Browsing by Author "Basu, Partha"

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    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.
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    Active Site Characterization of a Campylobacter jejuni Nitrate Reductase Variant Provides Insight into the Enzyme Mechanism
    (ACS, 2024) Yang, Jing; Mintmier, Breeanna; KC, Khadanand; Metzger, Mikayla C.; Radhakrishnan, Manohar; McGarry, Jennifer; Wilcoxen, Jarett; Basu, Partha; Kirk, Martin L.; Chemistry and Chemical Biology, School of Science
    Mo K-edge X-ray absorption spectroscopy (XAS) is used to probe the structure of wild-type Campylobacter jejuni nitrate reductase NapA and the C176A variant. The results of extended X-ray absorption fine structure (EXAFS) experiments on wt NapA support an oxidized Mo(VI) hexacoordinate active site coordinated by a single terminal oxo donor, four sulfur atoms from two separate pyranopterin dithiolene ligands, and an additional S atom from a conserved cysteine amino acid residue. We found no evidence of a terminal sulfido ligand in wt NapA. EXAFS analysis shows the C176A active site to be a 6-coordinate structure, and this is supported by EPR studies on C176A and small molecule analogs of Mo(V) enzyme forms. The SCys is replaced by a hydroxide or water ligand in C176A, and we find no evidence of a coordinated sulfhydryl (SH) ligand. Kinetic studies show that this variant has completely lost its catalytic activity toward nitrate. Taken together, the results support a critical role for the conserved C176 in catalysis and an oxygen atom transfer mechanism for the catalytic reduction of nitrate to nitrite that does not employ a terminal sulfido ligand in the catalytic cycle.
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    Campylobacter jejuni Periplasmic Nitrate Reductase NapA as a Medium for Elucidating Molybdenum Cofactor Reactivity
    (2025-05) Metzger, Mikayla; Basu, Partha; Blacklock, Brenda; Webb, Ian; Pu, Jingzhi
    Periplasmic nitrate reductase NapA is found within many gram-negative bacteria and catalyzes oxygen atom transfer reactions. NapA utilizes nitrate as a terminal electron acceptor in place of oxygen in low-air conditions, such as in the human gastrointestinal tract. Within the scope of this thesis, NapA from Campylobacter jejuni is primarily focused due to its reputation in poultry husbandry and antibiotic resistance. Although nitrate reduction aids in pathogen survival, it is also a geochemically essential process. Many enzymes closely related to NapA are involved in geochemical cycling and contain the same active site ligand structure. The ligand within these enzymes is called molybdenum cofactor, or Moco. The structure of the enzyme is influential on reactivity of the molybdenum cofactor. The rate of catalysis, electron and proton transfer, and substrate preference can be affected by the amino acids surrounding Moco. Elucidating details of Moco reactivity aids in understanding bacteria in relation to human health and geochemical cycles. The primary tools throughout this research were site-directed mutagenesis and steady-state kinetics.
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    Cervical cancer prevention and care in HIV clinics across sub-Saharan Africa: results of a facility-based survey
    (Wiley, 2024) Asangbeh-Kerman, Serra Lem; Davidović, Maša; Taghavi, Katayoun; Dhokotera, Tafadzwa; Manasyan, Albert; Sharma, Anjali; Jaquet, Antoine; Musick, Beverly; Twizere, Christella; Chimbetete, Cleophas; Murenzi, Gad; Tweya, Hannock; Muhairwe, Josephine; Wools-Kaloustian, Kara; Technau, Karl-Gunter; Anastos, Kathryn; Yotebieng, Marcel; Jousse, Marielle; Ezechi, Oliver; Orang’o, Omenge; Bosomprah, Samuel; Boni, Simon Pierre; Basu, Partha; Bohlius, Julia; IeDEA; Biostatistics and Health Data Science, Richard M. Fairbanks School of Public Health
    Introduction: To eliminate cervical cancer (CC), access to and quality of prevention and care services must be monitored, particularly for women living with HIV (WLHIV). We assessed implementation practices in HIV clinics across sub-Saharan Africa (SSA) to identify gaps in the care cascade and used aggregated patient data to populate cascades for WLHIV attending HIV clinics. Methods: Our facility-based survey was administered between November 2020 and July 2021 in 30 HIV clinics across SSA that participate in the International epidemiology Databases to Evaluate AIDS (IeDEA) consortium. We performed a qualitative site-level assessment of CC prevention and care services and analysed data from routine care of WLHIV in SSA. Results: Human papillomavirus (HPV) vaccination was offered in 33% of sites. Referral for CC diagnosis (42%) and treatment (70%) was common, but not free at about 50% of sites. Most sites had electronic health information systems (90%), but data to inform indicators to monitor global targets for CC elimination in WLHIV were not routinely collected in these sites. Data were collected routinely in only 36% of sites that offered HPV vaccination, 33% of sites that offered cervical screening and 20% of sites that offered pre-cancer and CC treatment. Conclusions: Though CC prevention and care services have long been available in some HIV clinics across SSA, patient and programme monitoring need to be improved. Countries should consider leveraging their existing health information systems and use monitoring tools provided by the World Health Organization to improve CC prevention programmes and access, and to track their progress towards the goal of eliminating CC.
