Stability Series for the Complexation of Six Key Siderophore Functional Groups with Uranyl Using Density Functional Theory.

Determining stability constants of uranyl complexes with the principal functional groups in siderophores and identifying stability series is of great importance to predict which siderophore classes preferentially bind to UVI and, hence, impact uranium speciation in the environment. It also helps to develop resins for scavenging UVI from aqueous solutions. Here, we apply a recently developed computational approach to calculate log ß values for a set of geochemically relevant uranium organometallic complexes using Density Functional Theory (DFT). We determined the stability series for catecholate, hydroxamate, α-hydroxycarboxylate, α-aminocarboxylate, hydroxy-phenyloxazolonate, and α-hydroxyimidazole with the uranyl cation. In this work, the stability constants (log ß110) of α-hydroxyimidazolate and hydroxy-phenyloxazolonate are calculated for the first time. Our approach employed the B3LYP density functional approximation, aug-cc-pVDZ basis set for ligand atoms, MDF60 ECP for UVI, and the IEFPCM solvation model. DFT calculated log ß110 were corrected using a previously established fitting equation. We find that the siderophore functional groups stability decreases in the order: α-hydroxycarboxylate bound via the α-hydroxy and carboxylate groups (log ß110 = 17.08), α-hydroxyimidazolate (log ß110 = 16.55), catecholate (log ß110 = 16.43), hydroxamate (log ß110 = 9.00), hydroxy-phenyloxazolonate (log ß110 = 8.43), α-hydroxycarboxylate bound via the carboxylate group (log ß110 = 7.51) and α-aminocarboxylate (log ß110 = 4.73). We confirm that the stability for the binding mode of the functional groups decrease in the order: bidentate, monodentate via ligand O atoms, and monodentate via ligand N atoms. The stability series strongly suggests that α-hydroxyimidazolate is an important functional group that needs to be included when assessing uranyl mobility and removal from aqueous solutions.

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.

Competition between photodetachment and autodetachment of the 2(1)ππ* state of the green fluorescent protein chromophore anion.

Using a combination of photoelectron spectroscopy measurements and quantum chemistry calculations, we have identified competing electron emission processes that contribute to the 350-315 nm photoelectron spectra of the deprotonated green fluorescent protein chromophore anion, p-hydroxybenzylidene-2,3-dimethylimidazolinone. As well as direct electron detachment from S0, we observe resonant excitation of the 2(1)ππ* state of the anion followed by autodetachment. The experimental photoelectron spectra are found to be significantly broader than photoelectron spectrum calculated using the Franck-Condon method and we attribute this to rapid (∼10 fs) vibrational decoherence, or intramolecular vibrational energy redistribution, within the neutral radical.

Lactonisation--a degradation pathway for active pharmaceutical compounds: an in silico study in amorphous trehalose.

The lactonisation of a CCR1 inhibitor (CC chemokine receptor 1, involved in autoimmune diseases) featuring a hydroxyl group in a gamma-position (gamma-OH) with respect to an amide group has been investigated in silico. The two key steps of the lactonisation reaction are (i) rearrangement to an optimal conformation and (ii) the formation of the lactone (ring closure) and expulsion of NH3. Quantum chemical calculations in the gas phase were employed to identify conformers of the molecule with favorable starting geometries for a lactonisation reaction. In total, calculations of 1296 conformers revealed that it is energetically feasible for an inhibitor molecule to adopt a conformation where the carbon atom of the amide group (C(amide)) is suitably close to the oxygen atom of the gamma-OH (O(gamma)) to facilitate a successful lactonisation reaction. Additionally, molecular dynamics methods were used to show that rearrangement to a suitable conformer for lactonisation to occur happens to a lesser extent when the CCR1 inhibitor was embedded in an amorphous trehalose matrix (a model carbohydrate excipient). The mechanism of the actual lactonisation was investigated using the complete Linear Synchronous Transit/Quadratic Synchronous Transit (LST/QST) method. This was performed in both the gas phase and in water and was found to be a concerted reaction.

