The 50 most-cited articles in The Journal of Physical Chemistry B, 2016

The accuracy of molecular dynamics simulations depends on the underlying force field, defined by the form and parametrization of the interparticle potential functions and the water model. The treatment of the solvent is crucial in molecular dynamics force fields, as hydrophobic interactions and hydrogen bonding are important molecular forces. The widely used CHARMM force field was originally parametrized using a modified version of the TIP3P water model (mTIP3P), including Lennard-Jones interactions between hydrogens and oxygens. The latest version, CHARMM36, was optimized using the standard TIP3P water model (sTIP3P) for proteins, while mTIP3P is still being used for lipids. Our replica exchange molecular dynamics simulations on dynamic peptides show that the CHARMM36 force field with mTIP3P water yields less realistic folding than with sTIP3P water. Analysis of the dimensions and hydrogen bonding of the unfolded state reveals that the peptides are more solvated and extended in mTIP3P, due to a higher solvation energy of the peptide in this water model. We recommend using CHARMM36…

This paper presents the computational assessment of the electrochemical stability of a series of alkyl methylimidazolium-based ionic liquids for their use as lithium battery electrolytes. The oxidation and reduction potentials of the constituent cation and anion of each ionic liquid with respect to a Li(+)/Li reference electrode were calculated using density functional theory following the method of thermodynamic cycles, and the electrochemical stability windows (ESW)s of these ionic liquids were obtained. The effect of varying the length of alkyl side chains of the methylimidazolium-based cations on the redox potentials and ESWs was investigated. The results show that the limits of the ESWs of these methylimidazolium-based ionic liquids are defined by the oxidation potential of the anions and the reduction potential of alkyl-methylimidazolium cations. Moreover, ionic liquids with [PF6](-) anion have a wider ESW. In addition to characterizing structure-function relationships, the accuracy of the computational approach was assessed through comparisons of the data against experimental…

Energetic thin films with high mass loadings of nanosized components have been recently fabricated using electrospray deposition. These films are composed of aluminum nanoparticles (nAl) homogeneously dispersed in an energetic fluoropolymer binder, poly(vinylidene fluoride) (PVDF). The nascent oxide shell of the nAl has been previously shown to undergo a preignition reaction (PIR) with fluoropolymers such as polytetrafluoroethylene (PTFE). This work examines the PIR between alumina and PVDF to further explain the reaction mechanism of the Al/PVDF system. Temperature jump (T-jump) ignition experiments in air, argon, and vacuum environments showed that the nAl is fluorinated by gas phase species due to a decrease in reactivity in a vacuum. Thermogravimetric analysis coupled with differential scanning calorimetry (TGA/DSC) was used to confirm the occurrence of a PIR, and gas phase products during the PIR and fluorination of nAl were investigated with temperature jump time-of-flight mass spectrometry (T-jump TOFMS). Results show a direct correlation between the amount of alumina in the…

Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in studies of enzymatic catalysis. Until recently, it has been cost prohibitive to determine the asymptotic limit of key energetic and structural properties with respect to increasingly large QM regions. Leveraging recent advances in electronic structure efficiency and accuracy, we investigate catalytic properties in catechol O-methyltransferase, a prototypical methyltransferase critical to human health. Using QM regions ranging in size from reactants-only (64 atoms) to nearly one-third of the entire protein (940 atoms), we show that properties such as the activation energy approach within chemical accuracy of the large-QM asymptotic limits rather slowly, requiring approximately 500-600 atoms if the QM residues are chosen simply by distance from the substrate. This slow approach to asymptotic limit is due to charge transfer from protein residues to the reacting substrates. Our large QM/MM calculations enable identification of charge separation for fragments in the transition state as a key component…

Designing thermally conductive polymer is of scientific interest and practical importance for applications like thermal interface materials, electronics packing, and plastic heat exchangers. In this work, we study the fundamental relationship between the molecular morphology and thermal conductivity in bulk amorphous polymers. We use polyethylene as a model system and performed systematic parametric study in molecular dynamics simulations. We find that the thermal conductivity is a strong function of the radius of gyration of the molecular chains, which is further correlated to persistence length, an intrinsic property of the molecule that characterizes molecular stiffness. Larger persistence length can lead to more extended chain morphology and thus higher thermal conductivity. Further thermal conductivity decomposition analysis shows that thermal transport through covalent bonds dominates the effective thermal conductivity over other contributions from nonbonded interactions (van der Waals) and translation of molecules disregarding the morphology. As a result, the more extended…

We recently showed for a large data set of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents [ Phys. Chem. Chem. Phys. 2015 , 17 , 2859 ]. In this paper, we significantly expand the scope of our study to examine the suitability of this approach for calculating general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMD-M062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems. This includes cluster-continuum schemes for pKa calculations as well as various neutral, radical, and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar-the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 and 25 kJ mol(-1), respectively. In systems where there are…

Understanding of how the stabilization mechanism of trehalose operates on biological molecules against different types of environmental stress could prove to gain great advancements in many different types of conservation techniques, such as cryopreservation or freeze-drying. Many theories exist that aim to explain why trehalose possesses an extraordinary ability to stabilize biomolecules. However, all of them just explain parts of its mechanism and a comprehensive picture is still lacking. In this study, we have used differential scanning calorimetry (DSC) and viscometry measurements to determine how the glass transition temperature Tg, the protein denaturation temperature Tden, and the dynamic viscosity depend on both the trehalose and the protein concentration in myoglobin-trehalose-water systems. The aim has been to determine whether these physical properties are related and to gain indirect structural insights from the limits of water crystallization at different concentration ratios. The results show that for systems without partial crystallization of water the addition of…

