defined, and a strategy to form EMLs based on noncovalent interactions was proposed. We verified the formation and investigated the properties, interaction sites, and interaction energies of the obtained 16 EMLs. Moreover, two new forms of noncovalent interactions, κ-hole and μ-hole bonding interactions, were proposed, which broaden the understanding of intermolecular interactions. Numerous EMLs can be strategically designed and prepared by simply mixing two parent molecule components based on noncovalent interactions, including hydrogen bonding interactions; π-π stacking; and σ-hole (halogen, chalcogen, pnicogen, and tetrel bonds), π-hole, κ-hole, and μ-hole bonding interactions. The properties of EMLs can be finely tailored by selecting or even designing appropriate parent compounds for task-specific applications. Our work presents a substantial step toward the innovative development of liquid systems.

The properties of higher n -alkanes and their mixtures is a topic of significant interest for the oil and chemical industry. However, the experimental data at high temperatures are scarce. The present study focuses on simulating n -dodecane, n -octacosane, their binary mixture at a n -dodecane mole fraction of 0.3, and a model mixture of the commercially available hydrocarbon wax SX-70 to evaluate the performance of several force fields on the reproduction of properties such as liquid densities, surface tension, and viscosities. Molecular dynamics simulations over a broad temperature range from 323.15 to 573.15 K were employed in examining a broad set of atomistic molecular models assessed for the reproduction of experimental data. The well-established united atom TraPPE (TraPPE-UA) was compared against the all atom optimized potentials for liquid simulations (OPLS) reparametrization for long n -alkanes, L-OPLS, as well as Lipid14 and MARTINI force fields. All models qualitatively reproduce the temperature dependence of the aforementioned properties, but TraPPE-UA was found to…

Abstract Long MD simulations are carried out using a detailed all-atom force field to investigate the effect of pH or, equivalently, degree of ionization α– (= 0, 50, 100%) and degree of polymerization N (= 20, 23, 46, 70, and 110) on the structure and dynamics of poly(acrylic acid) (PAA) at infinite dilution. To ensure the validity and add to the reliability of our research conclusions, a systematic validation of several molecular mechanics force fields is performed. It is observed that the generalized AMBER force field in combination with the RESP charge fitting method best describes both the structural and dynamical behavior of PAA in comparison to experimentally obtained data. It is found that ⟨Rg2⟩0.5changes with N as ⟨Rg2⟩0.5 ∼ Nν, with ν = 0.27 at α– = 0% degree of ionization (acidic conditions), ν = 0.94 at α– = 50% degree of ionization (neutral conditions), and ν = 0.87 at α– = 100% degree of ionization (basic conditions), which is in perfect agreement with theory. The global shape of the PAA chain in the solution is quantified in terms of the three eigenvalues of the…

Experiments and molecular dynamics (MD) simulations in the literature indicate that gaseous proteins generated by electrospray ionization (ESI) can retain native-like structures. However, the exact properties of these ions remain to be explored. Focusing on ubiquitin and lysozyme, we examined several pertinent questions. (1) We applied solvent MD runs to test whether the X-ray structures of both proteins are affected by crystal packing. Main and side-chain orientations were retained in solution, providing a justification for the hitherto unscrutinized approach of relying on crystal data for “solution” versus gas-phase comparisons. (2) Most earlier gas-phase protein MD investigations employed short (ns) simulation windows. By extending this time frame to 1 μs, we were able to observe rare unfolding/folding transitions in ubiquitin. These predicted fluctuations were consistent with a semi-unfolded subpopulation detected by ion mobility spectrometry (IMS). (3) Most earlier modeling studies did not account for the high H + mobility in gaseous proteins. For the first time, we compared…

