Chemistry Commons^™

Neural Network Ensemble For Computing Cross Sections Of Rotational Transitions In H2O + H2O Collisions, Bikramaditya Mandal, Dmitri Babikov, Phillip C. Stancil, Robert C. Forrey, Roman V. Krems, Naduvalath Balakrishnan

Chemistry Faculty Research and Publications

Water (H₂O) is one of the most abundant molecules in the universe and is found in a wide variety of astrophysical environments. Rotational transitions in H₂O + H₂O collisions are important for modeling environments rich in water molecules but they are computationally intractable using quantum mechanical methods. Here, we present a machine learning (ML) tool using an ensemble of neural networks (NNs) to predict cross sections to construct a database of rate coefficients for rotationally inelastic transitions in collisions of complex molecules such as water. The proposed methodology utilizes data computed with a mixed …

Mixed Quantum/Classical Theory For Rotational Excitation Of Hdo In Collisions With H2: Symmetry Breaking Effects And Time-Dependent Dynamics, Carolin Joy, Igor Gaidai, Alexandre Faure, Dmitri Babikov

Chemistry Faculty Research and Publications

The application of the mixed quantum/classical theory of inelastic scattering (MQCT) to the rotational excitation of the isotopically substituted water molecule, HDO, in collisions with hydrogen molecules is presented. Modification of the potential energy surface of thewater + hydrogen system, due to isotopic substitution, is described, and the effect of symmetry breaking is explored. It is found that the additional terms of potential expansion are significant and, therefore, are expected to play an important role during the collision process. The modeling of HDO + H₂ collision is carried out using both the MQCT method and the full-quantum CC method …

A Culturally Responsive Approach Toward Influencing General Chemistry Students’ Belonging And Perceptions Of Chemistry And Science: Metacognition Instruction Versus Role Model Narratives, Althea Berlyn, Rukayya Fall, Shanmugam Puvanendran, Jacinta M. Mutambuki

Chemistry Faculty Research and Publications

This study compared the influence of two distinct interventions, STEM role model narratives and metacognitive instruction, on students’ perceived sense of belonging in the General Chemistry 1 course and STEM program, as well as their perceptions of chemistry and science. We also investigated whether the influence reported differs between the two interventions and the manner in which students articulate this influence. Additionally, variations in the reported positive influence were analyzed based on gender, race/ethnicity, and first-generation status. Grounded in a culturally responsive teaching framework, the study utilized a randomized design to collect qualitative data through an open-ended questionnaire. One group …

Linking Core Concepts And Competencies In General Chemistry Via Gowin’S Theory Of Learning And Vee Heuristic, Vijay Vyas, Scott A. Reid

Chemistry Faculty Research and Publications

The content in introductory science courses has often been criticized as “miles wide and inches deep”. In general chemistry, several revisions have focused on framing around a set of core or anchoring concepts, and we recently adapted the anchoring concepts content map (ACCM) of the American Chemical Society (ACS) to develop an anchoring concept-based curriculum for our general chemistry courses. In this article, we describe efforts to connect this curriculum with laboratory learning using Gowin’s theory of learning and the associated knowledge Vee heuristic. Within this framework, the laboratories themselves become events connecting the conceptual and methodological domains, …

On The Chlorobenzene-Ammonia Cluster Reaction: Entrance Channel Dynamics, 2cr2pi Spectroscopy, And Ion Imaging Of The Reaction Dynamics, Ronald Mutete, Damian Kokkin, Natan Fessahaye, Thomas R. Howell, Richard A. Loomis, Scott A. Reid

Chemistry Faculty Research and Publications

Prior studies of halobenzene–ammonia complexes have shown that the nature of the cationic intermediate (i.e., Wheland-type vs ion-radical) may play a key role in determining the reaction products. To probe this link, we report here the reaction dynamics of the chlorobenzene-ammonia 1:1 complex (PhCl···NH₃) using product ion imaging following two-color resonant two-photon ionization. A threshold value of 8.863 ± 0.008 eV was determined for the appearance of protonated aniline, which accompanies Cl atom loss and is the dominant product channel at energies near threshold. Scanning down to energies close to threshold, we find no evidence for a roaming …

Flash Communication: Visible-Light-Driven, Cobalt-Mediated Selective C–H Arylation Of 2,2′-Bipyridine, Xi Chen, Eric R. Allen, Mckenzie L. Stack, Zachary M. Garozzo, Dian Wang

