The 50 most-cited articles in The Journal of Physical Chemistry B, 2017

The quality of the 1.14*CM1A and 1.20*CM5 charge models was evaluated for calculations of free energies of hydration. For a set of 426 neutral molecules, 1.14*CM1A and 1.20*CM5 yield MADs of 1.26 and 1.21 kcal/mol, respectively. The 1.14*CM1A charges, which can be readily obtained for large systems, exhibit large deviations only for a subset of functional groups. The results for these cases were systematically improved using localized bond-charge corrections (LBCC) by which offsetting adjustments are made to the partial charges for atoms in specified bond types. Only 19 LBCCs were needed to yield 1.14*CM1A-LBCC charges that reduce the errors for the 426 Δ G hyd values to only 0.61 kcal/mol. The modified charge method was also tested in computation of heats of vaporization and densities for pure organic liquids, yielding average errors of 1.40 kcal/mol and 0.024 g/cm 3, similar to those for 1.14*CM1A.

Ions differ in their ability to salt out proteins from solution as expressed in the lyotropic or Hofmeister series of cations and anions. Since its first formulation in 1888, this series has been invoked in a plethora of effects, going beyond the original salting out/salting in idea to include enzyme activities and the crystallization of proteins, as well as to processes not involving proteins like ion exchange, the surface tension of electrolytes, or bubble coalescence. Although it has been clear that the Hofmeister series is intimately connected to ion hydration in homogeneous and heterogeneous environments and to ion pairing, its molecular origin has not been fully understood. This situation could have been summarized as follows: Many chemists used the Hofmeister series as a mantra to put a label on ion-specific behavior in various environments, rather than to reach a molecular level understanding and, consequently, an ability to predict a particular effect of a given salt ion on proteins in solutions. In this Feature Article we show that the cationic and anionic Hofmeister…

Membrane permeability is a key property to consider during the drug design process, and particularly vital when dealing with small molecules that have intracellular targets as their efficacy highly depends on their ability to cross the membrane. In this work, we describe the use of umbrella sampling molecular dynamics (MD) computational modeling to comprehensively assess the passive permeability profile of a range of compounds through a lipid bilayer. The model was initially calibrated through in vitro validation studies employing a parallel artificial membrane permeability assay (PAMPA). The model was subsequently evaluated for its quantitative prediction of permeability profiles for a series of custom synthesized and closely related compounds. The results exhibited substantially improved agreement with the PAMPA data, relative to alternative existing methods. Our work introduces a computational model that underwent progressive molding and fine-tuning as a result of its synergistic collaboration with numerous in vitro PAMPA permeability assays. The presented computational model…

The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical force fields for simulation of proteins. We developed the AMBER-FB15 protein force field by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization. The optimized potential surface allows for more significant thermodynamic fluctuations away from local minima. In validation studies where simulation results are compared to experimental measurements, AMBER-FB15 in combination with the updated TIP3P-FB water model predicts equilibrium properties with equivalent accuracy, and temperature dependent properties with significantly improved accuracy, in comparison with published models. We also discuss the effect of changing the protein force field and water model on the simulation results.

Abstract The results of kinetic tests and ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) show the important role played by a ZnO–copper interface in the generation of CO and the synthesis of methanol from CO2 hydrogenation. The deposition of nanoparticles of ZnO on Cu(100) and Cu(111), θoxi < 0.3 monolayer, produces highly active catalysts. The catalytic activity of these systems increases in the sequence: Cu(111) < Cu(100) < ZnO/Cu(111) < ZnO/Cu(100). The structure of the copper substrate influences the catalytic performance of a ZnO–copper interface. Furthermore, size and metal–oxide interactions affect the chemical and catalytic properties of the oxide making the supported nanoparticles different from bulk ZnO. The formation of a ZnO–copper interface favors the binding and conversion of CO2 into a formate intermediate that is stable on the catalyst surface up to temperatures above 500 K. Alloys of Zn with Cu(111) and Cu(100) were not stable at the elevated temperatures (500–600 K) used for the CO2 hydrogenation reaction. Reaction with CO2 oxidized the zinc, enhancing…

First-principles molecular dynamics simulations in the canonical ensemble at temperatures of 333 and 363 K and at the corresponding experimental densities are carried out to investigate the behavior of the 1:2 choline chloride/urea (reline) deep eutectic solvent and its equimolar mixture with water. Analysis of atom-atom radial and spatial distribution functions and of the H-bond network reveals the microheterogeneous structure of these complex liquid mixtures. In neat reline, the structure is governed by strong H-bonds of the trans- and cis-H atoms of urea to the chloride ion. In hydrous reline, water competes for the anions, and the H atoms of urea have similar propensities to bond to the chloride ions and the O atoms of urea and water. The vibrational spectra exhibit relatively broad peaks reflecting the heterogeneity of the environment. Although the 100 ps trajectories allow only for a qualitative assessment of transport properties, the simulations indicate that water is more mobile than the other species and its addition also fosters faster motion of urea.

The effects of crowding in biological environments on biomolecular structure, dynamics, and function remain not well understood. Computer simulations of atomistic models of concentrated peptide and protein systems at different levels of complexity are beginning to provide new insights. Crowding, weak interactions with other macromolecules and metabolites, and altered solvent properties within cellular environments appear to remodel the energy landscape of peptides and proteins in significant ways including the possibility of native state destabilization. Crowding is also seen to affect dynamic properties, both conformational dynamics and diffusional properties of macromolecules. Recent simulations that address these questions are reviewed here and discussed in the context of relevant experiments.

