Chemistry Commons^™

Scattering Of Larger Molecules – Part 1: General Discussion, Dmitri Babikov

Chemistry Faculty Research and Publications

No abstract provided.

Autoregulatory Mechanism Of Enzyme Activity By The Nuclear Localization Signal Of Lysine-Specific Demethylase 1, Dulmi Senanayaka, Danyun Zeng, Sahar Alishiri, William J. Martin, Khadijah I. Moore, Roshni Patel, Zigmund Luka, Alexander Hirschi, Nicholas J. Reiter

Chemistry Faculty Research and Publications

The N-terminal region of the human lysine-specific demethylase 1 (LSD1) has no predicted structural elements, contains a nuclear localization signal (NLS), undergoes multiple posttranslational modifications (PTMs), and acts as a protein-protein interaction hub. This intrinsically disordered region (IDR) extends from core LSD1 structure, resides atop the catalytic active site, and is known to be dispensable for catalysis. Here, we show differential nucleosome binding between the full-length and an N terminus deleted LSD1 and identify that a conserved NLS and PTM containing element of the N terminus contains an alpha helical structure, and that this conserved element impacts demethylation. Enzyme assays …

Mixed Quantum/Classical Calculations Of Rotationally Inelastic Scattering In The Co + Co System: A Comparison With Fully Quantum Results, Dulat Bostan, Bikramaditya Mandal, Carolin Joy, Michał Żółtowski, François Lique, Jérôme Loreau, Ernesto Quintas-Sánchez, Adrian Batista-Planas, Richard Dawes, Dmitri Babikov

Chemistry Faculty Research and Publications

An updated version of the CO + CO potential energy surface from [R. Dawes, X. G. Wang and T. Carrington, J. Phys. Chem. A 2013, 117, 7612] is presented, that incorporates an improved treatment of the asymptotic behavior. It is found that this new surface is only slightly different from the other popular PES available for this system in the literature [G. W. M. Vissers, P. E. S. Wormer and A. Van Der Avoird, Phys. Chem. Chem. Phys. 2003, 5, 4767]. The differences are quantified by expanding both surfaces over a set of analytic functions and comparing the behavior of …

Mixed Quantum/Classical Theory For Rotationally Inelastic Scattering Of Identical Collision Partners: Revised, Dulat Bostan, Bikramaditya Mandal, Dmitri Babikov

Chemistry Faculty Research and Publications

Mixed quantum/classical theory (MQCT) for the treatment of rotationally inelastic transitions during collisions of two identical molecules, described either as indistinguishable or distinguishable partners, is reviewed. The treatment of two molecules as indistinguishable includes symmetrization of rotational wavefunctions, introduces exchange parity, and leads to state-to-state transition matrix elements different from those in the straightforward treatment of molecules as distinguishable. Moreover, the treatment of collision partners as indistinguishable is eight times faster. Numerical results presented herein for H₂ + H₂, CO + CO and H₂O + H₂O systems indicate good agreement of MQCT calculations …

Scattering In Extreme Environments: General Discussion, Dmitri Babikov

Chemistry Faculty Research and Publications

No abstract provided.

Scattering At Condensed-Phase Surfaces: General Discussion, Dmitri Babikov

Chemistry Faculty Research and Publications

No abstract provided.

Benzoquinone Ligand-Enabled Ruthenium-Catalyzed Deaminative Coupling Of 2-Aminoaryl Aldehydes And Ketones With Branched Amines For Regioselective Synthesis Of Quinoline Derivatives, Krishna Prasad Gnyawali, Aldiyar Shakenov, Pandula T. Kirinde Arachchige, Chae S. Yi

Chemistry Faculty Research and Publications

The catalytic system generated in situ from the cationic Ru–H complex [(C₆H₆)(PCy₃)(CO)RuH]⁺BF₄– (1) with 2,3,4,5-tetrachloro-1,2-benzoquinone (L1) was found to be highly effective for promoting the deaminative coupling reaction of 2-aminoaryl aldehydes with branched amines to form 2-substituted quinoline products. The analogous deaminative coupling reaction of 2-aminoaryl ketones with branched amines led to the regioselective formation of 2,4-disubstituted quinoline products. A number of biologically active quinoline derivatives including graveolinine and a triplex DNA intercalator have been synthesized by using the catalytic method.