The glass transition temperatures of amorphous trehalose-water mixtures and the mobility of water: an experimental and in silico study.

Isothermal-isobaric molecular dynamics simulations are used to calculate the specific volume of models of trehalose and three amorphous trehalose-water mixtures (2.9%, 4.5% and 5.3% (w/w) water, respectively) as a function of temperature. Plots of specific volume versus temperature exhibit a characteristic change in slope when the amorphous systems change from the glassy to the rubbery state and the intersection of the two regression lines provides an estimate of the glass transition temperature T(g). A comparison of the calculated and experimental T(g) values, as obtained from differential scanning calorimetry, shows that despite the predicted values being systematically higher (about 21-26K), the trend and the incremental differences between the T(g) values have been computed correctly: T(g)(5.3%(w/w))

Glass transition temperature of glucose, sucrose, and trehalose: an experimental and in silico study.

Isothermal-isobaric molecular dynamics simulations are used to calculate the specific volume of models of different amorphous carbohydrates (glucose, sucrose, and trehalose) as a function of temperature. Plots of specific volume vs temperature exhibit a characteristic change in slope when the amorphous systems change from the glassy to the rubbery state. The intersection of the regression lines of data below (glassy state) and above (rubbery state) the change in slope provides the glass transition temperature (T(g)). These predicted glass transition temperatures are compared to experimental T(g) values as obtained from differential scanning calorimetry measurements. As expected, the predicted values are systematically higher than the experimental ones (about 12-34 K) as the cooling rates of the modeling methods are about a factor of 10(12) faster. Nevertheless, the calculated trend of T(g) values agrees exactly with the experimental trend: T(g)(glucose) < T(g)(sucrose) < T(g)(trehalose). Furthermore, the relative differences between the glass transition temperatures were also computed precisely, implying that atomistic molecular dynamics simulations can reproduce trends of T(g) values in amorphous carbohydrates with high quality.

Adsorption of methanol on zeolites X and Y. An atomistic and quantum chemical study.

The adsorption of methanol on basic zeolites X and Y was investigated with both atomistic and quantum chemical methods. The Monte Carlo docking method was used to localize preferred adsorption sites within the framework. Sites were found adjacent to the interstitial alkali cations in the sites SI, SII, and SIII. We investigated the influence on adsorption behavior of all possible interstitial alkali metal cations, i.e., Li(+), Na(+), K(+), Rb(+), and Cs(+), and in the case of site SII also the influence of varying the Si/Al ratio and distribution. Clusters were cut from the periodic framework in a way that the topological character of the different sites was preserved. DFT calculations yielded geometries and energetic data, which are analyzed with respect to the nature of the cation and to the Si/Al ratio. Adsorption of the methanol molecule is influenced mainly by the identity of the alkali metal cation. Other factors, including Si/Al ratio, are of secondary importance, though there is evidence of weak hydrogen bonding between methanol hydrogen and framework. Cation positions are displaced only slightly by interaction with methanol, although somewhat more at the SIII sites than the SII. We propose that the SIII sites may be a more likely location for methanol activation, particularly in the reaction with toluene, which favors the SII site.

Hypothetical binodal zeolitic frameworks.

Hypothetical binodal zeolitic structures (structures containing two kinds of tetrahedral sites) were systematically enumerated using tiling theory and characterized by computational chemistry methods. Each of the 109 refineable topologies based on "simple tilings" was converted into a silica polymorph and its energy minimized using the GULP program with the Sanders-Catlow silica potential. Optimized structural parameters, framework energies relative to alpha-quartz and volumes accessible to sorption have been calculated. Eleven of the 30 known binodal topologies listed in the Atlas of Zeolite Framework Types were found, leaving 98 topologies that were unknown previously. The chemical feasibility of each structure as a zeolite was evaluated by means of a feasibility factor derived from the correlation between lattice energy and framework density. Structures are divided into 15 families, based on common structural features. Many "feasible" structures contain only small pores. Several very open structures were also enumerated, although they contain three-membered rings which are thermodynamically disfavoured and not found in conventional zeolites. We believe that such topologies may be realizable as framework materials, but with different elemental compositions to those normally associated with zeolites.

