Dendrimers as Functional Materials. A Molecular Simulation Study of Poly(propylene) Imine Starburst Molecules

Abstract

Dendritic macromolecules are hyperbranched polymers that emanate from a central core, have a defined number of generations and functional end groups, and are synthesized in a stepwise process by a repetitive reaction sequence. This hyperbranched topology results in a unique series of physical and chemical properties exhibited by these molecules which, in turn, could be exploited in a number of diverse possible applications, such as nanoscale catalysis, micelle mimics, immuno-diagnostic and NMR imaging agents, chemical sensors, molecular antennae, just to name a few.

Nonetheless, if on one hand the synthesis procedure allows for control over parameters such as size, shape and reactivity (and hence, on final properties), on the other hand it really hampers the production of large quantities of these materials. Accordingly, their cost is still quite high and, therefore, the materials available for characterization is still rather limited.

Since, however, their full application potentials (particularly in material science and engineering) will not be realized before the understanding of their physical properties is considerably more advanced, in this work we report the results obtained on structural details and related properties of several amine- and nitrile-terminated poly(propylene)imine dendrimer generations by computer simulation studies and discuss them in the light of (scarce) available experimental data.     

Investigations of Nematic-Isotropic Transition by Means of Constant Pressure Molecular Dynamics Simulations

Abstract

Constant pressure molecular dynamics simulations, which secure the system to be under hydrostatic pressure, are used to simulate the behavior of liquid crystals consisting of anisotropic molecules with both translational and orientational freedom. In order to investigate to what extent can the properties known to real liquid crystalline phases be explained by the anisotropy of the shape of the molecules alone, the molecular dynamic (MD) simulation uses purely repulsive short-range pair potentials representing soft spherocylinders. A clear change in the microscopic as well as the macroscopic physical properties are observed near the phase transition from nematic liquid crystal to isotropic liquid.     

Molecular simulation for predicting the rheological properties of polymer melts

ABSTRACT

Bottom-up prediction that links materials chemistry to their properties is a constant theme in polymer simulation. Rheological properties are particularly challenging to predict because of the extended time scales involved as well as large uncertainty in the stress output from molecular simulation. This review focuses on the application of molecular simulation in the prediction of such properties, including approaches solely based on molecular simulation and its integration with rheological models. Most attention is given to the prediction of quantitative properties, in particular, those most studied such as shear viscosity and linear viscoelasticity. Studies on the fundamental understanding of rheology are referenced only when they are directly relevant to the property prediction. The review starts with an overview of the major methods for extracting rheological properties from molecular simulation, using bead-spring chain models as a sandbox system. It then discusses materials-specific prediction using chemically-realistic models, including systematically coarse-grained models that allow the mapping between scales. Finally, integrating molecular simulation with rheological models extends the prediction to highly entangled polymers. Recent development of several multiscale predictive frameworks allowed the successful prediction of rheological properties from the chemical structure for polymers of experimentally relevant molecular weights.     

Promotion of Crystal Phase Transitions by Mass-of-cell Control in Molecular Dynamics Simulations: Phase Transitions in Benzene Crystals

Abstract

The promotion of crystal phase transitions in molecular dynamics (MD) simulations was realized by controlling the momentum of the MD cell. It was implemented by increasing the mass or velocity of the MD cell instantaneously during simulations within the framework of the constant-pressure method by Parrinello and Rahman. This method induced phase transitions in benzene crystals which have not been obtained in conventional MD simulations. This method is useful for the global search of stable (and metastable) crystal structures.     

Molecular Dynamics Study of BaB2O4 in Crystalline and Molten States

Abstract

Structural aspects of BaB₂O₄ liquids have been investigated by the molecular dynamics simulation including the determination on the parameters of the interatomic potential applicable to BaB₂O₄ in both crystalline and molten states. The structure and physical properties of BaB₂O₄ crystals were successfully reproduced by the MD simulation for both α and β phases. The simulated interference function in the liquid state was also in good agreement with the experimental one. Several interesting features on the relaxation phenomena just after melting were reproduced by the simulation that the structure factors of simulated liquid maintain the characteristic features of the original crystal structure for more than 40ps after melting, and the variation of the number of rings formed by B-O bondings was found to increase after melting.     