We report quantum chemical calculations performed on three popular deep eutectic solvents (DESs) in order to elucidate the molecular interactions, charge transfer interactions, and thermodynamics associated with these systems. The DESs studied comprise 1:2 choline chloride/urea (reline), 1:2 choline chloride/ethylene glycol (ethaline), and 1:1 choline chloride/malonic acid (maloline). The excellent correlation between calculated and experimental vibrational spectra allowed for identification of dominant interactions in the DES systems. The DESs were found to be stabilized by both conventional hydrogen bonds and C-H···O/C-H···π interactions between the components. The hydrogen-bonding network established in the DES is clearly distinct from that which exists within the neat hydrogen-bond donor dimer. Charge decomposition analysis indicates significant charge transfer from choline and chloride to the hydrogen-bond donor with a higher contribution from the cation, and a density of states analysis confirms the direction of the charge transfer. Consequently, the sum of the bond orders of…

We report a theoretical description and numerical tests of the extended-system adaptive biasing force method (eABF), together with an unbiased estimator of the free energy surface from eABF dynamics. Whereas the original ABF approach uses its running estimate of the free energy gradient as the adaptive biasing force, eABF is built on the idea that the exact free energy gradient is not necessary for efficient exploration, and that it is still possible to recover the exact free energy separately with an appropriate estimator. eABF does not directly bias the collective coordinates of interest, but rather fictitious variables that are harmonically coupled to them; therefore is does not require second derivative estimates, making it easily applicable to a wider range of problems than ABF. Furthermore, the extended variables present a smoother, coarse-grain-like sampling problem on a mollified free energy surface, leading to faster exploration and convergence. We also introduce CZAR, a simple, unbiased free energy estimator from eABF trajectories. eABF/CZAR converges to the physical free…

Select ionic liquids (ILs) dissolve significant quantities of cellulose through disruption and solvation of inter- and intramolecular hydrogen bonds. In this study, thermodynamic solid-liquid equilibrium was measured with microcrystalline cellulose in a model IL, 1-ethyl-3-methylimidazolium diethyl phosphate ([EMIm][DEP]) and mixtures with protic antisolvents and aprotic cosolvents between 40 and 120 °C. The solubility of cellulose in pure [EMIm][DEP] exhibits an asymptotic maximum of approximately 20 mass % above 100 °C. Solubility studies conducted on antisolvent mixtures with [EMIm][DEP] and [BMIm][Cl] indicate that protic solvents, ethanol, methanol, and water, significantly reduce the cellulose capacity of IL mixtures by 38-100% even at small antisolvent loadings (<5 mass %). Alternatively, IL-aprotic cosolvent (dimethyl sulfoxide, dimethylformamide, and 1,3-dimethyl-2-imidazolidinone) mixtures at mass ratios up to 1:1 enhance cellulose dissolution by 20-60% compared to pure [EMIm][DEP] at select temperatures. Interactions between the IL and molecular solvents were investigated…

In this article, we report a molecular dynamics simulation study on the X-ray and neutron scattering structures of deep eutectic solvents (DESs) and show that the DESs studied possess unique spatial heterogeneity on molecular length scales. The simulated X-ray and neutron scattering structure functions (S(q)s) of the DESs made of alkylamide + Li(+)/ClO4(-) display two peaks in the intermolecular region of the S(q)s. As a signature of nanoscale structural organization/heterogeneity, a prepeak is observed at 0.1 < q/Å(-1) < 0.4. The principal peak observed at around 1.2 < q/Å(-1) < 2 is rendered by short-distance inter- and intraspecies correlations. For the DESs studied, we demonstrate that nanoscale spatial heterogeneity is exhibited profoundly by the segregated domains of the constituent electrolyte, and the principal peak in S(q) is because of all sorts of close-contact correlations. The extent of nanoscale morphology as well as the strength of ion pairing is enhanced for the longer-tail alkylamide DES.

Atomistic molecular dynamics simulations have become an important source of information for the structure and dynamics of biomembranes at molecular detail difficult to access in experiments. A number of force fields for lipid membrane simulations have been derived in the past; the choice of the most suitable force field is, however, frequently hampered by the availability of parameters for specific lipids. Additionally, the comparison of different quantities among force fields is often aggravated by varying simulation parameters. Here, we compare four atomistic lipid force fields, namely, the united-atom GROMOS54a7 and the all-atom force fields CHARMM36, Slipids, and Lipid14, for a broad range of structural and dynamical properties of saturated and monounsaturated phosphatidylcholine bilayers (DMPC and POPC) as well as for monounsaturated phosphatidylethanolamine bilayers (POPE). Additionally, the ability of the different force fields to describe the gel-liquid crystalline phase transition is compared and their computational efficiency estimated. Moreover, membrane properties like…

