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

PubMed

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

2012-01-01

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

Comparison of binding energies of SrcSH2-phosphotyrosyl peptides with structure-based prediction using surface area based empirical parameterization.

PubMed Central

Henriques, D. A.; Ladbury, J. E.; Jackson, R. M.

2000-01-01

The prediction of binding energies from the three-dimensional (3D) structure of a protein-ligand complex is an important goal of biophysics and structural biology. Here, we critically assess the use of empirical, solvent-accessible surface area-based calculations for the prediction of the binding of Src-SH2 domain with a series of tyrosyl phosphopeptides based on the high-affinity ligand from the hamster middle T antigen (hmT), where the residue in the pY+ 3 position has been changed. Two other peptides based on the C-terminal regulatory site of the Src protein and the platelet-derived growth factor receptor (PDGFR) are also investigated. Here, we take into account the effects of proton linkage on binding, and test five different surface area-based models that include different treatments for the contributions to conformational change and protein solvation. These differences relate to the treatment of conformational flexibility in the peptide ligand and the inclusion of proximal ordered solvent molecules in the surface area calculations. This allowed the calculation of a range of thermodynamic state functions (deltaCp, deltaS, deltaH, and deltaG) directly from structure. Comparison with the experimentally derived data shows little agreement for the interaction of SrcSH2 domain and the range of tyrosyl phosphopeptides. Furthermore, the adoption of the different models to treat conformational change and solvation has a dramatic effect on the calculated thermodynamic functions, making the predicted binding energies highly model dependent. While empirical, solvent-accessible surface area based calculations are becoming widely adopted to interpret thermodynamic data, this study highlights potential problems with application and interpretation of this type of approach. There is undoubtedly some agreement between predicted and experimentally determined thermodynamic parameters: however, the tolerance of this approach is not sufficient to make it ubiquitously applicable. PMID:11106171

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

Rapid assessment of oxidation via middle-down LCMS correlates with methionine side-chain solvent-accessible surface area for 121 clinical stage monoclonal antibodies.

PubMed

Yang, Rong; Jain, Tushar; Lynaugh, Heather; Nobrega, R Paul; Lu, Xiaojun; Boland, Todd; Burnina, Irina; Sun, Tingwan; Caffry, Isabelle; Brown, Michael; Zhi, Xiaoyong; Lilov, Asparouh; Xu, Yingda

Susceptibility of methionine to oxidation is an important concern for chemical stability during the development of a monoclonal antibody (mAb) therapeutic. To minimize downstream risks, leading candidates are usually screened under forced oxidation conditions to identify oxidation-labile molecules. Here we report results of forced oxidation on a large set of in-house expressed and purified mAbs with variable region sequences corresponding to 121 clinical stage mAbs. These mAb samples were treated with 0.1% H 2 O 2 for 24 hours before enzymatic cleavage below the hinge, followed by reduction of inter-chain disulfide bonds for the detection of the light chain, Fab portion of heavy chain (Fd) and Fc by liquid chromatography-mass spectrometry. This high-throughput, middle-down approach allows detection of oxidation site(s) at the resolution of 3 distinct segments. The experimental oxidation data correlates well with theoretical predictions based on the solvent-accessible surface area of the methionine side-chains within these segments. These results validate the use of upstream computational modeling to predict mAb oxidation susceptibility at the sequence level.

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

Hydrophobic potential of mean force as a solvation function for protein structure prediction.

PubMed

Lin, Matthew S; Fawzi, Nicolas Lux; Head-Gordon, Teresa

2007-06-01

We have developed a solvation function that combines a Generalized Born model for polarization of protein charge by the high dielectric solvent, with a hydrophobic potential of mean force (HPMF) as a model for hydrophobic interaction, to aid in the discrimination of native structures from other misfolded states in protein structure prediction. We find that our energy function outperforms other reported scoring functions in terms of correct native ranking for 91% of proteins and low Z scores for a variety of decoy sets, including the challenging Rosetta decoys. This work shows that the stabilizing effect of hydrophobic exposure to aqueous solvent that defines the HPMF hydration physics is an apparent improvement over solvent-accessible surface area models that penalize hydrophobic exposure. Decoys generated by thermal sampling around the native-state basin reveal a potentially important role for side-chain entropy in the future development of even more accurate free energy surfaces.

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

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

On-the-fly Numerical Surface Integration for Finite-Difference Poisson-Boltzmann Methods.

PubMed

Cai, Qin; Ye, Xiang; Wang, Jun; Luo, Ray

2011-11-01

Most implicit solvation models require the definition of a molecular surface as the interface that separates the solute in atomic detail from the solvent approximated as a continuous medium. Commonly used surface definitions include the solvent accessible surface (SAS), the solvent excluded surface (SES), and the van der Waals surface. In this study, we present an efficient numerical algorithm to compute the SES and SAS areas to facilitate the applications of finite-difference Poisson-Boltzmann methods in biomolecular simulations. Different from previous numerical approaches, our algorithm is physics-inspired and intimately coupled to the finite-difference Poisson-Boltzmann methods to fully take advantage of its existing data structures. Our analysis shows that the algorithm can achieve very good agreement with the analytical method in the calculation of the SES and SAS areas. Specifically, in our comprehensive test of 1,555 molecules, the average unsigned relative error is 0.27% in the SES area calculations and 1.05% in the SAS area calculations at the grid spacing of 1/2Å. In addition, a systematic correction analysis can be used to improve the accuracy for the coarse-grid SES area calculations, with the average unsigned relative error in the SES areas reduced to 0.13%. These validation studies indicate that the proposed algorithm can be applied to biomolecules over a broad range of sizes and structures. Finally, the numerical algorithm can also be adapted to evaluate the surface integral of either a vector field or a scalar field defined on the molecular surface for additional solvation energetics and force calculations.

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.

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.

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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

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.

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.

Reliable solution processed planar perovskite hybrid solar cells with large-area uniformity by chloroform soaking and spin rinsing induced surface precipitation

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

Chern, Yann-Cherng; Wu, Hung-Ruei; Chen, Yen-Chu

2015-08-15

A solvent soaking and rinsing method, in which the solvent was allowed to soak all over the surface followed by a spinning for solvent draining, was found to produce perovskite layers with high uniformity on a centimeter scale and with much improved reliability. Besides the enhanced crystallinity and surface morphology due to the rinsing induced surface precipitation that constrains the grain growth underneath in the precursor films, large-area uniformity with film thickness determined exclusively by the rotational speed of rinsing spinning for solvent draining was observed. With chloroform as rinsing solvent, highly uniform and mirror-like perovskite layers of area asmore » large as 8 cm × 8 cm were produced and highly uniform planar perovskite solar cells with power conversion efficiency of 10.6 ± 0.2% as well as much prolonged lifetime were obtained. The high uniformity and reliability observed with this solvent soaking and rinsing method were ascribed to the low viscosity of chloroform as well as its feasibility of mixing with the solvent used in the precursor solution. Moreover, since the surface precipitation forms before the solvent draining, this solvent soaking and rinsing method may be adapted to spinless process and be compatible with large-area and continuous production. With the large-area uniformity and reliability for the resultant perovskite layers, this chloroform soaking and rinsing approach may thus be promising for the mass production and commercialization of large-area perovskite solar cells.« less

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.

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

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

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.

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.

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

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.

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.

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...

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.

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.

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.

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

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.

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.

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).

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

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

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.

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.

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

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.

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.

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...

Assessing the Impact of Chlorinated-Solvent Sites on Metropolitan Groundwater Resources

PubMed Central

Brusseau, Mark L.; Narter, Matthew

2014-01-01

Chlorinated-solvent compounds are among the most common groundwater contaminants in the U.S.A. The majority of the many sites contaminated by chlorinated-solvent compounds are located in metropolitan areas, and most such areas have one or more chlorinated-solvent contaminated sites. Thus, contamination of groundwater by chlorinated-solvent compounds may pose a potential risk to the sustainability of potable water supplies for many metropolitan areas. The impact of chlorinated-solvent sites on metropolitan water resources was assessed for Tucson, AZ, by comparing the aggregate volume of extracted groundwater for all pump-and-treat systems associated with contaminated sites in the region to the total regional groundwater withdrawal. The analysis revealed that the aggregate volume of groundwater withdrawn for the pump-and-treat systems operating in Tucson, all of which are located at chlorinated-solvent contaminated sites, was 20% of the total groundwater withdrawal in the city for the study period. The treated groundwater was used primarily for direct delivery to local water supply systems or for reinjection as part of the pump-and-treat system. The volume of the treated groundwater used for potable water represented approximately 13% of the total potable water supply sourced from groundwater, and approximately 6% of the total potable water supply. This case study illustrates the significant impact chlorinated-solvent contaminated sites can have on groundwater resources and regional potable-water supplies. PMID:24116872

Atomistic characterization of the active-site solvation dynamics of a model photocatalyst

DOE PAGES

van Driel, Tim B.; Kjær, Kasper S.; Hartsock, Robert W.; ...

2016-11-28

The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir 2(dimen) 4] 2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute–solvent pair distribution function, enabling themore » solvation dynamics around the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis.« less

Intermolecular interaction of thiosemicarbazone derivatives to solvents and a potential Aedes aegypti target

NASA Astrophysics Data System (ADS)

da Silva, João Bosco P.; Hallwass, Fernando; da Silva, Aluizio G.; Moreira, Diogo Rodrigo; Ramos, Mozart N.; Espíndola, José Wanderlan P.; de Oliveira, Ana Daura T.; Brondani, Dalci José; Leite, Ana Cristina L.; Merz, Kenneth M.

2015-08-01

DFT calculations were used to access information about structure, energy and electronic properties of series of phenyl- and phenoxymethyl-(thio)semicarbazone derivatives with demonstrated activity against the larvae of Aedes aegypti in stage L4. The way as the thiosemicarbazone derivatives can interact with solvents like DMSO and water were analyzed from the comparison between calculated and experimental 1H NMR chemical shifts. The evidences of thiosemicarbazone derivatives making H-bond interaction to solvent have provide us insights on how they can interact with a potential A. aegypti's biological target, the Sterol Carrier Protein-2.

Determination of water traces in various organic solvents using Karl Fischer method under FIA conditions.

PubMed

Dantan, N; Frenzel, W; Küppers, S

2000-05-31

Flow injection methods utilising the Karl Fischer (KF) reaction with spectrophotometric and potentiometric detection are described for the determination of the trace water content in various organic solvents. Optimisation of the methods resulted in an accessible (linear) working range of 0.01-0.2% water for many solvents studied with a typical precision of 1-2% R.S.D. Only 50 mul of organic solvent was injected and the sampling frequency was about 120 samples per h. Since the slopes of the calibration curves were different for different solvents appropriate calibration was required. Problems associated with spectrophotometric detection and caused by refractive index changes were pointed out and a nested-loop configuration was proposed to overcome this kind of interference. The potentiometric method with a novel flow-through detector cell was shown to surpass the performance of spectrophotometric detection in any respect. The characteristics of the procedures developed made them well applicable for on-line monitoring of technical solvent distillations in an industrial plant.

Peptide chain dynamics in light and heavy water: zooming in on internal friction.

PubMed

Schulz, Julius C F; Schmidt, Lennart; Best, Robert B; Dzubiella, Joachim; Netz, Roland R

2012-04-11

Frictional effects due to the chain itself, rather than the solvent, may have a significant effect on protein dynamics. Experimentally, such "internal friction" has been investigated by studying folding or binding kinetics at varying solvent viscosity; however, the molecular origin of these effects is hard to pinpoint. We consider the kinetics of disordered glycine-serine and α-helix forming alanine peptides and a coarse-grained protein folding model in explicit-solvent molecular dynamics simulations. By varying the solvent mass over more than two orders of magnitude, we alter only the solvent viscosity and not the folding free energy. Folding dynamics at the near-vanishing solvent viscosities accessible by this approach suggests that solvent and internal friction effects are intrinsically entangled. This finding is rationalized by calculation of the polymer end-to-end distance dynamics from a Rouse model that includes internal friction. An analysis of the friction profile along different reaction coordinates, extracted from the simulation data, demonstrates that internal as well as solvent friction varies substantially along the folding pathways and furthermore suggests a connection between friction and the formation of hydrogen bonds upon folding. © 2012 American Chemical Society

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

Effects of dilute aqueous NaCl solution on caffeine aggregation

NASA Astrophysics Data System (ADS)

Sharma, Bhanita; Paul, Sandip

2013-11-01

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

Effects of dilute aqueous NaCl solution on caffeine aggregation

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

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

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

X-ray diffraction measurement of cosolvent accessible volume in rhombohedral insulin crystals

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

Soares, Alexei S.; Caspar, Donald L. D.

We report x-ray crystallographic measurement of the number of solvent electrons in the unit cell of a protein crystal equilibrated with aqueous solutions of different densities provides information about preferential hydration in the crystalline state. Room temperature and cryo-cooled rhombohedral insulin crystals were equilibrated with 1.2 M trehalose to study the effect of lowered water activity. The native and trehalose soaked crystals were isomorphous and had similar structures. Including all the low resolution data, the amplitudes of the structure factors were put on an absolute scale (in units of electrons per asymmetric unit) by constraining the integrated number of electronsmore » inside the envelope of the calculated protein density map to equal the number deduced from the atomic model. This procedure defines the value of F(0 0 0), the amplitude at the origin of the Fourier transform, which is equal to the total number of electrons in the asymmetric unit (i.e. protein plus solvent). Comparison of the F(0 0 0) values for three isomorphous pairs of room temperature insulin crystals, three with trehalose and three without trehalose, indicates that 75 ± 12 electrons per asymmetric unit were added to the crystal solvent when soaked in 1.2 M trehalose. If all the water in the crystal were available as solvent for the trehalose, 304 electrons would have been added. Thus, the co-solvent accessible volume is one quarter of the total water in the crystal. Finally, determination of the total number of electrons in a protein crystal is an essential first step for mapping the average density distribution of the disordered solvent.« less

X-ray diffraction measurement of cosolvent accessible volume in rhombohedral insulin crystals

DOE PAGES

Soares, Alexei S.; Caspar, Donald L. D.

2017-08-31

We report x-ray crystallographic measurement of the number of solvent electrons in the unit cell of a protein crystal equilibrated with aqueous solutions of different densities provides information about preferential hydration in the crystalline state. Room temperature and cryo-cooled rhombohedral insulin crystals were equilibrated with 1.2 M trehalose to study the effect of lowered water activity. The native and trehalose soaked crystals were isomorphous and had similar structures. Including all the low resolution data, the amplitudes of the structure factors were put on an absolute scale (in units of electrons per asymmetric unit) by constraining the integrated number of electronsmore » inside the envelope of the calculated protein density map to equal the number deduced from the atomic model. This procedure defines the value of F(0 0 0), the amplitude at the origin of the Fourier transform, which is equal to the total number of electrons in the asymmetric unit (i.e. protein plus solvent). Comparison of the F(0 0 0) values for three isomorphous pairs of room temperature insulin crystals, three with trehalose and three without trehalose, indicates that 75 ± 12 electrons per asymmetric unit were added to the crystal solvent when soaked in 1.2 M trehalose. If all the water in the crystal were available as solvent for the trehalose, 304 electrons would have been added. Thus, the co-solvent accessible volume is one quarter of the total water in the crystal. Finally, determination of the total number of electrons in a protein crystal is an essential first step for mapping the average density distribution of the disordered solvent.« less

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.

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.

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

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.

Molecular accessibility in solvent swelled coal

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

Kispert, L.D.

1991-08-01

Research continued on the determination of pore size and number distribution changes after swelling the coal samples with various solvents. A paper has just been submitted to the journal Fuel on the Low temperature Swelling of Argonne Premium Coal samples using solvents of varying polarity. The variation in the shape of the pore was followed as a function of temperature and swelling solvent polarity. This change in pore structure was attributed to break-up of the hydrogen bonding network in coal by polar solvents. The modification in pore shape from spherical to cylindrical was attributed to anisotropy in hydrogen bond densities.more » A copy of this paper has been attached to this report. Wojciech Sady has determine the structural changes in the pores that occur when APCS coal is dehydrated prior to swelling with polar solvents. These changes are different from those that occur in the absence of prior dehydration. He has also completed a study on the variation in the hydrogen bonding character of the pore wall as the coals are swelled with various polar solvents. A statistical analysis of the data is currently underway to determine important trends in his data. 9 refs.« less

Comparative study of corn stover pretreated by dilute acid and cellulose solvent-based lignocellulose fractionation: Enzymatic hydrolysis, supramolecular structure, and substrate accessibility.

PubMed

Zhu, Zhiguang; Sathitsuksanoh, Noppadon; Vinzant, Todd; Schell, Daniel J; McMillan, James D; Zhang, Y-H Percival

2009-07-01

Liberation of fermentable sugars from recalcitrant biomass is among the most costly steps for emerging cellulosic ethanol production. Here we compared two pretreatment methods (dilute acid, DA, and cellulose solvent and organic solvent lignocellulose fractionation, COSLIF) for corn stover. At a high cellulase loading [15 filter paper units (FPUs) or 12.3 mg cellulase per gram of glucan], glucan digestibilities of the corn stover pretreated by DA and COSLIF were 84% at hour 72 and 97% at hour 24, respectively. At a low cellulase loading (5 FPUs per gram of glucan), digestibility remained as high as 93% at hour 24 for the COSLIF-pretreated corn stover but reached only approximately 60% for the DA-pretreated biomass. Quantitative determinations of total substrate accessibility to cellulase (TSAC), cellulose accessibility to cellulase (CAC), and non-cellulose accessibility to cellulase (NCAC) based on adsorption of a non-hydrolytic recombinant protein TGC were measured for the first time. The COSLIF-pretreated corn stover had a CAC of 11.57 m(2)/g, nearly twice that of the DA-pretreated biomass (5.89 m(2)/g). These results, along with scanning electron microscopy images showing dramatic structural differences between the DA- and COSLIF-pretreated samples, suggest that COSLIF treatment disrupts microfibrillar structures within biomass while DA treatment mainly removes hemicellulose. Under the tested conditions COSLIF treatment breaks down lignocellulose structure more extensively than DA treatment, producing a more enzymatically reactive material with a higher CAC accompanied by faster hydrolysis rates and higher enzymatic digestibility. (c) 2009 Wiley Periodicals, Inc.

Structural Refinement of Membrane Proteins by Restrained Molecular Dynamics and Solvent Accessibility Data

PubMed Central

Sompornpisut, Pornthep; Roux, Benoît; Perozo, Eduardo

2008-01-01

We present an approach for incorporating solvent accessibility data from electron paramagnetic resonance experiments in the structural refinement of membrane proteins through restrained molecular dynamics simulations. The restraints have been parameterized from oxygen (ΠO2) and nickel-ethylenediaminediacetic acid (ΠNiEdda) collision frequencies, as indicators of lipid or aqueous exposed spin-label sites. These are enforced through interactions between a pseudoatom representation of the covalently attached Nitroxide spin-label and virtual “solvent” particles corresponding to O2 and NiEdda in the surrounding environment. Interactions were computed using an empirical potential function, where the parameters have been optimized to account for the different accessibilities of the spin-label pseudoatoms to the surrounding environment. This approach, “pseudoatom-driven solvent accessibility refinement”, was validated by refolding distorted conformations of the Streptomyces lividans potassium channel (KcsA), corresponding to a range of 2–30 Å root mean-square deviations away from the native structure. Molecular dynamics simulations based on up to 58 electron paramagnetic resonance restraints derived from spin-label mutants were able to converge toward the native structure within 1–3 Å root mean-square deviations with minimal computational cost. The use of energy-based ranking and structure similarity clustering as selection criteria helped in the convergence and identification of correctly folded structures from a large number of simulations. This approach can be applied to a variety of integral membrane protein systems, regardless of oligomeric state, and should be particularly useful in calculating conformational changes from a known reference crystal structure. PMID:18676641

A fluorescent paramagnetic Mn metal–organic framework based on semi-rigid pyrene tetra­carboxylic acid: sensing of solvent polarity and explosive nitroaromatics

PubMed Central

Bajpai, Alankriti; Mukhopadhyay, Arindam; Krishna, Manchugondanahalli Shivakumar; Govardhan, Savitha; Moorthy, Jarugu Narasimha

2015-01-01

An Mn metal–organic framework (Mn-MOF), Mn-L, based on a pyrene-tetraacid linker (H4 L), displays a respectable fluorescence quantum yield of 8.3% in spite of the presence of the paramagnetic metal ions, due presumably to fixation of the metal ions in geometries that do not allow complete energy/charge-transfer quenching. Remarkably, the porous Mn-L MOF with ∼25% solvent-accessible volume exhibits a heretofore unprecedented solvent-dependent fluorescence emission maximum, permitting its use as a probe of solvent polarity; the emission maxima in different solvents correlate excellently with Reichardt’s solvent polarity parameter (E T N). Further, the applicability of Mn-L to the sensing of nitroaromatics via fluorescence quenching is demonstrated; the detection limit for TNT is shown to be 125 p.p.m. The results bring out the fact that MOFs based on paramagnetic metal ions can indeed find application when the quenching mechanisms are attenuated by certain geometries of the organic linkers of the MOF. PMID:26306197

A fluorescent paramagnetic Mn metal-organic framework based on semi-rigid pyrene tetra-carboxylic acid: sensing of solvent polarity and explosive nitroaromatics.

PubMed

Bajpai, Alankriti; Mukhopadhyay, Arindam; Krishna, Manchugondanahalli Shivakumar; Govardhan, Savitha; Moorthy, Jarugu Narasimha

2015-09-01

An Mn metal-organic framework (Mn-MOF), Mn-L, based on a pyrene-tetraacid linker (H4 L), displays a respectable fluorescence quantum yield of 8.3% in spite of the presence of the paramagnetic metal ions, due presumably to fixation of the metal ions in geometries that do not allow complete energy/charge-transfer quenching. Remarkably, the porous Mn-L MOF with ∼25% solvent-accessible volume exhibits a heretofore unprecedented solvent-dependent fluorescence emission maximum, permitting its use as a probe of solvent polarity; the emission maxima in different solvents correlate excellently with Reichardt's solvent polarity parameter (E T (N)). Further, the applicability of Mn-L to the sensing of nitroaromatics via fluorescence quenching is demonstrated; the detection limit for TNT is shown to be 125 p.p.m. The results bring out the fact that MOFs based on paramagnetic metal ions can indeed find application when the quenching mechanisms are attenuated by certain geometries of the organic linkers of the MOF.

Fluorescent pseudorotaxanes of a quinodicarbocyanine dye with gamma cyclodextrin

NASA Astrophysics Data System (ADS)

Bernstein, Olivia M.; McGee, Tiffany E.; Silzel, Lisa E.; Silzel, John W.

2018-01-01

Spectrophotometric titration of buffered solutions of gamma cyclodextrin (γCD) and 1,1‧-diethyl,2,2‧-dicarbocyanine (DDI) demonstrates extension of the known 1:2 host:guest complex to form a previously unreported 2:2 complex near the γCD solubility limit. Though DDI is predominantly hosted as a non-fluorescent H-aggregate, both complexes exist in respective equilibria with two secondary complexes hosting unaggregated DDI as 1:1 and 2:1 complexes. The 2:1 complex exhibits significant fluorescence emission, with a quantum yield six times that of DDI in organic solvents, but ten times lower than that of an analogous indodicarbocyanine. Fragment Molecular Orbital calculations suggest that the 2:1 complex has the tail-to-tail conformation, and that solvent access to the dye strongly favors photoisomerization. In the host-guest complex, γCD limits solvent access to the dye and hinders rotation of the quinolyl terminal groups, but nevertheless pairwise rotation of methine carbons within the γCD cavity likely remains as a significant nonradiative relaxation pathway for the excited state.

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.

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.

Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility.

PubMed

Zhang, Hua; Zhang, Tuo; Gao, Jianzhao; Ruan, Jishou; Shen, Shiyi; Kurgan, Lukasz

2012-01-01

Proteins fold through a two-state (TS), with no visible intermediates, or a multi-state (MS), via at least one intermediate, process. We analyze sequence-derived factors that determine folding types by introducing a novel sequence-based folding type predictor called FOKIT. This method implements a logistic regression model with six input features which hybridize information concerning amino acid composition and predicted secondary structure and solvent accessibility. FOKIT provides predictions with average Matthews correlation coefficient (MCC) between 0.58 and 0.91 measured using out-of-sample tests on four benchmark datasets. These results are shown to be competitive or better than results of four modern predictors. We also show that FOKIT outperforms these methods when predicting chains that share low similarity with the chains used to build the model, which is an important advantage given the limited number of annotated chains. We demonstrate that inclusion of solvent accessibility helps in discrimination of the folding kinetic types and that three of the features constitute statistically significant markers that differentiate TS and MS folders. We found that the increased content of exposed Trp and buried Leu are indicative of the MS folding, which implies that the exposure/burial of certain hydrophobic residues may play important role in the formation of the folding intermediates. Our conclusions are supported by two case studies.

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

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

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.

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

Impact of solvent granularity and layering on tracer hydrodynamics in confinement.

PubMed

Bollinger, Jonathan A; Carmer, James; Jain, Avni; Truskett, Thomas M

2016-11-28

Classic hydrodynamic arguments establish that when a spherical tracer particle is suspended between parallel walls, tracer-wall coupling mediated by the solvent will cause the tracer to exhibit position-dependent diffusivity. We investigate how the diffusivity profiles of confined tracers are impacted by the diameter size-ratio of the tracer to solvent: starting from the classic limit of infinite size-ratio (i.e., continuum solvent), we consider size-ratios of four or less to examine how hydrodynamic predictions are disrupted for systems where the tracer and solvent are of similar scale. We use computer simulations and techniques based on the Fokker-Planck formalism to calculate the diffusivity profiles of hard-sphere tracer particles in hard-sphere solvents, focusing on the dynamics perpendicular to the walls. Given wall separations of several tracer diameters, we first consider confinement between hard walls, where anisotropic structuring at the solvent lengthscale generates inhomogeneity in the tracer free-energy landscape and undermines hydrodynamic predictions locally. We then introduce confining planes that we term transparent walls, which restrict tracer and solvent center-accessibilities while completely eliminating static anisotropy, and reveal position-dependent signatures in tracer diffusivity solely attributable to confinement. With or without suppressing static heterogeneity, we find that tracer diffusivity increasingly deviates on a local basis from hydrodynamic predictions at smaller size-ratios. However, hydrodynamic theory still approximately captures spatially-averaged dynamics across the pores even for very small tracer-solvent size-ratios over a wide range of solvent densities and wall separations.

Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins

PubMed Central

Shcherbakova, Inna; Mitra, Somdeb; Beer, Robert H.; Brenowitz, Michael

2006-01-01

‘Footprinting’ describes assays in which ligand binding or structure formation protects polymers such as nucleic acids and proteins from either cleavage or modification; footprinting allows the accessibility of individual residues to be mapped in solution. Equilibrium and time-dependent footprinting links site-specific structural information with thermodynamic and kinetic transitions. The hydroxyl radical (·OH) is a particularly valuable footprinting probe by virtue of it being among the most reactive of chemical oxidants; it reports the solvent accessibility of reactive sites on macromolecules with as fine as a single residue resolution. A novel method of millisecond time-resolved ·OH footprinting has been developed based on the Fenton reaction, Fe(II) + H2O2 → Fe(III) + ·OH + OH−. This method can be implemented in laboratories using widely available three-syringe quench flow mixers and inexpensive reagents to study local changes in the solvent accessibility of DNA, RNA and proteins associated with their biological function. PMID:16582097

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.

Hazardous Waste Cleanup: Pride Solvents and Chemicals Incorporated in West Babylon, New York

EPA Pesticide Factsheets

Pride Solvents and Chemicals, Inc. (Pride Solvents) is located at 78 and 88 Lamar Street within the West Babylon Industrial Area of Suffolk County, New York. The site consists of two buildings, adjacent parking lots, and a loading dock on a 1.38 acre

Elman RNN based classification of proteins sequences on account of their mutual information.

PubMed

Mishra, Pooja; Nath Pandey, Paras

2012-10-21

In the present work we have employed the method of estimating residue correlation within the protein sequences, by using the mutual information (MI) of adjacent residues, based on structural and solvent accessibility properties of amino acids. The long range correlation between nonadjacent residues is improved by constructing a mutual information vector (MIV) for a single protein sequence, like this each protein sequence is associated with its corresponding MIVs. These MIVs are given to Elman RNN to obtain the classification of protein sequences. The modeling power of MIV was shown to be significantly better, giving a new approach towards alignment free classification of protein sequences. We also conclude that sequence structural and solvent accessible property based MIVs are better predictor. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

Structural changes in block copolymer micelles induced by cosolvent mixtures†

PubMed Central

Kelley, Elizabeth G.; Smart, Thomas P.; Jackson, Andrew J.; Sullivan, Millicent O.

2013-01-01

We investigated the influence of tetrahydrofuran (THF) addition on the structure of poly(1,2-butadiene-b-ethylene oxide) [PB-PEO] micelles in aqueous solution. Our studies showed that while the micelles remained starlike, the micelle core-corona interfacial tension and micelle size decreased upon THF addition. The detailed effects of the reduction in interfacial tension were probed using contrast variations in small angle neutron scattering (SANS) experiments. At low THF contents (high interfacial tensions), the SANS data were fit to a micelle form factor that incorporated a radial density distribution of corona chains to account for the starlike micelle profile. However, at higher THF contents (low interfacial tensions), the presence of free chains in solution affected the scattering at high q and required the implementation of a linear combination of micelle and Gaussian coil form factors. These SANS data fits indicated that the reduction in interfacial tension led to broadening of the core-corona interface, which increased the PB chain solvent accessibility at intermediate THF solvent fractions. We also noted that the micelle cores swelled with increasing THF addition, suggesting that previous assumptions of the micelle core solvent content in cosolvent mixtures may not be accurate. Control over the size, corona thickness, and extent of solvent accessible PB in these micelles can be a powerful tool in the development of targeting delivery vehicles. PMID:24282441

Structural changes in block copolymer micelles induced by cosolvent mixtures

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

Kelley, Elizabeth G.; Smart, Thomas P.; Jackson, Andrew J.

2012-11-26

We investigated the influence of tetrahydrofuran (THF) addition on the structure of poly(1,2-butadiene-b-ethylene oxide) [PB-PEO] micelles in aqueous solution. Our studies showed that while the micelles remained starlike, the micelle core-corona interfacial tension and micelle size decreased upon THF addition. The detailed effects of the reduction in interfacial tension were probed using contrast variations in small angle neutron scattering (SANS) experiments. At low THF contents (high interfacial tensions), the SANS data were fit to a micelle form factor that incorporated a radial density distribution of corona chains to account for the starlike micelle profile. However, at higher THF contents (lowmore » interfacial tensions), the presence of free chains in solution affected the scattering at high q and required the implementation of a linear combination of micelle and Gaussian coil form factors. These SANS data fits indicated that the reduction in interfacial tension led to broadening of the core-corona interface, which increased the PB chain solvent accessibility at intermediate THF solvent fractions. We also noted that the micelle cores swelled with increasing THF addition, suggesting that previous assumptions of the micelle core solvent content in cosolvent mixtures may not be accurate. Control over the size, corona thickness, and extent of solvent accessible PB in these micelles can be a powerful tool in the development of targeting delivery vehicles.« less

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.

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.

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.

Studying the Structure and Dynamics of Biomolecules by Using Soluble Paramagnetic Probes

PubMed Central

Hocking, Henry G; Zangger, Klaus; Madl, Tobias

2013-01-01

Characterisation of the structure and dynamics of large biomolecules and biomolecular complexes by NMR spectroscopy is hampered by increasing overlap and severe broadening of NMR signals. As a consequence, the number of available NMR spectroscopy data is often sparse and new approaches to provide complementary NMR spectroscopy data are needed. Paramagnetic relaxation enhancements (PREs) obtained from inert and soluble paramagnetic probes (solvent PREs) provide detailed quantitative information about the solvent accessibility of NMR-active nuclei. Solvent PREs can be easily measured without modification of the biomolecule; are sensitive to molecular structure and dynamics; and are therefore becoming increasingly powerful for the study of biomolecules, such as proteins, nucleic acids, ligands and their complexes in solution. In this Minireview, we give an overview of the available solvent PRE probes and discuss their applications for structural and dynamic characterisation of biomolecules and biomolecular complexes. PMID:23836693

Localized conformational interrogation of antibody and antibody-drug conjugates by site-specific carboxyl group footprinting.

