Physical Chemistry Commons^™

Robust Thermodynamic Analysis Of Flexible Protein-Ligand Binding Using Statistical Mechanics, Mitchell Dulaney

Create@State

Understanding how proteins bind small molecules is essential for accurate computational modeling of biological systems. However, calculating binding free energy (delta G), enthalpy (delta H), and entropy (delta S) becomes unreliable when proteins are flexible, and ligands are between multiple binding positions. This motion causes traditional computational methods to produce inconsistent thermodynamic values.

A computational workflow was implemented that included docking to predict likely binding positions, molecular dynamics simulations to sample how the protein and ligand move over time, and statistical mechanics analysis to calculate thermodynamic quantities. A new theoretical framework was developed and implemented in a custom program to …

Kinetic Analysis Of 2-Methylpentan-2-Ol*, Nicole Seheult

Campus Research Month

This experiment investigated the kinetics of 2-methylpentan-2-ol using UV-visible spectroscopy under strongly acidic conditions (96% sulfuric acid). The dehydration of the tert-amyl alcohol produced a carbocation intermediate whose absorbance at 300 nm was evaluated at various temperatures. An Arrhenius plot of ln(k) versus 1/T produced a linear relationship with a calculated activation energy of 90.0 kJ/mol. This value is consistent with literature expectations for tertiary carbocation formation and supports the acid-catalyzed dehydration mechanism predicted for this molecule.

Calculating Potential Energy Curves Of Molecular Hydrogen And Its Ion Using Psi4 For Blinc Fusion Applications*, Angelina Castillo, Oscar Coral, Canaan Hercules, Blake Laing, Vola Andrianarijaona

Campus Research Month

Southern Adventist University’s Beamline for Ionic and Neutral Collisions (BLINC) is investigating the interactions between hydrogen molecules and fusion particles. To perform in-house theoretical calculations, the BLINC Theory and Analysis Group is testing Psi4 as a viable computational method for BLINC fusion research. Successful calculations of the potential energy curves and dissociation energies of H₂ and H₂⁺ have been completed and compared to known values. Preliminary results align with known values, demonstrating Psi4’s potential for BLINC research. Future work will focus on the vibrational energies, wavefunctions, and transition probabilities of H₂ and H₂⁺.

Asphalt Pavement Rejuvenation Investigated By Nuclear Magnetic Resonance Relaxometry, Catherine Skaggs

Miners Solving for Tomorrow Research Conference

Asphalt is a relatively inexpensive material commonly used for road pavements; however, asphalt ages from exposure to oxygen and UV radiation, leading to loss of elasticity, which leads to cracks and potholes. To slow or reverse asphalt aging, pavement preservation treatments are in use. It’s unclear whether these treatments truly rejuvenate the pavement structure or merely offer a short-term benefit. Nuclear Magnetic Resonance (NMR) relaxometry is an analytical technique that uses the recovery of excited nuclear magnetization as a parameter to gain insights into molecular environments. Recovery-time distributions gathered from asphalt materials show differences between regular and rejuvenated asphalt samples, …

Computational Study Of The Proton Transfer In The H7o3+ Cluster, Anna James, Martina Kaledin

Symposium of Student Scholars

Proton transfer (PT) from one molecule to another is among the most studied phenomena in chemistry. PT requires the bond cleavage and the formation of a new one, AH⁺ + B -> A+ BH⁺. In protonated water clusters, such a process consists of the interconversion of hydrogen bonds. Experimentally, such a process can be observed as a significant increase of a dipole moment. However, other vibrational transitions often occur with small changes in the dipole moment while large changes in polarizability. In this work, we study the PT process in a protonated water cluster, H₇O …

An Open-Framework Iron-Selenite As Cathode For Li- Ion Batteries, Sutapa Bhattacharya, Aleksandr V. Chernatynskiy, Amitava Choudhury

Miners Solving for Tomorrow Research Conference

No abstract provided.

The Effect Of Nanomorphology As Quantified Via The K‑Index On The Drug Delivery Properties Of Isocyanate-Derived Aerogels, Stephen Y. Owusu, A. B. M. Shaheen Ud Doulah, Vaibhav A. Edlabadkar, Kamden J. George, Chariklia Sotiriou-Leventis

Miners Solving for Tomorrow Research Conference

No abstract provided.

