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Multiwalled carbon nanotubes (MWCNTs) were grown on the fibers of a commercial porous carbon paper used as carbon-collecting electrodes in fuel cells. The tubes were then covered with Pt nanoparticles in order to test these gas diffusion electrodes (GDEs) for oxygen reduction in H2SO4 solution and in H2/O2 fuel cells. The Pt nanoparticles were characterized by cyclic voltammetry, transmission electron microscopy, and X-ray photoelectron spectroscopy. The majority of the Pt particles are 3 nm in size with a mean size of 4.1 nm. They have an electrochemically active surface area of 60 m2/g Pt for Pt loadings of 0.1-0.45 mg Pt/cm2. Although the electroactive Pt surface area is larger for commercial electrodes of similar loadings, Pt/MWCNT electrodes largely outperform the commercial electrode for the oxygen reduction reaction in GDE experiments using H2SO4 at pH 1. On the other hand, when the same electrodes are used as the cathode in a H2/O2 fuel cell, they perform only slightly better than the commercial electrodes in the potential range going from approximately 0.9 to approximately 0.7 V and have a lower performance at lower voltages.

In the preceding paper of this series [Leontidis, E. Aroti, A. Belloni, L. J. Phys. Chem. B 2009, 113, 1447], we considered and modeled the increase of the surface pressure of dipalmitoyl phosphatidylcholine (DPPC) monolayers over electrolyte solutions of various monovalent sodium salts. The experimental results for salts with large, less hydrophilic anions can be successfully described by models treating ionic specificity either as specific partitioning in the interfacial lipid layer or as a result of ion-lipid dispersion interactions. However, the results for salts with more hydrophilic anions, such as chloride and fluoride, cannot be fitted by any of these models, while they clearly demonstrate the existence of a specific sodium-DPPC interaction. In the present paper, we first prove that the experimental results for sodium fluoride (NaF) can be fitted by a model that is based on simultaneous complexation of sodium ions with up to three lipid molecules, as suggested by recent molecular dynamics simulations. We then return to the experimental results of sodium salts with more hydrophobic anions, treated in the preceding paper, and prove that these can be fitted equally well with a complex model, which accounts for both sodium complexation with the lipid head groups and anion partitioning within the lipid monolayers. The partitioning parameters obtained from this more complete model correlate well with several measures of ion specificity, such as ionic volume, von Hippel chromatographic parameters, or viscosity B-coefficients. A model for these partitioning chemical potentials is created based on the competition of cavity and ion hydration terms. The model leads to an excellent correlation of the partitioning chemical potentials with a function of the ionic radius, suggesting that specific anion effects on this lipid model system are mostly a matter of ionic size. Two notable exceptions from this correlation are thiocyanate and acetate ions, the charge distribution of which is not spherically symmetric, so that they are expected to have orientational-dependent interactions with the water-lipid interface. The implications of the present results on ion specificity in general are discussed. © 2009 American Chemical Society. 113 5 1460 1467 Cited By :43

In this paper, we obtained various water-soluble polymer functionalized graphene in dimethyl sulfoxide under ultrasonication. The atomic force microscope analysis and control experiment shows the water-soluble polymer is the crucial part to help solvent molecules separate interlayer. Such polymer/graphene exhibits high conductivity and tunable surface property, as confirmed by the selected area electron diffraction and Raman and electrochemical impedance spectroscopy. As a result, a catalyst based on polyvinyl pyrrolidone (PVP)/graphene shows better methanol oxidation performance than that based on PVP/reduced graphene oxide. By changing to another polymer, poly(4-vinylpyridine)/graphene shows a stable and reversible response to pH, and demonstrates its potential for sensor application.

With unique structure and extraordinary electronic, thermal, and mechanical properties, graphene fascinates the scientific community. Due to its hydrophobic feature, preparation of a stable and highly concentrated graphene dispersion without the assistance of dispersing agents has generally been considered a challenge. Chemical reduction of graphene oxide (GO) is one of the most important methods for preparing a graphene dispersion. The aggregation of graphene sheets is a key reason to destabilize the resulting dispersion during conversion of aqueous GO dispersion to graphene. In this study, by replacing mechanical stirring with ultrasonic irradiation, the aggregation of various intermediates is effectively suppressed during the process of reduction of GO. Hence, a stable graphene dispersion with a high concentration of 1 mg.mL(-1) and relatively pure graphene sheets are achieved, and the as-prepared graphene paper exhibits a high electric conductivity of 712 S.m(-1). Ultraviolet-visible absorption spectroscopy and X-ray photoelectron spectroscopy show that ultrasound is the essence of enhancing chemical reaction rate. Fourier transformed infrared spectra and Raman spectra indicate that ultrasound has less damage to the chemical and crystal structures of graphene.

Filter paper, loaded with catalyst precursor, is burned to generate catalyst nanoparticles for single-wall nanotube (SWNT) synthesis in a two-stage flame. A first-stage diffusion flame creates the Fe nanoparticles as an aerosol in the post-flame gases for catalysis. A second-stage flame is formed by the first-stage diffusion flame gases plus added fuel exiting into the combustion gases of a fuel-rich, premixed flame. Both catalyst conditioning and SWNT synthesis occurs within the post-flame reacting flow of this second-stage flame system.

