Direct Evaluation of Vapour-Liquid Equilibria of Mixtures by Molecular Dynamics Using Gibbs-Duhem Integration

Abstract

We present an extension of the Gibbs-Duhem integration method that permits direct evaluation of vapour-liquid equilibria of mixtures by molecular dynamics. The Gibbs-Duhem integration combines the best elements of the Gibbs ensemble Monte Carlo technique and thermodynamic integration. Given conditions of coexistence of pure substances, simultaneous but independent molecular dynamics simulations of each phase at constant number of particles, constant pressure, constant temperature and constant fugacity fraction of species 2 are carried out in succession along coexistence lines. In each simulation, the coexistence pressure is adjusted to satisfy the Clapeyron-type equation. The Clapeyron-type equation is a first-order nonlinear differential equation that prescribes how the pressure must change with the fugacity fraction of species 2 to maintain coexistence at constant temperature. The Clapeyron-type equation is solved by the predictor-corrector method. Running averages of mole fraction and compressibility factor for the two phases are used to evaluate the right-hand side of the Clapeyron-type equation. The Gibbs-Duhem integration method is applied to three prototypes of binary mixtures of the two-centre Lennard-Jones fluid having various elongations. The starting points on the coexistence curve were taken from published data.     

An Extended Gibbs Ensemble

Abstract

A general extended Gibbs ensemble, obtained by augmenting the standard Gibbs ensemble by intermediate states in the spirit of the scaled particle method of Nezbeda and Kolafa [Molec. Simul., 5, 391 (1991)], is introduced. The intermediate states span the states with different number of particles in the simulation boxes and facilitate the transfer of particles even in such complex systems as e.g., mixtures of very different components, systems of flexible polymeric molecules, or systems at very high densities. A general formulation of the ensemble is given and two implementations are considered in detail. The method is very general and is exemplified by studying the fluid-fluid coexistence in a dense binary mixture of the hard-sphere and square-well fluids. It is found that its efficiency is about by factor three greater in comparison with the standard Gibbs ensemble simulations.     

New potential model for molecular dynamic simulation of liquid HF. I—Parameter optimization for charge equilibration method

In order to build a complete potential model to perform classical molecular dynamic simulations of liquid HF, a new optimization method is proposed to obtain transferable parameters for charge equilibration method on the basis of ab initio reference data. The optimized parameters (the electronegativity χ and the Slater orbital exponent ζ for H and F atoms) appear to be able to reproduce the variations of the electrostatic potential calculated from an ab initio method in a liquid phase of HF molecules for different thermodynamic conditions. It is concluded that the proposed method is general, precise and efficient to obtain transferable and realistic parameters.     

Molecular Dynamics/Free Energy Perturbation Studies of the Thermostable V74I Mutant of Ribonuclease HI

Abstract

Recent site-directed mutagenesis and thermodynamic studies have shown that the V74I mutant of Escherichia coli ribonuclease HI (RNase HI) is more stable than the wild type protein [Ishikawa et al., Biochemistry 32, 6171 (1993)]. In order to clarify the stabilization mechanism of this mutant, we calculated the free energy change due to the mutation Val 74→Ile in both the native and denatured states by free energy perturbations based on molecular dynamics (MD) simulations. We carried out inclusive MD simulations for the protein in water; i.e., fully solvated, no artificial constraints applied, and all long-range Coulomb interactions included. We found that the free energy of the mutant increased slightly relative to the wild type, in the native state by 1.60 kcal/mol, and in the denatured state by 2.25 kcal/mol. The unfolding free energy increment of the mutant (0.66 ± 0.19 kcal/mol) was in good agreement with the experimental value (0.6 kcal/mol). The hysteresis error in the free energy calculations, i.e., forward and reverse perturbations, was only ±0.19 kcal/mol. These results show that the V74I mutant is stabilized relative to the wild type by the increased free energy of the denatured state and not by a decrease in the free energy of the native state as had been proposed earlier based on the mutant X-ray structure. It was found that the stabilization was caused by a loss of solvation energy in the mutant denatured state and not by improved packing interactions inside the native protein.     

MODIFIED ETHANOL INJECTION METHOD FOR LIPOSOMES CONTAINING β-SITOSTEROL β-D-GLUCOSIDE

A modified ethanol injection method for liposomes containing soybean phosphatidylcholine (SPC), cholesterol (Ch), β-sitosterol β-D-glucoside (Sit-G) and oleic acid (OA) was developed, that can produce homogeneous unilamellar liposomes without the use of sonication and dialysis. In this method, water is poured into a concentrated lipid-ethanol solution and then ethanol is removed in an evaporator. Dilution with water causes spontaneous formation of small and homogenous unilamellar vesicles from micellar aggregate. The size of liposomes can be controlled by the ratio of ethanol to water. OA and Sit-G were distributed at the surface of liposomes and were recognized by Concanavalin A, respectively. This easy and quick method for preparation of liposomes may be applicable in many areas.     