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    Design, Synthesis, and Structure of Copper Dithione Complexes: Redox‐Dependent Charge Transfer
    (Wiley, 2019-12) Colston, Kyle J.; Dille, Sara A.; Mogesa, Benjamin; Astashkin, Andrei V.; Brant, Jacilynn A.; Zeller, Matthias; Basu, Partha; Chemistry and Chemical Biology, School of Science
    Redox‐active ligands impart versatility in transition metal complexes, which are attractive for photosensitizers, dye sensitized solar cells, photothermal therapy, etc. Dithiolene (Dt) ligands can transition between fully reduced and fully oxidized states. Herein, we report the syntheses, characterization, crystal structures and electronic properties of four [Cu(R2Dt0)2]+/2+ (R = Me, iPr) complexes, [Cu(iPr2Dt0)2][PF6] (1a), [Cu(iPr2Dt0)2][PF6]2 (1b), and [Cu(Me2Dt0)2][PF6] (2a), [Cu(Me2Dt0)2][PF6]2 (2b), where iPr2Dt0 = N,N′‐diisopropyl‐1,2‐piperazine dithione and Me2Dt0 = N,N′‐dimethyl‐1,2‐piperazine dithione. In addition, the molecular structure of [Cu(iPr2Dt0)2][BF4]2(1c) is also reported. Complexes 1a and 2a crystallized in the triclinic, P1 space group, and 1c crystallized in the monoclinic crystal system, space group C2/c. The single‐crystal X‐ray diffraction measurements show that the Cu(I) complexes have a distorted tetrahedral geometry, whereas the Cu(II) complex exhibits a true square‐planar geometry. Cu(I) complexes exhibit a low energy charge‐transfer band (450–650 nm), which are not observed in Cu(II) complexes. Electrochemical studies of these complexes show both ligand‐ and metal‐based redox couples.
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    Dithione, the antipodal redox partner of ene-1,2-dithiol ligands and their metal complexes
    (Elsevier, 2020) Basu, Partha; Colston, Kyle J.; Mogesa, Benjamin; Chemistry and Chemical Biology, School of Science
    Defining the oxidation state of the central atom in a coordination compound is fundamental in understanding the electronic structure and provides a starting point for elucidating molecular properties. The presence of non-innocent ligand(s) can obscure the oxidation state of the central atom as the ligand contribution to the electronic structure is difficult to ascertain. Redox-active ligands, such as dithiolene ligands, are well known non-innocent ligands that can exist in both a fully reduced (Dt2−) and fully oxidized (Dt0) states. Complexes containing the fully oxidized dithione state of the ligand are uncommon and only a few have been completely characterized. Dithione ligands are of interest due to their electron-deficient nature and ability to act as an electron acceptor for more electron-rich moieties, such as other dithiolene ligands or metal centers. This article focuses the syntheses, structures, and metal coordination, particularly coordination compounds, of dithione ligands. Various examples of mono, bis, and tris dithione complexes are discussed.
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    Influence of the Ligand-Field on EPR Parameters of cis- and trans-Isomers in MoV Systems Relevant to Molybdenum Enzymes: Experimental and Density Functional Theory Study
    (Elsevier, 2023) Nemykin, Victor N.; Sabin, Jared R.; Kail, Brian W.; Upadhyay, Anup; Hendrich, Michael P.; Basu, Partha; Chemistry and Chemical Biology, School of Science
    The electron paramagnetic resonance (EPR) investigation of mononuclear cis- and trans-(L1O)MoOCl2 complexes [L1OH = bis(3,5-dimethylpyrazolyl)-3-tert-butyl-2-hydroxy-5-methylphenyl)methane] reveals a significant difference in their spin Hamiltonian parameters which reflect different equatorial and axial ligand fields created by the heteroscorpionate donor atoms. Density functional theory (DFT) was used to calculate the values of principal components and relative orientations of the g and A tensors, and the molecular framework in four pairs of isomeric mononuclear oxo‑molybdenum(V) complexes (cis- and trans-(L1O)MoOCl2, cis,cis- and cis,trans-(L-N2S2)MoOCl [L-N2S2H2 = N,N'-dimethyl-N,N'-bis(mercaptophenyl)ethylenediamine], cis,cis- and cis,trans-(L-N2S2)MoO(SCN), and cis- and trans-[(dt)2MoO(OMe)]2- [dtH2 = 2,3-dimercapto-2-butene]). Scalar relativistic DFT calculations were conducted using three different exchange-correlation functionals. It was found that the use of hybrid exchange-correlation functional with 25% of the Hartree-Fock exchange leads to the best quantitative agreement between theory and experiment. A simplified ligand-field approach was used to analyze the influence of the ligand fields in all cis- and trans-isomers on energies and contributions of molybdenum d-orbital manifold to g and A tensors and relative orientations. Specifically, contributions that originated from the spin-orbit coupling of the dxz, dyz, and dx2-y2 orbitals into the ground state have been discussed. The new findings are discussed in the context of the experimental data of mononuclear molybdoenzyme, DMSO reductase.