We examine the nucleation kinetics of Au clusters on graphene and explore the relationship with layer number and underlying supporting substrate of graphene. Using the mean field theory of diffusion-limited aggregation, morphology patterns are semiquantitatively analyzed to obtain Au adatom effective diffusion constants and activation energies. Under specified assumptions, the Au adatom diffusion constant for single-layer graphene supported on SiO2 is ∼50 times smaller than that for hexagonal boron nitride (h-BN)-supported graphene and on the order of 800 times smaller than that for multilayer graphite. Bilayer graphene on SiO2 shows a Au adatom diffusion constant similar to single-layer graphene on h-BN. Scanning probe data show that single-layer graphene is far flatter on h-BN than on SiO2. Two factors are proposed as contributing to the observed lower diffusion constants on single-layer graphene: local surface roughness and homogeneous loss of dispersion/van der Waals electronic stability in multilayers. Graphene Raman spectroscopy shows little charge transfer between Au nanoparticles and graphene.

Loading of graphite oxide (GO) with tris(2,2'-bipyridyl) iron(II) ions and subsequent calcination affords a novel graphene-based composite with magnetic and electrically conductive properties. The pH of the starting aqueous suspension and the washing procedure play a crucial role in the successful immobilization of the iron precursor, which is mainly governed by ion exchange. The complex is intercalated between the graphene oxide layers, where it adopts a distorted conformation. Rapid heating of this solid results in the deflagration of GO and the formation of ultrafine ( d = 2-14 nm) Fe2O3 particles with maghemite as the dominant phase. The superparamagnetic maghemite crystals are dispersed uniformly in the high-surface-area diamagnetic matrix built up from single or turbostratic stacked graphenes.

Composite thin films consisting of silicon oxide and tin oxide have been deposited on polycarbonate substrates as gas barrier films, using a thermal evaporation process in an oxygen gas environment. Water vapor permeation through the composite films is significantly affected by the chemical interaction of water vapor with the composite oxide films and the microstructure of the composite oxide films. The chemical interaction of water vapor with oxide films has been investigated by the considering the refractive index obtained from ellipsometry and the OH group peak from X-ray photoelectron spectroscopy, and the microstructure of the composite oxide films has been characterized using atomic force microscopy. As the tin oxide is added to the silicon oxide, the refractive index and OH group peak intensity of the composite films increase, and the water vapor transmission rate through the composite oxide films shows a lower value than that through the single-element oxide films, such as tin oxide and silicon ox...

In this paper, atomistic molecular dynamics simulations are performed for the systems consisting of functionalized gold nanoparticles (NPs) in a toluene medium. Gold NPs are coated with ligand molecules that have different terminal groups, that is, polar carboxyl (COOH), hydroxyl (OH), amine (NH2), and nonpolar methyl (CH3). These functional groups are selected to understand the relation between the aggregation behavior of functionalized gold NPs in toluene and the polarity of terminal groups of ligand molecules. The center-of-mass distances between NP pairs, the radial distribution functions, the mean square displacements, the radius of gyration, and the number of hydrogen bonds (H-bond) between ligand molecules are computed. Our simulation results indicate that functionalized gold NPs exhibit different aggregation/dispersion behaviors depending upon the terminal group of ligands., TUBITAK (Turkish Agency) [117F246], This work has been supported by TUBITAK (Turkish Agency) under Research Project number 117F246. The numerical calculations reported in this paper were fully performed at the TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources).

Sharp and intense vibrational bands are characterized with conspicuous dispersion of complex refractive indices. Based on the quantitative data of dispersion in the preceding paper, this paper clarifies the influence of the dispersion on the sum frequency generation (SFG) spectroscopy. As a consequence of the large dispersion, the lineshapes of SFG spectra could be influenced by the frequency dependence of the Fresnel factor as well as the nonlinear susceptibility. This paper argues the relative importance of the two factors in general cases and provides a useful criterion to evaluate their importance. The effect of Fresnel dispersion becomes significant when the SFG spectrum involves a sharp and intense vibrational band as well as a large non-resonant background susceptibility, typically in some solid-liquid interfaces. A possible way to correct the effect of Fresnel dispersion is suggested using the heterodyne measurement.

This paper reviews the dispersion of complex refractive indices for representative intense vibrational bands of organic liquids in the absolute scale. Conspicuous variations in both real and imaginary refractive indices over the intense bands are precisely determined as a function of infrared wavenumber by attenuated total reflection infrared absorption measurement. The accurate spectral data offer an excellent reference to calibrate the absolute infrared intensities by various quantum chemical calculations, and thus, critical comparison between the present experiment and computation was reported to clarify the general accuracy of the quantum chemical calculations. The precise data of the dispersion will be utilized to clarify their impact on the analysis of vibrational spectroscopy of interfaces in the subsequent paper.

Various spatiotemporal patterns were created on the surface or in the body of cation-exchange resin beads which were loaded with the catalyst of the Belousov-Zhabotinsky (BZ) reaction. Either global oscillations (GO) or traveling waves (TW) and the switching between them were observed in the previous papers, but it was not clear how chemicals contribute to the reaction inside/around the BZ bead. In this paper, we scanned the electrical potential, E, from +1 to -1 V (negative scan) and then turned from -1 to +1 V (positive scan) to control the switching between GO and TW. We found that the electrical switching potential from TW to GO, ETG, and from GO to TW, EGT, depended on the scanning direction of E and the diameter of the bead, d. The present study suggests that the electrode-induced increase of the inhibitor, Br-, and the activator, HBrO2, around the BZ bead plays an important role in determining ETG and EGT.

In this paper, for the first time, the influence of the $BaTiO_{3}$ particles on the antiferroelectric liquid crystalline phase was shown. Low concentrations and two different sizes of $BaTiO_{3}$ particles (nano- and submicroparticles) were used. It was found that admixture of the ferroelectric particles causes a decrease in the concentration of free ions in the liquid crystal matrix. Despite the small amount of admixture, a decrease in spontaneous polarization, switching time and rotational viscosity, was observed, while the tilt angle of molecules and the smectic layer thickness did not change. It turns out that $BaTiO_{3}$ particles have a very large impact on the dielectric spectra not only in the antiferroelectric phase but also in the ferroelectric and paraelectric phases of the polymorphic mixture studied. The dopants affect also the complex conductivity. In this paper, we explain why some properties are modified by $BaTiO_{3}$ particles and others are not.