PubMed

Pan, Lucy Yan; Salas-Solano, Oscar; Valliere-Douglass, John F

Establishing and maintaining conformational integrity of monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs) during development and manufacturing is critical for ensuring their clinical efficacy. As presented here, we applied site-specific carboxyl group footprinting (CGF) for localized conformational interrogation of mAbs. The approach relies on covalent labeling that introduces glycine ethyl ester tags onto solvent-accessible side chains of protein carboxylates. Peptide mapping is used to monitor the labeling kinetics of carboxyl residues and the labeling kinetics reflects the conformation or solvent-accessibility of side chains. Our results for two case studies are shown here. The first study was aimed at defining the conformational changes of mAbs induced by deglycosylation. We found that two residues in C H 2 domain (D268 and E297) show significantly enhanced side chain accessibility upon deglycosylation. This site-specific result highlighted the advantage of monitoring the labeling kinetics at the amino acid level as opposed to the peptide level, which would result in averaging out of highly localized conformational differences. The second study was designed to assess conformational effects brought on by conjugation of mAbs with drug-linkers. All 59 monitored carboxyl residues displayed similar solvent-accessibility between the ADC and mAb under native conditions, which suggests the ADC and mAb share similar side chain conformation. The findings are well correlated and complementary with results from other assays. This work illustrated that site-specific CGF is capable of pinpointing local conformational changes in mAbs or ADCs that might arise during development and manufacturing. The methodology can be readily implemented within the industry to provide comprehensive conformational assessment of these molecules.

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.

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

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.

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.

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.

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.

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.

Measuring Solvent Content of Macromolecular Crystals Using Fluorescence Recovery after Photobleaching

NASA Astrophysics Data System (ADS)

Siewny, Matthew; Kmetko, Jan

2010-10-01

We work out a novel protocol for measuring the solvent content (the fraction of crystal volume occupied by solvent) in biological crystals by the technique of fluorescence recovery after photobleaching (FRAP). Crystals of proteins with widely varying known solvent content (lysozyme, thaumatin, catalase, and ferritin) were grown in their native solution doped with sodium fluorescein dye and hydroxylamine (to prevent dye from binding to amine groups of the proteins.) The crystals were irradiated by a broadband, high intensity light through knife slits, leaving a rectangular area of bleached dye within the crystals. Measuring the flow of dye out of the bleached area allowed us to construct a curve relating the diffusion coefficient of dye to the channel size within the crystals, by solving the diffusion equation analytically. This curve may be used to measure the solvent content of any biological crystal in its native solution and help determine the number of proteins in the crystallographic asymmetric unit cell in x-ray structure solving procedures.

Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase.

PubMed

Sen, Kakali; Horrell, Sam; Kekilli, Demet; Yong, Chin W; Keal, Thomas W; Atakisi, Hakan; Moreau, David W; Thorne, Robert E; Hough, Michael A; Strange, Richard W

2017-07-01

Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (Asp CAT and His CAT ) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the Asp CAT protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site 'capping residue' (Ile CAT ), a determinant of ligand binding, are influenced both by temperature and by the protonation state of Asp CAT . A previously unobserved conformation of Ile CAT is seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom.

Direct construction of diverse metallophthalocyanines by manifold substrates in a deep eutectic solvent

NASA Astrophysics Data System (ADS)

Shaabani, Ahmad; Hooshmand, Seyyed Emad; Afshari, Ronak; Shaabani, Shabnam; Ghasemi, Vahid; Atharnezhad, Mojtaba; Akbari, Masoud

2018-02-01

Direct access to a wide range of metal-free phthalocyanines and metallophthalocyanines in deep eutectic solvents (DESs), is reported. Substituted and unsubstituted phthalocyanines of Mn, Fe, Co, Ni, Cu, Zn, Pd, In, and Pt with various raw materials such as phthalonitriles, phthalimides, phthalic anhydrides and phthalic acids are successfully prepared in the DES based on choline chloride and urea in a very short reaction time with appropriate yields. It has been shown that DES as a green and rapidly degraded reaction medium in the environment plays a triple role as a solvent, organocatalyst, and reactant in this process. Moreover, the DES system could be separated and reused in four consecutive reaction runs with no considerable loss in catalytic activity.

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.

MoleculaRnetworks: an integrated graph theoretic and data mining tool to explore solvent organization in molecular simulation.

PubMed

Mooney, Barbara Logan; Corrales, L René; Clark, Aurora E

2012-03-30

This work discusses scripts for processing molecular simulations data written using the software package R: A Language and Environment for Statistical Computing. These scripts, named moleculaRnetworks, are intended for the geometric and solvent network analysis of aqueous solutes and can be extended to other H-bonded solvents. New algorithms, several of which are based on graph theory, that interrogate the solvent environment about a solute are presented and described. This includes a novel method for identifying the geometric shape adopted by the solvent in the immediate vicinity of the solute and an exploratory approach for describing H-bonding, both based on the PageRank algorithm of Google search fame. The moleculaRnetworks codes include a preprocessor, which distills simulation trajectories into physicochemical data arrays, and an interactive analysis script that enables statistical, trend, and correlation analysis, and other data mining. The goal of these scripts is to increase access to the wealth of structural and dynamical information that can be obtained from molecular simulations. Copyright © 2012 Wiley Periodicals, Inc.

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.

51. BUILDING NO. 533, SOLVENT RECOVERY BUILDING, LOOKING WEST AT ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

51. BUILDING NO. 533, SOLVENT RECOVERY BUILDING, LOOKING WEST AT SOUTHEAST (REAR) ELEVATION. - Picatinny Arsenal, 500 Area, Powder Factory & Power House, State Route 15 near I-80, Dover, Morris County, NJ

Anionic microemulsion to solvent stacking for on-line sample concentration of cationic analytes in capillary electrophoresis.

PubMed

Kukusamude, Chunyapuk; Srijaranai, Supalax; Quirino, Joselito P

2014-05-01

The common SDS microemulsion (i.e. 3.3% SDS, 0.8% octane, and 6.6% butanol) and organic solvents were investigated for the stacking of cationic drugs in capillary zone electrophoresis using a low pH separation electrolyte. The sample was prepared in the acidic microemulsion and a high percentage of organic solvent was included in the electrolyte at anodic end of capillary. The stacking mechanism was similar to micelle to solvent stacking where the micelles were replaced by the microemulsion for the transport of analytes to the organic solvent rich boundary. This boundary is found between the microemulsion and anodic electrolyte. The effective electrophoretic mobility of the cations reversed from the direction of the anode in the microemulsion to the cathode in the boundary. Microemulsion to solvent stacking was successfully achieved with 40% ACN in the anodic electrolyte and hydrodynamic sample injection of 21 s at 1000 mbar (equivalent to 30% of the effective length). The sensitivity enhancement factors in terms of peak height and corrected peak area were 15 to 35 and 21 to 47, respectively. The linearity R(2) in terms of corrected peak area were >0.999. Interday precisions (%RSD, n = 6) were 3.3-4.0% for corrected peak area and 2.0-3.0% for migration time. Application to spiked real sample is also presented. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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

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.

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.

Solvent and substituent effects on aggregation constants of perylene bisimide π-stacks--a linear free energy relationship analysis.

PubMed

Chen, Zhijian; Fimmel, Benjamin; Würthner, Frank

2012-08-14

A series of six perylene bisimides (PBIs) with hydrophilic and hydrophobic side chains at the imide nitrogens were applied for a comparative study of the solvent and structural effects on the aggregation behaviour of this class of dyes. A comparison of the binding constants in tetrachloromethane at room temperature revealed the highest binding constant of about 10(5) M(-1) for a PBI bearing 3,4,5-tridodecyloxyphenyl substituents at the imide nitrogens, followed by 3,4,5-tridodecylphenyl and alkyl-substituted PBIs, whereas no aggregation could be observed in the accessible concentration range for PBIs equipped with bulky 2,6-diisopropylphenyl substituents at the imide nitrogens. The aggregation behaviour of three properly soluble compounds was investigated in 17 different solvents covering a broad polarity range from nonpolar n-hexane to highly polar DMSO and water. Linear free energy relationships (LFER) revealed a biphasic behaviour between Gibbs free energies of aggregation and common empirical solvent polarity scales indicating particularly strong π-π stacking interactions in nonpolar aliphatic and polar alcoholic solvents whilst the weakest binding is observed in dichloromethane and chloroform. Accordingly, PBI aggregation is dominated by electrostatic interactions in nonpolar solvents and by solvophobic interactions in protic solvents. In water, the aggregation constant is increased far beyond LFER expectations pointing at a pronounced hydrophobic effect.

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.

25. BUILDING NO. 527, DEHYDRATING HOUSE, DETAIL OF SOLVENT RECOVERY ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

25. BUILDING NO. 527, DEHYDRATING HOUSE, DETAIL OF SOLVENT RECOVERY DUCTS. SOUTH SIDE OF BUILDING. - Picatinny Arsenal, 500 Area, Powder Factory & Power House, State Route 15 near I-80, Dover, Morris County, NJ

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

Organic solvent tolerance of an α-amylase from haloalkaliphilic bacteria as a function of pH, temperature, and salt concentrations.

PubMed

Pandey, Sandeep; Singh, S P

2012-04-01

A haloalkaliphilic bacterium was isolated from salt-enriched soil of Mithapur, Gujarat (India) and identified as Bacillus agaradhaerens Mi-10-6₂ based on 16S rRNA sequence analysis (NCBI gene bank accession, GQ121032). The bacterium was studied for its α-amylase characteristic in the presence of organic solvents. The enzyme was quite active and it retained considerable activity in 30% (v/v) organic solvents, dodecane, decane, heptane, n-hexane, methanol, and propanol. At lower concentrations of solvents, the catalysis was quite comparable to control. Enzyme catalysis at wide range of alkanes and alcohol was an interesting finding of the study. Mi-10-6₂ amylase retained activity over a broader alkaline pH range, with the optimal pH at 10-11. Two molars of salt was optimum for catalysis in the presence of most of the tested solvents, though the enzyme retained significant activity even at 4 M salt. With dodecane, the optimum temperature shifted from 50 °C to 60 °C, while the enzyme was active up to 80 °C. Over all, the present study focused on the effect of organic solvents on an extracellular α-amylase from haloalkaliphilic bacteria under varying conditions of pH, temperature, and salt.

Solvent Effects of Model Polymeric Corrosion Control Coatings on Water Transport and Corrosion Rate

NASA Astrophysics Data System (ADS)

Konecki, Christina

Industrial coating formulations are often made for volatile organic content compliance and ease of application, with little regard for the solvent impact on resultant performance characteristics. Our research objective was to understand the effect of both solvent retention and chemical structure on water transport through polymer films and resultant corrosion area growth of coated steel substrates. A clear, unpigmented Phenoxy(TM) thermoplastic polymer (PKHH) was formulated into resin solutions with three separate solvent blends selected by Hansen solubility parameter (HSP), boiling point, and ability to solubilize PKHH. Polymer films cast from MEK/PGME (methyl ethyl ketone/ propylene glycol methyl ether), dried under ambient conditions (AMB, > 6wt.% residual solvent) produced a porous morphology, which resulted in a corrosion area greater than 50%. We attributed this to the water-soluble solvent used in film preparation, which enabled residual PGME to be extracted by water. The resin solution prepared with CYCOH/DXL (Cyclohexanol/ 1,3 dioxolane) was selected because CYCOH is a solid at room temperature which acts as a pigment in the final film. Therefore, increasing the tortuosity of water transport, as well as a high hydrogen bonding character, which caused more interactions with water, slowing diffusion, producing a nodular morphology, and 37% less corrosion area than MEK/PGME AMB. The HSP of PKHH and EEP (ethyl 3-ethoxypropionate) are within 5% of each other, which produced a homogeneous morphology and resulted in comparable corrosion rates regardless of residual solvent content. We utilized electrochemical techniques and attenuated total reflectance- Fourier transform infrared spectroscopy to elucidate dynamic water absorption and solvent extraction in the exposed model formulations. We found that water absorption resulted in a loss of barrier properties, and increased corrosion due to the voids formed by solvent extraction. The polymer films were rejuvenated (removal of water) as an attempt to decrease the number of water transport pathways during exposure. Results found that samples rejuvenated at temperatures above the glass transition temperature of the samples achieved lower moisture content and consequently, lower corrosion growth rates. In commercial systems, rejuvenation lowered the corrosion rate up to 60% indicating better coating formulations and maintenance cycles would control the corrosion rate.

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.

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.

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

Determination of Selected Distillate Blending Solvents in Simple and Complex Aircraft Fuel Matrices Via Glass Capillary Gas Chromatography.

DTIC Science & Technology

1981-06-01

Division OCT 1 5 1981 June 1981 B Final Report for Period January 1979 - December 1979 j Approved for Public Release; Distribution Unlimited.-I AERO...Solvent 2040 *2040 Blending Solvent Xylene Bottoms *Xylene Bottoms Blending Solvent *Reference: Gleason, C. C., Oller , T. L. Shayeson, M. W., and Bahr...Table 4) was realistic for a 0% by volume point, 17 AFWAL- TR-80-2082 U J & J 18, AFWAL-TR-80-2082 TABLE 4 PEAK AREA PERCENTAGES FOUND IN EACH UNIQUE

Exploiting Deep Eutectic Solvents and Organolithium Reagent Partnerships: Chemoselective Ultrafast Addition to Imines and Quinolines Under Aerobic Ambient Temperature Conditions.

PubMed

Vidal, Cristian; García-Álvarez, Joaquín; Hernán-Gómez, Alberto; Kennedy, Alan R; Hevia, Eva

2016-12-23

Shattering the long-held dogma that organolithium chemistry needs to be performed under inert atmospheres in toxic organic solvents, chemoselective addition of organolithium reagents to non-activated imines and quinolines has been accomplished in green, biorenewable deep eutectic solvents (DESs) at room temperature and in the presence of air, establishing a novel and sustainable access to amines. Improving on existing methods, this approach proceeds in the absence of additives; occurs without competitive enolization, reduction or coupling processes; and reactions were completed in seconds. Comparing RLi reactivities in DESs with those observed in pure glycerol or THF suggests a kinetic anionic activation of the alkylating reagents occurs, favoring nucleophilic addition over competitive hydrolysis. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Hydroperoxide Traces in Common Cyclic Ethers as Initiators for Controlled RAFT Polymerizations.

PubMed

Eggers, Steffen; Abetz, Volker

2018-04-01

Herein, a reversible addition-fragmentation chain transfer (RAFT) polymerization is introduced for reactive monomers like N-acryloylpyrrolidine or N,N-dimethylacrylamide working without a conventional radical initiator. As a very straightforward proof of principle, the method takes advantage of the usually inconvenient radical-generating hydroperoxide contaminations in cyclic ethers like tetrahydrofuran or 1,4-dioxane, which are very common solvents in polymer sciences. The polymerizations are surprisingly well controlled and the polymers can be extended with a second block, indicating their high livingness. "Solvent-initiated" RAFT polymerizations hence prove to be a feasible access to tailored materials with minimal experimental effort and standard laboratory equipment, only requiring the following ingredients: hydroperoxide-contaminated solvent, monomer, and RAFT agent. In other respects, however, the potential coinitiating ability of the used solvent is to be considered when investigating the kinetics of RAFT polymerizations or aiming for the synthesis of high-livingness polymers, e.g., multiblock copolymers. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigation of the potential source area, contamination pathway, and probable release history of chlorinated-solvent-contaminated groundwater at the Capital City Plume Site, Montgomery, Alabama, 2008-2010

USGS Publications Warehouse

Landmeyer, James E.; Miller, Scott; Campbell, Bruce G.; Vroblesky, Don A.; Gill, Amy C.; Clark, Athena P.

2011-01-01

Detection of the organic solvent perchloroethylene (PCE) in a shallow public-supply well in 1991 and exposure of workers in 1993 to solvent vapors during excavation activities to depths near the water table provided evidence that the shallow aquifer beneath the capital city of Montgomery, Alabama, was contaminated. Investigations conducted from 1993 to 1999 by State and Federal agencies confirmed the detection of PCE in the shallow aquifer, as well as the detection of the organic solvent trichloroethylene (TCE) and various inorganic compounds, but the source of the groundwater contamination was not determined. In May 2000 the U.S. Environmental Protection Agency proposed that the site, called the Capital City Plume (CCP) Site, be a candidate for the National Priorities List. Between 2000 and 2007, numerous site-investigation activities also did not determine the source of the groundwater contamination. In 2008, additional assessments were conducted at the CCP Site to investigate the potential source area, contamination pathway, and the probable release history of the chlorinated-solvent-contaminated groundwater. The assessments included the collection of (1) pore water in 2008 from the hyporheic zone of a creek using passive-diffusion bag samplers; (2) tissue samples in 2008 and 2009 from trees growing in areas of downtown Montgomery characterized by groundwater contamination and from trees growing in riparian zones along the Alabama River and Cypress Creek; and (3) groundwater samples in 2009 and 2010. The data collected were used to investigate the potential source area of contaminants detected in groundwater, the pathway of groundwater contamination, and constraints on the probable contaminant-release history. The data collected between 2008 and 2010 indicate that the PCE and TCE contamination of the shallow aquifer beneath the CCP Site most likely resulted from the past use and disposal of industrial wastewater from printing operations containing chlorinated solvents into the sanitary sewer and (or) stormwater systems of Montgomery. Moreover, chlorinated-solvent use and disposal occurred at least between the 1940s and 1970s at several locations occupied by printing operations. The data also indicate that PCE and TCE contamination continues to occur in the shallow subsurface near potential release areas and that PCE and TCE have been transported to the intermediate part of the shallow aquifer.

Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

PubMed

Gaines, J C; Acebes, S; Virrueta, A; Butler, M; Regan, L; O'Hern, C S

2018-05-01

We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins. © 2018 Wiley Periodicals, Inc.

Mechanism of reactant and product dissociation from the anthrax edema factor: a locally enhanced sampling and steered molecular dynamics study.

PubMed

Martínez, Leandro; Malliavin, Thérèse E; Blondel, Arnaud

2011-05-01

The anthrax edema factor is a toxin overproducing damaging levels of cyclic adenosine monophosphate (cAMP) and pyrophosphate (PPi) from ATP. Here, mechanisms of dissociation of ATP and products (cAMP, PPi) from the active site are studied using locally enhanced sampling (LES) and steered molecular dynamics simulations. Various substrate conformations and ionic binding modes found in crystallographic structures are considered. LES simulations show that PPi and cAMP dissociate through different solvent accessible channels, while ATP dissociation requires significant active site exposure to solvent. The ionic content of the active site directly affects the dissociation of ATP and products. Only one ion dissociates along with ATP in the two-Mg(2+) binding site, suggesting that the other ion binds EF prior to ATP association. Dissociation of reaction products cAMP and PPi is impaired by direct electrostatic interactions between products and Mg(2+) ions. This provides an explanation for the inhibitory effect of high Mg(2+) concentrations on EF enzymatic activity. Breaking of electrostatic interactions is dependent on a competitive binding of water molecules to the ions, and thus on the solvent accessibility of the active site. Consequently, product dissociation seems to be a two-step process. First, ligands are progressively solvated while preserving the most important electrostatic interactions, in a process that is dependent on the flexibility of the active site. Second, breakage of the electrostatic bonds follows, and ligands diffuse into solvent. In agreement with this mechanism, product protonation facilitates dissociation.

Does the cation really matter? The effect of modifying an ionic liquid cation on an SN2 process.

PubMed

Tanner, Eden E L; Yau, Hon Man; Hawker, Rebecca R; Croft, Anna K; Harper, Jason B

2013-09-28

The rate of reaction of a Menschutkin process in a range of ionic liquids with different cations was investigated, with temperature-dependent kinetic data giving access to activation parameters for the process in each solvent. These data, along with molecular dynamics simulations, demonstrate the importance of accessibility of the charged centre on the cation and that the key interactions are of a generalised electrostatic nature.

Human telomere sequence DNA in water-free and high-viscosity solvents: G-quadruplex folding governed by Kramers rate theory.

PubMed

Lannan, Ford M; Mamajanov, Irena; Hud, Nicholas V

2012-09-19

Structures formed by human telomere sequence (HTS) DNA are of interest due to the implication of telomeres in the aging process and cancer. We present studies of HTS DNA folding in an anhydrous, high viscosity deep eutectic solvent (DES) comprised of choline choride and urea. In this solvent, the HTS DNA forms a G-quadruplex with the parallel-stranded ("propeller") fold, consistent with observations that reduced water activity favors the parallel fold, whereas alternative folds are favored at high water activity. Surprisingly, adoption of the parallel structure by HTS DNA in the DES, after thermal denaturation and quick cooling to room temperature, requires several months, as opposed to less than 2 min in an aqueous solution. This extended folding time in the DES is, in part, due to HTS DNA becoming kinetically trapped in a folded state that is apparently not accessed in lower viscosity solvents. A comparison of times required for the G-quadruplex to convert from its aqueous-preferred folded state to its parallel fold also reveals a dependence on solvent viscosity that is consistent with Kramers rate theory, which predicts that diffusion-controlled transitions will slow proportionally with solvent friction. These results provide an enhanced view of a G-quadruplex folding funnel and highlight the necessity to consider solvent viscosity in studies of G-quadruplex formation in vitro and in vivo. Additionally, the solvents and analyses presented here should prove valuable for understanding the folding of many other nucleic acids and potentially have applications in DNA-based nanotechnology where time-dependent structures are desired.

Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme

PubMed Central

Ahalawat, Navjeet; Pandit, Subhendu; Kay, Lewis E.

2018-01-01

Ligand binding sites in proteins are often localized to deeply buried cavities, inaccessible to bulk solvent. Yet, in many cases binding of cognate ligands occurs rapidly. An intriguing system is presented by the L99A cavity mutant of T4 Lysozyme (T4L L99A) that rapidly binds benzene (~106 M-1s-1). Although the protein has long served as a model system for protein thermodynamics and crystal structures of both free and benzene-bound T4L L99A are available, the kinetic pathways by which benzene reaches its solvent-inaccessible binding cavity remain elusive. The current work, using extensive molecular dynamics simulation, achieves this by capturing the complete process of spontaneous recognition of benzene by T4L L99A at atomistic resolution. A series of multi-microsecond unbiased molecular dynamics simulation trajectories unequivocally reveal how benzene, starting in bulk solvent, diffuses to the protein and spontaneously reaches the solvent inaccessible cavity of T4L L99A. The simulated and high-resolution X-ray derived bound structures are in excellent agreement. A robust four-state Markov model, developed using cumulative 60 μs trajectories, identifies and quantifies multiple ligand binding pathways with low activation barriers. Interestingly, none of these identified binding pathways required large conformational changes for ligand access to the buried cavity. Rather, these involve transient but crucial opening of a channel to the cavity via subtle displacements in the positions of key helices (helix4/helix6, helix7/helix9) leading to rapid binding. Free energy simulations further elucidate that these channel-opening events would have been unfavorable in wild type T4L. Taken together and via integrating with results from experiments, these simulations provide unprecedented mechanistic insights into the complete ligand recognition process in a buried cavity. By illustrating the power of subtle helix movements in opening up multiple pathways for ligand access, this work offers an alternate view of ligand recognition in a solvent-inaccessible cavity, contrary to the common perception of a single dominant pathway for ligand binding. PMID:29775455

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

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.

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.

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

High Anodic Performance of Co 1,3,5-Benzenetricarboxylate Coordination Polymers for Li-Ion Battery.

PubMed

Li, Chao; Lou, Xiaobing; Shen, Ming; Hu, Xiaoshi; Guo, Zhi; Wang, Yong; Hu, Bingwen; Chen, Qun

2016-06-22

We report the designed synthesis of Co 1,3,5-benzenetricarboxylate coordination polymers (CPs) via a straightforward hydrothermal method, in which three kinds of reaction solvents are selected to form CPs with various morphologies and dimensions. When tested as anode materials in Li-ion battery, the cycling stabilities of the three CoBTC CPs at a current density of 100 mA g(-1) have not evident difference; however, the reversible capacities are widely divergent when the current density is increased to 2 A g(-1). The optimized product CoBTC-EtOH maintains a reversible capacity of 473 mAh g(-1) at a rate of 2 A g(-1) after 500 galvanostatic charging/discharging cycles while retaining a nearly 100% Coulombic efficiency. The hollow microspherical morphology, accessible specific area, and the absence of coordination solvent of CoBTC-EtOH might be responsible for such difference. Furthermore, the ex situ soft X-ray absorption spectroscopy studies of CoBTC-EtOH under different states-of-charge suggest that the Co ions remain in the Co(2+) state during the charging/discharging process. Therefore, Li ions are inserted to the organic moiety (including the carboxylate groups and the benzene ring) of CoBTC without the direct engagement of Co ions during electrochemical cycling.

FIELD EVALUATION OF THE SOLVENT EXTRACTION RESIDUAL BIOTREATMENT (SERB) TECHNOLOGY

EPA Science Inventory

The Solvent Extraction Residual Biotreatment (SERB) technology was demonstrated at the former Sage's Dry Cleaner site in Jacksonville, FL where an area of PCE (tetrachloroethylene) contamination was identified. The SERB technology is a treatment train approach to complete site...

Solution Kinetics Database on the Web

National Institute of Standards and Technology Data Gateway

SRD 40 NDRL/NIST Solution Kinetics Database on the Web (Web, free access)   Data for free radical processes involving primary radicals from water, inorganic radicals and carbon-centered radicals in solution, and singlet oxygen and organic peroxyl radicals in various solvents.

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

Optimization Review: Lockwood Operable Unit 1 - Beall Source Area, Billings, Montana

EPA Pesticide Factsheets

The Lockwood Solvent Groundwater Plume Site (LSGPS) consists of two operable units (OUs) and is located on the outskirts of Billings, Montana in EPA Region 8. OU1 consists of contaminated soils and a chlorinated solvent groundwater plume associated with...

Comparison of direct and alternating current vacuum ultraviolet lamps in atmospheric pressure photoionization.

PubMed

Vaikkinen, Anu; Haapala, Markus; Kersten, Hendrik; Benter, Thorsten; Kostiainen, Risto; Kauppila, Tiina J

2012-02-07

A direct current induced vacuum ultraviolet (dc-VUV) krypton discharge lamp and an alternating current, radio frequency (rf) induced VUV lamp that are essentially similar to lamps in commercial atmospheric pressure photoionization (APPI) ion sources were compared. The emission distributions along the diameter of the lamp exit window were measured, and they showed that the beam of the rf lamp is much wider than that of the dc lamp. Thus, the rf lamp has larger efficient ionization area, and it also emits more photons than the dc lamp. The ionization efficiencies of the lamps were compared using identical spray geometries with both lamps in microchip APPI mass spectrometry (μAPPI-MS) and desorption atmospheric pressure photoionization-mass spectrometry (DAPPI-MS). A comprehensive view on the ionization was gained by studying six different μAPPI solvent compositions, five DAPPI spray solvents, and completely solvent-free DAPPI. The observed reactant ions for each solvent composition were very similar with both lamps except for toluene, which showed a higher amount of solvent originating oxidation products with the rf lamp than with the dc lamp in μAPPI. Moreover, the same analyte ions were detected with both lamps, and thus, the ionization mechanisms with both lamps are similar. The rf lamp showed a higher ionization efficiency than the dc lamp in all experiments. The difference between the lamp ionization efficiencies was greatest when high ionization energy (IE) solvent compositions (IEs above 10 eV), i.e., hexane, methanol, and methanol/water, (1:1 v:v) were used. The higher ionization efficiency of the rf lamp is likely due to the larger area of high intensity light emission, and the resulting larger efficient ionization area and higher amount of photons emitted. These result in higher solvent reactant ion production, which in turn enables more efficient analyte ion production. © 2012 American Chemical Society

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

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

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.

Semiautomatic sequential extraction of polycyclic aromatic hydrocarbons and elemental bio-accessible fraction by accelerated solvent extraction on a single particulate matter sample.

PubMed

Astolfi, Maria Luisa; Di Filippo, Patrizia; Gentili, Alessandra; Canepari, Silvia

2017-11-01

We describe the optimization and validation of a sequential extractive method for the determination of the polycyclic aromatic hydrocarbons (PAHs) and elements (Al, As, Cd, Cr, Cu, Fe, Mn, Ni, Pb, Se, V and Zn) that are chemically fractionated into bio-accessible and mineralized residual fractions on a single particulate matter filter. The extraction is performed by automatic accelerated solvent extraction (ASE); samples are sequentially treated with dichloromethane/acetone (4:1) for PAHs extraction and acetate buffer (0.01M; pH 4.5) for elements extraction (bio-accessible fraction). The remaining solid sample is then collected and subjected to acid digestion with HNO 3 :H 2 O 2 (2:1) to determine the mineralized residual element fraction. We also describe a homemade ASE cell that reduces the blank values for most elements; in this cell, the steel frit was replaced by a Teflon pierced disk and a Teflon cylinder was used as the filler. The performance of the proposed method was evaluated in terms of recovery from standard reference material (SRM 1648 and SRM 1649a) and repeatability. The equivalence between the new ASE method and conventional methods was verified for PAHs and for bio-accessible and mineralized residual fractions of elements on PM 10 twin filters. Copyright © 2017 Elsevier B.V. All rights reserved.

Approximately 800-nm-Thick Pinhole-Free Perovskite Films via Facile Solvent Retarding Process for Efficient Planar Solar Cells.

PubMed

Yuan, Zhongcheng; Yang, Yingguo; Wu, Zhongwei; Bai, Sai; Xu, Weidong; Song, Tao; Gao, Xingyu; Gao, Feng; Sun, Baoquan

2016-12-21

Device performance of organometal halide perovskite solar cells significantly depends on the quality and thickness of perovskite absorber films. However, conventional deposition methods often generate pinholes within ∼300 nm-thick perovskite films, which are detrimental to the large area device manufacture. Here we demonstrated a simple solvent retarding process to deposit uniform pinhole free perovskite films with thicknesses up to ∼800 nm. Solvent evaporation during the retarding process facilitated the components separation in the mixed halide perovskite precursors, and hence the final films exhibited pinhole free morphology and large grain sizes. In addition, the increased precursor concentration after solvent-retarding process led to thick perovskite films. Based on the uniform and thick perovskite films prepared by this convenient process, a champion device efficiency up to 16.8% was achieved. We believe that this simple deposition procedure for high quality perovskite films around micrometer thickness has a great potential in the application of large area perovskite solar cells and other optoelectronic devices.

Structural protein descriptors in 1-dimension and their sequence-based predictions.

PubMed

Kurgan, Lukasz; Disfani, Fatemeh Miri

2011-09-01

The last few decades observed an increasing interest in development and application of 1-dimensional (1D) descriptors of protein structure. These descriptors project 3D structural features onto 1D strings of residue-wise structural assignments. They cover a wide-range of structural aspects including conformation of the backbone, burying depth/solvent exposure and flexibility of residues, and inter-chain residue-residue contacts. We perform first-of-its-kind comprehensive comparative review of the existing 1D structural descriptors. We define, review and categorize ten structural descriptors and we also describe, summarize and contrast over eighty computational models that are used to predict these descriptors from the protein sequences. We show that the majority of the recent sequence-based predictors utilize machine learning models, with the most popular being neural networks, support vector machines, hidden Markov models, and support vector and linear regressions. These methods provide high-throughput predictions and most of them are accessible to a non-expert user via web servers and/or stand-alone software packages. We empirically evaluate several recent sequence-based predictors of secondary structure, disorder, and solvent accessibility descriptors using a benchmark set based on CASP8 targets. Our analysis shows that the secondary structure can be predicted with over 80% accuracy and segment overlap (SOV), disorder with over 0.9 AUC, 0.6 Matthews Correlation Coefficient (MCC), and 75% SOV, and relative solvent accessibility with PCC of 0.7 and MCC of 0.6 (0.86 when homology is used). We demonstrate that the secondary structure predicted from sequence without the use of homology modeling is as good as the structure extracted from the 3D folds predicted by top-performing template-based methods.

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.

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.

First-Principles Molecular Dynamics Studies of Organometallic Complexes and Homogeneous Catalytic Processes.

