Characterization of the organic ligand shell of semiconductor quantum dots by fluorescence quenching experiments.

PubMed

Boldt, Klaus; Jander, Sebastian; Hoppe, Kathrin; Weller, Horst

2011-10-25

We present the characterization of the organic ligand shell of CdSe/Cd(x)Zn(1-x)S/ZnS nanoparticles by means of fluorescence quenching experiments. Both electron scavengers and acceptors for resonance energy transfer were employed as probes. Different quenching behavior for short and long chain thiol ligands in water was found. It could be shown that poly(ethylene oxide) (PEO)-capping of the particles comprises a densely packed inner shell and a loosely packed outer shell in which ions and small molecules diffuse unhindered. A quantitative uptake of quencher molecules into the PEO shell was observed, through which the particle volume including the ligand sphere could be determined.

Modeling the interactions of phthalocyanines in water: from the Cu(II)-tetrasulphonate to the metal-free phthalocyanine.

PubMed

Martín, Elisa I; Martínez, Jose M; Sánchez Marcos, Enrique

2011-01-14

A quantum and statistical study on the effects of the ions Cu(2+) and SO(3)(-) in the solvent structure around the metal-free phthalocyanine (H(2)Pc) is presented. We developed an ab initio interaction potential for the system CuPc-H(2)O based on quantum chemical calculations and studied its transferability to the H(2)Pc-H(2)O and [CuPc(SO(3))(4)](4-)-H(2)O interactions. The use of the molecular dynamics technique allows the determination of energetic and structural properties of CuPc, H(2)Pc, and [CuPc(SO(3))(4)](4-) in water and the understanding of the keys for the different behaviors of the three phthalocyanine (Pc) derivatives in water. The inclusion of the Cu(2+) cation in the Pc structure reinforces the appearance of two axial water molecules and second-shell water molecules in the solvent structure, whereas the presence of SO(3)(-) anions implies a well defined hydration shell of about eight water molecules around them making the macrocycle soluble in water. Debye-Waller factors for axial water molecules have been obtained in order to examine the potential sensitivity of the extended x-ray absorption fine structure technique to detect the axial water molecules.

Binding Preferences of Amino Acids for Gold Nanoparticles: A Molecular Simulation Study.

PubMed

Shao, Qing; Hall, Carol K

2016-08-09

A better understanding of the binding preference of amino acids for gold nanoparticles of different diameters could aid in the design of peptides that bind specifically to nanoparticles of a given diameter. Here we identify the binding preference of 19 natural amino acids for three gold nanoparticles with diameters of 1.0, 2.0, and 4.0 nm, and investigate the mechanisms that govern these preferences. We calculate potentials of mean force between 36 entities (19 amino acids and 17 side chains) and the three gold nanoparticles in explicit water using well-tempered metadynamics simulations. Comparing these potentials of mean force determines the amino acids' nanoparticle binding preferences and if these preferences are controlled by the backbone, the side chain, or both. Twelve amino acids prefer to bind to the 4.0 nm gold nanoparticle, and seven prefer to bind to the 2.0 nm one. We also use atomistic molecular dynamics simulations to investigate how water molecules near the nanoparticle influence the binding of the amino acids. The solvation shells of the larger nanoparticles have higher water densities than those of the smaller nanoparticles while the orientation distributions of the water molecules in the shells of all three nanoparticles are similar. The nanoparticle preferences of the amino acids depend on whether their binding free energy is determined mainly by their ability to replace or to reorient water molecules in the nanoparticle solvation shell. The amino acids whose binding free energy depends mainly on the replacement of water molecules are likely to prefer to bind to the largest nanoparticle and tend to have relatively simple side chain structures. Those whose binding free energy depends mainly on their ability to reorient water molecules prefer a smaller nanoparticle and tend to have more complex side chain structures.

Development of magnetic luminescent core/shell nanocomplex particles with fluorescence using Rhodamine 6G

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Hee Uk; Song, Yoon Seok; Park, Chulhwan

2012-12-15

Graphical abstract: Display Omitted Highlights: ► A simple method was developed to synthesize Co-B/SiO{sub 2}/dye/SiO{sub 2} composite particles. ► The magnetic particle shows that highly luminescent and core/shell particles are formed. ► Such core/shell particles can be easily suspended in water. ► The magnetic particles could detect fluorescence for the application of biosensor. -- Abstract: A simple and reproducible method was developed to synthesize a novel class of Co-B/SiO{sub 2}/dye/SiO{sub 2} composite core/shell particles. Using a single cobalt core, Rhodamine 6G of organic dye molecules was entrapped in a silica shell, resulting in core/shell particles of ∼200 nm diameter. Analysesmore » using a variety of techniques such as transmission electron microscopy, X-ray photoelectron spectroscopy, vibration sample magnetometry, confocal laser scanning microscopy, and fluorescence intensity demonstrated that dye molecules were trapped inside the core/shell particles. A photoluminescence investigation showed that highly luminescent and photostable core/shell particles were formed. Such core/shell particles can be easily suspended in water. The synthesized magnetic particles could be used to detect fluorescence on glass substrate arrays for bioassay and biosensor applications.« less

Origin of the blueshift of water molecules at interfaces of hydrophilic cyclic compounds

PubMed Central

Tomobe, Katsufumi; Yamamoto, Eiji; Kojić, Dušan; Sato, Yohei; Yasui, Masato; Yasuoka, Kenji

2017-01-01

Water molecules at interfaces of materials exhibit enigmatic properties. A variety of spectroscopic studies have observed a high-frequency motion in these water molecules, represented by a blueshift, at both hydrophobic and hydrophilic interfaces. However, the molecular mechanism behind this blueshift has remained unclear. Using Raman spectroscopy and ab initio molecular dynamics simulations, we reveal the molecular mechanism of the blueshift of water molecules around six monosaccharide isomers. In the first hydration shell, we found weak hydrogen-bonded water molecules that cannot have a stable tetrahedral water network. In the water molecules, the vibrational state of the OH bond oriented toward the bulk solvent strongly contributes to the observed blueshift. Our work suggests that the blueshift in various solutions originates from the vibrational motions of these observed water molecules. PMID:29282448

Solvation of Na^+ in water from first-principles molecular dynamics

NASA Astrophysics Data System (ADS)

White, J. A.; Schwegler, E.; Galli, G.; Gygi, F.

2000-03-01

We have carried out ab initio molecular dynamics (MD) simulations of the Na^+ ion in water with an MD cell containing a single alkali ion and 53 water molecules. The electron-electron and electron-ion interactions were modeled by density functional theory with a generalized gradient approximation for the exchange-correlation functional. The computed radial distribution functions, coordination numbers, and angular distributions are consistent with available experimental data. The first solvation shell contains 5.2±0.6 water molecules, with some waters occasionally exchanging with those of the second shell. The computed Na^+ hydration number is larger than that from calculations for water clusters surrounding an Na^+ ion, but is consistent with that derived from x-ray measurements. Our results also indicate that the first hydration shell is better defined for Na^+ than for K^+ [1], as indicated by the first minimum in the Na-O pair distribution function. [1] L.M. Ramaniah, M. Bernasconi, and M. Parrinello, J. Chem. Phys. 111, 1587 (1999). This work was performed for DOE under contract W-7405-ENG-48.

Animated molecular dynamics simulations of hydrated caesium-smectite interlayers

PubMed Central

Sutton, Rebecca; Sposito, Garrison

2002-01-01

Computer animation of center of mass coordinates obtained from 800 ps molecular dynamics simulations of Cs-smectite hydrates (1/3 and 2/3 water monolayers) provided information concerning the structure and dynamics of the interlayer region that could not be obtained through traditional simulation analysis methods. Cs+ formed inner sphere complexes with the mineral surface, and could be seen to jump from one attracting location near a layer charge site to the next, while water molecules were observed to migrate from the hydration shell of one ion to that of another. Neighboring ions maintained a partial hydration shell by sharing water molecules, such that a single water molecule hydrated two ions simultaneously for hundreds of picoseconds. Cs-montmorillonite hydrates featured the largest extent of this sharing interaction, because interlayer ions were able to inhabit positions near surface cavities as well as at their edges, close to oxygen triads. The greater positional freedom of Cs+ within the montmorillonite interlayer, a result of structural hydroxyl orientation and low tetrahedral charge, promoted the optimization of distances between cations and water molecules required for water sharing. Preference of Cs+ for locations near oxygen triads was observed within interlayer beidellite and hectorite. Water molecules also could be seen to interact directly with the mineral surface, entering its surface cavities to approach attracting charge sites and structural hydroxyls. With increasing water content, water molecules exhibited increased frequency and duration of both cavity habitation and water sharing interactions. Competition between Cs+ and water molecules for surface sites was evident. These important cooperative and competitive features of interlayer molecular behavior were uniquely revealed by animation of an otherwise highly complex simulation output.

Interruption of Hydrogen Bonding Networks of Water in Carbon Nanotubes Due to Strong Hydration Shell Formation.

PubMed

Oya, Yoshifumi; Hata, Kenji; Ohba, Tomonori

2017-10-24

We present the structures of NaCl aqueous solution in carbon nanotubes with diameters of 1, 2, and 3 nm based on an analysis performed using X-ray diffraction and canonical ensemble Monte Carlo simulations. Anomalously longer nearest-neighbor distances were observed in the electrolyte for the 1-nm-diameter carbon nanotubes; in contrast, in the 2 and 3 nm carbon nanotubes, the nearest-neighbor distances were shorter than those in the bulk electrolyte. We also observed similar properties for water in carbon nanotubes, which was expected because the main component of the electrolyte was water. However, the nearest-neighbor distances of the electrolyte were longer than those of water in all of the carbon nanotubes; the difference was especially pronounced in the 2-nm-diameter carbon nanotubes. Thus, small numbers of ions affected the entire structure of the electrolyte in the nanopores of the carbon nanotubes. The formation of strong hydration shells between ions and water molecules considerably interrupted the hydrogen bonding between water molecules in the nanopores of the carbon nanotubes. The hydration shell had a diameter of approximately 1 nm, and hydration shells were thus adopted for the nanopores of the 2-nm-diameter carbon nanotubes, providing an explanation for the large difference in the nearest-neighbor distances between the electrolyte and water in these nanopores.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chatterjee, Anupam; Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076; Higham, Jonathan

A range of methods are presented to calculate a solute’s hydration shell from computer simulations of dilute solutions of monatomic ions and noble gas atoms. The methods are designed to be parameter-free and instantaneous so as to make them more general, accurate, and consequently applicable to disordered systems. One method is a modified nearest-neighbor method, another considers solute-water Lennard-Jones overlap followed by hydrogen-bond rearrangement, while three methods compare various combinations of water-solute and water-water forces. The methods are tested on a series of monatomic ions and solutes and compared with the values from cutoffs in the radial distribution function, themore » nearest-neighbor distribution functions, and the strongest-acceptor hydrogen bond definition for anions. The Lennard-Jones overlap method and one of the force-comparison methods are found to give a hydration shell for cations which is in reasonable agreement with that using a cutoff in the radial distribution function. Further modifications would be required, though, to make them capture the neighboring water molecules of noble-gas solutes if these weakly interacting molecules are considered to constitute the hydration shell.« less

Why are ionic liquid ions mainly associated in water? A Car-Parrinello study of 1-ethyl-3-methyl-imidazolium chloride water mixture

NASA Astrophysics Data System (ADS)

Spickermann, C.; Thar, J.; Lehmann, S. B. C.; Zahn, S.; Hunger, J.; Buchner, R.; Hunt, P. A.; Welton, T.; Kirchner, B.

2008-09-01

In this study we present the results of a first principles molecular dynamics simulation of a single 1-ethyl-3-methyl-imidazolium chloride [C2C1im][Cl] ion pair dissolved in 60 water molecules. We observe a preference of the in plane chloride coordination with respect to the cation ring plane as compared to the energetic slightly more demanding on top coordination. Evaluation of the different radial distribution functions demonstrates that the structure of the hydration shell around the ion pair differs significantly from bulk water and that no true ion pair dissociation in terms of completely autonomous solvation shells takes place on the timescale of the simulation. In addition, dipole moment distributions of the solvent in distinct solvation shells around different functional parts of the [C2C1im][Cl] ion pair are calculated from maximally localized Wannier functions. The analysis of these distributions gives evidence for a depolarization of water molecules close to the hydrophobic parts of the cation as well as close to the anion. Examination of the angular distribution of different OH(H2O )-X angles in turn shows a linear coordination of chloride accompanied by a tangential orientation of water molecules around the hydrophobic groups, being a typical feature of hydrophobic hydration. Based on these orientational aspects, a structural model for the obvious preference of ion pair association is developed, which justifies the associating behavior of solvated [C2C1im][Cl] ions in terms of an energetically favorable interface between the solvation shells of the anion and the hydrophobic parts of the cation.

Why are ionic liquid ions mainly associated in water? A Car-Parrinello study of 1-ethyl-3-methyl-imidazolium chloride water mixture.

PubMed

Spickermann, C; Thar, J; Lehmann, S B C; Zahn, S; Hunger, J; Buchner, R; Hunt, P A; Welton, T; Kirchner, B

2008-09-14

In this study we present the results of a first principles molecular dynamics simulation of a single 1-ethyl-3-methyl-imidazolium chloride [C(2)C(1)im][Cl] ion pair dissolved in 60 water molecules. We observe a preference of the in plane chloride coordination with respect to the cation ring plane as compared to the energetic slightly more demanding on top coordination. Evaluation of the different radial distribution functions demonstrates that the structure of the hydration shell around the ion pair differs significantly from bulk water and that no true ion pair dissociation in terms of completely autonomous solvation shells takes place on the timescale of the simulation. In addition, dipole moment distributions of the solvent in distinct solvation shells around different functional parts of the [C(2)C(1)im][Cl] ion pair are calculated from maximally localized Wannier functions. The analysis of these distributions gives evidence for a depolarization of water molecules close to the hydrophobic parts of the cation as well as close to the anion. Examination of the angular distribution of different OH(H(2)O)-X angles in turn shows a linear coordination of chloride accompanied by a tangential orientation of water molecules around the hydrophobic groups, being a typical feature of hydrophobic hydration. Based on these orientational aspects, a structural model for the obvious preference of ion pair association is developed, which justifies the associating behavior of solvated [C(2)C(1)im][Cl] ions in terms of an energetically favorable interface between the solvation shells of the anion and the hydrophobic parts of the cation.

Isotope effect in heavy/light water suspensions of optically active gold nanoparticles

NASA Astrophysics Data System (ADS)

Kutsenko, V. Y.; Artykulnyi, O. P.; Petrenko, V. I.; Avdeev, M. V.; Marchenko, O. A.; Bulavin, L. A.; Snegir, S. V.

2018-04-01

Aqueous suspensions of optically active gold nanoparticles coated with trisodium citrate were synthesized in light (H2O) water and mixture of light and heavy (H2O/D2O) water using the modified Turkevich protocol. The objective of the paper was to verify sensitivity of neutron scattering methods (in particular, neutron reflectometry) to the potential isotope H/D substitution in the stabilizing organic shell around particles in colloidal solutions. First, the isotope effect was studied with respect to the changes in the structural properties of metal particles (size, shape, crystalline morphology) in solutions by electron microscopy including high-resolution transmission electron microscopy from dried systems. The structural factors determining the variation in the adsorption spectra in addition to the change in the optical properties of surrounding medium were discussed. Then, neutron reflectometry was applied to the layered nanoparticles anchored on a silicon wafer via 3-aminopropyltriethoxysilane molecules to reveal the presence of deuterated water molecules in the shell presumably formed by citrate molecules around the metallic core.

X-ray and simulation studies of water

NASA Astrophysics Data System (ADS)

Nilsson, A.; Schlesinger, D.; G. M. Pettersson, L.

Here we present a picture that combines discussions regarding the thermodynamic anomalies in ambient and supercooled water with recent interpretations of X-ray spectroscopy and scattering data of water. At ambient temperatures most molecules favor a closer packing than tetrahedral, with strongly distorted hydrogen bonds, which allows the quantized librational modes to be excited and contribute to the entropy, but with enthalpically favored tetrahedrally bonded water patches appearing as fluctuations, a competition between entropy and enthalpy. Upon cooling water the amount of molecules participating in tetrahedral structures and the size of the tetrahedral patches increase. The two local structures are connected to the liquid-liquid critical point hypothesis in supercooled water corresponding to high-density liquid (HDL) and low-density liquid (LDL). We demonstrate that the HDL local structure deviates from a tetrahedral coordination not only through a collapse of the 2nd shell but also through severe distortions around the 1st coordination shell.

Nuclear quantum effects in water exchange around lithium and fluoride ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, David M.; Manolopoulos, David E.; Dang, Liem X.

2015-02-14

We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell ismore » found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the exchange processes are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium.« less

TMAO and urea in the hydration shell of the protein SNase.

PubMed

Smolin, Nikolai; Voloshin, Vladimir P; Anikeenko, Alexey V; Geiger, Alfons; Winter, Roland; Medvedev, Nikolai N

2017-03-01

We performed all-atom MD simulations of the protein SNase in aqueous solution and in the presence of two major osmolytes, trimethylamine-N-oxide (TMAO) and urea, as cosolvents at various concentrations and compositions and at different pressures and temperatures. The distributions of the cosolvent molecules and their orientation in the surroundings of the protein were analyzed in great detail. The distribution of urea is largely conserved near the protein. It varies little with pressure and temperature, and does practically not depend on the addition of TMAO. The slight decrease with temperature of the number of urea molecules that are in contact with the SNase molecule is consistent with the view that the interaction of the protein with urea is mainly of enthalpic nature. Most of the TMAO molecules tend to be oriented to the protein by its methyl groups, a small amount of these molecules contact the protein by its oxygen, forming hydrogen bonds with the protein, only. Unlike urea, the fraction of TMAO in the hydration shell of SNase slightly increases with temperature (a signature of a prevailing hydrophobic interaction between TMAO and SNase), and decreases significantly upon the addition of urea. This behavior reflects the diverse nature of the interaction of the two osmolytes with the protein. Using the Voronoi volume of the atoms of the solvent molecules (water, urea, TMAO), we compared the fraction of the volume occupied by a given type of solvent molecule in the hydration shell and in the bulk solvent. The volume fraction of urea in the hydration shell is more than two times larger than in the bulk, whereas the volume fraction of TMAO in the hydration shell is only slightly larger in the binary solvent (TMAO + water) and becomes even less than in the bulk in the ternary solvent (TMAO + water + urea). Thus, TMAO tends to be excluded from the hydration shell of the protein. The behavior of the two cosolvents in the vicinity of the protein does not change much with pressure (from 1 to 5000 bar) and temperature (from 280 to 330 K). This is also in line with the conception of the "osmophobic effect" of TMAO to protect proteins from denaturation also at harsh environmental conditions. We also calculated the volumetric parameters of SNase and found that the cosolvents have a small but significant effect on the apparent volume and its contributions, i.e. the intrinsic, molecular and thermal volumes.

Synthesis of fullerene@gold core-shell nanostructures.

PubMed

Ren, Yupeng; Paira, Priyankar; Nayak, Tapas Ranjan; Ang, Wee Han; Pastorin, Giorgia

2011-07-21

A "direct encapsulation" method was developed for the synthesis of highly stable water-soluble fullerene@gold core-shell nanostructures, with gold nanoshells showing either closed or porous morphology. This gold nano-shell coating formed a "nano-oven", capable of decomposing encapsulated fullerene molecules rapidly when irradiated by laser. We envisaged this being a useful tool for chemical reactions as well as a novel scaffold for nano-material synthesis.

The geometry of protein hydration

NASA Astrophysics Data System (ADS)

Persson, Filip; Söderhjelm, Pär; Halle, Bertil

2018-06-01

Based on molecular dynamics simulations of four globular proteins in dilute aqueous solution, with three different water models, we examine several, essentially geometrical, aspects of the protein-water interface that remain controversial or incompletely understood. First, we compare different hydration shell definitions, based on spatial or topological proximity criteria. We find that the best method for constructing monolayer shells with nearly complete coverage is to use a 5 Å water-carbon cutoff and a 4 Å water-water cutoff. Using this method, we determine a mean interfacial water area of 11.1 Å2 which appears to be a universal property of the protein-water interface. We then analyze the local coordination and packing density of water molecules in the hydration shells and in subsets of the first shell. The mean polar water coordination number in the first shell remains within 1% of the bulk-water value, and it is 5% lower in the nonpolar part of the first shell. The local packing density is obtained from additively weighted Voronoi tessellation, arguably the most physically realistic method for allocating space between protein and water. We find that water in all parts of the first hydration shell, including the nonpolar part, is more densely packed than in the bulk, with a shell-averaged density excess of 6% for all four proteins. We suggest reasons why this value differs from previous experimental and computational results, emphasizing the importance of a realistic placement of the protein-water dividing surface and the distinction between spatial correlation and packing density. The protein-induced perturbation of water coordination and packing density is found to be short-ranged, with an exponential decay "length" of 0.6 shells. We also compute the protein partial volume, analyze its decomposition, and argue against the relevance of electrostriction.

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory

PubMed Central

Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-ichi; Sugimoto, Naoki

2015-01-01

In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water–water interactions, (ii) ethylene glycol more effectively disrupted water–water interactions around Watson–Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson–Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. PMID:26538600

The structure of liquid water up to 360 MPa from x-ray diffraction measurements using a high Q-range and from molecular simulation

DOE PAGES

Skinner, L. B.; Galib, M.; Fulton, J. L.; ...

2016-04-04

In this study, x-ray diffraction measurements of liquid water are reported at pressures up to 360 MPa corresponding to a density of 0.0373 molecules per Å 3. The measurements were conducted at a spatial resolution corresponding to Q max = 16 Å -1. The method of data analysis and measurement in this study follows the earlier benchmark results reported for water under ambient conditions having a density of 0.0333 molecules per Å 3 and Q max = 20 Å -1 [J. Chem. Phys. 138, 074506 (2013)] and at 70°C having a density of 0.0327 molecules per Å 3 and Qmore » max = 20 Å -1 [J. Chem. Phys. 141, 214507 (2014)]. The structure of water is very different at these three different T and P state points and thus they provide the basis for evaluating the fidelity of molecular simulation. Measurements show that at 360 MPa, the 4 waters residing in the region between 2.3 and 3 Å are nearly unchanged: the peak position, shape, and coordination number are nearly identical to their values under ambient conditions. However, in the region above 3 Å, large structural changes occur with the collapse of the well-defined 2nd shell and shifting of higher shells to shorter distances. The measured structure is compared to simulated structure using intermolecular potentials described by both first-principles methods (revPBE-D3) and classical potentials (TIP4P/2005, MB-pol, and mW). The DFT-based, revPBE-D3, method and the many-body empirical potential model, MB-pol, provide the best overall representation of the ambient, high-temperature, and high-pressure data. Finally, the revPBE-D3, MB-pol, and the TIP4P/2005 models capture the densification mechanism, whereby the non-bonded 5th nearest neighbor molecule, which partially encroaches the 1st shell at ambient pressure, is pushed further into the local tetrahedral arrangement at higher pressures by the more distant molecules filling the void space in the network between the 1st and 2nd shells.« less

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

PubMed

Fogarty, Aoife C; Laage, Damien

2014-07-17

Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra.

Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

PubMed Central

2014-01-01

Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.

PubMed

Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-Ichi; Sugimoto, Naoki

2015-12-02

In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water-water interactions, (ii) ethylene glycol more effectively disrupted water-water interactions around Watson-Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson-Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Molecular mechanisms of decomposition of hydrated Na+Cl- ion pairs under planar nanopore conditions

NASA Astrophysics Data System (ADS)

Shevkunov, S. V.

2017-02-01

The decomposition of Na+Cl- ion pairs under the conditions of a nanoscopic planar pore with structureless walls in a material contact with water vapor at 298 K is simulated by Monte Carlo method. The transition from the state of a contact ion pair (CIP) to the state of solvent-separated ion pair (SSIP) is shown to occur as a result of an increase in the vapor pressure over a pore after exceeding the threshold number of molecules in a hydrate shell. It is found that the planar form of a molecular cluster under the conditions of a narrow pore does not level an abrupt structural transition and the formation of hydrogen bonds in the hydrate shell starts after three molecules are added. The hydrogen bond length under pore conditions is found to be resistant to variations in the hydrate shell size and coincides with that in water under normal conditions.

Neutron Nucleic Acid Crystallography.

PubMed

Chatake, Toshiyuki

2016-01-01

The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.

Dissecting the THz spectrum of liquid water from first principles via correlations in time and space.

PubMed

Heyden, Matthias; Sun, Jian; Funkner, Stefan; Mathias, Gerald; Forbert, Harald; Havenith, Martina; Marx, Dominik

2010-07-06

Solvation of molecules in water is at the heart of a myriad of molecular phenomena and of crucial importance to understanding such diverse issues as chemical reactivity or biomolecular function. Complementing well-established approaches, it has been shown that laser spectroscopy in the THz frequency domain offers new insights into hydration from small solutes to proteins. Upon introducing spatially-resolved analyses of the absorption cross section by simulations, the sensitivity of THz spectroscopy is traced back to characteristic distance-dependent modulations of absorption intensities for bulk water. The prominent peak at approximately 200 cm(-1) is dominated by first-shell dynamics, whereas a concerted motion involving the second solvation shell contributes most significantly to the absorption at about 80 cm(-1) approximately 2.4 THz. The latter can be understood in terms of an umbrella-like motion of two hydrogen-bonded tetrahedra along the connecting hydrogen bond axis. Thus, a modification of the hydrogen bond network, e.g., due to the presence of a solute, is expected to affect vibrational motion and THz absorption intensity at least on a length scale that corresponds to two layers of solvating water molecules. This result provides a molecular mechanism explaining the experimentally determined sensitivity of absorption changes in the THz domain in terms of distinct, solute-induced dynamical properties in solvation shells of (bio)molecules--even in the absence of well-defined resonances.

On the intermolecular vibrational coupling, hydrogen bonding, and librational freedom of water in the hydration shell of mono- and bivalent anions.

PubMed

Ahmed, Mohammed; Namboodiri, V; Singh, Ajay K; Mondal, Jahur A

2014-10-28

The hydration energy of an ion largely resides within the first few layers of water molecules in its hydration shell. Hence, it is important to understand the transformation of water properties, such as hydrogen-bonding, intermolecular vibrational coupling, and librational freedom in the hydration shell of ions. We investigated these properties in the hydration shell of mono- (Cl(-) and I(-)) and bivalent (SO4(2-) and CO3(2-)) anions by using Raman multivariate curve resolution (Raman-MCR) spectroscopy in the OH stretch, HOH bend, and [bend+librational] combination bands of water. Raman-MCR of aqueous Na-salt (NaCl, NaI, Na2SO4, and Na2CO3) solutions provides ion-correlated spectra (IC-spectrum) which predominantly bear the vibrational characteristics of water in the hydration shell of respective anions. Comparison of these IC-spectra with the Raman spectrum of bulk water in different spectral regions reveals that the water is vibrationally decoupled with its neighbors in the hydration shell. Hydrogen-bond strength and librational freedom also vary with the nature of anion: hydrogen-bond strength, for example, decreases as CO3(2-) > SO4(2-) > bulk water ≈ Cl(-) > I(-); and the librational freedom increases as CO3(2-) ≈ SO4(2-) < bulk water < Cl(-) < I(-). It is believed that these structural perturbations influence the dynamics of coherent energy transfer and librational reorientation of water in the hydration shell of anions.

Dock 'n roll: folding of a silk-inspired polypeptide into an amyloid-like beta solenoid.

PubMed

Zhao, Binwu; Cohen Stuart, Martien A; Hall, Carol K

2016-04-20

Polypeptides containing the motif ((GA)mGX)n occur in silk and have a strong tendency to self-assemble. For example, polypeptides containing (GAGAGAGX)n, where X = G or H have been observed to form filaments; similar sequences but with X = Q have been used in the design of coat proteins (capsids) for artificial viruses. The structure of the (GAGAGAGX)m filaments has been proposed to be a stack of peptides in a β roll structure with the hydrophobic side chains pointing outwards (hydrophobic shell). Another possible configuration, a β roll or β solenoid structure which has its hydrophobic side chains buried inside (hydrophobic core) was, however, overlooked. We perform ground state analysis as well as atomic-level molecular dynamics simulations, both on single molecules and on two-molecule stacks of the silk-inspired sequence (GAGAGAGQ)10, to decide whether the hydrophobic core or the hydrophobic shell configuration is the most stable one. We find that a stack of two hydrophobic core molecules is energetically more favorable than a stack of two hydrophobic shell molecules. A shell molecule initially placed in a perfect β roll structure tends to rotate its strands, breaking in-plane hydrogen bonds and forming out-of-plane hydrogen bonds, while a core molecule stays in the β roll structure. The hydrophobic shell structure has type II' β turns whereas the core configuration has type II β turns; only the latter secondary structure agrees well with solid-state NMR experiments on a similar sequence (GA)15. We also observe that the core stack has a higher number of intra-molecular hydrogen bonds and a higher number of hydrogen bonds between stack and water than the shell stack. Hence, we conclude that the hydrophobic core configuration is the most likely structure. In the stacked state, each peptide has more intra-molecular hydrogen bonds than a single folded molecule, which suggests that stacking provides the extra stability needed for molecules to reach the folded state.

Atomistic simulations of cation hydration in sodium and calcium montmorillonite nanopores

NASA Astrophysics Data System (ADS)

Yang, Guomin; Neretnieks, Ivars; Holmboe, Michael

2017-08-01

During the last four decades, numerous studies have been directed to the swelling smectite-rich clays in the context of high-level radioactive waste applications and waste-liners for contaminated sites. The swelling properties of clay mineral particles arise due to hydration of the interlayer cations and the diffuse double layers formed near the negatively charged montmorillonite (MMT) surfaces. To accurately study the cation hydration in the interlayer nanopores of MMT, solvent-solute and solvent-clay surface interactions (i.e., the solvation effects and the shape effects) on the atomic level should be taken into account, in contrast to many recent electric double layer based methodologies using continuum models. Therefore, in this research we employed fully atomistic simulations using classical molecular dynamics (MD) simulations, the software package GROMACS along with the CLAYFF forcefield and the SPC/E water model. We present the ion distributions and the deformation of the hydrated coordination structures, i.e., the hydration shells of Na+ and Ca2+ in the interlayer, respectively, for MMT in the first-layer, the second-layer, the third-layer, the fourth-layer, and the fifth-layer (1W, 2W, 3W, 4W, and 5W) hydrate states. Our MD simulations show that Na+ in Na-MMT nanopores have an affinity to the ditrigonal cavities of the clay layers and form transient inner-sphere complexes at about 3.8 Å from clay midplane at water contents less than the 5W hydration state. However, these phenomena are not observed in Ca-MMT regardless of swelling states. For Na-MMT, each Na+ is coordinated to four water molecules and one oxygen atom of the clay basal-plane in the first hydration shell at the 1W hydration state, and with five to six water molecules in the first hydration shell within a radius of 3.1 Å at all higher water contents. In Ca-MMT, however each Ca2+ is coordinated to approximately seven water molecules in the first hydration shell at the 1W hydration state and about eight water molecules in the first hydration shell within a radius of 3.3 Å at all higher hydration states. Moreover, the MD results show that the complete hydration shells are nearly spherical with an orthogonal coordination sphere. They could only be formed when the basal spacing d001 ≥ 18.7 Å, i.e., approximately, the interlayer separation h ≥ 10 Å. Comparison between DFT and MD simulations shows that DFT failed to reproduce the outer-sphere complexes in the Stern-layer (within ˜5.0 Å from the clay basal-plane), observed in the MD simulations.

Nuclear quantum effects in water exchange around lithium and fluoride ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, David M.; Manolopoulos, David; Dang, Liem X.

2015-02-14

We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell ismore » found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the water exchange reactions are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium, and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium. LXD was supported by US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.« less

Size-tunable drug-delivery capsules composed of a magnetic nanoshell.

PubMed

Fuchigami, Teruaki; Kitamoto, Yoshitaka; Namiki, Yoshihisa

2012-01-01

Nano-sized FePt capsules with two types of ultrathin shell were fabricated using a template method for use in a nano-scale drug delivery system. One capsule was composed of an inorganic-organic hybrid shell of a water-soluble polymer and FePt nanoparticles, and the other capsule was composed of a network of fused FePt nanoparticles. We demonstrated that FePt nanoparticles selectively accumulated on the polymer molecules adsorbed on the template silica particles, and investigated the morphologies of the particle accumulation by changing the concentration of the polymer solution with which the template particles were treated. Capsular size was reduced from 340 to less than 90 nm by changing the size of the silica template particles, and the shell thickness was controlled by changing the amount of FePt nanoparticles adsorbed on the template particles. The hybrid shell was maintained by the connection of FePt nanoparticles and polymer molecules, and the shell thickness was 10 nm at the maximum. The FePt network shell was fabricated by hydrothermal treatment of the FePt/polymer-modified silica composite particles. The FePt network shell was produced from only the FePt alloy, and the shell thickness was 3 nm. Water-soluble anti-cancer drugs could be loaded into the hollow space of FePt network capsules, and lipid-coated FePt network capsules loaded with anti-cancer drugs showed cellular toxicity. The nano-sized capsular structure and the ultrathin shell suggest applicability as a drug carrier in magnetically guided drug delivery systems.

Size-tunable drug-delivery capsules composed of a magnetic nanoshell

PubMed Central

Fuchigami, Teruaki; Kitamoto, Yoshitaka; Namiki, Yoshihisa

2012-01-01

Nano-sized FePt capsules with two types of ultrathin shell were fabricated using a template method for use in a nano-scale drug delivery system. One capsule was composed of an inorganic-organic hybrid shell of a water-soluble polymer and FePt nanoparticles, and the other capsule was composed of a network of fused FePt nanoparticles. We demonstrated that FePt nanoparticles selectively accumulated on the polymer molecules adsorbed on the template silica particles, and investigated the morphologies of the particle accumulation by changing the concentration of the polymer solution with which the template particles were treated. Capsular size was reduced from 340 to less than 90 nm by changing the size of the silica template particles, and the shell thickness was controlled by changing the amount of FePt nanoparticles adsorbed on the template particles. The hybrid shell was maintained by the connection of FePt nanoparticles and polymer molecules, and the shell thickness was 10 nm at the maximum. The FePt network shell was fabricated by hydrothermal treatment of the FePt/polymer-modified silica composite particles. The FePt network shell was produced from only the FePt alloy, and the shell thickness was 3 nm. Water-soluble anti-cancer drugs could be loaded into the hollow space of FePt network capsules, and lipid-coated FePt network capsules loaded with anti-cancer drugs showed cellular toxicity. The nano-sized capsular structure and the ultrathin shell suggest applicability as a drug carrier in magnetically guided drug delivery systems. PMID:23507895

An experimental point of view on hydration/solvation in halophilic proteins

PubMed Central

Talon, Romain; Coquelle, Nicolas; Madern, Dominique; Girard, Eric

2014-01-01

Protein-solvent interactions govern the behaviors of proteins isolated from extreme halophiles. In this work, we compared the solvent envelopes of two orthologous tetrameric malate dehydrogenases (MalDHs) from halophilic and non-halophilic bacteria. The crystal structure of the MalDH from the non-halophilic bacterium Chloroflexus aurantiacus (Ca MalDH) solved, de novo, at 1.7 Å resolution exhibits numerous water molecules in its solvation shell. We observed that a large number of these water molecules are arranged in pentagonal polygons in the first hydration shell of Ca MalDH. Some of them are clustered in large networks, which cover non-polar amino acid surface. The crystal structure of MalDH from the extreme halophilic bacterium Salinibacter ruber (Sr) solved at 1.55 Å resolution shows that its surface is strongly enriched in acidic amino acids. The structural comparison of these two models is the first direct observation of the relative impact of acidic surface enrichment on the water structure organization between a halophilic protein and its non-adapted counterpart. The data show that surface acidic amino acids disrupt pentagonal water networks in the hydration shell. These crystallographic observations are discussed with respect to halophilic protein behaviors in solution PMID:24600446

An experimental point of view on hydration/solvation in halophilic proteins.

PubMed

Talon, Romain; Coquelle, Nicolas; Madern, Dominique; Girard, Eric

2014-01-01

Protein-solvent interactions govern the behaviors of proteins isolated from extreme halophiles. In this work, we compared the solvent envelopes of two orthologous tetrameric malate dehydrogenases (MalDHs) from halophilic and non-halophilic bacteria. The crystal structure of the MalDH from the non-halophilic bacterium Chloroflexus aurantiacus (Ca MalDH) solved, de novo, at 1.7 Å resolution exhibits numerous water molecules in its solvation shell. We observed that a large number of these water molecules are arranged in pentagonal polygons in the first hydration shell of Ca MalDH. Some of them are clustered in large networks, which cover non-polar amino acid surface. The crystal structure of MalDH from the extreme halophilic bacterium Salinibacter ruber (Sr) solved at 1.55 Å resolution shows that its surface is strongly enriched in acidic amino acids. The structural comparison of these two models is the first direct observation of the relative impact of acidic surface enrichment on the water structure organization between a halophilic protein and its non-adapted counterpart. The data show that surface acidic amino acids disrupt pentagonal water networks in the hydration shell. These crystallographic observations are discussed with respect to halophilic protein behaviors in solution.

Stabilities of protonated water-ammonia clusters

NASA Astrophysics Data System (ADS)

Sundén, A. E. K.; Støchkel, K.; Hvelplund, P.; Brøndsted Nielsen, S.; Dynefors, B.; Hansen, K.

2018-05-01

Branching ratios of water and ammonia evaporation have been measured for spontaneous evaporation from protonated mixed clusters H+(H2O)n(NH3)m in the size range 0 ≤ n ≤ 11 and 0 ≤ m ≤ 7. Mixed clusters evaporate water except for clusters containing six or more ammonia molecules, indicating the formation of a stable core of one ammonium ion surrounded by four ammonia molecules and a second shell consisting predominantly of water. We relate evaporative branching ratios to free energy differences between the products of competing channels and determine the free energy differences for clusters with up to seven ammonia molecules. Clusters containing up to five ammonia molecules show a very strong scaling of these free energy differences.

The structure of liquid water up to 360 MPa from x-ray diffraction measurements using a high Q-range and from molecular simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Skinner, L. B.; Mineral Physics Institute, Stony Brook University, Stony Brook, New York, New York 11794-2100; Galib, M.

2016-04-07

X-ray diffraction measurements of liquid water are reported at pressures up to 360 MPa corresponding to a density of 0.0373 molecules per Å{sup 3}. The measurements were conducted at a spatial resolution corresponding to Q{sub max} = 16 Å{sup −1}. The method of data analysis and measurement in this study follows the earlier benchmark results reported for water under ambient conditions having a density of 0.0333 molecules per Å{sup 3} and Q{sub max} = 20 Å{sup −1} [J. Chem. Phys. 138, 074506 (2013)] and at 70 °C having a density of 0.0327 molecules per Å{sup 3} and Q{sub max} = 20more » Å{sup −1} [J. Chem. Phys. 141, 214507 (2014)]. The structure of water is very different at these three different T and P state points and thus they provide the basis for evaluating the fidelity of molecular simulation. Measurements show that at 360 MPa, the 4 waters residing in the region between 2.3 and 3 Å are nearly unchanged: the peak position, shape, and coordination number are nearly identical to their values under ambient conditions. However, in the region above 3 Å, large structural changes occur with the collapse of the well-defined 2nd shell and shifting of higher shells to shorter distances. The measured structure is compared to simulated structure using intermolecular potentials described by both first-principles methods (revPBE-D3) and classical potentials (TIP4P/2005, MB-pol, and mW). The DFT-based, revPBE-D3, method and the many-body empirical potential model, MB-pol, provide the best overall representation of the ambient, high-temperature, and high-pressure data. The revPBE-D3, MB-pol, and the TIP4P/2005 models capture the densification mechanism, whereby the non-bonded 5th nearest neighbor molecule, which partially encroaches the 1st shell at ambient pressure, is pushed further into the local tetrahedral arrangement at higher pressures by the more distant molecules filling the void space in the network between the 1st and 2nd shells.« less

Multicompartmental Microcapsules with Orthogonal Programmable Two-Way Sequencing of Hydrophobic and Hydrophilic Cargo Release.

PubMed

Xu, Weinan; Ledin, Petr A; Iatridi, Zacharoula; Tsitsilianis, Constantinos; Tsukruk, Vladimir V

2016-04-11

Multicompartmental responsive microstructures with the capability for the pre-programmed sequential release of multiple target molecules of opposite solubility (hydrophobic and hydrophilic) in a controlled manner have been fabricated. Star block copolymers with dual-responsive blocks (temperature for poly(N-isopropylacrylamide) chains and pH for poly(acrylic acid) and poly(2-vinylpyridine) arms) and unimolecular micellar structures serve as nanocarriers for hydrophobic molecules in the microcapsule shell. The interior of the microcapsule can be loaded with water-soluble hydrophilic macromolecules. For these dual-loaded microcapsules, a programmable and sequential release of hydrophobic and hydrophilic molecules from the shell and core, respectively, can be triggered independently by temperature and pH variations. These stimuli affect the hydrophobicity and chain conformation of the star block copolymers to initiate out-of-shell release (elevated temperature), or change the overall star conformation and interlayer interactions to trigger increased permeability of the shell and out-of-core release (pH). Reversing stimulus order completely alters the release process. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Core-shell biopolymer nanoparticle delivery systems: synthesis and characterization of curcumin fortified zein-pectin nanoparticles.

PubMed

Hu, Kun; Huang, Xiaoxia; Gao, Yongqing; Huang, Xulin; Xiao, Hang; McClements, David Julian

2015-09-01

Biopolymer core-shell nanoparticles were fabricated using a hydrophobic protein (zein) as the core and a hydrophilic polysaccharide (pectin) as the shell. Particles were prepared by coating cationic zein nanoparticles with anionic pectin molecules using electrostatic deposition (pH 4). The core-shell nanoparticles were fortified with curcumin (a hydrophobic bioactive molecule) at a high loading efficiency (>86%). The resulting nanoparticles were spherical, relatively small (diameter ≈ 250 nm), and had a narrow size distribution (polydispersity index ≈ 0.24). The encapsulated curcumin was in an amorphous (rather than crystalline form) as detected by differential scanning calorimetry (DSC). Fourier transform infrared (FTIR) and Raman spectra indicated that the encapsulated curcumin interacted with zein mainly through hydrophobic interactions. The nanoparticles were converted into a powdered form that had good water-dispersibility. These core-shell biopolymer nanoparticles could be useful for incorporating curcumin into functional foods and beverages, as well as dietary supplements and pharmaceutical products. Copyright © 2015 Elsevier Ltd. All rights reserved.

Miscibility at the immiscible liquid/liquid interface: A molecular dynamics study of thermodynamics and mechanism

NASA Astrophysics Data System (ADS)

Karnes, John J.; Benjamin, Ilan

2018-01-01

Molecular dynamics simulations are used to study the dissolution of water into an adjacent, immiscible organic liquid phase. Equilibrium thermodynamic and structural properties are calculated during the transfer of water molecule(s) across the interface using umbrella sampling. The net free energy of transfer agrees reasonably well with experimental solubility values. We find that water molecules "prefer" to transfer into the adjacent phase one-at-a-time, without co-transfer of the hydration shell, as in the case of evaporation. To study the dynamics and mechanism of transfer of water to liquid nitrobenzene, we collected over 400 independent dissolution events. Analysis of these trajectories suggests that the transfer of water is facilitated by interfacial protrusions of the water phase into the organic phase, where one water molecule at the tip of the protrusion enters the organic phase by the breakup of a single hydrogen bond.

Solvation structures and dynamics of alkaline earth metal halides in supercritical water: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Keshri, Sonanki; Mandal, Ratnamala; Tembe, B. L.

2016-09-01

Constrained molecular dynamics simulations of alkaline earth metal halides have been carried out to investigate their structural and dynamical properties in supercritical water. Potentials of mean force (PMFs) for all the alkaline earth metal halides in supercritical water have been computed. Contact ion pairs (CIPs) are found to be more stable than all other configurations of the ion pairs except for MgI2 where solvent shared ion pair (SShIP) is more stable than the CIP. There is hardly any difference in the PMFs between the M2+ (M = Mg, Ca, Sr, Ba) and the X- (X = F, Cl, Br, I) ions whether the second X- ion is present in the first coordination shell of the M2+ ion or not. The solvent molecules in the solvation shells diffuse at a much slower rate compared to the bulk. Orientational distribution functions of solvent molecules are sharper for smaller ions.

Molecular dynamics study of the solvation of calcium carbonate in water.

PubMed

Bruneval, Fabien; Donadio, Davide; Parrinello, Michele

2007-10-25

We performed molecular dynamics simulations of diluted solutions of calcium carbonate in water. To this end, we combined and tested previous polarizable models. The carbonate anion forms long-living hydrogen bonds with water and shows an amphiphilic character, in which the water molecules are expelled in a region close to its C(3) symmetry axis. The calcium cation forms a strongly bound ion pair with the carbonate. The first hydration shell around the CaCO(3) pair is found to be very similar to the location of the water molecules surrounding CaCO(3) in ikaite, the hydrated mineral.

Dock ’n Roll: Folding of a Silk-Inspired Polypeptide into an Amyloid-like Beta Solenoid

PubMed Central

Zhao, Binwu; Cohen Stuart, Martien A.; Hall, Carol K.

2016-01-01

Polypeptides containing the motif ((GA)mGX)n occur in silk (we refer to them as ‘silk-like’) and have a strong tendency to self-assemble. For example, polypeptides containing (GAGAGAGX)n, where X = G or H have been observed to form filaments; similar sequences but with X = Q have been used in the design of coat proteins (capsids) for artificial viruses. The structure of the (GAGAGAGX)m filaments has been proposed to be a stack of peptides in a β roll structure with the hydrophobic side chains pointing outwards (hydrophobic shell). Another possible configuration, a β roll or β solenoid structure which has its hydrophobic side chains buried inside (hydrophobic core) was, however, overlooked. We perform ground state analysis as well as atomic-level molecular dynamics simulations, both on single molecules and on two-molecule stacks of the silk-inspired sequence (GAGAGAGQ)10, to decide whether the hydrophobic core or the hydrophobic shell configuration is the most stable one. We find that a stack of two hydrophobic core molecules is energetically more favorable than a stack of two shell molecules. A shell molecule initially placed in a perfect β roll structure tends to rotate its strands, breaking in-plane hydrogen bonds and forming out-of-plane hydrogen bonds, while a core molecule stays in the β roll structure. The hydrophobic shell structure has type II’ β turns whereas the core configuration has type II β turns; only the latter secondary structure agrees well with solid-state NMR experiments on a similar sequence (GA)15. We also observe that the core stack has a higher number of intra-molecular hydrogen bonds and a higher number of hydrogen bonds between stack and water than the shell stack. Hence, we conclude that the hydrophobic core configuration is the most likely structure. In the stacked state, each peptide has more intra-molecular hydrogen bonds than a single folded molecule, which suggests that stacking provides the extra stability needed for molecules to reach the folded state. PMID:26947809

Core-Shell-Corona Micelles with a Responsive Shell.

PubMed

Gohy, Jean-François; Willet, Nicolas; Varshney, Sunil; Zhang, Jian-Xin; Jérôme, Robert

2001-09-03

A reactor for the synthesis of gold nanoparticles is one of the uses of a poly(styrene)-block-poly(2-vinylpyridine)-block-poly(ethylene oxide) triblock copolymer (PS-b-P2VP-b-PEO) which forms core-shell-corona micelles in water. Very low polydispersity spherical micelles are observed that consist of a PS core surrounded by a pH-sensitive P2VP shell and a corona of PEO chains end-capped by a hydroxyl group. The corona can act as a site for attaching responsive or sensing molecules. © 2001 WILEY-VCH Verlag GmbH, Weinheim, Fed. Rep. of Germany.

First Principles Simulations fo the Supercritical Behavior of Ore Forming Fluids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weare, John H

2013-04-19

Abstract of Selected Research Progress: I. First-principles simulation of solvation structure and deprotonation reactions of ore forming metal ions in very nonideal solutions: Advances in algorithms and computational performance achieved in this grant period have allowed the atomic level dynamical simulation of complex nanoscale materials using interparticle forces calculated directly from an accurate density functional solution to the electronic Schr dinger equation (ab-initio molecular dynamics, AIMD). Focus of this program was on the prediction and analysis of the properties of environmentally important ions in aqueous solutions. AIMD methods have provided chemical interpretations of these very complex systems with an unprecedentedmore » level of accuracy and detail. The structure of the solvation region neighboring a highly charged metal ion (e.g., 3+) in an aqueous solution is very different from that of bulk water. The many-body behaviors (polarization, charge transfer, etc.) of the ion-water and water-water interactions in this region are difficult to capture with conventional empirical potentials. However, a large numbers of waters (up to 128 waters) are required to fully describe chemical events in the extended hydrations shells and long simulation times are needed to reliably sample the system. Taken together this makes simulation at the 1st principles level a very large computational problem. Our AIMD simulation results using these methods agree with the measured octahedral structure of the 1st solvation shell of Al3+ at the 1st shell boundary and a calculated radius of 1.937 (exp. 1.9). Our calculated average 2nd shell radius agrees remarkably well with the measured radius, 4.093 calculated vs. the measured value of 4.0-4.15 . Less can be experimentally determined about the structure of the 2nd shell. Our simulations show that this shell contains roughly 12 water molecules, which are trigonally coordinated to the 1st shell waters. This structure cannot be measured directly. However, the number of 2nd shell water molecules predicted by the simulation is consistent with experimental estimates. Tetrahedral bulk water coordination reappears just after the 2nd shell. Simulations with 128 waters are close to the maximum size that can effectively be performed with present day methods. While the time scale of our simulation are not long enough to observe transfers of waters from the 1st to the 2nd shell, we do see transfers occurring on a picosecond time scale between the 2nd shell and 3rd shell via an associative mechanism. This is faster than, but consistent with, the results of measurements on the more tightly bound Cr3+ system. For high temperature simulations, proton transfers occur in the solvation shells leading to transient hydrolysis species. The reaction coordinate for proton transfer involves the coordinates of neighboring solvent waters as in the Grotis mechanism for proton transfer in bulk water. Directly removing a proton from the hexaqua Al3+ ion leads to a much more labile solvation shell and to a five coordinated Al3+ ion. This is consistent with very recent rate measurements of ligand exchange and the conjugate base labilization effect. For the Al3+-H2O system results for high but subcritical temperatures are qualitatively similar to room temperature simulations. However, preliminary simulations for supercritical temperatures (750K) suggest that there may be a dramatic change in behavior in the hydration structure of ions for these temperatures. For transition metal ions the presence of d valence electrons plays a significant role in the behavior of the system. Our preliminary results for the Fe3+ ion suggest that this ion which is larger radius than the Al3+ ion has somewhat less rigid 1st and 2nd solvation shell. II. Gibbs Ensemble Monte Carlo Simulation of Vapor/Liquid and Metastable Liquid/Liquid Phase Equilibria in the CO2-CH4-N2 System Many fluid inclusions have compositions in the system CO2-CH4-N2. Estimates of the saturation pressures, compositions and volumetric properties of coexisting phases in the unaries, binaries and the ternary of this system have been obtained from simulations using the Gibbs Ensemble Monte Carlo method. The temperature and pressure range considered include liquid/vapor, gas/gas and metastable liquid/liquid regions. All the molecular interactions in the system were described with two-body Lennard-Jones potentials requiring only two temperature independent parameters for interactions between like molecules. The Berthhelot-Lorentz rules are used to define the Lennard-Jones interactions for unlike molecules with one additional temperature independent mixing parameter. The equilibrium compositions and molar volumes of the coexisting phases in all the mixtures are predicted with accuracy close to that of the data. These results, particularly for the phase densities and critical parameters, are considerably closer to the observed values than those that have been reported using equation of state methods(116). For very low temperatures liquid/metastable liquid/vapor coexistence was observed for the CO2-N2 and the CH4-CO2 systems, e.g. the L1L2V line. The possibility of gas-gas coexistence for the binary N2-CO2 at high temperatures and pressures was also investigated but not observed.« less

Dynamics of water solutions of natural polysaccharides by fast field cycling nmr relaxometry

NASA Astrophysics Data System (ADS)

Prusova, Alena; Conte, Pellegrino; Kucerik, Jiri; de Pasquale, Claudio; Alonzo, Giuseppe

2010-05-01

Cryobiology studies the effect of low temperatures on living systems such as microorganisms and plants. In particular, plants growing in cold or frozen environments can survive such extreme conditions due to the cold hardening process. Hardening is a three step process during which, first, translocation of polysaccharides to the plant roots affects water structure in the cell-soil surface. For this reason, increase of cell-membrane permeability and resistance to temperatures from -5°C to -10°C is achieved. In a second step, chemical alteration of cell membrane arises and resistance to temperatures up to -20°C is obtained. The last hardening step consists in the vitrification of the plant tissues which allow plants to survive at temperatures as low as -50°C. Since polysaccharides play a very important role in the initial part of the cold hardening process, it is of paramount importance to study the effect of such natural biopolymers on water structure. Here, we present preliminary data obtained by fast field cycling NMR relaxometry on the effect of hyaluronan (an anionic, non-sulfated glycosaminoglycan) on water structure at different concentrations of the polysaccharide. Although hyaluronan is a polysaccharide found exceptionally in animal, human or bacterial bodies, in the present work it was used as a model "pilot" compound. In fact, it has an unique ability to hold water and it contains both polysaccharide and protein-like acetamido functionalities. For this reason, hyaluronan promotes the future research on other plant biopolymers such as, for instance, starch and other very specific proteins. Results revealed that different water-structure systems surround the molecule of hyaluronan in diluted and semidiluted systems. Namely, at the lowest hyaluronan concentration, three hydration shells can be recognized. The first hydration shell is made by bound water (BW) which is strongly fixed to the hyaluronan surface mainly through electrostatic interactions. A second hydration shell contains water molecules, also recognized as partly-bound (PBW), which are not directly interacting with the hyaluronan chains but with BW. Finally, water molecules, which dynamics is resembling that of the pure and undisturbed water, are indicated either as a bulk water or free water (FW). As hyaluronan concentration is increased the third FW hydration shell is lost and all water molecules are affected by the presence of hyaluronan molecules. This work showed the great potential of FFC-NMR relaxometry in revealing water nature in polysaccharide solutions and the possibility for future applications on complex biological systems. Acknowledgements A.P. gratefully acknowledges a bilateral Erasmus project between Brno University of Technology and University of Palermo which provided grant sustainment for working in Italy. Ministry of Education of the Czech Republic, project MSM 0021630501 is also acknwledged. This work was partially funded by Ce.R.T.A. s.c.r.l. (Centri Regionali per le Tecnologie Alimentari; Italy). Authors kindly acknowledge Dr. Vladimír Velebný (CPN company, Dolní Dobrouč, Czech Republic) for providing of hyaluronan sample.

CuCl Complexation in the Vapor Phase: Insights from Ab Initio Molecular Dynamics Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mei, Yuan; Liu, Weihua; Migdiov, A. A.

We invesmore » tigated the hydration of the CuCl 0 complex in HCl-bearing water vapor at 350°C and a vapor-like fluid density between 0.02 and 0.09 g/cm 3 using ab initio molecular dynamics (MD) simulations. The simulations reveal that one water molecule is strongly bonded to Cu(I) (first coordination shell), forming a linear [H 2O-Cu-Cl] 0 moiety. The second hydration shell is highly dynamic in nature, and individual configurations have short life-spans in such low-density vapors, resulting in large fluctuations in instantaneous hydration numbers over a timescale of picoseconds. The average hydration number in the second shell (m) increased from ~0.5 to ~3.5 and the calculated number of hydrogen bonds per water molecule increased from 0.09 to 0.25 when fluid density (which is correlated to water activity) increased from 0.02 to 0.09 g/cm 3 ( f H 2O 1.72 to 2.05). These changes of hydration number are qualitatively consistent with previous solubility studies under similar conditions, although the absolute hydration numbers from MD were much lower than the values inferred by correlating experimental Cu fugacity with water fugacity. This could be due to the uncertainties in the MD simulations and uncertainty in the estimation of the fugacity coefficients for these highly nonideal “vapors” in the experiments. Finally, our study provides the first theoretical confirmation that beyond-first-shell hydrated metal complexes play an important role in metal transport in low-density hydrothermal fluids, even if it is highly disordered and dynamic in nature.« less

CuCl Complexation in the Vapor Phase: Insights from Ab Initio Molecular Dynamics Simulations

DOE PAGES

Mei, Yuan; Liu, Weihua; Migdiov, A. A.; ...

2018-05-02

We invesmore » tigated the hydration of the CuCl 0 complex in HCl-bearing water vapor at 350°C and a vapor-like fluid density between 0.02 and 0.09 g/cm 3 using ab initio molecular dynamics (MD) simulations. The simulations reveal that one water molecule is strongly bonded to Cu(I) (first coordination shell), forming a linear [H 2O-Cu-Cl] 0 moiety. The second hydration shell is highly dynamic in nature, and individual configurations have short life-spans in such low-density vapors, resulting in large fluctuations in instantaneous hydration numbers over a timescale of picoseconds. The average hydration number in the second shell (m) increased from ~0.5 to ~3.5 and the calculated number of hydrogen bonds per water molecule increased from 0.09 to 0.25 when fluid density (which is correlated to water activity) increased from 0.02 to 0.09 g/cm 3 ( f H 2O 1.72 to 2.05). These changes of hydration number are qualitatively consistent with previous solubility studies under similar conditions, although the absolute hydration numbers from MD were much lower than the values inferred by correlating experimental Cu fugacity with water fugacity. This could be due to the uncertainties in the MD simulations and uncertainty in the estimation of the fugacity coefficients for these highly nonideal “vapors” in the experiments. Finally, our study provides the first theoretical confirmation that beyond-first-shell hydrated metal complexes play an important role in metal transport in low-density hydrothermal fluids, even if it is highly disordered and dynamic in nature.« less

High Level ab initio Predictions of the Energetics of mCO2•(H2O)n (n = 1-3, m = 1-12) Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thanthiriwatte, Sahan; Duke, Jessica R.; Jackson, Virgil E.

Electronic structure calculations at the correlated molecular orbital theory and density functional theory levels have been used to generate a reliable set of clustering energies for up to three water molecules in carbon dioxide clusters up to n = 12. The structures and energetics are dominated by Lewis acid-base interactions with hydrogen bonding interactions playing a lesser energetic role. The actual binding energies are somewhat larger than might be expected. The correlated molecular orbital MP2 method and density functional theory with the ωB97X exchange-correlation functional provide good results for the energetics of the clusters but the B3LYP and ωB97X-D functionalsmore » do not. Seven CO2 molecules form the first solvent shell about a single H2O with four CO2 molecules interacting with the H2O via Lewis acid-base interactions, two CO2 interacting with the H2O by hydrogen bonds, and the seventh CO2 completing the shell. The Lewis acid-base and weak hydrogen bond interactions between the water molecules and the CO2 molecules are strong enough to disrupt the trimer ring configuration for as few as seven CO2 molecules. Calculated 13C NMR chemical shifts for mCO2•(H2O)n show little change with respect to the number of H2O or CO2 molecules in the cluster. The O-H stretching frequencies do exhibit shifts that can provide information about the interactions between water and CO2 molecules.« less

A shell-resolved analysis of preferential solvation of coffee ingredients in aqueous mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate

NASA Astrophysics Data System (ADS)

Zeindlhofer, Veronika; Berger, Magdalena; Steinhauser, Othmar; Schröder, Christian

2018-05-01

Ionic liquids increase the solubility of various coffee ingredients in aqueous solution but little is known about the underlying mechanism. Kirkwood-Buff integrals as well as the potential of mean force indicate that the imidazolium cations are accumulated at the surface of the solutes, removing water molecules from the solute surface. Although hydrogen bonding of the anions to hydroxy groups of the solutes can be detected, their concentration at the surface is less enhanced compared to the cations. The decomposition into solvation shells by Voronoi tessellation reveals that structural features are only observed in the first solvation shell. Nevertheless, the depletion of water and the excess concentration of the ions and, in particular, of the cations are visible in the next solvation shells as well. Therefore, classical arguments of hydrotropic theory fail to explain this behavior.

Inner and Outer Coordination Shells of Mg(2+) in CorA Selectivity Filter from Molecular Dynamics Simulations.

PubMed

Kitjaruwankul, Sunan; Wapeesittipan, Pattama; Boonamnaj, Panisak; Sompornpisut, Pornthep

2016-01-28

Structural data of CorA Mg(2+) channels show that the five Gly-Met-Asn (GMN) motifs at the periplasmic loop of the pentamer structure form a molecular scaffold serving as a selectivity filter. Unfortunately, knowledge about the cation selectivity of Mg(2+) channels remains limited. Since Mg(2+) in aqueous solution has a strong first hydration shell and apparent second hydration sphere, the coordination structure of Mg(2+) in a CorA selectivity filter is expected to be different from that in bulk water. Hence, this study investigated the hydration structure and ligand coordination of Mg(2+) in a selectivity filter of CorA using molecular dynamics (MD) simulations. The simulations reveal that the inner-shell structure of Mg(2+) in the filter is not significantly different from that in aqueous solution. The major difference is the characteristic structural features of the outer shell. The GMN residues engage indirectly in the interactions with the metal ion as ligands in the second shell of Mg(2+). Loss of hydrogen bonds between inner- and outer-shell waters observed from Mg(2+) in bulk water is mostly compensated by interactions between waters in the first solvation shell and the GMN motif. Some water molecules in the second shell remain in the selectivity filter and become less mobile to support the metal binding. Removal of Mg(2+) from the divalent cation sensor sites of the protein had an impact on the structure and metal binding of the filter. From the results, it can be concluded that the GMN motif enhances the affinity of the metal binding site in the CorA selectivity filter by acting as an outer coordination ligand.

Near-infrared studies of glucose and sucrose in aqueous solutions: water displacement effect and red shift in water absorption from water-solute interaction.

PubMed

Jung, Youngeui; Hwang, Jungseek

2013-02-01

We used near infrared spectroscopy to obtain concentration dependent glucose absorption spectra in aqueous solutions in the near-infrared range (3800-7500 cm(-1)). Here we introduce a new method to obtain reliable glucose absorption bands from aqueous glucose solutions without measuring the water displacement coefficients of glucose separately. Additionally, we were able to extract the water displacement coefficients of glucose, and this may offer a new general method using spectroscopy techniques applicable to other water-soluble materials. We also observed red shifts in the absorption bands of water in the hydration shell around solute molecules, which comes from the contribution of the interacting water molecules around the glucose molecules in solutions. The intensity of the red shift gets larger as the concentration increases, which indicates that as the concentration increases more water molecules are involved in the interaction. However, the red shift in frequency does not seem to depend significantly on the concentration. We also performed the same measurements and analysis with sucrose instead of glucose as solute and compared.

Density functional theory and molecular dynamics study of the uranyl ion (UO₂)²⁺.

PubMed

Rodríguez-Jeangros, Nicolás; Seminario, Jorge M

2014-03-01

The detection of uranium is very important, especially in water and, more importantly, in the form of uranyl ion (UO₂)²⁺, which is one of its most abundant moieties. Here, we report analyses and simulations of uranyl in water using ab initio modified force fields for water with improved parameters and charges of uranyl. We use a TIP4P model, which allows us to obtain accurate water properties such as the boiling point and the second and third shells of water molecules in the radial distribution function thanks to a fictitious charge that corrects the 3-point models by reproducing the exact dipole moment of the water molecule. We also introduced non-bonded interaction parameters for the water-uranyl intermolecular force field. Special care was taken in testing the effect of a range of uranyl charges on the structure of uranyl-water complexes. Atomic charges of the solvated ion in water were obtained using density functional theory (DFT) calculations taking into account the presence of nitrate ions in the solution, forming a neutral ensemble. DFT-based force fields were calculated in such a way that water properties, such as the boiling point or the pair distribution function stand. Finally, molecular dynamics simulations of a water box containing uranyl cations and nitrate anions are performed at room temperature. The three peaks in the oxygen-oxygen radial distribution function for water were found to be kept in the presence of uranyl thanks to the improvement of interaction parameters and charges. Also, we found three shells of water molecules surrounding the uranyl ion instead of two as was previously thought.

Evidence for Reduced Hydrogen-Bond Cooperativity in Ionic Solvation Shells from Isotope-Dependent Dielectric Relaxation

NASA Astrophysics Data System (ADS)

Cota, Roberto; Ottosson, Niklas; Bakker, Huib J.; Woutersen, Sander

2018-05-01

We find that the reduction in dielectric response (depolarization) of water caused by solvated ions is different for H2O and D2O . This isotope dependence allows us to reliably determine the kinetic contribution to the depolarization, which is found to be significantly smaller than predicted by existing theory. The discrepancy can be explained from a reduced hydrogen-bond cooperativity in the solvation shell: we obtain quantitative agreement between theory and experiment by reducing the Kirkwood correlation factor of the solvating water from 2.7 (the bulk value) to ˜1.6 for NaCl and ˜1 (corresponding to completely uncorrelated motion of water molecules) for CsCl.

High-temperature stability of the hydrate shell of a Na+ cation in a flat nanopore with hydrophobic walls

NASA Astrophysics Data System (ADS)

Shevkunov, S. V.

2017-11-01

The effect of elevated temperature has on the hydrate shell of a singly charged sodium cation inside a flat nanopore with smooth walls is studied using the Monte Carlo method. The free energy and the entropy of vapor molecule attachment are calculated by means of a bicanonical statistical ensemble using a detailed model of interactions. The nanopore has a stabilizing effect on the hydrate shell with respect to fluctuations and a destabilizing effect with respect to complete evaporation. At the boiling point of water, behavior is observed that is qualitatively similar to behavior at room temperature, but with a substantial shift in the vapor pressure and shell size.

Quantum Calculations on Salt Bridges with Water: Potentials, Structure, and Properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liao, Sing; Green, Michael E.

2011-01-01

Salt bridges are electrostatic links between acidic and basic amino acids in a protein; quantum calculations are used here to determine the energetics and other properties of one form of these species, in the presence of water molecules. The acidic groups are carboxylic acids (aspartic and glutamic acids); proteins have two bases with pK above physiological pH: one, arginine, with a guanidinium basic group, the other lysine, which is a primary amine. Only arginine is modeled here, by ethyl guanidinium, while propionic acid is used as a model for either carboxylic acid. The salt bridges are accompanied by 0-12 watermore » molecules; for each of the 13 systems, the energy-bond distance relation, natural bond orbitals (NBO), frequency calculations allowing thermodynamic corrections to room temperature, and dielectric constant dependence, were all calculated. The water molecules were found to arrange themselves in hydrogen bonded rings anchored to the oxygens of the salt bridge components. This was not surprising in itself, but it was found that the rings lead to a periodicity in the energy, and to a 'water addition' rule. The latter shows that the initial rings, with four oxygen atoms, become five member rings when an additional water molecule becomes available, with the additional water filling in at the bond with the lowest Wiberg index, as calculated using NBO. The dielectric constant dependence is the expected hyperbola, and the fit of the energy to the inverse dielectric constant is determined. There is an energy periodicity related to ring formation upon addition of water molecules. When 10 water molecules have been added, all spaces near the salt bridge are filled, completing the first hydration shell, and a second shell starts to form. The potentials associated with salt bridges depend on their hydration, and potentials assigned without regard to local hydration are likely to cause errors as large as or larger than kBT, thus suggesting a serious problem if these potentials are used in Molecular Dynamics simulations.« less

Solvation of Cr 3+ cation in water-acetonitrile mixture studied by IR spectroscopy: molecular penetration into the solvation shells

NASA Astrophysics Data System (ADS)

Jamróz, Dorota; Wójcik, Marek; Lindgren, Jan

2000-09-01

Infrared spectra of mixtures of water and deuteroacetonitrile containing the Cr 3+ cation have been studied as a function of concentration, time and temperature. The CN stretching vibration of CD 3CN molecules has been used as a probe of the structural environments. The CN band in the spectra of the solutions is a superposition of four subbands, which may be attributed to CD 3CN bound in the first, second, and third solvation shells of the cation and to non-bound CD 3CN. The character of changes of the integral intensities of the subbands with time for various H 2O:Cr 3+ molar ratios are explained by suggesting mechanisms of molecular replacement within the solvation shells of Cr 3+.

On the nature of hydrogen bonding between the phosphatidylcholine head group and water and dimethylsulfoxide

NASA Astrophysics Data System (ADS)

Dabkowska, Aleksandra P.; Lawrence, M. Jayne; McLain, Sylvia E.; Lorenz, Christian D.

2013-01-01

Molecular dynamics simulations are used to provide a detailed investigation of the hydrogen bond networks around the phosphatidylcholine (PC) head group in 1,2-dipropionyl-sn-glycero-3-phosphocholine in pure water, 10 mol.% and 30 mol.% dimethylsulfoxide (DMSO)-water solutions. Specifically, it is observed that DMSO replaces those water molecules that are within the first solvation shell of the choline, phosphate and ester groups of the PC head group, but are not hydrogen-bonded to the group. The effect of the presence of DMSO on the hydrogen bond network around the PC head groups of the lipid changes with the concentration of DMSO. In comparison to the hydrogen bond network observed in the pure water system, the number of hydrogen-bonded chains of solvent molecules increases slightly for the 10 mol.% DMSO system, while, in the 30 mol.% DMSO system, the number of hydrogen-bonded chains of solvent molecules decreases.

The structure of liquid water up to 360 MPa from x-ray diffraction measurements using a high Q-range and from molecular simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Skinner, L. B.; Galib, M.; Fulton, J. L.

2016-04-07

X-ray diffraction measurements of liquid water are reported at pressures up to 360 MPa corresponding to a density of 0.0373 molecules per Å3. The measurements were conducted at a spatial resolution corresponding to Qmax = 16 Å-1. The method of data analysis and measurement in this study follows the earlier benchmark results reported for water under ambient conditions having density of 0.0333 molecules per Å3 and Qmax = 20 Å-1 [J Chem Phys 138, 074506 (2013)]1 and at 70°C having density of 0.0327 molecules per Å3 and Qmax = 20 Å-1. [J Chem Phys 141, 214507 (2014)]2 The structure ofmore » water is very different at these three different T and P state points and thus they provide basis for evaluating the fidelity of molecular simulation. Measurements show that at 360 MPa, the 4 waters residing in the region between 2.3-3 Å are nearly unchanged: the peak position, shape and coordination number are nearly identical to their values under ambient conditions. However, in the region above 3 Å, large structural changes occur with the collapse of the well-defined 2nd shell and shifting of higher shells to shorter distances. The measured structure is compared to simulated structure using intermolecular potentials described by both first-principles methods (revPBE-D3) and classical potentials (TIP4P/2005 and mW). The DFT-based, revPBE-D3 provides the best overall representation of the ambient, high-temperature and high-pressure data while the TIP4P/2005 also captures the densification mechanism, whereby the non-bonded 5th nearest neighbor molecule, which encroaches the 1st shell at ambient pressure, is pushed further into the local tetrahedral arrangement at higher pressures by the more distant molecules filling the void space in the network between the 1st and 2nd shells. Acknowledgments: Thanks to Rick Spence and Doug Robinson for support with the beamline equipment at the Advanced Photon Source. The helpful comments of Valeria Molinero are acknowledged. This work was supported by the U.S. Department of Energy (DOE) office of Basic Energy Sciences grant Number BES DE-FG02-09ER46650 which supported, MD simulations, data analysis and manuscript preparation (LBS and JBP). DOE contract DE-AC02-06CH11357 supports operation of the Advanced Photon Source at Argonne National Laboratory. Work by JLF, MG, GSK and CJM was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.« less

Monodisperse Magneto-Fluorescent Bifunctional Nanoprobes for Bioapplications

NASA Astrophysics Data System (ADS)

Zhang, Hongwang; Huang, Heng; Pralle, Arnd; Zeng, Hao

2013-03-01

We present the work on the synthesis of dye-doped monodisperse Fe/SiO2 core/shell nanoparticles as bifunctional probes for bioapplications. Magnetic nanoparticles (NP) have been widely studied as nano-probes for bio-imaging, sensing as well as for cancer therapy. Among all the NPs, Fe NPs have been the focus because they have very high magnetization. However, Fe NPs are usually not stable in ambient due to the fast surface oxidation of the NPs. On the other hand, dye molecules have long been used as probes for bio-imaging. But they are sensitive to environmental conditions. It requires passivation for both so that they can be stable for applications. In this work, monodisperse Fe NPs with sizes ranging from 13-20 nm have been synthesized through the chemical thermal-decomposition in a solution. Silica shells were then coated on the Fe NPs by a two-phase oil-in-water method. Dye molecules were first bonded to a silica precursor and then encapsulated into the silica shell during the coating process. The silica shells protect both the Fe NPs and dye molecules, which makes them as robust probes. The dye doped Fe/SiO2 core/shell NPs remain both highly magnetic and highly fluorescent. The stable dye doped Fe/SiO2NPs have been used as a dual functional probe for both magnetic heating and local nanoscale temperature sending, and their performance will be reported. Research supported by NSF DMR 0547036, DMR1104994.

Exploration of the Ca2+ interaction modes of the nifedipine calcium channel antagonist.

PubMed

Liu, Huichun; Zhang, Liang; Li, Ping; Cukier, Robert I; Bu, Yuxiang

2007-02-02

A comprehensive study is carried out using quantum chemical computation and molecular dynamics (MD) simulations to gain insight into the interaction between Ca(2+) ions and the most important class of calcium channel antagonists--nifedipine. First, the chelating structures and energetic characters of nifedipine-Ca(2+) in the gas phase are explored, and 25 isomers are found. The most favorable chelating mode is a tridentate one, that is, Ca(2+) binds to two carbonyl O atoms and one nitryl O atom, where Ca(2+) is above the plane of the three O atoms to form a pyramidal structure. Accurate geometric structures, relative stabilities, vertical and adiabatic binding energies, and charge distributions are discussed. The differences in the geometries and energies among these isomers are analyzed from the contributions of chelating sites, electrostatics and polarizations, steric repulsions, and charge distributions. The interconversions among isomers with similar geometries and energies are also investigated because of the importance of the geometric transformation in the biological system. Furthermore, certain numbers of water molecules are added to the nifedipine-Ca(2+) system to probe the effect of water. A detailed study is performed on the hydrated geometries on the basis of the most stable isomer 1. Stepwise hydration can weaken the nifedipine-Ca(2+) interaction, and the chelating sites of nifedipine are gradually replaced by the added water molecules. Hexacoordination is found to be the most favorable geometry no matter how many water molecules were added, which can be verified by the MD simulations. The transfer of water molecules from the inner shell to the outer shell is also supported by MD simulations of the hexahydrated complexes.

Region-specific role of water in collagen unwinding and assembly.

PubMed

Ravikumar, Krishnakumar M; Hwang, Wonmuk

2008-09-01

Conformational stability of the collagen triple helix affects its turnover and determines tissue homeostasis. Although it is known that the presence of imino acids (prolines or hydroxyprolines) confer stability to the molecule, little is known regarding the stability of the imino-poor region lacking imino acids, which plays a key role in collagen cleavage. In particular, there have been continuing debates about the role of water in collagen stability. We addressed these issues using molecular dynamics simulations on 30-residue long collagen triple helices, including a structure that has a biologically relevant 9-residue imino-poor region from type III collagen (PDB ID: 1BKV). A torsional map approach was used to characterize the conformational motion of the molecule that differ between imino-rich and imino-poor regions. At temperatures 300 K and above, unwinding initiates at a common cleavage site, the glycine-isoleucine bond in the imino-poor region. This provides a linkage between previous observations that unwinding of the imino-poor region is a requirement for collagenase cleavage, and that isolated collagen molecules are unstable at body temperature. We found that unwinding of the imino-poor region is controlled by dynamic water bridges between backbone atoms with average lifetimes on the order of a few picoseconds, as the degree of unwinding strongly correlated with the loss of water bridges, and unwinding could be either prevented or enhanced, respectively by enforcing or forbidding water bridge formation. While individual water bridges were short-lived in the imino-poor region, the hydration shell surrounding the entire molecule was stable even at 330 K. The diameter of the hydrated collagen including the first hydration shell was about 14 A, in good agreement with the experimentally measured inter-collagen distances. These results elucidate the general role of water in collagen turnover: water not only affects collagen cleavage by controlling its torsional motion, but it also forms a larger-scale lubrication layer mediating collagen self-assembly. 2008 Wiley-Liss, Inc.

Near-membrane electric field calcium ion dehydration.

PubMed

Barger, James P; Dillon, Patrick F

2016-12-01

The dehydration of ion-water complexes prior to ion channel transit has focused on channel protein-mediated dissociation of water. Ion dehydration by the membrane electric field has not previously been considered. Near membrane electric fields have previously been shown to cause the disassociation of non-covalently bound small molecule-small molecule, small molecule-protein, and protein-protein complexes. It is well known that cosmotropic, structure making ions such as calcium and sodium significantly bind multiple water ions in solution. It is also known that these ions are often not hydrated as they pass through membrane ion channels. Using capillary electrophoresis, the range of electric fields needed to strip water molecules from calcium ions has been measured. Ion migration velocity is a linear function of the electric field. At low electric fields, the migration rate of calcium ion was shown to be linearly related to the applied electric field. Using a form of the Stoke's equation applicable to ion migration, the hydrated calcium radius was found to be 0.334nm, corresponding to a water hydration shell of 5.09 water molecules. At higher electric fields, the slope of the calcium migration velocity as a function of the electric field increased, which was modeled as a decrease in the radius of the migrating ion as the water was removed. Using a tanh function to model the transition of the ion from a hydrated to a stripped state, the transition had a midpoint at 446V/cm, and was 88% complete at 587V/cm with a correlation coefficient of 0.9996. The migration velocity of the stripped calcium ion was found to be a function of both the decrease in radius and an increase in the effective, electronic viscosity of the dipole medium through which the dehydrated ion moved. The size of the electric field needed to dehydrate calcium occurs 6-7nm from the cell membrane. Calcium ions within this distance from the membrane will be devoid of water molecules when they reach the calcium selective channel pore entrances, all known to be approximately 1-2nm from the membrane. No matter what the calcium pore structure, calcium ions reaching the channel entrance will be devoid of a water shell. Copyright © 2016 Elsevier Ltd. All rights reserved.

Reduced Point Charge Models of Proteins: Effect of Protein-Water Interactions in Molecular Dynamics Simulations of Ubiquitin Systems.

PubMed

Leherte, Laurence; Vercauteren, Daniel P

2017-10-26

We investigate the influence of various solvent models on the structural stability and protein-water interface of three ubiquitin complexes (PDB access codes: 1Q0W , 2MBB , 2G3Q ) modeled using the Amber99sb force field (FF) and two different point charge distributions. A previously developed reduced point charge model (RPCM), wherein each amino acid residue is described by a limited number of point charges, is tested and compared to its all-atom (AA) version. The complexes are solvated in TIP4P-Ew or TIP3P type water molecules, involving either the scaling of the Lennard-Jones protein-O water interaction parameters, or the coarse-grain (CG) SIRAH water description. The best agreements between the RPCM and AA models were obtained for structural, protein-water, and ligand-ubiquitin properties when using the TIP4P-Ew water FF with a scaling factor γ of 0.7. At the RPCM level, a decrease in γ, or the inclusion of SIRAH particles, allows weakening of the protein-water interactions. It results in a slight collapse of the protein structure and a less compact hydration shell and, thus, in a decrease in the number of protein-water and water-water H-bonds. The dynamics of the surface protein atoms and of the water shell molecules are also slightly refrained, which allow the generation of stable RPCM trajectories.

Variations of water's local-structure induced by solvation of NaCl

NASA Astrophysics Data System (ADS)

Gu, Bin; Zhang, Feng-Shou; Huang, Yu-Gai; Fang, Xia

2010-03-01

The researches on the structure of water and its changes induced by solutes are of enduring interests. The changes of the local structure of liquid water induced by NaCl solute under ambient conditions are studied and presented quantitatively with some order parameters and visualized with 2-body and 3-body correlation functions. The results show that, after the NaCl are solvated, the translational order t of water is decreased for the suppression of the second hydration shells around H2O molecules; the tetrahedral order (q) of water is also decreased and its favorite distribution peak moves from 0.76 to 0.5. In addition, the orientational freedom k and the diffusion coefficient D of water molecules are reduced because of new formed hydrogen-bonding structures between water and solvated ions.

Molecular basis for competitive solvation of the Burkholderia cepacia lipase by sorbitol and urea.