Orange carotenoid proteins (OCPs) are photoswitchable macromolecules playing an important role in nonphotochemical quenching of excess energy in cyanobacterial light harvesting. Upon absorption of a blue photon (450–500 nm), OCPs undergo a structural change from the ground state OCPO to the active state OCPR, but high-resolution structures of the active state OCPR are not yet available. Here, we use small-angle scattering methods combined with simulation tools to determine low-resolution structures of the active state at low protein concentrations via two approaches: first, directly by in situ illumination of wild-type OCP achieving a turnover to the active state of >90% and second, by using the mutant OCPW288A anticipated to mimic the active state structure. Data fits assuming the shape of an ellipsoid yield three ellipsoidal radii of about 9, 29, and 51 ± 1 Å, in the case of the ground state OCPO. In the active state, however, the molecule becomes somewhat narrower with the two smaller radii being 9 and only 19 ± 3 Å, while the third dimension of the ellipsoid is significantly elongated to 85–92 ± 5 Å. Reconstitutions of the active state structure corroborate that OCPR is significantly elongated compared to the ground state OCPO and characterized by a separation of the N-terminal and C-terminal domains with unfolded N-terminal extension. By direct comparison of small-angle scattering data, we directly show that the mutant OCPW288A can be used as a structural analogue of the active state OCPR. The small-angle experiments are repeated for OCPO and the mutant OCPW288A at high protein concentrations of 50–65 mg/mL required for neutron spectroscopy investigating the molecular dynamics of OCP (see accompanying paper). The results reveal that the OCPO and OCPW288A samples for dynamics experiments are preferentially dimeric and widely resemble the structures of the ground and active states of OCP, respectively. This enables us to properly characterize the molecular dynamics of both states of OCP in the accompanying paper.

Solution acidity measured by pH is an important environmental factor that affects protein structure. It influences the protonation state of protein residues, which in turn may be coupled to protein conformational changes, unfolding, and ligand binding. It remains difficult to compute and measure the p Ka of individual residues, as well as to relate them to pH-dependent protein transitions. This paper presents a hierarchical approach to compute the p Ka of individual protonatable residues, specifically histidines, coupled with underlying structural changes of a protein. A fast and efficient free energy perturbation (FEP) algorithm has also been developed utilizing a fast implementation of standard molecular dynamics (MD) algorithms. Specifically, a CUDA version of the AMBER MD engine is used in this paper. Eight histidine p Ka's are computed in a diverse set of pH stable proteins to demonstrate the proposed approach's utility and assess the predictive quality of the AMBER FF99SB force field. A reference molecule is carefully selected and tested for convergence. A hierarchical approach is used to model p Ka's of the six histidine residues of the diphtheria toxin translocation domain (DTT), which exhibits a diverse ensemble of individual conformations and pH-dependent unfolding. The hierarchical approach consists of first sampling equilibrium conformational ensembles of a protein with protonated and neutral histidine residues via long equilibrium MD simulations (Flores-Canales, J. C.; et al. bioRxiv, 2019, 572040). A clustering method is then used to identify sampled protein conformations, and p Ka's of histidines in each protein conformation are computed. Finally, an ensemble averaging formalism is developed to compute weighted average histidine p Ka's. These can be compared with an apparent experimentally measured p Ka of the DTT protein and thus allows us to propose a mechanism of pH-dependent unfolding of the DTT protein.

The study of triacylglycerols (TAGs) in their molten state is of fundamental importance for a deeper understanding of the TAG crystallization processes, being highly relevant for both manufacturing and medical applications. Although different models have been proposed to explain the nanostructured nature of the fluid state of TAGs, none of them are fully satisfactory. In this paper, we propose a new model consisting of positionally uncorrelated lamellar TAG assemblies embedded in an isotropic medium that assist as prenucleating structures. This model was validated by applying a novel global fitting method, resulting in an excellent agreement with the small-angle X-ray scattering data. A deeper analysis of the scattering patterns at different temperatures, both in cooling and heating directions, allowed us further to detect the crystalline traces of TAGs even after heating to 40 °C and record, on cooling, the onset of crystallization at 30-25 °C. The application of the presented novel model not only explains the outstandingly structured fluid of molten TAGs, but also lays the basis for analyzing first the crystallization steps in greater detail, which is outlined in our follow-up paper "Global Small-Angle X-ray Scattering Data Analysis of Triacylglycerols in the α-Phase (Part II)".

Cyclization is the first step in the chromophore maturation process of the green fluorescent protein (GFP). In our previous paper [J. Phys. Chem. B 2012, 116, 1426-1436], the results of molecular dynamics simulation suggested the possibility that the amide nitrogen atom of Gly67 attacks the carbonyl carbon of Ser65 directly to complete the cyclization process (one-step mechanism). In this paper, density functional theory (DFT) and quantum mechanical/molecular mechanical (QM/MM) calculations were undertaken to study this step reaction in detail. Three cluster model systems (model A, model B, and model C) and large protein system were set up to investigate the cyclization process. Our results indicate that the one-step mechanism only exists in the two minimum models. However, in model C and the large protein system, the cyclization mechanism involves two steps: the first step is proton of Gly67 amide nitrogen transferring to carbonyl oxygen of Ser65, generating protonated amide, which is stabilized by a hydrogen bond interaction with a crystallographic water molecule, and the second step is Gly67 amide nitrogen attacking the carbonyl carbon of Ser65. Arg96 plays an important role in promoting the cyclization. The energy of cyclized product relative to reactant is about 10.0 kcal/mol endothermic, which is in line with the experimental results.