Molecular Dynamics Simulations With First Order Coupling to a Bath of Constant Chemical Potential

Abstract

In molecular dynamics simulations the temperature or pressure can be controlled by applying a weak first-order coupling to a bath of constant temperature or pressure. This weak coupling technique to control system properties using a first-order relaxation equation is analyzed from a statistical mechanics point of view. It is shown, how the weak coupling scheme can be generalized and applied to a bath of contstant chemical potential. The presented method, to which in the following will be referred to as chemical potential weak coupling, is applied and tested on a Lennard-Jones fluid. The thermodynamic quantities known from the literature are accuratly reproduced.

The temperature and chemical potential weak coupling methods aim to sample the canonical and grand canonical ensembles respectively. By analyzing the fluctuations in energy and number of particles, the tight relation between the ensembles and the distributions obtained from the weak coupling simulations is demonstrated. The influence of the choice of the coupling parameters on the quality of the approximation of the ensemble distribution is discussed.     

The Implementation of the Iterative Diagonalization Scheme and ab initio Molecular Dynamics Simulation with the LAPW Method

Abstract

A new ab initio molecular dynamics method based on the full-potential linearized-augmented-plane-wave (LAPW) basis set has been implemented. The LAPW basis set has been successfully employed for systems containing localized electrons such as first row atoms and transition metals. In our implementation of the LAPW-MD scheme, iterative residual minimization algorithm is used to solve the electronic states problem. The atoms are moved according to forces derived from the Hellman–Feynman theorem and incomplete basis set correction terms. The performance of the program is further enhanced by parallelization. We will discuss technical details of the program implementation and present results obtained from this code to the equilibrium structures and vibrational properties of simple diatomic molecules.     

Molecular Dynamics Simulation of CaF2 Structure in Crystalline,Superionic and Molten Phases

Abstract

We describe here a number of molecular dynamics simulations on calcium fluoride over a range of temperatures spanning the transitions to the superionic and molten state. The simulation temperatures are 1400, 1590, 1800, 2000, 2200 K. By using the bond spherical harmonics method with equal neighbor number, we have studied the structure and bond orientation of cation sublattice and anion sublattice in superionic conductor CaF₂. The bond order parameters Q₁ have been calculated both for the computer generated instataneous configurations from the simulation system and for the standard configurations from the normal distribution model of bond orientation. The comparison of Q₁ between the molecular dynamics simulation and the normal distribution model shows that not only the cation sublattice but also the anion sublattice can be described by the normal distribution model. The cations keep their original fcc frame, but in the anion case there is a great deal of random distortions from the original anion sublattice.     

Synthesis and Characterization of Templated Mesoporous Materials Using Molecular Simulation

Abstract

Lattice Monte Carlo simulations are used to calculate equilibrium properties of surfactant-solvent-silica liquid-crystal systems under no-polymerization conditions. The formation of a high-surfactant high-silica concentration phase in equilibrium with a dilute phase is observed when the surfactant-silica interactions are stronger than the surfactant-solvent interactions. Different silica structures that are similar to the M41 family are observed, depending on the overall concentration of the system. The formation of a hexagonal phase is favored at a surfactant/silica ratio of 0.2, whereas a lamellar phase is observed a surfactant/silica ratio of 1.

Argon adsorption properties on a model porous structure of the MCM-41 type prepared using this mimetic simulation protocol are calculated using grand canonical Monte Carlo simulation. Heats of adsorption are calculated from fluctuations in the energy and number of molecules [1] following the work of Nicholson and Parsonage [Computer Simulation and the Statistical Mechanics of Adsorption (Academic Press, London), 1982, p 97 8 pp]. A decrease in the heats of adsorption for coverage less than one statistical monolayer is evidence of surface heterogeneity. The results are in qualitative agreement with experimental measurements for argon on MCM-41.     