In a previous work, we have found that the pseudo -protic ionic liquid N -methylimidazolium acetate, [C 1 HIm][OAc] or [Hmim][OAc], mainly consists of the electrically neutral molecular species N -methylimidazole, C 1 Im, and acetic acid, AcOH, even though the mixture has significant ionic conductivity. This system was revisited by employing isotopic substitution Raman spectroscopy (ISRS) and pulsed field gradient (PFG) NMR self-diffusion measurements. The ISRS and PFG-NMR results obtained fully confirm our earlier findings. In particular, the self-diffusion coefficient of the hydroxyl hydrogen atom in AcOH is identical to that of the methyl hydrogen atoms within the experimental uncertainty, consistent with very little ionization. Therefore, a proton conduction mechanism similar to the Grotthuss mechanism for aqueous acid solutions is postulated to be responsible for the observed electrical conductivity. Laity resistance coefficients ( r ij ) are calculated from the transport properties, and the negative values obtained for the like-ion interactions are consistent with the pseudo…

Amino acid choline-based ionic liquids (AACBILs) have high biodegradability, low toxicity, availability, low cost, and high thermal stability compared to the traditional ionic liquids (ILs). In this work, the volumetric, structural, and dynamical properties of three AACBILs, that is, choline alanine ([CH][Ala]), choline β-alanine ([CH][β-Ala]), and choline phenylalanine ([CH][Phe]) were investigated using the quantum mechanical calculations and also molecular dynamics simulations in both gas and liquid phases. The density functional theory calculations, noncovalent interactions, and also the quantum theory of atoms in molecules methods have been used to investigate the hydrogen bonds, interaction energies, and also charge transfers between the ions of the studied ILs. Density, isobaric expansion coefficient, mean square displacement (MSD), self-diffusivity, viscosity, electrical conductivity, and transference numbers have been computed for the studied AACBILs in different temperatures and at 0.1 MPa. There is a satisfactory agreement between the calculated data with the…

We present first results on triazolium-based ionic liquids (ILs) as a novel class of nonderivatizing solvents for cellulose. Despite their chemical similarity to imidazolium cations, the 1,2,3-triazolium cation lacks the isolated ring proton, leading to reduced formation of N-heterocyclic carbenes (NHCs) and therefore to lower reactivity and less unwanted side reactions. We synthesized six ILs based on 1,2,3-triazolium and 1,2,4-triazolium cations. The acetates are room-temperature ionic liquids and dissolve a similar amount of cellulose as the corresponding imidazolium salt. From NMR spectroscopy of the solution, we rule out polymer degradation. The cellulose solubility rises with increasing anion basicity, while being almost independent of the cation. We perform molecular dynamics simulations and compute enthalpies of solvation, which quantitatively fit the experimental solubilities. Trajectory analysis reveals strong hydrogen bonds between acetate anions and cellulose hydroxyl groups, while the cations do not form strong hydrogen bonds with cellulose. Thus, the simulations…

The carbonyl groups of glycerolipid monolayers on water play an important role in the formation of the interfacial hydrogen bond network, which in turn influences the interactions of lipids with, for example, metabolites. As the frequency of the carbonyl absorption band strongly depends on the hydration state of the lipid headgroups, the carbonyl band is a sensitive reporter of changes in the headgroup environment. Here, we use phase-resolved sum frequency generation spectroscopy to obtain information about the orientation and hydration of the carbonyl groups in lipid monolayers. We find that there are two distinct carbonyl moieties in the lipid monolayers, oppositely oriented relative to the surface plane, that experience substantially different hydrogen-bonding environments.

Ion mobility spectrometry-mass spectrometry methods offer the potential to correlate protein tertiary and quaternary structures to variations in their amino acid sequences and post-translational modifications. Because ion mobility spectrometry measures cross sections of ions in the gas phase, however, the structure of protein systems detected by ion mobility spectrometry will generally differ from their native solution structures. While it is now established that ion mobility spectrometry does not typically detect equilibrium gas-phase structures of protein systems, what remains disputed is which aspects, if any, of the detected ions resemble the native state present in solution. Here, we develop the structure relaxation approximation (SRA) method to predict charge-state specific ion mobility spectra from an ensemble of solution structures. This allows us to predict the "global" trends observed in the experiments for various experimental conditions and charge states, thereby enabling detailed structure elucidation. The SRA predicts (RMSD to experiment ∼4%) that even the small…

