Biological and Chemical Physics Commons^™

Jwst: Deuterated Pahs, Pah-Nitriles, And Pah 4 Overtone And Combination Bands I: Program Description And First Look, C. Boersma, L. J. Allamandola, Vincent J. Esposito, A. Maragkoudakis, J. D. Bregman, P. Temi, T. J. Lee, R. C. Fortenberry, E. Peeters

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

A first look is taken at the NIRSpec 1–5 μm observations from James Webb Space Telescope program 1591 that targets seven objects along the low-mass stellar life cycle with polycyclic aromatic hydrocarbon (PAH) emission. Spectra extracted from a 1'.'5 radius circular aperture are explored, showing a wealth of features, including the 3 μm PAH complex, the PAH continuum, and atomic and molecular emission lines from H i, He, H₂, and other species. CO₂- and H₂O-ice absorption and CO emission is also seen. Focusing on the bright-PDR position in M17, the PAH CH stretch falls …

Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost

All Dissertations

In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …

Contributions Of Tunneling In 8Π-6Π Electrocyclic Cascade Reactions Of Bicyclo[4.2.0]Octa-2,4-Diene Moieties, Ishika Jain, Claire Castro, William L. Karney

Featured Student Work

Six-electron electrocyclic reactions usually require relatively high temperatures; however recent research has shown that such reactions can occur at significantly lower temperatures in biosynthetic and biomimetic pathways. Pathways resulting in bicyclo[4.2.0]octa-2,4-diene moieties arise from thermally allowed 8π-6π electrocyclization cascade reactions of 1,3,5,7-octatetraenes, as in the biosynthesis of endiandric acids, elysiapyrones, and numerous other natural products. We report multidimensional tunneling calculations to explore the possible contribution of heavy-atom tunneling (e.g. by carbon) to biosynthetic pathways and biomimetic syntheses, and thus to provide a more complete picture of biochemical kinetics. M06-2X/cc-pVDZ calculations on the 8π-6π cascade cyclizations of methylated octatetraene model systems …

Anharmonic Ir Absorption Spectra Of The Prototypical Interstellar Pahs Phenanthrene, Pyrene, And Pentacene In Their Neutral And Cation States, Vincent J. Esposito, Louis J. Allamandola, Christiaan Boersma, Jesse D. Bregman, Ryan C. Fortenberry, Alexandros Maragkoudakis, Pasquale Temi

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Combination band and overtone transitions of polycyclic aromatic hydrocarbon (PAH) cations in the 2000–2900 cm^-1 (5-3.5 µm) region are implicated as carriers of the ‘quasi-continuum’ observed in the near-infrared (IR) emission spectra of many astronomical objects. In neutral PAHs, the strongest absorption features are concentrated in the 700–900 cm^-1 (14–11 µm) range, which are associated with CH out-of-plane bending motions. Upon ionization, this shifts to the 1000–1600 cm^-1 (10–6 µm) range, where bands are associated with C=C stretches and CH in-plane bends. Anharmonicity is required to accurately characterize the IR absorption spectrum of PAHs, indicated herein by …

Anharmonicity And Deuteration In The Ir Absorption And Emission Spectra Of Phenylacetylene, Vincent J. Esposito, Pierro Ferrari, Wybren Jan Buma, Christiaan Boersma, Cameron J. Mackie, Alessandra Candian, Ryan C. Fortenberry, Alexander G. G. M. Tielens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Anharmonic cascade emission simulations, herein evinced by full reproduction and deep insights into recent emission spectroscopy experiments of phenylacetylene, are integral to the future successful analysis of JWST observational spectra. Experimental infrared absorption experiments conducted in this study reveal a complex spectrum dominated by quantum effects that are uncovered by anharmonic computational analysis. From this work, it becomes clear that phenylacetylene exhibits strong resonance coupling between fundamental and two-quanta combination modes as well as giving indication for coupling with higher-order, three-quanta combination bands. This study benchmarks the development of advanced computational methods that will be extended to larger systems of …

The Influence Of Allostery Governing The Changes In Protein Dynamics Upon Substitution, Joseph Hess

