Properties of the manganese(II) binding site in ternary complexes of Mnter dot ADP and Mnter dot ATP with chloroplast coupling factor 1: Magnetic field dependence of solvent sup 1 H and sup 2 H NMR relaxation rates

Energy Technology Data Exchange (ETDEWEB)

Haddy, A.E.; Frasch, W.D.; Sharp, R.R. (Univ. of Michigan, Ann Arbor (USA))

1989-05-02

The influence of the binding of ADP and ATP on the high-affinity Mn(II) binding site of chloroplast coupling factor 1 (CF{sub 1}) was studied by analysis of field-dependent solvent proton and deuteron spin-lattice relaxation data. In order to characterize metal-nucleotide complexes of CF{sub 1} under conditions similar to those of the NMR experiments, the enzyme was analyzed for bound nucleotides and Mn(II) after incubation with AdN and MnCl{sub 2} and removal of labile ligands by extensive gel filtration chromatography. In the field-dependent NMR experiments, the Mn(II) binding site of CF{sub 1} was studied for three mole ratios of added Mn(II) to CF{sub 1}, 0.5, 1.0, and 1.5, in the presence of an excess of either ADP or ATP. The results were extrapolated to zero Mn(II) concentration to characterize the environment of the first Mn(II) binding site of Cf{sub 1}. In the presence of both adenine nucleotides, pronounced changes in the Mn(II) environment relative to that in Mn(II)-CF{sub 1} were evident; the local relaxation rate maxima were more pronounced and shifted to higher field strengths, and the relaxation rate per bound Mn(II) increased at all field strengths. Analysis of the data revealed that the number of exchangeable water molecules liganded to bound Mn(II) increased from one in the binary Mn(II)-CF{sub 1} complex to three and two in the ternary Mn(II)-ADP-CF{sub 1} and Mn(II)-ATP-CF{sub 1} complexes, respectively; these results suggest that a water ligand to bound Mn(II) in the Mn(II)-ADP-CF{sub 1} complex is replaced by the {gamma}-phosphate of ATP in the Mn(II)-ATP-CF{sub 1} complex. A binding model is presented to account for these observations.

Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.

Science.gov (United States)

Katkova, E V; Onufriev, A V; Aguilar, B; Sulimov, V B

2017-03-01

In this study several commonly used implicit solvent models are compared with respect to their accuracy of estimating solvation energies of small molecules and proteins, as well as desolvation penalty in protein-ligand binding. The test set consists of 19 small proteins, 104 small molecules, and 15 protein-ligand complexes. We compared predicted hydration energies of small molecules with their experimental values; the results of the solvation and desolvation energy calculations for small molecules, proteins and protein-ligand complexes in water were also compared with Thermodynamic Integration calculations based on TIP3P water model and Amber12 force field. The following implicit solvent (water) models considered here are: PCM (Polarized Continuum Model implemented in DISOLV and MCBHSOLV programs), GB (Generalized Born method implemented in DISOLV program, S-GB, and GBNSR6 stand-alone version), COSMO (COnductor-like Screening Model implemented in the DISOLV program and the MOPAC package) and the Poisson-Boltzmann model (implemented in the APBS program). Different parameterizations of the molecules were examined: we compared MMFF94 force field, Amber12 force field and the quantum-chemical semi-empirical PM7 method implemented in the MOPAC package. For small molecules, all of the implicit solvent models tested here yield high correlation coefficients (0.87-0.93) between the calculated solvation energies and the experimental values of hydration energies. For small molecules high correlation (0.82-0.97) with the explicit solvent energies is seen as well. On the other hand, estimated protein solvation energies and protein-ligand binding desolvation energies show substantial discrepancy (up to 10kcal/mol) with the explicit solvent reference. The correlation of polar protein solvation energies and protein-ligand desolvation energies with the corresponding explicit solvent results is 0.65-0.99 and 0.76-0.96 respectively, though this difference in correlations is caused

A simple model for solvation in mixed solvents. Applications to the stabilization and destabilization of macromolecular structures.

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Schellman, J A

1990-08-31

The properties of a simple model for solvation in mixed solvents are explored in this paper. The model is based on the supposition that solvent replacement is a simple one-for-one substitution reaction at macromolecular sites which are independent of one another. This leads to a new form for the binding polynomial in which all terms are associated with ligand interchange rather than ligand addition. The principal solvent acts as one of the ligands. Thermodynamic analysis then shows that thermodynamic binding (i.e., selective interaction) depends on the properties of K'-1, whereas stoichiometric binding (site occupation) depends on K'. K' is a 'practical' interchange equilibrium constant given by (f3/f1)K, where K is the true equilibrium constant for the interchange of components 3 and 1 on the site and f3 and f4 denote their respective activity coefficients on the mole fraction scale. Values of K' less than unity lead to negative selective interaction. It is selective interaction and not occupation number which determines the thermodynamic effects of solvation. When K' greater than 100 on the mole fraction scale or K' greater than 2 on the molality scale (in water), the differences between stoichiometric binding and selective interaction become less than 1%. The theory of this paper is therefore necessary only for very weak binding constants. When K'-1 is small, large concentrations of the added solvent component are required to produce a thermodynamic effect. Under these circumstances the isotherms for the selective interaction and for the excess (or transfer) free energy are strongly dependent on the behavior of the activity coefficients of both solvent components. Two classes of behavior are described depending on whether the components display positive or negative deviations from Raoult's law. Examples which are discussed are aqueous solutions of urea and guanidinium chloride for positive deviations and of sucrose and glucose for negative deviations

Modification of crystal habit of ibuprofen using the phase partition technique: effect of aerosil and tween 80 in binding solvent.

Science.gov (United States)

Umprayn, K; Luengtummuen, A; Kitiyadisai, C; Pornpiputsakul, T

2001-11-01

A ternary diagram, representing the solubility of binding solvent (chloroform) in a mixture of ethanol and water, was constructed. For this study, the solvent mixture that gave the best ibuprofen pellets (IPs) was composed of chloroform.ethanol:water at a ratio of 1.5%:8%:90.5%. The suitable agitator speed, temperature, and mixing time were found to be 1,500 rpm, 25 degrees C +/- 2 degrees C, and 20 min, respectively. In addition, suitable stirring time when the phase partition process of IPs began was 15 min. IPs obtained from these conditions were small and round, approximately 1 mm; surface determination by scanning electron microscopy (SEM) indicated that the IPs were composed of drug microcrystals rearranged on the surface. For the dissolution, IPs showed lower drug release when compared with pure ibuprofen crystal (IC) (f2 analysis). An attempt to modify the dissolution property of IP by incorporating various concentrations of Aerosil and Tween 80 in the binding solvent was made. Microscopic appearance showed that both Aerosil and Tween 80 gave less spherical pellets when compared with the use of binding solvent alone. For both the Aerosil and Tween 80 employed, the results indicated a change in rearrangement of drug microcrystals and a change in crystal habit. However, Tween 80 gave more change of the crystallographic direction of drug microcrystals than Aerosil. In term of dissolution, the results showed that employing Tween 80 at 1.2% gave the highest drug release compared to the use of Aerosil and IC alone (f2 analysis). These pellets had a good flow property, as indicated by Carr's compressibility, flow rate, and angle of repose, and they can be compressed into a tablet, encapsulated by suitable polymer, or pulverized to obtain micronized crystals. In the case of compression into tablets, the dissolution profiles of these tablets compared with those of commercial product meet the USP 24 requirement (Q > or = 80% at 60 min).

Reactivity of solvent alcohol on degradation of CFC113

International Nuclear Information System (INIS)

Nakagawa, Seiko

2003-01-01

1,1,2-Trichloro-trifluoroethane (CFC113) was dissolved in alkaline 1-butanol, 2-butanol, iso-butyl alcohol, and phenyl ethyl alcohol and irradiated with 60 Co gamma rays after purged with pure nitrogen gas. In all these solvents, the concentration of CFC113 and hydroxide ion decreased and that of chloride ion increased with a dose observed in 2-propanol solution. The reaction efficiency increases in order of 1-butanol< iso-butyl alcohol< phenyl ethyl alcohol<2-butanol<2-propanol. The solvent effect will depend on the binding energy of the αC-H of the alcohol molecule and electron affinity and dipole moment of the ketones or aldehydes produced from the alcohols

Changing the Mechanism for CO ₂ Hydrogenation Using Solvent-Dependent Thermodynamics

Energy Technology Data Exchange (ETDEWEB)

Burgess, Samantha A. [Catalysis Science Group, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Appel, Aaron M. [Catalysis Science Group, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Linehan, John C. [Catalysis Science Group, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Wiedner, Eric S. [Catalysis Science Group, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA

2017-10-23

A critical scientific challenge for utilization of CO2 is the development of catalyst systems that do not depend upon expensive or environmentally unfriendly reagents, such as precious metals, strong organic bases, and organic solvents. We have used thermodynamic insights to predict and demonstrate that the HCoI(dmpe)2 catalyst system, previously described for use in organic solvents, can hydrogenate CO2 to formate in water with bicarbonate as the only added reagent. Replacing tetrahydrofuran as the solvent with water changes the mechanism for catalysis by altering the thermodynamics for hydride transfer to CO2 from a key dihydride intermediate. The need for a strong organic base was eliminated by performing catalysis in water due to the change in mechanism. These studies demonstrate that the solvent plays a pivotal role in determining the reaction thermodynamics and thereby catalytic mechanism and activity. The research was supported by 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 is operated by Battelle for the U.S. Department of Energy.

NMR determination of solvent dependent behavior and XRD structural properties of 4-carboxy phenylboronic acid: A DFT supported study

Science.gov (United States)

Dikmen, Gökhan; Alver, Özgür; Parlak, Cemal

2018-04-01

Solvent dependent structural properties of 4-carboxy phenylboronic acid (4-cpba) were investigated by X-ray diffraction (XRD) and nuclear magnetic resonance (NMR) spectroscopic methods. The molecular structure and geometric parameters were determined by some computational methods such as B3LYP/6-31 + G(3df,p), HF/aug-cc-pvtz and MP2/6-31G(d). Detailed elucidation of the structural and spectroscopic properties of 4-cpba was carried out with 1H, HETCOR and DOSY NMR experiments. Solvent effects on the structural properties were monitored on the changes of 1H NMR spectra by using various solvents and it was observed that 4-cpba shows serious structural preferences depending on the solvent used.

Solvent dependence of organic exciplex fluorescence studied by magnetic effect on reaction yield (M.A.R.Y) spectroscopy

International Nuclear Information System (INIS)

Pal, K.

2011-01-01

This work aims at understanding the various facets of one of the elementary reactions in nature, the electron transfer reaction using MARY (Magnetic effect on Reaction Yield) spectroscopy as a tool. The prime focus of study by the use this technique was the solvent dependence of organic exciplex fluorescence. Apart from that temperature dependent measurements using MARY spectroscopy have been performed to extract the activation energy parameters of electron transfer reaction. The discovery of magnetic field effect on new system was also a part of our study. The study of solvent dependence of organic exciplex fluorescence using MARY spectroscopy was carried out on the system of 9,10-dimethylanthracene (as the fluorophore) and N,N'-dimethylaniline and 4,4'-Bis(dimethylamino) diphenylmethane (as quenchers) in binary solvent mixtures of toluene/dimethylsulfoxide, benzylacetate/dimethylsulfoxide, toluene/propylenecarbonate and propylacetate/butyronitrile. The work focuses on the use of solvent mixtures rather than pure solvents. The solvent mixtures, tailored to simulate different microenvironemets, were employed to find out the effect of preferential solvation on electron transfer reaction. The contrast in the absolute field effect and linewidth values of the MARY spectra obtained in the four system as a function of dielectric constant scan suggest the imperative effect of concentration fluctuation on the electron transfer reaction. Temperature dependent measurements were performed on the system of N,N,N',N'- tetramethylparaphenylendiamin, photo-ionizing in a mixture of toluene/dimethylsulfoxide. However the sluggish response of the system to temperature changes does not really permit us to extract fruitful results. The magnetic field effect on the much studied system of Perylene/ N.N'-dimethylaniline was discovered for the first time. (author) [de

Effect of hydrogen bonding of a solvent on the thermodynamic stability of cadmium complexes of ethylenediamine

International Nuclear Information System (INIS)

Ledenkov, S.F.; Sharnin, V.A.; Chistyakova, G.V.

2004-01-01

The composition and stability of cadmium(II) ethylenediamine complexes in water-dimethylsulfoxide (DMSO) mixed solvents, depending on the content of organic component, were studied by the methods of pH-metry and calorimetry. It is shown that increase in DMSO content in the solvent gives rise to higher stability of cadmium complexes. The greatest growth of stability constant was pointed out for coordination-saturated compounds. The complexing thermodynamics was discussed from the viewpoint of solvation approach. Protolytic solvents were shown to produce destabilizing effect on the polyligand complexes owing to participation of coordination sphere in H-binding [ru

Prediction of Water Binding to Protein Hydration Sites with a Discrete, Semiexplicit Solvent Model.

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Setny, Piotr

2015-12-08

Buried water molecules are ubiquitous in protein structures and are found at the interface of most protein-ligand complexes. Determining their distribution and thermodynamic effect is a challenging yet important task, of great of practical value for the modeling of biomolecular structures and their interactions. In this study, we present a novel method aimed at the prediction of buried water molecules in protein structures and estimation of their binding free energies. It is based on a semiexplicit, discrete solvation model, which we previously introduced in the context of small molecule hydration. The method is applicable to all macromolecular structures described by a standard all-atom force field, and predicts complete solvent distribution within a single run with modest computational cost. We demonstrate that it indicates positions of buried hydration sites, including those filled by more than one water molecule, and accurately differentiates them from sterically accessible to water but void regions. The obtained estimates of water binding free energies are in fair agreement with reference results determined with the double decoupling method.

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

Energy Technology Data Exchange (ETDEWEB)

Rocklin, Gabriel J. [Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550, USA and Biophysics Graduate Program, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550 (United States); Mobley, David L. [Departments of Pharmaceutical Sciences and Chemistry, University of California Irvine, 147 Bison Modular, Building 515, Irvine, California 92697-0001, USA and Department of Chemistry, University of New Orleans, 2000 Lakeshore Drive, New Orleans, Louisiana 70148 (United States); Dill, Ken A. [Laufer Center for Physical and Quantitative Biology, 5252 Stony Brook University, Stony Brook, New York 11794-0001 (United States); Hünenberger, Philippe H., E-mail: phil@igc.phys.chem.ethz.ch [Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich (Switzerland)

2013-11-14

-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol{sup −1}). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pK{sub a} and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

Science.gov (United States)

Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.

2013-11-01

calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol-1). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects.

Science.gov (United States)

Rocklin, Gabriel J; Mobley, David L; Dill, Ken A; Hünenberger, Philippe H

2013-11-14

calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol(-1)). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

Unexpected solvent effects on the UV/Vis absorption spectra of o-cresol in toluene and benzene: in contrast with non-aromatic solvents.

Science.gov (United States)

Zheng, Dong; Yuan, Xiang-Ai; Ma, Haibo; Li, Xiaoxiong; Wang, Xizhang; Liu, Ziteng; Ma, Jing

2018-03-01

Cresol is a prototype molecule in understanding intermolecular interactions in material and biological systems, because it offers different binding sites with various solvents and protonation states under different pH values. It is found that the UV/Vis absorption spectra of o -cresol in aromatic solvents (benzene, toluene) are characterized by a sharp peak, unlike the broad double-peaks in 11 non-aromatic solvents. Both molecular dynamics simulations and electronic structure calculations revealed the formation of intermolecular π-complexation between o -cresol and aromatic solvents. The thermal movements of solvent and solute molecules render the conformations of o -cresol changing between trans and cis isomers. The π-interaction makes the cis configuration a dominant isomer, hence leading to the single keen-edged UV/Vis absorption peak at approximately 283 nm. The free conformation changes between trans and cis in aqueous solution rationalize the broader absorption peaks in the range of 260-280 nm. The pH dependence of the UV/Vis absorption spectra in aqueous solutions is also rationalized by different protonation states of o -cresol. The explicit solvent model with long-ranged interactions is vital to describe the effects of π-complexation and electrostatic interaction on the UV/Vis absorption spectra of o -cresol in toluene and alkaline aqueous (pH > 10.3) solutions, respectively.

Detection of Specific Solvent Rearrangement Regions of an Enzyme: NMR and ITC Studies with Aminoglycoside Phosphotransferase(3 )-IIIa

International Nuclear Information System (INIS)

Ozen, C.; Norris, Adrianne; Land, Miriam Louise; Tjioe, Elina; Serpersu, Engin H

2008-01-01

This work describes differential effects of solvent in complexes of the aminoglycoside phosphotransferase(3 and cent;)-IIIa (APH) with different aminoglycosides and the detection of change in solvent structure at specific sites away from substrates. Binding of kanamycins to APH occurs with a larger negative and cent;H in H2O relative to D2O ( and cent; and cent;H(H2O-D2O) < 0), while the reverse is true for neomycins. Unusually large negative and cent;Cp values were observed for binding of aminoglycosides to APH. and cent;Cp for the APHneomycin complex was -1.6 kcal and acirc;mol-1 and acirc;deg-1. A break at 30 C was observed in the APH-kanamycin complex yielding and cent;Cp values of -0.7 kcal and acirc;mol-1 and acirc;deg-1 and -3.8 kcal and acirc;mol-1 and acirc;deg-1 below and above 30 C, respectively. Neither the change in accessible surface area ( and cent;ASA) nor contributions from heats of ionization were sufficient to explain the large negative and cent;Cp values. Most significantly, 15N-1H HSQC experiments showed that temperature-dependent shifts of the backbone amide protons of Leu 88, Ser 91, Cys 98, and Leu143 revealed a break at 30 C only in the APH-kanamycin complex in spectra collected between 21 C and 38 C. These amino acids represent solVent reorganization sites that experience a change in solvent structure in their immediate environment as structurally different ligands bind to the enzyme. These residues were away from the substrate binding site and distributed in three hydrophobic patches in APH. Overall, our results show that a large number of factors affect and cent;Cp and binding of structurally different ligand groups cause different solvent structure in the active site as well as differentially affecting specific sites away from the ligand binding site

Influence of Solvent Polarity and DNA-Binding on Spectral Properties of Quaternary Benzo[c]phenanthridine Alkaloids.

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Michal Rájecký

Full Text Available Quaternary benzo[c]phenanthridine alkaloids are secondary metabolites of the plant families Papaveraceae, Rutaceae, and Ranunculaceae with anti-inflammatory, antifungal, antimicrobial and anticancer activities. Their spectral changes induced by the environment could be used to understand their interaction with biomolecules as well as for analytical purposes. Spectral shifts, quantum yield and changes in lifetime are presented for the free form of alkaloids in solvents of different polarity and for alkaloids bound to DNA. Quantum yields range from 0.098 to 0.345 for the alkanolamine form and are below 0.033 for the iminium form. Rise of fluorescence lifetimes (from 2-5 ns to 3-10 ns and fluorescence intensity are observed after binding of the iminium form to the DNA for most studied alkaloids. The alkanolamine form does not bind to DNA. Acid-base equilibrium constant of macarpine is determined to be 8.2-8.3. Macarpine is found to have the highest increase of fluorescence upon DNA binding, even under unfavourable pH conditions. This is probably a result of its unique methoxy substitution at C12 a characteristic not shared with other studied alkaloids. Association constant for macarpine-DNA interaction is 700000 M(-1.

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.

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Goh, Garrett B; Hulbert, Benjamin S; Zhou, Huiqing; Brooks, Charles L

2014-07-01

pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible. © 2013 Wiley Periodicals, Inc.

Effect of solvent alcohol on degradation of chlorinated hydrocarbons by γ-irradiation

International Nuclear Information System (INIS)

Nakagawa, Seiko

2002-01-01

1,1,2-Trichloro-trifluoroethane (CFC113) was dissolved in alkaline 1-butanol, 2-butanol, iso-butyl alcohol, and phenyl ethyl alcohol and irradiated with 60 Co gamma rays after being purged with pure nitrogen gas. In all these solvents, the concentration of CFC113 and hydroxide ion decreased and that of chloride ion increased with a dose observed in 2-propanol solution. The reaction efficiency increases in the following order: 1-butanol < iso-butyl alcohol < phenyl ethyl alcohol < 2-butanol < 2-propanol. The solvent effect will depend on the binding energy of the αC-H of the alcohol molecule and electron affinity and dipole moment of the ketones or aldehydes produced from the alcohols. (author)

Deltamethrin Binding to Triatoma infestans (Hemiptera: Reduviidae) Lipoproteins. Analysis by Solvent Bar Microextraction Coupled to Gas Chromatography.

Science.gov (United States)

Dulbecco, A B; Mijailovsky, S J; Girotti, J R; Juárez, M P

2015-11-01

The binding of deltamethrin (DLM) to the hemipteran Triatoma infestans (Klug) hemolymph lipoproteins was evaluated in vitro. After DLM incubation with the insect hemolymph, lipoproteins were fractioned by ultracentrifugation. DLM binding was analyzed by a microextractive technique-solvent bar microextraction-a solventless methodology to extract DLM from each lipoprotein fraction. This is a novel use of the technique applied to extract an insecticide from an insect fluid. Capillary gas chromatography with microelectron capture detection was used to detect DLM bound by the T. infestans hemolymph lipoproteins and to identify the preferred DLM carrier. We show that Lp and VHDLp I lipoproteins are mainly responsible for DLM transport in T. infestans, both in DLM-resistant and DLM-susceptible bugs. Our results also indicate that DLM amounts transported are not related to DLM susceptibility. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Mapping the surface of Escherichia coli peptide deformylase by NMR with organic solvents.

Science.gov (United States)

Byerly, Douglas W; McElroy, Craig A; Foster, Mark P

2002-07-01

Identifying potential ligand binding sites on a protein surface is an important first step for targeted structure-based drug discovery. While performing control experiments with Escherichia coli peptide deformylase (PDF), we noted that the organic solvents used to solubilize some ligands perturbed many of the same resonances in PDF as the small molecule inhibitors. To further explore this observation, we recorded (15)N HSQC spectra of E. coli peptide deformylase (PDF) in the presence of trace quantities of several simple organic solvents (acetone, DMSO, ethanol, isopropanol) and identified their sites of interaction from local perturbation of amide chemical shifts. Analysis of the protein surface structure revealed that the ligand-induced shift perturbations map to the active site and one additional surface pocket. The correlation between sites of solvent and inhibitor binding highlights the utility of organic solvents to rapidly and effectively validate and characterize binding sites on proteins prior to designing a drug discovery screen. Further, the solvent-induced perturbations have implications for the use of organic solvents to dissolve candidate ligands in NMR-based screens.

Solvent-Dependent Dual Fluorescence of the Push-Pull System 2-Diethylamino-7-Nitrofluorene

KAUST Repository

Larsen, Martin A. B.

2018-01-31

The solvent-dependent excited state behavior of the molecular push-pull system 2-diethylamino-7-nitrofluorene has been explored using femtosecond transient absorption spectroscopy in combination with density functional theory calculations. Several excited state minima have been identified computationally, all possessing significant intramolecular charge transfer character. The experimentally observed dual fluorescence is suggested to arise from a planar excited state minimum and another minimum reached by twisting of the aryl-nitrogen bond of the amino group. The majority of the excited state population, however, undergo non-radiative transitions and potential excited deactivation pathways are assessed in the computational investigation. A third excited state conformer, characterized by twisting around the aryl-nitrogen bond of the nitro group, is reasoned to be responsible for the majority of the non-radiative decays and a crossing between the excited state and ground state is localized. Additionally, ultrafast intersystem crossing is observed in the apolar solvent cyclohexane and rationalized to occur via an El-Sayed assisted transition from one of the identified excited state minima. The solvent thus determines more than just the fluorescence lifetime and shapes the potential energy landscape, thereby dictating the available excited state pathways.

Solvent-Dependent Dual Fluorescence of the Push-Pull System 2-Diethylamino-7-Nitrofluorene

KAUST Repository

Larsen, Martin A. B.; Stephansen, Anne B.; Alarousu, Erkki; Pittelkow, Michael; Mohammed, Omar F.; Sø lling, Theis I

2018-01-01

The solvent-dependent excited state behavior of the molecular push-pull system 2-diethylamino-7-nitrofluorene has been explored using femtosecond transient absorption spectroscopy in combination with density functional theory calculations. Several excited state minima have been identified computationally, all possessing significant intramolecular charge transfer character. The experimentally observed dual fluorescence is suggested to arise from a planar excited state minimum and another minimum reached by twisting of the aryl-nitrogen bond of the amino group. The majority of the excited state population, however, undergo non-radiative transitions and potential excited deactivation pathways are assessed in the computational investigation. A third excited state conformer, characterized by twisting around the aryl-nitrogen bond of the nitro group, is reasoned to be responsible for the majority of the non-radiative decays and a crossing between the excited state and ground state is localized. Additionally, ultrafast intersystem crossing is observed in the apolar solvent cyclohexane and rationalized to occur via an El-Sayed assisted transition from one of the identified excited state minima. The solvent thus determines more than just the fluorescence lifetime and shapes the potential energy landscape, thereby dictating the available excited state pathways.

Solvent Dependency in the Quantum Efficiency of 4-[(4-Aminophenyl)-(4-imino-1-cyclohexa-2, 5- dienylidene) methyl] Aniline Hydrochloride.

Science.gov (United States)

Pathrose, Bini; Nampoori, V P N; Radhakrishnan, P; Sahira, H; Mujeeb, A

2015-05-01

In the present work dual beam thermal lens technique is used for studying the solvent dependency on the quantum efficiency of a novel dye used for biomedical applications. The role of solvent in the absolute fluorescence quantum yield of 4-[(4-Aminophenyl)-(4-imino-1-cyclohexa-2, 5- dienylidene) methyl] aniline hydrochloride is studied using thermal lens technique. It is observed that the variation in solvents and its concentration results considerable variations in the fluorescence quantum yield. These variations are due to the non-radiative relaxation of the absorbed energy and because of the different solvent properties. The highest quantum yield of the dye is observed in the polar protic solvent-water.

Comparative studies on the human serum albumin binding of the clinically approved EGFR inhibitors gefitinib, erlotinib, afatinib, osimertinib and the investigational inhibitor KP2187.

Science.gov (United States)

Dömötör, Orsolya; Pelivan, Karla; Borics, Attila; Keppler, Bernhard K; Kowol, Christian R; Enyedy, Éva A

2018-05-30

Binding interactions between human serum albumin (HSA) and four approved epidermal growth factor receptor (EGFR) inhibitors gefitinib (GEF), erlotinib (ERL), afatinib (AFA), osimertinib (OSI), as well as the experimental drug KP2187, were investigated by means of spectrofluorometric and molecular modelling methods. Steady-state and time resolved spectrofluorometric techniques were carried out, including direct quenching of protein fluorescence and site marker displacement measurements. Proton dissociation processes and solvent dependent fluorescence properties were investigated as well. The EGFR inhibitors were predominantly presented in their single protonated form (HL + ) at physiological pH except ERL, which is charge-neutral. Significant solvent dependent fluorescence properties were found for GEF, ERL and KP2187, namely their emission spectra show strong dependence on the polarity and the hydrogen bonding ability of the solvents. The inhibitors proved to be bound at site I of HSA (in subdomain IIA) in a weak-to-moderate fashion (logK' 3.9-4.9) using spectrofluorometry. OSI (logK' 4.3) and KP2187 can additionally bind in site II (in subdomain IIIA), while GEF, ERL and AFA clearly show no interaction here. Docking methods qualitatively confirmed binding site preferences of compounds GEF and KP2187, and indicated that they probably bind to HSA in their neutral forms. Binding constants calculated on the basis of the various experimental data indicate a weak-to-moderate binding on HSA, only OSI exhibits somewhat higher affinity towards this protein. However, model calculations performed at physiological blood concentrations of HSA resulted in high (ca. 90%) bound fractions for the inhibitors, highlighting the importance of plasma protein binding. Copyright © 2018 Elsevier B.V. All rights reserved.

The solvent effects on dimethyl phthalate investigated by FTIR characterization, solvent parameter correlation and DFT computation

Science.gov (United States)

Chen, Yi; Zhang, Hui; Zhou, Wenzhao; Deng, Chao; Liao, Jian

2018-06-01

This study set out with the aim of investigating the solvent effects on dimethyl phthalate (DMP) using FTIR characterization, solvent parameter correlation and DFT calculation. DMP exposed to 17 organic solvents manifested varying shift in the carbonyl stretching vibration frequency (νCdbnd O). Non-alkanols induced Band I and alkanols produced Band I and Band II. Through correlating the νCdbnd O with the empirical solvent scales including acceptor parameter (AN), Schleyer's linear free energy parameter (G), and linear free salvation energy relationships (LSER), Band I was mainly ascribed to non-specific effects from either non-alkanols or alkanol polymers ((alkanol)n). νCdbnd O of the latter indicated minor red shift and less variability compared to the former. An assumption was made and validated about the sequestering of hydroxyl group by the bulky hydrophobic chain in (alkanol)n, creating what we refer to as "screening effects". Ab initio calculation, on the other hand, provided insights for possible hydrogen binding between DMP and (ethanol)n or between ethanol monomers. The two components of Band I observed in inert solvents were assigned to the two Cdbnd O groups adopting differentiated conformations. This in turn prompted our consideration that hydrogen binding was highly selective in favor of lowly associated (alkanol)n and the particular Cdbnd O group having relatively less steric hindrance and stronger electron-donating capacity. Band II was therefore believed to derive from hydrogen-bond interactions mainly in manner of 1:1 and 1:2 DMP-(alkanol)n complexes.

Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation

Science.gov (United States)

Pandey, R. B.; Jacobs, D. J.; Farmer, B. L.

2017-05-01

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ˜ 1.3), random-coil (D ˜ 1.75), and globular (D ˜ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.

Solvent-dependent excited-state hydrogen transfer and intersystem crossing in 2-(2′-hydroxyphenyl)-benzothiazole

KAUST Repository

Aly, Shawkat Mohammede

2015-02-12

The excited-state intramolecular hydrogen transfer (ESIHT) of 2-(2′-hydroxyphenyl) benzothiazole (HBT) has been investigated in a series of nonpolar, polar aprotic, and polar protic solvents. A variety of state-of-the-art experimental methods were employed, including femto- and nanosecond transient absorption and fluorescence upconversion spectroscopy with broadband capabilities. We show that the dynamics and mechanism of ESIHT of the singlet excited HBT are strongly solvent-dependent. In nonpolar solvents, the data demonstrate that HBT molecules adopt a closed form stabilized by O-H⋯N chelated hydrogen bonds with no twisting angle, and the photoinduced H transfer occurs within 120 fs, leading to the formation of a keto tautomer. In polar solvents, owing to dipole-dipole cross talk and hydrogen bonding interactions, the H transfer process is followed by ultrafast nonradiative deactivation channels, including ultrafast internal conversion (IC) and intersystem crossing (ISC). This is likely to be driven by the twisting motion around the C-C bond between the hydroxyphenyl and thiazole moieties, facilitating the IC back to the enol ground state or to the keto triplet state. In addition, our femtosecond time-resolved fluorescence experiments indicate, for the first time, that the lifetime of the enol form in ACN is approximately 280 fs. This observation indicates that the solvent plays a crucial role in breaking the H bond and deactivating the excited state of the HBT. Interestingly, the broadband transient absorption and fluorescence up-conversion data clearly demonstrate that the intermolecular proton transfer from the excited HBT to the DMSO solvent is about 190 fs, forming the HBT anion excited state.

Solvent-dependent excited-state hydrogen transfer and intersystem crossing in 2-(2′-hydroxyphenyl)-benzothiazole

KAUST Repository

Aly, Shawkat Mohammede; Usman, Anwar; Alzayer, Maytham; Hamdi, Ghada A.; Alarousu, Erkki; Mohammed, Omar F.

2015-01-01

The excited-state intramolecular hydrogen transfer (ESIHT) of 2-(2′-hydroxyphenyl) benzothiazole (HBT) has been investigated in a series of nonpolar, polar aprotic, and polar protic solvents. A variety of state-of-the-art experimental methods were employed, including femto- and nanosecond transient absorption and fluorescence upconversion spectroscopy with broadband capabilities. We show that the dynamics and mechanism of ESIHT of the singlet excited HBT are strongly solvent-dependent. In nonpolar solvents, the data demonstrate that HBT molecules adopt a closed form stabilized by O-H⋯N chelated hydrogen bonds with no twisting angle, and the photoinduced H transfer occurs within 120 fs, leading to the formation of a keto tautomer. In polar solvents, owing to dipole-dipole cross talk and hydrogen bonding interactions, the H transfer process is followed by ultrafast nonradiative deactivation channels, including ultrafast internal conversion (IC) and intersystem crossing (ISC). This is likely to be driven by the twisting motion around the C-C bond between the hydroxyphenyl and thiazole moieties, facilitating the IC back to the enol ground state or to the keto triplet state. In addition, our femtosecond time-resolved fluorescence experiments indicate, for the first time, that the lifetime of the enol form in ACN is approximately 280 fs. This observation indicates that the solvent plays a crucial role in breaking the H bond and deactivating the excited state of the HBT. Interestingly, the broadband transient absorption and fluorescence up-conversion data clearly demonstrate that the intermolecular proton transfer from the excited HBT to the DMSO solvent is about 190 fs, forming the HBT anion excited state.

Temperature-dependent binding of cyclosporine to an erythrocyte protein

International Nuclear Information System (INIS)

Agarwal, R.P.; Threatte, G.A.; McPherson, R.A.

1987-01-01

In this competitive binding assay to measure endogenous binding capacity for cyclosporine (CsA) in erythrocyte lysates, a fixed amount of [ 3 H]CsA plus various concentrations of unlabeled CsA is incubated with aliquots of a test hemolysate. Free CsA is then adsorbed onto charcoal and removed by centrifugation; CsA complexed with a cyclosporine-binding protein (CsBP) remains in the supernate. We confirmed the validity of this charcoal-separation mode of binding analysis by comparison with equilibrium dialysis. Scatchard plot analysis of the results at 4 degrees C yielded a straight line with slope corresponding to a binding constant of 1.9 X 10(7) L/mol and a saturation capacity of approximately 4 mumol per liter of packed erythrocytes. Similar analysis of binding data at 24 degrees C and 37 degrees C showed that the binding constant decreased with increasing temperature, but the saturation capacity did not change. CsBP was not membrane bound but appeared to be freely distributed within erythrocytes. 125 I-labeled CsA did not complex with the erythrocyte CsBP. Several antibiotics and other drugs did not inhibit binding between CsA and CsBP. These findings may explain the temperature-dependent uptake of CsA by erythrocytes in whole blood and suggest that measurement of CsBP in erythrocytes or lymphocytes may help predict therapeutic response or toxicity after administration of CsA

Calcium-dependent binding of Escherichia coli alpha-hemolysin to erythrocytes

International Nuclear Information System (INIS)

Boehm, D.F.

1989-01-01

Alpha hemolysin (AH), a protein secreted by certain strains of Escherichia coli, causes lysis of erythrocytes (RBCs) and is cytotoxic for other cells. The primary structure of AH contains an eight amino acid sequence tandemly repeated 13 times near the C-terminus. These repeated sequences are essential for hemolytic activity. AH also requires an unknown modification by an accessory protein, Hly C, for hemolytic activity. The role of calcium in the interaction of Ah with RBCs was investigated using recombinant strains which produced active and inactive forms of the toxin. Hemolytic activity was calcium-dependent. Osmotic protection experiments and immunoblots of SDS-PAGE separated proteins from washed, toxin-treated RBCs showed that the binding of active AH to RBCs was calcium-dependent. Binding of active AH to RBCs increased the calcium permeability of RBC membranes and resulted in changes in membrane protein profiles. The changes in membrane proteins did not cause the lysis of the cells. These results were consistent with a mechanism of lysis involving the formation of cation-selective pores in the membranes of target cells. 45 Ca-autoradiography of the recombinant hemolysins separated by SDS-PAGE and transferred to nitrocellulose showed that active AH bound calcium. The domain involved in binding calcium was identified as the tandemly repeated sequences since a deletion hemolysin missing 11 of the 13 repeated sequences did not bind calcium. This deletion hemolysin was non-hemolytic and did not bind to RBC membranes. Hemolysin lacking the Hly C modification was also non-hemolytic and did not bind to RBC membranes. This unmodified AH contained the repeated sequences and bound calcium as efficiently as active AH

Passivating ligand and solvent contribution to the electronics properties of semiconductor nanocrystals

Energy Technology Data Exchange (ETDEWEB)

Tretiak, Sergei [Los Alamos National Laboratory; Crotty, Angela [Los Alamos National Laboratory; Fischer, Sean [Los Alamos National Laboratory; Kilina, Svetlana [NON LANL

2010-10-04

Expanding on previous work, we examine in detail the impact passivating ligands have on the electronic properties of CdSe quantum dots (QDs). We also explore the importance of the inclusion of solvent in simulating passivated QDs. Most ligand states are found well removed from the band edges, with pyridine being the exception and contributing states that sit right on the conduction band edge. Localized trap states are found for trimethylphosphine and pyridine capped QDs, with solvent helping to eliminate these. The effect of losing a ligand on the electronic properties of the system is observed to vary in proportion with the binding energy and steric bulk of the ligand. More disruption of the electronic properties is seen for tight-binding, sterically large ligands. We also look at the validity of using the single-particle Kohn-Sham (KS) representation to approximate optical absorption spectra. Besides a systematic blue-shift relative to the time-dependent density functional theory spectra, the KS spectra are in very good agreement with the more accurate method for these systems. Such agreement here justifies the use of the KS approach for calculating absorption spectra of QD systems.

Predicting the activity coefficients of free-solvent for concentrated globular protein solutions using independently determined physical parameters.

Directory of Open Access Journals (Sweden)

Devin W McBride

Full Text Available The activity coefficient is largely considered an empirical parameter that was traditionally introduced to correct the non-ideality observed in thermodynamic systems such as osmotic pressure. Here, the activity coefficient of free-solvent is related to physically realistic parameters and a mathematical expression is developed to directly predict the activity coefficients of free-solvent, for aqueous protein solutions up to near-saturation concentrations. The model is based on the free-solvent model, which has previously been shown to provide excellent prediction of the osmotic pressure of concentrated and crowded globular proteins in aqueous solutions up to near-saturation concentrations. Thus, this model uses only the independently determined, physically realizable quantities: mole fraction, solvent accessible surface area, and ion binding, in its prediction. Predictions are presented for the activity coefficients of free-solvent for near-saturated protein solutions containing either bovine serum albumin or hemoglobin. As a verification step, the predictability of the model for the activity coefficient of sucrose solutions was evaluated. The predicted activity coefficients of free-solvent are compared to the calculated activity coefficients of free-solvent based on osmotic pressure data. It is observed that the predicted activity coefficients are increasingly dependent on the solute-solvent parameters as the protein concentration increases to near-saturation concentrations.

Symmetry- and Solvent-Dependent Photophysics of Fluorenes Containing Donor and Acceptor Groups (Postprint)

Science.gov (United States)

2014-07-01

for exciplex forma- tion.29,30 Solvent-dependent studies by Belfield et al. on similar dyes31 and BT2F32 revealed strong solvatochromism on the emission...Swiger, R. N.; Orseno, D. L.; Haley, J. E.; Cooper, T. M.; Tan, L.-S. Exciplex Formation in Solid State Blends of Charge-Transfer-Type Afx Dyes and...Tan, L.-S. Exciplex Formation in Blended Spin-Cast Films of Fluorene-Linked Dyes and Bisphthalimide Quenchers. J. Phys. Chem. A 2013, 117, 3909−3917

Methylene blue binding to DNA with alternating AT base sequence: minor groove binding is favored over intercalation.

Science.gov (United States)

Rohs, Remo; Sklenar, Heinz

2004-04-01

The results presented in this paper on methylene blue (MB) binding to DNA with AT alternating base sequence complement the data obtained in two former modeling studies of MB binding to GC alternating DNA. In the light of the large amount of experimental data for both systems, this theoretical study is focused on a detailed energetic analysis and comparison in order to understand their different behavior. Since experimental high-resolution structures of the complexes are not available, the analysis is based on energy minimized structural models of the complexes in different binding modes. For both sequences, four different intercalation structures and two models for MB binding in the minor and major groove have been proposed. Solvent electrostatic effects were included in the energetic analysis by using electrostatic continuum theory, and the dependence of MB binding on salt concentration was investigated by solving the non-linear Poisson-Boltzmann equation. We find that the relative stability of the different complexes is similar for the two sequences, in agreement with the interpretation of spectroscopic data. Subtle differences, however, are seen in energy decompositions and can be attributed to the change from symmetric 5'-YpR-3' intercalation to minor groove binding with increasing salt concentration, which is experimentally observed for the AT sequence at lower salt concentration than for the GC sequence. According to our results, this difference is due to the significantly lower non-electrostatic energy for the minor groove complex with AT alternating DNA, whereas the slightly lower binding energy to this sequence is caused by a higher deformation energy of DNA. The energetic data are in agreement with the conclusions derived from different spectroscopic studies and can also be structurally interpreted on the basis of the modeled complexes. The simple static modeling technique and the neglect of entropy terms and of non-electrostatic solute-solvent

Solvent Composition-Dependent Signal-Reduction of Molecular Ions Generated from Aromatic Compounds in (+) Atmospheric Pressure Photo Ionization Mass Spectrometry.

Science.gov (United States)

Lee, Seulgidaun; Ahmed, Arif; Kim, Sunghwan

2018-03-30

The ionization process is essential for successful mass spectrometry (MS) analysis because of its influence on selectivity and sensitivity. In particular, certain solvents reduce the ionization of the analyte, thereby reducing the overall sensitivity in APPI. Since the sensitivity varies greatly depending on the solvents, a fundamental understanding of the mechanism is required. Standard solutions were analyzed by (+) Atmospheric pressure photo ionization (APPI) QExactive ion trap mass spectrometer (Thermo Scientific). Each solution was infused directly to the APPI source at a flow rate 100 μl/min and the APPI source temperature was 300 °C. Other operating mass spectrometric parameters were maintained under the same conditions. Quantum mechanical calculations were carried out using the Gaussian 09 suite program. Density functional theory was used to calculate the reaction enthalpies (∆H) of reaction between toluene and other solvents. The experimental and theoretical results showed good agreement. The abundances of analyte ions were well correlated with the calculated ∆H values. Therefore, the results strongly support the suggested signal reduction mechanism. In addition, linear correlations between the abundance of toluene and analyte molecular ions were observed, which also supports the suggested mechanism. A solvent composition-dependent signal reduction mechanism was suggested and evaluated for the (+) atmospheric pressure photo ionization (APPI) mass spectrometry analysis of poly-aromatic hydrocarbons (PAHs) generating mainly molecular ions. Overall, the evidence provided in this work suggests that reactions between solvent cluster(s) and toluene molecular ions are responsible for the observed signal reductions. This article is protected by copyright. All rights reserved.

Dimensionality of hallucinogen and inhalant/solvent abuse and dependence criteria: implications for the Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition.

Science.gov (United States)

Kerridge, Bradley T; Saha, Tulshi D; Smith, Sharon; Chou, Patricia S; Pickering, Roger P; Huang, Boji; Ruan, June W; Pulay, Attila J

2011-09-01

Prior research has demonstrated the dimensionality of Diagnostic and Statistical Manual of Mental Disorders-Fourth Edition (DSM-IV) alcohol, nicotine, cannabis, cocaine and amphetamine abuse and dependence criteria. The purpose of this study was to examine the dimensionality of hallucinogen and inhalant/solvent abuse and dependence criteria. In addition, we assessed the impact of elimination of the legal problems abuse criterion on the information value of the aggregate abuse and dependence criteria, another proposed change for DSM-IV currently lacking empirical justification. Factor analyses and item response theory (IRT) analyses were used to explore the unidimisionality and psychometric properties of hallucinogen and inhalant/solvent abuse and dependence criteria using a large representative sample of the United States (U.S.) general population. Hallucinogen and inhalant/solvent abuse and dependence criteria formed unidimensional latent traits. For both substances, IRT models without the legal problems abuse criterion demonstrated better fit than the corresponding model with the legal problem abuse criterion. Further, there were no differences in the information value of the IRT models with and without the legal problems abuse criterion, supporting the elimination of that criterion. No bias in the new diagnoses was observed by sex, age and race-ethnicity. Consistent with findings for alcohol, nicotine, cannabis, cocaine and amphetamine abuse and dependence criteria, hallucinogen and inhalant/solvent criteria reflect underlying dimensions of severity. The legal problems criterion associated with each of these substance use disorders can be eliminated with no loss in informational value and an advantage of parsimony. Taken together, these findings support the changes to substance use disorder diagnoses recommended by the DSM-V Substance and Related Disorders Workgroup, that is, combining DSM-IV abuse and dependence criteria and eliminating the legal problems abuse

Reversibly Switchable, pH-Dependent Peptide Ligand Binding via 3,5-Diiodotyrosine Substitutions.

Science.gov (United States)

Ngambenjawong, Chayanon; Sylvestre, Meilyn; Gustafson, Heather H; Pineda, Julio Marco B; Pun, Suzie H

2018-04-20

Cell type-specific targeting ligands utilized in drug delivery applications typically recognize receptors that are overexpressed on the cells of interest. Nonetheless, these receptors may also be expressed, to varying extents, on off-target cells, contributing to unintended side effects. For the selectivity profile of targeting ligands in cancer therapy to be improved, stimuli-responsive masking of these ligands with acid-, redox-, or enzyme-cleavable molecules has been reported, whereby the targeting ligands are exposed in specific environments, e.g., acidic tumor hypoxia. One possible drawback of these systems lies in their one-time, permanent trigger, which enables the "demasked" ligands to bind off-target cells if released back into the systemic circulation. A promising strategy to address the aforementioned problem is to design ligands that show selective binding based on ionization state, which may be microenvironment-dependent. In this study, we report a systematic strategy to engineer low pH-selective targeting peptides using an M2 macrophage-targeting peptide (M2pep) as an example. 3,5-Diiodotyrosine mutagenesis into native tyrosine residues of M2pep confers pH-dependent binding behavior specific to acidic environment (pH 6) when the amino acid is protonated into the native tyrosine-like state. At physiological pH of 7.4, the hydroxyl group of 3,5-diiodotyrosine on the peptide is deprotonated leading to interruption of the peptide native binding property. Our engineered pH-responsive M2pep (Ac-Y-Î-Î) binds target M2 macrophages more selectively at pH 6 than at pH 7.4. In addition, 3,5-diiodotyrosine substitutions also improve serum stability of the peptide. Finally, we demonstrate pH-dependent reversibility in target binding via a postbinding peptide elution study. The strategy presented here should be applicable for engineering pH-dependent functionality of other targeting peptides with potential applications in physiology-dependent in vivo targeting

Theoretical investigation of the weak interaction between graphene and alcohol solvents

Science.gov (United States)

Wang, Haining; Chen, Sian; Lu, Shanfu; Xiang, Yan

2017-05-01

The dispersion of graphene in five different alcohol solvents was investigated by evaluating the binding energy between graphene and alcohol molecules using DFT-D method. The calculation showed the most stable binding energy appeared at the distance of ∼3.5 Å between graphene and alcohol molecules and increased linearly as changing the alcohol from methanol to 1-pentanol. The weak interaction was further graphically illustrated using the reduced density gradient method. The theoretical study revealed alcohols with more carbon atoms could be a good starting point for screening suitable solvents for graphene dispersion.

Solvent-Dependent Self-Assembly of 4,7-Dibromo-5,6-bis(octyloxybenzo[c][1,2,5] Thiadiazole on Graphite Surface by Scanning Tunneling Microscopy

Directory of Open Access Journals (Sweden)

Bao Zha

2013-01-01

Full Text Available Solvent effect on self-assembly of 4,7-dibromo-5,6-bis(octyloxybenzo[c][1,2,5] thiadiazole (DBT on a highly oriented graphite (HOPG surface was investigated by scanning tunneling microscopy (STM by using 1-phenyloctane, 1-octanoic acid, and 1-octanol as the solvents. Two different patterns were obtained in 1-phenyloctane and 1-octanoic acid, suggesting that the self-assembly of DBT was solvent dependent. At the 1-phenyloctane/HOPG interface, a linear structure was revealed due to the intermolecular halogen bonding. When 1-octanoic acid and 1-octanol are used as the solvents, the coadsorption of solvent molecules resulting from the hydrogen bonding between DBT and solvent made an important contribution to the formation of a lamellar structure. The results demonstrate that solvents could affect the molecular self-assembly according to the variational intermolecular interactions.

Caustic-Side Solvent Extraction: Chemical and Physical Properties of the Optimized Solvent

Energy Technology Data Exchange (ETDEWEB)

Delmau, L.H.

2002-10-08

This work was undertaken to optimize the solvent used in the Caustic Side Solvent Extraction (CSSX) process and to measure key chemical and physical properties related to its performance in the removal of cesium from the alkaline high-level salt waste stored in tanks at the Savannah River Site. The need to adjust the solvent composition arose from the prior discovery that the previous baseline solvent was supersaturated with respect to the calixarene extractant. The following solvent-component concentrations in Isopar{reg_sign} L diluent are recommended: 0.007 M calix[4]arene-bis(tert-octylbenzo-crown-6) (BOBCalixC6) extractant, 0.75 M 1-(2,2,3,3-tetrafluoropropoxy)-3-(4-sec-butylphenoxy)-2-propanol (Cs-7SB) phase modifier, and 0.003 M tri-n-octylamine (TOA) stripping aid. Criteria for this selection included BOBCalixC6 solubility, batch cesium distribution ratios (D{sub Cs}), calculated flowsheet robustness, third-phase formation, coalescence rate (dispersion numbers), and solvent density. Although minor compromises within acceptable limits were made in flowsheet robustness and solvent density, significant benefits were gained in lower risk of third-phase formation and lower solvent cost. Data are also reported for the optimized solvent regarding the temperature dependence of D{sub Cs} in extraction, scrubbing, and stripping (ESS); ESS performance on recycle; partitioning of BOBCalixC6, Cs-7SB, and TOA to aqueous process solutions; partitioning of organic anions; distribution of metals; solvent phase separation at low temperatures; solvent stability to elevated temperatures; and solvent density and viscosity. Overall, the technical risk of the CSSX process has been reduced by resolving previously identified issues and raising no new issues.

Investigation on the pH-dependent binding of Eosin Y and bovine serum albumin by spectral methods

International Nuclear Information System (INIS)

Gao Dejiang; Tian Yuan; Liang Fanghui; Jin Danhong; Chen Yanhua; Zhang Hanqi; Yu Aimin

2007-01-01

In this paper, the pH-dependent binding of Eosin Y and bovine serum albumin (BSA) was investigated by spectral methods, including resonance light scattering (RLS), absorption and fluorescence spectrometry. Due to the pH-dependent structure of Eosin Y and BSA, the interaction of BSA and Eosin Y depended on the solution pH value. Especially at pH 2.6 and 9.2, the RLS intensity of BSA was obviously enhanced in the presence of Eosin Y. However, the fluorescence intensity of BSA was quenched in the presence of Eosin Y. To fully understand the pH-dependent binding of BSA and Eosin Y, fluorescence quenching technique was introduced. Based on the fluorescence data obtained, the style of binding, the binding constant, the binding site number and the thermodynamic parameters for the interaction of BSA and Eosin Y were studied. Based on Foerster non-radiation energy transfer theory, the distance between donor BSA and acceptor Eosin Y was obtained

Investigation on the pH-dependent binding of Eosin Y and bovine serum albumin by spectral methods

Energy Technology Data Exchange (ETDEWEB)

Gao Dejiang; Tian Yuan [College of Chemistry, Jilin University, Changchun 130012 (China); Liang Fanghui; Jin Danhong [Changchun Medical College, Changchun 130031 (China); Chen Yanhua; Zhang Hanqi [College of Chemistry, Jilin University, Changchun 130012 (China); Yu Aimin [College of Chemistry, Jilin University, Changchun 130012 (China)], E-mail: analchem@mail.jlu.edu.cn

2007-12-15

In this paper, the pH-dependent binding of Eosin Y and bovine serum albumin (BSA) was investigated by spectral methods, including resonance light scattering (RLS), absorption and fluorescence spectrometry. Due to the pH-dependent structure of Eosin Y and BSA, the interaction of BSA and Eosin Y depended on the solution pH value. Especially at pH 2.6 and 9.2, the RLS intensity of BSA was obviously enhanced in the presence of Eosin Y. However, the fluorescence intensity of BSA was quenched in the presence of Eosin Y. To fully understand the pH-dependent binding of BSA and Eosin Y, fluorescence quenching technique was introduced. Based on the fluorescence data obtained, the style of binding, the binding constant, the binding site number and the thermodynamic parameters for the interaction of BSA and Eosin Y were studied. Based on Foerster non-radiation energy transfer theory, the distance between donor BSA and acceptor Eosin Y was obtained.

Rifampicin-dependent antibodies bind a similar or identical epitope to glycoprotein IX-specific quinine-dependent antibodies

NARCIS (Netherlands)

Burgess, Janette K.; Lopez, Jose A.; Gaudry, Leonie E.; Chong, Beng H.

2000-01-01

The drug-dependent antibody of a patient with rifampicin-induced thrombocytopenia was characterized using the antigen-capture enzyme-linked immunosorbent assay (MAIPA assay), flow cytometry, and immunoprecipitation. The antibody was found to bind glycoprotein (GP) Ib-IX but not GPIIb-IIIa because

Characterization and antioxidant activity of bovine serum albumin and sulforaphane complex in different solvent systems

Energy Technology Data Exchange (ETDEWEB)

Dong, Xueyan; Zhou, Rui; Jing, Hao, E-mail: h200521@cau.edu.cn

2014-02-15

Modes and influencing factors of bovine serum albumin (BSA) and sulforaphane (SFN) interaction will help us understand the interaction mechanisms and functional changes of bioactive small molecule and biomacromolecule. This study investigated interaction mechanisms of BSA and SFN and associated antioxidant activity in three solvent systems of deionized water (dH{sub 2}O), dimethyl sulfoxide (DMSO) and ethanol (EtOH), using Fourier transform infrared spectroscopy (FT-IR), fluorescence spectroscopy, synchronous fluorescence spectroscopy, DPPH and ABTS radical scavenging assays. The results revealed that SFN had ability to quench BSA's fluorescence in static modes, and to interact with BSA at both tyrosine (Tyr) and tryptophan (Trp) residues, while the Trp residues were highly sensitive, which was demonstrated by fluorescence at 340 nm. Hydrophobic forces, hydrogen bonds and van der Waals interactions were all involved in BSA and SFN interaction, which were not significantly changed by three solvents. The binding constant values and binding site numbers were in a descending order of dH{sub 2}O>DMSO>EtOH. The values of free energy change were in a descending order of dH{sub 2}O>DMSO>EtOH, which indicated that the binding forces were in a descending order of dH{sub 2}O>DMSO>EtOH. There was no significant difference in antioxidant activity between SFN and BSA–SFN. Moreover, three solvents had not significant influence on antioxidant activity of SFN and BSA–SFN. -- Highlights: • We report interaction mechanisms of BSA and sulforaphane in three solvent systems. • We report antioxidant activity of BSA–sulforaphane complex in three solvent systems. • Decreasing the solvent polarity will decrease the binding of BSA and sulforaphane. • Three solvents had not influence on antioxidant activity of BSA–sulforaphane.

COMPUTER-AIDED SOLVENT DESIGN FOR POLLUTION PREVENTION: PARIS II

Science.gov (United States)

Solvent substitution is an attractive way of elijminating the use of regulated solvents because it usually does not require major chanages in existing processes, equipment or operations. Successful solvent substitution is dependent on finding solvents that are as effective or be...

Solvent sorting in (mixed solvent electrolyte) systems: Time-resolved ...

Indian Academy of Sciences (India)

lar solvents as an effective single component dipo- lar liquid that is characterized ... and time (t) dependent solvation energy of mobile dipo- lar solute with density ..... Even though this way for modification of C is purely ad- hoc, the observation ...

Influence of Solvent-Solvent and Solute-Solvent Interaction Properties on Solvent-Mediated Potential

International Nuclear Information System (INIS)

Zhou Shiqi

2005-01-01

A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones (LJ) or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.

Recent Advances in Anhydrous Solvents for CO2 Capture: Ionic Liquids, Switchable Solvents, and Nanoparticle Organic Hybrid Materials

International Nuclear Information System (INIS)

Park, Youngjune; Lin, Kun-Yi Andrew; Park, Ah-Hyung Alissa; Petit, Camille

2015-01-01

CO 2 capture by amine scrubbing, which has a high CO 2 capture capacity and a rapid reaction rate, is the most employed and investigated approach to date. There are a number of recent large-scale demonstrations including the Boundary Dam Carbon Capture Project by SaskPower in Canada that have reported successful implementations of aqueous amine solvent in CO 2 capture from flue gases. The findings from these demonstrations will significantly advance the field of CO 2 capture in the coming years. While the latest efforts in aqueous amine solvents are exciting and promising, there are still several drawbacks to amine-based CO 2 capture solvents including high volatility and corrosiveness of the amine solutions as well as the high parasitic energy penalty during the solvent regeneration step. Thus, in a parallel effort, alternative CO 2 capture solvents, which are often anhydrous, have been developed as the third-generation CO 2 capture solvents. These novel classes of liquid materials include ionic liquids, CO 2 -triggered switchable solvents (i.e., CO 2 -binding organic liquids, reversible ionic liquids), and nanoparticle organic hybrid materials. This paper provides a review of these various anhydrous solvents and their potential for CO 2 capture. Particular attention is given to the mechanisms of CO 2 absorption in these solvents, their regeneration and their processability – especially taking into account their viscosity. While not intended to provide a complete coverage of the existing literature, this review aims at pointing the major findings reported for these new classes of CO 2 capture media.

Solubility-Parameter-Guided Solvent Selection to Initiate Ostwald Ripening for Interior Space-Tunable Structures with Architecture-Dependent Electrochemical Performance.

Science.gov (United States)

Mao, Baoguang; Guo, Donglei; Qin, Jinwen; Meng, Tao; Wang, Xin; Cao, Minhua

2018-01-08

Despite significant advancement in preparing various hollow structures by Ostwald ripening, one common problem is the intractable uncontrollability of initiating Ostwald ripening due to the complexity of the reaction processes. Here, a new strategy on Hansen solubility parameter (HSP)-guided solvent selection to initiate Ostwald ripening is proposed. Based on this comprehensive principle for solvent optimization, N,N-dimethylformamide (DMF) was screened out, achieving accurate synthesis of interior space-tunable MoSe 2 spherical structures (solid, core-shell, yolk-shell and hollow spheres). The resultant MoSe 2 structures exhibit architecture-dependent electrochemical performances towards hydrogen evolution reaction and sodium-ion batteries. This pre-solvent selection strategy can effectively provide researchers great possibility in efficiently synthesizing various hollow structures. This work paves a new pathway for deeply understanding Ostwald ripening. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Behavior of solvent-exposed hydrophobic groove in the anti-apoptotic Bcl-XL protein: clues for its ability to bind diverse BH3 ligands from MD simulations.

Directory of Open Access Journals (Sweden)

Dilraj Lama

Full Text Available Bcl-XL is a member of Bcl-2 family of proteins involved in the regulation of intrinsic pathway of apoptosis. Its overexpression in many human cancers makes it an important target for anti-cancer drugs. Bcl-XL interacts with the BH3 domain of several pro-apoptotic Bcl-2 partners. This helical bundle protein has a pronounced hydrophobic groove which acts as a binding region for the BH3 domains. Eight independent molecular dynamics simulations of the apo/holo forms of Bcl-XL were carried out to investigate the behavior of solvent-exposed hydrophobic groove. The simulations used either a twin-range cut-off or particle mesh Ewald (PME scheme to treat long-range interactions. Destabilization of the BH3 domain-containing helix H2 was observed in all four twin-range cut-off simulations. Most of the other major helices remained stable. The unwinding of H2 can be related to the ability of Bcl-XL to bind diverse BH3 ligands. The loss of helical character can also be linked to the formation of homo- or hetero-dimers in Bcl-2 proteins. Several experimental studies have suggested that exposure of BH3 domain is a crucial event before they form dimers. Thus unwinding of H2 seems to be functionally very important. The four PME simulations, however, revealed a stable helix H2. It is possible that the H2 unfolding might occur in PME simulations at longer time scales. Hydrophobic residues in the hydrophobic groove are involved in stable interactions among themselves. The solvent accessible surface areas of bulky hydrophobic residues in the groove are significantly buried by the loop LB connecting the helix H2 and subsequent helix. These observations help to understand how the hydrophobic patch in Bcl-XL remains stable in the solvent-exposed state. We suggest that both the destabilization of helix H2 and the conformational heterogeneity of loop LB are important factors for binding of diverse ligands in the hydrophobic groove of Bcl-XL.

Structure-dependent binding and activation of perfluorinated compounds on human peroxisome proliferator-activated receptor γ

Energy Technology Data Exchange (ETDEWEB)

Zhang, Lianying [State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, 18 Shuangqing Road, Beijing 100085 (China); College of Life Science, Dezhou University, Dezhou 253023 (China); Ren, Xiao-Min; Wan, Bin [State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, 18 Shuangqing Road, Beijing 100085 (China); Guo, Liang-Hong, E-mail: LHGuo@rcees.ac.cn [State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, 18 Shuangqing Road, Beijing 100085 (China)

2014-09-15

Perfluorinated compounds (PFCs) have been shown to disrupt lipid metabolism and even induce cancer in rodents through activation of peroxisome proliferator-activated receptors (PPARs). Lines of evidence showed that PPARα was activated by PFCs. However, the information on the binding interactions between PPARγ and PFCs and subsequent alteration of PPARγ activity is still limited and sometimes inconsistent. In the present study, in vitro binding of 16 PFCs to human PPARγ ligand binding domain (hPPARγ-LBD) and their activity on the receptor in cells were investigated. The results showed that the binding affinity was strongly dependent on their carbon number and functional group. For the eleven perfluorinated carboxylic acids (PFCAs), the binding affinity increased with their carbon number from 4 to 11, and then decreased slightly. The binding affinity of the three perfluorinated sulfonic acids (PFSAs) was stronger than their PFCA counterparts. No binding was detected for the two fluorotelomer alcohols (FTOHs). Circular dichroim spectroscopy showed that PFC binding induced distinctive structural change of the receptor. In dual luciferase reporter assays using transiently transfected Hep G2 cells, PFCs acted as hPPARγ agonists, and their potency correlated with their binding affinity with hPPARγ-LBD. Molecular docking showed that PFCs with different chain length bind with the receptor in different geometry, which may contribute to their differences in binding affinity and transcriptional activity. - Highlights: • Binding affinity between PFCs and PPARγ was evaluated for the first time. • The binding strength was dependent on fluorinated carbon chain and functional group. • PFC binding induced distinctive structural change of the receptor. • PFCs could act as hPPARγ agonists in Hep G2 cells.