At temperatures below the nominal glass transition temperature Tgα, the structural α-relaxation and the Johari-Goldstein (JG) β-relaxation are too slow to contribute to susceptibility measured at frequencies higher than 1 GHz. This is particularly clear in the neighborhood of the secondary glass transition temperature Tgβ, which can be obtained directly by positronium annihilation lifetime spectroscopy (PALS) and adiabatic calorimetry, or deduced from the temperature at which the JG β-relaxation time τβ reaches 1000 s. The fast process at such high frequencies comes from the vibrations and caged molecules dynamics manifested as the nearly constant loss (NCL) in susceptibility measurements, elastic scattering intensity, I(Q, T), or the mean-square-displacement, ⟨u(2)(T)⟩, in quasielastic neutron scattering experiment. Remarkably, we find for many different glass-formers that the NCL, I, or ⟨u(2)⟩ measured in the glassy state changes its temperature dependence at temperature THF near Tgβ. In paper I (Capaccioli, S.; et al. J. Phys. Chem. B 2015, 119 (28), 8800-8808) we have made known this property in the case of the polyalcohols and a pharmaceutical glass former, flufenamic acid studied by THz dielectric spectroscopy, and explained it by the coupling of the NCL to the JG β-relaxation, and the density dependence of these processes. In this paper II, we extend the consideration of the high frequency response to broader range from 100 MHz to THz in the glassy state of many polymers observed by quasielastic light scattering, Brillouin scattering, quasielastic neutron scattering, and GHz-THz dielectric relaxation. In all cases, the NCL changes its T-dependence at some temperature, THF, below Tgα, which is approximately the same as Tgβ. The latter is independently determined by PALS, or adiabatic calorimetry, or low frequency dielectric and mechanical spectroscopy. The property, THF ≈ Tgβ, had not been pointed out before by others or in any of the quasielastic neutron and light scattering studies of various amorphous polymers and van der Waals small molecular glass-formers over the past three decades. The generality and fundamental importance of this novel property revitalize the data from these previous publications, making it necessary to be reckoned with in any attempt to solve the glass transition problem. In our rationalization, the property arises first from the fact that the JG β-relaxation and the caged dynamics both depends on density and entropy. Second, the JG β-relaxation is the terminator of the caged dynamics, and hence the two processes are inseparable or effectively coupled. Consequently, the occurrence of the secondary glass transition at Tgβ necessarily is accompanied by corresponding change in the temperature dependence of the NCL, I, or ⟨u(2)⟩ of the fast caged dynamics at THF ≈ Tgβ.

This paper presents a simple but general analytical estimate of the characteristic time of crossing a long, high, and arbitrary bumpy free energy barrier in the course of a sequential (one-dimensional) chemical, biochemical, or physical reaction. This estimate is based on a generalized steady-state approach developed in this paper.

In this paper, the interaction of rhodamine123 (R123) with calf thymus DNA has been studied using molecular modeling and other biophysical methods like UV-vis spectroscopy, fluoremetry, optical melting, isothermal titration calorimetry, and circular dichroic studies. Results showed that the binding energy is about -6 to -8 kcal/mol, and the binding process is favored by both negative enthalpy change and positive entropy change. A new method to determine different thermodynamic properties like calorimetric enthalpy and heat capacity change has been introduced in this paper. The obtained data has been crossed-checked by other methods. After dissecting the free-energy contribution, it was observed that the binding was favored by both negative hydrophobic free energy and negative molecular free energy which compensated for the positive free energies due to the conformational change loss of rotational and transitional freedom of the DNA helix.

Polyelectrolytes continue to find wide interest and application in science and engineering, including areas such as water purification, drug delivery, and multilayer thin films. We have been interested in the dynamics of small molecules in a variety of polyelectrolyte (PE) environments; in this paper, we report simulations and analysis of the small dye molecule rhodamine B (RB) in several very simple polyelectrolyte solutions. Translational diffusion of the RB zwitterion has been measured in fully atomistic, 2 μs long molecular dynamics simulations in four different polyelectrolyte solutions. Two solutions contain the common polyanion sodium poly(styrene sulfonate) (PSS), one with a 30-mer chain and the other with 10 trimers. The other two solutions contain the common polycation poly(allyldimethylammonium) chloride (PDDA), one with two 15-mers and the other with 10 trimers. RB diffusion was also simulated in several polymer-free solutions to verify its known experimental value for the translational diffusion coefficient

Two selected ammonium-based ionic liquids, 2-hydroxyethyltrimethylammonium L-(+)-lactate and tris(2-hydroxyethyl)methylammonium methylsulfate, were fully characterized. The most relevant thermophysical properties of pure fluids were measured and analyzed as a function of temperature. Structural features were inferred from solvatochromic and Fourier transform infrared (FTIR) studies. Moisture absorption ability was also studied by gravimetric, spectroscopic, and Karl Fischer methods. Likewise, the water effect on fluids properties was analyzed. Polarity was studied by approaches based on solvatochromic measurements and on the water effect on FTIR spectra. Moreover, as computational work, quantum chemistry and molecular dynamics simulation methods were used to analyze the main molecular-level structural features in these fluids. The work is divided into two parts; in this first paper, the main objective is fully characterizing these ionic liquids in the pure state, and in the second paper CO(2) absorption will be analyzed, therefore leading to a deep knowledge of factors controlling structuring, properties, and CO(2) absorption for this family of ionic liquids in comparison with available information for other relevant types of ionic liquids.

