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Reverse micelles as nanoreactors have been most successful in designing nanostructures of different sizes and shapes. Nevertheless, important questions regarding the explicit roles of intrinsic parameters in modifying soft colloid templates which eventually give rise to variety of nanostructures are still unresolved. In this paper, we have focused on this challenging aspect of microemulsion based synthesis of nanostructures, i.e., how the tunable parameters like water to surfactant molar ratio, solvent properties, and surfactant structure modify the microstructure (size/shape) of reverse micelles (surfactant/cosurfactant/oil/water). Further, we have elucidated the correlation between these nanoreactors with the size and morphology of the evolving nanostructures within the aqueous core (using in situ studies) as well as the finally obtained nanostructures. We have employed fluorescence correlation spectroscopy (FCS), small-angle X-ray scattering (SAXS), dynamic light scattering (DLS), and transmission electron microscopy (TEM) to obtain details on the microstructural transformation of reverse micelles and their templating behavior on designing nanostructures, at (near) single droplet level and in an ensemble. The structure (size/shape) of nanoreactors, i.e., reverse micelles, finally guides the size and shape of nanostructures. As the water content increases, it induces the micellar growth and subsequently the growth of nanostructures develops linearly up to a critical value beyond which the finite bending modulus of surfactant film triggers the structural rearrangement of microemulsion droplets (MEDs) and the linear plot shows deviation. Bulkiness of the solvent molecules modulates the ME droplets, and MEDs encapsulates nanostructures by influencing the curvature and rigidity of the surfactant film and results in smaller dimensions of the micellar core, which leads to nanostructures with large aspect ratio. The origin of this structural evolution may be explained in terms of solvent molecular structure, which affects the penetrability of solvent molecules into the surfactant tail region. Interestingly, MEDs with cationic surfactants feature the onset of one-dimensional micellar growth and the shape evolves into a nearly prolate spheriod. Consequently, the growth of the micellar core and dynamical exchange in an anisotropic manner leads to the formation of nanorods. The implication of such studies could be far reaching due to the geometry-dependent novel properties and potential applications of anisotropic nanostructures.

Iodide-based ionic liquids have been widely employed as iodide sources in electrolytes for applications utilizing the triiodide/iodide redox couple. While adding a low-viscosity solvent such as water to ionic liquids can greatly enhance their usefulness, mixtures of highly viscous iodide-containing ILs with water have never been studied. This paper investigates, for the first time, mixtures of water and the ionic liquid 1-butyl-3-methylimidazolium iodide ([BMIM][I]) through a combined experimental and molecular dynamics study. The density, melting point, viscosity, and conductivity of these mixtures were measured by experiment. The composition region below 50% water by mole was found to differ dramatically from the region above 50% water, with trends in density and melting point differing before and after that point. Water was found to have a profound effect on viscosity and conductivity of the IL, and the effect of hydrogen bonding was discussed. Molecular dynamics simulations representing the same mixture compositions were performed. Molecular ordering was observed, as were changes in this ordering corresponding to water content. Molecular ordering was related to the experimentally measured mixture properties, providing a possible explanation for the two distinct composition regions identified by experiment.

In this paper, we present the first computer simulation of methanol exchange dynamics between the first and second solvation shells around different cations and anions. After water, methanol is the most frequently used solvent for ions. Methanol has different structural and dynamical properties than water, so its ion solvation process is different. To this end, we performed molecular dynamics simulations using polarizable potential models to describe methanol-methanol and ion-methanol interactions. In particular, we computed methanol exchange rates by employing the transition state theory, the Impey-Madden-McDonald method, the reactive flux approach, and the Grote-Hynes theory. We observed that methanol exchange occurs at a nanosecond time scale for Na(+) and at a picosecond time scale for Cs(+), Cl(-), and I(-). We also observed a trend in which, for like charges, the exchange rate is slower for smaller ions because they are more strongly bound to methanol.

Charge transfer and proton transfer in DNA have attracted wide attention due to their relevance in biological processes and so on. Especially, excess-electron transfer (EET) in DNA has strong relation to DNA repair. However, our understanding on EET in DNA still remains limited. Herein, by using a strongly electron-donating photosensitizer, trimer of 3,4-ethylenedioxythiophene (3E), and an electron acceptor, diphenylacetylene (DPA), two series of functionalized DNA oligomers were synthesized for investigation of EET dynamics in DNA. The transient absorption measurements during femtosecond laser flash photolysis showed that guanine:cytosine (G:C) base pair affects EET dynamics in DNA by two possible mechanisms: the excess-electron quenching by proton transfer with the complementary G after formation of C(•-) and the EET hindrance by inserting a G:C base pair as a potential barrier in consecutive thymines (T's). In the present paper, we provided useful information based on the direct kinetic measurements, which allowed us to discuss EET through oligonucleotides for the investigation of DNA damage/repair.

The understanding of the interaction of nanoplastics with living organisms is crucial both to assess the health hazards of degraded plastics and to design functional polymer nanoparticles with biomedical applications. In this paper, we develop two coarse-grained models of everyday use polymers, polyethylene (PE) and polypropylene (PP), aimed at the study of the interaction of hydrophobic plastics with lipid membranes. The models are compatible with the popular MARTINI force field for lipids, and they are developed using both structural and thermodynamic properties as targets in the parametrization. The models are then validated by showing their reliability at reproducing structural properties of the polymers, both linear and branched, in dilute conditions, in the melt, and in a PE-PP blend. PE and PP radius of gyration is correctly reproduced in all conditions, while PE-PP interactions in the blend are slightly overestimated. Partitioning of PP and PE oligomers in phosphatidylcholine membranes as obtained at CG level reproduces well atomistic data.

Mixtures of methyltetrahydrofuran (MTHF) with tristyrene and high molecular weight polystyrene involve an exceptionally large difference in the glass transition temperatures of the two components not realized in other binary mixtures studied before. The extensive study of the molecular dynamics of these mixtures by various experimental techniques by Blochowicz et al. has revealed the presence of a new α'-relaxation not found before in other mixtures and also the more familiar α- and β-relaxations, but their properties are more extreme. Attention was focused on the new α'-relaxation by Blochowicz et al. in interpreting it to originate from MTHF in confinement and explaining its properties by the Mode Coupling Theory. In a different direction, we concentrate on the highly unusual properties of the α- and β-relaxations. Earlier, we had success in explaining the properties of these two relaxations and their connection in other mixtures by the coupling model. In this paper, we apply the same model to explain the highly unusual dynamics of the α- and β-relaxations found in the mixtures of MTHF with tristyrene and polystyrene. Possible relation between the α'- and the β-relaxations also is explored.

Superhydrophobic/hydrophobic surfaces have attracted wide attention because of their broad applications in various regions, including coating, textile, packaging, electronic devices, and bioengineering. Many studies have been focused on the fabrication of superhydrophobic/hydrophobic surfaces using natural materials. In this paper, superhydrophobic/hydrophobic surfaces were formed by an amphiphilic natural protein, zein, using electrospinning. Water contact angle (WCA) and scanning electron microscopy (SEM) were used to characterize the hydrophobicity and surface morphology of the electrospun structures. The highest WCA of the zein electrospun surfaces could reach 155.5 ± 1.4°. To further understand the mechanism of superhydrophobic surface formation from amphiphiles using electrospinning, a synthetic amphiphilic polymer was selected, and also, a method similar to electrospinning, spray drying, was tried. The electrospun amphiphilic polymer surface showed a high hydrophobicity with a WCA of 141.4 ± 0.7°. WCA of the spray-dried zein surface could reach 125.3 ± 2.1°. The secondary structures of the zein in the electrospun film and cast-dried film were studied using ATR-FTIR, showing that α-helix to β-sheet transformation happened during the solvent evaporation in the cast drying process but not in the electrospinning process. A formation mechanism was proposed on the basis of the orientation of the amphiphiles during the solvent evaporation of different fabrication methods. The droplet-based or jet-based evaporation during electrospinning and spray drying led to the formation of the superhydrophobic/hydrophobic surface by the accumulation of the hydrophobic groups of the amphiphiles on the surface, while the surface-based evaporation during cast drying led to the formation of the hydrophilic surface by the accumulation of the hydrophilic groups of the amphiphiles on the surface.

