Open Access. Powered by Scholars. Published by Universities.®
- Institution
- Keyword
-
- 3D printing (1)
- Artificial intelligence (1)
- Astrochemistry (1)
- Binding energetics (1)
- Characterization (1)
-
- Chemistry education (1)
- Computational methods (1)
- Covalent adaptable network (1)
- DNA repair (1)
- Drug design (1)
- Encoder–decoder (1)
- Evolutionary mechanisms (1)
- Gateway cloning techniques (1)
- Genome instability (1)
- Hardener (1)
- Homologous recombination (1)
- Isolation (1)
- Molecular docking (1)
- Molecular dynamics (1)
- Molecular orbitals (1)
- Molecular spectroscopy (1)
- Mutational scanning (1)
- Natural Product Chemistry (1)
- Novel cysteine (1)
- Novel molecules (1)
- Nuclear Magnetic Resonance Spectroscopy (1)
- Protein stability (1)
- Quantitative estimate of drug-likeness (QED) (1)
- RecQ helicases (1)
- Reinforcement learning (1)
- Publication
- Publication Type
Articles 1 - 15 of 15
Full-Text Articles in Computational Chemistry
Spectroscopy And Photochemistry Of The Astrochemical Molecules Sicp And Alcp, Vincent J. Esposito, Tarek Trabelsi, Rebecca Firth, Ryan C. Fortenberry, Joseph S. Francisco
Spectroscopy And Photochemistry Of The Astrochemical Molecules Sicp And Alcp, Vincent J. Esposito, Tarek Trabelsi, Rebecca Firth, Ryan C. Fortenberry, Joseph S. Francisco
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Through characterization of the electronic excited-state topology, linear-SiCP is predicted to be photostable in the UV region, whereas linear-AlCP is predicted to undergo photodissociation to form Al+CP products after absorption of light in the 200–250 nm range, representing a catalytic process for freeing aluminum molecules from a solid dust grain. Both SiCP and AlCP are predicted to have electronic transitions with large absorption cross sections (∼10–17 cm2) and to undergo fluorescence from bound excited states. The total electronic absorption spectrum is provided to inform electronic spectroscopy experiments. Silicon (SiC) and aluminum (Al2O3) dust …
Ensemble-Based Binding Free Energy Profiling And Network Analysis Of The Kras Interactions With Darpin Proteins Targeting Distinct Binding Sites: Revealing Molecular Determinants And Universal Architecture Of Regulatory Hotspots And Allosteric Binding, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker
Ensemble-Based Binding Free Energy Profiling And Network Analysis Of The Kras Interactions With Darpin Proteins Targeting Distinct Binding Sites: Revealing Molecular Determinants And Universal Architecture Of Regulatory Hotspots And Allosteric Binding, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker
Mathematics, Physics, and Computer Science Faculty Articles and Research
KRAS is a pivotal oncoprotein that regulates cell proliferation and survival through interactions with downstream effectors such as RAF1. Despite significant advances in understanding KRAS biology, the structural and dynamic mechanisms of KRAS allostery remain poorly understood. In this study, we employ microsecond molecular dynamics simulations, mutational scanning, and binding free energy calculations together with dynamic network modeling to dissect how engineered DARPin proteins K27, K55, K13, and K19 engage KRAS through diverse molecular mechanisms ranging from effector mimicry to conformational restriction and allosteric modulation. Mutational scanning across all four DARPin systems identifies a core set of evolutionarily constrained residues …
Trade-Off Between Limonene & Geraniol-Based Reprocessable And Non-Reprocessable Epoxy Thermosets: Role Of Aliphatic Diamines In Polymer Networks Design, Priyankkumar Kanubhai Patel
Trade-Off Between Limonene & Geraniol-Based Reprocessable And Non-Reprocessable Epoxy Thermosets: Role Of Aliphatic Diamines In Polymer Networks Design, Priyankkumar Kanubhai Patel
Electronic Theses & Dissertations
The growing demand for sustainable materials, driven by environmental concerns and the rapid depletion of fossil fuels, has garnered significant attention in the fabrication of bio-based epoxy thermosets as renewable alternatives to petroleum-derived thermosetting polymers. The present study focuses on the synthesis and characterization of epoxy prepolymer resins derived from limonene and geraniol via a two-step process, followed by the fabrication of thermally cross-linked flexible epoxy thermoset films using various traditional aliphatic diamine curing agents, namely 1,2-ethylenediamine (EDA), 1,4-butylenediamine (BDA), and 1,6-hexamethylenediamine (HDA). Additionally, the incorporation of cystamine, a disulfide-containing diamine, enabled the formation of a covalent adaptable network through …