PubMed

Oliveira, Ivan P; Martínez, Leandro

2016-08-21

Increasing the stability of proteins is important for their application in industrial processes. In the intracellular environment many small molecules, called osmolytes, contribute to protein stabilization under physical or chemical stress. Understanding the nature of the interactions of these osmolytes with proteins can help the design of solvents and mutations to increase protein stability in extracellular media. One of the most common stabilizing osmolyes is sorbitol and one of the most common chemical denaturants is urea. In this work, we use molecular dynamics simulations to obtain a detailed picture of the solvation of the Burkholderia cepacia lipase (BCL) in the presence of the protecting osmolyte sorbitol and of the urea denaturant. We show that both sorbitol and urea compete with water for interactions with the protein surface. Overall, sorbitol promotes the organization of water in the first solvation shell and displaces water from the second solvation shell, while urea causes opposite effects. These effects are, however, highly heterogeneous among residue types. For instance, the depletion of water from the first protein solvation shell by urea can be traced down essentially to the side chain of negatively charged residues. The organization of water in the first solvation shell promoted by sorbitol occurs at polar (but not charged) residues, where the urea effect is minor. By contrast, sorbitol depletes water from the second solvation shell of polar residues, while urea promotes water organization at the same distances. The interactions of urea with negatively charged residues are insensitive to the presence of sorbitol. This osmolyte removes water and urea particularly from the second solvation shell of polar and non-polar residues. In summary, we provide a comprehensive description of the diversity of protein-solvent interactions, which can guide further investigations on the stability of proteins in non-conventional media, and assist solvent and protein design.

Hydration Dynamics of Hyaluronan and Dextran

PubMed Central

Hunger, Johannes; Bernecker, Anja; Bakker, Huib J.; Bonn, Mischa; Richter, Ralf P.

2012-01-01

Hyaluronan is a polysaccharide, which is ubiquitous in vertebrates and has been reported to be strongly hydrated in a biological environment. We study the hydration of hyaluronan in solution using the rotational dynamics of water as a probe. We measure these dynamics with polarization-resolved femtosecond-infrared and terahertz time-domain spectroscopies. Both experiments reveal that a subensemble of water molecules is slowed down in aqueous solutions of hyaluronan amounting to ∼15 water molecules per disaccharide unit. This quantity is consistent with what would be expected for the first hydration shell. Comparison of these results to the water dynamics in aqueous dextran solution, a structurally similar polysaccharide, yields remarkably similar results. This suggests that the observed interaction with water is a common feature for hydrophilic polysaccharides and is not specific to hyaluronan. PMID:22828349

How the shape of an H-bonded network controls proton-coupled water activation in HONO formation.

PubMed

Relph, Rachael A; Guasco, Timothy L; Elliott, Ben M; Kamrath, Michael Z; McCoy, Anne B; Steele, Ryan P; Schofield, Daniel P; Jordan, Kenneth D; Viggiano, Albert A; Ferguson, Eldon E; Johnson, Mark A

2010-01-15

Many chemical reactions in atmospheric aerosols and bulk aqueous environments are influenced by the surrounding solvation shell, but the precise molecular interactions underlying such effects have rarely been elucidated. We exploited recent advances in isomer-specific cluster vibrational spectroscopy to explore the fundamental relation between the hydrogen (H)-bonding arrangement of a set of ion-solvating water molecules and the chemical activity of this ensemble. We find that the extent to which the nitrosonium ion (NO+)and water form nitrous acid (HONO) and a hydrated proton cluster in the critical trihydrate depends sensitively on the geometrical arrangement of the water molecules in the network. Theoretical analysis of these data details the role of the water network in promoting charge delocalization.

On the structure and dynamics of the hydrated sulfite ion in aqueous solution--an ab initio QMCF MD simulation and large angle X-ray scattering study.

PubMed

Eklund, Lars; Hofer, Thomas S; Pribil, Andreas B; Rode, Bernd M; Persson, Ingmar

2012-05-07

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism has been applied in conjunction to experimental large angle X-ray scattering to study the structure and dynamics of the hydrated sulfite ion in aqueous solution. The results show that there is a considerable effect of the lone electron-pair on sulfur concerning structure and dynamics in comparison with the sulfate ion with higher oxidation number and symmetry of the hydration shell. The S-O bond distance in the hydrated sulfite ion has been determined to 1.53(1) Å by both methods. The hydrogen bonds between the three water molecules bound to each sulfite oxygen are only slightly stronger than those in bulk water. The sulfite ion can therefore be regarded as a weak structure maker. The water exchange rate is somewhat slower for the sulfite ion than for the sulfate ion, τ(0.5) = 3.2 and 2.6 ps, respectively. An even more striking observation in the angular radial distribution (ARD) functions is that the for sulfite ion the water exchange takes place in close vicinity of the lone electron-pair directed at its sides, while in principle no water exchange did take place of the water molecules hydrogen bound to sulfite oxygens during the simulation time. This is also confirmed when detailed pathway analysis is conducted. The simulation showed that the water molecules hydrogen bound to the sulfite oxygens can move inside the hydration shell to the area outside the lone electron-pair and there be exchanged. On the other hand, for the hydrated sulfate ion in aqueous solution one can clearly see from the ARD that the distribution of exchange events is symmetrical around the entire hydration sphere.

Ion Association in AlCl3 Aqueous Solutions from Constrained First-Principles Molecular Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cauet, Emilie L.; Bogatko, Stuart A.; Bylaska, Eric J.

2012-10-15

Ab initio molecular dynamics was used to investigate the ion pairing behavior between Cl- and the Al3+ ion in an aqueous AlCl3 solution containing 63 water molecules. A series of constrained simulations was carried out at 300 K for up to 16 ps each, by fixing the inter-nuclear separation (rAl-Cl) between the Al3+ ion and one of the Cl- ions. The calculated potential of mean force of the Al3+-Cl- ion pair shows a pronounced minimum at rAl-Cl = 2.3 Å corresponding to a contact ion pair (CIP). Two local minima assigned to solvent separated ion pairs (SSIP) are identified atmore » rAl-Cl= 4.4 and 6.0 Å. The positions of the free energy minima coincide with the hydration shell intervals of the Al3+ cation suggesting that the Cl- ion is inclined to reside in regions of low concentration of waters, i.e. between the 1st and 2nd shells of Al3+ and between the 2nd shell and bulk. A detailed analysis of solvent structure around the Al3+ and Cl- ions as a function of rAl-Cl is presented. The results are compared to structure data from X-ray measurements and unconstrained AIMD simulations of single ions Al3+ and Cl- and AlCl3 solutions. The dipole moment of the water molecules inside the 1st and 2nd hydration shells of Al3+ and in the bulk region and those of the Clion were calculated as a function of rAl-Cl. Major changes in the electronic structure of the system result from the removal of Cl- from the 1st hydration shell of the Al3+ cation. Finally, two unconstrained AIMD simulations of aqueous AlCl3 solutions corresponding to CIP and SSIP configurations were performed (17 ps, 300 K). Only minor structural changes are observed in these systems, confirming their stability.« less

Dynamics of Hydration Water in Sugars and Peptides Solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perticaroli, Stefania; Nakanishi, Masahiro; Pashkovski, Eugene

2013-01-01

We analyzed solute and solvent dynamics of sugars and peptides aqueous solutions using extended epolarized light scattering (EDLS) and broadband dielectric spectroscopies (BDS). Spectra measured with both techniques reveal the same mechanism of rotational diffusion of peptides molecules. In the case of sugars, this solute reorientational relaxation can be isolated by EDLS measurements, whereas its ontribution to the dielectric spectra is almost negligible. In the presented analysis, we characterize the hydration water in terms of hydration number and retardation ratio between relaxation times of hydration and bulk water. Both techniques provide similar estimates of . The retardation imposed on themore » hydration water by sugars is 3.3 1.3 and involves only water molecules hydrogen-bonded (HB) to solutes ( 3 water molecules per sugar OH-group). In contrast, polar peptides cause longer range erturbations beyond the first hydration shell, and between 2.8 and 8, increasing with the number of chemical groups engaged in HB formation. We demonstrate that chemical heterogeneity and specific HB interactions play a crucial role in hydration dynamics around polar solutes. The obtained results help to disentangle the role of excluded volume and enthalpic contributions in dynamics of hydration water at the interface with biological molecules.« less

Direct characterization of hydrophobic hydration during cold and pressure denaturation.

PubMed

Das, Payel; Matysiak, Silvina

2012-05-10

Cold and pressure denaturation are believed to have their molecular origin in hydrophobic interactions between nonpolar groups and water. However, the direct characterization of the temperature- and pressure-dependent variations of those interactions with atomistic simulations remains challenging. We investigated the role of solvent in the cold and pressure denaturation of a model hydrophobic 32-mer polymer by performing extensive coarse-grained molecular dynamics simulations including explicit solvation. Our simulations showed that the water-excluded folded state of this polymer is marginally stable and can be unfolded by heating or cooling, as well as by applying pressure, similar to globular proteins. We further detected essential population of a hairpin-like configuration prior to the collapse, which is consistently accompanied by a vapor bubble at the elbow of the kink. Increasing pressure suppresses formation of this vapor bubble by reducing water fluctuations in the hydration shell of the polymer, thus promoting unfolding. Further analysis revealed a slight reduction of water tetrahedrality in the polymer hydration shell compared to the bulk. Cold denaturation is driven by an enhanced tetrahedral ordering of hydration shell water than bulk water. At elevated pressures, the strikingly reduced fluctuations combined with the increase in interstitial water molecules in the polymer hydration shell contribute to weakening of hydrophobic interactions, thereby promoting pressure unfolding. These findings provide critical molecular insights into the changes in hydrophobic hydration during cold and pressure unfolding of a hydrophobic polymer, which is strongly related to the cold and pressure denaturation of globular proteins.

Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects.

PubMed

Lomize, Andrei L; Pogozheva, Irina D; Mosberg, Henry I

2011-04-25

A new implicit solvation model was developed for calculating free energies of transfer of molecules from water to any solvent with defined bulk properties. The transfer energy was calculated as a sum of the first solvation shell energy and the long-range electrostatic contribution. The first term was proportional to solvent accessible surface area and solvation parameters (σ(i)) for different atom types. The electrostatic term was computed as a product of group dipole moments and dipolar solvation parameter (η) for neutral molecules or using a modified Born equation for ions. The regression coefficients in linear dependencies of solvation parameters σ(i) and η on dielectric constant, solvatochromic polarizability parameter π*, and hydrogen-bonding donor and acceptor capacities of solvents were optimized using 1269 experimental transfer energies from 19 organic solvents to water. The root-mean-square errors for neutral compounds and ions were 0.82 and 1.61 kcal/mol, respectively. Quantification of energy components demonstrates the dominant roles of hydrophobic effect for nonpolar atoms and of hydrogen-bonding for polar atoms. The estimated first solvation shell energy outweighs the long-range electrostatics for most compounds including ions. The simplicity and computational efficiency of the model allows its application for modeling of macromolecules in anisotropic environments, such as biological membranes.

Aqueous solvation of Mg(ii) and Ca(ii): A Born-Oppenheimer molecular dynamics study of microhydrated gas phase clusters

NASA Astrophysics Data System (ADS)

León-Pimentel, C. I.; Amaro-Estrada, J. I.; Hernández-Cobos, J.; Saint-Martin, H.; Ramírez-Solís, A.

2018-04-01

The hydration features of [Mg(H2O)n ] 2 + and [Ca(H2O)n ] 2 + clusters with n = 3-6, 8, 18, and 27 were studied by means of Born-Oppenheimer molecular dynamics simulations at the B3LYP/6-31+G** level of theory. For both ions, it is energetically more favorable to have all water molecules in the first hydration shell when n ≤ 6, but stable lower coordination average structures with one water molecule not directly interacting with the ion were found for Mg2+ at room temperature, showing signatures of proton transfer events for the smaller cation but not for the larger one. A more rigid octahedral-type structure for Mg2+ than for Ca2+ was observed in all simulations, with no exchange of water molecules to the second hydration shell. Significant thermal effects on the average structure of clusters were found: while static optimizations lead to compact, spherically symmetric hydration geometries, the effects introduced by finite-temperature dynamics yield more prolate configurations. The calculated vibrational spectra are in agreement with infrared spectroscopy results. Previous studies proposed an increase in the coordination number (CN) from six to eight water molecules for [Ca(H2O)n ] 2 + clusters when n ≥ 12; however, in agreement with recent measurements of binding energies, no transition to a larger CN was found when n > 8. Moreover, the excellent agreement found between the calculated extended X-ray absorption fine structure spectroscopy spectra for the larger cluster and the experimental data of the aqueous solution supports a CN of six for Ca2+.

New insights into the photocatalytic activity of 3-D core-shell P25@silica nanocomposites: impact of mesoporous coating.

PubMed

Gong, Yichao; Wang, Dan Ping; Wu, Renbing; Gazi, Sarifuddin; Soo, Han Sen; Sritharan, Thirumany; Chen, Zhong

2017-04-11

In this report, a three-dimensional (3-D) network of core-shell TiO 2 (P25)-mesoporous SiO 2 (P25@mSiO 2 ) nanocomposites was prepared via a controllable surfactant-assisted sol-gel method. The nanocomposites were investigated for photocatalytic reactions of organic dye degradation, water splitting, and CO 2 reduction to understand the roles of the mSiO 2 shell in these photocatalytic reactions. It was found that the mSiO 2 shell accelerates the photodegradation of the organic dye, but dramatically reduces the photocatalytic activity of P25 in water splitting and CO 2 reduction. The roles played by the mSiO 2 shell in the photocatalytic reactions are summarized as: (1) effective prevention of agglomeration of P25 nanoparticles, (2) facilitating the transfer of uncharged photo-generated ˙OH radicals via the abundant -OH groups on the mesoporous surface, (3) provision of increased reaction sites between ˙OH radicals and dye molecules by its mesoporous nanostructure and large surface area, and (4) prevention of diffusion of the photo-generated charge carriers (photoelectrons and photoholes) because of its insulating nature.

Membrane electrode assembly fabricated with the combination of Pt/C and hollow shell structured-Pt-SiO2@ZrO2 sphere for self-humidifying proton exchange membrane fuel cell

NASA Astrophysics Data System (ADS)

Ko, Y. D.; Yang, H. N.; Züttel, Andreas; Kim, S. D.; Kim, W. J.

2017-11-01

The Pt-supported hollow structured Pt-HZrO2 with the shell thickness of 27 nm is successfully synthesized. The water retention ability of Pt-HZrO2 is significantly enhanced compared with that of SiO2@ZrO2 due to the hydrophilic hollow structured HZrO2with high BET surface area. Pt-C and Pt-HZrO2 are combined with different weight fractions to prepare the double catalyst electrode (DCE). The membrane electrode assembly with the DCE is fabricated and applied to both anode and cathode or anode side only. The water flooding and thus rapid voltage drop is affected by the presence/or absence of the DCE at the cathode side. The cell test and visual experiment suggests that the Pt-HZrO2 layer adsorb the water molecules generated by the oxygen reduction reaction (ORR), preventing the water flooding. The power generation under RH 0% strongly suggests the back-diffusion of water molecules generated by the ORR. The flow rate to the cathode significantly affects the water flooding and cell performance. Higher flow rate to the cathode is advantageous to expel the water generated by the ORR, thus preventing water flooding and enhancing the cell performance. Therefore, the weight fraction of Pt-C to Pt-HZrO2 and the flow rate to the cathode should be well balanced.

A molecular dynamics study of the relaxation of an excited molecule in crystalline nitromethane

NASA Astrophysics Data System (ADS)

Rivera-Rivera, Luis A.; Siavosh-Haghighi, Ali; Sewell, Thomas D.; Thompson, Donald L.

2014-07-01

Classical molecular dynamics simulations were used to study the relaxation of an excited nitromethane molecule in perfect crystalline nitromethane at 250 K and 1 atm pressure. The molecule was instantaneously excited by statistically distributing energy E∗ between 25.0 kcal/mol and 125.0 kcal/mol among the 21 degrees of freedom of the molecule. The relaxation occurs exponentially with time constants between 11.58 ps and 13.57 ps. Energy transfer from the excited molecule to surrounding quasi-spherical shells of molecules occurs concurrently to both the nearest and next-nearest neighbor shells, but with more energy per molecule transferred more rapidly to the first shell.

Solvation of actinide salts in water using a polarizable continuum model.

PubMed

Kumar, Narendra; Seminario, Jorge M

2015-01-29

In order to determine how actinide atoms are dressed when solvated in water, density functional theory calculations have been carried out to study the equilibrium structure of uranium plutonium and thorium salts (UO2(2+), PuO2(2+), Pu(4+), and Th(4+)) both in vacuum as well as in solution represented by a conductor-like polarizable continuum model. This information is of paramount importance for the development of sensitive nanosensors. Both UO2(2+) and PuO2(2+) ions show coordination number of 4-5 with counterions replacing one or two water molecules from the first coordination shell. On the other hand, Pu(4+), has a coordination number of 8 both when completely solvated and also in the presence of chloride and nitrate ions with counterions replacing water molecules in the first shell. Nitrates were found to bind more strongly to Pu(IV) than chloride anions. In the case of the Th(IV) ion, the coordination number was found to be 9 or 10 in the presence of chlorides. Moreover, the Pu(IV) ion shows greater affinity for chlorides than the Th(IV) ion. Adding dispersion and ZPE corrections to the binding energy does not alter the trends in relative stability of several conformers because of error cancelations. All structures and energetics of these complexes are reported.

Stabilizing effects of hydrated fullerenes C₆₀ in a wide range of concentrations on luciferase, alkaline phosphatase, and peroxidase in vitro.

PubMed

Voeikov, Vladimir L; Yablonskaya, Olga I

2015-01-01

Hydrated fullerene (HyFnC60) is a highly hydrophilic supra-molecular complex consisting of unmodified С60 fullerene molecule enclosed into a hydrated shell. It has been shown in numerous experiments that aqueous solutions of HyFnC60 manifest a wide range of biological activities both in vivo and in vitro even at very low concentrations of HyFnC60. We used a spectrophotometric method and a method of biochemoluminescence to demonstrate that HyFnC60 in concentrations below 10(-9) M down to 10(-23) M stabilizes peroxidase, alkaline phosphatase, and bacterial luciferase against inactivation due to long-term incubation of the enzymes at room temperature and also against heat inactivation. In addition, HyFnC60 was able to "revive" heat inactivated enzymes. These effects cannot be explained by the direct action of the fullerene molecules upon the enzymes. We suggest that the effects of HyFnC60 on the enzymes are related to the ability of hydrated fullerene C60 molecules to organize thick aqueous shells around them. One of the specific properties of water phase in these shells is its ability to optimize redox reactions, which can support enzyme stability against factors deteriorating their structure.

Compressibility of the protein-water interface

NASA Astrophysics Data System (ADS)

Persson, Filip; Halle, Bertil

2018-06-01

The compressibility of a protein relates to its stability, flexibility, and hydrophobic interactions, but the measurement, interpretation, and computation of this important thermodynamic parameter present technical and conceptual challenges. Here, we present a theoretical analysis of protein compressibility and apply it to molecular dynamics simulations of four globular proteins. Using additively weighted Voronoi tessellation, we decompose the solution compressibility into contributions from the protein and its hydration shells. We find that positively cross-correlated protein-water volume fluctuations account for more than half of the protein compressibility that governs the protein's pressure response, while the self correlations correspond to small (˜0.7%) fluctuations of the protein volume. The self compressibility is nearly the same as for ice, whereas the total protein compressibility, including cross correlations, is ˜45% of the bulk-water value. Taking the inhomogeneous solvent density into account, we decompose the experimentally accessible protein partial compressibility into intrinsic, hydration, and molecular exchange contributions and show how they can be computed with good statistical accuracy despite the dominant bulk-water contribution. The exchange contribution describes how the protein solution responds to an applied pressure by redistributing water molecules from lower to higher density; it is negligibly small for native proteins, but potentially important for non-native states. Because the hydration shell is an open system, the conventional closed-system compressibility definitions yield a pseudo-compressibility. We define an intrinsic shell compressibility, unaffected by occupation number fluctuations, and show that it approaches the bulk-water value exponentially with a decay "length" of one shell, less than the bulk-water compressibility correlation length. In the first hydration shell, the intrinsic compressibility is 25%-30% lower than in bulk water, whereas its self part is 15%-20% lower. These large reductions are caused mainly by the proximity to the more rigid protein and are not a consequence of the perturbed water structure.

Compressibility of the protein-water interface.

PubMed

Persson, Filip; Halle, Bertil

2018-06-07

The compressibility of a protein relates to its stability, flexibility, and hydrophobic interactions, but the measurement, interpretation, and computation of this important thermodynamic parameter present technical and conceptual challenges. Here, we present a theoretical analysis of protein compressibility and apply it to molecular dynamics simulations of four globular proteins. Using additively weighted Voronoi tessellation, we decompose the solution compressibility into contributions from the protein and its hydration shells. We find that positively cross-correlated protein-water volume fluctuations account for more than half of the protein compressibility that governs the protein's pressure response, while the self correlations correspond to small (∼0.7%) fluctuations of the protein volume. The self compressibility is nearly the same as for ice, whereas the total protein compressibility, including cross correlations, is ∼45% of the bulk-water value. Taking the inhomogeneous solvent density into account, we decompose the experimentally accessible protein partial compressibility into intrinsic, hydration, and molecular exchange contributions and show how they can be computed with good statistical accuracy despite the dominant bulk-water contribution. The exchange contribution describes how the protein solution responds to an applied pressure by redistributing water molecules from lower to higher density; it is negligibly small for native proteins, but potentially important for non-native states. Because the hydration shell is an open system, the conventional closed-system compressibility definitions yield a pseudo-compressibility. We define an intrinsic shell compressibility, unaffected by occupation number fluctuations, and show that it approaches the bulk-water value exponentially with a decay "length" of one shell, less than the bulk-water compressibility correlation length. In the first hydration shell, the intrinsic compressibility is 25%-30% lower than in bulk water, whereas its self part is 15%-20% lower. These large reductions are caused mainly by the proximity to the more rigid protein and are not a consequence of the perturbed water structure.

Water's hydrogen bonds in the hydrophobic effect: a simple model.

PubMed

Xu, Huafeng; Dill, Ken A

2005-12-15

We propose a simple analytical model to account for water's hydrogen bonds in the hydrophobic effect. It is based on computing a mean-field partition function for a water molecule in the first solvation shell around a solute molecule. The model treats the orientational restrictions from hydrogen bonding, and utilizes quantities that can be obtained from bulk water simulations. We illustrate the principles in a 2-dimensional Mercedes-Benz-like model. Our model gives good predictions for the heat capacity of hydrophobic solvation, reproduces the solvation energies and entropies at different temperatures with only one fitting parameter, and accounts for the solute size dependence of the hydrophobic effect. Our model supports the view that water's hydrogen bonding propensity determines the temperature dependence of the hydrophobic effect. It explains the puzzling experimental observation that dissolving a nonpolar solute in hot water has positive entropy.

Biomimetic synthesis of raspberry-like hybrid polymer-silica core-shell nanoparticles by templating colloidal particles with hairy polyamine shell.

PubMed

Pi, Mengwei; Yang, Tingting; Yuan, Jianjun; Fujii, Syuji; Kakigi, Yuichi; Nakamura, Yoshinobu; Cheng, Shiyuan

2010-07-01

The nanoparticles composed of polystyrene core and poly[2-(diethylamino)ethyl methacrylate] (PDEA) hairy shell were used as colloidal templates for in situ silica mineralization, allowing the well-controlled synthesis of hybrid silica core-shell nanoparticles with raspberry-like morphology and hollow silica nanoparticles by subsequent calcination. Silica deposition was performed by simply stirring a mixture of the polymeric core-shell particles in isopropanol, tetramethyl orthosilicate (TMOS) and water at 25 degrees C for 2.5h. No experimental evidence was found for nontemplated silica formation, which indicated that silica deposition occurred exclusively in the PDEA shell and formed PDEA-silica hybrid shell. The resulting hybrid silica core-shell particles were characterized by transmission electron microscopy (TEM), thermogravimetry, aqueous electrophoresis, and X-ray photoelectron spectroscopy. TEM studies indicated that the hybrid particles have well-defined core-shell structure with raspberry morphology after silica deposition. We found that the surface nanostructure of hybrid nanoparticles and the composition distribution of PDEA-silica hybrid shell could be well controlled by adjusting the silicification conditions. These new hybrid core-shell nanoparticles and hollow silica nanoparticles would have potential applications for high-performance coatings, encapsulation and delivery of active organic molecules. 2010 Elsevier B.V. All rights reserved.

Evaluation of the influence of the internal aqueous solvent structure on electrostatic interactions at the protein-solvent interface by nonlocal continuum electrostatic approach.

PubMed

Rubinstein, Alexander; Sherman, Simon

The dielectric properties of the polar solvent on the protein-solvent interface at small intercharge distances are still poorly explored. To deconvolute this problem and to evaluate the pair-wise electrostatic interaction (PEI) energies of the point charges located at the protein-solvent interface we used a nonlocal (NL) electrostatic approach along with a static NL dielectric response function of water. The influence of the aqueous solvent microstructure (determined by a strong nonelectrostatic correlation effect between water dipoles within the orientational Debye polarization mode) on electrostatic interactions at the interface was studied in our work. It was shown that the PEI energies can be significantly higher than the energies evaluated by the classical (local) consideration, treating water molecules as belonging to the bulk solvent with a high dielectric constant. Our analysis points to the existence of a rather extended, effective low-dielectric interfacial water shell on the protein surface. The main dielectric properties of this shell (effective thickness together with distance- and orientation-dependent dielectric permittivity function) were evaluated. The dramatic role of this shell was demonstrated when estimating the protein association rate constants.

Insight into the molecular mechanism of water evaporation via the finite temperature string method.

PubMed

Musolino, Nicholas; Trout, Bernhardt L

2013-04-07

The process of water's evaporation at its liquid/air interface has proven challenging to study experimentally and, because it constitutes a rare event on molecular time scales, presents a challenge for computer simulations as well. In this work, we simulated water's evaporation using the classical extended simple point charge model water model, and identified a minimum free energy path for this process in terms of 10 descriptive order parameters. The measured free energy change was 7.4 kcal/mol at 298 K, in reasonable agreement with the experimental value of 6.3 kcal/mol, and the mean first-passage time was 1375 ns for a single molecule, corresponding to an evaporation coefficient of 0.25. In the observed minimum free energy process, the water molecule diffuses to the surface, and tends to rotate so that its dipole and one O-H bond are oriented outward as it crosses the Gibbs dividing surface. As the water molecule moves further outward through the interfacial region, its local density is higher than the time-averaged density, indicating a local solvation shell that protrudes from the interface. The water molecule loses donor and acceptor hydrogen bonds, and then, with its dipole nearly normal to the interface, stops donating its remaining hydrogen bond. At that point, when the final, accepted hydrogen bond is broken, the water molecule is free. We also analyzed which order parameters are most important in the process and in reactive trajectories, and found that the relative orientation of water molecules near the evaporating molecule, and the number of accepted hydrogen bonds, were important variables in reactive trajectories and in kinetic descriptions of the process.

Molecular dynamics of ion hydration in the presence of small carboxylated molecules and implications for calcification.

PubMed

Hamm, Laura M; Wallace, Adam F; Dove, Patricia M

2010-08-19

The aspartate-rich macromolecules found at nucleation sites of calcifying organisms are widely implicated in regulating biomineral formation. Anecdotal evidence suggests that their ability to influence the onset of nucleation and composition of calcified structures may arise from effects on ion hydration. This study investigates the interactions of acidic amino acids and dipeptides with hydrated cations using molecular dynamics. By monitoring the hydration states of Mg2+, Ca2+, and Sr2+ during their approach to negatively charged molecules, we show that carboxylate moieties of Asp promote dehydration of Ca2+ and Sr2+. A contact ion pair (CIP) is not required to disrupt cation hydration, and we demonstrate that reductions and rearrangements of first shell water can begin at ion-Asp separation distances as large as approximately 4.9 A for Ca2+ and approximately 5.1 A for Sr2+. CIP formation between Ca2+ and Sr2+ and carboxylate groups decreases the total first shell coordination number from an average of 8.0 and 8.4 in bulk water to 7.5 and 8.0, respectively. The energy barrier to physically replacing waters about Ca2+ with carboxylate oxygen atoms is small (approximately 2 kcal/mol) as compared to a somewhat larger barrier for Sr2+ (approximately 4 kcal/mol). This may be explained by differences in the strength of Coulombic interactions between the cations and the Asp, resulting in different paths of approach toward Asp for Ca2+ and Sr2+. In contrast, the primary solvation shell of Mg2+ remains largely unchanged during interactions with Asp until the abrupt physical replacement of water by carboxylate oxygen atoms, which comes at a high energetic cost. These insights support the claim that carboxylated biomolecules increase the growth rate of calcite by lowering the energy barrier to Ca2+ dehydration. The findings also suggest a physical basis for the idea that ion-specific behaviors of Ca2+ and Mg2+ in cellular systems arise from a critical balance between water binding in the ion hydration shells versus their interactions with ligands present in intracellular environments.

Tuning the tetrahedrality of the hydrogen-bonded network of water: Comparison of the effects of pressure and added salts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prasad, Saurav, E-mail: saurav7188@gmail.com, E-mail: cyz118212@chemistry.iitd.ac.in; Chakravarty, Charusita

Experiments and simulations demonstrate some intriguing equivalences in the effect of pressure and electrolytes on the hydrogen-bonded network of water. Here, we examine the extent and nature of equivalence effects between pressure and salt concentration using relationships between structure, entropy, and transport properties based on two key ideas: first, the approximation of the excess entropy of the fluid by the contribution due to the atom-atom pair correlation functions and second, Rosenfeld-type excess entropy scaling relations for transport properties. We perform molecular dynamics simulations of LiCl–H{sub 2}O and bulk SPC/E water spanning the concentration range 0.025–0.300 molefraction of LiCl at 1more » atm and pressure range from 0 to 7 GPa, respectively. The temperature range considered was from 225 to 350 K for both the systems. To establish that the time-temperature-transformation behaviour of electrolyte solutions and water is equivalent, we use the additional observation based on our simulations that the pair entropy behaves as a near-linear function of pressure in bulk water and of composition in LiCl–H{sub 2}O. This allows for the alignment of pair entropy isotherms and allows for a simple mapping of pressure onto composition. Rosenfeld-scaling implies that pair entropy is semiquantitatively related to the transport properties. At a given temperature, equivalent state points in bulk H{sub 2}O and LiCl–H{sub 2}O (at 1 atm) are defined as those for which the pair entropy, diffusivity, and viscosity are nearly identical. The microscopic basis for this equivalence lies in the ability of both pressure and ions to convert the liquid phase into a pair-dominated fluid, as demonstrated by the O–O–O angular distribution within the first coordination shell of a water molecule. There are, however, sharp differences in local order and mechanisms for the breakdown of tetrahedral order by pressure and electrolytes. Increasing pressure increases orientational disorder within the first neighbour shell while addition of ions shifts local orientational order from tetrahedral to close-packed as water molecules get incorporated in ionic hydration shells. The variations in local order within the first hydration shell may underlie ion-specific effects, such as the Hofmeister series.« less

Tuning the tetrahedrality of the hydrogen-bonded network of water: Comparison of the effects of pressure and added salts

NASA Astrophysics Data System (ADS)

Prasad, Saurav; Chakravarty, Charusita

2016-06-01

Experiments and simulations demonstrate some intriguing equivalences in the effect of pressure and electrolytes on the hydrogen-bonded network of water. Here, we examine the extent and nature of equivalence effects between pressure and salt concentration using relationships between structure, entropy, and transport properties based on two key ideas: first, the approximation of the excess entropy of the fluid by the contribution due to the atom-atom pair correlation functions and second, Rosenfeld-type excess entropy scaling relations for transport properties. We perform molecular dynamics simulations of LiCl-H2O and bulk SPC/E water spanning the concentration range 0.025-0.300 molefraction of LiCl at 1 atm and pressure range from 0 to 7 GPa, respectively. The temperature range considered was from 225 to 350 K for both the systems. To establish that the time-temperature-transformation behaviour of electrolyte solutions and water is equivalent, we use the additional observation based on our simulations that the pair entropy behaves as a near-linear function of pressure in bulk water and of composition in LiCl-H2O. This allows for the alignment of pair entropy isotherms and allows for a simple mapping of pressure onto composition. Rosenfeld-scaling implies that pair entropy is semiquantitatively related to the transport properties. At a given temperature, equivalent state points in bulk H2O and LiCl-H2O (at 1 atm) are defined as those for which the pair entropy, diffusivity, and viscosity are nearly identical. The microscopic basis for this equivalence lies in the ability of both pressure and ions to convert the liquid phase into a pair-dominated fluid, as demonstrated by the O-O-O angular distribution within the first coordination shell of a water molecule. There are, however, sharp differences in local order and mechanisms for the breakdown of tetrahedral order by pressure and electrolytes. Increasing pressure increases orientational disorder within the first neighbour shell while addition of ions shifts local orientational order from tetrahedral to close-packed as water molecules get incorporated in ionic hydration shells. The variations in local order within the first hydration shell may underlie ion-specific effects, such as the Hofmeister series.

A Plasmonic Colloidal Photocatalyst Composed of a Metal-Organic Framework Core and a Gold/Anatase Shell for Visible-Light-Driven Wastewater Purification from Antibiotics and Hydrogen Evolution.

PubMed

Tilgner, Dominic; Kempe, Rhett

2017-03-02

Porous coordination polymers (PCP) or metal- organic frameworks (MOF) are promising materials for the generation of photocatalytically active composite materials. Here, a novel synthesis concept is reported, which permits the formation of PCP/MOF-core-Au/anatase-shell materials. These materials are photocatalysts for wastewater purification and hydrogen generation from water under visible-light illumination. MIL-101 (Cr) is utilized as the core material, which directs the size of the core-shell compound and ensures the overall stability. In addition, its excellent reversible large molecule sorption behavior allows the materials synthesis. The crystalline anatase shell is generated stepwise under mild conditions using titanium(IV) isopropoxide as a precursor. The high degree of control of the vapor phase deposition process permits the precise anatase shell formation. The generation of plasmonic active gold particles on the TiO 2 shell leads to an efficient material for visible-light-driven photocatalysis with a higher activity than gold-decorated P25 (Degussa). © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The mechanism of water/ion exchange at a protein surface: a weakly bound chloride in Helicobacter pylori apoflavodoxin.

PubMed

Galano-Frutos, Juan J; Morón, M Carmen; Sancho, Javier

2015-11-21

Binding/unbinding of small ligands, such as ions, to/from proteins influences biochemical processes such as protein folding, enzyme catalysis or protein/ligand recognition. We have investigated the mechanism of chloride/water exchange at a protein surface (that of the apoflavodoxin from Helicobacter pylori) using classical all-atom molecular dynamics simulations. They reveal a variety of chloride exit routes and residence times; the latter is related to specific coordination modes of the anion. The role of solvent molecules in the mechanism of chloride unbinding has been studied in detail. We see no temporary increase in chloride coordination along the release process. Instead, the coordination of new water molecules takes place in most cases after the chloride/protein atom release event has begun. Moreover, the distribution function of water entrance events into the first chloride solvation shell peaks after chloride protein atom dissociation events. All these observations together seem to indicate that water molecules simply fill the vacancies left by the previously coordinating protein residues. We thus propose a step-by-step dissociation pathway in which protein/chloride interactions gradually break down before new water molecules progressively fill the vacant positions left by protein atoms. As observed for other systems, water molecules associated with bound chloride or with protein atoms have longer residence times than those bound to the free anion. The implications of the exchange mechanism proposed for the binding of the FMN (Flavin Mononucleotide) protein cofactor are discussed.

Nanocrystalline p-hydroxyacetanilide (paracetamol) and gold core-shell structure as a model drug deliverable organic-inorganic hybrid nanostructure

NASA Astrophysics Data System (ADS)

Das, Subhojit; Paul, Anumita; Chattopadhyay, Arun

2013-09-01

We report on the generation of core-shell nanoparticles (NPs) having an organic nanocrystal (NC) core coated with an inorganic metallic shell, being dispersed in aqueous medium. First, NCs of p-hydroxyacetanilide (pHA)--known also as paracetamol--were generated in an aqueous medium. Transmission electron microscopy (TEM) and powder X-ray diffraction (XRD) evidenced the formation of pHA NCs and of their crystalline nature. The NCs were then coated with Au to form pHA@Au core-shell NPs, where the thickness of the Au shell was on the order of nanometers. The formation of Au nanoshell--surrounding pHA NC--was confirmed from its surface plasmon resonance (SPR) band in the UV/Vis spectrum and by TEM measurements. Further, on treatment of the core-shell particles with a solution comprising NaCl and HCl (pH < 3), the Au shell could be dissolved, subsequently releasing pHA molecules. The dissolution of Au shell was marked by a gradual diminishing of its SPR band, while the release of pHA molecules in the solution was confirmed from TEM and FTIR studies. The findings suggest that the core-shell NP could be hypothesized to be a model for encapsulating drug molecules, in their crystalline forms, for slow as well as targeted release.We report on the generation of core-shell nanoparticles (NPs) having an organic nanocrystal (NC) core coated with an inorganic metallic shell, being dispersed in aqueous medium. First, NCs of p-hydroxyacetanilide (pHA)--known also as paracetamol--were generated in an aqueous medium. Transmission electron microscopy (TEM) and powder X-ray diffraction (XRD) evidenced the formation of pHA NCs and of their crystalline nature. The NCs were then coated with Au to form pHA@Au core-shell NPs, where the thickness of the Au shell was on the order of nanometers. The formation of Au nanoshell--surrounding pHA NC--was confirmed from its surface plasmon resonance (SPR) band in the UV/Vis spectrum and by TEM measurements. Further, on treatment of the core-shell particles with a solution comprising NaCl and HCl (pH < 3), the Au shell could be dissolved, subsequently releasing pHA molecules. The dissolution of Au shell was marked by a gradual diminishing of its SPR band, while the release of pHA molecules in the solution was confirmed from TEM and FTIR studies. The findings suggest that the core-shell NP could be hypothesized to be a model for encapsulating drug molecules, in their crystalline forms, for slow as well as targeted release. Electronic supplementary information (ESI) available: See DOI: 10.1039/c3nr03566b

Molecular hydrogen solvated in water – A computational study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Śmiechowski, Maciej, E-mail: Maciej.Smiechowski@pg.gda.pl

2015-12-28

The aqueous hydrogen molecule is studied with molecular dynamics simulations at ambient temperature and pressure conditions, using a newly developed flexible and polarizable H{sub 2} molecule model. The design and implementation of this model, compatible with an existing flexible and polarizable force field for water, is presented in detail. The structure of the hydration layer suggests that first-shell water molecules accommodate the H{sub 2} molecule without major structural distortions and two-dimensional, radial-angular distribution functions indicate that as opposed to strictly tangential, the orientation of these water molecules is such that the solute is solvated with one of the free electronmore » pairs of H{sub 2}O. The calculated self-diffusion coefficient of H{sub 2}(aq) agrees very well with experimental results and the time dependence of mean square displacement suggests the presence of caging on a time scale corresponding to hydrogen bond network vibrations in liquid water. Orientational correlation function of H{sub 2} experiences an extremely short-scale decay, making the H{sub 2}–H{sub 2}O interaction potential essentially isotropic by virtue of rotational averaging. The inclusion of explicit polarizability in the model allows for the calculation of Raman spectra that agree very well with available experimental data on H{sub 2}(aq) under differing pressure conditions, including accurate reproduction of the experimentally noted trends with solute pressure or concentration.« less

Angular resolution and range of dipole-dipole correlations in water

NASA Astrophysics Data System (ADS)

Mathias, Gerald; Tavan, Paul

2004-03-01

We investigate the dipolar correlations in liquid water at angular resolution by molecular-dynamics simulations of a large periodic simulation system containing about 40 000 molecules. Because we are particularly interested in the long-range ordering, we use a simple three-point model for these molecules. The electrostatics is treated both by Ewald summation and by minimum image truncation combined with a reaction field approach. To gain insight into the angular dependence of the simulated dipolar ordering we introduce a suitable expansion of the molecular pair distribution function into a set of two-dimensional correlation functions. We show that these functions enable detailed insights into the shell structure of the dipolar ordering around a given water molecule. For these functions we derive analytical expressions in the particular case in which liquid water is conceived as a dielectric continuum. Comparisons of these continuum models with the correlation functions derived from the simulations yield the key result that liquid water behaves like a continuum dielectric beyond distances of about 15 Å from a given water molecule. We argue that this should be a generic property of water independent of our modeling. By comparison of the results of the two different electrostatics treatments with the continuum description we show that the boundary artifacts occurring in both methods are isotropically distributed and are locally small in the respective boundary regions.

17O nuclear quadrupole coupling constants of water bound to a metal ion: A gadolinium(III) case study

NASA Astrophysics Data System (ADS)

Yazyev, Oleg V.; Helm, Lothar

2006-08-01

Rotational correlation times of metal ion aqua complexes can be determined from O17 NMR relaxation rates if the quadrupole coupling constant of the bound water oxygen-17 nucleus is known. The rotational correlation time is an important parameter for the efficiency of Gd3+ complexes as magnetic resonance imaging contrast agents. Using a combination of density functional theory with classical and Car-Parrinello molecular dynamics simulations we performed a computational study of the O17 quadrupole coupling constants in model aqua ions and the [Gd(DOTA)(H2O)]- complex used in clinical diagnostics. For the inner sphere water molecule in the [Gd(DOTA)(H2O)]- complex the determined quadrupole coupling parameter χ√1+η2/3 of 8.7MHz is very similar to that of the liquid water (9.0MHz ). Very close values were also predicted for the the homoleptic aqua ions of Gd3+ and Ca2+. We conclude that the O17 quadrupole coupling parameters of water molecules coordinated to closed shell and lanthanide metal ions are similar to water molecules in the liquid state.

A coarse grained molecular dynamics simulation study on the structural properties of carbon nanotube-dendrimer composites.

PubMed

Kavyani, Sajjad; Dadvar, Mitra; Modarress, Hamid; Amjad-Iranagh, Sepideh

2018-04-25

By employing coarse grained (CG) molecular dynamics (MD) simulation, the effect of the size and hydrophilic/hydrophobic properties of the interior/exterior structures of the dendrimers in carbon nanotube (CNT)-dendrimer composites has been studied, to find a stable composite with high solubility in water and the capability to be used in drug delivery applications. For this purpose, composites consisting of core-shell dendrimer complexes including: [PPI{core}-PAMAM{shell}], [PAMAM{core}-polyethyleneglycol (PEG){shell}] and [PAMAM{core}-fattyacid (FTA){shell}] were constructed. A new CG model for the fatty acid (FTA) molecules as functionalized to the dendrimer was developed, which, unlike the previous models, could generate the structural conformations of the FTA properly. The obtained results indicated that the dendrimer complexes with short FTA chains can form stable composites with the CNT. Also, it was found that the pristine PAMAM and PPI-PAMAM with small PPI, and PAMAM-PEG dendrimers with short PEG chains, can distribute their chains into the water medium and interact with the CNT efficiently, to form a stable water-soluble CNT-dendrimer composite. The results demonstrated that the structural difference between the interior and exterior of a core-shell dendrimer complex can prevent the core and the interior layers of the dendrimer complex from interacting with the CNT. An overall analysis of the results manifested that the CNT-PAMAM:4-PEG:4 is the most stable composite, due to strong binding of the dendrimer with the CNT while also having high solubility in water, and its core retains its structure properly and unchanged, suitable for encapsulating drugs in the targeted delivery applications.

Visible photoelectrochemical water splitting into H 2 and O 2 in a dye-sensitized photoelectrosynthesis cell

DOE PAGES

Alibabaei, Leila; Sherman, Benjamin D.; Norris, Michael R.; ...

2015-04-27

A hybrid strategy for solar water splitting is exploited here based on a dye-sensitized photoelectrosynthesis cell (DSPEC) with a mesoporous SnO 2/TiO 2 core/shell nanostructured electrode derivatized with a surface-bound Ru(II) polypyridyl-based chromophore–catalyst assembly. The assembly, [(4,4’-(PO 3H 2) 2bpy) 2Ru(4-Mebpy-4’-bimpy)Ru(tpy)(OH 2)] 4+ ([RuaII-RubII-OH 2] 4+, combines both a light absorber and a water oxidation catalyst in a single molecule. It was attached to the TiO 2 shell by phosphonate-surface oxide binding. The oxide-bound assembly was further stabilized on the surface by atomic layer deposition (ALD) of either Al 2O 3 or TiO 2 overlayers. Illumination of the resulting fluorine-dopedmore » tin oxide (FTO)|SnO 2/TiO 2|-[Ru a II-Ru b II-OH 2] 4+(Al 2O 3 or TiO 2) photoanodes in photoelectrochemical cells with a Pt cathode and a small applied bias resulted in visible-light water splitting as shown by direct measurements of both evolved H 2 and O 2. The performance of the resulting DSPECs varies with shell thickness and the nature and extent of the oxide overlayer. Use of the SnO 2/TiO 2 core/shell compared with nanoITO/TiO 2 with the same assembly results in photocurrent enhancements of ~5. In conclusion, systematic variations in shell thickness and ALD overlayer lead to photocurrent densities as high as 1.97 mA/cm 2 with 445-nm, ~90-mW/cm 2 illumination in a phosphate buffer at pH 7.« less

Qualitative assessment of ultra-fast non-Grotthuss proton dynamics in S1 excited state of liquid H2O from ab initio time-dependent density functional theory★

NASA Astrophysics Data System (ADS)

Ziaei, Vafa; Bredow, Thomas

2017-11-01

We study qualitatively ultra-fast proton transfer (PT) in the first singlet (S1) state of liquid water (absorption onset) through excited-state dynamics by means of time-dependent density functional theory and ab initio Born-Oppenheimer molecular dynamics. We find that after the initial excitation, a PT occurs in S1 in form of a rapid jump to a neighboring water molecule, on which the proton either may rest for a relatively long period of time (as a consequence of possible defect in the hydrogen bond network) followed by back and forth hops to its neighboring water molecule or from which it further moves to the next water molecule accompanied by back and forth movements. In this way, the proton may become delocalized over a long water wire branch, followed again by back and forth jumps or short localization on a water molecule for some femtoseconds. As a result, the mechanism of PT in S1 is in most cases highly non-Grotthuss-like, delayed and discrete. Furthermore, upon PT an excess charge is ejected to the solvent trap, the so-called solvated electron. The spatial extent of the ejected solvated electron is mainly localized within one solvent shell with overlappings on the nearest neighbor water molecules and delocalizing (diffuse) tails extending beyond the first solvent sphere. During the entire ultra-short excited-state dynamics the remaining OH radical from the initially excited water molecule exhibits an extremely low mobility and is non-reactive. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjb/e2017-80329-7.

Core-shell designed scaffolds for drug delivery and tissue engineering.

PubMed

Perez, Roman A; Kim, Hae-Won

2015-07-01

Scaffolds that secure and deliver therapeutic ingredients like signaling molecules and stem cells hold great promise for drug delivery and tissue engineering. Employing a core-shell design for scaffolds provides a promising solution. Some unique methods, such as co-concentric nozzle extrusion, microfluidics generation, and chemical confinement reactions, have been successful in producing core-shelled nano/microfibers and nano/microspheres. Signaling molecules and drugs, spatially allocated to the core and/or shell part, can be delivered in a controllable and sequential manner for optimal therapeutic effects. Stem cells can be loaded within the core part on-demand, safely protected from the environments, which ultimately affords ex vivo culture and in vivo tissue engineering. The encapsulated cells experience three-dimensional tissue-mimic microenvironments in which therapeutic molecules are secreted to the surrounding tissues through the semi-permeable shell. Tuning the material properties of the core and shell, changing the geometrical parameters, and shaping them into proper forms significantly influence the release behaviors of biomolecules and the fate of the cells. This topical issue highlights the immense usefulness of core-shell designs for the therapeutic actions of scaffolds in the delivery of signaling molecules and stem cells for tissue regeneration and disease treatment. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Protons in non-ionic aqueous reverse micelles.

PubMed

Rodriguez, Javier; Martí, Jordi; Guàrdia, Elvira; Laria, Daniel

2007-05-03

Using molecular dynamics techniques, we investigate the solvation of an excess proton within an aqueous reverse micelle in vacuo, with the neutral surfactant diethylene glycol monodecyl ether [CH3(CH2)11(OC2H4)2OH]. The simulation experiments were performed using a multistate empirical valence bond Hamiltonian model. Our results show that the stable solvation environments for the excess proton are located in the water-surfactant interface and that its first solvation shell is composed exclusively by water molecules. The relative prevalence of Eigen- versus Zundel-like solvation structures is investigated; compared to bulk results, Zundel-like structures in micelles become somewhat more stable. Characteristic times for the proton translocation jumps have been computed using population relaxation time correlation functions. The micellar rate for proton transfer is approximately 40x smaller than that found in bulk water at ambient conditions. Differences in the computed rates are examined in terms of the hydrogen-bond connectivity involving the first solvation shell of the excess charge with the rest of the micellar environment. Simulation results would indicate that proton transfers are correlated with rare episodes during which the HB connectivity between the first and second solvation shells suffers profound modifications.

The effect of water on the microstructure of 1-butyl-3-methylimidazolium tetrafluoroborate/TX-100/benzene ionic liquid microemulsions.

PubMed

Gao, Yan'an; Li, Na; Zheng, Liqiang; Zhao, Xueyan; Zhang, Jin; Cao, Quan; Zhao, Mingwei; Li, Zhen; Zhang, Gaoyong

2007-01-01

The ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF4]) forms nonaqueous microemulsions with benzene with the aid of nonionic surfactant TX-100. The phase diagram of the ternary system was prepared, and the microstructures of the microemulsion were recognized. On the basis of the phase diagram, a series of ionic liquid-in-oil (IL/O) microemulsions were chosen and characterized by dynamic light scattering (DLS), which shows a similar swelling behavior to typical water-in-oil (W/O) microemulsions. The existence of IL pools in the IL/O microemulsion was confirmed by UV/Vis spectroscopic analysis with CoCl2 and methylene blue (MB) as the absorption probes. A constant polarity of the IL pool is observed, even if small amounts of water are added to the microemulsion, thus suggesting that the water molecules are solubilized in the polar outer shell of the microemulsion, as confirmed by FTIR spectra. 1H NMR spectroscopic analysis shows that these water molecules interact with the electronegative oxygen atoms of the oxyethylene (OE) units of TX-100 through hydrogen-bonding interactions, and the electronegative oxygen atoms of the water molecules attract the electropositive imidazolium rings of [bmim][BF4]. Hence, the water molecules are like a glue that stick the IL and OE units more tightly together and thus make the microemulsion system more stable. Considering the unique solubilization behavior of added water molecules, the IL/O microemulsion system may be used as a medium to prepare porous or hollow nanomaterials by hydrolysis reactions.

Adsorption of insulin peptide on charged single-walled carbon nanotubes: significant role of ordered water molecules.

PubMed

Shen, Jia-Wei; Wu, Tao; Wang, Qi; Kang, Yu; Chen, Xin

2009-06-02

Ordered hydration shells: The more ordered hydration shells outside the charged CNT surfaces prevent more compact adsorption of the peptide in the charged CNT systems [picture: see text], but peptide binding strengths on the charged CNT surfaces are stronger due to the electrostatic interaction.Studies of adsorption dynamics and stability for peptides/proteins on single-walled carbon nanotubes (SWNTs) are of great importance for a better understanding of the properties and nature of nanotube-based biosystems. Herein, the dynamics and mechanism of the adsorption of the insulin chain B peptide on different charged SWNTs are investigated by explicit solvent molecular dynamics simulations. The results show that all types of surfaces effectively attract the model peptide. Water molecules play a significant role in peptide adsorption on the surfaces of charged carbon nanotubes (CNTs). Compared to peptide adsorption on neutral CNT surfaces, the more ordered hydration shells outside the tube prevent more compact adsorption of the peptide in charged CNT systems. This shield effect leads to a smaller conformational change and van der Waals interaction between the peptide and surfaces, but peptide binding strengths on charged CNT surfaces are stronger than those on the neutral CNT surface due to the strong electrostatic interaction. The result of these simulations implies the possibility of improving the binding strength of peptides/proteins on CNT surfaces, as well as keeping the integrity of the peptide/protein conformation in peptide/protein-CNT complexes by charging the CNTs.

The hydration structure of the heavy-alkalines Rb+ and Cs+ through molecular dynamics and X-ray absorption spectroscopy: surface clusters and eccentricity.

PubMed

Caralampio, Daniel Z; Martínez, José M; Pappalardo, Rafael R; Marcos, Enrique Sánchez

2017-11-01

Physicochemical properties of the two heaviest stable alkaline cations, Rb + and Cs + , in water have been examined from classical molecular dynamics (MD) simulations. Alkaline cation-water intermolecular potentials have been built from ab initio interaction energies of [M(H 2 O) n ] + clusters. Unlike in the case of other monatomic metal cations, the sampling needed the inclusion of surface clusters to properly describe the interactions. The first coordination shell is found at an average M-O distance of 2.87 Å and 3.12 Å for Rb + and Cs + , respectively, with coordination numbers of 8 and 10. Structural, dynamical and energetic properties are discussed on the basis of the delicate compromise among the ion-water and water-water interactions which contribute almost on the same foot to the definition of the solvent structure around the ions. A significant asymmetry is detected in the Rb + and Cs + first hydration shell. Reorientational times of first-shell water molecules for Cs + support a clear structure-breaking nature for this cation, whereas the Rb + values do not differ from pure water behavior. Experimental EXAFS and XANES spectra have been compared to simulated ones, obtained by means of application of the FEFF code to a set of statistically significant structures taken from the MD simulations. Due to the presence of multi-excitations in the absorption spectra, theoretical-experimental agreement for the EXAFS spectra is reached when the multi-excitations are removed from the experimental spectra.

Rationalization of the solvation effects on the AtO+ ground-state change.

PubMed

Ayed, Tahra; Réal, Florent; Montavon, Gilles; Galland, Nicolas

2013-09-12

(211)At radionuclide is of considerable interest as a radiotherapeutic agent for targeted alpha therapy in nuclear medicine, but major obstacles remain because the basic chemistry of astatine (At) is not well understood. The AtO(+) cationic form might be currently used for (211)At-labeling protocols in aqueous solution and has proved to readily react with inorganic/organic ligands. But AtO(+) reactivity must be hindered at first glance by spin restriction quantum rules: the ground state of the free cation has a dominant triplet character. Investigating AtO(+) clustered with an increasing number of water molecules and using various flavors of relativistic quantum methods, we found that AtO(+) adopts in solution a Kramers restricted closed-shell configuration resembling a scalar-relativistic singlet. The ground-state change was traced back to strong interactions, namely, attractive electrostatic interactions and charge transfer, with water molecules of the first solvation shell that lift up the degeneracy of the frontier π* molecular orbitals (MOs). This peculiarity brings an alternative explanation to the highly variable reproducibility reported for some astatine reactions: depending on the production protocols (with distillation in gas-phase or "wet chemistry" extraction), (211)At may or may not readily react.

Neutron Scattering Studies of the Hydration Structure of Li +

DOE PAGES

Mason, P. E.; Ansell, S.; Neilson, G. W.; ...

2015-01-05

New results derived from the experimental method of neutron diffraction and isotopic substitution (NDIS) are presented for the hydration structure of the lithium cation (Li +) in aqueous solutions of lithium chloride in heavy water (D 2O) at concentrations of 6, 3 and 1 molal and at 1.5 molal lithium sulphate. By introducing new and more accurate data reduction procedures than in our earlier studies (Howell and Neilson, (1996)), we find in the first hydration shell of Li +,~4.3(2) water molecules at 6 molal, 4.9(3) at 3 molal, 4.8(3) at 1 molal in the LiCl solutions, and 5.0(3) water moleculesmore » in the case of Li 2SO 4 solution. The general form of the first hydration shell is similar in all four solutions, with the correlations for Li-O and Li-D sited at 1.96 (0.02) Å and 2.58 (0.02) Å, respectively. The results resemble those presented in 1996 in terms of ion-water distances and local coordination, but the hydration number is significantly lower for the case at 1 molal than the 6.5 (1.0) given at that time. Thus, experimental and theoretical results now agree that lithium is hydrated by a small number of waters (4-5) in the nearest coordination shell.« less

HF in clusters of molecular hydrogen. I. Size evolution of quantum solvation by parahydrogen molecules.

PubMed

Jiang, Hao; Bacić, Zlatko

2005-06-22

We present a theoretical study of the quantum solvation of the HF molecule by a small number of parahydrogen molecules, having n = 1-13 solvent particles. The minimum-energy cluster structures determined for n = 1-12 have all of the H(2) molecules in the first solvent shell. The first solvent shell closes at n = 12 and its geometry is icosahedral, with the HF molecule at the center. The quantum-mechanical ground-state properties of the clusters are calculated exactly using the diffusion Monte Carlo method. The zero-point energy of (p-H(2))(n)HF clusters is unusually large, amounting to 86% of the potential well depth for n > 7. The radial probability distribution functions (PDFs) confirm that the first solvent shell is complete for n = 12, and that the 13th p-H(2) molecule begins to fill the second solvent shell. The p-H(2) molecules execute large-amplitude motions and are highly mobile, making the solvent cage exceptionally fluxional. The anisotropy of the solvent, very pronounced for small clusters, decreases rapidly with increasing n, so that for n approximately 8-9 the solvent environment is practically isotropic. The analysis of the pair angular PDF reveals that for a given n, the parahydrogen solvent density around the HF is modulated in a pattern which clearly reflects the lowest-energy cluster configuration. The rigidity of the solvent clusters displays an interesting size dependence, increasing from n = 6 to 9, becoming floppier for n = 10, and increasing again up to n = 12, as the solvent shell is filled. The rigidity of the solvent cage appears to reach its maximum for n = 12, the point at which the first solvent shell is closed.

Simulations of polymorphic icosahedral shells assembling around many cargo molecules

NASA Astrophysics Data System (ADS)

Mohajerani, Farzaneh; Perlmutter, Jason; Hagan, Michael

Bacterial microcompartments (BMCs) are large icosahedral shells that sequester the enzymes and reactants responsible for particular metabolic pathways in bacteria. Although different BMCs vary in size and encapsulate different cargoes, they are constructed from similar pentameric and hexameric shell proteins. Despite recent groundbreaking experiments which visualized the formation of individual BMCs, the detailed assembly pathways and the factors which control shell size remain unclear. In this talk, we describe theoretical and computational models that describe the dynamical encapsulation of hundreds of cargo molecules by self-assembling icosahedral shells. We present phase diagrams and analysis of dynamical simulation trajectories showing how the thermodynamics, assembly pathways, and emergent structures depend on the interactions among shell proteins and cargo molecules. Our model suggests a mechanism for controlling insertion of the 12 pentamers required for a closed shell topology, and the relationship between assembly pathway and BMC size polydispersity. In addition to elucidating how native BMCs assemble,our results establish principles for reengineering BMCs or viral capsids as customizable nanoreactors that can assemble around a programmable set of enzymes and reactants. Supported by NIH R01GM108021 and Brandeis MRSEC DMR-1420382.

Fabrication of superhydrophobic fluorinated silica nanoparticles for multifunctional liquid marbles

NASA Astrophysics Data System (ADS)

Shang, Qianqian; Hu, Lihong; Hu, Yun; Liu, Chengguo; Zhou, Yonghong

2018-01-01

A facile one-pot method for the fabrication of superhydrophobic fluorinated silica nanoparticles is reported. Fluorinated aggregated silica (A-SiO2/FAS) nanoparticles were synthesized by controlling the nanoparticles assembly, in situ fixation and overgrowth of particle seeds with the assist of tetraethoxysilane (TEOS) in ethanol/water solution and then modification with fluoroalkylsilane (FAS) molecules. Such kind of A-SiO2/FAS nanoparticles showed superhydrophobicity and was not wetted by water, thus it could be served as the encapsulating shells to manipulate liquid droplets. Liquid marbles fabricated from A-SiO2/FAS nanoparticles were used for ammonia gas sensing or emitting by taking advantage of the porosity and superhydrophobicity of the liquid marble shells. In addition, the posibility of A-SiO2/FAS-based liquid marbles as microreactor for dopamine polymerization also was explored.

Development of hydrogel TentaGel shell-core beads for ultrahigh throughput solution-phase screening of encoded OBOC combinatorial small molecule libraries.

PubMed

Baek, Hyoung Gee; Liu, Ruiwu; Lam, Kit S

2009-01-01

The one-bead one-compound (OBOC) combinatorial library method enables the rapid generation and screening of millions of discrete chemical compounds on beads. Most of the OBOC screening methods require the library compounds to remain tethered to the bead during screening process. Methods have also been developed to release library compounds from immobilized beads for in situ solution phase or "lawn" assays. However, this latter approach, while extremely powerful, is severely limited by the lack of suitable solid supports for such assays. Here, we report on the development of a novel hydrogel TentaGel shell-core (HTSC) bead in which hydrogel is grafted onto the polystyrene-based TentaGel (TG) bead as an outer shell (5-80 mum thick) via free radical surface-initiated polymerization. This novel shell-core bilayer resin enables the preparation of encoded OBOC combinatorial small molecule libraries, such that the library compounds reside on the highly hydrophilic outer layer and the coding tags reside in the polystyrene-based TG core. Using fluorescein as a model small molecule compound, we have demonstrated that fluorescein molecules that have been linked covalently to the hydrogel shell via a disulfide bond could readily diffuse out of the hydrogel layer into the bead surrounding after reduction with dithiothreitol. In contrast, under identical condition, the released fluorescein molecules remained bound to unmodified TG bead. We have prepared an encoded OBOC small molecule library on the novel shell-core beads and demonstrated that the beads can be readily decoded.

Very Facile Polarity Umpolung and Noncovalent Functionalization of Inorganic Nanoparticles: A Tool Kit for Supramolecular Materials Chemistry.

PubMed

Zeininger, Lukas; Petzi, Stefanie; Schönamsgruber, Jörg; Portilla, Luis; Halik, Marcus; Hirsch, Andreas

2015-09-28

The facile assembly of shell-by-shell (SbS)-coated nanoparticles [TiO2-PAC16]@shell 1-7 (PAC16 = hexadecylphosphonic acid), which are soluble in water and can be isolated as stable solids, is reported. In these functional architectures, an umpolung of dispersibility (organic apolar versus water) was accomplished by the noncovalent binding of ligands 1-7 to titania nanoparticles [TiO2-PAC16] containing a first covalent coating with PAC16. Ligands 1-7 are amphiphilic and form the outer second shell of [TiO2-PAC16]@shell 1-7. The tailor-designed dendritic building blocks 3-5 contain negative and positive charges in the same molecule, and ligands 6 and 7 contain a perylenetetracarboxylic acid dimide (PDI) core (6/7) as a photoactive reporter component. In the redox and photoactive system [TiO2-PAC16]@shell 7, electronic communication between the inorganic core to the PDI ligands was observed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The catalytic effect of H2O on the hydrolysis of CO32- in hydrated clusters and its implication in the humidity driven CO2 air capture.

PubMed

Xiao, Hang; Shi, Xiaoyang; Zhang, Yayun; Liao, Xiangbiao; Hao, Feng; Lackner, Klaus S; Chen, Xi

2017-10-18

The hydration of ions in nanoscale hydrated clusters is ubiquitous and essential in many physical and chemical processes. Here we show that the hydrolysis reaction is strongly affected by relative humidity. The hydrolysis of CO 3 2- with n = 1-8 water molecules is investigated using an ab initio method. For n = 1-5 water molecules, all the reactants follow a stepwise pathway to the transition state. For n = 6-8 water molecules, all the reactants undergo a direct proton transfer to the transition state with overall lower activation free energy. The activation free energy of the reaction is dramatically reduced from 10.4 to 2.4 kcal mol -1 as the number of water molecules increases from 1 to 6. Meanwhile, the degree of hydrolysis of CO 3 2- is significantly increased compared to the bulk water solution scenario. Incomplete hydration shells facilitate the hydrolysis of CO 3 2- with few water molecules to be not only thermodynamically favorable but also kinetically favorable. We showed that the chemical kinetics is not likely to constrain the speed of CO 2 air capture driven by the humidity-swing. Instead, the pore-diffusion of ions is expected to be the time-limiting step in the humidity driven CO 2 air capture. The effect of humidity on the speed of CO 2 air capture was studied by conducting a CO 2 absorption experiment using IER with a high ratio of CO 3 2- to H 2 O molecules. Our result is able to provide valuable insights into designing efficient CO 2 air-capture sorbents.

Quantum mechanics/molecular mechanics study of the catalytic cycle of water splitting in photosystem II.

PubMed

Sproviero, Eduardo M; Gascón, José A; McEvoy, James P; Brudvig, Gary W; Batista, Victor S

2008-03-19

This paper investigates the mechanism of water splitting in photosystem II (PSII) as described by chemically sensible models of the oxygen-evolving complex (OEC) in the S0-S4 states. The reaction is the paradigm for engineering direct solar fuel production systems since it is driven by solar light and the catalyst involves inexpensive and abundant metals (calcium and manganese). Molecular models of the OEC Mn3CaO4Mn catalytic cluster are constructed by explicitly considering the perturbational influence of the surrounding protein environment according to state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, in conjunction with the X-ray diffraction (XRD) structure of PSII from the cyanobacterium Thermosynechococcus elongatus. The resulting models are validated through direct comparisons with high-resolution extended X-ray absorption fine structure spectroscopic data. Structures of the S3, S4, and S0 states include an additional mu-oxo bridge between Mn(3) and Mn(4), not present in XRD structures, found to be essential for the deprotonation of substrate water molecules. The structures of reaction intermediates suggest a detailed mechanism of dioxygen evolution based on changes in oxidization and protonation states and structural rearrangements of the oxomanganese cluster and surrounding water molecules. The catalytic reaction is consistent with substrate water molecules coordinated as terminal ligands to Mn(4) and calcium and requires the formation of an oxyl radical by deprotonation of the substrate water molecule ligated to Mn(4) and the accumulation of four oxidizing equivalents. The oxyl radical is susceptible to nucleophilic attack by a substrate water molecule initially coordinated to calcium and activated by two basic species, including CP43-R357 and the mu-oxo bridge between Mn(3) and Mn(4). The reaction is concerted with water ligand exchange, swapping the activated water by a water molecule in the second coordination shell of calcium.

Curie-type paramagnetic NMR relaxation in the aqueous solution of Ni(II).

PubMed

Mareš, Jiří; Hanni, Matti; Lantto, Perttu; Lounila, Juhani; Vaara, Juha

2014-04-21

Ni(2+)(aq) has been used for many decades as a model system for paramagnetic nuclear magnetic resonance (pNMR) relaxation studies. More recently, its magnetic properties and also nuclear magnetic relaxation rates have been studied computationally. We have calculated electron paramagnetic resonance and NMR parameters using quantum-mechanical (QM) computation of molecular dynamics snapshots, obtained using a polarizable empirical force field. Statistical averages of hyperfine coupling, g- and zero-field splitting tensors, as well as the pNMR shielding terms, are compared to the available experimental and computational data. In accordance with our previous work, the isotropic hyperfine coupling as well as nuclear shielding values agree well with experimental measurements for the (17)O nuclei of water molecules in the first solvation shell of the nickel ion, whereas larger deviations are found for (1)H centers. We report, for the first time, the Curie-type contribution to the pNMR relaxation rate using QM calculations together with Redfield relaxation theory. The Curie relaxation mechanism is analogous to chemical shift anisotropy relaxation, well-known in diamagnetic NMR. Due to the predominance of other types of paramagnetic relaxation mechanisms for this system, it is possible to extract the Curie term only computationally. The Curie mechanism alone would result in around 16 and 20 s(-1) of relaxation rates (R1 and R2 respectively) for the (1)H nuclei of water molecules bonded to the Ni(2+) center, in a magnetic field of 11.7 T. The corresponding (17)O relaxation rates are around 33 and 38 s(-1). We also report the Curie contribution to the relaxation rate for molecules beyond the first solvation shell in a 1 M solution of Ni(2+) in water.

Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

NASA Astrophysics Data System (ADS)

Carnevale, V.; Raugei, S.

2009-12-01

Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

Molecular Dynamics Simulations of the Initial-State Predict Product Distributions of Dediazoniation of Aryldiazonium in Binary Solvents.

PubMed

Cruz, Gustavo N; Lima, Filipe S; Dias, Luís G; El Seoud, Omar A; Horinek, Dominik; Chaimovich, Hernan; Cuccovia, Iolanda M

2015-09-04

The dediazoniation of aryldiazonium salts in mixed solvents proceeds by a borderline SN1 and SN2 pathway, and product distribution should be proportional to the composition of the solvation shell of the carbon attached to the -N2 group (ipso carbon). The rates of dediazoniation of 2,4,6-trimethylbenzenediazonium in water, methanol, ethanol, propanol, and acetonitrile were similar, but measured product distributions were noticeably dependent on the nature of the water/cosolvent mixture. Here we demonstrated that solvent distribution in the first solvation shell of the ipso carbon, calculated from classical molecular dynamics simulations, is equal to the measured product distribution. Furthermore, we showed that regardless of the charge distribution of the initial state, i.e., whether the positive charge is smeared over the molecule or localized on phenyl moiety, the solvent distribution around the reaction center is nearly the same.

An extension of the fenske-hall LCAO method for approximate calculations of inner-shell binding energies of molecules

NASA Astrophysics Data System (ADS)

Zwanziger, Ch.; Reinhold, J.

1980-02-01

The approximate LCAO MO method of Fenske and Hall has been extended to an all-election method allowing the calculation of inner-shell binding energies of molecules and their chemical shifts. Preliminary results are given.

Simulation of water solutions of Ni 2+ at infinite dilution

NASA Astrophysics Data System (ADS)

Natália, M.; Cordeiro, D. S.; Ignaczak, Anna; Gomes, José A. N. F.

1993-10-01

A new ab initio pair potential is developed to describe the nickel—water interactions in Ni(II) aqueous solutions. Results of Monte Carlo simulations for the Ni(II)(H 2O) 200 system are presented for this pair potential with and without three-body classical polarization terms (the water—water interaction is described by the ab initio MCY potential). The structure of the solution around Ni(II) is discussed in terms of radial distribution functions, coordination numbers and thermal ellipsoids. The results show that the three-body terms have a non-negligible effect on the simulated solution. In fact, the experimental coordination number of six is reproduced with the full potential while a higher value is predicted when the simple pairwise-additive potential is used. The equilibrium NiO distance for the first hydration shell is also dependent on the use of the three-body terms. Comparison of our distribution functions with those obtained by neutron-diffraction experiments shows a reasonable quantitative agreement. Statistical pattern recognition analysis has also been applied to our simulations in order to better understand the local thermal motion of the water molecules around the metal ion. In this way, thermal ellipsoids have been computed (and graphically displayed) for each atom of the water molecules belonging to the Ni(II) first hydration shell. This analysis revealed that the twisting and bending motions are greater than the radial motion, and that the hydrogens have a higher mobility than the oxygens. In addition, a thermodynamic perturbation method has been incorporated in our Monte Carlo procedure in order to compute the free energy of hydration for the Ni(II) ion. Agreement between these results and the experimental ones is also sufficiently reasonable to demonstrate the feasibility of this new potential for the nickel—water interactions.

The anomalous halogen bonding interactions between chlorine and bromine with water in clathrate hydrates.

PubMed

Dureckova, Hana; Woo, Tom K; Udachin, Konstantin A; Ripmeester, John A; Alavi, Saman

2017-10-13

Clathrate hydrate phases of Cl 2 and Br 2 guest molecules have been known for about 200 years. The crystal structure of these phases was recently re-determined with high accuracy by single crystal X-ray diffraction. In these structures, the water oxygen-halogen atom distances are determined to be shorter than the sum of the van der Waals radii, which indicates the action of some type of non-covalent interaction between the dihalogens and water molecules. Given that in the hydrate phases both lone pairs of each water oxygen atom are engaged in hydrogen bonding with other water molecules of the lattice, the nature of the oxygen-halogen interactions may not be the standard halogen bonds characterized recently in the solid state materials and enzyme-substrate compounds. The nature of the halogen-water interactions for the Cl 2 and Br 2 molecules in two isolated clathrate hydrate cages has recently been studied with ab initio calculations and Natural Bond Order analysis (Ochoa-Resendiz et al. J. Chem. Phys. 2016, 145, 161104). Here we present the results of ab initio calculations and natural localized molecular orbital analysis for Cl 2 and Br 2 guests in all cage types observed in the cubic structure I and tetragonal structure I clathrate hydrates to characterize the orbital interactions between the dihalogen guests and water. Calculations with isolated cages and cages with one shell of coordinating molecules are considered. The computational analysis is used to understand the nature of the halogen bonding in these materials and to interpret the guest positions in the hydrate cages obtained from the X-ray crystal structures.

Density functional theory based molecular dynamics study of hydration and electronic properties of aqueous La(3+).

PubMed

Terrier, Cyril; Vitorge, Pierre; Gaigeot, Marie-Pierre; Spezia, Riccardo; Vuilleumier, Rodolphe

2010-07-28

Structural and electronic properties of La(3+) immersed in bulk water have been assessed by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations. Correct structural properties, i.e., La(III)-water distances and La(III) coordination number, can be obtained within the framework of Car-Parrinello simulations providing that both the La pseudopotential and conditions of the dynamics (fictitious mass and time step) are carefully set up. DFT-MD explicitly treats electronic densities and is shown here to provide a theoretical justification to the necessity of including polarization when studying highly charged cations such as lanthanoids(III) with classical MD. La(3+) was found to strongly polarize the water molecules located in the first shell, giving rise to dipole moments about 0.5 D larger than those of bulk water molecules. Finally, analyzing Kohn-Sham orbitals, we found La(3+) empty 4f orbitals extremely compact and to a great extent uncoupled from the water conduction band, while the 5d empty orbitals exhibit mixing with unoccupied states of water.

The influence of trehalose on hydrophobic interactions of small nonpolar solute: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Paul, Subrata; Paul, Sandip

2013-07-01

Molecular dynamics simulations were carried out to investigate the influences of aqueous trehalose solution on the hydrophobic interactions between neopentane molecules. In this study, we consider six different trehalose concentrations ranging from 0% to 56%. We observe that with increasing trehalose concentration the dispersion of solute neopentane takes place. The neopentane-neopentane association constant value decreases with addition of trehalose. Our preferential interaction calculations suggest that with increasing trehalose concentration neopentane interacts preferentially with water over trehalose. Site-site neopentane-trehalose rdfs indicate that trehalose molecules are expelled out from the neopentane surface. Also observed are (i) trehalose induced second shell collapse of water network (ii) decrease in average number of water-water and water-trehalose hydrogen bonds with increasing trehalose concentration. We also find that addition of trehalose decreases the translational motion of all the solution species. The decrease in diffusion coefficient value is more pronounced for trehalose. We, further, observe that the ratio of the diffusion coefficient values of water and trehalose increases with increasing trehalose concentration.

Aqueous route to facile, efficient and functional silica coating of metal nanoparticles at room temperature

NASA Astrophysics Data System (ADS)

Shah, Kwok Wei; Sreethawong, Thammanoon; Liu, Shu-Hua; Zhang, Shuang-Yuan; Tan, Li Sirh; Han, Ming-Yong

2014-09-01

Various metal (Ag, Au, and Pt)@thiol-functionalized silica (SiO2-SH) nanoparticles (NPs) are successfully prepared at room temperature by a facile, efficient, functional, universal and scalable coating process in alcohol-free aqueous solution using pre-hydrolyzed 3-(mercaptopropyl)trimethoxysilane (MPTMS). The controlled pre-hydrolysis of the silane precursor in water and the consecutive condensation processes are the key to achieve the effective and uniform silica coating on metal NPs in aqueous solution. The thickness of the silica shell is tuned by simply varying the coating time. The silica shell can act as an effective protecting layer for Ag NPs in Ag@SiO2-SH NPs under conditions for silica coating in aqueous solution; however, it leads to a directional dissolution of Ag NPs in a more strongly basic ammonia solution. The environmentally friendly silica coating process in water is also applied to prepare highly surface-enhanced Raman scattering (SERS)-active Ag@SiO2-SH NPs with different types of Raman molecules for highly sensitive SERS-based applications in various fields.Various metal (Ag, Au, and Pt)@thiol-functionalized silica (SiO2-SH) nanoparticles (NPs) are successfully prepared at room temperature by a facile, efficient, functional, universal and scalable coating process in alcohol-free aqueous solution using pre-hydrolyzed 3-(mercaptopropyl)trimethoxysilane (MPTMS). The controlled pre-hydrolysis of the silane precursor in water and the consecutive condensation processes are the key to achieve the effective and uniform silica coating on metal NPs in aqueous solution. The thickness of the silica shell is tuned by simply varying the coating time. The silica shell can act as an effective protecting layer for Ag NPs in Ag@SiO2-SH NPs under conditions for silica coating in aqueous solution; however, it leads to a directional dissolution of Ag NPs in a more strongly basic ammonia solution. The environmentally friendly silica coating process in water is also applied to prepare highly surface-enhanced Raman scattering (SERS)-active Ag@SiO2-SH NPs with different types of Raman molecules for highly sensitive SERS-based applications in various fields. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr03306j

Computational studies on self-assembled paclitaxel structures: templates for hierarchical block copolymer assemblies and sustained drug release.

PubMed

Guo, Xin D; Tan, Jeremy P K; Kim, Sung H; Zhang, Li J; Zhang, Ying; Hedrick, James L; Yang, Yi Y; Qian, Yu

2009-11-01

Paclitaxel-loaded poly(ethylene oxide)-b-poly(lactide) (PEO-b-PLA) systems have been observed to assemble into fiber structures with remarkably different properties using different chirality and molecular weight of PLA segments. In this study, dissipative particle dynamics (DPD) simulations were carried out to elaborate the microstructures and properties of pure paclitaxel and paclitaxel-loaded PEO-b-PLA systems. Paclitaxel molecules formed ribbon or fiber like structures in water. With the addition of PEO-b-PDLA, PEO-b-PLLA and their stereocomplex, paclitaxel acted as a template and polymer molecules assembled around the paclitaxel structure to form core/shell structured fibers having a PEO shell. For PEO19-b-PDLA27 and PEO19-b-PLLA27 systems, PLA segments and paclitaxel molecules were distributed homogeneously in the core of fibers based on the hydrophobic interactions. In the stereocomplex formulation, paclitaxel molecules were more concentrated in the inner PLA stereocomplex core, which led to slower release of paclitaxel. By increasing the length of PLA segments (e.g. 8,16,22 and 27), the crystalline structure of paclitaxel was gradually weakened and destroyed, which was further proved by X-ray diffraction studies. All the simulation results agreed well with experimental data, suggesting that the DPD simulations may provide a powerful tool for designing drug delivery systems.

Exploring Closed-Shell Cationic Phenalenyl: From Catalysis to Spin Electronics.

PubMed

Mukherjee, Arup; Sau, Samaresh Chandra; Mandal, Swadhin K

2017-07-18

The odd alternant hydrocarbon phenalenyl (PLY) can exist in three different forms, a closed-shell cation, an open-shell radical, and a closed-shell anion, using its nonbonding molecular orbital (NBMO). The chemistry of PLY-based molecules began more than five decades ago, and so far, the progress has mainly involved the open-shell neutral radical state. Over the last two decades, we have witnessed the evolution of a range of PLY-based radicals generating an array of multifunctional materials. However, it has been admitted that the practical applications of PLY radicals are greatly challenged by the low stability of the open-shell (radical) state. Recently, we took a different route to establish the utility of these PLY molecules using the closed-shell cationic state. In such a design, the closed-shell unit of PLY can readily accept free electrons, stabilizing in its NBMO upon generation of the open-shell state of the molecule. Thus, one can synthetically avoid the unstable open-shell state but still take advantage of this state by in situ generating the radical through external electron transfer or spin injection into the empty NBMO. It is worth noting that such approaches using closed-shell phenalenyl have been missing in the literature. This Account focuses on our recent developments using the closed-shell cationic state of the PLY molecule and its application in broad multidisciplinary areas spanning from catalysis to spin electronics. We describe how this concept has been utilized to develop a variety of homogeneous catalysts. For example, this concept was used in designing an iron(III) PLY-based electrocatalyst for a single-compartment H 2 O 2 fuel cell, which delivered the best electrocatalytic activity among previously reported iron complexes, organometallic catalysts for various homogeneous organic transformations (hydroamination and polymerization), an organic Lewis acid catalyst for the ring opening of epoxides, and transition-metal-free C-H functionalization catalysts. Moreover, this concept of using the empty NBMO present in the closed-shell cationic state of the PLY moiety to capture electron(s) was further extended to an entirely different area of spin electronics to design a PLY-based spin-memory device, which worked by a spin-filtration mechanism using an organozinc compound based on a PLY backbone deposited over a ferromagnetic substrate. In this Account, we summarize our recent efforts to understand how this unexplored closed-shell state of the phenalenyl molecule, which has been known for over five decades, can be utilized in devising an array of materials that not only are important from an organometallic chemistry or organic chemistry point of view but also provide new understanding for device physics.

Cooperative effects in spherical spasers: Ab initio analytical model

NASA Astrophysics Data System (ADS)

Bordo, V. G.

