Showing papers in "Journal of Physical Chemistry B in 2011"
TL;DR: It is concluded that using partition functions computed for molecules optimized in solution is a correct and useful approach for averaging over solute degrees of freedom when computing free energies of solutes in solution, and it is moreover recommended for cases where liquid and gas-phase solute structures differ appreciably or when stationary points present in liquid solution do not exist in the gas phase.
Abstract: We find that vibrational contributions to a solute’s free energy are in general insensitive to whether the solute vibrational frequencies are computed in the gas phase or in solution. In most cases, the difference is smaller than the intrinsic error in solvation free energies associated with the continuum approximation to solvation modeling, although care must be taken to avoid spurious results associated with limitations in the quantum-mechanical harmonic-oscillator approximation for very low-frequency molecular vibrations. We compute solute vibrational partition functions in aqueous and carbon tetrachloride solution and compare them to gas-phase molecular partition functions computed with the same level of theory and the same quasiharmonic approximation for the diverse and extensive set of molecules and ions included in the training set of the SMD continuum solvation model, and we find mean unsigned differences in vibrational contributions to the solute free energy of only about 0.2 kcal/mol. On the bas...
767 citations
TL;DR: A small change in the Hamiltonian scaling in Replica Exchange with Solute Tempering (REST) is found to improve its sampling efficiency greatly, especially for the sampling of aqueous protein solutions in which there are large-scale solute conformation changes.
Abstract: A small change in the Hamiltonian scaling in Replica Exchange with Solute Tempering (REST) is found to improve its sampling efficiency greatly, especially for the sampling of aqueous protein solutions in which there are large-scale solute conformation changes. Like the original REST (REST1), the new version (which we call REST2) also bypasses the poor scaling with system size of the standard Temperature Replica Exchange Method (TREM), reducing the number of replicas (parallel processes) from what must be used in TREM. This reduction is accomplished by deforming the Hamiltonian function for each replica in such a way that the acceptance probability for the exchange of replica configurations does not depend on the number of explicit water molecules in the system. For proof of concept, REST2 is compared with TREM and with REST1 for the folding of the trpcage and β-hairpin in water. The comparisons confirm that REST2 greatly reduces the number of CPUs required by regular replica exchange and greatly increases...
561 citations
TL;DR: Graphene nanosheets may potentially serve as an encapsulating material for delivery of such microorganisms and as an effective photothermal agent for inactivation of the graphene-wrapped microorganisms.
Abstract: Bioactivity of Escherichia coli bacteria (as a simple model for microorganisms) and interaction of them with the environment were controlled by their capturing within aggregated graphene nanosheets. The oxygen-containing functional groups of chemically exfoliated single-layer graphene oxide nanosheets were reduced by melatonin as a biocompatible antioxidant. While each one of the graphene (oxide) suspension and melatonin solution did not separately show any considerable inactivation effects on the bacteria, aggregation of the sheets in the melatonin–bacterial suspension resulted in trapping the bacteria within the aggregated sheets, i.e., a kind of inactivation. The bacteria trapped within the aggregated sheets were biologically disconnected from their environment, because they could not proliferate in a culture medium and consume the glucose of their environment. However, after removing the sheets from the surface of the microorganisms by using sonication, they could again interact with their environment...
545 citations
TL;DR: A method that involves the deconvolution of the individual processes from the overall differential kinetic curves obtained under linear heating rate conditions, followed by the kinetic analysis of the discrete processes using combined kinetic analysis, is proposed.
Abstract: The kinetic analysis of complex solid-state reactions that involve simultaneous overlapping processes is challenging. A method that involves the deconvolution of the individual processes from the overall differential kinetic curves obtained under linear heating rate conditions, followed by the kinetic analysis of the discrete processes using combined kinetic analysis, is proposed. Different conventional mathematical fitting functions have been tested for deconvolution, paying special attention to the shape analysis of the kinetic curves. It has been shown that many conventional mathematical curves such as the Gaussian and Lorentzian ones fit kinetic curves inaccurately and the subsequent kinetic analysis yields incorrect kinetic parameters. Alternatively, other fitting functions such as the Fraser-Suzuki one properly fit the kinetic curves independently of the kinetic model followed by the reaction and their kinetic parameters, and moreover, the subsequent kinetic analysis yields the correct kinetic parameters. The method has been tested with the kinetic analysis of complex processes, both simulated and experimental.