PubMed

Vidossich, Pietro; Lledós, Agustí; Ujaque, Gregori

2016-06-21

Computational chemistry is a valuable aid to complement experimental studies of organometallic systems and their reactivity. It allows probing mechanistic hypotheses and investigating molecular structures, shedding light on the behavior and properties of molecular assemblies at the atomic scale. When approaching a chemical problem, the computational chemist has to decide on the theoretical approach needed to describe electron/nuclear interactions and the composition of the model used to approximate the actual system. Both factors determine the reliability of the modeling study. The community dedicated much effort to developing and improving the performance and accuracy of theoretical approaches for electronic structure calculations, on which the description of (inter)atomic interactions rely. Here, the importance of the model system used in computational studies is highlighted through examples from our recent research focused on organometallic systems and homogeneous catalytic processes. We show how the inclusion of explicit solvent allows the characterization of molecular events that would otherwise not be accessible in reduced model systems (clusters). These include the stabilization of nascent charged fragments via microscopic solvation (notably, hydrogen bonding), transfer of charge (protons) between distant fragments mediated by solvent molecules, and solvent coordination to unsaturated metal centers. Furthermore, when weak interactions are involved, we show how conformational and solvation properties of organometallic complexes are also affected by the explicit inclusion of solvent molecules. Such extended model systems may be treated under periodic boundary conditions, thus removing the cluster/continuum (or vacuum) boundary, and require a statistical mechanics simulation technique to sample the accessible configurational space. First-principles molecular dynamics, in which atomic forces are computed from electronic structure calculations (namely, density functional theory), is certainly the technique of choice to investigate chemical events in solution. This methodology is well established and thanks to advances in both algorithms and computational resources simulation times required for the modeling of chemical events are nowadays accessible, though the computational requirements use to be high. Specific applications reviewed here include mechanistic studies of the Shilov and Wacker processes, speciation in Pd chemistry, hydrogen bonding to metal centers, and the dynamics of agostic interactions.

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.

Effects of Polymer Hydrophobicity on Protein Structure and Aggregation Kinetics in Crowded Milieu.

PubMed

Breydo, Leonid; Sales, Amanda E; Frege, Telma; Howell, Mark C; Zaslavsky, Boris Y; Uversky, Vladimir N

2015-05-19

We examined the effects of water-soluble polymers of various degrees of hydrophobicity on the folding and aggregation of proteins. The polymers we chose were polyethylene glycol (PEG) and UCON (1:1 copolymer of ethylene glycol and propylene glycol). The presence of additional methyl groups in UCON makes it more hydrophobic than PEG. Our earlier analysis revealed that similarly sized PEG and UCON produced different changes in the solvent properties of water in their solutions and induced morphologically different α-synuclein aggregates [Ferreira, L. A., et al. (2015) Role of solvent properties of aqueous media in macromolecular crowding effects. J. Biomol. Struct. Dyn., in press]. To improve our understanding of molecular mechanisms defining behavior of proteins in a crowded environment, we tested the effects of these polymers on secondary and tertiary structure and aromatic residue solvent accessibility of 10 proteins [five folded proteins, two hybrid proteins; i.e., protein containing ordered and disordered domains, and three intrinsically disordered proteins (IDPs)] and on the aggregation kinetics of insulin and α-synuclein. We found that effects of both polymers on secondary and tertiary structures of folded and hybrid proteins were rather limited with slight unfolding observed in some cases. Solvent accessibility of aromatic residues was significantly increased for the majority of the studied proteins in the presence of UCON but not PEG. PEG also accelerated the aggregation of protein into amyloid fibrils, whereas UCON promoted aggregation to amyloid oligomers instead. These results indicate that even a relatively small change in polymer structure leads to a significant change in the effect of this polymer on protein folding and aggregation. This is an indication that protein folding and especially aggregation are highly sensitive to the presence of other macromolecules, and an excluded volume effect is insufficient to describe their effect.

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.

Synchrotron Protein Footprinting Supports Substrate Translocation by ClpA via ATP-Induced Movements of the D2 Loop

PubMed Central

Bohon, Jen; Jennings, Laura D.; Phillips, Christine M.; Licht, Stuart; Chance, Mark R.

2010-01-01

SUMMARY Synchrotron x-ray protein footprinting is used to study structural changes upon formation of the ClpA hexamer. Comparative solvent accessibilities between ClpA monomer and ClpA hexamer samples are in agreement throughout most of the sequence with calculations based on two previously proposed hexameric models. The data differ substantially from the proposed models in two parts of the structure: the D1 sensor 1 domain and the D2 loop region. The results suggest that these two regions can access alternate conformations in which their solvent protection is greater than in the structural models based on crystallographic data. In combination with previously reported structural data, the footprinting data provide support for a revised model in which the D2 loop contacts the D1 sensor 1 domain in the ATP-bound form of the complex. These data provide the first direct experimental support for the nucleotide-dependent D2 loop conformational change previously proposed to mediate substrate translocation. PMID:18682217

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).

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.

Bench-Scale Development of a Non-Aqueous Solvent (NAS) CO2 Capture Process for Coal-Fired Power Plants

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

Lail, Marty

The project aimed to advance RTI’s non-aqueous amine solvent technology by improving the solvent to reduce volatility, demonstrating long-term continuous operation at lab- (0.5 liters solvent) and bench-scale (~120 liters solvent), showing low reboiler heat duty measured during bench-scale testing, evaluating degradation products, building a rate-based process model, and evaluating the techno-economic performance of the process. The project team (RTI, SINTEF, Linde Engineering) and the technology performed well in each area of advancement. The modifications incorporated throughout the project enabled the attainment of target absorber and regenerator conditions for the process. Reboiler duties below 2,000 kJt/kg CO2 were observed inmore » a bench-scale test unit operated at RTI.« less

Nonflammable, Nonaqueous, Low Atmospheric Impact, High Performance Cleaning Solvents

NASA Technical Reports Server (NTRS)

Dhooge, P. M.; Glass, S. M.; Nimitz, J. S.

2001-01-01

For many years, chlorofluorocarbon (CFC) and chlorocarbon solvents have played an important part in aerospace operations. These solvents found extensive use as cleaning and analysis (EPA) solvents in precision and critical cleaning. However, CFCs and chlorocarbon solvents have deleterious effects on the ozone layer, are relatively strong greenhouse gases, and some are suspect or known carcinogens. Because of their ozone-depletion potential (ODP), the Montreal Protocol and its amendments, as well as other environmental regulations, have resulted in the phaseout of CFC-113 and 1,1,1-trichloroethane (TCA). Although alternatives have been recommended, they do not perform as well as the original solvents. In addition, some analyses, such as the infrared analysis of extracted hydrocarbons, cannot be performed with the substitute solvents that contain C-H bonds. CFC-113 solvent has been used for many critical aerospace applications. CFC-113, also known as Freon (registered) TF, has been used extensively in NASA's cleaning facilities for precision and critical cleaning, in particular the final rinsing in Class 100 areas, with gas chromatography analysis of rinse residue. While some cleaning can be accomplished by other processes, there are certain critical applications where CFC-113 or a similar solvent is highly cost-effective and ensures safety. Oxygen system components are one example where a solvent compatible with oxygen and capable of removing fluorocarbon grease is needed. Electronic components and precision mechanical components can also be damaged by aggressive cleaning solvents.

Effect of the deletion of the C region on the structure and hydration of insulin-like growth factor 1: a molecular dynamics investigation

NASA Astrophysics Data System (ADS)

Degreve, Leo; Silva, Luciene B.

The structure and hydration of insulin-like growth factor 1 and an inactive mutant lacking the C region have been investigated in aqueous solution by molecular dynamics simulation. The overall structures of the two polypeptide resemble those determined by NMR spectroscopy. The deletion of the C region in the wild polypeptide introduces structural stability in the mutant, leading to a better definition of the secondary structure elements. A detailed hydration analysis was performed using the radial distribution functions and energy distributions. The backbone of the mutant is in general more solvent accessible than the wild polypeptide backbone. The structural rearrangements induced in the mutant led to changes in the solvent exposition of Tyr24 and Tyr60, which are residues important for ligand-receptor complex formation. Tyr24 exhibited a similar degree of solvent exposition in both IGF-1 and in the mutant; however, its hydroxyl group in the wild polypeptide is better solvated than in the mutant. Tyr60 was found to be solvent exposed in the wild protein, while in the mutant the involvement of its hydroxyl group in intramolecular hydrogen bonds led to it being buried away from the solvent.

The role of proton shuttling mechanisms in solvent-free and catalyst-free acetalization reactions of imines.

PubMed

Lillo, Victor J; Mansilla, Javier; Saá, José M

2018-06-06

Proton transfer is central to the understanding of chemical processes. More so in addition reactions of the type NuH + E → Nu-EH taking place under solvent-free and catalyst-free conditions. Herein we show that the addition of alcohols or amines (the NuH component) to imine derivatives (the E component), in 1 : 1 ratio, under solvent-free and catalyst-free conditions, are efficient methods to access N,O and N,N-acetal derivatives. In addition, computational studies reveal that they are catalyzed reactions involving two or even three NuH molecules operating in a cooperative manner as H-bonded NuH(NuH)nNuH associates (many body effects) in the transition state through a concerted proton shuttling mechanism (addition of alcohols) or stepwise proton shuttling mechanism (addition of amines), thereby facilitating the key proton transfer step.

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.

Metabolomic analysis-Addressing NMR and LC-MS related problems in human feces sample preparation.

PubMed

Moosmang, Simon; Pitscheider, Maria; Sturm, Sonja; Seger, Christoph; Tilg, Herbert; Halabalaki, Maria; Stuppner, Hermann

2017-10-31

Metabolomics is a well-established field in fundamental clinical research with applications in different human body fluids. However, metabolomic investigations in feces are currently an emerging field. Fecal sample preparation is a demanding task due to high complexity and heterogeneity of the matrix. To gain access to the information enclosed in human feces it is necessary to extract the metabolites and make them accessible to analytical platforms like NMR or LC-MS. In this study different pre-analytical parameters and factors were investigated i.e. water content, different extraction solvents, influence of freeze-drying and homogenization, ratios of sample weight to extraction solvent, and their respective impact on metabolite profiles acquired by NMR and LC-MS. The results indicate that profiles are strongly biased by selection of extraction solvent or drying of samples, which causes different metabolites to be lost, under- or overstated. Additionally signal intensity and reproducibility of the measurement were found to be strongly dependent on sample pre-treatment steps: freeze-drying and homogenization lead to improved release of metabolites and thus increased signals, but at the same time induced variations and thus deteriorated reproducibility. We established the first protocol for extraction of human fecal samples and subsequent measurement with both complementary techniques NMR and LC-MS. Copyright © 2017 Elsevier B.V. All rights reserved.

Green analytical chemistry - the use of surfactants as a replacement of organic solvents in spectroscopy

NASA Astrophysics Data System (ADS)

Pharr, Daniel Y.

2017-07-01

This chapter gives an introduction to the many practical uses of surfactants in analytical chemistry in replacing organic solvents to achieve greener chemistry. Taking a holistic approach, it covers some background of surfactants as chemical solvents, their properties and as green chemicals, including their environmental effects. The achievements of green analytical chemistry with micellar systems are reviewed in all the major areas of analytical chemistry where these reagents have been found to be useful.

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

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.

16 CFR 1302.5 - Findings.

Code of Federal Regulations, 2010 CFR

2010-01-01

... sources summarized in the Hazard Analysis reveal that contact adhesive fires often result in a high... point (20 °F or below), a rapid evaporation rate (as a result of a high percentage of solvents, 70-90... to high solvent ratio, evaporation rate, size of the application area, and rate of application are...

Feasibility of Surfactant-Free Supported Emulsion Liquid Membrane Extraction

NASA Technical Reports Server (NTRS)

Hu, Shih-Yao B.; Li, Jin; Wiencek, John M.

2001-01-01

Supported emulsion liquid membrane (SELM) is an effective means to conduct liquid-liquid extraction. SELM extraction is particularly attractive for separation tasks in the microgravity environment where density difference between the solvent and the internal phase of the emulsion is inconsequential and a stable dispersion can be maintained without surfactant. In this research, dispersed two-phase flow in SELM extraction is modeled using the Lagrangian method. The results show that SELM extraction process in the microgravity environment can be simulated on earth by matching the density of the solvent and the stripping phase. Feasibility of surfactant-free SELM (SFSELM) extraction is assessed by studying the coalescence behavior of the internal phase in the absence of the surfactant. Although the contacting area between the solvent and the internal phase in SFSELM extraction is significantly less than the area provided by regular emulsion due to drop coalescence, it is comparable to the area provided by a typical hollow-fiber membrane. Thus, the stripping process is highly unlikely to become the rate-limiting step in SFSELM extraction. SFSELM remains an effective way to achieve simultaneous extraction and stripping and is able to eliminate the equilibrium limitation in the typical solvent extraction processes. The SFSELM design is similar to the supported liquid membrane design in some aspects.

The CoFactor database: organic cofactors in enzyme catalysis.

PubMed

Fischer, Julia D; Holliday, Gemma L; Thornton, Janet M

2010-10-01

Organic enzyme cofactors are involved in many enzyme reactions. Therefore, the analysis of cofactors is crucial to gain a better understanding of enzyme catalysis. To aid this, we have created the CoFactor database. CoFactor provides a web interface to access hand-curated data extracted from the literature on organic enzyme cofactors in biocatalysis, as well as automatically collected information. CoFactor includes information on the conformational and solvent accessibility variation of the enzyme-bound cofactors, as well as mechanistic and structural information about the hosting enzymes. The database is publicly available and can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/CoFactor.

Ca(OH)2-Catalyzed Condensation of Aldehydes with Methyl ketones in Dilute Aqueous Ethanol: A Comprehensive Access to α,β-Unsaturated Ketones

NASA Astrophysics Data System (ADS)

Yu, Lei; Han, Mengting; Luan, Jie; Xu, Lin; Ding, Yuanhua; Xu, Qing

2016-07-01

Cheap, abundant but seldom-employed Ca(OH)2 was found to be an excellent low-loading (5-10 mol%) catalyst for Claisen-Schmidt condensation of aldehydes with methyl ketones under mild conditions. It was interesting that dilute aqueous ethanol (20 v/v%) was unexpectedly discovered to be the optimal solvent. The reaction was scalable at least to 100 mmol and calcium could be precipitated by CO2 and removed by filtration. Evaporation of solvent directly afforded the product in the excellent 96% yield with high purity, as confirmed by its 1H NMR spectrum.

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.

Solvent recyclability in a multistep direct liquefaction process

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

Hetland, M.D.; Rindt, J.R.

1995-12-31

Direct liquefaction research at the Energy & Environmental Research Center (EERC) has, for a number of years, concentrated on developing a direct liquefaction process specifically for low-rank coals (LRCs) through the use of hydrogen-donating solvents and solvents similar to coal-derived liquids, the water/gas shift reaction, and lower-severity reaction conditions. The underlying assumption of all of the research was that advantage could be taken of the reactivity and specific qualities of LRCs to produce a tetrahydrofuran (THF)-soluble material that might be easier to upgrade than the soluble residuum produced during direct liquefaction of high-rank coals. A multistep approach was taken tomore » produce the THF-soluble material, consisting of (1) preconversion treatment to prepare the coal for solubilization, (2) solubilization of the coal in the solvent, and (3) polishing to complete solubilization of the remaining material. The product of these three steps can then be upgraded during a traditional hydrotreatment step. The results of the EERC`s research indicated that additional studies to develop this process more fully were justified. Two areas were targeted for further research: (1) determination of the recyclability of the solvent used during solubilization and (2) determination of the minimum severity required for hydrotreatment of the liquid product. The current project was funded to investigate these two areas.« less

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.

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.

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…

MICROWAVE-ASSISTED CU (I) CATALYZED SOLVENT-FREE THREE COMPONENT COUPLING OF ALDEHYDE, ALKYNE AND AMINE

EPA Science Inventory

Direct Grignard type addition of terminal alkynes to in situ generated imines, from aldehydes and amines, occurs under microwave irradiation using CuBr alone in a one-pot operation. This solventless approach provides ready access to propargylamines and is applicable both...

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

Monitored natural attenuation of chlorinated solvents—Moving beyond reductive dechlorination

USGS Publications Warehouse

Vangelas, Karen M.; Looney, Brian B.; Early, Tom O.; Gilmore, Tyler; Chapelle, Francis H.; Adams, Karen M.; Sink, Claire H.

2006-01-01

Monitored natural attenuation (MNA), while a remedy of choice for many sites, can be challenging when the contaminants are chlorinated solvents. Even with many high-quality technical guidance references available, there continue to be challenges implementing MNA at some chlorinated solvent sites. The U.S. Department of Energy, as one organization facing such challenges, is leading a project that will incorporate developing concepts and tools into the existing toolbox for selecting and implementing MNA as a remediation option at sites with chlorinated solvent contamination. The structure and goals of this project were introduced in an article in the Winter 2004 issue of Remediation (Sink et al., 2004). This article is a summary of the three technical areas being developed through the project: mass balance, enhanced attenuation, and characterization and monitoring supporting the first two areas.

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

Studies of the effect of selected nondonor solvents on coal liquefaction yields

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

Jolley, R. L.; Rodgers, B. R.; Benjamin, B. M.

The objective of this research program was to evaluate the effectiveness of selected nondonor solvents (i.e., solvents that are not generally considered to have hydrogen available for hydrogenolysis reactions) for the solubilization of coals. Principal criteria for selection of candidate solvents were that the compound should be representative of a major chemical class, should be present in reasonable concentration in coal liquid products, and should have the potential to participate in hydrogen redistribution reactions. Naphthalene, phenanthrene, pyrene, carbazole, phenanthridine, quinoline, 1-naphthol, and diphenyl ether were evaluated to determine their effect on coal liquefaction yields and were compared with phenol andmore » two high-quality process solvents, Wilsonville SRC-I recycle solvent and Lummus ITSL heavy oil solvent. The high conversion efficacy of 1-naphthol may be attributed to its condensation to binaphthol and the consequent availability of hydrogen. The effectiveness of both the nitrogen heterocycles and the polycyclic aromatic hydrocarbon (PAH) compounds may be due to their polycyclic aromatic nature (i.e., possible hydrogen shuttling or transfer agents) and their physical solvent properties. The relative effectiveness for coal conversion of the Lummus ITSL heavy oil solvent as compared with the Wilsonville SRC-I process solvent may be attributed to the much higher concentration of 3-, 4-, and 5-ring PAH and hydroaromatic constituents in Lummus solvent. The chemistry of coal liquefaction and the development of recycle, hydrogen donor, and nondonor solvents are reviewed. The experimental methodology for tubing-bomb tests is outlined, and experimental problem areas are discussed.« less

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.

Strengthening of the Coordination Shell by Counter Ions in Aqueous Th 4+ Solutions

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

Atta-Fynn, Raymond; Bylaska, Eric J.; de Jong, Wibe A.

The presence of counter ions in solutions containing highly charged metal cations can trigger processes such as ion-pair formation, hydrogen bond breakages and subsequent reformation, and ligand exchanges. In this work, it is shown how halide (Cl-, Br-) and perchlorate (ClO4-) anions affect the strength of the primary solvent coordination shells around Th4+ using explicit solvent and finite temperature ab initio molecular dynamics modeling methods. The 9-fold solvent geometry was found to be the most stable hydration structure in each aqueous solution. Relative to the dilute aqueous solution, the presence of the counter ions did not significantly alter the geometrymore » of the primary hydration shell. However, the free energy analyses indicated that the 10-fold hydrated states were thermodynamically accessible in dilute and bromide aqueous solutions within 1 kcal/mol. Analysis of the results showed that the hydrogen bond lifetimes were longer and solvent exchange energy barriers were larger in solutions with counter ions in comparison with the solution with no counter ions. This implies that the presence of the counter ions induces a strengthening of the Th4+ hydration shell.« less

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.

[Chemical hazards when working with solvent glues].

PubMed

Domański, Wojciech; Makles, Zbigniew

2012-01-01

Solvent glues are used in a wide variety of industries, e.g., textile, footwear and rubber. The problem of workers' exposure to solvent vapors is rarely tackled within the area of occupational safety and health in small and medium-sized enterprises. In order to assess exposure to solvents, organic solvents emitted by glues were identified in the samples of workplace air. The concentration of acetone, benzene, cyclohexane, ethylbenzene, n-hexane, methylcyclohexane, butyl acetate and toluene were determined. The obtained results evidenced the presence of cyclohexane, ethylbenzene, ethylcyclohexane, heptane, n-hexane, o-xylene, methylcyclohexane, methylcyclopentane, butyl acetate and toluene in workplace air. The concentration of those compounds in workplace air was low, usually below 0.15 of MAC. At some workstations the presence of benzene was also observed. Occupational risk was assessed at workstations where gluing took place. It showed that the risk at those workstations was medium or low.

A low viscosity, low boiling point, clean solvent system for the rapid crystallisation of highly specular perovskite films

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

Noel, Nakita K.; Habisreutinger, Severin N.; Wenger, Bernard

2017-01-01

Perovskite-based photovoltaics have, in recent years, become poised to revolutionise the solar industry. While there have been many approaches taken to the deposition of this material, one-step spin-coating remains the simplest and most widely used method in research laboratories. Although spin-coating is not recognised as the ideal manufacturing methodology, it represents a starting point from which more scalable deposition methods, such as slot-dye coating or ink-jet printing can be developed. Here, we introduce a new, low-boiling point, low viscosity solvent system that enables rapid, room temperature crystallisation of methylammonium lead triiodide perovskite films, without the use of strongly coordinating aproticmore » solvents. Through the use of this solvent, we produce dense, pinhole free films with uniform coverage, high specularity, and enhanced optoelectronic properties. We fabricate devices and achieve stabilised power conversion efficiencies of over 18% for films which have been annealed at 100 degrees C, and over 17% for films which have been dried under vacuum and have undergone no thermal processing. This deposition technique allows uniform coating on substrate areas of up to 125 cm2, showing tremendous promise for the fabrication of large area, high efficiency, solution processed devices, and represents a critical step towards industrial upscaling and large area printing of perovskite solar cells.« less

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

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

Halogenated solvent remediation

DOEpatents

Sorenson, Jr., Kent S.

2008-11-11

Methods for enhancing bioremediation of ground water contaminated with nonaqueous halogenated solvents are disclosed. An illustrative method includes adding an electron donor for microbe-mediated anaerobic reductive dehalogenation of the halogenated solvents, which electron donor enhances mass transfer of the halogenated solvents from residual source areas into the aqueous phase of the ground water. Illustrative electron donors include C.sub.2-C.sub.4 carboxylic acids and hydroxy acids, salts thereof, esters of C.sub.2-C.sub.4 carboxylic acids and hydroxy acids, and mixtures thereof, of which lactic acid, salts of lactic acid--such as sodium lactate, lactate esters, and mixtures thereof are particularly illustrative. The microbes are either indigenous to the ground water, or such microbes can be added to the ground water in addition to the electron donor.

Docking glycosaminoglycans to proteins: analysis of solvent inclusion

NASA Astrophysics Data System (ADS)

Samsonov, Sergey A.; Teyra, Joan; Pisabarro, M. Teresa

2011-05-01

Glycosaminoglycans (GAGs) are anionic polysaccharides, which participate in key processes in the extracellular matrix by interactions with protein targets. Due to their charged nature, accurate consideration of electrostatic and water-mediated interactions is indispensable for understanding GAGs binding properties. However, solvent is often overlooked in molecular recognition studies. Here we analyze the abundance of solvent in GAG-protein interfaces and investigate the challenges of adding explicit solvent in GAG-protein docking experiments. We observe PDB GAG-protein interfaces being significantly more hydrated than protein-protein interfaces. Furthermore, by applying molecular dynamics approaches we estimate that about half of GAG-protein interactions are water-mediated. With a dataset of eleven GAG-protein complexes we analyze how solvent inclusion affects Autodock 3, eHiTs, MOE and FlexX docking. We develop an approach to de novo place explicit solvent into the binding site prior to docking, which uses the GRID program to predict positions of waters and to locate possible areas of solvent displacement upon ligand binding. To investigate how solvent placement affects docking performance, we compare these results with those obtained by taking into account information about the solvent position in the crystal structure. In general, we observe that inclusion of solvent improves the results obtained with these methods. Our data show that Autodock 3 performs best, though it experiences difficulties to quantitatively reproduce experimental data on specificity of heparin/heparan sulfate disaccharides binding to IL-8. Our work highlights the current challenges of introducing solvent in protein-GAGs recognition studies, which is crucial for exploiting the full potential of these molecules for rational engineering.

Effects of solvent evaporation conditions on solvent vapor annealed cylinder-forming block polymer thin films

NASA Astrophysics Data System (ADS)

Grant, Meagan; Jakubowski, William; Nelson, Gunnar; Drapes, Chloe; Baruth, A.

Solvent vapor annealing is a less time and energy intensive method compared to thermal annealing, to direct the self-assembly of block polymer thin films. Periodic nanostructures have applications in ultrafiltration, magnetic arrays, or other structures with nanometer dimensions, driving its continued interest. Our goal is to create thin films with hexagonally packed, perpendicular aligned cylinders of poly(lactide) in a poly(styrene) matrix that span the thickness of the film with low anneal times and low defect densities, all with high reproducibility, where the latter is paramount. Through the use of our computer-controlled, pneumatically-actuated, purpose-built solvent vapor annealing chamber, we have the ability to monitor and control vapor pressure, solvent concentration within the film, and solvent evaporation rate with unprecedented precision and reliability. Focusing on evaporation, we report on two previously unexplored areas, chamber pressure during solvent evaporation and the flow rate of purging gas aiding the evaporation. We will report our exhaustive results following atomic force microscopy analysis of films exposed to a wide range of pressures and flow rates. Reliably achieving well-ordered films, while occurring within a large section of this parameter space, was correlated with high-flow evaporation rates and low chamber pressures. These results have significant implications on other methods of solvent annealing, including ``jar'' techniques.

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

How amide hydrogens exchange in native proteins.

PubMed

Persson, Filip; Halle, Bertil

2015-08-18

Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N-H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N-H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion.

How amide hydrogens exchange in native proteins

PubMed Central

Persson, Filip; Halle, Bertil

2015-01-01

Amide hydrogen exchange (HX) is widely used in protein biophysics even though our ignorance about the HX mechanism makes data interpretation imprecise. Notably, the open exchange-competent conformational state has not been identified. Based on analysis of an ultralong molecular dynamics trajectory of the protein BPTI, we propose that the open (O) states for amides that exchange by subglobal fluctuations are locally distorted conformations with two water molecules directly coordinated to the N–H group. The HX protection factors computed from the relative O-state populations agree well with experiment. The O states of different amides show little or no temporal correlation, even if adjacent residues unfold cooperatively. The mean residence time of the O state is ∼100 ps for all examined amides, so the large variation in measured HX rate must be attributed to the opening frequency. A few amides gain solvent access via tunnels or pores penetrated by water chains including native internal water molecules, but most amides access solvent by more local structural distortions. In either case, we argue that an overcoordinated N–H group is necessary for efficient proton transfer by Grotthuss-type structural diffusion. PMID:26195754

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.

Mass spectrometry-based carboxyl footprinting of proteins: Method evaluation

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

Zhang, Hao; Wen, Jianzhong; Huang, Richard Y-C.

2012-02-01

Protein structure determines function in biology, and a variety of approaches have been employed to obtain structural information about proteins. Mass spectrometry-based protein footprinting is one fast-growing approach. One labeling-based footprinting approach is the use of a water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and glycine ethyl ester (GEE) to modify solvent-accessible carboxyl groups on glutamate (E) and aspartate (D). This paper describes method development of carboxyl-group modification in protein footprinting. The modification protocol was evaluated by using the protein calmodulin as a model. Because carboxyl-group modification is a slow reaction relative to protein folding and unfolding, there is an issue that modificationsmore » at certain sites may induce protein unfolding and lead to additional modification at sites that are not solvent-accessible in the wild-type protein. We investigated this possibility by using hydrogen deuterium amide exchange (H/DX). The study demonstrated that application of carboxyl group modification in probing conformational changes in calmodulin induced by Ca{sup 2+} binding provides useful information that is not compromised by modification-induced protein unfolding.« less

Acquired Color Vision Defects and Hexane Exposure: A Study of San Francisco Bay Area Automotive Mechanics

PubMed Central

Beckman, Stella; Eisen, Ellen A.; Bates, Michael N.; Liu, Sa; Haegerstrom-Portnoy, Gunilla; Hammond, S. Katharine

2016-01-01

Occupational exposure to solvents, including n-hexane, has been associated with acquired color vision defects. Blue-yellow defects are most common and may be due to neurotoxicity or retinal damage. Acetone may potentiate the neurotoxicity of n-hexane. We present results on nonhexane solvent and hexane exposure and color vision from a cross-sectional study of 835 automotive repair workers in the San Francisco Bay Area, California (2007–2013). Cumulative exposure was estimated from self-reported work history, and color vision was assessed using the Lanthony desaturated D-15 panel test. Log-binomial regression was used to estimate prevalence ratios for color vision defects. Acquired color vision defects were present in 29% of participants, of which 70% were blue-yellow. Elevated prevalence ratios were found for nonhexane solvent exposure, with a maximum of 1.31 (95% confidence interval (CI): 0.86, 2.00) for blue-yellow. Among participants aged ≤50 years, the prevalence ratio for blue-yellow defects was 2.17 (95% CI: 1.03, 4.56) in the highest quartile of nonhexane solvent exposure and 1.62 (95% CI: 0.97, 2.72) in the highest category of exposure to hexane with acetone coexposure. Cumulative exposures to hexane and nonhexane solvents in the highest exposure categories were associated with elevated prevalence ratios for color vision defects in younger participants. PMID:27188942

Occupational solvent exposure and brain function: an fMRI study.

PubMed

Tang, Cheuk Ying; Carpenter, David M; Eaves, Emily L; Ng, Johnny; Ganeshalingam, Nimalya; Weisel, Clifford; Qian, Hua; Lange, Gudrun; Fiedler, Nancy L

2011-07-01

Deficits in cognitive function have been demonstrated among workers chronically exposed to solvents, but the neural basis for these deficits has not been shown. We used functional magnetic resonance imaging (fMRI) to compare pathophysiological changes in brain function between solvent-exposed and control workers. Painters, drywall tapers, and carpenters were recruited from the International Union of Painters and Allied Trades, District Council 9 in New York City and District Council 21 in Philadelphia, Pennsylvania, and from the Carpenters Union in New Jersey. Twenty-seven solvent-exposed and 27 control subjects of similar age, education, and occupational status completed the N-Back working memory test during fMRI. After controlling for confounders (age; lifetime marijuana, cocaine, and alcohol use; blood lead; symptoms of depression; verbal intelligence), voxelwise group analysis and regional activation levels were compared and then correlated with an index of lifetime solvent exposure. Solvent-exposed workers' performance on the N-Back was significantly worse than that of controls. Activation of the anterior cingulate, prefrontal, and parietal cortices--areas serving working memory function and attention--was also significantly lower for solvent-exposed workers relative to controls. After controlling for confounders, we observed a negative correlation between lifetime solvent exposure and activation in these same regions among the solvent-exposed workers. This study is one of the few to document neural structures affected by exposure to solvents. Our findings provide a biological mechanism for the neurobehavioral deficits in working memory and attention that have previously been reported by other groups studying the effects of chronic exposure to solvents. These imaging markers, which are consistent with the neurobehavioral measures in our subject population, are consistent with altered brain pathology caused by prolonged exposure to solvent mixtures during construction work.

Occupational Solvent Exposure and Brain Function: An fMRI Study

PubMed Central

Carpenter, David M.; Eaves, Emily L.; Ng, Johnny; Ganeshalingam, Nimalya; Weisel, Clifford; Qian, Hua; Lange, Gudrun; Fiedler, Nancy L.

