Computational Tools for Calculating log ß Values of Geochemically Relevant Uranium Organometallic Complexes.

Uranium (UVI) interacts with organic ligands, subsequently controlling its aqueous chemistry. It is therefore imperative to assess the binding ability of natural organic molecules. We evidence that density functional theory (DFT) can be used as a practical protocol for predicting the stability of UVI organic ligand complexes, allowing for the development of a relative stability series for organic complexes with limited experimental data. Solvation methods and DFT settings were benchmarked to suggest a suitable off-the-shelf solution. The results indicate that the IEFPCM solvation method should be employed. A mixed solvation approach improves the accuracy of the calculated stability constant (log ß); however, the calculated log ß are approximately five times more favorable than experimental data. Different basis sets, functionals, and effective core potentials were tested to check that there were no major changes in molecular geometries and Δr G. The recommended method employed is the B3LYP functional, aug-cc-pVDZ basis set for ligands, MDF60 ECP and basis set for UVI, and the IEFPCM solvation model. Using the fitting approach employed in the literature with these updated DFT settings allows fitting of 1:1 UVI complexes with root-mean-square deviation of 1.38 log ß units. Fitting multiple bound carboxylate ligands indicates a second, separate fitting for 1:2 and 1:3 complexes.

Proteins with Intrinsically Disordered Domains Are Preferentially Recruited to Polyglutamine Aggregates.

Intracellular protein aggregation is the hallmark of several neurodegenerative diseases. Aggregates formed by polyglutamine (polyQ)-expanded proteins, such as Huntingtin, adopt amyloid-like structures that are resistant to denaturation. We used a novel purification strategy to isolate aggregates formed by human Huntingtin N-terminal fragments with expanded polyQ tracts from both yeast and mammalian (PC-12) cells. Using mass spectrometry we identified the protein species that are trapped within these polyQ aggregates. We found that proteins with very long intrinsically-disordered (ID) domains (≥ 100 amino acids) and RNA-binding proteins were disproportionately recruited into aggregates. The removal of the ID domains from selected proteins was sufficient to eliminate their recruitment into polyQ aggregates. We also observed that several neurodegenerative disease-linked proteins were reproducibly trapped within the polyQ aggregates purified from mammalian cells. Many of these proteins have large ID domains and are found in neuronal inclusions in their respective diseases. Our study indicates that neurodegenerative disease-associated proteins are particularly vulnerable to recruitment into polyQ aggregates via their ID domains. Also, the high frequency of ID domains in RNA-binding proteins may explain why RNA-binding proteins are frequently found in pathological inclusions in various neurodegenerative diseases.

Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology.

The rates of intramolecular proton transfer are calculated on a full-dimensional reactive electronic potential energy surface that incorporates high level ab initio calculations along the reaction path and by using classical Transition State theory, Path-Integral Quantum Transition State Theory, and the Quantum Instanton approach. The specific example problem studied is malonaldehyde. Estimates of the kinetic isotope effect using the latter two methods are found to be in reasonable agreement with each other. Improvements and extensions of this practical, yet chemically accurate framework for the calculations of quantized, reactive dynamics are also discussed.

Theoretical studies of An(II)(2)(C(8)H(8))(2) (An = Th, Pa, U, and Np) complexes: the search for double-stuffed actinide metallocenes.

