InterProSurf: a web server for predicting interacting sites on protein surfaces

PubMed Central

Negi, Surendra S.; Schein, Catherine H.; Oezguen, Numan; Power, Trevor D.; Braun, Werner

2009-01-01

Summary A new web server, InterProSurf, predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex. The prediction method is based on solvent accessible surface area of residues in the isolated subunits, a propensity scale for interface residues and a clustering algorithm to identify surface regions with residues of high interface propensities. Here we illustrate the application of InterProSurf to determine which areas of Bacillus anthracis toxins and measles virus hemagglutinin protein interact with their respective cell surface receptors. The computationally predicted regions overlap with those regions previously identified as interface regions by sequence analysis and mutagenesis experiments. PMID:17933856

Surface characterization and chemical analysis of bamboo substrates pretreated by alkali hydrogen peroxide.

PubMed

Song, Xueping; Jiang, Yan; Rong, Xianjian; Wei, Wei; Wang, Shuangfei; Nie, Shuangxi

2016-09-01

The surface characterization and chemical analysis of bamboo substrates by alkali hydrogen peroxide pretreatment (AHPP) were investigated in this study. The results tended to manifest that AHPP prior to enzymatic and chemical treatment was potential for improving accessibility and reactivity of bamboo substrates. The inorganic components, organic solvent extractives and acid-soluble lignin were effectively removed by AHPP. X-ray photoelectron spectroscopy (XPS) analysis indicated that the surface of bamboo chips had less lignin but more carbohydrate after pre-treatment. Fiber surfaces became etched and collapsed, and more pores and debris on the substrate surface were observed with Scanning Electron Microscopy (SEM). Brenauer-Emmett-Teller (BET) results showed that both of pore volume and surface area were increased after AHPP. Although XRD analysis showed that AHPP led to relatively higher crystallinity, pre-extraction could overall enhance the accessibility of enzymes and chemicals into the bamboo structure. Copyright © 2016. Published by Elsevier Ltd.

Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites

NASA Astrophysics Data System (ADS)

Lu, Cheng-Tsung; Chen, Shu-An; Bretaña, Neil Arvin; Cheng, Tzu-Hsiu; Lee, Tzong-Yi

2011-10-01

In proteins, glutamate (Glu) residues are transformed into γ-carboxyglutamate (Gla) residues in a process called carboxylation. The process of protein carboxylation catalyzed by γ-glutamyl carboxylase is deemed to be important due to its involvement in biological processes such as blood clotting cascade and bone growth. There is an increasing interest within the scientific community to identify protein carboxylation sites. However, experimental identification of carboxylation sites via mass spectrometry-based methods is observed to be expensive, time-consuming, and labor-intensive. Thus, we were motivated to design a computational method for identifying protein carboxylation sites. This work aims to investigate the protein carboxylation by considering the composition of amino acids that surround modification sites. With the implication of a modified residue prefers to be accessible on the surface of a protein, the solvent-accessible surface area (ASA) around carboxylation sites is also investigated. Radial basis function network is then employed to build a predictive model using various features for identifying carboxylation sites. Based on a five-fold cross-validation evaluation, a predictive model trained using the combined features of amino acid sequence (AA20D), amino acid composition, and ASA, yields the highest accuracy at 0.874. Furthermore, an independent test done involving data not included in the cross-validation process indicates that in silico identification is a feasible means of preliminary analysis. Additionally, the predictive method presented in this work is implemented as Carboxylator (http://csb.cse.yzu.edu.tw/Carboxylator/), a web-based tool for identifying carboxylated proteins with modification sites in order to help users in investigating γ-glutamyl carboxylation.

Predicting the Activity Coefficients of Free-Solvent for Concentrated Globular Protein Solutions Using Independently Determined Physical Parameters

PubMed Central

McBride, Devin W.; Rodgers, Victor G. J.

2013-01-01

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. PMID:24324733

Denaturation of RNA secondary and tertiary structure by urea: simple unfolded state models and free energy parameters account for measured m-values

PubMed Central

Lambert, Dominic; Draper, David E.

2012-01-01

To investigate the mechanism by which urea destabilizes RNA structure, urea-induced unfolding of four different RNA secondary and tertiary structures was quantified in terms of an m-value, the rate at which the free energy of unfolding changes with urea molality. From literature data and our osmometric study of a backbone analog, we derived average interaction potentials (per Å2 of solvent accessible surface) between urea and three kinds of RNA surfaces: phosphate, ribose, and base. Estimates of the increases in solvent accessible surface areas upon RNA denaturation were based on a simple model of unfolded RNA as a combination of helical and single strand segments. These estimates, combined with the three interaction potentials and a term to account for urea interactions with released ions, yield calculated m-values in good agreement with experimental values (200 mm monovalent salt). Agreement was obtained only if single-stranded RNAs were modeled in a highly stacked, A form conformation. The primary driving force for urea induced denaturation is the strong interaction of urea with the large surface areas of bases that become exposed upon denaturation of either RNA secondary or tertiary structure, though urea interactions with backbone and released ions may account for up to a third of the m-value. Urea m-values for all four RNA are salt-dependent, which we attribute to an increased extension (or decreased charge density) of unfolded RNAs with increased urea concentration. The sensitivity of the urea m-value to base surface exposure makes it a potentially useful probe of the conformations of RNA unfolded states. PMID:23088364

Models of the solvent-accessible surface of biopolymers

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

Smith, R.E.

1996-09-01

Many biopolymers such as proteins, DNA, and RNA have been studied because they have important biomedical roles and may be good targets for therapeutic action in treating diseases. This report describes how plastic models of the solvent-accessible surface of biopolymers were made. Computer files containing sets of triangles were calculated, then used on a stereolithography machine to make the models. Small (2 in.) models were made to test whether the computer calculations were done correctly. Also, files of the type (.stl) required by any ISO 9001 rapid prototyping machine were written onto a CD-ROM for distribution to American companies.

Percolation characteristics of solvent invasion in rough fractures under miscible conditions

NASA Astrophysics Data System (ADS)

Korfanta, M.; Babadagli, T.; Develi, K.

2017-10-01

Surface roughness and flow rate effects on the solvent transport under miscible conditions in a single fracture are studied. Surface replicas of seven different rocks (marble, granite, and limestone) are used to represent different surface roughness characteristics each described by different mathematical models including three fractal dimensions. Distribution of dyed solvent is investigated at various flow rate conditions to clarify the effect of roughness on convective and diffusive mixing. After a qualitative analysis using comparative images of different rocks, the area covered by solvent with respect to time is determined to conduct a semi-quantitative analysis. In this exercise, two distinct zones are identified, namely the straight lines obtained for convective (early times) and diffusive (late times) flow. The bending point between these two lines is used to point the transition between the two zones. Finally, the slopes of the straight lines and the bending points are correlated to five different roughness parameters and the rate (Peclet number). It is observed that both surface roughness and flow rate have significant effect on solvent spatial distribution. The largest area covered is obtained at moderate flow rates and hence not only the average surface roughness characteristic is important, but coessentially total fracture surface area needs to be considered when evaluating fluid distribution. It is also noted that the rate effect is critically different for the fracture samples of large grain size (marbles and granite) compared to smaller grain sizes (limestones). Variogram fractal dimension exhibits the strongest correlation with the maximum area covered by solvent, and display increasing trend at the moderate flow rates. Equations with variogram surface fractal dimension in combination with any other surface fractal parameter coupled with Peclet number can be used to predict maximum area covered by solvent in a single fracture, which in turn can be utilized to model oil recovery, waste disposal, and groundwater contamination processes in the presence of fractures.

Interactions of urea with native and unfolded proteins: a volumetric study.

PubMed

Son, Ikbae; Shek, Yuen Lai; Tikhomirova, Anna; Baltasar, Eduardo Hidalgo; Chalikian, Tigran V

2014-11-26

We describe a statistical thermodynamic approach to analyzing urea-dependent volumetric properties of proteins. We use this approach to analyze our urea-dependent data on the partial molar volume and adiabatic compressibility of lysozyme, apocytochrome c, ribonuclease A, and α-chymotrypsinogen A. The analysis produces the thermodynamic properties of elementary urea-protein association reactions while also yielding estimates of the effective solvent-accessible surface areas of the native and unfolded protein states. Lysozyme and apocytochrome c do not undergo urea-induced transitions. The former remains folded, while the latter is unfolded between 0 and 8 M urea. In contrast, ribonuclease A and α-chymotrypsinogen A exhibit urea-induced unfolding transitions. Thus, our data permit us to characterize urea-protein interactions in both the native and unfolded states. We interpreted the urea-dependent volumetric properties of the proteins in terms of the equilibrium constant, k, and changes in volume, ΔV0, and compressibility, ΔKT0, for a reaction in which urea binds to a protein with a concomitant release of two waters of hydration to the bulk. Comparison of the values of k, ΔV0, and ΔKT0 with the similar data obtained on small molecules mimicking protein groups reveals lack of cooperative effects involved in urea-protein interactions. In general, the volumetric approach, while providing a unique characterization of cosolvent-protein interactions, offers a practical way for evaluating the effective solvent accessible surface area of biologically significant fully or partially unfolded polypeptides.

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

PubMed Central

2012-01-01

Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent–solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom–specific solvation parameter σiSASA. A procedure for the determination of values for the σiSASA parameters through matching of explicit and implicit solvation forces is proposed. Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the σiSASA parameters for atom types i of the standard amino acids in the GROMOS force field have been determined. A simplified representation based on groups of atom types σgSASA was obtained via partitioning of the atom–type σiSASA distributions by dynamic programming. Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces. PMID:23180979

Solvent mimicry with methylene carbene to probe protein topography.

PubMed

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.

A template-free solvent-mediated synthesis of high surface area boron nitride nanosheets for aerobic oxidative desulfurization.

PubMed

Wu, Peiwen; Zhu, Wenshuai; Chao, Yanhong; Zhang, Jinshui; Zhang, Pengfei; Zhu, Huiyuan; Li, Changfeng; Chen, Zhigang; Li, Huaming; Dai, Sheng

2016-01-04

Hexagonal boron nitride nanosheets (h-BNNs) with rather high specific surface area (SSA) are important two-dimensional layer-structured materials. Here, a solvent-mediated synthesis of h-BNNs revealed a template-free lattice plane control strategy that induced high SSA nanoporous structured h-BNNs with outstanding aerobic oxidative desulfurization performance.

Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility.

PubMed

Heffernan, Rhys; Yang, Yuedong; Paliwal, Kuldip; Zhou, Yaoqi

2017-09-15

The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions between amino acid residues that are close in three-dimensional structural space but far from each other in their sequence positions. All existing machine-learning techniques relied on a sliding window of 10-20 amino acid residues to capture some 'short to intermediate' non-local interactions. Here, we employed Long Short-Term Memory (LSTM) Bidirectional Recurrent Neural Networks (BRNNs) which are capable of capturing long range interactions without using a window. We showed that the application of LSTM-BRNN to the prediction of protein structural properties makes the most significant improvement for residues with the most long-range contacts (|i-j| >19) over a previous window-based, deep-learning method SPIDER2. Capturing long-range interactions allows the accuracy of three-state secondary structure prediction to reach 84% and the correlation coefficient between predicted and actual solvent accessible surface areas to reach 0.80, plus a reduction of 5%, 10%, 5% and 10% in the mean absolute error for backbone ϕ , ψ , θ and τ angles, respectively, from SPIDER2. More significantly, 27% of 182724 40-residue models directly constructed from predicted C α atom-based θ and τ have similar structures to their corresponding native structures (6Å RMSD or less), which is 3% better than models built by ϕ and ψ angles. We expect the method to be useful for assisting protein structure and function prediction. The method is available as a SPIDER3 server and standalone package at http://sparks-lab.org . yaoqi.zhou@griffith.edu.au or yuedong.yang@griffith.edu.au. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

DMG-α--a computational geometry library for multimolecular systems.

PubMed

Szczelina, Robert; Murzyn, Krzysztof

2014-11-24

The DMG-α library grants researchers in the field of computational biology, chemistry, and biophysics access to an open-sourced, easy to use, and intuitive software for performing fine-grained geometric analysis of molecular systems. The library is capable of computing power diagrams (weighted Voronoi diagrams) in three dimensions with 3D periodic boundary conditions, computing approximate projective 2D Voronoi diagrams on arbitrarily defined surfaces, performing shape properties recognition using α-shape theory and can do exact Solvent Accessible Surface Area (SASA) computation. The software is written mainly as a template-based C++ library for greater performance, but a rich Python interface (pydmga) is provided as a convenient way to manipulate the DMG-α routines. To illustrate possible applications of the DMG-α library, we present results of sample analyses which allowed to determine nontrivial geometric properties of two Escherichia coli-specific lipids as emerging from molecular dynamics simulations of relevant model bilayers.

Template-directed assembly of metal-chalcogenide nanocrystals into ordered mesoporous networks.

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

Vamvasakis, Ioannis; Subrahmanyam, Kota S.; Kanatzidis, Mercouri G.

Although great progress in the synthesis of porous networks of metal and metal oxide nanoparticles with highly accessible pore surface and ordered mesoscale pores has been achieved, synthesis of assembled 3D mesostructures of metal-chalcogenide nanocrystals is still challenging. In this work we demonstrate that ordered mesoporous networks, which comprise well-defined interconnected metal sulfide nanocrystals, can be prepared through a polymer-templated oxidative polymerization process. The resulting self-assembled mesostructures that were obtained after solvent extraction of the polymer template impart the unique combination of light-emitting metal chalcogenide nanocrystals, three-dimensional open-pore structure, high surface area, and uniform pores. We show that the poremore » surface of these materials is active and accessible to incoming molecules, exhibiting high photocatalytic activity and stability, for instance, in oxidation of 1-phenylethanol into acetophenone. We demonstrate through appropriate selection of the synthetic components that this method is general to prepare ordered mesoporous materials from metal chalcogenide nanocrystals with various sizes and compositions.« less

Covalent Surface Modification of Silicon Oxides with Alcohols in Polar Aprotic Solvents.

PubMed

Lee, Austin W H; Gates, Byron D

2017-09-05

Alcohol-based monolayers were successfully formed on the surfaces of silicon oxides through reactions performed in polar aprotic solvents. Monolayers prepared from alcohol-based reagents have been previously introduced as an alternative approach to covalently modify the surfaces of silicon oxides. These reagents are readily available, widely distributed, and are minimally susceptible to side reactions with ambient moisture. A limitation of using alcohol-based compounds is that previous reactions required relatively high temperatures in neat solutions, which can degrade some alcohol compounds or could lead to other unwanted side reactions during the formation of the monolayers. To overcome these challenges, we investigate the condensation reaction of alcohols on silicon oxides carried out in polar aprotic solvents. In particular, propylene carbonate has been identified as a polar aprotic solvent that is relatively nontoxic, readily accessible, and can facilitate the formation of alcohol-based monolayers. We have successfully demonstrated this approach for tuning the surface chemistry of silicon oxide surfaces with a variety of alcohol containing compounds. The strategy introduced in this research can be utilized to create silicon oxide surfaces with hydrophobic, oleophobic, or charged functionalities.

A template-free solvent-mediated synthesis of high surface area boron nitride nanosheets for aerobic oxidative desulfurization

DOE PAGES

Wu, Peiwen; Zhu, Wenshuai; Chao, Yanhong; ...

2015-10-16

Hexagonal boron nitride nanosheets (h-BNNs) with rather high specific surface area (SSA) are important two-dimensional layer-structured materials. Here in this study, a solvent-mediated synthesis of h-BNNs revealed a template-free lattice plane control strategy that induced high SSA nanoporous structured h-BNNs with outstanding aerobic oxidative desulfurization performance.

Surface area generation and droplet size control in solvent extraction systems utilizing high intensity electric fields

DOEpatents

Scott, Timothy C.; Wham, Robert M.

1988-01-01

A method and system for solvent extraction where droplets are shattered by a high intensity electric field. These shattered droplets form a plurality of smaller droplets which have a greater combined surface area than the original droplet. Dispersion, coalescence and phase separation are accomplished in one vessel through the use of the single pulsing high intensity electric field. Electric field conditions are chosen so that simultaneous dispersion and coalescence are taking place in the emulsion formed in the electric field. The electric field creates a large amount of interfacial surface area for solvent extraction when the droplet is disintegrated and is capable of controlling droplet size and thus droplet stability. These operations take place in the presence of a counter current flow of the continuous phase.

Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution.

PubMed

Kleinjung, J; Bayley, P; Fraternali, F

2000-03-31

A molecular simulation scheme, called Leap-dynamics, that provides efficient sampling of protein conformational space in solution is presented. The scheme is a combined approach using a fast sampling method, imposing conformational 'leaps' to force the system over energy barriers, and molecular dynamics (MD) for refinement. The presence of solvent is approximated by a potential of mean force depending on the solvent accessible surface area. The method has been successfully applied to N-acetyl-L-alanine-N-methylamide (alanine dipeptide), sampling experimentally observed conformations inaccessible to MD alone under the chosen conditions. The method predicts correctly the increased partial flexibility of the mutant Y35G compared to native bovine pancreatic trypsin inhibitor. In particular, the improvement over MD consists of the detection of conformational flexibility that corresponds closely to slow motions identified by nuclear magnetic resonance techniques.

Nanostructure and surface activation of mayenite (12CaO·7Al2O3) ceramics via femtosecond laser irradiation in solvents

NASA Astrophysics Data System (ADS)

Visbal, Heidy; Hirano, Minami; Omura, Takuya; Shimizu, Masahiro; Takaishi, Taigo; Hirao, Kazuyuki

2017-07-01

Mayenite (12CaO·7Al2O3) is a highly interesting functional material due to the wide variety of its possible future applications. In this study, we used femtosecond laser irradiation in several solvents with varying polarities to increase the specific surface area of 12CaO·7Al2O3 ceramics and reduce their particle size without any structural degradation or loss of crystallinity. We observed that when femtosecond laser irradiation was applied to solvents bearing hydroxyl groups, a smaller particle size was obtained with the particle size decreasing as the polarity of the solvent increased. Using infrared spectroscopy, we confirmed the presence of hydroxyl and carbonyl surface functional groups at the surface of 12CaO·7Al2O3 ceramics after femtosecond laser irradiation. This is attributed to the direct chemical bonds breaking of the solvent via multiphoton ionization and/or tunneling ionization, followed by the Coulomb explosion and the subsequent production of ions that are adsorbed on the surfaces of 12CaO·7Al2O3 ceramics. Femtosecond laser irradiation in polar solvents with hydroxyl groups can reduce the particle size and increase the specific surface area without degradation or loss of crystallinity of 12CaO·7Al2O3 ceramics. Additionally, this method can be used for the surface modification and introduction of functional groups on the 12CaO·7Al2O3 ceramics surface.

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

PubMed

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

2011-04-25

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

High temperature adhesive silicone foam composition, foam generating system and method of generating foam. [For access denial

DOEpatents

Mead, J.W.; Montoya, O.J.; Rand, P.B.; Willan, V.O.

1983-12-21

Access to a space is impeded by generation of a sticky foam from a silicone polymer and a low boiling solvent such as a halogenated hydrocarbon. In a preferred aspect, the formulation is polydimethylsiloxane gel mixed with F502 Freon as a solvent and blowing agent, and pressurized with CO/sub 2/ in a vessel to about 250 PSI, whereby when the vessel is opened, a sticky and solvent resistant foam is deployed. The foam is deployable, over a wide range of temperatures, adhering to wet surfaces as well as dry, is stable over long periods of time and does not propagate flame or lose adhesive properties during an externally supported burn.

Synthesis of porous Cu-BTC with ultrasonic treatment: Effects of ultrasonic power and solvent condition.

PubMed

Israr, Farrukh; Kim, Duk Kyung; Kim, Yeongmin; Oh, Seung Jin; Ng, Kim Choon; Chun, Wongee

2016-03-01

Cu-BTC (BTC=1,3,5-benzenetricarboxylate) metal organic framework (MOF) was synthesized using different solvent conditions with ultrasonic treatment. Solvent mixtures of water/N,N-dimethylformamide (DMF), water/ethanol were used for the reactions with or without a variety of bases under 20 kHz ultrasonically treated conditions. Prepared crystals were purified through 30 min of sonication to remove unreacted chemicals. Treatment time and ultrasonic power effects were compared to get optimum synthetic condition. The characterization of MOF powders was performed by scanning electron microscopy, X-ray powder diffraction, infrared-spectroscopy, thermo-gravimetric analysis and specific surface determination using the BET method. Isolated crystal yields varied with different solvent and applied ultrasonic power conditions. A high isolated crystal yield of 86% was obtained from water/ethanol/DMF solvent system after 120 min of ultrasonic treatment at 40% power of 750 W. Different solvent conditions led to the formation of Cu-BTC with different surface area, and an extremely high surface area of 1430 m(2)/g was obtained from the crystals taken with the solvent condition of water:DMF=70:30. Copyright © 2015 Elsevier B.V. All rights reserved.

Protein Solvent-Accessibility Prediction by a Stacked Deep Bidirectional Recurrent Neural Network.

PubMed

Zhang, Buzhong; Li, Linqing; Lü, Qiang

2018-05-25

Residue solvent accessibility is closely related to the spatial arrangement and packing of residues. Predicting the solvent accessibility of a protein is an important step to understand its structure and function. In this work, we present a deep learning method to predict residue solvent accessibility, which is based on a stacked deep bidirectional recurrent neural network applied to sequence profiles. To capture more long-range sequence information, a merging operator was proposed when bidirectional information from hidden nodes was merged for outputs. Three types of merging operators were used in our improved model, with a long short-term memory network performing as a hidden computing node. The trained database was constructed from 7361 proteins extracted from the PISCES server using a cut-off of 25% sequence identity. Sequence-derived features including position-specific scoring matrix, physical properties, physicochemical characteristics, conservation score and protein coding were used to represent a residue. Using this method, predictive values of continuous relative solvent-accessible area were obtained, and then, these values were transformed into binary states with predefined thresholds. Our experimental results showed that our deep learning method improved prediction quality relative to current methods, with mean absolute error and Pearson's correlation coefficient values of 8.8% and 74.8%, respectively, on the CB502 dataset and 8.2% and 78%, respectively, on the Manesh215 dataset.

Solvent Reaction Field Potential inside an Uncharged Globular Protein: A Bridge between Implicit and Explicit Solvent Models?

PubMed Central

Baker, Nathan A.; McCammon, J. Andrew

2008-01-01

The solvent reaction field potential of an uncharged protein immersed in Simple Point Charge/Extended (SPC/E) explicit solvent was computed over a series of molecular dynamics trajectories, intotal 1560 ns of simulation time. A finite, positive potential of 13 to 24 kbTec−1 (where T = 300K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0 Å from the solute surface, on average 0.008 ec/Å3, which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit-solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99. PMID:17949217

Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?

NASA Astrophysics Data System (ADS)

Cerutti, David S.; Baker, Nathan A.; McCammon, J. Andrew

2007-10-01

The solvent reaction field potential of an uncharged protein immersed in simple point charge/extended explicit solvent was computed over a series of molecular dynamics trajectories, in total 1560ns of simulation time. A finite, positive potential of 13-24 kbTec-1 (where T =300K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0Å from the solute surface, on average 0.008ec/Å3, which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99.

Innovative eco-friendly bio- solvent for combating sea surface and sedimented oil pollution

NASA Astrophysics Data System (ADS)

Theodorou, Paraskevas

2017-04-01

The combating of oil spill at sea surface by chemical dispersants accelerates the evaporation and disperse the oil into the water column, where it is broken down by natural processes and/or is sedimented at the sea bottom, especially at near coastal shallow areas, ports and marinas. The usual methodology for cleaning the sedimented oil from the sea bottom is mainly carried out via excavation and dumping of the polluted sediment into deeper sea areas, where the contamination is transferred from one area to another. The eco-friendly bio-solvent MSL Aqua 250 is an innovative new solution based mainly on natural constituents. The action mechanism and the effectiveness of this eco-friendly solvent is based on the high surface tension process. Organic compounds, including hydrocarbons upon coming in contact with MSL Aqua 250 solvent generate a significant surface tension reaction, which is able to alter the organic compounds to liquid form and then to drastically evaporate it. The use of MSL Aqua 250 solvent, both at sea surface and at the bottom, has the following advantages compared to the dispersants: • Efficient solution without transferring the pollution from sea surface to the water column and to the bottom or disturbing the Aquatic Eco System. • Non-Toxic. • Environmentally friendly with a restoration of marine life in the Eco System. • Cost effective. The MSL Aqua 250 solvent has been tested in cooperation with the Cyprus Department of Fisheries and Marine Research and the Technological University of Cyprus and used during the years 2015 and 2016 in marinas and fishing shelters in Cyprus faced oil pollution, with high concentration in the sea water and at the sea bottom of chemical parameters (BOD5, COD, FOG, TKN, TP, TPH), with excellent results.

Can solvent induced surface modifications applied to screen-printed platforms enhance their electroanalytical performance?

PubMed

Blanco, Elias; Foster, Christopher W; Cumba, Loanda R; do Carmo, Devaney R; Banks, Craig E

2016-04-25

In this paper the effect of solvent induced chemical surface enhancements upon graphitic screen-printed electrodes (SPEs) is explored. Previous literature has indicated that treating the working electrode of a SPE with the solvent N,N-dimethylformamide (DMF) offers improvements within the electroanalytical response, resulting in a 57-fold increment in the electrode surface area compared to their unmodified counterparts. The protocol involves two steps: (i) the SPE is placed into DMF for a selected time, and (ii) it is cured in an oven at a selected time and temperature. Beneficial electroanalytical outputs are reported to be due to the increased surface area attributed to the binder within the bulk surface of the SPEs dissolving out during the immersion step (step i). We revisit this exciting concept and explore these solvent induced chemical surface enhancements using edge- and basal-plane like SPEs and a new bespoke SPE, utilising the solvent DMF and explore, in detail, the parameters utilised in steps (i) and (ii). The electrochemical performance following steps (i) and (ii) is evaluated using the outer-sphere redox probe hexaammineruthenium(iii) chloride/0.1 M KCl, where it is found that the largest improvement is obtained using DMF with an immersion time of 10 minutes and a curing time of 30 minutes at 100 °C. Solvent induced chemical surface enhancement upon the electrochemical performance of SPEs is also benchmarked in terms of their electroanalytical sensing of NADH (dihydronicotinamide adenine dinucleotide reduced form) and capsaicin both of which are compared to their unmodified SPE counterparts. In both cases, it is apparent that a marginal improvement in the electroanalytical sensitivity (i.e. gradient of calibration plots) of 1.08-fold and 1.38-fold are found respectively. Returning to the original exciting concept, interestingly it was found that when a poor experimental technique was employed, only then significant increases within the working electrode area are evident. In this case, the insulating layer that defines the working electrode surface, which was not protected from the solvent (step (i)) creates cracks within the insulating layer exposing the underlying carbon connections and thus increasing the electrode area by an unknown quantity. We infer that the origin of the response reported within the literature, where an extreme increase in the electrochemical surface area (57-fold) was reported, is unlikely to be solely due to the binder dissolving but rather poor experimental control over step (i).

Organic solvent desorption from two tegafur polymorphs.

PubMed

Bobrovs, Raitis; Actiņš, Andris

2013-11-30

Desorption behavior of 8 different solvents from α and β tegafur (5-fluoro-1-(tetrahydro-2-furyl)uracil) has been studied in this work. Solvent desorption from samples stored at 95% and 50% relative solvent vapor pressure was studied in isothermal conditions at 30 °C. The results of this study demonstrated that: solvent desorption rate did not differ significantly for both phases; solvent desorption in all cases occurred faster from samples with the largest particle size; and solvent desorption in most cases occurred in two steps. Structure differences and their surface properties were not of great importance on the solvent desorption rates because the main factor affecting desorption rate was sample particle size and sample morphology. Inspection of the structure packing showed that solvent desorption rate and amount of solvent adsorbed were mainly affected by surface molecule arrangement and ability to form short contacts between solvent molecule electron donor groups and freely accessible tegafur tetrahydrofuran group hydrogens, as well as between solvents molecule proton donor groups and fluorouracil ring carbonyl and fluoro groups. Solvent desorption rates of acetone, acetonitrile, ethyl acetate and tetrahydrofuran multilayers from α and β tegafur were approximately 30 times higher than those of solvent monolayers. Scanning electron micrographs showed that sample storage in solvent vapor atmosphere promotes small tegafur particles recrystallization to larger particles. Copyright © 2013 Elsevier B.V. All rights reserved.

Improving the Efficiency of Non-equilibrium Sampling in the Aqueous Environment via Implicit-Solvent Simulations.

PubMed

Liu, Hui; Chen, Fu; Sun, Huiyong; Li, Dan; Hou, Tingjun

2017-04-11

By means of estimators based on non-equilibrium work, equilibrium free energy differences or potentials of mean force (PMFs) of a system of interest can be computed from biased molecular dynamics (MD) simulations. The approach, however, is often plagued by slow conformational sampling and poor convergence, especially when the solvent effects are taken into account. Here, as a possible way to alleviate the problem, several widely used implicit-solvent models, which are derived from the analytic generalized Born (GB) equation and implemented in the AMBER suite of programs, were employed in free energy calculations based on non-equilibrium work and evaluated for their abilities to emulate explicit water. As a test case, pulling MD simulations were carried out on an alanine polypeptide with different solvent models and protocols, followed by comparisons of the reconstructed PMF profiles along the unfolding coordinate. The results show that when employing the non-equilibrium work method, sampling with an implicit-solvent model is several times faster and, more importantly, converges more rapidly than that with explicit water due to reduction of dissipation. Among the assessed GB models, the Neck variants outperform the OBC and HCT variants in terms of accuracy, whereas their computational costs are comparable. In addition, for the best-performing models, the impact of the solvent-accessible surface area (SASA) dependent nonpolar solvation term was also examined. The present study highlights the advantages of implicit-solvent models for non-equilibrium sampling.

Morphometric approach to thermodynamic quantities of solvation of complex molecules: Extension to multicomponent solvent

NASA Astrophysics Data System (ADS)

Kodama, Ryota; Roth, Roland; Harano, Yuichi; Kinoshita, Masahiro

2011-07-01

The morphometric approach (MA) is a powerful tool for calculating a solvation free energy (SFE) and related quantities of solvation thermodynamics of complex molecules. Here, we extend it to a solvent consisting of m components. In the integral equation theories, the SFE is expressed as the sum of m terms each of which comprises solute-component j correlation functions (j = 1, …, m). The MA is applied to each term in a formally separate manner: The term is expressed as a linear combination of the four geometric measures, excluded volume, solvent-accessible surface area, and integrated mean and Gaussian curvatures of the accessible surface, which are calculated for component j. The total number of the geometric measures or the coefficients in the linear combinations is 4m. The coefficients are determined in simple geometries, i.e., for spherical solutes with various diameters in the same multicomponent solvent. The SFE of the spherical solutes are calculated using the radial-symmetric integral equation theory. The extended version of the MA is illustrated for a protein modeled as a set of fused hard spheres immersed in a binary mixture of hard spheres. Several mixtures of different molecular-diameter ratios and compositions and 30 structures of the protein with a variety of radii of gyration are considered for the illustration purpose. The SFE calculated by the MA is compared with that by the direct application of the three-dimensional integral equation theory (3D-IET) to the protein. The deviations of the MA values from the 3D-IET values are less than 1.5%. The computation time required is over four orders of magnitude shorter than that in the 3D-IET. The MA thus developed is expected to be best suited to analyses concerning the effects of cosolvents such as urea on the structural stability of a protein.

Method for the preparation of high surface area high permeability carbons

DOEpatents

Lagasse, Robert R.; Schroeder, John L.

1999-05-11

A method for preparing carbon materials having high surface area and high macropore volume to provide high permeability. These carbon materials are prepared by dissolving a carbonizable polymer precursor, in a solvent. The solution is cooled to form a gel. The solvent is extracted from the gel by employing a non-solvent for the polymer. The non-solvent is removed by critical point drying in CO.sub.2 at an elevated pressure and temperature or evaporation in a vacuum oven. The dried product is heated in an inert atmosphere in a first heating step to a first temperature and maintained there for a time sufficient to substantially cross-link the polymer material. The cross-linked polymer material is then carbonized in an inert atmosphere.

Microfluidic process monitor for industrial solvent extraction system

DOEpatents

Gelis, Artem; Pereira, Candido; Nichols, Kevin Paul Flood

2016-01-12

The present invention provides a system for solvent extraction utilizing a first electrode with a raised area formed on its surface, which defines a portion of a microfluidic channel; a second electrode with a flat surface, defining another portion of the microfluidic channel that opposes the raised area of the first electrode; a reversibly deformable substrate disposed between the first electrode and second electrode, adapted to accommodate the raised area of the first electrode and having a portion that extends beyond the raised area of the first electrode, that portion defining the remaining portions of the microfluidic channel; and an electrolyte of at least two immiscible liquids that flows through the microfluidic channel. Also provided is a system for performing multiple solvent extractions utilizing several microfluidic chips or unit operations connected in series.

iview: an interactive WebGL visualizer for protein-ligand complex.

PubMed

Li, Hongjian; Leung, Kwong-Sak; Nakane, Takanori; Wong, Man-Hon

2014-02-25

Visualization of protein-ligand complex plays an important role in elaborating protein-ligand interactions and aiding novel drug design. Most existing web visualizers either rely on slow software rendering, or lack virtual reality support. The vital feature of macromolecular surface construction is also unavailable. We have developed iview, an easy-to-use interactive WebGL visualizer of protein-ligand complex. It exploits hardware acceleration rather than software rendering. It features three special effects in virtual reality settings, namely anaglyph, parallax barrier and oculus rift, resulting in visually appealing identification of intermolecular interactions. It supports four surface representations including Van der Waals surface, solvent excluded surface, solvent accessible surface and molecular surface. Moreover, based on the feature-rich version of iview, we have also developed a neat and tailor-made version specifically for our istar web platform for protein-ligand docking purpose. This demonstrates the excellent portability of iview. Using innovative 3D techniques, we provide a user friendly visualizer that is not intended to compete with professional visualizers, but to enable easy accessibility and platform independence.

Characterizing monoclonal antibody structure by carbodiimide/GEE footprinting

PubMed Central

Kaur, Parminder; Tomechko, Sara; Kiselar, Janna; Shi, Wuxian; Deperalta, Galahad; Wecksler, Aaron T; Gokulrangan, Giridharan; Ling, Victor; Chance, Mark R

2014-01-01

Amino acid-specific covalent labeling is well suited to probe protein structure and macromolecular interactions, especially for macromolecules and their complexes that are difficult to examine by alternative means, due to size, complexity, or instability. Here we present a detailed account of carbodiimide-based covalent labeling (with GEE tagging) applied to a glycosylated monoclonal antibody therapeutic, which represents an important class of biologic drugs. Characterization of such proteins and their antigen complexes is essential to development of new biologic-based medicines. In this study, the experiments were optimized to preserve the structural integrity of the protein, and experimental conditions were varied and replicated to establish the reproducibility and precision of the technique. Homology-based models were generated and used to compare the solvent accessibility of the labeled residues, which include D, E, and the C-terminus, against the experimental surface accessibility data in order to understand the accuracy of the approach in providing an unbiased assessment of structure. Data from the protein were also compared to reactivity measures of several model peptides to explain sequence or structure-based variations in reactivity. The results highlight several advantages of this approach. These include: the ease of use at the bench top, the linearity of the dose response plots at high levels of labeling (indicating that the label does not significantly perturb the structure of the protein), the high reproducibility of replicate experiments (<2 % variation in modification extent), the similar reactivity of the 3 target probe residues (as suggested by analysis of model peptides), and the overall positive and significant correlation of reactivity and solvent accessible surface area (the latter values predicted by the homology modeling). Attenuation of reactivity, in otherwise solvent accessible probes, is documented as arising from the effects of positive charge or bond formation between adjacent amine and carboxyl groups, the latter accompanied by observed water loss. The results are also compared with data from hydroxyl radical-mediated oxidative footprinting on the same protein, showing that complementary information is gained from the 2 approaches, although the number of target residues in carbodiimide/GEE labeling is fewer. Overall, this approach is an accurate and precise method for assessing protein structure of biologic drugs. PMID:25484052

Stereolithographic models of the solvent-accessible surface of biopolymers. Topical report

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

Bradford, J.; Noel, P.; Emery, J.D.

1996-11-01

The solvent-accessible surfaces of several biopolymers were calculated. As part of the DOE education outreach activity, two high school students participated in this project. Computer files containing sets of triangles were produced. These files are called stl files and are the ISO 9001 standard. They have been written onto CD-ROMs for distribution to American companies. Stereolithographic models were made of some of them to ensure that the computer calculations were done correctly. Stereolithographic models were made of interleukin 1{beta} (IL-1{beta}), three antibodies (an anti-p-azobenzene arsonate, an anti-Brucella A cell wall polysaccharide, and an HIV neutralizing antibody), a triple stranded coiledmore » coil, and an engrailed homeodomain. Also, the biopolymers and their files are described.« less

Target specific proteochemometric model development for BACE1 - protein flexibility and structural water are critical in virtual screening.

PubMed

Manoharan, Prabu; Chennoju, Kiranmai; Ghoshal, Nanda

2015-07-01

BACE1 is an attractive target in Alzheimer's disease (AD) treatment. A rational drug design effort for the inhibition of BACE1 is actively pursued by researchers in both academic and pharmaceutical industries. This continued effort led to the steady accumulation of BACE1 crystal structures, co-complexed with different classes of inhibitors. This wealth of information is used in this study to develop target specific proteochemometric models and these models are exploited for predicting the prospective BACE1 inhibitors. The models developed in this study have performed excellently in predicting the computationally generated poses, separately obtained from single and ensemble docking approaches. The simple protein-ligand contact (SPLC) model outperforms other sophisticated high end models, in virtual screening performance, developed during this study. In an attempt to account for BACE1 protein active site flexibility information in predictive models, we included the change in the area of solvent accessible surface and the change in the volume of solvent accessible surface in our models. The ensemble and single receptor docking results obtained from this study indicate that the structural water mediated interactions improve the virtual screening results. Also, these waters are essential for recapitulating bioactive conformation during docking study. The proteochemometric models developed in this study can be used for the prediction of BACE1 inhibitors, during the early stage of AD drug discovery.

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

Ivanov, Ilia N.; Simpson, John T.

A method of preparing a network comprises disposing a solution comprising particulate materials in a solvent onto a superhydrophobic surface comprising a plurality of superhydrophobic features and interfacial areas between the superhydrophobic features. The plurality of superhydrophobic features has a water contact angle of at least about 150.degree.. The method of preparing the network also comprises removing the solvent from the solution of the particulate materials, and forming a network of the particulate materials in the interfacial areas, the particulate materials receding to the interfacial areas as the solvent is removed.

Method for the preparation of high surface area high permeability carbons

DOEpatents

Lagasse, R.R.; Schroeder, J.L.

1999-05-11

A method for preparing carbon materials having high surface area and high macropore volume to provide high permeability. These carbon materials are prepared by dissolving a carbonizable polymer precursor, in a solvent. The solution is cooled to form a gel. The solvent is extracted from the gel by employing a non-solvent for the polymer. The non-solvent is removed by critical point drying in CO{sub 2} at an elevated pressure and temperature or evaporation in a vacuum oven. The dried product is heated in an inert atmosphere in a first heating step to a first temperature and maintained there for a time sufficient to substantially cross-link the polymer material. The cross-linked polymer material is then carbonized in an inert atmosphere. 3 figs.

Lipid solvation effects contribute to the affinity of Gly-xxx-Gly motif-mediated helix-helix interactions.

PubMed

Johnson, Rachel M; Rath, Arianna; Melnyk, Roman A; Deber, Charles M

2006-07-18

Interactions between transmembrane helices are mediated by the concave Gly-xxx-Gly motif surface. Whether Gly residues per se are sufficient for selection of this motif has not been established. Here, we used the in vivo TOXCAT assay to measure the relative affinities of all 18 combinations of Gly, Ala, and Ser "small-xxx-small" mutations in glycophorin A (GpA) and bacteriophage M13 major coat protein (MCP) homodimers. Affinity values were compared with the accessibility to a methylene-sized probe of the total surface area of each helix monomer as a measure of solvation by membrane components. A strong inverse correlation was found between nonpolar-group lipid accessibility and dimer affinity (R = 0.75 for GpA, p = 0.013, and R = 0.81 for MCP, p = 0.004), suggesting that lipid as a poor membrane protein solvent, conceptually analogous to water in soluble protein folding, can contribute to dimer stability and help to define helix-helix interfaces.

Free energy landscape of protein folding in water: explicit vs. implicit solvent.

PubMed

Zhou, Ruhong

2003-11-01

The Generalized Born (GB) continuum solvent model is arguably the most widely used implicit solvent model in protein folding and protein structure prediction simulations; however, it still remains an open question on how well the model behaves in these large-scale simulations. The current study uses the beta-hairpin from C-terminus of protein G as an example to explore the folding free energy landscape with various GB models, and the results are compared to the explicit solvent simulations and experiments. All free energy landscapes are obtained from extensive conformation space sampling with a highly parallel replica exchange method. Because solvation model parameters are strongly coupled with force fields, five different force field/solvation model combinations are examined and compared in this study, namely the explicit solvent model: OPLSAA/SPC model, and the implicit solvent models: OPLSAA/SGB (Surface GB), AMBER94/GBSA (GB with Solvent Accessible Surface Area), AMBER96/GBSA, and AMBER99/GBSA. Surprisingly, we find that the free energy landscapes from implicit solvent models are quite different from that of the explicit solvent model. Except for AMBER96/GBSA, all other implicit solvent models find the lowest free energy state not the native state. All implicit solvent models show erroneous salt-bridge effects between charged residues, particularly in OPLSAA/SGB model, where the overly strong salt-bridge effect results in an overweighting of a non-native structure with one hydrophobic residue F52 expelled from the hydrophobic core in order to make better salt bridges. On the other hand, both AMBER94/GBSA and AMBER99/GBSA models turn the beta-hairpin in to an alpha-helix, and the alpha-helical content is much higher than the previously reported alpha-helices in an explicit solvent simulation with AMBER94 (AMBER94/TIP3P). Only AMBER96/GBSA shows a reasonable free energy landscape with the lowest free energy structure the native one despite an erroneous salt-bridge between D47 and K50. Detailed results on free energy contour maps, lowest free energy structures, distribution of native contacts, alpha-helical content during the folding process, NOE comparison with NMR, and temperature dependences are reported and discussed for all five models. Copyright 2003 Wiley-Liss, Inc.

Evaluation of various molecular parameters as predictors of bioconcentration in fish

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

Connell, D.W.; Schueuermann G3

1988-06-01

A reliable set of data on the bioconcentration factors (KB) of a diverse range of compounds in fish was selected from the literature. Using the structures of these compounds, the following molecular parameters were calculated: molecular weight (MW), solvent accessible molecular surface area (SASA), solvent accessible molecular volume (SAV), molar refraction (MR), largest principal moment of inertia (LPMI) and several molecular connectivity indices of the Randic type (1 chi, 2 chi, 3 chi, 1 chi vr, 3 chi c). The relationships between these parameters and log KB were evaluated for all compounds and the following subgroups: chlorinated hydrocarbons (CHC), polyaromaticmore » hydrocarbons (PAH), and CHC and PAH combined. These relationships indicated that SASA, SAV, and MR were good predictors of log KB for the CHC and PAH combined or alone and the other parameters were less satisfactory with these groups. In addition with the CHC, the log of these parameters displayed an improved correlation with log KB due to apparent nonlinearity in the log to linear relationship. Thus, with these groups of compounds, calculated values of SASA, SAV, and MR provide a satisfactory means of estimating log KB without measured data.« less

In Cell Footprinting Coupled with Mass Spectrometry for the Structural Analysis of Proteins in Live Cells.

PubMed

Espino, Jessica A; Mali, Vishaal S; Jones, Lisa M

2015-08-04

Protein footprinting coupled with mass spectrometry has become a widely used tool for the study of protein-protein and protein-ligand interactions and protein conformational change. These methods provide residue-level analysis on protein interaction sites and have been successful in studying proteins in vitro. The extension of these methods for in cell footprinting would open an avenue to study proteins that are not amenable for in vitro studies and would probe proteins in their native environment. Here we describe the application of an oxidative-based footprinting approach inside cells in which hydroxyl radicals are used to oxidatively modify proteins. Mass spectrometry is used to detect modification sites and to calculate modification levels. The method is probing biologically relevant proteins in live cells, and proteins in various cellular compartments can be oxdiatively modified. Several different amino acid residues are modified making the method a general labeling strategy for the study of a variety of proteins. Further, comparison of the extent of oxidative modification with solvent accessible surface area reveals the method successfully probes solvent accessibility. This marks the first time protein footprinting has been performed in live cells.

Hydrogen/deuterium (H/D) exchange of gelatinized starch studied by two-dimensional (2D) near-infrared (NIR) correlation spectroscopy

NASA Astrophysics Data System (ADS)

Shinzawa, Hideyuki; Mizukado, Junji

2018-05-01

Hydrogen/deuterium (H/D) exchange of gelatinized starch was probed by in-situ near-infrared (NIR) monitoring coupled with two-dimensional (2D) correlation spectroscopy. Gelatinized starch undergoes spontaneous H/D exchange in D2O. During the substitution, the exchange rate essentially becomes different depending on solvent accessibility of various parts of the molecule. Thus, by analyzing the change in the NIR feature observed during the substitution, it becomes possible to sort out local structure and dynamics of the system. 2D correlation analysis of the time-dependent NIR spectra reveals the presence of different local structure of the starch, each having different solvent accessibility. For example, during the H/D exchange, the D2O is first absorbed by starch molecules especially around the surface area between the starch and water, where the water molecules are weakly interacted with the starch molecules. This absorption is quickly followed by the development of HDO species. Further absorption of the D2O results in the penetration of the molecules inside the starch and eventually develops the relatively strong interaction between the HDO and starch molecules because of the presence of dominant starch molecules.

l-Proline and RNA Duplex m-Value Temperature Dependence.

PubMed

Schwinefus, Jeffrey J; Baka, Nadia L; Modi, Kalpit; Billmeyer, Kaylyn N; Lu, Shutian; Haase, Lucas R; Menssen, Ryan J

2017-08-03

The temperature dependence of l-proline interactions with the RNA dodecamer duplex surface exposed after unfolding was quantified using thermal and isothermal titration denaturation monitored by uv-absorbance. The m-value quantifying proline interactions with the RNA duplex surface area exposed after unfolding was measured using RNA duplexes with GC content ranging between 17 and 83%. The m-values from thermal denaturation decreased with increasing GC content signifying increasingly favorable proline interactions with the exposed RNA surface area. However, m-values from isothermal titration denaturation at 25.0 °C were independent of GC content and less negative than those from thermal denaturation. The m-value from isothermal titration denaturation for a 50% GC RNA duplex decreased (became more negative) as the temperature increased and was in nearly exact agreement with the m-value from thermal denaturation. Since RNA duplex transition temperatures increased with GC content, the more favorable proline interactions with the high GC content duplex surface area observed from thermal denaturation resulted from the temperature dependence of proline interactions rather than the RNA surface chemical composition. The enthalpy contribution to the m-value was positive and small (indicating a slight increase in duplex unfolding enthalpy with proline) while the entropic contribution to the m-value was positive and increased with temperature. Our results will facilitate proline's use as a probe of solvent accessible surface area changes during biochemical reactions at different reaction temperatures.

Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.

PubMed

Marenich, Aleksandr V; Cramer, Christopher J; Truhlar, Donald G

2009-05-07

We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the "D" stands for "density" to denote that the full solute electron density is used without defining partial atomic charges. "Continuum" denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where "universal" denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaqueous organic solvents and water), and 143 transfer free energies for 93 neutral solutes between water and 15 organic solvents. The elements present in the solutes are H, C, N, O, F, Si, P, S, Cl, and Br. The SMD model employs a single set of parameters (intrinsic atomic Coulomb radii and atomic surface tension coefficients) optimized over six electronic structure methods: M05-2X/MIDI!6D, M05-2X/6-31G, M05-2X/6-31+G, M05-2X/cc-pVTZ, B3LYP/6-31G, and HF/6-31G. Although the SMD model has been parametrized using the IEF-PCM protocol for bulk electrostatics, it may also be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space. This includes, for example, the conductor-like screening algorithm. With the 6-31G basis set, the SMD model achieves mean unsigned errors of 0.6-1.0 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 4 kcal/mol on average for ions with either Gaussian03 or GAMESS.

Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions

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

Marenich, Aleksandr; Cramer, Christopher J; Truhlar, Donald G

2009-04-30

We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the “D” stands for “density” to denote that the full solute electron density is used without defining partial atomic charges. “Continuum” denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where “universal” denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which amore » few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaqueous organic solvents and water), and 143 transfer free energies for 93 neutral solutes between water and 15 organic solvents. The elements present in the solutes are H, C, N, O, F, Si, P, S, Cl, and Br. The SMD model employs a single set of parameters (intrinsic atomic Coulomb radii and atomic surface tension coefficients) optimized over six electronic structure methods: M05-2X/MIDI!6D, M05-2X/6-31G*, M05-2X/6-31+G**, M05-2X/cc-pVTZ, B3LYP/6-31G*, and HF/6-31G*. Although the SMD model has been parametrized using the IEF-PCM protocol for bulk electrostatics, it may also be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space. This includes, for example, the conductor-like screening algorithm. With the 6-31G* basis set, the SMD model achieves mean unsigned errors of 0.6-1.0 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 4 kcal/mol on average for ions with either Gaussian03 or GAMESS.« less

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

NASA Astrophysics Data System (ADS)

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.

Group extraction of organic compounds present in liquid samples

NASA Technical Reports Server (NTRS)

Jahnsen, Vilhelm J. (Inventor)

1976-01-01

An extraction device is disclosed comprising a tube containing a substantially inert, chemically non-reactive packing material with a large surface area to volume ratio. A sample which consists of organic compounds dissolved in a liquid, is introduced into the tube. As the sample passes through the packing material it spreads over the material's large surface area to form a thin liquid film which is held on the packing material in a stationary state. A particular group or family of compounds is extractable from the sample by passing a particular solvent system consisting of a solvent and selected reagents through the packing material. The reagents cause optimum conditions to exist for the compounds of the particular family to pass through the phase boundary between the sample liquid and the solvent of the solvent system. Thus, the compounds of the particular family are separated from the sample liquid and become dissolved in the solvent of the solvent system. The particular family of compounds dissolved in the solvent, representing an extract, exits the tube together with the solvent through the tube's nozzle, while the rest of the sample remains on the packing material in a stationary state. Subsequently, a different solvent system may be passed through the packing material to extract another family of compounds from the remaining sample on the packing material.

Replica exchange molecular dynamics simulations provide insight into substrate recognition by small heat shock proteins.

PubMed

Patel, Sunita; Vierling, Elizabeth; Tama, Florence

2014-06-17

The small heat shock proteins (sHSPs) are a virtually ubiquitous and diverse group of molecular chaperones that can bind and protect unfolding proteins from irreversible aggregation. It has been suggested that intrinsic disorder of the N-terminal arm (NTA) of sHSPs is important for substrate recognition. To investigate conformations of the NTA that could recognize substrates we performed replica exchange molecular dynamics simulations. Behavior at normal and stress temperatures of the dimeric building blocks of dodecameric HSPs from wheat (Ta16.9) and pea (Ps18.1) were compared because they display high sequence similarity, but Ps18.1 is more efficient in binding specific substrates. In our simulations, the NTAs of the dimer are flexible and dynamic; however, rather than exhibiting highly extended conformations they retain considerable α-helical character and contacts with the conserved α-crystallin domain (ACD). Network analysis and clustering methods reveal that there are two major conformational forms designated either "open" or "closed" based on the relative position of the two NTAs and their hydrophobic solvent accessible surface area. The equilibrium constant for the closed to open transition is significantly different for Ta16.9 and Ps18.1, with the latter showing more open conformations at elevated temperature correlated with its more effective chaperone activity. In addition, the Ps18.1 NTAs have more hydrophobic solvent accessible surface than those of Ta16.9. NTA hydrophobic patches are comparable in size to the area buried in many protein-protein interactions, which would enable sHSPs to bind early unfolding intermediates. Reduced interactions of the Ps18.1 NTAs with each other and with the ACD contribute to the differences in dynamics and hydrophobic surface area of the two sHSPs. These data support a major role for the conformational equilibrium of the NTA in substrate binding and indicate features of the NTA that contribute to sHSP chaperone efficiency. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

p53 R175H hydrophobic patch and H-bond reorganization observed by MD simulation.

PubMed

Thayer, Kelly M; Quinn, Taylor R

2016-03-01

Molecular dynamics simulations probe the origins of aberrant functionality of R175H p53, which normally prevent tumorigenesis. This hotspot mutation exhibits loss of its essential zinc cofactor, aggregation, and activation of gain of function promoters, characteristics contributing to the loss of normal p53 activity. This study provided molecular level insight into the reorganization of the hydrogen bonding network and the formation of a hydrophobic patch on the surface of the protein. The hydrogen bonding network globally redistributes at the expense of the stability of the β-sandwich structure, and surface residues reorganize to expose a 250 Å(2) hydrophobic patch of residues covering approximately 2% of the solvent accessible surface. These changes could both stabilize the protein in the conformation exposing the patch to solvent to mediate the reported aggregation, and cause a destabilization in the area associated with DNA binding residues to affect the specificity. The development of the patch prior to loss of zinc indicates that stabilizing the patch quickly may prevent zinc loss. Considerations for rational design of small molecule therapeutics in light of the structural insight has been discussed and it suggest the positive ring around the hydrophobic patch and conserved residues may constitute a druggable site. © 2015 Wiley Periodicals, Inc.

Identification of protein–protein interfaces by decreased amide proton solvent accessibility

PubMed Central

Mandell, Jeffrey G.; Falick, Arnold M.; Komives, Elizabeth A.

1998-01-01

Matrix-assisted laser desorption ionization–time-of-flight mass spectrometry was used to identify peptic fragments from protein complexes that retained deuterium under hydrogen exchange conditions due to decreased solvent accessibility at the interface of the complex. Short deuteration times allowed preferential labeling of rapidly exchanging surface amides so that primarily solvent accessibility changes and not conformational changes were detected. A single mass spectrum of the peptic digest mixture was analyzed to determine the deuterium content of all proteolytic fragments of the protein. The protein–protein interface was reliably indicated by those peptides that retained more deuterons in the complex compared with control experiments in which only one protein was present. The method was used to identify the kinase inhibitor [PKI(5–24)] and ATP-binding sites in the cyclic-AMP-dependent protein kinase. Three overlapping peptides identified the ATP-binding site, three overlapping peptides identified the glycine-rich loop, and two peptides identified the PKI(5–24)-binding site. A complex of unknown structure also was analyzed, human α-thrombin bound to an 83-aa fragment of human thrombomodulin [TMEGF(4–5)]. Five peptides from thrombin showed significantly decreased solvent accessibility in the complex. Three peptides identified the anion-binding exosite I, confirming ligand competition experiments. Two peptides identified a new region of thrombin near the active site providing a potential mechanism of how thrombomodulin alters thrombin substrate specificity. PMID:9843953

Interfacial Interaction in Anodic Aluminum Oxide Templates Modifies Morphology, Surface Area, and Crystallization of Polyamide-6 Nanofibers.

PubMed

Xue, Junhui; Xu, Yizhuang; Jin, Zhaoxia

2016-03-08

Here, we demonstrated that, when the precipitation process of polyamide-6 (PA6) solution happens in cylindrical channels of an anodized aluminum oxide membrane (AAO), interface interactions between a solid surface, solvent, non-solvent, and PA6 will influence the obtained polymer nanostructures, resulting in complex morphologies, increased surface area, and crystallization changes. With the enhancing interaction of PA6 and the AAO surface, the morphology of PA6 nanostructures changes from solid nanofibers, mesoporous, to bamboo-like, while at the same time, metastable γ-phase domains increase in these PA6 nanostructures. Brunauer-Emmett-Teller (BET) surface areas of solid, bamboo-like, and mesoporous PA6 nanofibers rise from 16, 20.9, to 25 m(2)/g. This study shows that interfacial interaction in AAO template fabrication can be used in manipulating the morphology and crystallization of one-dimensional polymer nanostructures. It also provides us a simple and novel method to create porous PA6 nanofibers with a large surface area.

Effects of geometry and chemistry on hydrophobic solvation

PubMed Central

Harris, Robert C.; Pettitt, B. Montgomery

2014-01-01

Inserting an uncharged van der Waals (vdw) cavity into water disrupts the distribution of water and creates attractive dispersion interactions between the solvent and solute. This free-energy change is the hydrophobic solvation energy (ΔGvdw). Frequently, it is assumed to be linear in the solvent-accessible surface area, with a positive surface tension (γ) that is independent of the properties of the molecule. However, we found that γ for a set of alkanes differed from that for four configurations of decaalanine, and γ = −5 was negative for the decaalanines. These findings conflict with the notion that ΔGvdw favors smaller A. We broke ΔGvdw into the free energy required to exclude water from the vdw cavity (ΔGrep) and the free energy of forming the attractive interactions between the solute and solvent (ΔGatt) and found that γ < 0 for the decaalanines because −γatt > γrep and γatt < 0. Additionally, γatt and γrep for the alkanes differed from those for the decaalanines, implying that none of ΔGatt, ΔGrep, and ΔGvdw can be computed with a constant surface tension. We also showed that ΔGatt could not be computed from either the initial or final water distributions, implying that this quantity is more difficult to compute than is sometimes assumed. Finally, we showed that each atom’s contribution to γrep depended on multibody interactions with its surrounding atoms, implying that these contributions are not additive. These findings call into question some hydrophobic models. PMID:25258413

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

PubMed

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.

Insilico modeling and molecular dynamic simulation of claudin-1 point mutations in HCV infection.

PubMed

Vipperla, Bhavaniprasad; Dass, J Febin Prabhu; Jayanthi, S

2014-01-01

Claudin-1 (CLDN1) in association with envelope glycoprotein (CD81) mediates the fusion of HCV into the cytosol. Recent studies have indicated that point mutations in CLDN1 are important for the entry of hepatitis C virus (HCV). To validate these findings, we employed a computational platform to investigate the structural effect of two point mutations (I32M and E48K). Initially, three-dimensional co-ordinates for CLDN1 receptor sequence were generated. Then, three mutant models were built using the point mutation including a double mutant (I32M/E48K) model from the native model structure. Finally, all the four model structures including the native and three mutant models were subjected to molecular dynamics (MD) simulation for a period of 25 ns to appreciate their dynamic behavior. The MD trajectory files were analyzed using cluster and principal component method. The analysis suggested that either of the single mutation has negligible effect on the overall structure of CLDN1 compared to the double mutant form. However, the double mutant model of CLDN1 shows significant negative impact through the impairment of H-bonds and the simultaneous increase in solvent accessible surface area. Our simulation results are visibly consistent with the experimental report suggesting that the CLDN1 receptor distortion is prominent due to the double mutation with large surface accessibility. This increase in accessible surface area due to the coexistence of double mutation may be presumed as one of the key factor that results in permissive action of HCV attachment and infection.

Lid dynamics of porcine pancreatic lipase in non-aqueous solvents.

PubMed

Haque, Neshatul; Prabhu, N Prakash

2016-10-01

Understanding the dynamics of enzymes in organic solvents has wider implications on their industrial applications. Pancreatic lipases, which show activity in their lid open-state, demonstrate enhanced activity in organic solvents at higher temperatures. However, the lid dynamics of pancreatic lipases in non-aqueous environment is yet to be clearly understood. Dynamics of porcine pancreatic lipase (PPL) in open and closed conformations was followed in ethanol, toluene, and octanol using molecular simulation methods. In silico double mutant D250V and E254L of PPL (PPLmut-Cl) was created and its lid opening dynamics in water and in octanol was analyzed. PPL showed increase in solvent accessible surface area and decrease in packing density as the polarity of the surrounded solvent decreased. Breaking the interactions between D250-Y115, and D250-E254 in PPLmut-Cl directed the lid to attain open-state conformation. Major energy barriers during the lid movement in water and in octanol were identified. Also, the trajectories of lid movement were found to be different in these solvents. Only the double mutant at higher temperature showed lid opening movement suggesting the essential role of the three residues in holding the lid in closed conformation. The lid opening dynamics was faster in octanol than water suggesting that non-polar solvents favor open conformation of the lid. This study identifies important interactions between the lid and the residues in domain 1 which possibly keeps the lid in closed conformation. Also, it explains the rearrangements of residue-residue interactions during lid opening movement in water and in octanol. Copyright © 2016 Elsevier B.V. All rights reserved.

The new view of hydrophobic free energy.

PubMed

Baldwin, Robert L

2013-04-17

In the new view, hydrophobic free energy is measured by the work of solute transfer of hydrocarbon gases from vapor to aqueous solution. Reasons are given for believing that older values, measured by solute transfer from a reference solvent to water, are not quantitatively correct. The hydrophobic free energy from gas-liquid transfer is the sum of two opposing quantities, the cavity work (unfavorable) and the solute-solvent interaction energy (favorable). Values of the interaction energy have been found by simulation for linear alkanes and are used here to find the cavity work, which scales linearly with molar volume, not accessible surface area. The hydrophobic free energy is the dominant factor driving folding as judged by the heat capacity change for transfer, which agrees with values for solvating hydrocarbon gases. There is an apparent conflict with earlier values of hydrophobic free energy from studies of large-to-small mutations and an explanation is given. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Experimental and modeling study on charge storage/transfer mechanism of graphene-based supercapacitors

NASA Astrophysics Data System (ADS)

Ban, Shuai; Jing, Xie; Zhou, Hongjun; Zhang, Lei; Zhang, Jiujun

2014-12-01

A symmetrical graphene-based supercapacitor is constructed for studying the charge-transfer mechanism within the graphene-based electrodes using both experiment measurements and molecular simulation. The in-house synthesized graphene is characterized by XRD, SEM and BET measurements for morphology and surface area. It is observed that the electric capacity of graphene electrode can be reduced by both high internal resistance and limited mass transfer. Computer modeling is conducted at the molecular level to characterize the diffusion behavior of electrolyte ions to the interior of electrode with emphasis on the unique 2D confinement imposed by graphene layers. Although graphene powder poses a moderate internal surface of 400 m2 g-1, the capacitance performance of graphene electrode can be as good as that of commercial activated carbon which has an overwhelming surface area of 1700 m2 g-1. An explanation to this abnormal correlation is that graphene material has an intrinsic capability of adaptively reorganizing its microporous structure in response to intercalation of ions and immergence of electrolyte solvent. The accessible surface of graphene is believed to be dramatically enlarged for ion adsorption during the charging process of capacitor.

Functionalization of Cadmium Selenide Quantum Dots with Poly(ethylene glycol): Ligand Exchange, Surface Coverage, and Dispersion Stability.

PubMed

Wenger, Whitney Nowak; Bates, Frank S; Aydil, Eray S

2017-08-22

Semiconductor quantum dots synthesized using rapid mixing of precursors by injection into a hot solution of solvents and surfactants have surface ligands that sterically stabilize the dispersions in nonpolar solvents. Often, these ligands are exchanged to disperse the quantum dots in polar solvents, but quantitative studies of quantum dot surfaces before and after ligand exchange are scarce. We studied exchanging trioctylphosphine (TOP) and trioctylphosphine oxide (TOPO) ligands on as-synthesized CdSe quantum dots dispersed in hexane with a 2000 g/mol thiolated poly(ethylene glycol) (PEG) polymer. Using infrared spectroscopy we quantify the absolute surface concentration of TOP/TOPO and PEG ligands per unit area before and after ligand exchange. While 50-85% of the TOP/TOPO ligands are removed upon ligand exchange, only a few are replaced with PEG. Surprisingly, the remaining TOP/TOPO ligands outnumber the PEG ligands, but these few PEG ligands are sufficient to disperse the quantum dots in polar solvents such as chloroform, tetrahydrofuran, and water. Moreover, as-synthesized quantum dots once easily dispersed in hexane are no longer dispersible in nonpolar solvents after ligand exchange. A subtle coverage-dependent balance between attractive PEG-solvent interactions and repulsive TOP/TOPO-solvent interactions determines the dispersion stability.

Activation of porous MOF materials

DOEpatents

Hupp, Joseph T; Farha, Omar K

2013-04-23

A method for the treatment of solvent-containing MOF material to increase its internal surface area involves introducing a liquid into the MOF in which liquid the solvent is miscible, subjecting the MOF to supercritical conditions for a time to form supercritical fluid, and releasing the supercritical conditions to remove the supercritical fluid from the MOF. Prior to introducing the liquid into the MOF, occluded reaction solvent, such as DEF or DMF, in the MOF can be exchanged for the miscible solvent.

Activation of porous MOF materials

DOEpatents

Hupp, Joseph T; Farha, Omar K

2014-04-01

A method for the treatment of solvent-containing MOF material to increase its internal surface area involves introducing a liquid into the MOF in which liquid the solvent is miscible, subjecting the MOF to supercritical conditions for a time to form supercritical fluid, and releasing the supercritical conditions to remove the supercritcal fluid from the MOF. Prior to introducing the liquid into the MOF, occluded reaction solvent, such as DEF or DMF, in the MOF can be exchanged for the miscible solvent.

Enhanced ion signals in desorption electrospray ionization using surfactant spray solutions.

PubMed

Badu-Tawiah, Abraham; Cooks, R Graham

2010-08-01

Solvent optimization is an important procedure in desorption electrospray ionization (DESI) and in this study the effects of solvent surface tension are explored. Data are presented for methanol/water/surfactant solvent systems, which show increases in ion signals of more than an order of magnitude when low concentrations of surfactants are added to the standard methanol/water (1:1) spray solvent. Examples of analytes tested include food chemicals, peptides, pharmaceuticals, and drugs of abuse. The improvement in ion intensity is mainly attributed to the effect of surface tension in producing smaller spray droplets, which are shown to cover a larger surface area. Surfactant-containing spray solutions allowed extension of DESI-MS analysis to previously intractable analytes like melamine and highly hydrophobic compounds like the sudan dyes. Copyright 2010 American Society for Mass Spectrometry. Published by Elsevier Inc. All rights reserved.

Evaluation of Chemical Warfare Agent Wipe Sampling ...

EPA Pesticide Factsheets

Report This investigation tested specific (CWAs), including sarin (GB), soman (GD), cyclosarin (GF), sulfur mustard (HD), and O-ethyl-S-(2-diisopropylaminoethyl) methylphosphonothioate (VX) on the non-ideal (e.g., porous and permeable) surfaces of drywall, vinyl tile, wood, laminate, and coated glass. Pesticides (diazinon and malathion) were used so that a comparison is possible with existing literature data (1). Experiments included testing with coupons having surface areas of 10 cm2 and 100 cm2. The 10-cm2 coupons were of a size that could easily be extracted in a 2 oz jar (to provide comparative data for CWA recoveries generated by direct extraction) and the 100-cm2 coupons better represented the area of a surface that might typically be sampled by wipe extraction. In addition, CWA, at a normalized surface concentration of 0.1 µg per cm2 surface area, were spiked on coupons of the tested surfaces. Wipes were wetted with either dichloromethane (DCM) or isopropanol (IPA) before sampling for CWA. Experimental parameters include multiple wipe types, porous/permeable surfaces, coupon surface area, solvent used to wet the wipe (i.e., wetting solvent), and the utility of VX-d14 as an extracted internal standard.

Determination of protein secondary structure and solvent accessibility using site-directed fluorescence labeling. Studies of T4 lysozyme using the fluorescent probe monobromobimane.

PubMed

Mansoor, S E; McHaourab, H S; Farrens, D L

1999-12-07

We report an investigation of how much protein structural information could be obtained using a site-directed fluorescence labeling (SDFL) strategy. In our experiments, we used 21 consecutive single-cysteine substitution mutants in T4 lysozyme (residues T115-K135), located in a helix-turn-helix motif. The mutants were labeled with the fluorescent probe monobromobimane and subjected to an array of fluorescence measurements. Thermal stability measurements show that introduction of the label is substantially perturbing only when it is located at buried residue sites. At buried sites (solvent surface accessibility of <40 A(2)), the destabilizations are between 3 and 5.5 kcal/mol, whereas at more exposed sites, DeltaDeltaG values of < or = 1.5 kcal/mol are obtained. Of all the fluorescence parameters that were explored (excitation lambda(max), emission lambda(max), fluorescence lifetime, quantum yield, and steady-state anisotropy), the emission lambda(max) and the steady-state anisotropy values most accurately reflect the solvent surface accessibility at each site as calculated from the crystal structure of cysteine-less T4 lysozyme. The parameters we identify allow the classification of each site as buried, partially buried, or exposed. We find that the variations in these parameters as a function of residue number reflect the sequence-specific secondary structure, the determination of which is a key step for modeling a protein of unknown structure.

Coupling of protein surface hydrophobicity change to ATP hydrolysis by myosin motor domain.

PubMed Central

Suzuki, M; Shigematsu, J; Fukunishi, Y; Harada, Y; Yanagida, T; Kodama, T

1997-01-01

Dielectric spectroscopy with microwaves in the frequency range between 0.2 and 20 GHz was used to study the hydration of myosin subfragment 1 (S1). The data were analyzed by a method recently devised, which can resolve the total amount of water restrained by proteins into two components, one with a rotational relaxation frequency (fc) in the gigahertz region (weakly restrained water) and the other with lower fc (strongly restrained water). The weight ratio of total restrained water to S1 protein thus obtained (0.35), equivalent to 2100 water molecules per S1 molecule, is not much different from the values (0.3-0.4) for other proteins. The weakly restrained component accounts for about two-thirds of the total restrained water, which is in accord with the number of water molecules estimated from the solvent-accessible surface area of alkyl groups on the surface of the atomic model of S1. The number of strongly restrained water molecules coincides with the number of solvent-accessible charged or polar atoms. The dynamic behavior of the S1-restrained water during the ATP hydrolysis was also examined in a time-resolved mode. The result indicates that when S1 changes from the S1.ADP state into the S1.ADP.P1 state (ADP release followed by ATP binding and cleavage), about 9% of the weakly restrained waters are released, which are restrained again on slow P1 release. By contrast, there is no net mobilization of strongly restrained component. The observed changes in S1 hydration are quantitatively consistent with the accompanying large entropy and heat capacity changes estimated by calorimetry (Kodama, 1985), indicating that the protein surface hydrophobicity change plays a crucial role in the enthalpy-entropy compensation effects observed in the steps of S1 ATP hydrolysis. Images FIGURE 4 PMID:8994589

Formation of stable submicron peptide or protein particles by thin film freezing

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

Johnston, Keith P.; Engstrom, Joshua; Williams, III, Robert O.