Systolic Loop Methods for Molecular Dynamics Simulation,Generalised for Macromolecules

Abstract

Systolic loop programs have been shown to be very efficient for molecular dynamics simulations of liquid systems on distributed memory parallel computers. The original methods address the case where the number of molecules simulated exceeds the number of processors used. Simulations of large flexible molecules often do not meet this condition, requiring the three- and four-body terms used to model chemical bonds within a molecule to be distributed over several processors. This paper discusses how the systolic loop methods may be generalised to accommodate such systems, and describes the implementation of a computer program for simulation of protein dynamics. Performance figures are given for this program running typical simulations on a Meiko Computing Surface using different number of processors.     

Molecular Dynamics Simulations of NaCl-type Solid Solution Crystals: The First Application of Molecular Dynamics to Solid Solutions

Abstract

Solid solution crystals appear widely in the fields of earth sciences and inorganic material sciences. The physical properties of solid solutions may vary continuously with chemical composition. Sometimes, linear relationships of the properties with composition are assumed. However, this approximation is not always applicable (e.g., [1], [2], [3]). In order to elucidate the properties of solid solutions, studies on the relation between the macroscopic properties and the atomic configurations (microscopic property) in the crystal are desirable. One of the most effective approaches to the subject is molecular dynamics (MD). However, as far as the authors are aware there have been no molecular dynamics studies on solid solution crystals.     

Isobaric and Isothermal Molecular Dynamics Simulations of Diatomic Systems

Abstract

Isobaric molecular dynamics simulations were carried out for diatomic systems using different algorithms available in the literature. Two-centered Lennard-Jones potentials with and without quadrupolar interactions were used. Thermodynamic properties obtained from the isobaric algorithms compared very well with those of an equivalent simulation in the microcanonical ensemble; however, some differences were observed when similar comparisons were carried out for dynamic properties. More specifically, the constant pressure constraint affects the translational dynamics of the system because of the non-negligible differences between the momenta and the instantaneous velocities of the molecules.

Furthermore, the following studies were carried out using isobaric MD simulations: 1. Low temperature spontaneous FCC-orthorhombic (and vice versa) transition of a diatomic system with quadrupolar interactions as a function of the molecular bond length. 2. Effect of quadrupolar interaction on isobaric melting of a model diatomic system. 3. Effect of pressure on melting properties of a model diatomic system with quadrupolar interactions.     

Molecular properties of a bent-core nematic liquid crystal A131 by multi-level theory simulations

ABSTRACT

Multi-level theory simulations have been performed to model a number of important molecular properties of a bent-core nematic liquid crystal (LC) A131. These important properties include molecular conformations, molecular Raman spectra, differential polarisability ratios, molecular crystals packing, atomic LC structures, order parameters, and Raman depolarisation spectra. The simulations contain four theory levels, involving molecular quantum chemistry, molecular crystal packing, super cell density functional based tight binding optimisation, and super cell molecular dynamics calculations. To heat initial optimised super cell structures, molecular dynamics simulations reveal phase transitions to uniaxial and biaxial nematic phases from molecular crystals. LC atomic structures result in direct calculations on order parameters, which can be further applied to computations on Raman depolarisation spectra with differential polarisability ratios, obtained in the molecular quantum chemistry theory level. The good agreement of simulated Raman depolarisation spectra with the experiment provides a detailed analysis on the unusually low values of experimental uniaxial order parameters.     

Molecular Dynamics Study of Zinc-Blende GaN,AIN and InN

Abstract

We present a result of the molecular dynamics calculations with used a three-body empirical Tersoff potential. The parameters of the Tersoff potential are determined for nitride compound semiconductors such as GaN, AlN and InN. The structural and thermodynamic properties of GaN, AlN and InN in zinc-blende structure are presented. We report the equilibrium lattice constants, the bulk moduli, the cubic clastic constants, thermal expansion coefficient and specific heat. Good agreement is obtained with recent experimental and theoretical results for all constants.     

