Isothermalisobaric molecular dynamics simulation of diatomic liquids and their mixtures

Isothermalisobaric ensemble molecular dynamics simulations have been performed for systems of two-center Lennard-Jones molecules for pure fluids as well as binary mixtures. The results obtained from various ensemble averages have been compared for pure fluid simulations of Lennard-Jones model diatomic fluids. The excess enthalpy and excess volume of three equimolar mixtures (argonnitrogen, argonoxygen, and nitrogenoxygen) have been calculated and compared with values obtained from previous NVT molecular dynamics and perturbation theory. Pair distribution functions obtained from various methods are compared for the equimolar mixture of nitrogen and oxygen and used to study the effect of attractive forces on the local structure. For four other systems (argonethane, methaneethane, carbon disulfidecarbon tetrachloride, and carbon disulfidetetrachloroethylene), excess enthalpies and excess volumes from NPT simulations are used to test the ability of perturbation theory to predict these properties and are also compared with experimental data. The comparison of simulation and experiment clearly shows the need to improve the available parameters for cross interactions in binary mixtures.     

Influence of temperature on thermodynamic properties of acid–base liquid mixtures

Ultrasonic velocity, u density, ?? and viscosity, ?? of mixtures of N,N-dimethyl acetamide with equimolar mixture of ethanol?+?isopropyl alcohol/isobutyl alcohol/isoamyl alcohol, including those of pure liquids over the entire composition have been measured at T?=?308.15, 313.15, and 318.15?K. Using this data, various thermo-acoustic parameters such as deviations in ultrasonic velocity, ?u, isentropic compressibility, ?k _s , viscosity, ????, excess molar volume, $ V_{\text{m}}^{\text{E}} $ and excess Gibb??s free energy of activation for viscous flow, ??G ^*E have been calculated at different temperatures. The calculated deviation and excess functions have been fitted to the Redlich?CKister type polynomial equation. The influence of temperature on the observed negative and positive values of deviation and excess thermodynamic properties has been explained in terms of molecular interactions present in the investigated acid?Cbase liquid mixtures. The experimental data of ultrasonic velocity have been used to check the applicability of velocity models of Nomoto, Van Dael and Vangeel and Junjie and viscosity data have also been availed to test the applicability of standard viscosity models of Grunberg-Nissan, Hind-Mc Laughlin, and Katti-Chaudhary for all the systems investigated at various temperatures.     

Vapor–liquid equilibrium,fluid state,and zero-pressure solid properties of chlorine from anisotropic interaction potential by molecular dynamics

Extensive examination of the anisotropic interaction potential of chlorine by Rodger et al. [P.M. Rodger, A.J. Stone, D.J. Tildesley, J. Chem. Soc., Faraday Trans. 2, 83 (1987) 1689–1702] (with interaction sites located at the positions of atoms in a molecule and the electrostatic part found by ab initio calculations) for its predictive power has been performed. We have calculated (i) the second virial coefficient by using a non-product algorithm, (ii) a series of liquid-phase state points in the temperature and pressure ranges of 200 to 400 K and 0 to 6.2 MPa, respectively, by the constant pressure–constant temperature molecular dynamics simulations, (iii) vapor–liquid equilibrium and heat of vaporization from the triple point (172 K) to 300 K by the Gibbs–Duhem integration method combined with simultaneous (but independent) constant pressure–constant temperature molecular dynamics simulations of the vapor and liquid phases, and (iv) the properties of the zero-pressure crystal structures by molecular dynamics technique due to Parinello and Rahman [M. Parrinello, A. Rahman, Phys. Rev. Lett. 45 (1980) 1196–1199]. Generally, good to excellent agreement of the calculated properties with the corresponding values for real chlorine was observed. The results obtained from the investigated interaction potential are equivalent to (or even better than) those reported for a more complicated potential by Wheatley and Price [R.J. Wheatley, S.L. Price, Mol. Phys. 71 (1990) 1381–1404].     

