Diastereoselective Hydroxylation of --Butanesulfinyl Imines with 2-(Phenylsulfonyl)-3-phenyloxaziridine (Davis Oxaziridine).

The diastereoselective α-hydroxylation of --butanesulfinyl metallodienenamine and metalloenamines with Davis oxaziridine affords α-hydroxy -sulfinyl imines with 50-88% yield and up to 98:2 diastereomeric ratio. Dramatic changes in diastereoselectivity and stereoselectivity were observed by choice of metal bases. The mechanistic understanding for the switch in diastereoselectivity was assisted by DFT computational modeling, which suggests the facial approach is governed by aza-enolate geometry.

Intramolecular Natural Energy Decomposition Analysis: Applications to the Rational Design of Foldamers.

We describe an intramolecular version of the natural energy decomposition analysis (NEDA), with the aim of evaluating interactions between molecular fragments across covalent bonds. The electronic energy in intramolecular natural energy decomposition analysis (INEDA) is divided into electrical, core, and charge transfer components. The INEDA method describes the fragments using the nonfragmented electronic density, and, therefore, there are no limitations in how to choose the boundary orbital.

A DFT/B3LYP study of the mechanisms of the O formation reaction catalyzed by the [(terpy)(HO)Mn(O)Mn(OH)(terpy)](NO) complex: A paradigm for photosystem II.

We present a theoretical study of the reaction pathway for dioxygen molecular formation catalyzed by the [(terpy)(HO)Mn(O)Mn(OH) (terpy)](NO) (terpy=2,2':6',2″-terpyridine) complex based on DFT-B3LYP calculations. In the initial state of the reaction, a partial oxido radical (0.44 spins) is formed ligated to Mn.

Geometrical properties of the manganese(iv)/iron(iii) cofactor of Chlamydia trachomatis ribonucleotide reductase unveiled by simulations of XAS spectra.

Using simulations of Mn/Fe K-edge X-ray absorption spectroscopy (XAS), combined with DFT-optimized structural models and direct comparisons with available experimental data, we determine geometrical and electronic properties of the Mn-Fe active site of Chlamydia trachomatis (Ct) of ribonucleotide reductase (RNR). In the post-edge XAS energy range, we use extended X-ray absorption fine structure (EXAFS) data, to acquire absorber-scatterer geometrical information around each absorber metal center. For this task, we apply a protocol that evaluates Debye-Waller factors in scattering paths instead of scattering shells to fit the experimental EXAFS.

Opsin Effect on the Electronic Structure of the Retinylidene Chromophore in Rhodopsin.

Direct examination of experimental NMR parameters combined with electronic structure analysis was used to provide a first-principle interpretation of NMR experiments and give a precise evaluation of how the electronic perturbation of the protein environment affects the electronic properties of the retinylidene chromophere in rhodopsin. To this end, we pursued a theoretical analysis using a combination of tools including quantum mechanics/molecular mechanics (QM/MM) at the Density Functional Theory (DFT) level, in conjunction with gauge independent atomic orbital (GIAO) calculations of (13)C NMR chemical shieldings and (1)J(CC) spin-spin coupling constants obtained with the Coupled Perturbed DFT (CPDFT) method. The opsin effect on the retinylidene chromophere is interpreted as an inductive effect of Glu-113 which readjusts the weighting factors of resonance substructures of the conjugated chain of the chromophere.

Reversible visible-light photooxidation of an oxomanganese water-oxidation catalyst covalently anchored to TiO2 nanoparticles.

Several polynuclear transition-metal complexes, including our own dinuclear di-μ-oxo manganese compound [H(2)O(terpy)Mn(III)(μ-O)(2)Mn(IV)(terpy)H(2)O](NO(3))(3) (1, terpy = 2,2':6',2''-terpyridine), have been reported to be homogeneous catalysts for water oxidation. This paper reports the covalent attachment of 1 onto nanoparticulate TiO(2) surfaces using a robust chromophoric linker L. L, a phenylterpy ligand attached to a 3-phenyl-acetylacetonate anchoring moiety via an amide bond, absorbs visible light and leads to photoinduced interfacial electron transfer into the TiO(2) conduction band.

The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules.

Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and structural refinement of macrobiomolecules (e.g., proteins and nucleic acids).

