Molecular dynamics study on homonuclear and heteronuclear chains of Lennard–Jones segments

We report molecular dynamics (MD) simulation data for three simulated fluids: a homopolymer with 16 tangent Lennard–Jones (LJ) segments at the reduced temperature of 1.25, an equimolar binary homopolymer fluid with eight tangent LJ segments at 15 state points, and three corresponding copolymers with equimolar segment fraction and varying segment distribution at 15 state points. We find that the compressibility factors and energies do not change as the segment distribution varies in the copolymer example. The simulation data are compared with thermodynamic perturbation theory (TPT1) calculations. The TPT1 compressibility factors compare favorably with the MD data at high reduced temperatures but differ significantly at lower temperatures.     

Molecular dynamics simulation study of friction and diffusion of a tracer in a Lennard–Jones solvent

The friction and diffusion coefficients of a tracer in a Lennard–Jones (LJ) solvent are evaluated by equilibrium molecular dynamics simulations in a microcanonical ensemble. The solvent molecules interact through a repulsive LJ force each other and the tracer of diameter σ₂ interacts with the solvent molecules through the same repulsive LJ force with a different LJ parameter σ. Positive deviation of the diffusion coefficient D of the tracer from a Stokes–Einstein behavior is observed and the plot of 1/D versus σ₂ shows a linear behavior. It is also observed that the friction coefficient ζ of the tracer varies linearly with σ₂ in accord with the prediction of the Stokes formula but shows a smaller slope than the Stokes prediction. When the values of ratios of sizes between the tracer and solvent molecules are higher than 5 approximately, the behavior of the friction and diffusion coefficients is well described by the Einstein relation D = k _B T/ζ, from which the tracer is considered as a Brownian particle.     

On the study of nonlinear dynamics of complex chemical reaction systems

When driven far from equilibrium,nonlinear chemical reactions often show a variety of self-organization behavior,including chemical oscillations,waves,chaos and patterns[1].Recently,the study of such nonlinear phenomena in‘complex’systems,such as the li…     

Molecular dynamics assessment of doxorubicin–carbon nanotubes molecular interactions for the design of drug delivery systems

Carbon nanotubes (CNTs) constitute an interesting material for nanomedicine applications because of their unique properties, especially their ability to penetrate membranes, to transport drugs specifically and to be easily functionalized. In this work, the energies of the intermolecular interactions of single-walled CNTs and the anticancer drug doxorubicin (DOX) were determined using the AMBER 12 molecular dynamics MM/PBSA and MM/GBSA methods with the aim of better understanding how the structural parameters of the nanotube can improve the interactions with the drug and to determine which structural parameters are more important for increasing the stability of the complexes formed between the CNTs and DOX. The armchair, zigzag, and chiral nanotubes were finite hydrogen-terminated open tubes, and the DOX was encapsulated inside the tube or adsorbed on the nanotube surface. Pentagon/heptagon bumpy defects and polyethylene glycol (PEG) nanotube functionalization were also studied. The best interaction occurred when the drug was located inside the cavity of the nanotube. Armchair and zigzag nanotubes doped with nitrogen, favored interaction with the drug, whereas chiral nanotubes exhibited better drug interactions when having bumpy defects. The π-π stacking and N-H…π electrostatic interactions were important components of the attractive drug-nanotube forces, enabling significant flattening of the nanotube to favor a dual strong interaction with the encapsulated drug, with DOX–CNT equilibrium distances of 3.1–3.9 Å. These results can contribute to the modeling of new drug-nanotube delivery systems.

     

Molecular dynamics investigations on Lennard–Jones systems near the gas–liquid critical point

NVT simulations on Lennard–Jones (L–J) systems near the gas–liquid critical point were performed by a direct approach. As a result, the two necessary conditions for simulating the systems in accordance with the thermodynamic limit were proposed: (i) L/ξ≳20 (L: the box-length, ξ: the correlation length), (ii) the total time of evolution, t_E>500 L–J units, for ξ≈3.5. The proposed conditions are probably very close to the sufficient ones. The influence of finite-size effects on pressure and density of small systems was qualitatively predicted. The prediction was confirmed by the simulations but only for L markedly lower than the length of typical critical wave, 2πξ. For L markedly higher, the evolutions were dominated by an effect called here the instability effect. The effect became negligible just when the condition for L/ξ was fulfilled. The ξ₀′ constant for L–J fluid was estimated from direct measurements of ξ to be 0.27±0.02 (L–J units). The thermodynamic parameters of the critical point, obtained from extrapolation, were in agreement with the results of other authors. The β_C exponent was estimated from minimization for a high range of temperatures to be 0.346. A comparison of the efficiency of NVT and NpT methods was also performed and no distinct differences were noted.     