319 citations
TL;DR: The native state of ubiquitin is preserved in the transition from solution to the desolvated state during the ESI process and survives for >100 ms in a 294 K solvent-free environment; the A state is charged more extensively than the native state during ESI and decays more rapidly following ESI.
Abstract: The conformations of desolvated ubiquitin ions, lifted into the gas phase by electrospray ionization (ESI), were characterized by ion mobility spectrometry (IMS) and compared to the solution structures they originated from. The IMS instrument combining a two-meter helium drift tube with a quadrupole time-of-flight mass spectrometer was built in-house. Solutions stabilizing the native state of ubiquitin yielded essentially one family of tightly folded desolvated ubiquitin structures with a cross section matching the size of the native state (1000 A2). Solutions favoring the A state yielded several well-defined families of significantly unfolded conformations (1800–2000 A2) matching in size conformations between the A state and a fully unfolded state. On the basis of these results and a wealth of data available in the literature, we conclude that the native state of ubiquitin is preserved in the transition from solution to the desolvated state during the ESI process and survives for >100 ms in a 294 K solve...
301 citations
TL;DR: This work provides a straightforward method to prepare flexible films with high conductivity and good mechanical properties, which could be applied in sensors, flexible electrodes, and flexible displays, and opens a new field of potential applications of BC materials.
Abstract: The novel conductive polyaniline/bacterial cellulose (PANI/BC) nanocomposite membranes have been synthesized in situ by oxidative polymerization of aniline with ammonium persulfate as an oxidant and BC as a template. The resulting PANI-coated BC nanofibrils formed a uniform and flexible membrane. It was found that the PANI nanoparticles deposited on the surface of BC connected to form a continuous nanosheath by taking along the BC template, which greatly increases the thermal stability of BC. The content of PANI and the electrical conductivity of composites increased with increasing reaction time from 30 to 90 min, while the conductivity decreased because of the aggregation of PANI particles by further prolonging the reaction time. In addition, the acids remarkably improve the accessibility and reactivity of the hydroxyl groups of BC. The results indicate that the composites exhibit excellent electrical conductivity (the highest value was 5.0 × 10–2 S/cm) and good mechanical properties (Young’s modulus wa...
287 citations
TL;DR: This paper presents a two-state statistical mechanical model of boron speciation in which addition of network modifiers leads to a competition between the formation of nonbridging oxygen and the conversion ofboron from trigonal to tetrahedral configuration, and derives a detailed topological representation of alkali-alkaline earth-borosilicate glasses that enables the accurate prediction of properties such as glass transition temperature, liquid fragility, and hardness.
Abstract: Borosilicate glasses display a rich complexity of chemical behavior depending on the details of their composition and thermal history. Noted for their high chemical durability and thermal shock resistance, borosilicate glasses have found a variety of important uses from common household and laboratory glassware to high-tech applications such as liquid crystal displays. In this paper, we investigate the topological principles of borosilicate glass chemistry covering the extremes from pure borate to pure silicate end members. Based on NMR measurements, we present a two-state statistical mechanical model of boron speciation in which addition of network modifiers leads to a competition between the formation of nonbridging oxygen and the conversion of boron from trigonal to tetrahedral configuration. Using this model, we derive a detailed topological representation of alkali–alkaline earth–borosilicate glasses that enables the accurate prediction of properties such as glass transition temperature, liquid fragi...
287 citations
TL;DR: A diffusion model was developed which incorporated activity-dependent diffusivity, volume expansion, and the interfacial resistance, and was used to resolve the water activity profiles in the membrane, and suggested a change in the connectivity of the hydrophilic domains absorbed water occurs at λ ∼ 4.
Abstract: Water absorption, membrane swelling, and self-diffusivity of water in 1100 equivalent weight Nafion were measured as functions of temperature and water activity. Free volume per water at 80 °C, determined from water uptake and volume expansion data, decreases with water content in the membrane from 12 cm3/mol at λ = 0.5 H2O/SO3 to 1.5 cm3/mol at λ = 4. The change in free volume with water content displays a transition at λ = 4. Limiting water self-diffusivity in Nafion was determined by pulsed gradient spin echo NMR at long delay times. The limiting self-diffusivity increases exponentially with water activity; the rate of increase of diffusivity with water content shows a transition at λ = 4. The tortuosity of the hydrophilic domains in Nafion decreased from 20 at low membrane water activity to 3 at λ = 4. It suggested a change in the connectivity of the hydrophilic domains absorbed water occurs at λ ∼ 4. The diffusivity results were employed to separate the contributions of diffusional and interfacial re...
