A computational investigation of thermodynamics, structure, dynamics and solvation behavior in modified water models

We investigate the properties of geometrically modified water models by performing molecular dynamics simulations of perturbations of the extended simple point charge (SPC/E) model of water over a wide range of temperatures at 1 bar. The geometric modification consists of altering the H-O-H angle in SPC/E. The dipole moment is held constant by altering the O-H bond length, while the electrostatic charges are left unchanged. We find that a H-O-H angle of at least 100 degrees is necessary for the appearance of density anomalies and of solubility extrema with respect to temperature for small apolar solutes. We observe the occurrence of two incompatible types of structural order in these models: Tetrahedral, with waterlike translational order for bent models with H-O-H angles in excess of 100 degrees ; and linear, with Lennard-Jones-like orientationally averaged translational order for smaller H-O-H angles. Increasing the H-O-H angle causes the density to increase, while at the same time shifting waterlike anomalies to progressively higher temperatures. For bent models with H-O-H angle greater than SPC/E's, we observe arrest of translational motion at 300 K (115 degrees) and 330 K (120 degrees).     

Multiple conformational states in crystals and in solution in alphagamma hybrid peptides. Fragility of the C12 helix in short sequences

The conformational properties of foldamers generated from alphagamma hybrid peptide sequences have been probed in the model sequence Boc-Aib-Gpn-Aib-Gpn-NHMe. The choice of alpha-aminoisobutyryl (Aib) and gabapentin (Gpn) residues greatly restricts sterically accessible conformational space. This model sequence was anticipated to be a short segment of the alphagamma C12 helix, stabilized by three successive 4-->1 hydrogen bonds, corresponding to a backbone-expanded analogue of the alpha polypeptide 3(10)-helix. Unexpectedly, three distinct crystalline polymorphs were characterized in the solid state by X-ray diffraction. In one form, two successive C12 hydrogen bonds were obtained at the N-terminus, while a novel C17 hydrogen-bonded gamma alpha gamma turn was observed at the C-terminus. In the other two polymorphs, isolated C9 and C7 hydrogen-bonded turns were observed at Gpn (2) and Gpn (4). Isolated C12 and C9 turns were also crystallographically established in the peptides Boc-Aib-Gpn-Aib-OMe and Boc-Gpn-Aib-NHMe, respectively. Selective line broadening of NH resonances and the observation of medium range NH(i) <--> NH(i+2) NOEs established the presence of conformational heterogeneity for the tetrapeptide in CDCl3 solution. The NMR results are consistent with the limited population of the continuous C12 helix conformation. Lengthening of the (alphagamma) n sequences in the nonapeptides Boc-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Xxx (Xxx = Aib, Leu) resulted in the observation of all of the sequential NOEs characteristic of an alphagamma C12 helix. These results establish that conformational fragility is manifested in short hybrid alphagamma sequences despite the choice of conformationally constrained residues, while stable helices are formed on chain extension.     

Decavanadates with [Et3NH] and [Me2HN(CH2)2NHMe2]: Variation in protonation state and self-assembly

Synthesis, thermal behaviour and crystal structures of [Et₃NH]₄[V₁₀O₂₆(OH)₂] (1) and [Me₂HN(CH₂)₂NHMe₂]₃[V₁₀O₂₈] · 4H₂O (2) are reported. In the crystal lattice of 1, the anions form discrete dimers via O–H···O hydrogen bonds and the cations are connected to the respective anions through N–H···O hydrogen bonds. On the other hand, 2 forms a complex three-dimensional network due to involvement of the cations, the anions and the lattice water in O–H···O and N–H···O hydrogen bonds.     

Tuning of Microenvironment in Covalent Organic Framework via Fluorination Strategy promotes Selective CO2 Capture

Herein, we have designed and synthesized two heteroatom (N, O) rich covalent organic frameworks (COF), PD-COF and TF-COF , respectively, to demonstrate their relative effect on CO₂ adsorption capacity and also CO₂/N₂ selectivity. Compared to the non-fluorinated PD-COF (BET surface area 805 m² g⁻¹, total pore volume 0.3647 ccg⁻¹), a decrease in BET surface area and also pore volume have been observed for fluorinated TF-COF due to the incorporation of fluorine to the porous framework (BET surface area 451 m² g⁻¹, total pore volume 0.2978 ccg⁻¹). This fact leads to an enormous decrease in the CO₂ adsorption capacity and CO₂/N₂ selectivity of TF-COF , though it shows stronger affinity towards CO₂ with a Qst of 37.76 KJ/mol. The more CO₂ adsorption capacity by PD-COF can be attributed to the large specific surface area with considerable amount of micropore volume compared to the TF-COF . Further, PD-COF exhibited CO₂/N₂ selectivity of 16.8, higher than that of TF-COF (CO₂/N₂ selectivity 13.4).     