Porous fiber formation in polymer-solvent system undergoing solvent evaporation

Science.gov (United States)

Dayal, Pratyush; Kyu, Thein

2006-08-01

Temporal evolution of the fiber morphology during dry spinning has been investigated in the framework of Cahn-Hilliard equation [J. Chem. Phys. 28, 258 (1958)] pertaining to the concentration order parameter or volume fraction given by the Flory-Huggins free energy of mixing [P. J. Flory, Principles of Polymer Chemistry (Cornell University Press, Ithaca, NY, 1953), p. 672] in conjunction with the solvent evaporation rate. To guide the solvent evaporation induced phase separation, equilibrium phase diagram of the starting polymer solution was established on the basis of the Flory-Huggins free energy of mixing. The quasi-steady-state approximation has been adopted to account for the nonconserved nature of the concentration field caused by the solvent loss. The process of solvent evaporation across the fiber skin-air interface was treated in accordance with the classical Fick's law [R. B. Bird et al., Transport Phenomena (J. Wiley, New York, 1960), p. 780]. The simulated morphologies include gradient type, hollow fiber type, bicontinuous type, and host-guest type. The development of these diverse fiber morphologies is explicable in terms of the phase diagram of the polymer solution in a manner dependent on the competition between the phase separation dynamics and rate of solvent evaporation.

Role of excited state solvent fluctuations on time-dependent fluorescence Stokes shift

Energy Technology Data Exchange (ETDEWEB)

Li, Tanping, E-mail: tanping@lsu.edu, E-mail: revatik@lsu.edu; Kumar, Revati, E-mail: tanping@lsu.edu, E-mail: revatik@lsu.edu [Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803 (United States)

2015-11-07

We explore the connection between the solvation dynamics of a chromophore upon photon excitation and equilibrium fluctuations of the solvent. Using molecular dynamics simulations, fluorescence Stokes shift for the tryptophan in Staphylococcus nuclease was examined using both nonequilibrium calculations and linear response theory. When the perturbed and unperturbed surfaces exhibit different solvent equilibrium fluctuations, the linear response approach on the former surface shows agreement with the nonequilibrium process. This agreement is excellent when the perturbed surface exhibits Gaussian statistics and qualitative in the case of an isomerization induced non-Gaussian statistics. However, the linear response theory on the unperturbed surface breaks down even in the presence of Gaussian fluctuations. Experiments also provide evidence of the connection between the excited state solvent fluctuations and the total fluorescence shift. These observations indicate that the equilibrium statistics on the excited state surface characterize the relaxation dynamics of the fluorescence Stokes shift. Our studies specifically analyze the Gaussian fluctuations of the solvent in the complex protein environment and further confirm the role of solvent fluctuations on the excited state surface. The results are consistent with previous investigations, found in the literature, of solutes dissolved in liquids.

Green and Bio-Based Solvents.

Science.gov (United States)

Calvo-Flores, Francisco G; Monteagudo-Arrebola, María José; Dobado, José A; Isac-García, Joaquín

2018-04-24

Chemical reactions and many of the procedures of separation and purification employed in industry, research or chemistry teaching utilize solvents massively. In the last decades, with the birth of Green Chemistry, concerns about the employment of solvents and the effects on human health, as well as its environmental impacts and its dependence on non-renewable raw materials for manufacturing most of them, has drawn the attention of the scientific community. In this work, we review the concept of green solvent and the properties and characteristics to be considered green. Additionally, we discuss the different possible routes to prepare many solvents from biomass, as an alternative way to those methods currently applied in the petrochemical industry.

Calcium-dependent and -independent binding of the pentraxin serum amyloid P component to glycosaminoglycans and amyloid proteins

DEFF Research Database (Denmark)

Danielsen, B; Sørensen, I J; Nybo, Mads

1997-01-01

precursor protein beta2M was observed. This binding was also enhanced at slightly acid pH, most pronounced at pH 5.0. The results of this study indicate that SAP can exhibit both Ca2(+)-dependent and -independent binding to ligands involved in amyloid fibril formation and that the binding is enhanced under...... and beta2M) by ELISA. An increase in the dose-dependent binding of SAP to heparan sulfate, AA-protein and beta2M was observed as the pH decreased from 8.0 to 5.0. Furthermore, a lower, but significant Ca2(+)-independent binding of SAP to heparan sulfate, dermatan sulfate, AA protein and the amyloid...

Systematic studies of binding energy dependence of neutron-proton momentum correlation function

International Nuclear Information System (INIS)

Wei, Y B; Ma, Y G; Shen, W Q; Ma, G L; Wang, K; Cai, X Z; Zhong, C; Guo, W; Chen, J G; Fang, D Q; Tian, W D; Zhou, X F

2004-01-01

Hanbury Brown-Twiss (HBT) results of the neutron-proton correlation function have been systematically investigated for a series of nuclear reactions with light projectiles with the help of the isospin-dependent quantum molecular dynamics model. The relationship between the binding energy per nucleon of the projectiles and the strength of the neutron-proton HBT at small relative momentum has been obtained. Results show that neutron-proton HBT results are sensitive to the binding energy per nucleon

Effect of Ca2+ on the promiscuous target-protein binding of calmodulin.

Directory of Open Access Journals (Sweden)

Annie M Westerlund

2018-04-01

Full Text Available Calmodulin (CaM is a calcium sensing protein that regulates the function of a large number of proteins, thus playing a crucial part in many cell signaling pathways. CaM has the ability to bind more than 300 different target peptides in a Ca2+-dependent manner, mainly through the exposure of hydrophobic residues. How CaM can bind a large number of targets while retaining some selectivity is a fascinating open question. Here, we explore the mechanism of CaM selective promiscuity for selected target proteins. Analyzing enhanced sampling molecular dynamics simulations of Ca2+-bound and Ca2+-free CaM via spectral clustering has allowed us to identify distinct conformational states, characterized by interhelical angles, secondary structure determinants and the solvent exposure of specific residues. We searched for indicators of conformational selection by mapping solvent exposure of residues in these conformational states to contacts in structures of CaM/target peptide complexes. We thereby identified CaM states involved in various binding classes arranged along a depth binding gradient. Binding Ca2+ modifies the accessible hydrophobic surface of the two lobes and allows for deeper binding. Apo CaM indeed shows shallow binding involving predominantly polar and charged residues. Furthermore, binding to the C-terminal lobe of CaM appears selective and involves specific conformational states that can facilitate deep binding to target proteins, while binding to the N-terminal lobe appears to happen through a more flexible mechanism. Thus the long-ranged electrostatic interactions of the charged residues of the N-terminal lobe of CaM may initiate binding, while the short-ranged interactions of hydrophobic residues in the C-terminal lobe of CaM may account for selectivity. This work furthers our understanding of the mechanism of CaM binding and selectivity to different target proteins and paves the way towards a comprehensive model of CaM selectivity.

Alpha-amylase inhibitor, CS-1036 binds to serum amylase in a concentration-dependent and saturable manner.

Science.gov (United States)

Honda, Tomohiro; Kaneno-Urasaki, Yoko; Ito, Takashi; Kimura, Takako; Matsushima, Nobuko; Okabe, Hiromi; Yamasaki, Atsushi; Izumi, Takashi

2014-03-01

(2R,3R,4R)-4-hydroxy-2-(hydroxymethyl)pyrrolidin-3-yl 4-O-(6-deoxy-β-D-glucopyranosyl)-α-D-glucopyranoside (CS-1036), which is an α-amylase inhibitor, exhibited biphasic and sustained elimination with a long t1/2 (18.4-30.0 hours) in rats and monkeys, but exhibited a short t1/2 (3.7-7.9 hours) in humans. To clarify the species differences in the t1/2, the plasma protein binding of CS-1036 was evaluated by ultrafiltration. A concentration-dependent and saturable plasma protein binding of CS-1036 was observed in rats and monkeys with the dissociation rate constant (KD) of 8.95 and 27.2 nM, and maximal binding capacity (Bmax) of 52.8 and 22.1 nM, respectively. By the assessments of the recombinant amylase and immunoprecipitation, the major binding protein of CS-1036 in rats was identified as salivary amylase (KD 5.64 nM). CS-1036 also showed concentration-dependent and saturable binding to human salivary and pancreatic amylase, with similar binding affinity in rats. However, the protein binding of CS-1036 was constant in human plasma (≤10.2%) due to the lower serum amylase level compared with rats and monkeys. From the calculation of the unbound fraction (fu) in plasma based on in vitro KD and Bmax, the dose-dependent increase in fu after oral administration is speculated to lead to a dose-dependent increase in total body clearance and a high area under the curve/dose at lower doses, such as 0.3 mg/kg in rats.

SN2 fluorination reactions in ionic liquids: a mechanistic study towards solvent engineering.

Science.gov (United States)

Oh, Young-Ho; Jang, Hyeong Bin; Im, Suk; Song, Myoung Jong; Kim, So-Yeon; Park, Sung-Woo; Chi, Dae Yoon; Song, Choong Eui; Lee, Sungyul

2011-01-21

In the catalysis of S(N)2 fluorination reactions, the ionic liquid anion plays a key role as a Lewis base by binding to the counterion Cs(+) and thereby reducing the retarding Coulombic influence of Cs(+) on the nucleophile F(-). The reaction rates also depend critically on the structures of ionic liquid cation, for example, n-butyl imidazolium gives no S(N)2 products, whereas n-butylmethyl imidazolium works well. The origin of the observed phenomenal synergetic effects by the ionic liquid [mim-(t)OH][OMs], in which t-butanol is bonded covalently to the cation [mim], is that the t-butanol moiety binds to the leaving group of the substrate, moderating the retarding interactions between the acidic hydrogen and F(-). This work is a significant step toward designing and engineering solvents for promoting specific chemical reactions.

Recent Advances in Anhydrous Solvents for CO2 Capture: Ionic Liquids, Switchable Solvents, and Nanoparticle Organic Hybrid Materials

Directory of Open Access Journals (Sweden)

YOUNGJUNE ePARK

2015-10-01

Full Text Available CO2 capture by amine scrubbing, which has a high CO2 capture capacity and a rapid reaction rate, is the most employed and investigated approach to date. There are a number of recent large-scale demonstrations including the Boundary Dam Carbon Capture Project by SaskPower in Canada that have reported successful implementations of aqueous amine solvent in CO2 capture from flue gases. The findings from these demonstrations will significantly advance the field of CO2 capture in the coming years. While the latest efforts in aqueous amine solvents are exciting and promising, there are still several drawbacks to amine-based CO2 capture solvents including high volatility and corrosiveness of the amine solutions, as well as the high parasitic energy penalty during the solvent regeneration step. Thus, in a parallel effort, alternative CO2 capture solvents, which are often anhydrous, have been developed as the third-generation CO2 capture solvents. These novel classes of liquid materials include: Ionic Liquids (ILs, CO2-triggered switchable solvents (i.e., CO2 Binding Organic Liquids (CO2BOLs, Reversible Ionic Liquids (RevILs, and Nanoparticle Organic Hybrid Materials (NOHMs. This paper provides a review of these various anhydrous solvents and their potential for CO2 capture. Particular attention is given to the mechanisms of CO2 absorption in these solvents, their regeneration and their processability – especially taking into account their viscosity. While not intended to provide a complete coverage of the existing literature, this review aims at pointing the major findings reported for these new classes of CO2 capture media.

Temperature dependence of charge-transfer fluorescence from extended and U-shaped donor-bridge-acceptor systems in glass-forming solvents.

NARCIS (Netherlands)

Goes, M.; de Groot, M.; Koeberg, M.; Verhoeven, J.W.; Lokan, N.R.; Shephard, M.J.; Paddon-Row, M.N.

2001-01-01

Abstract: The behavior is reported of three fluorescent D-bridge-A systems that display a fascinating temperature dependence in glass forming solvents over the temperature range between 77 and 293 K. In two of these systems, a rigid, saturated alkane bridge maintains an extended conformation, and as

Determination of solvent concentration-dependent dispersion in the vapor extraction (VAPEX) process

Energy Technology Data Exchange (ETDEWEB)

Abukhalifeh, H.; Lohi, A.; Upreti, S. [Ryerson Polytechnic Univ., Toronto, ON (Canada)

2008-07-01

This paper presented the results of a computational algorithm that revealed the optimal conditions required for vapor extraction (VAPEX) for a solvent gas-heavy oil system. VAPEX is a promising recovery process because it requires low energy use and emits fewer greenhouse gases to the atmosphere compared to other enhanced oil recovery methods. The process is governed by the dispersion of solvent gases into heavy oil and bitumen. As such, it is essential to accurately determine solvent dispersion in VAPEX in order to effectively predict the amount and time scale of oil recovery, and to optimize field operations. VAPEX experiments were conducted in this study to determined the dispersion coefficient of a solvent as a function of its concentration in heavy oil and bitumen. The principles of variational calculus were used together with a mass transfer model of the experimental process. It was concluded that the oil production determined by the model should agree with its experimental counterpart, given the optimal gas dispersion versus concentration function.

Phosphopeptide binding by Sld3 links Dbf4-dependent kinase to MCM replicative helicase activation.

Science.gov (United States)

Deegan, Tom D; Yeeles, Joseph Tp; Diffley, John Fx

2016-05-02

The initiation of eukaryotic DNA replication requires the assembly of active CMG (Cdc45-MCM-GINS) helicases at replication origins by a set of conserved and essential firing factors. This process is controlled during the cell cycle by cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK), and in response to DNA damage by the checkpoint kinase Rad53/Chk1. Here we show that Sld3, previously shown to be an essential CDK and Rad53 substrate, is recruited to the inactive MCM double hexamer in a DDK-dependent manner. Sld3 binds specifically to DDK-phosphorylated peptides from two MCM subunits (Mcm4, 6) and then recruits Cdc45. MCM mutants that cannot bind Sld3 or Sld3 mutants that cannot bind phospho-MCM or Cdc45 do not support replication. Moreover, phosphomimicking mutants in Mcm4 and Mcm6 bind Sld3 without DDK and facilitate DDK-independent replication. Thus, Sld3 is an essential "reader" of DDK phosphorylation, integrating signals from three distinct protein kinase pathways to coordinate DNA replication during S phase. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

Quantum mechanics/molecular mechanics modeling of photoelectron spectra: the carbon 1s core-electron binding energies of ethanol-water solutions.

Science.gov (United States)

Löytynoja, T; Niskanen, J; Jänkälä, K; Vahtras, O; Rinkevicius, Z; Ågren, H

2014-11-20

Using ethanol-water solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solute-solvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics model-electrostatic, polarization, and van der Waals-with atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

Electric Dipole Transition Moments and Solvent-Dependent Interactions of Fluorescent Boron-Nitrogen Substituted Indole Derivatives.

Science.gov (United States)

Saif, Mari; Widom, Julia R; Xu, Senmiao; Abbey, Eric R; Liu, Shih-Yuan; Marcus, Andrew H

2015-06-25

Fluorescent analogues of the indole side chain of tryptophan can be useful spectroscopic probes of protein-protein and protein-DNA interactions. Here we present linear dichroism and solvent-dependent spectroscopic studies of two fluorescent analogues of indole, in which the organic C═C unit is substituted with the isosteric inorganic B-N unit. We studied the so-called "external" BN indole, which has C2v symmetry, and the "fused" BN indole with Cs symmetry. We performed a combination of absorption and fluorescence spectroscopy, ultraviolet linear dichroism (UV-LD) in stretched poly(ethylene) (PE) films, and quantum chemical calculations on both BN indole compounds. Our measurements allowed us to characterize the degree of alignment for both molecules in stretched PE films. We thus determined the orientations and magnitudes of the two lowest energy electric dipole transition moments (EDTMs) for external BN indole, and the two lowest energy EDTMs for fused BN indole within the 30 000-45 000 cm(-1) spectral range. We compared our experimental results to those of quantum chemical calculations using standard density functional theory (DFT). Our theoretical predictions for the low-energy EDTMs are in good agreement with our experimental data. The absorption and fluorescence spectra of the external and the fused BN indoles are sensitive to solvent polarity. Our results indicate that the fused BN indole experiences much greater solvation interactions with polar solvents than does the external BN indole.

Recent Advances in Anhydrous Solvents for CO{sub 2} Capture: Ionic Liquids, Switchable Solvents, and Nanoparticle Organic Hybrid Materials

Energy Technology Data Exchange (ETDEWEB)

Park, Youngjune [School of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju (Korea, Republic of); Lin, Kun-Yi Andrew [Department of Environmental Engineering, National Chung Hsing University, Taichung City (China); Park, Ah-Hyung Alissa, E-mail: ap2622@columbia.edu [Department of Earth and Environmental Engineering, Lenfest Center for Sustainable Energy, Columbia University, New York, NY (United States); Department of Chemical Engineering, Lenfest Center for Sustainable Energy, Columbia University, New York, NY (United States); Petit, Camille, E-mail: ap2622@columbia.edu [Department of Chemical Engineering, Imperial College London, London (United Kingdom)

2015-10-01

CO{sub 2} capture by amine scrubbing, which has a high CO{sub 2} capture capacity and a rapid reaction rate, is the most employed and investigated approach to date. There are a number of recent large-scale demonstrations including the Boundary Dam Carbon Capture Project by SaskPower in Canada that have reported successful implementations of aqueous amine solvent in CO{sub 2} capture from flue gases. The findings from these demonstrations will significantly advance the field of CO{sub 2} capture in the coming years. While the latest efforts in aqueous amine solvents are exciting and promising, there are still several drawbacks to amine-based CO{sub 2} capture solvents including high volatility and corrosiveness of the amine solutions as well as the high parasitic energy penalty during the solvent regeneration step. Thus, in a parallel effort, alternative CO{sub 2} capture solvents, which are often anhydrous, have been developed as the third-generation CO{sub 2} capture solvents. These novel classes of liquid materials include ionic liquids, CO{sub 2}-triggered switchable solvents (i.e., CO{sub 2}-binding organic liquids, reversible ionic liquids), and nanoparticle organic hybrid materials. This paper provides a review of these various anhydrous solvents and their potential for CO{sub 2} capture. Particular attention is given to the mechanisms of CO{sub 2} absorption in these solvents, their regeneration and their processability – especially taking into account their viscosity. While not intended to provide a complete coverage of the existing literature, this review aims at pointing the major findings reported for these new classes of CO{sub 2} capture media.

Maximizing in vivo target clearance by design of pH-dependent target binding antibodies with altered affinity to FcRn.

Science.gov (United States)

Yang, Danlin; Giragossian, Craig; Castellano, Steven; Lasaro, Marcio; Xiao, Haiguang; Saraf, Himanshu; Hess Kenny, Cynthia; Rybina, Irina; Huang, Zhong-Fu; Ahlberg, Jennifer; Bigwarfe, Tammy; Myzithras, Maria; Waltz, Erica; Roberts, Simon; Kroe-Barrett, Rachel; Singh, Sanjaya

2017-10-01

Antibodies with pH-dependent binding to both target antigens and neonatal Fc receptor (FcRn) provide an alternative tool to conventional neutralizing antibodies, particularly for therapies where reduction in antigen level is challenging due to high target burden. However, the requirements for optimal binding kinetic framework and extent of pH dependence for these antibodies to maximize target clearance from circulation are not well understood. We have identified a series of naturally-occurring high affinity antibodies with pH-dependent target binding properties. By in vivo studies in cynomolgus monkeys, we show that pH-dependent binding to the target alone is not sufficient for effective target removal from circulation, but requires Fc mutations that increase antibody binding to FcRn. Affinity-enhanced pH-dependent FcRn binding that is double-digit nM at pH 7.4 and single-digit nM at pH 6 achieved maximal target reduction when combined with similar target binding affinities in reverse pH directions. Sustained target clearance below the baseline level was achieved 3 weeks after single-dose administration at 1.5 mg/kg. Using the experimentally derived mechanistic model, we demonstrate the essential kinetic interplay between target turnover and antibody pH-dependent binding during the FcRn recycling, and identify the key components for achieving maximal target clearance. These results bridge the demand for improved patient dosing convenience with the "know-how" of therapeutic modality by design.

Species dependence of [64Cu]Cu-Bis(thiosemicarbazone) radiopharmaceutical binding to serum albumins

International Nuclear Information System (INIS)

Basken, Nathan E.; Mathias, Carla J.; Lipka, Alexander E.; Green, Mark A.

2008-01-01

Introduction: Interactions of three copper(II) bis(thiosemicarbazone) positron emission tomography radiopharmaceuticals with human serum albumin, and the serum albumins of four additional mammalian species, were evaluated. Methods: 64 Cu-labeled diacetyl bis(N 4 -methylthiosemicarbazonato)copper(II) (Cu-ATSM), pyruvaldehyde bis(N 4 -methylthiosemicarbazonato)copper(II) (Cu-PTSM) and ethylglyoxal bis(thiosemicarbazonato)copper(II) (Cu-ETS) were synthesized and their binding to human, canine, rat, baboon and porcine serum albumins quantified by ultrafiltration. Protein binding was also measured for each tracer in human, porcine, rat and mouse serum. Results: The interaction of these neutral, lipophilic copper chelates with serum albumin is highly compound- and species-dependent. Cu-PTSM and Cu-ATSM exhibit particularly high affinity for human serum albumin (HSA), while the albumin binding of Cu-ETS is relatively insensitive to species. At HSA concentrations of 40 mg/ml, '% free' (non-albumin-bound) levels of radiopharmaceutical were 4.0±0.1%, 5.3±0.2% and 38.6±0.8% for Cu-PTSM, Cu-ATSM and Cu-ETS, respectively. Conclusions: Species-dependent variations in radiopharmaceutical binding to serum albumin may need to be considered when using animal models to predict the distribution and kinetics of these compounds in humans

Solvent-dependent transformation of aflatoxin B1 in soil.

Science.gov (United States)

Starr, James M; Rushing, Blake R; Selim, Mustafa I

2017-08-01

To date, all studies of aflatoxin B 1 (AFB 1 ) transformation in soil or in purified mineral systems have identified aflatoxins B 2 (AFB 2 ) and G 2 (AFG 2 ) as the primary transformation products. However, identification in these studies was made using thin layer chromatography which has relatively low resolution, and these studies did not identify a viable mechanism by which such transformations would occur. Further, the use of methanol as the solvent delivery vehicle in these studies may have contributed to formation of artifactual transformation products. In this study, we investigated the role of the solvent vehicle in the transformation of AFB 1 in soil. To do this, we spiked soils with AFB 1 dissolved in water (93:7, water/methanol) or methanol and used HPLC-UV and HPLC-MS to identify the transformation products. Contrasting previous published reports, we did not detect AFB 2 or AFG 2 . In an aqueous-soil environment, we identified aflatoxin B 2a (AFB 2a ) as the single major transformation product. We propose that AFB 2a is formed from hydrolysis of AFB 1 with the soil acting as an acid catalyst. Alternatively, when methanol was used, we identified methoxy aflatoxin species likely formed via acid-catalyzed addition of methanol to AFB 1 . These results suggest that where soil moisture is adequate, AFB 1 is hydrolyzed to AFB 2a and that reactive organic solvents should be avoided when replicating natural conditions to study the fate of AFB 1 in soil.

A fluorescent glycolipid-binding peptide probe traces cholesterol dependent microdomain-derived trafficking pathways.

Directory of Open Access Journals (Sweden)

Steffen Steinert

Full Text Available BACKGROUND: The uptake and intracellular trafficking of sphingolipids, which self-associate into plasma membrane microdomains, is associated with many pathological conditions, including viral and toxin infection, lipid storage disease, and neurodegenerative disease. However, the means available to label the trafficking pathways of sphingolipids in live cells are extremely limited. In order to address this problem, we have developed an exogenous, non-toxic probe consisting of a 25-amino acid sphingolipid binding domain, the SBD, derived from the amyloid peptide Abeta, and conjugated by a neutral linker with an organic fluorophore. The current work presents the characterization of the sphingolipid binding and live cell trafficking of this novel probe, the SBD peptide. SBD was the name given to a motif originally recognized by Fantini et al in a number of glycolipid-associated proteins, and was proposed to interact with sphingolipids in membrane microdomains. METHODOLOGY/PRINCIPAL FINDINGS: In accordance with Fantini's model, optimal SBD binding to membranes depends on the presence of sphingolipids and cholesterol. In synthetic membrane binding assays, SBD interacts preferentially with raft-like lipid mixtures containing sphingomyelin, cholesterol, and complex gangliosides in a pH-dependent manner, but is less glycolipid-specific than Cholera toxin B (CtxB. Using quantitative time-course colocalization in live cells, we show that the uptake and intracellular trafficking route of SBD is unlike that of either the non-raft marker Transferrin or the raft markers CtxB and Flotillin2-GFP. However, SBD traverses an endolysosomal route that partially intersects with raft-associated pathways, with a major portion being diverted at a late time point to rab11-positive recycling endosomes. Trafficking of SBD to acidified compartments is strongly disrupted by cholesterol perturbations, consistent with the regulation of sphingolipid trafficking by cholesterol

Characterization of molecularly imprinted polymers using a new polar solvent titration method.

Science.gov (United States)

Song, Di; Zhang, Yagang; Geer, Michael F; Shimizu, Ken D

2014-07-01

A new method of characterizing molecularly imprinted polymers (MIPs) was developed and tested, which provides a more accurate means of identifying and measuring the molecular imprinting effect. In the new polar solvent titration method, a series of imprinted and non-imprinted polymers were prepared in solutions containing increasing concentrations of a polar solvent. The polar solvent additives systematically disrupted the templation and monomer aggregation processes in the prepolymerization solutions, and the extent of disruption was captured by the polymerization process. The changes in binding capacity within each series of polymers were measured, providing a quantitative assessment of the templation and monomer aggregation processes in the imprinted and non-imprinted polymers. The new method was tested using three different diphenyl phosphate imprinted polymers made using three different urea functional monomers. Each monomer had varying efficiencies of templation and monomer aggregation. The new MIP characterization method was found to have several advantages. To independently verify the new characterization method, the MIPs were also characterized using traditional binding isotherm analyses. The two methods appeared to give consistent conclusions. First, the polar solvent titration method is less susceptible to false positives in identifying the imprinting effect. Second, the method is able to differentiate and quantify changes in binding capacity, as measured at a fixed guest and polymer concentration, arising from templation or monomer aggregation processes in the prepolymerization solution. Third, the method was also easy to carry out, taking advantage of the ease of preparing MIPs. Copyright © 2014 John Wiley & Sons, Ltd.

Oxygen dependency of epidermal growth factor receptor binding and DNA synthesis of rat hepatocytes

International Nuclear Information System (INIS)

Hirose, Tetsuro; Terajima, Hiroaki; Yamauchi, Akira

1997-01-01

Background/Aims: Changes in oxygen availability modulate replicative responses in several cell types, but the effects on hepatocyte replication remain unclear. We have studied the effects of transient nonlethal hypoxia on epidermal growth factor receptor binding and epidermal growth factor-induced DNA synthesis of rat hepatocytes. Methods: Lactate dehydrogenase activity in culture supernatant, intracellular adenosine triphosphate content, 125 I-epidermal growth factor specific binding, epidermal growth factor receptor protein expression, and 3 H-thymidine incorporation were compared between hepatocytes cultured in hypoxia and normoxia. Results: Hypoxia up to 3 h caused no significant increase in lactate dehydrogenase activity in the culture supernatant, while intracellular adenosine triphosphate content decreased time-dependently and was restored to normoxic levels by reoxygenation (nonlethal hypoxia). Concomitantly, 125 I-epidermal growth factor specific binding to hepatocytes decreased time-dependently (to 54.1% of normoxia) and was restored to control levels by reoxygenation, although 125 I-insulin specific binding was not affected. The decrease in 125 I-epidermal growth factor specific binding was explained by the decrease in the number or available epidermal growth factor receptors (21.37±3.08 to 12.16±1.42 fmol/10 5 cells), while the dissociation constant of the receptor was not affected. The change in the number of available receptors was not considered to be due to receptor degradation-resynthesis, since immuno-detection of the epidermal growth factor receptor revealed that the receptor protein expression did not change during hypoxia and reoxygenation, and since neither actinomycin D nor cycloheximide affected the recovery of 125 I-epidermal growth factor binding by reoxygenation. Inhibition of epidermal growth factor-induced DNA synthesis after hypoxia (to 75.4% of normoxia by 3 h hypoxia) paralleled the decrease in 125 I-epidermal growth factor binding

Organic solvent topical report

International Nuclear Information System (INIS)

COWLEY, W.L.

1999-01-01

This report provides the basis for closing the organic solvent safety issue. Sufficient information is presented to conclude that risk posed by an organic solvent fire is within risk evaluation guidelines. This report updates information contained in Analysis of Consequences of Postulated Solvent Fires in Hanford Site Waste Tanks. WHC-SD-WM-CN-032. Rev. 0A (Cowley et al. 1996). However, this document will not replace Cowley et al (1996) as the primary reference for the Basis for Interim Operation (BIO) until the recently submitted BIO amendment (Hanson 1999) is approved by the US Department of Energy. This conclusion depends on the use of controls for preventing vehicle fuel fires and for limiting the use of flame cutting in areas where hot metal can fall on the waste surface.The required controls are given in the Tank Waste Remediation System Technical Safety Requirements (Noorani 1997b). This is a significant change from the conclusions presented in Revision 0 of this report. Revision 0 of this calcnote concluded that some organic solvent fire scenarios exceeded risk evaluation guidelines, even with controls imposed

Organic solvent topical report

Energy Technology Data Exchange (ETDEWEB)

COWLEY, W.L.

1999-05-13

This report provides the basis for closing the organic solvent safety issue. Sufficient information is presented to conclude that risk posed by an organic solvent fire is within risk evaluation guidelines. This report updates information contained in Analysis of Consequences of Postulated Solvent Fires in Hanford Site Waste Tanks. WHC-SD-WM-CN-032. Rev. 0A (Cowley et al. 1996). However, this document will not replace Cowley et al (1996) as the primary reference for the Basis for Interim Operation (BIO) until the recently submitted BIO amendment (Hanson 1999) is approved by the US Department of Energy. This conclusion depends on the use of controls for preventing vehicle fuel fires and for limiting the use of flame cutting in areas where hot metal can fall on the waste surface.The required controls are given in the Tank Waste Remediation System Technical Safety Requirements (Noorani 1997b). This is a significant change from the conclusions presented in Revision 0 of this report. Revision 0 of this calcnote concluded that some organic solvent fire scenarios exceeded risk evaluation guidelines, even with controls imposed.

Comparative responses of river biofilms at the community level to common organic solvent and herbicide exposure.

Science.gov (United States)

Paule, A; Roubeix, V; Swerhone, G D W; Roy, J; Lauga, B; Duran, R; Delmas, F; Paul, E; Rols, J L; Lawrence, J R

2016-03-01

Residual pesticides applied to crops migrate from agricultural lands to surface and ground waters. River biofilms are the first aquatic non-target organisms which interact with pesticides. Therefore, ecotoxicological experiments were performed at laboratory scale under controlled conditions to investigate the community-level responses of river biofilms to a chloroacetanilide herbicide (alachlor) and organic solvent (methanol) exposure through the development referenced to control. Triplicate rotating annular bioreactors, inoculated with river water, were used to cultivate river biofilms under the influence of 1 and 10 μg L(-1) of alachlor and 25 mg L(-1) of methanol. For this purpose, functional (thymidine incorporation and carbon utilization spectra) and structural responses of microbial communities were assessed after 5 weeks of development. Structural aspects included biomass (chlorophyll a, confocal laser scanning microscopy) and composition (fluor-conjugated lectin binding, molecular fingerprinting, and diatom species composition). The addition of alachlor resulted in a significant reduction of bacterial biomass at 1 μg L(-1), whereas at 10 μg L(-1), it induced a significant reduction of exopolymer lectin binding, algal, bacterial, and cyanobacterial biomass. However, there were no changes in biofilm thickness or thymidine incorporation. No significant difference between the bacterial community structures of control and alachlor-treated biofilms was revealed by terminal restriction fragment length polymorphism (T-RFLP) analyses. However, the methanol-treated bacterial communities appeared different from control and alachlor-treated communities. Moreover, methanol treatment resulted in an increase of bacterial biomass and thymidine incorporation as well. Changes in dominant lectin binding suggested changes in the exopolymeric substances and community composition. Chlorophyll a and cyanobacterial biomass were also altered by methanol. This study suggested

Solvent effects in ionic liquids: empirical linear energy-density relationships.

Science.gov (United States)

Cerda-Monje, A; Aizman, A; Tapia, R A; Chiappe, C; Contreras, R

2012-07-28

Multiparameter linear energy-density relationships to model solvent effects in room temperature ionic liquids (RTILs) are introduced and tested. The model incorporates two solvent dependent and two specific solute-solvent parameters represented by a set of electronic indexes derived from the conceptual density functional theory. The specific solute-solvent interactions are described in terms of the electronic chemical potential for proton migration between the anion or cation and the transition state structure of a specific reaction. These indexes provide a quantitative estimation of the hydrogen bond (HB) acceptor basicity and the hydrogen bond donor acidity of the ionic solvent, respectively. A sound quantitative scale of HB strength is thereby obtained. The solvent dependent contributions are described by the global electrophilicity of the cation and nucleophilicity of the anion forming the ionic liquid. The model is illustrated for the kinetics of cycloaddition of cyclopentadiene towards acrolein. In general, cation HB acidity outweighs the remaining parameters for this reaction.

Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations

Energy Technology Data Exchange (ETDEWEB)

Zhou, Shenggao, E-mail: sgzhou@suda.edu.cn, E-mail: bli@math.ucsd.edu [Department of Mathematics and Mathematical Center for Interdiscipline Research, Soochow University, 1 Shizi Street, Jiangsu, Suzhou 215006 (China); Sun, Hui; Cheng, Li-Tien [Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112 (United States); Dzubiella, Joachim [Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, 14109 Berlin, Germany and Institut für Physik, Humboldt-Universität zu Berlin, 12489 Berlin (Germany); Li, Bo, E-mail: sgzhou@suda.edu.cn, E-mail: bli@math.ucsd.edu [Department of Mathematics and Quantitative Biology Graduate Program, University of California, San Diego, La Jolla, California 92093-0112 (United States); McCammon, J. Andrew [Department of Chemistry and Biochemistry, Department of Pharmacology, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365 (United States)

2016-08-07

Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the “normal velocity” that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the

Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding

Science.gov (United States)

Newcomer, Rebecca L.; Fraser, LaTasha C.R.; Teschke, Carolyn M.; Alexandrescu, Andrei T.

2015-01-01

The I-domain is an insertion domain of the bacteriophage P22 coat protein that drives rapid folding and accounts for over half of the stability of the full-length protein. We sought to determine the role of hydrogen bonds (H-bonds) in the unfolding of the I-domain by examining 3JNC’ couplings transmitted through H-bonds, the temperature and urea-concentration dependence of 1HN and 15N chemical shifts, and native-state hydrogen exchange at urea concentrations where the domain is predominantly folded. The native-state hydrogen-exchange data suggest that the six-stranded β-barrel core of the I-domain is more stable against unfolding than a smaller subdomain comprised of a short α-helix and three-stranded β-sheet. H-bonds, separately determined from solvent protection and 3JNC’ H-bond couplings, are identified with an accuracy of 90% by 1HN temperature coefficients. The accuracy is improved to 95% when 15N temperature coefficients are also included. In contrast, the urea dependence of 1HN and 15N chemical shifts is unrelated to H-bonding. The protein segments with the largest chemical-shift changes in the presence of urea show curved or sigmoidal titration curves suggestive of direct urea binding. Nuclear Overhauser effects to urea for these segments are also consistent with specific urea-binding sites in the I-domain. Taken together, the results support a mechanism of urea unfolding in which denaturant binds to distinct sites in the I-domain. Disordered segments bind urea more readily than regions in stable secondary structure. The locations of the putative urea-binding sites correlate with the lower stability of the structure against solvent exchange, suggesting that partial unfolding of the structure is related to urea accessibility. PMID:26682823

Species dependence of [{sup 64}Cu]Cu-Bis(thiosemicarbazone) radiopharmaceutical binding to serum albumins

Energy Technology Data Exchange (ETDEWEB)

Basken, Nathan E. [Division of Nuclear Pharmacy, Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN 47907 (United States)], E-mail: nbasken@purdue.edu; Mathias, Carla J. [Division of Nuclear Pharmacy, Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN 47907 (United States); Lipka, Alexander E. [Department of Statistics, Purdue University, West Lafayette, IN 47907 (United States); Green, Mark A. [Division of Nuclear Pharmacy, Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN 47907 (United States)], E-mail: magreen@purdue.edu

2008-04-15

Introduction: Interactions of three copper(II) bis(thiosemicarbazone) positron emission tomography radiopharmaceuticals with human serum albumin, and the serum albumins of four additional mammalian species, were evaluated. Methods: {sup 64}Cu-labeled diacetyl bis(N{sup 4}-methylthiosemicarbazonato)copper(II) (Cu-ATSM), pyruvaldehyde bis(N{sup 4}-methylthiosemicarbazonato)copper(II) (Cu-PTSM) and ethylglyoxal bis(thiosemicarbazonato)copper(II) (Cu-ETS) were synthesized and their binding to human, canine, rat, baboon and porcine serum albumins quantified by ultrafiltration. Protein binding was also measured for each tracer in human, porcine, rat and mouse serum. Results: The interaction of these neutral, lipophilic copper chelates with serum albumin is highly compound- and species-dependent. Cu-PTSM and Cu-ATSM exhibit particularly high affinity for human serum albumin (HSA), while the albumin binding of Cu-ETS is relatively insensitive to species. At HSA concentrations of 40 mg/ml, '% free' (non-albumin-bound) levels of radiopharmaceutical were 4.0{+-}0.1%, 5.3{+-}0.2% and 38.6{+-}0.8% for Cu-PTSM, Cu-ATSM and Cu-ETS, respectively. Conclusions: Species-dependent variations in radiopharmaceutical binding to serum albumin may need to be considered when using animal models to predict the distribution and kinetics of these compounds in humans.

Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water

International Nuclear Information System (INIS)

Oshima, Hiraku; Kinoshita, Masahiro

2015-01-01

In earlier works, we showed that the entropic effect originating from the translational displacement of water molecules plays the pivotal role in protein folding and denaturation. The two different solvent models, hard-sphere solvent and model water, were employed in theoretical methods wherein the entropic effect was treated as an essential factor. However, there were similarities and differences in the results obtained from the two solvent models. In the present work, to unveil the physical origins of the similarities and differences, we simultaneously consider structural transition, cold denaturation, and pressure denaturation for the same protein by employing the two solvent models and considering three different thermodynamic states for each solvent model. The solvent-entropy change upon protein folding/unfolding is decomposed into the protein-solvent pair (PA) and many-body (MB) correlation components using the integral equation theories. Each component is further decomposed into the excluded-volume (EV) and solvent-accessible surface (SAS) terms by applying the morphometric approach. The four physically insightful constituents, (PA, EV), (PA, SAS), (MB, EV), and (MB, SAS), are thus obtained. Moreover, (MB, SAS) is discussed by dividing it into two factors. This all-inclusive investigation leads to the following results: (1) the protein-water many-body correlation always plays critical roles in a variety of folding/unfolding processes; (2) the hard-sphere solvent model fails when it does not correctly reproduce the protein-water many-body correlation; (3) the hard-sphere solvent model becomes problematic when the dependence of the many-body correlation on the solvent number density and temperature is essential: it is not quite suited to studies on cold and pressure denaturating of a protein; (4) when the temperature and solvent number density are limited to the ambient values, the hard-sphere solvent model is usually successful; and (5) even at the ambient

MIT domain of Vps4 is a Ca2+-dependent phosphoinositide-binding domain.

Science.gov (United States)

Iwaya, Naoko; Takasu, Hirotoshi; Goda, Natsuko; Shirakawa, Masahiro; Tanaka, Toshiki; Hamada, Daizo; Hiroaki, Hidekazu

2013-05-01

The microtubule interacting and trafficking (MIT) domain is a small protein module that is conserved in proteins of diverged function, such as Vps4, spastin and sorting nexin 15 (SNX15). The molecular function of the MIT domain is protein-protein interaction, in which the domain recognizes peptides containing MIT-interacting motifs. Recently, we identified an evolutionarily related domain, 'variant' MIT domain at the N-terminal region of the microtubule severing enzyme katanin p60. We found that the domain was responsible for binding to microtubules and Ca(2+). Here, we have examined whether the authentic MIT domains also bind Ca(2+). We found that the loop between the first and second α-helices of the MIT domain binds a Ca(2+) ion. Furthermore, the MIT domains derived from Vps4b and SNX15a showed phosphoinositide-binding activities in a Ca(2+)-dependent manner. We propose that the MIT domain is a novel membrane-associating domain involved in endosomal trafficking.

Adsorption decontamination of radioactive waste solvent by activated alumina and bauxites

International Nuclear Information System (INIS)

Hassan, N.M.; Marra, J.C.; Kyser, E.A.

1994-01-01

An adsorption process utilizing activated alumina and activated bauxite adsorbents was evaluated as a function of operating parameters for the removal of low level radioactive contaminants from organic waste solvent generated in the fuel reprocessing facilities and support operations at Savannah River Site. The waste solvent, 30% volume tributyl phosphate in n-paraffin diluent, was degraded due to hydrolysis and radiolysis reactions of tributyl phosphate and n-paraffin diluent, producing fission product binding degradation impurities. The process, which has the potential for removing these activity-binding degradation impurities from the solvent, was operated downflow through glass columns packed with activated alumina and activated bauxite adsorbents. Experimental breakthrough curves were obtained under various operating temperatures and flow rates. The results show that the adsorption capacity of the activated alumina was in the order 10 4 dpm/g and the capacity of the activated bauxite was 10 5 dpm/g. The performance of the adsorption process was evaluated in terms of dynamic parameters (i.e. adsorption capacity, the height and the efficiency of adsorption zone) in such a way as to maximize the adsorption capacity and to minimize the height of the mass transfer or adsorption zone

Modeling of Salt Solubilities in Mixed Solvents

DEFF Research Database (Denmark)

Chiavone-Filho, O.; Rasmussen, Peter

2000-01-01

A method to correlate and predict salt solubilities in mixed solvents using a UNIQUAC+Debye-Huckel model is developed. The UNIQUAC equation is applied in a form with temperature-dependent parameters. The Debye-Huckel model is extended to mixed solvents by properly evaluating the dielectric...... constants and the liquid densities of the solvent media. To normalize the activity coefficients, the symmetric convention is adopted. Thermochemical properties of the salt are used to estimate the solubility product. It is shown that the proposed procedure can describe with good accuracy a series of salt...

MOLECULAR DYNAMICS SIMULATION OF KINETIC RESOLUTION OF RACEMIC ALCOHOL USING BURKHOLDERIA CEPACIA LIPASE IN ORGANIC SOLVENTS

Directory of Open Access Journals (Sweden)

A. C. Mathpati

2018-03-01

Full Text Available Lipases, a subclass of hydrolases, have gained a lot of importance as they can catalyze esterification, transesterification and hydrolysis reaction in non-aqueous media. Lipases are also widely used for kinetic resolution of racemic alcohols into enantiopure compounds. The lipase activity is affected by organic solvents due to changes in the conformational rigidity of enzymes, the active site, or altering the solvation of the transition state. The activity of lipases strongly depends on the logP value of solvents. Molecular dynamics (MD can help to understand the effect of solvents on lipase conformation as well as protein-ligand complex. In this work, MD simulations of Burkholderia cepacia lipase (BCL and complex between R and S conformation of acetylated form of 1-phenylethanol with BCL using gromacs have been carried in various organic solvents. The RMSD values were within the range of 0.15 to 0.20 nm and radius of gyration was found to be with 1.65 to 1.9 nm. Major changes in the B factor compared to reference structure were observed between residues 60 to 80, 120 to 150 and 240 to 260. Higher unfolding was observed in toluene and diethyl ether compared to hexane and acetonitrile. R acetylated complex was found to favorably bind BCL compared to S form. The predicted enantioselectivity were in good agreement with the experimental data.

Reformulation of Maxwell's equations to incorporate near-solute solvent structure.

Science.gov (United States)

Yang, Pei-Kun; Lim, Carmay

2008-09-04

Maxwell's equations, which treat electromagnetic interactions between macroscopic charged objects in materials, have explained many phenomena and contributed to many applications in our lives. Derived in 1861 when no methods were available to determine the atomic structure of macromolecules, Maxwell's equations assume the solvent to be a structureless continuum. However, near-solute solvent molecules are highly structured, unlike far-solute bulk solvent molecules. Current methods cannot treat both the near-solute solvent structure and time-dependent electromagnetic interactions in a macroscopic system. Here, we derive "microscopic" electrodynamics equations that can treat macroscopic time-dependent electromagnetic field problems like Maxwell's equations and reproduce the solvent molecular and dipole density distributions observed in molecular dynamics simulations. These equations greatly reduce computational expense by not having to include explicit solvent molecules, yet they treat the solvent electrostatic and van der Waals effects more accurately than continuum models. They provide a foundation to study electromagnetic interactions between molecules in a macroscopic system that are ubiquitous in biology, bioelectromagnetism, and nanotechnology. The general strategy presented herein to incorporate the near-solute solvent structure would enable studies on how complex cellular protein-ligand interactions are affected by electromagnetic radiation, which could help to prevent harmful electromagnetic spectra or find potential therapeutic applications.

How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

Science.gov (United States)

Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle

2015-06-09

Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations

Science.gov (United States)

2016-01-01

Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

Mechanistic pathways of recognition of a solvent-inaccessible cavity of protein by a ligand

Science.gov (United States)

Mondal, Jagannath; Pandit, Subhendu; Dandekar, Bhupendra; Vallurupalli, Pramodh

One of the puzzling questions in the realm of protein-ligand recognition is how a solvent-inaccessible hydrophobic cavity of a protein gets recognized by a ligand. We address the topic by simulating, for the first time, the complete binding process of benzene from aqueous media to the well-known buried cavity of L99A T4 Lysozyme at an atomistic resolution. Our multiple unbiased microsecond-long trajectories, which were completely blind to the location of target binding site, are able to unequivocally identify the kinetic pathways along which benzene molecule meanders across the solvent and protein and ultimately spontaneously recognizes the deeply buried cavity of L99A T4 Lysozyme at an accurate precision. Our simulation, combined with analysis based on markov state model and free energy calculation, reveals that there are more than one distinct ligand binding pathways. Intriguingly, each of the identified pathways involves the transient opening of a channel of the protein prior to ligand binding. The work will also decipher rich mechanistic details on unbinding kinetics of the ligand as obtained from enhanced sampling techniques.

Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components.

Science.gov (United States)

Timasheff, Serge N

2002-07-23

Solvent additives (cosolvents, osmolytes) modulate biochemical reactions if, during the course of the reaction, there is a change in preferential interactions of solvent components with the reacting system. Preferential interactions can be expressed in terms of preferential binding of the cosolvent or its preferential exclusion (preferential hydration). The driving force is the perturbation by the protein of the chemical potential of the cosolvent. It is shown that the measured change of the amount of water in contact with protein during the course of the reaction modulated by an osmolyte is a change in preferential hydration that is strictly a measure of the cosolvent chemical potential perturbation by the protein in the ternary water-protein-cosolvent system. It is not equal to the change in water of hydration, because water of hydration is a reflection strictly of protein-water forces in a binary system. There is no direct relation between water of preferential hydration and water of hydration.

Permeability of commercial solvents through living human skin

DEFF Research Database (Denmark)

Ursin, C; Hansen, C M; Van Dyk, J W

1995-01-01

A procedure has been developed for measuring the steady state rate of permeation of commercial solvents through living human skin. To get the most consistent results, it was necessary with some solvents to normalize the solvent permeation rate of a given skin sample with its [3H]water permeation...... rate. For other solvents this was not necessary, so the un-normalized data were used. High [3H]water permeation rate also was used as a criterion for "defective" skin samples that gave erroneous permeability rates, especially for solvents having slow permeability. The linearity of the steady state data...... of DMSO and octyl acetate were measured. No octyl acetate was detected and the permeability of DMSO was proportional to its mole fraction in the mixture. The effect of two hours of solvent exposure on the viability of skin (based on DNA synthesis) was measured and found to be very dependent on the solvent....

Substituent Effects on the Coordination Chemistry of Metal-Binding Pharmacophores

Energy Technology Data Exchange (ETDEWEB)

Craig, Whitney R. [Department; Baker, Tessa W. [Department; Marts, Amy R. [Department; DeGenova, Daniel T. [Department; Martin, David P. [Department; Reed, Garrett C. [Department; McCarrick, Robert M. [Department; Crowder, Michael W. [Department; Cohen, Seth M. [Department; Tierney, David L. [Department

2017-09-12

A combination of XAS, UV–vis, NMR, and EPR was used to examine the binding of a series of α-hydroxythiones to CoCA. All three appear to bind preferentially in their neutral, protonated forms. Two of the three clearly bind in a monodentate fashion, through the thione sulfur alone. Thiomaltol (TM) appears to show some orientational preference, on the basis of the NMR, while it appears that thiopyromeconic acid (TPMA) retains rotational freedom. In contrast, allothiomaltol (ATM), after initially binding in its neutral form, presumably through the thione sulfur, forms a final complex that is five-coordinate via bidentate coordination of ATM. On the basis of optical titrations, we speculate that this may be due to the lower initial pKa of ATM (8.3) relative to those of TM (9.0) and TPMA (9.5). Binding through the thione is shown to reduce the hydroxyl pKa by ~0.7 pH unit on metal binding, bringing only ATM’s pKa close to the pH of the experiment, facilitating deprotonation and subsequent coordination of the hydroxyl. The data predict the presence of a solvent-exchangeable proton on TM and TPMA, and Q-band 2-pulse ESEEM experiments on CoCA + TM suggest that the proton is present. ESE-detected EPR also showed a surprising frequency dependence, giving only a subset of the expected resonances at X-band.

LRRK2 kinase activity is dependent on LRRK2 GTP binding capacity but independent of LRRK2 GTP binding.

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Jean-Marc Taymans

Full Text Available Leucine rich repeat kinase 2 (LRRK2 is a Parkinson's disease (PD gene that encodes a large multidomain protein including both a GTPase and a kinase domain. GTPases often regulate kinases within signal transduction cascades, where GTPases act as molecular switches cycling between a GTP bound "on" state and a GDP bound "off" state. It has been proposed that LRRK2 kinase activity may be increased upon GTP binding at the LRRK2 Ras of complex proteins (ROC GTPase domain. Here we extensively test this hypothesis by measuring LRRK2 phosphorylation activity under influence of GDP, GTP or non-hydrolyzable GTP analogues GTPγS or GMPPCP. We show that autophosphorylation and lrrktide phosphorylation activity of recombinant LRRK2 protein is unaltered by guanine nucleotides, when co-incubated with LRRK2 during phosphorylation reactions. Also phosphorylation activity of LRRK2 is unchanged when the LRRK2 guanine nucleotide binding pocket is previously saturated with various nucleotides, in contrast to the greatly reduced activity measured for the guanine nucleotide binding site mutant T1348N. Interestingly, when nucleotides were incubated with cell lysates prior to purification of LRRK2, kinase activity was slightly enhanced by GTPγS or GMPPCP compared to GDP, pointing to an upstream guanine nucleotide binding protein that may activate LRRK2 in a GTP-dependent manner. Using metabolic labeling, we also found that cellular phosphorylation of LRRK2 was not significantly modulated by nucleotides, although labeling is significantly reduced by guanine nucleotide binding site mutants. We conclude that while kinase activity of LRRK2 requires an intact ROC-GTPase domain, it is independent of GDP or GTP binding to ROC.

Vibrationally resolved UV/Vis spectroscopy with time-dependent density functional based tight binding

NARCIS (Netherlands)

Ruger, R.; Niehaus, T.; van Lenthe, E.; Heine, T.; Visscher, L.

2016-01-01

We report a time-dependent density functional based tight-binding (TD-DFTB) scheme for the calculation of UV/Vis spectra, explicitly taking into account the excitation of nuclear vibrations via the adiabatic Hessian Franck-Condon method with a harmonic approximation for the nu- clear wavefunction.

Involvement of histidine residues in the pH-dependent β-galactoside binding activity of human galectin-1.

Science.gov (United States)

Hiramatsu, Hirotsugu; Takeuchi, Katsuyuki; Takeuchi, Hideo

2013-04-02

The pH dependence of the β-galactoside binding activity of human galectin-1 (hGal-1) was investigated by fluorescence spectroscopy using lactose as a ligand. The obtained binding constant Kb was 2.94 ± 0.10 mM(-1) at pH 7.5. The Kb value decreased at acidic pH with a midpoint of transition at pH 6.0 ± 0.1. To elucidate the molecular mechanism of the pH dependence, we investigated the structures of hGal-1 and its two His mutants (H44Q and H52Q) using fluorescence, circular dichroism, UV absorption, and UV resonance Raman spectroscopy. Analysis of the spectra has shown that the pKa values of His44 and His52 are 5.7 ± 0.2 and 6.3 ± 0.1, respectively. The protonation of His52 below pH 6.3 induces a small change in secondary structure and partly reduces the galactoside binding activity. On the other hand, the protonation of His44 below pH 5.7 exerts a cation-π interaction with Trp68 and largely diminishes the galactoside binding activity. With reference to the literature X-ray structures at pH 7.0 and 5.6, protonated His52 is proposed to move slightly away from the galactoside-binding region with a partial unfolding of the β-strand containing His52. On the other hand, protonated His44 becomes unable to form a hydrogen bond with galactoside and additionally induces a reorientation and/or displacement of Trp68 through cation-π interaction, leading to a loosening of the galactoside-binding pocket. These structural changes associated with His protonation are likely to be the origin of the pH dependence of the galactoside binding activity of hGal-1.

Photo-isomerization and oxidation of bilirubin in mammals is dependent on albumin binding.

Science.gov (United States)

Goncharova, Iryna; Jašprová, Jana; Vítek, Libor; Urbanová, Marie

2015-12-01

The bilirubin (BR) photo-conversion in the human body is a protein-dependent process; an effective photo-isomerization of the potentially neurotoxic Z,Z-BR as well as its oxidation to biliverdin in the antioxidant redox cycle is possible only when BR is bound on serum albumin. We present a novel analytical concept in the study of linear tetrapyrroles metabolic processes based on an in-depth mapping of binding sites in the structure of human serum albumin (HSA). A combination of fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and molecular modeling methods was used for recognition of the binding site for BR, its derivatives (mesobilirubin and bilirubin ditaurate), and the products of the photo-isomerization and oxidation (lumirubin, biliverdin, and xanthobilirubic acid) on HSA. The CD spectra and fluorescent quenching of the Trp-HSA were used to calculate the binding constants. The results of the CD displacement experiments performed with hemin were interpreted together with the findings of molecular docking performed on the pigment-HSA complexes. We estimated that Z,Z-BR and its metabolic products bind on two independent binding sites. Our findings support the existence of a reversible antioxidant redox cycle for BR and explain an additional pathway of the photo-isomerization process (increase of HSA binding capacity; the excess free [unbound] BR can be converted and also bound to HSA). Copyright © 2015 Elsevier Inc. All rights reserved.

Heavy atoms as molecular probes in studying the solvent dependence of the dynamics of triplet exciplexes

International Nuclear Information System (INIS)

Steiner, U.; Winter, G.

1981-01-01

Electron transfer reactions between thiopyronine triplet (acceptor 3 A + ) and the electron donors (D), aniline, p-Br-aniline and p-I-aniline, are investigated by flash spectroscopy in solvents of different viscosity and polarity. Due to the heavy-atom effect the radical yield becomes very sensitive to the solvent influence, which can be explained by the dynamic properties of a triplet exciplex ( 3 (AD + )) formed as a primary product in the reaction between acceptor triplet and donor. Whereas on variation of solvent viscosity the solvent cage effect on the dissociation of 3 (AD + ) is observed, a change in solvent polarity is suggested to affect the radiationless deactivation of 3 (AD + ) to the ground state of the components. (author)

Dendritic brushes under theta and poor solvent conditions

Science.gov (United States)

Gergidis, Leonidas N.; Kalogirou, Andreas; Charalambopoulos, Antonios; Vlahos, Costas

2013-07-01

The effects of solvent quality on the internal stratification of polymer brushes formed by dendron polymers up to third generation were studied by means of molecular dynamics simulations with Langevin thermostat. The distributions of polymer units, of the free ends, the radii of gyration, and the back folding probabilities of the dendritic spacers were studied at the macroscopic states of theta and poor solvent. For high grafting densities we observed a small decrease in the height of the brush as the solvent quality decreases. The internal stratification in theta solvent was similar to the one we found in good solvent, with two and in some cases three kinds of populations containing short dendrons with weakly extended spacers, intermediate-height dendrons, and tall dendrons with highly stretched spacers. The differences increase as the grafting density decreases and single dendron populations were evident in theta and poor solvent. In poor solvent at low grafting densities, solvent micelles, polymeric pinned lamellae, spherical and single chain collapsed micelles were observed. The scaling dependence of the height of the dendritic brush at high density brushes for both solvents was found to be in agreement with existing analytical results.

Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics

Science.gov (United States)

2015-01-01

We present a strategy for carrying out high-precision calculations of binding free energy and binding enthalpy values from molecular dynamics simulations with explicit solvent. The approach is used to calculate the thermodynamic profiles for binding of nine small molecule guests to either the cucurbit[7]uril (CB7) or β-cyclodextrin (βCD) host. For these systems, calculations using commodity hardware can yield binding free energy and binding enthalpy values with a precision of ∼0.5 kcal/mol (95% CI) in a matter of days. Crucially, the self-consistency of the approach is established by calculating the binding enthalpy directly, via end point potential energy calculations, and indirectly, via the temperature dependence of the binding free energy, i.e., by the van’t Hoff equation. Excellent agreement between the direct and van’t Hoff methods is demonstrated for both host–guest systems and an ion-pair model system for which particularly well-converged results are attainable. Additionally, we find that hydrogen mass repartitioning allows marked acceleration of the calculations with no discernible cost in precision or accuracy. Finally, we provide guidance for accurately assessing numerical uncertainty of the results in settings where complex correlations in the time series can pose challenges to statistical analysis. The routine nature and high precision of these binding calculations opens the possibility of including measured binding thermodynamics as target data in force field optimization so that simulations may be used to reliably interpret experimental data and guide molecular design. PMID:26523125

Cu(II) bis(thiosemicarbazone) radiopharmaceutical binding to serum albumin: further definition of species dependence and associated substituent effects

International Nuclear Information System (INIS)

Basken, Nathan E.; Green, Mark A.

2009-01-01

Introduction: The pyruvaldehyde bis(N 4 -methylthiosemicarbazonato)copper(II) (Cu-PTSM) and diacetyl bis(N 4 -methylthiosemicarbazonato)copper(II) (Cu-ATSM) radiopharmaceuticals exhibit strong, species-dependent binding to the IIA site of human serum albumin (HSA), while the related ethylglyoxal bis(thiosemicarbazonato)copper(II) (Cu-ETS) radiopharmaceutical appears to exhibit only nonspecific binding to HSA and animal serum albumins. Methods: To further probe the structural basis for the species dependence of this albumin binding interaction, we examined protein binding of these three radiopharmaceuticals in solutions of albumin and/or serum from a broader array of mammalian species (rat, sheep, donkey, rabbit, cow, pig, dog, baboon, mouse, cat and elephant). We also evaluated the albumin binding of several copper(II) bis(thiosemicarbazone) chelates offering more diverse substitution of the ligand backbone. Results: Cu-PTSM and Cu-ATSM exhibit a strong interaction with HSA that is not apparent with the albumins of other species, while the binding of Cu-ETS to albumin is much less species dependent. The strong interaction of Cu-PTSM with HSA does not appear to simply correlate with variation, relative to the animal albumins, of a single amino acid lining HSA's IIA site. Those agents that selectively interact with HSA share the common feature of only methyl or hydrogen substitution at the carbon atoms of the diimine fragment of the ligand backbone. Conclusions: The interspecies variations in albumin binding of Cu-PTSM and Cu-ATSM are not simply explained by unique amino acid substitutions in the IIA binding pocket of the serum albumins. However, the specific affinity for this region of HSA is disrupted when substituents bulkier than a methyl group appear on the imine carbons of the copper bis(thiosemicarbazone) chelate.

Cu(II) bis(thiosemicarbazone) radiopharmaceutical binding to serum albumin: further definition of species dependence and associated substituent effects

Energy Technology Data Exchange (ETDEWEB)

Basken, Nathan E. [Division of Nuclear Pharmacy, Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN 47907 (United States); Green, Mark A. [Division of Nuclear Pharmacy, Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN 47907 (United States)], E-mail: magreen@purdue.edu

2009-07-15

Introduction: The pyruvaldehyde bis(N{sup 4}-methylthiosemicarbazonato)copper(II) (Cu-PTSM) and diacetyl bis(N{sup 4}-methylthiosemicarbazonato)copper(II) (Cu-ATSM) radiopharmaceuticals exhibit strong, species-dependent binding to the IIA site of human serum albumin (HSA), while the related ethylglyoxal bis(thiosemicarbazonato)copper(II) (Cu-ETS) radiopharmaceutical appears to exhibit only nonspecific binding to HSA and animal serum albumins. Methods: To further probe the structural basis for the species dependence of this albumin binding interaction, we examined protein binding of these three radiopharmaceuticals in solutions of albumin and/or serum from a broader array of mammalian species (rat, sheep, donkey, rabbit, cow, pig, dog, baboon, mouse, cat and elephant). We also evaluated the albumin binding of several copper(II) bis(thiosemicarbazone) chelates offering more diverse substitution of the ligand backbone. Results: Cu-PTSM and Cu-ATSM exhibit a strong interaction with HSA that is not apparent with the albumins of other species, while the binding of Cu-ETS to albumin is much less species dependent. The strong interaction of Cu-PTSM with HSA does not appear to simply correlate with variation, relative to the animal albumins, of a single amino acid lining HSA's IIA site. Those agents that selectively interact with HSA share the common feature of only methyl or hydrogen substitution at the carbon atoms of the diimine fragment of the ligand backbone. Conclusions: The interspecies variations in albumin binding of Cu-PTSM and Cu-ATSM are not simply explained by unique amino acid substitutions in the IIA binding pocket of the serum albumins. However, the specific affinity for this region of HSA is disrupted when substituents bulkier than a methyl group appear on the imine carbons of the copper bis(thiosemicarbazone) chelate.

