A quasichemical approach for protein-cluster free energies in dilute solution

Reversible formation of protein oligomers or small clusters is a key step in processes such as protein polymerization, fibril formation, and protein phase separation from dilute solution. A straightforward, statistical mechanical approach to accurately calculate cluster free energies in solution is presented using a cell-based, quasichemical (QC) approximation for the partition function of proteins in an implicit solvent. The inputs to the model are the protein potential of mean force (PMF) and the corresponding subcell degeneracies up to relatively low particle densities. The approach is tested using simple two and three dimensional lattice models in which proteins interact with either isotropic or anisotropic nearest-neighbor attractions. Comparison with direct Monte Carlo simulation shows that cluster probabilities and free energies of oligomer formation (DeltaG(i) (0)) are quantitatively predicted by the QC approach for protein volume fractions approximately 10(-2) (weight/volume concentration approximately 10 g l(-1)) and below. For small clusters, DeltaG(i) (0) depends weakly on the strength of short-ranged attractive interactions for most experimentally relevant values of the normalized osmotic second virial coefficient (b(2) (*)). For larger clusters (i"2), there is a small but non-negligible b(2) (*) dependence. The results suggest that nonspecific, hydrophobic attractions may not significantly stabilize prenuclei in processes such as non-native aggregation. Biased Monte Carlo methods are shown to accurately provide subcell degeneracies that are intractable to obtain analytically or by direct enumeration, and so offer a means to generalize the approach to mixtures and proteins with more complex PMFs.     

Thiacyclophane cages and related bi- and tripodal molecules via transient polysulfenic acids

A series of bis- and tris-bridged thiacyclophane S-oxides, as racemates or meso products, have been synthesized with a new procedure. Starting from the corresponding thiols, in three steps, transient polyarene- and polyarylmethane-sulfenic acids were generated in the presence of di- and triethynylbenzenes. The thermal syn-addition of these sulfenic acids onto the triple bonds of the unsaturated acceptors was conducted in CH2Cl2 at 40 degrees C. The concentration of sulfoxide precursors of sulfenic acid and the sulfoxide/acceptor molar ratio addressed the syn-addition toward open-chain benzene sulfoxides or thiacyclophane S-oxides. Complete stereochemical control was observed in some reactions between polysulfenic acids and ethynylbenzenes, where the meso dithiacyclophane S,S'-dioxides were obtained exclusively, whereas 1:1 mixtures of meso/rac dithiacyclophanes S,S'-dioxides were isolated as products of other reactions. In almost all the cases, the obtained compounds were separated by column chromatography. The structure assignment of the new heterophanes was done on the basis of their diagnostic NMR spectra and X-ray crystallographic analysis of some of them. Open-chain polysulfinyl and polysulfinylmethyl benzenes, obtained as meso/rac mixtures, were separated and the products were fully characterized. Both synthesized cages, including trithia[3(3)](1,3,5)cyclophane S,S',S' '-trioxides, and bi- and tripodal benzene sulfoxides, appear promising in the field of coordination and material chemistry.     

Reactivity of 2,3-bis(2-pyridyl)pyrazine with [Re2(CO)8(CH3CN)2]: Molecular structures of [Re2(CO)8(C14H10N4)] and [Re2(CO)8(C14H10N4)Re2(CO)8]

The reaction of the labile compound [Re₂(CO)₈(CH₃CN)₂] with 2,3-bis(2-pyridyl)pyrazine in dichloromethane solution at reflux temperature afforded the structural dirhenium isomers [Re₂(CO)₈(C₁₄H₁₀N₄)] (1 and 2), and the complex [Re₂(CO)₈(C₁₄H₁₀N₄)Re₂(CO)₈] (3). In 1, the ligand is σ,σ′-N,N′-coordinated to a Re(CO)₃ fragment through pyridine and pyrazine to form a five-membered chelate ring. A seven-membered ring is obtained for isomer 2 by N-coordination of the 2-pyridyl groups while the pyrazine ring remains uncoordinated. For 2, isomers 2a and 2b are found in a dynamic equilibrium ratio [2a]/[2b]  =  7 in solution, detected by ¹H NMR (−50 °C, CD₃COCD₃), coalescence being observed above room temperature. The ligand in 3 behaves as an 8e-donor bridge bonding two Re(CO)₃ fragments through two (σ,σ′-N,N′) interactions. When the reaction was carried out in refluxing tetrahydrofuran, complex [Re₂(CO)₆(C₁₄H₁₀N₄)₂] (4) was obtained in addition to compounds 1-3. The dinuclear rhenium derivative 4 contains two units of the organic ligand σ,σ′-N,N′-coordinated in a chelate form to each rhenium core. The X-ray crystal structures for 1 and 3 are reported.     

