Molecular dynamics study of phase transition and nucleation in supercooled clusters of potassium iodide

In a series of molecular dynamics (MD) runs on (KI)₁₀₈ clusters, the Born–Mayer–Huggins potential function is employed to study structural, energetic, and kinetic aspects of phase change and the homogeneous nucleation of KI clusters. Melting and freezing are reproducible when clusters are heated and cooled. The melted clusters are not spherical in shape no matter the starting cluster is cubic or spherical. Quenching a melted (KI)₁₀₈ cluster from 960 K in a bath with temperature range 200–400 K for a time period of 80 ps both nucleation and crystallization are observed. Nucleation rates exceeding 10³⁶ critical nuclei m⁻³ s⁻¹ are determined at 200, 250, 300, 350, and 400 K. Results are interpreted in terms of the classical theory of nucleation of Turnbull and Fisher and of Buckle. Interfacial free energies of the liquid–solid phase derived from the nucleation rates are 7–10 mJ m⁻². This quantity is 0.19 of the heat of transition per unit area from solid to liquid, or about two-thirds of the corresponding ratio which Turnbull proposed for freezing transition. The temperature dependence of σ_sl(T) of (KI)₁₀₈ clusters can be expressed as σ_sl(T)∝T^0.34.     

Molecular dynamics simulation of the kinetics of nucleation of supercooled NaCl melt clusters

Approaches to describing the structure of metastable liquids are considered. A criterion for the classification of particles in a supercooled NaCl melt is suggested. The criterion is based on the Q₆ method and structural features of salt crystals. It was applied to analyze the configurations of clusters calculated by the molecular dynamics method. The results were interpreted using classic nucleation theory and the probabilistic approach. It was shown that crystalline phase nuclei with subcritical sizes existed in a metastable liquid. The evolution of nucleus sizes follows a complex mechanism. Along with monomer attachment and detachment reactions, collective structural fluctuations play a noticeable role.     

Molecular dynamics studies of homogeneous nucleation in solid-state transitions

Simulations of clusters containing 100 to 250 molecules of TeF₆ successfully reproduce the crystalline packing arrangements observed in electron diffraction investigations of large molecular clusters (～ 10⁴ molecules) of the same material. More remarkably, when the clusters are cooled step by step in MD computations at a rate of ca. 10¹¹ K/s they spontaneously undergo the same bcc to monoclinic phase transition that has been observed experimentally in supersonic flow, despite the million-fold difference in the timescales involved. The existence of such a correspondence over so many orders of magnitude, in itself, imposes severe constraints on what type of molecular mechanism can underlie the transformation. Even more revealing evidence about the molecular behavior associated with the phase change is provided by the simulations. They show the formation of the actual transition complexes along the transition pathway, namely, the critical nuclei of the new phase. These nuclei, which are made up of approximately 20 molecules, can be recognized in the midst of the surrounding matter. Techniques based on molecular orientations, involving Pawley-Fuchs projections and orientational angular distribution functions, make it possible to estimate the size of critical nuclei. One noteworthy result established in the simulations is that the solid-state transition temperature from bcc to monoclinic depends upon particle size in the same manner as does the freezing point.     

Molecular dynamics implementation in MSINDO: study of silicon clusters

Born-Oppenheimer molecular dynamics is implemented in the semiempirical self-consistent field molecular orbital method MSINDO. The method is employed for the investigation of the structure and dynamics of silicon clusters of various sizes. The reliability of the present parameterization for silicon compounds is demonstrated by a comparison of the results of simulated annealing and of density functional calculations of Si(n) clusters (n = 5-7). The melting behavior of the Si(7) cluster is investigated and the MSINDO results are compared to previous high-level calculations. The efficiency of the present approach for the treatment of large systems is demonstrated by an extensive simulated annealing study of the Si(45) and Si(60) clusters. New Si(45) and Si(60) structures are found and evaluated. The relative stability of various energy minimum structures is compared with density functional calculations and available literature data.     

