This book discusses the fundamentals of molecular simulation, starting with the basics of statistical mechanics and providing introductions to Monte Carlo and molecular dynamics simulation techniques. It also offers an overview of force-field models for molecular simulations and their parameterization, with a discussion of specific aspects. The book then summarizes the available know-how for analyzing molecular simulation outputs to derive information on thermophysical and structural properties. Both the force-field modeling and the analysis of simulation outputs are illustrated by various examples. Simulation studies on recently introduced HFO compounds as working fluids for different technical applications demonstrate the value of molecular simulations in providing predictions for poorly understood compounds and gaining a molecular-level understanding of their properties. This book will prove a valuable resource to researchers and students alike.

This book is concerned with the prediction of thermodynamic and transport properties of gases and liquids. The prediction of such properties is essential for the solution of many problems encountered in chemical and process engineering as well as in other areas of science and technology. The book aims to present the best of those modern methods which are capable of practical application. It begins with basic scientific principles and formal results which are subsequently developed into practical methods of prediction. Numerous examples, supported by a suite of computer programmes, illustrate applications of the methods. The book is aimed primarily at the student market (for both undergraduate and taught postgraduate courses) but it will also be useful for those engaged in research and for chemical and process engineering professionals.

There are many tools available to measure the thermophysical properties of compounds. Experimental measurements have been evolving for many years and are very accurate at determining the properties of most compounds. However, many of the measurements are unreliable when the compound of interest is thermally unstable. Throughout the years molecular simulation techniques have been developed to understand the thermophysical properties of thermally unstable compounds. There are primarily two methods to study Vapor-Liquid Equilibrium by molecular simulation Gibbs Ensemble Monte Carlo and Molecular Dynamics. MD is a technique that allows one to simulate the vapor and the liquid in the same simulation cell. The advantage to having the vapor and liquid in the same simulation cell is that an interface forms and properties not available by GEMC can be investigated. However, the inclusion of the interface complicates the determination of the phase densities. There are two methods available in the literature to determine the phase densities from a two-phase MD simulation. The first utilizes a hyperbolic tangent function to fit the density profile across the axis normal to the interface. The second method calculates the average of a local property spatially and then determines the resulting distribution function. The distribution function is used to determine the phases from user defined phase cut-offs. These methods only work well far from the critical point and have many adjustable parameters. These adjustable parameters make it difficult to reliably obtain accurate results. This lack of reliability is one of the main driving forces behind this dissertation. In order to correct the limitations of previous methods, a new technique is presented and tested against three cases. The new technique utilizes Voronoi tessellations to calculate the volume of every molecule in the simulation cell. The molecular volumes generated can be interpreted by simple statistical parameters such as the mean and variance to determine the density on the two phase envelope. In this dissertation a new method is presented and applied to three test cases, a simple fluid, and two polyatomic cases.

This dissertation, "Molecular Dynamics Simulations of Thermodynamic Properties of Selected Polymeric and Biological Molecules" by Liangxu, Xie, 谢良旭, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Molecular dynamics (MD) simulations have been widely applied to study equilibrium and dynamical properties of macromolecular systems. In this thesis MD simulations are applied to important macromolecular processes, including conformation transformation in macromolecular systems and enzymatic catalysis, molecular details of which are inaccessible to experimental methods. A fundamental investigation of macromolecular processes is presented in this dissertation. Different computational methods, such as integrated tempering sampling (ITS), umbrella sampling (US), and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, have been applied to study conformation changes of macromolecules including those in an enzyme catalyzed reaction. Three representative topics are investigated in this dissertation: (1) structural and dynamic relaxation behavior of polyelectrolytes confined in metal-organic framework (MOF) MIL-53(Al); (2) switch of peptide conformations between α-helix and β-hairpin states; and (3) chorismate rearrangement reaction catalyzed by ―isochorismate-pyruvate lyase from Pseudomonas aeruginosa‖ (PchB). Conformation and dynamical properties of polyelectrolytes threaded in MOF are investigated by MD simulations. A polymer threaded inside MOF was reported to have augmented conductivity and high ion-exchange kinetics. Basic understanding of confinement effect on polyelectrolytes is critical for designing novel polyelectrolyte MOF composites. Three polyelectrolytes, sodium polyacrylate acid, sodium poly (4-vinylbenzonic acid), and polydiallyldimethylammonium chloride (PDADMA), have been introduced into MIL-53(Al) channels to elucidate the confinement effect with variation of charged groups and molecular structures. Quantitative analysis demonstrates that confinement effects include (1) increasing order and size of polyelectrolytes, (2) enabling uniform counter-ion distribution, and (3) changing dynamic relaxation and configurational entropy of polyelectrolytes in the polyelectrolyte MIL-53(Al) composites. To efficiently sample conformation transformations of peptide, the ITS method has been used to investigate secondary structure transformation process of peptides. Proteins undergo conformational changes to fulfill their functions. Secondary structure changes between α-helix and β-hairpin, an essential feature of proteins, is explored by the ITS method. Results demonstrate that ITS can widely sample peptide conformational space, without prior knowledge of the structure or the use of a bias potential. The obtained free energy landscape is used reliably to characterize conformations changes of the peptide between α-helix and β-hairpin states. Finally, chorismate mutate reaction has been a central topic of the enzyme catalysis for decades. This reaction has attracted studies using the QM/MM scheme. However, it is still unclear whether the reaction is enthalpy driven or entropy driven. In this dissertation, the free energy changes of reaction in water are compared to corresponding enzymatic reaction catalyzed by PchB. This reaction is also studied by long timescale US simulations to illustrate the enthalpy/entropy scheme in this enzyme. Comparing the uncatalyzed reaction with the catalyzed reaction in PchB, we conclude that both enthalpy and entropy contribute to catalysis. The stable structure of bound chorismate and the enthalpy/