All Dissertations

The focus of this research is to investigate the effects of allostery on the function/activity of an enzyme, human immunodeficiency virus type 1 (HIV-1) protease, using well-defined statistical analyses of the dynamic changes of the protein and variants with unique single point substitutions ¹. The experimental data¹ evaluated here only characterized HIV-1 protease with one of its potential target substrates. Probing the dynamic interactions of the residues of an enzyme and its variants can offer insight of the developmental importance for allosteric signaling and their connection to a protein’s function. The realignment of the secondary structure elements can …

Vibrational, Rotational And Electronic Spectroscopy For Possible Interstellar Detection Of Alnh2 And Halnh, Tarek Trabelsi, Vincent J. Esposito, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We obtained accurate vibrational frequencies, rotational constants, and vertical transition energy for AlNH₂(X¹A₁) and HAlNH(X¹A′) isomers using ab initio calculations at various levels of theory. These two isomers are potential candidates for astronomical observation. AlNH₂ and HAlNH are thermodynamically stable, with Al-NH₂ and HAl-NH bond dissociation energies predicted to be 4.39 and 3.60 eV, respectively. The two isomers are characterized by sizable dipole moments of 1.211 and 3.64 D, respectively. The anharmonic frequencies and spectroscopic constants reported for the two isomers should facilitate their experimental differentiation. In addition, we evaluated …

Photoisomerizable Membrane Active Peptides, Cristina Ventura

Seton Hall University Dissertations and Theses (ETDs)

Membrane active peptides (MAPs) bind and partition into the cell membrane thus causing permeabilization. Many α-helical membrane active peptides contain central proline residues that distinguish the hydrophobic and hydrophilic faces of the helix. The proline induces a bend that produces a helix-hinge-helix motif. Mutation of these proline residues has a significant effect on the activity of the MAP. Azobenzene is a photoisomerizable molecule that switches from its trans to cis isomer upon excitation with ultraviolet (UV) light and from its cis to trans isomer upon excitation with visible light (VL). In this work it is hypothesized that the hinge function …

Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel

Honors Scholar Theses

Among structural biology techniques, Nuclear Magnetic Resonance (NMR) provides a holistic view of structure that is close to protein structure in situ. Namely, NMR imaging allows for the solution state of the protein to be observed, derived from Nuclear Overhauser Effect restraints (NOEs). NOEs are a distance range in which hydrogen pairs are observed to stay within range of, and therefore experimental data which computational models can be compared against. To that end, we investigated the effects of adding the NOE restraints as distance restraints in Molecular Dynamics (MD) simulations on the 24 residue HP24stab derived villin headpiece subdomain to …

Modeling Excited State Processes In Molecular Aggregates By Constructing An Adaptive Basis For The Hierarchy Of Pure States, Leonel Varvelo

Chemistry Theses and Dissertations

Simulating excitation energy transfer (EET) in molecular materials is of crucial importance for the development of and understanding of materials such as organic photovoltaics and photosynthetic systems and further development of novel materials. The Hierarchy of Pure States (HOPS) is an exact framework for the time evolution of an open quantum system in which a hierarchy of stochastic wave functions are propagated in time. The adaptive HOPS (adHOPS) method achieves size-invariant scaling with the number of simulated molecules for sufficiently large aggregates by using an adaptive basis that moves with the excitation through the material. To demonstrate the power of …

First Review Of Equilibrium Landscape Of Ingress/Egress Channels And Gating Residues Of The Cytochrome P450 3a4, Edward Ackad Ph.D, Maria Kontoyianni

SIUE Faculty Research, Scholarship, and Creative Activity

The review document and changes made to "Equilibrium Landscape of Ingress/Egress Channels and Gating Residues of the Cytochrome P450 3A4".

Photoionization Energetics And Dissociation Pathways Of Hydroperoxyethyl Formate Produced In The Reaction Of Ch3Choo + Formic Acid, Vincent J. Esposito, Trent A. Mchenry, Marsha I. Lester

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The bimolecular reaction of Criegee intermediates, zwitterionic carbonyl oxide species produced in alkene ozonolysis, with organic acids leads to formation of functional hydroperoxides implicated in the generation of atmospheric aerosols. This theoretical study using high-level explicitly correlated coupled-cluster theory examines the low energy conformers of hydroperoxyethyl formate [HOOCH(CH₃)OCHO, HPEF] formed in the bimolecular reaction of CH₃CHOO, a simple alkyl-substituted Criegee intermediate, with formic acid, and the detection of HPEF via photoionization. The vertical and adiabatic ionization energies of HPEF are computed, along with the pathways for dissociative ionization that produce HO₂ or OCHO fragments with …

