Promotion of oxygen atom transfer in Mo and W enzymes by bicyclic forms of the pterin cofactor

Density functional theory calculations suggest that bicyclic structures of the "molybdopterin" in DMSO reductases may have an important catalytic role in oxygen atom transfer reactions.     

Atom probe tomography characterization of thin copper layers on aluminum deposited by galvanic displacement

″Ultrathin″ metallization layers on the order of nanometers in thickness are increasingly used in semiconductor interconnects and other nanostructures. Aqueous deposition methods are attractive methods to produce such layers due to their low cost, but formation of ultrathin layers has proven challenging, particularly on oxide-coated substrates. This work focused on the formation of thin copper layers on aluminum, by galvanic displacement from alkaline aqueous solutions. Analysis by atom probe tomography (APT) showed that continuous copper films of approximately 1 nm thickness were formed, apparently the first demonstration of deposition of ultrathin metal layers on oxidized substrates from aqueous solutions. The APT reconstructions indicate that deposited copper replaced a portion of the surface oxide film on aluminum. The results are consistent with mechanisms in which surface hydride species on aluminum mediate deposition, either by directly reducing cupric ions or by inducing electronic conduction in the oxide, thus enabling cupric ion reduction by Al metal.     

Structure and redox properties of the protein, rubredoxin, and its ligand and metal mutants studied by electronic structure calculation

The changes in the structural and electronic properties accompanying metal ionization of the iron-containing protein, rubredoxin, and of some ligand and metal mutants, have been explored using density functional theory (DFT) calculations of the metal atom coordinated to the four immediate residues. Both isolated and embedded cluster studies have been carried out, the latter using the hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The replacement of a cysteine by a serine residue has a considerable effect on both the electronic and geometric structure of the core, which can be qualitatively understood on the basis of the isolated cluster studies. The modulation of these properties caused by the protein environment is quite accurately described by the QM/MM calculations. The predicted core geometries are in good accord with both X-ray and EXAFS data, and the changes in the redox potentials are predicted, at least semiquantitatively, by considering only the core part of the protein.     

Interplay of structure and reactivity in a most unusual furan Diels-Alder reaction

Difluorinated alkenoate ethyl 3,3-difluoro-2-(N,N-diethylcarbamoyloxy)-2-propenoate reacts rapidly and in high yield with furan and a range of substituted furans in the presence of a tin(IV) catalyst. Non-fluorinated congener 2-(N,N-diethylcarbamoyloxy)-2-propenoate fails to react at all under the same conditions. These reactions have been explored using density functional theory (DFT) calculations. They reveal a highly polar transition state, which is stabilized by the Lewis acid catalyst SnCl(4) and by polar solvents. In the presence of both catalyst and solvent, a two-step reaction is predicted, corresponding to the stepwise formation of the two new carbon-carbon bonds via transition states which have similar energies in all cases. Our experimental observations of the lack of reaction of the non-fluorinated dienophile, the stereochemical outcomes, and the rate acceleration accompanying furan methylation are all well predicted by our calculations. The calculated free energy barriers generally correlate well with measured reaction rates, supporting a reaction mechanism in which zwitterionic character is developed strongly. An in situ ring opening reaction of exo-cycloadduct ethyl exo-2-(N,N-diethylcarbamoyloxy)-3,3-difluoro-7-oxabicyclo[2.2.1]hept-5-enyl-2-endo-carboxylate, which results in the formation of cyclic carbonate ethyl 4,4-difluoro-5-hydroxy-2-oxo-5,7a-dihydro-4H-benzo[1,3]dioxole-3a-carboxylate by a Curtin-Hammett mechanism, has also been examined. Substantial steric opposition to Lewis acid binding prevents carbonate formation from 2-substituted furans.     