Molecular Dynamics Study of Li2SiO3 in the Liquid and Glassy States

Abstract

Molecular dynamics simulation (MD) has been carried out for Li₂SiO₃ in the molten and glassy states. The parameters of the pair potential functions were determined by a trial and error method so that the results of X-ray diffraction analysis could be well reproduced.

The changes in the structure and dynamic properties accompanied by lowering temperature revealed that the glass transition of this simulated system occurred between 973 and 700 K. The ratio of the bridging oxygens to non-bridging oxygens was nearly constant over the investigated temperature range, while a small change in the pattern of branching of the -Si-O-framework was found. The second peaks in the pair correlation functions g_Si-O(r) and g_Si-Si(r) split at lower temperature. These splittings suggest that the motion changing the relative orientations of two neighboring SiO₄ units may be nearly frozen at lower temperature.     

Molecular Dynamics Simulation of Nucleation and Growth of a Binary Quasicrystal

Abstract

The quasicrystal structure is considered to be a new type of ordered phase because its Fourier transform has Laue spots with icosahedral symmetry, which is inconsistent with crystal structure. Computer simulation of the formation process of a quasicrystal was performed by the molecular dynamics method. On the basis of the Strandburg type of quasicrystal model, we developed an algorithm of the formation process of binary quasicrystal reflecting the procedure as realistically as possible. The Fourier transform of some of the obtained structures has shown decagonal symmetry although the spots are rather diffused. It has been shown that the potential parameter and experimental condition should be limited to produce a perfect quasicrystal structure.     

On the Approximation of Solvent Effects on the Conformation and Dynamics of Cyclosporin A by Stochastic Dynamics Simulation Techniques

Abstract

The molecular simulation technique of stochastic dynamics (SD) is tested by application to the immunosuppressive drug cyclosporin A (CPA). Two stochastic dynamics simulations are performed, one (SD_CCl4 ) with atomic friction coefficients proportional to the viscosity of the nonpolar solvent CCl₄, and one (SD_H2O) with atomic friction coefficients corresponding to an aqueous solution. The atomic friction coefficients are also taken proportional to an approximate expression for the atomic accessible surface area. The properties of both stochastic dynamics simulations are compared to those of two full molecular dynamics (MD) simulations of cyclosporin A, one in a box with 591 CCl₄ molecules, and one in a box with 632 H₂O molecules.

The properties of cyclosporin A as found in the molecular dynamics simulation in CCl₄ are well reproduced by the SD_CCl4 simulation. This indicates that the neglect of a mean force reresenting the average solvent effects on the solute is justified in the case of nonpolar solvents. For polar solvents, like water, this mean force may not be neglected. The SD_H2O simulation of cyclosporin A clearly fails to reproduce the amount of hydrogen bonding found in the molecular dynamics stimulation of cyclosporin A in water.

A comparison with a molecular dynamics simulation of cyclosporin A in vacuo shows that both the SD_CCl4 and the SD_H2O simulation come closer to the properties of the molecular dynamics simulations in CCl₄ and in H₂O than a molecular dynamics simulation in vacuo.     

Structure of Supercritical Fluid Krypton at Small Scattering Angle Using Parallel Molecular Dynamics Simulation

Abstract

We present a parallel algorithm for molecular dynamics involving short-range two- and three-body potentials and the pair-correlation function, g(r). The method is based on a spatial decomposition of the simulation box that takes advantage of a linked-cell list, and allows a load balanced partition of the computations of both the forces and g(r) over the processors. The tests of the program is conducted by evaluating the efficiency for both the thermalization phase and the production phase of the simulation. This method is successfully applied to the calculation of the direct correlation function of fluid krypton at small scattering angle along the T = 297 K supercritical isotherm.     

The Role of Molecular Dynamics Simulations for the Study of Slow Dynamics

Abstract

A two step strategy is proposed to study dynamical properties of a physical system much slower than the time scales accessible by molecular dynamics simulations. The strategy is applied to investigate the slow dynamics of supercooled liquids.