Showing papers in "Journal of Physical Chemistry B in 2014"

The Most Effective Gold Nanorod Size for Plasmonic Photothermal Therapy: Theory and In Vitro Experiments

Abstract: The development of new and improved photothermal contrast agents for the successful treatment of cancer (or other diseases) via plasmonic photothermal therapy (PPTT) is a crucial part of the application of nanotechnology in medicine. Gold nanorods (AuNRs) have been found to be the most effective photothermal contrast agents, both in vitro and in vivo. Therefore, determining the optimum AuNR size needed for applications in PPTT is of great interest. In the present work, we utilized theoretical calculations as well as experimental techniques in vitro to determine this optimum AuNR size by comparing plasmonic properties and the efficacy as photothermal contrast agents of three different sizes of AuNRs. Our theoretical calculations showed that the contribution of absorbance to the total extinction, the electric field, and the distance at which this field extends away from the nanoparticle surface all govern the effectiveness of the amount of heat these particles generate upon NIR laser irradiation. Comparing between three different AuNRs (38 × 11, 28 × 8, and 17 × 5 nm), we determined that the 28 × 8 nm AuNR is the most effective in plasmonic photothermal heat generation. These results encouraged us to carry out in vitro experiments to compare the PPTT efficacy of the different sized AuNRs. The 28 × 8 nm AuNR was found to be the most effective photothermal contrast agent for PPTT of human oral squamous cell carcinoma. This size AuNR has the best compromise between the total amount of light absorbed and the fraction of which is converted to heat. In addition, the distance at which the electric field extends from the particle surface is most ideal for this size AuNR, as it is sufficient to allow for coupling between the fields of adjacent particles in solution (i.e., particle aggregates), resulting in effective heating in solution.

Structure and aggregation in the 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquid homologous series.

Abstract: A new comprehensive Molecular Dynamics study using large simulation boxes has been performed in order to complete and extend the structural analysis on the mesoscopic segregation observed in the ionic liquids of the 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide homologous series, [CnC1im][Ntf2] (2 ≤ n ≤ 10). The analysis includes the discussion along the whole family of the corresponding structure factors, S(q), in the low-q range (1.6 ≤ q/nm–1 ≤ 20); the confirmation of the periodicity of the polar network of the ionic liquid and its intermediate low-q peak equivalence; and the introduction of five statistical functions that probe the existence and characterize the polar network and the nonpolar aggregates that are formed along the [CnC1im][Ntf2] series. The later functions comprise aggregate size distributions, average number of contact neighbors within an aggregate, neighbor distributions, distributions of aggregate maximum length, and distributions of aggregate volume.

Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation.

Abstract: Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these co...

Dissolution Mechanism of Cellulose in N,N-Dimethylacetamide/Lithium Chloride: Revisiting through Molecular Interactions

Abstract: Understanding the interactions between solvent molecules and cellulose at a molecular level is still not fully achieved in cellulose/N,N-dimethylacetamide (DMAc)/LiCl system. In this paper, cellobiose was used as the model compound of cellulose to investigate the interactions in cellulose/DMAc/LiCl solution by using Fourier transform infrared spectroscopy (FTIR), 13C, 35Cl, and 7Li nuclear magnetic resonance (NMR) spectroscopy and conductivity measurements. It was found that when cellulose is dissolved in DMAc/LiCl cosolvent system, the hydroxyl protons of cellulose form strong hydrogen bonds with the Cl–, during which the intermolecular hydrogen bonding networks of cellulose is broken with simultaneous splitting of the Li+–Cl– ion pairs. Simultaneously, the Li+ cations are further solvated by free DMAc molecules, which accompany the hydrogen-bonded Cl– to meet electric balance. Thereafter, the cellulose chains are dispersed in molecular level in the solvent system to form homogeneous solution. This work ...