Spectroscopic Properties Of The Astrochemical Molecules [Al, O, Si]X (X = 0, +1), Jacqueline M. Friskey, Vincent J. Esposito, Tarek Trabelsi, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Aluminum and silicon are present in large quantities in the interstellar medium, making the triatomic species consisting of both elements intriguing with regard to the foundations of astrochemistry. Spectroscopic parameters have been calculated via high-level ab initio methods to assist with laboratory and observational detection of [Al, O, Si]^x(x = 0,+1). All [Al, O, Si]M^x(x = 0,+1) isomers exist in the linear geometry, with linear AlOSi (X ²Π) and linear AlOSi⁺ (X¹Δ) being the most stable neutral and cationic species, respectively. Formation of the neutral species most likely occurs via reaction of …

The Interaction Of Different Primary Producers And Physical And Chemical Dynamics Of An Urban Shallow Lake, Majid Sahin

Dissertations, Theses, and Capstone Projects

An artificial urban shallow lake, Prospect Park Lake (PPL), is situated on a terminal moraine in Brooklyn New York, and supplied with municipal water treated with ortho-phosphates. The constant input of the phosphate nutrient is the primary source of eutrophication in the lake. The numerous pools along the water course houses various aquatic phototrophs, which influence the water quality and the state of the system, driving conditions into favoring the survival of their species. In the first half of the dissertation, the focus of the project is on analyzing how the different primary producers in different regions of PPL affect …

The Photoionization Dynamics, Electronic Spectroscopy, And Excited State Photochemistry Of Alco And Aloc, Vincent J. Esposito, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The high cosmic abundance of carbon monoxide (CO) and the ubiquitous nature of aluminum-coated dust grains sets the stage for the production of weakly bound triatomic molecules AlCO (X ²Π) and AlOC (X ²Π) in circumstellar envelopes of evolved stars. Following desorption of cold AlCO and AlOC from the dust grain surface, incoming stellar radiation in the 2–9 eV wavelength range (visible to vacuum ultraviolet) will drive various photochemical processes. Ionization to the singlet cation state will cause an immediate Al–X (X = C, O) bond dissociation to form Al⁺ (¹S) and CO (X ^{1 …}

Dr. Lawrence J. Berliner, Anit Tyagi

DU Undergraduate Research Journal Archive

An interview with Dr. Lawrence J. Berliner.

Insights Into Molecular Recognition And Reactivity From Molecular Simulations Of Protein-Ligand Interactions Using Md And Qm/Mm, Jerrano L. Bowleg

Theses and Dissertations

In this thesis, we have employed two computational methods, molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) MD simulations with umbrella sampling (US), to gain insights into the molecular mechanism governing the molecular recognition and reactivity in several protein-ligand complexes. Three systems involving protein-ligand interactions are examined in this dissertation utilizing well-established computational methodologies and mathematical modeling. The three proteins studied here are acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1). These enzymes are known to interact with a variety of ligands. AChE dysfunction caused by organophosphorus (OP) chemicals is a severe hazard since AChE is …

Aloso: Spectroscopy And Structure Of A New Group Of Astrochemical Molecules, Vincent J. Esposito, Tarek Trabelsi, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

No abstract provided.

Growth Kinetics Determine The Polydispersity And Size Of Pbs And Pbse Nanocrystals, Michael P. Campos, Jonathan De Roo, Matthew W. Greenberg, Brandon M. Mcmurtry, Mark P. Hendricks, Ellie Bennett, Natalie Saenz, Matthew Y. Sfeir, Benjamin Abecassis, Sanjit K. Ghose, Jonathan S. Owen

Advanced Science Research Center

A library of thio- and selenourea derivatives is used to adjust the kinetics of PbE (E = S, Se) nanocrystal formation across a 1000-fold range (kr = 10−1 to 10−4 s−1), at several temperatures (80–120 °C), under a standard set of conditions (Pb : E = 1.2 : 1, [Pb(oleate)2] = 10.8 mM, [chalcogenourea] = 9.0 mM). An induction delay (tind) is observed prior to the onset of nanocrystal absorption during which PbE solute is observed using in situ X-ray total scattering. Density functional theory models fit to the X-ray pair distribution function (PDF) support a Pb2(μ2-S)2(Pb(O2CR)2)2 structure. Absorption spectra …