Mechanistic Investigation Of C—C Bond Activation Of Phosphaalkynes With Pt(0) Complexes, Roberto M. Escobar, Abdurrahman C. Ateşin, Christian Müller, William D. Jones, Tülay Ateşin

Research Symposium

Carbon–carbon (C–C) bond activation has gained increased attention as a direct method for the synthesis of pharmaceuticals. Due to the thermodynamic stability and kinetic inaccessibility of the C–C bonds, however, activation of C–C bonds by homogeneous transition-metal catalysts under mild homogeneous conditions is still a challenge. Most of the systems in which the activation occurs either have aromatization or relief of ring strain as the primary driving force. The activation of unstrained C–C bonds of phosphaalkynes does not have this advantage. This study employs Density Functional Theory (DFT) calculations to elucidate Pt(0)-mediated C–CP bond activation mechanisms in phosphaalkynes. Investigating the …

Predicting The Reactions Of Cs2, Ocs, And Co2 With Group Iv And Group Vi Transition Metal Oxides, Marissa Shea Blair, Zachary Ryan Lee Phd, David A. Dixon Phd

Posters-at-the-Capitol

Building on a recent serious of high level electronic structure studies of Lewis acid gas reactions with metal oxide sorbents, DFT (B3LYP and ωB97X-D) and CCSD(T) methods are being used to predict the Lewis acid-base addition (physisorption) and formation of metal oxide carbonate/thiocarbonate formation (chemisorption) reactions of CS2, OCS, and CO2 of CS2, OCS, and CO2 with Group IV (MO2)n and Group VI (MO3)n (n = 1 - 3) nanoclusters. For the Group IV oxides, chemisorption to form terminal carbonates and thiocarbonates is predicted to be the most favored, with thiocarbonate ligand binding energies slightly more exothermic than their carbonate …

Probing The Effect Of Nitrogen And Boron Doping On Structures, Properties, And Stability Of C20 Clusters, Ramsay Revennaugh, Martina Kaledin

Symposium of Student Scholars

Fullerenes are carbon molecules arranged in a closed hollow shell to form spherical-like structures. These clusters exist in various sizes, C_n, with the smallest being C₂₀. C₂₀, often when doped with other elements, has shown promise in creating new materials as a catalyst and as energy storage material. Here, we look at the existence of C₂₀ doped with nitrogen or boron atoms using density functional theory (DFT). C₂₀ is doped with one to three boron or nitrogen atoms, respectively, including the five different C₁₈N₂ / C₁₈B_{2 …}

Ab Initio Calculations Of Vibrational Spectra Of Model Peptides, Katheryn Foust, Martina Kaledin

Symposium of Student Scholars

The function of biological molecules is closely related to their spatial structure and conformational dynamics. Therefore, understanding the structure and functions of small peptides contributes to gaining insight into the behavior of more complex systems. The peptide bond (-CO-NH-) is among the very important binding patterns in biochemistry. It links amino acids together, specifies rigidity to the protein backbone, and includes the two essential docking sites for hydrogen-bond-mediated protein folding and protein aggregation, namely, the C=O acceptor and the N-H donor parts. Therefore, the C=O (amide-I) and N-H (amide-A) vibrations provide sensitive and widely used probes into the structure of …

A Comparative Study Of Specific Enthalpy Of Aromatic Hydrocarbons With Simple Carbohydrates, Kohl D. Kervin, Subha Pratihar

ATU Scholars Symposium

Calorimetry is an aspect of chemistry primarily focused on determining the enthalpy of reactions (∆Hrxn). In the bomb calorimetry technique, the heat of combustion of chemical compounds can be measured experimentally. From this data and the application of Hess’s Law, ∆the Hrxn of several chemical reactions can be determined. The technique of bomb calorimetry can be applied to food, fuels, pharmaceuticals, and many other fields. The objective of the present project is to determine the specific enthalpy of various simple carbohydrates (naturally occurring sugars) through bomb calorimetry and compare it with that of aromatic hydrocarbons.

By performing benzoic acid standardization …

Hydrogen Bonding In Small Model Peptides; The Dft And Mp2 Study, Gracie Smith, Martina Kaledin

Symposium of Student Scholars

Formamide is a small model compound for the study of the peptide bond. The peptide bond links amino acids together, specifies rigidity to the protein backbone, and includes the essential docking sites for hydrogen-bond-mediated protein folding and protein aggregation, namely, the C=O acceptor and the N-H donor parts. Therefore, the infrared C=O (amide-I) and N-H (amide-A) vibrations provide sensitive and widely used probes into the structure of peptides. This computational chemistry work, we study hydrogen bonds in formamide dimer isomers. We evaluate the accuracy of the density functional theory (DFT) and many-body perturbation theory to the 2^nd order (MP2) …