254 citations
TL;DR: Neutron contrast variation experiments enhance the description of this nanoaggregate in terms of core-shell disk organization, giving insight into core and shell dimensions and chemical compositions.
Abstract: Complementary neutron and X-ray small angle scattering results give prominent information on the asphaltene nanostructure. Precise SANS and SAXS measurements on a large q-scale were performed on the same dilute asphaltene–toluene solution, and absolute intensity scaling was carried out. Direct comparison of neutron and X-ray spectra enables description of a fractal organization made from the aggregation of small entities of 16 kDa, exhibiting an internal fine structure. Neutron contrast variation experiments enhance the description of this nanoaggregate in terms of core–shell disk organization, giving insight into core and shell dimensions and chemical compositions. The nanoaggregates are best described by a disk of total radius 32 A with 30% polydispersity and a height of 6.7 A. Composition and density calculations show that the core is a dense and aromatic structure, contrary to the shell, which is highly aliphatic. These results show a good agreement with the general view of the Yen model (Yen, T. F.; ...
253 citations
TL;DR: A fluorescent compound, 9,10-bis(2-(10-hexyl-10H-phenothiazin-3-yl)vinyl) anthracene, has been synthesized and studied and the results show that the compound possesses piezofluorochromic properties as well as aggregation-induced emission enhancement effect.
Abstract: A fluorescent compound, 9,10-bis(2-(10-hexyl-10H-phenothiazin-3-yl)vinyl) anthracene, has been synthesized and studied. The results show that the compound possesses piezofluorochromic properties as well as aggregation-induced emission enhancement effect. The spectroscopic properties and morphological structures are reversibly exhibited upon pressing (or grinding) or annealing (or fuming). The piezofluorochromic nature is generated through phase transformation under the stimulus of external pressure. The reason for the phase transformation caused by external pressure is ascribed to the twisted conformation of the molecule which leads to poor solid molecular packing and weak interactions in the interfaces of lamellar layers confirmed by its single-crystal X-ray diffraction analysis.
247 citations
TL;DR: The findings demonstrate that molecular modeling is a powerful technique for determining the solubility parameters and predicting miscibility of pharmaceutical compounds, and are in reasonable agreement with those calculated using group contribution methods.
Abstract: The objectives of this study were (i) to develop a computational model based on molecular dynamics technique to predict the miscibility of indomethacin in carriers (polyethylene oxide, glucose, and sucrose) and (ii) to experimentally verify the in silico predictions by characterizing the drug-carrier mixtures using thermoanalytical techniques. Molecular dynamics (MD) simulations were performed using the COMPASS force field, and the cohesive energy density and the solubility parameters were determined for the model compounds. The magnitude of difference in the solubility parameters of drug and carrier is indicative of their miscibility. The MD simulations predicted indomethacin to be miscible with polyethylene oxide and to be borderline miscible with sucrose and immiscible with glucose. The solubility parameter values obtained using the MD simulations values were in reasonable agreement with those calculated using group contribution methods. Differential scanning calorimetry showed melting point depression...
TL;DR: Room-temperature calculations of the excited-state dynamics in FMO are reported on using a combination of molecular dynamics simulations and electronic structure calculations to obtain trajectories for the Hamiltonian of this system which contains time-dependent vertical excitation energies of the individual bacteriochlorophyll molecules and their mutual electronic couplings.
Abstract: The experimental observation of long-lived quantum coherences in the Fenna-Matthews-Olson (FMO) light-harvesting complex at low temperatures has challenged general intuition in the field of complex molecular systems and provoked considerable theoretical effort in search of explanations. Here we report on room-temperature calculations of the excited-state dynamics in FMO using a combination of molecular dynamics simulations and electronic structure calculations. Thus we obtain trajectories for the Hamiltonian of this system which contains time-dependent vertical excitation energies of the individual bacteriochlorophyll molecules and their mutual electronic couplings. The distribution of energies and couplings is analyzed together with possible spatial correlations. It is found that in contrast to frequent assumptions the site energy distribution is non-Gaussian. In a subsequent step, averaged wave packet dynamics is used to determine the exciton dynamics in the system. Finally, with the time-dependent Hamiltonian, linear and two-dimensional spectra are determined. The thus-obtained linear absorption line shape agrees well with experimental observation and is largely determined by the non-Gaussian site energy distribution. The two-dimensional spectra are in line with what one would expect by extrapolation of the experimental observations at lower temperatures and indicate almost total loss of long-lived coherences.