Self-assembly of Aβ peptides into amyloid aggregates has been suggested as the major cause of Alzheimer's disease (AD). Nowadays, there is no medication for AD, but experimental data indicate that reversion of the process of amyloid aggregation reduces the symptoms of disease. In this paper, all 8000 tripeptides were studied for their ability to destroy Aβ fibrils. The docking method and the more sophisticated MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) method were employed to calculate the binding affinity and mode of tripeptides to Aβ fibrils. The ability of these peptides to depolymerize Aβ fibrils was also investigated experimentally using atomic force microscopy and fluorescence spectroscopy (Thioflavin T assay). It was shown that tripeptides prefer to bind to hydrophobic regions of 6Aβ9-40 fibrils. Tripeptides WWW, WWP, WPW and PWW were found to be the most potent binders. In vitro experiments showed that tight-binding tripeptides have significant depolymerizing activities and their DC50 values determined from dose-response curves were in micromolar range. The ability of nonbinding (GAM, AAM) and weak-binding (IVL and VLA) tripeptides to destroy Aβ fibrils was negligible. In vitro data of tripeptide depolymerizing activities support the predictions obtained by molecular docking and all-atom simulation methods. Our results suggest that presence of multiple complexes of heterocycles forming by tryptophan and proline residues in tripeptides is crucial for their tight binding to Aβ fibrils as well as for extensive fibril depolymerization. We recommend PWW for further studies as it has the lowest experimental binding constant.

In the present paper, the impact of dodecyl maltoside (C12G2) on the association of sodium poly(styrenesulfonate) (PSS) with dodecyl- and hexadecyltrimethylammonium bromides (DTAB and CTAB) was studied. A low amount of nonionic surfactant enhances the binding of the investigated cationic amphiphiles on PSS, reducing the cationic surfactant-to-polyanion ratio needed for charge neutralization and precipitation. This effect is more pronounced for DTAB than for CTAB due to the considerably higher free surfactant concentration of the former cationic amphiphile. The synergistic surfactant binding also affects the nonequilibrium features of PSS/CTAB association via enhancing the kinetically stable concentration range of overcharged polyion/surfactant nanoparticle dispersions. With increasing C12G2 concentration, however, an opposite effect of the uncharged additive dominates. Namely, the CTAB molecules are solubilized excessively into mixed surfactant micelles, which reduces the surface charge of the PSS/CTAB/C12G2 nanoparticles and thus destabilizes their dispersion. At appropriately large nonionic surfactant concentrations, the binding of CTAB is largely reduced, resulting in the redissolution of the precipitate. In contrast, neither the destabilization nor the resolubilization effects of the added dodecyl maltoside were observed for the PSS/DTAB system due to the much lower driving force of DTAB binding compared to CTAB. Our results clearly demonstrate that the alkyl chain length of the ionic amphiphile has a pronounced effect on both the equilibrium and nonequilibrium aspects of polyion/mixed surfactant complexation which might be further exploited in various next generation applications.

G-quadruplexes are four-stranded structures of nucleic acids that are formed from the association of guanine nucleobases into cyclical arrangements known as tetrads. G-quadruplexes are involved in a host of biological processes and are of interest in nanomaterial applications. However, not much is known about their electronic properties. In this paper, we analyze electronic excited states of G-quadruplexes using a combination of time-dependent DFT calculations and molecular dynamics simulations. We systematically consider experimentally observed arrangements of stacked guanine tetrads. The effects of structural features on exciton delocalization and photoinduced charge separation are explored using a quantitative analysis of the transition electron density. It is shown that collective coherent excitations shared between two guanine nucleobases dominate in the absorption spectrum of stacked G-tetrads. These excitations may also include a significant contribution of charge transfer states. Large variation in exciton localization is also observed between different structures with a general propensity toward localization between two bases. We reveal large differences in how charge separation occurs within different nucleobase arrangements, with some geometries favoring separation within a single tetrad and others favoring separation between tetrads. We also investigate the effects of the coordinating K+ ion located in the central cavity of G-quadruplexes on the relative excited state properties of such systems. Our results demonstrate how the nature of excited states in G-quadruplexes depends on the nucleobase stacking geometry resulting from the mutual arrangement of guanine tetrads his research was funded by Nanyang Technological grants (A.T.P. and M.-E.M.-B.) and by the grant CTQ2011-26573 from Ministry of Science and Innovation, Spain (A.A.V.)

In this paper, we report a micelle-to-vesicle transition in aqueous solution of the anionic single-tailed surfactant (STS) sodium dodecylbenzenesulfonate (SDBS), with the mediation of a rough glass surface (RGS) in the absence of cosurfactants or additives. This transition produced a mixed solution of vesicles and micelles. Interestingly, the obtained SDBS vesicles in the solution displayed good stability during a long-term storage (at least 6 months at room temperature), exposure to high temperature (80 °C for 2 h), and freeze-thawing (-20 or -196 °C for 2 h to approximately 25 °C) after the RGS was removed. Our results confirmed that SDBS could adsorb on the RGS to form bilayers, in which the molecular packing parameter of SDBS was in the range of 1/2-1. The bilayer adsorption and the roughness of the solid surface played an important role in the vesicle formation. In addition, we propose a possible mechanism for the RGS-mediated transition of micelle-to-vesicle in SDBS solutions: SDBS micelles and molecules adsorb on the RGS to form curved bilayers; the curved bilayers detach from the RGS, and then close to form vesicles.

The flavin-containing enzyme monoamine oxidase (MAO) is essential for the enzymatic decomposition of amine neurotransmitters. The exact mechanism of the oxidative deamination of amines to aldehydes by the enzyme has not yet been fully understood despite extensive research on the area. The rate limiting step is the reductive half-reaction where the Hα together with two electrons of the amine substrate is transferred to the flavin cofactor. However, it is still not known whether the hydrogen is transferred as a proton or a hydride. Experimental results cannot be fully explained by either of those mechanisms. In our previous work, theoretical results based on QM/MM calculations of the full enzyme show an intermediate situation between these two cases. In this paper, we report on an in-depth computational analysis concerning the role of the enzymatic environment for the reaction mechanism of human MAO-B with different p-substituted benzylamines as substrates. Our results show that steric and electrostatic effects from the active site environment turn the mechanism closer to an asynchronous polar nucleophilic mechanism. We found indications that the protein environment of MAO-A enhances the polar nucleophilic character of the mechanism compared to that of MAO-B.

We develop a model to probe the relative orientation of two second-order polarizable daunomycin molecules that are intercalated into a DNA duplex using optical second-harmonic (SH) generation. The SH field generated by the daunomycin molecules interfere with each other. Because the interference depends on the relative orientation of the daunomycin molecules, we can control the interference by changing the number of base pairs separating them. The relative orientation changes as the number of base pairs separating them, multiplied by 36°, which is the twist angle between neighboring base pairs. In this paper, we derive a set of relationships between the relative angle of the molecules and the nonlinear susceptibility elements, and we calculate the SH field generated by the DNA/molecular-pair complex attached to an isotropic dielectric sphere. Calculations reveal that the SH intensity varies periodically with the relative orientation of the two chromophores in the plane perpendicular to the helical axis. The predicted periodicity is in close agreement with experimental results. Structural changes induced by foreign molecules binding to DNA will change the relative orientation of the two chromophores and thereby change the SH interference pattern. We discuss the potential of this SH interference method in providing a new way to probe structural changes induced by the formation of biomolecule complexes. An important feature of the method is that it is label-free, that is, the binding molecule, in this case, daunomycin, is not tagged.

