Density functional theory and DFT+U study of transition metal porphines adsorbed on Au(111) surfaces and effects of applied electric fields

We apply Density Functional Theory (DFT) and the DFT+U technique to study the adsorption of transition metal porphine molecules on atomistically flat Au(111) surfaces. DFT calculations using the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional correctly predict the palladium porphine (PdP) low-spin ground state. PdP is found to adsorb preferentially on gold in a flat geometry, not in an edgewise geometry, in qualitative agreement with experiments on substituted porphyrins. It exhibits no covalent bonding to Au(111), and the binding energy is a small fraction of an eV. The DFT+U technique, parameterized to B3LYP predicted spin state ordering of the Mn d-electrons, is found to be crucial for reproducing the correct magnetic moment and geometry of the isolated manganese porphine (MnP) molecule. Adsorption of Mn(II)P on Au(111) substantially alters the Mn ion spin state. Its interaction with the gold substrate is stronger and more site-specific than PdP. The binding can be partially reversed by applying an electric potential, which leads to significant changes in the electronic and magnetic properties of adsorbed MnP, and ~ 0.1 Angstrom, changes in the Mn-nitrogen distances within the porphine macrocycle. We conjecture that this DFT+U approach may be a useful general method for modeling first row transition metal ion complexes in a condensed-matter setting.Comment: 14 pages, 6 figure

Theoretical EXAFS studies of a model of the oxygen-evolving complex of photosystem II obtained with the quantum cluster approach

The oxygen-evolving complex (OEC) of photosystem II is the only natural system that can form O2 from water and sunlight and it consists of a Mn4Ca cluster. In a series of publications, Siegbahn has developed a model of the OEC with the quantum mechanical (QM) cluster approach that is compatible with available crystal structures, able to form O2 with a reasonable energetic barrier, and has a significantly lower energy than alternative models. In this investigation, we present a method to restrain a QM geometry optimization toward experimental polarized extended X-ray absorption fine structure (EXAFS) data. With this method, we show that the cluster model is compatible with the EXAFS data and we obtain a refined cluster model that is an optimum compromise between QM and polarized EXAFS data. (C) 2012 Wiley Periodicals, Inc

Stereoelectronic interactions and molecular properties: An NBO-based study of uracil

The contributions of stereoelectronic interactions to several molecular properties are used to analyze the propagation of information between different parts of the uracil molecule with a method that is based on the natural bond orbital (NBO) deletion technique. The emphasis is not on the effect of the contributions of localized orbitals to selected properties but rather on their interactions, giving information that is complementary to that resulting from a standard localized molecular orbital contribution. The analysis of how information between orbitals is transmitted throughout the molecule allows interpretation of the ways in which an interaction can affect a molecular property localized in the same region or in a different region of the molecule. A network of stereoelectronic interactions was identified in the uracil molecule, and the relative influences of the interactions that transmit information between different parts of the molecule were evaluated. An analysis was performed over localized properties on atoms and bonds of the two carbonyl groups, namely bond orders, distribution of electronic charge, and NMR shielding tensors. Interactions n(N3) → π*(C4=O) and n(N1) → π*(C5=C6) were the most important delocalizations that carry information concerning the change of substituents at C-5, whereas interactions n(N1) → π*(C2=O) and n(N3) rarr; π*(C2=O) were those mainly responsible for transmitting this information to the C-2 uracil carbonyl (C2=O) properties.Fil: Sproviero, Eduardo M.. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Orgánica; ArgentinaFil: Burton, Gerardo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Orgánica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Unidad de Microanálisis y Métodos Físicos en Química Orgánica. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Unidad de Microanálisis y Métodos Físicos en Química Orgánica; Argentin

Computational insights into the O2-evolving complex of photosystem II

Mechanistic investigations of the water-splitting reaction of the oxygen-evolving complex (OEC) of photosystem II (PSII) are fundamentally informed by structural studies. Many physical techniques have provided important insights into the OEC structure and function, including X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy as well as mass spectrometry (MS), electron paramagnetic resonance (EPR) spectroscopy, and Fourier transform infrared spectroscopy applied in conjunction with mutagenesis studies. However, experimental studies have yet to yield consensus as to the exact configuration of the catalytic metal cluster and its ligation scheme. Computational modeling studies, including density functional (DFT) theory combined with quantum mechanics/molecular mechanics (QM/MM) hybrid methods for explicitly including the influence of the surrounding protein, have proposed chemically satisfactory models of the fully ligated OEC within PSII that are maximally consistent with experimental results. The inorganic core of these models is similar to the crystallographic model upon which they were based, but comprises important modifications due to structural refinement, hydration, and proteinaceous ligation which improve agreement with a wide range of experimental data. The computational models are useful for rationalizing spectroscopic and crystallographic results and for building a complete structure-based mechanism of water-splitting in PSII as described by the intermediate oxidation states of the OEC. This review summarizes these recent advances in QM/MM modeling of PSII within the context of recent experimental studies. © 2008 Springer Science+Business Media B.V

Quantum mechanics/molecular mechanics study of the catalytic cycle of water splitting in photosystem II