Chemistry Faculty Research and Publications

Herein, we report a visible-light-driven, cobalt-mediated, highly selective C–H arylation method to afford aryl-2,2′-bipyridine, a widely used class of ancillary ligands in transition metal catalysis. This arylation reaction exhibits good-to-excellent C6 selectivity for a variety of aryl groups, allowing for isolation of the 6-isomer in its pure form. Mechanistic studies provided evidence for the generation of an aryl radical by the joint action of [Co(bpy)₃] species and visible light, enabling arylation under mild conditions. Compared to previous work, this method employs cost-effective reagents and provides one-step, direct access from 2,2′-bipyridine to a broad range of electronically varied 6-aryl-2,2′-bipyridine …

Magnetospectroscopic Studies Of A Series Of Fe(Ii) Scorpionate Complexes: Assessing The Relationship Between Halide Identity And Zero-Field Splitting, Daniel J. Santa Lucia, Laxmi Devkota, Sergey Lindeman, Andrew Ozarowski, J. Krzystek, Mykhaylo Ozerov, Samuel M. Greer, Daniel C. Cummins, Klaus H. Theopold, Mihail Atanasov, Joshua Telser, Adam T. Fiedler

Chemistry Faculty Research and Publications

Ferrous ions in four-coordinate environments are common in protein structures, synthetic catalysts, and molecular magnets. The 3d⁶ configuration of high-spin Fe(II) imparts an S = 2 ground state, whose analysis using conventional spectroscopic methods is often hindered by substantial zero-field splitting (ZFS). Herein, we provide detailed electronic-structure descriptions for [Fe^IIX(Tp^tBu,Me)] (1-X; X = F, Cl, Br, I), where (Tp^tBu,Me)− is hydrotris(3-tert-butyl-5-methyl-pyrazol-1-yl)borate. The three pyrazolyl N-donors of the “scorpionate” ligand facially coordinate to Fe(II), giving idealized C_3v symmetry with the halide occupying the axial position. Although originally reported …

Direct Photopatterning Of Quantum Dots Via Thiol-Yne Click Chemistry, Nicholas Langer, Ofer Kedem

Chemistry Faculty Research and Publications

Functional nanomaterials are revolutionizing electronic devices such as displays and photovoltaics, yet existing semiconductor manufacturing methods struggle to adapt to the unique properties of nanoparticles. In particular, quantum dots (QDs) display density-dependent properties such as tunable energy transfer, yet current preferred methods of producing QD patterns lack control over the density of QDs deposited in specific locations on a surface. Here, we present a photochemical method to generate QD patterns directly from solution onto a functionalized surface, which enables density control. The overall dose of light used in the pattern (visible or UV) determines the surface density of deposited QDs …

Quantum Simulation Of Molecular Dynamics Processes─A Benchmark Study Using A Classical Simulator And Present-Day Quantum Hardware, Tamila Kuanysheva, Brian K. Kendrick, Lukasz Cincio, Dmitri Babikov

Chemistry Faculty Research and Publications

We explore how the fundamental problems in quantum molecular dynamics can be modeled using classical simulators (emulators) of quantum computers and the actual quantum hardware available to us today. The list of problems we tackle includes propagation of a free wave packet, vibration of a harmonic oscillator, and tunneling through a barrier. Each of these problems starts with the initial wave packet setup. Although Qiskit provides a general method for initializing wave functions, in most cases it generates deep quantum circuits. While these circuits perform well on noiseless simulators, they suffer from excessive noise on quantum hardware. To overcome this …

Mixed Quantum/Classical Theory Approach To Rotationally Inelastic Molecular Collisions Implemented On A Quantum Computer, Jonathan Andrade-Plascencia, Tamila Kuanysheva, Dulat Bostan, Brian K. Kendrick, Dmitri Babikov

Chemistry Faculty Research and Publications

All elements of a quantum algorithm for calculations of rotationally inelastic molecule + atom scattering within the framework of a mixed quantum/classical theory are outlined. In this approach, the rotational motion of the molecule is described quantum mechanically using the time-dependent Schrödinger equation, while the scattering process of two collision partners is treated classically. The matrix of potential coupling is precomputed on a classical processor, whereas the quantum hardware is used to propagate the system of coupled equations for the rotational state-to-state transitions. All quantum circuits needed for practical implementation of the algorithm are presented. First, the quantum codes written …

Visible-Light-Driven Catalytic Dehalogenation Of Trichloroacetic Acid And Α-Halocarbonyl Compounds: Multiple Roles Of Copper, Abigail J. Thillman, Erin C. Kill, Alexander N. Erickson, Dian Wang

Chemistry Faculty Research and Publications

Herein, we report the reaction development and mechanistic studies of visible-light-driven Cu-catalyzed dechlorination of trichloroacetic acid for the highly selective formation of monochloroacetic acid. Visible-light-driven transition metal catalysis via an inner-sphere pathway features the dual roles of transition metal species in photoexcitation and substrate activation steps, and a detailed mechanistic understanding of their roles is crucial for the further development of light-driven catalysis. This catalytic method, which features environmentally desired ascorbic acid as the hydrogen atom source and water/ethanol as the solvent, can be further applied to the dehalogenation of a variety of halocarboxylic acids and amides. Spectroscopic, X-ray crystallographic, …