New developments in the studies of the reactivity of cyclometallated palladium(II) compounds with homo- ([P,P],[As,As]) and heterobidentate ([P,N],[P,O]) ligands

Treatment of the chloro-bridged dinuclear compounds [{Pd[RC₆H₃C(H)NCy-C2,N]}(μ-Cl)]₂ (R = 4-(COH), 1; R = 5-(COH), 2) with bidentate phosphorus or arsenic diphosphines or diarsine ligands in 1:1 molar ratio gave the dinuclear complexes [{Pd[RC₆H₃C(H)NCy-C2,N](Cl)}₂{μ-(o-Tol)₂P(CH₂)₂P(o-Tol)₂}] (R = 4-(COH), 3; R = 5-(COH), 4), [{Pd[RC₆H₃C(H)NCy-C2,N](Cl)}₂{μ-Ph₂PC₄H₂(NH)CH₂PPh₂}] (R = 4-(COH), 5; R = 5-(COH), 6) and [{Pd[RC₆H₃C(H)NCy-C2,N](Cl)}₂{μ-Ph₂As(CH₂)₂AsPh₂}] (R = 4-(COH), 7; R = 5-(COH), 8) with the homobidentate [P,P] and [As,As] ligands in a bridging mode. Treatment of 1 and 2 with the aminophosphine Ph₂P(CH₂)₂NH₂ yields the dinuclear complexes [{Pd[RC₆H₃C(H)NCy-C2,N](Cl)}₂{μ-Ph₂P(CH₂)₂NH₂}] (R = 4-(COH), 9; R = 5-(COH), 10). The analogous reactions carried out in a 1:2 molar ratio, in the presence of NH₄PF₆ or NaClO₄, gave the mononuclear compounds [Pd{RC₆H₃C(H)NCy-C2,N}{(o-Tol)₂P(CH₂)₂P(o-Tol)₂-P,P}][PF₆] (R = 4-(COH), 11; R = 5-(COH), 12), [Pd{RC₆H₃C(H)NCy-C2,N}{Ph₂PC₄H₂(NH)CH₂PPh₂-P,P}][ClO₄] (R = 4-(COH), 13; R = 5-(COH), 14) and [Pd{RC₆H₃C(H)NCy-C2,N}{Ph₂As(CH₂)₂AsPh₂-As,As}][ClO₄](R = 4-(COH), 15; R = 5-(COH), 16), with the [P,P] and [As,As] ligands chelated to the palladium atom.Treatment of 2 with Ph₂P(CH₂)₃NH₂ in a 1:2 molar ratio in acetone in the presence of NH₄PF₆ afforded the mononuclear compound [Pd{5-(COH)C₆H₃C(H)NCy-C2,N}{Ph₂P(CH₂)₃N(Me₂)-P,N}][PF₆], 17, via intermolecular condensation between the aminophosphine and the solvent. Condensation was precluded using toluene as solvent to give [Pd{RC₆H₃C(H)NCy-C2,N}{Ph₂P(CH₂)_nNH₂-P,N}][PF₆], (n = 3, R = 5-(COH), 18; n = 2, R = 4-(COH), 19; n = 2, R = 5-(COH), 20). Treatment of 1 and 2 with Ph₂P(C₆H₄)CHO in a 1:2 molar ratio in the presence of NH₄PF₆ gave the mononuclear complexes [Pd{RC₆H₃C(H)NCy-C2,N}{2-(Ph₂P)C₆H₄CHO-P,O}][PF₆] (R = 4-(COH), 21; R = 5-(COH), 22) with the palladium atom bonded to four different atoms (C, N, P, O) and a chelating [P,O] ligand. The crystal structures of compounds 7, 11, 15 and 21 have been determined by X-ray crystallography.     

MgNb2O6 Modified K0.5Na0.5NbO3 Eco-Piezoceramics: Scalable Processing,Structural Distortion and Complex Impedance at Resonance

In this work, piezoceramics of the lead-free composition K_0.5Na_0.5NbO₃ with an increasing amount of MgNb₂O₆ (0, 0.5, 1, 2 wt.%) were prepared through conventional solid-state synthesis and sintered in air atmosphere at 1100 °C. The effect of magnesium niobate addition on structure, microstructure and piezoelectric properties was evaluated. The ceramics maintain the orthorhombic Amm2 phase for all compositions, while an orthorhombic Pbcm secondary phase was found for increasing the concentration of MgNb₂O₆. Our results show that densification of these ceramics can be significantly improved up to 94.9 % of theoretical density by adding a small amount of magnesium-based oxide (1 wt.%). Scanning electron microscopy morphology of the 1 wt.% system reveals a well-packed structure with homogeneous grain size of ∼2.72 μm. Dielectric and piezoelectric properties become optimal for 0.5–1.0 wt.% of MgNb₂O₆ that shows, with respect to the unmodified composition, either higher piezoelectric coefficients, lower anisotropy and relatively low piezoelectric losses (d₃₃=97 pC N⁻¹; d₃₁=−36.99 pC N⁻¹ and g₃₁=−14.04×10⁻³ mV N⁻¹; Q_p(d₃₁)=76 and Q_p(g₃₁)=69) or enhanced electromechanical coupling factors (k_p=29.06 % and k₃₁=17.25 %).     

