Thermodynamic Estimation Research Articles

Fast estimation of protein conformational preference at air/water interface via molecular dynamics simulations

Abstract Understanding the protein structural stability and thus its functional integrity at interface are critical for its biotechnology application development. Conventionally, it requires two extensive free energy calculations of protein in bulk and at interface to evaluate the conformational preference change during the adsorption. In this work, we derive an estimation of adsorption free energy at air/water interface for a protein in a defined conformation with the contributions of partial desolvation ΔGdesolv and surface energy ΔGa/w, which can be quickly evaluated from equilibrium MD trajectories. Via thermodynamics cycle, the free energy variation of α-helix to β-hairpin transition during the adsorption Δ Δ G w a t → i n t α → β can be obtained from the difference between the adsorption free energies of the two conformations. Applying the method, we estimate Δ Δ G w a t → i n t α → β of 6.31kJ/mol for DP5, in excellent agreement with the MD free energy data of 6.35 kJ/mol. Consistent results for four other tested proteins compared with MD free energy calculation further validate the derived adsorption model. The combination of MD simulations and thermodynamic estimations provide valuable physical insights for protein interfacial folding behaviors and serve as basis for developing prediction tools of protein conformations at interface.

Thermal stability of xylose reductase from Debaryomyces nepalensis NCYC 3413: deactivation kinetics and structural studies

Abstract Deactivation kinetics, as well as the operational stability of enzymes, is crucial in economic feasibility of industrial enzymatic processes. In this study, thermal inactivation profiles of Debaryomyces nepalensis NCYC 3413 xylose reductase (DnXR) were obtained at different temperatures. Thermodynamic parameters of the deactivation process were determined by measuring the residual activity of the enzyme. Structural characteristics of the enzyme were determined using circular dichroism, differential scanning calorimetric techniques. Enzyme retained 75–80% activity at 35 °C after incubation for 5 h. At higher temperatures, the residual activity reduced at a faster rate where only 10% of the initial activity was retained in 10 min at 50 °C. Values of ΔH* (-300.47 kJmole−1), ΔG* (−530.66 kJ mole−1) and ΔS* (714.51 × 10−3 kJ K−1 mole−1) indicated that thermal deactivation of DnXR is enthalpy driven. In the presence of cofactor NADPH, melting temperature of the enzyme increased by 2 °C with a decrease in rate of thermal deactivation. Substrate found not to have a positive effect on thermal stability. This is the first report providing information on the thermal deactivation kinetics, thermodynamic parameter estimation and the influence of cofactor on thermal stability of Debaryomyces nepalensis NCYC 3413 xylose reductase.

АТОМЫ УГЛЕРОДА В МЕЖДОУЗЛИЯХ КРИСТАЛЛИЧЕСКОЙ РЕШЁТКИ ЦЕМЕНТИТА: AB INITIO МОДЕЛИРОВАНИЕ

It was shown in previous works that iron sublattice in the structure of cementite Fe3C has four different types of interstitial sites that may potentially be occupied by carbon atoms, viz. ‘normal’ and ‘distorted’ prismatic (NP, DP) and ‘normal’ and ‘distorted’ octahedral (NO, DO) sites. Distances between their centres and the centres of z nearest-neighbour iron atoms are 1.99–2.04 A (NP sites, z = 6); 1.80–1.87 A (NO sites, z = 6); 1.62 A (DP sites, z = 4) and 1.25 A (DO sites, z = 2). It is usually believed that all carbon atoms are located in NP positions. In this work other possible variants are considered by ab initio calculations using FP-LAPW full-potential method as realized in WIEN2k program package and a cementite supercell containing 16 atoms (4 formula units). It is found that the structure containing all carbon atoms in NP positions has the lowest energy and volume. The structure with all carbon atoms in NO positions has the energy 0.267 eV/f.u. higher and the volume 9.20 % greater. If only one of the four carbon atoms in the supercell is shifted from NP to NO site the energy and volume increase by 0.233 eV/f.u. and 3.59 % correspondingly. The structure with one carbon atoms located in DP site and the other three in DO sites has the energy 0.452 eV and the volume 3.75 % higher than those of cementite with all carbon atoms in NP sites. The structures with all carbon atoms in DP sites and one or all carbon atoms in DO sites are mecha-nically unstable and transform spontaneously to conventional NP structure. Thermodynamic estima-tion based on these data shows that even at temperatures below 1000 K the fraction of carbon atoms that may move from NP sites to other ones may be as great as 20 %. Evaluation of the vacancy formation energy in cementite (supercell of 128 atoms containing 96 atoms of Fe and 32 atoms of C) resulted in the values of 0.50 eV for carbon vacancy and 1.34 (FeG) or 1.60 eV (FeS) for iron vacancy. In all these cases vacancy formation did not result in volume change of the system.