Biological structures consist of lipid bilayers immersed in the aqueous phase. They can be considered as a two-phase system where the two phases are separated (connected) by the transition regions (interphases), which properties are affected by both lipid and aqueous phases. Interphase structure and dynamics might influence properties and/or functioning of the lipid bilayer core, including osmotically induced water flow. It has been shown previously that the osmotically induced water flow depends on the membrane lipid composition, which determines the packing of the membrane core, but the role of the aqueous phase composition has not been studied previously. Ionic composition of an aqueous phase may affect behavior of biological structures. Chaotropic ions interact strongly with a lipid bilayer affecting its molecular packing whereas kosmotropic ions have only limited effect. In the paper result of studies on the dependence of the osmotically induced water flow on the ionic composition of the aqueous phase are presented. The stopped flow technique, with the light scattering as the detection quantity, was adopted, and a new experimental design was developed for the monitoring of the intravesicle salt concentration. Obtained results show that the strength of selected anions interactions with the lipid bilayer does not correlate with their capacity to affect the osmotically induced water flow. Specifically, the measured water permeability coefficient does not depend on the quantity and type of ions present in the aqueous phase.

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

As plasma membranes of animal cells are known to be asymmetric, the transmembrane lipid asymmetry, being essential for many membranes' properties and functions, should be properly accounted for in model membrane systems. In this paper, we employ atomic-scale molecular dynamics simulations to explore electroporation phenomena in asymmetric model membranes comprised of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipid monolayers that mimic the outer and inner leaflets of plasma membranes, respectively. Our findings clearly demonstrate that the molecular mechanism of electroporation in asymmetric phospholipid membranes differs considerably from the picture observed for their single-component symmetric counterparts: The initial stages of electric-field-induced formation of a water-filled pore turn out to be asymmetric and occur mainly on the PC side of the PC/PE membrane. In particular, water molecules penetrate in the membrane interior mostly from the PC side, and the reorientation of lipid head groups, being crucial for stabilizing the hydrophilic pore, also takes place in the PC leaflet. In contrast, the PE lipid head groups do not enter the central region of the membrane until the water pore becomes rather large and partly stabilized by PC head groups. Such behavior implies that the PE leaflet is considerably more robust against an electric field most likely due to interlipid hydrogen bonding. We also show that an electric field induces asymmetric changes in the lateral pressure profile of PC/PE membranes, decreasing the cohesion between lipid molecules predominantly in the PC membrane leaflet. Overall, our simulations provide compelling evidence that the transmembrane lipid asymmetry can be essential for understanding electroporation phenomena in living cells.

Homodimeric cyanine dyes are DNA intercalators that display a large enhancement of fluorescence emission when bound to double-stranded DNA. However, other different interaction modes are possible, such as H-type molecular aggregates of the dye, templated by the nucleic acid. In this paper, we study in depth the formation of nonfluorescent H-aggregates of the cyanine homodimer YOYO-3 with two different DNA templates using absorption and both steady-state and time-resolved fluorescence spectroscopy. First, a nonfluorescent YOYO-3 H-aggregate complex was found to form in single-stranded polycytidine chains, resulting in the appearance of a new absorption band at approximately 500 nm. The specific interaction of cytosine bases suggests the involvement of the C-rich i-motif in facilitating the formation of the H-aggregate complex. Second, the interaction of YOYO-3 with double-stranded poly(A·T) tracts also led to the appearance of a new absorption band at approximately 500 nm, and hence of a different type of H-aggregate. We found that the aggregate is formed mainly in double-stranded regions with consecutive adenine bases in the same strand (and thymine bases in the complementary strand). These poly(A·T) tracts provide narrow minor grooves and enhanced electrostatic negative potential to promote the aggregation of the negatively charged cyanine. As the YOYO-3 H-aggregates are nonfluorescent, our results provide an important basis to quantitatively understand the fluorescence emission of this cyanine dye in the presence of DNA strands.

The mutual solubilities of [C2C1im][Ntf2] ionic liquid and aromatic molecules (benzene and its fluorinated derivatives) can be correlated to the dipolar and quadrupolar moments of the latter molecules. This fact can be interpreted as a consequence of the charge-induced structuration of the IL ions around the aromatic molecules. In this paper we demonstrate that we can follow the above-mentioned structural changes in the mixtures using different NMR-based techniques, namely 1D (1)H and (13)C NMR and 2D (1)H-(1)H NOESY NMR spectroscopy. These have been complemented by more detailed structural analyses of the different (IL plus aromatic solute) mixtures using MD simulations. Such systematic studies included eight systems, namely mixtures of the 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquid with benzene, fluorobenzene, 1,2-difluorobenzene, 1,4-difluorobenzene, 1,3,5-trifluorobenzene, 1,2,4,5-tetrafluorobenzene, penta-fluorobenzene, and hexafluorobenzene.

Amphiphilic block copolymers have emerged during last years as a fascinating substrate material to develop micellar nanocontainers able to solubilize, protect, transport, and release under external or internal stimuli different classes of cargos to diseased cells or tissues. However, this class of materials can also induce biologically relevant actions, which complement the therapeutic activity of their cargo molecules through their mutual interactions with biologically relevant entities (cellular membranes, proteins, organelles...); these interactions at the same time, are regulated by the nature, conformation, and state of the copolymeric chains. For these reasons, in this paper we investigated the self-assembly process and physico-chemcial properties of two reverse triblock poly(butylene oxide)-poly(ethylene oxide)-poly(butylene oxide) block copolymers, BO14EO378BO14 and BO21EO385BO21, which have been recently found to be very useful as drug delivery nanovehicles and biological response modifiers under certain conditions (A. Cambón et al. Int. J. Pharm. 2013, 445, 47-57) in order to obtain a clear picture of the solution behavior of this class or block copolymers and to understand their biological activity. These block copolymers are characterized by possessing long BO blocks and extremely lengthy central EO ones, which provide them with a rich rheological behavior characterized by the formation of flowerlike micelles with sizes ranging from 20 to 40 nm in aqueous solution and the presence of intermicellar bridging even at low copolymers concentrations as denoted by atomic force microscopy. Bridging is also clearly observed by analyzing the rheological response of these block copolymers both storage and loss moduli upon changes on time, temperature, and or concentration. Strikingly, the relatively wide Poisson distribution of the polymeric chains make the present copolymers behave rather distinctly to conventional associative thickeners. The observed rich rheological behavior and their tunability also make these copolymers promising materials to configure drug gelling depots.

