Evaluation Of Log P, Pka, And Log D Predictions From The Sampl7 Blind Challenge,
2021
University of California, Irvine
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 pKa 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 pKa 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 …
Multiple Wetting−Dewetting States Of A Water Droplet On Dual-
Scale Hierarchical Structured Surfaces,
2021
University of Nebraska-Lincoln
Multiple Wetting−Dewetting States Of A Water Droplet On Dual- Scale Hierarchical Structured Surfaces, Yurui Gao, Yuan Liu, Jian Jiang, Chongqin Zhu, Craig Zuhlke, Dennis Alexander, Joseph S. Francisco, Xiao Cheng Zeng
Xiao Cheng Zeng Publications
Surfaces with microscale roughness can entail dualscale hierarchical structures such as the recently reported nano/ microstructured surfaces produced in the laboratory (Wang et al. Nature 2020, 582, 55−57). However, how the dual-scale hierarchical structured surface affects the apparent wetting/ dewetting states of a water droplet, and the transitions between the states are still largely unexplored. Here, we report a systematic large-scale molecular dynamics (MD) simulation study on the wetting/dewetting states of water droplets on various dual-scale nano/near-submicrometer structured surfaces. To this end, we devise slab-water/slab-substrate model systems with a variety of dual-scale surface structures and with different degrees of intrinsic …
Lanthanide Interactions With Ligands And Biomolecules: Spectroscopic And Extraction Studies,
2021
Florida International University
Lanthanide Interactions With Ligands And Biomolecules: Spectroscopic And Extraction Studies, Setareh Sakhdari
FIU Electronic Theses and Dissertations
Lanthanides (Ln), also known as rare earth metals, have been utilized for industrial and biological purposes and are commonly encountered in the 3+ oxidation state as Ln3+. The presence of Ln in spent nuclear fuel introduces problems during the transmutation and partitioning of actinides (An) due to the Ln high neutron cross-sections. Therefore, designing ligands for Ln3+ complexation, can be helpful for their separation from An3+ in nuclear technology. Also, the biomimetic roles of Ln3+ could be suitable for studying the biological macromolecules, such as the Ca2+-binding EF-hand proteins that are otherwise inaccessible …
Recovery Of High Specific Activity Molybdenum-99 From Accelerator-Induced Fission On Low-Enriched Uranium For Technetium-99m Generators,
2021
Argonne National Laboratory
Recovery Of High Specific Activity Molybdenum-99 From Accelerator-Induced Fission On Low-Enriched Uranium For Technetium-99m Generators, M. Alex Brown, Nathan Johnson, Artem V. Gelis, Milan Stika, Anna G. Servis, Alex Bakken, Christine Krizmanich, Kristin Shannon, Peter Kozak, Amanda Barnhart, Chad Denbrock, Nicolas Luciani, Terry Grimm, Peter Tkac
Chemistry and Biochemistry Faculty Research
A new process was developed to recover high specific activity (no carrier added) 99Mo from electron-accelerator irradiated U3O8 or uranyl sulfate targets. The process leverages a novel solvent extraction scheme to recover Mo using di(2-ethylhexyl) phosphoric acid following uranium and transuranics removal with tri-n-butyl phosphate. An anion-exchange concentration column step provides a final purification, generating pure 99Mo intended for making 99Mo/99mTc generators. The process was demonstrated with irradiated uranium targets resulting in more than 95% 99Mo recovery and without presence of fission products or actinides in the product.
