Physical Sciences and Mathematics Commons^™

Microstructural Origin Of The High-Energy Storage Performance In Epitaxial Lead-Free Ba(Zr 0.2 Ti 0.8 )O 3 Thick Films, Jun Ouyang, Xianke Wang, Changtao Shao, Hongbo Cheng, Hanfei Zhu, Yuhang Ren

Publications and Research

In our previous work, epitaxial Ba(Zr 0.2 Ti 0.8 )O 3 thick films (~1–2 μ m) showed an excellent energy storage performance with a large recyclable energy density (~58 J/cc) and a high energy efficiency (~92%), which was attributed to a nanoscale entangled heterophase polydomain structure. Here, we propose a detailed analysis of the structure–property relationship in these film materials, using an annealing process to illustrate the effect of nanodomain entanglement on the energy storage performance. It is revealed that an annealing-induced stress relaxation led to the segregation of the nanodomains (via detailed XRD analyses), and a degraded energy storage …

Markovnikov Alcohols Via Epoxide Hydroboration By Molecular Alkali Metal Catalysts, Guoqi Zhang, Haisu Zeng, Shengping Zheng, Michelle C. Neary, Los Alamos National Laboratory

Publications and Research

Summary

Evolution Of Microscopic Heterogeneity And Dynamics In Choline Chloride-Based Deep Eutectic Solvents, Stephanie Spittle, Derrick Poe, Brain Doherty, Charles Kolodziej, Luke Heroux, Md Ashraful Haque, Henry Squire, Tyler Cosby, Yong Zhang, Carla Fraenza, Sahana Bhattacharyya, Madhusudan Tyagi, Jing Peng, Ramez A. Elgammal, Thomas Zawodzinski, Mark Tuckerman, Steve Greenbaum, Burcu Gurkan, Clemens Burda, Mark Dadmun, Edward J. Maginn, Joshua Sangoro

Publications and Research

Deep eutectic solvents (DESs) are an emerging class of non-aqueous solvents that are potentially scalable, easy to prepare and functionalize for many applications ranging from biomass processing to energy storage technologies. Predictive understanding of the fundamental correlations between local structure and macroscopic properties is needed to exploit the large design space and tunability of DESs for specific applications. Here, we employ a range of computational and experimental techniques that span length-scales from molecular to macroscopic and timescales from picoseconds to seconds to study the evolution of structure and dynamics in model DESs, namely Glyceline and Ethaline, starting from the parent …

Biomedical Applications Of Lanthanide Nanomaterials, For Imaging, Sensing And Therapy, Qize Zhang, Stephen O'Brien, Jan Grimm

Publications and Research

The application of nanomaterials made of rare earth elements within biomedical sciences continues to make significant progress. The rare earth elements, also called the lanthanides, play an essential role in modern life through materials and electronics. As we learn more about their utility, function, and underlying physics, we can contemplate extending their applications to biomedicine. This particularly applies to diagnosis and radiation therapy due to their relatively unique features, such as an ultra-wide Stokes shift in the luminescence, variable magnetism and potentially tunable properties, due to the library of lanthanides available and their multivalent oxidation state chemistry. The ability to …

Probing The Production Of Intracellular Vesicles Containing Reactive Oxygen And Nitrogen Species By Electrochemical Resistive-Pulse Sensing, Rui Jia

Publications and Research

No abstract provided.

High-Resolution Cryo-Electron Microscopy Structure Of Photosystem Ii From The Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803, Christopher J. Gisriel, Jimin Wang, Jinchan Liu, David A. Flesher, Krystle M. Reiss, Hao-Li Huang, Ke R. Yang, William H. Armstrong, M. R. Gunner, Victor S. Batista, Richard J. Debus, Gary W. Brudvig

Publications and Research

Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a highresolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the …

Me3al-Mediated Domino Nucleophilic Addition/Intramolecular Cyclisation Of 2-(2-Oxo-2-Phenylethyl)Benzonitriles With Amines; A Convenient Approach For The Synthesis Of Substituted 1-Aminoisoquinolines, Krishna M. S. Adusumalli, Lakshmi N.S. Konidena, Hima B. Gandham, Krishnaiah Kumari, Krishan R. Valluru, Satya K.R. Nidasanametla, Venkateswara R. Battula, Hari K. Namballa

Publications and Research

A simple and efficient protocol for the construction of 1-aminoisoquinolines was achieved by treating 2-(2-oxo-2- phenylethyl)benzonitriles with amines in the presence of Me 3 Al. The reaction proceeds via a domino nucleophilic addition with subsequent intramolecular cyclisation. This method provides a wide variety of substituted 1-aminoisoquinolines with good func- tional group tolerance. Furthermore, the synthetic utility of this protocol was demonstrated in the successful synthesis of the anti- tumor agent CWJ-a-5 in gram scale.