Chemically Tunable Ionic Liquids with Aprotic Heterocyclic Anion (AHA) for CO2 Capture

Abstract: Ionic liquids (ILs) with aprotic heterocyclic anions, or AHAs, can bind CO2 with reaction enthalpies that are suitable for gas separations and without suffering large viscosity increases. In the present work, we have synthesized ILs bearing an alkyl-phosphonium cation with indazolide, imidazolide, pyrrolide, pyrazolide and triazolide-based anions that span a wide range of predicted reaction enthalpies with CO2. Each AHA-based IL was characterized by NMR spectroscopy and their physical properties (viscosity, glass transition, and thermal decomposition temperature) determined. In addition, the influence of substituent groups on the reaction enthalpy was investigated by measuring the CO2 solubility in each IL at pressures between 0 and 1 bar at 22 °C using a volumetric method. The isotherm-derived enthalpies range between −37 and −54 kJ mol–1 of CO2, and these values are in good agreement with computed enthalpies of gas-phase IL-CO2 reaction products from molecular electronic structure calculations. The AHA ...

Hidden scale invariance in condensed matter.

Abstract: Recent developments show that many liquids and solids have an approximate “hidden” scale invariance that implies the existence of lines in the thermodynamic phase diagram, so-called isomorphs, alon...

Secondary structure of corona proteins determines the cell surface receptors used by nanoparticles.

Abstract: Nanoparticles used for biological and biomedical applications encounter a host of extracellular proteins. These proteins rapidly adsorb onto the nanoparticle surface, creating a protein corona. Poly(ethylene glycol) can reduce, but not eliminate, the nonspecific adsorption of proteins. As a result, the adsorbed proteins, rather than the nanoparticle itself, determine the cellular receptors used for binding, the internalization mechanism, the intracellular transport pathway, and the subsequent immune response. Using fluorescence microscopy and flow cytometry, we first characterize a set of polystyrene nanoparticles in which the same adsorbed protein, bovine serum albumin, leads to binding to two different cell surface receptors: native albumin receptors and scavenger receptors. Using a combination of circular dichroism spectroscopy, isothermal titration calorimetry, and fluorescence spectroscopy, we demonstrate that the secondary structure of the adsorbed bovine serum albumin protein controls the cellular ...

Chelate effects in glyme/lithium bis(trifluoromethanesulfonyl)amide solvate ionic liquids. I. Stability of solvate cations and correlation with electrolyte properties.

Abstract: To develop a basic understanding of a new class of ionic liquids (ILs), “solvate” ILs, the transport properties of binary mixtures of lithium bis(trifluoromethanesulfonyl)amide (Li[TFSA]) and oligoethers (tetraglyme (G4), triglyme (G3), diglyme (G2), and monoglyme (G1)) or tetrahydrofuran (THF) were studied. The self-diffusion coefficient ratio of the solvents and Li+ ions (Dsol/DLi) was a good metric for evaluating the stability of the complex cations consisting of Li+ and the solvent(s). When the molar ratio of Li+ ions and solvent oxygen atoms ([O]/[Li+]) was adjusted to 4 or 5, Dsol/DLi always exceeded unity for THF and G1-based mixtures even at the high concentrations, indicating the presence of uncoordinating or highly exchangeable solvents. In contrast, long-lived complex cations were evidenced by a Dsol/DLi ∼ 1 for the longer G3 and G4. The binary mixtures studied were categorized into two different classes of liquids: concentrated solutions and solvate ILs, based on Dsol/DLi. Mixtures with G2 exh...

New Insights into the Mechanism of the DNA/Doxorubicin Interaction

Abstract: Doxorubicin (DOX) is an important anthracycline antibiotic whose intricate features of binding to DNAs, not yet fully understood, have been the object of intense debate. The dimerization equilibrium has been studied at pH = 7.0, I = 2.5 mM, and T = 25 °C. A thermodynamic and kinetic study of the binding of doxorubicin to DNA, carried out by circular dichroism, viscometry, differential scanning calorimetry, fluorescence, isothermal titration calorimetry, and T-jump relaxation measurements, has enabled us to characterize for the first time two different types of calf thymus DNA (ctDNA)/DOX complexes: PD1 for C(DOX)/C(DNA) < 0.3, and PD2 for higher drug content. The nature of the PD1 complex is described better in light of the affinity of DOX with the synthetic copolymers [poly(dA-dT)]2 and [poly(dG-dC)]2. The formation of PD1 has been categorized kinetically as a two-step mechanism in which the fast step is the groove binding in the AT region, and the slow step is the intercalation into the GC region. This bifunctional nature provides a plausible explanation for the high PD1 constant obtained (K1 = 2.3 × 10(8) M(-1)). Moreover, the formation of an external aggregate complex ctDNA/DOX (PD2) at the expense of PD1, with K2 = 9.3 × 10(5) M(-1), has been evinced.