2011-01-01

Background: Deficits in cognitive function have been demonstrated among workers chronically exposed to solvents, but the neural basis for these deficits has not been shown. Objectives: We used functional magnetic resonance imaging (fMRI) to compare pathophysiological changes in brain function between solvent-exposed and control workers. Methods: Painters, drywall tapers, and carpenters were recruited from the International Union of Painters and Allied Trades, District Council 9 in New York City and District Council 21 in Philadelphia, Pennsylvania, and from the Carpenters Union in New Jersey. Twenty-seven solvent-exposed and 27 control subjects of similar age, education, and occupational status completed the N-Back working memory test during fMRI. After controlling for confounders (age; lifetime marijuana, cocaine, and alcohol use; blood lead; symptoms of depression; verbal intelligence), voxelwise group analysis and regional activation levels were compared and then correlated with an index of lifetime solvent exposure. Results: Solvent-exposed workers’ performance on the N-Back was significantly worse than that of controls. Activation of the anterior cingulate, prefrontal, and parietal cortices—areas serving working memory function and attention—was also significantly lower for solvent-exposed workers relative to controls. After controlling for confounders, we observed a negative correlation between lifetime solvent exposure and activation in these same regions among the solvent-exposed workers. Conclusions: This study is one of the few to document neural structures affected by exposure to solvents. Our findings provide a biological mechanism for the neurobehavioral deficits in working memory and attention that have previously been reported by other groups studying the effects of chronic exposure to solvents. These imaging markers, which are consistent with the neurobehavioral measures in our subject population, are consistent with altered brain pathology caused by prolonged exposure to solvent mixtures during construction work. PMID:21296712

Chemical Speciation and Bond Lengths of Organic Solutes by Core-Level Spectroscopy: pH and Solvent Influence on p-Aminobenzoic Acid.

PubMed

Stevens, Joanna S; Gainar, Adrian; Suljoti, Edlira; Xiao, Jie; Golnak, Ronny; Aziz, Emad F; Schroeder, Sven L M

2015-05-04

Through X-ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near-edge X-ray absorption fine structure (NEXAFS) and resonant inelastic X-ray scattering (RIXS) measurements at the nitrogen K-edge of para-aminobenzoic acid reveal both pH- and solvent-dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO-LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs and σ* shape resonances in the NEXAFS spectra. This provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute-solvent interactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Determination of zearalenone and its metabolites in endometrial cancer by coupled separation techniques.

PubMed

Gadzała-Kopciuch, Renata; Cendrowski, Krzysztof; Cesarz, Anna; Kiełbasa, Paweł; Buszewski, Bogusław

2011-10-01

This study presents a selective method of isolation of zearalenone (ZON) and its metabolite, α-zearalenol (α-ZOL), in neoplastically changed human tissue by accelerated solvent and ultrasonic extractions using a mixture of acetonitrile/water (84/16% v/v) as the extraction solvent. Extraction effectiveness was determined through the selection of parameters (composition of the solvent mixture, temperature, pressure, number of cycles) with tissue contamination at the level of nanograms per gram. The produced acetonitrile/water extracts were purified, and analytes were enriched in columns packed with homemade molecularly imprinted polymers. Purified extracts were determined by liquid chromatography (LC) coupled with different detection systems (diode array detection--DAD and mass spectrometry--MS) involving the Ascentis RP-Amide as a stationary phase and gradient elution. The combination of UE-MISPE-LC (ultrasonic extraction--molecularly imprinted solid-phase extraction--liquid chromatography) produced high (R≈95-98%) and repeatable (RSD<3%) recovery values for ZON and α-ZOL. © The Author(s) 2011. This article is published with open access at Springerlink.com

Cosolvent pretreatment in cellulosic biofuel production: Effect of tetrahydrofuran-water on lignin structure and dynamics

DOE PAGES

Smith, Micholas Dean; Mostofian, Barmak; Cheng, Xiaolin; ...

2015-10-05

The deconstruction of cellulose is an essential step in the production of ethanol from lignocellulosic biomass. However, the presence of lignin hinders this process. Recently, a novel cosolvent based biomass pretreatment method called CELF (Cosolvent Enhanced Lignocellulosic Fractionation) which employs tetrahydrofuran (THF) in a single phase mixture with water, was found to be highly effective at solubilizing and extracting lignin from lignocellulosic biomass and achieving high yields of fermentable sugars. Here, using all-atom molecular-dynamics simulation, we find that THF preferentially solvates lignin, and in doing so, shifts the equilibrium configurational distribution of the biopolymer from a crumpled globule to coil,more » independent of temperature. Whereas pure water is a bad solvent for lignin, the THF : water cosolvent acts as a "theta" solvent, in which solvent : lignin and lignin : lignin interactions are approximately equivalent in strength. Furthermore, under these conditions, polymers do not aggregate, thus providing a mechanism for the observed lignin solubilization that facilitates unfettered access of celluloytic enzymes to cellulose.« less

Chemical Speciation and Bond Lengths of Organic Solutes by Core-Level Spectroscopy: pH and Solvent Influence on p -Aminobenzoic Acid

DOE PAGES

Stevens, Joanna S.; Gainar, Adrian; Suljoti, Edlira; ...

2015-03-18

Through X-ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near-edge X-ray absorption fine structure (NEXAFS) and resonant inelastic X-ray scattering (RIXS) measurements at the nitrogen K-edge of para-aminobenzoic acid reveal both pH- and solvent-dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO–LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs andmore » σ* shape resonances in the NEXAFS spectra. Finally, this provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute–solvent interactions.« less

Redox active polymers and colloidal particles for flow batteries

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

Gavvalapalli, Nagarjuna; Moore, Jeffrey S.; Rodriguez-Lopez, Joaquin

The invention provides a redox flow battery comprising a microporous or nanoporous size-exclusion membrane, wherein one cell of the battery contains a redox-active polymer dissolved in the non-aqueous solvent or a redox-active colloidal particle dispersed in the non-aqueous solvent. The redox flow battery provides enhanced ionic conductivity across the electrolyte separator and reduced redox-active species crossover, thereby improving the performance and enabling widespread utilization. Redox active poly(vinylbenzyl ethylviologen) (RAPs) and redox active colloidal particles (RACs) were prepared and were found to be highly effective redox species. Controlled potential bulk electrolysis indicates that 94-99% of the nominal charge on different RAPsmore » is accessible and the electrolysis products are stable upon cycling. The high concentration attainable (>2.0 M) for RAPs in common non-aqueous battery solvents, their electrochemical and chemical reversibility, and their hindered transport across porous separators make them attractive materials for non-aqueous redox flow batteries based on size-selectivity.« less

Solutions Remediate Contaminated Groundwater

NASA Technical Reports Server (NTRS)

2010-01-01

During the Apollo Program, NASA workers used chlorinated solvents to clean rocket engine components at launch sites. These solvents, known as dense non-aqueous phase liquids, had contaminated launch facilities to the point of near-irreparability. Dr. Jacqueline Quinn and Dr. Kathleen Brooks Loftin of Kennedy Space Center partnered with researchers from the University of Central Florida's chemistry and engineering programs to develop technology capable of remediating the area without great cost or further environmental damage. They called the new invention Emulsified Zero-Valent Iron (EZVI). The groundwater remediation compound is cleaning up polluted areas all around the world and is, to date, NASA's most licensed technology.

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.

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.

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.

Operation of the solvent-refined-coal pilot plant, Wilsonville, Alabama. Annual technical report, January-December 1980

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

Lewis, H.E.

1981-08-01

The plant was in operation for the equivalent of 247 days, an on-stream factor of 67.7%. Kentucky 9 coals from the Lafayette, Dotiki and Fies mines were processed. During 1980, the operating conditions and equipment were adjusted to evaluate potential process improvements. These experiments produced significant results in the following areas: Operating V103 High Pressure Separator in the hot mode; varying T102 Vacuum Column operating temperature; adding light SRC (LSRC), a product of the third stage of the Critical Solvent Deashing (CSD) unit, to the process solvent; investigating the effects of the chlorine content of the feed coal on corrosionmore » in the process vessels; evaluating the effects of adding sodium carbonate on corrosion rates; operating under conditions of low severity; i.e., low reactor temperature and long residence time; and testing an alternate CSD deashing solvent. A series of simulation runs investigating the design operating conditions for a planned 6000 ton per day SRC-I demonstation plant were also completed. Numerous improvements were made in the CSD processing area, and the components for a hydrotreating unit were installed.« less

To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent

PubMed Central

Dahanayake, Jayangika N.; Gautam, Devaki N.; Verma, Rajni; Mitchell-Koch, Katie R.

2016-01-01

The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties. However, a common protocol for non-aqueous enzyme simulations does not exist. If you want to simulate enzymes in non-aqueous solutions, how many and which crystallographic waters do you keep? In the present work, this question is addressed by determining which crystallographic water molecules lead most quickly to an equilibrated protein structure. Five different methods of selecting and keeping crystallographic waters are used in order to discover which crystallographic waters lead the protein structure to reach an equilibrated structure more rapidly in organic solutions. It is found that buried waters contribute most to rapid equilibration in organic solvent, with slow-diffusing waters giving similar results. PMID:27403032

METRICS OF PERFORMANCE FOR THE SABRE MICROCOSM STUDY (ABSTRACT ONLY)

EPA Science Inventory

The SABRE (Source Area BioREmediation) project will evaluate accelerated anaerobic bioremediation of chlorinated solvents in areas of high concentration, such as DNAPL source areas. In preparation for a field scale pilot test, a laboratory microcosm study was conducted to provide...

CHARACTERIZING THE MICROBIAL COMMUNITY IN SABRE MICROCOSM STUDIES (ABSTRACT ONLY)

EPA Science Inventory

The SABRE (Source Area BioREmediation) project will evaluate accelerated anaerobic bioremediation of chlorinated solvents in areas of high concentration, such as DNAPL source areas. In preparation for a field scale pilot test, laboratory microcosm and column studies were conducte...

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…

Quenching of Tryptophan Fluorescence in Unfolded Cytochrome "c": A Biophysics Experiment for Physical Chemistry Students

ERIC Educational Resources Information Center

Schlamadinger, Diana E.; Kats, Dina I.; Kim, Judy E.

2010-01-01

Laboratory experiments that focus on protein folding provide excellent opportunities for undergraduate students to learn important topics in the expanding interdisciplinary field of biophysics. Here, we describe the use of Stern-Volmer plots to determine the extent of solvent accessibility of the single tryptophan residue (trp-59) in unfolded and…

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.

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.

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.

Evaluation of the effect of extraction solvent and organ selection on the chemical profile of Astragalus spinosus using HPTLC- multivariate image analysis.

PubMed

Shawky, Eman; Selim, Dina A

2017-09-01

The evaluation of extraction protocols for untargeted and targeted metabolomics was implemented for root and aerial organs of Astragalus spinosus in this work. The efficiency and complementarity of commonly used extraction solvents, namely petroleum ether, methylene chloride, ethyl acetate and n-butanol were considered for method evaluation using chemometric techniques in conjunction with new, simple, and fast high performance thin layer chromatography (HPTLC) method for fingerprint analysis by extracting information from a digitalized HPTLC plate using ImageJ software. A targeted approach was furtherly implemented by developing and validating an HPTLC method allowing the quantification of three saponin glycosides. The results of untargeted and targeted principle component analysis (PCA) and hierarchical cluster analysis (HCA) revealed that the apparent saponins profile seems to depend on a combined effect of matrix composition and the properties of the selected solvent for extraction, where both the biological matrix of the investigated plant organs, as well as the extraction solvent can influence the precision of metabolite abundances. Although, the aerial part is frequently discarded as waste, it is shown hereby that it has similar chemical profile compared to the medicinal part, roots, yet a different extraction solvents pattern is recognized between the two organs which can be attributed to the differences in the composition, permeability or accessibility of the sample matrix/organ tissues, rather than the chemical structures of the detected metabolites. Copyright © 2017 Elsevier B.V. All rights reserved.

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).

An easy access to nanocrystalline alkaline earth metal fluorides - just by shaking

NASA Astrophysics Data System (ADS)

Dreger, M.; Scholz, G.; Kemnitz, E.

2012-04-01

High energy ball milling as fast, direct and solvent free method allows an easy access to nanocrystalline alkaline earth metal fluorides MF2 (M: Mg, Ca, Sr, Ba). Comparable metal sources (acetates, carbonates, hydroxides, alkoxides) were used for the reaction with NH4F as fluorinating agent. Even very simple manual shaking experiments between NH4F and the corresponding hydroxides in the stoichiometric ratio (M:F = 1:2, M: Ca, Sr, Ba) give phase pure fluorides. Moreover, comparable classical thermal reactions in closed crucibles at higher temperatures provide phase pure crystalline fluorides in nearly all cases as well.

Emulsified Zero-Valent Nano-Scale Iron Treatment of Chlorinated Solvent DNAPL Source Areas

DTIC Science & Technology

2010-09-01

Significant laboratory and field research has demonstrated that zero-valent metals will reductively dehalogenate dissolved chlorinated solvents such as...Eekert, Servé W. M. Kengen, Gosse Schraa, and Alfons J. M. Stams. 1999. Anaerobic Microbial Reductive Dehalogenation of Chlorinated Ethenes...and T. Holdsworth. 2005. Field Demonstration of DNAPL Dehalogenation Using Emulsified Zero-Valent Iron. Environmental Science Technology, vol 39

The second evolution of ionic liquids: from solvents and separations to advanced materials--energetic examples from the ionic liquid cookbook.

PubMed

Smiglak, Marcin; Metlen, Andreas; Rogers, Robin D

2007-11-01

In this Account of the small portion of the recent research in ionic liquids (ILs) by the Rogers Group, we fast forward through the first evolution of IL research, where ILs were studied for their unique set of physical properties and the resulting potential for tunable "green solvents", to the second evolution of ILs, where the tunability of the cation and anion independently offers almost unlimited access to targeted combinations of physical and chemical properties. This approach is demonstrated here with the field of energetic ionic liquids (EILs), which utilizes this design flexibility to find safe synthetic routes to ILs with high energy content and targeted physical properties.

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.

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.

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.

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.

Multiprobe Spectroscopic Inverstigation of Molecular-level Behavior within Aqueous 1-Butyl-3-methylimidazolium Tetrafluoroborate

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

Sarkar, Abhra; Ali, Maroof; Baker, Gary A

2009-01-01

In this work, an array of molecular-level solvent featuressincluding solute-solvent/solvent-solvent interactions, dipolarity, heterogeneity, dynamics, probe accessibility, and diffusionswere investigated across the entire composition of ambient mixtures containing the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate, [bmim][BF4], and pH 7.0 phosphate buffer, based on results assembled for nine different molecular probes utilized in a range of spectroscopic modes. These studies uncovered interesting and unusual solvatochromic probe behavior within this benchmark mixture. Solvatochromic absorbance probessa watersoluble betaine dye (betaine dye 33), N,N-diethyl-4-nitroaniline, and 4-nitroanilineswere employed to determine ET (a blend of dipolarity/polarizability and hydrogen bond donor contributions) and the Kamlet-Taft indices * (dipolarity/polarizability), R (hydrogenmore » bond donor acidity), and (hydrogen bond acceptor basicity) characterizing the [bmim][BF4] + phosphate buffer system. These parameters each showed a marked deviation from ideality, suggesting selective solvation of the individual probe solutes by [bmim][BF4]. Similar conclusions were derived from the responses of the fluorescent polarity-sensitive probes pyrene and pyrene-1-carboxaldehyde. Importantly, the fluorescent microfluidity probe 1,3-bis(1-pyrenyl)propane senses a microviscosity within the mixture that significantly exceeds expectations derived from simple interpolation of the behavior in the neat solvents. On the basis of results from this probe, a correlation between microviscosity and bulk viscosity was established; pronounced solvent-solvent hydrogen-bonding interactions were implicit in this behavior. The greatest deviation from ideal additive behavior for the probes studied herein was consistently observed to occur in the buffer-rich regime. Nitromethane-based fluorescence quenching of pyrene within the [bmim][BF4] + phosphate buffer system showed unusual compliance with a sphere-of-action quenching model, a further manifestation of the microheterogeneity of the system. Fluorescence correlation spectroscopic results for both small (BODIPY FL) and macromolecular (Texas Red-10 kDa dextran conjugate) diffusional probes provide additional evidence in support of microphase segregation inherent to aqueous [bmim][BF4].« less

Cluster-continuum quasichemical theory calculation of the lithium ion solvation in water, acetonitrile and dimethyl sulfoxide: an absolute single-ion solvation free energy scale.

PubMed

Carvalho, Nathalia F; Pliego, Josefredo R

2015-10-28

Absolute single-ion solvation free energy is a very useful property for understanding solution phase chemistry. The real solvation free energy of an ion depends on its interaction with the solvent molecules and on the net potential inside the solute cavity. The tetraphenyl arsonium-tetraphenyl borate (TATB) assumption as well as the cluster-continuum quasichemical theory (CC-QCT) approach for Li(+) solvation allows access to a solvation scale excluding the net potential. We have determined this free energy scale investigating the solvation of the lithium ion in water (H2O), acetonitrile (CH3CN) and dimethyl sulfoxide (DMSO) solvents via the CC-QCT approach. Our calculations at the MP2 and MP4 levels with basis sets up to the QZVPP+diff quality, and including solvation of the clusters and solvent molecules by the dielectric continuum SMD method, predict the solvation free energy of Li(+) as -116.1, -120.6 and -123.6 kcal mol(-1) in H2O, CH3CN and DMSO solvents, respectively (1 mol L(-1) standard state). These values are compatible with the solvation free energy of the proton of -253.4, -253.2 and -261.1 kcal mol(-1) in H2O, CH3CN and DMSO solvents, respectively. Deviations from the experimental TATB scale are only 1.3 kcal mol(-1) in H2O and 1.8 kcal mol(-1) in DMSO solvents. However, in the case of CH3CN, the deviation reaches a value of 9.2 kcal mol(-1). The present study suggests that the experimental TATB scale is inconsistent for CH3CN. A total of 125 values of the solvation free energy of ions in these three solvents were obtained. These new data should be useful for the development of theoretical solvation models.

Solventless and solvent-minimized sample preparation techniques for determining currently used pesticides in water samples: a review.

PubMed

Tankiewicz, Maciej; Fenik, Jolanta; Biziuk, Marek

2011-10-30

The intensification of agriculture means that increasing amounts of toxic organic and inorganic compounds are entering the environment. The pesticides generally applied nowadays are regarded as some of the most dangerous contaminants of the environment. Their presence in the environment, especially in water, is hazardous because they cause human beings to become more susceptible to disease. For these reasons, it is essential to monitor pesticide residues in the environment with the aid of all accessible analytical methods. The analysis of samples for the presence of pesticides is problematic, because of the laborious and time-consuming operations involved in preparing samples for analysis, which themselves may be a source of additional contaminations and errors. To date, it has been standard practice to use large quantities of organic solvents in the sample preparation process; but as these solvents are themselves hazardous, solventless and solvent-minimized techniques are coming into use. This paper discusses the most commonly used over the last 15 years sample preparation techniques for monitoring organophosphorus and organonitrogen pesticides residue in water samples. Furthermore, a significant trend in sample preparation, in accordance with the principles of 'Green Chemistry' is the simplification, miniaturization and automation of analytical techniques. In view of this aspect, several novel techniques are being developed in order to reduce the analysis step, increase the sample throughput and to improve the quality and the sensitivity of analytical methods. The paper describes extraction techniques requiring the use of solvents - liquid-liquid extraction (LLE) and its modifications, membrane extraction techniques, hollow fibre-protected two-phase solvent microextraction, liquid phase microextraction based on the solidification of a floating organic drop (LPME-SFO), solid-phase extraction (SPE) and single-drop microextraction (SDME) - as well as solvent-free techniques - solid phase microextraction (SPME) and stir bar sorptive extraction (SBSE). The advantages and drawbacks of these techniques are also discussed, and some solutions to their limitations are proposed. Copyright © 2011 Elsevier B.V. All rights reserved.

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.

Halogenated solvent remediation

DOEpatents

Sorenson, Kent S.

2004-08-31

Methods for enhancing bioremediation of ground water contaminated with nonaqueous halogenated solvents are disclosed. A preferred method includes adding a composition to the ground water wherein the composition is an electron donor for microbe-mediated reductive dehalogenation of the halogenated solvents and enhances mass transfer of the halogenated solvents from residual source areas into the aqueous phase of the ground water. Illustrative compositions effective in these methods include surfactants such as C.sub.2 -C.sub.4 carboxylic acids and hydroxy acids, salts thereof, esters of C.sub.2 -C.sub.4 carboxylic acids and hydroxy acids, and mixtures thereof. Especially preferred compositions for use in these methods include lactic acid, salts of lactic acid, such as sodium lactate, lactate esters, and mixtures thereof. The microbes are either indigenous to the ground water, or such microbes can be added to the ground water in addition to the composition.

Fundamental investigation of stress corrosion cracking

NASA Technical Reports Server (NTRS)

Beck, T. R.; Blackburn, M. J.; Smyrl, W. H.

1972-01-01

Two principle areas studied were stress corrosion crack growth rates of a titanium alloy in liquid environments containing halide ions and pitting corrosion of titanium in bromide solutions. Two initial assumptions were made, that the rate of propagation was controlled by a macroscopic solution parameter and that this parameter was viscosity. A series of solutions were prepared using lithium chloride as the solute and water, methanol, glycerin, formic acid, acetone, dimethyl sulphoxide, etc. As solvents, these solutions were prepared with a 5:1 solvent-solute ratio. Viscosity was varied by changing the temperature and it was found: (1) In all solvents the velocity of cracking was proportional to the reciprocal of the viscosity. (2) Each solvent gave a separate relationship, (3) The temperature dependence and numerical values for the apparent activation energy of cracking and viscosity were the same.

50 CFR 648.59 - Sea Scallop Access Areas.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Sea Scallop Access Areas. 648.59 Section... Atlantic Sea Scallop Fishery § 648.59 Sea Scallop Access Areas. (a) Delmarva Sea Scallop Access Area. (1... in or from the area known as the Delmarva Sea Scallop Access Area, described in paragraph (a)(2) of...

50 CFR 648.59 - Sea Scallop Access Areas.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 12 2013-10-01 2013-10-01 false Sea Scallop Access Areas. 648.59 Section... Atlantic Sea Scallop Fishery § 648.59 Sea Scallop Access Areas. (a) [Reserved] (b) Closed Area I Access... whereby the vessel gains a Closed Area I Access Area trip and gives up a trip into another Sea Scallop...

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.

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.

Solvent exposure and related work practices amongst apprentice spray painters in automotive body repair workshops.

PubMed

Winder, C; Turner, P J

1992-08-01

As part of a multidisciplinary study into the health effects of solvents, workplace assessments and airborne solvent vapour monitoring was conducted in 46 spray painting workshops in the Sydney metropolitan area. Breathing-zone samples were taken from 50 apprentices and 14 experienced spray painters. An interview schedule was developed to obtain information about the use of acrylic or two-pack paint systems, the use of engineering controls, the use of personal protective equipment and the availability of material safety data sheets. Contaminants typical of the chemical products used in this industry were encountered (aromatic hydrocarbons, C5-C7 aliphatic hydrocarbons, ketones, esters). The results of airborne solvent monitoring indicate a total solvent exposure in the range 1-99% of a combined Worksafe Australia exposure standard, with a mean of 19%. Solvent exposure was highest when spraying acrylic paint in the open workshop and lowest when spraying two pack paint in a spray booth. Much the same personal protective equipment was available in all workshops, but wide variation in its use was observed. Material safety data sheets were not observed in any of the workshops.

Characterizing The Microbial Community In A TCE DNAPL Site: SABRE Column And Field Studies

EPA Science Inventory

The SABRE (Source Area BioREmediation) project is evaluating accelerated anaerobic bioremediation of chlorinated solvents in areas of high concentration, such as DNAPL source areas. In support of a field scale pilot test, column studies were conducted to design the system and ob...

Spatial And Temporal Distribution Of Microbial Communities In A TCE DNAPL Site: SABRE Field Studies

EPA Science Inventory

The SABRE (Source Area BioREmediation) project was conducted to evaluate accelerated anaerobic bioremediation of chlorinated solvents in areas of high concentration, such as DNAPL source areas. To study performance of this technology, a test cell was constructed with a longitudi...

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

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

50 CFR 648.59 - Sea Scallop Access Areas.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 10 2011-10-01 2011-10-01 false Sea Scallop Access Areas. 648.59 Section... Atlantic Sea Scallop Fishery § 648.59 Sea Scallop Access Areas. (a) Delmarva Sea Scallop Access Area. (1... Sea Scallop Access Area, described in paragraph (a)(2) of this section, only if the vessel is...

50 CFR 648.59 - Sea Scallop Access Areas.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 12 2012-10-01 2012-10-01 false Sea Scallop Access Areas. 648.59 Section... Atlantic Sea Scallop Fishery § 648.59 Sea Scallop Access Areas. (a) Delmarva Sea Scallop Access Area. (1... Sea Scallop Access Area, described in paragraph (a)(2) of this section, only if the vessel is...

Implementation of picoSpin Benchtop NMR Instruments into Organic Chemistry Teaching Laboratories through Spectral Analysis of Fischer Esterification Products

ERIC Educational Resources Information Center

Yearty, Kasey L.; Sharp, Joseph T.; Meehan, Emma K.; Wallace, Doyle R.; Jackson, Douglas M.; Morrison, Richard W.

2017-01-01

[Superscript 1]H NMR analysis is an important analytical technique presented in introductory organic chemistry courses. NMR instrument access is limited for undergraduate organic chemistry students due to the size of the instrument, price of NMR solvents, and the maintenance level required for instrument upkeep. The University of Georgia Chemistry…

A rapid, one-pot, microwave-influenced synthesis of spiro-2,5-diketopiperazines via a cascade Ugi/6-exo-trig aza-Michael reaction.

PubMed

Santra, Soumava; Andreana, Peter R

2011-04-01

A rapid, cascade reaction process has been developed to access biologically validated spiro-2,5-diketopiperazines. The facile and environmentally benign method capitalizes on commercially available starting reagents for a sequential Ugi/6-exo-trig aza-Michael reaction, water as a solvent, and microwave irradiation without any extraneous additives.

Classes of organic molecules targeted by a methanogenic microbial consortium grown on sedimentary rocks of various maturities

PubMed Central

Meslé, Margaux; Dromart, Gilles; Haeseler, Frank; Oger, Philippe M.

2015-01-01

Organic-rich shales are populated by methanogenic consortia that are able to degrade the fossilized organic matter into methane gas. To identify the organic fraction effectively degraded, we have sequentially depleted two types of organic-rich sedimentary rocks, shale, and coal, at two different maturities, by successive solvent extractions to remove the most soluble fractions (maltenes and asphaltenes) and isolate kerogen. We show the ability of the consortia to produce methane from all rock samples, including those containing the most refractory organic matter, i.e., the kerogen. Shales yielded higher methane production than lignite and coal. Mature rocks yielded more methane than immature rocks. Surprisingly, the efficiency of the consortia was not influenced by the removal of the easily biodegradable fractions contained in the maltenes and asphaltenes. This suggests that one of the limitations of organic matter degradation in situ may be the accessibility to the carbon and energy source. Indeed, bitumen has a colloidal structure that may prevent the microbial consortia from reaching the asphaltenes in the bulk rock. Solvent extractions might favor the access to asphaltenes and kerogen by modifying the spatial organization of the molecules in the rock matrix. PMID:26136731

A layered microchip conductance detector with through-layer access to detection fields and high sensitivity to dielectric constant.

PubMed

Suganuma, Y; Dhirani, A-A

2011-04-01

The present study explores a novel apertured microchip conductance detector (AMCD) that is sensitive to dielectric constant. Fashioned on silicon oxide/silicon using optical microlithography, the detector has novel parallel-plate geometry with a top mesh electrode, a middle apertured insulator, and a bottom conducting electrode. This monolithic apertured architecture is planar and may be provided with a thin insulator layer enabling large capacitances, while the top mesh electrode and middle apertured-insulator enable access to regions of the capacitor where electric fields are strong. Hence, the detector is sensitive yet mechanically robust. To test its response, the AMCD was immersed in various solvents, namely water, methanol, acetonitrile, and hexanes. Its response was found to vary in proportion to the solvents' respective dielectric constants. The AMCD was also able to distinguish quantitatively the presence of various molecules in solution, including molecules with chromophores [such as acetylsalicylic acid (ASA)] in methanol and those without chrompohores [such as polyethylene glycol 200 Daltons (PEG200)] in methanol or water. The universal nature of dielectric constant and the microchip detector's sensitivity point to a wide range of potential applications. © 2011 American Institute of Physics

Field comparison of thermal and non-thermal ultra-low-volume applications using water and diesel as solvents for managing dengue vector, Aedes aegypti.

PubMed

Harburguer, Laura; Lucia, Alejandro; Licastro, Susana; Zerba, Eduardo; Masuh, Héctor

2012-10-01

To compare the effectiveness on Aedes aegypti (Linneo) (Diptera: Culicidae) of a larvicide-adulticide ULV formulation applied by a thermal or a cold fogger using different solvents. We applied, in field conditions, a ULV formulation containing pyriproxyfen and permethrin, using a thermal and a cold fogger and water or diesel as solvent. We determined the effectiveness of these applications on Ae. aegypti adults and larvae by different bioassays and measuring Breteau, house and adult indices. When water was used as solvent, the treatments applied with the cold or the thermal foggers were equally effective on adult mortality (close to 90%) and adult emergence inhibition (% EI) (close to 70%). When the thermal fogger was used with water as solvent, the adult mortality outside the houses (85%) was higher, but not significantly different, than with diesel (65%). The contrary happens inside (22%vs. 58%), while there were no differences in %EI. Adult and larval indices behaved similarly in all areas, with a slight tendency for the treatments applied using water as solvent to be more effective. Water-based formulations are equally or more effective than the one applied with diesel as solvent. The use of water as solvent will not only improve the effectiveness of this formulation but also reduce the environmental impact and costs of spraying compared to the use of diesel. © 2012 Blackwell Publishing Ltd.

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.

Bottom-up view of water network-mediated CO2 reduction using cryogenic cluster ion spectroscopy and direct dynamics simulations.

PubMed

Breen, Kristin J; DeBlase, Andrew F; Guasco, Timothy L; Voora, Vamsee K; Jordan, Kenneth D; Nagata, Takashi; Johnson, Mark A

2012-01-26

The transition states of a chemical reaction in solution are generally accessed through exchange of thermal energy between the solvent and the reactants. As such, an ensemble of reacting systems approaches the transition state configuration of reactant and surrounding solvent in an incoherent manner that does not lend itself to direct experimental observation. Here we describe how gas-phase cluster chemistry can provide a detailed picture of the microscopic mechanics at play when a network of six water molecules mediates the trapping of a highly reactive "hydrated electron" onto a neutral CO(2) molecule to form a radical anion. The exothermic reaction is triggered from a metastable intermediate by selective excitation of either the reactant CO(2) or the water network, which is evidenced by the evaporative decomposition of the product cluster. Ab initio molecular dynamics simulations of energized CO(2)·(H(2)O)(6)(-) clusters are used to elucidate the nature of the network deformations that mediate intracluster electron capture, thus revealing the detailed solvent fluctuations implicit in the Marcus theory for electron-transfer kinetics in solution.

Psychophysical Evaluation of Achromatic and Chromatic Vision of Workers Chronically Exposed to Organic Solvents

PubMed Central

Lacerda, Eliza Maria da Costa Brito; Lima, Monica Gomes; Rodrigues, Anderson Raiol; Teixeira, Cláudio Eduardo Correa; de Lima, Lauro José Barata; Ventura, Dora Fix; Silveira, Luiz Carlos de Lima

2012-01-01

The purpose of this paper was to evaluate achromatic and chromatic vision of workers chronically exposed to organic solvents through psychophysical methods. Thirty-one gas station workers (31.5 ± 8.4 years old) were evaluated. Psychophysical tests were achromatic tests (Snellen chart, spatial and temporal contrast sensitivity, and visual perimetry) and chromatic tests (Ishihara's test, color discrimination ellipses, and Farnsworth-Munsell 100 hue test—FM100). Spatial contrast sensitivities of exposed workers were lower than the control at spatial frequencies of 20 and 30 cpd whilst the temporal contrast sensitivity was preserved. Visual field losses were found in 10–30 degrees of eccentricity in the solvent exposed workers. The exposed workers group had higher error values of FM100 and wider color discrimination ellipses area compared to the controls. Workers occupationally exposed to organic solvents had abnormal visual functions, mainly color vision losses and visual field constriction. PMID:22220188

An overview of NASA testing requirements for alternate cleaning solvents used in liquid and gaseous oxygen environments

NASA Technical Reports Server (NTRS)

Strickland, John W.; Davis, S. Eddie

1995-01-01

The elimination of CFC-containing cleaning solvents for oxygen systems has prompted the development of a number of alternative cleaning solvents that must now be evaluated not only for cleanability, but compatibility as well. NASA Handbook 8060.1(NHB 8060.1) establishes the requirements for evaluation, testing, and selection of materials for use in oxygen rich environments. Materials intended for use in space vehicles, specified test facilities, and ground support equipment must meet the requirements of this document. In addition to the requirements of NHB 8060.1 for oxygen service, alternative cleaning solvents must also be evaluated in other areas (such as corrosivity, non-metals compatibility, non-volatile residue contamination, etc.). This paper will discuss the testing requirements of NHB 8060.1 and present preliminary results from early screening tests performed at Marshall Space Flight Center's Materials Combustion Research Facility.