Singlet exciton fission (SF) is a promising strategy for increasing photovoltaic efficiency, but in order for SF to be useful in solar cells, it should take place in a chromophore that is air-stable, highly absorptive, solution processable, and inexpensive. Unlike many SF chromophores, diketopyrrolopyrrole (DPP) conforms to these criteria, and here we investigate SF in DPP for the first time. SF yields in thin films of DPP derivatives, which are widely used in organic electronics and photovoltaics, are shown to depend critically on crystal morphology. Time-resolved spectroscopy of three DPP derivatives with phenyl (3,6-diphenylpyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione, PhDPP), thienyl (3,6-di(thiophen-2-yl)pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione, TDPP), and phenylthienyl (3,6-di(5-phenylthiophen-2-yl)pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione, PhTDPP) aromatic substituents in 100-200 nm thin films reveals that efficient SF occurs only in TDPP and PhTDPP (τSF = 220 ± 20 ps), despite the fact that SF is most exoergic in PhDPP. This result correlates well with the greater degree of π-overlap…

In this work, pendant drop techniques and molecular dynamics (MD) simulations were employed to investigate the effect of asphaltene concentrations on the interfacial tension (IFT) of the oil/water interface. Here, oil and asphaltene were represented by, respectively, common organic solvents and Violanthrone-79, and two types of concentration, i.e., bulk concentration and surface concentration, were examined. Correlations between the IFTs from experiments and MD simulations revealed that surface concentration, rather than the commonly used bulk concentration, determines the reduction of oil/water IFTs. Through analyzing the hydrogen bonding, the underlying mechanism for the IFT reduction was proposed. Our discussions here not only enable the direct comparison between experiments and MD simulations on the IFTs but also help with future interfacial studies using combined experimental and simulation approaches. The methodologies used in this work can be extended to many other oil/water interfaces in the presence of interfacially active compounds.

Ionic liquids (ILs) have been widely considered and used as "green solvents" for more than two decades. However, their ecotoxicity results have contradicted this view, as ILs, particularly hydrophobic ones, are reported to exhibit high toxicity. Yet the origin of their toxicology remains unclear. In this work, we have investigated the interaction of amphiphilic ILs with a lipid bilayer as a model cell membrane to understand their cytotoxicity at a molecular level. By employing fluorescence imaging and light and X-ray scattering techniques, we have found that amphiphilic ILs could disrupt the lipid bilayer by IL insertion, end-capping the hydrophobic edge of the lipid bilayer, and eventually disintegrating the lipid bilayer at high IL concentration. The insertion of ILs to cause the swelling of the lipid bilayer shows strong dependence on the hydrophobicity of IL cationic alky chain and anions and is strongly correlated with the reported IL cytotoxicity.

Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT), a physically based model that accounts for different molecular interactions explicitly, was applied to describe for the first time the phase behavior of deep eutectic solvents (DESs) with CO2 at temperatures from 298.15 to 318.15 K and pressures up to 2 MPa. DESs are mixtures of two solid compounds, a hydrogen bond donor (HBD) and a hydrogen bond acceptor (HBA), which form liquids upon mixing with melting points far below that of the individual compounds. In this work, the HBD is lactic acid and the HBAs are tetramethylammonium chloride, tetraethylammonium chloride, and tetrabutylammonium chloride. Two different modeling strategies were considered for the PC-SAFT modeling. In the first strategy, the so-called pseudo-pure component approach, a DES was considered as a pseudo-pure compound, and its pure-component parameters were obtained by fitting to pure DES density data. In the second strategy, the so-called individual-component approach, a DES was considered to consist of two individual components (HBA and HBD), and…

Combining broadband impedance spectroscopy, differential scanning calorimetry, and nuclear magnetic resonance we analyzed charge and mass transport in two polymerized ionic liquids and one of their monomeric precursors. In order to establish a general procedure for extracting single-particle diffusivity from their conductivity spectra, we critically assessed several approaches previously employed to describe the onset of diffusive charge dynamics and of the electrode polarization in ion conducting materials. Based on the analysis of the permittivity spectra, we demonstrate that the conductivity relaxation process provides information on ion diffusion and the magnitude of cross-correlation effects between ionic motions. A new approach is introduced which is able to estimate ionic diffusivities from the characteristic times of conductivity relaxation and ion concentration without any adjustable parameters. This opens the venue for a deeper understanding of charge transport in concentrated and diluted electrolyte solutions.

Although QM/MM calculations are the primary current tool for modeling enzymatic reactions, the reliability of such calculations can be limited by the size of the QM region. Thus, we examine in this work the dependence of QM/MM calculations on the size of the QM region, using the reaction of catechol-O-methyl transferase (COMT) as a test case. Our study focuses on the effect of adding residues to the QM region on the activation free energy, obtained with extensive QM/MM sampling. It is found that the sensitivity of the activation barrier to the size of the QM is rather limited, while the dependence of the reaction free energy is somewhat larger. Of course, the results depend on the inclusion of the first solvation shell in the QM regions. For example, the inclusion of the Mg(2+) ion can change the activation barrier due to charge transfer effects. However, such effects can easily be included in semiempirical approaches by proper parametrization. Overall, we establish that QM/MM calculations of activation barriers of enzymatic reactions are not highly sensitive to the size of the QM…

The recently described ionic liquid structure of the three equivalent hydrate of zinc chloride (ZnCl2·R H2O, R = 3, existing as [Zn(OH2)6][ZnCl4]) explains the solubility of cellulose in this medium. Only hydrate compositions in the narrow range of 3 - x < R < 3 + x with x ≈ 1 dissolve cellulose. Once dissolved, the cellulose remains in solution up to the R = 9 hydrate. Neutron diffraction and differential pair distribution function analysis of cellulose and model compound solutions (1 wt % cellulose in the R = 3 hydrate and 1 wt % ethanol in the R = 3 hydrate and the ZnCl2·3 ethanol liquid) coupled with detailed solubility measurements suggest that cellulose solubility occurs via coordination of the primary OH to the hydrated zinc cation with ring hydroxyls forming part of a second coordination shell around the cation of the ionic liquid.

