MedeA® Application Notes for Chemical & Petrochemical

The effect of resin molecular architecture on the small strain elastic constants of diamine-cured epoxy thermosets has been studied using classical all-atom simulations conducted within the MedeA simulation environment. Batches of thermoset systems have been created using chemically similar di, tri and tetrafunctional resins, followed by calculation of stiffness and compliance matrices for each individual model. Analysis of the batches of topologically and geometrically distinct structures using the Hill-Walpole approach yields upper and lower bounds estimates of the moduli differing by typically 1%, enabling critical comparison with experimentally-measured values.

Effect of Resin Molecular Architecture on Epoxy Thermoset Mechanical Properties

The formation of micelles by surfactants was followed by molecular dynamics calculations performed with MedeA-LAMMPS and using the PCFF+ forcefield. An initial model with a random distribution of C9TAC surfactant molecules was built using the MedeA building capabilities, such as the Molecular Builder and the Amorphous Materials Builder. Results are in agreement with previous simulation studies and available experimental data.

This application note describes the calculation of densities, cohesive energy densities (CED), and enthalpies of vaporization for a range of straight chain hydrocarbon fluids. The construction, simulation, and analysis methodologies employed are reviewed; and the accuracy of atomistic simulation for organic materials and polymers illustrated. Mean absolute errors are 0.23% and 0.28% for densities and heats of vaporization respectively for the PCFF+ forcefield.

Organic Materials Properties: Densities,  Cohesive Energies, and Heats of Vaporization

In this note, we compare computed structural properties of clay minerals with experimental data, wherever such data is available. Calculated properties include cell parameters, atomic positions (in particular H positions) and internal surface areas.

Structural Properties And Surface Area of Clay Minerals

Faujasitic zeolites are employed in a range of industrial contexts including separation processes, gas purification and dehydration, and shape selective catalysis. The simulation of the interaction of small molecules with faujasite based zeolites is increasingly practical and the resulting information provides the basis for efficient materials selection and design. When experimental data are scarce and empirical models insufficiently accurate, the MedeA software environment can be employed to provide quantitative property data for faujasitic zeolite systems.

The colloidal behavior of asphaltenes explains the high viscosity of heavy oils and the occurrence of solid deposits in reservoir rocks, production wells or transport lines.
Asphaltenes make refining more difficult because they cause coke deposits and tend to lower the yield in high quality fuels or chemicals. Due to their significant content of sulfur and metals (Ni, V) and high aromaticity, energy-intensive conversion and hydrotreatment processes are required.

Colloidal behavior of confined model asphaltenes using molecular dynamics

Typical HP-HT conditions may be defined by fluid pressures in excess of 50 MPa or temperatures above 150°C, as encountered in deep reservoirs below the North Sea, the Caspian Sea, the Gulf of Mexico and offshore Brazil, among others. Under these conditions natural gas may contain hydrocarbons with chain length of as much as 30 carbon atoms and a methane content higher than 60% (molar concentration). Because of the high temperature, water content may be significant, and further, H2S or CO2 contents may be elevated in some HP-HT reservoirs.

Properties of Natural Gases in Classical and High Pressure-High Temperature Conditions

The structure of the Fe₂O₃ (0001) surface as a function of oxygen partial pressure and temperature is computed using first-principles thermodynamics. The results reveal an active four-fold coordinated surface Fe atom which releases oxygen atoms at approximately 850 K at ambient oxygen partial pressure. This property is likely to be related to the catalytic activity of hematite for selective oxidation reactions such as the oxidation from ethylbenzene to styrene.

Structure of an iron oxide (Fe₂O₃) surface as function of temperature and O₂ pressure

First-principles calculations reveal the atomistic structures of the active phases of CoMoS and NiMoS hydrodesulfurization catalysts. The reliable determination of the catalyst surface is critical, as it represents the starting point for subsequent adsorption and reaction path simulations. The predicted dominant structures are consistent with experimental STM, EXAFS and magnetic susceptibility measurements.

Atomic Structure of Hydrodesulfurization (HDS) Catalysts

First-principles calculations reveal the dominant acid sites on the amorphous silica-alumina (ASA) catalyst surface. Based on the strength of interaction with Lewis base probe molecules, the bridging and pseudo-bridging silanol (PBS) species are determined to be the most acidic and therefore catalytically active groups. Evident in the calculations is the interplay between the Lewis acid and the Brønsted acid sites on the ASA catalyst surface, giving rise to the enhanced acidity of the PBS species. This work provides mechanistic insight to inform efforts at rationally engineering enhanced ASA-based solid acids.

Acidity of Amorphous Silica-Alumina (ASA) Catalysts

First-principles calculations using VASP reveal the lowest energy reaction pathway for the catalyzed skeletal isomerization of 2-pentene by the acidic zeolite H-ZSM. Three potential mechanisms were evaluated: an ethyl-shift pathway, a dimethylcyclopropane (DMCP) intermediate pathway and a pathway involving an edge-protonated DMCP species. The results indicate that the DMCP intermediate pathway is the kinetically preferred pathway with a classical barrier height of 98 kJ/mol. Evident in the calculations is the influence of the transient intermediate stability along the reaction path; with secondary carbenium ions leading to energetically favored mechanisms.

Catalytic Isomerization of 2-pentene in H-ZSM-22

The energy of adsorption and dissociation of molecules on surfaces plays a critical role in technological processes such as chemical vapor deposition, catalysis, and corrosion. The present case shows the calculation of the energy of the dissociative chemisorption of a silane molecule on a Si (001) surface.

Energy of Dissociative Chemisorption of SiH₄ on Si (001) Surface

Increasingly stringent environmental regulations require a lowering of sulfur in Diesel fuels. This is accomplished by a catalytic process transforming sulfur-containing molecules into H2S, which is removed from the liquid phase. Larger sulfur-organic molecules are more difficult to attack and new catalytic materials are needed. The present screening study demonstrates how the combination of experimental activity data, crystallographic information from structural databases and first- principles computation of binding energies are used to identify potential new candidates.

Screening of desulfurization catalysts

The performance of catalytic materials depends on complex phenomena linked to chemical
composition, preparation, activation procedures, and surface conditions under operational
conditions. This complexity requires a comprehensive arsenal of R&D approaches including
theoretical and computational methods. While many fundamental research efforts are
currently directed at a detailed understanding of surface reaction mechanisms, PREDIBOND™
focuses on bond strength and local chemical environment as central descriptors of chemical

PREDIBOND™ in Heterogeneous Catalysis: Predicting Activity Patterns

This application note deals with positioning molecules on surfaces. As an example we will investigate the adsorption of ethyl alcohol (ethanol) on a Cu (111) surface. In doing so we will consider two possible configurations for the adsorbed molecule:
1. adsorbed ethanol
2. dehydrogenated ethanol, i.e. an ethoxygen.
Running structure relaxations using VASP produces a first estimate of the relative stability of these two systems.

Dehydrogenation Energy of Ethyl Alcohol (Ethanol) on a Cu (111) Surface