Working with benchmark datasets in the Cuby framework.

The development and benchmarking of computational chemistry methods rely on comparison with benchmark data. More and larger benchmark datasets are becoming available, and working efficiently with them is a necessity. The Cuby framework provides rich functionality for working with datasets, comes with many ready-to-use predefined benchmark sets, and interfaces with a wide range of computational chemistry software packages. Here, we review the tools Cuby provides for working with datasets and provide examples of more advanced workflows, such as handling large numbers of computations on high performance computing resources and reusing previously computed data. Cuby has also been extended recently to include two important benchmark databases, NCIAtlas and GMTKN55.

Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin.

As the field of nanoelectronics based on biomolecules such as peptides and proteins rapidly grows, there is a need for robust computational methods able to reliably predict charge transfer properties at bio/metallic interfaces. Traditionally, hybrid quantum-mechanical/molecular-mechanical techniques are employed for systems where the electron hopping transfer mechanism is applicable to determine physical parameters controlling the thermodynamics and kinetics of charge transfer processes. However, these approaches are limited by a relatively high computational cost when extensive sampling of a configurational space is required, like in the case of soft biomatter. For these applications, semi-empirical approaches such as the perturbed matrix method (PMM) have been developed and successfully used to study charge-transfer processes in biomolecules. Here, we explore the performance of PMM on prototypical redox-active protein azurin in various environments, from solution to vacuum interfaces with gold surfaces and protein junction. We systematically benchmarked the robustness and convergence of the method with respect to the quantum-centre size, size of the Hamiltonian, number of samples, and level of theory. We show that PMM can adequately capture all the trends associated with the structural and electronic changes related to azurin oxidation at bio/metallic interfaces.

Reorganization free energy of copper proteins in solution, in vacuum, and on metal surfaces.

Metalloproteins, known to efficiently transfer electronic charge in biological systems, recently found their utilization in nanobiotechnological devices where the protein is placed into direct contact with metal surfaces. The feasibility of oxidation/reduction of the protein redox sites is affected by the reorganization free energies, one of the key parameters determining the transfer rates. While their values have been measured and computed for proteins in their native environments, i.e., in aqueous solution, the reorganization free energies of dry proteins or proteins adsorbed to metal surfaces remain unknown. Here, we investigate the redox properties of blue copper protein azurin, a prototypical redox-active metalloprotein previously probed by various experimental techniques both in solution and on metal/vacuum interfaces. We used a hybrid quantum mechanical/molecular mechanical computational technique based on density functional theory to explore protein dynamics, flexibility, and corresponding reorganization free energies in aqueous solution, vacuum, and on vacuum gold interfaces. Surprisingly, the reorganization free energy only slightly decreases when azurin is dried because the loss of the hydration shell leads to larger flexibility of the protein near its redox site. At the vacuum gold surfaces, the energetics of the structure relaxation depends on the adsorption geometry; however, significant reduction of the reorganization free energy was not observed. These findings have important consequences for the charge transport mechanism in vacuum devices, showing that the free energy barriers for protein oxidation remain significant even under ultra-high vacuum conditions.

Functional panchromatic BODIPY dyes with near-infrared absorption: design, synthesis, characterization and use in dye-sensitized solar cells.

We report two novel functional dyes based on a boron-dipyrromethene (BODIPY) core displaying a panchromatic absorption with an extension to the near-infrared (NIR) range. An innovative synthetic approach for preparing the 2,3,5,6-tetramethyl-BODIPY unit is disclosed, and a versatile way to further functionalize this unit has been developed. The optoelectronic properties of the two dyes were computed by density functional theory modelling (DFT) and characterized through UV-vis spectroscopy and cyclic voltammetry (CV) measurements. Finally, we report preliminary results obtained using these functional dyes as photosensitizers in dye-sensitized solar cells (DSSCs).