LOBSTER: Local orbital projections,atomic charges,and chemical-bonding analysis from projector-augmented-wave-based density-functional theory

We present an update on recently developed methodology and functionality in the computer program Local Orbital Basis Suite Toward Electronic-Structure Reconstruction (LOBSTER) for chemical-bonding analysis in periodic systems. LOBSTER is based on an analytic projection from projector-augmented wave (PAW) density-functional theory (DFT) computations (Maintz et al., J. Comput. Chem. 2013 , 34, 2557), reconstructing chemical information in terms of local, auxiliary atomic orbitals and thereby opening the output of PAW-based DFT codes to chemical interpretation. We demonstrate how LOBSTER has been improved by taking into account time-reversal symmetry, thereby speeding up the DFT and LOBSTER calculations by a factor of 2. Over the recent years, the functionalities have also been continually expanded, including accurate projected densities of states (DOSs), crystal orbital Hamilton population (COHP) analysis, atomic and orbital charges, gross populations, and the recently introduced k -dependent COHP. The software is offered free-of-charge for non-commercial research.     

Tuning Aqueous Supramolecular Polymerization by an Acid-Responsive Conformational Switch

Besides their widespread use in coordination chemistry, 2,2’-bipyridines are known for their ability to undergo cis–trans conformational changes in response to metal ions and acids, which has been primarily investigated at the molecular level. However, the exploitation of such conformational switching in self-assembly has remained unexplored. In this work, the use of 2,2’-bipyridines as acid-responsive conformational switches to tune supramolecular polymerization processes has been demonstrated. To achieve this goal, we have designed a bipyridine-based linear bolaamphiphile, 1 , that forms ordered supramolecular polymers in aqueous media through cooperative aromatic and hydrophobic interactions. Interestingly, addition of acid (TFA) induces the monoprotonation of the 2,2’-bipyridine moiety, leading to a switch in the molecular conformation from a linear (trans) to a V-shaped (cis) state. This increase in molecular distortion along with electrostatic repulsions of the positively charged bipyridine-H⁺ units attenuate the aggregation tendency and induce a transformation from long fibers to shorter thinner fibers. Our findings may contribute to opening up new directions in molecular switches and stimuli-responsive supramolecular materials.     

A Phosphine Functionalized β-Diketimine Ligand for the Synthesis of Manifold Metal Complexes

A bis(diphenyl)-phosphine functionalized β-diketimine (PNac-H) was synthesized as a flexible ligand for transition metal complexes. The newly designed ligand features symmetrically placed phosphine moieties around a β-diketimine unit, forming a PNNP-type pocket. Due to the hard and soft donor atoms (N vs. P) the ligand can stabilize various coordination polyhedra. A complete series ranging from coordination numbers 2 to 6 was realized. Linear, trigonal planar, square planar, tetrahedral, square pyramidal, and octahedral coordination arrangements containing the PNac-ligand around the metal center were observed by using suitable metal sources. Hereby, PNac-H or its anion PNac⁻ acts as mono-, bi- and tetradendate ligand. Such a broad flexibility is unusual for a rigid tetradentate system. The structural motifs were realized by treatment of PNac-H with a series of late transition metal precursors, for example, silver, gold, nickel, copper, platinum, and rhodium. The new complexes have been fully characterized by single crystal X-ray diffraction, NMR, IR, UV/Vis spectroscopy, mass spectrometry as well as elemental analysis. Additionally, selected complexes were investigated regarding their photophysical properties. Thus, PNac-H proved to be an ideal ligand platform for the selective coordination and stabilization of various metal ions in diverse polyhedra and oxidation states.     

