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https://www.readbyqxmd.com/read/28943441/a-combined-experimental-and-molecular-simulation-study-of-factors-influencing-interaction-of-quinoa-proteins-carrageenan
#1
Natalia Montellano Duran, Darío Spelzini, Natael Wayllace, Valeria Boeris, Fernando L Barroso da Silva
The interaction between quinoa proteins isolate (QP isolate) and the negatively charged polysaccharide ι-Carragennan (Carr) as a function of pH was studied. Experimental measurements as turbidity, hydrophobic surface, ζ-potential, and hydrodynamic size were carried out. Associative interaction between QP and Carr was found in the pH range between 1 and 2.9. When both molecules are negatively charged (pH>5,5), a pure Coulombic repulsion regime is observed and the self-association of QP due to the Carr exclusion is proposed...
September 21, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28942641/extracting-aggregation-free-energies-of-mixed-clusters-from-simulations-of-small-systems-application-to-ionic-surfactant-micelles
#2
Xiaokun Zhang, Lara A Patel, Olivia Beckwith, Robert Schneider, Christopher J Weeden, James T Kindt
Micelle cluster distributions from molecular dynamics simulations of a solvent-free coarse-grained model of sodium octyl sulfate (SOS) have been analyzed using an improved method to extract equilibrium association constants from small-system simulations, containing one or two micelle clusters at equilibrium with free surfactants and counterions. The statistical-thermodynamic and mathematical foundations of this "Partition-Enabled Analysis of Cluster Histograms" (PEACH) approach are presented. A dramatic reduction in computational time for analysis is achieved through a strategy similar to the "selector variable method" to circumvent the need for exhaustive enumeration of the possible partitions of surfactants and counterions into clusters...
September 25, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28942529/dft-study-of-benzyl-alcohol-tio2-interfacial-surface-complex-reaction-pathway-and-mechanism-of-visible-light-absorption
#3
Lei Zhao, Feng Long Gu, Minjae Kim, Maosheng Miao, Rui-Qin Zhang
We propose a new pathway for the adsorption of benzyl alcohol on the surface of TiO2 and the formation of interfacial surface complex (ISC). The reaction free energies and reaction kinetics were thoroughly investigated by density functional calculations. The TiO2 surfaces were modeled by clusters consisting of 4 Ti atoms and 18 O atoms passivated by H, OH group and H2O molecules. Compared with solid-state calculations utilizing the periodicity of the materials, such cluster modeling allows inclusion of the high-order correlation effects that seem to be essential for the adsorption of organic molecules onto solid surfaces...
September 24, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28940242/a-component-analysis-of-the-free-energies-of-folding-of-35-proteins-a-consensus-view-on-the-thermodynamics-of-folding-at-the-molecular-level
#4
Debarati DasGupta, Varun Mandalaparthy, Bhyravabhotla Jayaram
What factors favor protein folding? This is a textbook question. Parsing the experimental free energies of folding/unfolding into diverse enthalpic and entropic components of solute and solvent favoring or disfavoring folding is not an easy task. In this study, we present a computational protocol for estimating the free energy contributors to protein folding semi-quantitatively using ensembles of unfolded and native states generated via molecular dynamics simulations. We tested the methodology on 35 proteins with diverse structural motifs and sizes and found that the calculated free energies correlate well with experiment (correlation coefficient ∼ 0...
September 22, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28939814/equilibrium-kinetic-and-thermodynamic-study-of-removal-of-eosin-yellow-from-aqueous-solution-using-teak-leaf-litter-powder
#5
Emmanuel O Oyelude, Johannes A M Awudza, Sylvester K Twumasi
Low-cost teak leaf litter powder (TLLP) was prepared as possible substitute for activated carbon. The feasibility of using the adsorbent to remove eosin yellow (EY) dye from aqueous solution was investigated through equilibrium adsorption, kinetic and thermodynamic studies. The removal of dye from aqueous solution was feasible but influenced by temperature, pH, adsorbent dosage and contact time. Variation in the initial concentration of dye did not influence the equilibrium contact time. Optimum adsorption of dye occurred at low adsorbent dosages, alkaline pH and high temperatures...