Binding of biguanides to β-lactoglobulin: molecular-docking and molecular dynamics simulation studies

Biguanides are a class of drugs derived from biguanide and they are the most widely used drugs for diabetes mellitus or pre-diabetes treatment. An investigation of their interaction and a transport protein such as β-lactoglobulin (BLG) at atomic level could be a valuable factor in controlling their transport to biological sites. Molecular-docking and molecular dynamics simulation methods were used to study the interaction of metformin, phenformin and buformin as biguanides and BLG as transport protein. The molecular-docking results revealed that these biguanides bind to BLG and that the BLG affinity for binding the biguanides decreases in the following order: phenformin — buformin — metformin. The docking results also show the hydrophobic interactions to have a significant role in the BLG-biguanides complex stability. Analysis of molecular dynamic simulation trajectories shows that the root mean square deviation of various systems attained equilibrium and fluctuated around the mean value at various times. The time evolution of the radius of gyration and the total solvent-accessible surface of the protein showed that BLG and BLG-biguanide complexes became stable at approximately 2500 ps and that there was not any conformational change in the BLG-biguanide complexes. In addition, the profiles of atomic fluctuations show the rigidity of the ligand-binding site during the simulation.     

Hydration of β-cyclodextrin: A molecular dynamics simulation study

We study by molecular dynamics simulations the hydration of -cyclodextrin. Our simulations show that within these barrel-shaped molecules hydrophobicity dominates, while at the top and bottom sides of the barrel interactions with water are mostly hydrophilic in nature. These results agree with crystallographic data at 120 K and, in particular, with the spontaneous hydration process of a cyclodextrin crystal in wet atmosphere. The predicted structure of the hydration shells is discussed and compared with previous molecular mechanics calculations which report an overall hydrophobic behavior. Moreover, the temperature dependence of the hydration process is discussed.     

Effect of pressure on the structure and dynamics of hydrogen bonds in ethylene glycol–water mixtures: Numerical simulation data

Water?ethylene glycol mixtures containing from 0.002 to 0.998 mole fractions of ethylene glycol at T = 298.15 K and P = 0.1 and 100 MPa are simulated by means of classical molecular dynamics. Such structural and dynamic characteristics of hydrogen bonds as the average number and lifetime, along with the distribution of molecules over the number of hydrogen bonds, are calculated; their changes are analyzed, depending on the mixture’s composition and pressure. It is shown that the components are characterized by a high degree of interpenetration and form a uniform infinite hydrogen-bonded cluster over the range of concentrations. It is found that the higher the concentration of ethylene glycol, the greater the stability of all hydrogen bonds. It is concluded that an increase in pressure lowers the number of hydrogen bonds, while the average lifetime of the remaining hydrogen bonds grows.     

Comparison of perturbation theory and mean spherical approximation for polar fluids and ion–dipole mixtures based on molecular simulation data

A comprehensive study on various internal energies, pressures and chemical potentials for the pure dipolar hard sphere fluids, pure Stockmayer fluids, the Lennard–Jones and Stockmayer mixtures, the Stockmayer and Stockmayer mixtures and the ion–dipole mixtures is reported based on the perturbation theory (PT) and mean spherical approximation (MSA). Compared with the results of molecular simulations, it is shown that the PT is superior to MSA in most cases.     

Prediction of thermodynamic properties of some polymeric systems using an extended LJ potential-based equation of state up to high temperature–high pressure conditions

In this work, the extended Lennard-Jones potential-based equation of state (ELJ-based EoS) on which the effective near-neighbour pair interactions are LJ (12,6,3) type has been used to predict the specific volume and other thermodynamic properties of some semi-crystalline and liquid polymers and copolymers up to extremely high temperature–high pressure conditions. It seems that, at least in the dense regions, there are no upper- and lower-specific volume limitations in the applicability of the model for different polymeric systems. The parameters can be determined at any temperature for each compound using the temperature dependence of the parameters of ELJ-based EoS. The calculated parameters have been used to calculate the specific volume and other derived thermodynamic properties of different polymeric systems at any temperature and pressure. The ELJ-based EoS has been also compared with some previous studies.     

