Department of Chemistry and Chemical Biology

Permanent URI for this community

https://hdl.handle.net/1805/4562

Browse

Now showing 1 - 10 of 243

7 Things You Should Know About Virtual Labs
(2020-08-14) Badillo, Joseph; Londino-Smolar, Gina; Savvides, Philippos; Chemistry and Chemical Biology, School of Science
Virtual labs are interactive, digital simulations of activities that typically take place in physical laboratory settings.
A 24-year longitudinal study on a STEM gateway general chemistry course and the reduction of achievement disparities
(Public Library of Science, 2025-02-26) Basu, Partha; Malik, David J.; Graunke, Steven; Chemistry and Chemical Biology, School of Science
The "First Year Experience" is a critical component of retention of STEM majors. Often, general chemistry has been labeled as a "gatekeeper" course for STEM careers due to a high attrition rate and a course that leads to increased time for graduation when students are inadequately prepared. We demonstrate that the active learning strategy Peer-Led Team Learning (PLTL) model increases student retention (%DFW calculated from earned grades A through F plus withdrawals, W) and success (%ABC calculated from earned grades A through F). We have analyzed approximately 24 years of data in general chemistry I (~20,000 students), using Analysis of Covariance (ANCOVA), which showed progressive, significant improvement in both student success and completion metrics. A Hierarchical Linear Modeling (HLM), using a combination of course and student-level variables, demonstrated the impact of PLTL on internal exam metrics and overall course grades. Further, HLM modeling assessed the impact of PLTL controlling for various student demographics. PLTL strongly impacted URM student completion rates to a greater degree than well-represented students, reducing the URM/non-URM achievement gap.
A systematic study of the absorbance of the nitro functional group in the vacuum UV region
(Elsevier, 2021-11-15) Cruse, Courtney A.; Goodpaster, John V.; Chemistry and Chemical Biology, School of Science
The nitro functional group (NO) features strongly in compounds such as explosives, pharmaceuticals, and fragrances. However, its gas phase absorbance characteristics in the vacuum UV region (120-200 nm) have not been systematically studied. Gas chromatography/vacuum UV spectroscopy (GC/VUV) was utilized to study the gas phase VUV spectra of various nitrated compounds (e.g., nitrate esters (-R-O-NO), nitramines (R-N-NO), nitroaromatics (Ar-NO), and nitroalkanes (R-NO)). The nitro absorption maximum appeared over a wide range (170-270 nm) and its wavelength and intensity were highly dependent upon the structure of the rest of the molecule. For example, the nitroalkanes exhibited a trend in that the ratio of the relative absorption intensity between these two absorption features between the alkyl group (<150 nm) and the nitro group (200 nm) increases as the molecular weight increases. It was observed that the addition of multiple nitro functional groups on benzene or toluene resulted in an increase in intensity and blue shift from approximately 240 nm-210 nm. Nitrate esters exhibited an absorption between 170 nm and 210 nm and absorbance increased with increasing nitrogen content. The relative diversity of the spectra obtained was analyzed by Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA). These calculations revealed that the spectra of all the compounds analyzed could be reliably differentiated without any misclassifications.
Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching
(The Royal Society of Chemistry, 2019-08-15) Pan, Xiaoliang; Li, Pengfei; Ho, Junming; Pu, Jingzhi; Mei, Ye; Shao, Yihan; Chemistry and Chemical Biology, School of Science
An efficient and accurate reference potential simulation protocol is proposed for producing ab initio quantum mechanical molecular mechanical (AI-QM/MM) quality free energy profiles for chemical reactions in a solvent or macromolecular environment. This protocol involves three stages: (a) using force matching to recalibrate a semi-empirical quantum mechanical (SE-QM) Hamiltonian for the specific reaction under study; (b) employing the recalibrated SE-QM Hamiltonian (in combination with molecular mechanical force fields) as the reference potential to drive umbrella samplings along the reaction pathway; and (c) computing AI-QM/MM energy values for collected configurations from the sampling and performing weighted thermodynamic perturbation to acquire AI-QM/MM corrected reaction free energy profile. For three model reactions (identity SN2 reaction, Menshutkin reaction, and glycine proton transfer reaction) in aqueous solution and one enzyme reaction (Claisen arrangement in chorismate mutase), our simulations using recalibrated PM3 SE-QM Hamiltonians well reproduced QM/MM free energy profiles at the B3LYP/6–31G* level of theory all within 1 kcal/mol with a 20 to 45 fold reduction in the computer time.
Accelerating ab initio QM/MM Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semi-empirical QM/MM Hamiltonian
(American Chemical Society, 2022-06-02) Pan, Xiaoliang; Van, Richard; Epifanovsky, Evgeny; Liu, Jian; Pu, Jingzhi; Nam, Kwangho; Shao, Yihan; Chemistry and Chemical Biology, School of Science