September 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28939517/purification-physicochemical-and-thermodynamic-studies-of-antifungal-chitinase-with-production-of-bioactive-chitosan-oligosaccharide-from-newly-isolated-aspergillus-griseoaurantiacus-kx010988
#6
Abeer N Shehata, Abeer A Abd El Aty, Doaa A Darwish, Walaa A Abdel Wahab, Faten A Mostafa
In our search for chitinase and chitosanase producer from unconventional sources, the marine-derived fungus Aspergillus griseoaurantiacus KX010988 was obviously the best producer of the highest chitinase and chitosanase activities by solid state fermentation of potato shells. Chitinase was purified in three steps involving ammonium sulphate precipitation, DEAE-cellulose ion-exchange chromatography and Sephacryl S-300 gel chromatography. 12.55 fold increase in purity with a recovery of 17.6 was obtained. The molecular mass of the purified chitinase was found to be 130kDa...
September 19, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28939339/design-virtual-screening-molecular-docking-and-molecular-dynamics-studies-of-novel-urushiol-derivatives-as-potential-hdac2-selective-inhibitors
#7
Hao Zhou, Chengzhang Wang, Jianzhong Ye, Hongxia Chen, Ran Tao
Three series of novel urushiol derivatives were designed by introducing a hydroxamic acid moiety into the tail of an alkyl side chain and substituents with differing electronic properties or steric bulk onto the benzene ring and alkyl side chain. The binding affinity toward HDAC2 of the compounds was screened by Glide docking. The best scoring compounds were processed further with molecular docking, MD simulations and binding free energy studies to analyze the binding modes and mechanisms. Six compounds, 21, 23, 10, 19, 9 and 30, gave Glide scores of -7...
September 19, 2017: Gene
https://www.readbyqxmd.com/read/28938860/pharmacophore-generation-atom-based-3d-qsar-molecular-docking-and-molecular-dynamics-simulation-studies-on-benzamide-analogues-as-ftsz-inhibitors
#8
Swayansiddha Tripathy, Mohammed Afzal Azam, Srikanth Jupudi, Susanta Kumar Sahu
FtsZ is an appealing target for the design of antimicrobial agent that can be used to defeat the multidrug-resistant (MDR) bacterial pathogens. Pharmacophore modelling, molecular docking, and molecular dynamics (MD) simulation studies were performed on a series of 3-substituted benzamide derivatives. In the present study a five-featured pharmacophore model with one hydrogen bond acceptors (A), one hydrogen bond donors (D), one hydrophobic (H) and two aromatic rings (RR) was developed using 97 molecules having MIC values ranging from 0...
September 22, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28938825/on-the-applicability-of-a-wavefunction-free-energy-based-procedure-for-generating-first-order-non-adiabatic-couplings-around-conical-intersections
#9
Benjamin Gonon, Aurelie Perveaux, Fabien Gatti, David Lauvergnat, Benjamin Lasorne
The primal definition of first-order non-adiabatic couplings among electronic states relies on the knowledge of how electronic wavefunctions vary with nuclear coordinates. However, the non-adiabatic coupling between two electronic states can be obtained in the vicinity of a conical intersection from energies only, as this vector spans the branching plane along which degeneracy is lifted to first order. The gradient difference and derivative coupling are responsible of the two-dimensional cusp of a conical intersection between both potential-energy surfaces and can be identified to the non-trivial eigenvectors of the second derivative of the square energy difference, as first pointed out in Köppel and Schubert [Mol...
September 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28938819/a-general-method-for-the-derivation-of-the-functional-forms-of-the-effective-energy-terms-in-coarse-grained-energy-functions-of-polymers-ii-backbone-local-potentials-of-coarse-grained-o1%C3%A2-4-bonded-polyglucose-chains
#10
Emilia A Lubecka, Adam Liwo
Based on the theory of the construction of coarse-grained force fields for polymer chains described in our recent work [A. K. Sieradzan et al., J. Chem. Phys. 146, 124106 (2017)], in this work effective coarse-grained potentials, to be used in the SUGRES-1P model of polysaccharides that is being developed in our laboratory, have been determined for the O⋯O⋯O virtual-bond angles (θ) and for the dihedral angles for rotation about the O⋯O virtual bonds (γ) of 1 → 4-linked glucosyl polysaccharides, for all possible combinations of [α,β]-[d,l]-glucose...