Rationalization of Anomalous Pseudocontact Shifts and Their Solvent Dependence in a Series of C3-Symmetric Lanthanide Complexes.

Science.gov (United States)

Vonci, Michele; Mason, Kevin; Suturina, Elizaveta A; Frawley, Andrew T; Worswick, Steven G; Kuprov, Ilya; Parker, David; McInnes, Eric J L; Chilton, Nicholas F

2017-10-11

Bleaney's long-standing theory of magnetic anisotropy has been employed with some success for many decades to explain paramagnetic NMR pseudocontact shifts, and has been the subject of many subsequent approximations. Here, we present a detailed experimental and theoretical investigation accounting for the anomalous solvent dependence of NMR shifts for a series of lanthanide(III) complexes, namely [LnL 1 ] (Ln = Eu, Tb, Dy, Ho, Er, Tm, and Yb; L 1 : 1,4,7-tris[(6-carboxypyridin-2-yl)methyl]-1,4,7-triazacyclononane), taking into account the effect of subtle ligand flexibility on the electronic structure. We show that the anisotropy of the room temperature magnetic susceptibility tensor, which in turn affects the sign and magnitude of the pseudocontact chemical shift, is extremely sensitive to minimal structural changes in the first coordination sphere of L 1 . We show that DFT structural optimizations do not give accurate structural models, as assessed by the experimental chemical shifts, and thus we determine a magnetostructural correlation and employ this to evaluate the accurate solution structure for each [LnL 1 ]. This approach allows us to explain the counterintuitive pseudocontact shift behavior, as well as a striking solvent dependence. These results have important consequences for the analysis and design of novel magnetic resonance shift and optical emission probes that are sensitive to the local solution environment and polarity.

Solvent effects in time-dependent self-consistent field methods. II. Variational formulations and analytical gradients

International Nuclear Information System (INIS)

Bjorgaard, J. A.; Velizhanin, K. A.; Tretiak, S.

2015-01-01

This study describes variational energy expressions and analytical excited state energy gradients for time-dependent self-consistent field methods with polarizable solvent effects. Linear response, vertical excitation, and state-specific solventmodels are examined. Enforcing a variational ground stateenergy expression in the state-specific model is found to reduce it to the vertical excitation model. Variational excited state energy expressions are then provided for the linear response and vertical excitation models and analytical gradients are formulated. Using semiempiricalmodel chemistry, the variational expressions are verified by numerical and analytical differentiation with respect to a static external electric field. Lastly, analytical gradients are further tested by performing microcanonical excited state molecular dynamics with p-nitroaniline

Cesium Concentration in MCU Solvent

International Nuclear Information System (INIS)

Walker, D

2006-01-01

During Modular Caustic-Side Solvent Extraction (CSSX) Unit (MCU) operations, Cs-137 concentrations in product streams will vary depending on the location in the process and on the recent process conditions. Calculations of cesium concentrations under a variety of operating conditions reveal the following: (1) Under nominal operations with salt solution feed containing 1.1 Ci Cs-137 per gallon, the maximum Cs-137 concentration in the process will occur in the strip effluent (SE) and equal 15-16.5 Ci/gal. (2) Under these conditions, the majority of the solvent will contain 0.005 to 0.01 Ci/gal, with a limited portion of the solvent in the contactor stages containing ∼4 Ci/gal. (3) When operating conditions yield product near 0.1 Ci Cs-137/gal in the decontaminated salt solution (DSS), the SE cesium concentration will be the same or lower than in nominal operations, but majority of the stripped solvent will increase to ∼2-3 Ci/gal. (4) Deviations in strip and waste stream flow rates cause the largest variations in cesium content: (a) If strip flow rates deviate by -30% of nominal, the SE will contain ∼23 Ci/gal, although the cesium content of the solvent will increase to only 0.03 Ci/gal; (b) If strip flow rate deviates by -77% (i.e., 23% of nominal), the SE will contain 54 Ci/gal and solvent will contain 1.65 Ci/gal. At this point, the product DSS will just reach the limit of 0.1 Ci/gal, causing the DSS gamma monitors to alarm; and (c) Moderate (+10 to +30%) deviations in waste flow rate cause approximately proportional increases in the SE and solvent cesium concentrations. Recovery from a process failure due to poor cesium stripping can achieve any low cesium concentration required. Passing the solvent back through the contactors while recycling DSS product will produce a ∼70% reduction during one pass through the contactors (assuming the stripping D value is no worse than 0.36). If the solvent is returned to the solvent hold tank (containing additional

Ionic magnetic fluids in polar solvents with tuned counter-ions

Energy Technology Data Exchange (ETDEWEB)

Lopes Filomeno, C. [Sorbonne Universités, UPMC Univ Paris 06, CNRS, Lab. PHENIX, Paris (France); Grupo de Fluidos Complexos Inst. de Quimica, Univ. de Brasília, Brasília (DF) (Brazil); Kouyaté, M. [Sorbonne Universités, UPMC Univ Paris 06, CNRS, Lab. PHENIX, Paris (France); Cousin, F. [Lab. Léon Brillouin – CE-Saclay, Gif-sur-Yvette (France); Demouchy, G. [Sorbonne Universités, UPMC Univ Paris 06, CNRS, Lab. PHENIX, Paris (France); Dpt de physique, Univ. de Cergy Pontoise, Cergy-Pontoise (France); Dubois, E.; Michot, L.; Mériguet, G. [Sorbonne Universités, UPMC Univ Paris 06, CNRS, Lab. PHENIX, Paris (France); Perzynski, R., E-mail: regine.perzynski@upmc.fr [Sorbonne Universités, UPMC Univ Paris 06, CNRS, Lab. PHENIX, Paris (France); Peyre, V.; Sirieix-Plénet, J. [Sorbonne Universités, UPMC Univ Paris 06, CNRS, Lab. PHENIX, Paris (France); Tourinho, F.A. [Grupo de Fluidos Complexos Inst. de Quimica, Univ. de Brasília, Brasília (DF) (Brazil)

2017-06-01

The aim of the present study is to propose a new reproducible method for preparing colloidal dispersions of electrostatically charged nanoparticles (NPs) in polar solvents with different kinds of counter-ions. Maghemite NPs are here dispersed in solvents of different dielectric constant, namely water, dimethylsulfoxide (DMSO) and an ionic liquid, ethylammonium nitrate (EAN). If the existence of a NP superficial charge happens to be necessary for the colloidal stability of the dispersions in these three solvents, the standard DLVO theory cannot be used any more to describe the colloidal stability in EAN. The structure of the dispersions and the strength of the interparticle repulsion are investigated by small angle X-ray scattering measurements, in association with Ludwig–Soret coefficient determinations. Specificities, associated to the nature of the counter-ions are identified in this work on the colloidal stability, on the interparticle repulsion and on the Ludwig–Soret coefficient. - Highlights: • A controlled synthesis of ionic magnetic fluids in three polar solvents is proposed. • Colloidal repulsion in the magnetic fluids depends on the counter-ion nature. • Soret coefficient of citrate-coated maghemite nanoparticles is probed in water-pH7. • Thermophilicity of nanoparticles depends on the nature of their counter-ions. • Nanoparticles dressed with same counter-ions have solvent-dependent thermoproperties.

Molecular and ionic hydrogen bond formation in fluorous solvents.

Science.gov (United States)

O'Neal, Kristi L; Weber, Stephen G

2009-01-08

There are only a few studies of noncovalent association in fluorous solvents and even fewer that are quantitative. A full understanding, particularly of stoichiometry and binding strength of noncovalent interactions in fluorous solvents could be very useful in improved molecular-receptor-based extractions, advancements in sensor technologies, crystal engineering, and supramolecular chemistry. This work investigates hydrogen bonding between heterocyclic bases and a perfluoropolyether with a terminal carboxylic acid group (Krytox 157FSH (1)), chiefly in FC-72 (a mixture of perfluorohexanes). In particular, we were interested in whether or not proton transfer occurs, and if so, under what conditions in H-bonded complexes. Continuous variations experiments show that in FC-72 weaker bases (pyrazine, pyrimidine, and quinazoline) form 1:1 complexes with 1, whereas stronger bases (quinoline, pyridine, and isoquinoline) form 1:3 complexes. Ultraviolet and infrared spectral signatures reveal that the 1:1 complexes are molecular (B.HA) whereas the 1:3 complexes are ionic (BH+.A-HAHA). Infrared spectra of 1:3 ionic complexes are discussed in detail. Literature and experimental data on complexes between N-heterocyclic bases and carboxylic acids in a range of solvents are compiled to compare solvent effects on proton transfer. Polar solvents support ionic hydrogen bonds at a 1:1 mol ratio. In nonpolar organic solvents, ionic hydrogen bonds are only observed in complexes with 1:2 (base/acid) stoichiometries. In fluorous solvents, a larger excess of acid, 1:3, is necessary to facilitate proton transfer in hydrogen bonds between carboxylic acids and the bases studied.

Indium recovery by solvent extraction

International Nuclear Information System (INIS)

Fortes, Marilia Camargos Botelho

1999-04-01

Indium has been recovered as a byproduct from residues generated from the sulfuric acid leaching circuits in mineral plants for zinc recovery. Once its recovery comes from the slags of other metals recovery, it is necessary to separate it from the other elements which usually are present in high concentrations. Many works have been approaching this separation and indicate the solvent extraction process as the main technique used. In Brazilian case, indium recovery depends on the knowledge of this technique and its development. This paper describes the solvent extraction knowledge for the indium recovery from aqueous solutions generated in mineral plants. The results for determination of the best experimental conditions to obtain a high indium concentration solution and minimum iron poisoning by solvent extraction with di (2-ethylhexyl)-phosphoric acid (D2EHPA) solubilized in isoparafin and exxsol has been presented. (author)

Activity of cAMP-dependent protein kinases and cAMP-binding proteins of rat kidney cytosol during dehydration

International Nuclear Information System (INIS)

Zelenina, M.N.; Solenov, E.I.; Ivanova, L.N.

1985-01-01

The activity of cAMP-dependent protein kinases, the binding of cAMP, and the spectrum of cAMP-binding proteins in the cytosol of the renal papilla was studied in intact rats and in rats after 24 h on a water-deprived diet. It was found that the activation of protein kinases by 10 -6 M cAMP is significantly higher in the experimental animals than in the intact animals. In chromatography on DEAE-cellulose, the positions of the peaks of specific reception of cAMP corresponded to the peaks of the regulatory subunits of cAMP-dependent protein kinases of types I and II. In this case, in intact animals more than 80% of the binding activity was detected in peaks II, whereas in rats subjected to water deprivation, more than 60% of the binding was observed in peak I. The general regulatory activity of the cytosol was unchanged in the experimental animals in comparison with intact animals. It is suggested that during dehydration there is an induction of the synthesis of the regulatory subunit of type I cAMP-dependent protein kinase in the renal papilla

The Potato Nucleotide-binding Leucine-rich Repeat (NLR) Immune Receptor Rx1 Is a Pathogen-dependent DNA-deforming Protein*

Science.gov (United States)

Fenyk, Stepan; Townsend, Philip D.; Dixon, Christopher H.; Spies, Gerhard B.; de San Eustaquio Campillo, Alba; Slootweg, Erik J.; Westerhof, Lotte B.; Gawehns, Fleur K. K.; Knight, Marc R.; Sharples, Gary J.; Goverse, Aska; Pålsson, Lars-Olof; Takken, Frank L. W.; Cann, Martin J.

2015-01-01

Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable cells to respond to pathogen attack. Several NLRs act in the nucleus; however, conserved nuclear targets that support their role in immunity are unknown. Previously, we noted a structural homology between the nucleotide-binding domain of NLRs and DNA replication origin-binding Cdc6/Orc1 proteins. Here we show that the NB-ARC (nucleotide-binding, Apaf-1, R-proteins, and CED-4) domain of the Rx1 NLR of potato binds nucleic acids. Rx1 induces ATP-dependent bending and melting of DNA in vitro, dependent upon a functional P-loop. In situ full-length Rx1 binds nuclear DNA following activation by its cognate pathogen-derived effector protein, the coat protein of potato virus X. In line with its obligatory nucleocytoplasmic distribution, DNA binding was only observed when Rx1 was allowed to freely translocate between both compartments and was activated in the cytoplasm. Immune activation induced by an unrelated NLR-effector pair did not trigger an Rx1-DNA interaction. DNA binding is therefore not merely a consequence of immune activation. These data establish a role for DNA distortion in Rx1 immune signaling and define DNA as a molecular target of an activated NLR. PMID:26306038

Full scale solvent extraction remedial results

International Nuclear Information System (INIS)

Cash, A.B.

1992-01-01

Sevenson Extraction Technology, Inc. has completed the development of the Soil Restoration Unit (initially developed by Terra-Kleen Corporation), a mobile, totally enclosed solvent extraction treatment facility for the removal of organic contaminated media is greater by a closed loop, counter current process that recycles all solvents. The solvents used are selected for the individual site dependant upon the contaminants, such as PCB's, oil, etc. and the soil conditions. A mixture of up to fourteen non-toxic solvents can be used for complicated sites. The full scale unit has been used to treat one superfund site, the Traband Site in Tulsa, Oklahoma, and is currently treating another superfund site, the Pinette's Salvage Yard Site in Washburn, Maine. The full scale Soil Restoration Unit has also been used at a non-superfund site, as part of a TSCA Research and Development permit. The results from these sites will be discussed in brief herein, and in more detail in the full paper

Insight into the Local Solvent Environment of Biologically Relevant Iron-nitroysl Systems through Two-Dimensional Infrared Spectroscopy

Science.gov (United States)

Brookes, Jennifer Faith

Iron-nitrosyl systems, particularly in the form of heme proteins, with their iron metal active sites play an important role in biological systems. Heme proteins act as storage, transporters, and receptors for nitric oxide (NO), a signaling molecule that is important in immune, nervous, and cardiovascular systems of mammals. By better understanding the local environment of the active site of NO binding heme proteins we can gain insight into disease in which the NO pathways have been implicated. This is an important step to being able to develop pharmaceuticals targeting NO pathways in humans. Sodium nitroprusside ((SNP, Na2[Fe(CN)5is NO]·2H 2O) investigated as a model system for the active site of nitric oxide binding heme proteins. Using two-dimensional infrared spectroscopy (2D IR) to obtain dephasing dynamics of the nitrosyl stretch (nuNO) in a series of solvents we are able to better understand the local environment of the more complicated metalloproteins. Rigorous line shape analysis is performed by using nonlinear response theory to simulate 2D IR spectra which are then fit to experimental data in an iterative process to extract frequency-frequency correlation functions (FFCFs). The time scales obtained are then correlated to empirical solvent polarity parameters. The analysis of the 2D IR lineshapes reveal that the spectral diffusion timescale of the nuNO in SNP varies from 0.8 -- 4 ps and is negatively correlated with the empirical solvent polarity scales. We continue to investigate NO binding of metalloproteins through 2D IR experiments on nitrophorin 4 (NP4). NP4 is a pH-sensitive NO transporter protein present in the salivary gland of the blood sucking insect Rhodius prolixus which undergoes a pH sensitive structural change between a closed and open conformation allowing for the storage and delivery of NO. The two structures are observed spectroscopically as two distinct pH-dependent nu NO frequencies at ~1904 and ~1917 cm-1. We obtain FFCFs by globally

Time-dependent recovery of in vivo binding sites after drug dosing: A method for radiotracer evaluation

International Nuclear Information System (INIS)

Kilbourn, Michael R.

1997-01-01

The recovery of in vivo binding sites for (±)-α-[ 11 C]methoxytetrabenazine, a radioligand for the monoamine vesicular transporter (VMAT2), was determined in mouse brain at various times following a pharmacological dose of tetrabenazine. Concentrations of in vivo radioligand binding sites progressively increased and had reached control values by 8.5 h, and this recovery was consistent with the pharmacokinetics of the competing drug tetrabenazine and its active metabolite, dihydrotetrabenazine. This study demonstrates a simple experimental protocol of using a single dose of a reversible competing drug and time-dependent measurements of in vivo binding of a radioligand. This protocol is suitable for testing the sensitivity of an in vivo radiotracer for measurement of varying concentrations of in vivo binding sites

Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA.

Science.gov (United States)

Mori, Tetsuya; Saveliev, Sergei V; Xu, Yao; Stafford, Walter F; Cox, Michael M; Inman, Ross B; Johnson, Carl H

2002-12-24

KaiC from Synechococcus elongatus PCC 7942 (KaiC) is an essential circadian clock protein in cyanobacteria. Previous sequence analyses suggested its inclusion in the RecADnaB superfamily. A characteristic of the proteins of this superfamily is that they form homohexameric complexes that bind DNA. We show here that KaiC also forms ring complexes with a central pore that can be visualized by electron microscopy. A combination of analytical ultracentrifugation and chromatographic analyses demonstrates that these complexes are hexameric. The association of KaiC molecules into hexamers depends on the presence of ATP. The KaiC sequence does not include the obvious DNA-binding motifs found in RecA or DnaB. Nevertheless, KaiC binds forked DNA substrates. These data support the inclusion of KaiC into the RecADnaB superfamily and have important implications for enzymatic activity of KaiC in the circadian clock mechanism that regulates global changes in gene expression patterns.

Dependence of the surface roughness of MAPLE-deposited films on the solvent parameters

Science.gov (United States)

Caricato, A. P.; Leggieri, G.; Martino, M.; Vantaggiato, A.; Valerini, D.; Cretì, A.; Lomascolo, M.; Manera, M. G.; Rella, R.; Anni, M.

2010-12-01

Matrix-assisted pulsed laser evaporation (MAPLE) was used to deposit layers of poly(9,9-dioctylfluorene) (PFO) to study the relation between the solvent properties (laser light absorption, boiling temperature and solubility parameters) and the morphology of the deposited films. To this end, the polymer was diluted (0.5 wt%) in tetrahydrofuran—THF, toluene and toluene/hexane mixtures. The thickness of the films was equal to 70±20 nm. The morphology and uniformity of the films was investigated by Atomic Force Microscopy and by the photoluminescence emission properties of the polymer films, respectively. It is shown that, although the solubility parameters of the solvents are important in controlling the film roughness and morphology, the optical absorption properties and boiling temperature play a very important role, too. In fact, for matrices characterized by the same total solubility parameter, lower roughness values are obtained for films prepared using solvents with lower penetration depth of the laser radiation and higher boiling temperatures.

Pressure-dependent shallow donor binding energy in InGaN/GaN square QWWs

International Nuclear Information System (INIS)

Ghazi, Haddou El; Jorio, Anouar; Zorkani, Izeddine

2013-01-01

Using a variational approach, we perform a theoretical study of hydrostatic pressure effect on the ground-state of axial hydrogenic shallow-donor impurity binding energy in InGaN/GaN square quantum well wire (SQWWs) as a function of the side length within the effective-mass scheme and finite potential barrier. The pressure dependence of wire length, effective mass, dielectric constant and potential barrier are taken into account. Numerical results show that: (i) the binding energy is strongly affected by the wire length and the external applied pressure and (ii) its maximum moves to the narrow wire in particular for height pressure.

Solvent selection methodology for pharmaceutical processes: Solvent swap

DEFF Research Database (Denmark)

Papadakis, Emmanouil; Kumar Tula, Anjan; Gani, Rafiqul

2016-01-01

A method for the selection of appropriate solvents for the solvent swap task in pharmaceutical processes has been developed. This solvent swap method is based on the solvent selection method of Gani et al. (2006) and considers additional selection criteria such as boiling point difference...... in pharmaceutical processes as well as new solvent swap alternatives. The method takes into account process considerations such as batch distillation and crystallization to achieve the swap task. Rigorous model based simulations of the swap operation are performed to evaluate and compare the performance...

Solvents effect on n→π*and π→π* transition of 9- fluorenone

African Journals Online (AJOL)

STORAGESEVER

2008-08-04

Aug 4, 2008 ... tation to bind with the excited state charge distribution. Blue shift will therefore ... of fluorenone by oxime formation test on the spectra. The disappearance of ... ties and the oscillator strength of 9-fluorenone in various solvents.

The Potato Nucleotide-binding Leucine-rich Repeat (NLR) Immune Receptor Rx1 Is a Pathogen-dependent DNA-deforming Protein.

Science.gov (United States)

Fenyk, Stepan; Townsend, Philip D; Dixon, Christopher H; Spies, Gerhard B; de San Eustaquio Campillo, Alba; Slootweg, Erik J; Westerhof, Lotte B; Gawehns, Fleur K K; Knight, Marc R; Sharples, Gary J; Goverse, Aska; Pålsson, Lars-Olof; Takken, Frank L W; Cann, Martin J

2015-10-09

Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable cells to respond to pathogen attack. Several NLRs act in the nucleus; however, conserved nuclear targets that support their role in immunity are unknown. Previously, we noted a structural homology between the nucleotide-binding domain of NLRs and DNA replication origin-binding Cdc6/Orc1 proteins. Here we show that the NB-ARC (nucleotide-binding, Apaf-1, R-proteins, and CED-4) domain of the Rx1 NLR of potato binds nucleic acids. Rx1 induces ATP-dependent bending and melting of DNA in vitro, dependent upon a functional P-loop. In situ full-length Rx1 binds nuclear DNA following activation by its cognate pathogen-derived effector protein, the coat protein of potato virus X. In line with its obligatory nucleocytoplasmic distribution, DNA binding was only observed when Rx1 was allowed to freely translocate between both compartments and was activated in the cytoplasm. Immune activation induced by an unrelated NLR-effector pair did not trigger an Rx1-DNA interaction. DNA binding is therefore not merely a consequence of immune activation. These data establish a role for DNA distortion in Rx1 immune signaling and define DNA as a molecular target of an activated NLR. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

On the Evaporation Kinetics of [60] Fullerene in Aromatic Organic Solvents

KAUST Repository

Amer, Maher S.; Wang, Wenhu; Kollins, Kaitlin N; Altalebi, Hasanain; Schwingenschlö gl, Udo

2018-01-01

We investigate the effect of C60 fullerene nanospheres on the evaporation kinetics of a number of aromatic solvents with different levels of molecular association, namely, benzene, toluene, and chlorobenzene. The dependence of the evaporation rate on the fullerene concentration is not monotonic but rather exhibits maxima and minima. The results strongly support the notion of molecular structuring within the liquid solvent controlled by the nature of fullerene/solvent interaction and the level of molecular association within the solvent itself.

On the Evaporation Kinetics of [60] Fullerene in Aromatic Organic Solvents

KAUST Repository

Amer, Maher S.

2018-04-03

We investigate the effect of C60 fullerene nanospheres on the evaporation kinetics of a number of aromatic solvents with different levels of molecular association, namely, benzene, toluene, and chlorobenzene. The dependence of the evaporation rate on the fullerene concentration is not monotonic but rather exhibits maxima and minima. The results strongly support the notion of molecular structuring within the liquid solvent controlled by the nature of fullerene/solvent interaction and the level of molecular association within the solvent itself.

Kinetics and thermodynamics of small molecule binding to pincer-PCP rhodium(I) complexes

KAUST Repository

Doherty, Mark D.

2013-04-15

The kinetics and thermodynamics of the binding of several small molecules, L (L = N2, H2, D2, and C2H 4), to the coordinatively unsaturated pincer-PCP rhodium(I) complexes Rh[tBu2PCH2(C6H3)CH 2PtBu2] (1) and Rh[tBu 2P(CH2)2(CH)(CH2)2P tBu2] (2) in organic solvents (n-heptane, toluene, THF, and cyclohexane-d12) have been investigated by a combination of kinetic flash photolysis methods, NMR equilibrium studies, and density functional theory (DFT) calculations. Using various gas mixtures and monitoring by NMR until equilibrium was established, the relative free energies of binding of N2, H2, and C2H4 in cyclohexane-d12 were found to increase in the order C 2H4 < N2 < H2. Time-resolved infrared (TRIR) and UV-vis transient absorption spectroscopy revealed that 355 nm excitation of 1-L and 2-L results in the photoejection of ligand L. The subsequent mechanism of binding of L to 1 and 2 to regenerate 1-L and 2-L is determined by the structure of the PCP ligand framework and the nature of the solvent. In both cases, the primary transient is a long-lived, unsolvated species (τ = 50-800 ns, depending on L and its concentration in solution). For 2, this so-called less-reactive form (LRF) is in equilibrium with a more-reactive form (MRF), which reacts with L at diffusion-controlled rates to regenerate 2-L. These two intermediates are proposed to be different conformers of the three-coordinate (PCP)Rh fragment. For 1, a similar mechanism is proposed to occur, but the LRF to MRF step is irreversible. In addition, a parallel reaction pathway was observed that involves the direct reaction of the LRF of 1 with L, with second-order rate constants that vary by almost 3 orders of magnitude, depending on the nature of L (in n-heptane, k = 6.7 × 10 5 M-1 s-1 for L = C2H4; 4.0 × 106 M-1 s-1 for L = N2; 5.5 × 108 M-1 s-1 for L = H2). Experiments in the more coordinating solvent, THF, revealed the binding of THF to 1 to generate 1-THF, and its subsequent reaction with L, as a

Kinetics and thermodynamics of small molecule binding to pincer-PCP rhodium(I) complexes

KAUST Repository

Doherty, Mark D.; Grills, David C.; Huang, Kuo-Wei; Muckerman, James T.; Polyansky, Dmitry E.; Van Eldik, Rudi V.; Fujita, Etsuko

2013-01-01

The kinetics and thermodynamics of the binding of several small molecules, L (L = N2, H2, D2, and C2H 4), to the coordinatively unsaturated pincer-PCP rhodium(I) complexes Rh[tBu2PCH2(C6H3)CH 2PtBu2] (1) and Rh[tBu 2P(CH2)2(CH)(CH2)2P tBu2] (2) in organic solvents (n-heptane, toluene, THF, and cyclohexane-d12) have been investigated by a combination of kinetic flash photolysis methods, NMR equilibrium studies, and density functional theory (DFT) calculations. Using various gas mixtures and monitoring by NMR until equilibrium was established, the relative free energies of binding of N2, H2, and C2H4 in cyclohexane-d12 were found to increase in the order C 2H4 < N2 < H2. Time-resolved infrared (TRIR) and UV-vis transient absorption spectroscopy revealed that 355 nm excitation of 1-L and 2-L results in the photoejection of ligand L. The subsequent mechanism of binding of L to 1 and 2 to regenerate 1-L and 2-L is determined by the structure of the PCP ligand framework and the nature of the solvent. In both cases, the primary transient is a long-lived, unsolvated species (τ = 50-800 ns, depending on L and its concentration in solution). For 2, this so-called less-reactive form (LRF) is in equilibrium with a more-reactive form (MRF), which reacts with L at diffusion-controlled rates to regenerate 2-L. These two intermediates are proposed to be different conformers of the three-coordinate (PCP)Rh fragment. For 1, a similar mechanism is proposed to occur, but the LRF to MRF step is irreversible. In addition, a parallel reaction pathway was observed that involves the direct reaction of the LRF of 1 with L, with second-order rate constants that vary by almost 3 orders of magnitude, depending on the nature of L (in n-heptane, k = 6.7 × 10 5 M-1 s-1 for L = C2H4; 4.0 × 106 M-1 s-1 for L = N2; 5.5 × 108 M-1 s-1 for L = H2). Experiments in the more coordinating solvent, THF, revealed the binding of THF to 1 to generate 1-THF, and its subsequent reaction with L, as a

Phospho-dependent binding of the clathrin AP2 adaptor complex to GABAA receptors regulates the efficacy of inhibitory synaptic transmission.

Science.gov (United States)

Kittler, Josef T; Chen, Guojun; Honing, Stephan; Bogdanov, Yury; McAinsh, Kristina; Arancibia-Carcamo, I Lorena; Jovanovic, Jasmina N; Pangalos, Menelas N; Haucke, Volker; Yan, Zhen; Moss, Stephen J

2005-10-11

The efficacy of synaptic inhibition depends on the number of gamma-aminobutyric acid type A receptors (GABA(A)Rs) expressed on the cell surface of neurons. The clathrin adaptor protein 2 (AP2) complex is a critical regulator of GABA(A)R endocytosis and, hence, surface receptor number. Here, we identify a previously uncharacterized atypical AP2 binding motif conserved within the intracellular domains of all GABA(A)R beta subunit isoforms. This AP2 binding motif (KTHLRRRSSQLK in the beta3 subunit) incorporates the major sites of serine phosphorylation within receptor beta subunits, and phosphorylation within this site inhibits AP2 binding. Furthermore, by using surface plasmon resonance, we establish that a peptide (pepbeta3) corresponding to the AP2 binding motif in the GABA(A)R beta3 subunit binds to AP2 with high affinity only when dephosphorylated. Moreover, the pepbeta3 peptide, but not its phosphorylated equivalent (pepbeta3-phos), enhanced the amplitude of miniature inhibitory synaptic current and whole cell GABA(A)R current. These effects of pepbeta3 on GABA(A)R current were occluded by inhibitors of dynamin-dependent endocytosis supporting an action of pepbeta3 on GABA(A)R endocytosis. Therefore phospho-dependent regulation of AP2 binding to GABA(A)Rs provides a mechanism to specify receptor cell surface number and the efficacy of inhibitory synaptic transmission.

Thermodynamics of 4’-bromomethyl-2-cyanobiphenyl in different solvents

International Nuclear Information System (INIS)

Yang, Jingxiang; Wu, Hong; Wang, Yongli; Luan, Qinghua; Zhang, Jie; Wang, Guan; Hao, Hongxun

2015-01-01

Highlights: • The melting properties of OTBNBr were investigated. • The solubility of OTBNBr in eight selected organic solvents has been determined. • The interaction of solvents molecules plays a dominated role in the dissolving behavior. • The experimental solubility data in pure solvents were well correlated by four models. • The activity coefficient and temperature dependence of van’t Hoff enthalpy were investigated. - Abstract: The melting properties and the heat capacity of the solid state and the melt state 4’-bromomethyl-2-cyanobiphenyl (OTBNBr) were determined. The enthalpy, entropy and Gibbs free energy of fusion were also calculated. The solubility of OTBNBr in eight organic solvents was experimentally measured at temperatures from (283.15 to 323.15) K by using a static method. The reasons for the differences of the solubility of OTBNBr in various solvents are discussed by using the intermolecular interaction. Furthermore, the experimental solubility values were well correlated by the modified Apelblat equation, the λh equation, the Wilson model and the van’t Hoff equation. Finally, the temperature dependence of the activity coefficient and the van’t Hoff enthalpy in the tested solutions was investigated and is discussed

Effect of solvent polarity and temperature on the spectral and thermodynamic properties of exciplexes of 1-cyanonaphthalene with hexamethylbenzene in organic solvents

International Nuclear Information System (INIS)

Asim, Sadia; Mansha, Asim; Grampp, Günter; Landgraf, Stephan; Zahid, Muhammad; Bhatti, Ijaz Ahmad

2014-01-01

Study of the effect of solvent polarity and temperature is done on the exciplex emission spectra of 1-cyanonaphthalene with hexamethylbenzene. Exciplex system is studied in the range of partially polar solvents and in solvent mixture of propyl acetate and butyronitrile. The unique feature of this solvent mixture is that only the solvent polarity changes (6.0≤ε s ≤24.7) with the change in the mole fraction of solvents whereas the solvent viscosity and refractive index remains unaffected. Thermodynamic properties are calculated according to the models developed by Weller and Kuzmin. Fluorescence lifetimes for both the fluorophore as well as the exciplex are evaluated in all used solvents. Exciplex energetics as a function of solvent polarity and temperature are also discussed. Kuzmin model of self-consistent polarization is used for the explanation of the exciplex emission spectra. The effects of solvent polarity and temperature on energy of zero–zero transitions (hv 0 / ), Huang–Rhys factor (S), Gauss broadening of vibronic level (σ) and the dominant high-frequency vibration (hν ν ) are investigated. The strong dependence of exciplex stability and energetics upon the solvent polarity and temperature are observed. Full charge transfer exciplexes were observed in solvents of all polarities and stronger exciplex with large emission intensities were found in solvents of low polarities but with the increase in solvent polarity the exciplex becomes weak and they dissociate fastly into radical ion pairs. The kinetic model of Kuzmin was observed to reduce into the Weller kinetic model for this exciplex system with ∆G ET = −0.22 eV and the spectral shift, h∆ν>0.2 eV. - Highlights: • Exciplex formed as a result of mixing of charge transfer and locally excited states. • Effect of solvents polarity and temperature on the exciplex stability and thermodynamics. • Solvent polarity will decide the formation of contact radical ion pair or solvent separated

Influences of surface and solvent on retention of HEMA/mixture components after evaporation.

Science.gov (United States)

Garcia, Fernanda C P; Wang, Linda; Pereira, Lúcia C G; de Andrade e Silva, Safira M; Júnior, Luiz M; Carrilho, Marcela Rocha de Oliveira

2010-01-01

This study examined the retention of solvents within experimental HEMA/solvent primers after two conditions for solvent evaporation: from a free surface or from dentine surface. Experimental primers were prepared by mixing 35% HEMA with 65% water, methanol, ethanol or acetone (v/v). Aliquots of each primer (50 microl) were placed on glass wells or they were applied to the surface of acid-etched dentine cubes (2mm x 2mm x 2mm) (n=5). For both conditions (i.e. from free surface or dentine cubes), change in primers mass due to solvent evaporation was gravimetrically measured for 10min at 51% RH and 21 degrees C. The rate of solvent evaporation was calculated as a function of loss of primers mass (%) over time. Data were analysed by two-way ANOVA and Student-Newman-Keuls (pevaporation rate (%/min) depending on the solvent present in the primer and the condition for evaporation (from free surface or dentine cubes) (pevaporation for HEMA/acetone primer was almost 2- to 10-times higher than for HEMA/water primer depending whether evaporation occurred, respectively, from a free surface or dentine cubes. The rate of solvent evaporation varied with time, being in general highest at the earliest periods. The rate of solvent evaporation and its retention into HEMA/solvent primers was influenced by the type of the solvent and condition allowed for their evaporation.

Chiral halogenated Schiff base compounds: green synthesis, anticancer activity and DNA-binding study

Science.gov (United States)

Ariyaeifar, Mahnaz; Amiri Rudbari, Hadi; Sahihi, Mehdi; Kazemi, Zahra; Kajani, Abolghasem Abbasi; Zali-Boeini, Hassan; Kordestani, Nazanin; Bruno, Giuseppe; Gharaghani, Sajjad

2018-06-01

Eight enantiomerically pure halogenated Schiff base compounds were synthesized by reaction of halogenated salicylaldehydes with 3-Amino-1,2-propanediol (R or S) in water as green solvent at ambient temperature. All compounds were characterized by elemental analyses, NMR (1H and 13C), circular dichroism (CD) and FT-IR spectroscopy. FS-DNA binding studies of these compounds carried out by fluorescence quenching and UV-vis spectroscopy. The obtained results revealed that the ligands bind to DNA as: (Rsbnd ClBr) > (Rsbnd Cl2) > (Rsbnd Br2) > (Rsbnd I2) and (Ssbnd ClBr) > (Ssbnd Cl2) > (Ssbnd Br2) > (Ssbnd I2), indicating the effect of halogen on binding constant. In addition, DNA-binding constant of the Ssbnd and R-enantiomers are different from each other. The ligands can form halogen bonds with DNA that were confirmed by molecular docking. This method was also measured the bond distances and bond angles. The study of obtained data can have concluded that binding affinity of the ligands to DNA depends on strength of halogen bonds. The potential anticancer activity of ligands were also evaluated on MCF-7 and HeLa cancer cell lines by using MTT assay. The results showed that the anticancer activity and FS-DNA interaction is significantly dependent on the stereoisomers of Schiff base compounds as R-enantiomers displayed significantly higher activity than S-enantiomers. The molecular docking was also used to illustrate the specific DNA-binding of synthesized compounds and groove binding mode of DNA interaction was proposed for them. In addition, molecular docking results indicated that there are three types of bonds (Hsbnd and X-bond and hX-bond) between synthesized compounds and base pairs of DNA.

Solvent extraction

Energy Technology Data Exchange (ETDEWEB)

Coombs, D.M.; Latimer, E.G.

1988-01-05

It is an object of this invention to provide for the demetallization and general upgrading of heavy oil via a solvent extracton process, and to improve the efficiency of solvent extraction operations. The yield and demetallization of product oil form heavy high-metal content oil is maximized by solvent extractions which employ either or all of the following techniques: premixing of a minor amount of the solvent with feed and using countercurrent flow for the remaining solvent; use of certain solvent/free ratios; use of segmental baffle tray extraction column internals and the proper extraction column residence time. The solvent premix/countercurrent flow feature of the invention substantially improves extractions where temperatures and pressures above the critical point of the solvent are used. By using this technique, a greater yield of extract oil can be obtained at the same metals content or a lower metals-containing extract oil product can be obtained at the same yield. Furthermore, the premixing of part of the solvent with the feed before countercurrent extraction gives high extract oil yields and high quality demetallization. The solvent/feed ratio features of the invention substanially lower the captial and operating costs for such processes while not suffering a loss in selectivity for metals rejection. The column internals and rsidence time features of the invention further improve the extractor metals rejection at a constant yield or allow for an increase in extract oil yield at a constant extract oil metals content. 13 figs., 3 tabs.

ATP binding cassette G1-dependent cholesterol efflux during inflammation.

Science.gov (United States)

de Beer, Maria C; Ji, Ailing; Jahangiri, Anisa; Vaughan, Ashley M; de Beer, Frederick C; van der Westhuyzen, Deneys R; Webb, Nancy R

2011-02-01

ATP binding cassette transporter G1 (ABCG1) mediates the transport of cellular cholesterol to HDL, and it plays a key role in maintaining macrophage cholesterol homeostasis. During inflammation, HDL undergoes substantial remodeling, acquiring lipid changes and serum amyloid A (SAA) as a major apolipoprotein. In the current study, we investigated whether remodeling of HDL that occurs during acute inflammation impacts ABCG1-dependent efflux. Our data indicate that lipid free SAA acts similarly to apolipoprotein A-I (apoA-I) in mediating sequential efflux from ABCA1 and ABCG1. Compared with normal mouse HDL, acute phase (AP) mouse HDL containing SAA exhibited a modest but significant 17% increase in ABCG1-dependent efflux. Interestingly, AP HDL isolated from mice lacking SAA (SAAKO mice) was even more effective in promoting ABCG1 efflux. Hydrolysis with Group IIA secretory phospholipase A(2) (sPLA(2)-IIA) significantly reduced the ability of AP HDL from SAAKO mice to serve as a substrate for ABCG1-mediated cholesterol transfer, indicating that phospholipid (PL) enrichment, and not the presence of SAA, is responsible for alterations in efflux. AP human HDL, which is not PL-enriched, was somewhat less effective in mediating ABCG1-dependent efflux compared with normal human HDL. Our data indicate that inflammatory remodeling of HDL impacts ABCG1-dependent efflux independent of SAA.

Solvent induced supramolecular anisotropy in molecular gels

Energy Technology Data Exchange (ETDEWEB)

Rogers, Michael A., E-mail: mroger09@uoguelph.ca [Department of Food Science, University of Guelph, Guelph, Ontario, N3C3X9 (Canada); Corradini, Maria G. [Department of Food Science, University of Massachusetts Amherst, Amherst, MA, 01003 (United States); Emge, Thomas [Department of Chemistry and Biochemistry, Rutgers University, New Brunswick, NJ, 08901 (United States)

2017-06-15

Herein is the first report of solvent induced anisotropy in 12-hydroxystearic acid self-assembled fibrillar networks. Increasing the chain length of polar solvent, such as nitriles and ketones, tailored the anisotropy of the fibrillar aggregates. 12HSA molecular gels, comprised of alkanes, exhibited an isotropic fibrillar network irrespective of the alkane chain length. In polar solvents, anisotropy, observed using 2D powder x-ray diffraction profiles, is correlated to a fibrillar supramolecular morphologies in long chain nitriles and ketones while sphereulitic crystals are correlated to x-ray diffraction patterns with an isotropic scatter intensity in short chain ketones and nitriles. These changes directly modify the final physical properties of the gels. - Highlights: • 12-HSA self-assembles into crystalline supramolecular morphologies depending on the solvent. • Alkanes, short chain nitriles and ketones led to 12-HSA displaying supramolecular isotropy. • In long chain nitriles and ketones, 12-HSA displays supramolecular anisotropy.

Solvent induced supramolecular anisotropy in molecular gels

International Nuclear Information System (INIS)

Rogers, Michael A.; Corradini, Maria G.; Emge, Thomas

2017-01-01

Herein is the first report of solvent induced anisotropy in 12-hydroxystearic acid self-assembled fibrillar networks. Increasing the chain length of polar solvent, such as nitriles and ketones, tailored the anisotropy of the fibrillar aggregates. 12HSA molecular gels, comprised of alkanes, exhibited an isotropic fibrillar network irrespective of the alkane chain length. In polar solvents, anisotropy, observed using 2D powder x-ray diffraction profiles, is correlated to a fibrillar supramolecular morphologies in long chain nitriles and ketones while sphereulitic crystals are correlated to x-ray diffraction patterns with an isotropic scatter intensity in short chain ketones and nitriles. These changes directly modify the final physical properties of the gels. - Highlights: • 12-HSA self-assembles into crystalline supramolecular morphologies depending on the solvent. • Alkanes, short chain nitriles and ketones led to 12-HSA displaying supramolecular isotropy. • In long chain nitriles and ketones, 12-HSA displays supramolecular anisotropy.

A new combined computational and NMR-spectroscopical strategy for the identification of additional conformational constraints of the bound ligand in an aprotic solvent

NARCIS (Netherlands)

Vliegenthart, J.F.G.; Siebert, H.-C; André, S.; Asensio, J.l.; Cañada, F.J.; Dong, X.; Espinosa, M.; Frank, M.

2000-01-01

This study documents the feasibility of switching to an aprotic medium in sugar receptor research. The solvent change offers additional insights into mechanistic details of receptor-carbohydrate ligand interactions. If a receptor retained binding capacity in an aprotic medium, solvent-exchangeable

A hierarchy of functionally important relaxations within myoglobin based on solvent effects, mutations and kinetic model.

Science.gov (United States)

Dantsker, David; Samuni, Uri; Friedman, Joel M; Agmon, Noam

2005-06-01

Geminate CO rebinding in myoglobin is studied for two viscous solvents, trehalose and sol-gel (bathed in 100% glycerol) at several temperatures. Mutations in key distal hemepocket residues are used to eliminate or enhance specific relaxation modes. The time-resolved data are analyzed with a modified Agmon-Hopfield model which is capable of providing excellent fits in cases where a single relaxation mode is dominant. Using this approach, we determine the relaxation rate constants of specific functionally important modes, obtaining also their Arrhenius activation energies. We find a hierarchy of distal pocket modes controlling the rebinding kinetics. The "heme access mode" (HAM) is responsible for the major slow-down in rebinding. It is a solvent-coupled cooperative mode which restricts ligand return from the xenon cavities. Bulky side-chains, like those His64 and Trp29 (in the L29W mutant), operate like overdamped pendulums which move over and block the binding site. They may be either unslaved (His64) or moderately slaved (Trp29) to the solvent. Small side-chain relaxations, most notably of leucines, are revealed in some mutants (V68L, V68A). They are conjectured to facilitate inter-cavity ligand motion. When all relaxations are arrested (H64L in trehalose), we observe pure inhomogeneous kinetics with no temperature dependence, suggesting that proximal relaxation is not a factor on the investigated timescale.

Solvent Extraction and Characterization of Neutral Lipids in Oocystis sp.

Directory of Open Access Journals (Sweden)

Renil eAnthony

2015-01-01

Full Text Available Microalgae are a favorable feedstock for bioproducts and biofuels due to their high oil content, fast growth rates and low resource demands. Solvent lipid extraction efficiency from microalgae is dependent on algal strain and the extraction solvent. Four non-polar extraction solvents were evaluated for the recovery of neutral cellular lipids from microalgae Oocystis sp. (UTEX LB2396. Methylene chloride, hexane, diethyl ether, and cyclohexane were selected as the extraction solvents. All solvent extracts contained hexadecanoic acid, linoleic acid and linolenic acid; accounting for 70% of total lipid content with a proportional wt% composition of the three fatty acids, except for the hexane extracts that showed only hexadecanoic acid and linoleic acid. While not statistically differentiated, methylene chloride proved to be the most effective solvent for Oocystis sp. among the four solvents tested with a total average neutral lipid recovery of 0.25% of dry weight followed by diethyl ether (0.18%, cyclohexane (0.14% and hexane (0.11%. This research presents a simple methodology to optimize the selection of lipid specific extraction solvents for the microalgal strain selected.

Carbohydrate-dependent binding of langerin to SodC, a cell wall glycoprotein of Mycobacterium leprae.

Science.gov (United States)

Kim, Hee Jin; Brennan, Patrick J; Heaslip, Darragh; Udey, Mark C; Modlin, Robert L; Belisle, John T

2015-02-01

Langerhans cells participate in the immune response in leprosy by their ability to activate T cells that recognize the pathogen, Mycobacterium leprae, in a langerin-dependent manner. We hypothesized that langerin, the distinguishing C-type lectin of Langerhans cells, would recognize the highly mannosylated structures in pathogenic Mycobacterium spp. The coding region for the extracellular and neck domain of human langerin was cloned and expressed to produce a recombinant active trimeric form of human langerin (r-langerin). Binding assays performed in microtiter plates, by two-dimensional (2D) Western blotting, and by surface plasmon resonance demonstrated that r-langerin possessed carbohydrate-dependent affinity to glycoproteins in the cell wall of M. leprae. This lectin, however, yielded less binding to mannose-capped lipoarabinomannan (ManLAM) and even lower levels of binding to phosphatidylinositol mannosides. However, the superoxide dismutase C (SodC) protein of the M. leprae cell wall was identified as a langerin-reactive ligand. Tandem mass spectrometry verified the glycosylation of a recombinant form of M. leprae SodC (rSodC) produced in Mycobacterium smegmatis. Analysis of r-langerin affinity by surface plasmon resonance revealed a carbohydrate-dependent affinity of rSodC (equilibrium dissociation constant [KD] = 0.862 μM) that was 20-fold greater than for M. leprae ManLAM (KD = 18.69 μM). These data strongly suggest that a subset of the presumptively mannosylated M. leprae glycoproteins act as ligands for langerin and may facilitate the interaction of M. leprae with Langerhans cells. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Distribution of multi-component solvents in solvent vapor extraction chamber

Energy Technology Data Exchange (ETDEWEB)

Das, S. [Society of Petroleum Engineers, Richardson, TX (United States)]|[Marathon Oil Corp., Houston, TX (United States)

2008-10-15

Vapex process performance is sensitive to operating pressures, temperatures and the types of solvent used. The hydrocarbon solvents used in Vapex processes typically have between 5 and 10 per cent hydrocarbon impurities, and the accumulation of dense phases inside the vapor chamber reduces gravity drainage potential. This study investigated the partitioning of solvent compounds inside the vapor chamber during in situ Vapex processes.The aim of the study was to examine how the different components of the mixed solvent partitioned inside the extracted chamber during the oil and vapor phase. A 2-D homogenous reservoir model was used to simulate the Vapex process with a solvent mixture comprised of propane and methane at various percentages. The effect of injecting a hot solvent vapor was also investigated. The study showed that injected methane accumulated at both the top and the extraction interface. Accumulations near the top had a positive impact on solvent confinement in thin reservoirs. Diffusion of the solvent component was controlled by gas phase molecular diffusion, and was much faster than the diffusion of solvent molecules in the liquid phase. The use of hot solvent mixtures slowed the extraction process due to lower solvent solubility in the oil phase. It was concluded that the negative impact on viscosity reduction by dilution was not compensated by rises in temperature. 6 refs., 11 figs.

A Central Nervous System-Dependent Intron-Embedded Gene Encodes a Novel Murine Fyn Binding Protein.

Science.gov (United States)

Ben Khalaf, Noureddine; Taha, Safa; Bakhiet, Moiz; Fathallah, M Dahmani

2016-01-01

The interplay between the nervous and immune systems is gradually being unraveled. We previously reported in the mouse the novel soluble immune system factor ISRAA, whose activation in the spleen is central nervous system-dependent. We also showed that ISRAA plays a role in modulating anti-infection immunity. Herein, we report the genomic description of the israa locus, along with some insights into the structure-function relationship of the protein. Our findings revealed that israa is nested within intron 6 of the mouse zmiz1 gene. Protein sequence analysis revealed a typical SH2 binding motif (Y102TEV), with Fyn being the most likely binding partner. Docking simulation showed a favorable conformation for the ISRAA-Fyn complex, with a specific binding mode for the binding of the YTEV motif to the SH2 domain. Experimental studies showed that in vitro, recombinant ISRAA is phosphorylated by Fyn at tyrosine 102. Cell transfection and pull-down experiments revealed Fyn as a binding partner of ISRAA in the EL4 mouse T-cell line. Indeed, we demonstrated that ISRAA downregulates T-cell activation and the phosphorylation of an activation tyrosine (Y416) of Src-family kinases in mouse splenocytes. Our observations highlight ISRAA as a novel Fyn binding protein that is likely to be involved in a signaling pathway driven by the nervous system.

A Central Nervous System-Dependent Intron-Embedded Gene Encodes a Novel Murine Fyn Binding Protein.

Directory of Open Access Journals (Sweden)

Noureddine Ben Khalaf

Full Text Available The interplay between the nervous and immune systems is gradually being unraveled. We previously reported in the mouse the novel soluble immune system factor ISRAA, whose activation in the spleen is central nervous system-dependent. We also showed that ISRAA plays a role in modulating anti-infection immunity. Herein, we report the genomic description of the israa locus, along with some insights into the structure-function relationship of the protein. Our findings revealed that israa is nested within intron 6 of the mouse zmiz1 gene. Protein sequence analysis revealed a typical SH2 binding motif (Y102TEV, with Fyn being the most likely binding partner. Docking simulation showed a favorable conformation for the ISRAA-Fyn complex, with a specific binding mode for the binding of the YTEV motif to the SH2 domain. Experimental studies showed that in vitro, recombinant ISRAA is phosphorylated by Fyn at tyrosine 102. Cell transfection and pull-down experiments revealed Fyn as a binding partner of ISRAA in the EL4 mouse T-cell line. Indeed, we demonstrated that ISRAA downregulates T-cell activation and the phosphorylation of an activation tyrosine (Y416 of Src-family kinases in mouse splenocytes. Our observations highlight ISRAA as a novel Fyn binding protein that is likely to be involved in a signaling pathway driven by the nervous system.

Effect of solvent polarity and temperature on the spectral and thermodynamic properties of exciplexes of 1-cyanonaphthalene with hexamethylbenzene in organic solvents

Energy Technology Data Exchange (ETDEWEB)

Asim, Sadia [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad (Pakistan); Mansha, Asim [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Department of Chemistry, Government College University, Faisalabad (Pakistan); Grampp, Günter, E-mail: grampp@tugraz.at [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Landgraf, Stephan [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Zahid, Muhammad [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad (Pakistan); Bhatti, Ijaz Ahmad [Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad (Pakistan)

2014-09-15

Study of the effect of solvent polarity and temperature is done on the exciplex emission spectra of 1-cyanonaphthalene with hexamethylbenzene. Exciplex system is studied in the range of partially polar solvents and in solvent mixture of propyl acetate and butyronitrile. The unique feature of this solvent mixture is that only the solvent polarity changes (6.0≤ε{sub s}≤24.7) with the change in the mole fraction of solvents whereas the solvent viscosity and refractive index remains unaffected. Thermodynamic properties are calculated according to the models developed by Weller and Kuzmin. Fluorescence lifetimes for both the fluorophore as well as the exciplex are evaluated in all used solvents. Exciplex energetics as a function of solvent polarity and temperature are also discussed. Kuzmin model of self-consistent polarization is used for the explanation of the exciplex emission spectra. The effects of solvent polarity and temperature on energy of zero–zero transitions (hv{sub 0}{sup /}), Huang–Rhys factor (S), Gauss broadening of vibronic level (σ) and the dominant high-frequency vibration (hν{sub ν}) are investigated. The strong dependence of exciplex stability and energetics upon the solvent polarity and temperature are observed. Full charge transfer exciplexes were observed in solvents of all polarities and stronger exciplex with large emission intensities were found in solvents of low polarities but with the increase in solvent polarity the exciplex becomes weak and they dissociate fastly into radical ion pairs. The kinetic model of Kuzmin was observed to reduce into the Weller kinetic model for this exciplex system with ∆G{sub ET} = −0.22 eV and the spectral shift, h∆ν>0.2 eV. - Highlights: • Exciplex formed as a result of mixing of charge transfer and locally excited states. • Effect of solvents polarity and temperature on the exciplex stability and thermodynamics. • Solvent polarity will decide the formation of contact radical ion pair

Reverse Non-Equilibrium Molecular Dynamics Demonstrate That Surface Passivation Controls Thermal Transport at Semiconductor-Solvent Interfaces.

Science.gov (United States)

Hannah, Daniel C; Gezelter, J Daniel; Schaller, Richard D; Schatz, George C

2015-06-23

We examine the role played by surface structure and passivation in thermal transport at semiconductor/organic interfaces. Such interfaces dominate thermal transport in semiconductor nanomaterials owing to material dimensions much smaller than the bulk phonon mean free path. Utilizing reverse nonequilibrium molecular dynamics simulations, we calculate the interfacial thermal conductance (G) between a hexane solvent and chemically passivated wurtzite CdSe surfaces. In particular, we examine the dependence of G on the CdSe slab thickness, the particular exposed crystal facet, and the extent of surface passivation. Our results indicate a nonmonotonic dependence of G on ligand-grafting density, with interfaces generally exhibiting higher thermal conductance for increasing surface coverage up to ∼0.08 ligands/Å(2) (75-100% of a monolayer, depending on the particular exposed facet) and decreasing for still higher coverages. By analyzing orientational ordering and solvent penetration into the ligand layer, we show that a balance of competing effects is responsible for this nonmonotonic dependence. Although the various unpassivated CdSe surfaces exhibit similar G values, the crystal structure of an exposed facet nevertheless plays an important role in determining the interfacial thermal conductance of passivated surfaces, as the density of binding sites on a surface determines the ligand-grafting densities that may ultimately be achieved. We demonstrate that surface passivation can increase G relative to a bare surface by roughly 1 order of magnitude and that, for a given extent of passivation, thermal conductance can vary by up to a factor of ∼2 between different surfaces, suggesting that appropriately tailored nanostructures may direct heat flow in an anisotropic fashion for interface-limited thermal transport.

Potential of mean force for ion pairs in non-aqueous solvents. Comparison of polarizable and non-polarizable MD simulations

Science.gov (United States)

Odinokov, A. V.; Leontyev, I. V.; Basilevsky, M. V.; Petrov, N. Ch.

2011-01-01

Potentials of mean force (PMF) are calculated for two model ion pairs in two non-aqueous solvents. Standard non-polarizable molecular dynamics simulation (NPMD) and approximate polarizable simulation (PMD) are implemented and compared as tools for monitoring PMF profiles. For the polar solvent (dimethylsulfoxide, DMSO) the PMF generated in terms of the NPMD reproduces fairly well the refined PMD-PMF profile. For the non-polar solvent (benzene) the conventional NPMD computation proves to be deficient. The validity of the correction found in terms of the approximate PMD approach is verified by its comparison with the result of the explicit PMD computation in benzene. The shapes of the PMF profiles in DMSO and in benzene are quite different. In DMSO, owing to dielectric screening, the PMF presents a flat plot with a shallow minimum positioned in the vicinity of the van der Waals contact of the ion pair. For the benzene case, the observed minimum proves to be unexpectedly deep, which manifests the formation of a tightly-binded contact ion pair. This remarkable effect arises owing to the strong electrostatic interaction that is incompletely screened by a non-polar medium. The PMFs for the binary benzene/DMSO mixtures display intermediate behaviour depending on the DMSO content.

Endogenously generated plasmin at the vascular wall injury site amplifies lysine binding site-dependent plasminogen accumulation in microthrombi.

Directory of Open Access Journals (Sweden)

Tomasz Brzoska

Full Text Available The fibrinolytic system plays a pivotal role in the regulation of hemostasis; however, it remains unclear how and when the system is triggered to induce thrombolysis. Using intra-vital confocal fluorescence microscopy, we investigated the process of plasminogen binding to laser-induced platelet-rich microthrombi generated in the mesenteric vein of transgenic mice expressing green fluorescent protein (GFP. The accumulation of GFP-expressing platelets as well as exogenously infused Alexa Fluor 568-labeled Glu-plasminogen (Glu-plg on the injured vessel wall was assessed by measuring the increase in the corresponding fluorescence intensities. Glu-plg accumulated in a time-dependent manner in the center of the microthrombus, where phosphatidylserine is exposed on platelet surfaces and fibrin formation takes place. The rates of binding of Glu-plg in the presence of ε-aminocaproic acid and carboxypeptidase B, as well as the rates of binding of mini-plasminogen lacking kringle domains 1-4 and lysine binding sites, were significantly lower than that of Glu-plg alone, suggesting that the binding was dependent on lysine binding sites. Furthermore, aprotinin significantly suppressed the accumulation of Glu-plg, suggesting that endogenously generated plasmin activity is a prerequisite for the accumulation. In spite of the endogenous generation of plasmin and accumulation of Glu-plg in the center of microthrombi, the microthrombi did not change in size during the 2-hour observation period. When human tissue plasminogen activator was administered intravenously, Glu-plg further accumulated and the microthrombi were lysed. Glu-plg appeared to accumulate in the center of microthrombi in the early phase of microthrombus formation, and plasmin activity and lysine binding sites were required for this accumulation.

Effect of solvent extraction on Tunisian esparto wax composition

Directory of Open Access Journals (Sweden)

Saâd Inès

2016-08-01

Full Text Available The increase of needs for renewable and vegetable based materials will help to drive the market growth of vegetable waxes. Because of their highly variable composition and physicochemical properties, plant waxes have found numerous applications in the: food, cosmetic, candle, coating, polish etc... The aim of this project is to determine the effect of solvent extraction (petroleum ether and ethanol on Tunisian esparto wax composition. The GC-MS was applied in order to determine the waxes compositions. Then, physicochemical parameters of these two samples of waxes: acid value, saponification value, iodine value and melting point were measured in order to deduct their properties and possible fields of uses. Results showed that esparto wax composition depended on the solvent extraction and that major components of the two samples of waxes were: alkanes, esters of fatty acids and phenols. Furthermore, esparto waxes were characterized by an antioxidant and antibacterial activities but the potential of these activities depended on the solvent of wax extraction.

Solvent Extraction and Characterization of Neutral Lipids in Oocystis sp

Energy Technology Data Exchange (ETDEWEB)

Anthony, Renil [Department of Mechanical Engineering, Ohio University, Athens, OH (United States); Stuart, Ben, E-mail: stuart@ohio.edu [Department of Civil Engineering, Ohio University, Athens, OH (United States)

2015-01-20

Microalgae are a favorable feedstock for bioproducts and biofuels due to their high oil content, fast growth rates, and low resource demands. Solvent lipid extraction efficiency from microalgae is dependent on algal strain and the extraction solvent. Four non-polar extraction solvents were evaluated for the recovery of neutral cellular lipids from microalgae Oocystis sp. (University of Texas at Austin LB2396). Methylene chloride, hexane, diethyl ether, and cyclohexane were selected as the extraction solvents. The lipid extracts were derivatized and analyzed using gas chromatography–mass spectroscopy. All solvent extracts contained hexadecanoic acid, linoleic acid, and linolenic acid; accounting for 70% of total lipid content with a proportional wt% composition of the three fatty acids, except for the hexane extracts that showed only hexadecanoic acid and linoleic acid. While not statistically differentiated, methylene chloride proved to be the most effective solvent for Oocystis sp. among the four solvents tested with a total average neutral lipid recovery of 0.25% of dry weight followed by diethyl ether (0.18%), cyclohexane (0.14%), and hexane (0.11%). This research presents a simple methodology to optimize the selection of lipid specific extraction solvents for the microalgal strain selected.

Solvent Extraction and Characterization of Neutral Lipids in Oocystis sp

International Nuclear Information System (INIS)

Anthony, Renil; Stuart, Ben

2015-01-01

Microalgae are a favorable feedstock for bioproducts and biofuels due to their high oil content, fast growth rates, and low resource demands. Solvent lipid extraction efficiency from microalgae is dependent on algal strain and the extraction solvent. Four non-polar extraction solvents were evaluated for the recovery of neutral cellular lipids from microalgae Oocystis sp. (University of Texas at Austin LB2396). Methylene chloride, hexane, diethyl ether, and cyclohexane were selected as the extraction solvents. The lipid extracts were derivatized and analyzed using gas chromatography–mass spectroscopy. All solvent extracts contained hexadecanoic acid, linoleic acid, and linolenic acid; accounting for 70% of total lipid content with a proportional wt% composition of the three fatty acids, except for the hexane extracts that showed only hexadecanoic acid and linoleic acid. While not statistically differentiated, methylene chloride proved to be the most effective solvent for Oocystis sp. among the four solvents tested with a total average neutral lipid recovery of 0.25% of dry weight followed by diethyl ether (0.18%), cyclohexane (0.14%), and hexane (0.11%). This research presents a simple methodology to optimize the selection of lipid specific extraction solvents for the microalgal strain selected.

Photo-dynamics of roseoflavin and riboflavin in aqueous and organic solvents

International Nuclear Information System (INIS)

Zirak, P.; Penzkofer, A.; Mathes, T.; Hegemann, P.

2009-01-01

Roseoflavin (8-dimethylamino-8-demethyl-D-riboflavin) and riboflavin in aqueous and organic solvents are studied by optical absorption spectroscopy, fluorescence spectroscopy, and fluorescence decay kinetics. Solvent polarity dependent absorption shifts are observed. The fluorescence quantum yields are solvent dependent. For roseoflavin the fluorescence decay shows a bi-exponential dependence (ps to sub-ps time constant, and 100 ps to a few ns time constant). The roseoflavin photo-dynamics is explained in terms of fast intra-molecular charge transfer (diabatic electron transfer) from the dimethylamino electron donor group to the pteridin carbonyl electron acceptor followed by intra-molecular charge recombination. The fast fluorescence component is due to direct locally-excited-state emission, and the slow fluorescence component is due to delayed locally-excited-state emission and charge transfer state emission. The fluorescence decay of riboflavin is mono-exponential. The S 1 -state potential energy surface is determined by vibronic relaxation and solvation dynamics due to excited-state dipole moment changes (adiabatic optical electron transfer).