While many numerical and experimental works were focused on water-ethanol mixtures at low ethanol concentration, this work reports predictions of a few physical properties (thermodynamical, interfacial, dynamical, and dielectrical properties) of water-ethanol mixture at high alcohol concentrations by means of molecular dynamics simulations. By using a standard force field a good agreement was found between experiment and molecular simulation. This was allowed us to explore the dynamics, structure, and interplay between both hydrogen-bonding networks of water and ethanol.

We review the latest developments in computational methods for direct simulation of fully fluctuating field theories of polymeric assemblies. In this context, we describe a newly developed theoretical and computational framework for accurately computing fluctuation-corrected phase diagrams of mesostructured polymer systems and report the first such complete phase diagram for a diblock copolymer melt. The method is based on complex Langevin sampling of a UV regularized field-theoretic model, with Helmholtz free energies computed using thermodynamic integration. UV regularization ensures that the free energies do not have an arbitrary reference; they can be compared between incommensurate phases, permitting for the first time the computation of order-order transitions with fluctuation corrections. We further demonstrate that computed free energies are accurate in the disordered phase by comparison to perturbation theory on the one-loop level. Importantly, we note that our method uses no uncontrolled approximations beyond the initial definition of a coarse-grained molecular model for…

Protein aggregation into highly structured amyloid fibrils is associated with various diseases including Alzheimer's disease, Parkinson's disease, and type II diabetes. Amyloids can also have normal biological functions and, in the future, could be used as the basis for novel nanoscale materials. However, a full understanding of the physicochemical forces that drive protein aggregation is still lacking. Such understanding is crucial for the development of drugs that can effectively inhibit aberrant amyloid aggregation and for the directed design of functional amyloids. Atomistic simulations can help understand protein aggregation. In particular, atomistic simulations can be used to study the initial formation of toxic oligomers which are hard to characterize experimentally and to understand the difference in aggregation behavior between different amyloidogenic peptides. Here, we review the latest atomistic simulations of protein aggregation, concentrating on amyloidogenic protein fragments, and provide an outlook for the future in this field.

Polyamide (PA) membrane-based reverse-osmosis (RO) serves as one of the most important techniques for water desalination and purification. Fundamental understanding of PA RO membranes at the atomistic level is critical to enhance their separation capabilities, leading to significant societal and commercial benefits. In this paper, a fully atomistic molecular dynamics simulation was performed to investigate PA membrane. Our simulated cross-linked membrane exhibits structural properties similar to those reported in experiments. Our results also reveal the presence of small local two-layer slip structures in PA membrane with 70% cross-linking, primarily due to short-range anisotropic interactions among aromatic benzene rings. Inside the inhomogeneous polymeric structure of the membrane, water molecules show heterogeneous diffusivities and converge adjacent to polar groups. Increased diffusion of water molecules is observed through the less cross-linked pathways. The existence of the fast pathways for water permeation has no effect on membrane's salt rejections.

Amphiphilic ionic liquids (ILs) based on 3-hexadecyl-1-methyl imidazolium cation, [C16mim](+), having aromatic anions, 4-hydroxybenzenesulfonate, [HBS], benzenesulfonate, [BS], and p-toluenesulfonate, [PTS], as counterions have been synthesized and investigated for their micellization behavior in aqueous medium. The surface activity of investigated ILs has been established by surface tension measurements, whereas bulk behavior has been investigated by conductivity and steady-state fluorescence measurements. The investigated ILs exhibited 2-3 fold lower critical micelle concentration (cmc) as compared to analogous ILs or conventional surfactants with nonaromatic counterions. The polarity of the cybotactic region of pyrene decreases along with decrease in extent of water penetration toward palisade layer of micelle with increase in hydrophobicity of counterion. Relatively more hydrophobic anions, i.e., [BS](-) and [PTS](-), have been found to form excimer in palisade layer of micelle, whereas [HBS](-) remains in close vicinity of imidazolium head groups of micelle as established from…

It has been found in many experiments that the mean square displacement of a Brownian particle x(T) diffusing in a rearranging environment is strictly Fickian, obeying ⟨(x(T))(2)⟩ ∝ T, but the probability distribution function for the displacement is not Gaussian. An explanation of this is that the diffusivity of the particle itself is changing as a function of time. Models for this diffusing diffusivity have been solved analytically in the limit of small time, but simulations were necessary for intermediate and large times. We show that one of the diffusing diffusivity models is equivalent to Brownian motion in the presence of a sink and introduce a class of models for which it is possible to find analytical solutions. Our solution gives ⟨(x(T))(2)⟩ ∝ T for all times and at short times the probability distribution function of the displacement is exponential which crosses over to a Gaussian in the limit of long times and large displacements.