Energy gap method (EGM) to increase energy efficiency in industrial processes: Successful cases in polymer processing

A novel strategic decision methodology to increase energy efficiency in industrial processes, the Energy Gap Method (EGM), is presented. For this methodology, six different specific energy consumption levels are proposed; four of them are based on historical plant data and measurements in production processes, and the other two levels are based on benchmark references and thermodynamic minimum estimations. Five gaps or differences between specific energy consumptions can be calculated: production, quality, process, technological, and R&D gaps. Actions aiming at the reduction of the largest gaps are prioritized, taking into account the required resources and payback analyses. Four successful industrial case studies applying EGM in polymer processing are presented. In the first study, a blow molding process was diagnosed and the interventions obtained a specific energy consumption (SEC) reduction of 14%. For the second study, the same process used in the first study was employed to intervene in a second machine, obtaining an SEC reduction of 65%. For the third and fourth studies, an automotive part injection molding process was diagnosed and improved, obtaining SEC savings of 16% for the part production and around 7% for the whole production plant. EGM is not limited to polymer processing plants, and it could be adapted to other mass production processes.

Thermodynamic Estimate of the Number of Solvent Molecules Displaced by a Solute Molecule for Enthalpy-Driven Adsorption: Phenobarbital and Activated Carbons as the Model System

A Modified Crisp Equation, describing the differential Gibbs free energy of the adsorption process, is being proposed, which considers multiple sites available on the surface for adsorption and their relative fractions. The differential Gibbs free energy can be calculated by the van't Hoff Equation, which depends on the affinity constant in the Langmuir-like equation. To consider the number of solvent molecules displaced by a solute molecule in the adsorption process, a new derivative of the Langmuir-like equation is being proposed as well. By comparing the differential Gibbs free energies obtained from the 2 thermodynamic relationships, it can be determined that a phenobarbital molecule displaces 5 water molecules on the activated carbon surface for site-specific adsorption from solution. For the series of experimental conditions studied, including 4 activated carbons, pH effects, temperature effects, and solvent effects, the corrected differential Gibbs free energies using n1 = 5 for site-specific adsorption are quite consistent between the 2 thermodynamic relationships. The difference between the estimates of the differential Gibbs free energies by the Modified Crisp Equation and the van't Hoff Equation provides a new experimental method to calculate the number of solvent molecules displaced by an adsorbing solute molecule.

Thermodynamical estimation of the bounds on performance of irreversible binary distillation

The limits of the ability of a distillation system to seperate a binary mixture are considered for two different cases. In the first case the heat supply solely takes place at the column bottom and the heat removal at the condenser. In the second case the heat supply and removal is distributed over the column height. For both cases, the limiting column capacity and the minimum heat consumption are related to the external stream compositions and to the heat and mass transfer coefficients.

Water structuring inside the cavities of cucurbit[n]urils (n = 5–8): a quantum-chemical forecast

In this work we report findings of the quantum-chemical examination of water structuring in the cavities of cucurbit[n]urils (CB[n]), n = 5–8 obtained within the density functional theory. The thermodynamically most stable structures of inclusion compounds (H2O)m@CB[n] were determined for different numbers m of H2O molecules inside the cavities. From the viewpoint of thermodynamics, the most probable numbers m of water molecules in the CB[n] homologues are the following: m = 2 for CB[5], m = 4 for CB[6], m = 8 for CB[7] and m = 10 for CB[8]. For the case of CB[6] synthesized in aqueous solution, we compared its experimental IR spectrum with that calculated quantum-chemically for the model inclusion systems (H2O)m@CB[6] where m ranges from 1 to 6. The best agreement between the experimental and theoretical spectra was observed for (H2O)4@CB[6], in complete agreement with the conclusion made based on the thermodynamic estimations. Our results are also in good agreement with other available estimates of the most probable number of water molecules in CB[n].

