Basicity of bisperhalophenyl aurates toward closed-shell metal ions: metallophilicity and additional interactions

The interaction of bisperhalophenyl aurates [AuR₂]^? (R?=?C₆F₅, C₆F₃Cl₂, and C₆Cl₅) with the closed-shell Ag⁺, Cu⁺, and Tl⁺ ions has been studied theoretically and compared with the experimentally known X-ray diffraction crystal structures. Initially, the aurates have been fully optimized at MP2 level of theory in a D _2h symmetry. The analysis of the basicity of the three aurates [AuR₂]^? (R?=?C₆F₅, C₆F₃Cl₂ and C₆Cl₅) against Ag⁺ ions in a C _2v symmetry has been calculated in point-by-point bsse-corrected interaction energy analysis at HF and MP2 levels of theory. Taking into account the experimental observation of additional interactions between the heterometals and C _ipso atoms at the perhalophenyl rings or halogen atoms at the ortho position of the perhalophenyl rings, dinuclear models of the type [AuR₂]^?···Ag⁺ (R?=?C₆Cl₅, and C₆F₅); [AuR₂]^?···Cu⁺ (R?=?C₆F₅, and C₆Cl₅) and [AuR₂]^?···Tl⁺ (R?=?C₆F₅, and C₆Cl₅) with a C _2v , C ₂ , and C _s symmetries have been optimized at DFT-B3LYP level. The interaction energies have been computed through bsse-corrected single point HF and MP2 calculations. The energy stabilization provided and the heterometal preference have been analyzed and compared with the experimental results.     

Molecular structure of cyanidin metal complexes: Al(III) versus Mg(II)

Metal complexation by anthocyanins is a very efficient mechanism for protecting plants. While Mg is an essential metal for life, typically found bound to anthocyanins, Al interferes with the metabolism of the former. Density functional theory and the polarizable continuum model are used to study cyanin (the simplest anthocyanin bearing a catechol unit) complexes with Mg(II) and Al(III), considering different metal ligand stoichiometries. Results obtained for metal-binding energies indicate that Al(III) complexes are always more stable than those of Mg(II). Furthermore, reaction energies for the metal exchange process show that free Al(III) (hexaaquo complex) is always able to displace Mg(II). This displacement is more favored when the metal ligand ratio decreases. Thus, anthocyanins are implied in suppressing Al(III) toxicity by enabling its accumulation and reducing its migration to ecosystems. The characteristics of Al(III)?Ccyanidin and Mg(II)?Ccyanidin bonds are investigated using the quantum theory of atoms in molecules. We find these complexes are more stabilized by ion?Cdipole electrostatic interactions than by electron pair sharing, as predicted by the Hard and Soft Acids Theory. Globally, two factors increase the covalent character: replacement of Mg(II) by Al(III) and replacement of water by cyanidin ligands.     

On the mechanism of the N-glycosydic bond hydrolysis of 2��-deoxyguanosine: insights from first principles calculations

The effect of the activation of the nucleobase (leaving group) or the activation of the water molecule (nucleophile) by a general acid or a general base on the hydrolysis of the N-glycosydic bond of 2??-deoxyguanosine has been analyzed by means of density functional methods. First, we have considered two limiting cases: (1) the activation of the guanine by protonation at N7 and (2) the nucleophile attack by a hydroxyl ion, to separately evaluate the two kinds of activation. Next, we have studied the simultaneous activation of the leaving group and the nucleophile by introducing models of amino acid residues such as a formic acid (HCOOH) and imidazolium (C₃N₂H₅ ⁺), methylammonium (CH₃NH₃ ⁺) and formate (HCOO^?) ions in the system. It is shown that protonation of the nucleobase greatly catalyzes the hydrolysis of the N-glycosydic bond, the reaction occurring through a stepwise (D_N*A_N) mechanism with a discrete oxocarbenium ion intermediate. However, when a H₂O nucleophile molecule is activated by a formate anion, the reaction mechanism is a concerted A_ND_N but with different degrees of dissociative character of the transition structure depending on the acid that is activating the nucleobase.     