Complexes of the form An(2)(C(8)H(8))(2) (An = Th, Pa, U, and Np) were investigated using density functional theory with scalar-relativistic effective core potentials. For uranium, a coaxial isomer with D(8h) symmetry is found to be more stable than a C(s) isomer in which the dimetal unit is perpendicular to the C(8) ring axis. Similar coaxial structures are predicted for Pa(2)(C(8)H(8))(2) and Np(2)(C(8)H(8))(2), while in Th(2)(C(8)H(8))(2), the C(8)H(8) rings tilt away from the An-An axis. Going from Th(2)(C(8)H(8))(2) to Np(2)(C(8)H(8))(2), the An-An bond length decreases from 2.81 A to 2.19 A and the An-An stretching frequency increases from 249 to 354 cm(-1). This is a result of electrons populating An-An 5f pi- and delta-type bonding orbitals and varphi nonbonding orbitals, thereby increasing in An-An bond order. U(2)(C(8)H(8))(2) is stable with respect to dissociation into U(C(8)H(8)) monomers. Disproportionation of U(2)(C(8)H(8))(2) into uranocene and the U atom is endothermic but is slightly exothermic for uranocene plus (1)/(2)U(2), suggesting that it might be possible to prepare double stuffed uranocene if suitable conditions can be found to avoid disproportionation.

Distributed Gaussian Valence Bond Surface Derived from Ab Initio Calculations.

The experimental and computational results for the tautomerization reaction of 2-pyridone are reviewed. G3, G4, CBS-APNO, and W1 model chemistries are used to generate state-of-the-art reaction energetics for the tautomerization reaction with and without catalytic water molecules in both the gas and aqueous phases. Reactive, electronic potential energy surface surfaces for use in molecular dynamics simulations were generated for these reactions following a recently improved empirical valence bond formulation. The form of molecular mechanics potentials needed for a satisfactory fit is also discussed.

A definitive example of a geometric "entatic state" effect: electron-transfer kinetics for a copper(II/I) complex involving A quinquedentate macrocyclic trithiaether-bipyridine ligand.

The quinquedentate macrocyclic ligand cyclo-6,6'-[1,9-(2,5,8-trithianonane)]-2,2'-bipyridine ([15]aneS3bpy = L), containing two pyridyl nitrogens and three thiaether sulfurs as donor atoms, has been synthesized and complexed with copper. The CuII/IL redox potential, the stabilities of the oxidized and reduced complex, and the oxidation and reduction electron-transfer kinetics of the complex reacting with a series of six counter reagents have been studied in acetonitrile at 25 degrees C, mu = 0.10 M (NaClO4). The Marcus cross relationship has been applied to the rate constants obtained for the reactions with each of the six counter reagents to permit the evaluation of the electron self-exchange rate constant, k11. The latter value has also been determined independently from NMR line-broadening experiments. The cumulative data are consistent with a value of k11 = 1 x 10(5) M(-1) s(-1), ranking this among the fastest-reacting CuII/I systems, on a par with the blue copper proteins known as cupredoxins. The resolved crystal structures show that the geometry of the CuIIL and CuIL complexes are nearly identical, both exhibiting a five-coordinate square pyramidal geometry with the central sulfur donor atom occupying the apical site. The most notable geometric difference is a puckering of an ethylene bridge between two sulfur donor atoms in the CuIL complex. Theoretical calculations suggest that the reorganizational energy is relatively small, with the transition-state geometry more closely approximating the geometry of the CuIIL ground state. The combination of a nearly constant geometry and a large self-exchange rate constant implies that this CuII/I redox system represents a true geometric "entatic state."

Automated approach to couple solubility with final pH and crystallinity for pharmaceutical discovery compounds.

The design and validation of a novel high-throughput system for thermodynamic solubility determination requiring only 5 mg of sample is described. The system uses a sintered nickel filter assembly to recover excess solids from saturated solutions for rapid crystallinity assessment via powder X-ray diffraction (PXRD). Moreover, the system measures the pH of filtrates to provide a final pH value with the solubility measurement. The limit of detection for the UV-vis plate reader used on this system is approximately 0.001 mg/ml, while the practical upper limit is approximately 3 mg/mL. The solubility measurements of 60 proprietary Pfizer compounds were used to validate the nickel filter assembly against a more conventional polyvinylidenedifluoride (PVDF) filter. Additionally, a comparison was made between a subset of 10 compounds run on the automated system and a more traditional shake-flask method employing HPLC analysis. In both cases, a favorable comparison was obtained.

Empirical Valence-Bond Models for Reactive Potential Energy Surfaces Using Distributed Gaussians.