Little is presently known about the unique nanostructure of deep eutectic solvents (DES). The order of the liquid-solid phase transition is contended and whether DES-water mixtures are merely aqueous solutions, or have properties dominated by the eutectic pair, is unclear. Here, we unambiguously show the structure of choline chloride-malic acid (malicine) as a liquid, and also in solid and hydrated forms, using neutron total scattering on D/H isotope-substituted samples, and quasi-elastic neutron scattering (QENS). Data were refined using empirical potential structure refinement. We show evidence for a stoichiometric complex ion cluster in the disordered liquid, with strong choline-chloride bonding and a hydrogen bond donor (HBD) contribution. The 1:1 eutectic stoichiometry makes these ionic domains more well-defined, with less HBD clustering than seen previously for reline. There is minimal structural difference for the solidified material, demonstrating that this DES solidification is a glass transition rather than a first order phase change. QENS data support this by showing a…

Infrared (IR) imaging provides chemical-specific information without the need for exogenous labels. Conventional far-field IR imaging techniques are diffraction limited, which means an effective spatial resolution of >5 μm with currently available optics. In this article, we present a novel far-field IR imaging technique based on photothermal heterodyne imaging (IR-PHI). In our version of IR-PHI, an IR pump laser excites the sample, causing a small temperature rise that is detected by a counterpropagating visible probe beam. Images and spectra of several different types of soft matter systems (polystyrene beads, thin polymer films, and single Escherichia coli bacterial cells) are presented to demonstrate the sensitivity and versatility of the technique. Importantly, the spatial resolution in the IR-PHI measurements is determined by the visible probe beam: a spatial resolution of 0.3 μm was achieved with a 0.53 μm probe wavelength and a high numerical aperture focusing objective. This is the highest spatial resolution reported to date for far-field IR imaging. Analysis of the…

The dimer of the amyloid-β peptide Aβ of 42 residues is the smallest toxic species in Alzheimer's disease, but its equilibrium structures are unknown. Here we determined the equilibrium ensembles generated by the four atomistic OPLS-AA, CHARMM22*, AMBER99sb-ildn, and AMBERsb14 force fields with the TIP3P water model. On the basis of 144 μs replica exchange molecular dynamics simulations (with 750 ns per replica), we find that the four force fields lead to random coil ensembles with calculated cross-collision sections, hydrodynamics properties, and small-angle X-ray scattering profiles independent of the force field. There are, however, marked differences in secondary structure, with the AMBERsb14 and CHARMM22* ensembles overestimating the CD-derived helix content, and the OPLS-AA and AMBER99sb-ildn secondary structure contents in agreement with CD data. Also the intramolecular beta-hairpin content spanning residues 17-21 and 30-36 varies between 1.5% and 13%. Overall, there are significant differences in tertiary and quaternary conformations among all force fields, and the key…

Nanocellulose extracted from wood pulps using TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl radical)-mediated oxidation and sulfuric acid hydrolysis methods was characterized by small-angle neutron scattering (SANS), small-angle X-ray scattering (SAXS), and dynamic light scattering (DLS) techniques. The dimensions of this nanocellulose (TEMPO-oxidized cellulose nanofiber (TOCN) and sulfuric acid hydrolyzed cellulose nanocrystal (SACN)) revealed by the different scattering methods were compared with those characterized by transmission electron microscopy (TEM). The SANS and SAXS data were analyzed using a parallelepiped-based form factor. The width and thickness of the nanocellulose cross section were ∼8 and ∼2 nm for TOCN and ∼20 and ∼3 nm for SACN, respectively, where the fitting results from SANS and SAXS profiles were consistent with each other. DLS was carried out under both the V V mode with the polarizer and analyzer parallel to each other and the H V mode having them perpendicular to each other. Using rotational and translational diffusion coefficients obtained under the H V…

Hydronium (H 3 O + ) and hydroxide (OH – ) ions have anomalously large diffusion constants in aqueous solutions due to their combination of vehicular and Grotthuss hopping diffusion mechanisms. An improvement of the ReaxFF reactive water force field on the basis of our first-generation water force field (water-2010) is presented to describe the proton transfer (PT) mechanisms of H 3 O + and OH – in water. Molecular dynamics simulation studies with the water-2017 force field support the Eigen–Zundel–Eigen mechanism for PT in acidic aqueous solution and reproduce the hypercoordinated solvation structure of the OH – in a basic environment. In particular, it predicts the correct order of the diffusion constants of H 2 O, H 3 O +, and OH – and their values are in agreement with the experimental data. Another interesting observation is that the diffusion constants of H 3 O + and OH – are close to each other at high concentration due to the strong correlation between OH – ions in basic aqueous solution. On the basis of our results, it is shown that ReaxFF provides a novel approach to study…

Abstract Water is an extensively self-associated liquid due to its extensive hydrogen bond (H-bond) forming ability. The resulting H-bonded network fluid exhibits nearly continuous absorption of light from the terahertz to the near-IR region. The relatively weak bend+libration water combination band (centered at 2130 cm–1) has been largely overlooked as a reporter of liquid water’s structure and dynamics despite its location in a convenient region of the IR for spectroscopic study. The intermolecular nature of the combination band leads to a unique absorption signal that reports collectively on the rigidity of the H-bonding network in the presence of many different solutes. This study reports comprehensively how the combination band acts as an intrinsic and collective probe in various chemically and biologically relevant solutions, including salts of varying character, denaturants, osmolytes, crowders, and surfactants that form reverse micelles and micelles. While we remark on changes in the line width and intensity of this combination band, we mainly focus on the frequency and how…

