Anion–arene adducts: C–H hydrogen bonding, anion– interaction, and carbon bonding motifs

This article summarizes experimental and theoretical evidence for the existence of four distinct binding modes for complexes of anions with charge-neutral arenes. These include C–H hydrogen bonding and three motifs involving the arene– system—the noncovalent anion– interaction, weakly covalent interaction, and strongly covalent interaction

Computational Study of Copper(II) Complexation and Hydrolysis in Aqueous Solutions Using Mixed Cluster/Continuum Models

We use density functional theory (B3LYP) and the COSMO continuum solvent model to characterize the structure and stability of the hydrated Cu(II) complexes [Cu(MeNH_2)(H_2O)_(n−1)]^(2+) and [Cu(OH)_x(H_2O)_(n−x)]^(2−x) (x = 1−3) as a function of metal coordination number (4−6) and cluster size (n = 4−8, 18). The small clusters with n = 4−8 are found to be the most stable in the nearly square-planar four-coordinate configuration, except for [Cu(OH)_3(H_2O)]^−, which is three-coordinate. In the presence of the two full hydration shells (n = 18), however, the five-coordinate square-pyramidal geometry is the most favorable for Cu(MeNH_2)^(2+) (5, 6) and Cu(OH)^+ (5, 4, 6), and the four-coordinate geometry is the most stable for Cu(OH)_2 (4, 5) and Cu(OH)_3^− (4). (Other possible coordination numbers for these complexes in the aqueous phase are shown in parentheses.) A small energetic difference between these structures (0.23−2.65 kcal/mol) suggests that complexes with different coordination numbers may coexist in solution. Using two full hydration shells around the Cu^(2+) ion (18 ligands) gives Gibbs free energies of aqueous reactions that are in excellent agreement with experiment. The mean unsigned error is 0.7 kcal/mol for the three consecutive hydrolysis steps of Cu^(2+) and the complexation of Cu^(2+) with methylamine. Conversely, calculations for the complexes with only one coordination shell (four equatorial ligands) lead to a mean unsigned error that is >6.0 kcal/mol. Thus, the explicit treatment of the first and the second shells is critical for the accurate prediction of structural and thermodynamic properties of Cu(II) species in aqueous solution

Tissue-specific diversity of the Muscleblind expression in adult flies.

Department of Molecular and Cellular Biology, Kennesaw State University The muscleblind (mbl) family of RNA-binding proteins regulates alternative splicing, determining mRNA transcript composition for various types of tissue, and has been implicated in myotonic dystrophy. The mbl gene is subject to alternative splicing in Drosophila, leading to multiple isoforms, and has several paralogs in humans. Mbl proteins vary significantly in length, although the significance of such diversity and the role of specific isoforms have not been fully explored. Using immunofluorescence microscopy and polyclonal serum, we analyzed Mbl protein expression across adult Drosophila tissues. Mbl was detected in various locations, including the brain, gonads, muscle, and gut epithelium. Skeletal muscles demonstrated the greatest diversity in Mbl expression, with other tissues showing more homogenous expression. Mbl was present at low levels in flight and jump muscles, while other thoracic muscles and abdominal muscles showed high Mbl levels. Intracellular localization of Mbl was typically nuclear, however in the nervous system the protein was strongly expressed in the cytoplasm. During early adult development in the pupa, in various tissues Mbl was initially detected in discrete nuclear bodies, before it assumed more general nuclear staining. Our study reveals natural locations that have drastically different levels of Mbl as well as its intracellular localization. Our further aim is to supplement these findings with molecular analysis of Mbl isoforms to create the basis for functional interrogation of the Mbl diversity and its relation to tissue-specific regulation of alternative RNA splicing