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.

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

Towards sustainable and safe apparel cleaning methods: A review.

PubMed

Troynikov, Olga; Watson, Christopher; Jadhav, Amit; Nawaz, Nazia; Kettlewell, Roy

2016-11-01

Perchloroethylene (PERC) is a compound commonly used as a solvent in dry cleaning, despite its severe health and environmental impacts. In recent times chemicals such as hydrocarbons, GreenEarth(®), acetal and liquid carbon dioxide have emerged as less damaging substitutes for PERC, and an even more sustainable water-based wet cleaning process has been developed. We employed a systematic review approach to provide a comprehensive overview of the existing research evidence in the area of sustainable and safe apparel cleaning methods and care. Our review describes traditional professional dry cleaning methods, as well as those that utilise solvents other than PERC, and their ecological attributes. In addition, the new professional wet cleaning process is discussed. Finally, we address the health hazards of the various solvents used in dry cleaning and state-of-the-art solvent residue trace analysis techniques. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

Combining Crystallography and Hydrogen-Deuterium Exchange to Study Galectin-Ligand Complexes.

PubMed

Ruiz, Federico M; Gilles, Ulrich; Lindner, Ingo; André, Sabine; Romero, Antonio; Reusch, Dietmar; Gabius, Hans-Joachim

2015-09-21

The physiological significance arising from translating information stored in glycans into cellular effects explains the interest in structurally defining lectin-carbohydrate recognition. The relatively small set of adhesion/growth-regulatory galectins in chicken makes this system attractive to study the origins of specificity and divergence. Cell binding by using glycosylation mutants reveals binding of the N-terminal domain of chicken galectin-8 (CG-8N) to α-2,3-sialylated and galactose-terminated glycan chains. Cocrystals with lactose and its 3'-sialylated derivative disclose Arg58 as a key contact for the carboxylic acid and differences in loop lengths to the three homodimeric chicken galectins. Monitoring hydrogen-deuterium exchange by mass spectrometry revealed an effective reduction of deuteration after ligand binding within the contact area. In addition, evidence for changes in solvent accessibility of amide protons beyond this site was obtained. Their detection, which highlights the sensor capacity of this technique, encourages systematic studies on galectins and beyond. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Ultra-large supramolecular coordination cages composed of endohedral Archimedean and Platonic bodies

NASA Astrophysics Data System (ADS)

Byrne, Kevin; Zubair, Muhammad; Zhu, Nianyong; Zhou, Xiao-Ping; Fox, Daniel S.; Zhang, Hongzhou; Twamley, Brendan; Lennox, Matthew J.; Düren, Tina; Schmitt, Wolfgang

2017-05-01

Pioneered by Lehn, Cram, Peterson and Breslow, supramolecular chemistry concepts have evolved providing fundamental knowledge of the relationships between the structures and reactivities of organized molecules. A particular fascinating class of metallo-supramolecular molecules are hollow coordination cages that provide cavities of molecular dimensions promoting applications in diverse areas including catalysis, enzyme mimetics and material science. Here we report the synthesis of coordination cages with exceptional cross-sectional diameters that are composed of multiple sub-cages providing numerous distinctive binding sites through labile coordination solvent molecules. The building principles, involving Archimedean and Platonic bodies, renders these supramolecular keplerates as a class of cages whose composition and topological aspects compare to characteristics of edge-transitive {Cu2} MOFs with A3X4 stoichiometry. The nature of the cavities in these double-shell metal-organic polyhedra and their inner/outer binding sites provide perspectives for post-synthetic functionalizations, separations and catalysis. Transmission electron microscopy studies demonstrate that single molecules are experimentally accessible.

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.

Ultra-large supramolecular coordination cages composed of endohedral Archimedean and Platonic bodies

PubMed Central

Byrne, Kevin; Zubair, Muhammad; Zhu, Nianyong; Zhou, Xiao-Ping; Fox, Daniel S.; Zhang, Hongzhou; Twamley, Brendan; Lennox, Matthew J.; Düren, Tina; Schmitt, Wolfgang

2017-01-01

Pioneered by Lehn, Cram, Peterson and Breslow, supramolecular chemistry concepts have evolved providing fundamental knowledge of the relationships between the structures and reactivities of organized molecules. A particular fascinating class of metallo-supramolecular molecules are hollow coordination cages that provide cavities of molecular dimensions promoting applications in diverse areas including catalysis, enzyme mimetics and material science. Here we report the synthesis of coordination cages with exceptional cross-sectional diameters that are composed of multiple sub-cages providing numerous distinctive binding sites through labile coordination solvent molecules. The building principles, involving Archimedean and Platonic bodies, renders these supramolecular keplerates as a class of cages whose composition and topological aspects compare to characteristics of edge-transitive {Cu2} MOFs with A3X4 stoichiometry. The nature of the cavities in these double-shell metal-organic polyhedra and their inner/outer binding sites provide perspectives for post-synthetic functionalizations, separations and catalysis. Transmission electron microscopy studies demonstrate that single molecules are experimentally accessible. PMID:28485392

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.

Acquired Color Vision Defects and Hexane Exposure: A Study of San Francisco Bay Area Automotive Mechanics.

PubMed

Beckman, Stella; Eisen, Ellen A; Bates, Michael N; Liu, Sa; Haegerstrom-Portnoy, Gunilla; Hammond, S Katharine

2016-06-01

Occupational exposure to solvents, including n-hexane, has been associated with acquired color vision defects. Blue-yellow defects are most common and may be due to neurotoxicity or retinal damage. Acetone may potentiate the neurotoxicity of n-hexane. We present results on nonhexane solvent and hexane exposure and color vision from a cross-sectional study of 835 automotive repair workers in the San Francisco Bay Area, California (2007-2013). Cumulative exposure was estimated from self-reported work history, and color vision was assessed using the Lanthony desaturated D-15 panel test. Log-binomial regression was used to estimate prevalence ratios for color vision defects. Acquired color vision defects were present in 29% of participants, of which 70% were blue-yellow. Elevated prevalence ratios were found for nonhexane solvent exposure, with a maximum of 1.31 (95% confidence interval (CI): 0.86, 2.00) for blue-yellow. Among participants aged ≤50 years, the prevalence ratio for blue-yellow defects was 2.17 (95% CI: 1.03, 4.56) in the highest quartile of nonhexane solvent exposure and 1.62 (95% CI: 0.97, 2.72) in the highest category of exposure to hexane with acetone coexposure. Cumulative exposures to hexane and nonhexane solvents in the highest exposure categories were associated with elevated prevalence ratios for color vision defects in younger participants. © The Author 2016. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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.

Solvent-Free Toner Printing of Organic Semiconductor Layer in Flexible Thin-Film Transistors

NASA Astrophysics Data System (ADS)

Sakai, Masatoshi; Koh, Tokuyuki; Toyoshima, Kenji; Nakamori, Kouta; Okada, Yugo; Yamauchi, Hiroshi; Sadamitsu, Yuichi; Shinamura, Shoji; Kudo, Kazuhiro

2017-07-01

A solvent-free printing process for printed electronics is successfully developed using toner-type patterning of organic semiconductor toner particles and the subsequent thin-film formation. These processes use the same principle as that used for laser printing. The organic thin-film transistors are prepared by electrically distributing the charged toner onto a Au electrode on a substrate film, followed by thermal lamination. The thermal lamination is effective for obtaining an oriented and crystalline thin film. Toner printing is environmentally friendly compared with other printing technologies because it is solvent free, saves materials, and enables easy recycling. In addition, this technology simultaneously enables both wide-area and high-resolution printing.

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.

Brazing method

DOEpatents

McCormick, James T.; Ferry, Paul B.; Hall, John C.

1981-10-06

There is disclosed a positive cathode electrode structure formed by brazing a thin porous membrane to a backing material by preselecting a predetermined area of the thin porous membrane and thereafter providing a braze flow barrier throughout the remainder of the membrane and electrolessly plating a nickel-phosphide alloy on the backing material, or in this case the honeycomb structure. The preselected area of the thin porous membrane is placed in intimate contact with the electrolessly plated portion of the backing material and heated to elevated temperatures in the absence of oxygen to form a brazed joint limited to a preselected area. If the braze flow barrier is provided by application of a liquid organic solvent, then the organic solvent is driven off by maintaining the thin porous membrane at elevated temperatures for an extended period of time prior to the brazing operation.

Study on the Preparation Process and Influential Factors of Large Area Environment-friendly Molten Carbonate Fuel Cell Matrix

NASA Astrophysics Data System (ADS)

Zhang, Ruiyun; Xu, Shisen; Cheng, Jian; Wang, Hongjian; Ren, Yongqiang

2017-07-01

Low-cost and high-performance matrix materials used in mass production of molten carbonate fuel cell (MCFC) were prepared by automatic casting machine with α-LiAlO2 powder material synthesized by gel-solid method, and distilled water as solvent. The single cell was assembled for generating test, and the good performance of the matrix was verified. The paper analyzed the factors affecting aqueous tape casting matrix preparation, such as solvent content, dispersant content, milling time, blade height and casting machine running speed, providing a solid basis for the mass production of large area environment-friendly matrix used in molten carbonate fuel cell.

Quality of Chemical Safety Information in Printing Industry.

PubMed

Tsai, Chung-Jung; Mao, I-Fang; Ting, Jo-Yu; Young, Chi-Hsien; Lin, Jhih-Sian; Li, Wei-Lun

2016-04-01

Employees in printing industries can be exposed to multiple solvents in their work environment. The objectives of this study were to investigate the critical components of chemical solvents by analyzing the components of the solvents and collecting the Safety data sheets (SDSs), and to evaluate the hazard communication implementation status in printing industries. About 152 printing-related industries were recruited by area-stratified random sampling and included 23 plate-making, 102 printing and 27 printing-assistance companies in Taiwan. We analyzed company questionnaires (n = 152), SDSs (n = 180), and solvents (n = 20) collected from this sample of printing-related companies. Analytical results indicated that benzene and ethylbenzene, which were carcinogen and possibly carcinogen, were detectable in the cleaning solvents, and the detection rate were 54.5% (concentrations: <0.011-0.035 wt%) and 63.6% (concentrations: <0.011-6.22 wt%), respectively; however, neither compound was disclosed in the SDS for the solvents. Several other undisclosed components, including methanol, isopropanol and n-butanol, were also identified in the printing inks, fountain solutions and dilution solvents. We noted that, of the companies we surveyed, only 57.2% had a hazard communication program, 61.8% had SDSs on file and 59.9% provided employee safety and health training. We note that hazard communication programs were missing or ineffective in almost half of the 152 printing industries surveyed. Current safety information of solvents components in printing industries was inadequate, and many hazardous compounds were undisclosed in the SDSs of the solvents or the labels of the containers. The implementation of hazard communications in printing industries was still not enough for protecting the employees' safety and health. © The Author 2015. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

Quality of Chemical Safety Information in Printing Industry

PubMed Central

Tsai, Chung-Jung; Mao, I-Fang; Ting, Jo-Yu; Young, Chi-Hsien; Lin, Jhih-Sian; Li, Wei-Lun

2016-01-01

Objectives: Employees in printing industries can be exposed to multiple solvents in their work environment. The objectives of this study were to investigate the critical components of chemical solvents by analyzing the components of the solvents and collecting the Safety data sheets (SDSs), and to evaluate the hazard communication implementation status in printing industries. Method: About 152 printing-related industries were recruited by area-stratified random sampling and included 23 plate-making, 102 printing and 27 printing-assistance companies in Taiwan. We analyzed company questionnaires (n = 152), SDSs (n = 180), and solvents (n = 20) collected from this sample of printing-related companies. Results: Analytical results indicated that benzene and ethylbenzene, which were carcinogen and possibly carcinogen, were detectable in the cleaning solvents, and the detection rate were 54.5% (concentrations: <0.011–0.035 wt%) and 63.6% (concentrations: <0.011–6.22 wt%), respectively; however, neither compound was disclosed in the SDS for the solvents. Several other undisclosed components, including methanol, isopropanol and n-butanol, were also identified in the printing inks, fountain solutions and dilution solvents. We noted that, of the companies we surveyed, only 57.2% had a hazard communication program, 61.8% had SDSs on file and 59.9% provided employee safety and health training. We note that hazard communication programs were missing or ineffective in almost half of the 152 printing industries surveyed. Conclusions: Current safety information of solvents components in printing industries was inadequate, and many hazardous compounds were undisclosed in the SDSs of the solvents or the labels of the containers. The implementation of hazard communications in printing industries was still not enough for protecting the employees’ safety and health. PMID:26568584

50 CFR 648.60 - Sea scallop access area program requirements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 12 2013-10-01 2013-10-01 false Sea scallop access area program... Management Measures for the Atlantic Sea Scallop Fishery § 648.60 Sea scallop access area program requirements. (a) A limited access scallop vessel may only fish in the Sea Scallop Access Areas specified in...

50 CFR 648.60 - Sea scallop access area program requirements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 12 2014-10-01 2014-10-01 false Sea scallop access area program... Management Measures for the Atlantic Sea Scallop Fishery § 648.60 Sea scallop access area program requirements. (a) A limited access scallop vessel may only fish in the Sea Scallop Access Areas specified in...

50 CFR 648.60 - Sea scallop area access program requirements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 10 2011-10-01 2011-10-01 false Sea scallop area access program... Management Measures for the Atlantic Sea Scallop Fishery § 648.60 Sea scallop area access program requirements. (a) A limited access scallop vessel may only fish in the Sea Scallop Access Areas specified in...

50 CFR 648.60 - Sea scallop access area program requirements.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 12 2012-10-01 2012-10-01 false Sea scallop access area program... Management Measures for the Atlantic Sea Scallop Fishery § 648.60 Sea scallop access area program requirements. (a) A limited access scallop vessel may only fish in the Sea Scallop Access Areas specified in...

50 CFR 648.60 - Sea scallop area access program requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Sea scallop area access program... Management Measures for the Atlantic Sea Scallop Fishery § 648.60 Sea scallop area access program requirements. (a) A limited access scallop vessel may only fish in the Sea Scallop Access Areas specified in...

50 CFR 648.59 - Sea Scallop Access Areas.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 12 2014-10-01 2014-10-01 false Sea Scallop Access Areas. 648.59 Section... Atlantic Sea Scallop Fishery § 648.59 Sea Scallop Access Areas. (a) [Reserved] (b) Closed Area I Access... not fish for, possess, or land scallops in or from the area known as the Closed Area II Sea Scallop...

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

PubMed

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

2005-06-01

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

Orthogonal protection of saccharide polyols through solvent-free one-pot sequences based on regioselective silylations

PubMed Central

Traboni, Serena; Bedini, Emiliano

2016-01-01

tert-Butyldimethylsilyl (TBDMS) and tert-butyldiphenylsilyl (TBDPS) are alcohol protecting groups widely employed in organic synthesis in view of their compatibility with a wide range of conditions. Their regioselective installation on polyols generally requires lengthy reactions and the use of high boiling solvents. In the first part of this paper we demonstrate that regioselective silylation of sugar polyols can be conducted in short times with the requisite silyl chloride and a very limited excess of pyridine (2–3 equivalents). Under these conditions, that can be regarded as solvent-free conditions in view of the insolubility of the polyol substrates, the reactions are faster than in most examples reported in the literature, and can even be further accelerated with a catalytic amount of tetrabutylammonium bromide (TBAB). The strategy proved also useful for either the selective TBDMS protection of secondary alcohols or the fast per-O-trimethylsilylation of saccharide polyols. In the second part of the paper the scope of the silylation approach was significantly extended with the development of unprecedented “one-pot” and “solvent-free” sequences allowing the regioselective silylation/alkylation (or the reverse sequence) of saccharide polyols in short times. The developed methodologies represent a very useful and experimentally simple tool for the straightforward access to saccharide building-blocks useful in organic synthesis. PMID:28144345

Biomass Processing using Ionic Liquids for Jet Fuel Production

DTIC Science & Technology

2014-04-09

lignocellulosic biomass. Biomass consists predominantly of three biopolymers— lignin , hemicellulose and cellulose. For fuel production, it is necessary to...hydrocarbons. The lignin and cellulose, however, have very low solubility in conventional solvents making processing difficult. Typically a pretreatment step...is used to break up the lignin and make the cellulose accessible to further hydrolysis to glucose. Pretreatment, however, is one of the most

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.

Mixed aqueous solutions as dilution media in the determination of residual solvents by static headspace gas chromatography.

PubMed

D'Autry, Ward; Zheng, Chao; Wolfs, Kris; Yarramraju, Sitaramaraju; Hoogmartens, Jos; Van Schepdael, Ann; Adams, Erwin

2011-06-01

Static headspace (HS) sampling has been commonly used to test for volatile organic chemicals, usually referred to as residual solvents (RS) in pharmaceuticals. If the sample is not soluble in water, organic solvents are used. However, these seriously reduce the sensitivity in the determination of some RS. Here, mixed aqueous dilution media (a mixture of water and an organic solvent like dimethyl formamide, dimethyl sulfoxide or dimethyl acetamide) were studied as alternative media for static HS-gas chromatographic analysis. Although it has been known that mixed aqueous dilution media can often improve sensitivity for many RS, this study used a systematic approach to investigate phase volumes and the organic content in the HS sampling media. Reference solutions using 18 different class 1, 2 and 3 RS were evaluated. The effect of salt addition was also studied in this work. A significant increase in the peak area was observed for all RS using mixed aqueous dilution media, when compared with organic solvents alone. Matrix effects related to the mixed aqueous dilution media were also investigated and reported. Repeatability and linearity obtained with mixed aqueous dilution media were found to be similar to those observed with pure organic solvents. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solvent exposure and cognitive function in automotive technicians.

PubMed

Bates, Michael N; Reed, Bruce R; Liu, Sa; Eisen, Ellen A; Hammond, S Katharine

2016-12-01

Automotive technicians are commonly exposed to organic and chlorinated solvents, particularly through use of cleaning products. Occupational solvent exposures have been associated with deficits in cognitive function but, to our knowledge, no previous studies have investigated automotive technicians. The purpose of the present study was to investigate whether previous exposures to n-hexane, in particular, or general solvents posed a persistent neurotoxic hazard to automotive workers. Enrolled in the study were 830 San Francisco Bay Area automotive repair workers. Each participant underwent a battery of cognitive function tests to investigate central nervous system impairment, with a primary focus on the domains of psychomotor speed, fine motor function, memory and mood. Cognitive test results regressed against estimated hexane and total solvent exposures showed little evidence of associations. Exposures to both solvents and hexane were well below the occupational exposure limits. Our results provide some reassurance about persistent neuropsychological effects in automotive workers who use solvent-based products and those who previously used hexane-containing automotive cleaning products, since this solvent is believed no longer to be used in automotive cleaning products. The lack of observed effect in this study may be attributable to low exposures, or it may reflect improved cognitive function since hexane use in automotive cleaning products was discontinued. However, impacts on results of exposure misclassification and/or the healthy worker survivor effect cannot be discounted. Irrespective of the outcome of this study, the main known neurologic effect of n-hexane is peripheral neuropathy, and such an association in automotive technicians is not excluded by these results. Copyright © 2016 Elsevier B.V. All rights reserved.

Gas discharge visualization evaluation of ultramolecular doses of homeopathic medicines under blinded, controlled conditions.

PubMed

Bell, Iris R; Lewis, Daniel A; Brooks, Audrey J; Lewis, Sabrina E; Schwartz, Gary E

2003-02-01

To determine the feasibility of using a computerized biophysical method, gas discharge visualization (GDV), to differentiate ultramolecular doses of homeopathic remedies from solvent controls and from each other. Blinded, randomized assessment of four split samples each of 30c potencies of three homeopathic remedies from different kingdoms, for example, Natrum muriaticum (mineral), Pulsatilla (plant), and Lachesis (animal), dissolved in a 20% alcohol-water solvent versus two different control solutions (that is, solvent with untreated lactose/sucrose pellets and unsuccussed solvent alone). GDV measurements, involving application of a brief electrical impulse at four different voltage levels, were performed over 10 successive images on each of 10 drops from each bottle (total 400 images per test solution per voltage). The dependent variables were the quantified image characteristics of the liquid drops (form coefficient, area, and brightness) from the resultant burst of electron-ion emission and optical radiation in the visual and ultraviolet ranges. The procedure generated measurable images at the two highest voltage levels. At 17 kV, the remedies exhibited overall lower image parameter values compared with solvents (significant for Pulsatilla and Lachesis), as well as differences from solvents in fluctuations over repeated images (exposures to the same voltage). At 24 kV, other patterns emerged, with individual remedies showing higher or lower image parameters compared with other remedies and the solvent controls. GDV technology may provide an electromagnetic probe into the properties of homeopathic remedies as distinguished from solvent controls. However, the present findings also highlight the need for additional research to evaluate factors that may affect reproducibility of results.

Worker exposure to volatile organic compounds in the vehicle repair industry.

PubMed

Wilson, Michael P; Hammond, S Katharine; Nicas, Mark; Hubbard, Alan E

2007-05-01

This study evaluated exposures among vehicle repair technicians to hexane, acetone, toluene, and total volatile organic compounds (VOCs). On randomly selected workdays, we observed a characteristic pattern of solvent use among 36 technicians employed in 10 repair shops, each of which used an aerosol solvent product. We obtained quantitative exposure measurements from a subset of nine technicians (employed in three of these shops) who used an aerosol product containing hexane (25-35%), acetone (45-55%), and toluene (5-10%). The time-weighted average (TWA) exposure concentration for task-length breathing zone (BZ) samples (n = 23) was 36 mg/m(3) for hexane, 50 mg/m(3) for acetone, and 10 mg/m(3) for toluene. The TWA area concentrations (n = 49) obtained contemporaneously with BZ samples ranged from 25% to 35% of the BZ concentrations. The solvent emission rate (grams emitted/task time) was correlated with the total VOC exposure concentration (R(2) = 0.45). The proportions of VOCs in the BZ samples were highly correlated (r = 0.89 to 0.95) and were similar to those of the bulk product. Continuous exposure measurements for total VOCs (n = 1238) during 26 tasks produced a mean BZ VOC "pulse" of 394 mg/m(3) within 1 min following initiation of solvent spraying. The geometric mean air speed was 5.2 meters/min in the work areas (n = 870) and was associated with 0.8 air changes per minute in the BZ. The findings suggest that vehicle repair technicians who use aerosol solvent products experience episodic, inhalation exposures to the VOCs contained in these products, and the proportions of VOCs in the breathing zone are similar to those of the bulk product. Because acetone appears to amplify the severity and duration of the neurotoxic effects of n-hexane, products formulated with both hexane and acetone should be avoided. Further evaluation of exposures to VOCs is needed in this industry, along with information on effective alternatives to aerosol solvent products.

Direct Push Optical Screening Tool for High-Resolution, Real-Time Mapping of Chlorinated Solvent DNAPL Architecture

DTIC Science & Technology

2016-04-01

due to higher densities, lower viscosities , and increased weathering (mass depletion) of residual chlorinated solvent DNAPL compared to those other...demonstration area can be generally classified as stratified layers of fine sand and silt with few clay layers. A silt layer was penetrated consistently at...toxic and carcinogenic. Another potential issue evaluated was that in plastic soils (stiff clays for example) there is potential for the thickness of

Highly crystalline films of PCPDTBT with branched side chains by solvent vapor crystallization: influence on opto-electronic properties.

PubMed

Fischer, Florian S U; Trefz, Daniel; Back, Justus; Kayunkid, Navaphun; Tornow, Benjamin; Albrecht, Steve; Yager, Kevin G; Singh, Gurpreet; Karim, Alamgir; Neher, Dieter; Brinkmann, Martin; Ludwigs, Sabine

2015-02-18

PCPDTBT, a marginally crystallizable polymer, is crystallized into a new crystal structure using solvent-vapor annealing. Highly ordered areas with three different polymer-chain orientations are identified using TEM/ED, GIWAXS, and polarized Raman spectroscopy. The optical and structural properties differ significantly from films prepared by standard device preparation protocols. Bilayer solar cells, however, show similar performance. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

28. BUILDING NO. 527, DEHYDRATING HOUSE, LOOKING SOUTH AT NORTH ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

28. BUILDING NO. 527, DEHYDRATING HOUSE, LOOKING SOUTH AT NORTH (REAR) ELEVATION OF PRELIMINARY SOLVENT RECOVERY WING. RAILS LEADING FROM DOORS CARRIED STANDARD GUAGE R.R. CARTS ONTO SMALL FLATCARS RIDING IN TRACKS IN FOREGROUND. FROM HERE THE CARS WERE TAKEN TO BUILDING NO. 533, SOLVENT RECOVERY. BUILDING NO. 540, LOADING DOCK (STORAGE FOR POWDER BUGGIES) IN BACKGROUND LEFT. - Picatinny Arsenal, 500 Area, Powder Factory & Power House, State Route 15 near I-80, Dover, Morris County, NJ

Installation Restoration Program. Phase I. Records Search Columbus Air force Base, Mississippi.

DTIC Science & Technology

1985-04-01

with the river flood plains and pine plantations on drier upland areas. Loblolly pine ( Pinus taeda) is the dominant planted pine and is used for pulp...Maintenance MCL maximum contaminant level Methyl ethyl ketone A solvent used in paint thinner, stripper, and a (MEK) wide variety of industrial...l milligrams per liter A-3 Methyl isobutyl A solvent used in paint stripper, thinner, and a - ketone (MIBK) wide variety of industrial applications

Gold Nanoparticle Microwave Synthesis

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

Krantz, Kelsie E.; Christian, Jonathan H.; Coopersmith, Kaitlin

At the nanometer scale, numerous compounds display different properties than those found in bulk material that can prove useful in areas such as medicinal chemistry. Gold nanoparticles, for example, display promise in newly developed hyperthermia therapies for cancer treatment. Currently, gold nanoparticle synthesis is performed via the hot injection technique which has large variability in final particle size and a longer reaction time. One underdeveloped area by which these particles could be produced is through microwave synthesis. To initiate heating, microwaves agitate polar molecules creating a vibration that gives off the heat energy needed. Previous studies have used microwaves formore » gold nanoparticle synthesis; however, polar solvents were used that partially absorbed incident microwaves, leading to partial thermal heating of the sample rather than taking full advantage of the microwave to solely heat the gold nanoparticle precursors in a non-polar solution. Through this project, microwaves were utilized as the sole heat source, and non-polar solvents were used to explore the effects of microwave heating only as pertains to the precursor material. Our findings show that the use of non-polar solvents allows for more rapid heating as compared to polar solvents, and a reduction in reaction time from 10 minutes to 1 minute; this maximizes the efficiency of the reaction, and allows for reproducibility in the size/shape of the fabricated nanoparticles.« less

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.

AIR TOXICS ASSESSMENT REFINEMENT IN RAPCA'S JURISDICTION - DAYTON, OH AREA

EPA Science Inventory

RAPCA has receive two grants to conduct this project. As part of the original project, RAPCA has improved and expanded their point source inventory by converting the following area sources to point sources: dry cleaners, gasoline throughput processes and halogenated solvent clea...

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.

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.

Fast Printing and In-Situ Morphology Observation of Organic Photovoltaics using Slot-Die Coating

NASA Astrophysics Data System (ADS)

Liu, Feng; Ferdous, Sunzida; Wang, Cheng; Hexamer, Alexander; Russell, Thomas; Cheng Wang Collaboration; Thomas Russell Team

2014-03-01

The solvent-processibility of polymer semiconductors is a key advantage for the fabrication of large area, organic bulk-heterojunction (BHJ) photovoltaic devices. Most reported power conversion efficiencies (PCE) are based on small active areas, fabricated by spin-coating technique. In general, this does not reflect device fabrication in an industrial setting. To realize commercial viability, devices need to be fabricated in a roll-to-roll fashion. The evolution of the morphology associated with different processing parameters, like solvent choice, concentration and temperature, needs to be understood and controlled. We developed a mini slot-die coater, to fabricate BHJ devices using various low band gap polymers mixed with phenyl-C71-butyric acid methyl ester (PCBM). Solvent choice, processing additives, coating rate and coating temperatures were used to control the final morphology. Efficiencies comparable to lab-setting spin-coated devices are obtained. The evolution of the morphology was monitored by in situ scattering measurements, detecting the onset of the polymer chain packing in solution that led to the formation of a fibrillar network in the film.

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.

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.

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.

Liquefaction of Biopolymers: Solvent-free Liquids and Liquid Crystals from Nucleic Acids and Proteins.

PubMed

Liu, Kai; Ma, Chao; Göstl, Robert; Zhang, Lei; Herrmann, Andreas

2017-05-16

Biomacromolecules, such as nucleic acids, proteins, and virus particles, are persistent molecular entities with dimensions that exceed the range of their intermolecular forces hence undergoing degradation by thermally induced bond-scission upon heating. Consequently, for this type of molecule, the absence of a liquid phase can be regarded as a general phenomenon. However, certain advantageous properties usually associated with the liquid state of matter, such as processability, flowability, or molecular mobility, are highly sought-after features for biomacromolecules in a solvent-free environment. Here, we provide an overview over the design principles and synthetic pathways to obtain solvent-free liquids of biomacromolecular architectures approaching the topic from our own perspective of research. We will highlight the milestones in synthesis, including a recently developed general surfactant complexation method applicable to a large variety of biomacromolecules as well as other synthetic principles granting access to electrostatically complexed proteins and DNA. These synthetic pathways retain the function and structure of the biomacromolecules even under extreme, nonphysiological conditions at high temperatures in water-free melts challenging the existing paradigm on the role of hydration in structural biology. Under these conditions, the resulting complexes reveal their true potential for previously unthinkable applications. Moreover, these protocols open a pathway toward the assembly of anisotropic architectures, enabling the formation of solvent-free biomacromolecular thermotropic liquid crystals. These ordered biomaterials exhibit vastly different mechanical properties when compared to the individual building blocks. Beyond the preparative aspects, we will shine light on the unique potential applications and technologies resulting from solvent-free biomacromolecular fluids: From charge transport in dehydrated liquids to DNA electrochromism to biocatalysis in the absence of a protein hydration shell. Moreover, solvent-free biological liquids containing viruses can be used as novel storage and process media serving as a formulation technology for the delivery of highly concentrated bioactive compounds. We are confident that this new class of hybrid biomaterials will fuel further studies and applications of biomacromolecules beyond water and other solvents and in a much broader context than just the traditional physiological conditions.

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.

Structure-wise discrimination of adenine and guanine by proteins on the basis of their nonbonded interactions.

PubMed

Usha, S; Selvaraj, S

2015-01-01

We have analyzed the nonbonded interactions of the structurally similar moieties, adenine and guanine forming complexes with proteins. The results comprise (a) the amino acid-ligand atom preferences, (b) solvent accessibility of ligand atoms before and after complex formation with proteins, and (c) preferred amino acid residue atoms involved in the interactions. We have observed that the amino acid preferences involved in the hydrogen bonding interactions vary for adenine and guanine. The structural variation between the purine atoms is clearly reflected by their burial tendency in the solvent environment. Correlation of the mean amino acid preference values show the variation that exists between adenine and guanine preferences of all the amino acid residues. All our observations provide evidence for the discriminating nature of the proteins in recognizing adenine and guanine.

An eco-compatible strategy for the diversity-oriented synthesis of macrocycles exploiting carbohydrate-derived building blocks.

