Physical Sciences and Mathematics Commons^™

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 …

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 …

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 …

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 …

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 …

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, …

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 …

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 …

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 …

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 …

Mixed Quantum/Classical Theory For Collisional Quenching Of Pahs In The Interstellar Media, Bikramaditya Mandal, Carolin Joy, Alexander Semenov, Dmitri Babikov

Chemistry Faculty Research and Publications

A computationally affordable methodology is developed to predict cross sections and rate coefficients for collisional quenching and excitation of large molecules in space, such as PAHs. Mixed quantum/classical theory of inelastic scattering (MQCT) is applied, in which quantum state-to-state transitions between the internal states of the molecule are described using a time-dependent Schrodinger equation, while the scattering of collision partners is described classically using mean-field trajectories. To boost the numerical performance even further, a decoupling scheme for the equations of motion and a Monte Carlo sampling of the initial conditions are implemented. The method is applied to compute cross sections …

Reversible Dioxygen Binding To Co(Ii) Complexes With Noninnocent Ligands, Praveen Kumar, Laxmi Devkota, Maximilian C. Casey, Anne A. Fischer, Sergey V. Lindeman, Adam T. Fiedler

Chemistry Faculty Research and Publications

A series of mononuclear Co(II) complexes with noninnocent (redox-active) ligands are prepared that exhibit metal–ligand cooperativity during the reversible binding of O₂. The complexes have the general formula, [Co^II(L^S,N)(Tp^R2)] (R = Me, Ph), where L^S,N is a bidentate o-aminothiophenolate and Tp^R2 is a hydrotris(pyrazol-1-yl)borate scorpionate with R-substituents at the 3- and 5-positions. Exposure to O₂ at room temperature results in one-electron oxidation and deprotonation of L^S,N. The oxidized derivatives possess substantial “singlet diradical” character arising from antiferromagnetic coupling between an iminothiosemiquinonate (ITSQ^•–) …

Effect Of Ligands And Their Removal On The Au Nanoparticle-Catalyzed Reduction Of 4-Nitrophenol, Nicholas Langer, Ofer Kedem

Chemistry Faculty Research and Publications

The catalytic activity of gold nanoparticles (Au NPs) is strongly affected by the organic ligands coating them, which afford colloidal stability and are most commonly attached during the synthesis of the Au NPs. However, different ligands also produce Au NPs of different sizes and morphologies, complicating the study of the impact of the ligands themselves. Alternatively, postsynthetic ligand exchange risks incomplete exchanges and a mixed ligand shell, as well as colloidal instability. Here, Au NPs are immobilized on glass supports to afford truly ligand-free, solvent-stable Au nanoislands (NIs). The catalytic activity of Au NIs, uncoated and coated with a variety …

Enantioselective Synthesis Of Enantioisotopomers With Quantitative Chiral Analysis By Chiral Tag Rotational Spectroscopy, Mitchell D. Mills, Reilly E. Sonstrom, Zoua Pa Vang, Justin L. Neill, Haley N. Scolati, Channing T. West, Brooks H. Pate, Joseph R. Clark

Chemistry Faculty Research and Publications

Fundamental to the synthesis of enantioenriched chiral molecules is the ability to assign absolute configuration at each stereogenic center, and to determine the enantiomeric excess for each compound. While determination of enantiomeric excess and absolute configuration is often considered routine in many facets of asymmetric synthesis, the same determinations for enantioisotopomers remains a formidable challenge. Here, we report the first highly enantioselective metal-catalyzed synthesis of enantioisotopomers that are chiral by virtue of deuterium substitution along with the first general spectroscopic technique for assignment of the absolute configuration and quantitative determination of the enantiomeric excess of isotopically chiral molecules. Chiral tag …

Uv- And Visible-Light Photopatterning Of Molecular Gradients Using The Thiol–Yne Click Reaction, Mark Mitmoen, Ofer Kedem

Chemistry Faculty Research and Publications

The rational design of chemical coatings is used to control surface interactions with small molecules, biomolecules, nanoparticles, and liquids as well as optical and other properties. Specifically, micropatterned surface coatings have been used in a wide variety of applications, including biosensing, cell growth assays, multiplexed biomolecule interaction arrays, and responsive surfaces. Here, a maskless photopatterning process is studied, using the photocatalyzed thiol–yne “click” reaction to create both binary and gradient patterns on thiolated surfaces. Nearly defect-free patterns are produced by first coating glass surfaces with mercaptopropylsilatrane, a silanizing agent that forms smoother self-assembled monolayers than the commonly used 3-mercaptopropyltrimethoxysilane. Photopatterning …