Photo-dynamics of roseoflavin and riboflavin in aqueous and organic solvents

Science.gov (United States)

Zirak, P.; Penzkofer, A.; Mathes, T.; Hegemann, P.

2009-03-01

Roseoflavin (8-dimethylamino-8-demethyl- D-riboflavin) and riboflavin in aqueous and organic solvents are studied by optical absorption spectroscopy, fluorescence spectroscopy, and fluorescence decay kinetics. Solvent polarity dependent absorption shifts are observed. The fluorescence quantum yields are solvent dependent. For roseoflavin the fluorescence decay shows a bi-exponential dependence (ps to sub-ps time constant, and 100 ps to a few ns time constant). The roseoflavin photo-dynamics is explained in terms of fast intra-molecular charge transfer (diabatic electron transfer) from the dimethylamino electron donor group to the pteridin carbonyl electron acceptor followed by intra-molecular charge recombination. The fast fluorescence component is due to direct locally-excited-state emission, and the slow fluorescence component is due to delayed locally-excited-state emission and charge transfer state emission. The fluorescence decay of riboflavin is mono-exponential. The S 1-state potential energy surface is determined by vibronic relaxation and solvation dynamics due to excited-state dipole moment changes (adiabatic optical electron transfer).

Photo-dynamics of roseoflavin and riboflavin in aqueous and organic solvents

Energy Technology Data Exchange (ETDEWEB)

Zirak, P. [Institut II - Experimentelle und Angewandte Physik, Universitaet Regensburg, Universitaetstrasse 31, D-93053 Regensburg (Germany); Penzkofer, A., E-mail: alfons.penzkofer@physik.uni-regensburg.de [Institut II - Experimentelle und Angewandte Physik, Universitaet Regensburg, Universitaetstrasse 31, D-93053 Regensburg (Germany); Mathes, T.; Hegemann, P. [Institut fuer Biologie/Experimentelle Biophysik, Humboldt Universitaet zu Berlin, Invalidenstrasse 42, D-10115 Berlin (Germany)

2009-03-30

Roseoflavin (8-dimethylamino-8-demethyl-D-riboflavin) and riboflavin in aqueous and organic solvents are studied by optical absorption spectroscopy, fluorescence spectroscopy, and fluorescence decay kinetics. Solvent polarity dependent absorption shifts are observed. The fluorescence quantum yields are solvent dependent. For roseoflavin the fluorescence decay shows a bi-exponential dependence (ps to sub-ps time constant, and 100 ps to a few ns time constant). The roseoflavin photo-dynamics is explained in terms of fast intra-molecular charge transfer (diabatic electron transfer) from the dimethylamino electron donor group to the pteridin carbonyl electron acceptor followed by intra-molecular charge recombination. The fast fluorescence component is due to direct locally-excited-state emission, and the slow fluorescence component is due to delayed locally-excited-state emission and charge transfer state emission. The fluorescence decay of riboflavin is mono-exponential. The S{sub 1}-state potential energy surface is determined by vibronic relaxation and solvation dynamics due to excited-state dipole moment changes (adiabatic optical electron transfer).

Effect of solvent blending on cycling characteristics of lithium

Energy Technology Data Exchange (ETDEWEB)

Morita, Masayuki; Matsuda, Yoshiharu

1987-07-01

The suitability of electrolytes using mixed solvents has been examined for ambient temperature, rechargeable lithium batteries. Sulfolane (S) and dimethylsulfoxide (DMSO) have been used as base solvents because of their high permittivity, and ethers such as 1,2-dimethoxyethane (DME) have been blended as a low viscosity co-solvent. This blending has been found to yield electrolytes with a high conductivity, and maximum values are observed in solutions with 40-90 mol% ether. The cycling characteristics of lithium are also improved by blending the ethers. The coulombic efficiencies on a nickel substrate are greater than or equal to 80% in S-DME/LiPF/sub 6/ and DMSO-DME/LiPF/sub 6/ solutions. The lithium electrode characteristics are markedly dependent on the type of co-solvent ether, as well as on the electrolytic salt. The results of the conductance behaviour and the electrode characteristics are discussed in terms of ionic structure in the mixed solvent and the state of the electrode/electrolyte interphase.

Aerosols released from solvent fire accidents in reprocessing plants

International Nuclear Information System (INIS)

Jordan, S.; Lindner, W.

1985-01-01

Thermodynamic, aerosol characterizing and radiological data of solvent fires in reprocessing plants have been established in experiments. These are the main results: Depending on the ventilation in the containment, kerosene-TBP mixtures burn at a rate up to 120 kg/m 2 h. The aqueous phase of inorganic-organic mixtures might be released during the fire. The gaseous reaction products contain unburnable acidic compounds. Solvents with TBP-nitrate complex shows higher (up to 25%) burning rates than pure solvents (kerosene-TBP). The nitrate complex decomposes violently at about 130 0 C with a release of acid and unburnable gases. Up to 20% of the burned kerosene-TBP solvents are released during the fire in the form of soot particles, phosphoric acid and TBP decomposition products. The particles have an aerodynamic mass median diameter of about 0.5 μm and up to 1.5% of the uranium fixed in the TBP-nitrate complex is released during solvent fires. (orig.)

Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes.

Science.gov (United States)

Moritsugu, Kei; Kidera, Akinori; Smith, Jeremy C

2014-07-24

Protein solvation dynamics has been investigated using atom-dependent Langevin friction coefficients derived directly from molecular dynamics (MD) simulations. To determine the effect of solvation on the atomic friction coefficients, solution and vacuum MD simulations were performed for lysozyme and staphylococcal nuclease and analyzed by Langevin mode analysis. The coefficients thus derived are roughly correlated with the atomic solvent-accessible surface area (ASA), as expected from the fact that friction occurs as the result of collisions with solvent molecules. However, a considerable number of atoms with higher friction coefficients are found inside the core region. Hence, the influence of solvent friction propagates into the protein core. The internal coefficients have large contributions from the low-frequency modes, yielding a simple picture of the surface-to-core long-range damping via solvation governed by collective low-frequency modes. To make use of these findings in implicit-solvent modeling, we compare the all-atom friction results with those obtained using Langevin dynamics (LD) with two empirical representations: the constant-friction and the ASA-dependent (Pastor-Karplus) friction models. The constant-friction model overestimates the core and underestimates the surface damping whereas the ASA-dependent friction model, which damps protein atoms only on the solvent-accessible surface, reproduces well the friction coefficients for both the surface and core regions observed in the explicit-solvent MD simulations. Therefore, in LD simulation, the solvent friction coefficients should be imposed only on the protein surface.

Probing protein surface with a solvent mimetic carbene coupled to detection by mass spectrometry.

Science.gov (United States)

Gómez, Gabriela E; Mundo, Mariana R; Craig, Patricio O; Delfino, José M

2012-01-01

Much knowledge into protein folding, ligand binding, and complex formation can be derived from the examination of the nature and size of the accessible surface area (SASA) of the polypeptide chain, a key parameter in protein science not directly measurable in an experimental fashion. To this end, an ideal chemical approach should aim at exerting solvent mimicry and achieving minimal selectivity to probe the protein surface regardless of its chemical nature. The choice of the photoreagent diazirine to fulfill these goals arises from its size comparable to water and from being a convenient source of the extremely reactive methylene carbene (:CH(2)). The ensuing methylation depends primarily on the solvent accessibility of the polypeptide chain, turning it into a valuable signal to address experimentally the measurement of SASA in proteins. The superb sensitivity and high resolution of modern mass spectrometry techniques allows us to derive a quantitative signal proportional to the extent of modification (EM) of the sample. Thus, diazirine labeling coupled to electrospray mass spectrometry (ESI-MS) detection can shed light on conformational features of the native as well as non-native states, not easily addressable by other methods. Enzymatic fragmentation of the polypeptide chain at the level of small peptides allows us to locate the covalent tag along the amino acid sequence, therefore enabling the construction of a map of solvent accessibility. Moreover, by subsequent MS/MS analysis of peptides, we demonstrate here the feasibility of attaining amino acid resolution in defining the target sites. © American Society for Mass Spectrometry, 2011

Solvent-mediated pathways to gelation and phase separation in suspensions of grafted nanoparticles

KAUST Repository

Anyfantakis, Manos; Bourlinos, Athanasios; Vlassopoulos, Dimitris; Fytas, George; Giannelis, Emmanuel; Kumar, Sanat K.

2009-01-01

, rheology and visual observations, and different routes to gelation, depending on the solvent used. In agreement with earlier works, the solvent quality for the grafted chains at a given temperature controls the balance between attractions and repulsions

Predicting accurate absolute binding energies in aqueous solution

DEFF Research Database (Denmark)

Jensen, Jan Halborg

2015-01-01

Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic. In this paper I summarize some of the many factors that could easily contribute 1-3 kcal......-represented by continuum models. While I focus on binding free energies in aqueous solution the approach also applies (with minor adjustments) to any free energy difference such as conformational or reaction free energy differences or activation free energies in any solvent....

Solvent wash solution

International Nuclear Information System (INIS)

Neace, J.C.

1986-01-01

This patent describes a process for removing diluent degradation products from a solvent extraction solution comprising an admixture of an organic extractant for uranium and plutonium and a non-polar organic liquid diluent, which has been used to recover uranium and plutonium from spent nuclear fuel. Comprising combining a wash solution consisting of: (a) water; and (b) a positive amount up to about, an including, 50 volume percent of at least one highly-polar water-miscible organic solvent, based on the total volume of the water and the highly-polar organic solvent, with the solvent extraction solution after uranium and plutonium values have been stripped from the solvent extraction solution, the diluent degradation products dissolving in the highly-polar organic solvent and the extractant and diluent of the extraction solution not dissolving in the highly-polar organic solvent, and separating the highly-polar organic solvent and the extraction solution to obtain a purified extraction solution

Mechanistic Insights into Solvent and Ligand Dependency in Cu(I)-Catalyzed Allylic Alkylation with gem-Diborylalkanes.

Science.gov (United States)

Zhang, Qi; Wang, Bing; Liu, Jia-Qin; Fu, Yao; Wu, Yu-Cheng

2018-01-19

The recent Cu-catalyzed allylic substitution reaction between gem-diboryalkane and allyl electrophiles shows intriguing solvent and ligand-controlled regioselectivity. The α-alkylation product was obtained in DMF solvent, while γ-alkylation product was obtained in dioxane solvent and the dioxane and NHC ligand situation. In the present study, density functional theory calculations have been used to investigate the reaction mechanism and origin of the regioselectivity. For both dioxane and DMF, γ-alkylation undergoes successive oxidative addition (CH 2 Bpin trans to leaving group) and direct Cγ-C reductive elimination. The α-alkylation is found to undergo oxidative addition (CH 2 Bpin trans to leaving group), isomerization, and Cα-C reductive elimination rather than the previously proposed oxidative addition (-CH 2 Bpin cis to the leaving group) and Cα-C reductive elimination. The γ-alkylation and α-alkylation is, respectively, favorable for dioxane and DMF solvent, which is consistent with the γ- and α-selectivity in experiment. The solvent interferes the isomerization step, thereby affects the relative facility of the α- and γ-alkylation. Further investigation shows that η 1 -intermediate formation promoted by solvent is the rate-determining step of the isomerization. The stronger electron-donating ability of DMF than dioxane facilitates the η 1 -intermediate formation and finally results in the easier isomerization in DMF. For dioxane and NHC situation, in the presence of neutral NHC ligand, the -PO 4 Et 2 group tightly coordinates with the Cu center after the oxidative addition, preventing the isomerization process. The regioselectivity is determined by the relative facility of the oxidative addition step. Therefore, the favorable oxidative addition (in which -CH 2 Bpin trans to the leaving group) results in the facility of γ-alkylation.

Effect of solvent composition on dispersing ability of reaction sialon suspensions.

Science.gov (United States)

Xu, Xin; Oliveira, Marta; Ferreira, José M F

2003-03-15

This work focuses on the optimization of the rheological behavior of suspensions considering different solvent compositions. The effects of methyl ethyl ketone (MEK)/ethanol (E) solvent mixtures on reaction sialon suspensions were investigated by measuring sedimentation behavior, adsorption of dispersant, and flow behavior. It was shown that both the flow behavior and the sedimentation behavior strongly depended on selection of solvent composition. Using 3 wt% KD1 as dispersant, well-dispersed colloidal suspensions could be obtained in MEK-rich solvents. The suspensions with 60 vol% MEK/40 vol% E as solvent could be fitted to the Bingham model with very low yield stress, while suspensions with pure MEK or ethanol-rich mixtures as solvent showed pseudo plastic behavior with relatively high yield stress values. A model was proposed to explain the different flow behaviors of suspensions considering the different configurations of dispersant at particles' surfaces.

EXPRESSION OF CALCIUM-BINDING PROTEINS IN THE NEUROTROPHIN-3-DEPENDENT SUBPOPULATION OF RAT EMBRYONIC DORSAL-ROOT GANGLION-CELLS IN CULTURE

NARCIS (Netherlands)

COPRAY, JCVM; MANTINGHOTTER, IJ; BROUWER, N

1994-01-01

In this study we have examined the calcium-binding protein expression in rat embryonic (E16) dorsal root ganglia (DRG) neurons in vitro in the presence of neurotrophin-3 (NT-3). A comparison was made with the expression of calcium-binding proteins in DRG subpopulations that depended in vitro on

Paxillin and embryonic PolyAdenylation Binding Protein (ePABP) engage to regulate androgen-dependent Xenopus laevis oocyte maturation - A model of kinase-dependent regulation of protein expression.

Science.gov (United States)

Miedlich, Susanne U; Taya, Manisha; Young, Melissa Rasar; Hammes, Stephen R

2017-06-15

Steroid-triggered Xenopus laevis oocyte maturation is an elegant physiologic model of nongenomic steroid signaling, as it proceeds completely independent of transcription. We previously demonstrated that androgens are the main physiologic stimulator of oocyte maturation in Xenopus oocytes, and that the adaptor protein paxillin plays a crucial role in mediating this process through a positive feedback loop in which paxillin first enhances Mos protein translation, ensued by Erk2 activation and Erk-dependent phosphorylation of paxillin on serine residues. Phosphoserine-paxillin then further augments Mos protein translation and downstream Erk2 activation, resulting in meiotic progression. We hypothesized that paxillin enhances Mos translation by interacting with embryonic PolyAdenylation Binding Protein (ePABP) on polyadenylated Mos mRNA. Knockdown of ePABP phenocopied paxillin knockdown, with reduced Mos protein expression, Erk2 and Cdk1 activation, as well as oocyte maturation. In both Xenopus oocytes and mammalian cells (HEK-293), paxillin and ePABP constitutively interacted. Testosterone (Xenopus) or EGF (HEK-293) augmented ePABP-paxillin binding, as well as ePABP binding to Mos mRNA (Xenopus), in an Erk-dependent fashion. Thus, ePABP and paxillin work together in an Erk-dependent fashion to enhance Mos protein translation and promote oocyte maturation. Copyright © 2017 Elsevier B.V. All rights reserved.

Metal retention in human transferrin: consequences of solvent composition in analytical sample preparation methods.

Science.gov (United States)

Quarles, C Derrick; Randunu, K Manoj; Brumaghim, Julia L; Marcus, R Kenneth

2011-10-01

The analysis of metal-binding proteins requires careful sample manipulation to ensure that the metal-protein complex remains in its native state and the metal retention is preserved during sample preparation or analysis. Chemical analysis for the metal content in proteins typically involves some type of liquid chromatography/electrophoresis separation step coupled with an atomic (i.e., inductively coupled plasma-optical emission spectroscopy or -mass spectrometry) or molecular (i.e., electrospray ionization-mass spectrometry) analysis step that requires altered-solvent introduction techniques. UV-VIS absorbance is employed here to monitor the iron content in human holo-transferrin (Tf) under various solvent conditions, changing polarity, pH, ionic strength, and the ionic and hydrophobic environment of the protein. Iron loading percentages (i.e. 100% loading equates to 2 Fe(3+):1 Tf) were quantitatively determined to evaluate the effect of solvent composition on the retention of Fe(3+) in Tf. Maximum retention of Fe(3+) was found in buffered (20 mM Tris) solutions (96 ± 1%). Exposure to organic solvents and deionized H(2)O caused release of ~23-36% of the Fe(3+) from the binding pocket(s) at physiological pH (7.4). Salt concentrations similar to separation conditions used for ion exchange had little to no effect on Fe(3+) retention in holo-Tf. Unsurprisingly, changes in ionic strength caused by additions of guanidine HCl (0-10 M) to holo-Tf resulted in unfolding of the protein and loss of Fe(3+) from Tf; however, denaturing and metal loss was found not to be an instantaneous process for additions of 1-5 M guanidinium to Tf. In contrast, complete denaturing and loss of Fe(3+) was instantaneous with ≥6 M additions of guanidinium, and denaturing and loss of iron from Tf occurred in parallel proportions. Changes to the hydrophobicity of Tf (via addition of 0-14 M urea) had less effect on denaturing and release of Fe(3+) from the Tf binding pocket compared to changes

Epithelial binding of 1,1,2,2-tetrachloroethane in the respiratory and upper alimentary tract

International Nuclear Information System (INIS)

Eriksson, C.; Brittebo, E.B.

1991-01-01

The bioactivation and binding of 14 C-labelled 1,1,2,2-tetrachloroethane (TCE) in the tissues of C57B1 mice were studied. As shown by autoradiography with heated and organic solvent-extracted tissue sections of i.v. injected mice, a high and selective localization of bound metabolites occurred in the nasal olfactory mucosa, preferentially in the Bowman's glands. High levels of bound metabolites were also present in epithelia of the trachea, bronchi and bronchioli and in the squamous epithelia of the oral cavity, tongue and esophagus. An epithelial binding was observed in tissue slices incubated with 14 C-TCE. Incubation of 14 C-TCE with homogenates of the olfactory mucosa and liver showed that the olfactory mucosa had a higher ability to activate 14 C-TCE into products that become irreversibly bound to protein. Addition of metyrapone, glutathione or sodium dithionite to the incubations decreased the level of irreversible binding, suggesting that the activation of TCE to reactive products is mediated via an oxidative cytochrome P-450 dependent process in the olfactory mucosa. (orig.)

FcγRII-binding Centyrins mediate agonism and antibody-dependent cellular phagocytosis when fused to an anti-OX40 antibody.

Science.gov (United States)

Zhang, Di; Whitaker, Brian; Derebe, Mehabaw G; Chiu, Mark L

2018-04-01

Immunostimulatory antibodies against the tumor necrosis factor receptors (TNFR) are emerging as promising cancer immunotherapies. The agonism activity of such antibodies depends on crosslinking to Fc gamma RIIB receptor (FcγRIIB) to enable the antibody multimerization that drives TNFR activation. Previously, Fc engineering was used to enhance the binding of such antibodies to Fcγ receptors. Here, we report the identification of Centyrins as alternative scaffold proteins with binding affinities to homologous FcγRIIB and FcγRIIA, but not to other types of Fcγ receptors. One Centyrin, S29, was engineered at distinct positions of an anti-OX40 SF2 antibody to generate bispecific and tetravalent molecules named as mAbtyrins. Regardless of the position of S29 on the SF2 antibody, SF2-S29 mAbtyrins could bind FcγRIIB and FcγRIIA specifically while maintaining binding to OX40 receptors. In a NFκB reporter assay, attachment of S29 Centyrin molecules at the C-termini, but not the N-termini, resulted in SF2 antibodies with increased agonism owing to FcγRIIB crosslinking. The mAbtyrins also showed agonism in T-cell activation assays with immobilized FcγRIIB and FcγRIIA, but this activity was confined to mAbtyrins with S29 specifically at the C-termini of antibody heavy chains. Furthermore, regardless of the position of the molecule, S29 Centyrin could equip an otherwise Fc-silent antibody with antibody-dependent cellular phagocytosis activity without affecting the antibody's intrinsic antibody-dependent cell-meditated cytotoxicity and complement-dependent cytotoxicity. In summary, the appropriate adoption FcγRII-binding Centyrins as functional modules represents a novel strategy to engineer therapeutic antibodies with improved functionalities.

Uranium reextraction from D2EHPA-TOPO solvent

International Nuclear Information System (INIS)

Duarte Neto, J.

1985-01-01

A comparative study for recovering uranium from the solvent D 2 EHPA-TOPO (di-2-ethyl hexyl phosphoric acid - tri-n-octyl phosphine oxide) with ammonium carbonate and sodium carbonate solutions has been made. The paper discusses the precipitation of iron during stripping and the extracctant solubilization in the aqueous phases. Continuous tests showed that uranium is efficiently stripped from the solvent by using both solutions and that the choice of a specific system is dependent on the uranium precipitation mechanism to be employed. (Author) [pt

Solvent Flux Method (SFM): A Case Study of Water Access to Candida antarctica Lipase B.

Science.gov (United States)

Benson, Sven P; Pleiss, Jürgen

2014-11-11

The solvent flux method (SFM) was developed to comprehensively characterize the influx of solvent molecules from the solvent environment into the active site of a protein in the framework of molecular dynamics simulations. This was achieved by introducing a solvent concentration gradient as well as partially reorienting and rescaling the velocity vector of all solvent molecules contained within a spherical volume enclosing the protein, thus inducing an accelerated solvent influx toward the active site. In addition to the detection of solvent access pathway within the protein structure, it is hereby possible to identify potential amino acid positions relevant to solvent-related enzyme engineering with high statistical significance. The method is particularly aimed at improving the reverse hydrolysis reaction rates in nonaqueous media. Candida antarctica lipase B (CALB) binds to a triglyceride-water interface with its substrate entrance channel oriented toward the hydrophobic substrate interface. The lipase-triglyceride-water system served as a model system for SFM to evaluate the influx of water molecules to the active site. As a proof of principle for SFM, a previously known water access pathway in CALB was identified as the primary water channel. In addition, a secondary water channel and two pathways for water access which contribute to water leakage between the protein and the triglyceride-water interface were identified.

Superinsulating Polyisocyanate Based Aerogels: A Targeted Search for the Optimum Solvent System.

Science.gov (United States)

Zhu, Zhiyuan; Snellings, Geert M B F; Koebel, Matthias M; Malfait, Wim J

2017-05-31

Polyisocyanate based aerogels combine ultralow thermal conductivities with better mechanical properties than silica aerogel, but these properties critically depend on the nature of the gelation solvent, perhaps more so than on any other parameter. Here, we present a systematic study of the relationship between the polyurethane-polyisocyanurate (PUR-PIR) aerogel microstructure, surface area, thermal conductivity, and density and the gelation solvent's Hansen solubility parameters for an industrially relevant PUR-PIR rigid foam formulation. We first investigated aerogels prepared in acetone-dimethyl sulfoxide (DMSO) blends and observed a minimum in thermal conductivity (λ) and maximum in specific surface area for an acetone:DMSO ratio of 85:15 v/v. We then prepared PUR-PIR aerogels in 32 different solvent blends, divided into three series with δ Dispersion , δ Polarity , and δ H-bonding fixed at 15.94, 11.30, and 7.48 MPa 1/2 , respectively, corresponding to the optimum parameters for the acetone:DMSO series. The aerogel properties display distinct dependencies on the various solubility parameters: aerogels with low thermal conductivity can be synthesized in solvents with a high δ H-bonding parameter (above 7.2) and δ Dispersion around 16.3 MPa 1/2 . In contrast, the δ Polarity parameter is of lesser importance. Our study highlights the importance of the gelation solvent, clarifies the influence of the different solvent properties, and provides a methodology for a targeted search across the solvent chemical space based on the Hansen solubility parameters.

Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

Directory of Open Access Journals (Sweden)

Clarisse Gravina Ricci

2018-02-01

Full Text Available Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes.

Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

Science.gov (United States)

Ricci, Clarisse Gravina; Li, Bo; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J. Andrew

2018-01-01

Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed) solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes. PMID:29484300

Mechanistic study on lowering the sensitivity of positive atmospheric pressure photoionization mass spectrometric analyses: size-dependent reactivity of solvent clusters.

Science.gov (United States)

Ahmed, Arif; Choi, Cheol Ho; Kim, Sunghwan

2015-11-15

Understanding the mechanism of atmospheric pressure photoionization (APPI) is important for studies employing APPI liquid chromatography/mass spectrometry (LC/MS). In this study, the APPI mechanism for polyaromatic hydrocarbon (PAH) compounds dissolved in toluene and methanol or water mixture was investigated by use of MS analysis and quantum mechanical simulation. In particular, four different mechanisms that could contribute to the signal reduction were considered based on a combination of MS data and quantum mechanical calculations. The APPI mechanism is clarified by combining MS data and density functional theory (DFT) calculations. To obtain MS data, a positive-mode (+) APPI Q Exactive Orbitrap mass spectrometer was used to analyze each solution. DFT calculations were performed using the general atomic and molecular electronic structure system (GAMESS). The experimental results indicated that methanol significantly reduced the signal in (+) APPI, but no significative signal reduction was observed when water was used as a co-solvent with toluene. The signal reduction is more significant especially for molecular ions than for protonated ions. Therefore, important information about the mechanism of methanol-induced signal reduction in (+) APPI-MS can be gained due its negative impact on APPI efficiency. The size-dependent reactivity of methanol clusters ((CH3 OH)n , n = 1-8) is an important factor in determining the sensitivity of (+) APPI-MS analyses. Clusters can compete with toluene radical ions for electrons. The reactivity increases as the sizes of the methanol clusters increase and this effect can be caused by the size-dependent ionization energy of the solvent clusters. The resulting increase in cluster reactivity explains the flow rate and temperature-dependent signal reduction observed in the analytes. Based on the results presented here, minimizing the sizes of methanol clusters can improve the sensitivity of LC/(+)-APPI-MS. Copyright © 2015 John

Molecular simulations of electrolyte structure and dynamics in lithium-sulfur battery solvents

Science.gov (United States)

Park, Chanbum; Kanduč, Matej; Chudoba, Richard; Ronneburg, Arne; Risse, Sebastian; Ballauff, Matthias; Dzubiella, Joachim

2018-01-01

The performance of modern lithium-sulfur (Li/S) battery systems critically depends on the electrolyte and solvent compositions. For fundamental molecular insights and rational guidance of experimental developments, efficient and sufficiently accurate molecular simulations are thus in urgent need. Here, we construct a molecular dynamics (MD) computer simulation model of representative state-of-the art electrolyte-solvent systems for Li/S batteries constituted by lithium-bis(trifluoromethane)sulfonimide (LiTFSI) and LiNO3 electrolytes in mixtures of the organic solvents 1,2-dimethoxyethane (DME) and 1,3-dioxolane (DOL). We benchmark and verify our simulations by comparing structural and dynamic features with various available experimental reference systems and demonstrate their applicability for a wide range of electrolyte-solvent compositions. For the state-of-the-art battery solvent, we finally calculate and discuss the detailed composition of the first lithium solvation shell, the temperature dependence of lithium diffusion, as well as the electrolyte conductivities and lithium transference numbers. Our model will serve as a basis for efficient future predictions of electrolyte structure and transport in complex electrode confinements for the optimization of modern Li/S batteries (and related devices).

Acyl-CoA-binding protein (ACBP) localizes to the endoplasmic reticulum and Golgi in a ligand-dependent manner in mammalian cells

DEFF Research Database (Denmark)

Hansen, Jesper S; Færgeman, Nils J; Kragelund, Birthe B

2008-01-01

showed that ACBP targeted to the ER (endoplasmic reticulum) and Golgi in a ligand-binding-dependent manner. A variant Y28F/K32A-FACI-50, which is unable to bind acyl-CoA, did no longer show association with the ER and became segregated from the Golgi, as analysed by intensity correlation calculations....... Depletion of fatty acids from cells by addition of FAFBSA (fatty-acid-free BSA) significantly decreased FACI-50 association with the Golgi, whereas fatty acid overloading increased Golgi association, strongly supporting that ACBP associates with the Golgi in a ligand-dependent manner. FRAP (fluorescence...... recovery after photobleaching) showed that the fatty-acid-induced targeting of FACI-50 to the Golgi resulted in a 5-fold reduction in FACI-50 mobility. We suggest that ACBP is targeted to the ER and Golgi in a ligand-binding-dependent manner in living cells and propose that ACBP may be involved...

Solvent extraction of Zn and metals in Zn ores by nonphosphorous solvents

International Nuclear Information System (INIS)

Auchapt, J.M.; Tostain, Jacqueline.

1975-07-01

This bibliography follows a first work on Zn solvent extraction by organo-phosphorous compounds. The other solvents used in Zn extraction, are studied: oxygenated nonphosphorous solvents (ketones, alcohols, carboxylic acids, sulfonates), nitrogenous solvents and hydrocarbons [fr

Glutathione reductase: solvent equilibrium and kinetic isotope effects

International Nuclear Information System (INIS)

Wong, K.K.; Vanoni, M.A.; Blanchard, J.S.

1988-01-01

Glutathione reductase catalyzes the NADPH-dependent reduction of oxidized glutathione (GSSG). The kinetic mechanism is ping-pong, and we have investigated the rate-limiting nature of proton-transfer steps in the reactions catalyzed by the spinach, yeast, and human erythrocyte glutathione reductases using a combination of alternate substrate and solvent kinetic isotope effects. With NADPH or GSSG as the variable substrate, at a fixed, saturating concentration of the other substrate, solvent kinetic isotope effects were observed on V but not V/K. Plots of Vm vs mole fraction of D 2 O (proton inventories) were linear in both cases for the yeast, spinach, and human erythrocyte enzymes. When solvent kinetic isotope effect studies were performed with DTNB instead of GSSG as an alternate substrate, a solvent kinetic isotope effect of 1.0 was observed. Solvent kinetic isotope effect measurements were also performed on the asymmetric disulfides GSSNB and GSSNP by using human erythrocyte glutathione reductase. The Km values for GSSNB and GSSNP were 70 microM and 13 microM, respectively, and V values were 62 and 57% of the one calculated for GSSG, respectively. Both of these substrates yield solvent kinetic isotope effects greater than 1.0 on both V and V/K and linear proton inventories, indicating that a single proton-transfer step is still rate limiting. These data are discussed in relationship to the chemical mechanism of GSSG reduction and the identity of the proton-transfer step whose rate is sensitive to solvent isotopic composition. Finally, the solvent equilibrium isotope effect measured with yeast glutathione reductase is 4.98, which allows us to calculate a fractionation factor for the thiol moiety of GSH of 0.456

Solvent substitution

International Nuclear Information System (INIS)

1990-01-01

The DOE Environmental Restoration and Waste Management Office of Technology Development and the Air Force Engineering and Services Center convened the First Annual International Workshop on Solvent Substitution on December 4--7, 1990. The primary objectives of this joint effort were to share information and ideas among attendees in order to enhance the development and implementation of required new technologies for the elimination of pollutants associated with industrial use of hazardous and toxic solvents; and to aid in accelerating collaborative efforts and technology transfer between government and industry for solvent substitution. There were workshop sessions focusing on Alternative Technologies, Alternative Solvents, Recovery/Recycling, Low VOC Materials and Treatment for Environmentally Safe Disposal. The 35 invited papers presented covered a wide range of solvent substitution activities including: hardware and weapons production and maintenance, paint stripping, coating applications, printed circuit boards, metal cleaning, metal finishing, manufacturing, compliance monitoring and process control monitoring. This publication includes the majority of these presentations. In addition, in order to further facilitate information exchange and technology transfer, the US Air Force and DOE solicited additional papers under a general ''Call for Papers.'' These papers, which underwent review and final selection by a peer review committee, are also included in this combined Proceedings/Compendium. For those involved in handling, using or managing hazardous and toxic solvents, this document should prove to be a valuable resource, providing the most up-to-date information on current technologies and practices in solvent substitution. Individual papers are abstracted separated

Purification, crystallization and preliminary X-ray diffraction analysis of the putative ABC transporter ATP-binding protein from Thermotoga maritima

International Nuclear Information System (INIS)

Ethayathulla, Abdul S.; Bessho, Yoshitaka; Shinkai, Akeo; Padmanabhan, Balasundaram; Singh, Tej P.; Kaur, Punit; Yokoyama, Shigeyuki

2008-01-01

The putative ABC transporter ATP-binding protein TM0222 from T. maritima was cloned, overproduced, purified and crystallized. A complete MAD diffraction data set has been collected to 2.3 Å resolution. Adenosine triphosphate (ATP) binding cassette transporters (ABC transporters) are ATP hydrolysis-dependent transmembrane transporters. Here, the overproduction, purification and crystallization of the putative ABC transporter ATP-binding protein TM0222 from Thermotoga maritima are reported. The protein was crystallized in the hexagonal space group P6 4 22, with unit-cell parameters a = b = 148.49, c = 106.96 Å, γ = 120.0°. Assuming the presence of two molecules in the asymmetric unit, the calculated V M is 2.84 Å 3 Da −1 , which corresponds to a solvent content of 56.6%. A three-wavelength MAD data set was collected to 2.3 Å resolution from SeMet-substituted TM0222 crystals. Data sets were collected on the BL38B1 beamline at SPring-8, Japan

Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site

Science.gov (United States)

Dolenc, Jožica; Oostenbrink, Chris; Koller, Jože; van Gunsteren, Wilfred F.

2005-01-01

Molecular dynamics simulations have been performed on netropsin in two different charge states and on distamycin binding to the minor groove of the DNA duplex d(CGCGAAAAACGCG)·d(CGCGTTTTTCGCG). The relative free energy of binding of the two non-covalently interacting ligands was calculated using the thermodynamic integration method and reflects the experimental result. From 2 ns simulations of the ligands free in solution and when bound to DNA, the mobility and the hydrogen-bonding patterns of the ligands were studied, as well as their hydration. It is shown that even though distamycin is less hydrated than netropsin, the loss of ligand–solvent interactions is very similar for both ligands. The relative mobilities of the ligands in their bound and free forms indicate a larger entropic penalty for distamycin when binding to the minor groove compared with netropsin, partially explaining the lower binding affinity of the distamycin molecule. The detailed structural and energetic insights obtained from the molecular dynamics simulations allow for a better understanding of the factors determining ligand–DNA binding. PMID:15687382

Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site.

Science.gov (United States)

Dolenc, Jozica; Oostenbrink, Chris; Koller, Joze; van Gunsteren, Wilfred F

2005-01-01

Molecular dynamics simulations have been performed on netropsin in two different charge states and on distamycin binding to the minor groove of the DNA duplex d(CGCGAAAAACGCG).d(CGCGTTTTTCGCG). The relative free energy of binding of the two non-covalently interacting ligands was calculated using the thermodynamic integration method and reflects the experimental result. From 2 ns simulations of the ligands free in solution and when bound to DNA, the mobility and the hydrogen-bonding patterns of the ligands were studied, as well as their hydration. It is shown that even though distamycin is less hydrated than netropsin, the loss of ligand-solvent interactions is very similar for both ligands. The relative mobilities of the ligands in their bound and free forms indicate a larger entropic penalty for distamycin when binding to the minor groove compared with netropsin, partially explaining the lower binding affinity of the distamycin molecule. The detailed structural and energetic insights obtained from the molecular dynamics simulations allow for a better understanding of the factors determining ligand-DNA binding.

Single molecule studies of solvent-dependent diffusion and entrapment in poly(dimethylsiloxane) thin films.

Science.gov (United States)

Lange, Jeffrey J; Culbertson, Christopher T; Higgins, Daniel A

2008-12-15

Single molecule microscopic and spectroscopic methods are employed to probe the mobility and physical entrapment of dye molecules in dry and solvent-loaded poly(dimethylsiloxane) (PDMS) films. PDMS films of approximately 220 nm thickness are prepared by spin casting dilute solutions of Sylgard 184 onto glass coverslips, followed by low temperature curing. A perylene diimide dye (BPPDI) is used to probe diffusion and molecule-matrix interactions. Two classes of dye-loaded samples are investigated: (i) those incorporating dye dispersed throughout the films ("in film" samples) and (ii) those in which the dye is restricted primarily to the PDMS surface ("on film" samples). Experiments are performed under dry nitrogen and at various levels of isopropyl alcohol (IPA) loading from the vapor phase. A PDMS-coated quartz-crystal microbalance is employed to monitor solvent loading and drying of the PDMS and to ensure equilibrium conditions are achieved. Single molecules are shown to be predominantly immobile under dry conditions and mostly mobile under IPA-saturated conditions. Quantitative methods for counting the fluorescent spots produced by immobile single molecules in optical images of the samples demonstrate that the population of mobile molecules increases nonlinearly with IPA loading. Even under IPA saturated conditions, the population of fixed molecules is found to be greater than zero and is greatest for "in film" samples. Fluorescence correlation spectroscopy is used to measure the apparent diffusion coefficient for the mobile molecules, yielding a mean value of D = 1.4(+/-0.4) x 10(-8) cm(2)/s that is virtually independent of IPA loading and sample class. It is concluded that a nonzero population of dye molecules is physically entrapped within the PDMS matrix under all conditions. The increase in the population of mobile molecules under high IPA conditions is attributed to the filling of film micropores with solvent, rather than by incorporation of molecularly

Item-location binding in working memory: is it hippocampus-dependent?

Science.gov (United States)

Allen, Richard J; Vargha-Khadem, Faraneh; Baddeley, Alan D

2014-07-01

A general consensus is emerging that the hippocampus has an important and active role in the creation of new long-term memory representations of associations or bindings between elements. However, it is less clear whether this contribution can be extended to the creation of temporary bound representations in working memory, involving the retention of small numbers of items over short delays. We examined this by administering a series of recognition and recall tests of working memory for colour-location binding and object-location binding to a patient with highly selective hippocampal damage (Jon), and groups of control participants. Jon achieved high levels of accuracy in all working memory tests of recognition and recall binding across retention intervals of up to 10s. In contrast, Jon performed at chance on an unexpected delayed test of the same object-location binding information. These findings indicate a clear dissociation between working memory and long-term memory, with no evidence for a critical hippocampal contribution to item-location binding in working memory. Copyright © 2014 Elsevier Ltd. All rights reserved.

Distinct roles of beta1 metal ion-dependent adhesion site (MIDAS), adjacent to MIDAS (ADMIDAS), and ligand-associated metal-binding site (LIMBS) cation-binding sites in ligand recognition by integrin alpha2beta1.

Science.gov (United States)

Valdramidou, Dimitra; Humphries, Martin J; Mould, A Paul

2008-11-21

Integrin-ligand interactions are regulated in a complex manner by divalent cations, and previous studies have identified ligand-competent, stimulatory, and inhibitory cation-binding sites. In collagen-binding integrins, such as alpha2beta1, ligand recognition takes place exclusively at the alpha subunit I domain. However, activation of the alphaI domain depends on its interaction with a structurally similar domain in the beta subunit known as the I-like or betaI domain. The top face of the betaI domain contains three cation-binding sites: the metal-ion dependent adhesion site (MIDAS), the ADMIDAS (adjacent to MIDAS), and LIMBS (ligand-associated metal-binding site). The role of these sites in controlling ligand binding to the alphaI domain has yet to be elucidated. Mutation of the MIDAS or LIMBS completely blocked collagen binding to alpha2beta1; in contrast mutation of the ADMIDAS reduced ligand recognition but this effect could be overcome by the activating monoclonal antibody TS2/16. Hence, the MIDAS and LIMBS appear to be essential for the interaction between alphaI and betaI, whereas occupancy of the ADMIDAS has an allosteric effect on the conformation of betaI. An activating mutation in the alpha2 I domain partially restored ligand binding to the MIDAS and LIMBS mutants. Analysis of the effects of Ca(2+), Mg(2+), and Mn(2+) on ligand binding to these mutants showed that the MIDAS is a ligand-competent site through which Mn(2+) stimulates ligand binding, whereas the LIMBS is a stimulatory Ca(2+)-binding site, occupancy of which increases the affinity of Mg(2+) for the MIDAS.

Solvent/Non-Solvent Sintering To Make Microsphere Scaffolds

Science.gov (United States)

Laurencin, Cato T.; Brown, Justin L.; Nair, Lakshmi

2011-01-01

A solvent/non-solvent sintering technique has been devised for joining polymeric microspheres to make porous matrices for use as drug-delivery devices or scaffolds that could be seeded with cells for growing tissues. Unlike traditional sintering at elevated temperature and pressure, this technique is practiced at room temperature and pressure and, therefore, does not cause thermal degradation of any drug, protein, or other biochemical with which the microspheres might be loaded to impart properties desired in a specific application. Also, properties of scaffolds made by this technique are more reproducible than are properties of comparable scaffolds made by traditional sintering. The technique involves the use of two miscible organic liquids: one that is and one that is not a solvent for the affected polymer. The polymeric microspheres are placed in a mold having the size and shape of the desired scaffold, then the solvent/non-solvent mixture is poured into the mold to fill the void volume between the microspheres, then the liquid mixture is allowed to evaporate. Some of the properties of the resulting scaffold can be tailored through choice of the proportions of the liquids and the diameter of the microspheres.

Solvent substitution

Energy Technology Data Exchange (ETDEWEB)

1990-01-01

The DOE Environmental Restoration and Waste Management Office of Technology Development and the Air Force Engineering and Services Center convened the First Annual International Workshop on Solvent Substitution on December 4--7, 1990. The primary objectives of this joint effort were to share information and ideas among attendees in order to enhance the development and implementation of required new technologies for the elimination of pollutants associated with industrial use of hazardous and toxic solvents; and to aid in accelerating collaborative efforts and technology transfer between government and industry for solvent substitution. There were workshop sessions focusing on Alternative Technologies, Alternative Solvents, Recovery/Recycling, Low VOC Materials and Treatment for Environmentally Safe Disposal. The 35 invited papers presented covered a wide range of solvent substitution activities including: hardware and weapons production and maintenance, paint stripping, coating applications, printed circuit boards, metal cleaning, metal finishing, manufacturing, compliance monitoring and process control monitoring. This publication includes the majority of these presentations. In addition, in order to further facilitate information exchange and technology transfer, the US Air Force and DOE solicited additional papers under a general Call for Papers.'' These papers, which underwent review and final selection by a peer review committee, are also included in this combined Proceedings/Compendium. For those involved in handling, using or managing hazardous and toxic solvents, this document should prove to be a valuable resource, providing the most up-to-date information on current technologies and practices in solvent substitution. Individual papers are abstracted separated.

Characterization of little skate (Leucoraja erinacea) recombinant transthyretin: Zinc-dependent 3,3',5-triiodo-l-thyronine binding.

Science.gov (United States)

Suzuki, Shunsuke; Kasai, Kentaro; Yamauchi, Kiyoshi

2015-01-01

Transthyretin (TTR) diverged from an ancestral 5-hydroxyisourate hydrolase (HIUHase) by gene duplication at some early stage of chordate evolution. To clarify how TTR had participated in the thyroid system as an extracellular thyroid hormone (TH) binding protein, TH binding properties of recombinant little skate Leucoraja erinacea TTR was investigated. At the amino acid level, skate TTR showed 37-46% identities with the other vertebrate TTRs. Because the skate TTR had a unique histidine-rich segment in the N-terminal region, it could be purified by Ni-affinity chromatography. The skate TTR was a 46-kDa homotetramer of 14.5kDa subunits, and had one order of magnitude higher affinity for 3,3',5-triiodo-l-thyronine (T3) and some halogenated phenols than for l-thyroxine. However, the skate TTR had no HIUHase activity. Ethylenediaminetetraacetic acid (EDTA) treatment inhibited [(125)I]T3 binding activity whereas the addition of Zn(2+) to the EDTA-treated TTR recovered [(125)I]T3 binding activity in a Zn(2+) concentration-dependent manner. Scatchard analysis revealed the presence of two classes of binding site for T3, with dissociation constants of 0.24 and 17nM. However, the high-affinity sites were completely abolished with 1mM EDTA, whereas the remaining low-affinity sites decreased binding capacity. The number of zinc per TTR was quantified to be 4.5-6.3. Our results suggest that skate TTR has tight Zn(2+)-binding sites, which are essential for T3 binding to at least the high-affinity sites. Zn(2+) binding to the N-terminal histidine-rich segment may play an important role in acquisition or reinforcement of TH binding ability during early evolution of TTR. Copyright © 2015 Elsevier Inc. All rights reserved.

DNA Binding in High Salt: Analysing the Salt Dependence of Replication Protein A3 from the Halophile Haloferax volcanii

Directory of Open Access Journals (Sweden)

Jody A. Winter

2012-01-01

Full Text Available Halophilic archaea maintain intracellular salt concentrations close to saturation to survive in high-salt environments and their cellular processes have adapted to function under these conditions. Little is known regarding halophilic adaptation of the DNA processing machinery, particularly intriguing since protein-DNA interactions are classically salt sensitive. To investigate such adaptation, we characterised the DNA-binding capabilities of recombinant RPA3 from Haloferax volcanii (HvRPA3. Under physiological salt conditions (3 M KCl, HvRPA3 is monomeric, binding 18 nucleotide ssDNA with nanomolar affinity, demonstrating that RPAs containing the single OB-fold/zinc finger architecture bind with broadly comparable affinity to two OB-fold/zinc finger RPAs. Reducing the salt concentration to 1 M KCl induces dimerisation of the protein, which retains its ability to bind DNA. On circular ssDNA, two concentration-dependent binding modes are observed. Conventionally, increased salt concentration adversely affects DNA binding but HvRPA3 does not bind DNA in 0.2 M KCl, although multimerisation may occlude the binding site. The single N-terminal OB-fold is competent to bind DNA in the absence of the C-terminal zinc finger, albeit with reduced affinity. This study represents the first quantitative characterisation of DNA binding in a halophilic protein in extreme salt concentrations.

CO₂ Binding Organic Liquids Gas Capture with Polarity Swing Assisted Regeneration

Energy Technology Data Exchange (ETDEWEB)

Heldebrant, David [Battelle Memorial Institute, Columbus, OH (United States)

2014-05-31

This report outlines the comprehensive bench-scale testing of the CO₂-binding organic liquids (CO₂BOLs) solvent platform and its unique Polarity Swing Assisted Regeneration (PSAR). This study outlines all efforts on a candidate CO₂BOL solvent molecule, including solvent synthesis, material characterization, preliminary toxicology studies, and measurement of all physical, thermodynamic and kinetic data, including bench-scale testing. Equilibrium and kinetic models and analysis were made using Aspen Plus™. Preliminary process configurations, a technoeconomic assessment and solvent performance projections for separating CO₂ from a subcritical coal-fired power plant are compared to the U.S. Department of Energy's Case 10 monoethanolamine baseline.

Solvents and solvent effects in organic chemistry

National Research Council Canada - National Science Library

Reichardt, C; Welton, T

2011-01-01

.../guest complexation equilibria and reactions in biphasic solvent systems and neoteric solvents, respectively. More than 900 new references have been added, giving preference to review articles, and many older ones have been deleted. New references either replace older ones or are added to the end of the respective reference list of each chapter. Th...

Extraction of Aromatics from Heavy Naphtha Using Different Solvents

International Nuclear Information System (INIS)

EI-Bassuoni, A.A.; Esmael, K.K.

2004-01-01

Aromatic hydrocarbons are very important to the petrochemical industry. Among these are benzene, toluene and xylene (BTX), which are basic raw materials for the production of a number of important petrochemicals. There are many processes used to separate aromatic from non aromatic such as fractionation, azeotropic distillation and liquid I liquid extraction, etc. Liquid - liquid extraction is unique, efficiently used for heat sensitive, close boiling components and for separation of components not possible by other unit operations and it could be done at ambient temperature makes it more energy efficient. The choice of solvent depends on the properties and boiling range of the feedstock. Through the years, a lot of selective solvents has been proposed and selected for the physical separation of aromatics in liquid liquid extraction. Among the selection criteria are the stability,. chemical compatibility, availability, environmental hazards and price of the solvent. But the basic solvent properties that make it efficient are selectivity and capacity

Heparin-independent, PF4-dependent binding of HIT antibodies to platelets: implications for HIT pathogenesis.

Science.gov (United States)

Padmanabhan, Anand; Jones, Curtis G; Bougie, Daniel W; Curtis, Brian R; McFarland, Janice G; Wang, Demin; Aster, Richard H

2015-01-01

Antibodies specific for platelet factor 4 (PF4)/heparin complexes are the hallmark of heparin-induced thrombocytopenia and thrombosis (HIT), but many antibody-positive patients have normal platelet counts. The basis for this is not fully understood, but it is believed that antibodies testing positive in the serotonin release assay (SRA) are the most likely to cause disease. We addressed this issue by characterizing PF4-dependent binding of HIT antibodies to intact platelets and found that most antibodies testing positive in the SRA, but none of those testing negative, bind to and activate platelets when PF4 is present without any requirement for heparin (P HIT antibodies recognize PF4 in a complex with heparin, only a subset of these antibodies recognize more subtle epitopes induced in PF4 when it binds to CS, the major platelet glycosaminoglycan. Antibodies having this property could explain "delayed HIT" seen in some individuals after discontinuation of heparin and the high risk for thrombosis that persists for weeks in patients recovered from HIT. © 2015 by The American Society of Hematology.

Conserved epitope on several human vitamin K-dependent proteins: location of the antigenic site and influence of metal ions on antibody binding

International Nuclear Information System (INIS)

Church, W.R.; Messier, T.; Howard, P.R.; Amiral, J.; Meyer, D.; Mann, K.G.

1988-01-01

A murine monoclonal antibody (designated H-11) produced by injecting mice with purified human protein C was found to bind several human vitamin K-dependent proteins. Using a solid-phase competitive radioimmunoassay with antibody immobilized onto microtiter plates, binding of 125 I-labeled protein C to the antibody was inhibited by increasing amounts of protein C, prothrombin, and Factors X and VII over a concentration range of 1 x 10 -8 to 1 x 10 -6 M. Chemical treatment of prothrombin with a variety of agents did not destroy the antigenic site recognized by the antibody as measured by immunoblotting of prothrombin or prothrombin derivative immobilized onto nitrocellulose. Immunoblotting of purified vitamin K-dependent polypeptides with the monoclonal antibody following sodium dodecyl sulfate-polyacrylamide gel electrophoresis and electrophoretic transfer to nitrocellulose indicated that the antigenic site was found on the light chains of protein C and Factor X. The exact location of the antigenic determinant for antibody H-11 was established using synthetic peptides. Comparison of protein sequences of bovine and human vitamin K-dependent proteins suggests that the sequence Phe-Leu-Glu-Glu-Xaa-Arg/Lys is required for antibody binding. Increasing concentrations of Ca 2+ , Mg 2+ , or Mn 2+ partially inhibited binding of 125 I-protein C to the antibody in a solid-phase assay system with half-maximal binding observed at divalent metal ion concentrations of 2, 4, and 0.6 mM, respectively. The antigenic site thus recognized by monoclonal antibody H-11 is located at the amino-terminal region in the highly conserved γ-carboxyglutamic acid-containing domains of several, but not all, vitamin K-dependent proteins

The chemistry of nonaqueous solvents v.4 solution phenomena and aprotic solvents

CERN Document Server

Lagowski, J J

1976-01-01

The Chemistry of Nonaqueous Solvents, Volume IV: Solution Phenomena and Aprotic Solvents focuses on the chemistry of nonaqueous solvents, with emphasis on solution phenomena and aprotic solvents such as tetramethylurea, inorganic acid chlorides, cyclic carbonates, and sulfolane. This book is organized into seven chapters and begins with an overview of the theory of electrical conductivity and elementary experimental considerations, along with some of the interesting research on nonaqueous solvents. It then turns to a discussion on hydrogen bonding phenomena in nonaqueous systems as probed

Crystal structure of the botulinum neurotoxin type G binding domain: insight into cell surface binding.

Science.gov (United States)

Stenmark, Pål; Dong, Min; Dupuy, Jérôme; Chapman, Edwin R; Stevens, Raymond C

2010-04-16

Botulinum neurotoxins (BoNTs) typically bind the neuronal cell surface via dual interactions with both protein receptors and gangliosides. We present here the 1.9-A X-ray structure of the BoNT serotype G (BoNT/G) receptor binding domain (residues 868-1297) and a detailed view of protein receptor and ganglioside binding regions. The ganglioside binding motif (SxWY) has a conserved structure compared to the corresponding regions in BoNT serotype A and BoNT serotype B (BoNT/B), but several features of interactions with the hydrophilic face of the ganglioside are absent at the opposite side of the motif in the BoNT/G ganglioside binding cleft. This may significantly reduce the affinity between BoNT/G and gangliosides. BoNT/G and BoNT/B share the protein receptor synaptotagmin (Syt) I/II. The Syt binding site has a conserved hydrophobic plateau located centrally in the proposed protein receptor binding interface (Tyr1189, Phe1202, Ala1204, Pro1205, and Phe1212). Interestingly, only 5 of 14 residues that are important for binding between Syt-II and BoNT/B are conserved in BoNT/G, suggesting that the means by which BoNT/G and BoNT/B bind Syt diverges more than previously appreciated. Indeed, substitution of Syt-II Phe47 and Phe55 with alanine residues had little effect on the binding of BoNT/G, but strongly reduced the binding of BoNT/B. Furthermore, an extended solvent-exposed hydrophobic loop, located between the Syt binding site and the ganglioside binding cleft, may serve as a third membrane association and binding element to contribute to high-affinity binding to the neuronal membrane. While BoNT/G and BoNT/B are homologous to each other and both utilize Syt-I/Syt-II as their protein receptor, the precise means by which these two toxin serotypes bind to Syt appears surprisingly divergent. Copyright (c) 2010. Published by Elsevier Ltd.

Effect of trastuzumab interchain disulfide bond cleavage on Fcγ receptor binding and antibody-dependent tumour cell phagocytosis.

Science.gov (United States)

Suzuki, Mami; Yamanoi, Ayaka; Machino, Yusuke; Ootsubo, Michiko; Izawa, Ken-ichi; Kohroki, Junya; Masuho, Yasuhiko

2016-01-01

The Fc domain of human IgG1 binds to Fcγ receptors (FcγRs) to induce effector functions such as phagocytosis. There are four interchain disulfide bonds between the H and L chains. In this study, the disulfide bonds within the IgG1 trastuzumab (TRA), which is specific for HER2, were cleaved by mild S-sulfonation or by mild reduction followed by S-alkylation with three different reagents. The cleavage did not change the binding activities of TRA to HER2-bearing SK-BR-3 cells. The binding activities of TRA to FcγRIIA and FcγRIIB were greatly enhanced by modification with mild reduction and S-alkylation with ICH2CONH2 or N-(4-aminophenyl) maleimide, while the binding activities of TRA to FcγRI and FcγRIIIA were decreased by any of the four modifications. However, the interchain disulfide bond cleavage by the different modifications did not change the antibody-dependent cell-mediated phagocytosis (ADCP) of SK-BR-3 cells by activated THP-1 cells. The order of FcγR expression levels on the THP-1 cells was FcγRII > FcγRI > FcγRIII and ADCP was inhibited by blocking antibodies against FcγRI and FcγRII. These results imply that the effect of the interchain disulfide bond cleavage on FcγRs binding and ADCP is dependent on modifications of the cysteine residues and the FcγR isotypes. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Hemin binding by Porphyromonas gingivalis strains is dependent on the presence of A-LPS.

Science.gov (United States)

Rangarajan, M; Aduse-Opoku, J; Paramonov, N A; Hashim, A; Curtis, M A

2017-10-01

Porphyromonas gingivalis is a Gram-negative black pigmenting anaerobe that is unable to synthesize heme [Fe(II)-protoporphyrin IX] or hemin [Fe(III)-protoporphyrin IX-Cl], which are important growth/virulence factors, and must therefore derive them from the host. Porphyromonas gingivalis expresses several proteinaceous hemin-binding sites, which are important in the binding/transport of heme/hemin from the host. It also synthesizes several virulence factors, namely cysteine-proteases Arg- and Lys-gingipains and two lipopolysaccharides (LPS), O-LPS and A-LPS. The gingipains are required for the production of the black pigment, μ-oxo-bisheme {[Fe(III)PPIX] 2 O}, which is derived from hemoglobin and deposited on the bacterial cell-surface leading to the characteristic black colonies when grown on blood agar. In this study we investigated the role of LPS in the deposition of μ-oxo-bisheme on the cell-surface. A P. gingivalis mutant defective in the biosynthesis of Arg-gingipains, namely rgpA/rgpB, produces brown colonies on blood agar and mutants defective in Lys-gingipain (kgp) and LPS biosynthesis namely porR, waaL, wzy, and pg0129 (α-1, 3-mannosyltransferase) produce non-pigmented colonies. However, only those mutants lacking A-LPS showed reduced hemin-binding when cells in suspension were incubated with hemin. Using native, de-O-phosphorylated and de-lipidated LPS from P. gingivalis W50 and porR strains, we demonstrated that hemin-binding to O-polysaccharide (PS) and to the lipid A moiety of LPS was reduced compared with hemin-binding to A-PS. We conclude that A-LPS in the outer-membrane of P. gingivalis serves as a scaffold/anchor for the retention of μ-oxo-bisheme on the cell surface and pigmentation is dependent on the presence of A-LPS. © 2017 The Authors. Molecular Oral Microbiology Published by John Wiley & Sons Ltd.

Revealing kinetics and state-dependent binding properties of IKur-targeting drugs that maximize atrial fibrillation selectivity

Science.gov (United States)

Ellinwood, Nicholas; Dobrev, Dobromir; Morotti, Stefano; Grandi, Eleonora

2017-09-01

The KV1.5 potassium channel, which underlies the ultra-rapid delayed-rectifier current (IKur) and is predominantly expressed in atria vs. ventricles, has emerged as a promising target to treat atrial fibrillation (AF). However, while numerous KV1.5-selective compounds have been screened, characterized, and tested in various animal models of AF, evidence of antiarrhythmic efficacy in humans is still lacking. Moreover, current guidelines for pre-clinical assessment of candidate drugs heavily rely on steady-state concentration-response curves or IC50 values, which can overlook adverse cardiotoxic effects. We sought to investigate the effects of kinetics and state-dependent binding of IKur-targeting drugs on atrial electrophysiology in silico and reveal the ideal properties of IKur blockers that maximize anti-AF efficacy and minimize pro-arrhythmic risk. To this aim, we developed a new Markov model of IKur that describes KV1.5 gating based on experimental voltage-clamp data in atrial myocytes from patient right-atrial samples in normal sinus rhythm. We extended the IKur formulation to account for state-specificity and kinetics of KV1.5-drug interactions and incorporated it into our human atrial cell model. We simulated 1- and 3-Hz pacing protocols in drug-free conditions and with a [drug] equal to the IC50 value. The effects of binding and unbinding kinetics were determined by examining permutations of the forward (kon) and reverse (koff) binding rates to the closed, open, and inactivated states of the KV1.5 channel. We identified a subset of ideal drugs exhibiting anti-AF electrophysiological parameter changes at fast pacing rates (effective refractory period prolongation), while having little effect on normal sinus rhythm (limited action potential prolongation). Our results highlight that accurately accounting for channel interactions with drugs, including kinetics and state-dependent binding, is critical for developing safer and more effective pharmacological anti

Human IGF-I propeptide A promotes articular chondrocyte biosynthesis and employs glycosylation-dependent heparin binding.

Science.gov (United States)

Shi, Shuiliang; Kelly, Brian J; Wang, Congrong; Klingler, Ken; Chan, Albert; Eckert, George J; Trippel, Stephen B

2018-03-01

Insulin-like growth factor I (IGF-I) is a key regulator of chondrogenesis, but its therapeutic application to articular cartilage damage is limited by rapid elimination from the repair site. The human IGF-I gene gives rise to three IGF-I propeptides (proIGF-IA, proIGF-IB and proIGF-IC) that are cleaved to create mature IGF-I. In this study, we elucidate the processing of IGF-I precursors by articular chondrocytes, and test the hypotheses that proIGF-I isoforms bind to heparin and regulate articular chondrocyte biosynthesis. Human IGF-I propeptides and mutants were overexpressed in bovine articular chondrocytes. IGF-I products were characterized by ELISA, western blot and FPLC using a heparin column. The biosynthetic activity of IGF-I products on articular chondrocytes was assayed for DNA and glycosaminoglycan that the cells produced. Secreted IGF-I propeptides stimulated articular chondrocyte biosynthetic activity to the same degree as mature IGF-I. Of the three IGF-I propeptides, only one, proIGF-IA, strongly bound to heparin. Interestingly, heparin binding of proIGF-IA depended on N-glycosylation at Asn92 in the EA peptide. To our knowledge, this is the first demonstration that N-glycosylation determines the binding of a heparin-binding protein to heparin. The biosynthetic and heparin binding abilities of proIGF-IA, coupled with its generation of IGF-I, suggest that proIGF-IA may have therapeutic value for articular cartilage repair. These data identify human pro-insulin-like growth factor IA as a bifunctional protein. Its combined ability to bind heparin and augment chondrocyte biosynthesis makes it a promising therapeutic agent for cartilage damage due to trauma and osteoarthritis. Copyright © 2017 Elsevier B.V. All rights reserved.

Whole blood-oxygen binding properties of four cold-temperate marine fishes: blood affinity is independent of pH-dependent binding, routine swimming performance, and environmental hypoxia

DEFF Research Database (Denmark)

Herbert, Neill A; Skov, Peter V; Wells, Rufus M G

2006-01-01

performance and the predicted low O(2) response of each species. The ecotype of the four marine species was also unrelated to pH-dependent binding because no difference in the Bohr effect was apparent ( Phi varied insignificantly from -0.90 to -1.06), and differences in the magnitude of the cooperative...

Directed Assembly of Janus Cylinders by Controlling the Solvent Polarity.