Anticancer Drugs Of Lysine Specific Histone Demethylase-1 (Lsd1) Display Variable Inhibition On Nucleosome Substrates, Dulmi Senanayaka, Danyun Zeng, Emre Deniz, Indunil K. Priyankara, Joceline Helmbreck, Owen Schneider, Aashay Mardikar, Aykut Uren, Nicholas J. Reiter

Chemistry Faculty Research and Publications

Lysine specific demethylase-1 (LSD1) serves as a regulator of transcription and represents a promising epigenetic target for anticancer treatment. LSD1 inhibitors are in clinical trials for the treatment of Ewing’s sarcoma (EWS), acute myeloid leukemia, and small cell lung cancer, and the development of robust inhibitors requires accurate methods for probing demethylation, potency, and selectivity. Here, the inhibition kinetics on the H3K4me2 peptide and nucleosome substrates was examined, comparing the rates of demethylation in the presence of reversible [CC-90011 (PD) and SP-2577 (SD)] and irreversible [ORY-1001 (ID) and tranylcypromine (TCP)] inhibitors. Inhibitors were also subject to viability studies in three …

Synthesis And Evaluation Of 5-(Heteroarylmethylene)Hydantoins As Glycogen Synthase Kinase-3Β Inhibitors, Nicholas O. Schneider, Keandra Gilreath, Daniel J. Burkett, Martin St. Maurice, William A. Donaldson

Chemistry Faculty Research and Publications

Glycogen synthase kinase-3 (GSK-3) is a serine/threonine kinase which plays a center role in the phosphorylation of a wide variety of proteins, generally leading to their inactivation. As such, GSK-3 is viewed as a therapeutic target. An ever-increasing number of small organic molecule inhibitors of GSK-3 have been reported. Phenylmethylene hydantoins are known to exhibit a wide range of inhibitory activities including for GSK-3β. A family of fourteen 2-heterocycle substituted methylene hydantoins (14, 17–29) were prepared and evaluated for the inhibition of GSK-3β at 25 μM. The IC50 values of five of these compounds was determined; the two best inhibitors …

Efficient Synthesis Of Thiazole-Fused Bisnoralcohol Derivatives As Potential Therapeutic Agents, Subrata Roy, Hansa Raj Kc, Sanjay Adhikary, Alexander N. Erickson, Mohammad Abrar Alam

Chemistry Faculty Research and Publications

Thiazole derivatives are known for a wide range of therapeutic properties. Bisnoralcohol is an inexpensive natural product obtained by the biodegradation of sterols. This article describes an efficient synthesis of a library of thiazole-fused bisnoralcohol derivatives. These novel compounds have been studied for their antineoplastic and antibacterial properties, which led to the discovery of hit compounds with therapeutic potential. The antibacterial compound is noncytotoxic and nonhemolytic against cancer cell lines and sheep red blood cells, respectively. Several of the antineoplastic compounds showed activity against human cancer cell lines with growth inhibition at submicromolar concentration.

Mechanism Of Action Of Kl-50, A Candidate Imidazotetrazine For The Treatment Of Drug-Resistant Brain Cancers, Eric D. Huseman, Anna Lo, Olga Fedorova, James L. Elia, Susan E. Gueble, Kingson Lin, Ranjini K. Sundaram, Jooneseok Oh, Jinchan Liu, Fabian Menges, Matthew G. Rees, Melissa M. Ronan, Jennifer A. Roth, Victor S. Batista, Jason M. Crawford, Anna M. Pyle, Ranjit S. Bindra, Seth B. Herzon

