Generalized hybrid orbital for the treatment of boundary atoms in combined quantum mechanical and molecular mechanical calculations using the semiempirical parameterized model 3 method

The application of combined quantum mechanical (QM) and molecular mechanical methods to large molecular systems requires an adequate treatment of the boundary between the two approaches. In this article, we extend the generalized hybrid orbital (GHO) method to the semiempirical parameterized model 3 (PM3) Hamiltonian combined with the CHARMM force field. The GHO method makes use of four hybrid orbitals, one of which is included in the QM region in self-consistent field optimization and three are treated as auxiliary orbitals that do not participate in the QM optimization, but they provide an effective electric field for interactions. An important feature of the GHO method is that the semiempirical parameters for the boundary atom are transferable, and these parameters have been developed for a carbon boundary atom consistent with the PM3 model. The combined GHO-PM3/CHARMM model has been tested on molecular geometry and proton affinity for a series of organic compounds.Acknowledgement We thank the National Institutes of Health for support of this research.Contribution to the Jacopo Tomasi Honorary Issue     

A multi-scale approach to spin crossover in Fe(II) compounds

We report here for the first time a multi-scale study on the concept of spin-crossover compounds, which integrates improved density functionals, a polarizable force field and hybrid QM/MM calculations. This multi-scale setup is applied to the temperature dependence of spin states of a Fe(II) compound with trispyrazolylborate ligands that exhibits spin-crossover. Our study shows a transition temperature of around 290 K, which is in perfect agreement with experimental results. Moreover, based on our data we provide the origin of why spin transition occurs in this iron-compound: it results directly from spin-state changes in the iron-compound that lead to more favourable electrostatic interactions for the high-spin state.     

Characterization of fan spray atomizers through numerical simulation

The present paper focuses on the mathematical modeling of industrial fan spray atomizers. The two-phase flow taking place inside the nozzle’s tip and the exterior region near the outlet of three different industrial nozzle designs has been modeled and simulated. As a result, valuable information has been obtained regarding the influence of the inner geometry on the flow and also the formation and development of the liquid sheet. Characteristic magnitudes such as the discharge coefficient and the liquid sheet thickness factor have been obtained and validated through experimental measurements. The accumulation of liquid at the border of fan-shaped liquid sheets, also known as rim, has been studied in the analyzed designs, revealing the presence of a tangential velocity component in the liquid sheet and a relationship between the incoming flow rate of the rim and the angle of the liquid sheet. The dependence of the results on turbulence modeling has also been analyzed, drawing interesting conclusions regarding their influence on the liquid sheet mean flow characteristics and on the surrounding gas. Thus, the mathematical model developed has been proved to be a useful tool for nozzle manufacturers; it provides the most important characteristic parameters of the liquid sheet formed given certain nozzle geometry and, additionally, those data necessary to carry out studies of instability, breakup and atomization of the liquid sheet.     

Strategic Capture of the {Nb7} Polyoxometalate

Group V Nb-polyoxometalate (Nb-POM) chemistry generally lacks the elegant pH-controlled speciation exhibited by group VI (Mo, W) POM chemistry. Here three Nb-POM clusters were isolated and structurally characterized; [Nb₁₄O₄₀(O₂)₂H₃]¹⁴⁻, [((UO₂)(H₂O))₃Nb₄₆(UO₂)₂O₁₃₆H₈(H₂O)₄]²⁴⁻, and [(Nb₇O₂₂H₂)₄(UO₂)₇(H₂O)₆]²²⁻, that effectively capture the aqueous Nb-POM species from pH 7 to pH 10. These Nb-POMs illustrate a reaction pathway for control over speciation that is driven by counter-cations (Li⁺) rather than pH. The two reported heterometallic POMs (with UO₂²⁺ moieties) are stabilized by replacing labile H₂O/HO−Nb=O with very stable O=U=O. The third isolated Nb-POM features cis-yl-oxos, prior observed only in group VI POM chemistry. Moreover, with these actinide-heterometal contributions to the burgeoning Nb-POM family, it now transects all major metal groups of the periodic table.     