In Memoriam - Nora Sabelli: Master Orchestrator Of Grant Programs And Mentor For Advancing The Interdisciplinary Learning Sciences Field, Eric Hamilton, Jeremy Roschelle, Roy Pea, Barbara Means, Louis Gomez, Kim Gomez, Nancy Butler Songer
In Memoriam - Nora Sabelli: Master Orchestrator Of Grant Programs And Mentor For Advancing The Interdisciplinary Learning Sciences Field, Eric Hamilton, Jeremy Roschelle, Roy Pea, Barbara Means, Louis Gomez, Kim Gomez, Nancy Butler Songer
Education Division Scholarship
On Friday, September 6, 2024, the learning sciences field lost a giant in Dr. Nora Sabelli, 87 years old, a personal mentor to many researchers and an inspiration to so many learning scientists and STEM leaders. Nora’s first professional career was as a computational chemist, and later she became a passionate leader in research for improving STEM education. Nora’s time as a senior program officer at the National Science Foundation’s (NSF) Education and Human Resources (EHR) directorate was legendary; she was a force of nature who reshaped funding priorities for stronger science and a stronger connection of science to education …
Demystifying Misconceptions In Introductory Undergraduate Chemistry Education With 3d Printed Molecular Orbitals, Hiwot Endeshaw, Daniel J. O'Leary
Demystifying Misconceptions In Introductory Undergraduate Chemistry Education With 3d Printed Molecular Orbitals, Hiwot Endeshaw, Daniel J. O'Leary
Pomona Senior Theses
Spatial abilities are invaluable skills for the science, technology, engineering, and mathematics (STEM) subjects. However, women, people from low socioeconomic backgrounds, and ethnic minorities are more likely to have less developed spatial abilities, which is one of the many contributing factors for the lack of diversity in STEM subjects like chemistry. Teaching spatial skills to undergraduate chemistry students may address this issue and help increase the diversity of students who go on to continue their education in the subject. 3D printing technology in higher education has exploded in recent years, presenting a unique opportunity to teach “hard to grasp” concepts …
Phytochemistry Of Dalea Candida Var. Oligophylla, Ryan E. Galperin
Phytochemistry Of Dalea Candida Var. Oligophylla, Ryan E. Galperin
All Master's Theses
The focus of this project was the plant Dalea candida and its phytochemistry. The plant compounds were isolated and purified by an array of chromatographic techniques. The structures of the pure compounds were determined by one-dimensional and two-dimensional 1H and 13C NMR spectroscopy, supported by infrared and ultraviolet spectroscopy, experimental and calculated circular dichroism spectroscopy, and mass spectrometry. Plant parts were worked on separately since they typically differ in content. Purified compounds will be tested for biological activities. Based on our results, eight new or known compound were isolated, specifically four new compounds and four known compounds. Compound …
Response To Replication Stress And Maintenance Of Genome Stability By Wrn, The Werner Syndrome Protein, David K. Orren, Amrita Machwe
Response To Replication Stress And Maintenance Of Genome Stability By Wrn, The Werner Syndrome Protein, David K. Orren, Amrita Machwe
Markey Cancer Center Faculty Publications
Werner syndrome (WS) is an autosomal recessive disease caused by loss of function of WRN. WS is a segmental progeroid disease and shows early onset or increased frequency of many characteristics of normal aging. WRN possesses helicase, annealing, strand exchange, and exonuclease activities and acts on a variety of DNA substrates, even complex replication and re- combination intermediates. Here, we review the genetics, biochemistry, and probably physiological functions of the WRN protein. Although its precise role is unclear, evidence suggests WRN plays a role in pathways that respond to replication stress and maintain genome stability particularly in telomeric regions.