Sustainable Peptide Synthesis Enabled by a Transient Protecting Group

The growing interest in synthetic peptides has prompted the development of viable methods for their sustainable production. Currently, large amounts of toxic solvents are required for peptide assembly from protected building blocks, and switching to water as a reaction medium remains a major hurdle in peptide chemistry. We report an aqueous solid‐phase peptide synthesis strategy that is based on a water‐compatible 2,7‐disulfo‐9‐fluorenylmethoxycarbonyl (Smoc) protecting group. This approach enables peptide assembly under aqueous conditions, real‐time monitoring of building block coupling, and efficient postsynthetic purification. The procedure for the synthesis of all natural and several non‐natural Smoc‐protected amino acids is described, as well as the assembly of 22 peptide sequences and the fundamental issues of SPPS, including the protecting group strategy, coupling and cleavage efficiency, stability under aqueous conditions, and crucial side reactions.     

Determining elemental strontium distribution in rat bones treated with strontium ranelate and strontium citrate using 2D micro-XRF and 3D dual energy K-edge subtraction synchrotron imaging

Strontium-based medications, such as strontium ranelate, have been suggested to have therapeutic effects in patients with osteoporosis. Strontium salts available off-shelf in stores across North America are assumed to provide similar effects as strontium ranelate and thus should lead to similar distributions of elemental strontium incorporated in bone. The objective of this study was to compare the spatial distribution of strontium in animal bones following the administration of strontium ranelate and strontium citrate. Seventeen-week-old Sprague–Dawley rats were split into three groups over 10 weeks and given 625 mg/kg/day of strontium ranelate and 676 mg/kg/day of strontium citrate; the control group received no additional supplementary strontium. The humeri were collected from all animals, and strontium distribution was mapped using 2D micro-XRF and 3D dual energy K-edge subtraction (KES) imaging. 2D and 3D elemental mapping methods demonstrated that strontium delivered during treatment by both salts had the same spatial distribution. 3D elemental strontium maps of treated animal bones showed that strontium was largely observed in the trabecular regions under the epiphyseal (growth) plate. The thickness of the strontium layers in both the strontium ranelate and strontium citrate sample was not significantly different (p = .9201). 2D micro-XRF and 3D dual-energy KES images effectively elucidated the spatial distribution of elemental strontium in calcified tissue. These methods provide a novel approach to evaluating the potential efficacy of strontium supplements in the treatment of osteoporosis.     

Acceleration of the cationic polymerization of an epoxy with hexanediol

Thin films of 3,4-epoxycyclohexylmethyl 3',4'-epoxycyclohexane carboxylate were UV irradiated (1.1 J cm^-2) under isothermal conditions ranging from 0 to 50°C. Under these conditions the polymerization advanced quickly but only to a conversion level of less than 10% before the reaction rate slowed by more than an order of magnitude. This drop off in rate was not caused by the glass transition temperature, T _g, reaching or exceeding the reaction temperature, T _rxn, since the epoxide's T _g remained at least 40°C below T _rxn. Raising the sample temperature above 60°C caused a sharp increase in the conversion level. At 100°C conversion exceeds 80% and the ultimate T _g approaches 190°C. The addition of 10 mass% 1,6-hexanediol, HD, to the epoxy caused the conversion at room temperature to quintuple over the level obtained without the alcohol present. The heat liberated from this alcohol epoxy blend during cure on a UV conveyor belt system caused the sample's temperature to increase by about 100°C above ambient whereas the epoxy alone under these conditions only experienced a modest temperature rise of about 26°C. If the amount of HD in the blend is increased above 10% the heat of reaction at 23°C decreases due to HD being trapped in a nonreactive crystalline phase. Boosting reaction temperatures above 50°C melts the HD crystals and yields significantly improved conversion ratios. As the level of alcohol blended with the epoxy is raised its ultimate T _g is lowered and when the concentration of alcohol in the blend nears 30 mass%T _g drops below room temperature. This revised version was published online in July 2006 with corrections to the Cover Date.     

