Physical Chemistry Commons^™

Single Fluorogens And Orientation-Localization Microscopy For Quantifying Chemical And Biomolecular Dynamics At The Nanoscale, Yiyang Chen, Yuanxin Qiu, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Many chemical systems look uniform only because ensemble measurements average over their most interesting molecules. Electron-transfer rates vary across electrode surfaces; lipid membranes contain nanodomains with distinct packing and fluidity; peptide aggregates exhibit local polymorphism; and biomolecular condensates contain transient networks of interactions that are blurred in ensemble images. A central challenge in chemical imaging is not simply to see smaller structures, but to measure chemical variables such as polarity, redox potential, and molecular confinement at the single-molecule level. In this Account, we describe how fluorogens, molecules whose brightness, blinking, spectral shifts, orientation, rotational mobility, and motion are directly shaped …

Enhanced Transdermal Immunization Via Solid-In-Oil Nanodispersions Incorporating Dendritic Cell-Targeting Peptide, Md Samiul Islam, Md. Shahin Ekka Sarker, Yoshirou Kawaguchi, Rie Wakabayashi, Noriho Kamiya, Muhammad Moniruzzaman, Masahiro Goto

Publications and Research

Transdermal immunization represents a promising needle-free alternative to conventional vaccination. However, efficient antigen delivery and robust immune activation remain major challenges. In this study, a solid-in-oil (S/O) nanodispersion system comprising a dendritic cell-targeting peptide (HR8), ovalbumin (OVA), and an adjuvant was developed for transdermal immunization. The HR8 peptide along with OVA was successfully incorporated into an S/O nanodispersion with an optimal hydrodynamic diameter of particles (< 200 nm) and exhibited stable physical properties for up to 90 days. In vitro and in vivo studies demonstrated enhanced antigen delivery with insignificant skin irritation in C57BL/6N mice. Moreover, in vivo transdermal immunization studies demonstrated that the addition of the HR8 peptide enhanced OVA-specific IgG responses (~1.5-fold). Notably, the HR8 peptide also promoted an approximately 2.5-fold increase in IgG2c levels, suggesting a shift toward a more T helper type 1-biased immune response, as reflected by an increased IgG2c/IgG1 ratio. Overall, these findings demonstrate that the incorporation of HR8 peptide into an S/O nanodispersion enables efficient transdermal antigen delivery and improved immunogenicity, highlighting its potential as a simple, non-invasive, and patient-friendly immunization strategy.

Laminarin-Loaded Solid-In-Oil Nanodispersion For Enhanced Non-Invasive Transdermal Immunization, Md. Shahin Ekka Sarker, Yoshirou Kawaguchi, Rie C. Wakabayashi, Noriho J. Kamiya, Muhammad Moniruzzaman, Masahiro Goto

Publications and Research

Simple and non-invasive transdermal vaccination is an attractive alternative to conventional injection-based immunization. However, the effectiveness of transdermal vaccines is often constrained by the stratum corneum barrier. Although the use of solid-in-oil (S/O) nanodispersion technology has successfully facilitated skin permeation to induce an immunological response, the antibody titers remain suboptimal. Herein, a dectin-1 selective ligand, laminarin, was used as an immunostimulatory adjuvant to enhance the immune response. S/O nanodispersions loaded with laminarin and ovalbumin (OVA) were systematically developed and characterized in terms of particle size, in vitro OVA release behavior, and skin permeation performance using excised mouse skin. In vivo …

Structure And Spectroscopy Of Free Base, Copper, And Zinc Tetrapentylporphyrin, Christopher J. Ziegler, Nneka Damola Ajayi, Victor N. Nemkyin, G Richard Geier Iii

University Research

Synthetic porphyrins have been crucial as models for heme units and other biological porphyrins, as well as components of advanced materials and catalysts. Much of the work on synthetic porphyrins has focused on the meso-substituted 5,10,15,20-tetraphenylporphyrin (TPP) or the pyrrole-substituted 2,3,7,8,12,13,17,18-octaethylporphyrin (OEP). In this report, we present a comprehensive spectroscopic, electrochemical, and computational study of free-base, zinc(II), and copper(II) 5,10,15,20-tetrapentylporphyrin (TPeP). TPeP can be prepared via a two-step, one-flask reaction of pyrrole and hexanal mediated by Montmorillonite K10, followed by oxidation with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) in yields of around 40%. Similar to TPP, the TPeP systems have the highest occupied molecular …