Molecular dynamics (MD) simulations employing ab initio quantum mechanical and molecular mechanical (ai-QM/MM) potentials are considered to be the state of the art, but the high computational cost associated with the ai-QM calculations remains a theoretical challenge for their routine application. Here, we present a modified protocol of the multiple time step (MTS) method for accelerating ai-QM/MM MD simulations of condensed-phase reactions. Within a previous MTS protocol [Nam J. Chem. Theory Comput. 2014, 10, 4175], reference forces are evaluated using a low-level (semiempirical QM/MM) Hamiltonian and employed at inner time steps to propagate the nuclear motions. Correction forces, which arise from the force differences between high-level (ai-QM/MM) and low-level Hamiltonians, are applied at outer time steps, where the MTS algorithm allows the time-reversible integration of the correction forces. To increase the outer step size, which is bound by the highest-frequency component in the correction forces, the semiempirical QM Hamiltonian is recalibrated in this work to minimize the magnitude of the correction forces. The remaining high-frequency modes, which are mainly bond stretches involving hydrogen atoms, are then removed from the correction forces. When combined with a Langevin or SIN(R) thermostat, the modified MTS-QM/MM scheme remains robust with an up to 8 (with Langevin) or 10 fs (with SIN(R)) outer time step (with 1 fs inner time steps) for the chorismate mutase system. This leads to an over 5-fold speedup over standard ai-QM/MM simulations, without sacrificing the accuracy in the predicted free energy profile of the reaction.
Achieving biosensing at attomolar concentrations of cardiac troponin T in human biofluids by developing a label-free nanoplasmonic analytical assay
(RSC, 2017) Liyanage, Thaksila; Sangha, Andeep; Sardar, Rajesh; Chemistry and Chemical Biology, School of Science
Acute myocardial infarction (heart attack) is the fifth leading cause of death in the United States (Dariush et al., Circulation, 2015, 131, e29–e322). This highlights the need for early, rapid, and sensitive detection of its occurrence and severity through assaying cardiac biomarkers in human fluids. Herein we report chip-based fabrication of the first label-free, nanoplasmonic biosensor to assay cardiac troponin T (cTnT) in human biofluids (plasma, serum, and urine) with high specificity. The sensing mechanism is based on the adsorption model that measures the localized surface plasmon resonance (LSPR) wavelength shift of anti-cTnT functionalized gold triangular nanoprisms (Au TNPs) induced by a change of their local dielectric environment upon binding of cTnT. We demonstrate that controlled manipulation of the sensing volume and decay length of Au TNPs together with an appropriate surface functionalization and immobilization of anti-cTnT onto TNPs allows us to achieve a limit of detection (LOD) of our cTnT assay at attomolar concentration (∼15 aM) in human plasma. This LOD is at least 50-fold more sensitive than that of other label-free techniques. Furthermore, we demonstrate excellent sensitivity of our sensors in human serum and urine. Importantly, our chip-based fabrication strategy is extremely reproducible. We believe our powerful analytical tool for detection of cTnT directly in human biofluids using this highly reproducible, label-free LSPR sensor will have great potential for early diagnosis of heart attack and thus increase patients’ survival rate.
Advances in Optical Contrast Agents for Medical Imaging: Fluorescent Probes and Molecular Imaging
(MDPI, 2025-03-18) Tripathi, Divya; Hardaniya, Mayurakshi; Pande, Suchita; Maity, Dipak; Chemistry and Chemical Biology, School of Science
Optical imaging is an excellent non-invasive method for viewing visceral organs. Most importantly, it is safer as compared to ionizing radiation-based methods like X-rays. By making use of the properties of photons, this technique generates high-resolution images of cells, molecules, organs, and tissues using visible, ultraviolet, and infrared light. Moreover, optical imaging enables real-time evaluation of soft tissue properties, metabolic alterations, and early disease markers in real time by utilizing a variety of techniques, including fluorescence and bioluminescence. Innovative biocompatible fluorescent probes that may provide disease-specific optical signals are being used to improve diagnostic capabilities in a variety of clinical applications. However, despite these promising advancements, several challenges remain unresolved. The primary obstacle includes the difficulty of developing efficient fluorescent probes, and the tissue autofluorescence, which complicates signal detection. Furthermore, the depth penetration restrictions of several imaging modalities limit their use in imaging of deeper tissues. Additionally, enhancing biocompatibility, boosting fluorescent probe signal-to-noise ratios, and utilizing cutting-edge imaging technologies like machine learning for better image processing should be the main goals of future research. Overcoming these challenges and establishing optical imaging as a fundamental component of modern medical diagnoses and therapeutic treatments would require cooperation between scientists, physicians, and regulatory bodies.