Deep eutectic solvents (DESs) have emerged as nontoxic and inexpensive alternatives not only to the common organic solvents but to the ionic liquids as well. Some of the common and popular, and perhaps the most investigated, DESs are the ones comprising an ammonium salt and an appropriate hydrogen bond (HB) donor in a predetermined mole ratio. The formation of the DES is attributed to the H-bonding interaction(s) present between the salt and the HB donor. Consequently, addition of a predominantly HB donor or a predominantly HB acceptor cosolvent to such DESs may result in intriguing features and properties. We present investigation of two DESs constituted of salt choline chloride along with HB donors urea and glycerol, respectively, in 1:2 mol ratio, named reline and glyceline as the cosolvent of very high HB donating acidity and no HB accepting basicity 2,2,2-trifluoroethanol (TFE) and of very high HB accepting basicity and no HB donating acidity hexamethylphosphoramide (HMPA), respectively, is added. TFE shows up to 0.25 mole fraction miscibility with both reline and glyceline.…

The detailed structure and crystallization behavior of poly(butylene succinate) (PBS) have been investigated by Fourier transform infrared (FTIR) and other methods systematically. For the first time, we confirmed that the C═O stretching modes of PBS can respond to three distinguish absorption bands in the FTIR spectrum, at around 1736, 1720, and 1714 cm –1 respectively. The 1736 cm –1 band is adopted as the stretching mode of C═O groups in free amorphous fraction (MAF); the 1714 cm –1 band which is relevant to more stable structure, displays more anisotropic in polarized FTIR spectra, and has been confirmed as stretching vibrations of hydrogen-bonded C═O groups in the crystalline phase. The 1720 cm –1 band is linked to crystallization but comes from less ordered structure. Moreover, the 1720 cm –1 band can be destroyed prior to 1714 cm –1 band during heating and constructed behind 1714 cm –1 band during cooling. Thus, the 1720 cm –1 band is reasonably ascribed to the C═O groups in rigid amorphous fraction (RAF) or intermediate phase which locates between MAF and crystalline phase.…

Cosolvents modulate aqueous solubility, hydrophobic interactions, and the stability and function of most proteins in the living cell. Our molecular-level understanding of cosolvent effects is incomplete, not only at the level of complex systems such as proteins, but also at the level of very fundamental interactions that underlie the hydrophobic effect. This Feature Article discusses cosolvent effects on the aqueous solubility of nonpolar solutes, hydrophobic interactions, and hydrophobic self-assembly/collapse of aqueous polymers, recently studied with molecular dynamics simulations. It is shown that direct interactions of cosolvents with nonpolar solutes and aqueous polymers can strengthen hydrophobic interactions and can contribute to stabilizing collapsed globular structures. The molecular-level explanation of these observations requires a better understanding of the entropy associated with fluctuations of attractive solute-solvent interactions and of length-scale dependencies of this quantity.

Molecular details of BSA adsorption on a silica surface are revealed by fully atomistic molecular dynamics (MD) simulations (with a 0.5 μs trajectory), supported by dynamic light scattering (DLS), zeta potential, multiparametric surface plasmon resonance (MP-SPR), and contact angle experiments. The experimental and theoretical methods complement one another and lead to a wider understanding of the mechanism of BSA adsorption across a range of pH 3-9. The MD results show how the negatively charged BSA at pH7 adsorbs to the negatively charged silica surface, and reveal a unique orientation with preserved secondary and tertiary structure. The experiments then show that the protein forms complete monolayers at ∼ pH6, just above the protein's isoelectric point (pH5.1). The surface contact angle is maximum when it is completely coated with protein, and the hydrophobicity of the surface is understood in terms of the simulated protein conformation. The adsorption behavior at higher pH > 6 is also consistently interpreted using the MD picture; both the contact angle and the adsorbed protein…

Abstract The high precious metal loading and high overpotential of the oxygen evolution reaction (OER) prevents the widespread utilization of polymer electrolyte membrane (PEM) water electrolyzers. Herein we explore the OER activity and stability in acidic electrolyte of a combined IrOx/RuO2 system consisting of RuO2 thin films with submonolayer (1, 2, and 4 Å) amounts of IrOx deposited on top. Operando extended X-ray absorption fine structure (EXAFS) on the Ir L-3 edge revealed a rutile type IrO2 structure with some Ir sites occupied by Ru, IrOx being at the surface of the RuO2 thin film. We monitor corrosion on IrOx/RuO2 thin films by combining electrochemical quartz crystal microbalance (EQCM) with inductively coupled mass spectrometry (ICP-MS). We elucidate the importance of submonolayer surface IrOx in minimizing Ru dissolution. Our work shows that we can tune the surface properties of active OER catalysts, such as RuO2, aiming to achieve higher electrocatalytic stability in PEM electrolyzers.

We introduce a computational framework that is able to describe general many-body coarse-grained (CG) interactions of molecules and use it to model the free energy surface of molecular liquids as a cluster expansion in terms of monomer, dimer, and trimer terms. The contributions to the free energy due to these terms are inferred from all-atom molecular dynamics (MD) data using Gaussian Approximation Potentials, a type of machine-learning model that employs Gaussian process regression. The resulting CG model is much more accurate than those possible using pair potentials. Though slower than the latter, our model can still be faster than all-atom simulations for solvent-free CG models commonly used in biomolecular simulations.

