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Articles 1 - 15 of 15
Full-Text Articles in Physical Sciences and Mathematics
Dark-Binding Process Relevant To Preventing Photosensitized Oxidation: Conformation-Dependent Light And Dark Mechanisms By A Dual-Functioning Diketone, Sarah J. Belh, Niluksha Walalawela, Stas Lekhtman, Alexander Greer
Dark-Binding Process Relevant To Preventing Photosensitized Oxidation: Conformation-Dependent Light And Dark Mechanisms By A Dual-Functioning Diketone, Sarah J. Belh, Niluksha Walalawela, Stas Lekhtman, Alexander Greer
Publications and Research
Few photosensitizers function in both light and dark processes as they usually have no function when the lights are turned off. We hypothesized that light and dark mechanisms in an α-diketone will be decoupled by dihedral rotation in a conformation- dependent binding process. Successful decoupling of these two functions is now shown. Namely, anti- and syn-skewed conformations of 4,4′-dimethylbenzil promote photosensitized alkoxy radical production, whereas the syn conformation promotes a binding shutoff reaction with trimethyl phosphite. Less rotation of the diketone is better suited to the photosensitizing function since phosphite binding arises through the syn conformer of lower stability. The …
Building Mof Nanocomposites With Oxidized Graphitic Carbon Nitride Nanospheres: The Effect Of Framework Geometry On The Structural Heterogeneity, Dimitrios A. Giannakoudakis, Teresa J. Bandosz
Building Mof Nanocomposites With Oxidized Graphitic Carbon Nitride Nanospheres: The Effect Of Framework Geometry On The Structural Heterogeneity, Dimitrios A. Giannakoudakis, Teresa J. Bandosz
Publications and Research
Composite of two MOFs, copper-based Cu-BTC (HKUST-1) and zirconium-based Zr-BDC (UiO-66), with oxidized graphitic carbon nitride nanospheres were synthesized. For comparison, pure MOFs were also obtained. The surface features were analyzed using x-ray diffraction (XRD), sorption of nitrogen, thermal analysis, and scanning electron microscopy (SEM). The incorporation of oxidized g-C3N4 to the Cu-BTC framework caused the formation of a heterogeneous material of a hierarchical pores structure, but a decreased surface area when compared to that of the parent MOF. In the case of UiO-66, functionalized nanospheres were acting as seeds around which the crystals grew. Even though the MOF phases …
Tio2/S-Doped Carbons Hybrids: Analysis Of Their Interfacial And Surface Features, Teresa Bandosz, Alfonso Policicchio, Marc Florent, Po S. Poon, Juan Matos
Tio2/S-Doped Carbons Hybrids: Analysis Of Their Interfacial And Surface Features, Teresa Bandosz, Alfonso Policicchio, Marc Florent, Po S. Poon, Juan Matos
Publications and Research
Hybrids containing approximately equal amounts of P25 TiO2 and S-doped porous carbons were prepared using a water-based slurry mixing method. The materials were extensively characterized by adsorption of nitrogen, potentiometric titration, thermal analysis in air and in helium, XRD, XPS and SEM. The collected results showed the significant blockage of carbon micropores by TiO2 particles deposited on their outer surface. The formation of a new interface, especially for the S-rich samples, might also contribute to the porosity alteration. Analysis of surface chemistry suggested the presence of Ti-S bonds with an involvement of sulfur from thiophenic species in the carbon phase. …
Hidden Bias In The Dud-E Dataset Leads To Misleading Performance Of Deep Learning In Structure-Based Virtual Screening, Lieyang Chen, Anthony Cruz, Steven Ramsey, Callum J. Dickson, Jose S. Duca, Viktor Hornak, David R. Koes, Tom Kurtzman