State-free reversible VAMPnets (SRVs) are a neural network-based framework capable of learning the leading eigenfunctions of the transfer operator of a dynamical system from trajectory data. In molecular dynamics simulations, these data-driven collective variables capture the slowest modes of the dynamics and are useful for enhanced sampling and free energy estimation. In this work, we employ SRV coordinates as a feature set for Markov state model (MSM) construction. Compared to the current state-of-the-art, MSMs constructed from SRV coordinates are more robust to the choice of input features, exhibit faster implied time scale convergence, and permit the use of shorter lagtimes to construct higher kinetic resolution models. We apply this methodology to study the folding kinetics and conformational landscape of the Trp-cage miniprotein. Folding and unfolding mean first passage times are in good agreement with the prior literature, and a nine macrostate model is presented. The unfolded ensemble comprises a central kinetic hub with interconversions to several metastable unfolded…

It is important to study the bactericidal mechanism with nanostructures for the design and preparation of high-efficiency sterilization materials. In this paper, the interfacial energy gradient between cells and nanopillars is proposed to be the driving force to promote cells to migrate into nanostructures and get killed. The expressions of interfacial energy and its gradient were first established, then the deformation of cells pressured by nanostructures was calculated. The results show that the interfacial energy gradient or the pressure on cells is influenced by nanopillar parameters substantially. The smaller the nanopillar diameter and the larger the pitch, the greater the pressure on cells. Only high enough nanocolumns can ensure sufficient cell creep deformation and become punctured. Furthermore, a cell volume and its adhesion morphology also influence the interaction between cells and nanostructures. The smaller the cell volume, the greater the pressure on it. And the larger the contact angle of adhered cells, the greater the pressure on the cells by nanopillars. Besides,…

The thermal stability of collagen has an important effect on its practical applications. Many believe that hydroxyproline (Hyp) improves the structural stability of collagen molecules. In this study, for the first time, a method of building natural collagen molecular models was described. We constructed a collagen model with typical triple-helix structure and calculated the hydrogen bond energy between collagen α chains. The calculated hydrogen bond energy was consistent with the experimental results of differential scanning calorimetry. After the calculation simulation, we verified that the hydrogen bond energy between collagen chains was positively correlated with Hyp content in the models and an increased Hyp content in the model was beneficial in improving the thermal resistance of the structure. In addition, we found that thermal unfolding did not occur simultaneously along the entire molecule but started in the regions with less Hyp content. This study provides a collagen model with a natural collagen amino acid sequence, which will be helpful for further investigation of the…

Boron dipyrromethene (BODIPY) molecular rotors have shown sensitivity toward viscosity, polarity, and temperature. Here, we report a 1,3,5,7-tetramethyl-8-phenyl-BODIPY modified with a polyethylene glycol (PEG) chain, for temperature sensing and live cell imaging. This new PEG-BODIPY dye presents an increase in nonradiative decay as temperature increases, which directly influences its lifetime. This change in lifetime is dependent on changes in both temperature and viscosity at low viscosity values, but is only dependent on temperature at high viscosity values. The dependence of fluorescence lifetime with temperature allows for temperature monitoring in vitro and in cells, with sub degree resolution. When in contact with cells, the PEG-BODIPY spontaneously penetrates and stains the cell but not the nucleus. Furthermore, no significant cell toxicity was found even at 100 μM concentration. Using fluorescence lifetime imaging microscopy (FLIM), we were able to observe the changes in the lifetime of PEG-BODIPY within the cell at different temperatures. The use of FLIM and molecular…

We present the results of the atomistic molecular dynamics modeling of different protonation states of Nafion at varying hydration levels. Previous experiments have shown that the degree of deprotonation (DDP) of the sulfonic acid groups in a Nafion membrane varies significantly upon hydration. Our goal is to provide insights into the effects of variable protonation states and water content on the internal structure and vehicular transport inside the Nafion membrane. The Nafion side chain lengths showed a weak increasing trend with increasing DDP at all hydration levels, exposing more of the sulfonic acid groups to the hydrophilic/water phase. The water-phase characteristic size/diameter decreased with increasing DDP, but, interestingly, the average number of water molecules per cluster increased. The probability of water-hydronium hydrogen bond formation decreased with increasing DDP, despite an increase in the total number of such hydrogen bonds. The water diffusion was largely unaffected by the state of deprotonation. In contrast to that, the hydronium ion diffusion slowed down…

