Estimation of molecular diffusivity in liquid phase systems by the Wilke-Chang equation

This study deals with the application of the Wilke-Chang equation to the estimation of molecular diffusivity (Dm) in liquid phase systems including polar solutes and/or solvents. First, Dm of benzene in six different organic solvents was experimentally measured by the peak parking method. The value of association coefficient (α) was calculated from the Dm values by assuming that Dm can be represented by the Wilke-Chang equation. Then, the α value was correlated with the solubility parameter (δ) and ET of the solvents. Two different curved correlations were observed between α and the two physico-chemical parameters. This means that α of given solutes and solvents can be obtained from the values of δ and/or ET. Finally, Dm was estimated by a modified Wilke-Chang equation, which is derived by considering the aggregation of not only solvent molecules but also solute molecules. Although α is necessary for the estimation, it was calculated from δ for various solutes and solvents. The Dm values estimated were compared with those reported in literature. The mean square deviation between the Dm values was calculated less than 19% for 71 Dm data. It was demonstrated that the modified Wilke-Chang equation can be used for estimating Dm in liquid phase systems containing polar solutes and solvents.     

Peak parking method for measurement of molecular diffusivity in liquid phase systems

The combination of series of measurements of band broadening made with the peak parking (PP) method, using successively an open capillary tube and a HPLC column, gives a convenient procedure for the measurement of the molecular diffusivity (D_m) of compounds in solutions, of their axial dispersion coefficient (D_ax,m) in chromatographic columns, and of the tortuosity or obstructive factor of the column bed. The molecular diffusivity measured for benzene in methanol was in excellent agreement with literature data. The ratio of the axial dispersion coefficient to this diffusivity gives the obstructive factor (γ_m) of the packed bed, which was 0.74 for the column used. The values of D_m in other solutions were obtained from the D_ax,m values measured by the PP method, by correcting the D_ax,m values with the γ_m value. The D_m values determined by this method were in good agreement with those previously reported or estimated using literature correlations. These results showed that the PP method is effective for the experimental measurement of D_m.     

Equations of states for an ionic liquid under high pressure: A molecular dynamics simulation study

The high-pressure dependence of density given by empirical equation of states (EoS) for the ionic liquid 1-butyl-3-methylimidazolium trifluoromethanesulfonate (or triflate), [C₄C₁im][TfO], is compared with results obtained by molecular dynamics (MD) simulations. Two EoS proposed for [C₄C₁im][TfO] in the pressure range of tens of MPa, which give very different densities when extrapolated to pressures beyond the original experiments, are compared with a group contribution model (GCM). The MD simulations provide support that one of the empirical EoS and the GCM is valid in the pressure range of hundreds of MPa. As an alternative to these EoS that are based on modified Tait equations, it is shown that a perturbed hard-sphere EoS based on the Carnahan–Starling–van der Waals equation also fits the densities calculated by MD simulations of [C₄C₁im][TfO] up to ∼1.0 GPa.     

Phase behavior of amphiphiles at liquid crystals/water interface: A coarse-grained molecular dynamics study

We present a coarse-grained molecular dynamics simulation study of phase behavior of amphiphilic monolayers at the liquid crystal （LC）/water interface. The results revealed that LCs at interface can influence the lateral ordering of amphiphiles. Particularly, the amphiphile tails along with perpendicularly penetrated LCs between tails undergo a two-dimension phase transition from liquid-expanded into a liquid-condensed phase as their area density at interface reaches 0.93. While, the liquid-condensed phase of the monolayer never appears at oil/water interface with isotropic shape oil particles. These findings reveal the penetration of anisotropic LC can promote ordered lateral organization of amphiphiles. Moreover, we find the phase transition point is shifted to lower surface coverage of amphiphiles when the LCs have larger affinity to the amphiphile tails.     