Scope And Mechanism Of The Ruthenium-Catalyzed Sp3 C–H Coupling Reaction Of 2-Alkylindoles With Enones For The Synthesis Of Carbazole Derivatives, Krishna Prasad Gnyawali, Mina Son, Donghun Hwang, Nuwan Asanka Pannilawithana, Mu-Hyun Baik, Chase S. Yi

Chemistry Faculty Research and Publications

The catalytic system consisting of a cationic Ru–H complex 1 and 3,4,5,6-tetrachloro-1,2-benzoquinone (L1) was found to be highly effective for the dehydrative sp³ C–H coupling reaction of 2-alkyl substituted indoles with enones to form 2,4-disubstituted carbazole products. The analogous coupling reaction of 2-alkylindoles with linear enones bearing the cyclic olefinic group afforded tetracyclic carbazole products. A normal deuterium kinetic isotope effect was measured from the coupling reaction of 1,2-dimethylindole versus 1-methyl-2-(methyl-d₃)indole with (E)-3-penten-2-one (k_H/k_D = 2.5). The Hammett plot was constructed from the reaction of para-substituted …

Stereoselective Synthesis Of (Z)-Acrylic Nitriles From The Ruthenium-Catalyzed Coupling Reaction Of Nitriles With Unsaturated Carbonyl Compounds Via C–C Bond Cleavage, Aldiyar Shakenov, Krishna Prasad Gnyawali, Chae S. Yi

Chemistry Faculty Research and Publications

Acrylic nitriles are a versatile class of synthetic precursors for a variety of pharmaceutically active compounds, as well as for nitrile polymers. We devised a stereoselective synthesis of (Z)-acrylic nitriles from the Ru-catalyzed coupling reaction of nitriles with unsaturated carbonyl compounds via C–C bond cleavage. Both carbon KIE and Hammett correlation data indicated that C–C bond cleavage is the rate-determining step for the coupling reaction. Several bioactive (Z)-acrylic nitriles were synthesized by using the catalytic coupling method.

Rate Coefficients For Rotational State-To-State Transitions In H2O + H2 Collisions As Predicted By Mixed Quantum–Classical Theory, Carolin Joy, Dulat Bostan, Bikramaditya Mandal, Dmitri Babikov

Chemistry Faculty Research and Publications

Aims. A new dataset of collisional rate coefficients for transitions between the rotational states of H₂O collided with H₂ background gas is developed. The goal is to expand over the other existing datasets in terms of the rotational states of water (200 states are included here) and the rotational states of hydrogen (10 states). All four symmetries of ortho- and para-water combined with ortho- and para-hydrogen are considered.

Methods. The mixed quantum–classical theory of inelastic scattering implemented in the code MQCT was employed. A detailed comparison with previous datasets was conducted to ensure that this …

The Novel Estrogen Receptor Beta Agonist Egx358 And Apoe Genotype Influence Memory, Vasomotor, And Anxiety Outcomes In An Alzheimer’S Mouse Model, M. R. Schwabe, A. W. Fleischer, R. K. Kuehn, S. Chaudhury, J. M. York, D. S. Sem, William A. Donaldson, M. J. Ladu, K. M. Frick

Chemistry Faculty Research and Publications

Introduction: Alzheimer’s disease (AD) prevalence and severity are associated with increased age, female sex, and apolipoprotein E4 (APOE4) genotype. Although estrogen therapy (ET) effectively reduces symptoms of menopause including hot flashes and anxiety, and can reduce dementia risk, it is associated with increased risks of breast and uterine cancer due to estrogen receptor alpha (ERα)-mediated increases in cancer cell proliferation. Because ERβ activation reduces this cell proliferation, selective targeting of ERβ may provide a safer method of improving memory and reducing hot flashes in menopausal women, including those with AD. APOE genotype influences the response to ET, although it is …

Observation Of Oxygenated Intermediates In Functional Mimics Of Aminophenol Dioxygenase, Laxmi Devkota, Jin Xiong, Anne A. Fischer, Kate Murphy, Praveen Kumar, Ellie L. Balensiefen, Sergey V. Lindeman, Cordina V. Popescu, Adam T. Fiedler