The properties of room-temperature ionic liquids (ILs) may be viewed as resulting from a balance of electrostatic interactions that can be tuned at short range but constrained to satisfy universal, asymptotic screening conditions. Short-range interactions and ion packing provide ample opportunity for chemical tunability, while asymptotic sum rules dictate that the long-range structure and charge oscillation be similar to those of molten alkali halide salts. In this work, we study the structure factors and long-range electrostatic interactions in six ILs. The cation in all cases is 1-butyl-3-methylimidazolium (BMIM + ), and we study six anions, namely, tetrafluoroborate (BF 4 – ), hexafluorophosphate (PF 6 – ), nitrate (NO 3 – ), triflate (CF 3 SO 3 – ), bisfluorosulfonylimide [(FSO 2 ) 2 N – ], and bistriflimide [(CF 3 SO 2 ) 2 N – ]. To gain insight, we perform similar computer simulations of a primitive molten salt model with and without electronic polarization. We emphasize universal similarities among ionic liquids and molten salts in the long-range ion ordering and the…

Conformational memory in single-molecule dynamics has attracted recent attention and, in particular, has been invoked as a possible explanation of some of the intriguing properties of transition paths observed in single-molecule force spectroscopy (SMFS) studies. Here we study one candidate for a non-Markovian model that can account for conformational memory, the generalized Langevin equation with a friction force that depends not only on the instantaneous velocity but also on the velocities in the past. The memory in this model is determined by a time-dependent friction memory kernel. We propose a method for extracting this kernel directly from an experimental signal and illustrate its feasibility by applying it to a generalized Rouse model of a SMFS experiment, where the memory kernel is known exactly. Using the same model, we further study how memory affects various statistical properties of transition paths observed in SMFS experiments and evaluate the performance of recent approximate analytical theories of non-Markovian dynamics of barrier crossing. We argue that the same type…

Abstract Classical molecular dynamics simulations have been performed in polarizable and nonpolarizable force fields for series of electrolytes based on MeTFSI (Me = Li, Na) salts dissolved in EMIM–TFSI ionic liquid. Structure and dynamics of the solvation shell of Me+ ions have been investigated. Contributions to the total conductivity of the electrolyte arising from motions of different ions and cross-correlations between them have been analyzed. The analysis has indicated that regardless of the type of Me+ cation, motions of Me+ ions and ionic liquid anions are positively correlated, contributing toward conductivity decrease and leading to negative transference numbers of metal ions. The results have confirmed experimental findings of negative transference numbers of Li+ and have suggested that the effect of Me-anion correlations in certain concentration range is a general feature of Me+ solutions in ionic liquids.

The oligomerization of Aβ 16–22 peptide, which is the hydrophobic core region of full-length Aβ 1–42, causes Alzheimer’s disease (AD). This progressive neurodegenerative disease affects over 44 million people worldwide. However, very few synthesized drug molecules are available to inhibit the aggregation of Aβ. Recently, experimental studies have shown that the biological ATP molecule prevents Aβ fibrillation at the millimolar scale; however, the significance of ATP molecules on Aβ fibrillation and the mechanism behind it remain elusive. We have carried out a total of 7.5 μs extensive all-atom molecular dynamics and 8.82 μs of umbrella sampling in explicit water using AMBER14SB, AMBER99SB-ILDN, and AMBER-FB15 force fields for Aβ 16–22 peptide, to investigate the role of ATP on the disruption of Aβ 16–22 prefibrils. From various analyses, such as secondary structure analysis, residue-wise contact map, SASA, and interaction energies, we have observed that, in the presence of ATP, the aggregation of Aβ 16–22 peptide is very unfavorable. Moreover, the biological molecule ATP interacts…