Spectral unmixing and clustering algorithms for assessment of single cells by Raman microscopic imaging

A detailed comparison of six multivariate algorithms is presented to analyze and generate Raman microscopic images that consist of a large number of individual spectra. This includes the segmentation algorithms for hierarchical cluster analysis, fuzzy C-means cluster analysis, and k-means cluster analysis and the spectral unmixing techniques for principal component analysis and vertex component analysis (VCA). All algorithms are reviewed and compared. Furthermore, comparisons are made to the new approach N-FINDR. In contrast to the related VCA approach, the used implementation of N-FINDR searches for the original input spectrum from the non-dimension reduced input matrix and sets it as the endmember signature. The algorithms were applied to hyperspectral data from a Raman image of a single cell. This data set was acquired by collecting individual spectra in a raster pattern using a 0.5-??m step size via a commercial Raman microspectrometer. The results were also compared with a fluorescence staining of the cell including its mitochondrial distribution. The ability of each algorithm to extract chemical and spatial information of subcellular components in the cell is discussed together with advantages and disadvantages.     

Probing vibrational wave packets in molecular excited states

A time-dependent theoretical method is used to describe a UV pump?CUV probe strategy to trace, at a femtosecond time scale, the motion of vibrational wave packets created in excited states of the hydrogen molecule by measuring single ionization probabilities. We use a spectral method to solve the time-dependent Schr?dinger equation in full dimensionality, including correlation and all electronic and vibrational degrees of freedom. A pump pulse initially creates a vibrational wave packet in the intermediate electronic excited states of $\hbox{H}_2$ . The frequency of the probe is chosen to ionize the target leaving the ion in a bound vibrational state. By varying the time delay between pulses, non-dissociative single ionization is enhanced or suppressed. Energy differential ionization probabilities are reported and compared with a model based on the Franck?CCondon approximation.     

Predicting binding energies of CDK6 inhibitors in the hit-to-lead process

The main challenge for the ??hit-to-lead?? stage in the drug discovery process relies on the accuracy of existing docking methods. In fact, accuracy of docking methods depends not only on the scoring function used to rank the poses but also on the ability of the docking method to reproduce the experimental binding mode. At this purpose, the performance of different approximations to properly dock and score compounds with known activity in a narrow range of IC₅₀ values was analyzed. A set of five ATP-competitive CDK6 inhibitors and three receptor conformations for CDK6 were considered for analysis, and three methodologies were used and analyzed in order to include different degrees of receptor flexibility. Thus, a completely rigid receptor is considered when using Glide, while the so-called Induced Fit Docking Protocol accounts for receptor sidechain rearrangements. Finally, force field calculations were also performed in order to consider a completely flexible receptor.     

Improved valence basis sets for divalent lanthanide 4f-in-core pseudopotentials

Improved energy-optimized (6s5p4d) and (7s6p5d) primitive valence basis sets have been derived for energy-consistent scalar-relativistic 4f-in-core pseudopotentials of the Stuttgart-Cologne variety modeling divalent lanthanides with a $4\hbox{f}^{n+1}$ occupation (n = 0?C13 for La?CYb). Segmented contracted basis sets covering the range of polarized double-, triple-, and quadruple-zeta quality, augmented by 2f1g correlation sets, were created for use in molecular calculations. The basis sets contain smaller (4s4p3d) and (5s5p4d) primitive subsets, which are designed in particular for solid state calculations of crystals containing divalent lanthanide ions. Hartree?CFock, density functional theory and coupled cluster results obtained with the new basis sets for lanthanide atomic ionization potentials as well as of geometry optimizations of various test molecules, i.e. selected lanthanide mono- and dihydrides, mono- and difluorides, and monooxides, show a satisfactory agreement with experimental data as well as with corresponding scalar-relativistic all-electron results. Core-polarization potentials are found to improve the results, especially for the atomic first and second ionization potentials.     