Olefin cis‐Dihydroxylation and Aliphatic C?H Bond Oxygenation by a Dioxygen‐Derived Electrophilic Iron–Oxygen Oxidant

Many iron‐containing enzymes involve metal–oxygen oxidants to carry out O₂‐dependent transformation reactions. However, the selective oxidation of C H and CC bonds by biomimetic complexes using O₂ remains a major challenge in bioinspired catalysis. The reactivity of iron–oxygen oxidants generated from an Fe^II–benzilate complex of a facial N₃ ligand were thus investigated. The complex reacted with O₂ to form a nucleophilic oxidant, whereas an electrophilic oxidant, intercepted by external substrates, was generated in the presence of a Lewis acid. Based on the mechanistic studies, a nucleophilic Fe^II–hydroperoxo species is proposed to form from the benzilate complex, which undergoes heterolytic O O bond cleavage in the presence of a Lewis acid to generate an Fe^IV–oxo–hydroxo oxidant. The electrophilic iron–oxygen oxidant selectively oxidizes sulfides to sulfoxides, alkenes to cis‐diols, and it hydroxylates the C H bonds of alkanes, including that of cyclohexane.     

Shear and extensional rheology of carbon nanofiber suspensions

The morphology and rheology of carbon nanofiber (CNF) suspensions were studied. The CNFs, produced by decomposing organic vapors at elevated temperature in the presence of metal catalysts, have characteristic diameter and length of 100 nm and 20–100 m, respectively. The CNFs, as delivered, have a strong tendency to clump into mm-sized agglomerates. The efficacy of CNF/glycerol-water suspensions was studied vs. two processing parameters: mechanical sonication and chemical treatment. Experimental measurements revealed that sonication alone reduces the size of CNF clumps from millimeter to micrometer scale, but cannot achieve uniform dispersion. The chemically untreated sonicated suspensions contain clumps of nanofibers with a characteristic size of 20×50 m, together with smaller aggregations of partially dispersed nanofibers. In response to this unsatisfactory dispersion, the effect of acid treatment before dispersion was investigated. This acid treatment, which makes the surface of the CNFs more hydrophilic, greatly improves dispersion in the aqueous solution: treatment followed by sonication results in a uniform dispersion of individual nanofibers. At the same time, however, we observed that surface treatment and subsequent sonication greatly shorten the nanofibers.The rheology of CNF/glycerol-water suspensions is highly non-Newtonian both in shear and extensional flows, with strong dependence on the dispersion, particle length, and concentration of the CNFs. As the solvent is Newtonian, all of the elastic and strain-rate dependent behavior in the CNF/aqueous suspensions derives from the addition of nanofibers. The steady shear viscosity of the untreated-sonicated (poorly dispersed, with longer fibers) suspensions is highly shear thinning with a viscosity that increases three orders of magnitude as concentration varies from 0.5 wt% to 5 wt%. Beyond 5 wt% the suspensions are too viscous to be effectively mixed by sonication. When the CNFs are chemically treated and then sonicated (resulting in much better dispersion but shorter fibers), the viscosity exhibits little shear thinning, and only varies by a factor of two from pure solvent to 5 wt%. In small amplitude oscillatory shear measurements, we found strong indications of elastic behavior in both the treated and untreated suspensions, with elastic modulus G greater than loss modulus G. In particular, for both systems G exhibits a low-frequency plateau when nanofiber concentration is 3 wt% or above, a characteristic of elastic solidlike response. Again, there is a strong dependence on CNF dispersion and fiber length: At low frequencies, the elastic modulus of the 5 wt% untreated suspension (with agglomerates and longer fibers) is four orders of magnitude larger than that of the 5 wt% treated suspension (with uniformly dispersed, shorter fibers). In addition, G of untreated suspensions is a much stronger function of concentration than that of treated suspensions, indicative of network formation.The rheology and morphology of nanofiber suspensions were related by identifying morphology of the suspensions with the assumptions of the kinetic theory-based elastic and rigid dumbbell constitutive models; the approach is to specify the parameters in the kinetic theory models in terms of microscale morphological features measured in the SEM. Of those investigated, the elastic dumbbell model with anisotropic hydrodynamic drag is the most successful, effectively modeling the small amplitude oscillatory shear and steady shear behavior of the treated sonicated suspensions. As for the treated unsonicated and untreated sonicated suspensions, which contain mesoscale agglomerates not present in the underlying assumptions of the dumbbell models, it is discovered that the elastic dumbbell with parameters assigned from morphological measurements predicts the correct trends in the steady shear experiments, but fails to accurately predict the small amplitude oscillatory shear experiments.     