Halogens are present in a significant number of drugs, contributing favorably to ligand-protein binding. Currently, the contribution of halogens, most notably chlorine and bromine, is largely attributed to halogen bonds involving favorable interactions with hydrogen bond acceptors. However, we show that halogens acting as hydrogen bond acceptors potentially make a more favorable contribution to ligand binding than halogen bonds based on quantum mechanical calculations. In addition, bioinformatics analysis of ligand-protein crystal structures shows the presence of significant numbers of such interactions. It is shown that interactions between halogens and hydrogen bond donors (HBDs) are dominated by perpendicular C-X···HBD orientations. Notably, the orientation dependence of the halogen-HBD (X-HBD) interactions is minimal over greater than 100° with favorable interaction energies ranging from -2 to -14 kcal/mol. This contrasts halogen bonds in that X-HBD interactions are substantially more favorable, being comparable to canonical hydrogen bonds, with a smaller orientation dependence,…

Magnesium and zinc dications possess the same charge and have an almost identical size, yet they behave very differently in aqueous solutions and play distinct biological roles. It is thus crucial to identify the origins of such different behaviors and to assess to what extent they can be captured by force-field molecular dynamics simulations. In this work, we combine neutron scattering experiments in a specific mixture of H 2 O and D 2 O (the so-called null water) with ab initio molecular dynamics simulations to probe the difference in the hydration structure and ion-pairing properties of chloride solutions of the two cations. The obtained data are used as a benchmark to develop a scaled-charge force field for Mg 2+ that includes electronic polarization in a mean field way. We show that using this electronic continuum correction we can describe aqueous magnesium chloride solutions well. However, in aqueous zinc chloride specific interaction terms between the ions need to be introduced to capture ion pairing quantitatively.

The highly crystalline nature of cellulose results in poor processability and solubility, necessitating the search for solvents that can efficiently dissolve this material. Thus, ionic liquids (ILs) have recently been shown to be well suited for this purpose, although the corresponding dissolution mechanism has not been studied in detail. Herein, we adopt a molecular dynamics (MD) approach to study the dissolution of model cellulose crystal structures in imidazolium-based ILs and gain deep mechanistic insights, demonstrating that dissolution involves IL penetration-induced cleavage of hydrogen bonds between cellulose molecular chains. Moreover, we reveal that in ILs with high cellulose dissolving power (powerful solvents, such as 1-allyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium chloride), the above molecular chains are peeled from the crystal phase and subsequently dispersed in the solvent, whereas no significant structural changes are observed in poor-dissolving-power solvents. Finally, we utilize MD trajectory analysis to show that the solubility of…

The generation of singlet oxygen ( 1 O 2 ) has been established as the principal mechanism of photodynamic therapy (PDT). Various dyes, metal nanoparticles, and clusters have been shown to sensitize 1 O 2 . However, metal nanoclusters are even more promising candidates as photosensitizers for this purpose. By understanding the optical properties that lead to efficient 1 O 2 generation, one can fully realize their potential as PDT photosensitizers. Three different metal nanoclusters, Au 25, Ag 32, and Au 144, are investigated for their 1 O 2 generation efficiency. The Au 144 showed a 1 O 2 generation rate that is 2 orders of magnitude higher than that for Au 25 and Ag 32, and several orders of magnitude higher than nanoparticles (>5 nm) due to Au 144 ’s high absorption cross section-to-volume ratio. The effectiveness of PDT in live cells with nanoclusters was demonstrated by two-photon excitation compared to one-photon excitation. The implication of these results points toward new efficient two-photon 1 O 2 sensitizers for photodynamic therapy.

Abstract The free energy profile of the piperidine catalyzed Knoevenagel condensation reaction of acetylacetone with benzaldehyde has been obtained by theoretical calculations. The carbinolamine formation step involves catalysis by methanol solvent, and its decomposition takes place via hydroxide ion elimination without a classical transition state, leading to the iminium ion. Hydroxide ion deprotonates the acetylacetone, forming an enolate that attacks the iminium ion and leads to an addition intermediate. The final step involves elimination of piperidine catalyst. Our analysis suggests the iminium ion formation has the highest barrier and the catalytic effect of piperidine is facilitating the elimination step rather than activation of the benzaldehyde electrophile. Experimental measures of the kinetics lead to an observed free energy barrier of 20.0 kcal mol–1, in good agreement with the theoretical value of 21.8 kcal mol–1 based on the free energy profile.

Machine learning (ML) is increasingly becoming a helpful tool in the search for novel functional compounds. Here we use classification via random forests to predict the stability of half-Heusler (HH) compounds, using only experimentally reported compounds as a training set. Cross-validation yields an excellent agreement between the fraction of compounds classified as stable and the actual fraction of truly stable compounds in the ICSD. The ML model is then employed to screen 71 178 different 1:1:1 compositions, yielding 481 likely stable candidates. The predicted stability of HH compounds from three previous high-throughput ab initio studies is critically analyzed from the perspective of the alternative ML approach. The incomplete consistency among the three separate ab initio studies and between them and the ML predictions suggests that additional factors beyond those considered by ab initio phase stability calculations might be determinant to the stability of the compounds. Such factors can include configurational entropies and quasiharmonic contributions.