A Bacterial Inflammation Sensor Regulates C-Di-Gmp Signaling, Adhesion, And Biofilm Formation,
2021
University of Oregon
A Bacterial Inflammation Sensor Regulates C-Di-Gmp Signaling, Adhesion, And Biofilm Formation, Arden Perkins, Dan A. Tudorica, Raphael D. Teixeira, Tilman Schirmer, Lindsay Zumwalt, O. Maduka Ogba, C. Keith Cassidy, Phillip J. Stansfeld, Karen Guillemin
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Bacteria that colonize animals must overcome, or coexist, with the reactive oxygen species products of inflammation, a front-line defense of innate immunity. Among these is the neutrophilic oxidant bleach, hypochlorous acid (HOCl), a potent antimicrobial that plays a primary role in killing bacteria through nonspecific oxidation of proteins, lipids, and DNA. Here, we report that in response to increasing HOCl levels, Escherichia coli regulates biofilm production via activation of the diguanylate cyclase DgcZ. We identify the mechanism of DgcZ sensing of HOCl to be direct oxidation of its regulatory chemoreceptor zinc-binding (CZB) domain. Dissection of CZB signal transduction reveals that …
Analysis And Differentiation Of Uniform And Localized Corrosion Of Cu,
2021
The University of Western Ontario
Analysis And Differentiation Of Uniform And Localized Corrosion Of Cu, Roshan J. Daljeet
Electronic Thesis and Dissertation Repository
The current plan for disposal of used nuclear fuel in Canada involves sealing the waste in steel containers coated with 3 mm of copper and burying them in a deep geologic repository (DGR). The purpose of the copper coating is to provide corrosion resistance. To achieve long term containment, it is necessary that the copper layer corrodes slowly and predictably via active dissolution rather than passivating due to film formation. Film formation could allow pitting corrosion to occur in early phase repository conditions when groundwater ions such as Cl– , SO4 2– and HCO3 – play a dominant role in …
Fragment-Based In Silico Design Of Sars-Cov-2 Main Protease Inhibitors,
2021
Drug Design Development Research Group, Department of Chemistry, Faculty of Science, Universiti Malaya
Fragment-Based In Silico Design Of Sars-Cov-2 Main Protease Inhibitors, Sarfraz Ahmad, Muhammad Usman Mirza, Lee Yean Kee, Mamoona Nazir, Noorsaadah Abd Rahman, John F. Trant, Iskandar Abdullah
Chemistry and Biochemistry Publications
3CLpro is essential for SARS-CoV-2 replication and infection; its inhibition using small molecules is a potential therapeutic strategy. In this study, a comprehensive crystallography-guided fragment-based drug discovery approach was employed to design new inhibitors for SARS-CoV-2 3CLpro. All small molecules co-crystallized with SARS-CoV-2 3CLpro with structures deposited in the Protein Data Bank were used as inputs. Fragments sitting in the binding pocket (87) were grouped into eight geographical types. They were interactively coupled using various synthetically reasonable linkers to generate larger molecules with divalent binding modes taking advantage of two different fragments' interactions. In total, 1,251 compounds were proposed, and …
A Fret Flow Cytometry-Based Screening Assay For Multiplex Analysis Of Metabolites In T. Brucei,
2021
Brigham Young University
A Fret Flow Cytometry-Based Screening Assay For Multiplex Analysis Of Metabolites In T. Brucei, Ronald A. Zegarra
Undergraduate Honors Theses
Kinetoplastid parasites are a significant public health issue in some tropical and subtropical regions of the world. Kinetoplastid parasites all require glycolysis for survival, with host glucose key for ATP production. One such parasite, Trypanosoma brucei, exclusively metabolizes glucose in its bloodstream form. Trypanosomal glycolysis is unique because it displays unconventional structural features. Hence, glucose metabolism has been studied extensively in T. brucei and is a therapeutic target in kinetoplastid parasites.The lack of in vivo analytical techniques for measuring vital glycolytic metabolites in situ has restricted the ability of researchers to test, with high sensitivity and specificity, the essential roles …
Special Issue Editorial: Current Advances In Liquid Crystals,
2021
University of Nevada, Las Vegas
Special Issue Editorial: Current Advances In Liquid Crystals, Pradip K. Bhowmik
Chemistry and Biochemistry Faculty Research
No abstract provided.