Hidden Bias In The Dud-E Dataset Leads To Misleading Performance Of Deep Learning In Structure-Based Virtual Screening, Lieyang Chen, Anthony Cruz, Steven Ramsey, Callum J. Dickson, Jose S. Duca, Viktor Hornak, David R. Koes, Tom Kurtzman
Publications and Research
Recently much effort has been invested in using convolutional neural network (CNN) models trained on 3D structural images of protein-ligand complexes to distinguish binding from non-binding ligands for virtual screening. However, the dearth of reliable protein-ligand x-ray structures and binding affinity data has required the use of constructed datasets for the training and evaluation of CNN molecular recognition models. Here, we outline various sources of bias in one such widely-used dataset, the Directory of Useful Decoys: Enhanced (DUDE). We have constructed and performed tests to investigate whether CNN models developed using DUD-E are properly learning the underlying physics of molecular …
Hidden Bias In The Dud-E Dataset Leads To Misleading Performance Of Deep Learning In Structure-Based Virtual Screening, Lieyang Chen, Anthony Cruz, Steven Ramsey, Callum J. Dickson, Jose S. Duca, Viktor Hornak, David R. Koes, Tom Kurtzman
Hidden Bias In The Dud-E Dataset Leads To Misleading Performance Of Deep Learning In Structure-Based Virtual Screening, Lieyang Chen, Anthony Cruz, Steven Ramsey, Callum J. Dickson, Jose S. Duca, Viktor Hornak, David R. Koes, Tom Kurtzman
Publications and Research
Recently much effort has been invested in using convolutional neural network (CNN) models trained on 3D structural images of protein-ligand complexes to distinguish binding from non-binding ligands for virtual screening. However, the dearth of reliable protein-ligand x-ray structures and binding affinity data has required the use of constructed datasets for the training and evaluation of CNN molecular recognition models. Here, we outline various sources of bias in one such widely-used dataset, the Directory of Useful Decoys: Enhanced (DUDE). We have constructed and performed tests to investigate whether CNN models developed using DUD-E are properly learning the underlying physics of molecular …
Synthesis And Evaluations Of “1,4-Triazolyl Combretacoumarins” And Desmethoxy Analogs, Tashrique A. Khandaker, Jessica D. Hess, Renato Aguilera, Graciela Andrei, Robert Snoeck, Dominique Schols, Padmanava Pradhan, Mahesh K. Lakshman
Synthesis And Evaluations Of “1,4-Triazolyl Combretacoumarins” And Desmethoxy Analogs, Tashrique A. Khandaker, Jessica D. Hess, Renato Aguilera, Graciela Andrei, Robert Snoeck, Dominique Schols, Padmanava Pradhan, Mahesh K. Lakshman
Publications and Research
1,4-Triazolyl combretacoumarins have been prepared by linking the trimethoxyarene unit of combretastatin A4 with coumarins, via a 1,2,3-triazole. For this, 4-azidocoumarins were accessed by a sequential two-step, one-pot reaction of 4-hydroxycoumarins with (benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP), followed by reaction with NaN3. In the reaction with BOP, a coumarin-derived phosphonium ion intermediate seems to form, leading to an O4-(benzotriazolyl)coumarin derivative. For the CuAAC reaction of azidocoumarins with 5-ethynyl-1,2,3-trimethoxybenzene, catalytic [(MeCN)4Cu]PF6 in CH2Cl2/MeOH with 2,6-lutidine, at 50 oC, was suitable. The 4-azidocoumarins were less reactive as compared to PhN3 and …
Unconventional Anticancer Metallodrugs And Strategies To Improve Their Pharmacological Profile, Maria Contel
Unconventional Anticancer Metallodrugs And Strategies To Improve Their Pharmacological Profile, Maria Contel
Publications and Research
No abstract provided.