VDAC electronics: 4. Novel electrical mechanism and thermodynamic estimations of glucose repression of yeast respiration

Inhibition of cell respiration by high concentrations of glucose (glucose repression), known as “Crabtree effect”, has been demonstrated for various cancerous strains, highly proliferating cells and yeast lines. Although significant progress in understanding metabolic events associated with the glucose repression of cell respiration has been achieved, it is not yet clear whether the Crabtree effect is the result of a limited activity of the respiratory chain, or of some glucose-mediated regulation of mitochondrial metabolic state. In this work we propose an electrical mechanism of glucose repression of the yeast S. cerevisiae, resulting from generation of the mitochondrial outer membrane potential (OMP) coupled to the direct oxidation of cytosolic NADH in mitochondria. This yeast-type mechanism of OMP generation is different from the earlier proposed VDAC-hexokinase-mediated voltage generation of cancer-type, associated with the mitochondrial outer membrane. The model was developed assuming that VDAC is more permeable to NADH than to NAD+. Thermodynamic estimations of OMP, generated as a result of NADH(2-)/NAD+(1-) turnover through the outer membrane, demonstrated that the values of calculated negative OMP match the known range of VDAC voltage sensitivity, thus suggesting a possibility of OMP-dependent VDAC-mediated regulation of cell energy metabolism. According to the proposed mechanism, we suggest that the yeast-type Crabtree effect is the result of a fast VDAC-mediated electrical repression of mitochondria due to a decrease in the outer membrane permeability to charged metabolites and owing their redistribution between the mitochondrial intermembrane space and the cytosol, both controlled by metabolically-derived OMP.

Термодинамическая оценка топливной эффективности высокоскоростного прямоточного воздушно-реактивного двигателя на углеводородном топливе с добавками бора и гидрида бериллия

Термодинамическая оценка топливной эффективности высокоскоростного прямоточного воздушно-реактивного двигателя на углеводородном топливе с добавками бора и гидрида бериллия

In Silico Prediction of the Toxic Potential of Lupeol.

Lupeol is a natural triterpenoid found in many plant species such as mango. This compound is the principal active component of many traditional herbal medicines. In the past decade, a considerable number of publications dealt with lupeol and its analogues due to the interest in their pharmacological activities against cancer, inflammation, arthritis, diabetes, and heart disease. To identify further potential applications of lupeol and its analogues, it is necessary to investigate their mechanisms of action, particularly their interaction with off-target proteins that may trigger adverse effects or toxicity. In this study, we simulated and quantified the interaction of lupeol and 11 of its analogues toward a series of 16 proteins known or suspected to trigger adverse effects employing the VirtualToxLab. This software provides a thermodynamic estimate of the binding affinity, and the results were challenged by molecular-dynamics simulations, which allow probing the kinetic stability of the underlying protein-ligand complexes. Our results indicate that there is a moderate toxic potential for lupeol and some of its analogues, by targeting and binding to nuclear receptors involved in fertility, which could trigger undesired adverse effects.

Thermokinetic Investigations of High Temperature Carbon Capture Using a Coal Fly Ash Doped Sorbent

Carbon capture (CC) employing novel sorbents at high temperature is highly significant to address the serious concerns of global warming. In this work, thermodynamic and kinetic studies have been conducted on the carbonation using doped sorbents of CaO–MgO–CFA (coal fly ash). The thermodynamic estimations not only proved the feasibility and spontaneity of the reaction but also reinforced the positive role played by CFA in not only enhancing the CC but also reducing the regeneration temperatures. Regarding the kinetic studies, a model has been proposed for both the reaction and diffusion kinetic control regimes and has been validated with experimental data at optimal conditions. Various kinetic and Arrhenius parameters have been estimated and compared with the reported values. The rate constants at 650 °C and activation energies estimated for reaction and diffusion controlled regimes were 2.5 min−1, 23 kJ/mol and 0.8 min−1, 30 kJ/mol, respectively. Our values clearly indicate the enhanced rate achieved by ...

