molSimplify: A toolkit for automating discovery in inorganic chemistry

We present an automated, open source toolkit for the first‐principles screening and discovery of new inorganic molecules and intermolecular complexes. Challenges remain in the automatic generation of candidate inorganic molecule structures due to the high variability in coordination and bonding, which we overcome through a divide‐and‐conquer tactic that flexibly combines force‐field preoptimization of organic fragments with alignment to first‐principles‐trained metal‐ligand distances. Exploration of chemical space is enabled through random generation of ligands and intermolecular complexes from large chemical databases. We validate the generated structures with the root mean squared (RMS) gradients evaluated from density functional theory (DFT), which are around 0.02 Ha/au across a large 150 molecule test set. Comparison of molSimplify results to full optimization with the universal force field reveals that RMS DFT gradients are improved by 40%. Seamless generation of input files, preparation and execution of electronic structure calculations, and post‐processing for each generated structure aids interpretation of underlying chemical and energetic trends. © 2016 Wiley Periodicals, Inc.     

Ultra‐Fast Degradation of Chemical Warfare Agents Using MOF–Nanofiber Kebabs

The threat associated with chemical warfare agents (CWAs) motivates the development of new materials to provide enhanced protection with a reduced burden. Metal–organic frame‐works (MOFs) have recently been shown as highly effective catalysts for detoxifying CWAs, but challenges still remain for integrating MOFs into functional filter media and/or protective garments. Herein, we report a series of MOF–nanofiber kebab structures for fast degradation of CWAs. We found TiO₂ coatings deposited via atomic layer deposition (ALD) onto polyamide‐6 nanofibers enable the formation of conformal Zr‐based MOF thin films including UiO‐66, UiO‐66‐NH₂, and UiO‐67. Cross‐sectional TEM images show that these MOF crystals nucleate and grow directly on and around the nanofibers, with strong attachment to the substrates. These MOF‐functionalized nanofibers exhibit excellent reactivity for detoxifying CWAs. The half‐lives of a CWA simulant compound and nerve agent soman (GD) are as short as 7.3 min and 2.3 min, respectively. These results therefore provide the earliest report of MOF–nanofiber textile composites capable of ultra‐fast degradation of CWAs.     

Crystal polymorphism of protein GB1 examined by solid-state NMR spectroscopy and X-ray diffraction

The study of micro- or nanocrystalline proteins by magic-angle spinning (MAS) solid-state NMR (SSNMR) gives atomic-resolution insight into structure in cases when single crystals cannot be obtained for diffraction studies. Subtle differences in the local chemical environment around the protein, including the characteristics of the cosolvent and the buffer, determine whether a protein will form single crystals. The impact of these small changes in formulation is also evident in the SSNMR spectra; however, the changes lead only to correspondingly subtle changes in the spectra. Here, we demonstrate that several formulations of GB1 microcrystals yield very high quality SSNMR spectra, although only a subset of conditions enable growth of single crystals. We have characterized these polymorphs by X-ray powder diffraction and assigned the SSNMR spectra. Assignments of the 13C and 15N SSNMR chemical shifts confirm that the backbone structure is conserved, indicative of a common protein fold, but side chain chemical shifts are changed on the surface of the protein, in a manner dependent upon crystal packing and electrostatic interactions with salt in the mother liquor. Our results demonstrate the ability of SSNMR to reveal minor structural differences among crystal polymorphs. This ability has potential practical utility for studying the formulation chemistry of industrial and therapeutic proteins, as well as for deriving fundamental insights into the phenomenon of single-crystal growth.     

Modified active site coordination in a clinical mutant of sulfite oxidase

The molybdenum site of the Arginine 160 --> Glutamine clinical mutant of the physiologically vital enzyme sulfite oxidase has been investigated by a combination of X-ray absorption spectroscopy and density functional theory calculations. We conclude that the mutant enzyme has a six-coordinate pseudo-octahedral active site with coordination of Glutamine Oepsilon to molybdenum. This contrasts with the wild-type enzyme which is five-coordinate with approximately square-based pyramidal geometry. This difference in the structure of the molybdenum site explains many of the properties of the mutant enzyme which have previously been reported.     

