Physical Sciences and Mathematics | Open Access Articles

An Assessment Of Computational Methods For Calculating Accurate Structures And Energies Of Bio-Relevant Polysulfur/Selenium-Containing Compounds, Sahar Nikoo, Paul Meister, John Hayward, James Gauld

Chemistry and Biochemistry Publications

The heavier chalcogens sulfur and selenium are important in organic and inorganic chemistry, and the role of such chalcogens in biological systems has recently gained more attention. Sulfur and, to a lesser extent selenium, are involved in diverse reactions from redox signaling to antioxidant activity and are considered essential nutrients. We investigated the ability of the DFT functionals (B3LYP, B3PW91, ωB97XD, M06-2X, and M08-HX) relative to electron correlation methods MP2 and QCISD to produce reliable and accurate structures as well as thermochemical data for sulfur/selenium-containing systems. Bond lengths, proton affinities (PA), gas phase basicities (GPB), chalcogen–chalcogen bond dissociation enthalpies (BDE), …

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Computational, Experimental Details, And Biological Raw Data Accompanying The Publication: “The Synthesis And Characterization Of A Nanomagnetite With Potent Antibacterial Activity And Low Mammalian Toxicity”, Seyedeh Maryamdokht Taimoory, Abbas Rahdar, Mousa Aliahmad, Fardin Sadeghfar, Mohammad Reza Hajinezhad, Mohammad Jahantigh, Parisa Shahbazi, John F. Trant

Chemistry and Biochemistry Publications

This data file includes experimental details on how to make uncoated iron oxide nanoparticles using a green electrochemical method. It provides the raw data on the antibacterial activity of one of these formulations, and the full computational data and methodology used to generate that data, of several different magnetite clusters of specific spin multiplicities for 4, 5, 7 and 9 iron atom magnetite clusters. This data will assist other researchers wishing to replicate or expand on these results for the investigation and use of nanomagnetite for antibacterial applications.

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The Effect Of Ionic Liquid Adsorption On The Electronic And Optical Properties Of Fluorographene Nanosheets, Mehdi Shakourian-Fard, S. Maryamdokht Taimoory, Volodymyr Semeniuchenko, Ganesh Kamath, John F. Trant

Chemistry and Biochemistry Publications

In the present study, we investigate the adsorption characteristics of six different ionic liquids (ILs) on a fully-fluorinated graphene (fluorographene, FG) surface using electronic structure studies and associated analysis methods. A systematic comparison of differences in IL binding energies (ΔEb) with fluorographene, graphene and hexagonal boron nitride surfaces indicates that fluorination strongly decreases the binding energy compared to the other two surfaces, hence resulting in the binding energetics: ΔEb (Graphene…IL) > ΔEb (Hexagonal boron-nitride…IL) > ΔEb (Fluorographene…IL). To probe the reasons for this difference, quantum theory of atoms in molecules (QTAIM) analysis and non-covalent interactions (NCI) analyses were carried out. Results indicate …

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The Synthesis And Characterization Of A Magnetite Nanoparticle With Potent Antibacterial Activity And Low Mammalian Toxicity, Seyedeh Maryamdokht Taimoory, Abbas Rahdar, Mousa Aliahmad, Fardin Sadeghfar, Mohammad Reza Hajinezhad, Mohammad Jahantigh, Parisa Shahbazi, John F. Trant

Chemistry and Biochemistry Publications

Magnetite has shown some promise as a biomedical material and antibacterial agent; however the benefits are normally only realized when it is used in combination with other metals or drugs. Unfunctionalized magnetite may be a biocompatible alternative. This report discusses the synthesis and potent antibacterial activity, with low associated mammalian organ toxicity, of nanomagnetite particles. Magnetite (Fe3O4) nanoparticles were electrochemically prepared in a green surfactant-free, closed water loop system. These materials, characterized by X-ray diffraction, FTIR, and vibrational magnetometry, also appear contaminated with Fe-O-O-H functionalities. This physical characterization is accompanied by a computational investigation of truncated clusters showing that a …

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Bring Training Forward For Undergraduate Researchers, John Trant

Chemistry and Biochemistry Publications

No abstract provided.