Influence of connectivity and porosity on ligand-based luminescence in zinc metal-organic frameworks

Applications of metal-organic frameworks (MOFs) require close correlation between their structure and function. We describe the preparation and characterization of two zinc MOFs based on a flexible and emissive linker molecule, stilbene, which retains its luminescence within these solid materials. Reaction of trans-4,4'-stilbene dicarboxylic acid and zinc nitrate in N,N-dimethylformamide (DMF) yielded a dense 2-D network, 1, featuring zinc in both octahedral and tetrahedral coordination environments connected by trans-stilbene links. Similar reaction in N,N-diethylformamide (DEF) at higher temperatures resulted in a porous, 3-D framework structure, 2. This framework consists of two interpenetrating cubic lattices, each featuring basic zinc carboxylate vertices joined by trans-stilbene, analogous to the isoreticular MOF (IRMOF) series. We demonstrate that the optical properties of both 1 and 2 correlate with the local ligand environments observed in the crystal structures. Steady-state and time-resolved spectroscopic measurements reveal that the stilbene linkers in the dense structure 1 exhibit a small degree of interchromophore coupling. In contrast, the stilbenoid units in 2 display very little interaction in this low-density 3-D framework, with excitation and emission spectra characteristic of monomeric stilbenes, similar to the dicarboxylic acid in dilute solution. In both cases, the rigidity of the stilbene linker increases upon coordination to the inorganic units through inhibition of torsion about the central ethylene bond, resulting in luminescent crystals with increased emission lifetimes compared to solutions of trans-stilbene. The emission spectrum of 2 is found to depend on the nature of the incorporated solvent molecules, suggesting use of this or related materials in sensor applications.     

Adsorption, desorption, and surface-promoted hydrolysis of glucose-1-phosphate in aqueous goethite (α-FeOOH) suspensions

Adsorption, desorption, and precipitation reactions at environmental interfaces govern the fate of phosphorus in terrestrial and aquatic environments. Typically, a substantial part of the total pool of phosphorus consists of organophosphate, and in this study we have focused on the interactions between glucose-1-phosphate (G1P) and goethite (α-FeOOH) particles. The adsorption and surface-promoted hydrolysis reactions have been studied at room temperature as a function of pH, time, and total concentration of G1P by means of quantitative batch experiments in combination with infrared spectroscopy. A novel simultaneous infrared and potentiometric titration (SIPT) technique has also been used to study the rates and mechanisms of desorption of the surface complexes. The results have shown that G1P adsorption occurs over a wide pH interval and at pH values above the isoelectric point of goethite (IEP(goethite) = 9.4), indicating a comparatively strong interaction with the particle surfaces. As evidenced by IR spectroscopy, G1P formed pH-dependent surface complexes on goethite, and investigations of both adsorption and desorption processes were consistent with a model including three types of surface complexes. These complexes interact monodentately with surface Fe but differ in hydrogen bonding interactions via the auxiliary oxygens of the phosphate group. The apparent desorption rates were shown to be influenced by reaction pathways that include interconversion of surface species, which highlights the difficulty in determining the intrinsic desorption rates of individual surface complexes. Desorption results have also indicated that the molecular structures of surface complexes and the surface charge are two important determinants of G1P desorption rates. Finally, this study has shown that surface-promoted hydrolysis of G1P by goethite is base-catalyzed but that the extent of hydrolysis was small.     

Switching in Metal–Organic Frameworks

In recent years, metal–organic frameworks (MOFs) have become an area of intense research interest because of their adjustable pores and nearly limitless structural diversity deriving from the design of different organic linkers and metal structural building units (SBUs). Among the recent great challenges for scientists include switchable MOFs and their corresponding applications. Switchable MOFs are a type of smart material that undergo distinct, reversible, chemical changes in their structure upon exposure to external stimuli, yielding interesting technological applicability. Although the process of switching shares similarities with flexibility, very limited studies have been devoted specifically to switching, while a fairly large amount of research and a number of Reviews have covered flexibility in MOFs. This Review focuses on the properties and general design of switchable MOFs. The switching activity has been delineated based on the cause of the switching: light, spin crossover (SCO), redox, temperature, and wettability.