Thermodynamic estimation of the Rehbinder effect in the case of adsorption according to the Frumkin isotherm

The adsorption Rehbinder effect is determined using an earlier-suggested thermodynamical adsorption theory on a solid surface taking into account its deformation. Single-component adsorption is considered for the case in which the adsorption isotherm on an undeformed surface is the Frumkin isotherm. The dependence of the value of the effect on the adsorbate-bulk concentration and the effect of the attraction constant on The Frumkin isotherm on it are analyzed. The concentration selectivity of the adsorption effect and the condition of the dome shape of the dependence of this value on the bulk concentration are explained in terms of isotherm parameters.

Estimating the proportionality coefficient in Rusanov’s formula for surface tension using kinetic data on the rates of nanoparticle evaporation and vacancy pore shrinkage

Confidence intervals for proportionality coefficient K in Rusanov’s linear dependence σ = Kr between surface tension σ and particle radius r are estimated for the first time using experimental data on the rates of small metal particle evaporation and vacancy pore shrinkage. The results are compared to earlier estimates by E.N. Vitol (1992) and thermodynamic estimates of other authors.

Interaction of Amino Acids and Graphene Oxide: Trends in Thermodynamic Properties

Recent studies on interaction of graphene oxide with proteins and peptides has attracted a lot of attention in biomedical applications. Hence, fundamental and experimental estimation of binding thermodynamics between various amino acids and graphene oxide is highly significant for many aspects. In this study, the interaction of graphene oxide (GO) with amino acids bearing variable charge, hydrophobicity, and aromatic moieties are studied by using isothermal titration calorimetry. To explore the effect of lateral size and degree of oxidation in GO, we employ two different sizes of GO. The results show that the interactions of GO with amino acids are mainly governed by electrostatic and π–π interaction with variable enthalpy and entropy values. The highest complex stability is observed in the case of tryptophan and arginine followed by other amino acids containing either positive charge or aromatic moieties. Amino acids bearing other functional groups either exhibit very weak interaction or did not show any...

Extending Reaction Mechanism Generator to Silicon Hydride Chemistry

Understanding the gas-phase chemistry of silicon hydrides is the first step to building a realistic kinetic model for chemical vapor deposition (CVD). Functionality for thermodynamic and kinetic data estimation of silicon hydrides was added to the open-source software Reaction Mechanism Generator (RMG). Using the updated RMG, a detailed kinetic model was built for SiH4 thermal decomposition. The generated model was used to perform reactor simulations at various process conditions for comparison to prior SiH4 decomposition experiments in a flow tube. Results show that the RMG-generated model can reasonably replicate experimental results for SiH4 concentration profiles at different temperatures and residence times. While the effect of changing initial SiH4 concentration is not captured, a first pass sensitivity analysis reveals that reasonable errors in reaction rates could contribute to the discrepancy.

Application of thermodynamics in designing of advanced automotive steels

Advanced automotive steels were designed with alloy concept and thermodynamics. Several phases were taken for the designing of transformation induced plasticity(TRIP) steels in accordance with the practical metallurgy process. Al was firstly chosen to substitute Si for improving galvanizing property, afterwards P was proved to be another alternative of Si by thermodynamic calculation and kinetic estimation. Thermodynamic investigation in the third phase revealed the effective function of Al to increase carbon solubility in austenite as well as TRIP effect of steel. Stack fault energy was calculated, in combination with heat treatment and microstructure measurement, which led to a successful composition designing of twin induced plasticity (TWIP) steel.

A New Process of Manufacturing “Oxygen-free” Gd

“Oxygen-free” Gd was fabricated by hydrogen plasma arc melting (HPAM). The HPAM is more different than the traditional Ar plasma arc melting (PAM) in Oxygen removal. It is attributable to the hydrogen atoms dissociated and activated in high temperature HPAM. In addition an increased diffusion of oxygen in Gd-O solid solution to the surface also plays an important role in removal of oxygen. The substances are confirmed by optical emission spectroscopy (OES), which are involved in the plasma like Ar I, Ar II and H I and some possible reactions. The effect of H with thermodynamic estimation was discussed in detail.

Effective interactions between nanoparticles: Creating temperature-independent solvation environments for self-assembly.