On the stability and lifetime of GaO2+ in the gas phase

The electronic structure, stability, and lifetime of GaO²⁺ have been investigated using high-level ab initio calculations. The potential energy curves have been calculated at the CCSD(T)/aug-cc-pV5Z and at the MS-CASPT2/ANO-RCC levels of theory. Lifetimes were evaluated using the Exterior Complex Scaling (ECS) method and B-spline basis functions. Our calculations show that GaO²⁺ is a metastable species in the gas phase, since the diatomic dication, in its ground state, lies 97.1?kcal/mol above the Ga⁺ (¹S)?+?O⁺ (⁴S) dissociation limit. However, the energy barrier that has to be overcome to reach this limit is 3?kcal/mol high so that five vibrational resonances can be accommodated between the bottom of the well and the top of the barrier. The evaluated lifetimes vary from hundreds of femtoseconds to approximately 1?s, so at least two of them have long enough lifetimes (1?s and 91???s) to be detected using mass spectrometry techniques, in agreement with the experimental evidence. In the experiment (Fiser et al. in Eur J Mass Spectrom 15:315?C324, 2009), GaO²⁺ was observed for an ion flight time of about ~12???s through a magnetic-sector mass spectrometer and unambiguously identified by its isotopic abundance. Our results also show that isotopic effects on the resonances?? energies and on their lifetimes, when ⁷⁰Ga is replaced by ⁶⁹Ga or ⁷¹Ga, are very small (~0.1 and ~1%, respectively), reflecting the large mass of the system.     

A fluidic-muscle driven force-controlled parallel platform for physical simulation of virtual spatial force-displacement laws

Described in this paper is a six-legged Stewart-Gough parallel platform driven by a relatively new type of fluidic muscles. The advantage of the platform is that it is virtually free of stick-slip effects. Thus, the device is well-suited for fine-tuned force control and for physical simulation of virtual force-displacement laws. The legs of the platform are of type RRPS and are equipped with a coaxial coil spring and a fluidic muscle providing push and pull forces. Each leg is equipped with a force sensor, a pressure sensor, and a magnetostrictive position encoder. The control for the platform consists of six control loops for the six operated actuators with model-based force control comprising individual gas models as well as the rubber nonlinearities for each leg. The control law also includes the gas flow in the proportional directional control valve in 3/3-way function. The present paper describes the basic architecture of the platform, the dynamic models, as well as testbed results for the existing fluidic-muscle parallel platform DynaHex. It is shown that the presented control scheme leads to a stable force control of the platform for quasi-static motion. As an application, the device will be employed in fields of biomechanics, as well as in general environments requiring physical simulation.     

Prediction of steady-state viscous and elastic properties of polyolefin melts in shear and elongation

The linear and nonlinear steady-state viscosities and elastic compliances were measured in shear and elongational flows for two low-density polyethylenes, a linear polypropylene, and two metallocene catalyzed polyethylenes (one linear and one long-chain branched) by Wolff et al. (Rheol Acta 49:95?C103, 2010) and Resch (dissertation, 2010). Comprehensive data of this type are rarely found in the literature, and comprehensive modeling of both viscous and elastic effects is even rarer. In this contribution, the reliability of a modeling approach proposed by Laun (J Rheol 30(3):459?C501, 1986) and based on the damping function concept is tested. The strain hardening seen for the long-chain branched polymers and its absence in the case of the linear polymer, the stronger decrease of the tensile compliance in comparison to the shear compliance with increasing stress, as well as the extended linear-viscoelastic regime of the shear viscosity in contrast to the shear compliance are correctly modeled. While the modeling of the nonlinear response in shear can be achieved with only one material parameter for most of the polymers considered here, the nonlinear modeling in elongation is achieved with two parameters. The same parameter values are shown to describe viscous as well as elastic properties of the melts, and thus the relations of Laun can be used to test the consistency of viscosity and compliance measurements.