Ethanol injection method for hydrophilic and lipophilic drug-loaded liposome preparation

In this article, a hydrophobic (beclomethasone dipropionate; BDP) and a hydrophilic (cytarabine; Ara-C) drugs have been encapsulated in liposomes in order to be administered via the pulmonary route. For this aim, a liposome preparation method, which is easy to scale up, the ethanol injection method, has been selected. The effects of critical process and formulation parameters have been investigated. The drug-loaded liposomes were prepared and characterized in terms of size, zeta potential, encapsulation efficiency, release study, cell uptake, and aerodynamic behavior. Small multilamellar vesicles, with sizes ranging from about 80 to 170?nm, were successfully obtained. Results indicated a significant influence of phospholipid and cholesterol amounts on liposome size and encapsulation efficiency. The higher encapsulation efficiencies were about 100% for the hydrophobic drug (BDP) and about 16% for the hydrophilic one (Ara-C). The in vitro release study showed a prolonged release profile for BDP, in contrast with Ara-C, which was released more rapidly. The cell-uptake test revealed that fluorescent liposomes have been well internalized into the cytoplasm of SW-1573 human lung carcinoma cells, confirming the possibility to use liposomes for lung cell targeting. Nebulized Ara-C and BDP liposomes presented aerodynamic diameters compatible with deep lung deposition. In conclusion, the elaborated liposomes seem to be promising carriers for both Ara-C and BDP pulmonary delivery.     

Effect of Diglucosamine on the Entrapment of Protein into Liposomes

Liposomes, which had entrapped bovine serum albumin (BSA), were modified with diglucosamine by two methods. The liposome was prepared by a freeze-thawing method in the presence of the disaccharide, or the disaccharide was added to the liposome prepared in advance without it. To examine the effects of diglucosamine, the morphology, mean particle size, and zeta potential of both liposomes were compared with those of BSA-entrapping liposome prepared without the disaccharide. Diglucosamine caused no remarkable change in shape and no aggregation of the liposome. The presence of the disaccharide was confirmed on the surfaces of modified liposomes, and the entrapment of BSA into the liposomes was increased by the disaccharide. The entrapment behavior was affected by the way the disaccharide was added, and the difference in the way the BSA was entrapped was also indicated.     

Gene Re-annotation in Genome of the Extremophile Pyrobaculum Aerophilum by Using Bioinformatics Methods

Abstract

In this paper, we re-annotated the genome of Pyrobaculum aerophilum str. IM2, particularly for hypothetical ORFs. The annotation process includes three parts. Firstly and most importantly, 23 new genes, which were missed in the original annotation, are found by combining similarity search and the ab initio gene finding approaches. Among these new genes, five have significant similarities with function-known genes and the rest have significant similarities with hypothetical ORFs contained in other genomes. Secondly, the coding potentials of the 1645 hypothetical ORFs are re-predicted by using 33 Z curve variables combined with Fisher linear discrimination method. With the accuracy being 99.68%, 25 originally annotated hypothetical ORFs are recognized as non-coding by our method. Thirdly, 80 hypothetical ORFs are assigned with potential functions by using similarity search with BLAST program. Re-annotation of the genome will benefit related researches on this hyperthermophilic crenarchaeon. Also, the re-annotation procedure could be taken as a reference for other archaeal genomes. Details of the revised annotation are freely available at http://cobi.uestc.edu.cn/resource/paero/     

Improved Chiral SFC Screening for Analytical Method Development

In this study we describe the evaluation of a recently developed supercritical fluid chromatography (SFC) instrument for automated chiral SFC method development. The greatly improved gradient dwell volume and liquid flow control of the new instrument in combination with the use of shorter columns containing smaller stationary phase particles affords chiral SFC method development that is faster and more universal than previous systems. Chirality 25:799–804, 2013. © 2013 Wiley Periodicals, Inc.     

Postfledging parental care and unexpected foraging behaviour of juvenile Sooty Terns Onychoprion fuscata in the southern Mozambique Channel

The Berlese funnel method, and its variations, is commonly used for the extraction of arthropods from various substrates such as nest material. However, little is known about its effectivity in extracting ectoparasites from penguin nests. This study aimed to assess the efficacy of a modified Berlese funnel method in extracting ectoparasites from African Penguin Spheniscus demersus nests and to determine differences in extraction capacity across parasite taxa and life stages. African Penguin nests (n = 278) were sampled at five penguin colonies along the south-west coast of South Africa in 2017. Nest samples were subjected to a modified Berlese funnel method with naphthalene as a repellent. Thereafter, all remaining ectoparasites were removed by hand sorting. Ectoparasite abundance was positively correlated between the two extraction methods (Spearman’s r = 0.73–0.89). Compared to total counts, flea (combined life stages and larvae) and total ectoparasite abundance and prevalence were significantly lower with the modified Berlese funnel method. In addition, adult flea and tick prevalence (but not abundance) was significantly lower with the modified Berlese funnel method compared with total counts. The modified Berlese funnel method fails as a quantitative method and can only provide a crude indication of the incidence of ectoparasites in penguin nests.