Science.gov (United States)

Kim, Jongmin; Choi, Chang-Hyung; Yeom, Su-Jin; Eom, Naye; Kang, Kyoung-Ku; Lee, Chang-Soo

2017-08-01

This study demonstrates the possibility of controlling the directed self-assembly of microsized Janus cylinders by changing the solvent polarity of the assembly media. Experimental results are analyzed and theoretical calculations of the free energy of adhesion (ΔG ad ) are performed to elucidate the underlying basic principles and investigate the effects of the solvent on the self-assembled structures. This approach will pave a predictive route for controlling the structures of assembly depending on the solvent polarity. In particular, we find that a binary solvent system with precisely controlled polarity induces directional assembly of the microsized Janus cylinders. Thus, the formation of two-dimensional (2D) and three-dimensional (3D) assembled clusters can be reliably tuned by controlling the numbers of constituent Janus cylinders in a binary solvent system. Finally, this approach is expanded to stepwise assembly, which forms unique microstructures via secondary growth of primary seed clusters formed by the Janus cylinders. We envision that this investigation is highly promising for the construction of desired superstructures using a wide variety of polymeric Janus microparticles with chemical and physical multicompartments.

Photophysical properties of coumarin-120: Unusual behavior in nonpolar solvents

International Nuclear Information System (INIS)

Pal, Haridas; Nad, Sanjukta; Kumbhakar, Manoj

2003-01-01

Photophysical properties of coumarin-120 (C120; 7-amino-4-methyl-1,2-benzopyrone) dye have been investigated in different solvents using steady-state and time-resolved fluorescence and picosecond laser flash photolysis (LFP) and nanosecond pulse radiolysis (PR) techniques. C120 shows unusual photophysical properties in nonpolar solvents compared to those in other solvents of moderate to higher polarities. Where the Stokes shifts (Δν-bar=ν-bar abs -ν-bar fl ), fluorescence quantum yields (Φ f ), and fluorescence lifetimes (τ f ) show more or less linear correlation with the solvent polarity function Δf={(ε-1)/(2ε+1)-(n 2 -1)/(2n 2 +1)}, all these parameters are unusually lower in nonpolar solvents. Unlike in other solvents, both Φ f and τ f in nonpolar solvents are also strongly temperature dependent. It is indicated that the excited singlet (S 1 ) state of C120 undergoes a fast activation-controlled nonradiative deexcitation in nonpolar solvents, which is absent in all other solvents. LFP and PR studies indicate that the intersystem crossing process is negligible for the present dye in all the solvents studied. Photophysical behavior of C120 in nonpolar solvent has been rationalized assuming that in these solvents the dye exists in a nonpolar structure, with its 7-NH 2 group in a pyramidal configuration. In this structure, since the 7-NH 2 group is bonded to the 1,2-benzopyrone moiety by a single bond, the former group can undergo a fast flip-flop motion, which in effect causes the fast nonradiative deexcitation of the dye excited state. In moderate to higher polarity solvents, it is indicated that the dye exists in an intramolecular charge-transfer structure, where the bond between 7-NH 2 group and the 1,2-benzopyrone moiety attains substantial double bond character. In this structure, the flip-flop motion of the 7-NH 2 group is highly restricted and thus there is no fast nonradiative deexcitation process for the excited dye

Characterization of inclusion complexes of organic ions with hydrophilic hosts by ion transfer voltammetry with solvent polymeric membranes.

Science.gov (United States)

Olmos, José Manuel; Laborda, Eduardo; Ortuño, Joaquín Ángel; Molina, Ángela

2017-03-01

The quantitative characterization of inclusion complexes formed in aqueous phase between organic ions and hydrophilic hosts by ion-transfer voltammetry with solvent polymeric membrane ion sensors is studied, both in a theoretical and experimental way. Simple analytical solutions are presented for the determination of the binding constant of the complex from the variation with the host concentration of the electrochemical signal. These solutions are valid for any voltammetric technique and for solvent polymeric membrane ion sensors comprising one polarisable interface (1PI) and also, for the first time, two polarisable interfaces (2PIs). Suitable experimental conditions and data analysis procedures are discussed and applied to the study of the interactions of a common ionic liquid cation (1-octyl-3-metyl-imidazolium) and an ionisable drug (clomipramine) with two hydrophilic cyclodextrins: α-cyclodextrin and 2-hydroxypropyl-β-cyclodextrin. The experimental study is performed via square wave voltammetry with 2PIs and 1PI solvent polymeric membranes and in both cases the electrochemical experiments enable the detection of inclusion complexes and the determination of the corresponding binding constant. Copyright © 2016 Elsevier B.V. All rights reserved.

Solvent-dependent self-assembly and ordering in slow-drying semi-crystalline conjugated polymer solutions

KAUST Repository

Zhao, Kui

2015-09-07

The mechanistic understanding of the intrinsic molecular self-assembly of conjugated polymers is of immense importance to controlling the microstructure development in organic semiconducting thin films, with meaningful impact on charge transport and optoelectronic properties. Yet, to date the vast majority of studies have focused on the fast solution process itself, with studies of slower intrinsic molecular self-assembly in formulations lagging behind. Here we have investigated molecular self-assembly during spontaneous organization and uncovered how changes in formulation influence the microstructure, morphology and transport properties of conjugated polymer thin films. Our results suggest that the polymer-solvent interaction is the key factor for the molecular self-assembly and changes in macroscopic charge transport, which is in contrast with most solution processes, such as spin-coating and blade coating, where solvent drying kinetics dominates the aggregation and crystallization processes. Energetically favourable interactions between the polymer and its solvent are shown to cause chain expansion, resulting in a large hydrodynamic volume and few chain entanglements in solution. This provides molecular freedom for self-assembly and is shown to greatly enhance the local and long range order of the polymer, intra-chain backbone planarity and crystallite size. These improvements, in turn, are shown to endow the conjugated polymer with high carrier transport, as demonstrated by organic thin film transistors.

A solvent/non-solvent system for achieving solution-processed multilayer organic light-emitting devices

Energy Technology Data Exchange (ETDEWEB)

Yu, Yue; Wu, Zhaoxin, E-mail: zhaoxinwu@mail.xjtu.edu.cn; He, Lin; Jiao, Bo; Hou, Xun

2015-08-31

We developed a solvent/non-solvent system to fabricate the multilayer organic light-emitting devices (OLEDs) based on poly(N-vinylcarbazole) (PVK) by solution-process. This solvent system consists of both the solvent and non-solvent of PVK, in which fluorescent small molecules could be fully dissolved and directly spin-coated on top of the PVK layer; it could effectively avoid the redissolution of PVK during the spin-coating process of small molecules emitting layer. In the further investigation of this system, we also demonstrated the three-component solvent system, and found out that the third component, a less volatile solvent of PVK, was crucial for preparing a smoother interface between PVK and emitting layer. Compared with OLEDs through the vacuum deposition, the devices fabricated by solution-process from the solvent/non-solvent system showed comparable efficiency, which indicate that the solvent/non-solvent system can be used as an alternative process to prepare the polymer and small molecule multilayer devices through all-solution-process. - Highlights: • We fabricate the multilayer OLEDs by solution-process using a novel system. • We develop a solvent/non-solvent system of polymer (PVK) to avoid redissolution. • Small molecules could be fully dissolved and directly spin-coated on PVK layer. • The devices fabricated by the system and vacuum deposition show comparable efficiency.

The C-terminus of H-Ras as a target for the covalent binding of reactive compounds modulating Ras-dependent pathways.

Directory of Open Access Journals (Sweden)

Clara L Oeste

2011-01-01

Full Text Available Ras proteins are crucial players in differentiation and oncogenesis and constitute important drug targets. The localization and activity of Ras proteins are highly dependent on posttranslational modifications at their C-termini. In addition to an isoprenylated cysteine, H-Ras, but not other Ras proteins, possesses two cysteine residues (C181 and C184 in the C-terminal hypervariable domain that act as palmitoylation sites in cells. Cyclopentenone prostaglandins (cyPG are reactive lipidic mediators that covalently bind to H-Ras and activate H-Ras dependent pathways. Dienone cyPG, such as 15-deoxy-Δ(12,14-PGJ(2 (15d-PGJ(2 and Δ(12-PGJ(2 selectively bind to the H-Ras hypervariable domain. Here we show that these cyPG bind simultaneously C181 and C184 of H-Ras, thus potentially altering the conformational tendencies of the hypervariable domain. Based on these results, we have explored the capacity of several bifunctional cysteine reactive small molecules to bind to the hypervariable domain of H-Ras proteins. Interestingly, phenylarsine oxide (PAO, a widely used tyrosine phosphatase inhibitor, and dibromobimane, a cross-linking agent used for cysteine mapping, effectively bind H-Ras hypervariable domain. The interaction of PAO with H-Ras takes place in vitro and in cells and blocks modification of H-Ras by 15d-PGJ(2. Moreover, PAO treatment selectively alters H-Ras membrane partition and the pattern of H-Ras activation in cells, from the plasma membrane to endomembranes. These results identify H-Ras as a novel target for PAO. More importantly, these observations reveal that small molecules or reactive intermediates interacting with spatially vicinal cysteines induce intramolecular cross-linking of H-Ras C-terminus potentially contributing to the modulation of Ras-dependent pathways.

Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

Energy Technology Data Exchange (ETDEWEB)

Cheng, Xiaofei [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036 (China); Deng, Ping; Cui, Hongguang [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); Wang, Aiming, E-mail: aiming.wang@agr.gc.ca [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada)

2015-11-15

Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

International Nuclear Information System (INIS)

Cheng, Xiaofei; Deng, Ping; Cui, Hongguang; Wang, Aiming

2015-01-01

Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

Temperature dependence and GABA modulation of [3H]triazolam binding in the rat brain

International Nuclear Information System (INIS)

Earle, M.E.; Concas, A.; Wamsley, J.K.; Yamamura, H.I.

1987-01-01

The hypnotic triazolam (TZ), a triazolobenzodiazepine displays a short physiological half life and has been used for the treatment of insomnia related to anxiety states. The authors major objectives were the direct measurement of the temperature dependence and the gamma-aminobutyric acid (GABA) effect of [ 3 H]TZ binding in the rat brain. Saturation studies showed a shift to lower affinity with increasing temperatures (K/sub d/ = 0.27 +/- 08 nM at 0 0 C; K/sub d/ = 1.96 +/- 0.85 nM at 37 0 C) while the B/sub max/ values remained unchanged (1220 +/- 176 fmoles/mg protein at 0 0 C and 1160 +/- 383 fmoles/mg protein at 37 0 C). Saturation studies of [ 3 H]TZ binding in the presence or absence of GABA (100μM) showed a GABA-shift. At 0 0 C the K/sub d/ values were (K/sub d/ = 0.24 +/- 0.03 nM/-GABA; K/sub d/ = 0.16 +/- 0.04/+GABA) and at 37 0 C the K/sub d/ values were (K/sub d/ = 1.84 +/- 0.44 nM/-GABA; K/sub d/ = 0.95 +/- 0.29 nM/+GABA). In contrast to reported literature, the authors findings show that TZ interacts with benzodiazepine receptors with a temperature dependence and GABA-shift consistent with predicted behavior for benzodiazepine agonists. 20 references, 3 tables

Lamellar Diblock Copolymer Thin Films during Solvent Vapor Annealing Studied by GISAXS

DEFF Research Database (Denmark)

Zhang, Jianqi; Posselt, Dorthe; Smilgies, Detlef-M.

2014-01-01

The reorientation of lamellae and the dependence of the lamellar spacing, Dlam, on polymer volume fraction, ϕP, Dlam ∝ ϕP–β, in diblock copolymer thin films during solvent vapor annealing (SVA) are examined by combining white light interferometry (WLI) and grazing-incidence small-angle X-ray scat......The reorientation of lamellae and the dependence of the lamellar spacing, Dlam, on polymer volume fraction, ϕP, Dlam ∝ ϕP–β, in diblock copolymer thin films during solvent vapor annealing (SVA) are examined by combining white light interferometry (WLI) and grazing-incidence small-angle X...

Drug and Solvent Abuse Among Ahwaz\\'s Elderlies

Directory of Open Access Journals (Sweden)

Abdolrahim Asadollahi

2007-10-01

Full Text Available Objectives: There are researches to point epidemiology of addiction to drugs, chemical and solvent abuse in elderlies. Drug and Solvent abuse is considered as one of these addictions. This study was point to chemical abuse among elderly population of Ahwaz an Iranian city during year of 2007. Methods & Materials: Research method is description-exploration with use to questionnaire, clinical interview and survey of medical and clinical reports among volunteer clients. Statistical community is all elderly population at one of citizen region in Ahwaz city (Iran. Seventy four dossiers were considered via random sampling; with 30 Elder volunteer clients been interviewed and replied to Elderly Drug Abuse Questionnaire (EDAQ. Results: Signification of hypothesis with X2 test was considered significant relation between age and addiction record variables to solvent abuse; this relation is very significant to second value of drug's derivations such as Morphine, Codeine, Tebaine and Heroine. Interview showed psychological dependent due to appeal them to solvent abuse. Kind of abuse among elderly was snuffing and abuse of medicine drugs which were been recommended to them by their physician. Conclusion: Although study of solvent and chemical abuse's epidemiology pointed less average of this addiction in samples, should be considered important and notice in studies. Finally, researchers were suggested to avoid of this new drug abuse and so to control behavior and interaction of these addicted and their behavior development; it's better to control on distribution of solvent and glue materials and recommending of medicine drug via physicians visiting exderlies.

Characterization of binding of N'-nitrosonornicotine to protein

International Nuclear Information System (INIS)

Hughes, M.F.

1986-01-01

The NADPH-dependent activation of the carcinogenic nitrosamine, N'-nitrosonornicotine (NNN) to a reactive intermediate which binds covalently to protein was assessed using male Sprague-Dawley rat liver and lung microsomes. The NADPH-dependent covalent binding of [ 14 C]NNN to liver and lung microsomes was linear with time up to 90 and 45 min, respectively and was also linear with protein concentrations up to 3.0 and 2.0 mg/ml, respectively. The apparent K/sub m/ and V/sub max/ of the NADPH-dependent binding to liver microsomes were determined from the initial velocities. Addition of the thiols glutathione, cystein, N-acetylcysteine or 2-mercapthoethanol significantly decreased the non-NADPH-dependent binding to liver microsomal protein, but did not affect the NADPH-dependent binding. Glutathione was required in order to observe any NADPH-dependent binding to lung microsomal protein. In lung microsomes, SKF-525A significantly decreased the NADPH-dependent binding by 79%. Replacement of an air atmosphere with N 2 or CO:O 2 (8:2) significantly decreased the NADPH-dependent binding of [ 14 C]NNN to liver microsomal protein by 40% or 27% respectively. Extensive covalent binding of [ 14 C]NNN to liver and muscle microsomal protein occurred in the absence of an NADPH-generating system, in the presence of 50% methanol and also to bovine serum albumin, indicating a nonenzymatic reaction. These data indicate that cytochrome P-450 is at least in part responsible for the metabolic activation of the carcinogen NNN, but also suggest additional mechanisms of activation

Crystal Nucleation of Tolbutamide in Solution: Relationship to Solvent, Solute Conformation, and Solution Structure.

Science.gov (United States)

Zeglinski, Jacek; Kuhs, Manuel; Khamar, Dikshitkumar; Hegarty, Avril C; Devi, Renuka K; Rasmuson, Åke C

2018-04-03

The influence of the solvent in nucleation of tolbutamide, a medium-sized, flexible and polymorphic organic molecule, has been explored by measuring nucleation induction times, estimating solvent-solute interaction enthalpies using molecular modelling and calorimetric data, probing interactions and clustering with spectroscopy, and modelling solvent-dependence of molecular conformation in solution. The nucleation driving force required to reach the same induction time is strongly solvent-dependent, increasing in the order: acetonitrilenucleation difficulty is a function of the strength of solvent-solute interaction, with emphasis on the interaction with specific H-bonding polar sites of importance in the crystal structure. A clear exception from this rule is the most difficult nucleation in toluene despite the weakest solvent-solute interactions. However molecular dynamics modelling predicts that tolbutamide assumes an intramolecularly H-bonded conformation in toluene, substantially different from and more stable than the conformation in the crystal structure, and thus presenting an additional barrier to nucleation. This explains why nucleation in toluene is the most difficult and why the relatively higher propensity for aggregation of tolbutamide molecules in toluene solution, as observed with FTIR spectroscopy, does not translate into easier nucleation. Thus, our combined experimental and molecular modelling study suggests that the solvent can influence on the nucleation not only via differences in the desolvation but also through the influence on molecular conformation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of solvent extracts from coal liquefaction in a flowing solvent reactor

Energy Technology Data Exchange (ETDEWEB)

Li, Wen-Ying; Feng, Jie; Xie, Ke-Chang [Key Laboratory of Coal Science and Technology, Taiyuan University of Technology, Ministry of Education and Shanxi Province, No. 79 Yingze West Street, Taiyuan 030024 (China); Kandiyoti, R. [Department of Chemical Engineering and Chemical Technology, Imperial College, University of London, London SW7 2BY (United Kingdom)

2004-10-15

Point of Ayr coal has been extracted using three solvents, tetralin, quinoline and 1-methyl-2-pyrrolidinone (NMP) at two temperatures 350 and 450 C, corresponding approximately to before and after the onset of massive covalent bond scission by pyrolysis. The three solvents differ in solvent power and the ability to donate hydrogen atoms to stabilise free radicals produced by pyrolysis of the coal. The extracts were prepared in a flowing solvent reactor to minimise secondary thermal degradation of the primary extracts. Analysis of the pentane-insoluble fractions of the extracts was achieved by size exclusion chromatography, UV-fluorescence spectroscopy in NMP solvent and probe mass. With increasing extraction temperature, the ratio of the amount having big molecular weight to that having small molecular weight in tetralin extracts was increased; the tetralin extract yield increased from 12.8% to 75.9%; in quinoline, increasing extraction temperature did not have an effect on the molecular weight of products but there was a big increase in extract yield. The extracts in NMP showed the enhanced solvent extraction power at both temperatures, with a shift in the ratio of larger molecules to smaller molecules with increasing extraction temperature and with the highest conversion of Point of Ayr coal among these three solvents at both temperatures. Solvent adducts were detected in the tetralin and quinoline extracts by probe mass spectrometry; solvent products were formed from NMP at both temperatures.

Solvent cleanup using base-treated silica gel solid adsorbent

International Nuclear Information System (INIS)

Tallent, O.K.; Mailen, J.C.; Pannell, K.D.

1984-06-01

A solvent cleanup method using silica gel columns treated with either sodium hydroxide (NaOH) or lithium hydroxide (LiOH) has been investigated. Its effectiveness compares favorably with that of traditional wash methods. After treatment with NaOH solution, the gels adsorb HNO 3 , dibutyl phosphate (DBP), UO 2 2+ , Pu 4+ , various metal-ion fission products, and other species from the solvent. Adsorption mechanisms include neutralization, hydrolysis, polymerization, and precipitation, depending on the species adsorbed. Sodium dibutyl phosphate, which partially distributes to the solvent from the gels, can be stripped with water; the stripping coefficient ranges from 280 to 540. Adsorption rates are diffusion controlled such that temperature effects are relatively small. Recycle of the gels is achieved either by an aqueous elution and recycle sequence or by a thermal treatment method, which may be preferable. Potential advantages of this solvent cleanup method are that (1) some operational problems are avoided and (2) the amount of NaNO 3 waste generated per metric ton of nuclear fuel reprocessed would be reduced significantly. 19 references, 6 figures, 12 tables

Binding-dependent disorder-order transition in PKI alpha: a fluorescence anisotropy study.

Science.gov (United States)

Hauer, J A; Taylor, S S; Johnson, D A

1999-05-25

The conformational flexibility of peptidyl ligands may be an essential element of many peptide-macromolecular interactions. Consequently, the alpha-carbonyl backbone flexibility of the 8 kDa protein kinase inhibitor (PKI alpha) peptide of cAMP-dependent protein kinase (cAPK) free in solution and bound to cAPK was assessed by time-resolved fluorescence anisotropy. Specifically, three full-length, single-site PKI alpha mutants (V3C, S28C, and S59C) were prepared, and fluorescein iodoacetamide (FI) was selectively conjugated to the side chains of each substituted cysteine. The time-resolved anisotropy decay profiles of the labeled mutants were well fit to a model-free nonassociative biexponential equation. Free in solution, the three labeled proteins had very similar anisotropy decays arising primarily from local alpha-carbonyl backbone movements. Only a small fraction of the anisotropy decay was associated with slower, whole-body tumbling, confirming that PKI alpha is highly disordered at all three locations. Complexation of the mutants with the catalytic (C) subunit of cAPK decreased the rate of whole-body tumbling for all three mutants. The effects on the rapid decay processes, however, were dependent upon the site of conjugation. The anisotropy decay profiles of both FI-V3C- and FI-S28C-PKI alpha were associated with significantly reduced contributions from the fast decay processes, while that of FI-S59C-PKI alpha was largely unaffected by binding to the C-subunit. The results suggest that the cAPK-binding domain of PKI alpha extends from the its N-terminus to residues beyond Ser28 but does not include the segment around Ser59, which is still part of a highly flexible domain when bound to the C-subunit.

Time-dependent density-functional tight-binding method with the third-order expansion of electron density.

Science.gov (United States)

Nishimoto, Yoshio

2015-09-07

We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of the third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well.

Effect of the Solvent Temperatures on Dynamics of Serine Protease Proteinase K

Directory of Open Access Journals (Sweden)

Peng Sang

2016-02-01

Full Text Available To obtain detailed information about the effect of the solvent temperatures on protein dynamics, multiple long molecular dynamics (MD simulations of serine protease proteinase K with the solute and solvent coupled to different temperatures (either 300 or 180 K have been performed. Comparative analyses demonstrate that the internal flexibility and mobility of proteinase K are strongly dependent on the solvent temperatures but weakly on the protein temperatures. The constructed free energy landscapes (FELs at the high solvent temperatures exhibit a more rugged surface, broader spanning range, and higher minimum free energy level than do those at the low solvent temperatures. Comparison between the dynamic hydrogen bond (HB numbers reveals that the high solvent temperatures intensify the competitive HB interactions between water molecules and protein surface atoms, and this in turn exacerbates the competitive HB interactions between protein internal atoms, thus enhancing the conformational flexibility and facilitating the collective motions of the protein. A refined FEL model was proposed to explain the role of the solvent mobility in facilitating the cascade amplification of microscopic motions of atoms and atomic groups into the global collective motions of the protein.

LIGAND-BINDING SITES ON THE MYCOBACTERIUM TUBERCULOSIS UREASE

Directory of Open Access Journals (Sweden)

Lisnyak Yu. V.

2017-10-01

Full Text Available Introduction. Mycobacterium tuberculosis is the causative agent of tuberculosis that remains a serious medical and social health problem. Despite intensive efforts have been made in the past decade, there are no new efficient anti-tuberculosis drugs today, and that need is growing due to the spread of drug-resistant strains of M.tuberculosis. M. tuberculosis urease (MTU, being an important factor of the bacterium viability and virulence, is an attractive target for anti-tuberculosis drugs acting by inhibition of urease activity. However, the commercially available urease inhibitors are toxic and unstable, that prevent their clinical use. Therefore, new more potent anti-tuberculosis drugs inhibiting new targets are urgently needed. A useful tool for the search of novel inhibitors is a computational drug design. The inhibitor design is significantly easier if binding sites on the enzyme are identified in advance. This paper aimed to determine the probable ligand binding sites on the surface of M. tuberculosis urease. Methods. To identify ligand binding sites on MTU surface, сomputational solvent mapping method FTSite was applied by the use of MTU homology model we have built earlier. The method places molecular probes (small organic molecules containing various functional groups on a dense grid defined around the enzyme, and for each probe finds favorable positions. The selected poses are refined by free energy minimization, the low energy conformations are clustered, and the clusters are ranked on the basis of the average free energy. FTSite server outputs the protein residues delineating a binding sites and the probe molecules representing each cluster. To predict allosteric pockets on MTU, AlloPred and AlloSite servers were applied. AlloPred uses the normal mode analysis (NMA and models how the dynamics of a protein would be altered in the presence of a modulator at a specific pocket. Pockets on the enzyme are predicted using the Fpocket

Thin porphyrin composite membranes with enhanced organic solvent transport

KAUST Repository

Phuoc, Duong

2018-05-01

Extending the stability of polymeric membranes in organic solvents is important for applications in chemical and pharmaceutical industry. Thin-film composite membranes with enhanced solvent permeance are proposed, using porphyrin as a building block. Hybrid polyamide films are formed by interfacial polymerization of 5,10,15,20-(tetra-4-aminophenyl)porphyrin/m-phenylene diamine (MPD) mixtures with trimesoyl chloride. Porphyrin is a non-planar molecule, containing a heterocyclic tetrapyrrole unit. Its incorporation into a polyamide film leads to higher free volume than that of a standard polyamide film. Polyamide films derived from porphyrin and MPD amines with a fixed total amine concentration of 1wt% and various porphyrin/MPD ratios were fabricated and characterized. The porphyrin/MPD polyamide film was complexed with Cu(II), due to the binding capacity of porphyrin to metal ions. By coupling scanning transmission electron microscopy (STEM) with electron energy-loss spectroscopy (EELS), Cu mapping was obtained, revealing the distribution of porphyrin in the interfacial polymerized layer. By using porphyrin as amine-functionalized monomer a membrane with thin selective skin and enhanced solvent transport is obtained, with good dye selectivity in the nanofiltration range. For instance, an ultra-fast hexane permeance, 40-fold increased, was confirmed when using 0.5/0.5 porphyrin/MPD mixtures, instead of only MPD as amine monomer. A rejection of 94.2% Brilliant Blue R (826g/mol) in methanol was measured.

The Solvent Selection framework: solvents for organic synthesis, separation processes and ionic-organic synthesis

DEFF Research Database (Denmark)

Mitrofanov, Igor; Sansonetti, Sascha; Abildskov, Jens

2012-01-01

This paper presents a systematic integrated framework for solvent selection and solvent design. The framework is divided into several modules, which can tackle specific problems in various solvent-based applications. In particular, three modules corresponding to the following solvent selection pr...

Nonspecific DNA Binding and Bending by HUαβ: Interfaces of the Three Binding Modes Characterized by Salt Dependent Thermodynamics

Science.gov (United States)

Koh, Junseock; Shkel, Irina; Saecker, Ruth M.; Record, M. Thomas

2011-01-01

Previous ITC and FRET studies demonstrated that Escherichia coli HUαβ binds nonspecifically to duplex DNA in three different binding modes: a tighter-binding 34 bp mode which interacts with DNA in large (>34 bp) gaps between bound proteins, reversibly bending it 140° and thereby increasing its flexibility, and two weaker, modestly cooperative small-site-size modes (10 bp, 6 bp) useful for filling gaps between bound proteins shorter than 34 bp. Here we use ITC to determine the thermodynamics of these binding modes as a function of salt concentration, and deduce that DNA in the 34 bp mode is bent around but not wrapped on the body of HU, in contrast to specific binding of IHF. Analyses of binding isotherms (8, 15, 34 bp DNA) and initial binding heats (34, 38, 160 bp DNA) reveal that all three modes have similar log-log salt concentration derivatives of the binding constants (Ski) even though their binding site sizes differ greatly; most probable values of Ski on 34 bp or larger DNA are − 7.5 ± 0.5. From the similarity of Ski values, we conclude that binding interfaces of all three modes involve the same region of the arms and saddle of HU. All modes are entropy-driven, as expected for nonspecific binding driven by the polyelectrolyte effect. The bent-DNA 34 bp mode is most endothermic, presumably because of the cost of HU-induced DNA bending, while the 6 bp mode is modestly exothermic at all salt concentrations examined. Structural models consistent with the observed Ski values are proposed. PMID:21513716

Solvent effects in the synergistic solvent extraction of Co2+

International Nuclear Information System (INIS)

Kandil, A.T.; Ramadan, A.

1979-01-01

The extraction of Co 2+ from a 0.1M ionic strength aqueous phase (Na + , CH 3 COOH) of pH = 5.1 was studied using thenoyltrifluoroacetone, HTTA, in eight different solvents and HTTA + trioctylphosphine oxide, TOPO, in the same solvents. A comparison of the effect of solvent dielectric constant on the equilibrium constant shows a synergism as a result of the increased hydrophobic character imparted to the metal complex due to the formation of the TOPO adduct. (author)

An organic solvent-, detergent-, and thermo-stable alkaline protease from the mesophilic, organic solvent-tolerant Bacillus licheniformis 3C5.

Science.gov (United States)

Rachadech, W; Navacharoen, A; Ruangsit, W; Pongtharangkul, T; Vangnai, A S

2010-01-01

Bacillus licheniformis 3C5, isolated as mesophilic bacterium, exhibited tolerance towards a wide range of non-polar and polar organic solvents at 45 degrees C. It produced an extracellular organic solvent-stable protease with an apparent molecular mass of approximately 32 kDa. The inhibitory effect of PMSF and EDTA suggested it is likely to be an alkaline serine protease. The protease was active over abroad range of temperatures (45-70 degrees C) and pH (8-10) range with an optimum activity at pH 10 and 65 degrees C. It was comparatively stable in the presence ofa relatively high concentration (35% (v/v)) of organic solvents and various types of detergents even at a relatively high temperature (45 degrees C). The protease production by B. licheniformis 3C5 was growth-dependent. The optimization of carbon and nitrogen sources for cell growth and protease production revealed that yeast extract was an important medium component to support both cell growth and the protease production. The overall properties of the protease produced by B. licheniformis 3C5 suggested that this thermo-stable, solvent-stable, detergent-stable alkaline protease is a promising potential biocatalyst for industrial and environmental applications.

Plasma-polymerized films providing selective affinity to the polarity of vaporized organic solvents

International Nuclear Information System (INIS)

Akimoto, Takuo; Ikeshita, Yusuke; Terashima, Ryo; Karube, Isao

2009-01-01

Plasma-polymerized films (PPFs) were fabricated as recognition membranes for a vapor-sensing device, and their affinity to vaporized organic solvents was evaluated with surface plasmon resonance. The affinity we intended to create is the selective sorption of the vaporized organic solvents depending on their polarity. For this purpose, acetonitrile, ethylenediamine (EDA), styrene, hexamethyldisiloxane (HMDSO), and hexamethyldisilazane were used to fabricate PPFs. Vaporized methanol, ethanol, and 1-propanol were used as high-polar solvents to be analyzed. Hexane, toluene, and p-xylene were used as low-polar solvents. As a result, the HMDSO-PPF with 97.3 o of contact angle was found to provide affinity to the low-polar solvents. In contrast, the EDA-PPF with 7.1 o of contact angle provided affinity to the high-polar solvents. Observations of the surface morphology of the HMDSO- and EDA-PPFs with a scanning electron microscope revealed that they are composed of nano-scale islands.

SOLVENT FIRE BY-PRODUCTS

Energy Technology Data Exchange (ETDEWEB)

Walker, D; Samuel Fink, S

2006-05-22

Southwest Research Institute (SwRI) conducted a burn test of the Caustic-Side Solvent Extraction (CSSX) solvent to determine the combustion products. The testing showed hydrogen fluoride gas is not a combustion product from a solvent fire when up to 70% of the solvent is consumed. The absence of HF in the combustion gases may reflect concentration of the modifier containing the fluoride groups in the unburned portion. SwRI reported results for other gases (CO, HCN, NOx, formaldehyde, and hydrocarbons). The results, with other supporting information, can be used for evaluating the consequences of a facility fire involving the CSSX solvent inventory.

An overview of industrial solvent use or is there life after chlorinated solvents?

International Nuclear Information System (INIS)

Green, B.

1991-01-01

Everyone using industrial chemicals has been affected by the fire- storm of new regulations governing solvent use. How will companies currently using hazardous solvents prepare for the changes ahead? What will the impact be on commonly used industrial solvents? What effect are environmental pressures having on solvent use and disposal? Are the responsible individuals in your company up-to-date on phase-out schedules? This paper is written for an audience of compliance coordinators, consultants, production engineers and corporate management. In it, the either addresses the above questions and discusses the specific products affected. The author reviews currently available alternatives to chlorinated and hazardous solvents and introduces a simple system for rating alternatives. The program also includes a discussion of solvent minimization programs and worker reeducation

Influence of Solvent Composition on the Performance of Spray-Dried Co-Amorphous Formulations

DEFF Research Database (Denmark)

Mishra, Jaya; Rades, Thomas; Löbmann, Korbinian

2018-01-01

Ball-milling is usually used to prepare co-amorphous drug–amino acid (AA) mixtures. In this study, co-amorphous drug–AA mixtures were produced using spray-drying, a scalable industrially preferred preparation method. The influence of the solvent type and solvent composition was investigated....... Mixtures of indomethacin (IND) and each of the three AAs arginine, histidine, and lysine were ball-milled and spray-dried at a 1:1 molar ratio, respectively. Spray-drying was performed at different solvent ratios in (a) ethanol and water mixtures and (b) acetone and water mixtures. Different ratios...... that using spray-drying as a preparation method, all IND–AA mixtures could be successfully converted into the respective co-amorphous forms, irrespective of the type of solvent used, but depending on the solvent mixture ratios. Both ball-milled and spray-dried co-amorphous samples showed an enhanced...

Solvent mimicry with methylene carbene to probe protein topography.

Science.gov (United States)

Gómez, Gabriela Elena; Monti, José Luis E; Mundo, Mariana Rocío; Delfino, José María

2015-10-06

The solvent accessible surface area (SASA) of the polypeptide chain plays a key role in protein folding, conformational change, and interaction. This fundamental biophysical parameter is elusive in experimental measurement. Our approach to this problem relies on the reaction of the minimal photochemical reagent diazirine (DZN) with polypeptides. This reagent (i) exerts solvent mimicry because its size is comparable to water and (ii) shows scant chemical selectivity because it generates extremely reactive methylene carbene. Methylation gives rise to the EM (extent of modification) signal, which is useful for scrutinizing the conformational change triggered by Ca(2+) binding to calmodulin (CaM). The increased EM observed for the full protein is dominated by the enhanced exposure of hydrophobic area in Ca(2+)-CaM. Fragmentation allowed us to quantify the methylene incorporation at specific sites. Peptide 91-106 reveals a major reorganization around the calcium 151 binding site, resulting in local ordering and a greater exposure of the hydrophobic surface. Additionally, this technique shows a high sensitivity to probe recognition between CaM and melittin (Mel). The large decrease in EM indicates the occlusion of a significant hydrophobic area upon complexation. Protection from labeling reveals a larger involvement of the N-terminal and central regions of CaM in this interaction. Despite its smaller size, Mel's differential exposure can also be quantified. Moreover, MS/MS fragmentation realizes the goal of extending the resolution of labeled sites at the amino acid level. Overall, DZN labeling emerges as a useful footprinting method capable of shedding light on physiological conformational changes and interactions.

Influence of solvent addition on the physicochemical properties of Brazilian gasoline

Energy Technology Data Exchange (ETDEWEB)

E.V. Takeshita; R.V.P. Rezende; S.M.A. Guelli; U. de Souza; A.A. Ulson de Souza [Federal University of Santa Catarina, Florianopolis (Brazil). Chemical Engineering Department

2008-08-15

The influence of several solvents (anhydrous ethanol, white spirit, alkylbenzene AB9, diesel) on the physicochemical parameters of gasoline was studied according to ASTM international standard methods. The parameters investigated (distillation curves, density, Reid vapor pressure) showed differentiated behavior, depending on the class of the solvent (oxygenated, light and heavy aliphatic, aromatic) and the quantity added to the gasoline. The azeotropic mixtures formed by ethanol and hydrocarbons showed a strong influence on the behavior of the distillation curves and the location of the point of a sudden change in temperature was shown to be a possible way to detect adulterations and determine the quantity of solvent added to the gasoline. 28 refs., 9 figs., 5 tabs.

Binding and thermodynamics of REV peptide-ctDNA interaction.

Science.gov (United States)

Upadhyay, Santosh Kumar

2017-03-01

driven. ITC based analysis of salt dependence of binding constant gave a charge value (Z) = +4.01, as determined for the δlnK/δln[Na + ] parameter, suggesting the participation of only 3-4 Arg out of 11 Arg charge from REV peptide. The stoichiometry observed for the complex was three molar charge of REV peptide binding per molar charge of ctDNA. ITC based analysis further confirmed that the binding between ctDNA and REV peptide is governed by electrostatic interaction. Molecular interactions including H-bonding, van der Waals forces, and solvent molecules rearrangement, underlie the binding of REV peptide to ctDNA. © 2016 Wiley Periodicals, Inc.

Low Operational Stability of Enzymes in Dry Organic Solvents: Changes in the Active Site Might Affect Catalysis

Directory of Open Access Journals (Sweden)

Gabriel Barletta

2012-02-01

Full Text Available The potential of enzyme catalysis in organic solvents for synthetic applications has been overshadowed by the fact that their catalytic properties are affected by organic solvents. In addition, it has recently been shown that an enzyme’s initial activity diminishes considerably after prolonged exposure to organic media. Studies geared towards understanding this last drawback have yielded unclear results. In the present work we decided to use electron paramagnetic resonance spectroscopy (EPR to study the motion of an active site spin label (a nitroxide free radical during 96 h of exposure of the serine protease subtilisin Carlsberg to four different organic solvents. Our EPR data shows a typical two component spectra that was quantified by the ratio of the anisotropic and isotropic signals. The isotropic component, associated with a mobile nitroxide free radical, increases during prolonged exposure to all solvents used in the study. The maximum increase (of 43% was observed in 1,4-dioxane. Based on these and previous studies we suggest that prolonged exposure of the enzyme to these solvents provokes a cascade of events that could induce substrates to adopt different binding conformations. This is the first EPR study of the motion of an active-site spin label during prolonged exposure of an enzyme to organic solvents ever reported.

Expression, purification, crystallization and structure of human adipocyte lipid-binding protein (aP2)

International Nuclear Information System (INIS)

Marr, Eric; Tardie, Mark; Carty, Maynard; Brown Phillips, Tracy; Wang, Ing-Kae; Soeller, Walt; Qiu, Xiayang; Karam, George

2006-01-01

The crystal structure of human adipocyte lipid-binding protein (aP2) with a bound palmitate is reported at 1.5 Å resolution. Human adipocyte lipid-binding protein (aP2) belongs to a family of intracellular lipid-binding proteins involved in the transport and storage of lipids. Here, the crystal structure of human aP2 with a bound palmitate is described at 1.5 Å resolution. Unlike the known crystal structure of murine aP2 in complex with palmitate, this structure shows that the fatty acid is in a folded conformation and that the loop containing Phe57 acts as a lid to regulate ligand binding by excluding solvent exposure to the central binding cavity

Phospho-dependent binding of the clathrin AP2 adaptor complex to GABAA receptors regulates the efficacy of inhibitory synaptic transmission

OpenAIRE

Kittler, Josef T.; Chen, Guojun; Honing, Stephan; Bogdanov, Yury; McAinsh, Kristina; Arancibia-Carcamo, I. Lorena; Jovanovic, Jasmina N.; Pangalos, Menelas N.; Haucke, Volker; Yan, Zhen; Moss, Stephen J.

2005-01-01

The efficacy of synaptic inhibition depends on the number of γ-aminobutyric acid type A receptors (GABAARs) expressed on the cell surface of neurons. The clathrin adaptor protein 2 (AP2) complex is a critical regulator of GABAAR endocytosis and, hence, surface receptor number. Here, we identify a previously uncharacterized atypical AP2 binding motif conserved within the intracellular domains of all GABAAR β subunit isoforms. This AP2 binding motif (KTHLRRRSSQLK in the β3 subunit) incorporates...

Photoaffinity labeling with cholesterol analogues precisely maps a cholesterol-binding site in voltage-dependent anion channel-1.

Science.gov (United States)

Budelier, Melissa M; Cheng, Wayland W L; Bergdoll, Lucie; Chen, Zi-Wei; Janetka, James W; Abramson, Jeff; Krishnan, Kathiresan; Mydock-McGrane, Laurel; Covey, Douglas F; Whitelegge, Julian P; Evers, Alex S

2017-06-02

Voltage-dependent anion channel-1 (VDAC1) is a highly regulated β-barrel membrane protein that mediates transport of ions and metabolites between the mitochondria and cytosol of the cell. VDAC1 co-purifies with cholesterol and is functionally regulated by cholesterol, among other endogenous lipids. Molecular modeling studies based on NMR observations have suggested five cholesterol-binding sites in VDAC1, but direct experimental evidence for these sites is lacking. Here, to determine the sites of cholesterol binding, we photolabeled purified mouse VDAC1 (mVDAC1) with photoactivatable cholesterol analogues and analyzed the photolabeled sites with both top-down mass spectrometry (MS), and bottom-up MS paired with a clickable, stable isotope-labeled tag, FLI -tag. Using cholesterol analogues with a diazirine in either the 7 position of the steroid ring (LKM38) or the aliphatic tail (KK174), we mapped a binding pocket in mVDAC1 localized to Thr 83 and Glu 73 , respectively. When Glu 73 was mutated to a glutamine, KK174 no longer photolabeled this residue, but instead labeled the nearby Tyr 62 within this same binding pocket. The combination of analytical strategies employed in this work permits detailed molecular mapping of a cholesterol-binding site in a protein, including an orientation of the sterol within the site. Our work raises the interesting possibility that cholesterol-mediated regulation of VDAC1 may be facilitated through a specific binding site at the functionally important Glu 73 residue. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Solvent - solute interaction

International Nuclear Information System (INIS)

Urbanczyk, A.; Kalinowski, M.K.

1983-01-01

The electronic absorption spectrum of vanadyl acetylacetonate has been studied in 15 organic solvents. It has been found that wavenumbers and molar absorptivities of the long-wavelength bands (d-d transitions) can be well described by a complementary Lewis acid-base model including Gutmann's donor number [Gutmann V., Wychera E., Inorg. Nucl. Chem. Letters 2, 257 (1966)] and acceptor number [Mayer U., Gutmann V., Gerger W., Monatsh. Chem. 106, 1235 (1975)] of a solvent. This model describes also the solvent effect of the hyperfine splitting constant, Asub(iso)( 51 V), from e.s.r. spectra of VOacac 2 . These observations are discussed in terms of the donor-acceptor concept for solvent-solute interactions. (Author)

Thermodynamics of ligand binding to acyl-coenzyme A binding protein studied by titration calorimetry

DEFF Research Database (Denmark)

Færgeman, Nils J.; Sigurskjold, B W; Kragelund, B B

1996-01-01

Ligand binding to recombinant bovine acyl-CoA binding protein (ACBP) was examined using isothermal microcalorimetry. Microcalorimetric measurements confirm that the binding affinity of acyl-CoA esters for ACBP is strongly dependent on the length of the acyl chain with a clear preference for acyl-...

Effects of concentration, temperature and solvent composition on density and apparent molar volume of the binary mixtures of cationic-anionic surfactants in methanol-water mixed solvent media.

Science.gov (United States)

Bhattarai, Ajaya; Chatterjee, Sujeet Kumar; Niraula, Tulasi Prasad

2013-01-01

The accurate measurements on density of the binary mixtures of cetyltrimethylammonium bromide and sodium dodecyl sulphate in pure water and in methanol(1) + water (2) mixed solvent media containing (0.10, 0.20, and 0.30) volume fractions of methanol at 308.15, 318.15, and 323.15 K are reported. The concentrations are varied from (0.03 to 0.12) mol.l(-1) of sodium dodecyl sulphate in presence of ~ 5.0×10(-4) mol.l(-1) cetyltrimethylammonium bromide. The results showed almost increase in the densities with increasing surfactant mixture concentration, also the densities are found to decrease with increasing temperature over the entire concentration range, investigated in a given mixed solvent medium and these values are found to decrease with increasing methanol content in the solvent composition. The concentration dependence of the apparent molar volumes appear to be negligible over the entire concentration range, investigated in a given mixed solvent medium and the apparent molar volumes increase with increasing temperature and are found to decrease with increasing methanol content in the solvent composition.

Deasphalting solvents

International Nuclear Information System (INIS)

Carrillo, J. A; Caceres, J; Vela, G; Bueno, H

1996-01-01

This paper describes how the deasphalted oil (DMO) or demetalized oil (DMO) quality (CCR, Ni, V end asphaltenes contents) changes with: DAO or DMO yield, solvent/feed ratio, type of vacuum reside (from paraffinic to blends with vis breaking bottoms), extraction temperature and extraction solvent (propane, propylene, n-butane and I butane)

Solvent effects on the fluorescence and effective three-photon absorption of a Zn(II)-[meso-tetrakis(4-octyloxyphenyl)porphyrin

Science.gov (United States)

Wan, Yong; Xue, Yuxiong; Sheng, Ning; Rui, Guanghao; Lv, Changgui; He, Jun; Gu, Bing; Cui, Yiping

2018-06-01

The fluorescence and effective three-photon absorption (3PA) properties of Zn(II)-[meso-tetrakis(4-octyloxyphenyl)porphyrin] (labeled Zn(II)-porphyrin) dissolved in three different polar solvents were systematically investigated. The electrochemical and photophysical properties of Zn(II)-porphyrin were investigated by 1H NMR spectra, IR spectra, mass spectroscopy, and electronic absorption spectra. The fluorescence emission of Zn(II)-porphyrin in three different solvents excited at the wavelengths of 420 nm (Soret band) and 550 nm (Q-band) were analyzed. By performing Z-scan experiments with femtosecond laser pulses at a wavelength of 800 nm, the effective 3PA process of Zn(II)-porphyrin in three different solvents was observed and the underlying mechanism was discussed in detail. It is found that the fluorescence spectra slightly depend on the polarity of the solvent. Interestingly, the effective 3PA properties of Zn(II)-porphyrin strongly depend on the solvent polarity. The lower the solvent polarity is, the larger effective 3PA cross-section is. Low polar solvents are beneficial to applications of Zn(II)-porphyrin in optical limiting, photodynamic therapy, etc.

Cyclophilin B binding to platelets supports calcium-dependent adhesion to collagen.

Science.gov (United States)

Allain, F; Durieux, S; Denys, A; Carpentier, M; Spik, G

1999-08-01

We have recently reported that cyclophilin B (CyPB), a secreted cyclosporine-binding protein, could bind to T lymphocytes through interactions with two types of binding sites. The first ones, referred to as type I, involve interactions with the conserved domain of CyPB and promote the endocytosis of surface-bound ligand, while the second type of binding sites, termed type II, are represented by glycosaminoglycans (GAG). Here, we further investigated the interactions of CyPB with blood cell populations. In addition to lymphocytes, CyPB was found to interact mainly with platelets. The binding is specific, with a dissociation constant (kd) of 9 +/- 3 nmol/L and the number of sites estimated at 960 +/- 60 per cell. Platelet glycosaminoglycans are not required for the interactions, but the binding is dramatically reduced by active cyclosporine derivatives. We then analyzed the biologic effects of CyPB and found a significant increase in platelet adhesion to collagen. Concurrently, CyPB initiates a transmembranous influx of Ca(2+) and induces the phosphorylation of the P-20 light chains of myosin. Taken together, the present results demonstrate for the first time that extracellular CyPB specifically interacts with platelets through a functional receptor related to the lymphocyte type I binding sites and might act by regulating the activity of a receptor-operated membrane Ca(2+) channel.

Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.

Science.gov (United States)

Deng, Nanjie; Zhang, Bin W; Levy, Ronald M

2015-06-09

The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions, and protein–ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ∼3 kcal/mol at only ∼8% of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the implicit/explicit thermodynamic cycle.

Gate dielectric strength dependent performance of CNT MOSFET and CNT TFET: A tight binding study

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Md. Shamim Sarker

Full Text Available This paper presents a comparative study between CNT MOSFET and CNT TFET taking into account of different dielectric strength of gate oxide materials. Here we have studied the transfer characteristics, on/off current (ION/IOFF ratio and subthreshold slope of the device using Non Equilibrium Greens Function (NEGF formalism in tight binding frameworks. The results are obtained by solving the NEGF and Poisson’s equation self-consistently in NanoTCADViDES environment and found that the ON state performance of CNT MOSFET and CNT TFET have significant dependency on the dielectric strength of the gate oxide materials. The figure of merits of the devices also demonstrates that the CNT TFET is promising for high-speed and low-power logic applications. Keywords: CNT TFET, Subthreshold slop, Barrier width, Conduction band (C.B and Valance band (V.B, Oxide dielectric strength, Tight binding approach

Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses.

Science.gov (United States)

Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

2017-02-22

Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation.

Reversible and Irreversible Binding of Nanoparticles to Polymeric Surfaces

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Wolfgang H. Binder

2009-01-01

Full Text Available Reversible and irreversible binding of CdSe-nanoparticles and nanorods to polymeric surfaces via a strong, multiple hydrogen bond (= Hamilton-receptor/barbituric acid is described. Based on ROMP-copolymers, the supramolecular interaction on a thin polymer film is controlled by living polymerization methods, attaching the Hamilton-receptor in various architectures, and concentrations. Strong binding is observed with CdSe-nanoparticles and CdSe-nanorods, whose surfaces are equipped with matching barbituric acid-moieties. Addition of polar solvents, able to break the hydrogen bonds leads to the detachment of the nanoparticles from the polymeric film. Irreversible binding is observed if an azide/alkine-“click”-reaction is conducted after supramolecular recognition of the nanoparticles on the polymeric surface. Thus reversible or irreversible attachment of the nanosized objects can be achieved.

Solvent cleaning system and method for removing contaminants from solvent used in resin recycling

Science.gov (United States)

Bohnert, George W [Harrisonville, MO; Hand, Thomas E [Lee's Summit, MO; DeLaurentiis, Gary M [Jamestown, CA

2009-01-06

A two step solvent and carbon dioxide based system that produces essentially contaminant-free synthetic resin material and which further includes a solvent cleaning system for periodically removing the contaminants from the solvent so that the solvent can be reused and the contaminants can be collected and safely discarded in an environmentally safe manner.

Solvation-based vapour pressure model for (solvent + salt) systems in conjunction with the Antoine equation

International Nuclear Information System (INIS)

Senol, Aynur

2013-01-01

Highlights: • Vapour pressures of (solvent + salt) systems have been estimated through a solvation-based model. • Two structural forms of the generalized solvation model using the Antoine equation have been performed. • A simplified concentration-dependent vapour pressure model has been also processed. • The model reliability analysis has been performed in terms of a log-ratio objective function. • The reliability of the models has been interpreted in terms of the statistical design factors. -- Abstract: This study deals with modelling the vapour pressure of a (solvent + salt) system on the basis of the principles of LSER. The solvation model framework clarifies the simultaneous impact of several physical variables such as the vapour pressure of a pure solvent estimated by the Antoine equation, the solubility and solvatochromic parameters of the solvent and the physical properties of the ionic salt. It has been analyzed independently the performance of two structural forms of the generalized model, i.e., a relation depending on an integration of the properties of the solvent and the ionic salt and a relation on a reduced property-basis. A simplified concentration-dependent vapour pressure model has been also explored and implemented on the relevant systems. The vapour pressure data of sixteen (solvent + salt) systems have been processed to analyze statistically the reliability of existing models in terms of a log–ratio objective function. The proposed vapour pressure models match relatively well the observed performance, yielding the overall design factors of 1.066 and 1.073 for the solvation-based models with the integrated and reduced properties, and 1.008 for the concentration-based model, respectively

Quantifying the molecular origins of opposite solvent effects on protein-protein interactions.

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Vincent Vagenende

Full Text Available Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments.

Carbon nanotube functionalized with dodecylamine for the effective dispersion in solvents

International Nuclear Information System (INIS)

Ferreira, Filipe Vargas; Francisco, Wesley; Menezes, Beatriz Rossi Canuto de; Cividanes, Luciana De Simone; Coutinho, Aparecido dos Reis; Thim, Gilmar Patrocínio

2015-01-01

Highlights: • The functionalized carbon nanotubes exhibit the formation of a shell structure with nanotubes in the center. • Graphitic structures (sp 2 ) reduce simultaneously with the change of textures on the surface of carbon nanotubes. • The nonpolar chain of dodecylamine improves the carbon nanotube interaction with the nonpolar solvent. - Abstract: In this work, it was performed a dispersion study of carbon nanotubes (CNTs) functionalized with carboxylic and alkane groups in various solvents. CNT was functionalized using H 2 SO 4 /HNO 3 and subsequently functionalized by dodecylamine (DDA). Fourier transform infrared, X-ray photoelectron spectroscopy, thermogravimetric analysis and transmission electron microscopy were used to characterize the CNTs at each step of the surface modification. The dispersion state of CNTs in the solvents was evaluated by Optical microscopy and visual observations. The evaluation of the solvent influence itself was also made. Results confirmed the presence of oxygen-containing and alkane groups on CNTs surfaces. The dispersion stability was strongly dependent on the solvent and carbon nanotubes surface interactions, which can vary with the chemical nature of the solvent. The study of the surface modifications and the degree of carbon nanotubes dispersion is relevant to enhance the full understanding of its applications.

Structure of an N276-Dependent HIV-1 Neutralizing Antibody Targeting a Rare V5 Glycan Hole Adjacent to the CD4 Binding Site

Energy Technology Data Exchange (ETDEWEB)

Wibmer, Constantinos Kurt; Gorman, Jason; Anthony, Colin S.; Mkhize, Nonhlanhla N.; Druz, Aliaksandr; York, Talita; Schmidt, Stephen D.; Labuschagne, Phillip; Louder, Mark K.; Bailer, Robert T.; Karim, Salim S. Abdool; Mascola, John R.; Williamson, Carolyn; Moore, Penny L.; Kwong, Peter D.; Morris, Lynn (NHLS-South Africa); (NIH); (Witwatersrand); (KwaZulu-Natal)

2016-08-31

All HIV-1-infected individuals develop strain-specific neutralizing antibodies to their infecting virus, which in some cases mature into broadly neutralizing antibodies. Defining the epitopes of strain-specific antibodies that overlap conserved sites of vulnerability might provide mechanistic insights into how broadly neutralizing antibodies arise. We previously described an HIV-1 clade C-infected donor, CAP257, who developed broadly neutralizing plasma antibodies targeting an N276 glycan-dependent epitope in the CD4 binding site. The initial CD4 binding site response potently neutralized the heterologous tier 2 clade B viral strain RHPA, which was used to design resurfaced gp120 antigens for single-B-cell sorting. Here we report the isolation and structural characterization of CAP257-RH1, an N276 glycan-dependent CD4 binding site antibody representative of the early CD4 binding site plasma response in donor CAP257. The cocrystal structure of CAP257-RH1 bound to RHPA gp120 revealed critical interactions with the N276 glycan, loop D, and V5, but not with aspartic acid 368, similarly to HJ16 and 179NC75. The CAP257-RH1 monoclonal antibody was derived from the immunoglobulin-variable IGHV3-33 and IGLV3-10 genes and neutralized RHPA but not the transmitted/founder virus from donor CAP257. Its narrow neutralization breadth was attributed to a binding angle that was incompatible with glycosylated V5 loops present in almost all HIV-1 strains, including the CAP257 transmitted/founder virus. Deep sequencing of autologous CAP257 viruses, however, revealed minority variants early in infection that lacked V5 glycans. These glycan-free V5 loops are unusual holes in the glycan shield that may have been necessary for initiating this N276 glycan-dependent CD4 binding site B-cell lineage.

IMPORTANCEThe conserved CD4 binding site on gp120 is a major target for HIV-1 vaccine design, but key events in the elicitation and maturation of

Dishevelled binds the Discs large 'Hook' domain to activate GukHolder-dependent spindle positioning in Drosophila.

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Joshua D Garcia

Full Text Available Communication between cortical cell polarity cues and the mitotic spindle ensures proper orientation of cell divisions within complex tissues. Defects in mitotic spindle positioning have been linked to various developmental disorders and have recently emerged as a potential contributor to tumorigenesis. Despite the importance of this process to human health, the molecular mechanisms that regulate spindle orientation are not fully understood. Moreover, it remains unclear how diverse cortical polarity complexes might cooperate to influence spindle positioning. We and others have demonstrated spindle orientation roles for Dishevelled (Dsh, a key regulator of planar cell polarity, and Discs large (Dlg, a conserved apico-basal cell polarity regulator, effects which were previously thought to operate within distinct molecular pathways. Here we identify a novel direct interaction between the Dsh-PDZ domain and the alternatively spliced "I3-insert" of the Dlg-Hook domain, thus establishing a potential convergent Dsh/Dlg pathway. Furthermore, we identify a Dlg sequence motif necessary for the Dsh interaction that shares homology to the site of Dsh binding in the Frizzled receptor. Expression of Dsh enhanced Dlg-mediated spindle positioning similar to deletion of the Hook domain. This Dsh-mediated activation was dependent on the Dlg-binding partner, GukHolder (GukH. These results suggest that Dsh binding may regulate core interdomain conformational dynamics previously described for Dlg. Together, our results identify Dlg as an effector of Dsh signaling and demonstrate a Dsh-mediated mechanism for the activation of Dlg/GukH-dependent spindle positioning. Cooperation between these two evolutionarily-conserved cell polarity pathways could have important implications to both the development and maintenance of tissue homeostasis in animals.

Ultrasonication-Assisted Solvent Extraction of Quercetin Glycosides from ‘Idared’ Apple Peels

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Gwendolyn M. Huber

2011-11-01

Full Text Available Quercetin and quercetin glycosides are physiologically active flavonol molecules that have been attributed numerous health benefits. Recovery of such molecules from plant matrices depends on a variety of factors including polarity of the extraction solvent. Among the solvents of a wide range of dielectric constants, methanol recovered the most quercetin and its glycosides from dehydrated ‘Idared’ apple peels. When ultra-sonication was employed to facilitate the extraction, exposure of 15 min of ultrasound wavelengths of dehydrated apple peel powder in 80% to 100% (v/v methanol in 1:50 (w:v solid to solvent ratio provided the optimum extraction conditions for quercetin and its glycosides. Acidification of extraction solvent with 0.1% (v/v or higher concentrations of HCl led to hydrolysis of naturally occurring quercetin glycosides into the aglycone as an extraction artifact.

Extrastriatal binding of [123I]FP-CIT in the thalamus and pons: gender and age dependencies assessed in a European multicentre database of healthy controls

International Nuclear Information System (INIS)

Koch, Walter; Unterrainer, Marcus; Xiong, Guoming; Bartenstein, Peter; Diemling, Markus; Varrone, Andrea; Dickson, John C.; Tossici-Bolt, Livia; Sera, Terez; Asenbaum, Susanne; Booij, Jan; Kapucu, Ozlem L.; Kluge, Andreas; Ziebell, Morten; Darcourt, Jacques; Nobili, Flavio; Pagani, Marco; Hesse, Swen; Borght, Thierry Vander; Laere, Koen van; Tatsch, Klaus; La Fougere, Christian

2014-01-01

Apart from binding to the dopamine transporter (DAT), [ 123 I]FP-CIT shows moderate affinity for the serotonin transporter (SERT), allowing imaging of both monoamine transporters in a single imaging session in different brain areas. The aim of this study was to systematically evaluate extrastriatal binding (predominantly due to SERT) and its age and gender dependencies in a large cohort of healthy controls. SPECT data from 103 healthy controls with well-defined criteria of normality acquired at 13 different imaging centres were analysed for extrastriatal binding using volumes of interest analysis for the thalamus and the pons. Data were examined for gender and age effects as well as for potential influence of striatal DAT radiotracer binding. Thalamic binding was significantly higher than pons binding. Partial correlations showed an influence of putaminal DAT binding on measured binding in the thalamus but not on the pons. Data showed high interindividual variation in extrastriatal binding. Significant gender effects with 31 % higher binding in women than in men were observed in the thalamus, but not in the pons. An age dependency with a decline per decade (±standard error) of 8.2 ± 1.3 % for the thalamus and 6.8 ± 2.9 % for the pons was shown. The potential to evaluate extrastriatal predominant SERT binding in addition to the striatal DAT in a single imaging session was shown using a large database of [ 123 I]FP-CIT scans in healthy controls. For both the thalamus and the pons, an age-related decline in radiotracer binding was observed. Gender effects were demonstrated for binding in the thalamus only. As a potential clinical application, the data could be used as a reference to estimate SERT occupancy in addition to nigrostriatal integrity when using [ 123 I]FP-CIT for DAT imaging in patients treated with selective serotonin reuptake inhibitors. (orig.)

Solvent, isotope, and magnetic field effects in the geminate recombination of radical ion pairs

International Nuclear Information System (INIS)

Werner, H.; Staerk, H.; Weller, A.

1978-01-01

The magnetic field dependence of the geminate recombination triplet yield of radical ion pairs generated via photoinduced electron transfer in polar solvents is investigated for the systems pyrene/N,N-dimethylaniline (Py/DMA), pyrene/3,5-dimethoxy-N,N-dimethylaniline (Py/DMDMA), and the perdeuterated system Py-d 10 /DMA-d 11 . The magnetic field dependence characterized through its B/sub 1/2/ value is found to be dependent on the sum of the hyperfine coupling constants in the radical pair in agreement with previous theoretical predictions. A drastic reduction of the B/sub 1/2/ value is observed with the perdeuterated system. By means of measurements of the radical ion and triplet absorption signals with nanosecond time resolution, the influence of the solvent on the geminate singlet and triplet recombination yields is investigated. Complementary measurements of exciplex lifetimes and quantum yields are carried out in a series of solvents with different polarities in order to determine the rate constants of fluorescence emission and intersystem crossing in the exciplexes

New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces.

Science.gov (United States)

Simões, Inês C M; Costa, Inês P D; Coimbra, João T S; Ramos, Maria J; Fernandes, Pedro A

2017-01-23

Knowing how proteins make stable complexes enables the development of inhibitors to preclude protein-protein (P:P) binding. The identification of the specific interfacial residues that mostly contribute to protein binding, denominated as hot spots, is thus critical. Here, we refine an in silico alanine scanning mutagenesis protocol, based on a residue-dependent dielectric constant version of the Molecular Mechanics/Poisson-Boltzmann Surface Area method. We have used a large data set of structurally diverse P:P complexes to redefine the residue-dependent dielectric constants used in the determination of binding free energies. The accuracy of the method was validated through comparison with experimental data, considering the per-residue P:P binding free energy (ΔΔG binding ) differences upon alanine mutation. Different protocols were tested, i.e., a geometry optimization protocol and three molecular dynamics (MD) protocols: (1) one using explicit water molecules, (2) another with an implicit solvation model, and (3) a third where we have carried out an accelerated MD with explicit water molecules. Using a set of protein dielectric constants (within the range from 1 to 20) we showed that the dielectric constants of 7 for nonpolar and polar residues and 11 for charged residues (and histidine) provide optimal ΔΔG binding predictions. An overall mean unsigned error (MUE) of 1.4 kcal mol -1 relative to the experiment was achieved in 210 mutations only with geometry optimization, which was further reduced with MD simulations (MUE of 1.1 kcal mol -1 for the MD employing explicit solvent). This recalibrated method allows for a better computational identification of hot spots, avoiding expensive and time-consuming experiments or thermodynamic integration/ free energy perturbation/ uBAR calculations, and will hopefully help new drug discovery campaigns in their quest of searching spots of interest for binding small drug-like molecules at P:P interfaces.