Structure And Spectroscopy Of Free Base, Copper, And Zinc Tetrapentylporphyrin, Christopher J. Ziegler, Nneka Damola Ajayi, Victor N. Nemkyin, G Richard Geier Iii

University Research

Synthetic porphyrins have been crucial as models for heme units and other biological porphyrins, as well as components of advanced materials and catalysts. Much of the work on synthetic porphyrins has focused on the meso-substituted 5,10,15,20-tetraphenylporphyrin (TPP) or the pyrrole-substituted 2,3,7,8,12,13,17,18-octaethylporphyrin (OEP). In this report, we present a comprehensive spectroscopic, electrochemical, and computational study of free-base, zinc(II), and copper(II) 5,10,15,20-tetrapentylporphyrin (TPeP). TPeP can be prepared via a two-step, one-flask reaction of pyrrole and hexanal mediated by Montmorillonite K10, followed by oxidation with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) in yields of around 40%. Similar to TPP, the TPeP systems have the highest occupied molecular …

Interview With Orca Winner Xiao Cheng Zeng; Unl Chemistry; Computational/Theoretical; Nebraska Ice & Gold Nanocages, Mark Griep, Xiao Cheng Zeng

UNL ORCA Interview Series

Xiao Cheng Zeng became a chemistry professor at the University of Nebraska-Lincoln in 1993, quickly rose through the ranks, and was in the department for 29 years. In 2022, he left to become head of the Department of Materials Science and Engineering at the City University of Hong Kong. Xiao was born in Beijing and earned a bachelor’s in physics at the University of Beijing in 1984. Next, he traveled 6800 miles east to Ohio State University in Columbus where he earned his doctorate in condensed matter physics. He followed that up with two postdoctoral experiences, first at the University …

Elucidating The Structure And Binding Nature Of Thianaphthene Dimers Using Gas-Phase Infrared Spectroscopy, Gaia Zucali, Vincent J. Esposito, Sandra Brünken, Piero Ferrari

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Crucial for many biological systems, in astrochemistry, and for fundamental chemistry in general, the conformations adopted by weakly bound complexes of polycyclic aromatic hydrocarbons (PAHs) have been the focus of debate for decades. Still, there are great challenges in forming such complexes in the laboratory, measuring accurate spectroscopic information sensitive to structure, and computing molecular properties for systems subtly bound by dispersive interactions. Here, we employ a combination of gas-phase infrared spectroscopy with extensive density functional theory (DFT) calculations to unambiguously determine the preferred conformation adopted by dimers of neutral thianaphthene, a PAH composed of one six- and one five-membered …

Non-Redundant Rovibrational Hamiltonians By Molien Generating Functions And Gröbner-Basis Reduction, Leandro Ajo

University Libraries Undergraduate Research Award

High-resolution molecular spectroscopy requires an effective Hamiltonian whose operator content is both complete, containing every term allowed by molecular symmetry and nonredundant, free of any algebraically dependent operators that would cause ill-conditioned parameter fits. Traditional derivations based on Van Vleck contact transformations satisfy neither criterion automatically. This paper develops a rigorous, algorithmic pipeline that guarantees both properties simultaneously. Starting from the permutation– inversion (PI) group GPI of a molecule (Longuet-Higgins, 1963), we apply Molien’s theorem (Molien, 1897) to the symplectic normal-coordinate representation to obtain the vibrational generating function Φvib(t); integrate over the Haar measure of SO(3) (Weyl, 1946) to obtain …

2026 Research Day Program, Lincoln Memorial University

Research Day

This program contains abstracts and presentation summaries from LMU's 2026 Annual Research Day conference.

Intramolecular Nonbonding Interactions And Geared Phenyl Twisting In Para-Disubstituted 1,4-Diphenylazines: Electron Correlation Effects On Molecular Conformations And Enantiomerization, Kaidi Yang, Harmeet Bhoday, Rainer Glaser

Chemistry Faculty Research & Creative Works

The results are reported of potential energy surface (PES) analyses of six symmetrical azines Y_p − Ph − RC=N − N=CR − Ph − Y_p, namely, the benzaldehyde azines 1H, 2H, and 8H with R = H and the acetophenone azines 1M, 2M, and 8M with R = Me. The Y substituents Cl (1), Br (2), and Me (8) were studied because sets of polymorphs I (C2-symmetry, azine twist τ ≈ 135 ± 10°, disrotatory phenyl twists ϕi ≠ 0°) and II (Ci-symmetry, τ = 180°, conrotatory ϕi ≠ 0°) were crystallized for these three azines. The …