PAMAM Dendrimers Undergo pH Responsive Conformational Changes without Swelling

Atomistic molecular dynamics (MD) simulations of a G4-NH2 PAMAM dendrimer were carried out in aqueous solution using explicit water molecules and counterions (with the Dreiding III force field optimized using quantum mechanics). Our simulations predict that the radius of gyration (R_g) of the dendrimer changes little with pH from 21.1 Å at pH 10 (uncharged PAMAM) to 22.1 Å at pH 5 (charged with 126 protons), which agrees quantitatively with recent small angle neutron scattering (SANS) experiments (from 21.4 Å at pH 10 to 21.5 Å at pH 5). Even so we predict a dramatic change in the conformation. The ion pairing in the low pH form leads to a locally compact dense shell with an internal surface area only 37% of the high pH form with a dense core. This transformation from “dense core” at high pH to “dense shell” at low pH could facilitate the encapsulation and release of guest molecules (e.g., drugs) using pH as the trigger, making dendrimers a unique drug delivery vehicle

Evaluation of B3LYP, X3LYP, and M06-class density functionals for predicting the binding energies of neutral, protonated, and deprotonated water clusters

In this paper we assess the accuracy of the B3LYP, X3LYP, and newly developed M06-L, M06-2X, and M06 functionals to predict the binding energies of neutral and charged water clusters including (H_2O)_n, n = 2−8, 20), H_3O+(H_2O_)n, n = 1−6, and OH−(H_2O)_n, n = 1−6. We also compare the predicted energies of two ion hydration and neutralization reactions on the basis of the calculated binding energies. In all cases, we use as benchmarks calculated binding energies of water clusters extrapolated to the complete basis set limit of the second-order Møller−Plesset perturbation theory with the effects of higher order correlation estimated at the coupled-cluster theory with single, double, and perturbative triple excitations in the aug-cc-pVDZ basis set. We rank the accuracy of the functionals on the basis of the mean unsigned error (MUE) between calculated benchmark and density functional theory energies. The corresponding MUE (kcal/mol) for each functional is listed in parentheses. We find that M06-L (0.73) and M06 (0.84) give the most accurate binding energies using very extended basis sets such as aug-cc-pV5Z. For more affordable basis sets, the best methods for predicting the binding energies of water clusters are M06-L/aug-cc-pVTZ (1.24), B3LYP/6-311++G(2d,2p) (1.29), and M06/aug-cc-PVTZ (1.33). M06-L/aug-cc-pVTZ also gives more accurate energies for the neutralization reactions (1.38), whereas B3LYP/6-311++G(2d,2p) gives more accurate energies for the ion hydration reactions (1.69)

pK_a Calculations of Aliphatic Amines, Diamines, and Aminoamides via Density Functional Theory with a Poisson−Boltzmann Continuum Solvent Model

In order to make reliable predictions of the acid−base properties of macroligands with a large number of ionizable sites such as dendrimers, one needs to develop and validate computational methods that accurately estimate the acidity constants (pK_a) of their chemical building blocks. In this article, we couple density functional theory (B3LYP) with a Poisson−Boltzmann continuum solvent model to calculate the aqueous pK_a of aliphatic amines, diamines, and aminoamides, which are building blocks for several classes of dendrimers. No empirical correction terms were employed in the calculations except for the free energy of solvation of the proton (H^+) adjusted to give the best match with experimental data. The use of solution-phase optimized geometries gives calculated pK_a values in excellent agreement with experimental measurements. The mean absolute error is 0.5 pK_a unit compared to experimental measurements. We find that geometry optimization in solution is essential for making accurate pK_a predictions for systems possessing intramolecular hydrogen bonds

Development and Validation of a ReaxFF Reactive Force Field for Cu Cation/Water Interactions and Copper Metal/Metal Oxide/Metal Hydroxide Condensed Phases