In this paper, a theoretical model for diffusion in Lennard-Jones fluids over a larger density range is proposed. Instead of looking at molecular transport in real space, we treat molecular transport in radial distribution function space. Specifically, the radial distribution function, which reflects the static properties of the system, is used to calculate the mean free path of molecules, a key physical quantity for diffusion modeling. Then, on the basis of the rarefied hard sphere gas diffusion model, and with consideration of the correction of collision frequency and backscattering effect caused by the higher density, the expression of self-diffusion coefficient in Lennard-Jones fluid is obtained. Molecular dynamics was used to simulate the diffusion in Lennard-Jones fluids in a wide range of reduced densities from 0.298 to 1.19 and reduced temperatures from 0.833 to 1.67. Except for small deviations at very high densities, the simulation results agree with the model predictions when the temperature is not too low.

The 3D reference interaction site model (3DRISM) provides an efficient grid-based solvation model to compute the structural and thermodynamic properties of biomolecules in aqueous solutions. However, it remains challenging for existing 3DRISM methods to correctly predict water distributions around negatively charged solute molecules. In this paper, we first show that this challenge is mainly due to the orientation of water molecules in the first solvation shell of the negatively charged solute molecules. To properly consider this orientational preference, position-dependent two-body intramolecular correlations of solvent need to be included in the 3DRISM theory, but direct evaluations of these position-dependent two-body intramolecular correlations remain numerically intractable. To address this challenge, we introduce the Ion-Dipole Correction (IDC) to the 3DRISM theory, in which we incorporate the orientation preference of water molecules via an additional solute-solvent interaction term (i.e., the ion-dipole interaction) while keeping the formulism of the 3DRISM equation unchanged. We prove that this newly introduced IDC term is equivalent to an effective direct correlation function which can effectively consider the orientation effect that arises from position dependent two-body correlations. We first quantitatively validate our 3DRISM-IDC theory combined with the PSE3 closure on Cl

Graphene oxide (GO), a nanomaterial with promising applications that range from water purification to enzyme immobilization, is actively present in scientific research since its discovery. GO studies with computational methodologies such as molecular dynamics are frequently reported in the literature; however, the models used often rely on approximations, such as randomly placing functional groups and the use of generalized force fields. Therefore, it is important to develop new MD models that provide a more accurate description of GO structures and their interaction with an aqueous solvent and other adsorbate molecules. In this paper, we derived new force field non-bonded parameters from linear-scaling density functional theory calculations of nanoscale GO sheets with more than 10,000 atoms through an atoms-in-molecules (AIM) partitioning scheme. The resulting GAFF2-AIM force field, derived from the bonded terms of GAFF2 parameterization, reproduces the solvent structure reported in ab initio MD simulations better than the force field nowadays widely used in the literature. Additionally, we analyzed the effect of the ionic strength of the medium and of the C/O ratio on the distribution of charges surrounding the GO sheets. Finally, we simulated the adsorption of natural amino acid molecules to a GO sheet and estimated their free energy of binding, which compared very favorably to their respective experimental values, validating the force field presented in this work.

Polarizability, or the tendency of the electron distribution to distort under an electric field, often depends on the local chemical environment. For example, the polarizability of a chloride ion is larger in gas phase compared to a chloride ion solvated in water. This effect is due to the restriction the Pauli exclusion principle places on the allowed electron states. Because no two electrons can occupy the same state, when a highly polarizable atom comes in close contact with other atoms or molecules, the space of allowed states can dramatically decrease. This constraint suggests that an accurate molecular mechanics polarizability model should depend on the radial distance between neighboring atoms. This paper introduces a variable polarizability model within the framework of the HIPPO (Hydrogen-like Intermolecular Polarizable Potential) force field, by damping the polarizability as a function of the orbital overlap of two atoms. This effectively captures the quantum mechanical exchange polarization effects, without explicit utilization of antisymmetrized wave functions. We show that the variable polarizability model remarkably improves the two-body polarization energies and three-body energies of ion-ion and ion-water systems. Under this model, no manual tuning of atomic polarizabilities for monatomic ions is required; the gas-phase polarizability can be used because an appropriate damping function is able to correct the polarizability at short range.

One of the most important areas of medical science is oncology, which is responsible for both the diagnostics and treatment of cancer diseases. Over the years, there has been an intensive development of cancer diagnostics and treatment. This paper shows the comparison of normal (CCD-18Co) and cancerous (CaCo-2) cell lines of the human gastrointestinal tract on the basis of nanomechanical and biochemical properties in order to obtain information on the cancer biomarkers useful in oncological diagnostics. The research techniques used were: Atomic Force Microscopy and Raman spectroscopy and imaging. In addition, the studies included also the effect of the statins compounds: mevastatin, lovastatin and simvastatin and their influence on nanomechanical and biochemical changes of properties of cells tracking using AFM and Raman imaging techniques. The cytotoxicity of mevastatin and lovastatin was determined by using XTT tests.