Enhancing oil–water emulsion separation using improved styrene–acrylonitrile copolymer membrane: Experimental and thermodynamic study of the impact of solvent mixtures

This study investigated the fabrication of styrene–acrylonitrile copolymer (SAN) membrane using the nonsolvent-induced phase separation (NIPS) method with a combination of solvents, namely N-methyl-2-pyrrolidone (NMP) and dimethylformamide (DMF) and water as the nonsolvent. Since the impact of varying solvent ratios on SAN membrane performance remained unexplored, this study aimed to address this knowledge gap in the context of oil–water emulsion separation. Experimental results demonstrated that employing a solvent mixture, rather than a pure solvent, led to improved membrane performance. The primary objective of this work was to experimentally determine the optimal solvent ratio for enhancing SAN copolymer membrane performance. Additionally, the Flory–Huggins thermodynamic model was applied to investigate the possibility of predicting membrane binodal data. The thermodynamic analysis revealed a strong agreement between calculated and experimental binodal data, with an error of less than 3.8%. Notably, membranes produced with an equal solvent ratio exhibited the most hydrophilic properties, resulting in increased permeability. The permeate flux for distilled water reached 320 L/(m² h) (LMH), and water contact angle of the membrane was 22°. Furthermore, mechanical resistance increased up to 50%. These results highlight the promising potential of fabricating SAN membrane using solvent mixtures for oil–water emulsion separation.     

How do trehalose, maltose, and sucrose influence some structural and dynamical properties of lysozyme? Insight from molecular dynamics simulations

The influence of three well-known disaccharides, namely, trehalose, maltose, and sucrose, on some structural and dynamical properties of lysozyme has been investigated by means of molecular dynamics computer simulations in the 37-60 wt % concentration range. The effects of sugars on the protein conformation are found to be relatively weak, in agreement with the preferential hydration of lysozyme. Conversely, sugars seem to increase significantly the relaxation times of the protein. These effects are shown to be correlated to the fractional solvent accessibilities of lysozyme residues and further support the slaving of protein dynamics. Moreover, a significant increase in the relaxation times of lysozyme, sugars, and water molecules is observed within the studied concentration range and may result from the percolation of the hydrogen-bond network of sugar molecules. This percolation appears to be of primary importance to explain the influence of sugars on the dynamical properties of lysozyme and water.     

Structural analysis of polymer-brush-type cellulose β-ketoesters by molecular dynamics simulation

The reason for anomalous NMR patterns of cellulose β-ketoesters, which were prepared by reaction between cellulose and ketene dimers having long alkyl chains (AKDs) under homogeneous conditions using a cellulose solvent system, was studied by molecular dynamics simulation. Cellulose/AKD β-ketoester models with degree of substitution (DS) 2.0 and degree of polymerization (DP) 5, 10, 20 or 40, and cellulose/fatty acid ester models with DS 3.0 and DP 5, 10, 20 or 40 were assembled in the simulation. The calculated results were compared with those obtained by NMR and conformation analyses of the actually prepared cellulose derivatives. The molecular dynamics simulation data showed that the average velocities of anhydroglucose units in cellulose/AKD β-ketoesters were approximately one tenth of those in cellulose/fatty acid esters. Thus, cellulose chains in the cellulose/AKD β-ketoesters are extremely restricted in motion by the β-ketoester substituents. The solid-like behavior of cellulose chains in cellulose/AKD β-ketoesters in solution state is, therefore, explainable by strong restriction in motion of cellulose chains by long, branched and bulky substituents introduced into cellulose hydroxyls in high densities via β-ketoester bonds.     