Krokinobacter eikastus rhodopsin 2 (KR2) is a light-driven sodium ion pump that was discovered in marine bacteria. Although KR2 is able to pump lithium ions similarly, it is converted into a proton pump in potassium chloride or salts of larger cations. In this paper, we applied light-induced difference Fourier-transform infrared (FTIR) spectroscopy to KR2, a compatible sodium ion-proton pump, at 77 K. The first structural study of the functional cycle showed that the structure and structural changes in the primary processes of KR2 are common to all microbial rhodopsins. The red shifted K formation (KR2K) was accompanied by retinal photoisomerization from an all-trans to a 13-cis form, resulting in a distorted retinal chromophore. The observed hydrogen out-of-plane vibrations were H/D exchangeable, indicating that the chromophore distortion by retinal isomerization is located near the Schiff base region in KR2. This tendency was also the case for bacteriorhodopsin and halorhodopsin but not the case for sensory rhodopsin I and II. Therefore, ion pumps such as proton, chloride, and sodium pumps exhibit local structural perturbations of retinal at the Schiff base moiety, while photosensors show more extended structural perturbations of retinal. The retinal Schiff base of KR2 forms a hydrogen bond that is stronger than in BR. KR2 possesses more protein-bound water molecules than other microbial rhodopsins and contains strongly hydrogen-bonded water (O-D stretch at 2333 cm(-1) in D2O). The light-induced difference FTIR spectra at 77 K were identical between the two states functioning as light-driven sodium ion and proton pumps, indicating that the structural changes in the primary processes are identical between different ion pump functions in KR2. In other words, it is unknown which ions are transported by molecules when they absorb photons and photoisomerize. It is likely that the relaxation processes from the K state lead to an alternative function, namely a sodium ion pump or proton pump, depending on the environment.

Liquid crystal (LC) droplets dispersed in aqueous solution have emerged as an optical probe for sensing the adsorption and interaction of biological species at the LC/aqueous interface. In this paper, we modify the surface of 4-n-pentyl-4'-cyanobiphenyl (5CB) LC droplets by the adsorption of positively charged poly(diallyldimethylammonium chloride) (PDADMAC) and poly(ethylenimine) (PEI) with different molecular weights at the 5CB/water interface. The PDADMAC and PEI-modified 5CB droplets show a radial director configuration in aqueous solution with salt concentrations above 150 mM. The adsorption of negatively charged bovine serum albumin (BSA) on the positively charged PDADMAC and PEI-modified 5CB droplets through electrostatic interaction can induce the radial-to-bipolar configuration transition of the 5CB inside the droplets. We find that the concentration of BSA required to induce the configuration transition increases linearly with the decrease of the molecular weight of PDAMAC and PEI. Our results highlight the capability of the director configuration of LC droplets as an optical probe for sensing the interaction between proteins and polyelectrolytes at the LC/aqueous interface.

In this paper, we propose a new and complete mechanism for dual fluorescence of methyl salicylate (MS) under different conditions using a combined experimental (i.e., steady-state absorption and emission spectra and time-resolved fluorescence spectra) and theoretical (i.e., time-dependent density function theory) study. First, our theoretical study indicates that the barrier height for excited state intramolecular proton transfer (ESIPT) reaction of ketoB depends on the solvent polarity. In nonpolar solvents, the ESIPT reaction of ketoB is barrierless; the barrier height will increase with increasing solvent polarity. Second, we found that, in alcoholic solvents, intermolecular hydrogen bonding plays a more important role. The ketoB form of MS can form two hydrogen bonds with alcoholic solvents; one will facilitate ESIPT and produce the emission band in the blue region; the other one precludes ESIPT and produces the emission band in the near-UV region. Our proposed new mechanism can well explain previous results as well as our new experimental results.

Numerous recent investigations have been devoted to the determination of the equilibrium phase behavior and packing characteristics of hard nonspherical particles, including ellipsoids, superballs, and polyhedra, to name but just a few shapes. Systems of hard nonspherical particles exhibit a variety of stable phases with different degrees of translational and orientational order, including isotropic liquid, solid crystal, rotator and a variety of liquid crystal phases. In this paper, we employ a Monte Carlo implementation of the adaptive-shrinking-cell (ASC) numerical scheme and free-energy calculations to ascertain with high precision the equilibrium phase behavior of systems of congruent Archimedean truncated tetrahedra over the entire range of possible densities up to the maximal nearly space-filling density. In particular, we find that the system undergoes two first-order phase transitions as the density increases: first a liquid-solid transition and then a solid-solid transition. The isotropic liquid phase coexists with the Conway-Torquato (CT) crystal phase at intermediate densities, verifying the result of a previous qualitative study [ J. Chem. Phys. 2011 , 135 , 151101 ]. The freezing- and melting-point packing fractions for this transition are respectively ϕF = 0.496 ± 0.006 and ϕM = 0.591 ± 0.005. At higher densities, we find that the CT phase undergoes another first-order phase transition to one associated with the densest-known crystal, with coexistence densities in the range ϕ ∈ [0.780 ± 0.002, 0.802 ± 0.003]. We find no evidence for stable rotator (or plastic) or nematic phases. We also generate the maximally random jammed (MRJ) packings of truncated tetrahedra, which may be regarded to be the glassy end state of a rapid compression of the liquid. Specifically, we systematically study the structural characteristics of the MRJ packings, including the centroidal pair correlation function, structure factor and orientational pair correlation function. We find that such MRJ packings are hyperuniform with an average packing fraction of 0.770, which is considerably larger than the corresponding value for identical spheres (≈ 0.64). We conclude with some simple observations concerning what types of phase transitions might be expected in general hard-particle systems based on the particle shape and which would be good glass formers.

Fluctuations of NMR resonance frequency shifts and their relation with protein exchanging conformations are usually analyzed in terms of simple two-site jump processes. However, this description is unable to account for the presence of multiple time scale dynamics. In this work, we present an alternative model for the interpretation of the stochastic processes underlying these fluctuations of resonance frequencies. Time correlation functions of 15 N amide chemical shifts computed from molecular dynamics simulations (MD) were analyzed in terms of a transiently fractional diffusion process. The analysis of MD trajectories spanning dramatically different time scales (∼200 ns and 1 ms (Shaw, D. E.; et al. Science 2010, 330, 341−346)) allowed us to show that our model could capture the multiple scale structure of chemical shift fluctuations. Moreover, the predicted exchange contribution Rex to the NMR transverse relaxation rate is in qualitative agreement with experimental results. These observations suggest that the proposed fractional diffusion model may provide significative improvement to the analysis of NMR dispersion experiments. relaxation. 17 In this paper, we investigate the stochastic properties of the fluctuations of the nuclei frequencies at a more fundamental level. We present a combined analysis of chemical shift trajectories computed from a 1 ms MD trajectory of the small protein BPTI, 16 together with a short 200 ns simulation of the same protein performed by us in similar conditions. Chemical shift correlation functions computed from these trajectories are analyzed in terms of a transiently fractional diffusion process. We show that, when quality permits, data are consistent with a variable order fractional diffusion equation. 18 Moreover, in these favorable cases, similar fractional orders are found in both simulations. This suggests that in spite of the dramatically different sampling rates (2 ps and 25 ns) and lengths (200 ns and 1 ms), the same fractional structure of stochastic process underlying the chemical shift fluctuations can be identified. Such processes imply a distribution of time scales, as typically occurs in complex systems, 19 and associated with a power law decay of the correlation function. However, this kind of decay occurs at intermediate rather than asymptotically long

Water-soluble chlorophyll-binding proteins (WSCPs) are interesting model systems for the study of pigment-pigment and pigment-protein interactions. While class IIa WSCP has been extensively studied by spectroscopic and theoretical methods, a comprehensive spectroscopic study of class IIb WSCP was lacking so far despite the fact that its structure was determined by X-ray crystallography. In this paper, results of two-dimensional electronic spectroscopy applied to the class IIb WSCP from Lepidium virginicum are presented. Global analysis of 2D data allowed determination of energy levels and excitation energy transfer pathways in the system. Some additional pathways, not present in class IIa WSCP, were observed. The data were interpreted in terms of a model comprising two interacting chlorophyll dimers. In addition, oscillatory signals were observed and identified as coherent beatings of vibrational origin.