Synthesis And Characterization Of A Novel Reaction-Based Azaborine Fluorescent Probe Capable Of Selectively Detect Carbon Monoxide Based On Palladium-Mediated Carbonylation Chemistry, Samuel Moore, Carl Jacky Saint-Louis

Symposium of Student Scholars

Azaborines are fascinating compounds because they possess valuable properties such as photochemical stability, have high molar absorption coefficient and high fluorescent quantum yields, as well as large Stokes shifts and tunable absorption/emission spectra. Here, we designed, synthesized, and will examine a novel reaction-based azaborine fluorescent probe capable of selectively detect carbon monoxide (CO) based on palladium-mediated carbonylation chemistry. This novel azaborine fluorescent probe will exhibit high selectivity for CO and display a robust turn-on fluorescent response in the presence of CO in aqueous buffer solution.

Ketal-Azaborine Versus Ketal-Azaborine With A Spacer: Structural Effects On The Photophysical Properties Of Tunable Heteroaromatic Polycyclic Chromophores, Albert Campbell, Janiyah Riley, Samuel Moore, Albert Campbell

Symposium of Student Scholars

Flat-structured heteroaromatic polycyclic compounds with extended conjugated π-systems such as azaborines are in high demand in the material and imaging technology markets because of their unique features such as simultaneous tunability of fluorescence color and intensity. We have designed, synthesized, and investigated a series of novel conjugated thermally stable ketal-azaborine chromophores that contain a phenyl ring as a spacer between electronic moieties and the ketal-azaborine core as easily tunable high-luminescent organic materials. We investigated the impact of the phenyl spacer on the ketal-azaborine unit. We examined the structural effects on their photophysical properties by incorporating electron –donating and –withdrawing substituents …

Azaborine Versus Azaborine With A Spacer: Structural Effects On The Photophysical Properties Of Tunable Azaborine Chromophores, Kaia Ellis, Janiyah Riley, Lyric Gordon, Janiyah Riley

Symposium of Student Scholars

Azaborines are fascinating compounds because of their valuable and interesting optical properties making them suitable to be utilized in many optoelectronic devices. We have designed, synthesized, and investigated a series of novel conjugated thermally stable azaborine chromophores by incorporating a phenyl ring as a spacer linking the chromophore to different electronic moieties as easily tunable high-luminescent organic materials. We investigated the effect of the phenyl spacer on the azaborine unit. The substituent effects of different electronic moieties were investigated by the insertion of electron –withdrawing and –donating moieties to the phenyl spacer. We examined the role of the electron –donating …

Gravimetric Determination Of The Adsorption Capacity Of Zirconium Hydroxide For Isopropanol, Riley Bennett

Symposium of Student Scholars

Zirconium hydroxide’s adsorption properties make it useful for the decomposition of chemical warfare agents and toxic industrial chemicals. In the current study, isopropanol is used to examine the adsorption behavior of the zirconium hydroxide surface sites through a series of microreactor experiments. Initially, the mass delivery of isopropanol is calibrated as a function of temperature and gas flow rate. Separate experiments can then be done by flowing the isopropanol mixture through a sample of zirconium hydroxide to quantitatively determine the amount of isopropanol that can adsorb onto a sample of zirconium hydroxide. FT-IR spectra of the gas mixtures flowing from …

The Investigation Of Geologically Relevant Metal Phosphites As A Plausible Source Of Phosphorus In Prebiotic Chemistry, James Quarles, Amelia Shengaout, Kimberly Meyberg, Heather Abbott-Lyon

Symposium of Student Scholars

To understand the origin of life, the abiotic incorporation of phosphorus in energy-promoting molecules like adenosine triphosphate (ATP) need to be identified. However, a consensus has not been reached on the source of phosphorus for prebiotic chemistry on Archaean Earth. One hypothesis is that metal phosphites were an important source of phosphorus for prebiotic chemistry. The primary issue with this hypothesis is the lack of phosphites in the geological rock record, where different phosphorus compounds (mostly inorganic phosphates) are observed instead. Two geologically relevant metal phosphites with varying waters of hydration, CaHPO3 and MgHPO3, were synthesized, structurally characterized, and thermally …

Computer Simulation Of Raman Spectra And Mode Assignment: Application To Methane, Oluwaseun Omodemi, Ciara Tyler, Martina Kaledin