2017-06-01

A fully analytical semiclassical theory of cooperative optical processes which occur in an ensemble of molecules embedded in a spherical core-shell nanoparticle is developed from first principles. Both the plasmonic Dicke effect and spaser generation are investigated for the designs in which a shell/core contains an arbitrarily large number of active molecules in the vicinity of a metallic core/shell. An essential aspect of the theory is an ab initio account of the feedback from the core/shell boundaries which significantly modifies the molecular dynamics. The theory provides rigorous, albeit simple and physically transparent, criteria for both plasmonic superradiance and surface plasmon generation.

Transition energy and potential energy curves for ionized inner-shell states of CO, O2 and N 2 calculated by several inner-shell multiconfigurational approaches.

PubMed

Moura, Carlos E V de; Oliveira, Ricardo R; Rocha, Alexandre B

2013-05-01

Potential energy curves and inner-shell ionization energies of carbon monoxide, oxygen and nitrogen molecules were calculated using several forms of the inner-shell multiconfigurational self-consistent field (IS-MCSCF) method-a recently proposed protocol to obtain specifically converged inner-shell states at this level. The particular forms of the IS-MCSCF method designated IS-GVB-PP, IS-FVBL and IS-CASSCF stand for perfect pairing generalized valence bond, full valence bond-like MCSCF and complete active space self consistent field, respectively. A comparison of these different versions of the IS-MCSCF method was carried out for the first time. The results indicate that inner-shell states are described accurately even for the simplest version of the method (IS-GVB-PP). Dynamic correlation was recovered by multireference configuration interaction or multireference perturbation theory. For molecules not having equivalent atoms, all methods led to comparable and accurate transition energies. For molecules with equivalent atoms, the most accurate results were obtained by multireference perturbation theory. Scalar relativistic effects were accounted for using the Douglas-Kroll-Hess Hamiltonian.

"Structure-making" ability of Na+ in dilute aqueous solution: an ONIOM-XS MD simulation study.

PubMed

Sripa, Pattrawan; Tongraar, Anan; Kerdcharoen, Teerakiat

2013-02-28

An ONIOM-XS MD simulation has been performed to characterize the "structure-making" ability of Na(+) in dilute aqueous solution. The region of most interest, i.e., a sphere that includes Na(+) and its surrounding water molecules, was treated at the HF level of accuracy using LANL2DZ and DZP basis sets for the ion and waters, respectively, whereas the rest of the system was described by classical pair potentials. Detailed analyzes of the ONIOM-XS MD trajectories clearly show that Na(+) is able to order the structure of waters in its surroundings, forming two prevalent Na(+)(H(2)O)(5) and Na(+)(H(2)O)(6) species. Interestingly, it is observed that these 5-fold and 6-fold coordinated complexes can convert back and forth with some degrees of flexibility, leading to frequent rearrangements of the Na(+) hydrates as well as numerous attempts of inner-shell water molecules to interchange with waters in the outer region. Such a phenomenon clearly demonstrates the weak "structure-making" ability of Na(+) in aqueous solution.

Nonideality in diffusion of ionic and hydrophobic solutes and pair dynamics in water-acetone mixtures of varying composition.

PubMed

Gupta, Rini; Chandra, Amalendu

2007-07-14

We have performed a series of molecular dynamics simulations of water-acetone mixtures containing either an ionic solute or a neutral hydrophobic solute to study the extent of nonideality in the dynamics of these solutes with variation of composition of the mixtures. The diffusion coefficients of the charged solutes, both cationic and anionic, are found to change nonmonotonically with the composition of the mixtures showing strong nonideality of their dynamics. Also, the extent of nonideality in the diffusion of these charged solutes is found to be similar to the nonideality that is observed for the diffusion and orientational relaxation of water and acetone molecules in these mixtures which show a somewhat similar changes in the solvation characteristics of charged and dipolar solutes with changes of composition of water-acetone mixtures. The diffusion of the hydrophobic solute, however, shows a monotonic increase with increase of acetone concentration showing its different solvation characteristics as compared to the charged and dipolar solutes. The links between the nonideality in diffusion and solvation structures are further confirmed through calculations of the relevant solute-solvent and solvent-solvent radial distribution functions for both ionic and hydrophobic solutes. We have also calculated various pair dynamical properties such as the relaxation of water-water and acetone-water hydrogen bonds and residence dynamics of water molecules in water and acetone hydration shells. The lifetimes of both water-water and acetone-water hydrogen bonds and also the residence times of water molecules are found to increase steadily with increase in acetone concentration. No maximum or minimum was found in the composition dependence of these pair dynamical quantities. The lifetimes of water-water hydrogen bonds are always found to be longer than that of acetone-water hydrogen bonds in these mixtures. The residence times of water molecules are also found to follow a similar trend.

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. II. Fullerenes.

PubMed

Calvo, F; Yurtsever, E

2016-08-28

The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C60 (+) and C70 (+) are close to 49 and 51, respectively, and agree with mass spectrometry experiments.

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. II. Fullerenes

NASA Astrophysics Data System (ADS)

Calvo, F.; Yurtsever, E.

2016-08-01

The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C 60+ and C 70+ are close to 49 and 51, respectively, and agree with mass spectrometry experiments.

Preparation of keratin-based microcapsules for encapsulation of hydrophilic molecules.

PubMed

Rajabinejad, Hossein; Patrucco, Alessia; Caringella, Rosalinda; Montarsolo, Alessio; Zoccola, Marina; Pozzo, Pier Davide

2018-01-01

The interest towards microcapsules based on non-toxic, biodegradable and biocompatible polymers, such as proteins, is increasing considerably. In this work, microcapsules were prepared using water soluble keratin, known as keratoses, with the aim of encapsulating hydrophilic molecules. Keratoses were obtained via oxidizing extraction of pristine wool, previously degreased by Soxhlet. In order to better understand the shell part of microcapsules, pristine wool and obtained keratoses were investigated by FT-IR, gel-electrophoresis and HPLC. Production of the microcapsules was carried out by a sonication method. Thermal properties of microcapsules were investigated by DSC. Microencapsulation and dye encapsulation yields were obtained by UV-spectroscopy. Morphological structure of microcapsules was studied by light microscopy, SEM, and AFM. The molecular weights of proteins analyzed using gel-electrophoresis resulted in the range of 38-62kDa. The results confirmed that the hydrophilic dye (Telon Blue) was introduced inside the keratoses shells by sonication and the final microcapsules diameter ranged from 0.5 to 4µm. Light microscope investigation evidenced the presence of the dye inside the keratoses vesicles, confirming their capability of encapsulating hydrophilic molecules. The microcapsule yield and dye encapsulation yield were found to be 28.87±3% and 83.62±5% respectively. Copyright © 2017 Elsevier B.V. All rights reserved.

Preparation and characterisation of core-shell CNTs@MIPs nanocomposites and selective removal of estrone from water samples.

PubMed

Gao, Ruixia; Su, Xiaoqian; He, Xiwen; Chen, Langxing; Zhang, Yukui

2011-01-15

This paper reports the preparation of carbon nanotubes (CNTs) functionalized with molecularly imprinted polymers (MIPs) for advanced removal of estrone. CNTs@Est-MIPs nanocomposites with a well-defined core-shell structure were obtained using a semi-covalent imprinting strategy, which employed a thermally reversible covalent bond at the surface of silica-coated CNTs for a large-scale production. The morphology and structure of the products were characterised by transmission electron microscopy and Fourier transform infrared spectroscopy. The adsorption properties were demonstrated by equilibrium rebinding experiments and Scatchard analysis. The results demonstrate that the imprinted nanocomposites possess favourable selectivity, high capacity and fast kinetics for template molecule uptake, yielding an adsorption capacity of 113.5 μmol/g. The synthetic process is quite simple, and the different batches of synthesized CNTs@Est-MIPs nanocomposites showed good reproducibility in template binding. The feasibility of removing estrogenic compounds from environmental water using the CNTs@Est-MIPs nanocomposites was demonstrated using water samples spiked with estrone. Copyright © 2010 Elsevier B.V. All rights reserved.

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations.

PubMed

Černý, Jiří; Schneider, Bohdan; Biedermannová, Lada

2017-07-14

Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures. The crystal-derived data include 3D maps of water distribution around amino-acids and probability of occurrence of each of the identified hydration sites. The quantum mechanics calculations validate and extend this primary description by optimizing the water position for each hydration site, by providing hydrogen atom positions and by quantifying the interaction energy that stabilizes the water molecule at the particular hydration site position. The calculations show that the majority of experimentally derived hydration sites are positioned near local energy minima for water, and the calculated interaction energies help to assess the preference of water for the individual hydration sites. We propose that the atlas can be used to validate water placement in electron density maps in crystallographic refinement, to locate water molecules mediating protein-ligand interactions in drug design, and to prepare and evaluate molecular dynamics simulations. WatAA: Atlas of Protein Hydration is freely available without login at .

Dual-Shell Fluorescent Nanoparticles for Self-Monitoring of pH-Responsive Molecule-Releasing in a Visualized Way.

PubMed

Yang, Lingang; Cui, Chuanfeng; Wang, Lingzhi; Lei, Juying; Zhang, Jinlong

2016-07-27

The rational design and controlled synthesis of a smart device with flexibly tailored response ability is all along desirable for bioapplication but long remains a considerable challenge. Here, a pH-stimulated valve system with a visualized "on-off" mode is constructed through a dual-shell fluorescence resonance energy transfer (FRET) strategy. The dual shells refer to carbon dots and fluorescent molecules embedded polymethacrylic acid (F-PMAA) layers successively coating around a SiO2 core (ca. 120 nm), which play the roles as energy donor and acceptor, respectively. The total thickness of the dual-shell in the solid composite is ca. 10 nm. The priorities of this dual-shell FRET nanovalve stem from three facts: (1) the thin shell allows the formation of efficient FRET system without chemical bonding between energy donor and acceptor; (2) the maximum emission wavelength of CD layer is tunable in the range of 400-600 nm, thus providing a flexible energy donor for a wide variety of energy acceptors; (3) the outer F-PMAA shell with a pH-sensitive swelling-shrinking (on-off) behavior functions as a valve for regulating the FRET process. As such, a sensitive and stable pH ratiometric sensor with a working pH range of 3-6 has been built by simply encapsulating pH-responsive fluorescein isothiocyanate (FITC) into PMAA; a pH-dependent swelling-shrinking shuttle carrier with a finely controllable molecule-release behavior has been further fabricated using rhodamine B isothiocyanate (RBITC) as the energy donor and model guest molecule. Significantly, the controlled releasing process is visually self-monitorable.

Differences in Hydration Structure Around Hydrophobic and Hydrophilic Model Peptides Probed by THz Spectroscopy

NASA Astrophysics Data System (ADS)

Wirtz, Hanna; Schäfer, Sarah; Hoberg, Claudius; Havenith, Martina

2018-03-01

We have recorded the THz spectra of the peptides NALA and NAGA as well as the amino acid leucine as model systems for hydrophobic and hydrophilic hydration. The spectra were recorded as a function of temperature and concentration and were analyzed in terms of a principal component analysis approach. NAGA shows positive absorptions with an increasing effective absorption coefficient for increasing concentrations. We conclude that NAGA due to its polar and hydrophilic structure does not have a significant influence on the surrounding water network, but is instead integrated into the water network forming a supramolecular complex. In contrast, for NALA, one hydrogen atom is substituted by a hydrophobic iso-butyl chain. We observe for NALA a decrease in absorption below 1.5 THz and a nonlinearity with a turning point around 0.75 M. Our measurements indicate that the first hydration shell of NALA is still intact at 0.75 M (corresponding to 65 water molecules per NALA). However, for larger concentrations the hydration shells can overlap, which explains the nonlinearity. For leucine, the changes in the spectrum occur at smaller concentrations. This might indicate that leucine exhibits a long-range effect on the solvating water network.

Role of specific cations and water entropy on the stability of branched DNA motif structures.

PubMed

Pascal, Tod A; Goddard, William A; Maiti, Prabal K; Vaidehi, Nagarajan

2012-10-11

DNA three-way junctions (TWJs) are important intermediates in various cellular processes and are the simplest of a family of branched nucleic acids being considered as scaffolds for biomolecular nanotechnology. Branched nucleic acids are stabilized by divalent cations such as Mg(2+), presumably due to condensation and neutralization of the negatively charged DNA backbone. However, electrostatic screening effects point to more complex solvation dynamics and a large role of interfacial waters in thermodynamic stability. Here, we report extensive computer simulations in explicit water and salt on a model TWJ and use free energy calculations to quantify the role of ionic character and strength on stability. We find that enthalpic stabilization of the first and second hydration shells by Mg(2+) accounts for 1/3 and all of the free energy gain in 50% and pure MgCl(2) solutions, respectively. The more distorted DNA molecule is actually destabilized in pure MgCl(2) compared to pure NaCl. Notably, the first shell, interfacial waters have very low translational and rotational entropy (i.e., mobility) compared to the bulk, an entropic loss that is overcompensated by increased enthalpy from additional electrostatic interactions with Mg(2+). In contrast, the second hydration shell has anomalously high entropy as it is trapped between an immobile and bulklike layer. The nonmonotonic entropic signature and long-range perturbations of the hydration shells to Mg(2+) may have implications in the molecular recognition of these motifs. For example, we find that low salt stabilizes the parallel configuration of the three-way junction, whereas at normal salt we find antiparallel configurations deduced from the NMR. We use the 2PT analysis to follow the thermodynamics of this transition and find that the free energy barrier is dominated by entropic effects that result from the decreased surface area of the antiparallel form which has a smaller number of low entropy waters in the first monolayer.

Microscopic structural descriptor of liquid water

NASA Astrophysics Data System (ADS)

Shi, Rui; Tanaka, Hajime

2018-03-01

The microscopic structure of liquid water has been believed to be the key to the understanding of the unique properties of this extremely important substance. Many structural descriptors have been developed for revealing local structural order in water, but their properties are still not well understood. The essential difficulty comes from structural fluctuations due to thermal noise, which are intrinsic to the liquid state. The most popular and widely used descriptors are the local structure index (LSI) and d5. Recently, Russo and Tanaka [Nat. Commun. 3, 3556 (2014)] introduced a new descriptor ζ which measures the translational order between the first and second shells considering hydrogen bonding (H-bonding) in the first shell. In this work, we compare the performance of these three structural descriptors for a popular water model known as TIP5P water. We show that local structural ordering can be properly captured only by the structural descriptor ζ, but not by the other two descriptors particularly at a high temperature, where thermal noise effects are severe. The key difference of ζ from LSI and d5 is that only ζ considers H-bonding which is crucial to detect high translational and tetrahedral order of not only oxygen but also hydrogen atoms. The importance of H-bonding is very natural, considering the fact that the locally favored structures are stabilized by energy gain due to the formation of four hydrogen bonds between the central water molecule and its neighboring ones in the first shell. Our analysis of the water structure by using ζ strongly supports the two-state model of water: water is a dynamic mixture of locally favored (ordered) and normal-liquid (disordered) structures. This work demonstrates the importance of H-bonding in the characterization of water's structures and provides a useful structural descriptor for water-type tetrahedral liquids to study their structure and dynamics.

Local structure of dilute aqueous DMSO solutions, as seen from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Idrissi, Abdenacer; Marekha, Bogdan A.; Barj, Mohammed; Miannay, François Alexandre; Takamuku, Toshiyuki; Raptis, Vasilios; Samios, Jannis; Jedlovszky, Pál

2017-06-01

The information about the structure of dimethyl sulfoxide (DMSO)-water mixtures at relatively low DMSO mole fractions is an important step in order to understand their cryoprotective properties as well as the solvation process of proteins and amino acids. Classical MD simulations, using the potential model combination that best reproduces the free energy of mixing of these compounds, are used to analyze the local structure of DMSO-water mixtures at DMSO mole fractions below 0.2. Significant changes in the local structure of DMSO are observed around the DMSO mole fraction of 0.1. The array of evidence, based on the cluster and the metric and topological parameters of the Voronoi polyhedra distributions, indicates that these changes are associated with the simultaneous increase of the number of DMSO-water and decrease of water-water hydrogen bonds with increasing DMSO concentration. The inversion between the dominance of these two types of H-bonds occurs around XDMSO = 0.1, above which the DMSO-DMSO interactions also start playing an important role. In other words, below the DMSO mole fraction of 0.1, DMSO molecules are mainly solvated by water molecules, while above it, their solvation shell consists of a mixture of water and DMSO. The trigonal, tetrahedral, and trigonal bipyramidal distributions of water shift to lower corresponding order parameter values indicating the loosening of these orientations. Adding DMSO does not affect the hydrogen bonding between a reference water molecule and its first neighbor hydrogen bonded water molecules, while it increases the bent hydrogen bond geometry involving the second ones. The close-packed local structure of the third, fourth, and fifth water neighbors also is reinforced. In accordance with previous theoretical and experimental data, the hydrogen bonding between water and the first, the second, and the third DMSO neighbors is stronger than that with its corresponding water neighbors. At a given DMSO mole fraction, the behavior of the intensity of the high orientational order parameter values indicates that water molecules are more ordered in the vicinity of the hydrophilic group while their structure is close-packed near the hydrophobic group of DMSO.

Sugar-influenced water diffusion, interaction, and retention in clay interlayer nanopores probed by theoretical simulations and experimental spectroscopies

NASA Astrophysics Data System (ADS)

Aristilde, Ludmilla; Galdi, Stephen M.; Kelch, Sabrina E.; Aoki, Thalia G.

2017-08-01

Understanding the hydrodynamics in clay nanopores is important for gaining insights into the trapping of water, nutrients, and contaminants in natural and engineered soils. Previous investigations have focused on the interlayer organization and molecular diffusion coefficients (D) of cations and water molecules in cation-saturated interlayer nanopores of smectite clays. Little is known, however, about how these interlayer dynamic properties are influenced by the ubiquitous presence of small organic compounds such as sugars in the soil environment. Here we probed the effects of glucose molecules on montmorillonite interlayer properties. Molecular dynamics simulations revealed re-structuring of the interlayer organization of the adsorptive species. Water-water interactions were disrupted by glucose-water H-bonding interactions. ;Dehydration; of the glucose-populated nanopore led to depletion in the Na solvation shell, which resulted in the accumulation of both Na ions (as inner-sphere complexes) and remaining hydrated water molecules at the mineral surface. This accumulation led to a decrease in both DNa and Dwater. In addition, the reduction in Dglucose as a function of increasing glucose content can be explained by the aggregation of glucose molecules into organic clusters H-bonded to the mineral surface on both walls of the nanopore. Experimental nuclear magnetic resonance and X-ray diffraction data were consistent with the theoretical predictions. Compared to clay interlayers devoid of glucose, increased intensities and new peaks in the 23Na nuclear magnetic resonance spectra confirmed increasing immobilization of Na as a function of increasing glucose content. And, the X-ray diffraction data indicated a reduced collapse of glucose-populated interlayers exposed to decreasing moisture conditions, which led to the maintenance of hydrated clay nanopores. The coupling of theoretical and experimental findings sheds light on the molecular to nanoscale mechanisms that control the enhanced trapping of water molecules and solutes within sugar-enriched clay nanopores.

Time-resolved inner-shell photoelectron spectroscopy: From a bound molecule to an isolated atom

NASA Astrophysics Data System (ADS)

Brauße, Felix; Goldsztejn, Gildas; Amini, Kasra; Boll, Rebecca; Bari, Sadia; Bomme, Cédric; Brouard, Mark; Burt, Michael; de Miranda, Barbara Cunha; Düsterer, Stefan; Erk, Benjamin; Géléoc, Marie; Geneaux, Romain; Gentleman, Alexander S.; Guillemin, Renaud; Ismail, Iyas; Johnsson, Per; Journel, Loïc; Kierspel, Thomas; Köckert, Hansjochen; Küpper, Jochen; Lablanquie, Pascal; Lahl, Jan; Lee, Jason W. L.; Mackenzie, Stuart R.; Maclot, Sylvain; Manschwetus, Bastian; Mereshchenko, Andrey S.; Mullins, Terence; Olshin, Pavel K.; Palaudoux, Jérôme; Patchkovskii, Serguei; Penent, Francis; Piancastelli, Maria Novella; Rompotis, Dimitrios; Ruchon, Thierry; Rudenko, Artem; Savelyev, Evgeny; Schirmel, Nora; Techert, Simone; Travnikova, Oksana; Trippel, Sebastian; Underwood, Jonathan G.; Vallance, Claire; Wiese, Joss; Simon, Marc; Holland, David M. P.; Marchenko, Tatiana; Rouzée, Arnaud; Rolles, Daniel

2018-04-01

Due to its element and site specificity, inner-shell photoelectron spectroscopy is a widely used technique to probe the chemical structure of matter. Here, we show that time-resolved inner-shell photoelectron spectroscopy can be employed to observe ultrafast chemical reactions and the electronic response to the nuclear motion with high sensitivity. The ultraviolet dissociation of iodomethane (CH3I ) is investigated by ionization above the iodine 4 d edge, using time-resolved inner-shell photoelectron and photoion spectroscopy. The dynamics observed in the photoelectron spectra appear earlier and are faster than those seen in the iodine fragments. The experimental results are interpreted using crystal-field and spin-orbit configuration interaction calculations, and demonstrate that time-resolved inner-shell photoelectron spectroscopy is a powerful tool to directly track ultrafast structural and electronic transformations in gas-phase molecules.

Fabrication of Uniform Hydrogel Microparticles with Alternate Polyelectrolyte/Silica Shell Layers for Applications of Controlled Loading and Releasing

NASA Astrophysics Data System (ADS)

Jeong, Eun Sook; Kim, Jin Woong

2015-03-01

Hydrogel particles, also known as microgels, consist of cross-linked three-dimensional water-soluble polymer networks. They play an essential role in loading and delivering active ingredients in medicine, cosmetics, and foods. Despite their excellent biocompatibility as well as structural diversity, much wider applications are limited due mainly to their intrinsically loose network nature. This study introduces a practical and straightforward method that enables fabrication of hydrogel microparticles layered with a mechanically robust hybrid thin shell. Basically highly monodisperse hydrogel microparticles were produced in microcapillary devices. Then, their surface was coated with alternate polyelectrolyte layers through the layer-by-layer deposition. Finally a thin silica layer was again formed by reduction of silicate on the amino-functionalized polyelectrolyte layer. We have figured out that these hybrid hydrogel microparticles showed controlled loading and releasing behaviors for water-soluble probe molecules. Moreover, we have demonstrated that they can be applied for immobilization of biomacromolecules, such as bacteria and living cells, and even for targeted releasing.

Recovery of bioactive molecules from chestnut (Castanea sativa Mill.) by-products through extraction by different solvents.

PubMed

Vella, Filomena Monica; Laratta, Bruna; La Cara, Francesco; Morana, Alessandra

2018-05-01

The underutilised forest and industrial biomass of Castanea sativa (Mill.) is generally discarded during post-harvest and food processing, with high impact on environmental quality. The searching on alternative sources of natural antioxidants from low-cost supplies, by methods involving environment-friendly techniques, has become a major goal of numerous researches in recent times. The aim of the present study was the set-up of a biomolecules extraction procedure from chestnut leaves, burs and shells and the assessing of their potential antioxidant activity. Boiling water was the best extraction solvent referring to polyphenols from chestnut shells and burs, whereas the most efficient for leaves resulted 60% ethanol at room temperature. Greatest polyphenol contents were 90.35, 60.01 and 17.68 mg gallic acid equivalents g -1 in leaves, burs and shells, respectively. Moreover, flavonoids, tannins and antioxidant activity were assessed on the best extract obtained from each chestnut by-product.

Structure and properties of silk from the African wild silkmoth Gonometa postica reared indoors

PubMed Central

Teshome, Addis; Raina, S. K.; Vollrath, Fritz

2014-01-01

Abstract African wild silkmoth, Gonometa postica Walker (Lepidoptera: Lasiocampidae), were reared indoors in order to examine the influence of rearing conditions on the structure and properties of silk cocoon shells and degummed fibers by using a scanning electron microscope, an Instron tensile tester, and a thermogravimetric analyzer. The cocoons reared indoors showed inferior quality in weight, length, width, and cocoon shell ratio compared to cocoons reared outdoors. There were no differences in cocoon shell and fiber surfaces and cross sectional structures. Cocoon shells were covered with calcium oxalate crystals with few visible fibers on their surface. Degummed fibers were smooth with minimum unfractured surfaces and globular to triangular cross sections. Indoor-reared cocoon shells had a significantly higher breaking strain, while the breaking stress was higher for cocoons reared outdoors. Fibers from indoor cocoons had a significantly higher breaking stress while outdoor fibers had higher breaking strain. Thermogravimetric analysis curves showed two main thermal reactions revealing the dehydration of water molecules and ir-reversible decomposition of the crystallites in both cocoons and fibers reared indoors and outdoors. Cocoon shells underwent additional peaks of decomposition with increased temperature. The total weight loss was higher for cocoon shells and degummed fibers from indoors. Rearing conditions (temperature and relative humidity), feeding method used, changes in total life span, days to molting, and spinning might have influenced the variation in the properties observed.The ecological and commercial significances of indoor rearing of G. postica are discussed. PMID:25373183

Many-molecule encapsulation by an icosahedral shell

PubMed Central

Perlmutter, Jason D; Mohajerani, Farzaneh; Hagan, Michael F

2016-01-01

We computationally study how an icosahedral shell assembles around hundreds of molecules. Such a process occurs during the formation of the carboxysome, a bacterial microcompartment that assembles around many copies of the enzymes ribulose 1,5-bisphosphate carboxylase/ oxygenase and carbonic anhydrase to facilitate carbon fixation in cyanobacteria. Our simulations identify two classes of assembly pathways leading to encapsulation of many-molecule cargoes. In one, shell assembly proceeds concomitantly with cargo condensation. In the other, the cargo first forms a dense globule; then, shell proteins assemble around and bud from the condensed cargo complex. Although the model is simplified, the simulations predict intermediates and closure mechanisms not accessible in experiments, and show how assembly can be tuned between these two pathways by modulating protein interactions. In addition to elucidating assembly pathways and critical control parameters for microcompartment assembly, our results may guide the reengineering of viruses as nanoreactors that self-assemble around their reactants. DOI: http://dx.doi.org/10.7554/eLife.14078.001 PMID:27166515

Inner-shell excitation and ionic fragmentation of molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hitchcock, A.P.; Tyliszczak, T.; Cavell, R.G.

1997-04-01

Inner-shell excitation and associated decay spectroscopies are site specific probes of electronic and geometrical structure and photoionization dynamics. X-ray absorption probes the geometric and electronic structure, while time-of-flight mass spectrometry with multi-coincidence detection provides information on the photofragmentation dynamics of the initially produced inner-shell state. Auger decay of inner-shell excited and ionised states is an efficient source of multiply charged ions. The charge separation and fragmentation of these species, studied by photoelectron-photoion-photoion coincidence (also called charge separation mass spectrometry) gives insights into bonding and electronic structure. In molecules, the dependence of the fragmentation process on the X-ray energy can revealmore » cases of site and/or state selective fragmentation. At the ALS the authors have examined the soft X-ray spectroscopy and ionic fragmentation of a number of molecules, including carboranes, silylenes, phosphorus halides, SF{sub 6} and CO{sub 2}. Their work is illustrated using results from the carborane and PF{sub 3} studies.« less

Proposed Ancestors of Phage Nucleic Acid Packaging Motors (and Cells)

PubMed Central

Serwer, Philip

2011-01-01

I present a hypothesis that begins with the proposal that abiotic ancestors of phage RNA and DNA packaging systems (and cells) include mobile shells with an internal, molecule-transporting cavity. The foundations of this hypothesis include the conjecture that current nucleic acid packaging systems have imprints from abiotic ancestors. The abiotic shells (1) initially imbibe and later also bind and transport organic molecules, thereby providing a means for producing molecular interactions that are links in the chain of events that produces ancestors to the first molecules that are both information carrying and enzymatically active, and (2) are subsequently scaffolds on which proteins assemble to form ancestors common to both shells of viral capsids and cell membranes. Emergence of cells occurs via aggregation and merger of shells and internal contents. The hypothesis continues by using proposed imprints of abiotic and biotic ancestors to deduce an ancestral thermal ratchet-based DNA packaging motor that subsequently evolves to integrate a DNA packaging ATPase that provides a power stroke. PMID:21994778

Crystalline order of a water/glycine film coadsorbed on the (104) calcite surface.

PubMed

Magdans, Uta; Torrelles, Xavier; Angermund, Klaus; Gies, Hermann; Rius, Jordi

2007-04-24

For biomineralization processes, the interaction of the surface of calcite crystals with organic molecules is of particular importance. Especially, biologically controlled biomineralization as in exoskeletons of mollusks and echinoderms, e.g., sea urchin with single-crystal-like spines and shells,1-3 requires molecular control of seed formation and growth process. So far, experiments showing the obvious influence of organic molecules on the morphology and habit of calcite crystals have demonstrated the molecular dimension of the interaction.4-7 Details of the kinetics of growth and dissolution of mineral surfaces influenced by additives are available,8,9 but other experimental data about the structure of the organic/inorganic interface on the atomic scale are rare. On the other hand, complicated organic macromolecules which are involved in biomineralization are numerous, with only a small fraction solved in structure and function so far.10-13 Therefore, model systems have to be designed to provide a basic understanding for the interaction process.14 Using grazing incidence X-ray diffraction combined with molecular modeling techniques, we show that glycine molecules order periodically on the calcite (104) face in competition with the solvent water when exposed to an aqueous solution of the most simple amino acid. In contrast to the general concept of the charge-matching fit of organic molecules on mineral surfaces,4,14 glycine is not attached to the calcite surface directly but substitutes for water molecules in the second hydration layer.

Molecular Design of Branched and Binary Molecules at Ordered Interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Genson, Kirsten Larson

2005-01-01

This study examined five different branched molecular architectures to discern the effect of design on the ability of molecules to form ordered structures at interfaces. Photochromic monodendrons formed kinked packing structures at the air-water interface due to the cross-sectional area mismatch created by varying number of alkyl tails and the hydrophilic polar head group. The lower generations formed orthorhombic unit cell with long range ordering despite the alkyl tails tilted to a large degree. Favorable interactions between liquid crystalline terminal groups and the underlying substrate were observed to compel a flexible carbosilane dendrimer core to form a compressed elliptical conformationmore » which packed stagger within lamellae domains with limited short range ordering. A twelve arm binary star polymer was observed to form two dimensional micelles at the air-water interface attributed to the higher polystyrene block composition. Linear rod-coil molecules formed a multitude of packing structures at the air-water interface due to the varying composition. Tree-like rod-coil molecules demonstrated the ability to form one-dimensional structures at the air-water interface and at the air-solvent interface caused by the preferential ordering of the rigid rod cores. The role of molecular architecture and composition was examined and the influence chemically competing fragments was shown to exert on the packing structure. The amphiphilic balance of the different molecular series exhibited control on the ordering behavior at the air-water interface and within bulk structures. The shell nature and tail type was determined to dictate the preferential ordering structure and molecular reorganization at interfaces with the core nature effect secondary.« less

Elucidating hydrogen oxidation/evolution kinetics in base and acid by enhanced activities at the optimized Pt shell thickness on the Ru core

DOE PAGES

Elbert, Katherine; Hu, Jue; Ma, Zhong; ...

2015-10-05

Hydrogen oxidation and evolution on Pt in acid are facile processes, while in alkaline electrolytes, they are 2 orders of magnitude slower. Thus, developing catalysts that are more active than Pt for these two reactions is important for advancing the performance of anion exchange membrane fuel cells and water electrolyzers. Herein, we detail a 4-fold enhancement of Pt mass activity that we achieved using single-crystalline Ru@Pt core–shell nanoparticles with two-monolayer-thick Pt shells, which doubles the activity on Pt–Ru alloy nanocatalysts. For Pt specific activity, the two- and one-monolayer-thick Pt shells exhibited enhancement factors of 3.1 and 2.3, respectively, compared tomore » the Pt nanocatalysts in base, differing considerably from the values of 1 and 0.4, respectively, in acid. To explain such behavior and the orders of magnitude difference in activity on going from acid to base, we performed kinetic analyses of polarization curves over a wide range of potential from –250 to 250 mV using the dual-pathway kinetic equation. From acid to base, the activation free energies increase the most for the Volmer reaction, resulting in a switch of the rate-determining step from the Tafel to the Volmer reaction, and a shift to a weaker optimal hydrogen binding energy. Furthermore, the much higher activation barrier for the Volmer reaction in base than in acid is ascribed to one or both of the two catalyst-insensitive factors: slower transport of OH – than H + in water and a stronger O–H bond in water molecules (HO–H) than in hydrated protons (H 2O–H +).« less

Studies of protein-protein and protein-water interactions by small angle x-ray scattering, terahertz spectroscopy, ASMOS, and computer simulation

NASA Astrophysics Data System (ADS)

Kim, Seung Joong

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 microm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

Tetrahedrality and hydrogen bonds in water

NASA Astrophysics Data System (ADS)

Székely, Eszter; Varga, Imre K.; Baranyai, András

2016-06-01

We carried out extensive calculations of liquid water at different temperatures and pressures using the BK3 model suggested recently [P. T. Kiss and A. Baranyai, J. Chem. Phys. 138, 204507 (2013)]. In particular, we were interested in undercooled regions to observe the propensity of water to form tetrahedral coordination of closest neighbors around a central molecule. We compared the found tetrahedral order with the number of hydrogen bonds and with the partial pair correlation functions unfolded as distributions of the closest, the second closest, etc. neighbors. We found that contrary to the number of hydrogen bonds, tetrahedrality changes substantially with state variables. Not only the number of tetrahedral arrangements increases with lowering the pressure, the density, and the temperature but the domain size of connecting tetrahedral structures as well. The difference in tetrahedrality is very pronounced between the two sides of the Widom line and even more so between the low density amorphous (LDA) and high density amorphous (HDA) phases. We observed that in liquid water and in HDA, the 5th water molecule, contrary to ice and LDA, is positioned between the first and the second coordination shell. We found no convincing evidence of structural heterogeneity or regions referring to structural transition.

Optical oscillator strengths of the valence-shell excitations of atoms and molecules determined by the dipole ( γ,γ) method

NASA Astrophysics Data System (ADS)

Xu, Long-Quan; Liu, Ya-Wei; Xu, Xin; Ni, Dong-Dong; Yang, Ke; Zhu, Lin-Fan

2017-07-01

The dipole (γ,γ) method, which is the inelastic X-ray scattering operated at a negligibly small momentum transfer, has been developed to determine the absolute optical oscillator strengths of the valence-shell excitations of atoms and molecules. This new method is free from the line saturation effect, and its Bethe-Born conversion factor varies much more slowly with the excitation energy than that of the dipole (e, e) method. Thus the dipole (γ,γ) method provides a reliable approach to obtain the benchmark optical oscillator strengths of the valence-shell excitations for gaseous atoms and molecules. In this paper, we give a review of the dipole (γ,γ) method and some recent measurements of absolute optical oscillator strengths of gaseous atoms and molecules. Contribution to the Topical Issue "Atomic and Molecular Data and their Applications", edited by Gordon W.F. Drake, Jung-Sik Yoon, Daiji Kato, Grzegorz Karwasz.

Dynamics of water in synthetic saponite clays: Effect of trivalent ion substitution

NASA Astrophysics Data System (ADS)

Mitra, S.; Prabhudesai, S. A.; Chakrabarty, D.; Sharma, V. K.; Vicente, M. A.; Embs, J. P.; Mukhopadhyay, R.

2013-06-01

Saponite clay belongs to the phyllosilicate family and is comprised of layers of Si(IV) tetrahedra and Al(III) or Mg(II) octahedra with definite interlayer spacing. In these systems, the trivalent ion substitutions in the tetrahedral layers lead to negative charge on the layers. Here we report the dynamics of water contained in [Si6.97Al1.03][Ni6.00]O20(OH)4[Na1.03]·28H2O (SAP-1) and [Si7.13Fe0.86][Ni6.00]O20(OH)4[Na0.86]·14H2O (SAP-2) saponite clays in the temperature range 200-310 K as studied by quasielastic neutron scattering technique. Particularly the effect of the ion substitution towards the dynamics of water is addressed here. Data analysis is carried out using the relaxing cage model. The existence of distribution in relaxation times indicated that the water molecules in saponite clay have a different local environment which leads to complex diffusion behavior. It is found that water exists in a supercooled state in the temperature range up to 235 K. However, some of the water molecules are found to be immobile in the temperature range 240-285 K. The fraction of immobile water decreases with increase in temperature. At higher temperatures, some of the water molecules in the hydration shells or those near the surface start participating in the diffusion process and at 293 K, almost all water molecules contribute to the dynamics. Diffusivity of water in both SAP-1 and SAP-2 are found to be lower in comparison to the bulk, and within the two samples of saponite clay diffusivity in SAP-1 is found to be lower compared to SAP-2; this has been explained on the basis of the charge on the tetrahedral layers and the charge balancing cations in the interlayer spacing.

A hydrophobic dye-encapsulated nano-hybrid as an efficient fluorescent probe for living cell imaging.

PubMed

Chang, Shu; Wu, Xumeng; Li, Yongsheng; Niu, Dechao; Ma, Zhi; Zhao, Wenru; Gu, Jinlou; Dong, Wenjie; Ding, Feng; Zhu, Weihong; Shi, Jianlin

2012-07-01

Water-soluble hydrophobic-dye@nano-hybrids (DPN@NHs) with extraordinarily enhanced fluorescent performance were fabricated by encapsulating the hydrophobic dye molecules into the core of the hybrid nanospheres based on the self-assembly of amphiphilic block copolymers followed by shell cross-linking using 3-mercaptopropyltrimethoxy-silane. The DPN@NHs are 50 nm in size, are monodispersed in aqueous solution and have a quantum yield enhanced by 30 times. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Water reorientation in the hydration shells of hydrophilic and hydrophobic solutes

NASA Astrophysics Data System (ADS)

Laage, Damien; Stirnemann, Guillaume; Hynes, James T.

2010-06-01

We discuss some key aspects of our recent theoretical work on water reorientation dynamics, which is important in a wide range of phenomena, including aqueous phase chemical reactions, protein folding, and drug binding to proteins and DNA. It is shown that, contrary to the standard conception that these dynamics are diffusional, the reorientation of a water molecule occurs by sudden, large amplitude angular jumps. The mechanism involves the exchange of one hydrogen bond for another by the reorienting water, and the process can be fruitfully viewed as a chemical reaction. The results for reorientation times, which can be well described analytically, are discussed in the context of the molecular level interpretation of recent ultrafast infrared spectroscopic results, focusing on the concepts of structure making/breaking and solvent ‘icebergs’.

Cooperation and Environment Characterize the Low-Lying Optical Spectrum of Liquid Water.

PubMed

P, Sudheer Kumar; Genova, Alessandro; Pavanello, Michele

2017-10-19

The optical spectrum of liquid water is analyzed by subsystem time-dependent density functional theory. We provide simple explanations for several important (and so far elusive) features. Due to the disordered environment surrounding each water molecule, the joint density of states of the liquid is much broader than that of the vapor, thus explaining the red-shifted Urbach tail of the liquid compared to the gas phase. Confinement effects provided by the first solvation shell are responsible for the blue shift of the first absorption peak compared to the vapor. In addition, we also characterize many-body excitonic effects. These dramatically affect the spectral weights at low frequencies, contributing to the refractive index by a small but significant amount.

Computational investigation of longitudinal diffusion, eddy dispersion, and trans-particle mass transfer in bulk, random packings of core-shell particles with varied shell thickness and shell diffusion coefficient.

PubMed

Daneyko, Anton; Hlushkou, Dzmitry; Baranau, Vasili; Khirevich, Siarhei; Seidel-Morgenstern, Andreas; Tallarek, Ulrich

2015-08-14

In recent years, chromatographic columns packed with core-shell particles have been widely used for efficient and fast separations at comparatively low operating pressure. However, the influence of the porous shell properties on the mass transfer kinetics in core-shell packings is still not fully understood. We report on results obtained with a modeling approach to simulate three-dimensional advective-diffusive transport in bulk random packings of monosized core-shell particles, covering a range of reduced mobile phase flow velocities from 0.5 up to 1000. The impact of the effective diffusivity of analyte molecules in the porous shell and the shell thickness on the resulting plate height was investigated. An extension of Giddings' theory of coupled eddy dispersion to account for retention of analyte molecules due to stagnant regions in porous shells with zero mobile phase flow velocity is presented. The plate height equation involving a modified eddy dispersion term excellently describes simulated data obtained for particle-packings with varied shell thickness and shell diffusion coefficient. It is confirmed that the model of trans-particle mass transfer resistance of core-shell particles by Kaczmarski and Guiochon [42] is applicable up to a constant factor. We analyze individual contributions to the plate height from different mass transfer mechanisms in dependence of the shell parameters. The simulations demonstrate that a reduction of plate height in packings of core-shell relative to fully porous particles arises mainly due to reduced trans-particle mass transfer resistance and transchannel eddy dispersion. Copyright © 2015 Elsevier B.V. All rights reserved.

Effects of Near Infrared Radiation on DNA. DLS and ATR-FTIR Study

NASA Astrophysics Data System (ADS)

Szymborska-Małek, Katarzyna; Komorowska, Małgorzata; Gąsior-Głogowska, Marlena

2018-01-01

We presume that the primary effect of Near Infrared (NIR) radiation on aqueous solutions of biological molecules concerns modification of hydrogen bonded structures mainly the global and the hydration shell water molecules. Since water has a significant influence on the DNA structure, we expect that the thermal stability of DNA could be modified by NIR radiation. The herring sperm DNA was exposed to NIR radiation (700-1100 nm) for 5, 10, and 20 min periods. The temperature dependent infrared measurements were done for the thin films formed on the diamond ATR crystal from evaporated DNA solutions exposed and unexposed to NIR radiation. For the NIR-treated samples (at room temperature) the B form was better conserved than in the control sample independently of the irradiation period. Above 50 °C a considerable increase in the A form was only observed for 10 min NIR exposed samples. The hydrodynamic radius, (Rh), studied by the dynamic light scattering, showed drastic decrease with the increasing irradiation time. Principal components analysis (PCA) allowed to detect the spectral features correlated with the NIR effect and thermal stability of the DNA films. Obtained results strongly support the idea that the photoionization of water by NIR radiation in presence of DNA molecules is the main factor influencing on its physicochemical properties.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ganesh, Panchapakesan; Kent, Paul R; Mochalin, Vadym N

We simulate the experimentally observed graphitization of nanodiamonds into multi-shell onion-like carbon nanostructures, also called carbon onions, at different temperatures, using reactive force fields. The simulations include long-range Coulomb and van der Waals interactions. Our results suggest that long-range interactions play a crucial role in the phase-stability and the graphitization process. Graphitization is both enthalpically and entropically driven and can hence be controlled with temperature. The outer layers of the nanodiamond have a lower kinetic barrier toward graphitization irrespective of the size of the nanodiamond and graphitize within a few-hundred picoseconds, with a large volume increase. The inner core ofmore » the nanodiamonds displays a large size-dependent kinetic barrier, and graphitizes much more slowly with abrupt jumps in the internal energy. It eventually graphitizes by releasing pressure and expands once the outer shells have graphitized. The degree of transformation at a particular temperature is thereby determined by a delicate balance between the thermal energy, long-range interactions, and the entropic/enthalpic free energy gained by graphitization. Upon full graphitization, a multi-shell carbon nanostructure appears, with a shell-shell spacing of about {approx}3.4 {angstrom} for all sizes. The shells are highly defective with predominantly five- and seven-membered rings to curve space. Larger nanodiamonds with a diameter of 4 nm can graphitize into spiral structures with a large ({approx}29-atom carbon ring) pore opening on the outermost shell. Such a large one-way channel is most attractive for a controlled insertion of molecules/ions such as Li ions, water, or ionic liquids, for increased electrochemical capacitor or battery electrode applications.« less

Global molecular identification from graphs. Neutral and ionized main-group diatomic molecules.

PubMed

James, Bryan; Caviness, Ken; Geach, Jonathan; Walters, Chris; Hefferlin, Ray

2002-01-01

Diophantine equations and inequalities are presented for main-group closed-shell diatomic molecules. Specifying various bond types (covalent, dative, ionic, van der Waals) and multiplicities, it becomes possible to identify all possible molecules. While many of the identified species are probably unstable under normal conditions, they are interesting and present a challenge for computational or experimental analysis. Ionized molecules with net charges of -1, 1, and 2 are also identified. The analysis applies to molecules with atoms from periods 2 and 3 but can be generalized by substituting isovalent atoms. When closed-shell neutral diatomics are positioned in the chemical space (with axes enumerating the numbers of valence electrons of the free atoms), it is seen that they lie on a few parallel isoelectronic series.

Glass shell manufacturing in space. [residual gases in spherical shells made from metal-organic gels

NASA Technical Reports Server (NTRS)

Nolen, R. J.; Ebner, M. A.; Downs, R. L.

1980-01-01

Residual gases always found in glass shells are CO2, O2 and N2. In those cases where high water vapor pressure is maintained in the furnace, water is also found in the shells. Other evidence for the existence of water in shells is the presence of water-induced surface weathering of the interior shell surface. Water and CO2 are the predominant volatiles generated by the pyrolysis of both inorganic and hydrolyzed metal-organic gels. The pyrolysates of unhydrolyzed metal-organic gels also contain, in addition to water and CO2, significant levels of organic volatiles, such as ethanol and some hydrocarbons; on complete oxidation, these produce CO2 and water as well. Water is most likely the initial blowing agent, it is produced copiously during the initial stages of heating. In the later stages, CO2 becomes the dominant gas as H2O is lost at increasing rates. Water in the shell arises mainly from gel dehydration, CO2 by sodium bicarbonate/carbonate decomposition and carbon oxidation, and O2 and N2 by permeation of the ambient furnace air through the molten shell wall.

Incorporation of local structure into kriging models for the prediction of atomistic properties in the water decamer.

PubMed

Davie, Stuart J; Di Pasquale, Nicodemo; Popelier, Paul L A

2016-10-15

Machine learning algorithms have been demonstrated to predict atomistic properties approaching the accuracy of quantum chemical calculations at significantly less computational cost. Difficulties arise, however, when attempting to apply these techniques to large systems, or systems possessing excessive conformational freedom. In this article, the machine learning method kriging is applied to predict both the intra-atomic and interatomic energies, as well as the electrostatic multipole moments, of the atoms of a water molecule at the center of a 10 water molecule (decamer) cluster. Unlike previous work, where the properties of small water clusters were predicted using a molecular local frame, and where training set inputs (features) were based on atomic index, a variety of feature definitions and coordinate frames are considered here to increase prediction accuracy. It is shown that, for a water molecule at the center of a decamer, no single method of defining features or coordinate schemes is optimal for every property. However, explicitly accounting for the structure of the first solvation shell in the definition of the features of the kriging training set, and centring the coordinate frame on the atom-of-interest will, in general, return better predictions than models that apply the standard methods of feature definition, or a molecular coordinate frame. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Hydrogen bonding in hydrates with one acetic acid molecule.

PubMed

Pu, Liang; Sun, Yueming; Zhang, Zhibing

2010-10-14

Hydrogen bonding (H-bond) interaction significantly influences the separation of acetic acid (HAc) from the HAc/H(2)O mixtures, especially the dilute solution, in distillation processes. It has been examined from the HAc mono-, di-, tri-, and tetrahydrates by analyzing the structures, binding energies, and infrared vibrational frequencies from quantum chemical calculations. For the first coordinate shell the 6-membered head-on ring is surely the most favorable structure because it has (1) the most favorable H-bonding parameters, (2) almost the largest binding energy per H-bond, (3) the biggest wavenumber shifts, and (4) the highest ring distribution (the AIMD simulations). Moreover, the comparison of the calculations with the experiments (the X-ray scattering data and IR frequencies) suggests that the possible structures in dilute aqueous solution are those involving two or more coordinate shells. The H-bonding in these water-surrounded HAc hydrates are the origin of the low-efficiency problem of isolating HAc from the dilute HAc/H(2)O mixtures. It is apparently a tougher work to break the H-bonds among HAc and the surrounded H(2)O molecules with respect to the case of more concentrated solutions, where the dominant structures are HAc or H(2)O aggregates.

Shell extracts of the edible mussel and oyster induce an enhancement of the catabolic pathway of human skin fibroblasts, in vitro.

PubMed

Latire, Thomas; Legendre, Florence; Bouyoucef, Mouloud; Marin, Frédéric; Carreiras, Franck; Rigot-Jolivet, Muriel; Lebel, Jean-Marc; Galéra, Philippe; Serpentini, Antoine

2017-10-01

Mollusc shells are composed of more than 95% calcium carbonate and less than 5% organic matrix consisting mostly of proteins, glycoproteins and polysaccharides. In this study, we investigated the effects of matrix macromolecular components extracted from the shells of two edible molluscs of economic interest, i.e., the blue mussel Mytilus edulis and the Pacific oyster Crassostrea gigas. The potential biological activities of these organic molecules were analysed on human dermal fibroblasts in primary culture. Our results demonstrate that shell extracts of the two studied molluscs modulate the metabolic activities of the cells. In addition, the extracts caused a decrease of type I collagen and a concomitant increase of active MMP-1, both at the mRNA and the protein levels. Therefore, our results suggest that shell extracts from M. edulis and C. gigas contain molecules that promote the catabolic pathway of human dermal fibroblasts. This work emphasises the potential use of these shell matrices in the context of anti-fibrotic strategies, particularly against scleroderma. More generally, it stresses the usefulness to valorise bivalve shells that are coproducts of shellfish farming activity.

Preferential solvation, ion pairing, and dynamics of concentrated aqueous solutions of divalent metal nitrate salts

NASA Astrophysics Data System (ADS)

Yadav, Sushma; Chandra, Amalendu

2017-12-01

We have investigated the characteristics of preferential solvation of ions, structure of solvation shells, ion pairing, and dynamics of aqueous solutions of divalent alkaline-earth metal nitrate salts at varying concentration by means of molecular dynamics simulations. Hydration shell structures and the extent of preferential solvation of the metal and nitrate ions in the solutions are investigated through calculations of radial distribution functions, tetrahedral ordering, and also spatial distribution functions. The Mg2+ ions are found to form solvent separated ion-pairs while the Ca2+ and Sr2+ ions form contact ion pairs with the nitrate ions. These findings are further corroborated by excess coordination numbers calculated through Kirkwood-Buff G factors for different ion-ion and ion-water pairs. The ion-pairing propensity is found to be in the order of Mg(NO3) 2 < C a (NO3) 2 < S r (NO3) 2, and it follows the trend given by experimental activity coefficients. It is found that proper modeling of these solutions requires the inclusion of electronic polarization of the ions which is achieved in the current study through electronic continuum correction force fields. A detailed analysis of the effects of ion-pairs on the structure and dynamics of water around the hydrated ions is done through classification of water into different subspecies based on their locations around the cations or anions only or bridged between them. We have looked at the diffusion coefficients, relaxation of orientational correlation functions, and also the residence times of different subspecies of water to explore the dynamics of water in different structural environments in the solutions. The current results show that the water molecules are incorporated into fairly well-structured hydration shells of the ions, thus decreasing the single-particle diffusivities and increasing the orientational relaxation times of water with an increase in salt concentration. The different structural motifs also lead to the presence of substantial dynamical heterogeneity in these solutions of strongly interacting ions. The current study helps us to understand the molecular details of hydration structure, ion pairing, and dynamics of water in the solvation shells and also of ion diffusion in aqueous solutions of divalent metal nitrate salts.

How proteins modify water dynamics

NASA Astrophysics Data System (ADS)

Persson, Filip; Söderhjelm, Pär; Halle, Bertil

2018-06-01

Much of biology happens at the protein-water interface, so all dynamical processes in this region are of fundamental importance. Local structural fluctuations in the hydration layer can be probed by 17O magnetic relaxation dispersion (MRD), which, at high frequencies, measures the integral of a biaxial rotational time correlation function (TCF)—the integral rotational correlation time. Numerous 17O MRD studies have demonstrated that this correlation time, when averaged over the first hydration shell, is longer than in bulk water by a factor 3-5. This rotational perturbation factor (RPF) has been corroborated by molecular dynamics simulations, which can also reveal the underlying molecular mechanisms. Here, we address several outstanding problems in this area by analyzing an extensive set of molecular dynamics data, including four globular proteins and three water models. The vexed issue of polarity versus topography as the primary determinant of hydration water dynamics is resolved by establishing a protein-invariant exponential dependence of the RPF on a simple confinement index. We conclude that the previously observed correlation of the RPF with surface polarity is a secondary effect of the correlation between polarity and confinement. Water rotation interpolates between a perturbed but bulk-like collective mechanism at low confinement and an exchange-mediated orientational randomization (EMOR) mechanism at high confinement. The EMOR process, which accounts for about half of the RPF, was not recognized in previous simulation studies, where only the early part of the TCF was examined. Based on the analysis of the experimentally relevant TCF over its full time course, we compare simulated and measured RPFs, finding a 30% discrepancy attributable to force field imperfections. We also compute the full 17O MRD profile, including the low-frequency dispersion produced by buried water molecules. Computing a local RPF for each hydration shell, we find that the perturbation decays exponentially with a decay "length" of 0.3 shells and that the second and higher shells account for a mere 3% of the total perturbation measured by 17O MRD. The only long-range effect is a weak water alignment in the electric field produced by an electroneutral protein (not screened by counterions), but this effect is negligibly small for 17O MRD. By contrast, we find that the 17O TCF is significantly more sensitive to the important short-range perturbations than the other two TCFs examined here.

Exploring the Counteracting Mechanism of Trehalose on Urea Conferred Protein Denaturation: A Molecular Dynamics Simulation Study.

PubMed

Paul, Subrata; Paul, Sandip

2015-07-30

To provide the underlying mechanism of the inhibiting effect of trehalose on the urea denatured protein, we perform classical molecular dynamics simulations of N-methylacetamide (NMA) in aqueous urea and/or trehalose solution. The site-site radial distribution functions and hydrogen bond properties indicate in binary urea solution the replacement of NMA-water hydrogen bonds by NMA-urea hydrogen bonds. On the other hand, in ternary urea and trehalose solution, trehalose does not replace the NMA-urea hydrogen bonds significantly; rather, it forms hydrogen bonds with the NMA molecule. The calculation of a preferential interaction parameter shows that, at the NMA surface, trehalose molecules are preferred and the preference for urea decreases slightly in ternary solution with respect to the binary solution. The exclusion of urea molecules in the ternary urea-NMA-trehalose system causes alleviation in van der Waals interaction energy between urea and NMA molecules. Our findings also reveal the following: (a) trehalose and urea induced second shell collapse of water structure, (b) a reduction in the mean trehalose cluster size in ternary solution, and (c) slowing down of translational motion of solution species in the presence of osmolytes. Implications of these results for the molecular explanations of the counteracting mechanism of trehalose on urea induced protein denaturation are discussed.

Organic ion association in aqueous phase and ab initio-based force fields: The case of carboxylate/ammonium salts

NASA Astrophysics Data System (ADS)

Houriez, Céline; Vallet, Valérie; Réal, Florent; Meot-Ner Mautner, Michael; Masella, Michel

2017-10-01

We performed molecular dynamics simulations of carboxylate/methylated ammonium ion pairs solvated in bulk water and of carboxylate/methylated ammonium salt solutions at ambient conditions using an ab initio-based polarizable force field whose parameters are assigned to reproduce only high end quantum computations, at the Møller-Plesset second-order perturbation theory/complete basis set limit level, regarding single ions and ion pairs as isolated and micro-hydrated in gas phase. Our results agree with the available experimental results regarding carboxylate/ammonium salt solutions. For instance, our force field approach predicts the percentage of acetate associated with ammonium ions in CH3 COO-/CH3 NH3+ solutions at the 0.2-0.8M concentration scale to range from 14% to 35%, in line with the estimates computed from the experimental ion association constant in liquid water. Moreover our simulations predict the number of water molecules released from the ion first hydration shell to the bulk upon ion association to be about 2.0 ± 0.6 molecules for acetate/protonated amine ion pairs, 3.1 ± 1.5 molecules for the HCOO-/NH4+ pair and 3.3 ± 1.2 molecules for the CH3COO-/(CH3)4N+ pair. For protonated amine-based ion pairs, these values are in line with experiment for alkali/halide pairs solvated in bulk water. All these results demonstrate the promising feature of ab initio-based force fields, i.e., their capacity in accurately modeling chemical systems that cannot be readily investigated using available experimental techniques.

Mass spectrometric and theoretical investigation of sulfate clusters in nanoscale water droplets

NASA Astrophysics Data System (ADS)

Lemke, K.

2017-12-01

The solvation of sulfate clusters of varying size and charge in water clusters and in nanoscale water droplets has been studied using electrospray ionization (ESI) FT-MS and density functional theory (DFT) molecular simulations. ESI mass spectra of solvated [Mg(MgSO4)m]2+(H2O)n with m≤10 and up to 15 water molecules have been recorded, and ion cluster experiments have been undertaken using a custom-modified FT-ICR mass spectrometer with the ability of IRMPD for ion dissociation. We present equilibrium geometries and energies for [Mg(MgSO4)m]2+(H2O)n, water-free and solvated with up to 100 water molecules, using swarm-based optimizers and DFT level calculations. Dominant cluster species identified following ESI of dilute (1-5 mM) MgSO4 solutions include hexa- and octa-nuclear magnesium sulfate ions, water-free and with a full first shell of water molecules. The largest clusters identified are magnesium sulfate decamers, i.e. [Mg(MgSO4)10]2+(H2O)n, with n≤15. As a very first step towards understanding the distribution and intensity of ESI ion mass spectra, we have identified the global minima of [Mg(MgSO4)m]2+(H2O)n with m≤10 and n≤100, and located likely global minima of magnesium sulfate clusters in the gas phase and in nano-scale water droplets. We will present a summary of the structural and energetic trends of solvated magnesium sulfate clusters, with a particular focus on structural transitions induced by cluster growth and solvation, the occurrence of "magic" number cluster species, their energetic properties and their potential role as atmospheric aqueous species.

Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water.

PubMed

Paschek, Dietmar; Nymeyer, Hugh; García, Angel E

2007-03-01

We simulate the folding/unfolding equilibrium of the 20-residue miniprotein Trp-cage. We use replica exchange molecular dynamics simulations of the AMBER94 atomic detail model of the protein explicitly solvated by water, starting from a completely unfolded configuration. We employ a total of 40 replicas, covering the temperature range between 280 and 538 K. Individual simulation lengths of 100 ns sum up to a total simulation time of about 4 micros. Without any bias, we observe the folding of the protein into the native state with an unfolding-transition temperature of about 440 K. The native state is characterized by a distribution of root mean square distances (RMSD) from the NMR data that peaks at 1.8A, and is as low as 0.4A. We show that equilibration times of about 40 ns are required to yield convergence. A folded configuration in the entire extended ensemble is found to have a lifetime of about 31 ns. In a clamp-like motion, the Trp-cage opens up during thermal denaturation. In line with fluorescence quenching experiments, the Trp-residue sidechain gets hydrated when the protein opens up, roughly doubling the number of water molecules in the first solvation shell. We find the helical propensity of the helical domain of Trp-cage rather well preserved even at very high temperatures. In the folded state, we can identify states with one and two buried internal water molecules interconnecting parts of the Trp-cage molecule by hydrogen bonds. The loss of hydrogen bonds of these buried water molecules in the folded state with increasing temperature is likely to destabilize the folded state at elevated temperatures.

Conformational Changes of the Alanine Dipeptide in Water-Ethanol Binary Mixtures.

PubMed

Almeida, Glauco G; Cordeiro, João M M; Martín, M Elena; Aguilar, Manuel A

2016-04-12

Experimental work developed in the last years has evidenced the capacity of alcohols and polyalcohols to modify the energy landscape of peptides and proteins. However, the mechanism underlying this effect is not clear. Taking as a model system the alanine dipeptide (AD) we perform a QM/MM study in water, ethanol, and a 40-60% in volume water-ethanol mixture. The AD molecule was described at the MP2/aug-cc-pVDZ level. In polar solution, only αR and PPII conformers contribute in an appreciable way to the conformational equilibrium. The final in solution αR-PPII free energy difference is determined from the interplay between the internal energy of the dipeptide and the solute-solvent interaction free energy. Internal energy favors the formation of PPII, whereas, on the contrary, solute-solvent interaction is favorable to αR, so any factor that decreases the solute-solvent interaction free energy will increase the PPII population. The addition of ethanol increases the stability of the PPII conformer. Our results point to the presence of preferential solvation in this system, the composition of the first solvation shell in the binary mixture being dominated by water molecules. Remarkably, this fact does not affect the differential conformational stability that is controlled by long-range interactions. From the analysis of solvent density maps it is concluded that, in the water-ethanol mixture, ethanol molecules are more likely found around the alanine side chain and the carbonyl group, but while in PPII ethanol molecules interact mainly with the carbonyl group of the N-terminal end, in C5 the interaction is with the carbonyl group of the C-terminal end. In αR, ethanol interacts with both carbonyl groups.

Effects of dilute aqueous NaCl solution on caffeine aggregation

NASA Astrophysics Data System (ADS)

Sharma, Bhanita; Paul, Sandip

2013-11-01

The effect of salt concentration on association properties of caffeine molecule was investigated by employing molecular dynamics simulations in isothermal-isobaric ensemble of eight caffeine molecules in pure water and three different salt (NaCl) concentrations, at 300 K temperature and 1 atm pressure. The concentration of caffeine was taken almost at the solubility limit. With increasing salt concentration, we observe enhancement of first peak height and appearance of a second peak in the caffeine-caffeine distribution function. Furthermore, our calculated solvent accessible area values and cluster structure analyses suggest formation of higher order caffeine cluster on addition of salt. The calculated hydrogen bond properties reveal that there is a modest decrease in the average number of water-caffeine hydrogen bonds on addition of NaCl salt. Also observed are: (i) decrease in probability of salt contact ion pair as well as decrease in the solvent separated ion pair formation with increasing salt concentration, (ii) a modest second shell collapse in the water structure, and (iii) dehydration of hydrophobic atomic sites of caffeine on addition of NaCl.

Effects of dilute aqueous NaCl solution on caffeine aggregation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Bhanita; Paul, Sandip, E-mail: sandipp@iitg.ernet.in

The effect of salt concentration on association properties of caffeine molecule was investigated by employing molecular dynamics simulations in isothermal-isobaric ensemble of eight caffeine molecules in pure water and three different salt (NaCl) concentrations, at 300 K temperature and 1 atm pressure. The concentration of caffeine was taken almost at the solubility limit. With increasing salt concentration, we observe enhancement of first peak height and appearance of a second peak in the caffeine-caffeine distribution function. Furthermore, our calculated solvent accessible area values and cluster structure analyses suggest formation of higher order caffeine cluster on addition of salt. The calculated hydrogenmore » bond properties reveal that there is a modest decrease in the average number of water-caffeine hydrogen bonds on addition of NaCl salt. Also observed are: (i) decrease in probability of salt contact ion pair as well as decrease in the solvent separated ion pair formation with increasing salt concentration, (ii) a modest second shell collapse in the water structure, and (iii) dehydration of hydrophobic atomic sites of caffeine on addition of NaCl.« less

Preparation of paclitaxel/chitosan co-assembled core-shell nanofibers for drug-eluting stent

NASA Astrophysics Data System (ADS)

Tang, Jing; Liu, Yongjia; Zhu, Bangshang; Su, Yue; Zhu, Xinyuan

2017-01-01

The paclitaxel/chitosan (PTX/CS) core-shell nanofibers (NFs) are easily prepared by co-assembly of PTX and CS and used in drug-eluting stent. The mixture solution of PTX (dissolved in ethanol) and CS (dissolved in 1% acetic acid water solution) under sonication will make the formation of NFs, in which small molecule PTX co-assembles with biomacromolecular CS through non-covalent interactions. The obtained NFs are tens to hundreds nanometers in diameter and millimeter level in length. Furthermore, the structure of PTX/CS NFs was characterized by confocal laser scanning microscopy (CLSM), zeta potential, X-ray photoelectron spectroscopy (XPS) and nanoscale infra-red (nanoIR), which provided evidences demonstrated that PTX/CS NFs are core-shell structures. The 'shell' of CS wrapped outside of the NFs, while PTX is located in the core. Thus it resulted in high drug loading content (>40 wt.%). The well-controlled drug release, low cytotoxicity and good haemocompatibility were also found in drug carrier system of PTX/CS NFs. In addition, the hydrophilic and flexible properties of NFs make them easily coating and filming on stent to prepare drug-eluting stent (DES). Therefore, this study provides a convenient method to prepare high PTX loaded NFs, which is a promising nano-drug carrier used for DES and other biomedical applications. The possible molecular mechanism of PTX and CS co-assembly and core-shell nanofiber formation is also explored.

Regulation of Extracellular Matrix Synthesis by Shell Extracts from the Marine Bivalve Pecten maximus in Human Articular Chondrocytes- Application for Cartilage Engineering.

PubMed

Bouyoucef, Mouloud; Rakic, Rodolphe; Gómez-Leduc, Tangni; Latire, Thomas; Marin, Frédéric; Leclercq, Sylvain; Carreiras, Franck; Serpentini, Antoine; Lebel, Jean-Marc; Galéra, Philippe; Legendre, Florence

2018-04-07

The shells of the bivalve mollusks are organo-mineral structures predominantly composed of calcium carbonate, but also of a minor organic matrix, a mixture of proteins, glycoproteins, and polysaccharides. These proteins are involved in mineral deposition and, more generally, in the spatial organization of the shell crystallites in well-defined microstructures. In this work, we extracted different organic shell extracts (acid-soluble matrix, acid-insoluble matrix, water-soluble matrix, guanidine HCl/EDTA-extracted matrix, referred as ASM, AIM, WSM, and EDTAM, respectively) from the shell of the scallop Pecten maximus and studied their biological activities on human articular chondrocytes (HACs). We found that these extracts differentially modulate the biological activities of HACs, depending on the type of extraction and the concentration used. Furthermore, we showed that, unlike ASM and AIM, WSM promotes maintenance of the chondrocyte phenotype in monolayer culture. WSM increased the expression of chondrocyte-specific markers (aggrecan and type II collagen), without enhancing that of the main chondrocyte dedifferentiation marker (type I collagen). We also demonstrated that WSM could favor redifferentiation of chondrocyte in collagen sponge scaffold in hypoxia. Thus, this study suggests that the organic matrix of Pecten maximus, particularly WSM, may contain interesting molecules with chondrogenic effects. Our research emphasizes the potential use of WSM of Pecten maximus for cell therapy of cartilage.

Pt@Ag and Pd@Ag core/shell nanoparticles for catalytic degradation of Congo red in aqueous solution.

PubMed

Salem, Mohamed A; Bakr, Eman A; El-Attar, Heba G

2018-01-05

Platinum/silver (Pt@Ag) and palladium/silver (Pd@Ag) core/shell NPs have been synthesized in two steps reaction using the citrate method. The progress of nanoparticle formation was followed by the UV/Vis spectroscopy. Transmission electron microscopy revealed spherical shaped core/shell nanoparticles with average particle diameter 32.17nm for Pt@Ag and 8.8nm for Pd@Ag. The core/shell NPs were further characterized by FT-IR and XRD. Reductive degradation of the Congo red dye was chosen to demonstrate the excellent catalytic activity of these core/shell nanostructures. The nanocatalysts act as electron mediators for the transfer of electrons from the reducing agent (NaBH 4 ) to the dye molecules. Effect of reaction parameters such as nanocatalyst dose, dye and NaBH 4 concentrations on the dye degradation was investigated. A comparison between the catalytic activities of both nanocatalysts was made to realize which of them the best in catalytic performance. Pd@Ag was the higher in catalytic activity over Pt@Ag. Such greater activity is originated from the smaller particle size and larger surface area. Pd@Ag nanocatalyst was catalytically stable through four subsequent reaction runs under the utilized reaction conditions. These findings can thus be considered as possible economical alternative for environmental safety against water pollution by dyes. Copyright © 2017. Published by Elsevier B.V.

Pt@Ag and Pd@Ag core/shell nanoparticles for catalytic degradation of Congo red in aqueous solution

NASA Astrophysics Data System (ADS)

Salem, Mohamed A.; Bakr, Eman A.; El-Attar, Heba G.

2018-01-01

Platinum/silver (Pt@Ag) and palladium/silver (Pd@Ag) core/shell NPs have been synthesized in two steps reaction using the citrate method. The progress of nanoparticle formation was followed by the UV/Vis spectroscopy. Transmission electron microscopy revealed spherical shaped core/shell nanoparticles with average particle diameter 32.17 nm for Pt@Ag and 8.8 nm for Pd@Ag. The core/shell NPs were further characterized by FT-IR and XRD. Reductive degradation of the Congo red dye was chosen to demonstrate the excellent catalytic activity of these core/shell nanostructures. The nanocatalysts act as electron mediators for the transfer of electrons from the reducing agent (NaBH4) to the dye molecules. Effect of reaction parameters such as nanocatalyst dose, dye and NaBH4 concentrations on the dye degradation was investigated. A comparison between the catalytic activities of both nanocatalysts was made to realize which of them the best in catalytic performance. Pd@Ag was the higher in catalytic activity over Pt@Ag. Such greater activity is originated from the smaller particle size and larger surface area. Pd@Ag nanocatalyst was catalytically stable through four subsequent reaction runs under the utilized reaction conditions. These findings can thus be considered as possible economical alternative for environmental safety against water pollution by dyes.

Influence of Electrostatics on Small Molecule Flux through a Protein Nanoreactor.

PubMed

Glasgow, Jeff E; Asensio, Michael A; Jakobson, Christopher M; Francis, Matthew B; Tullman-Ercek, Danielle

2015-09-18

Nature uses protein compartmentalization to great effect for control over enzymatic pathways, and the strategy has great promise for synthetic biology. In particular, encapsulation in nanometer-sized containers to create nanoreactors has the potential to elicit interesting, unexplored effects resulting from deviations from well-understood bulk processes. Self-assembled protein shells for encapsulation are especially desirable for their uniform structures and ease of perturbation through genetic mutation. Here, we use the MS2 capsid, a well-defined porous 27 nm protein shell, as an enzymatic nanoreactor to explore pore-structure effects on substrate and product flux during the catalyzed reaction. Our results suggest that the shell can influence the enzymatic reaction based on charge repulsion between small molecules and point mutations around the pore structure. These findings also lend support to the hypothesis that protein compartments modulate the transport of small molecules and thus influence metabolic reactions and catalysis in vitro.

Amino Acid Side Chain Interactions in the Presence of Salts

PubMed Central

Hassan, Sergio A.

2005-01-01

The effects of salt on the intermolecular interactions between polar/charged amino acids are investigated through molecular dynamics simulations. The mean forces and associated potentials are calculated for NaCl salt in the 0–2 M concentration range at 298 K. It is found that the addition of salt may stabilize or destabilize the interactions, depending on the nature of the interacting molecules. The degree of (de)stabilization is quantified, and the origin of the salt-dependent modulation is discussed based upon an analysis of solvent density profiles. To gain insight into the molecular origin of the salt modulation, spatial distribution functions (sdf’s) are calculated, revealing a high degree of solvent structuredness in all cases. The peaks in the sdf’s are consistent with long-range hydrogen-bonding networks connecting the solute hydrophilic groups, and that contribute to their intermolecular solvent-induced forces. The restructuring of water around the solutes as they dissociate from close contact is analyzed. This analysis offers clues on how the solvent structure modulates the effective intermolecular interactions in complex solutes. This modulation results from a critical balance between bulk electrostatic forces and those exerted by (i) the water molecules in the structured region between the monomers, which is disrupted by ions that transiently enter the hydration shells, and (ii) the ions in the hydration shells in direct interactions with the solutes. The implications of these findings in protein/ligand (noncovalent) association/dissociation mechanisms are briefly discussed. PMID:16479276

Viewpoint 9--molecular structure of aqueous interfaces

NASA Technical Reports Server (NTRS)

Pohorille, A.; Wilson, M. A.

1993-01-01

In this review we summarize recent progress in our understanding of the structure of aqueous interfaces emerging from molecular level computer simulations. It is emphasized that the presence of the interface induces specific structural effects which, in turn, influence a wide variety of phenomena occurring near the phase boundaries. At the liquid-vapor interface, the most probable orientations of a water molecule is such that its dipole moment lies parallel to the interface, one O-H bond points toward the vapor and the other O-H bond is directed toward the liquid. The orientational distributions are broad and slightly asymmetric, resulting in an excess dipole moment pointing toward the liquid. These structural preferences persist at interfaces between water and nonpolar liquids, indicating that the interactions between the two liquids in contact are weak. It was found that liquid-liquid interfaces are locally sharp but broadened by capillary waves. One consequence of anisotropic orientations of interfacial water molecules is asymmetric interactions, with respect to the sign of the charge, of ions with the water surface. It was found that even very close to the surface ions retain their hydration shells. New features of aqueous interfaces have been revealed in studies of water-membrane and water-monolayer systems. In particular, water molecules are strongly oriented by the polar head groups of the amphiphilic phase, and they penetrate the hydrophilic head-group region, but not the hydrophobic core. At infinite dilution near interfaces, amphiphilic molecules exhibit behavior different from that in the gas phase or in bulk water. This result sheds new light on the nature of hydrophobic effect in the interfacial regions. The presence of interfaces was also shown to affect both equilibrium and dynamic components of rates of chemical reactions. Applications of continuum models to interfacial problems have been, so far, unsuccessful. This, again, underscores the importance of molecular-level information about interfaces.

Pressure dependence of viscosity in supercooled water and a unified approach for thermodynamic and dynamic anomalies of water

PubMed Central

Singh, Lokendra P.; Issenmann, Bruno; Caupin, Frédéric

2017-01-01

The anomalous decrease of the viscosity of water with applied pressure has been known for over a century. It occurs concurrently with major structural changes: The second coordination shell around a molecule collapses onto the first shell. Viscosity is thus a macroscopic witness of the progressive breaking of the tetrahedral hydrogen bond network that makes water so peculiar. At low temperature, water at ambient pressure becomes more tetrahedral and the effect of pressure becomes stronger. However, surprisingly, no data are available for the viscosity of supercooled water under pressure, in which dramatic anomalies are expected based on interpolation between ambient pressure data for supercooled water and high pressure data for stable water. Here we report measurements with a time-of-flight viscometer down to 244K and up to 300MPa, revealing a reduction of viscosity by pressure by as much as 42%. Inspired by a previous attempt [Tanaka H (2000) J Chem Phys 112:799–809], we show that a remarkably simple extension of a two-state model [Holten V, Sengers JV, Anisimov MA (2014) J Phys Chem Ref Data 43:043101], initially developed to reproduce thermodynamic properties, is able to accurately describe dynamic properties (viscosity, self-diffusion coefficient, and rotational correlation time) as well. Our results support the idea that water is a mixture of a high density, “fragile” liquid, and a low density, “strong” liquid, the varying proportion of which explains the anomalies and fragile-to-strong crossover in water. PMID:28404733

The synthesis of four-layer gold-silver-polymer-silver core-shell nanomushroom with inbuilt Raman molecule for surface-enhanced Raman scattering

NASA Astrophysics Data System (ADS)

Jiang, Tao; Wang, Xiaolong; Zhou, Jun

2017-12-01

A facial two-step reduction method was proposed to synthesize four-layer gold-silver-polymer-silver (Au@Ag@PSPAA@Ag) core-shell nanomushrooms (NMs) with inbuilt Raman molecule. The surface-enhanced Raman scattering (SERS) intensity of 4MBA adhered on the surface of Au core gradually increased with the modification of middle Ag shell and then Ag mushroom cap due to the formation of two kinds of ultra-small interior nanogap. Compared with the initial Au nanoparticles, the SERS enhancement ratio of the Au@Ag@PSPAA@Ag NMs approached to nearly 40. The novel core-shell NMs also exhibited homogeneous SERS signals for only one sample and reproducible signals for 10 different samples, certified by the low relative standard deviation values of less than 10% and 15% for the character peaks of 4-mercaptobenzoic acid, respectively. Such a novel four-layer core-shell nanostructure with reliable SERS performance has great potential application in quantitative SERS-based immunoassay.

Active ester functional single core magnetic nanostructures as a versatile immobilization matrix for effective bioseparation and catalysis.

PubMed

Gelbrich, Thorsten; Reinartz, Michael; Schmidt, Annette M

2010-03-08

Multifunctional nanocarriers for amino functional targets with a high density of accessible binding sites are obtained in a single polymerization step by grafting from copolymerization of an active ester monomer from superparamagnetic cores. As a result of the brush-like structure of the highly dispersed shell, the nano-objects exhibit an available capture capacity for amines that is found to be up to 2 orders of magnitude higher than for commercial magnetic beads, and the functional brush shell can serve as a template for many types of pendant functional groups and molecules. As comonomer, oligo(ethylene glycol) methacrylate allows for excellent water solubility at room temperature, biocompatibility, and thermoflocculation. We demonstrate the biorelated applicability of the hybrid nanoparticles by two different approaches. In the first approach, the immobilization of trypsin to the core-shell nanoparticles results in highly active, nanoparticulate biocatalysts that can easily be separated magnetically. Second, we demonstrate that the obtained nanoparticles are suitable for the effective labeling of cell membranes, opening a novel pathway for the easy and effective isolation of membrane proteins.

The solvation study of carbon, silicon and their mixed nanotubes in water solution.

PubMed

Hashemi Haeri, Haleh; Ketabi, Sepideh; Hashemianzadeh, Seyed Majid

2012-07-01

Nanotubes are believed to open the road toward different modern fields, either technological or biological. However, the applications of nanotubes have been badly impeded for the poor solubility in water which is especially essential for studies in the presence of living cells. Therefore, water soluble samples are in demand. Herein, the outcomes of Monte Carlo simulations of different sets of multiwall nanotubes immersed in water are reported. A number of multi wall nanotube samples, comprised of pure carbon, pure silicon and several mixtures of carbon and silicon are the subjects of study. The simulations are carried out in an (N,V,T) ensemble. The purpose of this report is to look at the effects of nanotube size (diameter) and nanotube type (pure carbon, pure silicon or a mixture of carbon and silicon) variation on solubility of multiwall nanotubes in terms of number of water molecules in shell volume. It is found that the solubility of the multi wall carbon nanotube samples is size independent, whereas multi wall silicon nanotube samples solubility varies with diameter of the inner tube. The higher solubility of samples containing silicon can be attributed to the larger atomic size of silicon atom which provides more direct contact with the water molecules. The other affecting factor is the bigger inter space (the space between inner and outer tube) in the case of silicon samples. Carbon type multi wall nanotubes appeared as better candidates for transporting water molecules through a multi wall nanotube structure, while in the case of water adsorption problems it is better to use multi wall silicon nanotubes or a mixture of multi wall carbon/ silicon nanotubes.

Simultaneous tracking of drug molecules and carriers using aptamer-functionalized fluorescent superstable gold nanorod-carbon nanocapsules during thermo-chemotherapy

NASA Astrophysics Data System (ADS)

Wang, Xue-Wei; Gao, Wei; Fan, Huanhuan; Ding, Ding; Lai, Xiao-Fang; Zou, Yu-Xiu; Chen, Long; Chen, Zhuo; Tan, Weihong

2016-04-01

Controlling and monitoring the drug delivery process is critical to its intended therapeutic function. Many nanocarrier systems for drug delivery have been successfully developed. However, biocompatibility, stability, and simultaneously tracing drugs and nanocarriers present significant limitations. Herein, we have fabricated a multifunctional nanocomposite by coating the gold nanorod (AuNR) with a biocompatible, superstable and fluorescent carbon layer, obtaining the AuNR@carbon core-shell nanocapsule. In this system, the carbon shell, originally obtained in aqueous glucose solutions and, therefore, biocompatible in physiological environments, could be simply loaded with cell-specific aptamers and therapeutic molecules through π-π interactions, a useful tool for cancer-targeted cellular imaging and therapy. Moreover, such a stable and intrinsic fluorescence effect of the AuNR@carbon enabled simultaneous tracking of released therapeutic molecules and nanocarriers under thermo-chemotherapy. The AuNR@carbons had high surface areas and stable shells, as well as unique optical and photothermal properties, making them promising nanostructures for biomedical applications.Controlling and monitoring the drug delivery process is critical to its intended therapeutic function. Many nanocarrier systems for drug delivery have been successfully developed. However, biocompatibility, stability, and simultaneously tracing drugs and nanocarriers present significant limitations. Herein, we have fabricated a multifunctional nanocomposite by coating the gold nanorod (AuNR) with a biocompatible, superstable and fluorescent carbon layer, obtaining the AuNR@carbon core-shell nanocapsule. In this system, the carbon shell, originally obtained in aqueous glucose solutions and, therefore, biocompatible in physiological environments, could be simply loaded with cell-specific aptamers and therapeutic molecules through π-π interactions, a useful tool for cancer-targeted cellular imaging and therapy. Moreover, such a stable and intrinsic fluorescence effect of the AuNR@carbon enabled simultaneous tracking of released therapeutic molecules and nanocarriers under thermo-chemotherapy. The AuNR@carbons had high surface areas and stable shells, as well as unique optical and photothermal properties, making them promising nanostructures for biomedical applications. Electronic supplementary information (ESI) available: Experimental details and characterization data for all new compounds. See DOI: 10.1039/c6nr00369a

Teaching Valence Shell Electron Pair Repulsion (VSEPR) Theory

ERIC Educational Resources Information Center

Talbot, Christopher; Neo, Choo Tong

2013-01-01

This "Science Note" looks at the way that the shapes of simple molecules can be explained in terms of the number of electron pairs in the valence shell of the central atom. This theory is formally known as valence shell electron pair repulsion (VSEPR) theory. The article explains the preferred shape of chlorine trifluoride (ClF3),…

Hydration and dielectrical properties of aqueous pyrrolidinium trifluoroacetate solutions

NASA Astrophysics Data System (ADS)

Lyashchenko, A. K.; Balakaeva, I. V.; Simonova, Yu. A.; Timofeeva, L. M.

