Sebastian Metz

ChemShell—a modular software package for QM/MM simulations

ChemShell is a modular computational chemistry package with a particular focus on hybrid quantum mechanical/molecular mechanical (QM/MM) simulations. A core set of chemical data handling modules and scripted interfaces to a large number of quantum chemistry and molecular modeling packages underpin a flexible QM/MM scheme. ChemShell has been used in the study of small molecules, molecular crystals, biological macromolecules such as enzymes, framework materials including zeolites, ionic solids, and surfaces. We outline the range of QM/MM coupling schemes and supporting functions for system setup, geometry optimization, and transition‐state location (including those from the open‐source DL‐FIND optimization library). We discuss recently implemented features allowing a more efficient treatment of long range electrostatic interactions, X‐ray based quantum refinement of crystal structures, free energy methods, and excited‐state calculations. ChemShell has been ported to a range of parallel computers and we describe a number of options including parallel execution based on the message‐passing capabilities of the interfaced packages and task‐farming for applications in which a number of individual QM, MM, or QM/MM calculations can performed simultaneously. We exemplify each of the features by brief reference to published applications.

DL_MESO: highly scalable mesoscale simulations

DL_MESO is a parallel mesoscale simulation package capable of dissipative particle dynamics and the lattice Boltzmann equation method. It has been developed at Daresbury Laboratory for the United Kingdom Collaborative Computational Project known as CCP5. Capable of addressing industrially relevant tasks, but written to support academic research, it has a wide range of applications and scales to thousands of processors on high-performance computing platforms yet runs efficiently on smaller commodity clusters and single processor personal computers. This article serves as a guide to a variety of users, describing the functionality, performance and structure of this simulation package. Representative examples highlighting the capabilities of DL_MESO are given for each of the two methodologies available. Future directions for the package are discussed towards the end of the article.

Graphene-based acceptor molecules for organic photovoltaic cells: a predictive study identifying high modularity and morphological stability

Ideal donor:acceptor pairs are required to improve organic photovoltaic lifetimes and efficiencies. Here an idealized donor:acceptor for organic solar cells is predicted. Circular and triangular graphene-based hexabenzocoronenes are shown, in conjunction with the energetically well-placed poly(3-oxypentylthiophene), to provide requisite HOMO/LUMO levels for efficient charge transfer through columnar structures and hole/electron extraction. Circular hexabenzocoronenes are furthermore adaptable to energy-level modulation by targeted substitutions.

A perspective on using experiment and theory to identify design principles in dye-sensitized solar cells

ABSTRACT Dye-sensitized solar cells (DSCs) have been the subject of wide-ranging studies for many years because of their potential for large-scale manufacturing using roll-to-roll processing allied to their use of earth abundant raw materials. Two main challenges exist for DSC devices to achieve this goal; uplifting device efficiency from the 12 to 14% currently achieved for laboratory-scale ‘hero’ cells and replacement of the widely-used liquid electrolytes which can limit device lifetimes. To increase device efficiency requires optimized dye injection and regeneration, most likely from multiple dyes while replacement of liquid electrolytes requires solid charge transporters (most likely hole transport materials – HTMs). While theoretical and experimental work have both been widely applied to different aspects of DSC research, these approaches are most effective when working in tandem. In this context, this perspective paper considers the key parameters which influence electron transfer processes in DSC devices using one or more dye molecules and how modelling and experimental approaches can work together to optimize electron injection and dye regeneration. Graphical Abstract This paper provides a perspective that theory and experiment are best used in tandem to study DSC devices

Cooperative Modes of Action of Antimicrobial Peptides Characterized with Atomistic Simulations: A Study on Cecropin B

Antimicrobial peptides (AMPs) are widely occurring host defense agents of interest as one route for addressing the growing problem of multidrug-resistant pathogens. Understanding the mechanisms behind their antipathogen activity is instrumental in designing new AMPs. Herein, we present an all-atom molecular dynamics and free energy study on cecropin B (CB) and its constituent domains. We find a cooperative mechanism in which CB inserts into an anionic model membrane with its amphipathic N-terminal segment, supported by the hydrophobic C-terminal segment of a second peptide. The two peptides interact via a Glu···Lys salt bridge and together sustain a pore in the membrane. Using a modified membrane composition, we demonstrate that when the lower leaflet is overall neutral, insertion of the cationic segment is retarded and thus this mode of action is membrane specific. The observed mode of action utilizes a flexible hinge, a common structural motif among AMPs, which allows CB to insert into the membrane using either or both termini. Data from both unbiased trajectories and enhanced sampling simulations indicate that a requirement for CB to be an effective AMP is the interaction of its hydrophobic C-terminal segment with the membrane. Simulations of these segments in isolation reveal their aggregation in the membrane and a different mechanism of supporting pore formation. Together, our results show the complex interaction of different structural motifs of AMPs and, in particular, a potential role for electronegative side chains in an overall cationic AMP.