The aqueous cationic system sodium undecenoate-dodecyltrimethylammonium bromide at low concentration

The aqueous sodium undecenoate (SUD) –dodecyltrimethylammonium bromide (DTAB) catanionic system was studied at low concentration. The system did not precipitate, even at a 1:1 SUD:DTAB proportion, but showed the formation of a coacervate in a range of surfactant mixture compositions. Micelles have a preferential composition of 0.37 mole fraction of SUD. This behavior is attributed to the presence of the double bond at the distal extreme of the SUD molecule, which can form hydrogen bonds with water. Consequently, the –CH=CH₂ group is situated at the interface between the hydrocarbon micelle core and water, reducing the interfacial free energy. Structural computations demonstrate that the mentioned SUD proportion produces complete coverage of the micelle surface by the double bonds.     

Molecular modeling and dynamics of neuropeptide Y

Summary A combination of molecular modeling and molecular dynamics (MD) is used to determine a theoretical structure for neuropeptide Y (NPY). Starting with the X-ray structure for avian pancreatic polypeptide (APP), the substituted amino acids were mutated, the side chains oriented to local potential energy minima, and the entire structure minimized and subjected to an MD simulation. Comparison of the resulting NPY structure with APP X-ray and MD results showed secondary structural elements to be maintained and RMS fluctuations to be similar, although differences in both were observed. The approach presented offers a means to study the structure-function relationships of NPY and other similar polypeptides when combined with pharmacological measurements.Abbreviations NPY Neuropeptide Y - APP Avian pancreatic polypeptide - ABNR Adopted-basis Newton Raphson - MD Molecular dynamics     

Importance of heat capacity determination in homogeneous nucleation: application to progesterone

Progesterone is known to exist under different crystallographic forms in the solid state. The thermodynamic stable form (I), melts at 129.2 °C (402.35 K) under atmospheric pressure. After melting and cooling a metastable form (II) can be obtained which melts at 122 °C (395.15 K). This uncommon behaviour can be explained with the theory of nucleation, only if heat capacity of the different forms are known.     

Molecular dynamics study of selective adsorption of PCB on activated carbon

The selectivity of PCB adsorption from fish oil onto activated carbon (AC) was investigated by means of molecular dynamics to determine the importance of molecular planarity. PCB congeners 77 and 118 were selected for comparison purposes due to pronounced differences in mean adsorption efficiency and molecular geometry; triolein, a triacylglycerol of oleic acid (C18:1), was used as the representative fish oil component. Graphitic carbon structure was set up to serve as activated carbon model. Molecular force fields employed in the simulations combined short-range parameters from the OPLS with partial atomic charges obtained via quantum chemical calculations using DFT/B3LYP/6-31**G+ and Solvation Model 6. We modified the dihedral angle potential between the PCB aromatic rings and applied Schrödinger's Jaguar package to evaluate the required force field constants. Our complete system comprised a number of PCB molecules dissolved in triacylglycerol that overlaid and filled the pores of an AC structure. The production run of 4 ns provided strong indications that smaller pores will be conductive to better selectivity though also resulted in certain doubts concerning the estimation and assignment of partial atomic charges on the activated carbon. The majority of PCB molecules trapped in pores were attached via cl-AC “bonding”, leaving the main part of the PCB molecule free to interact with triolein. The cl-AC adsorption energy was found to surpass the energy criteria conventionally used for hydrogen bonds. Planar orientation assumed by a PCB molecule in a very energetically favored position on top of the graphite sheet clearly supported the π-cloud overlap hypothesis.     

Molecular dynamics simulation of quasi-two-dimensional water clusters on ice nucleation protein

We performed molecular dynamics simulations of systems that consisted of the ice nucleation protein and the quasi-two-dimensional water cluster on it. The angle distributions, percolation probabilities, mean cluster sizes, cluster size distributions, and hydrogen bond relaxation times were analyzed. We concluded that the behavior of the water clusters on the ice nucleation protein was elaborately intertwined by the interaction between the ice nucleation protein and water, the interaction between the water molecules and the effect of temperature. The percolation probability and mean cluster size depended on the interactions and temperatures.     