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    Interligand communication in a metal mediated LL′CT system – a case study
    (RSC, 2021) Dille, Sara A.; Colston, Kyle J.; Ratvasky, Stephen C.; Pu, Jingzhi; Basu, Partha; Chemistry and Chemical Biology, School of Science
    A series of oxo-Mo(IV) complexes, [MoO(Dt2−)(Dt0)] (where Dt2− = benzene-1,2-dithiol (bdt), toluene-3,4-dithiol (tdt), quinoxaline-2,3-dithiol (qdt), or 3,6-dichloro-benzene-1,2-dithiol (bdtCl2); Dt0 = N,N′-dimethylpiperazine-2,3-dithione (Me2Dt0) or N,N′-diisopropylpiperazine-2,3-dithione (iPr2Dt0)), possessing a fully oxidized and a fully reduced dithiolene ligand have been synthesized and characterized. The assigned oxidation states of coordinated dithiolene ligands are supported with spectral and crystallographic data. The molecular structure of [MoO(tdt)(iPr2Dt0)] (6) demonstrates a large ligand fold angle of 62.6° along the S⋯S vector of the Dt0 ligand. The electronic structure of this system is probed by density functional theory (DFT) calculations. The HOMO is largely localized on the Dt2− ligand while virtual orbitals are mostly Mo and Dt0 in character. Modeling the electronic spectrum of 6 with time dependent (TD) DFT calculations attributes the intense low energy transition at ∼18 000 cm−1 to a ligand-to-ligand charge transfer (LL′CT). The electron density difference map (EDDM) for the low energy transition depicts the electron rich Dt2− ligand donating charge density to the redox-active orbitals of the electron deficient Dt0 ligand. Electronic communication between dithiolene ligands is facilitated by a Mo-monooxo center and distortion about its primary coordination sphere.
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    Investigating the Photophysical Properties of Potential Organic Lead Sensors
    (2023) Quinones, Carlos; Basu, Partha; Deng, Yongming; Pu , Jingzhi
    LeadGlow (LG) was reported in 2009 for its ability to both sensitively and selectively detect Pb2+ in aqueous solutions. Utilizing the synthetic approach of LG, it is possible to generate a class of novel fluorophores. A derivative of first-generation LG was synthesized and reported here for the first time, intuitively named LG2. Both compounds contain interesting photophysical properties that have not been extensively researched prior to this work. Because of this, photophysical properties of both LG and LG2 are unveiled here for the first time. These properties were investigated by determinations of quantum yield (QY), average fluorescence lifetime, and DFT calculations. LG was found to have a higher QY (0.057) than LG2 (0.011); however, LG2 displays an average fluorescence lifetime (3.186 ns) 5x greater than that of LG. Both LG and LG2 are synthesized via Hg2+-facilitated desulfurization of their respective thiocarbonyls, resulting in a turn-on fluorescence feature. The thiocarbonyl-containing fluorophores (SLG and SLG2) display quenched fluorescence compared to their oxo-derivatives (LG and LG2), this work attempts to investigate the mechanism(s) responsible. A whole class of LeadGlow compounds can be synthesized and could be potentially used as fluorescence-based sensors.
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    Kinetic consequences of the endogenous ligand to molybdenum in the DMSO reductase family: a case study with periplasmic nitrate reductase
    (Springer, 2021-02) Mintmier, Breeanna; McGarry, Jennifer M.; Bain, Daniel J.; Basu, Partha; Chemistry and Chemical Biology, School of Science
    The molybdopterin enzyme family catalyzes a variety of substrates and plays a critical role in the cycling of carbon, nitrogen, arsenic, and selenium. The dimethyl sulfoxide reductase (DMSOR) subfamily is the most diverse family of molybdopterin enzymes and the members of this family catalyze a myriad of reactions that are important in microbial life processes. Enzymes in the DMSOR family can transform multiple substrates; however, quantitative information about the substrate preference is sparse, and, more importantly, the reasons for the substrate selectivity are not clear. Molybdenum coordination has long been proposed to impact the catalytic activity of the enzyme. Specifically, the molybdenum-coordinating residue may tune substrate preference. As such, molybdopterin enzyme periplasmic nitrate reductase (Nap) is utilized as a vehicle to understand the substrate preference and delineate the kinetic underpinning of the differences imposed by exchanging the molybdenum ligands. To this end, NapA from Campylobacter jejuni has been heterologously overexpressed, and a series of variants, where the molybdenum coordinating cysteine has been replaced with another amino acid, has been produced. The kinetic properties of these variants are discussed and compared with those of the native enzyme, providing quantitative information to understand the function of the molybdenum-coordinating residue.