Erik E. Santiso

A general set of order parameters for molecular crystals

Crystallization is fundamental to many aspects of physics and chemistry in addition to being of technological relevance, for example, in the chemical, food, and pharmaceutical industries. However, the design of crystalline materials and crystallization processes is often challenging due to the many variables that can influence the process. As a part of an effort to gain a molecular-level understanding of the way molecules aggregate and organize themselves into crystal structures, in this work we present a new method to construct order parameters suitable for the study of crystallization and polymorph transformations in molecular systems. Our order parameters can be systematically defined for complex systems using information that can be obtained from simple molecular dynamics simulations of the crystals. We show how to construct the order parameters for the study of three different systems: the formation of α-glycine crystals in solution, the crystallization of benzene from the melt, and the polymorph transformation of terephthalic acid. Finally, we suggest how these order parameters could be used to study order-disorder transitions in molecular systems.

Multi-scale Molecular Modeling of Chemical Reactivity

We present a review of the most widely used methods to model chemical reactions, at both the electronic and atomistic levels. While, in principle, ab initio methods alone should provide the required prediction of reaction mechanisms, yields and rates, in practice this can rarely be achieved due to the intensive nature of the computations and the poor scaling of the computational burden with the number of electrons. In many applications a combination of ab initio and semi-classical atomistic simulations will be needed. Specialized atomistic simulation methods are necessary, since the reactions are themselves rare events, and the free energy landscape for the reaction is often rugged with many possible reaction paths. We provide a survey of these methods, with comments on their applicability and a description of their strengths and weaknesses.

Molecular modeling of freezing of simple fluids confined within carbon nanotubes

We report Monte Carlo simulation results for freezing of Lennard-Jones carbon tetrachloride confined within model multiwalled carbon nanotubes of different diameters. The structure and thermodynamic stability of the confined phases, as well as the transition temperatures, were determined from parallel tempering grand canonical Monte Carlo simulations and free-energy calculations. The simulations show that the adsorbate forms concentric molecular layers that solidify into defective quasi-two-dimensional hexagonal crystals. Freezing in such concentric layers occurs via intermediate phases that show remnants of hexatic behavior, similar to the freezing mechanism observed for slit pores in previous works. The adsorbate molecules in the inner regions of the pore also exhibit changes in their properties upon reduction of temperature. The structural changes in the different regions of adsorbate occur at temperatures above or below the bulk freezing point, depending on pore diameter and distance of the adsorbate molecules from the pore wall. The simulations show evidence of a rich phase behavior in confinement; a number of phases, some of them inhomogeneous, were observed for the pore sizes considered. The multiple transition temperatures obtained from the simulations were found to be in good agreement with recent dielectric relaxation spectroscopy experiments for CCl(4) confined within multiwalled carbon nanotubes.

Dense packing of binary and polydisperse hard spheres

The packing of binary and polydisperse unimodal and bimodal ensembles of hard spheres in the limit of high pressure is studied using a sequential addition algorithm. Upon fixing the number of particles, and their size distribution, the average (maximum) packing fraction is determined for systems of up to 20 000 particles. The structures obtained correspond to amorphous states close to the dense random close packing density. Binary distributions obtained are denser than the equivalent monodisperse distribution and agree with the theoretical prediction for an infinite size ratio limit. Unimodal normal and lognormal polydisperse distributions obtained compare favourably with available simulation and experimental data. Results for bimodal lognormal distributions are presented. In all cases it is seen how an increase in polydispersity increases the packing fraction of the system. The results can be employed to gain insight into optimal formulations for dense emulsions.

Separation of Chemical Reaction Intermediates by Metal–Organic Frameworks

HPLC columns custom-packed with metal-organic framework (MOF) materials are used for the separation of four small intermediates and byproducts found in the commercial synthesis of an important active pharmaceutical ingredient in methanol. In particular, two closely related amines can be separated in the methanol reaction medium using MOFs, but not with traditional C18 columns using an optimized aqueous mobile phase. Infrared spectroscopy, UV-vis spectroscopy, X-ray diffraction, and thermogravimetric analysis are used in combination with molecular dynamic simulations to study the separation mechanism for the best-performing MOF materials. It is found that separation with ZIF-8 is the result of an interplay between the thermodynamic driving force for solute adsorption within the framework pores and the kinetics of solute diffusion into the material pores, while the separation with Basolite F300 is achieved because of the specific interactions between the solutes and Fe(3+) sites. This work, and the exceptional ability to tailor the porous properties of MOF materials, points to prospects for using MOF materials for the continuous separation and synthesis of pharmaceutical compounds.

