The protein folding transition state: insights from kinetics and thermodynamics

We perform extensive lattice Monte Carlo simulations of protein folding to construct and compare the equilibrium and the kinetic transition state ensembles of a model protein that folds to the native state with two-state kinetics. The kinetic definition of the transition state is based on the folding probability analysis method, and therefore on the selection of conformations with 0.4相似文献   

Electron diffraction study of the equilibrium structure of hexamethylenetetramine involving data from quantum chemistry and vibrational spectroscopy

The equilibrium structure of the urotropine molecule is characterized by means of gas electron diffraction (GED) with the involvement of quantum chemistry and vibrational spectroscopy. A structural analysis of the GED data is performed based on the parameters of the intramolecular potential function using of the program complex SYMM/DISP/ELDIFF/LARGE. The quadratic and cubic force constants of the urotropine molecule were obtained earlier on the basis of calculations at the MP2(full)/cc-pVTZ level and assuming molecular symmetry T _d . The values of the equilibrium geometric parameters r _e of the urotropine molecule are found. The experimental structural parameters are in good agreement with those calculated at the MP2(full)/cc-pVTZ level.     

关于弯曲界面气液两相相平衡化学势相等热力学判据的讨论

Thermodynamic criterion of equal chemical potential for phase equilibrium between gas and liquid in curved interface has been introduced in many textbooks and papers. In this paper, the process of the derivation of the criterion is proved to be wrong with analysis. In order to solve the problem, a proof procedure for the thermodynamic criterion of equal chemical potential is provided based on the definition of chemical potential. At the same time, a new thermodynamic criterion of two-phase equilibrium in curved interface is established using Gibbs interface thermodynamics and a new method for derivation of Kelvin equation is put forward based on the thermodynamic criterion of two-phase equilibrium. The new criterion which is derived directly from the second law of thermodynamics has a specific thermodynamic significance and clear physical model.     

Quantitative 2H NMR spectroscopy. 1. Thermodynamic H/D isotope effects in N,N-dimethylformamide and cyclopentadiene molecules

A new method for quantification of the relative distribution of deuterium in molecules is proposed. The technique is based on the lineshape analysis in the ²H NMR spectra obtained at the natural abundance level of deuterium with allowance for inhomogeneity of the magnetic field. The equilibrium thermodynamic H/D isotope effects for hindered rotation about the C—N bond in the N,N-dimethylformamide molecule and for prototropic exchange in the cyclopentadiene molecule were determined. The results obtained agree with those of DFT calculations of the vibrational energies.     

Essential energy space random walks to accelerate molecular dynamics simulations: convergence improvements via an adaptive-length self-healing strategy

Recently, accelerated molecular dynamics (AMD) technique was generalized to realize essential energy space random walks so that further sampling enhancement and effective localized enhanced sampling could be achieved. This method is especially meaningful when essential coordinates of the target events are not priori known; moreover, the energy space metadynamics method was also introduced so that biasing free energy functions can be robustly generated. Despite the promising features of this method, due to the nonequilibrium nature of the metadynamics recursion, it is challenging to rigorously use the data obtained at the recursion stage to perform equilibrium analysis, such as free energy surface mapping; therefore, a large amount of data ought to be wasted. To resolve such problem so as to further improve simulation convergence, as promised in our original paper, we are reporting an alternate approach: the adaptive-length self-healing (ALSH) strategy for AMD simulations; this development is based on a recent self-healing umbrella sampling method. Here, the unit simulation length for each self-healing recursion is increasingly updated based on the Wang-Landau flattening judgment. When the unit simulation length for each update is long enough, all the following unit simulations naturally run into the equilibrium regime. Thereafter, these unit simulations can serve for the dual purposes of recursion and equilibrium analysis. As demonstrated in our model studies, by applying ALSH, both fast recursion and short nonequilibrium data waste can be compromised. As a result, combining all the data obtained from all the unit simulations that are in the equilibrium regime via the weighted histogram analysis method, efficient convergence can be robustly ensured, especially for the purpose of free energy surface mapping.     

Modeling Biomass Gasification Using Thermodynamic Equilibrium Approach

In this paper, the thermodynamic equilibrium models for biomass gasification applicable to various gasifier types have been developed, with and without considering char. The equilibrium models were then modified closely matching the CH₄ only or both CH₄ and CO compositions from experimental data. It is shown that the modified model presented here based on thermodynamic equilibrium and taking into account local heat and mass considerations can be used to simulate the performance of a downdraft gasifier. The model can also be used to estimate the equilibrium composition of the syngas. Depending on the gasifier type and internal fluid flow, heat and mass transfer characteristics, with proper modification of the equilibrium model, a simple tool to simulate the operation and performance of varying types of biomass gasifier can be developed.     

