Lev Sarkisov

Computational structure characterisation tools in application to ordered and disordered porous materials

In this article, we present a set of computational tools for systematic characterisation of ordered and disordered porous materials. These tools include calculation of the accessible surface area and geometric pore size distribution, analysis of the structure connectivity and percolation analysis of the porous space. We briefly discuss the algorithms behind these calculations. To demonstrate the capabilities of the tools and the type of insights that can be gained from their application, we consider a series of case studies. These case studies include small molecular fragments, several crystalline metal-organic materials, and variants of these materials with induced defects and disorder in their structure. The simulation package is available upon request.

Capillary condensation in disordered porous materials: hysteresis versus equilibrium behavior

We study the interplay between hysteresis and equilibrium behavior in capillary condensation of fluids in mesoporous disordered materials via a mean-field density functional theory of a disordered lattice-gas model. The approach reproduces all major features observed experimentally. We show that the simple van der Waals picture of metastability fails due to the appearance of a complex free-energy landscape with a large number of metastable states. In particular, hysteresis can occur both with and without an underlying equilibrium transition, and thermodynamic consistency is not satisfied along the hysteresis loop.

On the flexibility of metal-organic frameworks.

Occasional, large amplitude flexibility in metal-organic frameworks (MOFs) is one of the most intriguing recent discoveries in chemistry and material science. Yet, there is at present no theoretical framework that permits the identification of flexible structures in the rapidly expanding universe of MOFs. Here, we propose a simple method to predict whether a MOF is flexible, based on treating it as a system of rigid elements, connected by hinges. This proposition is correct in application to MOFs based on rigid carboxylate linkers. We validate the method by correctly classifying known experimental MOFs into rigid and flexible groups. Applied to hypothetical MOFs, the method reveals an abundance of flexibility phenomena, and this seems to be at odds with the proportion of flexible structures among experimentally known MOFs. We speculate that the flexibility of a MOF may constitute an intrinsic impediment on its experimental realization. This highlights the importance of systematic prediction of large amplitude flexibility regimes in MOFs.

Molecular modelling of adsorption in novel nanoporous metal–organic materials

Grand canonical Monte Carlo and molecular dynamics simulations have been performed for methane, n-alkanes, cyclohexane and benzene in two novel nanoporous metal–organic materials. The first material, bipyridine molecular squares, consists of discrete square molecules with corners formed by rhenium complexes and edges formed by bipyridine links, giving a small cavity within each square. The material is considered in both its crystalline form and an amorphous packing of squares. The second material is IRMOF-1, a periodic, crystalline structure also with metal corners and organic bridging units. Adsorption isotherms and self-diffusion coefficients are reported and provide insight into molecular interactions in these materials.

Structure and Phase Transformations of DPPC Lipid Bilayers in the Presence of Nanoparticles: Insights from Coarse-Grained Molecular Dynamics Simulations

In this article, we investigate fluid-gel transformations of a DPPC lipid bilayer in the presence of nanoparticles, using coarse-grained molecular dynamics. Two types of nanoparticles are considered, specifically a 3 nm hydrophobic nanoparticle located in the core of the bilayer and a 6 nm charged nanoparticle located at the interface between the bilayer and water phase. Both negatively and positively charged nanoparticles at the bilayer interface are investigated. We demonstrate that the presence of all types of nanoparticles induces disorder effects in the structure of the lipid bilayer. These effects are characterized using computer visualization of the gel phase in the presence of nanoparticles, radial distribution functions, and order parameters. The 3 nm hydrophobic nanoparticle immersed in the bilayer core and the positively charged nanoparticle at the bilayer surface have no effect on the temperature of the fluid-gel transformation, compared to the bulk case. Interestingly, a negatively charged hydrophobic nanoparticle located at the surface of the bilayer causes slight shift of the fluid-gel transformation to a lower temperature, compared to the bulk bilayer case.

Computer simulation of volatile organic compound adsorption in atomistic models of molecularly imprinted polymers.