The present invention includes compositions and methods for preparing micron-sized or submicron-sized particles by dissolving a water soluble effective ingredient in one or more solvents; spraying or dripping droplets solvent such that the effective ingredient is exposed to a vapor-liquid interface of less than 50, 100, 150, 200, 250, 200, 400 or 500 cm.sup.-1 area/volume to, e.g., increase protein stability; and contacting the droplet with a freezing surface that has a temperature differential of at least 30.degree. C. between the droplet and the surface, wherein the surface freezes the droplet into a thin film with a thickness of less thanmore » 500 micrometers and a surface area to volume between 25 to 500 cm.sup.-1.« less

Clean Transfer of Wafer-Scale Graphene via Liquid Phase Removal of Polycyclic Aromatic Hydrocarbons.

PubMed

Kim, Hyun Ho; Kang, Boseok; Suk, Ji Won; Li, Nannan; Kim, Kwang S; Ruoff, Rodney S; Lee, Wi Hyoung; Cho, Kilwon

2015-05-26

Pentacene (C22H14), a polycyclic aromatic hydrocarbon, was used as both supporting and sacrificing layers for the clean and doping-free graphene transfer. After successful transfer of graphene to a target substrate, the pentacene layer was physically removed from the graphene surface by using intercalating organic solvent. This solvent-mediated removal of pentacene from graphene surface was investigated by both theoretical calculation and experimental studies with various solvents. The uses of pentacene and appropriate intercalation solvent enabled graphene transfer without forming a residue from the supporting layer. Such residues tend to cause charged impurity scattering and unintentional graphene doping effects. As a result, this clean graphene exhibited extremely homogeneous surface potential profiles over a large area. A field-effect transistor fabricated using this graphene displayed a high hole (electron) mobility of 8050 cm(2)/V·s (9940 cm(2)/V·s) with a nearly zero Dirac point voltage.

High surface area nanocrystalline hausmannite synthesized by a solvent-free route

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

Herrera-Miranda, Daniel; Ponrouch, Alexandre; Pons, Josefina

Highlights: ► High surface area Mn{sub 3}O{sub 4} nanoparticles obtained by a solvent-free low temperature route. ► 3,6,9-Trioxadecanoic acid allows to obtain nanocrystalline hausmannite. ► Tape casted electrodes show up to 300 mAh g{sup −1} capacity after more than 40 cycles at a C/3 rate. ► Upper cut off voltage strongly influences capacity retention upon cycling at high C rates. -- Abstract: Nanocrystalline high surface area Mn{sub 3}O{sub 4} powder was obtained at low temperature by a solvent-free route. The precursor was a mixture of manganese (II) acetate, 3,6,9-trioxadecanoic acid (TODA) and ammonium acetate that were intimately mixed by groundingmore » in an agate mortar. Nanocrystalline Mn{sub 3}O{sub 4} was obtained by thermal treatment at 120 °C. Powder X-ray diffraction, selected area electron diffraction, high resolution transmission electron microscopy, and Fourier transformed infrared characterization confirmed the formation of the hausmannite phase. The as-prepared mesoporous material has high specific surface area (120 m{sup 2} g{sup −1}). The performances of tape casted Mn{sub 3}O{sub 4} nanopowder electrodes were investigated as anode material for lithium ion batteries. High capacity values were achieved at diverse C rates. Capacity fading was found to be dependent on the upper cut off voltage, the presence of a plateau at 2.25 V vs. Li{sup +}/Li being detrimental for long term cyclability.« less

High temperature adhesive silicone foam composition, foam generating system and method of generating foam

DOEpatents

Mead, Judith W.; Montoya, Orelio J.; Rand, Peter B.; Willan, Vernon O.

1984-01-01

Access to a space is impeded by generation of a sticky foam from a silicone polymer and a low boiling solvent such as a halogenated hydrocarbon. In a preferred aspect, the formulation is polydimethylsiloxane gel mixed with F502 Freon as a solvent and blowing agent, and pressurized with CO.sub.2 in a vessel to about 250 PSI, whereby when the vessel is opened, a sticky and solvent resistant foam is deployed. The foam is deployable, over a wide range of temperatures, adhering to wet surfaces as well as dry, is stable over long periods of time and does not propagate flame or lose adhesive properties during an externally supported burn.

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

PubMed

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.

Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations.

PubMed

Zerze, Gül H; Best, Robert B; Mittal, Jeetain

2015-11-19

We use all-atom molecular simulation with explicit solvent to study the properties of selected intrinsically disordered proteins and unfolded states of foldable proteins, which include chain dimensions and shape, secondary structure propensity, solvent accessible surface area, and contact formation. We find that the qualitative scaling behavior of the chains matches expectations from theory under ambient conditions. In particular, unfolded globular proteins tend to be more collapsed under the same conditions than charged disordered sequences of the same length. However, inclusion of explicit solvent in addition naturally captures temperature-dependent solvation effects, which results in an initial collapse of the chains as temperature is increased, in qualitative agreement with experiment. There is a universal origin to the collapse, revealed in the change of hydration of individual residues as a function of temperature: namely, that the initial collapse is driven by unfavorable solvation free energy of individual residues, which in turn has a strong temperature dependence. We also observe that in unfolded globular proteins, increased temperature also initially favors formation of native-like (rather than non-native-like) structure. Our results help to establish how sequence encodes the degree of intrinsic disorder or order as well as its response to changes in environmental conditions.

The Effect of Complex Solvents on the Structure and Dynamics of Protein Solutions: the case of Lysozyme in Trehalose/Water Mixtures

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

Ghattyvenkatakrishna, Pavan K; Carri, Gustavo A.

We present a Molecular Dynamics simulation study of the effect of trehalose concentration on the structure and dynamics of individual proteins immersed in trehalose/water mixtures. Hen Egg White Lysozyme is used in this study and trehalose concentrations of 0%, 10%, 20%, 30% and 100% by weight are explored. Surprisingly, we have found that changes in trehalose concentration do not change the global structural characteristics of the protein as measured by standard quantities like the mean square deviation, radius of gyration, solvent accessible surface area, inertia tensor and asphericity. Only in the limit of pure trehalose these metrics change significantly. Specifically,more » we found that the protein is compressed by 2% when immersed in pure trehalose. At the amino acid level there is noticeable rearrangement of the surface residues due to the change in polarity of the surrounding environment with the addition of trehalose. From a dynamic perspective, our computation of the Incoherent Intermediate Scattering Function shows that the protein slows down with increasing trehalose concentration; however, this slowdown is not monotonic. Finally, we also report in-depth results for the hydration layer around the protein including its structure, hydrogen- bonding characteristics and dynamic behavior at different length scales.« less

Characterizing monoclonal antibody structure by carboxyl group footprinting

PubMed Central

Kaur, Parminder; Tomechko, Sara E; Kiselar, Janna; Shi, Wuxian; Deperalta, Galahad; Wecksler, Aaron T; Gokulrangan, Giridharan; Ling, Victor; Chance, Mark R

2015-01-01

Structural characterization of proteins and their antigen complexes is essential to the development of new biologic-based medicines. Amino acid-specific covalent labeling (CL) is well suited to probe such structures, especially for cases that are difficult to examine by alternative means due to size, complexity, or instability. We present here a detailed account of carboxyl group labeling (with glycine ethyl ester (GEE) tagging) applied to a glycosylated monoclonal antibody therapeutic (mAb). The experiments were optimized to preserve the structural integrity of the mAb, and experimental conditions were varied and replicated to establish the reproducibility of the technique. Homology-based models were generated and used to compare the solvent accessibility of the labeled residues, which include aspartic acid (D), glutamic acid (E), and the C-terminus (i.e., the target probes), with the experimental data in order to understand the accuracy of the approach. Data from the mAb were compared to reactivity measures of several model peptides to explain observed variations in reactivity. Attenuation of reactivity in otherwise solvent accessible probes is documented as arising from the effects of positive charge or bond formation between adjacent amine and carboxyl groups, the latter accompanied by observed water loss. A comparison of results with previously published data by Deperalta et al using hydroxyl radical footprinting showed that 55% (32/58) of target residues were GEE labeled in this study whereas the previous study reported 21% of the targets were labeled. Although the number of target residues in GEE labeling is fewer, the two approaches provide complementary information. The results highlight advantages of this approach, such as the ease of use at the bench top, the linearity of the dose response plots at high levels of labeling, reproducibility of replicate experiments (<2% variation in modification extent), the similar reactivity of the three target probes, and significant correlation of reactivity and solvent accessible surface area. PMID:25933350

The use of chemometrics to study multifunctional indole alkaloids from Psychotria nemorosa (Palicourea comb. nov.). Part I: Extraction and fractionation optimization based on metabolic profiling.

PubMed

Klein-Júnior, Luiz C; Viaene, Johan; Salton, Juliana; Koetz, Mariana; Gasper, André L; Henriques, Amélia T; Vander Heyden, Yvan

2016-09-09

Extraction methods evaluation to access plants metabolome is usually performed visually, lacking a truthful method of data handling. In the present study the major aim was developing reliable time- and solvent-saving extraction and fractionation methods to access alkaloid profiling of Psychotria nemorosa leaves. Ultrasound assisted extraction was selected as extraction method. Determined from a Fractional Factorial Design (FFD) approach, yield, sum of peak areas, and peak numbers were rather meaningless responses. However, Euclidean distance calculations between the UPLC-DAD metabolic profiles and the blank injection evidenced the extracts are highly diverse. Coupled with the calculation and plotting of effects per time point, it was possible to indicate thermolabile peaks. After screening, time and temperature were selected for optimization, while plant:solvent ratio was set at 1:50 (m/v), number of extractions at one and particle size at ≤180μm. From Central Composite Design (CCD) results modeling heights of important peaks, previously indicated by the FFD metabolic profile analysis, time was set at 65min and temperature at 45°C, thus avoiding degradation. For the fractionation step, a solid phase extraction method was optimized by a Box-Behnken Design (BBD) approach using the sum of peak areas as response. Sample concentration was consequently set at 150mg/mL, % acetonitrile in dichloromethane at 40% as eluting solvent, and eluting volume at 30mL. Summarized, the Euclidean distance and the metabolite profiles provided significant responses for accessing P. nemorosa alkaloids, allowing developing reliable extraction and fractionation methods, avoiding degradation and decreasing the required time and solvent volume. Copyright © 2016 Elsevier B.V. All rights reserved.

Analytical electron tomography mapping of the SiCporeoxidation at the nanoscale

NASA Astrophysics Data System (ADS)

Florea, Ileana; Ersen, Ovidiu; Hirlimann, Charles; Roiban, Lucian; Deneuve, Adrien; Houllé, Matthieu; Janowska, Izabela; Nguyen, Patrick; Pham, Charlotte; Pham-Huu, Cuong

2010-12-01

Silicon carbide is a ceramic material that has been widely studied because of its potential applications, ranging from electronics to heterogeneous catalysis. Recently, a new type of SiC materials with a medium specific surface area and thermal conductivity, called β-SiC, has attracted overgrowing interest as a new class of catalyst support in several catalytic reactions. A primary electron tomography study, performed in usual mode, has revealed a dual surface structure defined by two types of porosities made of networks of connected channels with sizes larger than 50 nm and ink-bottled pores with sizes spanning from 4 to 50 nm. Depending on the solvent nature, metal nanoparticles could be selectively deposited inside one of the two porosities, a fact that illustrates a selective wetting titration of the two types of surfaces by different liquids. The explaining hypothesis that has been put forward was that this selectivity against solvents is related to the pore surface oxidation degree of the two types of pores. A new technique of analytical electron tomography, where the series of projections used to reconstruct the volume of an object is recorded in energy filtered mode (EFTEM), has been implemented to map the poreoxidation state and to correlate it with the morphology and the accessibility of the porous network. Applied, for the first time, at a nanoscale resolution, this technique allowed us to obtain 3D elemental maps of different elements present in the analysed porous grains, in particular oxygen; we found thus that the interconnected channelpores are more rapidly oxidized than the ink-bottled ones. Alternatively, our study highlights the great interest of this method that opens the way for obtaining precise information on the chemical composition of a 3D surface at a nanometer scale.Silicon carbide is a ceramic material that has been widely studied because of its potential applications, ranging from electronics to heterogeneous catalysis. Recently, a new type of SiC materials with a medium specific surface area and thermal conductivity, called β-SiC, has attracted overgrowing interest as a new class of catalyst support in several catalytic reactions. A primary electron tomography study, performed in usual mode, has revealed a dual surface structure defined by two types of porosities made of networks of connected channels with sizes larger than 50 nm and ink-bottled pores with sizes spanning from 4 to 50 nm. Depending on the solvent nature, metal nanoparticles could be selectively deposited inside one of the two porosities, a fact that illustrates a selective wetting titration of the two types of surfaces by different liquids. The explaining hypothesis that has been put forward was that this selectivity against solvents is related to the pore surface oxidation degree of the two types of pores. A new technique of analytical electron tomography, where the series of projections used to reconstruct the volume of an object is recorded in energy filtered mode (EFTEM), has been implemented to map the poreoxidation state and to correlate it with the morphology and the accessibility of the porous network. Applied, for the first time, at a nanoscale resolution, this technique allowed us to obtain 3D elemental maps of different elements present in the analysed porous grains, in particular oxygen; we found thus that the interconnected channelpores are more rapidly oxidized than the ink-bottled ones. Alternatively, our study highlights the great interest of this method that opens the way for obtaining precise information on the chemical composition of a 3D surface at a nanometer scale. Electronic supplementary information (ESI) available: SI-1-SI-4. See DOI: 10.1039/c0nr00449a

PRince: a web server for structural and physicochemical analysis of protein-RNA interface.

PubMed

Barik, Amita; Mishra, Abhishek; Bahadur, Ranjit Prasad

2012-07-01

We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in '.pdb' format). They should also mention the chain identifiers of interacting protein and RNA molecules. The size of the protein-RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein-RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters generated by the server are presented in a tabular format. The interacting surfaces can also be visualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic coordinates of the interacting protein, RNA and interface water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical parameters for better understanding the specificity of the protein-RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free for use. Available at http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html.

3D Printing of Protein Models in an Undergraduate Laboratory: Leucine Zippers

ERIC Educational Resources Information Center

Meyer, Scott C.

2015-01-01

An upper-division undergraduate laboratory experiment is described that explores the structure/function relationship of protein domains, namely leucine zippers, through a molecular graphics computer program and physical models fabricated by 3D printing. By generating solvent accessible surfaces and color-coding hydrophobic, basic, and acidic amino…

Improved Detection Technique for Solvent Rinse Cleanliness Verification

NASA Technical Reports Server (NTRS)

Hornung, S. D.; Beeson, H. D.

2001-01-01

The NASA White Sands Test Facility (WSTF) has an ongoing effort to reduce or eliminate usage of cleaning solvents such as CFC-113 and its replacements. These solvents are used in the final clean and cleanliness verification processes for flight and ground support hardware, especially for oxygen systems where organic contaminants can pose an ignition hazard. For the final cleanliness verification in the standard process, the equivalent of one square foot of surface area of parts is rinsed with the solvent, and the final 100 mL of the rinse is captured. The amount of nonvolatile residue (NVR) in the solvent is determined by weight after the evaporation of the solvent. An improved process of sampling this rinse, developed at WSTF, requires evaporation of less than 2 mL of the solvent to make the cleanliness verification. Small amounts of the solvent are evaporated in a clean stainless steel cup, and the cleanliness of the stainless steel cup is measured using a commercially available surface quality monitor. The effectiveness of this new cleanliness verification technique was compared to the accepted NVR sampling procedures. Testing with known contaminants in solution, such as hydraulic fluid, fluorinated lubricants, and cutting and lubricating oils, was performed to establish a correlation between amount in solution and the process response. This report presents the approach and results and discusses the issues in establishing the surface quality monitor-based cleanliness verification.

Three-dimensional simulation of rivulet and film flows over an inclined plate: Effects of solvent properties and contact angle

DOE PAGES

Singh, Rajesh K.; Galvin, Janine E.; Sun, Xin

2015-12-10

We numerically investigated the film flow down an inclined plate using the volume of fluid (VOF) method. The flow simulations have been systematically carried out for a wide range of parameters, such as inlet size, inclination angle, contact angle, flow rates and solvent properties (viscosity and surface tension). Based on the simulation results, scaling theory is proposed for both interfacial area and for film thickness in terms of the Kapitza number (Ka).The Kapitza number is advantageous because it depends only on solvent properties. The Kapitza number decreases with increased solvent viscosity and is fixed for a given fluid. Here, tomore » investigate the effects of solvent properties on interfacial area a small inlet cross-section was used. The interfacial area decreases with increased value of Ka. The time to reach pseudo-steady state of rivulet is also observed to increase with decreasing Ka. For a fixed flow rate, the inlet cross-section has marginal effect on the interfacial area; however, the developed width of the rivulet remains unchanged. In addition to inlet size, flow rate and solvent properties, the impact of contact angle on film thickness and interfacial area was also investigated. The contact angle has negligible effect for a fully wetted plate, but it significantly affects the interfacial area of the rivulet. Finally, a scaling theory for interfacial area in terms of the contact angle and Ka is presented.« less

Competitive interactions and controlled release of a natural antioxidant from halloysite nanotubes.

PubMed

Hári, József; Gyürki, Ádám; Sárközi, Márk; Földes, Enikő; Pukánszky, Béla

2016-01-15

Halloysite nanotubes used as potential carrier material for a controlled release stabilizer in polyethylene were thoroughly characterized with several techniques including the measurement of specific surface area, pore volume and surface energy. The high surface energy of the halloysite results in the strong bonding of the additive to the surface. Dissolution experiments carried out with eight different solvents for the determination of the effect of solvent characteristics on the amount of irreversibly bonded quercetin proved that adsorption and dissolution depend on competitive interactions prevailing in the system. Solvents with low polarity dissolve only surplus quercetin adsorbed in multilayers. Polyethylene is a very apolar polymer forming weak interactions with every substance; quercetin dissolves into it from the halloysite surface only above a critical surface coverage. Stabilization experiments confirmed that strong adhesion prevents dissolution and results in limited stabilization efficiency. At larger adsorbed amounts better stability and extended effect were measured indicating dissolution and controlled release. Copyright © 2015 Elsevier Inc. All rights reserved.

An analytical method for computing atomic contact areas in biomolecules.

PubMed

Mach, Paul; Koehl, Patrice

2013-01-15

We propose a new analytical method for detecting and computing contacts between atoms in biomolecules. It is based on the alpha shape theory and proceeds in three steps. First, we compute the weighted Delaunay triangulation of the union of spheres representing the molecule. In the second step, the Delaunay complex is filtered to derive the dual complex. Finally, contacts between spheres are collected. In this approach, two atoms i and j are defined to be in contact if their centers are connected by an edge in the dual complex. The contact areas between atom i and its neighbors are computed based on the caps formed by these neighbors on the surface of i; the total area of all these caps is partitioned according to their spherical Laguerre Voronoi diagram on the surface of i. This method is analytical and its implementation in a new program BallContact is fast and robust. We have used BallContact to study contacts in a database of 1551 high resolution protein structures. We show that with this new definition of atomic contacts, we generate realistic representations of the environments of atoms and residues within a protein. In particular, we establish the importance of nonpolar contact areas that complement the information represented by the accessible surface areas. This new method bears similarity to the tessellation methods used to quantify atomic volumes and contacts, with the advantage that it does not require the presence of explicit solvent molecules if the surface of the protein is to be considered. © 2012 Wiley Periodicals, Inc. Copyright © 2012 Wiley Periodicals, Inc.

Integrated Geophysical Investigation of Preferential Flow Paths at the Former Tyson Valley Powder Farm near Eureka, Missouri, May 2006

USGS Publications Warehouse

Burton, Bethany L.; Ball, Lyndsay B.; Stanton, Gregory P.; Hobza, Christopher M.

2009-01-01

In May 2006, the U.S. Geological Survey, in cooperation with the U.S. Army Corps of Engineers, conducted surface and borehole geophysical surveys at the former Tyson Valley Powder Farm near Eureka, Mo., to identify preferential pathways for potential contaminant transport along the bedrock surface and into dissolution-enhanced fractures. The Tyson Valley Powder Farm was formerly used as a munitions storage and disposal facility in the 1940s and 1950s, and the site at which the surveys were performed was a disposal area for munitions and waste solvents such as trichloroethylene and dichloroethylene. Direct-current resistivity and seismic refraction data were acquired on the surface; gamma, electromagnetic induction, and full waveform sonic logs were acquired in accessible boreholes. Through the combined interpretation of the seismic refraction tomographic and resistivity inversion results and borehole logs, inconsistencies in the bedrock surface were identified that may provide horizontal preferential flow paths for dense nonaqueous phase liquid contaminants. These results, interpreted and displayed in georeferenced three-dimensional space, should help to establish more effective monitoring and remediation strategies.

Method for removing organic liquids from aqueous solutions and mixtures

DOEpatents

Hrubesh, Lawrence W.; Coronado, Paul R.; Dow, Jerome P.

2004-03-23

A method for removing organic liquids from aqueous solutions and mixtures. The method employs any porous material preferably in granular form and having small pores and a large specific surface area, that is hydrophobic so that liquid water does not readily wet its surface. In this method, organics, especially organic solvents that mix with and are more volatile than water, are separated from aqueous solution by preferentially evaporating across the liquid/solid boundary formed at the surfaces of the hydrophobic porous materials. Also, organic solvents that are immiscible with water, preferentially wet the surfaces of the hydrophobic material and are drawn within the porous materials by capillary action.

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

Tande, Brian; Seames, Wayne; Benson, Steve

The objective of this project was to evaluate the use of composite polymer membranes and porous membrane contactors to regenerate physical and chemical solvents for capture of carbon dioxide (CO 2) from synthesis gas or flue gas, with the goal of improving the energy efficiency of carbon capture. Both a chemical solvent (typical for a post-combustion capture of CO 2 from flue gas) and a physical solvent (typical for pre- combustion capture of CO 2 from syngas) were evaluated using two bench-scale test systems constructed for this project. For chemical solvents, polytetrafluoroethylene and polypropylene membranes were found to be ablemore » to strip CO 2 from a monoethanolamine (MEA) solution with high selectivity without significant degradation of the material. As expected, the regeneration temperature was the most significant parameter affecting the CO 2 flux through the membrane. Pore size was also found to be important, as pores larger than 5 microns lead to excessive pore wetting. For physical solvents, polydimethyl-siloxane (PDMS)-based membranes were found to have a higher CO 2 permeability than polyvinylalcohol (PVOH) based membranes, while also minimizing solvent loss. Overall, however, the recovery of CO 2 in these systems is low – less than 2% for both chemical and physical solvents – primarily due to the small surface area of the membrane test apparatus. To obtain the higher regeneration rates needed for this application, a much larger surface area would be needed. Further experiments using, for example, a hollow fiber membrane module could determine if this process could be commercially viable.« less

Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces.

PubMed

Bardhan, Jaydeep P; Altman, Michael D; Willis, David J; Lippow, Shaun M; Tidor, Bruce; White, Jacob K

2007-07-07

Surface formulations of biophysical modeling problems offer attractive theoretical and computational properties. Numerical simulations based on these formulations usually begin with discretization of the surface under consideration; often, the surface is curved, possessing complicated structure and possibly singularities. Numerical simulations commonly are based on approximate, rather than exact, discretizations of these surfaces. To assess the strength of the dependence of simulation accuracy on the fidelity of surface representation, here methods were developed to model several important surface formulations using exact surface discretizations. Following and refining Zauhar's work [J. Comput.-Aided Mol. Des. 9, 149 (1995)], two classes of curved elements were defined that can exactly discretize the van der Waals, solvent-accessible, and solvent-excluded (molecular) surfaces. Numerical integration techniques are presented that can accurately evaluate nonsingular and singular integrals over these curved surfaces. After validating the exactness of the surface discretizations and demonstrating the correctness of the presented integration methods, a set of calculations are presented that compare the accuracy of approximate, planar-triangle-based discretizations and exact, curved-element-based simulations of surface-generalized-Born (sGB), surface-continuum van der Waals (scvdW), and boundary-element method (BEM) electrostatics problems. Results demonstrate that continuum electrostatic calculations with BEM using curved elements, piecewise-constant basis functions, and centroid collocation are nearly ten times more accurate than planar-triangle BEM for basis sets of comparable size. The sGB and scvdW calculations give exceptional accuracy even for the coarsest obtainable discretized surfaces. The extra accuracy is attributed to the exact representation of the solute-solvent interface; in contrast, commonly used planar-triangle discretizations can only offer improved approximations with increasing discretization and associated increases in computational resources. The results clearly demonstrate that the methods for approximate integration on an exact geometry are far more accurate than exact integration on an approximate geometry. A MATLAB implementation of the presented integration methods and sample data files containing curved-element discretizations of several small molecules are available online as supplemental material.

Fluorescence Determination of Tryptophan Side-Chain Accessibility and Dynamics in Triple-Helical Collagen-Like Peptides

PubMed Central

Simon-Lukasik, Kristine V.; Persikov, Anton V.; Brodsky, Barbara; Ramshaw, John A. M.; Laws, William R.; Alexander Ross, J. B.; Ludescher, Richard D.

2003-01-01

We report tryptophan fluorescence measurements of emission intensity, iodide quenching, and anisotropy that describe the environment and dynamics at X and Y sites in stable collagen-like peptides of sequence (Gly-X-Y)n. About 90% of tryptophans at both sites have similar solvent exposed fluorescence properties and a lifetime of 8.5–9 ns. Analysis of anisotropy decays using an associative model indicates that these long lifetime populations undergo rapid depolarizing motion with a 0.5 ns correlation time; however, the extent of fast motion at the Y site is considerably less than the essentially unrestricted motion at the X site. About 10% of tryptophans at both sites have a shorter (∼3 ns) lifetime indicating proximity to a protein quenching group; these minor populations are immobile on the peptide surface, depolarizing only by overall trimer rotation. Iodide quenching indicates that tryptophans at the X site are more accessible to solvent. Side chains at X sites are more solvent accessible and considerably more mobile than residues at Y sites and can more readily fluctuate among alternate intermolecular interactions in collagen fibrils. This fluorescence analysis of collagen-like peptides lays a foundation for studies on the structure, dynamics, and function of collagen and of triple-helical junctions in gelatin gels. PMID:12524302

Compressed air-assisted solvent extraction (CASX) for metal removal.

PubMed

Li, Chi-Wang; Chen, Yi-Ming; Hsiao, Shin-Tien

2008-03-01

A novel process, compressed air-assisted solvent extraction (CASX), was developed to generate micro-sized solvent-coated air bubbles (MSAB) for metal extraction. Through pressurization of solvent with compressed air followed by releasing air-oversaturated solvent into metal-containing wastewater, MSAB were generated instantaneously. The enormous surface area of MSAB makes extraction process extremely fast and achieves very high aqueous/solvent weight ratio (A/S ratio). CASX process completely removed Cr(VI) from acidic electroplating wastewater under A/S ratio of 115 and extraction time of less than 10s. When synthetic wastewater containing Cd(II) of 50mgl(-1) was treated, A/S ratios of higher than 714 and 1190 could be achieved using solvent with extractant/diluent weight ratio of 1:1 and 5:1, respectively. Also, MSAB have very different physical properties, such as size and density, compared to the emulsified solvent droplets, making separation and recovery of solvent from treated effluent very easy.

Effects of the Pathogenic Mutation A117V and the Protective Mutation H111S on the Folding and Aggregation of PrP106-126: Insights from Replica Exchange Molecular Dynamics Simulations.

PubMed

Ning, Lulu; Pan, Dabo; Zhang, Yan; Wang, Shaopeng; Liu, Huanxiang; Yao, Xiaojun

2015-01-01

The fragment 106-126 of prion protein exhibits similar properties to full-length prion. Experiments have shown that the A117V mutation enhances the aggregation of PrP106-126, while the H111S mutation abolishes the assembly. However, the mechanism of the change in the aggregation behavior of PrP106-126 upon the two mutations is not fully understood. In this study, replica exchange molecular dynamics simulations were performed to investigate the conformational ensemble of the WT PrP106-126 and its two mutants A117V and H111S. The obtained results indicate that the three species are all intrinsically disordered but they have distinct morphological differences. The A117V mutant has a higher propensity to form β-hairpin structures than the WT, while the H111S mutant has a higher population of helical structures. Furthermore, the A117V mutation increases the hydrophobic solvent accessible surface areas of PrP106-126 and the H111S mutation reduces the exposure of hydrophobic residues. It can be concluded that the difference in populations of β-hairpin structures and the change of hydrophobic solvent accessible areas may induce the different aggregation behaviors of the A117V and the H111S mutated PrP106-126. Understanding why the two mutations have contrary effects on the aggregation of PrP106-126 is very meaningful for further elucidation of the mechanism underlying aggregation and design of inhibitor against aggregation process.

Effects of the Pathogenic Mutation A117V and the Protective Mutation H111S on the Folding and Aggregation of PrP106-126: Insights from Replica Exchange Molecular Dynamics Simulations

PubMed Central

Ning, Lulu; Pan, Dabo; Zhang, Yan; Wang, Shaopeng; Liu, Huanxiang; Yao, Xiaojun

2015-01-01

The fragment 106-126 of prion protein exhibits similar properties to full-length prion. Experiments have shown that the A117V mutation enhances the aggregation of PrP106-126, while the H111S mutation abolishes the assembly. However, the mechanism of the change in the aggregation behavior of PrP106-126 upon the two mutations is not fully understood. In this study, replica exchange molecular dynamics simulations were performed to investigate the conformational ensemble of the WT PrP106-126 and its two mutants A117V and H111S. The obtained results indicate that the three species are all intrinsically disordered but they have distinct morphological differences. The A117V mutant has a higher propensity to form β-hairpin structures than the WT, while the H111S mutant has a higher population of helical structures. Furthermore, the A117V mutation increases the hydrophobic solvent accessible surface areas of PrP106-126 and the H111S mutation reduces the exposure of hydrophobic residues. It can be concluded that the difference in populations of β-hairpin structures and the change of hydrophobic solvent accessible areas may induce the different aggregation behaviors of the A117V and the H111S mutated PrP106-126. Understanding why the two mutations have contrary effects on the aggregation of PrP106-126 is very meaningful for further elucidation of the mechanism underlying aggregation and design of inhibitor against aggregation process. PMID:25993001

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.

PubMed

Ochoa, David; García-Gutiérrez, Ponciano; Juan, David; Valencia, Alfonso; Pazos, Florencio

2013-01-27

A widespread family of methods for studying and predicting protein interactions using sequence information is based on co-evolution, quantified as similarity of phylogenetic trees. Part of the co-evolution observed between interacting proteins could be due to co-adaptation caused by inter-protein contacts. In this case, the co-evolution is expected to be more evident when evaluated on the surface of the proteins or the internal layers close to it. In this work we study the effect of incorporating information on predicted solvent accessibility to three methods for predicting protein interactions based on similarity of phylogenetic trees. We evaluate the performance of these methods in predicting different types of protein associations when trees based on positions with different characteristics of predicted accessibility are used as input. We found that predicted accessibility improves the results of two recent versions of the mirrortree methodology in predicting direct binary physical interactions, while it neither improves these methods, nor the original mirrortree method, in predicting other types of interactions. That improvement comes at no cost in terms of applicability since accessibility can be predicted for any sequence. We also found that predictions of protein-protein interactions are improved when multiple sequence alignments with a richer representation of sequences (including paralogs) are incorporated in the accessibility prediction.

Predictive Sampling of Rare Conformational Events in Aqueous Solution: Designing a Generalized Orthogonal Space Tempering Method.

PubMed

Lu, Chao; Li, Xubin; Wu, Dongsheng; Zheng, Lianqing; Yang, Wei

2016-01-12

In aqueous solution, solute conformational transitions are governed by intimate interplays of the fluctuations of solute-solute, solute-water, and water-water interactions. To promote molecular fluctuations to enhance sampling of essential conformational changes, a common strategy is to construct an expanded Hamiltonian through a series of Hamiltonian perturbations and thereby broaden the distribution of certain interactions of focus. Due to a lack of active sampling of configuration response to Hamiltonian transitions, it is challenging for common expanded Hamiltonian methods to robustly explore solvent mediated rare conformational events. The orthogonal space sampling (OSS) scheme, as exemplified by the orthogonal space random walk and orthogonal space tempering methods, provides a general framework for synchronous acceleration of slow configuration responses. To more effectively sample conformational transitions in aqueous solution, in this work, we devised a generalized orthogonal space tempering (gOST) algorithm. Specifically, in the Hamiltonian perturbation part, a solvent-accessible-surface-area-dependent term is introduced to implicitly perturb near-solute water-water fluctuations; more importantly in the orthogonal space response part, the generalized force order parameter is generalized as a two-dimension order parameter set, in which essential solute-solvent and solute-solute components are separately treated. The gOST algorithm is evaluated through a molecular dynamics simulation study on the explicitly solvated deca-alanine (Ala10) peptide. On the basis of a fully automated sampling protocol, the gOST simulation enabled repetitive folding and unfolding of the solvated peptide within a single continuous trajectory and allowed for detailed constructions of Ala10 folding/unfolding free energy surfaces. The gOST result reveals that solvent cooperative fluctuations play a pivotal role in Ala10 folding/unfolding transitions. In addition, our assessment analysis suggests that because essential conformational events are mainly driven by the compensating fluctuations of essential solute-solvent and solute-solute interactions, commonly employed "predictive" sampling methods are unlikely to be effective on this seemingly "simple" system. The gOST development presented in this paper illustrates how to employ the OSS scheme for physics-based sampling method designs.

Evaluation of Advanced Reactive Surface Area Estimates for Improved Prediction of Mineral Reaction Rates in Porous Media

NASA Astrophysics Data System (ADS)

Beckingham, L. E.; Mitnick, E. H.; Zhang, S.; Voltolini, M.; Yang, L.; Steefel, C. I.; Swift, A.; Cole, D. R.; Sheets, J.; Kneafsey, T. J.; Landrot, G.; Anovitz, L. M.; Mito, S.; Xue, Z.; Ajo Franklin, J. B.; DePaolo, D.

2015-12-01

CO2 sequestration in deep sedimentary formations is a promising means of reducing atmospheric CO2 emissions but the rate and extent of mineral trapping remains difficult to predict. Reactive transport models provide predictions of mineral trapping based on laboratory mineral reaction rates, which have been shown to have large discrepancies with field rates. This, in part, may be due to poor quantification of mineral reactive surface area in natural porous media. Common estimates of mineral reactive surface area are ad hoc and typically based on grain size, adjusted several orders of magnitude to account for surface roughness and reactivity. This results in orders of magnitude discrepancies in estimated surface areas that directly translate into orders of magnitude discrepancies in model predictions. Additionally, natural systems can be highly heterogeneous and contain abundant nano- and micro-porosity, which can limit connected porosity and access to mineral surfaces. In this study, mineral-specific accessible surface areas are computed for a sample from the reservoir formation at the Nagaoka pilot CO2 injection site (Japan). Accessible mineral surface areas are determined from a multi-scale image analysis including X-ray microCT, SEM QEMSCAN, XRD, SANS, and SEM-FIB. Powder and flow-through column laboratory experiments are performed and the evolution of solutes in the aqueous phase is tracked. Continuum-scale reactive transport models are used to evaluate the impact of reactive surface area on predictions of experimental reaction rates. Evaluated reactive surface areas include geometric and specific surface areas (eg. BET) in addition to their reactive-site weighted counterparts. The most accurate predictions of observed powder mineral dissolution rates were obtained through use of grain-size specific surface areas computed from a BET-based correlation. Effectively, this surface area reflects the grain-fluid contact area, or accessible surface area, in the powder dissolution experiment. In the model of the flow-through column experiment, the accessible mineral surface area, computed from the multi-scale image analysis, is evaluated in addition to the traditional surface area estimates.

Vibrational energy transfer between carbon nanotubes and liquid water: a molecular dynamics study.

PubMed

Nelson, Tammie R; Chaban, Vitaly V; Kalugin, Oleg N; Prezhdo, Oleg V

2010-04-08

The rates and magnitudes of vibrational energy transfer between single-wall carbon nanotubes (CNTs) and water are investigated by classical molecular dynamics. The interactions between the CNT and solvent confined inside of the tube, the CNT and solvent surrounding the tube, as well as the solvent inside and outside of the tube are considered for the (11,11), (15,15), and (19,19) armchair CNTs. The vibrational energy transfer exhibits two time scales, subpicosecond and picosecond, of roughly equal importance. Solvent molecules confined within CNTs are more strongly coupled to the tubes than the outside molecules. The energy exchange is facilitated by slow collective motions, including CNT radial breathing modes (RBM). The transfer rate between CNTs and the inside solvent shows strong dependence on the CNT diameter. In smaller tubes, the transfer is faster and the solvent coupling to RBMs is stronger. The magnitude of the CNT-outside solvent interaction scales with the CNT surface area, while that of the CNT-inside solvent exhibits scaling that is intermediate between the CNT volume and surface. The Coulomb interaction between the solvent molecules inside and outside of the CNTs is much weaker than the CNT-solvent interactions. The results indicate that the excitation energy supplied to CNTs in chemical and biological applications is rapidly deposited to the active molecular agents and should remain localized sufficiently long in order to perform the desired function.

The role of advanced reactive surface area characterization in improving predictions of mineral reaction rates

NASA Astrophysics Data System (ADS)

Beckingham, L. E.; Zhang, S.; Mitnick, E.; Cole, D. R.; Yang, L.; Anovitz, L. M.; Sheets, J.; Swift, A.; Kneafsey, T. J.; Landrot, G.; Mito, S.; Xue, Z.; Steefel, C. I.; DePaolo, D. J.; Ajo Franklin, J. B.

2014-12-01

Geologic sequestration of CO2 in deep sedimentary formations is a promising means of mitigating carbon emissions from coal-fired power plants but the long-term fate of injected CO2 is challenging to predict. Reactive transport models are used to gain insight over long times but rely on laboratory determined mineral reaction rates that have been difficult to extrapolate to field systems. This, in part, is due to a lack of understanding of mineral reactive surface area. Many models use an arbitrary approximation of reactive surface area, applying orders of magnitude scaling factors to measured BET or geometric surface areas. Recently, a few more sophisticated approaches have used 2D and 3D image analyses to determine mineral-specific reactive surface areas that account for the accessibility of minerals. However, the ability of these advanced surface area estimates to improve predictions of mineral reaction rates has yet to be determined. In this study, we fuse X-ray microCT, SEM QEMSCAN, XRD, SANS, and SEM-FIB analysis to determine mineral-specific accessible reactive surface areas for a core sample from the Nagaoka pilot CO2 injection site (Japan). This sample is primarily quartz, plagioclase, smectite, K-feldspar, and pyroxene. SEM imaging shows abundant smectite cement and grain coatings that decrease the fluid accessibility of other minerals. However, analysis of FIB-SEM images reveals that smectite nano-pores are well connected such that access to underlying minerals is not occluded by smectite coatings. Mineral-specific accessible surfaces are determined, accounting for the connectivity of the pore space with and without connected smectite nano-pores. The large-scale impact of variations in accessibility and dissolution rates are then determined through continuum scale modeling using grid-cell specific information on accessible surface areas. This approach will be compared with a traditional continuum scale model using mineral abundances and common surface area estimates. Ultimately, the effectiveness of advanced surface area characterization to improve mineral dissolution rates will be evaluated by comparison of model results with dissolution rates measured from a flow-through column experiment.

HippDB: a database of readily targeted helical protein-protein interactions.

PubMed

Bergey, Christina M; Watkins, Andrew M; Arora, Paramjit S

2013-11-01

HippDB catalogs every protein-protein interaction whose structure is available in the Protein Data Bank and which exhibits one or more helices at the interface. The Web site accepts queries on variables such as helix length and sequence, and it provides computational alanine scanning and change in solvent-accessible surface area values for every interfacial residue. HippDB is intended to serve as a starting point for structure-based small molecule and peptidomimetic drug development. HippDB is freely available on the web at http://www.nyu.edu/projects/arora/hippdb. The Web site is implemented in PHP, MySQL and Apache. Source code freely available for download at http://code.google.com/p/helidb, implemented in Perl and supported on Linux. arora@nyu.edu.

Spectroscopy and computational studies on the interaction of octyl, dodecyl, and hexadecyl derivatives of anionic and cationic surfactants with adenosine deaminase.

PubMed

Ajloo, Davood; Mahmoodabadi, Najmeh; Ghadamgahi, Maryam; Saboury, Ali Akbar

2016-07-01

Effects of sodium (octyl, dodecyl, hexadecyl) sulfate and their cationic analogous on the structure of adenosine deaminase (ADA) were investigated by fluorescence and circular dichroism spectroscopy as well as molecular dynamics simulation and docking calculation. Root-mean-square derivations, radius of gyration, solvent accessible surface area, and radial distribution function were obtained. The results showed that anionic and cationic surfactants reduce protein stability. Cationic surfactants have more effect on the ADA structure in comparison with anionic surfactants. More concentration and longer surfactants are parallel to higher denaturation. Furthermore, aggregation in the presence of anionic surfactants is more than cationic surfactants. Docking data showed that longer surfactants have more interaction energy and smaller ones bound to the active site.

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

PubMed

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.

Synthesis and characterization of binary titania-silica mixed oxides

NASA Astrophysics Data System (ADS)

Budhi, Sridhar

A series of binary titania-silica mixed oxides were synthesized by the sol-gel method at room temperature. The mixed oxides were prepared that involved the hydrolysis of titanium isopropoxide and tetraethylorthosilicate (TEOS) by co-solvent induced gelation usually in acidic media. The resulting gels were dried, calcined and then characterized by powder X-ray diffractometric studies, nitrogen sorption studies (at 77K), diffuse reflectance spectroscopy, Raman microscopy and transmission electron microscopic studies. The nitrogen sorption studies indicate that the specific surface areas, pore volume, pore diameter and pore size distribution of the mixed oxides were substantially enhanced when non-polar solvents such as toluene, p-xylene or mesitylene were added as co-solvents to the synthesis gel. Transmission electron microscopic (TEM) studies confirm the results obtained from the nitrogen sorption studies. Our results indicate that we can obtain binary metal oxides possessing high surface area and large pore volumes with tunable pore size distribution at room temperature. Photocatalytic evaluation of the mixed oxides is currently in progress.

Anti-solvent derived non-stacked reduced graphene oxide for high performance supercapacitors.

PubMed

Yoon, Yeoheung; Lee, Keunsik; Baik, Chul; Yoo, Heejoun; Min, Misook; Park, Younghun; Lee, Sae Mi; Lee, Hyoyoung

2013-08-27

An anti-solvent for graphene oxide (GO), hexane, is introduced to increase the surface area and the pore volume of the non-stacked GO/reduced GO 3D structure and allows the formation of a highly crumpled non-stacked GO powder, which clearly shows ideal supercapacitor behavior. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hazardous particle binder, coagulant and re-aerosolization inhibitor

DOEpatents

Krauter, Paula [Livermore, CA; Zalk, David [San Jose, CA; Hoffman, D Mark [Livermore, CA

2011-04-12

A copolymer and water/ethanol solvent solution capable of binding with airborne contaminants or potential airborne contaminants, such as biological weapon agents or toxic particulates, coagulating as the solvent evaporates, and adhering the contaminants to a surface so as to inhibit the re-suspension of such contaminants. The solution uses a water or ethanol/water mixture for the solvent, and a copolymer having one of several functional group sets so as to have physical and chemical characteristics of high adhesion, low viscosity, low surface tension, negative electrostatic charge, substantially neutral pH, and a low pKa. Use of the copolymer solution prevents re-aerosolization and transport of unwanted, reactive species thus increasing health and safety for personnel charged with decontamination of contaminated buildings and areas.

Hazardous particle binder, coagulant and re-aerosolization inhibitor

DOEpatents

Krauter, Paula; Zalk, David; Hoffman, D. Mark

2012-07-10

A copolymer and water/ethanol solvent solution capable of binding with airborne contaminants or potential airborne contaminants, such as biological weapon agents or toxic particulates, coagulating as the solvent evaporates, and adhering the contaminants to a surface so as to inhibit the re-suspension of such contaminants. The solution uses a water or ethanol/water mixture for the solvent, and a copolymer having one of several functional group sets so as to have physical and chemical characteristics of high adhesion, low viscosity, low surface tension, negative electrostatic charge, substantially neutral pH, and a low pKa. Use of the copolymer solution prevents re-aerosolization and transport of unwanted, reactive species thus increasing health and safety for personnel charged with decontamination of contaminated buildings and areas.

Surveying implicit solvent models for estimating small molecule absolute hydration free energies

PubMed Central

Knight, Jennifer L.

2011-01-01

Implicit solvent models are powerful tools in accounting for the aqueous environment at a fraction of the computational expense of explicit solvent representations. Here, we compare the ability of common implicit solvent models (TC, OBC, OBC2, GBMV, GBMV2, GBSW, GBSW/MS, GBSW/MS2 and FACTS) to reproduce experimental absolute hydration free energies for a series of 499 small neutral molecules that are modeled using AMBER/GAFF parameters and AM1-BCC charges. Given optimized surface tension coefficients for scaling the surface area term in the nonpolar contribution, most implicit solvent models demonstrate reasonable agreement with extensive explicit solvent simulations (average difference 1.0-1.7 kcal/mol and R2=0.81-0.91) and with experimental hydration free energies (average unsigned errors=1.1-1.4 kcal/mol and R2=0.66-0.81). Chemical classes of compounds are identified that need further optimization of their ligand force field parameters and others that require improvement in the physical parameters of the implicit solvent models themselves. More sophisticated nonpolar models are also likely necessary to more effectively represent the underlying physics of solvation and take the quality of hydration free energies estimated from implicit solvent models to the next level. PMID:21735452

Structure and dynamics of human vimentin intermediate filament dimer and tetramer in explicit and implicit solvent models.

PubMed

Qin, Zhao; Buehler, Markus J

2011-01-01

Intermediate filaments, in addition to microtubules and microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells, and play an important role in mechanotransduction as well as in providing mechanical stability to cells at large stretch. The molecular structures, mechanical and dynamical properties of the intermediate filament basic building blocks, the dimer and the tetramer, however, have remained elusive due to persistent experimental challenges owing to the large size and fibrillar geometry of this protein. We have recently reported an atomistic-level model of the human vimentin dimer and tetramer, obtained through a bottom-up approach based on structural optimization via molecular simulation based on an implicit solvent model (Qin et al. in PLoS ONE 2009 4(10):e7294, 9). Here we present extensive simulations and structural analyses of the model based on ultra large-scale atomistic-level simulations in an explicit solvent model, with system sizes exceeding 500,000 atoms and simulations carried out at 20 ns time-scales. We report a detailed comparison of the structural and dynamical behavior of this large biomolecular model with implicit and explicit solvent models. Our simulations confirm the stability of the molecular model and provide insight into the dynamical properties of the dimer and tetramer. Specifically, our simulations reveal a heterogeneous distribution of the bending stiffness along the molecular axis with the formation of rather soft and highly flexible hinge-like regions defined by non-alpha-helical linker domains. We report a comparison of Ramachandran maps and the solvent accessible surface area between implicit and explicit solvent models, and compute the persistence length of the dimer and tetramer structure of vimentin intermediate filaments for various subdomains of the protein. Our simulations provide detailed insight into the dynamical properties of the vimentin dimer and tetramer intermediate filament building blocks, which may guide the development of novel coarse-grained models of intermediate filaments, and could also help in understanding assembly mechanisms.

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

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

Ozen, C.; Norris, Adrianne; Land, Miriam L

2008-01-01

This work describes differential effects of solvent in complexes of the aminoglycoside phosphotransferase(3¢)-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 ¢H in H2O relative to D2O (¢¢H(H2O-D2O) < 0), while the reverse is true for neomycins. Unusually large negative ¢Cp values were observed for binding of aminoglycosides to APH. ¢Cp for the APHneomycin complex was -1.6 kcalâmol-1âdeg-1. A break at 30 C was observed in the APH-kanamycin complex yielding ¢Cp values of -0.7 kcalâmol-1âdeg-1 and -3.8 kcalâmol-1âdeg-1 below andmore » above 30 C, respectively. Neither the change in accessible surface area (¢ASA) nor contributions from heats of ionization were sufficient to explain the large negative ¢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 ¢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.« less

Materials Compatibility Testing in RSRM ODC: Free Cleaner Selection

NASA Technical Reports Server (NTRS)

Keen, Jill M.; Sagers, Neil W.; McCool, Alex (Technical Monitor)

2001-01-01

Government regulations have mandated production phase-outs of a number of solvents, including 1,1,1-trichloroethane, an ozone-depleting chemical (ODC). This solvent was used extensively in the production of the Reusable Solid Rocket Motors (RSRMs) for the Space Shuttle. Many tests have been performed to identify replacement cleaners. One major area of concern in the selection of a new cleaner has been compatibility. Some specific areas considered included cleaner compatibility with non-metallic surfaces, painted surfaces, support materials such as gloves and wipers as well as corrosive properties of the cleaners on the alloys used on these motors. The intent of this paper is to summarize the test logic, methodology, and results acquired from testing the many cleaner and material combinations.

Examination and Manipulation of Protein Surface Charge in Solution with Electrospray Ionization Mass Spectrometry

ERIC Educational Resources Information Center

Gross, Deborah S.; Van Ryswyk, Hal

2014-01-01

Electrospray ionization mass spectrometry (ESI-MS) is a powerful tool for examining the charge of proteins in solution. The charge can be manipulated through choice of solvent and pH. Furthermore, solution-accessible, protonated lysine side chains can be specifically tagged with 18-crown-6 ether to form noncovalent adducts. Chemical derivatization…

A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction.

PubMed

Deng, Lei; Fan, Chao; Zeng, Zhiwen

2017-12-28

Direct prediction of the three-dimensional (3D) structures of proteins from one-dimensional (1D) sequences is a challenging problem. Significant structural characteristics such as solvent accessibility and contact number are essential for deriving restrains in modeling protein folding and protein 3D structure. Thus, accurately predicting these features is a critical step for 3D protein structure building. In this study, we present DeepSacon, a computational method that can effectively predict protein solvent accessibility and contact number by using a deep neural network, which is built based on stacked autoencoder and a dropout method. The results demonstrate that our proposed DeepSacon achieves a significant improvement in the prediction quality compared with the state-of-the-art methods. We obtain 0.70 three-state accuracy for solvent accessibility, 0.33 15-state accuracy and 0.74 Pearson Correlation Coefficient (PCC) for the contact number on the 5729 monomeric soluble globular protein dataset. We also evaluate the performance on the CASP11 benchmark dataset, DeepSacon achieves 0.68 three-state accuracy and 0.69 PCC for solvent accessibility and contact number, respectively. We have shown that DeepSacon can reliably predict solvent accessibility and contact number with stacked sparse autoencoder and a dropout approach.

Residue solvent accessibilities in the unfolded polypeptide chain.

PubMed Central

Zielenkiewicz, P; Saenger, W

1992-01-01

The difference of solvent accessibilities in the native and unfolded states of the protein is used as a measure of the hydrophobic contribution to the free energy of folding. We present a new approximation of amino acids solvent accessibilities in the unfolded state based on the 1-ns molecular dynamics simulation of Ala-X-Ala tripeptides at a temperature of 368 K. The standard accessibility values averaged from the molecular dynamics study are significantly lower from those previously obtained by considering only selected conformations of Ala-X-Ala tripeptides. PMID:1489908

A QSPR study on the solvent-induced frequency shifts of acetone and dimethyl sulfoxide in organic solvents.

PubMed

Ou, Yu Heng; Chang, Chia Ming; Chen, Ying Shao

2016-06-05

In this study, solvent-induced frequency shifts (SIFS) in the infrared spectrum of acetone and dimethyl sulfoxide in organic solvents were investigated by using four types of quantum-chemical reactivity descriptors. The results showed that the SIFS of acetone is mainly affected by the electron-acceptance chemical potential and the maximum nucleophilic condensed local softness of organic solvents, which represent the electron flow and the polarization between acetone and solvent molecules. On the other hand, the SIFS of dimethyl sulfoxide changes with the maximum positive charge of hydrogen atom and the inverse of apolar surface area of solvent molecules, showing that the electrostatic and hydrophilic interactions are main mechanisms between dimethyl sulfoxide and solvent molecules. The introduction of the four-element theory model-based quantitative structure-property relationship approach improved the assessing quality and provided a basis for interpreting the solute-solvent interactions. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular surface area based predictive models for the adsorption and diffusion of disperse dyes in polylactic acid matrix.

PubMed

Xu, Suxin; Chen, Jiangang; Wang, Bijia; Yang, Yiqi

2015-11-15

Two predictive models were presented for the adsorption affinities and diffusion coefficients of disperse dyes in polylactic acid matrix. Quantitative structure-sorption behavior relationship would not only provide insights into sorption process, but also enable rational engineering for desired properties. The thermodynamic and kinetic parameters for three disperse dyes were measured. The predictive model for adsorption affinity was based on two linear relationships derived by interpreting the experimental measurements with molecular structural parameters and compensation effect: ΔH° vs. dye size and ΔS° vs. ΔH°. Similarly, the predictive model for diffusion coefficient was based on two derived linear relationships: activation energy of diffusion vs. dye size and logarithm of pre-exponential factor vs. activation energy of diffusion. The only required parameters for both models are temperature and solvent accessible surface area of the dye molecule. These two predictive models were validated by testing the adsorption and diffusion properties of new disperse dyes. The models offer fairly good predictive ability. The linkage between structural parameter of disperse dyes and sorption behaviors might be generalized and extended to other similar polymer-penetrant systems. Copyright © 2015 Elsevier Inc. All rights reserved.

Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR.

PubMed

Westermaier, Yvonne; Ruiz-Carmona, Sergio; Theret, Isabelle; Perron-Sierra, Françoise; Poissonnet, Guillaume; Dacquet, Catherine; Boutin, Jean A; Ducrot, Pierre; Barril, Xavier

2017-08-01

The knowledge of the free energy of binding of small molecules to a macromolecular target is crucial in drug design as is the ability to predict the functional consequences of binding. We highlight how a molecular dynamics (MD)-based approach can be used to predict the free energy of small molecules, and to provide priorities for the synthesis and the validation via in vitro tests. Here, we study the dynamics and energetics of the nuclear receptor REV-ERBα with its co-repressor NCoR and 35 novel agonists. Our in silico approach combines molecular docking, molecular dynamics (MD), solvent-accessible surface area (SASA) and molecular mechanics poisson boltzmann surface area (MMPBSA) calculations. While docking yielded initial hints on the binding modes, their stability was assessed by MD. The SASA calculations revealed that the presence of the ligand led to a higher exposure of hydrophobic REV-ERB residues for NCoR recruitment. MMPBSA was very successful in ranking ligands by potency in a retrospective and prospective manner. Particularly, the prospective MMPBSA ranking-based validations for four compounds, three predicted to be active and one weakly active, were confirmed experimentally.

Numerical Integration Techniques for Curved-Element Discretizations of Molecule–Solvent Interfaces

PubMed Central

Bardhan, Jaydeep P.; Altman, Michael D.; Willis, David J.; Lippow, Shaun M.; Tidor, Bruce; White, Jacob K.

2012-01-01

Surface formulations of biophysical modeling problems offer attractive theoretical and computational properties. Numerical simulations based on these formulations usually begin with discretization of the surface under consideration; often, the surface is curved, possessing complicated structure and possibly singularities. Numerical simulations commonly are based on approximate, rather than exact, discretizations of these surfaces. To assess the strength of the dependence of simulation accuracy on the fidelity of surface representation, we have developed methods to model several important surface formulations using exact surface discretizations. Following and refining Zauhar’s work (J. Comp.-Aid. Mol. Des. 9:149-159, 1995), we define two classes of curved elements that can exactly discretize the van der Waals, solvent-accessible, and solvent-excluded (molecular) surfaces. We then present numerical integration techniques that can accurately evaluate nonsingular and singular integrals over these curved surfaces. After validating the exactness of the surface discretizations and demonstrating the correctness of the presented integration methods, we present a set of calculations that compare the accuracy of approximate, planar-triangle-based discretizations and exact, curved-element-based simulations of surface-generalized-Born (sGB), surface-continuum van der Waals (scvdW), and boundary-element method (BEM) electrostatics problems. Results demonstrate that continuum electrostatic calculations with BEM using curved elements, piecewise-constant basis functions, and centroid collocation are nearly ten times more accurate than planartriangle BEM for basis sets of comparable size. The sGB and scvdW calculations give exceptional accuracy even for the coarsest obtainable discretized surfaces. The extra accuracy is attributed to the exact representation of the solute–solvent interface; in contrast, commonly used planar-triangle discretizations can only offer improved approximations with increasing discretization and associated increases in computational resources. The results clearly demonstrate that our methods for approximate integration on an exact geometry are far more accurate than exact integration on an approximate geometry. A MATLAB implementation of the presented integration methods and sample data files containing curved-element discretizations of several small molecules are available online at http://web.mit.edu/tidor. PMID:17627358

Efficient minimization of multipole electrostatic potentials in torsion space

PubMed Central

Bodmer, Nicholas K.

2018-01-01

The development of models of macromolecular electrostatics capable of delivering improved fidelity to quantum mechanical calculations is an active field of research in computational chemistry. Most molecular force field development takes place in the context of models with full Cartesian coordinate degrees of freedom. Nevertheless, a number of macromolecular modeling programs use a reduced set of conformational variables limited to rotatable bonds. Efficient algorithms for minimizing the energies of macromolecular systems with torsional degrees of freedom have been developed with the assumption that all atom-atom interaction potentials are isotropic. We describe novel modifications to address the anisotropy of higher order multipole terms while retaining the efficiency of these approaches. In addition, we present a treatment for obtaining derivatives of atom-centered tensors with respect to torsional degrees of freedom. We apply these results to enable minimization of the Amoeba multipole electrostatics potential in a system with torsional degrees of freedom, and validate the correctness of the gradients by comparison to finite difference approximations. In the interest of enabling a complete model of electrostatics with implicit treatment of solvent-mediated effects, we also derive expressions for the derivative of solvent accessible surface area with respect to torsional degrees of freedom. PMID:29641557

Evaluation of accessible mineral surface areas for improved prediction of mineral reaction rates in porous media

NASA Astrophysics Data System (ADS)

Beckingham, Lauren E.; Steefel, Carl I.; Swift, Alexander M.; Voltolini, Marco; Yang, Li; Anovitz, Lawrence M.; Sheets, Julia M.; Cole, David R.; Kneafsey, Timothy J.; Mitnick, Elizabeth H.; Zhang, Shuo; Landrot, Gautier; Ajo-Franklin, Jonathan B.; DePaolo, Donald J.; Mito, Saeko; Xue, Ziqiu

2017-05-01

The rates of mineral dissolution reactions in porous media are difficult to predict, in part because of a lack of understanding of mineral reactive surface area in natural porous media. Common estimates of mineral reactive surface area used in reactive transport models for porous media are typically ad hoc and often based on average grain size, increased to account for surface roughness or decreased by several orders of magnitude to account for reduced surface reactivity of field as opposed to laboratory samples. In this study, accessible mineral surface areas are determined for a sample from the reservoir formation at the Nagaoka pilot CO2 injection site (Japan) using a multi-scale image analysis based on synchrotron X-ray microCT, SEM QEMSCAN, XRD, SANS, and FIB-SEM. This analysis not only accounts for accessibility of mineral surfaces to macro-pores, but also accessibility through connected micro-pores in smectite, the most abundant clay mineral in this sample. While the imaging analysis reveals that most of the micro- and macro-pores are well connected, some pore regions are unconnected and thus inaccessible to fluid flow and diffusion. To evaluate whether mineral accessible surface area accurately reflects reactive surface area a flow-through core experiment is performed and modeled at the continuum scale. The core experiment is performed under conditions replicating the pilot site and the evolution of effluent solutes in the aqueous phase is tracked. Various reactive surface area models are evaluated for their ability to capture the observed effluent chemistry, beginning with parameter values determined as a best fit to a disaggregated sediment experiment (Beckingham et al., 2016) described previously. Simulations that assume that all mineral surfaces are accessible (as in the disaggregated sediment experiment) over-predict the observed mineral reaction rates, suggesting that a reduction of RSA by a factor of 10-20 is required to match the core flood experimental data. While the fit of the effluent chemistry (and inferred mineral dissolution rates) greatly improve when the pore-accessible mineral surface areas are used, it was also necessary to include highly reactive glass phases to match the experimental observations, in agreement with conclusions from the disaggregated sediment experiment. It is hypothesized here that the 10-20 reduction in reactive surface areas based on the limited pore accessibility of reactive phases in core flood experiment may be reasonable for poorly sorted and cemented sediments like those at the Nagaoka site, although this reflects pore rather than larger scale heterogeneity.

Residual contamination and corrosion on electrochemically marked uranium

NASA Astrophysics Data System (ADS)

Seals, R. D.; Bullock, J. S.; Cristy, S. S.; Bennett, R. K.

Residual contamination and potential corrosion problems on uranium parts electrochemically marked with PHB-1 and PHB-1E electroetchants have been investigated using ion microprobe mass analysis (IMMA), scanning electron microscopy (SEM), and light microscopy (LM). The effectiveness of various solvent-cleaning sequences and the influence of the use of an abrasive cleaner were evaluated. The corrosion depths and chlorine distributions resulting from the electroetching process were determined. To meet the objective, the surfaces of uranium coupons, which had been processed according to production procedures for parts, i.e., machining, cleaning, marking, inspecting and coating with Shell Vitrea-29® oil, were studied. The greater surface wetting capability of the PHB-1E electroetchant solution relative to PHB-1 resulted in less localized corrosion at the point of attack which provided a more legible mark. Components of the electroetchants (aluminum, potassium and chromium) were found in the marked areas of both types of electroetched samples. Chromium, resulting from the corrosion inhibitor in the electroetchants, was found in the etched areas as well as on the coupon away from the electroetched areas. Depth profile data indicated that the major etching action (marking thickness) of the electroetchants penetrated to a depth of approximately 200 nm. Trace amounts of chlorine were present primarily within the first 65 nm of the marked surface. Comparison of the solvent rinsing sequences revealed that the most effective cleaning process included a degreaser, such as perchloroethylene, followed by a polar solvent, such as alcohol. Evaluation of the use of an abrasive cleaner on the electroetched areas indicates that this process removed residual contaminants, increased mark legibility and did not introduce significant residuals from the abrading material or cause significant surface damage.

Nonadiabatic dynamics of electron transfer in solution: Explicit and implicit solvent treatments that include multiple relaxation time scales

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

Schwerdtfeger, Christine A.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon, E-mail: shs3@illinois.edu

2014-01-21

The development of efficient theoretical methods for describing electron transfer (ET) reactions in condensed phases is important for a variety of chemical and biological applications. Previously, dynamical dielectric continuum theory was used to derive Langevin equations for a single collective solvent coordinate describing ET in a polar solvent. In this theory, the parameters are directly related to the physical properties of the system and can be determined from experimental data or explicit molecular dynamics simulations. Herein, we combine these Langevin equations with surface hopping nonadiabatic dynamics methods to calculate the rate constants for thermal ET reactions in polar solvents formore » a wide range of electronic couplings and reaction free energies. Comparison of explicit and implicit solvent calculations illustrates that the mapping from explicit to implicit solvent models is valid even for solvents exhibiting complex relaxation behavior with multiple relaxation time scales and a short-time inertial response. The rate constants calculated for implicit solvent models with a single solvent relaxation time scale corresponding to water, acetonitrile, and methanol agree well with analytical theories in the Golden rule and solvent-controlled regimes, as well as in the intermediate regime. The implicit solvent models with two relaxation time scales are in qualitative agreement with the analytical theories but quantitatively overestimate the rate constants compared to these theories. Analysis of these simulations elucidates the importance of multiple relaxation time scales and the inertial component of the solvent response, as well as potential shortcomings of the analytical theories based on single time scale solvent relaxation models. This implicit solvent approach will enable the simulation of a wide range of ET reactions via the stochastic dynamics of a single collective solvent coordinate with parameters that are relevant to experimentally accessible systems.« less

Method for producing high surface area chromia materials for catalysis

DOEpatents

Gash, Alexander E [Brentwood, CA; Satcher, Joe [Patterson, CA; Tillotson, Thomas [Tracy, CA; Hrubesh, Lawrence [Pleasanton, CA; Simpson, Randall [Livermore, CA

2007-05-01

Nanostructured chromium(III)-oxide-based materials using sol-gel processing and a synthetic route for producing such materials are disclosed herein. Monolithic aerogels and xerogels having surface areas between 150 m.sup.2/g and 520 m.sup.2/g have been produced. The synthetic method employs the use of stable and inexpensive hydrated-chromium(III) inorganic salts and common solvents such as water, ethanol, methanol, 1-propanol, t-butanol, 2-ethoxy ethanol, and ethylene glycol, DMSO, and dimethyl formamide. The synthesis involves the dissolution of the metal salt in a solvent followed by an addition of a proton scavenger, such as an epoxide, which induces gel formation in a timely manner. Both critical point (supercritical extraction) and atmospheric (low temperature evaporation) drying may be employed to produce monolithic aerogels and xerogels, respectively.

1D vs. 2D shape selectivity in the crystallization-driven self-assembly of polylactide block copolymers.

PubMed

Inam, Maria; Cambridge, Graeme; Pitto-Barry, Anaïs; Laker, Zachary P L; Wilson, Neil R; Mathers, Robert T; Dove, Andrew P; O'Reilly, Rachel K

2017-06-01

2D materials such as graphene, LAPONITE® clays or molybdenum disulfide nanosheets are of extremely high interest to the materials community as a result of their high surface area and controllable surface properties. While several methods to access 2D inorganic materials are known, the investigation of 2D organic nanomaterials is less well developed on account of the lack of ready synthetic accessibility. Crystallization-driven self-assembly (CDSA) has become a powerful method to access a wide range of complex but precisely-defined nanostructures. The preparation of 2D structures, however, particularly those aimed towards biomedical applications, is limited, with few offering biocompatible and biodegradable characteristics as well as control over self-assembly in two dimensions. Herein, in contrast to conventional self-assembly rules, we show that the solubility of polylactide (PLLA)-based amphiphiles in alcohols results in unprecedented shape selectivity based on unimer solubility. We use log  P oct analysis to drive solvent selection for the formation of large uniform 2D diamond-shaped platelets, up to several microns in size, using long, soluble coronal blocks. By contrast, less soluble PLLA-containing block copolymers yield cylindrical micelles and mixed morphologies. The methods developed in this work provide a simple and consistently reproducible protocol for the preparation of well-defined 2D organic nanomaterials, whose size and morphology are expected to facilitate potential applications in drug delivery, tissue engineering and in nanocomposites.

Semiconductor surface protection material

NASA Technical Reports Server (NTRS)

Packard, R. D. (Inventor)

1973-01-01

A method and a product for protecting semiconductor surfaces is disclosed. The protective coating material is prepared by heating a suitable protective resin with an organic solvent which is solid at room temperature and converting the resulting solution into sheets by a conventional casting operation. Pieces of such sheets of suitable shape and thickness are placed on the semiconductor areas to be coated and heat and vacuum are then applied to melt the sheet and to drive off the solvent and cure the resin. A uniform adherent coating, free of bubbles and other defects, is thus obtained exactly where it is desired.

PACSY, a relational database management system for protein structure and chemical shift analysis.

PubMed

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

2012-10-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

Thermodynamic properties of water solvating biomolecular surfaces

NASA Astrophysics Data System (ADS)

Heyden, Matthias

Changes in the potential energy and entropy of water molecules hydrating biomolecular interfaces play a significant role for biomolecular solubility and association. Free energy perturbation and thermodynamic integration methods allow calculations of free energy differences between two states from simulations. However, these methods are computationally demanding and do not provide insights into individual thermodynamic contributions, i.e. changes in the solvent energy or entropy. Here, we employ methods to spatially resolve distributions of hydration water thermodynamic properties in the vicinity of biomolecular surfaces. This allows direct insights into thermodynamic signatures of the hydration of hydrophobic and hydrophilic solvent accessible sites of proteins and small molecules and comparisons to ideal model surfaces. We correlate dynamic properties of hydration water molecules, i.e. translational and rotational mobility, to their thermodynamics. The latter can be used as a guide to extract thermodynamic information from experimental measurements of site-resolved water dynamics. Further, we study energy-entropy compensations of water at different hydration sites of biomolecular surfaces. This work is supported by the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft.

Deep eutectic-solvothermal synthesis of nanostructured ceria

PubMed Central

Hammond, Oliver S.; Edler, Karen J.; Bowron, Daniel T.; Torrente-Murciano, Laura

2017-01-01

Ceria is a technologically important material with applications in catalysis, emissions control and solid-oxide fuel cells. Nanostructured ceria becomes profoundly more active due to its enhanced surface area to volume ratio, reactive surface oxygen vacancy concentration and superior oxygen storage capacity. Here we report the synthesis of nanostructured ceria using the green Deep Eutectic Solvent reline, which allows morphology and porosity control in one of the less energy-intensive routes reported to date. Using wide Q-range liquid-phase neutron diffraction, we elucidate the mechanism of reaction at a molecular scale at considerably milder conditions than the conventional hydrothermal synthetic routes. The reline solvent plays the role of a latent supramolecular catalyst where the increase in reaction rate from solvent-driven pre-organization of the reactants is most significant. This fundamental understanding of deep eutectic-solvothermal methodology will enable future developments in low-temperature synthesis of nanostructured ceria, facilitating its large-scale manufacturing using green, economic, non-toxic solvents. PMID:28120829

Aromatic Rings Commonly Used in Medicinal Chemistry: Force Fields Comparison and Interactions With Water Toward the Design of New Chemical Entities.