The interactions of two highly positively charged short peptide sequences with negatively charged lipid bilayers were explored by fluorescence binding assays and all-atom molecular dynamics simulations. The bilayers consisted of mixtures of phosphatidylglycerol (PG) and phosphatidylcholine (PC) lipids as well as a fluorescence probe that was sensitive to the interfacial potential. The first peptide contained nine arginine repeats (Arg9), and the second one had nine lysine repeats (Lys9). The experimentally determined apparent dissociation constants and Hill cooperativity coefficients demonstrated that the Arg9 peptides exhibited weakly anticooperative binding behavior at the bilayer interface at lower PG concentrations, but this anticooperative effect vanished once the bilayers contained at least 20 mol % PG. By contrast, Lys9 peptides showed strongly anticooperative binding behavior at all PG concentrations, and the dissociation constants with Lys9 were approximately 2 orders of magnitude higher than with Arg9. Moreover, only arginine-rich peptides could bind to the phospholipid…

Human ubiquitin has been extensively characterized using a variety of experimental and computational methods and has become an important model for studying protein dynamics. Nevertheless, it has proven difficult to characterize the microsecond time scale dynamics of this protein with atomistic resolution. Here we use an unbiased computer simulation to describe the structural dynamics of ubiquitin on the picosecond to millisecond time scale. In the simulation, ubiquitin interconverts between a small number of distinct states on the microsecond to millisecond time scale. We find that the conformations visited by free ubiquitin in solution are very similar to those found various crystal structures of ubiquitin in complex with other proteins, a finding in line with previous experimental studies. We also observe weak but statistically significant correlated motions throughout the protein, including long-range concerted movement across the entire β sheet, consistent with recent experimental observations. We expect that the detailed atomistic description of ubiquitin dynamics provided by…

The periodic Saffman–Delbrück (PSD) model, an extension of the Saffman–Delbrück model developed to describe the effects of periodic boundary conditions on the diffusion constants of lipids and proteins obtained from simulation, is tested using the coarse-grained Martini and all-atom CHARMM36 (C36) force fields. Simulations of pure Martini dipalmitoylphosphatidylcholine (DPPC) bilayers and those with one embedded gramicidin A (gA) dimer or one gA monomer with sizes ranging from 512 to 2048 lipids support the PSD model. Underestimates of D ∞ (the value of the diffusion constant for an infinite system) from the 512-lipid system are 35% for DPPC, 45% for the gA monomer, and 70% for the gA dimer. Simulations of all-atom DPPC and dioleoylphosphatidylcholine (DOPC) bilayers yield diffusion constants not far from experiment. However, the PSD model predicts that diffusion constants at the sizes of the simulation should underestimate experiment by approximately a factor of 3 for DPPC and 2 for DOPC. This likely implies a deficiency in the C36 force field. A Bayesian method for extrapolating…

How proteins adsorb to inorganic material surfaces is critically important for the development of new biotechnologies, since the orientation and structure of the adsorbed proteins impacts their functionality. While it is known that many negatively charged proteins readily adsorb to negatively charged oxide surfaces, a detailed understanding of how this process occurs is lacking. In this work we study the adsorption of BSA, an important transport protein that is negatively charged at physiological conditions, to a model silica surface that is also negatively charged. We use fully atomistic molecular dynamics to provide detailed understanding of the noncovalent interactions that bind the BSA to the silica surface. Our results provide new insight into the competing roles of long-range electrostatics and short-range forces, and the consequences this has for the orientation and structure of the adsorbed proteins.

Abstract Potential of mean force (PMF) calculations are used to characterize the free energy landscape of protein–lipid and protein–protein association within membranes. Coarse-grained simulations allow binding free energies to be determined with reasonable statistical error. This accuracy relies on defining a good collective variable to describe the binding and unbinding transitions, and upon criteria for assessing the convergence of the simulation toward representative equilibrium sampling. As examples, we calculate protein–lipid binding PMFs for ANT/cardiolipin and Kir2.2/PIP2, using umbrella sampling on a distance coordinate. These highlight the importance of replica exchange between windows for convergence. The use of two independent sets of simulations, initiated from bound and unbound states, provide strong evidence for simulation convergence. For a model protein–protein interaction within a membrane, center-of-mass distance is shown to be a poor collective variable for describing transmembrane helix–helix dimerization. Instead, we employ an alternative intermolecular…

The focus of this study was to understand and unravel the interaction of silver nanoparticles (AgNPs) with different types of Deoxyribonucleic acid (DNA), mammalian and bacterial, having different base pair compositions. Binding of spherical silver nanoparticles (AgNPs) to Calf thymus (CT) DNA, Escherichia coli (EC) DNA and Micrococcus lysodeikticus (ML) DNA has been studied to gain insights into their mode of interaction and specificity. Interaction of AgNPs with synthetic DNA has also been carried out. On the basis of absorption, thermal melting, isothermal calorimetry and viscosity studies, we could establish the mode of binding and specificity of the synthesized silver nanoparticles with mammalian and bacterial DNA. Thermal melting (Tm) studies indicated a decrease in the Tm of all the DNAs, confirming the destabilization of DNA stacks on interaction with AgNPs. Comparative interaction studies with single stranded (ss) and double stranded (ds) DNAs further confirmed the specificity of the particles toward ds DNA. On the basis of the results we could confirm that the synthesized…

We have investigated the interactions between polygalacturonate (polyGal) and four divalent cations (M(2+) = Ba(2+), Ca(2+), Mg(2+), Zn(2+)) that differ in size and affinity for water. Our results evidence that M(2+)-polyGal interactions are intimately linked to the affinity of M(2+) for water. Mg(2+) interacts so strongly with water that it remains weakly bound to polyGal (polycondensation) by sharing water molecules from its first coordination shell with the carboxylate groups of polyGal. In contrast, the other cations form transient ionic pairs with polyGal by releasing preferentially one water molecule (for Zn(2+)) or two (for Ca(2+) and Ba(2+)), which corresponds to monodentate and bidentate binding modes with carboxylates, respectively. The mechanism for the binding of these three divalent cations to polyGal can be described by two steps: (i) monocomplexation and formation of point-like cross-links between polyGal chains (at low M(2+)/Gal molar ratios, R) and (ii) dimerization (at higher R). The threshold molar ratio, R*, between these two steps depends on the nature of…