This paper presents a general protocol for the interpretation of the electric surface potential of Langmuir monolayers based on a three-layer capacitor model. The measured values were correlated with the results from DFT molecular dynamics simulations, and, as a result, the local dielectric permittivities and dipole-moment components of molecules organized in the monolayer were obtained. The main advantage of the developed approach is applicability to amphiphiles of any type; irrespective of the structure of the polar head as well as the molecular organization and inclination in the surface film. The developed methodology was successively applied to an atypical surface-active compound, perfluorodecyldecane, and its derivatives containing the hydroxyl, thiol, and carboxyl moiety. The following contributions to the apparent dipole moments connected with the reorientation of water molecules and local dielectric permittivities in the vicinity of polar and apolar molecule parts, respectively, were determined: μ

Vibrational sum frequency generation (SFG) spectroscopy can specifically probe molecular species non-centrosymmetrically arranged in a centrosymmetric or isotropic medium. This capability has been extensively utilized to detect and study molecular species present at the two-dimensional (2D) interface at which the centrosymmetry or isotropy of bulk phases is naturally broken. The same principle has been demonstrated to be very effective for the selective detection of non-centrosymmetric crystalline nanodomains interspersed in three-dimensional (3D) amorphous phases. However, the full spectral interpretation of SFG features has been difficult due to the complexity associated with the theoretical calculation of SFG responses of such 3D systems. This paper describes a numerical method to predict the relative SFG intensities of non-centrosymmetric nanodomains in 3D systems as functions of their size and concentration as well as their assembly patterns, i.e., the distributions of tilt, azimuth, and rotation angles with respect to the lab coordinate. We applied the developed method to predict changes in the CH and OH stretch modes characteristic to crystalline cellulose microfibrils distributed with various orders, which are relevant to plant cell wall structures. The same algorithm can also be applied to any SFG-active nanodomains interspersed in 3D amorphous matrices.

The earlier paper of this same title demonstrated a collapse of relaxation data of fragile supercooled glass forming liquids [\textit{J. Phys. Chem. B} \textbf{113}, 5563-5567 (2009)]. For temperature $T$ below that of the onset to supercooled behavior, $T_{\mathrm{o}}$, the logarithm of structural relaxation time, $\log \tau$, is given by the parabolic form $\log (\tau/\tau_{\mathrm{o}}) \, =\, J^2(1/T - 1/T_{\mathrm{o}})^{2}$, where $J$ and $\tau_{\mathrm{o}}$ are temperature independent. This paper presents further applications of this formula. In particular, it is shown that the effects of attractive forces in numerical simulation of glass forming liquids can be logically organized in terms of $J$ and $T_{\mathrm{o}}$. Further, analysis of experimental data for several systems suggests that $J$ and $T_{\mathrm{o}}$ are material properties. In contrast, values of similar parameters for other fitting formulas are shown to depend not only upon the material but also upon the range of data used in fitting these formulas. Expressions demonstrated to fail in this way include the Vogel-Fulcher-Tammann formula, a double-exponential formula, and a fractional exponential formula., Comment: 9 pages, 6 figures

Due to its unmatched hardness and chemical inertia, diamond offers many advantages over other materials for extreme conditions and routine analysis by attenuated total reflection (ATR) infrared spectroscopy. Its low refractive index can offer up to a 6-fold absorbance increase compared to germanium. Unfortunately, it also results for strong bands in spectral distortions compared to transmission experiments. The aim of this paper is to present a methodological approach to determine quantitatively the degree of the spectral distortions in ATR spectra. This approach requires the determination of the optical constants (refractive index and extinction coefficient) of the investigated sample. As a typical example, the optical constants of the fibroin protein of the silk worm Bombyx mori have been determined from the polarized ATR spectra obtained using both diamond and germanium internal reflection elements. The positions found for the amide I band by germanium and diamond ATR are respectively 6 and 17 cm(-1) lower than the true value dtermined from the k(nu) spectrum, which is calculated to be 1659 cm(-1). To determine quantitatively the effect of relevant parameters such as the film thickness and the protein concentration, various spectral simulations have also been performed. The use of a thinner film probed by light polarized in the plane of incidence and diluting the protein sample can help in obtaining ATR spectra that are closer to their transmittance counterparts. To extend this study to any system, the ATR distortion amplitude has been evaluated using spectral simulations performed for bands of various intensities and widths. From these simulations, a simple empirical relationship has been found to estimate the band shift from the experimental band height and width that could be of practical use for ATR users. This paper shows that the determination of optical constants provides an efficient way to recover the true spectrum shape and band frequencies of distorted ATR spectra.

Structural information such as orientations of interfacial proteins and peptides is important for understanding properties and functions of such biological molecules, which play crucial roles in biological applications and processes such as antimicrobial selectivity, membrane protein activity, biocompatibility, and biosensing performance. The alpha-helical and beta-sheet structures are the most widely encountered secondary structures in peptides and proteins. In this paper, for the first time, a method to quantify the orientation of the interfacial beta-sheet structure using a combined attenuated total reflectance Fourier transformation infrared spectroscopic (ATR-FTIR) and sum frequency generation (SFG) vibrational spectroscopic study was developed. As an illustration of the methodology, the orientation of tachyplesin I, a 17 amino acid peptide with an antiparallel beta-sheet, adsorbed to polymer surfaces as well as associated with a lipid bilayer was determined using the regular and chiral SFG spectra, together with polarized ATR-FTIR amide I signals. Both the tilt angle (theta) and the twist angle (psi) of the beta-sheet at interfaces are determined. The developed method in this paper can be used to obtain in situ structural information of beta-sheet components in complex molecules. The combination of this method and the existing methodology that is currently used to investigate alpha-helical structures will greatly broaden the application of optical spectroscopy in physical chemistry, biochemistry, biophysics, and structural biology.