Solvatochromic probe behavior within choline chloride-based deep eutectic solvents: effect of temperature and water.

Abstract: Deep eutectic solvents (DESs) have shown potential as promising environmentally friendly alternatives to conventional solvents. Many common and popular DESs are obtained by simply mixing a salt and a H-bond donor. Properties of such a DES depend on its constituents. Change in temperature and addition of water, a benign cosolvent, can change the physicochemical properties of DESs. The effect of changing temperature and addition of water on solvatochromic probe behavior within three DESs formed from choline chloride combined with 1,2-ethanediol, glycerol, and urea, respectively, in 1:2 mol ratios termed ethaline, glyceline, and reline is presented. Increase in temperature results in reduced H-bond donating acidity of the DESs. Dipolarity/polarizability and H-bond accepting basicity do not change with changing temperature of the DESs. The response of the fluorescence probe pyrene also indicates a decrease in the polarity of the DESs as temperature is increased. Addition of water to DES results in increased d...

Thermodynamics of block copolymers with and without salt.

Abstract: Ion-containing block copolymers are of interest for applications such as electrolytes in rechargeable lithium batteries. The addition of salt to these materials is necessary to make them conductive; however, even small amounts of salt can have significant effects on the phase behavior of these materials and consequently on their ion-transport and mechanical properties. As a result, the effect of salt addition on block copolymer thermodynamics has been the subject of significant interest over the past decade. This feature article describes a comprehensive study of the thermodynamics of block copolymer/salt mixtures over a wide range of molecular weights, compositions, salt concentrations, and temperatures. The Flory-Huggins interaction parameter was determined by fitting small-angle X-ray scattering data of disordered systems to predictions based on the random phase approximation. Experiments on neat block copolymers revealed that the Flory-Huggins parameter is a strong function of chain length. Experiments on block copolymer/salt mixtures revealed a highly nonlinear dependence of the Flory-Huggins parameter on salt concentration. These findings are a significant departure from previous results and indicate the need for improved theories for describing thermodynamic interactions in neat and salt-containing block copolymers.

Radical Scavenging Ability of Gallic Acid toward OH and OOH Radicals. Reaction Mechanism and Rate Constants from the Density Functional Theory

Abstract: Gallic acid is a ubiquitous compound, widely distributed in the vegetal kingdom and frequently found in the human diet. In the present work, its primary antioxidant activity has been investigated using the density functional theory (DFT), and the quantum mechanics-based test for overall free radical scavenging activity (QM-ORSA) protocol. It was found that gallic acid is a better antioxidant than the reference compound, Trolox, regardless of the polarity of the environment. In addition, gallic acid is predicted to be among the best peroxyl radical scavengers identified so far in nonpolar (lipid) media. This compound is capable of scavenging hydroxyl radicals at diffusion-limited rates, and hydroperoxyl radicals with rate constants in the order of 105 M–1 s–1. The deprotonation of gallic acid, in aqueous solution, is predicted to increase the protective action of this compound against oxidative stress. Gallic acid was also identified as a versatile scavenger, capable of rapidly deactivating a wide variety ...

Molecular mechanisms for the reaction between (˙)OH radicals and proline: insights on the role as reactive oxygen species scavenger in plant stress.

Abstract: The accumulation of proline (Pro) and overproduction of reactive oxygen species (ROS) by plants exposed to stress is well-documented. In vitro assays show that enzyme inactivation by hydroxyl radicals ((•)OH) can be avoided in the presence of Pro, suggesting this amino acid might act as a (•)OH scavenger. Although production of hydroxyproline (Hyp) has been hypothesized in connection with such antioxidant activity, no evidence on the detailed mechanism of scavenging has been reported. To elucidate whether and how Hyp might be produced, we used density functional theory calculations coupled to a polarizable continuum model to explore 27 reaction channels including H-abstraction by (•)OH and (•)OH/H2O addition. The structure and energetics of stable species and transition states for each reaction channel were characterized at the PCM-(U)M06/6-31G(d,p) level in aqueous solution. Evidence is found for a main pathway in which Pro scavenges (•)OH by successive H-abstractions (ΔG(‡,298) = 4.1 and 7.5 kcal mol(-1)) to yield 3,4-Δ-Pro. A companion pathway with low barriers yielding Δ(1)-pyrroline-5-carboxylate (P5C) is also supported, linking with 5-Hyp through hydration. However, this connection remains unlikely in stressed plants because P5C would be efficiently recycled to Pro (contributing to its accumulation) by P5C reductase, hypothesis coined here as the "Pro-Pro cycle".