PubMed

Maurya, Sushil K; Rana, Rohit

2017-01-01

An efficient, eco-compatible diversity-oriented synthesis (DOS) approach for the generation of library of sugar embedded macrocyclic compounds with various ring size containing 1,2,3-triazole has been developed. This concise strategy involves the iterative use of readily available sugar-derived alkyne/azide-alkene building blocks coupled through copper catalyzed azide-alkyne cycloaddition (CuAAC) reaction followed by pairing of the linear cyclo-adduct using greener reaction conditions. The eco-compatibility, mild reaction conditions, greener solvents, easy purification and avoidance of hazards and toxic solvents are advantages of this protocol to access this important structural class. The diversity of the macrocycles synthesized (in total we have synthesized 13 macrocycles) using a set of standard reaction protocols demonstrate the potential of the new eco-compatible approach for the macrocyclic library generation.

Novel Paradigm Supercapacitors V: Significance of Organic Polar Solvents and Salt Identities

DTIC Science & Technology

2017-06-01

CM/Baker.pdf. Accessed May 13, 2017. 156 [36] Lithium - ion battery . (n.d.). Wikipedia. [Online]. Available: https://en.wikipedia.org/wiki/ Lithium ...interested in the electrolytic components of lithium batteries and high performance non-nanotube SDM (NTSDM) capacitors. This is because these... lithium batteries and various commercial non- NTSDM capacitors. Table 3. List of Lithium Battery and Electrolytic Capacitors. Adapted from [34]–[36

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

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

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

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

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.

49 CFR 1560.105 - Denial of transport or sterile area access; designation for enhanced screening.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 9 2010-10-01 2010-10-01 false Denial of transport or sterile area access... Matching § 1560.105 Denial of transport or sterile area access; designation for enhanced screening. (a...-traveling individuals, including denial of transport or sterile area access or designation for enhanced...

75 FR 22073 - Fisheries of the Northeastern United States; Atlantic Sea Scallop Fishery; Framework Adjustment 21

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-27

... Elephant Trunk Access Area (ETAA), and one trip in the Delmarva Access Area (Delmarva). A part-time scallop... area trips into the Delmarva and Elephant Trunk Access Areas, as specified in Sec. 648.59(a) and (e... Delmarva and Elephant Trunk Access Areas specified in Sec. 648.59(a) and (e) during the period June 15...

Estimation of absolute solvent and solvation shell entropies via permutation reduction

NASA Astrophysics Data System (ADS)

Reinhard, Friedemann; Grubmüller, Helmut

2007-01-01

Despite its prominent contribution to the free energy of solvated macromolecules such as proteins or DNA, and although principally contained within molecular dynamics simulations, the entropy of the solvation shell is inaccessible to straightforward application of established entropy estimation methods. The complication is twofold. First, the configurational space density of such systems is too complex for a sufficiently accurate fit. Second, and in contrast to the internal macromolecular dynamics, the configurational space volume explored by the diffusive motion of the solvent molecules is too large to be exhaustively sampled by current simulation techniques. Here, we develop a method to overcome the second problem and to significantly alleviate the first one. We propose to exploit the permutation symmetry of the solvent by transforming the trajectory in a way that renders established estimation methods applicable, such as the quasiharmonic approximation or principal component analysis. Our permutation-reduced approach involves a combinatorial problem, which is solved through its equivalence with the linear assignment problem, for which O(N3) methods exist. From test simulations of dense Lennard-Jones gases, enhanced convergence and improved entropy estimates are obtained. Moreover, our approach renders diffusive systems accessible to improved fit functions.

Behavior of anionic molybdenum(IV, VI) and tungsten(IV, VI) complexes containing bulky hydrophobic dithiolate ligands and intramolecular NH···S hydrogen bonds in nonpolar solvents.

PubMed

Hasenaka, Yuki; Okamura, Taka-aki; Tatsumi, Miki; Inazumi, Naoya; Onitsuka, Kiyotaka

2014-11-07

Molybdenum(IV, VI) and tungsten(IV, VI) complexes, (Et4N)2[M(IV)O{1,2-S2-3,6-(RCONH)2C6H2}2] and (Et4N)2[M(VI)O2{1,2-S2-3,6-(RCONH)2C6H2}2] (M = Mo, W; R = (4-(t)BuC6H4)3C), with bulky hydrophobic dithiolate ligands containing NH···S hydrogen bonds were synthesized. These complexes are soluble in nonpolar solvents like toluene, which allows the detection of unsymmetrical coordination structures and elusive intermolecular interactions in solution. The (1)H NMR spectra of the complexes in toluene-d8 revealed an unsymmetrical coordination structure, and proximity of the counterions to the anion moiety was suggested at low temperatures. The oxygen-atom-transfer reaction between the molybdenum(IV) complex and Me3NO in toluene was considerably accelerated in nonpolar solvents, and this increase was attributed to the favorable access of the substrate to the active center in the hydrophobic environment.

Biochemical and Structural Basis for Inhibition of Enterococcus faecalis Hydroxymethylglutaryl-CoA Synthase, mvaS, by Hymeglusin

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

Skaff, D. Andrew; Ramyar, Kasra X.; McWhorter, William J.

Hymeglusin (1233A, F244, L-659-699) is established as a specific {beta}-lactone inhibitor of eukaryotic hydroxymethylglutaryl-CoA synthase (HMGCS). Inhibition results from formation of a thioester adduct to the active site cysteine. In contrast, the effects of hymeglusin on bacterial HMG-CoA synthase, mvaS, have been minimally characterized. Hymeglusin blocks growth of Enterococcus faecalis. After removal of the inhibitor from culture media, a growth curve inflection point at 3.1 h is observed (vs 0.7 h for the uninhibited control). Upon hymeglusin inactivation of purified E. faecalis mvaS, the thioester adduct is more stable than that measured for human HMGCS. Hydroxylamine cleaves the thioester adduct;more » substantial enzyme activity is restored at a rate that is 8-fold faster for human HMGCS than for mvaS. Structural results explain these differences in enzyme-inhibitor thioester adduct stability and solvent accessibility. The E. faecalis mvaS-hymeglusin cocrystal structure (1.95 {angstrom}) reveals virtually complete occlusion of the bound inhibitor in a narrow tunnel that is largely sequestered from bulk solvent. In contrast, eukaryotic (Brassica juncea) HMGCS binds hymeglusin in a more solvent-exposed cavity.« less

A carbohydrate-anion recognition system in aprotic solvents.

PubMed

Ren, Bo; Dong, Hai; Ramström, Olof

2014-05-01

A carbohydrate-anion recognition system in nonpolar solvents is reported, in which complexes form at the B-faces of β-D-pyranosides with H1-, H3-, and H5-cis patterns similar to carbohydrate-π interactions. The complexation effect was evaluated for a range of carbohydrate structures; it resulted in either 1:1 carbohydrate-anion complexes, or 1:2 complex formation depending on the protection pattern of the carbohydrate. The interaction was also evaluated with different anions and solvents. In both cases it resulted in significant binding differences. The results indicate that complexation originates from van der Waals interactions or weak CH⋅⋅⋅A(-) hydrogen bonds between the binding partners and is related to electron-withdrawing groups of the carbohydrates as well as increased hydrogen-bond-accepting capability of the anions. © 2014 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Molecular simulations of self-assembly processes of amphiphiles in dilute solutions: the challenge for quantitative modelling

NASA Astrophysics Data System (ADS)

Jusufi, Arben

2013-11-01

We report on two recent developments in molecular simulations of self-assembly processes of amphiphilic solutions. We focus on the determination of micelle formation of ionic surfactants which exhibit the archetype of self-assembling compounds in solution. The first approach is centred on the challenge in predicting micellisation properties through explicit solvent molecular dynamics simulations. Even with a coarse-grained (CG) approach and the use of highly optimised software packages run on graphics processing unit hardware, it remains in many cases computationally infeasible to directly extract the critical micelle concentration (cmc). However, combined with a recently presented theoretical mean-field model this task becomes resolved. An alternative approach to study self-assembly is through implicit solvent modelling of the surfactants. Here we review some latest results and present new ones regarding capabilities of such a modelling approach in determining the cmc, and the aggregate structures in the dilute regime, that is currently not accessible through explicit solvent simulations, neither through atomistic nor through CG approaches. A special focus is put on surfactant concentration effects and surfactant correlations quantified by scattering intensities that are compared to recently published small-angle X-ray scattering data.

21 CFR 1240.3 - General definitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... characteristics of milk, cream, or whey by using enzymes, solvents, heat, pressure, cooling, vacuum, genetic... that includes activities such as classification of molluscan shellfish growing areas, enforcement of...

Structure and Dynamics of Solvent Landscapes in Charge-Transfer Reactions

NASA Astrophysics Data System (ADS)

Leite, Vitor B. Pereira

The dynamics of solvent polarization plays a major role in the control of charge transfer reactions. The success of Marcus theory describing the solvent influence via a single collective quadratic polarization coordinate has been remarkable. Onuchic and Wolynes have recently proposed (J. Chem Phys 98 (3) 2218, 1993) a simple model demonstrating how a many-dimensional-complex model composed by several dipole moments (representing solvent molecules or polar groups in proteins) can be reduced under the appropriate limits into the Marcus Model. This work presents a dynamical study of the same model, which is characterized by two parameters, an average dipole-dipole interaction as a term associated with the potential energy landscape roughness. It is shown why the effective potential, obtained using a thermodynamic approach, is appropriate for the dynamics of the system. At high temperatures, the system exhibits effective diffusive one-dimensional dynamics, where the Born-Marcus limit is recovered. At low temperatures, a glassy phase appears with a slow non-self-averaging dynamics. At intermediate temperatures, the concept of equivalent diffusion paths and polarization dependence effects are discussed. This approach is extended to treat more realistic solvent models. Real solvents are discussed in terms of simple parameters described above, and an analysis of how different regimes affect the rate of charge transfer is presented. Finally, these ideas are correlated to analogous problems in other areas.

Application of natural deep eutectic solvents to the extraction of anthocyanins from Catharanthus roseus with high extractability and stability replacing conventional organic solvents.

PubMed

Dai, Yuntao; Rozema, Evelien; Verpoorte, Robert; Choi, Young Hae

2016-02-19

Natural deep eutectic solvents (NADES) have attracted a great deal of attention in recent times as promising green media. They are generally composed of neutral, acidic or basic compounds that form liquids of high viscosity when mixed in certain molar ratio. Despite their potential, viscosity and acid or basic nature of some ingredients may affect the extraction capacity and stabilizing ability of the target compounds. To investigate these effects, extraction with a series of NADES was employed for the analysis of anthocyanins in flower petals of Catharanthus roseus in combination with HPLC-DAD-based metabolic profiling. Along with the extraction yields of anthocyanins their stability in NADES was also studied. Multivariate data analysis indicates that the lactic acid-glucose (LGH), and 1,2-propanediol-choline chloride (PCH) NADES present a similar extraction power for anthocyanins as conventional organic solvents. Furthermore, among the NADES employed, LGH exhibits an at least three times higher stabilizing capacity for cyanidins than acidified ethanol, which facilitates their extraction and analysis process. Comparing NADES to the conventional organic solvents, in addition to their reduced environmental impact, they proved to provide higher stability for anthocyanins, and therefore have a great potential as possible alternatives to those organic solvents in health related areas such as food, pharmaceuticals and cosmetics. Copyright © 2016 Elsevier B.V. All rights reserved.

47 CFR 54.806 - Calculation by the Administrator of interstate access universal service support for areas served...

Code of Federal Regulations, 2010 CFR

2010-10-01

... access universal service support for areas served by price cap local exchange carriers. 54.806 Section 54... Administrator of interstate access universal service support for areas served by price cap local exchange... calculate the Interstate Access Universal Service Support for areas served by price cap local exchange...

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 physical properties and operating parameters on hydrodynamics in Centrifugal Partition Chromatography.

PubMed

Adelmann, S; Schembecker, G

2011-08-12

Besides the selection of a suitable biphasic solvent system the separation efficiency in Centrifugal Partition Chromatography (CPC) is mainly influenced by the hydrodynamics in the chambers. The flow pattern, the stationary phase retention and the interfacial area for mass transfer strongly depend on physical properties of the solvent system and operating parameters. In order to measure these parameters we visualized the hydrodynamics in a FCPC-chamber for five different solvent systems with an optical measurement system and calculated the stationary phase retention, interfacial area and the distribution of mobile phase thickness in the chamber. Although inclined chambers were used we found that the Coriolis force always deflected the mobile phase towards the chamber wall reducing the interfacial area. This effect increased for systems with low density difference. We also have shown that the stability of phase systems (stationary phase retention) and its tendency to disperse increased for smaller values of the ratio of interfacial tension and density difference. But also the viscosity ratio and the flow pattern itself had a significant effect on retention and dispersion of the mobile phase. As a result operating parameters should be chosen carefully with respect to physical properties for a CPC system. In order to reduce the effect of the Coriolis force CPC devices with greater rotor radius are desirable. Copyright © 2011 Elsevier B.V. All rights reserved.

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.

29 CFR 1915.91 - Housekeeping.

Code of Federal Regulations, 2011 CFR

2011-07-01

...) All working areas on or immediately surrounding vessels and dry docks, graving docks, or marine... boxes or fire-extinguishing equipment. (e) All oils, paints thinners, solvents, waste, rags, or other...

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.

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.

The effect of solvent relaxation time constants on free energy gap law for ultrafast charge recombination following photoinduced charge separation.

PubMed

Mikhailova, Valentina A; Malykhin, Roman E; Ivanov, Anatoly I

2018-05-16

To elucidate the regularities inherent in the kinetics of ultrafast charge recombination following photoinduced charge separation in donor-acceptor dyads in solutions, the simulations of the kinetics have been performed within the stochastic multichannel point-transition model. Increasing the solvent relaxation time scales has been shown to strongly vary the dependence of the charge recombination rate constant on the free energy gap. In slow relaxing solvents the non-equilibrium charge recombination occurring in parallel with solvent relaxation is very effective so that the charge recombination terminates at the non-equilibrium stage. This results in a crucial difference between the free energy gap laws for the ultrafast charge recombination and the thermal charge transfer. For the thermal reactions the well-known Marcus bell-shaped dependence of the rate constant on the free energy gap is realized while for the ultrafast charge recombination only a descending branch is predicted in the whole area of the free energy gap exceeding 0.2 eV. From the available experimental data on the population kinetics of the second and first excited states for a series of Zn-porphyrin-imide dyads in toluene and tetrahydrofuran solutions, an effective rate constant of the charge recombination into the first excited state has been calculated. The obtained rate constant being very high is nearly invariable in the area of the charge recombination free energy gap from 0.2 to 0.6 eV that supports the theoretical prediction.

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

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.

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

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.

Role of Geography and Nurse Practitioner Scope-of-Practice in Efforts to Expand Primary Care System Capacity: Health Reform and the Primary Care Workforce.

PubMed

Graves, John A; Mishra, Pranita; Dittus, Robert S; Parikh, Ravi; Perloff, Jennifer; Buerhaus, Peter I

2016-01-01

Little is known about the geographic distribution of the overall primary care workforce that includes both physician and nonphysician clinicians--particularly in areas with restrictive nurse practitioner scope-of-practice laws and where there are relatively large numbers of uninsured. We investigated whether geographic accessibility to primary care clinicians (PCCs) differed across urban and rural areas and across states with more or less restrictive scope-of-practice laws. An observational study. 2013 Area Health Resource File (AHRF) and US Census Bureau county travel data. The measures included percentage of the population in low-accessibility, medium-accessibility, and high-accessibility areas; number of geographically accessible primary care physicians (PCMDs), nurse practitioners (PCNPs), and physician assistants (PCPAs) per 100,000 population; and number of uninsured per PCC. We found divergent patterns in the geographic accessibility of PCCs. PCMDs constituted the largest share of the workforce across all settings, but were relatively more concentrated within urban areas. Accessibility to nonphysicians was highest in rural areas: there were more accessible PCNPs per 100,000 population in rural areas of restricted scope-of-practice states (21.4) than in urban areas of full practice states (13.9). Despite having more accessible nonphysician clinicians, rural areas had the largest number of uninsured per PCC in 2012. While less restrictive scope-of-practice states had up to 40% more PCNPs in some areas, we found little evidence of differences in the share of the overall population in low-accessibility areas across scope-of-practice categorizations. Removing restrictive scope-of-practice laws may expand the overall capacity of the primary care workforce, but only modestly in the short run. Additional efforts are needed that recognize the locational tendencies of physicians and nonphysicains.

Spatial access disparities to primary health care in rural and remote Australia.

PubMed

McGrail, Matthew Richard; Humphreys, John Stirling

2015-11-04

Poor spatial access to health care remains a key issue for rural populations worldwide. Whilst geographic information systems (GIS) have enabled the development of more sophisticated access measures, they are yet to be adopted into health policy and workforce planning. This paper provides and tests a new national-level approach to measuring primary health care (PHC) access for rural Australia, suitable for use in macro-level health policy. The new index was constructed using a modified two-step floating catchment area method framework and the smallest available geographic unit. Primary health care spatial access was operationalised using three broad components: availability of PHC (general practitioner) services; proximity of populations to PHC services; and PHC needs of the population. Data used in its measurement were specifically chosen for accuracy, reliability and ongoing availability for small areas. The resultant index reveals spatial disparities of access to PHC across rural Australia. While generally more remote areas experienced poorer access than more populated rural areas, there were numerous exceptions to this generalisation, with some rural areas close to metropolitan areas having very poor access and some increasingly remote areas having relatively good access. This new index provides a geographically-sensitive measure of access, which is readily updateable and enables a fine granulation of access disparities. Such an index can underpin national rural health programmes and policies designed to improve rural workforce recruitment and retention, and, importantly, health service planning and resource allocation decisions designed to improve equity of PHC access.

78 FR 27088 - Fisheries of the Northeastern United States; Atlantic Sea Scallop Fishery and Northeast...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-09

...). Framework 24 also continues the closures of the Delmarva and Elephant Trunk scallop access areas, refines... Scallop Access Areas Framework 24 closes both the Elephant Trunk (ET) area and the Delmarva Access Area...

Protease activation in glycerol-based deep eutectic solvents.

PubMed

Zhao, Hua; Baker, Gary A; Holmes, Shaletha

2011-11-01

Deep eutectic solvents (DESs) consisting of mixtures of a choline salt (chloride or acetate form) and glycerol are prepared as easily accessible, biodegradable, and inexpensive alternatives to conventional aprotic cation-anion paired ionic liquids. These DES systems display excellent fluidity coupled with thermal stability to nearly 200 °C. In this work, the transesterification activities of cross-linked proteases (subtilisin and α-chymotrypsin), immobilized on chitosan, were individually examined in these novel DESs. In the 1:2 molar ratio mixture of choline chloride/glycerol containing 3% (v/v) water, cross-linked subtilisin exhibited an excellent activity (2.9 μmo l min(-1) g(-1)) in conjunction with a selectivity of 98% in the transesterification reaction of N-acetyl-L-phenylalanine ethyl ester with 1-propanol. These highly encouraging results advocate more extensive exploration of DESs in protease-mediated biotransformations of additional polar substrates and use of DESs in biocatalysis more generally.

Easy Access to Supramolecular Gels of the Nonsteroidal Anti-inflammatory Drug Diflunisal: Synthesis, Characterization, and Plausible Biomedical Applications.

PubMed

Parveen, Rumana; Dastidar, Parthasarathi

2015-11-01

By exploiting salt formation, a new series of primary ammonium monocarboxylate salts of a nonsteroidal anti-inflammatory drug, namely, diflunisal, was synthesized. The majority of the salts thus synthesized turned out to be good gelators of various solvents, including the solvents (e.g., methyl salicylate and pure water) typically used for topical gel formulation. Single-crystal X-ray diffraction studies of a few gelator and nongelator salts in the series revealed details of the hydrogen-bonding networks present in the salts. Furthermore, one such gelator salt, namely, the diflunisal salt of serinol, was found to be biocompatible (MTT assay), and its anti-inflammatory (PGE2 assay) response turned out to be as good as that of the parent drug, which is indicative of its potential in biomedical applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solute-solvent interactions and dynamics probed by THz light

NASA Astrophysics Data System (ADS)

Schwaab, Gerhard; Böhm, Fabian; Ma, Chun-Yu; Havenith, Martina

The THz range (1-12 THz, 30-400 cm-1) is especially suited to probe changes in the solvent dynamics induced by solutes of different character (hydrophobic, hydrophilic, charged, neutral). In recent years we have investigated a large variety of such solutes and found characteristic spectral fingerprints for ions, but also for uncharged solutes, such as alcohols. We will present a status report on our current understanding of the observed spectral changes and how they relate to physico-chemical parameters like hydration shell size or the lifetime of an excited intermolecular oscillation. In addition, we will show, that in some cases the spectral changes are closely related to the partition function yielding access to a microscopic understanding of macroscopic thermodynamic functions. The authors gratefully acknowledge financial support from the Cluster of Excellence RESOLV (Ruhr-Universität, EXC1069) funded by the Deutsche Forschungsgemeinschaft.

Evolution of an adenine-copper cluster to a highly porous cuboidal framework: solution-phase ripening and gas-adsorption properties.

PubMed

Venkatesh, V; Pachfule, Pradip; Banerjee, Rahul; Verma, Sandeep

2014-09-15

The synthesis and directed evolution of a tetranuclear copper cluster, supported by 8-mercapto-N9-propyladenine ligand, to a highly porous three-dimensional cubic framework in the solid state is reported. The structure of this porous framework was unambiguously characterized by X-ray crystallography. The framework contains about 62 % solvent-accessible void; the presence of a free exocyclic amino group in the porous framework facilitates reversible adsorption of gas and solvent molecules. Oriented growth of framework in solution was also tracked by force and scanning electron microscopy studies, leading to identification of an intriguing ripening process, over a period of 30 days, which also revealed formation of cuboidal aggregates in solution. The elemental composition of these cuboidal aggregates was ascertained by EDAX analysis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Designing cooperatively folded abiotic uni- and multimolecular helix bundles

NASA Astrophysics Data System (ADS)

de, Soumen; Chi, Bo; Granier, Thierry; Qi, Ting; Maurizot, Victor; Huc, Ivan

2018-01-01

Abiotic foldamers, that is foldamers that have backbones chemically remote from peptidic and nucleotidic skeletons, may give access to shapes and functions different to those of peptides and nucleotides. However, design methodologies towards abiotic tertiary and quaternary structures are yet to be developed. Here we report rationally designed interactional patterns to guide the folding and assembly of abiotic helix bundles. Computational design facilitated the introduction of hydrogen-bonding functionalities at defined locations on the aromatic amide backbones that promote cooperative folding into helix-turn-helix motifs in organic solvents. The hydrogen-bond-directed aggregation of helices not linked by a turn unit produced several thermodynamically and kinetically stable homochiral dimeric and trimeric bundles with structures that are distinct from the designed helix-turn-helix. Relative helix orientation within the bundles may be changed from parallel to tilted on subtle solvent variations. Altogether, these results prefigure the richness and uniqueness of abiotic tertiary structure behaviour.

Field demonstration of foam injection to confine a chlorinated solvent source zone.

PubMed

Portois, Clément; Essouayed, Elyess; Annable, Michael D; Guiserix, Nathalie; Joubert, Antoine; Atteia, Olivier

2018-05-01

A novel approach using foam to manage hazardous waste was successfully demonstrated under active site conditions. The purpose of the foam was to divert groundwater flow, that would normally enter the source zone area, to reduce dissolved contaminant release to the aquifer. During the demonstration, foam was pre generated and directly injected surrounding the chlorinated solvent source zone. Despite the constraints related to the industrial activities and non-optimal position of the injection points, the applicability and effectiveness of the approach have been highlighted using multiple metrics. A combination of measurements and modelling allowed definition of the foam extent surrounding each injection point, and this appears to be the critical metric to define the success of the foam injection approach. Information on the transport of chlorinated solvents in groundwater showed a decrease of contaminant flux by a factor of 4.4 downstream of the confined area. The effective permeability reduction was maintained over a period of three months. The successful containment provides evidence for consideration of the use of foam to improve traditional flushing techniques, by increasing the targeting of contaminants by remedial agents. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

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

Structural and dynamical properties of the porins OmpF and OmpC: insights from molecular simulations

NASA Astrophysics Data System (ADS)

Kumar, Amit; Hajjar, Eric; Ruggerone, Paolo; Ceccarelli, Matteo

2010-11-01

In this paper we investigate the structural and dynamical properties of the two major porins (OmpF and OmpC) in Escherichia coli, using molecular dynamics (MD) simulations. In particular we characterized the atomic fluctuations, correlated motions, temperature dependence, solvent-accessible cross-sectional area and water dynamics in the key regions of the two channels. Our in-depth analysis allows us to highlight the importance of both the key conserved and substituted residues between OmpF and OmpC. The latter is characterized by a narrower and longer constriction region with respect to OmpF. OmpC also showed a higher stability upon increasing temperature. We then present the results of transport properties by using accelerated MD simulations to probe the diffusion of norfloxacin (a fluoroquinolone antibiotic) through the two porins OmpF/OmpC. Our study constitutes a step forward towards understanding the structure-function relationship of the two porins' channels. This will benefit the research of antibacterials with improved permeation properties and nanopores that aim to use these porins as sensing systems.

Chemically Responsive Elastomers Exhibiting Unity-Order Refractive Index Modulation.

PubMed

Wu, Di M; Solomon, Michelle L; Naik, Gururaj V; García-Etxarri, Aitzol; Lawrence, Mark; Salleo, Alberto; Dionne, Jennifer A

2018-02-01

Chameleons are masters of light, expertly changing their color, pattern, and reflectivity in response to their environment. Engineered materials that share this tunability can be transformative, enabling active camouflage, tunable holograms, and novel colorimetric medical sensors. While progress has been made in creating artificial chameleon skin, existing schemes often require external power, are not continuously tunable, and may prove too stiff or bulky for applications. Here, a chemically tunable, large-area metamaterial is demonstrated that accesses a wide range of colors and refractive indices. An ordered monolayer of nanoresonators is fabricated, then its optical response is dynamically tuned by infiltrating its polymer substrate with solvents. The material shows a strong magnetic response with a dependence on resonator spacing that leads to a highly tunable effective permittivity, permeability, and refractive index spanning negative and positive values. The unity-order index tuning exceeds that of traditional electro-optic and photochromic materials and is robust to cycling, providing a path toward programmable optical elements and responsive light routing. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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).

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.

MDTRA: a molecular dynamics trajectory analyzer with a graphical user interface.

PubMed

Popov, Alexander V; Vorobjev, Yury N; Zharkov, Dmitry O

2013-02-05

Most of existing software for analysis of molecular dynamics (MD) simulation results is based on command-line, script-guided processes that require the researchers to have an idea about programming language constructions used, often applied to the one and only product. Here, we describe an open-source cross-platform program, MD Trajectory Reader and Analyzer (MDTRA), that performs a large number of MD analysis tasks assisted with a graphical user interface. The program has been developed to facilitate the process of search and visualization of results. MDTRA can handle trajectories as sets of protein data bank files and presents tools and guidelines to convert some other trajectory formats into such sets. The parameters analyzed by MDTRA include interatomic distances, angles, dihedral angles, angles between planes, one-dimensional and two-dimensional root-mean-square deviation, solvent-accessible area, and so on. As an example of using the program, we describe the application of MDTRA to analyze the MD of formamidopyrimidine-DNA glycosylase, a DNA repair enzyme from Escherichia coli. Copyright © 2012 Wiley Periodicals, Inc.

Generation of tricyclic imidazo[1,2-a]pyrazines as novel PI3K inhibitors by application of a conformational restriction strategy.

PubMed

Martínez González, Sonia; Rodríguez-Arístegui, Sonsoles; Hernández, Ana Isabel; Varela, Carmen; González Cantalapiedra, Esther; Álvarez, Rosa María; Rodríguez Hergueta, Antonio; Bischoff, James R; Albarrán, María Isabel; Cebriá, Antonio; Cendón, Elena; Cebrián, David; Alfonso, Patricia; Pastor, Joaquín

2017-06-01

The involvement of the phosphoinositide 3-kinases (PI3Ks) in several diseases, especially in the oncology area, has singled it as one of the most explored therapeutic targets in the last two decades. Many different inhibitor classes have been developed by the industry and academia with a diverse selectivity profile within the PI3K family. In the present manuscript we report a further exploration of our lead PI3K inhibitor ETP-46321 (Martínez González et al., 2012) 1 by the application of a conformational restriction strategy. For that purpose we have successfully synthesized novel tricyclic imidazo[1,2-a]pyrazine derivatives as PI3K inhibitors. This new class of compounds had enable the exploration of the solvent-accessible region within PI3K and resulted in the identification of molecule 8q with the best selectivity PI3Kα/δ isoform profile in vitro, and promising in vivo PK data. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

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

46 CFR 154.340 - Access to tanks and spaces in the cargo area.

Code of Federal Regulations, 2010 CFR

2010-10-01

... access from the weather deck to gas-safe spaces in the cargo area must be at least 2.4 m (7.9 ft.) above... 46 Shipping 5 2010-10-01 2010-10-01 false Access to tanks and spaces in the cargo area. 154.340... Equipment Ship Arrangements § 154.340 Access to tanks and spaces in the cargo area. (a) Each cargo tank must...

46 CFR 154.340 - Access to tanks and spaces in the cargo area.

Code of Federal Regulations, 2011 CFR

2011-10-01

... access from the weather deck to gas-safe spaces in the cargo area must be at least 2.4 m (7.9 ft.) above... 46 Shipping 5 2011-10-01 2011-10-01 false Access to tanks and spaces in the cargo area. 154.340... Equipment Ship Arrangements § 154.340 Access to tanks and spaces in the cargo area. (a) Each cargo tank must...

46 CFR 154.340 - Access to tanks and spaces in the cargo area.

Code of Federal Regulations, 2014 CFR

2014-10-01

... access from the weather deck to gas-safe spaces in the cargo area must be at least 2.4 m (7.9 ft.) above... 46 Shipping 5 2014-10-01 2014-10-01 false Access to tanks and spaces in the cargo area. 154.340... Equipment Ship Arrangements § 154.340 Access to tanks and spaces in the cargo area. (a) Each cargo tank must...

46 CFR 154.340 - Access to tanks and spaces in the cargo area.

Code of Federal Regulations, 2012 CFR

2012-10-01

... access from the weather deck to gas-safe spaces in the cargo area must be at least 2.4 m (7.9 ft.) above... 46 Shipping 5 2012-10-01 2012-10-01 false Access to tanks and spaces in the cargo area. 154.340... Equipment Ship Arrangements § 154.340 Access to tanks and spaces in the cargo area. (a) Each cargo tank must...

46 CFR 154.340 - Access to tanks and spaces in the cargo area.

Code of Federal Regulations, 2013 CFR

2013-10-01

... access from the weather deck to gas-safe spaces in the cargo area must be at least 2.4 m (7.9 ft.) above... 46 Shipping 5 2013-10-01 2013-10-01 false Access to tanks and spaces in the cargo area. 154.340... Equipment Ship Arrangements § 154.340 Access to tanks and spaces in the cargo area. (a) Each cargo tank must...

Solvent hold tank sample results for MCU-16-1488-1493 (December 2016), MCU-17-86-88 (January 2017), and MCU-17-119-121 (February 2017): Quarterly Report

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

Fondeur, F. F.; Jones, D. H.

A trend summary of three Solvent Hold Tank (SHT) monthly samples; MCU-16-1488-1493 (December 2016), MCU-17-86-88 (January 2017), and MCU-17-119-121 (February 2017) are reported. Analyses indicate that the modifier (CS-7SB) and the extractant (MaxCalix) concentrations are at their nominal recommended levels (169,000 mg/L and 46,300 mg/L respectively). The suppressor (TiDG) level has decreased to a steady state level of 673 mg/L well above the minimum recommended level (479 mg/L). This analysis confirms the Isopar™ addition to the solvent in January 18, 2017. This analysis also indicates the solvent did not require further additions. Based on the current monthly sample, the levelsmore » of TiDG, Isopar™L, MaxCalix, and modifier are sufficient for continuing operation but are expected to decrease with time. Periodic characterization and trimming additions to the solvent are recommended. No impurities above the 1000 ppm level were found in this solvent by the Semi-Volatile Organic Analysis (SVOA). No impurities were observed in the Hydrogen Nuclear Magnetic Resonance (HNMR). Another impurity observed in the samples was mercury. Up to 38 ± 8 micrograms of mercury per mL of solvent was detected in these samples (the average of the CV-AA and XRF methods). The higher mercury concentration in the solvent (as determined in the last three monthly samples) is possibly due to the higher mercury concentration in Salt Batches 8 and 9 (Tank 49H) or mixing of previously undisturbed areas of high mercury concentration in Tank 49H. The gamma level (0.21E5 dpm/mL) measured in the February SHT sample was one order of magnitude lower than the gamma levels observed in the December and January SHT samples. The February gamma level is consistent with the solvent being idle (since January 10, 2017). The gamma levels observed in the December and January SHT samples were consistent with previous monthly measurements where the process operated normally. The laboratory will continue to monitor the quality of the solvent in particular for any new impurities or degradation of the solvent components.« less

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.

