Browsing by Subject "Molecular simulations"

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    Simulation setup for Enthalpy of Mixing and Liquid Structure for Mixtures of Primary and Secondary Alcohols: Molecular Simulations and COSMO-SAC Calculations
    (2023-10-05) Chang, Chun-Kai; Siepmann, J. Ilja; chan1843@umn.edu; Chang, Chun-Kai; Siepmann Group
    The enthalpy of mixing provides information on the favorability of cross-interactions between two different chemical compounds, and it can be included in the training of activity coefficient models to capture the temperature dependence. Recently, Mathias highlighted that certain mixtures of primary and secondary alcohols exhibit exothermic mixing behavior, whereas mixtures of primary alcohols show the more common endothermic mixing behavior [Ind. Eng. Chem. Res. 2019, 58, 12465]. Here, we probe the mixing behavior of short-chain alcohols at T = 298 K and p = 1 atm through molecular simulations with the TraPPE–UA force field and molecular modeling with the COSMO-SAC activity coefficient model. Using their predictive modes (i.e., without tuning of the models), neither of these two computational approaches yields the exothermic mixing behavior for primary and secondary alcohols. To capture the exothermic mixing, we explore modifications of the TraPPE–UA force-field parameters to make the secondary CHOH group a better hydrogen-bond acceptor(through an increase of the partial charge on the oxygen atom), but also adding steric hindrance for hydrogen-bond formation between two secondary alcohols (through an increase of the Lennard-Jones diameter on the α-CH pseudoatom). Detailed analysis of the liquid structures for the neat phases and mixtures indicates that the tuned model yields slightly enhanced cross-association which results in a more significant shift from tetrameric to larger hydrogen-bonded aggregates than for the TraPPE–UA model, whereas neither model exhibits a significant change in the number of hydrogen bonds upon mixing. Thus, the simulations point to a shift from cyclic tetramers and pentamers with strained hydrogen bonds to larger, less strained aggregates as the underlying structural change for the exothermic mixing behavior of primary and secondary alcohols.
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    Toward Simulation of Complex Reactive Systems: Development and Application of Enhanced Sampling Methods
    (2018-03) Fetisov, Evgenii
    redictive modeling of fluid phase and sorption equilibria for reacting systems presents one of the grand challenges in the field of molecular simulation. Difficulties in the study of such systems arise from the need (i) to accurately model both strong, short-ranged interactions leading to the formation of chemical bonds and weak interactions representing the environment, and (ii) to sample the range of time scales involving frequent molecular collisions, slow diffusion, and infrequent reactive events. This thesis showcases some of my efforts in developing and applying advanced simulation methods to a variety of important systems. Chapters 2 and 3 describe how a novel Monte Carlo method (reactive first principles Monte Carlo or RxFPMC) can be used to overcome some limitations of existing methods for simulation of reactive systems. Chapter 4 shows how advanced sampling techniques in combination with sophisticated interatomic potentials can be used to elucidate nucleation pathways. Chapters 5 and 6 manifest how first principles simulations can be leveraged to understand liquid structure of novel complex solvents as well as reactive processes in such solvents. Finally, the last chapter discusses the use of smart sampling algorithms to study chemisorption of mixed ligands on nanoparticles.