Chemistry Faculty Research and Publications

Aberrant DNA repair is a hallmark of cancer, and many tumors display reduced DNA repair capacities that sensitize them to genotoxins. Here, we demonstrate that the differential DNA repair capacities of healthy and transformed tissue may be exploited to obtain highly selective chemotherapies. We show that the novel N3-(2-fluoroethyl)imidazotetrazine “KL-50” is a selective toxin toward tumors that lack the DNA repair protein O⁶-methylguanine-DNA-methyltransferase (MGMT), which reverses the formation of O⁶-alkylguanine lesions. We establish that KL-50 generates DNA interstrand cross-links (ICLs) by a multistep process comprising DNA alkylation to generate an O⁶-(2-fluoroethyl)guanine (O⁶FEtG) …

Terra-Lsd1 Phase Separation Promotes R-Loop Formation For Telomere Maintenance In Alt Cancer Cells, Nicholas J. Reiter

Chemistry Faculty Research and Publications

The telomere repeat-containing RNA (TERRA) forms R-loops to promote homology-directed DNA synthesis in the alternative lengthening of telomere (ALT) pathway. Here we report that TERRA contributes to ALT via interacting with the lysine-specific demethylase 1A (LSD1 or KDM1A). We show that LSD1 localizes to ALT telomeres in a TERRA dependent manner and LSD1 function in ALT is largely independent of its demethylase activity. Instead, LSD1 promotes TERRA recruitment to ALT telomeres via RNA binding. In addition, LSD1 and TERRA undergo phase separation, driven by interactions between the RNA binding properties of LSD1 and the G-quadruplex structure of TERRA. Importantly, the …

Surface-Modified Pd/Ceo2 Single-Atom Catalyst Shows Increased Activity For Suzuki Cross-Coupling, Audrey Vice, Nicholas Langer, Benjamin J. Reinhart, Ofer Kedem

Chemistry Faculty Research and Publications

Single-atom catalysts (SACs) comprise catalytically active atoms dispersed on supports; they combine the high activity and site uniformity of homogeneous catalysts with the ease of separability of heterogeneous catalysts. However, SACs lack fine control over the active site, provided by ligands in homogeneous catalysts. In this work, we demonstrate that modification of the support with an organic monolayer is a viable approach to improving the catalytic performance. The addition of catechol-type monolayers to a Pd/CeO2 SAC increases its catalytic activity for Suzuki cross-coupling, a central reaction in the synthesis of fine chemicals and pharmaceuticals. Kinetic trials reveal that the coating …

Scope And Mechanism Of The Ruthenium-Catalyzed Deaminative Coupling Reaction Of Enones With Amines Via Regioselective CΑ–CΒ Bond Cleavage, Marat R. Talipov, Dulanjali S. Thennakoon, Chae S. Yi

Chemistry Faculty Research and Publications

A highly regioselective C–C bond cleavage method of enones has been devised from the ruthenium-catalyzed deaminative coupling reaction with simple amines. The analogous catalytic coupling reaction of enones with anilines has led to a regioselective C_α–C_β bond cleavage of enones in forming N-alkylanilines and 2,4-disubstituted quinolines. The reaction profile study showed the formation of a β-aminoimine intermediate prior to the C–C cleavage product formation. A Hammett plot from the reaction of (E)-2-octen-4-one with a series of para-substituted benzylamines established a strong promotional effect by an electron-donating group (ρ = −0.77 ± 0.1). The …

Improved Temperature Dependence Of Rate Coefficients For Rotational State-To-State Transitions In H2O + H2O Collisions, Bikramaditya Mandal, Dmitri Babikov

Chemistry Faculty Research and Publications

Aims. We present an improved database of temperature-dependent rate coefficients for rotational state-to-state transitions in H₂O + H₂O collisions. The database includes 231 transitions between the lower para-states of H₂O and 210 transitions between its lower ortho-states (up to j = 7) and can be employed in cometary and planetary applications up to the temperature of 1000 K.