TL;DR: The most important result of this study is that the viscosity of [P(66614)][Pro] only increased by a factor of 2 when fully complexed with 1 bar of CO(2) at room temperature, in stark contrast to the other chemically reacted ILs investigated here and all other amino acid-based ILs reported in the literature, which dramatically increase in Viscosity.
Abstract: Amine-functionalized anion-tethered ionic liquids (ILs) trihexyl(tetradecyl)phosphonium asparaginate [P66614][Asn], glutaminate [P66614][Gln], lysinate [P66614][Lys], methioninate [P66614][Met], prolinate [P66614][Pro], taurinate [P66614][Tau], and threoninate [P66614][Thr] were synthesized and investigated as potential absorbents for CO2 capture from postcombustion flue gas. Their physical properties, including density, viscosity, glass transition temperature, and thermal decomposition temperature were determined. Furthermore, the CO2 absorption isotherms of [P66614][Lys], [P66614][Tau], [P66614][Pro], and [P66614][Met] were measured using a volumetric method, and the results were modeled with two different Langmuir-type absorption models. The most important result of this study is that the viscosity of [P66614][Pro] only increased by a factor of 2 when fully complexed with 1 bar of CO2 at room temperature. This is in stark contrast to the other chemically reacted ILs investigated here and all other amin...
TL;DR: Both experimental and computational results indicate an energetic differentiation between the cation and the anion to the ionic pair, and it was found that the quantum chemical calculations can describe the trend obtained for the electrostatic cation-anion attraction potential.
Abstract: Electrospray ionization mass spectrometry with variable collision induced dissociation of the isolated [(cation)2anion]+ and/or [(anion)2cation]− ions of imidazolium-, pyridinium-, pyrrolidinium-, and piperidinium-based ionic liquids (ILs) combined with a large set of anions, such as chloride, tetrafluoroborate, hexafluorophosphate, trifluoromethanesulfonate, and bis[(trifluoromethyl)sulfonyl]imide, was used to carry out a systematic and comprehensive study on the ionic liquids relative interaction energies. The results are interpreted in terms of main influences derived from the structural characteristics of both anion and cation. On the basis of quantum chemical calculations, the effect of the anion upon the dissociation energies of the ionic liquid pair, and isolated [(cation)2anion]+ and/or [(anion)2cation]− aggregates, were estimated and are in good agreement with the experimental data. Both experimental and computational results indicate an energetic differentiation between the cation and the anion ...
TL;DR: It is found that the fluorescence of BSA at λ(ex) 230 nm arising from aromatic amino acids Trp and Tyr is almost as sensitive as that achieved at η 280 nm for elucidating the protein conformational changes, which provides a valid and new probe for the investigation of binding kinetics between molecules/ions and proteins.
Abstract: The interactions of imidazolium ionic liquids (ILs), i.e., dibutylimidazolium chloride, 1-butyl-3-methylimidazolium chloride, and 1-butyl-3-methylimidazolium nitrate, with bovine serum albumin (BSA) were studied by monitoring the spectral behaviors of IL-BSA aqueous systems. The intrinsic fluorescence of BSA at 340 nm excited at 230 nm is obviously quenched by these ILs due to complex dynamic collision and their quenching constants are at the order of 10(2) L mol(-1). However, no fluorescence quenching is observed within the same region when excited at 280 nm, which is widely used for probing protein conformations. Thermodynamic investigations reveal that the combination between ILs and BSA is entropy driven by predominantly hydrophobic and electrostatic interactions, leading to the unfolding of polypeptides within BSA. The influence of the ILs on the conformation of BSA follows a sequence of BmimNO(3) > BmimCl ≈ BbimCl. Molecular docking shows that cationic imidazolium moieties of ILs enter the subdomains of protein and interact with the hydrophobic residues of domain III. An agreement between fluorescence spectroscopic investigations and molecular docking is reached. It is found that the fluorescence of BSA at λ(ex) 230 nm arising from aromatic amino acids Trp and Tyr is almost as sensitive as that achieved at λ(ex) 280 nm for elucidating the protein conformational changes, which provides a valid and new probe for the investigation of binding kinetics between molecules/ions and proteins.
TL;DR: Investigation of the impact of vibronic couplings on the electronic structures and relaxation mechanisms of two cyanobacterial light-harvesting proteins suggests that the distinct behaviors of these closely related proteins are understood on the same footing only in a basis of joint electronic-nuclear states.