A comparative study of vibrational dynamics of α- and β-forms of poly(β-hydroxybutyrate)

Normal modes and their dispersion are obtained for planar zig-zag form of poly(β-hydroxybutyrate) using Urey-Bradley force field. A comparison is made with the spectra of its helical form. Apart from detailed assignment of modes, various characteristic features of dispersion curves have been explained as arising due to internal symmetry in energy momentum space. The density-of-states have been used to calculate heat capacity in the temperature range 10-450 K using Debye's formalism.     

Molecular dynamics and ion mobility spectrometry study of model β-hairpin peptide, trpzip1

Here, we explore the conformations of gas phase, protonated tryptophan zipper 1 (trpzip1) ions and its six derivatives by an enhanced sampling molecular dynamics, specially the integrated tempering sampling molecular dynamics simulation (ITS-MDS). The structural distributions obtained from ITS-MDS are compared with results obtained from matrix-assisted laser desorption ionization (MALDI)-ion mobility-mass spectrometry (IM-MS). The IM-MS measured collision cross-section (CCS) profiles compare well with the calculated CCS profiles obtained from ITS-MDS. Although β-turn structures are preferred for solution phase species, the ITS-MDS and IM-MS structural analysis suggests that the γ-turn structures are preferred for gas-phase, unsolvated trpzip1 [M + H](+) ions. In addition, the data suggests that the energy landscape of the gas phase peptide ions is sensitive to the site of protonation as well as intramolecular interactions involving the lysine side chain.     

Molecular dynamics, density functional and second-order Møller–Plesset theory study of the structure and conformation of acetylcholine in vacuo and in solution

 Molecular mechanics minimizations based on the CVFF force field and molecular dynamics simulation for a time of 2.5 ns were performed to examine the conformational behaviour and the molecular motion of acetylcholine in vacuo and in aqueous solution. Five low-lying conformations, namely the TT, TG, GG, G*G and GT, were obtained from molecular mechanics computations with the GT structure as the absolute minimum. Molecular dynamics trajectories in vacuo and in water show that only four (GT, GG, G*G and TG) and three (TG, TT and GT) conformations are present in the simulation time, respectively. Density functional B3LYP and second-order M?ller–Plesset (MP2) methods were then used to study all the five lowest-lying conformers of acetylcholine neurotransmitter in vacuo and in water by the polarizable continuum model approach. The B3LYP and MP2 computations show that in the gas phase all minima lie in a narrow range of energy with the G*G conformer as the most stable one. The relative minima GG, GT, TG and TT are located at 1.1 (3.3), 1.8 (4.2), 2.1 (4.5) and 4.3 (7.3) kcal/mol above the absolute one at the B3LYP (MP2) level. The preferred conformation in water is the TG. Solvation reduces the relative energy differences between the five minima in both computations. Received: 4 April 2001 / Accepted: 5 July 2001 / Published online: 30 October 2001     

Physicochemical characterization and molecular modeling study of host–guest systems of aripiprazole and functionalized cyclodextrins

Journal of Thermal Analysis and Calorimetry - Aripiprazole (ARP), an innovative atypical antipsychotic drug, exhibits very low aqueous solubility, affecting its dissolution and absorption and high...     