This paper presents a methodology that allows the fine refinement of the crystal and molecular structure for compounds for which the data deposited in the crystallographic bases are of poor quality. Such species belong to the group of samples with molecular disorder. In the Cambridge Crystallographic Data Center (CCDC), there are approximately 22,000 deposited structures with an R-factor over 10. The powerful methodology we present employs crystal data for Leu-enkephalin (two crystallographic forms) with R-factor values of 14.0 and 8.9 and for Met-enkephalin (one form) with an R-factor of 10.5. NMR crystallography was employed in testing the X-ray data and the quality of the structure refinement. The GIPAW (gauge invariant projector augmented wave) method was used to optimize the coordinates of the enkephalins and to compute NMR parameters. As we reveal, this complementary approach makes it possible to generate a reasonable set of new coordinates that better correlate to real samples. This methodology is general and can be employed in the study of each compound possessing magnetically active nuclei.

Glutamine--a popular nutritional supplement, non-toxic amino acid, and an essential interorgan and intercellular ammonia transporter--can destroy the neurons' mitochondria. When glutamine enters (like a Trojan horse) into the mitochondria, in the presence of glutaminase, it reacts with water and yields glutamate and excess ammonia which opens gates in the membrane of the mitochondria and thereby destroys it. The mechanistic details underlying the molecular basis of the catabolic production of excess ammonia remain unclear. In the present paper, both 5-oxoproline-mediated and direct pathways for glutamine deamidation are studied using wave function and density functional theories. The mechanisms are studied both in the gas phase and in aqueous solution using the polarizable continuum model (PCM) and solvent model on density (SMD) solvation models. Among three glutamine deamidation pathways, a two-step pathway, GDB, shows the lowest gas phase barrier height of 189 kJ/mol with the G3MP2B3 level of theory. Incorporation of solvent through PCM and SMD models reduces the barrier height to 183 and 174 kJ/mol, respectively. For the hydrolysis of 5-oxoproline, a two-step mechanism, pathway PH-B, provides a lower gas phase energy barrier (187 kJ/mol) compared to one-step (201 kJ/mol) and three-step (227 kJ/mol) pathways at G3MP2B3. Although direct hydrolysis with OH(-), pathway DHE, has the lowest gas phase barrier of 135 kJ/mol, the solvent has little effect on the barrier. For the direct hydrolysis with OH(-)/H2O, pathway DHF, the overall barrier is 143 kJ/mol, in the gas phase at G3MP2B3. In aqueous solution, the overall barrier decreases to 76 and 75 kJ/mol with PCM and SMD, respectively, at B3LYP/6-31+G(d,p), making this the most plausible mechanism. Compared to PCM, SMD predicts lower barriers for nearly all pathways investigated.

Protein sedimentation sans cryoprotection is a new approach to magic angle spinning (MAS) and dynamic nuclear polarization (DNP) nuclear magnetic resonance (NMR) spectroscopy of proteins. It increases the sensitivity of the experiments by a factor of ∼4.5 in comparison to the conventional DNP sample preparation and circumvents intense background signals from the cryoprotectant. In this paper, we investigate sedimented samples and concentrated frozen solutions of natural abundance bovine serum albumin (BSA) in the absence of a glycerol-based cryoprotectant. We observe DNP signal enhancements of ε ∼ 66 at 140 GHz in a BSA pellet sedimented from an aqueous solution containing the biradical polarizing agent TOTAPOL and compare this with samples prepared using the conventional protocol (i.e., dissolution of BSA in a glycerol/water cryoprotecting mixture). The dependence of DNP parameters on the radical concentration points to the presence of an interaction between TOTAPOL and BSA, so much so that a frozen solution sans cryoprotectant still gives ε ∼ 50. We have studied the interaction of BSA with another biradical, SPIROPOL, that is more rigid than TOTAPOL and has been reported to give higher enhancements. SPIROPOL was also found to interact with BSA, and to give ε ∼ 26 close to its maximum achievable concentration. Under the same conditions, TOTAPOL gives ε ∼ 31, suggesting a lesser affinity of BSA for SPIROPOL with respect to TOTAPOL. Altogether, these results demonstrate that DNP is feasible in self-cryoprotecting samples.

In this paper we provide a computational study of the l-methionine conformational landscape and VCD spectra in the gas phase and a water environment simulated by implicit PCM and the hybrid model, i.e., a combination of explicit "microsolvation" and implicit models. In the gas phase, two groups of conformers differing in H-bonding, i.e., OH···NH2 and NH···O═C, could be distinguished based solely on the IR ν(OH) and ν(NH) stretching vibrations range. On the other hand, VCD better reflected chain differences. The most stable OH···NH2 conformer was predicted to be easily detected, and the presence of two out of four NH···O═C conformers could be confirmed. Three zwitterionic methionine conformers were shown to dominate in water. Their VCD spectra, simulated within the hybrid model at the B3LYP-IEF-PCM/aug-cc-pVDZ level of theory, indicated that they could be recognized in the mixture. Use of the hybrid model is crucial for good reproduction of the hydrogen bonding pattern in the VCD spectra of methionine in water solution. However, the 1300-800 cm(-1) region of the skeleton vibrations of methionine appeared to be relatively insensitive to the model of the solvent.

A relevant number of experiments on short peptides has been performed in recent years. One of the major problems rises from the simultaneous presence of slightly different conformers at equilibrium in solution. In the present paper, the conformational characteristics of the Gly-l-Ala-Methyl amide dipeptide in D2O and DMSO solutions are investigated by nonlinear IR spectroscopy. The pump-probe scheme with ultrashort mid-infrared pulses, in the Amide I region, is used to determine the mutual orientation of the two C═O bonds and the dynamics due to solute-solvent interactions. The coupling between Amide I modes is evaluated from both linear and 2D spectra. The interconversion between the different conformations occurs on time scales longer than the vibrational lifetime, and the spectral diffusion observed in 2D spectra is attributed to the solvent dynamics. Quantum mechanical calculations and molecular dynamics simulations are performed to identify the most stable geometries. By comparing the experimental and the theoretical data, we establish the prevalence of β-like polar conformers in both water and DMSO solvents.

The use of forward osmosis (FO) process for seawater desalination has attracted tremendous interest in recent years. Besides the manufacture of suitable membranes, the major technical challenge in the efficient deployment of the FO technology lies in the development of a suitable "draw solute". Owing to its inherent advantages, poly(aspartic acid) has arisen to be an attractive candidate for this purpose. However, an investigation of its molecular level properties has not been studied in detail. In this paper, the dynamics of poly(aspartic acid) and its sodium salt in the dilute concentration regime have been reported. The quantification of the polymer conformational properties, its solvation behavior, and the counterion dynamics are studied. The neutral polymer shows a preferentially coiled structure whereas the fully ionized polymer has an extended structure. Upon comparing with poly(acrylic acid) polymer, another polymer which has been used as a draw solute, poly(aspartic acid) forms more number of hydrogen bonds as well as fewer ion pairs.

We propose an equilibrium embryo definition for homogeneous bubble nucleation within the pure component superheated Lennard-Jones liquid. The suggested embryo definition serves as an improvement to a previous (n,v) embryo model (Uline and Corti 2007). In that model, the constrained equilibrium between the bubble and the surrounding superheated liquid was maintained by placing n particles within a spherical volume v, without concern for the redundant counting of configurations and the relevance of the model to the dynamics of a nucleation process. To eliminate this redundancy, while only considering those embryos that should most likely appear at a transitional state, we now define the volume of the embryo via the use of a shell particle and only include n particles inside the volume that are deemed to be "vapor-like". The underlying free energy surface of formation of the new (n,v) embryo model is generated via Monte Carlo simulation and also approximately by a suggested density functional theory method. The resulting surface implies that small and locally confined regions of near-zero density serve as precursors initiating homogeneous bubble nucleation. Furthermore, the nonredundant counting of the embryo configurations yields a well-defined and sharp conduit in the free energy surface that directs the initially formed embryos toward the critical nucleus. We discuss how the suggested equilibrium embryo model aids in both the identification of the transitional configurations and calculation of the average number density of the critical nuclei within the superheated liquid phase, which is the focus of the companion paper (DOI 10.1021/jp404151h).