Photoisomerization Dynamics and Pathways of trans- and cis-Azobenzene in Solution from Broadband Femtosecond Spectroscopies and Calculations

Abstract: The photoisomerization of azobenzene in solution was studied experimentally and by calculations. trans-to-cis and cis-to-trans dynamics are described through broadband transient absorption, fluorescence, and stimulated Raman spectroscopy. Transient absorption was extended to cover not only the nπ* band but also the ππ* band in the ultraviolet. Isomerization yields are used for a quantitative comparison of trans and cis transient spectra under different excitation. For the trans-to-cis path upon nπ*(S1) excitation, the evolution develops with 0.3, 3, and 16 ps. The first two times reflect population relaxation to a local minimum S1tL and subsequent transition to a dark intermediate S1tD over an 8 kJ/mol barrier. The existence of stationary points S1tL and S1tD is confirmed by quantum-chemical calculations. The third time corresponds to S1tD → S0 relaxation to the ground state via an S1/S0 conical intersection over a 12 kJ/mol barrier. Thus, the 16 ps time constant is attributed to the isomerization process...

Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

Abstract: The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn2+, Zn2+, Mg2+, and Ca2+, as well as providing new parameters for Ni2+, Co2+, and Fe2+. In all the cases, we are able to reproduce both M2+–O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase I as showcase systems, as both enzymes are active with a range of transition metals. The ...

Extending Single-Molecule Microscopy Using Optical Fourier Processing

Abstract: This article surveys the recent application of optical Fourier processing to the long-established but still expanding field of single-molecule imaging and microscopy. A variety of single-molecule studies can benefit from the additional image information that can be obtained by modulating the Fourier, or pupil, plane of a widefield microscope. After briefly reviewing several current applications, we present a comprehensive and computationally efficient theoretical model for simulating single-molecule fluorescence as it propagates through an imaging system. Furthermore, we describe how phase/amplitude-modulating optics inserted in the imaging pathway may be modeled, especially at the Fourier plane. Finally, we discuss selected recent applications of Fourier processing methods to measure the orientation, depth, and rotational mobility of single fluorescent molecules.

Molecular dynamics simulations of sodium dodecyl sulfate micelles in water-the effect of the force field.

Abstract: Molecular dynamic (MD) simulations of preassembled sodium dodecyl sulfate (SDS) micelles are carried out using three versions of GROMOS, as well as CHARMM36, OPLS-AA, and OPLS-UA force fields at different aggregation numbers and box sizes. The differences among force fields have little effect on the overall micelle structure of small aggregates of size 60 or 100, but for micelles of an aggregation number of 300 or higher, bicelle structures with ordered tails, rather than the more realistic rodlike or cylindrical micelles with disordered tails, occur when using versions of GROMOS45A3 or the OPLS-AA force fields that are adapted to model the sulfate head group atoms using methods given in the literature. We find that the Lennard-Jones (L-J) parameters for the sodium ions and the ionic oxygens of the SDS head group, as well as the water model, control the transition to bicelles, regardless of other L-J parameters. A closer binding of the sodium ions to the head group ionic oxygens screens the electrostatic ...

CHARMM36 united atom chain model for lipids and surfactants.

Abstract: Molecular simulations of lipids and surfactants require accurate parameters to reproduce and predict experimental properties. Previously, a united atom (UA) chain model was developed for the CHARMM27/27r lipids (Henin, J., et al. J. Phys. Chem. B. 2008, 112, 7008–7015) but suffers from the flaw that bilayer simulations using the model require an imposed surface area ensemble, which limits its use to pure bilayer systems. A UA-chain model has been developed based on the CHARMM36 (C36) all-atom lipid parameters, termed C36-UA, and agreed well with bulk, lipid membrane, and micelle formation of a surfactant. Molecular dynamics (MD) simulations of alkanes (heptane and pentadecane) were used to test the validity of C36-UA on density, heat of vaporization, and liquid self-diffusion constants. Then, simulations using C36-UA resulted in accurate properties (surface area per lipid, X-ray and neutron form factors, and chain order parameters) of various saturated- and unsaturated-chain bilayers. When mixed with the ...

Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.

Abstract: We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree–Fock (HF), (2) second order Moller–Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the ...

Accurate description of calcium solvation in concentrated aqueous solutions.

Abstract: Calcium is one of the biologically most important ions; however, its accurate description by classical molecular dynamics simulations is complicated by strong electrostatic and polarization interactions with surroundings due to its divalent nature. Here, we explore the recently suggested approach for effectively accounting for polarization effects via ionic charge rescaling and develop a new and accurate parametrization of the calcium dication. Comparison to neutron scattering and viscosity measurements demonstrates that our model allows for an accurate description of concentrated aqueous calcium chloride solutions. The present model should find broad use in efficient and accurate modeling of calcium in aqueous environments, such as those encountered in biological and technological applications.

Computational and Experimental Investigation of Li-Doped Ionic Liquid Electrolytes: [pyr14][TFSI], [pyr13][FSI], and [EMIM][BF4]

Abstract: We employ molecular dynamics (MD) simulation and experiment to investigate the structure, thermodynamics, and transport of N-methyl-N-butylpyrrolidinium bis(trifluoromethylsufonyl)imide ([pyr14][TFSI]), N-methyl-N-propylpyrrolidinium bis(fluorosufonyl)imide ([pyr13][FSI]), and 1-ethyl-3-methylimidazolium boron tetrafluoride ([EMIM][BF4]), as a function of Li-salt mole fraction (0.05 ≤ xLi(+) ≤ 0.33) and temperature (298 K ≤ T ≤ 393 K). Structurally, Li(+) is shown to be solvated by three anion neighbors in [pyr14][TFSI] and four anion neighbors in both [pyr13][FSI] and [EMIM][BF4], and at all levels of xLi(+) we find the presence of lithium aggregates. Pulsed field gradient spin-echo NMR measurements of diffusion and electrochemical impedance spectroscopy measurements of ionic conductivity are made for the neat ionic liquids as well as 0.5 molal solutions of Li-salt in the ionic liquids. Bulk ionic liquid properties (density, diffusion, viscosity, and ionic conductivity) are obtained with MD simulations and show excellent agreement with experiment. While the diffusion exhibits a systematic decrease with increasing xLi(+), the contribution of Li(+) to ionic conductivity increases until reaching a saturation doping level of xLi(+) = 0.10. Comparatively, the Li(+) conductivity of [pyr14][TFSI] is an order of magnitude lower than that of the other liquids, which range between 0.1 and 0.3 mS/cm. Our transport results also demonstrate the necessity of long MD simulation runs (∼200 ns) to converge transport properties at room temperature. The differences in Li(+) transport are reflected in the residence times of Li(+) with the anions (τ(Li/-)), which are revealed to be much larger for [pyr14][TFSI] (up to 100 ns at the highest doping levels) than in either [EMIM][BF4] or [pyr13][FSI]. Finally, to comment on the relative kinetics of Li(+) transport in each liquid, we find that while the net motion of Li(+) with its solvation shell (vehicular) significantly contributes to net diffusion in all liquids, the importance of transport through anion exchange increases at high xLi(+) and in liquids with large anions.