Effect of zeolite structure on the selective catalytic reduction of NO with ammonia over Mn-Fe supported on ZSM-5, BEA,MOR and FER

A series of catalysts based on Mn-Fe loaded zeolites was prepared by impregnation and their activity in the selective catalytic reduction of NO with ammonia (NH₃-SCR) was investigated. The highest catalytic conversion was recorded for MnFe-ZSM-5 (MnFe-Z), followed by MnFe-BEA (MnFe-B) and MnFe-MOR (MnFe-M), while MnFe-FER (MnFe-F) showed a very poor activity over the entire temperature range. In order to evidence a correlation between the structure and acidity of the zeolites and NO conversion, the prepared samples were characterized by various techniques (ICP-AES, N₂ physisorption at 77 K, XRD, ²⁷NMR, Raman, FTIR spectroscopy of adsorbed ammonia, H₂-TPR, DRS UV–Vis, EPR and XPS). The superior catalytic activity of MnFe-Z at low temperature is attributed to the abundance of Mn⁴⁺ concentration as revealed by XPS, the highest NH₃-L/NH₄⁺ ratio indicative of the contribution of metals in generating Lewis acidic centers as evidenced by IR-NH3, and the better reducibility of manganese and iron on ZSM-5 which increases the kinetics for red-ox cycles as confirmed in TPR analysis. Fe₃Mn₃O₈ mixed oxide phase is also detected by XRD and XPS and can be associated with the high reducibility of MnFe-Z which generates a high oxidation ability favoring NO to NO₂ oxidation. Raman spectroscopy was also used to confirm the existence of a strong synergy between metals and ZSM-5 support revealed by the shift in the signal position and the decrease in band intensities. The results showed that the zeolite framework and acidity generate catalysts with different textural and structural properties which influence the metal dispersion and speciation and hence influence the catalytic performances.

     

Investigation on Optical and Biological Properties of 2-(4-Dimethylaminophenyl)benzothiazole Based Cycloplatinated Complexes

The optical and biological properties of 2-(4-dimethylaminophenyl)benzothiazole cycloplatinated complexes featuring bioactive ligands ([{Pt(Me₂N-pbt)(C₆F₅)}L] [L=Me₂N-pbtH 1 , p-dpbH (4-(diphenylphosphino)benzoic acid) 2 , o-dpbH (2-(diphenylphosphino)benzoic acid) 3 ), [Pt(Me₂N-pbt)(o-dpb)] 4 , [{Pt(Me₂N-pbt)(C₆F₅)}₂(μ-PR_nP)] [PR₄P=O(CH₂CH₂OC(O)C₆H₄PPh₂)₂ 5 , PR₁₂P=O{(CH₂CH₂O)₃C(O)C₆H₄PPh₂}₂ 6 ] are presented. Complexes 1 – 6 display ¹ILCT and metal-perturbed ³ILCT dual emissions. The ratio between both bands is excitation dependent, accomplishing warm-white emissions for 2 , 5 and 6 . The phosphorescent emission is lost in aerated solutions owing to photoinduced electron transfer to ³O₂ and the formation of ¹O₂, as confirmed in complexes 2 and 4 . They also exhibit photoinduced phosphorescence enhancement in non-degassed DMSO due to local oxidation of DMSO by sensitized ¹O₂, which causes a local degassing. Me₂N-pbtH and the complexes specifically accumulate in the Golgi apparatus, although only 2 , 3 and 6 were active against A549 and HeLa cancer cell lines, 6 being highly selective in respect to nontumoral cells. The potential photodynamic property of these complexes was demonstrated with complex 4 .     

Using Flow Cytometry to Evaluate the Stress Physiological Response of the Yeast <Emphasis Type="Italic">Saccharomyces carlsbergensis</Emphasis> ATCC 6269 to the Presence of 5-Hydroxymethylfurfural During Ethanol Fermentations

Lignocellulosic materials have been considered low-cost effective substrates for bioethanol production. However, lignocellulosic pretreatment releases toxic compounds such as 5-hydroxymethylfurfural (HMF) that is known to inhibit the yeast growth and ethanol production. In this work, flow cytometry was used to monitor the physiological response of the yeast Saccharomyces carlsbergensis ATCC 6269 in the presence of different initial HMF concentrations within the range of 0–15 g/L, in terms of cell membrane integrity, potential, and intracellular lipids. It was observed that the HMF presence affected more significantly the yeast growth than the ethanol production. At 15 g/L HMF, the yeast growth and fermentation ability were completely inhibited. The cell membrane integrity and potential decreased as the initial HMF concentration increased. At the end of the fermentation process with 10 g/L HMF, the yeast culture contained 45 % of cells with depolarized plasma membrane, 52 % of cells with permeabilized plasma membrane, and 53 % of cells with increasing reactive oxygen species (ROS) levels. Using the Nile Red stain, it was observed that intracellular polar lipids were more affected by the initial HMF concentration than the neutral lipids, probably due to the extensive membrane damage.     

Practical computational toolkits for dendrimers and dendrons structure design

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.