PubMed

Polêto, Marcelo D; Rusu, Victor H; Grisci, Bruno I; Dorn, Marcio; Lins, Roberto D; Verli, Hugo

2018-01-01

The identification of lead compounds usually includes a step of chemical diversity generation. Its rationale may be supported by both qualitative (SAR) and quantitative (QSAR) approaches, offering models of the putative ligand-receptor interactions. In both scenarios, our understanding of which interactions functional groups can perform is mostly based on their chemical nature (such as electronegativity, volume, melting point, lipophilicity etc.) instead of their dynamics in aqueous, biological solutions (solvent accessibility, lifetime of hydrogen bonds, solvent structure etc.). As a consequence, it is challenging to predict from 2D structures which functional groups will be able to perform interactions with the target receptor, at which intensity and relative abundance in the biological environment, all of which will contribute to ligand potency and intrinsic activity. With this in mind, the aim of this work is to assess properties of aromatic rings, commonly used for drug design, in aqueous solution through molecular dynamics simulations in order to characterize their chemical features and infer their impact in complexation dynamics. For this, common aromatic and heteroaromatic rings were selected and received new atomic charge set based on the direction and module of the dipole moment from MP2/6-31G * calculations, while other topological terms were taken from GROMOS53A6 force field. Afterwards, liquid physicochemical properties were simulated for a calibration set composed by nearly 40 molecules and compared to their respective experimental data, in order to validate each topology. Based on the reliance of the employed strategy, we expanded the dataset to more than 100 aromatic rings. Properties in aqueous solution such as solvent accessible surface area, H-bonds availability, H-bonds residence time, and water structure around heteroatoms were calculated for each ring, creating a database of potential interactions, shedding light on features of drugs in biological solutions, on the structural basis for bioisosterism and on the enthalpic/entropic costs for ligand-receptor complexation dynamics.

The solvent dependent shift of the amide I band of a fully solvated peptide in methanol/water mixtures as a local probe for the solvent composition in the peptide/solvent interface

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

Gnanakaran, S

2008-01-01

We determine the shift and line-shape of the amide I band of a model AK-peptide from molecular dynamics (MD) simulations of the peptide dissolved in methanol/water mixtures with varying composition. The IR-spectra are determined from a transition dipole coupling exciton model. A simplified empirical model Hamiltonian is employed, taking both the effect of hydrogen bonding, as well as intramolecular vibrational coupling into account. We consider a single isolated AK-peptide in a mostly helical conformation, while the solvent is represented by 2600 methanol or water molecules, simulated for a pressure of 1 bar and a temperature of 300 K. Over themore » course of the simulations minor reversible conformational changes at the termini are observed, which are found to only slightly affect the calculated spectral properties. Over the entire composition range, varying from pure water to the pure methanol solvent, a monotonous blue-shift of the IR amide I band of about 8 wavenumbers is observed. The shift is found to be caused by two counter-compensating effects: An intramolecular red-shift of about 1.2 wavenumbers, due to stronger intramolecular hydrogen-bonding in a methanol-rich environment. Dominating, however, is the intermolecular solvent-dependent blue-shift of about 10 wavenumbers, being attributed to the less effective hydrogen bond donor capabilities of methanol compared to water. The importance of solvent-contribution to the IR-shift, as well as the significantly different hydrogen formation capabilities of water and methanol make the amide I band sensitive to composition changes in the local environment close the peptide/solvent interface. This allows, in principle, an experimental determination of the composition of the solvent in close proximity to the peptide surface. For the AK-peptide case they observe at low methanol concentrations a significantly enhanced methanol concentration at the peptide/solvent-interface, supposedly promoted by the partially hydrophobic character of the AK-peptide's solvent accessible surface.« less

Long-range single domain array of a 5 nm pattern of supramolecules via solvent annealing in a double-sandwich cell.

PubMed

Kwon, Kiok; Park, Kangho; Jung, Hee-Tae

2018-05-10

In nanotechnology and microelectronics research, the generation of an ultradense, single-grain nanostructure with a long-range lateral order is challenging. In this paper, we report upon a new solvent-annealing method using a double-sandwich confinement to promote the formation of a large-area, single-domain array (>0.3 × 0.3 mm2) of supramolecular cylinders with a small feature size (4.7 nm). The in situ GISAXS experiment result shows the ordering process during solvent evaporation. The diffusion of the solvent molecules led to the disassembly of the supramolecules confined between the top and bottom surfaces and their subsequent mobilization, thereby producing a highly ordered hexagonal array of supramolecular materials under the double-sandwich confinement upon solvent evaporation. In addition, two key factors were found to be crucial in this process for generating highly-ordered supramolecular building blocks: (i) the presence of a top coat during solvent evaporation to provide a geometric confinement template, and (ii) the control of the solvent evaporation rate during the solvent evaporation step to provide the dendrimer sufficient time to self-assemble into the highly ordered state over a large area. Our developed approach, which can be extended to be used for a large family of supramolecules, is of critical importance in providing a new bottom-up lithographic method based on supramolecular self-assembly.

10.6% Certified Colloidal Quantum Dot Solar Cells via Solvent-Polarity-Engineered Halide Passivation.

PubMed

Lan, Xinzheng; Voznyy, Oleksandr; García de Arquer, F Pelayo; Liu, Mengxia; Xu, Jixian; Proppe, Andrew H; Walters, Grant; Fan, Fengjia; Tan, Hairen; Liu, Min; Yang, Zhenyu; Hoogland, Sjoerd; Sargent, Edward H

2016-07-13

Colloidal quantum dot (CQD) solar cells are solution-processed photovoltaics with broad spectral absorption tunability. Major advances in their efficiency have been made via improved CQD surface passivation and device architectures with enhanced charge carrier collection. Herein, we demonstrate a new strategy to improve further the passivation of CQDs starting from the solution phase. A cosolvent system is employed to tune the solvent polarity in order to achieve the solvation of methylammonium iodide (MAI) and the dispersion of hydrophobic PbS CQDs simultaneously in a homogeneous phase, otherwise not achieved in a single solvent. This process enables MAI to access the CQDs to confer improved passivation. This, in turn, allows for efficient charge extraction from a thicker photoactive layer device, leading to a certified solar cell power conversion efficiency of 10.6%, a new certified record in CQD photovoltaics.

Preparation and Characterization of Single Ion Conductors from High Surface Area Fumed Silica

NASA Technical Reports Server (NTRS)

Zhang, H.; Maitra, P.; Liu, B.; Wunder, S. L.; Lin, H.-P.; Salomon, M.; Hagedorn, Norman H. (Technical Monitor)

2002-01-01

Anions that can form dissociative salts with Li(+) have been prepared and covalently attached to high surface area fumed silica. When blended with polyethylene oxide (PEO), the functionalized fumed silica suppresses the crystallization of the PEO, provides dimensional stability, and serves as a single ion conductor. Since functionalized fumed silica is easily dispersed in common polar solvents, it can be incorporated in both the polymer electrolyte and the electrodes.

Role of solvent in metal-on-metal surface diffusion: A case for rational solvent selection for materials synthesis

NASA Astrophysics Data System (ADS)

Imandi, Venkataramana; Jagannath, Mantha Sai Pavan; Chatterjee, Abhijit

2018-09-01

The effect of solvent on diffusion at metal surfaces is poorly understood despite its importance to morphological evolution during materials processing, corrosion and catalysis. In this article, we probe the metal-solvent interfacial structure, effective nature of interactions and dynamics when a solvent is in contact with a metal using a novel accelerated molecular dynamics simulation technique called temperature programmed molecular dynamics (TPMD). TPMD simulations reveal that surface diffusion of metal-on-metal can be made to vary over orders-of-magnitude by tuning the metal-solvent interaction. Ultimately, the solvent can have an indirect effect on diffusion. As the solvent tugs at the metal surface the separation between the adsorbed metal atom (adatom) and the surface layer can be modulated via metal-solvent interactions. The resulting adatom-surface separation can cause stronger/weaker binding of the adatom to the metal surface, which in turn results in the observed slower/enhanced diffusion in the presence of solvent. We believe this effect is ubiquitous in pure metal and metal alloys and in principle one could rationally select solvent to control the material structural evolution. Implications on materials synthesis are discussed in the context of formation of nanoporous materials.

Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure.

PubMed

Olechnovic, Kliment; Margelevicius, Mindaugas; Venclovas, Ceslovas

2011-03-01

We present Voroprot, an interactive cross-platform software tool that provides a unique set of capabilities for exploring geometric features of protein structure. Voroprot allows the construction and visualization of the Apollonius diagram (also known as the additively weighted Voronoi diagram), the Apollonius graph, protein alpha shapes, interatomic contact surfaces, solvent accessible surfaces, pockets and cavities inside protein structure. Voroprot is available for Windows, Linux and Mac OS X operating systems and can be downloaded from http://www.ibt.lt/bioinformatics/voroprot/.

Mesoporous-silica films, fibers, and powders by evaporation

DOEpatents

Bruinsma, Paul J.; Baskaran, Suresh; Bontha, Jagannadha R.; Liu, Jun

2008-05-06

This invention pertains to surfactant-templated nanometer-scale porosity of a silica precursor solution and forming a mesoporous material by first forming the silica precursor solution into a preform having a high surface area to volume ratio, then rapid drying or evaporating a solvent from the silica precursor solution. The mesoporous material may be in any geometric form, but is preferably in the form of a film, fiber, powder or combinations thereof. The rapid drying or evaporation of solvent from the solution is accomplished by layer thinning, for example spin casting, liquid drawing, and liquid spraying respectively. Production of a film is by layer thinning, wherein a layer of the silica precursor solution is formed on a surface followed by removal of an amount of the silica precursor solution and leaving a geometrically thinner layer of the silica precursor solution from which the solvent quickly escapes via evaporation. Layer thinning may be by any method including but not limited to squeegeeing and/or spin casting. In powder formation by spray drying, the same conditions of fast drying exists as in spin-casting (as well as in fiber spinning) because of the high surface-area to volume ratio of the product. When a powder is produced by liquid spraying, the particles or micro-bubbles within the powder are hollow spheres with walls composed of mesoporous silica. Mesoporous fiber formation starts with a similar silica precursor solution but with an added pre-polymer making a pituitous mixture that is drawn into a thin strand from which solvent is evaporated leaving the mesoporous fiber(s).

Mesoporous-silica films, fibers, and powders by evaporation

DOEpatents

Bruinsma, Paul J.; Baskaran, Suresh; Bontha, Jagannadha R.; Liu, Jun

1999-01-01

This invention pertains to surfactant-templated nanometer-scale porosity of a silica precursor solution and forming a mesoporous material by first forming the silica precursor solution into a preform having a high surface area to volume ratio, then rapid drying or evaporating a solvent from the silica precursor solution. The mesoporous material may be in any geometric form, but is preferably in the form of a film, fiber, powder or combinations thereof. The rapid drying or evaporation of solvent from the solution is accomplished by layer thinning, for example spin casting, liquid drawing, and liquid spraying respectively. Production of a film is by layer thinning, wherein a layer of the silica precursor solution is formed on a surface followed by removal of an amount of the silica precursor solution and leaving a geometrically thinner layer of the silica precursor solution from which the solvent quickly escapes via evaporation. Layer thinning may be by any method including but not limited to squeegeeing and/or spin casting. In powder formation by spray drying, the same conditions of fast drying exists as in spin-casting (as well as in fiber spinning) because of the high surface-area to volume ratio of the product. When a powder is produced by liquid spraying, the particles or micro-bubbles within the powder are hollow spheres with walls composed of mesoporous silica. Mesoporous fiber formation starts with a similar silica precursor solution but with an added pre-polymer making a pituitous mixture that is drawn into a thin strand from which solvent is evaporated leaving the mesoporous fiber(s).

Mesoporous-silica films, fibers, and powders by evaporation

DOEpatents

Bruinsma, P.J.; Baskaran, S.; Bontha, J.R.; Liu, J.

1999-07-13

This invention pertains to surfactant-templated nanometer-scale porosity of a silica precursor solution and forming a mesoporous material by first forming the silica precursor solution into a preform having a high surface area to volume ratio, then rapid drying or evaporating a solvent from the silica precursor solution. The mesoporous material may be in any geometric form, but is preferably in the form of a film, fiber, powder or combinations thereof. The rapid drying or evaporation of solvent from the solution is accomplished by layer thinning, for example spin casting, liquid drawing, and liquid spraying respectively. Production of a film is by layer thinning, wherein a layer of the silica precursor solution is formed on a surface followed by removal of an amount of the silica precursor solution and leaving a geometrically thinner layer of the silica precursor solution from which the solvent quickly escapes via evaporation. Layer thinning may be by any method including but not limited to squeegeeing and/or spin casting. In powder formation by spray drying, the same conditions of fast drying exists as in spin-casting (as well as in fiber spinning) because of the high surface-area to volume ratio of the product. When a powder is produced by liquid spraying, the particles or micro-bubbles within the powder are hollow spheres with walls composed of mesoporous silica. Mesoporous fiber formation starts with a similar silica precursor solution but with an added pre-polymer making a pituitous mixture that is drawn into a thin strand from which solvent is evaporated leaving the mesoporous fiber(s). 24 figs.

Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents

PubMed Central

Mohamad Ali, Mohd Shukuri; Salleh, Abu Bakar; Rahman, Raja Noor Zaliha Raja Abd; Normi, Yahaya M.; Mohd Shariff, Fairolniza

2017-01-01

The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD) of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol) and water mixture systems to a concentration of 50%. On the basis of the MD results, the structural deviations of the backbone atoms elucidated the dynamic effects of water/organic solvent mixtures on the equilibrium state of the protein simulations in decreasing solvent polarity. The results show that the solvent mixture gives rise to deviations in enzyme structure from the native one simulated in water. The drop in the flexibility in H2O, MtOH, EtOH and PrOH simulation mixtures shows that greater motions of residues were influenced in BtOH and PtOH simulation mixtures. Comparing the root mean square fluctuations value with the accessible solvent area (SASA) for every residue showed an almost correspondingly high SASA value of residues to high flexibility and low SASA value to low flexibility. The study further revealed that the organic solvents influenced the formation of more hydrogen bonds in MtOH, EtOH and PrOH and thus, it is assumed that increased intraprotein hydrogen bonding is ultimately correlated to the stability of the protein. However, the solvent accessibility analysis showed that in all solvent systems, hydrophobic residues were exposed and polar residues tended to be buried away from the solvent. Distance variation of the tetrahedral intermediate packing of the active pocket was not conserved in organic solvent systems, which could lead to weaknesses in the catalytic H-bond network and most likely a drop in catalytic activity. The conformational variation of the lid domain caused by the solvent molecules influenced its gradual opening. Formation of additional hydrogen bonds and hydrophobic interactions indicates that the contribution of the cooperative network of interactions could retain the stability of the protein in some solvent systems. Time-correlated atomic motions were used to characterize the correlations between the motions of the atoms from atomic coordinates. The resulting cross-correlation map revealed that the organic solvent mixtures performed functional, concerted, correlated motions in regions of residues of the lid domain to other residues. These observations suggest that varying lengths of polar organic solvents play a significant role in introducing dynamic conformational diversity in proteins in a decreasing order of polarity. PMID:28533982

Practical implications of some recent studies in electrospray ionization fundamentals.

PubMed

Cech, N B; Enke, C G

2001-01-01

In accomplishing successful electrospray ionization analyses, it is imperative to have an understanding of the effects of variables such as analyte structure, instrumental parameters, and solution composition. Here, we review some fundamental studies of the ESI process that are relevant to these issues. We discuss how analyte chargeability and surface activity are related to ESI response, and how accessible parameters such as nonpolar surface area and reversed phase HPLC retention time can be used to predict relative ESI response. Also presented is a description of how derivitizing agents can be used to maximize or enable ESI response by improving the chargeability or hydrophobicity of ESI analytes. Limiting factors in the ESI calibration curve are discussed. At high concentrations, these factors include droplet surface area and excess charge concentration, whereas at low concentrations ion transmission becomes an issue, and chemical interference can also be limiting. Stable and reproducible non-pneumatic ESI operation depends on the ability to balance a number of parameters, including applied voltage and solution surface tension, flow rate, and conductivity. We discuss how changing these parameters can shift the mode of ESI operation from stable to unstable, and how current-voltage curves can be used to characterize the mode of ESI operation. Finally, the characteristics of the ideal ESI solvent, including surface tension and conductivity requirements, are discussed. Analysis in the positive ion mode can be accomplished with acidified methanol/water solutions, but negative ion mode analysis necessitates special constituents that suppress corona discharge and facilitate the production of stable negative ions. Copyright 2002 Wiley Periodicals, Inc.

Synthesis and Properties of Cross-Linked Polyamide Aerogels

NASA Technical Reports Server (NTRS)

Williams, Jarrod; Meador, Mary Ann; McCorkle, Linda

2014-01-01

We report our ongoing research on polyamide aerogels made by step growth polymerization using a combination of terephthaloyl chloride, isophthaloyl chloride and m-phenylenediamine. Crosslinking of the amine capped polymer chains with 1,3,5-benzenetricarbonyl trichloride causes gelation in as little as two to five minutes. Removing the reaction solvent is accomplished through solvent exchange, followed by drying using supercritical CO2 extraction to give colorless aerogels with densities ranging from 0.07 to 0.33 grams per cubic centimeter and surface areas as high as 440 square meters per gram. Statistical experimental design methodology has been utilized to investigate dependence of properties of these aerogels, such as density, compressive modulus, and surface area, on changes in fabrication parameters including formulated number of amide oligomer repeat units (n-value), acid chloride (meta, para or combination), and solids concentration of solution used for gelation. For example, the density of these materials was found to be dependent on the acid chloride type and the solids concentration, but n was not a significant variable. However, surface area was significantly influenced by all three parameters. The polyamide aerogels represent a potential cost savings over previously reported polyimide aerogels, since monomers are all inexpensive and commercially available. Surface area and density were both highest when 100 terephthaloyl chloride was used but a combination of 5 solid concentration, 100 terephthaloyl chloride and n of 20 gave the best combination of properties.

Exploration of crystal simulation potential by fluconazole isomorphism and its application in improvement of pharmaceutical properties

NASA Astrophysics Data System (ADS)

Thakur, Amitha; Kumar, Dinesh; Thipparaboina, Rajesh; Shastri, Nalini R.

2014-11-01

Control of crystal morphology during crystallization is a paramount challenge in pharmaceutical processing. Hence, there is need to introduce computational methods for morphology prediction to manage production cost of drugs and improve related pharmaceutical and biopharmaceutical properties. Layer docking approach with molecular dynamics opens a new avenue for crystal habit prediction in presence of solvent. In the present study, attempts were made to correlate predicted and experimental crystal habits of fluconazole considering solvent interactions using layer docking approach. Simulated results from layer docking approach with methanol as solvent gave two dominant facets (0 1 1) and (1 0 1) with a surface area 22.43% and 19.82% respectively, which were in agreement with the experimental results. Experimentally grown modified crystal habit of fluconazole in methanol showed enhanced dissolution rate (p<0.05) when compared to plain drug. This was attributed to the increased surface area on the specified facets caused by interactions with the solvent. Furthermore, Differential Scanning Calorimetry, Fourier Transform Infrared (FTIR) Spectroscopy and powder X-ray Diffraction of recrystallized samples confirmed only a habit change and absence of any polymorphs, hydrates or solvates. Flow and compressibility of fluconazole recrystallized in methanol was significantly improved when compared to plain drug. This study demonstrates a methodical approach using computational tools for prediction and modification of crystal habit, to enhance dissolution of poorly soluble drugs, for future pharmaceutical applications.

Spine-like Nanostructured Carbon Interconnected by Graphene for High-performance Supercapacitors

NASA Astrophysics Data System (ADS)

Park, Sang-Hoon; Yoon, Seung-Beom; Kim, Hyun-Kyung; Han, Joong Tark; Park, Hae-Woong; Han, Joah; Yun, Seok-Min; Jeong, Han Gi; Roh, Kwang Chul; Kim, Kwang-Bum

2014-08-01

Recent studies on supercapacitors have focused on the development of hierarchical nanostructured carbons by combining two-dimensional graphene and other conductive sp2 carbons, which differ in dimensionality, to improve their electrochemical performance. Herein, we report a strategy for synthesizing a hierarchical graphene-based carbon material, which we shall refer to as spine-like nanostructured carbon, from a one-dimensional graphitic carbon nanofiber by controlling the local graphene/graphitic structure via an expanding process and a co-solvent exfoliation method. Spine-like nanostructured carbon has a unique hierarchical structure of partially exfoliated graphitic blocks interconnected by thin graphene sheets in the same manner as in the case of ligaments. Owing to the exposed graphene layers and interconnected sp2 carbon structure, this hierarchical nanostructured carbon possesses a large, electrochemically accessible surface area with high electrical conductivity and exhibits high electrochemical performance.

Spine-like nanostructured carbon interconnected by graphene for high-performance supercapacitors.

PubMed

Park, Sang-Hoon; Yoon, Seung-Beom; Kim, Hyun-Kyung; Han, Joong Tark; Park, Hae-Woong; Han, Joah; Yun, Seok-Min; Jeong, Han Gi; Roh, Kwang Chul; Kim, Kwang-Bum

2014-08-19

Recent studies on supercapacitors have focused on the development of hierarchical nanostructured carbons by combining two-dimensional graphene and other conductive sp(2) carbons, which differ in dimensionality, to improve their electrochemical performance. Herein, we report a strategy for synthesizing a hierarchical graphene-based carbon material, which we shall refer to as spine-like nanostructured carbon, from a one-dimensional graphitic carbon nanofiber by controlling the local graphene/graphitic structure via an expanding process and a co-solvent exfoliation method. Spine-like nanostructured carbon has a unique hierarchical structure of partially exfoliated graphitic blocks interconnected by thin graphene sheets in the same manner as in the case of ligaments. Owing to the exposed graphene layers and interconnected sp(2) carbon structure, this hierarchical nanostructured carbon possesses a large, electrochemically accessible surface area with high electrical conductivity and exhibits high electrochemical performance.

Spine-like Nanostructured Carbon Interconnected by Graphene for High-performance Supercapacitors

PubMed Central

Park, Sang-Hoon; Yoon, Seung-Beom; Kim, Hyun-Kyung; Han, Joong Tark; Park, Hae-Woong; Han, Joah; Yun, Seok-Min; Jeong, Han Gi; Roh, Kwang Chul; Kim, Kwang-Bum

2014-01-01

Recent studies on supercapacitors have focused on the development of hierarchical nanostructured carbons by combining two-dimensional graphene and other conductive sp2 carbons, which differ in dimensionality, to improve their electrochemical performance. Herein, we report a strategy for synthesizing a hierarchical graphene-based carbon material, which we shall refer to as spine-like nanostructured carbon, from a one-dimensional graphitic carbon nanofiber by controlling the local graphene/graphitic structure via an expanding process and a co-solvent exfoliation method. Spine-like nanostructured carbon has a unique hierarchical structure of partially exfoliated graphitic blocks interconnected by thin graphene sheets in the same manner as in the case of ligaments. Owing to the exposed graphene layers and interconnected sp2 carbon structure, this hierarchical nanostructured carbon possesses a large, electrochemically accessible surface area with high electrical conductivity and exhibits high electrochemical performance. PMID:25134517

Single chain structure of a poly(N-isopropylacrylamide) surfactant in water.

PubMed

Abbott, Lauren J; Tucker, Ashley K; Stevens, Mark J

2015-03-05

We present atomistic simulations of a single PNIPAM-alkyl copolymer surfactant in aqueous solution at temperatures below and above the LCST of PNIPAM. We compare properties of the surfactant with pure PNIPAM oligomers of similar lengths, such as the radius of gyration and solvent accessible surface area, to determine the differences in their structures and transition behavior. We also explore changes in polymer-polymer and polymer-water interactions, including hydrogen bond formation. The expected behavior is observed in the pure PNIPAM oligomers, where the backbone folds onto itself above the LCST in order to shield the hydrophobic groups from water. The surfactant, on the other hand, does not show much conformational change as a function of temperature, but instead folds to bring the hydrophobic alkyl tail and PNIPAM headgroup together at all temperatures. The atomic detail available from these simulations offers important insight into understanding how the transition behavior is changed in PNIPAM-based systems.

PACSY, a relational database management system for protein structure and chemical shift analysis

PubMed Central

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

Interaction of three new tetradentates Schiff bases containing N2O2 donor atoms with calf thymus DNA.

PubMed

Ajloo, Davood; Shabanpanah, Sajede; Shafaatian, Bita; Ghadamgahi, Maryam; Alipour, Yasin; Lashgarbolouki, Taghi; Saboury, Ali Akbar

2015-01-01

Interaction of 1,3-bis(2-hydroxy-benzylidene)-urea (H2L1), 1,3-bis(2-hydroxy-3-methoxy-benzylidene)-urea (H2L2) and 1,3-bis(2-hydroxy-3-methoxy-benzylidene)-urea nickel(II) (NiL2) with calf-thymus DNA were investigated by UV-vis absorption, fluorescence emission and circular dichroism (CD) spectroscopy as well as cyclic voltammetry, viscosity measurements, molecular docking and molecular dynamics simulation. Binding constants were determined using UV-vis absorption and fluorescence spectra. The results indicated that studied Schiff-bases bind to DNA in the intercalative mode in which the metal derivative is more effective than non metals. Their interaction trend is further determined by molecular dynamics (MD) simulation. MD results showed that Ni derivative reduces oligonucleotide intermolecular hydrogen bond and increases solvent accessible surface area more than other compounds. Copyright © 2015 Elsevier B.V. All rights reserved.

Evaluation of the physi- and chemisorption of hydrogen in alkali (Na, Li) doped fullerenes

DOE PAGES

Ward, Patrick A.; Teprovich, Jr., Jospeph A.; Compton, Robert N.; ...

2015-01-11

Here, alkali doped fullerenes synthesized by two different solvent assisted mixing techniques are compared for their hydrogen uptake activity. In this study we investigated the interaction of hydrogen with alkali doped fullerenes via physisorption. In addition, we present the first mass spectrometric evidence for the formation of C 60H 60 via chemisorption. Hydrogen physisorption isotherms up to 1 atm at temperatures ranging from 77-303 K were measured demonstrating an increase in hydrogen uptake versus pure C 60 and increased isosteric heats of adsorption for the lithium doped fullerene Li 12C 60. However, despite these improvements the low amount of physisorbedmore » hydrogen at 1 atm and 77 K in these materials suggests that fullerenes do not possess enough accessible surface area to effectively store hydrogen due to their close packed crystalline nature.« less

Topological distribution of four-alpha-helix bundles.

PubMed Central

Presnell, S R; Cohen, F E

1989-01-01

The four-alpha-helix bundle, a common structural motif in globular proteins, provides an excellent forum for the examination of predictive constraints for protein backbone topology. An exhaustive examination of the Brookhaven Crystallographic Protein Data Bank and other literature sources has lead to the discovery of 20 putative four-alpha-helix bundles. Application of an analytical method that examines the difference between solvent-accessible surface areas in packed and partially unpacked bundles reduced the number of structures to 16. Angular requirements further reduced the list of bundles to 13. In 12 of these bundles, all pairs of neighboring helices were oriented in an anti-parallel fashion. This distribution is in accordance with structure types expected if the helix macro dipole effect makes a substantial contribution to the stability of the native structure. The characterizations and classifications made in this study prompt a reevaluation of constraints used in structure prediction efforts. Images PMID:2771946

MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?

PubMed

Fogolari, Federico; Moroni, Elisabetta; Wojciechowski, Marcin; Baginski, Maciej; Ragona, Laura; Molinari, Henriette

2005-04-01

The pH-driven opening and closure of beta-lactoglobulin EF loop, acting as a lid and closing the internal cavity of the protein, has been studied by molecular dynamics (MD) simulations and free energy calculations based on molecular mechanics/Poisson-Boltzmann (PB) solvent-accessible surface area (MM/PBSA) methodology. The forms above and below the transition pH differ presumably only in the protonation state of residue Glu89. MM/PBSA calculations are able to reproduce qualitatively the thermodynamics of the transition. The analysis of MD simulations using a combination of MM/PBSA methodology and the colony energy approach is able to highlight the driving forces implied in the transition. The analysis suggests that global rearrangements take place before the equilibrium local conformation is reached. This conclusion may bear general relevance to conformational transitions in all lipocalins and proteins in general. (c) 2005 Wiley-Liss, Inc.

Quantitative Protein Topography Analysis and High-Resolution Structure Prediction Using Hydroxyl Radical Labeling and Tandem-Ion Mass Spectrometry (MS)*

PubMed Central

Kaur, Parminder; Kiselar, Janna; Yang, Sichun; Chance, Mark R.

2015-01-01

Hydroxyl radical footprinting based MS for protein structure assessment has the goal of understanding ligand induced conformational changes and macromolecular interactions, for example, protein tertiary and quaternary structure, but the structural resolution provided by typical peptide-level quantification is limiting. In this work, we present experimental strategies using tandem-MS fragmentation to increase the spatial resolution of the technique to the single residue level to provide a high precision tool for molecular biophysics research. Overall, in this study we demonstrated an eightfold increase in structural resolution compared with peptide level assessments. In addition, to provide a quantitative analysis of residue based solvent accessibility and protein topography as a basis for high-resolution structure prediction; we illustrate strategies of data transformation using the relative reactivity of side chains as a normalization strategy and predict side-chain surface area from the footprinting data. We tested the methods by examination of Ca+2-calmodulin showing highly significant correlations between surface area and side-chain contact predictions for individual side chains and the crystal structure. Tandem ion based hydroxyl radical footprinting-MS provides quantitative high-resolution protein topology information in solution that can fill existing gaps in structure determination for large proteins and macromolecular complexes. PMID:25687570

Entropy in molecular recognition by proteins

PubMed Central

Caro, José A.; Harpole, Kyle W.; Kasinath, Vignesh; Lim, Jackwee; Granja, Jeffrey; Valentine, Kathleen G.; Sharp, Kim A.

2017-01-01

Molecular recognition by proteins is fundamental to molecular biology. Dissection of the thermodynamic energy terms governing protein–ligand interactions has proven difficult, with determination of entropic contributions being particularly elusive. NMR relaxation measurements have suggested that changes in protein conformational entropy can be quantitatively obtained through a dynamical proxy, but the generality of this relationship has not been shown. Twenty-eight protein–ligand complexes are used to show a quantitative relationship between measures of fast side-chain motion and the underlying conformational entropy. We find that the contribution of conformational entropy can range from favorable to unfavorable, which demonstrates the potential of this thermodynamic variable to modulate protein–ligand interactions. For about one-quarter of these complexes, the absence of conformational entropy would render the resulting affinity biologically meaningless. The dynamical proxy for conformational entropy or “entropy meter” also allows for refinement of the contributions of solvent entropy and the loss in rotational-translational entropy accompanying formation of high-affinity complexes. Furthermore, structure-based application of the approach can also provide insight into long-lived specific water–protein interactions that escape the generic treatments of solvent entropy based simply on changes in accessible surface area. These results provide a comprehensive and unified view of the general role of entropy in high-affinity molecular recognition by proteins. PMID:28584100

Interplay of Electrostatics and Hydrophobic Effects in the Metamorphic Protein Human Lymphotactin.

PubMed

Korkmaz, Elif Nihal; Volkman, Brian F; Cui, Qiang

2015-07-30

The human lymphotactin (hLtn) is a protein that features two native states both of which are physiologically relevant: it is a monomer (hLtn10) at 10 °C with 200 mM salt and a dimer (hLtn40) at 40 °C and without salt. Here we focus on the networks of electrostatic and hydrophobic interactions that display substantial changes upon the conversion from hLtn10 to hLtn40 since they are expected to modulate the relative stability of the two folds. In addition to the Arg 23-Arg 43 interaction discussed in previous work, we find several other like-charge pairs that are likely important to the stability of hLtn10. Free energy perturbation calculations are carried out to explicitly evaluate the contribution of the Arg 23-Arg 43 interaction to the hLtn10 stability. hLtn40 features a larger number of salt bridges, and a set of hydrophobic residues undergo major changes in the solvent accessible surface area between hLtn10 and hLtn40, pointing to their importance to the relative stability of the two folds. We also discuss the use of explicit and implicit solvent simulations for characterizing the conformational ensembles under different solution conditions.

Entropy in molecular recognition by proteins.

PubMed

Caro, José A; Harpole, Kyle W; Kasinath, Vignesh; Lim, Jackwee; Granja, Jeffrey; Valentine, Kathleen G; Sharp, Kim A; Wand, A Joshua

2017-06-20

Molecular recognition by proteins is fundamental to molecular biology. Dissection of the thermodynamic energy terms governing protein-ligand interactions has proven difficult, with determination of entropic contributions being particularly elusive. NMR relaxation measurements have suggested that changes in protein conformational entropy can be quantitatively obtained through a dynamical proxy, but the generality of this relationship has not been shown. Twenty-eight protein-ligand complexes are used to show a quantitative relationship between measures of fast side-chain motion and the underlying conformational entropy. We find that the contribution of conformational entropy can range from favorable to unfavorable, which demonstrates the potential of this thermodynamic variable to modulate protein-ligand interactions. For about one-quarter of these complexes, the absence of conformational entropy would render the resulting affinity biologically meaningless. The dynamical proxy for conformational entropy or "entropy meter" also allows for refinement of the contributions of solvent entropy and the loss in rotational-translational entropy accompanying formation of high-affinity complexes. Furthermore, structure-based application of the approach can also provide insight into long-lived specific water-protein interactions that escape the generic treatments of solvent entropy based simply on changes in accessible surface area. These results provide a comprehensive and unified view of the general role of entropy in high-affinity molecular recognition by proteins.

Electronic and Structural Elements That Regulate the Excited-State Dynamics in Purine Nucleobase Derivatives

PubMed Central

2015-01-01

The excited-state dynamics of the purine free base and 9-methylpurine are investigated using experimental and theoretical methods. Femtosecond broadband transient absorption experiments reveal that excitation of these purine derivatives in aqueous solution at 266 nm results primarily in ultrafast conversion of the S2(ππ*) state to the vibrationally excited 1nπ* state. Following vibrational and conformational relaxation, the 1nπ* state acts as a doorway state in the efficient population of the triplet manifold with an intersystem crossing lifetime of hundreds of picoseconds. Experiments show an almost 2-fold increase in the intersystem crossing rate on going from polar aprotic to nonpolar solvents, suggesting that a solvent-dependent energy barrier must be surmounted to access the singlet-to-triplet crossing region. Ab initio static and surface-hopping dynamics simulations lend strong support to the proposed relaxation mechanism. Collectively, the experimental and computational results demonstrate that the accessibility of the nπ* states and the topology of the potential energy surfaces in the vicinity of conical intersections are key elements in controlling the excited-state dynamics of the purine derivatives. From a structural perspective, it is shown that the purine chromophore is not responsible for the ultrafast internal conversion in the adenine and guanine monomers. Instead, C6 functionalization plays an important role in regulating the rates of radiative and nonradiative relaxation. C6 functionalization inhibits access to the 1nπ* state while simultaneously facilitating access to the 1ππ*(La)/S0 conical intersection, such that population of the 1nπ* state cannot compete with the relaxation pathways to the ground state involving ring puckering at the C2 position. PMID:25763596

AcconPred: Predicting Solvent Accessibility and Contact Number Simultaneously by a Multitask Learning Framework under the Conditional Neural Fields Model.

PubMed

Ma, Jianzhu; Wang, Sheng

2015-01-01

The solvent accessibility of protein residues is one of the driving forces of protein folding, while the contact number of protein residues limits the possibilities of protein conformations. The de novo prediction of these properties from protein sequence is important for the study of protein structure and function. Although these two properties are certainly related with each other, it is challenging to exploit this dependency for the prediction. We present a method AcconPred for predicting solvent accessibility and contact number simultaneously, which is based on a shared weight multitask learning framework under the CNF (conditional neural fields) model. The multitask learning framework on a collection of related tasks provides more accurate prediction than the framework trained only on a single task. The CNF method not only models the complex relationship between the input features and the predicted labels, but also exploits the interdependency among adjacent labels. Trained on 5729 monomeric soluble globular protein datasets, AcconPred could reach 0.68 three-state accuracy for solvent accessibility and 0.75 correlation for contact number. Tested on the 105 CASP11 domain datasets for solvent accessibility, AcconPred could reach 0.64 accuracy, which outperforms existing methods.

AcconPred: Predicting Solvent Accessibility and Contact Number Simultaneously by a Multitask Learning Framework under the Conditional Neural Fields Model

PubMed Central

Ma, Jianzhu; Wang, Sheng

2015-01-01

Motivation. The solvent accessibility of protein residues is one of the driving forces of protein folding, while the contact number of protein residues limits the possibilities of protein conformations. The de novo prediction of these properties from protein sequence is important for the study of protein structure and function. Although these two properties are certainly related with each other, it is challenging to exploit this dependency for the prediction. Method. We present a method AcconPred for predicting solvent accessibility and contact number simultaneously, which is based on a shared weight multitask learning framework under the CNF (conditional neural fields) model. The multitask learning framework on a collection of related tasks provides more accurate prediction than the framework trained only on a single task. The CNF method not only models the complex relationship between the input features and the predicted labels, but also exploits the interdependency among adjacent labels. Results. Trained on 5729 monomeric soluble globular protein datasets, AcconPred could reach 0.68 three-state accuracy for solvent accessibility and 0.75 correlation for contact number. Tested on the 105 CASP11 domain datasets for solvent accessibility, AcconPred could reach 0.64 accuracy, which outperforms existing methods. PMID:26339631

Evidence for Conformationa1 Heterogeneity of Fission Protein Fis1 from Saccharomyces cerevisiae†

PubMed Central

Picton, Lora K.; Casares, Salvador; Monahan, Ann C.; Majumdar, Ananya; Hill, R. Blake

2009-01-01

Fission 1 (Fis1) is an evolutionarily conserved, type II integral membrane protein implicated in maintaining the proper morphology of mitochondria and peroxisomes. A concave surface on the cytosolic domain of Fis1 from Saccharomyces cerevisiae is implicated in binding other fission proteins, yet structural studies reveal that this surface is sterically occluded by its N-terminal arm. Here we address the question of whether the N-terminal arm of yeast Fis1 exists in a dynamic equilibrium that would allow access to this functionally important surface. NMR measurements sensitive to dynamics occurring on a wide range of time scales (picoseconds to minutes) were used to assess whether the Fis1 arm is dynamic. Hydrogen–deuterium exchange experiments revealed that the Fis1 arm, α-helix 6, and proximal loops were not protected from solvent exchange, consistent with motions on the second to minute time scale. An engineered cysteine, I85C, located on the concave surface that lies underneath the Fis1 arm, was readily modified by a fluorescent probe, revealing more solvent accessibility of this position than would be predicted from the structure. Chemical denaturation, NMR chemical shift perturbation, and residual dipolar coupling experiments support the idea that the dynamic equilibrium can be shifted on the basis of changing pH and temperature, with the changes primarily localizing to the Fis1 arm and proximal regions. The data as a whole are consistent with the Fis1 arm adopting a primarily “closed” conformational state able to undergo dynamic excursions that reveal the concave surface and therefore may be important for binding other fission factors and for Fis1 function. PMID:19522466

Analysis of the binding loops configuration and surface adaptation of different crystallized single-domain antibodies in response to various antigens.

PubMed

Al Qaraghuli, Mohammed M; Ferro, Valerie A

2017-04-01

Monoclonal antibodies have revolutionized the biomedical field through their ubiquitous utilization in different diagnostics and therapeutic applications. Despite this widespread use, their large size and structural complexity have limited their versatility in specific applications. The antibody variable region that is responsible for binding antigen is embodied within domains that can be rescued individually as single-domain antibody (sdAb) fragments. Because of the unique characteristics of sdAbs, such as low molecular weight, high physicochemical stability, and the ability to bind antigens inaccessible to conventional antibodies, they represent a viable alternative to full-length antibodies. Consequently, 149 crystal structures of sdAbs, originating from human (VH), camelids (VHH), or sharks (VNAR), were retrieved from the Protein Data Bank, and their structures were compared. The 3 types of sdAbs displayed complementarity determining regions (CDRs) with different lengths and configurations. CDR3 of the VHH and VNAR domains were dominated by pleated and extended orientations, respectively. Although VNAR showed the smallest average molecular weight and molecular surface area compared with VHH and VH antibodies. However, the solvent accessible surface area measurements of the 3 tested sdAbs types were very similar. All the antihapten VHH antibodies showed pleated CDR3, which were sufficient to create a binding pocket to accommodate haptens (methotrexate and azo dyes) in terms of shape and electrostatic potential. The sdAbs that recognized lysozyme showed more diversity in their CDR3 orientation to enable them to recognize various topographies of lysozyme. Subsequently, the three sdAb classes were different in size and surface area and have shown distinguishable ability to optimize their CDR length and orientation to recognize different antigen classes. Copyright © 2016 John Wiley & Sons, Ltd.

Molecular receptors in metal oxide sol-gel materials prepared via molecular imprinting

DOEpatents

Sasaki, Darryl Y.; Brinker, C. Jeffrey; Ashley, Carol S.; Daitch, Charles E.; Shea, Kenneth J.; Rush, Daniel J.

2000-01-01

A method is provided for molecularly imprinting the surface of a sol-gel material, by forming a solution comprised of a sol-gel material, a solvent, an imprinting molecule, and a functionalizing siloxane monomer of the form Si(OR).sub.3-n X.sub.n, wherein n is an integer between zero and three and X is a functional group capable of reacting with the imprinting molecule, evaporating the solvent, and removing the imprinting molecule to form the molecularly imprinted metal oxide sol-gel material. The use of metal oxide sol-gels allows the material porosity, pore size, density, surface area, hardness, electrostatic charge, polarity, optical density, and surface hydrophobicity to be tailored and be employed as sensors and in catalytic and separations operations.

Large-Area Atomic Oxygen Facility Used to Clean Fire-Damaged Artwork

NASA Technical Reports Server (NTRS)

Rutledge, Sharon K.; Banks, Bruce A.; Steuber, Thomas J.; Sechkar, Edward A.

2000-01-01

In addition to completely destroying artwork, fires in museums and public buildings can soil a displayed artwork with so much accumulated soot that it can no longer be used for study or be enjoyed by the public. In situations where the surface has not undergone extensive charring or melting, restoration can be attempted. However, soot deposits can be very difficult to remove from some types of painted surfaces, particularly when the paint is fragile or flaking or when the top surface of the paint binder has been damaged. Restoration typically involves the use of organic solvents to clean the surface, but these solvents may cause the paint layers to swell or leach out. Also, immersion of the surface or swabbing during solvent cleaning may move or remove pigment through mechanical contact, especially if the fire damage extends into the paint binder. A noncontact technique of removing organic deposits from surfaces was developed out of NASA research on the effects of oxygen atoms on various materials. Atomic oxygen is present in the atmosphere surrounding the Earth at the altitudes where satellites typically orbit. It can react chemically with surface coatings or deposits that contain carbon. In the reaction, the carbon is converted to carbon monoxide and some carbon dioxide. Water vapor is also a byproduct of the reaction if the surface contains carbon-hydrogen bonds. To study this reaction, NASA developed Earth-based facilities to produce atomic oxygen for material exposure and testing. A vacuum facility designed and built by the Electro-Physics Branch of the NASA Glenn Research Center at Lewis Field to provide atomic oxygen over a large area for studying reactions in low Earth orbit has been used to successfully clean several full-size paintings. (This facility can accommodate paintings up to 1.5 by 2.1 m. The atomic oxygen plasma is produced between two large parallel aluminum plates using a radiofrequency power source operating at roughly 400 W. Atomic oxygen is generated uniformly over this area at an operating pressure of 1 to 5 mtorr.

Nonhazardous solvent composition and method for cleaning metal surfaces

DOEpatents

Googin, John M.; Simandl, Ronald F.; Thompson, Lisa M.

1993-01-01

A solvent composition for displacing greasy and oily contaminants as well as water and/or aqueous residue from metallic surfaces, especially surfaces of radioactive materials so that such surfaces can be wiped clean of the displaced contaminants, water and/or aqueous residue. The solvent composition consists essentially of a blend of nonpolar aliphatic hydrocarbon solvent having a minimum flash point of about 140.degree. F. and 2 to 25 volume percent of a polar solvent having a flash point sufficiently high so as to provide the solvent composition with a minimum flash point of at least 140.degree. F. The solvent composition is nonhazardous so that when it is used to clean the surfaces of radioactive materials the waste in the form of paper or cloth wipes, lab coats and the like used in the cleaning operation is not considered to be mixed waste composed of a hazardous solvent and a radioactive material.

Nonhazardous solvent composition and method for cleaning metal surfaces

DOEpatents

Googin, J.M.; Simandl, R.F.; Thompson, L.M.

1993-05-04

A solvent composition for displacing greasy and oily contaminants as well as water and/or aqueous residue from metallic surfaces, especially surfaces of radioactive materials so that such surfaces can be wiped clean of the displaced contaminants, water and/or aqueous residue. The solvent composition consists essentially of a blend of nonpolar aliphatic hydrocarbon solvent having a minimum flash point of about 140 F and 2 to 25 volume percent of a polar solvent having a flash point sufficiently high so as to provide the solvent composition with a minimum flash point of at least 140 F. The solvent composition is nonhazardous so that when it is used to clean the surfaces of radioactive materials the waste in the form of paper or cloth wipes, lab coats and the like used in the cleaning operation is not considered to be mixed waste composed of a hazardous solvent and a radioactive material.

Self-assembly of short amyloidogenic peptides at the air-water interface.

PubMed

Chaudhary, Nitin; Nagaraj, Ramakrishnan

2011-08-01

Short peptide stretches in amyloidogenic proteins can form amyloid fibrils in vitro and have served as good models for studying amyloid fibril formation. Recently, these amyloidogenic peptides have gained considerable attention, as non-amyloid ordered structures can be obtained from these peptides by carefully tuning the conditions of self-assembly, especially pH, temperature and presence of organic solvents. We have examined the effect of surface pressure on the self-assembled structures of two amyloidogenic peptides, Pβ(2)m (Ac-DWSFYLLYYTEFT-am) and AcPHF6 (Ac-VQIVYK-am) at the air-water interface when deposited from different solvents. Both the peptides are surface-active and form Thioflavin T (ThT) positive structures at the air-water interface. There is considerable hysteresis in the compression and expansion isotherms, suggesting the occurrence of structural rearrangements during compression. Preformed Pβ(2)m fibrillar structures at the air-water interface are disrupted as peptide is compressed to lower molecular areas but restored if the film is expanded, suggesting that the process is reversible. AcPHF6, on the other hand, shows largely sheet-like structures at lower molecular areas. The solvents used for dissolution of the peptides appear to influence the nature of the aggregates formed. Our results show that like hydrostatic pressure, surface pressure can also be utilized for modulating the self-assembly of the amyloidogenic and self-assembling peptides. Copyright © 2011 Elsevier Inc. All rights reserved.

Issues Related to Cleaning Complex Geometry Surfaces with ODC-Free Solvents

NASA Technical Reports Server (NTRS)

Bradford, Blake F.; Wurth, Laura A.; Nayate, Pramod D.; McCool, Alex (Technical Monitor)

2001-01-01

Implementing ozone depleting chemicals (ODC)-free solvents into full-scale reusable solid rocket motor cleaning operations has presented problems due to the low vapor pressures of the solvents. Because of slow evaporation, solvent retention is a problem on porous substrates or on surfaces with irregular geometry, such as threaded boltholes, leak check ports, and nozzle backfill joints. The new solvents are being evaluated to replace 1,1,1-trichloroethane, which readily evaporates from these surfaces. Selection of the solvents to be evaluated on full-scale hardware was made based on results of subscale tests performed with flat surface coupons, which did not manifest the problem. Test efforts have been undertaken to address concerns with the slow-evaporating solvents. These concerns include effects on materials due to long-term exposure to solvent, potential migration from bolthole threads to seal surfaces, and effects on bolt loading due to solvent retention in threads. Tests performed to date have verified that retained solvent does not affect materials or hardware performance. Process modifications have also been developed to assist drying, and these can be implemented if additional drying becomes necessary.

Indolylarylsulfones carrying a heterocyclic tail as very potent and broad spectrum HIV-1 non-nucleoside reverse transcriptase inhibitors.

PubMed

Famiglini, Valeria; La Regina, Giuseppe; Coluccia, Antonio; Pelliccia, Sveva; Brancale, Andrea; Maga, Giovanni; Crespan, Emmanuele; Badia, Roger; Riveira-Muñoz, Eva; Esté, José A; Ferretti, Rosella; Cirilli, Roberto; Zamperini, Claudio; Botta, Maurizio; Schols, Dominique; Limongelli, Vittorio; Agostino, Bruno; Novellino, Ettore; Silvestri, Romano

2014-12-11

We synthesized new indolylarylsulfone (IAS) derivatives carrying a heterocyclic tail at the indole-2-carboxamide nitrogen as potential anti-HIV/AIDS agents. Several new IASs yielded EC50 values <1.0 nM against HIV-1 WT and mutant strains in MT-4 cells. The (R)-11 enantiomer proved to be exceptionally potent against the whole viral panel; in the reverse transcriptase (RT) screening assay, it was remarkably superior to NVP and EFV and comparable to ETV. The binding poses were consistent with the one previously described for the IAS non-nucleoside reverse transcriptase inhibitors. Docking studies showed that the methyl group of (R)-11 points toward the cleft created by the K103N mutation, different from the corresponding group of (S)-11. By calculating the solvent-accessible surface, we observed that the exposed area of RT in complex with (S)-11 was larger than the area of the (R)-11 complex. Compounds 6 and 16 and enantiomer (R)-11 represent novel robust lead compounds of the IAS class.

Effect of dynamic surface polarization on the oxidative stability of solvents in nonaqueous Li-O 2 batteries

NASA Astrophysics Data System (ADS)

Khetan, Abhishek; Pitsch, Heinz; Viswanathan, Venkatasubramanian

2017-09-01

Polarization-induced renormalization of the frontier energy levels of interacting molecules and surfaces can cause significant shifts in the excitation and transport behavior of electrons. This phenomenon is crucial in determining the oxidative stability of nonaqueous electrolytes in high-energy density electrochemical systems such as the Li-O2 battery. On the basis of partially self-consistent first-principles Sc G W0 calculations, we systematically study how the electronic energy levels of four commonly used solvent molecules, namely, dimethylsulfoxide (DMSO), dimethoxyethane (DME), tetrahydrofuran (THF), and acetonitrile (ACN), renormalize when physisorbed on the different stable surfaces of Li2O2 , the main discharge product. Using band level alignment arguments, we propose that the difference between the solvent's highest occupied molecular orbital (HOMO) level and the surface's valence-band maximum (VBM) is a refined metric of oxidative stability. This metric and a previously used descriptor, solvent's gas phase HOMO level, agree quite well for physisorbed cases on pristine surfaces where ACN is oxidatively most stable followed by DME, THF, and DMSO. However, this effect is intrinsically linked to the surface chemistry of the solvent's interaction with the surface states and defects, and depends strongly on their nature. We conclusively show that the propensity of solvent molecules to oxidize will be significantly higher on Li2O2 surfaces with defects as compared to pristine surfaces. This suggests that the oxidative stability of a solvent is dynamic and is a strong function of surface electronic properties. Thus, while gas phase HOMO levels could be used for preliminary solvent candidate screening, a more refined picture of solvent stability requires mapping out the solvent stability as a function of the state of the surface under operating conditions.

Optimization of instantaneous solvent exchange/surface modification process for ambient synthesis of monolithic silica aerogels.

PubMed

Hwang, Sung-Woo; Kim, Tae-Youn; Hyun, Sang-Hoon

2008-06-01

The instantaneous solvent exchange/surface modification (ISE/SM) process for the ambient synthesis of crack-free silica aerogel monoliths with a high production yield was optimized. Monolithic forms of silica wet gels were obtained from aqueous colloidal silica sols prepared via the ion exchange of sodium silicate solutions. Crack-free silica aerogel monoliths were synthesized via an ISE/SM process using isopropyl alcohol/trimethylchlorosilane as a modification agent and n-hexane as a main solvent, followed by ambient drying. The optimum process conditions of the ISE/SM process were investigated by clarifying the reaction mechanism and phenomena. Most effective ranges of process variables on the ISE/SM stage were determined as 0.2500-0.3567 of TMCS/H2O (pore water) in molar ratio and 15-30 of n-hexane/TMCS in volumetric ratio, with a reaction temperature below 283 K. Crack-free silica aerogel monoliths synthesized via these conditions had a well-developed mesoporous structure and excellent properties (bulk density of 0.12-0.14 g/cm3, specific surface area of 724 m2/g), and a high yield (nearly 80%).

Local phase separation of co-solvents enhances pretreatment of biomass for bioenergy applications

DOE PAGES

Mostofian, Barmak; Cai, Charles M.; Smith, Micholas Dean; ...

2016-08-02

Pretreatment facilitates more complete deconstruction of plant biomass to enable more economic production of lignocellulosic biofuels and byproducts. Various co-solvent pretreatments have demonstrated advantages relative to aqueous-only methods by enhancing lignin removal to allow unfettered access to cellulose. However, there is a limited mechanistic understanding of the interactions between the co-solvents and cellulose that impedes further improvement of such pretreatment methods. Recently, tetrahydrofuran (THF) has been identified as a highly effective co-solvent for the pretreatment and fractionation of biomass. Here, to elucidate the mechanism of the THF water interactions with cellulose, we pair simulation and experimental data demonstrating that enhancedmore » solubilization of cellulose can be achieved by the THF water co-solvent system at equivolume mixtures and moderate temperatures (≤445 K). The simulations show that THF and water spontaneously phase separate on the local surface of a cellulose fiber, owing to hydrogen bonding of water molecules with the hydrophilic cellulose faces and stacking of THF molecules on the hydrophobic faces. Furthermore, a single fully solvated cellulose chain is shown to be preferentially bound by water molecules in the THF water mixture. In light of these findings, co-solvent reactions were performed on microcrystalline cellulose and maple wood to show that THF significantly enhanced cellulose deconstruction and lignocellulose solubilization at simulation conditions, enabling a highly versatile and efficient biomass pretreatment and fractionation method.« less

Ionic Liquids and Poly(ionic liquid)s for Morphosynthesis of Inorganic Materials.

PubMed

Gao, Min-Rui; Yuan, Jiayin; Antonietti, Markus

2017-04-24

Ionic liquids (ILs) are new, innovative ionic solvents with rich physicochemical properties and intriguing pre-organized solvent structures; these materials offer great potential to impact across versatile areas of scientific research, for example, synthetic inorganic chemistry. Recent use of ILs as precursors, templates, and solvents has led to inorganic materials with tailored sizes, dimensionalities, morphologies, and functionalities that are difficult to obtain, or even not accessible, by using conventional solvents. Poly(ionic liquid)s (PILs) polymerized from IL monomers also raise the prospect of modifying nucleation, growth, and crystallization of inorganic objects, shedding light on the synthesis of a wide range of new materials. Here we survey recent key progress in using ILs and PILs in the field of synthetic inorganic chemistry. As well as highlighting the unique features of ILs and PILs that enable advanced synthesis, the effects of adding other solvents to the final products, along with the emerging applications of the created inorganic materials will be discussed. We finally provide an outlook on several development opportunities that could lead to new advancements of this exciting research field. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solvent-dependent gating motions of an extremophilic lipase from Pseudomonas aeruginosa

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

Johnson, Quentin R.; Nellas, Ricky B.; Shen, Tongye

2012-07-25

Understanding how organic solvent-stable proteins can function in anhydrous and often complex solutions is essential for the study of the interaction of protein and molecular immiscible interfaces and the design of efficient industrial enzymes in nonaqueous solvents. Using an extremophilic lipase from Pseudomonas aeruginosa as an example, we investigated the conformational dynamics of an organic solvent-tolerant enzyme in complex solvent milieux. Four 100-ns molecular dynamics simulations of the lipase were performed in solvent systems: water, hexane, and two mixtures of hexane and water, 5% and 95% (w/w) hexane. Our results show a solvent-dependent structural change of the protein, especially inmore » the region that regulates the admission of the substrate. We observed that the lipase is much less flexible in hexane than in aqueous solution or at the immiscible interface. Quantified by the size of the accessible channel, the lipase in water has a closed-gate conformation and no access to the active site, while in the hexane-containing systems, the lipase is at various degrees of open-gate state, with the immiscible interface setup being in the widely open conformation ensembles. Furthermore, the composition of explicit solvents in the access channel showed a significant influence on the conformational dynamics of the protein. Interestingly, the slowest step (bottleneck) of the hexane-induced conformational switch seems to be correlated with the slow dehydration dynamics of the channel.« less

Supercritical processing as a route to high internal surface areas and permanent microporosity in metal-organic framework materials.

PubMed

Nelson, Andrew P; Farha, Omar K; Mulfort, Karen L; Hupp, Joseph T

2009-01-21

Careful processing of four representative metal-organic framework (MOF) materials with liquid and supercritical carbon dioxide (ScD) leads to substantial, or in some cases spectacular (up to 1200%), increases in gas-accessible surface area. Maximization of surface area is key to the optimization of MOFs for many potential applications. Preliminary evidence points to inhibition of mesopore collapse, and therefore micropore accessibility, as the basis for the extraordinarily efficacious outcome of ScD-based activation.

Surface and Bulk Phase Separations in Block Copolymers and Their Blends.

DTIC Science & Technology

1984-03-01

research effort in _. the biomedical area to study polymeric surfaces which may be applied where biocompatibility (particularly, blood compatibilty) is...elasticity(thermoplastic) and good biocompatibility . Two such commercially available polyurethanes-, Avcothane and Biomer, have been used in this...the biocompatible properties depended considerably on the rate of evaporation of solvent during the film preparation. ATR-IR spectroscopy showed that

The preparation of large surface area lanthanum based perovskite supports for AuPt nanoparticles: tuning the glycerol oxidation reaction pathway by switching the perovskite B site

PubMed Central

Evans, Christopher D.; Smith, Paul J.; Manning, Troy D.; Miedziak, Peter J.; Brett, Gemma L.; Armstrong, Robert D.; Bartley, Jonathan K.; Taylor, Stuart H.; Rosseinsky, Matthew J.; Hutchings, Graham J.

2016-01-01

Gold and gold alloys, in the form of supported nanoparticles, have been shown over the last three decades to be highly effective oxidation catalysts. Mixed metal oxide perovskites, with their high structural tolerance, are ideal for investigating how changes in the chemical composition of supports affect the catalysts' properties, while retaining similar surface areas, morphologies and metal co-ordinations. However, a significant disadvantage of using perovskites as supports is their high crystallinity and small surface area. We report the use of a supercritical carbon dioxide anti-solvent precipitation methodology to prepare large surface area lanthanum based perovskites, making the deposition of 1 wt% AuPt nanoparticles feasible. These catalysts were used for the selective oxidation of glycerol. By changing the elemental composition of the perovskite B site, we dramatically altered the reaction pathway between a sequential oxidation route to glyceric or tartronic acid and a dehydration reaction pathway to lactic acid. Selectivity profiles were correlated to reported oxygen adsorption capacities of the perovskite supports and also to changes in the AuPt nanoparticle morphologies. Extended time on line analysis using the best oxidation catalyst (AuPt/LaMnO3) produced an exceptionally high tartronic acid yield. LaMnO3 produced from alternative preparation methods was found to have lower activities, but gave comparable selectivity profiles to that produced using the supercritical carbon dioxide anti-solvent precipitation methodology. PMID:27074316

The preparation of large surface area lanthanum based perovskite supports for AuPt nanoparticles: tuning the glycerol oxidation reaction pathway by switching the perovskite B site.

PubMed

Evans, Christopher D; Kondrat, Simon A; Smith, Paul J; Manning, Troy D; Miedziak, Peter J; Brett, Gemma L; Armstrong, Robert D; Bartley, Jonathan K; Taylor, Stuart H; Rosseinsky, Matthew J; Hutchings, Graham J

2016-07-04

Gold and gold alloys, in the form of supported nanoparticles, have been shown over the last three decades to be highly effective oxidation catalysts. Mixed metal oxide perovskites, with their high structural tolerance, are ideal for investigating how changes in the chemical composition of supports affect the catalysts' properties, while retaining similar surface areas, morphologies and metal co-ordinations. However, a significant disadvantage of using perovskites as supports is their high crystallinity and small surface area. We report the use of a supercritical carbon dioxide anti-solvent precipitation methodology to prepare large surface area lanthanum based perovskites, making the deposition of 1 wt% AuPt nanoparticles feasible. These catalysts were used for the selective oxidation of glycerol. By changing the elemental composition of the perovskite B site, we dramatically altered the reaction pathway between a sequential oxidation route to glyceric or tartronic acid and a dehydration reaction pathway to lactic acid. Selectivity profiles were correlated to reported oxygen adsorption capacities of the perovskite supports and also to changes in the AuPt nanoparticle morphologies. Extended time on line analysis using the best oxidation catalyst (AuPt/LaMnO3) produced an exceptionally high tartronic acid yield. LaMnO3 produced from alternative preparation methods was found to have lower activities, but gave comparable selectivity profiles to that produced using the supercritical carbon dioxide anti-solvent precipitation methodology.

Solvent polarity effect on quality of n-octadecanethiol self-assembled monolayers on copper and oxidized copper

NASA Astrophysics Data System (ADS)

Zhang, Yaozhong; Zhou, Jun; Zhang, Xiaoli; Hu, Jun; Gao, Han

2014-11-01

This article reports the effect of solvent polarity on the formation of n-octadecanethiol self-assembled monolayers (C18SH-SAMs) on pure copper surface and oxidized copper surface. The quality of SAMs prepared in different solvents (n-hexane, toluene, trichloroethylene, chloroform, acetone, acetonitrile, ethanol) was monitored by EIS, RAIRS and XPS. The results indicated that C18SH-SAMs formed in these solvents were in good barrier properties on pure copper surface and the structures of monolayers formed in high polarity solvents were more compact and orderly than that formed in low polarity solvents. For comparison, C18SH adsorbed on the surface of oxidized copper in these solvents were studied and the results indicated that C18SH could be adsorbed on oxidized copper surface after the reduction of copper oxide layer by thiols. Compared with high polarity solvents, a limited reduction process of oxidized copper by thiols led to the incompletely formation of monolayers in low polarity solvents. This can be interpreted that the generated water on solid-liquid interface and a smaller reaction force restrict the continuous reduction reaction in low polarity solvents

Method for forming a nano-textured substrate

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

Jeong, Sangmoo; Hu, Liangbing; Cui, Yi

A method for forming a nano-textured surface on a substrate is disclosed. An illustrative embodiment of the present invention comprises dispensing of a nanoparticle ink of nanoparticles and solvent onto the surface of a substrate, distributing the ink to form substantially uniform, liquid nascent layer of the ink, and enabling the solvent to evaporate from the nanoparticle ink thereby inducing the nanoparticles to assemble into an texture layer. Methods in accordance with the present invention enable rapid formation of large-area substrates having a nano-textured surface. Embodiments of the present invention are well suited for texturing substrates using high-speed, large scale,more » roll-to-roll coating equipment, such as that used in office product, film coating, and flexible packaging applications. Further, embodiments of the present invention are well suited for use with rigid or flexible substrates.« less

An anatomical study comparing two surgical approaches for isolated talonavicular arthrodesis.

PubMed

Higgs, Zoe; Jamal, Bilal; Fogg, Quentin A; Kumar, C Senthil

2014-10-01

Two operative approaches are commonly used for isolated talonavicular arthrodesis: the medial and the dorsal approach. It is recognized that access to the lateral aspect of the talonavicular joint can be limited when using the medial approach, and it is our experience that using the dorsal approach addresses this issue. We performed an anatomical study using cadaver specimens, to compare the amount of articular surface that can be accessed by each operative approach. Medial and dorsal approaches to the talonavicular joint were performed on each of 11 cadaveric specimens (10 fresh frozen, 1 embalmed). Distraction of the joint was performed as used intraoperatively and the accessible area of articular surfaces was marked for each of the 2 approaches using a previously reported technique. Disarticulation was performed and the marked surface area was quantified using an immersion digital microscribe, allowing a 3-dimensional virtual model of the articular surfaces to be assessed. The median percentage of total accessible talonavicular articular surface area for the medial and dorsal approaches was 71% and 92%, respectively (Wilcoxon signed-rank test, P < .001). This study provides quantifiable measurements of the articular surface accessible by the medial and dorsal approaches to the talonavicular joint. These data support for the use of the dorsal approach for talonavicular arthrodesis, particularly in cases where access to the lateral half of the joint is necessary. © The Author(s) 2014.

Apparatus to measure adsorption of condensable solvents on technical surfaces by photothermal deflection

NASA Astrophysics Data System (ADS)

Plimmer, M. D.; du Colombier, D.; Iraqi Houssaini, N.; Silvestri, Z.; Pinot, P.; Hannachi, R.

2012-11-01

This article describes an instrument for the measurement of the mirage effect as a tool to determine the molar adsorption per unit surface area Y1 of condensable solvents in the presence of a non-condensable carrier gas. The present apparatus is a much improved version of previous prototypes developed in our laboratory and elsewhere with a higher surface bake-out temperature (150 °C rather than 40 °C), lower residual vacuum (3 Pa versus 100 Pa), greater sample surface (40 mm diameter instead of 10 mm), more powerful optical pump beam (150 W cf. 50 W), and larger saturated vapour preparation volume (4 L instead of 1 L). The new set-up also includes the in situ monitoring of the surface via a reflected HeNe laser beam for the real-time detection of the onset of condensation. Here, we give a detailed description of the various components, outline the experimental procedure, show typical results, and suggest some straightforward improvements.

Apparatus to measure adsorption of condensable solvents on technical surfaces by photothermal deflection.

PubMed

Plimmer, M D; du Colombier, D; Iraqi Houssaini, N; Silvestri, Z; Pinot, P; Hannachi, R

2012-11-01

This article describes an instrument for the measurement of the mirage effect as a tool to determine the molar adsorption per unit surface area Y(1) of condensable solvents in the presence of a non-condensable carrier gas. The present apparatus is a much improved version of previous prototypes developed in our laboratory and elsewhere with a higher surface bake-out temperature (150 °C rather than 40 °C), lower residual vacuum (3 Pa versus 100 Pa), greater sample surface (40 mm diameter instead of 10 mm), more powerful optical pump beam (150 W cf. 50 W), and larger saturated vapour preparation volume (4 L instead of 1 L). The new set-up also includes the in situ monitoring of the surface via a reflected HeNe laser beam for the real-time detection of the onset of condensation. Here, we give a detailed description of the various components, outline the experimental procedure, show typical results, and suggest some straightforward improvements.

Relating saturation capacity to charge density in strong cation exchangers.

PubMed

Steinebach, Fabian; Coquebert de Neuville, Bertrand; Morbidelli, Massimo

2017-07-21

In this work the relation between physical and chemical resin characteristics and the total amount of adsorbed protein (saturation capacity) for ion-exchange resins is discussed. Eleven different packing materials with a sulfo-functionalization and one multimodal resin were analyzed in terms of their porosity, pore size distribution, ligand density and binding capacity. By specifying the ligand density and binding capacity by the total and accessible surface area, two different groups of resins were identified: Below a ligand density of approx. 2.5μmol/m 2 area the ligand density controls the saturation capacity, while above this limit the accessible surface area becomes the limiting factor. This results in a maximum protein uptake of around 2.5mg/m 2 of accessible surface area. The obtained results allow estimating the saturation capacity from independent resin characteristics like the saturation capacity mainly depends on "library data" such as the accessible and total surface area and the charge density. Hence these results give an insight into the fundamentals of protein adsorption and help to find suitable resins, thus limiting the experimental effort in early process development stages. Copyright © 2017 Elsevier B.V. All rights reserved.

Phytoremediation of Trichloroethylene and Perchloroethylene at the Savannah River Site

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

Brigmon, R.L.

Bioremediation of chlorinated solvents, both natural and accelerated, is exemplified by phytoremediation and biodegradation by rhizosphere microorganisms. Phytoremediation is the use of vegetation for the treatment of contaminated soils, sediments, and water. The potential for phytoremediation of chlorinated solvents has been demonstrated at the Savannah River Site (SRS) Miscellaneous Chemical Basin, Southern Sector of A/M Area and TNX/D-Area. Recent characterization work at the SRS has delineated widespread plumes (1-2 miles) of low concentration (40 ppb -10-ppm range) trichloroethylene (TCE) and perchloroethylene (PCE) contaminated groundwater. Phytoremediation deployments are underway for TCE and PCE phytoremediation in select SRS areas. Phytoremediation appears tomore » be an excellent technology to intercept and control plume migration. The ongoing Southern Sector treatability study is part of a multi-year field study of SRS seepline-soil systems maintained under saturated conditions. The primary focus is on determining how trees, seepline groundcover, soil microbial communities, and geochemical and surface-volatilization processes affect TCE and PCE in contaminated groundwater that flows through surface seepline areas. Therefore, FY00 represented an initial acclimation phase for soil and plant systems and will facilitate examination of seepline phyto- and bioactivity in subsequent growth season in FY01.« less

Mapping bedrock surface contours using the horizontal-to-vertical spectral ratio (HVSR) method near the middle quarter srea, Woodbury, Connecticut

USGS Publications Warehouse

Brown, Craig J.; Voytek, Emily B.; Lane, John W.; Stone, Janet R.

2013-01-01

The bedrock surface contours in Woodbury, Connecticut, were determined downgradient of a commercial zone known as the Middle Quarter area (MQA) using the novel, noninvasive horizontal-to-vertical (H/V) spectral ratio (HVSR) passive seismic geophysical method. Boreholes and monitoring wells had been drilled in this area to characterize the shallow subsurface to within 20 feet (ft) of the land surface, but little was known about the deep subsurface, including sediment thicknesses and depths to bedrock (Starn and Brown, 2007; Brown and others, 2009). Improved information on the altitude of the bedrock surface and its spatial variation was needed for assessment and remediation of chlorinated solvents that have contaminated the overlying glacial aquifer that supplies water to wells in the area.

Membrane-Based Emitter for Coupling Microfluidics with Ultrasensitive Nanoelectrospray Ionization-Mass Spectrometry

PubMed Central

Sun, Xuefei; Kelly, Ryan T.; Tang, Keqi; Smith, Richard D.