Chemistry Faculty Research and Publications

Aminophenol dioxygenases (APDO) are mononuclear nonheme iron enzymes that utilize dioxygen (O₂) to catalyze the conversion of o-aminophenols to 2-picolinic acid derivatives in metabolic pathways. This study describes the synthesis and O₂ reactivity of two synthetic models of substrate-bound APDO: [Fe^II(Tp^Me2)(^tBu2APH)] (1) and [Fe^II(Tp^Me2)(^tBuAPH)] (2), where Tp^Me2 = hydrotris(3,5-dimethylpyrazole-1-yl)borate, ^tBu2APH = 4,6-di-tert-butyl-2-aminophenolate, and ^tBuAPH₂ = 4-tert-butyl-2-aminophenolate. Both Fe(II) complexes behave as functional APDO mimics, as exposure to O₂ results in oxidative …

Rotational State-To-State Transition Rate Coefficients For H2O + H2O Collisions At Nonequilibrium Conditions, Bikramaditya Mandal, Michal Zoltowski, Martin Cordiner, François Lique, Dmitri Babikov

Chemistry Faculty Research and Publications

Aims. The goal is to develop a database of rate coefficients for rotational state-to-state transitions in H₂O + H₂O collisions that is suitable for the modeling of energy transfer in nonequilibrium conditions, in which the distribution of rotational states of H₂O deviates from local thermodynamic equilibrium.

Methods. A two-temperature model was employed that assumed that although there is no equilibrium between all possible degrees of freedom in the system, the translational and rotational degrees of freedom can be expected to achieve their own equilibria independently, and that they can be approximately characterized by Boltzmann …

Mixed Quantum/Classical Theory (Mqct) Approach To The Dynamics Of Molecule–Molecule Collisions In Complex Systems, Carolin Joy, Bikramaditya Mandal, Dulat Bostan, Marie-Lise Dubernet, Dmitri Babikov

Chemistry Faculty Research and Publications

We developed a general theoretical approach and a user-ready computer code that permit study of the dynamics of collisional energy transfer and ro-vibrational energy exchange in complex molecule–molecule collisions. The method is a mixture of classical and quantum mechanics. The internal ro-vibrational motion of collision partners is treated quantum mechanically using a time-dependent Schrödinger equation that captures many quantum phenomena including state quantization and zero-point energy, propensity and selection rules for state-to-state transitions, quantum symmetry and interference phenomena. A significant numerical speed up is obtained by describing the translational motion of collision partners classically, using the Ehrenfest mean-field trajectory approach. …

Preferential Crystallization Of (±)-Pinenyllithium·Tmeda, Alexander N. Erickson, Curtis Haltiwanger, Masoumeh Rahim, Charles M. Garner

Chemistry Faculty Research and Publications

(±)-Pinenyllithium·TMEDA or (tetra­methyl­ethylenedi­amine-κ²N,N′)(η³-6,6-di­methyl-2-methylenebi­cyclo­[3.1.1]hept­yl)lithium, [Li(C₁₀H₁₅)(C₆H₁₆N₂)], is readily pre­pared from β-pinene, butyl­lithium and TMEDA, and the racemic material pre­fer­entially crystallizes even from 96:4 (92% ee) mixtures of (−)- and (+)-β-pinene, respectively. The structure is monomeric, with the geminal-dimethyl bridge of the bicyclic structure shielding one face of the allyl system, restricting the lithium to the opposite face and preventing the Li–all­yl–Li aggregation observed with some other allyl­lithium systems. The symmetry of the allyl system, bond lengths, bond angles and out-of-plane deviations …

Characterizing Modulators Of Protease-Activated Receptors With A Calcium Mobilization Assay Using A Plate Reader, Jacob T. Derousse, Chris Dockendorff

Chemistry Faculty Research and Publications

Changes in calcium concentration in cells are rapidly monitored in a high-throughput fashion with the use of intracellular, fluorescent, calcium-binding dyes and imaging instruments that can measure fluorescent emissions from up to 1,536 wells simultaneously. However, these instruments are much more expensive and can be challenging to maintain relative to widely available plate readers that scan wells individually. Described here is an optimized plate reader assay for use with an endothelial cell line (EA.hy926) to measure the protease-activated receptor (PAR)-driven activation of G_αq signaling and subsequent calcium mobilization using the calcium-binding dye Fluo-4. This assay has been used to …

Basecol2023 Scientific Content, Dmitri Babikov

Chemistry Faculty Research and Publications

Context. The global context of making numerous data produced by researchers available requires collecting and organising the data, assigning meaningful metadata, and presenting the data in a meaningful and homogeneous way. The BASECOL database, which collects inelastic rate coefficients for application to the interstellar medium and to circumstellar and cometary atmospheres, meets those requirements.

Aims. We aim to present the scientific content of the BASECOL2023 edition.

Methods. While the previous versions relied on finding rate coefficients in the literature, the current version is populated with published results sent by the producers of data. The paper presents the …

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 Of Larger Molecules – Part 1: 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.

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 …

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 …

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 …