A method to estimate the Gibbs free energy of non-equilibrium alloys by thermal analysis

A method has been developed to estimate the Gibbs free energy $ \left( {G_{\text{S}}^{\text{NE}} } \right) $ of the non-equilibrium solid alloys with multicomponents based on differential scanning calorimetry (DSC) analysis. In this method, the DSC curves of the non-equilibrium and equilibrium alloys during heating up to fully melting and those of the alloys during solidifying were measured. Then the thermal effects of the solid phase transformations from non-equilibrium to equilibrium states and the equilibrium solidification could be calculated. By evolving the traditional equal-G curve principle to equal-G point, the Gibbs free energy of the equilibrium solid alloy with multicomponents could be obtained on condition that the free energy of the liquid alloy was known. Considering the thermal effects of the solid phase transformations from non-equilibrium to equilibrium states, the Gibbs free energy value of the non-equilibrium alloys with a given composition could be achieved although the phase constitution of the equilibrium solid alloys and the Gibbs free energy of each phase were not known, and the calculation errors could be reduced by dividing the alloys into many infinitesimal virtual pure metals. The Gibbs free energy of the non-equilibrium Al?CSi?CMn alloys was calculated by using this method, confirming the validity of this method.     

Graph Theoretic Techniques in the Theory of Classical Fluids

Abstract

The mathematical ideas underlying the graph theoretic approach to the equilibrium theory of classical fluids are treated from an elementary point of view. The emphasis is placed on modern developments based on the techniques of functional differentiation and topological reduction. The aim is to provide the non-expert reader with a mathematical guide to recent papers which employ graph theoretic methods, particularly to those dealing with perturbation theory.     

Configurational statistics of ethylene-propylene copolymers: stereochemical equilibrium on the tertiary carbon atoms

The average dimensions and thermodynamic properties of unperturbed ethylene-propylene copolymer chains have been evaluated according to a theory based on a pseudostereochemical equilibrium among the different monomer units. The frequency of occurrence of the ethylene-propylene pairs has been adjusted to the value to be expected from the chemical composition and from the product of the reactivity ratios, while stereochemical equilibrium is assumed for the propylene-propylene sequences. The calculated unperturbed dimensions agree satisfactorily with experimental data. Our results are also in substantial agreement with those recently obtained by Mark who used a different method based on a Monte Carlo routine for sequence generation.     

A modular fluorimetric stopped-flow system for use in clinical chemistry

Summary A simple, versatile modular stopped-flow system described elsewhere was applied to clinical analyses. The instrument was tested for detection limits, selectivity, precision, dynamic range and sampling rate with conventional rate and equilibrium methods. For this purpose, the determination of copper based on its accelerating effect on a new indicator reaction involving the imidazole/hydrogen peroxide system, was chosen and satisfactorily applied to the analysis of copper in serum. The results obtained show that the stopped-flow method is more advantageous and adequate for routine analysis than two other methods (conventional kinetic and equilibrium techniques).

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Modulares fluorimetrisches Stopped-Flow-System für die klinische Chemie

     

Estimation of Aluminum Speciation in Surface Waters of Low Ionic Strength by a Simple Computer Model

Abstract

A simple computer model based on chemical equilibrium calculation for evaluating the aluminum speciation in surface waters of low ionic strength (I < 1 × 10^?4 M) was presented in this paper. The speciations of aluminum obtained by this model have been compared with those obtained experimentally and the reasons for the observed differences have been discussed. This model has been applied to the estimation of aluminum speciation in practical surface waters sampling from areas of the United Kingdom, United States and People's Republic of China. Some valuable conclusions are obtained.     

Plasma models applicable to low pressure discharges

Electron, ionization and excitation temperatures are often used to characterize discharge plasmas. These temperatures are determined using a plasma model, which generally is based on the assumption of equilibrium in the plasma. The assumptions that are used in the development of the equilibrium model are critically discussed, especially with regard to the application of this model to a low pressure plasma. A steady state model based on a set of assumptions much more applicable to a low pressure plasma is presented. A ratioing technique is developed which allows this model to be straight-forwardly applied to spectroscopic data. Results obtained for the application of the steady state model to a hollow cathode discharge are presented and shown to be more realistic than those obtained using the equilibrium model.     

Liquid–liquid equilibria of alkane (C10/C12/C14)+1,4-diisopropylbenzene+sulfolane at 323.15, 348.15 and 373.15 K

Tie line data have been determined at 323.15, 348.15 and 373.15 K for the ternary liquid–liquid equilibria (LLE) of alkane (C10/C12/C14)+1,4-diisopropylbenzene+sulfolane systems. The addition of 1,4-diisopropylbenzene to sulfolane is found to increase the solubility of alkanes in the order of n-decane>n-dodecane>n-tetradecane and the relative mutual solubility of 1,4-diisopropylbenzene is higher in n-decane+sulfolane than in n-dodecane+sulfolane or n-tetradecane+sulfolane mixtures. The tie line data were correlated with the well-known UNIQUAC and NRTL models. The calculated equilibrium mole fractions based on the UNIQUAC model are better than those based on the NRTL model. The values of selectivity and distribution coefficient were derived from the equilibrium data.     