A new method for constructing empirical valence bond potential energy surfaces for reactions is presented. Building on the generalized Gaussian approach of Chang-Miller, V12(2)(q) is represented by a Gaussian times a polynomial at the transition state and generalized to handle any number of data points on the potential energy surface. The method is applied to two model surfaces and the HCN isomerization reaction. The applications demonstrate that the present method overcomes the divergence problems encountered in some other approaches. The use of Cartesian versus internal or redundant internal coordinates is discussed.

Theoretical investigations of uranyl-ligand bonding: four- and five-coordinate uranyl cyanide, isocyanide, carbonyl, and hydroxide complexes.

The coordination and bonding of equatorial hydroxide, carbonyl, cyanide (CN-), and isocyanide (NC-) ligands with uranyl dication, [UO2]2+, has been studied using density functional theory with relativistic effective core potentials. Good agreement is seen between experimental and calculated geometries of [UO2(OH)4]2-. Newly predicted ground-state structures of [UO2(OH)5]3-, [UO2(CO)4]2+, [UO2(CO)5]2+, [UO2(CN)4]2-, [UO2(CN)5]3-, [UO2(NC)4]2-, and [UO2(NC)5]3- are reported. Four-coordinate uranyl isocyanide complexes are the predicted gas-phase species while five-coordinate uranyl cyanide complexes are energetically favorable in aqueous solution. Small energy differences between cyanide and isocyanide complexes indicate the energetic feasibility of mixed cyanide and isocyanide complexes. A D2d uranyl tetrahydroxide is the dominant gas-phase and aqueous species, but formation of uranyl carbonyl complexes is seen to be exothermic in the gas-phase and endothermic in aqueous solution.

Theoretical investigation of uranyl dihydroxide: oxo ligand exchange, water catalysis, and vibrational spectra.

Density functional theory is employed to investigate uranyl dihydroxide, UO2(OH)2, isomerization reaction energy barriers, including those occurring via proton shuttles. The ground-state structure of a uranyl dihydroxide complex containing a uranyl moiety with a near 90 degrees O=U=O bond angle is reported for the first time. Furthermore, we predict the vibrational spectra of these compounds. Scalar-relativistic effects for uranium are treated by employing a relativistic effective core potential.

Density and wave function analysis of actinide complexes: what can fuzzy atom, atoms-in-molecules, Mulliken, Lowdin, and natural population analysis tell us?

Recent advances in computational methods have made it possible to calculate the wave functions for a wide variety of simple actinide complexes. Equally important is the ability to analyze the information contained therein and produce a chemically meaningful understanding of the electronic structure. Yet the performance of the most common wave function analyses for the calculation of atomic charge and bond order has not been thoroughly investigated for actinide systems. This is particularly relevant because the calculation of charge and bond order even in transition metal complexes is known to be fraught with difficulty. Here we use Mulliken, Lowdin, natural population analysis, atoms-in-molecules (AIM), and fuzzy atom techniques to determine the charges and bond orders of UO(2)(2+), PuO(2)(2+), UO(2), UO(2)Cl(4)(2-), UO(2)(CO)(5)(2+), UO(2)(CO)(4)(2+), UO(2)(CN)(5)(3-), UO(2)(CN)(4)(2-), UO(2)(OH)(5)(3-), and UO(2)(OH)(4)(2-). This series exhibits a clear experimental and computational trend in bond lengths and vibrational frequencies. The results indicate that Mulliken and Lowdin populations and bond orders are unreliable for the actinyls. Natural population analysis performs well after modification of the partitioning of atomic orbitals to include the 6d in the valence space. The AIM topological partitioning is insensitive to the electron donating ability of the equatorial ligands and the relative atomic volume of the formally U(VI) center is counterintuitively larger than that of O(2-) in the UO(2)(2+) core. Lastly, the calibrated fuzzy atom method yields reasonable bond orders for the actinyls at significantly reduced computational cost relative to the AIM analysis.