2011-01-01

An integrated poly(dimethylsiloxane) (PDMS) membrane-based microfluidic emitter for high performance nanoelectrospray ionization-mass spectrometry (nanoESI-MS) has been fabricated and evaluated. The ~100-μm-thick emitter was created by cutting a PDMS membrane that protrudes beyond the bulk substrate. The reduced surface area at the emitter enhances the electric field and reduces wetting of the surface by the electrospray solvent. As such, the emitter enables highly stable electrosprays at flow rates as low as 10 nL/min, and is compatible with electrospray solvents containing a large organic component (e.g., 90% methanol). This approach enables facile emitter construction, and provides excellent stability, reproducibility and sensitivity, as well as compatibility with multilayer soft lithography. PMID:21657269

Water based on a molecular model behaves like a hard-sphere solvent for a nonpolar solute when the reference interaction site model and related theories are employed

NASA Astrophysics Data System (ADS)

Hayashi, Tomohiko; Oshima, Hiraku; Harano, Yuichi; Kinoshita, Masahiro

2016-09-01

For neutral hard-sphere solutes, we compare the reduced density profile of water around a solute g(r), solvation free energy μ, energy U, and entropy S under the isochoric condition predicted by the two theories: dielectrically consistent reference interaction site model (DRISM) and angle-dependent integral equation (ADIE) theories. A molecular model for water pertinent to each theory is adopted. The hypernetted-chain (HNC) closure is employed in the ADIE theory, and the HNC and Kovalenko-Hirata (K-H) closures are tested in the DRISM theory. We also calculate g(r), U, S, and μ of the same solute in a hard-sphere solvent whose molecular diameter and number density are set at those of water, in which case the radial-symmetric integral equation (RSIE) theory is employed. The dependences of μ, U, and S on the excluded volume and solvent-accessible surface area are analyzed using the morphometric approach (MA). The results from the ADIE theory are in by far better agreement with those from computer simulations available for g(r), U, and μ. For the DRISM theory, g(r) in the vicinity of the solute is quite high and becomes progressively higher as the solute diameter d U increases. By contrast, for the ADIE theory, it is much lower and becomes further lower as d U increases. Due to unphysically positive U and significantly larger |S|, μ from the DRISM theory becomes too high. It is interesting that μ, U, and S from the K-H closure are worse than those from the HNC closure. Overall, the results from the DRISM theory with a molecular model for water are quite similar to those from the RSIE theory with the hard-sphere solvent. Based on the results of the MA analysis, we comparatively discuss the different theoretical methods for cases where they are applied to studies on the solvation of a protein.

Linear regression models for solvent accessibility prediction in proteins.

PubMed

Wagner, Michael; Adamczak, Rafał; Porollo, Aleksey; Meller, Jarosław

2005-04-01

The relative solvent accessibility (RSA) of an amino acid residue in a protein structure is a real number that represents the solvent exposed surface area of this residue in relative terms. The problem of predicting the RSA from the primary amino acid sequence can therefore be cast as a regression problem. Nevertheless, RSA prediction has so far typically been cast as a classification problem. Consequently, various machine learning techniques have been used within the classification framework to predict whether a given amino acid exceeds some (arbitrary) RSA threshold and would thus be predicted to be "exposed," as opposed to "buried." We have recently developed novel methods for RSA prediction using nonlinear regression techniques which provide accurate estimates of the real-valued RSA and outperform classification-based approaches with respect to commonly used two-class projections. However, while their performance seems to provide a significant improvement over previously published approaches, these Neural Network (NN) based methods are computationally expensive to train and involve several thousand parameters. In this work, we develop alternative regression models for RSA prediction which are computationally much less expensive, involve orders-of-magnitude fewer parameters, and are still competitive in terms of prediction quality. In particular, we investigate several regression models for RSA prediction using linear L1-support vector regression (SVR) approaches as well as standard linear least squares (LS) regression. Using rigorously derived validation sets of protein structures and extensive cross-validation analysis, we compare the performance of the SVR with that of LS regression and NN-based methods. In particular, we show that the flexibility of the SVR (as encoded by metaparameters such as the error insensitivity and the error penalization terms) can be very beneficial to optimize the prediction accuracy for buried residues. We conclude that the simple and computationally much more efficient linear SVR performs comparably to nonlinear models and thus can be used in order to facilitate further attempts to design more accurate RSA prediction methods, with applications to fold recognition and de novo protein structure prediction methods.

Synthesis of metal oxide nanoparticles via a robust ``solvent-deficient'' method

NASA Astrophysics Data System (ADS)

Smith, Stacey J.; Huang, Baiyu; Liu, Shengfeng; Liu, Qingyuan; Olsen, Rebecca E.; Boerio-Goates, Juliana; Woodfield, Brian F.

2014-11-01

We report an efficient, general methodology for producing high-surface area metal oxide nanomaterials for a vast range of metal oxides, including at least one metal oxide nanomaterial from nearly every transition metal and semi-metal group in the periodic table (groups 3-4 and 6-15) as well as several from the lanthanide group (see Table 1). The method requires only 2-3 simple steps; a hydrated metal salt (usually a nitrate or chloride salt) is ground with bicarbonate (usually NH4HCO3) for 10-30 minutes to form a precursor that is then either untreated or rinsed before being calcined at relatively low temperatures (220-550 °C) for 1-3 hours. The method is thus similar to surfactant-free aqueous methods such as co-precipitation but is unique in that no solvents are added. The resulting ``solvent-deficient'' environment has interesting and unique consequences, including increased crystallinity of the products over other aqueous methods and a mesoporous nature in the inevitable agglomerates. The products are chemically pure and phase pure with crystallites generally 3-30 nm in average size that aggregate into high surface area, mesoporous agglomerates 50-300 nm in size that would be useful for catalyst and gas sensing applications. The versatility of products and efficiency of the method lend its unique potential for improving the industrial viability of a broad family of useful metal oxide nanomaterials. In this paper, we outline the methodology of the solvent-deficient method using our understanding of its mechanism, and we describe the range and quality of nanomaterials it has produced thus far.We report an efficient, general methodology for producing high-surface area metal oxide nanomaterials for a vast range of metal oxides, including at least one metal oxide nanomaterial from nearly every transition metal and semi-metal group in the periodic table (groups 3-4 and 6-15) as well as several from the lanthanide group (see Table 1). The method requires only 2-3 simple steps; a hydrated metal salt (usually a nitrate or chloride salt) is ground with bicarbonate (usually NH4HCO3) for 10-30 minutes to form a precursor that is then either untreated or rinsed before being calcined at relatively low temperatures (220-550 °C) for 1-3 hours. The method is thus similar to surfactant-free aqueous methods such as co-precipitation but is unique in that no solvents are added. The resulting ``solvent-deficient'' environment has interesting and unique consequences, including increased crystallinity of the products over other aqueous methods and a mesoporous nature in the inevitable agglomerates. The products are chemically pure and phase pure with crystallites generally 3-30 nm in average size that aggregate into high surface area, mesoporous agglomerates 50-300 nm in size that would be useful for catalyst and gas sensing applications. The versatility of products and efficiency of the method lend its unique potential for improving the industrial viability of a broad family of useful metal oxide nanomaterials. In this paper, we outline the methodology of the solvent-deficient method using our understanding of its mechanism, and we describe the range and quality of nanomaterials it has produced thus far. Electronic supplementary information (ESI) available: (1) Preliminary Netzsch milling results for Al2O3 and CeO2, (2) XRD patterns/analyses of the dried and rinsed precursors plotted with the ICDD standard patterns of the materials they contain, (3) all TG/DTA-MS data. See DOI: 10.1039/c4nr04964k

Modification of the crystal habit of celecoxib for improved processability.

PubMed

Banga, Sheere; Chawla, Garima; Varandani, Deepak; Mehta, B R; Bansal, Arvind K

2007-01-01

Crystallization is often used in the pharmaceutical industry for purification and isolation of drugs, and also as a means of generating polymorphs or isomorphs. The aim of this study was to investigate the role of extrinsic crystallization parameters on the crystallized product, with special emphasis on improving the mechanical properties of acicular celecoxib. Celecoxib isomorphs were prepared using different techniques (solvent crystallization and vapour diffusion) and crystallization conditions (solvents, stirring, degree of supersaturation, crystallization temperature and seeding). Powder X-ray diffractometry, spectroscopic and thermal methods were used to investigate physical characteristics of crystals. Growth kinetics and aggregation dynamics of crystallization in polar and non-polar solvents were simulated using a dynamic light scattering method. The quick appearance of broad peaks over the range of 10-8000 nm in chloroform during crystallization simulation studies indicated faster aggregation in non-polar solvents. Aspect ratio, flow, compressibility and surface area of recrystallized products were also determined. Surface topography was determined by atomic force microscopy and the lath-shaped crystals (aspect ratio of 2-4) exhibited a roughness index of 1.79 in comparison with 2.92 for needles. Overall, the lath-shaped isomorphs exhibited improved flow and better compressibility.

How wood adhesives work and where are the areas for improvement

Treesearch

Charles R. Frihart

2013-01-01

Invoking normal adhesion theory, bonding of wood would seem to be easy in that the surface has plenty of roughness for mechanical interlocking with high enough surface energy, there is an abundance of hydroxyl groups on the wood for hydrogen bonding to the adhesives, and the aqueous solvent in the adhesive can readily soak into the wood. In fact most adhesives will...

Carborane-Based Metal-Organic Framework with High Methane and Hydrogen Storage Capacities

DTIC Science & Technology

2013-01-01

guest solvent molecules were removed via supercritical CO2 (see the Supporting Information for activation details),30,31 the samples were further...unique geometry of the carborane unit, NU-135 has a very high volumetric BET surface area of ca. 1900 m2/cm3. CH4, CO2 , and H2 adsorption isotherms...NU-135 has a very high volumetric BET surface area of ca. 1900 m2/cm3. CH4, CO2 , and H2 adsorption isotherms were measured over a broad range of

On the Hofmeister effect: fluctuations at the protein-water interface and the surface tension.

PubMed

Bogár, Ferenc; Bartha, Ferenc; Násztor, Zoltán; Fábián, László; Leitgeb, Balázs; Dér, András

2014-07-24

We performed molecular dynamics simulations on the tryptophane-cage miniprotein using a nonpolarizable force field, in order to model the effect of concentrated water solutions of neutral salts on protein conformation, which is a manifestation of Hofmeister effects. From the equilibrium values and the fluctuations of the solvent accessible surface area of the miniprotein, the salt-induced changes of the mean value of protein-water interfacial tension were determined. At 300 K, the chaotropic ClO4(-) and NO3(-) decreased the interfacial tension according to their position in the Hofmeister series (by approximately 5 and 2.7 mN/m, respectively), while the kosmotropic F(-) increased it (by 1 mN/m). These values were compared to those obtained from the Gibbs equation using the excess surface adsorption calculated from the probability distribution of the water molecules and ions around the miniprotein, and the two sets were found to be very close to each other. Our results present a direct evidence for the central role of interfacial tension and fluctuations at the protein-water interface in Hofmeister phenomena, and provide a computational method for the determination of the protein-water interfacial tension, establishing a link between the phenomenological and microscopic description of protein-water interfaces.

Are Water-lean Solvent Systems Viable for Post-Combustion CO 2 Capture?

DOE PAGES

Heldebrant, David J.; Koech, Phillip K.; Rousseau, Roger; ...

2017-08-18

Here, we present here an overview of water-lean solvents that compares their projected costs and performance to aqueous amine systems, emphasizing critical areas of study needed to evaluate their performance against their water-based brethren. The work presented her focuses on bridging these knowledge gaps. Because the majority of water-lean solvents are still at the lab scale, substantial studies are still needed to model their performance at scale. This presents a significant challenge as eachformulation has different physical and thermodynamic properties and behavior, and quantifying how these different properties manifest themselves in conventional absorber-stripper configurations, or identifying new configurations that aremore » specific for a solvent’s signature behavior. We identify critical areas of study that are needed, and our efforts (e.g. custom infrastructure, molecular models) to predict, measure, and model these behaviors. Such findings are critical for determining the rheology required for heat exchanger design; absorber designs and packing to accommodate solvents with gradient changes (e.g. viscosity, contact angle, surface tension), and stripper configurations without direct steam utilization or water reflux. Another critical area of research need is to understand the molecular structure of the liquid interface and bulk as a function of CO 2 loading, and to assess whether conventional film theories accurately quantify solvent behavior, or if thermodynamic models adequately quantify activity coefficients of ions in solution. We conclude with an assessment of our efforts to aid in bridging the knowledge gaps in understanding water-lean solvents, and suggestions of what is needed to enable large-scale demonstrations to meet the United States Department of Energy’s year 2030 goal.« less

Are Water-lean Solvent Systems Viable for Post-Combustion CO 2 Capture?

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

Heldebrant, David J.; Koech, Phillip K.; Rousseau, Roger

Here, we present here an overview of water-lean solvents that compares their projected costs and performance to aqueous amine systems, emphasizing critical areas of study needed to evaluate their performance against their water-based brethren. The work presented her focuses on bridging these knowledge gaps. Because the majority of water-lean solvents are still at the lab scale, substantial studies are still needed to model their performance at scale. This presents a significant challenge as eachformulation has different physical and thermodynamic properties and behavior, and quantifying how these different properties manifest themselves in conventional absorber-stripper configurations, or identifying new configurations that aremore » specific for a solvent’s signature behavior. We identify critical areas of study that are needed, and our efforts (e.g. custom infrastructure, molecular models) to predict, measure, and model these behaviors. Such findings are critical for determining the rheology required for heat exchanger design; absorber designs and packing to accommodate solvents with gradient changes (e.g. viscosity, contact angle, surface tension), and stripper configurations without direct steam utilization or water reflux. Another critical area of research need is to understand the molecular structure of the liquid interface and bulk as a function of CO 2 loading, and to assess whether conventional film theories accurately quantify solvent behavior, or if thermodynamic models adequately quantify activity coefficients of ions in solution. We conclude with an assessment of our efforts to aid in bridging the knowledge gaps in understanding water-lean solvents, and suggestions of what is needed to enable large-scale demonstrations to meet the United States Department of Energy’s year 2030 goal.« less

Meletin sustained-release gliadin nanoparticles prepared via solvent surface modification on blending electrospraying

NASA Astrophysics Data System (ADS)

Yang, Yao-Yao; Zhang, Man; Liu, Zhe-Peng; Wang, Ke; Yu, Deng-Guang

2018-03-01

Almost all electrospraying processes are carried out under an air-solution interface, thereby overlooking the potential influence of an additional solvent surface modification between air and the working solution. A pure solvent was explored to temporarily and dynamically surround the solutions utilized for blending electrospraying, which contained a guest drug meletin and a protein drug carrier gliadin. The new modified processes created protein-based medicated nanoparticles (P2) with higher quality than their counterparts (P1) from blending processes, as demonstrated by the SEM and TEM images. Although the particles from the two processes were similar (nanocomposites), and the particles P1 were larger than P2, the later provided a better meletin sustained-release profile than the former. This finding was verified by the smaller initial burst release, longer sustained-release time period, and shorter late leveling-off stage. These unanticipated results were attributed to the rounder surface, the more uniform size distribution, and the smaller total surface area of particles P2 than P1. The microformation mechanism of the modified coaxial process was suggested. The protocols reported here paved a new way for the development of new kinds of functional nanoparticles by modifying the interfaces of working fluids during electrospraying.

POLLUTION PREVENTION RESEARCH FOR ORGANIC AIR EMISSIONS

EPA Science Inventory

The paper gives an overview of the U.S. EPA's pollution prevention (P2) research in three areas: (1) Surface Coating, such as wood furniture finishing, printing, and the use of adhesives and radiation-cured coatings; (2) Solvent Cleaning, such as vapor degreasing, process equipme...

Effect of structural changes of lignocelluloses material upon pre-treatment using green solvents

NASA Astrophysics Data System (ADS)

Gunny, Ahmad Anas Nagoor; Arbain, Dachyar; Jamal, Parveen

2017-04-01

The Malaysia Biomass strategy 2020 stated that the key step of biofuel production from biomass lies on the pretreatment process. Conventional `pre-treatment' methods are `non-green" and costly. The recent green and cost-effective biomass pretreatment is using new generation of Ionic Liquids also known as Deep Eutectic Solvents (DESs). DESs are made of renewable components are cheaper, greener and the process synthesis are easier. Thus, the present paper concerns with the preparation of various combination of DES and to study the effect of DESs pretreatment process on microcrystalline cellulose (MCC), a model substrate. The crystalline structural changes were studied using using X-ray Diffraction Methods, Fourier Transformed Infrared Spectroscopy (FTIR) and surface area and pore size analysis. Results showed reduction of crystalline structure of MCC treated with the DESs and increment of surface area and pore size of MCC after pre-treatment process. These results indicated the DES has successfully converted the lignocelluloses material in the form suitable for hydrolysis and conversion to simple sugar.

Shape-Dependent Photocatalytic Activity of Hydrothermally Synthesized Cadmium Sulfide Nanostructures.

PubMed

Kundu, Joyjit; Khilari, Santimoy; Pradhan, Debabrata

2017-03-22

The effective surface area of the nanostructured materials is known to play a prime role in catalysis. Here we demonstrate that the shape of the nanostructured materials plays an equally important role in their catalytic activity. Hierarchical CdS microstructures with different morphologies such as microspheres assembled of nanoplates, nanorods, nanoparticles, and nanobelts are synthesized using a simple hydrothermal method by tuning the volume ratio of solvents, i.e., water or ethylenediamine (en). With an optimum solvent ratio of 3:1 water:en, the roles of other synthesis parameters such as precursor's ratio, temperature, and precursor combinations are also explored and reported here. Four selected CdS microstructures are used as photocatalysts for the degradation of methylene blue and photoelectrochemical water splitting for hydrogen generation. In spite of smaller effective surface area of CdS nanoneedles/nanorods than that of CdS nanowires network, the former exhibits higher catalytic activity under visible light irradiation which is ascribed to the reduced charge recombination as confirmed from the photoluminescence study.

How ion properties determine the stability of a lipase enzyme in ionic liquids: a molecular dynamics study.

PubMed

Klähn, Marco; Lim, Geraldine S; Wu, Ping

2011-11-07

The influence of eight different ionic liquid (IL) solvents on the stability of the lipase Candida antarctica lipase B (CAL-B) is investigated with molecular dynamics (MD) simulations. Considered ILs contain cations that are based either on imidazolium or guanidinium as well as nitrate, tetrafluoroborate or hexafluorophosphate anions. Partial unfolding of CAL-B is observed during high-temperature MD simulations and related changes of CAL-B regarding its radius of gyration, surface area, secondary structure, amount of solvent close to the backbone and interaction strength with the ILs are evaluated. CAL-B stability is influenced primarily by anions in the order NO(3)(-)≪ BF(4)(-) < PF(6)(-) of increasing stability, which agrees with experiments. Cations influence protein stability less than anions but still substantially. Long decyl side chains, polar methoxy groups and guanidinium-based cations destabilize CAL-B more than short methyl groups, other non-polar groups and imidazolium-based cations, respectively. Two distinct causes for CAL-B destabilization are identified: a destabilization of the protein surface is facilitated mostly by strong Coulomb interactions of CAL-B with anions that exhibit a localized charge and strong polarization as well as with polar cation groups. Surface instability is characterized by an unraveling of α-helices and an increase of surface area, radius of gyration and protein-IL total interaction strength of CAL-B, all of which describe a destabilization of the folded protein state. On the other hand, a destabilization of the protein core is facilitated when direct core-IL interactions are feasible. This is the case when long alkyl chains are involved or when particularly hydrophobic ILs induce major conformational changes that enable ILs direct access to the protein core. This core instability is characterized by a disintegration of β-sheets, diffusion of ions into CAL-B and increasing protein-IL van der Waals interactions. This process describes a stabilization of the unfolded protein state. Both of these processes reduce the folding free energy and thus destabilize CAL-B. The results of this work clarify the impact of ions on CAL-B stabilization. An extrapolation of the observed trends enables proposing novel ILs in which protein stability could be enhanced further. This journal is © the Owner Societies 2011

Effects of Solvent Diols on the Synthesis of ZnFe2O4 Particles and Their Use as Heterogeneous Photo-Fenton Catalysts

PubMed Central

Anchieta, Chayene Gonçalves; Cancelier, Adriano; Mazutti, Marcio Antonio; Jahn, Sérgio Luiz; Kuhn, Raquel Cristine; Gündel, Andre; Chiavone-Filho, Osvaldo; Foletto, Edson Luiz

2014-01-01

A solvothermal method was used to prepare zinc ferrite spinel oxide (ZnFe2O4) using ethylene glycol and 1,4 butanediol as solvent diols, and the influence of diols on the physical properties of ZnFe2O4 particles was investigated. The produced particles were characterized by X-ray powder diffraction (XRD), atomic force microscopy (AFM), Fourier transform infrared spectroscopy (FTIR) and nitrogen adsorption isotherms, and the catalytic activity for the organic pollutant decomposition by heterogeneous photo-Fenton reaction was investigated. Both solvents produced particles with cubic spinel structure. Microporous and mesoporous structures were obtained when ethylene glycol and 1,4 butanediol were used as diols, respectively. A higher pore volume and surface area, as well as a higher catalytic activity for the pollutant degradation were found when 1,4 butanediol was used as solvent. PMID:28788191

Effects of different force fields on the structural character of α synuclein β-hairpin peptide (35-56) in aqueous environment.

PubMed

Kundu, Sangeeta

2018-02-01

The hallmark of Parkinson's disease (PD) is the intracellular protein aggregation forming Lewy Bodies (LB) and Lewy neuritis which comprise mostly of a protein, alpha synuclein (α-syn). Molecular dynamics (MD) simulation methods can augment experimental techniques to understand misfolding and aggregation pathways with atomistic resolution. The quality of MD simulations for proteins and peptides depends greatly on the accuracy of empirical force fields. The aim of this work is to investigate the effects of different force fields on the structural character of β hairpin fragment of α-syn (residues 35-56) peptide in aqueous solution. Six independent MD simulations are done in explicit solvent using, AMBER03, AMBER99SB, GROMOS96 43A1, GROMOS96 53A6, OPLS-AA, and CHARMM27 force fields with CMAP corrections. The performance of each force field is assessed from several structural parameters such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), formation of β-turn, the stability of folded β-hairpin structure, and the favourable conformations obtained for different force fields. In this study, CMAP correction of CHARMM27 force field is found to overestimate the helical conformation, while GROMOS96 53A6 is found to most successfully capture the conformational dynamics of α-syn β-hairpin fragment as elicited from NMR.

Haloalkane hydrolysis with an immobilized haloalkane dehalogenase.

PubMed

Dravis, B C; Swanson, P E; Russell, A J

2001-11-20

Haloalkane dehalogenase from Rhodococcus rhodochrous was covalently immobilized onto a polyethyleneimine impregnated gamma-alumina support. The dehalogenating enzyme was found to retain greater than 40% of its original activity after immobilization, displaying an optimal loading (max. activity/supported protein) of 70 to 75 mg/g with an apparent maximum (max. protein/support) of 156 mg/g. The substrate, 1,2,3-trichloropropane, was found to favorably partition (adsorb) onto the inorganic alumina carrier (10 to 20 mg/g), thereby increasing the local reactant concentration with respect to the catalyst's environment, whereas the product, 2,3-dichloropropan-1-ol, demonstrated no affinity. Additionally, the inorganic alumina support exhibited no adverse effects because of solvent/component incompatibilities or deterioration due to pH variance (pH 7.0 to 10.5). As a result of the large surface area to volume ratio of the support matrix and the accessibility of the bound protein, the immobilized biocatalyst was not subject to internal mass transfer limitations. External diffusional restrictions could be eliminated with simple agitation (mixing speed: 50 rpm; flux: 4.22 cm/min). The pH-dependence of the immobilized dehalogenase was essentially the same as that for the native enzyme. Finally, both the thermostability and resistance toward inactivation by organic solvent were improved by more than an order of magnitude after immobilization. Copyright 2001 John Wiley & Sons, Inc.

Synthesis and Characterization of Functionalized Metal-organic Frameworks

PubMed Central

Karagiaridi, Olga; Bury, Wojciech; Sarjeant, Amy A.; Hupp, Joseph T.; Farha, Omar K.

2014-01-01

Metal-organic frameworks have attracted extraordinary amounts of research attention, as they are attractive candidates for numerous industrial and technological applications. Their signature property is their ultrahigh porosity, which however imparts a series of challenges when it comes to both constructing them and working with them. Securing desired MOF chemical and physical functionality by linker/node assembly into a highly porous framework of choice can pose difficulties, as less porous and more thermodynamically stable congeners (e.g., other crystalline polymorphs, catenated analogues) are often preferentially obtained by conventional synthesis methods. Once the desired product is obtained, its characterization often requires specialized techniques that address complications potentially arising from, for example, guest-molecule loss or preferential orientation of microcrystallites. Finally, accessing the large voids inside the MOFs for use in applications that involve gases can be problematic, as frameworks may be subject to collapse during removal of solvent molecules (remnants of solvothermal synthesis). In this paper, we describe synthesis and characterization methods routinely utilized in our lab either to solve or circumvent these issues. The methods include solvent-assisted linker exchange, powder X-ray diffraction in capillaries, and materials activation (cavity evacuation) by supercritical CO2 drying. Finally, we provide a protocol for determining a suitable pressure region for applying the Brunauer-Emmett-Teller analysis to nitrogen isotherms, so as to estimate surface area of MOFs with good accuracy. PMID:25225784

The Use of Solar Heating and Heat Cured Polymers for Lunar Surface Stabilization

NASA Technical Reports Server (NTRS)

Hintze, Paul; Curran, Jerry; Back, Reddy

2008-01-01

Dust ejecta can affect visibility during a lunar landing, erode nearby coated surfaces and get into mechanical assemblies of in-place infrastructure. Regolith erosion was observed at many of the Apollo landing sites. This problem needs to be addressed at the beginning of the lunar base missions, as the amount of infrastructure susceptible to problems will increase with each landing. Protecting infrastructure from dust and debris is a crucial step in its long term functionality. A proposed way to mitigate these hazards is to build a lunar launch pad. Other areas of a lunar habitat will also need surface stabilization methods to help mitigate dust hazards. Roads would prevent dust from being lifted during movement and dust free zones might be required for certain areas critical to crew safety or to critical science missions. Work at NASA Kennedy Space Center (KSC) is investigating methods of stabilizing the lunar regolith including: sintering the regolith into a solid and using heat or UV cured polymers to stabilize the surface. Sintering, a method in which powders are heated until fusing into solids, has been proposed as one way of building a Lunar launch/landing pad. A solar concentrator has been built and used in the field to sinter JSC-1 Lunar stimulant. Polymer palliatives are used by the military to build helicopter landing pads and roads in dusty and sandy areas. Those polymers are dispersed in a solvent (water), making them unsuitable for lunar use. Commercially available, solvent free, polymer powders are being investigated to determine their viability to work in the same way as the solvent borne terrestrial analog. This presentation will describe the ongoing work at KSC in this field. Results from field testing will be presented. Physical testing results, including compression and abrasion, of field and laboratory prepared samples will be presented.

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

NASA Astrophysics Data System (ADS)

Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

2016-09-01

We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.

PubMed

Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

2016-09-01

We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

Bioremediation of a Large Chlorinated Solvent Plume, Dover AFB, DE

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

Bloom, Aleisa C

2015-01-01

Bioremediation of a Large Chlorinated Solvent Plume, Dover AFB, DE Aleisa Bloom, (Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA) Robert Lyon (bob.lyon@aecom.com), Laurie Stenberg, and Holly Brown (AECOM, Germantown, Maryland, USA) ABSTRACT: Past disposal practices at Dover Air Force Base (AFB), Delaware, created a large solvent plume called Area 6 (about 1 mile long, 2,000 feet wide, and 345 acres). The main contaminants are PCE, TCE, and their degradation products. The remedy is in-situ accelerated anaerobic bioremediation (AAB). AAB started in 2006 and is focusing on source areas and downgradient plume cores. Direct-push injections occurred in source areas wheremore » contamination is typically between 5 and 20 feet below ground surface. Lower concentration dissolved-phased contamination is present downgradient at 35 and 50 feet below ground surface. Here, permanent injection/extraction wells installed in transects perpendicular to the flow of groundwater are used to apply AAB. The AAB substrate is a mix of sodium lactate, emulsified vegetable oil, and nutrients. After eight years, dissolved contaminant mass within the main 80-acre treatment area has been reduced by over 98 percent. This successful application of AAB has stopped the flux of contaminants to the more distal portions of the plume. While more time is needed for effects to be seen in the distal plume, AAB injections will soon cease, and the remedy will transition to natural attenuation. INTRODUCTION Oak Ridge National Laboratory Environmental Science Division (ORNL) and AECOM (formerly URS Corporation) have successfully implemented in situ accelerated anaerobic bioremediation (AAB) to remediate chlorinated solvent contamination in a large, multi-sourced groundwater plume at Dover Air Force Base (AFB). AAB has resulted in significant reductions of dissolved phase chlorinated solvent concentrations. This plume, called Area 6, was originally over 1 mile in length and over 2,000 feet wide (Figure 1). It originated from at least four separate source areas that comingled in the subsurface to form the large plume. The major contaminants of concern (COCs) are tetrachloroethene (PCE), trichloroethene (TCE), and 1,1,1-trichloroethane (1,1,1-TCA), which were historically used for degreasing operations in the maintenance of aircraft and support vehicles. Relatively small areas of elevated PCE, TCE, and 1,1,1-TCA were delineated in the shallow portion of the water table aquifer by direct-push groundwater sampling. Focused direct-push AAB treatment occurred in March 2006 at these source areas (Figure 1). Downgradient of the these areas and deeper in the aquifer, AAB treatment was implemented using rows of extraction/injection wells oriented perpendicular to groundwater flow to create multiple reductive zones across the plume cores, defined as areas where more than 1,000 micrograms per liter (ug/L) total solvent concentrations were present. Initial indications of successful degradation were observed within 6 months of starting injections. FIGURE 1. Dover AFB Area 6 plume. This paper describes the AAB implementation and progress of remediation after 8 years of treatment and periodic groundwater monitoring. SITE LITHOLOGY Contamination at the site is limited to the surficial aquifer, which consists of 35 to 50 feet (ft) (11 to 15 meters [m]) of unconsolidated Pleistocene deposits of the Columbia Formation. The Columbia Formation consists of fine to coarse sand with silt and clay lenses and less common gravel lenses. Silts and silty sands are generally encountered to a depth of 10 to 12 ft (3.05 to 3.65 m) below ground surface (bgs) and grade to medium- and coarse-grained sands to a depth of 35 to 50 ft (11 to 15 m) bgs. There is a clay and silt unit (part of the Calvert Formation) below the surficial aquifer that acts as an aquitard to the downward migration of contaminants. The depth to the water table varies across the site but usually ranges from 8 to 15 ft (2.4 to 4.5 m) bgs in the treatment area. REMEDIAL APPROACH AND OPERATIONS Because the Columbia Aquifer is used as a source of potable water off base, the remedial goal is to restore the aquifer to usable condition, i.e., reduce all chemicals of concern to below drinking water maximum contaminant levels (MCLs). To achieve this goal, AAB was selected as the best remedial alternative to reduce the solvent contamination. Source areas with high solvent concentrations were present in the shallow portion of the aquifer. From the source areas, dissolved solvents migrated downgradient and deeper in the aquifer with the flow of groundwater. In the deeper portion of the aquifer, the individual plumes comingle to form the larger Area 6 Plume, which covers approximately 345 acres. Types of Substrate. Previous AAB pilot tests at Dover AFB used either sodium lactate or emulsified vegetable oil (EVO) as substrates to stimulate microbial growth. The best results were obtained with...« less

Synthesis, fractionation, and thin film processing of nanoparticles using the tunable solvent properties of carbon dioxide gas expanded liquids

NASA Astrophysics Data System (ADS)

Anand, Madhu

Nanoparticles have received significant attention because of their unusual characteristics including high surface area to volume ratios. Materials built from nanoparticles possess unique chemical, physical, mechanical and optical properties. Due to these properties, they hold potential in application areas such as catalysts, sensors, semiconductors and optics. At the same time, CO 2 in the form of supercritical fluid or CO2 gas-expanded liquid mixtures has gained significant attention in the area of processing nanostructures. This dissertation focuses on the synthesis and processing of nanoparticles using CO2 tunable solvent systems. Nanoparticle properties depend heavily on their size and, as such, the ability to finely control the size and uniformity of nanoparticles is of utmost importance. Solution based nanoparticle formation techniques are attractive due to their simplicity, but they often result in the synthesis of particles with a wide size range. To address this limitation, a post-synthesis technique has been developed in this dissertation to fractionate polydisperse nanoparticles ( s . = 30%) into monodisperse fractions ( s . = 8%) using tunable physicochemical properties of CO 2 expanded liquids, where CO2 is employed as an antisolvent. This work demonstrates that by controlling the addition of CO2 (pressurization) to an organic dispersion of nanoparticles, the ligand stabilized nanoparticles can be size selectively precipitated within a novel high pressure apparatus that confines the particle precipitation to a specified location on a surface. Unlike current techniques, this CO2 expanded liquid approach provides faster and more efficient particle size separation, reduction in organic solvent usage, and pressure tunable size selection in a single process. To improve our fundamental understanding and to further refine the size separation process, a detailed study has been performed to identify the key parameters enabling size separation of various nanoparticle populations. This study details the influence of various factors on the size separation process, such as the types of nanoparticles, ligand type and solvent type as well as the use of recursive fractionation and the time allowed for settling during each fractionation step. This size selective precipitation technique was also applied to fractionate and separate polydisperse dispersions of CdSe/ZnS semiconductor nanocrystals into very distinct size and color fractions based solely on the pressure tunable solvent properties of CO2 expanded liquids. This size selective precipitation of nanoparticles is achieved by finely tuning the solvent strength of the CO2/organic solvent medium by simply adjusting the applied CO2 pressure. These subtle changes affect the balance between osmotic repulsive and van der Waals attractive forces thereby allowing fractionation of the nanocrystals into multiple narrow size populations. Thermodynamic analysis of nanoparticle size selective fractionation was performed to develop a theoretical model based on the thermodynamic properties of gas expanded liquids. We have used the general phenomenon of nanoparticle precipitation with CO2 expanded liquids to create dodecanethiol stabilized gold nanoparticle thin films. This method utilizes CO2 as an anti-solvent for low defect, wide area gold nanoparticle film formation employing monodisperse gold nanoparticles. Dodecanethiol stabilized gold particles are precipitated from hexane by controllably expanding the solution with carbon dioxide. Subsequent addition of carbon dioxide as a dense supercritical fluid then provides for removal of the organic solvent while avoiding the dewetting effects common to evaporating solvents. Unfortunately, the use of carbon dioxide as a neat solvent in nanoparticles synthesis and processing is limited by the very poor solvent strength of dense phase CO2. As a result, most current techniques employed to synthesize and disperse nanoparticles in neat carbon dioxide require the use of environmentally persistent fluorinated compounds as metal precursors and/or stabilizing ligands. This dissertation presents the first report of the simultaneous synthesis and stabilization of metallic nanoparticles in carbon dioxide solvent without the use of any fluorinated compounds thereby further enabling the use of CO 2 as a green solvent medium in nanomaterials synthesis and processing.

33 CFR 165.776 - Security Zone; Coast Guard Base San Juan, San Juan Harbor, Puerto Rico

Code of Federal Regulations, 2010 CFR

2010-07-01

... GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PORTS AND WATERWAYS SAFETY REGULATED NAVIGATION AREAS AND LIMITED ACCESS AREAS Specific Regulated Navigation Areas and Limited Access Areas Seventh Coast...) Location. The following area is a security zone: All waters from surface to bottom, encompassed by an...

Ultrafast adsorption and selective desorption of aqueous aromatic dyes by graphene sheets modified by graphene quantum dots

NASA Astrophysics Data System (ADS)

Ying, Yulong; He, Peng; Ding, Guqiao; Peng, Xinsheng

2016-06-01

Graphene modified by graphene quantum dots (GQDs) has been employed to remove toxic organic dyes. An excellent removal capacity (497 mg g-1) and record-breaking adsorption rate (475 mg g-1 min-1 at 20 °C) were demonstrated for Rhodamine B. The enhancement in performance by nearly a factor of three compared to that of graphene was ascribed to the greatly increased accessible surface area of graphene in aqueous solution as well as the increase in surface charges with the modification with GQDs. Besides, this unique adsorption behavior of the modified graphene was expanded to other typical toxic aqueous aromatic dyes such as Evans Blue, Methyl Orange, Malachite Green and Rose Bengal. What is more, a unique desorption behavior of dyes was first observed when employing different solvents, which enabled the GQD-modified graphene to be exploited for selective extraction of dyes and recycling of the adsorbent. The adsorption and desorption mechanism were further investigated. Combining high removal capacity, rapid adsorption kinetics, good recyclability and unique selective desorption, GQD-modified graphene has potential applications in both water purification and separation of aromatic dyes.

Insights into the effects of solvent properties in graphene based electric double-layer capacitors with organic electrolytes

NASA Astrophysics Data System (ADS)

Zhang, Shuo; Bo, Zheng; Yang, Huachao; Yang, Jinyuan; Duan, Liangping; Yan, Jianhua; Cen, Kefa

2016-12-01

Organic electrolytes are widely used in electric double-layer capacitors (EDLCs). In this work, the microstructure of planar graphene-based EDLCs with different organic solvents are investigated with molecular dynamics simulations. Results show that an increase of solvent polarity could weaken the accumulation of counter-ions nearby the electrode surface, due to the screen of electrode charges and relatively lower ionic desolvation. It thus suggests that solvents with low polarity could be preferable to yield high EDL capacitance. Meanwhile, the significant effects of the size and structure of solvent molecules are reflected by non-electrostatic molecule-electrode interactions, further influencing the adsorption of solvent molecules on electrode surface. Compared with dimethyl carbonate, γ-butyrolactone, and propylene carbonate, acetonitrile with relatively small-size and linear structure owns weak non-electrostatic interactions, which favors the easy re-orientation of solvent molecules. Moreover, the shift of solvent orientation in surface layer, from parallel orientation to perpendicular orientation relative to the electrode surface, deciphers the solvent twin-peak behavior near negative electrode. The as-obtained insights into the roles of solvent properties on the interplays among particles and electrodes elucidate the solvent influences on the microstructure and capacitive behavior of EDLCs using organic electrolytes.

40 CFR 761.389 - Testing parameter requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... variable testing parameters described in this section which may be used in the validation study. The conditions demonstrated in the validation study for these variables shall become the required conditions for.... During the validation study, use the same ratio of contaminated surface area to soak solvent volume as...

40 CFR 761.389 - Testing parameter requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... variable testing parameters described in this section which may be used in the validation study. The conditions demonstrated in the validation study for these variables shall become the required conditions for.... During the validation study, use the same ratio of contaminated surface area to soak solvent volume as...

40 CFR 761.389 - Testing parameter requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... variable testing parameters described in this section which may be used in the validation study. The conditions demonstrated in the validation study for these variables shall become the required conditions for.... During the validation study, use the same ratio of contaminated surface area to soak solvent volume as...

Solvent-Induced Cadmium(II) Metal-Organic Frameworks with Adjustable Guest-Evacuated Porosity: Application in the Controllable Assembly of MOF-Derived Porous Carbon Materials for Supercapacitors.

PubMed

Yue, Man-Li; Jiang, Yi-Fan; Zhang, Lin; Yu, Cheng-Yan; Zou, Kang-Yu; Li, Zuo-Xi

2017-11-07

In this work, five new cadmium metal-organic frameworks (Cd-MOFs 1-5) have been synthesized from solvothermal reactions of Cd(NO 3 ) 2 ⋅4 H 2 O with isophthalic acid and 1,4-bis(imidazol-1-yl)-benzene under different solvent systems of CH 3 OH, C 2 H 5 OH, (CH 3 ) 2 CHOH, DMF, and N-methyl-2-pyrrolidone (NMP), respectively. Cd-MOF 1 shows a 3D diamondoid framework with 1D rhombic and hexagonal channels, and the porosity is 12.9 %. Cd-MOF 2 exhibits a 2D (4,4) layer with a 1D parallelogram channel and porosity of 23.6 %. Cd-MOF 3 has an 8-connected dense network with the Schäfli symbol of [4 24 ⋅6 4 ] based on the Cd 6 cluster. Cd-MOFs 4-5 are isomorphous, and display an absolutely double-bridging 2D (4,4) layer with 1D tetragonal channels and porosities of 29.2 and 28.2 %, which are occupied by DMF and NMP molecules, respectively. Followed by the calcination-thermolysis procedure, Cd-MOFs 1-5 are employed as precursors to prepare MOF-derived porous carbon materials (labeled as PC-me, PC-eth, PC-ipr, PC-dmf and PC-nmp), which have the BET specific surface area of 23, 51, 10, 122, and 96 m 2  g -1 , respectively. The results demonstrate that the specific surface area of PCs is tuned by the porosity of Cd-MOFs, where the later is highly dependent on the solvent. Thereby, the specific surface area of PCs could be adjusted by the solvent used in the synthese of MOF precusors. Significantly, PCs have been further activated by KOH to obtain activated carbon materials (APCs), which possess even higher specific surface area and larger porosity. After a series of characterization and electrochemical investigations, the APC-dmf electrode exhibits the best porous properties and largest specific capacitances (153 F g -1 at 5 mV s -1 and 156 F g -1 at 0.5 Ag -1 ). Meanwhile, the APC-dmf electrode shows excellent cycling stability (ca. 84.2 % after 5000 cycles at 1 Ag -1 ), which can be applied as a suitable electrode material for supercapacitors. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pyrite footprinting of RNA

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

Schlatterer, Joerg C., E-mail: joerg.schlatterer@einstein.yu.edu; Wieder, Matthew S.; Jones, Christopher D.

2012-08-24

Highlights: Black-Right-Pointing-Pointer RNA structure is mapped by pyrite mediated {sup {center_dot}}OH footprinting. Black-Right-Pointing-Pointer Repetitive experiments can be done in a powdered pyrite filled cartridge. Black-Right-Pointing-Pointer High {sup {center_dot}}OH reactivity of nucleotides imply dynamic role in Diels-Alderase catalysis. -- Abstract: In RNA, function follows form. Mapping the surface of RNA molecules with chemical and enzymatic probes has revealed invaluable information about structure and folding. Hydroxyl radicals ({sup {center_dot}}OH) map the surface of nucleic acids by cutting the backbone where it is accessible to solvent. Recent studies showed that a microfluidic chip containing pyrite (FeS{sub 2}) can produce sufficient {sup {center_dot}}OH tomore » footprint DNA. The 49-nt Diels-Alder RNA enzyme catalyzes the C-C bond formation between a diene and a dienophile. A crystal structure, molecular dynamics simulation and atomic mutagenesis studies suggest that nucleotides of an asymmetric bulge participate in the dynamic architecture of the ribozyme's active center. Of note is that residue U42 directly interacts with the product in the crystallized RNA/product complex. Here, we use powdered pyrite held in a commercially available cartridge to footprint the Diels-Alderase ribozyme with single nucleotide resolution. Residues C39 to U42 are more reactive to {sup {center_dot}}OH than predicted by the solvent accessibility calculated from the crystal structure suggesting that this loop is dynamic in solution. The loop's flexibility may contribute to substrate recruitment and product release. Our implementation of pyrite-mediated {sup {center_dot}}OH footprinting is a readily accessible approach to gleaning information about the architecture of small RNA molecules.« less

The Importance of Non-accessible Crosslinks and Solvent Accessible Surface Distance in Modeling Proteins with Restraints From Crosslinking Mass Spectrometry*

PubMed Central

Bullock, Joshua Matthew Allen; Schwab, Jannik; Thalassinos, Konstantinos; Topf, Maya

2016-01-01

Crosslinking mass spectrometry (XL-MS) is becoming an increasingly popular technique for modeling protein monomers and complexes. The distance restraints garnered from these experiments can be used alone or as part of an integrative modeling approach, incorporating data from many sources. However, modeling practices are varied and the difference in their usefulness is not clear. Here, we develop a new scoring procedure for models based on crosslink data—Matched and Nonaccessible Crosslink score (MNXL). We compare its performance with that of other commonly-used scoring functions (Number of Violations and Sum of Violation Distances) on a benchmark of 14 protein domains, each with 300 corresponding models (at various levels of quality) and associated, previously published, experimental crosslinks (XLdb). The distances between crosslinked lysines are calculated either as Euclidean distances or Solvent Accessible Surface Distances (SASD) using a newly-developed method (Jwalk). MNXL takes into account whether a crosslink is nonaccessible, i.e. an experimentally observed crosslink has no corresponding SASD in a model due to buried lysines. This metric alone is shown to have a significant impact on modeling performance and is a concept that is not considered at present if only Euclidean distances are used. Additionally, a comparison between modeling with SASD or Euclidean distance shows that SASD is superior, even when factoring out the effect of the nonaccessible crosslinks. Our benchmarking also shows that MNXL outperforms the other tested scoring functions in terms of precision and correlation to Cα-RMSD from the crystal structure. We finally test the MNXL at different levels of crosslink recovery (i.e. the percentage of crosslinks experimentally observed out of all theoretical ones) and set a target recovery of ∼20% after which the performance plateaus. PMID:27150526

Evaluating and modeling the effects of surface sampling factors on the recovery of organic chemical attribution signatures using the accelerated diffusion sampler and solvent extraction

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

Mo, Kai-For; Heredia-Langner, Alejandro; Fraga, Carlos G.

In this study, an experimental design matrix was created and executed in order to test the effects of various real-world factors on the ability of the (1) accelerated diffusion sampler with solid phase micro-extraction (ADS-SPME) and (2) solvent extraction to capture organic chemical attribution signatures (CAS) from dimethyl methylphosphonate (DMMP) spiked onto painted wall board (PWB) surfaces. The DMMP CAS organic impurities sampled by ADS-SPME and solvent extraction were analyzed by gas chromatography/mass spectrometry (GC/MS). The number of detected DMMP CAS impurities and their respective GC/MS peak areas were determined as a function of DMMP stock, DMMP spiked volume, exposuremore » time, SPME sampling time, and ADS headspace pressure. Based on the statistical analysis of experimental results, several general conclusions are made: (1) ADS-SPME with vacuum (i.e., reduced pressure) increased the amount of detected CAS impurity, as measured by GC/MS peak area, by a factor of 1.7 to 1.9 for PWB under certain experimental conditions, (2) the amount of detected CAS impurity was most influenced by spiked volume, stock, and ADS headspace pressure, (3) the ADS had no measurable effect on the number of detected DMMP impurities, that is, the ADS (with and without reduced pressure) had no practical effect on the DMMP impurity profile collected from spiked PWB, and (4) solvent extraction out performed ADS-SPME in terms of consistently capturing all or most of the targeted DMMP impurities from spiked PWB.« less

Evaluating and modeling the effects of surface sampling factors on the recovery of organic chemical attribution signatures using the accelerated diffusion sampler and solvent extraction.

PubMed

Mo, Kai-For; Heredia-Langner, Alejandro; Fraga, Carlos G

2017-03-01

In this study, an experimental design matrix was created and executed to test the effects of various real-world factors on the ability of (1) the accelerated diffusion sampler with solid phase micro-extraction (ADS-SPME) and (2) solvent extraction to capture organic chemical attribution signatures (CAS) from dimethyl methylphosphonate (DMMP) spiked onto painted wall board (PWB) surfaces. The DMMP CAS organic impurities sampled by ADS-SPME and solvent extraction were analyzed by gas chromatography/mass spectrometry (GC/MS). The number of detected DMMP CAS impurities and their respective GC/MS peak areas were determined as a function of DMMP stock, DMMP spiked volume, exposure time, SPME sampling time, and ADS headspace pressure. Based on the statistical analysis of experimental results, several general conclusions are made: (1) the amount of CAS impurity detected using ADS-SPME and GC/MS was most influenced by spiked volume, stock, and ADS headspace pressure, (2) reduced ADS headspace pressure increased the amount of detected CAS impurity, as measured by GC/MS peak area, by up to a factor of 1.7-1.9 compared to ADS at ambient headspace pressure, (3) the ADS had no measurable effect on the number of detected DMMP impurities, that is, ADS (with and without reduced pressure) had no practical effect on the DMMP impurity profile collected from spiked PWB, and (4) solvent extraction out performed ADS-SPME in terms of consistently capturing all or most of the targeted DMMP impurities from spiked PWB. Copyright © 2016 Elsevier B.V. All rights reserved.

Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

NASA Astrophysics Data System (ADS)

Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

1998-08-01

A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

Application of a statistically enhanced, novel, organic solvent stable lipase from Bacillus safensis DVL-43.

PubMed

Kumar, Davender; Parshad, Rajinder; Gupta, Vijay Kumar

2014-05-01

This paper presents the molecular identification of a newly isolated bacterial strain producing a novel and organic solvent stable lipase, statistical optimization of fermentation medium, and its application in the synthesis of ethyl laurate. On the basis of nucleotide homology and phylogenetic analysis of 16S rDNA sequence, the strain was identified as Bacillus safensis DVL-43 (Gen-bank accession number KC156603). Optimization of fermentation medium using Plackett-Burman design and response surface methodology led to 11.4-fold increase in lipase production. The lipase from B. safensis DVL-43 exhibited excellent stability in various organic solvents. The enzyme retained 100% activity after 24h incubation in xylene, DMSO and toluene, each solvent being used at a concentration of 25% (v/v). The use of partially purified DVL-43 lipase as catalyst in the synthesis of ethyl laurate, an esterification product of lauric acid and ethanol, resulted in 80% esterification in 12h under optimized conditions. The formation of ethyl laurate was confirmed using TLC and (1)H NMR. Organic solvent stable lipases exhibiting potential application in enzymatic esterification are in great demand in flavor, fine chemicals and pharma industries. We could not find any report on lipase production from B. safensis strain and its application in esterification. Copyright © 2014 Elsevier B.V. All rights reserved.

Accessibility of Nitroxide Side Chains: Absolute Heisenberg Exchange Rates from Power Saturation EPR

PubMed Central

Altenbach, Christian; Froncisz, Wojciech; Hemker, Roy; Mchaourab, Hassane; Hubbell, Wayne L.

2005-01-01

In site-directed spin labeling, the relative solvent accessibility of spin-labeled side chains is taken to be proportional to the Heisenberg exchange rate (Wex) of the nitroxide with a paramagnetic reagent in solution. In turn, relative values of Wex are determined by continuous wave power saturation methods and expressed as a proportional and dimensionless parameter Π. In the experiments presented here, NiEDDA is characterized as a paramagnetic reagent for solvent accessibility studies, and it is shown that absolute values of Wex can be determined from Π, and that the proportionality constant relating them is independent of the paramagnetic reagent and mobility of the nitroxide. Based on absolute exchange rates, an accessibility factor is defined (0 < ρ < 1) that serves as a quantitative measure of side-chain solvent accessibility. The accessibility factors for a nitroxide side chain at 14 different sites in T4 lysozyme are shown to correlate with a structure-based accessibility parameter derived from the crystal structure of the protein. These results provide a useful means for relating crystallographic and site-directed spin labeling data, and hence comparing crystal and solution structures. PMID:15994891

Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution

PubMed Central

Zhang, Dawei; Lazim, Raudah

2017-01-01

In this study, we had exploited the advancement in computer technology to determine the stability of four apomyoglobin variants namely wild type, E109A, E109G and G65A/G73A by conducting conventional molecular dynamics simulations in explicit urea solution. Variations in RMSD, native contacts and solvent accessible surface area of the apomyoglobin variants during the simulation were calculated to probe the effect of mutation on the overall conformation of the protein. Subsequently, the mechanism leading to the destabilization of the apoMb variants was studied through the calculation of correlation matrix, principal component analyses, hydrogen bond analyses and RMSF. The results obtained here correlate well with the study conducted by Baldwin and Luo which showed improved stability of apomyoglobin with E109A mutation and contrariwise for E109G and G65A/G73A mutation. These positive observations showcase the feasibility of exploiting MD simulation in determining protein stability prior to protein expression. PMID:28300210

Molecular dynamics simulation analysis of Focal Adhesive Kinase (FAK) docked with solanesol as an anti-cancer agent

PubMed Central

Daneial, Betty; Joseph, Jacob Paul Vazhappilly; Ramakrishna, Guruprasad

2017-01-01

Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been associated in a series of cellular processes like cell migration and survival. FAK inhibition by an anti cancer agent is critical. Therefore, it is of interest to identify, modify, design, improve and develop molecules to inhibit FAK. Solanesol is known to have inhibitory activity towards FAK. However, the molecular principles of its binding with FAK is unknown. Solanesol is a highly flexible ligand (25 rotatable bonds). Hence, ligand-protein docking was completed using AutoDock with a modified contact based scoring function. The FAK-solanesol complex model was further energy minimized and simulated in GROMOS96 (53a6) force field followed by post simulation analysis such as Root mean square deviation (RMSD), root mean square fluctuations (RMSF) and solvent accessible surface area (SASA) calculations to explain solanesol-FAK binding. PMID:29081606

vmdICE: a plug-in for rapid evaluation of molecular dynamics simulations using VMD.

PubMed

Knapp, Bernhard; Lederer, Nadja; Omasits, Ulrich; Schreiner, Wolfgang

2010-12-01

Molecular dynamics (MD) is a powerful in silico method to investigate the interactions between biomolecules. It solves Newton's equations of motion for atoms over a specified period of time and yields a trajectory file, containing the different spatial arrangements of atoms during the simulation. The movements and energies of each single atom are recorded. For evaluating of these simulation trajectories with regard to biomedical implications, several methods are available. Three well-known ones are the root mean square deviation (RMSD), the root mean square fluctuation (RMSF) and solvent accessible surface area (SASA). Herein, we present a novel plug-in for the software "visual molecular dynamics" (VMD) that allows an interactive 3D representation of RMSD, RMSF, and SASA, directly on the molecule. On the one hand, our plug-in is easy to handle for inexperienced users, and on the other hand, it provides a fast and flexible graphical impression of the spatial dynamics of a system for experts in the field. © 2010 Wiley Periodicals, Inc.

Single Chain Structure of a Poly(N-isopropylacrylamide) Surfactant in Water

DOE PAGES

Abbott, Lauren J.; Tucker, Ashley K.; Stevens, Mark J.

2015-02-10

In this paper, we present atomistic simulations of a single PNIPAM–alkyl copolymer surfactant in aqueous solution at temperatures below and above the LCST of PNIPAM. We compare properties of the surfactant with pure PNIPAM oligomers of similar lengths, such as the radius of gyration and solvent accessible surface area, to determine the differences in their structures and transition behavior. We also explore changes in polymer–polymer and polymer–water interactions, including hydrogen bond formation. The expected behavior is observed in the pure PNIPAM oligomers, where the backbone folds onto itself above the LCST in order to shield the hydrophobic groups from water.more » The surfactant, on the other hand, does not show much conformational change as a function of temperature, but instead folds to bring the hydrophobic alkyl tail and PNIPAM headgroup together at all temperatures. Finally, the atomic detail available from these simulations offers important insight into understanding how the transition behavior is changed in PNIPAM-based systems.« less

Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution

NASA Astrophysics Data System (ADS)

Zhang, Dawei; Lazim, Raudah

2017-03-01

In this study, we had exploited the advancement in computer technology to determine the stability of four apomyoglobin variants namely wild type, E109A, E109G and G65A/G73A by conducting conventional molecular dynamics simulations in explicit urea solution. Variations in RMSD, native contacts and solvent accessible surface area of the apomyoglobin variants during the simulation were calculated to probe the effect of mutation on the overall conformation of the protein. Subsequently, the mechanism leading to the destabilization of the apoMb variants was studied through the calculation of correlation matrix, principal component analyses, hydrogen bond analyses and RMSF. The results obtained here correlate well with the study conducted by Baldwin and Luo which showed improved stability of apomyoglobin with E109A mutation and contrariwise for E109G and G65A/G73A mutation. These positive observations showcase the feasibility of exploiting MD simulation in determining protein stability prior to protein expression.

Structure-Based Prediction of Unstable Regions in Proteins: Applications to Protein Misfolding Diseases

NASA Astrophysics Data System (ADS)

Guest, Will; Cashman, Neil; Plotkin, Steven

2009-03-01

Protein misfolding is a necessary step in the pathogenesis of many diseases, including Creutzfeldt-Jakob disease (CJD) and familial amyotrophic lateral sclerosis (fALS). Identifying unstable structural elements in their causative proteins elucidates the early events of misfolding and presents targets for inhibition of the disease process. An algorithm was developed to calculate the Gibbs free energy of unfolding for all sequence-contiguous regions of a protein using three methods to parameterize energy changes: a modified G=o model, changes in solvent-accessible surface area, and solution of the Poisson-Boltzmann equation. The entropic effects of disulfide bonds and post-translational modifications are treated analytically. It incorporates a novel method for finding local dielectric constants inside a protein to accurately handle charge effects. We have predicted the unstable parts of prion protein and superoxide dismutase 1, the proteins involved in CJD and fALS respectively, and have used these regions as epitopes to prepare antibodies that are specific to the misfolded conformation and show promise as therapeutic agents.

Identifying Unstable Regions of Proteins Involved in Misfolding Diseases

NASA Astrophysics Data System (ADS)

Guest, Will; Cashman, Neil; Plotkin, Steven

2009-05-01

Protein misfolding is a necessary step in the pathogenesis of many diseases, including Creutzfeldt-Jakob disease (CJD) and familial amyotrophic lateral sclerosis (fALS). Identifying unstable structural elements in their causative proteins elucidates the early events of misfolding and presents targets for inhibition of the disease process. An algorithm was developed to calculate the Gibbs free energy of unfolding for all sequence-contiguous regions of a protein using three methods to parameterize energy changes: a modified G=o model, changes in solvent-accessible surface area, and all-atoms molecular dynamics. The entropic effects of disulfide bonds and post-translational modifications are treated analytically. It incorporates a novel method for finding local dielectric constants inside a protein to accurately handle charge effects. We have predicted the unstable parts of prion protein and superoxide dismutase 1, the proteins involved in CJD and fALS respectively, and have used these regions as epitopes to prepare antibodies that are specific to the misfolded conformation and show promise as therapeutic agents.

Computational insight into the capacitive performance of graphene edge planes

DOE PAGES

Zhan, Cheng; Zhang, Yu; Cummings, Peter T.; ...

2017-02-01

Recent experiments have shown that electric double-layer capacitors utilizing electrodes consisting of graphene edge plane exhibit higher capacitance than graphene basal plane. However, theoretical understanding of this capacitance enhancement is still limited. Here we applied a self-consistent joint density functional theory calculation on the electrode/electrolyte interface and found that the capacitance of graphene edge plane depends on the edge type: zigzag edge has higher capacitance than armchair edge due to the difference in their electronic structures. We further examined the quantum, dielectric, and electric double-layer (EDL) contributions to the total capacitance of the edge-plane electrodes. Classical molecular dynamics simulation foundmore » that the edge planes have higher EDL capacitance than the basal plane due to better adsorption of counter-ions and higher solvent accessible surface area. Finally, our work therefore has elucidated the capacitive energy storage in graphene edge planes that take into account both the electrode's electronic structure and the EDL structure.« less

Significantly enhancing enzymatic hydrolysis of rice straw after pretreatment using renewable ionic liquid-water mixtures.

PubMed

Hou, Xue-Dan; Li, Ning; Zong, Min-Hua

2013-05-01

Pretreatment of rice straw by using renewable cholinium lysine ionic liquid ([Ch][Lys] IL)-water mixtures and subsequent enzymatic hydrolysis of the residues were conducted in this work. There is a clear correlation between the delignification capacity of the pretreatment solvent and its basicity. After pretreatment, surface area and pore volume of rice straw increased significantly, which substantially improved polysaccharides accessibility to enzymes and thus enhanced polysaccharides digestion. By carefully controlling the pretreatment severity (IL content, temperature and duration), loss of readily extractable xylan could be minimized. The sugar yields of 81% for glucose and 48% for xylose were achieved in the enzymatic hydrolysis of rice straw after pretreatment with 20% [Ch][Lys]-water mixture at 90 °C for 1 h. This pretreatment process is highly promising for industrial application because of high sugar yields, low energy input, short pretreatment time, and being environmentally benign and highly tolerant to moisture. Copyright © 2013 Elsevier Ltd. All rights reserved.

Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution.

PubMed

Zhang, Dawei; Lazim, Raudah

2017-03-16

In this study, we had exploited the advancement in computer technology to determine the stability of four apomyoglobin variants namely wild type, E109A, E109G and G65A/G73A by conducting conventional molecular dynamics simulations in explicit urea solution. Variations in RMSD, native contacts and solvent accessible surface area of the apomyoglobin variants during the simulation were calculated to probe the effect of mutation on the overall conformation of the protein. Subsequently, the mechanism leading to the destabilization of the apoMb variants was studied through the calculation of correlation matrix, principal component analyses, hydrogen bond analyses and RMSF. The results obtained here correlate well with the study conducted by Baldwin and Luo which showed improved stability of apomyoglobin with E109A mutation and contrariwise for E109G and G65A/G73A mutation. These positive observations showcase the feasibility of exploiting MD simulation in determining protein stability prior to protein expression.

Molecular dynamics simulation analysis of Focal Adhesive Kinase (FAK) docked with solanesol as an anti-cancer agent.

PubMed

Daneial, Betty; Joseph, Jacob Paul Vazhappilly; Ramakrishna, Guruprasad

2017-01-01

Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been associated in a series of cellular processes like cell migration and survival. FAK inhibition by an anti cancer agent is critical. Therefore, it is of interest to identify, modify, design, improve and develop molecules to inhibit FAK. Solanesol is known to have inhibitory activity towards FAK. However, the molecular principles of its binding with FAK is unknown. Solanesol is a highly flexible ligand (25 rotatable bonds). Hence, ligand-protein docking was completed using AutoDock with a modified contact based scoring function. The FAK-solanesol complex model was further energy minimized and simulated in GROMOS96 (53a6) force field followed by post simulation analysis such as Root mean square deviation (RMSD), root mean square fluctuations (RMSF) and solvent accessible surface area (SASA) calculations to explain solanesol-FAK binding.

Ultrathin Hydrophobic Coatings Obtained on Polyethylene Terephthalate Materials in Supercritical Carbon Dioxide with Co-Solvents

NASA Astrophysics Data System (ADS)

Kumeeva, T. Yu.; Prorokova, N. P.

2018-02-01

The surface properties of ultradisperse polytetrafluoroethylene coatings on polyethylene terephthalate materials modified in a supercritical carbon dioxide medium with co-solvent additions (aliphatic alcohols) were analyzed. An atomic force microscopy study revealed the peculiarities of the morphology of the hydrophobic coatings formed in the presence of co-solvents. The contribution of the co-solvents to the formation of the surface layer with a low surface energy was evaluated from the surface energy components of the modified polyester material. The stability of the coatings against dry friction was analyzed.

Method for cleaning and passivating a metal surface

NASA Technical Reports Server (NTRS)

Alexander, George B. (Inventor); Carpenter, Norman F. (Inventor)

1976-01-01

A cleaning solvent useful in the cleaning of metal surfaces, e.g. nickle-iron alloys, contains sulfamic acid, citric acid, a solvent for hydrocarbon residues, and a surfactant. Metal surfaces are cleaned by contacting the surface with the cleaning solvent and then passivated by contact with aqueous solutions of citric acid or sodium nitrite or a combination of the two.

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

PubMed

Oshima, Hiraku; Kinoshita, Masahiro

2015-04-14

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 values, however, the many-body correlation plays significant roles in the β-sheet formation and argument of relative stabilities of very similar structures of a protein. These results are argued in detail with respect to the four physically insightful constituents and the two factors mentioned above. The relevance to the absence or presence of hydrogen-bonding properties in the solvent is also discussed in detail.

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

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

Oshima, Hiraku; Kinoshita, Masahiro, E-mail: kinoshit@iae.kyoto-u.ac.jp

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 modelsmore » 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 values, however, the many-body correlation plays significant roles in the β-sheet formation and argument of relative stabilities of very similar structures of a protein. These results are argued in detail with respect to the four physically insightful constituents and the two factors mentioned above. The relevance to the absence or presence of hydrogen-bonding properties in the solvent is also discussed in detail.« less

Solid-Supported Lipid Membranes: Formation, Stability and Applications

NASA Astrophysics Data System (ADS)

Goh, Haw Zan

This thesis presents a comprehensive investigation of the formation of supported lipid membranes with vesicle hemifusion, their stability under detergents and organic solvents and their applications in molecular biology. In Chapter 3, we describe how isolated patches of DOPC bilayers supported on glass surfaces are dissolved by various detergents (decyl maltoside, dodecyl maltoside, CHAPS, CTAB, SDS, TritonX-100 and Tween20) at their CMC, as investigated by fluorescence video microscopy. In general, detergents partition into distal leaflets of bilayers and lead to the expansion of the bilayers through a rolling motion of the distal over the proximal leaflets, in agreement with the first stage of the established 3-stage model of lipid vesicle solubilization by detergents. Subsequently, we study the partitioning of organic solvents (methanol, ethanol, isopropanol, propanol, acetone and chloroform) into isolated bilayer patches on glass in Chapter 4 with fluorescence microscopy. The area expansion of bilayers due to the partitioning of organic solvents is measured. From the titration of organic solvents, we measured the rate of area expansion as a function of the volume fraction of organic solvents, which is proposed to be a measure of strength of interactions between solvents and membranes. From the same experiments, we also measure the maximum expansion of bilayers (or the maximum binding stoichiometry between organic solvents and lipids) before structural breakdown, which depends on the depth of penetration of solvents to the membranes. In Chapter 5, we investigate the formation of sparsely-tethered bilayer lipid membranes (stBLMs) with vesicle hemifusion. In vesicle hemifusion, lipid vesicles in contact with a hydrophobic alkyl-terminated self-assembled monolayer (SAM) deposit a lipid monolayer to the SAM surface, thus completing the bilayer. Electrical Impedance Spectroscopy and Neutron Reflectivity are used to probe the integrity of stBLMs in terms of their insulating and structural properties. Preparation conditions are screened for those that are optimal for stBLM formation. Concentrations of lipid vesicles, hydrophobicity of SAMs, the presence of calcium and high concentrations of salt are identified as the key parameters. We show that stBLMs can be formed with vesicles of different compositions. Vesicle hemifusion opens up a new route in preserving the chemical compositions of stBLMs and facilitating membrane proteins incorporation. In Chapter 6, we visualize the hemifusion pathway of giant unilamellar vesicles (GUVs) with planar hydrophobic surfaces at the single vesicle level with fluorescence video microscopy. When a GUV hemifuses to a surface, its outer leaflet breaks apart and remains connected to the surface presumably through a hemifusion diaphragm. Lipids from the outer leaflet are transferred to the surface as a lipid monolayer that expands radially outward from the hemifusion diaphragm, thereby forming the loosely packed outer hemifusion zone. In Chapter 7, we develop an in vitro assay employing stBLMs and lipid vesicles to examine the functionality of GRASP in membrane tethering. Membrane-bound GRASP on opposing membranes dimerizes and tethers fluorescently-labeled vesicles to stBLMs. The fluorescence intensity of images taken at stBLM surfaces is used to quantify the tethering activity. Both wild type and mutant proteins were studied to shed light on the molecular mechanism of tethering. We show that the GRASP domain is sufficient and necessary for membrane tethering. In addition, the tethering capability of GRASP is impaired when the internal ligands and the binding pockets participating in dimerization are deleted and mutated. Membrane anchors, sizes of vesicles and membrane compositions are explored for their influence on the outcomes of the assay. Furthermore, preliminary analysis from neutron reflectivity measurements shows that both the internal ligands and binding pockets are exposed instead of buried toward the membrane surface. In summary, we establish a functional assay for studying GRASP activity in vitro. (Abstract shortened by UMI.)

Prediction of Protein-Protein Interaction Sites Using Electrostatic Desolvation Profiles

PubMed Central

Fiorucci, Sébastien; Zacharias, Martin

2010-01-01

Abstract Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces. PMID:20441756

Smoothing Polymer Surfaces by Solvent-Vapor Exposure

NASA Astrophysics Data System (ADS)

Anthamatten, Mitchell

2003-03-01

Ultra-smooth polymer surfaces are of great importance in a large body of technical applications such as optical coatings, supermirrors, waveguides, paints, and fusion targets. We are investigating a simple approach to controlling surface roughness: by temporarily swelling the polymer with solvent molecules. As the solvent penetrates into the polymer, its viscosity is lowered, and surface tension forces drive surface flattening. To investigate sorption kinetics and surface-smoothing phenomena, a series of vapor-deposited poly(amic acid) films were exposed to dimethyl sulfoxide vapors. During solvent exposure, the surface topology was continuously monitored using light interference microscopy. The resulting power spectra indicate that high-frequency defects smooth faster than low-frequency defects. This frequency dependence was studied by depositing polymer films onto a series of 2D sinusoidal surfaces and performing smoothing experiments. Results show that the amplitudes of the sinusoidal surfaces decay exponentially with solvent exposure time, and the exponential decay constants are proportional to surface frequency. This work was performed under the auspices of the U.S. Department of Energy by the University of California Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48.

Molecular dynamics simulations reveal the assembly mechanism of polysaccharides in marine aerosols.

PubMed

Sun, Lu; Li, Xin; Hede, Thomas; Tu, Yaoquan; Leck, Caroline; Ågren, Hans

2014-12-21

The high Arctic marine environment has recently detected polymer gels in atmospheric aerosol particles and cloud water originating from the surface microlayer of the open leads within the pack ice area. These polysaccharide molecules are water insoluble but water solvated, highly surface-active and highly hydrated (99% water). In order to add to the understanding and to complement missing laboratory characterization of marine polymer gels we have in this work performed an atomistic study of the assembly process and interfacial properties of polysaccharides. Our study reveals a number of salient features of the microscopic process behind polysaccharide assembly into nanogels. With three- and four-repeating units the polysaccharides assemble into a cluster in 50 ns. The aggregates grow quicker by absorbing one or two polymers each time, depending on the unit length and the type of inter-bridging cation. Although both the hydrophobic and hydrophilic domains are contracted, the latter dominates distinctly upon the contraction of solvent accessible surface areas. The establishment of inter-chain hydrogen-bonds is the key to the assembly while ionic bridges can further promote aggregation. During the assembly of the more bent four-unit polymers, intra-chain hydrogen bonds are significantly diminished by Ca(2+). Meanwhile, the percentage of Ca(2+) acting as an ionic bridge is more eminent, highlighting the significance of Ca(2+) ions for longer-chain polysaccharides. The aggregates are able to enhance surface tension more in the presence of Ca(2+) than in the presence of Na(+) owing to their more compact structure. These conclusions all demonstrate that studies of the present kind provide insight into the self-assembly process and interfacial properties of marine gels. We hope this understanding will keep up the interest in the complex and the fascinating relationship between marine microbiology, atmospheric aerosols, clouds and climate.