In this paper, we analyze the internal picosecond dynamics of enantiomeric ((S)-) and racemic ((R,S)-) ibuprofen (IBP), when forming inclusion complexes, in solid state, with methyl-β-cyclodextrin (Me-β-CD), by inelastic and quasi elastic neutron scattering. The study was aimed at understanding, by the analysis of the vibrational and relaxational properties of the inclusion complexes also with respect to the single components, if and how the differences in the structural properties of the hydrogen bond (HB) network of (S)- and (R,S)-IBP can have influence on the complexation process triggered by "host-guest" interactions, whose detailed knowledge is retained as a prerequisite for enantiodiscrimination. From the results, a similar complexation mechanism for (S)- and (R,S)-IBP is argued, with a preferred penetration mode involving the isopropyl group of IBP.

The nonradiative relaxation of both the exciton and biexciton in CdSe/ZnS core-shell nanoparticles have complicated, nonexponential kinetics. This paper presents data on this system from multiple population-period transient spectroscopy (MUPPETS), a method for two-dimensional kinetics. An initial report of a dispersed (nonexponential) biexciton decay [J. Am. Chem. Soc. 2013, 135, 1002] is confirmed in a more rigorous analysis. Additional transient-grating data allow a quantitative treatment of the full, complex MUPPETS data set. The MUPPETS signal has a strong fluence dependence. With extrapolation to the low fluence limit, the ratio of cross sections for ground-to-exciton and exciton-to-biexciton absorption is found to be close to the predictions of the uncorrelated-electron model. The full two-dimensional MUPPETS data set is reported for the first time and is analyzed to detect heterogeneity in the exciton decay. The exciton has a substantial (>40%) nonradiative decay, but it is not due to a subset of defective particles. A surface relaxation in response to formation of the exciton is suggested. This data set is the first capable of detecting correlations between the biexciton and exciton decay mechanism. None is found.

Multiple population-period transient spectroscopy (MUPPETS) is a six-pulse experiment with two time dimensions that is capable of adding information about systems with complicated kinetics. The core theory for MUPPETS focuses on the χ(5) response of the chromophores. This theory was used to analyze the dynamics of excitons and biexcitons in CdSe/ZnS core-shell nanoparticles in part I of this paper [J. Phys. Chem. B 2013, DOI:10.1021/jp405785a]. In real experiments, the potential role of additional processes must also be considered, in particular, the χ(7), "saturation" of the MUPPETS signal and nonresonant signals from heating of the solvent. A pathway method for calculating fluence effects in MUPPETS is developed. The fluence dependence of the biexciton signal and its sign reversal, as found in part I, are explained without invoking higher excitons or unexpected species. A method is presented for quantitatively predicting the magnitude of signals from solvent heating using an external standard. Thermal effects in this system are found to be too small to affect the conclusions in part I. Their small size, combined with small, systematic errors in the data, also makes it difficult to measure the yield of solvent heat in these experiments.

Bioactive phosphate-based glasses (PBGs) have several possible biomedical applications because of the chemical reactions they undergo with their surroundings when implanted into the body. The dissolution rate of PBGs in physiological conditions is a crucial parameter for these applications, to ensure, e.g., delivery of drugs or nutrients to the body at the correct rate. While it has been well-known that increasing the CaO content of these glasses at the expense of Na2O slows the dissolution rate, this paper provides an atomistic explanation of this for the first time. In this work, molecular dynamics simulations of five ternary P2O5-CaO-Na2O glasses reveal the structural properties at the atomic level that enhance the durability of PBGs as more Ca is added: (i) Ca binds together more fragments of the phosphate glass network than Na, (ii) Ca binds together more PO4 tetrahedra than Na, and (iii) Ca has a lower concentration of intratetrahedral phosphate bonding than Na. This behavior is rooted in the calcium ion's higher charge and field strength. These results open the path to precise control and optimization of the PBG dissolution rate for specific biomedical applications.

Hydroxyethyl starch (HES) is an important industrial additive in the paper, textile, food, and cosmetic industries and has been shown to be an effective cryoprotectant for red blood cells; however, little is known about its thermodynamic solution properties. In many applications, in particular those in biology, HES is used in an aqueous solution with sodium chloride (NaCl). The osmotic virial solution thermodynamics approach accurately captures the dependence of osmolality on molality for many types of solutes in aqueous systems, including electrolytes, sugars, alcohols, proteins, and starches. Elliott et al. proposed mixing rules for the osmotic virial equation to be used for osmolality of multisolute aqueous solutions [Elliott, J. A. W.; et al. J. Phys. Chem. B 2007, 111, 1775-1785] and recently applied this approach to the fitting of one set of aqueous HES-NaCl solution data reported by Jochem and Körber [Cryobiology 1987, 24, 513-536], indicating that the HES osmotic virial coefficients are dependent on HES-to-NaCl mass ratios. The current study reports new aqueous HES-NaCl vapor pressure osmometry data which are analyzed using the osmotic virial equation. HES modifications were measured after dialysis (membrane cut off: 10,000 g/mol) and freeze-drying using vapor pressure osmometry at different mass ratios of HES to NaCl for HES up to 50% and NaCl up to 25% with three different HES modifications (weight average molecular weights [g/mol]/degree of substitution: 40,000/0.5; 200,000/0.5; 450,000/0.7). Equations were then fit to the data to provide a model for HES osmotic virial coefficient dependence on mass ratio of HES to NaCl. The osmolality data of the three HES modifications were accurately described over a broad range of HES-to-NaCl mass ratios using only four parameters, illustrating the power of the osmotic virial approach in analyzing complex data sets. As expected, the second osmotic virial coefficients increase with molecular weight of the HES and increase with HES-to-NaCl mass ratio.

The nucleation rate from classical nucleation theory is independent of sample size. In the past decades, several experimental and theoretical studies argued that the homogeneous nucleation rate of ice in supercooled droplets increases when the drop size is decreased. In this paper, we investigate the nucleation of ice in nanoscale water films using molecular dynamics simulations. We found that the nucleation rate of ice actually decreases when the film thickness decreases in the nanoscale regime. A theoretical model is presented to interpret the mechanism of nucleation rate decrease, which agrees well with the simulation results. The model divides films into the near-surface and the middle regions that are characterized by relatively low and high nucleation rates, respectively. The middle region dominates the nucleation process of films, whereas its effect is continuously weakened when increasing volume fraction of the near-surface region by decreasing the film size, leading to a decrease of the total nucleation rate. The structural and thermodynamic analyses indicate that the high stress induced by the surface layering slows down the diffusion and increases the nucleation barrier in the near-surface region, which is responsible for the low nucleation rate and eventually the decrease of the total nucleation rate.