Abstract Ionic-liquid (IL) mixtures hold great promise, as they allow liquids with a wide range of properties to be formed by mixing two common components rather than by synthesizing a large array of pure ILs with different chemical structures. In addition, these mixtures can exhibit a range of properties and structural organization that depend on their composition, which opens up new possibilities for the composition-dependent control of IL properties for particular applications. However, the fundamental properties, structure, and dynamics of IL mixtures are currently poorly understood, which limits their more widespread application. This article presents the first comprehensive investigation into the bulk and surface properties of IL mixtures formed from two commonly encountered ILs: 1-ethyl-3-methylimidazolium and 1-dodecyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C2mim][Tf2N] and [C12mim][Tf2N]). Physical property measurements (viscosity, conductivity, and density) reveal that these IL mixtures are not well described by simple mixing laws, implying that their…

For a long time, the effect of a crowded cellular environment on protein dynamics has been largely ignored. Recent experiments indicate that proteins diffuse more slowly in a living cell than in a diluted solution, and further studies suggest that the diffusion depends on the local surroundings. Here, detailed insight into how diffusion depends on protein-protein contacts is presented based on extensive all-atom molecular dynamics simulations of concentrated villin headpiece solutions. After force field adjustments in the form of increased protein-water interactions to reproduce experimental data, translational and rotational diffusion was analyzed in detail. Although internal protein dynamics remained largely unaltered, rotational diffusion was found to slow down more significantly than translational diffusion as the protein concentration increased. The decrease in diffusion is interpreted in terms of a transient formation of protein clusters. These clusters persist on sub-microsecond time scales and follow distributions that increasingly shift toward larger cluster size with…

Abstract We present a combined experimental and theoretical study to demonstrate that the electrocatalytic activity of NiFe layered double hydroxides (NiFe LDHs) for the oxygen evolution reaction (OER) can be significantly enhanced by systematic cobalt incorporation using coprecipitation and/or intercalation. Electrochemical measurements show that cobalt modified NiFe LDH possesses an enhanced activity for the OER relative to pristine NiFe LDH. The Co-modified NiFe LDH exhibits overpotentials in the range of 290–322 mV (at 10 mA cm–2), depending on the degree of cobalt content. The best catalyst, cobalt intercalated NiFe LDH achieved a current density of 10 mA cm–2 at an overpotential of ∼265 mV (compared to 310 mV for NiFe LDH), with a near unity (99%) faradaic efficiency and long-term stability. Density functional theory calculations revealed that enhanced activity of Co-modified NiFe LDH could be attributed to the ability of Co to tune the electronic structure of the NiFe LDH so that optimal binding of OER reaction intermediates could be achieved.

Polymerized ionic liquids (PolyILs) are promising candidates for a wide range of technological applications due to their single ion conductivity and good mechanical properties. Tuning the glass transition temperature ( T g ) in these materials constitutes a major strategy to improve room temperature conductivity while controlling their mechanical properties. In this work, we show experimental and simulation results demonstrating that in these materials T g does not follow a universal scaling behavior with the volume of the structural units V m (including monomer and counterion). Instead, T g is significantly influenced by the chain flexibility and polymer dielectric constant. We propose a simplified empirical model that includes the electrostatic interactions and chain flexibility to describe T g in PolyILs. Our model enables design of new functional PolyILs with the desired T g .

Abstract Recent advances of ambient pressure X-ray photoelectron spectroscopy (AP-XPS) have enabled the chemical composition and the electrical potential profile at a liquid/electrode interface under electrochemical reaction conditions to be directly probed. In this work, we apply this operando technique to study the surface chemical composition evolution on a Co metal electrode in 0.1 M KOH aqueous solution under various electrical biases. It is found that an ∼12.2 nm-thick layer of Co­(OH)2 forms at a potential of about −0.4 VAg/AgCl, and upon increasing the anodic potential to about +0.4 VAg/AgCl, this layer is partially oxidized into cobalt oxyhydroxide (CoOOH). A CoOOH/Co­(OH)2 mixture layer is formed on the top of the electrode surface. Finally, the oxidized surface layer can be reduced to Co0 at a cathodic potential of −1.35 VAg/Cl. These observations indicate that the ultrathin layer containing cobalt oxyhydroxide is the active phase for oxygen evolution reaction (OER) on a Co electrode in an alkaline electrolyte, consistent with previous studies.

blend electrolytes. Second, the results for different plasticizers, such as ethylene carbonate, propylene carbonate, and dimethyle carbonate, on the conductivity and relaxation in these blend electrolytes are compared. We have followed a new approach for the analysis of the conductivity data. The frequency dependent conductivity is analyzed using random free-energy barrier model, taking into consideration the low frequency polarization effect. The temperature dependences of the ionic conductivity and the relaxation time obtained from the model exhibit Vogel-Tammann-Fulcher behavior. Using the scaling of the ac conductivity spectra it is observed that the relaxation dynamics of charge carriers in blend electrolytes are independent of temperature but depend on the nature of plasticizers. The electric modulus is studied using Havriliak-Negami function for the understanding of ionic relaxation. The modulus data are also analyzed using nonexponential Kohlrausch-Williams-Watts function. The temperature dependence of the relaxation time obtained from modulus analysis follows…

Obtaining exact solutions to the Schrödinger equation for atoms, molecules, and extended systems continues to be a “Holy Grail” problem which the fields of theoretical chemistry and physics have been striving to solve since inception. Recent breakthroughs have been made in the development of hardware-efficient quantum optimizers and coherent Ising machines capable of simulating hundreds of interacting spins with an Ising-type Hamiltonian. One of the most vital questions pertaining to these new devices is, “Can these machines be used to perform electronic structure calculations?” Within this work, we review the general procedure used by these devices and prove that there is an exact mapping between the electronic structure Hamiltonian and the Ising Hamiltonian. Additionally, we provide simulation results of the transformed Ising Hamiltonian for H 2, He 2, HeH +, and LiH molecules, which match the exact numerical calculations. This demonstrates that one can map the molecular Hamiltonian to an Ising-type Hamiltonian which could easily be implemented on currently available quantum…