RaptorX-Property: a web server for protein structure property prediction.

PubMed

Wang, Sheng; Li, Wei; Liu, Shiwang; Xu, Jinbo

2016-07-08

RaptorX Property (http://raptorx2.uchicago.edu/StructurePropertyPred/predict/) is a web server predicting structure property of a protein sequence without using any templates. It outperforms other servers, especially for proteins without close homologs in PDB or with very sparse sequence profile (i.e. carries little evolutionary information). This server employs a powerful in-house deep learning model DeepCNF (Deep Convolutional Neural Fields) to predict secondary structure (SS), solvent accessibility (ACC) and disorder regions (DISO). DeepCNF not only models complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent property labels. Our experimental results show that, tested on CASP10, CASP11 and the other benchmarks, this server can obtain ∼84% Q3 accuracy for 3-state SS, ∼72% Q8 accuracy for 8-state SS, ∼66% Q3 accuracy for 3-state solvent accessibility, and ∼0.89 area under the ROC curve (AUC) for disorder prediction. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Probing the Self-Assembly and the Accompanying Structural Changes of Hydrophobin SC3 on a Hydrophobic Surface by Mass Spectrometry

PubMed Central

Wang, X.; Permentier, H. P.; Rink, R.; Kruijtzer, J. A. W.; Liskamp, R. M. J.; Wösten, H. A. B.; Poolman, B.; Robillard, G. T.

2004-01-01

The fungal class I hydrophobin SC3 self-assembles into an amphipathic membrane at hydrophilic-hydrophobic interfaces such as the water-air and water-Teflon interface. During self-assembly, the water-soluble state of SC3 proceeds via the intermediate α-helical state to the stable end form called the β-sheet state. Self-assembly of the hydrophobin at the Teflon surface is arrested in the α-helical state. The β-sheet state can be induced at elevated temperature in the presence of detergent. The structural changes of SC3 were monitored by various mass spectrometry techniques. We show that the so-called second loop of SC3 (C39–S72) has a high affinity for Teflon. Binding of this part of SC3 to Teflon was accompanied by the formation of α-helical structure and resulted in low solvent accessibility. The solvent-protected region of the second loop extended upon conversion to the β-sheet state. In contrast, the C-terminal part of SC3 became more exposed to the solvent. The results indicate that the second loop of class I hydrophobins plays a pivotal role in self-assembly at the hydrophilic-hydrophobic interface. Of interest, this loop is much smaller in case of class II hydrophobins, which may explain the differences in their assembly. PMID:15345568

Readily available titania nanostructuring routines based on mobility and polarity controlled phase separation of an amphiphilic diblock copolymer.

PubMed

Hohn, Nuri; Schlosser, Steffen J; Bießmann, Lorenz; Grott, Sebastian; Xia, Senlin; Wang, Kun; Schwartzkopf, Matthias; Roth, Stephan V; Müller-Buschbaum, Peter

2018-03-15

The amphiphilic diblock copolymer polystyrene-block-polyethylene oxide is combined with sol-gel chemistry to control the structure formation of blade-coated foam-like titania thin films. The influence of evaporation time before immersion into a poor solvent bath and polarity of the poor solvent bath are studied. Resulting morphological changes are quantified by scanning electron microscopy (SEM) and grazing incidence small angle X-ray scattering (GISAXS) measurements. SEM images surface structures while GISAXS accesses inner film structures. Due to the correlation of evaporation time and mobility of the polymer template during the phase separation process, a decrease in the distances of neighboring titania nanostructures from 50 nm to 22 nm is achieved. Furthermore, through an increase of polarity of an immersion bath the energetic incompatibility of the hydrophobic block and the solvent can be enhanced, leading to an increase of titania nanostructure distances from 35 nm to 55 nm. Thus, a simple approach is presented to control titania nanostructure in foam-like films prepared via blade coating, which enables an easy upscaling of film preparation.

Synthesis and characterization of gold nanodogbones by the seeded mediated growth method

NASA Astrophysics Data System (ADS)

Huang, Chien-Jung; Chiu, Pin-Hsiang; Wang, Yeong-Her; Meen, Teen-Hang; Yang, Cheng-Fu

2007-10-01

Novel gold nanodogbones (GDBs) are successfully fabricated using a simple seeded mediated growth (SMG) method. The shapes of GDBs depend on the amount of added vitamin C solvent. The amount of vitamin C solvent was varied from 10 to 40 µl to investigate the influence of vitamin C solvent on the GDBs. It is found that the aspect ratios (R) of GDBs were in the range from 2.34 to 1.46, and the UV-vis absorption measurement revealed a pronounced blueshift on the longitudinal surface plasmon resonance (SPR) band from 713 to 676 nm. The GDBs were determined by x-ray diffraction (XRD) to be single-crystalline with a face-centered cubic (fcc) structure. The lattice constant calculated from this selected-area electron diffraction (SAED) pattern is 4.068 Å.

Solvophobic and solvophilic contributions in the water-to-aqueous guanidinium chloride transfer free energy of model peptides

NASA Astrophysics Data System (ADS)

Tomar, Dheeraj S.; Ramesh, Niral; Asthagiri, D.

2018-06-01

We study the solvation free energy of two different conformations (helix and extended) of two different peptides (deca-alanine and deca-glycine) in two different solvents (water and aqueous guanidinium chloride, GdmCl). The free energies are obtained using the quasichemical organization of the potential distribution theorem, an approach that naturally provides the repulsive (solvophobic or cavity) and attractive (solvophilic) contributions to solvation. The solvophilic contribution is further parsed into a chemistry contribution arising from solute interaction with the solvent in the first solvation shell and a long-range contribution arising from non-specific interactions between the solute and the solvent beyond the first solvation shell. The cavity contribution is obtained for two different envelopes, ΣS E, which theory helps identify as the solvent excluded volume, and ΣG, a larger envelope beyond which solute-solvent interactions are Gaussian. The ΣS E envelope is independent of the solvent, as expected on the basis of the insensitivity to the solvent type of the distance of closest approach between protein heavy atoms and solvent heavy atoms, but contrary to the intuition based on treating solvent constituents as spheres of some effective radii. For both envelopes, the cavity contribution in water is proportional to the surface area of the envelope. The same does not hold for GdmCl(aq), revealing the limitation of using molecular area to assess solvation energetics. The ΣG-cavity contribution predicts that GdmCl(aq) should favor the more compact state, contrary to the role of GdmCl in unfolding proteins. The chemistry contribution attenuates this effect, but still the net local (chemistry plus ΣG-packing) contribution is inadequate in capturing the role of GdmCl. With the inclusion of the long-range contribution, which is dominated by van der Waals interaction, aqueous GdmCl favors the extended conformation over the compact conformation. Our finding emphasizes the importance of weak, but attractive, long-range dispersion interactions in protein solution thermodynamics.

Solvophobic and solvophilic contributions in the water-to-aqueous guanidinium chloride transfer free energy of model peptides.

PubMed

Tomar, Dheeraj S; Ramesh, Niral; Asthagiri, D

2018-06-14

We study the solvation free energy of two different conformations (helix and extended) of two different peptides (deca-alanine and deca-glycine) in two different solvents (water and aqueous guanidinium chloride, GdmCl). The free energies are obtained using the quasichemical organization of the potential distribution theorem, an approach that naturally provides the repulsive (solvophobic or cavity) and attractive (solvophilic) contributions to solvation. The solvophilic contribution is further parsed into a chemistry contribution arising from solute interaction with the solvent in the first solvation shell and a long-range contribution arising from non-specific interactions between the solute and the solvent beyond the first solvation shell. The cavity contribution is obtained for two different envelopes, Σ SE , which theory helps identify as the solvent excluded volume, and Σ G , a larger envelope beyond which solute-solvent interactions are Gaussian. The Σ SE envelope is independent of the solvent, as expected on the basis of the insensitivity to the solvent type of the distance of closest approach between protein heavy atoms and solvent heavy atoms, but contrary to the intuition based on treating solvent constituents as spheres of some effective radii. For both envelopes, the cavity contribution in water is proportional to the surface area of the envelope. The same does not hold for GdmCl(aq), revealing the limitation of using molecular area to assess solvation energetics. The Σ G -cavity contribution predicts that GdmCl(aq) should favor the more compact state, contrary to the role of GdmCl in unfolding proteins. The chemistry contribution attenuates this effect, but still the net local (chemistry plus Σ G -packing) contribution is inadequate in capturing the role of GdmCl. With the inclusion of the long-range contribution, which is dominated by van der Waals interaction, aqueous GdmCl favors the extended conformation over the compact conformation. Our finding emphasizes the importance of weak, but attractive, long-range dispersion interactions in protein solution thermodynamics.

Lipophilicity of a series of 1,2-benzisothiazol-3(2H)-ones determined by reversed-phase thin-layer chromatography.

PubMed

Sławik, Tomasz; Kowalski, Cezary

2002-04-05

The lipophilicity (R(Mo)) and specific hydrophobic surface area of seven 1,2-benzisothiazol-3(2H)-ones have been determined by reversed-phase TLC and the effect of different mobile-phase modifiers (acetone, acetonitrile, methanol) on the retention has been studied. The linear correlations between the volume fraction of the organic solvent and the R(M) values over a limited range were established for each solute with high values of correlation coefficients (>0.99). The influence of solvent pH on R(M) values was investigated.

Simultaneous tuning of chemical composition and topography of copolymer surfaces: micelles as building blocks.

PubMed

Zhao, Ning; Zhang, Xiaoyan; Zhang, Xiaoli; Xu, Jian

2007-05-14

A simple method is described for controlling the surface chemical composition and topography of the diblock copolymer poly(styrene)-b-poly(dimethylsiloxane)(PS-b-PDMS) by casting the copolymer solutions from solvents with different selectivities. The surface morphology and chemical composition were characterized by scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS), respectively, and the wetting behavior was studied by water contact angle (CA) and sliding angle (SA) and by CA hysteresis. Chemical composition and morphology of the surface depend on solvent properties, humidity of the air, solution concentration, and block lengths. If the copolymer is cast from a common solvent, the resultant surface is hydrophobic, with a flat morphology, and dominated by PDMS on the air side. From a PDMS-selective solvent, the surface topography depends on the morphology of the micelles. Starlike micelles give rise to a featureless surface nearly completely covered by PDMS, while crew-cut-like micelles lead to a rough surface with a hierarchical structure that consists partly of PDMS. From a PS-selective solvent, however, surface segregation of PDMS was restricted, and the surface morphology can be controlled by vapor-induced phase separation. On the basis of the tunable surface roughness and PDMS concentration on the air side, water repellency of the copolymer surface could be tailored from hydrophobic to superhydrophobic. In addition, reversible switching behavior between hydrophobic and superhydrophobic can be achieved by exposing the surface to solvents with different selectivities.

Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses.

PubMed

Chang, Hsiao-Han; Huber, Roland G; Bond, Peter J; Grad, Yonatan H; Camerini, David; Maurer-Stroh, Sebastian; Lipsitch, Marc

2017-07-01

To analyse the proportions of protein identity between Zika virus and dengue, Japanese encephalitis, yellow fever, West Nile and chikungunya viruses as well as polymorphism between different Zika virus strains. We used published protein sequences for the Zika virus and obtained protein sequences for the other viruses from the National Center for Biotechnology Information (NCBI) protein database or the NCBI virus variation resource. We used BLASTP to find regions of identity between viruses. We quantified the identity between the Zika virus and each of the other viruses, as well as within-Zika virus polymorphism for all amino acid k -mers across the proteome, with k ranging from 6 to 100. We assessed accessibility of protein fragments by calculating the solvent accessible surface area for the envelope and nonstructural-1 (NS1) proteins. In total, we identified 294 Zika virus protein fragments with both low proportion of identity with other viruses and low levels of polymorphisms among Zika virus strains. The list includes protein fragments from all Zika virus proteins, except NS3. NS4A has the highest number (190 k -mers) of protein fragments on the list. We provide a candidate list of protein fragments that could be used when developing a sensitive and specific serological test to detect previous Zika virus infections.

High Surface Area, Thermally Stable, Hydrophobic, Microporous, Rigid Gels Generated at Ambient from MeSi(OEt)3 /(EtO)3 SiCH2 CH2 Si(OEt)3 Mixtures by F- -Catalyzed Hydrolysis.

PubMed

Furgal, Joseph C; Yamane, Honami; Odykirk, Timothy R; Yi, Eongyu; Chujo, Yoshiki; Laine, Richard M

2018-01-02

High surface area materials are of considerable interest for gas storage/capture, molecular sieving, catalyst supports, as well as for slow-release drug-delivery systems. We report here a very simple and fast route to very high surface area, mechanically robust, hydrophobic polymer gels prepared by fluoride-catalyzed hydrolysis of mixtures of MeSi(OEt) 3 and bis-triethoxysilylethane (BTSE) at room temperature. These materials offer specific surface areas up to 1300 m 2  g -1 , peak pore sizes of 0.8 nm and thermal stabilities above 200 °C. The gelation times and surface areas can be controlled by adjusting the solvent volume (dichloromethane), percent fluoride (as nBu 4 NF or TBAF) and the BTSE contents. Polymers with other corners and linkers were also explored. These materials will further expand the materials databank for use in vacuum insulation panels and as thermally stable release and capture media. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spatial-Temporal dynamics of surface water flooding and consequences for emergency services accessibility

NASA Astrophysics Data System (ADS)

Pattison, Ian; Green, Daniel; Yu, Dapeng; Bosher, Lee; Wilby, Rob; Yang, Lili; Ryley, Tim

2016-04-01

Urban areas are increasingly susceptible to surface water flooding, with more intense precipitation and intensification of land development. Flooding has both direct impacts i.e. locations inundated with water, and indirect impacts i.e. transport networks, utility e.g. electricity/water services etc. The direct areas flooded evolve in space through the event, and are predicted by standard inundation models. However, the wider indirect impacts and the spatial-temporal patterns are less constrained and it is these that are needed to manage the impacts in real-time. This paper focusses on the Category One responders of the Fire and Rescue and Ambulance Services in the City of Leicester, East Midlands, UK. Leicester is ranked 16th out of 4215 settlements at risk of surface water flooding in the UK based upon the population at risk (15,200 people) (DEFRA, 2009). The analysis undertaken involved overlaying the flood extent with the Integrated Transport Network (ITN) data within a GIS framework. Then a simple transport routing algorithm was used to predict the travel time from specific nodes representing ambulance or fire stations to different parts of the city. Flood magnitudes with 1:20, 1:100 and 1:1000 return periods have been investigated. Under a scenario of no flooding, 100% of the city is accessible by the six fire stations in the city. However, in the 1 in 20 year surface water flood event the peak inundation results in 66.5% being accessible in the 10 minute permitted time and 6% is totally inaccessible. This falls to 40% and 13% respectively for the 1 in 100 year event. Maps show the area of the city that are accessible by two or more stations within the permitted response time, which shows these areas are the most resilient to surface water flooding. However, it isn't just the peak water depths at every location which impacts accessibility within the city but the spatial-temporal patterns of the inundation. The areas within the 10 minute response time expand and contract through the event as the inundated area makes roads in different parts of the city inaccessible through the event. These maps also allow key access roads to be identified. Key stakeholders, within the City of Leicester, have highlighted the potential benefit of such dynamic accessibility maps for their multi-agency planning and response for surface water flooding.

Surface properties of adipocyte lipid-binding protein: Response to lipid binding, and comparison with homologous proteins.

PubMed

LiCata, V J; Bernlohr, D A

1998-12-01

Adipocyte lipid-binding protein (ALBP) is one of a family of intracellular lipid-binding proteins (iLBPs) that bind fatty acids, retinoids, and other hydrophobic ligands. The different members of this family exhibit a highly conserved three-dimensional structure; and where structures have been determined both with (holo) and without (apo) bound lipid, observed conformational changes are extremely small (Banaszak, et al., 1994, Adv. Prot. Chem. 45, 89; Bernlohr, et al., 1997, Annu. Rev. Nutr. 17, 277). We have examined the electrostatic, hydrophobic, and water accessible surfaces of ALBP in the apo form and of holo forms with a variety of bound ligands. These calculations reveal a number of previously unrecognized changes between apo and holo ALBP, including: 1) an increase in the overall protein surface area when ligand binds, 2) expansion of the binding cavity when ligand is bound, 3) clustering of individual residue exposure increases in the area surrounding the proposed ligand entry portal, and 4) ligand-binding dependent variation in the topology of the electrostatic potential in the area surrounding the ligand entry portal. These focused analyses of the crystallographic structures thus reveal a number of subtle but consistent conformational and surface changes that might serve as markers for differential targeting of protein-lipid complexes within the cell. Most changes are consistent from ligand to ligand, however there are some ligand-specific changes. Comparable calculations with intestinal fatty-acid-binding protein and other vertebrate iLBPs show differences in the electrostatic topology, hydrophobic topology, and in localized changes in solvent exposure near the ligand entry portal. These results provide a basis toward understanding the functional and mechanistic differences among these highly structurally homologous proteins. Further, they suggest that iLBPs from different tissues exhibit one of two predominant end-state structural distributions of the ligand entry portal.

Thermal Motion and Forced Migration of Colloidal Particles Generate Hydrostatic Pressure in Solvent

PubMed Central

Hammel, H. T.; Scholander, P. F.

1973-01-01

A colloidal solution of ferrite particles in an osmometer has been used to demonstrate that the property that propels water across the semipermeable membrane is the decrease in hydrostatic pressure in the water of the solution. A magnetic field gradient directed so as to force the ferrite particles away from the semipermeable membrane of the osmometer and toward the free surface of the solution enhanced the colloidal osmotic pressure. The enhancement of this pressure was always exactly equal to the augmentation of the pressure as measured by the outward force of the particles, against the area of the free surface. Contrariwise, directing the magnetic field gradient so as to force the ferrite particles away from the free surface and toward the semipermeable membrane diminished the colloidal osmotic pressure of the solution. For a sufficiently forceful field gradient, the initial colloidal osmotic pressure could be negative, followed by an equilibrium pressure approaching zero regardless of the force of the particles against the membrane. Thus, the osmotic pressure of a solution is to be attributed to the pressure in the solvent generated in opposition to the pressure of the solute particles caused by their interaction with the free surface (Brownian motion and/or an external field force), or by their viscous shear when they migrate through the solvent, or both. PMID:16592046

Super-hydrophobic coatings based on non-solvent induced phase separation during electro-spraying.

PubMed

Gao, Jiefeng; Huang, Xuewu; Wang, Ling; Zheng, Nan; Li, Wan; Xue, Huaiguo; Li, Robert K Y; Mai, Yiu-Wing

2017-11-15

The polymer solution concentration determines whether electrospinning or electro-spraying occurs, while the addition of the non-solvent into the polymer solution strongly influences the surface morphology of the obtained products. Both smooth and porous surfaces of the electro-sprayed microspheres can be harvested by choosing different non-solvent and its amount as well as incorporating polymeric additives. The influences of the solution concentration, weight ratio between the non-solvent and the copolymer, and the polymeric additives on the surface morphology and the wettability of the electro-sprayed products were systematically studied. Surface pores and/or asperities on the microsphere surface were mainly caused by the non-solvent induced phase separation (NIPS) and subsequent evaporation of the non-solvent during electro-spraying. With increasing polymer solution concentration, the microsphere was gradually changed to the bead-on-string geometry and finally to a nanofiber form, leading to a sustained decrease of the contact angle (CA). It was found that the substrate coatings derived from the microspheres possessing hierarchical surface pores or dense asperities had high surface roughness and super-hydrophobicity with CAs larger than 150° while sliding angles smaller than 10°; but coatings composed of microspheres with smooth surfaces gave relatively low CAs. Copyright © 2017 Elsevier Inc. All rights reserved.

Cathepsin B Cleavage of vcMMAE-Based Antibody-Drug Conjugate Is Not Drug Location or Monoclonal Antibody Carrier Specific.

PubMed

Gikanga, Benson; Adeniji, Nia S; Patapoff, Thomas W; Chih, Hung-Wei; Yi, Li

2016-04-20

Antibody-drug conjugates (ADCs) require thorough characterization and understanding of product quality attributes. The framework of many ADCs comprises one molecule of antibody that is usually conjugated with multiple drug molecules at various locations. It is unknown whether the drug release rate from the ADC is dependent on drug location, and/or local environment, dictated by the sequence and structure of the antibody carrier. This study addresses these issues with valine-citrulline-monomethylauristatin E (vc-MMAE)-based ADC molecules conjugated at reduced disulfide bonds, by evaluating the cathepsin B catalyzed drug release rate of ADC molecules with different drug distributions or antibody carriers. MMAE drug release rates at different locations on ADC I were compared to evaluate the impact of drug location. No difference in rates was observed for drug released from the V(H), V(L), or C(H)2 domains of ADC I. Furthermore, four vc-MMAE ADC molecules were chosen as substrates for cathepsin B for evaluation of Michaelis-Menten parameters. There was no significant difference in K(M) or k(cat) values, suggesting that different sequences of the antibody carrier do not result in different drug release rates. Comparison between ADCs and small molecules containing vc-MMAE moieties as substrates for cathepsin B suggests that the presence of IgG1 antibody carrier, regardless of its bulkiness, does not impact drug release rate. Finally, a molecular dynamics simulation on ADC II revealed that the val-cit moiety at each of the eight possible conjugation sites was, on average, solvent accessible over 50% of its maximum solvent accessible surface area (SASA) during a 500 ns trajectory. Combined, these results suggest that the cathepsin cleavage sites for conjugated drugs are exposed enough for the enzyme to access and that the drug release rate is rather independent of drug location or monoclonal antibody carrier. Therefore, the distribution of drug conjugation at different sites is not a critical parameter to control in manufacturing of the vc-MMAE-based ADC conjugated at reduced disulfide bonds.

Experimental and theoretical aspects of studying themodynamics and mass transport in polymer-solvent systems

NASA Astrophysics Data System (ADS)

Davis, Peter Kennedy

Mass transport and thermodynamics in polymer-solvent systems are two key areas of importance to the polymer industry. Numerous processes including polymerization reactors, membrane separations, foam production, devolatilization processes, film and coating drying, supercritical extractions, drug delivery, and even nano-technology require fundamental phase equilibria and diffusion information. Although such information is vital in equipment design and optimization, acquisition and modeling of these data are still in the research and development stages. This thesis is rather diverse as it addresses many realms of this broad research area. From high pressure to low pressure, experimental to theoretical, and infinite dilution to finite concentration, the thesis covers a wide range of topics that are of current importance to the industrial and academic polymer community. Chapter 1 discusses advances in the development of a new volumetric sorption pressure decay technique to make phase equilibrium and diffusion measurements in severe temperature-pressure environments. Chapter 2 provides the derivations and results of a new completely predictive Group Contribution Lattice Fluid Equation of State for multi-component polymer-solvent systems. The remaining four chapters demonstrate advances in the modeling of inverse gas chromatography (IGC) experiments. IGC has been used extensively of the last 50 years to make low pressure sorption and diffusion measurements at infinitely dilute and finite solvent concentrations. Chapter 3 proposes a new IGC experiment capable of obtaining ternary vapor-liquid equilibria in polymer-solvent-solvent systems. Also in that chapter, an extensive derivation is provided for a continuum model capable of describing the results of such an experiment. Chapter 4 presents new data collected on a packed column IGC experiment and a new model that can be used with those experimental data to obtain diffusion and partition coefficients. Chapter 5 addresses a rather controversial topic about IGC experiments near the polymer glass transition temperature. Using a new IGC model capable of describing both bulk absorption and surface adsorption, IGC behavior around the glass transition was able to be better understood. Finally, Chapter 6 presents an IGC model that can be used to separate bulk effects from surface effects in capillary column IGC experiments.

Deep eutectic solvents: sustainable media for nanoscale and functional materials.

PubMed

Wagle, Durgesh V; Zhao, Hua; Baker, Gary A

2014-08-19

Deep eutectic solvents (DESs) represent an alternative class of ionic fluids closely resembling room-temperature ionic liquids (RTILs), although, strictly speaking, they are distinguished by the fact that they also contain an organic molecular component (typically, a hydrogen bond donor like a urea, amide, acid, or polyol), frequently as the predominant constituent. Practically speaking, DESs are attractive alternatives to RTILs, sharing most of their remarkable qualities (e.g., tolerance to humidity, negligible vapor pressure, thermostability, wide electrochemical potential windows, tunability) while overcoming several limitations associated with their RTIL cousins. Particularly, DESs are typically, less expensive, more synthetically accessible (typically, from bulk commodity chemicals using solvent/waste-free processes), nontoxic, and biodegradable. In this Account, we provide an overview of DESs as designer solvents to create well-defined nanomaterials including shape-controlled nanoparticles, electrodeposited films, metal-organic frameworks, colloidal assemblies, hierarchically porous carbons, and DNA/RNA architectures. These breakthroughs illustrate how DESs can fulfill multiple roles in directing chemistry at the nanoscale: acting as supramolecular template, metal/carbon source, sacrificial agent (e.g., ammonia release from urea), and/or redox agent, all in the absence of formal stabilizing ligand (here, solvent and stabilizer are one and the same). The ability to tailor the physicochemical properties of DESs is central to controlling their interfacial behavior. The preorganized "supramolecular" nature of DESs provides a soft template to guide the formation of bimodal porous carbon networks or the evolution of electrodeposits. A number of essential parameters (viscosity, polarity, surface tension, hydrogen bonding), plus coordination with solutes/surfaces, all play significant roles in modulating species reactivity and mass transport properties governing the genesis of nanostructure. Furthermore, DES components may modulate nucleation and growth mechanisms by charge neutralization, modification of reduction potentials (or chemical activities), and passivation of particular crystal faces, dictating growth along preferred crystallographic directions. Broad operational windows for electrochemical reactions coupled with their inherent ionic nature facilitate the electrodeposition of alloys and semiconductors inaccessible to classical means and the use of cosolvents or applied potential control provide under-explored strategies for mediating interfacial interactions leading to control over film characteristics. The biocompatibility of DESs suggests intriguing potential for the construction of biomolecular architectures in these novel media. It has been demonstrated that nucleic acid structures can be manipulated in the ionic, crowded, dehydrating (low water activity) DES environment-including the adoption of duplex helical structures divergent from the canonical B form and parallel G-quadruplex DNA persisting near water's boiling point-challenging the misconception that water is a necessity for maintenance of nucleic acid structure/functionality and suggesting an enticing trajectory toward DNA/RNA-based nanocatalysis within a strictly anhydrous medium. DESs offer tremendous opportunities and open intriguing perspectives for generating sophisticated nanostructures within an anhydrous or low-water medium. We conclude this Account by offering our thoughts on the evolution of the field, pointing to areas of clear and compelling utility which will surely see fruition in the coming years. Finally, we highlight a few hurdles (e.g., need for a universal nomenclature, absence of water-immiscible, oriented-phase, and low-viscosity DESs) which, once navigated, will hasten progress in this area.

Wetting and phase separation in soft adhesion

PubMed Central

Jensen, Katharine E.; Sarfati, Raphael; Style, Robert W.; Boltyanskiy, Rostislav; Chakrabarti, Aditi; Chaudhury, Manoj K.; Dufresne, Eric R.

2015-01-01

In the classic theory of solid adhesion, surface energy drives deformation to increase contact area whereas bulk elasticity opposes it. Recently, solid surface stress has been shown also to play an important role in opposing deformation of soft materials. This suggests that the contact line in soft adhesion should mimic that of a liquid droplet, with a contact angle determined by surface tensions. Consistent with this hypothesis, we observe a contact angle of a soft silicone substrate on rigid silica spheres that depends on the surface functionalization but not the sphere size. However, to satisfy this wetting condition without a divergent elastic stress, the gel phase separates from its solvent near the contact line. This creates a four-phase contact zone with two additional contact lines hidden below the surface of the substrate. Whereas the geometries of these contact lines are independent of the size of the sphere, the volume of the phase-separated region is not, but rather depends on the indentation volume. These results indicate that theories of adhesion of soft gels need to account for both the compressibility of the gel network and a nonzero surface stress between the gel and its solvent. PMID:26553989

ODC-Free Solvent Implementation for Phenolics Cleaning

NASA Technical Reports Server (NTRS)

Wurth, Laura; Biegert, Lydia; Lamont, DT; McCool, Alex (Technical Monitor)

2001-01-01

During phenolic liner manufacture, resin-impregnated (pre-preg) bias tape of silica, glass, or carbon cloth is tape-wrapped, cured, machined, and then wiped with 1,1,1 tri-chloroethane (TCA) to remove contaminants that may have been introduced during machining and handling. Following the TCA wipe, the machined surface is given a resin wet-coat and over-wrapped with more prepreg and cured. A TCA replacement solvent for these wiping operations must effectively remove both surface contaminants, and sub-surface oils and greases while not compromising the integrity of this interface. Selection of a TCA replacement solvent for phenolic over-wrap interface cleaning began with sub-scale compatibility tests with cured phenolics. Additional compatibility tests included assessment of solvent retention in machined phenolic surfaces. Results from these tests showed that, while the candidate solvent did not degrade the cured phenolics, it was retained in higher concentrations than TCA in phenolic surfaces. This effect was most pronounced with glass and silica cloth phenolics with steep ply angles relative to the wiped surfaces.

Deployment of Phytotechnology in the 317/319 Area at Argonne National Laboratory-East, Innovative Technology Evaluation Report

EPA Science Inventory

Hybrid poplar and hybrid willow trees were planted for several environmental objectives at the Argonne National Laboratory - East, near Chicago, IL. Some trees were planted to clean TCE and other solvents from soil, some were planted to control surface water flow on a landfill, a...

Process for electrospinning chitin fibers from chitinous biomass solution

DOEpatents

Swatloski, Richard P.; Barber, Patrick S.; Opichka, Terrance; Bonner, Jonathan R.; Gurau, Gabriela; Griggs, Christopher Scott; Rogers, Robin D.

2017-06-20

Disclosed are methods for electrospinning chitinous biomass solution to form chitin fibers, using ionic liquids or other ion-containing liquids as solvent. Chitin fibers produced thereby and articles containing such chitin fibers are also disclosed. The chitin fiber thus obtained has very high surface area and improved strength over currently commercially available chitin materials.

Application of two dimensional periodic molecular dynamics to interfaces.

NASA Astrophysics Data System (ADS)

Gay, David H.; Slater, Ben; Catlow, C. Richard A.

1997-08-01

We have applied two-dimensional molecular dynamics to the surface of a crystalline aspartame and the interface between the crystal face and a solvent (water). This has allowed us to look at the dynamic processes at the surface. Understanding the surface structure and properties are important to controlling the crystal morphology. The thermodynamic ensemble was constant Number, surface Area and Temperature (NAT). The calculations have been carried out using a 2D Ewald summation and 2D periodic boundary conditions for the short range potentials. The equations of motion integration has been carried out using the standard velocity Verlet algorithm.

Preparation and characterization of uniform nanosized cephradine by combination of reactive precipitation and liquid anti-solvent precipitation under high gravity environment.

PubMed

Zhong, Jie; Shen, Zhigang; Yang, Yan; Chen, Jianfeng

2005-09-14

In this work, a novel direct method, which was combined with reactive precipitation and liquid anti-solvent precipitation under high gravity environment, had been developed to prepare nanosized cephradine with narrow particle size distribution. Compared with commercial crude cephradine, the prepared cephradine showed a significant decrease in particle size, a significant increase in the specific surface area and shorter dissolving time when used for injection. The characteristic particle size was between 200-400 nm. The specific surface area increased from 2.95 to 10.87 m2/g after micronization. When the amount of L-arginin decreased from 0.25 to 0.18 g, the mixture of nanosized cephradine and L-arginine could still dissolve in 1 min. The X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FT-IR) analysis indicated that the physical characteristics and molecular states remained unchanged after the recrystallization process. This method had potential application in industrial fields because of its low cost, efficient processing and the ease of scaling-up.

Polyacrylonitrile nanofiber as polar solvent N,N-dimethyl formamide sensor based on quartz crystal microbalance technique

NASA Astrophysics Data System (ADS)

Rianjanu, A.; Julian, T.; Hidayat, S. N.; Suyono, E. A.; Kusumaatmaja, A.; Triyana, K.

2018-04-01

Here, we describe an N,N-dimethyl formamide (DMF) vapour sensor fabricated by coating polyacrylonitrile (PAN) nanofiber structured on quartz crystal microbalance (QCM). The PAN nanofiber sensors with an average diameter of 225 nm to 310 nm were fabricated via electrospinning process with different mass deposition on QCM substrate. The nanostructured of PAN nanofiber offers a high specific surface area that improved the sensing performance of nanofiber sensors. Benefiting from that fine structure, and high polymer-solvent affinity between PAN and DMF, the development of DMF sensors presented good response at ambient temperature. Since there is no chemical reaction between PAN nanofiber and DMF vapour, weak physical interaction such absorption and swelling were responsible for the sensing behavior. The results are indicating that the response of PAN nanofiber sensors has more dependency on the nanofiber structure (specific surface area) rather than its mass deposition. The sensor also showed good stability after a few days sensing. These findings have significant implications for developing DMF vapour sensor based on QCM coated polymer nanofibers.

Ultra-lightweight and highly porous carbon aerogels from bamboo pulp fibers as an effective sorbent for water treatment

NASA Astrophysics Data System (ADS)

Yuan, Wei; Zhang, Xiaofang; Zhao, Jiangqi; Li, Qingye; Ao, Chenghong; Xia, Tian; Zhang, Wei; Lu, Canhui

Sorbents derived from biomass provide a novel approach to settle issues of organic solvent and/or oil leakage. In this work, a novel carbon aerogel (CA) was prepared as sorbents using the cheap and abundant bamboo pulp fibers as precursors through the pyrolysis method. The CA displayed an ultra-low density (5.65 mg cm-3), high hydrophobicity (water contact angle of 135.9°) and a large specific surface area (379.39 m2 g-1) as well as great mechanical properties. The absorption capacities of CA for organic solvents/oils were extraordinary (50-150 g/g). Particularly, its absorption on organic solvents was superior to many other bio-based CAs. The reusability of CA was also found impressive. For over five absorption-desorption cycles, the CA still showed excellent absorption behaviors on organic solvents and oils. Importantly, the fabrication process of CA is quite simple and environmentally friendly, demonstrating high potentials for future water treatment applications.

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

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

Li, Tanping, E-mail: tanping@lsu.edu, E-mail: revatik@lsu.edu; Kumar, Revati, E-mail: tanping@lsu.edu, E-mail: revatik@lsu.edu

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 breaksmore » 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.« less

Chemically exfoliating large sheets of phosphorene via choline chloride urea viscosity-tuning

NASA Astrophysics Data System (ADS)

Ng, A.; Sutto, T. E.; Matis, B. R.; Deng, Y.; Ye, P. D.; Stroud, R. M.; Brintlinger, T. H.; Bassim, N. D.

2017-04-01

Exfoliation of two-dimensional phosphorene from bulk black phosphorous through chemical means is demonstrated where the solvent system of choice (choline chloride urea diluted with ethanol) has the ability to successfully exfoliate large-area multi-layer phosphorene sheets and further protect the flakes from ambient degradation. The intercalant solvent molecules, aided by low-powered sonication, diffuse between the layers of the bulk black phosphorus, allowing for the exfoliation of the multi-layer phosphorene through breaking of the interlayer van der Waals bonds. Through viscosity tuning, the optimal parameters (1:1 ratio between the intercalant and the diluting solvent) at which the exfoliation takes place is determined. Our exfoliation technique is shown to produce multi-layer phosphorene flakes with surface areas greater than 3 μm2 (a factor of three larger than what has previously been reported for a similar exfoliation method) while limiting exposure to the ambient environment, thereby protecting the flakes from degradation. Characterization techniques such as optical microscopy, Raman spectroscopy, ultraviolet-visible spectroscopy, and (scanning) transmission electron microscopy are used to investigate the quality, quantity, and thickness of the exfoliated flakes.

Rapid and selective adsorption of cationic dyes by a unique metal-organic framework with decorated pore surface

NASA Astrophysics Data System (ADS)

Zhang, Jie; Li, Fan; Sun, Qian

2018-05-01

Organic dye pollutants become a big headache due to their toxic nature to the environment, and it should be one of the best solutions if we can remove and separate them. Here, a metal-organic framework (MOF) (denoted as Zn-MOF) with carbonyl group based on fluorenone-2,7-dicarboxylate ligand, was directly synthesized without post-synthesis method and applied to selectively absorb cationic dyes such as MB, CV, RhB from aqueous solution, while anionic or neutral dyes were excluded. Characterization of the Zn-MOF was achieved by X-ray diffraction, scanning electron microscope, Fourier transform infrared spectrometry and elemental analysis. The Zn-MOF mainly possesses open pore channels, high surface area, big pore volume, and most important, the pore surface is furnished with carbonyl groups arising from the ligand and pointing toward the centers of the large chambers of the framework, which are benefit for the adsorption of the cationic dyes. The MB maximum adsorption capacities can attain 326 mg g-1, which is probably due to the suitable pore size, higher solvent-accessible void, and the prominent adsorption capacity of the mesoporous material. The dye adsorption process for the material is proven to be charge-selective and size-selective, and the adsorption isotherms, as well as kinetics characteristic of dye adsorption onto the Zn-MOF were also investigated.

Hydration structure of the α-chymotrypsin substrate binding pocket: the impact of constrained geometry

NASA Astrophysics Data System (ADS)

Carey, Christina; Cheng, Yuen-Kit; Rossky, Peter J.

2000-08-01

The concave substrate binding pocket of α-chymotrypsin binds specifically hydrophobic side chains. In order to understand the hydration structure present in the absence of substrate, and elucidate the character of the solvent displaced on binding, molecular dynamics computer simulation of the solvent in a fully hydrated protein has been carried out and analyzed. The pocket is found to be characterized in terms of a mixed polar and apolar macromolecular surface. It is shown that the simulated solvent structure within it is spatially consistent with that seen via crystallography. The solvent structure is energetically characterized by large losses in hydrogen bonding among solvent molecules except at the mouth of the pocket where exposure to bulk-like solvent is possible. The loss in hydrogen bonding is attributed to the highly constrained geometry available to the solvent, preventing formation of a hydrogen bonding network, with only partial compensation by interactions with the macromolecular surface. The solvent displacement concomitant with substrate binding will therefore be associated with a large enthalpic driving force. This result is at the extreme of a continuum of variable cases of "hydrophobic" hydration, which differ most basically in surface curvature. These range from convex solute surfaces, inducing clathrate-like structures, with negligible hydrogen bond loss, to flat surfaces with significant interfacial loss, to the present concave case with hydrogen bonding losses exceeding 50%.

C{sub 60}-dyad aggregates: Self-organized structures in aqueous solutions

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

Guskova, O. A., E-mail: guskova@ipfdd.de, E-mail: s.raovaranasi@uq.edu.au; Varanasi, S. R., E-mail: guskova@ipfdd.de, E-mail: s.raovaranasi@uq.edu.au; Sommer, J.-U.

2014-10-14

Extensive full-atomistic molecular dynamics simulations are performed to study the self-organization of C{sub 60}-fullerene dyad molecules in water, namely phenyl-C{sub 61}-butyric acid methyl ester and fulleropyrrolidines, which have two elements of ordering, the hydrophobic fullerene cage and the hydrophilic/ionic group. While pristine fullerene or phenyl-C{sub 61}-butyric acid methyl ester forms spherical droplets in order to minimize the surface tension, the amphiphilic nature of charged solute molecules leads to the formation of supramolecular assemblies having cylindrical shape driven by charge repulsion between the ionic groups located on the surface of the aggregates. We show that formation of non-spherical micelles is themore » geometrical consequence if the fullerene derivatives are considered as surfactants where the ionized groups are only hydrophilic unit. The agglomeration behavior of fullerenes is evaluated by determining sizes of the clusters, solvent accessible surface areas, and shape parameters. By changing the size of the counterions from chloride over iodide to perchlorate we find a thickening of the cylinder-like structures which can be explained by stronger condensation of larger ions and thus partial screening of the charge repulsion on the cluster surface. The reason for the size dependence of counterion condensation is the formation of a stronger hydration shell in case of small ions which in turn are repelled from the fullerene aggregates. Simulations are also in good agreement with the experimentally observed morphologies of decorated C{sub 60}-nanoparticles.« less

Effects of copolymer composition, film thickness, and solvent vapor annealing time on dewetting of ultrathin block copolymer films.

PubMed

Huang, Changchun; Wen, Gangyao; Li, Jingdan; Wu, Tao; Wang, Lina; Xue, Feifei; Li, Hongfei; Shi, Tongfei

2016-09-15

Effects of copolymer composition, film thickness, and solvent vapor annealing time on dewetting of spin-coated polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) films (<20nm thick) were mainly investigated by atomic force microscopy. Surface chemical analysis of the ultrathin films annealed for different times were performed using X-ray photoelectron spectroscopy and contact angle measurement. With the annealing of acetone vapor, dewetting of the films with different thicknesses occur via the spinodal dewetting and the nucleation and growth mechanisms, respectively. The PS-b-PMMA films rupture into droplets which first coalesce into large ones to reduce the surface free energy. Then the large droplets rupture into small ones to increase the contact area between PMMA blocks and acetone molecules resulting from ultimate migration of PMMA blocks to droplet surface, which is a novel dewetting process observed in spin-coated films for the first time. Copyright © 2016 Elsevier Inc. All rights reserved.

Surface tension driven aggregation of organic nanowires via lab in a droplet.

PubMed

Gu, Jianmin; Yin, Baipeng; Fu, Shaoyan; Feng, Man; Zhang, Ziming; Dong, Haiyun; Gao, Faming; Zhao, Yong Sheng

2018-06-05

Directing the architecture of complex organic nanostructures is desirable and still remains a challenge in areas of materials science due to their structure-dependent collective optoelectronic properties. Herein, we demonstrate a simple and versatile solution strategy that allows surface tension to drive low-dimensional nanostructures to aggregate into complex structures via a lab in a droplet technique. By selecting a suitable combination of a solvent and an anti-solvent with controllable surface tension difference, the droplets can be automatically cracked into micro-droplets, which provides an aggregation force directed toward the centre of the droplet to drive the low-dimensional building blocks to form the special aggregations during the self-assembly process. This synthetic strategy has been shown to be universal for organic materials, which is beneficial for further optimizing the optoelectronic properties. These results contribute to gaining an insightful understanding on the detailed growth mechanism of complex organic nanostructures and greatly promoting the development of organic nanophotonics.

Non-encapsulation approach for high-performance Li-S batteries through controlled nucleation and growth

NASA Astrophysics Data System (ADS)

Pan, Huilin; Chen, Junzheng; Cao, Ruiguo; Murugesan, Vijay; Rajput, Nav Nidhi; Han, Kee Sung; Persson, Kristin; Estevez, Luis; Engelhard, Mark H.; Zhang, Ji-Guang; Mueller, Karl T.; Cui, Yi; Shao, Yuyan; Liu, Jun

2017-10-01

High-surface-area, nanostructured carbon is widely used for encapsulating sulfur and improving the cyclic stability of Li-S batteries, but the high carbon content and low packing density limit the specific energy that can be achieved. Here we report an approach that does not rely on sulfur encapsulation. We used a low-surface-area, open carbon fibre architecture to control the nucleation and growth of the sulfur species by manipulating the carbon surface chemistry and the solvent properties, such as donor number and Li+ diffusivity. Our approach facilitates the formation of large open spheres and prevents the production of an undesired insulating sulfur-containing film on the carbon surface. This mechanism leads to 100% sulfur utilization, almost no capacity fading, over 99% coulombic efficiency and high energy density (1,835 Wh kg-1 and 2,317 Wh l-1). This finding offers an alternative approach for designing high-energy and low-cost Li-S batteries through controlling sulfur reaction on low-surface-area carbon.

Synthesis of porous inorganic hollow fibers without harmful solvents.

PubMed

Shukla, Sushumna; de Wit, Patrick; Luiten-Olieman, Mieke W J; Kappert, Emiel J; Nijmeijer, Arian; Benes, Nieck E

2015-01-01

A route for the fabrication of porous inorganic hollow fibers with high surface-area-to-volume ratio that avoids harmful solvents is presented. The approach is based on bio-ionic gelation of an aqueous mixture of inorganic particles and sodium alginate during wet spinning. In a subsequent thermal treatment, the bio-organic material is removed and the inorganic particles are sintered. The method is applicable to the fabrication of various inorganic fibers, including metals and ceramics. The route completely avoids the use of organic solvents, such as N-methyl-2-pyrrolidone, and additives associated with the currently used fiber fabrication methods. In addition, it inherently avoids the manifestation of so-called macro voids and allows the facile incorporation of additional metal oxides in the inorganic hollow fibers. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photoisomers of Azobenzene Star with a Flat Core: Theoretical Insights into Multiple States from DFT and MD Perspective.

PubMed

Koch, Markus; Saphiannikova, Marina; Santer, Svetlana; Guskova, Olga

2017-09-21

This study focuses on comparing physical properties of photoisomers of an azobenzene star with benzene-1,3,5-tricarboxamide core. Three azobenzene arms of the molecule undergo a reversible trans-cis isomerization upon UV-vis light illumination giving rise to multiple states from the planar all-trans one, via two mixed states to the kinked all-cis isomer. Employing density functional theory, we characterize the structural and photophysical properties of each state indicating a role the planar core plays in the coupling between azobenzene chromophores. To characterize the light-triggered switching of solvophilicity/solvophobicity of the star, the difference in solvation free energy is calculated for the transfer of an azobenzene star from its gas phase to implicit or explicit solvents. For the latter case, classical all-atom molecular dynamics simulations of aqueous solutions of azobenzene star are performed employing the polymer consistent force field to shed light on the thermodynamics of explicit hydration as a function of the isomerization state and on the structuring of water around the star. From the analysis of two contributions to the free energy of hydration, the nonpolar van der Waals and the electrostatic terms, it is concluded that isomerization specificity largely determines the polarity of the molecule and the solute-solvent electrostatic interactions. This convertible hydrophilicity/hydrophobicity together with readjustable occupied volume and the surface area accessible to water, affects the self-assembly/disassembly of the azobenzene star with a flat core triggered by light.

Protein structure modeling and refinement by global optimization in CASP12.

PubMed

Hong, Seung Hwan; Joung, InSuk; Flores-Canales, Jose C; Manavalan, Balachandran; Cheng, Qianyi; Heo, Seungryong; Kim, Jong Yun; Lee, Sun Young; Nam, Mikyung; Joo, Keehyoung; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

2018-03-01

For protein structure modeling in the CASP12 experiment, we have developed a new protocol based on our previous CASP11 approach. The global optimization method of conformational space annealing (CSA) was applied to 3 stages of modeling: multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain re-modeling. For better template selection and model selection, we updated our model quality assessment (QA) method with the newly developed SVMQA (support vector machine for quality assessment). For 3D chain building, we updated our energy function by including restraints generated from predicted residue-residue contacts. New energy terms for the predicted secondary structure and predicted solvent accessible surface area were also introduced. For difficult targets, we proposed a new method, LEEab, where the template term played a less significant role than it did in LEE, complemented by increased contributions from other terms such as the predicted contact term. For TBM (template-based modeling) targets, LEE performed better than LEEab, but for FM targets, LEEab was better. For model refinement, we modified our CASP11 molecular dynamics (MD) based protocol by using explicit solvents and tuning down restraint weights. Refinement results from MD simulations that used a new augmented statistical energy term in the force field were quite promising. Finally, when using inaccurate information (such as the predicted contacts), it was important to use the Lorentzian function for which the maximal penalty arising from wrong information is always bounded. © 2017 Wiley Periodicals, Inc.

Solvent free tin oxide nanoparticle for gas sensing application

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

Ranjan, Pranay, E-mail: pranjan@iitp.ac.in; Thakur, Ajay D.; Centre for Energy and Environment, Indian Institute of Technology Patna, Patliputra, Patna 800013 India

2016-05-06

A new modified technique of synthesizing tin oxide nanoparticles with crystallite size of 2 nm to 6 nm has been developed. Surface area of the nanoparticle has been increased as we approached towards the Debye length. Such a techniques for approaching the Debye length is expected to bring remarkable changes in the properties of resistive based gas sensors. The technique used here is less toxic, economical and has high yield. Phase purity, size, shape and composition has been investigated using x-ray diffraction, micro Raman, scanning electron microscopy and energy dispersive x ray spectroscopy. While surface area has been calculated through Brunaur-Emmett-Teller (BET).

Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review

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

Wei, Guowei; Baker, Nathan A.

2016-11-11

This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, electrostatic potential, ion density, electron density, etc. Recently, differential geometry theory has been used to define the surfaces that separate the microscopic (solute) domains for biomolecules from the macroscopic (solvent) domains. In thesemore » approaches, the microscopic domains are modeled with atomistic or quantum mechanical descriptions, while continuum mechanics models (including fluid mechanics, elastic mechanics, and continuum electrostatics) are applied to the macroscopic domains. This multiphysics description is integrated through an energy functional formalism and the resulting Euler-Lagrange equation is employed to derive a variety of governing partial differential equations for different solvation and transport processes; e.g., the Laplace-Beltrami equation for the solvent-solute interface, Poisson or Poisson-Boltzmann equations for electrostatic potentials, the Nernst-Planck equation for ion densities, and the Kohn-Sham equation for solute electron density. Extensive validation of these models has been carried out over hundreds of molecules, including proteins and ion channels, and the experimental data have been compared in terms of solvation energies, voltage-current curves, and density distributions. We also propose a new quantum model for electrolyte transport.« less

Solvent effects on adsorption of CO over CuCl(1 1 1) surface: A density functional theory study

NASA Astrophysics Data System (ADS)

Zhang, Riguang; Ling, Lixia; Wang, Baojun; Huang, Wei

2010-09-01

DFT calculations have been performed to investigate the effect of dielectric responses of the solvent environment on the CO adsorption over CuCl(1 1 1) surface by using COSMO (conductor-like solvent model) model in Dmol 3. Different dielectric constants, including vacuum, liquid paraffin, methylene chloride, methanol and water solution, are considered. The effects of solvent model on the structural parameters, adsorption energies and vibrational frequency of CO adsorption over CuCl(1 1 1) surface have been investigated. The calculation results suggest that solvent effects can improve the stability of CO adsorption and reduce the intensity of C-O bond, which might mean that solvent is in favor of C-O bond activation and improve the reaction activity of oxidative carbonylation in a slurry reactor.

Rectification of nanopores in aprotic solvents - transport properties of nanopores with surface dipoles

NASA Astrophysics Data System (ADS)

Plett, Timothy; Shi, Wenqing; Zeng, Yuhan; Mann, William; Vlassiouk, Ivan; Baker, Lane A.; Siwy, Zuzanna S.

2015-11-01

Nanopores have become a model system to understand transport properties at the nanoscale. We report experiments and modeling of ionic current in aprotic solvents with different dipole moments through conically shaped nanopores in a polycarbonate film and through glass nanopipettes. We focus on solutions of the salt LiClO4, which is of great importance in modeling lithium based batteries. Results presented suggest ion current rectification observed results from two effects: (i) adsorption of Li+ ions to the pore walls, and (ii) a finite dipole moment rendered by adsorbed solvent molecules. Properties of surfaces in various solvents were probed by means of scanning ion conductance microscopy, which confirmed existence of an effectively positive surface potential in aprotic solvents with high dipole moments.Nanopores have become a model system to understand transport properties at the nanoscale. We report experiments and modeling of ionic current in aprotic solvents with different dipole moments through conically shaped nanopores in a polycarbonate film and through glass nanopipettes. We focus on solutions of the salt LiClO4, which is of great importance in modeling lithium based batteries. Results presented suggest ion current rectification observed results from two effects: (i) adsorption of Li+ ions to the pore walls, and (ii) a finite dipole moment rendered by adsorbed solvent molecules. Properties of surfaces in various solvents were probed by means of scanning ion conductance microscopy, which confirmed existence of an effectively positive surface potential in aprotic solvents with high dipole moments. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06340j

Molecular dynamic simulation of Trastuzumab F(ab’)2 structure in corporation with HER2 as a theranostic agent of breast cancer

NASA Astrophysics Data System (ADS)

Hermanto, S.; Yusuf, M.; Mutalib, A.; Hudiyono, S.

2017-05-01

Trastuzumab as intact IgG are well researched for theranostic agent in HER2 overexpressed breast cancer. However, due to the relatively large of molecules it is slowly moved and weak penetration of the target cells. Fragmentation of trastzumab has been developed by pepsin cleavages to get the F(ab’)2 fragments. To observe the stability and accessibility of F(ab’)2 structure in corporation with HER2 (human epidermal growth factor receptor-2), the structure of antibody modeling had been developed with 1IGT as a template. Molecular dynamics (MD) of the F(ab’)2 structure simulation has been done in the aqueous phase with AMBER trajectories for 20 ns. Computational visualization by VMD (Visual Molecular Dynamics) were applied to identify binding site interaction details between trastuzumab F(ab’)2 and HER2 receptor. The results of MD simulations indicated that the fragmentation of trastuzumab F(ab’)2 did not change the structure and conformation of F(ab’)2 as a whole, especially in the CDR (Complementarity Determining Region) area. SASA (solvent accessibility surface area) analysis on lysine residues showed that formation of conjugate DOTA-F(ab’)2 predicted occur on outside of the CDR regions so its not interfered with binding affinity for the HER2 receptor. The molecular dynamic simulation of DOTA-F(ab’)2 with HER2 receptor in aqueous system generated ΔGbinding more highly (15.5066 kkal/mol) than positive control HER2-Fab (-45.1446 kkal/mol).

In Search of Functional Advantages of Knots in Proteins.

PubMed

Dabrowski-Tumanski, Pawel; Stasiak, Andrzej; Sulkowska, Joanna I

2016-01-01

We analysed the structure of deeply knotted proteins representing three unrelated families of knotted proteins. We looked at the correlation between positions of knotted cores in these proteins and such local structural characteristics as the number of intra-chain contacts, structural stability and solvent accessibility. We observed that the knotted cores and especially their borders showed strong enrichment in the number of contacts. These regions showed also increased thermal stability, whereas their solvent accessibility was decreased. Interestingly, the active sites within these knotted proteins preferentially located in the regions with increased number of contacts that also have increased thermal stability and decreased solvent accessibility. Our results suggest that knotting of polypeptide chains provides a favourable environment for the active sites observed in knotted proteins. Some knotted proteins have homologues without a knot. Interestingly, these unknotted homologues form local entanglements that retain structural characteristics of the knotted cores.

Non-encapsulation approach for high-performance Li–S batteries through controlled nucleation and growth

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

Pan, Huilin; Chen, Junzheng; Cao, Ruiguo

Sulfur encapsulation in high surface area, nanoporous carbon is currently the most widely studied approach to improve the cycling stability of Li-S batteries. However, the relatively large amount of high surface area carbon decreases the overall volumetric energy density in the system and makes it difficult to compete with other battery chemistries. In this paper, we report a new approach that does not depend on sulfur encapsulation and high surface area carbon. We investigate the nucleation and deposition of sulfur using low surface area carbon in the cathode (surface area 17 m2 g-1). Optimization of the solvent properties and themore » deposition condition produce large spherical porous agglomerated particles rather than thin films. A solution mediated nucleation and growth mechanism is identified to form the large porous polysulfide particles. This new mechanism leads to close to 100% sulfur utilization, almost no capacity fading, over 99% coulombic efficacy, and high energy density (2350 Wh kg-1 and 2600 Wh L-1 based on overall mass/volume of cathode). This study may open a fundamentally new approach of using a low surface area carbon host for designing high energy Li-S battery by controlling the nucleation/growth pathway and morphology of sulfur species.« less

Prediction of protein-protein interaction sites using electrostatic desolvation profiles.

PubMed

Fiorucci, Sébastien; Zacharias, Martin

2010-05-19

Protein-protein complex formation involves removal of water from the interface region. Surface regions with a small free energy penalty for water removal or desolvation may correspond to preferred interaction sites. A method to calculate the electrostatic free energy of placing a neutral low-dielectric probe at various protein surface positions has been designed and applied to characterize putative interaction sites. Based on solutions of the finite-difference Poisson equation, this method also includes long-range electrostatic contributions and the protein solvent boundary shape in contrast to accessible-surface-area-based solvation energies. Calculations on a large set of proteins indicate that in many cases (>90%), the known binding site overlaps with one of the six regions of lowest electrostatic desolvation penalty (overlap with the lowest desolvation region for 48% of proteins). Since the onset of electrostatic desolvation occurs even before direct protein-protein contact formation, it may help guide proteins toward the binding region in the final stage of complex formation. It is interesting that the probe desolvation properties associated with residue types were found to depend to some degree on whether the residue was outside of or part of a binding site. The probe desolvation penalty was on average smaller if the residue was part of a binding site compared to other surface locations. Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization.

PubMed

Beuming, Thijs; Che, Ye; Abel, Robert; Kim, Byungchan; Shanmugasundaram, Veerabahu; Sherman, Woody

2012-03-01

Water plays an essential role in determining the structure and function of all biological systems. Recent methodological advances allow for an accurate and efficient estimation of the thermodynamic properties of water molecules at the surface of proteins. In this work, we characterize these thermodynamic properties and relate them to various structural and functional characteristics of the protein. We find that high-energy hydration sites often exist near protein motifs typically characterized as hydrophilic, such as backbone amide groups. We also find that waters around alpha helices and beta sheets tend to be less stable than waters around loops. Furthermore, we find no significant correlation between the hydration site-free energy and the solvent accessible surface area of the site. In addition, we find that the distribution of high-energy hydration sites on the protein surface can be used to identify the location of binding sites and that binding sites of druggable targets tend to have a greater density of thermodynamically unstable hydration sites. Using this information, we characterize the FKBP12 protein and show good agreement between fragment screening hit rates from NMR spectroscopy and hydration site energetics. Finally, we show that water molecules observed in crystal structures are less stable on average than bulk water as a consequence of the high degree of spatial localization, thereby resulting in a significant loss in entropy. These findings should help to better understand the characteristics of waters at the surface of proteins and are expected to lead to insights that can guide structure-based drug design efforts. Copyright © 2011 Wiley Periodicals, Inc.

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

PubMed Central

Sankararamakrishnan, Ramasubbu

2013-01-01

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. PMID:23468841

Apparatus for diffusion-gap thermal desalination

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

Lowenstein, Andrew

A thermal distillation apparatus including evaporation surfaces that are wetted with a solution, and from which at least some of the volatile solvent contained in the solution evaporates, condensers having an external surface in close proximity to, but not touching, a corresponding one of the one or more evaporation surfaces, and on which vapors of the solvent condense, releasing thermal energy that heats a flow of the solution moving upward within the condensers, spacers that prevent contact between the evaporating surfaces and the condensers, wherein spaces between the evaporating surfaces and the condensers are filled with a gaseous mixture composedmore » of solvent vapor and one or more non-condensable gases, and except for diffusion of the solvent vapor relative to the non-condensable gases, the gaseous mixture is stationary.« less

Variational Implicit Solvation with Solute Molecular Mechanics: From Diffuse-Interface to Sharp-Interface Models.

PubMed

Li, Bo; Zhao, Yanxiang

2013-01-01

Central in a variational implicit-solvent description of biomolecular solvation is an effective free-energy functional of the solute atomic positions and the solute-solvent interface (i.e., the dielectric boundary). The free-energy functional couples together the solute molecular mechanical interaction energy, the solute-solvent interfacial energy, the solute-solvent van der Waals interaction energy, and the electrostatic energy. In recent years, the sharp-interface version of the variational implicit-solvent model has been developed and used for numerical computations of molecular solvation. In this work, we propose a diffuse-interface version of the variational implicit-solvent model with solute molecular mechanics. We also analyze both the sharp-interface and diffuse-interface models. We prove the existence of free-energy minimizers and obtain their bounds. We also prove the convergence of the diffuse-interface model to the sharp-interface model in the sense of Γ-convergence. We further discuss properties of sharp-interface free-energy minimizers, the boundary conditions and the coupling of the Poisson-Boltzmann equation in the diffuse-interface model, and the convergence of forces from diffuse-interface to sharp-interface descriptions. Our analysis relies on the previous works on the problem of minimizing surface areas and on our observations on the coupling between solute molecular mechanical interactions with the continuum solvent. Our studies justify rigorously the self consistency of the proposed diffuse-interface variational models of implicit solvation.

40 CFR 52.253 - Metal surface coating thinner and reducer.

Code of Federal Regulations, 2010 CFR

2010-07-01

... PROGRAMS (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS California § 52.253 Metal surface... conform to paragraph (k) of § 52.254 so as to be defined as a nonphotochemically reactive solvent. (d...-photochemically reactive solvent. (e) If there is an inadequate supply of necessary solvent ingredients needed in...

Rapid and enhanced activation of microporous coordination polymers by flowing supercritical CO.sub.2

DOEpatents

Matzger, Adam J.; Liu, Baojian; Wong-Foy, Antek G.

2016-07-19

Flowing supercritical CO.sub.2 is used to activate metal organic framework materials (MOF). MOFs are activated directly from N,N-dimethylformamide (DMF) thus avoiding exchange with a volatile solvent. Most MCPs display increased surface areas directly after treatment although those with coordinatively unsaturated metal centers benefit from additional heating.

Influence of solvent polarity and supersaturation on template-induced nucleation of carbamazepine crystal polymorphs

NASA Astrophysics Data System (ADS)

Parambil, Jose V.; Poornachary, Sendhil K.; Tan, Reginald B. H.; Heng, Jerry Y. Y.

2017-07-01

Studies on the use of template surfaces to induce heterogeneous crystal nucleation have gained momentum in recent years-with potential applications in selective crystallisation of polymorphs and in the generation of seed crystals in a continuous crystallisation process. In developing a template-assisted solution crystallisation process, the kinetics of homogeneous versus heterogeneous crystal nucleation could be influenced by solute-solvent, solute-template, and solvent-template interactions. In this study, we report the effect of solvents of varying polarity on the nucleation of carbamazepine (CBZ) crystal polymorphs, a model active pharmaceutical ingredient. The experimental results demonstrate that functionalised template surfaces are effective in promoting crystallisation of either the metastable (form II) or stable (form III) polymorphs of CBZ only in moderately (methanol, ethanol, isopropanol) and low polar (toluene) solvents. A solvent with high polarity (acetonitrile) is thought to mask the template effect on heterogeneous nucleation due to strong solute-solvent and solvent-template interactions. The current study highlights that a quality-by-design (QbD) approach-considering the synergistic effects of solute concentration, solvent type, solution temperature, and template surface chemistry on crystal nucleation-is critical to the development of a template-induced crystallisation process.

On the theory of electric double layer with explicit account of a polarizable co-solvent.

PubMed

Budkov, Yu A; Kolesnikov, A L; Kiselev, M G

2016-05-14

We present a continuation of our theoretical research into the influence of co-solvent polarizability on a differential capacitance of the electric double layer. We formulate a modified Poisson-Boltzmann theory, using the formalism of density functional approach on the level of local density approximation taking into account the electrostatic interactions of ions and co-solvent molecules as well as their excluded volume. We derive the modified Poisson-Boltzmann equation, considering the three-component symmetric lattice gas model as a reference system and minimizing the grand thermodynamic potential with respect to the electrostatic potential. We apply present modified Poisson-Boltzmann equation to the electric double layer theory, showing that accounting for the excluded volume of co-solvent molecules and ions slightly changes the main result of our previous simplified theory. Namely, in the case of small co-solvent polarizability with its increase under the enough small surface potentials of electrode, the differential capacitance undergoes the significant growth. Oppositely, when the surface potential exceeds some threshold value (which is slightly smaller than the saturation potential), the increase in the co-solvent polarizability results in a differential capacitance decrease. However, when the co-solvent polarizability exceeds some threshold value, its increase generates a considerable enhancement of the differential capacitance in a wide range of surface potentials. We demonstrate that two qualitatively different behaviors of the differential capacitance are related to the depletion and adsorption of co-solvent molecules at the charged electrode. We show that an additive of the strongly polarizable co-solvent to an electrolyte solution can shift significantly the saturation potential in two qualitatively different manners. Namely, a small additive of strongly polarizable co-solvent results in a shift of saturation potential to higher surface potentials. On the contrary, a sufficiently large additive of co-solvent shifts the saturation potential to lower surface potentials. We obtain that an increase in the co-solvent polarizability makes the electrostatic potential profile longer-ranged. However, increase in the co-solvent concentration in the bulk leads to non-monotonic behavior of the electrostatic potential profile. An increase in the co-solvent concentration in the bulk at its sufficiently small values makes the electrostatic potential profile longer-ranged. Oppositely, when the co-solvent concentration in the bulk exceeds some threshold value, its further increase leads to decrease in electrostatic potential at all distances from the electrode.

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

Lei, Huan; Yang, Xiu; Zheng, Bin

Biomolecules exhibit conformational fluctuations near equilibrium states, inducing uncertainty in various biological properties in a dynamic way. We have developed a general method to quantify the uncertainty of target properties induced by conformational fluctuations. Using a generalized polynomial chaos (gPC) expansion, we construct a surrogate model of the target property with respect to varying conformational states. We also propose a method to increase the sparsity of the gPC expansion by defining a set of conformational “active space” random variables. With the increased sparsity, we employ the compressive sensing method to accurately construct the surrogate model. We demonstrate the performance ofmore » the surrogate model by evaluating fluctuation-induced uncertainty in solvent-accessible surface area for the bovine trypsin inhibitor protein system and show that the new approach offers more accurate statistical information than standard Monte Carlo approaches. Further more, the constructed surrogate model also enables us to directly evaluate the target property under various conformational states, yielding a more accurate response surface than standard sparse grid collocation methods. In particular, the new method provides higher accuracy in high-dimensional systems, such as biomolecules, where sparse grid performance is limited by the accuracy of the computed quantity of interest. Finally, our new framework is generalizable and can be used to investigate the uncertainty of a wide variety of target properties in biomolecular systems.« less

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

Lei, Huan; Yang, Xiu; Zheng, Bin

Biomolecules exhibit conformational fluctuations near equilibrium states, inducing uncertainty in various biological properties in a dynamic way. We have developed a general method to quantify the uncertainty of target properties induced by conformational fluctuations. Using a generalized polynomial chaos (gPC) expansion, we construct a surrogate model of the target property with respect to varying conformational states. We also propose a method to increase the sparsity of the gPC expansion by defining a set of conformational “active space” random variables. With the increased sparsity, we employ the compressive sensing method to accurately construct the surrogate model. We demonstrate the performance ofmore » the surrogate model by evaluating fluctuation-induced uncertainty in solvent-accessible surface area for the bovine trypsin inhibitor protein system and show that the new approach offers more accurate statistical information than standard Monte Carlo approaches. Further more, the constructed surrogate model also enables us to directly evaluate the target property under various conformational states, yielding a more accurate response surface than standard sparse grid collocation methods. In particular, the new method provides higher accuracy in high-dimensional systems, such as biomolecules, where sparse grid performance is limited by the accuracy of the computed quantity of interest. Our new framework is generalizable and can be used to investigate the uncertainty of a wide variety of target properties in biomolecular systems.« less

How PEGylation enhances the stability and potency of insulin: a molecular dynamics simulation.

PubMed

Yang, Cheng; Lu, Diannan; Liu, Zheng

2011-04-05

While the effectiveness of PEGylation in enhancing the stability and potency of protein pharmaceuticals has been validated for years, the underlying mechanism remains poorly understood, particularly at the molecular level. A molecular dynamics simulation was developed using an annealing procedure that allowed an all-atom level examination of the interaction between PEG polymers of different chain lengths and a conjugated protein represented by insulin. It was shown that PEG became entangled around the protein surface through hydrophobic interaction and concurrently formed hydrogen bonds with the surrounding water molecules. In addition to enhancing its structural stability, as indicated by the root-mean-square difference (rmsd) and secondary structure analyses, conjugation increased the size of the protein drug while decreasing the solvent accessible surface area of the protein. All these thus led to prolonged circulation life despite kidney filtration, proteolysis, and immunogenic side effects, as experimentally demonstrated elsewhere. Moreover, the simulation results indicated that an optimal chain length exists that would maximize drug potency underpinned by the parameters mentioned above. The simulation provided molecular insight into the interaction between PEG and the conjugated protein at the all-atom level and offered a tool that would allow for the design of PEGylated protein pharmaceuticals for given applications.

Energetic basis for selective recognition of T*G mismatched base pairs in DNA by imidazole-rich polyamides.

PubMed

Lacy, Eilyn R; Nguyen, Binh; Le, Minh; Cox, Kari K; OHare, Caroline; Hartley, John A; Lee, Moses; Wilson, W David

2004-01-01

To complement available structure and binding results and to develop a detailed understanding of the basis for selective molecular recognition of T.G mismatches in DNA by imidazole containing polyamides, a full thermodynamic profile for formation of the T.G-polyamide complex has been determined. The amide-linked heterocycles f-ImImIm and f-PyImIm (where f is formamido group, Im is imidazole and Py is pyrrole) were studied by using biosensor-surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) with a T.G mismatch containing DNA hairpin duplex and a similar DNA with only Watson-Crick base pairs. Large negative binding enthalpies for all of the polyamide-DNA complexes indicate that the interactions are enthalpically driven. SPR results show slower complex formation and stronger binding of f-ImImIm to the T.G than to the match site. The thermodynamic analysis indicates that the enhanced binding to the T.G site is the result of better entropic contributions. Negative heat capacity changes for the complex are correlated with calculated solvent accessible surface area changes and indicate hydrophobic contributions to complex formation. DNase I footprinting analysis in a long DNA sequence provided supporting evidence that f-ImImIm binds selectively to T.G mismatch sites.

