SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Gibbs free energy

202

A water drop on a superhydrophobic surface that is pinned by wire loops can be reproducibly cut without formation of satellite droplets. Drops placed on low-density polyethylene surfaces and Teflon-coated glass slides were cut with superhydrophobic knives of low-density polyethylene and treated copper or zinc sheets, respectively. Distortion of drop shape by the superhydrophobic knife enables a clean break. The driving force for droplet formation arises from the lower surface free energy for two separate drops, and it is modeled as a 2-D system. An estimate of the free energy change serves to guide when droplets will form based on the variation of drop volume, loop spacing and knife depth. Combining the cutting process with an electrofocusing driving force could enable a reproducible biomolecular separation without troubling satellite drop formation.

Concepts: Energy, Liquid, Surface tension, Drop, Gibbs free energy, Rainbow, Liquids, Globule

176

Integrin clustering plays a pivotal role in a host of cell functions. Hetero-dimeric integrin adhesion receptors regulate cell migration, survival, and differentiation by communicating signals bidirectionally across the plasma membrane. Thus far, crystallographic structures of integrin components are solved only separately, and for some integrin types. Also, the sequence of interactions that leads to signal transduction remains ambiguous. Particularly, it remains controversial whether the homo-dimerization of integrin transmembrane domains occurs following the integrin activation (i.e. when integrin ectodomain is stretched out) or if it regulates integrin clustering. This study employs molecular dynamics modeling approaches to address these questions in molecular details and sheds light on the crucial effect of the plasma membrane. Conducting a normal mode analysis of the intact αllbβ3 integrin, it is demonstrated that the ectodomain and transmembrane-cytoplasmic domains are connected via a membrane-proximal hinge region, thus merely transmembrane-cytoplasmic domains are modeled. By measuring the free energy change and force required to form integrin homo-oligomers, this study suggests that the β-subunit homo-oligomerization potentially regulates integrin clustering, as opposed to α-subunit, which appears to be a poor regulator for the clustering process. If α-subunits are to regulate the clustering they should overcome a high-energy barrier formed by a stable lipid pack around them. Finally, an outside-in activation-clustering scenario is speculated, explaining how further loading the already-active integrin affects its homo-oligomerization so that focal adhesions grow in size.

Concepts: Protein, Signal transduction, Cell membrane, Cell biology, Cell signaling, G protein-coupled receptor, Gibbs free energy, Normal mode

146

Previous experimental study measuring the binding affinities of biotin to the wild type streptavidin (WT) and three mutants (S45A, D128A and S45A/D128A double mutant) has shown that the loss of binding affinity from the double mutation is larger than the direct sum of those from two single mutations. The origin of this cooperativity has been investigated in this work through molecular dynamics simulations and the end-state free energy method using the polarized protein-specific charge. The results show that this cooperativity comes from both the enthalpy and entropy contributions. The former contribution mainly comes from the alternations of solvation free energy. Decomposition analysis shows that the mutated residues nearly have no contributions to the cooperativity. Instead, N49 and S88, which are located at the entry of the binding pocket and interact with the carboxyl group of biotin, make the dominant contribution among all the residues in the first binding shell around biotin.

Concepts: DNA, Mutation, Energy, Mutant, Chemistry, Entropy, Gibbs free energy, Affinity

137

Molecular dynamics (MD) simulation in the explicit water is performed to study the interaction mechanism of trypsin-ligand binding under the AMBER force field and polarized protein-specific charge (PPC) force field combined the new developed highly efficient interaction entropy (IE) method for calculation of entropy change. And the detailed analysis and comparison of the results of MD simulation for two trypsin-ligand systems show that the root-mean-square deviation (RMSD) of backbone atoms, B-factor, intra-protein and protein-ligand hydrogen bonds are more stable under PPC force field than AMBER force field. Our results demonstrate that the IE method is superior than the traditional normal mode (Nmode) method in the calculation of entropy change and the calculated binding free energy under the PPC force field combined with the IE method is more close to the experimental value than other three combinations (AMBER-Nmode, AMBER-IE and PPC-Nmode). And three critical hydrogen bonds between trypsin and ligand are broken under AMBER force field. However, they are well preserved under PPC force field. Detailed binding interactions of ligands with trypsin are further analyzed. The present work demonstrates that the polarized force field combined the highly efficient IE method is critical in MD simulation and free energy calculation.

Concepts: Energy, Molecular dynamics, Fundamental physics concepts, Chemistry, Atom, Entropy, Gibbs free energy, AMBER

104

Thioesters and thioacetic acid (TAA) have been invoked as key reagents for the origin of life as activated forms of acetate analogous to acetyl-CoA. These species could have served as high-energy group-transfer reagents and allowed carbon insertions to form higher molecular weight compounds such as pyruvate. The apparent antiquity of the Wood-Ljungdahl CO2 fixation pathway and its presence in organisms which inhabit hydrothermal (HT) environments has also led to suggestions that there may be a connection between the abiotic chemistry of compounds similar to TAA and the origins of metabolism. These compounds' apparent chemical simplicity has made their prebiotic availability assumed, however, although the kinetic behavior and thermochemical properties of TAA and analogous esters have been preliminarily explored in other contexts, the geochemical relevance of these compounds merits further evaluation. Therefore, the chemical behavior of the simplest thiolated acetic acid derivatives, TAA and methylthioacetate (MTA) were explored here. Using laboratory measurements, literature data, and thermochemical models, we examine the plausibility of the accumulation of these compounds in various geological settings. Due to the high free energy change of their hydrolysis and corresponding low equilibrium constants, it is unlikely that these species could have accumulated abiotically to any significant extant.