The gap between the time scale of interesting behavior in macromolecular systems and that which our computational resources can afford often limits molecular dynamics (MD) from understanding experimental results and predicting what is inaccessible in experiments. In this paper, we introduce a new sampling scheme, named diffusion-map-directed MD (DM-d-MD), to rapidly explore molecular configuration space. The method uses a diffusion map to guide MD on the fly. DM-d-MD can be combined with other methods to reconstruct the equilibrium free energy, and here, we used umbrella sampling as an example. We present results from two systems: alanine dipeptide and alanine-12. In both systems, we gain tremendous speedup with respect to standard MD both in exploring the configuration space and reconstructing the equilibrium distribution. In particular, we obtain 3 orders of magnitude of speedup over standard MD in the exploration of the configurational space of alanine-12 at 300 K with DM-d-MD. The method is reaction coordinate free and minimally dependent on a priori knowledge of the system. We expect wide applications of DM-d-MD to other macromolecular systems in which equilibrium sampling is not affordable by standard MD.

This paper discusses the phase behavior, rheology, and structure of self-assembled sodium bis(2-ethylhexyl) sulfosuccinate (AOT) reverse micelle systems at high AOT concentrations. When the amount of AOT and w(o) (the molar ratio of water to AOT) were changed, many different phases were found, a fact which is not discussed in the literature. Opaque gel-like phase (phase separation) occurred with high concentrations of AOT in organic solvents without water. When the AOT concentration and w(o) were increased to 18-72 m and 2, respectively, the samples were gel-like and translucent. Dynamic rheological results indicate that the viscoelastic transition agreed with a multirelaxation time model. Small-angle X-ray scattering (SAXS) results imply that these samples showed a hexagonally close-packed cylindrical structure in which the diameter of a cylinder was ~2.5-3.0 nm, depending on the water contents. Moreover, these AOT cylinders self-assembled into fiber bundles with a diameter of 1-10 μm, as determined using a polarized optical microscope. As w(o) was increased to 2-6 in 72 m AOT samples, similar rheological and SAXS results were obtained. However, a different type of viscoelastic transition occurred, from multirelaxation to single-relaxation, when w(o) was increased to 7-11. The samples were in the transparent gel-like phase, and the structures determined by SAXS were a combination of hexagonally packed cylindrical and lamellar structure. The close-packed cylindrical structures had larger radii and shorter lengths with increasing w(o). Furthermore, when w(o) was increased to 12, the gel-like phase disappeared and a highly viscous solution was observed. This is because all the cylindrical structures collapsed and transformed into lamellar structures when the amount of water was further increased.

We have previously demonstrated that arginine increases the solubility of aromatic compounds that have poor water solubility, an effect referred to as the "arginine-assisted solubilization system (AASS)". In the current study, we utilized a molecular dynamics simulation to examine the solubilization effects of arginine on caffeic acid, which has a tendency to aggregate in aqueous solution. Caffeic acid has a hydrophobic moiety containing a π-conjugated system that includes an aromatic ring and a hydrophilic moiety with hydroxyl groups and a carboxyl group. While its solubility increases at higher pH values due to the acquisition of a negative charge, the solubility was greatly enhanced by the addition of 1 M arginine hydrochloride at any pH. The results of the simulation indicated that the caffeic acid aggregates were dissociated by the arginine hydrochloride, which is consistent with the experimental data. The binding free energy calculation for two caffeic acid molecules in an aqueous 1 M arginine hydrochloride solution indicated that arginine stabilized the dissociated state due to the interaction between its guanidinium group and the π-conjugated system of the caffeic acid. The binding free energy of two caffeic acid molecules in the arginine hydrochloride solution exhibited a local minimum at approximately 8 Å, at which the arginine intervened between the caffeic acid molecules, causing a stabilization of the dissociated state of caffeic acid. Such stabilization by arginine likely led to the caffeic acid solubilization, as observed in both the experiment and the MD simulation. The results reported in this paper suggest that AASS can be attributed to the stabilization resulting from the intervention of arginine in the interaction between the aromatic compounds.

The hydrogen ion is one of the most important species in aqueous solutions, as well as in protic ionic liquids (PILs). PILs are important potential alternatives to H2O for swelling the proton exchange membranes (PEMs) and improving the high-temperature performance of fuel cells. The hydrogen ion (H(+)) or hydronium (H3O(+)) solvation mechanism is not only a fundamental principle of acid/base chemistry in ionic liquids but also key to understanding the charge- and proton-transport properties of the PIL solutions. In this paper, a PIL system was prepared by mixing 1-butyl-3-methyl-imidazolium tetrafluoroborate (BMIBF4) IL with an aqueous solution of a strong acid, HBF4. Water can be partially evaporated from the solution under a vacuum at room temperature. Conductivity and vibrational spectroscopy (IR and Raman) measurements were used in combination with density functional theory (DFT) calculations to characterize the molecular-level solvation of H(+) and H2O in the IL solution. When water is present at high molar fraction, the cations (BMI(+) and H(+)) and anions (BF4(-)) are both solvated by water and the solutions have high conductivity. After water evaporation, the PIL solution has excess H(+) and reduced conductivity, which is still significantly higher than that of pure BMIBF4. Vibrational spectroscopy suggests that the BMI(+) and BF4(-) ions are desolvated from water during the water evaporation. DFT calculations assist the interpretation of the vibrational spectroscopy and show that the remaining water is in the form of H3O(+) solvated by the IL molecular ions. Hence, the species remaining after evaporation is a ternary PIL consisting of BMI(+) cation, BF4(-) anion, and H3O(+) cation. The H3O(+) may be the principle charge carrier in the PIL solution and responsible for the high solution conductivity.

Sum-frequency-generation (SFG) vibration spectroscopy selectively detects noncentrosymmetric vibrational modes in crystalline cellulose inside intact lignocellulose. However, SFG peak assignment in biomass samples is challenging due to the complexity of the SFG processes and the lack of reference SFG spectra from the two crystal forms synthesized in nature, cellulose Iα and Iβ. This paper compares SFG spectra of laterally aligned cellulose Iα and Iβ crystals with vibration frequencies calculated from density functional theory with dispersion corrections (DFT-D2). Two possible hydrogen-bond networks A and B ( Nishiyama et al. Biomacromolecules 2008 , 9 , 3133 ) were investigated for both polymorphs. From DFT-D2 calculations the energetically favorable structures for cellulose Iα and Iβ had CH2OH groups in tg conformations and network A hydrogen bonding. The calculated frequencies of C-H stretch modes agreed reasonably well with the peak positions observed with SFG and were localized vibrations; thus, peak assignments to specific alkyl groups were proposed. DFT-D2 calculations underestimated the distances between hydrogen-bonded oxygen atoms compared to the experimentally determined values; therefore, the OH stretching calculated frequencies were ~100 cm(-1) lower than observed. The SFG peak assignments through comparison with DFT-D2 calculations will guide the SFG analysis of the crystalline cellulose structure in plant cell walls and lignocellulose biomass.

We present a computer simulation-molecular-thermodynamic (CSMT) framework to model the micellization behavior of mixtures of surfactants in which hydration information from all-atomistic simulations of surfactant mixed micelles and monomers in aqueous solution is incorporated into a well-established molecular-thermodynamic framework for mixed surfactant micellization. In addition, we address the challenges associated with the practical implementation of the CSMT framework by formulating a simpler mixture CSMT model based on a composition-weighted average approach involving single-component micelle simulations of the mixture constituents. We show that the simpler mixture CSMT model works well for all of the binary surfactant mixtures considered, except for those containing alkyl ethoxylate surfactants, and rationalize this finding molecularly. The mixture CSMT model is then utilized to predict mixture CMCs, and we find that the predicted CMCs compare very well with the experimental CMCs for various binary mixtures of linear surfactants. This paper lays the foundation for the mixture CSMT framework, which can be used to predict the micellization properties of mixtures of surfactants that possess a complex chemical architecture, and are therefore not amenable to traditional molecular-thermodynamic modeling.