Methods. We developed and applied a new general method that allows the generation of rate coefficients for excitation and quenching processes that automatically satisfy the principle of microscopic reversibility and also helps to cover …

Scope And Mechanistic Studies On The Ruthenium-Catalyzed Multicomponent Deaminative C–H Coupling Reaction Of Phenols With Aldehydes And Enamines For The Formation Of Xanthene And Dioxacyclic Derivatives, Nuwan Asanka Pannilawithana, Mina Son, Donghun Hwang, Mu-Hyun Baik, Chase S. Yi

Chemistry Faculty Research and Publications

The in situ generated catalytic system from the tetranuclear Ru–H complex [(PCy₃)(CO)RuH]₄(O)(OH)₂ (1) with 3,4,5,6-tetrachloro-1,2-benzoquinone (L1) has been found to mediate a multicomponent deaminative coupling reaction of phenols with aldehydes and enamines to form xanthene products. The multicomponent C–H coupling reaction of phenols with 2-hydroxybenzaldehydes and cyclic enamines efficiently installed the tricyclic 1,3-dioxacin derivatives, while the analogous coupling reaction of phenols with 2-hydroxybenzaldehydes and triethylamine selectively formed bicyclic 1,5-dioxacyclic derivatives. The density functional theory (DFT) calculations established two energetically viable mechanistic pathways for the formation of xanthene products, in which both …

Scope And Mechanistic Studies Of Ruthenium Catalyzed C-C And C-N Bond Activation Reactions, Dulanjali Thennakoon

Dissertations (1934 -)

Transition metal catalyzed selective C–C and C–N bond activation reactions emerged as an effective synthetic tool in organic chemistry. Reorganization of these bond connections allows access to complex molecular scaffolds from readily available starting materials which are immensely useful for organic synthesis of pharmaceutical agents. While enormous progress has been achieved to date, major challenges still remain in desigining broad applicable catalytic bond activation methods. The well-defined cationic Ru–H complex with a benzoquinone ligand was found to be an effective catalytic system for the deaminative coupling reaction of enones with amines which enable regioselective cleavage of unstrained Cα–Cβ bond of …

Elucidating The Structure And Regulatory Interactions Of The Hotair Non-Coding Rna And The Bacterial Rnase P. Holoenzyme, Ainur Abzhanova

Dissertations (1934 -)

RNA structures and RNA-protein interactions are studied as potential drug targets, biomarkers in cancer, and can be administered as vaccines. The cancer associated HOTAIR (HOX transcript antisense RNA) exists in higher vertebrates and interacts with chromatin remodeling enzymes. We examined the thermodynamic folding properties and structural propensity of the exonic regions of HOTAIR using biophysical methods and NMR spectroscopy. Different exons of HOTAIR contain variable degrees of structural heterogeneity. We identify one exonic region, exon 4, that adopts a stable and compact fold under low magnesium concentrations. Close agreement of NMR spectroscopy and chemical probing confirm conserved base pair interactions …

Photophysical And Photocatalytic Properties Of Covalent Organic Frameworks, Daniel Streater H.

Dissertations (1934 -)

This dissertation is most interested in how a class of materials known as covalent organic frameworks (COFs) can be designed to capture photon energy to initiate chemical reactions. Different COF designs change how long the energy is held, how it migrates, and how it is dispersed – and these differences can be used to change their performance as artificial photosynthesis platforms. Thus, it is helpful to have an informative discussion about the processes behind natural photosynthesis, that is, nature’s light harvesting strategies and photocatalytic schemes (Section 1.2) and will lead into an introduction of COFs and why they possess unique …

Identification Of The Autoregulatory Properties And Molecular Interactions Of The Lysine-Specific Histone Demethylase 1 Enzyme, Dulmi Senanayaka

Dissertations (1934 -)