2017-10-01

Results from microwave measurements of the dielectrical properties of aqueous pyrrolidinium trifluoroacetate solutions at maximum water dispersion frequencies (13-25 GHz) and temperatures of 288, 298, and 308 K are given. The static dielectrical constants, times, and activation parameters of the dielectrical relaxation of solutions are calculated. The enthalpy and time of dielectrical relaxation activation are increased by deceleration of the motion of water molecules in the hydrate shells of ions. The changes in dielectrical parameters are in this case minimal in a series of aqueous solutions of diallylammonium salts with cations of different structures and degrees of substitution. It is shown that pyrrolidinium ions are characterized by weak hydrophobic hydration.

Thermodynamic properties and diffusion of water + methane binary mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shvab, I.; Sadus, Richard J., E-mail: rsadus@swin.edu.au

2014-03-14

Thermodynamic and diffusion properties of water + methane mixtures in a single liquid phase are studied using NVT molecular dynamics. An extensive comparison is reported for the thermal pressure coefficient, compressibilities, expansion coefficients, heat capacities, Joule-Thomson coefficient, zero frequency speed of sound, and diffusion coefficient at methane concentrations up to 15% in the temperature range of 298–650 K. The simulations reveal a complex concentration dependence of the thermodynamic properties of water + methane mixtures. The compressibilities, heat capacities, and diffusion coefficients decrease with increasing methane concentration, whereas values of the thermal expansion coefficients and speed of sound increase. Increasing methanemore » concentration considerably retards the self-diffusion of both water and methane in the mixture. These effects are caused by changes in hydrogen bond network, solvation shell structure, and dynamics of water molecules induced by the solvation of methane at constant volume conditions.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elbert, Katherine; Hu, Jue; Ma, Zhong

Hydrogen oxidation and evolution on Pt in acid are facile processes, while in alkaline electrolytes, they are 2 orders of magnitude slower. Thus, developing catalysts that are more active than Pt for these two reactions is important for advancing the performance of anion exchange membrane fuel cells and water electrolyzers. Herein, we detail a 4-fold enhancement of Pt mass activity that we achieved using single-crystalline Ru@Pt core–shell nanoparticles with two-monolayer-thick Pt shells, which doubles the activity on Pt–Ru alloy nanocatalysts. For Pt specific activity, the two- and one-monolayer-thick Pt shells exhibited enhancement factors of 3.1 and 2.3, respectively, compared tomore » the Pt nanocatalysts in base, differing considerably from the values of 1 and 0.4, respectively, in acid. To explain such behavior and the orders of magnitude difference in activity on going from acid to base, we performed kinetic analyses of polarization curves over a wide range of potential from –250 to 250 mV using the dual-pathway kinetic equation. From acid to base, the activation free energies increase the most for the Volmer reaction, resulting in a switch of the rate-determining step from the Tafel to the Volmer reaction, and a shift to a weaker optimal hydrogen binding energy. Furthermore, the much higher activation barrier for the Volmer reaction in base than in acid is ascribed to one or both of the two catalyst-insensitive factors: slower transport of OH – than H + in water and a stronger O–H bond in water molecules (HO–H) than in hydrated protons (H 2O–H +).« less

How High Pressure Unifies Solvation Processes in Liquid Chromatography.

PubMed

Bocian, Szymon; Škrinjar, Tea; Bolanca, Tomislav; Buszewski, Bogusław

2017-11-01

A series of core-shell-based stationary phases of varying surface chemistry were subjected to solvent adsorption investigation under ultra-HPLC conditions. Acetonitrile and water excess isotherms were measured using a minor disturbance method. It was observed that adsorption of organic solvent is unified under high pressure. Preferential solvation due to specific interactions between the stationary phases and solvent molecules was limited. The obtained results showed that the solvation process is almost independent of surface chemistry, in contrast to HPLC conditions in which specific interactions differentiate solvation processes.

Alkali-ion microsolvation with benzene molecules.

PubMed

Marques, J M C; Llanio-Trujillo, J L; Albertí, M; Aguilar, A; Pirani, F

2012-05-24

The target of this investigation is to characterize by a recently developed methodology, the main features of the first solvation shells of alkaline ions in nonpolar environments due to aromatic rings, which is of crucial relevance to understand the selectivity of several biochemical phenomena. We employ an evolutionary algorithm to obtain putative global minima of clusters formed with alkali-ions (M(+)) solvated with n benzene (Bz) molecules, i.e., M(+)-(Bz)(n). The global intermolecular interaction has been decomposed in Bz-Bz and in M(+)-Bz contributions, using a potential model based on different decompositions of the molecular polarizability of benzene. Specifically, we have studied the microsolvation of Na(+), K(+), and Cs(+) with benzene molecules. Microsolvation clusters up to n = 21 benzene molecules are involved in this work and the achieved global minimum structures are reported and discussed in detail. We observe that the number of benzene molecules allocated in the first solvation shell increases with the size of the cation, showing three molecules for Na(+) and four for both K(+) and Cs(+). The structure of this solvation shell keeps approximately unchanged as more benzene molecules are added to the cluster, which is independent of the ion. Particularly stable structures, so-called "magic numbers", arise for various nuclearities of the three alkali-ions. Strong "magic numbers" appear at n = 2, 3, and 4 for Na(+), K(+), and Cs(+), respectively. In addition, another set of weaker "magic numbers" (three per alkali-ion) are reported for larger nuclearities.

Dendritic core-shell nickel-iron-copper metal/metal oxide electrode for efficient electrocatalytic water oxidation.

PubMed

Zhang, Peili; Li, Lin; Nordlund, Dennis; Chen, Hong; Fan, Lizhou; Zhang, Biaobiao; Sheng, Xia; Daniel, Quentin; Sun, Licheng

2018-01-26

Electrochemical water splitting requires efficient water oxidation catalysts to accelerate the sluggish kinetics of water oxidation reaction. Here, we report a promisingly dendritic core-shell nickel-iron-copper metal/metal oxide electrode, prepared via dealloying with an electrodeposited nickel-iron-copper alloy as a precursor, as the catalyst for water oxidation. The as-prepared core-shell nickel-iron-copper electrode is characterized with porous oxide shells and metallic cores. This tri-metal-based core-shell nickel-iron-copper electrode exhibits a remarkable activity toward water oxidation in alkaline medium with an overpotential of only 180 mV at a current density of 10 mA cm -2 . The core-shell NiFeCu electrode exhibits pH-dependent oxygen evolution reaction activity on the reversible hydrogen electrode scale, suggesting that non-concerted proton-electron transfers participate in catalyzing the oxygen evolution reaction. To the best of our knowledge, the as-fabricated core-shell nickel-iron-copper is one of the most promising oxygen evolution catalysts.

Thermodynamic and structural signatures of water-driven methane-methane attraction in coarse-grained mW water.

PubMed

Song, Bin; Molinero, Valeria

2013-08-07

Hydrophobic interactions are responsible for water-driven processes such as protein folding and self-assembly of biomolecules. Microscopic theories and molecular simulations have been used to study association of a pair of methanes in water, the paradigmatic example of hydrophobic attraction, and determined that entropy is the driving force for the association of the methane pair, while the enthalpy disfavors it. An open question is to which extent coarse-grained water models can still produce correct thermodynamic and structural signatures of hydrophobic interaction. In this work, we investigate the hydrophobic interaction between a methane pair in water at temperatures from 260 to 340 K through molecular dynamics simulations with the coarse-grained monatomic water model mW. We find that the coarse-grained model correctly represents the free energy of association of the methane pair, the temperature dependence of free energy, and the positive change in entropy and enthalpy upon association. We investigate the relationship between thermodynamic signatures and structural order of water through the analysis of the spatial distribution of the density, energy, and tetrahedral order parameter Qt of water. The simulations reveal an enhancement of tetrahedral order in the region between the first and second hydration shells of the methane molecules. The increase in tetrahedral order, however, is far from what would be expected for a clathrate-like or ice-like shell around the solutes. This work shows that the mW water model reproduces the key signatures of hydrophobic interaction without long ranged electrostatics or the need to be re-parameterized for different thermodynamic states. These characteristics, and its hundred-fold increase in efficiency with respect to atomistic models, make mW a promising water model for studying water-driven hydrophobic processes in more complex systems.

Water vapor permeability of the rigid-shelled gecko egg.

PubMed

Andrews, Robin M

2012-07-01

The vast majority of squamate reptiles (lizards and snakes) produce parchment-shelled eggs that absorb water during incubation, and thus increase in mass, volume, and surface area. In contrast, females from a single monophyletic lineage of gekkotan lizards produce rigid-shelled eggs. These eggs are functionally comparable to those of birds, that is, at oviposition, eggs contain all the water needed for development, and their mass decreases during incubation via the diffusion of water vapor through the shell. I determined patterns of water loss and shell permeability to water vapor from oviposition to hatching for the rigid-shelled eggs of the gekkonid Chrondrodactylus turneri and compared permeability of C. turneri eggs to those of birds and other squamates. Chrondrodactylus turneri eggs incubated at 28.5°C and 40% relative humidity (RH) decreased in mass by 14% over the course of a 68-day incubation period. The rate of water loss varied during incubation; egg mass decreased rapidly during the first 8 days of incubation, declined at a low constant rate during the next 35 days, and then decreased rapidly during the final 25 days of incubation. Overall permeability was 0.17 mg/day/kPa/cm(2) . Percent water loss of rigid-shelled gecko eggs during incubation is similar to that exhibited by birds, but water vapor permeability is about one-third that of bird eggs and several orders of magnitude lower than that of parchment-shelled squamate eggs. In general, the water economy of their eggs may be associated with the adaptive radiation of the rigid-shelled sphaerodactylid, phyllodactylid, and gekkonid geckos. © 2012 WILEY PERIODICALS, INC.

Structure and properties of silk from the African wild silkmoth Gonometa postica reared indoors.

PubMed

Teshome, Addis; Raina, S K; Vollrath, Fritz

2014-03-07

African wild silkmoth, Gonometa postica Walker (Lepidoptera: Lasiocampidae), were reared indoors in order to examine the influence of rearing conditions on the structure and properties of silk cocoon shells and degummed fibers by using a scanning electron microscope, an Instron tensile tester, and a thermogravimetric analyzer. The cocoons reared indoors showed inferior quality in weight, length, width, and cocoon shell ratio compared to cocoons reared outdoors. There were no differences in cocoon shell and fiber surfaces and cross sectional structures. Cocoon shells were covered with calcium oxalate crystals with few visible fibers on their surface. Degummed fibers were smooth with minimum unfractured surfaces and globular to triangular cross sections. Indoor-reared cocoon shells had a significantly higher breaking strain, while the breaking stress was higher for cocoons reared outdoors. Fibers from indoor cocoons had a significantly higher breaking stress while outdoor fibers had higher breaking strain. Thermogravimetric analysis curves showed two main thermal reactions revealing the dehydration of water molecules and ir-reversible decomposition of the crystallites in both cocoons and fibers reared indoors and outdoors. Cocoon shells underwent additional peaks of decomposition with increased temperature. The total weight loss was higher for cocoon shells and degummed fibers from indoors. Rearing conditions (temperature and relative humidity), feeding method used, changes in total life span, days to molting, and spinning might have influenced the variation in the properties observed.The ecological and commercial significances of indoor rearing of G. posticaare discussed. This is an open access paper. We use the Creative Commons Attribution 3.0 license that permits unrestricted use, provided that the paper is properly attributed.

Formation, characterization, and dynamics of onion-like carbon structures for electrical energy storage from nanodiamonds using reactive force fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ganesh, P.; Kent, P. R. C.; Mochalin, V.

We simulate the experimentally observed graphitization of nanodiamonds into multi-shell onion-like carbonnanostructures, also called carbon onions, at different temperatures, using reactive force fields. The simulations include long-range Coulomb and van der Waals interactions. Our results suggest that long-range interactions play a crucial role in the phase-stability and the graphitization process. Graphitization is both enthalpically and entropically driven and can hence be controlled with temperature. The outer layers of the nanodiamond have a lower kinetic barrier toward graphitization irrespective of the size of the nanodiamond and graphitize within a few-hundred picoseconds, with a large volume increase. The inner core of themore » nanodiamonds displays a large size-dependent kinetic barrier, and graphitizes much more slowly with abrupt jumps in the internal energy. It eventually graphitizes by releasing pressure and expands once the outer shells have graphitized. The degree of transformation at a particular temperature is thereby determined by a delicate balance between the thermal energy, long-range interactions, and the entropic/enthalpic free energy gained by graphitization. Upon full graphitization, a multi-shell carbonnanostructure appears, with a shell-shell spacing of about ~3.4 Å for all sizes. The shells are highly defective with predominantly five- and seven-membered rings to curve space. Larger nanodiamonds with a diameter of 4 nm can graphitize into spiral structures with a large (~29-atom carbon ring) pore opening on the outermost shell. Such a large one-way channel is most attractive for a controlled insertion of molecules/ions such as Li ions, water, or ionic liquids, for increased electrochemical capacitor or battery electrode applications.« less

Formation, characterization and dynamics of onion like carbon structures from nanodiamonds using reactive force-fields for electrical energy storage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kent, Paul R

We simulate the experimentally observed graphitization of nanodiamonds into multi-shell onion-like carbon nanostructures, also called carbon onions, at different temperatures, using reactive force fields. The simulations include long-range Coulomb and van der Waals interactions. Our results suggest that long-range interactions play a crucial role in the phase-stability and the graphitization process. Graphitization is both enthalpically and entropically driven and can hence be controlled with temperature. The outer layers of the nanodiamond have a lower kinetic barrier toward graphitization irrespective of the size of the nanodiamond and graphitize within a few-hundred picoseconds, with a large volume increase. The inner core ofmore » the nanodiamonds displays a large size-dependent kinetic barrier, and graphitizes much more slowly with abrupt jumps in the internal energy. It eventually graphitizes by releasing pressure and expands once the outer shells have graphitized. The degree of transformation at a particular temperature is thereby determined by a delicate balance between the thermal energy, long-range interactions, and the entropic/enthalpic free energy gained by graphitization. Upon full graphitization, a multi-shell carbon nanostructure appears, with a shell-shell spacing of about {approx}3.4 {angstrom} for all sizes. The shells are highly defective with predominantly five- and seven-membered rings to curve space. Larger nanodiamonds with a diameter of 4 nm can graphitize into spiral structures with a large ({approx}29-atom carbon ring) pore opening on the outermost shell. Such a large one-way channel is most attractive for a controlled insertion of molecules/ions such as Li ions, water, or ionic liquids, for increased electrochemical capacitor or battery electrode applications.« less

Olive-oil nanocapsules stabilized by HSA: influence of processing variables on particle properties

NASA Astrophysics Data System (ADS)

Molina-Bolívar, J. A.; Galisteo-González, F.

2015-10-01

Liquid lipid nanocapsules (LLN) are considered to be promising drug carriers in the medical field. The size and the surface charge of these nanocarriers are of major importance, affecting their bioavailability and the in vivo behaviour after intravenous injection. This research provides a comprehensive study on the preparation of olive-oil nanocapsules stabilized with a human serum albumin shell (HSA). LLN were prepared by modified solvent-displacement method. Numerous experimental variables were examined in order to characterize their impact on LLN size, distribution, and electrophoretic mobility. Physicochemical parameters of LLN were controlled by adjusting the nanodroplet stabilizing shell of adsorbed protein molecules, which was affected by the oil:HSA ratio, pH, and ionic strength of aqueous medium. The stronger the repulsion between adsorbed HSA molecules, the smaller and more monodisperse the particles proved. Other process parameters, including the ethanol:acetone ratio, organic:aqueous phase ratio, speed of organic-phase injection, and stirring rate were examined to achieve optimum preparation conditions. LLN produced by our standardized formulation were in the range of 170-175 nm with low polydispersity index (<0.1). Long-term colloidal stability of samples was evaluated after 6 months of storage. Efficient incorporation of curcumin, a model for a water-insoluble drug, into olive-oil nanocapsules was achieved (90 %). Encapsulation of curcumin into LLN had a stabilizing effect with respect to drug photodecomposition compared to that of the free molecule in solution.

Enhancing the humidity sensitivity of Ga2O3 /SnO2 core/shell microribbon by applying mechanical strain and its application as a flexible strain sensor.

PubMed

Liu, Kewei; Sakurai, Makoto; Aono, Masakazu

2012-12-07

The humidity sensitivity of a single β-Ga(2) O(3) /amorphous SnO(2) core/shell microribbon on a flexible substrate is enhanced by the application of tensile strain and increases linearly with the strain. The strain-induced enhancement originates from the increase in the effective surface area where water molecules are adsorbed. This strain dependence of humidity sensitivity can be used to monitor the external strain. The strain sensing of the microribbon device under various amounts of mechanical loading shows excellent reliability and reproducibility with a gauge factor of -41. The flexible device has high potential to detect both humidity and strain at room temperature. These findings and the mechanism involved are expected to pave the way for new flexible strain and multifunctional sensors. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Biedermannová, Lada, E-mail: lada.biedermannova@ibt.cas.cz; Schneider, Bohdan

2015-10-27

The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. Themore » results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.« less

Vibrational Sum Frequency Generation Spectroscopy Study of Hydrous Species in Soda Lime Silica Float Glass.

PubMed

Luo, Jiawei; Banerjee, Joy; Pantano, Carlo G; Kim, Seong H

2016-06-21

It is generally accepted that the mechanical properties of soda lime silica (SLS) glass can be affected by the interaction between sodium ions and hydrous species (silanol groups and water molecules) in its surface region. While the amount of these hydrous species can be estimated from hydrogen profiles and infrared spectroscopy, their chemical environment in the glass network is still not well understood. This work employed vibrational sum frequency generation (SFG) spectroscopy to investigate the chemical environment of hydrous species in the surface region of SLS float glass. SLS float glass shows sharp peaks in the OH stretching vibration region in SFG spectra, while the OH stretch peaks of glasses that do not have leachable sodium ions and the OH peaks of water molecules in condensed phases are normally broad due to fast hydrogen bonding dynamics. The hydrous species responsible for the sharp SFG peaks for the SLS float glass were found to be thermodynamically more stable than physisorbed water molecules, did not exchange with D2O, and were associated with the sodium concentration gradient in the dealkalized subsurface region. These results suggested that the hydrous species reside in static solvation shells defined by the silicate network with relatively slow hydrogen bonding dynamics, compared to physisorbed water layers on top of the glass surface. A putative radial distribution of the hydrous species within the SLS glass network was estimated based on the OH SFG spectral features, which could be compared with theoretical distributions calculated from computational simulations.

Dynamical properties of the hydration shell of fully deuterated myoglobin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Achterhold, Klaus; Parak, Fritz G.; Ostermann, Andreas

2011-10-15

Freeze-dried perdeuterated sperm whale myoglobin was kept in a water-saturated atmosphere in order to obtain a hydration degree of 335 {sup 1}H{sub 2}O molecules per one myoglobin molecule. Incoherent neutron scattering was performed at the neutron spectrometer TOFTOF at the FRM II in an angular range of q from 0.6 to 1.8 A{sup -1} and a temperature range from 4 to 297 K. We used neutrons with a wavelength of {lambda}{alpha}E 6 A and an energy resolution of about 65 {mu}eV corresponding to motions faster than 10 ps. At temperatures above 225 K, broad lines appear in the spectra causedmore » by quasielastic scattering. For an explanation of these lines, we assumed that there are only two types of protons, those that are part of the hydration water (72%) and those that belong to the protein (28%). The protons of the hydration water were analyzed with the diffusion model of Singwi and Sjoelander [Phys. Rev. 119, 863 (1960)]. In this model, a water molecule stays for a time {tau}{sub 0} in a bound state performing oscillatory motions. Thereafter, the molecule performs free diffusion for the time {tau}{sub 1} in a nonbound state followed again by the oscillatory motions for {tau}{sub 0} and so forth. We used the general formulation with no simplifications as {tau}{sub 0}>>{tau}{sub 1} or {tau}{sub 1}>>{tau}{sub 0}. At room temperature, we obtained {tau}{sub 0} {alpha}E 104 ps and {tau}{sub 1} {alpha}E 37 ps. For the protein bound hydrogen, the dynamics is described by a Brownian oscillator where the protons perform overdamped motions in limited space.« less

Multi-Shell Hollow Nanogels with Responsive Shell Permeability

PubMed Central

Schmid, Andreas J.; Dubbert, Janine; Rudov, Andrey A.; Pedersen, Jan Skov; Lindner, Peter; Karg, Matthias; Potemkin, Igor I.; Richtering, Walter

2016-01-01

We report on hollow shell-shell nanogels with two polymer shells that have different volume phase transition temperatures. By means of small angle neutron scattering (SANS) employing contrast variation and molecular dynamics (MD) simulations we show that hollow shell-shell nanocontainers are ideal systems for controlled drug delivery: The temperature responsive swelling of the inner shell controls the uptake and release, while the thermoresponsive swelling of the outer shell controls the size of the void and the colloidal stability. At temperatures between 32 °C < T < 42 °C, the hollow nanocontainers provide a significant void, which is even larger than the initial core size of the template, and they possess a high colloidal stability due to the steric stabilization of the swollen outer shell. Computer simulations showed, that temperature induced switching of the permeability of the inner shell allows for the encapsulation in and release of molecules from the cavity. PMID:26984478

Encapsulation of small ionic molecules within alpha-cyclodextrins.

PubMed

Rodriguez, Javier; Elola, M Dolores

2009-02-05

Results from molecular dynamics experiments pertaining to the encapsulation of ClO4- within the hydrophobic cavity of an aqueous alpha-cyclodextrin (alpha-CD) are presented. Using a biased sampling procedure, we constructed the Gibbs free energy profile associated with the complexation process. The profile presents a global minimum at the vicinity of the primary hydroxyl groups, where the ion remains tightly coordinated to four water molecules via hydrogen bonds. Our estimate for the global free energy of encapsulation yields DeltaGenc approximately -2.5 kBT. The decomposition of the average forces acting on the trapped ion reveals that the encapsulation is controlled by Coulomb interactions between the ion and OH groups in the CD, with a much smaller contribution from the solvent molecules. Changes in the previous results, arising from the partial methylation of the host CD and modifications in the charge distribution of the guest molecule are also discussed. The global picture that emerges from our results suggests that the stability of the ClO4- encapsulation involves not only the individual ion but also its first solvation shell.

Self-assembly of core-polyethylene glycol-lipid shell (CPLS) nanoparticles and their potential as drug delivery vehicles.

PubMed

Shen, Zhiqiang; Loe, David T; Awino, Joseph K; Kröger, Martin; Rouge, Jessica L; Li, Ying

2016-08-21

Herein a new multifunctional formulation, referred to as a core-polyethylene glycol-lipid shell (CPLS) nanoparticle, has been proposed and studied in silico via large scale coarse-grained molecular dynamics simulations. A PEGylated core with surface tethered polyethylene glycol (PEG) chains is used as the starting configuration, where the free ends of the PEG chains are covalently bonded with lipid molecules (lipid heads). A complete lipid bilayer is formed at the surface of the PEGylated particle core upon addition of free lipids, driven by the hydrophobic properties of the lipid tails, leading to the formation of a CPLS nanoparticle. The self-assembly process is found to be sensitive to the grafting density and molecular weight of the tethered PEG chains, as well as the amount of free lipids added. At low grafting densities the assembly of CPLS nanoparticles cannot be accomplished. As demonstrated by simulations, a lipid bud/vesicle can be formed on the surface when an excess amount of free lipids is added at high grafting density. Therefore, the CPLS nanoparticles can only be formed under appropriate conditions of both PEG and free lipids. The CPLS nanoparticle has been recognized to be able to store a large quantity of water molecules, particularly with high molecular weight of PEG chains, indicating its capacity for carrying hydrophilic molecules such as therapeutic biomolecules or imaging agents. Under identical size and surface chemistry conditions of a liposome, it has been observed that the CPLS particle can be more efficiently wrapped by the lipid membrane, indicating its potential for a greater efficiency in delivering its hydrophilic cargo. As a proof-of-concept, the experimental realization of CPLS nanoparticles is explicitly demonstrated in this study. To test the capacity of the CPLS to store small molecule cargo a hydrophilic dye was successfully encapsulated in the particles' water soluble layer. The results of this study show the power and potential of simulation-driven approaches for guiding the design of more efficient nanomaterial delivery platforms.

Dendritic core-shell nickel-iron-copper metal/metal oxide electrode for efficient electrocatalytic water oxidation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Peili; Li, Lin; Nordlund, Dennis

Electrochemical water splitting requires efficient water oxidation catalysts to accelerate the sluggish kinetics of water oxidation reaction. Here in this paper, we report a promisingly dendritic core-shell nickel-iron-copper metal/metal oxide electrode, prepared via dealloying with an electrodeposited nickel-iron-copper alloy as a precursor, as the catalyst for water oxidation. The as-prepared core-shell nickel-iron-copper electrode is characterized with porous oxide shells and metallic cores. This tri-metal-based core-shell nickel-iron-copper electrode exhibits a remarkable activity toward water oxidation in alkaline medium with an overpotential of only 180 mV at a current density of 10 mA cm -2. The core-shell NiFeCu electrode exhibits pH-dependent oxygenmore » evolution reaction activity on the reversible hydrogen electrode scale, suggesting that non-concerted proton-electron transfers participate in catalyzing the oxygen evolution reaction. To the best of our knowledge, the as-fabricated core-shell nickel-iron-copper is one of the most promising oxygen evolution catalysts.« less

Dendritic core-shell nickel-iron-copper metal/metal oxide electrode for efficient electrocatalytic water oxidation

DOE PAGES

Zhang, Peili; Li, Lin; Nordlund, Dennis; ...

2018-01-26

Electrochemical water splitting requires efficient water oxidation catalysts to accelerate the sluggish kinetics of water oxidation reaction. Here in this paper, we report a promisingly dendritic core-shell nickel-iron-copper metal/metal oxide electrode, prepared via dealloying with an electrodeposited nickel-iron-copper alloy as a precursor, as the catalyst for water oxidation. The as-prepared core-shell nickel-iron-copper electrode is characterized with porous oxide shells and metallic cores. This tri-metal-based core-shell nickel-iron-copper electrode exhibits a remarkable activity toward water oxidation in alkaline medium with an overpotential of only 180 mV at a current density of 10 mA cm -2. The core-shell NiFeCu electrode exhibits pH-dependent oxygenmore » evolution reaction activity on the reversible hydrogen electrode scale, suggesting that non-concerted proton-electron transfers participate in catalyzing the oxygen evolution reaction. To the best of our knowledge, the as-fabricated core-shell nickel-iron-copper is one of the most promising oxygen evolution catalysts.« less

Effect of sub- and supercritical water treatments on the physicochemical properties of crab shell chitin and its enzymatic degradation.

PubMed

Osada, Mitsumasa; Miura, Chika; Nakagawa, Yuko S; Kaihara, Mikio; Nikaido, Mitsuru; Totani, Kazuhide

2015-12-10

This study examined the effects of sub- and supercritical water pretreatments on the physicochemical properties of crab shell α-chitin and its enzymatic degradation to obtain N,N'-diacetylchitobiose (GlcNAc)2. Following sub- and supercritical water pretreatments, the protein in the crab shell was removed and the residue of crab shell contained α-chitin and CaCO3. Prolonged pretreatment led to α-chitin decomposition. The reaction of pure α-chitin in sub- and supercritical water pretreatments was investigated separately; we observed lower mean molecular weight and weaker hydrogen bonds compared with untreated α-chitin. (GlcNAc)2 yields from enzymatic degradation of subcritical (350 °C, 7 min) and supercritical water (400 °C, 2.5 min) pretreated crab shell were 8% and 6%, compared with 0% without any pretreatment. This study shows that sub- and supercritical water pretreatments of crab shell provide to an alternative method to the use of acid and base for decalcification and deproteinization of crab shell required for (GlcNAc)2 production. Copyright © 2015 Elsevier Ltd. All rights reserved.

Study on collision resistance characteristics of the side tanks with water inside

NASA Astrophysics Data System (ADS)

Liu, Yuxi; Hu, Jinwen; Liu, Ting; Wu, Can

2018-05-01

When we evaluate the safety performance of ships against external events, one of the most important indicator is the collision resistance to which water inside the side tanks also make some contributions because of the water effect. To further analyze the interaction mechanism, different collision velocities and side tank waterlines are set for the analysis model. Results indicate the outside shell and the inner shell of the side structure significantly enhanced the collision resistance performance to a certain extension. The water effect on the failure of the outside shell is unobvious, while, it performs a great influence on the destructive reaction force of the inner shell. When the velocity of the coming bulbous bow gradually increases, the destructive reaction forces of the outside shell and the inner shell increase with a decreasing rate. Besides, water influence the collision characteristics of the inner shell a lot when the waterlines are below the upper rib of the strong frame.

Facile synthesis of terminal-alkyne bioorthogonal molecules for live -cell surface-enhanced Raman scattering imaging through Au-core and silver/dopamine-shell nanotags.

PubMed

Chen, Meng; Zhang, Ling; Yang, Bo; Gao, Mingxia; Zhang, Xiangmin

2018-03-01

Alkyne is unique, specific and biocompatible in the Raman-silent region of the cell, but there still remains a challenge to achieve ultrasensitive detection in living systems due to its weak Raman scattering. Herein, a terminal alkyne ((E)-2-[4-(ethynylbenzylidene)amino]ethane-1-thiol (EBAE)) with surface-enhanced Raman scattering is synthesized. The EBAE molecule possesses S- and C-termini, which can be directly bonded to gold nanoparticles and dopamine/silver by forming the Au-S chemical bond and the carbon-metal bond, respectively. The distance between Raman reporter and AuNPs/AgNPs can be reduced, contributing to forming hot-spot-based SERS substrate. The alkyne functionalized nanoparticles are based on Au core and encapsulating polydopamine shell, defined as Au-core and dopamine/Ag-shell (ACDS). The bimetallic ACDS induce strong SERS signals for molecular imaging that arise from the strong electromagnetic field. Furthermore, the EBAE provides a distinct peak in the cellular Raman-silent region with nearly zero background interference. The EBAE Raman signals could be tremendously enhanced when the Raman reporter is located at the middle of the Au-core and dopamine/Ag-shell. Therefore, this work could have huge potential benefits for the highly sensitive detection of intercellular information delivery by connecting the recognition molecules in biomedical diagnostics. Graphical abstract Terminal-alkyne-functionalized Au-core and silver/dopamine-shell nanotags for live-cell surface-enhanced Raman scattering imaging.

Computational modeling of the effective Young's modulus values of fullerene molecules: a combined molecular dynamics simulation and continuum shell model.

PubMed

Ghavanloo, Esmaeal; Izadi, Razie; Nayebi, Ali

2018-02-28

Estimating the Young's modulus of a structure in the nanometer size range is a difficult task. The reliable determination of this parameter is, however, important in both basic and applied research. In this study, by combining molecular dynamics (MD) simulations and continuum shell theory, we designed a new approach to determining the Young's modulus values of different spherical fullerenes. The results indicate that the Young's modulus values of fullerene molecules decrease nonlinearly with increasing molecule size and understandably tend to the Young's modulus of an ideal flat graphene sheet at large molecular radii. To the best of our knowledge, this is first time that a combined atomistic-continuum method which can predict the Young's modulus values of fullerene molecules with high precision has been reported.

Solute rotational dynamics at the water liquid/vapor interface.

PubMed

Benjamin, Ilan

2007-11-28

The rotational dynamics of a number of diatomic molecules adsorbed at different locations at the interface between water and its own vapors are studied using classical molecular dynamics computer simulations. Both equilibrium orientational and energy correlations and nonequilibrium orientational and energy relaxation correlations are calculated. By varying the dipole moment of the molecule and its location, and by comparing the results with those in bulk water, the effects of dielectric and mechanical frictions on reorientation dynamics and on rotational energy relaxation can be studied. It is shown that for nonpolar and weekly polar solutes, the equilibrium orientational relaxation is much slower in the bulk than at the interface. As the solute becomes more polar, the rotation slows down and the surface and bulk dynamics become similar. The energy relaxation (both equilibrium and nonequilibrium) has the opposite trend with the solute dipole (larger dipoles relax faster), but here again the bulk and surface results converge as the solute dipole is increased. It is shown that these behaviors correlate with the peak value of the solvent-solute radial distribution function, which demonstrates the importance of the first hydration shell structure in determining the rotational dynamics and dependence of these dynamics on the solute dipole and location.

Ultrafast dynamics of liquid water: Energy relaxation and transfer processes of the OH stretch and the HOH bend

DOE Office of Scientific and Technical Information (OSTI.GOV)

Imoto, Sho; Xantheas, Sotiris S.; Saito, Shinji

2015-08-27

The vibrational energy relaxation and transfer processes of the OH stretching and the HOH bending vibrations in liquid water are investigated via the theoretical calculation of the pump-probe spectra obtained from non-equilibrium molecular dynamics simulations with the TTM3-F interaction potential. The excitation of the OH stretch induces an instantaneous response of the high frequency librational motions in the 600-1000 cm-1 range. In addition, the excess energy of the OH stretch of a water molecule quickly transfers to the OH stretches of molecules in its first hydration shell with a time constant of ~50 fs, followed by relaxation to the HOHmore » bends of the surrounding molecules with a time constant of 230 fs. The excitation of the HOH bend also results in the ultrafast excitation of the high frequency librational motions. The energy of the excited HOH bend of a water molecule decays, with a time constant of 200 fs, mainly to the relaxation of the HOH bends of its surrounding molecules. The energies of the HOH bends were found to transfer quickly to the intermolecular motions via the coupling with the high frequency librational motions. The excess energy of the OH stretch or the HOH bend relaxes to the high frequency intermolecular librational motions and eventually to the hot ground state with a time scale of ~1 ps via the coupling with the librational and translational motions. The energy relaxation and transfer processes were found to depend on the local hydrogen bonding network; the relaxations of the excess energy of the OH stretch and the HOH bend of four- and five-coordinated molecules are faster than those of a three-coordinated molecule due to the delocalization of the vibrational motions of the former (four- and five-coordinated molecules) compared to those of the later (three-coordinated molecules). The present results highlight the importance of the high frequency intermolecular librational modes in facilitating the ultrafast energy relaxation process in liquid water via their strong nonlinear couplings with the intramolecular OH stretching and HOH bending vibrations. S.S.X. acknowledges the support of the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. The calculation was carried out using the computing resources at the Research Center for Computational Science in Okazaki, Japan.« less

Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

NASA Astrophysics Data System (ADS)

Zhang, Junfang; Rivero, Mayela; Choi, S. K.

2007-02-01

We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 Å. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.

Water repellency in hydrophobic nanocapsules--molecular view on dewetting.

PubMed

Müller, Achim; Garai, Somenath; Schäffer, Christian; Merca, Alice; Bögge, Hartmut; Al-Karawi, Ahmed Jasim M; Prasad, Thazhe Kootteri

2014-05-26

The hydrophobic effect plays a major role in a variety of important phenomena in chemistry, materials science and biology, for instance in protein folding and protein-ligand interactions. Studies--performed within cavities of the unique metal oxide based porous capsules of the type {(pentagon)12(linker)30}≡{(W)W5}12{Mo2(ligand)}30 with different acetate/water ligand ratios--have provided unprecedented results revealing segregation/repellency of the encapsulated "water" from the internal hydrophobic ligand walls of the capsules, while the disordered water molecules, interacting strongly with each other via hydrogen bonding, form in all investigated cases the same type of spherical shell. The present results can be (formally) compared--but only regarding the repellency effect--with the amazing "action" of the (super)hydrophobic Lotus (Nelumbo) leaves, which are self-cleaning based on water repellency resulting in the formation of water droplets picking up dirt. The present results were obtained by constructing deliberately suitable hydrophobic interiors within the mentioned capsules. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Utilization of wasted cockle shell as a natural coagulant and a neutralizer of polluted water in Bangka Belitung islands, Indonesia

NASA Astrophysics Data System (ADS)

Tiandho, Y.; Aldila, H.; Mustari; Megiyo; Afriani, F.

2018-05-01

Bangka Belitung Islands is the largest tin producer in Indonesia. The high activity of tin mining caused the environmental damage which had an impact on the emergence of clean water crisis in some areas in this province. In this paper, a simple water quality improvement method based on wasted cockle shell was developed. Based on x-ray diffraction analysis it is known that calcination of cockle shell powder at 700°C will decompose the powder into calcium oxide compound. The addition of calcined cockle shell powder into acidic water from Merawang Sub-district will increase the pH of water through the process of forming hydroxide groups in the water. The calcined cockle shell powder can also coagulate pollutants in some polluted water from Koba Sub-district. The coagulation results were analyzed using SEM/EDS.

Self-assembly of core-polyethylene glycol-lipid shell (CPLS) nanoparticles and their potential as drug delivery vehicles

NASA Astrophysics Data System (ADS)

Shen, Zhiqiang; Loe, David T.; Awino, Joseph K.; Kröger, Martin; Rouge, Jessica L.; Li, Ying

2016-08-01

Herein a new multifunctional formulation, referred to as a core-polyethylene glycol-lipid shell (CPLS) nanoparticle, has been proposed and studied in silico via large scale coarse-grained molecular dynamics simulations. A PEGylated core with surface tethered polyethylene glycol (PEG) chains is used as the starting configuration, where the free ends of the PEG chains are covalently bonded with lipid molecules (lipid heads). A complete lipid bilayer is formed at the surface of the PEGylated particle core upon addition of free lipids, driven by the hydrophobic properties of the lipid tails, leading to the formation of a CPLS nanoparticle. The self-assembly process is found to be sensitive to the grafting density and molecular weight of the tethered PEG chains, as well as the amount of free lipids added. At low grafting densities the assembly of CPLS nanoparticles cannot be accomplished. As demonstrated by simulations, a lipid bud/vesicle can be formed on the surface when an excess amount of free lipids is added at high grafting density. Therefore, the CPLS nanoparticles can only be formed under appropriate conditions of both PEG and free lipids. The CPLS nanoparticle has been recognized to be able to store a large quantity of water molecules, particularly with high molecular weight of PEG chains, indicating its capacity for carrying hydrophilic molecules such as therapeutic biomolecules or imaging agents. Under identical size and surface chemistry conditions of a liposome, it has been observed that the CPLS particle can be more efficiently wrapped by the lipid membrane, indicating its potential for a greater efficiency in delivering its hydrophilic cargo. As a proof-of-concept, the experimental realization of CPLS nanoparticles is explicitly demonstrated in this study. To test the capacity of the CPLS to store small molecule cargo a hydrophilic dye was successfully encapsulated in the particles' water soluble layer. The results of this study show the power and potential of simulation-driven approaches for guiding the design of more efficient nanomaterial delivery platforms.Herein a new multifunctional formulation, referred to as a core-polyethylene glycol-lipid shell (CPLS) nanoparticle, has been proposed and studied in silico via large scale coarse-grained molecular dynamics simulations. A PEGylated core with surface tethered polyethylene glycol (PEG) chains is used as the starting configuration, where the free ends of the PEG chains are covalently bonded with lipid molecules (lipid heads). A complete lipid bilayer is formed at the surface of the PEGylated particle core upon addition of free lipids, driven by the hydrophobic properties of the lipid tails, leading to the formation of a CPLS nanoparticle. The self-assembly process is found to be sensitive to the grafting density and molecular weight of the tethered PEG chains, as well as the amount of free lipids added. At low grafting densities the assembly of CPLS nanoparticles cannot be accomplished. As demonstrated by simulations, a lipid bud/vesicle can be formed on the surface when an excess amount of free lipids is added at high grafting density. Therefore, the CPLS nanoparticles can only be formed under appropriate conditions of both PEG and free lipids. The CPLS nanoparticle has been recognized to be able to store a large quantity of water molecules, particularly with high molecular weight of PEG chains, indicating its capacity for carrying hydrophilic molecules such as therapeutic biomolecules or imaging agents. Under identical size and surface chemistry conditions of a liposome, it has been observed that the CPLS particle can be more efficiently wrapped by the lipid membrane, indicating its potential for a greater efficiency in delivering its hydrophilic cargo. As a proof-of-concept, the experimental realization of CPLS nanoparticles is explicitly demonstrated in this study. To test the capacity of the CPLS to store small molecule cargo a hydrophilic dye was successfully encapsulated in the particles' water soluble layer. The results of this study show the power and potential of simulation-driven approaches for guiding the design of more efficient nanomaterial delivery platforms. Electronic supplementary information (ESI) available: Simulation protocol, simulation results for the self-assembly of CPLS nanoparticles, membrane wrapping and free energy change of grafted PEG polymers. See DOI: 10.1039/C6NR04134E

Electrophoretic manipulation of multiple-emulsion droplets

NASA Astrophysics Data System (ADS)

Schoeler, Andreas M.; Josephides, Dimitris N.; Chaurasia, Ankur S.; Sajjadi, Shahriar; Mesquida, Patrick

2014-02-01

Electrophoretic manipulation of multiple-emulsion oil-in-water-in-oil (O/W)/O and water-in-oil-in-water-in-oil (W/O/W)/O core-shell droplets is shown. It was found that the electrophoretic mobility of the droplets is determined solely by the outer water shell, regardless of size or composition of the inner droplets. It was observed that the surface charge of the outer water shell can be changed and the polarity can be reversed through contact with a biased electrode in a similar way as with simple W/O droplets. Furthermore, addition of the anionic surfactant, sodium dodecyl sulfate to the outer water shell reverses the initial polarity and hence, electrophoretic mobility of the core-shell droplets before contact with an electrode. The results have practical implications for the manipulation of oil droplets in a continuous oil phase.

Lifetime of inner-shell hole states of Ar (2p) and Kr (3d) using equation-of-motion coupled cluster method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghosh, Aryya; Vaval, Nayana, E-mail: np.vaval@ncl.res.in; Pal, Sourav

2015-07-14

Auger decay is an efficient ultrafast relaxation process of core-shell or inner-shell excited atom or molecule. Generally, it occurs in femto-second or even atto-second time domain. Direct measurement of lifetimes of Auger process of single ionized and double ionized inner-shell state of an atom or molecule is an extremely difficult task. In this paper, we have applied the highly correlated complex absorbing potential-equation-of-motion coupled cluster (CAP-EOMCC) approach which is a combination of CAP and EOMCC approach to calculate the lifetime of the states arising from 2p inner-shell ionization of an Ar atom and 3d inner-shell ionization of Kr atom. Wemore » have also calculated the lifetime of Ar{sup 2+}(2p{sup −1}3p{sup −1}) {sup 1}D, Ar{sup 2+}(2p{sup −1}3p{sup −1}) {sup 1}S, and Ar{sup 2+}(2p{sup −1}3s{sup −1}) {sup 1}P double ionized states. The predicted results are compared with the other theoretical results as well as experimental results available in the literature.« less

High ink absorption performance of inkjet printing based on SiO2@Al13 core-shell composites

NASA Astrophysics Data System (ADS)

Chen, YiFan; Jiang, Bo; Liu, Li; Du, Yunzhe; Zhang, Tong; Zhao, LiWei; Huang, YuDong

2018-04-01

The increasing growth of the inkjet market makes the inkjet printing more necessary. A composite material based on core-shell structure has been developed and applied to prepare inkjet printing layer. In this contribution, the ink printing record layers based on SiO2@Al13 core-shell composite was elaborated. The prepared core-shell composite materials were characterized by X-ray photoelectron spectroscopy (XPS), zeta potential, X-ray diffraction (XRD), scanning electron microscopy (SEM). The results proved the presence of electrostatic adsorption between SiO2 molecules and Al13 molecules with the formation of the well-dispersed system. In addition, based on the adsorption and the liquid permeability analysis, SiO2@Al13 ink printing record layer achieved a relatively high ink uptake (2.5 gmm-1) and permeability (87%), respectively. The smoothness and glossiness of SiO2@Al13 record layers were higher than SiO2 record layers. The core-shell structure facilitated the dispersion of the silica, thereby improved its ink absorption performance and made the clear printed image. Thus, the proposed procedure based on SiO2@Al13 core-shell structure of dye particles could be applied as a promising strategy for inkjet printing.

Glass polymorphism in glycerol-water mixtures: I. A computer simulation study.

PubMed

Jahn, David A; Wong, Jessina; Bachler, Johannes; Loerting, Thomas; Giovambattista, Nicolas

2016-04-28

We perform out-of-equilibrium molecular dynamics (MD) simulations of water-glycerol mixtures in the glass state. Specifically, we study the transformations between low-density (LDA) and high-density amorphous (HDA) forms of these mixtures induced by compression/decompression at constant temperature. Our MD simulations reproduce qualitatively the density changes observed in experiments. Specifically, the LDA-HDA transformation becomes (i) smoother and (ii) the hysteresis in a compression/decompression cycle decreases as T and/or glycerol content increase. This is surprising given the fast compression/decompression rates (relative to experiments) accessible in MD simulations. We study mixtures with glycerol molar concentration χ(g) = 0-13% and find that, for the present mixture models and rates, the LDA-HDA transformation is detectable up to χ(g) ≈ 5%. As the concentration increases, the density of the starting glass (i.e., LDA at approximately χ(g) ≤ 5%) rapidly increases while, instead, the density of HDA remains practically constant. Accordingly, the LDA state and hence glass polymorphism become inaccessible for glassy mixtures with approximately χ(g) > 5%. We present an analysis of the molecular-level changes underlying the LDA-HDA transformation. As observed in pure glassy water, during the LDA-to-HDA transformation, water molecules within the mixture approach each other, moving from the second to the first hydration shell and filling the first interstitial shell of water molecules. Interestingly, similar changes also occur around glycerol OH groups. It follows that glycerol OH groups contribute to the density increase during the LDA-HDA transformation. An analysis of the hydrogen bond (HB)-network of the mixtures shows that the LDA-HDA transformation is accompanied by minor changes in the number of HBs of water and glycerol. Instead, large changes in glycerol and water coordination numbers occur. We also perform a detailed analysis of the effects that the glycerol force field (FF) has on our results. By comparing MD simulations using two different glycerol models, we find that glycerol conformations indeed depend on the FF employed. Yet, the thermodynamic and microscopic mechanisms accompanying the LDA-HDA transformation and hence, our main results, do not. This work is accompanied by an experimental report where we study the glass polymorphism in glycerol-water mixtures prepared by isobaric cooling at 1 bar.

Well-defined magnetic surface imprinted nanoparticles for selective enrichment of 2,4-dichlorophenoxyacetic acid in real samples.

PubMed

Sheng, Le; Jin, Yulong; He, Yonghuan; Huang, Yanyan; Yan, Liushui; Zhao, Rui

2017-11-01

Superparamagnetic core-shell molecularly imprinted polymer nanoparticles (MIPs) were prepared via surface initiated reversible-addition fragmentation chain transfer (si-RAFT) polymerization for the selective recognition of 2,4-dichlorophenoxyacetic acid (2,4-D) in real samples. The construction of uniform core-shell structure with a 50nm MIP layer was successfully accomplished, which favored mass transfer and resulted in fast recognition kinetics. The static equilibrium experiments revealed the satisfied adsorption capacity and imprinting efficiency of Fe 3 O 4 @MIP. Moreover, the Fe 3 O 4 @MIP exhibited high selectivity and affinity towards 2,4-D over structural analogues. The prepared Fe 3 O 4 @MIP nanoparticles were used for the selective enrichment of 2,4-D in tap water and Chinese cabbage samples. Combined with RP-HPLC, the recoveries of 2,4-D were calculated from 93.1% to 103.3% with RSD of 1.7-5.4% (n = 3) in Chinese cabbage samples. This work provides a versatile approach for fabricating well-constructed core-shell MIP nanoparticles for rapid enrichment and highly selective separation of target molecules in real samples. Copyright © 2017 Elsevier B.V. All rights reserved.

General route for the assembly of functional inorganic capsules.

PubMed

Akartuna, Ilke; Tervoort, Elena; Studart, André R; Gauckler, Ludwig J

2009-11-03

Semipermeable, hollow capsules are attractive materials for the encapsulation and delivery of active agents in food processing, pharmaceutical and agricultural industries, and biomedicine. These capsules can be produced by forming a solid shell of close packed colloidal particles, typically polymeric particles, at the surface of emulsion droplets. However, current methods to prepare such capsules may involve multistep chemical procedures to tailor the surface chemistry of particles or are limited to particles that exhibit inherently the right hydrophobic-hydrophilic balance to adsorb around emulsion droplets. In this work, we describe a general and simple method to fabricate semipermeable, inorganic capsules from emulsion droplets stabilized by a wide variety of colloidal metal oxide particles. The assembly of particles at the oil-water interface is induced by the in situ hydrophobization of the particle surface through the adsorption of short amphiphilic molecules. The adsorption of particles at the interface leads to stable capsules comprising a single layer of particles in the outer shell. Such capsules can be used in the wet state or can be further processed into dry capsules. The permeability of the capsules can be modified by filling the interstices between the shell particles with polymeric or inorganic species. Functional capsules with biocompatible, bioresorbable, heat-resistant, chemical-resistant, and magnetic properties were prepared using alumina, silica, iron oxide, or tricalcium phosphate as particles in the shell.

Influences of external vs. core-shell mixing on aerosol optical properties at various relative humidities.

PubMed

Ramachandran, S; Srivastava, Rohit

2013-05-01

Aerosol optical properties of external and core-shell mixtures of aerosol species present in the atmosphere are calculated in this study for different relative humidities. Core-shell Mie calculations are performed using the values of radii, refractive indices and densities of aerosol species that act as core and shell, and the core-shell radius ratio. The single scattering albedo (SSA) is higher when the absorbing species (black carbon, BC) is the core, while for a sulfate core SSA does not vary significantly as the BC in the shell dominates the absorption. Absorption gets enhanced in core-shell mixing of absorbing and scattering aerosols when compared to their external mixture. Thus, SSA is significantly lower for a core-shell mixture than their external mixture. SSA is more sensitive to core-shell ratio than mode radius when BC is the core. The extinction coefficient, SSA and asymmetry parameter are higher for external mixing when compared to BC (core)-water soluble aerosol (shell), and water soluble aerosol (core)-BC (shell) mixtures in the relative humidity range of 0 to 90%. Spectral SSA exhibits the behaviour of the species which acts as a shell in core-shell mixing. The asymmetry parameter for an external mixture of water soluble aerosol and BC is higher than BC (core)-water soluble aerosol (shell) mixing and increases as function of relative humidity. The asymmetry parameter for the water soluble aerosol (core)-BC (shell) is independent of relative humidity as BC is hydrophobic. The asymmetry parameter of the core-shell mixture decreases when BC aerosols are involved in mixing, as the asymmetry parameter of BC is lower. Aerosol optical depth (AOD) of core-shell mixtures increases at a higher rate when the relative humidity exceeds 70% in continental clean and urban aerosol models, whereas AOD remains the same when the relative humidity exceeds 50% in maritime aerosol models. The SSA for continental aerosols varies for core-shell mixing of water soluble aerosol (core)-shell (BC) when compared to their external mixture, while the SSA for maritime aerosols does not vary significantly for different mixing scenarios because of the dominance of sea salt aerosols. Thus, these results confirm that aerosol mixing can modify the physical and optical characteristics of aerosols, which vary as a function of relative humidity. These calculations will be useful in parameterising the effect of core-shell vs. external mixing of aerosols in global climate models, and in the evaluation of aerosol radiative effects.

Evaluation of sanitizers for inactivating Salmonella on in-shell pecans and pecan nutmeats.

PubMed

Beuchat, Larry R; Mann, David A; Alali, Walid Q

2012-11-01

Chlorine, organic acids, and water extracts of inedible pecan components were tested for effectiveness in killing Salmonella on pecans. In-shell pecans and nutmeats (U.S. Department of Agriculture medium pieces) were immersion inoculated with a mixture of five Salmonella serotypes, dried to 3.7% moisture, and stored at 4°C for 3 to 6 weeks. In-shell nuts were immersed in chlorinated water (200, 400, and 1,000 μg/ml), lactic acid (0.5, 1, and 2%), and levulinic acid (0.5, 1, and 2%) with and without 0.05% sodium dodecyl sulfate (SDS), and a mixed peroxyacid sanitizer (Tsunami 200, 40 μg/ml) for up to 20 min at 21°C. The rate of reduction of free chlorine in conditioning water decreased as the ratio of in-shell nuts/water was increased. The rate of reduction was more rapid when nuts were not precleaned before treatment. The initial population of Salmonella on in-shell nuts (5.9 to 6.3 log CFU/g) was reduced by 2.8 log CFU/g after treating with chlorinated water (1,000 μg/ml). Treatment with 2% lactic acid plus SDS or 2% levulinic acid plus SDS reduced the pathogen by 3.7 and 3.4 log CFU/g, respectively. Lactic and levulinic acids (2%) without SDS were less effective (3.3- and 2.1-log CFU/g reductions, respectively) than acids with SDS. Treatment with Tsunami 200 resulted in a 2.4-log CFU/g reduction. In-shell nuts and nutmeats were immersed in water extracts of ground pecan shucks (hulls), shells, a mixture of shells and pith, and pith. The general order of lethality of extracts to Salmonella was shuck < shell-pith ≤ shell ≤ pith < chlorine (400 μg/ml) and shuck < shell ≤ pith = shell-pith < chlorine (400 μg/ml). Results emphasize the importance of removing soil and dust on in-shell pecans before conditioning in chlorinated water and the need for sanitizers with increased effectiveness in killing Salmonella on pecans.

Tenofovir Containing Thiolated Chitosan Core/Shell Nanofibers: In Vitro and in Vivo Evaluations.

PubMed

Meng, Jianing; Agrahari, Vivek; Ezoulin, Miezan J; Zhang, Chi; Purohit, Sudhaunshu S; Molteni, Agostino; Dim, Daniel; Oyler, Nathan A; Youan, Bi-Botti C

2016-12-05

It is hypothesized that thiolated chitosan (TCS) core/shell nanofibers (NFs) can enhance the drug loading of tenofovir, a model low molecular weight and highly water-soluble drug molecule, and improve its mucoadhesivity and in vivo safety. To test this hypothesis, poly(ethylene oxide) (PEO) core with TCS and polylactic acid (PLA) shell NFs are fabricated by a coaxial electrospinning technique. The morphology, drug loading, drug release profiles, cytotoxicity and mucoadhesion of the NFs are analyzed using scanning and transmission electron microscopies, liquid chromatography, cytotoxicity assays on VK2/E6E7 and End1/E6E7 cell lines and Lactobacilli crispatus, fluorescence imaging and periodic acid colorimetric method, respectively. In vivo safety studies are performed in C57BL/6 mice followed by H&E and immunohistochemical (CD45) staining analysis of genital tract. The mean diameters of PEO, PEO/TCS, and PEO/TCS-PLA NFs are 118.56, 9.95, and 99.53 nm, respectively. The NFs exhibit smooth surface. The drug loading (13%-25%, w/w) increased by 10-fold compared to a nanoparticle formulation due to the application of the electrospinning technique. The NFs are noncytotoxic at the concentration of 1 mg/mL. The PEO/TCS-PLA core/shell NFs mostly exhibit a release kinetic following Weibull model (r 2 = 0.9914), indicating the drug release from a matrix system. The core/shell NFs are 40-60-fold more bioadhesive than the pure PEO based NFs. The NFs are nontoxic and noninflammatory in vivo after daily treatment for up to 7 days. Owing to their enhanced drug loading and preliminary safety profile, the TCS core/shell NFs are promising candidates for the topical delivery of HIV/AIDS microbicides such as tenofovir.

Deep-sea ostracode shell chemistry (Mg:Ca ratios) and late Quaternary Arctic Ocean history

USGS Publications Warehouse

Cronin, T. M.; Dwyer, Gary S.; Baker, P.A.; Rodriguez-Lazaro, J.; Briggs, W.M.; ,

1996-01-01

The magnesium:calcium (Mg:Ca) and strontium:calcium (Sr:Ca) ratios were investigated in shells of the benthic ostracode genus Krithe obtained from 64 core-tops from water depths of 73 to 4411 m in the Arctic Ocean and Nordic seas to determine the potential of ostracode shell chemistry for palaeoceanographic study. Shells from the Polar Surface Water (−1 to −1.5°C) had Mg:Ca molar ratios of about 0.006–0.008; shells from Arctic Intermediate Water (+0.3 to +2.0°C) ranged from 0.09 to 0.013. Shells from the abyssal plain and ridges of the Nansen, Amundsen and Makarov basins and the Norwegian and Greenland seas had a wide scatter of Mg:Ca ratios ranging from 0.007 to 0.012 that may signify post-mortem chemical alteration of the shells from Arctic deep-sea environments below about 1000 m water depth. There is a positive correlation (r2 = 0.59) between Mg:Ca ratios and bottom-water temperature in Krithe shells from Arctic and Nordic seas from water depths <900 m. Late Quaternary Krithe Mg:Ca ratios were analysed downcore using material from the Gakkel Ridge (water depths 3047 and 3899 m), the Lomonosov Ridge (water depth 1051 m) and the Amundsen Basin (water depth 4226 m) to test the core-top Mg:Ca temperature calibration. Cores from the Gakkel and Lomonosov ridges display a decrease in Mg:Ca ratios during the interval spanning the last glacial/deglacial transition and the Holocene, perhaps related to a decrease in bottom water temperatures or other changes in benthic environments.

Silica diatom shells tailored with Au nanoparticles enable sensitive analysis of molecules for biological, safety and environment applications.

PubMed

Onesto, V; Villani, M; Coluccio, M L; Majewska, R; Alabastri, A; Battista, E; Schirato, A; Calestani, D; Coppedé, N; Cesarelli, M; Amato, F; Di Fabrizio, E; Gentile, F

2018-04-10

Diatom shells are a natural, theoretically unlimited material composed of silicon dioxide, with regular patterns of pores penetrating through their surface. For their characteristics, diatom shells show promise to be used as low cost, highly efficient drug carriers, sensor devices or other micro-devices. Here, we demonstrate diatom shells functionalized with gold nanoparticles for the harvesting and detection of biological analytes (bovine serum albumin-BSA) and chemical pollutants (mineral oil) in low abundance ranges, for applications in bioengineering, medicine, safety, and pollution monitoring.

Computational smart polymer design based on elastin protein mutability.

PubMed

Tarakanova, Anna; Huang, Wenwen; Weiss, Anthony S; Kaplan, David L; Buehler, Markus J

2017-05-01

Soluble elastin-like peptides (ELPs) can be engineered into a range of physical forms, from hydrogels and scaffolds to fibers and artificial tissues, finding numerous applications in medicine and engineering as "smart polymers". Elastin-like peptides are attractive candidates as a platform for novel biomaterial design because they exhibit a highly tunable response spectrum, with reversible phase transition capabilities. Here, we report the design of the first virtual library of elastin-like protein models using methods for enhanced sampling to study the effect of peptide chemistry, chain length, and salt concentration on the structural transitions of ELPs, exposing associated molecular mechanisms. We describe the behavior of the local molecular structure under increasing temperatures and the effect of peptide interactions with nearest hydration shell water molecules on peptide mobility and propensity to exhibit structural transitions. Shifts in the magnitude of structural transitions at the single-molecule scale are explained from the perspective of peptide-ion-water interactions in a library of four unique elastin-like peptide systems. Predictions of structural transitions are subsequently validated in experiment. This library is a valuable resource for recombinant protein design and synthesis as it elucidates mechanisms at the single-molecule level, paving a feedback path between simulation and experiment for smart material designs, with applications in biomedicine and diagnostic devices. Copyright © 2017. Published by Elsevier Ltd.

Electronic spectroscopy and photodissociation dynamics of Co(2+)-methanol clusters: Co2+ (CH3OH)n (n = 4-7).

PubMed

Thompson, Christopher J; Faherty, Kieron P; Stringer, Kay L; Metz, Ricardo B

2005-03-07

Solvated cluster ions Co2+ (CH3OH)n (n = 4-7) have been produced by electrospray and studied using photofragment spectroscopy. There are notable differences between the photodissociation spectra of these complexes and the analogous water complexes. Co2+ (CH3OH)6 absorbs significantly more strongly than Co2+ (H2O)6. The photodissociation spectra of Co2+ (CH3OH)n (n = 4, 5 and 6) are very similar, which suggests that they share the Co2+ (CH3OH)4 chromophore, with additional solvent molecules in the second shell. In contrast, our earlier studies indicate that Co2+ (H2O)6 is six coordinate, and its spectrum is significantly different from that of Co2+ (H2O)4. The larger clusters Co2+ (CH3OH)n (n = 5-7) dissociate by simple loss of one or more solvent molecules. Larger clusters tend to lose more solvent molecules, especially at higher photon energies. As with the corresponding water cluster, Co2+ (CH3OH)4 photodissociates by proton transfer through a salt-bridge intermediate. This is accompanied by a modest kinetic energy release of 170 kJ mol(-1) and occurs with a lifetime of 145 ns.

Enzyme microheterogeneous hydration and stabilization in supercritical carbon dioxide.

PubMed

Silveira, Rodrigo L; Martínez, Julian; Skaf, Munir S; Martínez, Leandro

2012-05-17

Supercritical carbon dioxide is a promising green-chemistry solvent for many enzyme-catalyzed chemical reactions, yet the striking stability of some enzymes in such unconventional environments is not well understood. Here, we investigate the stabilization of the Candida antarctica Lipase B (CALB) in supercritical carbon dioxide-water biphasic systems using molecular dynamics simulations. The preservation of the enzyme structure and optimal activity depend on the presence of small amounts of water in the supercritical dispersing medium. When the protein is at least partially hydrated, water molecules bind to specific sites on the enzyme surface and prevent carbon dioxide from penetrating its catalytic core. Strikingly, water and supercritical carbon dioxide cover the protein surface quite heterogeneously. In the first solvation layer, the hydrophilic residues at the surface of the protein are able to pin down patches of water, whereas carbon dioxide solvates preferentially hydrophobic surface residues. In the outer solvation shells, water molecules tend to cluster predominantly on top of the larger water patches of the first solvation layer instead of spreading evenly around the remainder of the protein surface. For CALB, this exposes the substrate-binding region of the enzyme to carbon dioxide, possibly facilitating diffusion of nonpolar substrates into the catalytic funnel. Therefore, by means of microheterogeneous solvation, enhanced accessibility of hydrophobic substrates to the active site can be achieved, while preserving the functional structure of the enzyme. Our results provide a molecular picture on the nature of the stability of proteins in nonaqueous media.

The initiation and persistence of cracks in Enceladus' ice shell

NASA Astrophysics Data System (ADS)

Rudolph, M. L.; Jordan, J.; Manga, M.; Hawkins, E. K.; Grannan, A. M.; Reinhard, A.; Farough, A.; Mittal, T.; Hernandez, J. A.

2016-12-01

The eruption of water from a global ocean underlying Enceladus' ice shell requires; i. a mechanism to create stresses sufficient to produce cracks that reach the ocean, ii. that the ascent of water through the crack must be fast enough to keep the crack from freezing. We develop models for the evolution of stresses in the ice shell and overpressure in the ocean, the propagation of cracks into the ice shell, and the melting of ice caused by the eruption of water through the cracks. We show that modest cooling of Enceladus' interior can produce extensional stresses in the ice shell sufficient to overcome the tensile strength of ice. We show that the resultant ice shell cracks can penetrate to depths greater than 10 km. Cracks of 10 km are required to reach the interior oceans of Enceladus in the polar regions. After crack formation, we show that the present eruption rate is sufficient to keep cracks from freezing below the water-table, at which water boils and subsequently erupts. The ascent of warm water from Enceladus' ocean widens the cracks and thins the ice shell in the South Polar Terrain (SPT). Model predictions show that a crack with the minimum, sufficient heat flow to persist without freezing, would thin the surrounding ice shell by about a factor of two. This calculation for heat flow is consistent with observed heat fluxes at the surface and recent inferences of the ice shell thickness in the SPT based on the shape and gravity of Enceladus.

Aspects of Weak Interactions between Folate and Glycine Betaine.

PubMed

Bhojane, Purva P; Duff, Michael R; Bafna, Khushboo; Rimmer, Gabriella P; Agarwal, Pratul K; Howell, Elizabeth E

2016-11-15

Folate, or vitamin B 9 , is an important compound in one-carbon metabolism. Previous studies have found weaker binding of dihydrofolate to dihydrofolate reductase in the presence of osmolytes. In other words, osmolytes are more difficult to remove from the dihydrofolate solvation shell than water; this shifts the equilibrium toward the free ligand and protein species. This study uses vapor-pressure osmometry to explore the interaction of folate with the model osmolyte, glycine betaine. This method yields a preferential interaction potential (μ 23 /RT value). This value is concentration-dependent as folate dimerizes. The μ 23 /RT value also tracks the deprotonation of folate's N3-O4 keto-enol group, yielding a pK a of 8.1. To determine which folate atoms interact most strongly with betaine, the interaction of heterocyclic aromatic compounds (as well as other small molecules) with betaine was monitored. Using an accessible surface area approach coupled with osmometry measurements, deconvolution of the μ 23 /RT values into α values for atom types was achieved. This allows prediction of μ 23 /RT values for larger molecules such as folate. Molecular dynamics simulations of folate show a variety of structures from extended to L-shaped. These conformers possess μ 23 /RT values from -0.18 to 0.09 m -1 , where a negative value indicates a preference for solvation by betaine and a positive value indicates a preference for water. This range of values is consistent with values observed in osmometry and solubility experiments. As the average predicted folate μ 23 /RT value is near zero, this indicates folate interacts almost equally well with betaine and water. Specifically, the glutamate tail prefers to interact with water, while the aromatic rings prefer betaine. In general, the more protonated species in our small molecule survey interact better with betaine as they provide a source of hydrogens (betaine is not a hydrogen bond donor). Upon deprotonation of the small molecule, the preference swings toward water interaction because of its hydrogen bond donating capacities.

Probe conformational dynamics of proteins in aqueous solutions by terahertz spectroscopy

NASA Astrophysics Data System (ADS)

Vinh, Nguyen Q.

2016-10-01

Proteins solvated in their biologically milieu are expected to exhibit strong absorption in the terahertz frequencies, that contain information on their global and sub-global collective vibrational modes (conformational dynamics) and global dynamic correlations among solvent water and proteins. The dynamics play an important role in enzymatic activities of proteins, but obtaining an accurate and quantitative pictures of these activities, however, is challenging due to the strong absorption of water. In response, we have developed the world's highest precision, highest sensitivity terahertz-frequency domain spectrometer and a standard terahertz-time domain system to probe the collective dynamics of proteins in aqueous solutions. Operating over the frequency range from 5 GHz up to 3 THz, our spectrometers provide an unparalleled ability to probe directly such questions as the hydration level, the dynamics of water and hydrated proteins over the 100 fs to 1 ns timescale. Employing an effective medium approximation to describe the complex dielectric response of the solvated proteins in solution we find that proteins are surrounded by a loosely and tightly held layers of water molecules that behave as if they are an integral part of the protein. The number of water molecules in the protein hydration shells varies with proteins, which can tell us the average surface structure of proteins. These measurements shed light on the macromolecular motions of proteins in their biologically relevant environment.

Microsolvation of the potassium ion with aromatic rings: comparison between hexafluorobenzene and benzene.

PubMed

Marques, J M C; Llanio-Trujillo, J L; Albertí, M; Aguilar, A; Pirani, F

2013-08-22

We employ a recently developed methodology to study structural and energetic properties of the first solvation shells of the potassium ion in nonpolar environments due to aromatic rings, which is important to understand the selectivity of several biochemical phenomena. Our evolutionary algorithm is used in the global optimization study of clusters formed of K(+) solvated with hexafluorobenzene (HFBz) molecules. The global intermolecular interaction for these clusters has been decomposed in HFBz-HFBz and in K(+)-HFBz contributions, using a potential model based on different decompositions of the molecular polarizability of hexafluorobenzene. Putative global minimum structures of microsolvation clusters up to 21 hexafluorobenzene molecules were obtained and compared with the analogous K(+)-benzene clusters reported in our previous work (J. Phys. Chem. A 2012, 116, 4947-4956). We have found that both K(+)-(Bz)n and K(+)-(HFBz)n clusters show a strong magic number around the closure of the first solvation shell. Nonetheless, all K(+)-benzene clusters have essentially the same first solvation shell geometry with four solvent molecules around the ion, whereas the corresponding one for K(+)-(HFBz)n is completed with nine HFBz species, and its structural motif varies as n increases. This is attributed to the ion-solvent interaction that has a larger magnitude for K(+)-Bz than in the case of K(+)-HFBz. In addition, the ability of having more HFBz than Bz molecules around K(+) in the first solvation shell is intimately related to the inversion in the sign of the quadrupole moment of the two solvent species, which leads to a distinct ion-solvent geometry of approach.

Rotating shell eggs immersed in hot water for the purpose of pasteurization

USDA-ARS?s Scientific Manuscript database

Pasteurization of shell eggs for inactivation of Salmonella using hot water immersion can be used to improve their safety. The rotation of a shell egg immersed in hot water has previously been simulated by computational fluid dynamics (CFD); however, experimental data to verify the results do not ex...

Infrared light-induced protein crystallization. Structuring of protein interfacial water and periodic self-assembly

NASA Astrophysics Data System (ADS)

Kowacz, Magdalena; Marchel, Mateusz; Juknaité, Lina; Esperança, José M. S. S.; Romão, Maria João; Carvalho, Ana Luísa; Rebelo, Luís Paulo N.

2017-01-01

We show that a physical trigger, a non-ionizing infrared (IR) radiation at wavelengths strongly absorbed by liquid water, can be used to induce and kinetically control protein (periodic) self-assembly in solution. This phenomenon is explained by considering the effect of IR light on the structuring of protein interfacial water. Our results indicate that the IR radiation can promote enhanced mutual correlations of water molecules in the protein hydration shell. We report on the radiation-induced increase in both the strength and cooperativeness of H-bonds. The presence of a structured dipolar hydration layer can lead to attractive interactions between like-charged biomacromolecules in solution (and crystal nucleation events). Furthermore, our study suggests that enveloping the protein within a layer of structured solvent (an effect enhanced by IR light) can prevent the protein non-specific aggregation favoring periodic self-assembly. Recognizing the ability to affect protein-water interactions by means of IR radiation may have important implications for biological and bio-inspired systems.

Chemical complexity in the winds of the oxygen-rich supergiant star VY Canis Majoris

NASA Astrophysics Data System (ADS)

Ziurys, L. M.; Milam, S. N.; Apponi, A. J.; Woolf, N. J.

2007-06-01

The interstellar medium is enriched primarily by matter ejected from old, evolved stars. The outflows from these stars create spherical envelopes, which foster gas-phase chemistry. The chemical complexity in circumstellar shells was originally thought to be dominated by the elemental carbon to oxygen ratio. Observations have suggested that envelopes with more carbon than oxygen have a significantly greater abundance of molecules than their oxygen-rich analogues. Here we report observations of molecules in the oxygen-rich shell of the red supergiant star VY Canis Majoris (VY CMa). A variety of unexpected chemical compounds have been identified, including NaCl, PN, HNC and HCO+. From the spectral line profiles, the molecules can be distinguished as arising from three distinct kinematic regions: a spherical outflow, a tightly collimated, blue-shifted expansion, and a directed, red-shifted flow. Certain species (SiO, PN and NaCl) exclusively trace the spherical flow, whereas HNC and sulphur-bearing molecules (amongst others) are selectively created in the two expansions, perhaps arising from shock waves. CO, HCN, CS and HCO+ exist in all three components. Despite the oxygen-rich environment, HCN seems to be as abundant as CO. These results suggest that oxygen-rich shells may be as chemically diverse as their carbon counterparts.

Chemical complexity in the winds of the oxygen-rich supergiant star VY Canis Majoris.

PubMed

Ziurys, L M; Milam, S N; Apponi, A J; Woolf, N J

2007-06-28

The interstellar medium is enriched primarily by matter ejected from old, evolved stars. The outflows from these stars create spherical envelopes, which foster gas-phase chemistry. The chemical complexity in circumstellar shells was originally thought to be dominated by the elemental carbon to oxygen ratio. Observations have suggested that envelopes with more carbon than oxygen have a significantly greater abundance of molecules than their oxygen-rich analogues. Here we report observations of molecules in the oxygen-rich shell of the red supergiant star VY Canis Majoris (VY CMa). A variety of unexpected chemical compounds have been identified, including NaCl, PN, HNC and HCO+. From the spectral line profiles, the molecules can be distinguished as arising from three distinct kinematic regions: a spherical outflow, a tightly collimated, blue-shifted expansion, and a directed, red-shifted flow. Certain species (SiO, PN and NaCl) exclusively trace the spherical flow, whereas HNC and sulphur-bearing molecules (amongst others) are selectively created in the two expansions, perhaps arising from shock waves. CO, HCN, CS and HCO+ exist in all three components. Despite the oxygen-rich environment, HCN seems to be as abundant as CO. These results suggest that oxygen-rich shells may be as chemically diverse as their carbon counterparts.

Glass polymorphism in glycerol–water mixtures: I. A computer simulation study

PubMed Central

Jahn, David A.; Wong, Jessina; Bachler, Johannes; Loerting, Thomas

2016-01-01

We perform out-of-equilibrium molecular dynamics (MD) simulations of water–glycerol mixtures in the glass state. Specifically, we study the transformations between low-density (LDA) and high-density amorphous (HDA) forms of these mixtures induced by compression/decompression at constant temperature. Our MD simulations reproduce qualitatively the density changes observed in experiments. Specifically, the LDA–HDA transformation becomes (i) smoother and (ii) the hysteresis in a compression/decompression cycle decreases as T and/or glycerol content increase. This is surprising given the fast compression/decompression rates (relative to experiments) accessible in MD simulations. We study mixtures with glycerol molar concentration χ g = 0–13% and find that, for the present mixture models and rates, the LDA–HDA transformation is detectable up to χ g ≈ 5%. As the concentration increases, the density of the starting glass (i.e., LDA at approximately χ g ≤ 5%) rapidly increases while, instead, the density of HDA remains practically constant. Accordingly, the LDA state and hence glass polymorphism become inaccessible for glassy mixtures with approximately χ g > 5%. We present an analysis of the molecular-level changes underlying the LDA–HDA transformation. As observed in pure glassy water, during the LDA-to-HDA transformation, water molecules within the mixture approach each other, moving from the second to the first hydration shell and filling the first interstitial shell of water molecules. Interestingly, similar changes also occur around glycerol OH groups. It follows that glycerol OH groups contribute to the density increase during the LDA–HDA transformation. An analysis of the hydrogen bond (HB)-network of the mixtures shows that the LDA–HDA transformation is accompanied by minor changes in the number of HBs of water and glycerol. Instead, large changes in glycerol and water coordination numbers occur. We also perform a detailed analysis of the effects that the glycerol force field (FF) has on our results. By comparing MD simulations using two different glycerol models, we find that glycerol conformations indeed depend on the FF employed. Yet, the thermodynamic and microscopic mechanisms accompanying the LDA–HDA transformation and hence, our main results, do not. This work is accompanied by an experimental report where we study the glass polymorphism in glycerol–water mixtures prepared by isobaric cooling at 1 bar. PMID:27063705

The environmental effect on the radial breathing mode of carbon nanotubes. II. Shell model approximation for internally and externally adsorbed fluids

NASA Astrophysics Data System (ADS)

Longhurst, M. J.; Quirke, N.

2006-11-01

We have previously shown that the upshift in the radial breathing mode (RBM) of closed (or infinite) carbon nanotubes in solution is almost entirely due to coupling of the RBM with an adsorbed layer of fluid on the nanotube surface. The upshift can be modeled analytically by considering the adsorbed fluid as an infinitesimally thin shell, which interacts with the nanotube via a continuum Lennard-Jones potential. Here we extend the model to include internally as well as externally adsorbed waterlike molecules, and find that filling the nanotubes leads to an additional upshift of two to six wave numbers. We show that using molecular dynamics, the RBM can be accurately reproduced by replacing the fluid molecules with a mean field harmonic shell potential, greatly reducing simulation times.

Records of River Variation in the Shells of Freshwater Bivalves

NASA Astrophysics Data System (ADS)

Carroll, M.; Romanek, C.

2005-12-01

The skeletons of hard-shelled invertebrates such as corals and bivalves are commonly used in marine settings as archives of environmental information. They are less commonly used in freshwater settings where variability in water chemistry makes it more difficult to calibrate chemical proxies such as the Sr:Ca in a shell. Our objective is to evaluate whether trace element concentrations in freshwater bivalve shells contain information on environmental conditions. Multiple elements (Ba, Cu, Mn and Sr) were analyzed within the shells of modern bivalves from four streams on DOE's Savannah River Site in S.C. Laser Ablation ICP-MS was used to measure elemental concentrations across five aragonitic shells from each site. These elements were chosen because they are present in detectable concentrations (ppm) in the shell and they have been suggested as useful proxies for temperature, rainfall, productivity and pollution. Results were compared to historical monthly site records of water chemistry and chemical analyses of water samples collected from the streams where the clams were found. The average shell concentrations of Sr and Mn were significantly different between sites and increased proportionally to water concentration. This was not observed for Ba and Cu. For example, the Ba concentrations of shells collected at a site downstream of a lake were higher than those for shells from stream sites with significantly higher dissolved Ba concentrations. Copper was only detected at dark growth lines with the number of lines and shell material between them varying between shells within the same stream. Intrashell profiles of Ba, Sr and Mn concentrations exhibited cyclical variation. The magnitude of cyclical variation for Mn and Sr within a shell corresponds with the annual variation in monthly water sample concentrations. Again, this pattern was not observed for Ba, especially in shells from the site downstream of a lake. This supports suggestions that particulate organic matter, to which Ba preferentially partitions, plays a role in bivalve Ba uptake. Finally, variations in Ba, Cu, Mn and Sr profiles across shells are not in unison. The individual elemental responses to biological and physicochemical effects suggest that the elemental records in freshwater bivalve shells can be interpreted as environmental proxies.

Dehydration of multilamellar fatty acid membranes: Towards a computational model of the stratum corneum

NASA Astrophysics Data System (ADS)

MacDermaid, Christopher M.; DeVane, Russell H.; Klein, Michael L.; Fiorin, Giacomo

2014-12-01

The level of hydration controls the cohesion between apposed lamellae of saturated free fatty acids found in the lipid matrix of stratum corneum, the outermost layer of mammalian skin. This multilamellar lipid matrix is highly impermeable to water and ions, so that the local hydration shell of its fatty acids may not always be in equilibrium with the acidity and relative humidity, which significantly change over a course of days during skin growth. The homeostasis of the stratum corneum at each moment of its growth likely requires a balance between two factors, which affect in opposite ways the diffusion of hydrophilic species through the stratum corneum: (i) an increase in water order as the lipid lamellae come in closer contact, and (ii) a decrease in water order as the fraction of charged fatty acids is lowered by pH. Herein molecular dynamics simulations are employed to estimate the impact of both effects on water molecules confined between lamellae of fatty acids. Under conditions where membrane undulations are energetically favorable, the charged fatty acids are able to sequester cations around points of contact between lamellae that are fully dehydrated, while essentially maintaining a multilamellar structure for the entire system. This observation suggests that the undulations of the fatty acid lamellae control the diffusion of hydrophilic species through the water phase by altering the positional and rotational order of water molecules in the embedded/occluded "droplets."

Two-state protein model with water interactions: Influence of temperature on the intrinsic viscosity of myoglobin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bakk, Audun

2001-06-01

We describe a single-domain protein as a two-state system with water interactions. Around the unfolded apolar parts of the protein we incorporate the hydration effect by introducing hydrogen bonds between the water molecules in order to mimic the {open_quotes}icelike{close_quotes} shell structure. Intrinsic viscosity, proportional to the effective hydrodynamic volume, for sperm whale metmyoglobin is assigned from experimental data in the folded and in the denaturated state. By weighing statistically the two states against the degree of folding, we express the total intrinsic viscosity. The temperature dependence of the intrinsic viscosity, for different chemical potentials, is in good correspondence with experimentalmore » data [P. L. Privalov , J. Mol. Biol. >190, 487 (1986)]. Cold and warm unfolding, common to small globular proteins, is also a result of the model.« less

Facile synthesis of Cu(II) impregnated biochar with enhanced adsorption activity for the removal of doxycycline hydrochloride from water.