Abstract: Transport processes and spectroscopic phenomena in light harvesting proteins depend sensitively on the characteristics of electron-phonon couplings. Decoherence imposed by low-frequency nuclear motion generally suppresses the delocalization of electronic states, whereas the Franck-Condon progressions of high-frequency intramolecular modes underpin a hierarchy of vibronic Coulombic interactions between pigments. This Article investigates the impact of vibronic couplings on the electronic structures and relaxation mechanisms of two cyanobacterial light-harvesting proteins, allophycocyanin (APC) and C-phycocyanin (CPC). Both APC and CPC possess three pairs of pigments (i.e., dimers) that undergo electronic relaxation on the subpicosecond time scale. Electronic relaxation is ~10 times faster in APC than in CPC despite the nearly identical structures of their pigment dimers. We suggest that the distinct behaviors of these closely related proteins are understood on the same footing only in a basis of joint electronic-nuclear states (i.e., vibronic excitons). A vibronic exciton model predicts well-defined rate enhancements in APC at realistic values of the site reorganization energies, whereas a purely electronic exciton model points to faster dynamics in CPC. Calculated exciton sizes (i.e., participation ratios) show that wave function delocalization underlies the rate enhancement predicted by the vibronic exciton model. Strong vibronic coupling and heterogeneity in the pigment sites are the key ingredients of the vibronic delocalization mechanism. In contrast, commonly employed purely electronic exciton models see heterogeneity as only a localizing influence. This work raises the possibility that similar vibronic effects, which are often neglected, may generally have a significant influence on energy transport in molecular aggregates and photosynthetic complexes.
TL;DR: The thermodynamic results reported in the present article constitute the first quantitative experimental evidence of the structural percolation phenomenon and make a significant contribution to better understanding of the relationship among cohesive energies, volatilities, and liquid structures of ionic liquids.
Abstract: For the first time, two distinct trends are clearly evidenced for the enthalpies and entropies of vaporization along the [Cnmim][Ntf2] ILs series. The trend shifts observed for ΔlgHmo and ΔlgSmo, which occur at [C6mim][Ntf2], are related to structural modifications. The thermodynamic results reported in the present article constitute the first quantitative experimental evidence of the structural percolation phenomenon and make a significant contribution to better understanding of the relationship among cohesive energies, volatilities, and liquid structures of ionic liquids. A new Knudsen effusion apparatus, combined with a quartz crystal microbalance, was used for the high-accuracy volatility study of the 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide series ([Cnmim][Ntf2], where n = 2, 3, 4, 5, 6, 7, 8, 10, 12). Vapor pressures in the (450–500) K temperature range were measured, and the molar standard enthalpies, entropies, and Gibbs energies of vaporization were derived. The thermodynamic...
TL;DR: This simulations of electroporation show that the S. aureus cell membrane is less resistant to poration than the E. coli outer membrane, and identifies the extended network of lipid-lipid interactions that stabilize the membranes.
Abstract: Bacterial membranes are complex organelles composed of a variety of lipid types. The differences in their composition are a key factor in determining their relative permeabilities. The success of antibacterial agents depends upon their interaction with bacterial membranes, yet little is known about the molecular-level interactions within membranes of different bacterial species. To address this, we have performed molecular dynamics simulations of two bacterial membranes: the outer membrane of E. coli and the cell membrane of S. aureus. We have retained the chemical complexity of the membranes by considering the details of their lipidic components. We identify the extended network of lipid–lipid interactions that stabilize the membranes. Our simulations of electroporation show that the S. aureus cell membrane is less resistant to poration than the E. coli outer membrane. The mechanisms of poration for the two membranes have subtle differences; for the E. coli outer membrane, relative differences in mobilit...
TL;DR: This study provides new insights into the molecular interactions that form the structural basis of cellulose, which is the primary building block of plant cell walls, and highlights the need for experimentally determining microfibril shape at the nanometer length scale when comparing conversion rates of cellulOSE polymorphs by enzymes.
Abstract: Cellulose is a crystalline polymer of β1,4-d-glucose that is difficult to deconstruct to sugars by enzymes. The recalcitrance of cellulose microfibrils is a function of both the shape of cellulose microfibrils and the intrinsic work required to decrystallize individual chains, the latter of which is calculated here from the surfaces of four crystalline cellulose polymorphs: cellulose Iβ, cellulose Iα, cellulose II, and cellulose IIII. For edge chains, the order of decrystallization work is as follows (from highest to lowest): Iβ, Iα, ΙΙΙΙ, and II. For cellulose Iβ, we compare chains from three different locations on the surface and find that an increasing number of intralayer hydrogen bonds (from 0 to 2) increases the intrinsic decrystallization work. From these results, we propose a microkinetic model for the deconstruction of cellulose (and chitin) by processive enzymes, which when taken with a previous study [Horn et al.Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 18089] identifies the thermodynamic and ki...