基于分子对接的thanatin与NDM-1分子动力学模拟研究

耐碳青霉烯类抗生素的超级细菌给人类健康带来了严重威胁,其所携带的金属 β-内酰胺酶编码基因是耐药性的主要来源。NDM-1作为其中传播最广、活性最强的 β-内酰胺酶,其抑制剂的研发刻不容缓。具有广谱作用的抗菌肽thanatin对NDM-1展现出了较好的抑制效果,但抑制机理并不清楚。本文使用HPEPDOCK与Rosetta FlexPepDock服务器,将thanatin与NDM-1进行了分子对接,并使用Desmond软件包对对接模型进行了分子动力学模拟。结果表明,thanatin与NDM-1活性中心的Zn2+ 并无直接相互作用,而作为竞争性抑制剂结合于NDM-1的活性口袋,阻止抗生素分子进入活性口袋与Zn2+ 结合,从而抑制NDM-1的水解活性。本文为研发有效的NDM临床抑制剂探索了可行的方法。     

Molecular dynamics on distributed memory (MIMD) parallel computers

Summary Several algorithms are described that have been applied to molecular dynamics simulations and their merits discussed. The subject matter is confined to distributed (MIMD) algorithms. A simple mathematical model is used to illustrate the performance characteristics of a parallel MD algorithm.     

Elution dynamics of adsorption of Chladon 113 and methyl bromide on active carbons

The elution dynamics of adsorption of Chladon 113 (at high contents of the adsorptive) and methyl bromide on active carbons with different lengths of the layer was studied. The adsorption isotherms were described by the equation of the theory of volume filling of micropores. The elution curves were calculated using the model of the equilibrium adsorption layer. The effective kinetic constant calculated in the framework of the model is 1.5 cm for Chladon 113 at a linear velocity of vapor-air flow of 1250 cm min⁻¹ and 1.0 cm for methyl bromide at the velocity of 700 cm min⁻¹. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1353–1355, July, 1998.     

Molecular dynamics simulation of the aggregation of colloidal particles

The spontaneous time evolution of systems containing N colloidal particles (N = 12, 24, 100) in a spherical cell of volume V at a constant volume fraction φ=0.1 was studied by a molecular dynamics method in the NVT ensemble. The starting velocities of the particles are allocated according to the Maxwell distribution at T=273 K.

Pairwise interaction of the particles was specified by molecular, electrostatic and elastic forces. The changes in the potential energy of the systems were calculated during the establishment of dynamic equilibrium. Coagulation takes place at sufficiently high values of the Hamaker constant. The value of the coefficient of Brownian diffusion, which is calculated from the half-time of coagulation, is found to be close to the known value for aqueous dispersions. The inclusion of electrostatic forces prevents coagulation.

The results obtained are in agreement with those obtained using theories of aggregate formation. Some structural characteristics of aggregates and stable systems are discussed.     

Extended study of molecular dynamics simulation of homogeneous vapor-liquid nucleation of water

Using the simple point charge/extended water model, we performed molecular dynamics simulations of homogeneous vapor-liquid nucleation at various values of temperature T and supersaturation S, from which the nucleation rate J, critical nucleus size n(*), and the cluster formation free energy DeltaG were derived. As well as providing lots of simulation data, the results were compared with theories on homogeneous nucleation, including the classical, semi-phenomenological, and scaled models, but none of these gave a satisfactory explanation for our results. It was found that two main factors made the theories fail: (1) The average cluster structure including the nonspherical shape and the core structure that is not like the bulk liquid and (2) the forward rate which is larger than assumed by the theories by about one order of magnitude. The quantitative evaluation of these factors is left for future investigations.     