PubMed

Liu, Su; Xu, Wei-Hua; Liu, Yun-Guo; Tan, Xiao-Fei; Zeng, Guang-Ming; Li, Xin; Liang, Jie; Zhou, Zan; Yan, Zhi-Li; Cai, Xiao-Xi

2017-08-15

In this study, the effect factors and mechanisms of doxycycline hydrochloride (DOX) adsorption on copper nitrate modified biochar (Cu-BC) was investigated. Cu-BC absorbent was synthesized through calcination of peanut shells biomass at 450°C and then impregnation with copper nitrate. The Cu-BC has exhibited excellent sorption efficiency about 93.22% of doxycycline hydrochloride from aqueous solution, which was double higher than that of the unmodified biochar. The experimental results suggest that the adsorption efficiency of DOX on the Cu-BC is dominated by the strong complexation, electrostatic interactions between DOX molecules and the Cu-BC samples. Comprehensively considering the cost, efficiency and the application to realistic water, the Cu-BC hold the significant potential for enhancing the effectiveness to remove DOX from water. Copyright © 2017 Elsevier B.V. All rights reserved.

Efficient geometry optimization by Hellmann-Feynman forces with the anti-Hermitian contracted Schrödinger equation

NASA Astrophysics Data System (ADS)

Foley, Jonathan J.; Mazziotti, David A.

2010-10-01

An efficient method for geometry optimization based on solving the anti-Hermitian contracted Schrödinger equation (ACSE) is presented. We formulate a reduced version of the Hellmann-Feynman theorem (HFT) in terms of the two-electron reduced Hamiltonian operator and the two-electron reduced density matrix (2-RDM). The HFT offers a considerable reduction in computational cost over methods which rely on numerical derivatives. While previous geometry optimizations with numerical gradients required 2M evaluations of the ACSE where M is the number of nuclear degrees of freedom, the HFT requires only a single ACSE calculation of the 2-RDM per gradient. Synthesizing geometry optimization techniques with recent extensions of the ACSE theory to arbitrary electronic and spin states provides an important suite of tools for accurately determining equilibrium and transition-state structures of ground- and excited-state molecules in closed- and open-shell configurations. The ability of the ACSE to balance single- and multi-reference correlation is particularly advantageous in the determination of excited-state geometries where the electronic configurations differ greatly from the ground-state reference. Applications are made to closed-shell molecules N2, CO, H2O, the open-shell molecules B2 and CH, and the excited state molecules N2, B2, and BH. We also study the HCN ↔ HNC isomerization and the geometry optimization of hydroxyurea, a molecule which has a significant role in the treatment of sickle-cell anaemia.

Nanofiber Based Optical Sensors for Oxygen Determination

NASA Astrophysics Data System (ADS)

Xue, Ruipeng

Oxygen sensors based on luminescent quenching of nanofibers were developed for measurement of both gaseous and dissolved oxygen concentrations. Electrospinning was used to fabricate "core-shell" fiber configurations in which oxygen-sensitive transition metal complexes are embedded into a polymer 'core' while a synthetic biocompatible polymer provides a protective 'shell.' Various matrix polymers and luminescent probes were studied in terms of their sensitivity, linear calibration, reversibility, response time, stability and probe-matrix interactions. Due to the small size and high surface area of these nanofibers, all samples showed rapid response and a highly linear response to oxygen. The sensitivity and photostability of the sensors were controlled by the identity of both the probe molecule and the polymer matrix. Such nanofiber sensor forms are particularly suitable in biological applications due to the fact that they do not consume oxygen, are biocompatible and biomimetic and can be easily incorporated into cell culture. Applications of these fibers in cancer cell research, wound healing, breath analysis and waste water treatment were explored.

Identification of Multiple Water-Iodide Species in Concentrated NaI Solutions Based on the Raman Bending Vibration of Water.

PubMed

Besemer, Matthieu; Bloemenkamp, Rob; Ariese, Freek; van Manen, Henk-Jan

2016-02-11

The influence of aqueous electrolytes on the water bending vibration was studied with Raman spectroscopy. For all salts investigated (NaI, NaBr, NaCl, and NaSCN), we observed a nonlinear intensity increase of the water bending vibration with increasing concentration. Different lasers and a tunable frequency-doubled optical parametric oscillator system were used to achieve excitation wavelengths between 785 and 374 nm. Focusing on NaI solutions, the relative enhancement of the water bending vibration was found to increase strongly with excitation photon energy, in line with a preresonance effect from the iodide-water charge-transfer transition. We used multivariate curve resolution (MCR) to decompose the measured Raman spectra of NaI solutions into three interconverting spectral components assigned to bulk water and water molecules interacting with one (X···H-O-H···O) and two (X···H-O-H···X) iodide ions (X = I(-)). The Raman spectrum of solid sodium iodide dihydrate supports the assignment of the latter. Using the MCR results, relative Raman scattering cross sections of 4.0 ± 0.6 and 14.0 ± 0.1 were calculated for the mono- and di-iodide species, respectively (compared to that of bulk water set to unity). In addition, it was found that at relatively low concentrations each iodide ion affects the Raman spectrum of roughly 22 surrounding water molecules, indicating that the influence of iodide extends beyond the first solvation shell. Our results demonstrate that the Raman bending vibration of water is a sensitive probe, providing new insights into anion solvation in aqueous environments.

Charge and Spin Currents in Open-Shell Molecules:  A Unified Description of NMR and EPR Observables.

PubMed

Soncini, Alessandro

2007-11-01

The theory of EPR hyperfine coupling tensors and NMR nuclear magnetic shielding tensors of open-shell molecules in the limit of vanishing spin-orbit coupling (e.g., for organic radicals) is analyzed in terms of spin and charge current density vector fields. The ab initio calculation of the spin and charge current density response has been implemented at the Restricted Open-Shell Hartree-Fock, Unrestricted Hartree-Fock, and unrestricted GGA-DFT level of theory. On the basis of this formalism, we introduce the definition of nuclear hyperfine coupling density, a scalar function of position providing a partition of the EPR observable over the molecular domain. Ab initio maps of spin and charge current density and hyperfine coupling density for small radicals are presented and discussed in order to illustrate the interpretative advantages of the newly introduced approach. Recent NMR experiments providing evidence for the existence of diatropic ring currents in the open-shell singlet pancake-bonded dimer of the neutral phenalenyl radical are directly assessed via the visualization of the induced current density.

Au-Ag-Au double shell nanoparticles-based localized surface plasmon resonance and surface-enhanced Raman scattering biosensor for sensitive detection of 2-mercapto-1-methylimidazole.

PubMed

Liao, Xue; Chen, Yanhua; Qin, Meihong; Chen, Yang; Yang, Lei; Zhang, Hanqi; Tian, Yuan

2013-12-15

In this paper, Au-Ag-Au double shell nanoparticles were prepared based on the reduction of the metal salts HAuCl4 and AgNO3 at the surface of seed particles. Due to the synergistic effect between Au and Ag, the hybrid nanoparticles are particularly stable and show excellent performances on the detection of 2-mercapto-1-methylimidazole (methimazole). The binding of target molecule at the surface of Au-Ag-Au double shell nanoparticles was demonstrated based on both localized surface plasmon resonance (LSPR) and surface-enhanced Raman scattering (SERS) spectra. The LSPR intensity is directly proportional to the methimazole concentration in the range of 0.10-3.00×10(-7) mol L(-1). The SERS spectrum can be applied in identification of methimazole molecule. The LSPR coupled with SERS based on the Au-Ag-Au double shell nanoparticles would be very attractive for the quantitative determination and qualitative analysis of the analytes in medicines. © 2013 Elsevier B.V. All rights reserved.

Hexakis(3,6-di-tert-butyl-4-oxo-2,5-cyclohexadien-1-ylidene)cyclohexane: Closed-shell [6]Radialene or Open-shell Hexa-radicaloid?

PubMed

Wu, Jishan; Feng, Jiaqi; Gopalakrishna, Tullimilli Y; Phan, Hoa

2018-04-19

We report a star-shaped hexaquinocyclohexane molecule 4c, which turns out to be a closed-shell extended [6]radialene with a twisted-boat conformation according to X-ray crystallographic analysis. It was formed by an unusually slow decay of its in situ generated open-shell valence isomer, the hexa-radicaloid 4o, with a half-life time of about 156 min at room temperature. Reaction progress kinetic analysis revealed a large energy barrier of about 95.5 ± 4.3 kJ/mol at room temperature from the hexa-radical form 4o to the contorted [6]radialene form 4c, because the transformation need overcome large steric repulsion between the neighbouring phenoxyl units. Compound 4c can be chemically reduced to radical anion and dianion, and the dianion is actually a diradical dianion, with a calculated diradical character of 71.9%. This study demonstrated the unique chemical bonding nature of contorted quinoidal π-conjugated molecules and a very unusual valence isomerization process. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Folic acid-functionalized magnetic ZnFe2O4 hollow microsphere core/mesoporous silica shell composite particles: synthesis and application in drug release.

PubMed

Yang, Dandan; Wei, Kaiwei; Liu, Qi; Yang, Yong; Guo, Xue; Rong, Hongren; Cheng, Mei-Ling; Wang, Guoxiu

2013-07-01

A drug delivery system was designed by deliberately combining the useful functions into one entity, which was composed of magnetic ZnFe2O4 hollow microsphere as the core, and mesoporous silica with folic acid molecules as the outer shell. Amine groups coated magnetic ZnFe2O4 hollow microsphere core/mesoporous silica shell (MZHM-MSS-NH2) composite particles were first synthesized by a one-pot direct co-condensation method. Subsequently a novel kind of folic acid-functionalized magnetic ZnFe2O4 hollow microsphere core/mesoporous silica shell (MZHM-MSS-NHFA) composite particles were synthesized by conjugating folic acid as targeted molecule to MZHM-MSS-NH2. Ibuprofen, a well-known antiphlogistic drug, was used as a model drug to assess the loading and releasing behavior of the composite microspheres. The results show that the MZHM-MSS-NHFA system has the higher capacity of drug storage and good sustained drug-release property. Copyright © 2013 Elsevier B.V. All rights reserved.

Ethanol Gas Detection Using a Yolk-Shell (Core-Shell) α-Fe2O3 Nanospheres as Sensing Material.

PubMed

Wang, LiLi; Lou, Zheng; Deng, Jianan; Zhang, Rui; Zhang, Tong

2015-06-17

Three-dimensional (3D) nanostructures of α-Fe2O3 materials, including both hollow sphere-shaped and yolk-shell (core-shell)-shaped, have been successfully synthesized via an environmentally friendly hydrothermal approach. By expertly adjusting the reaction time, the solid, hollow, and yolk-shell shaped α-Fe2O3 can be selectively synthesized. Yolk-shell α-Fe2O3 nanospheres display outer diameters of 350 nm, and the interstitial hollow spaces layer is intimately sandwiched between the inner and outer shell of α-Fe2O3 nanostructures. The possible growth mechanism of the yolk-shell nanostructure is proposed. The results showed that the well-defined bilayer interface effectively enhanced the sensing performance of the α-Fe2O3 nanostructures (i.e., yolk-shell α-Fe2O3@α-Fe2O3), owing predominantly to the unique nanostructure, thus facilitated the transport rate and augmented the adsorption quantity of the target gas molecule under gas detection.

Analysis of experimental heats of dilution of aqueous solutions of NaBPh 4 by use of the mean spherical approximation and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

M'halla, Jalel; M'halla, Sondes; Wipff, Georges

2003-03-01

Calorimetric measurements of heats of dilution: QDC→0 =- nsφL,sexp, of aqueous solutions of NaBPh 4 are determined at 25 °C in the concentration range: 0

Single molecule conductivity: the role of junction-orbital degeneracy in the artificially high currents predicted by ab initio approaches.

PubMed

Solomon, Gemma C; Reimers, Jeffrey R; Hush, Noel S

2004-10-08

A priori evaluations, using Hartree-Fock self-consistent-field (SCF) theory or density-functional theory (DFT), of the current passing between two electrodes through a single bridging molecule result in predicted conductivities that may be up to one to two orders of magnitude larger than observed ones. We demonstrate that this is, in part, often due to the improper application of the computational methods. Conductivity is shown to arise from tunneling between junction states of the electrodes through the molecule; these states are inherently either quasi two-fold or four-fold degenerate and always comprise the (highest occupied molecular orbital) HOMO band at the Fermi energy of the system. Frequently, in previous cluster based molecular conduction calculations, closed-shell SCF or Kohn-Sham DFT methods have been applied to systems that we demonstrate to be intrinsically open shell in nature. Such calculations are shown to induce artificial HOMO-LUMO (LUMO-lowest unoccupied molecular orbital) band splittings that Landauer-based formalisms for steady-state conduction interpret as arising from extremely rapid through-molecule tunneling at the Fermi energy, hence, overestimating the low-voltage conductivity. It is demonstrated that these shortcomings can be eliminated, dramatically reducing calculated current magnitudes, through the alternate use of electronic-structure calculations based on the spin-restricted open-shell formalism and related multiconfigurational SCF of DFT approaches. Further, we demonstrate that most anomalies arising in DFT implementations arise through the use of hybrid density functionals such as B3LYP. While the enhanced band-gap properties of these functionals have made them the defacto standard in molecular conductivity calculations, we demonstrate that it also makes them particularly susceptible to open-shell anomalies.

Microcavity surface plasmon resonance bio-sensors

NASA Astrophysics Data System (ADS)

Mosavian, Nazanin

This work discusses a miniature surface plasmon biosensor which uses a dielectric sub- micron diameter core with gold spherical shell. The shell has a subwavelength nanoaperture believed to excite stationary plasmon resonances at the biosensor's surface. The sub-micron cavity enhances the measurement sensitivity of molecules binding to the sensor surface. We used visible-range optical spectroscopy to study the wavelength shift as bio-molecules absorbed-desorbed at the shell surface. We also used Scanning Electron Microscopy (SEM) and Focused Ion Beam (FIB) ablation to study the characteristics of microcavity surface plasmon resonance sensor (MSPRS) and the inner structure formed with metal deposition and its spectrum. We found that resonances at 580 nm and 670 nm responded to bound test agents and that Surface Plasmon Resonance (SPR) sensor intensity could be used to differentiate between D-glucose and L-glucose. The responsiveness of the system depended upon the mechanical integrity of the metallic surface coating.

Stable Radical Materials for Energy Applications.

PubMed

Wilcox, Daniel A; Agarkar, Varad; Mukherjee, Sanjoy; Boudouris, Bryan W

2018-06-07

Although less studied than their closed-shell counterparts, materials containing stable open-shell chemistries have played a key role in many energy storage and energy conversion devices. In particular, the oxidation-reduction (redox) properties of these stable radicals have made them a substantial contributor to the progress of organic batteries. Moreover, the use of radical-based materials in photovoltaic devices and thermoelectric systems has allowed for these emerging molecules to have impacts in the energy conversion realm. Additionally, the unique doublet states of radical-based materials provide access to otherwise inaccessible spin states in optoelectronic devices, offering many new opportunities for efficient usage of energy in light-emitting devices. Here, we review the current state of the art regarding the molecular design, synthesis, and application of stable radicals in these energy-related applications. Finally, we point to fundamental and applied arenas of future promise for these designer open-shell molecules, which have only just begun to be evaluated in full.

rPM6 parameters for phosphorous and sulphur-containing open-shell molecules

NASA Astrophysics Data System (ADS)

Saito, Toru; Takano, Yu

2018-03-01

In this article, we have introduced a reparameterisation of PM6 (rPM6) for phosphorus and sulphur to achieve a better description of open-shell species containing the two elements. Two sets of the parameters have been optimised separately using our training sets. The performance of the spin-unrestricted rPM6 (UrPM6) method with the optimised parameters is evaluated against 14 radical species, which contain either phosphorus or sulphur atom, comparing with the original UPM6 and the spin-unrestricted density functional theory (UDFT) methods. The standard UPM6 calculations fail to describe the adiabatic singlet-triplet energy gaps correctly, and may cause significant structural mismatches with UDFT-optimised geometries. Leaving aside three difficult cases, tests on 11 open-shell molecules strongly indicate the superior performance of UrPM6, which provides much better agreement with the results of UDFT methods for geometric and electronic properties.

The effect of the condensed-phase environment on the vibrational frequency shift of a hydrogen molecule inside clathrate hydrates

NASA Astrophysics Data System (ADS)

Powers, Anna; Scribano, Yohann; Lauvergnat, David; Mebe, Elsy; Benoit, David M.; Bačić, Zlatko

2018-04-01

We report a theoretical study of the frequency shift (redshift) of the stretching fundamental transition of an H2 molecule confined inside the small dodecahedral cage of the structure II clathrate hydrate and its dependence on the condensed-phase environment. In order to determine how much the hydrate water molecules beyond the confining small cage contribute to the vibrational frequency shift, quantum five-dimensional (5D) calculations of the coupled translation-rotation eigenstates are performed for H2 in the v =0 and v =1 vibrational states inside spherical clathrate hydrate domains of increasing radius and a growing number of water molecules, ranging from 20 for the isolated small cage to over 1900. In these calculations, both H2 and the water domains are treated as rigid. The 5D intermolecular potential energy surface (PES) of H2 inside a hydrate domain is assumed to be pairwise additive. The H2-H2O pair interaction, represented by the 5D (rigid monomer) PES that depends on the vibrational state of H2, v =0 or v =1 , is derived from the high-quality ab initio full-dimensional (9D) PES of the H2-H2O complex [P. Valiron et al., J. Chem. Phys. 129, 134306 (2008)]. The H2 vibrational frequency shift calculated for the largest clathrate domain considered, which mimics the condensed-phase environment, is about 10% larger in magnitude than that obtained by taking into account only the small cage. The calculated splittings of the translational fundamental of H2 change very little with the domain size, unlike the H2 j = 1 rotational splittings that decrease significantly as the domain size increases. The changes in both the vibrational frequency shift and the j = 1 rotational splitting due to the condensed-phase effects arise predominantly from the H2O molecules in the first three complete hydration shells around H2.

Chemical and thermal stability of core-shelled magnetite nanoparticles and solid silica

NASA Astrophysics Data System (ADS)

Cendrowski, Krzysztof; Sikora, Pawel; Zielinska, Beata; Horszczaruk, Elzbieta; Mijowska, Ewa

2017-06-01

Pristine nanoparticles of magnetite were coated by solid silica shell forming core/shell structure. 20 nm thick silica coating significantly enhanced the chemical and thermal stability of the iron oxide. Chemical and thermal stability of this structure has been compared to the magnetite coated by mesoporous shell and pristine magnetite nanoparticles. It is assumed that six-membered silica rings in a solid silica shell limit the rate of oxygen diffusion during thermal treatment in air and prevent the access of HCl molecules to the core during chemical etching. Therefore, the core/shell structure with a solid shell requires a longer time to induce the oxidation of iron oxide to a higher oxidation state and, basically, even strong concentrated acid such as HCl is not able to dissolve it totally in one month. This leads to the desired performance of the material in potential applications such as catalysis and environmental protection.

QM/MM investigation of the concentration effects on the second-order nonlinear optical responses of solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hidalgo Cardenuto, Marcelo, E-mail: marcelo.hidalgo@unamur.be, E-mail: benoit.champagne@unamur.be; Instituto de Física, Universidade de São Paulo, CP 66318, 05314-970 São Paulo, SP; Champagne, Benoît, E-mail: marcelo.hidalgo@unamur.be, E-mail: benoit.champagne@unamur.be

2014-12-21

A multiscale approach combining quantum mechanics (QM) and molecular mechanics methods has been employed to investigate the effects of solute-solute interactions and therefore of concentration on the first hyperpolarizability of solutions of nitrobenzene in benzene. First, spatial distributions of solute and solvent molecules are generated using Monte Carlo simulations where the intermolecular interactions are described using the Lennard-Jones potentials and Coulomb terms. Then, a reduced number of statistically-uncorrelated configurations are sampled and submitted to time-dependent Hartree-Fock calculations of the first hyperpolarizability. When only one molecule is described quantum-mechanically and is embedded in the electrostatic polarization field of the solution describedmore » by point charges, β{sub HRS} and β{sub //} as well as the depolarization ratio increase in parallel with the concentration in nitrobenzene. This effect is attributed to the increase of the polarization field associated with the presence of polar nitrobenzene molecules in the surrounding. Then, the first solvation shell is considered explicitly in the QM calculation to address solute-solute interactions effects. When the number of nitrobenzenes in the first solvation shell increases, β{sub HRS} and β{sub //} normalized to the number of nitrobenzene molecules decrease and this decrease attains roughly 50% when there are 3 nitrobenzene molecules in the first solvation shell. These drastic reductions of the first hyperpolarizability result from (partial) centro-symmetric arrangements between the nitrobenzene molecules, as supported by the relationship between β and the angle between the nitrobenzene charge transfer axes. Moreover, these β decreases originate mostly from the reduction of the dipolar β component, whereas the octupolar one is rather constant as a function of the nitrobenzene concentration.« less

N(2)O in small para-hydrogen clusters: Structures and energetics.

PubMed

Zhu, Hua; Xie, Daiqian

2009-04-30

We present the minimum-energy structures and energetics of clusters of the linear N(2)O molecule with small numbers of para-hydrogen molecules with pairwise additive potentials. Interaction energies of (p-H(2))-N(2)O and (p-H(2))-(p-H(2)) complexes were calculated by averaging the corresponding full-dimensional potentials over the H(2) angular coordinates. The averaged (p-H(2))-N(2)O potential has three minima corresponding to the T-shaped and the linear (p-H(2))-ONN and (p-H(2))-NNO structures. Optimization of the minimum-energy structures was performed using a Genetic Algorithm. It was found that p-H(2) molecules fill three solvation rings around the N(2)O axis, each of them containing up to five p-H(2) molecules, followed by accumulation of two p-H(2) molecules at the oxygen and nitrogen ends. The first solvation shell is completed at N = 17. The calculated chemical potential oscillates with cluster size up to the completed first solvation shell. These results are consistent with the available experimental measurements. (c) 2009 Wiley Periodicals, Inc.

Evaluation of aqueous and alcohol-based quaternary ammonium sanitizers for inactivating Salmonella spp., Escherichia coli O157:H7, and Listeria monocytogenes on peanut and pistachio shells.

PubMed

McEgan, Rachel; Danyluk, Michelle D

2015-05-01

This study evaluated the efficacy of aqueous (aQUAT) and isopropyl alcohol-based quaternary ammonium (ipQUAT) sanitizers for reducing Salmonella spp., Escherichia coli O157:H7, or Listeria monocytogenes populations on peanut and pistachio shell pieces. Inoculated nutshells were mixed with QUAT sanitizers, water, or 70% ethanol and enumerated immediately or after incubation at 30 °C for 48 h. None of the treatments had any immediate effect on Salmonella or E. coli O157:H7 populations on the peanut or pistachio shells. L. monocytogenes populations declined immediately on the peanut and pistachio shells treated with aQUAT or ipQUAT. After incubation, Salmonella and E. coli O157:H7 populations increased significantly on the water- or aQUAT-treated peanut and pistachio shells. L. monocytogenes populations also increased significantly on the water- or aQUAT-treated peanut shells, but levels did not change on the water-treated pistachio shells and levels were just above the limit of detection on the aQUAT-treated pistachio shells. After treatment with ipQUAT and 48-h incubation, Salmonella and E. coli O157:H7 populations decreased to or below the limit of detection on both shell types; L. monocytogenes populations remained at or below the limit of detection on both shell types. Copyright © 2014 Elsevier Ltd. All rights reserved.

Empirical calibration of shell chemistry of Cyprideis torosa (Jones, 1850) (Crustacea: Ostracoda)

NASA Astrophysics Data System (ADS)

Marco-Barba, J.; Ito, E.; Carbonell, E.; Mesquita-Joanes, F.

2012-09-01

Cyprideis torosa is a species of ostracode that inhabits a wide range of aquatic habitats in which its low Alk/Ca requirement is met. Its fossil remains are widely used in palaeoecological studies of coastal environments and inland salt lakes. We collected C. torosa from 20 water bodies near Valencia, Spain. Temperature, chlorophyll a concentration, electrical conductivity, and the concentration of major ions and oxygen isotopes were measured at each site. Between 2 and 20 live individuals of C. torosa were collected per site, their instar stage and sex determined and their shell chemistry (Mg/Ca, Sr/Ca and carbon and oxygen isotope composition) analyzed. Three of these sites were sampled monthly for one year, and ostracode population structure and shell chemistry (20-40 shells) were analyzed. The water chemistry varied widely between sites. TDS (total dissolved solids) ranged from 0.5 to 71.8 g/L but chloride was always the dominant anion. There is a significant positive relationship between ostracode and water δ18O except at high TDS (>20 g/L) when shell δ18O values are lower than expected. No effect of either temperature or water Mg/Ca is observed on the Mg/Ca in the ostracode calcite in waters with Mg/Ca < 6 (molar ratio). Ostracode shell Sr/Ca is strongly and significantly related to water Sr/Ca. δ13C values in C. torosa shells are ˜2‰ lower than observed δ13CDIC. These results provide new and more accurate quantification tools to reconstruct past hydrochemistry from C. torosa shells.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borodin, Oleg; Price, David L.; Aoun, Bachir

The influence of water on the structure of a prototype ionic liquid (IL) 1-octyl-3-methyimidazolium tetrafluoroborate (C8mimBF4) is examined in the IL-rich regime using high-energy x-ray diffraction (HEXRD) and molecular dynamics (MD) simulations. A many-body polarizable force field APPLE&P was developed for C8mimBF4 water mixture. It predicts structure factors of pure IL and IL-water mixture in excellent agreement with the HEXRD experiments. The MD results provide detailed insights into the structural changes from the partial structure factors, 2-D projections of the simulation box and 3-D distribution functions. Water partitioning with IL and its competition with BF4- for complexing the imidazolium ringsmore » was examined. The added water molecules occupy a diffuse coordination shell around the imidazolium ring but are not present around the alkyl tail. The strong coordination of the fluorine atoms of the BF4- anions to the imidazolium ring is not significantly changed by the addition of water. These results are consistent with the very small differences in the average structure between the pure IL and the mixture.« less

Water solvent effects using continuum and discrete models: The nitromethane molecule, CH3NO2.

PubMed

Modesto-Costa, Lucas; Uhl, Elmar; Borges, Itamar

2015-11-15

The first three valence transitions of the two nitromethane conformers (CH3NO2) are two dark n → π* transitions and a very intense π → π* transition. In this work, these transitions in gas-phase and solvated in water of both conformers were investigated theoretically. The polarizable continuum model (PCM), two conductor-like screening (COSMO) models, and the discrete sequential quantum mechanics/molecular mechanics (S-QM/MM) method were used to describe the solvation effect on the electronic spectra. Time dependent density functional theory (TDDFT), configuration interaction including all single substitutions and perturbed double excitations (CIS(D)), the symmetry-adapted-cluster CI (SAC-CI), the multistate complete active space second order perturbation theory (CASPT2), and the algebraic-diagrammatic construction (ADC(2)) electronic structure methods were used. Gas-phase CASPT2, SAC-CI, and ADC(2) results are in very good agreement with published experimental and theoretical spectra. Among the continuum models, PCM combined either with CASPT2, SAC-CI, or B3LYP provided good agreement with available experimental data. COSMO combined with ADC(2) described the overall trends of the transition energy shifts. The effect of increasing the number of explicit water molecules in the S-QM/MM approach was discussed and the formation of hydrogen bonds was clearly established. By including explicitly 24 water molecules corresponding to the complete first solvation shell in the S-QM/MM approach, the ADC(2) method gives more accurate results as compared to the TDDFT approach and with similar computational demands. The ADC(2) with S-QM/MM model is, therefore, the best compromise for accurate solvent calculations in a polar environment. © 2015 Wiley Periodicals, Inc.

Does the 4f-shell contribute to bonding in tetravalent lanthanide halides?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ji, Wen-Xin; School of Chemistry and Chemical Engineering, Ningxia University, 750015 Yinchuan; Xu, Wei

2014-12-28

Lanthanide tetrahalide molecules LnX{sub 4} (Ln = Ce, Pr, Tb; X = F, Cl, Br, I) have been investigated by density functional theory at the levels of the relativistic Zero Order Regular Approximation and the relativistic energy-consistent pseudopotentials, using frozen small- and medium-cores. The calculated bond lengths and vibrational frequencies are close to the experimental data. Our calculations indicate 4f shell contributions to bonding in LnX{sub 4}, in particular for the early lanthanides, which show significant overlap between the Ln 4f-shell and the halogen np-shells. The 4f shells contribute to Ln-X bonding in LnX{sub 4} about one third more thanmore » in LnX{sub 3}.« less

Spectroscopic Observation of Water-Mediated Deformation of the CARBOXYLATE-M2+ (M= Mg, Ca) Contact Ion Pair

NASA Astrophysics Data System (ADS)

Kelleher, Patrick J.; DePalma, Joseph W.; Johnson, Mark

2016-06-01

The binding of alkaline earth dications to the biologically relevant carboxylate ligand has previously been studied using vibrational sum frequency generation (VSFG) spectroscopy of the air-water interface, infrared multiple photon dissociation (IRMPD) spectroscopy of clusters, and DFT methods. These results suggest the presence of both monodentate and bidentate binding motifs of the M2+ ions to the cayboxyl head groups depending on the extent of solvation. We revisit these systems using vibrational predissociation spectroscopy to measure the gas-phase vibrational spectra of the D2-tagged microhydrated [MgOAc(H2O)n=1-5]+ and [CaOAc(H2O)n=1-6]+ clusters. The spectra show that [MgOAc(H2O)n]+ switches from bidentate to monodentate binding promptly at n = 5, while [CaOAc(H2O)n]+ retains its bidentate attachment such that the sixth water molecule initiates the second solvation shell. The difference in binding behavior between these two divalent metal ions is analyzed in the context of the local acidity of the solvent water molecules and the strength of the metal-carboxylate and metal-water interactions. This cluster study provides insight into the chemical physics underlying the unique and surprising impacts of Mg2+ and Ca2+ on the chemistry mediated by sea spray aerosols. Funding for this work was provided by the NSF's Center for Aerosol Impacts on Climate and the Environment.

Gastropod shell size and architecture influence the applicability of methods used to estimate internal volume.

PubMed

Ragagnin, Marilia Nagata; Gorman, Daniel; McCarthy, Ian Donald; Sant'Anna, Bruno Sampaio; de Castro, Cláudio Campi; Turra, Alexander

2018-01-11

Obtaining accurate and reproducible estimates of internal shell volume is a vital requirement for studies into the ecology of a range of shell-occupying organisms, including hermit crabs. Shell internal volume is usually estimated by filling the shell cavity with water or sand, however, there has been no systematic assessment of the reliability of these methods and moreover no comparison with modern alternatives, e.g., computed tomography (CT). This study undertakes the first assessment of the measurement reproducibility of three contrasting approaches across a spectrum of shell architectures and sizes. While our results suggested a certain level of variability inherent for all methods, we conclude that a single measure using sand/water is likely to be sufficient for the majority of studies. However, care must be taken as precision may decline with increasing shell size and structural complexity. CT provided less variation between repeat measures but volume estimates were consistently lower compared to sand/water and will need methodological improvements before it can be used as an alternative. CT indicated volume may be also underestimated using sand/water due to the presence of air spaces visible in filled shells scanned by CT. Lastly, we encourage authors to clearly describe how volume estimates were obtained.

Synthesis and spectroscopic properties of silica-dye-semiconductor nanocrystal hybrid particles.

PubMed

Ren, Ting; Erker, Wolfgang; Basché, Thomas; Schärtl, Wolfgang

2010-12-07

We prepared silica-dye-nanocrystal hybrid particles and studied the energy transfer from semiconductor nanocrystals (= donor) to organic dye molecules (= acceptor). Multishell CdSe/CdS/ZnS semiconductor nanocrystals were adsorbed onto monodisperse Stöber silica particles with an outer silica shell of thickness 2-23 nm containing organic dye molecules (Texas Red). The thickness of this dye layer has a strong effect on the energy transfer efficiency, which is explained by the increase in the number of dye molecules homogeneously distributed within the silica shell, in combination with an enhanced surface adsorption of nanocrystals with increasing dye amount. Our conclusions were underlined by comparison of the experimental results with numerically calculated FRET efficiencies and by control experiments confirming attractive interaction between the nanocrystals and Texas Red freely dissolved in solution.

A Facile Strategy for In Situ Core-Template-Functionalizing Siliceous Hollow Nanospheres for Guest Species Entrapment

PubMed Central

2009-01-01

The shell wall-functionalized siliceous hollow nanospheres (SHNs) with functional molecules represent an important class of nanocarriers for a rich range of potential applications. Herein, a self-templated approach has been developed for the synthesis of in situ functionalized SHNs, in which the biocompatible long-chain polycarboxylates (i.e., polyacrylate, polyaspartate, gelatin) provide the framework for silica precursor deposition by simply controlling chain conformation with divalent metal ions (i.e., Ca2+, Sr2+), without the intervention of any external templates. Metal ions play crucial roles in the formation of organic vesicle templates by modulating the long chains of polymers and preventing them from separation by washing process. We also show that, by in situ functionalizing the shell wall of SHNs, it is capable of entrapping nearly an eightfold quantity of vitamin Bc in comparison to the bare bulk silica nanospheres. These results confirm the feasibility of guest species entrapment in the functionalized shell wall, and SHNs are effective carriers of guest (bio-)molecules potentially for a variety of biomedical applications. By rationally choosing the functional (self-templating) molecules, this concept may represent a general strategy for the production of functionalized silica hollow structures. PMID:20596316

Solvation of carbonaceous molecules by para-H{sub 2} and ortho-D{sub 2} clusters. I. Polycyclic aromatic hydrocarbons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Calvo, F., E-mail: florent.calvo@univ-grenoble-alpes.fr; Yurtsever, E.

This work theoretically examines the progressive coating of planar polycyclic aromatic hydrocarbon (PAH) molecules ranging from benzene to circumcoronene (C{sub 54}H{sub 18}) by para-hydrogen and ortho-deuterium. The coarse-grained Silvera-Goldman potential has been extended to model the interactions between hydrogen molecules and individual atoms of the PAH and parametrized against quantum chemical calculations for benzene-H{sub 2}. Path-integral molecular dynamics simulations at 2 K were performed for increasingly large amounts of hydrogen coating the PAH up to the first solvation shell and beyond. From the simulations, various properties were determined such as the size of the first shell and its thickness asmore » well as the solvation energy. The degree of delocalization was notably quantified from an energy landscape perspective, by monitoring the fluctuations among inherent structures sampled by the trajectories. Our results generally demonstrate a high degree of localization owing to relatively strong interactions between hydrogen and the PAH, and qualitatively minor isotopic effects. In the limit of large hydrogen amounts, the shell size and solvation energy both follow approximate linear relations with the numbers of carbon and hydrogen in the PAH.« less

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. I. Polycyclic aromatic hydrocarbons.

PubMed

Calvo, F; Yurtsever, E

2016-06-14

This work theoretically examines the progressive coating of planar polycyclic aromatic hydrocarbon (PAH) molecules ranging from benzene to circumcoronene (C54H18) by para-hydrogen and ortho-deuterium. The coarse-grained Silvera-Goldman potential has been extended to model the interactions between hydrogen molecules and individual atoms of the PAH and parametrized against quantum chemical calculations for benzene-H2. Path-integral molecular dynamics simulations at 2 K were performed for increasingly large amounts of hydrogen coating the PAH up to the first solvation shell and beyond. From the simulations, various properties were determined such as the size of the first shell and its thickness as well as the solvation energy. The degree of delocalization was notably quantified from an energy landscape perspective, by monitoring the fluctuations among inherent structures sampled by the trajectories. Our results generally demonstrate a high degree of localization owing to relatively strong interactions between hydrogen and the PAH, and qualitatively minor isotopic effects. In the limit of large hydrogen amounts, the shell size and solvation energy both follow approximate linear relations with the numbers of carbon and hydrogen in the PAH.

Detection of MgCn in IRC + 10216: A new metal-bearing free radical

NASA Technical Reports Server (NTRS)

Ziurys, L. M.; Apponi, A. J.; Guelin, M.; Cernicharo, J.

1995-01-01

A new metal-containing molecule, MgCN, has been detected toward the late-type star IRC + 10216, using the NRAO 12 m and IRAM 30 m telescopes. The N = 11 approaches 10, 10 approaches 9, and 9 approaches 8 transtions of this species which has a (sup 2)Sigma(sup +) ground state, have been observed in the outer envelope of this object at 3 mm. For the N = 11 approaches 10 transitions, the two spin-rotation components are clearly resolved and conclusively identify this new radical. These measurements imply a column of density for MgCN of N(sub tot) approximately 10(exp 12)/sq cm in the outer shell, which corresponds to a fractional abundance of f approximately 7x10(exp -10). This molecule, the metastable isomer of MgNC, is the third metal-bearing species thus far identified in the outer shell of IRC + 10216, and its detection implies a ratio of MgNC/MgCN approximately 22/1. MgCN may be formed through a reaction scheme involving magnesium and HNC or CN, both prominent outer shell molecules, or through synthesis on grains.

Core-shell microspheres with porous nanostructured shells for liquid chromatography.

PubMed

Ahmed, Adham; Skinley, Kevin; Herodotou, Stephanie; Zhang, Haifei

2018-01-01

The development of new stationary phases has been the key aspect for fast and efficient high-performance liquid chromatography separation with relatively low backpressure. Core-shell particles, with a solid core and porous shell, have been extensively investigated and commercially manufactured in the last decade. The excellent performance of core-shell particles columns has been recorded for a wide range of analytes, covering small and large molecules, neutral and ionic (acidic and basic), biomolecules and metabolites. In this review, we first introduce the advance and advantages of core-shell particles (or more widely known as superficially porous particles) against non-porous particles and fully porous particles. This is followed by the detailed description of various methods used to fabricate core-shell particles. We then discuss the applications of common silica core-shell particles (mostly commercially manufactured), spheres-on-sphere particles and core-shell particles with a non-silica shell. This review concludes with a summary and perspective on the development of stationary phase materials for high-performance liquid chromatography applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Composition Formulas of Inorganic Compounds in Terms of Cluster Plus Glue Atom Model.

PubMed

Ma, Yanping; Dong, Dandan; Wu, Aimin; Dong, Chuang

2018-01-16

The present paper attempts to identify the molecule-like structural units in inorganic compounds, by applying the so-called "cluster plus glue atom model". This model, originating from metallic glasses and quasi-crystals, describes any structure in terms of a nearest-neighbor cluster and a few outer-shell glue atoms, expressed in the cluster formula [cluster](glue atoms). Similar to the case for normal molecules where the charge transfer occurs within the molecule to meet the commonly known octet electron rule, the octet state is reached after matching the nearest-neighbor cluster with certain outer-shell glue atoms. These kinds of structural units contain information on local atomic configuration, chemical composition, and electron numbers, just as for normal molecules. It is shown that the formulas of typical inorganic compounds, such as fluorides, oxides, and nitrides, satisfy a similar octet electron rule, with the total number of valence electrons per unit formula being multiples of eight.

Thin silica shell coated Ag assembled nanostructures for expanding generality of SERS analytes

PubMed Central

Kang, Yoo-Lee; Lee, Minwoo; Kang, Homan; Kim, Jaehi; Pham, Xuan-Hung; Kim, Tae Han; Hahm, Eunil; Lee, Yoon-Sik; Jeong, Dae Hong

2017-01-01

Surface-enhanced Raman scattering (SERS) provides a unique non-destructive spectroscopic fingerprint for chemical detection. However, intrinsic differences in affinity of analyte molecules to metal surface hinder SERS as a universal quantitative detection tool for various analyte molecules simultaneously. This must be overcome while keeping close proximity of analyte molecules to the metal surface. Moreover, assembled metal nanoparticles (NPs) structures might be beneficial for sensitive and reliable detection of chemicals than single NP structures. For this purpose, here we introduce thin silica-coated and assembled Ag NPs (SiO2@Ag@SiO2 NPs) for simultaneous and quantitative detection of chemicals that have different intrinsic affinities to silver metal. These SiO2@Ag@SiO2 NPs could detect each SERS peak of aniline or 4-aminothiophenol (4-ATP) from the mixture with limits of detection (LOD) of 93 ppm and 54 ppb, respectively. E-field distribution based on interparticle distance was simulated using discrete dipole approximation (DDA) calculation to gain insight into enhanced scattering of these thin silica coated Ag NP assemblies. These NPs were successfully applied to detect aniline in river water and tap water. Results suggest that SiO2@Ag@SiO2 NP-based SERS detection systems can be used as a simple and universal detection tool for environment pollutants and food safety. PMID:28570633

Predicting performance of almonds shells for cleanup of almond soil fumigants from potable water.

USDA-ARS?s Scientific Manuscript database

Almond shell strength and bulk density were determined to differ significantly among almond varieties, and further research demonstrated that granular activated carbons (GAC) produced from shells of different varieties had similar abilities to adsorb DBCP from contaminated water. As an extension of...

Inactivation of salmonella in shell eggs by hot water immersion and its effect on quality

USDA-ARS?s Scientific Manuscript database

Thermal inactivation kinetics of heat resistant strains of Salmonella Enteritidis in shell eggs processed by hot water immersion were determined, and the effects of the processing on egg quality were evaluated. Shell eggs were inoculated with a composite of heat resistant Salmonella Enteritidis (SE)...

Growth history of cultured pearl oysters based on stable oxygen isotope analysis

NASA Astrophysics Data System (ADS)

Nakashima, R.; Furuta, N.; Suzuki, A.; Kawahata, H.; Shikazono, N.

2007-12-01

We investigated the oxygen isotopic ratio in shells of the pearl oyster Pinctada martensii cultivated in embayments in Mie Prefecture, central Japan, to evaluate the biomineralization of shell structures of the species and its pearls in response to environmental change. Microsamples for oxygen isotope analysis were collected from the surfaces of shells (outer, middle, and inner shell layers) and pearls. Water temperature variations were estimated from the oxygen isotope values of the carbonate. Oxygen isotope profiles of the prismatic calcite of the outer shell layer reflected seasonal variations of water temperature, whereas those of nacreous aragonites of the middle and inner shell layers and pearls recorded temperatures from April to November, June to September, and July to September, respectively. Lower temperatures in autumn and winter might slow the growth of nacreous aragonites. The oxygen isotope values are controlled by both variations of water temperature and shell structures; the prismatic calcite of this species is useful for reconstructing seasonal changes of calcification temperature.

Factors affecting the yield of bio-oil from the pyrolysis of coconut shell.

PubMed

Gao, Yun; Yang, Yi; Qin, Zhanbin; Sun, Yi

2016-01-01

Coconut is a high-quality agricultural product of the Asia-Pacific region. In this paper, coconut shell which mainly composed of cellulose, hemicellulose, lignin was used as a raw material for coconut shell oil from coconut shell pyrolysis. The influence of the pyrolysis temperature, heating rate and particle size on coconut oil yield was investigated, and the effect of heating rate on coconut oil components was discussed. Experimental results show that the maximum oil yield of 75.74 wt% (including water) were obtained under the conditions that the final pyrolysis temperature 575 °C, heating rate 20 °C/min, coconut shell diameter about 5 mm. Thermal gravimetric analysis was used and it can be seen that coconut shell pyrolysis process can be divided into three stages: water loss, pyrolysis and pyrocondensation. The main components of coconut-shell oil are water (about 50 wt%), aromatic, phenolic, acid, ketone and ether containing compounds.

Sonoluminescence in an Acoustically Levitated Water Filled Shell

NASA Astrophysics Data System (ADS)

Rivera, P. J.; Stephens, R. B.; Jones, J. P.

1998-11-01

The possibility of using shells levitated by acoustic waves to improve the conditions to study sonoluminescence was conducted. Single bubble sonoluminescence (SBSL) was generated using a 2 mm diameter water filled plastic shell, supported in air with 1 MHz sound waves. The bubble was generated and compressed with a separate transducer emitting pulsed 5 MHz acoustic waves which were focussed on the center of the suspended shell. This approach is considerably different from the typical generation technique of SBSL in that the acoustic power is coupled through the air rather than by a solid bond to the container. With this configuration, the water container can be substantially reduced in size and the luminescence pulse rate is probably not connected with cavity resonances. As a result, optical access to the spark is improved, water attenuation is reduced (water thickness ~1 mm), and repetition rate can be considerably higher. This geometry presents problems and opportunities in controlling the gas content and temperature of the water. It might also be sensitive to the perfection of the enclosing plastic shell, so success is erratic. Details will be discussed.

Effects of Soil Water Deficit on Insecticidal Protein Expression in Boll Shells of Transgenic Bt Cotton and the Mechanism.

PubMed

Zhang, Xiang; Wang, Jian; Peng, Sheng; Li, Yuan; Tian, Xiaofeng; Wang, Guangcheng; Zhang, Zhongning; Dong, Zhaodi; Chen, Yuan; Chen, Dehua

2017-01-01

This study was conducted to investigate the effects of soil water deficit on insecticidal protein expression in boll shells of cotton transgenic for a Bt gene. In 2014, Bt cotton cultivars Sikang 1 (a conventional cultivar) and Sikang 3 (a hybrid cultivar) were planted in pots and five soil water content treatments were imposed at peak boll stage: 15% (G1), 35% (G2), 40% (G3), 60% (G4), and 75% field capacity (CK), respectively. Four treatments (G2, G3, G4, and CK) were repeated in 2015 in the field. Results showed that the insecticidal protein content of boll shells decreased with increasing water deficit. Compared with CK, boll shell insecticidal protein content decreased significantly when soil water content was below 60% of maximum water holding capacity for Sikang 1 and Sikang 3. However, increased Bt gene expression was observed when boll shell insecticidal protein content was significantly reduced. Activity assays of key enzymes in nitrogen metabolism showed that boll shell protease and peptidase increased but nitrogen reductase and glutamic-pyruvic transaminase (GPT) decreased. Insecticidal protein content exhibited significant positive correlation with nitrogen reductase and GPT activities; and significant negative correlation with protease and peptidase activities. These findings suggest that the decrease of insecticidal protein content associated with increasing water deficit was a net result of decreased synthesis and increased decomposition.

On the microscopic fluctuations driving the NMR relaxation of quadrupolar ions in water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carof, Antoine; Salanne, Mathieu; Rotenberg, Benjamin, E-mail: benjamin.rotenberg@upmc.fr

Nuclear Magnetic Resonance (NMR) relaxation is sensitive to the local structure and dynamics around the probed nuclei. The Electric Field Gradient (EFG) is the key microscopic quantity to understand the NMR relaxation of quadrupolar ions, such as {sup 7}Li{sup +}, {sup 23}Na{sup +}, {sup 25}Mg{sup 2+}, {sup 35}Cl{sup −}, {sup 39}K{sup +}, or {sup 133}Cs{sup +}. Using molecular dynamics simulations, we investigate the statistical and dynamical properties of the EFG experienced by alkaline, alkaline Earth, and chloride ions at infinite dilution in water. Specifically, we analyze the effect of the ionic charge and size on the distribution of the EFGmore » tensor and on the multi-step decay of its auto-correlation function. The main contribution to the NMR relaxation time arises from the slowest mode, with a characteristic time on the picosecond time scale. The first solvation shell of the ion plays a dominant role in the fluctuations of the EFG, all the more that the ion radius is small and its charge is large. We propose an analysis based on a simplified charge distribution around the ion, which demonstrates that the auto-correlation of the EFG, hence the NMR relaxation time, reflects primarily the collective translational motion of water molecules in the first solvation shell of the cations. Our findings provide a microscopic route to the quantitative interpretation of NMR relaxation measurements and open the way to the design of improved analytical theories for NMR relaxation for small ionic solutes, which should focus on water density fluctuations around the ion.« less

Gold core@silver semishell Janus nanoparticles prepared by interfacial etching

NASA Astrophysics Data System (ADS)

Chen, Limei; Deming, Christopher P.; Peng, Yi; Hu, Peiguang; Stofan, Jake; Chen, Shaowei

2016-07-01

Gold core@silver semishell Janus nanoparticles were prepared by chemical etching of Au@Ag core-shell nanoparticles at the air/water interface. Au@Ag core-shell nanoparticles were synthesized by chemical deposition of a silver shell onto gold seed colloids followed by the self-assembly of 1-dodecanethiol onto the nanoparticle surface. The nanoparticles then formed a monolayer on the water surface of a Langmuir-Blodgett trough, and part of the silver shell was selectively etched away by the mixture of hydrogen peroxide and ammonia in the water subphase, where the etching was limited to the side of the nanoparticles that was in direct contact with water. The resulting Janus nanoparticles exhibited an asymmetrical distribution of silver on the surface of the gold cores, as manifested in transmission electron microscopy, UV-vis absorption, and X-ray photoelectron spectroscopy measurements. Interestingly, the Au@Ag semishell Janus nanoparticles exhibited enhanced electrocatalytic activity in oxygen reduction reactions, as compared to their Au@Ag and Ag@Au core-shell counterparts, likely due to a synergistic effect between the gold cores and silver semishells that optimized oxygen binding to the nanoparticle surface.Gold core@silver semishell Janus nanoparticles were prepared by chemical etching of Au@Ag core-shell nanoparticles at the air/water interface. Au@Ag core-shell nanoparticles were synthesized by chemical deposition of a silver shell onto gold seed colloids followed by the self-assembly of 1-dodecanethiol onto the nanoparticle surface. The nanoparticles then formed a monolayer on the water surface of a Langmuir-Blodgett trough, and part of the silver shell was selectively etched away by the mixture of hydrogen peroxide and ammonia in the water subphase, where the etching was limited to the side of the nanoparticles that was in direct contact with water. The resulting Janus nanoparticles exhibited an asymmetrical distribution of silver on the surface of the gold cores, as manifested in transmission electron microscopy, UV-vis absorption, and X-ray photoelectron spectroscopy measurements. Interestingly, the Au@Ag semishell Janus nanoparticles exhibited enhanced electrocatalytic activity in oxygen reduction reactions, as compared to their Au@Ag and Ag@Au core-shell counterparts, likely due to a synergistic effect between the gold cores and silver semishells that optimized oxygen binding to the nanoparticle surface. Electronic supplementary information (ESI) available: Additional TEM, UV-vis, XPS, and electrochemical data. See DOI: 10.1039/c6nr03368g

Staged depressurization system

DOEpatents

Schulz, T.L.

1993-11-02

A nuclear reactor having a reactor vessel disposed in a containment shell is depressurized in stages using depressurizer valves coupled in fluid communication with the coolant circuit. At least one sparger submerged in the in-containment refueling water storage tank which can be drained into the containment sump communicates between one or more of the valves and an inside of the containment shell. The depressurizer valves are opened in stages, preferably at progressively lower coolant levels and for opening progressively larger flowpaths to effect depressurization through a number of the valves in parallel. The valves can be associated with a pressurizer tank in the containment shell, coupled to a coolant outlet of the reactor. At least one depressurization valve stage openable at a lowest pressure is coupled directly between the coolant circuit and the containment shell. The reactor is disposed in the open sump in the containment shell, and a further valve couples the open sump to a conduit coupling the refueling water storage tank to the coolant circuit for adding water to the coolant circuit, whereby water in the containment shell can be added to the reactor from the open sump. 4 figures.

Staged depressurization system

DOEpatents

Schulz, Terry L.

1993-01-01

A nuclear reactor having a reactor vessel disposed in a containment shell is depressurized in stages using depressurizer valves coupled in fluid communication with the coolant circuit. At least one sparger submerged in the in-containment refueling water storage tank which can be drained into the containment sump communicates between one or more of the valves and an inside of the containment shell. The depressurizer valves are opened in stages, preferably at progressively lower coolant levels and for opening progressively larger flowpaths to effect depressurization through a number of the valves in parallel. The valves can be associated with a pressurizer tank in the containment shell, coupled to a coolant outlet of the reactor. At least one depressurization valve stage openable at a lowest pressure is coupled directly between the coolant circuit and the containment shell. The reactor is disposed in the open sump in the containment shell, and a further valve couples the open sump to a conduit coupling the refueling water storage tank to the coolant circuit for adding water to the coolant circuit, whereby water in the containment shell can be added to the reactor from the open sump.

Characterizing hydrophobicity at the nanoscale: a molecular dynamics simulation study.

PubMed

Bandyopadhyay, Dibyendu; Choudhury, Niharendu

2012-06-14

We use molecular dynamics (MD) simulations of water near nanoscopic surfaces to characterize hydrophobic solute-water interfaces. By using nanoscopic paraffin like plates as model solutes, MD simulations in isothermal-isobaric ensemble have been employed to identify characteristic features of such an interface. Enhanced water correlation, density fluctuations, and position dependent compressibility apart from surface specific hydrogen bond distribution and molecular orientations have been identified as characteristic features of such interfaces. Tetrahedral order parameter that quantifies the degree of tetrahedrality in the water structure and an orientational order parameter, which quantifies the orientational preferences of the second solvation shell water around a central water molecule, have also been calculated as a function of distance from the plate surface. In the vicinity of the surface these two order parameters too show considerable sensitivity to the surface hydrophobicity. The potential of mean force (PMF) between water and the surface as a function of the distance from the surface has also been analyzed in terms of direct interaction and induced contribution, which shows unusual effect of plate hydrophobicity on the solvent induced PMF. In order to investigate hydrophobic nature of these plates, we have also investigated interplate dewetting when two such plates are immersed in water.

Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade

NASA Astrophysics Data System (ADS)

Samanta, Sudipta; Mukherjee, Sanchita

2018-01-01

The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.

Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade.

PubMed

Samanta, Sudipta; Mukherjee, Sanchita

2018-01-28

The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.

Outer organic layer and internal repair mechanism protects pteropod Limacina helicina from ocean acidification

NASA Astrophysics Data System (ADS)

Peck, Victoria L.; Tarling, Geraint A.; Manno, Clara; Harper, Elizabeth M.; Tynan, Eithne

2016-05-01

Scarred shells of polar pteropod Limacina helicina collected from the Greenland Sea in June 2012 reveal a history of damage, most likely failed predation, in earlier life stages. Evidence of shell fracture and subsequent re-growth is commonly observed in specimens recovered from the sub-Arctic and further afield. However, at one site within sea-ice on the Greenland shelf, shells that had been subject to mechanical damage were also found to exhibit considerable dissolution. It was evident that shell dissolution was localised to areas where the organic, periostracal sheet that covers the outer shell had been damaged at some earlier stage during the animal's life. Where the periostracum remained intact, the shell appeared pristine with no sign of dissolution. Specimens which appeared to be pristine following collection were incubated for four days. Scarring of shells that received periostracal damage during collection only became evident in specimens that were incubated in waters undersaturated with respect to aragonite, ΩAr≤1. While the waters from which the damaged specimens were collected at the Greenland Sea sea-ice margin were not ΩAr≤1, the water column did exhibit the lowest ΩAr values observed in the Greenland and Barents Seas, and was likely to have approached ΩAr≤1 during the winter months. We demonstrate that L. helicina shells are only susceptible to dissolution where both the periostracum has been breached and the aragonite beneath the breach is exposed to waters of ΩAr≤1. Exposure of multiple layers of aragonite in areas of deep dissolution indicate that, as with many molluscs, L. helicina is able to patch up dissolution damage to the shell by secreting additional aragonite internally and maintain their shell. We conclude that, unless breached, the periostracum provides an effective shield for pteropod shells against dissolution in waters ΩAr≤1, and when dissolution does occur the animal has an effective means of self-repair. We suggest that future studies of pteropod shell condition are undertaken on specimens from which the periostracum has not been removed in preparation.

Water Mediated Ligand Functional Group Cooperativity: The Contribution of a Methyl Group to Binding Affinity is Enhanced by a COO− Group Through Changes in the Structure and Thermo dynamics of the Hydration Waters of Ligand-Thermolysin Complexes

PubMed Central

Nasief, Nader N; Tan, Hongwei; Kong, Jing; Hangauer, David

2012-01-01

Ligand functional groups can modulate the contributions of one another to the ligand-protein binding thermodynamics, producing either positive or negative cooperativity. Data presented for four thermolysin phosphonamidate inhibitors demonstrate that the differential binding free energy and enthalpy caused by replacement of a H with a Me group, which binds in the well-hydrated S2′ pocket, are more favorable in presence of a ligand carboxylate. The differential entropy is however less favorable. Dissection of these differential thermodynamic parameters, X-ray crystallography, and density-functional theory calculations suggest that these cooperativities are caused by variations in the thermodynamics of the complex hydration shell changes accompanying the H→Me replacement. Specifically, the COO− reduces both the enthalpic penalty and the entropic advantage of displacing water molecules from the S2′ pocket, and causes a subsequent acquisition of a more enthalpically, less entropically, favorable water network. This study contributes to understanding the important role water plays in ligand-protein binding. PMID:22894131

The influence of polarizability and charge transfer on specific ion effects in the dynamics of aqueous salt solutions

NASA Astrophysics Data System (ADS)

Nguyen, Mary; Rick, Steven W.

2018-06-01

The diffusion rates for water molecules in salt solutions depend on the identity of the ions, as well as their concentration. Among the alkali metal ions, cesium and potassium increase and sodium strongly decreases the diffusion constant of water. The origin of the difference can be understood by examining the simulation results using different potential models. In this work, aqueous solutions of salts are simulated with a variety of models. Commonly used non-polarizable models, which otherwise reproduce many experimental properties, do not capture the trend in the diffusion constant, while models which include polarization and/or charge transfer interactions do. For the non-polarizable models, the diffusion constant decreases too strongly with salt concentration. The changes in the water diffusion constant with increasing salt concentration match the diffusion constant of the ion. The ion diffusion constant is dependent on the residence time for water in the ion solvation shell. The non-polarizable models over-estimate the residence time, relative to the translational diffusion constant and so tend to under-estimate the ion and water diffusion constants.

Shell architecture: a novel proxy for paleotemperature reconstructions?

NASA Astrophysics Data System (ADS)

Milano, Stefania; Nehrke, Gernot; Wanamaker, Alan D., Jr.; Witbaard, Rob; Schöne, Bernd R.

2017-04-01

Mollusk shells are unique high-resolution paleoenvironmental archives. Their geochemical properties, such as oxygen isotope composition (δ18Oshell) and element-to-calcium ratios, are routinely used to estimate past environmental conditions. However, the existing proxies have certain drawbacks that can affect paleoreconstruction robustness. For instance, the estimation of water temperature of brackish and near-shore environments can be biased by the interdependency of δ18Oshell from multiple environmental variables (water temperature and δ18Owater). Likely, the environmental signature can be masked by physiological processes responsible for the incorporation of trace elements into the shell. The present study evaluated the use of shell structural properties as alternative environmental proxies. The sensitivity of shell architecture at µm and nm-scale to the environment was tested. In particular, the relationship between water temperature and microstructure formation was investigated. To enable the detection of potential structural changes, the shells of the marine bivalves Cerastoderma edule and Arctica islandica were analyzed with Scanning Electron Microscopy (SEM), nanoindentation and Confocal Raman Microscopy (CRM). These techniques allow a quantitative approach to the microstructural analysis. Our results show that water temperature induces a clear response in shell microstructure. A significant alteration in the morphometric characteristics and crystallographic orientation of the structural units was observed. Our pilot study suggests that shell architecture records environmental information and it has potential to be used as novel temperature proxy in near-shore and open ocean habitats.

Fabrication of PLA/CaCO3 hybrid micro-particles as carriers for water-soluble bioactive molecules.

PubMed

Kudryavtseva, Valeriya L; Zhao, Li; Tverdokhlebov, Sergei I; Sukhorukov, Gleb B

2017-09-01

We propose the use of polylactic acid/calcium carbonate (PLA/CaCO 3 ) hybrid micro-particles for achieving improved encapsulation of water-soluble substances. Biodegradable porous CaCO 3 microparticles can be loaded with wide range of bioactive substance. Thus, the formation of hydrophobic polymeric shell on surface of these loaded microparticles results on encapsulation and, hence, sealing internal cargo and preventing their release in aqueous media. In this study, to encapsulate proteins, we explore the solid-in-oil-in-water emulsion method for fabricating core/shell PLA/CaCO 3 systems. We used CaCO 3 particles as a protective core for encapsulated bovine serum albumin, which served as a model protein system. We prepared a PLA coating using dichloromethane as an organic solvent and polyvinyl alcohol as a surfactant for emulsification; in addition, we varied experimental parameters such as surfactant concentration and polymer-to-CaCO 3 ratio to determine their effect on particle-size distribution, encapsulation efficiency and capsule permeability. The results show that the particle size decreased and the size distribution narrowed as the surfactant concentration increased in the external aqueous phase. In addition, when the CaCO 3 /PLA mass ratio dropped below 0.8, the hybrid micro-particles were more likely to resist treatment by ethylenediaminetetraacetic acid and thus retained their bioactive cargos within the polymer-coated micro-particles. Copyright © 2017 Elsevier B.V. All rights reserved.

Ecology and shell chemistry of Loxoconcha matagordensis

USGS Publications Warehouse

Cronin, T. M.; Kamiya, T.; Dwyer, G.S.; Belkin, H.; Vann, C.D.; Schwede, S.; Wagner, R.

2005-01-01

Studies of the seasonal ecology and shell chemistry of the ostracode Loxoconcha matagordensis and related species of Loxoconcha from regions off eastern North America reveal that shell size and trace elemental (Mg/Ca ratio) composition are useful in paleothermometry using fossil populations. Seasonal sampling of populations from Chesapeake Bay, augmented by samples from Florida Bay, indicate that shell size is inversely proportional to water temperature and that Mg/Ca ratios are positively correlated with the water temperature in which the adult carapace was secreted. Microprobe analyses of sectioned valves reveal intra-shell variability in Mg/Ca ratios but this does not strongly influence the utility of whole shell Mg/Ca analyses for paleoclimate application.

Synthesis, characterization and evaluation of uniformly sized core-shell imprinted microspheres for the separation trans-resveratrol from giant knotweed

NASA Astrophysics Data System (ADS)

Zhang, Zhaohui; Liu, Li; Li, Hui; Yao, Shouzhuo

2009-09-01

A novel core-shell molecularly imprinting microspheres (MIMs) with trans-resveratrol as the template molecule; acrylamide (AA) as functional monomer and ethylene glycol dimethacrylate (EGDMA) as cross-linker, was prepared based on SiO 2 microspheres with surface imprinting technique. These core-shell trans-resveratrol imprinted microspheres were characterized by infrared spectra (IR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and high performance liquid chromatography (HPLC). The results showed that these core-shell imprinted microspheres, which take on perfect spherical shape with average shell thickness of 150 nm, exhibit especially selective recognition for trans-resveratrol. These imprinted microspheres were applied as solid-phase extraction materials for selective extraction of trans-resveratrol from giant knotweed extracting solution successfully.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohanta, Dayanidhi; Jana, Madhurima, E-mail: janam@nitrkl.ac.in

A series of atomistic molecular dynamics (MD) simulations of a small enzymatic protein Chymotrypsin Inhibitor 2 (CI2) in water-ethanol mixed solutions were carried out to explore the underlying mechanism of ethanol driven conformational changes of the protein. Efforts have been made to probe the influence of ethanol concentrations ranging from 0% to 75% (v/v) at ambient condition (300 K (T1)) and at elevated temperatures (375 K (T2) and 450 K (T3)) to investigate the temperature induced conformational changes of the protein further. Our study showed that the effect of varying ethanol concentrations on protein’s structure is almost insignificant at T1more » and T2 temperatures whereas at T3 temperature, partial unfolding of CI2 in 10% ethanol solution followed by full unfolding of the protein at ethanol concentrations above 25% occurs. However, interestingly, at T3 temperature CI2’s native structure was found to be retained in pure water (0% ethanol solution) indicating that the cosolvent ethanol do play an important role in thermal denaturation of CI2. Such observations were quantified in the light of root-mean-square deviations (RMSDs) and radius of gyration. Although higher RMSD values of β-sheet over α-helix indicate complete destruction of the β-structure of CI2 at high ethanol concentrations, the associated time scale showed that the faster melting of α-helix happens over β-sheet. Around 60%-80% of initial native contacts of the protein were found broken with the separation of hydrophobic core consisting eleven residues at ethanol concentrations greater than 25%. This leads protein to expand with the increase in solvent accessible surface area. The interactions between protein and solvent molecules showed that protein’s solvation shell preferred to accommodate ethanol molecules as compared to water thereby excluded water molecules from CI2’s surface. Further, concentration dependent differential self-aggregation behavior of ethanol is likely to regulate the replacement of relatively fast diffused water by low diffused ethanol molecules from protein’s surface during the unfolding process.« less

Aspects of Weak Interactions between Folate and Glycine Betaine

PubMed Central

2016-01-01

Folate, or vitamin B9, is an important compound in one-carbon metabolism. Previous studies have found weaker binding of dihydrofolate to dihydrofolate reductase in the presence of osmolytes. In other words, osmolytes are more difficult to remove from the dihydrofolate solvation shell than water; this shifts the equilibrium toward the free ligand and protein species. This study uses vapor-pressure osmometry to explore the interaction of folate with the model osmolyte, glycine betaine. This method yields a preferential interaction potential (μ23/RT value). This value is concentration-dependent as folate dimerizes. The μ23/RT value also tracks the deprotonation of folate’s N3–O4 keto–enol group, yielding a pKa of 8.1. To determine which folate atoms interact most strongly with betaine, the interaction of heterocyclic aromatic compounds (as well as other small molecules) with betaine was monitored. Using an accessible surface area approach coupled with osmometry measurements, deconvolution of the μ23/RT values into α values for atom types was achieved. This allows prediction of μ23/RT values for larger molecules such as folate. Molecular dynamics simulations of folate show a variety of structures from extended to L-shaped. These conformers possess μ23/RT values from −0.18 to 0.09 m–1, where a negative value indicates a preference for solvation by betaine and a positive value indicates a preference for water. This range of values is consistent with values observed in osmometry and solubility experiments. As the average predicted folate μ23/RT value is near zero, this indicates folate interacts almost equally well with betaine and water. Specifically, the glutamate tail prefers to interact with water, while the aromatic rings prefer betaine. In general, the more protonated species in our small molecule survey interact better with betaine as they provide a source of hydrogens (betaine is not a hydrogen bond donor). Upon deprotonation of the small molecule, the preference swings toward water interaction because of its hydrogen bond donating capacities. PMID:27768285

Effect of ethanol concentrations on temperature driven structural changes of chymotrypsin inhibitor 2

NASA Astrophysics Data System (ADS)

Mohanta, Dayanidhi; Jana, Madhurima

2016-04-01

A series of atomistic molecular dynamics (MD) simulations of a small enzymatic protein Chymotrypsin Inhibitor 2 (CI2) in water-ethanol mixed solutions were carried out to explore the underlying mechanism of ethanol driven conformational changes of the protein. Efforts have been made to probe the influence of ethanol concentrations ranging from 0% to 75% (v/v) at ambient condition (300 K (T1)) and at elevated temperatures (375 K (T2) and 450 K (T3)) to investigate the temperature induced conformational changes of the protein further. Our study showed that the effect of varying ethanol concentrations on protein's structure is almost insignificant at T1 and T2 temperatures whereas at T3 temperature, partial unfolding of CI2 in 10% ethanol solution followed by full unfolding of the protein at ethanol concentrations above 25% occurs. However, interestingly, at T3 temperature CI2's native structure was found to be retained in pure water (0% ethanol solution) indicating that the cosolvent ethanol do play an important role in thermal denaturation of CI2. Such observations were quantified in the light of root-mean-square deviations (RMSDs) and radius of gyration. Although higher RMSD values of β-sheet over α-helix indicate complete destruction of the β-structure of CI2 at high ethanol concentrations, the associated time scale showed that the faster melting of α-helix happens over β-sheet. Around 60%-80% of initial native contacts of the protein were found broken with the separation of hydrophobic core consisting eleven residues at ethanol concentrations greater than 25%. This leads protein to expand with the increase in solvent accessible surface area. The interactions between protein and solvent molecules showed that protein's solvation shell preferred to accommodate ethanol molecules as compared to water thereby excluded water molecules from CI2's surface. Further, concentration dependent differential self-aggregation behavior of ethanol is likely to regulate the replacement of relatively fast diffused water by low diffused ethanol molecules from protein's surface during the unfolding process.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lehmann, C. S.; Picón, A.; Bostedt, C.

The availability at x-ray free electron lasers of generating two intense, femtosecond x-ray pulses with controlled time delay opens the possibility of performing time-resolved experiments for x-ray induced phenomena. We have applied this capability to molecular dynamics. In diatomic molecules composed of low-Z elements, K-shell ionization creates a core-hole state in which the main decay is an Auger process involving two electrons in the valence shell. After Auger decay, the nuclear wavepackets of the transient two-valence-hole states continue evolving on the femtosecond timescale, leading either to separated atomic ions or long-lived quasi-bound states. By using an x-ray pump and anmore » x-ray probe pulse tuned above the K-shell ionization threshold of the nitrogen molecule, we are able to observe ion dissociation in progress by measuring the time-dependent kinetic energy releases of different breakup channels. We simulated the measurements on N2 with a molecular dynamics model that accounts for K-shell ionization, Auger decay, and time evolution of the nuclear wavepackets. In addition to explaining the time-dependent feature in the measured kinetic energy release distributions from the dissociative states, the simulation also reveals the contributions of quasi-bound states.« less

Synthesis of robust water-soluble ZnS:Mn/SiO2 core/shell nanoparticles

NASA Astrophysics Data System (ADS)

Sun, Jing; Zhuang, Jiaqi; Guan, Shaowei; Yang, Wensheng

2008-04-01

Water-soluble Mn doped ZnS (ZnS:Mn) nanocrystals synthesized by using 3-mercaptopropionic acid (MPA) as stabilizer were homogeneously coated with a dense silica shell through a multi-step procedure. First, 3-mercaptopropyl triethoxy silane (MPS) was used to replace MPA on the particle surface to form a vitreophilic layer for further silica deposition under optimal experimental conditions. Then a two-step silica deposition was performed to form the final water-soluble ZnS:Mn/SiO2 core/shell nanoparticles. The as-prepared core/shell nanoparticles show little change in fluorescence intensity in a wide range of pH value.

Quantum Chemistry on Quantum Computers: A Polynomial-Time Quantum Algorithm for Constructing the Wave Functions of Open-Shell Molecules.

PubMed

Sugisaki, Kenji; Yamamoto, Satoru; Nakazawa, Shigeaki; Toyota, Kazuo; Sato, Kazunobu; Shiomi, Daisuke; Takui, Takeji

2016-08-18

Quantum computers are capable to efficiently perform full configuration interaction (FCI) calculations of atoms and molecules by using the quantum phase estimation (QPE) algorithm. Because the success probability of the QPE depends on the overlap between approximate and exact wave functions, efficient methods to prepare accurate initial guess wave functions enough to have sufficiently large overlap with the exact ones are highly desired. Here, we propose a quantum algorithm to construct the wave function consisting of one configuration state function, which is suitable for the initial guess wave function in QPE-based FCI calculations of open-shell molecules, based on the addition theorem of angular momentum. The proposed quantum algorithm enables us to prepare the wave function consisting of an exponential number of Slater determinants only by a polynomial number of quantum operations.

Water resources of the Fort Berthold Indian Reservation, west-central North Dakota

USGS Publications Warehouse

Cates, Steven W.; Macek-Rowland, Kathleen M.

1998-01-01

Water resources of the Fort Berthold Indian Reservation in west-central North Dakota occur as ground water in bedrock and buried-valley aquifers and as surface water in streams and Lake Sakakawea. The bedrock aquifers-the Fox Hills-Hell Creek, Tongue River, and Sentinel Butte store about 93 million acre-feet of water under the Reservation. The Fox Hills-Hell Creek aquifer is composed mainly of very fine to medium-grained sandstone and stores about 51 million acrefeet of water. Water levels in the aquifer declined from 1976 through 1992. The Tongue River aquifer is composed mainly of claystones and siltstones and has widely distributed pockets of sandstone or lignite layers. The aquifer stores about 24 million acre-feet of water. The Sentinel Butte aquifer is composed mainly of interbedded claystones, siltstones, shale, lignite, and sandstone and stores about 18 million acre-feet of water. Yields from the lignite beds are highly variable. Water in the aquifers was predominantly a sodium bicarbonate type. Mean dissolved solids concentrations were 1,530 milligrams per liter in water from the Fox Hills-Hell Creek aquifer, 2,110 milligrams per liter in water from the Tongue River aquifer, and 1,300 milligrams per liter in water from the Sentinel Butte aquifer. The East Fork Shell Creek, Shell Creek, White Shield, New Town, and Sanish aquifers occur within buried valleys and store about 1,414,000 acre-feet of water. The East Fork Shell Creek and Shell Creek aquifers are composed of sand and gravel lenses that are surrounded by less permeable till. Water in the East Fork Shell Creek aquifer is a sodium sulfate bicarbonate type, and water in the Shell Creek aquifer is a sodium bicarbonate sulfate type. Mean dissolved-solids concentrations were 3,220 milligrams per liter in water from the East Fork Shell Creek aquifer and 1,470 milligrams per liter in water from the Shell Creek aquifer.The White Shield aquifer is composed of very fine to coarse sand and fine to coarse gravel. Water in the aquifer varies from a sodium bicarbonate sulfate type to a mixed calcium magnesium sodium bicarbonate sulfate type. Mean dissolved-solids concentrations were 1,080 milligrams per liter in water from the eastern part of the aquifer and 1,430 milligrams per liter in water from the western part of the aquifer. Water levels in the western part of the aquifer rose during 1970-92. The New Town aquifer is composed of lenticular deposits of sand and gravel. Water in the aquifer is a calcium sodium bicarbonate sulfate type and had a mean dissolved-solids concentration of 1,390 milligrams per liter. Data indicate a close correspondence between ground-water levels and lake stage of Lake Sakakawea, implying a hydraulic connection between the aquifer and the lake.The Sanish aquifer is composed of sand, clayey sand, and thin gravels that are poorly cemented and highly permeable. Water in the aquifer is a mixed calcium magnesium bicarbonate sulfate type and had a mean dissolved-solids concentration of 1,350 milligrams per liter.Major streams on the Reservation are Bear Den Creek, Shell Creek, East Fork Shell Creek, Deepwater Creek, Moccasin Creek, and Squaw Creek. Mean streamflow for Bear Den Creek for June 1966 through September 1992 was 6.72 cubic feet per second. Mean streamflow for Shell Creek for September 1965 through September 1981 was 12.9 cubic feet per second. Streamflow measurements for East Fork Shell Creek for April 1990 through June 1991 ranged from zero to 3.65 cubic feet per second, measurements for Deepwater Creek for April 1990 through May 1991 ranged from zero to 4.28 cubic feet per second, measurements for Moccasin Creek for April 1990 through September 1992 ranged from zero to 7.07 cubic feet per second, and measurements for Squaw Creek for April 1990 through September 1992 ranged from zero to 4.22 cubic feet per second. Lake Sakakawea has a maximum surface area of 390,000 acres. The surface area is variable in relation to lake stage, which was unusually low during this study. The mean lake elevation for Lake Sakakawea for 1970-92 was 1,837.08 feet, and the mean lake elevation for 1990-92 was 1,821.14 feet.

A 100 au Wide Bipolar Rotating Shell Emanating from the HH 212 Protostellar Disk: A Disk Wind?

NASA Astrophysics Data System (ADS)

Lee, Chin-Fei; Li, Zhi-Yun; Codella, Claudio; Ho, Paul T. P.; Podio, Linda; Hirano, Naomi; Shang, Hsien; Turner, Neal J.; Zhang, Qizhou

2018-03-01

HH 212 is a Class 0 protostellar system found to host a “hamburger”-shaped dusty disk with a rotating disk atmosphere and a collimated SiO jet at a distance of ∼400 pc. Recently, a compact rotating outflow has been detected in SO and SO2 toward the center along the jet axis at ∼52 au (0.″13) resolution. Here we resolve the compact outflow into a small-scale wide-opening rotating outflow shell and a collimated jet, with the observations in the same S-bearing molecules at ∼16 au (0.″04) resolution. The collimated jet is aligned with the SiO jet, tracing the shock interactions in the jet. The wide-opening outflow shell is seen extending out from the inner disk around the SiO jet and has a width of ∼100 au. It is not only expanding away from the center, but also rotating around the jet axis. The specific angular momentum of the outflow shell is ∼40 au km s‑1. Simple modeling of the observed kinematics suggests that the rotating outflow shell can trace either a disk wind or disk material pushed away by an unseen wind from the inner disk or protostar. We also resolve the disk atmosphere in the same S-bearing molecules, confirming the Keplerian rotation there.

Flash Nanoprecipitation: Particle Structure and Stability

PubMed Central

Pustulka, Kevin M.; Wohl, Adam R.; Lee, Han Seung; Michel, Andrew R.; Han, Jing; Hoye, Thomas R.; McCormick, Alon V.; Panyam, Jayanth; Macosko, Christopher W.

2013-01-01

Flash nanoprecipitation (FNP) is a process that, through rapid mixing, stabilizes an insoluble low molecular weight compound in a nano-sized, polymer-stabilized delivery vehicle. The polymeric components are typically amphiphilic diblock copolymers (BCPs). In order to fully exploit the potential of FNP, factors affecting particle structure, size, and stability must be understood. Here we show that polymer type, hydrophobicity and crystallinity of the small molecule, and small molecule loading levels all affect particle size and stability. Of the four block copolymers (BCP) that we have studied here, poly(ethylene glycol)-b-poly(lactic-co-glycolic acid) (PEG-b-PLGA) was most suitable for potential drug delivery applications due to its ability to give rise to stable nanoparticles, its biocompatibility, and its degradability. We found little difference in particle size when using PLGA block sizes over the range of 5 to 15kDa. The choice of hydrophobic small molecule was important, as molecules with a calculated water-octanol partition coefficient (clogP) below 6 gave rise to particles that were unstable and underwent rapid Ostwald ripening. Studies probing the internal structure of nanoparticles were also performed. Analysis of differential scanning calorimetry (DSC), cryogenic transmission electron microscopy (cryo-TEM), and 1H-NMR experiments support a three-layer core-shell-corona nanoparticle structure. PMID:24053447

Shell-corona microgels from double interpenetrating networks.

PubMed

Rudyak, Vladimir Yu; Gavrilov, Alexey A; Kozhunova, Elena Yu; Chertovich, Alexander V

2018-04-18

Polymer microgels with a dense outer shell offer outstanding features as universal carriers for different guest molecules. In this paper, microgels formed by an interpenetrating network comprised of collapsed and swollen subnetworks are investigated using dissipative particle dynamics (DPD) computer simulations, and it is found that such systems can form classical core-corona structures, shell-corona structures, and core-shell-corona structures, depending on the subchain length and molecular mass of the system. The core-corona structures consisting of a dense core and soft corona are formed at small microgel sizes when the subnetworks are able to effectively separate in space. The most interesting shell-corona structures consist of a soft cavity in a dense shell surrounded with a loose corona, and are found at intermediate gel sizes; the area of their existence depends on the subchain length and the corresponding mesh size. At larger molecular masses the collapsing network forms additional cores inside the soft cavity, leading to the core-shell-corona structure.

Bandgap Engineering of InP QDs Through Shell Thickness and Composition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dennis, Allison M.; Mangum, Benjamin D.; Piryatinski, Andrei

2012-06-21

Fields as diverse as biological imaging and telecommunications utilize the unique photophysical and electronic properties of nanocrystal quantum dots (NQDs). The development of new NQD compositions promises material properties optimized for specific applications, while addressing material toxicity. Indium phosphide (InP) offers a 'green' alternative to the traditional cadmium-based NQDs, but suffers from extreme susceptibility to oxidation. Coating InP cores with more stable shell materials significantly improves nanocrystal resistance to oxidation and photostability. We have investigated several new InP-based core-shell compositions, correlating our results with theoretical predictions of their optical and electronic properties. Specifically, we can tailor the InP core-shell QDsmore » to a type-I, quasi-type-II, or type-II bandgap structure with emission wavelengths ranging from 500-1300 nm depending on the shell material used (ZnS, ZnSe, CdS, or CdSe) and the thickness of the shell. Single molecule microscopy assessments of photobleaching and blinking are used to correlate NQD properties with shell thickness.« less

Theoretical study of the H2 reaction with a Pt4 (111) cluster

NASA Astrophysics Data System (ADS)

Cruz, A.; Bertin, V.; Poulain, E.; Benitez, J. I.; Castillo, S.

