Establishing methods to accurately assess and model the binding strength of surfactants around a given-chirality single-walled carbon nanotube (SWNT) are crucial for selective enrichment, targeted functionalization, and spectrally sharp nanodevices. Unlike surfactant exchange, which is subject to interferences from the second surfactant, we herein introduce a thermal dissociation method based on reversible H(+)/O2 doping to determine SWNT/surfactant thermodynamic stability values with greater fidelity. Thermodynamic values were reproduced using molecular mechanics augmented by ab initio calculations in order to better assess π-π interactions. This afforded detailed quantification of the flavin binding strength in terms of π-π stacking (55-58%), with the remaining portion roughly split 3:1 between electrostatic plus van der Waals flavin mononucleotide (FMN) interdigitation and H-bonding interactions, respectively. Quasi-epitaxial π-π alignment between the near-armchair FMN helix and the underlying nanotube lattice plays a crucial role in stabilizing these assemblies. The close resemblance of the thermal dissociation method to helix-coil and ligand-binding transitions of DNA opens up a unique insight into the molecular engineering of self-organizing surfactants around various-chirality nanotubes.

A sonochemical method was employed in the synthesis of nickel aluminum layered double hydroxides (NiAl-LDH) and the materials were used as adsorbents for the removal of the reactive azo dye, Remazol Brilliant Violet (RBV-5r). The experimental data obtained for microstructure were compared and both the arrangement and orientation of the intercalated dye species were examined using molecular dynamics (MD) simulations. The obtained materials were characterized by X-ray diffraction (XRD), nitrogen sorption (BET), scanning electron microscopy (SEM), transmission electron microscopy (TEM), thermogravimetric analysis (TGA) and Fourier transformation infrared spectroscopy (FTIR). The adsorption characteristics were studied in a batch process by optimizing different parameters such as calcination temperature, contact time, initial dye concentration, solution pH, and solution temperature. NiAl-LDH material synthesized by sonochemical (SC) methods and calcined at 250 °C (NiAl-C250SC) showed the best dye removal efficiency (100% removal in 6 min) with an adsorption capacity of 150 mg/g at 25 °C and at pH = 6. The reusability of the dye loaded material was investigated by replicating the adsorption−desorption cycle. The results show that the material could regenerate without significant loss of the adsorption capacity. The regenerated adsorbent showed 95.9%, and 95.7% of the initial adsorption capacity after the first and the second regeneration cycles, respectively. XRD and FTIR results for LDH before and after the dye adsorption showed removal of the dye is due to intercalation of the organic dye molecule into the LDH structure where a net increase in the basal spacing from 7.48 to 8.71 Å is observed. Molecular dynamics (MD) simulations further suggest that the dye molecules arrange in the interlayer space as a monolayer with the main axis horizontal to the layer plane. The calculated d-spacing values were in good agreement with the experimental results.

Liquid chromatography coupled with electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) is a major analytical technique used for nontargeted identification of metabolites in biological fluids. Typically, in LC-ESI-MS/MS based database assisted structure elucidation pipelines, the exact mass of an unknown compound is used to mine a chemical structure database to acquire an initial set of possible candidates. Subsequent matching of the collision induced dissociation (CID) spectrum of the unknown to the CID spectra of candidate structures facilitates identification. However, this approach often fails because of the large numbers of potential candidates (i.e., false positives) for which CID spectra are not available. To overcome this problem, CID fragmentation predication programs have been developed, but these also have limited success if large numbers of isomers with similar CID spectra are present in the candidate set. In this study, we investigated the use of a retention index (RI) predictive model as an orthogonal method to help improve identification rates. The model was used to eliminate candidate structures whose predicted RI values differed significantly from the experimentally determined RI value of the unknown compound. We tested this approach using a set of ninety-one endogenous metabolites and four in silico CID fragmentation algorithms: CFM-ID, CSI:FingerID, Mass Frontier, and MetFrag. Candidate sets obtained from PubChem and the Human Metabolite Database (HMDB) were ranked with and without RI filtering followed by in silico spectral matching. Upon RI filtering, 12 of the ninetyone metabolites were eliminated from their respective candidate sets, i.e., were scored incorrectly as negatives. For the remaining seventy-nine compounds, we show that RI filtering eliminated an average of 58% from PubChem candidate sets. This resulted in an approximately 2-fold improvement in average rankings when using CFM-ID, Mass Frontier, and MetFrag. In addition, RI filtering slightly increased the occurrence of number one rankings for all 4 fragmentation algorithms. However, RI filtering did not significantly improve average rankings when HMDB was used as the candidate database, nor did it significantly improve average rankings when using CSI:FingerID. Overall, we show that the current RI model incorrectly eliminated more true positives (12) than were expected (4−5) on the basis of the filtering method. However, it slightly improved the number of correct first place rankings and improved overall average rankings when using CFM-ID, Mass Frontier, and MetFrag.

Molecular dynamics (MD) simulations were performed to calculate free energies of sorption (ΔG sorb) of cationic aromatic amines to Ca-montmorillonite. We applied the linear interaction energy (LIE) method, well-established in the biochemistry field, to derive ΔG sorb. We obtained a mean average error of 0.3 kcal mol–1 within the compound training set and an error of 0.41 kcal mol–1 for a validation test set. We were able to reproduce absolute ΔG sorb values for a variety of compound structures, including the zwitterionic antibiotic oxytetracycline. MD simulations also provided atomistic level insights into the underlying driving forces that modulate sorption. Importantly, our approach provides a compelling alternative to polyparameter linear free energy relationship methods, which have shown limited success in capturing the sorption of ionogenic compounds with polar and/or charged moieties. We conclude that the LIE method can be used as a robust and tractable method to predict ΔG sorb within families of organic cations bound to aluminosilicate clay minerals.

Syntheses and optical properties of mono- and bis-chromene-annulated bacteriochlorins are described. Known monochromene-annulated meso-(pentafluorophenyl)chlorin is susceptible to a regioselective OsO4-mediated dihydroxylation, generating two monochromene-annulated trihydroxybacteriochlorin stereoisomers: either the newly introduced vic-cis-diol functionality is on the same side as the vic-cis-diol moiety the chromene-annulation was based on or on the opposite side. Treatment of the two isomers with heat or base generates different sets of bis-chromene-annulated bacteriochlorin stereo- and regioisomers. Detailed 1D and 2D (1)H and (19)F NMR spectroscopic investigations allowed the characterization of the isomers that formed. The regioselectivity of the second annulation reaction was rationalized computationally on steric grounds. The bacteriochlorin-type optical spectra of the mono- and bis-chromene-annulated bacteriochlorins are modulated as a result of the annulation, with each isomer possessing a unique spectrum, attributed to the effects the regiochemically distinct annulations have on the conformation of the chromophore. The formation of a bis-chromene-annulated chlorin from the bacteriochlorins is also described, including its X-ray crystal structure, revealing some details of the metrics of the chromene-annulated moiety. The vic-diol functionality of monochromene-annulated trihydroxybacteriochlorins is also susceptible to oxidation and ring-expansion reactions, generating chromene-annulated pyrrole-modified chlorins incorporating oxazolone and morpholine moieties. The work expands the body of work on the synthesis and optical fine-tuning of meso-aryl-substituted bacteriochlorins.