Amide Synthesis through the In Situ Generation of Chloro- and Imido-Phosphonium Salts
(ACS, 2020-06) Irving, Charles D.; Floreancig, Jack T.; Laulhé, Sébastien; Chemistry and Chemical Biology, School of Science
We describe a methodology for the amidation of carboxylic acids by generating phosphonium salts in situ from N-chlorophthalimide and triphenylphosphine. Aliphatic, benzylic, and aromatic carboxylic acids can be transformed into their amide counter parts using primary and secondary amines. This functional group interconversion is achieved at room temperature in good to excellent yields. Mechanistic work shows the in situ formation of chloro- and imido-phosphonium salts that react as activating agents for carboxylic acids and generate an acyloxy-phosphonium species.
Amplification-Free, High-Throughput Nanoplasmonic Quantification of Circulating MicroRNAs in Unprocessed Plasma Microsamples for Earlier Pancreatic Cancer Detection
(ACS, 2023-03) Masterson, Adrianna N.; Chowdhury, Nayela N.; Yang, Yue; Yip-Schneider, Michele T.; Hati, Sumon; Gupta, Prashant; Cao, Sha; Wu, Huangbing; Schmidt, C. Max; Fishel, Melissa L.; Sardar, Rajesh; Chemistry and Chemical Biology, School of Science
Pancreatic ductal adenocarcinoma (PDAC) is a deadly malignancy that is often detected at an advanced stage. Earlier diagnosis of PDAC is key to reducing mortality. Circulating biomarkers such as microRNAs are gaining interest, but existing technologies require large sample volumes, amplification steps, extensive biofluid processing, lack sensitivity, and are low-throughput. Here, we present an advanced nanoplasmonic sensor for the highly sensitive, amplification-free detection and quantification of microRNAs (microRNA-10b, microRNA-let7a) from unprocessed plasma microsamples. The sensor construct utilizes uniquely designed −ssDNA receptors attached to gold triangular nanoprisms, which display unique localized surface plasmon resonance (LSPR) properties, in a multiwell plate format. The formation of −ssDNA/microRNA duplex controls the nanostructure–biomolecule interfacial electronic interactions to promote the charge transfer/exciton delocalization processes and enhance the LSPR responses to achieve attomolar (10–18 M) limit of detection (LOD) in human plasma. This improve LOD allows the fabrication of a high-throughput assay in a 384-well plate format. The performance of nanoplasmonic sensors for microRNA detection was further assessed by comparing with the qRT-PCR assay of 15 PDAC patient plasma samples that shows a positive correlation between these two assays with the Pearson correlation coefficient value >0.86. Evaluation of >170 clinical samples reveals that oncogenic microRNA-10b and tumor suppressor microRNA-let7a levels can individually differentiate PDAC from chronic pancreatitis and normal controls with >94% sensitivity and >94% specificity at a 95% confidence interval (CI). Furthermore, combining both oncogenic and tumor suppressor microRNA levels significantly improves differentiation of PDAC stages I and II versus III and IV with >91% and 87% sensitivity and specificity, respectively, in comparison to the sensitivity and specificity values for individual microRNAs. Moreover, we show that the level of microRNAs varies substantially in pre- and post-surgery PDAC patients (n = 75). Taken together, this ultrasensitive nanoplasmonic sensor with excellent sensitivity and specificity is capable of assaying multiple biomarkers simultaneously and may facilitate early detection of PDAC to improve patient care.
An Overview of α-Aminoalkyl Radical Mediated Halogen-Atom Transfer
(Wiley, 2023-11-08) Sachidanandan, Krishnakumar; Niu, Ben; Laulhé, Sébastien; Chemistry and Chemical Biology, School of Science
The merging of photocatalysis with halogen-atom transfer (XAT) processes has proven to be a versatile tool for the generation of carbon-centered radicals in organic synthesis. XAT processes are unique in that they generate radicals without requiring the use of strong reductants necessary for the traditional single electron transfer (SET) activation of halides. Pathways to achieve XAT in synthetic applications can be categorized into three major sections: i) heteroatom-based activators, ii) metal-based activators, and iii) carbon-based activators among which α-aminoalkyl radicals have taken the center stage. Access to these α-aminoalkyl radicals as XAT reagents has gained significant attention in the past few years due to the robustness of the reactions, the simplicity of the reagents required, and the broadness of their applications. Generation of these α-aminoalkyl radicals is simply achieved through the single electron oxidation of tertiary amines, which after deprotonation at the α-position generates the α-aminoalkyl radicals. Due to the wide scope of tertiary amines available and the tunable nucleophilicity of α-aminoalkyl radical formed, this strategy has become an attractive alternative to heteroatom/metal-based radicals for XAT. In this minireview, we focus our attention on recent (2020–2023) developments and uses of this robust technology to mediate XAT processes.

Browse

Browsing Department of Chemistry and Chemical Biology by Title

Results Per Page

Sort Options