2004-04-01

The Cs symmetry reaction of the H2 molecule on a Pt4 (111) clusters, has been studied using ab initio multiconfiguration self-consistent field plus extensive multireference configuration interaction variational and perturbative calculations. The H2 interaction by the vertex and by the base of a tetrahedral Pt4 cluster were studied in ground and excited triplet and singlet states (closed and open shells), where the reaction curves are obtained through many avoided crossings. The Pt4 cluster captures and activates the hydrogen molecule; it shows a similar behavior compared with other Ptn (n=1,2,3) systems. The Pt4 cluster in their lowest five open and closed shell electronic states: 3B2, 1B2, 1A1 3A1, 1A1, respectively, may capture and dissociate the H2 molecule without activation barriers for the hydrogen molecule vertex approach. For the threefolded site reaction, i.e., by the base, the situation is different, the hydrogen adsorption presents some barriers. The potential energy minima occur outside and inside the cluster, with strong activation of the H-H bond. In all cases studied, the Pt4 cluster does not absorb the hydrogen molecule.

Synthesis and characterization of core-shell gold nanoparticles with poly(vinyl pyrrolidone) from a new precursor salt

NASA Astrophysics Data System (ADS)

Behera, M.; Ram, S.

2013-02-01

In this article, we report a facile one-step chemical synthesis of gold (Au) nanoparticles (GNPs) from a new precursor salt i.e., gold hydroxide in the presence of poly(vinyl pyrrolidone) (PVP) polymer. The non-aqueous dispersion of GNPs was comprehensively characterized by UV-Visible, FTIR, zeta potential, and transmission electron microscope (TEM). A strong surface plasmon resonance band at 529 nm in the UV-Visible spectrum confirms the formation of GNPs in the Au colloid. The FTIR spectroscopic results showed that PVP molecules get chemisorbed onto the surface of GNP via O-atom of carbonyl group. A negative zeta potential of (-)16 mV reveals accumulation of nonbonding electrons of O-atom of carbonyl group of PVP molecules on the nanosurface of GNP. TEM images demonstrate a core-shell nanostructure with an Au-crystalline core covered by a thin amorphous PVP-shell. PVP-capped GNPs could be a potential candidate for bio-sensing, catalysis, and other applications.

On the Highest Oxidation States of Metal Elements in MO4 Molecules (M = Fe, Ru, Os, Hs, Sm, and Pu).

PubMed

Huang, Wei; Xu, Wen-Hua; Schwarz, W H E; Li, Jun

2016-05-02

Metal tetraoxygen molecules (MO4, M = Fe, Ru, Os, Hs, Sm, Pu) of all metal atoms M with eight valence electrons are theoretically studied using density functional and correlated wave function approaches. The heavier d-block elements Ru, Os, Hs are confirmed to form stable tetraoxides of Td symmetry in (1)A1 electronic states with empty metal d(0) valence shell and closed-shell O(2-) ligands, while the 3d-, 4f-, and 5f-elements Fe, Sm, and Pu prefer partial occupation of their valence shells and peroxide or superoxide ligands at lower symmetry structures with various spin couplings. The different geometric and electronic structures and chemical bonding types of the six iso-stoichiometric species are explained in terms of atomic orbital energies and orbital radii. The variations found here contribute to our general understanding of the periodic trends of oxidation states across the periodic table.

Theory and practice of uncommon molecular electronic configurations.

PubMed

Gryn'ova, Ganna; Coote, Michelle L; Corminboeuf, Clemence

2015-01-01

The electronic configuration of the molecule is the foundation of its structure and reactivity. The spin state is one of the key characteristics arising from the ordering of electrons within the molecule's set of orbitals. Organic molecules that have open-shell ground states and interesting physicochemical properties, particularly those influencing their spin alignment, are of immense interest within the up-and-coming field of molecular electronics. In this advanced review, we scrutinize various qualitative rules of orbital occupation and spin alignment, viz., the aufbau principle, Hund's multiplicity rule, and dynamic spin polarization concept, through the prism of quantum mechanics. While such rules hold in selected simple cases, in general the spin state of a system depends on a combination of electronic factors that include Coulomb and Pauli repulsion, nuclear attraction, kinetic energy, orbital relaxation, and static correlation. A number of fascinating chemical systems with spin states that fluctuate between triplet and open-shell singlet, and are responsive to irradiation, pH, and other external stimuli, are highlighted. In addition, we outline a range of organic molecules with intriguing non-aufbau orbital configurations. In such quasi-closed-shell systems, the singly occupied molecular orbital (SOMO) is energetically lower than one or more doubly occupied orbitals. As a result, the SOMO is not affected by electron attachment to or removal from the molecule, and the products of such redox processes are polyradicals. These peculiar species possess attractive conductive and magnetic properties, and a number of them that have already been developed into molecular electronics applications are highlighted in this review. WIREs Comput Mol Sci 2015, 5:440-459. doi: 10.1002/wcms.1233 For further resources related to this article, please visit the WIREs website.

A Stable Graphitic, Nanocarbon-Encapsulated, Cobalt-Rich Core–Shell Electrocatalyst as an Oxygen Electrode in a Water Electrolyzer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sivanantham, Arumugam; Ganesan, Pandian; Estevez,

2018-01-11

The oxygen electrode plays a vital role in the successful commercialization of renewable energy technologies, such as fuel cells and water electrolyzers. In this study, the Prussian blue analogue-derived nitrogen-doped nanocarbon (NC) layer-trapped, cobalt-rich, core–shell nanostructured electrocatalysts (core–shell Co@NC) are reported. The electrode exhibits an improved oxygen evolution activity and stability compared to that of the commercial noble electrodes. The core–shell Co@NC-loaded nickel foam exhibits a lower overpotential of 330 mV than that of IrO2 on nickel foam at 10 mA cm−2 and has a durability of over 400 h. The commercial Pt/C cathode-assisted, core–shell Co@NC–anode water electrolyzer delivers 10more » mA cm−2 at a cell voltage of 1.59 V, which is 70 mV lower than that of the IrO2–anode water electrolyzer. Over the long-term chronopotentiometry durability testing, the IrO2–anode water electrolyzer shows a cell voltage loss of 230 mV (14%) at 95 h, but the loss of the core–shell Co@NC–anode electrolyzer is only 60 mV (4%) even after 350 h cell-operation. The findings indicate that the Prussian blue analogue is a class of inorganic nanoporous materials that can be used to derive metal-rich, core–shell electrocatalysts with enriched active centers.« less

A Stable Graphitic, Nanocarbon-Encapsulated, Cobalt-Rich Core-Shell Electrocatalyst as an Oxygen Electrode in a Water Electrolyzer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sivanantham, Arumugam; Ganesan, Pandian; Estevez, Luis

The oxygen electrode plays a vital role in the successful commercialization of renewable energy technologies, such as fuel cells and water electrolyzers. In this study, the Prussian blue analogue-derived nitrogen-doped nanocarbon (NC) layer-trapped, cobalt-rich, core–shell nanostructured electrocatalysts (core–shell Co@NC) are reported. The electrode exhibits an improved oxygen evolution activity and stability compared to that of the commercial noble electrodes. The core–shell Co@NC-loaded nickel foam exhibits a lower overpotential of 330 mV than that of IrO2 on nickel foam at 10 mA cm-2 and has a durability of over 400 h. The commercial Pt/C cathode-assisted, core–shell Co@NC–anode water electrolyzer delivers 10more » mA cm-2 at a cell voltage of 1.59 V, which is 70 mV lower than that of the IrO2–anode water electrolyzer. Over the long-term chronopotentiometry durability testing, the IrO2–anode water electrolyzer shows a cell voltage loss of 230 mV (14%) at 95 h, but the loss of the core–shell Co@NC–anode electrolyzer is only 60 mV (4%) even after 350 h cell-operation. The findings indicate that the Prussian blue analogue is a class of inorganic nanoporous materials that can be used to derive metal-rich, core–shell electrocatalysts with enriched active centers.« less

Binding of Divalent Cations to Polygalacturonate: A Mechanism Driven by the Hydration Water.

PubMed

Huynh, Uyen T D; Lerbret, Adrien; Neiers, Fabrice; Chambin, Odile; Assifaoui, Ali

2016-02-11

We have investigated the interactions between polygalacturonate (polyGal) and four divalent cations (M(2+) = Ba(2+), Ca(2+), Mg(2+), Zn(2+)) that differ in size and affinity for water. Our results evidence that M(2+)-polyGal interactions are intimately linked to the affinity of M(2+) for water. Mg(2+) interacts so strongly with water that it remains weakly bound to polyGal (polycondensation) by sharing water molecules from its first coordination shell with the carboxylate groups of polyGal. In contrast, the other cations form transient ionic pairs with polyGal by releasing preferentially one water molecule (for Zn(2+)) or two (for Ca(2+) and Ba(2+)), which corresponds to monodentate and bidentate binding modes with carboxylates, respectively. The mechanism for the binding of these three divalent cations to polyGal can be described by two steps: (i) monocomplexation and formation of point-like cross-links between polyGal chains (at low M(2+)/Gal molar ratios, R) and (ii) dimerization (at higher R). The threshold molar ratio, R*, between these two steps depends on the nature of divalent cations and is lower for calcium ions (R* < 0.1) than for zinc and barium ions (R* > 0.3). This difference may be explained by the intermediate affinity of Ca(2+) for water with respect to those of Zn(2+) and Ba(2+), which may induce the formation of cross-links of intermediate flexibility. By comparison, the lower and higher flexibilities of the cross-links formed by Zn(2+) and Ba(2+), respectively, may shift the formation of dimers to higher molar ratios (R*).

Propagation of flexural and membrane waves with fluid loaded NASTRAN plate and shell elements

NASA Technical Reports Server (NTRS)

Kalinowski, A. J.; Wagner, C. A.

1983-01-01

Modeling of flexural and membrane type waves existing in various submerged (or in vacuo) plate and/or shell finite element models that are excited with steady state type harmonic loadings proportioned to e(i omega t) is discussed. Only thin walled plates and shells are treated wherein rotary inertia and shear correction factors are not included. More specifically, the issue of determining the shell or plate mesh size needed to represent the spatial distribution of the plate or shell response is of prime importance towards successfully representing the solution to the problem at hand. To this end, a procedure is presented for establishing guide lines for determining the mesh size based on a simple test model that can be used for a variety of plate and shell configurations such as, cylindrical shells with water loading, cylindrical shells in vacuo, plates with water loading, and plates in vacuo. The procedure for doing these four cases is given, with specific numerical examples present only for the cylindrical shell case.

Description of Hydration Water in Protein (Green Fluorescent Protein) Solution

DOE PAGES

Perticaroli, Stefania; Ehlers, Georg; Stanley, Christopher B.; ...

2016-10-26

The structurally and dynamically perturbed hydration shells that surround proteins and biomolecules have a substantial influence upon their function and stability. This makes the extent and degree of water perturbation of practical interest for general biological study and industrial formulation. Here, we present an experimental description of the dynamical perturbation of hydration water around green fluorescent protein in solution. Less than two shells (~5.5 Å) were perturbed, with dynamics a factor of 2–10 times slower than bulk water, depending on their distance from the protein surface and the probe length of the measurement. Furthermore, this dependence on probe length demonstratesmore » that hydration water undergoes subdiffusive motions (τ ∝ q –2.5 for the first hydration shell, τ ∝ q –2.3 for perturbed water in the second shell), an important difference with neat water, which demonstrates diffusive behavior (τ ∝ q –2). Our results help clarify the seemingly conflicting range of values reported for hydration water retardation as a logical consequence of the different length scales probed by the analytical techniques used.« less

Multifunctional core-shell silica microspheres and their performance in self-carrier decomposition, sustained drug release and fluorescent bioimaging

NASA Astrophysics Data System (ADS)

Mehdi, Yamina Ait; Itatahine, Asma; Fizir, Meriem; Xiao, Deli; Dramou, Pierre; He, Hua

2018-07-01

An ideal nanocarrier system for drug delivery is that one made from biocompatible and biodegradable materials for safe excretion from the biological system, and often with additional imaging abilities. In the present work, new core-shell silica microspheres have been prepared, with carrier decomposition after drug release. Paclitaxel, which is one of the most efficient drugs against a wide range of malignancies was integrated into the silica core. The carrier decomposition resulted from the escape of drug molecules with loading capacity about 16.95%. To achieve the fluorescents properties of the synthesized material a biocompatible photoluminescent prepared carbon dots were inserted in a silica shell around the Ptx-SiO2 core. The resultant silica core-shell (Ptx-SiO2CDs-SiO2) NPs with average particle size around 100 nm showed high fluorescent properties from the confocal laser scanning microscope observation. Further observation under UV-light at 365 nm also confirmed the photoluminescence. The Ptx-SiO2@CDs-SiO2 NPs were highly water soluble, and provide a sustained drug release as well as pH sensitivity. The incubation of A549 cells line with Ptx-SiO2@CDs-SiO2 NPs exhibits high cellular uptake as shown by CDs imaging. These properties in addition to the biocompatibility of Ptx-SiO2@CDs-SiO2 NPs and biodegradability of the silica core contributed simultaneously with the drug release process for easy body excretion after its functionality via renal system.

Emission Behavior of Fluorescently Labeled Silver Nanoshell: Enhanced Self-Quenching by Metal Nanostructure.

PubMed

Zhang, Jian; Fu, Yi; Lakowicz, Joseph R

2007-02-08

Labeled silica beads with an average diameter of 100 nm were synthesized by incorporating with 20-600 μM Ru(bpy)(3) (2+) complexes. Silver shells were deposited on the beads layer-by-layer with the shell thickness of 5-50 nm. The emission band became narrower and the intensity was enhanced depending on the shell thickness. Self-quenching of the probe was observed at high concentration. Poisson statistics were employed to analyze self-quenching of the fluorophores. The estimated quenching distance was extended from 6 to 16 nm with shell growth from 0 to 50 nm. Moreover, the silver shells were also labeled with Rhodamine 6G. Fluorescence enhancement and reduced lifetime were also observed for silver-silica shell containing R6G. We found that by adjustment of probe concentration and silver shell thickness, a Ru(bpy)(3) (2+)-labeled particle could be 600 times brighter than an isolated Ru(bpy)(3) (2+) molecule. We expect labeled metal core-shell structures can become useful probes for high sensitivity and/or single particle assay.

Ferritin cage for encapsulation and delivery of bioactive nutrients: From structure, property to applications.

PubMed

Zang, Jiachen; Chen, Hai; Zhao, Guanghua; Wang, Fudi; Ren, Fazheng

2017-11-22

Ferritin is a class of naturally occurring iron storage proteins, which is distributed widely in animal, plant, and bacteria. It usually consists of 24 subunits that form a hollow protein shell with high symmetry. One holoferritin molecule can store up to 4500 iron atom within its inner cavity, and it becomes apoferritin upon removal of iron from the cavity. Recently, scientists have subverted these nature functions and used reversibly self-assembled property of apoferritin cage controlled by pH for the encapsulation and delivery of bioactive nutrients or anticancer drug. In all these cases, the ferritin cages shield their cargo from the influence of external conditions and provide a controlled microenvironment. More importantly, upon encapsulation, ferritin shell greatly improved the water solubility, thermal stability, photostability, and cellular uptake activity of these small bioactive compounds. This review aims to highlight recent advances in applications of ferritin cage as a novel vehicle in the field of food science and nutrition. Future outlooks are highlighted with the aim to suggest a research line to follow for further studies.

Authentic Assessment Tool for the Measurement of Students' Understanding of the Valence Shell Electron Pair Repulsion Theory

ERIC Educational Resources Information Center

Wuttisela, Karntarat

2017-01-01

There are various types of instructional media related to Valence Shell Electron Pair Repulsion (VSEPR) but there is a lack of diversity of resources devoted to assessment. This research presents an assessment and comparison of students' understanding of VSEPR theory before and after tuition involving the use of the foam molecule model (FMM) and…

Flexible 3D Fe@VO2 core-shell mesh: A highly efficient and easy-recycling catalyst for the removal of organic dyes.

PubMed

Li, Jing; Wang, Ruoqi; Su, Zhen; Zhang, Dandan; Li, Heping; Yan, Youwei

2018-10-01

Nowadays, it is extremely urgent to search for efficient and effective catalysts for water purification due to the severe worldwide water-contamination crises. Here, 3D Fe@VO 2 core-shell mesh, a highly efficient catalyst toward removal of organic dyes with excellent recycling ability in the dark is designed and developed for the first time. This novel core-shell structure is actually 304 stainless steel mesh coated by VO 2 , fabricated by an electrophoretic deposition method. In such a core-shell structure, Fe as the core allows much easier separation from the water, endowing the catalyst with a flexible property for easy recycling, while VO 2 as the shell is highly efficient in degradation of organic dyes with the addition of H 2 O 2 . More intriguingly, the 3D Fe@VO 2 core-shell mesh exhibits favorable performance across a wide pH range. The 3D Fe@VO 2 core-shell mesh can decompose organic dyes both in a light-free condition and under visible irradiation. The possible catalytic oxidation mechanism of Fe@VO 2 /H 2 O 2 system is also proposed in this work. Considering its facile fabrication, remarkable catalytic efficiency across a wide pH range, and easy recycling characteristic, the 3D Fe@VO 2 core-shell mesh is a newly developed high-performance catalyst for addressing the universal water crises. Copyright © 2018 Elsevier B.V. All rights reserved.

Investigations of the Interactions of Radiation with Matter.

DTIC Science & Technology

1986-07-31

Process in Atoms, Molecules and Solids, eds. A. Mei-el and J. Finster , (Karl-Marx Universitat, Leipzig, 1984), p. 58. 10. S.T. Manson in High Enery Ion...H. Toburen, and S. T. Manson in X-Ra and Inner-Shell Process in Atoms, Molecules and Solids, eds. A. Meisel and J. Finster , (Karl-Marx- Universitat

Biosensing via light scattering from plasmonic core-shell nanospheres coated with DNA molecules

NASA Astrophysics Data System (ADS)

Xie, Huai-Yi; Chen, Minfeng; Chang, Yia-Chung; Moirangthem, Rakesh Singh

2017-05-01

We present both experimental and theoretical studies for investigating DNA molecules attached on metallic nanospheres. We have developed an efficient and accurate numerical method to investigate light scattering from plasmonic nanospheres on a substrate covered by a shell, based on the Green's function approach with suitable spherical harmonic basis. Next, we use this method to study optical scattering from DNA molecules attached to metallic nanoparticles placed on a substrate and compare with experimental results. We obtain fairly good agreement between theoretical predictions and the measured ellipsometric spectra. The metallic nanoparticles were used to detect the binding with DNA molecules in a microfluidic setup via spectroscopic ellipsometry (SE), and a detectable change in ellipsometric spectra was found when DNA molecules are captured on Au nanoparticles. Our theoretical simulation indicates that the coverage of Au nanosphere by a submonolayer of DNA molecules, which is modeled by a thin layer of dielectric material (which may absorb light), can lead to a small but detectable spectroscopic shift in both the Ψ and Δ spectra with more significant change in Δ spectra in agreement with experimental results. Our studies demonstrated the ultrasensitive capability of SE for sensing submonolayer coverage of DNA molecules on Au nanospheres. Hence the spectroscopic ellipsometric measurements coupled with theoretical analysis via an efficient computation method can be an effective tool for detecting DNA molecules attached on Au nanoparticles, thus achieving label-free, non-destructive, and high-sensitivity biosensing with nanoscale resolution.

Temperature effects on prevalent structures of hydrated Fe{sup +} complexes: Infrared spectroscopy and DFT calculations of Fe{sup +}(H{sub 2}O){sub n} (n = 3–8)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ohashi, Kazuhiko, E-mail: kazu@chem.kyushu-univ.jp; Sekiya, Hiroshi; Sasaki, Jun

2014-12-07

Hydrated Fe{sup +} ions are produced in a laser-vaporization cluster source of a triple quadrupole mass spectrometer. The Fe{sup +}(H{sub 2}O){sub n} (n = 3–8) complexes are mass-selected and probed with infrared (IR) photodissociation spectroscopy in the OH-stretch region. Density functional theory (DFT) calculations are also carried out for analyzing the experimental IR spectra and for evaluating thermodynamic quantities of low-lying isomers. Solvation through H-bonding instead of direct coordination to Fe{sup +} is observed already at n = 3, indicating the completion of the first hydration shell with two H{sub 2}O molecules. Size dependent variations in the spectra for nmore » = 5–7 provide evidence for the second-shell completion at n = 6, where a linearly coordinated Fe{sup +}(H{sub 2}O){sub 2} subunit is solvated with four H{sub 2}O molecules. Overall spectral features for n = 3–8 agree well with those predicted for 2-coordinated structures. DFT calculations predict that such 2-coordinated structures are lowest in energy for smaller n. However, 4-coordinated isomers are predicted to be more stable for n = 7 and 8; the energy ordering is in conflict with the IR spectroscopic observation. Examination of free energy as a function of temperature suggests that the ordering of the isomers at warmer temperatures can be different from the ordering near 0 K. For n = 7 and 8, the 4-coordinated isomers should be observed at low temperatures because they are lowest in enthalpy. Meanwhile, outer-shell waters in the 2-coordinated structures are bound less rigidly; their contribution to entropy is rather large. The 2-coordinated structures become abundant at warmer temperatures, owing to the entropy effect.« less

Biometric studies on the bivalves Astarte elliptica, A. borealis and A. montagui in Kiel Bay (Western Baltic Sea)

NASA Astrophysics Data System (ADS)

Schaefer, R.; Trutschler, K.; Rumohr, H.

1985-09-01

The three Astarte species were studied in June 1983 at two sites in Kiel Bay, “Süderfahrt” and “Schleimünde”, at 20 m depth. Shell length to live wet weight correlations are given for all three species; for A. elliptica also shell-free dry weight, shell dry weight, ash-free dry weight of the soft body and ash-free dry weight of the shell are recorded as functions of the shell length. In the logarithmic length/weight regression analysis the coefficients of slope for A. elliptica and A. borealis are 3. For A. montagui, that coefficient is significantly greater than 3. Weight conversion factors, calculated for A. elliptica, revealed a mean weight composition of 31.5 % water in the mantle cavity and tissue water, 64.5 % shell ash, 2.1 % organic content of shell, 1.7 % organic content of the soft body and 0.4 % ash of the soft body. An isometric growth of shell length and shell breadth is confirmed for A. borealis, while A. montagui exhibits positive allometric shell growth and changes its shape during life.

Metal coated colloidosomes as carriers for an antibiotic

NASA Astrophysics Data System (ADS)

Sun, Qian; Zhao, Ziyan; Hall, Elizabeth A. H.; Routh, Alexander F.

2018-06-01

Colloidosomes are polymer shell microcapsules. They are stable and easy to prepare and have been used to encapsulate drugs for release at specific areas in the body. Traditional polymer shell capsules cannot totally seal drugs, since they are porous and small molecules diffuse through the polymer shell. In this paper, we report a method for encapsulating an antibiotic kanamycin using gold or silver coated colloidosomes. The colloidosomes are impermeable and can be triggered using ultrasound. To investigate the application of the capsules in a biological system, Escherichia Coli (E.coli) was chosen as a model organism. After triggering, the released antibiotic, as well as the metal shell fragments, kill E.coli. Both the silver and gold shells colloidosomes are toxic to this bacterial system and the gold coated colloidosomes can load a higher concentration of kanamycin.

A novel superparamagnetic surface molecularly imprinted nanoparticle adopting dummy template: an efficient solid-phase extraction adsorbent for bisphenol A.

PubMed

Lin, Zhenkun; Cheng, Wenjing; Li, Yanyan; Liu, Zhiren; Chen, Xiangping; Huang, Changjiang

2012-03-30

Leakage of the residual template molecules is one of the biggest challenges for application of molecularly imprinted polymer (MIP) in solid-phase extraction (SPE). In this study, bisphenol F (BPF) was adopted as a dummy template to prepare MIP of bisphenol A (BPA) with a superparamagnetic core-shell nanoparticle as the supporter, aiming to avoid residual template leakage and to increase the efficiency of SPE. Characterization and test of the obtained products (called mag-DMIP beads) revealed that these novel nanoparticles not only had excellent magnetic property but also displayed high selectivity to the target molecule BPA. As mag-DMIP beads were adopted as the adsorbents of solid-phase extraction for detecting BPA in real water samples, the recoveries of spiked samples ranged from 84.7% to 93.8% with the limit of detection of 2.50 pg mL(-1), revealing that mag-DMIP beads were efficient SPE adsorbents. Copyright © 2012 Elsevier B.V. All rights reserved.

X-Ray Absorption Spectra of Amorphous Ices from GW Quasiparticle Calculation

NASA Astrophysics Data System (ADS)

Kong, Lingzhu; Car, Roberto

2013-03-01

We use a GW approach[2] to compute the x-ray absorption spectra of model low- and high-density amorphous ice structures(LDA and HDA)[3]. We include the structural effects of quantum zero point motion using colored-noise Langevin molecular dynamics[4]. The calculated spectra differences in the main and post edge region between LDA and HDA agree well with experimental observations. We attribute these differences to the presence of interstitial molecules within the first coordination shell range in HDA. This assignment is further supported by a calculation of the spectrum of ice VIII, a high-pressure structure that maximizes the number of interstitial molecules and, accordingly, shows a much weaker post-edge feature. We further rationalize the spectral similarity between HDA and liquid water, and between LDA and ice Ih in terms of the respective similarities in the H-bond network topology and bond angle distributions. Supported by grants DOE-DE-SC0005180, DOE DE-SC0008626 and NSF-CHE-0956500.

Quasielastic small-angle neutron scattering from heavy water solutions of cyclodextrins

NASA Astrophysics Data System (ADS)

Kusmin, André; Lechner, Ruep E.; Saenger, Wolfram

2011-01-01

We present a model for quasielastic neutron scattering (QENS) by an aqueous solution of compact and inflexible molecules. This model accounts for time-dependent spatial pair correlations between the atoms of the same as well as of distinct molecules and includes all coherent and incoherent neutron scattering contributions. The extension of the static theory of the excluded volume effect [A. K. Soper, J. Phys.: Condens. Matter 9, 2399 (1997)] to the time-dependent (dynamic) case allows us to obtain simplified model expressions for QENS spectra in the low Q region in the uniform fluid approximation. The resulting expressions describe the quasielastic small-angle neutron scattering (QESANS) spectra of D _2O solutions of native and methylated cyclodextrins well, yielding in particular translational and rotational diffusion coefficients of these compounds in aqueous solution. Finally, we discuss the full potential of the QESANS analysis (that is, beyond the uniform fluid approximation), in particular, the information on solute-solvent interactions (e.g., hydration shell properties) that such an analysis can provide, in principle.

Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle.

PubMed

Salorinne, Kirsi; Malola, Sami; Wong, O Andrea; Rithner, Christopher D; Chen, Xi; Ackerson, Christopher J; Häkkinen, Hannu

2016-01-21

Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of (1)H and (13)C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional theory calculations and molecular dynamics simulations. Molecular dynamics simulations augment the data by giving information about the ligand disorder and visualization of possible distinct ligand conformations of the most dynamic ligands. The method demonstrated here opens a way to controllable strategies for functionalization of ligated nanoparticles for applications.

Nanoparticles with photoinduced precipitation for the extraction of pollutants from water and soil

PubMed Central

Brandl, Ferdinand; Bertrand, Nicolas; Lima, Eliana Martins; Langer, Robert

2015-01-01

Nanotechnology may offer fast and effective solutions for environmental clean-up. Herein, amphiphilic diblock copolymers are used to develop a platform of photosensitive core-shell nanoparticles. Irradiation with ultraviolet light removes the protective layer responsible for colloidal stability; as a result, the nanoparticles are rapidly and irreversibly converted to macroscopic aggregates. The associated phase separation allows measuring the partitioning of small molecules between the aqueous phase and nanoparticles; data suggests that interactions are enhanced by decreasing the particle size. Adsorption onto nanoparticles can be exploited to efficiently remove hydrophobic pollutants from water and contaminated soil. Preliminary in vivo experiments suggest that treatment with photocleavable nanoparticles can significantly reduce the teratogenicity of bisphenol A, triclosan and 17α-ethinyl estradiol without generating obviously toxic byproducts. Small-scale pilot experiments on wastewater, thermal printing paper and contaminated soil demonstrate the applicability of the approach. PMID:26196119

Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle

PubMed Central

Salorinne, Kirsi; Malola, Sami; Wong, O. Andrea; Rithner, Christopher D.; Chen, Xi; Ackerson, Christopher J.; Häkkinen, Hannu

2016-01-01

Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of 1H and 13C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional theory calculations and molecular dynamics simulations. Molecular dynamics simulations augment the data by giving information about the ligand disorder and visualization of possible distinct ligand conformations of the most dynamic ligands. The method demonstrated here opens a way to controllable strategies for functionalization of ligated nanoparticles for applications. PMID:26791253

Indirect double photoionization of water

NASA Astrophysics Data System (ADS)

Resccigno, T. N.; Sann, H.; Orel, A. E.; Dörner, R.

2011-05-01

The vertical double ionization thresholds of small molecules generally lie above the dissociation limits corresponding to formation of two singly charged fragments. This gives the possibility of populating singly charged molecular ions by photoionization in the Franck-Condon region at energies below the lowest dication state, but above the dissociation limit into two singly charged fragment ions. This process can produce a superexcited neutral fragment that autoionizes at large internuclear separation. We study this process in water, where absorption of a photon produces an inner-shell excited state of H2O+ that fragments to H++OH*. The angular distribution of secondary electrons produced by OH* when it autoionizes produces a characteristic asymmetric pattern that reveals the distance, and therefore the time, at which the decay takes place. LBNL, Berkeley, CA, J. W. Goethe Universität, Frankfurt, Germany. Work performed under auspices of US DOE and supported by OBES, Div. of Chemical Sciences.

Nanoparticles with photoinduced precipitation for the extraction of pollutants from water and soil

NASA Astrophysics Data System (ADS)

Brandl, Ferdinand; Bertrand, Nicolas; Lima, Eliana Martins; Langer, Robert

2015-07-01

Nanotechnology may offer fast and effective solutions for environmental clean-up. Herein, amphiphilic diblock copolymers are used to develop a platform of photosensitive core-shell nanoparticles. Irradiation with ultraviolet light removes the protective layer responsible for colloidal stability; as a result, the nanoparticles are rapidly and irreversibly converted to macroscopic aggregates. The associated phase separation allows measuring the partitioning of small molecules between the aqueous phase and nanoparticles; data suggests that interactions are enhanced by decreasing the particle size. Adsorption onto nanoparticles can be exploited to efficiently remove hydrophobic pollutants from water and contaminated soil. Preliminary in vivo experiments suggest that treatment with photocleavable nanoparticles can significantly reduce the teratogenicity of bisphenol A, triclosan and 17α-ethinyl estradiol without generating obviously toxic byproducts. Small-scale pilot experiments on wastewater, thermal printing paper and contaminated soil demonstrate the applicability of the approach.

Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems

PubMed Central

Huang, Xuhui; Hagen, Morten; Kim, Byungchan; Friesner, Richard A.; Zhou, Ruhong; Berne, B. J.

2009-01-01

We apply the recently developed replica exchange with solute tempering (REST) to three large solvated peptide systems: an α-helix, a β-hairpin, and a TrpCage, with these peptides defined as the “central group”. We find that our original implementation of REST is not always more efficient than the replica exchange method (REM). Specifically, we find that exchanges between folded (F) and unfolded (U) conformations with vastly different structural energies are greatly reduced by the nonappearance of the water self-interaction energy in the replica exchange acceptance probabilities. REST, however, is expected to remain useful for a large class of systems for which the energy gap between the two states is not large, such as weakly bound protein–ligand complexes. Alternatively, a shell of water molecules can be incorporated into the central group, as discussed in the original paper. PMID:17439169

The use of nutshell carbons in drinking water filters for removal of trace metals.

PubMed

Ahmedna, Mohamed; Marshall, Wayne E; Husseiny, Abdo A; Rao, Ramu M; Goktepe, Ipek

2004-02-01

Filtration of drinking water by point-of-use (POU) or point-of-entry (POE) systems is becoming increasingly popular in the United States. Drinking water is filtered to remove both organic and inorganic contaminants. The objective of this study was to evaluate the use of granular activated carbon from nutshells (almond, English walnut, pecan) in a POU water filtration system to determine its effectiveness in removing select, potentially toxic metal ions, namely, copper (Cu2+), lead (Pb2+) or zinc (Zn2+) found in drinking water. The nutshell-based carbon system was designated "Envirofilter" and was compared to four commercial POU systems with brand names of BRITA, Omni Filter, PUR and Teledyne Water Pik. Eight prototype "Envirofilters", consisting of individual or binary mixtures of carbons made from acid-activated almond or pecan shells and steam-activated pecan or walnut shells were constructed and evaluated for adsorption of the three metal ions. The results indicated that a binary mixture of carbons from acid-activated almond and either steam-activated pecan or walnut shells were the most effective in removing these metals from drinking water of all the POU systems evaluated. Binary mixtures of acid-activated almond shell-based carbon with either steam-activated pecan shell- or walnut shell-based carbon removed nearly 100% of lead ion, 90-95% of copper ion and 80-90% of zinc ion. Overall the performance data on the "Envirofilters" suggest that these prototypes require less carbon than commercial filters to achieve the same metal adsorption efficiency and may also be a less expensive product.

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

NASA Astrophysics Data System (ADS)

Fogarty, Aoife C.; Potestio, Raffaello; Kremer, Kurt

2015-05-01

A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations.

H{sub 2} MOLECULAR CLUSTERS WITH EMBEDDED MOLECULES AND ATOMS AS THE SOURCE OF THE DIFFUSE INTERSTELLAR BANDS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernstein, L. S.; Clark, F. O.; Lynch, D. K., E-mail: larry@spectral.com, E-mail: dave@thulescientific.com

2013-05-01

We suggest that the diffuse interstellar bands (DIBs) arise from absorption lines of electronic transitions in molecular clusters primarily composed of a single molecule, atom, or ion ({sup s}eed{sup )}, embedded in a single-layer shell of H{sub 2} molecules. Less abundant variants of the cluster, including two seed molecules and/or a two-layer shell of H{sub 2} molecules, may also occur. The lines are broadened, blended, and wavelength-shifted by interactions between the seed and surrounding H{sub 2} shell. We refer to these clusters as contaminated H{sub 2} clusters (CHCs). We show that CHC spectroscopy matches the diversity of observed DIB spectralmore » profiles and provides good fits to several DIB profiles based on a rotational temperature of 10 K. CHCs arise from {approx}centimeter-sized, dirty H{sub 2} ice balls, called contaminated H{sub 2} ice macro-particles (CHIMPs), formed in cold, dense, giant molecular clouds (GMCs), and later released into the interstellar medium (ISM) upon GMC disruption. Attractive interactions, arising from Van der Waals and ion-induced dipole potentials, between the seeds and H{sub 2} molecules enable CHIMPs to attain centimeter-sized dimensions. When an ultraviolet (UV) photon is absorbed in the outer layer of a CHIMP, it heats the icy matrix and expels CHCs into the ISM. While CHCs are quickly destroyed by absorbing UV photons, they are replenished by the slowly eroding CHIMPs. Since CHCs require UV photons for their release, they are most abundant at, but not limited to, the edges of UV-opaque molecular clouds, consistent with the observed, preferred location of DIBs. An inherent property of CHCs, which can be characterized as nanometer size, spinning, dipolar dust grains, is that they emit in the radio-frequency region. We also show that the CHCs offer a natural explanation for the anomalous microwave emission feature in the {approx}10-100 GHz spectral region.« less

The influence of shell thickness of Au@TiO2 core-shell nanoparticles on the plasmonic enhancement effect in dye-sensitized solar cells.

PubMed

Liu, Wei-Liang; Lin, Fan-Cheng; Yang, Yu-Chen; Huang, Chen-Hsien; Gwo, Shangjr; Huang, Michael H; Huang, Jer-Shing

2013-09-07

Plasmonic core-shell nanoparticles (PCSNPs) can function as nanoantennas and improve the efficiency of dye-sensitized solar cells (DSSCs). To achieve maximum enhancement, the morphology of PCSNPs needs to be optimized. Here we precisely control the morphology of Au@TiO2 PCSNPs and systematically study its influence on the plasmonic enhancement effect. The enhancement mechanism was found to vary with the thickness of the TiO2 shell. PCSNPs with a thinner shell mainly enhance the current, whereas particles with a thicker shell improve the voltage. While pronounced plasmonic enhancement was found in the near infrared regime, wavelength-independent enhancement in the visible range was observed and attributed to the plasmonic heating effect. Emission lifetime measurement confirms that N719 molecules neighboring nanoparticles with TiO2 shells exhibit a longer lifetime than those in contact with metal cores. Overall, PCSNPs with a 5 nm shell give the highest efficiency enhancement of 23%. Our work provides a new synthesis route for well-controlled Au@TiO2 core-shell nanoparticles and gains insight into the plasmonic enhancement in DSSCs.

Hyperfine structure of 2Σ molecules containing alkaline-earth-metal atoms

NASA Astrophysics Data System (ADS)

Aldegunde, Jesus; Hutson, Jeremy M.

2018-04-01

Ultracold molecules with both electron spin and an electric dipole moment offer new possibilities in quantum science. We use density-functional theory to calculate hyperfine coupling constants for a selection of molecules important in this area, including RbSr, LiYb, RbYb, CaF, and SrF. We find substantial hyperfine coupling constants for the fermionic isotopes of the alkaline-earth-metal and Yb atoms. We discuss the hyperfine level patterns and Zeeman splittings expected for these molecules. The results will be important both to experiments aimed at forming ultracold open-shell molecules and to their applications.

Interfacial complexation in microfluidic droplets for single-step fabrication of microcapsule

NASA Astrophysics Data System (ADS)

Kaufman, Gilad; Nejati, Siamak; Sarfati, Raphael; Boltyanskiy, Rostislav; Williams, Danielle; Liu, Wei; Schloss, Ashley; Regan, Lynn; Yan, Elsa; Dufrense, Eric; Loewenberg, Michael; Osuji, Chinedum

We present microfluidic interfacial complexation in emulsion droplets as a simple single-step approach for fabricating a large variety of stable monodisperse microcapsules with tailored mechanical properties, protein binding and controlled release behavior. We rely on electrostatic interactions and hydrogen bonding to direct the assembly of complementary species at oil-water droplet interfaces to form microcapsules with polyelectrolyte shells, composite polyelectrolyte-nanoparticle shells, and copolymer-nanofiber shells. Additionally, we demonstrate the formation of microcapsules by adsorption of an amphiphilic bacterial hydrophobin, BslA, at oil-in-water and water-in-oil droplets, and protein capture on these capsules using engineered variants of the hydrophobin. We discuss the composition dependence of mechanical properties, shell thickness and release behavior, and regimes of stability for microcapsule fabrication. Nanoparticle based microcapsules display an intriguing plastic deformation response which enables the formation of large aspect ratio asperities by pipette aspiration of the shell.

Water-soluble core/shell nanoparticles for proton therapy through particle-induced radiation

NASA Astrophysics Data System (ADS)

Park, Jeong Chan; Jung, Myung-Hwan; Kim, Maeng Jun; Kim, Kye-Ryung

2015-02-01

Metallic nanoparticles have been used in biomedical applications such as magnetic resonance imaging (MRI), therapy, and drug delivery systems. Metallic nanoparticles as therapeutic tools have been demonstrated using radio-frequency magnetic fields or near-infrared light. Recently, therapeutic applications of metallic nanomaterials combined with proton beams have been reported. Particle-induced radiation from metallic nanoparticles, which can enhance the therapeutic effects of proton therapy, was released when the nanoparticles were bombarded by a high-energy proton beam. Core/shell nanoparticles, especially Au-coated magnetic nanoparticles, have drawn attention in biological applications due to their attractive characteristics. However, studies on the phase transfer of organic-ligand-based core/shell nanoparticles into water are limited. Herein, we demonstrated that hydrophobic core/shell structured nanomaterials could be successfully dispersed in water through chloroform/surfactant mixtures. The effects of the core/shell nanomaterials and the proton irradiation on Escherichia coli (E. coli) were also explored.

Evaluation of water displacement energetics in protein binding sites with grid cell theory.

PubMed

Gerogiokas, G; Southey, M W Y; Mazanetz, M P; Heifetz, A; Hefeitz, A; Bodkin, M; Law, R J; Michel, J

2015-04-07

Excess free energies, enthalpies and entropies of water in protein binding sites were computed via classical simulations and Grid Cell Theory (GCT) analyses for three pairs of congeneric ligands in complex with the proteins scytalone dehydratase, p38α MAP kinase and EGFR kinase respectively. Comparative analysis is of interest since the binding modes for each ligand pair differ in the displacement of one binding site water molecule, but significant variations in relative binding affinities are observed. Protocols that vary in their use of restraints on protein and ligand atoms were compared to determine the influence of protein-ligand flexibility on computed water structure and energetics, and to assess protocols for routine analyses of protein-ligand complexes. The GCT-derived binding affinities correctly reproduce experimental trends, but the magnitude of the predicted changes in binding affinities is exaggerated with respect to results from a previous Monte Carlo Free Energy Perturbation study. Breakdown of the GCT water free energies into enthalpic and entropic components indicates that enthalpy changes dominate the observed variations in energetics. In EGFR kinase GCT analyses revealed that replacement of a pyrimidine by a cyanopyridine perturbs water energetics up three hydration shells away from the ligand.

Translational and Rotational Diffusion in Water in the Gigapascal Range

NASA Astrophysics Data System (ADS)

Bove, L. E.; Klotz, S.; Strässle, Th.; Koza, M.; Teixeira, J.; Saitta, A. M.

2013-11-01

First measurements of the self-dynamics of liquid water in the GPa range are reported. The GPa range has here become accessible through a new setup for the Paris-Edinburgh press specially conceived for quasielastic neutron scattering studies. A direct measurement of both the translational and rotational diffusion coefficients of water along the 400 K isotherm up to 3 GPa, corresponding to the melting point of ice VII, is provided and compared with molecular dynamics simulations. The translational diffusion is observed to strongly decrease with pressure, though its variation slows down for pressures higher than 1 GPa and decouples from that of the shear viscosity. The rotational diffusion turns out to be insensitive to pressure. Through comparison with structural data and molecular dynamics simulations, we show that this is a consequence of the rigidity of the first neighbors shell and of the invariance of the number of hydrogen bonds of a water molecule under high pressure. These results show the inadequacy of the Stokes-Einstein-Debye equations to predict the self-diffusive behavior of water at high temperature and high pressure, and challenge the usual description of hot dense water behaving as a simple liquid.

Hybrid MC/QC simulations of water-assisted proton transfer in nucleosides. Guanosine and its analog acyclovir.

PubMed

Markova, Nadezhda; Pejov, Ljupco; Stoyanova, Nina; Enchev, Venelin

2017-05-01

To provide an in-depth insight into the molecular basis of spontaneous tautomerism in DNA and RNA base pairs, a hybrid Monte Carlo (MC)-quantum chemical (QC) methodology is implemented to map two-dimensional potential energy surfaces along the reaction coordinates of solvent-assisted proton transfer processes in guanosine and its analog acyclovir in aqueous solution. The solvent effects were simulated by explicit inclusion of water molecules that model the relevant part of the first hydration shell around the solute. The position of these water molecules was estimated by carrying out a classical Metropolis Monte Carlo simulation of dilute water solutions of the guanosine (Gs) and acyclovir (ACV) and subsequently analyzing solute-solvent intermolecular interactions in the statistically-independent MC-generated configurations. The solvent-assisted proton transfer processes were further investigated using two different ab initio MP2 quantum chemical approaches. In the first one, potential energy surfaces of the 'bare' finite solute-solvent clusters containing Gs/ACV and four water molecules (MP2/6-31+G(d,p) level) were explored, while within the second approach, these clusters were embedded in 'bulk' solvent treated as polarizable continuum (C-PCM/MP2/6-31+G(d,p) level of theory). It was found that in the gas phase and in water solution, the most stable tautomer for guanosine and acyclovir is the 1H-2-amino-6-oxo form followed by the 2-amino-6-(sZ)-hydroxy form. The energy barriers of the water-assisted proton transfer reaction in guanosine and in acyclovir are found to be very similar - 11.74 kcal mol -1 for guanosine and 11.16 kcal mol -1 for acyclovir, and the respective rate constants (k = 1.5 × 10 1 s -1 , guanosine and k = 4.09 × 10 1 s -1 , acyclovir), are sufficiently large to generate the 2-amino-6-(sZ)-hydroxy tautomer. The analysis of the reaction profiles in both compounds shows that the proton transfer processes occur through the asynchronous concerted mechanism.

Formation of Core-Shell Ethane-Silver Clusters in He Droplets.

PubMed

Loginov, Evgeny; Gomez, Luis F; Sartakov, Boris G; Vilesov, Andrey F

2017-08-17

Ethane core-silver shell clusters consisting of several thousand particles have been assembled in helium droplets upon capture of ethane molecules followed by Ag atoms. The composite clusters were studied via infrared laser spectroscopy in the range of the C-H stretching vibrations of ethane. The spectra reveal a splitting of the vibrational bands, which is ascribed to interaction with Ag. A rigorous analysis of band intensities for a varying number of trapped ethane molecules and Ag atoms indicates that the composite clusters consist of a core of ethane that is covered by relatively small Ag clusters. This metastable structure is stabilized due to fast dissipation in superfluid helium droplets of the cohesion energy of the clusters.

Molecular Dynamics Studies of Overbased Detergents on a Water Surface.

PubMed

Bodnarchuk, M S; Dini, D; Heyes, D M; Breakspear, A; Chahine, S

2017-07-25

Molecular dynamics (MD) simulations are reported of model overbased detergent nanoparticles on a model water surface which mimic their behavior on a Langmuir trough or large water droplet in engine oil. The simulations predict that the structure of the nanoparticle on a water surface is different to when it is immersed in a bulk hydrophobic solvent. The surfactant tails are partly directed out of the water, while the carbonate core maximizes its extent of contact with the water. Umbrella sampling calculations of the potential of mean force between two particles showed that they are associated with varying degrees with a maximum binding free energy of ca. 10 k B T for the salicylate stabilized particle, ca. 8 k B T for a sulfurized alkyl phenate stabilized particle, and ca. 5 k B T for a sulfonate stabilized particle. The differences in the strength of attraction depend on the proximity of nearest approach and the energy penalty associated with the disruption of the hydration shell of water molecules around the calcium carbonate core when the two particles approach. This is greatest for the sulfonate particle, which partially loses the surfactant ions to the solution, and least for the salicylate, which forms the weakest water "cage". The particles are separated by a water hydration layer, even at the point of closest approach.

Novel polymeric micelles for insect pest control: encapsulation of essential oil monoterpenes inside a triblock copolymer shell for head lice control.

PubMed

Lucia, Alejandro; Toloza, Ariel Ceferino; Guzmán, Eduardo; Ortega, Francisco; Rubio, Ramón G

2017-01-01

Essential oil components (EOCs) are molecules with interesting application in pest control, these have been evaluated against different insect pest from more than 100 years, but their practical use is rather limited. Thus, the enhancement of their bioavailability and manageability due to their dispersion in water can open new perspective for the preparation of formulations for the control of insect pest. In this work, we studied the encapsulation of different monoterpenes in a poloxamer shell in order to prepare aqueous formulations that can be used for the development of platforms used in pest control. Micellar systems containing a 5 wt% of poloxamer 407 and 1.25 wt% of the different monoterpenes were prepared. Dynamic Light Scattering (DLS) experiments were carried out to characterize the dispersion of the EOCs in water. The pediculicidal activity of these micellar systems was tested on head lice using an ex vivo immersion test. The poloxamers allowed the dispersion of EOCs in water due to their encapsulation inside the hydrophobic core of the copolymer micelles. From this study, we concluded that it is possible to make stable micellar systems containing water (>90 wt%), 1.25 wt% of different monoterpenes and a highly safe polymer (5wt% Poloxamer 407). These formulations were effective against head lice with mortality ranging from 30 to 60%, being the most effective emulsions those containing linalool, 1,8-cineole, α -terpineol, thymol, eugenol, geraniol and nonyl alcohol which lead to mortalities above 50%. Since these systems showed good pediculicidal activity and high physicochemical stability, they could be a new route for the green fabrication of biocompatible and biosustainable insecticide formulations.

Interactions of S-peptide analogue in aqueous urea and trimethylamine-N-oxide solutions: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Sarma, Rahul; Paul, Sandip

2013-07-01

The ability of the osmolyte, trimethylamine-N-oxide (TMAO), to protect proteins from deleterious effect of urea, another commonly available osmolyte, is well-established. However, the molecular mechanism of this counteraction is not understood yet. To provide a molecular level understanding of how TMAO protects proteins in highly concentrated urea solution, we report here molecular dynamics simulation results of a 15-residue model peptide in two different conformations: helix and extended. For both conformations, simulations are carried out in pure water as well as in binary and ternary aqueous solutions of urea and TMAO. Analysis of solvation characteristics reveals direct interactions of urea and TMAO with peptide residues. However, the number of TMAO molecules that enter in the first solvation shell of the peptide is significantly lower than that of urea, and, unlike water and urea, TMAO shows its inability to form hydrogen bond with backbone oxygen and negatively charged sidechains. Preferential accumulation of urea near the peptide surface and preferential exclusion of TMAO from the peptide surface are observed. Inclusion of osmolytes in the peptide solvation shell leads to dehydration of the peptide in binary and ternary solutions of urea and TMAO. Solvation of peptide residues are investigated more closely by calculating the number of hydrogen bonds between the peptide and solution species. It is found that number of hydrogen bonds formed by the peptide with solution species increases in binary urea solution (relative to pure water) and this relative enhancement in hydrogen bond number reduces upon addition of TMAO. Our simulation results also suggest that, in the ternary solution, the peptide solvation layer is better mixed in terms of water and urea as compared to binary urea solution. Implications of the results for counteraction mechanism of TMAO are discussed.

Novel polymeric micelles for insect pest control: encapsulation of essential oil monoterpenes inside a triblock copolymer shell for head lice control

PubMed Central

Guzmán, Eduardo; Ortega, Francisco; Rubio, Ramón G.

2017-01-01

Background Essential oil components (EOCs) are molecules with interesting application in pest control, these have been evaluated against different insect pest from more than 100 years, but their practical use is rather limited. Thus, the enhancement of their bioavailability and manageability due to their dispersion in water can open new perspective for the preparation of formulations for the control of insect pest. In this work, we studied the encapsulation of different monoterpenes in a poloxamer shell in order to prepare aqueous formulations that can be used for the development of platforms used in pest control. Methods Micellar systems containing a 5 wt% of poloxamer 407 and 1.25 wt% of the different monoterpenes were prepared. Dynamic Light Scattering (DLS) experiments were carried out to characterize the dispersion of the EOCs in water. The pediculicidal activity of these micellar systems was tested on head lice using an ex vivo immersion test. Results The poloxamers allowed the dispersion of EOCs in water due to their encapsulation inside the hydrophobic core of the copolymer micelles. From this study, we concluded that it is possible to make stable micellar systems containing water (>90 wt%), 1.25 wt% of different monoterpenes and a highly safe polymer (5wt% Poloxamer 407). These formulations were effective against head lice with mortality ranging from 30 to 60%, being the most effective emulsions those containing linalool, 1,8-cineole, α-terpineol, thymol, eugenol, geraniol and nonyl alcohol which lead to mortalities above 50%. Discussion Since these systems showed good pediculicidal activity and high physicochemical stability, they could be a new route for the green fabrication of biocompatible and biosustainable insecticide formulations. PMID:28439460

Study of clusters using negative ion photodetachment spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Yuexing

1995-12-01

The weak van der Waals interaction between an open-shell halogen atom and a closed-shell atom or molecule has been investigated using zero electron kinetic energy (ZEKE) spectroscopy. This technique is also applied to study the low-lying electronic states in GaAs and GaAs -. In addition, the spectroscopy and electron detachment dynamics of several small carbon cluster anions are studied using resonant multiphoton detachment spectroscopy.

Effects of scallop shell extract on scopolamine-induced memory impairment and MK801-induced locomotor activity.

PubMed

Hasegawa, Yasushi; Inoue, Tatsuro; Kawaminami, Satoshi; Fujita, Miho

2016-07-01

To evaluate the neuroprotective effects of the organic components of scallop shells (scallop shell extract) on memory impairment and locomotor activity induced by scopolamine or 5-methyl-10,11-dihydro-5H-dibenzo (a,d) cyclohepten-5,10-imine (MK801). Effect of the scallop shell extract on memory impairment and locomotor activity was investigated using the Y-maze test, the Morris water maze test, and the open field test. Scallop shell extract significantly reduced scopolamine-induced short-term memory impairment and partially reduced scopolamine-induced spatial memory impairment in the Morris water maze test. Scallop shell extract suppressed scopolamine-induced elevation of acetylcholine esterase activity in the cerebral cortex. Treatment with scallop shell extract reversed the increase in locomotor activity induced by scopolamine. Scallop shell extract also suppressed the increase in locomotor activity induced by MK801. Our results provide initial evidence that scallop shell extract reduces scopolamine-induced memory impairment and suppresses MK-801-induced hyperlocomotion. Copyright © 2016 Hainan Medical College. Production and hosting by Elsevier B.V. All rights reserved.

Gold core@silver semishell Janus nanoparticles prepared by interfacial etching.

PubMed

Chen, Limei; Deming, Christopher P; Peng, Yi; Hu, Peiguang; Stofan, Jake; Chen, Shaowei

2016-08-14

Gold core@silver semishell Janus nanoparticles were prepared by chemical etching of Au@Ag core-shell nanoparticles at the air/water interface. Au@Ag core-shell nanoparticles were synthesized by chemical deposition of a silver shell onto gold seed colloids followed by the self-assembly of 1-dodecanethiol onto the nanoparticle surface. The nanoparticles then formed a monolayer on the water surface of a Langmuir-Blodgett trough, and part of the silver shell was selectively etched away by the mixture of hydrogen peroxide and ammonia in the water subphase, where the etching was limited to the side of the nanoparticles that was in direct contact with water. The resulting Janus nanoparticles exhibited an asymmetrical distribution of silver on the surface of the gold cores, as manifested in transmission electron microscopy, UV-vis absorption, and X-ray photoelectron spectroscopy measurements. Interestingly, the Au@Ag semishell Janus nanoparticles exhibited enhanced electrocatalytic activity in oxygen reduction reactions, as compared to their Au@Ag and Ag@Au core-shell counterparts, likely due to a synergistic effect between the gold cores and silver semishells that optimized oxygen binding to the nanoparticle surface.

High Water Tolerance of a Core-Shell-Structured Zeolite for CO2 Adsorptive Separation under Wet Conditions.

PubMed

Miyamoto, Manabu; Ono, Shumpei; Kusukami, Kodai; Oumi, Yasunori; Uemiya, Shigeyuki

2018-06-11

Dehumidification in CO 2 adsorptive separation processes is an important issue, owing to its high energy consumption. However, available adsorbents such as low-silica zeolites show a significant decrease in CO 2 adsorption capacity when water vapor is present. A core-shell-structured MFI-type zeolite with a hydrophilic ZSM-5 coated with a hydrophobic silicalite-1 shell layer was applied in CO 2 adsorptive separation under wet conditions. This hybrid material demonstrated remarkably high water tolerance with stable CO 2 adsorption performance without additional thermal treatment for regeneration, whereas a significant decrease in the CO 2 adsorption amount because of water vapor was observed on the parent ZSM-5. The core-shell structure of zeolites with high pore volumes, such as LTA or CHA, could also be suitable candidates for high CO 2 adsorption capacity and high water tolerance for practical applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Preparation of core-shell CaCO3 capsules via Pickering emulsion templates.

PubMed

Wang, Xiaoli; Zhou, Weizheng; Cao, Jian; Liu, Weichang; Zhu, Shiping

2012-04-15

Micron size and food grade pristine CaCO(3) particles were used to stabilize an oil in water Pickering emulsion. The particles also acted as nucleation sites for the subsequent crystallization of CaCO(3) with the addition of CaCl(2) and CO(2) gas as precursors. After the controllable crystallization process, a dense CaCO(3) shell with a few microns in thickness was formed. The CaCO(3) shell was proven to be calcite without the presence of crystallization modifiers. The crystallization speed and the shell integrity were controlled by manipulating the addition of CaCl(2) amount during the different crystallization stages; therefore, the homogeneous nucleation in the bulk was almost inhibited, and the heterogeneous nucleation at the oil-water interface on pristine CaCO(3) particles was the main contribution to the growth of the shell. The encapsulated limonene flavor in CaCO(3) capsules showed a prolonged release in neutral water at 85°C, while a burst release at pH 2 water as expected. The method is a simple and scalable process for creating inorganic core-shell capsules and can be used for producing food grade capsules for controlling the flavor release or masking undesirable taste in mouth. Copyright © 2012 Elsevier Inc. All rights reserved.

Synthesis and characterization of triangulene

NASA Astrophysics Data System (ADS)

Pavliček, Niko; Mistry, Anish; Majzik, Zsolt; Moll, Nikolaj; Meyer, Gerhard; Fox, David J.; Gross, Leo

2017-05-01

Triangulene, the smallest triplet-ground-state polybenzenoid (also known as Clar's hydrocarbon), has been an enigmatic molecule ever since its existence was first hypothesized. Despite containing an even number of carbons (22, in six fused benzene rings), it is not possible to draw Kekulé-style resonant structures for the whole molecule: any attempt results in two unpaired valence electrons. Synthesis and characterization of unsubstituted triangulene has not been achieved because of its extreme reactivity, although the addition of substituents has allowed the stabilization and synthesis of the triangulene core and verification of the triplet ground state via electron paramagnetic resonance measurements. Here we show the on-surface generation of unsubstituted triangulene that consists of six fused benzene rings. The tip of a combined scanning tunnelling and atomic force microscope (STM/AFM) was used to dehydrogenate precursor molecules. STM measurements in combination with density functional theory (DFT) calculations confirmed that triangulene keeps its free-molecule properties on the surface, whereas AFM measurements resolved its planar, threefold symmetric molecular structure. The unique topology of such non-Kekulé hydrocarbons results in open-shell π-conjugated graphene fragments that give rise to high-spin ground states, potentially useful in organic spintronic devices. Our generation method renders manifold experiments possible to investigate triangulene and related open-shell fragments at the single-molecule level.

Sound-structure interaction analysis of an infinite-long cylindrical shell submerged in a quarter water domain and subject to a line-distributed harmonic excitation

NASA Astrophysics Data System (ADS)

Guo, Wenjie; Li, Tianyun; Zhu, Xiang; Miao, Yuyue

2018-05-01

The sound-structure coupling problem of a cylindrical shell submerged in a quarter water domain is studied. A semi-analytical method based on the double wave reflection method and the Graf's addition theorem is proposed to solve the vibration and acoustic radiation of an infinite cylindrical shell excited by an axially uniform harmonic line force, in which the acoustic boundary conditions consist of a free surface and a vertical rigid surface. The influences of the complex acoustic boundary conditions on the vibration and acoustic radiation of the cylindrical shell are discussed. It is found that the complex acoustic boundary has crucial influence on the vibration of the cylindrical shell when the cylindrical shell approaches the boundary, and the influence tends to vanish when the distances between the cylindrical shell and the boundaries exceed certain values. However, the influence of the complex acoustic boundary on the far-field sound pressure of the cylindrical shell cannot be ignored. The far-field acoustic directivity of the cylindrical shell varies with the distances between the cylindrical shell and the boundaries, besides the driving frequency. The work provides more understanding on the vibration and acoustic radiation behaviors of cylindrical shells with complex acoustic boundary conditions.

Molecular-dynamics simulations of alkaline-earth metal cations in water by atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Yang, Zhong-Zhi; Li, Xin

2005-09-01

Intermolecular potential for alkaline-earth metal (Be(2+), Mg(2+), and Ca(2+)) cations in water has been derived using the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), and it is consistent with what was previously applied to the hydration study of the monovalent cations. Parameters for the effective interaction between a cation and a water molecule were determined, reproducing the ab initio results. The static, dynamic, and thermodynamic properties of Be(2+)(aq), Mg(2+)(aq), and Ca(2+)(aq) were studied using these potential parameters. Be(2+) requires a more complicated form of the potential function than Mg(2+) and Ca(2+) in order to obtain better fits. Strong influences of the twofold charged cations on the structures of the hydration shells and some other properties of aqueous ionic solutions are discussed and compared with the results of a previous study of monovalent cations in water. At the same time, comparative study of the hydration properties of each cation is also discussed. This work demonstrates that ABEEM/MM provides a useful tool in the exploration of the hydration of double-charged cations in water.

Novel alginate-based nanocarriers as a strategy to include high concentrations of hydrophobic compounds in hydrogels for topical application.

PubMed

Nguyen, H T P; Munnier, E; Souce, M; Perse, X; David, S; Bonnier, F; Vial, F; Yvergnaux, F; Perrier, T; Cohen-Jonathan, S; Chourpa, I

2015-01-26

The cutaneous penetration of hydrophobic active molecules is of foremost concern in the dermatology and cosmetic formulation fields. The poor solubility in water of those molecules limits their use in hydrophilic forms such as gels, which are favored by patients with chronic skin disease. The aim of this work is to design a novel nanocarrier of hydrophobic active molecules and to determine its potential as an ingredient of a topical form. The nanocarrier consists of an oily core surrounded by a protective shell of alginate, a natural polysaccharide isolated from brown algae. These calcium alginate-based nanocarriers (CaANCs) were prepared at room temperature and without the use of organic solvent by an accelerated nanoemulsification-polymer crosslinking method. The size (hydrodynamic diameter ~200 nm) and surface charge (zeta potential ~ - 30 mV) of the CaANCs are both compatible with their application on skin. CaANCs loaded with a fluorescent label were stable in model hydrophilic galenic forms under different storage conditions. Curcumin was encapsulated in CaANCs with an efficiency of ~95%, fully retaining its antioxidant activity. The application of the curcumin-loaded CaANCs on excised human skin led to a significant accumulation of the active molecules in the upper layers of the skin, asserting the potential of these nanocarriers in active pharmaceutical and cosmetic ingredients topical delivery.

Novel alginate-based nanocarriers as a strategy to include high concentrations of hydrophobic compounds in hydrogels for topical application

NASA Astrophysics Data System (ADS)

Nguyen, H. T. P.; Munnier, E.; Souce, M.; Perse, X.; David, S.; Bonnier, F.; Vial, F.; Yvergnaux, F.; Perrier, T.; Cohen-Jonathan, S.; Chourpa, I.

2015-06-01

The cutaneous penetration of hydrophobic active molecules is of foremost concern in the dermatology and cosmetic formulation fields. The poor solubility in water of those molecules limits their use in hydrophilic forms such as gels, which are favored by patients with chronic skin disease. The aim of this work is to design a novel nanocarrier of hydrophobic active molecules and to determine its potential as an ingredient of a topical form. The nanocarrier consists of an oily core surrounded by a protective shell of alginate, a natural polysaccharide isolated from brown algae. These calcium alginate-based nanocarriers (CaANCs) were prepared at room temperature and without the use of organic solvent by an accelerated nanoemulsification-polymer crosslinking method. The size (hydrodynamic diameter ˜200 nm) and surface charge (zeta potential ˜ - 30 mV) of the CaANCs are both compatible with their application on skin. CaANCs loaded with a fluorescent label were stable in model hydrophilic galenic forms under different storage conditions. Curcumin was encapsulated in CaANCs with an efficiency of ˜95%, fully retaining its antioxidant activity. The application of the curcumin-loaded CaANCs on excised human skin led to a significant accumulation of the active molecules in the upper layers of the skin, asserting the potential of these nanocarriers in active pharmaceutical and cosmetic ingredients topical delivery.

Exploiting the spatial locality of electron correlation within the parametric two-electron reduced-density-matrix method

NASA Astrophysics Data System (ADS)

DePrince, A. Eugene; Mazziotti, David A.

2010-01-01

The parametric variational two-electron reduced-density-matrix (2-RDM) method is applied to computing electronic correlation energies of medium-to-large molecular systems by exploiting the spatial locality of electron correlation within the framework of the cluster-in-molecule (CIM) approximation [S. Li et al., J. Comput. Chem. 23, 238 (2002); J. Chem. Phys. 125, 074109 (2006)]. The 2-RDMs of individual molecular fragments within a molecule are determined, and selected portions of these 2-RDMs are recombined to yield an accurate approximation to the correlation energy of the entire molecule. In addition to extending CIM to the parametric 2-RDM method, we (i) suggest a more systematic selection of atomic-orbital domains than that presented in previous CIM studies and (ii) generalize the CIM method for open-shell quantum systems. The resulting method is tested with a series of polyacetylene molecules, water clusters, and diazobenzene derivatives in minimal and nonminimal basis sets. Calculations show that the computational cost of the method scales linearly with system size. We also compute hydrogen-abstraction energies for a series of hydroxyurea derivatives. Abstraction of hydrogen from hydroxyurea is thought to be a key step in its treatment of sickle cell anemia; the design of hydroxyurea derivatives that oxidize more rapidly is one approach to devising more effective treatments.

Spectrum of Slow and Super-Slow (Picosecond to Nanosecond) Water Dynamics around Organic and Biological Solutes.

PubMed

Ramakrishnan, Gopakumar; González-Jiménez, Mario; Lapthorn, Adrian J; Wynne, Klaas

2017-07-06

Water dynamics in the solvation shell of solutes plays a very important role in the interaction of biomolecules and in chemical reaction dynamics. However, a selective spectroscopic study of the solvation shell is difficult because of the interference of the solute dynamics. Here we report on the observation of heavily slowed down water dynamics in the solvation shell of different solutes by measuring the low-frequency spectrum of solvation water, free from the contribution of the solute. A slowdown factor of ∼50 is observed even for relatively low concentrations of the solute. We go on to show that the effect can be generalized to different solutes including proteins.

One-pot synthesis of iniferter-bound polystyrene core nanoparticles for the controlled grafting of multilayer shells

NASA Astrophysics Data System (ADS)

Marchyk, Nataliya; Maximilien, Jacqueline; Beyazit, Selim; Haupt, Karsten; Sum Bui, Bernadette Tse

2014-02-01

A novel approach using one-pot synthesis for the production of uniform, iniferter-bound polystyrene core nanoparticles of size 30-40 nm is described. Conventional oil-in-water emulsion polymerisation of styrene and divinylbenzene, combining a hybrid initiation system (thermal and UV), triggered sequentially, was employed to form the surface-bound thiocarbamate iniferters in situ. The iniferter cores were then used as seeds for re-initiating further polymerisation by UV irradiation to produce water-compatible core-shell nanoparticles. Grafting of various shell-types is demonstrated: linear polymers of poly(N-isopropylacrylamide) brushes, crosslinked polymers bearing different surface charges and molecularly imprinted polymers. The shell thickness was readily tuned by varying the monomers' concentration and polymerisation time. Our method is straightforward and in addition, gives access to the preparation of fluorescent seeds and the possibility of grafting nanosized multiple shells. The core-shell nanoparticles were fully characterised by dynamic light scattering, transmission electron microscopy, Fourier transform infrared spectroscopy and microelemental analysis.A novel approach using one-pot synthesis for the production of uniform, iniferter-bound polystyrene core nanoparticles of size 30-40 nm is described. Conventional oil-in-water emulsion polymerisation of styrene and divinylbenzene, combining a hybrid initiation system (thermal and UV), triggered sequentially, was employed to form the surface-bound thiocarbamate iniferters in situ. The iniferter cores were then used as seeds for re-initiating further polymerisation by UV irradiation to produce water-compatible core-shell nanoparticles. Grafting of various shell-types is demonstrated: linear polymers of poly(N-isopropylacrylamide) brushes, crosslinked polymers bearing different surface charges and molecularly imprinted polymers. The shell thickness was readily tuned by varying the monomers' concentration and polymerisation time. Our method is straightforward and in addition, gives access to the preparation of fluorescent seeds and the possibility of grafting nanosized multiple shells. The core-shell nanoparticles were fully characterised by dynamic light scattering, transmission electron microscopy, Fourier transform infrared spectroscopy and microelemental analysis. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr05295h

Effective Role of Magnetic Core-Shell Nanocomposites in Removing Organic and Inorganic Wastes from Water.

PubMed

Shah, Nasrullah; Claessyns, Frederick; Rimmer, Stephen; Arain, Muhammad Balal; Rehan, Touseef; Wazwaz, Aref; Ahmad, Mohammad Wasi; Ul-Islam, Mazhar

2016-01-01

Affordable and efficient water treatment process to produce water free from various contaminants is a big challenge. The presence of toxic heavy metals, dyes, hazardous chemicals and other toxins causes contamination of water sources and our food chain and make them hazardous to living organisms. The current water treatment processes are no longer sustainable due to high cost and low efficiency. Due to advantageous properties, nanotechnology based materials can play a great role in increasing the efficiency of water treatment processes. Magnetic nanocomposites use nano as well as magnetic properties and have the potential to provide a sophisticated system to overcome most of the impurities present in water. There is a diversity of magnetic nanocomposites, however presently we have focussed the core-shell magnetic nanocomposites because they have excellent magnetic and separation properties, stability, and good biocompatibility. We collected systematically the bibliographic data bases for peer-reviewed research literature focusing on the theme of our review. The quality of the included research papers are selected by standard tools. A conceptual frame work is designed to arrange the topics and extracted the interventions and findings of the included studies. The overall study was divided into sections and each section incorporated the most appropriate literature citation. Total one hundred and eight references were included of which 32 references were used for basic description/introduction of core-shell magnetic nanocomposites. One review paper containing the synthesis methods for core shell magnetic nanocomposites is included while majority (76) of the references are included for comprehensive description of applications of the core-shell nanocomposites among which 25 were for dyes removal, 27 for hazardous metals, 07 for hazardous chemicals, 12 for pesticides and biological contaminants removal and five other including patents were added as miscellaneous substances removal from water sources. This review identified the effective role of core-shell magnetic nanocomposites for environmental remediation in terms of removal of various hazardous substances from water resources. The outcome of the present review confirms that the magnetic core-shell nanocomposites provide a cost effective and efficient way for the removal of various toxic substances including dyes, heavy metals, toxic organic chemicals, pesticides and some biological contaminants from water sources.

Adsorbates in a Box: Titration of Substrate Electronic States

NASA Astrophysics Data System (ADS)

Cheng, Zhihai; Wyrick, Jonathan; Luo, Miaomiao; Sun, Dezheng; Kim, Daeho; Zhu, Yeming; Lu, Wenhao; Kim, Kwangmoo; Einstein, T. L.; Bartels, Ludwig

2010-08-01

Nanoscale confinement of adsorbed CO molecules in an anthraquinone network on Cu(111) with a pore size of ≈4nm arranges the CO molecules in a shell structure that coincides with the distribution of substrate confined electronic states. Molecules occupy the states approximately in the sequence of rising electron energy. Despite the sixfold symmetry of the pore boundary itself, the adsorbate distribution adopts the threefold symmetry of the network-substrate system, highlighting the importance of the substrate even for such quasi-free-electron systems.

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

PubMed Central

Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

2016-01-01

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method. PMID:27025410

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

NASA Astrophysics Data System (ADS)

Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

2016-03-01

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method.

Hydrology and water quality of Shell Lake, Washburn County, Wisconsin, with special emphasis on the effects of diversion and changes in water level on the water quality of a shallow terminal lake

USGS Publications Warehouse

Juckem, Paul F.; Robertson, Dale M.

2013-01-01

Shell Lake is a relatively shallow terminal lake (tributaries but no outlets) in northwestern Wisconsin that has experienced approximately 10 feet (ft) of water-level fluctuation over more than 70 years of record and extensive flooding of nearshore areas starting in the early 2000s. The City of Shell Lake (City) received a permit from the Wisconsin Department of Natural Resources in 2002 to divert water from the lake to a nearby river in order to lower water levels and reduce flooding. Previous studies suggested that water-level fluctuations were driven by long-term cycles in precipitation, evaporation, and runoff, although questions about the lake’s connection with the groundwater system remained. The permit required that the City evaluate assumptions about lake/groundwater interactions made in previous studies and evaluate the effects of the water diversion on water levels in Shell Lake and other nearby lakes. Therefore, a cooperative study between the City and U.S. Geological Survey (USGS) was initiated to improve the understanding of the hydrogeology of the area and evaluate potential effects of the diversion on water levels in Shell Lake, the surrounding groundwater system, and nearby lakes. Concerns over deteriorating water quality in the lake, possibly associated with changes in water level, prompted an additional cooperative project between the City and the USGS to evaluate efeffects of changes in nutrient loading associated with changes in water levels on the water quality of Shell Lake. Numerical models were used to evaluate how the hydrology and water quality responded to diversion of water from the lake and historical changes in the watershed. The groundwater-flow model MODFLOW was used to simulate groundwater movement in the area around Shell Lake, including groundwater/surface-water interactions. Simulated results from the MODFLOW model indicate that groundwater flows generally northward in the area around Shell Lake, with flow locally converging toward the lake. Total groundwater inflow to Shell Lake is small (approximately 5 percent of the water budget) compared with water entering the lake from precipitation (83 percent) and surface-water runoff (13 percent). The MODFLOW model also was used to simulate average annual hydrologic conditions from 1949 to 2009, including effects of the removal of 3 billion gallons of water during 2003–5. The maximum decline in simulated average annual water levels for Shell Lake due to the diversion alone was 3.3 ft at the end of the diversion process in 2005. Model simulations also indicate that although water level continued to decline through 2009 in response to local weather patterns (local drought), the effects of the diversion decreased after the diversion ceased; that is, after 4 years of recovery (2006–9), drawdown attributable to the diversion alone decreased by about 0.6 ft because of increased groundwater inflow and decreased lake-water outflow to groundwater caused by the artificially lower lake level. A delayed response in drawdown of less than 0.5 ft was transmitted through the groundwater-flow system to upgradient lakes. This relatively small effect on upgradient lakes is attributed in part to extensive layers of shallow clay that limit lake/groundwater interaction in the area. Data collected in the lake indicated that Shell Lake is polymictic (characterized by frequent deep mixing) and that its productivity is limited by the amount of phosphorus in the lake. The lake was typically classified as oligotrophic-mesotrophic in June, mesotrophic in July, and mesotrophic-eutrophic in August. In polymictic lakes like Shell Lake, phosphorus released from the sediments is not trapped near the bottom of the lake but is intermittently released to the shallow water, resulting in deteriorating water quality as summer progresses. Because the productivity of Shell Lake is limited by phosphorus, the sources of phosphorus to the lake were quantified, and the response in water quality to changes in phosphorus inputs were evaluated by means of eutrophication models. During 2009, the total input of phosphorus to Shell Lake was 1,730 pounds (lb), of which 1,320 lb came from external sources (76 percent) and 414 lb came from internal loading from sediments in the lake (24 percent). The largest external source was from surface-water runoff, which delivered about 52 percent of the total phosphorus load compared with about 13 percent of the water input. The second largest source was from precipitation (wetfall and dryfall), which delivered 19 percent of the load compared to about 83 percent of the water input. Contributions from septic systems and groundwater accounted for about 3 and 2 percent, respectively. Increased runoff raises water levels in the lake but does not necessarily increase phosphorus loading because phosphorus concentrations in the tributaries decline during increased flow, possibly because of shorter retention times in upstream wetlands. Phosphorus loading to the lake in 2009 represented what occurred after a series of dry years; therefore, this information was combined with data from 2011, a wet year, to estimate phosphorus loading during a range of hydrologic conditions by estimating loading from each component of the phosphorus budget for each year from 1949 to 2011. Comparisons of historical water-quality records with historical water levels and applications of a hydrodynamic model (Dynamic Lake Model, DLM) and empirical eutrophication models were used to understand how changes in water level and the coinciding changes in phosphorus loading affect the water quality of Shell Lake. DLM simulations indicate that large changes in water level (approximately 10 ft) affect the persistence of stratification in the lake. During periods with low water levels, the lake is a well-mixed, polymictic system, with water quality degrading slightly as summer progresses. During periods with high water levels, the lake is more stratified, and phosphorus from internal loading is trapped in the hypolimnion and released later in summer, which results in more extreme seasonality in water quality and better clarity in early summer. Results of eutrophication model simulations using a range in external phosphorus inputs illustrate how water quality in Shell Lake (phosphorus and chlorophyll a concentrations and Secchi depths) responds to changes in external phosphorus loading. Results indicate that a 50-percent reduction in external loading from that measured in 2009 would be required to change phosphorus concentrations from 0.018 milligram per liter (mg/L) (measured in 2009) to 0.012 mg/L (estimated for the mid-1800s from analysis of diatoms in sediment cores). Such reductions in phosphorus loading cannot be accomplished by targeting septic systems or internal loading alone because septic systems contribute only about 3 percent of the phosphorus input to the lake, and internal loading from the sediments of Shell Lake contributes only about 25 percent of phosphorus input. Complete elimination of phosphorus from septic systems and internal loading would decrease the phosphorus concentrations in the lake by 0.003–0.004 mg/L. Therefore, reducing phosphorus concentration in the lake more than by 0.004 mg/L requires decreasing phosphorus loading from surface-water contributions, primarily runoff to the lake. Reconstructed changes in water quality from 1860 to 2010, based on changes in the diatom communities archived in the sediments and eutrophication model simulations, suggest that anthropogenic changes in the watershed (sawmill construction in 1881; the establishment of the village of Shell Lake; and land-use changes in the 1920s, including increased agriculture) had a much larger effect on water quality than the natural changes associated with fluctuations in water level. Although the effects of natural changes in water level on water quality appear to be small, changes in water level do have a modest effect on water quality, primarily manifested as small improvements during higher water levels. Fluctuations in water level, however, have a larger effect on the seasonality of water-quality patterns, with better water quality, especially increased Secchi depths, in early summer during years with high water levels.

Marine bivalve shell geochemistry and ultrastructure from modern low pH environments: environmental effect versus experimental bias

NASA Astrophysics Data System (ADS)

Hahn, S.; Rodolfo-Metalpa, R.; Griesshaber, E.; Schmahl, W. W.; Buhl, D.; Hall-Spencer, J. M.; Baggini, C.; Fehr, K. T.; Immenhauser, A.

2012-05-01

Bivalve shells can provide excellent archives of past environmental change but have not been used to interpret ocean acidification events. We investigated carbon, oxygen and trace element records from different shell layers in the mussels Mytilus galloprovincialis combined with detailed investigations of the shell ultrastructure. Mussels from the harbour of Ischia (Mediterranean, Italy) were transplanted and grown in water with mean pHT 7.3 and mean pHT 8.1 near CO2 vents on the east coast of the island. Most prominently, the shells recorded the shock of transplantation, both in their shell ultrastructure, textural and geochemical record. Shell calcite, precipitated subsequently under acidified seawater responded to the pH gradient by an in part disturbed ultrastructure. Geochemical data from all test sites show a strong metabolic effect that exceeds the influence of the low-pH environment. These field experiments showed that care is needed when interpreting potential ocean acidification signals because various parameters affect shell chemistry and ultrastructure. Besides metabolic processes, seawater pH, factors such as salinity, water temperature, food availability and population density all affect the biogenic carbonate shell archive.

Small-angle-neutron-scattering from giant water-in-oil microemulsion droplets. II. Polymer-decorated droplets in a quaternary system

NASA Astrophysics Data System (ADS)

Foster, Tobias; Sottmann, Thomas; Schweins, Ralf; Strey, Reinhard

2008-02-01

Amphiphilic block copolymers of the type poly(ethylenepropylene)-co-poly(ethyleneoxide) dramatically enhance the solubilisation efficiency of non-ionic surfactants in microemulsions that contain equal volumes of water in oil. Consequently, the length scale of the microstructure of such bicontinuous microemulsions is dramatically increased up to the order of a few 100nm. In this paper, we show that this so-called efficiency boosting effect can also be applied to water-in-oil microemulsions with droplet microstructure. Such giant water-in-oil microemulsions would provide confined compartments in which chemical reactions of biological macromolecules can be performed on a single molecule level. With this motivation we investigated the phase behavior and the microstructure of oil-rich microemulsions containing D2O, n-decane(d22), C10E4 and the amphiphilic block copolymer PEP5-PEO5 [poly(ethylenepropylene)-co-poly(ethyleneoxide), weight per block of 5000g/mol]. We found that 15wt% of water can be solubilised by 5wt% of surfactant and block copolymer when about 6wt% of surfactant is replaced by the block copolymer. Small-angle-neutron-scattering experiments were performed to determine the length scales and microstructure topologies of the oil-rich microemulsions. To analyze the scattering data, we derived a novel form factor that also takes into account the scattering contribution of the hydrophobic part of the block copolymer molecules that reside in the surfactant shell. The quantitative analysis of the scattering data with this form factor shows that the radius of the largest droplets amounts up to 30nm. The novel form factor also yielded qualitative information on the stretching of the polymer chains in dependence on the polymer surface density and the droplet radius.

Fishing and bottom water temperature as drivers of change in maximum shell length in Atlantic surfclams (Spisula solidissima)

NASA Astrophysics Data System (ADS)

Munroe, D. M.; Narváez, D. A.; Hennen, D.; Jacobson, L.; Mann, R.; Hofmann, E. E.; Powell, E. N.; Klinck, J. M.

