Exploring the dynamics of calix[4]pyrrole: effect of solvent and fluorine substitution

Molecular dynamics simulations show that calix[4]pyrrole (CP) and octafluorocalix[4]pyrrole (8F-CP) are extremely flexible molecules. CP mainly adopts the 1,3-alternate conformation in all the solvents, although the percentage of alternative conformations increases in polar solvents, especially those with good hydrogen-bonding acceptor properties. However, in the case of 8F-CP, the cone conformation is the most populated in some solvents. Transitions between conformers are common and fast, and both CP and 8F-CP can adopt the cone conformation needed for optimum interaction with anions more easily than would be predicted on the basis of previous gas-phase calculations. Furthermore, the present studies show that when a fluoride anion is specifically placed initially in close proximity to CP and 8F-CP in their respective 1,3-alternate conformations, an extremely fast change to the cone conformation is observed in both cases. The results suggest that preorganization does not represent a major impediment to anion-binding for either CP or 8F-CP, and that ion-induced conformational changes can follow different mechanisms depending on the solvent and the chemical substituents present on the calix[4]pyrrole beta-pyrrolic positions.     

Influence of the variable thermophysical properties on the turbulent buoyancy-driven airflow inside open square cavities

The effects of the air variable properties (density, viscosity and thermal conductivity) on the buoyancy-driven flows established in open square cavities are investigated, as well as the influence of the stated boundary conditions at open edges and the employed differencing scheme. Two-dimensional, laminar, transitional and turbulent simulations are obtained, considering both uniform wall temperature and uniform heat flux heating conditions. In transitional and turbulent cases, the low-Reynolds k − ω turbulence model is employed. The average Nusselt number and the dimensionless mass-flow rate have been obtained for a wide and not yet covered range of the Rayleigh number varying from 10³ to 10¹⁶. The results obtained taking into account variable properties effects are compared with those calculated assuming constant properties and the Boussinesq approximation. For uniform heat flux heating, a correlation for the critical heating parameter above which the burnout phenomenon can be obtained is presented, not reported in previous works. The effects of variable properties on the flow patterns are analyzed.     

A barium perchlorate complex with a lateral macrobicycle derived from 4,13‐diaza‐18‐crown‐6 containing a pyridine Schiff base spacer

In the crystal structure of (perchlorato‐κ²O,O′))(28,31,36,39tetraoxa‐1,9,17,25,42‐penta­aza­penta­cyclo­[23.8.5.1^11,15.0^3,8.0^18,23]­nonatriaconta‐3,5,7,9,11,13,15,16,18,20,22‐un­decaene‐κ⁸N¹,N⁹, N¹⁷,N⁴²,O²⁸,O³¹,O³⁶,O³⁹)­barium(II) perchlorate, [Ba(ClO₄)(C₃₃H₄₁N₅O₄)](ClO₄), the Ba^II cation is situated in the macrobicyclic cavity, bound to only eight of the nine available donor atoms of the Schiff base macrobicyclic receptor. The pivotal N5 atom does not belong to the coordination sphere of the Ba^II ion, in spite of its endo conformation with the lone pair directed towards the inside of the cavity. The Ba^II ion completes its coordination core with two O atoms of one bidentate perchlorate group.     

Completing Lorentz violating massive gravity at high energies

Journal of Experimental and Theoretical Physics - Theories with massive gravitons are interesting for a variety of physical applications, ranging from cosmological phenomena to holographic modeling...     

Improving solution of discrete competitive facility location problems

We consider discrete competitive facility location problems in this paper. Such problems could be viewed as a search of nodes in a network, composed of candidate and customer demand nodes, which connections correspond to attractiveness between customers and facilities located at the candidate nodes. The number of customers is usually very large. For some models of customer behavior exact solution approaches could be used. However, for other models and/or when the size of problem is too high to solve exactly, heuristic algorithms may be used. The solution of discrete competitive facility location problems using genetic algorithms is considered in this paper. The new strategies for dynamic adjustment of some parameters of genetic algorithm, such as probabilities for the crossover and mutation operations are proposed and applied to improve the canonical genetic algorithm. The algorithm is also specially adopted to solve discrete competitive facility location problems by proposing a strategy for selection of the most promising values of the variables in the mutation procedure. The developed genetic algorithm is demonstrated by solving instances of competitive facility location problems for an entering firm.     