Long-Range Fit: A Software Package For The Representation And Study Of Long-Range Molecular Interactions, Adrian L. Batista-Planas, Ernesto Quintas-Sánchez, Richard Dawes

Chemistry Faculty Research & Creative Works

Describing intermolecular forces is fundamental to modeling and predicting the behavior of molecular systems. In particular, long-range molecular interactions with electrostatic, induction, and dispersion as the main components play a critical role, especially for low-temperature and low-density regimes. Long-range interactions are often described through perturbation theory, representing the electronic charge distribution via a multipolar series of the moments and polarizability tensors corresponding to each molecule. However, while the theory is well established, obtaining the resulting analytical expressions (and their practical implementation) constitutes a highly complex and system-dependent task. To address this challenge, we developed long-range-fit (LRF), an interactive and user-friendly …

Parameter-Free Determination Of Au Nanorod Dimensions Using Depolarized Dls And Genetic Optimization, Nehal Nupnar, Geofrey Nyabere, Claire M.B. Bolding, Kiril A. Streletzky, Michael J.A. Hore

Physics Faculty Publications

Gold nanorods (AuNRs) have received considerable attention for their distinctive optical properties and well-defined, low-polydispersity dimensions. These characteristics position them as promising candidates for diverse applications in imaging, sensing, and treating diseases. However, accurate characterization of AuNRs in their native solution state, which is crucial to many applications, presents many challenges─especially if AuNRs are coated with surface layers (e.g., surfactants or grafted polymers). When applied to AuNRs with functionalized surfaces, common techniques such as transmission electron microscopy (TEM), small-angle scattering, and dynamic light scattering (DLS) can present limitations such as small sample sizes, the inability to detect light elements, a …

Efficient Organic Molecular Crystal Structure Prediction Using The Density Functional Tight-Binding Method, Maureen M. Kitheka, Yan Jing, Yan Yao, Puja Goyal

Faculty Publications – Chemistry

Over the years, computational crystal structure prediction (CSP) for organic molecules has thrived as an area of research, spanning various scientific disciplines and having significant applications in industries such as pharmaceuticals and agrochemicals. Within the field of batteries, redox-active organic materials (ROMs) such as quinones have received increased attention as promising electrode materials for rechargeable batteries. However, experimental determination of the crystal structure of intermediate species formed during the discharge/charge cycle can often be challenging. Incomplete X-ray diffraction patterns can also lead to difficulties in crystal structure determination for ROMs used in batteries. Use of a semiempirical electronic structure method …

Hot Ground State Cooling Following Ultrafast Photoisomerization: Time-Resolved Infrared Spectroscopy, James N. Bull, Mark H. Stockett, Pratip Chakraborty, Eleanor K. Ashworth, Anam Fatima, Vincent J. Esposito, Gregory M. Greetham, Partha Malakar, Stephen R. Meech

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The ultrafast photophysics of many isomerizing molecules involves subpicosecond formation of a twisted hot ground state, which transfers energy to the environment through vibrational relaxation (cooling) over several picoseconds. In time-resolved infrared (TR-IR) spectroscopy, hot ground state transients show frequency shifts and band reshapings, which cannot be described through kinetic models that assume static spectral functions. We report a simple anharmonic cascade framework, which uses a single adjustable parameter associated with scaling the probability of vibrational energy transfer to the environment, for describing hot ground state cooling (HGSC) in TR-IR spectroscopy. The model is demonstrated against measurements on the cyan …

Catalytic Synthesis Of Iron-Doped Graphitic Aerogels From Poly(Phloroglucinol-Terephthalaldehyde – Urethane) Precursors, Stephen Yaw Owusu, Rushi U. Soni, Chariklia Sotiriou-Leventis

Chemistry Faculty Research & Creative Works

We report a new class of graphitic carbon aerogel precursors based on iron oxide-doped poly(phloroglucinol-terephthalaldehyde–urethane) (T-POL/PU-FeOx) networks. The hybrid polymeric network incorporates a rigid aromatic triisocyanate, tris(4-isocyanatophenyl)methane, which reacts in situ with the hydroxyl groups of phloroglucinol to form a polyurethane-containing framework. Monolithic aerogels derived from this system undergo catalytic graphitization at significantly reduced temperatures (800–1500 °C) compared to conventional graphitization (2500–3300 °C). An oxidative ring fusion aromatization step (240 °C, air) prior to pyrolysis enhanced the degree of graphitization. The resulting graphitic aerogels were characterized by XRD, Raman spectroscopy, TGA, TEM, SEM, XPS, and N₂ sorption porosimetry. Compared to …

