1,726 research outputs found
Simulation setup for Enthalpy of Mixing and Liquid Structure for Mixtures of Primary and Secondary Alcohols: Molecular Simulations and COSMO-SAC Calculations
No full textSource code, input files, and generic output files for molecular simulations in "Enthalpy of Mixing and Liquid Structure for Mixtures of Primary and Secondary Alcohols: Molecular Simulations and COSMO-SAC Calculations".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.National Science Foundation through the Chemical Measurement & Imaging program and the Interfacial Engineering program (Award CHE–2003246)Chang, Chun-Kai; Siepmann, J. Ilja. (2023). Simulation setup for Enthalpy of Mixing and Liquid Structure for Mixtures of Primary and Secondary Alcohols: Molecular Simulations and COSMO-SAC Calculations. Retrieved from the University Digital Conservancy, https://doi.org/10.13020/f13h-ax23
Whole-mount identification of gene transcripts in aphids: Protocols and evaluation of probe accessibility
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No full textIdentification of nuage-like structures in the panoistic ovarioles of the German cockroach Blattella germanica (Linnaeus)
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Germ-plasm specification and germline development in the parthenogenetic pea aphidAcyrthosiphon pisum: Vasa and Nanos as markers
No full textPopulation size and stocking contribution rates for marked and recaptured black porgy Acanthopagrus schlegelli, in Northwestern Taiwan, 2005-2008
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