Fourier transform infrared (FT-IR), X-ray diffraction (XRD), and transference number measurement (TNM) techniques were applied to investigate the complexation, structural, and ionic transport properties of and the dominant charge-carrier species in a solid biopolymer electrolyte (SBE) system based on carboxymethyl cellulose (CMC) doped with ammonium fluoride (NH 4 F), which was prepared via a solution casting technique. The SBEs were partially opaque in appearance, with no phase separation. The presence of interactions between the host polymer (CMC) and the ionic dopant (NH 4 F) was proven by FT-IR analysis at the C–O band. XRD spectra analyzed using Origin 8 software disclose that the degree of crystallinity (χ c %) of the SBEs decreased with the addition of NH 4 F, indicating an increase in the amorphous nature of the SBEs. Analysis of the ionic transport properties reveals that the ionic conductivity of the SBEs is dependent on the ionic mobility (μ) and diffusion of ions ( D ). TNM analysis confirms that the SBEs are proton conductors.

Stratum Corneum (SC), the outermost layer of skin, is mainly responsible for skin's barrier function. The complex lipid matrix of SC determines these barrier properties. In this study, the lipid matrix is modeled as an equimolar mixture of ceramide (CER), cholesterol (CHOL), and free fatty acid (FFA). The permeation of water, oxygen, ethanol, acetic acid, urea, butanol, benzene, dimethyl sulfoxide (DMSO), toluene, phenol, styrene, and ethylbenzene across this layer is studied using a constrained MD simulations technique. Several long constrained simulations are performed at a skin temperature of 310 K under NPT conditions. The free energy profiles and diffusion coefficients along the bilayer normal have been calculated for each molecule. Permeability coefficients are also calculated and compared with experimental data. The main resistance for the permeation of hydrophilic and hydrophobic permeants has been found to be in the interior of the lipid bilayer and near the lipid-water interface, respectively. The obtained permeability is found to be a few orders of magnitude higher than…

We present an experimental Raman study on how the addition of sodium chloride to CO2-hydrate-forming systems inhibits the hydrate formation thermodynamically. For this purpose, the molar enthalpy of reaction and the molar entropy of reaction for the reaction of weakly hydrogen-bonded water molecules to strongly hydrogen bonded water molecules are determined for different salinities from the Raman spectrum of the water-stretching vibration. Simultaneously, the influence of the salinity on the solubility of CO2 in the liquid water-rich phase right before the start of hydrate formation is analyzed. The results demonstrate that various mechanisms contribute to the inhibition of gas hydrate formation. For the highest salt concentration of 20 wt % investigated, the temperature of gas hydrate formation is lowered by 12 K. For this concentration the molar enthalpy and entropy of reaction become smaller by 50 and 20%, respectively. Concurrently, the solubility of carbon dioxide is reduced by 70%. These results are compared with data in literature for systems of sodium chloride in water…

Ion-stabilized gas nanobubbles (the so-termed "bubstons") and their clusters are investigated in bulk aqueous solutions of NaCl at different ion concentrations by four independent laser diagnostic methods. It turned out that in the range of NaCl concentration 10(-6) < C < 1 M the radius of bubston remains virtually unchanged at a value of 100 nm. Bubstons and their clusters are a thermodynamically nonequilibrium phase, which has been demonstrated in experiments with magnetic stirrer at different stirring rates. Different regimes of the bubston generation, resulting from various techniques of processing the liquid samples, were explored.

The function of biological macromolecules involves large-scale conformational dynamics spanning multiple time scales, from microseconds to seconds. Such conformational motions, which may involve whole domains or subunits of a protein, play a key role in allosteric regulation. There is an urgent need for experimental methods to probe the fastest of these motions. Single-molecule fluorescence experiments can in principle be used for observing such dynamics, but there is a lack of analysis methods that can extract the maximum amount of information from the data, down to the microsecond time scale. To address this issue, we introduce H 2 MM, a maximum likelihood estimation algorithm for photon-by-photon analysis of single-molecule fluorescence resonance energy transfer (FRET) experiments. H 2 MM is based on analytical estimators for model parameters, derived using the Baum–Welch algorithm. An efficient and effective method for the calculation of these estimators is introduced. H 2 MM is shown to accurately retrieve the reaction times from ∼1 s to ∼10 μs and even faster when applied to…

A strategy for decreasing the viscosity variation in the process of CO2 capture by amino-functionalized ionic liquids (ILs) through the formation of intramolecular hydrogen bond was reported. Different with the dramatic increase in viscosity during CO2 uptake by traditional amino-functionalized ILs, slight increase or even decrease in viscosity was achieved through introducing a N or O atom as hydrogen acceptor into amino-functionalized anion, which could stabilize the active hydrogen of produced carbamic acid. Quantum chemical calculations and spectroscopic investigations demonstrated that the formation of intramolecular hydrogen bond between introduced hydrogen acceptor and carbamic acid was the key to avoid the dramatic increase in viscosity during the capture of CO2 by these amino-functionalized ILs.