Modulation of fluorescence through coassembly of molecules in organic nanostructures

This paper describes the fluorescence of bimolecular coassemblies that form one-dimensional nanostructures. One molecule is a fluorescent peptide amphiphile containing its branched stilbene chromophore covalently linked to the hydrophilic end of the amphiphile, and the second molecule is a shorter, nonfluorescent peptide amphiphile of complementary charge. Using circular dichroism we observe that mixing both molecules results in coassemblies that exhibit a beta-sheet signature in the peptide region indicative of these types of nanostructures. The nature of the coassembly is dependent on the molar ratio of each component, and the changing CD spectra suggest the formation of domains along the length of the nanofibers with decreasing concentrations of the fluorescent component. In coassemblies with dilute concentrations of the fluorophore, we observe an increase in fluorescence intensity and quantum yield, as well as chiral transfer to the achiral segment of the fluorescent peptide amphiphile. The coassemblies studied containing a fluorescent component at a low molar ratio exhibit fluorescence resonance energy transfer to fluorescent acceptors in solution. When the nonfluorescent peptide amphiphile component is designed to bind the important bioactive polysaccharide heparin, a selective transfer of energy is observed between fluorescein-tagged heparin and the coassemblies in both dilute solution and in macroscopic gels.     

Intramolecular carbozincation of unactivated alkenes occurs through a zinc radical transfer mechanism

The cyclizations of a number of terminally unsaturated alkenyl zinc iodides to cyclopentylmethylzinc iodides, formerly believed to be nonradical in nature, have been revealed as radical chain cyclizations initiated by adventitious oxygen. Five cases are presented in which the published carbozincation cis/trans selectivities are essentially the same as those found for the cyclizations of the unsaturated alkyl iodide precursors of the alkylzinc iodides by the iodine atom transfer method at approximately the same temperatures. In addition, it has been found that one of the organozinc cyclizations does not occur in a system in which oxygen has been rigorously excluded. The combined findings strongly suggest that these organozinc cyclizations occur by a zinc radical transfer mechanism rather than by a conventional carbometallation that is thought to occur with the analogous organolithium and organomagnesium cyclizations.     

Determination of polybrominated diphenyl ethers in environmental standard reference materials

Standard reference materials (SRMs) are valuable tools in developing and validating analytical methods to improve quality assurance standards. The National Institute of Standards and Technology (NIST) has a long history of providing environmental SRMs with certified concentrations of organic and inorganic contaminants. Here we report on new certified and reference concentrations for 27 polybrominated diphenyl ether (PBDE) congeners in seven different SRMs: cod-liver oil, whale blubber, fish tissue (two materials), mussel tissue and sediment (two materials). PBDEs were measured in these SRMs, with the lowest concentrations measured in mussel tissue (SRM 1974b) and the highest in sediment collected from the New York/New Jersey Waterway (SRM 1944). Comparing the relative PBDE congener concentrations within the samples, we found the biota SRMs contained primarily tetrabrominated and pentabrominated diphenyl ethers, whereas the sediment SRMs contained primarily decabromodiphenyl ether (BDE 209). The cod-liver oil (SRM 1588b) and whale blubber (SRM 1945) materials were also found to contain measurable concentrations of two methoxylated PBDEs (MeO-BDEs). Certified and reference concentrations are reported for 12 PBDE congeners measured in the biota SRMs and reference values are available for two MeO-BDEs. Results from a sediment interlaboratory comparison PBDE exercise are available for the two sediment SRMs (1941b and 1944).     

Diamidonaphthalene-supported pnictogenium cations: synthesis of an N-heterocyclic stibenium cation by a novel protonation route

A 1,8-bis(alkylamido)naphthalene framework has been applied to the construction of N-heterocyclic arsenium and stibenium cations; a novel synthetic route, involving protonation of an ancillary amido ligand, was used to generate the base-stabilized stibenium cation.     

Competition between DPPC and SDS at the air-aqueous interface

Vibrational sum frequency generation spectroscopy is used to study the interactions of the charged soluble organic surfactant sodium dodecyl sulfate (SDS) with an insoluble 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) monolayer at the air-aqueous interface. Results indicate that the surfactant species compete for surface sites in the mixed system, with a lower monolayer number density of DPPC molecules being observed in the presence of dodecyl sulfate anions at the interface. Spectroscopic results also indicate that fewer dodecyl sulfate chains reside at the interface when the insoluble DPPC film is present. Increased conformational ordering of the acyl chains of both the DPPC molecules and the interfacial dodecyl sulfate anions is observed in the mixed system. Additionally, charged surfactant SDS promotes the alignment of the interfacial water molecules even in the presence of a DPPC monolayer.