Silica aerogels are nanostructured, highly porous solids which have, compared to other soft materials, special mechanical properties, such as extremely low densities. In the present work, the mechanical properties of silica aerogels have been studied with molecular dynamics (MD) simulations. The aerogel model of 192 000 atoms was created with different densities by direct expansion of β-cristobalite and subjected to series of thermal treatments. Because of the high number of atoms and improved modeling procedure, the proposed model was more stable and showed significant improvement in the smoothness of the resulting stress–strain curves in comparison to previous models. Resulting Poisson’s ratio values for silica aerogels lie between 0.18 and 0.21. The elasticity moduli display a power law dependence on the density, with the exponent estimated to be 3.25 ± 0.1. These results are in excellent agreement with reported experimental as well as computational values. Two different deformation scenarios have been discussed. Under tension, the low-density aerogels were more ductile while the…

We present the Simulation Enabled Estimation of Kinetic Rates (SEEKR) package, a suite of open-source scripts and tools designed to enable researchers to perform multiscale computation of the kinetics of molecular binding, unbinding, and transport using a combination of molecular dynamics, Brownian dynamics, and milestoning theory. To demonstrate its utility, we compute the k on, k off, and Δ G bind for the protein trypsin with its noncovalent binder, benzamidine, and examine the kinetics and other results generated in the context of the new software, and compare our findings to previous studies performed on the same system. We compute a k on estimate of (2.1 ± 0.3) × 10 7 M –1 s –1, a k off estimate of 83 ± 14 s –1, and a Δ G bind of −7.4 ± 0.1 kcal·mol –1, all of which compare closely to the experimentally measured values of 2.9 × 10 7 M –1 s –1, 600 ± 300 s –1, and −6.71 ± 0.05 kcal·mol –1, respectively.

Optogenetics has been, and will continue to be, a boon to mechanistic studies of cellular processes. Genetically encodable proteins that sensitize the production of reactive oxygen species (ROS) are expected to play an increasingly important role, particularly in elucidating mechanisms of temporally and spatially dependent cell signaling. However, a substantial challenge in developing such photosensitizing proteins has been to funnel the optical excitation energy into the initial selective production of only one ROS. Singlet molecular oxygen, O 2 (a 1 Δ g ), is a ROS known to have a wide range of effects on cell function. Nevertheless, mechanistic details of singlet oxygen’s behavior in a cell are lacking. On the basis of the rational optimization of a LOV-derived flavoprotein, we now report the development and photophysical characterization of a protein-encased photosensitizer that efficiently and selectively produces singlet oxygen at the expense of other ROS, especially ROS that derive from photoinduced electron transfer reactions. These results set the stage for a plethora of…

We perform molecular dynamics simulation study of CO 2, methane, and their mixture in the presence of brine over a broad range of temperature (311–473 K), pressure (up to about 100 MPa), and NaCl concentration (up to about 14 wt %). The general decrease in the interfacial tension (IFT) values of the CH 4 –brine system with pressure and temperature is similar to that obtained for the corresponding CH 4 –water system. The IFT of methane and brine is a linearly increasing function of salt concentration, and the resulting slopes are dependent on the pressure. A similar behavior as methane is observed for such systems containing CO 2 and CO 2 –CH 4 mixture. The IFT of CO 2 and brine increases linearly with increasing salt content; however, the resulting slopes are independent of pressure. The simulations show that the presence of CO 2 decreases the IFT values of the CH 4 –water and CH 4 –brine systems, but the degree of reduction depends on the amount of CO 2 in each sample, which is consistent with experimental evidence. These IFT values show a linear correlation with the amount of CO…

The host–guest complexation of hydrocarbons (22 guest molecules) with cucurbit[7]uril was investigated in aqueous solution using the indicator displacement strategy. The binding constants (10 3 –10 9 M –1 ) increased with guest size, pointing to the hydrophobic effect and dispersion interactions as driving forces. The measured affinities provide unique benchmark data for the binding of neutral guest molecules. Consequently, a computational blind challenge, the HYDROPHOBE challenge, was conducted to allow a comparison with state-of-the-art computational methods for predicting host–guest affinity constants. In total, three quantum-chemical (QM) data sets and two explicit-solvent molecular dynamics (MD) submissions were received. When searching for sources of uncertainty in predicting the host–guest affinities, the experimentally known hydration energies of the investigated hydrocarbons were used to test the employed solvation models (explicit solvent for MD and COSMO-RS for QM). Good correlations were obtained for both solvation models, but a rather constant offset was observed for…

Abstract We use ambient-pressure X-ray photoelectron spectroscopy (APXPS) to study chemical changes, including hydroxylation and water adsorption, at copper oxide surfaces from ultrahigh vacuum to ambient relative humidities of ∼5%. Polycrystalline CuO and Cu2O surfaces were prepared by selective oxidation of metallic copper foils. For both oxides, hydroxylation occurs readily, even at high-vacuum conditions. Hydroxylation on both oxides plateaus near ∼0.01% relative humidity (RH) at a coverage of ∼1 monolayer. In contrast to previous studies, neither oxide shows significant accumulation of molecular water; rather, both surfaces show a high affinity for adventitious carbon contaminants. Results of isobaric and isothermic experiments are compared, and the strengths and potential drawbacks of each method are discussed. We also provide critical evaluations of the effects of the hot filament of the ion pressure gauge on the reactivity of gas-phase species, the peak fitting procedure on the quantitative analysis of spectra, and rigorous accounting of carbon contamination on data analysis…