H- and J-Aggregation of Fluorene-Based Chromophores

Abstract: Understanding of H- and J-aggregation behaviors in fluorene-based polymers is significant both for determining the origin of various red-shifted emissions occurring in blue-emitting polyfluorenes and for developing polyfluorene-based device performance. In this contribution, we demonstrate a new theory of the H- and J-aggregation of polyfluorenes and oligofluorenes, and understand the influence of chromosphere aggregation on their photoluminescent properties. H- and J-aggregates are induced by a continuous increasing concentration of the oligofluorene or polyfluorene solution. A relaxed molecular configuration is simulated to illustrate the spatial arrangement of the bonding of fluorenes. It is indicated that the relaxed state adopts a 21 helical backbone conformation with a torsion angle of 18° between two connected repeat units. This configuration makes the formation of H- and J-aggregates through the strong π-π interaction between the backbone rings. A critical aggregation concentration is observed to form H- and J-aggregates for both polyfluorenes and oligofluorenes. These aggregates show large spectral shifts and distinct shape changes in photoluminescent excitation (PLE) and emission (PL) spectroscopy. Compared with "isolated" chromophores, H-aggregates induce absorption spectral blue-shift and fluorescence spectral red-shift but largely reduce fluorescence efficiency. "Isolated" chromophores not only refer to "isolated molecules" but also include those associated molecules if their conjugated backbones are not compact enough to exhibit perturbed absorption and emission. J-aggregates induce absorption spectral red-shift and fluorescence spectral red-shift but largely enhance fluorescence efficiency. The PLE and PL spectra also show that J-aggregates dominate in concentrated solutions. Different from the excimers, the H- and J-aggregate formation changes the ground-state absorption of fluorene-based chromophores. H- and J-aggregates show changeable absorption and emission derived from various interchain interactions, unlike the β phase, which has relatively fixed absorption and emission derived from an intrachain interaction.

Irreversible Catalyst Activation Enables Hyperpolarization and Water Solubility for NMR Signal Amplification by Reversible Exchange

Abstract: Activation of a catalyst [IrCl(COD)(IMes)] (IMes = 1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene; COD = cyclooctadiene)] for signal amplification by reversible exchange (SABRE) was monitored by in situ hyperpolarized proton NMR at 9.4 T. During the catalyst-activation process, the COD moiety undergoes hydrogenation that leads to its complete removal from the Ir complex. A transient hydride intermediate of the catalyst is observed via its hyperpolarized signatures, which could not be detected using conventional nonhyperpolarized solution NMR. SABRE enhancement of the pyridine substrate can be fully rendered only after removal of the COD moiety; failure to properly activate the catalyst in the presence of sufficient substrate can lead to irreversible deactivation consistent with oligomerization of the catalyst molecules. Following catalyst activation, results from selective RF-saturation studies support the hypothesis that substrate polarization at high field arises from nuclear cross-relaxation with hyp...

Electrostatic Unfolding and Interactions of Albumin Driven by pH Changes: A Molecular Dynamics Study

Abstract: A better understanding of protein aggregation is bound to translate into critical advances in several areas, including the treatment of misfolded protein disorders and the development of self-assembling biomaterials for novel commercial applications. Because of its ubiquity and clinical potential, albumin is one of the best-characterized models in protein aggregation research; but its properties in different conditions are not completely understood. Here, we carried out all-atom molecular dynamics simulations of albumin to understand how electrostatics can affect the conformation of a single albumin molecule just prior to self-assembly. We then analyzed the tertiary structure and solvent accessible surface area of albumin after electrostatically triggered partial denaturation. The data obtained from these single protein simulations allowed us to investigate the effect of electrostatic interactions between two proteins. The results of these simulations suggested that hydrophobic attractions and counterion binding may be strong enough to effectively overcome the electrostatic repulsions between the highly charged monomers. This work contributes to our general understanding of protein aggregation mechanisms, the importance of explicit consideration of free ions in protein solutions, provides critical new insights about the equilibrium conformation of albumin in its partially denatured state at low pH, and may spur significant progress in our efforts to develop biocompatible protein hydrogels driven by electrostatic partial denaturation.

Mechanism of Fast Pyrolysis of Lignin: Studying Model Compounds

Abstract: Fast pyrolysis of lignin is one of the most promising methods to convert the complex and irregular structure of lignin into renewable chemicals and fuel. During pyrolysis the complex set of radical reactions, rearrangements, and eliminations is influenced by temperature, pressure, and the lignin origin and structure. This model compound study aims to understand reaction pathways and how primary intermediates lead to the observed product selectivity. The pyrolysis microreactor directly connected to the gas chromatograph with a mass spectrometer (py-GC/MS) detects the final products, while imaging photoelectron photoion coincidence (iPEPICO) with VUV synchrotron radiation shows primary decomposition radicals. The tested model compounds, diphenylether (DPE) and ortho-methoxyphenol (guaiacol), represent a common lignin linkage and the most present subunit in lignin, respectively. Radical fragments, such as the hydroxycyclopentadienyl radical in guaiacol decomposition, are identified by mass-selected threshold...