Molecular recognition of endocrine disruptors by synthetic and natural 17β-estradiol receptors: a comparative study

A β-estradiol receptor binding mimic was synthesised using molecular imprinting. Bulk polymers and spherical polymer nanoparticles based on methacrylic acid and ethylene glycol dimethacrylate as the functional monomer and crosslinker, respectively, were prepared in acetonitrile. The selectivity was evaluated by radioligand binding assays. The imprinted polymers were very specific to β-estradiol since the control polymers bound virtually none of the radioligand. The bulk polymer was then employed to screen endocrine disrupting chemicals. Structurally related steroids like α-estradiol, estrone and ethynylestradiol showed, respectively, 14.0, 5.0 and 0.7% of relative binding to the β-estradiol polymer, whereas most unrelated chemicals did not bind at all. These results are compared to those obtained with a bioassay using stably transfected yeast cells in culture bearing the human estrogen receptor. The receptor was activated by several estrogen-like chemicals and to a lesser extent by some structurally related chemicals. Figure A molecularly imprinted polymer that was a synthetic receptor for beta-estradiol was used for the screening of endocrine disrupting chemicals that are structurally related or unrelated to beta-estradiol. The results were compared with the recognition of the compounds by the biological estrogen receptor expressed in yeast cells. Related steroids like alpha-estradiol, estrone and ethynylestradiol showed significant binding to the beta-estradiol imprinted polymer, whereas most unrelated chemicals did not bind. The biological receptor was activated by several estrogen-like chemicals, and to a lesser extent by some structurally related chemicals     

Unusual examples of methane hydrate nucleation in bilayer water–oil systems

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A comparative study of the structure and properties of β-galactosidases

A comparative study of β-galactosidase amino acid sequences of E. coli and another four out of 11 microorganisms selected at the first stage was performed. It was shown that the functional amino acid residues in the catalytic domain and the ligand environment of the magnesium cation for all five sequences are identical. The mechanism of the catalytic action of E. coli and K. lactis β-galactosidases was investigated by the method of nucleophilic competition. It was shown that the mechanism of the effects of nucleophilic agents is kinetically identical both enzymes: the presence of methanol or butanediols affects the stage of degalactosylation; the presence of magnesium cations promotes the activity of both β-galactosidases; and the mechanisms of the thermal inactivation of E. coli and K. lactis β-galactosidases are different.     

Molecular thermodynamics of salt effect in vapor–liquid equilibrium of ethanol–water systems

Scaled particle theory was used to derive a general expression for the salt effect parameter, K, of isobaric vapor–liquid equilibrium for ethanol–water-1-1 type electrolytic systems, which appears in the Furter equation. This expression was essentially a sum of two terms: 1, the hard sphere interaction term calculated by Masterton–Lee's equation, 2, the soft sphere interaction term calculated by Y. Hu's molecular thermodynamical model, in which the diameters of nacked ions were replaced by that of solvated ions, the solvation coefficients (i.e., in the radio of the latter to the former) were taken to be adjustable parameters, their magnitude implies the ionic solvation rules. A correlation equation for the local dielectrical constant around central ions with liquid concentration was obtained by mapping out experimental points. The calculated salt effect parameters of 9 ethanol–water-1–1 type electrolytic systems were in good agreement with the literature values within the wide range of liquid concentration.     

Molecular dynamics and the structure of macrocycles —Solvent acetonitrile interactions

Microwave complex permittivities,* = -J, are reported in the 1–90 GHz frequency range for the macrocycles 18-crown-6 (18C6) and 15C5 added to acetonitrile in stoichiometric proportions, in the solvent CCl₄ at 25°C. Digitized infrared spectra of the CN stretch ₂ vibration of acetonitrile for the same systems are reported in the 2300–2200 cm^–1 spectral region. The macrocycle 12C4 added to CH₃CN has also been investigated in the infrared. Both the dielectric relaxation and infrared results are interpreted in terms of macrocycle-acetonitrile interactions, probably involving a methyl-hydrogen to ethereal-oxygen interaction. These interactions with CH₃CN diminish in strength according to the sequence: 18C6 > 15C5 > 12C4.This paper is dedicated to the memory of the late Dr C. J. Pedersen.     

Molecular dynamics study of a new metastable allotropic crystalline form of gallium—supertetrahedral gallium

A new metastable crystalline form of gallium has been computationally designed using density functional calculations with imposing periodic boundary conditions. The geometric and electronic structures of the predicted new allotrope were calculated on the basis of a diamond lattice in which all carbon atoms are replaced by gallium Ga₄ tetrahedra. This form does not have any imaginary phonons, thus it is a metastable crystalline form of gallium. The new form of gallium is a metal and shows high plasticity and low-melting temperature. Molecular dynamics simulations show that this form of gallium will melt at about 273 K with a sharp increase in temperature in the system during the melting process from 273 to 1800 K. This melting process is very different from conventional melting, where temperature stays the same until complete melting. That unusual melting can be explained by the fact that supertetrahedral gallium is a metastable structure that has an excess of strain energy released during melting. If made this new material may find many useful applications as a new low density metal with stored internal energy. © 2019 Wiley Periodicals, Inc.     