Highly Regioselective Copper-Catalyzed Transfer Hydrodeuteration Of Unactivated Terminal Alkenes, Albert Reyes, Emanuel Rivera Torres, Zoua Pa Vang, Joseph R. Clark

Chemistry Faculty Research and Publications

Catalytic transfer hydrodeuteration of unactivated alkenes is challenging because of the requirement that similar hydrogen and deuterium undergo selective insertion across a π-bond. We now report a highly regioselective catalytic transfer hydrodeuteration of unactivated terminal alkenes across a variety of heteroatom- or heterocycle-containing substrates. The base-metal-catalyzed reaction is also demonstrated on two complex natural products. Reaction studies indicate modular conditions that can also be extended to perform either an alkene transfer hydrogenation or transfer deuteration.

Molecular Dynamics On Quantum Annealers, Igor Gaidai, Dmitri Babikov, Alexander Teplukhin, Brian K. Kendrick, Susan M. Mniszewski, Yu Zhang, Sergei Tretiak, Pavel A. Dub

Chemistry Faculty Research and Publications

In this work we demonstrate a practical prospect of using quantum annealers for simulation of molecular dynamics. A methodology developed for this goal, dubbed Quantum Differential Equations (QDE), is applied to propagate classical trajectories for the vibration of the hydrogen molecule in several regimes: nearly harmonic, highly anharmonic, and dissociative motion. The results obtained using the D-Wave 2000Q quantum annealer are all consistent and quickly converge to the analytical reference solution. Several alternative strategies for such calculations are explored and it was found that the most accurate results and the best efficiency are obtained by combining the quantum annealer with …

Triple Oxygen Isotope Constraints On Atmospheric O2 And Biological Productivity During The Mid-Proterozoic, Peng Liu, Jingjin Liu, Aoshaung Ji, Christopher T. Reinhard, Noah J. Planavsky, Dmitri Babikov, Raymond G. Najjar, James F. Kasting

Chemistry Faculty Research and Publications

Reconstructing the history of biological productivity and atmospheric oxygen partial pressure (pO₂) is a fundamental goal of geobiology. Recently, the mass-independent fractionation of oxygen isotopes (O-MIF) has been used as a tool for estimating pO₂ and productivity during the Proterozoic. O-MIF, reported as Δ′¹⁷O, is produced during the formation of ozone and destroyed by isotopic exchange with water by biological and chemical processes. Atmospheric O-MIF can be preserved in the geologic record when pyrite (FeS₂) is oxidized during weathering, and the sulfur is redeposited as sulfate. Here, sedimentary sulfates from …

2d Covalent Organic Frameworks With An Incorporated Manganese Complex For Light Driven Carbon Dioxide Reduction, Denan Wang, Daniel Streater, Yun Peng, Jier Huang

Chemistry Faculty Research and Publications

Covalent organic frameworks (COFs) have emerged as a novel class of crystalline porous photocatalytic materials due to their unique properties such as large surface area, tunable porosity, and rigid structure. In this work, we report the direct incorporation of a manganese CO₂ molecular catalyst (MC) into COFs (Mn−TTA-COF) and the evaluation of its capability as photocatalyst for visible light driven CO₂ reduction to form CO. We found that the photocatalytic activity of Mn−TTA-COF is quite low, which mainly results from the elimination of the CO ligand in the Mn MC upon light illumination, rendering its short duration in …

Spectrumsdt: A Program For Parallel Calculation Of Coupled Rotational-Vibrational Energies And Lifetimes Of Bound States And Scattering Resonances In Triatomic Systems, Igor Gayday, Alexander Teplukhin, Jonathan Moussa, Dmitri Babikov