Identification and Affinity-Quantification of ß-Amyloid and α-Synuclein Polypeptides Using On-Line SAW-Biosensor-Mass Spectrometry

Bioaffinity analysis using a variety of biosensors has become an established tool for detection and quantification of biomolecular interactions. Biosensors, however, are generally limited by the lack of chemical structure information of affinity-bound ligands. On-line bioaffinity-mass spectrometry using a surface-acoustic wave biosensor (SAW-MS) is a new combination providing the simultaneous affinity detection, quantification, and mass spectrometric structural characterization of ligands. We describe here an on-line SAW-MS combination for direct identification and affinity determination, using a new interface for MS of the affinity-isolated ligand eluate. Key element of the SAW-MS combination is a microfluidic interface that integrates affinity-isolation on a gold chip, in-situ sample concentration, and desalting with a microcolumn for MS of the ligand eluate from the biosensor. Suitable MS- acquisition software has been developed that provides coupling of the SAW-MS interface to a Bruker Daltonics ion trap-MS, FTICR-MS, and Waters Synapt-QTOF- MS systems. Applications are presented for mass spectrometric identifications and affinity (K_D) determinations of the neurodegenerative polypeptides, ß-amyloid (Aß), and pathophysiological and physiological synucleins (α- and ß-synucleins), two key polypeptide systems for Alzheimer’s disease and Parkinson’s disease, respectively. Moreover, first in vivo applications of αSyn polypeptides from brain homogenate show the feasibility of on-line affinity-MS to the direct analysis of biological material. These results demonstrate on-line SAW-bioaffinity-MS as a powerful tool for structural and quantitative analysis of biopolymer interactions.

Molecular clips with extended aromatic sidewalls as receptors for electron-acceptor molecules. Synthesis and NMR, photophysical, and electrochemical properties

We have synthesized molecular clips 1 comprising (i) two benzo[k]fluoranthene sidewalls and (ii) a dimethylene-connected benzene bridge that carries two acetoxy (1a), hydroxy (1b), or methoxy (1c) substituents in the para position. Their NMR spectra, single-crystal structures, and photophysical (fluorescence intensity, lifetime, depolarization) and electrochemical properties are discussed. For the purpose of comparison, similar compounds (2 and 3) containing only one benzo[k]fluoranthene unit have been prepared and studied. The strongly fluorescent clips 1 form stable complexes with electron-acceptor guests because of a highly negative electrostatic potential on the inner van der Waals surface of their cavity. The complexation constants in chloroform solution for a variety of guests, determined by NMR and fluorescence titration, are much larger than those of the corresponding anthracene and naphthalene clips (4 and 5), particularly in the case of extended aromatic guests. The effect of the substituents in the para position of the benzene spacer unit of clips 1 is discussed on the basis of the host-guest complex structures obtained by X-ray analysis and molecular mechanics simulations. In the case of 9-dicyanomethylene-2,4,7-trinitrofluorene (TNF) guest, complex formation with clip 1a causes dramatic changes in the photophysical and electrochemical properties: (i) a new charge-transfer band at 600 nm arises, (ii) a very efficient quenching of the strong benzo[k]fluoranthene fluorescence takes place, (iii) shifts of both the first oxidation (clip-centered) and reduction (TNF-centered) potentials are observed, and (iv) reversible disassembling of the complex can be obtained by electrochemical stimulation.     

Nanosized trigonal prismatic and antiprismatic CuII coordination cages based on tricarboxylate linkers

3D coordination cages have been synthesized via the supramolecular 3 + 2 self-assembly of macrocyclic dicopper molecular clips and tricarboxylate linkers, the nature of which allows the introduction of different functionalities to the 3D cages.