Until recently, it was believed that the CP29 protein from higher plant photosystem II (PSII) contains 8 chlorophylls (Chl's) per complex (Ahn et al. Science 2008, 320, 794-797; Bassi et al. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 10056-10061) in contrast to the 13 Chl's revealed by the recent X-ray structure (Pan et al. Nat. Struct. Mol. Biol. 2011, 18, 309-315). This disagreement presents a constraint on the interpretation of the underlying electronic structure of this complex. To shed more light on the interpretation of various experimental optical spectra discussed in the accompanying paper (part I, DOI 10.1021/jp4004328 ), we report here calculated low-temperature (5 K) absorption, fluorescence, hole-burned (HB), and 300 K circular dichroism (CD) spectra for CP29 complexes with a different number of pigments. We focus on excitonic structure and the nature of the low-energy state using modeling based on the X-ray structure of CP29 and Redfield theory. We show that the lowest energy state is mostly contributed to by a612, a611, and a615 Chl's. We suggest that in the previously studied CP29 complexes from spinach (Pieper et al. Photochem. Photobiol.2000, 71, 574-589) two Chl's could have been lost during the preparation/purification procedure, but it is unlikely that the spinach CP29 protein contains only eight Chl's, as suggested by the sequence homology-based study (Bassi et al. Proc. Natl. Acad. Sci. U.S.A.1999, 96, 10056-10061). The likely Chl's missing in wild-type (WT) CP29 complexes studied previously (Pieper et al. Photochem. Photobiol. 2000, 71, 574-589) include a615 and b607. This is why the nonresonant HB spectra shown in that reference were ~1 nm blue-shifted with the low-energy state mostly localized on about one Chl a (i.e., a612) molecule. Pigment composition of CP29 is discussed in the context of light-harvesting and excitation energy transfer.

The mechanism of neutral hydrolysis of ester has long been explored by theoretical studies. However, reliable theoretical calculations show that the usual bifunctional catalysis mechanism reported by different authors cannot explain the experimental kinetics. An important advance was recently reported by Gunaydin and Houk, suggesting that ions are involved in the mechanism and the process initiates by water autoionization followed by protonation of the ester (W(AI)A mechanism). However, this mechanism does not explain the hydrolysis of activated esters. In this work, we have used ab initio calculations, continuum solvation models, and intrinsic reaction coordinate method to support the W(AI)A mechanism for normal ester. In the case of activated esters, the process can also be viewed as water autoionization with formation of hydroxide ion aided by a second water molecule acting as a general base (W(AI)B mechanism). This is the mechanism that was proposed by Jencks and Carriuolo 50 years ago. Our analysis point out that the usual method for exploring mechanisms, searching for saddle points, may not work for problems like the present one, since there are no saddle points on the reaction pathway. Rather, the formation of a pair of ions from a neutral species may have an asymptotic barrier. The approach used in this paper allows the calculation of the free energy profile and enable us to explain the mechanism and kinetics of the neutral hydrolysis of normal (methyl acetate) and activated (methyl trifluoroacetate) esters. In addition, the present study suggests that formation of a pair of ions should always be considered in reactions in aqueous solution.

The adsorption properties of polyvinyl alcohol (PVA)-grafted silica gel particles PVA/SiO2 toward genistein are researched in this paper. The effects of the main factors on the adsorption properties are investigated, the adsorption mechanism is explored in depth, and the adsorption thermodynamics is researched. The experimental results show that the conventional hydrogen bond is formed between the hydroxyl groups with high density on the surfaces of PVA/SiO2 and the phenolic hydroxyl groups in genistein, while π-type hydrogen bond is formed between the hydroxyl groups of PVA/SiO2 and the conjugated aromatic rings. It is the two types of hydrogen bond that make the functional composite particles PVA/SiO2 produce very strong physical adsorption toward genistein. The competitive adsorption of the solvent can have severe negative impact on the adsorption capacity of genistein. Increasing temperature will weaken the hydrogen-bond interaction between PVA/SiO2 particles and genistein. The existence of electrolytes in the protic solvent will affect the adsorption negatively. The adsorption process of PVA/SiO2 particles toward genistein is exothermic and driven by enthalpy. The adsorption isotherm data matches the Langmuir model.

In this paper are presented the results of theoretical studies of the structure in proton motion in a very short O···O and two weak N-H···O intramolecular hydrogen bonds in the nitromalonamide crystal. The dynamics of proton motion in hydrogen bonds were investigated in the NVT ensemble at 298 K using the Car-Parrinello and the path integral molecular dynamics. A very large delocalization of proton in the slightly asymmetrical single well of free energy potential of O-H···O intramolecular hydrogen bond was noted especially in the path integral simulation where quantum effects are taken into account. This hydrogen bond is very strong with the estimated energy of hydrogen bond ca. -27 kcal/mol. The nature of intra- and intermolecular interactions was studied by means of quantum theory of atoms in molecules. The infrared spectra were calculated and compared with available experimental data. CPMD vibrational results appear to be in good agreement with the experimental ones.

The self-consistent charge density functional tight binding (SCC-DFTB) method has been applied to hydroxide water clusters and a hydroxide ion in bulk water. To determine the impact of various implementations of SCC-DFTB on the energetics and dynamics of a hydroxide ion in gas phase and condensed phase, the DFTB2, DFTB2-γ(h), DFTB2-γ(h)+gaus, DFTB3-diag, DFTB3-diag+gaus, DFTB3-Full+gaus, and DFTB3-3OB implementations have been tested. Energetic stabilities for small hydroxide clusters, OH(-)(H2O)n, where n = 4-7, are inconsistent with the results calculated with the B3LYP and second order Møller-Plesset (MP2) levels of ab initio theory. The condensed phase simulations, OH(-)(H2O)127, using the DFTB2, DFTB2-γ(h), DFTB2-γ(h)+gaus, DFTB3-diag, DFTB3-diag+gaus, DFTB3-Full+gaus and DFTB3-3OB methods are compared to Car-Parrinello molecular dynamics (CPMD) simulations using the BLYP functional. The SCC-DFTB method including a modified O-H repulsive potential and the third order correction (DFTB3-diag/Full+gaus) is shown to poorly reproduce the CPMD computational results, while the DFTB2 and DFTB2-γ(h) method somewhat more closely describe the structural and dynamical nature of the hydroxide ion in condensed phase. The DFTB3-3OB outperforms the MIO parameter set but is no more accurate than DFTB2. It is also shown that the overcoordinated water molecules lead to an incorrect bulk water density and result in unphysical water void formation. The results presented in this paper point to serious drawbacks for various DFTB extensions and corrections for a hydroxide ion in aqueous environments.

In many applications, Ionic liquids (ILs) work in a nonequilibrium steady state driven by an external electric field. However, how the electric field changes the structure and dynamics of ILs and its underlying mechanism still. remain poorly understood. In this paper, coarse-grained molecular dynamics simulations, were performed to investigate the structure and dynamics of 1-ethyl-3-methylimidaiolium nitrate ([EMIm][NO3]) under a static electric field. The Ion cage. structure was found to play an essential role in determining the structural and dynamic properties of the IL System. With a weak or moderate electric field (0-10(7) V/m), the external electric field is too weak to modify the ion Cage structure in an influential way and thus the changes of structural and dynamic properties are negligible. With a strong electric field (10(7)-10(9) V/m) applied, ion cages expand and deform apparently; leading to the increase of ion mobility and self diffusion coefficient with electric field, and the self diffusion of ions along the electric field becomes faster than the other two directions due to the anisotropic deformation of ion cages. In addition, the Einstein relation connecting diffusion and mobility breaks down at strong electric fields, and it also breaks down for a single ion species even at moderate electric fields (linear response region).