A Molecular Reconstruction Approach To Sitebased 3d-Rism And Comparison To Gist Hydration Thermodynamic Maps In An Enzyme Active Site, Crystal Nguyen, Takeshi Yamazaki, Andriy Kovalenko, David A. Case, Michael K. Gilson, Tom Kurtzman, Tyler Luchko
A Molecular Reconstruction Approach To Sitebased 3d-Rism And Comparison To Gist Hydration Thermodynamic Maps In An Enzyme Active Site, Crystal Nguyen, Takeshi Yamazaki, Andriy Kovalenko, David A. Case, Michael K. Gilson, Tom Kurtzman, Tyler Luchko
Publications and Research
Computed, high-resolution, spatial distributions of solvation energy and entropy can provide detailed information about the role of water in molecular recognition. While grid inhomogeneous solvation theory (GIST) provides rigorous, detailed thermodynamic information from explicit solvent molecular dynamics simulations, recent developments in the 3D reference interaction site model (3D-RISM) theory allow many of the same quantities to be calculated in a fraction of the time. However, 3D-RISM produces atomic-site, rather than molecular, density distributions, which are difficult to extract physical meaning from. To overcome this difficulty, we introduce a method to reconstruct molecular density distributions from atomic site density distributions. Furthermore, …
A Field Procedure To Screen Soil For Hazardous Lead, Franziska C. Landers, Anna Paltseva, Jennifer M. Sobolewski, Zhongqi Cheng, Tyler K. Ellis, Brian J. Mailloux, Alexander Van Geen
A Field Procedure To Screen Soil For Hazardous Lead, Franziska C. Landers, Anna Paltseva, Jennifer M. Sobolewski, Zhongqi Cheng, Tyler K. Ellis, Brian J. Mailloux, Alexander Van Geen
Publications and Research
Soils retain lead contamination from possible sources such as mining, smelting, battery recycling, waste incineration, leaded gasoline, and crumbling paint. Such contamination is often concentrated in toxic hot spots that need to be identified locally. To address this need, a simple field procedure was designed to screen soil for hazardous Pb for use by the general public. The procedure is a modification of the in vitro soil Pb extraction described by Drexler and Brattin (Hum. Ecol. Risk Assess. 2007, 13, 383) and EPA Method 1340, and uses a 0.4 M glycine solution at pH 1.5. A higher soil-to-solution ratio of …
Titanium Dioxide Sensitized With Porphyrin Dye As A Photocatalyst For The Degradation Of Water Pollutants, Kevin Reyes, Ivana Jovanovic
Titanium Dioxide Sensitized With Porphyrin Dye As A Photocatalyst For The Degradation Of Water Pollutants, Kevin Reyes, Ivana Jovanovic
Publications and Research
TiO2 was sensitized with a porphyrin, Tetra(4-carboxyphenyl) porphyrin(TCPP) and used as photocatalyst under visible light for degradation of aqueous solutions of methylene blue (MB) dye. The quantification of the degradation of MB was assessed by UV-Vis spectroscopy. The results of this procedure showed the decrease in concentration of MB over time when reaction is exposed to visible light. The TiO2-TCPP complex was tested as well for the recovery of metals from the AgNO3 aqueous solution. The reduction of silver cations to silver metal was observed through formation of black precipitate.
Ligand Selectivity In The Recognition Of Protoberberine Alkaloids By Hybrid-2 Human Telomeric G-Quadruplex: Binding Free Energy Calculation, Fluorescence Binding, And Nmr Experiments, Nanjie Deng, Junchao Xia, Lauren Wickstrom, Clement Lin, Kaibo Wang, Peng He, Yunting Yin, Danzhou Yang
Ligand Selectivity In The Recognition Of Protoberberine Alkaloids By Hybrid-2 Human Telomeric G-Quadruplex: Binding Free Energy Calculation, Fluorescence Binding, And Nmr Experiments, Nanjie Deng, Junchao Xia, Lauren Wickstrom, Clement Lin, Kaibo Wang, Peng He, Yunting Yin, Danzhou Yang
Publications and Research
The human telomeric G-quadruplex (G4) is an attractive target for developing anticancer drugs. Natural products protoberberine alkaloids are known to bind human telomeric G4 and inhibit telomerase. Among several structurally similar protoberberine alkaloids, epiberberine (EPI) shows the greatest specificity in recognizing the human telomeric G4 over duplex DNA and other G4s. Recently, NMR study revealed that EPI recognizes specifically the hybrid-2 form human telomeric G4 by inducing large rearrangements in the 50-flanking segment and loop regions to form a highly extensive four-layered binding pocket. Using the NMR structure of the EPI-human telomeric G4 complex, here we perform molecular dynamics free …