Non-polarizable force field of water based on the dielectric constant: TIP4P/ε.

Abstract: The static dielectric constant at room temperature and the temperature of maximum density are used as target properties to develop, by molecular dynamics simulations, the TIP4P/e force field of wat...

Single-Particle Spectroscopy Reveals Heterogeneity in Electrochemical Tuning of the Localized Surface Plasmon

Abstract: A hyperspectral imaging method was developed that allowed the identification of heterogeneous plasmon response from 50 nm diameter gold colloidal particles on a conducting substrate in a transparent three-electrode spectroelectrochemical cell under non-Faradaic conditions. At cathodic potentials, we identified three distinct behaviors from different nanoparticles within the same sample: irreversible chemical reactions, reversible chemical reactions, and reversible charge density tuning. The irreversible reactions in particular would be difficult to discern in alternate methodologies. Additional heterogeneity was observed when single nanoparticles demonstrating reversible charge density tuning in the cathodic regime were measured dynamically in anodic potential ranges. Some nanoparticles that showed charge density tuning in the cathodic range also showed signs of an additional chemical tuning mechanism in the anodic range. The expected changes in nanoparticle free-electron density were modeled using a char...

Differences in Cationic and Anionic Charge Densities Dictate Zwitterionic Associations and Stimuli Responses

Abstract: Zwitterionic materials have shown their excellent performance in many biological and chemical applications. Zwitterionic materials possess moieties that own both cationic and anionic groups. The associations among zwitterionic moieties through electrostatic interactions play an important role in properties of zwitterionic materials. However, the relationship between the molecular structures and associations of zwitterionic moieties are still not well understood. This work compared thermal- and salt-responsive behaviors of sulfobetaine and carboxybetaine polymers by examining their rheological properties as a function of temperature and their hydrodynamic sizes as a function of salt concentration. Results showed that carboxybetaine polymers do not exhibit stimuli responses as expected from the antipolyelectrolyte behavior of zwitterionic polymers as observed in sulfobetaine polymers. We studied and compared the associations among zwitterionic moieties in these two zwitterionic polymers using molecular dynamic simulations. Simulation results show that the charge-density difference between cationic and anionic groups determines the associations among zwitterionic moieties, which are responsible for different stimuli responses of carboxybetaine and sulfobetaine polymers.

Host–Guest Interactions in Fe(III)-Trimesate MOF Nanoparticles Loaded with Doxorubicin

Abstract: Doxorubicin (DOX) entrapment in porous Fe(III)–trimesate metal organic frameworks (MIL-100(Fe)) nanoparticles was investigated in neutral Tris buffer via UV–vis absorption, circular dichroism (CD), and fluorescence. The binding constants and the absolute spectra of the DOX-MIL-100(Fe) complexes were determined via absorption and fluorescence titrations. A binding model where DOX associates as monomer to the dehydrated Fe3O (OH)(H2O)2 [(C6H3)(CO2)3]2 structural unit in 1:1 stoichiometry, with apparent association constant of (1.1 to 1.8) × 104 M–1, was found to reasonably fit the experimental data. Spectroscopic data indicate that DOX binding occurs via the formation of highly stable coordination bonds between one or both deprotonated hydroxyl groups of the aglycone moiety and coordinatively unsaturated Fe(III) centers. Complete quenching of the DOX fluorescence and remarkable thermal and photochemical stability were observed for DOX incorporated in the MIL-100(Fe) framework.

Effect of bubble formation on the dissociation of methane hydrate in water: a molecular dynamics study.

Abstract: We investigate the dissociation of methane hydrate in liquid water using molecular dynamics simulations. As dissociation of the hydrate proceeds, methane molecules are released into the aqueous phase and eventually they form bubbles. It is shown that this bubble formation, which causes change in the methane concentration in the aqueous phase, significantly affects the dissociation kinetics of methane hydrate. A large system size employed in this study makes it possible to analyze the effects of the change in the methane concentration and the formation of bubbles on the dissociation kinetics in detail. It is found that the dissociation rate decreases with time until the bubble formation and then it turns to increase. It is also demonstrated that methane hydrate can exist as a metastable superheated solid if there exists no bubble.