Chemistry Faculty Research and Publications

We present SpectrumSDT – a program for calculations of energies and lifetimes of bound rotational-vibrational states below and scattering resonances above the dissociation threshold on a global potential energy surface of a triatomic system, which may include stable molecules, weekly-bound van-der-Waals complexes, and unbound atom + diatom scattering systems. Large-amplitude vibrational motion is treated explicitly using hyper-spherical coordinates. Three options for the rotational-vibrational interaction are supported: uncoupled (symmetric top rotor), partially coupled (to include interaction between several nearest states only) and full-coupled (vibrating asymmetric-top rotor). In addition to energies and lifetimes, SpectrumSDT is able to integrate ro-vibrational wave functions over …

Dissecting Monomer-Dimer Equilibrium Of An Rnase P Protein Provides Insight Into The Synergistic Flexibility Of 5’ Leader Pre-Trna Recognition, Danyun Zeng, Ainur Abzhanova, Benjamin P. Brown, Nicholas J. Reiter

Chemistry Faculty Research and Publications

Ribonuclease P (RNase P) is a universal RNA-protein endonuclease that catalyzes 5’ precursor-tRNA (ptRNA) processing. The RNase P RNA plays the catalytic role in ptRNA processing; however, the RNase P protein is required for catalysis in vivo and interacts with the 5’ leader sequence. A single P RNA and a P protein form the functional RNase P holoenzyme yet dimeric forms of bacterial RNase P can interact with non-tRNA substrates and influence bacterial cell growth. Oligomeric forms of the P protein can also occur in vitro and occlude the 5’ leader ptRNA binding interface, presenting a challenge in accurately defining …

Electronic Structures And Spectroscopic Signatures Of Diiron Intermediates Generated By O2 Activation Of Nonheme Iron(Ii)–Thiolate Complexes, Danushka M. Ekanayake, Dao Pham, Andrew L. Probst, Joshua R. Miller, Cordina V. Popescu, Adam T. Fiedler

Chemistry Faculty Research and Publications

The activation of O₂ at thiolate–ligated iron(II) sites is essential to the function of numerous metalloenzymes and synthetic catalysts. Iron–thiolate bonds in the active sites of nonheme iron enzymes arise from either coordination of an endogenous cysteinate residue or binding of a deprotonated thiol-containing substrate. Examples of the latter include sulfoxide synthases, such as EgtB and OvoA, that utilize O₂ to catalyze tandem S–C bond formation and S-oxygenation steps in thiohistidine biosyntheses. We recently reported the preparation of two mononuclear nonheme iron–thiolate complexes (1 and 2) that serve as structural active-site models of substrate-bound EgtB …

Covalent Immobilization Of Molecular Complexes On Metal-Organic Frameworks Towards Robust And Highly Efficient Heterogeneous Water Oxidation Catalysts, Xiangming Liang, Sizhou Yang, Junyi Yang, Wanjun Sun, Xiangyang Li, Baochun Ma, Jier Huang, Jiangwei Zhang, Lele Duan, Yong Ding

Chemistry Faculty Research and Publications

The major challenges to practical implementation of efficient noble metal based molecular water oxidation catalysts are their stability and recycle ability. Herein, noble metal Ru based molecular water oxidation catalysts were covalently anchored in MOFs through “amide bond” as bridges, which leads to the formation of high-efficiency and robust heterogeneous catalysts for water oxidation reaction. We show that the efficiency for Ce^IV-driven water oxidation was significantly enhanced by 120 times when the Ru molecules were immobilized on the frameworks of MIL-101(Cr). The relationship between recycle stability and the structure of the Ru complexes covalently anchored in MOFs was …

Catalytic Transfer Deuteration And Hydrodeuteration: Emerging Techniques To Selectively Transform Alkenes And Alkynes To Deuterated Alkanes, Zoua Pa Vang, Samuel J. Hintzsche, Joseph R. Clark

Chemistry Faculty Research and Publications

Increasing demand for deuterium-labeled organic molecules has spurred a renewed interest in selective methods for deuterium installation. Catalytic transfer deuteration and transfer hydrodeuteration are emerging as powerful techniques for the selective incorporation of deuterium into small molecules. These reactions not only obviate the use of D₂ gas and pressurized reaction setups but provide new opportunities for selectively installing deuterium into small molecules. Commercial or readily synthesized deuterium donors are typically employed as easy-to-handle reagents for transfer deuteration and hydrodeuteration reactions. In this minireview, recent advances in the catalytic transfer deuteration and hydrodeuteration of alkenes and alkynes for the selective …