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Host-Guest Complexes Of C-Propyl-2-Bromoresorcinarene With Aromatic N-Oxides*, Rakesh Puttreddy, Ngong Kodiah Beyeh, Pia Jurček, Lotta Turunen, John F. Trant, Robin H.A. Ras, Kari Rissanen

Chemistry and Biochemistry Publications

The host-guest complexes of C-propyl-2-bromoresorcinarene with pyridine N-oxide, 3-methylpyridine N-oxide, quinoline N-oxide and isoquinoline N-oxide are studied using single crystal X-ray crystallography and 1H NMR spectroscopy. The C-propyl-2-bromoresorcinarene forms endo-complexes with the aromatic N-oxides in the solid-state when crystallised from either methanol or acetone. In solution, the endo-complexes were observed only in methanol-d4. In DMSO the solvent itself is a good guest, and crystallisation provides only solvate endo-complexes. The C-propyl-2-bromoresorcinarene shows remarkable flexibility when crystallised from either methanol or acetone, and packs into one-dimensional self-included chains. Of special note, crystallising C-propyl-2-bromoresorcinarene with 3-methylpyridine N-oxide from acetone results in a 2:2 …

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Metal-Interface-Elastomer (Mine) Structures For Stretchable Electronics, Tricia Carmichael, Akhil Vohra, Kory Schlingman, R. Stephen Carmichael

Chemistry and Biochemistry Publications

The future of soft, conformable, and robust wearable electronics will require elastomers to provide mechanical stabilization, a soft surface to interact with human wearers, and a crucial physical barrier to protect stretchable devices from the environment. It is a difficult challenge, however, for a single elastomer to fulfill each of these needs. Here, we present a new approach that fuses a membrane of poly(dimethylsiloxane) (PDMS) onto the surface of a transparent butyl rubber (T-IIR) substrate using an organosilane-based molecular glue. The resulting membrane-interface-elastomer (MINE) structures uniquely combine the surface chemistry of PDMS with the intrinsically low gas permeability of T-IIR …

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Preparation And Characterization Of A Small Library Of Thermally-Labile End-Caps For Variable-Temperature Triggering Of Self-Immolative Polymers, S. Maryamdokht Taimoory, S. Iraj Sadraei, Rose Anne Fayoumi, Sarah Nasri, Matthew Revington, John F. Trant

Chemistry and Biochemistry Publications

The reaction between furans and maleimides has increasingly become a method of interest as its reversibility makes it a useful tool for applications ranging from self-healing materials, to self-immolative polymers, to hydrogels for cell culture and for the preparation of bone repair. However, most of these applications have relied on simple monosubstituted furans and simple maleimides and have not extensively evaluated the potential thermal variability inherent in the process that is achievable through simple substrate modification. A small library of cycloadducts suitable for the above applications was prepared, and the temperature dependence of the retro-Diels-Alder processes was determined through in …

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Diels-Alder Click-Cross-Linked Hydrogels With Increased Reactivity Enable 3d Cell Encapsulation, Laura J. Smith, S. Maryamdokht Taimoory, Roger Y. Tam, Alexander E.G. Baker, Niema Binth Mohammad, John F. Trant, Molly S. Shoichet

Chemistry and Biochemistry Publications

Engineered hydrogels have been extensively used to direct cell function in 3D cell culture models, which are more representative of the native cellular microenvironment than conventional 2D cell culture. Previously, hyaluronan-furan and bis-maleimide polyethylene glycol hydrogels were synthesized via Diels-Alder chemistry at acidic pH, which did not allow encapsulation of viable cells. In order to enable gelation at physiological pH, the reaction kinetics were accelerated by replacing the hyaluronan-furan with the more electron-rich hyaluronan-methylfuran. These new click-cross-linked hydrogels gel faster and at physiological pH, enabling encapsulation of viable cells, as demonstrated with 3D culture of 5 different cancer cell lines. …

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Solution Deposition Of Conformal Gold Coatings On Knitted Fabric For E-Textiles And Electroluminescent Clothing, Tricia Carmichael, Yunyun Wu, Sara S. Mechael, Yiting Chen