September 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28938812/single-molecule-translocation-in-smectics-illustrates-the-challenge-for-time-mapping-in-simulations-on-multiple-scales
#11
Biswaroop Mukherjee, Christine Peter, Kurt Kremer
Understanding the connections between the characteristic dynamical time scales associated with a coarse-grained (CG) and a detailed representation is central to the applicability of the coarse-graining methods to understand molecular processes. The process of coarse graining leads to an accelerated dynamics, owing to the smoothening of the underlying free-energy landscapes. Often a single time-mapping factor is used to relate the time scales associated with the two representations. We critically examine this idea using a model system ideally suited for this purpose...
September 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28936368/uncertainty-quantified-computational-analysis-of-the-energetics-of-virus-capsid-assembly
#12
N Clement, M Rasheed, C Bajaj
Most of the existing research in assembly pathway prediction/analysis of viral capsids makes the simplifying assumption that the configuration of the intermediate states can be extracted directly from the final configuration of the entire capsid. This assumption does not take into account the conformational changes of the constituent proteins as well as minor changes to the binding interfaces that continue throughout the assembly process until stabilization. This paper presents a statistical-ensemble based approach which samples the configurational space for each monomer with the relative local orientation between monomers, to capture the uncertainties in binding and conformations...
December 2016: Proceedings
https://www.readbyqxmd.com/read/28936029/silicon-nanoporous-membranes-as-a-rigorous-platform-for-validation-of-biomolecular-transport-models
#13
Benjamin J Feinberg, Jeff C Hsiao, Jaehyun Park, Andrew L Zydney, William H Fissell, Shuvo Roy
Microelectromechanical systems (MEMS), a technology that resulted from significant innovation in semiconductor fabrication, have recently been applied to the development of silicon nanopore membranes (SNM). In contrast to membranes fabricated from polymeric materials, SNM exhibit slit-shaped pores, monodisperse pore size, constant surface porosity, zero pore overlap, and sub-micron thickness. This development in membrane fabrication is applied herein for the validation of the XDLVO (extended Derjaguin, Landau, Verwey, and Overbeek) theory of membrane transport within the context of hemofiltration...
August 15, 2017: Journal of Membrane Science
https://www.readbyqxmd.com/read/28935998/theory-of-amyloid-fibril-nucleation-from-folded-proteins
#14
Lingyun Zhang, Jeremy D Schmit
We present a theoretical model for the nucleation of amyloid fibrils. In our model we use helix-coil theory to describe the equilibrium between a soluble native state and an aggregation-prone unfolded state. We then extend the theory to include oligomers with β-sheet cores and calculate the free energy of these states using estimates for the energies of H-bonds, steric zipper interactions, and the conformational entropy cost of forming secondary structure. We find that states with fewer than ~10 β-strands are unstable relative to the dissociated state and three β-strands is the highest free energy state...
July 2017: Israel Journal of Chemistry
https://www.readbyqxmd.com/read/28933853/exchange-hole-dipole-dispersion-model-for-accurate-energy-ranking-in-molecular-crystal-structure-prediction-ii-non-planar-molecules
#15
Sarah R Whittleton, Alberto Otero-de-la-Roza, Erin R Johnson
The crystal structure prediction (CSP) of a given compound from its molecular diagram is a fundamental challenge in computational chemistry with implications in relevant technological fields. A key component of CSP is the method to calculate the lattice energy of a crystal, which allows the ranking of candidate structures. This work is the second part of our investigation to assess the potential of the exchange-hole dipole moment dispersion (XDM) model for crystal structure prediction. In this article, we study the relatively large, non-planar, mostly flexible molecules in the first five blind tests held by the Cambridge Crystallographic Data Centre...