Experimental And Anharmonic Theoretical Spectroscopic Benchmarks Of Nitrogenated And Doubly-Nitrogenated Polycyclic Heterocycles, Selma Bejaoui, Brant E. Billinghurst, Christiaan Boersma, Vincent J. Esposito

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

In this study, we report the first high-resolution gas-phase infrared absorption spectra and anharmonic vibrational simulations for three nitrogenated aromatic molecules, namely indole (C₈H₇N), 1,5-diazabicyclo[4.3.0]non-5-ene (DBN; C₇H₁₂N₂), and 1,8- diazabicyclo[5.4.0]undec-7-ene (DBU; C₉H₁₆N₂) with excellent agreement between measurement and computation. Anharmonic cascade emission spectra (2–8 eV) of the three systems show that nitrogen substitution strongly modifies the emission spectra: indole reproduces the unidentified 3.3 μm emission in Titan’s atmosphere, while DBN and DBU exhibit redshifted aliphatic C–H stretches. In the 5–10 μm region, …

Collisional Excitation Of Hcn By Co To Refine The Modeling Of Cometary Comae, Francesca Tonolo, Ernesto Quintas-Sánchez, Adrian Batista-Planas, Richard Dawes, François Lique

Chemistry Faculty Research & Creative Works

We present the first dataset of collisional (de)-excitation rate coefficients of HCN induced by CO, one of the main perturbing gases in cometary atmospheres. The dataset spans the temperature range of 5–50 K. It includes both state-to-state rate coefficients involving the lowest ten and nine rotational levels of HCN and CO, respectively, and the so-called "thermalized" rate coefficients over the rotational population of CO at each kinetic temperature. The derivation of these coefficients exploited the good performance of the statistical adiabatic channel model (SACM) on top of an accurate interaction potential computed at the CCSD(T)-F12b/CBS level of theory. The reliability …

Revisiting The Spin–Lattice Relaxation Of Homonuclear In-Phase And Antiphase Nmr Magnetization, Lauren M. Kehoe, Zachary G. Mayes, Kelsey E. Brakensiek, Emma L. Ellis, Adam J. Alderfer, Lingyu Chi, Klaus Woelk

Chemistry Faculty Research & Creative Works

Hyperpolarization techniques such as dynamic nuclear polarization (DNP), chemically induced dynamic nuclear polarization (CIDNP), and parahydrogen-induced polarization (PHIP) enhance the sensitivity of NMR spectroscopy and MRI, but the associated antiphase magnetization patterns often relax faster than those of conventional in-phase signals. This study analyzes the spin–lattice relaxation matrix for single-quantum transitions in an isolated, weakly coupled two-spin AX system to identify eigenvectors and eigenvalues that govern the time evolution of in-phase and antiphase longitudinal magnetization. The analysis predicts that AX antiphase magnetization, such as that generated by PHIP hydrogenations in high magnetic field, can relax up to twice as fast …

Unveiling The Interplay Of Electronic And Phononic Excitations In Laser-Induced Oxygen Activation On Ru(0001), Xiangrui Wang, Jiamin Wang, Paul Spiering, Liping Liu, Jörg Meyer, Jerry L. Larue, Hongliang Xin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Understanding laser-induced dynamics on metal surfaces poses significant challenges due to the intricate interplay between electronic and phononic degrees of freedom, which evolve on distinct timescales. In this study, we introduce a machine learning-accelerated approach to molecular dynamics simulations that incorporates anisotropic electronic friction, providing deeper insights into these complex processes. Our framework extends the accessible time and length scales for nonadiabatic dynamics simulations, enabling a detailed investigation of the laser-induced activation of oxygen on the Ru(0001) surface. Statistical analysis reveals that strong electronic excitation dominates the first 800 fs after laser exposure. Beyond this timescale, energy deposited by electronic …

An Experiment In Electron Paramagnetic Resonance Spectroscopy For Undergraduate Labs In Physical Chemistry Or Physical Biochemistry, Evan A. Old, Matthew C. Rehak, Jefferson C. Thompson, Herbert J. Sipe Jr.