A sequential binding mechanism in a PDZ domain

DEFF Research Database (Denmark)

Chi, Celestine N; Bach, Anders; Engström, Åke

2009-01-01

that ligand binding involves at least a two-step process. By using an ultrarapid continuous-flow mixer, we then detected a hyperbolic dependence of binding rate constants on peptide concentration, corroborating the two-step binding mechanism. Furthermore, we found a similar dependence of the rate constants...

An investigation of influence of solvent on the degradation kinetics of carotenoids in oil extracts of Calendula officinalis

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DEJAN BEZBRADICA

2005-02-01

Full Text Available The stability of carotenoids was studied in marigold oil extracts prepared with following solvents: Myritol 312®, paraffin oil, almond oil, olive oil, sunflower oil, grape seed oil, and soybean oil. The concentration of the carotenoids was determined by spectroscopic measurement at 450 nm. Degradation rate showed a first order dependence on the concentration of carotenoids with a faster first stage (which lasted 35–50 days, depending on the solvent and a slower second stage. The highest degradation rates were observed in extracts prepared with linoleic acid rich solvents (sunflower oil, soybean oil and grape seed oil, while the lowest were found in oil with saturated fatty acids (Myritol 312® and paraffin oil. These results confirm the connection between the degradation of carotenoids and lipid autoxidation, and suggest that the influence of the oil solvents on the stability of oil extracts of Calendula officinalis is a factor that must be considered when selecting a solvent for the production of marigold oil extracts.

Solvent isotope effect on the fluorescence of azoalkanes

International Nuclear Information System (INIS)

Mirbach, M.J.; Mirbach, M.F.; Cherry, W.R.; Turro, N.J.; Engel, P.

1977-01-01

A study of fluorescence quantum yields and fluorescence lifetimes of two cyclic azoalkanes reveal a striking dependence of phisub(F) and tausub(F) on solvent and on isotopic substitution (OH → OD). A mechanism involving specific deactivation of the fluorescent state from a hydrogen bonded complex is proposed to rationalize the data. (orig./HK) [de

Hydrogenic-Donor Impurity Binding Energy Dependence of the Electric Field in GaAs/AlxGa1−xAs Quantum Rings

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Guangxin Wang

2013-01-01

Full Text Available Using a variational method with two-parameter trial wave function and the effective mass approximation, the binding energy of a donor impurity in GaAs/AlxGa1−xAs cylindrical quantum ring (QR subjected to an external field is calculated. It is shown that the donor impurity binding energy is highly dependent on the QR structure parameters (radial thickness and height, impurity position, and external electric field. The binding energy increases inchmeal as the QR parameters (radial thickness and height decrease until a maximum value for a central impurity and then begins to drop quickly. The applied electric field can significantly modify the spread of electronic wave function in the QR and shift electronic wave function from the donor position and then leads to binding energy changes. In addition, results for the binding energies of a hydrogenic donor impurity as functions of the impurity position and applied electric field are also presented.

Thermodynamics of cooperative binding of FAD to human NQO1: Implications to understanding cofactor-dependent function and stability of the flavoproteome.

Science.gov (United States)

Clavería-Gimeno, Rafael; Velazquez-Campoy, Adrian; Pey, Angel Luis

2017-12-15

The stability of human flavoproteins strongly depends on flavin levels, although the structural and energetic basis of this relationship is poorly understood. Here, we report an in-depth analysis on the thermodynamics of FAD binding to one of the most representative examples of such relationship, NAD(P)H:quinone oxidoreductase 1 (NQO1). NQO1 is a dimeric enzyme that tightly binds FAD, which triggers large structural changes upon binding. A common cancer-associated polymorphism (P187S) severely compromises FAD binding. We show that FAD binding is described well by a thermodynamic model explicitly incorporating binding cooperativity when applied to different sets of calorimetric analyses and NQO1 variants, thus providing insight on the effects in vitro and in cells of cancer-associated P187S, its suppressor mutation H80R and the role of NQO1 C-terminal domain to modulate binding cooperativity and energetics. Furthermore, we show that FAD binding to NQO1 is very sensitive to physiologically relevant environmental conditions, such as the presence of phosphate buffer and salts. Overall, our results contribute to understanding at the molecular level the link between NQO1 stability and fluctuations of FAD levels intracellularly, and supports the notion that FAD binding energetics and cooperativity are fundamentally linked with the dynamic nature of apo-NQO1 conformational ensemble. Copyright © 2017 Elsevier Inc. All rights reserved.

Enantiomeric and Diastereomeric Self-Assembled Multivalent (SAMul) Nanostructures - Understanding the Effects of Chirality on Binding to Polyanionic Heparin and DNA.

Science.gov (United States)

Thornalley, Kiri; Laurini, Erik; Pricl, Sabrina; Smith, David K

2018-05-15

A family of four self-assembling lipopeptides containing Ala-Lys peptides attached to a C16 aliphatic chain was synthesised. These compounds form two enantiomeric pairs that bear a diastereomeric relationship to one another (C16-L-Ala-L-Lys/C16-D-Ala-D-Lys) and (C16-D-Ala-L-Lys/C16-L-Ala-D-Lys). These diastereomeric pairs have very different critical micelle concentrations (CMCs), with LL/DD < DL/LD suggesting more effective assembly of the former. The self-assembled multivalent (SAMul) systems bind biological polyanions as result of the cationic lysine groups on their surfaces. Polyanion binding was investigated using dye displacement assays and isothermal calorimetry (ITC). On heparin binding, there was no significant enantioselectivity, but there was a binding preference for the diastereomeric assemblies with lower CMCs. Conversely, on binding DNA, there was a significant enantioselective preference for systems displaying D-lysine ligands, with a further slight preference for attachment to L-alanine, with the CMC being irrelevant. Binding to adaptive, ill-defined heparin has a large favourable entropic term, suggesting it depends primarily on the cationic SAMul nanostructure maximising surface contact with heparin, which can adapt, displacing solvent and other ions. Conversely, binding to well-defined, shape-persistent DNA has a larger favourable enthalpic term, and combined with the enantioselectivity, this allows us to suggest that its SAMul binding is based on optimised individual electrostatic interactions at the molecular level, with a preference for binding to D-lysine. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Selective solvent extraction of oils

Energy Technology Data Exchange (ETDEWEB)

1938-04-09

In the selective solvent extraction of naphthenic base oils, the solvent used consists of the extract obtained by treating a paraffinic base oil with a selective solvent. The extract, or partially spent solvent is less selective than the solvent itself. Selective solvents specified for the extraction of the paraffinic base oil are phenol, sulphur dioxide, cresylic acid, nitrobenzene, B:B/sup 1/-dichlorethyl ether, furfural, nitroaniline and benzaldehyde. Oils treated are Coastal lubricating oils, or naphthenic oils from the cracking, or destructive hydrogenation of coal, tar, lignite, peat, shale, bitumen, or petroleum. The extraction may be effected by a batch or counter-current method, and in the presence of (1) liquefied propane, or butane, or naphtha, or (2) agents which modify the solvent power such as, water, ammonia, acetonitrile, glycerine, glycol, caustic soda or potash. Treatment (2) may form a post-treatment effected on the extract phase. In counter-current treatment in a tower some pure selective solvent may be introduced near the raffinate outlet to wash out any extract therefrom.

Combined effect of solvents and gamma irradiation on the infrared absorption spectra of polyethylene terephthalate

International Nuclear Information System (INIS)

Rabie, S.M.; ElBially, A.; Elshourbaguie, S.

1991-01-01

The combined effect of solvents and gamma irradiation on the intensities of infrared absorption bands of polyethylene terephthalate, particularly the bands sensitive to conformational changes, were studied. The results revealed that solvent treatment of PET results in significant changes in the intensities of its infrared absorption bands and the exposure of PET to gamma radiation in the presence of solvents helps in the appearance of the two bands at 1550 and 1630 cm . Also, the combined effect of solvents and gamma irradiation on the intensities of the absorption bands is greater than the effect of each agent alone. The extent of the induced changes depends on the nature of solvent and the applied dosage. Further more, for any given solvent or dosage, the rate of change of the intensities of the trans band is not equal to that of the gauche bands.3 fig

Structure of the Mr 140,000 growth hormone-dependent insulin-like growth factor binding protein complex: Determination by reconstitution and affinity-labeling

International Nuclear Information System (INIS)

Baxter, R.C.; Martin, J.L.

1989-01-01

To determine the structure of the high molecular weight, growth hormone-dependent complex between the insulin-like growth factors (IGF-I and IGF-II) and their binding proteins in human serum, we have reconstituted the complex from its purified component proteins and analyzed it by gel electrophoresis and autoradiography after covalent cross-linking. The proteins tested in reconstitution mixtures were an acid-labile Mr 84,000-86,000 glycoprotein doublet (alpha subunit), an acid-stable Mr 47,000-53,000 glycoprotein doublet with IGF-binding activity (BP-53 or beta subunit), and IGF-I or IGF-II (gamma subunit). In incubations containing any one of the three subunits 125I-labeled and the other two unlabeled, identical 125I-labeled alpha-beta-gamma complexes of Mr 140,000 were formed. Minor bands of Mr 120,000 and 90,000 were also seen, thought to represent a partially deglycosylated form of the alpha-beta-gamma complex, and an alpha-gamma complex arising as a cross-linking artifact. When serum samples from subjects of various growth hormone status were affinity-labeled with IGF-II tracer, a growth hormone-dependent Mr 140,000 band was seen, corresponding to the reconstituted alpha-beta-gamma complex. Other growth hormone-dependent labeled bands, of Mr 90,000 (corresponding to alpha-gamma), Mr 55,000-60,000 (corresponding to labeled beta-subunit doublet), and smaller bands of Mr 38,000, 28,000, and 23,000-25,000 (corresponding to labeled beta-subunit degradation products), were also seen in the affinity-labeled serum samples and in the complex reconstituted from pure proteins. All were immunoprecipitable with an anti-BP-53 antiserum. We conclude that the growth hormone-dependent Mr 140,000 IGF-binding protein complex in human serum has three components: the alpha (acid-labile) subunit, the beta (binding) subunit, and the gamma (growth factor) subunit

Thermodynamic method for obtaining the solubilities of complex medium-sized chemicals in pure and mixed solvents

DEFF Research Database (Denmark)

Abildskov, Jens; O'Connell, J.P.

2005-01-01

This paper extends our previous simplified approach to using group contribution methods and limited data to determine differences in solubility of sparingly soluble complex chemicals as the solvent is changed. New applications include estimating temperature dependence and the effect of adding cos....... Though we present no new solution theory, the paper shows an especially efficient use of thermodynamic models for solvent and cosolvent selection for product formulations. Examples and discussion of applications are given. (c) 2004 Elsevier B.V. All rights reserved.......This paper extends our previous simplified approach to using group contribution methods and limited data to determine differences in solubility of sparingly soluble complex chemicals as the solvent is changed. New applications include estimating temperature dependence and the effect of adding...

Separation and identification of anthocyanin extracted from mulberry fruit and the pigment binding properties toward human serum albumin.

Science.gov (United States)

Sheng, Feng; Wang, Yuning; Zhao, Xingchen; Tian, Na; Hu, Huali; Li, Pengxia

2014-07-16

Purple pigments were isolated from mulberry extracts using preparative high-speed countercurrent chromatography (HSCCC) and identified by ESI-MS/MS and high performance liquid chromatography (HPLC) techniques. The solvent system containing methyl tert-butyl ether, 1-butanol, acetonitrile, water, and trifluoroacetic acid (10:30:10:50:0.05; %, v/v) was developed in order to separate anthocyanins with different polarities. Cyanidin 3-O-(6″-O-α-rhamnopyranosyl-β-galactopyranoside) (also known as keracyanin) is the major component present in mulberry (41.3%). Other isolated pigments are cyanidin 3-O-(6″-O-α-rhamnopyranosyl-β-glucopyranoside) and petunidin 3-O-β-glucopyranoside. The binding characteristics of keracyanin with human serum albumin (HSA) were investigated by fluorescence and circular dichroism (CD) spectroscopy. Spectroscopic analysis reveals that HSA fluorescence quenched by keracyanin follows a static mode. Binding of keracyanin to HSA mainly depends on van der Waals force or H-bonds with average binding distance of 2.82 nm. The results from synchronous fluorescence, three-dimensional fluorescence, and CD spectra show that adaptive structure rearrangement and decrease of α-helical structure occur in the presence of keracyanin.

Fluorescence spectroscopic studies on substituted porphyrins in homogeneous solvents and cationic micellar medium

International Nuclear Information System (INIS)

Phukan, Smritakshi; Mishra, Bhupendra; Chandra Shekar, K.P.; Kumar, Anil; Kumar, Dalip; Mitra, Sivaprasad

2013-01-01

Steady state and time-resolved fluorescence properties of porphyrin appended 1,3,4-oxadiazoles and thiazoles were described in homogeneous medium as well as in presence of cationic surfactant cetyltrimethylammonium bromide (CTAB). The electron withdrawing substituent on the porphyrin moiety in both the cases make a donor–spacer–acceptor type of intramolecular photoinduced electron transfer (PET) system resulting substantial quenching in porphyrin fluorescence due to partial energy migration towards the acceptor in the excited state. The increase in fluorescence yield as well as appreciable difference in fluorescence decay behavior in aqueous buffer solution of pH 4.2 from that in chloroform solution is believed due to partial protonation of the porphyrin ring. All the investigated systems show preferential binding into the interfacial region of the micellar sub-domain with varying degree of penetration depending on the nature of the substituent. Almost 2–4 fold increase in fluorescence yield for the probes is explained on the basis of restricted flexibility and corresponding decrease in total nonradiative rate inside the micellar interface layer. - Highlights: ► Synthesis and detail fluorescence studies of a series of porphyrin appended 1,3,4-oxadiazoles and thiazoles. ► Comparison of homogeneous solvent study with that in CTAB. ► Substantial porphyrin fluorescence quenching in donor–spacer–acceptor type system. ► Preferential binding of the substituted porphyrins in micellar sub-domain. ► Appreciable increase in fluorescence yield in micellar interface layer is due to decrease in total nonradiative rate.

pH-dependence of the specific binding of Cu(II) and Zn(II) ions to the amyloid-β peptide

International Nuclear Information System (INIS)

Ghalebani, Leila; Wahlström, Anna; Danielsson, Jens; Wärmländer, Sebastian K.T.S.; Gräslund, Astrid

2012-01-01

Highlights: ► Cu(II) and Zn(II) display pH-dependent binding to the Aβ(1–40) peptide. ► At pH 7.4 both metal ions display residue-specific binding to the Aβ peptide. ► At pH 5.5 the binding specificity is lost for Zn(II). ► Differential Cu(II) and Zn(II) binding may help explain metal-induced AD toxicity. -- Abstract: Metal ions like Cu(II) and Zn(II) are accumulated in Alzheimer’s disease amyloid plaques. The amyloid-β (Aβ) peptide involved in the disease interacts with these metal ions at neutral pH via ligands provided by the N-terminal histidines and the N-terminus. The present study uses high-resolution NMR spectroscopy to monitor the residue-specific interactions of Cu(II) and Zn(II) with 15 N- and 13 C, 15 N-labeled Aβ(1–40) peptides at varying pH levels. At pH 7.4 both ions bind to the specific ligands, competing with one another. At pH 5.5 Cu(II) retains its specific histidine ligands, while Zn(II) seems to lack residue-specific interactions. The low pH mimics acidosis which is linked to inflammatory processes in vivo. The results suggest that the cell toxic effects of redox active Cu(II) binding to Aβ may be reversed by the protective activity of non-redox active Zn(II) binding to the same major binding site under non-acidic conditions. Under acidic conditions, the protective effect of Zn(II) may be decreased or changed, since Zn(II) is less able to compete with Cu(II) for the specific binding site on the Aβ peptide under these conditions.

Solvent substitutes

International Nuclear Information System (INIS)

Evanoff, S.P.

1995-01-01

The environmental and industrial hygiene regulations promulgated since 1980, most notably the Superfund Amendments and Reauthorization Act (SARA), the Hazardous and Solid Waste Amendments to the Resources Conservation and Recovery Act (RCRA), and the Clean Air Act Amendments of 1990, have brought about an increased emphasis on user exposure, hazardous waste generation, and air emissions. As a result, industry is performing a fundamental reassessment of cleaning solvents, processes, and procedures. The more progressive organizations have made their goal the elimination of solvents that may pose significant potential human health and environmental hazards. This chapter discusses solvent cleaning in metal-finishing, metal-manufacturing, and industrial maintenance applications; precision cleaning; and electronics manufacturing. Nonmetallic cleaning, adhesives, coatings, inks, and aerosols also will be addressed, but in a more cursory manner

Calcium binding properties of calcium dependent protein kinase 1 (CaCDPK1) from Cicer arietinum.

Science.gov (United States)

Dixit, Ajay Kumar; Jayabaskaran, Chelliah

2015-05-01

Calcium plays a crucial role as a secondary messenger in all aspects of plant growth, development and survival. Calcium dependent protein kinases (CDPKs) are the major calcium decoders, which couple the changes in calcium level to an appropriate physiological response. The mechanism by which calcium regulates CDPK protein is not well understood. In this study, we investigated the interactions of Ca(2+) ions with the CDPK1 isoform of Cicer arietinum (CaCDPK1) using a combination of biophysical tools. CaCDPK1 has four different EF hands as predicted by protein sequence analysis. The fluorescence emission spectrum of CaCDPK1 showed quenching with a 5 nm red shift upon addition of calcium, indicating conformational changes in the tertiary structure. The plot of changes in intensity against calcium concentrations showed a biphasic curve with binding constants of 1.29 μM and 120 μM indicating two kinds of binding sites. Isothermal calorimetric (ITC) titration with CaCl2 also showed a biphasic curve with two binding constants of 0.027 μM and 1.7 μM. Circular dichroism (CD) spectra showed two prominent peaks at 208 and 222 nm indicating that CaCDPK1 is a α-helical rich protein. Calcium binding further increased the α-helical content of CaCDPK1 from 75 to 81%. Addition of calcium to CaCDPK1 also increased fluorescence of 8-anilinonaphthalene-1-sulfonic acid (ANS) indicating exposure of hydrophobic surfaces. Thus, on the whole this study provides evidence for calcium induced conformational changes, exposure of hydrophobic surfaces and heterogeneity of EF hands in CaCDPK1. Copyright © 2015 Elsevier GmbH. All rights reserved.

Kinetic investigations of emulsion- and solvent-mediated radiation induced graft copolymerization of glycidyl methacrylate onto nylon-6 fibres

International Nuclear Information System (INIS)

Teo Ming Ting; Paveswari Sithambaranathan

2017-01-01

Kinetic behaviour of graft copolymerisation of glycidyl methacrylate onto nylon-6 fibres in solvent- and emulsion- media was investigated. The order for the dependence of the initial rate of grafting on the monomer concentration for solvent and emulsion grafting systems were found to be 1.65 and 1.57, respectively. The order of dependence of the initial rate of grafting on the absorbed dose was found to be 1.55 for solvent and 0.62 emulsion grafting systems. The results showed that grafting in both systems is controlled by diffusion mechanism and the degree of grafting can be effectively tuned by variation of the grafting parameters. (author)

Next Generation Solvent Performance in the Modular Caustic Side Solvent Extraction Process - 15495

Energy Technology Data Exchange (ETDEWEB)

Smith, Tara E. [Savannah River Remediation, LLC., Aiken, SC (United States); Scherman, Carl [Savannah River Remediation, LLC., Aiken, SC (United States); Martin, David [Savannah River Remediation, LLC., Aiken, SC (United States); Suggs, Patricia [Savannah River Site (SRS), Aiken, SC (United States)

2015-01-14

Changes to the Modular Caustic Side Solvent Extraction Unit (MCU) flow-sheet were implemented in the facility. Implementation included changing the scrub and strip chemicals and concentrations, modifying the O/A ratios for the strip, scrub, and extraction contactor banks, and blending the current BoBCalixC6 extractant-based solvent in MCU with clean MaxCalix extractant-based solvent. During the successful demonstration period, the MCU process was subject to rigorous oversight to ensure hydraulic stability and chemical/radionuclide analysis of the key process tanks (caustic wash tank, solvent hold tank, strip effluent hold tank, and decontaminated salt solution hold tank) to evaluate solvent carryover to downstream facilities and the effectiveness of cesium removal from the liquid salt waste. Results indicated the extraction of cesium was significantly more effective with an average Decontamination Factor (DF) of 1,129 (range was 107 to 1,824) and that stripping was effective. The contactor hydraulic performance was stable and satisfactory, as indicated by contactor vibration, contactor rotational speed, and flow stability; all of which remained at or near target values. Furthermore, the Solvent Hold Tank (SHT) level and specific gravity was as expected, indicating that solvent integrity and organic hydraulic stability were maintained. The coalescer performances were in the range of processing results under the BOBCalixC6 flow sheet, indicating negligible adverse impact of NGS deployment. After the Demonstration period, MCU began processing via routine operations. Results to date reiterate the enhanced cesium extraction and stripping capability of the Next Generation Solvent (NGS) flow sheet. This paper presents process performance results of the NGS Demonstration and continued operations of MCU utilizing the blended BobCalixC6-MaxCalix solvent under the NGS flowsheet.

Purex process solvent: literature review

International Nuclear Information System (INIS)

Geier, R.G.

1979-10-01

This document summarizes the data on Purex process solvent presently published in a variety of sources. Extracts from these various sources are presented herein and contain the work done, the salient results obtained, and the original, unaltered conclusions of the author of each paper. Three major areas are addressed: solvent stability, solvent quality testing, and solvent treatment processes. 34 references, 44 tables

Purex process solvent: literature review

Energy Technology Data Exchange (ETDEWEB)

Geier, R.G.

1979-10-01

This document summarizes the data on Purex process solvent presently published in a variety of sources. Extracts from these various sources are presented herein and contain the work done, the salient results obtained, and the original, unaltered conclusions of the author of each paper. Three major areas are addressed: solvent stability, solvent quality testing, and solvent treatment processes. 34 references, 44 tables.

Canonical and Noncanonical Sites Determine NPT2A Binding Selectivity to NHERF1 PDZ1.

Directory of Open Access Journals (Sweden)

Tatyana Mamonova

Full Text Available Na+/H+ Exchanger Regulatory Factor-1 (NHERF1 is a scaffolding protein containing 2 PDZ domains that coordinates the assembly and trafficking of transmembrane receptors and ion channels. Most target proteins harboring a C-terminus recognition motif bind more-or-less equivalently to the either PDZ domain, which contain identical core-binding motifs. However some substrates such as the type II sodium-dependent phosphate co-transporter (NPT2A, uniquely bind only one PDZ domain. We sought to define the structural determinants responsible for the specificity of interaction between NHERF1 PDZ domains and NPT2A. By performing all-atom/explicit-solvent molecular dynamics (MD simulations in combination with biological mutagenesis, fluorescent polarization (FP binding assays, and isothermal titration calorimetry (ITC, we found that in addition to canonical interactions of residues at 0 and -2 positions, Arg at the -1 position of NPT2A plays a critical role in association with Glu43 and His27 of PDZ1 that are absent in PDZ2. Experimentally introduced mutation in PDZ1 (Glu43Asp and His27Asn decreased binding to NPT2A. Conversely, introduction of Asp183Glu and Asn167His mutations in PDZ2 promoted the formation of favorable interactions yielding micromolar KDs. The results describe novel determinants within both the PDZ domain and outside the canonical PDZ-recognition motif that are responsible for discrimination of NPT2A between two PDZ domains. The results challenge general paradigms for PDZ recognition and suggest new targets for drug development.

Extrastriatal binding of [{sup 123}I]FP-CIT in the thalamus and pons: gender and age dependencies assessed in a European multicentre database of healthy controls

Energy Technology Data Exchange (ETDEWEB)

Koch, Walter; Unterrainer, Marcus; Xiong, Guoming; Bartenstein, Peter [University of Munich, Department of Nuclear Medicine, Munich (Germany); Diemling, Markus [Hermes Medical Solutions, Stockholm (Sweden); Varrone, Andrea [Karolinska University Hospital, Karolinska Institutet, Department of Clinical Neuroscience, Centre for Psychiatry Research, Stockholm (Sweden); Dickson, John C. [UCLH NHS Foundation Trust and University College, Institute of Nuclear Medicine, London (United Kingdom); Tossici-Bolt, Livia [University Hospitals Southampton NHS Trust, Department of Medical Physics, Southampton (United Kingdom); Sera, Terez [University of Szeged, Department of Nuclear Medicine and Euromedic Szeged, Szeged (Hungary); Asenbaum, Susanne [Medical University of Vienna, Department of Neurology, Vienna (Austria); Booij, Jan [University of Amsterdam, Department of Nuclear Medicine, Academic Medical Centre, Amsterdam (Netherlands); Kapucu, Ozlem L. [Gazi University, Department of Nuclear Medicine, Faculty of Medicine, Ankara (Turkey); Kluge, Andreas [ABX-CRO, Dresden (Germany); Ziebell, Morten [Rigshospitalet and University of Copenhagen, Neurobiology Research Unit, Copenhagen (Denmark); Darcourt, Jacques [University of Nice-Sophia Antipolis, Nuclear Medicine Department, Centre Antoine Lacassagne, Nice (France); Nobili, Flavio [University of Genoa, Clinical Neurology Unit, Department of Neuroscience (DINOGMI), Genoa (Italy); Pagani, Marco [CNR, Institute of Cognitive Sciences and Technologies, Rome (Italy); Karolinska Hospital, Department of Nuclear Medicine, Stockholm (Sweden); Hesse, Swen [University of Leipzig, Department of Nuclear Medicine, Leipzig (Germany); Leipzig University Medical Centre, Molecular Neuroimaging IFB Adiposity Diseases, Leipzig (Germany); Borght, Thierry Vander [Universite Catholique de Louvain, Nuclear Medicine Division, CHU Dinant Godinne, Yvoir (Belgium); Laere, Koen van [University Hospital and K.U. Leuven, Nuclear Medicine, Leuven (Belgium); Tatsch, Klaus [Staedtisches Klinikum Karlsruhe, Department of Nuclear Medicine, Karlsruhe (Germany); La Fougere, Christian [University of Munich, Department of Nuclear Medicine, Munich (Germany); University of Tuebingen, Department of Nuclear Medicine, Tuebingen (Germany)

2014-10-15

Apart from binding to the dopamine transporter (DAT), [{sup 123}I]FP-CIT shows moderate affinity for the serotonin transporter (SERT), allowing imaging of both monoamine transporters in a single imaging session in different brain areas. The aim of this study was to systematically evaluate extrastriatal binding (predominantly due to SERT) and its age and gender dependencies in a large cohort of healthy controls. SPECT data from 103 healthy controls with well-defined criteria of normality acquired at 13 different imaging centres were analysed for extrastriatal binding using volumes of interest analysis for the thalamus and the pons. Data were examined for gender and age effects as well as for potential influence of striatal DAT radiotracer binding. Thalamic binding was significantly higher than pons binding. Partial correlations showed an influence of putaminal DAT binding on measured binding in the thalamus but not on the pons. Data showed high interindividual variation in extrastriatal binding. Significant gender effects with 31 % higher binding in women than in men were observed in the thalamus, but not in the pons. An age dependency with a decline per decade (±standard error) of 8.2 ± 1.3 % for the thalamus and 6.8 ± 2.9 % for the pons was shown. The potential to evaluate extrastriatal predominant SERT binding in addition to the striatal DAT in a single imaging session was shown using a large database of [{sup 123}I]FP-CIT scans in healthy controls. For both the thalamus and the pons, an age-related decline in radiotracer binding was observed. Gender effects were demonstrated for binding in the thalamus only. As a potential clinical application, the data could be used as a reference to estimate SERT occupancy in addition to nigrostriatal integrity when using [{sup 123}I]FP-CIT for DAT imaging in patients treated with selective serotonin reuptake inhibitors. (orig.)

Mapping the Binding Interface of VEGF and a Monoclonal Antibody Fab-1 Fragment with Fast Photochemical Oxidation of Proteins (FPOP) and Mass Spectrometry

Science.gov (United States)

Zhang, Ying; Wecksler, Aaron T.; Molina, Patricia; Deperalta, Galahad; Gross, Michael L.

2017-05-01

We previously analyzed the Fab-1:VEGF (vascular endothelial growth factor) system described in this work, with both native top-down mass spectrometry and bottom-up mass spectrometry (carboxyl-group or GEE footprinting) techniques. This work continues bottom-up mass spectrometry analysis using a fast photochemical oxidation of proteins (FPOP) platform to map the solution binding interface of VEGF and a fragment antigen binding region of an antibody (Fab-1). In this study, we use FPOP to compare the changes in solvent accessibility by quantitating the extent of oxidative modification in the unbound versus bound states. Determining the changes in solvent accessibility enables the inference of the protein binding sites (epitope and paratopes) and a comparison to the previously published Fab-1:VEGF crystal structure, adding to the top-down and bottom-up data. Using this method, we investigated peptide-level and residue-level changes in solvent accessibility between the unbound proteins and bound complex. Mapping these data onto the Fab-1:VEGF crystal structure enabled successful characterization of both the binding region and regions of remote conformation changes. These data, coupled with our previous higher order structure (HOS) studies, demonstrate the value of a comprehensive toolbox of methods for identifying the putative epitopes and paratopes for biotherapeutic antibodies.

Mannose-Binding Lectin Binds to Amyloid Protein and Modulates Inflammation

Directory of Open Access Journals (Sweden)

Mykol Larvie

2012-01-01

Full Text Available Mannose-binding lectin (MBL, a soluble factor of the innate immune system, is a pattern recognition molecule with a number of known ligands, including viruses, bacteria, and molecules from abnormal self tissues. In addition to its role in immunity, MBL also functions in the maintenance of tissue homeostasis. We present evidence here that MBL binds to amyloid β peptides. MBL binding to other known carbohydrate ligands is calcium-dependent and has been attributed to the carbohydrate-recognition domain, a common feature of other C-type lectins. In contrast, we find that the features of MBL binding to Aβ are more similar to the reported binding characteristics of the cysteine-rich domain of the unrelated mannose receptor and therefore may involve the MBL cysteine-rich domain. Differences in MBL ligand binding may contribute to modulation of inflammatory response and may correlate with the function of MBL in processes such as coagulation and tissue homeostasis.

HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information

Directory of Open Access Journals (Sweden)

Hu Jianjun

2011-05-01

Full Text Available Abstract Background Accurate prediction of binding residues involved in the interactions between proteins and small ligands is one of the major challenges in structural bioinformatics. Heme is an essential and commonly used ligand that plays critical roles in electron transfer, catalysis, signal transduction and gene expression. Although much effort has been devoted to the development of various generic algorithms for ligand binding site prediction over the last decade, no algorithm has been specifically designed to complement experimental techniques for identification of heme binding residues. Consequently, an urgent need is to develop a computational method for recognizing these important residues. Results Here we introduced an efficient algorithm HemeBIND for predicting heme binding residues by integrating structural and sequence information. We systematically investigated the characteristics of binding interfaces based on a non-redundant dataset of heme-protein complexes. It was found that several sequence and structural attributes such as evolutionary conservation, solvent accessibility, depth and protrusion clearly illustrate the differences between heme binding and non-binding residues. These features can then be separately used or combined to build the structure-based classifiers using support vector machine (SVM. The results showed that the information contained in these features is largely complementary and their combination achieved the best performance. To further improve the performance, an attempt has been made to develop a post-processing procedure to reduce the number of false positives. In addition, we built a sequence-based classifier based on SVM and sequence profile as an alternative when only sequence information can be used. Finally, we employed a voting method to combine the outputs of structure-based and sequence-based classifiers, which demonstrated remarkably better performance than the individual classifier alone

The molecular basis of FHA domain:phosphopeptide binding specificity and implications for phospho-dependent signaling mechanisms.

Science.gov (United States)

Durocher, D; Taylor, I A; Sarbassova, D; Haire, L F; Westcott, S L; Jackson, S P; Smerdon, S J; Yaffe, M B

2000-11-01

Forkhead-associated (FHA) domains are a class of ubiquitous signaling modules that appear to function through interactions with phosphorylated target molecules. We have used oriented peptide library screening to determine the optimal phosphopeptide binding motifs recognized by several FHA domains, including those within a number of DNA damage checkpoint kinases, and determined the X-ray structure of Rad53p-FHA1, in complex with a phospho-threonine peptide, at 1.6 A resolution. The structure reveals a striking similarity to the MH2 domains of Smad tumor suppressor proteins and reveals a mode of peptide binding that differs from SH2, 14-3-3, or PTB domain complexes. These results have important implications for DNA damage signaling and CHK2-dependent tumor suppression, and they indicate that FHA domains play important and unsuspected roles in S/T kinase signaling mechanisms in prokaryotes and eukaryotes.

Promiscuous ligand-dependent activation of the Ah receptor: chemicals in crude extracts from commercial and consumer products bind to and activate the Ah receptor and Ah receptor-dependent gene expression

Energy Technology Data Exchange (ETDEWEB)

Denison, M.; Rogers, W.; Bohonowych, J.; Zhao, B. [Dept. of Environmental Toxicology, Univ. of California, Davis (United States)

2004-09-15

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD, dioxin) and related halogenated and polycyclic aromatic hydrocarbons (HAHs and PAHs) produce a variety of toxic and biological effects, the majority of which are mediated by their ability to bind to and activate the Ah receptor (AhR) and AhR-dependent gene expression. While previous studies suggested that the physiochemical characteristics of AhR ligands (i.e. HAH and PAH agonists) must meet a defined set of criteria, it has recently become abundantly clear that the AhR can be bound and activated by structurally diverse range of synthetic and naturally occurring chemicals. Based on the spectrum of AhR ligands identified to date, the structural promiscuity of AhR ligands is significantly more diverse than that observed for other liganddependent nuclear receptors. However, a detailed understanding of the structural diversity of AhR ligands and their respective biological and toxicological activities remains to be established and could provide insights into the identity of endogenous ligands. Over the past several years we have developed and utilized several AhR-based in vitro and cell-based bioassay systems to screen pure chemicals and chemical libraries as well as mixtures of chemicals with the goal of defining the spectrum of chemicals that can bind to and activate/inhibit the AhR and AhR-dependent gene expression. In addition, demonstration of the presence of AhR agonists/antagonists in extracts containing complex mixtures of chemicals from a variety of biological and environmental samples, coupled with AhR bioassay-based fractionation procedures, provides an avenue in which to identify novel AhR ligands. In previous preliminary screening studies we demonstrated the presence of AhR agonists in extracts of commercial and consumer products using an in vitro guinea pig hepatic AhR DNA binding and mouse gene induction assays. Here we have extended these studies and have examined the ability of crude DMSO and ethanol extracts

The effect of solvent component on the discharge performance of Lithium-sulfur cell containing various organic electrolytes

International Nuclear Information System (INIS)

Kim, Seok; Jung, Yongju; Lim, Hong S.

2004-01-01

The effect of solvent component on the discharge performance of lithium-sulfur (Li/S) cell and the optimal composition of ternary electrolyte for the improved discharge performance of the cell have been investigated. The capacity value and capacity stability with cycle are dependent on the nature of solvent as well as the composition of mixed solvent. The change trend of discharge performance as a function of content of each solvent component is studied. Capacity value increases as the 1,3-dioxolane (DOX) content decreases. Average discharge voltage shows larger value when the 1,2-dimethoxy ethane (DME) content is small. Finally, we have obtained the optimal solvent composition by using a statistical method

Conventional and accelerated-solvent extractions of green tea (camellia sinensis) for metabolomics-based chemometrics.

Science.gov (United States)

Kellogg, Joshua J; Wallace, Emily D; Graf, Tyler N; Oberlies, Nicholas H; Cech, Nadja B

2017-10-25

Metabolomics has emerged as an important analytical technique for multiple applications. The value of information obtained from metabolomics analysis depends on the degree to which the entire metabolome is present and the reliability of sample treatment to ensure reproducibility across the study. The purpose of this study was to compare methods of preparing complex botanical extract samples prior to metabolomics profiling. Two extraction methodologies, accelerated solvent extraction and a conventional solvent maceration, were compared using commercial green tea [Camellia sinensis (L.) Kuntze (Theaceae)] products as a test case. The accelerated solvent protocol was first evaluated to ascertain critical factors influencing extraction using a D-optimal experimental design study. The accelerated solvent and conventional extraction methods yielded similar metabolite profiles for the green tea samples studied. The accelerated solvent extraction yielded higher total amounts of extracted catechins, was more reproducible, and required less active bench time to prepare the samples. This study demonstrates the effectiveness of accelerated solvent as an efficient methodology for metabolomics studies. Copyright © 2017. Published by Elsevier B.V.

Solvent/non-solvent sintering: a novel route to create porous microsphere scaffolds for tissue regeneration.

Science.gov (United States)

Brown, Justin L; Nair, Lakshmi S; Laurencin, Cato T

2008-08-01

Solvent/non-solvent sintering creates porous polymeric microsphere scaffolds suitable for tissue engineering purposes with control over the resulting porosity, average pore diameter, and mechanical properties. Five different biodegradable biocompatible polyphosphazenes exhibiting glass transition temperatures from -8 to 41 degrees C and poly (lactide-co-glycolide), (PLAGA) a degradable polymer used in a number of biomedical settings, were examined to study the versatility of the process and benchmark the process to heat sintering. Parameters such as: solvent/non-solvent sintering solution composition and submersion time effect the sintering process. PLAGA microsphere scaffolds fabricated with solvent/non-solvent sintering exhibited an interconnected porosity and pore size of 31.9% and 179.1 mum, respectively which was analogous to that of conventional heat sintered PLAGA microsphere scaffolds. Biodegradable polyphosphazene microsphere scaffolds exhibited a maximum interconnected porosity of 37.6% and a maximum compressive modulus of 94.3 MPa. Solvent/non-solvent sintering is an effective strategy for sintering polymeric microspheres, with a broad spectrum of glass transition temperatures, under ambient conditions making it an excellent fabrication route for developing tissue engineering scaffolds and drug delivery vehicles. (c) 2007 Wiley Periodicals, Inc.

Measurement and correlation of solubility of cefmenoxime hydrochloride in pure solvents and binary solvent mixtures

International Nuclear Information System (INIS)

Wang, Jinxiu; Xie, Chuang; Yin, Qiuxiang; Tao, Linggang; Lv, Jun; Wang, Yongli; He, Fang; Hao, Hongxun

2016-01-01

Highlights: • Solubility of cefmenoxime hydrochloride in pure and binary solvents was determined. • The experimental solubility data were correlated by thermodynamic models. • A model was employed to calculate the melting temperature of cefmenoxime hydrochloride. • Mixing thermodynamic properties of cefmenoxime hydrochloride were calculated. - Abstract: The solubility of cefmenoxime hydrochloride in pure solvents and binary solvent mixtures was measured at temperatures from (283.15 to 313.15) K by using the UV spectroscopic method. The results reveal that the solubility of cefmenoxime hydrochloride increases with increasing temperature in all solvent selected. The solubility of cefmenoxime hydrochloride reaches its maximum value when the mole fraction of isopropanol is 0.2 in the binary solvent mixtures of (isopropanol + water). The modified Apelblat equation and the NRTL model were successfully used to correlate the experimental solubility in pure solvents while the modified Apelblat equation, the CNIBS/R–K model and the Jouyban–Acree model were applied to correlate the solubility in binary solvent mixtures. In addition, the mixing thermodynamic properties of cefmenoxime hydrochloride in different solvents were also calculated based on the NRTL model and experimental solubility data.

Mycobacterial laminin-binding histone-like protein mediates collagen-dependent cytoadherence

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André Alves Dias

2012-12-01

Full Text Available When grown in the presence of exogenous collagen I, Mycobacterium bovis BCG was shown to form clumps. Scanning electron microscopy examination of these clumps revealed the presence of collagen fibres cross-linking the bacilli. Since collagen is a major constituent of the eukaryotic extracellular matrices, we assayed BCG cytoadherence in the presence of exogenous collagen I. Collagen increased the interaction of the bacilli with A549 type II pneumocytes or U937 macrophages, suggesting that BCG is able to recruit collagen to facilitate its attachment to host cells. Using an affinity chromatography approach, we have isolated a BCG collagen-binding protein corresponding to the previously described mycobacterial laminin-binding histone-like protein (LBP/Hlp, a highly conserved protein associated with the mycobacterial cell wall. Moreover, Mycobacterium leprae LBP/Hlp, a well-characterized adhesin, was also able to bind collagen I. Finally, using recombinant fragments of M. leprae LBP/Hlp, we mapped the collagen-binding activity within the C-terminal domain of the adhesin. Since this protein was already shown to be involved in the recognition of laminin and heparan sulphate-containing proteoglycans, the present observations reinforce the adhesive activities of LBP/Hlp, which can be therefore considered as a multifaceted mycobacterial adhesin, playing an important role in both leprosy and tuberculosis pathogenesis.

Measurement and prediction of dabigatran etexilate mesylate Form II solubility in mono-solvents and mixed solvents

International Nuclear Information System (INIS)

Xiao, Yan; Wang, Jingkang; Wang, Ting; Ouyang, Jinbo; Huang, Xin; Hao, Hongxun; Bao, Ying; Fang, Wen; Yin, Qiuxiang

2016-01-01

Highlights: • Solubility of DEM Form II in mono-solvents and binary solvent mixtures was measured. • Regressed UNIFAC model was used to predict the solubility in solvent mixtures. • The experimental solubility data were correlated by different models. - Abstract: UV spectrometer method was used to measure the solubility data of dabigatran etexilate mesylate (DEM) Form II in five mono-solvents (methanol, ethanol, ethane-1,2-diol, DMF, DMAC) and binary solvent mixtures of methanol and ethanol in the temperature range from 287.37 K to 323.39 K. The experimental solubility data in mono-solvents were correlated with modified Apelblat equation, van’t Hoff equation and λh equation. GSM model and Modified Jouyban-Acree model were employed to correlate the solubility data in mixed solvent systems. And Regressed UNIFAC model was used to predict the solubility of DEM Form II in the binary solvent mixtures. Results showed that the predicted data were consistent with the experimental data.

Effect of solvents on the enzyme mediated degradation of copolymers

International Nuclear Information System (INIS)

Banerjee, Aditi; Chatterjee, Kaushik; Madras, Giridhar

2015-01-01

The biodegradation of polycaprolactone (PCL), polylactic acid (PLA), polyglycolide (PGA) and their copolymers, poly (lactide-co-glycolide) and poly (D, L-lactide-co-caprolactone) (PLCL) was investigated. The influence of different solvents on the degradation of these polymers at 37 °C in the presence of two different lipases namely Novozym 435 and the free lipase of porcine pancreas was investigated. The rate coefficients for the polymer degradation and enzyme deactivation were determined using continuous distribution kinetics. Among the homopolymers, the degradation of PGA was nearly an order of magnitude lower than that for PCL and PLA. The overall rate coefficients of the copolymers were higher than their respective homopolymers. Thus, PLCL degraded faster than either PCL or PLA. The degradation was highly dependent on the viscosity of the solvent used with the highest degradation observed in acetone. The degradation of the polymers in acetone was nearly twice that observed in dimethyl sulfoxide indicating that the degradation decreases with increase in the solvent viscosity. The degradation of the polymers in water-solvent mixtures indicated an optimal water content of 2.5 wt% of water. (paper)

Photoaffinity studies of the tubulin-colchicine binding site

International Nuclear Information System (INIS)

Hahn, K.M.

1987-01-01

A variety of colchicine derivatives were synthesized and coupled with 3,3,3-trifluoro-2-diazapropionyl chloride (TFDP-Cl) to produce colchicine photoaffinity analogs for use in tubulin labelling studies. Photoaffinity analogs of allocolchicine and podophylotoxin were also made using the same photoreactive moiety. Several labels were found to be effective inhibitors of tubulin polymerization. The approximate tubulin binding constants of the labels, calculated from polymerization inhibition data, varied between 2.2 x 10 5 to 2.5 x 10 3 M -1 . The labels chosen for use in tubulin labelling experiments were (N-TFDP) deacetyl-thiocolchicine 1, (O-TFDP)thiocolchifoline 2, and (O-TFDP)-2-demethylthiocolchicine 3. Compound 1 was found to bind tubulin reversibly and to competitively inhibit colchicine binding. Methods for the incorporation of tritium and 14 C in these labels were developed. Conditions were found which caused labels to insert into solvent without photorearrangement of the colchicine skeleton. Catalytic base caused the α-diazo amide of 1 to rearrange to a triazole

The effect of deep eutectic solvents on catalytic function and structure of bovine liver catalase.

Science.gov (United States)

Harifi-Mood, Ali Reza; Ghobadi, Roohollah; Divsalar, Adeleh

2017-02-01

Aqueous solutions of reline and glyceline, the most common deep eutectic solvents, were used as a medium for Catalase reaction. By some spectroscopic methods such as UV-vis, fluorescence and circular dichroism (CD) function and structure of Catalase were investigated in aqueous solutions of reline and glyceline. These studies showed that the binding affinity of the substrate to the enzyme increased in the presence of 100mM glyceline solution, which contrasts with reline solution that probably relates to instructive changes in secondary structure of protein. Meanwhile, enzyme remained nearly 70% and 80% active in this concentration of glyceline and reline solutions respectively. In the high concentration of DES solutions, enzyme became mainly inactive but surprisingly stayed in nearly 40% active in choline chloride solution, which is the common ion species in reline and glyceline solvents. It is proposed that the chaotropic nature of choline cation might stop the reducing trend of activity in concentrated choline chloride solutions but this instructive effect is lost in aqueous deep eutectic solvents. In this regard, the presence of various concentrations of deep eutectic solvents in the aqueous media of human cells would be an activity adjuster for this important enzyme in its different operation conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

Characterization of microwave-induced electric discharge phenomena in metal-solvent mixtures.

Science.gov (United States)

Chen, Wen; Gutmann, Bernhard; Kappe, C Oliver

2012-02-01

Electric discharge phenomena in metal-solvent mixtures are investigated utilizing a high field density, sealed-vessel, single-mode 2.45 GHz microwave reactor with a built-in camera. Particular emphasis is placed on studying the discharges exhibited by different metals (Mg, Zn, Cu, Fe, Ni) of varying particle sizes and morphologies in organic solvents (e.g., benzene) at different electric field strengths. Discharge phenomena for diamagnetic and paramagnetic metals (Mg, Zn, Cu) depend strongly on the size of the used particles. With small particles, short-lived corona discharges are observed that do not lead to a complete breakdown. Under high microwave power conditions or with large particles, however, bright sparks and arcs are experienced, often accompanied by solvent decomposition and formation of considerable amounts of graphitized material. Small ferromagnetic Fe and Ni powders (discharges. Electric discharges were also observed when Cu metal or other conductive materials such as silicon carbide were exposed to the microwave field in the absence of a solvent in an argon or nitrogen atmosphere.

Chemical approach to solvent removal during nanoencapsulation: its application to preparation of PLGA nanoparticles with non-halogenated solvent

Energy Technology Data Exchange (ETDEWEB)

Lee, Youngme [Ewha Womans University, College of Pharmacy (Korea, Republic of); Sah, Eric [University of Notre Dame, College of Science (United States); Sah, Hongkee, E-mail: hsah@ewha.ac.kr [Ewha Womans University, College of Pharmacy (Korea, Republic of)

2015-11-15

The objective of this study was to develop a new oil-in-water emulsion-based nanoencapsulation method for the preparation of PLGA nanoparticles using a non-halogenated solvent. PLGA (60–150 mg) was dissolved in 3 ml of methyl propionate, which was vortexed with 4 ml of a 0.5–4 % polyvinyl alcohol solution. This premix was sonicated for 2 min, added into 30 ml of the aqueous polyvinyl alcohol solution, and reacted with 3 ml of 10 N NaOH. Solvent removal was achieved by the alkaline hydrolysis of methyl propionate dissolved in an aqueous phase into water-soluble methanol and sodium propionate. It was a simple but effective technique to quickly harden nanoemulsion droplets into nanoparticles. The appearing PLGA nanoparticles were recovered by ultracentrifugation and/or dialysis, lyophilized with trehalose, and redispersed by water. This nanoencapsulation technique permitted a control of their mean diameters over 151.7 ± 3.8 to 440.2 ± 22.2 nm at mild processing conditions. When the aqueous polyvinyl alcohol concentration was set at ≥1 %, nanoparticles showed uniform distributions with polydispersity indices below 0.1. There were no significant changes in their mean diameters and size distribution patterns before and after lyophilization. When mestranol was encapsulated into nanoparticles, the drug was completely nanoencapsulated: depending on experimental conditions, their encapsulation efficiencies were determined to be 99.4 ± 7.2 to 105.8 ± 6.3 %. This simple, facile nanoencapsulation technique might have versatile applications for the preparation of polymeric nanoparticulate dosage forms.Graphical AbstractSchematic illustration of an innovative chemical approach to solvent removal during nanoencapsulation. Methyl propionate present in the aqueous continuous phase reacts with sodium hydroxide, thereby producing methanol and sodium propionate. Its alkaline hydrolysis allows the continuous extraction of the solvent out of nanoemulsion

Chemical approach to solvent removal during nanoencapsulation: its application to preparation of PLGA nanoparticles with non-halogenated solvent

International Nuclear Information System (INIS)

Lee, Youngme; Sah, Eric; Sah, Hongkee

2015-01-01

The objective of this study was to develop a new oil-in-water emulsion-based nanoencapsulation method for the preparation of PLGA nanoparticles using a non-halogenated solvent. PLGA (60–150 mg) was dissolved in 3 ml of methyl propionate, which was vortexed with 4 ml of a 0.5–4 % polyvinyl alcohol solution. This premix was sonicated for 2 min, added into 30 ml of the aqueous polyvinyl alcohol solution, and reacted with 3 ml of 10 N NaOH. Solvent removal was achieved by the alkaline hydrolysis of methyl propionate dissolved in an aqueous phase into water-soluble methanol and sodium propionate. It was a simple but effective technique to quickly harden nanoemulsion droplets into nanoparticles. The appearing PLGA nanoparticles were recovered by ultracentrifugation and/or dialysis, lyophilized with trehalose, and redispersed by water. This nanoencapsulation technique permitted a control of their mean diameters over 151.7 ± 3.8 to 440.2 ± 22.2 nm at mild processing conditions. When the aqueous polyvinyl alcohol concentration was set at ≥1 %, nanoparticles showed uniform distributions with polydispersity indices below 0.1. There were no significant changes in their mean diameters and size distribution patterns before and after lyophilization. When mestranol was encapsulated into nanoparticles, the drug was completely nanoencapsulated: depending on experimental conditions, their encapsulation efficiencies were determined to be 99.4 ± 7.2 to 105.8 ± 6.3 %. This simple, facile nanoencapsulation technique might have versatile applications for the preparation of polymeric nanoparticulate dosage forms.Graphical AbstractSchematic illustration of an innovative chemical approach to solvent removal during nanoencapsulation. Methyl propionate present in the aqueous continuous phase reacts with sodium hydroxide, thereby producing methanol and sodium propionate. Its alkaline hydrolysis allows the continuous extraction of the solvent out of nanoemulsion

Enhancing Self-Assembly in Cellulose Nanocrystal Suspensions Using High-Permittivity Solvents.

Science.gov (United States)

Bruckner, Johanna R; Kuhnhold, Anja; Honorato-Rios, Camila; Schilling, Tanja; Lagerwall, Jan P F

2016-09-27

Helical liquid crystal self-assembly in suspensions of cellulose nanocrystals (CNCs), bioderived nanorods exhibiting excellent mechanical and optical properties, opens attractive routes to sustainable production of advanced functional materials. For convenience, in most studies until now, the CNCs were suspended in water, leaving a knowledge gap concerning the influence of the solvent. Using a novel approach for aggregation-free solvent exchange in CNC suspensions, here we show that protic solvents with a high dielectric permittivity εr significantly speed up self-assembly (from days to hours) at high CNC mass fraction and reduce the concentration dependence of the helix period (variation reducing from more than 30 μm to less than 1 μm). Moreover, our computer simulations indicate that the degree of order at constant CNC content increases with increasing εr, leading to a shorter pitch and a reduced threshold for liquid crystallinity. In low-εr solvents, the onset of long-range orientational order is coupled to kinetic arrest, preventing the formation of a helical superstructure. Our results show that the choice of solvent is a powerful parameter for tuning the behavior of CNC suspensions, enhancing our ability to control the self-assembly and thereby harvesting valuable novel cellulose-based materials.

Cyanide binding to ferrous and ferric microperoxidase-11.

Science.gov (United States)

Ascenzi, Paolo; Sbardella, Diego; Santucci, Roberto; Coletta, Massimo

2016-07-01

Microperoxidase-11 (MP11) is an undecapeptide derived from horse heart cytochrome c (cytc). MP11 is characterized by a covalently linked solvent-exposed heme group, the heme-Fe atom being axially coordinated by a histidyl residue. Here, the reactions of ferrous and ferric MP11 (MP11-Fe(II) and MP11-Fe(III), respectively) with cyanide have been investigated from the kinetic and thermodynamic viewpoints, at pH 7.0 and 20.0 °C. Values of the second-order rate constant for cyanide binding to MP11-Fe(II) and MP11-Fe(III) are 4.5 M(-1) s(-1) and 8.9 × 10(3) M(-1) s(-1), respectively. Values of the first-order rate constant for cyanide dissociation from ligated MP11-Fe(II) and MP11-Fe(III) are 1.8 × 10(-1) s(-1) and 1.5 × 10(-3) s(-1), respectively. Values of the dissociation equilibrium constant for cyanide binding to MP11-Fe(II) and MP11-Fe(III) are 3.7 × 10(-2) and 1.7 × 10(-7) M, respectively, matching very well with those calculated from kinetic parameters so that no intermediate species seem to be involved in the ligand-binding process. The pH-dependence of cyanide binding to MP11-Fe(III) indicates that CN(-) is the only binding species. Present results have been analyzed in parallel with those of several heme-proteins, suggesting that (1) the ligand accessibility to the metal center and cyanide ionization may modulate the formation of heme-Fe-cyanide complexes, and (2) the general polarity of the heme pocket and/or hydrogen bonding of the heme-bound ligand may affect cyanide exit from the protein matrix. Microperoxidase-11 (MP11) is an undecapeptide derived from horse heart cytochrome c. Penta-coordinated MP11 displays a very high reactivity towards cyanide, whereas the reactivity of hexa-coordinated horse heart cytochrome c is very low.

A fluorescence polarization binding assay to identify inhibitors of flavin-dependent monooxygenases.

Science.gov (United States)

Qi, Jun; Kizjakina, Karina; Robinson, Reeder; Tolani, Karishma; Sobrado, Pablo

2012-06-01

N-Hydroxylating monooxygenases (NMOs) are essential for pathogenesis in fungi and bacteria. NMOs catalyze the hydroxylation of sine and ornithine in the biosynthesis of hydroxamate-containing siderophores. Inhibition of kynurenine monooxygenase (KMO), which catalyzes the conversion of kynurenine to 3-hydroxykynurenine, alleviates neurodegenerative disorders such as Huntington's and Alzheimer's diseases and brain infections caused by the parasite Trypanosoma brucei. These enzymes are examples of flavin-dependent monooxygenases, which are validated drug targets. Here, we describe the development and optimization of a fluorescence polarization assay to identify potential inhibitors of flavin-dependent monooxygenases. Fluorescently labeled ADP molecules were synthesized and tested. An ADP-TAMRA chromophore bound to KMO with a K(d) value of 0.60 ± 0.05 μM and to the NMOs from Aspergillus fumigatus and Mycobacterium smegmatis with K(d) values of 2.1 ± 0.2 and 4.0 ± 0.2 μM, respectively. The assay was tested in competitive binding experiments with substrates and products of KMO and an NMO. Furthermore, we show that this assay can be used to identify inhibitors of NMOs. A Z' factor of 0.77 was calculated, and we show that the assay exhibits good tolerance to temperature, incubation time, and dimethyl sulfoxide concentration. Copyright © 2012 Elsevier Inc. All rights reserved.

Iodine removing method in organic solvent

International Nuclear Information System (INIS)

Suzuki, Takeo; Sakurai, Manabu

1988-01-01

Purpose: To effectively remove iodine in an organic solvent to thereby remove iodine in the solvent that can be re-used or put to purning treatment. Method: Organic solvent formed from wastes of nuclear facilities is mixed with basic lead acetate, or silica gel or activated carbon incorporated with such a compound to adsorb iodine in the organic solvent to the basic lead acetate. Then, iodine in the organic solvent is removed by separating to eliminate the basic lead acetate adsorbing iodine from the organic solvent or by passing the organic solvent through a tower or column charged or pre-coated with silica gel or activated carbon incorporated with lead acetate. By using basic lead acetate as the adsorbents, iodine can effective by adsorbed and eliminated. Thus, the possibility of circumstantial release of iodine can be reduced upon reusing or burning treatment of the organic solvent. (Kamimura, M.)

Sensibilidade do carrapato Boophilus microplus a solventes Sensibility of Boophilus microplus tick to solvents

Directory of Open Access Journals (Sweden)

Ana Carolina de Souza Chagas

2003-02-01

Full Text Available Os experimentos envolvendo o uso de acaricidas sintéticos ou naturais, geralmente necessitam da utilização de um solvente. Com a finalidade de verificar a sensibilidade do carrapato bovino Boophilus microplus a diferentes solventes, larvas e fêmeas ingurgitadas deste ectoparasito foram expostas a sete solventes em cinco diferentes concentrações, na ausência e presença de azeite de oliva. Os resultados mostraram que a utilização do azeite de oliva não produz resultados diferentes estatisticamente em testes de larvas com papel impregnado, fato não verificado em testes de imersão de adultos com compostos hidrofílicos. A mortalidade média causada pelos solventes foi menor nos testes com papel impregnado, aumentando nos testes de imersão de larvas e de adultos. Solventes de baixo peso molecular e pouca viscosidade como o álcool metílico e o álcool etílico, não interferiram na mortalidade média em testes biológicos de B. microplus, principalmente em concentrações inferiores a 76%.Experiments carried out with synthetic or natural acaricides usually use a solvent. To investigate the sensitivity of Boophilus microplus cattle tick to different solvents, larvae and engorged female were subjected to seven solvents in five different concentrations. It was done in the presence and absence of olive oil. The results showed that the utilization of olive oil doesn't produce different statistical results in impregnated paper larvae test. It did not happen in adults immersion test with hydrophilic compounds. The mean mortality caused by solvents was small in impregnated paper larvae test, increasing in immersion tests of larvae and adults. Solvents with low molecular weight and viscosity like ethyl alcohol and methyl alcohol did not cause interference in the mortality of B. microplus in biological tests, mainly in concentrations below 76%.

Photoreactivity of biologically active compounds. XVII. Influence of solvent interactions on spectroscopic properties and photostability of primaquine.

Science.gov (United States)

Kristensen, S

2005-06-01

The influence of solvent interactions on absorption properties, fluorescence properties (emission spectra and quantum yields) and relative photochemical degradation rates of primaquine has been investigated, in order to evaluate photochemical reaction mechanisms and chemical properties of the compound. The first absorption band (n - pi*) of primaquine is only slightly dependent on properties of the solvent, which can be ascribed to a strong, intramolecular hydrogen bond between the quinoline N and amine group in the ground state (S0). Amphiprotic solvents with predominant acidic properties (water and methanol) will to some extent stabilize the molecule and initiate hypsochromic shifts of the absorption band by protic interactions, while the other solvents (amphiprotic, basic and neutral) influence the absorption spectrum by general solvent effects only. The excited singlet (S1*) state of primaquine interacts more efficiently with the surrounding solvents than the S0 state, as evaluated by the Stokes shifts. The pKa value of the quinoline N is likely to increase in the S1* state, which is important for the observed protic interactions with amphiprotic solvents of predominant acidity. Specific solvent effects are highly important for the efficiency of the fluorescence (fluorescence quantum yields; phi f). The fluorescence is quenched by amphiprotic solvents, likely due to a rupture of the intramolecular bond and protonation of the quinolone N, and enhanced by polar, non-protic (basic) solvents, probably by stabilization of the delta intramolecular hydrogen bond. The observed photochemical degradation rates of primaquine in amphiprotic media are positively correlated with phi f, indicating that the photochemical degradation of primaquine is dependent on intramolecular hydrogen bonding and non protonated lone-pair electrons at the quinoline N. The intramolecular ring-formation with a subsequent increased lipophilic character and (lack of) interactions with the

Modeling coding-sequence evolution within the context of residue solvent accessibility.

Science.gov (United States)

Scherrer, Michael P; Meyer, Austin G; Wilke, Claus O

2012-09-12

Protein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues) tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues). Here, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94) model in which all model parameters can be functions of the relative solvent accessibility (RSA) of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratio ω that varies linearly with RSA provides a better model fit than an RSA-independent ω or an ω that is estimated separately in individual RSA bins. We further show that the branch length t and the transition-transverion ratio κ also vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94) model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship between ω and RSA, and gene expression level affects both the intercept and the slope. Structure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship between ω and RSA implies that genes are better characterized by their ω slope and intercept than by just their mean ω.

Modeling coding-sequence evolution within the context of residue solvent accessibility

Directory of Open Access Journals (Sweden)

Scherrer Michael P

2012-09-01

Full Text Available Abstract Background Protein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues. Results Here, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94 model in which all model parameters can be functions of the relative solvent accessibility (RSA of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratio ω that varies linearly with RSA provides a better model fit than an RSA-independent ω or an ω that is estimated separately in individual RSA bins. We further show that the branch length t and the transition-transverion ratio κ also vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94 model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship between ω and RSA, and gene expression level affects both the intercept and the slope. Conclusions Structure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship between ω and RSA implies that genes are better characterized by their ω slope and intercept than by just their mean ω.