2016-03-01

Maximum shell length of Atlantic surfclams (Spisula solidissima) on the Middle Atlantic Bight (MAB) continental shelf, obtained from federal fishery survey data from 1982-present, has decreased by 15-20 mm. Two potential causes of this decreasing trend, fishery removal of large animals and stress due to warming bottom temperatures, were investigated using an individual-based model for post-settlement surfclams and a fifty-year hindcast of bottom water temperatures on the MAB. Simulations showed that fishing and/or warming bottom water temperature can cause decreases in maximum surfclam shell length (body size) equivalent to those observed in the fished stock. Independently, either localized fishing rates of 20% or sustained bottom temperatures that are 2 °C warmer than average conditions generate the observed decrease in maximum shell length. However, these independent conditions represent extremes and are not sustained in the MAB. The combined effects of fishing and warmer temperatures can generate simulated length decreases that are similar to observed decreases. Interannual variability in bottom water temperatures can also generate fluctuations in simulated shell length of up to 20 mm over a period of 10-15 years. If the change in maximum size is not genotypic, simulations also suggest that shell size composition of surfclam populations can recover if conditions change; however, that recovery could take a decade to become evident.

Survival and growth of salmonella in high-moisture pecan nutmeats, in-shell pecans, inedible nut components, and orchard soil.

PubMed

Beuchat, Larry R; Mann, David A

2010-11-01

Outbreaks of salmonellosis associated with almonds have raised interest in better understanding the behavior of Salmonella on other tree nuts. We undertook a study to determine the survival and growth characteristics of Salmonella on high-moisture (water activity of 0.96 to 0.99) pecan nutmeats, in-shell pecans, and inedible components (shuck, shell, and middle septum tissue) of in-shell pecans. Salmonella did not grow on high-moisture nutmeat halves, pieces, or granules stored at 4°C for up to 48 h. Growth did occur, however, at 21, 30, and 37°C. Increases of 1.77 to 5.87 log CFU/g of nutmeats occurred within 48 h at 37°C; the order in which nutmeats supported growth was granules > pieces > halves. Populations of Salmonella on and in high-moisture in-shell pecans (kernel water activity of 0.94) stored at 4, 21, 30, and 37°C for 8 days decreased by 0.52 to 1.19 log CFU/g. The pathogen grew on the surface of high-moisture (water activity of 0.99) pecan shucks and shells but died on middle septum tissue stored at 21, 30, and 37°C for up to 6 days. Salmonella died in water extracts of shucks and in pecan orchard soil saturated with water or shuck extract, but survived well for at least 18 weeks in dry soil. The ability of the pathogen to grow on high-moisture nutmeats and some of the inedible components of pecans emphasizes the importance of controlling or limiting the time pecans are exposed to water in preharvest and postharvest environments.

Marine bivalve geochemistry and shell ultrastructure from modern low pH environments

NASA Astrophysics Data System (ADS)

Hahn, S.; Rodolfo-Metalpa, R.; Griesshaber, E.; Schmahl, W. W.; Buhl, D.; Hall-Spencer, J. M.; Baggini, C.; Fehr, K. T.; Immenhauser, A.

2011-10-01

Bivalve shells can provide excellent archives of past environmental change but have not been used to interpret ocean acidification events. We investigated carbon, oxygen and trace element records from different shell layers in the mussels Mytilus galloprovincialis (from the Mediterranean) and M. edulis (from the Wadden Sea) combined with detailed investigations of the shell ultrastructure. Mussels from the harbour of Ischia (Mediterranean, Italy) were transplanted and grown in water with mean pHT 7.3 and mean pHT 8.1 near CO2 vents on the east coast of the island of Ischia. The shells of transplanted mussels were compared with M. edulis collected at pH ~8.2 from Sylt (German Wadden Sea). Most prominently, the shells recorded the shock of transplantation, both in their shell ultrastructure, textural and geochemical record. Shell calcite, precipitated subsequently under acidified seawater responded to the pH gradient by an in part disturbed ultrastructure. Geochemical data from all test sites show a strong metabolic effect that exceeds the influence of the low-pH environment. These field experiments showed that care is needed when interpreting potential ocean acidification signals because various parameters affect shell chemistry and ultrastructure. Besides metabolic processes, seawater pH, factors such as salinity, water temperature, food availability and population density all affect the biogenic carbonate shell archive.

Molecular basis for polyol-induced protein stability revealed by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Liu, Fu-Feng; Ji, Luo; Zhang, Lin; Dong, Xiao-Yan; Sun, Yan

2010-06-01

Molecular dynamics simulations of chymotrypsin inhibitor 2 in different polyols (glycerol, xylitol, sorbitol, trehalose, and sucrose) at 363 K were performed to probe the molecular basis of the stabilizing effect, and the data in water, ethanol, and glycol were compared. It is found that protein protection by polyols is positively correlated with both the molecular volume and the fractional polar surface area, and the former contributes more significantly to the protein's stability. Polyol molecules have only a few direct hydrogen bonds with the protein, and the number of hydrogen bonds between a polyol and the protein is similar for different polyols. Thus, it is concluded that the direct interactions contribute little to the stabilizing effect. It is clarified that the preferential exclusion of the polyols is the origin of their protective effects, and it increases with increasing polyol size. Namely, there is preferential hydration on the protein surface (2 Å), and polyol molecules cluster around the protein at a distance of about 4 Å. The preferential exclusion of polyols leads to indirect interactions that prevent the protein from thermal unfolding. The water structure becomes more ordered with increasing the polyol size. So, the entropy of water in the first hydration shell decreases, and a larger extent of decrease is observed with increasing polyol size, leading to larger transfer free energy. The findings suggest that polyols protect the protein from thermal unfolding via indirect interactions. The work has thus elucidated the molecular mechanism of structural stability of the protein in polyol solutions.

Lanthanum(III) and Lutetium(III) in Nitrate-Based Ionic Liquids: A Theoretical Study of Their Coordination Shell.

PubMed

Bodo, Enrico

2015-09-03

By using ab initio molecular dynamics, we investigate the solvent shell structure of La(3+) and Lu(3+) ions immersed in two ionic liquids, ethylammonium nitrate (EAN) and its hydroxy derivative (2-ethanolammonium nitrate, HOEAN). We provide the first study of the coordination properties of these heavy metal ions in such a highly charged nonacqueous environment. We find, as expected, that the coordination in the liquid is mainly due to nitrate anions and that, due to the bidentate nature of the ligand, the complexation shell of the central ion has a nontrivial geometry and a coordination number in terms of nitrate molecules that apparently violates the decrease of ionic radii along the lanthanides series, since the smaller Lu(3+) ion seems to coordinate six nitrate molecules and the La(3+) ion only five. A closer inspection of the structural features obtained from our calculations shows, instead, that the first shell of oxygen atoms is more compact for Lu(3+) than for La(3+) and that the former coordinates 8 oxygen atoms while the latter 10 in accord with the typical lanthanide's trend along the series and that their first solvation shells have a slight irregular and complex geometrical pattern. When moving to the HOEAN solutions, we have found that the solvation of the central ion is possibly also due to the cation itself through the oxygen atom on the side chain. Also, in this liquid, the coordination numbers in terms of oxygen atoms in both solvents is 10 for La(3+) and 8 for Lu(3+).

Hydrogeology and water quality of the Shell Valley Aquifer, Rolette County, North Dakota

USGS Publications Warehouse

Strobel, M.L.

1997-01-01

The Shell Valley aquifer is the sole source of water for the city of Belcourt and the primary source of water for most of the Turtle Mountain Indian Reservation. The Turtle Mountain Band of Chippewa Indians is concerned about the quantity and quality of water in the Shell Valley aquifer, which underlies about 56 square miles in central Rolette County and has an average saturated thickness of about 35 feet. Water levels across most of the Shell Valley aquifer fluctuate with variations in precipitation but generally are stable. Withdrawals from the north well field decreased slightly during 1976-95, but withdrawals from the south well field increased during 1983-95. Water levels in the south well field declined as withdrawals increased. The average decline during the last 8 years was about 1.75 feet per year. The water level has reached the well screen in at least one of the production wells. Most of the water in the aquifer is a bicarbonate type and has dissolved-solids concentrations ranging from 479 to 1,510 milligrams per liter. None of the samples analyzed had detectable concentrations of pesticides, but hydrocarbons were detected in both ground- and surfacewater samples. Polycyclic aromatic hydrocarbons (PAH) were the most frequently detected hydrocarbons. Benzene, toluene, ethylbenzene, and xylene (BTEX), polychlorinated biphenyls (PCB), and pentachlorophenol (PCP) also were detected.Generally, the Shell Valley aquifer is an adequate source of water for current needs, but evaluation of withdrawals in relation to a knowledge of aquifer hydrology would be important in quantifying sustainable water supplies. Water quality in the aquifer generally is good; the Turtle Mountain Band of Chippewa Indians filters the water to reduce concentrations of dissolved constituents. Hydrocarbons, although present in the aquifer, have not been quantified and may not pose a general health risk. Further analysis of the quantity and distribution of the hydrocarbons would be useful to understand their sources and implications for water use.

Core-shell nanofibers of curcumin/cyclodextrin inclusion complex and polylactic acid: Enhanced water solubility and slow release of curcumin.

PubMed

Aytac, Zeynep; Uyar, Tamer

2017-02-25

Core-shell nanofibers were designed via electrospinning using inclusion complex (IC) of model hydrophobic drug (curcumin, CUR) with cyclodextrin (CD) in the core and polymer (polylactic acid, PLA) in the shell (cCUR/HPβCD-IC-sPLA-NF). CD-IC of CUR and HPβCD was formed at 1:2 molar ratio. The successful formation of core-shell nanofibers was revealed by TEM and CLSM images. cCUR/HPβCD-IC-sPLA-NF released CUR slowly but much more in total than PLA-CUR-NF at pH 1 and pH 7.4 due to the restriction of CUR in the core of nanofibers and solubility improvement shown in phase solubility diagram, respectively. Improved antioxidant activity of cCUR/HPβCD-IC-sPLA-NF in methanol:water (1:1) is related with the solubility enhancement achieved in water based system. The slow reaction of cCUR/HPβCD-IC-sPLA-NF in methanol is associated with the shell inhibiting the quick release of CUR. On the other hand, cCUR/HPβCD-IC-sPLA-NF exhibited slightly higher rate of antioxidant activity than PLA-CUR-NF in methanol:water (1:1) owing to the enhanced solubility. To conclude, slow release of CUR was achieved by core-shell nanofiber structure and inclusion complexation of CUR with HPβCD provides high solubility. Briefly, electrospinning of core-shell nanofibers with CD-IC core could offer slow release of drugs as well as solubility enhancement for hydrophobic drugs. Copyright © 2017 Elsevier B.V. All rights reserved.

Synthesis of water dispersible boron core silica shell (B@SiO2) nanoparticles

NASA Astrophysics Data System (ADS)

Walton, Nathan I.; Gao, Zhe; Eygeris, Yulia; Ghandehari, Hamidreza; Zharov, Ilya

2018-04-01

Water dispersible boron nanoparticles have great potential as materials for boron neutron capture therapy of cancer and magnetic resonance imaging, if they are prepared on a large scale with uniform size and shape and hydrophilic modifiable surface. We report the first method to prepare spherical, monodisperse, water dispersible boron core silica shell nanoparticles (B@SiO2 NPs) suitable for aforementioned biomedical applications. In this method, 40 nm elemental boron nanoparticles, easily prepared by mechanical milling and carrying 10-undecenoic acid surface ligands, are hydrosilylated using triethoxysilane, followed by base-catalyzed hydrolysis of tetraethoxysilane, which forms a 10-nm silica shell around the boron core. This simple two-step process converts irregularly shaped hydrophobic boron particles into the spherically shaped uniform nanoparticles. The B@SiO2 NPs are dispersible in water and the silica shell surface can be modified with primary amines that allow for the attachment of a fluorophore and, potentially, of targeting moieties. [Figure not available: see fulltext.

Processes of energy deposition by heavy-particle and electron impact. Final progress report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salop, A.; Smith, F.T.

1978-04-18

Progress is reported in three areas of reasearch during the present period: K-shell ionization in high energy collisions of heavy ions with light target atoms using the sudden (Magnus) approximation, K-L level matching phenomena associated with K-shell vacancy production in heavy-ion collisions, and studies of low energy collisions of electrons with molecules using semi-classical perturbation theory. A brief discussion of each of these activities is given.

Non-empirical Prediction of the Photophysical and Magnetic Properties of Systems with Open d- and f-Shells Based on Combined Ligand Field and Density Functional Theory (LFDFT).

PubMed

Daul, Claude

2014-09-01

Despite the important growth of ab initio and computational techniques, ligand field theory in molecular science or crystal field theory in condensed matter offers the most intuitive way to calculate multiplet energy levels arising from systems with open shells d and/or f electrons. Over the past decade we have developed a ligand field treatment of inorganic molecular modelling taking advantage of the dominant localization of the frontier orbitals within the metal-sphere. This feature, which is observed in any inorganic coordination compound, especially if treated by Density Functional Theory calculation, allows the determination of the electronic structure and properties with a surprising good accuracy. In ligand field theory, the theoretical concepts consider only a single atom center; and treat its interaction with the chemical environment essentially as a perturbation. Therefore success in the simple ligand field theory is no longer questionable, while the more accurate molecular orbital theory does in general over-estimate the metal-ligand covalence, thus yields wave functions that are too delocalized. Although LF theory has always been popular as a semi-empirical method when dealing with molecules of high symmetry e.g. cubic symmetry where the number of parameters needed is reasonably small (3 or 5), this is no more the case for molecules without symmetry and involving both an open d- and f-shell (# parameters ∼90). However, the combination of LF theory and Density Functional (DF) theory that we introduced twenty years ago can easily deal with complex molecules of any symmetry with two and more open shells. The accuracy of these predictions from 1(st) principles achieves quite a high accuracy (<5%) in terms of states energies. Hence, this approach is well suited to predict the magnetic and photo-physical properties arbitrary molecules and materials prior to their synthesis, which is the ultimate goal of each computational chemist. We will illustrate the performance of LFDFT for the design of phosphors that produces light similar to our sun and predict the magnetic anisotropy energy of single ion magnets.

Organic-dye-coupled magnetic nanoparticles encaged inside thermoresponsive PNIPAM Microcapsules.

PubMed

Guo, Jia; Yang, Wuli; Deng, Yonghui; Wang, Changchun; Fu, Shoukuan

2005-07-01

We present a new approach for the fabrication of thermoresponsive polymer microcapsules with mobile magnetic cores that undergo a volume phase-transition upon changing the temperature and are collected under an external magnetic field. We have prepared organic/inorganic composite microspheres with a well-defined core-shell structure that are composed of a crosslinked poly(N-isopropylacrylamide) (PNIPAM) shell and silica cores dotted centrally by magnetite nanoparticles. Since the infiltration of template-decomposed products is dependent on the permeability of PNIPAM shells triggered by changes of exterior temperature, the silica layer sandwiched between the magnetic core and the PNIPAM shell was quantitatively removed to generate PNIPAM microcapsules with mobile magnetic cores by treatment with aqueous NaOH solution. For development of the desired multifunctional microcapsules, modification of the unetched silica surface interiors can be realized by treatment with a silane coupling agent containing functional groups that can easily bind to catalysts, enzymes, or labeling molecules. Herein, fluorescein isothiocyanate (FITC), which is a common organic dye, is attached to the insides of the mobile magnetic cores to give PNIPAM microcapsules with FITC-labeled magnetic cores. In this system, it can be expected that an extension of the functionalization of the cavity properties of smart polymer microcapsules is to immobilize other target molecules onto the mobile cores in order to introduce other desired functions in the hollow cage.

Solvent Electrostatic Response: From Simple Solutes to Proteins

NASA Astrophysics Data System (ADS)

Dinpajooh, Mohammadhasan

How water behaves at interfaces is relevant to many scientific and technological applications; however, many subtle phenomena are unknown in aqueous solutions. In this work, interfacial structural transition in hydration shells of a polarizable solute at critical polarizabilities is discovered. The transition is manifested in maximum water response, the reorientation of the water dipoles at the interface, and an increase in the density of dangling OH bonds. This work also addresses the role of polarizability of the active site of proteins in biological catalytic reactions. For proteins, the hydration shell becomes very heterogeneous and involves a relatively large number of water molecules. The molecular dynamics simulations show that the polarizability, along with the atomic charge distribution, needs to be a part of the picture describing how enzymes work. Non Gaussian dynamics in time-resolved linear and nonlinear (correlation) 2D spectra are also analyzed. Additionally, a theoretical formalism is presented to show that when preferential orientations of water dipoles exist at the interface, electrophoretic charges can be produced without free charge carriers, i.e., neutral solutes can move in a constant electric field due to the divergence of polarization at the interface. Furthermore, the concept of interface susceptibility is introduced. It involves the fluctuations of the surface charge density caused by thermal motion and its correlation over the characteristic correlation length with the fluctuations of the solvent charge density. Solvation free energy and interface dielectric constant are formulated accordingly. Unlike previous approaches, the solvation free energy scales quite well in a broad range of ion sizes, namely in the range of 2-14 A. Interface dielectric constant is defined such that the boundary conditions in the Laplace equation describing a micro- or mesoscopic interface are satisfied. The effective dielectric constant of interfacial water is found to be significantly lower than its bulk value. Molecular dynamics simulation results show that the interface dielectric constant for a TIP3P water model changes from nine to four when the effective solute radius is increased from 5 Ato 18 A. The small value of the interface dielectric constant of water has potentially dramatic consequences for hydration.

High performance magneto-fluorescent nanoparticles assembled from terbium and gadolinium 1,3-diketones

PubMed Central

Zairov, Rustem; Mustafina, Asiya; Shamsutdinova, Nataliya; Nizameev, Irek; Moreira, Beatriz; Sudakova, Svetlana; Podyachev, Sergey; Fattakhova, Alfia; Safina, Gulnara; Lundstrom, Ingemar; Gubaidullin, Aidar; Vomiero, Alberto

2017-01-01

Polyelectrolyte-coated nanoparticles consisting of terbium and gadolinium complexes with calix[4]arene tetra-diketone ligand were first synthesized. The antenna effect of the ligand on Tb(III) green luminescence and the presence of water molecules in the coordination sphere of Gd(III) bring strong luminescent and magnetic performance to the core-shell nanoparticles. The size and the core-shell morphology of the colloids were studied using transmission electron microscopy and dynamic light scattering. The correlation between photophysical and magnetic properties of the nanoparticles and their core composition was highlighted. The core composition was optimized for the longitudinal relaxivity to be greater than that of the commercial magnetic resonance imaging (MRI) contrast agents together with high level of Tb(III)-centered luminescence. The tuning of both magnetic and luminescent output of nanoparticles is obtained via the simple variation of lanthanide chelates concentrations in the initial synthetic solution. The exposure of the pheochromocytoma 12 (PC 12) tumor cells and periphery human blood lymphocytes to nanoparticles results in negligible effect on cell viability, decreased platelet aggregation and bright coloring, indicating the nanoparticles as promising candidates for dual magneto-fluorescent bioimaging. PMID:28091590

Polymeric nanocapsules with up-converting nanocrystals cargo make ideal fluorescent bioprobes.

PubMed

Bazylińska, U; Wawrzyńczyk, D; Kulbacka, J; Frąckowiak, R; Cichy, B; Bednarkiewicz, A; Samoć, M; Wilk, K A

2016-07-13

An innovative approach for up-converting nanoparticles adaptation for bio-related and theranostic applications is presented. We have successfully encapsulated multiple, ~8 nm in size NaYF4 nanoparticles inside the polymeric nanocarriers with average size of ~150 nm. The initial coating of nanoparticles surfaces was preserved due to the hydrophobic environment inside the nanocapsules, and thus no single nanoparticle surface functionalization was necessary. The selection of biodegradable and sugar-based polyelectrolyte shells ensured biocompatibility of the nanostructures, while the choice of Tm(3+) and Yb(3+) NaYF4 nanoparticles co-doping allowed for near-infrared to near-infrared bioimaging of healthy and cancerous cell lines. The protective role of organic shell resulted in not only preserved high up-converted emission intensity and long luminescence lifetimes, without quenching from water environment, but also ensured low cytotoxicity and high cellular uptake of the engineered nanocapsules. The multifunctionality of the proposed nanocarriers is a consequence of both the organic exterior part that is accessible for conjugation with biologically important molecules, and the hydrophobic interior, which in future application may be used as a container for co-encapsulation of inorganic nanoparticles and anticancer drug cargo.

High performance magneto-fluorescent nanoparticles assembled from terbium and gadolinium 1,3-diketones

NASA Astrophysics Data System (ADS)

Zairov, Rustem; Mustafina, Asiya; Shamsutdinova, Nataliya; Nizameev, Irek; Moreira, Beatriz; Sudakova, Svetlana; Podyachev, Sergey; Fattakhova, Alfia; Safina, Gulnara; Lundstrom, Ingemar; Gubaidullin, Aidar; Vomiero, Alberto

2017-01-01

Polyelectrolyte-coated nanoparticles consisting of terbium and gadolinium complexes with calix[4]arene tetra-diketone ligand were first synthesized. The antenna effect of the ligand on Tb(III) green luminescence and the presence of water molecules in the coordination sphere of Gd(III) bring strong luminescent and magnetic performance to the core-shell nanoparticles. The size and the core-shell morphology of the colloids were studied using transmission electron microscopy and dynamic light scattering. The correlation between photophysical and magnetic properties of the nanoparticles and their core composition was highlighted. The core composition was optimized for the longitudinal relaxivity to be greater than that of the commercial magnetic resonance imaging (MRI) contrast agents together with high level of Tb(III)-centered luminescence. The tuning of both magnetic and luminescent output of nanoparticles is obtained via the simple variation of lanthanide chelates concentrations in the initial synthetic solution. The exposure of the pheochromocytoma 12 (PC 12) tumor cells and periphery human blood lymphocytes to nanoparticles results in negligible effect on cell viability, decreased platelet aggregation and bright coloring, indicating the nanoparticles as promising candidates for dual magneto-fluorescent bioimaging.

Polymeric nanocapsules with up-converting nanocrystals cargo make ideal fluorescent bioprobes

PubMed Central

Bazylińska, U.; Wawrzyńczyk, D.; Kulbacka, J.; Frąckowiak, R.; Cichy, B.; Bednarkiewicz, A.; Samoć, M.; Wilk, K. A.

2016-01-01

An innovative approach for up-converting nanoparticles adaptation for bio-related and theranostic applications is presented. We have successfully encapsulated multiple, ~8 nm in size NaYF4 nanoparticles inside the polymeric nanocarriers with average size of ~150 nm. The initial coating of nanoparticles surfaces was preserved due to the hydrophobic environment inside the nanocapsules, and thus no single nanoparticle surface functionalization was necessary. The selection of biodegradable and sugar-based polyelectrolyte shells ensured biocompatibility of the nanostructures, while the choice of Tm3+ and Yb3+ NaYF4 nanoparticles co-doping allowed for near-infrared to near-infrared bioimaging of healthy and cancerous cell lines. The protective role of organic shell resulted in not only preserved high up-converted emission intensity and long luminescence lifetimes, without quenching from water environment, but also ensured low cytotoxicity and high cellular uptake of the engineered nanocapsules. The multifunctionality of the proposed nanocarriers is a consequence of both the organic exterior part that is accessible for conjugation with biologically important molecules, and the hydrophobic interior, which in future application may be used as a container for co-encapsulation of inorganic nanoparticles and anticancer drug cargo. PMID:27406954

Polymeric nanocapsules with up-converting nanocrystals cargo make ideal fluorescent bioprobes

NASA Astrophysics Data System (ADS)

Bazylińska, U.; Wawrzyńczyk, D.; Kulbacka, J.; Frąckowiak, R.; Cichy, B.; Bednarkiewicz, A.; Samoć, M.; Wilk, K. A.

2016-07-01

An innovative approach for up-converting nanoparticles adaptation for bio-related and theranostic applications is presented. We have successfully encapsulated multiple, ~8 nm in size NaYF4 nanoparticles inside the polymeric nanocarriers with average size of ~150 nm. The initial coating of nanoparticles surfaces was preserved due to the hydrophobic environment inside the nanocapsules, and thus no single nanoparticle surface functionalization was necessary. The selection of biodegradable and sugar-based polyelectrolyte shells ensured biocompatibility of the nanostructures, while the choice of Tm3+ and Yb3+ NaYF4 nanoparticles co-doping allowed for near-infrared to near-infrared bioimaging of healthy and cancerous cell lines. The protective role of organic shell resulted in not only preserved high up-converted emission intensity and long luminescence lifetimes, without quenching from water environment, but also ensured low cytotoxicity and high cellular uptake of the engineered nanocapsules. The multifunctionality of the proposed nanocarriers is a consequence of both the organic exterior part that is accessible for conjugation with biologically important molecules, and the hydrophobic interior, which in future application may be used as a container for co-encapsulation of inorganic nanoparticles and anticancer drug cargo.

One-by-one imprinting in two eccentric layers of hollow core-shells: Sequential electroanalysis of anti-HIV drugs.

PubMed

Singh, Kislay; Jaiswal, Swadha; Singh, Richa; Fatma, Sana; Prasad, Bhim Bali

2018-07-15

Double layered one-by-one imprinted hollow core-shells@ pencil graphite electrode was fabricated for sequential sensing of anti-HIV drugs. For this, two eccentric layers were developed on the surface of vinylated silica nanospheres to obtain double layered one-by-one imprinted solid core-shells. This yielded hollow core-shells on treatment with hydrofluoric acid. The modified hollow core-shells (single layered dual imprinted) evolved competitive diffusion of probe/analyte molecules. However, the corresponding double layered one-by-one imprinted hollow core-shells (outer layer imprinted with Zidovudine, and inner layer with Lamivudine) were found relatively better owing to their bilateral diffusions into molecular cavities, without any competition. The entire work is based on differential pulse anodic stripping voltammetry at double layered one-by-one imprinted hollow core-shells. This resulted in indirect detection of electro inactive targets with limits of detection as low as 0.91 and 0.12 (aqueous sample), 0.94 and 0.13 (blood serum), and 0.99 and 0.20 ng mL -1 (pharmaceutics) for lamivudine and zidovudine, respectively in anti-HIV drug combination. Copyright © 2018 Elsevier B.V. All rights reserved.

Evolution of a compound droplet attached to a core-shell nozzle under the action of a strong electric field

NASA Astrophysics Data System (ADS)

Reznik, S. N.; Yarin, A. L.; Zussman, E.; Bercovici, L.

2006-06-01

The shape evolution of small compound droplets at the exit of a core-shell system in the presence of a sufficiently strong electric field is studied both experimentally and theoretically. It is shown that the jetting effect at the tip of the shell nozzle does not necessarily cause entrainment of the core fluid, in which case the co-electrospinning process fails to produce core-shell nanofibers. The remedy lies in extending the core nozzle outside its shell counterpart by about half the radius of the latter. The results also show that the free charges migrate very rapidly from both fluids and their interface to the free surface of the shell. This reflects the fact that most of the prejetting evolution of the droplet can be effectively described in terms of the perfect conductor model, even though the fluids can be characterized as leaky dielectrics. The stress level at the core-shell interface is of the order of 5×103g/(cms2), the relevant value in assessing the viability of viruses, bacteria, DNA molecules, drugs, enzymes, chromophores, and proteins to be encapsulated in nanofibers via co-electrospinning.

Extended fenske-hall calculation of inner-shell binding energies using ( Z + 1)-bazis sets: Sulfur-containing molecules

NASA Astrophysics Data System (ADS)

Zwanziger, Ch.; Zwanziger, H.; Szargan, R.; Reinhold, J.

1981-08-01

It is shown that the S1s and S2p binding energies and their chemical shifts in the molecules H 2S, SO 2, SF 6 and COS obtained with hole-state calculations using an extended Fenske-Hall method are in good agreement with experimental values if mixed ( Z + 1)-basis sets are applied.

Aggregation protects flexible-shelled reptile eggs from severe hydric stress.

PubMed

Marco, Adolfo; Díaz-Paniagua, Carmen

2008-03-01

Many reptiles lay eggs with flexible shells that can progressively lose water until lethal dehydration under dry soil conditions. The number of eggs that develop together may influence the water exchange in the nest. We hypothesise that egg aggregation could reduce water lost under dry conditions. We exposed aggregated and isolated eggs to severe hydric stress followed by a period of rehydration. Hydric stress caused a general loss of water in common chameleon eggs. Initial egg mass did not affect survival but eggs that had lost more water had higher mortality and produced smaller hatchlings. Mass loss was higher and even lethal for isolated Chamaeleo chameleon eggs. However, aggregated eggs lost less water and most survived this period. After hydric stress, all surviving eggs gained mass via water absorption, and aggregation negatively affected water uptake. Isolated eggs hatched at smaller sizes than aggregated eggs. Aggregation also favoured hatching synchrony. Large clutches may favour hatching success of terrestrial flexible-shelled eggs incubated under severe drought conditions.

On the molecular origin of the cooperative coil-to-globule transition of poly(N-isopropylacrylamide) in water† †Electronic supplementary information (ESI) available: Stereochemistry and initial conformation of PNIPAM 30-mer; pair distribution functions of PNIPAM methyl groups; average time of transitions of dihedral angles; distribution of methyl dihedral angles; temperature dependence of average number of hydration water molecules; correlation between hydrogen bonding of water molecules per repeating unit in the FHS and end to end distance and correlation between PNIPAM–water hydrogen bonding and end to end distance. Time evolution of PNIPAM with the first hydration shell: movie FHSpnipam.avi. See DOI: 10.1039/c8cp00537k

PubMed Central

Zaccarelli, E.

2018-01-01

By means of atomistic molecular dynamics simulations we investigate the behaviour of poly(N-isopropylacrylamide), PNIPAM, in water at temperatures below and above the lower critical solution temperature (LCST), including the undercooled regime. The transition between water soluble and insoluble states at the LCST is described as a cooperative process involving an intramolecular coil-to-globule transition preceding the aggregation of chains and the polymer precipitation. In this work we investigate the molecular origin of such cooperativity and the evolution of the hydration pattern in the undercooled polymer solution. The solution behaviour of an atactic 30-mer at high dilution is studied in the temperature interval from 243 to 323 K with a favourable comparison to available experimental data. In the water soluble states of PNIPAM we detect a correlation between polymer segmental dynamics and diffusion motion of bound water, occurring with the same activation energy. Simulation results show that below the coil-to-globule transition temperature PNIPAM is surrounded by a network of hydrogen bonded water molecules and that the cooperativity arises from the structuring of water clusters in proximity to hydrophobic groups. Differently, the perturbation of the hydrogen bond pattern involving water and amide groups occurs above the transition temperature. Altogether these findings reveal that even above the LCST PNIPAM remains largely hydrated and that the coil-to-globule transition is related with a significant rearrangement of the solvent in the proximity of the surface of the polymer. The comparison between the hydrogen bonding of water in the surrounding of PNIPAM isopropyl groups and in the bulk displays a decreased structuring of solvent at the hydrophobic polymer–water interface across the transition temperature, as expected because of the topological extension along the chain of such interface. No evidence of an upper critical solution temperature behaviour, postulated in theoretical and thermodynamics studies of PNIPAM aqueous solution, is observed in the low temperature domain. PMID:29619464

Preparation, process optimization and characterization of core-shell polyurethane/chitosan nanofibers as a potential platform for bioactive scaffolds.

PubMed

Maleknia, Laleh; Dilamian, Mandana; Pilehrood, Mohammad Kazemi; Sadeghi-Aliabadi, Hojjat; Hekmati, Amir Houshang

2018-06-01

In this paper, polyurethane (PU), chitosan (Cs)/polyethylene oxide (PEO), and core-shell PU/Cs nanofibers were produced at the optimal processing conditions using electrospinning technique. Several methods including SEM, TEM, FTIR, XRD, DSC, TGA and image analysis were utilized to characterize these nanofibrous structures. SEM images exhibited that the core-shell PU/Cs nanofibers were spun without any structural imperfections at the optimized processing conditions. TEM image confirmed the PU/Cs core-shell nanofibers were formed apparently. It that seems the inclusion of Cs/PEO to the shell, did not induce the significant variations in the crystallinity in the core-shell nanofibers. DSC analysis showed that the inclusion of Cs/PEO led to the glass temperature of the composition increased significantly compared to those of neat PU nanofibers. The thermal degradation of core-shell PU/Cs was similar to PU nanofibers degradation due to the higher PU concentration compared to other components. It was hypothesized that the core-shell PU/Cs nanofibers can be used as a potential platform for the bioactive scaffolds in tissue engineering. Further biological tests should be conducted to evaluate this platform as a three dimensional scaffold with the capabilities of releasing the bioactive molecules in a sustained manner.

Selective molecular transport through the protein shell of a bacterial microcompartment organelle

DOE PAGES

Chowdhury, Chiranjit; Chun, Sunny; Pang, Allan; ...

2015-02-23

Bacterial microcompartments are widespread prokaryotic organelles that have important and diverse roles ranging from carbon fixation to enteric pathogenesis. Current models for microcompartment function propose that their outer protein shell is selectively permeable to small molecules, but whether a protein shell can mediate selective permeability and how this occurs are unresolved questions. In this paper, biochemical and physiological studies of structure-guided mutants are used to show that the hexameric PduA shell protein of the 1,2-propanediol utilization (Pdu) microcompartment forms a selectively permeable pore tailored for the influx of 1,2-propanediol (the substrate of the Pdu microcompartment) while restricting the efflux ofmore » propionaldehyde, a toxic intermediate of 1,2-propanediol catabolism. Crystal structures of various PduA mutants provide a foundation for interpreting the observed biochemical and phenotypic data in terms of molecular diffusion across the shell. Finally and overall, these studies provide a basis for understanding a class of selectively permeable channels formed by nonmembrane proteins.« less

Testing the assumption of annual shell ring deposition in freshwater mussels

Treesearch

Wendell R. Haag; Amy M. Commens-Carson

2008-01-01

We tested the assumption of annual shell ring deposition by freshwater mussels in three rivers using 17 species. In 2000, we notched shell margins, returned animals to the water, and retrieved them in 2001. In 2003, we measured shells, affixed numbered tags, returned animals, and retrieved them in 2004 and 2005. We validated deposition of a single internal annulus per...

A new approach to the method of source-sink potentials for molecular conduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pickup, Barry T., E-mail: B.T.Pickup@sheffield.ac.uk, E-mail: P.W.Fowler@sheffield.ac.uk; Fowler, Patrick W., E-mail: B.T.Pickup@sheffield.ac.uk, E-mail: P.W.Fowler@sheffield.ac.uk; Borg, Martha

2015-11-21

We re-derive the tight-binding source-sink potential (SSP) equations for ballistic conduction through conjugated molecular structures in a form that avoids singularities. This enables derivation of new results for families of molecular devices in terms of eigenvectors and eigenvalues of the adjacency matrix of the molecular graph. In particular, we define the transmission of electrons through individual molecular orbitals (MO) and through MO shells. We make explicit the behaviour of the total current and individual MO and shell currents at molecular eigenvalues. A rich variety of behaviour is found. A SSP device has specific insulation or conduction at an eigenvalue ofmore » the molecular graph (a root of the characteristic polynomial) according to the multiplicities of that value in the spectra of four defined device polynomials. Conduction near eigenvalues is dominated by the transmission curves of nearby shells. A shell may be inert or active. An inert shell does not conduct at any energy, not even at its own eigenvalue. Conduction may occur at the eigenvalue of an inert shell, but is then carried entirely by other shells. If a shell is active, it carries all conduction at its own eigenvalue. For bipartite molecular graphs (alternant molecules), orbital conduction properties are governed by a pairing theorem. Inertness of shells for families such as chains and rings is predicted by selection rules based on node counting and degeneracy.« less

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

DOE PAGES

Wang, Xu; Le, Anh -Thu; Yu, Chao; ...

2016-03-30

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. Lastly, amore » simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method.« less

Size-Tunable and Functional Core-Shell Structured Silica Nanoparticles for Drug Release

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chi, Fangli; Guo, Ya Nan; Liu, Jun

2010-02-18

Size-tunable silica cross-linked micellar core-shell nanoparticles (SCMCSNs) were successfully synthesized from a Pluronic nonionic surfactant (F127) template system with organic swelling agents such as 1,3,5-trimethylbenzene (TMB) and octanoic acid at room temperature. The size and morphology of SCMCSNs were directly evidenced by TEM imaging and DLS measurements (up to ~90 nm). Pyrene and coumarin 153 (C153) were used as fluorescent probe molecules to investigate the effect and location of swelling agent molecules. Papaverine as a model drug was used to measure the loading capacity and release property of nanoparticles. The swelling agents can enlarge the nanoparticle size and improve themore » drug loading capacity of nanoparticles. Moreover, the carboxylic acid group of fatty acid can adjust the release behavior of the nanoparticles.« less

Ecological studies on the breeding of Aedes aegypti and other mosquitos in shells of the giant African snail Achatina fulica

PubMed Central

Trpis, Milan

1973-01-01

The breeding of larvae of Aedes aegypti, Aedes simpsoni, and Eretmapodites quinquevittatus in empty shells of Achatina fulica was studied in the coastal zone of Dar es Salaam, Tanzania. The average density of shells was estimated to be 228 per ha. From 11 to 35% were positive for mosquito larvae. A. aegypti were found in 82-84% of positive shells; A. simpsoni in 8-13%. On Msasani peninsula, during the 3-month rainy season April—June 1970, the larval density of A. aegypti in shells was estimated at 1 100 per ha, that of A. simpsoni and E. quinquevittatus being estimated at 60 and 280 larvae per ha, respectively. Empty shells of A. fulica may contain up to 250 ml of water (average: 56.5 ml). The number of larvae per shell varies from 1 to 35 (average: 8.4) and it was estimated that, depending on the availability of food, and other factors, approximately 10 ml of water are required per larva. Viable eggs of A. aegypti were still to be found in 4% of the shells at the end of the dry season. PMID:4148745

Developmental plasticity of shell morphology of quagga mussels from shallow and deep-water habitats of the Great Lakes

Treesearch

Suzanne Peyer; John C. Hermanson; Carol Eunmi Lee

2010-01-01

The invasive zebra mussel (Dreissena polymorpha) has quickly colonized shallow-water habitats in the North American Great Lakes since the 1980s but the quagga mussel (Dreissena bugensis) is becoming dominant in both shallow and deep-water habitats. While quagga mussel shell morphology differs between shallow and deep habitats, functional causes and consequences of such...

A cloud collision model for water maser excitation.

PubMed

Tarter, J C; Welch, W J

1986-06-01

High-velocity collisions between small, dense, neutral clouds or between a dense cloud and a dense shell can provide the energy source required to excite H2O maser emission. The radiative precursor from the surface of the collisional shock front rapidly diffuses through the cloud, heating the dust grains but leaving the H2 molecules cool. Transient maser emission occurs as the conditions for the Goldreich and Kwan "hot-dust cold-gas" maser pump scheme are realized locally within the cloud. In time the local maser action quenches due to the heating of the H2 molecules by collisions against the grains. Although this model cannot explain the very long-lived steady maser features, it is quite successful in explaining a number of the observed properties of the high-velocity features in such sources as Orion, W51, and W49. In particular, it provides a natural explanation for the rapid time variations, the narrow line widths, juxtaposition of high- and low-velocity features, and the short lifetimes which are frequently observed for the so-called high-velocity maser "bullets" thought to be accelerated by strong stellar winds.

Method of making foam-encapsulated laser targets

DOEpatents

Rinde, James A.; Fulton, Fred J.

1977-01-01

Foam-encapsulated laser fusion targets are fabricated by suspending fusion fuel filled shells in a solution of cellulose acetate, extruding the suspension through a small orifice into a bath of ice water, soaking the thus formed shell containing cellulose acetate gel in the water to extract impurities, freezing the gel, and thereafter freeze-drying wherein water and solvents sublime and the gel structure solidifies into a low-density microcellular foam containing one or more encapsulated fuel-filled shells. The thus formed material is thereafter cut and mounted on a support to provide laser fusion targets containing a fuel-filled shell surrounded by foam having a thickness of 10 to 60 .mu.m, a cell size of less than 2 .mu.m, and density of 0.08 to 0.6.times.10.sup.3 kg/m.sup.3. Various configured foam-encapsulated targets capable of being made by the encapsulation method are illustrated.

Biomineralization of Schlumbergerella floresiana, a significant carbonate-producing benthic foraminifer

NASA Astrophysics Data System (ADS)

Sabbatini, Anna; Bédouet, Laurent; Marie, Arul; Bartolini, Annachiara; Landemarre, Ludovic; Weber, Michele; Ngurah Kade Mahardika, Gusti; Berland, Sophie; Zito, Francesca; Vénec-Peyré, Marie-Thérèse

2016-04-01

Most foraminifera that produce a shell are efficient biomineralizers. They contribute to the global carbon cycle, and thus influence ocean-climate regulation. Calcification in foraminifera is likely biologically controlled and is potentially similar to shell formation in metazoan taxa (e.g. mollusks, corals, sea urchins). However, foraminiferal biomineralization processes and the molecules involved are still poorly understood. We analyzed the calcitic shell of the large tropical benthic foraminifer Schlumbergerella floresiana. We found a suite of macromolecules containing many charged and polar amino acids and glycine that are also abundant in biomineralization proteins of other phyla. As neither genomic nor transcriptomic data are available for foraminiferal biomineralization yet, de novo-generated sequences, obtained from organic matrices submitted to MS BLAST database search, led to the characterization of 156 peptides. Very few homologous proteins were matched in the proteomic database, implying that the peptides are derived from unknown proteins present in the foraminiferal organic matrices. The amino acid distribution of these peptides was queried against the UNIPROT database and the mollusk UNIPROT database for comparison. The mollusks compose a well-studied phylum that yield a large variety of biomineralization proteins. These results showed that proteins extracted from S. floresiana shells contained sequences enriched with glycine, alanine, and proline, making a set of residues that provided a signature unique to foraminifera. Three of the de novo peptides exhibited sequence similarities to peptides found in proteins such as pre-collagen-P and a group of P-type ATPases including a calcium-transporting ATPase. Surprisingly, the peptide that was most similar to the collagen-like protein was a glycine-rich peptide reported from the test and spine proteome of sea urchin. The molecules, identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses, included acid-soluble N-glycoproteins with its sugar moieties represented by high-mannose-type glycans and carbohydrates. Describing the nature of the proteins, and associated molecules in the skeletal structure of living foraminifera, can elucidate the biomineralization mechanisms of these major carbonate producers in marine ecosystems. Foraminifera constitute an important tool used for paleo-environmental reconstructions because of their nearly continuous fossil record and abundance. Many studies focus on their biomineralization process using a geochemical perspective to record environmental and climate changes from shell isotopic and trace element compositions. Our results are a first step toward understanding the functioning mechanism behind biomineralization and the molecules involved. Coupling geochemical and biological perspectives will enhance interpretation of the proxies used for climatic reconstructions and improve future modeling efforts.

Stable isotope ratios in freshwater mussel shells as high resolution recorders of riverine environmental variation

NASA Astrophysics Data System (ADS)

Kukolich, S.; Kendall, C.; Dettman, D. L.

2017-12-01

The geochemical record stored in growth increments of freshwater mussel shells reveals annual to sub-annual changes in environmental conditions during the lifetime of the organism. The carbon, nitrogen, and oxygen stable isotope composition of aragonite shells responds to changes in water chemistry, temperature, streamflow, turbidity, growth rate, size, age, and reproduction. The goals of this study are to determine how stable isotopes can be used to reconstruct the conditions in which the mussels lived and to illuminate any vital effects that might obscure the isotopic record of those conditions. Previous research has suggested that annual δ13C values decrease in older freshwater mussel shells due to lower growth rates and greater incorporation of dietary carbon into the shell with increasing age. However, a high-resolution, seasonal investigation of δ13C, δ15N, and δ18O as they relate to organism age has not yet been attempted in freshwater mussels. A total of 28 Unionid mussels of three different species were collected live in 2011 in the Tennessee River near Paducah, Kentucky, USA. In this study, we analyzed the shell nacre and external organic layers for stable carbon, nitrogen, and oxygen isotope ratios, focusing on growth bands formed between 2006 and 2011. We present a time series of shell δ13C, δ18O, and δ15N values with monthly resolution. We also compare the shell-derived geochemical time series to a time series of the δ13C and δ15N of particulate organic matter, δ13C of DIC, δ18OWater, and water temperature in which the mussels lived. Results show that environmental factors such as water temperature and primary productivity dominate shell chemistry while animal age has little or no effect.

Stereo and scanning electron microscopy of in-shell Brazil nut (Bertholletia excelsa H.B.K.): part two-surface sound nut fungi spoilage susceptibility.

PubMed

Scussel, Vildes M; Manfio, Daniel; Savi, Geovana D; Moecke, Elisa H S

2014-11-01

This work reports the in-shell Brazil nut spoilage susceptible morpho-histological characteristics and fungi infection (shell, edible part, and brown skin) through stereo and scanning electron microscopies (SEM). The following characteristics related to shell (a) morphology-that allow fungi and insects' entrance to inner nut, and (b) histology-that allow humidity absorption, improving environment conditions for living organisms development, were identified. (a.1) locule in testae-the nut navel, which is a cavity formed during nut detaching from pods (located at 1.0 to 2.0/4th of the shell B&C nut faces linkage). It allows the nut brown skin (between shell and edible part) first contact to the external environment, through the (a.2) nut channel-the locule prolongation path, which has the water/nutrients cambium function for their transport and distribution to the inner seed (while still on the tree/pod). Both, locule followed by the channel, are the main natural entrance of living organisms (fungi and insects), including moisture to the inner seed structures. In addition, the (a.3) nut shell surface-which has a crinkled and uneven surface morphology-allows water absorption, thus adding to the deterioration processes too. The main shell histological characteristic, which also allows water absorption (thus improving environment conditions for fungi proliferation), is the (b.1) cell wall porosity-the multilayered wall and porous rich cells that compose the shell faces double tissue layers and the (b.2) soft tissue-the mix of tissues 2 faces corner/linkage. This work also shows in details the SEM nut spoilage susceptible features highly fungi infected with hyphae and reproductive structures distribution. © 2014 Institute of Food Technologists®

Characteristics of global organic matrix in normal and pimpled chicken eggshells.

PubMed

Liu, Z; Song, L; Zhang, F; He, W; Linhardt, R J

2017-10-01

The organic matrix from normal and pimpled calcified chicken eggshells were dissociated into acid-insoluble, water-insoluble, and facultative-soluble (both acid- and water-soluble) components, to understand the influence of shell matrix on eggshell qualities. A linear correlation was shown among these 3 matrix components in normal eggshells but was not observed in pimpled eggshells. In pimpled eggshells, the percentage contents of all 4 groups of matrix (the total matrix, acid-insoluble matrix, water-insoluble matrix, and facultative-soluble matrix) were significantly higher than that in normal eggshells. The amounts of both total matrix and acid-insoluble matrix in individual pimpled calcified shells were high, even though their weight was much lower than a normal eggshell. In both normal and pimpled eggshells, the calcified eggshell weight and shell thickness significantly and positively correlated with the amounts of all 4 groups of matrix in an individual calcified shell. In normal eggshells, the calcified shell thickness and shell breaking strength showed no significant correlations with the percentage contents of all 4 groups of matrix. In normal eggshells, only the shell membrane weight significantly correlated with the constituent ratios of both acid-insoluble matrix and facultative-soluble matrix in the whole matrix. In pimpled eggshells, 3 variables (calcified shell weight, shell thickness, and breaking strength) were significantly correlated with the constituent proportions of both acid-insoluble matrix and facultative-matrix. This study suggests that mechanical properties of normal eggshells may not linearly depend on the organic matrix content in the calcified eggshells and that pimpled eggshells might result by the disequilibrium enrichment of some proteins with negative effects. © 2017 Poultry Science Association Inc.

The conformation of Pluronic block copolymers adsorbed on carbon nanotubes and their interaction with water studied by small-angle neutron scattering

NASA Astrophysics Data System (ADS)

Cohen, Yachin; Granite, Meirav; Pyckhout-Hintzen, Wim; Radulescu, Aurel

2010-03-01

Amphiphilic block copolymers are particularly useful in dispersing single-walled carbon nanotubes (SWCNT) in water. Small-angle neutron scattering measurements conducted at different D2O/H2O content of the dispersing medium provide quantitative information on the adsorption density and conformation of the polymer interacting with the nanotube surface. Data is presented on Pluronic F108 - (EO)132(PO)50(EO)132 and F127 (EO)100(PO)65(EO)100, where EO-ethylene oxide and PO-propylene oxide, well below the critical micellization temperature of the polymer. A dense coating of the PPO blocks on the nanotube surface is determined with the PEO chains extended from the cylindrical core-shell structure. The data from the two Pluronic systems show minimal scattering at about 70% D2O in the dispersing water, which exhibit a q -1 power law of the scattering vector (q ). This indicates near matching of the polymer chains at a surprisingly high scattering length density. The model fit required considerations of tight association of water molecules around PEO chains and slight isotopic selectivity.

Unraveling the role of water in the stereoselective step of aqueous proline-catalyzed aldol reactions.

PubMed

Ribas-Arino, Jordi; Carvajal, Maria Angels; Chaumont, Alain; Masia, Marco

2012-12-03

A multiscale computational study was performed with the aim of tracing the source of stereoselectivity and disclosing the role of water in the stereoselective step of propionaldehyde aldol self-condensation catalyzed by proline amide in water, a reaction that serves as a model for aqueous organocatalytic aldol condensations. Solvent mixing and hydration behavior were assessed by classical molecular dynamics simulations, which show that the reaction between propanal and the corresponding enamine takes place in a fully hydrated environment. First-principles molecular dynamics simulations were used to study the free-energy profile of four possible reaction paths, each of which yields a different stereoisomer, and high-level static first-principles calculations were employed to characterize the transition states for microsolvated species. The first solvation shell of the oxygen atom of the electrophilic aldehyde at the transition states contains two water molecules, each of which donates one hydrogen bond to the nascent alkoxide and thereby largely stabilizes its excess electron density. The stereoselectivity originates in an extra hydrogen bond donated by the amido group of proline amide in two reaction paths. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural insights into the light-driven auto-assembly process of the water-oxidizing Mn4CaO5-cluster in photosystem II.

PubMed

Zhang, Miao; Bommer, Martin; Chatterjee, Ruchira; Hussein, Rana; Yano, Junko; Dau, Holger; Kern, Jan; Dobbek, Holger; Zouni, Athina

2017-07-18

In plants, algae and cyanobacteria, Photosystem II (PSII) catalyzes the light-driven splitting of water at a protein-bound Mn 4 CaO 5 -cluster, the water-oxidizing complex (WOC). In the photosynthetic organisms, the light-driven formation of the WOC from dissolved metal ions is a key process because it is essential in both initial activation and continuous repair of PSII. Structural information is required for understanding of this chaperone-free metal-cluster assembly. For the first time, we obtained a structure of PSII from Thermosynechococcus elongatus without the Mn 4 CaO 5 -cluster. Surprisingly, cluster-removal leaves the positions of all coordinating amino acid residues and most nearby water molecules largely unaffected, resulting in a pre-organized ligand shell for kinetically competent and error-free photo-assembly of the Mn 4 CaO 5 -cluster. First experiments initiating (i) partial disassembly and (ii) partial re-assembly after complete depletion of the Mn 4 CaO 5 -cluster agree with a specific bi-manganese cluster, likely a di-µ-oxo bridged pair of Mn(III) ions, as an assembly intermediate.

Encapsulation of β-carotene within ferritin nanocages greatly increases its water-solubility and thermal stability.

PubMed

Chen, Lingli; Bai, Guangling; Yang, Rui; Zang, Jiachen; Zhou, Ting; Zhao, Guanghua

2014-04-15

Carotenoids may play a number of potential health benefits for human. However, their use in food industry is limited mostly because of their poor water-solubility and low thermal stability. Ferritins are widely distributed in nature with a shell-like structure which offers a great opportunity to improve the water-solubility and thermal stability of the carotenoids by encapsulation. In this work, recombinant human H-chain ferritin (rHuHF) was prepared and used to encapsulate β-carotene, a typical compound among carotenoids, by taking advantage of the reversible dissociation and reassembly characteristic of apoferritin in different pH environments. Results from high-performance liquid chromatography (HPLC), UV/Vis spectroscopy and transmission electron microscope (TEM) indicated that β-carotene molecules were successfully encapsulated within protein cages with a β-carotene/protein molar ratio of 12.4-1. Upon such encapsulation, these β-carotene-containing apoferritin nanocomposites were water-soluble. Interestingly, the thermal stability of the β-carotene encapsulated within apoferritin nanocages was markedly improved as compared to free β-carotene. These new properties might be favourable to the utilisation of β-carotene in food industry. Copyright © 2013 Elsevier Ltd. All rights reserved.

Adsorption of cadmium on cerium oxide nanoparticles and oyster shells

NASA Astrophysics Data System (ADS)

Ji, Yongbo; Liu, Zhuomiao; Dang, Yonghui; Xu, Lina; Ning, Fangyuan; Xue, Yinhao; Wei, Yongpeng; Dai, Yanhui

2018-03-01

This study investigated the adsorption of cadmium (Cd(II)) by cerium oxide nanoparticles (CeO2 NPs) and oyster shells in seawater. The results showed that the addition of Cd(II) significantly inhibited the agglomeration of CeO2 NPs both in DI water and seawater, increased the positive charges of CeO2 NPs in DI water and neutralized the negative charges of CeO2 NPs in seawater. Additionally, CeO2 NPs could adsorb Cd and the bioavailability of Cd was reduced in the presence of oyster shells. This study demonstrated that the adsorption of metals on shells should not be neglected for the accumulation of metals by shellfish.

Instruments for Characterizing Carbon and Sulfur-Resistant Core-Shell Redox Catalysts for Combined Hydrocarbon Reforming and Water-Splitting

DTIC Science & Technology

2015-11-22

SECURITY CLASSIFICATION OF: This project aims to investigate a novel core-shell redox catalyst for combined methane partial oxidation and water...Properly designed redox catalyst are shown to be highly effective for syngas production (from methane ) and water-splitting. The resulting syngas has a...27709-2211 redox catalyst, methane partial oxidation, water-splitting REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT NUMBER(S) 10. SPONSOR

Organic History and Ice-Rock Decoupling on Enceladus

NASA Astrophysics Data System (ADS)

Zolotov, M. Y.

2007-12-01

The Cassini detection of methane, propane and acetylene in the Enceladus plume, and condensed organic compounds (OC) on the south polar region imply an organic-bearing interior of the moon. At least a few wt. % of C is expected in rocks from which Enceladus accreted. By analogy with carbonaceous chondrites, the majority of accreted OC was in a polymer in which polyaromatic groups are linked by O-, N-, and S-bearing aliphatic units. If accreted, cometary-type materials also delivered CO2, CO(?), methanol, ethane, ethene, acetylene, and condensed OC. Subsequent water ice melting and hydrothermal processes driven by decay of short-lived radionuclides led to dissolution of CO, CO2 and methanol in water and transformations of the polymer and cometary OC. CO converted to formic acid, carbonate species, methanol and methane. Hydrous pyrolysis and oxidation of the polymer partially liberated aromatic molecules and led to the formation of O-bearing OC (carboxylic and amino acids, alcohols). Increase in temperature favored oxidation of OC to carbonate species and N2, and led to graphitization of the polymer. Despite net oxidation of OC driven by H2 escape, mineral- catalyzed Fisher-Tropsch like synthesis of hydrocarbons and methane occurred in H2-rich niches. As a result, an array of aromatic, aliphatic, and N-, O-, S-bearing OC, and methane was delivered into a primordial water ocean in hydrothermal fluids. Highly soluble OC (acids, alcohols) made multiple passes through hydrothermal systems causing further oxidation of OC in rocks and solutions. In contrast, hydrocarbons exolved from cold oceanic water and formed an organic layer below the ice shell. Subsequent cooling of ocean-entering fluids and ocean freezing from above led to further separation and accumulation of OC. Some OC was trapped in ice, and methane formed clathrates. After freezing of salt eutectic brines, the light oil (a solution/mixture of ethane, propane, butane, ethene, acetylene, methanol, toluene etc.) remained unfrozen and decoupled the ice shell from underlying salt deposits and rocks. Even after oil solidification, if it occurred, the organic layer had a lower viscosity than salts and ice. An uneven pressure and/or topography at the ice-salt boundary could have led to preferential oil (and salt?) accumulation below the south polar region. Throughout history (and today), the uneven oil-rich layer could have favored tidal motions and heat generation at the bottom of the ice shell.

A novel core-shell lipid nanoparticle for improving oral administration of water soluble chemotherapeutic agents: inhibited intestinal hydrolysis and enhanced lymphatic absorption.

PubMed

Wang, Tao; Shen, Liao; Zhang, Zhen; Li, Haiyan; Huang, Ri; Zhang, Yadan; Quan, Dongqin

2017-11-01

The oral administration of water-soluble chemotherapeutical agents is limited by their serious gastrointestinal side effects, instability at intestinal pH, and poor absorption. Aiming to solve these problems, we chose topotecan (TPT) as a model drug and developed a novel lipid formulation containing core-shell lipid nanoparticle (CLN) that makes the water-soluble drug to 'dissolve' in oil. TPT molecules can be encapsulated into nanoparticles surrounded by oil barrier while avoiding the direct contact with intestinal environment, thus easing the intestinal hydrolytic degradation and gastrointestinal (GI) irritation. Microstructure and mean particle size of TPT-CLN were characterized by Transmission Electron Microscope (TEM) and Dynamic Light Scattering (DLS), respectively. The average size of nanoparticles was approximately 60 nm with a homogeneous distribution in shapes of spheres or ellipsoid. According to in vitro stability studies, more initial form of TPT was observed in presence of lipid nanoparticle compared with free topotecan solution in artificial intestinal juice (pH 6.5). After oral administration of TPT-CLN in rats, AUC and C max of TPT were all increased compared with free TPT, indicating significant enhancement of oral absorption. Intestinal lymphatic transport was confirmed as the major way for CLN to enhance oral absorption of TPT by the treatment of blocking chylomicron flow. Lower GI irritation of TPT-CLN was observed in the gastrointestinal damage studies. The in vivo antitumor activity of TPT-CLN showed an improved antitumor efficacy by oral treatment of TPT-CLN compared to free TPT. From the obtained data, the systems appear an attractive progress in oral administration of topotecan.

Preparation of magnetic core mesoporous shell microspheres with C18-modified interior pore-walls for fast extraction and analysis of phthalates in water samples.

PubMed

Li, Zhongbo; Huang, Danni; Fu, Chinfai; Wei, Biwen; Yu, Wenjia; Deng, Chunhui; Zhang, Xiangmin

2011-09-16

In this study, core-shell magnetic mesoporous microspheres with C18-functionalized interior pore-walls were synthesized through coating Fe(3)O(4) microspheres with a mesoporous inorganic-organic hybrid layer with a n-octadecyltriethoxysilane (C18TES) and tetraethyl orthosilicate (TEOS) as the silica source and cetyltrimethylammonia bromide (CTAB) as a template. The obtained C18-functionalized Fe(3)O(4)@mSiO(2) microspheres possess numerous C18 groups anchored in the interior pore-walls, large surface area (274.7 m(2)/g, high magnetization (40.8 emu/g) and superparamagnetism, uniform mesopores (4.1 nm), which makes them ideal absorbents for simple, fast, and efficient extraction and enrichment of hydrophobic organic compounds in water samples. Several kinds of phthalates were used as the model hydrophobic organic compounds to systematically evaluate the performance of the C18-functionalized Fe(3)O(4)@mSiO(2) microspheres in extracting hydrophobic molecules by using a gas chromatography-mass spectrometry. Various parameters, including eluting solvent, the amounts of absorbents, extraction time and elution time were optimized. Hydrophobic extraction was performed in the interior pore of magnetic mesoporous microspheres, and the materials had the anti-interference ability to macromolecular proteins, which was also investigated in the work. Under the optimized conditions, C18-functionalized Fe(3)O(4)@mSiO(2) microspheres were successfully used to analyze the real water samples. The results indicated that this novel method was fast, convenient and efficient for the target compounds and could avoid being interfered by macromolecules. Copyright © 2011 Elsevier B.V. All rights reserved.

Active formation of `chaos terrain' over shallow subsurface water on Europa

NASA Astrophysics Data System (ADS)

Schmidt, B. E.; Blankenship, D. D.; Patterson, G. W.; Schenk, P. M.

2011-11-01

Europa, the innermost icy satellite of Jupiter, has a tortured young surface and sustains a liquid water ocean below an ice shell of highly debated thickness. Quasi-circular areas of ice disruption called chaos terrains are unique to Europa, and both their formation and the ice-shell thickness depend on Europa's thermal state. No model so far has been able to explain why features such as Conamara Chaos stand above surrounding terrain and contain matrix domes. Melt-through of a thin (few-kilometre) shell is thermodynamically improbable and cannot raise the ice. The buoyancy of material rising as either plumes of warm, pure ice called diapirs or convective cells in a thick (>10 kilometres) shell is insufficient to produce the observed chaos heights, and no single plume can create matrix domes. Here we report an analysis of archival data from Europa, guided by processes observed within Earth's subglacial volcanoes and ice shelves. The data suggest that chaos terrains form above liquid water lenses perched within the ice shell as shallow as 3kilometres. Our results suggest that ice-water interactions and freeze-out give rise to the diverse morphologies and topography of chaos terrains. The sunken topography of Thera Macula indicates that Europa is actively resurfacing over a lens comparable in volume to the Great Lakes in North America.

Reconsideration on Hydration of Sodium Ion: From Micro-Hydration to Bulk Hydration

NASA Astrophysics Data System (ADS)

Yongquan, Zhou; Chunhui, Fang; Yan, Fang; Fayan, Zhu; Haiwen, Ge; Hongyan, Liu

2017-12-01

Micro hydration structures of the sodium ion, [Na(H2O) n ]+, n = 1-12, were probed by density functional theory (DFT) at B3LYP/aug-cc-pVDZ level in both gaseous and aqueous phase. The predicted equilibrium sodium-oxygen distance of 0.240 nm at the present level of theory. The four-, five- and six-coordinated cluster can transform from each other at the ambient condition. The analysis of the successive water binding energy and natural charge population (NBO) on Na+ clearly shows that the influence of Na+ on the surrounding water molecules goes beyond the first hydration shell with the hydration number of 6. The Car-Parrinello molecular dynamic simulation shows that only the first hydration sphere can be found, and the hydration number of Na+ is 5.2 and the hydration distance ( r Na-O) is 0.235 nm. All our simulations mentioned in the present paper show an excellent agreement with the diffraction result from X-ray scattering study.

Putting prey back together again: integrating predator-induced behavior, morphology, and life history.

PubMed

Hoverman, Jason T; Auld, Josh R; Relyea, Rick A

2005-07-01

The last decade has seen an explosion in the number of studies exploring predator-induced plasticity. Recently, there has been a call for more comprehensive approaches that can identify functional relationships between traits, constraints on phenotypic responses, and the cost and benefits of alternative phenotypes. In this study, we exposed Helisoma trivolvis, a freshwater snail, to a factorial combination of three resource levels and five predator environments (no predator, one or two water bugs, and one or two crayfish) and examined ten traits including behavior, morphology, and life history. Each predator induced a unique suite of behavioral and morphological responses. Snails increased near-surface habitat use with crayfish but not with water bugs. Further, crayfish induced narrow and high shells whereas water bugs induced wide shells and wide apertures. In terms of life history, both predators induced delayed reproduction and greater mass at reproduction. However, crayfish induced a greater delay in reproduction that resulted in reduced fecundity whereas water bugs did not induce differences in fecundity. Resource levels impacted the morphology of H. trivolvis; snails reared with greater resource levels produced higher shells, narrower shells, and wider apertures. Resource levels also impacted snail life history; lower resources caused longer times to reproduction and reduced fecundity. Based on an analysis of phenotypic correlations, the morphological responses to each predator most likely represent phenotypic trade-offs. Snails could either produce invasion-resistant shells for defense against water bugs or crush-resistant shells for defense against crayfish, but not both. Our use of a comprehensive approach to examine the responses of H. trivolvis has provided important information regarding the complexity of phenotypic responses to different environments, the patterns of phenotypic integration across environments, and the potential costs and benefits associated with plastic traits.

Europa's Great Lakes

NASA Astrophysics Data System (ADS)

Schmidt, B. E.; Blankenship, D. D.; Patterson, G. W.; Schenk, P. M.

2012-04-01

Unique to the surface of Europa, chaos terrain is diagnostic of the properties and dynamics of its icy shell. While models have suggested that partial melt within a thick shell or melt-through of a thin shell may form chaos, neither model has been able to definitively explain all observations of chaos terrain. However, we present a new model that suggests large melt lenses form within the shell and that water-ice interactions above and within these lenses drive the production of chaos. Our analysis of the geomorphology of Conamara Chaos and Thera Macula, was used to infer and test a four-stage lens-collapse chaos formation model: 1) Thermal plumes of warm, pure ice ascend through the shell melting the impure brittle ice above, producing a lake of briny water and surface down draw due to volume reduction. 2) Surface deflection and driving force from the plume below hydraulically seals the water in place. 3) Extension of the brittle ice lid generates fractures from below, allowing brines to enter and fluidize the ice matrix. 4) As the lens and now brash matrix refreeze, thermal expansion creates domes and raises the chaos feature above the background terrain. This new "lense-collapse" model indicates that chaos features form in the presence of a great deal of liquid water, and that large liquid water bodies exist within 3km of Europa's surface comparable in volume to the North American Great Lakes. The detection of shallow subsurface "lakes" implies that the ice shell is recycling rapidly and that Europa may be currently active. In this presentation, we will explore environments on Europa and their analogs on Earth, from collapsing Antarctic ice shelves to to subglacial volcanos in Iceland. I will present these new analyses, and describe how this new perspective informs the debate about Europa's habitability and future exploration.

Lego Bricks and the Octet Rule: Molecular Models for Biochemical Pathways with Plastic, Interlocking Toy Bricks

ERIC Educational Resources Information Center

Lin, Henry J.; Lehoang, Jennifer; Kwan, Isabel; Baghaee, Anita; Prasad, Priya; Ha-Chen, Stephanie J.; Moss, Tanesha; Woods, Jeremy D.

2018-01-01

The 8 studs on a 2 × 4 Lego brick conveniently represent the outer shell of electrons for carbon, nitrogen, and oxygen atoms. We used Lego bricks to model these atoms, which are then joined together to form molecules by following the Lewis octet rule. A variety of small biological molecules can be modeled in this way, such as most amino acids,…

Europa's differentiated internal structure: inferences from four Galileo encounters.

PubMed

Anderson, J D; Schubert, G; Jacobson, R A; Lau, E L; Moore, W B; Sjogren, W L

1998-09-25

Radio Doppler data from four encounters of the Galileo spacecraft with the jovian moon Europa have been used to refine models of Europa's interior. Europa is most likely differentiated into a metallic core surrounded by a rock mantle and a water ice-liquid outer shell, but the data cannot eliminate the possibility of a uniform mixture of dense silicate and metal beneath the water ice-liquid shell. The size of a metallic core is uncertain because of its unknown composition, but it could be as large as about 50 percent of Europa's radius. The thickness of Europa's outer shell of water ice-liquid must lie in the range of about 80 to 170 kilometers.

Acute cold stress improved the transcription of pro-inflammatory cytokines of Chinese soft-shelled turtle against Aeromonas hydrophila.

PubMed

Zhang, Zuobing; Chen, Bojian; Yuan, Lin; Niu, Cuijuan

2015-03-01

Chinese soft-shelled turtle, Pelodiscus sinensis, is widely cultured in East and Southeast Asian countries. It frequently encounters the stress of abrupt temperature changes, which leads to mass death in most cases. However, the mechanism underlying the stress-elicited death remains unknown. We have suspected that the stress impaired the immune function of Chinese soft-shelled turtle, which could result in the mass death, as we noticed that there was a clinical syndrome of infection in dead turtles. To test our hypothesis, we first performed bioinformatic annotation of several pro-inflammatory molecules (IL-1β, TNFα, IL-6, IL-12β) of Chinese soft-shelled turtle. Then, we treated the turtles in six groups, injected with Aeromonas hydrophila before acute cold stress (25 °C) and controls, after acute cold stress (15 °C) and controls as well as after the temperature was restored to 25 °C and controls, respectively. Subsequently, real-time PCR for several pro-inflammatory cytokines (IL-1β, TNFα, IL-6, IL-12β, IL-8 and IFNγ) was performed to assess the turtle immune function in spleen and intestine, 24 hours after the injection. We found that the mRNA expression levels of the immune molecules were all enhanced after acute cold stress. This change disappeared when the temperature was restored back to 25 °C. Our results suggest that abrupt temperature drop did not suppress the immune function of Chinese soft-shelled turtle in response to germ challenge after abrupt temperature drop. In contrast, it may even increase the expression of various cytokines at least, within a short time after acute cold stress. Copyright © 2014 Elsevier Ltd. All rights reserved.

Freshwater Mussel Shell δ13C Values as a Proxy for δ13CDIC in a Polluted, Temperate River

NASA Astrophysics Data System (ADS)

Graniero, L. E.; Gillikin, D. P.; Surge, D. M.

2017-12-01

Freshwater mussel shell δ13C values have been examined as an indicator of ambient δ13C composition of dissolved inorganic carbon (DIC) in temperate rivers. However, shell δ13C values may be obscured by the assimilation of respired, metabolic carbon (CM) derived from the organism's diet. Water δ18O and δ13CDIC values were collected fortnightly from August 2015 through July 2017 from three sites (one agricultural, one downstream of a wastewater treatment plant, one urban) in the Neuse River, NC to test the reliability of Elliptio complanata shell δ13C values as a proxy for δ13CDIC values. Muscle, mantle, gill, and stomach δ13C values were analyzed to approximate the %CM incorporated into the shell. All tissue δ13C values were within 2‰ of each other, which equates to a ±1% difference in calculated %CM. As such, muscle tissue δ13C values will be used for calculating the %CM, because they have the slowest turnover rate of the tissues sampled. Water temperature and δ18O values were used to calculate predicted aragonite shell δ18O­ values (δ18O­ar) based on the aragonite-water fractionation relationship. To assign dates to each shell microsample, predicted δ18O­ar values were compared to high-resolution serially sampled shell values. Consistent with previous studies, E. complanata cease growth in winter when temperatures are below about 12ºC. Preliminary results indicate that during the growing season, shell δ13C values are lower than expected equilibrium values, reflecting the assimilation of 15% CM, on average. Shell δ13C values are not significantly different than δ13CDIC values, but do not capture the full range of δ13CDIC values during each growing season. Thus, δ13C values of E. complanata shells can be used to reliably reconstruct past δ13CDIC values within 2‰ of coeval values. Further research will investigate how differing land-use affects the relationship between shell δ13C, CM, and δ13CDIC values.

Engineering report single-shell tank farms interim measures to limit infiltration through the vadose zone

DOE Office of Scientific and Technical Information (OSTI.GOV)

HAASS, C.C.

1999-10-14

Identifies, evaluates and recommends interim measures for reducing or eliminating water sources and preferential pathways within the vadose zone of the single-shell tank farms. Features studied: surface water infiltration and leaking water lines that provide recharge moisture, and wells that could provide pathways for contaminant migration. An extensive data base, maps, recommended mitigations, and rough order of magnitude costs are included.

How many molecular layers of polar solvent molecules control chemistry? The concept of compensating dipoles.

PubMed

Langhals, Heinz; Braun, Patricia; Dietl, Christian; Mayer, Peter

2013-09-27

The extension of the solvent influence of the shell into the volume of a polar medium was examined by means of anti-collinear dipoles on the basis of the E(T)(30) solvent polarity scale (i.e., the molar energy of excitation of a pyridinium-N-phenolatebetaine dye; generally: E(T) =28,591 nm kcal mol(-1)/λmax) where no compensation effects were found. As a consequence, solvent polarity effects are concentrated to a very thin layer of a few thousand picometres around the solute where extensions into the bulk solvent become unimportant. A parallelism to the thin surface layer of water to the gas phase is discussed. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Laser-triggered release of encapsulated molecules from polylactic-co-glycolic acid microcapsules

NASA Astrophysics Data System (ADS)

Ariyasu, Kazumasa; Ishii, Atsuhiro; Umemoto, Taiga; Terakawa, Mitsuhiro

2016-08-01

The controlled release of encapsulated molecules from a microcapsule is a promising method of targeted drug delivery. Laser-triggered methods for the release of encapsulated molecules have the advantage of spatial and temporal controllability. In this study, we demonstrated the release of encapsulated molecules from biodegradable polymer-based microcapsules using near-infrared femtosecond laser pulses. The polylactic-co-glycolic acid microcapsules encapsulating fluorescein isothiocyanate-dextran molecules were fabricated using a dual-coaxial nozzle system. Irradiation of femtosecond laser pulses enhanced the release of the molecules from the microcapsules, which was accompanied by a decrease in the residual ratio of the microcapsules. The laser-induced modification of the surface of the shell of the microcapsules indicated the potential for sustained release as well as burst release.

Microbial Immobilization of Si, Mn, Fe, and Sr Ions in the Nacreous Layer of Sinohyliopsis schlegeli and Environmental Factors

NASA Astrophysics Data System (ADS)

Tazaki, Kazue; Morii, Issei

Environmental changes recorded in the shell nacre of Sinohyliopsis schlegeli were observed with elemental factors of characteristic water and nutrition for eight months in a cultivated drainage pond at Kanazawa University, Ishikawa Prefecture, Japan. Tetracycline as an indicator was injected into the shell nacre once every month from May to November in 2007. Water qualities such as the pH, redox potential, electrical conductivity, dissolved oxygen concentration, and water temperature were measured periodically, and the suspended solids in the water were removed by filtration for optical microscopy, X-ray fluorescence analysis, and scanning electron microscopy-energy dispersive X-ray (SEM-EDX) observations. X-ray fluorescence chemical analysis of shell nacre indicated layers with strong tetracycline accumulation corresponding to high concentrations of Si, Mn, Fe, and Sr ions. The redox potential and dissolved oxygen concentration measurements supported the existence of layers in the nacre. The suspended materials in the drainage pond water comprised mainly of Si, Mn, and Fe elements, which were the same elements involved in microbial immobilization in the shell nacre during the summer of 2007. SEM-EDX analyses confirmed that the ions originated from diatoms, Siderocapsa sp. and Gallionella ferruginea in the stomach. There was little microbial immobilization of the ions in winter. The results suggested elemental immobilization in the layered shell nacre and indicated that Sinohyliopsis schlegeli fed on the ions, to grow the nacre during summer. Sinohyliopsis schlegeli with these biogenic oxides might contribute to the scavenging of heavy metals in natural water.

High-resolution Measurement of Contact Ion-pair Structures in Aqueous RbCl Solutions from the Simultaneous Corefinement of their Rb and Cl K-edge XAFS and XRD Spectra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pham, Van-Thai; Fulton, John L.

2016-06-21

In concentrated solutions of aqueous RbCl, all of the Rb+ and Cl- ions exist as contact ion pairs. This full structural assessment is derived from the refinement of three independent experimental measurements: the Rb and Cl K-edge x-ray absorption fine structure (XAFS) and the x-ray diffraction spectra (XRD). This simultaneous refinement of the XAFS and XRD data provides high accuracy since each method probes the structure of different local regions about the ions with high sensitivity. At high RbCl concentration (6 m (mol/kg )) the solution is dominated by Rb+ - Cl- contact ion pairs yielding an average of 1.5more » pairs at an Rb-Cl distance of 3.24 Å. Upon formation of these ion pairs, approximately 1.1 waters molecules are displaced from the Rb+ and 1.4 water molecules from Cl-. The hydration shells about both the cation and anion are also determined. These results greatly improve the understanding of monovalent ions and provide a basis for testing the Rb+-Cl- interaction potentials used in molecular dynamics (MD) simulation. This research was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.« less

Revisit the landscape of protonated water clusters H+(H2O)n with n = 10-17: An ab initio global search.

PubMed

Shi, Ruili; Li, Keyao; Su, Yan; Tang, Lingli; Huang, Xiaoming; Sai, Linwei; Zhao, Jijun

2018-05-07

Using a genetic algorithm incorporated with density functional theory, we explore the ground state structures of protonated water clusters H + (H 2 O) n with n = 10-17. Then we re-optimize the isomers at B97-D/aug-cc-pVDZ level of theory. The extra proton connects with a H 2 O molecule to form a H 3 O + ion in all H + (H 2 O) 10-17 clusters. The lowest-energy structures adopt a monocage form at n = 10-16 and core-shell structure at n = 17 based on the MP2/aug-cc-pVTZ//B97-D/aug-cc-pVDZ+ZPE single-point-energy calculation. Using second-order vibrational perturbation theory, we further calculate the infrared spectra with anharmonic correction for the ground state structures of H + (H 2 O) 10-17 clusters at the PBE0/aug-cc-pVDZ level. The anharmonic correction to the spectra is crucial since it reproduces the experimental results quite well. The extra proton weakens the O-H bond strength in the H 3 O + ion since the Wiberg bond order of the O-H bond in the H 3 O + ion is smaller than that in H 2 O molecules, which causes a red shift of the O-H stretching mode in the H 3 O + ion.

Revisit the landscape of protonated water clusters H+(H2O)n with n = 10-17: An ab initio global search

NASA Astrophysics Data System (ADS)

Shi, Ruili; Li, Keyao; Su, Yan; Tang, Lingli; Huang, Xiaoming; Sai, Linwei; Zhao, Jijun

2018-05-01

Using a genetic algorithm incorporated with density functional theory, we explore the ground state structures of protonated water clusters H+(H2O)n with n = 10-17. Then we re-optimize the isomers at B97-D/aug-cc-pVDZ level of theory. The extra proton connects with a H2O molecule to form a H3O+ ion in all H+(H2O)10-17 clusters. The lowest-energy structures adopt a monocage form at n = 10-16 and core-shell structure at n = 17 based on the MP2/aug-cc-pVTZ//B97-D/aug-cc-pVDZ+ZPE single-point-energy calculation. Using second-order vibrational perturbation theory, we further calculate the infrared spectra with anharmonic correction for the ground state structures of H+(H2O)10-17 clusters at the PBE0/aug-cc-pVDZ level. The anharmonic correction to the spectra is crucial since it reproduces the experimental results quite well. The extra proton weakens the O-H bond strength in the H3O+ ion since the Wiberg bond order of the O-H bond in the H3O+ ion is smaller than that in H2O molecules, which causes a red shift of the O-H stretching mode in the H3O+ ion.

Reconstruction of seasonal temperature variability in the tropical Pacific Ocean from the shell of the scallop, Comptopallium radula

NASA Astrophysics Data System (ADS)

Thébault, Julien; Chauvaud, Laurent; Clavier, Jacques; Guarini, Jennifer; Dunbar, Robert B.; Fichez, Renaud; Mucciarone, David A.; Morize, Eric

2007-02-01

We investigated the oxygen isotope composition (δ 18O) of shell striae from juvenile Comptopallium radula (Mollusca; Pectinidae) specimens collected live in New Caledonia. Bottom-water temperature and salinity were monitored in-situ throughout the study period. External shell striae form with a 2-day periodicity in this scallop, making it possible to estimate the date of precipitation for each calcite sample collected along a growth transect. The oxygen isotope composition of shell calcite (δ 18O shell calcite) measured at almost weekly resolution on calcite accreted between August 2002 and July 2003 accurately tracks bottom-water temperatures. A new empirical paleotemperature equation for this scallop species relates temperature and δ 18O shell calcite: t(°C)=20.00(±0.61)-3.66(±0.39)×(δ18O-δ18O) The mean absolute accuracy of temperature estimated using this equation is 1.0 °C at temperatures between 20 and 30 °C. Uncertainties regarding the precise timing of CaCO 3 deposition and the actual variations in δ 18O water at our study sites probably contribute to this error. Comparison with a previously published empirical paleotemperature equation indicates that C. radula calcite is enriched in 18O by ˜0.7‰ relative to equilibrium. Given the direction of this offset and the lack of correlation between shell growth rate and δ 18O shell calcite, this disequilibrium is unlikely to be related to kinetic isotope effects. We suggest that this enrichment reflects (1) a relatively low pH in the scallop's marginal extrapallial fluid (EPF), (2) an isotopic signature of the EPF different from that of seawater, or (3) Rayleigh fractionation during the biocalcification process. Relative changes in δ 18O shell calcite reflect seawater temperature variability at this location and we suggest that the shell of C. radula may be useful as an archive of past seawater temperatures.