Vibrational echo spectroscopy of aqueous sodium bromide solutions from first principles simulations

A theoretical study of the time-dependent vibrational echo spectroscopy of sodium bromide solutions in deuterated water at two different concentrations of 0.5 and 5.0 M and at temperatures of 300 and 350 K is presented using the method of ab initio molecular dynamics simulations. The instantaneous fluctuations in frequencies of local OD stretch modes are calculated using time-series analysis of the simulated trajectories. The third-order polarization and intensities of three pulse photon-echo are calculated from ab initio simulations. The timescales of vibrational spectral diffusion are determined from the frequency time correlation functions (FTCF) and short-time slope of three pulse photon echo (S3PE) calculated within the second-order cumulant and Condon approximations. It is found that under ambient conditions, the rate of vibrational spectral diffusion becomes slower with increase in ionic concentration. Decay of S3PE calculated for different systems give timescales, which are in close agreement with those of FTCF and also with the results of experimental time-dependent vibrational spectroscopic experiments. © 2019 Wiley Periodicals, Inc.     

Aqueous two-phase extraction system of sodium perfluorooctanoate and dodecyltriethylammonium bromide mixture and its application to porphyrins and dyes

A new aqueous two-phase system is developed consisting of sodium perfluorooctanoate (SPFO) and dodecyltriethylammonium bromide (C₁₂NE) cationic–anionic surfactant mixture. The two phases with a clear interfacial boundary formed when SPFO to C₁₂NE molar ratio is 1.2:1 in the presence of 5% (v/v) nitric acid. The top phase is transparent and the bottom phase is opalescent. Extractions of dyes, porphyrin compounds with the two-phase system were performed. The results show that hydrophobic molecules were extracted into the surfactant-rich bottom phase with high extraction efficiencies. Positively charged porphyrins were extracted into the bottom phase with higher extraction efficiencies than negatively charged porphyrins. Such a new anionic surfactant two-phase system would be complementary to the C₁₂NE–SDS (sodium dodecyl sulfate) cationic two-phase which has been proven to be effective for extractions of porphyrins with substituted groups like carboxyl or sulfonic acid groups.     

Molecular dynamics and quantum chemical studies on nitroglycerine

A constant temperature molecular dynamics study has been performed on PM3 (RHF) geometry optimized nitroglycerine molecule. The dynamics was carried out by using MM+ method at 550 K which is above the explosion point of nitroglycerine. Some molecular orbital characteristics of nitroglycerine at elevated temperatures were computed.     

Molecular dynamics simulations of oligonucleotides in solution: Visualisation of intrinsic curvature

Summary We have undertaken molecular dynamics simulations on the d(CGCAAAAAAGCG)d(CGCTTTTTTGCG) dodecamer in solution. In this study, we focus on aspects of conformation and dynamics, including the possibility of cross-strand hydrogen bonds. We compare our results with those from crystallography as well as infrared, Raman and NMR spectroscopy and cyclization kinetics. Our method of analysis allows us to visualise the curvature of the helix as a function of time during the simulation. We find that the major distortions of the helix axis path occur at the junctions between the (essentially straight) A-tract and the CG-and GC-tracts, although at one junction this is due to hyperflexibility (i.e., regions of high flexibility with no preferred direction of curvature), while at the other junction a static curvature is found (i.e., a preferred, sustained direction of curvature).     

Unusual volumetric and hydration behavior of the catanionic system sodium undecenoate: sodecyltrimethylammonium bromide

Following the studies on the effect of double bonds in the surfactant hydrophobic tail on the formation of mixed surfactant aggregates, we studied the viscosity and density of the system Sodium 10-undecenoate (SUD)–decyltrimethylammonium bromide (DTAB)–water. We found that the partial molar volume (pmv) and intrinsic viscosity of both, micellised and unmicellised mixtures, are non-ideal, dependent on the mixture composition and related to structural changes in micelles. These phenomena are caused by the presence of the double bond at the distal extreme of the SUD molecule, which has some affinity with water by formation of hydrogen bonds. In particular, as far as we know, this is the first report on non-ideal behavior of the pmv in mixed micelles.