Structure and molecular dynamics of host–guest complexes of TEMPO with cucurbituryl: An ESR and DFT study

Host–guest complexes are of interest as promising nanodevices for molecular recognition and chemosensors. In this work, the structure and molecular dynamics of complexes of the nitroxyl radical TEMPO (I), as models of indicator and analyte, with cucurbituril CB[7] in solution and in the solid phase have been studied by ESR and DFT methods. The kinetic accessibility of the NO group of I for water-soluble reagents has been determined. By simulation of the ESR spectra of the complex, the rotational diffusion coefficients and the anisotropy of its rotation have been determined. To study the rotational mobility of the guest in the CB[7] cavity, solid solutions of I@CB[7] in the CB[7] matrix have been obtained. The ESR spectra indicate rapid jump-like rotation of I about an axis oriented along the normal to the CB[7] portals. The formation energy and the spatial structure of the complex have been calculated by the DFT method; a change in the spin density on the NO group with changing the orientation of I in the CB[7] cavity has been found.     

Molecular dynamics simulation of the equilibrium liquid–vapor interphase with solidification

The equilibrium structure of the finite, interphase interfacial region that exists between a liquid film and a bulk vapor is resolved by molecular dynamics simulation. Argon systems are considered for a temperature range that extends below the melting point. Physically consistent procedures are developed to define the boundaries between the interphase and the liquid and vapor phases. The procedures involve counting of neighboring molecules and comparing the results with boundary criteria that permit the boundaries to be precisely established. Two-dimensional radial distribution functions at the liquid and vapor boundaries and within the interphase region demonstrate the physical consistency of the boundary criteria and the state of transition within the region. The method developed for interphase boundary definitions can be extended to nonequilibrium systems. Spatial profiles of macroscopic properties across the interphase region are presented. A number of interfacial thermodynamic properties and profile curve-fit parameters are tabulated, including evaporation/condensation coefficients determined from molecular flux statistics. The evaporation/condensation coefficients away from the melting point compare more favorably with transition state theory than those of previous simulations. Near the melting point, transition theory approximations are less valid and the present results differ from the theory. The effects of film substrate wetting on evaporation/condensation coefficients are also presented.     

Molecular dynamics simulation study on zwitterionic structure to maintain the normal conformations of Glutathione

Molecular dynamics simulations were applied to normal conformational Glutathione (GSH) and GSH over zwitterionic and hydrophobic surfaces respectively. Conformational analysis of GSH during the simulation time on RMSD, conformational flexibility and dihedral distribution were performed. The re- sults showed that zwitterionic structure maintains the normal conformations of GSH to a better extent, which should be a first good proof of the hypothesis of "maintain of normal structure".     

A comparative study on characterization and photocatalytic activities of gadolinium–boron codoped and mono-doped TiO2 nanoparticles

Gadolinium?Cboron codoped and mono-doped TiO₂ nanoparticles were prepared using a sol?Cgel method, and tested for photocatalytic activity by the UV light after a further calcination process. For comparison, a pure TiO₂ sample was also prepared and tested under the same conditions. The prepared catalysts were characterized by X-ray diffraction, scanning electron microscope, and UV?CVis spectra. The photocatalytic activity of the samples was evaluated through the photo-degradation of three different dyes under UV light. The experiments demonstrated that the gadolinium?Cboron codoped TiO₂ (Gd?CB?CTiO₂) sample calcined at 500?°C possessed the best photocatalytic activity, and the photodegradation rate of the Reactive Brilliant Red K2G aqueous solution could reach to 95.7% under UV irradiation for 80?min. The results showed that Gd?CB?CTiO₂ has smaller crystallite size and higher photocatalytic activity than that of mono-doped TiO₂ samples and undoped TiO₂.