Energetic basis for selective recognition of T·G mismatched base pairs in DNA by imidazole-rich polyamides

PubMed Central

Lacy, Eilyn R.; Nguyen, Binh; Le, Minh; Cox, Kari K.; O'Hare, Caroline; Hartley, John A.; Lee, Moses; Wilson, W. David

2004-01-01

To complement available structure and binding results and to develop a detailed understanding of the basis for selective molecular recognition of T·G mismatches in DNA by imidazole containing polyamides, a full thermodynamic profile for formation of the T·G–polyamide complex has been determined. The amide-linked heterocycles f-ImImIm and f-PyImIm (where f is formamido group, Im is imidazole and Py is pyrrole) were studied by using biosensor-surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) with a T·G mismatch containing DNA hairpin duplex and a similar DNA with only Watson–Crick base pairs. Large negative binding enthalpies for all of the polyamide–DNA complexes indicate that the interactions are enthalpically driven. SPR results show slower complex formation and stronger binding of f-ImImIm to the T·G than to the match site. The thermodynamic analysis indicates that the enhanced binding to the T·G site is the result of better entropic contributions. Negative heat capacity changes for the complex are correlated with calculated solvent accessible surface area changes and indicate hydrophobic contributions to complex formation. DNase I footprinting analysis in a long DNA sequence provided supporting evidence that f-ImImIm binds selectively to T·G mismatch sites. PMID:15064359

The Hinge Region as a Key Regulatory Element of Androgen Receptor Dimerization, DNA Binding and Transactivation

DTIC Science & Technology

2006-05-01

Mutations in the human androgen receptor gene as a learning tool for molecular endocrinology’ III. Poster presentations at international meetings...nonconsensus half-site, the cognate half-complex buries slightly more surface area from solvent (1,230 Å2) than the noncognate one (960 Å2). AR Mutations ...energetic penalty in- Fig. 4. (A) The AR DBD dimer interface. The molecular surfaces of the AR subunits are shown in red and blue. Dashed black lines

Functionalization of CNTs surface with phosphonuim based deep eutectic solvents for arsenic removal from water

NASA Astrophysics Data System (ADS)

AlOmar, Mohamed Khalid; Alsaadi, Mohammed Abdulhakim; Hayyan, Maan; Akib, Shatirah; Hashim, Mohd Ali

2016-12-01

Herein, we present the use of deep eutectic solvent (DES) as functionalization agents for carbon nanotubes (CNTs) to form novel adsorbents for removal of arsenic ions (As3+) from water. Two DESs systems were prepared using methyltriphenylphosphonium bromide (MTPB) and benzyltriphenylphosphonium chloride (BTPC) as salts, in conjugation with glycerol (Gly) as a hydrogen bond donor. The resulting novel adsorbents were characterized using thermogravimetric analysis (TGA), Zeta potential, Raman spectroscopy, Fourier transform infrared (FTIR) spectroscopy, XRD, EDX, FESEM, and BET surface area. Optimization studies were carried out utilizing RSM-CCD experimental design to estimate the optimum removal conditions for each adsorbent. The adsorption experimental data of both adsorbents were found to fit well with pseudo-second-order kinetics model, as well as with Langmuir and Freundlich adsorption isotherm models. The maximum adsorption capacity of a MTPB-DES-functionalized CNTs adsorbent was 23.4 mg/g.

Computational screening of biomolecular adsorption and self-assembly on nanoscale surfaces.

PubMed

Heinz, Hendrik

2010-05-01

The quantification of binding properties of ions, surfactants, biopolymers, and other macromolecules to nanometer-scale surfaces is often difficult experimentally and a recurring challenge in molecular simulation. A simple and computationally efficient method is introduced to compute quantitatively the energy of adsorption of solute molecules on a given surface. Highly accurate summation of Coulomb energies as well as precise control of temperature and pressure is required to extract the small energy differences in complex environments characterized by a large total energy. The method involves the simulation of four systems, the surface-solute-solvent system, the solute-solvent system, the solvent system, and the surface-solvent system under consideration of equal molecular volumes of each component under NVT conditions using standard molecular dynamics or Monte Carlo algorithms. Particularly in chemically detailed systems including thousands of explicit solvent molecules and specific concentrations of ions and organic solutes, the method takes into account the effect of complex nonbond interactions and rotational isomeric states on the adsorption behavior on surfaces. As a numerical example, the adsorption of a dodecapeptide on the Au {111} and mica {001} surfaces is described in aqueous solution. Copyright 2009 Wiley Periodicals, Inc.

Adsorption behavior of acetone solvent at the HMX crystal faces: A molecular dynamics study.

PubMed

Liu, Yingzhe; Yu, Tao; Lai, Weipeng; Ma, Yiding; Kang, Ying; Ge, Zhongxue

2017-06-01

Molecular dynamics simulations have been performed to understand the adsorption behavior of acetone (AC) solvent at the three surfaces of 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctan (HMX) crystal, i.e. (011), (110), and (020) faces. The simulation results show that the structural features and electrostatic potentials of crystal faces are determined by the HMX molecular packing, inducing distinct mass density distribution, dipole orientation, and diffusion of solvent molecules in the interfacial regions. The solvent adsorption is mainly governed by the van der Waals forces, and the crystal-solvent interaction energies among three systems are ranked as (020)≈(110)>(011). The adsorption sites for solvent incorporation at the crystal surface were found and visualized with the aid of occupancy analysis. A uniform arrangement of adsorption sites is observed at the rough (020) surface as a result of ordered adsorption motif. Copyright © 2017 Elsevier Inc. All rights reserved.

Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics

NASA Astrophysics Data System (ADS)

Mansbach, Rachael A.; Ferguson, Andrew L.

2015-03-01

The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energy landscapes from molecular simulations, quantify changes to the landscape as a function of external conditions and molecular chemistry, and relate these changes to modifications of molecular structure and dynamics. In an application to an n-eicosane chain, we quantify the thermally accessible chain configurations as a function of temperature and solvent conditions. In an application to a family of polyglutamate-derivative homopeptides, we quantify helical stability as a function of side chain length, resolve the critical side chain length for the helix-coil transition, and expose the molecular mechanisms underpinning side chain-mediated helix stability. By quantifying single molecule responses through perturbations to the underlying free energy surface, our approach provides a quantitative bridge between experimentally controllable variables and microscopic molecular behavior, guiding and informing rational engineering of desirable molecular structure and function.

Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics.

PubMed

Mansbach, Rachael A; Ferguson, Andrew L

2015-03-14

The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energy landscapes from molecular simulations, quantify changes to the landscape as a function of external conditions and molecular chemistry, and relate these changes to modifications of molecular structure and dynamics. In an application to an n-eicosane chain, we quantify the thermally accessible chain configurations as a function of temperature and solvent conditions. In an application to a family of polyglutamate-derivative homopeptides, we quantify helical stability as a function of side chain length, resolve the critical side chain length for the helix-coil transition, and expose the molecular mechanisms underpinning side chain-mediated helix stability. By quantifying single molecule responses through perturbations to the underlying free energy surface, our approach provides a quantitative bridge between experimentally controllable variables and microscopic molecular behavior, guiding and informing rational engineering of desirable molecular structure and function.

40 CFR 63.5753 - How do I calculate the combined organic HAP content of aluminum wipedown solvents and aluminum...

Code of Federal Regulations, 2010 CFR

2010-07-01

... HAP content of aluminum wipedown solvents and aluminum recreational boat surface coatings? 63.5753... Standards for Hazardous Air Pollutants for Boat Manufacturing Standards for Aluminum Recreational Boat... wipedown solvents and aluminum recreational boat surface coatings? (a) Use equation 1 of this section to...

40 CFR 63.5753 - How do I calculate the combined organic HAP content of aluminum wipedown solvents and aluminum...

Code of Federal Regulations, 2011 CFR

2011-07-01

... HAP content of aluminum wipedown solvents and aluminum recreational boat surface coatings? 63.5753... Standards for Hazardous Air Pollutants for Boat Manufacturing Standards for Aluminum Recreational Boat... wipedown solvents and aluminum recreational boat surface coatings? (a) Use equation 1 of this section to...

High yield synthesis of Ni-BTC metal-organic framework with ultrasonic irradiation: Role of polar aprotic DMF solvent.

PubMed

Israr, Farrukh; Chun, Daye; Kim, Yeongmin; Kim, Duk Kyung

2016-07-01

Nickel based porous solid was synthesized with 20 kHz ultrasonic irradiation. The reaction of Ni(II) nitrate hexahydrate with 1,3,5-benzene tricarboxylic acid in N,N-Dimethylformamide (DMF) as the sole solvent under ultrasonic radiation produced porous Ni-BTC MOF. Choice of correct solvent for the ultrasonic treatment was proven important. The effect of varying ultrasonic powers (40%, 60% and 80% of 750 W) along with different temperature conditions (50 °C, 60 °C, 70 °C and 80 °C) influenced the respective yield. A very high yield of 88% Ni-BTC MOF was obtained from 80% ultrasonic power at 60 °C. BET surface areas of the MOF crystals measured by N2 gas adsorption isotherms were in the range of 960-1000 m(2)/g. Copyright © 2015 Elsevier B.V. All rights reserved.

Bubbles in solvent microextraction: the influence of intentionally introduced bubbles on extraction efficiency.

PubMed

Williams, D Bradley G; George, Mosotho J; Meyer, Riaan; Marjanovic, Ljiljana

2011-09-01

Significant improvements to microdrop extractions of triazine pesticides are realized by the intentional incorporation of an air bubble into the solvent microdroplet used in this microextraction technique. The increase is attributed partly to greater droplet surface area resulting from the air bubble being incorporated into the solvent droplet as opposed to it sitting thereon and partly to thin film phenomena. The method is useful at nanogram/liter levels (LOD 0.002-0.012 μg/L, LOQ 0.007-0.039 μg/L), is precise (7-12% at 10 μg/L concentration level), and is validated against certified reference materials containing 0.5 and 5.0 μg/L analyte. It tolerates water and fruit juice as matrixes without serious matrix effects. This new development brings a simple, inexpensive, and efficient preconcentration technique to bear which rivals solid phase microextraction methods.

Diffusion accessibility as a method for visualizing macromolecular surface geometry.

PubMed

Tsai, Yingssu; Holton, Thomas; Yeates, Todd O

2015-10-01

Important three-dimensional spatial features such as depth and surface concavity can be difficult to convey clearly in the context of two-dimensional images. In the area of macromolecular visualization, the computer graphics technique of ray-tracing can be helpful, but further techniques for emphasizing surface concavity can give clearer perceptions of depth. The notion of diffusion accessibility is well-suited for emphasizing such features of macromolecular surfaces, but a method for calculating diffusion accessibility has not been made widely available. Here we make available a web-based platform that performs the necessary calculation by solving the Laplace equation for steady state diffusion, and produces scripts for visualization that emphasize surface depth by coloring according to diffusion accessibility. The URL is http://services.mbi.ucla.edu/DiffAcc/. © 2015 The Protein Society.

Spectroscopic investigation of phenolic groups ionization in the vipoxin neurotoxic phospholipase A 2: comparison with the X-ray structure in the region of the tyrosyl residues

NASA Astrophysics Data System (ADS)

Georgieva, Dessislava Nikolova; Genov, Nicolay; Rajashankar, Kanagalaghatta R.; Aleksiev, Boris; Betzel, Christian

1998-12-01

The neurotoxin vipoxin is the major lethal component of the venom of Vipera ammodites meridionalis, the most toxic snake in Europe. It is a complex between a toxic phospholipase A 2 (PLA 2) and a non-toxic protein inhibitor (Inh). Tyrosyl residues are involved in the catalytic site (Tyr 52 and 73) and in the substrate binding (Tyr 22). Spectroscopic studies demonstrated differences in the ionization behavior of the various phenolic hydroxyl groups in the toxic PLA 2. The tyrosyl side chains of the enzyme can be classified into three groups: (a) three phenolic hydroxyls are accessible to the solvent and titrate normally, with a p Keff=10.45; (b) three residues are partially 'buried' and participate in hydrogen bonds with neighboring functional groups. They titrate anomalously with a p Keff=12.17; (c) two tyrosines with a p Keff=13.23 are deeply 'buried' in the hydrophobic interior of PLA 2. They became accessible to the titrating agent only after alkaline denaturation of the protein molecule. The spectroscopic data are related to the X-ray structure of the vipoxin PLA 2. The refined model was investigated in the region of the tyrosyl side chains. The accessible surface area of each tyrosyl residue and each phenolic hydroxyl group was calculated. A good correlation between the spectrophotometric and the crystallographic data was observed. The ionization behavior of the phenolic groups is explained by peculiarities of the protein three-dimensional structure and the participation of tyrosines in the catalytic site hydrogen bond network. Attempts are made to assign the calculated p Keff values to individual residues. The high degree of 'exposure' on the protein surface of Tyr 22 and 75 is probably important for their function as parts of the substrate binding and pharmacological sites.

Rectification of nanopores in aprotic solvents--transport properties of nanopores with surface dipoles.

PubMed

Plett, Timothy; Shi, Wenqing; Zeng, Yuhan; Mann, William; Vlassiouk, Ivan; Baker, Lane A; Siwy, Zuzanna S

2015-12-07

Nanopores have become a model system to understand transport properties at the nanoscale. We report experiments and modeling of ionic current in aprotic solvents with different dipole moments through conically shaped nanopores in a polycarbonate film and through glass nanopipettes. We focus on solutions of the salt LiClO4, which is of great importance in modeling lithium based batteries. Results presented suggest ion current rectification observed results from two effects: (i) adsorption of Li(+) ions to the pore walls, and (ii) a finite dipole moment rendered by adsorbed solvent molecules. Properties of surfaces in various solvents were probed by means of scanning ion conductance microscopy, which confirmed existence of an effectively positive surface potential in aprotic solvents with high dipole moments.

The National Shipbuilding Research Program. Update Handbook for Surface Preparation and Coatings in Tanks and Confined Areas

DTIC Science & Technology

2000-10-31

cleaning method are described in Naval Ships’ Technical Manual Chapter 631. 4.6.4 Citric Acid Cleaning The citric acid cleaning system is intended to...acquisition of necessary chemicals and tools, degreasing/cleaning, paint/stripping/removal, citric acid rust removal, passivation of bare steel, and drying...Figure 9-7 Hanging Explosion -Proof Light Box • Figure 9-8 Lighting in Tank • Figure 10-1 Hazardous Waste Storage Area • Figure 10-2 Solvent

An Experimental Approach to Controllably Vary Protein Oxidation While Minimizing Electrode Adsorption for Boron-Doped Diamond Electrochemical Surface Mapping Applications

PubMed Central

McClintock, Carlee S; Hettich, Robert L.

2012-01-01

Oxidative protein surface mapping has become a powerful approach for measuring the solvent accessibility of folded protein structures. A variety of techniques exist for generating the key reagent – hydroxyl radicals – for these measurements; however, these approaches range significantly in their complexity and expense of operation. This research expands upon earlier work to enhance the controllability of boron-doped diamond (BDD) electrochemistry as an easily accessible tool for producing hydroxyl radicals in order to oxidize a range of intact proteins. Efforts to modulate oxidation level while minimizing the adsorption of protein to the electrode involved the use of relatively high flow rates to reduce protein residence time inside the electrochemical flow chamber. Additionally, a different cell activation approach using variable voltage to supply a controlled current allowed us to precisely tune the extent of oxidation in a protein-dependent manner. In order to gain perspective on the level of protein adsorption onto the electrode surface, studies were conducted to monitor protein concentration during electrolysis and gauge changes in the electrode surface between cell activation events. This report demonstrates the successful use of BDD electrochemistry for greater precision in generating a target number of oxidation events upon intact proteins. PMID:23210708

Unified interpretation of exciplex formation and marcus electron transfer on the basis of two-dimensional free energy surfaces.

PubMed

Murata, Shigeo; Tachiya, M

2007-09-27

The mechanism of exciplex formation proposed in a previous paper has been refined to show how exciplex formation and Marcus electron transfer (ET) in fluorescence quenching are related to each other. This was done by making simple calculations of the free energies of the initial (DA*) and final (D+A-) states of ET. First it was shown that the decrease in D-A distance can induce intermolecular ET even in nonpolar solvents where solvent orientational polarization is absent, and that it leads to exciplex formation. This is consistent with experimental results that exciplex is most often observed in nonpolar solvents. The calculation was then extended to ET in polar solvents where the free energies are functions of both D-A distance and solvent orientational polarization. This enabled us to discuss both exciplex formation and Marcus ET in the same D-A pair and solvent on the basis of 2-dimensional free energy surfaces. The surfaces contain more information about the rates of these reactions, the mechanism of fluorescence quenching by ET, etc., than simple reaction schemes. By changing the parameters such as the free energy change of reaction, solvent dielectric constants, etc., one can construct the free energy surfaces for various systems. The effects of free energy change of reaction and of solvent polarity on the mechanism and relative importance of exciplex formation and Marcus ET in fluorescence quenching can be well explained. The free energy surface will also be useful for discussion of other phenomena related to ET reactions.

Continuum and atomistic description of excess electrons in TiO2

NASA Astrophysics Data System (ADS)

Maggio, Emanuele; Martsinovich, Natalia; Troisi, Alessandro

2016-02-01

The modelling of an excess electron in a semiconductor in a prototypical dye sensitised solar cell is carried out using two complementary approaches: atomistic simulation of the TiO2 nanoparticle surface is complemented by a dielectric continuum model of the solvent-semiconductor interface. The two methods are employed to characterise the bound (excitonic) states formed by the interaction of the electron in the semiconductor with a positive charge opposite the interface. Density-functional theory (DFT) calculations show that the excess electron in TiO2 in the presence of a counterion is not fully localised but extends laterally over a large region, larger than system sizes accessible to DFT calculations. The numerical description of the excess electron at the semiconductor-electrolyte interface based on the continuum model shows that the exciton is also delocalised over a large area: the exciton radius can have values from tens to hundreds of Ångströms, depending on the nature of the semiconductor (characterised by the dielectric constant and the electron effective mass in our model).

A thermodynamic study of Abeta(16-21) dissociation from a fibril using computer simulations

NASA Astrophysics Data System (ADS)

Dias, Cristiano; Mahmoudinobar, Farbod; Su, Zhaoqian

Here, I will discuss recent all-atom molecular dynamics simulations with explicit water in which we studied the thermodynamic properties of Abeta(16-21) dissociation from an amyloid fibril. Changes in thermodynamics quantities, e.g., entropy, enthalpy, and volume, are computed from the temperature dependence of the free-energy computed using the umbrella sampling method. We find similarities and differences between the thermodynamics of peptide dissociation and protein unfolding. Similarly to protein unfolding, Abeta(16-21) dissociation is characterized by an unfavorable change in enthalpy, a favorable change in the entropic energy, and an increase in the heat capacity. A main difference is that peptide dissociation is characterized by a weak enthalpy-entropy compensation. We characterize dock and lock states of the peptide based on the solvent accessible surface area. The Lennard-Jones energy of the system is observed to increase continuously in lock and dock states as the peptide dissociates. The electrostatic energy increases in the lock state and it decreases in the dock state as the peptide dissociates. These results will be discussed as well as their implication for fibril growth.

Alcohols Reduce Lateral Membrane Pressures: Predictions from Molecular Theory

PubMed Central

Frischknecht, Amalie L.; Frink, Laura J. Douglas

2006-01-01

We explore the effects of alcohols on fluid lipid bilayers using a molecular theory with a coarse-grained model. We show that the trends predicted from the theory in the changes in area per lipid, alcohol concentration in the bilayer, and area compressibility modulus, as a function of alcohol chain length and of the alcohol concentration in the solvent far from the bilayer, follow those found experimentally. We then use the theory to study the effect of added alcohol on the lateral pressure profile across the membrane, and find that added alcohol reduces the surface tensions at both the headgroup/solvent and headgroup/tailgroup interfaces, as well as the lateral pressures in the headgroup and tailgroup regions. These changes in lateral pressures could affect the conformations of membrane proteins, providing a nonspecific mechanism for the biological effects of alcohols on cells. PMID:16980354

The Effects of Secondary Oxides on Copper-Based Catalysts for Green Methanol Synthesis.

PubMed

Hayward, James S; Smith, Paul J; Kondrat, Simon A; Bowker, Michael; Hutchings, Graham J

2017-05-10

Catalysts for methanol synthesis from CO 2 and H 2 have been produced by two main methods: co-precipitation and supercritical anti-solvent (SAS) precipitation. These two methods are compared, along with the behaviour of copper supported on Zn, Mg, Mn, and Ce oxides. Although the SAS method produces initially active material with high Cu specific surface area, they appear to be unstable during reaction losing significant amounts of surface area and hence activity. The CuZn catalysts prepared by co-precipitation, however, showed much greater thermal and reactive stability than the other materials. There appeared to be the usual near-linear dependence of activity upon Cu specific area, though the initial performance relationship was different from that post-reaction, after some loss of surface area. The formation of the malachite precursor, as reported before, is important for good activity and stability, whereas if copper oxides are formed during the synthesis and ageing process, then a detrimental effect on these properties is seen.

The Effects of Secondary Oxides on Copper‐Based Catalysts for Green Methanol Synthesis

PubMed Central

Hayward, James S.; Smith, Paul J.; Kondrat, Simon A.; Bowker, Michael

2017-01-01

Abstract Catalysts for methanol synthesis from CO2 and H2 have been produced by two main methods: co‐precipitation and supercritical anti‐solvent (SAS) precipitation. These two methods are compared, along with the behaviour of copper supported on Zn, Mg, Mn, and Ce oxides. Although the SAS method produces initially active material with high Cu specific surface area, they appear to be unstable during reaction losing significant amounts of surface area and hence activity. The CuZn catalysts prepared by co‐precipitation, however, showed much greater thermal and reactive stability than the other materials. There appeared to be the usual near‐linear dependence of activity upon Cu specific area, though the initial performance relationship was different from that post‐reaction, after some loss of surface area. The formation of the malachite precursor, as reported before, is important for good activity and stability, whereas if copper oxides are formed during the synthesis and ageing process, then a detrimental effect on these properties is seen. PMID:28706570

The extraction of bitumen from western oil sands. Final report, July 1989--September 1993

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

Oblad, A.G.; Bunger, J.W.; Dahlstrom, D.A.

1994-03-01

Research and development of surface extraction and upgrading processes of western tar sands are described. Research areas included modified hot water, fluidized bed, and rotary kiln pyrolysis of tar sands for extraction of bitumen. Bitumen upgrading included solvent extraction of bitumen, and catalytic hydrotreating of bitumen. Characterization of Utah tar sand deposits is also included.

Experimental protocols for and studies of the effects of surface passivation and water isotopes on the gliding speed of microtubules propelled by kinesin-1

NASA Astrophysics Data System (ADS)

Maloney, Roger Andrew

This dissertation explores how the kinesin-1 and microtubule system is affected by surface passivation and water isotopes. Surface passivation was found to affect the gliding speed that microtubules exhibit in the gliding motility assay and the lengths of microtubules supported by the passivation. It was also found that gliding speeds of microtubules are very sensitive to temperature changes. Studies changing the water isotope were a first attempt to investigate if changing the solvent changed the osmotic pressure of the solution kinesin and microtubules were in. No osmotic pressure changes were observed, however, the experiments using different isotopes of water did illuminate the possibility that kinesin may be sensitive to viscosity changes in the solvent. This experiment also suggests further experiments that can be specifically designed to probe osmotic pressure changes. This thesis was also the first thesis ever, to the best of the author's knowledge, to be done in a completely open format. All information and notebook entries that are related to it, as well as the thesis itself, can be found on the website OpenWetWare. The thesis can also be found there including all the different versions that went into its editing. The philosophy and process of making data open and accessible to every one is also discussed.

Structure and Dynamics of Solvated Polymers near a Silica Surface: On the Different Roles Played by Solvent.

PubMed

Perrin, Elsa; Schoen, Martin; Coudert, François-Xavier; Boutin, Anne

2018-04-26

Whereas it is experimentally known that the inclusion of nanoparticles in hydrogels can lead to a mechanical reinforcement, a detailed molecular understanding of the adhesion mechanism is still lacking. Here we use coarse-grained molecular dynamics simulations to investigate the nature of the interface between silica surfaces and solvated polymers. We show how differences in the nature of the polymer and the polymer-solvent interactions can lead to drastically different behavior of the polymer-surface adhesion. Comparing explicit and implicit solvent models, we conclude that this effect cannot be fully described in an implicit solvent. We highlight the crucial role of polymer solvation for the adsorption of the polymer chain on the silica surface, the significant dynamics of polymer chains on the surface, and details of the modifications in the structure solvated polymer close to the interface.

Field performance testing of improved engineered wood fiber surfaces for accessible playground areas

Treesearch

Theodore L. Laufenberg; Jerrold E. Winandy

2003-01-01

Some engineered wood fiber (EWF) surfaces on playgrounds are soft and uneven, which creates difficulties for those who use mobility aids, such as wheelchairs and walkers. The outdoor field testing reported in this study is part of an effort to stabilize EWF to improve accessibility. The concept is to mix a binder with the upper surface of EWF to create a stiff (firm)...

Probing Contaminant Transport to and from Clay Surfaces in Organic Solvents and Water Using Solution Calorimetry.

PubMed

Pourmohammadbagher, Amin; Shaw, John M

2015-09-15

Clays, in tailings, are a significant ongoing environmental concern in the mining and oilsands production industries, and clay rehabilitation following contamination poses challenges episodically. Understanding the fundamentals of clay behavior can lead to better environmental impact mitigation strategies. Systematic calorimetric measurements are shown to provide a framework for parsing the synergistic and antagonistic impacts of trace (i.e., parts per million level) components on the surface compositions of clays. The enthalpy of solution of as-received and "contaminated" clays, in as-received and "contaminated" organic solvents and water, at 60 °C and atmospheric pressure, provides important illustrative examples. Clay contamination included pre-saturation of clays with water and organic liquids. Solvent contamination included the addition of trace water to organic solvents and trace organic liquids to water. Enthalpy of solution outcomes are interpreted using a quantitative mass and energy balance modeling framework that isolates terms for solvent and trace contaminant sorption/desorption and surface energy effects. Underlying surface energies are shown to dominate the energetics of the solvent-clay interaction, and organic liquids as solvents or as trace contaminants are shown to displace water from as-received clay surfaces. This approach can be readily extended to include pH, salts, or other effects and is expected to provide mechanistic and quantitative insights underlying the stability of clays in tailings ponds and the behaviors of clays in diverse industrial and natural environments.

Effect of surface hydroxyl groups on heat capacity of mesoporous silica

NASA Astrophysics Data System (ADS)

Marszewski, Michal; Butts, Danielle; Lan, Esther; Yan, Yan; King, Sophia C.; McNeil, Patricia E.; Galy, Tiphaine; Dunn, Bruce; Tolbert, Sarah H.; Hu, Yongjie; Pilon, Laurent

2018-05-01

This paper quantifies the effect of surface hydroxyl groups on the effective specific and volumetric heat capacities of mesoporous silica. To achieve a wide range of structural diversity, mesoporous silica samples were synthesized by various methods, including (i) polymer-templated nanoparticle-based powders, (ii) polymer-templated sol-gel powders, and (iii) ambigel silica samples dried by solvent exchange at room temperature. Their effective specific heat capacity, specific surface area, and porosity were measured using differential scanning calorimetry and low-temperature nitrogen adsorption-desorption measurements. The experimentally measured specific heat capacity was larger than the conventional weight-fraction-weighted specific heat capacity of the air and silica constituents. The difference was attributed to the presence of OH groups in the large internal surface area. A thermodynamic model was developed based on surface energy considerations to account for the effect of surface OH groups on the specific and volumetric heat capacity. The model predictions fell within the experimental uncertainty.

Synthesis and characterization of nanoporous silica aerogel beads using cheap industrial grade sodium silacte precursor

NASA Astrophysics Data System (ADS)

Khan, Tasneem M. A.; Khan, Asiya; Sarawade, Pradip B.

2018-05-01

We report a method to synthesize low-density transparent mesoporous silica aerogel beads by ambient pressure drying (APD). The beads were prepared by acid-base sol-gel polymerization of sodium silicate in via the ball dropping method (BDM). To minimize shrinkage during drying, wet silica beads were initially prepared; their surfaces were then modified using trimethylchlorosilane (TMCS) via simultaneous solvent exchange and surface modification. The specific surface area and cumulative pore volume of the silica aerogel beads increased with an increase in the %V of TMCS. Silica aerogel beads with low packing bed density, high surface area, and large cumulative pore volume was obtained when TMCS was used. Properties of the final product were examined by BET, and TG-DT analyses. The hydrophobic silica aerogel beads were thermally stable up to 350°C. We discuss our results and compare our findings for modified versus unmodified silica beads.

Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of small membranes using all atomistic and coarse-grained methods. The molecular interaction between common polymer chains used in biomedical applications and the cell membrane is unknown. This interaction may affect the biocompatibility of the polymer chains. Molecular dynamics simulations offer an emerging tool to characterize the interaction between common degradable polymer chains used in biomedical applications, such as polycaprolactone, and model cell membranes. We systematically characterize with long-time all-atomistic molecular dynamics simulations the interaction between single polycaprolactone chains of varying chain lengths with a model phospholipid membrane. We find that the length of polymer chain greatly affects the nature of interaction with the membrane, as well as the membrane properties. Furthermore, we next utilize advanced sampling techniques in molecular dynamics to characterize the two-dimensional free energy surface for the interaction of varying polymer chain lengths (short, intermediate, and long) with model cell membranes. We find that the free energy minimum shifts from the membrane-water interface to the hydrophobic core of the phospholipid membrane as a function of chain length. These results can be used to design polymer chain lengths and chemistries to optimize their interaction with cell membranes at the molecular level.

Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations.

PubMed

Godschalk, Frithjof; Genheden, Samuel; Söderhjelm, Pär; Ryde, Ulf

2013-05-28

Molecular mechanics with generalised Born and surface area solvation (MM/GBSA) is a popular method to calculate the free energy of the binding of ligands to proteins. It involves molecular dynamics (MD) simulations with an explicit solvent of the protein-ligand complex to give a set of snapshots for which energies are calculated with an implicit solvent. This change in the solvation method (explicit → implicit) would strictly require that the energies are reweighted with the implicit-solvent energies, which is normally not done. In this paper we calculate MM/GBSA energies with two generalised Born models for snapshots generated by the same methods or by explicit-solvent simulations for five synthetic N-acetyllactosamine derivatives binding to galectin-3. We show that the resulting energies are very different both in absolute and relative terms, showing that the change in the solvent model is far from innocent and that standard MM/GBSA is not a consistent method. The ensembles generated with the various solvent models are quite different with root-mean-square deviations of 1.2-1.4 Å. The ensembles can be converted to each other by performing short MD simulations with the new method, but the convergence is slow, showing mean absolute differences in the calculated energies of 6-7 kJ mol(-1) after 2 ps simulations. Minimisations show even slower convergence and there are strong indications that the energies obtained from minimised structures are different from those obtained by MD.

A novel carbon electrode material for highly improved EDLC performance.

PubMed

Fang, Baizeng; Binder, Leo

2006-04-20

Porous materials, developed by grafting functional groups through chemical surface modification with a surfactant, represent an innovative concept in energy storage. This work reports, in detail, the first practical realization of a novel carbon electrode based on grafting of vinyltrimethoxysilane (vtmos) functional group for energy storage in electric double layer capacitor (EDLC). Surface modification with surfactant vtmos enhances the hydrophobisation of activated carbon and the affinity toward propylene carbonate (PC) solvent, which improves the wettability of activated carbon in the electrolyte solution based on PC solvent, resulting in not only a lower resistance to the transport of electrolyte ions within micropores of activated carbon but also more usable surface area for the formation of electric double layer, and accordingly, higher specific capacitance, energy density, and power capability available from the capacitor based on modified carbon. Especially, the effects from surface modification become superior at higher discharge rate, at which much better EDLC performance (i.e., much higher energy density and power capability) has been achieved by the modified carbon, suggesting that the modified carbon is a novel and very promising electrode material of EDLC for large current applications where both high energy density and power capability are required.

Aqueous or solvent based surface modification: The influence of the combination solvent - organic functional group on the surface characteristics of titanium dioxide grafted with organophosphonic acids

NASA Astrophysics Data System (ADS)

Roevens, Annelore; Van Dijck, Jeroen G.; Geldof, Davy; Blockhuys, Frank; Prelot, Benedicte; Zajac, Jerzy; Meynen, Vera

2017-09-01

To alter the versatility of interactions at its surface, TiO2 is modified with organophosphonic acids (PA). A thorough understanding of the role of all synthesis conditions is necessary to achieve controlled functionalization. This study reports on the effect of using water, toluene and their mixtures when performing the modification of TiO2 with PA. Sorption and calorimetry measurements of surface interactions with various probing species clearly indicate that, by grafting PA in water, clear differences appear in the distribution of organic groups on the surface. Also the functional group of the PA determines the impact of using water as solvent. Modification in toluene results in a higher modification degree for propylphosphonic acid (3PA), as the solvent-solute interaction may hinder the grafting with phenylphosphonic acid (PhPA) in toluene. Water is preferred as solvent for PhPA modification as stabilizing π-OH interactions enhance surface grafting overcoming the competitive interaction of water at the surface as observed with 3PA. By using water in toluene mixtures for the functionalization of TiO2 with 3PA, the degree of functionalization is higher than when only water or toluene is used. Furthermore, adding small amounts of water leads to the formation of titanium propylphosphonates, next to surface grafting.

Molecular dynamics simulation of interactions between a sodium dodecyl sulfate micelle and a poly(ethylene oxide) polymer.

PubMed

Shang, Barry Z; Wang, Zuowei; Larson, Ronald G

2008-03-13

We have performed atomistic molecular dynamics simulations of an anionic sodium dodecyl sulfate (SDS) micelle and a nonionic poly(ethylene oxide) (PEO) polymer in aqueous solution. The micelle consisted of 60 surfactant molecules, and the polymer chain lengths varied from 20 to 40 monomers. The force field parameters for PEO were adjusted by using 1,2-dimethoxymethane (DME) as a model compound and matching its hydration enthalpy and conformational behavior to experiment. Excellent agreement with previous experimental and simulation work was obtained through these modifications. The simulated scaling behavior of the PEO radius of gyration was also in close agreement with experimental results. The SDS-PEO simulations show that the polymer resides on the micelle surface and at the hydrocarbon-water interface, leading to a selective reduction in the hydrophobic contribution to the solvent-accessible surface area of the micelle. The association is mainly driven by hydrophobic interactions between the polymer and surfactant tails, while the interaction between the polymer and sulfate headgroups on the micelle surface is weak. The 40-monomer chain is mostly wrapped around the micelle, and nearly 90% of the monomers are adsorbed at low PEO concentration. Simulations were also performed with multiple 20-monomer chains, and gradual addition of polymer indicates that about 120 monomers are required to saturate the micelle surface. The stoichiometry of the resulting complex is in close agreement with experimental results, and the commonly accepted "beaded necklace" structure of the SDS-PEO complex is recovered by our simulations.

The impact of surface area, volume, curvature, and Lennard-Jones potential to solvation modeling.

PubMed

Nguyen, Duc D; Wei, Guo-Wei

2017-01-05

This article explores the impact of surface area, volume, curvature, and Lennard-Jones (LJ) potential on solvation free energy predictions. Rigidity surfaces are utilized to generate robust analytical expressions for maximum, minimum, mean, and Gaussian curvatures of solvent-solute interfaces, and define a generalized Poisson-Boltzmann (GPB) equation with a smooth dielectric profile. Extensive correlation analysis is performed to examine the linear dependence of surface area, surface enclosed volume, maximum curvature, minimum curvature, mean curvature, and Gaussian curvature for solvation modeling. It is found that surface area and surfaces enclosed volumes are highly correlated to each other's, and poorly correlated to various curvatures for six test sets of molecules. Different curvatures are weakly correlated to each other for six test sets of molecules, but are strongly correlated to each other within each test set of molecules. Based on correlation analysis, we construct twenty six nontrivial nonpolar solvation models. Our numerical results reveal that the LJ potential plays a vital role in nonpolar solvation modeling, especially for molecules involving strong van der Waals interactions. It is found that curvatures are at least as important as surface area or surface enclosed volume in nonpolar solvation modeling. In conjugation with the GPB model, various curvature-based nonpolar solvation models are shown to offer some of the best solvation free energy predictions for a wide range of test sets. For example, root mean square errors from a model constituting surface area, volume, mean curvature, and LJ potential are less than 0.42 kcal/mol for all test sets. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain.

PubMed

Hou, Tingjun; Zhang, Wei; Case, David A; Wang, Wei

2008-02-29

Many important protein-protein interactions are mediated by peptide recognition modular domains, such as the Src homology 3 (SH3), SH2, PDZ, and WW domains. Characterizing the interaction interface of domain-peptide complexes and predicting binding specificity for modular domains are critical for deciphering protein-protein interaction networks. Here, we propose the use of an energetic decomposition analysis to characterize domain-peptide interactions and the molecular interaction energy components (MIECs), including van der Waals, electrostatic, and desolvation energy between residue pairs on the binding interface. We show a proof-of-concept study on the amphiphysin-1 SH3 domain interacting with its peptide ligands. The structures of the human amphiphysin-1 SH3 domain complexed with 884 peptides were first modeled using virtual mutagenesis and optimized by molecular mechanics (MM) minimization. Next, the MIECs between domain and peptide residues were computed using the MM/generalized Born decomposition analysis. We conducted two types of statistical analyses on the MIECs to demonstrate their usefulness for predicting binding affinities of peptides and for classifying peptides into binder and non-binder categories. First, combining partial least squares analysis and genetic algorithm, we fitted linear regression models between the MIECs and the peptide binding affinities on the training data set. These models were then used to predict binding affinities for peptides in the test data set; the predicted values have a correlation coefficient of 0.81 and an unsigned mean error of 0.39 compared with the experimentally measured ones. The partial least squares-genetic algorithm analysis on the MIECs revealed the critical interactions for the binding specificity of the amphiphysin-1 SH3 domain. Next, a support vector machine (SVM) was employed to build classification models based on the MIECs of peptides in the training set. A rigorous training-validation procedure was used to assess the performances of different kernel functions in SVM and different combinations of the MIECs. The best SVM classifier gave satisfactory predictions for the test set, indicated by average prediction accuracy rates of 78% and 91% for the binding and non-binding peptides, respectively. We also showed that the performance of our approach on both binding affinity prediction and binder/non-binder classification was superior to the performances of the conventional MM/Poisson-Boltzmann solvent-accessible surface area and MM/generalized Born solvent-accessible surface area calculations. Our study demonstrates that the analysis of the MIECs between peptides and the SH3 domain can successfully characterize the binding interface, and it provides a framework to derive integrated prediction models for different domain-peptide systems.

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

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

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

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

NASA Astrophysics Data System (ADS)

Mohanta, Dayanidhi; Jana, Madhurima

2016-04-01

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

Partially nanofibrous architecture of 3D tissue engineering scaffolds.

PubMed

Wei, Guobao; Ma, Peter X

2009-11-01

An ideal tissue-engineering scaffold should provide suitable pores and appropriate pore surface to induce desired cellular activities and to guide 3D tissue regeneration. In the present work, we have developed macroporous polymer scaffolds with varying pore wall architectures from smooth (solid), microporous, partially nanofibrous, to entirely nanofibrous ones. All scaffolds are designed to have well-controlled interconnected macropores, resulting from leaching sugar sphere template. We examine the effects of material composition, solvent, and phase separation temperature on the pore surface architecture of 3D scaffolds. In particular, phase separation of PLLA/PDLLA or PLLA/PLGA blends leads to partially nanofibrous scaffolds, in which PLLA forms nanofibers and PDLLA or PLGA forms the smooth (solid) surfaces on macropore walls, respectively. Specific surface areas are measured for scaffolds with similar macroporosity but different macropore wall architectures. It is found that the pore wall architecture predominates the total surface area of the scaffolds. The surface area of a partially nanofibrous scaffold increases linearly with the PLLA content in the polymer blend. The amounts of adsorbed proteins from serum increase with the surface area of the scaffolds. These macroporous scaffolds with adjustable pore wall surface architectures may provide a platform for investigating the cellular responses to pore surface architecture, and provide us with a powerful tool to develop superior scaffolds for various tissue-engineering applications.

Comparative molecular dynamics simulation studies for determining factors contributing to the thermostability of chemotaxis protein "CheY".

PubMed

Paul, Manish; Hazra, Mousumi; Barman, Arghya; Hazra, Saugata

2014-01-01

Comparative molecular dynamics simulations of chemotaxis protein "CheY" from thermophilic origin Thermotoga maritima and its mesophilic counterpart Salmonella enterica have been performed for 10 ns each at 300 and 350 K, and 20 ns each at 400 and 450 K. The trajectories were analyzed in terms of different factors like root-mean-square deviation, root-mean-square fluctuation, radius of gyration, solvent accessible surface area, H-bonds, salt bridge content, and protein-solvent interactions which indicate distinct differences between the two of them. The two proteins also follow dissimilar unfolding pathways. The overall flexibility calculated by the trace of the diagonalized covariance matrix displays similar flexibility of both the proteins near their optimum growth temperatures. However, at higher temperatures mesophilic protein shows increased overall flexibility than its thermophilic counterpart. Principal component analysis also indicates that the essential subspaces explored by the simulations of two proteins at different temperatures are nonoverlapping and they show significantly different directions of motion. However, there are significant overlaps within the trajectories and similar direction of motions are observed for both proteins at 300 K. Overall, the mesophilic protein leads to increased conformational sampling of the phase space than its thermophilic counterpart. This is the first ever study of thermostability of CheY protein homologs by using protein dynamism as a main impact. Our study might be used as a model for studying the molecular basis of thermostability of two homologous proteins from two organisms living at different temperatures with less visible differences.

MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch.

PubMed

Sharma, Monika; Bulusu, Gopalakrishnan; Mitra, Abhijit

2009-09-01

Riboswitches are structural cis-acting genetic regulatory elements in 5' UTRs of mRNAs, consisting of an aptamer domain that regulates the behavior of an expression platform in response to its recognition of, and binding to, specific ligands. While our understanding of the ligand-bound structure of the aptamer domain of the adenine riboswitches is based on crystal structure data and is well characterized, understanding of the structure and dynamics of the ligand-free aptamer is limited to indirect inferences from physicochemical probing experiments. Here we report the results of 15-nsec-long explicit-solvent molecular dynamics simulations of the add A-riboswitch crystal structure (1Y26), both in the adenine-bound (CLOSED) state and in the adenine-free (OPEN) state. Root-mean-square deviation, root-mean-square fluctuation, dynamic cross-correlation, and backbone torsion angle analyses are carried out on the two trajectories. These, along with solvent accessible surface area analysis of the two average structures, are benchmarked against available experimental data and are shown to constitute the basis for obtaining reliable insights into the molecular level details of the binding and switching mechanism. Our analysis reveals the interaction network responsible for, and conformational changes associated with, the communication between the binding pocket and the expression platform. It further highlights the significance of a, hitherto unreported, noncanonical W:H trans base pairing between A73 and A24, in the OPEN state, and also helps us to propose a possibly crucial role of U51 in the context of ligand binding and ligand discrimination.

Origins of protein denatured state compactness and hydrophobic clustering in aqueous urea: inferences from nonpolar potentials of mean force.

PubMed

Shimizu, Seishi; Chan, Hue Sun

2002-12-01

Free energies of pairwise hydrophobic association are simulated in aqueous solutions of urea at concentrations ranging from 0-8 M. Consistent with the expectation that hydrophobic interactions are weakened by urea, the association of relatively large nonpolar solutes is destabilized by urea. However, the association of two small methane-sized nonpolar solutes in water has the opposite tendency of being slightly strengthened by the addition of urea. Such size effects and the dependence of urea-induced stability changes on the configuration of nonpolar solutes are not predicted by solvent accessible surface area approaches based on energetic parameters derived from bulk-phase solubilities of model compounds. Thus, to understand hydrophobic interactions in proteins, it is not sufficient to rely solely on transfer experiment data that effectively characterize a single nonpolar solute in an aqueous environment but not the solvent-mediated interactions among two or more nonpolar solutes. We find that the m-values for the rate of change of two-methane association free energy with respect to urea concentration is a dramatically nonmonotonic function of the spatial separation between the two methanes, with a distance-dependent profile similar to the corresponding two-methane heat capacity of association in pure water. Our results rationalize the persistence of residual hydrophobic contacts in some proteins at high urea concentrations and explain why the heat capacity signature (DeltaC(P)) of a compact denatured state can be similar to DeltaC(P) values calculated by assuming an open random-coil-like unfolded state. Copyright 2002 Wiley-Liss, Inc.

Multibody correlations in the hydrophobic solvation of glycine peptides

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

Harris, Robert C.; Drake, Justin A.; Pettitt, B. Montgomery, E-mail: mpettitt@utmb.edu

2014-12-14

Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (ΔG{sub vdw}) that scales linearly with solvent-accessible surface area (A). In a previous study, we argued that ΔG{sub vdw}, as well as its attractive (ΔG{sub att}) and repulsive (ΔG{sub rep}) components, was not simply a linear function of A. We found that the surface tensions, γ{sub rep}, γ{sub att}, and γ{sub vdw}, gotten from ΔG{sub rep}, ΔG{sub att}, and ΔG{sub vdw} against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysismore » to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of γ{sub rep}. Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the γ{sub rep} for the intact decaglycines. Finally, γ{sub att} for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of γ{sub vdw} (−74 and −56 cal/mol/Å{sup 2} for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that ΔG{sub vdw} favors extended rather than compact structures for decaglycine. We find that ΔG{sub rep} and ΔG{sub vdw} have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms.« less

The inconsistency in adsorption properties and powder XRD data of MOF-5 is rationalized by framework interpenetration and the presence of organic and inorganic species in the nanocavities.

PubMed

Hafizovic, Jasmina; Bjørgen, Morten; Olsbye, Unni; Dietzel, Pascal D C; Bordiga, Silvia; Prestipino, Carmelo; Lamberti, Carlo; Lillerud, Karl Petter

2007-03-28

MOF-5 is the archetype metal-organic framework and has been subjected to numerous studies the past few years. The focal point of this report is the pitfalls related to the MOF-5 phase identification based on powder XRD data. A broad set of conditions and procedures have been reported for MOF-5 synthesis. These variations have led to materials with substantially different adsorption properties (specific surface areas in the range 700 to 3400 m(2)/g). The relatively low weight loss observed for some as synthesized samples upon solvent removal is also indicative of a low pore volume. Regrettably, these materials have all been described as MOF-5 without any further comments. Furthermore, the reported powder XRD patterns hint at structural differences: The variations in surface area are accompanied by peak splitting phenomena and rather pronounced changes in the relative peak intensities in the powder XRD patterns. In this work, we use single-crystal XRD to investigate structural differences between low and high surface area MOF-5. The low surface area MOF-5 sample had two different classes of crystals. For the dominant phase, Zn(OH)2 species partly occupied the cavities. The presence of Zn species makes the hosting cavity and possibly also adjacent cavities inaccessible and thus efficiently reduces the pore volume of the material. Furthermore, the minor phase consisted of doubly interpenetrated MOF-5 networks, which lowers the adsorption capacity. The presence of Zn species and lattice interpenetration changes the symmetry from cubic to trigonal and explains the peak splitting observed in the powder XRD patterns. Pore-filling effects from the Zn species (and partly the solvent molecules) are also responsible for the pronounced variations in powder XRD peak intensities. This latter conclusion is particularly useful for predicting the adsorption properties of a MOF-5-type material from powder XRD.

Communication: Contrasting effects of glycerol and DMSO on lipid membrane surface hydration dynamics and forces

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

Schrader, Alex M.; Cheng, Chi-Yuan; Israelachvili, Jacob N.

2016-07-28

Glycerol and dimethyl sulfoxide (DMSO) are commonly used cryoprotectants in cellular systems, but due to the challenges of measuring the properties of surface-bound solvent, fundamental questions remain regarding the concentration, interactions, and conformation of these solutes at lipid membrane surfaces. We measured the surface water diffusivity at gel-phase dipalmitoylphosphatidylcholine (DPPC) bilayer surfaces in aqueous solutions containing ≤7.5 mol. % of DMSO or glycerol using Overhauser dynamic nuclear polarization. We found that glycerol similarly affects the diffusivity of water near the bilayer surface and that in the bulk solution (within 20%), while DMSO substantially increases the diffusivity of surface water relativemore » to bulk water. We compare these measurements of water dynamics with those of equilibrium forces between DPPC bilayers in the same solvent mixtures. DMSO greatly decreases the range and magnitude of the repulsive forces between the bilayers, whereas glycerol increases it. We propose that the differences in hydrogen bonding capability of the two solutes leads DMSO to dehydrate the lipid head groups, while glycerol affects surface hydration only as much as it affects the bulk water properties. The results suggest that the mechanism of the two most common cryoprotectants must be fundamentally different: in the case of DMSO by decoupling the solvent from the lipid surface, and in the case of glycerol by altering the hydrogen bond structure and intermolecular cohesion of the global solvent, as manifested by increased solvent viscosity.« less

Observation of chain stretching in Langmuir diblock copolymer monolayers

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

Factor, B.J.; Lee, L.; Kent, M.S.

1993-10-01

We report observations of chain stretching in diblock copolymer monolayers on the surface of a selective solvent. Using neutron reflectivity, we have studied the concentration profile of the submerged block over a large range of surface density [sigma] (chains per area) for two different molecular weights. The observed increase in the layer thickness is weaker than the [sigma][sup 1/3] prediction of mean-field and scaling theories for the limiting behavior, but is in agreement with recent numerical self-consistent-field calculations by Whitmore and Noolandi [Macromolecules 23, 3321 (1990)].

Empirical correlation between hydrophobic free energy and aqueous cavity surface area

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

Reynolds, J.A.; Gilbert, D.B.; Tanford, C.

1974-08-01

The unitary free energy of transfer of a hydrocarbon molecule from a hydrocarbon solvent to an aqueous medium is a measure of the hydrophobic interaction in the aqueous medium. We have reexamined available data on this phenomenon and have confirmed that the free energy for saturated hydrocarbons is proportional to the surface area of the cavity created by the solute in the aqueous solution, with the same proportionality constant for linear, branched, and cyclic hydrocarbon molecules. The numerical value of the proportionality constant is uncertain because absolute and self-consistent area measurements are not available. We estimate that it falls betweenmore » 20 and 25 cal/mole per Angstrom/sup 2/ at 25/sup 0/ (for areas measured at the distance of closest approach of water molecules), which is significantly less than the figure of 33 cal/mole per Angstrom/sup 2/ that has been assigned to the same parameter by Hermann.« less

AFM fluid delivery/liquid extraction surface sampling/electrostatic spray cantilever probe

DOEpatents

Van Berkel, Gary J.

2015-06-23

An electrospray system comprises a liquid extraction surface sampling probe. The probe comprises a probe body having a liquid inlet and a liquid outlet, and having a liquid extraction tip. A solvent delivery conduit is provided for receiving solvent liquid from the liquid inlet and delivering the solvent liquid to the liquid extraction tip. An open liquid extraction channel extends across an exterior surface of the probe body from the liquid extraction tip to the liquid outlet. An electrospray emitter tip is in liquid communication with the liquid outlet of the liquid extraction surface sampling probe. A system for analyzing samples, a liquid junction surface sampling system, and a method of analyzing samples are also disclosed.

Solvent dependence of the activation energy of attachment determined by single molecule observations of surfactant adsorption.

PubMed

Honciuc, Andrei; Baptiste, Denver Jn; Campbell, Ian P; Schwartz, Daniel K

2009-07-07

Single-molecule total internal reflection fluorescence microscopy was used to obtain real-time images of fluorescently labeled hexadecanoic (palmitic) acid molecules as they adsorbed at the interface between fused silica and three different solvents: hexadecane (HD), tetrahydrofuran (THF), and water. These solvents were chosen to explore the effect of solvent polarity on the activation energy associated with the attachment rate, i.e., the rate at which molecules were transferred to the surface from the near-surface layer. Direct counting of single-molecule events, made under steady-state conditions at extremely low coverage, provided direct, model-independent measurements of this attachment rate, in contrast with conventional ensemble-averaged methods, which are influenced by bulk transport and competing detachment processes. We found that the attachment rate increased with increasing temperature for all solvents. Arrhenius analyses gave activation energies of 5+/-2 kJ/mol for adsorption from HD, 10+/-2 kJ/mol for adsorption from THF, and 19+/-2 kJ/mol for adsorption from water. These energies increased systematically with the solvent polarity and, therefore, with the expected strength of the solvent-substrate interaction. We hypothesize that the adsorption of amphiphilic solute molecules from solution can be regarded as a competitive exchange between solute molecules and surface-bound solvent. In this scenario, adsorption is an activated process, and the activation energy for attachment is associated with the solvent-substrate interaction energy.

Vibrational Stark effect spectroscopy reveals complementary electrostatic fields created by protein-protein binding at the interface of Ras and Ral.

PubMed

Walker, David M; Hayes, Ellen C; Webb, Lauren J

2013-08-07

Electrostatic fields at the interface of the GTPase H-Ras (Ras) docked with the Ras binding domain of the protein Ral guanine nucleoside dissociation stimulator (Ral) were measured with vibrational Stark effect (VSE) spectroscopy. Nine residues on the surface of Ras that participate in the protein-protein interface were systematically mutated to cysteine and subsequently converted to cyanocysteine in order to introduce a nitrile VSE probe into the protein-protein interface. The absorption energy of the nitrile was measured both on the surface of Ras in its monomeric state, then after incubation with the Ras binding domain of Ral to form the docked complex. Boltzmann-weighted structural snapshots of the nitrile-labeled Ras protein were generated both in monomeric and docked configurations from molecular dynamics simulations using enhanced sampling of the cyanocysteine side chain's χ2 dihedral angle. These snapshots were used to determine that on average, most of the nitrile probes were aligned along the Ras surface, parallel to the Ras-Ral interface. The average solvent-accessible surface areas (SASA) of the cyanocysteine side chain were found to be <60 Å(2) for all measured residues, and was not significantly different whether the nitrile was on the surface of the Ras monomer or immersed in the docked complex. Changes in the absorption energy of the nitrile probe at nine positions along the Ras-Ral interface were compared to results of a previous study examining this interface with Ral-based probes, and found a pattern of low electrostatic field in the core of the interface surrounded by a ring of high electrostatic field around the perimeter of the interface. These data are used to rationalize several puzzling features of the Ras-Ral interface.

Surface Texture-Induced Enhancement of Optical and Photoelectrochemical Activity of Cu2ZnSnS4 Photocathodes

NASA Astrophysics Data System (ADS)

Sarswat, Prashant K.; Deka, Nipon; Jagan Mohan Rao, S.; Free, Michael L.; Kumar, Gagan

2017-08-01

The objective of this work is to understand and improve the photocatalytic activity of Cu2ZnSnS4 (CZTS) through postgrowth modification techniques to create surface textures. This objective can be achieved using a combination of solvents, etching agents, and anodization techniques. One of the most effective surface treatments for enhancing the surface properties of photovoltaic materials is formation of nanoscale flakes, although other surface modifications were also evaluated. The superior performance of textured films can be attributed to enhanced surface area of absorber material exposed to electrolyte, ZnS deficiency, and high catalytic activity due to reduced charge-transfer resistance. Fine-tuning of ion flux and electrolyte stoichiometry can be used to create a controlled growth algorithm for CZTS thin films. The resulting information can be utilized to optimize film properties. The utility of nanostructured or engineered surfaces was evaluated using photoelectrochemical measurements. Finite-difference time-domain (FDTD)-assisted simulations were conducted for selected texturing, revealing enhanced surface area of absorbing medium that ultimately resulted in greater power loss of light in the medium.

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

PubMed

Vorobjev, Y N; Almagro, J C; Hermans, J

1998-09-01

A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximation by analysis of the covariance matrix. The implicit solvent (IS) dielectric continuum model is used to calculate the average solvation free energy as the sum of the free energies of creating the solute-size hydrophobic cavity, of the van der Waals solute-solvent interactions, and of the polarization of water solvent by the solute's charges. The reliability of the solvation free energy depends on a number of factors: the details of arrangement of the protein's charges, especially those near the surface; the definition of the molecular surface; and the method chosen for solving the Poisson equation. Molecular dynamics simulation in explicit solvent relaxes the protein's conformation and allows polar surface groups to assume conformations compatible with interaction with solvent, while averaging of internal energy and solvation free energy tend to enhance the precision. Two recently developed methods--SIMS, for calculation of a smooth invariant molecular surface, and FAMBE, for solution of the Poisson equation via a fast adaptive multigrid boundary element--have been employed. The SIMS and FAMBE programs scale linearly with the number of atoms. SIMS is superior to Connolly's MS (molecular surface) program: it is faster, more accurate, and more stable, and it smooths singularities of the molecular surface. Solvation free energies calculated with these two programs do not depend on molecular position or orientation and are stable along a molecular dynamics trajectory. We have applied this method to calculate the conformational free energy of native and intentionally misfolded globular conformations of proteins (the EMBL set of deliberately misfolded proteins) and have obtained good discrimination in favor of the native conformations in all instances.

Dispersing surface-modified imogolite nanotubes in polar and non-polar solvents

NASA Astrophysics Data System (ADS)

Li, Ming; Brant, Jonathan A.

2018-02-01

Furthering the development of nanocomposite structures, namely membranes for water treatment applications, requires that methods be developed to ensure nanoparticle dispersion in polar and non-polar solvents, as both are widely used in associated synthesis techniques. Here, we report on a two-step method to graft polyvinylpyrrolidone (PVP), and a one-step method for octadecylphosphonic acid (OPA), onto the outer surfaces of imogolite nanotubes. The goal of these approaches was to improve and maintain nanotube dispersion in polymer compatible polar and non-polar solvents. The PVP coating modified the imogolite surface charge from positive to weakly negative at pH ≤ 9; the OPA made it weakly positive at acidic pH values to negative at pH ≥ 7. The PVP surface coating stabilized the nanotubes through steric hindrance in polar protic, dipolar aprotic, and chloroform. In difference to the PVP, the OPA surface coating allowed the nanotubes to be dispersed in n-hexane and chloroform, but not in the polar solvents. The lack of miscibility in the polar solvents, as well as the better dispersion in n-hexane, was attributed to the stronger hydrophobicity of the OPA polymer relative to the PVP. [Figure not available: see fulltext.

Effect of stearic acid modified HAp nanoparticles in different solvents on the properties of Pickering emulsions and HAp/PLLA composites.

PubMed

Zhang, Ming; Wang, Ai-Juan; Li, Jun-Ming; Song, Na

2017-10-01

Stearic acid (Sa) was used to modify the surface properties of hydroxyapatite (HAp) in different solvents (water, ethanol or dichloromethane(CH 2 Cl 2 )). Effect of different solvents on the properties of HAp particles (activation ratio, grafting ratio, chemical properties), emulsion properties (emulsion stability, emulsion type, droplet morphology) as well as the cured materials (morphology, average pore size) were studied. FT-IR and XPS results confirmed the interaction occurred between stearic acid and HAp particles. Stable O/W and W/O type Pickering emulsions were prepared using unmodified and Sa modified HAp nanoparticles respectively, which indicated a catastrophic inversion of the Pickering emulsion happened possibly because of the enhanced hydrophobicity of HAp particles after surface modification. Porous materials with different structures and pore sizes were obtained using Pickering emulsion as the template via in situ evaporation solvent method. The results indicated the microstructures of cured samples are different form each other when HAp was surface modified in different solvents. HAp particles fabricated using ethanol as solvent has higher activation ratio and grafting ratio. Pickering emulsion with higher stability and cured porous materials with uniform morphology were obtained compared with samples prepared using water and CH 2 Cl 2 as solvents. In conclusion, surface modification of HAp in different solvents played a very important role for its stabilized Pickering emulsion as well as the microstructure of cured samples. It is better to use ethanol as the solvent for Sa modified HAp particles, which could increase the stability of Pickering emulsion and obtain cured samples with uniform pore size. Copyright © 2017 Elsevier B.V. All rights reserved.

Facile room-temperature solution-phase synthesis of a spherical covalent organic framework for high-resolution chromatographic separation.

PubMed

Yang, Cheng-Xiong; Liu, Chang; Cao, Yi-Meng; Yan, Xiu-Ping

2015-08-07

A simple and facile room-temperature solution-phase synthesis was developed to fabricate a spherical covalent organic framework with large surface area, good solvent stability and high thermostability for high-resolution chromatographic separation of diverse important industrial analytes including alkanes, cyclohexane and benzene, α-pinene and β-pinene, and alcohols with high column efficiency and good precision.

Design and performance of subgrade biogeochemical reactors.

PubMed

Gamlin, Jeff; Downey, Doug; Shearer, Brad; Favara, Paul

2017-12-15

Subgrade biogeochemical reactors (SBGRs), also commonly referred to as in situ bioreactors, are a unique technology for treatment of contaminant source areas and groundwater plume hot spots. SBGRs have most commonly been configured for enhanced reductive dechlorination (ERD) applications for chlorinated solvent treatment. However, they have also been designed for other contaminant classes using alternative treatment media. The SBGR technology typically consists of removal of contaminated soil via excavation or large-diameter augers, and backfill of the soil void with gravel and treatment amendments tailored to the target contaminant(s). In most cases SBGRs include installation of infiltration piping and a low-flow pumping system (typically solar-powered) to recirculate contaminated groundwater through the SBGR for treatment. SBGRs have been constructed in multiple configurations, including designs capable of meeting limited access restrictions at heavily industrialized sites, and at sites with restrictions on surface disturbance due to sensitive species or habitat issues. Typical performance results for ERD applications include 85 to 90 percent total molar reduction of chlorinated volatile organic compounds (CVOCs) near the SBGR and rapid clean-up of adjacent dissolved contaminant source areas. Based on a review of the literature and CH2M's field-scale results from over a dozen SBGRs with a least one year of performance data, important site-specific design considerations include: 1) hydraulic residence time should be long enough for sufficient treatment but not too long to create depressed pH and stagnant conditions (e.g., typically between 10 and 60 days), 2) reactor material should balance appropriate organic mulch as optimal bacterial growth media along with other organic additives that provide bioavailable organic carbon, 3) a variety of native bacteria are important to the treatment process, and 4) biologically mediated generation of iron sulfides along with addition of iron pyrite sands as an abiotic polishing step within the reactor has been observed to be an efficient treatment train for chlorinated solvent sites. Copyright © 2017 Elsevier Ltd. All rights reserved.

Improved strategies for DNP-enhanced 2D 1 H-X heteronuclear correlation spectroscopy of surfaces

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

Kobayashi, Takeshi; Perras, Frederic A.; Chaudhary, Umesh

We demonstrate that dynamic nuclear polarization (DNP)-enhanced 1H-X heteronuclear correlation (HETCOR) measurements of hydrogen-rich surface species are better accomplished by using proton-free solvents. This approach notably prevents HETCOR spectra from being obfuscated by the solvent-derived signals otherwise present in DNP measurements. Additionally, in the hydrogen-rich materials studied here, which included functionalized mesoporous silica nanoparticles and metal organic frameworks, the use of proton-free solvents afforded higher sensitivity gains than the commonly used solvents containing protons. Here, we also explored the possibility of using a solvent-free sample formulation and the feasibility of indirect detection in DNP-enhanced HETCOR experiments.

Improved strategies for DNP-enhanced 2D 1 H-X heteronuclear correlation spectroscopy of surfaces

DOE PAGES

Kobayashi, Takeshi; Perras, Frederic A.; Chaudhary, Umesh; ...

2017-08-12

We demonstrate that dynamic nuclear polarization (DNP)-enhanced 1H-X heteronuclear correlation (HETCOR) measurements of hydrogen-rich surface species are better accomplished by using proton-free solvents. This approach notably prevents HETCOR spectra from being obfuscated by the solvent-derived signals otherwise present in DNP measurements. Additionally, in the hydrogen-rich materials studied here, which included functionalized mesoporous silica nanoparticles and metal organic frameworks, the use of proton-free solvents afforded higher sensitivity gains than the commonly used solvents containing protons. Here, we also explored the possibility of using a solvent-free sample formulation and the feasibility of indirect detection in DNP-enhanced HETCOR experiments.

40 CFR 761.372 - Specific requirements for relatively clean surfaces.

Code of Federal Regulations, 2012 CFR

2012-07-01

... that each 900 cm2 (1 square foot) of the surface is always very wet for 1 minute. Wipe smooth surfaces with a solvent-soaked, disposable absorbent pad such that each 900 cm2 (1 square foot) is wiped for 1 minute. Any surface square foot shall also be wiped for 1 minute. Wipe, mop, and/or sorb the solvent...

40 CFR 761.372 - Specific requirements for relatively clean surfaces.

Code of Federal Regulations, 2014 CFR

2014-07-01

... that each 900 cm2 (1 square foot) of the surface is always very wet for 1 minute. Wipe smooth surfaces with a solvent-soaked, disposable absorbent pad such that each 900 cm2 (1 square foot) is wiped for 1 minute. Any surface square foot shall also be wiped for 1 minute. Wipe, mop, and/or sorb the solvent...

Green synthesis of mesoporous molecular sieve incorporated monoliths using room temperature ionic liquid and deep eutectic solvents.

PubMed

Zhang, Li-Shun; Zhao, Qing-Li; Li, Xin-Xin; Li, Xi-Xi; Huang, Yan-Ping; Liu, Zhao-Sheng

2016-12-01

A hybrid monolith incorporated with mesoporous molecular sieve MCM-41 of uniform pore structure and high surface area was prepared with binary green porogens in the first time. With a mixture of room temperature ionic liquids and deep eutectic solvents as porogens, MCM-41 was modified with 3-(trimethoxysilyl) propyl methacrylate (γ-MPS) and the resulting MCM-41-MPS was incorporated into poly (BMA-co-EDMA) monoliths covalently. Because of good dispersibility of MCM-41-MPS in the green solvent-based polymerization system, high permeability and homogeneity for the resultant hybrid monolithic columns was achieved. The MCM-41-MPS grafted monolith was characterized by scanning electron microscopy, energy dispersive spectrometer area scanning, transmission electron microscopy, FT-IR spectra and nitrogen adsorption tests. Chromatographic performance of MCM-41-MPS grafted monolith was characterized by separating small molecules in capillary electrochromatography, including phenol series, naphthyl substitutes, aniline series and alkyl benzenes. The maximum column efficiency of MCM-41-MPS grafted monolith reached 209,000 plates/m, which was twice higher than the corresponding MCM-41-MPS free monolith. Moreover, successful separation of non-steroidal anti-inflammatory drugs and polycyclic aromatic hydrocarbons demonstrated the capacity in broad-spectrum application of the MCM-41-MPS incorporated monolith. The results indicated that green synthesis using room temperature ionic liquid and deep eutectic solvents is an effective method to prepare molecular sieve-incorporated monolithic column. Copyright © 2016 Elsevier B.V. All rights reserved.

Supercapacitor Electrolyte Solvents with Liquid Range Below -80 C

NASA Technical Reports Server (NTRS)

Brandon, Erik; Smart, Marshall; West, William

2010-01-01

A previous NASA Tech Brief ["Low-Temperature Supercapacitors" (NPO-44386) NASA Tech Briefs, Vol. 32, No 7 (July 2008), page 32] detailed ongoing efforts to develop non-aqueous supercapacitor electrolytes capable of supporting operation at temperatures below commercially available cells (which are typically limited to charging and discharging at > or equal to -40 C). These electrolyte systems may enable energy storage and power delivery for systems operating in extreme environments, such as those encountered in the Polar regions on Earth or in the exploration of space. Supercapacitors using these electrolytes may also offer improved power delivery performance at moderately low temperatures (e.g. -40 to 0 C) relative to currently available cells, offering improved cold-cranking and cold-weather acceleration capabilities for electrical or hybrid vehicles. Supercapacitors store charge at the electrochemical double-layer, formed at the interface between a high surface area electrode material and a liquid electrolyte. The current approach to extending the low-temperature limit of the electrolyte focuses on using binary solvent systems comprising a high-dielectric-constant component (such as acetonitrile) in conjunction with a low-melting-point co-solvent (such as organic formates, esters, and ethers) to depress the freezing point of the system, while maintaining sufficient solubility of the salt. Recent efforts in this area have led to the identification of an electrolyte solvent formulation with a freezing point of -85.7 C, which is achieved by using a 1:1 by volume ratio of acetonitrile to 1,3-dioxolane

Facile preparation of polymer microspheres and fibers with a hollow core and porous shell for oil adsorption and oil/water separation

NASA Astrophysics Data System (ADS)

Gao, Jiefeng; Song, Xin; Huang, Xuewu; Wang, Ling; Li, Bei; Xue, Huaiguo

2018-05-01

Non-solvent assisted electrospinning was proposed for fabricating Polymethylmethacrylate (PMMA) microspheres and fibers with a hollow core and porous shell, which could be used for oil adsorption and oil/water separation. Propanediol was chosen as the non-solvent because of its high surface tension and viscosity as well as large phase separation tendency with polymer, which was beneficial to the formation of both the hollow core and porous shell during the electrospinning. With the increase of the polymer solution concentration, the microsphere gradually evolved to the bead-on-string geometry and finally to a continuous fiber form, indicating the transition from electro-spraying to electrospinning. The hollow core and dense surface pores enhanced the hydrophobicity, oleophilicity, permeability, and specific surface area of the fibers, and hence imparted the fibrous mat a high oil adsorption capacity. When the porous hollow microspheres were electro-sprayed onto the stainless steel mesh followed by the PDMS modification, the modified mesh became super-hydrophobic and super-oleophilic with the contact angle of 153° and sliding angle of 4°. The as-prepared mesh showed rapid oil/water separation with high efficiency and excellent recycling performance. The flux for separation of oil/water mixture could reach as high as 11,000 L m-2 h-1. This facile non-solvent assisted electrospinning method provides a new avenue for preparation of multifunctional porous materials which possess potential applications in large-scale oil/water separation.

Alcohols react with MCM-41 at room temperature and chemically modify mesoporous silica.

