Integrating open‐source software applications to build molecular dynamics systems

Three open‐source applications, NanoEngineer‐1, packmol, and mis2lmp are integrated using an open‐source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open‐source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol‐a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real‐world research requirements and integrated to create a new capability. © 2014 Wiley Periodicals, Inc.     

Cooperative Chemotaxis of Magnesium Microswimmers for Corrosion Spotting

Numerous artificial micro- and nanomotors, as well as various swimmers have been inspired by living organisms that are able to move in a coordinated manner. Their cooperation has also gained a lot of attention because the resulting clusters are able to adapt to changes in their environment and to perform complex tasks. However, mimicking such a collective behavior remains a challenge. In the present work, magnesium microparticles are used as chemotactic swimmers with pronounced collective features, allowing the gradual formation of macroscopic agglomerates. The formed clusters act like a single swimmer able to follow pH gradients. This dynamic behavior can be used to spot localized corrosion events in a straightforward way. The autonomous docking of the swimmers to the corrosion site leads to the formation of a local protection layer, thus increasing corrosion resistance and triggering partial self-healing.     

Characteristics of Dietary Fatty Acids Isolated from Historic Dental Calculus of the 17th- and 18th-Century Inhabitants of the Subcarpathian Region (Poland)

Dental calculus analysis can be a valuable source of archaeological knowledge, since it preserves not only microbial and host biomolecules but also dietary and environmental debris, as well as metabolic products likely originating from dietary and craft activities. Here we described GC-MS analysis of a set of historic dental calculus samples from the front teeth of the mandibles of seven individuals found in 17th- and 18th-century graves in the city of Rzeszow, located in South-eastern Poland. We have found that only saturated fatty acids, which are characteristic for fats of animal origin, were present in the tested samples. Our preliminary results indicate that the diet of modern-period inhabitants of Rzeszow was rich in animal products, such as meat and dairy products.     

The Ising version of the t–J model

The t–J model is analysed in the limit of strong anisotropy, where the transverse components of electron spin are neglected. We propose a slave-particle-type approach that is valid, in contradiction to many of the standard approaches, in the low-doping regime and becomes exact for a half-filled system. We describe an effective method that allows to numerically study the system with the no-double-occupancy constraint rigorously taken into account at each lattice site. Then, we use this approach to demonstrate the destruction of the antiferromagnetic order by increasing the doping and formation of Nagaoka polarons in the strong interaction regime.     

Palladium‐Catalyzed Stereoselective Intramolecular Oxidative Amidation of Alkenes in the Synthesis of 1,3‐ and 1,4‐Amino Alcohols and 1,3‐Diamines

An efficient and practical Pd‐catalyzed intramolecular oxidative allylic amidation provides facile access to derivatives of 1,3‐ and 1,4‐amino alcohols and 1,3‐diamines. The method operates under mild reaction conditions (RT) with molecular oxygen (1 atm) as the sole reoxidant of Pd. Excellent diastereoselectivities were attained with substrates bearing a secondary stereogenic center     

Ultrafast Photoswitching in a Copper‐Nitroxide‐Based Molecular Magnet

Molecular compounds with photoswitchable magnetic properties have been intensively investigated over the last decades due to their prospective applications in nanoelectronics, sensing and magnetic data storage. The family of copper‐nitroxide‐based molecular magnets represents a new promising type of photoswitchable compounds. We report the first study of these appealing systems using femtosecond optical spectroscopy. We unveil the mechanism of ultrafast (<50 fs) spin state photoswitching and establish its principal differences compared to other photoswitchable magnets. On this basis, we propose potential advantages of copper‐nitroxide‐based molecular magnets for the future design of ultrafast magnetic materials.     