Tetrahedral distortion and energetic packing penalty in "zeolite" frameworks: linked phenomena?

We report a computational study on the distortion of SiO4 tetrahedra in zeolite frameworks. For all previously observed frameworks, the tetrahedral mismatch was found to span a narrow range (1.0 x 10(-3) to 2.5 x 10(-2) angstroms2) of values, in contrast to the hypothetical frameworks, which were calculated to have a much wider range of mismatch values. The energy of the frameworks was not found to be a function of the tetrahedral distortion for the previously observed and moderately distorted (tetrahedral mismatch <2.5 x 10(-2) angstroms2) hypothetical frameworks. In contrast, the energy of the bulk of the hypothetical frameworks was shown to be a strong function of the tetrahedral distortion. The fact that the framework energies of some hypothetical frameworks lie much higher than both those of the observed frameworks and the values we would expect from our previously developed topological method (the so-called energetic packing penalty) is explained in terms of the tetrahedral distortion contribution to the framework energy which is negligible for the observed frameworks. Finally, it is hypothesized that the absence of tetrahedral distortion is pivotal for a framework to be experimentally realized, in which case a large fraction of hypothetical frameworks are unrealizable and will forever remain in the realms of the abstract.

Evidence for heterodimers of 2,4,5-trichlorophenol on planar lipid layers. A FTIR-ATR investigation.

Trichlorophenols are weak acids of high hydrophobicity and are able to transport protons across the mitochondrial membrane. Thus the proton motive force is dissipated and the ATP production decreased. In situ Fourier Transform Infrared-Attenuated Total Reflection (FTIR-ATR) experiments with 2,4,5-trichlorophenol (TCP) adsorbed to model membranes resulted in good evidence for the formation of the TCP-heterodimer. Two surfaces were examined: a dipalmitoyl phosphatidic acid (DPPA) monolayer and a planar DPPA/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. TCP was adsorbed from 1 to 3 mM solutions at pH 6.0 to the lipid layers leading to surface layers at the water/lipid interface. Difference spectra showed an effect on DPPA acyl chains even when it was covered with POPC. Time-resolved measurements revealed two distinct adsorption processes, which were assigned to TCP and its deprotonated anion (phenoxide), respectively. For DPPA/POPC bilayers, the adsorption of TCP was faster than that of its phenoxide, whereas adsorption of both species to DPPA monolayers proceeded with similar velocity. In both cases, phenoxide formation at the membrane was found to be delayed with respect to phenol adsorption. Phenoxide and phenol were retained after replacing the TCP solution with buffer. For the retained species, we estimated a phenol/phenoxide molar ratio of 1 at pH 6.0 (pKa=6.94 for TCP), demonstrating strong evidence for heterodimer formation.

Chemically feasible hypothetical crystalline networks.

Our systematic enumeration of 4-connected crystalline networks (that is, networks in which each atom is connected to exactly four neighbours) used recent advances in tiling theory to evolve over 900 topologies. The results are relevant to the structures of zeolites and other silicates, aluminophosphates (AlPOs), oxides, nitrides, chalcogenides, halides, carbon networks, and even to polyhedral bubbles in foams. Given their importance as molecular sieves, ion exchangers, catalysts and catalyst supports, we have applied the results to microporous aluminosilicates and aluminophosphates (zeolites). Zeolite chemistry has to date produced 152 distinct types of structure. However, it was always clear that although many further structures can be synthesised, only a fraction of the mathematically generated networks would be chemically feasible (many are 'strained' frameworks requiring unrealistic bond lengths and bond angles), and that an effective 'filtering' process is needed to identify the most plausible frameworks. Here, we describe the use of computational chemistry methods to calculate optimized structural parameters, framework energies relative to alpha-quartz, volumes accessible to sorption, and X-ray diffraction patterns for systematically enumerated hypothetical 4-connected crystalline frameworks. Structures were treated as silica polymorphs with the empirical formula SiO(2), and their energies were minimized.