To enable large-scale reactive dynamic simulations of copper oxide/water and copper ion/water interactions we have extended the ReaxFF reactive force field framework to Cu/O/H interactions. To this end, we employed a multistage force field development strategy, where the initial training set (containing metal/metal oxide/metal hydroxide condensed phase data and [Cu(H_2O)_n]^(2+) cluster structures and energies) is augmented by single-point quantum mechanices (QM) energies from [Cu(H_2O)_n]^(2+) clusters abstracted from a ReaxFF molecular dynamics simulation. This provides a convenient strategy to both enrich the training set and to validate the final force field. To further validate the force field description we performed molecular dynamics simulations on Cu^(2+)/water systems. We found good agreement between our results and earlier experimental and QM-based molecular dynamics work for the average Cu/water coordination, Jahn−Teller distortion, and inversion in [Cu(H_2O)_6]^(2+) clusters and first- and second-shell O−Cu−O angular distributions, indicating that this force field gives a satisfactory description of the Cu-cation/water interactions. We believe that this force field provides a computationally convenient method for studying the solution and surface chemistry of metal cations and metal oxides and, as such, has applications for studying protein/metal cation complexes, pH-dependent crystal growth/dissolution, and surface catalysis

Addition of H_2O and O_2 to Acetone and Dimethylsulfoxide Ligated Uranyl(V) Dioxocations

Gas-phase complexes of the formula [UO_2(lig)]^+ (lig = acetone (aco) or dimethylsulfoxide (dmso)) were generated by electrospray ionization (ESI) and studied by tandem ion-trap mass spectrometry to determine the general effect of ligand charge donation on the reactivity of UO_2^+ with respect to water and dioxygen. The original hypothesis that addition of O_2 is enhanced by strong σ-donor ligands bound to UO_2^+ is supported by results from competitive collision-induced dissociation (CID) experiments, which show near exclusive loss of H_2O from [UO_2(dmso)(H_2O)(O_2)]^+, whereas both H_2O and O_2 are eliminated from the corresponding [UO_2(aco)(H_2O)(O_2)]^+ species. Ligand-addition reaction rates were investigated by monitoring precursor and product ion intensities as a function of ion storage time in the ion-trap mass spectrometer: these experiments suggest that the association of dioxygen to the UO_2^+ complex is enhanced when the more basic dmso ligand was coordinated to the metal complex. Conversely, addition of H_2O is favored for the analogous complex ion that contains an aco ligand. Experimental rate measurements are supported by density function theory calculations of relative energies, which show stronger bonds between UO_2^+ and O_2 when dmso is the coordinating ligand, whereas bonds to H_2O are stronger for the aco complex

Candidate carriers and synthetic spectra of the 21- and 30-mu protoplanetary nebular bands

Computational chemistry is used here to determine the vibrational line spectrum of several candidate molecules. It is shown that the thiourea functional group, associated with various carbonaceous structures (mainly compact and linear aromatic clusters), is able to mimic the 21-$\mu$m band emitted by a number of proto-planetary nebulae. The combination of nitrogen and sulphur in thiourea is the essential source of emission in this model: the band disappears if these species are replaced by carbon. The astronomical 21-$\mu$m feature extends redward to merge with another prominent band peaking between 25 and 30 $\mu$m, also known as the 30-$\mu$m band. It is found that the latter can be modelled by the combined spectra of aliphatic chains, made of CH$_{2}$ groups, oxygen bridges and OH groups, which provide the 30-$\mu$m emission. The absence of oxygen all but extinguishes the 30-$\mu$m emission. The emission between the 21- and 30-$\mu$m bands is provided mainly by thiourea attached to linear aromatic clusters. The chemical software reveals that the essential role of the heteroatoms N, S and O stems from their large electronic charge. It also allows to determine the type of atomic vibration responsible for the different lines of each structure, which helps selecting the most relevant structures. A total of 22 structures have been selected here, but their list is far from being exhaustive; they are only intended as examples of 3 generic classes. When background dust emission is added, model spectra are obtained, which are able to satisfactorily reproduce recent observations of proto-planetary nebulae. The relative numbers of atomic species used in this model are typically H:C:O:N:S=53:36:8:2:1.Comment: 9 pages, 14 figure