Molecular simulation of the phase behaviour of ternary fluid mixtures: the effect of a third component on vapour–liquid and liquid–liquid coexistence

The Gibbs ensemble algorithm is implemented to determine the vapour–liquid and liquid–liquid phase coexistence of dilute ternary fluid mixtures interacting via a Lennard–Jones potential. Calculations are reported for mixtures with a third component characterised by different intermolecular potential energy parameters. Comparison with binary mixture data indicates that the choice of energy parameter for the third component affects the composition range of vapour–liquid substantially. The addition of a third component lowers the energy of liquid phase while slightly increasing the energy of the vapour phase.     

Vapour pressure and thermodynamic properties of hexamethyldisilane at 305–387 K

The Swietoslawski's differential ebulliometer has been minimized to be usable for ca. 13 cm³ of liquid. After a performance test with acetone, the vapour pressure of hexamethyldisilane is determined over the temperature range 304.61–386.74 K. The Antoine equation obtained is log₁₀(P/kPa) = 5.97097 − 1319.85/{(T/K) − 52.96} and the normal boiling point is 385.81 K. The present results agree with literature values of Suga and Seki at 287–310 K and Brockway and Davidson at 293–334 K.     

Tensile strength of Iβ crystalline cellulose predicted by molecular dynamics simulation

The mechanical properties of Iβ crystalline cellulose are studied using molecular dynamics simulation. A model Iβ crystal is deformed in the three orthogonal directions at three different strain rates. The stress–strain behaviors for each case are analyzed and then used to calculate mechanical properties. The results show that the elastic modulus, Poisson’s ratio, yield stress and strain, and ultimate stress and strain are highly anisotropic. In addition, while the properties that describe the elastic behavior of the material are independent of strain rate, the yield and ultimate properties increase with increasing strain rate. The deformation and failure modes associated with these properties and the relationships between the material’s response to tension and the evolution of the crystal structure are analyzed.     

An in silico approach to design peptide mimetics based on docking and molecular dynamics simulation of EGFR–matuzumab complex

Epidermal growth factor receptor (EGFR) plays an essential role in anticancer therapy. Matuzumab is an antibody for the treatment of colorectal, lung and stomach cancer. Matuzumab binds efficiently to EGFR and blocks its phosphorylation. The recent clinical successes have established application of peptides for cancer treatment. The present contribution introduces an in silico approach to design peptides based on molecular dynamics simulation (MDs) of the matuzumab-EGFR complex in water environment. Moreover, principal component analysis has been used to select multiple conformations of the complex in MDs for designing the peptides. The paratope and epitope in each conformation of the complex were determined, and the alanine scanning was used to identify the hot spots of EGFR conformers. The conformations of the peptides were optimized using PEP-FOLD server and MDs. The selected conformations were analyzed in a docking study to realize the binding site of the EGFR. Finally, pharmokinetics properties of the peptides were calculated. The designed oligopeptides were EWRSYYYWH, YYYWHNEWN, YYYWHNEWS and HNHSRNYGS with a higher affinity to the EGFR relative to the previously reported peptides. The newly designed peptides were investigated for their in vivo toxicities on rats, and all of them were non-toxic.     

Study of the surface properties and surface concentration of ionic liquid–alcohol mixtures

Surface properties for three binary mixtures containing a 1-butyl-3-methylimidazolium thiocyanate ([BMIM][SCN]) and a long-chain alcohol (1-butanol, 1-pentanol and 1-hexanol) were determined by surface tension data at the following temperatures: (298.15, 308.15, 318.15, 328.15 and 338.15) K. The surface tension data over the entire mole fraction range are correlated by the Fu et al.(FLW) and Myers-Scott (MS) models. There is good agreement between the experimental data and the results of correlations for 15 binary systems (the three systems at five temperatures) with an average relative error below 1.5%. In addition, the UNIFAC group contribution method is applied for calculation of activity coefficients of components in solution. Moreover, the relative adsorptions of alcohol at the air/liquid interface are determined using Gibbs adsorption isotherm. The obtained results show that the values of adsorption for mixtures of alcohols/[BMIM][SCN] increase with increasing the alkyl chain length of alcohol and decreasing temperature.