Surface diffusion in reversed-phase liquid chromatography

More than 40 years ago, Giddings pointed out in “Dynamics of Chromatography” that surface diffusion should become an important research topic in the kinetics of chromatographic phenomena. However, few studies on surface diffusion in adsorbents used in chromatography were published since then. Most scientists use ordinary rate equations to study mass transfer kinetics in chromatography. They take no account of surface diffusion and overlook the significant contributions of this mass transfer process to chromatographic behavior and to column efficiency at high mobile phase flow rate. Only recently did the significance of surface diffusion in separation processes begin to be recognized in connection with the development of new techniques of fast flow, high efficiency chromatography. In this review, we revisit the reports on experimental data on surface diffusion and introduce a surface-restricted molecular diffusion model, derived as a first approximation for the mechanism of surface diffusion, on the basis of the absolute rate theory. We also explain how this model accounts for many intrinsic characteristics of surface diffusion that cannot properly be explained by the conventional models of surface diffusion.     

Development of a model for the rational design of molecular imprinted polymer: Computational approach for combined molecular dynamics/quantum mechanics calculations

A new rational approach for the preparation of molecularly imprinted polymer (MIP) based on the combination of molecular dynamics (MD) simulations and quantum mechanics (QM) calculations is described in this work. Before performing molecular modeling, a virtual library of functional monomers was created containing forty frequently used monomers. The MD simulations were first conducted to screen the top three monomers from virtual library in each porogen-acetonitrile, chloroform and carbon tetrachloride. QM simulations were then performed with an aim to select the optimum monomer and progen solvent in which the QM simulations were carried out; the monomers giving the highest binding energies were chosen as the candidate to prepare MIP in its corresponding solvent. The acetochlor, a widely used herbicide, was chosen as the target analyte. According to the theoretical calculation results, the MIP with acetochlor as template was prepared by emulsion polymerization method using N,N-methylene bisacrylamide (MBAAM) as functional monomer and divinylbenzene (DVB) as cross-linker in chloroform. The synthesized MIP was then tested by equilibrium-adsorption method, and the MIP demonstrated high removal efficiency to the acetochlor. Mulliken charge distribution and ¹H NMR spectroscopy of the synthesized MIP provided insight on the nature of recognition during the imprinting process probing the governing interactions for selective binding site formation at a molecular level. We think the computer simulation method first proposed in this paper is a novel and reliable method for the design and synthesis of MIP.     

Correlation of thermodynamic modeling and molecular simulations for liquid-liquid equilibrium of ternary polymer mixtures based on a phenomenological scaling method

In our previous study [S.Y. Oh, Y.C. Bae, J. Phys. Chem. B 114 (2010) 8948-8953], we presented a new method to predict liquid-liquid equilibria in ternary simple liquid mixtures by using a combination of a thermodynamic model and molecular simulations. As a continuation of that effort, we extend our previously developed method to ternary polymer systems. In the simulations, we used the dummy atoms to calculate the pair interaction energy values between the polymer segments and the solvent molecules. Furthermore, a thermodynamic model scaling concept is introduced to consider the chain length dependence of the energy parameters. This method was applied to ternary mixtures incorporating low to high molecular weight polymers. The method presented here well described the experimental observations using one or no adjustable parameters.     

Poisson-Boltzmann calculations versus molecular dynamics simulations for calculating the electrostatic potential of a solvated peptide

We performed a very long molecular dynamics simulation of a peptide in explicit water molecules and ions and averaged the electrostatic potential caused by peptide, water and ions at eight points in the vicinity of the peptide. These electrostatic potential values were directly compared to the potential calculated by solving the non-linear Poisson-Boltzmann equation for the system, which describes the solvent using continuum electrostatics. We analyze the contribution of dielectric constant, conformational flexibility and solvation effects on the electrostatic potential at these eight points. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 23 November 1998     

Local elevation: A method for improving the searching properties of molecular dynamics simulation

Summary The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.     

Discovery of potential inhibitor against human acetylcholinesterase: a molecular docking and molecular dynamics investigation

Alzheimer’s disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for the degradation of acetylcholine which in turn prevents the post synaptic signal transmissions. hAChE has been an attractive target of drug discovery for the search of therapeutics against AD. In the recent past hAChE has become hot target for the investigation of new potential therapeutics. We performed virtual screening of entire database against hAChE. Further, the extra precision molecular docking was carried out to refine the docking results and the best complex was passed for molecular dynamics simulations in order of understanding the hAChE dynamics and its behavior in complex with the ligand which corroborate the outcomes of virtual screening. This also provides binding free energy data that establishes the ligands efficiency for inhibiting hAChE. The computational findings discussed in this paper provide initial information of inhibitory effects of ligand, (drugbank entry DB00983), over hAChE.     

Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution

Coupled advances in empirical force fields and classical molecular dynamics simulation methodologies, combined with the availability of faster computers, has lead to significant progress towards accurately representing the structure and dynamics of biomolecular systems, such as proteins, nucleic acids, and lipids in their native environments. Thanks to these advances, simulation results are moving beyond merely evaluating force fields, displaying expected structural fluctuations, or demonstrating low root-mean-squared deviations from experimental structures and now provide believable structural insight into a variety of processes such as the stabilization of A-DNA in mixed water and ethanol solution or reversible β-peptide folding in methanol. The purpose of this overview is to take stock of these recent advances in biomolecular simulation and point out some common deficiencies exposed in longer simulations. The most significant methodological advances relate to the development of fast methods to properly treat long-range electrostatic interactions, and in this regard the fast Ewald methods are becoming the de facto standard. Received: 9 April 1998 / Accepted: 21 May 1998 / Published online: 13 August 1998     

Dynamic conformational ensembles regulate casein kinase-1 isoforms: Insights from molecular dynamics and molecular docking studies

Casein kinase-1 (CK1) isoforms actively participate in the down-regulation of canonical Wnt signaling pathway; however recent studies have shown their active roles in oncogenesis of various tissues through this pathway. Functional loss of two isoforms (CK1-α/ε) has been shown to activate the carcinogenic pathway which involves the stabilization of of cytoplasmic β-catenin. Development of anticancer therapeutics is very laborious task and depends upon the structural and conformational details of the target. This study focuses on, how the structural dynamics and conformational changes of two CK1 isoforms are synchronized in carcinogenic pathway. The conformational dynamics in kinases is the responsible for their action as has been supported by the molecular docking experiments.     

The effect of corrugation of pore wall on the thermal diffusion in nanopores by molecular dynamics simulations

In this work we have studied the effect of corrugation on the thermal diffusion (soret effect) in isotopic and non-isotopic fluid mixtures confined in a slit pore. We used a boundary driven non-equilibrium molecular dynamics to simulate thermal diffusion in Lennard–Jones (LJ) binary mixtures confined in structureless Steele 10-4-3 and atomistic Lennard–Jones pore walls. The results showed that for the isotopic mixture thermal diffusion factor for both wall types agrees and the corrugation of the LJ wall has no effect in isotopic mixture. However, for non-isotopic mixture confined in atomistic LJ pore the component with stronger attraction adsorbs more to the wall than the structureless Steele wall. The effect of corrugation of pore wall on the thermal diffusion is noticeable in narrow slit pore and mixture with large difference in molecular attraction parameter of components.     

Dielectric relaxation in water–cholesterol mixture cluster: molecular dynamics simulation

Molecular dynamics (MD) studies of the cluster composed of cholesterol (C₂₇H₄₅OH) and water molecules are presented. We have investigated several dynamical quantities of cholesterol as a function of its concentration in the mixture cluster and the temperature. The main attention was focused on the temperature and concentration dependence of the calculated total dipole moment autocorrelation function and dielectric loss of the cluster.     

Forging of nicotine for the effective management of diabetic wounds: A hybrid of scaffold hopping and molecular dynamics simulation approaches