This paper investigates the mechanism of water splitting in photosystem II (PSII) as described by chemically sensible models of the oxygen-evolving complex (OEC) in the S0-S4 states. The reaction is the paradigm for engineering direct solar fuel production systems since it is driven by solar light and the catalyst involves inexpensive and abundant metals (calcium and manganese). Molecular models of the OEC Mn3CaO4Mn catalytic cluster are constructed by explicitly considering the perturbational influence of the surrounding protein environment according to state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, in conjunction with the X-ray diffraction (XRD) structure of PSII from the cyanobacterium Thermosynechococcus elongatus. The resulting models are validated through direct comparisons with high-resolution extended X-ray absorption fine structure spectroscopic data. Structures of the S3, S4, and S 0 states include an additional μ-oxo bridge between Mn(3) and Mn(4), not present in XRD structures, found to be essential for the deprotonation of substrate water molecules. The structures of reaction intermediates suggest a detailed mechanism of dioxygen evolution based on changes in oxidization and protonation states and structural rearrangements of the oxomanganese cluster and surrounding water molecules. The catalytic reaction is consistent with substrate water molecules coordinated as terminal ligands to Mn(4) and calcium and requires the formation of an oxyl radical by deprotonation of the substrate water molecule ligated to Mn(4) and the accumulation of four oxidizing equivalents. The oxyl radical is susceptible to nucleophilic attack by a substrate water molecule initially coordinated to calcium and activated by two basic species, including CP43-R357 and the μ-oxo bridge between Mn(3) and Mn(4). The reaction is concerted with water ligand exchange, swapping the activated water by a water molecule in the second coordination shell of calcium. © 2008 American Chemical Society

Quantum mechanics/molecular mechanics structural models of the oxygen-evolving complex of photosystem II

The annual production of 260 Gtonnes of oxygen, during the process of photosynthesis, sustains life on earth. Oxygen is produced in the thylakoid membranes of green-plant chloroplasts and the internal membranes of cyanobacteria by photocatalytic water oxidation at the oxygen-evolving complex (OEC) of photosystem II (PSII). Recent breakthroughs in X-ray crystallography and advances in quantum mechanics/molecular mechanics (QM/MM) hybrid methods have enabled the construction of chemically sensible models of the OEC of PSII. The resulting computational structural models suggest the complete ligation of the catalytic center by amino acid residues, water, hydroxide and chloride, as determined from the intrinsic electronic properties of the oxomanganese core and the perturbational influence of the surrounding protein environment. These structures are found to be consistent with available mechanistic data, and are also compatible with X-ray diffraction models and extended X-ray absorption fine structure measurements. It is therefore conjectured that these OEC models are particularly relevant for the elucidation of the catalytic mechanism of water oxidation. © 2006 Elsevier Ltd. All rights reserved

A model of the oxygen-evolving center of photosystem II predicted by structural refinement based on EXAFS simulations

A refined computational structural model of the oxygen-evolving complex (OEC) of photosystem II (PSII) is introduced. The model shows that the cuboidal core Mn3CaO4 with a dangler Mn ligated to a corner μ4-oxide ion is maximally consistent with the positioning of the amino acids around the metal cluster as characterized by XRD models and high-resolution spectroscopic data, including polarized EXAFS of oriented single crystals and isotropic EXAFS. It is, therefore, natural to expect that the proposed structural model should be particularly useful to establish the structure of the OEC, consistently with high-resolution spectroscopic data, and for elucidating the mechanism of water-splitting in PSII as described by the intermediate oxidation states of the EC along the catalytic cycle. Copyright © 2008 American Chemical Society

PHILOSOPHICAL TRANSACTIONS -OF THE ROYAL SOCIETY QM/MM computational studies of substrate water binding to the oxygen-evolving centre of photosystem II

This paper reports computational studies of substrate water binding to the oxygen-evolving centre (OEC) of photosystem II (PSII), completely ligated by amino acid residues, water, hydroxide and chloride. The calculations are based on quantum mechanics/molecular mechanics hybrid models of the OEC of PSII, recently developed in conjunction with the X-ray crystal structure of PSII from the cyanobacterium Thermosynechococcus elongatus. The model OEC involves a cuboidal Mn3Ca04Mn metal cluster with three closely associated manganese ions linked to a single |Li4-oxo-ligated Mn ion, often called the 'dangling manganese'. Two water molecules bound to calcium and the dangling manganese are postulated to be substrate molecules, responsible for dioxygen formation. It is found that the energy barriers for the Mn(4)-bound water agree nicely with those of model complexes. However, the barriers for Ca-bound waters are substantially larger. Water binding is not simply correlated to the formal oxidation states of the metal centres but rather to their corresponding electrostatic potential atomic charges as modulated by charge-transfer interactions. The calculations of structural rearrangements during water exchange provide support for the experimental finding that the exchange rates with bulk lsO-labelled water should be smaller for water molecules coordinated to calcium than for water molecules attached to the dangling manganese. The models also predict that the Sx->S2 transition should produce opposite effects on the two water exchange rates