Abstract Herein we present surface sensitive operando XAS L-edge measurements on IrOx/RuO2 thin films as well as mass-selected RuOx and Ru nanoparticles. We observed shifts of the white line XAS peak toward higher energies with applied electrochemical potential. Apart from the case of the metallic Ru nanoparticles, the observed potential dependencies were purely core-level shifts caused by a change in oxidation state, which indicates no structural changes. These findings can be explained by different binding energies of oxygenated species on the surface of IrOx and RuOx. Simulated XAS spectra show that the average Ir oxidation state change is strongly affected by the coverage of atomic O. The observed shifts in oxidation state suggest that the surface has a high coverage of O at potentials just below the potential where oxygen evolution is exergonic in free energy. This observation is consistent with the notion that the metal–oxygen bond is stronger than ideal.

Abstract The Schlenk equilibrium is a complex reaction governing the presence of multiple chemical species in solution of Grignard reagents. The full characterization at the molecular level of the transformation of CH3MgCl into MgCl2 and Mg(CH3)2 in tetrahydrofuran (THF) by means of ab initio molecular dynamics simulations with enhanced-sampling metadynamics is presented. The reaction occurs via formation of dinuclear species bridged by chlorine atoms. At room temperature, the different chemical species involved in the reaction accept multiple solvation structures, with two to four THF molecules that can coordinate the Mg atoms. The energy difference between all dinuclear solvated structures is lower than 5 kcal mol–1. The solvent is shown to be a direct key player driving the Schlenk mechanism. In particular, this study illustrates how the most stable symmetrically solvated dinuclear species, (THF)CH3Mg(μ-Cl)2MgCH3(THF) and (THF)CH3Mg(μ-Cl)(μ-CH3)MgCl(THF), need to evolve to less stable asymmetrically solvated species, (THF)CH3Mg(μ-Cl)2MgCH3(THF)2 and…

Excited-state proton transfer (ESPT) in Indigo and its monohexyl-substituted derivative (Ind and NHxInd, respectively) in solution was investigated experimentally as a function of solvent viscosity, polarity, and temperature, and theoretically by time-dependent density functional theory (TDDFT) calculations. Although a single emission band is observed, the fluorescence decays (collected at different wavelengths along the emission band using time-correlated single photon counting (TCSPC)) are biexponential, with two identical decay times but different pre-exponential factors, which is consistent with the existence of excited-state keto and enol species. The femtosecond (fs)-transient absorption data show that two similar decay components are present, in addition to a shorter (<3 ps) component associated with vibrational relaxation. From TDDFT calculations it was shown that with both Ind and NHxInd, the reaction proceeds through a single ESPT mechanism driven by an Arrhenius-type activation through a saddle point, which is enhanced by tunneling through the barrier. From the…

We investigate the mechanism of a typical kinetic hydrate inhibitor (KHI), polyvinylcaprolactam (PVCap), which has been applied to prevent hydrate plugs from forming in gas pipe lines, using molecular dynamics simulations of crystal growth of ethylene oxide hydrate. Water-soluble ethylene oxide is chosen as a guest species to avoid problems associated with the presence of the gas phase in the simulation cell such as slow crystal growth. A PVCap dodecamer adsorbs irreversibly on the hydrate surface which grows at supercooling of 3 K when the hydrophobic part of two pendent groups are trapped in open cages at the surface. The amide hydrogen bonds make no contribution to the adsorption. PVCap can adsorb on various crystallographic planes of sI hydrate. This is in contrast to antifreeze proteins, each of which prefers a specific plane of ice. The trapped PVCap gives rise to necessarily the concave surface of the hydrate. The crystal growth rate decreases with increasing surface curvature, indicating that the inhibition by PVCap is explained by the Gibbs-Thomson effect.

Antioxidant efficiency of all- trans -retinol has been studied on the basis of characteristic thermochemical properties using density functional theory. The influence of the solvent polarity has also been evaluated. It is found that retinol may act in parallel as an effective antioxidant via H atom donating as well as a pro-oxidant in yielding reactive hydroxyl radical. In fact, the lowest values of bond dissociation enthalpy were found at the C18–H and C18–OH positions. Retinol was also determined to be a good electron donor but bad acceptor in the single electron transfer (ET) reaction with hydroperoxyl (HOO • ) radical. In addition, potential energy surfaces of H atom transfer (HAT) and radical adduct formation (RAF) reactions between retinol and HOO • radical were also investigated in the gas phase and in the solvent. The results demonstrated that the RAF mechanism was generally more predominant than ET and HAT ones. The most favored radical addition position was found at the C2═C3 double bond in the cyclohexenyl ring. Moreover, the radical scavenging reactivity via RAF…

Abstract Förster resonance energy transfer (FRET) measurements from a donor, D, to an acceptor, A, fluorophore are frequently used in vitro and in live cells to reveal information on the structure and dynamics of DA labeled macromolecules. Accurate descriptions of FRET measurements by molecular models are complicated because the fluorophores are usually coupled to the macromolecule via flexible long linkers allowing for diffusional exchange between multiple states with different fluorescence properties caused by distinct environmental quenching, dye mobilities, and variable DA distances. It is often assumed for the analysis of fluorescence intensity decays that DA distances and D quenching are uncorrelated (homogeneous quenching by FRET) and that the exchange between distinct fluorophore states is slow (quasistatic). This allows us to introduce the FRET-induced donor decay, εD(t), a function solely depending on the species fraction distribution of the rate constants of energy transfer by FRET, for a convenient joint analysis of fluorescence decays of FRET and reference samples by…