On the Calculation of Solid-Fluid Contact Angles from Molecular Dynamics

A methodology for the determination of the solid-fluid contact angle, to be employed within molecular dynamics (MD) simulations, is developed and systematically applied. The calculation of the contact angle of a fluid drop on a given surface, averaged over an equilibrated MD trajectory, is divided in three main steps: (i) the determination of the fluid molecules that constitute the interface, (ii) the treatment of the interfacial molecules as a point cloud data set to define a geometric surface, using surface meshing techniques to compute the surface normals from the mesh, (iii) the collection and averaging of the interface normals collected from the post-processing of the MD trajectory. The average vector thus found is used to calculate the Cassie contact angle (i.e., the arccosine of the averaged normal z-component). As an example we explore the effect of the size of a drop of water on the observed solid-fluid contact angle. A single coarse- grained bead representing two water molecules and parameterized using the SAFT-γ Mie equation of state (EoS) is employed, meanwhile the solid surfaces are mimicked using integrated potentials. The contact angle is seen to be a strong function of the system size for small nano-droplets. The thermodynamic limit, corresponding to the infinite size (macroscopic) drop is only truly recovered when using an excess of half a million water coarse-grained beads and/or a drop radius of over 26 nm.

Computer simulations of homogeneous nucleation of benzene from the melt.

Nucleation is the key step in crystallization by which the molecules (or atoms or ions) aggregate together, find the right relative orientations, and start to grow to form the final crystal structure. Since nucleation is an activated step involving a large gap in time scales between molecular motions and the nucleation event itself, nucleation must be studied using rare events methods. We employ a technique developed previously in our group known as aimless shooting [Peters, B.; Trout, B. L. J. Chem. Phys., 2006, 125, 054108], which is based on transition path sampling, to generate reactive trajectories between the disordered and ordered phases of benzene. Using the likelihood maximization algorithm, we analyze the aimless shooting trajectories to identify the key order parameters or collective variables to describe the reaction coordinate for the nucleation of benzene from the melt. We find that the local bond orientation and local relative orientation order parameters are the most important collective variables in describing the reaction coordinate for homogeneous nucleation from the melt, as compared to cluster size and space-averaged order parameters. This study also demonstrates the utility of recently developed order parameters for molecular crystals [Santiso, E. E.; Trout, B. L. J. Chem. Phys., 2011, 134, 064109].

Catalytic role of carbons in methane decomposition for CO-and CO2-free hydrogen generation

Decomposition of methane is an environmentally attractive approach to CO- and CO(2)-free hydrogen production. Using first principles calculations at the density functional theory level, our studies demonstrate that the defective carbons can be used as catalysts for methane decomposition, without the need for other catalysts, such as transition metals or oxides, and the catalytic sites can be regenerated by the deposition of carbon decomposed from methane, to make the hydrogen production a continuous process. Additionally, since no other gases are produced in the process, the cost of CO(2) sequestration and hydrogen purification from CO contamination will be dramatically reduced.

A remarkable shape-catalytic effect of confinement on the rotational isomerization of small hydrocarbons

As part of an effort to understand the effect of confinement by porous carbons on chemical reactions, we have carried out density functional theory calculations on the rotational isomerization of three four-membered hydrocarbons: n-butane, 1-butene, and 1,3-butadiene. Our results show that the interactions with the carbon walls cause a dramatic change on the potential energy surface for pore sizes comparable to the molecular dimensions. The porous material enhances or hinders reactions depending on how similar is the shape of the transition state to the shape of the confining material. The structure of the stable states and their equilibrium distributions are also drastically modified by confinement. Our results are consistent with a doubly exponential behavior of the reaction rates as a function of pore size, illustrating how the shape of a catalytic support can dramatically change the efficiency of a catalyst.

Effect of confinement by porous carbons on the unimolecular decomposition of formaldehyde

As part of an effort to understand the effect of confinement by porous carbons on chemical reactions, we have carried out density functional theory calculations on the unimolecular decomposition of formaldehyde within graphitic carbons. Our results show that the interactions with the carbon walls result in a lowering of the reaction barrier. For larger pores, there is also a shift of the equilibrium towards the formation of carbon monoxide and hydrogen at low temperatures. This trend is reversed for small pore sizes.