Molecularly imprinted polymers (MIPs) offer a unique opportunity to significantly advance volatile organic compound (VOC) sensing technologies and a number of other applications. However, the development of these applications using MIPs has been hindered by poor understanding of the microstructure of MIPs, geometry of binding sites, and the details of molecular recognition processes in these materials. This is further complicated by the vast number of optimization parameters such as building components and processing conditions. Computer simulations and molecular modeling can help us understand adsorption and binding phenomena in MIPs on the molecular level and thus provide a route to more efficient MIP design strategies. So far, molecular models have been either oversimplified or severely limited in length scale, essentially focusing on a single binding site. Here, we propose a more general, atomistically detailed model that describes the microstructure of MIPs. We apply this model to investigate adsorption of pyridine, benzene, and toluene in MIPs and demonstrate that it is able to capture a number of essential experimental features. Therefore, this model can serve as a starting point in computational design and optimization of MIPs.

Interactions of Phospholipid Bilayers with Several Classes of Amphiphilic alpha-Helical Peptides: Insights from Coarse-Grained Molecular Dynamics Simulations

In this article, we focus on several types of interactions between lipid membranes and alpha-helical peptides, based on the distribution of hydrophobic and hydrophilic residues along the helix. We employ a recently proposed coarse-grained model MARTINI and test its ability to capture diverse types of behavior. MARTINI provides useful insights on the formation of barrel-stave and toroidal pores and on the relation between these two mechanisms. Amphipathic nonspanning peptides are also described with sufficient accuracy. The picture is not as clear for fusion and transmembrane peptides. For each class of peptides, we calculate the potential of mean force (PMF) for peptide translocation across the lipid bilayer and demonstrate that each class has a distinct shape of PMF. The reliability of these calculations, as well as wider implications of the results, is discussed.

Homogeneous Hydrophobic-Hydrophilic Surface Patterns Enhance Permeation of Nanoparticles through Lipid Membranes.

We employ coarse-grained molecular dynamics simulations to understand why certain interaction patterns on the surface of a nanoparticle promote its translocation through a lipid membrane. We demonstrate that switching from a random, heterogeneous distribution of hydrophobic and hydrophilic areas on the surface of a nanoparticle to even, homogeneous patterns substantially flattens the translocation free-energy profile and dramatically enhances permeation. We then proceed to construct a more detailed coarse-grained model of a nanoparticle with flexible hydrophobic and hydrophilic ligands arranged into striped domains. Molecular dynamics simulations of these nanoparticles show that the terminal groups of the ligands tend to arrange themselves into homogeneous patterns, despite the underlying striped domains. These observations are linked to recent experimental studies.

Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion

Intracellular uptake of nanoparticles (NPs) may induce phase transitions, restructuring, stretching, or even complete disruption of the cell membrane. Therefore, NP cytotoxicity assessment requires a thorough understanding of the mechanisms by which these engineered nanostructures interact with the cell membrane. In this study, extensive Coarse-Grained Molecular Dynamics (MD) simulations are performed to investigate the partitioning of an anionic, ligand-decorated NP in model membranes containing dipalmitoylphosphatidylcholine (DPPC) phospholipids and different concentrations of cholesterol. Spontaneous fusion and translocation of the anionic NP is not observed in any of the 10-µs unbiased MD simulations, indicating that longer timescales may be required for such phenomena to occur. This picture is supported by the free energy analysis, revealing a considerable free energy barrier for NP translocation across the lipid bilayer. 5-µs unbiased MD simulations with the NP inserted in the bilayer core reveal that the hydrophobic and hydrophilic ligands of the NP surface rearrange to form optimal contacts with the lipid bilayer, leading to the so-called snorkeling effect. Inside cholesterol-containing bilayers, the NP induces rearrangement of the structure of the lipid bilayer in its vicinity from the liquid-ordered to the liquid phase spanning a distance almost twice its core radius (8–10 nm). Based on the physical insights obtained in this study, we propose a mechanism of cellular anionic NPpartitioning, which requires structural rearrangements of both the NP and the bilayer, and conclude that the translocation of anionic NPs through cholesterol-rich membranes must be accompanied by formation of cholesterol-lean regions in the proximity of NPs.

Experiences with the publicly available multipurpose simulation code, Music

It has been 10 years since the original publication that presented Music, a multipurpose simulation code, written in Fortran 90. Since then, the code has been downloaded over 350 times and used in over 100 publications. In this study, we summarise the philosophy behind Music, its features and capabilities, and review some recent applications of the code to problems ranging from adsorption in porous materials to tribology and free energy analysis. We also reflect upon our experiences with having a computer simulation code available to the public and highlight some current needs in the development of flexible, versatile and well-documented software for Monte Carlo simulations.