September 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28933850/an-efficient-strategy-for-the-calculation-of-solvation-free-energies-in-water-and-chloroform-at-the-quantum-mechanical-molecular-mechanical-level
#16
Meiting Wang, Pengfei Li, Xiangyu Jia, Wei Liu, Yihan Shao, Wenxin Hu, Jun Zheng, Bernard R Brooks, Ye Mei
The partitioning of solute molecules between immiscible solvents with significantly different polarities is of great importance. The polarization between the solute and solvent molecules plays an essential role in determining the solubility of the solute, which makes computational studies utilizing molecular mechanics (MM) rather difficult. In contrast, quantum mechanics (QM) can provide more reliable predictions. In this work, the partition coefficients of the side chain analogs of some amino acids between water and chloroform were computed...
September 21, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28933553/bromide-photo-oxidation-sensitized-to-visible-light-in-consecutive-ion-pairs
#17
Guocan Li, Wesley B Swords, Gerald J Meyer
The titration of bromide into a [Ru(deeb)(bpz)2]2+ (Ru2+, deeb = 4,4'-diethylester-2,2'-bipyridine; bpz = 2,2'-bipyrazine) dichloromethane solution led to the formation of two consecutive ion-paired species, [Ru2+, Br]+ and [Ru2+, 2Br], each with distinct photophysical and electron transfer properties. Formation of the first ion pair was stoichiometric, Keq1 > 106 M1, and the second ion-pair equilibrium was estimated to be Keq2 = 2.4 ± 0.4  105 M‒1. The 1H NMR spectra recorded in deuterated dichloromethane indicated the presence of contact ion-pairs and provided insights into their structures that were complimented by density functional theory calculations...
September 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28933544/conformational-dynamics-and-exchange-kinetics-of-n-formyl-and-n-acetyl-groups-substituting-3-amino-3-6-dideoxy-%C3%AE-d-galactopyranose-a-sugar-found-in-bacterial-o-antigen-polysaccharides
#18
Olof Engström, Hani Mobarak, Jonas Ståhle, Göran Widmalm
Three dimensional shape and conformation of carbohydrates are important factors in molecular recognition events and the N-acetyl group of a monosaccharide residue can function as a conformational gatekeeper whereby it influences the overall shape of the oligosaccharide. NMR spectroscopy and quantum mechanics (QM) calculations are used herein to investigate both the conformational preferences and the dynamic behavior of N-acetyl and N-formyl substituents of 3-amino-3,6-dideoxy-α-D-galactopyranose, a sugar and substitution patterns found in bacterial O-antigen polysaccharides...
September 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28931328/kinetic-and-thermodynamic-parameters-and-partial-characterization-of-the-crude-extract-of-tannase-produced-by-saccharomyces-cerevisiae-ccmb-520
#19
Lúzia Morgana de Melo Lopes, Larissa Hayannyelly Costa Batista, Marcos Juliano Gouveia, Tonny Cley Campos Leite, Marcelo Rodrigues Figueira de Mello, Sandra Aparecida de Assis, Amanda Reges de Sena
Tannase can be used in different industrial sectors such as in food (juices and wine) and pharmaceutical production (trimethoprim) because it catalyses the hydrolysis of hydrolysable tannins. The aim of the current study is to assess the tannase found in the crude extract of Saccharomyces cerevisiae CCMB 520, and to set its catalytic and thermodynamic properties. The enzyme was optimally active at pH 6.0 and temperature 30 °C. Tannase was activated by Na(+), Ca(2+), K(+) at 5 × 10(-3) mol/L. The half-life at 30 °C was 3465...
September 20, 2017: Natural Product Research
https://www.readbyqxmd.com/read/28930630/assessing-the-structure-and-stability-of-transmembrane-oligomeric-intermediates-of-an-%C3%AE-helical-toxin
#20
Rajat Desikan, Prabal K K Maiti, K Ganapathy Ayappa
Protein membrane interactions play an important role in our understanding of diverse phenomena ranging from membrane assisted protein aggregation to oligomerization and folding. Pore forming toxins (PFTs) form the primary vehicle for infection by several strains of bacteria. These proteins expressed in a water soluble form (monomers) bind to the target membrane (protomer) to form a transmembrane pore complex through a process of oligomerization. Based on the structure of the transmembrane domains, PFTs are broadly classified into β or α toxins...
September 20, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
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