Symposium of Student Scholars

This work uses driven molecular dynamics (DMD) method, in conjunction with an analytic PES calculated using MP2/aug-cc-pVDZ energies to identify and assign Raman vibrational modes of methane. Recently, a new linearized approach was proposed for the Polarizability Tensor Surfaces (PTS) that yields a unique solution to the least-squares fitting problem and provides a competitive level of accuracy compared to the non-linear PTS model. We used the previously reported B3LYP/6-31+G(d) molecular geometries for CH₄ and generated a new PTS at the MP2/aug-cc-pVDZ level of theory. The performance of the linearly parametrized functional form for the CH₄ PTS is examined. …

Exploring The Geometric And Electronic Properties Of Palladium Doped Silicon Clusters, Madison Winkeler, Ciara N. Richardson

Scholars Week

Transition metal-doped silicon clusters have unique properties and have been studied as building blocks for nanomaterials and microelectronics. Here, the structure and properties of candidate palladium doped silicon clusters (SinPd2: n=1-17) were determined using global optimization techniques on a high performance computing cluster at the San Diego Supercomputing Center. Then geometric structures were further optimized utilizing the B3LYP method with 6-311+G(d) basis sets for silicon and lanl2dz pseudopotential for palladium, followed by the larger DSDPBEP86 method with 6-311+G(2d) basis sets for silicon and SDD pseudopotential for palladium, as implemented in the Gaussian 16 program package. The energetics for each cluster …

Investigating The Proton Transfer Dynamics And Vibrational Spectrum Of Hydrogen Oxalate Using Driven Molecular Dynamics Simulations, Martina Kaledin, Dominick Pierre-Jacques, Olivia Cochran, Dayana Salazar, Dalton Boutwell, Martina Kaledin

Symposium of Student Scholars

In this computational chemistry work, we describe ab initio calculations and assignment of infrared (IR) spectra of an intramolecular H-bonding system hydrogen oxalate, C₂O₄H^–. The mechanism and dynamics of proton transfer are of fundamental importance in chemistry and biology. In C₂O₄H^–, proton transfer occurs along the non-linear path. Previous experimental studies are signaling very strong coupling between OH stretch mode and low frequency motions. We calculated IR spectra at 300 K using the direct molecular dynamics (MD) method at the MP2/ aug-cc-pVDZ level of theory and assigned the …

Molecular Vibrations Of Symmetric Molecules: Raman Scattering Driven Molecular Dynamics Method, Martina Kaledin, Dominick Pierre-Jacques, Ciara Tyler, Jason Dyke

Symposium of Student Scholars

This project focuses on developing a novel computational technique to study molecular vibrations through infrared (IR) and Raman scattering Driven Molecular Dynamics (DMD) method. While the main criterion for IR absorption is a net change in the dipole moment in a molecule as it vibrates, presently we wish to predict and analyze vibrational spectra to study symmetric vibrational modes that are IR inactive or weakly active while strongly Raman active. A newly developed method was tested on CO₂, H₂O, CH₄, and C₂₀ molecules. Students optimized the molecular structures, obtained vibrational frequencies, and IR …

Probing Structure And Energetics Of Proton-Bound Complexes N2…Hco+ And N2h+…Oc Using Computational Chemistry Methods, Antonio Barrios, Dalton Boutwell, Onyi Okere, Monique Olocha, Oluwaseun Omodemi, Alexander Toledo, Antonio Barrios

Symposium of Student Scholars

N₂…HCO⁺ and N₂H⁺…OC are predicted to exist in interstellar clouds. These complexes involve HCO⁺ and N₂H⁺ fragments that are bound to N₂ and CO, respectively using hydrogen-bonded interaction. The reason these molecules are important is that the existence of nitrogen can be measured indirectly through ion-molecular complexes studied in this work. The measured vibrational spectra of molecules is an excellent way to characterize and detect molecules. We used B3LYP, MP2, and CCSD(T) computational methods to predict the structure and vibrational frequencies of N₂…HCO⁺ and N …

Theoretical Study On The Isomerization And Detection Of N2h+…Oc Complex In Interstellar Clouds, Dalton Boutwell, Martina Kaledin

Symposium of Student Scholars

In this study, we characterize N₂H⁺…OC linear complex using Driven Molecular Dynamics (DMD) and Vibrational Self-Consistent Field Theory (VSCF) methods due to its relevance in astrochemistry. A central challenge is the detection of the molecular complex in interstellar media (ISM). Computational chemistry approaches can predict vibrational spectra, hence facilitate prediction of its existence and stability in the ISM. N₂H⁺…OC involves the proton transfer process via hydrogen bonding interaction. Proton motion is highly anharmonic, therefore facing a significant challenge to characterize it accurately. Quantum mechanical variational methods are popular among many theoretical chemists …