The Temperature-Dependent Conformational Ensemble Of Sars-Cov-2 Main Protease (Mpro), Ali Ebrahim, Blake T. Riley, Desigan Kumaran, Babak Andi, Martin R. Fuchs, Sean Mcsweeney, Daniel A. Keedy

Publications and Research

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M^pro, is a promising target for development of novel antiviral therapeutics. Previous X-ray crystal structures of M^pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M^pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these datasets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a temperature-dependent conformational landscape for M^pro, including …

Designing Atomic Edge Structures In 2d Transition Metal Dichalcogenides For Improved Catalytic Activity, Raymond R. Unocic, Xiahan Sang, Guoxiang Hu, Victor Fung, Jingsong Huang, Matthew G. Boebinger, Kai Xiao, Panchapakesan Ganesh

Publications and Research

Designing new materials for functional applications depends upon our ability to understand and correlate the materials structure and chemistry to functional material properties. This is even more important for two-dimensional (2D) materials where thicknesses are on the order of a single atom to a few-atomic layers; therefore, any structural or chemical modification at these length scales can have a profound effect on modifying physical and chemical properties. 2D transition metal dichalcogenides (TMDs) such as MoS2 have emerged as a promising catalyst for the hydrogen evolution reaction with defects such as vacancies and edges being linked to high catalytic active sites …

Evaluation Of Log P, Pka, And Log D Predictions From The Sampl7 Blind Challenge, Teresa Danielle Bergazin, Nicolas Tielker, Yingying Zhang, Junjun Mao, M. R. Gunner, Karol Francisco, Carlo Ballatore, Stefan M. Kast, David L. Mobley

Publications and Research

The Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenges focuses the computational modeling community on areas in need of improvement for rational drug design. The SAMPL7 physical property challenge dealt with prediction of octanol-water partition coefficients and pK_a for 22 compounds. The dataset was composed of a series of N-acylsulfonamides and related bioisosteres. 17 research groups participated in the log P challenge, submitting 33 blind submissions total. For the pK_a challenge, 7 different groups participated, submitting 9 blind submissions in total. Overall, the accuracy of octanol-water log P predictions in the SAMPL7 challenge was …

Human Ace2‑Functionalized Gold “Virus‑Trap” Nanostructures For Accurate Capture Of Sars‑Cov‑2 And Single‑Virus Sers Detection, Yong Yang, Yusi Peng, Chenglong Lin, Li Long, Jingying Hu, Jun He, Hui Zeng, Zhengren Huang, Zhi-Yuan Li, Masaki Tanemura, Jianlin Shi, John R. Lombardi, Xiaoying Luo

Publications and Research

The current COVID-19 pandemic urges the extremely sensitive and prompt detection of SARS-CoV-2 virus. Here, we present a Human Angiotensin-converting-enzyme 2 (ACE2)-functionalized gold “virus traps” nanostructure as an extremely sensitive SERS biosensor, to selectively capture and rapidly detect S-protein expressed coronavirus, such as the current SARS-CoV-2 in the contaminated water, down to the single-virus level. Such a SERS sensor features extraordinary 106- fold virus enrichment originating from high-affinity of ACE2 with S protein as well as “virus-traps” composed of oblique gold nanoneedles, and 109- fold enhancement of Raman signals originating from multicomponent SERS effects. Furthermore, the identification standard of virus …

Alternative View Of Oxygen Reduction On Porous Carbon Electrocatalysts: The Substance Of Complex Oxygen-Surface Interactions, Giacomo De Falco, Marc Florent, Jacek Jagiello, Yongqiang Cheng, Luke L. Daemen, Anibal J. Ramirez-Cuesta, Teresa J. Bandosz

Publications and Research

Electrochemical oxygen reduction reaction (ORR) is an important energy-related process requiring alternative catalysts to expensive platinum-based ones. Although recently some advancements in carbon catalysts have been reported, there is still a lack of understanding which surface features might enhance their efficiency for ORR. Through a detailed study of oxygen adsorption on carbon molecular sieves and using inelastic neutron scattering, we demonstrated here that the extent of oxygen adsorption/interactions with surface is an important parameter affecting ORR. It was found that both the strength of O2 physical adsorption in small pores and its specific interactions with surface ether functionalities in the …

Exploring The Silent Aspect Of Carbon Nanopores, Teresa J. Bandosz

Publications and Research

Recently, owing to the discovery of graphene, porous carbons experienced a revitalization in their explorations. However, nowadays, the focus is more on search for suitable energy advancing catalysts sensing, energy storage or thermal/light absorbing features than on separations. In many of these processes, adsorption, although not emphasized sufficiently, can be a significant step. It can just provide a surface accumulation of molecules used in other application-driving chemical or physical phenomena or can be even an additional mechanism adding to the efficiency of the overall performance. However, that aspect of confined molecules in pores and their involvement in the overall performance …

Mapping Gadolinium Contrast In A Complex Ionic And Photosynthesis Environment Of Pineapple By Near-Infrared And X-Ray Imaging, Subhendra Sarkar, Zoya Vinokur, Chen Xu, Tetiana Soloviova, Amina Shahbaz, Aldona Gjoni