Active site structures and the redox properties of blue copper proteins: atomic resolution structure of azurin II and electronic structure calculations of azurin, plastocyanin and stellacyanin

Understanding how the active site structures of blue copper proteins determine their redox properties is the central structure-function relationship question of this important class of protein, also referred to as cupredoxins. We here describe both experimental and computational studies of azurin, plastocyanin and stellacyanin designed to define more accurately the geometric structures of the active site of the reduced and oxidized species, and thus to understand how these structures determine the redox potentials of these proteins. To this end the crystal structure of reduced azurin II has been determined at an atomic resolution of 1.13 Angstrom and is presented here. Co-ordinates and structure factors have been deposited in the RCSB Protein Data Bank with accession codes 2ccw and r2ccwsf respectively. The improved accuracy provided by the atomic resolution for the metal stereochemistry are utilised in conjunction with the EXAFS data for theoretical calculations. Multilevel calculations involving density functional theory and molecular mechanical potentials are used to predict both the geometric and electronic structure of the active sites of azurin, plastocyanin and stellacyanin and to estimate the relative redox potentials of these three proteins. We have also compared the relative energies of the structures obtained from experiment at varying resolutions, and from the isolated and embedded cluster calculations. We find significant energy differences between low and high (atomic) resolution structures arising primarily due to inaccuracies in the Cu-ligand distances in the lower resolution structures, emphasising the importance of accurate, very high resolution structural information. QM/MM structures are only approximately 1 kcal mol(-1) lower in energy than the 1.13 Angstrom structure while the optimized gas phase structure is 13.0 kcal mol(-1) lower in energy.     

Can the semiempirical PM3 scheme describe iron-containing bioinorganic molecules?

A set of iron parameters for use in the semiempirical PM3 method have been developed to allow the structure and redox properties of the active sites of iron-containing proteins to be accurately modeled, focussing on iron-sulfur, iron-heme, and iron-only hydrogenases. Data computed at the B3LYP/6-31G* level for a training set of 60 representative complexes have been employed. A gradient-based optimization algorithm has been used, and important modifications of the core repulsion function have been highlighted. The derived parameters lead in general to good predictions of the structure and energetics of molecules both within and outside the training set, and overcome the extensive deficiencies of a B3LYP/STO-3G model. Particularly encouraging is the success of the parameters in describing [4Fe-4S] cubanes. The derived parameter set provides a starting point should greater accuracy for a more restricted range of compounds be required.     

An adeno-associated viral vector transduces the rat hypothalamus and amygdala more efficient than a lentiviral vector

Background  

This study compared the transduction efficiencies of an adeno-associated viral (AAV) vector, which was pseudotyped with an AAV1 capsid and encoded the green fluorescent protein (GFP), with a lentiviral (LV) vector, which was pseudotyped with a VSV-G envelop and encoded the discosoma red fluorescent protein (dsRed), to investigate which viral vector transduced the lateral hypothalamus or the amygdala more efficiently. The LV-dsRed and AAV1-GFP vector were mixed and injected into the lateral hypothalamus or into the amygdala of adult rats. The titers that were injected were 1 × 10⁸ or 1 × 10⁹ genomic copies of AAV1-GFP and 1 × 10⁵ transducing units of LV-dsRed.     

Why is RCM Favoured Over Dimerisation? Predicting and Estimating Thermodynamic Effective Molarities by Solution Experiments and Electronic Structure Calculations

The thermodynamic effective molarities of a series of simple cycloalkenes, synthesised from α,ω-dienes by reaction with Grubbs' second generation precatalyst, have been evaluated. Effective molarities were measured from a series of small scale metathesis reactions and agreed well with empirical predictions derived from the number of rotors and the product ring strain. The use of electronic structure calculations (at the M06-L/6-311G** level of theory) was explored for predicting thermodynamic effective molarities in ring-closing metathesis. However, it was found that it was necessary to apply a correction to DFT-derived free energies to account for the entropic effects of solvation.     

Satellite peaks in the high energy photoelectron spectra of some small first row molecules

The gas phase high energy photoelectron spectra of CH₄, NH₃, H₂O, N₂, O₂, CO and CO₂ have been recorded, and in all cases weak satellite peaks to high binding energy of the main ionization peak are observed. These peaks are assigned to transitions to ionic states in which valence electron excitation as well as core ionization has occurred. The intensity and position of these peaks, relative to the main ionization peak have been estimated from ab initio UHF calculations on the core hole states, which in general allow assignment of the satellite peaks in terms of orbital transitions of the core hole ion.