33 CFR 104.107 - Employee access area.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., excluding cruise ships, may designate areas within the vessel as employee access areas. (b) An employee... measures for access control, of a ferry or passenger vessel that is open only to employees and not to...

33 CFR 104.107 - Employee access area.

Code of Federal Regulations, 2013 CFR

2013-07-01

..., excluding cruise ships, may designate areas within the vessel as employee access areas. (b) An employee... measures for access control, of a ferry or passenger vessel that is open only to employees and not to...

33 CFR 104.107 - Employee access area.

Code of Federal Regulations, 2011 CFR

2011-07-01

..., excluding cruise ships, may designate areas within the vessel as employee access areas. (b) An employee... measures for access control, of a ferry or passenger vessel that is open only to employees and not to...

33 CFR 104.106 - Passenger access area.

Code of Federal Regulations, 2011 CFR

2011-07-01

... measures for access control, of a ferry, passenger vessel, or cruise ship that is open to passengers. It is..., or cruise ship may designate areas within the vessel as passenger access areas. (b) A passenger...

33 CFR 104.106 - Passenger access area.

Code of Federal Regulations, 2010 CFR

2010-07-01

... measures for access control, of a ferry, passenger vessel, or cruise ship that is open to passengers. It is..., or cruise ship may designate areas within the vessel as passenger access areas. (b) A passenger...

33 CFR 104.107 - Employee access area.

Code of Federal Regulations, 2012 CFR

2012-07-01

..., excluding cruise ships, may designate areas within the vessel as employee access areas. (b) An employee... measures for access control, of a ferry or passenger vessel that is open only to employees and not to...

33 CFR 104.107 - Employee access area.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., excluding cruise ships, may designate areas within the vessel as employee access areas. (b) An employee... measures for access control, of a ferry or passenger vessel that is open only to employees and not to...

33 CFR 104.106 - Passenger access area.

Code of Federal Regulations, 2013 CFR

2013-07-01

... measures for access control, of a ferry, passenger vessel, or cruise ship that is open to passengers. It is..., or cruise ship may designate areas within the vessel as passenger access areas. (b) A passenger...

33 CFR 104.106 - Passenger access area.

Code of Federal Regulations, 2012 CFR

2012-07-01

... measures for access control, of a ferry, passenger vessel, or cruise ship that is open to passengers. It is..., or cruise ship may designate areas within the vessel as passenger access areas. (b) A passenger...

33 CFR 104.106 - Passenger access area.

Code of Federal Regulations, 2014 CFR

2014-07-01

... measures for access control, of a ferry, passenger vessel, or cruise ship that is open to passengers. It is..., or cruise ship may designate areas within the vessel as passenger access areas. (b) A passenger...

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.

O2 and Water Migration Pathways between the Solvent and Heme Pockets of Hemoglobin with Open and Closed Conformations of the Distal HisE7.

PubMed

Shadrina, Maria S; Peslherbe, Gilles H; English, Ann M

2015-09-01

Hemoglobin transports O2 by binding the gas at its four hemes. Hydrogen bonding between the distal histidine (HisE7) and heme-bound O2 significantly increases the affinity of human hemoglobin (HbA) for this ligand. HisE7 is also proposed to regulate the release of O2 to the solvent via a transient E7 channel. To reveal the O2 escape routes controlled by HisE7 and to evaluate its role in gating heme access, we compare simulations of O2 diffusion from the distal heme pockets of the T and R states of HbA performed with HisE7 in its open (protonated) and closed (neutral) conformations. Irrespective of HisE7's conformation, we observe the same four or five escape routes leading directly from the α- or β-distal heme pockets to the solvent. Only 21-53% of O2 escapes occur via these routes, with the remainder escaping through routes that encompass multiple internal cavities in HbA. The conformation of the distal HisE7 controls the escape of O2 from the heme by altering the distal pocket architecture in a pH-dependent manner, not by gating the E7 channel. Removal of the HisE7 side chain in the GlyE7 variant exposes the distal pockets to the solvent, and the percentage of O2 escapes to the solvent directly from the α- or β-distal pockets of the mutant increases to 70-88%. In contrast to O2, the dominant water route from the bulk solvent is gated by HisE7 because protonation and opening of this residue dramatically increase the rate of influx of water into the empty distal heme pockets. The occupancy of the distal heme site by a water molecule, which functions as an additional nonprotein barrier to binding of the ligand to the heme, is also controlled by HisE7. Overall, analysis of gas and water diffusion routes in the subunits of HbA and its GlyE7 variant sheds light on the contribution of distal HisE7 in controlling polar and nonpolar ligand movement between the solvent and the hemes.

Simplex optimization of headspace factors for headspace gas chromatography determination of residual solvents in pharmaceutical products.

PubMed

Grodowska, Katarzyna; Parczewski, Andrzej

2013-01-01

The purpose of the present work was to find optimum conditions of headspace gas chromatography (HS-GC) determination of residual solvents which usually appear in pharmaceutical products. Two groups of solvents were taken into account in the present examination. Group I consisted of isopropanol, n-propanol, isobutanol, n-butanol and 1,4-dioxane and group II included cyclohexane, n-hexane and n-heptane. The members of the groups were selected in previous investigations in which experimental design and chemometric methods were applied. Four factors were taken into consideration in optimization which describe HS conditions: sample volume, equilibration time, equilibrium temperature and NaCl concentration in a sample. The relative GC peak area served as an optimization criterion which was considered separately for each analyte. Sequential variable size simplex optimization strategy was used and the progress of optimization was traced and visualized in various ways simultaneously. The optimum HS conditions appeared different for the groups of solvents tested, which proves that influence of experimental conditions (factors) depends on analyte properties. The optimization resulted in significant signal increase (from seven to fifteen times).

Occupational exposure to solvents and risk of head and neck cancer in women: a population-based case-control study in France.

PubMed

Carton, Matthieu; Barul, Christine; Menvielle, Gwenn; Cyr, Diane; Sanchez, Marie; Pilorget, Corinne; Trétarre, Brigitte; Stücker, Isabelle; Luce, Danièle

2017-01-09

Our objective was to investigate the association between head and neck cancer and occupational exposure to chlorinated, oxygenated and petroleum solvents in women. Investigation of occupational and environmental CAuses of REspiratory cancers (ICARE), a French population-based case-control study, included 296 squamous cell carcinomas of the head and neck (HNSCC) in women and 775 female controls. Lifelong occupational history was collected. Job-exposure matrices allowed to assess exposure to 5 chlorinated solvents (carbon tetrachloride; chloroform; methylene chloride; perchloroethylene; trichloroethylene), 5 petroleum solvents (benzene; special petroleum product; gasoline; white spirits and other light aromatic mixtures; diesel, fuels and kerosene) and 5 oxygenated solvents (alcohols; ketones and esters; ethylene glycol; diethyl ether; tetrahydrofuran). OR and 95% CIs, adjusted for smoking, alcohol drinking, age and geographical area, were estimated with logistic models. Elevated ORs were observed among women ever exposed to perchloroethylene (OR=2.97, 95% CI 1.05 to 8.45) and trichloroethylene (OR=2.15, 95% CI 1.21 to 3.81). These ORs increased with exposure duration (OR=3.75, 95% CI 0.64 to 21.9 and OR=4.44, 95% CI 1.56 to 12.6 for 10 years or more, respectively). No significantly increased risk of HNSCC was found for occupational exposure to the other chlorinated, petroleum or oxygenated solvents. These findings suggest that exposure to perchloroethylene or trichloroethylene may increase the risk of HNSCC in women. In our study, there is no clear evidence that the other studied solvents are risk factors for HNSCC. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Urban-rural differences in the association between access to healthcare and health outcomes among older adults in China.

PubMed

Zhang, Xufan; Dupre, Matthew E; Qiu, Li; Zhou, Wei; Zhao, Yuan; Gu, Danan

2017-07-19

Studies have shown that inadequate access to healthcare is associated with lower levels of health and well-being in older adults. Studies have also shown significant urban-rural differences in access to healthcare in developing countries such as China. However, there is limited evidence of whether the association between access to healthcare and health outcomes differs by urban-rural residence at older ages in China. Four waves of data (2005, 2008/2009, 2011/2012, and 2014) from the largest national longitudinal survey of adults aged 65 and older in mainland China (n = 26,604) were used for analysis. The association between inadequate access to healthcare (y/n) and multiple health outcomes were examined-including instrumental activities of daily living (IADL) disability, ADL disability, cognitive impairment, and all-cause mortality. A series of multivariate models were used to obtain robust estimates and to account for various covariates associated with access to healthcare and/or health outcomes. All models were stratified by urban-rural residence. Inadequate access to healthcare was significantly higher among older adults in rural areas than in urban areas (9.1% vs. 5.4%; p < 0.01). Results from multivariate models showed that inadequate access to healthcare was associated with significantly higher odds of IADL disability in older adults living in urban areas (odds ratio [OR] = 1.58-1.79) and rural areas (OR = 1.95-2.30) relative to their counterparts with adequate access to healthcare. In terms of ADL disability, we found significant increases in the odds of disability among rural older adults (OR = 1.89-3.05) but not among urban older adults. Inadequate access to healthcare was also associated with substantially higher odds of cognitive impairment in older adults from rural areas (OR = 2.37-3.19) compared with those in rural areas with adequate access to healthcare; however, no significant differences in cognitive impairment were found among older adults in urban areas. Finally, we found that inadequate access to healthcare increased overall mortality risks in older adults by 33-37% in urban areas and 28-29% in rural areas. However, the increased risk of mortality in urban areas was not significant after taking into account health behaviors and baseline health status. Inadequate access to healthcare was significantly associated with higher rates of disability, cognitive impairment, and all-cause mortality among older adults in China. The associations between access to healthcare and health outcomes were generally stronger among older adults in rural areas than in urban areas. Our findings underscore the importance of providing adequate access to healthcare for older adults-particularly for those living in rural areas in developing countries such as China.

Molecular dynamics of conformation-specific dopamine transporter-inhibitor complexes.

PubMed

Jean, Bernandie; Surratt, Christopher K; Madura, Jeffry D

2017-09-01

The recreational psychostimulant cocaine inhibits dopamine reuptake from the synapse, resulting in excessive stimulation of postsynaptic dopamine receptors in brain areas associated with reward and addiction. Cocaine binds to and stabilizes the outward- (extracellular-) facing conformation of the dopamine transporter (DAT) protein, while the low abuse potential DAT inhibitor benztropine prefers the inward- (cytoplasmic-) facing conformation. A correlation has been previously postulated between psychostimulant abuse potential and preference for the outward-facing DAT conformation. The 3β-aryltropane cocaine analogs LX10 and LX11, however, differ only in stereochemistry and share a preference for the outward-facing DAT, yet are reported to vary widely in abuse potential in an animal model. In search of the molecular basis for DAT conformation preference, complexes of cocaine, benztropine, LX10 or LX11 bound to each DAT conformation were subjected to 100ns of all-atom molecular dynamics simulation. Results were consistent with previous findings from cysteine accessibility assays used to assess an inhibitor's DAT conformation preference. The respective 2β- and 2α-substituted phenyltropanes of LX10 and LX11 interacted with hydrophobic regions of the DAT S1 binding site that were inaccessible to cocaine. Solvent accessibility measurements also revealed subtle differences in inhibitor positioning within a given DAT conformation. This work serves to advance our understanding of the conformational selectivity of DAT inhibitors and suggests that MD may be useful in antipsychostimulant therapeutic design. Copyright © 2017 Elsevier Inc. All rights reserved.

Substance misuse in Aboriginal Australians.

PubMed

Gracey, M

1998-01-01

Australia's Aborigines lived in isolation from the rest of humanity as successful hunter-gatherers for tens of thousands of years. That isolation ended abruptly with British colonization in the late 18th century and was followed by a traumatic 200 years for Aborigines who are now seriously disadvantaged, socio-economically and in terms of their health standards. It has often been assumed that the Aborigines had no access to psychotropic substances before permanent European contact but several pieces of evidence dispute this view. The history of Aboriginal contact with and usage of intoxicating substances, including alcohol, is extremely complex and affected by a maze of restrictive government policies. These interact with a wide range of other Federal and State policies which have changed rapidly since the late 1960s when Aborigines were first granted the franchise; access to unrestricted drinking followed soon afterwards. Today Aborigines suffer disproportionately to other Australians from the physical and social consequences of excess alcohol consumption, tobacco usage, petrol and other solvent sniffing, usage of marijuana, amphetamines, cocaine and heroin, as well as other drugs. The Aboriginal population is dispersed in cities, towns, fringe settlements, rural and remote areas over this vast continent and there are different patterns of drug usage from place to place. This review attempts to synthesize some of this information in order to give an overview to the history, background, current status of substance misuse by Aborigines as well as some strategies being used to try to overcome this serious problem.

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

Determination of void volume in normal phase liquid chromatography.

PubMed

Jiang, Ping; Wu, Di; Lucy, Charles A

2014-01-10

Void volume is an important fundamental parameter in chromatography. Little prior discussion has focused on the determination of void volume in normal phase liquid chromatography (NPLC). Various methods to estimate the total void volume are compared: pycnometry; minor disturbance method based on injection of weak solvent; tracer pulse method; hold-up volume based on unretained compounds; and accessible volume based on Martin's rule and its descendants. These are applied to NPLC on silica, RingSep and DNAP columns. Pycnometry provides a theoretically maximum value for the total void volume and should be performed at least once for each new column. However, pycnometry does not reflect the volume of adsorbed strong solvent on the stationary phase, and so only yields an accurate void volume for weaker mobile phase conditions. 1,3,5-Tri-t-butyl benzene (TTBB) results in hold-up volumes that are convenient measures of the void volume for all eluent conditions on charge-transfer columns (RingSep and DNAP), but is weakly retained under weak eluent conditions on silica. Injection of the weak mobile phase component (hexane) may be used to determine void volume, but care must be exercised to select the appropriate disturbance feature. Accessible volumes, that are determined using a homologous series, are always biased low, and are not recommended as a measure of the void volume. Copyright © 2013 Elsevier B.V. All rights reserved.

Dynamics at Lys-553 of the acto-myosin interface in the weakly and strongly bound states.

PubMed Central

MacLean, J J; Chrin, L R; Berger, C L

2000-01-01

Lys-553 of skeletal muscle myosin subfragment 1 (S1) was specifically labeled with the fluorescent probe FHS (6-[fluorescein-5(and 6)-carboxamido]hexanoic acid succinimidyl ester) and fluorescence quenching experiments were carried out to determine the accessibility of this probe at Lys-553 in both the strongly and weakly actin-bound states of the MgATPase cycle. Solvent quenchers of varying charge [nitromethane, (2,2,6, 6-tetramethyl-1-piperinyloxy) (TEMPO), iodide (I(-)), and thallium (Tl(+))] were used to assess both the steric and electrostatic accessibilities of the FHS probe at Lys-553. In the strongly bound rigor (nucleotide-free) and MgADP states, actin offered no protection from solvent quenching of FHS by nitromethane, TEMPO, or thallium, but did decrease the Stern-Volmer constant by almost a factor of two when iodide was used as the quencher. The protection from iodide quenching was almost fully reversed with the addition of 150 mM KCl, suggesting this effect is ionic in nature rather than steric. Conversely, actin offered no protection from iodide quenching at low ionic strength during steady-state ATP hydrolysis, even with a significant fraction of the myosin heads bound to actin. Thus, the lower 50 kD subdomain of myosin containing Lys-553 appears to interact differently with actin in the weakly and strongly bound states. PMID:10692329

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

Printed environmentally friendly supercapacitors with ionic liquid electrolytes on paper

NASA Astrophysics Data System (ADS)

Pettersson, F.; Keskinen, J.; Remonen, T.; von Hertzen, L.; Jansson, E.; Tappura, K.; Zhang, Y.; Wilén, C.-E.; Österbacka, R.

2014-12-01

Environmentally friendly supercapacitors are fabricated using commercial grade aluminum coated paper as a substrate and symmetrical activated carbon electrodes as large area electrodes. Different choline chloride-based eutectic solvents are used as electrolyte. These are inexpensive, environmentally friendly and have a larger operating window compared to that of water electrolytes. As the entire device is printed and the materials used are inexpensive, both small- and large-area power sources can be fabricated to be used in cheap, disposable and recyclable devices. Supercapacitors with different eutectic solvents are measured using cyclic charge-discharge and impedance spectroscopy measurements and compared to one widely used and one "green" imidazolium ionic liquid; EMIM:TFSI and EcoEng 212™, respectively. A mixture of ethylene glycol and choline chloride, Glyceline™, show the highest capacitance and power densities of the electrolytes being tested, including the imidazolium alternatives.

Downstream Processing of Synechocystis for Biofuel Production

NASA Astrophysics Data System (ADS)

Sheng, Jie

Lipids and free fatty acids (FFA) from cyanobacterium Synechocystis can be used for biofuel (e.g. biodiesel or renewable diesel) production. In order to utilize and scale up this technique, downstream processes including culturing and harvest, cell disruption, and extraction were studied. Several solvents/solvent systems were screened for lipid extraction from Synechocystis. Chloroform + methanol-based Folch and Bligh & Dyer methods were proved to be "gold standard" for small-scale analysis due to their highest lipid recoveries that were confirmed by their penetration of the cell membranes, higher polarity, and stronger interaction with hydrogen bonds. Less toxic solvents, such as methanol and MTBE, or direct transesterification of biomass (without preextraction step) gave only slightly lower lipid-extraction yields and can be considered for large-scale application. Sustained exposure to high and low temperature extremes severely lowered the biomass and lipid productivity. Temperature stress also triggered changes of lipid quality such as the degree of unsaturation; thus, it affected the productivities and quality of Synechocystis-derived biofuel. Pulsed electric field (PEF) was evaluated for cell disruption prior to lipid extraction. A treatment intensity > 35 kWh/m3 caused significant damage to the plasma membrane, cell wall, and thylakoid membrane, and it even led to complete disruption of some cells into fragments. Treatment by PEF enhanced the potential for the low-toxicity solvent isopropanol to access lipid molecules during subsequent solvent extraction, leading to lower usage of isopropanol for the same extraction efficiency. Other cell-disruption methods also were tested. Distinct disruption effects to the cell envelope, plasma membrane, and thylakoid membranes were observed that were related to extraction efficiency. Microwave and ultrasound had significant enhancement of lipid extraction. Autoclaving, ultrasound, and French press caused significant release of lipid into the medium, which may increase solvent usage and make medium recycling difficult. Production of excreted FFA by mutant Synechocystis has the potential of reducing the complexity of downstream processing. Major problems, such as FFA precipitation and biodegradation by scavengers, account for FFA loss in operation. Even a low concentration of FFA scavengers could consume FFA at a high rate that outpaced FFA production rate. Potential strategies to overcome FFA loss include high pH, adsorptive resin, and sterilization techniques.

Solvent-Free Synthesis of Zeolites: Mechanism and Utility.

PubMed

Wu, Qinming; Meng, Xiangju; Gao, Xionghou; Xiao, Feng-Shou

2018-05-08

Zeolites have been extensively studied for years in different areas of chemical industry, such as shape selective catalysis, ion-exchange, and gas adsorption and separation. Generally, zeolites are prepared from solvothermal synthesis in the presence of a large amounts of solvents such as water and alcohols in sealed autoclaves under autogenous pressure. Water has been regarded as essential to synthesize zeolites for fast mass transfer of reactants, but it occupies a large space in autoclaves, which greatly reduces the yield of zeolite products. Furthermore, polluted wastes and relatively high pressure due to the presence of water solvent in the synthesis also leads to environmental and safety issues. Recently, inspired by great benefits of solvent-free synthesis, including the environmental concerns, energy consumption, safety, and economic cost, researchers continually challenge the rationale of the solvent and reconsider the age-old question "Do we actually need solvents at all in zeolite synthesis?" In this Account, we briefly summarize our efforts to rationally synthesize zeolites via a solvent-free route. Our research demonstrates that a series of silica, aluminosilicate, and aluminophosphate-based zeolites can be successfully prepared by mixing, grinding, and heating starting solid materials under solvent-free conditions. Combining an organotemplate-free synthesis with a solvent-free approach maximizes the advantages resulting in a more sustainable synthetic route, which avoids using toxic and costly organic templates and the formation of harmful gases by calcination of organic templates at high temperature. Furthermore, new insights into the solvent-free crystallization process of zeolites have been provided by modern techniques such as NMR and UV-Raman spectroscopy, which should be helpful in designing new zeolite structures and developing novel routes for synthesis of zeolites. The role of water and the vital intermediates during the crystallization of zeolites have been proposed and verified. In addition to a significant reduction in liquid wastes and a remarkable increase in zeolite yields, the solvent-free synthesis of zeolites exhibits more unprecedented benefits, including (i) the formation of hierarchical micro-, meso-, and macrostructures, which benefit the mass transfer in the reactions, (ii) rapid synthesis at higher temperatures, which greatly improve the space-time yields of zeolites, and (iii) construction of a novel catalytic system for encapsulation of metal nanoparticles and metal oxide particles within zeolite crystals synergistically combining the advantages of catalytic metal nanoparticles and metal oxide particles (high activity) and zeolites (shape selectivity). We believe that the concept of "solvent-free synthesis of zeolites" would open a door for deep understanding of zeolite crystallization and the design of efficient zeolitic catalysts.

Synthesis and characterization of lactose-based homopolymers, hydrophilic/hydrophobic copolymers, and hydrogels

NASA Astrophysics Data System (ADS)

Zhou, Wenjing

The focus of this dissertation is the synthesis and characterization of lactose-based functional polymers. Currently 60% of lactose, a by-product from the cheese industry, is being utilized and the remaining fraction represents a serious disposal problem because of the high biological oxygen demand. Therefore, further development of utilization of lactose is an important issue both for industry and environment. Herein, the syntheses of lactose-based polymers such glycopolymers, hydrophilic/hydrophobic copolymers, and hydrogels are reported. A brief review of lactose formation, physical properties, and production is presented in Chapter 1. Syntheses and applications of lactose derivatives such as lactitol, lactulose, lactaime, lactosylurea, lactosylamine, lactone, and barbituric derivative are documented. Previous work in lactose-based polymers include: (1) hydrogels from cross linking of LPEP, borate complexation of lactose-containing polymer, and copolymerization of lactose monomer with crosslinkers; (2) lactose-based polyurethane rigid foams and adhesives; and (3) lactose-containing glycopolymers are also included. Chapter 2 documents the synthesis of acrylamidolactamine and the free radical copolymerization of this monomer with N-isopropylacrylamide in the presence of BisA to make hydrogels. Swelling behavior of the hydrogels at different temperatures as well as DSC study of these hydrogels are also carried out to characterize the swelling transition and the organization of water in the copolymer hydrogels. In Chapter 3, novel monomer syntheses of N-lactosyl- N'-(4-vinylbenzyl)urea or N '-lactosyl-N,N-methyl(4-vinylbenzyl)urea are described. Polymerization of these new urea monomers using a redox initiator gave water-soluble homopolymers with molecular weights in the range of 1.9 x 103 to 5.3 x 106. Synthesis and polymerization of lactose-O-(p-vinylbenzyl)hydroxime are documented in Chapter 4. The resulting polymers had high molecular weight (106) and narrow polydispersity (Mw/Mn: 1.20--1.35). The Mark-Houwink equation was obtained as [eta] = 2.15 x 10-4Mv0.73. Hydrogels produced in the presence of N,N'-methylenebisacrylamide swelled as much as 21-fold in deionized water. Copolymerization of styrene with lactose-O-(vinylbenzyl)oxime in dimethylsulfoxide-toluene (1:1, v/v) using 2,2'-azobisisobutyronitrile as the initiator are discussed in Chapter 5. The resulting hydrophilic/hydrophobic copolymers were characterized by viscometry, TGA, DSC, GPC, and solubility tests in solvents of varied polarities. Chapter 6 documents the preparation of polystyrene beads with different length of oligo(ethylene glycol) crosslinkers. Swelling in different solvents, solvent accessibility, and reagent diffusion of these beads with different crosslinking density were studied and the results indicated that the PEG-crosslinked polymers showed slightly better solvent accessibility in polar solvents than the analogous DVB-crosslinked networks.

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).

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

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.

Solvent-Assisted Gel Printing for Micropatterning Thin Organic-Inorganic Hybrid Perovskite Films.

PubMed

Jeong, Beomjin; Hwang, Ihn; Cho, Sung Hwan; Kim, Eui Hyuk; Cha, Soonyoung; Lee, Jinseong; Kang, Han Sol; Cho, Suk Man; Choi, Hyunyong; Park, Cheolmin

2016-09-27

While tremendous efforts have been made for developing thin perovskite films suitable for a variety of potential photoelectric applications such as solar cells, field-effect transistors, and photodetectors, only a few works focus on the micropatterning of a perovskite film which is one of the most critical issues for large area and uniform microarrays of perovskite-based devices. Here we demonstrate a simple but robust method of micropatterning a thin perovskite film with controlled crystalline structure which guarantees to preserve its intrinsic photoelectric properties. A variety of micropatterns of a perovskite film are fabricated by either microimprinting or transfer-printing a thin spin-coated precursor film in soft-gel state with a topographically prepatterned elastomeric poly(dimethylsiloxane) (PDMS) mold, followed by thermal treatment for complete conversion of the precursor film to a perovskite one. The key materials development of our solvent-assisted gel printing is to prepare a thin precursor film with a high-boiling temperature solvent, dimethyl sulfoxide. The residual solvent in the precursor gel film makes the film moldable upon microprinting with a patterned PDMS mold, leading to various perovskite micropatterns in resolution of a few micrometers over a large area. Our nondestructive micropatterning process does not harm the intrinsic photoelectric properties of a perovskite film, which allows for realizing arrays of parallel-type photodetectors containing micropatterns of a perovskite film with reliable photoconduction performance. The facile transfer of a micropatterned soft-gel precursor film on other substrates including mechanically flexible plastics can further broaden its applications to flexible photoelectric systems.

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.

Directed Self-Assembly of Triblock Copolymer on Chemical Patterns for Sub-10-nm Nanofabrication via Solvent Annealing.

PubMed

Xiong, Shisheng; Wan, Lei; Ishida, Yoshihito; Chapuis, Yves-Andre; Craig, Gordon S W; Ruiz, Ricardo; Nealey, Paul F

2016-08-23

Directed self-assembly (DSA) of block copolymers (BCPs) is a leading strategy to pattern at sublithographic resolution in the technology roadmap for semiconductors and is the only known solution to fabricate nanoimprint templates for the production of bit pattern media. While great progress has been made to implement block copolymer lithography with features in the range of 10-20 nm, patterning solutions below 10 nm are still not mature. Many BCP systems self-assemble at this length scale, but challenges remain in simultaneously tuning the interfacial energy atop the film to control the orientation of BCP domains, designing materials, templates, and processes for ultra-high-density DSA, and establishing a robust pattern transfer strategy. Among the various solutions to achieve domains that are perpendicular to the substrate, solvent annealing is advantageous because it is a versatile method that can be applied to a diversity of materials. Here we report a DSA process based on chemical contrast templates and solvent annealing to fabricate 8 nm features on a 16 nm pitch. To make this possible, a number of innovations were brought in concert with a common platform: (1) assembling the BCP in the phase-separated, solvated state, (2) identifying a larger process window for solvated triblock vs diblock BCPs as a function of solvent volume fraction, (3) employing templates for sub-10-nm BCP systems accessible by lithography, and (4) integrating a robust pattern transfer strategy by vapor infiltration of organometallic precursors for selective metal oxide synthesis to prepare an inorganic hard mask.

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.

The structure of the Caenorhabditis elegans manganese superoxide dismutase MnSOD-3-azide complex

DOE PAGES

Hunter, Gary J.; Trinh, Chi H.; Bonetta, Rosalin; ...

2015-08-27

C. elegans MnSOD-3 has been implicated in the longevity pathway and its mechanism of catalysis is relevant to the aging process and carcinogenesis. The structures of MnSOD-3 provide unique crystallographic evidence of a dynamic region of the tetrameric interface (residues 41–54). We have determined the structure of the MnSOD-3-azide complex to 1.77-Å resolution. The analysis of this complex shows that the substrate analog, azide, binds end-on to the manganese center as a sixth ligand and that it ligates directly to a third and new solvent molecule also positioned within interacting distance to the His30 and Tyr34 residues of the substratemore » access funnel. This is the first structure of a eukaryotic MnSOD-azide complex that demonstrates the extended, uninterrupted hydrogen-bonded network that forms a proton relay incorporating three outer sphere solvent molecules, the substrate analog, the gateway residues, Gln142, and the solvent ligand. This configuration supports the formation and release of the hydrogen peroxide product in agreement with the 5-6-5 catalytic mechanism for MnSOD. The high product dissociation constant k₄ of MnSOD-3 reflects low product inhibition making this enzyme efficient even at high levels of superoxide.« less

Hydrothermal pre-treatment of oil palm empty fruit bunch into fermentable sugars

NASA Astrophysics Data System (ADS)

Muhd Ali, M. D.; Tamunaidu, P.; Nor Aslan, A. K. H.; Morad, N. A.; Sugiura, N.; Goto, M.; Zhang, Z.

2016-06-01

Presently oil palm empty fruit bunch (OPEFB) is one of the solid waste which is produced daily whereby it is usually left at plantation site to act as organic fertilizer for the plants to ensure the sustainability of fresh fruit bunch. The major drawback in biomass conversion technology is the difficulty of degrading the material in a short period of time. A pre-treatment step is required to break the lignocellulosic biomass to easily accessible carbon sources for further use in the production of fuels and fine chemicals. Therefore, this study investigated the effect of hydrothermal pre-treatment under different reaction temperatures (100 - 250°C), reaction time (10 - 40 min), solid to solvent ratio of (1:10 - 1:20 w/v) and particle size (0.15 - 1.00 mm) on the solubilization of OPEFB to produce soluble fermentable sugars. The maximum soluble sugars of 68.18 mg glucose per gram of OPEFB were achieved at 175°C of reaction temperature, 20 min of reaction time, 1:15 w/v of solid to solvent ratio for 30 mm of particle size. Results suggest that reaction temperature, reaction time, the amount of solid to solvent ratio and size of the particle are crucial parameters for hydrothermal pretreatment, in achieving a high yield of soluble fermentable sugars.

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.

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.

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.

10 CFR 20.1601 - Control of access to high radiation areas.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Control of access to high radiation areas. 20.1601 Section 20.1601 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Control of Exposure From External Sources in Restricted Areas § 20.1601 Control of access to high radiation areas. (a...

33 CFR 127.1325 - Access to marine transfer area for LHG.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false Access to marine transfer area... to marine transfer area for LHG. Each operator of a waterfront facility handling LHG shall ensure that— (a) Access to the marine transfer area for LHG from shoreside and waterside is limited to— (1...

33 CFR 127.1325 - Access to marine transfer area for LHG.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 33 Navigation and Navigable Waters 2 2013-07-01 2013-07-01 false Access to marine transfer area... to marine transfer area for LHG. Each operator of a waterfront facility handling LHG shall ensure that— (a) Access to the marine transfer area for LHG from shoreside and waterside is limited to— (1...

33 CFR 127.1325 - Access to marine transfer area for LHG.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Access to marine transfer area... to marine transfer area for LHG. Each operator of a waterfront facility handling LHG shall ensure that— (a) Access to the marine transfer area for LHG from shoreside and waterside is limited to— (1...

10 CFR 20.1601 - Control of access to high radiation areas.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Control of access to high radiation areas. 20.1601 Section 20.1601 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Control of Exposure From External Sources in Restricted Areas § 20.1601 Control of access to high radiation areas. (a...

10 CFR 20.1601 - Control of access to high radiation areas.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Control of access to high radiation areas. 20.1601 Section 20.1601 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Control of Exposure From External Sources in Restricted Areas § 20.1601 Control of access to high radiation areas. (a...