Laser-induced photochemical reduction of aqueous [AuCl 4 ] − is a green synthesis approach requiring no chemical reducing agents or stabilizers; but size control over the resulting gold nanoparticles remains a challenge. Under optical breakdown conditions producing hydrated electrons (e aq – ) and hydroxyl radicals (OH • ) through decomposition of water, [AuCl 4 ] − reduction kinetics follow an autocatalytic rate law, which is governed by rate constants: nucleation rate k 1, dependent on e aq –; and growth rate k 2, dependent on the OH • recombination product, H 2 O 2 . In this work, we add the hydroxyl radical scavengers isopropyl alcohol and sodium acetate to limit H 2 O 2 formation. Higher scavenger concentrations both lowered k 2 values and produced smaller gold nanoparticles with Gaussian size distributions and remarkably narrow mass-weighted size distributions. With sufficiently high scavenger concentrations, the mean nanoparticle size could be tuned from 3.8 to 6.1 nm with polydispersity indices below 0.08. Both the higher surface area-normalized catalytic activity of the…

Deep eutectic solvents (DES) are a new class of designer solvents with a wide range of possible applications. DESs are typically made from an ionic compound and a hydrogen bond donor, but lately DESs made of nonionic compounds with interesting properties have started to appear. This study focuses on describing the structure, dynamics, and interactions of a nonionic DES composed of N-methylacetamide (NMA) and lauric acid (LA). Linear IR and time-resolved IR experiments show that LA-NMA DES is the result of hydrogen bond interaction between the two molecular components, though the interaction energy is only favored by ∼1 kJ/mol with respect to the pure components. The IR experiments also reveal the presence of molecular heterogeneities produced by the nanosegregation of polar and nonpolar domains formed by N-methylacetamide and lauric acid, respectively. In addition, it is observed that the hydrogen bond interaction between components occurs at the interface of the two distinct polarity domains. The proposed molecular picture is also supported by the observation of nanodomains with…

Quantitative structure–property relationship (QSPR) analysis is a promising approach to correlate structural features with properties of glass materials that lack long-range order and usually have complex structures. By using carefully chosen descriptors based on structural models generated from molecular dynamics (MD) simulations, correlations with properties and insights on glass behaviors can be obtained. Zirconia can significantly alter glass properties including chemical durability, even in a small amount, and hence plays an important role in vitrification of nuclear waste where long-term chemical durability is desired. In this study, borosilicate glasses with the composition of x ZrO 2 –(61 – x )SiO 2 –17B 2 O 3 –18Na 2 O–4CaO with x = 0, 1, 2, 4, 6, and 8 were simulated using classical MD simulations with the recently developed composition-dependent potentials. Short-range (e.g., bond distance and coordination numbers) and medium-range (e.g., Q n distribution, network connectivity, and ring-size distribution) structural features altered by ZrO 2 were obtained and analyzed.…

To provide a more sustainable future, development and implementation of green electronics incorporating natural materials has become an essential requirement. In this study, we demonstrated a low-temperature and low-cost fabrication route to develop chitosan/PVP (CHP) substrate for flexible electronics device applications. A combination of natural polymer (chitosan) and synthetic polymer (poly(vinylpyrrolidone), PVP) has been used to fabricate biodegradable, low-cost, and flexible substrate. The CHP substrate has been prepared by the solution casting method. The CHP flexible substrate demonstrates a high optical transmittance (∼90% in the visible region), high-temperature stability (up to 250 °C), smooth surface, and good mechanical stability along with a high biodegradation rate (within 6 days) into the soil. Radio frequency (RF) sputtering and thermal evaporation techniques have been used to deposit high-quality ZnO thin films and Au/Ti electrodes over the CHP substrate. This fabricated metal-semiconductor-metal (MSM) device gives a clear indication about the accountability of the…