Optimization of Adsorbent Layer Type and Developing Solvent in Coccidiostats Sample Preparation with Procedure of Solvent Front Position Extraction

Coccidiostats are drugs used against coccidiosis, a common disease among breeding animals. Their widespread application leads to the appearance of their residues in food, which is potentially harmful for human health and life. The European Union has established limits of concentrations of these drugs in premixtures and food. Nowadays, there are many methods for monitoring coccidiostats’ presence in market products, but their frequent weakness is sample preparation. Solvent Front Position Extraction is a planar chromatography-based sample preparation method that allows for effective assay of samples with coccidiostats when coupled with LC-MS/MS. The purpose of this research was to find common conditions for the effective isolation of eight coccidiostats from biological sample components with both lower and higher retention than the substances of interest. The acquired results were used for effective isolation of monensin and salinomycin from the premixture samples and allowed for their quantitative determination. The application of a semi-automatic device for the development of chromatograms positively impacted the results, confirming the effectiveness of the method for determining coccidiostats in biological samples.     

Bases,solvates and salts: new benzimidazole‐ and pyridine‐scaffolded ligands

The intermolecular interactions in the structures of a series of Schiff base ligands have been thoroughly studied. These ligands can be obtained in different forms, namely, as the free base 2‐[(2E)‐2‐(1H‐imidazol‐4‐ylmethylidene)‐1‐methylhydrazinyl]pyridine, C₁₀H₁₁N₅, 1 , the hydrates 2‐[(2E)‐2‐(1H‐imidazol‐2‐ylmethylidene)‐1‐methylhydrazinyl]‐1H‐benzimidazole monohydrate, C₁₂H₁₂N₆·H₂O, 2 , and 2‐{(2E)‐1‐methyl‐2‐[(1‐methyl‐1H‐imidazol‐2‐yl)methylidene]hydrazinyl}‐1H‐benzimidazole 1.25‐hydrate, C₁₃H₁₄N₆·1.25H₂O, 3 , the monocationic hydrate 5‐{(1E)‐[2‐(1H‐1,3‐benzodiazol‐2‐yl)‐2‐methylhydrazinylidene]methyl}‐1H‐imidazol‐3‐ium trifluoromethanesulfonate monohydrate, C₁₂H₁₃N₆⁺·CF₃O₃S^?·H₂O, 5 , and the dicationic 2‐{(2E)‐1‐methyl‐2‐[(1H‐imidazol‐3‐ium‐2‐yl)methylidene]hydrazinyl}pyridinium bis(trifluoromethanesulfonate), C₁₀H₁₃N₅²⁺·2CF₃O₃S^?, 6 . The connection between the forms and the preferred intermolecular interactions is described and further studied by means of the calculation of the interaction energies between the neutral and charged components of the crystal structures. These studies show that, in general, the most important contribution to the stabilization energy of the crystal is provided by π–π interactions, especially between charged ligands, while the details of the crystal architecture are influenced by directional interactions, especially relatively strong hydrogen bonds. In one of the structures, a very interesting example of the nontypical F…O interaction was found and its length, 2.859 (2) Å, is one of the shortest ever reported.     

Synthesis,Crystal Structures,and Spectroscopic Properties of Novel Gadolinium and Erbium Triphenylsiloxide Coordination Entities

In alkali metal and lanthanide coordination chemistry, triphenylsiloxides seem to be unduly underappreciated ligands. This is as surprising as that such substituents play a crucial role, among others, in stabilizing rare oxidation states of lanthanide ions, taking a part of intramolecular and molecular interactions stabilizing metal-oxygen cores and many others. This paper reports the synthesis and characterization of new lithium [Li₄(OSiPh₃)₄(THF)₂] (1), and sodium [Na₄(OSiPh₃)₄] (2) species, which were later used in obtaining novel gadolinium [Gd(OSiPh₃)₃(THF)₃]·THF (3), and erbium [Er(OSiPh₃)₃(THF)₃]·THF (4) configuration, it can result in res were determined for all 1–4 compounds, and in addition, IR, Raman, absorption spectroscopy studies were conducted for 3 and 4 lanthanide compounds. Furthermore, direct current (dc) variable-temperature magnetic susceptibility measurements on polycrystalline samples of 3 and 4 were carried out in the temperature range 1.8–300 K. The 3 shows behavior characteristics for the paramagnetism of the Gd³⁺ ion. In contrast, the magnetic properties of 4 are dominated by the crystal field effect on the Er³⁺ ion, masking the magnetic interaction between magnetic centers of neighboring molecules.