10 CFR 20.1601 - Control of access to high radiation areas.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Control of access to high radiation areas. 20.1601 Section 20.1601 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Control of Exposure From External Sources in Restricted Areas § 20.1601 Control of access to high radiation areas. (a...

10 CFR 20.1601 - Control of access to high radiation areas.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Control of access to high radiation areas. 20.1601 Section 20.1601 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Control of Exposure From External Sources in Restricted Areas § 20.1601 Control of access to high radiation areas. (a...

14 CFR 1203a.103 - Access to security areas.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Access to security areas. 1203a.103 Section 1203a.103 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION NASA SECURITY AREAS § 1203a.103 Access to security areas. (a) Only those NASA employees, NASA contractor employees, and...

14 CFR 1203a.103 - Access to security areas.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 14 Aeronautics and Space 5 2011-01-01 2010-01-01 true Access to security areas. 1203a.103 Section 1203a.103 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION NASA SECURITY AREAS § 1203a.103 Access to security areas. (a) Only those NASA employees, NASA contractor employees, and...

Existence of a new emitting singlet state of proflavine: femtosecond dynamics of the excited state processes and quantum chemical studies in different solvents.

PubMed

Kumar, Karuppannan Senthil; Selvaraju, Chellappan; Malar, Ezekiel Joy Padma; Natarajan, Paramasivam

2012-01-12

Proflavine (3,6-diaminoacridine) shows fluorescence emission with lifetime, 4.6 ± 0.2 ns, in all the solvents irrespective of the solvent polarity. To understand this unusual photophysical property, investigations were carried out using steady state and time-resolved fluorescence spectroscopy in the pico- and femtosecond time domain. Molecular geometries in the ground and low-lying excited states of proflavine were examined by complete structural optimization using ab initio quantum chemical computations at HF/6-311++G** and CIS/6-311++G** levels. Time dependent density functional theory (TDDFT) calculations were performed to study the excitation energies in the low-lying excited states. The steady state absorption and emission spectral details of proflavine are found to be influenced by solvents. The femtosecond fluorescence decay of the proflavine in all the solvents follows triexponential function with two ultrafast decay components (τ(1) and τ(2)) in addition to the nanosecond component. The ultrafast decay component, τ(1), is attributed to the solvation dynamics of the particular solvent used. The second ultrafast decay component, τ(2), is found to vary from 50 to 215 ps depending upon the solvent. The amplitudes of the ultrafast decay components vary with the wavelength and show time dependent spectral shift in the emission maximum. The observation is interpreted that the time dependent spectral shift is not only due to solvation dynamics but also due to the existence of more than one emitting state of proflavine in the solvent used. Time resolved area normalized emission spectral (TRANES) analysis shows an isoemissive point, indicating the presence of two emitting states in homogeneous solution. Detailed femtosecond fluorescence decay analysis allows us to isolate the two independent emitting components of the close lying singlet states. The CIS and TDDFT calculations also support the existence of the close lying emitting states. The near constant lifetime observed for proflavine in different solvents is suggested to be due to the similar dipole moments of the ground and the evolved emitting singlet state of the dye from the Franck-Condon excited state.

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

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

DiStefano, Victoria H.; McFarlane, Joanna; Anovitz, Lawrence M.

This study is an attempt to understand how native organics are distributed with respect to pore size to determine the relationship between hydrocarbon chemistry and pore structure in shales, as the location and accessibility of hydrocarbons is key to understanding and improving the extractability of hydrocarbons in hydraulic fracturing. Selected shale cores from the Eagle Ford and Marcellus formations were subjected to pyrolysis gas chromatography (GC), thermogravimetric analysis, and organic solvent extraction with the resulting effluent analyzed by GC-mass spectrometry (MS). Organics representing the oil and gas fraction (0.1 to 1 wt. %) were observed by GC-MS. For most ofmore » the samples, the amount of native organic extracted directly related to the percentage of clay in the shale. The porosity and pore size distribution (0.95 nm to 1.35 m) in the Eagle Ford and Marcellus shales was measured before and after solvent extraction using small angle neutron scattering (SANS). An unconventional method was used to quantify the background from incoherent scattering as the Porod transformation obscures the Bragg peak from the clay minerals. Furthermore, the change in porosity from SANS is indicative of the extraction or breakdown of higher molecular weight bitumen with high C/H ratios (asphaltenes and resins). This is mostly likely attributed to complete dissolution or migration of asphaltenes and resins. These longer carbon chain lengths, C30-C40, were observed by pyrolysis GC, but either were too heavy to be analyzed in the extracts by GC-MS or were not effectively leached into the organic solvents. Thus, experimental limitations meant that the amount of extractable material could not be directly correlated to the changes in porosity measured by SANS. But, the observable porosity generally increased with solvent extraction. A decrease in porosity after extraction as observed in a shale with high clay content and low maturity was attributed to swelling of pores with solvent uptake or migration of resins and asphaltenes.« less

Extraction of organic compounds from representative shales and the effect on porosity

DOE PAGES

DiStefano, Victoria H.; McFarlane, Joanna; Anovitz, Lawrence M.; ...

2016-09-01

This study is an attempt to understand how native organics are distributed with respect to pore size to determine the relationship between hydrocarbon chemistry and pore structure in shales, as the location and accessibility of hydrocarbons is key to understanding and improving the extractability of hydrocarbons in hydraulic fracturing. Selected shale cores from the Eagle Ford and Marcellus formations were subjected to pyrolysis gas chromatography (GC), thermogravimetric analysis, and organic solvent extraction with the resulting effluent analyzed by GC-mass spectrometry (MS). Organics representing the oil and gas fraction (0.1 to 1 wt. %) were observed by GC-MS. For most ofmore » the samples, the amount of native organic extracted directly related to the percentage of clay in the shale. The porosity and pore size distribution (0.95 nm to 1.35 m) in the Eagle Ford and Marcellus shales was measured before and after solvent extraction using small angle neutron scattering (SANS). An unconventional method was used to quantify the background from incoherent scattering as the Porod transformation obscures the Bragg peak from the clay minerals. Furthermore, the change in porosity from SANS is indicative of the extraction or breakdown of higher molecular weight bitumen with high C/H ratios (asphaltenes and resins). This is mostly likely attributed to complete dissolution or migration of asphaltenes and resins. These longer carbon chain lengths, C30-C40, were observed by pyrolysis GC, but either were too heavy to be analyzed in the extracts by GC-MS or were not effectively leached into the organic solvents. Thus, experimental limitations meant that the amount of extractable material could not be directly correlated to the changes in porosity measured by SANS. But, the observable porosity generally increased with solvent extraction. A decrease in porosity after extraction as observed in a shale with high clay content and low maturity was attributed to swelling of pores with solvent uptake or migration of resins and asphaltenes.« less

Extended solvent-contact model approach to blind SAMPL5 prediction challenge for the distribution coefficients of drug-like molecules

NASA Astrophysics Data System (ADS)

Chung, Kee-Choo; Park, Hwangseo

2016-11-01

The performance of the extended solvent-contact model has been addressed in the SAMPL5 blind prediction challenge for distribution coefficient (LogD) of drug-like molecules with respect to the cyclohexane/water partitioning system. All the atomic parameters defined for 41 atom types in the solvation free energy function were optimized by operating a standard genetic algorithm with respect to water and cyclohexane solvents. In the parameterizations for cyclohexane, the experimental solvation free energy (Δ G sol ) data of 15 molecules for 1-octanol were combined with those of 77 molecules for cyclohexane to construct a training set because Δ G sol values of the former were unavailable for cyclohexane in publicly accessible databases. Using this hybrid training set, we established the LogD prediction model with the correlation coefficient ( R), average error (AE), and root mean square error (RMSE) of 0.55, 1.53, and 3.03, respectively, for the comparison of experimental and computational results for 53 SAMPL5 molecules. The modest accuracy in LogD prediction could be attributed to the incomplete optimization of atomic solvation parameters for cyclohexane. With respect to 31 SAMPL5 molecules containing the atom types for which experimental reference data for Δ G sol were available for both water and cyclohexane, the accuracy in LogD prediction increased remarkably with the R, AE, and RMSE values of 0.82, 0.89, and 1.60, respectively. This significant enhancement in performance stemmed from the better optimization of atomic solvation parameters by limiting the element of training set to the molecules with experimental Δ G sol data for cyclohexane. Due to the simplicity in model building and to low computational cost for parameterizations, the extended solvent-contact model is anticipated to serve as a valuable computational tool for LogD prediction upon the enrichment of experimental Δ G sol data for organic solvents.

10 CFR 20.1602 - Control of access to very high radiation areas.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Control of access to very high radiation areas. 20.1602 Section 20.1602 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Control of Exposure From External Sources in Restricted Areas § 20.1602 Control of access to very high radiation areas...

50 CFR 648.53 - Acceptable biological catch (ABC), annual catch limits (ACL), annual catch targets (ACT), DAS...

Code of Federal Regulations, 2011 CFR

2011-10-01

... be implemented as soon as possible after September 30 each year. (v) The Elephant Trunk Access Area shall change to an open area starting in fishing year 2011. For reference, the Elephant Trunk Access... chart depicting the area previously known as the Elephant Trunk Access Area are available from the...

50 CFR 648.53 - Acceptable biological catch (ABC), annual catch limits (ACL), annual catch targets (ACT), DAS...

Code of Federal Regulations, 2012 CFR

2012-10-01

... be implemented as soon as possible after September 30 each year. (v) The Elephant Trunk Access Area shall change to an open area starting in fishing year 2011. For reference, the Elephant Trunk Access... chart depicting the area previously known as the Elephant Trunk Access Area are available from the...

10 CFR 20.1602 - Control of access to very high radiation areas.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Control of access to very high radiation areas. 20.1602 Section 20.1602 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Control of Exposure From External Sources in Restricted Areas § 20.1602 Control of access to very high radiation areas...

10 CFR 20.1602 - Control of access to very high radiation areas.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Control of access to very high radiation areas. 20.1602 Section 20.1602 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Control of Exposure From External Sources in Restricted Areas § 20.1602 Control of access to very high radiation areas...

10 CFR 20.1602 - Control of access to very high radiation areas.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Control of access to very high radiation areas. 20.1602 Section 20.1602 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Control of Exposure From External Sources in Restricted Areas § 20.1602 Control of access to very high radiation areas...

10 CFR 20.1602 - Control of access to very high radiation areas.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Control of access to very high radiation areas. 20.1602 Section 20.1602 Energy NUCLEAR REGULATORY COMMISSION STANDARDS FOR PROTECTION AGAINST RADIATION Control of Exposure From External Sources in Restricted Areas § 20.1602 Control of access to very high radiation areas...

Small angle neutron scattering applications in fuel science

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

Thiyagarajan, P.; Cody, G.D.; Hunt, J.E.

1995-08-01

A wide range of physical and chemical methods have been used to study complex, multicomponent systems in fuel chemistry (crude oil, coal), and we are still far from complete understanding. Since chemical modification and/or solvent extraction of coal result in a number of different systems, it is important to understand the products in terms of their colloidal properties as a function of the solvent type, as well as other physical conditions. This would be helpful in design of processing techniques. Another area of research where SANS can be useful is characterization of the synthetic and modified clays being developed formore » processing in the petroleum industry. Major limitations for performing SANS experiments are nonavailability/high cost sof certain deuterated solvents and the paucity of beam time at the neutron scattering centers. This paper reports briefly on analysis of coal and asphaltenes.« less

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.

Driving Forces Controlling Host-Guest Recognition in Supercritical Carbon Dioxide Solvent.

PubMed

Ingrosso, Francesca; Altarsha, Muhannad; Dumarçay, Florence; Kevern, Gwendal; Barth, Danielle; Marsura, Alain; Ruiz-López, Manuel F

2016-02-24

The formation of supramolecular host-guest complexes is a very useful and widely employed tool in chemistry. However, supramolecular chemistry in non-conventional solvents such as supercritical carbon dioxide (scCO2 ), one of the most promising sustainable solvents, is still in its infancy. In this work, we explored a successful route to the development of green processes in supercritical CO2 by combining a theoretical approach with experiments. We were able to synthesize and characterize an inclusion complex between a polar aromatic molecule (benzoic acid) and peracetylated-β-cyclodextrin, which is soluble in the supercritical medium. This finding opens the way to wide, environmental friendly, applications of scCO2 in many areas of chemistry, including supramolecular synthesis, reactivity and catalysis, micro and nano-particle formation, molecular recognition, as well as enhanced extraction processes with increased selectivity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

An insight into non-emissive excited states in conjugated polymers

NASA Astrophysics Data System (ADS)

Hu, Zhongjian; Willard, Adam P.; Ono, Robert J.; Bielawski, Christopher W.; Rossky, Peter J.; vanden Bout, David A.

2015-09-01

Conjugated polymers in the solid state usually exhibit low fluorescence quantum yields, which limit their applications in many areas such as light-emitting diodes. Despite considerable research efforts, the underlying mechanism still remains controversial and elusive. Here, the nature and properties of excited states in the archetypal polythiophene are investigated via aggregates suspended in solvents with different dielectric constants (ε). In relatively polar solvents (ε>~ 3), the aggregates exhibit a low fluorescence quantum yield (QY) of 2-5%, similar to bulk films, however, in relatively nonpolar solvents (ε<~ 3) they demonstrate much higher fluorescence QY up to 20-30%. A series of mixed quantum-classical atomistic simulations illustrate that dielectric induced stabilization of nonradiative charge-transfer (CT) type states can lead to similar drastic reduction in fluorescence QY as seen experimentally. Fluorescence lifetime measurement reveals that the CT-type states exist as a competitive channel of the formation of emissive exciton-type states.

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.

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.

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.

Solubility Database

National Institute of Standards and Technology Data Gateway

SRD 106 IUPAC-NIST Solubility Database (Web, free access)   These solubilities are compiled from 18 volumes (Click here for List) of the International Union for Pure and Applied Chemistry(IUPAC)-NIST Solubility Data Series. The database includes liquid-liquid, solid-liquid, and gas-liquid systems. Typical solvents and solutes include water, seawater, heavy water, inorganic compounds, and a variety of organic compounds such as hydrocarbons, halogenated hydrocarbons, alcohols, acids, esters and nitrogen compounds. There are over 67,500 solubility measurements and over 1800 references.

Chemical Synthesis of Proteins

PubMed Central

Nilsson, Bradley L.; Soellner, Matthew B.; Raines, Ronald T.

2010-01-01

Proteins have become accessible targets for chemical synthesis. The basic strategy is to use native chemical ligation, Staudinger ligation, or other orthogonal chemical reactions to couple synthetic peptides. The ligation reactions are compatible with a variety of solvents and proceed in solution or on a solid support. Chemical synthesis enables a level of control on protein composition that greatly exceeds that attainable with ribosome-mediated biosynthesis. Accordingly, the chemical synthesis of proteins is providing previously unattainable insight into the structure and function of proteins. PMID:15869385

In Situ Bioremediation of Chlorinated Solvents Source Areas with Enhanced Mass Transfer

DTIC Science & Technology

2009-11-01

cells within NAPL Area 3 ................................. 22 Figure 6. Impact of whey injection on pH in the treatment cells...locations following 1% and 10% whey injections. ............................ 39 Figure 12. Total chlorinated ethene concentration contours at select time...points. ................ 40 Figure 13. Relationship between interfacial tension reduction and enhanced solubility of TCE DNAPL as a function of whey

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.

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.

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

Assessing potential spatial accessibility of health services in rural China: a case study of Donghai county

PubMed Central

2013-01-01

Introduction There is a great health services disparity between urban and rural areas in China. The percentage of people who are unable to access health services due to long travel times increases. This paper takes Donghai County as the study unit to analyse areas with physician shortages and characteristics of the potential spatial accessibility of health services. We analyse how the unequal health services resources distribution and the New Cooperative Medical Scheme affect the potential spatial accessibility of health services in Donghai County. We also give some advice on how to alleviate the unequal spatial accessibility of health services in areas that are more remote and isolated. Methods The shortest traffic times of from hospitals to villages are calculated with an O-D matrix of GIS extension model. This paper applies an enhanced two-step floating catchment area (E2SFCA) method to study the spatial accessibility of health services and to determine areas with physician shortages in Donghai County. The sensitivity of the E2SFCA for assessing variation in the spatial accessibility of health services is checked using different impedance coefficient valuesa. Geostatistical Analyst model and spatial analyst method is used to analyse the spatial pattern and the edge effect of potential spatial accessibility of health services. Results The results show that 69% of villages have access to lower potential spatial accessibility of health services than the average for Donghai County, and 79% of the village scores are lower than the average for Jiangsu Province. The potential spatial accessibility of health services diminishes greatly from the centre of the county to outlying areas. Using a smaller impedance coefficient leads to greater disparity among the villages. The spatial accessibility of health services is greater along highway in the county. Conclusions Most of villages are in underserved health services areas. An unequal distribution of health service resources and the reimbursement policies of the New Cooperative Medical Scheme have led to an edge effect regarding spatial accessibility of health services in Donghai County, whereby people living on the edge of the county have less access to health services. Comprehensive measures should be considered to alleviate the unequal spatial accessibility of health services in areas that are more remote and isolated. PMID:23688278

The continuing problem of youthful solvent abuse in New York State.

PubMed

Frank, B; Marel, R; Schmeidler, J

1988-01-01

The major finding in the comparison of surveys of New York State secondary school students is the increasing use of solvents in this population over time. What in 1974-75 seemed to be limited use, by 1983 was found to be of widespread use. Very much like the survey of 1974-75 and the findings in the literature, age of first use together with the recentness of use appears to cluster in the preteens or the early teen years and tapers off during the teen years. Of interest is the fact that, along with the general upward rate of use over the surveys, those 18 years or older also show an upward trend. Some evidence in the recent literature indicates that adults, too, are found to have a problem with inhalants. Similar to the 1974-75 survey, but unlike findings in the literature, males and females continue to show similar rates of solvent use. Although males do generally surpass females in these use rates, the differences are usually not significant. In light of the literature on solvent abuse among Hispanic youth, the 1978 and 1983 surveys indicated mixed findings. Hispanic students in New York City consistently showed intermediate levels of solvent use; whereas, in 1983, Hispanic students residing in areas of the state outside of New York City showed excessive rates of solvent use. To the extent that the problem of acculturation among poor Hispanic youth may contribute to solvent abuse, an explanation may be found in the contrasts between living in New York City and living in the rest of the State. In New York City, which has an extremely large Hispanic population (about 20 percent of the population), feelings of isolation and cultural distance may not be so profound. In the rest of the state, where the proportion of Hispanics is quite small (about 2 percent of the population), these cultural problems may be more of a factor. Reasons, however, for the extraordinary increase in solvent use among those Hispanic youth, specifically between 1978 and 1983, are difficult to offer. Again, very similar to the 1974-75 findings, the 1978 and 1983 surveys found a strong relationship between solvent use and poor academic performance. Furthermore, the early findings relating to solvent use to a lack of family cohesion was supported by the 1978 survey where comparable information was gathered. The pattern of drug-using or polydrug use found among solvent users in the 1974-75 survey was underscored by the findings in the subsequent surveys.(ABSTRACT TRUNCATED AT 400 WORDS)

Fluorescence quenching of human orosomucoid. Accessibility to drugs and small quenching agents.

PubMed Central

Friedman, M L; Schlueter, K T; Kirley, T L; Halsall, H B

1985-01-01

The fluorescence behaviour of human orosomucoid was investigated. The intrinsic fluorescence was more accessible to acrylamide than to the slightly larger succinimide, indicating limited accessibility to part of the tryptophan population. Although I- showed almost no quenching, that of Cs+ was enhanced, and suggested a region of negative charge proximal to an emitting tryptophan residue. Removal of more than 90% of sialic acid from the glycan chains led to no change in the Cs+, I-, succinimide or acrylamide quenching, indicating that the negatively charged region originates with the protein core. Quenching as a function of pH and temperature supported this view. The binding of chlorpromazine monitored by fluorescence quenching, in the presence and in the absence of the small quenching probes (above), led to a model of its binding domain on orosomucoid that includes two tryptophan residues relatively shielded from the bulk solvent, with the third tryptophan residue being on the periphery of the domain, or affected allotopically and near the negatively charged field. PMID:4091825

THERMAL REMEDIATION

EPA Science Inventory

Thermal remediation is being proposed by Region I for remediation of the overburden soil and groundwater at the Solvent Recovery Services New England Superfund site. This presentation at the public meeting will acquaint area residents with thermal remediation. The two types of ...

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

Access to recreational physical activities by car and bus: an assessment of socio-spatial inequalities in mainland Scotland.

PubMed

Ferguson, Neil S; Lamb, Karen E; Wang, Yang; Ogilvie, David; Ellaway, Anne

2013-01-01

Obesity and other chronic conditions linked with low levels of physical activity (PA) are associated with deprivation. One reason for this could be that it is more difficult for low-income groups to access recreational PA facilities such as swimming pools and sports centres than high-income groups. In this paper, we explore the distribution of access to PA facilities by car and bus across mainland Scotland by income deprivation at datazone level. GIS car and bus networks were created to determine the number of PA facilities accessible within travel times of 10, 20 and 30 minutes. Multilevel negative binomial regression models were then used to investigate the distribution of the number of accessible facilities, adjusting for datazone population size and local authority. Access to PA facilities by car was significantly (p<0.01) higher for the most affluent quintile of area-based income deprivation than for most other quintiles in small towns and all other quintiles in rural areas. Accessibility by bus was significantly lower for the most affluent quintile than for other quintiles in urban areas and small towns, but not in rural areas. Overall, we found that the most disadvantaged groups were those without access to a car and living in the most affluent areas or in rural areas.

How far will we need to go to reach HIV-infected people in rural South Africa?

PubMed

Wilson, David P; Blower, Sally

2007-06-19

The South African Government has outlined detailed plans for antiretroviral (ART) rollout in KwaZulu-Natal Province, but has not created a plan to address treatment accessibility in rural areas in KwaZulu-Natal. Here, we calculate the distance that People Living With HIV/AIDS (PLWHA) in rural areas in KwaZulu-Natal would have to travel to receive ART. Specifically, we address the health policy question 'How far will we need to go to reach PLWHA in rural KwaZulu-Natal?'. We developed a model to quantify treatment accessibility in rural areas; the model incorporates heterogeneity in spatial location of HCFs and patient population. We defined treatment accessibility in terms of the number of PLWHA that have access to an HCF. We modeled the treatment-accessibility region (i.e. catchment area) around an HCF by using a two-dimensional function, and assumed that treatment accessibility decreases as distance from an HCF increases. Specifically, we used a distance-discounting measure of ART accessibility based upon a modified form of a two-dimensional gravity-type model. We calculated the effect on treatment accessibility of: (1) distance from an HCF, and (2) the number of HCFs. In rural areas in KwaZulu-Natal even substantially increasing the size of a small catchment area (e.g. from 1 km to 20 km) around an HCF would have a negligible impact (~2%) on increasing treatment accessibility. The percentage of PLWHA who can receive ART in rural areas in this province could be as low as ~16%. Even if individuals were willing (and able) to travel 50 km to receive ART, only ~50% of those in need would be able to access treatment. Surprisingly, we show that increasing the number of available HCFs for ART distribution ~ threefold does not lead to a threefold increase in treatment accessibility in rural KwaZulu-Natal. Our results show that many PLWHA in rural KwaZulu-Natal are unlikely to have access to ART, and that the impact of an additional 37 HCFs on treatment accessibility in rural areas would be less substantial than might be expected. There is a great length to go before we will be able to reach many PLWHA in rural areas in South Africa, and specifically in KwaZulu-Natal.

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

47 CFR 54.807 - Interstate access universal service support.

Code of Federal Regulations, 2011 CFR

2011-10-01

... supported service within the study area of a price cap local exchange carrier shall receive Interstate Access Universal Service Support for each line that it serves within that study area. (b) In any study... Service Support Per Line by dividing Study Area Access Universal Service Support by twelve times all...

Fluorescence spectroscopy of Rhodamine 6G: concentration and solvent effects.

PubMed

Zehentbauer, Florian M; Moretto, Claudia; Stephen, Ryan; Thevar, Thangavel; Gilchrist, John R; Pokrajac, Dubravka; Richard, Katherine L; Kiefer, Johannes

2014-01-01

Rhodamine 6G (R6G), also known as Rhodamine 590, is one of the most frequently used dyes for application in dye lasers and as a fluorescence tracer, e.g., in the area of environmental hydraulics. Knowing the spectroscopic characteristics of the optical emission is key to obtaining high conversion efficiency and measurement accuracy, respectively. In this work, solvent and concentration effects are studied. A series of eight different organic solvents (methanol, ethanol, n-propanol, iso-propanol, n-butanol, n-pentanol, acetone, and dimethyl sulfoxide (DMSO)) are investigated at constant dye concentration. Relatively small changes of the fluorescence spectrum are observed for the different solvents; the highest fluorescence intensity is observed for methanol and lowest for DMSO. The shortest peak wavelength is found in methanol (568 nm) and the longest in DMSO (579 nm). Concentration effects in aqueous R6G solutions are studied over the full concentration range from the solubility limit to highly dilute states. Changing the dye concentration provides tunability between ∼550 nm in the dilute case and ∼620 nm at high concentration, at which point the fluorescence spectrum indicates the formation of R6G aggregates. Copyright © 2013 Elsevier B.V. All rights reserved.

Iodination of insulin in aqueous and organic solvents

PubMed Central

Massaglia, A.; Rosa, U.; Rialdi, G.; Rossi, C. A.

1969-01-01

1. The iodination of insulin was studied under various experimental conditions in aqueous media and in some organic solvents, by measuring separately the uptake of iodine by the four tyrosyl groups and the relative amounts of monoiodotyrosine and di-iodotyrosine that are formed. In aqueous media from pH1 to pH9 the iodination occurs predominantly on the tyrosyl groups of the A chain. Some organic solvents increase the iodine uptake of the B-chain tyrosyl groups. Their efficacy in promoting iodination of Tyr-B-16 and Tyr-B-26 is in the order: ethylene glycol and propylene glycol≃methanol and ethanol>dioxan>8m-urea. 2. It is suggested that each of the four tyrosyl groups in insulin has a different environment: Tyr-A-14 is fully exposed to the solvent; Tyr-A-19 is sterically influenced by the environmental structure, possibly by the vicinity of a disulphide interchain bond; Tyr-B-16 is embedded into a non-polar area whose stability is virtually independent of the molecular conformation; Tyr-B-26 is probably in a situation similar to Tyr-B-16 with the difference that its non-polar environment depends on the preservation of the native structure. PMID:5346365

Probing potential Li-ion battery electrolyte through first principles simulation of atomic clusters

NASA Astrophysics Data System (ADS)

Kushwaha, Anoop Kumar; Sahoo, Mihir Ranjan; Nayak, Saroj

2018-04-01

Li-ion battery has wide area of application starting from low power consumer electronics to high power electric vehicles. However, their large scale application in electric vehicles requires further improvement due to their low specific power density which is an essential parameter and is closely related to the working potential windows of the battery system. Several studies have found that these parameters can be taken care of by considering different cathode/anode materials and electrolytes. Recently, a unique approach has been reported on the basis of cluster size in which the use of Li3 cluster has been suggested as a potential component of the battery electrode material. The cluster based approach significantly enhances the working electrode potential up to 0.6V in the acetonitrile solvent. In the present work, using ab-initio quantum chemical calculation and the dielectric continuum model, we have investigated various dielectric solvent medium for the suitable electrolyte for the potential component Li3 cluster. This study suggests that high dielectric electrolytic solvent (ethylene carbonate and propylene carbonate) could be better for lithium cluster due to improvement in the total electrode potential in comparison to the other dielectric solvent.

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.

Alginate as immobilization matrix and stabilizing agent in a two-phase liquid system: application in lipase-catalysed reactions.

PubMed

Hertzberg, S; Kvittingen, L; Anthonsen, T; Skjåk-Braek, G

1992-01-01

Alginate was evaluated as an immobilization matrix for enzyme-catalyzed reactions in organic solvents. In contrast to most hydrogels, calcium alginate was found to be stable in a range of organic solvents and to retain the enzyme inside the gel matrix. In hydrophobic solvents, the alginate gel (greater than 95% water) thus provided a stable, two-phase liquid system. The lipase from Candida cylindracea, after immobilization in alginate beads, catalysed esterification and transesterification in n-hexane under both batch and continuous-flow conditions. The operational stability of the lipase was markedly enhanced by alginate entrapment. In the esterification of butanoic acid with n-butanol, better results were obtained in the typical hydrophilic calcium alginate beads than in less hydrophilic matrices. The effects of substrate concentration, matrix area, and polarity of the substrate alcohols and of the organic solvent on the esterification activity were examined. The transesterification of octyl 2-bromopropanoate with ethanol was less efficient than that of ethyl 2-bromopropanoate with octanol. By using the hydrophilic alginate gel as an immobilization matrix in combination with a mobile hydrophobic phase, a two-phase liquid system was achieved with definite advantages for a continuous, enzyme-catalysed process.

Dendronization-induced phase-transfer, stabilization and self-assembly of large colloidal Au nanoparticles

NASA Astrophysics Data System (ADS)

Malassis, Ludivine; Jishkariani, Davit; Murray, Christopher B.; Donnio, Bertrand

2016-07-01

The phase-transfer of CTAB-coated aqueous, spherical gold nanoparticles, with metallic core diameters ranging from ca. 27 to 54 nm, into organic solvents by exchanging the primitive polar bilayer with lipophilic, disulfide dendritic ligands is reported. The presence of such a thick nonpolar organic shell around these large nanoparticles enhances their stabilization against aggregation, in addition to enabling their transfer into a variety of solvents such as chloroform, toluene or tetrahydrofuran. Upon the slow evaporation of a chloroform suspension deposited on a solid support, the dendronized hybrids were found to self-assemble into ring structures of various diameters. Moreover, their self-assembly at the liquid-air interface affords the formation of fairly long-range ordered monolayers, over large areas, that can then be entirely transferred onto solid substrates.The phase-transfer of CTAB-coated aqueous, spherical gold nanoparticles, with metallic core diameters ranging from ca. 27 to 54 nm, into organic solvents by exchanging the primitive polar bilayer with lipophilic, disulfide dendritic ligands is reported. The presence of such a thick nonpolar organic shell around these large nanoparticles enhances their stabilization against aggregation, in addition to enabling their transfer into a variety of solvents such as chloroform, toluene or tetrahydrofuran. Upon the slow evaporation of a chloroform suspension deposited on a solid support, the dendronized hybrids were found to self-assemble into ring structures of various diameters. Moreover, their self-assembly at the liquid-air interface affords the formation of fairly long-range ordered monolayers, over large areas, that can then be entirely transferred onto solid substrates. Electronic supplementary information (ESI) available: TEM microscope images. See DOI: 10.1039/c6nr03404g

Use of plume mapping data to estimate chlorinated solvent mass loss

USGS Publications Warehouse

Barbaro, J.R.; Neupane, P.P.

2006-01-01

Results from a plume mapping study from November 2000 through February 2001 in the sand-and-gravel surficial aquifer at Dover Air Force Base, Delaware, were used to assess the occurrence and extent of chlorinated solvent mass loss by calculating mass fluxes across two transverse cross sections and by observing changes in concentration ratios and mole fractions along a longitudinal cross section through the core of the plume. The plume mapping investigation was conducted to determine the spatial distribution of chlorinated solvents migrating from former waste disposal sites. Vertical contaminant concentration profiles were obtained with a direct-push drill rig and multilevel piezometers. These samples were supplemented with additional ground water samples collected with a minipiezometer from the bed of a perennial stream downgradient of the source areas. Results from the field program show that the plume, consisting mainly of tetrachloroethylene (PCE), trichloroethene (TCE), and cis-1,2-dichloroethene (cis-1,2-DCE), was approximately 670 m in length and 120 m in width, extended across much of the 9- to 18-m thickness of the surficial aquifer, and discharged to the stream in some areas. The analyses of the plume mapping data show that losses of the parent compounds, PCE and TCE, were negligible downgradient of the source. In contrast, losses of cis-1,2-DCE, a daughter compound, were observed in this plume. These losses very likely resulted from biodegradation, but the specific reaction mechanism could not be identified. This study demonstrates that plume mapping data can be used to estimate the occurrence and extent of chlorinated solvent mass loss from biodegradation and assess the effectiveness of natural attenuation as a remedial measure.