PubMed

Björklund, Sebastian; Kocherbitov, Vitaly

2017-08-30

Mesoporous silica has received much attention due to its well-defined structural order, high surface area, and tunable pore diameter. To successfully employ mesoporous silica for nanotechnology applications it is important to consider how it is influenced by solvent molecules due to the fact that most preparation procedures involve treatment in various solvents. In the present work we contribute to this important topic with new results on how MCM-41 is affected by a simple treatment in alcohol at room temperature. The effects of alcohol treatment are characterized by TGA, FTIR, and sorption calorimetry. The results are clear and show that treatment of MCM-41 in methanol, ethanol, propanol, butanol, pentanol, or octanol at room temperature introduces alkoxy groups that are covalently bound to the silica surface. It is shown that alcohol treated MCM-41 becomes more hydrophobic and that this effect is sequentially more prominent going from methanol to octanol. Chemical formation of alkoxy groups onto MCM-41 occurs both for calcined and hydroxylated MCM-41 and the alkoxy groups are hydrolytically unstable and can be replaced by silanol groups after exposure to water. The results are highly relevant for mesoporous silica applications that involve contact or treatment in protic solvents, which is very common.

The Effects of Anchor Groups on (1) TiO2-Catalyzed Photooxidation and (2) Linker-Assisted Assembly on TiO2

NASA Astrophysics Data System (ADS)

Anderson, Ian Mark

Quantum dot-sensitized solar cells (QDSSCs) are a popular target for research due to their potential for highly efficient, easily tuned absorption. Typically, light is absorbed by quantum dots attached to a semiconductor substrate, such as TiO2, via bifunctional linker molecules. This research aims to create a patterned monolayer of linker molecules on a TiO2 film, which would in turn allow the attachment of a patterned layer of quantum dots. One method for the creation of a patterned monolayer is the functionalization of a TiO2 film with a linker molecule, followed by illumination with a laser at 355 nm. This initiates a TiO 2-catalyzed oxidation reaction, causing loss of surface coverage. A second linker molecule can then be adsorbed onto the TiO2 surface in the illuminated area. Towards that end, the behaviors of carboxylic and phosphonic acids adsorbed on TiO2 have been studied. TiO2 films were functionalized by immersion in solutions a single adsorbate and surface coverage was determined by IR spectroscopy. It is shown that phosphonic acids attain higher surface coverage than carboxylic acids, and will displace them from TiO2 when in a polar solvent. Alkyl chain lengths, which can influence stabilities of monolayers, are shown not to have an effect on this relationship. Equilibrium binding data for the adsorption of n-hexadecanoic acid to TiO2 from a THF solution are presented. It is shown that solvent polarity can affect monolayer stability; carboxylates and phosphonates undergo more desorption into polar solvents than nonpolar. Through illumination, it was possible to remove nearly all adsorbed linkers from TiO2. However, the illuminated areas were found not to be receptive to attachment by a second adsorbate. A possible reason for this behavior is presented. I also report on the synthesis and characterization of a straight-chain, thiol-terminated phosphonic acid. Initial experiments involving monolayer formation and quantum dot attachment are presented. Finally, it was found that quantum dots attach in high amounts to linker-functionalized TiO2 when suspended in pyridine. This increased surface attachment was present even when the linker molecule used lacked a functional group which would bind to the CdSe surface.

An easy-to-use approach for determining the disintegration ability of disintegrants by analysis of available surface area.

PubMed

Iwao, Yasunori; Tanaka, Shoko; Uchimoto, Takeaki; Noguchi, Shuji; Itai, Shigeru

2013-05-01

With the aim of directly predicting the functionality and mechanism of disintegrants during the disintegration and dissolution of tablets, we investigated an analysis method based on available surface area, which is the surface area of a drug in a formulation in direct contact with the external solvent during dissolution. We evaluated the following disintegrants in this study: sodium starch glycolate (Glycolys), crospovidone (Kollidon CL), carboxymethylcellulose calcium (CMC-Ca), low-substituted hydroxypropylcellulose (L-HPC), and croscarmellose sodium (Ac-Di-Sol). When disintegrant was added to a 50% ethenzamide tablet formulation, an increase in the dissolution rate dependent on disintegrant concentration was observed, according to the type of disintegrant. In addition, the available surface area also differed between disintegrants. For Glycolys, CMC-Ca, and Ac-Di-Sol, a rapid increase in available surface area and a large increase in maximum available surface area (Smax) were observed due to high swellability and wicking, even when the disintegrant concentration was only 1.0%. In contrast, for Kollidon CL and LH-21, a gradual increase in available surface area was observed, depending on the disintegrant concentration. To evaluate the disintegrant ability, Δtmax and ΔSmax were calculated by subtracting peak time (tmax) at 5.0% from that at 1.0% and subtracting Smax at 1.0% from that at 5.0%, respectively, and it was found that the water absorption ratio had strong negative correlations with Δtmax and ΔSmax. Therefore, this study demonstrates that analysis of only available surface area and parameters thereby obtained can directly provide useful information, especially about the disintegration ability of disintegrants. Copyright © 2013 Elsevier B.V. All rights reserved.

Electric field-driven, magnetically-stabilized ferro-emulsion phase contactor

DOEpatents

Scott, T.C.

1990-07-17

Methods and systems are disclosed for interfacial surface area contact between a dispersed phase liquid and a continuous phase liquid in counter-current flow for purposes such as solvent extraction. Initial droplets of a dispersed phase liquid material containing ferromagnetic particles functioning as a packing'' are introduced to a counter-current flow of the continuous phase. A high intensity pulsed electric field is applied so as to shatter the initial droplets into a ferromagnetic emulsion comprising many smaller daughter droplets having a greater combined total surface area than that of the initial droplets in contact with the continuous phase material. A magnetic field is applied to control the position of the ferromagnetic emulsion for enhanced coalescence of the daughter droplets into larger reformed droplets. 2 figs.

Electric field-driven, magnetically-stabilized ferro-emulsion phase contactor

DOEpatents

Scott, Timothy C.

1990-01-01

Methods and systems for interfacial surface area contact between a dispersed phase liquid and a continuous phase liquid in counter-current flow for purposes such as solvent extraction. Initial droplets of a dispersed phase liquid material containing ferromagnetic particles functioning as a "packing" are introduced to a counter-current flow of the continuous phase. A high intensity pulsed electric field is applied so as to shatter the initial droplets into a ferromagnetic emulsion comprising many smaller daughter droplets having a greater combined total surface area than that of the initial droplets in contact with the continuous phase material. A magnetic field is applied to control the position of the ferromagnetic emulsion for enhanced coalescence of the daughter droplets into larger reformed droplets.

Catalyst for hydrotreating carbonaceous liquids

DOEpatents

Berg, Lloyd; McCandless, Frank P.; Ramer, Ronald J.

1982-01-01

A catalyst for denitrogenating and desulfurating carbonaceous liquid such as solvent refined coal includes catalytic metal oxides impregnated within a porous base of mostly alumina with relatively large pore diameters, surface area and pore volume. The base material includes pore volumes of 0.7-0.85 ml/g, surface areas of 200-350 m.sup.2 /g and pore diameters of 85-200 Angstroms. The catalytic metals impregnated into these base materials include the oxides of Group VI metals, molybdenum and tungsten, and the oxides of Group VIII metals, nickel and cobalt, in various combinations. These catalysts and bases in combination have effectively promoted the removal of chemically combined sulfur and nitrogen within a continuous flowing mixture of carbonaceous liquid and hydrogen gas.

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics.

PubMed

Azuara, Cyril; Lindahl, Erik; Koehl, Patrice; Orland, Henri; Delarue, Marc

2006-07-01

We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized Poisson-Boltzmann-Langevin equation (GPBLE). We have implemented a web server (http://lorentz.immstr.pasteur.fr/pdb_hydro.php) that both numerically solves this equation and uses the resulting water density profiles to place water molecules at preferred sites of hydration. Surface atoms with high or low hydration preference can be easily displayed using a simple PyMol script, allowing for the tentative prediction of the dimerization interface in homodimeric proteins, or lipid binding regions in membrane proteins. The web site includes options that permit mutations in the sequence as well as reconstruction of missing side chain and/or main chain atoms. These tools are accessible independently from the electrostatics calculation, and can be used for other modeling purposes. We expect this web server to be useful to structural biologists, as the knowledge of solvent density should prove useful to get better fits at low resolution for X-ray diffraction data and to computational biologists, for whom these profiles could improve the calculation of interaction energies in water between ligands and receptors in docking simulations.

Free energy landscape of a minimalist salt bridge model.

PubMed

Li, Xubin; Lv, Chao; Corbett, Karen M; Zheng, Lianqing; Wu, Dongsheng; Yang, Wei

2016-01-01

Salt bridges are essential to protein stability and dynamics. Despite the importance, there has been scarce of detailed discussion on how salt bridge partners interact with each other in distinct solvent exposed environments. In this study, employing a recent generalized orthogonal space tempering (gOST) method, we enabled efficient molecular dynamics simulation of repetitive breaking and reforming of salt bridge structures within a minimalist salt-bridge model, the Asp-Arg dipeptide and thereby were able to map its detailed free energy landscape in aqueous solution. Free energy surface analysis shows that although individually-solvated states are more favorable, salt-bridge states still occupy a noticeable portion of the overall population. Notably, the competing forces, e.g. intercharge attractions that drive the formation of salt bridges and solvation forces that pull the charged groups away from each other, are energetically comparable. As the result, the salt bridge stability is highly tunable by local environments; for instance when local water molecules are perturbed to interact more strongly with each other, the population of the salt-bridge states is likely to increase. Our results reveal the critical role of local solvent structures in modulating salt-bridge partner interactions and imply the importance of water fluctuations on conformational dynamics that involves solvent accessible salt bridge formations. © 2015 The Protein Society.

Solvent coarsening around colloids driven by temperature gradients

NASA Astrophysics Data System (ADS)

Roy, Sutapa; Dietrich, Siegfried; Maciolek, Anna

2018-04-01

Using mesoscopic numerical simulations and analytical theory, we investigate the coarsening of the solvent structure around a colloidal particle emerging after a temperature quench of the colloid surface. Qualitative differences in the coarsening mechanisms are found, depending on the composition of the binary liquid mixture forming the solvent and on the adsorption preferences of the colloid. For an adsorptionwise neutral colloid, the phase next to its surface alternates as a function of time. This behavior sets in on the scale of the relaxation time of the solvent and is absent for colloids with strong adsorption preferences. A Janus colloid, with a small temperature difference between its two hemispheres, reveals an asymmetric structure formation and surface enrichment around it, even if the solvent is within its one-phase region and if the temperature of the colloid is above the critical demixing temperature Tc of the solvent. Our phenomenological model turns out to capture recent experimental findings according to which, upon laser illumination of a Janus colloid and due to the ensuing temperature gradient between its two hemispheres, the surrounding binary liquid mixture develops a concentration gradient.

Conversion of glycerol to polyglycerol over waste duck-bones as a catalyst in solvent free etherification process

NASA Astrophysics Data System (ADS)

Ayoub, Muhammad; Sufian, Suriati; Mekuria Hailegiorgis, Sintayehu; Ullah, Sami; Uemura, Yoshimitsu

2017-08-01

The alkaline catalyst derived from the duck-bones was used for conversion of glycerol to polyglycerol via solvent free etherification process. The physicochemical properties of prepared materials were duck-bones were systematically investigated as a catalyst by latest techniques of Thermo gravimetric analysis (TGA), X-ray diffraction (XRD), and Brunauer-Emmett-Teller (BET) surface properties. TGA showed different trends of duck-bones decomposition from room temperature to 1000C. XRD pattern showed a clear and sharp peaks of a crystalline phase of CaO. The activity of the catalysts was in line with the basic amount of the strong base sites, surface area, and crystalline phase in the catalysts. The prepared catalyst derived from duck-bones provided high activity (99 %) for glycerol conversion and around 68 % yield for polyglycerol production. These ample wastes of duck-bones have good potential to be used as polyglycerol production catalysts due to have high quantity of Ca compare to other types of bones like cow, chicken and fish bones.

40 CFR 63.5746 - How do I demonstrate compliance with the emission limits for aluminum wipedown solvents and...

Code of Federal Regulations, 2011 CFR

2011-07-01

...) to determine the density of each aluminum surface coating and wipedown solvent. (d) Compliance is... Hazardous Air Pollutants for Boat Manufacturing Standards for Aluminum Recreational Boat Surface Coating... of solids per liter of coating, or volume fraction) of each aluminum surface coating, including...

Low-Temperature Soft-Cover Deposition of Uniform Large-Scale Perovskite Films for High-Performance Solar Cells.

PubMed

Ye, Fei; Tang, Wentao; Xie, Fengxian; Yin, Maoshu; He, Jinjin; Wang, Yanbo; Chen, Han; Qiang, Yinghuai; Yang, Xudong; Han, Liyuan

2017-09-01

Large-scale high-quality perovskite thin films are crucial to produce high-performance perovskite solar cells. However, for perovskite films fabricated by solvent-rich processes, film uniformity can be prevented by convection during thermal evaporation of the solvent. Here, a scalable low-temperature soft-cover deposition (LT-SCD) method is presented, where the thermal convection-induced defects in perovskite films are eliminated through a strategy of surface tension relaxation. Compact, homogeneous, and convection-induced-defects-free perovskite films are obtained on an area of 12 cm 2 , which enables a power conversion efficiency (PCE) of 15.5% on a solar cell with an area of 5 cm 2 . This is the highest efficiency at this large cell area. A PCE of 15.3% is also obtained on a flexible perovskite solar cell deposited on the polyethylene terephthalate substrate owing to the advantage of presented low-temperature processing. Hence, the present LT-SCD technology provides a new non-spin-coating route to the deposition of large-area uniform perovskite films for both rigid and flexible perovskite devices. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

From microporous regular frameworks to mesoporous materials with ultrahigh surface area: dynamic reorganization of porous polymer networks.

PubMed

Kuhn, Pierre; Forget, Aurélien; Su, Dangsheng; Thomas, Arne; Antonietti, Markus

2008-10-08

High surface area organic materials featuring both micro- and mesopores were synthesized under ionothermal conditions via the formation of polyaryltriazine networks. While the polytrimerization of nitriles in zinc chloride at 400 degrees C produces microporous polymers, higher reaction temperatures induce the formation of additional spherical mesopores with a narrow dispersity. The nitrogen-rich carbonaceous polymer materials thus obtained present surface areas and porosities up to 3300 m(2) g(-1) and 2.4 cm(3) g(-1), respectively. The key point of this synthesis relies on the occurrence of several high temperature polymerization reactions, where irreversible carbonization reactions coupled with the reversible trimerization of nitriles allow the reorganization of the dynamic triazine network. The ZnCl2 molten salt fulfills the requirement of a high temperature solvent, but is also required as catalyst. Thus, this dynamic polymerization system provides not only highly micro- and mesoporous materials, but also allows controlling the pore structure in amorphous organic materials.

Constructing Surrogate Models of Complex Systems with Enhanced Sparsity: Quantifying the Influence of Conformational Uncertainty in Biomolecular Solvation

DOE PAGES

Lei, Huan; Yang, Xiu; Zheng, Bin; ...

2015-11-05

Biomolecules exhibit conformational fluctuations near equilibrium states, inducing uncertainty in various biological properties in a dynamic way. We have developed a general method to quantify the uncertainty of target properties induced by conformational fluctuations. Using a generalized polynomial chaos (gPC) expansion, we construct a surrogate model of the target property with respect to varying conformational states. We also propose a method to increase the sparsity of the gPC expansion by defining a set of conformational “active space” random variables. With the increased sparsity, we employ the compressive sensing method to accurately construct the surrogate model. We demonstrate the performance ofmore » the surrogate model by evaluating fluctuation-induced uncertainty in solvent-accessible surface area for the bovine trypsin inhibitor protein system and show that the new approach offers more accurate statistical information than standard Monte Carlo approaches. Further more, the constructed surrogate model also enables us to directly evaluate the target property under various conformational states, yielding a more accurate response surface than standard sparse grid collocation methods. In particular, the new method provides higher accuracy in high-dimensional systems, such as biomolecules, where sparse grid performance is limited by the accuracy of the computed quantity of interest. Finally, our new framework is generalizable and can be used to investigate the uncertainty of a wide variety of target properties in biomolecular systems.« less

Adsorption of soft and hard proteins onto OTCEs under the influence of an external electric field.

PubMed

Benavidez, Tomás E; Torrente, Daniel; Marucho, Marcelo; Garcia, Carlos D

2015-03-03

The adsorption behavior of hard and soft proteins under the effect of an external electric field was investigated by a combination of spectroscopic ellipsometry and molecular dynamics (MD) simulations. Optically transparent carbon electrodes (OTCE) were used as conductive, sorbent substrates. Lysozyme (LSZ) and ribonuclease A (RNase A) were selected as representative hard proteins, whereas myoglobin (Mb), α-lactalbumin (α-LAC), bovine serum albumin (BSA), glucose oxidase (GOx), and immunoglobulin G (IgG) were selected to represent soft proteins. In line with recent publications from our group, the experimental results revealed that while the adsorption of all investigated proteins can be enhanced by the potential applied to the electrode, the effect is more pronounced for hard proteins. In contrast with the incomplete monolayers formed at open-circuit potential, the application of +800 mV to the sorbent surface induced the formation of multiple layers of protein. These results suggest that this effect can be related to the intrinsic polarizability of the protein (induction of dipoles), the resulting surface accessible solvent area (SASA), and structural rearrangements induced upon the incorporation on the protein layer. The described experiments are critical to understand the relationship between the structure of proteins and their tendency to form (under electric stimulation) layers with thicknesses that greatly surpass those obtained at open-circuit conditions.

Insights into the species-specific TLR4 signaling mechanism in response to Rhodobacter sphaeroides lipid A detection

NASA Astrophysics Data System (ADS)

Anwar, Muhammad Ayaz; Panneerselvam, Suresh; Shah, Masaud; Choi, Sangdun

2015-01-01

TLR4 in complex with MD2 senses the presence of lipid A (LA) and initiates a signaling cascade that curb the infection. This complex is evolutionarily conserved and can initiate the immune system in response to a variety of LAs. In this study, molecular dynamics simulation (25 ns) was performed to elucidate the differential behavior of TLR4/MD2 complex in response to Rhodobacter sphaeroides lipid A (RsLA). Penta-acyl chain-containing RsLA is at the verge of agonist (6 acyl-chains) and antagonist (4 acyl-chains) structure, and activates the TLR4 pathway in horses and hamsters, while inhibiting in humans and murine. In the time-evolved coordinates, the promising factors that dictated the differential response included the local and global mobility pattern of complexes, solvent-accessible surface area of ligand, and surface charge distributions of TLR4 and MD2. We showed that the GlcN1-GlcN2 backbone acquires agonist (3FXI)-like configurations in horses and hamsters, while acquiring antagonist (2E59)-like configurations in humans and murine systems. Moreover, analysis of F126 behavior in the MD2 F126 loop (amino acids 123-129) and loop EF (81-89) suggested that certain sequence variations also contribute to species-specific response. This study underlines the TLR4 signaling mechanism and provides new therapeutic opportunities.

Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase

PubMed Central

Votapka, Lane; Demir, Özlem; Swift, Robert V; Walker, Ross C; Amaro, Rommie E

2012-01-01

Influenza A continues to be a major public health concern due to its ability to cause epidemic and pandemic disease outbreaks in humans. Computational investigations of structural dynamics of the major influenza glycoproteins, especially the neuraminidase (NA) enzyme, are able to provide key insights beyond what is currently accessible with standard experimental techniques. In particular, all-atom molecular dynamics simulations reveal the varying degrees of flexibility for such enzymes. Here we present an analysis of the relative flexibility of the ligand- and receptor-binding area of three key strains of influenza A: highly pathogenic H5N1, the 2009 pandemic H1N1, and a human N2 strain. Through computational solvent mapping, we investigate the various ligand- and receptor-binding “hot spots” that exist on the surface of NA which interacts with both sialic acid receptors on the host cells and antiviral drugs. This analysis suggests that the variable cavities found in the different strains and their corresponding capacities to bind ligand functional groups may play an important role in the ability of NA to form competent reaction encounter complexes with other species of interest, including antiviral drugs, sialic acid receptors on the host cell surface, and the hemagglutinin protein. Such considerations may be especially useful for the prediction of how such complexes form and with what binding capacity. PMID:22872804

Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes.

PubMed

Nandy, Suman Kumar; Seal, Alpana

2016-01-01

Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases.

Structural adaptations of octaheme nitrite reductases from haloalkaliphilic Thioalkalivibrio bacteria to alkaline pH and high salinity.

PubMed

Popinako, Anna; Antonov, Mikhail; Tikhonov, Alexey; Tikhonova, Tamara; Popov, Vladimir

2017-01-01

Bacteria Tv. nitratireducens and Tv. paradoxus from soda lakes grow optimally in sodium carbonate/NaCl brines at pH range from 9.5 to 10 and salinity from 0.5 to 1.5 M Na+. Octaheme nitrite reductases (ONRs) from haloalkaliphilic bacteria of genus Thioalkalivibrio are stable and active in a wide range of pH (up to 11) and salinity (up to 1 M NaCl). To establish adaptation mechanisms of ONRs from haloalkaliphilic bacteria a comparative analysis of amino acid sequences and structures of ONRs from haloalkaliphilic bacteria and their homologues from non-halophilic neutrophilic bacteria was performed. The following adaptation strategies were observed: (1) strategies specific for halophilic and alkaliphilic proteins (an increase in the number of aspartate and glutamate residues and a decrease in the number of lysine residues on the protein surface), (2) strategies specific for halophilic proteins (an increase in the arginine content and a decrease in the number of hydrophobic residues on the solvent-accessible protein surface), (3) strategies specific for alkaliphilic proteins (an increase in the area of intersubunit hydrophobic contacts). Unique adaptation mechanism inherent in the ONRs from bacteria of genus Thioalkalivibrio was revealed (an increase in the core in the number of tryptophan and phenylalanine residues, and an increase in the number of small side chain residues, such as alanine and valine, in the core).

Evidence for a pore-filling mechanism in the adsorption of aromatic hydrocarbons to a natural wood char.

PubMed

Nguyen, Thanh H; Cho, Hyun-Hee; Poster, Dianne L; Ball, William P

2007-02-15

Sorption isotherms for five aromatic hydrocarbons were obtained with a natural wood char (NC1) and its residue after solvent extraction (ENC1). Substantial isotherm nonlinearity was observed in all cases. ENC1 showed higher BET surface area, higher nitrogen-accessible micropore volume, and lower mass of extractable organic chemicals, including quantifiable polycyclic aromatic hydrocarbons (PAHs),while the two chars showed identical surface oxygen/ carbon (O/C) ratio. For two chlorinated benzenes that normally condense as liquids at the temperatures used, sorption isotherms with NC1 and ENC1 were found to be statistically identical. For the solid-phase compounds (1,4-dichlorobenzene (1,4-DCB) and two PAHs), sorption was statistically higher with ENC1, thus demonstrating sorption effects due to both (1) authigenic organic content in the sorbentand (2)the sorbate's condensed state. Polanyi-based isotherm modeling, pore size measurements, and comparisons with activated carbon showthe relative importance of adsorptive pore filling and help explain results. With both chars, maximum sorption increased in the order of decreasing molecular diameter: phenanthrene < naphthalene < 1,2-dichlorobenzene/1,2,4-trichlorobenzene < 1,4-DCB. Comparison of 1,4- and 1,2-DCB shows that the critical molecular diameter was apparently more important than the condensed state, suggesting that 1,4-DCB sorbed in the liquid state for ENC1.

Adsorption of Soft and Hard Proteins onto OTCEs under the influence of an External Electric Field

PubMed Central

Benavidez, Tomás E.; Torrente, Daniel; Marucho, Marcelo; Garcia, Carlos D.

2015-01-01

The adsorption behavior of hard and soft proteins under the effect of an external electric field was investigated by a combination of spectroscopic ellipsometry and molecular dynamics (MD) simulations. Optically transparent carbon electrodes (OTCE) were used as conductive, sorbent substrates. Lysozyme (LSZ) and ribonuclease A (RNase A) were selected as representative hard proteins whereas myoglobin (Mb), α-lactalbumin (α-LAC), bovine serum albumin (BSA), glucose oxidase (GOx), and immunoglobulin G (IgG) were selected to represent soft proteins. In line with recent publications from our group, the experimental results revealed that while the adsorption of all investigated proteins can be enhanced by the potential applied to the electrode, the effect is more pronounced for hard proteins. In contrast with the incomplete monolayers formed at open-circuit potential, the application of +800mV to the sorbent surface induced the formation of multiple layers of protein. These results also suggest that this effect can be related to the intrinsic polarizability of the protein (induction of dipoles), the resulting surface accessible solvent area (SASA), and structural rearrangements induced upon the incorporation on the protein layer. The described experiments are critical to understand the relationship between the structure of proteins and their tendency to form (under electric stimulation) layers with thicknesses that greatly surpass those obtained at open-circuit conditions. PMID:25658387

Synthesis by extrusion: continuous, large-scale preparation of MOFs using little or no solvent† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c4sc03217a Click here for additional data file.

PubMed Central

Crawford, Deborah; Casaban, José; Haydon, Robert; Giri, Nicola; McNally, Tony

2015-01-01

Grinding solid reagents under solvent-free or low-solvent conditions (mechanochemistry) is emerging as a general synthetic technique which is an alternative to conventional solvent-intensive methods. However, it is essential to find ways to scale-up this type of synthesis if its promise of cleaner manufacturing is to be realised. Here, we demonstrate the use of twin screw and single screw extruders for the continuous synthesis of various metal complexes, including Ni(salen), Ni(NCS)2(PPh3)2 as well as the commercially important metal organic frameworks (MOFs) Cu3(BTC)2 (HKUST-1), Zn(2-methylimidazolate)2 (ZIF-8, MAF-4) and Al(fumarate)(OH). Notably, Al(fumarate)(OH) has not previously been synthesised mechanochemically. Quantitative conversions occur to give products at kg h–1 rates which, after activation, exhibit surface areas and pore volumes equivalent to those of materials produced by conventional solvent-based methods. Some reactions can be performed either under completely solvent-free conditions whereas others require the addition of small amounts of solvent (typically 3–4 mol equivalents). Continuous neat melt phase synthesis is also successfully demonstrated by both twin screw and single screw extrusion for ZIF-8. The latter technique provided ZIF-8 at 4 kg h–1. The space time yields (STYs) for these methods of up to 144 × 103 kg per m3 per day are orders of magnitude greater than STYs for other methods of making MOFs. Extrusion methods clearly enable scaling of mechanochemical and melt phase synthesis under solvent-free or low-solvent conditions, and may also be applied in synthesis more generally. PMID:29308131

Debinding and Sintering of an Injection-Moulded Hypereutectic Al⁻Si Alloy.

PubMed

Ni, Jiaqi; Yu, Muhuo; Han, Keqing

2018-05-16

Hypereutectic Al⁻Si (20 wt.%) alloy parts were fabricated by employing a powder injection moulding (PIM) technique with a developed multi-component binder system composed of high-density polyethylene (35 wt.%), carnauba wax (62 wt.%) and stearic acid (3 wt.%). The feedstocks contained 83 wt.% metal powders. The debinding process was carried out by a combination of solvent extraction and thermal decomposition. The effects of solvent debinding variables such as kind of solvents, debinding temperatures and time, and the bulk surface area to volume ratios on the debinding process were investigated. Thermal debinding and the subsequent sintering process were carried out in a heating sequence under a nitrogen atmosphere. The influences of sintering temperature and sintering time on the mechanical properties and structure were considered. Under the optimal sintering condition, sintering at 550 °C for 3 h, the final sintering parts were free of distortion and exhibited good mechanical properties. Relative sintered density, Brinell hardness, and tensile strength were ~95.5%, 58 HBW and ~154, respectively.

Prevention of corrosion with polyaniline

NASA Technical Reports Server (NTRS)

Ahmad, Naseer (Inventor); MacDiarmid, Alan G. (Inventor)

1997-01-01

Methods for improving the corrosion inhibition of a metal or metal alloy substrate surface are provided wherein the substrate surface is coated with a polyaniline film. The polyaniline film coating is applied by contacting the substrate surface with a solution of polyaniline. The polyaniline is dissolved in an appropriate organic solvent and the solvent is allowed to evaporate from the substrate surface yielding the polyaniline film coating.

Relating Nanoscale Accessibility within Plant Cell Walls to Improved Enzyme Hydrolysis Yields in Corn Stover Subjected to Diverse Pretreatments.

PubMed

Crowe, Jacob D; Zarger, Rachael A; Hodge, David B

2017-10-04

Simultaneous chemical modification and physical reorganization of plant cell walls via alkaline hydrogen peroxide or liquid hot water pretreatment can alter cell wall structural properties impacting nanoscale porosity. Nanoscale porosity was characterized using solute exclusion to assess accessible pore volumes, water retention value as a proxy for accessible water-cell walls surface area, and solute-induced cell wall swelling to measure cell wall rigidity. Key findings concluded that delignification by alkaline hydrogen peroxide pretreatment decreased cell wall rigidity and that the subsequent cell wall swelling resulted increased nanoscale porosity and improved enzyme binding and hydrolysis compared to limited swelling and increased accessible surface areas observed in liquid hot water pretreated biomass. The volume accessible to a 90 Å dextran probe within the cell wall was found to be correlated to both enzyme binding and glucose hydrolysis yields, indicating cell wall porosity is a key contributor to effective hydrolysis yields.

Nanobubbles do not sit alone at the solid-liquid interface.

PubMed

Peng, Hong; Hampton, Marc A; Nguyen, Anh V

2013-05-21

The unexpected stability and anomalous contact angle of gaseous nanobubbles at the hydrophobic solid-liquid interface has been an issue of debate for almost two decades. In this work silicon-nitride tipped AFM cantilevers are used to probe the highly ordered pyrolytic graphite (HOPG)-water interface with and without solvent-exchange (a common nanobubble production method). Without solvent-exchange the force obtained by the single force and force mapping techniques is consistent over the HOPG atomic layers and described by DLVO theory (strong EDL repulsion). With solvent-exchange the force is non-DLVO (no EDL repulsion) and the range of the attractive jump-in (>10 nm) over the surface is grouped into circular areas of longer range, consistent with nanobubbles, and the area of shorter range. The non-DLVO nature of the area between nanobubbles suggests that the interaction is no longer between a silicon-nitride tip and HOPG. Interfacial gas enrichment (IGE) covering the entire area between nanobubbles is suggested to be responsible for the non-DLVO forces. The absence of EDL repulsion suggests that both IGE and nanobubbles are not charged. The coexistence of nanobubbles and IGE provides further evidence of nanobubble stability by dynamic equilibrium. The IGE cannot be removed by contact mode scanning of a cantilever tip in pure water, but in a surfactant (SDS) solution the mechanical action of the tip and the chemical action of the surfactant molecules can successfully remove the enrichment. Strong EDL repulsion between the tip and nanobubbles/IGE in surfactant solutions is due to the polar heads of the adsorbed surfactant molecules.

Surface Nanobubbles in Nonaqueous Media: Looking for Nanobubbles in DMSO, Formamide, Propylene Carbonate, Ethylammonium Nitrate, and Propylammonium Nitrate.

PubMed

An, Hongjie; Liu, Guangming; Atkin, Rob; Craig, Vincent S J

2015-07-28

Surface nanobubbles produced by supersaturation during the exchange of ethanol for water are routinely observed on hydrophobic surfaces, are stable for days, and have contact angles that are very much greater than observed macroscopically. Here, we test the hypothesis that nanobubbles can also be observed in nonaqueous solvents in order to ascertain if their anomalous lifetimes and contact angles are related to properties of the solvent. Nanobubbles were seen in the protic solvents formamide, ethylammonium nitrate, and propylammonium nitrate, but not in propylene carbonate or dimethyl sulfoxide. Solvents in which nanobubbles were observed exhibit a three-dimensional hydrogen-bonding network. Like in aqueous systems, the nanobubbles were stable for days and exhibited high contact angles (∼165°).

Prediction of the solvent affecting site and the computational design of stable Candida antarctica lipase B in a hydrophilic organic solvent.

PubMed

Park, Hyun June; Joo, Jeong Chan; Park, Kyungmoon; Kim, Yong Hwan; Yoo, Young Je

2013-02-10

Enzyme reactions in organic solvent such as for organic synthesis have great industrial potential. However, enzymes lose their stability in hydrophilic organic solvents due to the deformation of the enzyme by the solvent. It is thus important to enhance the stability of enzymes in hydrophilic organic solvents. Previous approaches have not considered on the interaction between enzymes and solvents due to the lack of information. In this study, the structural motions of the enzyme in methanol cosolvent and the interaction between the enzyme surface and the solvent molecule were investigated using molecular dynamics simulation (MD). By analyzing the MD simulation results, the surface residues of Candida antarctica lipase B (CalB) with higher root mean square deviation (RMSD) in a methanol solvent were considered as methanol affecting site and selected for site-directed mutagenesis. The methanol affecting site was computationally redesigned by lowering the RMSD. Among the candidate mutants, the A8T, A92E, N97Q and T245S mutants showed higher organic solvent stability at various methanol concentrations. The rational approach developed in this study could be applied to the stabilization of other industrial enzymes used in organic solvents. Copyright © 2012 Elsevier B.V. All rights reserved.

A robust and efficient method for the extraction of plant extracellular surface lipids as applied to the analysis of silks and seedling leaves of maize

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

Loneman, Derek M.; Peddicord, Layton; Al-Rashid, Amani

Aerial plant organs possess a diverse array of extracellular surface lipids, including both non-polar and amphipathic constituents that collectively provide a primary line of defense against environmental stressors. Extracellular surface lipids on the stigmatic silks of maize are composed primarily of saturated and unsaturated linear hydrocarbons, as well as fatty acids, and aldehydes. To efficiently extract lipids of differing polarities from maize silks, five solvent systems (hexanes; hexanes:diethyl ether (95:5); hexanes:diethyl ether (90:10); chloroform:hexanes (1:1) and chloroform) were tested by immersing fresh silks in solvent for different extraction times. Surface lipid recovery and the relative composition of individual constituents weremore » impacted to varying degrees depending on solvent choice and duration of extraction. Analyses were performed using both silks and leaves to demonstrate the utility of the solvent- and time-optimized protocol in comparison to extraction with the commonly used chloroform solvent. Overall, the preferred solvent system was identified as hexanes:diethyl ether (90:10), based on its effectiveness in extracting surface hydrocarbons and fatty acids as well as its reduced propensity to extract presumed internal fatty acids. Metabolite profiling of wildtype and glossy1 seedlings, which are impaired in surface lipid biosynthesis, demonstrated the ability of the preferred solvent to extract extracellular surface lipids rich in amphipathic compounds (aldehydes and alcohols). In addition to the expected deficiencies in dotriacontanal and dotriacontan-1-ol for gl1 seedlings, an unexpected increase in fatty acid recovery was observed in gl1 seedlings extracted in chloroform, suggesting that chloro-form extracts lipids from internal tissues of gl1 seedlings. This highlights the importance of extraction method when evaluating mutants that have altered cuticular lipid compositions. Lastly, metabolite profiling of silks from maize inbreds B73 and Mo17, exposed to different environments and harvested at different ages, revealed differences in hydrocarbon and fatty acid composition, demonstrating the dynamic nature of surface lipid accumulation on silks.« less

A robust and efficient method for the extraction of plant extracellular surface lipids as applied to the analysis of silks and seedling leaves of maize

DOE PAGES

Loneman, Derek M.; Peddicord, Layton; Al-Rashid, Amani; ...

2017-07-11

Aerial plant organs possess a diverse array of extracellular surface lipids, including both non-polar and amphipathic constituents that collectively provide a primary line of defense against environmental stressors. Extracellular surface lipids on the stigmatic silks of maize are composed primarily of saturated and unsaturated linear hydrocarbons, as well as fatty acids, and aldehydes. To efficiently extract lipids of differing polarities from maize silks, five solvent systems (hexanes; hexanes:diethyl ether (95:5); hexanes:diethyl ether (90:10); chloroform:hexanes (1:1) and chloroform) were tested by immersing fresh silks in solvent for different extraction times. Surface lipid recovery and the relative composition of individual constituents weremore » impacted to varying degrees depending on solvent choice and duration of extraction. Analyses were performed using both silks and leaves to demonstrate the utility of the solvent- and time-optimized protocol in comparison to extraction with the commonly used chloroform solvent. Overall, the preferred solvent system was identified as hexanes:diethyl ether (90:10), based on its effectiveness in extracting surface hydrocarbons and fatty acids as well as its reduced propensity to extract presumed internal fatty acids. Metabolite profiling of wildtype and glossy1 seedlings, which are impaired in surface lipid biosynthesis, demonstrated the ability of the preferred solvent to extract extracellular surface lipids rich in amphipathic compounds (aldehydes and alcohols). In addition to the expected deficiencies in dotriacontanal and dotriacontan-1-ol for gl1 seedlings, an unexpected increase in fatty acid recovery was observed in gl1 seedlings extracted in chloroform, suggesting that chloro-form extracts lipids from internal tissues of gl1 seedlings. This highlights the importance of extraction method when evaluating mutants that have altered cuticular lipid compositions. Lastly, metabolite profiling of silks from maize inbreds B73 and Mo17, exposed to different environments and harvested at different ages, revealed differences in hydrocarbon and fatty acid composition, demonstrating the dynamic nature of surface lipid accumulation on silks.« less

Systems and methods for laser assisted sample transfer to solution for chemical analysis

DOEpatents

Van Berkel, Gary J.; Kertesz, Vilmos; Ovchinnikova, Olga S.

2014-06-03

Systems and methods are described for laser ablation of an analyte from a specimen and capturing of the analyte in a dispensed solvent to form a testing solution. A solvent dispensing and extraction system can form a liquid microjunction with the specimen. The solvent dispensing and extraction system can include a surface sampling probe. The laser beam can be directed through the surface sampling probe. The surface sampling probe can also serve as an atomic force microscopy probe. The surface sampling probe can form a seal with the specimen. The testing solution including the analyte can then be analyzed using an analytical instrument or undergo further processing.

Systems and methods for laser assisted sample transfer to solution for chemical analysis

DOEpatents

Van Berkel, Gary J.; Kertesz, Vilmos; Ovchinnikova, Olga S.

2015-09-29

Systems and methods are described for laser ablation of an analyte from a specimen and capturing of the analyte in a dispensed solvent to form a testing solution. A solvent dispensing and extraction system can form a liquid microjunction with the specimen. The solvent dispensing and extraction system can include a surface sampling probe. The laser beam can be directed through the surface sampling probe. The surface sampling probe can also serve as an atomic force microscopy probe. The surface sampling probe can form a seal with the specimen. The testing solution including the analyte can then be analyzed using an analytical instrument or undergo further processing.

Systems and methods for laser assisted sample transfer to solution for chemical analysis

DOEpatents

Van Berkel, Gary J; Kertesz, Vilmos; Ovchinnikova, Olga S

2013-08-27

Systems and methods are described for laser ablation of an analyte from a specimen and capturing of the analyte in a dispensed solvent to form a testing solution. A solvent dispensing and extraction system can form a liquid microjunction with the specimen. The solvent dispensing and extraction system can include a surface sampling probe. The laser beam can be directed through the surface sampling probe. The surface sampling probe can also serve as an atomic force microscopy probe. The surface sampling probe can form a seal with the specimen. The testing solution including the analyte can then be analyzed using an analytical instrument or undergo further processing.

dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.

PubMed

Huang, Kai-Yao; Su, Min-Gang; Kao, Hui-Ju; Hsieh, Yun-Chung; Jhong, Jhih-Hua; Cheng, Kuang-Hao; Huang, Hsien-Da; Lee, Tzong-Yi

2016-01-04

Owing to the importance of the post-translational modifications (PTMs) of proteins in regulating biological processes, the dbPTM (http://dbPTM.mbc.nctu.edu.tw/) was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this 10th anniversary of dbPTM, the updated resource provides not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12 000 modified peptides, including the emerging S-nitrosylation, S-glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining. As the number of available PTM prediction methods increases, this work compiles a non-homologous benchmark dataset to evaluate the predictive power of online PTM prediction tools. An increasing interest in the structural investigation of PTM substrate sites motivated the mapping of all experimental PTM peptides to protein entries of Protein Data Bank (PDB) based on database identifier and sequence identity, which enables users to examine spatially neighboring amino acids, solvent-accessible surface area and side-chain orientations for PTM substrate sites on tertiary structures. Since drug binding in PDB is annotated, this update identified over 1100 PTM sites that are associated with drug binding. The update also integrates metabolic pathways and protein-protein interactions to support the PTM network analysis for a group of proteins. Finally, the web interface is redesigned and enhanced to facilitate access to this resource. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Influence of the type of solvent on the development of superhydrophobicity from silane-based solution containing nanoparticles

NASA Astrophysics Data System (ADS)

Pantoja, M.; Abenojar, J.; Martinez, M. A.

2017-03-01

Superhydrophobic surfaces are very appealing for numerous industrial applications due to their self-cleaning capacity. Although there are different methods to manufacture superhydrophobic surfaces, some of them do not keep the aesthetic appearance of the neat surface. Sol-gel processes are a valid alternative when transparent coatings are desired. The main goal of this research is to study the viability of this method by making superhydrophobic coatings from silane-based solution containing SiO2 nanoparticles. The effect of using different solvents is investigated, as well as the role played by the different components of the solution (silane, nanoparticles and solvent). Solutions of methyltrimethoxisilane (MTS) and tetraethoxysilane (TEOS) and 1% of SiO2 (%wt) were prepared with different solvents (ethanol, ethanol/water and white spirit). The hydrophobicity of the developed coatings is studied using contact angle measurements, while the aesthetic appearance is evaluated with gloss and color measurements. Also, infrared spectroscopy, dynamic light scattering (DSL), and surface tension measurements are used to study the silane solutions. The results show that the capacity of solvents to promote the dispersion of the nanoparticles is crucial to ensuring superhydrophobicity, since these agglomerates provide the micro- and nano- surface roughness required to get a hierarchical structure. However, the combined use of silanes and nanoparticles is key to make a superhydrophobic surface because physical (the surface roughness provided by nanoparticles) and chemical characteristics (hydrophobicity provided by silanes) are coupled.

40 CFR 63.5746 - How do I demonstrate compliance with the emission limits for aluminum wipedown solvents and...

Code of Federal Regulations, 2014 CFR

2014-07-01

...) to determine the density of each aluminum surface coating and wipedown solvent. (d) Compliance is... Surface Coating Operations § 63.5746 How do I demonstrate compliance with the emission limits for aluminum... (liters of solids per liter of coating, or volume fraction) of each aluminum surface coating, including...

40 CFR 63.5746 - How do I demonstrate compliance with the emission limits for aluminum wipedown solvents and...

Code of Federal Regulations, 2013 CFR

2013-07-01

...) to determine the density of each aluminum surface coating and wipedown solvent. (d) Compliance is... Surface Coating Operations § 63.5746 How do I demonstrate compliance with the emission limits for aluminum... (liters of solids per liter of coating, or volume fraction) of each aluminum surface coating, including...

Solvent jet desorption capillary photoionization-mass spectrometry.

PubMed

Haapala, Markus; Teppo, Jaakko; Ollikainen, Elisa; Kiiski, Iiro; Vaikkinen, Anu; Kauppila, Tiina J; Kostiainen, Risto

2015-03-17

A new ambient mass spectrometry method, solvent jet desorption capillary photoionization (DCPI), is described. The method uses a solvent jet generated by a coaxial nebulizer operated at ambient conditions with nitrogen as nebulizer gas. The solvent jet is directed onto a sample surface, from which analytes are extracted into the solvent and ejected from the surface in secondary droplets formed in collisions between the jet and the sample surface. The secondary droplets are directed into the heated capillary photoionization (CPI) device, where the droplets are vaporized and the gaseous analytes are ionized by 10 eV photons generated by a vacuum ultraviolet (VUV) krypton discharge lamp. As the CPI device is directly connected to the extended capillary inlet of the MS, high ion transfer efficiency to the vacuum of MS is achieved. The solvent jet DCPI provides several advantages: high sensitivity for nonpolar and polar compounds with limit of detection down to low fmol levels, capability of analyzing small and large molecules, and good spatial resolution (250 μm). Two ionization mechanisms are involved in DCPI: atmospheric pressure photoionization, capable of ionizing polar and nonpolar compounds, and solvent assisted inlet ionization capable of ionizing larger molecules like peptides. The feasibility of DCPI was successfully tested in the analysis of polar and nonpolar compounds in sage leaves and chili pepper.

Solvent-induced synthesis of nitrogen-doped hollow carbon spheres with tunable surface morphology for supercapacitors

NASA Astrophysics Data System (ADS)

Liu, Feng; Yuan, Ren-Lu; Zhang, Ning; Ke, Chang-Ce; Ma, Shao-Xia; Zhang, Ru-Liang; Liu, Lei

2018-04-01

Nitrogen doped hollow carbon spheres (NHCSs) with tunable surface morphology have been prepared through one-pot carbonization method by using melamine-formaldehyde spheres as template and resorcinol-based resin as carbon precursor in ethanol-water solution. Well-dispersed NHCSs with particle size of 800 nm were obtained and the surface of NHCSs turn from smooth to tough, wrinkled, and finally concave by increasing the ethanol concentration. The fabricated NHCSs possessed high nitrogen content (3.99-4.83%) and hierarchical micro-dual mesoporous structure with surface area range of 265-405 m2 g-1 and total pore volume of 0.18-0.29 cm3 g-1, which contributed to high specific capacitance, excellent rate capability and long cycle life.

Expansion of access tunnels and active-site cavities influence activity of haloalkane dehalogenases in organic cosolvents.

PubMed

Stepankova, Veronika; Khabiri, Morteza; Brezovsky, Jan; Pavelka, Antonin; Sykora, Jan; Amaro, Mariana; Minofar, Babak; Prokop, Zbynek; Hof, Martin; Ettrich, Rudiger; Chaloupkova, Radka; Damborsky, Jiri

2013-05-10

The use of enzymes for biocatalysis can be significantly enhanced by using organic cosolvents in the reaction mixtures. Selection of the cosolvent type and concentration range for an enzymatic reaction is challenging and requires extensive empirical testing. An understanding of protein-solvent interaction could provide a theoretical framework for rationalising the selection process. Here, the behaviour of three model enzymes (haloalkane dehalogenases) was investigated in the presence of three representative organic cosolvents (acetone, formamide, and isopropanol). Steady-state kinetics assays, molecular dynamics simulations, and time-resolved fluorescence spectroscopy were used to elucidate the molecular mechanisms of enzyme-solvent interactions. Cosolvent molecules entered the enzymes' access tunnels and active sites, enlarged their volumes with no change in overall protein structure, but surprisingly did not act as competitive inhibitors. At low concentrations, the cosolvents either enhanced catalysis by lowering K(0.5) and increasing k(cat), or caused enzyme inactivation by promoting substrate inhibition and decreasing k(cat). The induced activation and inhibition of the enzymes correlated with expansion of the active-site pockets and their occupancy by cosolvent molecules. The study demonstrates that quantitative analysis of the proportions of the access tunnels and active-sites occupied by organic solvent molecules provides the valuable information for rational selection of appropriate protein-solvent pair and effective cosolvent concentration. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

QSAR and docking studies on xanthone derivatives for anticancer activity targeting DNA topoisomerase IIα

PubMed Central

Alam, Sarfaraz; Khan, Feroz

2014-01-01

Due to the high mortality rate in India, the identification of novel molecules is important in the development of novel and potent anticancer drugs. Xanthones are natural constituents of plants in the families Bonnetiaceae and Clusiaceae, and comprise oxygenated heterocycles with a variety of biological activities along with an anticancer effect. To explore the anticancer compounds from xanthone derivatives, a quantitative structure activity relationship (QSAR) model was developed by the multiple linear regression method. The structure–activity relationship represented by the QSAR model yielded a high activity–descriptors relationship accuracy (84%) referred by regression coefficient (r2=0.84) and a high activity prediction accuracy (82%). Five molecular descriptors – dielectric energy, group count (hydroxyl), LogP (the logarithm of the partition coefficient between n-octanol and water), shape index basic (order 3), and the solvent-accessible surface area – were significantly correlated with anticancer activity. Using this QSAR model, a set of virtually designed xanthone derivatives was screened out. A molecular docking study was also carried out to predict the molecular interaction between proposed compounds and deoxyribonucleic acid (DNA) topoisomerase IIα. The pharmacokinetics parameters, such as absorption, distribution, metabolism, excretion, and toxicity, were also calculated, and later an appraisal of synthetic accessibility of organic compounds was carried out. The strategy used in this study may provide understanding in designing novel DNA topoisomerase IIα inhibitors, as well as for other cancer targets. PMID:24516330

Scanning tunneling microscopy studies of pulse deposition of dinuclear organometallic molecules on Au(111)

NASA Astrophysics Data System (ADS)

Guo, Song; Alex Kandel, S.

2008-01-01

Ultrahigh-vacuum scanning tunneling microscopy (STM) was used to study trans-[Cl(dppe)2Ru(CC)6Ru(dppe)2Cl] [abbreviated as Ru2, diphenylphosphinoethane (dppe)] on Au(111). This large organometallic molecule was pulse deposited onto the Au(111) surface under ultrahigh-vacuum (UHV) conditions. UHV STM studies on the prepared sample were carried out at room temperature and 77K in order to probe molecular adsorption and to characterize the surface produced by the pulse deposition process. Isolated Ru2 molecules were successfully imaged by STM at room temperature; however, STM images were degraded by mobile toluene solvent molecules that remain on the surface after the deposition. Cooling the sample to 77K allows the solvent molecules to be observed directly using STM, and under these conditions, toluene forms organized striped domains with regular domain boundaries and a lattice characterized by 5.3 and 2.7Å intermolecular distances. When methylene chloride is used as the solvent, it forms analogous domains on the surface at 77K. Mild annealing under vacuum causes most toluene molecules to desorb from the surface; however, this annealing process may lead to thermal degradation of Ru2 molecules. Although pulse deposition is an effective way to deposit molecules on surfaces, the presence of solvent on the surface after pulse deposition is unavoidable without thermal annealing, and this annealing may cause undesired chemical changes in the adsorbates under study. Preparation of samples using pulse deposition must take into account the characteristics of sample molecules, solvent, and surfaces.

Measuring and predicting the emission rate of phthalate plasticizer from vinyl flooring in a specially-designed chamber.

PubMed

Xu, Ying; Liu, Zhe; Park, Jinsoo; Clausen, Per A; Benning, Jennifer L; Little, John C

2012-11-20

The emission of di-2-ethylhexyl phthalate (DEHP) from vinyl flooring (VF) was measured in specially designed stainless steel chambers. In duplicate chamber studies, the gas-phase concentration in the chamber increased slowly and reached a steady state level of 0.8-0.9 μg/m(3) after about 20 days. By increasing the area of vinyl flooring and decreasing that of the stainless steel surface within the chamber, the time to reach steady state was significantly reduced, compared to a previous study (1 month versus 5 months). The adsorption isotherm of DEHP on the stainless steel chamber surfaces was explicitly measured using solvent extraction and thermal desorption. The strong partitioning of DEHP onto the stainless steel surface was found to follow a simple linear relationship. Thermal desorption resulted in higher recovery than solvent extraction. Investigation of sorption kinetics showed that it takes several weeks for the sorption of DEHP onto the stainless steel surface to reach equilibrium. The content of DEHP in VF was measured at about 15% (w/w) using pressurized liquid extraction. The independently measured or calculated parameters were used to validate an SVOC emission model, with excellent agreement between model prediction and the observed gas-phase DEHP chamber concentrations.

Electrostatic Unfolding and Interactions of Albumin Driven by pH Changes: A Molecular Dynamics Study

PubMed Central

2015-01-01

A better understanding of protein aggregation is bound to translate into critical advances in several areas, including the treatment of misfolded protein disorders and the development of self-assembling biomaterials for novel commercial applications. Because of its ubiquity and clinical potential, albumin is one of the best-characterized models in protein aggregation research; but its properties in different conditions are not completely understood. Here, we carried out all-atom molecular dynamics simulations of albumin to understand how electrostatics can affect the conformation of a single albumin molecule just prior to self-assembly. We then analyzed the tertiary structure and solvent accessible surface area of albumin after electrostatically triggered partial denaturation. The data obtained from these single protein simulations allowed us to investigate the effect of electrostatic interactions between two proteins. The results of these simulations suggested that hydrophobic attractions and counterion binding may be strong enough to effectively overcome the electrostatic repulsions between the highly charged monomers. This work contributes to our general understanding of protein aggregation mechanisms, the importance of explicit consideration of free ions in protein solutions, provides critical new insights about the equilibrium conformation of albumin in its partially denatured state at low pH, and may spur significant progress in our efforts to develop biocompatible protein hydrogels driven by electrostatic partial denaturation. PMID:24393011

Nano- to Formation-Scale Estimates of Mineral-Specific Reactive Surface Area

NASA Astrophysics Data System (ADS)

Cole, D. R.; Swift, A.; Sheets, J.; Anovitz, L. M.

2017-12-01

Predictions of changes in fluid composition, coupled with the evolution of the solid matrix, include the generation and testing of reactive transport models. However, translating a heterogeneous natural system into physical and chemical model parameters, including the critical but poorly-constrained metric of fluid-accessible surface area, continues to challenge Earth scientists. Studies of carbon storage capacity, permeability, rock strain due to mineral dissolution and precipitation, or the prediction of rock evolution through diagenesis and weathering each consider macroscale outcomes of processes that often are critically impacted by rock surface geometry at the nanoscale. The approach taken here is to consider the whole vertical extent of a saline reservoir and then to address two questions. First, what is the accessible surface area for each major mineral, and for all adjacent pore sizes from <2 nm on up, within each major lithofacies in that formation? Second, with the formation thus divided into units of analysis, parameterized, and placed into geologic context, what constraints can be placed on reactive surface area as a function of mineral composition? A complex sandstone covering a substantial fraction of the quartz-K-feldspar-illite ternary is selected and mineral-specific surface area quantified using neutron scattering, nitrogen and mercury porosimetry, multi-signal high-resolution mineral mapping, and other techniques. For neutron scattering, scale-specific pore geometries enable more accurate translation of volume into surface area. By applying this workflow to all end-member lithologies of this reservoir formation, equations and maps of surface area as a function of position on a quartz-feldspar-clay ternary plot are developed for each major mineral. Results from this work therefore advance our ability to parameterize models not just for the particular formation studied, but for similar geologic units as well.

The addition of nanostructured hydroxyapatite to an experimental adhesive resin.

PubMed

Leitune, Vicente Castelo Branco; Collares, Fabrício Mezzomo; Trommer, Rafael Mello; Andrioli, Daniela Guerra; Bergmann, Carlos Pérez; Samuel, Susana Maria Werner

2013-04-01

Was produced nanostructured hydroxyapatite (HAnano) and evaluated the influence of its incorporation in an adhesive resin. HAnano was produced by a flame-based process and was characterized by scanning electron microscopy. The surface area, particle size, micro-Raman and cytotoxicity were evaluated. The organic phase was formulated by mixing 50 wt.% Bis-GMA, 25 wt.% TEGDMA, and 25 wt.% HEMA. HAnano was added at seven different concentrations: 0; 0.5; 1; 2; 5; 10 and 20 wt.%. Adhesive resins with hydroxyapatite incorporation were evaluated for their radiopacity, degree of conversion, flexural strength, softening in solvent and microshear bond strength. The data were analyzed by one-way ANOVA and Tukey's post hoc test (α=0.05), except for softening in solvent (paired t-test) and cytotoxicity (two-way ANOVA and Bonferroni). HAnano presented 15.096 m(2)/g of specific surface area and a mean size of 26.7 nm. The radiopacity values were not different from those of 1-mm aluminium. The degree of conversion ranged from 52.2 to 63.8%. The incorporation of HAnano did not influence the flexural strength, which ranged from 123.3 to 143.4MPa. The percentage of reduction of the microhardness after immersion in the solvent became lower as the HAnano concentration increased. The addition of 2% nanostructured hydroxyapatite resulted in a higher value of microshear bond strength than the control group (p<0.05). The incorporation of 2% of nanostructured hydroxyapatite into an adhesive resin presented the best results. The incorporation of nanostructured hydroxyapatite increases the adhesive properties and may be a promising filler for adhesive resin. Copyright © 2013 Elsevier Ltd. All rights reserved.

Double-grooved nanofibre surfaces with enhanced anisotropic hydrophobicity.

PubMed

Liang, Meimei; Chen, Xin; Xu, Yang; Zhu, Lei; Jin, Xiangyu; Huang, Chen

2017-11-02

This study reports a facile method for fabricating double-grooved fibrous surfaces. The primary grooves of the surface are formed by aligned fibres, while the secondary grooves are achieved by oriented nanogrooves on the fibre surface. Investigation into the formation mechanism reveals that the nanogrooves can be readily tailored through adjusting the solvent ratio and relative humidity. With this understanding, a variety of polymers have been successfully electrospun into fibres having the same nanogrooved feature. These fibres show high resemblance to natural hierarchical structures, and thereby endowing the corresponding double-grooved surface with enhanced anisotropic hydrophobicity. A water droplet at a parallel direction to the grooves exhibits a much higher contact angle and a lower roll-off angle than the droplet at a perpendicular direction. The application potential of such anisotropic hydrophobicity has been demonstrated via a fog collection experiment, in which the double-grooved surface can harvest the largest amount of water. Moreover, the fabrication method requires neither post-treatment nor sophisticated equipment, making us anticipate that the double-grooved surface would be competitive in areas where a highly ordered surface, a large surface area and an anisotropic hydrophobicity are preferred.

'GREENER' SOLVENT-FREE CHEMICAL SYNTHESIS USING MICROWAVE IRRADIATION

EPA Science Inventory

Solvent-free approach that involves microwave (MW) irradiation of neat reactants (undiluted) catalyzed by the surfaces of less-expensive and recyclable mineral supports such as alumina, silica, clay, or 'doped' surfaces is presented which is applicable to a wide range of cleavage...

Clean Air Act Guidelines and Standards for Solvent Use and Surface Coating Industry

EPA Pesticide Factsheets

This page contains the stationary sources of air pollution for the solvent use and surface coating industries, and their corresponding air pollution regulations. To learn more about the regulations for each industry, just click on the links below.

Simultaneously 'pushing' and 'pulling' graphene oxide into low-polar solvents through a designed interface.

PubMed

Liu, Zhen; Liu, Jingquan; Wang, Yichao; Razal, Joselito M; Francis, Paul S; Biggs, Mark J; Barrow, Colin J; Yang, Wenrong

2018-08-03

Dispersing graphene oxide (GO) in low-polar solvents can realize a perfect self-assembly with functional molecules and application in removal of organic impurities that only dissolve in low-polar solvents. The surface chemistry of GO plays an important role in its dispersity in these solvents. The direct transfer of hydrophilic GO into low-polar solvents, however, has remained an experimental challenge. In this study, we design an interface to transfer GO by simultaneously 'pushing and pulling' the nanosheets into low-polar solvents. Our approach is outstanding due to the ability to obtain monolayers of chemically reduced GO (CRGO) with designed surface properties in the organic phase. Using the transferred GO or CRGO dispersions, we have fabricated GO/fullerene nanocomposites and assessed the ability of CRGOs for dye adsorption. We hope our work can provide a universal approach for the phase transfer of other nanomaterials.

Oxidative Gelation of Solvent-Accessible Arabinoxylans is the Predominant Consequence of Extensive Chlorination of Soft Wheat Flour

USDA-ARS?s Scientific Manuscript database

Solvent retention capacity (SRC) and Bostwick flow were used to explore the effects of milling yield, extent of chlorination, and flour particle size on cake flour functionality and batter viscosity. The effects of the extent of chlorination were dramatic, but milling yield and additional milling t...

Micro- and nano-porous surface patterns prepared by surface-confined directional melt crystallization of solvent

NASA Astrophysics Data System (ADS)

Kim, Byoung Soo; Kim, Hyun Jin; An, Suyeong; Chi, Sangwon; Kim, Junseok; Lee, Jonghwi

2017-07-01

Recently, numerous attempts have been made to engineer micro- and nano-porous surface patterns or to develop convenient preparation methods for the practical applications of self-cleaning surfaces, water-repellent surfaces, novel textures, etc. Herein, we introduce a simple, cheap, and repeatable crystallization-based method to produce porous surface structures, on any surface of already fabricated polymeric materials. Contact of the solvent phase with cooled polymer surfaces enabled the limited dissolution of the surfaces and the subsequent extremely fast melt crystallization of the solvent. After removing the crystals, various micro- and nano-porous patterns were obtained, whose pore sizes ranged over three orders of magnitude. Pore depth was linearly dependent on the dissolution time. Crystal growth was mainly directed normal to the surfaces, but it was also controlled in-plane, resulting in cylindrical or lamellar structures. Superhydrophobic surfaces were successfully prepared on both polystyrene and polycarbonate. This process offers a novel surface engineering tool for a variety of polymer surfaces, whose topology can be conveniently controlled over a wide range by crystal engineering.

VERU-SOLVE™ MARINE 200 HP

EPA Pesticide Factsheets

Technical product bulletin: this surface washing agent used in oil spill cleanups separates the oil and water from the sand or soiled surface. Suitable for treating shorelines, beaches, rocks, marshes, sensitive environments, and access limited areas.

STABILITY OF A CYLINDRICAL SOLUTE-SOLVENT INTERFACE: EFFECT OF GEOMETRY, ELECTROSTATICS, AND HYDRODYNAMICS.

PubMed

Li, B O; Sun, Hui; Zhou, Shenggao

The solute-solvent interface that separates biological molecules from their surrounding aqueous solvent characterizes the conformation and dynamics of such molecules. In this work, we construct a solvent fluid dielectric boundary model for the solvation of charged molecules and apply it to study the stability of a model cylindrical solute-solvent interface. The motion of the solute-solvent interface is defined to be the same as that of solvent fluid at the interface. The solvent fluid is assumed to be incompressible and is described by the Stokes equation. The solute is modeled simply by the ideal-gas law. All the viscous force, hydrostatic pressure, solute-solvent van der Waals interaction, surface tension, and electrostatic force are balanced at the solute-solvent interface. We model the electrostatics by Poisson's equation in which the solute-solvent interface is treated as a dielectric boundary that separates the low-dielectric solute from the high-dielectric solvent. For a cylindrical geometry, we find multiple cylindrically shaped equilibrium interfaces that describe polymodal (e.g., dry and wet) states of hydration of an underlying molecular system. These steady-state solutions exhibit bifurcation behavior with respect to the charge density. For their linearized systems, we use the projection method to solve the fluid equation and find the dispersion relation. Our asymptotic analysis shows that, for large wavenumbers, the decay rate is proportional to wavenumber with the proportionality half of the ratio of surface tension to solvent viscosity, indicating that the solvent viscosity does affect the stability of a solute-solvent interface. Consequences of our analysis in the context of biomolecular interactions are discussed.

Study on the disparate transition behaviors of the electrical/physical properties in PEDOT:PSS film depending on solvent species under a follow-up solution-treatment process

NASA Astrophysics Data System (ADS)

Yun, Dong-Jin; Kim, Jung-Hwa; Kim, Seong Heon; Seol, Minsu; Yu, DaEun; Kwon, Hyukju; Ham, Yongnam; Chung, JaeGwan; Kim, Yongsu; Heo, Sung

2016-04-01

In most solution-processed organic devices, a poly(3,4-ethylenedioxythiophene) (PEDOT) polymerized with poly(4-styrenesulfonate) (PSS) film is inevitably affected by various conditions during the subsequent solution-coating processes. To investigate the effects of direct solvent exposure on the properties of PEDOT polymerized with PSS (PEDOT:PSS) films, photoemission spectroscopy-based analytical methods were used before and after solvent-coating processes. Our results clearly indicate that PEDOT:PSS films undergo a different transition mechanism depending on the solubility of the solvent in water. The water-miscible solvents induce the solvation of hydrophilic PSS chains. As a result, this process allows the solvent to diffuse into the PEDOT:PSS film, and a conformational change between PEDOT and PSS occurs. On the other hand, the water-immiscible organic solvents cause the partial adsorption of solvent molecules at the PE surface, which leads to changes in the surface properties, including work function. Based on our finding, we demonstrate that the energy-level alignments at the organic semiconductor/electrode interface for the PEDOT:PSS films can be controlled by simple solvent treatments.

D-Area Drip Irrigation-Phytoremediation Project: SRTC Final Report

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

Wilde, E.W.

2003-01-14

Groundwater in D-Area at the Savannah River Site (SRS) is contaminated with trichloroethylene (TCE) and by-products resulting from discharges of this organic solvent during past operations. Several potential clean-up strategies are being or have been investigated, including a novel drip irrigation-phytoremediation process that is the focus of the treatability study described in this report. The contaminated groundwater in D-Area occurs primarily at depths of 30 to 50 feet below ground surface, well below the depths that are typically penetrated by plant roots. The system investigated in this study involved pumping water from the contaminated aquifer and discharging the water intomore » overlying test plots below the surface using drip irrigation. The test plots contained pines, cottonwoods, or no vegetation (controls). The primary objective was to determine the overall effectiveness of the process for TCE removal and to elucidate the biotic and abiotic pathways for its removal.« less

Superhydrophobic perfluoropolymer/polystyrene blend films induced by nonsolvent

NASA Astrophysics Data System (ADS)

Gengec, Nevin Atalay; Cengiz, Ugur; Erbil, H. Yildirim

2016-10-01

Statistical copolymers of perfluoroalkyl ethyl acrylate (Zonyl-TAN) and methyl methacrylate (MMA) were synthesized in a CO2 polymerization system where a CO2-expanded monomer mixture was formed at 13 MPa, and 80 °C by using AIBN as initiator. Flat and superhydrophobic surfaces were subsequently prepared on glass slides by applying a phase separation process where the synthesized p(TAN-co-MMA) copolymer and polystyrene (PS) were dissolved in THF solvent. Ethanol was added as the non-solvent to introduce superhydrophobicity during film formation. Water contact angle on the flat p(TAN-co-MMA) copolymer was 118° and increased up to 170° with the formation of surface roughness. The ratio of the ethanol non-solvent in the blend solution has an important effect on the magnitude of surface roughness during the phase separation process. Both pits and protrusions of 1-10 μm in size were formed on the surface when non-solvent was used. Surface roughness increased with the increase in the ethanol ratio and the PS content of the blend solution.

Scaling and self-organized criticality in proteins: Lysozyme c

NASA Astrophysics Data System (ADS)

Phillips, J. C.

2009-11-01

Proteins appear to be the most dramatic natural example of self-organized criticality (SOC), a concept that explains many otherwise apparently unlikely phenomena. Protein functionality is often dominated by long-range hydro(phobic/philic) interactions, which both drive protein compaction and mediate protein-protein interactions. In contrast to previous reductionist short-range hydrophobicity scales, the holistic Moret-Zebende hydrophobicity scale [Phys. Rev. E 75, 011920 (2007)] represents a hydroanalytic tool that bioinformatically quantifies SOC in a way fully compatible with evolution. Hydroprofiling identifies chemical trends in the activities and substrate binding abilities of model enzymes and antibiotic animal lysozymes c , as well as defensins, which have been the subject of tens of thousands of experimental studies. The analysis is simple and easily performed and immediately yields insights not obtainable by traditional methods based on short-range real-space interactions, as described either by classical force fields used in molecular-dynamics simulations, or hydrophobicity scales based on transference energies from water to organic solvents or solvent-accessible areas.

Structure of choline oxidase in complex with the reaction product glycine betaine.

PubMed

Salvi, Francesca; Wang, Yuan-Fang; Weber, Irene T; Gadda, Giovanni

2014-02-01

Choline oxidase from Arthrobacter globiformis, which is involved in the biosynthesis of glycine betaine from choline, has been extensively characterized in its mechanistic and structural properties. Despite the knowledge gained on the enzyme, the details of substrate access to the active site are not fully understood. The `loop-and-lid' mechanism described for the glucose-methanol-choline enzyme superfamily has not been confirmed for choline oxidase. Instead, a hydrophobic cluster on the solvent-accessible surface of the enzyme has been proposed by molecular dynamics to control substrate access to the active site. Here, the crystal structure of the enzyme was solved in complex with glycine betaine at pH 6.0 at 1.95 Å resolution, allowing a structural description of the ligand-enzyme interactions in the active site. This structure is the first of choline oxidase in complex with a physiologically relevant ligand. The protein structures with and without ligand are virtually identical, with the exception of a loop at the dimer interface, which assumes two distinct conformations. The different conformations of loop 250-255 define different accessibilities of the proposed active-site entrance delimited by the hydrophobic cluster on the other subunit of the dimer, suggesting a role in regulating substrate access to the active site.

CHEMISTRY UNDER 'GREENER' CONDITIONS: SOLVENT-FREE SYNTHESIS USING MICROWAVE IRRADIATION

EPA Science Inventory

Solvent-free approach is emphasized that involves microwave (MW) irradiation of neat reactants (undiluted) catalyzed by the surfaces of less-expensive and recyclable mineral supports such as alumina, silica, clay, or 'doped' surfaces which is applicable to a wide range of cleavag...

ORGANIC SYNTHESES IN SOLVENT-FREE AND AQUEOUS MEDIA USING MICROWAVES

EPA Science Inventory

A solvent-free approach that involves microwave (MW) exposure of neat reactants (undiluted) catalyzed by the surfaces of recyclable mineral supports such as alumina, silica, clay, or 'doped' surfaces is presented which is applicable to a wide range of cleavage, condensation, cycl...

Solvent/co-solvent effects on the electronic properties and adsorption mechanism of anticancer drug Thioguanine on Graphene oxide surface as a nanocarrier: Density functional theory investigation and a molecular dynamics

NASA Astrophysics Data System (ADS)

Hasanzade, Zohre; Raissi, Heidar

2017-11-01

In this work, the adsorption of Thioguanine (TG) anticancer drug on the surface of Graphene oxide (GO) nanosheet has investigated using density functional theory (DFT) and molecular dynamics simulation (MDs). Quantum mechanics calculations by two methods including M06-2X/6-31G**and ωB97X-D/6-31G** have been employed to calculate the details of energetic, geometric, and electronic properties of the TG molecule interacting with Graphene oxide nanosheet (GONS). DFT calculations confirmed that the strongest adsorption is observed when hydrogen bond interactions between TG molecule and the functional groups of Graphene oxide nanosheet are predominate. In all calculations, solvent effects have been considered in water using the PCM method. It is found that TG molecule can be adsorbed on Graphene oxide with negative solvation energy, indicating the TG adsorption on Graphene oxide surfaces is thermodynamically favored. Moreover, MD simulations are examined to understand the solvent/co-solvent effect (water, ethanol, nicotine) on the Thioguanine drug delivery through Graphene oxide. The results of RDF patterns and the van der Waals energy calculations show that interaction between TG drugs and the Graphene oxide surface is stronger in water solvent compared to the other co-solvent. The obtained MD results illustrate that when nicotine and ethanol exist in the system, the drug takes longer time to bind with GO nanosheet and the system becomes unstable. It can be concluded that Graphene oxide can be a promising candidate in water media for delivery the TG molecule.