The salting-out of molibdoferrats(II from aqueous solutions by the organic solvents

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Mykola V. Nikolenko

2016-12-01

Full Text Available The aim of this work was to develop a method for producing of molybdoferrate(II precipitates by salting-out them from aqueous solutions by means of organic solvents. Dependence of the composition of molybdoferrate(II precipitates on the pH of the reaction solutions was studied. Experiments on salting-out of molybdoferrate(II with various organic solvents were carried out. As a result it was found that the best reagent for the molybdoferrate(II salting-out is acetone. By its use, lowest quantity of the ammonium sulfate impurities was obtained. It is also of importance that by using of acetone the process of regeneration by distillation of the reaction solutions is characterized by the lowest energy consumption. A functional relationship between the solubility of molybdoferrates(II and dielectric constant of the medium was established. By increasing the dielectric constant of the solvent solubility of molybdoferrates(II rapidly increases. The linearized dependence ln(lnS–ln(1/e was proposed to predict the solubility of molybdoferrates(II in various aqueous-organic solutions.

Next Generation Solvent Development for Caustic-Side Solvent Extraction of Cesium

Energy Technology Data Exchange (ETDEWEB)

Moyer, Bruce A. [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Birdwell, Joseph F. [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Bonnesen, Peter V. [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Bruffey, Stephanie [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

2014-03-01

This report summarizes the FY 2010 and 2011 accomplishments at Oak Ridge National Laboratory (ORNL) in developing the Next Generation Caustic-Side Solvent Extraction (NG-CSSX) process, referred to commonly as the Next Generation Solvent (NGS), under funding from the U.S. Department of Energy, Office of Environmental Management (DOE-EM), Office of Technology Innovation and Development. The primary product of this effort is a process solvent and preliminary flowsheet capable of meeting a target decontamination factor (DF) of 40,000 for worst-case Savannah River Site (SRS) waste with a concentration factor of 15 or higher in the 18-stage equipment configuration of the SRS Modular Caustic-Side Solvent Extraction Unit (MCU). In addition, the NG-CSSX process may be readily adapted for use in the SRS Salt Waste Processing Facility (SWPF) or in supplemental tank-waste treatment at Hanford upon appropriate solvent or flowsheet modifications. Efforts in FY 2010 focused on developing a solvent composition and process flowsheet for MCU implementation. In FY 2011 accomplishments at ORNL involved a wide array of chemical-development activities and testing up through single-stage hydraulic and mass-transfer tests in 5-cm centrifugal contactors. Under subcontract from ORNL, Argonne National Laboratory (ANL) designed a preliminary flowsheet using ORNL cesium distribution data, and Tennessee Technological University confirmed a chemical model for cesium distribution ratios (DCs) as a function of feed composition. Inter laboratory efforts were coordinated with complementary engineering tests carried out (and reported separately) by personnel at Savannah River National Laboratory (SRNL) and Savannah River Remediation (SRR) with helpful advice by Parsons Engineering and General Atomics on aspects of possible SWPF implementation.

Selection and design of solvents

DEFF Research Database (Denmark)

Gani, Rafiqul

and design of solvents will be presented together with application examples. The selection problem is defined as finding known chemicals that match the desired functions of a solvent for a specified set of applications. The design problem is defined as finding the molecular structure (or mixture of molecules....... With increasing interest on issues such as waste, sustainability, environmental impact and green chemistry, the selection and design of solvents have become important problems that need to be addressed during chemical product-process design and development. Systematic methods and tools suitable for selection......) that match the desired functions of a solvent for a specified set of applications. Use of organic chemicals and ionic liquids as solvents will be covered....

Solvent polarity scale on the fluorescence spectra of a dansyl monomer copolymerizable in aqueous media

Science.gov (United States)

Ren, Biye; Gao, Feng; Tong, Zhen; Yan, Yu

1999-06-01

A copolymerizable fluorescent monomer N-[2-[[[5-(N,N-dimethylamino)-1-naphthalenyl]sulfonyl]-amino]ethyl]-2-propenamide (DANSAEP) was synthesized, which exhibits dual fluorescence due to the twisted intramolecular charge transfer in the excited state. The emission maximum λem shifts from 463.3 nm in n-hexane to 530.0 nm in water, showing solvent polarity dependence. The relations between λem and the conventional solvent polarity parameters ET(30) or Z are linear, dividing solvents into protic and aprotic groups. Kamlet's linear solvation energy relationship gives a good description for λem as a solvent polarity scale. The increment of dipole moment Δ μ at the excited state was estimated as 5.09 D with the solvatochromic analysis.

Critical solvent properties affecting the particle formation process and characteristics of celecoxib-loaded plga microparticles via spray-drying.

Science.gov (United States)

Wan, Feng; Bohr, Adam; Maltesen, Morten Jonas; Bjerregaard, Simon; Foged, Camilla; Rantanen, Jukka; Yang, Mingshi

2013-04-01

It is imperative to understand the particle formation mechanisms when designing advanced nano/microparticulate drug delivery systems. We investigated how the solvent power and volatility influence the texture and surface chemistry of celecoxib-loaded poly (lactic-co-glycolic acid) (PLGA) microparticles prepared by spray-drying. Binary mixtures of acetone and methanol at different molar ratios were applied to dissolve celecoxib and PLGA prior to spray-drying. The resulting microparticles were characterized with respect to morphology, texture, surface chemistry, solid state properties and drug release profile. The evaporation profiles of the feed solutions were investigated using thermogravimetric analysis (TGA). Spherical PLGA microparticles were obtained, irrespectively of the solvent composition. The particle size and surface chemistry were highly dependent on the solvent power of the feed solution. An obvious burst release was observed for the microparticles prepared by the feed solutions with the highest amount of poor solvent for PLGA. TGA analysis revealed distinct drying kinetics for the binary mixtures. The particle formation process is mainly governed by the PLGA precipitation rate, which is solvent-dependent, and the migration rate of celecoxib molecules during drying. The texture and surface chemistry of the spray-dried PLGA microparticles can therefore be tailored by adjusting the solvent composition.

Influence of Solvent Composition on the Performance of Spray-Dried Co-Amorphous Formulations

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Jaya Mishra

2018-04-01

Full Text Available Ball-milling is usually used to prepare co-amorphous drug–amino acid (AA mixtures. In this study, co-amorphous drug–AA mixtures were produced using spray-drying, a scalable industrially preferred preparation method. The influence of the solvent type and solvent composition was investigated. Mixtures of indomethacin (IND and each of the three AAs arginine, histidine, and lysine were ball-milled and spray-dried at a 1:1 molar ratio, respectively. Spray-drying was performed at different solvent ratios in (a ethanol and water mixtures and (b acetone and water mixtures. Different ratios of these solvents were chosen to study the effect of solvent mixtures on co-amorphous formulation. Residual crystallinity, thermal properties, salt/partial salt formation, and powder dissolution profiles of the IND–AA mixtures were investigated and compared to pure crystalline and amorphous IND. It was found that using spray-drying as a preparation method, all IND–AA mixtures could be successfully converted into the respective co-amorphous forms, irrespective of the type of solvent used, but depending on the solvent mixture ratios. Both ball-milled and spray-dried co-amorphous samples showed an enhanced dissolution rate and maintained supersaturation compared to the crystalline and amorphous IND itself. The spray-dried samples resulting in co-amorphous samples were stable for at least seven months of storage.

THE INFLUENCE OF THE SOLVENT ON THE THERMODYNAMICS OF ION ASSOCIATION

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Vitalii Chumak

2011-03-01

Full Text Available Abstract. Some approaches which allow to divide thermodynamic functions of the ion associationprocess in two components have been developed. The first component belongs to the process, the second oneis caused by the temperature dependence of the dielectric permittivity of the solvent. The theory is confirmedby numerous examples of the ion association process of different electrolytes in the binary mixed solvents.Keywords: covalent part of the constant of ionic association, electrostatic part of the constant of ionicassociation, enthalpy of the chemical equilibria in solution, enthropy of the chemical equilibria in solution,ionic association, ionic equilibrias, the equilibrium constant.

An investigation of influence of solvent on the degradation kinetics of carotenoids in oil extracts of Calendula officinalis

OpenAIRE

DEJAN BEZBRADICA; JELA MILIC-ASKRABIC; SLOBODAN D. PETROVIC; SLAVICA SILER-MARINKOVIC

2005-01-01

The stability of carotenoids was studied in marigold oil extracts prepared with following solvents: Myritol 312®, paraffin oil, almond oil, olive oil, sunflower oil, grape seed oil, and soybean oil. The concentration of the carotenoids was determined by spectroscopic measurement at 450 nm. Degradation rate showed a first order dependence on the concentration of carotenoids with a faster first stage (which lasted 3550 days, depending on the solvent) and a slower second stage. The highest degra...

Phospholipid electrospun nanofibers: effect of solvents and co-axial processing on morphology and fiber diameter

DEFF Research Database (Denmark)

Jørgensen, Lars; Qvortrup, Klaus; Chronakis, Ioannis S.

2015-01-01

Asolectin phospholipid nano-microfibers were prepared using electrospinning processing. The asolectin fibers were studied by scanning electron microscopy, and the fiber morphology was found to be strongly dependent on the phospholipid concentration and the solvents used. The solvents studied were...... chloroform : dimethylformamide (CHCl3 : DMF, 3 : 2 v/v), isooctane, cyclohexane and limonene, producing phospholipid fibers with average diameters in the range of 2.57 +/- 0.59 mu m, similar to 3-8 mu m, similar to 4-5 mu m and 14.3 +/- 2.7 mu m, respectively. The diameter of asolectin electrospun fibers...... solvent and the inner needle contains the asolectin solution in CHCl3: DMF, a substantial reduction in the average fiber diameter was observed. In particular, the average diameter of the fibers when DMF (a solvent with a high dielectric constant) was used as a sheath solvent was reduced by a factor...

Hazardous solvent substitution

International Nuclear Information System (INIS)

Twitchell, K.E.

1995-01-01

This article is an overview of efforts at INEL to reduce the generation of hazardous wastes through the elimination of hazardous solvents. To aid in their efforts, a number of databases have been developed and will become a part of an Integrated Solvent Substitution Data System. This latter data system will be accessible through Internet

Organic Solvent Tropical Report

International Nuclear Information System (INIS)

COWLEY, W.L.

2000-01-01

This report provides the basis for closing the organic solvent safety issue. Sufficient information is presented to conclude that risk posed by an unmitigated organic solvent fire is within risk evaluation guidelines

An in silico analysis of the binding modes and binding affinities of small molecule modulators of PDZ-peptide interactions.

Directory of Open Access Journals (Sweden)

Garima Tiwari

Full Text Available Inhibitors of PDZ-peptide interactions have important implications in a variety of biological processes including treatment of cancer and Parkinson's disease. Even though experimental studies have reported characterization of peptidomimetic inhibitors of PDZ-peptide interactions, the binding modes for most of them have not been characterized by structural studies. In this study we have attempted to understand the structural basis of the small molecule-PDZ interactions by in silico analysis of the binding modes and binding affinities of a set of 38 small molecules with known K(i or K(d values for PDZ2 and PDZ3 domains of PSD-95 protein. These two PDZ domains show differential selectivity for these compounds despite having a high degree of sequence similarity and almost identical peptide binding pockets. Optimum binding modes for these ligands for PDZ2 and PDZ3 domains were identified by using a novel combination of semi-flexible docking and explicit solvent molecular dynamics (MD simulations. Analysis of the binding modes revealed most of the peptidomimectic ligands which had high K(i or K(d moved away from the peptide binding pocket, while ligands with high binding affinities remained in the peptide binding pocket. The differential specificities of the PDZ2 and PDZ3 domains primarily arise from differences in the conformation of the loop connecting βB and βC strands, because this loop interacts with the N-terminal chemical moieties of the ligands. We have also computed the MM/PBSA binding free energy values for these 38 compounds with both the PDZ domains from multiple 5 ns MD trajectories on each complex i.e. a total of 228 MD trajectories of 5 ns length each. Interestingly, computational binding free energies show good agreement with experimental binding free energies with a correlation coefficient of approximately 0.6. Thus our study demonstrates that combined use of docking and MD simulations can help in identification of potent inhibitors

Comparative Study on Electronic, Emission, Spontaneous Property of Porous Silicon in Different Solvents

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M. Naziruddin Khan

2014-01-01

Full Text Available Luminescent porous silicon (Psi fabricated by simple chemical etching technique in different organic solvents was studied. By quantifying the silicon wafer piece, optical properties of the Psi in solutions were investigated. Observation shows that no photoluminescence light of Psi in all solvents is emitted. Morphology of Psi in different solvents indicates that the structure and distribution of Psi are differently observed. Particles are uniformly dispersive with the sizes around more or less 5–8 nm. The crystallographic plane and high crystalline nature of Psi is observed by selected area diffraction (SED and XRD. Electronic properties of Psi in solutions are influenced due to the variation of quantity of wafer and nature of solvent. Influence in band gaps of Psi calculated by Tauc’s method is obtained due to change of absorption edge of Psi in solvents. PL intensities are observed to be depending on quantity of silicon wafer, etched cross-section area on wafer surface. Effects on emission peaks and bands of Psi under temperature annealing are observed. The spontaneous signals of Psi measured under high power Pico second laser 355 nm source are significant, influenced by the nature of solvent, pumped energy, and quantity of Si wafer piece used in etching process.

Binding energy effects in cascade evolution and sputtering

International Nuclear Information System (INIS)

Robinson, M.T.

1995-06-01

The MARLOWE model was extended to include a binding energy dependent on the local crystalline order, so that atoms are bound less strongly to their lattice sites near surfaces or associated damage. Sputtering and cascade evolution were studied on the examples of self-ion irradiations of Cu and Au monocrystals. In cascades, the mean binding energy is reduced ∼8% in Cu with little dependence on the initial recoil energy; in Au, it is reduced ∼9% at 1 keV and ∼15% at 100 keV. In sputtering, the mean binding energy is reduced ∼8% in Cu and ∼15% in Au with little energy dependence; the yields are increased about half as much. Most sites from which sputtered atoms originate are isolated in both metals. Small clusters of such sites occur in Cu, but there are some large clusters in Au, especially in [111] targets. There are always more large clusters with damage-dependent binding than with a constant binding energy, but only a few clusters are compact enough to be regarded as pits

Physical organogels: mechanism and kinetics of evaporation of the solvents entrapped within network scaffolding

International Nuclear Information System (INIS)

Markovic, Nov; Dutta, Naba K.

2005-01-01

A series of hydrocarbon gels (based on leaded petrol and decalin) using physically crosslinked networks have been prepared using Al-salt of fatty acid as the physical gelling agent. The effects of gel network scaffolding on the mechanism and kinetics of evaporation of the solvents from the gels were investigated using conventional, isothermal and modulated thermogravimetric analysis. It has been clearly observed that the evaporation of solvent from gels followed a complex evaporation pattern compared to the pure solvent. It appears that with increase in network scaffolding the maximum rate of evaporation of the solvent decreases and its distribution become broader. The activation energy of evaporation for these solvents was found not to be dramatically dependent on the concentration of the gelator and tightness of the network scaffolding. Amongst different methods employed, isothermal measurements provided reliable information about the mechanism of evaporation. Modulated thermogravimetric analysis proved to be an efficient method to achieve kinetic parameters of evaporation from a single dynamic experiment. Scanning electron microscopy was used to probe for both dry gelator and gel network after evaporation of the solvents for evaluation of their surface morphology

Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes.

Science.gov (United States)

Gkionis, Konstantinos; Kruse, Holger; Šponer, Jiří

2016-04-12

Modern dispersion-corrected DFT methods have made it possible to perform reliable QM studies on complete nucleic acid (NA) building blocks having hundreds of atoms. Such calculations, although still limited to investigations of potential energy surfaces, enhance the portfolio of computational methods applicable to NAs and offer considerably more accurate intrinsic descriptions of NAs than standard MM. However, in practice such calculations are hampered by the use of implicit solvent environments and truncation of the systems. Conventional QM optimizations are spoiled by spurious intramolecular interactions and severe structural deformations. Here we compare two approaches designed to suppress such artifacts: partially restrained continuum solvent QM and explicit solvent QM/MM optimizations. We report geometry relaxations of a set of diverse double-quartet guanine quadruplex (GQ) DNA stems. Both methods provide neat structures without major artifacts. However, each one also has distinct weaknesses. In restrained optimizations, all errors in the target geometries (i.e., low-resolution X-ray and NMR structures) are transferred to the optimized geometries. In QM/MM, the initial solvent configuration causes some heterogeneity in the geometries. Nevertheless, both approaches represent a decisive step forward compared to conventional optimizations. We refine earlier computations that revealed sizable differences in the relative energies of GQ stems computed with AMBER MM and QM. We also explore the dependence of the QM/MM results on the applied computational protocol.

Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses

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Jinxiang Xi

2018-03-01

Full Text Available Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of

Molecular Binding Contributes to Concentration Dependent Acrolein Deposition in Rat Upper Airways: CFD and Molecular Dynamics Analyses.

Science.gov (United States)

Xi, Jinxiang; Hu, Qin; Zhao, Linlin; Si, Xiuhua April

2018-03-27

Existing in vivo experiments show significantly decreased acrolein uptake in rats with increasing inhaled acrolein concentrations. Considering that high-polarity chemicals are prone to bond with each other, it is hypothesized that molecular binding between acrolein and water will contribute to the experimentally observed deposition decrease by decreasing the effective diffusivity. The objective of this study is to quantify the probability of molecular binding for acrolein, as well as its effects on acrolein deposition, using multiscale simulations. An image-based rat airway geometry was used to predict the transport and deposition of acrolein using the chemical species model. The low Reynolds number turbulence model was used to simulate the airflows. Molecular dynamic (MD) simulations were used to study the molecular binding of acrolein in different media and at different acrolein concentrations. MD results show that significant molecular binding can happen between acrolein and water molecules in human and rat airways. With 72 acrolein embedded in 800 water molecules, about 48% of acrolein compounds contain one hydrogen bond and 10% contain two hydrogen bonds, which agreed favorably with previous MD results. The percentage of hydrogen-bonded acrolein compounds is higher at higher acrolein concentrations or in a medium with higher polarity. Computational dosimetry results show that the size increase caused by the molecular binding reduces the effective diffusivity of acrolein and lowers the chemical deposition onto the airway surfaces. This result is consistent with the experimentally observed deposition decrease at higher concentrations. However, this size increase can only explain part of the concentration-dependent variation of the acrolein uptake and acts as a concurrent mechanism with the uptake-limiting tissue ration rate. Intermolecular interactions and associated variation in diffusivity should be considered in future dosimetry modeling of high

Nonequilibrium quantum solvation with a time-dependent Onsager cavity

Science.gov (United States)

Kirchberg, H.; Nalbach, P.; Thorwart, M.

2018-04-01

We formulate a theory of nonequilibrium quantum solvation in which parameters of the solvent are explicitly depending on time. We assume in a simplest approach a spherical molecular Onsager cavity with a time-dependent radius. We analyze the relaxation properties of a test molecular point dipole in a dielectric solvent and consider two cases: (i) a shrinking Onsager sphere and (ii) a breathing Onsager sphere. Due to the time-dependent solvent, the frequency-dependent response function of the dipole becomes time-dependent. For a shrinking Onsager sphere, the dipole relaxation is in general enhanced. This is reflected in a temporally increasing linewidth of the absorptive part of the response. Furthermore, the effective frequency-dependent response function shows two peaks in the absorptive part which are symmetrically shifted around the eigenfrequency. By contrast, a breathing sphere reduces damping as compared to the static sphere. Interestingly, we find a non-monotonous dependence of the relaxation rate on the breathing rate and a resonant suppression of damping when both rates are comparable. Moreover, the linewidth of the absorptive part of the response function is strongly reduced for times when the breathing sphere reaches its maximal extension.

Magnetic field-dependent of binding energy in GaN/InGaN/GaN spherical QDQW nanoparticles

International Nuclear Information System (INIS)

El Ghazi, Haddou; Jorio, Anouar; Zorkani, Izeddine

2013-01-01

Simultaneous study of magnetic field and impurity's position effects on the ground-state shallow-donor binding energy in GaN|InGaN|GaN (core|well|shell) spherical quantum dot–quantum well (SQDQW) as a function of the ratio of the inner and the outer radius is reported. The calculations are investigated within the framework of the effective-mass approximation and an infinite deep potential describing the quantum confinement effect. A Ritz variational approach is used taking into account of the electron-impurity correlation and the magnetic field effect in the trial wave-function. It appears that the binding energy depends strongly on the external magnetic field, the impurity's position and the structure radius. It has been found that: (i) the magnetic field effect is more marked in large layer than in thin layer and (ii) it is more pronounced in the spherical layer center than in its extremities

Calorimetric study of binding of some disaccharides with crown ethers

Energy Technology Data Exchange (ETDEWEB)

Davydova, Olga I.; Lebedeva, Nataliya Sh.; Parfenyuk, Elena V

2004-11-01

Isothermal titration calorimetry has been applied to the determination of the thermodynamic parameters of binding of {beta}-lactose, {alpha},{alpha}-trehalose and sucrose with 15-crown-5 and 18-crown-6 in water at 298.15 K. The formation of 1:1 molecular associates has been found for the systems studied except 18-crown-6 and {beta}-lactose. The associates are preferentially or completely entropy stabilized. The most stable associate is formed between {alpha},{alpha}-trehalose and 18-crown-6. The obtained values of thermodynamic parameters of binding are discussed from the point of view of solute-solvent interactions as well as conformational and structural peculiarities of the disaccharides (DS) and crown ethers (CE)

Calorimetric study of binding of some disaccharides with crown ethers

International Nuclear Information System (INIS)

Davydova, Olga I.; Lebedeva, Nataliya Sh.; Parfenyuk, Elena V.

2004-01-01

Isothermal titration calorimetry has been applied to the determination of the thermodynamic parameters of binding of β-lactose, α,α-trehalose and sucrose with 15-crown-5 and 18-crown-6 in water at 298.15 K. The formation of 1:1 molecular associates has been found for the systems studied except 18-crown-6 and β-lactose. The associates are preferentially or completely entropy stabilized. The most stable associate is formed between α,α-trehalose and 18-crown-6. The obtained values of thermodynamic parameters of binding are discussed from the point of view of solute-solvent interactions as well as conformational and structural peculiarities of the disaccharides (DS) and crown ethers (CE)

The effect of the electrode material on the electrodeposition of zinc from deep eutectic solvents

International Nuclear Information System (INIS)

Vieira, L.; Schennach, R.; Gollas, B.

2016-01-01

Highlights: • Mechanistic insight into zinc electrodeposition from deep eutectic solvents. • Overpotential for hydrogen evolution affects the electrodeposition of zinc. • Electrodeposited zinc forms surface alloys on Cu, Au, and Pt. • In situ PM-IRRAS of a ZnCl_2 containing deep eutectic solvent on glassy carbon. - Abstract: The voltammetric behaviour of the ZnCl_2 containing deep eutectic solvent choline chloride/ethylene glycol 1:2 was investigated on glassy carbon, stainless steel, Au, Pt, Cu, and Zn electrodes. While cyclic voltammetry on glassy carbon and stainless steel showed a cathodic peak for zinc electrodeposition only in the anodic reverse sweep, a cathodic peak was found also in the cathodic forward sweep on Au, Pt, Cu, and Zn. This behaviour is in agreement with the proposed mechanism of zinc deposition from an intermediate species Z, whose formation depends on the cathodic reduction potential of the solvent. The voltammetric reduction of the electrolyte involves hydrogen evolution and as a result the formation of Z and its reduction to zinc depend on the hydrogen overpotential for each electrode material. On Au, Pt, and Cu also the anodic stripping was different from that on glassy carbon and steel due to the formation of surface zinc alloys with the three former metals. The morphology of the zinc layers on Cu has been characterised by scanning electron microscopy and focussed ion beam. X-ray diffraction confirmed the presence of crystalline zinc and a Cu_4Zn phase. Spectroelectrochemistry by means of polarization modulation reflection-absorption spectroscopy (PM-IRRAS) on a glassy carbon electrode in the ZnCl_2 containing deep eutectic solvent showed characteristic potential dependent changes. The variation of band intensities at different applied potentials correlate with the voltammetry and suggest the formation of a compact blocking layer on the electrode surface, which inhibits the electrodeposition of zinc at sufficiently negative

High-yield exfoliation of tungsten disulphide nanosheets by rational mixing of low-boiling-point solvents

Science.gov (United States)

Sajedi-Moghaddam, Ali; Saievar-Iranizad, Esmaiel

2018-01-01

Developing high-throughput, reliable, and facile approaches for producing atomically thin sheets of transition metal dichalcogenides is of great importance to pave the way for their use in real applications. Here, we report a highly promising route for exfoliating two-dimensional tungsten disulphide sheets by using binary combination of low-boiling-point solvents. Experimental results show significant dependence of exfoliation yield on the type of solvents as well as relative volume fraction of each solvent. The highest yield was found for appropriate combination of isopropanol/water (20 vol% isopropanol and 80 vol% water) which is approximately 7 times higher than that in pure isopropanol and 4 times higher than that in pure water. The dramatic increase in exfoliation yield can be attributed to perfect match between the surface tension of tungsten disulphide and binary solvent system. Furthermore, solvent molecular size also has a profound impact on the exfoliation efficiency, due to the steric repulsion.

Conformation Analysis of T1 Lipase on Alcohols Solvent using Molecular Dynamics Simulation

Science.gov (United States)

Putri, A. M.; Sumaryada, T.; Wahyudi, S. T.

2017-07-01

Biodiesel usually is produced commercially via a transesterification reaction of vegetable oil with alcohol and alkali catalyst. The alkali catalyst has some drawbacks, such as the soap formation during the reaction. T1 Lipase enzyme had been known as a thermostable biocatalyst which is able to produce biodiesel through a cleaner process. In this paper the performance of T1 lipase enzyme as catalyst for transesterification reaction in pure ethanol, methanol, and water solvents were studied using a Molecular Dynamics (MD) Simulation at temperature of 300 K for 10 nanoseconds. The results have shown that in general the conformation of T1 lipase enzyme in methanol is more dynamics as shown by the value of root mean square deviation (RMSD), root mean squared fluctuation (RMSF), and radius of gyration. The highest solvent accessible surface area (SASA) total was also found in methanol due to the contribution of non-polar amino acid in the interior of the protein. Analysis of MD simulation has also revealed that the enzyme structure tend to be more rigid in ethanol environment. The analysis of electrostatic interactions have shown that Glu359-Arg270 salt-bridge pair might hold the key of thermostability of T1 lipase enzyme as shown by its strong and stable binding in all three solvents.

Insecticide solvents: interference with insecticidal action.

Science.gov (United States)

Brattsten, L B; Wilkinson, C F

1977-06-10

Several commercial solvent mixtures commonly used as insecticide carriers in spray formulations increase by more than threefold the microsomal N-demethylation of p-chloro N-methylaniline in midgut preparations of southern army-worm (Spodoptera eridania) larvae exposed orally to the test solvents. Under laboratory conditions, the same solvent mixtures exhibit a protective action against the in vivo toxicity of the insecticide carbaryl to the larvae. The data are discussed with respect to possible solvent-insecticide interactions occurring under field conditions and, more broadly, to potential toxicological hazards of these solvents to humans.

Phospholipid-binding protein EhC2A mediates calcium-dependent translocation of transcription factor URE3-BP to the plasma membrane of Entamoeba histolytica.

Science.gov (United States)

Moreno, Heriberto; Linford, Alicia S; Gilchrist, Carol A; Petri, William A

2010-05-01

The Entamoeba histolytica upstream regulatory element 3-binding protein (URE3-BP) is a transcription factor that binds DNA in a Ca(2+)-inhibitable manner. The protein is located in both the nucleus and the cytoplasm but has also been found to be enriched in the plasma membrane of amebic trophozoites. We investigated the reason for the unusual localization of URE3-BP at the amebic plasma membrane. Here we identify and characterize a 22-kDa Ca(2+)-dependent binding partner of URE3-BP, EhC2A, a novel member of the C2-domain superfamily. Immunoprecipitations of URE3-BP and EhC2A showed that the proteins interact and that such interaction was enhanced in the presence of Ca(2+). Recombinant and native EhC2A bound phospholipid liposomes in a Ca(2+)-dependent manner, with half-maximal binding occurring at 3.4 muM free Ca(2+). A direct interaction between EhC2A and URE3-BP was demonstrated by the ability of recombinant EhC2A to recruit recombinant URE3-BP to phospholipid liposomes in a Ca(2+)-dependent manner. URE3-BP and EhC2A were observed to translocate to the amebic plasma membrane upon an increase in the intracellular Ca(2+) concentration of trophozoites, as revealed by subcellular fractionation and immunofluorescent staining. Short hairpin RNA-mediated knockdown of EhC2A protein expression significantly modulated the mRNA levels of URE3-BP-regulated transcripts. Based on these results, we propose a model for EhC2A-mediated regulation of the transcriptional activities of URE3-BP via Ca(2+)-dependent anchoring of the transcription factor to the amebic plasma membrane.

The HTLV-1 Tax protein binding domain of cyclin-dependent kinase 4 (CDK4 includes the regulatory PSTAIRE helix

Directory of Open Access Journals (Sweden)

Grassmann Ralph

2005-09-01

Full Text Available Abstract Background The Tax oncoprotein of human T-cell leukemia virus type 1 (HTLV-1 is leukemogenic in transgenic mice and induces permanent T-cell growth in vitro. It is found in active CDK holoenzyme complexes from adult T-cell leukemia-derived cultures and stimulates the G1- to-S phase transition by activating the cyclin-dependent kinase (CDK CDK4. The Tax protein directly and specifically interacts with CDK4 and cyclin D2 and binding is required for enhanced CDK4 kinase activity. The protein-protein contact between Tax and the components of the cyclin D/CDK complexes increases the association of CDK4 and its positive regulatory subunit cyclin D and renders the complex resistant to p21CIP inhibition. Tax mutants affecting the N-terminus cannot bind cyclin D and CDK4. Results To analyze, whether the N-terminus of Tax is capable of CDK4-binding, in vitro binding -, pull down -, and mammalian two-hybrid analyses were performed. These experiments revealed that a segment of 40 amino acids is sufficient to interact with CDK4 and cyclin D2. To define a Tax-binding domain and analyze how Tax influences the kinase activity, a series of CDK4 deletion mutants was tested. Different assays revealed two regions which upon deletion consistently result in reduced binding activity. These were isolated and subjected to mammalian two-hybrid analysis to test their potential to interact with the Tax N-terminus. These experiments concurrently revealed binding at the N- and C-terminus of CDK4. The N-terminal segment contains the PSTAIRE helix, which is known to control the access of substrate to the active cleft of CDK4 and thus the kinase activity. Conclusion Since the N- and C-terminus of CDK4 are neighboring in the predicted three-dimensional protein structure, it is conceivable that they comprise a single binding domain, which interacts with the Tax N-terminus.

CO2-Binding Organic Liquids Gas Capture with Polarity-Swing-Assisted Regeneration Full Technology Feasibility Study B1 - Solvent-based Systems

Energy Technology Data Exchange (ETDEWEB)

Heldebrant, David J

2014-08-31

PNNL, Fluor Corporation and Queens University (Kingston, ON) successfully completed a three year comprehensive study of the CO2BOL water-lean solvent platform with Polarity Swing Assisted Regeneration (PSAR). This study encompassed solvent synthesis, characterization, environmental toxicology, physical, thermodynamic and kinetic property measurements, Aspen Plus™ modeling and bench-scale testing of a candidate CO2BOL solvent molecule. Key Program Findings The key program findings are summarized as follows: • PSAR favorably reduced stripper duties and reboiler temperatures with little/no impact to absorption column • >90% CO2 capture was achievable at reasonable liquid-gas ratios in the absorber • High rich solvent viscosities (up to 600 cP) were successfully demonstrated in the bench-scale system. However, the projected impacts of high viscosity to capital cost and operational limits compromised the other levelized cost of electricity benefits. • Low thermal conductivity of organics significantly increased the required cross exchanger surface area, and potentially other heat exchange surfaces. • CO2BOL had low evaporative losses during bench-scale testing • There was no evidence of foaming during bench scale testing • Current CO2BOL formulation costs project to be $35/kg • Ecotoxicity (Water Daphnia) was comparable between CO2BOL and MEA (169.47 versus 103.63 mg/L) • Full dehydration of the flue gas was determined to not be economically feasible. However, modest refrigeration (13 MW for the 550 MW reference system) was determined to be potentially economically feasible, and still produce a water-lean condition for the CO2BOLs (5 wt% steady-state water loading). • CO2BOLs testing with 5 wt% water loading did not compromise anhydrous performance behavior, and showed actual enhancement of CO2 capture performance. • Mass transfer of CO2BOLs was not greatly impeded by viscosity • Facile separation of antisolvent from lean CO2BOL was

Investigations on the role of mixed-solvent for improved efficiency in perovskite solar cell

Science.gov (United States)

Singh, Ranbir; Suranagi, Sanjaykumar R.; Kumar, Manish; Shukla, Vivek Kumar

2017-12-01

The morphology of the spin-coated photoactive layer is one of the major factors affecting the performance of perovskite solar cells. In this work, we have employed a mixed-solvent strategy to obtain a high quality MAPbI3 (MA = CH3NH3) perovskite film, without pinholes and reduced grain boundaries. Perovskite films formed with single and mixed-solvents are systematically characterized for their optical, structural, and morphological properties using UV-vis absorption, photoluminescence (PL), X-ray diffraction (XRD), atomic force microscopy (AFM), and scanning electron microscopy (SEM) tools. The power conversion efficiency (PCE) of the devices fabricated using the mixed-solvent showed better performance than the devices made using the single solvent. The best-optimized mixed-solvent perovskite film exhibited a PCE of 15.2% with uniform film coverage on the substrate, better charge generation, and a high hole mobility of 1.16 × 10-4cm2/V s. The disparities in photovoltaic properties have been analyzed with the intensity dependent current density-voltage (J-V), transient photovoltage (TPV), and relationship between photocurrent (Jph) and effective voltage (Veff).

Asymmetric cation-binding catalysis

DEFF Research Database (Denmark)

Oliveira, Maria Teresa; Lee, Jiwoong

2017-01-01

The employment of metal salts is quite limited in asymmetric catalysis, although it would provide an additional arsenal of safe and inexpensive reagents to create molecular functions with high optical purity. Cation chelation by polyethers increases the salts' solubility in conventional organic...... solvents, thus increasing their applicability in synthesis. The expansion of this concept to chiral polyethers led to the emergence of asymmetric cation-binding catalysis, where chiral counter anions are generated from metal salts, particularly using BINOL-based polyethers. Alkali metal salts, namely KF...... highly enantioselective silylation reactions in polyether-generated chiral environments, and leading to a record-high turnover in asymmetric organocatalysis. This can lead to further applications by the asymmetric use of other inorganic salts in various organic transformations....

Quaternary Benzyltriethylammonium Ion Binding to the Na,K-ATPase: a Tool to Investigate Extracellular K+ Binding Reactions†

Science.gov (United States)

Peluffo, R. Daniel; González-Lebrero, Rodolfo M.; Kaufman, Sergio B.; Kortagere, Sandhya; Orban, Branly; Rossi, Rolando C.; Berlin, Joshua R.

2009-01-01

This study examined how the quaternary organic ammonium ion, benzyltriethylamine (BTEA), binds to the Na,K-ATPase to produce membrane potential (VM)-dependent inhibition and tested the prediction that such a VM-dependent inhibitor would display electrogenic binding kinetics. BTEA competitively inhibited K+ activation of Na,K-ATPase activity and steady-state 86Rb+ occlusion. The initial rate of 86Rb+ occlusion was decreased by BTEA to a similar degree whether it was added to the enzyme prior to or simultaneously with Rb+, a demonstration that BTEA inhibits the Na,K-ATPase without being occluded. Several BTEA structural analogues reversibly inhibited Na,K-pump current, but none blocked current in a VM-dependent manner except BTEA and its para-nitro derivative, pNBTEA. Under conditions that promoted electroneutral K+-K+ exchange by the Na,K-ATPase, step changes in VM elicited pNBTEA-activated ouabain-sensitive transient currents that had similarities to those produced with the K+ congener, Tl+. pNBTEA- and Tl+-dependent transient currents both displayed saturation of charge moved at extreme negative and positive VM, equivalence of charge moved during and after step changes in VM, and similar apparent valence. The rate constant (ktot) for Tl+-dependent transient current asymptotically approached a minimum value at positive VM. In contrast, ktot for pNBTEA-dependent transient current was a “U”-shaped function of VM with a minimum value near 0 mV. Homology models of the Na,K-ATPase alpha subunit suggested that quaternary amines can bind to two extracellularly-accessible sites, one of them located at K+ binding sites positioned between transmembrane helices 4, 5, and 6. Altogether, these data revealed important information about electrogenic ion binding reactions of the Na,K-ATPase that are not directly measurable during ion transport by this enzyme. PMID:19621894

Next Generation Solvent (NGS): Development for Caustic-Side Solvent Extraction of Cesium

Energy Technology Data Exchange (ETDEWEB)

Moyer, Bruce A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Birdwell, Jr, Joseph F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bonnesen, Peter V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bruffey, Stephanie H. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Delmau, Laetitia Helene [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Duncan, Nathan C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ensor, Dale [Tennessee Technological Univ., Cookeville, TN (United States); Hill, Talon G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Denise L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Rajbanshi, Arbin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Roach, Benjamin D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Szczygiel, Patricia L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sloop, Jr., Frederick V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Stoner, Erica L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Williams, Neil J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2014-03-01

This report summarizes the FY 2010 and 2011 accomplishments at Oak Ridge National Laboratory (ORNL) in developing the Next Generation Caustic-Side Solvent Extraction (NG-CSSX) process, referred to commonly as the Next Generation Solvent (NGS), under funding from the U.S. Department of Energy, Office of Environmental Management (DOE-EM), Office of Technology Innovation and Development. The primary product of this effort is a process solvent and preliminary flowsheet capable of meeting a target decontamination factor (DF) of 40,000 for worst-case Savannah River Site (SRS) waste with a concentration factor of 15 or higher in the 18-stage equipment configuration of the SRS Modular Caustic-Side Solvent Extraction Unit (MCU). In addition, the NG-CSSX process may be readily adapted for use in the SRS Salt Waste Processing Facility (SWPF) or in supplemental tank-waste treatment at Hanford upon appropriate solvent or flowsheet modifications. Efforts in FY 2010 focused on developing a solvent composition and process flowsheet for MCU implementation. In FY 2011 accomplishments at ORNL involved a wide array of chemical-development activities and testing up through single-stage hydraulic and mass-transfer tests in 5-cm centrifugal contactors. Under subcontract from ORNL, Argonne National Laboratory (ANL) designed a preliminary flowsheet using ORNL cesium distribution data, and Tennessee Technological University confirmed a chemical model for cesium distribution ratios (DCs) as a function of feed composition. Interlaboratory efforts were coordinated with complementary engineering tests carried out (and reported separately) by personnel at Savannah River National Laboratory (SRNL) and Savannah River Remediation (SRR) with helpful advice by Parsons Engineering and General Atomics on aspects of possible SWPF implementation.

Ionic Liquids in Selective Oxidation: Catalysts and Solvents.

Science.gov (United States)

Dai, Chengna; Zhang, Jie; Huang, Chongpin; Lei, Zhigang

2017-05-24

Selective oxidation has an important role in environmental and green chemistry (e.g., oxidative desulfurization of fuels and oxidative removal of mercury) as well as chemicals and intermediates chemistry to obtain high-value-added special products (e.g., organic sulfoxides and sulfones, aldehydes, ketones, carboxylic acids, epoxides, esters, and lactones). Due to their unique physical properties such as the nonvolatility, thermal stability, nonexplosion, high polarity, and temperature-dependent miscibility with water, ionic liquids (ILs) have attracted considerable attention as reaction solvents and media for selective oxidations and are considered as green alternatives to volatile organic solvents. Moreover, for easy separation and recyclable utilization, IL catalysts have attracted unprecedented attention as "biphasic catalyst" or "immobilized catalyst" by immobilizing metal- or nonmetal-containing ILs onto mineral or polymer supports to combine the unique properties of ILs (chemical and thermal stability, capacity for extraction of polar substrates and reaction products) with the extended surface of the supports. This review highlights the most recent outcomes on ILs in several important typical oxidation reactions. The contents are arranged in the series of oxidation of sulfides, oxidation of alcohols, epoxidation of alkenes, Baeyer-Villiger oxidation reaction, oxidation of alkanes, and oxidation of other compounds step by step involving ILs as solvents, catalysts, reagents, or their combinations.

Selective nonspecific solvation under dielectric saturation and fluorescence spectra of dye solutions in binary solvents.

Science.gov (United States)

Bakhshiev, N G; Kiselev, M B

1991-09-01

The influence of selective nonspecific solvation on the fluorescence spectra of three substitutedN-methylphthalimides in a binary solvent system consisting of a nonpolar (n-heptane) and a polar (pyridine) component has been studied under conditions close to dielectric saturation. The substantially nonlinearity of the effect is confirmation that the spectral shifts of fluorescence bands depend on the number of polar solvent molecules involved in solvating the dye molecule. The measured fluorescence spectral shifts determined by substituting one nonpolar solvent molecula with a polar one in the proximity of the dye molecule agree quantitatively with the forecasts of the previously proposed semiempirical theory which describes this nonlinear solvation phenomenon.

Computer Aided Solvent Selection and Design Framework

DEFF Research Database (Denmark)

Mitrofanov, Igor; Conte, Elisa; Abildskov, Jens

and computer-aided tools and methods for property prediction and computer-aided molecular design (CAMD) principles. This framework is applicable for solvent selection and design in product design as well as process design. The first module of the framework is dedicated to the solvent selection and design...... in terms of: physical and chemical properties (solvent-pure properties); Environment, Health and Safety (EHS) characteristic (solvent-EHS properties); operational properties (solvent–solute properties). 3. Performing the search. The search step consists of two stages. The first is a generation and property...... identification of solvent candidates using special software ProCAMD and ProPred, which are the implementations of computer-aided molecular techniques. The second consists of assigning the RS-indices following the reaction–solvent and then consulting the known solvent database and identifying the set of solvents...

Binding of Diphtheria Toxin to Phospholipids in Liposomes

Science.gov (United States)

Alving, Carl R.; Iglewski, Barbara H.; Urban, Katharine A.; Moss, Joel; Richards, Roberta L.; Sadoff, Jerald C.

1980-04-01

Diphtheria toxin bound to the phosphate portion of some, but not all, phospholipids in liposomes. Liposomes consisting of dimyristoyl phosphatidylcholine and cholesterol did not bind toxin. Addition of 20 mol% (compared to dimyristoyl phosphatidylcholine) of dipalmitoyl phosphatidic acid, dicetyl phosphate, phosphatidylinositol phosphate, cardiolipin, or phosphatidylserine in the liposomes resulted in substantial binding of toxin. Inclusion of phosphatidylinositol in dimyristol phosphatidylcholine / cholesterol liposomes did not result in toxin binding. The calcium salt of dipalmitoyl phosphatidic acid was more effective than the sodium salt, and the highest level of binding occurred with liposomes consisting only of dipalmitoyl phosphatidic acid (calcium salt) and cholesterol. Binding of toxin to liposomes was dependent on pH, and the pattern of pH dependence varied with liposomes having different compositions. Incubation of diphtheria toxin with liposomes containing dicetyl phosphate resulted in maximal binding at pH 3.6, whereas binding to liposomes containing phosphatidylinositol phosphate was maximal above pH 7. Toxin did not bind to liposomes containing 20 mol% of a free fatty acid (palmitic acid) or a sulfated lipid (3-sulfogalactosylceramide). Toxin binding to dicetyl phosphate or phosphatidylinositol phosphate was inhibited by UTP, ATP, phosphocholine, or p-nitrophenyl phosphate, but not by uracil. We conclude that (a) diphtheria toxin binds specifically to the phosphate portion of certain phospholipids, (b) binding to phospholipids in liposomes is dependent on pH, but is not due only to electrostatic interaction, and (c) binding may be strongly influenced by the composition of adjacent phospholipids that do not bind toxin. We propose that a minor membrane phospholipid (such as phosphatidylinositol phosphate or phosphatidic acid), or that some other phosphorylated membrane molecule (such as a phosphoprotein) may be important in the initial binding of

Volatile solvents as drugs of abuse: focus on the cortico-mesolimbic circuitry.

Science.gov (United States)

Beckley, Jacob T; Woodward, John J

2013-12-01

Volatile solvents such as those found in fuels, paints, and thinners are found throughout the world and are used in a variety of industrial applications. However, these compounds are also often intentionally inhaled at high concentrations to produce intoxication. While solvent use has been recognized as a potential drug problem for many years, research on the sites and mechanisms of action of these compounds lags behind that of other drugs of abuse. In this review, we first discuss the epidemiology of voluntary solvent use throughout the world and then consider what is known about their basic pharmacology and how this may explain their use as drugs of abuse. We next present data from preclinical and clinical studies indicating that these substances induce common addiction sequelae such as dependence, withdrawal, and cognitive impairments. We describe how toluene, the most commonly studied psychoactive volatile solvent, alters synaptic transmission in key brain circuits such as the mesolimbic dopamine system and medial prefrontal cortex (mPFC) that are thought to underlie addiction pathology. Finally, we make the case that activity in mPFC circuits is a critical regulator of the mesolimbic dopamine system's ability to respond to volatile solvents like toluene. Overall, this review provides evidence that volatile solvents have high abuse liability because of their selective effects on critical nodes of the addiction neurocircuitry, and underscores the need for more research into how these compounds induce adaptations in neural circuits that underlie addiction pathology.

Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain.

Directory of Open Access Journals (Sweden)

Tingjun Hou

2006-01-01

Full Text Available Protein-protein interactions, particularly weak and transient ones, are often mediated by peptide recognition domains, such as Src Homology 2 and 3 (SH2 and SH3 domains, which bind to specific sequence and structural motifs. It is important but challenging to determine the binding specificity of these domains accurately and to predict their physiological interacting partners. In this study, the interactions between 35 peptide ligands (15 binders and 20 non-binders and the Abl SH3 domain were analyzed using molecular dynamics simulation and the Molecular Mechanics/Poisson-Boltzmann Solvent Area method. The calculated binding free energies correlated well with the rank order of the binding peptides and clearly distinguished binders from non-binders. Free energy component analysis revealed that the van der Waals interactions dictate the binding strength of peptides, whereas the binding specificity is determined by the electrostatic interaction and the polar contribution of desolvation. The binding motif of the Abl SH3 domain was then determined by a virtual mutagenesis method, which mutates the residue at each position of the template peptide relative to all other 19 amino acids and calculates the binding free energy difference between the template and the mutated peptides using the Molecular Mechanics/Poisson-Boltzmann Solvent Area method. A single position mutation free energy profile was thus established and used as a scoring matrix to search peptides recognized by the Abl SH3 domain in the human genome. Our approach successfully picked ten out of 13 experimentally determined binding partners of the Abl SH3 domain among the top 600 candidates from the 218,540 decapeptides with the PXXP motif in the SWISS-PROT database. We expect that this physical-principle based method can be applied to other protein domains as well.

Improvements in solvent extraction columns

International Nuclear Information System (INIS)

Aughwane, K.R.

1987-01-01

Solvent extraction columns are used in the reprocessing of irradiated nuclear fuel. For an effective reprocessing operation a solvent extraction column is required which is capable of distributing the feed over most of the column. The patent describes improvements in solvent extractions columns which allows the feed to be distributed over an increased length of column than was previously possible. (U.K.)

Incremental binding free energies of aluminum (III) vs. magnesium (II) complexes

International Nuclear Information System (INIS)

Mercero, Jose M.; Mujika, Jon I.; Matxain, Jon M.; Lopez, Xabier; Ugalde, Jesus M.

2003-01-01

A sequential ligand addition to the aluminum (III) cation has been studied using the B3LYP functional and a combined all-electron/pseudopotentials basis set. The aluminum complexes are compared with analogous magnesium (II) complexes. Different thermodynamical data, such as incremental binding energies, enthalpies, entropies and free energies, are presented for these addition reactions. While the magnesium (II) cation can only accommodate three negatively charged ligands, aluminum (III) accommodates four even after including bulk solvent effects. The main differences between both cations complexing with the neutral ligands, is that aluminum (III) is not able to form complexes with methanol until the number of methanol ligands is equal to 3. Magnesium (II) prefers to bind methanol and formamide when the number of ligands is small, while aluminum prefers formamide. For the largest complexes both cations prefer to bind water

Effect of organic solvents on dissolution process of mechano-chemically activated molybdenum by inorganic acid solutions

International Nuclear Information System (INIS)

Shevtsova, I.Ya.; Chernyak, A.S.; Khal'zov, A.A.

1992-01-01

The process of chemical dissolution of mechanochemically activated and nonactivated molybdenite by inorganic acid solutions in certain organic solvents of different nature was considered. It is shown that the highest extraction of molybdenum in solution is achieved in the presence of nitric acid. The dissociation constant of the acid used in the given organic solvent does not affect molybdenite solubility. When dissolving molybdenite by solutions of nitric acid in carbonic acids, alcohols and esters, the solubility of the concentrate depends on the length of hydrocarbon chain of the organic solvent and dispersion degree of mineral source material

Calcium ion binding properties of Medicago truncatula calcium/calmodulin-dependent protein kinase.

Science.gov (United States)

Swainsbury, David J K; Zhou, Liang; Oldroyd, Giles E D; Bornemann, Stephen

2012-09-04

A calcium/calmodulin-dependent protein kinase (CCaMK) is essential in the interpretation of calcium oscillations in plant root cells for the establishment of symbiotic relationships with rhizobia and mycorrhizal fungi. Some of its properties have been studied in detail, but its calcium ion binding properties and subsequent conformational change have not. A biophysical approach was taken with constructs comprising either the visinin-like domain of Medicago truncatula CCaMK, which contains EF-hand motifs, or this domain together with the autoinhibitory domain. The visinin-like domain binds three calcium ions, leading to a conformational change involving the exposure of hydrophobic surfaces and a change in tertiary but not net secondary or quaternary structure. The affinity for calcium ions of visinin-like domain EF-hands 1 and 2 (K(d) = 200 ± 50 nM) was appropriate for the interpretation of calcium oscillations (~125-850 nM), while that of EF-hand 3 (K(d) ≤ 20 nM) implied occupancy at basal calcium ion levels. Calcium dissociation rate constants were determined for the visinin-like domain of CCaMK, M. truncatula calmodulin 1, and the complex between these two proteins (the slowest of which was 0.123 ± 0.002 s(-1)), suggesting the corresponding calcium association rate constants were at or near the diffusion-limited rate. In addition, the dissociation of calmodulin from the protein complex was shown to be on the same time scale as the dissociation of calcium ions. These observations suggest that the formation and dissociation of the complex between calmodulin and CCaMK would substantially mirror calcium oscillations, which typically have a 90 s periodicity.

Gas separation by composite solvent-swollen membranes

Science.gov (United States)

Matson, Stephen L.; Lee, Eric K. L.; Friesen, Dwayne T.; Kelly, Donald J.

1989-01-01

There is disclosed a composite immobulized liquid membrane of a solvent-swollen polymer and a microporous organic or inorganic support, the solvent being at least one highly polar solvent containing at least one nitrogen, oxygen, phosphorous or sulfur atom, and having a boiling point of at least 100.degree. C. and a specified solubility parameter. The solvent or solvent mixture is homogeneously distributed through the solvent-swollen polymer from 20% to 95% by weight. The membrane is suitable for acid gas scrubbing and oxygen/nitrogen separation.

Gas separation by composite solvent-swollen membranes

Science.gov (United States)

Matson, S.L.; Lee, E.K.L.; Friesen, D.T.; Kelly, D.J.

1989-04-25

There is disclosed a composite immobilized liquid membrane of a solvent-swollen polymer and a microporous organic or inorganic support, the solvent being at least one highly polar solvent containing at least one nitrogen, oxygen, phosphorus or sulfur atom, and having a boiling point of at least 100 C and a specified solubility parameter. The solvent or solvent mixture is homogeneously distributed through the solvent-swollen polymer from 20% to 95% by weight. The membrane is suitable for acid gas scrubbing and oxygen/nitrogen separation. 3 figs.

Combining Solvent Isotope Effects with Substrate Isotope Effects in Mechanistic Studies of Alcohol and Amine Oxidation by Enzymes*

Science.gov (United States)

Fitzpatrick, Paul F.

2014-01-01

Oxidation of alcohols and amines is catalyzed by multiple families of flavin-and pyridine nucleotide-dependent enzymes. Measurement of solvent isotope effects provides a unique mechanistic probe of the timing of the cleavage of the OH and NH bonds, necessary information for a complete description of the catalytic mechanism. The inherent ambiguities in interpretation of solvent isotope effects can be significantly decreased if isotope effects arising from isotopically labeled substrates are measured in combination with solvent isotope effects. The application of combined solvent and substrate (mainly deuterium) isotope effects to multiple enzymes is described here to illustrate the range of mechanistic insights that such an approach can provide. PMID:25448013

Alkali-assisted coal extraction with polar aprotic solvents

Energy Technology Data Exchange (ETDEWEB)

Makgato, M.H.; Moitsheki, L.J.; Shoko, L.; Kgobane, B.L.; Morgan, D.L.; Focke, W.W. [SARChI Chair in Carbon Technology and Materials, Institute of Applied Materials, University of Pretoria, Pretoria 0002 (South Africa)

2009-04-15

Coal extraction experiments were conducted using a coal, containing ca. 10% ash, from the Tshikondeni mine in South Africa. This coal dissolves only to a limited extent in pure polar aprotic solvents such as dimethylformamide (DMF) and N-methyl-2-pyrrolidinone (NMP). However, the addition of a strong base, e.g. sodium hydroxide (NaOH) or sodium tert-butoxide increased the degree of coal dissolution in these organic solvents. Depending on the extraction conditions, carbon extraction efficiencies of up to 90% were obtained. Carbon precursor material was recovered from the solution as a gel by precipitation with water. Ash content was reduced from 10% in the coal to less than 1.6% in the coal extracts. Sodium sulfide (Na{sub 2}S) addition further reduced ash content and aided the recovery of carbon precursors that led to graphitizable cokes but the degree of extraction was significantly reduced. (author)

Solvent-mediated pathways to gelation and phase separation in suspensions of grafted nanoparticles

KAUST Repository

Anyfantakis, Manos

2009-01-01

We explore the role of the solvent medium on the interplay between gelation and phase separation in suspensions of organosilicate planar hybrids grafted with hydrocarbon chains. We establish their phase diagram by means of dynamic light scattering, rheology and visual observations, and different routes to gelation, depending on the solvent used. In agreement with earlier works, the solvent quality for the grafted chains at a given temperature controls the balance between attractions and repulsions, and hence the phase diagram of the nanoparticles and their tendency to gel. Here we show how to tune the suspension state and hence its rheology. For decane, a good solvent for the hydrocarbon chains, gelation occurs at rather low volume fractions in the presence of phase separation. This is due to the interdigitation of solvent molecules with the grafted chains, resulting in their crystalline packing that promotes the attraction between particles. For toluene, a solvent of reduced quality for the hydrocarbon chains, no interdigitation takes place, and hence gelation is triggered by clustering at higher volume fractions before phase separation. Our results support the generic picture of complex kinetic arrest/phase separation interplay in soft matter, where phase separation can proceed, be interrupted or be completely inhibited. A number of interesting possibilities for tailoring the rheology of grafted colloidal systems emerge. © 2009 The Royal Society of Chemistry.

Processing of polymers using reactive solvents

NARCIS (Netherlands)

Lemstra, P.J.; Kurja, J.; Meijer, H.E.H.; Meijer, H.E.H.

1997-01-01

A review with many refs. on processing of polymers using reactive solvents including classification of synthetic polymers, guidelines for the selection of reactive solvents, basic aspects of processing, examples of intractable and tractable polymer/reactive solvent system

Magnetic field-dependent of binding energy in GaN/InGaN/GaN spherical QDQW nanoparticles

Energy Technology Data Exchange (ETDEWEB)

El Ghazi, Haddou, E-mail: hadghazi@gmail.com [Solid State Laboratory, Faculty of science, Dhar EL Mehrez, BP 1796 Fes-Atlas (Morocco); Special mathematics, CPGE Kénitra, Chakib Arsalane Street (Morocco); Jorio, Anouar; Zorkani, Izeddine [Solid State Laboratory, Faculty of science, Dhar EL Mehrez, BP 1796 Fes-Atlas (Morocco)

2013-10-15

Simultaneous study of magnetic field and impurity's position effects on the ground-state shallow-donor binding energy in GaN|InGaN|GaN (core|well|shell) spherical quantum dot–quantum well (SQDQW) as a function of the ratio of the inner and the outer radius is reported. The calculations are investigated within the framework of the effective-mass approximation and an infinite deep potential describing the quantum confinement effect. A Ritz variational approach is used taking into account of the electron-impurity correlation and the magnetic field effect in the trial wave-function. It appears that the binding energy depends strongly on the external magnetic field, the impurity's position and the structure radius. It has been found that: (i) the magnetic field effect is more marked in large layer than in thin layer and (ii) it is more pronounced in the spherical layer center than in its extremities.

40 CFR Table 4 to Subpart Oooo of... - Default Organic HAP Mass Fraction for Solvents and Solvent Blends

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 12 2010-07-01 2010-07-01 true Default Organic HAP Mass Fraction for... 63—Default Organic HAP Mass Fraction for Solvents and Solvent Blends You may use the mass fraction... formulation data. Solvent/solvent blend CAS. No. Averageorganic HAP mass fraction Typical organic HAP, percent...

Morphological control in polymer solar cells using low-boiling-point solvent additives

Science.gov (United States)

Mahadevapuram, Rakesh C.

In the global search for clean, renewable energy sources, organic photovoltaics (OPVs) have recently been given much attention. Popular modern-day OPVs are made from solution-processible, carbon-based polymers (e.g. the model poly(3-hexylthiophene) that are intimately blended with fullerene derivatives (e.g. [6,6]-phenyl-C71-butyric acid methyl ester) to form what is known as the dispersed bulk-heterojunction (BHJ). This BHJ architecture has produced some of the most efficient OPVs to date, with reports closing in on 10% power conversion efficiency. To push efficiencies further into double digits, many groups have identified the BHJ nanomorphology---that is, the phase separations and grain sizes within the polymer: fullerene composite---as a key aspect in need of control and improvement. As a result, many methods, including thermal annealing, slow-drying (solvent) annealing, vapor annealing, and solvent additives, have been developed and studied to promote BHJ self-organization. Processing organic photovoltaic (OPV) blend solutions with high-boiling-point solvent additives has recently been used for morphological control in BHJ OPV cells. Here we show that even low-boiling-point solvents can be effective additives. When P3HT:PCBM OPV cells were processed with a low-boiling-point solvent tetrahydrafuran as an additive in parent solvent o-dichlorobenzene, charge extraction increased leading to fill factors as high as 69.5%, without low work-function cathodes, electrode buffer layers or thermal treatment. This was attributed to PCBM demixing from P3HT domains and better vertical phase separation, as indicated by photoluminescence lifetimes, hole mobilities, and shunt leakage currents. Dependence on solvent parameters and applicability beyond P3HT system was also investigated.

Effects of solvent and structure on the reactivity of 6-substituted nicotinic acids with diazodiphenylmethane in aprotic solvents

Directory of Open Access Journals (Sweden)

BRATISLAV Ž. JOVANOVIĆ

2009-12-01

Full Text Available The rate constants for the reactions of diazodiphenylmethane (DDM with 6-substituted nicotinic acids in aprotic solvents at 30 °C were determined. The obtained second order rate constants in aprotic solvents, together with literature data for benzoic and nicotinic acids in protic solvents, were used for the calculation of solvent effects, employing the Kamlet-Taft solvatochromic equation (linear solvation energy relationship – LSER in the form: log k = log k0 + s* + a + b. The correlations of the kinetic data were performed by means of multiple linear regression analysis taking appropriate solvent parameters. The sign of the equation coefficients (s, a and b were in agreement with the postulated reaction mechanism, and the mode of the solvent influences on the reaction rate is discussed based on the correlation results. A similar contribution of the non-specific solvent effect and electrophilic solvation was observed for all acids, while the highest contribution of nucleophilic solvation was influenced by their high acidity. Correlation analysis of the rate data with substituent p parameters in an appropriate solvent using the Hammett equation was also performed. The substituent effect on the acid reactivity was higher in aprotic solvents of higher dipolarity/polarizability. The mode of the transmission of the substituent effect is discussed in light of the contribution of solute–solvent interaction on the acid reactivity.

Effects of solvents on the radiation grafting reaction of vinyl compounds on poly (3-hydroxybutyrate)

International Nuclear Information System (INIS)

Torres, Maykel González; Talavera, José Rogelio Rodríguez; Muñoz, Susana Vargas; Pérez, Manuel González; Castro, Ma. Pilar. Carreón.; Cortes, Jorge Cerna

2015-01-01

Vinyl Acetate was grafted onto poly (3-hydroxybutyrate) by the simultaneous gamma irradiation method using different types of solvents and in bulk (solvent free), at 10 kGy and 1.62 kGy/h dose and dose rate respectively. Subsequent complete hydrolysis allowed the conversion of grafted chains from poly (vinyl acetate) to poly (vinyl alcohol). The aim of this study is to determine the effect of solvent through the estimation of the dependence of the degree of grafting with the choice of solvent, the calculation of the degree of crystallinity, and to study the biodegradation of the products. The results showed a greater degree of grafting in bulk, while the more suitable solvent was hexane. Characterization of the grafted copolymer indicated that crystallinity percentage decreased by an increase in grafting, while the biodegradability was promoted by the increment in poly (vinyl alcohol) grafted. - Highlights: • PHB was indirectly grafted with PVA, by complete hydrolysis of grafted PVAc. • The effect of solvents on the grafting, crystallinity and biodegradation was studied. • The characterizations of the products were obtained by SEM, TGA, and DSC

40 CFR Table 3 to Subpart IIIi of... - Default Organic HAP Mass Fraction for Solvents and Solvent Blends

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 12 2010-07-01 2010-07-01 true Default Organic HAP Mass Fraction for... Organic HAP Mass Fraction for Solvents and Solvent Blends You may use the mass fraction values in the... Solvent/solvent blend CAS. No. Averageorganic HAP mass fraction Typical organic HAP, percent by mass 1...

40 CFR Table 5 to Subpart Qqqq of... - Default Organic HAP Mass Fraction for Solvents and Solvent Blends

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 12 2010-07-01 2010-07-01 true Default Organic HAP Mass Fraction for... HAP Mass Fraction for Solvents and Solvent Blends You may use the mass fraction values in the.... Solvent/solvent blend CAS. No. Average organic HAP mass fraction Typical organic HAP, percent by mass 1...