Elucidation Of The Combination Bands And Anharmonic Features In The Vibrational Spectra Of C2o4h- And C2o4d- With Driven Classical Trajectories, Dalton Boutwell, Martina Kaledin

Symposium of Student Scholars

Hydrogen bonds are strong electrostatic interactions characterized by the anharmonic shift of vibrational modes of atoms involved with this intramolecular force. The low energy barrier of the H⁺ transfer in hydrogen oxalate (C₂O₄H^-), predicted to be ~2.98 kcal/mol at the MP2/aVDZ level of theory, allows for rapid proton exchange in the system and confounds the experimental vibrational spectrum of the molecule with broad spectral features in the O-H stretching region. The molecule is planar and exhibits several torsional motions among some of its lower frequency fundamental vibrational transitions. Because H-bonding and torsional motions …

Model Calculations Of H/D Isotope Substitution In Hydrogen Oxalate Anion Using The Normal Mode Analysis, Dominick Pierre-Jacques, Olivia Cochran, Dayana Salazar, Martina Kaledin

Symposium of Student Scholars

In this computational chemistry work, we describe ab initio calculations and assignment of infrared (IR) spectra of an intramolecular H-bonding system hydrogen oxalate, C₂O₄H^–. The study of H/D isotope effects can provide useful information on a proton’s location inside a non-linear pathway. In C₂O₄H^–, a normal mode analysis was performed at the MP2/aug-cc-pVDZ and B3LYP/aug-cc-pVDZ levels of theory. Previous experimental studies suggest a frequency shift ~1000 cm^-1 for the OH stretch mode upon the H/D isotopic substitution. Isotope calculations resulted in a shift of 842 cm^{-1 …}

Transmission Ir Of Phosphorus In Water-Ice, Kerrigan Greene

Symposium of Student Scholars

The possibility of life on other planets has prompted philosophical debate and scientific research for years. As more of space is explored, and more is discovered about the origin of life, various planets and moons have come under speculation for the possibility of life. The icy moons of Saturn and Jupiter are prime examples. This is because of the presence of water-ice on their surfaces. However, there are many other important chemicals and elements necessary for life to develop and thrive. One such element is phosphorus. In order to analyze the ice on the surface of these moons and other …

The Reactivity Of Metal Phosphites: Oxidative Rate Analysis, Jamie Kitchens

Symposium of Student Scholars

Phosphorous compounds are involved in many of the biomolecular processes deemed fundamental for life. DNA, ATP, and phospholipids are a few of the molecules where phosphates can be found in the body. Phosphates are geochemically characterized by their low solubility and poor reactivity. This has led to the investigation of reaction mechanisms that could lead to the formation of the phosphorous compounds found in organisms. The oxidation of phosphite into phosphate could be how phosphates were introduced to life, due to phosphites being more soluble and more reactive than phosphates. We will present the synthesis and oxidation reactivity of four …

Energy Requirements For Abiotic Production Of Phosphorous Compounds At The Ice-Schreibersite Interface, Lindsay M. Hicks

Symposium of Student Scholars

Energy Requirements for Abiotic Production of Phosphorous Compounds at the

Ice-Schreibersite Interface

The Abbott-Lyon Lab is investigating the chemistry at the interface of simple ices and a meteoritic mineral analogue. Phosphorous is a key component of numerous biomolecules necessary for life. Lack of an abundance of biologically accessible mineral sources of phosphates on Earth, termed “The Phosphorous Problem,” has led some origin-of-life scientists to look to extraterrestrial sources like meteoritic metal phosphides as possible sources of available phosphates. Schreibersite (Fe₂NiP) is a common mineral in iron meteorites and a plausible source of biologically accessible phosphorous. This study will …

Investigation Of Chemistry At Ice-Mineral Interfaces Of Phosphorus-Containing Meteorites Analogues, Kimberly Meyberg

Symposium of Student Scholars

The search for life outside of Earth has raised questions about how life began have intrigued origin-of-life researchers, such as the incorporation of phosphorus into biomolecules. Phosphorus exists on Earth mostly as phosphate, PO₄^3-, which is insoluble and unreactive in the geochemical conditions of the early Earth. The challenge of incorporating phosphorus into biomolecules is known as the “phosphorus problem,” prompting investigations of reactive phosphorus species delivered to the prebiotic Earth. Phosphorus-laden meteorites delivered schreibersite (Fe,Ni)₃P, a possible mineral source of phosphorus recognized for its redox chemistry potential and observed reactivity with aqueous …