Amino acids and peptides are often used as "model" segments of proteins for studying their behavior in various types of environments, and/or elaborating functional surfaces. Indeed, though the protein behavior is much more complex than that of their isolated segments, knowledge of the binding mode as well as of the chemical structure of peptides on metal or oxide surfaces is a significant step toward the control of materials in a biological environment. Such knowledge has considerably increased in the past few years, thanks to the combination of advanced characterization techniques and of modeling methods. Investigations of biomolecule-surface interactions in water/solvent environments are quite numerous, but only in a few cases is it possible to reach an understanding of the molecule-(water)-surface interaction with a level of detail comparable to that of the UHV studies. This contribution aims at reviewing the recent data describing the amino acid and peptide interaction with metal or oxide surfaces in the presence of water.

Mixed-solvent molecular dynamics (MixMD) is a hotspot-mapping technique that relies on molecular dynamics simulations of proteins in binary solvent mixtures. Previous work on MixMD has established the technique's effectiveness in capturing binding sites of small organic compounds. In this work, we show that MixMD can identify both competitive and allosteric sites on proteins. The MixMD approach embraces full protein flexibility and allows competition between solvent probes and water. Sites preferentially mapped by probe molecules are more likely to be binding hotspots. There are two important requirements for the identification of ligand-binding hotspots: (1) hotspots must be mapped at very high signal-to-noise ratio and (2) the hotspots must be mapped by multiple probe types. We have developed our mapping protocol around acetonitrile, isopropanol, and pyrimidine as probe solvents because they allowed us to capture hydrophilic, hydrophobic, hydrogen-bonding, and aromatic interactions. Charged probes were needed for mapping one target, and we introduce them in this work. In order to…

Hydrofluoroethers have recently been used as the diluent to a lithium battery electrolyte solution to increase and decrease the ionic conductivity and the solution viscosity, respectively. In order to clarify the Li(+) local structure in the 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (HFE) diluted [Li(G4)][TFSA] (G4, tetraglyme; TFSA, bis(trifluoromethanesulfonyl)amide) solvate ionic liquid, Raman spectroscopic study has been done with the DFT calculations. It has turned out that the HFE never coordinates to the Li(+) directly, and that the solvent (G4) shared ion pair of Li(+) with TFSA anion (SSIP) and the contact ion pair between Li(+) and TFSA anion (CIP) are found in the neat and HFE diluted [Li(G4)][TFSA] solvate ionic liquid. It is also revealed that the two kinds of the CIP in which TFSA anion coordinates to the Li(+) in monodentate and bidentate manners (hereafter, we call them the monodentate CIP and the bidentate CIP, respectively) exist with the SSIP of predominant [Li(G4)](+) ion-pair species in the neat [Li(G4)][TFSA] solvate ionic liquid, and that the…

Molecular dynamics (MD) simulations and Brillouin light scattering (BLS) spectroscopy experiments have been carried to study the structure of sodium silicate glasses (SiO 2 ) (100– X ) (Na 2 O) X, where X ranges from 0 to 45 at room temperature. The MD-obtained glass structures have been subjected to energy minimization at zero temperature to extract the elastic constants also obtained by BLS spectroscopy. The structures obtained are in good agreement with the structural experimental data realized by different techniques. The simulations show that the values of the elastic constants as a function of X (i.e., Na 2 O mol %) agree well with those measured by BLS spectroscopy. The variations of elastic constants C 11 and C 44 as a function of Na 2 O mol % are discussed and correlated to structural results and potential energies of oxygen atoms.

The valence-excited states of ferric and ferrous hexacyanide ions in aqueous solution were mapped by resonant inelastic X-ray scattering (RIXS) at the Fe L2,3 and N K edges. Probing of both the central Fe and the ligand N atoms enabled identification of the metal- and ligand-centered excited states, as well as ligand-to-metal and metal-to-ligand charge-transfer excited states. Ab initio calculations utilizing the RASPT2 method were used to simulate the Fe L2,3-edge RIXS spectra and enabled quantification of the covalencies of both occupied and empty orbitals of π and σ symmetry. We found that π back-donation in the ferric complex is smaller than that in the ferrous complex. This is evidenced by the relative amounts of Fe 3d character in the nominally 2π CN(-) molecular orbital of 7% and 9% in ferric and ferrous hexacyanide, respectively. Utilizing the direct sensitivity of Fe L3-edge RIXS to the Fe 3d character in the occupied molecular orbitals, we also found that the donation interactions are dominated by σ bonding. The latter was found to be stronger in the ferric complex, with…

Noncovalent interactions, in particular the hydrogen bonds and nonspecific long-range electrostatic interactions are fundamental to biomolecular functions. A molecular understanding of the local electrostatic environment, consistently for both specific (hydrogen-bonding) and nonspecific electrostatic (local polarity) interactions, is essential for a detailed understanding of these processes. Vibrational Stark Effect (VSE) has proven to be an extremely useful method to measure the local electric field using infrared spectroscopy of carbonyl and nitrile based probes. The nitrile chemical group would be an ideal choice because of its absorption in an infrared spectral window transparent to biomolecules, ease of site-specific incorporation into proteins, and common occurrence as a substituent in various drug molecules. However, the inability of VSE to describe the dependence of IR frequency on electric field for hydrogen-bonded nitriles to date has severely limited nitrile's utility to probe the noncovalent interactions. In this work, using infrared spectroscopy and atomistic molecular…