GTP-dependent binding and nuclear transport of RNA polymerase II by Npa3 protein

DEFF Research Database (Denmark)

Staresincic, Lidija; Walker, Jane; Dirac-Svejstrup, A Barbara

2011-01-01

in yeast extracts. Indeed, Npa3 depletion in vivo affects nuclear localization of RNAPII; the polymerase accumulates in the cytoplasm. Npa3 is a member of the GPN-LOOP family of GTPases. Npa3 mutants that either cannot bind GTP or that bind but cannot hydrolyze it are inviable and unable to support nuclear...... transport of RNAPII. Surprisingly, we were unable to detect interactions between Npa3 and proteins in the classical importin a/ß pathway for nuclear import. Interestingly, Npa3-RNAPII binding is significantly increased by the addition of GTP or its slowly hydrolyzable analogue guanosine 5'-3-O......-(thio)triphosphate (GTP¿S). Moreover, the Npa3 mutant that binds GTP, but cannot hydrolyze it, binds RNAPII even in the absence of added GTP, whereas the mutant that cannot bind GTP is unable to bind the polymerase. Together, our data suggest that Npa3 defines an unconventional pathway for nuclear import of RNAPII, which...

Solubility of daidzin in different organic solvents and (ethyl alcohol + water) mixed solvents

International Nuclear Information System (INIS)

Fan, Jie-Ping; Yang, Dan; Xu, Xiao-Kang; Guo, Xiao-Jie; Zhang, Xue-Hong

2015-01-01

Highlights: • The solubilities of daidzin were measured in various solvents. • The solubility data were correlated by three models. • The thermodynamic properties of the dissolution process were also determined. - Abstract: The solubility of daidzin in different organic solvents and (ethyl alcohol + water) mixed solvents was measured by high performance liquid chromatography (HPLC) analysis method from T = (283.2 to 323.2) K at atmosphere pressure. The results show that at higher temperature more daidzin dissolves, and moreover, the solubility increases with the ethyl alcohol mole fraction increase in the (ethyl alcohol + water) mixed solvents. The experimental solubility values were correlated by a simplified thermodynamic equation, λh equation and modified Apelblat equation. Based on the solubility of daidzin, the enthalpy and entropy of solution were also evaluated by van’t Hoff equation. The results illustrated that the dissolution process of daidzin is endothermic and entropy driven

Morphological transformations of diblock copolymers in binary solvents: A simulation study

Science.gov (United States)

Wang, Zheng; Yin, Yuhua; Jiang, Run; Li, Baohui

2017-12-01

Morphological transformations of amphiphilic AB diblock copolymers in mixtures of a common solvent (S1) and a selective solvent (S2) for the B block are studied using the simulated annealing method. We focus on the morphological transformation depending on the fraction of the selective solvent C S2, the concentration of the polymer C p , and the polymer-solvent interactions ɛ ij ( i = A, B; j = S1, S2). Morphology diagrams are constructed as functions of C p , C S2, and/or ɛ AS2. The copolymer morphological sequence from dissolved → sphere → rod → ring/cage → vesicle is obtained upon increasing C S2 at a fixed C p . This morphology sequence is consistent with previous experimental observations. It is found that the selectivity of the selective solvent affects the self-assembled microstructure significantly. In particular, when the interaction ɛ BS2 is negative, aggregates of stacked lamellae dominate the diagram. The mechanisms of aggregate transformation and the formation of stacked lamellar aggregates are discussed by analyzing variations of the average contact numbers of the A or B monomers with monomers and with molecules of the two types of solvent, as well as the mean square end-to-end distances of chains. It is found that the basic morphological sequence of spheres to rods to vesicles and the stacked lamellar aggregates result from competition between the interfacial energy and the chain conformational entropy. Analysis of the vesicle structure reveals that the vesicle size increases with increasing C p or with decreasing C S2, but remains almost unchanged with variations in ɛ AS2.

Solution and gas phase evidence of anion binding through the secondary bonding interactions of a bidentate bis-antimony(iii) anion receptor.

Science.gov (United States)

Qiu, J; Song, B; Li, X; Cozzolino, A F

2017-12-20

The solution and gas phase halide binding to a bis-antimony(iii) anion receptor was studied. This new class of anion receptors utilizes the strong Sb-centered secondary bonding interactions (SBIs) that are formed opposite to the polar Sb-O primary bond. 1 H NMR titration data were fitted statistically to binding models and solution-phase binding energetics were extracted, while the formation of anion-to-receptor complexes was observed using ESI-MS. Density functional theory calculations suggest that their affinity towards binding halide anions is mitigated by the strong explicit solvation effect in DMSO, which gives insights into future designs that circumvent direct solvent binding and are anticipated to yield tighter and perhaps more selectivity in anion binding.

Adaptive Resolution Simulation of MARTINI Solvents

NARCIS (Netherlands)

Zavadlav, Julija; Melo, Manuel N.; Cunha, Ana V.; de Vries, Alex H.; Marrink, Siewert J.; Praprotnik, Matej

We present adaptive resolution dynamics simulations of aqueous and apolar solvents coarse-grained molecular models that are compatible with the MARTINI force field. As representatives of both classes solvents we have chosen liquid water and butane, respectively, at ambient temperature. The solvent

Physicochemical and catalytic properties of Au nanorods micro-assembled in solvents of varying dipole moment and refractive index

Energy Technology Data Exchange (ETDEWEB)

Kaur, Rupinder; Pal, Bonamali, E-mail: bpal@thapar.edu

2015-02-15

Highlights: • Physicochemical activities of Au nanorods in water largely differ from organic solvents. • Au nanorods agglomeration increased with dipole moments of different polar solvents. • Refractive indexes of Au nanorods dispersion in various polar solvents are enhanced. • Electrokinetics significantly altered depending on agglomerated size of Au nanorods. • Catalysis or co-catalysis activity is varied as per the extent of Au nanorods coagulation. - Abstract: This paper deals with the impact of dipole moment (1.66–3.96 D) and refractive index (1.333–1.422) of the dispersion solvent on the plasmon absorption, surface charge, zeta potential, and adsorption properties of Au nanorods (AuNRs). AuNRs (length ≈ 53 nm and width ≈ 20 nm) undergo agglomeration (size 50–180 nm) with increase in the dipole moment of solvent (iPrOH < MeOH < DMF < DMSO). Whereas, no such coagulation occurs in H{sub 2}O and CCl{sub 4} suspension as confirmed by DLS and TEM size distribution. The electrostatic interaction of AuNRs with its surface adsorbed solvent dipoles leads to alteration of the their ionic state, absolute electronic charge and zeta potential (+49.79 mV in H{sub 2}O, +8.99 mV in DMF and −4.65 mV in MeOH dispersion) to a greater extent. This interaction distinctly modifies the adsorption behavior of polar molecules like p-nitrophenol and salicylic acid on AuNRs surface, as evidenced by the measured changes in their electro-kinetic parameters. As a result, we observe a substantial difference in catalytic and co-catalytic activities of AuNRs dispersed in various solvents as mentioned above because the catalytic properties of AuNRs are strongly dependent on the type of solvent in which they are dispersed.

Solvent Extraction of Furfural From Biomass

Science.gov (United States)

Humphrey, M. F.

1984-01-01

Solvent-extraction method reduces energy required to remove furfural produced during acid hydrolysis of biomass. Acid hydrolysis performed in vessel containing both solvents and reacting ingredients. With intimate contact between solvents and aqueous hydrolyis liqour, furfural removed form liquor almost as fast as it forms.

Solvent Isotope-induced Equilibrium Perturbation for Isocitrate Lyase

Science.gov (United States)

Quartararo, Christine E.; Hadi, Timin; Cahill, Sean M.; Blanchard, John S.

2014-01-01

Isocitrate lyase (ICL) catalyzes the reversible retro-aldol cleavage of isocitrate to generate glyoxylate and succinate. ICL is the first enzyme of the glyoxylate shunt, which allows for the anaplerosis of citric acid cycle intermediates under nutrient limiting conditions. In Mycobacterium tuberculosis, the source of ICL for these studies, ICL is vital for the persistence phase of the bacteria’s life cycle. Solvent kinetic isotope effects (KIEs) in the direction of isocitrate cleavage of D2OV = 2.0 ± 0.1 and D2O[V/Kisocitrate] = 2.2 ± 0.3 arise from the initial deprotonation of the C2 hydroxyl group of isocitrate or the protonation of the aci-acid of succinate product of the isocitrate aldol cleavage by a solvent-derived proton. This KIE suggested that an equilibrium mixture of all protiated isocitrate, glyoxylate and succinate prepared in D2O, would undergo transient changes in equilibrium concentrations as a result of the solvent KIE and solvent-derived deuterium incorporation into both succinate and isocitrate. No change in the isotopic composition of glyoxylate was expected or observed. We have directly monitored the changing concentrations of all isotopic species of all reactants and products using a combination of NMR spectroscopy and mass spectrometry. Continuous monitoring of glyoxylate by 1H NMR spectroscopy shows a clear equilibrium perturbation in D2O. The final equilibrium isotopic composition of reactants in D2O revealed di-deuterated succinate, protiated glyoxylate, and mono-deuterated isocitrate, with the transient appearance and disappearance of mono-deuterated succinate. A model for the equilibrium perturbation of substrate species, and their time-dependent isotopic composition is presented. PMID:24261638

Biodiesel production from ethanolysis of palm oil using deep eutectic solvent (DES) as co-solvent

Science.gov (United States)

Manurung, R.; Winarta, A.; Taslim; Indra, L.

2017-06-01

Biodiesel produced from ethanolysis is more renewable and have better properties (higher oxidation stability, lower cloud and pour point) compared to methanolysis, but it has a disadvantage such as complicated purification. To improve ethanolysis process, deep eutectic solvent (DES) can be prepared from choline chloride and glycerol and used as co-solvent in ethanolysis. The deep eutectic solvent is formed from a quaternary ammonium salt (choline chloride) and a hydrogen bond donor (Glycerol), it is a non-toxic, biodegradable solvent compared to a conventional volatile organic solvent such as hexane. The deep eutectic solvent is prepared by mixing choline chloride and glycerol with molar ratio 1:2 at temperature 80 °C, stirring speed 300 rpm for 1 hour. The DES is characterized by its density and viscosity. The ethanolysis is performed at a reaction temperature of 70 °C, ethanol to oil molar ratio of 9:1, potassium hydroxide as catalyst concentration of 1.2 wt. DES as co-solvent with concentration 0.5 to 3 wt. stirring speed 400 rpm, and a reaction time 1 hour. The obtained biodiesel is then characterized by its density, viscosity, and ester content. The oil - ethanol phase condition is observed in the reaction tube. The oil - ethanol phase with DES tends to form meniscus compared to without DES, showed that oil and ethanol become more slightly miscible, which favors the reaction. Using DES as co-solvent in ethanolysis showed increasing in yield and easier purification. The esters properties meet the international standards ASTM D6751, with the highest yield achieved 83,67 with 99,77 conversion at DES concentration 2 . Increasing DES concentration above 2 in ethanolysis decrease the conversion and yield, because of the excessive glycerol in the systems makes the reaction equilibrium moves to the reactant side.

Carcinogenicity of petroleum lubricating oil distillates: effects of solvent refining, hydroprocessing, and blending.

Science.gov (United States)

Halder, C A; Warne, T M; Little, R Q; Garvin, P J

1984-01-01

Certain refining processes were investigated to determine their influence on the dermal carcinogenic activity of petroleum-derived lubricating oil distillates. Specifically, the effects of solvent refining, hydroprocessing, a combination of both processes, and the blending of oils processed using each technique were evaluated in standard mouse skin-painting bioassays. The refining process used as well as the level or severity of treatment greatly influenced the carcinogenic outcome of processed lubricating oils. Solvent refining at severities normally used appeared to eliminate carcinogenicity. In contrast, hydroprocessing alone at mild levels of treatment was successful only in reducing the carcinogenic potency; severe hydroprocessing conditions were necessary to eliminate carcinogenic activity without the use of additional refining processes. Carcinogenic activity could also be eliminated by following moderate solvent refining with mild hydroprocessing. Blending of hydroprocessed oils with solvent-refined oils resulted in a substantial reduction or even elimination of carcinogenic activity. However, the degree of protection obtained varied with the particular distillates used and appeared largely dependent on the inherent biological activity of the hydroprocessed oil.

Organic Solvent Tolerant Lipases and Applications

Directory of Open Access Journals (Sweden)

Shivika Sharma

2014-01-01

Full Text Available Lipases are a group of enzymes naturally endowed with the property of performing reactions in aqueous as well as organic solvents. The esterification reactions using lipase(s could be performed in water-restricted organic media as organic solvent(s not only improve(s the solubility of substrate and reactant in reaction mixture but also permit(s the reaction in the reverse direction, and often it is easy to recover the product in organic phase in two-phase equilibrium systems. The use of organic solvent tolerant lipase in organic media has exhibited many advantages: increased activity and stability, regiospecificity and stereoselectivity, higher solubility of substrate, ease of products recovery, and ability to shift the reaction equilibrium toward synthetic direction. Therefore the search for organic solvent tolerant enzymes has been an extensive area of research. A variety of fatty acid esters are now being produced commercially using immobilized lipase in nonaqueous solvents. This review describes the organic tolerance and industrial application of lipases. The main emphasis is to study the nature of organic solvent tolerant lipases. Also, the potential industrial applications that make lipases the biocatalysts of choice for the present and future have been presented.

Acetone-based cellulose solvent.

Science.gov (United States)

Kostag, Marc; Liebert, Tim; Heinze, Thomas

2014-08-01

Acetone containing tetraalkylammonium chloride is found to be an efficient solvent for cellulose. The addition of an amount of 10 mol% (based on acetone) of well-soluble salt triethyloctylammonium chloride (Et3 OctN Cl) adjusts the solvent's properties (increases the polarity) to promote cellulose dissolution. Cellulose solutions in acetone/Et3 OctN Cl have the lowest viscosity reported for comparable aprotic solutions making it a promising system for shaping processes and homogeneous chemical modification of the biopolymer. Recovery of the polymer and recycling of the solvent components can be easily achieved. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computer-aided tool for solvent selection in pharmaceutical processes: Solvent swap

DEFF Research Database (Denmark)

Papadakis, Emmanouil; K. Tula, Anjan; Gernaey, Krist V.

-liquid equilibria). The application of the developed model-based framework is highlighted through several cases studies published in the literature. In the current state, the framework is suitable for problems where the original solvent is exchanged by distillation. A solvent selection guide for fast of suitable......-aided framework with the objective to assist the pharmaceutical industry in gaining better process understanding. A software interface to improve the usability of the tool has been created also....

Improving the industrial production of 6-APA: enzymatic hydrolysis of penicillin G in the presence of organic solvents.

Science.gov (United States)

Abian, Olga; Mateo, César; Fernández-Lorente, Gloria; Guisán, José M; Fernández-Lafuente, Roberto

2003-01-01

The hydrolysis of penicillin G in the presence of an organic solvent, used with the purpose of extracting it from the culture medium, may greatly simplify the industrial preparation of 6-APA. However, under these conditions, PGA immobilized onto Eupergit displays very low stability (half-life of 5 h in butanone-saturated water) and a significant degree of inhibition by the organic solvent (30%). The negative effect of the organic solvent strongly depended on the type of solvent utilized: water saturated with butanone (around 28% v/v) had a much more pronounced negative effect than that of methylisobutyl ketone (MIBK) (solubility in water was only 2%). These problems were sorted out by using a new penicillin G acylase derivative designed to work in the presence of organic solvents (with each enzyme molecule surrounded by an hydrophilic artificial environment) and a suitable organic solvent (MIBK). Using such solvent, this derivative kept its activity unaltered for 1 week at 32 degrees C. Moreover, the enzyme activity was hardly inhibited by the presence of the organic solvent. In this way, the new enzyme derivative thus prepared enables simplification of the industrial hydrolysis of penicillin G.

Effects of solvent evaporation conditions on solvent vapor annealed cylinder-forming block polymer thin films

Science.gov (United States)

Grant, Meagan; Jakubowski, William; Nelson, Gunnar; Drapes, Chloe; Baruth, A.

Solvent vapor annealing is a less time and energy intensive method compared to thermal annealing, to direct the self-assembly of block polymer thin films. Periodic nanostructures have applications in ultrafiltration, magnetic arrays, or other structures with nanometer dimensions, driving its continued interest. Our goal is to create thin films with hexagonally packed, perpendicular aligned cylinders of poly(lactide) in a poly(styrene) matrix that span the thickness of the film with low anneal times and low defect densities, all with high reproducibility, where the latter is paramount. Through the use of our computer-controlled, pneumatically-actuated, purpose-built solvent vapor annealing chamber, we have the ability to monitor and control vapor pressure, solvent concentration within the film, and solvent evaporation rate with unprecedented precision and reliability. Focusing on evaporation, we report on two previously unexplored areas, chamber pressure during solvent evaporation and the flow rate of purging gas aiding the evaporation. We will report our exhaustive results following atomic force microscopy analysis of films exposed to a wide range of pressures and flow rates. Reliably achieving well-ordered films, while occurring within a large section of this parameter space, was correlated with high-flow evaporation rates and low chamber pressures. These results have significant implications on other methods of solvent annealing, including ``jar'' techniques.

Photophysical properties and excited state intramolecular proton transfer in 2-hydroxy-5-[(E)-(4-methoxyphenyl)diazenyl]benzoic acid in homogeneous solvents and micro-heterogeneous environments

Energy Technology Data Exchange (ETDEWEB)

Gashnga, Pynsakhiat Miki [Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, Shillong 793022, Meghalaya (India); Singh, T. Sanjoy [Department of Chemistry, Assam University, Silchar 788011, Assam (India); Baul, Tushar S. Basu [Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, Shillong 793022, Meghalaya (India); Mitra, Sivaprasad, E-mail: smitra@nehu.ac.in [Centre for Advanced Studies, Department of Chemistry, North-Eastern Hill University, Shillong 793022, Meghalaya (India)

2014-04-15

A systematic study on the photophysical properties and excited state intramolecular proton transfer (ESIPT) behavior of 2-hydroxy-5-[(E)-(4-methoxyphenyl)diazenyl]benzoic acid, is reported using steady-state and time-resolved fluorescence spectroscopy in homogeneous solvents as well as in different micro-heterogeneous environments. Depending on the nature of intramolecular hydrogen bond (IHB), the salicylic acid derivative may exist in two different ground state conformers (I and II). Structure I having IHB between the carbonyl oxygen and phenolic hydrogen can undergo ESIPT upon excitation as evidenced by largely Stokes-shifted fluorescence at ∼455 nm; whereas, normal fluorescence in the blue side of the spectrum (∼410 nm) is due to the spontaneous emission from conformer II. The results in homogeneous solvents were compared with those in bio-mimicking environments of β-cyclodextrin (CD) and surfactants. The intensity of the ESIPT fluorescence increases substantially upon encapsulation of the probe into the cyclodextrin as well as micellar nano-cavities. Detailed analysis of the spectroscopic data indicates that the probe forms 1:1 complex with CD in aqueous medium. Binding constant of the probe with the micelles as well as critical micelle concentration was obtained from the variation of fluorescence intensity on increasing concentration of different surfactants in aqueous medium. -- Highlights: • Steady state and time resolved fluorescence study on ESIPT in HMBA. • Dual fluorescence corresponding to the pro- and non-ESIPT structures. • Modulation of ESIPT fluorescence in micro-heterogeneous environments. • 1:1 stoichiometry for interaction with cyclodextrin. • Calculation of binding constant and other physico-chemical properties from fluorescence titration data in surfactants.

Photophysical properties and excited state intramolecular proton transfer in 2-hydroxy-5-[(E)-(4-methoxyphenyl)diazenyl]benzoic acid in homogeneous solvents and micro-heterogeneous environments

International Nuclear Information System (INIS)

Gashnga, Pynsakhiat Miki; Singh, T. Sanjoy; Baul, Tushar S. Basu; Mitra, Sivaprasad

2014-01-01

A systematic study on the photophysical properties and excited state intramolecular proton transfer (ESIPT) behavior of 2-hydroxy-5-[(E)-(4-methoxyphenyl)diazenyl]benzoic acid, is reported using steady-state and time-resolved fluorescence spectroscopy in homogeneous solvents as well as in different micro-heterogeneous environments. Depending on the nature of intramolecular hydrogen bond (IHB), the salicylic acid derivative may exist in two different ground state conformers (I and II). Structure I having IHB between the carbonyl oxygen and phenolic hydrogen can undergo ESIPT upon excitation as evidenced by largely Stokes-shifted fluorescence at ∼455 nm; whereas, normal fluorescence in the blue side of the spectrum (∼410 nm) is due to the spontaneous emission from conformer II. The results in homogeneous solvents were compared with those in bio-mimicking environments of β-cyclodextrin (CD) and surfactants. The intensity of the ESIPT fluorescence increases substantially upon encapsulation of the probe into the cyclodextrin as well as micellar nano-cavities. Detailed analysis of the spectroscopic data indicates that the probe forms 1:1 complex with CD in aqueous medium. Binding constant of the probe with the micelles as well as critical micelle concentration was obtained from the variation of fluorescence intensity on increasing concentration of different surfactants in aqueous medium. -- Highlights: • Steady state and time resolved fluorescence study on ESIPT in HMBA. • Dual fluorescence corresponding to the pro- and non-ESIPT structures. • Modulation of ESIPT fluorescence in micro-heterogeneous environments. • 1:1 stoichiometry for interaction with cyclodextrin. • Calculation of binding constant and other physico-chemical properties from fluorescence titration data in surfactants

On linear correlation between interfacial tension of water-solvent interface solubility of water in organic solvents and parameters of diluent effect scale

International Nuclear Information System (INIS)

Mezhov, Eh.A.; Khananashvili, N.L.; Shmidt, V.S.

1988-01-01

Presence of linear correlation between water solubility in nonmiscible with it organic solvents, interfacial tension of water-solvent interface, on the one hand, and solvent effect scale parameters and these solvents π* - on the other hand, is established. It allows, using certain tabular parameters of solvent effect or each solvent π*, to predict values of interfacial tension and water solubility for corresponding systems. It is shown, that solvent effect scale allows to predict values more accurately, than other known solvent scales, as it in contrast to other scales characterizes solvents, which are in equilibrium with water

Photophysics of Curcumin excited state in toluene-polar solvent mixtures: Role of H-bonding properties of the polar solvent

Energy Technology Data Exchange (ETDEWEB)

Saini, R.K.; Das, K., E-mail: kaustuv@rrcat.gov.in

2014-01-15

Excited state dynamics of Curcumin in binary solvent mixtures of toluene and polar H-bonding solvents were compared by using an instrument endowed with 40 ps time resolution. The solvation time constant of Curcumin increases significantly (and can therefore be measured) in polar solvents which have, either, both H-bond donating and accepting ability, or, only H-bond donating ability. These results suggest that the rate limiting step in the excited state dynamics of the pigment might be the formation and reorganization of the intermolecular H-bonding between the keto group of the pigment and the H-bond donating moieties of the polar solvent. -- Highlights: • Excited state dynamics of Curcumin in a binary solvent mixture of toluene and three polar H-bonding solvents were compared. • The solvation time constant increases significantly with polar solvents having, H-bond donating and accepting, or, H-bond donating ability. • Observed results suggest that H-bonding property of polar solvent plays an important role in the excited state dynamics. • Intermolecular H-bonding between the keto group of the pigment and polar solvent may be the rate limiting step.

Photophysics of Curcumin excited state in toluene-polar solvent mixtures: Role of H-bonding properties of the polar solvent

International Nuclear Information System (INIS)

Saini, R.K.; Das, K.

2014-01-01

Excited state dynamics of Curcumin in binary solvent mixtures of toluene and polar H-bonding solvents were compared by using an instrument endowed with 40 ps time resolution. The solvation time constant of Curcumin increases significantly (and can therefore be measured) in polar solvents which have, either, both H-bond donating and accepting ability, or, only H-bond donating ability. These results suggest that the rate limiting step in the excited state dynamics of the pigment might be the formation and reorganization of the intermolecular H-bonding between the keto group of the pigment and the H-bond donating moieties of the polar solvent. -- Highlights: • Excited state dynamics of Curcumin in a binary solvent mixture of toluene and three polar H-bonding solvents were compared. • The solvation time constant increases significantly with polar solvents having, H-bond donating and accepting, or, H-bond donating ability. • Observed results suggest that H-bonding property of polar solvent plays an important role in the excited state dynamics. • Intermolecular H-bonding between the keto group of the pigment and polar solvent may be the rate limiting step

Excited-state dynamics of mononucleotides and DNA strands in a deep eutectic solvent.

Science.gov (United States)

Zhang, Yuyuan; de La Harpe, Kimberly; Hariharan, Mahesh; Kohler, Bern

2018-04-17

The photophysics of several mono- and oligonucleotides were investigated in a deep eutectic solvent for the first time. The solvent glyceline, prepared as a 1 : 2 mole ratio mixture of choline chloride and glycerol, was used to study excited-state deactivation in a non-aqueous solvent by the use of steady-state and time-resolved spectroscopy. DNA strands in glyceline retain the secondary structures that are present in aqueous solution to some degree, thus enabling a study of the effects of solvent properties on the excited states of stacked bases and stacked base pairs. The excited-state lifetime of the mononucleotide 5'-AMP in glyceline is 630 fs, or twice as long as in aqueous solution. Even slower relaxation is seen for 5'-TMP in glyceline, and a possible triplet state with a lifetime greater than 3 ns is observed. Circular dichroism spectra show that the single strand (dA)18 and the duplex d(AT)9·d(AT)9 adopt similar structures in glyceline and in aqueous solution. Despite having similar conformations in both solvents, femtosecond transient absorption experiments reveal striking changes in the dynamics. Excited-state decay and vibrational cooling generally take place more slowly in glyceline than in water. Additionally, the fraction of long-lived excited states in both oligonucleotide systems is lower in glyceline than in aqueous solution. For a DNA duplex, water is suggested to favor decay pathways involving intrastrand charge separation, while the deep eutectic solvent favors interstrand deactivation channels involving neutral species. Slower solvation dynamics in the viscous deep eutectic solvent may also play a role. These results demonstrate that the dynamics of excitations in stacked bases and stacked base pairs depend not only on conformation, but are also highly sensitive to the solvent.

Linear correlation of interfacial tension at water-solvent interface, solubility of water in organic solvents, and SE* scale parameters

International Nuclear Information System (INIS)

Mezhov, E.A.; Khananashvili, N.L.; Shmidt, V.S.

1988-01-01

A linear correlation has been established between the solubility of water in water-immiscible organic solvents and the interfacial tension at the water-solvent interface on the one hand and the parameters of the SE* and π* scales for these solvents on the other hand. This allows us, using the known tabulated SE* or π* parameters for each solvent, to predict the values of the interfacial tension and the solubility of water for the corresponding systems. We have shown that the SE* scale allows us to predict these values more accurately than other known solvent scales, since in contrast to other scales it characterizes solvents found in equilibrium with water

Human telomere sequence DNA in water-free and high-viscosity solvents: G-quadruplex folding governed by Kramers rate theory.

Science.gov (United States)

Lannan, Ford M; Mamajanov, Irena; Hud, Nicholas V

2012-09-19

Structures formed by human telomere sequence (HTS) DNA are of interest due to the implication of telomeres in the aging process and cancer. We present studies of HTS DNA folding in an anhydrous, high viscosity deep eutectic solvent (DES) comprised of choline choride and urea. In this solvent, the HTS DNA forms a G-quadruplex with the parallel-stranded ("propeller") fold, consistent with observations that reduced water activity favors the parallel fold, whereas alternative folds are favored at high water activity. Surprisingly, adoption of the parallel structure by HTS DNA in the DES, after thermal denaturation and quick cooling to room temperature, requires several months, as opposed to less than 2 min in an aqueous solution. This extended folding time in the DES is, in part, due to HTS DNA becoming kinetically trapped in a folded state that is apparently not accessed in lower viscosity solvents. A comparison of times required for the G-quadruplex to convert from its aqueous-preferred folded state to its parallel fold also reveals a dependence on solvent viscosity that is consistent with Kramers rate theory, which predicts that diffusion-controlled transitions will slow proportionally with solvent friction. These results provide an enhanced view of a G-quadruplex folding funnel and highlight the necessity to consider solvent viscosity in studies of G-quadruplex formation in vitro and in vivo. Additionally, the solvents and analyses presented here should prove valuable for understanding the folding of many other nucleic acids and potentially have applications in DNA-based nanotechnology where time-dependent structures are desired.

29 CFR 1915.32 - Toxic cleaning solvents.

Science.gov (United States)

2010-07-01

... 29 Labor 7 2010-07-01 2010-07-01 false Toxic cleaning solvents. 1915.32 Section 1915.32 Labor... Preservation § 1915.32 Toxic cleaning solvents. (a) When toxic solvents are used, the employer shall employ one or more of the following measures to safeguard the health of employees exposed to these solvents. (1...

MeCP2 regulates Tet1-catalyzed demethylation, CTCF binding, and learning-dependent alternative splicing of the BDNF gene in Turtle

Science.gov (United States)

Zheng, Zhaoqing; Ambigapathy, Ganesh; Keifer, Joyce

2017-01-01

MECP2 mutations underlying Rett syndrome cause widespread misregulation of gene expression. Functions for MeCP2 other than transcriptional are not well understood. In an ex vivo brain preparation from the pond turtle Trachemys scripta elegans, an intraexonic splicing event in the brain-derived neurotrophic factor (BDNF) gene generates a truncated mRNA transcript in naïve brain that is suppressed upon classical conditioning. MeCP2 and its partners, splicing factor Y-box binding protein 1 (YB-1) and methylcytosine dioxygenase 1 (Tet1), bind to BDNF chromatin in naïve but dissociate during conditioning; the dissociation correlating with decreased DNA methylation. Surprisingly, conditioning results in new occupancy of BDNF chromatin by DNA insulator protein CCCTC-binding factor (CTCF), which is associated with suppression of splicing in conditioning. Knockdown of MeCP2 shows it is instrumental for splicing and inhibits Tet1 and CTCF binding thereby negatively impacting DNA methylation and conditioning-dependent splicing regulation. Thus, mutations in MECP2 can have secondary effects on DNA methylation and alternative splicing. DOI: http://dx.doi.org/10.7554/eLife.25384.001 PMID:28594324

Analysis of recovered solvents from coal liquefaction in a flowing-solvent reactor by SEC and UV-fluorescence

Energy Technology Data Exchange (ETDEWEB)

Li, W.Y.; Feng, J.; Xie, K.C.; Kandiyoti, R. [Taiyuan University of Technology, Taiyuan (China)

2005-08-01

Point of Ayr coal has been extracted using three solvents: tetralin, quinoline and 1-methyl-2-pyrrolidinone (NMP); at two temperatures: 350 {sup o}C and 450{sup o}C, corresponding approximately to before and after the onset of massive covalent bond scission by pyrolysis. These solvents differ in solvent power and the ability to donate hydrogen atoms to stabilize free radicals produced by pyrolysis of the coal. Analysis of the fresh solvents and recovered solvents from coal liquefaction was achieved by size exclusion chromatography and UV-fluorescence spectroscopy. In the blank run, it was testified that the filling material sand and the steel powder did not react with solvent with increasing reaction temperature. The role of hydrogen donation in the tetralin extracts was to increase the proportion of large molecules with increasing extraction temperature. Quinoline and NMP both have the powerful extracting capability to get more materials out of coal with increasing extraction temperature.

Analysis of recovered solvents from coal liquefaction in a flowing-solvent reactor by SEC and UV-fluorescence

Energy Technology Data Exchange (ETDEWEB)

Wen-Ying Li; Jie Feng; Ke-Chang Xie; R. Kandiyoti [Taiyuan University of Technology, Taiyuan (China). Key Laboratory of Coal Science and Technology for Ministry of Education and Shanxi Province

2005-08-01

Point of Ayr coal has been extracted using three solvents: tetralin, quinoline and 1-methyl-2-pyrrolidinone (NMP); at two temperatures: 350{sup o}C and 450{sup o}C, corresponding approximately to before and after the onset of massive covalent bond scission by pyrolysis. These solvents differ in solvent power and the ability to donate hydrogen atoms to stabilize free radicals produced by pyrolysis of the coal. Analysis of the fresh solvents and recovered solvents from coal liquefaction was achieved by size exclusion chromatography and UV-fluorescence spectroscopy. In the blank run, it was testified that the filling material sand and the steel powder did not react with solvent with increasing reaction temperature. The role of hydrogen donation in the tetralin extracts was to increase the proportion of large molecules with increasing extraction temperature. Quinoline and NMP both have the powerful extracting capability to get more materials out of coal with increasing extraction temperature.

Evidence of two different Na/sup +/-dependent (/sup 3/H)-ouabain binding sites of a Na/sup +/-K/sup +/-ATPase of guinea-pig hearts

Energy Technology Data Exchange (ETDEWEB)

Fricke, U; Klaus, W [Koeln Univ. (Germany, F.R.)

1977-11-01

The influence of various Na/sup +/ concentrations on (/sup 3/H)-ouabain binding was studied in experiments on a microsomal Na/sup +/-K/sup +/-adenosine triphosphatase (ATPase) from guinea-pig hearts. The ATP-independent cardiac glycoside binding was not influenced by increasing Na/sup +/ concentrations. However, a good correlation was found between the ATP-dependent (/sup 3/H)-ouabain binding and Na/sup +/ concentration. A more detailed analysis of these results revealed two distinct processes involved in this interaction: one ouabain binding process was activated at rather low Na/sup +/ concentrations, (Ksub(0.5) = 4.5 mM); this type of (/sup 3/H)-ouabain binding was strongly correlated to the Na/sup +/ concentration necessary for half maximum phosphorylation (Ksub(0.5) = 1 mM). The other ouabain binding process was predominant at high Na/sup +/ concentrations (Ksub(0.5 = 69 mM). On the basis of the commonly accepted ATPase reaction cycle a model for the interaction of cardiac glycosides with the Na/sup +/-K/sup +/-ATPase is proposed, assuming two different binding sites for cardiac glycosides (E/sub 2/ -P and Esub(l) -P) and involving a translocation of these drugs from an outer to an inner compartment of the cell membrane.

Direct Probing of Solvent Accessibility and Mobility at the Binding Interface of Polymerase (Dpo4)-DNA Complex

OpenAIRE

Qin, Yangzhong; Yang, Yi; Zhang, Luyuan; Fowler, Jason D.; Qiu, Weihong; Wang, Lijuan; Suo, Zucai; Zhong, Dongping

2013-01-01

Water plays essential structural and dynamical roles in protein-DNA recognition through contributing to enthalpic or entropic stabilization of binding complex and by mediating intermolecular interactions and fluctuations for biological function. These interfacial water molecules are confined by the binding partners in nanospace but in many cases they are highly mobile and exchange with outside bulk solution. Here, we report our studies of the interfacial water dynamics in the binary and terna...

Variation in one residue associated with the metal ion-dependent adhesion site regulates αIIbβ3 integrin ligand binding affinity.

Directory of Open Access Journals (Sweden)

Joel Raborn

Full Text Available The Asp of the RGD motif of the ligand coordinates with the β I domain metal ion dependent adhesion site (MIDAS divalent cation, emphasizing the importance of the MIDAS in ligand binding. There appears to be two distinct groups of integrins that differ in their ligand binding affinity and adhesion ability. These differences may be due to a specific residue associated with the MIDAS, particularly the β3 residue Ala(252 and corresponding Ala in the β1 integrin compared to the analogous Asp residue in the β2 and β7 integrins. Interestingly, mutations in the adjacent to MIDAS (ADMIDAS of integrins α4β7 and αLβ2 increased the binding and adhesion abilities compared to the wild-type, while the same mutations in the α2β1, α5β1, αVβ3, and αIIbβ3 integrins demonstrated decreased ligand binding and adhesion. We introduced a mutation in the αIIbβ3 to convert this MIDAS associated Ala(252 to Asp. By combination of this mutant with mutations of one or two ADMIDAS residues, we studied the effects of this residue on ligand binding and adhesion. Then, we performed molecular dynamics simulations on the wild-type and mutant αIIbβ3 integrin β I domains, and investigated the dynamics of metal ion binding sites in different integrin-RGD complexes. We found that the tendency of calculated binding free energies was in excellent agreement with the experimental results, suggesting that the variation in this MIDAS associated residue accounts for the differences in ligand binding and adhesion among different integrins, and it accounts for the conflicting results of ADMIDAS mutations within different integrins. This study sheds more light on the role of the MIDAS associated residue pertaining to ligand binding and adhesion and suggests that this residue may play a pivotal role in integrin-mediated cell rolling and firm adhesion.

Binding and distribution studies in the SENCAR mouse of compounds demonstrating a route-dependent tumorigenic effect

International Nuclear Information System (INIS)

Carlson, G.P.; Fossa, A.A.; Morse, M.A.; Weaver, P.M.

1986-01-01

Previous investigators have determined that benzo(a)pyrene [B(a)P] was much more effective in causing skin papillomas if applied topically than when administered orally in the initiation-promotion assay in SENCAR mouse. Conversely, urethane and acrylamide caused a higher percentage of mice to develop papillomas and induced more tumors per mouse when given orally. In an attempt to understand the reason for this discrepancy in route dependency, 3 H-benzo(a)pyrene, 14 C-acrylamide were administered as single doses orally or topically to male SENCAR mice. Distribution in skin, stomach, liver, and lung was determined for time periods up to 48 hr. The binding of these compounds to DNA, RNA, and protein in these tissues was determined 6 and 48 hr after administration. For all three compounds, high concentrations were found in the skin following topical application, but very little material reached this target organ following oral administration. In contrast, the internal organs generally contained more material after oral administration. The binding of label compounds to DNA, RNA, and protein generally reflected the distribution data, thus more compound was bound in the stomach, liver, and lung after oral administration compared to topical application, whereas the opposite was true for the skin. This finding was particularly evident for B(a)P. The results suggest that differences in distribution to the skin and binding to macromolecules following oral or topical administration cannot explain the greater tumorigenicity of urethane and acrylamide after oral administration in the SENCAR mouse

Dual Function of Novel Pollen Coat (Surface) Proteins: IgE-binding Capacity and Proteolytic Activity Disrupting the Airway Epithelial Barrier

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Bashir, Mohamed Elfatih H.; Ward, Jason M.; Cummings, Matthew; Karrar, Eltayeb E.; Root, Michael; Mohamed, Abu Bekr A.; Naclerio, Robert M.; Preuss, Daphne

2013-01-01

Background The pollen coat is the first structure of the pollen to encounter the mucosal immune system upon inhalation. Prior characterizations of pollen allergens have focused on water-soluble, cytoplasmic proteins, but have overlooked much of the extracellular pollen coat. Due to washing with organic solvents when prepared, these pollen coat proteins are typically absent from commercial standardized allergenic extracts (i.e., “de-fatted”), and, as a result, their involvement in allergy has not been explored. Methodology/Principal Findings Using a unique approach to search for pollen allergenic proteins residing in the pollen coat, we employed transmission electron microscopy (TEM) to assess the impact of organic solvents on the structural integrity of the pollen coat. TEM results indicated that de-fatting of Cynodon dactylon (Bermuda grass) pollen (BGP) by use of organic solvents altered the structural integrity of the pollen coat. The novel IgE-binding proteins of the BGP coat include a cysteine protease (CP) and endoxylanase (EXY). The full-length cDNA that encodes the novel IgE-reactive CP was cloned from floral RNA. The EXY and CP were purified to homogeneity and tested for IgE reactivity. The CP from the BGP coat increased the permeability of human airway epithelial cells, caused a clear concentration-dependent detachment of cells, and damaged their barrier integrity. Conclusions/Significance Using an immunoproteomics approach, novel allergenic proteins of the BGP coat were identified. These proteins represent a class of novel dual-function proteins residing on the coat of the pollen grain that have IgE-binding capacity and proteolytic activity, which disrupts the integrity of the airway epithelial barrier. The identification of pollen coat allergens might explain the IgE-negative response to available skin-prick-testing proteins in patients who have positive symptoms. Further study of the role of these pollen coat proteins in allergic responses is

Dual function of novel pollen coat (surface proteins: IgE-binding capacity and proteolytic activity disrupting the airway epithelial barrier.

Directory of Open Access Journals (Sweden)

Mohamed Elfatih H Bashir

Full Text Available BACKGROUND: The pollen coat is the first structure of the pollen to encounter the mucosal immune system upon inhalation. Prior characterizations of pollen allergens have focused on water-soluble, cytoplasmic proteins, but have overlooked much of the extracellular pollen coat. Due to washing with organic solvents when prepared, these pollen coat proteins are typically absent from commercial standardized allergenic extracts (i.e., "de-fatted", and, as a result, their involvement in allergy has not been explored. METHODOLOGY/PRINCIPAL FINDINGS: Using a unique approach to search for pollen allergenic proteins residing in the pollen coat, we employed transmission electron microscopy (TEM to assess the impact of organic solvents on the structural integrity of the pollen coat. TEM results indicated that de-fatting of Cynodon dactylon (Bermuda grass pollen (BGP by use of organic solvents altered the structural integrity of the pollen coat. The novel IgE-binding proteins of the BGP coat include a cysteine protease (CP and endoxylanase (EXY. The full-length cDNA that encodes the novel IgE-reactive CP was cloned from floral RNA. The EXY and CP were purified to homogeneity and tested for IgE reactivity. The CP from the BGP coat increased the permeability of human airway epithelial cells, caused a clear concentration-dependent detachment of cells, and damaged their barrier integrity. CONCLUSIONS/SIGNIFICANCE: Using an immunoproteomics approach, novel allergenic proteins of the BGP coat were identified. These proteins represent a class of novel dual-function proteins residing on the coat of the pollen grain that have IgE-binding capacity and proteolytic activity, which disrupts the integrity of the airway epithelial barrier. The identification of pollen coat allergens might explain the IgE-negative response to available skin-prick-testing proteins in patients who have positive symptoms. Further study of the role of these pollen coat proteins in allergic

Probing binding hot spots at protein-RNA recognition sites.

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Barik, Amita; Nithin, Chandran; Karampudi, Naga Bhushana Rao; Mukherjee, Sunandan; Bahadur, Ranjit Prasad

2016-01-29

We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein-RNA interfaces to probe the binding hot spots at protein-RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein-protein and protein-RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein-RNA recognition sites with desired affinity. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Activity and conformation of lysozyme in molecular solvents, protic ionic liquids (PILs) and salt-water systems.

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Wijaya, Emmy C; Separovic, Frances; Drummond, Calum J; Greaves, Tamar L

2016-09-21

Improving protein stabilisation is important for the further development of many applications in the pharmaceutical, specialty chemical, consumer product and agricultural sectors. However, protein stabilization is highly dependent on the solvent environment and, hence, it is very complex to tailor protein-solvent combinations for stable protein maintenance. Understanding solvent features that govern protein stabilization will enable selection or design of suitable media with favourable solution environments to retain protein native conformation. In this work the structural conformation and activity of lysozyme in 29 solvent systems were investigated to determine the role of various solvent features on the stability of the enzyme. The solvent systems consisted of 19 low molecular weight polar solvents and 4 protic ionic liquids (PILs), both at different water content levels, and 6 aqueous salt solutions. Small angle X-ray scattering, Fourier transform infrared spectroscopy and UV-vis spectroscopy were used to investigate the tertiary and secondary structure of lysozyme along with the corresponding activity in various solvation systems. At low non-aqueous solvent concentrations (high water content), the presence of solvents and salts generally maintained lysozyme in its native structure and enhanced its activity. Due to the presence of a net surface charge on lysozyme, electrostatic interactions in PIL-water systems and salt solutions enhanced lysozyme activity more than the specific hydrogen-bond interactions present in non-ionic molecular solvents. At higher solvent concentrations (lower water content), solvents with a propensity to exhibit the solvophobic effect, analogous to the hydrophobic effect in water, retained lysozyme native conformation and activity. This solvophobic effect was observed particularly for solvents which contained hydroxyl moieties. Preferential solvophobic effects along with bulky chemical structures were postulated to result in less

Presenilins Regulate Neurotrypsin Gene Expression and Neurotrypsin-dependent Agrin Cleavage via Cyclic AMP Response Element-binding Protein (CREB) Modulation*

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Almenar-Queralt, Angels; Kim, Sonia N.; Benner, Christopher; Herrera, Cheryl M.; Kang, David E.; Garcia-Bassets, Ivan; Goldstein, Lawrence S. B.

2013-01-01

Presenilins, the catalytic components of the γ-secretase complex, are upstream regulators of multiple cellular pathways via regulation of gene transcription. However, the underlying mechanisms and the genes regulated by these pathways are poorly characterized. In this study, we identify Tequila and its mammalian ortholog Prss12 as genes negatively regulated by presenilins in Drosophila larval brains and mouse embryonic fibroblasts, respectively. Prss12 encodes the serine protease neurotrypsin, which cleaves the heparan sulfate proteoglycan agrin. Altered neurotrypsin activity causes serious synaptic and cognitive defects; despite this, the molecular processes regulating neurotrypsin expression and activity are poorly understood. Using γ-secretase drug inhibitors and presenilin mutants in mouse embryonic fibroblasts, we found that a mature γ-secretase complex was required to repress neurotrypsin expression and agrin cleavage. We also determined that PSEN1 endoproteolysis or processing of well known γ-secretase substrates was not essential for this process. At the transcriptional level, PSEN1/2 removal induced cyclic AMP response element-binding protein (CREB)/CREB-binding protein binding, accumulation of activating histone marks at the neurotrypsin promoter, and neurotrypsin transcriptional and functional up-regulation that was dependent on GSK3 activity. Upon PSEN1/2 reintroduction, this active epigenetic state was replaced by a methyl CpG-binding protein 2 (MeCP2)-containing repressive state and reduced neurotrypsin expression. Genome-wide analysis revealed hundreds of other mouse promoters in which CREB binding is similarly modulated by the presence/absence of presenilins. Our study thus identifies Tequila and neurotrypsin as new genes repressed by presenilins and reveals a novel mechanism used by presenilins to modulate CREB signaling based on controlling CREB recruitment. PMID:24145027

Presenilins regulate neurotrypsin gene expression and neurotrypsin-dependent agrin cleavage via cyclic AMP response element-binding protein (CREB) modulation.

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Almenar-Queralt, Angels; Kim, Sonia N; Benner, Christopher; Herrera, Cheryl M; Kang, David E; Garcia-Bassets, Ivan; Goldstein, Lawrence S B

2013-12-06

Presenilins, the catalytic components of the γ-secretase complex, are upstream regulators of multiple cellular pathways via regulation of gene transcription. However, the underlying mechanisms and the genes regulated by these pathways are poorly characterized. In this study, we identify Tequila and its mammalian ortholog Prss12 as genes negatively regulated by presenilins in Drosophila larval brains and mouse embryonic fibroblasts, respectively. Prss12 encodes the serine protease neurotrypsin, which cleaves the heparan sulfate proteoglycan agrin. Altered neurotrypsin activity causes serious synaptic and cognitive defects; despite this, the molecular processes regulating neurotrypsin expression and activity are poorly understood. Using γ-secretase drug inhibitors and presenilin mutants in mouse embryonic fibroblasts, we found that a mature γ-secretase complex was required to repress neurotrypsin expression and agrin cleavage. We also determined that PSEN1 endoproteolysis or processing of well known γ-secretase substrates was not essential for this process. At the transcriptional level, PSEN1/2 removal induced cyclic AMP response element-binding protein (CREB)/CREB-binding protein binding, accumulation of activating histone marks at the neurotrypsin promoter, and neurotrypsin transcriptional and functional up-regulation that was dependent on GSK3 activity. Upon PSEN1/2 reintroduction, this active epigenetic state was replaced by a methyl CpG-binding protein 2 (MeCP2)-containing repressive state and reduced neurotrypsin expression. Genome-wide analysis revealed hundreds of other mouse promoters in which CREB binding is similarly modulated by the presence/absence of presenilins. Our study thus identifies Tequila and neurotrypsin as new genes repressed by presenilins and reveals a novel mechanism used by presenilins to modulate CREB signaling based on controlling CREB recruitment.

Solvent-annealing-induced nanowetting in templates: towards tailored polymer nanostructures.

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Chen, Jiun-Tai; Lee, Chih-Wei; Chi, Mu-Huan; Yao, I-Chun

2013-02-25

We study the solvent-annealing-induced nanowetting in templates using porous anodic aluminum oxide membranes. The morphology of polystyrene and poly(methyl methacrylate) nanostructures can be controlled, depending on whether the swollen polymers are in the partial or complete wetting regimes, which are characterized by the spreading coefficient. When the swollen polymers are in the partial wetting regime, polymers wet the nanopores by capillary action, resulting in the formation of polymer nanorods. When the swollen polymers are in the complete wetting regime, polymers form wetting layers in the nanopores, resulting in the formation of polymer nanotubes. The solubility parameters of polymers and solvents are also used to predict the wetting behavior of swollen polymers in cylindrical geometry. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adaptive evolution of transcription factor binding sites

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Berg Johannes

2004-10-01

Full Text Available Abstract Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution of complex regulatory networks. We study a theoretical model for the sequence evolution of binding sites by point mutations. The approach is based on biophysical models for the binding of transcription factors to DNA. Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection. Results We show that the selection for factor binding generically leads to specific correlations between nucleotide frequencies at different positions of a binding site. We demonstrate the possibility of rapid adaptive evolution generating a new binding site for a given transcription factor by point mutations. The evolutionary time required is estimated in terms of the neutral (background mutation rate, the selection coefficient, and the effective population size. Conclusions The efficiency of binding site formation is seen to depend on two joint conditions: the binding site motif must be short enough and the promoter region must be long enough. These constraints on promoter architecture are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive evolution of genetic switches and of signal integration through binding cooperativity between different sites. Experimental tests of this picture involving the statistics of polymorphisms and phylogenies of sites are discussed.

Simultaneous fluorescence light-up and selective multicolor nucleobase recognition based on sequence-dependent strong binding of berberine to DNA abasic site.

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Wu, Fei; Shao, Yong; Ma, Kun; Cui, Qinghua; Liu, Guiying; Xu, Shujuan

2012-04-28

Label-free DNA nucleobase recognition by fluorescent small molecules has received much attention due to its simplicity in mutation identification and drug screening. However, sequence-dependent fluorescence light-up nucleobase recognition and multicolor emission with individual emission energy for individual nucleobases have been seldom realized. Herein, an abasic site (AP site) in a DNA duplex was employed as a binding field for berberine, one of isoquinoline alkaloids. Unlike weak binding of berberine to the fully matched DNAs without the AP site, strong binding of berberine to the AP site occurs and the berberine's fluorescence light-up behaviors are highly dependent on the target nucleobases opposite the AP site in which the targets thymine and cytosine produce dual emission bands, while the targets guanine and adenine only give a single emission band. Furthermore, more intense emissions are observed for the target pyrimidines than purines. The flanking bases of the AP site also produce some modifications of the berberine's emission behavior. The binding selectivity of berberine at the AP site is also confirmed by measurements of fluorescence resonance energy transfer, excited-state lifetime, DNA melting and fluorescence quenching by ferrocyanide and sodium chloride. It is expected that the target pyrimidines cause berberine to be stacked well within DNA base pairs near the AP site, which results in a strong resonance coupling of the electronic transitions to the particular vibration mode to produce the dual emissions. The fluorescent signal-on and emission energy-modulated sensing for nucleobases based on this fluorophore is substantially advantageous over the previously used fluorophores. We expect that this approach will be developed as a practical device for differentiating pyrimidines from purines by positioning an AP site toward a target that is available for readout by this alkaloid probe. This journal is © The Royal Society of Chemistry 2012

Nuclear size is sensitive to NTF2 protein levels in a manner dependent on Ran binding

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Vuković, Lidija D.; Jevtić, Predrag; Zhang, Zhaojie; Stohr, Bradley A.; Levy, Daniel L.

2016-01-01

ABSTRACT Altered nuclear size is associated with many cancers, and determining whether cancer-associated changes in nuclear size contribute to carcinogenesis necessitates an understanding of mechanisms of nuclear size regulation. Although nuclear import rates generally positively correlate with nuclear size, NTF2 levels negatively affect nuclear size, despite the role of NTF2 (also known as NUTF2) in nuclear recycling of the import factor Ran. We show that binding of Ran to NTF2 is required for NTF2 to inhibit nuclear expansion and import of large cargo molecules in Xenopus laevis egg and embryo extracts, consistent with our observation that NTF2 reduces the diameter of the nuclear pore complex (NPC) in a Ran-binding-dependent manner. Furthermore, we demonstrate that ectopic NTF2 expression in Xenopus embryos and mammalian tissue culture cells alters nuclear size. Finally, we show that increases in nuclear size during melanoma progression correlate with reduced NTF2 expression, and increasing NTF2 levels in melanoma cells is sufficient to reduce nuclear size. These results show a conserved capacity for NTF2 to impact on nuclear size, and we propose that NTF2 might be a new cancer biomarker. PMID:26823604

Implicit solvent simulations of DNA and DNA-protein complexes: Agreement with explicit solvent vs experiment

Czech Academy of Sciences Publication Activity Database

Chocholoušová, Jana; Feig, M.

2006-01-01

Roč. 110, č. 34 (2006), s. 17240-17251 ISSN 1520-6106 Keywords : implicit solvent * explicit solvent * protein DNA complex Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.115, year: 2006

Theory of polyelectrolytes in solvents.

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Chitanvis, Shirish M

2003-12-01

Using a continuum description, we account for fluctuations in the ionic solvent surrounding a Gaussian, charged chain and derive an effective short-ranged potential between the charges on the chain. This potential is repulsive at short separations and attractive at longer distances. The chemical potential can be derived from this potential. When the chemical potential is positive, it leads to a meltlike state. For a vanishingly low concentration of segments, this state exhibits scaling behavior for long chains. The Flory exponent characterizing the radius of gyration for long chains is calculated to be approximately 0.63, close to the classical value obtained for second order phase transitions. For short chains, the radius of gyration varies linearly with N, the chain length, and is sensitive to the parameters in the interaction potential. The linear dependence on the chain length N indicates a stiff behavior. The chemical potential associated with this interaction changes sign, when the screening length in the ionic solvent exceeds a critical value. This leads to condensation when the chemical potential is negative. In this state, it is shown using the mean-field approximation that spherical and toroidal condensed shapes can be obtained. The thickness of the toroidal polyelectrolyte is studied as a function of the parameters of the model, such as the ionic screening length. The predictions of this theory should be amenable to experimental verification.

Biomolecular-solvent stereodynamic coupling probed by deuteration

International Nuclear Information System (INIS)

Fornili, S.L.; Leone, M.; Madonia, F.; Migliore, M.; Palma-Vittorelli, M.B.; Palma, M.U.; San Biagio, P.L.

1983-01-01

Thermodynamic interpretation of experiments with isotopically perturbed solvent supports the view that solvent stereodynamics is directly relevant to thermodynamic stability of biomolecules. According with the current understanding of the structure of the aqueous solvent, in any stereodynamic configuration of the latter, connectivity pathways are identifiable for their topologic and order properties. Perturbing the solvent by isotopic substitution or, e.g., by addition of co-solvents, can therefore be viewed as reinforcing or otherwise perturbing these topologic structures. This microscopic model readily visualizes thermodynamic interpretation. In conclusion, the topologic stereodynamic structures of connectivity pathways in the solvent, as modified by interaction with solutes, acquire a specific thermodynamic and biological significance, and the problem of thermodynamic and functional stability of biomolecules is seen in its full pertinent phase space

Understanding dissolution behavior of 193nm photoresists in organic solvent developers

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Lee, Seung-Hyun; Park, Jong Keun; Cardolaccia, Thomas; Sun, Jibin; Andes, Cecily; O'Connell, Kathleen; Barclay, George G.

2012-03-01

Herein, we investigate the dissolution behavior of 193-nm chemically amplified resist in different organic solvents at a mechanistic level. We previously reported the effect of solvent developers on the negative tone development (NTD) process in both dry and immersion lithography, and demonstrated various resist performance parameters such as photospeed, critical dimension uniformity, and dissolution rate contrast are strongly affected by chemical nature of the organic developer. We further pursued the investigation by examining the dependence of resist dissolution behavior on their solubility properties using Hansen Solubility Parameter (HSP). The effects of monomer structure, and resist composition, and the effects of different developer chemistry on dissolution behaviors were evaluated by using laser interferometry and quartz crystal microbalance. We have found that dissolution behaviors of methacrylate based resists are significantly different in different organic solvent developers such as OSDTM-1000 Developer* and n-butyl acetate (nBA), affecting their resist performance. This study reveals that understanding the resist dissolution behavior helps to design robust NTD materials for higher resolution imaging.

Structural transition of a homopolymer in solvents mixture

International Nuclear Information System (INIS)

Guettari, Moez; Aschi, Adel; Gomati, Riadh; Gharbi, Abdelhafidh

2008-01-01

The present work is aimed at studying the thermodynamic behaviour of a polymer in solvents mixture. Dynamic light scattering is used to measure the hydrodynamic radius of polyvinylpyrrolidone (M w = 360,000 g/mol), in water/methanol solvents mixture, versus the mixed solvents composition at 25 deg. C. Then, we show that the polymer conformation adopts the Coil-Globule-Coil structure when the methanol molar fraction X A is varied. This transition is attributed to solvent quality change which result from water and methanol complex formation. The polymer contraction rate calculated for each composition takes its maximum value at X A = 0.17. Hildebrand theory assuming the solvents mixture as an equivalent solvent was used to analyze the change in mixed solvents quality. These changes can be attributed to dispersive forces in solvents mixture

A New Class of Solvents for TRU Dissolution and Separation: Ionic Liquids. Project No. 81891

International Nuclear Information System (INIS)

Rogers, Robin D.

2004-01-01

Through the current EMSP funding, solvent extraction technologies based on liquid-liquid partitioning of TRU to an Ionic Liquid phase containing conventional complexants has been shown to be viable. The growing understanding of the role that the different components of an ionic liquid can have on the partitioning mechanism, and on the nature of the subsequent dissolved species indicates strongly that ionic liquids are not necessarily direct replacements for volatile or otherwise hazardous organic solvents. Separations and partitioning can be exceptionally complex with competing solvent extraction, cation, anion and sacrificial ion exchange mechanisms are all important, depending on the selection of components for formation of the ionic liquid phase, and that control of these competing mechanisms can be utilized to provide new, alternative separations schemes

Absorption and emission behaviour of trans- p-coumaric acid in aqueous solutions and some organic solvents

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Putschögl, M.; Zirak, P.; Penzkofer, A.

2008-01-01

The absorption and fluorescence behaviour of trans- p-coumaric acid ( trans-4-hydroxycinnamic acid) is investigated in buffered aqueous solution over a wide range from pH 1 to pH 12, in un-buffered water, and in some organic solvents. Absorption cross-section spectra, fluorescence quantum distributions, fluorescence quantum yields, and degrees of fluorescence polarisation are measured. p-Coumaric acid exists in different ionic forms in aqueous solution depending on the pH. There is an equilibrium between the neutral form ( p-CAH 2) and the single anionic form ( p-CAH -) at low pH (p Kna ≈ 4.9), and between the single anionic and the double anionic form ( p-CA 2-) at high pH (p Kaa ≈ 9.35). In the organic solvents studied trans- p-coumaric acid is dissolved in its neutral form. The fluorescence quantum yield of trans- p-coumaric acid in aqueous solution is ϕF ≈ 1.4 × 10 -4 for the neutral and the single anionic form, while it is ϕF ≈ 1.3 × 10 -3 for the double anionic form. For trans- p-coumaric acid in organic solvents fluorescence quantum yields in the range from 4.8 × 10 -5 (acetonitrile) to 1.5 × 10 -4 (glycerol) were measured. The fluorescence spectra are 7700-10,000 cm -1 Stokes shifted in aqueous solution, and 5400-8200 cm -1 Stokes shifted in the studied organic solvents. Decay paths responsible for the low fluorescence quantum yields are discussed (photo-isomerisation and internal conversion for p-CA 2-, solvent-assisted intra-molecular charge-transfer or ππ ∗ to nπ ∗ transfer and internal conversion for p-CAH 2 and p-CAH -). The solvent dependence of the first ππ ∗ electronic transition frequency and of the fluorescence Stokes shift of p-CAH 2 is discussed in terms of polar solute-solvent interaction effects. Thereby the ground-state and excite-state molecular dipole moments are extracted.

Absorption and emission behaviour of trans-p-coumaric acid in aqueous solutions and some organic solvents

International Nuclear Information System (INIS)

Putschoegl, M.; Zirak, P.; Penzkofer, A.

2008-01-01

The absorption and fluorescence behaviour of trans-p-coumaric acid (trans-4-hydroxycinnamic acid) is investigated in buffered aqueous solution over a wide range from pH 1 to pH 12, in un-buffered water, and in some organic solvents. Absorption cross-section spectra, fluorescence quantum distributions, fluorescence quantum yields, and degrees of fluorescence polarisation are measured. p-Coumaric acid exists in different ionic forms in aqueous solution depending on the pH. There is an equilibrium between the neutral form (p-CAH 2 ) and the single anionic form (p-CAH - ) at low pH (pK na ∼ 4.9), and between the single anionic and the double anionic form (p-CA 2- ) at high pH (pK aa ∼ 9.35). In the organic solvents studied trans-p-coumaric acid is dissolved in its neutral form. The fluorescence quantum yield of trans-p-coumaric acid in aqueous solution is φ F ∼ 1.4 x 10 -4 for the neutral and the single anionic form, while it is φ F ∼ 1.3 x 10 -3 for the double anionic form. For trans-p-coumaric acid in organic solvents fluorescence quantum yields in the range from 4.8 x 10 -5 (acetonitrile) to 1.5 x 10 -4 (glycerol) were measured. The fluorescence spectra are 7700-10,000 cm -1 Stokes shifted in aqueous solution, and 5400-8200 cm -1 Stokes shifted in the studied organic solvents. Decay paths responsible for the low fluorescence quantum yields are discussed (photo-isomerisation and internal conversion for p-CA 2- , solvent-assisted intra-molecular charge-transfer or ππ* to nπ* transfer and internal conversion for p-CAH 2 and p-CAH - ). The solvent dependence of the first ππ* electronic transition frequency and of the fluorescence Stokes shift of p-CAH 2 is discussed in terms of polar solute-solvent interaction effects. Thereby the ground-state and excite-state molecular dipole moments are extracted