First-principle molecular dynamics with ultrasoft pseudopotentials: parallel implementation and application to extended bio-inorganic system

We present a plane-wave ultrasoft pseudopotential implementation of first-principle molecular dynamics, which is well suited to model large molecular systems containing transition metal centers. We describe an efficient strategy for parallelization that includes special features to deal with the augmented charge in the contest of Vanderbilt's ultrasoft pseudopotentials. We also discuss a simple approach to model molecular systems with a net charge and/or large dipole/quadrupole moments. We present test applications to manganese and iron porphyrins representative of a large class of biologically relevant metallorganic systems. Our results show that accurate Density-Functional Theory calculations on systems with several hundred atoms are feasible with access to moderate computational resources.Comment: 29 pages, 4 Postscript figures, revtex

Porphyrin-based metal-organic frameworks for solar fuel synthesis photocatalysis: band gap tuning via iron substitutions

Photocatalysts based on metal-organic frameworks (MOFs) are very promising due to a combination of high tuneability and convenient porous structure. Introducing porphyrin units within MOFs is a potential route to engineer these natural photosynthesis molecular catalysts into artificial photosynthesis heterogeneous catalysts. Using computer simulations based on density functional theory, we explore how to modify the electronic structure of porphyrin-based MOFs to make them suitable for the photocatalysis of solar fuel synthesis via water splitting or carbon dioxide reduction. In particular we have investigated the effect that Fe substitutions have on the electronic properties of porphyrin-based metal organic frameworks. By aligning the electron levels with a vacuum reference, we show that Fe at the porphyrin metal centre has the effect of slightly raising the position of the valence band edge, whereas Fe at the octahedral metal node has the ability to significantly lower the position of the conduction band edge on the absolute scale. Iron is therefore a very useful dopant to engineer the band structure and alignment of these MOFs. We find that the porphyrin-based structure with Al in the octahedral sites and Zn in the porphyrin centres has a band gap that is slightly too wide to take advantage of visible-light solar radiation, while the structure with Fe in the octahedral sites has bandgaps that are too narrow for water splitting photocatalysis. We then show that the optimal composition is achieved by partial substitution of Al by Fe at the octahedral sites, while keeping Zn at the porphyrin centres. Our study demonstrates that porphyrin-based MOFs can be engineered to display intrinsic photocatalytic activity in solar fuel synthesis reactions

Resolving transition metal chemical space: feature selection for machine learning and structure-property relationships

Machine learning (ML) of quantum mechanical properties shows promise for accelerating chemical discovery. For transition metal chemistry where accurate calculations are computationally costly and available training data sets are small, the molecular representation becomes a critical ingredient in ML model predictive accuracy. We introduce a series of revised autocorrelation functions (RACs) that encode relationships between the heuristic atomic properties (e.g., size, connectivity, and electronegativity) on a molecular graph. We alter the starting point, scope, and nature of the quantities evaluated in standard ACs to make these RACs amenable to inorganic chemistry. On an organic molecule set, we first demonstrate superior standard AC performance to other presently-available topological descriptors for ML model training, with mean unsigned errors (MUEs) for atomization energies on set-aside test molecules as low as 6 kcal/mol. For inorganic chemistry, our RACs yield 1 kcal/mol ML MUEs on set-aside test molecules in spin-state splitting in comparison to 15-20x higher errors from feature sets that encode whole-molecule structural information. Systematic feature selection methods including univariate filtering, recursive feature elimination, and direct optimization (e.g., random forest and LASSO) are compared. Random-forest- or LASSO-selected subsets 4-5x smaller than RAC-155 produce sub- to 1-kcal/mol spin-splitting MUEs, with good transferability to metal-ligand bond length prediction (0.004-5 {\AA} MUE) and redox potential on a smaller data set (0.2-0.3 eV MUE). Evaluation of feature selection results across property sets reveals the relative importance of local, electronic descriptors (e.g., electronegativity, atomic number) in spin-splitting and distal, steric effects in redox potential and bond lengths.Comment: 43 double spaced pages, 11 figures, 4 table

Electrocatalytic and Photoelectrosynthetic Hydrogen Production using Metalloporphyrins and Molecular-modified Gallium Phosphide Photocathodes

abstract: Metalloporphyrins represent a class of molecular electrocatalysts for driving energy relevant half-reactions, including hydrogen evolution and carbon dioxide reduction. As electrocatalysts, they provide a strategy, and potential structural component, for linking renewable energy sources with the production of fuels and other value-added chemicals. In this work, porphyrins are used as structural motifs for exploring structure-function relationships in electrocatalysis and as molecular building blocks for assembling photoelectrochemical assemblies leveraging the light capture and conversion properties of a gallium phosphide (GaP) semiconductor. These concepts are further covered in Chapter 1. A direct one-step method to chemically graft metalloporphyrins to GaP surfaces is described in Chapter 2. Structural characterization of the hybrid assemblies is achieved using surface-sensitive spectroscopic methods, and functional performance for photoinduced hydrogen production is demonstrated via three-electrode electrochemical measurement combined with product analysis using gas chromatography. In Chapter 3, preparation of a novel cobalt porphyrin modified with 3-fluorophenyl groups at all four meso-positions of the porphyrin ring and a single 4-vinylphenyl surface attachment group at one of the β-positions is described. Electrochemical measurements show the 3-fluorophenyl groups perturb the reduction potentials of the complex to more positive values as compared to non-fluorinated analogs, illustrating synthetic control over the redox properties of the catalysts. The use of grazing angle attenuated total reflectance Fourier transform infrared spectroscopy to characterize chemically modified GaP surfaces containing grafted cobalt fluoro-porphyrins is presented in Chapter 4. In these hybrid constructs, porphyrin surface attachment is achieved using either a two-step method involving coordination of cobalt fluoro-porphyrin metal centers to nitrogen sites on an initially applied thin-film polypyridyl surface coating, or via a direct modification strategy using a cobalt fluoro-porphyrin precursor bearing a covalently bonded 4- vinylphenyl surface attachment group. Finally, Chapter 5 describes binuclear copper porphyrins in which two copper porphyrin macrocycles are doubly fused at the meso-β positions are shown to be active electrocatalysts for the hydrogen evolution reaction. The enhancement in catalytic performance over analogous non-fused copper porphyrins indicates extended macrocycles provide an advantageous structural motif and design element for preparing electrocatalysts that activate small molecules of consequence to renewable energy.Dissertation/ThesisDoctoral Dissertation Chemistry 201

Bioinorganic Chemistry

This book covers material that could be included in a one-quarter or one-semester course in bioinorganic chemistry for graduate students and advanced undergraduate students in chemistry or biochemistry. We believe that such a course should provide students with the background required to follow the research literature in the field. The topics were chosen to represent those areas of bioinorganic chemistry that are mature enough for textbook presentation. Although each chapter presents material at a more advanced level than that of bioinorganic textbooks published previously, the chapters are not specialized review articles. What we have attempted to do in each chapter is to teach the underlying principles of bioinorganic chemistry as well as outlining the state of knowledge in selected areas. We have chosen not to include abbreviated summaries of the inorganic chemistry, biochemistry, and spectroscopy that students may need as background in order to master the material presented. We instead assume that the instructor using this book will assign reading from relevant sources that is appropriate to the background of the students taking the course. For the convenience of the instructors, students, and other readers of this book, we have included an appendix that lists references to reviews of the research literature that we have found to be particularly useful in our courses on bioinorganic chemistry