Water transport in epoxy-aliphatic amine networks - Influence of curing cycles

In this work, polyepoxide network based on an aliphatic amine hardener were cured under different curing temperatures and their water sorption characteristics was systematically investigated as function of cure conditions. Attention was focused on the analysis of equilibrium properties, swelling behaviour and thermomechanical properties.For the undercured systems (epoxide conversion around 0.90), additional crosslinking reactions take part during water immersion, even at 20 °C. This effect was found to be mainly related to plasticizing of the network by water molecules.Local dynamics and plasticization effects were also monitored by dynamic mechanical analysis (DMA). The changes in the glass transition for the two well-crosslinked epoxies were greater than those predicted by considering the free volume changes only. The β process was significantly affected by the absorbed water. A decrease of the average relaxation time with moisture uptake was observed. The disruptions of the α and β relaxations were found to be reversible after re-drying of the wet material for the nearly fully cured epoxies.The fully crosslinked network was found to absorb slightly more water and at a greater rate than a slightly less crosslinked network (conversion around 0.98). This anomalous behaviour was analysed and a tentative explanation was presented in this paper.     

The nature of thermodynamic compatibility of components of aqueous solutions of starch and cellulose carboxymethyl derivatives

The Gibbs free energy, enthalpy, and entropy of mixing of starch and carboxymethyl derivatives of starch and cellulose with water were determined by sorption and calorimetry methods at 25°C throughout the entire range of compositions. The contributions due to the equilibrium intermolecular interactions and relaxation of a metastable glassy structure were separated. The relaxation of the metastable structure taking place during physical adsorption of the first portions of water on polymers makes a negative contribution to all thermodynamic functions of mixing. The contribution of equilibrium interactions, which includes pair nonviolent interactions of units and water molecules and electrostatic interactions of ions, is positive for the enthalpy and entropy of mixing. In this case, the positive entropy values exceed those of enthalpy, which is responsible for the thermodynamic compatibility. Thermodynamic analysis of the processes of dissolution of starch, carboxymethyl starch and carboxymethyl cellulose sodium salts showed that, contrary to the popular point of view, the compatibility of polysaccharides and their derivatives with water is based not on the enthalpy, but entropy nature and is strengthened additionally owing to relaxation of the metastable glassy structure of polymers.     

Liquid–liquid equilibria of alkane (C10–C14)+octylbenzene+sulfolane

The liquid–liquid equilibria (LLE) data are presented for mixtures of alkane (C10/C12/C14)+octylbenzene+sulfolane at 323.15, 348.15 and 373.15 K. The addition of octylbenzene to sulfolane is found to increase the solubility of alkanes in the order of decane>dodecane>tetradecane. The tie line data were correlated with the well-known UNIQUAC and NRTL models. The calculated values based on the UNIQUAC model were found to be better than those based on the NRTL model. The values of selectivity and distribution coefficient were derived from the equilibrium data.     

Application of a single model to study the adsorption equilibrium of prednisolone on six carbonaceous materials

The knowledge of sorption processes of nonelectrolytes in solution by solid adsorbents implies the study of kinetics, equilibrium, and thermodynamic functions. However, quite frequently the equilibrium isotherms are studied by comparing them with those corresponding to the Giles et al. classification (1); these isotherms are also analyzed by fitting them to equations based on thermodynamic or kinetic criteria, and even to empirical equations. Nevertheless, information obtained is more coherent and satisfactory if the adsorption isotherms are fitted by using an equation describing the equilibrium isotherms according to the kinetic laws. These mentioned laws would determine each one of the unitary processes (one or more) which condition the global process. In this paper, an adsorption process of prednisolone in solution by six carbonaceous materials is explained according to a previously proposed single model, which allows to establish a kinetic law which fits satisfactorily most of C vs t isotherms (2). According to the above-mentioned kinetic law, equations describing sorption equilibrium processes have been deducted, and experimental data points have been fitted to these equations; such a fitting yields to different values of adsorption capacity and kinetic equilibrium constants for the different processes at several temperatures. However, in spite of their practical interest, these constants have no thermodynamic signification. Thus, the thermodynamic equilibrium constant (K) has been calculated by using a modified expression of the Gaines et al. equation (3). Global average values of the thermodynamic functions have also been calculated from the K values. Information related to variations of DeltaH and DeltaS with the surface coverage fraction was obtained by using the corresponding Clausius-Clapeyron equations.     

Gibbs energy based procedure for the correlation of type 3 ternary systems including a three-liquid phase region

Equilibrium data for type 3 ternary systems comprising a liquid–liquid–liquid equilibrium region (LLLE tie-triangle) are not frequently correlated, as is evidenced by a lack of studies in the literature. In the present paper, a robust algorithm to calculate or correlate equilibrium data for this type of system is proposed. This algorithm is based on geometric aspects related to the Gibbs energy of mixing (g^M) and possesses some interesting advantages that are discussed in the text. The methodology put forward is applied to correlate the equilibrium data of three type 3 ternary systems. The NRTL model is used to define g^M, and the common tangent plane criterion to define the equilibrium condition for the calculations. The lack in flexibility of the NRTL equation to model these systems is discussed.