Computational studies of the O(2)-evolving complex of photosystem II and biomimetic oxomanganese complexes.

In recent years, there has been considerable interest in studies of catalytic metal clusters in metalloproteins based on Density Functional Theory (DFT) quantum mechanics/molecular mechanics (QM/MM) hybrid methods. These methods explicitly include the perturbational influence of the surrounding protein environment on the structural/functional properties of the catalytic centers. In conjunction with recent breakthroughs in X-ray crystallography and advances in spectroscopic and biophysical studies, computational chemists are trying to understand the structural and mechanistic properties of the oxygen-evolving complex (OEC) embedded in photosystem II (PSII).

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.

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 mu4-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.

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.

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 Mn3CaO4Mn metal cluster with three closely associated manganese ions linked to a single mu4-oxo-ligated Mn ion, often called the 'dangling manganese'.

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.

QM/MM Models of the O2-Evolving Complex of Photosystem II.

This paper introduces structural models of the oxygen-evolving complex of photosystem II (PSII) in the dark-stable S1 state, as well as in the reduced S0 and oxidized S2 states, with complete ligation of the metal-oxo cluster by amino acid residues, water, hydroxide, and chloride. The models are developed according to state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, applied in conjunction with the X-ray crystal structure of PSII from the cyanobacterium Thermosynechococcus elongatus, recently reported at 3.5 Å resolution.

Computational studies of the primary phototransduction event in visual rhodopsin.

This Account addresses recent advances in the elucidation of the detailed molecular rearrangements due to the primary photochemical event in rhodopsin, a prototypical G-protein-coupled receptor (GPCR) responsible for the signal transmission cascade in the vertebrate vision process. The reviewed studies provide fundamental insight on long-standing problems regarding the assembly and function of the individual residues and bound water molecules that form the rhodopsin active site, a center that catalyzes the 11-cis/all-trans isomerization of the retinyl chromophore in the primary step of the phototransduction mechanism. Emphasis is placed on the authors' recent computational studies, based on state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, addressing the structural refinement of the retinyl chromophore binding site in high-resolution X-ray structures of bovine visual rhodopsin, the energy storage mechanism, and the molecular origin of spectroscopic changes due to the primary photochemical event.

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 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.

Characterization of synthetic oxomanganese complexes and the inorganic core of the O2-evolving complex in photosystem II: evaluation of the DFT/B3LYP level of theory.

The capabilities and limitations of the Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional are investigated as applied to studies of mixed-valent multinuclear oxomanganese complexes. Benchmark calculations involve the analysis of structural, electronic and magnetic properties of di-, tri- and tetra-nuclear Mn complexes, previously characterized both chemically and spectroscopically, including the di-mu-oxo bridged dimers [Mn(III)Mn(IV)(mu-O)(2)(H(2)O)(2)(terpy)(2)](3+) (terpy=2,2':6,2''-terpyridine) and [Mn(III)Mn(IV)(mu-O)(2)(phen)(4)](3+) (phen=1,10-phenanthroline), the Mn trimer [Mn(3)O(4)(bpy)(4)(H(2)O)(2)](4+) (bpy=2,2'-bipyridine), and the tetramer [Mn(4)O(4)L(6)](+) with L=Ph(2)PO(2)(-). Furthermore, the density functional theory (DFT) B3LYP level is applied to analyze the hydrated Mn(3)O(4)CaMn cluster completely ligated by water, OH(-), Cl(-), carboxylate and imidazole ligands, analogous to the '3+1 Mn tetramer' of the oxygen-evolving complex of photosystem II.

QM/MM Study of the NMR Spectroscopy of the Retinyl Chromophore in Visual Rhodopsin.

The (1)H and (13)C nuclear magnetic resonance (NMR) spectra of the retinyl chromophore in rhodopsin are investigated by using quantum mechanics/molecular mechanics (QM/MM) hybrid methods at the density functional theory (DFT) B3LYP/6-31G*:Amber level of theory, in conjunction with the gauge independent atomic orbital (GIAO) method for the ab initio self-consistent-field (SCF) calculation of NMR chemical shifts. The study provides a first-principle interpretation of solid-state NMR experiments based on recently developed QM/MM computational models of rhodopsin and bathorhodopsin [Gascón, J. A.