Structure Determination of [Au18(SR)14]

Unravelling the atomic structures of small gold clusters is the key to understanding the origin of metallic bonds and the nucleation of clusters from organometallic precursors. Herein we report the X‐ray crystal structure of a charge‐neutral [Au₁₈(SC₆H₁₁)₁₄] cluster. This structure exhibits an unprecedented bi‐octahedral (or hexagonal close packing) Au₉ kernel protected by staple‐like motifs including one tetramer, one dimer, and three monomers. Until the present, the [Au₁₈(SC₆H₁₁)₁₄] cluster is the smallest crystallographically characterized gold cluster protected by thiolates and provides important insight into the structural evolution with size. Theoretical calculations indicate charge transfer from surface to kernel for the HOMO–LUMO transition.     

Design of Photocaged Puromycin for Nascent Polypeptide Release and Spatiotemporal Monitoring of Translation

The antibiotic puromycin, which inhibits protein translation, is used in a broad range of biochemical applications. The synthesis, characterization, and biological applications of NVOC‐puromycin, a photocaged derivative that is activated by UV illumination, are presented. The caged compound had no effect either on prokaryotic or eukaryotic translation or on the viability of HEK 293 cells. Furthermore, no significant release of ribosome‐bound polypeptide chains was detected in vitro. Upon illumination, cytotoxic activity, in vitro translation inhibition, and polypeptide release triggered by the uncaging of NVOC‐puromycin were equivalent to those of the commercial compound. The quantum yield of photolysis was determined to be 1.1±0.2 % and the NVOC‐puromycin was applied to the detection of newly translated proteins with remarkable spatiotemporal resolution by using two‐photon laser excitation, puromycin immunohistochemistry, and imaging in rat hippocampal neurons.     

Olefin cis‐Dihydroxylation and Aliphatic CH Bond Oxygenation by a Dioxygen‐Derived Electrophilic Iron–Oxygen Oxidant

Many iron‐containing enzymes involve metal–oxygen oxidants to carry out O₂‐dependent transformation reactions. However, the selective oxidation of C? H and C?C bonds by biomimetic complexes using O₂ remains a major challenge in bioinspired catalysis. The reactivity of iron–oxygen oxidants generated from an Fe^II–benzilate complex of a facial N₃ ligand were thus investigated. The complex reacted with O₂ to form a nucleophilic oxidant, whereas an electrophilic oxidant, intercepted by external substrates, was generated in the presence of a Lewis acid. Based on the mechanistic studies, a nucleophilic Fe^II–hydroperoxo species is proposed to form from the benzilate complex, which undergoes heterolytic O? O bond cleavage in the presence of a Lewis acid to generate an Fe^IV–oxo–hydroxo oxidant. The electrophilic iron–oxygen oxidant selectively oxidizes sulfides to sulfoxides, alkenes to cis‐diols, and it hydroxylates the C? H bonds of alkanes, including that of cyclohexane.     

Influence of Arrestin on the Photodecay of Bovine Rhodopsin

Continued activation of the photocycle of the dim‐light receptor rhodopsin leads to the accumulation of all‐trans‐retinal in the rod outer segments (ROS). This accumulation can damage the photoreceptor cell. For retinal homeostasis, deactivation processes are initiated in which the release of retinal is delayed. One of these processes involves the binding of arrestin to rhodopsin. Here, the interaction of pre‐activated truncated bovine visual arrestin (Arr^Tr) with rhodopsin in 1,2‐diheptanoyl‐sn‐glycero‐3‐phosphocholine (DHPC) micelles is investigated by solution NMR techniques and flash photolysis spectroscopy. Our results show that formation of the rhodopsin–arrestin complex markedly influences partitioning in the decay kinetics of rhodopsin, which involves the simultaneous formation of a meta II and a meta III state from the meta I state. Binding of Arr^Tr leads to an increase in the population of the meta III state and consequently to an approximately twofold slower release of all‐trans‐retinal from rhodopsin.