A Microfluidic Approach For Synthesis And Kinetic Profiling Of Branched Gold Nanostructures, Qi Cai, Valentina Castagnola, Luca Boselli, Alirio Moura, Hender Lopez, Wei Zhang, João M. De Araújo, Kenneth A. Dawson

Articles

Automatized approaches for nanoparticle synthesis and characterization represent a great asset to their applicability in the biomedical field by improving reproducibility and standardization, which help to meet the selection criteria of regulatory authorities. The scaled-up production of nanoparticles with carefully defined characteristics, including intrinsic morphological features, and minimal intra-batch, batch-to-batch, and operator variability, is an urgent requirement to elevate nanotechnology towards more trustable biological and technological applications. In this work, microfluidic approaches were employed to achieve fast mixing and good reproducibility in synthesizing a variety of gold nanostructures. The microfluidic setup allowed exploiting spatial resolution to investigate the growth evolution …

Spectroscopic Properties Relevant To Astronomical And Laboratory Detection Of Mch And Mch+ (M = Al, Mg), Vincent J. Esposito, Tarek Trabelsi, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

New spectroscopic parameters have been calculated to aid in the laboratory and observational detection of AlCH, AlCH⁺, MgCH, MgCH⁺, and their deuterated analogs. All species exist in linear geometry except for AlCH+, which exhibits a bent structure. Rotational frequencies have been calculated and the transition with maximum intensity is discussed for three temperature regions present in space: 100 K for a central circumstellar envelope (CSE), 30 K for an outer CSE, and 3 K indicative of the interstellar medium. Pertinent frequencies range from 25 to 250 GHz, depending on the species. At 30 K, the most …

Inhibitors Of Alpha-Synuclein Aggregation, Jemil Ahmed

Electronic Theses and Dissertations

Alpha-Synuclein (αS) – a neuronal, disordered, presynaptic protein – aggregates into amyloid fibrils and accumulates in the substantia nigra pars compacta of Parkinson's Disease (PD) patients. The aggregation and accumulation of αS amyloid fibrils leads to death of dopaminergic neurons; a hallmark of PD. Although it’s not clear why αS aggregates, prior studies have found that intrastriatal injection of fibril alone is sufficient to cause PD pathology in mouse and non-human primates models. These observations implicate αS as a therapeutic target against PD.

Unfortunately, there are three caveats when attempting to target αS. First, αS is a neuronal protein expressed …

Characterization Of Nanoparticles Using Inductively-Coupled Plasma Mass Spectrometry, Jabez D. Campbell

Graduate Theses/Dissertations

Nanomaterials are a relatively new class of materials that have many applications which span a wide host of fields from medical products to consumer products. The possible compositions and forms of nanomaterials are just as varied as the applications. Therefore, a versatile characterization method is needed for researchers and regulators alike to ensure nanomaterials are properly used. Single Particle Inductively Coupled Plasma Mass Spectrometry (SP-ICP-MS) is a functional method that could fill the characterization need in the nanomaterial research field. Using data from both SP-ICP-MS tests and data from literature established characterization methods, the viability of making SP-ICP-MS the standard …

Stratospheric Aerosol Composition Observed By The Atmospheric Chemistry Experiment Following The 2019 Raikoke Eruption, Chris D. Boone, Peter F. Bernath, Keith Labelle, Jeff Crouse

Chemistry & Biochemistry Faculty Publications

Infrared aerosol spectra derived from Atmospheric Chemistry Experiment measurements following the June 2019 Raikoke volcanic eruption are used to evaluate the composition of stratospheric aerosols in the Arctic. A blanket of aerosols, spanning an altitude range from the tropopause (8–11 km) to 20 km, persisted in the stratosphere over northern latitudes for many months. The aerosols within this blanket were almost exclusively sulfates. The percentage of sulfuric acid in the aerosols decreased over time, dropping below 50% H₂SO₄ concentration at some altitudes by March 2020. Contrary to previous reports, the aerosol blanket was not comprised of smoke …

Self-Assembly Of Black Cumin Oil-Based Nanoemulsion On Various Surfactants: A Molecular Dynamics Study, Aulia Fikri Hidayat, Taufik Muhammad Fakih