Publications and Research

This work explores the diffusivity of a lanthanide complex, Eovist (Gadolinium-Ethoxy Benzyl Diethylenetriamine pentaacetate) that is stable in neutral media but is not in acidic environment. In the current work an acidic fruit model like pineapple that is rich in transition metals was used and a possible transmetallation reaction among Eovist and transition metal complexes was tested using X-ray imaging. Another goal of this work was to perturb the usual and the unusual photosynthesis systems that pineapple has maintained for millions of years during the evolution of circadian genes for efficient water conservation by dark photosynthesis. To detect such photosynthesis …

Challenges In Quantifying Air‐Water Carbon Dioxide Flux Using Estuarine Water Quality Data: Case Study For Chesapeake Bay, Maria Herrmann, Raymond G. Najjar, Fei Da, Jaclyn R. Friedman, Marjorie A. M. Friedrichs, Sreece Goldberger, Alana Menendez, Elizabeth H. Shadwick, Edward G. Stets, Pierre St-Laurent

Publications and Research

Estuaries play an uncertain but potentially important role in the global carbon cycle via CO₂ outgassing. The uncertainty mainly stems from the paucity of studies that document the full spatial and temporal variability of estuarine surface water partial pressure of carbon dioxide ( pCO₂). Here, we explore the potential of utilizing the abundance of pH data from historical water quality monitoring programs to fill the data void via a case study of the mainstem Chesapeake Bay (eastern United States). We calculate pCO₂ and the air-water CO₂ flux at monthly resolution from 1998 to …

Uptake Of Co(Ii) Ions From Aqueous Solutions By Low-Cost Biopolymers And Their Hybrid, Mohamdia Nassar, Abel E. Navarro

Publications and Research

Alginate hydrogel beads (AB), spent peppermint leaf (PM), and a hybrid adsorbent of these two materials (ABPM), were studied as potential adsorbents of Cobalt (II) ions from aqueous solutions in batch system at room temperature. Equilibrium parameters such as solution pH, mass of adsorbent and the presence of a crowding agent on the adsorption of Co(II) ions were investigated. The results indicate that Co(II) uptake is maximized at pH values higher than 5, with adsorbent doses in the range 120-200 mg. Co(II) adsorption followed the trend AB > ABPM > PM with adsorption percentages of 77%, 71% and 64%, respectively.

Polymers For Extrusion‐Based 3d Printing Of Pharmaceuticals: A Holistic Materials–Process Perspective, Mohammad A. Azad, Deborah Olawuni, Georgia Kimbell, Abu Zayed Badruddoza, Md. Shahadat Hossain, Tasnim Sultana

Publications and Research

Three dimensional (3D) printing as an advanced manufacturing technology is progressing to be established in the pharmaceutical industry to overcome the traditional manufacturing regime of ʹone size fits for allʹ. Using 3D printing, it is possible to design and develop complex dosage forms that can be suitable for tuning drug release. Polymers are the key materials that are necessary for 3D printing. Among all 3D printing processes, extrusion‐based (both fused deposition modeling (FDM) and pressure‐assisted microsyringe (PAM)) 3D printing is well researched for pharmaceutical manufacturing. It is important to understand which polymers are suitable for extrusion‐based 3D printing of pharmaceuticals …

Singlet Fission In A Hexacene Dimer: Energetics Dictate Dynamics, Samuel N. Sanders, Elango Kumarasamy, Kealan J. Fallon, Matthew Y. Sfeir, Luis M. Campos

Publications and Research

Singlet fission (SF) is an exciton multiplication process with the potential to raise the efficiency limit of single junction solar cells from 33% to up to 45%. Most chromophores generally undergo SF as solid-state crystals. However, when such molecules are covalently coupled, the dimers can be used as model systems to study fundamental photophysical dynamics where a singlet exciton splits into two triplet excitons within individual molecules. Here we report the synthesis and photophysical characterization of singlet fission of a hexacene dimer. Comparing the hexacene dimer to analogous tetracene and pentacene dimers reveals that excess exoergicity slows down singlet fission, …

Triflic Acid Mediated Sequential Cyclization Of Ortho-Alkynylarylesters With Ammonium Acetate, Maciej E. Domaradzki, Xiaochen Liu, Jiye Ong, Gyeongah Yu, Gan Zhang, Ariel Simantov, Eliyahu Perl, Yu Chen

Publications and Research

A triflic acid (TfOH) mediated sequential cyclization of ortho-alkynylarylesters and ammonium acetate (NH₄OAc) was reported. The reaction took place via a Brønsted acid-mediated intramolecular cyclization of ortho-alkynylarylesters followed by an ammonium acetate participated substitution reaction, forming isoquinolin-1-ones as the major products. Different from most of the known synthetic methods of isoquinolin-1-ones, no metal catalyst was required in the reported reaction. The regioisomers – isoindolin-1-ones were obtained together with isoquinolin-1-ones in a few cases. The intermediate compounds – isochromen-1-ones and isobenzofuran-1-ones were also isolated. The interconversion experiments showed that the regioisomers formed during the Brønsted acid induced …

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

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

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

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

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

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

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

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

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

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

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 …