Diabetic wound (DW) is a huge threat to the health care community and is always challenging to treat. The main biochemical culprits in DW recalcitrance are elevated inflammatory mediators, proteases, cell proliferation and migration suppressors, anti-angiogenic factors, and bacterial infections. In this scenario, using a scaffold to target important factors at each stage of pathogenesis can accelerate the healing process. Many shreds of evidence disclosed the role of nicotine scaffold in handling inflammation, infection, proliferation, migration, and angiogenesis. All these factors made us forge nicotine by employing a scaffold hopping approach. The hops were then subjected to molecular docking and binding free energy calculations against Matrix metallopeptidase 9, Glycogen synthase kinase 3 beta, Tumor necrosis factor alpha, MurC and ParE enzymes. Gratifyingly, molecule H1 was found to possess significant inhibitory activity against the selected receptors as evidenced by their high negative glide score and binding energy. Furthermore, 100 ns of molecular dynamics simulation studies (MD) was performed for the five H1/4XCT, H1/5F95, H1/2AZ5, H1/4C13 and H1/4MOT complexes to get insight into the binding modes and stability. The MD results showed significant stability as evidenced by the low conformational changes of the H1 with the chosen receptors. Hence, H1 might be a druggable candidate in the therapeutic management of DW. However, further research is strongly recommended to advance the drug into the therapeutic pipeline.     

Structure,thermodynamics and diffusion in asymmetric binary mixtures: a molecular dynamics simulation study

Structural and thermodynamic properties as well as diffusion coefficients of binary fluid mixtures with asymmetry in mass, size, charge and their combinations have been studied using classical molecular dynamics simulations. The fluid mixture is modelled as spherical particles interacting via the Weeks–Chandler–Andersen and Coulomb potential. The diameter, charge and mass of the fluid particles are in the range 6–60 Å, 1–10e and 1—500 amu, respectively. Systematic variations in pair-correlation functions, thermodynamic properties as well as the self-diffusion coefficient are found with the size, charge and mass ratio of the particles. The self-diffusion coefficient for systems having more than one type of asymmetry is calculated and expressed in terms of diffusion coefficients of systems with only one type of asymmetry.     

Estimation of molecular diffusivity in aqueous solution of acetonitrile by the Wilke-Chang equation

It was tried to estimate the molecular diffusivity (D(m)) of solutes in the mixtures of acetonitrile (ACN) and water by the Wilke-Chang equation. Although the information about association coefficient (α) is necessary for the calculation, it has never been proposed for ACN. The value of α was estimated as 1.37 from D(m) of benzene in ACN at 303 K experimentally measured by the peak parking method. The values of α, i.e. 2.6, 1.9, 1.5, and 1.0, which have respectively been proposed for four solvents, i.e. water, methanol, ethanol, and benzene, were correlated with two physico-chemical parameters of the solvents, i.e. solubility parameter and E(T) value. The α value for ACN was plotted around the two correlations, indicating its appropriateness. The values of D(m) calculated by the Wilke-Chang equation using the α value for ACN were compared with those measured by the peak parking method and the Aris-Taylor method in aqueous solutions of ACN. The mean square deviation of the estimation of D(m) was calculated as 8.8 and 14%. It was demonstrated that the Wilke-Chang equation can be used for estimating D(m) with a reasonable accuracy in the mixtures consisting of ACN and water.     

Partition coefficients of organic molecules in squalane and water/ethanol mixtures by molecular dynamics simulations

Accurate partition coefficient data of migrants between a polymer and a solvent are of paramount importance for estimating the migration of the migrant over time, including the concentration of the migrant at infinite time in the two solvents. In this article it is shown how this partition coefficient can be estimated for both a small hydrophilic and a hydrophobic organic molecules between squalane (used here to mimic low density poly ethylene) and water/ethanol solutes using thermodynamic integration to calculate the free energy of solvation. Molecular dynamics simulations are performed, using the GROMACS software, by slowly decoupling of firstly the electrostatic and then the Lennard-Jones interactions between molecules in the simulation box. These calculations depend very much on the choice of force field. Two force fields have been tested in this work, the TraPPE-UA (united-atom) and the OPLS-AA (all-atom). The computational cheaper TraPPE-UA force field showed to be more accurate over the whole range of systems compared to the OPLS-AA force field. Moreover, some of the calculations were done with five different water models to investigate the influence of the specific water model on the calculations. It was found that the combination of the TraPPE-UA force field and the TIP4p water model gave the best results. Based on the methodology proposed in this article, it is possible to obtain good partition coefficients only knowing the chemical structure of the molecules in the system.