The extent to which solvent-mediated effective interactions between nanoparticles can be predicted based on structure and associated thermodynamic estimators for bulk solvents and for solvation of single and pairs of nanoparticles is studied here. As a test of the approach, we analyse the strategy for creating temperature-independent solvent environments using a series of homologous chain fluids as solvents, as suggested by an experimental paper [M. I. Bodnarchuk et al., J. Am. Chem. Soc. 132, 11967 (2010)]. Our conclusions are based on molecular dynamics simulations of Au140(SC10H21)62 nanoparticles in n-alkane solvents, specifically hexane, octane, decane and dodecane, using the TraPPE-UA potential to model the alkanes and alkylthiols. The 140-atom gold core of the nanocrystal is held rigid in a truncated octahedral geometry and the gold-thiolate interaction is modeled using a Morse potential. The experimental observation was that the structural and rheological properties of n-alkane solvents are constant over a temperature range determined by equivalent solvent vapour pressures. We show that this is a consequence of the fact that long chain alkane liquids behave to a good approximation as simple liquids formed by packing of monomeric methyl/methylene units. Over the corresponding temperature range (233-361 K), the solvation environment is approximately constant at the single and pair nanoparticle levels under good solvent conditions. However, quantitative variations of the order of 10%-20% do exist in various quantities, such as molar volume of solute at infinite dilution, entropy of solvation, and onset distance for soft repulsions. In the opposite limit of a poor solvent, represented by vacuum in this study, the effective interactions between nanoparticles are no longer temperature-independent with attractive interactions increasing by up to 50% on decreasing the temperature from 361 K to 290 K, accompanied by an increase in emergent anisotropy due to correlation of mass dipoles on the two nanoparticles. One expects therefore that during self-assembly using solvent evaporation, temperature can be used as a structure-directing factor as long as good solvent conditions are maintained. It also suggests that disordered configurations may emerge as solvent quality decreases due to increasing role of short-range attractions and ligand fluctuation-driven anisotropy. The possibilities of using structural estimators of various thermodynamic quantities to analyse the interplay of ligand fluctuations and solvent quality in self-assembly as well as to design solvation environments are discussed.

Defining the Thermodynamic Efficiency in a Wave Rotor

A wave rotor enhances the performance of a gas turbine with its internal compression and expansion, yet the thermodynamic efficiency estimation has been troubling because the efficiency definition is unclear. This paper put forward three new thermodynamic efficiency definitions to overcome the trouble: the adiabatic efficiency, the weighted-pressure mixed efficiency, and the pressure pre-equilibrated efficiency. They were all derived from multistream control volumes. As a consequence, they could correct the efficiency values and make the values for compression and expansion independent. Moreover, the latter two incorporated new models of pre-equilibration inside a control volume, and modified the hypothetical “ideal” thermodynamic processes. Parametric analyses based on practical wave rotor data demonstrated that the trends of those efficiency values reflected the energy losses in wave rotors. Essentially, different thermodynamic efficiency definitions indicated different ideal thermal cycle that an optimal wave rotor can provide for a gas turbine, and they were recommended to application based on that essence.

Structural insights into chaperone-activity enhancement by a K354E mutation in tomato acidic leucine aminopeptidase.

Tomato plants express acidic leucine aminopeptidase (LAP-A) in response to various environmental stressors. LAP-A not only functions as a peptidase for diverse peptide substrates, but also displays chaperone activity. A K354E mutation has been shown to abolish the peptidase activity but to enhance the chaperone activity of LAP-A. To better understand this moonlighting function of LAP-A, the crystal structure of the K354E mutant was determined at 2.15 Å resolution. The structure reveals that the K354E mutation destabilizes an active-site loop and causes significant rearrangement of active-site residues, leading to loss of the catalytic metal-ion coordination required for the peptidase activity. Although the mutant was crystallized in the same hexameric form as wild-type LAP-A, gel-filtration chromatography revealed an apparent shift from the hexamer to lower-order oligomers for the K354E mutant, showing a mixture of monomers to trimers in solution. In addition, surface-probing assays indicated that the K354E mutant has more accessible hydrophobic areas than wild-type LAP-A. Consistently, computational thermodynamic estimations of the interfaces between LAP-A monomers suggest that increased exposure of hydrophobic surfaces occurs upon hexamer breakdown. These results suggest that the K354E mutation disrupts the active-site loop, which also contributes to the hexameric assembly, and destabilizes the hexamers, resulting in much greater hydrophobic areas accessible for efficient chaperone activity than in the wild-type LAP-A.