The dissipative vibrational dynamics of a symmetric triatomic ABA molecule is extensively studied in a series of three papers. The momentum-dependent rotor model is used to describe the dynamical behavior of an ABA molecule with a single 1:1 nonlinear resonant coupling. Four characteristic modes, including symmetric normal modes, asymmetric normal modes, local modes, and quasi-local modes, are identified at different energy regimes. Under the influence of thermal noise, an ABA molecule switches between the four distinct modes intermittently along its dynamic trajectory, resulting in blinking of vibrational bond energy. The statistics of these dynamic transitions (i.e., "vibrational blinking") is obtained from numerical integration of stochastic equations in this paper and will be analyzed within the theoretical framework of noise-induced symmetry breaking and activated barrier crossing in the next two papers. This study demonstrates the rich dynamic behavior of a highly nonlinear system in a dissipative environment and is instructive for understanding the stability and stochasticity of energy localization in complex systems ranging from polyatomic molecules to nanostructures and micromechanical oscillators.

This paper has been withdrawn by the authors due to a copyright conflict with the Journal of Physical Chemistry B, to which it has been submitted., Comment: This paper is withdrawn due to copyright issues; the paper can be found at J. Phys. Chem. B 114, 5404 (2010)

In this paper two kinds of Bragg reflections from oriented mesogenic crystals are considered. Bragg reflections behave differently for ...ABABA... and ...ABCABCA... layer stacking. We call them black and white reflections. Black reflections are characterized by the fact that they behave identical for the two kinds of stacking. Therefore, the message is the following: Black rods should not be used to identify the two kinds of stacking. By contrast, white reflections show a different behavior for ...ABABA... and ...ABCABCA... stacking and for the resulting hexagonal close-packed (hcp) and face-centered cubic (fcc) crystals. White reflections can be used to distinguish the two kinds of crystals. For an application of this method the crystals should be oriented. It will be shown that orienting by flow is possible in a Couette cell. Flow ordering occurs in all rotation cells which are often applied in rheology. The scattering presented is therefore closely related to rheology. Details and experimental results will be given in the paper.

It is demonstrated that it is possible to coat the individual fibers of wood-based nanocellulose with polypyrrole using in situ chemical polymerization to obtain an electrically conducting continuous high-surface-area composite. The experimental results indicate that the high surface area of the water dispersed material, to a large extent, is maintained upon normal drying without the use of any solvent exchange. Thus, the employed chemical polymerization of polypyrrole on the microfibrillated cellulose (MFC) nanofibers in the hydrogel gives rise to a composite, the structure of which-unlike that of uncoated MFC paper-does not collapse upon drying. The dry composite has a surface area of approximately 90 m(2)/g and a conductivity of approximately 1.5 S/cm, is electrochemically active, and exhibits an ion-exchange capacity for chloride ions of 289 C/g corresponding to a specific capacity of 80 mAh/g. The straightforwardness of the fabrication of the present nanocellulose composites should significantly facilitate industrial manufacturing of highly porous, electroactive conductive paper materials for applications including ion-exchange and paper-based energy storage devices.

This paper addresses the experimentally observed mechanistic differences between the cytochrome P450-catalyzed N-demethylation of substituted N,N-dimethylanilines (DMA) and of N,N-dimethylbenzamides (DMBA). The two reactions of these substrates are initiated by C-H activation of the methyl groups on the nitrogen. Thus, the DMA reactions exhibit small deuterium kinetic isotope effects (KIEs), and these KIEs and the corresponding reaction rates exhibit a linear response to the electronic nature of the para substituent. By contrast, the DMBA reactions exhibit large KIEs; the KIEs and reaction rates do not at all respond to the nature of the para substituent. Accordingly, the present paper uses density functional theoretical calculations to address these reactivity patterns in para-substituted DMBA and compare these results to those obtained for the DMA reactions previously (Wang, Y.; Kumar, D.; Yang, C. L.; Han, K. L.; Shaik, S. J. Phys. Chem. B 2007, 111, 7700). The theoretical calculations reproduce the experimental trends of narrow variations in rates and KIEs. It is shown that the above mechanistic differences between the two reaction series of DMA and DMBA are caused by the ability of the para substituent to maintain a conjugation path between the C-H reaction center and the aryl moiety. Furthermore, the computational results show a new feature of reactivity, namely, that the N-demethylation of DMBA proceeds by a spin-selective reaction via the high spin state of the active species of the enzyme. This conclusion is reinforced by the match of the calculated and experimental KIE values.

This paper offers a theoretical explanation of the coupling effect phenomenon between mechanical loading and chemical reactions based on linear nonequilibrium thermodynamics and also discusses the classical method of obtaining restrictions on the phenomenological coefficients. The question whether static or dynamic loading influences biochemical processes is addressed-the necessity of dynamic loading as a stimulatory mechanism is shown. Further, the presented paper suggests that chemical and mechanical processes do not only facilitate or support one another but they may also play a triggering role for the other coupled process-some biochemical processes may need mechanical stimulation to run and vice versa as well-chemical reactions may provide energy for some mechanical processes. As an example, a detailed analysis of a model for controlled autocatalytic reproduction is presented, where the coupling effect, i.e. the influence of dynamic loading on reaction kinetics, is demonstrated.

In this paper, we study the collapse of a mixed insoluble monolayer formed by a cationic matrix, dioctadecyl-dimethylammonium bromide (DOMA), and a tetra-anionic porphyrin, tetrakis(4-sulfonatophenyl)porphyrin (TSPP), in a molar ratio TSPP/DOMA = 1:4. During the collapse of this system, we visualized the formation of circular domains consisting exclusively of trilayer, although the domains coalescence was not observed. The coexistence of trilayer and monolayer at the final step of the collapse cannot be interpreted exclusively in terms of a thermodynamic phase equilibrium, intervening as an additional factor the anisotropic line tension of the domain. A high line tension implies a high resistance to the domain deformation, and the anisotropy of the line tension implies the lack of coalescence between these domains, which has been experimentally observed by Brewster angle microscopy for us. Under these circumstances, the domains of collapsed material could enclose monolayer regions where the local surface pressure drops thus stopping the collapse process. The collapse of the TSPP/DOMA system is reversible, that is, the return of the three-dimensional material to the monolayer fits into a simple kinetics according to the nucleation-growth-collision theory. As for the collapse, the reverse process is also affected by the line tension of the domains. This paper relates the high line tension and the anisotropic line tension of a given domains with the reversible nature of the collapse process.