In Situ Activated Co3–XNiXO4 As A Highly Active And Ultrastable Electrocatalyst For Hydrogen Generation, Kailu Guo, Yantao Wang, Junfeng Huang, Min Lu, Hua Li, Yong Peng, Pinxian Xi, Haoli Zhang, Jier Huang, Siyu Lu, Cailing Xu

Chemistry Faculty Research and Publications

The spinel Co₃O₄ has emerged as a promising alternative to noble-metal-based electrocatalysts for electrochemical water electrolysis in alkaline medium. However, pure Co₃O₄, despite having high activity in anodic water oxidation, remains inactive toward the hydrogen evolution reaction (HER). Here, a Ni-doped Co₃O₄(Co_3–xNi_xO₄) prepared by a simple method exhibits favorable HER activity and stability (>300 h, whether in 1 M KOH or the realistic 30 wt % KOH solution) after in situ electrochemical activation, outperforming almost all of the oxide-based electrocatalysts. More …

Efficient Method For An Approximate Treatment Of The Coriolis Effect In Calculations Of Quantum Dynamics And Spectroscopy, With Application To Scattering Resonances In Ozone, Igor Gayday, Dmitri Babikov

Chemistry Faculty Research and Publications

A numerical approach is developed to capture the effect of rotation–vibration coupling in a practically affordable way. In this approach only a limited number of adjacent rotational components are considered to be coupled, while the couplings to other rotational components are neglected. This partially coupled (PC) approach permits to reduce the size of Hamiltonian matrix significantly, which enables the calculations of ro-vibrational states above dissociation threshold (scattering resonances) for large values of total angular momentum. This method is employed here to reveal the role of the Coriolis effect in the ozone formation reaction at room temperature, dominated by large values …

Four Isotope-Labeled Recombination Pathways Of Ozone Formation, Dmitri Babikov, Elizaveta Grushnikova, Igor Gayday, Alexander Teplukhin

Chemistry Faculty Research and Publications

A theoretical approach is developed for the description of all possible recombination pathways in the ozone forming reaction, without neglecting any process a priori, and without decoupling the individual pathways one from another. These pathways become physically distinct when a rare isotope of oxygen is introduced, such as ¹⁸O, which represents a sensitive probe of the ozone forming reaction. Each isotopologue of O₃ contains two types of physically distinct entrance channels and two types of physically distinct product wells, creating four recombination pathways. Calculations are done for singly and doubly substituted isotopologues of ozone, eight rate coefficients …

Unraveling A Trifecta Of Weak Non-Covalent Interactions: The Dissociation Energy Of The Anisole-Ammonia 1:1 Complex, John L. Loman, James T. Makuvaza, Damian L. Kokkin, Scott A. Reid

Chemistry Faculty Research and Publications

The anisole-ammonia 1:1 complex is a challenge for both experiment and theory. Early studies supported a non-planar structure, involving a trifecta of weak non-covalent interactions: N-H/O, N-H/π, and C-H/N. The calculated structure and binding energy of the complex proved remarkably sensitive to the level of theory employed. Here, we report the first experimental measurement of the ground state dissociation energy of the complex, and derive an excited (S₁) state dissociation energy that is in excellent agreement with the cutoff observed in the experimental excitation spectrum. Results are compared with previous predictions and new calculations based on benchmarked Density …

The Electronic Properties Of Ni(Pnn) Pincer Complexes Modulate Activity In Catalytic Hydrodehalogenation Reactions, Denan Wang, James R. Gardinier

Chemistry Faculty Research and Publications

Three chloronickel(II) complexes of PNN‐ pincer ligands with pyrazolyl and diphenylphosphino donors appended to different arms of diarylamido anchors were prepared and fully characterized. The three derivatives (1‐OMe, 1‐Me, 1‐CF₃) differ only by the identity of the para‐aryl substituent on the pyrazolyl arm with 1‐OMe being 310 mV easier to oxidize than 1‐CF₃. All three complexes are competent catalysts for hydrodehalogenation reactions of 1‐bromooctane and a variety of aryl halides in dimethylacetamide using NaBH₄ as both base and hydride source. Comparative studies using diverse substrates showed that catalytic activity correlates with electron donor properties; …