TL;DR: The SAFT-γ top-down approach to coarse-grained techniques resolves a key challenge with coarse- graining techniques: the provision of a direct robust link between the microscopic and macroscopic scales.
Abstract: An application of the “top-down” concept for the development of accurate coarse-grained intermolecular potentials of complex fluids is presented. With the more common “bottom-up” procedure, coarse-grained models are constructed from a suitable simplification of a detailed atomistic representation, and small adjustments to the intermolecular parameters are made by comparison with limited experimental data where necessary. In contrast, in the top-down approach, a molecular-based equation of state is used to obtain an effective coarse-grained intermolecular potential that reproduces the macroscopic experimental thermophysical properties over a wide range of conditions. These coarse-grained intermolecular potentials can then be used in conventional molecular simulation to obtain properties (such as structure or dynamics) that are not directly accessible from the equation of state or at extreme conditions where the theory is expected to fail. To demonstrate our procedure, a coarse-grained model for carbon diox...
TL;DR: This work presents a set of equations that in the case of ionic liquids and molten salts can be used to obtain from direct measurements of impedance and NMR the distinct part of the diffusion coefficient matrix in the barycentric reference frame.
Abstract: In this article we show that, analyzed in a barycentric reference frame, the deviation in conductivity measured directly from impedance experiments with respect to that estimated indirectly from NMR diffusion experiments has different origins in electrolyte solutions and pure salts. In the case of electrolyte solutions, the momentum conservation law is satisfied by solvent + ions. Instead, in a molten salt or ionic liquid momentum conservation must be satisfied solely by the ions. This has significant implications. While positively correlated motion of ions of opposite charge is a well justified explanation for the reduction in impedance conductivity in the case of electrolyte solutions, it is not so in the case of ionic liquids and molten salts. This work presents a set of equations that in the case of ionic liquids and molten salts can be used to obtain from direct measurements of impedance and NMR the distinct part of the diffusion coefficient matrix in the barycentric reference frame. In other words, ...
TL;DR: In the presence of disorder and for T > 0 K, λ2S(R) is closely approximated by the exciton coherence number N( coh), thereby providing a simple and direct way of extracting N(coh) from the photoluminescence spectrum.
Abstract: Exciton coherence in a J-aggregate with exciton−phonon coupling involving a single intramolecular vibration is studied. For linear aggregates with no disorder and periodic boundary conditions, the 0−0 to 0−1 line strength ratio, SR, corresponding to the low-temperature photoluminescence spectrum is rigorously equal to N/λ2, where N is the number of chromophores comprising the aggregate and λ2 is the Huang−Rhys factor of the coupled vibrational mode. The result is independent of exciton bandwidth and therefore remains exact from the weak to strong exciton−phonon coupling regimes. The simple relation between SR and N also holds for more complex morphologies, as long as the transition from the lowest exciton state to the vibrationless ground state is symmetry-allowed. For example, in herringbone aggregates with monoclinic unit cells, the line strength ratio, defined as SR ≡ Ib0−0/Ib0−1 (where Ib0−0 and Ib0−1 correspond to the b-polarized 0−0 and 0−1 line strengths, respectively) is rigorously equal to N/λ2....
TL;DR: RAF has been identified as the main mechanism involved in the direct ROS scavenging activity of CAF, and excellent agreement with the available experimental data supports the reliability of the present calculations.
Abstract: The reactions of caffeine (CAF) with different reactive oxygen species (ROS) have been studied using density functional theory. Five mechanisms of reaction have been considered, namely, radical adduct formation (RAF), hydrogen atom transfer (HAT), single electron transfer (SET), sequential electron proton transfer (SEPT), and proton coupled electron transfer (PCET). The SET, SEPT, and PCET mechanisms have been ruled out for the reactions of CAF with •OH, O2•−, ROO•, and RO• radicals. It was found that caffeine is inefficient for directly scavenging O2•− and •OOCH3 radicals and most likely other alkyl peroxyl radicals. The overall reactivity of CAF toward •OH was found to be diffusion-controlled, regardless of the polarity of the environment, supporting the excellent •OH scavenging activity of CAF. On the other hand, it is predicted to be a modest scavenger of •OCH3, and probably of other alkoxyl radicals, and a poor scavenger of HOO•. RAF has been identified as the main mechanism involved in the direct RO...