Identification of key residues for the binding of glucagon to the N-terminal domain of its receptor: an alanine scan and modeling study.

PubMed

Prévost, M; Vertongen, P; Waelbroeck, M

2012-10-01

Glucagon plays an essential role in the glycemia maintenance during fasting, but also aggravates hyperglycemia in diabetic patients. A series of analogues of glucagon were synthesized replacing each amino acid of the C-terminal region (residues 15-29) with alanine. The residues affecting the binding to the glucagon receptor are found to be located on one face of the glucagon helix. Several 3-dimensional models of the N-terminal domain of the glucagon receptor in complex with its ligand peptide were built and used to analyze the peptide-receptor interface in terms of the nature of the peptide residues and the interactions they form with the receptor. The models suggest that glucagon keeps its native helical structure upon binding, and that a large part of the interface formed with the receptor is hydrophobic. We find that in the C-terminal region, F22, V23, M27, and D15 are the most important residues for peptide binding. They bury a large portion of their solvent accessible surface area and make numerous interactions with the receptor mainly of the hydrophobic type. © Georg Thieme Verlag KG Stuttgart · New York.

Adaptive resolution simulation of an atomistic protein in MARTINI water

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

Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J., E-mail: s.j.marrink@rug.nl

2014-02-07

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecularmore » dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.« less

Adaptive resolution simulation of an atomistic protein in MARTINI water.

PubMed

Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J; Praprotnik, Matej

2014-02-07

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.

regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution.

PubMed

Zhang, Xinjun; Li, Meng; Lin, Hai; Rao, Xi; Feng, Weixing; Yang, Yuedong; Mort, Matthew; Cooper, David N; Wang, Yue; Wang, Yadong; Wells, Clark; Zhou, Yaoqi; Liu, Yunlong

2017-09-01

While synonymous single-nucleotide variants (sSNVs) have largely been unstudied, since they do not alter protein sequence, mounting evidence suggests that they may affect RNA conformation, splicing, and the stability of nascent-mRNAs to promote various diseases. Accurately prioritizing deleterious sSNVs from a pool of neutral ones can significantly improve our ability of selecting functional genetic variants identified from various genome-sequencing projects, and, therefore, advance our understanding of disease etiology. In this study, we develop a computational algorithm to prioritize sSNVs based on their impact on mRNA splicing and protein function. In addition to genomic features that potentially affect splicing regulation, our proposed algorithm also includes dozens structural features that characterize the functions of alternatively spliced exons on protein function. Our systematical evaluation on thousands of sSNVs suggests that several structural features, including intrinsic disorder protein scores, solvent accessible surface areas, protein secondary structures, and known and predicted protein family domains, show significant differences between disease-causing and neutral sSNVs. Our result suggests that the protein structure features offer an added dimension of information while distinguishing disease-causing and neutral synonymous variants. The inclusion of structural features increases the predictive accuracy for functional sSNV prioritization.

Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound to a Partner by Combined ESI-IM-MS and Modeling

NASA Astrophysics Data System (ADS)

D'Urzo, Annalisa; Konijnenberg, Albert; Rossetti, Giulia; Habchi, Johnny; Li, Jinyu; Carloni, Paolo; Sobott, Frank; Longhi, Sonia; Grandori, Rita

2015-03-01

Intrinsically disordered proteins (IDPs) form biologically active complexes that can retain a high degree of conformational disorder, escaping structural characterization by conventional approaches. An example is offered by the complex between the intrinsically disordered NTAIL domain and the phosphoprotein X domain (PXD) from measles virus (MeV). Here, distinct conformers of the complex are detected by electrospray ionization-mass spectrometry (ESI-MS) and ion mobility (IM) techniques yielding estimates for the solvent-accessible surface area (SASA) in solution and the average collision cross-section (CCS) in the gas phase. Computational modeling of the complex in solution, based on experimental constraints, provides atomic-resolution structural models featuring different levels of compactness. The resulting models indicate high structural heterogeneity. The intermolecular interactions are predominantly hydrophobic, not only in the ordered core of the complex, but also in the dynamic, disordered regions. Electrostatic interactions become involved in the more compact states. This system represents an illustrative example of a hydrophobic complex that could be directly detected in the gas phase by native mass spectrometry. This work represents the first attempt to modeling the entire NTAIL domain bound to PXD at atomic resolution.

Alginate-based hybrid aerogel microparticles for mucosal drug delivery.

PubMed

Gonçalves, V S S; Gurikov, P; Poejo, J; Matias, A A; Heinrich, S; Duarte, C M M; Smirnova, I

2016-10-01

The application of biopolymer aerogels as drug delivery systems (DDS) has gained increased interest during the last decade since these structures have large surface area and accessible pores allowing for high drug loadings. Being biocompatible, biodegradable and presenting low toxicity, polysaccharide-based aerogels are an attractive carrier to be applied in pharmaceutical industry. Moreover, some polysaccharides (e.g. alginate and chitosan) present mucoadhesive properties, an important feature for mucosal drug delivery. This feature allows to extend the contact of DDS with biological membranes, thereby increasing the absorption of drugs through the mucosa. Alginate-based hybrid aerogels in the form of microparticles (<50μm) were investigated in this work as carriers for mucosal administration of drugs. Low methoxyl pectin and κ-carrageenan were co-gelled with alginate and further dried with supercritical CO2 (sc-CO2). Spherical mesoporous aerogel microparticles were obtained for alginate, hybrid alginate/pectin and alginate/κ-carrageenan aerogels, presenting high specific surface area (370-548m(2)g(-1)) and mucoadhesive properties. The microparticles were loaded with ketoprofen via adsorption from its solution in sc-CO2, and with quercetin via supercritical anti-solvent precipitation. Loading of ketoprofen was in the range between 17 and 22wt% whereas quercetin demonstrated loadings of 3.1-5.4wt%. Both the drugs were present in amorphous state. Loading procedure allowed the preservation of antioxidant activity of quercetin. Release of both drugs from alginate/κ-carrageenan aerogel was slightly faster compared to alginate/pectin. The results indicate that alginate-based aerogel microparticles can be viewed as promising matrices for mucosal drug delivery applications. Copyright © 2016 Elsevier B.V. All rights reserved.

The X-Ray Crystal Structure of the Keratin 1-Keratin 10 Helix 2B Heterodimer Reveals Molecular Surface Properties and Biochemical Insights into Human Skin Disease

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

Bunick, Christopher G.; Milstone, Leonard M.

Keratins 1 (K1) and 10 (K10) are the primary keratins expressed in differentiated epidermis. Mutations in K1/K10 are associated with human skin diseases. We determined the crystal structure of the complex between the distal (2B) helices of K1 and K10 to better understand how human keratin structure correlates with function. The 3.3 Å resolution structure confirms many features inferred by previous biochemical analyses, but adds unexpected insights. It demonstrates a parallel, coiled-coil heterodimer with a predominantly hydrophobic intermolecular interface; this heterodimer formed a higher order complex with a second K1-K10-2B heterodimer via a Cys401K10 disulfide link, although the bond anglemore » is unanticipated. The molecular surface analysis of K1-K10-2B identified several pockets, one adjacent to the disulfide linkage and conserved in K5-K14. The solvent accessible surface area of the K1-K10 structure is 20–25% hydrophobic. The 2B region contains mixed acidic and basic patches proximally (N-terminal), whereas it is largely acidic distally (C-terminal). Mapping of conserved and nonconserved residues between K1-K10 and K5-K14 onto the structure demonstrated the majority of unique residues align along the outer helical ridge. Finally, the structure permitted a fresh analysis of the deleterious effects caused by K1/K10 missense mutations found in patients with phenotypic skin disease.« less

Increased rate of solvent diffusion in a prototypical supramolecular gel measured on the picosecond timescale.

PubMed

Seydel, Tilo; Edkins, Robert M; Jones, Christopher D; Foster, Jonathan A; Bewley, Robert; Aguilar, Juan A; Edkins, Katharina

2018-06-14

Solvent diffusion in a prototypical supramolecular gel probed by quasi-elastic neutron scattering on the picosecond timescale is faster than that in the respective bulk solvent. This phenomenon is hypothesized to be due to disruption of the hydrogen bonding of the solvent by the large hydrophobic surface of the gel network.

Low-cost and fast synthesis of nanoporous silica cryogels for thermal insulation applications.

PubMed

Su, Li Fen; Miao, Lei; Tanemura, Sakae; Xu, Gang

2012-06-01

Nanoporous silica cryogels with a high specific surface area of 1095 m 2 g -1 were fabricated using tert-butyl alcohol as a reaction solvent, via a cost-effective sol-gel process followed by vacuum freeze drying. The total time of cryogel production was reduced markedly to one day. The molar ratio of solvent/precursor, which was varied from 5 to 13, significantly affected the porous structure and thermal insulating properties of the cryogels. The silica cryogels with low densities in the range of 0.08-0.18 g cm -3 and thermal conductivities as low as 6.7 mW (m·K) -1 at 100 Pa and 28.3 mW (m·K) -1 at 10 5 Pa were obtained using this new technique.

Molecular description of the LCST behavior of an elastin-like polypeptide.

PubMed

Li, Nan K; García Quiroz, Felipe; Hall, Carol K; Chilkoti, Ashutosh; Yingling, Yaroslava G

2014-10-13

Elastin-like polypeptides (ELPs) with the repeat sequence of VPGVG are widely used as a model system for investigation of lower critical solution temperature (LCST) transition behavior. In this paper, the effect of temperature on the structure, dynamics and association of (VPGVG)18 in aqueous solution is investigated using atomistic molecular dynamics simulations. Our simulations show that as the temperature increases the ELP backbones undergo gradual conformational changes, which are attributed to the formation of more ordered secondary structures such as β-strands. In addition, increasing temperature changes the hydrophobicity of the ELP by exposure of hydrophobic valine-side chains to the solvent and hiding of proline residues. Based on our simulations, we conclude that the transition behavior of (VPGVG)18 can be attributed to a combination of thermal disruption of the water network that surrounds the polypeptide, reduction of solvent accessible surface area of the polypeptide, and increase in its hydrophobicity. Simulations of the association of two (VPGVG)18 molecules demonstrated that the observed gradual changes in the structural properties of the single polypeptide chain are enough to cause the aggregation of polypeptides above the LCST. These results lead us to propose that the LCST phase behavior of poly(VPGVG) is a collective phenomenon that originates from the correlated gradual changes in single polypeptide structure and the abrupt change in properties of hydration water around the peptide and is a result of a competition between peptide-peptide and peptide-water interactions. This is a computational study of an important intrinsically disordered peptide system that provides an atomic-level description of structural features and interactions that are relevant in the LCST phase behavior.

Impact of deglycosylation and thermal stress on conformational stability of a full length murine IgG2a monoclonal antibody: observations from molecular dynamics simulations.

PubMed

Wang, Xiaoling; Kumar, Sandeep; Buck, Patrick M; Singh, Satish K

2013-03-01

With the rise of antibody based therapeutics as successful medicines, there is an emerging need to understand the fundamental antibody conformational dynamics and its implications towards stability of these medicines. Both deglycosylation and thermal stress have been shown to cause conformational destabilization and aggregation in monoclonal antibodies. Here, we study instabilities caused by deglycosylation and by elevated temperature (400 K) by performing molecular dynamic simulations on a full length murine IgG2a mAb whose crystal structure is available in the Protein Data bank. C(α)-atom root mean square deviation and backbone root mean square fluctuation calculations show that deglycosylation perturbs quaternary and tertiary structures in the C(H) 2 domains. In contrast, thermal stress pervades throughout the antibody structure and both Fabs and Fc regions are destabilized. The thermal stress applied in this study was not sufficient to cause large scale unfolding within the simulation time and most amino acid residues showed similar average solvent accessible surface area and secondary structural conformations in all trajectories. C(H) 3 domains were the most successful at resisting the conformational destabilization. The simulations helped identify aggregation prone regions, which may initiate cross-β motif formation upon deglycosylation and upon applying thermal stress. Deglycosylation leads to increased backbone fluctuations and solvent exposure of a highly conserved APR located in the edge β-strand A of the C(H) 2 domains. Aggregation upon thermal stress is most likely initiated by two APRs that overlap with the complementarity determining regions. This study has important implications for rational design of antibody based therapeutics that are resistant towards aggregation. Copyright © 2012 Wiley Periodicals, Inc.

Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.

PubMed

Arnautova, Yelena A; Abagyan, Ruben A; Totrov, Maxim

2011-02-01

We report the development of internal coordinate mechanics force field (ICMFF), new force field parameterized using a combination of experimental data for crystals of small molecules and quantum mechanics calculations. The main features of ICMFF include: (a) parameterization for the dielectric constant relevant to the condensed state (ε = 2) instead of vacuum, (b) an improved description of hydrogen-bond interactions using duplicate sets of van der Waals parameters for heavy atom-hydrogen interactions, and (c) improved backbone covalent geometry and energetics achieved using novel backbone torsional potentials and inclusion of the bond angles at the C(α) atoms into the internal variable set. The performance of ICMFF was evaluated through loop modeling simulations for 4-13 residue loops. ICMFF was combined with a solvent-accessible surface area solvation model optimized using a large set of loop decoys. Conformational sampling was carried out using the biased probability Monte Carlo method. Average/median backbone root-mean-square deviations of the lowest energy conformations from the native structures were 0.25/0.21 Å for four residues loops, 0.84/0.46 Å for eight residue loops, and 1.16/0.73 Å for 12 residue loops. To our knowledge, these results are significantly better than or comparable with those reported to date for any loop modeling method that does not take crystal packing into account. Moreover, the accuracy of our method is on par with the best previously reported results obtained considering the crystal environment. We attribute this success to the high accuracy of the new ICM force field achieved by meticulous parameterization, to the optimized solvent model, and the efficiency of the search method. © 2010 Wiley-Liss, Inc.

HCl, KCl and KOH solvation resolved solute-solvent interactions and solution surface stress

NASA Astrophysics Data System (ADS)

Zhang, Xi; Xu, Yan; Zhou, Yong; Gong, Yinyan; Huang, Yongli; Sun, Chang Q.

2017-11-01

An incorporation of the hydrogen bond (O:Hsbnd O or HB) cooperativity notion, contact angle detection, and the differential phonon spectrometrics (DPS) has enabled us to gain refined information on the HCl, KCl and KOH solvation resolved solute-solvent molecular interactions and the solution surface stresses. Results show that ionic polarization stiffens the solvent Hsbnd O bond phonon from 3200 to 3480 cm-1 in the hydration shells. The HO- in alkaline solution, however, shares not only the same Hsbnd O phonon redshift of compressed water from 3200 to < 3100 cm-1 but also the dangling bonds of H2O surface featured at 3610 cm-1. Salt and alkaline solvation enhances the solution surface stress by K+ and Cl- ionic polarization. The excessive H+ proton in acid solution forms a H↔H anti-HB that depresses the solution surface stress, instead. The solute capability of transforming the fraction of the O:Hsbnd O bonds of the solvent matrix is featured by: fH = 0 and fx ∝ 1-exp(-C/C0) (x = HO-, K+ and Cl-) towards saturation. Exercises not only confirm the presence of the H↔H anti-HB point fragilization, the O:⇔:O super-HB point compression, and ionic polarization dominating the performance of the respective HCl, KOH, and KCl solutions, but also demonstrate the power of the DPS that enables high resolution of solute-solute-solvent interactions and correlation between HB relaxation and solution surface stress.

Laboratory evaluation of a prospective remediation method for PCB-contaminated paint

PubMed Central

2014-01-01

Background Paint laden with polychlorinated biphenyls (PCBs) often acts as a point source for environmental contamination. It is advantageous to address contaminated paint before the PCBs transport to surrounding media; however, current disposal methods of painted material introduce a variety of complications. Previous work demonstrates that PCBs can be broken down at ambient temperatures and pressures through a degradation process involving magnesium metal and acidified ethanol. This report is an extension of that work by describing the development of a delivery system for said reaction in preparation for a field test. Two treatment options including the Activated Metal Treatment System (AMTS) and the Non-Metal Treatment System (NMTS) remove and degrade PCBs from painted surfaces. Findings AMTS decreased the Aroclor® concentration of a solution by more than 97% within 120 minutes and the Aroclor® concentration of industrial paint chips by up to 98% over three weeks. After removing up to 76% of PCBs on a painted surface after seven days, NMTS also removed trace amounts of PCBs in the paint’s concrete substrate. The evaporation rate of the solvent (ethanol) from the treatment system was reduced when the application area was increased. The solvent system’s ability to remove more than 90% of PCBs was maintained after losing 36% of its mass to solvent evaporation. Conclusions The delivery systems, AMTS and NMTS, are able to support the hydrodechlorination reaction necessary for PCB degradation and are therefore attractive options for further studies regarding the remediation of contaminated painted surfaces. PMID:24602329

40 CFR 63.5749 - How do I calculate the organic HAP content of aluminum wipedown solvents?

Code of Federal Regulations, 2011 CFR

2011-07-01

... the past 12 months, liters. Dj= density of aluminum wipedown solvent j, kilograms per liter. Wj= mass fraction of organic HAP in aluminum wipedown solvent j. m = number of different aluminum surface coatings...

CHEMISTRY UNDER NON-TRADITIONAL CONDITIONS: SOLVENT-FREE SYNTHESIS USING MICROWAVE IRRADIATION

EPA Science Inventory

A solvent-free approach that involves microwave (MW) irradiation of neat reactants (undiluted) catalyzed by the surfaces of less-expensive and recyclable mineral supports such as alumina, silica, clay, or "doped" surfaces is presented which is applicable to a wide range of cleava...

'GREENER' CHEMICAL SYNTHESES USING MICROWAVES UNDER SOLVENT-FREE CONDITIONS OR AQUEOUS MEDIA

EPA Science Inventory

A solvent-free approach that involves microwave (MW) exposure of neat reactants (undiluted) catalyzed by the surfaces of recyclable mineral supports such as alumina, silica, clay, or 'doped' surfaces is presented which is applicable to a wide range of cleavage, condensation, cycl...

Hybrid Membrane/Absorption Process for Post-combustion CO2 Capture

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

Li, Shiguang; Shou, S.; Pyrzynski, Travis

2013-12-31

This report summarizes scientific/technical progress made for bench-scale membrane contactor technology for post-combustion CO2 capture from DOE Contract No. DE-FE-0004787. Budget Period 1 (BP1) membrane absorber, Budget Period 2 (BP2) membrane desorber and Budget Period 3 (BP3) integrated system and field testing studies have been completed successfully and met or exceeded the technical targets (≥ 90% CO2 removal and CO2 purity of 97% in one membrane stage). Significant breakthroughs are summarized below: BP1 research: The feasibility of utilizing the poly (ether ether ketone), PEEK, based hollow fiber contractor (HFC) in combination with chemical solvents to separate and capture at leastmore » 90% of the CO2 from simulated flue gases has been successfully established. Excellent progress has been made as we have achieved the BP1 goal: ≥ 1,000 membrane intrinsic CO2 permeance, ≥ 90% CO2 removal in one stage, ≤ 2 psi gas side pressure drop, and ≥ 1 (sec)-1 mass transfer coefficient. Initial test results also show that the CO2 capture performance, using activated Methyl Diethanol Amine (aMDEA) solvent, was not affected by flue gas contaminants O2 (~3%), NO2 (66 ppmv), and SO2 (145 ppmv). BP2 research: The feasibility of utilizing the PEEK HFC for CO2-loaded solvent regeneration has been successfully established High CO2 stripping flux, one order of magnitude higher than CO2 absorption flux, have been achieved. Refined economic evaluation based on BP1 membrane absorber and BP2 membrane desorber laboratory test data indicate that the CO2 capture costs are 36% lower than DOE’s benchmark amine absorption technology. BP3 research: A bench-scale system utilizing a membrane absorber and desorber was integrated into a continuous CO2 capture process using contactors containing 10 to 20 ft2 of membrane area. The integrated process operation was stable through a 100-hour laboratory test, utilizing a simulated flue gas stream. Greater than 90% CO2 capture combined with 97% CO2 product purity was achieved throughout the test. Membrane contactor modules have been scaled from bench scale 2-inch diameter by 12-inch long (20 ft2 membrane surface area) modules to 4-inch diameter by 60-inch long pilot scale modules (165 ft2 membrane surface area). Pilot scale modules were tested in an integrated absorption/regeneration system for CO2 capture field tests at a coal-fired power plant (Midwest Generation’s Will County Station located in Romeoville, IL). Absorption and regeneration contactors were constructed utilizing high performance super-hydrophobic, nano-porous PEEK membranes with CO2 gas permeance of 2,000 GPU and a 1,000 GPU, respectively. Field tests using aMDEA solvent achieved greater than 90% CO2 removal in a single stage. The absorption mass transfer coefficient was 1.2 (sec)-1, exceeding the initial target of 1.0 (sec)-1. This mass transfer coefficient is over one order of magnitude greater than that of conventional gas/liquid contacting equipment. The economic evaluation based on field tests data indicates that the CO2 capture cost associated with membrane contactor technology is $54.69 (Yr 2011$)/tonne of CO2 captured when using aMDEA as a solvent. It is projected that the DOE’s 2025 cost goal of $40 (Yr 2011$)/tonne of CO2 captured can be met by decreasing membrane module cost and by utilizing advanced CO2 capture solvents. In the second stage of the field test, an advanced solvent, Hitachi’s H3-1 was utilized. The use of H3-1 solvent increased mass transfer coefficient by 17% as compared to aMDEA solvent. The high mass transfer coefficient of H3-1 solvent combined with much more favorable solvent regeneration requirements, indicate that the projected savings achievable with membrane contactor process can be further improved. H3-1 solvent will be used in the next pilot-scale development phase. The integrated absorption/regeneration process design and high performance membrane contactors developed in the current bench-scale program will be used as the base technology for future pilot-scale development.« less

Tailoring magnetic nanoparticle for transformers application.

PubMed

Morais, P C; Silva, A S; Leite, E S; Garg, V K; Oliveira, A C; Viali, W R; Sartoratto, P P C

2010-02-01

In this study photoacoustic spectroscopy was used to investigate the effect of dilution of an oil-based magnetic fluid sample on the magnetic nanoparticle surface-coating. Changes of the photoacoustic signal intensity on the band-L region (640 to 830 nm) upon dilution of the stock magnetic fluid sample were discussed in terms of molecular surface desorption. The model proposed here assumes that the driving force taking the molecules out from the nanoparticle surface into the bulk solvent is the gradient of osmotic pressure. This gradient of osmotic pressure is established between the nanoparticle surface and the bulk suspension. It is further assumed that the photoacoustic signal intensity (area under the photoacoustic spectra) scales linearly with the number of coating molecules (surface grafting) at the nanoparticle surface. This model picture provides a non-linear analytical description for the reduction of the surface grafting coefficient upon dilution, which was successfully-used to curve-fit the photoacoustic experimental data.

Small-Molecule Organic Photovoltaic Modules Fabricated via Halogen-Free Solvent System with Roll-to-Roll Compatible Scalable Printing Method.

PubMed

Heo, Youn-Jung; Jung, Yen-Sook; Hwang, Kyeongil; Kim, Jueng-Eun; Yeo, Jun-Seok; Lee, Sehyun; Jeon, Ye-Jin; Lee, Donmin; Kim, Dong-Yu

2017-11-15

For the first time, the photovoltaic modules composed of small molecule were successfully fabricated by using roll-to-roll compatible printing techniques. In this study, blend films of small molecules, BTR and PC 71 BM were slot-die coated using a halogen-free solvent system. As a result, high efficiencies of 7.46% and 6.56% were achieved from time-consuming solvent vapor annealing (SVA) treatment and roll-to-roll compatible solvent additive approaches, respectively. After successful verification of our roll-to-roll compatible method on small-area devices, we further fabricated large-area photovoltaic modules with a total active area of 10 cm 2 , achieving a power conversion efficiency (PCE) of 4.83%. This demonstration of large-area photovoltaic modules through roll-to-roll compatible printing methods, even based on a halogen-free solvent, suggests the great potential for the industrial-scale production of organic solar cells (OSCs).

Lithium modified zeolite synthesis for conversion of biodiesel-derived glycerol to polyglycerol

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

Ayoub, Muhammad, E-mail: muhammad.ayoub@petronas.com.my; Abdullah, Ahmad Zuhairi, E-mail: chzuhairi@usm.my; Inayat, Abrar, E-mail: abrar.inayat@petronas.com.my

Basic zeolite has received significant attention in the catalysis community. These zeolites modified with alkaline are the potential replacement for existing zeolite catalysts due to its unique features with added advantages. The present paper covers the preparation of lithium modified zeolite Y (Li-ZeY) and its activity for solvent free conversion of biodiesel-derived glycerol to polyglycerol via etherification process. The modified zeolite was well characterized by X-ray diffraction (XRD), Scanning Electron Microscope (SEM) and Nitrogen Adsorption. The SEM images showed that there was no change in morphology of modified zeolite structure after lithium modification. XRD patterns showed that the structure ofmore » zeolite was sustained after lithium modification. The surface properties of parent and modified zeolite was also observed N{sub 2} adsortion-desorption technique and found some changes in surface area and pore size. In addition, the basic strength of prepared materials was measured by Hammet indicators and found that basic strength of Li-ZeY was highly improved. This modified zeolite was found highly thermal stable and active heterogamous basic catalyst for conversion of solvent free glycerol to polyglycerol. This reaction was conducted at different temperatures and 260 °C was found most active temperature for this process for reaction time from 6 to 12 h over this basic catalyst in the absence of solvent.« less

Rational engineering of a mesohalophilic carbonic anhydrase to an extreme halotolerant biocatalyst

PubMed Central

Warden, Andrew C.; Williams, Michelle; Peat, Thomas S.; Seabrook, Shane A.; Newman, Janet; Dojchinov, Greg; Haritos, Victoria S.

2015-01-01

Enzymes expressed by highly salt-tolerant organisms show many modifications compared with salt-affected counterparts including biased amino acid and lower α-helix content, lower solvent accessibility and negative surface charge. Here, we show that halotolerance can be generated in an enzyme solely by modifying surface residues. Rational design of carbonic anhydrase II is undertaken in three stages replacing 18 residues in total, crystal structures confirm changes are confined to surface residues. Catalytic activities and thermal unfolding temperatures of the designed enzymes increase at high salt concentrations demonstrating their shift to halotolerance, whereas the opposite response is found in the wild-type enzyme. Molecular dynamics calculations reveal a key role for sodium ions in increasing halotolerant enzyme stability largely through interactions with the highly ordered first Na+ hydration shell. For the first time, an approach to generate extreme halotolerance, a trait with broad application in industrial biocatalysis, in a wild-type enzyme is demonstrated. PMID:26687908

Reconciling the discrepancies between crystallographic porosity and guest access as exemplified by Zn-HKUST-1.

PubMed

Feldblyum, Jeremy I; Liu, Ming; Gidley, David W; Matzger, Adam J

2011-11-16

There are several compounds for which there exists a disconnect between porosity as predicted by crystallography and porosity measured by gas sorption analysis. In this paper, the Zn-based analogue of Cu(3)(btc)(2) (HKUST-1), Zn(3)(btc)(2) (Zn-HKUST-1; btc = 1,3,5-benzenetricarboxylate) is investigated. Conventional analysis of Zn-HKUST-1 by powder X-ray diffraction and gas sorption indicates retention of crystalline structure but negligible nitrogen uptake at 77 K. By using positron annihilation lifetime spectroscopy, a densified surface layer preventing the entry of even small molecular species into the crystal framework is revealed. The material is shown to have inherent surface instability after solvent removal, rendering it impermeable to molecular guests irrespective of handling and processing methods. This previously unobserved surface instability may provide insight into the failure of other microporous coordination polymers to exhibit significant porosity despite crystal structures indicative of regular, interconnected, microporous networks.

'GREENER' ORGANIC SYNTHESES AND TRANSFORMATIONS USING MICROWAVES UNDER SOLVENT-FREE CONDITIONS OR AQUEOUS MEDIA

EPA Science Inventory

A solvent-free approach that involves microwave (MW) exposure of neat reactants (undiluted) catalyzed by the surfaces of recyclable mineral supports such as alumina, silica, clay, or 'doped' surfaces is presented which is applicable to a wide range of cleavage, condensation, cycl...

Determination of Macrolide Antibiotics Using Dispersive Liquid-Liquid Microextraction Followed by Surface-Assisted Laser Desorption/Ionization Mass Spectrometry

NASA Astrophysics Data System (ADS)

Chen, Kuan-Yu; Yang, Thomas C.; Chang, Sarah Y.

2012-06-01

A novel method for the determination of macrolide antibiotics using dispersive liquid-liquid microextraction coupled to surface-assisted laser desorption/ionization mass spectrometric detection was developed. Acetone and dichloromethane were used as the disperser solvent and extraction solvent, respectively. A mixture of extraction solvent and disperser solvent were rapidly injected into a 1.0 mL aqueous sample to form a cloudy solution. After the extraction, macrolide antibiotics were detected using surface-assisted laser desorption/ionization mass spectrometry (SALDI/MS) with colloidal silver as the matrix. Under optimum conditions, the limits of detection (LODs) at a signal-to-noise ratio of 3 were 2, 3, 3, and 2 nM for erythromycin (ERY), spiramycin (SPI), tilmicosin (TILM), and tylosin (TYL), respectively. This developed method was successfully applied to the determination of macrolide antibiotics in human urine samples.

On a Multiphase Multicomponent Model of Biofilm Growth

NASA Astrophysics Data System (ADS)

Friedman, Avner; Hu, Bei; Xue, Chuan

2014-01-01

Biofilms are formed when free-floating bacteria attach to a surface and secrete polysaccharide to form an extracellular polymeric matrix (EPS). A general model of biofilm growth needs to include the bacteria, the EPS, and the solvent within the biofilm region Ω( t), and the solvent in the surrounding region D( t). The interface between the two regions, Γ( t), is a free boundary. In this paper, we consider a mathematical model that consists of a Stokes equation for the EPS with bacteria attached to it, a Stokes equation for the solvent in Ω( t) and another for the solvent in D( t). The volume fraction of the EPS is another unknown satisfying a reaction-diffusion equation. The entire system is coupled nonlinearly within Ω( t) and across the free surface Γ( t). We prove the existence and uniqueness of a solution, with a smooth surface Γ( t), for a small time interval.

Enhancement of room temperature ferromagnetism in tin oxide nanocrystal using organic solvents

NASA Astrophysics Data System (ADS)

Sakthiraj, K.; Hema, M.; Balachandra Kumar, K.

2017-10-01

The effect of organic solvents (ethanol & ethylene glycol) on the room temperature ferromagnetism in nanocrystalline tin oxide has been studied. The samples were synthesized using sol-gel method with the mixture of water & organic liquid as solvent. It is found that pristine SnO2 nanocrystal contain two different types of paramagnetic centres over their surface:(i) surface chemisorbed oxygen species and (ii) Sn interstitial & oxygen vacancy defect pair. The magnetic moment induced in the as-prepared samples is mainly contributed by the alignment of local spin moments resulting from these defects. These surface defect states are highly activated by the usage of ethylene glycol solvent rather than ethylene in tin oxide nanostructure synthesis. Powder X-ray diffraction, transmission electron microscope imaging, energy dispersive spectrometry, Fourier transformed infrared spectroscopy, UV-vis absorption spectroscopy, photoluminescence spectroscopy, vibrating sample magnetometer measurement and electron spin resonance spectroscopy were employed to characterize the nanostructured tin oxide materials.

Resonant infrared matrix-assisted pulsed laser evaporation of TiO2 nanoparticle films

NASA Astrophysics Data System (ADS)

Mayo, Daniel C.; Paul, Omari; Airuoyo, Idemudia J.; Pan, Zhengda; Schriver, Kenneth E.; Avanesyan, Sergey M.; Park, Hee K.; Mu, Richard R.; Haglund, Richard F.

2013-03-01

The successful development of flexible, high performance thin films that are competitive with silicon-based technology will likely require fabricating films of hybrid materials that incorporate nanomaterials, glasses, ceramics, polymers, and thin films. Resonant infrared matrix-assisted pulsed laser evaporation (RIR-MAPLE) is an ideal method for depositing organic materials and nanoparticles with minimal photochemical or photothermal damage to the deposited material. Furthermore, there are many nonhazardous solvents containing chemical functional groups with infrared absorption bands that are accessible using IR lasers. We report here results of recent work in which RIR-MAPLE has been employed successfully to deposit thin films of TiO2 nanoparticles on Si substrates. Using an Er:YAG laser ( λ=2.94 μm), we investigated a variety of MAPLE matrices containing -OH moieties, including water and all four isomers of butyl alcohol. The alcohol isomers are shown to provide effective and relatively nontoxic solvents for use in the RIR-MAPLE process. In addition, we examine the effects of varying concentration and laser fluence on film roughness and surface coverage.

Classifying neighbourhoods by level of access to stores selling fresh fruit and vegetables and groceries: identifying problematic areas in the city of Gatineau, Quebec.

PubMed

Gould, Adrian C; Apparicio, Philippe; Cloutier, Marie-Soleil

2012-11-06

Physical access to stores selling groceries, fresh fruit and vegetables (FV) is essential for urban dwellers. In Canadian cities where low-density development practices are common, social and material deprivation may be compounded by poor geographic access to healthy food. This case study examines access to food stores selling fresh FV in Gatineau, Quebec, to identify areas where poor access is coincident with high deprivation. Food retailers were identified using two secondary sources and each store was visited to establish the total surface area devoted to the sale of fresh FV. Four population-weighted accessibility measures were then calculated for each dissemination area (DA) using road network distances. A deprivation index was created using variables from the 2006 Statistics Canada census, also at the scale of the DA. Finally, six classes of accessibility to a healthy diet were constructed using a k-means classification procedure. These were mapped and superimposed over high deprivation areas. Overall, deprivation is positively correlated with better accessibility. However, more than 18,000 residents (7.5% of the population) live in high deprivation areas characterized by large distances to the nearest retail food store (means of 1.4 km or greater) and virtually no access to fresh FV within walking distance (radius of 1 km). In this research, we identified areas where poor geographic access may introduce an additional constraint for residents already dealing with the challenges of limited financial and social resources. Our results may help guide local food security policies and initiatives.

A novel organic solvent-based coupling method for the preparation of covalently immobilized proteins on gold.

PubMed Central

Parker, M. C.; Patel, N.; Davies, M. C.; Roberts, C. J.; Tendler, S. J.; Williams, P. M.

1996-01-01

A novel organic solvent-based coupling method has been developed for the covalent immobilization of biological material to gold surfaces. The method employs the polar organic solvent anhydrous 2,2,2-trifluoroethanol as the reaction medium and involves dissolution of the protein (catalase) in the solvent allowing protein coupling to proceed under basic conditions in a dry organic environment. The advantage of this method is that protein attachment is favored over hydrolysis of the coupling reagent. We have shown qualitatively and quantitatively that following attachment to the gold surface a significant proportion of the enzyme catalase remains catalytically active (at least 20-31%). PMID:8931151

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

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

Heldebrant, David J

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 600more » 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 demonstrated on the bench cart • No measurable solvent degradation was observed over 4 months of testing – even with 5 wt% water present« less

Solvent Exchange Leading to Nanobubble Nucleation: A Molecular Dynamics Study

PubMed Central

2017-01-01

The solvent exchange procedure has become the most-used protocol to produce surface nanobubbles, while the molecular mechanisms behind the solvent exchange are far from being fully understood. In this paper, we build a simple model and use molecular dynamics simulations to investigate the dynamic characteristics of solvent exchange for producing nanobubbles. We find that at the first stage of solvent exchange, there exists an interface between interchanging solvents of different gas solubility. This interface moves toward the substrate gradually as the exchange process proceeds. Our simulations reveal directed diffusion of gas molecules against the gas concentration gradient, driven by the solubility gradient of the liquid composition across the moving solvent–solvent interface. It is this directed diffusion that causes gas retention and produces a local gas oversaturation much higher near the substrate than far from it. At the second stage of solvent exchange, the high local gas oversaturation leads to bubble nucleation either on the solid surface or in the bulk solution, which is found to depend on the substrate hydrophobicity and the degree of local gas oversaturation. Our findings suggest that solvent exchange could be developed into a standard procedure to produce oversaturation and used to a variety of nucleation applications other than generating nanobubbles. PMID:28742364

Development of high capacity, high rate lithium ion batteries utilizing metal fiber conductive additives

NASA Astrophysics Data System (ADS)

Ahn, Soonho; Kim, Youngduk; Kim, Kyung Joon; Kim, Tae Hyung; Lee, Hyungkeun; Kim, Myung H.

As lithium ion cells dominate the battery market, the performance improvement is an utmost concern among developers and researchers. Conductive additives are routinely employed to enhance electrode conductivity and capacity. Carbon particulates—graphite or carbon black powders—are conventional and popular choices as conductive fillers. However, percolation requirements of particles demand significant volumetric content of impalpable, and thereby high area conductive fillers. As might be expected, the electrode active surface area escalates unnecessarily, resulting in overall increase in reaction with electrolytes and organic solvents. The increased reactions usually manifest as an irreversible loss of anode capacity, gradual oxidation and consumption of electrolyte on the cathode—which causes capacity decline during cycling—and an increased threat to battery safety by gas evolution and exothermic solvent oxidation. In this work we have utilized high aspect ratio, flexible, micronic metal fibers as low active area and high conductivity additives. The metal fibers appear well dispersed within the electrode and to satisfy percolation requirements very efficiently at very low volumetric content compared to conventional carbon-based conductive additives. Results from 18650-type cells indicate significant enhancements in electrode capacity and high rate capability while the irreversible capacity loss is negligible.

Particle sensor array

NASA Technical Reports Server (NTRS)

Buehler, Martin G. (Inventor); Blaes, Brent R. (Inventor); Lieneweg, Udo (Inventor)

1994-01-01

A particle sensor array which in a preferred embodiment comprises a static random access memory having a plurality of ion-sensitive memory cells, each such cell comprising at least one pull-down field effect transistor having a sensitive drain surface area (such as by bloating) and at least one pull-up field effect transistor having a source connected to an offset voltage. The sensitive drain surface area and the offset voltage are selected for memory cell upset by incident ions such as alpha-particles. The static random access memory of the present invention provides a means for selectively biasing the memory cells into the same state in which each of the sensitive drain surface areas is reverse biased and then selectively reducing the reversed bias on these sensitive drain surface areas for increasing the upset sensitivity of the cells to ions. The resulting selectively sensitive memory cells can be used in a number of applications. By way of example, the present invention can be used for measuring the linear energy transfer of ion particles, as well as a device for assessing the resistance of CMOS latches to Cosmic Ray induced single event upsets. The sensor of the present invention can also be used to determine the uniformity of an ion beam.

Spatial organization of surface nanobubbles and its implications in their formation process.

PubMed

Lhuissier, Henri; Lohse, Detlef; Zhang, Xuehua

2014-02-21

We study the size and spatial distribution of surface nanobubbles formed by the solvent exchange method to gain insight into the mechanism of their formation. The analysis of Atomic Force Microscopy (AFM) images of nanobubbles formed on a hydrophobic surface reveals that the nanobubbles are not randomly located, which we attribute to the role of the history of nucleation during the formation. Moreover, the size of each nanobubble is found to be strongly correlated with the area of the bubble-depleted zone around it. The precise correlation suggests that the nanobubbles grow by diffusion of the gas from the bulk rather than by diffusion of the gas adsorbed on the surface. Lastly, the size distribution of the nanobubbles is found to be well described by a log-normal distribution.

Effect of Urea on G-Quadruplex Stability.

PubMed

Aslanyan, Lusine; Ko, Jordan; Kim, Byul G; Vardanyan, Ishkhan; Dalyan, Yeva B; Chalikian, Tigran V

2017-07-13

G-quadruplexes represent a class of noncanonical nucleic acid structures implicated in transcriptional regulation, cellular function, and disease. An understanding of the forces involved in stabilization and destabilization of the G-quadruplex conformation relative to the duplex or single-stranded conformation is a key to elucidating the biological role of G-quadruplex-based genomic switches and the quest for therapeutic means for controlled induction or suppression of a G-quadruplex at selected genomic loci. Solute-solvent interactions provide a ubiquitous and, in many cases, the determining thermodynamic force in maintaining and modulating the stability of nucleic acids. These interactions involve water as well as water-soluble cosolvents that may be present in the solution or in the crowded environment in the cell. We present here the first quantitative investigation of the effect of urea, a destabilizing cosolvent, on the conformational preferences of a G-quadruplex formed by the telomeric d[A(G 3 T 2 A) 3 G 3 ] sequence (Tel22). At 20 mM NaCl and room temperature, Tel22 undergoes a two-state urea-induced unfolding transition. An increase in salt mitigates the deleterious effect of urea on Tel22. The urea m-value of Tel22 normalized per change in solvent-accessible surface area, ΔS A , is similar to those for other DNA and RNA structures while being several-fold larger than that of proteins. Our results suggest that urea can be employed as an analytical tool in thermodynamic characterizations of G-quadruplexes in a manner similar to the use of urea in protein studies. We emphasize the need for further studies involving a larger selection of G-quadruplexes varying in sequence, topology (parallel, antiparallel, hybrid), and molecularity (monomolecular, bimolecular, tetramolecular) to outline the advantages and the limits of the use of urea in G-quadruplex studies. A deeper understanding of the effect of solvent and cosolvents on the differential stability of the G-quadruplex and duplex conformations is a step toward elucidation of the modulating influence of different types of cosolvents on duplex-G-quadruplex molecular switches triggering genomic events.

Connecting Free Energy Surfaces in Implicit and Explicit Solvent: an Efficient Method to Compute Conformational and Solvation Free Energies

PubMed Central

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

2015-01-01

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 explicit/implicit thermodynamic cycle. PMID:26236174

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

PubMed

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.

Quantum Monte Carlo studies of solvated systems

NASA Astrophysics Data System (ADS)

Schwarz, Kathleen; Letchworth Weaver, Kendra; Arias, T. A.; Hennig, Richard G.

2011-03-01

Solvation qualitatively alters the energetics of diverse processes from protein folding to reactions on catalytic surfaces. An explicit description of the solvent in quantum-mechanical calculations requires both a large number of electrons and exploration of a large number of configurations in the phase space of the solvent. These problems can be circumvented by including the effects of solvent through a rigorous classical density-functional description of the liquid environment, thereby yielding free energies and thermodynamic averages directly, while eliminating the need for explicit consideration of the solvent electrons. We have implemented and tested this approach within the CASINO Quantum Monte Carlo code. Our method is suitable for calculations in any basis within CASINO, including b-spline and plane wave trial wavefunctions, and is equally applicable to molecules, surfaces, and crystals. For our preliminary test calculations, we use a simplified description of the solvent in terms of an isodensity continuum dielectric solvation approach, though the method is fully compatible with more reliable descriptions of the solvent we shall employ in the future.

Insights into the effect of dilute acid, hot water or alkaline pretreatment on cellulose accessible surface area and the overall porosity of Populus

DOE PAGES

Meng, Xianzhi; Wells, Tyrone; Sun, Qining; ...

2015-06-19

Pretreatment is known to render biomass more reactive to cellulase by altering the chemical compositions as well as physical structures of biomass. Simons stain technique along with mercury porosimetry were applied on the acid, neutral, and alkaline pretreated materials to measure the accessible surface area of cellulose and pore size distribution of Populus. Results indicated that acid pretreatment is much more effective than water and alkaline pretreatment in terms of cellulose accessibility increase. Further investigation suggests that lignin does not dictate cellulose accessibility to the extent that hemicellulose does, but it does restrict xylan accessibility which in turn controls themore » access of cellulase to cellulose. The most interesting finding is that severe acid pretreatment significantly decreases the average pore size, i.e., 90% average size decrease could be observed after 60 min dilute acid pretreatment at 160 °C; moreover, the nano-pore space formed between coated microfibrils is increased after pretreatment, especially for the acid pretreatment, suggesting this particular type of biomass porosity is probably the most fundamental barrier to effective enzymatic hydrolysis.« less

Assessing Ink Transfer Performance of Gravure-Offset Fine-Line Circuitry Printing

NASA Astrophysics Data System (ADS)

Cheng, Hsien-Chie; Chen, You-Wei; Chen, Wen-Hwa; Lu, Su-Tsai; Lin, Shih-Ming

2018-03-01

In this study, the printing mechanism and performance of gravure-offset fine-line circuitry printing technology are investigated in terms of key printing parameters through experimental and theoretical analyses. First, the contact angles of the ink deposited on different substrates, blankets, and gravure metal plates are experimentally determined; moreover, their temperature and solvent content dependences are analyzed. Next, the ink solvent absorption and evaporation behaviors of the blankets at different temperatures, times, and numbers of printing repetitions are characterized by conducting experiments. In addition, while printing repeatedly, the surface characteristics of the blankets, such as the contact angle, vary with the amount of absorbed ink solvent, further affecting the ink transfer performance (ratio) and printing quality. Accordingly, the surface effect of the blanket due to ink solvent absorption on the ink contact angle is analyzed. Furthermore, the amount of ink transferred from the gravure plate to the blanket in the "off process" and from the blanket to the substrate in the "set process" is evaluated by conducting a simplified plate-to-plate experiment. The influences of loading rate (printing velocity), temperature, and solvent content on the ink transfer performance are addressed. Finally, the ink transfer mechanism is theoretically analyzed for different solvent contents using Surface Evolver. The calculation results are compared with those of the experiment.

Adsorption of flexible polymer chains on a surface: Effects of different solvent conditions

NASA Astrophysics Data System (ADS)

Martins, P. H. L.; Plascak, J. A.; Bachmann, M.

2018-05-01

Polymer chains undergoing a continuous adsorption-desorption transition are studied through extensive computer simulations. A three-dimensional self-avoiding walk lattice model of a polymer chain grafted onto a surface has been treated for different solvent conditions. We have used an advanced contact-density chain-growth algorithm, in which the density of contacts can be directly obtained. From this quantity, the order parameter and its fourth-order Binder cumulant are computed, as well as the corresponding critical exponents and the adsorption-desorption transition temperature. As the number of configurations with a given number of surface contacts and monomer-monomer contacts is independent of the temperature and solvent conditions, it can be easily applied to get results for different solvent parameter values without the need of any extra simulations. In analogy to continuous magnetic phase transitions, finite-size-scaling methods have been employed. Quite good results for the critical properties and phase diagram of very long single polymer chains have been obtained by properly taking into account the effects of corrections to scaling. The study covers all solvent effects, going from the limit of super-self-avoiding walks, characterized by effective monomer-monomer repulsion, to poor solvent conditions that enable the formation of compact polymer structures.

Porous structures of polymer films prepared by spin coating with mixed solvents under humid condition.

PubMed

Park, Min Soo; Joo, Wonchul; Kim, Jin Kon

2006-05-09

We investigate the effects of interfacial energy between water and solvent as well as polymer concentration on the formation of porous structures of polymer films prepared by spin coating of cellulose acetate butyrate (CAB) in mixed solvent of tetrahydrofuran (THF) and chloroform under humid condition. The interfacial energy between water and the solvent was gradually changed by the addition of chloroform to the solvent. At a high polymer concentration (0.15 g/cm3 in THF), porous structures were limited only at the top surfaces of CAB films, regardless of interfacial energies, due to the high viscosity of the solution. At a medium concentration (approximately 0.08 g/cm3 in THF), CAB film had relatively uniform pores at the top surface and very small pores inside the film because of the mixing of the water droplets with THF solution. When chloroform was added to THF, pores at the inner CAB film had a comparable size with those at the top surface because of the reduced degree of the mixing between the water droplets and the mixed solvent. A further decrease in polymer concentration (0.05 g/cm3 in THF) caused the final films to have a two-layer porous structure, and the size of pores at each layer was almost the same.

Formation of thin film like assembly of exfoliated C3N4 nanoflakes by solvent non-evaporative method using centrifuge

NASA Astrophysics Data System (ADS)

Tejasvi, Ravi; Basu, Suddhasatwa

2017-12-01

A simple method for depositing a thin film of nanomaterial on a substrate using centrifugation technique has been developed, whereby solvent evaporation is prevented and solvent reuse is possible. The centrifuge technique of deposition yields uniform, smooth thin film irrespective of substrate surface texture. The deposited TiO2/eC3N4 film studied, through field emission scanning electron microscope, atomic force microscope, and optical surface profilometer, shows variation in surface roughness on the basis of centrifugation speeds. Initially film coverage improves and surface roughness decreases with the increase in rpm of the centrifuge and the surface roughness slightly increases with further increase in rpm. The photoelectrochemical studies of TiO2/eC3N4 films suggest that the centrifuge technique forms better heterojunctions compared to that by spin coating technique leading to enhanced photoelectrochemical water splitting.

Self-Assembly of Rod-Coil Block Copolymers on Carbon Nanotubes: A Route toward Diverse Surface Nanostructures.

PubMed

Han, Yang; Cai, Chunhua; Lin, Jiaping; Gong, Shuting; Xu, Wenheng; Hu, Rui

2018-04-14

In this work, it is reported that poly(γ-benzyl-l-glutamate)-block-poly(ethylene glycol) (PBLG-b-PEG) rod-coil block copolymers (BCPs) can disperse carbon nanotubes (CNTs) in solution and form various surface nanostructures on the CNTs via solution self-assembly. In an organic solvent that dissolves the BCPs, the PBLG rod blocks adsorb on CNT surfaces, and the BCPs form conformal coatings. Then, by the introduction of water, a selective solvent for PEG blocks, the BCPs in the coatings further self-assemble into diverse surface nanostructures, such as helices (left-handed or right-handed), gyros, spheres, and rings. The morphology of the surface nanostructure can be tailored by initial organic solvent composition, preparation temperature, feeding ratio of BCPs to CNTs, degree of polymerization of PBLG blocks, and diameter of the CNTs. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An implicit boundary integral method for computing electric potential of macromolecules in solvent

NASA Astrophysics Data System (ADS)

Zhong, Yimin; Ren, Kui; Tsai, Richard

2018-04-01

A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equation that arises in mathematical models for the electrostatics of molecules in solvent. The proposed method uses an implicit boundary integral formulation to derive a linear system defined on Cartesian nodes in a narrowband surrounding the closed surface that separates the molecule and the solvent. The needed implicit surface is constructed from the given atomic description of the molecules, by a sequence of standard level set algorithms. A fast multipole method is applied to accelerate the solution of the linear system. A few numerical studies involving some standard test cases are presented and compared to other existing results.

Synthesis of silica aerogel monoliths with controlled specific surface areas and pore sizes

NASA Astrophysics Data System (ADS)

Gao, Bingying; Lu, Shaoxiang; Kalulu, Mulenga; Oderinde, Olayinka; Ren, Lili

2017-07-01

To replace traditional preparation methods of silica aerogels, a small-molecule 1,2-epoxypropane (PO) has been introduced into the preparation process instead of using ammonia as the cross-linking agent, thus generating a lightweight, high porosity, and large surface area silica aerogel monolithic. We put forward a simple solution route for the chemical synthesis of silica aerogels, which was characterized by scanning electron microscopy (SEM), TEM, XRD, FTIR, thermogravimetric analysis (TGA) and the Brunauer-Emmett-Teller (BET) method In this paper, the effect of the amount of PO on the microstructure of silica aerogels is discussed. The BET surface areas and pore sizes of the resulting silica aerogels can be freely adjusted by changing the amount of PO, which will be helpful in promoting the development of silica aerogels to fabricate other porous materials with similar requirements. We also adopted a new organic solvent sublimation drying (OSSD) method to replace traditional expensive and dangerous drying methods such as critical point drying and freeze drying. This simple approach is easy to operate and has good repeatability, which will further facilitate actual applications of silica aerogels.

Versatile Vials

NASA Technical Reports Server (NTRS)

2001-01-01

Advanced Fuel Research, Inc. (AFR) developed a new sol-gel material coating for sample vials to be used in surface-enhanced Raman (SER) spectroscopy. In the fields of biomedical and forensic science, the coated vials are used to identify physiological chemicals present in blood and urine. The vials are used in the pharmaceutical industry in the area of drug development and discovery. In the drug enforcement field, using the vials helps with detection of trace amounts of drugs on surfaces. The SER vials will also help to identify contaminants in water sources, such as various inorganics and pesticides. The new vials have advantages over other SER materials. Former products required that samples be pre-mixed or dissolved into specific solvents or reagents. The SER vials do not have these limitations, and measurements can be performed using any solvent. Furthermore, the signal appears in less than one second. The sol-gel material will stay active for at least one year and the vials are compatible with any Raman spectrometer. Most importantly, the SER activity can be duplicated from vial-to-vial, allowing for reproducible results.

Adsorption and desorption of carbaryl on hexadecyl trimethyl ammonium bromide modified zeolite NaY using RGB portable photometer

NASA Astrophysics Data System (ADS)

Patdhanagul, Nopbhasinthu; Chanpaka, Saiphon; Intharaksa, Orapan; Sirival, Rujikarn; Thanomsith, Kannikar; Wongkwanklom, Sarayuth

2018-04-01

The carbaryl adsorption-desorption isotherms of zeolite NaY and hexadecyl trimethyl ammonium bromide (HTAB) modified zeolite NaY were investigated. Zeolite NaY was synthesized and modified by HTAB in the concentration range 0.1 - 10.0 mM. The adsorption isotherms indicated that zeolite modified with HTAB could significantly enhance the carbaryl adsorption capacity. Zeolite NaY modified with 5.0 mM HTAB gave great carbaryl adsorption because of hydrophilic surface. The 5.0 mM HTAB could adsorb up to 145.75 ppm g-1 of carbaryl which was equivalent to a 36.7% increase. The Surface area characterization showed the remaining of pore volume and pore size diameter and external surface area whereas the BET surface area and micropore surface area of modified zeolite slightly decreased. The XRD results indicate that modification of zeolite NaY with HTAB does not change the crystallinity of the starting zeolite. The elemental analysis indicated that the Si/Al ratio of synthesized zeolite NaY was close to 2.43. Desorption of carbaryl was tested by organic solvents such as methanol, ethanol, tetrahydrofuran, hexane and Deionized water. The results demonstrated that the percentage desorption of methanol is the highest. Carbaryl was quantitatively desorbed with percentage desorption of 82-100 %. It indicated sorption mechanism of carbaryl on the modified sorbent which was principally driven by hydrophobic forces.

Observing structural reorientations at solvent–nanoparticle interfaces by X-ray diffraction – putting water in the spotlight

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

Zobel, Mirijam

Nanoparticles are attractive in a wide range of research genres due to their size-dependent properties, which can be in contrast to those of micrometre-sized colloids or bulk materials. This may be attributed, in part, to their large surface-to-volume ratio and quantum confinement effects. There is a growing awareness that stress and strain at the particle surface contribute to their behaviour and this has been included in the structural models of nanoparticles for some time. One significant oversight in this field, however, has been the fact that the particle surface affects its surroundings in an equally important manner. It should bemore » emphasized here that the surface areas involved are huge and, therefore, a significant proportion of solvent molecules are affected. Experimental evidence of this is emerging, where suitable techniques to probe the structural correlations of liquids at nanoparticle surfaces have only recently been developed. The recent validation of solvation shells around nanoparticles has been a significant milestone in advancing this concept. Restructured ordering of solvent molecules at the surfaces of nanoparticles has an influence on the entire panoply of solvent–particle interactions during, for example, particle formation and growth, adhesion forces in industrial filtration, and activities of nanoparticle–enzyme complexes. This article gives an overview of the advances made in solvent–nanoparticle interface research in recent years: from description of the structure of bulk solids and liquidsviamacroscopic planar surfaces, to the detection of nanoscopic restructuring effects. Water–nanoparticle interfaces are given specific attention to illustrate and highlight their similarity to biological systems.« less

Direct in situ measurement of specific capacitance, monolayer tension, and bilayer tension in a droplet interface bilayer

DOE PAGES

Taylor, Graham J.; Venkatesan, Guru A.; Collier, C. Patrick; ...

2015-08-05

In this study, thickness and tension are important physical parameters of model cell membranes. However, traditional methods to measure these quantities require multiple experiments using separate equipment. This work introduces a new multi-step procedure for directly accessing in situ multiple physical properties of droplet interface bilayers (DIB), including specific capacitance (related to thickness), lipid monolayer tension in the Plateau-Gibbs border, and bilayer tension. The procedure employs a combination of mechanical manipulation of bilayer area followed by electrowetting of the capacitive interface to examine the sensitivities of bilayer capacitance to area and contact angle to voltage, respectively. These data allow formore » determining the specific capacitance of the membrane and surface tension of the lipid monolayer, which are then used to compute bilayer thickness and tension, respectively. The use of DIBs affords accurate optical imaging of the connected droplets in addition to electrical measurements of bilayer capacitance, and it allows for reversibly varying bilayer area. After validating the accuracy of the technique with diphytanoyl phosphatidylcholine (DPhPC) DIBs in hexadecane, the method is applied herein to quantify separately the effects on membrane thickness and tension caused by varying the solvent in which the DIB is formed and introducing cholesterol into the bilayer. Because the technique relies only on capacitance measurements and optical images to determine both thickness and tension, this approach is specifically well-suited for studying the effects of peptides, biomolecules, natural and synthetic nanoparticles, and other species that accumulate within membranes without altering bilayer conductance.« less

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

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

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

2015-10-27

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

Lipid and Lipid-Polymer Mixtures at an Interface

NASA Astrophysics Data System (ADS)

Kim, Joon Heon; Kim, Mahn Won

2000-03-01

The surface pressure (Π) and surface area/molecule (A) isotherms of a mixture of DMPC (DL-α-phosphatidylcholine,Dimyristoyl) and PEG-DMPE (1,2-Diacyl-sn-Glycero-3-Phosphoethanolamine-N-[Poly(ethylene glycol)5000]) system were measured at various compositions by the Langmuir surface balance technique at an air/water interface. In the range where the surface pressure is less than about 8 dynes/cm, a PEG polymer chain of PEG-DMPE molecules remains on the surface and the isotherm can be explained by the 2-D power law behavior of chains in a good solvent. In the range above 8 dynes/cm, a part of the PEG polymer segment is dissolved into the water phase, and the surface pressure can be explained as the sum of the 2-D component and 3-D component. Furthermore, the mixing energy is negative, which indicates an attractive interaction between DMPC and PEG-DMPE.

Lipid and lipid-polymer mixtures at an interface

NASA Astrophysics Data System (ADS)

Kim, Joon Heon; Kim, Mahn Won

2000-06-01

The surface pressure (Π) and surface area/molecule (A) isotherms of a mixture of DMPC (DL-α-phosphatidylcholine, Dimyristoyl) and PEG-DMPE (1,2-Diacyl-sn-Glycero-3-Phosphoethanolamine-N-[Poly(ethylene glycol)5000]) system were measured at various compositions by the Langmuir surface balance technique at an air/water interface. In the range where the surface pressure is less than about 8 dynes/cm, a PEG polymer chain of PEG-DMPE molecules remains on the surface and the isotherm can be explained by the 2-D power law behavior of chains in a good solvent. In the range above 8 dynes/cm, a part of the PEG polymer segment is dissolved into the water phase, and the surface pressure can be explained as the sum of the 2-D component and 3-D component. Furthermore, the mixing energy is negative, which indicates an attractive interaction between DMPC and PEG-DMPE. .

Control of morphology and function of low band gap polymer–bis-fullerene mixed heterojunctions in organic photovoltaics with selective solvent vapor annealing

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

Chen, Huipeng; Hsiao, Yu-Che; Hu, Bin

2014-05-07

We reported how by replacing PCBM with a bis-adduct fullerene (i.e. ICBA) we significantly improve the open circuit voltage (VOC) and power conversion efficiency (PCE) in P3HT bulk heterojunctions. But, for the most promising low band-gap polymer (LBP) systems, replacing PCBM with ICBA results in very poor shortcircuit current (JSC) and PCE although the VOC is significantly improved. Therefore, in this work, we have completed small angle neutron scattering and neutron reflectometry experiments to study the impact of post-deposition solvent annealing (SA) with control of solvent quality on the morphology and performance of LBP bis-fullerene BHJ photovoltaics. Our results showmore » that SA in a solvent that is selective for the LBP results in a depletion of bis-fullerene near the air surface, which limits device performance. SA in a solvent vapor which has similar solubility for polymer and bis-fullerene results in a higher degree of polymer ordering, bis-fullerene phase separation, and segregation of the bis-fullerene to the air surface, which facilitates charge transport and increases power conversion efficiency (PCE) by 100%. The highest degree of polymer ordering combined with significant bis-fullerene phase separation and segregation of bis-fullerene to the air surface is obtained by SA in a solvent vapor that is selective for the bis-fullerene. The resultant morphology increases PCE by 190%. These results indicate that solvent annealing with judicious solvent choice provides a unique tool to tune the morphology of LBP bisfullerene BHJ system, providing sufficient polymer ordering, formation of a bis-fullerene pure phase, and segregation of bis-fullerene to the air surface to optimize the morphology of the active layer. Furthermore, this process is broadly applicable to improving current disappointing LBP bis-fullerene systems to optimize their morphology and OPV performance post-deposition, including higher VOC and power conversion efficiency.« less

Effect of Solvent and Substrate on the Surface Binding Mode of Carboxylate-Functionalized Aromatic Molecules

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

Domenico, Janna; Foster, Michael E.; Spoerke, Erik D.

Here, the efficiency of dye-sensitized solar cells (DSSCs) is strongly influenced by dye molecule orientation and interactions with the substrate. Understanding the factors controlling the surface orientation of sensitizing organic molecules will aid in the improvement of both traditional DSSCs and other devices that integrate molecular linkers at interfaces. Here, we describe a general approach to understand relative dye–substrate orientation and provide analytical expressions predicting orientation. We consider the effects of substrate, solvent, and protonation state on dye molecule orientation. In the absence of solvent, our model predicts that most carboxylic acid-functionalized molecules prefer to lie flat (parallel) on themore » surface, due to van der Waals interactions, as opposed to a tilted orientation with respect to the surface that is favored by covalent bonding of the carboxylic acid group to the substrate. When solvation effects are considered, however, the molecules are predicted to orient perpendicular to the surface. We extend this approach to help understand and guide the orientation of metal–organic framework (MOF) thin-film growth on various metal–oxide substrates. A two-part analytical model is developed on the basis of the results of DFT calculations and ab initio MD simulations that predicts the binding energy of a molecule by chemical and dispersion forces on rutile and anatase TiO 2 surfaces, and quantifies the dye solvation energy for two solvents. The model is in good agreement with the DFT calculations and enables rapid prediction of dye molecule and MOF linker binding preference on the basis of the size of the adsorbing molecule, identity of the surface, and the solvent environment. We establish the threshold molecular size, governing dye molecule orientation, for each condition.« less

Effect of Solvent and Substrate on the Surface Binding Mode of Carboxylate-Functionalized Aromatic Molecules

DOE PAGES

Domenico, Janna; Foster, Michael E.; Spoerke, Erik D.; ...

2018-04-25

Here, the efficiency of dye-sensitized solar cells (DSSCs) is strongly influenced by dye molecule orientation and interactions with the substrate. Understanding the factors controlling the surface orientation of sensitizing organic molecules will aid in the improvement of both traditional DSSCs and other devices that integrate molecular linkers at interfaces. Here, we describe a general approach to understand relative dye–substrate orientation and provide analytical expressions predicting orientation. We consider the effects of substrate, solvent, and protonation state on dye molecule orientation. In the absence of solvent, our model predicts that most carboxylic acid-functionalized molecules prefer to lie flat (parallel) on themore » surface, due to van der Waals interactions, as opposed to a tilted orientation with respect to the surface that is favored by covalent bonding of the carboxylic acid group to the substrate. When solvation effects are considered, however, the molecules are predicted to orient perpendicular to the surface. We extend this approach to help understand and guide the orientation of metal–organic framework (MOF) thin-film growth on various metal–oxide substrates. A two-part analytical model is developed on the basis of the results of DFT calculations and ab initio MD simulations that predicts the binding energy of a molecule by chemical and dispersion forces on rutile and anatase TiO 2 surfaces, and quantifies the dye solvation energy for two solvents. The model is in good agreement with the DFT calculations and enables rapid prediction of dye molecule and MOF linker binding preference on the basis of the size of the adsorbing molecule, identity of the surface, and the solvent environment. We establish the threshold molecular size, governing dye molecule orientation, for each condition.« less

Greener and rapid access to bio-active heterocycles: one-pot solvent-free synthesis of 1,3,4-oxadiazoles and 1,3,4-thiadiazoles

EPA Science Inventory

A novel one-pot solvent free synthesis of 1,3,4-oxadiazoles and 1,3,4-thiadiazoles by condensation of acid hydrazide and triethyl orthoalkanates under microwave irradiations is reported. This green protocol was catalyzed efficiently by solid supported Nafion®NR50 and phosphorus p...

High-yield production of graphene by liquid-phase exfoliation of graphite.

PubMed

Hernandez, Yenny; Nicolosi, Valeria; Lotya, Mustafa; Blighe, Fiona M; Sun, Zhenyu; De, Sukanta; McGovern, I T; Holland, Brendan; Byrne, Michele; Gun'Ko, Yurii K; Boland, John J; Niraj, Peter; Duesberg, Georg; Krishnamurthy, Satheesh; Goodhue, Robbie; Hutchison, John; Scardaci, Vittorio; Ferrari, Andrea C; Coleman, Jonathan N

2008-09-01

Fully exploiting the properties of graphene will require a method for the mass production of this remarkable material. Two main routes are possible: large-scale growth or large-scale exfoliation. Here, we demonstrate graphene dispersions with concentrations up to approximately 0.01 mg ml(-1), produced by dispersion and exfoliation of graphite in organic solvents such as N-methyl-pyrrolidone. This is possible because the energy required to exfoliate graphene is balanced by the solvent-graphene interaction for solvents whose surface energies match that of graphene. We confirm the presence of individual graphene sheets by Raman spectroscopy, transmission electron microscopy and electron diffraction. Our method results in a monolayer yield of approximately 1 wt%, which could potentially be improved to 7-12 wt% with further processing. The absence of defects or oxides is confirmed by X-ray photoelectron, infrared and Raman spectroscopies. We are able to produce semi-transparent conducting films and conducting composites. Solution processing of graphene opens up a range of potential large-area applications, from device and sensor fabrication to liquid-phase chemistry.

Systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions

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

Cooks, Robert Graham; Li, Anyin; Luo, Qingjie

The invention generally relates to systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions. In certain aspects, the invention provides methods that involve providing a metal and a solvent. The methods additionally involve applying voltage to the solvated metal to thereby produce solvent droplets including ions of the metal containing compound, and directing the solvent droplets including the metal ions to a target. In certain embodiments, once at the target, the metal ions can react directly or catalyze reactions.

Systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions

DOEpatents

Cooks, Robert Graham; Li, Anyin; Luo, Qingjie

2017-01-24

The invention generally relates to systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions. In certain aspects, the invention provides methods that involve providing a metal and a solvent. The methods additionally involve applying voltage to the solvated metal to thereby produce solvent droplets including ions of the metal containing compound, and directing the solvent droplets including the metal ions to a target. In certain embodiments, once at the target, the metal ions can react directly or catalyze reactions.

How High Pressure Unifies Solvation Processes in Liquid Chromatography.

PubMed

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

2017-11-01

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

Synthesis and electrochemical properties of polyaniline nanofibers by interfacial polymerization.

PubMed

Manuel, James; Ahn, Jou-Hyeon; Kim, Dul-Sun; Ahn, Hyo-Jun; Kim, Ki-Won; Kim, Jae-Kwang; Jacobsson, Per

2012-04-01

Polyaniline nanofibers were prepared by interfacial polymerization with different organic solvents such as chloroform and carbon tetrachloride. Field emission scanning electron microscopy and transmission electron microscopy were used to study the morphological properties of polyaniline nanofibers. Chemical characterization was carried out using Fourier transform infrared spectroscopy, UV-Vis spectroscopy, and X-ray diffraction spectroscopy and surface area was measured using BET isotherm. Polyaniline nanofibers doped with lithium hexafluorophosphate were prepared and their electrochemical properties were evaluated.

Supported Silver Nanoparticle and Near-Interface Solution Dynamics in a Deep Eutectic Solvent

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

Hammons, Joshua A.; Ustarroz, Jon; Muselle, Thibault

2016-01-28

Type III deep eutectic solvents (DES) have attracted significant interest as both environmentally friendly and functional solvents that are, in some ways, advantageous to traditional aqueous systems. While these solvents continue to produce remarkable thin films and nanoparticle assemblies, their interactions with metallic surfaces are complex and difficult to manipulate. In this study, the near-surface region (2–600 nm) of a carbon surface is investigated immediately following silver nanoparticle nucleation and growth. This is accomplished, in situ, using a novel grazing transmission small-angle X-ray scattering approach with simultaneous voltammetry and electrochemical impedance spectroscopy. With this physical and electrochemical approach, the timemore » evolution of three distinct surface interaction phenomena is observed: aggregation and coalescence of Ag nanoparticles, multilayer perturbations induced by nonaggregated Ag nanoparticles, and a stepwise transport of dissolved Ag species from the carbon surface. The multilayer perturbations contain charge-separated regions of positively charged choline-ethylene and negatively charged Ag and Cl species. Both aggregation-coalescence and the stepwise decrease in Ag precursor near the surface are observed to be very slow (~2 h) processes, as both ion and particle transport are significantly impeded in a DES as compared to aqueous electrolytes. Finally, altogether, this study shows how the unique chemistry of the DES changes near the surface and in the presence of nanoparticles that adsorb the constituent species.« less