TeachEPR Submissions

We report a biochemically based EPR experiment for undergraduate laboratories that will serve as instruction for learning EPR sample preparation, spectral observation, and spectral analysis. There is a current lack of EPR instructional experiments that present complex spectra in which computational analysis may be required. The biochemical oxidation system of horse radish peroxidase (HRP) activated by H₂O₂ acts on 2,6-di-t-butyl-4-hydroxyanisole (DTBHA) to form phenoxyl radicals. This experiment produces moderately complex spectra of moderately long-lived radicals using relatively small amounts of readily available reactants. Spectrum analysis and simulation is accomplished using software freely available on-line. If desired, EPR …

High-Capacity, Reversible, And Energy-Efficient Water Vapor Sorption By Hierarchical Micro-To-Macroporous Carbon Aerogels From Polybenzoxazine And Polybenzodiazine, Vaibhav A. Edlabadkar, Rushi U. Soni, Stephen Y. Owusu, A. B.M.Shaheen Ud Doulah, Nicholas Leventis, Chariklia Sotiriou-Leventis

Chemistry Faculty Research & Creative Works

Quantitative, reversible water vapor sorption is in rising demand for applications ranging from home appliances to atmospheric water harvesting. However, most sorbents suffer from low water-uptake capacities, nonreusability, and especially high regeneration temperatures. This study addresses this challenge by introducing polybenzoxazine- (PBO) and polybenzodiazine-derived (PBDAZ) carbon aerogels as reversible high-capacity desiccants. PBO and PBDAZ aerogels were prepared from structurally related monomers via HCl-catalyzed ring opening polymerization. Both types of aerogels were first aromatized at 200–240 °C under air or O2 and then were carbonized at 800 °C under Ar. These as-prepared carbon aerogels were further etched at 1000 °C under …

Simulating Chemiluminescence Spectra Of Oh Radical Using Quantum Dynamical Simulations, Triet M. Cao

Research from the Berry Summer Thesis Institute, 2025

Chemiluminescence is a phenomenon of light emission that occurs when molecules transition from an excited state to the ground state. This phenomenon is widely utilized in applications ranging from quantifying product yields in chemical reactions to biological imaging and atmospheric chemistry studies. It has also been used in many crucial applications in the scarce conditions of heat and electricity, such as light sources for astronomy discovery or deep-sea diving. A notable example of such reactions is combustion, where highly reactive hydroxyl radicals (OH) are products. These radicals exhibit a chemiluminescence spectrum because of the interaction between their ground state and …

Efficient Decontamination Of Organophosphate-Based Pesticides And Nerve Agent Simulants Mediated By N-Containing Nucleophiles, Emmanuel Kingsley Darkwah, Puspa Aryal, Saidulu Todeti, Jared Kenik, Samuel Insall, V. Prakash Reddy, Chariklia Sotiriou-Leventis

Chemistry Faculty Research & Creative Works

There is a growing interest in developing safer and more effective decontaminating agents for organophosphate-based pesticides and nerve agents. In this study, we present an effective method for the nonaqueous decontamination of these compounds using small-molecule-based decontaminating agents under ambient conditions. Our approach utilizes aryl and heteroaryl carboxaldehyde hydrazones and hydrazides to effectively hydrolyze nerve agent simulants into their nontoxic degradation products. The effectiveness of this method was evaluated using a range of nerve agent simulants, including dimethyl 4-nitrophenyl phosphate (DMNP), dimethyl methyl phosphonate (DMMP), and triphenyl phosphate (TPhP). In the presence of the heteroaryl hydrazone, the rate of hydrolysis …

Dynamic Mutational Profiling Of Binding Interactions And Allosteric Networks In Conformational Ensembles Of The Sars-Cov-2 Spike Protein Complexes With Classes Of Antibodies Targeting Cryptic Binding Sites: Confluence Of Binding And Allostery Determines Molecular Mechanisms And Hotspots Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The ongoing evolution of SARS-CoV-2 variants has underscored the need to understand not only the structural basis of antibody recognition but also the dynamic and allosteric mechanisms that could underlie complexity of broad and escape-resistant neutralization. In this study, we employed a multi-scale approach integrating structural analysis, hierarchical molecular simulations, mutational scanning and network-based allosteric modeling to dissect how Class 4 antibodies (represented by S2X35, 25F9, and SA55) and Class 5 antibodies (represented by S2H97, WRAIR-2063 and WRAIR-2134) can modulate conformational behavior, binding energetics, allosteric interactions and immune escape patterns of the SARS-CoV-2 spike protein. Using hierarchical simulations of the …

Assembly Of Non-Close-Packed Poly(N-Isopropylacrylamide) Microgels On Metal Halide Perovskite Films, Amal Alruwaili, Osama M. Alkhudhari, Ran Wang, Zhenyu Jia, Jennifer M. Saunders, Eugenio Picheo, Daniel T.W. Toolan, L. Andrew Lyon, Brian R. Saunders