The coassembly of different building blocks into supramolecular copolymers provides a promising avenue to control their properties and to thereby expand the potential of supramolecular polymers in applications. However, contrary to covalent copolymerization which nowadays can be well controlled, the control over sequence, polymer length, and morphology in supramolecular copolymers is to date less developed, and their structures are more determined by the delicate balance in binding free energies between the distinct building blocks than by kinetics. Consequently, to rationalize the structures of supramolecular copolymers, a thorough understanding of their thermodynamic behavior is needed. Though this is well established for single-component assemblies and over the past years several models have been proposed for specific copolymerization cases, a generally applicable model for supramolecular cooperative copolymers is still lacking. Here, we provide a generalization of our earlier mass-balance models for supramolecular copolymerizations that encompasses all our earlier models. In…

Lithium ion battery (LIB) technology is undoubtedly indispensable to modern life. However, despite enormous and extended effort to improve LIB performance, our understanding of the underlying principles and mechanisms of lithium ion transport in nonaqueous LIB electrolytes remained limited until recently. There is a particular lack of knowledge of the microscopic solvation structures and fluctuation dynamics around charge carriers in real electrolytes. Typical electrolytes found in commercially available LIBs consist of lithium salts and mixed carbonate solvents, with the latter playing an essential role in promoting lithium ion transport and forming an electrically stable solid electrolyte interphase. Although a number of linear spectroscopic studies of LIB electrolytes aiming at understanding the complex nature of lithium ion solvation processes have been reported, the notion that each lithium ion is strongly solvated by carbonate molecules to form a long-lasting solvation sheath structure has remained the subject of intense debate. Here, we present the results of FTIR, fs IR…

We report relaxation dynamics of glycerol-water mixtures as probed by megahertz-to-terahertz dielectric spectroscopy in a frequency range from 50 MHz to 0.5 THz at room temperature. The dielectric relaxation spectra reveal several polarization processes at the molecular level with different time constants and dielectric strengths, providing an understanding of the hydrogen-bonding network in glycerol-water mixtures. We have determined the structure of hydration shells around glycerol molecules and the dynamics of bound water as a function of glycerol concentration in solutions using the Debye relaxation model. The experimental results show the existence of a critical glycerol concentration of ∼7.5 mol %, which is related to the number of water molecules in the hydration layer around a glycerol molecule. At higher glycerol concentrations, water molecules dispersed in a glycerol network become abundant and eventually dominate, and four distinct relaxation processes emerge in the mixtures. The relaxation dynamics and hydration structure in glycerol-water mixtures are further probed…

This Article covers the influence of the concentration of gold nanoparticles on laser-induced water decomposition. It was established that addition of gold nanoparticles intensifies laser-induced water decomposition by almost 2 orders of magnitude. The water decomposition rate was shown to be maximal at a nanoparticle concentration around 10 10 NP/mL, whereas a decrease or increase of nanoparticle concentration leads to a decrease of water decomposition rate. It was demonstrated that, if the concentration of nanoparticles in water-based colloid was less than 10 10 NP/mL, laser irradiation of the colloid caused formation of molecular hydrogen, hydrogen peroxide, and molecular oxygen. If the concentration of nanoparticles exceeded 10 11 NP/mL, only two products, molecular hydrogen and hydrogen peroxide, were formed. Correlations between the water decomposition rate and the main optical and acoustic parameters of optical breakdown-generated plasma were investigated. Variants of laser-induced decomposition of colloidal solutions of nanoparticles based on organic solvents (ethanol,…

Cyclodextrin complexes were used as simple model systems to explore the enthalpy-entropy compensation phenomenon, which is often observed in biomolecular processes, e.g., in protein-ligand binding. The complexation thermodynamics for the binding of a series of adamantane derivatives to several cyclodextrin hosts were determined by isothermal titration calorimetry in the temperature range 10-55 °C. As for other cyclodextrin complexes, the thermodynamic parameters depended systematically on the structural modifications of the cyclodextrins. Hydroxypropyl chains at the rims of the cyclodextrin hosts changed the thermodynamic fingerprint of binding to all guests by inducing significant increases in the complexation enthalpies and entropies. Similarly, the heat capacity changes upon complexation also showed a linear dependence on the number of hydroxypropyl chains. The altered complexation thermodynamics was ascribed to the increased dehydration of polar groups on the guest by the hydroxypropyl chains on the host. This unfavorable interaction destabilized the complexes as the enthalpic…