Β-Sheets Mediate The Conformational Change And Allosteric Signal Transmission Between The Aslov2 Termini, Sian Xiao, Mayar Terek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao
Β-Sheets Mediate The Conformational Change And Allosteric Signal Transmission Between The Aslov2 Termini, Sian Xiao, Mayar Terek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao
Mathematics, Physics, and Computer Science Faculty Articles and Research
Avena sativa phototropin 1 light-oxygen-voltage 2 domain (AsLOV2) is a model protein of Per-Arnt-Sim (PAS) superfamily, characterized by conformational changes in response to external environmental stimuli. This conformational change begins with the unfolding of the N-terminal A'α helix in the dark state followed by the unfolding of the C-terminal Jα helix. The light state is characterized by the unfolded termini and the subsequent modifications in hydrogen bond patterns. In this photoreceptor, β-sheets are identified as crucial components for mediating allosteric signal transmission between the two termini. Through combined experimental and computational investigations, the Hβ …
De Novo Drug Design Using Transformer-Based Machine Translation And Reinforcement Learning Of An Adaptive Monte Carlo Tree Search, Dony Ang, Cyril Rakovski, Hagop S. Atamian
De Novo Drug Design Using Transformer-Based Machine Translation And Reinforcement Learning Of An Adaptive Monte Carlo Tree Search, Dony Ang, Cyril Rakovski, Hagop S. Atamian
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
The discovery of novel therapeutic compounds through de novo drug design represents a critical challenge in the field of pharmaceutical research. Traditional drug discovery approaches are often resource intensive and time consuming, leading researchers to explore innovative methods that harness the power of deep learning and reinforcement learning techniques. Here, we introduce a novel drug design approach called drugAI that leverages the Encoder–Decoder Transformer architecture in tandem with Reinforcement Learning via a Monte Carlo Tree Search (RL-MCTS) to expedite the process of drug discovery while ensuring the production of valid small molecules with drug-like characteristics and strong binding affinities towards …
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
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
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 …
Cloning And Characterization Of Sas0754, A Hypothetical Protein From Community Associated Staphylococcus Aureus, Unknown Unknown
Cloning And Characterization Of Sas0754, A Hypothetical Protein From Community Associated Staphylococcus Aureus, Unknown Unknown
Symposium 2012
Community associated Staphylococcus aureus (strain MSSA476) is a gram positive cocci capable of infecting many different parts of the body and known to cause serious infections that can be fatal, such as bacterial arthritis and acute endocarditis. To find effective ways of fighting against CA-MRSA strains we must learn more about their ability to infect. The focus of this study was cloning and characterization of a protein referred to as SAS0754. The size of SAS0754 is 340 amino acids and the gene sequence is 1023 nucleotides. The hypothetical function of this protein is that it is an extracellular matrix binding …
A Convenient Synthesis Of 2,6-Dichlorohomonicotinic Acid, Chase Buchanan, Richard W. Fitch
A Convenient Synthesis Of 2,6-Dichlorohomonicotinic Acid, Chase Buchanan, Richard W. Fitch
Symposium 2012
In our synthetic efforts toward the alkaloid phantasmidine, we required a convenient source of the title compound. Herein, we describe a short synthesis of 2,6-dichlorohomonicotinic acid by direct allylation of 2,6-dichloropyridine with LDA/allyl chloride, followed by permanganate oxidation of the side chain [figure1]. Yields for the allylation are high, while permanganate oxidation required more adjustment. Successful conditions require the modest acidification of the mixture with acetic acid and cleanup by acid base workup. No chromatography is needed.
Convenient Parallel Synthesis Of Alkyl- And Aryl-S-Tert-Butyl Thiothers, Rebecca Norcross, Jessica Stanfield, Richard W. Fitch
Convenient Parallel Synthesis Of Alkyl- And Aryl-S-Tert-Butyl Thiothers, Rebecca Norcross, Jessica Stanfield, Richard W. Fitch
Symposium 2012
While preparing novel cysteine derivatives as oxidation catalysts, we needed S-tert-butylcysteine. We also examined acid-promoted tert-butylation of thiols using tert-butanol as reagent and solvent. While cysteine and aminoethanethiol work well using tBuOH in 4M HCl, other thiols fail in the aqueous environment and aerobic conditions. We examined a variety of aliphatic and aromatic thiols in tBuOH with H2SO4 catalysis and found that argon sparging and the use of 1 eq of acid led to good yields in a parallel format.
Diffusion And Random Walks, Lewis Ludwig, Annabel Edwards
Diffusion And Random Walks, Lewis Ludwig, Annabel Edwards
Faculty Publications
No abstract provided.