The conserved chromatin-remodeling enzyme, Lysine-Specific histone1/2 Demethylase 1 (LSD1) primarily demethylates Histone H3K4me , acting as a transcriptional repressor. It plays pivotal roles in various physiological processes including cancer and interacts with many regulatory proteins, non-coding RNAs, and small metabolites. However, little biochemical information is known about LSD1’s N-terminal intrinsically disordered region (IDR) and how LSD1 interacts with various biomolecules in the context of nucleosome. I present evidence that the IDR of LSD1, containing multiple post translational modifications (PTMs) and a nuclear localization signal (NLS), can act as a reversible competitive autoinhibitor of LSD1’s activity. This autoinhibition can be relieved …

Cationic Polymer Coating Increases The Catalytic Activity Of Gold Nanoparticles Toward Anionic Substrates, Nicholas Langer, Mason Legrand, Ofer Kedem

Chemistry Faculty Research and Publications

Organic coatings on catalytic metal nanoparticles (NPs) typically hinder their activity due to the blocking of active sites. Therefore, considerable effort is made to remove organic ligands when preparing supported NP catalytic materials. Here, cationic polyelectrolyte coatings are shown to increase the catalytic activity of partially embedded gold nanoislands (Au NIs) toward transfer hydrogenation and oxidation reactions with anionic substrates compared to the activity of identical but uncoated Au NIs. Any potential steric hindrance caused by the coating is countered by a decrease in the activation energy of the reaction by half, resulting in overall enhancement. The direct comparison to …

Exploring New Techniques For Precision Deuteration Of Alkenes And Alkynes, Zoua Pa Vang

Dissertations (1934 -)

Deuterium labeled compounds are often utilized in chemical research as internal standards in mass spectrometry, to study reaction mechanisms and in the pharmaceutical industry to slow the rate of metabolism. With the increase interest for deuterium labeled molecules, there is a renewed interest in selective methods for the installation of deuterium atoms into small organic molecules. However, current methods to incorporate deuterium atoms into organic molecules can lead to isotopic mixtures such as isotopologues and isotopomers. These isotopic species are indistinguishable due to their similar physical properties, leading to inseparable products by common purification techniques. Furthermore, common spectroscopic techniques to …

Rate Coefficients For Rotational State-To-State Transitions In H2O + H2O Collisions For Cometary And Planetary Applications, As Predicted By Mixed Quantum-Classical Theory, Bikramaditya Mandal, Dmitri Babikov

Chemistry Faculty Research and Publications

Aims. We present new calculations of collision cross sections for state-to-state transitions between the rotational states in an H₂O + H₂O system, which are used to generate a new database of collisional rate coefficients for cometary and planetary applications.

Methods. Calculations were carried out using a mixed quantum-classical theory approach that is implemented in the code MQCT. The large basis set of rotational states used in these calculations permits us to predict thermally averaged cross sections for 441 transitions in para- and ortho-H₂O in a broad range of temperatures.

Results. It is found that …

What Moves The Needle On Dfw Rates And Student Success In General Chemistry? A Quarter-Century Perspective, Vijay Vyas, Scott A. Reid

Chemistry Faculty Research and Publications

Second-term general chemistry is a key gateway course at our institution for a variety of STEM (Science, Technology, Engineering, and Mathematics) majors. Herein, we examine data on DFW% (i.e., % of D and F grades and withdrawals) in our general chemistry courses over roughly a quarter-century period, focusing on sections taught by the authors. The data are discussed in light of changes in curriculum, pedagogy, and assessments, which included introduction of recitation sections, classroom response systems (clickers), and online homework, restructuring of course content into a modular format, followed by a redesign of the course modules along an anchoring concepts …

Design, Evolution, And Evaluation Of A General Chemistry-Bridging Course, Scott A. Reid

Chemistry Faculty Research and Publications

General chemistry I/II courses are important gateway courses for a variety of STEM majors, as poor performance in these courses is often associated with lower rates of student success and retention. Much research has explored preparatory or remedial strategies to improve student outcomes. In this article, we report a different approach, which involved the development of a bridging or intervention course designed to capture students who are not or have not succeeded in general chemistry I and prepare them to retake the course in the following semester or summer. The course was initially developed as an eight-week module in the …