Chemistry and Biochemistry Publications

The vision for wearable electronics involves creating an imperceptible boundary between humans and devices. Integrating electronic devices into clothing represents an important path to this vision; however, combining conductive materials with textiles is challenging due to the porous structure of knitted textiles. Stretchability depends on maintaining the void structure between the yarns of the fabric; filling these voids with conductive materials stiffens the textile and can lead to detrimental cracking. The authors demonstrate the solution-based metallization of a knitted textile that conformally coats individual fibers with gold, leaving the void structure intact. The resulting gold-coated textile is highly conductive, with …

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Intrinsic Curvature-Mediated Transbilayer Coupling In Asymmetric Lipid Vesicles, Barbara Eicher, Drew Marquardt, Frederick A. Heberle, Ilse Letofsky-Papst, Gerald N. Rechberger, Marie Sousai Appavou, John Katsaras, Georg Pabst

Chemistry and Biochemistry Publications

© 2017 Biophysical Society We measured the effect of intrinsic lipid curvature, J0, on structural properties of asymmetric vesicles made of palmitoyl-oleoyl-phosphatidylethanolamine (POPE; J0<0) and palmitoyl-oleoyl-phosphatidylcholine (POPC; J0∼0). Electron microscopy and dynamic light scattering were used to determine vesicle size and morphology, and x-ray and neutron scattering, combined with calorimetric experiments and solution NMR, yielded insights into leaflet-specific lipid packing and melting processes. Below the lipid melting temperature we observed strong interleaflet coupling in asymmetric vesicles with POPE inner bilayer leaflets and outer leaflets enriched in POPC. This lipid arrangement manifested itself by lipids melting cooperatively in both leaflets, and a rearrangement of lipid packing in both monolayers. On the other hand, no coupling was observed in vesicles with POPC inner bilayer leaflets and outer leaflets enriched in POPE. In this case, the leaflets melted independently and did not affect each other's acyl chain packing. Furthermore, we found no evidence for transbilayer structural coupling above the melting temperature of either sample preparation. Our results are consistent with the energetically preferred location of POPE residing in the inner leaflet, where it also resides in natural membranes, most likely causing the coupling of both leaflets. The loss of this coupling in the fluid bilayers is most likely the result of entropic contributions.

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Bamboo-Like Chained Cavities And Other Halogen-Bonded Complexes From Tetrahaloethynyl Cavitands With Simple Ditopic Halogen Bond Acceptors, Lotta Turunen, Fangfang Pan, Ngong Kodiah Beyeh, John F. Trant, Robin H.A. Ras, Kari Rissanen

Chemistry and Biochemistry Publications

Halogen bonding provides a useful complement to hydrogen bonding and metal-coordination as a tool for organizing supramolecular systems. Resorcinarenes, tetrameric bowl-shaped cavitands, have been previously shown to function as efficient scaffolds for generating dimeric capsules in both solution and solid-phase, and complicated one-, two-, and three-dimensional frameworks in the solid phase. Tetrahaloethynyl resorcinarenes (bromide and iodide) position the halogen atoms in a very promising "crown-like" orientation for acting as organizing halogen-bond donors to help build capsules and higher-order networks. Symmetric divalent halogen bond acceptors including bipyridines, 1,4-dioxane, and 1,4-diazabicyclo[2.2.2]octane are very promising halogen bond accepting partners for creating these systems. …

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High-Affinity And Selective Detection Of Pyrophosphate In Water By A Resorcinarene Salt Receptor, Ngong Kodiah Beyeh, Isabel Díez, S. Maryamdokht Taimoory, Daniel Meister, Andrew I. Feig, John F. Trant, Robin H.A. Ras, Kari Rissanen

Chemistry and Biochemistry Publications

Pyrophosphate (PPi) is a byproduct of DNA and RNA synthesis, and abnormal levels are indicative of disease. We report the high-affinity binding of PPi in water by N-alkyl ammonium resorcinarene chloride receptors. Experimental analysis using 1H and 31P NMR, isothermal titration calorimetry, mass spectrometry, and UV-vis spectroscopy all support exceptional selectivity of these systems for PPi in water. The measured affinity of K1 = 1.60 × 107 M-1 for PPi is three orders of magnitude larger than that observed for binding to another phosphate, ATP. This exceptional anion-binding affinity in water is explored through a detailed density functional theory computational …