TL;DR: In this paper, the effect of residue-specific TMAO interactions on small fragments of solvent-exposed conformations of denatured states of proteins was investigated, and it was shown that TMAOs preferentially formed hydrogen bonds with the exposed dipeptide backbone but generally not with nonpolar or polar side chains.
Abstract: The osmolyte trimethylamine N-oxide (TMAO) accumulates in the cell in response to osmotic stress and increases the thermodynamic stability of folded proteins. To understand the mechanism of TMAO induced stabilization of folded protein states, we systematically investigated the action of TMAO on several model dipeptides (leucine, L2, serine, S2, glutamine, Q2, lysine, K2, and glycine, G2) in order to elucidate the effect of residue-specific TMAO interactions on small fragments of solvent-exposed conformations of the denatured states of proteins. We find that TMAO preferentially hydrogen bonds with the exposed dipeptide backbone but generally not with nonpolar or polar side chains. However, interactions with the positively charged Lys are substantially greater than with the backbone. The dipeptide G2 is a useful model of the pure amide backbone; interacts with TMAO by forming a hydrogen bond between the amide nitrogen and the oxygen in TMAO. In contrast, TMAO is depleted from the protein backbone in the hex...
TL;DR: The ReaxFF potential developed in this work provides an accurate description of proton transfer in glycine and thus provides a useful methodology for simulating protonTransfer reactions in organic molecules in the aqueous environment.
Abstract: Tautomerization of amino acids between the neutral form (NF) and the zwitterionic form (ZW) in water has been extensively studied, often using glycine as a model to understand this fundamental process In spite of many advanced studies, the tautomerization reaction remains poorly understood because of the intrinsic complexities of the system, including multiple accessible reaction pathways, charge transfer, and variations of solvation structure To establish an accurate model that can be used for molecular dynamics simulations, a ReaxFF reactive force field has been developed for glycine A training set for the ReaxFF hydrocarbon potential was augmented with several glycine conformers and glycine−water complexes The force field parameters were optimized to reproduce the quantum mechanically derived energies of the species in the training set The optimized potential could accurately describe the properties of gas-phase glycine It was applied to investigate the effect of solvation on the conformational d
TL;DR: By simulations, the relationship between aggregation rates and binding affinity is clarified and it is predicted that LPFFD inhibits/degrades the fibrillogenesis of full-length amyloid peptides better than KLVFF.
Abstract: The effects of beta-sheet breaker peptides KLVFF and LPFFD on the oligomerization of amyloid peptides were studied by all-atom simulations. It was found that LPFFD interferes the aggregation of Aβ(16-22) peptides to a greater extent than does KLVFF. Using the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method, we found that the former binds more strongly to Aβ(16-22). Therefore, by simulations, we have clarified the relationship between aggregation rates and binding affinity: the stronger the ligand binding, the slower the oligomerization process. The binding affinity of pentapeptides to full-length peptide Aβ(1-40) and its mature fibrils has been considered using the Autodock and MM-PBSA methods. The hydrophobic interaction between ligands and receptors plays a more important role for association than does hydrogen bonding. The influence of beta-sheet breaker peptides on the secondary structures of monomer Aβ(1-40) was studied in detail, and it turns out that, in their presence, the total beta-sheet content can be enhanced. However, the aggregation can be slowed because the beta-content is reduced in fibril-prone regions. Both pentapeptides strongly bind to monomer Aβ(1-40), as well as to mature fibrils, but KLVFF displays a lower binding affinity than LPFFD. Our findings are in accord with earlier experiments that both of these peptides can serve as prominent inhibitors. In addition, we predict that LPFFD inhibits/degrades the fibrillogenesis of full-length amyloid peptides better than KLVFF. This is probably related to a difference in their total hydrophobicities in that the higher the hydrophobicity, the lower the inhibitory capacity. The GROMOS96 43a1 force field with explicit water and the force field proposed by Morris et al. (Morris et al. J. Comput. Chem. 1998, 19, 1639 ) were employed for all-atom molecular dynamics simulations and Autodock experiments, respectively.
TL;DR: It is shown that constant potential simulations indicate time scales of hundreds of picoseconds required for electrode charge/discharge and EDL formation.