Carbonic, lactic, and pyruvic acids have been generated in aqueous solution by the transient protonation of their corresponding conjugate bases by a tailor-made photoacid, the 6-hydroxy-1-sulfonate pyrene sodium salt molecule. A particular goal is to establish the pK(a) of carbonic acid H2CO3. The on-contact proton transfer (PT) reaction rate from the optically excited photoacid to the carboxylic bases was derived, with unprecedented precision, from time-correlated single-photon-counting measurements of the fluorescence lifetime of the photoacid in the presence of the proton acceptors. The time-dependent diffusion-assisted PT rate was analyzed using the Szabo-Collins-Kimball equation with a radiation boundary condition. The on-contact PT rates were found to follow the acidity order of the carboxylic acids: the stronger was the acid, the slower was the PT reaction to its conjugate base. The pK(a) of carbonic acid was found to be 3.49 ± 0.05 using both the Marcus and Kiefer-Hynes free energy correlations. This establishes H2CO3 as being 0.37 pK(a) units stronger and about 1 pK(a) unit…

Gangliosides are glycolipids in which an oligosaccharide headgroup containing one or more sialic acids is connected to a ceramide. Gangliosides reside in the outer leaflet of the plasma membrane and play a crucial role in various physiological processes such as cell signal transduction and neuronal differentiation by modulating structures and functions of membrane proteins. Because the detailed behavior of gangliosides and protein-ganglioside interactions are poorly known, we investigated the interactions between the gangliosides GM1 and GM3 and the proteins aquaporin (AQP1) and WALP23 using equilibrium molecular dynamics simulations and potential of mean force calculations at both coarse-grained (CG) and atomistic levels. In atomistic simulations, on the basis of the GROMOS force field, ganglioside aggregation appears to be a result of the balance between hydrogen bond interactions and steric hindrance of the headgroups. GM3 clusters are slightly larger and more ordered than GM1 clusters due to the smaller headgroup of GM3. The different structures of GM1 and GM3 clusters from…

In liquid phase chemistry dynamic solute-solvent interactions often govern the path, ultimate outcome, and efficiency of chemical reactions. These steps involve many-body movements on subpicosecond time scales and thus ultrafast structural tools capable of capturing both intramolecular electronic and structural changes, and local solvent structural changes are desired. We have studied the intra- and intermolecular dynamics of a model chromophore, aqueous [Fe(bpy)3](2+), with complementary X-ray tools in a single experiment exploiting intense XFEL radiation as a probe. We monitored the ultrafast structural rearrangement of the solute with X-ray emission spectroscopy, thus establishing time zero for the ensuing X-ray diffuse scattering analysis. The simultaneously recorded X-ray diffuse scattering patterns reveal slower subpicosecond dynamics triggered by the intramolecular structural dynamics of the photoexcited solute. By simultaneous combination of both methods only, we can extract new information about the solvation dynamic processes unfolding during the first picosecond (ps). The…

In this work, we investigate the effect of salt and water on plasticization and thermal properties of hydrated poly(diallyldimethylammonium chloride) (PDAC) and poly(sodium 4-styrenesulfonate) (PSS) assemblies via molecular dynamics simulations and modulated differential scanning calorimetry (MDSC). Commonly, both water and salt are considered to be plasticizers of hydrated polyelectrolyte assemblies. However, the simulation results presented here show that while water has a plasticizing effect, salt can also have an opposite effect on the PE assemblies. On one hand, the presence of salt ions provides additional free volume for chain motion and weakens PDAC–PSS ion pairing due to electrostatic screening, which contributes toward plasticization of the complex. On the other hand, salt ions bind water in their hydration shells, which decreases water mobility and reduces the plasticization by hydration. Our MDSC results connect the findings to macroscopic PE plasticization and the glass-transition-like thermal transition T tr under controlled PE hydration and salt content. This work…

IR and Raman frequency shifts have been reported for numerous probes of enzyme transition states, leading to diverse interpretations. In the case of the model enzyme ketosteroid isomerase (KSI), we have argued that IR spectral shifts for a carbonyl probe at the active site can provide a connection between the active site electric field and the activation free energy (Fried et al. Science 2014, 346, 1510-1514). Here we generalize this approach to a much broader set of carbonyl probes (e.g., oxoesters, thioesters, and amides), first establishing the sensitivity of each probe to an electric field using vibrational Stark spectroscopy, vibrational solvatochromism, and MD simulations, and then applying these results to reinterpret data already in the literature for enzymes such as 4-chlorobenzoyl-CoA dehalogenase and serine proteases. These results demonstrate that the vibrational Stark effect provides a general framework for estimating the electrostatic contribution to the catalytic rate and may provide a metric for the design or modification of enzymes. Opportunities and limitations of…

So-called "weak" protein-protein interactions are important for the control of solution properties and stability at elevated protein concentrations (c2) but are not practical to capture in atomistic simulations. This report focuses on a series of coarse-grained models for predicting second osmotic virial coefficients (B22) and high-concentration Rayleigh scattering (osmotic compressibility) as a function of c2 for monoclonal antibodies (MAbs) that are of interest in biotechnology. B22 and molecular volume along with c2-dependent osmotic compressibility were calculated for a series of models with increasing structural detail. Models were refined to include contributions from sterics, short-ranged van der Waals and hydrophobic attractions, screened electrostatics, and the flexibility of the mAb hinge region. The results highlight shortcomings for spherical models of MAbs and a useful balance between numerical accuracy and computational burden offered by models based on 6 or 12 spherical, partly overlapping domains. The results provide bounds for realistic values of effective charges…