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Full-Text Articles in Physical Sciences and Mathematics

An Assessment Of Computational Methods For Calculating Accurate Structures And Energies Of Bio-Relevant Polysulfur/Selenium-Containing Compounds, Sahar Nikoo, Paul Meister, John Hayward, James Gauld

Chemistry and Biochemistry Publications

Chemistry and Biochemistry Publications

The Effect Of Ionic Liquid Adsorption On The Electronic And Optical Properties Of Fluorographene Nanosheets, Mehdi Shakourian-Fard, S. Maryamdokht Taimoory, Volodymyr Semeniuchenko, Ganesh Kamath, John F. Trant

Chemistry and Biochemistry Publications

The Synthesis And Characterization Of A Magnetite Nanoparticle With Potent Antibacterial Activity And Low Mammalian Toxicity, Seyedeh Maryamdokht Taimoory, Abbas Rahdar, Mousa Aliahmad, Fardin Sadeghfar, Mohammad Reza Hajinezhad, Mohammad Jahantigh, Parisa Shahbazi, John F. Trant

Chemistry and Biochemistry Publications

Bring Training Forward For Undergraduate Researchers, John Trant

Chemistry and Biochemistry Publications

Host-Guest Complexes Of C-Propyl-2-Bromoresorcinarene With Aromatic N-Oxides*, Rakesh Puttreddy, Ngong Kodiah Beyeh, Pia Jurček, Lotta Turunen, John F. Trant, Robin H.A. Ras, Kari Rissanen

Chemistry and Biochemistry Publications

Metal-Interface-Elastomer (Mine) Structures For Stretchable Electronics, Tricia Carmichael, Akhil Vohra, Kory Schlingman, R. Stephen Carmichael

Chemistry and Biochemistry Publications

Preparation And Characterization Of A Small Library Of Thermally-Labile End-Caps For Variable-Temperature Triggering Of Self-Immolative Polymers, S. Maryamdokht Taimoory, S. Iraj Sadraei, Rose Anne Fayoumi, Sarah Nasri, Matthew Revington, John F. Trant

Chemistry and Biochemistry Publications

Diels-Alder Click-Cross-Linked Hydrogels With Increased Reactivity Enable 3d Cell Encapsulation, Laura J. Smith, S. Maryamdokht Taimoory, Roger Y. Tam, Alexander E.G. Baker, Niema Binth Mohammad, John F. Trant, Molly S. Shoichet

Chemistry and Biochemistry Publications

Solution Deposition Of Conformal Gold Coatings On Knitted Fabric For E-Textiles And Electroluminescent Clothing, Tricia Carmichael, Yunyun Wu, Sara S. Mechael, Yiting Chen

Chemistry and Biochemistry Publications

Intrinsic Curvature-Mediated Transbilayer Coupling In Asymmetric Lipid Vesicles, Barbara Eicher, Drew Marquardt, Frederick A. Heberle, Ilse Letofsky-Papst, Gerald N. Rechberger, Marie Sousai Appavou, John Katsaras, Georg Pabst

Chemistry and Biochemistry Publications

Bamboo-Like Chained Cavities And Other Halogen-Bonded Complexes From Tetrahaloethynyl Cavitands With Simple Ditopic Halogen Bond Acceptors, Lotta Turunen, Fangfang Pan, Ngong Kodiah Beyeh, John F. Trant, Robin H.A. Ras, Kari Rissanen

Chemistry and Biochemistry Publications

High-Affinity And Selective Detection Of Pyrophosphate In Water By A Resorcinarene Salt Receptor, Ngong Kodiah Beyeh, Isabel Díez, S. Maryamdokht Taimoory, Daniel Meister, Andrew I. Feig, John F. Trant, Robin H.A. Ras, Kari Rissanen

Chemistry and Biochemistry Publications