Silica is both ubiquitous in nature and important in a wide range of applications ranging from drug delivery to catalysis. This has spawned significant interest in modeling silica, particularly the amorphous solid, and its interactions with liquids, adsorbates, and embedded active sites. One of the challenges is developing descriptions that accurately represent the synthesized materials used in experiments when key properties, such as the surface roughness and distribution of silanol groups, cannot be readily measured. Here, we implement a simple, tunable melt-cleave-quench-functionalize approach to create amorphous silica slabs with variable characteristics. We use it to generate 2000 atomistically distinct slab models, based on the widely used the van Beest, Kramer, van Santen (BKS) potential, that differ in their atomistic roughness, defect site density, ring distribution, silanol density, and spatial arrangement of silanols. The surfaces are demonstrated to be consistent with available experimental data and stable within the ReaxFF bond order-based reactive force field. These amorphous silica slab models should thus be of use in a variety of computational studies of interfacial properties.

The use of gene therapeutics, including short interfering RNA (siRNA), is limited by the lack of efficient delivery systems. An appealing approach to deliver gene therapeutics involves noncovalent complexation with cell penetrating peptides (CPPs) which are able to penetrate the cell membranes of mammals. Although a number of CPPs have been discovered, our understanding of their complexation and translocation of siRNA is as yet insufficient. Here, we report on computational studies comparing the binding affinities of CPPs with siRNA, considering a variety of CPPs. Specifically, seventeen CPPs from three different categories, cationic, amphipathic, and hydrophobic CPPs, were studied. Molecular mechanics were used to minimize structures, while molecular docking calculations were used to predict the orientation and favorability of sequentially binding multiple peptides to siRNA. Binding scores from docking calculations were highest for amphipathic peptides over cationic and hydrophobic peptides. Results indicate that initial complexation of peptides will likely occur along the major groove of the siRNA, driven by electrostatic interactions. Subsequent binding of CPPs is likely to occur in the minor groove and later on bind randomly, to siRNA or previously bound CPPs, through hydrophobic interactions. However, hydrophobic CPPs do not show this binding pattern. Ultimately binding yields a positively charged nanoparticle capable of noninvasive cellular import of therapeutic molecules.

Anions play significant roles in the separation of lanthanides and actinides. The molecular-scale details of how these anions behave at aqueous interfaces are not well understood, especially at high ionic strengths. Here, we describe the interfacial structure of thiocyanate anions at a soft charged interface up to 5 M bulk concentration with combined classical and phase-sensitive vibrational sum frequency generation (PS-VSFG) spectroscopy, and molecular dynamics (MD) simulations. At low concentrations thiocyanate ions are mostly oriented with their sulfur end pointing towards the charged surfactants. VSFG signal reaches a plateau around 100 mM bulk concentration, followed by significant changes above 1 M. At high concentrations a new thiocyanate population emerges with their sulfur end pointing towards the bulk liquid. The -CN stretch frequency is different for up and down oriented SCNions, indicating different coordination environments. These results provide key molecular-level insights for the interfacial behavior of complex anions in highly concentrated solutions.

Extractant aggregation in liquid–liquid extraction organic phases impacts extraction energetics and is related to the deleterious efficiency-limiting liquid–liquid phase transition known as third phase formation.

Molecular metal complexes such as MCl x react readily with hydroxyl-terminated surfaces to produce some of the “single-atom” catalysts used in important large-scale commercial reactions, including olefin metathesis, polymerization, and epoxidation. While the local oxide environment can vary at each metal site, the manner and degree to which these differences impact the catalytic activities of individual sites are poorly understood. In this work, we develop a computational framework to model the grafting of metal complexes onto amorphous supports and apply the framework to examine TiCl4 grafting onto amorphous silica. We use density functional theory (DFT) to calculate free energies for TiCl4 reactions at vicinal silanol sites. The kinetics and thermodynamics depend on the dihedral angle between the silanols. Vicinal silanol pairs with small dihedral angles are predicted to yield bipodal [(SiO)2TiCl2] sites initially, but they react further with TiCl4 vapor to give vicinal pairs of monopodal sites, [  SiOTiCl3]. In contrast, silanol pairs with large dihedral angles yield vicinal pairs of monopodal Ti sites directly. The DFT results were used to construct a population balance model to describe the kinetics of TiCl4 grafting onto nonuniform sites of an atomistic model for amorphous silica. The solution of the population balance model predicts that the majority of the vicinal pairs graft as bipodal [(SiO)2TiCl2] sites first and then slowly convert to monopodal [SiOTiCl3] sites. The predictions provide a plausible explanation for the variability in the populations of monopodal and bipodal sites previously reported for TiCl4 grafting.