Concepts: Carbon dioxide, Life, Molecule, Chemistry, Acid dissociation constant, Acetic acid, Carboxylic acid, Gibbs free energy

29

The term ‘stress’ - coined in 1936 - has many definitions, but until now has lacked a theoretical foundation. Here we present an information-theoretic approach - based on the ‘free energy principle’ - defining the essence of stress; namely, uncertainty. We address three questions: What is uncertainty? What does it do to us? What are our resources to master it? Mathematically speaking, uncertainty is entropy or ‘expected surprise’. The ‘free energy principle’ rests upon the fact that self-organizing biological agents resist a tendency to disorder and must therefore minimize the entropy of their sensory states. Applied to our everyday life, this means that we feel uncertain, when we anticipate that outcomes will turn out to be something other than expected - and that we are unable to avoid surprise. As all cognitive systems strive to reduce their uncertainty about future outcomes, they face a critical constraint: Reducing uncertainty requires cerebral energy. The characteristic of the vertebrate brain to prioritize its own high energy is captured by the notion of the ‘selfish brain’. Accordingly, in times of uncertainty, the selfish brain demands extra energy from the body. If, despite all this, the brain cannot reduce uncertainty, a persistent cerebral energy crisis may develop, burdening the individual by ‘allostatic load’ that contributes to systemic and brain malfunction (impaired memory, atherogenesis, diabetes and subsequent cardio- and cerebrovascular events). Based on the basic tenet that stress originates from uncertainty, we discuss the strategies our brain uses to avoid surprise and thereby resolve uncertainty.

Concepts: Brain, Energy, Physics, Cognition, Entropy, Gibbs free energy, Statistical mechanics, Conservation of energy

28

The effect of two fly ashes as soil amendment on the adsorption-desorption of metolachlor [2-chloro-N-(2-ethyl-6-methylphenyl)-N-(2-methoxy-1-methylphenyl)] and atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) was studied in alluvial and laterite soils. The adsorption data for both the herbicides fitted well the Freundlich equation, and Freundlich adsorption coefficient (K (f)) increased with an increase of fly ash amount. Both the fly ashes differed in their extent to increase herbicide sorption, and the effect was different in different soils. Atrazine was sorbed more in the soils/soils + fly ash mixtures than the metolachlor. The K (f) values showed significant correlation with the amount of fly ash amendment (correlation coefficient, R > 0.982). The desorption isotherms also fitted the Freundlich equation, and desorption showed hysteresis which increased with an increase in the content of fly ash amendment. The free energy change (ΔG) indicated that the sorption process is exothermic, spontaneous, and physical in nature. The study has shown that fly ash as soil amendment significantly increased the sorption of metolachlor and atrazine, but the effect is soil- and fly ash-specific.

Concepts: Soil, Adsorption, Gibbs free energy, Freundlich equation, Surface runoff, Herbicide, Atrazine, Herbicides

28

In this study, a method was proposed for calculating the thermodynamic entropy increase ΔS in a water body after receiving excess discharge of organics and nutrients in order to quantitatively assess the impact of pollutants discharge on aquatic systems. The enthalpy change was evaluated using the standard thermodynamic data according to the possible chemical and/or biochemical reactions such as organic oxidation, nitrification/denitrification, and phosphorus precipitation, for the recovery of water quality to the background level. A series of equations were established for calculating the ΔS associated with the decomposition or removal of TOC, NO(3)-N, NO(2)-N, NH(3)-N and TP. The values of ΔS corresponding to unit mass (per g) of these pollutants were calculated as 54.0 kJ/K, 2.91 kJ/K, 10.01 kJ/K, 28.51 kJ/K and 2.81 kJ/K, respectively. Besides, the applicability of the proposed method was proved by a scenario analysis regarding effluent quality control and surface water quality protection in China.

Concepts: Energy, Evaluation, Water, Thermodynamics, Entropy, Gibbs free energy, Enthalpy, Thermodynamic databases for pure substances

28

Rates of hydride transfer from several hydride donors to benzhydrylium ions have been measured at 20 °C and used for the determination of empirical nucleophilicity parameters N and s(N) according to the linear free energy relationship log k(20 °C) =s(N) (N+E). Comparison of the rate constants of hydride abstraction by tritylium ions with those calculated from the reactivity parameters s(N) , N, and E showed fair agreement. Therefore, it was possible to convert the large number of literature data on hydride abstraction by tritylium ions into N and s(N) parameters for the corresponding hydride donors, and construct a reactivity scale for hydride donors covering more than 20 orders of magnitude.

Concepts: Hydrogen, Rates, Hydride, Gibbs free energy, Free-energy relationship, Large numbers, Logarithmic scale, Order of magnitude

28

Comparison of the results of Car-Parrinello molecular dynamics simulations of isolated benzene, pyrimidine and 1,2,4-triazine molecules reveals that the unusually low population of planar geometry of the benzene ring is caused by entropy effects despite its high aromaticity. The decrease in symmetry of the molecule results in smaller changes in entropy and Gibbs free energy due to out-of-plane deformations of the ring, leading to an increase in the population of planar geometry of the ring. This leads to differences in the topology of potential energy and Gibbs free energy surfaces.

Concepts: DNA, Energy, Atom, Benzene, Entropy, Gibbs free energy, Aromaticity, Electrophilic aromatic substitution