Abstract: Molecular dynamics simulations were performed on N-methyl-N-propylpyrrolidinium bis(fluorosulfonyl)imide (pyr13FSI) room temperature ionic liquid (RTIL) confined between graphite electrodes as a function of applied potential at 393 and 453 K using an accurate force field developed in this work. The electric double layer (EDL) structure and differential capacitance (DC) of pyr13FSI was compared with the results of the previous study of a similar RTIL pyr13bis(trifluoromethanesulfonyl)imide (pyr13TFSI) with a significantly larger anion [Vatamanu, J.; Borodin, O.; Smith, G. D.J. Am. Chem. Soc. 2010, 132, 14825]. Intriguingly, the smaller size of the FSI anion compared to TFSI did not result in a significant increase of the DC on the positive electrode. Instead, a 30% higher DC was observed on the negative electrode for pyr13FSI compared to pyr13TFSI. The larger DC observed on the negative electrode for pyr13FSI compared to pyr13TFSI was associated with two structural features of the EDL: (a) a closer approac...
TL;DR: How the structural heterogeneities and physical properties of these ILs are consistent with alkyl tail segregation is discussed, and an even-odd effect previously observed in molecular dynamics simulations is confirmed by viscosity measurements.
Abstract: In this paper, the morphology and bulk physical properties of 1,3-dialkylimidazolium bis{(trifluoromethane)sulfonyl}amide ([(CN/2)2im][NTf2]) are compared to that of 1-alkyl-3-methylimidazolium bis{(trifluoromethane)sulfonyl}amide ([CN–1C1im][NTf2]) for N = 4, 6, 8, and 10. For a given pair of ionic liquids (ILs) with the same N, the ILs differ only in the symmetry of the alkyl substitution on the imidazolium ring of the cation. Small-wide-angle X-ray scattering measurements indicate that, for a given symmetric/asymmetric IL pair, the structural heterogeneities are larger in the asymmetric IL than in the symmetric IL. The correlation length of structural heterogeneities for the symmetric and asymmetric salts, however, is described by the same linear equation when plotted versus the single alkyl chain length. Symmetric ILs with N = 4 and 6 easily crystallize, whereas longer alkyl chains and asymmetry hinder crystallization. Interestingly, the glass transition temperature is found to vary inversely with the...
TL;DR: This work has developed a nonadiabatic excited-state molecular dynamics (NA-ESMD) framework incorporating quantum transitions and identifies specific slow and fast nuclear motions that are strongly coupled to the electronic degrees of freedom, namely, torsion and bond length alternation.
Abstract: Nonadiabatic dynamics generally defines the entire evolution of electronic excitations in optically active molecular materials. It is commonly associated with a number of fundamental and complex processes such as intraband relaxation, energy transfer, and light harvesting influenced by the spatial evolution of excitations and transformation of photoexcitation energy into electrical energy via charge separation (e.g., charge injection at interfaces). To treat ultrafast excited-state dynamics and exciton/charge transport we have developed a nonadiabatic excited-state molecular dynamics (NA-ESMD) framework incorporating quantum transitions. Our calculations rely on the use of the Collective Electronic Oscillator (CEO) package accounting for many-body effects and actual potential energy surfaces of the excited states combined with Tully’s fewest switches algorithm for surface hopping for probing nonadiabatic processes. This method is applied to model the photoinduced dynamics of distyrylbenzene (a small oligo...
TL;DR: The findings suggest that the conformational conversion occurs in the oligomers that serve as precursors to amyloid fibrils and precedes the overall fibrillar growth.
Abstract: We have investigated the fibrillation propensity of different conformational isomers of an archetypal, all α-helical protein, namely, bovine serum albumin (BSA), under different pH conditions and ionic strengths using fluorescence and circular dichroism (CD) spectroscopy. At low pH and higher protein concentration, the partially folded conformers associate to form oligomers that are converted into ordered amyloid-like fibrils when incubated at elevated temperature. We have elucidated the mechanism of fibril formation, especially the early steps, by monitoring the kinetics of structural changes during the aggregation process. Various structural probes in tandem were utilized to decipher the temporal evolution of both conformational and size changes by measuring the time dependence of fluorescence intensity and anisotropy of intrinsic tryptophans and several extrinsic fluorophores during the aggregation. Additionally, CD spectroscopy was utilized to monitor the changes in protein secondary structural content during fibrillation. Our findings suggest that the conformational conversion occurs in the oligomers that serve as precursors to amyloid fibrils and precedes the overall fibrillar growth.