Symmetry Breaking: A Classic Example Of Quantum Interference Captured By Mixed Quantum/Classical Theory, Kayla Imanzi, Dulat Bostan, Max Mccrea, Josh Featherstone, Mark Brouard, Dmitri Babikov

Chemistry Faculty Research and Publications

The phenomena of propensity and inverse propensity are explored using time-dependent mixed quantum classical theory, MQCT, in which the rotational motion of the molecule is treated quantum mechanically, whereas the scattering process is described classically. Good agreement with the results of accurate full-quantum calculations is reported for a closed shell approximation to the NO + Ar system. It is shown that MQCT reproduces both phenomena in a broad range of the final states of the molecule and for various initial rotational states, offering a unique time-dependent insight. It permits seeing that both propensity and inverse propensity occur due to efficient …

Mixed Quantum/Classical Theory For Rotational Energy Exchange In Symmetric-Top-Rotor + Linear-Rotor Collisions And A Case Study Of The Nd3 + D2 System, Carolin Joy, Bikramaditya Mandal, Dulat Bostan, Dmitri Babikov

Chemistry Faculty Research and Publications

Manifestation of the quantum interference effect in the oscillation of scattering cross section is explored using the N2 + O system as a case study. Calculations are carried out for two electronic PESs of the system, for various initial rotational states of N2, in a broad range of N2 + O collision energies and using three theoretical methods: two versions of the approximate mixed quantum/classical theory (MQCT and AT-MQCT) and the accurate full-quantum coupled-channel method (implemented in MOLSCAT). A good agreement between different methods is observed, especially at high energies. Elastic scattering cross-sections oscillate as a function of collision energy, …

Description Of Quantum Interference Using Mixed Quantum/Classical Theory Of Inelastic Scattering, Dulat Bostan, Bikramaditya Mandal, Carolin Joy, Dmitri Babikov

Chemistry Faculty Research and Publications

Manifestation of the quantum interference effect in the oscillation of scattering cross section is explored using the N₂ + O system as a case study. Calculations are carried out for two electronic PESs of the system, for various initial rotational states of N2, in a broad range of N₂ + O collision energies and using three theoretical methods: two versions of the approximate mixed quantum/classical theory (MQCT and AT-MQCT) and the accurate full-quantum coupled-channel method (implemented in MOLSCAT). A good agreement between different methods is observed, especially at high energies. Elastic scattering cross-sections oscillate as a function of …

Adiabatic Trajectory Approximation: A New General Method In The Toolbox Of Mixed Quantum/Classical Theory For Collisional Energy Transfer, Bikramaditya Mandal, Carolin Joy, Dulat Bostan, Alexander Eng, Dmitri Babikov

Chemistry Faculty Research and Publications

A new version of the MQCT program is presented, which includes an important addition, adiabatic trajectory approximation (AT-MQCT), in which the equations of motion for the classical and quantum parts of the system are decoupled. This method is much faster, which permits calculations for larger molecular systems and at higher collision energies than was possible before. AT-MQCT is general and can be applied to any molecule + molecule inelastic scattering problem. A benchmark study is presented for H₂O + H₂O rotational energy transfer, an important asymmetric-top rotor + asymmetric-top rotor collision process, a very difficult problem …

Impact Of A Low-Stakes Assessments Model With Retake In General Chemistry: Connecting To Student Attitudes And Self-Concept, Vijay Vyas, Llanie Nobile, James R. Gardinier, Scott A. Reid

Chemistry Faculty Research and Publications

Across a variety of fields, the use of low-stakes assessments has led to reductions in achievement gaps and improved student success. Here, we probe the use of a low-stakes assessment model with a retake option for failed quizzes in a two-semester general chemistry sequence. We find that the quiz-retake rate in general chemistry II was significantly higher for students who had completed a retake in a general chemistry I section, and the percentage of students who failed at least one quiz in general chemistry I but passed all quizzes in general chemistry II was significantly higher for students who had …