Mimicking Tyrosine Phosphorylation in Human Cytochrome c by the Evolved tRNA Synthetase Technique

Phosphorylation of tyrosine 48 of cytochrome c is related to a wide range of human diseases due to the pleiotropic role of the heme‐protein in cell life and death. However, the structural conformation and physicochemical properties of phosphorylated cytochrome c are difficult to study as its yield from cell extracts is very low and its kinase remains unknown. Herein, we report a high‐yielding synthesis of a close mimic of phosphorylated cytochrome c, developed by optimization of the synthesis of the non‐canonical amino acid p‐carboxymethyl‐L ‐phenylalanine (pCMF) and its efficient site‐specific incorporation at position 48. It is noteworthy that the Y48pCMF mutation significantly destabilizes the Fe?Met bond in the ferric form of cytochrome c, thereby lowering the pK_a value for the alkaline transition of the heme‐protein. This finding reveals the differential ability of the phosphomimic protein to drive certain events. This modified cytochrome c might be an important tool to investigate the role of the natural protein following phosphorylation.     

Molecular simulation of model liquid crystals in a strong aligning field

We report a computer simulation study of systems of perfectly aligned molecules interacting through the Gay–Berne (GB) potential model for two different values of the molecular anisotropy parameter κ, namely 3 and 4.4. The models are appropriate to gauge the effects of strong aligning fields on the thermodynamics and structural properties of thermotropic liquid crystals. According to our results, one of the main effects of the external field is to increase the range of stability of the smectic A phase, which indicates the existence of a strong coupling between orientational and translational order. For the κ?=?3?GB model the smectic phase, which is not stable in the absence of the field, is promoted when the molecules are constrained to be parallel. According to the simulation results, the smectic A-nematic transition is, in general, continuous; however, this transition appears to be first order at low pressure for the κ?=?4.4?GB fluid model.     

Multi-timescale investigation of radiation damage near TiO2 rutile grain boundaries

To understand the interactions between defects and grain boundaries (GBs) in oxides, two atomistic modeling methods were used to examine the role of GBs in a model system, rutile TiO₂, in modifying radiation-induced defect production and annealing. Molecular dynamics was used to investigate defect production near a symmetric tilt GB at both 300?K and 1000?K. The damage production is found to be sensitive to the initial distance of the primary knock-on atom from the GB. We find three distinct regimes in which GBs have different effects. Similar to GBs in metals, the GB absorbs more interstitials than vacancies at certain distances while this behavior of biased loading of interstitials diminishes at other distances. Further, we obtain the statistics of both interstitial and vacancy clusters produced in collision cascades in terms of their compositions at two temperatures. Perfectly stoichiometric defect clusters represent a small fraction of the total clusters produced. Moreover, a significant reduction in the number of interstitial clusters at 1000?K compared to 300?K is thought to be a consequence of enhanced migration of interstitials towards the GB. Finally, the kinetic properties of certain defect clusters were investigated with temperature accelerated dynamics, without any a priori assumptions of migration mechanisms. Small interstitial clusters become mobile at high temperatures while small vacancy clusters do not. Multiple migration pathways exist and are typically complex and non-intuitive. We use this kinetic information to explain experimental observations and predict their long-time migration behavior near GBs.     

{4,10‐Bis[2‐(2‐oxidobenzyl­idene­amino‐κ2N,O)benz­yl]‐1,7‐dioxa‐4,10‐diaza­cyclo­dodecane‐κ4O1,N4,O3,N10}ytterbium(III) perchlorate acetonitrile solvate

In the crystal structure of the title compound, [Yb(C₃₆H₃₈N₄O₄)]ClO₄·CH₃CN, the ytterbium ion is eight‐coordinated and deeply buried in the cavity of the dianionic Schiff base ligand. The coordination polyhedron may be described as a distorted square anti­prism that shows a twist angle of 29.5 (1)° between the two square planes. The receptor adopts a syn arrangement, with both pendent arms on the same side of the crown group, and there are two helicities (one associated with this layout of the pendent arms and the other with the conformation of the crown ring), which give rise to enantiomeric pairs of diastereoisomers, viz. Δ(λλλλ) and Λ(δδδδ).