Makara Journal of Science

Black cumin is commonly used as traditional medicine due to its wide range of pharmacological potential. Black cumin oil (BCO) was often prepared as nanoemulsion to improve its solubility, stability, and bioavailability. This study was conducted to investigate the molecular behavior as well as structural evolution of BCO-surfactant systems during self-assembly micellization using molecular dynamics (MD) simulations. Several BCO constituents and variations of surfactants were employed to model BCO-surfactant systems. 50 ns of MD simulations were performed to elucidate their evolution of structures and physicochemical properties during formation. Results showed that BCO-tween20 and BCO-lecithin were able to form spherical-shaped micelles …

A Nanoscale Shape-Discovery Framework Supporting Systematic Investigations Of Shape-Dependent Biological Effects And Immunomodulation, Wei Zhang, Hender Lopez, Luca Boselli, Paolo Bigini, André Perez-Potti, Zengchun Xie, Valentina Castagnola, Qi Cai, Camila P. Silveira, Joao M. De Araujo, Laura Talamini, Nicolò Panini, Giuseppe Ristagno, Martina B. Violatto, Stéphanie Devineau, Marco P. Monopoli, Mario Salmona, Valeria A. Giannone, Sandra Lara, Kenneth A. Dawson, Yan Yan

Articles

Since it is now possible to make, in a controlled fashion, an almost unlimited variety of nanostructure shapes, it is of increasing interest to understand the forms of biological control that nanoscale shape allows. However, a priori rational investigation of such a vast universe of shapes appears to present intractable fundamental and practical challenges. This has limited the useful systematic investigation of their biological interactions and the development of innovative nanoscale shape-dependent therapies. Here, we introduce a concept of biologically relevant inductive nanoscale shape discovery and evaluation that is ideally suited to, and will ultimately become, a vehicle for machine …

Reinvigorating A Technical Countering Weapons Of Mass Destruction Distance Learning Graduate Certificate Program, James C. Petrosky, Gaiven Varshney, Jeremy Slagley, Sara Shaghaghi

Faculty Publications

Current Countering Weapons of Mass Destruction (CWMD) demands can be divided broadly into policy and science. The science of chemical, biological, and radiological/nuclear weapons informs the limits of development, production, employment, operation, detection, risk characterization, human and material protection, and medical intervention. In short, the science of weapons of mass destruction (WMD) should precede and inform the development of policy. It is to this end that the Air Force Institute of Technology (AFIT) CWMD program was re-established, providing a technical educational option for practitioners to understand the science behind a very technically challenging subject.

Molecular Dynamics Simulations Of Self-Assemblies In Nature And Nanotechnology, Phu Khanh Tang

Dissertations, Theses, and Capstone Projects

Nature usually divides complex systems into smaller building blocks specializing in a few tasks since one entity cannot achieve everything. Therefore, self-assembly is a robust tool exploited by Nature to build hierarchical systems that accomplish unique functions. The cell membrane distinguishes itself as an example of Nature’s self-assembly, defining and protecting the cell. By mimicking Nature’s designs using synthetically designed self-assemblies, researchers with advanced nanotechnological comprehension can manipulate these synthetic self-assemblies to improve many aspects of modern medicine and materials science. Understanding the competing underlying molecular interactions in self-assembly is always of interest to the academic scientific community and industry. …

Thermal Properties Of 18f-Fdg Uptake And Imaging In Positron Emission Tomography Scans Of Cancerous Cells, Carleigh R. Eagle

PANDION: The Osprey Journal of Research and Ideas

Positron Emission Tomography (PET) scans can utilize a radioactive tracer, in this case 2-deoxy2-[fluorine-18] fluoro-D-glucose (¹⁸F-FDG), to visualize malignant tumors in cancer patients. The uptake was compared to glucose to understand the difference in thermal properties, which contribute to the ability to image the cancerous cells. The uptake of ¹⁸F-FDG by cancer cells and the imaging process of positron emission tomography were reviewed from a thermodynamic perspective. Gastrointestinal and neurological imaging techniques were reviewed to understand the role of PET imaging in different areas of the human body.

Bridging The 12-6-4 Model And The Fluctuating Charge Model, Pengfei Li

Chemistry: Faculty Publications and Other Works

Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r …