Annihilator Dimers Enhance Triplet Fusion Upconversion, Andrew B. Pun, Samuel N. Sanders, Matthew Y. Sfeir, Luis M. Campos, Daniel N. Congreve
Annihilator Dimers Enhance Triplet Fusion Upconversion, Andrew B. Pun, Samuel N. Sanders, Matthew Y. Sfeir, Luis M. Campos, Daniel N. Congreve
Publications and Research
Optical upconversion is a net process by which two low energy photons are converted into one higher energy photon. There is vast potential to exploit upconversion in applications ranging from solar energy and biological imaging to data storage and photocatalysis. Here, we link two upconverting chromophores together to synthesize a series of novel tetracene dimers for use as annihilators. When compared with the monomer annihilator, TIPS–tetracene, the dimers yield a strong enhancement in the triplet fusion process, also known as triplet–triplet annihilation, as demonstrated via a large increase in upconversion efficiency and an order of magnitude reduction of the threshold …
Self-Assembled Bismuth Selenide (Bi2se3) Quantum Dots Grown By Molecular Beam Epitaxy, Marcel S. Claro, Ido Levy, Abhinandan Gangopadhyay, David J. Smith, Maria C. Tamargo
Self-Assembled Bismuth Selenide (Bi2se3) Quantum Dots Grown By Molecular Beam Epitaxy, Marcel S. Claro, Ido Levy, Abhinandan Gangopadhyay, David J. Smith, Maria C. Tamargo
Publications and Research
We report the growth of self-assembled Bi2se3 quantum dots (QDs) by molecular beam epitaxy on GaAs substrates using the droplet epitaxy technique. The QD formation occurs after anneal of Bismuth droplets under Selenium flux. Characterization by atomic force microscopy, scanning electron microscopy, X-ray diffraction, high-resolution transmission electron microscopy and X-ray reflectance spectroscopy is presented. Raman spectra confirm the QD quality. The quantum dots are crystalline, with hexagonal shape, and have average dimensions of 12-nm height (12 quintuple layers) and 46-nm width, and a density of 8.5 × 109 cm−2. this droplet growth technique provides a means to produce topological insulator …
Extraction Of Acids And Bases From Aqueous Phase To A Pseudoprotic Ionic Liquid, Nikolas Patsos, Karin Lewis, Francesco Picchioni, Mark N. Kobrak
Extraction Of Acids And Bases From Aqueous Phase To A Pseudoprotic Ionic Liquid, Nikolas Patsos, Karin Lewis, Francesco Picchioni, Mark N. Kobrak
Publications and Research
We report experiments on the extraction of acids and bases from an aqueous phase to a pseudoprotic ionic liquid phase consisting of an equimolar mixture of trihexylamine and octanoic acid. We observed the extraction of a wide range of acids and bases, and investigated the mechanism of extraction in detail. Our results confirmed the observation of the Hofmeister effect in these systems reported in our previous work, where the extent of the extraction of copper salts was significantly influenced by the interactions between extracted inorganic anions and the organic phase. Our results further demonstrated that the organic layer served as …
Teaching With Technology: Using A Virtual Learning Community And Peer Mentoring To Create An Interdisciplinary Intervention, Rebecca Mazumdar, Nadia Benakli, Pamela Brown
Teaching With Technology: Using A Virtual Learning Community And Peer Mentoring To Create An Interdisciplinary Intervention, Rebecca Mazumdar, Nadia Benakli, Pamela Brown
Publications and Research
This paper describes the development and implementation of engaging and supportive experiences to promote student engagement, persistence and success at a commuter, open enrollment, public, minority serving institution. Project components included faculty development at the SENCER Summer Institute (SSI) 2016, attended by a team comprised of an academic administrator, full-time faculty from English and math, and part-time faculty in chemistry; creation of a virtual learning community of freshmen enrolled in chemistry, English, and math linked by the specific theme of the environmental impacts of deicing roads with salt and the overarching theme of the impacts of human activities on the …