Morphology of the conducting polymer PEDOT:TOS (poly(3,4-ethylenedioxythiophene) doped with molecular tosylate) and its crystallization in aqueous solution were studied using atomistic molecular dynamics simulations. It was found that (a) PEDOT comprises crystallite aggregates consisting of 3–6 π–π stacked chains. The crystallites are linked by interpenetrating π–π stacked chains such that percolative paths in the structure are formed. (b) The size of the crystallites depends on the water content, but the π–π stacking distance is practically independent of the chain length, charge concentration and water content. (c) TOS counterions are located either on the top of the chains or on the side of the crystallites and their distribution depends on the charge concentration but is practically independent of the water content; (d) PEDOT chains and crystallites exhibit bending that depends on their length and water content.

Flavonoids have emerged to be an important molecular frame for chemical sensors, due to their capability to give dual emission and their compatibility to biological cells. Two flavonoid compounds with Me 2 N- and Et 2 N-substituents were examined by acquiring their fluorescence at different temperatures, in order to evaluate the impact of intramolecular charge transfer (ICT) on ESIPT. By freezing the sample solution in liquid N 2, the study detected the “locally excited” state at λ em ≈ 460 nm, in which both ICT and ESIPT processes were not present. As temperature was warmed up (to about −90 °C), ICT process became gradually allowed and emission was shifted to λ em ≈ 510 nm, which was attributed to the normal form N* of flavonoid. Emission from tautomeric form T* (λ em ≈ 575 nm) could only be observed at a higher temperature, when ESIPT became allowed. With the aid of a model compound (without R 2 N-substituent) and computational study, the study led to improved understanding on the photophysical properties of flavonoid materials in general.

A comparative study of binding interaction between Safranin O (SO) and Neutral Red (NR) with lysozyme (Lyz) has been reported using several spectroscopic methods along with computational approaches. Steady-state fluorescence measurements revealed static quenching as the major quenching mechanism in Lyz-SO and Lyz-NR interaction, which is further supported by time-resolved fluorescence and UV-vis measurements. Additionally, binding and thermodynamic parameters of these interactions are calculated from temperature dependent fluorescence data. Moreover, conformational changes of protein upon binding with SO and NR are provided by synchronous and circular dichroism (CD) measurements. Molecular docking study provided the exact binding location of SO and NR in lysozyme. Along with this study, molecular dynamics simulation is carried out to measure the stability of Lyz, Lyz-SO, and Lyz-NR complex. The present study revealed the strong binding affinity of dyes with lysozyme, and this study would be helpful toward medical and environmental science.

We report the transition dipole strengths and frequencies of the amyloid β-sheet amide I mode for the aggregated proteins amyloid-β 1–40, calcitonin, α-synuclein, and glucagon. According to standard vibrational coupling models for proteins, the frequencies of canonical β-sheets are set by their size and structural and environmental disorder, which determines the delocalization length of the vibrational excitons. The larger the delocalization the lower the frequency of the main infrared-allowed transition, A ⊥ . The models also predict an accompanying increase in transition dipole strength. For the proteins measured here, we find no correlation between transition dipole strengths and amyloid β-sheet transition frequency. To understand this observation, we have extracted from the protein data bank crystal structures of amyloid peptides from which we calculate the amide I vibrational couplings, and we use these in a model β-sheet Hamiltonian to simulate amyloid vibrational spectra. We find that the variations in amyloid β-sheet structures (e.g., dihedral angles, interstrand distances,…

Nitrogenase is the only enzyme that can break the triple bond in N 2 to form two molecules of ammonia. The enzyme has been thoroughly studied with both experimental and computational methods, but there is still no consensus regarding the atomic details of the reaction mechanism. In the most common form, the active site is a MoFe 7 S 9 C(homocitrate) cluster. The homocitrate ligand contains one alcohol and three carboxylate groups. In water solution, the triply deprotonated form dominates, but because the alcohol (and one of the carboxylate groups) coordinate to the Mo ion, this may change in the enzyme. We have performed a series of computational calculations with molecular dynamics (MD), quantum mechanical (QM) cluster, combined QM and molecular mechanics (QM/MM), QM/MM with Poisson–Boltzmann and surface area solvation, QM/MM thermodynamic cycle perturbations, and quantum refinement methods to settle the most probable protonation state of the homocitrate ligand in nitrogenase. The results quite conclusively point out a triply deprotonated form (net charge −3) with a proton shared…

Weak interchain interactions have been considered to be a bottleneck for heat transfer in polymers, while covalent bonds are believed to give a high thermal conductivity to polymer chains. For this reason, cross-linkers have been explored as a means to enhance polymer thermal conductivity; however, results have been inconsistent. Some studies show an enhancement in the thermal conductivity for polymers upon cross-linking, while others show the opposite trend. In this work we study the mechanisms of heat transfer in cross-linked polymers in order to understand the reasons for these discrepancies, in particular examining the relative contributions of covalent (referred to here as "bonding") and nonbonding (e.g., van der Waals and electrostatic) interactions. Our results indicate cross-linkers enhance thermal conductivity primarily when they are short in length and thereby bring polymer chains closer to each other, leading to increased interchain heat transfer by enhanced nonbonding interactions between the chains (nonbonding interactions being highly dependent on interchain distance).…