Reduction of the Radiating Sound of a Submerged Finite Cylindrical Shell Structure by Active Vibration Control

PubMed Central

Kim, Heung Soo; Sohn, Jung Woo; Jeon, Juncheol; Choi, Seung-Bok

2013-01-01

In this work, active vibration control of an underwater cylindrical shell structure was investigated, to suppress structural vibration and structure-borne noise in water. Finite element modeling of the submerged cylindrical shell structure was developed, and experimentally evaluated. Modal reduction was conducted to obtain the reduced system equation for the active feedback control algorithm. Three Macro Fiber Composites (MFCs) were used as actuators and sensors. One MFC was used as an exciter. The optimum control algorithm was designed based on the reduced system equations. The active control performance was then evaluated using the lab scale underwater cylindrical shell structure. Structural vibration and structure-borne noise of the underwater cylindrical shell structure were reduced significantly by activating the optimal controller associated with the MFC actuators. The results provide that active vibration control of the underwater structure is a useful means to reduce structure-borne noise in water. PMID:23389344

Reduction of the radiating sound of a submerged finite cylindrical shell structure by active vibration control.

PubMed

Kim, Heung Soo; Sohn, Jung Woo; Jeon, Juncheol; Choi, Seung-Bok

2013-02-06

In this work, active vibration control of an underwater cylindrical shell structure was investigated, to suppress structural vibration and structure-borne noise in water. Finite element modeling of the submerged cylindrical shell structure was developed, and experimentally evaluated. Modal reduction was conducted to obtain the reduced system equation for the active feedback control algorithm. Three Macro Fiber Composites (MFCs) were used as actuators and sensors. One MFC was used as an exciter. The optimum control algorithm was designed based on the reduced system equations. The active control performance was then evaluated using the lab scale underwater cylindrical shell structure. Structural vibration and structure-borne noise of the underwater cylindrical shell structure were reduced significantly by activating the optimal controller associated with the MFC actuators. The results provide that active vibration control of the underwater structure is a useful means to reduce structure-borne noise in water.

Enceladus' tidal dissipation revisited

NASA Astrophysics Data System (ADS)

Tobie, Gabriel; Behounkova, Marie; Choblet, Gael; Cadek, Ondrej; Soucek, Ondrej

2016-10-01

A series of chemical and physical evidence indicates that the intense activity at Enceladus' South Pole is related to a subsurface salty water reservoir underneath the tectonically active ice shell. The detection of a significant libration implies that this water reservoir is global and that the average ice shell thickness is about 20-25km (Thomas et al. 2016). The interpretation of gravity and topography data further predicts large variations in ice shell thickness, resulting in a shell potentially thinner than 5 km in the South Polar Terrain (SPT) (Cadek et al. 2016). Such an ice shell structure requires a very strong heat source in the interior, with a focusing mechanism at the SPT. Thermal diffusion through the ice shell implies that at least 25-30 GW is lost into space by passive diffusion, implying a very efficient dissipation mechanism in Enceladus' interior to maintain such an ocean/ice configuration thermally stable.In order to determine in which conditions such a large dissipation power may be generated, we model the tidal response of Enceladus including variable ice shell thickness. For the rock core, we consider a wide range of rheological parameters representative of water-saturated porous rock materials. We demonstrate that the thinning toward the South Pole leads to a strong increase in heat production in the ice shell, with a optimal thickness obtained between 1.5 and 3 km, depending on the assumed ice viscosity. Our results imply that the heat production in the ice shell within the SPT may be sufficient to counterbalance the heat loss by diffusion and to power eruption activity. However, outside the SPT, a strong dissipation in the porous core is required to counterbalance the diffusive heat loss. We show that about 20 GW can be generated in the core, for an effective viscosity of 1012 Pa.s, which is comparable to the effective viscosity estimated in water-saturated glacial tills on Earth. We will discuss the implications of this revisited tidal budget for the activity of Enceladus and the long-term evolution of its interior.

Comparative Spectra of Oxygen-Rich Versus Carbon-Rich Circumstellar Shells: VY Canis Majoris and IRC(plus)10216 at 215-285 GHz

NASA Technical Reports Server (NTRS)

Tenebaum, E. D.; Dodd, J. L.; Milam, S. N.; Woolf, N. J.; Ziurys, L. M.

2010-01-01

A sensitive (1sigma rms at 1 MHz resolution approx.3 mK) 1 mm spectral line survey (214.5-285.5 GHz) of VY Canis Majoris (VY CMa) and IRC +10216 has been conducted to compare the chemistries of oxygen- and carbon-rich circumstellar envelopes. This study was carried out using the Submillimeter Telescope of the Arizona Radio Observatory with a new Atacama Large Millimeter Array type receiver. This survey is the first to chemically characterize an O-rich circumstellar shell at millimeter wavelengths. In VY CMa, 128 emission features were detected arising from 18 different molecules; and in IRC +10216, 720 lines were observed, assigned to 32 different species. The 1 mm spectrum of VY CMa is dominated by SO, and SiS; in IRC +10216, C4H and SiC2 are the most recurrent species. Ten molecules were common to both sources: CO, SiS, SiO, CS, CN, HCN, HNC, NaCl, PN, and HCO(+). Sulfur plays an important role in VY CMa, but saturated/ unsaturated carbon dominates the molecular content of IRC +102.16, producing CH2NH, for example. Although the molecular complexity of IRC +10216 is greater, VY CMa supports a unique "inorganic" chemistry leading to the oxides PO, AlO, and AlOH. Only diatomic and triatomic compounds were observed in VY CMa, while species with four or more atoms are common in IRC +10216, reflecting carbon's ability to form multiple strong bonds, unlike oxygen. In VY CMa, a new water maser (v2 = 2) has been found, as well as vibrationally excited NaCl. Toward IRC +10216, vibrationally excited CCH was detected for the first time.

Comparative Spectra of Oxygen-rich Versus Carbon-rich Circumstellar Shells: VY Canis Majoris and IRC +10216 at 215-285 GHz

NASA Astrophysics Data System (ADS)

Tenenbaum, E. D.; Dodd, J. L.; Milam, S. N.; Woolf, N. J.; Ziurys, L. M.

2010-09-01

A sensitive (1σ rms at 1 MHz resolution ~3 mK) 1 mm spectral line survey (214.5-285.5 GHz) of VY Canis Majoris (VY CMa) and IRC +10216 has been conducted to compare the chemistries of oxygen- and carbon-rich circumstellar envelopes. This study was carried out using the Submillimeter Telescope of the Arizona Radio Observatory with a new Atacama Large Millimeter Array type receiver. This survey is the first to chemically characterize an O-rich circumstellar shell at millimeter wavelengths. In VY CMa, 128 emission features were detected arising from 18 different molecules; and in IRC +10216, 720 lines were observed, assigned to 32 different species. The 1 mm spectrum of VY CMa is dominated by SO2 and SiS; in IRC +10216, C4H and SiC2 are the most recurrent species. Ten molecules were common to both sources: CO, SiS, SiO, CS, CN, HCN, HNC, NaCl, PN, and HCO+. Sulfur plays an important role in VY CMa, but saturated/unsaturated carbon dominates the molecular content of IRC +10216, producing CH2NH, for example. Although the molecular complexity of IRC +10216 is greater, VY CMa supports a unique "inorganic" chemistry leading to the oxides PO, AlO, and AlOH. Only diatomic and triatomic compounds were observed in VY CMa, while species with four or more atoms are common in IRC +10216, reflecting carbon's ability to form multiple strong bonds, unlike oxygen. In VY CMa, a new water maser (v 2 = 2) has been found, as well as vibrationally excited NaCl. Toward IRC +10216, vibrationally excited CCH was detected for the first time.

Structural characterization of the phospholipid stabilizer layer at the solid-liquid interface of dispersed triglyceride nanocrystals with small-angle x-ray and neutron scattering

NASA Astrophysics Data System (ADS)

Schmiele, Martin; Schindler, Torben; Unruh, Tobias; Busch, Sebastian; Morhenn, Humphrey; Westermann, Martin; Steiniger, Frank; Radulescu, Aurel; Lindner, Peter; Schweins, Ralf; Boesecke, Peter

2013-06-01

Dispersions of crystalline nanoparticles with at least one sufficiently large unit cell dimension can give rise to Bragg reflections in the small-angle scattering range. If the nanocrystals possess only a small number of unit cells along these particular crystallographic directions, the corresponding Bragg reflections will be broadened. In a previous study of phospholipid stabilized dispersions of β-tripalmitin platelets [Unruh, J. Appl. Crystallogr.JACGAR0021-889810.1107/S0021889807044378 40, 1008 (2007)], the x-ray powder pattern simulation analysis (XPPSA) was developed. The XPPSA method facilitates the interpretation of the rather complicated small-angle x-ray scattering (SAXS) curves of such dispersions of nanocrystals. The XPPSA method yields the distribution function of the platelet thicknesses and facilitates a structural characterization of the phospholipid stabilizer layer at the solid-liquid interface between the nanocrystals and the dispersion medium from the shape of the broadened 001 Bragg reflection. In this contribution an improved and extended version of the XPPSA method is presented. The SAXS and small-angle neutron scattering patterns of dilute phospholipid stabilized tripalmitin dispersions can be reproduced on the basis of a consistent simulation model for the particles and their phospholipid stabilizer layer on an absolute scale. The results indicate a surprisingly flat arrangement of the phospholipid molecules in the stabilizer layer with a total thickness of only 12 Å. The stabilizer layer can be modeled by an inner shell for the fatty acid chains and an outer shell including the head groups and additional water. The experiments support a dense packing of the phospholipid molecules on the nanocrystal surfaces rather than isolated phospholipid domains.

Disinfection of the Water Borne Pathogens Escherichia coli and Staphylococcus aureus by Solar Photocatalysis Using Sonochemically Synthesized Reusable Ag@ZnO Core-Shell Nanoparticles.

PubMed

Das, Sourav; Ranjana, Neha; Misra, Ananyo Jyoti; Suar, Mrutyunjay; Mishra, Amrita; Tamhankar, Ashok J; Lundborg, Cecilia Stålsby; Tripathy, Suraj K

2017-07-10

Water borne pathogens present a threat to human health and their disinfection from water poses a challenge, prompting the search for newer methods and newer materials. Disinfection of the Gram-negative bacterium Escherichia coli and the Gram-positive coccal bacterium Staphylococcus aureus in an aqueous matrix was achieved within 60 and 90 min, respectively, at 35 °C using solar-photocatalysis mediated by sonochemically synthesized Ag@ZnO core-shell nanoparticles. The efficiency of the process increased with the increase in temperature and at 55 °C the disinfection for the two bacteria could be achieved in 45 and 60 min, respectively. A new ultrasound-assisted chemical precipitation technique was used for the synthesis of Ag@ZnO core-shell nanoparticles. The characteristics of the synthesized material were established using physical techniques. The material remained stable even at 400 °C. Disinfection efficiency of the Ag@ZnO core-shell nanoparticles was confirmed in the case of real world samples of pond, river, municipal tap water and was found to be better than that of pure ZnO and TiO₂ (Degussa P25). When the nanoparticle- based catalyst was recycled and reused for subsequent disinfection experiments, its efficiency did not change remarkably, even after three cycles. The sonochemically synthesized Ag@ZnO core-shell nanoparticles thus have a good potential for application in solar photocatalytic disinfection of water borne pathogens.

Disinfection of the Water Borne Pathogens Escherichia coli and Staphylococcus aureus by Solar Photocatalysis Using Sonochemically Synthesized Reusable Ag@ZnO Core-Shell Nanoparticles

PubMed Central

Das, Sourav; Ranjana, Neha; Misra, Ananyo Jyoti; Suar, Mrutyunjay; Mishra, Amrita; Tripathy, Suraj K.

2017-01-01

Water borne pathogens present a threat to human health and their disinfection from water poses a challenge, prompting the search for newer methods and newer materials. Disinfection of the Gram-negative bacterium Escherichia coli and the Gram-positive coccal bacterium Staphylococcus aureus in an aqueous matrix was achieved within 60 and 90 min, respectively, at 35 °C using solar-photocatalysis mediated by sonochemically synthesized Ag@ZnO core-shell nanoparticles. The efficiency of the process increased with the increase in temperature and at 55 °C the disinfection for the two bacteria could be achieved in 45 and 60 min, respectively. A new ultrasound-assisted chemical precipitation technique was used for the synthesis of Ag@ZnO core-shell nanoparticles. The characteristics of the synthesized material were established using physical techniques. The material remained stable even at 400 °C. Disinfection efficiency of the Ag@ZnO core-shell nanoparticles was confirmed in the case of real world samples of pond, river, municipal tap water and was found to be better than that of pure ZnO and TiO2 (Degussa P25). When the nanoparticle- based catalyst was recycled and reused for subsequent disinfection experiments, its efficiency did not change remarkably, even after three cycles. The sonochemically synthesized Ag@ZnO core-shell nanoparticles thus have a good potential for application in solar photocatalytic disinfection of water borne pathogens. PMID:28698514

A molecular dynamics study of water nucleation using the TIP4P/2005 model

NASA Astrophysics Data System (ADS)

Pérez, Alejandro; Rubio, Angel

2011-12-01

Extensive molecular dynamics simulations were conducted using the TIP4P/2005 water model of Abascal and Vega [J. Chem. Phys. 123, 234505 (2005)] to investigate its condensation from supersaturated vapor to liquid at 330 K. The mean first passage time method [J. Wedekind, R. Strey, and D. Reguera, J. Chem. Phys. 126, 134103 (2007); L. S. Bartell and D. T. Wu, 125, 194503 (2006)] was used to analyze the influence of finite size effects, thermostats, and charged species on the nucleation dynamics. We find that the Nosé-Hoover thermostat and the one proposed by Bussi et al. [J. Chem. Phys. 126, 014101 (2007)] give essentially the same averages. We identify the maximum thermostat coupling time to guarantee proper thermostating for these simulations. The presence of charged species has a dramatic impact on the dynamics, inducing a marked change towards a pure growth regime, which highlights the importance of ions in the formation of liquid droplets in the atmosphere. It was found a small but noticeable sign preference at intermediate cluster sizes (between 5 and 30 water molecules) corresponding mostly to the formation of the second solvation shell around the ion. The TIP4P/2005 water model predicts that anions induce faster formation of water clusters than cations of the same magnitude of charge.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Varanasi, S. R., E-mail: s.raovaranasi@uq.edu.au, E-mail: guskova@ipfdd.de; John, A.; Guskova, O. A., E-mail: s.raovaranasi@uq.edu.au, E-mail: guskova@ipfdd.de

Fullerene C{sub 60} sub-colloidal particle with diameter ∼1 nm represents a boundary case between small and large hydrophobic solutes on the length scale of hydrophobic hydration. In the present paper, a molecular dynamics simulation is performed to investigate this complex phenomenon for bare C{sub 60} fullerene and its amphiphilic/charged derivatives, so called shape amphiphiles. Since most of the unique properties of water originate from the pattern of hydrogen bond network and its dynamics, spatial, and orientational aspects of water in solvation shells around the solute surface having hydrophilic and hydrophobic regions are analyzed. Dynamical properties such as translational-rotational mobility, reorientationalmore » correlation and occupation time correlation functions of water molecules, and diffusion coefficients are also calculated. Slower dynamics of solvent molecules—water retardation—in the vicinity of the solutes is observed. Both the topological properties of hydrogen bond pattern and the “dangling” –OH groups that represent surface defects in water network are monitored. The fraction of such defect structures is increased near the hydrophobic cap of fullerenes. Some “dry” regions of C{sub 60} are observed which can be considered as signatures of surface dewetting. In an effort to provide molecular level insight into the thermodynamics of hydration, the free energy of solvation is determined for a family of fullerene particles using thermodynamic integration technique.« less

Report on the 18th International Conference on X-ray and Inner-Shell Processes (X99).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gemmell, D. S.; Physics

2000-01-01

The 18th conference of the series served as a forum for discussing fundamental issues in the field of x-ray and inner-shell processes and their application in various disciplines of science and technology. Special emphasis was given to the opportunities offered by modern synchrotron x-ray sources. The program included plenary talks, progress reports and poster presentations relating to new developments in the field of x-ray and inner-shell processes. The range of topics included: X-ray interactions with atoms, molecules, clusters, surfaces and solids; Decay processes for inner-shell vacancies; X-ray absorption and emission spectroscopy - Photoionization processes; Phenomena associated with highly charged ionsmore » and collisions with energetic particles; Electron-spin and -momentum spectroscopy; X-ray scattering and spectroscopy in the study of magnetic systems; Applications in materials science, biology, geosciences, and other disciplines; Elastic and inelastic x-ray scattering processes in atoms and molecules; Threshold phenomena (post-collision interaction, resonant Raman processes, etc.); Nuclear absorption and scattering of x-rays; 'Fourth-generation' x-ray sources; Processes exploiting the polarization and coherence properties of x-ray beams; Developments in experimental techniques (x-ray optics, temporal techniques, detectors); Microscopy, spectromicroscopy, and various imaging techniques; Non-linear processes and x-ray lasers; Ionization and excitation induced by charged particles and by x-rays; and Exotic atoms (including 'hollow' atoms and atoms that contain 'exotic' particles).« less

Triple-functional core-shell structured upconversion luminescent nanoparticles covalently grafted with photosensitizer for luminescent, magnetic resonance imaging and photodynamic therapy in vitro

NASA Astrophysics Data System (ADS)

Qiao, Xiao-Fei; Zhou, Jia-Cai; Xiao, Jia-Wen; Wang, Ye-Fu; Sun, Ling-Dong; Yan, Chun-Hua

2012-07-01

Upconversion luminescent nanoparticles (UCNPs) have been widely used in many biochemical fields, due to their characteristic large anti-Stokes shifts, narrow emission bands, deep tissue penetration and minimal background interference. UCNPs-derived multifunctional materials that integrate the merits of UCNPs and other functional entities have also attracted extensive attention. Here in this paper we present a core-shell structured nanomaterial, namely, NaGdF4:Yb,Er@CaF2@SiO2-PS, which is multifunctional in the fields of photodynamic therapy (PDT), magnetic resonance imaging (MRI) and fluorescence/luminescence imaging. The NaGdF4:Yb,Er@CaF2 nanophosphors (10 nm in diameter) were prepared via sequential thermolysis, and mesoporous silica was coated as shell layer, in which photosensitizer (PS, hematoporphyrin and silicon phthalocyanine dihydroxide) was covalently grafted. The silica shell improved the dispersibility of hydrophobic PS molecules in aqueous environments, and the covalent linkage stably anchored the PS molecules in the silica shell. Under excitation at 980 nm, the as-fabricated nanomaterial gave luminescence bands at 550 nm and 660 nm. One luminescent peak could be used for fluorescence imaging and the other was suitable for the absorption of PS to generate singlet oxygen for killing cancer cells. The PDT performance was investigated using a singlet oxygen indicator, and was investigated in vitro in HeLa cells using a fluorescent probe. Meanwhile, the nanomaterial displayed low dark cytotoxicity and near-infrared (NIR) image in HeLa cells. Further, benefiting from the paramagnetic Gd3+ ions in the core, the nanomaterial could be used as a contrast agent for magnetic resonance imaging (MRI). Compared with the clinical commercial contrast agent Gd-DTPA, the as-fabricated nanomaterial showed a comparable longitudinal relaxivities value (r1) and similar imaging effect.Upconversion luminescent nanoparticles (UCNPs) have been widely used in many biochemical fields, due to their characteristic large anti-Stokes shifts, narrow emission bands, deep tissue penetration and minimal background interference. UCNPs-derived multifunctional materials that integrate the merits of UCNPs and other functional entities have also attracted extensive attention. Here in this paper we present a core-shell structured nanomaterial, namely, NaGdF4:Yb,Er@CaF2@SiO2-PS, which is multifunctional in the fields of photodynamic therapy (PDT), magnetic resonance imaging (MRI) and fluorescence/luminescence imaging. The NaGdF4:Yb,Er@CaF2 nanophosphors (10 nm in diameter) were prepared via sequential thermolysis, and mesoporous silica was coated as shell layer, in which photosensitizer (PS, hematoporphyrin and silicon phthalocyanine dihydroxide) was covalently grafted. The silica shell improved the dispersibility of hydrophobic PS molecules in aqueous environments, and the covalent linkage stably anchored the PS molecules in the silica shell. Under excitation at 980 nm, the as-fabricated nanomaterial gave luminescence bands at 550 nm and 660 nm. One luminescent peak could be used for fluorescence imaging and the other was suitable for the absorption of PS to generate singlet oxygen for killing cancer cells. The PDT performance was investigated using a singlet oxygen indicator, and was investigated in vitro in HeLa cells using a fluorescent probe. Meanwhile, the nanomaterial displayed low dark cytotoxicity and near-infrared (NIR) image in HeLa cells. Further, benefiting from the paramagnetic Gd3+ ions in the core, the nanomaterial could be used as a contrast agent for magnetic resonance imaging (MRI). Compared with the clinical commercial contrast agent Gd-DTPA, the as-fabricated nanomaterial showed a comparable longitudinal relaxivities value (r1) and similar imaging effect. Electronic supplementary information (ESI) available: More TEM, emission spectra, longitudinal and transverse relaxation times, t2-weighted MR images of the as-prepared nanomaterial, and confocal fluorescent images of HeLa cells. See DOI: 10.1039/c2nr30938f

Mussel Shell Evaluation as Bioindicator For Heavy Metals

NASA Astrophysics Data System (ADS)

Andrello, Avacir Casanova; Lopes, Fábio; Galvão, Tiago Dutra

2010-05-01

Recently, in Brazil, it has appeared a new and unusual "plague" in lazer and commercial fishing. It is caused by the parasitic larval phase of certain native bivalve mollusks of fresh water known as "Naiades" and its involves the presence of big bivalve of fresh water, mainly Anodontites trapesialis, in the tanks and dams of the fish creation. These bivalve mollusks belong to the Unionoida Order, Mycetopodidae Family. The objective of the present work was to analyze the shells of these mollusks to verify the possibility of use as bioindicators for heavy metals in freshwater. The mollusks shells were collected in a commercial fishing at Londrina-PR. A qualitative analysis was made to determine the chemical composition of the shells and verify a possible correlation with existent heavy metals in the aquatic environment. In the inner part of the shells were identified the elements Ca, P, Fe, Mn and Sr and in the outer part were identified Ca, P, Fe, Mn, Sr and Cu. The Ca ratio of the outer part by inner part of the analyzed shells is around of 1, as expected, because Ca is the main compound of mollusks shells. The ratio of P, Fe, Mn, and Sr to the Ca were constant in all analyzed shells, being close to 0.015. The ratio Cu/Ca varied among the shells, showing that this mollusk is sensitive to concentration of this element in the aquatic environment.

Facile method for preparing organic/inorganic hybrid capsules using amino-functional silane coupling agent in aqueous media.

PubMed

Kurayama, Fumio; Suzuki, Satoru; Oyamada, Tetsuro; Furusawa, Takeshi; Sato, Masahide; Suzuki, Noboru

2010-09-01

A new and facile method for preparing microcapsules with 3-aminopropyltriethoxysilane (APTES)/alginate hybrid shell (AP-capsule) is proposed based on gelling and sol-gel processes. In this method, conventional capsules with alginate shells (Alg-capsule) are produced by dripping carboxymethyl cellulose solution containing calcium chloride into a sodium alginate solution. Subsequently, addition of the Alg-capsules to an aqueous APTES solution induces the formation of APTES/alginate hybrid shells. The optical observation shows that the texture of AP-capsules is more glossy and transparent than that of Alg-capsules. The surface morphology and elemental composition of microcapsules were characterized by Scanning Electron Microscopy (SEM), Fourier Transform Infrared Spectroscopy (FT-IR) and X-ray Photoelectron Spectroscopy (XPS). The results suggest that APTES molecules are incorporated to the framework of the alginate shells via electrostatic interaction between amino groups of APTES and carboxyl groups of alginate and the hybrid shells have a dense and homogeneous structure. In the formation reaction, the shrinking of the capsule shells occurs and the accumulation of APTES in the capsule shells proceeds with pseudo first-order kinetics. Moreover, these behaviors are greatly influenced by pH of the reaction solution, especially promoted under acidic and alkaline conditions. Copyright 2010 Elsevier Inc. All rights reserved.

Sub-seasonal oxygen and carbon isotope variations in shells of modern Radix sp. (Gastropoda) from the Tibetan Plateau: potential of a new archive for palaeoclimatic studies

NASA Astrophysics Data System (ADS)

Taft, Linda; Wiechert, Uwe; Riedel, Frank; Weynell, Marc; Zhang, Hucai

2012-02-01

Carbon and oxygen isotope ratios have been measured for nine aragonite shells of the gastropod genus Radix from the lake Bangda Co (30°29'N, 97°04'E, 4450 m a.s.l.) at the south-eastern edge and from two characteristic sites at the lake Kyaring Co (31°09'N, 88°17'E, 4650 m a.s.l.) on the central Tibetan Plateau. Radix shells were sampled for isotope ratio analysis with high spatial resolution along the ontogenetic spiral of growth providing the basis of isotope records with a sub-seasonal time-resolution. δ18O values of shells from Bangda Co are on average ˜-15.0‰ relative to PDB and the pattern exhibits a clear onset and progression of the summer monsoon precipitation indicated by a strong "amount effect". This pattern mirrors the precipitation pattern in the respective year and region as expected for a small (surface area ca 0.3 km2) and shallow (<5 m) lake or habitat with short water residence times and little evaporative 18O enrichment of the lake water. In contrast, δ18O values of Radix shells from Kyaring Co habitat A which is connected to the deep (several tens of metres) and big (surface area ca 660 km2) lake, average at ˜-13.0‰ consistent with a higher evaporation rate and longer water residence time. The latter is supported by more 18O enriched water in this habitat. The δ18O values of Radix shells from Kyaring Co habitat B are nearly as low as shells from Bangda Co due to the similar habitat characteristic but isotopic patterns of these shells exhibit a weaker "amount effect". In both lake systems δ13C values of the shells are coupled with oxygen isotopes because a large amount of isotopically light carbon is washed from mountain slopes into the lake during the rainy season. Although other processes influence the isotopic patterns, e.g. biological productivity (δ13C) or temperature (δ18O), these influences are minor compared with the monsoon signal or the effect of evaporation in the Radix shell records. The overall weaker amount effect in Radix shells from Kyaring Co habitat B compared with shells from Bangda Co are consistent with a current decreasing monsoon influence from the south-eastern edge towards the central Tibetan Plateau. Thus, fossil shells of the gastropod genus Radix are a valuable archive for reconstructing climatic and environmental changes on the Tibetan Plateau and provide information about former habitat sizes and depths.

SERS microscopy: plasmonic nanoparticle probes and biomedical applications

NASA Astrophysics Data System (ADS)

Gellner, M.; Schütz, M.; Salehi, M.; Packeisen, J.; Ströbel, P.; Marx, A.; Schmuck, C.; Schlücker, S.

2010-08-01

Nanoparticle probes for use in targeted detection schemes and readout by surface-enhanced Raman scattering (SERS) comprise a metal core, Raman reporter molecules and a protective shell. One design of SERS labels specifically optimized for biomedical applications in conjunction with red laser excitation is based on tunable gold/silver nanoshells, which are completely covered by a self-assembled monolayer (SAM) of Raman reporters. A shell around the SAM-coated metal core stabilizes the colloid and prevents particle aggregation. The optical properties and SERS efficiencies of these plasmonic nanostructures are characterized both experimentally and theoretically. Subsequent bioconjugation of SERS probes to ligands such as antibodies is a prerequisite for the selective detection of the corresponding target molecule via the characteristic Raman signature of the label. Biomedical imaging applications of SERS-labeled antibodies for tumor diagnostics by SERS microscopy are presented, using the localization of the tumor suppressor p63 in prostate tissue sections as an example.

Ultrafast isomerization initiated by X-ray core ionization

NASA Astrophysics Data System (ADS)

Liekhus-Schmaltz, Chelsea E.; Tenney, Ian; Osipov, Timur; Sanchez-Gonzalez, Alvaro; Berrah, Nora; Boll, Rebecca; Bomme, Cedric; Bostedt, Christoph; Bozek, John D.; Carron, Sebastian; Coffee, Ryan; Devin, Julien; Erk, Benjamin; Ferguson, Ken R.; Field, Robert W.; Foucar, Lutz; Frasinski, Leszek J.; Glownia, James M.; Gühr, Markus; Kamalov, Andrei; Krzywinski, Jacek; Li, Heng; Marangos, Jonathan P.; Martinez, Todd J.; McFarland, Brian K.; Miyabe, Shungo; Murphy, Brendan; Natan, Adi; Rolles, Daniel; Rudenko, Artem; Siano, Marco; Simpson, Emma R.; Spector, Limor; Swiggers, Michele; Walke, Daniel; Wang, Song; Weber, Thorsten; Bucksbaum, Philip H.; Petrovic, Vladimir S.

2015-09-01

Rapid proton migration is a key process in hydrocarbon photochemistry. Charge migration and subsequent proton motion can mitigate radiation damage when heavier atoms absorb X-rays. If rapid enough, this can improve the fidelity of diffract-before-destroy measurements of biomolecular structure at X-ray-free electron lasers. Here we study X-ray-initiated isomerization of acetylene, a model for proton dynamics in hydrocarbons. Our time-resolved measurements capture the transient motion of protons following X-ray ionization of carbon K-shell electrons. We Coulomb-explode the molecule with a second precisely delayed X-ray pulse and then record all the fragment momenta. These snapshots at different delays are combined into a `molecular movie' of the evolving molecule, which shows substantial proton redistribution within the first 12 fs. We conclude that significant proton motion occurs on a timescale comparable to the Auger relaxation that refills the K-shell vacancy.

Chemical Understanding of the Limited Site-Specificity in Molecular Inner-Shell Photofragmentation

DOE PAGES

Inhester, Ludger; Oostenrijk, Bart; Patanen, Minna; ...

2018-02-14

In many cases fragmentation of molecules upon inner-shell ionization is very unspecific with respect to the initially localized ionization site. Often this finding is interpreted in terms of an equilibration of internal energy into vibrational degrees of freedom after Auger decay. In this paper, we investigate the X-ray photofragmentation of ethyl trifluoroacetate upon core electron ionization at environmentally distinct carbon sites using photoelectron–photoion–photoion coincidence measurements and ab initio electronic structure calculations. For all four carbon ionization sites, the Auger decay weakens the same bonds and transfers the two charges to opposite ends of the molecule, which leads to a rapidmore » dissociation into three fragments, followed by further fragmentation steps. Finally, the lack of site specificity is attributed to the character of the dicationic electronic states after Auger decay instead of a fast equilibration of internal energy.« less

Electronic spectrum of the UO and UO(+) molecules.

PubMed

Tyagi, Rajni; Zhang, Zhiyong; Pitzer, Russell M

2014-12-18

Electronic theory calculations are applied to the study of the UO molecule and the UO(+) ion. Relativistic effective core potentials are used along with the accompanying valence spin-orbit operators. Polarized double-ς and triple-ς basis sets are used. Molecular orbitals are obtained from state-averaged multiconfiguration self-consistent field calculations and then used in multireference spin-orbit configuration interaction calculations with a number of millions of terms. The ground state of UO has open shells of 5f(3)7s(1), angular momentum Ω = 4, and a spin-orbit-induced avoided crossing near the equilibrium internuclear distance. Many UO excited states are studied with rotational constants, intensities, and experimental comparisons. The ground state of UO(+) is of 5f(3) nature with Ω = 9/2. Many UO(+) excited states are also studied. The open-shell nature of both UO and UO(+) leads to many low-lying excited states.

Influence of drug binding on DNA hydration: acoustic and densimetric characterizations of netropsin binding to the poly(dAdT).poly(dAdT) and poly(dA).poly(dT) duplexes and the poly(dT).poly(dA).poly(dT) triplex at 25 degrees C.

PubMed

Chalikian, T V; Plum, G E; Sarvazyan, A P; Breslauer, K J

1994-07-26

We use high-precision acoustic and densimetric techniques to determine, at 25 degrees C, the changes in volume, delta V, and adiabatic compressibility, delta Ks, that accompany the binding of netropsin to the poly(dAdT).poly(dAdT) and poly(dA).poly(dT) duplexes, as well as to the poly(dT).poly(dA).poly(dT) triplex. We find that netropsin binding to the heteropolymeric poly(dAdT).poly(dAdT) duplex is accompanied by negative changes in volume, delta V, and small positive changes in compressibility, delta Ks. By contrast, netropsin binding to the homopolymeric poly(dA).poly(dT) duplex is accompanied by large positive changes in both volume, delta V, and compressibility, delta Ks. Furthermore, netropsin binding to the poly(dT).poly(dA).poly(dT) triplex causes changes in both volume and compressibility that are nearly twice as large as those observed when netropsin binds to the poly(dA).poly(dT) duplex. We interpret these macroscopic data in terms of binding-induced microscopic changes in the hydration of the DNA structures and the drug. Specifically, we find that netropsin binding induces the release of approximately 22 waters from the hydration shell of the poly(dAdT).poly(dAdT) heteropolymeric duplex, approximately 40 waters from the hydration shell of the poly(dA).poly(dT) homopolymeric duplex, and about 53 waters from the hydration shell of the poly(dA).poly(dT), induces the release of 18 more water molecules than netropsin binding to the heteropolymeric duplex, poly(dAdT).poly(dAdT). On the basis of apparent molar volume, phi V, and apparent molar adiabatic compressibility, phi Ks, values for the initial drug-free and final drug-bound states of the two all-AT duplexes, we propose that the larger dehydration of the poly(dA).poly(dT) duplex reflects, in part, the formation of a less hydrated poly(dA).poly(dT)-netropsin complex compared with the corresponding poly(dAdT).poly(dAdT)-netropsin complex. In conjunction with our previously published entropy data [Marky, L. A., & Breslauer, K. J. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 4359-4363], we calculate that each water of hydration released to the bulk solvent by ligand binding contributes 1.6 cal K-1 mol-1 to the entropy of binding. This value corresponds to the average difference between the partial molar entropy of water in the bulk state and water in the hydration shells of the two all-AT duplexes. When netropsin binds to the poly(dT).poly(dA).poly(dT) triplex, the changes in both volume and compressibility suggest that the binding event induces more dehydration of the triplex than of the duplex state. Specifically, we calculate that netropsin binding to the poly(dT).poly(dA).poly(dT) triplex causes the release of 13 more waters than netropsin binding to the poly(dA).poly(dT) duplex.(ABSTRACT TRUNCATED AT 400 WORDS)

Highly aqueous soluble CaF2:Ce/Tb nanocrystals: effect of surface functionalization on structural, optical band gap, and photoluminescence properties.

PubMed

Ansari, Anees A; Parchur, Abdul K; Kumar, Brijesh; Rai, S B

2016-12-01

The design of nanostructured materials with highly stable water-dispersion and luminescence efficiency is an important concern in nanotechnology and nanomedicine. In this paper, we described the synthesis and distinct surface modification on the morphological structure and optical (optical absorption, band gap energy, excitation, emission, decay time, etc.) properties of highly crystalline water-dispersible CaF 2 :Ce/Tb nanocrystals (core-nanocrystals). The epitaxial growth of inert CaF 2 and silica shell, respectively, on their surface forming as CaF 2 :Ce/Tb@CaF 2 (core/shell) and CaF 2 :Ce/Tb@CaF 2 @SiO 2 (core/shell/SiO 2 ) nanoarchitecture. X-ray diffraction and transmission electron microscope image shows that the nanocrystals were in irregular spherical phase, highly crystalline (~20 nm) with narrow size distribution. The core/shell nanocrystals confirm that the surface coating is responsible in the change of symmetrical nanostructure, which was determined from the band gap energy and luminescent properties. It was found that an inert inorganic shell formation effectively enhances the luminescence efficiency and silica shell makes the nanocrystals highly water-dispersible. In addition, Ce 3+ /Tb 3+ -co-doped CaF 2 nanocrystals show efficient energy transfer from Ce 3+ to Tb 3+ ion and strong green luminescence of Tb 3+ ion at 541 nm( 5 D 4 → 7 F 5 ). Luminescence decay curves of core and core/shell nanocrystals were fitted using mono and biexponential equations, and R 2 regression coefficient criteria were used to discriminate the goodness of the fitted model. The lifetime values for the core/shell nanocrystals are higher than core-nanocrystals. Considering the high stable water-dispersion and intensive luminescence emission in the visible region, these luminescent core/shell nanocrystals could be potential candidates for luminescent bio-imaging, optical bio-probe, displays, staining, and multianalyte optical sensing. A newly designed CaF 2 :Ce/Tb nanoparticles via metal complex decomposition rout shows high dispersibility in aqueous solvents with enhanced photoluminescence. The epitaxial growth of inert CaF 2 shell and further amorphous silica, respectively, enhanced their optical and luminescence properties, which is highly usable for luminescent biolabeling, and optical bioprobe etc.

The problem of hole localization in inner-shell states of N2 and CO2 revisited with complete active space self-consistent field approach.

PubMed

Rocha, Alexandre B; de Moura, Carlos E V

2011-12-14

Potential energy curves for inner-shell states of nitrogen and carbon dioxide molecules are calculated by inner-shell complete active space self-consistent field (CASSCF) method, which is a protocol, recently proposed, to obtain specifically converged inner-shell states at multiconfigurational level. This is possible since the collapse of the wave function to a low-lying state is avoided by a sequence of constrained optimization in the orbital mixing step. The problem of localization of K-shell states is revisited by calculating their energies at CASSCF level based on both localized and delocalized orbitals. The localized basis presents the best results at this level of calculation. Transition energies are also calculated by perturbation theory, by taking the above mentioned MCSCF function as zeroth order wave function. Values for transition energy are in fairly good agreement with experimental ones. Bond dissociation energies for N(2) are considerably high, which means that these states are strongly bound. Potential curves along ground state normal modes of CO(2) indicate the occurrence of Renner-Teller effect in inner-shell states. © 2011 American Institute of Physics

Broken Chains: The Effect of Ocean Acidification on Bivalve and Echinoid Development

NASA Astrophysics Data System (ADS)

Richardson, K.

2016-12-01

Global warming is one of the most urgent issues facing the interconnected systems of our planet. One important impact of global warming is ocean acidification, which is a change in the pH of the oceans due to increased levels of carbon dioxide in the atmosphere. This can harm ocean life in many ways, including the disintegration of reef structures and the weakening of many types of sea animals' shells. The purpose of this project is to assess the efficacy of a novel method of raising the pH of increasingly acidic ocean waters. The experiment was set up with water of varying pH levels. There were three different experiment groups, including current ocean water (pH 8.1), increased acidity ocean water (pH 7.5), and an increased acidity ocean water with an activated carbon filter (pH 7.5). Six bivalve shells were placed in each solution . Mass loss data was taken from bivalve shells every three days over the course of thirty days (for a total of ten measurements). I hypothesized that the carbon filter would improve the pH of the ocean water (by raising the pH from 7.5) to that of normal ocean water (pH 8.1). The data showed that while the acidic ocean water shell's weight decreased (by 13%), the acidic water with the filter and current ocean water decreased by 0.3% and 0.5%, respectively. Overall, the activated carbon filter decreased the amount of weight change from the acidic water. The data is applicable to helping solve ocean acidification - activated charcoal greatly improved the effects of very acidic ocean water, which could be used in the future to help offset the impact of ocean acidification on its creatures.

Structural, dynamical, and transport properties of the hydrated halides: How do At{sup −} bulk properties compare with those of the other halides, from F{sup −} to I{sup −}?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Réal, Florent, E-mail: florent.real@univ-lille1.fr; Severo Pereira Gomes, André; Guerrero Martínez, Yansel Omar

2016-03-28

The properties of halides from the lightest, fluoride (F{sup −}), to the heaviest, astatide (At{sup −}), have been studied in water using a polarizable force-field approach based on molecular dynamics (MD) simulations at the 10 ns scale. The selected force-field explicitly treats the cooperativity within the halide-water hydrogen bond networks. The force-field parameters have been adjusted to ab initio data on anion/water clusters computed at the relativistic Möller-Plesset second-order perturbation theory level of theory. The anion static polarizabilities of the two heaviest halides, I{sup −} and At{sup −}, were computed in the gas phase using large and diffuse atomic basis sets,more » and taking into account both electron correlation and spin-orbit coupling within a four-component framework. Our MD simulation results show the solvation properties of I{sup −} and At{sup −} in aqueous phase to be very close. For instance, their first hydration shells are structured and encompass 9.2 and 9.1 water molecules at about 3.70 ± 0.05 Å, respectively. These values have to be compared to the F{sup −}, Cl{sup −}, and Br{sup −} ones, i.e., 6.3, 8.4, and 9.0 water molecules at 2.74, 3.38, and 3.55 Å, respectively. Moreover our computations predict the solvation free energy of At{sup −} in liquid water at ambient conditions to be 68 kcal mol{sup −1}, a value also close the I{sup −} one, about 70 kcal mol{sup −1}. In all, our simulation results for I{sup −} are in excellent agreement with the latest neutron- and X-ray diffraction studies. Those for the At{sup −} ion are predictive, as no theoretical or experimental data are available to date.« less

Dual reorientation relaxation routes of water molecules in oxyanion’s hydration shell: A molecular geometry perspective

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn

2015-12-14

In this study, we examine how complex ions such as oxyanions influence the dynamic properties of water and whether differences exist between simple halide anions and oxyanions. Nitrate anion is taken as an example to investigate the hydration properties of oxyanions. Reorientation relaxation of its hydration water can occur through two different routes: water can either break its hydrogen bond with the nitrate to form one with another water or switch between two oxygen atoms of the same nitrate. The latter molecular mechanism increases the residence time of oxyanion’s hydration water and thus nitrate anion slows down the translational motionmore » of neighbouring water. But it is also a “structure breaker” in that it accelerates the reorientation relaxation of hydration water. Such a result illustrates that differences do exist between the hydration of oxyanions and simple halide anions as a result of different molecular geometries. Furthermore, the rotation of the nitrate solute is coupled with the hydrogen bond rearrangement of its hydration water. The nitrate anion can either tilt along the axis perpendicularly to the plane or rotate in the plane. We find that the two reorientation relaxation routes of the hydration water lead to different relaxation dynamics in each of the two above movements of the nitrate solute. The current study suggests that molecular geometry could play an important role in solute hydration and dynamics.« less

Shell Condition and Survival of Puget Sound Pteropods Are Impaired by Ocean Acidification Conditions

PubMed Central

Busch, D. Shallin; Maher, Michael; Thibodeau, Patricia; McElhany, Paul

2014-01-01

We tested whether the thecosome pteropod Limacina helicina from Puget Sound, an urbanized estuary in the northwest continental US, experiences shell dissolution and altered mortality rates when exposed to the high CO2, low aragonite saturation state (Ωa) conditions that occur in Puget Sound and the northeast Pacific Ocean. Five, week-long experiments were conducted in which we incubated pteropods collected from Puget Sound in four carbon chemistry conditions: current summer surface (∼460–500 µatm CO2, Ωa≈1.59), current deep water or surface conditions during upwelling (∼760 and ∼1600–1700 µatm CO2, Ωa≈1.17 and 0.56), and future deep water or surface conditions during upwelling (∼2800–3400 µatm CO2, Ωa≈0.28). We measured shell condition using a scoring regime of five shell characteristics that capture different aspects of shell dissolution. We characterized carbon chemistry conditions in statistical analyses with Ωa, and conducted analyses considering Ωa both as a continuous dataset and as discrete treatments. Shell dissolution increased linearly as aragonite saturation state decreased. Discrete treatment comparisons indicate that shell dissolution was greater in undersaturated treatments compared to oversaturated treatments. Survival increased linearly with aragonite saturation state, though discrete treatment comparisons indicated that survival was similar in all but the lowest saturation state treatment. These results indicate that, under starvation conditions, pteropod survival may not be greatly affected by current and expected near-future aragonite saturation state in the NE Pacific, but shell dissolution may. Given that subsurface waters in Puget Sound’s main basin are undersaturated with respect to aragonite in the winter and can be undersaturated in the summer, the condition and persistence of the species in this estuary warrants further study. PMID:25162395

Shell condition and survival of Puget Sound pteropods are impaired by ocean acidification conditions.

PubMed

Busch, D Shallin; Maher, Michael; Thibodeau, Patricia; McElhany, Paul

2014-01-01

We tested whether the thecosome pteropod Limacina helicina from Puget Sound, an urbanized estuary in the northwest continental US, experiences shell dissolution and altered mortality rates when exposed to the high CO2, low aragonite saturation state (Ωa) conditions that occur in Puget Sound and the northeast Pacific Ocean. Five, week-long experiments were conducted in which we incubated pteropods collected from Puget Sound in four carbon chemistry conditions: current summer surface (∼460-500 µatm CO2, Ωa≈1.59), current deep water or surface conditions during upwelling (∼760 and ∼1600-1700 µatm CO2, Ωa≈1.17 and 0.56), and future deep water or surface conditions during upwelling (∼2800-3400 µatm CO2, Ωa≈0.28). We measured shell condition using a scoring regime of five shell characteristics that capture different aspects of shell dissolution. We characterized carbon chemistry conditions in statistical analyses with Ωa, and conducted analyses considering Ωa both as a continuous dataset and as discrete treatments. Shell dissolution increased linearly as aragonite saturation state decreased. Discrete treatment comparisons indicate that shell dissolution was greater in undersaturated treatments compared to oversaturated treatments. Survival increased linearly with aragonite saturation state, though discrete treatment comparisons indicated that survival was similar in all but the lowest saturation state treatment. These results indicate that, under starvation conditions, pteropod survival may not be greatly affected by current and expected near-future aragonite saturation state in the NE Pacific, but shell dissolution may. Given that subsurface waters in Puget Sound's main basin are undersaturated with respect to aragonite in the winter and can be undersaturated in the summer, the condition and persistence of the species in this estuary warrants further study.

Mechanisms to Explain the Elemental Composition of the Initial Aragonite Shell of Larval Oysters

NASA Astrophysics Data System (ADS)

Haley, Brian A.; Hales, Burke; Brunner, Elizabeth L.; Kovalchik, Kevin; Waldbusser, George G.

2018-04-01

Calcifying organisms face increasing stress from the changing carbonate chemistry of an acidifying ocean, particularly bivalve larvae that live in upwelling regions of the world, such as the coastal and estuarine waters of Oregon (USA). Arguably the first and most significant developmental hurdle faced by larval oysters is formation of their initial prodissoconch I (PDI) shell, upon which further ontological development depends. We measured the minor metal compositions (Sr/Ca, Mg/Ca) of this aragonitic PDI shell and of post-PDI larval Crassostrea gigas shell, as well as the water they were reared in, over ˜20 days for a May and an August cohort in 2011, during which time there was no period of carbonate under-saturation. After testing various methods, we successfully isolated the shell from organic tissue using a 5% active chlorine bleach solution. Elemental compositions (Sr, Mg, C, N) of the shells post-treatment showed that shell Sr/Ca ranged from 1.55 to 1.82 mmol/mol; Mg/Ca from 0.60 to 1.11 mmol/mol, similar to the few comparable published data for larval oyster aragonite compositions. We compare these data in light of possible biomineralization mechanisms: an amorphous calcium carbonate (ACC) path, an intercellular path, and a direct-from-seawater path to shell formation via biologically induced inorganic precipitation of aragonite. The last option provides a mechanistic explanation for: (1) the accelerated precipitation rates of biogenic calcification in the absence of a calcifying fluid; (2) consistently elevated precipitation rates at varying ambient-water saturation states; and (3) the high Ca-selectivity of the early larval calcification despite rapid precipitation rates.

Conformational relaxation and water penetration coupled to ionization of internal groups in proteins.

PubMed

Damjanović, Ana; Brooks, Bernard R; García-Moreno, Bertrand

2011-04-28

Molecular dynamics simulations were used to examine the effects of ionization of internal groups on the structures of eighteen variants of staphylococcal nuclease (SNase) with internal Lys, Asp, or Glu. In most cases the RMSD values of internal ionizable side chains were larger when the ionizable moieties were charged than when they were neutral. Calculations of solvent-accessible surface area showed that the internal ionizable side chains were buried in the protein interior when they were neutral and moved toward crevices and toward the protein-water interface when they were charged. The only exceptions are Lys-36, Lys-62, and Lys-103, which remained buried even after charging. With the exception of Lys-38, the number of internal water molecules surrounding the ionizable group increased upon charging: the average number of water oxygen atoms within the first hydration shell increased by 1.7 for Lys residues, by 5.2 for Asp residues, and by 3.2 for Glu residues. The polarity of the microenvironment of the ionizable group also increased when the groups were charged: the average number of polar atoms of any kind within the first hydration shell increased by 2.7 for Lys residues, by 4.8 for Asp residues, and by 4.0 for Glu residues. An unexpected correlation was observed between the absolute value of the shifts in pK(a) values measured experimentally, and several parameters of structural relaxation: the net difference in the polarity of the microenvironment of the charged and neutral forms of the ionizable groups, the net difference in hydration of the charged and neutral forms of the ionizable groups, and the difference in RMSD values of the charged and neutral forms of the ionizable groups. The effects of ionization of internal groups on the conformation of the backbone were noticeable but mostly small and localized to the area immediately next to the internal ionizable moiety. Some variants did exhibit local unfolding.

Permeability-diffusivity modeling vs. fractional anisotropy on white matter integrity assessment and application in schizophrenia.

PubMed

Kochunov, P; Chiappelli, J; Hong, L E

2013-01-01

Diffusion tensor imaging (DTI) assumes a single pool of anisotropically diffusing water to calculate fractional anisotropy (FA) and is commonly used to ascertain white matter (WM) deficits in schizophrenia. At higher b-values, diffusion-signal decay becomes bi-exponential, suggesting the presence of two, unrestricted and restricted, water pools. Theoretical work suggests that semi-permeable cellular membrane rather than the presence of two physical compartments is the cause. The permeability-diffusivity (PD) parameters measured from bi-exponential modeling may offer advantages, over traditional DTI-FA, in identifying WM deficits in schizophrenia. Imaging was performed in N = 26/26 patients/controls (age = 20-61 years, average age = 40.5 ± 12.6). Imaging consisted of fifteen b-shells: b = 250-3800 s/mm(2) with 30 directions/shell, covering seven slices of mid-sagittal corpus callosum (CC) at 1.7 × 1.7 × 4.6 mm. 64-direction DTI was also collected. Permeability-diffusivity-index (PDI), the ratio of restricted to unrestricted apparent diffusion coefficients, and the fraction of unrestricted compartment (Mu) were calculated for CC and cingulate gray matter (GM). FA values for CC were calculated using tract-based-spatial-statistics. Patients had significantly reduced PDI in CC (p ≅ 10(- 4)) and cingulate GM (p = 0.002), while differences in CC FA were modest (p ≅ .03). There was no group-related difference in Mu. Additional theoretical-modeling analysis suggested that reduced PDI in patients may be caused by reduced cross-membrane water molecule exchanges. PDI measurements for cerebral WM and GM yielded more robust patient-control differences than DTI-FA. Theoretical work offers an explanation that patient-control PDI differences should implicate abnormal active membrane permeability. This would implicate abnormal activities in ion-channels that use water as substrate for ion exchange, in cerebral tissues of schizophrenia patients.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bazalova, M; Ahmad, M; Fahrig, R

Purpose: To evaluate x-ray fluorescence computed tomography induced with proton beams (pXFCT) for imaging of gold contrast agent. Methods: Proton-induced x-ray fluorescence was studied by means of Monte Carlo (MC) simulations using TOPAS, a MC code based on GEANT4. First, proton-induced K-shell and L-shell fluorescence was studied as a function of proton beam energy and 1) depth in water and 2) size of contrast object. Second, pXFCT images of a 2-cm diameter cylindrical phantom with four 5- mm diameter contrast vials and of a 20-cm diameter phantom with 1-cm diameter vials were simulated. Contrast vials were filled with water andmore » water solutions with 1-5% gold per weight. Proton beam energies were varied from 70-250MeV. pXFCT sinograms were generated based on the net number of gold K-shell or L-shell x-rays determined by interpolations from the neighboring 0.5keV energy bins of spectra collected with an idealized 4π detector. pXFCT images were reconstructed with filtered-back projection, and no attenuation correction was applied. Results: Proton induced x-ray fluorescence spectra showed very low background compared to x-ray induced fluorescence. Proton induced L-shell fluorescence had a higher cross-section compared to K-shell fluorescence. Excitation of L-shell fluorescence was most efficient for low-energy protons, i.e. at the Bragg peak. K-shell fluorescence increased with increasing proton beam energy and object size. The 2% and 5% gold contrast vials were accurately reconstructed in K-shell pXFCT images of both the 2-cm and 20-cm diameter phantoms. Small phantom L-shell pXFCT image required attenuation correction and had a higher sensitivity for 70MeV protons compared to 250MeV protons. With attenuation correction, L-shell pXFCT might be a feasible option for imaging of small size (∼2cm) objects. Imaging doses for all simulations were 5-30cGy. Conclusion: Proton induced x-ray fluorescence CT promises to be an alternative quantitative imaging technique to the commonly considered XFCT imaging with x-ray beams.« less

Ferroelectric hydration shells around proteins: electrostatics of the protein-water interface.

PubMed

LeBard, David N; Matyushov, Dmitry V

2010-07-22

Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric layer with large values of the average dipole moment magnitude and the dipole moment variance. The emergence of the new polarized mesophase dramatically alters the statistics of electrostatic fluctuations at the protein-water interface. The linear response relation between the average electrostatic potential and its variance breaks down, with the breadth of the electrostatic fluctuations far exceeding the expectations of the linear response theories. The dynamics of these non-Gaussian electrostatic fluctuations are dominated by a slow (approximately = 1 ns) component that freezes in at the temperature of the dynamical transition of proteins. The ferroelectric shell propagates 3-5 water diameters into the bulk.

Active formation of 'chaos terrain' over shallow subsurface water on Europa.

PubMed

Schmidt, B E; Blankenship, D D; Patterson, G W; Schenk, P M

2011-11-16

Europa, the innermost icy satellite of Jupiter, has a tortured young surface and sustains a liquid water ocean below an ice shell of highly debated thickness. Quasi-circular areas of ice disruption called chaos terrains are unique to Europa, and both their formation and the ice-shell thickness depend on Europa's thermal state. No model so far has been able to explain why features such as Conamara Chaos stand above surrounding terrain and contain matrix domes. Melt-through of a thin (few-kilometre) shell is thermodynamically improbable and cannot raise the ice. The buoyancy of material rising as either plumes of warm, pure ice called diapirs or convective cells in a thick (>10 kilometres) shell is insufficient to produce the observed chaos heights, and no single plume can create matrix domes. Here we report an analysis of archival data from Europa, guided by processes observed within Earth's subglacial volcanoes and ice shelves. The data suggest that chaos terrains form above liquid water lenses perched within the ice shell as shallow as 3 kilometres. Our results suggest that ice-water interactions and freeze-out give rise to the diverse morphologies and topography of chaos terrains. The sunken topography of Thera Macula indicates that Europa is actively resurfacing over a lens comparable in volume to the Great Lakes in North America. ©2011 Macmillan Publishers Limited. All rights reserved

Application of molluscan analyses to the reconstruction of past environmental conditions in estuaries: Chapter 15

USGS Publications Warehouse

Wingard, G. Lynn; Surge, Donna

2017-01-01

Molluscs possess a number of attributes that make them an excellent source of past environmental conditions in estuaries: they are common in estuarine environments; they typically have hard shells and are usually well preserved in sediments; they are relatively easy to detect in the environment; they have limited mobility as adults; they grow by incremental addition of layers to their shells; and they are found in all the major environments surrounding estuaries—terrestrial, freshwater, brackish, and marine waters. Analysis of molluscan assemblages can contribute information about past changes in sea level, climate, land use patterns, anthropogenic alterations, salinity, and other parameters of the benthic habitat and water chemistry within the estuary. High-resolution (from less than a day to annual) records of changes in environmental parameters can be obtained by analyzing the incremental growth layers in mollusc shells (sclerochronology). The shell layers retain information on changes in water temperature, salinity, seasonality, climate, river discharge, productivity, pollution and human activity. Isotopic analyses of mollusc shell growth layers can be problematic in estuaries where water temperatures and isotopic ratios can vary simultaneously; however, methods are being developed to overcome these problems. In addition to sclerochronology, molluscs are important to Holocene and Pleistocene estuarine palaeoenvironmental studies because of their use in the development of age models through radiocarbon dating, amino acid racemization, uranium-thorium series dating, and electron spin resonance (ESR) dating.

The effect of different anti-solvent and coconut shell content on properties of coconut shell regenerated cellulose biocomposite films

NASA Astrophysics Data System (ADS)

Hahary, Farah Norain; Husseinsyah, Salmah; Mostapha@Zakaria, Marliza

2016-07-01

In this study, coconut shell (CS) regenerated cellulose (RC) biocomposite films was prepared using dimethylacetamide/lithium chloride (DMAc/LiCl) solvent system. The effect of anti-solvents such as water and methanol for regeneration of cellulose and coconut shell content on properties of CS-RC biocomposite films was investigated. The used of water as anti-solvent for cellulose regeneration was found to have higher tensile properties compared to regenerated cellulose using methanol. Besides, the X-Ray diffraction (XRD) analysis also revealed that RC using water as anti-solvent have higher crystallinity index (CrI) than CS-RC biocomposite film using methanol. The tensile strength and modulus elasticity of CS-RC biocomposite films increased up to 3 wt% CS and decreased with further addition of CS. The elongation at break of CS-RC biocomposite films decreased with the increment of CS. The CrI of CS-RC bioocmposite films up to 3 wt% and decreased with at higher content of CS.

Tandem Core–Shell Si–Ta 3N 5 Photoanodes for Photoelectrochemical Water Splitting

DOE PAGES

Narkeviciute, Ieva; Chakthranont, Pongkarn; Mackus, Adriaan J. M.; ...

2016-11-22

Here, nanostructured core–shell Si–Ta 3N 5 photoanodes were designed and synthesized to overcome charge transport limitations of Ta 3N 5 for photoelectrochemical water splitting. The core–shell devices were fabricated by atomic layer deposition of amorphous Ta 2O 5 onto nanostructured Si and subsequent nitridation to crystalline Ta 3N 5. Nanostructuring with a thin shell of Ta 3N 5 results in a 10-fold improvement in photocurrent compared to a planar device of the same thickness. In examining thickness dependence of the Ta 3N 5 shell from 10 to 70 nm, superior photocurrent and absorbed-photon-to-current efficiencies are obtained from the thinner Tamore » 3N 5 shells, indicating minority carrier diffusion lengths on the order of tens of nanometers. The fabrication of a heterostructure based on a semiconducting, n-type Si core produced a tandem photoanode with a photocurrent onset shifted to lower potentials by 200 mV. CoTiO x and NiO x water oxidation cocatalysts were deposited onto the Si–Ta 3N 5 to yield active photoanodes that with NiO x retained 50–60% of their maximum photocurrent after 24 h chronoamperometry experiments and are thus among the most stable Ta 3N 5 photoanodes reported to date.« less

Insight into the electrical properties and chain conformation of spherical polyelectrolyte brushes by dielectric spectroscopy

NASA Astrophysics Data System (ADS)

Guo, Xiaoxia; Zhao, Kongshuang

2017-02-01

We report here a dielectric study on three kinds of anionic spherical polyelectrolyte brush (SPBs, consisting of a polystyrene (PS) core and three different poly (acrylic acid) chains grafted onto the core) suspensions over a frequency ranging from 40 Hz to 110 MHz. The relaxation behavior of the SPB suspensions shows significant changes in the brush-layer properties when the mass fraction of SPBs and the pH of the suspensions change. Two definite relaxations related to the interfacial polarization are observed around 100 kHz and 10 MHz. A single-layer spherical-shell model is applied to describe the SPB suspensions wherein the suspended SPB is modeled as a spherical-shell composite particle in which an insulated PS sphere is surrounded by a conducting ion-permeable shell (the polyelectrolyte chain layer). We developed the curve-fitting procedure to analyze the dielectric spectrum in order to obtain the dielectric properties of the components of the SPBs, especially the properties of the polyelectrolyte brush. Based on this method and model, the permittivity and conductivity of the brush layer, ζ potential, etc are calculated. The ordered orientation of the water molecules in the layer leads to an additional electrical dipole moment; increasing pH causes the brush layer to swell. In addition, the repulsive force between the SPB particles are evaluated using the brush-layer thickness, which is obtained by fitting dielectric spectra, combined with relative theoretical formulas. Increasing PH values or SPB concentration would improve the stability of the SPBs dispersion.

Size-selective QD@MOF core-shell nanocomposites for the highly sensitive monitoring of oxidase activities.

PubMed

Wang, Ke; Li, Nan; Zhang, Jing; Zhang, Zhiqi; Dang, Fuquan

2017-01-15

In this work, we proposed a novel and facile method to monitor oxidase activities based on size-selective fluorescent quantum dot (QD)@metal-organic framework (MOF) core-shell nanocomposites (CSNCPs). The CSNCPs were synthesized from ZIF-8 and CdTe QDs in aqueous solution in 40min at room temperature with stirring. The prepared CdTe@ZIF-8 CSNCPs , which have excellent water dispersibility and stability, displays distinct fluorescence responses to hole scavengers of different molecular sizes (e.g., H 2 O 2 , substrate, and oxidase) due to the aperture limitation of the ZIF-8 shell. H 2 O 2 can efficiently quench the fluorescence of CdTe@ZIF-8 CSNCPs over a linearity range of 1-100nM with a detection limit of 0.29nM, whereas large molecules such as substrate and oxidase have very little effect on its fluorescence. Therefore, the highly sensitive detection of oxidase activities was achieved by monitoring the fluorescence quenching of CdTe@ZIF-8 CSNCPs by H 2 O 2 produced in the presence of substrate and oxidase, which is proportional to the oxidase activities. The linearity ranges of the uricase and glucose oxidase activity are 0.1-50U/L and 1-100U/L, respectively, and their detection limits are 0.024U/L and 0.26U/L, respectively. Therefore, the current QD@MOF CSNCPs based sensing system is a promising, widely applicable means of monitoring oxidase activities in biochemical research. Copyright © 2016 Elsevier B.V. All rights reserved.

Polyfibroblast: A Self-Healing and Galvanic Protection Additive

DTIC Science & Technology

2013-06-25

polyurea shell. The degradation was so slow over the course of one month that it was easier to monitor IPD1 degradation instead. We found first order...dependence of water diffusion through the shell. Note that the polyurea shell in this case contains silica inclusions. -13.6 -14.0 -14.4 -14.8 -15.2

Pasteurization of shell eggs using radio frequency heating

USDA-ARS?s Scientific Manuscript database

The USDA-FSIS estimates that pasteurization of all shell eggs in the U.S. would reduce the annual number of illnesses by more than 110,000, yet less than 1% of shell eggs are commercially pasteurized. One of the main reasons for this is that the current process, hot water immersion, requires approxi...

Effect of Chitin Isolated from Crustaceans and Cephalopods on Denaturation of Fish Myofibrillar Protein and the State of Water during Frozen Storage

NASA Astrophysics Data System (ADS)

Arredondo Romero, Eduardo; Nakamura, Yukio; Yamashita, Yasumitsu; Ichikawa, Hisashi; Goto, Shingi; Osatomi, Kiyoshi; Nozaki, Yukinori

From the point of view of utilization of shells as a waste product of fishery industry, the cryoprotective effect of chitin made from shell of crustaceans (Japanese fan lobster and Japanese swimming crab) and cartilage of cephalopods (spear squid) are studied. Chitin from the shells and cartilage were added to lizard fish myofibrils, and the changes of unfrozen water in myofibrils and ATPase activity of myofibrillar protein were observed during frozen storage at -250°C for 120days. The amount of unfrozen water were increased by addition of three kinds of chitin, and decreased moderately during forzen storage. Whereas, in the chitin free sample, the amount of unfrozen water were decreased rapidly during frozen storage. Changes of ATPase activity of samples showed similar tendency to that of the amount of unfrozen water. The present moderate cryoprotective effect of chitin and data of unfrozen water and ATPase activity of myofibrillar protein suggest the importance of the amount of unfrozen water in frozen matrix.

Thermoresponsive Cellulose Acetate-Poly(N-isopropylacrylamide) Core-Shell Fibers for Controlled Capture and Release of Moisture.

PubMed

Thakur, Neha; Sargur Ranganath, Anupama; Sopiha, Kostiantyn; Baji, Avinash

2017-08-30

In this study, we used core-shell electrospinning to fabricate cellulose acetate-poly(N-isopropylacrylamide) (CA-PNIPAM) fibrous membranes and demonstrated the ability of these fibers to capture water from a high humid atmosphere and release it when thermally stimulated. The wettability of the fibers was controlled by using thermoresponsive PNIPAM as the shell layer. Scanning electron and fluorescence microscopes are used to investigate the microstructure of the fibers and confirm the presence of the core and shell phases within the fibers. The moisture capturing and releasing ability of these core-shell CA-PNIPAM fibers was compared with those of the neat CA and neat PNIPAM fibers at room temperature as well as at an elevated temperature. At room temperature, the CA-PNIPAM core-shell fibers are shown to have the maximum moisture uptake capacity among the three samples. The external temperature variations which trigger the moisture response behavior of these CA-PNIPAM fibers fall within the range of typical day and night cycles of deserts, demonstrating the potential use of these fibers for water harvesting applications.

Phase Equilibria and Ionic Solvation in the Lithium Tetrafluoroborate-Dimethylsulfoxide System

NASA Astrophysics Data System (ADS)

Gafurov, M. M.; Kirillov, S. A.; Gorobets, M. I.; Rabadanov, K. Sh.; Ataev, M. B.; Tretyakov, D. O.; Aydemirov, K. M.

2015-01-01

The phase diagram and electrical conductivity isotherms for the lithium tetrafluoroborate (LiBF4)-dimethylsulfoxide (DMSO) system and Raman spectra of DMSO and the LiBF4-DMSO solution were studied. Spectroscopic signatures of a H-bond between DMSO and BF4 - ions were found. The bonds of Li+ ions to the solvent were stronger than the bonds in DMSO dimers because formation of the solvate destroyed dimeric DMSO molecules. The τω values for DMSO molecules in the Li+-ion solvate shell of the LiBF4-DMSO system were similar to those for associated solvent molecules.

Shell Structure Water Cellar’s Rapid Construct Technology

NASA Astrophysics Data System (ADS)

Xian Zhuang, Wen; Qing Yin, De; Chen, Shu Fa

2018-05-01

Tradition concrete water cellar’s problems, such as high cost, long construction term, easy to crack, are pointed out. A new construct method, and it’s matching airbag mould, of constructing concrete shell structure water cellars, are introduced. Combine with full-scale verifying cellar’s construct test, full-load water storage test, analyzed the technology in terms of construction term, cost, crack resistance, air bag pressure etc. It is believed that this new technology can successfully solve the problems that tradition technology has, and it will have a good prospect in rainfall resources utilization.

Hydrochemical effects on the life cycle, shell size, thickness, and chemistry of ostracode Cyprideis torosa

NASA Astrophysics Data System (ADS)

Marco-Barba, J.; Ito, E.; Mezquita, F.; Carbonell, E.

2006-12-01

Cyprideis torosa is a species of ostracode that inhabits and reproduces in wide range of ionic concentrations as long as (carbonate alkalinity)/Ca ratio is low. It is found in inland springs, lakes, estuaries, wetlands and seawater evaporation ponds as long as its Alk/Ca requirement is met. We collected C. torosa from 20 sites near Valencia, Spain in early spring 2004. Main environmental variables were analyzed in situ or in the lab, including temperature and concentration of major ions and oxygen isotopes. Several (2-20) live individuals were sorted out, their growth instar, sex and size measured and their shell chemistry (Mg/Ca, Sr/Ca and oxygen isotopes) analyzed. Three of these 20 sites were sampled monthly for an entire year, and its population structure, juvenile and adult shell chemistry (between 20 and 40 shells) analyzed. The chemistry of the single-visit sites varied widely with TDS from 9 to 2200 meq/L. Generally, Cl was the most dominant anion, with an averaged value of 76% (16% - 94%). CO3 plus HCO3 varied between 0.4 and 64% and SO4 between 4 and 26%. Principal Components Analysis showed that all waters follow a similar solute evolution trend of increasing Cl and SO4 and decreasing carbonate alkalinity with increasing TDS. Water δ18O also increase with TDS suggesting evaporation is the dominant driver of solute evolution. Among the sites sampled monthly, U1 is a HCO3>Ca>Mg>SO4 spring with the TDS of 9 meq/L. Sites P5 and P7 are part of a coastal wetland system of Cl>Na>Mg~SO4>Ca>HCO3 composition with TDS of 1700meq/L and 270meq/L, respectively. Water temperature varies from 12 to 30°C in P5, 13 to 33°C in P7 and 16 to 30°C in U1. At all 3 sites, the highest temperature occurred in July. The longest animals have the highest shell Ca content, and size is related to water chemistry. Both males and females are smaller in high TDS waters, and in particular, in high SO4 waters. The shell-water oxygen isotope fractionation decreases drastically at higher TDS. Cation composition of the shells show a trend of decreasing values of Mg/Cashell/Mg/Cawater with TDS as might be expected since ostracodes form low-Mg calcite shells. This trend is also observed between Sr/Cashell/Sr/ Cawater and TDS albeit with a large scatter. The changes in the population structure suggest that in U1, moulting from A-1 to A occur throughout the year whereas in P5 and P7, this moulting process is restricted to spring and fall months. This is corroborated by oxygen isotope values and Mg/Ca and Sr/Ca of adult and juvenile shells from all 3 sites: observed changes in U1 shells parallel the changes in U1 water; for P5 and P7, no such parallel is observed probably because A-1 juveniles live longer and do not moult until favorable conditions occur, and all the adults collected over the course of the year had calcified during a narrower time window. This is in agreement with the trend observed in the whole dataset.

Vertical Electron Detachment Energies for Octahedral Closed-Shell Multiply Charged Anions

DTIC Science & Technology

1994-04-22

however, at low theoretical levels, motivating us to extend the investigations to: a) higher levels of theory, b) analogous closed-shell singly- and...hundredths of an eV. This further supports our choice of SBKJ+diff as the basis set for the production runs. The SCF relaxation energies for F- and Cl...intensities for the product molecules ML 5(’)" (D3h) and ML 4 (n-2 )" 15 (Td) were determined at the SCF/SBKJ level and are reported in Table V

A computer simulation study of the temperature dependence of the hydrophobic hydration

NASA Astrophysics Data System (ADS)

Guillot, B.; Guissani, Y.

1993-11-01

The test particle method is used to evaluate by molecular dynamics calculations the solubility of rare gases and of methane in water between the freezing point and the critical point. A quantitative agreement is obtained between solubility data and simulation results when the simulated water is modeled by the extended simple point charge model (SPCE). From a thermodynamical point of view, it is shown that the hierarchy of rare gases solubilities in water is governed by the solute-water interaction energy while an entropic term of cavity formation is found to be responsible for the peculiar temperature dependence of the solubility along the coexistence curve, and more precisely, of the solubility minimum exhibited by all the investigated solutes. Near the water critical point, the asymptotic behaviors of the Henry's constant and of the vapor-liquid partition coefficient, respectively, as deduced from the simulation data follow with a good accuracy the critical laws recently proposed in the literature for these quantities. Moreover, the calculated partial molar volume of the solute shows a steep increase above 473 K and becomes proportional to the isothermal compressibility of the pure solvent in the vicinity of the critical point as it is observed experimentally. From a microscopic point of view, the evaluation of the solute-solvent pair distribution functions permits to establish a relationship between the increase of the solubility with the decrease of the temperature in cold water on the one hand, and the formation of cages of the clathrate-type around the solute on the other hand. Nevertheless, as soon as the boiling point of water is reached the computer simulation shows that the water molecules of the first hydration shell are no longer oriented tangentially to the solute and tend to reorientate towards the bulk. At higher temperatures a deficit of water molecules progressively appears around the solute, a deficit which is directly associated with an increase of the partial molar volume. Although this phenomenon could be related to what is observed in supercritical mixtures it is emphasized that no long range critical fluctuation is present in the simulated sample.

Surfactant Effect on Hydrate Crystallization at the Oil-Water Interface.

PubMed

Dann, Kevin; Rosenfeld, Liat

2018-05-29

Gas hydrates pose economic and environmental risks to the oil and gas industry when plug formation occurs in pipelines. A novel approach was applied to understand cyclopentane clathrate hydrate formation in the presence of nonionic surfactant to achieve hydrate inhibition at low percent weight compared to thermodynamic inhibitors. The hydrate-inhibiting performance of low (CMC) concentrations of Span 20, Span 80, Pluronic L31, and Tween 65 at 2 °C on a manually nucleated 2 μL droplet showed a morphological shift in crystallization from planar shell growth to conical growth. Monitoring the internal pressure of the water droplet undergoing hydrate crystallization provides information on the change in interfacial tension during the crystallization process. The results of this study will provide information on the surfactant effect on hydrate crystallization and inhibition. At low surfactant concentrations (below CMC), a planar hydrate crystal was formed. Decreasing interfacial tension was observed, which can be related to the shrinking area of the water-cyclopentane interface. At high surfactant concentration, the crystal morphology was shifted to conical. Interfacial tension measurements reveal oscillations of the interfacial tension during the crystallization process. The oscillations of the interfacial tension result from the fact that once the crystal has reached a critical size a portion of the cone breaks free from the droplet surface, which results in a sudden increase in the available surface for the surfactant molecules. Hence, a temporary increase in the interfacial tension can be observed. The oscillatory behavior of the interfacial tension is a result of the growth and release of the hydrate cones from the surface of the droplet. We have found that the most efficient surfactant in hydrate inhibition would be the one with HLB closest to 10 (equal hydrophilic-hydrophobic parts). In this way, the surfactant molecules will stay at the interface as they observe equal affinities for both the oil and water phases. Surfactant molecules that have the strongest affinity to the interface will be able to inhibit the growth of the crystal as they will force the cones to break and will not allow them to grow.

Radiolarians decreased silicification as an evolutionary response to reduced Cenozoic ocean silica availability.

PubMed

Lazarus, David B; Kotrc, Benjamin; Wulf, Gerwin; Schmidt, Daniela N

2009-06-09

It has been hypothesized that increased water column stratification has been an abiotic "universal driver" affecting average cell size in Cenozoic marine plankton. Gradually decreasing Cenozoic radiolarian shell weight, by contrast, suggests that competition for dissolved silica, a shared nutrient, resulted in biologic coevolution between radiolaria and marine diatoms, which expanded dramatically in the Cenozoic. We present data on the 2 components of shell weight change--size and silicification--of Cenozoic radiolarians. In low latitudes, increasing Cenozoic export of silica to deep waters by diatoms and decreasing nutrient upwelling from increased water column stratification have created modern silica-poor surface waters. Here, radiolarian silicification decreases significantly (r = 0.91, P < 0.001), from approximately 0.18 (shell volume fraction) in the basal Cenozoic to modern values of approximately 0.06. A third of the total change occurred rapidly at 35 Ma, in correlation to major increases in water column stratification and abundance of diatoms. In high southern latitudes, Southern Ocean circulation, present since the late Eocene, maintains significant surface water silica availability. Here, radiolarian silicification decreased insignificantly (r = 0.58, P = 0.1), from approximately 0.13 at 35 Ma to 0.11 today. Trends in shell size in both time series are statistically insignificant and are not correlated with each other. We conclude that there is no universal driver changing cell size in Cenozoic marine plankton. Furthermore, biologic and physical factors have, in concert, by reducing silica availability in surface waters, forced macroevolutionary changes in Cenozoic low-latitude radiolarians.

Insight into hydrogen bonds and characterization of interlayer spacing of hydrated graphene oxide.

PubMed

Liu, Liyan; Zhang, Ruifeng; Liu, Ying; Tan, Wei; Zhu, Guorui

2018-05-28

The number of hydrogen bonds and detailed information on the interlayer spacing of graphene oxide (GO) confined water molecules were calculated through experiments and molecular dynamics simulations. Experiments play a crucial role in the modeling strategy and verification of the simulation results. The binding of GO and water molecules is essentially controlled by hydrogen bond networks involving functional groups and water molecules confined in the GO layers. With the increase in the water content, the clusters of water molecules are more evident. The water molecules bounding to GO layers are transformed to a free state, making the removal of water molecules from the system difficult at low water contents. The diffuse behaviors of the water molecules are more evident at high water contents. With an increase in the water content, the functional groups are surrounded by fewer water molecules, and the distance between the functional groups and water molecules increases. As a result, the water molecules adsorbed into the GO interlamination will enlarge the interlayer spacing. The interlayer spacing is also affected by the number of GO layers. These results were confirmed by the calculations of number of hydrogen bonds, water state, mean square displacement, radial distribution function, and interlayer spacing of hydrated GO. Graphical Abstract This work research the interaction between GO functional groups and confined water molecules. The state of water molecules and interlayer spacing of graphene oxide were proved to be related to the number of hydrogen bonds.

Interactions and aggregation of apoferritin molecules in solution: effects of added electrolytes.

PubMed Central

Petsev, D N; Thomas, B R; Yau, S; Vekilov, P G

2000-01-01

We have studied the structure of the protein species and the protein-protein interactions in solutions containing two apoferritin molecular forms, monomers and dimers, in the presence of Na(+) and Cd(2+) ions. We used chromatographic, and static and dynamic light scattering techniques, and atomic force microscopy (AFM). Size-exclusion chromatography was used to isolate these two protein fractions. The sizes and shapes of the monomers and dimers were determined by dynamic light scattering and AFM. Although the monomer is an apparent sphere with a diameter corresponding to previous x-ray crystallography determinations, the dimer shape corresponds to two, bound monomer spheres. Static light scattering was applied to characterize the interactions between solute molecules of monomers and dimers in terms of the second osmotic virial coefficients. The results for the monomers indicate that Na(+) ions cause strong intermolecular repulsion even at concentrations higher than 0.15 M, contrary to the predictions of the commonly applied Derjaguin-Landau-Verwey-Overbeek theory. We argue that the reason for such behavior is hydration force due to the formation of a water shell around the protein molecules with the help of the sodium ions. The addition of even small amounts of Cd(2+) changes the repulsive interactions to attractive but does not lead to oligomer formation, at least at the protein concentrations used. Thus, the two ions provide examples of strong specificity of their interactions with the protein molecules. In solutions of the apoferritin dimer, the molecules attract even in the presence of Na(+) only, indicating a change in the surface of the apoferritin molecule. In view of the strong repulsion between the monomers, this indicates that the dimers and higher oligomers form only after partial denaturation of some of the apoferritin monomers. These observations suggest that aggregation and self-assembly of protein molecules or molecular subunits may be driven by forces other than those responsible for crystallization and other phase transitions in the protein solution. PMID:10733984

Construction of homogenous/heterogeneous hollow mesoporous silica nanostructures by silica-etching chemistry: principles, synthesis, and applications.

PubMed

Chen, Yu; Chen, Hang-Rong; Shi, Jian-Lin

2014-01-21

Colloidal hollow mesoporous silica nanoparticles (HMSNs) are aspecial type of silica-based nanomaterials with penetrating mesopore channels on their shells. HMSNs exhibit unique structural characteristics useful for diverse applications: Firstly, the hollow interiors can function as reservoirs for enhanced loading of guest molecules, or as nanoreactors for the growth of nanocrystals or for catalysis in confined spaces. Secondly, the mesoporous silica shell enables the free diffusion of guest molecules through the intact shell. Thirdly, the outer silica surface is ready for chemical modifications, typically via its abundant Si-OH bonds. As early as 2003, researchers developed a soft-templating methodto prepare hollow aluminosilicate spheres with penetrating mesopores in a cubic symmetry pattern on the shells. However, adapting this method for applications on the nanoscale, especially for biomedicine, has proved difficult because the soft templating micelles are very sensitive to liquid environments, making it difficult to tune key parameters such as dispersity, morphology and structure. In this Account, we present the most recent developments in the tailored construction of highly dispersive and monosized HMSNs using simple silica-etching chemistry, and we discuss these particles' excellent performance in diverse applications. We first introduce general principles of silica-etching chemistry for controlling the chemical composition and the structural parameters (particle size, pore size, etching modalities, yolk-shell nanostructures, etc.) of HMSNs. Secondly, we include recent progress in constructing heterogeneous, multifunctional, hollow mesoporous silica nanorattles via several methods for diverse applications. These elaborately designed HMSNs could be topologically transformed to prepare hollow mesoporous carbon nanoparticles or functionalized to produce HMSN-based composite nanomaterials. Especially in biomedicine, HMSNs are excellent as carriers to deliver either hydrophilic or hydrophobic anti-cancer drugs, to tumor cells, offering enhanced chemotherapeutic efficacy and diminished toxic side effects. Most recently, research has shown that loading one or more anticancer drugs into HMSNs can inhibit metastasis or reverse multidrug resistance of cancer cells. HMSNs could also deliver hydrophobic perfluorohexane (PFH) molecules to improve high intensity focused ultrasound (HIFU) cancer surgery by changing the tissue acoustic environment; and HMSNs could act as nanoreactors for enhanced catalytic activity and/or durability. The versatility of silica-etching chemistry, a simple but scalable synthetic methodology, offers great potential for the creation of new types of HMSN-based nanostructures in a range of applications.