Cationic Boron Formazanate Complexes,
2021
The University of Western Ontario
Cationic Boron Formazanate Complexes, Benjamin D. Katzman
Electronic Thesis and Dissertation Repository
This thesis describes the synthesis and characterization of various three- and four-coordinate cationic and dicationic boron complexes supported by formazanate ([R1-N-N=C(Ph)-N=N-R5]− ligands. The first chapter provides a review of various three-coordinate and cationic boron complexes and related applications. Chapter two examines the effect of several variations (i.e., charge, coordination number and boron-bound substituents) on the electronic structure of cationic boron formazanate complexes. Absorption spectroscopy measurements reveal that the wavelengths, intensities, and type of the first electronic transitions in cationic boron complexes can be modulated by these structural variations. Chapter three exploits the electron deficiency …
Characterization Of Extracellular Vesicles Derived From Mesenchymal Stromal Cells By Surface-Enhanced Raman Spectroscopy.,
2021
Western University
Characterization Of Extracellular Vesicles Derived From Mesenchymal Stromal Cells By Surface-Enhanced Raman Spectroscopy., Nina M Ćulum, Tyler T Cooper, Gillian I Bell, David A Hess, François Lagugné-Labarthet
Chemistry Publications
Extracellular vesicles (EVs) are secreted by all cells into bodily fluids and play an important role in intercellular communication through the transfer of proteins and RNA. There is evidence that EVs specifically released from mesenchymal stromal cells (MSCs) are potent cell-free regenerative agents. However, for MSC EVs to be used in therapeutic practices, there must be a standardized and reproducible method for their characterization. The detection and characterization of EVs are a challenge due to their nanoscale size as well as their molecular heterogeneity. To address this challenge, we have fabricated gold nanohole arrays of varying sizes and shapes by …
Characterization Of Extracellular Vesicles Derived From Mesenchymal Stromal Cells By Surface-Enhanced Raman Spectroscopy.,
2021
Western University
Characterization Of Extracellular Vesicles Derived From Mesenchymal Stromal Cells By Surface-Enhanced Raman Spectroscopy., Nina M Ćulum, Tyler T Cooper, Gillian I Bell, David A Hess, François Lagugné-Labarthet
Chemistry Publications
Extracellular vesicles (EVs) are secreted by all cells into bodily fluids and play an important role in intercellular communication through the transfer of proteins and RNA. There is evidence that EVs specifically released from mesenchymal stromal cells (MSCs) are potent cell-free regenerative agents. However, for MSC EVs to be used in therapeutic practices, there must be a standardized and reproducible method for their characterization. The detection and characterization of EVs are a challenge due to their nanoscale size as well as their molecular heterogeneity. To address this challenge, we have fabricated gold nanohole arrays of varying sizes and shapes by …
Data From: Chemical Bonding Analysis Of Excited States Using The Adaptive Natural Density Partitioning Method,
2021
Utah State University
Data From: Chemical Bonding Analysis Of Excited States Using The Adaptive Natural Density Partitioning Method, Alexander I. Boldyrev, Nikolay Tkachenko
Browse all Datasets
A novel approach to chemical bond analysis for excited states has been developed. Using an extended adaptive natural density partitioning method (AdNDP) as implemented in AdNDP 2.0 code, we obtained chemically intuitive bonding patterns for the excited states of H2O, B5+, and C2H4+ molecules. The deformation pathway in the excited states could be easily predicted based on the analysis of the chemical bond pattern. We expect that this new method of chemical bonding analysis would be very helpful for photochemistry, photoelectron spectroscopy, electron spectroscopy and other chemical applications that involved excited states.
Characterization Of Extracellular Vesicles Derived From Mesenchymal Stromal Cells By Surface-Enhanced Raman Spectroscopy.,
2021
The University of Western Ontario
Characterization Of Extracellular Vesicles Derived From Mesenchymal Stromal Cells By Surface-Enhanced Raman Spectroscopy., Nina M. Culum, Tyler T. Cooper, Gillian I. Bell, David A. Hess, François Lagugné-Labarthet
Chemistry Publications
Extracellular vesicles (EVs) are secreted by all cells into bodily fluids and play an important role in intercellular communication through the transfer of proteins and RNA. There is evidence that EVs specifically released from mesenchymal stromal cells (MSCs) are potent cell-free regenerative agents. However, for MSC EVs to be used in therapeutic practices, there must be a standardized and reproducible method for their characterization. The detection and characterization of EVs are a challenge due to their nanoscale size as well as their molecular heterogeneity. To address this challenge, we have fabricated gold nanohole arrays of varying sizes and shapes by …
Data From: Stability, Electronic, And Optical Properties Of Two-Dimensional Phosphoborane,
2021
Utah State University
Data From: Stability, Electronic, And Optical Properties Of Two-Dimensional Phosphoborane, Alexander I. Boldyrev, Nikolay Tkachenko