Engineering Faculty Articles and Research

Hypothesis

Experiments

A Promising Statistical Approach For Studying The Collisional Excitation Induced By Co: Application To The Cs-Co System, Amélie Godard Palluet, Richard Dawes, Ernesto Quintas-Sánchez, Adrian Batista-Planas, François Lique

Chemistry Faculty Research & Creative Works

The calculations of rate coefficients for the interpretation of molecular spectra are a recognized computationally expensive task. This is particularly true for media like comets, where the dominant species (CO, CO₂, and H₂O) have relatively high masses. Currently, no clear methodology exists to treat the collisional excitation of heavy species at low temperatures, thus limiting the number of collisional studies on such species. We present here a promising statistical approach to determine collisional rate coefficients of heavy systems as an alternative to fully quantum calculations when heavy projectiles such as CO are considered. This is illustrated …

Nuclear Magnetic Resonance Dynamics Of Pyrazole-Litfsi Eutectic Solvents As Promising Electrolytes, Emilia Pelegano-Titmuss, Giselle De Araujo Lima E Souza, Muhammad Zulqarnain, Ramez Elgammal, Thomas Zawodzinski, Steven Greenbaum

Undergraduate Research

Deep Eutectic Solvents (DESs) have emerged as promising candidates to replace conventional organic solvents in various technological applications due to their low vapor pressure, non-flammability, and ease of preparation at low costs. In particular, Type IV DESs, which are composed of metal salts and hydrogen bond donors, are possible replacements for lithium-ion battery electrolytes due to their potential of having high lithium transference numbers. In this study, we investigated solvents of Pyrazole and LiTFSI at varying molar ratios using Fast Field Cycling (FFC) NMR Relaxometry. Notably, the 1:2 LiTFSI: Pyrazole sample shows distinct behavior, exhibiting enhanced relaxation rates for ^{1 …}

A Catalytic Pathway For The Formation Of Cyanobenzene In Nitrogen-Rich Environments And The Spectroscopy Of The Reactive Intermediates, Vincent J. Esposito, Silvia Alessandrini, David Dubois, Ryan Fortenberry

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The catalytic reaction of isocyanobenzene (C₆H₅NC) with NCN⁻ produces cyanobenzene (C₆H₅NC) through various highly stable reactive intermediate species. Nitrogen-rich environments such as Titan’s atmosphere serve as favorable locations to study reaction pathways involving nitrogenated species contributing to organic growth. Formation pathways of cyanobenzene have been characterized, but none with the contribution of anions or phenyl groups. In regions with a high abundance of nitrogen anions, such as Titan’s atmosphere, reactions with species such as NCN⁻ may play a role in the formation of cyanobenzene. Highly accurate computational methods are used …

A Study Of Ultrafast, Intense-Field Photodynamics In Carbon Dioxide, Carbon Disulfide, And Select Substituted Benzenes, Joshua Edwin Beck

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The study of the photodynamics of molecules in ultrashort pulses of intense radiation continues to be of interest. Electric field strengths in such pulses can approach or exceed the typical electric field strengths binding the electrons to the nuclear framework (ke/a²₀ ≈ 5 × 10⁹ V/cm). The resulting excitation, ionization, and dissociation of molecular targets is of interest in many areas including attosecond science, femtochemistry, atmospheric science, high harmonic generation, and many other fields.

This dissertation investigates the photoionization and photofragmentation behavior of carbon dioxide, carbon disulfide, and the substituted benzenes nitrobenzene, aniline, as …

Predicting PkA Of Flexible Polybasic Tetra-Aza Macrocycles, Tatum K. Harvey, Kristof Pota, Magy Mekhail, David M. Freire, Donatus A. Agbaglo, Benjamin G. Janesko, Kayla N. Green

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We present physics-based pK_a predictions for a library of tetra-aza macrocycles. These flexible, polybasic molecules exhibit highly charged states and substantial prototropic tautomerism, presenting a challenge for pK_a prediction. Our computational protocol combines CREST/xTB conformational sampling, density functional theory (DFT) refinement in continuum solvent, and a linear empirical correction (LEC). This approach predicts known tetra-aza macrocycle pK_a to within a root-mean-square deviation 1.2 log units. This approach also provides reasonable predictions for the most stable protomers at different pH. We use this protocol to predict pK_a values for four novel, synthetically achievable, …