In this paper we explore the effects of water dissociation and CO2 contamination on the electrical conductivity of salt-free concentrated suspensions in static electric fields. The conductivity model here presented is based on a new description of the equilibrium double layer for particles in "realistic" salt-free suspensions recently developed by the authors to account for the latter effects (Ruiz-Reina, E.; Carrique, F. J. Phys. Chem. B 2008, 112, 11960). It was shown that in most of the cases the neglecting of those effects would lead to a very poor description of common salt-free suspensions, especially, but not only, if the suspensions have been in contact with air. As shown in this paper, the presence of only water dissociation ions suffices to provoke very important changes in the standard salt-free predictions. A realistic aqueous salt-free suspension consists of an aqueous suspension without any electrolyte added during the preparation but including the following ionic species: (i) the "added counterions" stemming from the particle charging process that counterbalance their surface charge (with just this ionic species, the suspension can be considered as an ideal or pure salt-free one), (ii) the H+ and OH- ions from water dissociation, and (iii) the ions produced by the atmospheric CO2 contamination. The model is based on the classical Poisson-Boltzmann theory, the appropriate local chemical reactions, the standard electrokinetic equations, and the cell model approximation to account for electro-hydrodynamic particle-particle interactions. Thus, we have studied the electrical conductivity of such realistic salt-free suspensions for different particle volume fraction phi and surface charge density sigma, and compared it with results of pure salt-free conductivity predictions. The numerical results have shown that water dissociation ions and/or CO2 contamination has an extreme influence on the suspension conductivity values at low-moderate particle volume fractions. In these situations the role of the added counterions is screened by the other ionic species. Even if the suspensions have not been exposed to the atmosphere, the quantitative changes in conductivity at low volume fractions associated with the presence of water dissociation ions over the added counterions are enormous. It is concluded that it is necessary to take into account the water dissociation influence for phi lower than approximately 10(-2)-10(-3), whereas the atmospheric CO2 contamination is not negligible if phi

The loop 287-290 (Ile, Phe, Arg, and Phe) of the protein acetylcholinesterase (AChE) changes its structure upon interaction of AChE with diisopropylphosphorofluoridate (DFP). Reversible dissociation measurements suggest that the free-energy (F) penalty for the loop displacement is DeltaF=Ffree-Fbound approximately -4 kcal/mol. Therefore, this loop has been the target of two studies by Olson's group for testing the efficiency of procedures for calculating F. In this paper, we test for the first time the performance of our "hypothetical scanning molecular dynamics" (HSMD) method and the validity of the related modeling for a loop with bulky side chains in explicit water. Thus, we consider only atoms of the protein that are the closest to the loop (they constitute the "template"), where the rest of the atoms are ignored. The template's atoms are fixed in the X-ray coordinates of the free protein, and the loop is capped with a sphere of TIP3P water molecules; also, the X-ray structure of the bound loop is attached to the free template. We carry out two separate MD simulations starting from the free and bound X-ray structures, where only the atoms of the loop and water are allowed to move while the template-water and template-loop (AMBER) interactions are considered. The absolute Ffree and Fbound (of the loop and water) are calculated from the corresponding trajectories. A main objective of this paper is to assess the reliability of this model, and for this several template sizes are studied capped with 80-220 water molecules. We find that consistent results for the free energy (which also agree with the experimental data above) require a template larger than a minimal size and a number of water molecules approximately equal to the experimental density of bulk water. For example, we obtain DeltaFtotal=DeltaFwater+DeltaFloop=-3.1+/-2.5 and -3.6+/-4 kcal/mol for a template consisting of 944 atoms and a sphere containing 160 and 180 waters, respectively. Our calculations demonstrate the important contribution of water to the total free energy. Namely, for water densities close to the experimental value, DeltaFwater is always negative leading thereby to a negative DeltaFtotal (while DeltaFloop is always positive). Also, the contribution of the water entropy TDeltaSwater to DeltaFtotal is significant. Various aspects related to the efficiency of HSMD are tested and improved, and plans for future studies are discussed.

This paper reports a methodology for analyzing the solvent effect from empirical measurements of solvent acidity (SA), basicity (SB), dipolarity (SdP), and polarizability (SP). The proposed methodology departs from the traditional single-parameter procedures for estimating nonspecific solvent effects by splitting them into a polarizability term and a dipolarity term. In this work, we examined the SA, SB, SP, and SdP values for 160 solvents, the gas phase (the absence of solvent) being the origin of these scales. As shown in this paper, this information allows one not only to accurately describe the solvent effect experienced by any solute whether polar or nonpolar and exhibiting some or no specific interaction with the solvent but also to understand the nature of the well-known solvent parameters E(T)(30), pi, S', and SPP, which are frequently used to describe the overall nonspecific contribution of solvents in terms of a single parameter. The high potential of the proposed empirical methodology is illustrated with its application to the solvatochromic analysis of the spectroscopic behavior of molecular chromophores, thus explaining, for example, the influence of solvent effects in the twist intramolecular charge transfer (TICT), the excited-state intramolecular proton transfer (ESIPT), or LASER (light amplification by stimulated emission of radiation) emissions. Also, this methodology is applied to understanding for the indole chromophore the feasible inversion of the electronic nature for the first electronic excited state due to solvent effects.