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The structure and properties of two-dimensional phosphoborane sheets were computationally investigated using Density Functional Theory calculations. The calculated phonon spectrum and band structure point to dynamic stability and allowed characterization of the predicted two-dimensional material as a direct-gap semiconductor with a band gap of ~1.5 eV. The calculation of the optical properties showed that the two-dimensional material has a relatively small absorptivity coefficient. The parameters of the mechanical properties characterize the two-dimensional phosphoborane as a relatively soft material, similar to the monolayer of MoS2. Assessment of thermal stability by the method of molecular dynamics indicates sufficient stability of the predicted …
Data From: Novel Strongly Correlated Europium Superhydrides,
2021
Utah State University
Data From: Novel Strongly Correlated Europium Superhydrides, Alexander I. Boldyrev, Nikolay Tkachenko
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We conducted a joint experimental–theoretical investigation of the high-pressure chemistry of europium polyhydrides at pressures of 86–130 GPa. We discovered several novel magnetic Eu superhydrides stabilized by anharmonic effects: cubic EuH9, hexagonal EuH9, and an unexpected cubic (Pm3n) clathrate phase, Eu8H46. Monte Carlo simulations indicate that cubic EuH9 has antiferromagnetic ordering with TN of up to 24 K, whereas hexagonal EuH9 and Pm3n-Eu8H46 possess ferromagnetic ordering with TC = 137 and 336 K, respectively. The electron–phonon interaction is weak in all studied europium hydrides, and their magnetic ordering excludes s-wave superconductivity, except, perhaps, for distorted pseudohexagonal EuH9. The equations of …
Data From: A Sandwich-Type Cluster Containing Ge@Pd3 Planar Fragment Flanked By Aromatic Nonagermanide Caps,
2021
Utah State University
Data From: A Sandwich-Type Cluster Containing Ge@Pd3 Planar Fragment Flanked By Aromatic Nonagermanide Caps, Alexander I. Boldyrev, Nikolay Tkachenko
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Sandwich-type clusters with the planar fragment containing a heterometallic sheet have remained elusive. In this work, we introduce the [K(2,2,2-crypt)]4{(Ge9)2[η6-Ge(PdPPh3)3]} complex that contains a heterometallic sandwich fragment. The title compound is structurally characterized by means of single-crystal X-ray diffraction, which reveals the presence of an unusual heteroatomic metal planar fragment Ge@Pd3. The planar fragment contains a rare formal zerovalent germanium core and a peculiar bonding mode of sp2-Ge@(PdPPh3)3 trigonal planar structure, whereas the nonagermanide fragments act as capping ligands. The chemical bonding pattern of the planar fragment consists of three 2c-2e Pd-Ge σ-bonds attaching Pd atoms to the core Ge …
Exploration Of Fluorinated Α,Β-Dehydroamino Acids And Their Structure,
2021
Brigham Young University
Exploration Of Fluorinated Α,Β-Dehydroamino Acids And Their Structure, Austin Lesueur
Undergraduate Honors Theses
This thesis explores the synthesis of fluorinated α,β-dehydroamino acids, specifically a fluorinated dehydrovaline derivative. Previous work has been done on the equivalent dehydrovaline derivative without fluorine present and this work builds toward the fluorinated version with the goal of comparing the two structurally. The synthesis presented here pulls from previous synthetic strategies employed for dehydrovaline while also exploring the synthetic impact of the electronegative fluorine atoms.
Dataset For: Multiple Local Σ-Aromaticity Of Nonagermanide Clusters,
2021
Utah State University
Dataset For: Multiple Local Σ-Aromaticity Of Nonagermanide Clusters, Alexander I. Boldyrev, Nikolay Tkachenko
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Nonagermanide clusters are widely used in inorganic synthesis and are actively studied by experimentalists and theoreticians. However, chemical bonding of such versatile species is still not completely understood. In our work we deciphered a bonding pattern for various experimentally obtained nonagermanide species. We localized the electron density via the AdNDP algorithm for the model structures ([Ge9]4−, [Ge9{P(NH2)2}3]−, Cu[Ge9{P(NH2)2}3] and Cu(NHC)[Ge9{P(NH2)2}3]) and obtained a simple and chemically intuitive bonding pattern which can explain the variety of active sites and the existence of both D3h and C4v geometries for such clusters. Moreover, the [Ge9]4− core is found to be a unique example …
Data For: Record Low Ionization Potentials Of Alkali Metal Complexes With Crown Ethers And Cryptands,
2021
Utah State University
Data For: Record Low Ionization Potentials Of Alkali Metal Complexes With Crown Ethers And Cryptands, Alexander I. Boldyrev, Nikolay Tkachenko
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Electronic properties of series of alkali metals complexes with crown ethers and cryptands were studied via DFT hybrid functionals. For [M([2.2.2]crypt)] (M=Li, Na, K) extremely low (1.70–1.52 eV) adiabatic ionization potentials were found. Such low values of ionization energies are significantly lower than those of alkali metal atoms. Thus, the investigated complexes can be defined as superalkalis. As a result, our investigation opens up new directions in the designing of chemical species with record low ionization potentials and extends the explanation of the ability of the cryptates and alkali crown ether complexes to stabilize multiple charged Zintl ions.
