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Njoo Research @ ASDRP

Chemistry & Chemical Biology

Our lab utilizes computational chemistry methods, including density functional theory (DFT) to run ab initio quantum mechanical calculations with predictive power on chemical systems. We also utilize molecular dynamics simulations to better understand macromolecular behavior. 

Computational Chemistry

We are interested in the synthesis of biologically-active molecules from readily-available and renewable feedstocks. Additionally, we are interested in the utilization of green chemistry principles in synthetic chemistry, and in regioselectivity of common organic reactions.

Targeted Organic Synthesis & Catalysis

We are big fans of spectroscopy as a tool for probing molecular-level phenomena. We utilize UV-VIS, NMR (nuclear magnetic resonance), FT-IR (Fourier transform infrared spectroscopy) and fluorescence spectroscopy.

Molecular Spectroscopy

We are interested in understanding UV-VIS behavior of novel azo dyes synthesized through a diazonium coupling reaction from both experimental values and ab initio excited state theoretical calculations. Further, we seek to investigate the effects of solvents on UV-VIS absorbance spectra.

Parallel Empirical - Theoretical Characterization of Novel Azo Dyes

In this research, we use a combination of computational approaches (transition state theory, saddle point scans) and timescale 1H NMR analysis to understand the mechanism of chlorination of terpenes under different halogenating conditions.

Selective Radical-Initiated Chlorination of Asymmetric Terpenes by Tricholoisocyanuric acid

We are interested in understanding the rates and selectivities of various protease enzymes on N-acetylated amino acids and synthetic small molecule peptide mimics. The structure-activity relationship elucidated here can provide insight into the role of proteases in metabolite or drug degradation.

Kinetics and Selectivity of Amide Hydrolysis in Proteases

We utilize a combination of spectroscopy and combinatorial synthesis, as well as computational justification from transition state DFT calculations to understand and develop Lewis Acid catalysts for 4+2 cycloaddition reactions. Further, DFT is utilized to justify regiocontrol over the diels-alder adducts. 

Transition State Analysis of Iron (III) Catalyzed Diels-Alder and Hetero-DA 4+2 Cycloaddition Reactions

Here, we aim to develop a green and cost-effective total synthesis route for etoposide, a molecule first isolated from the wild mandrake, and which is clinically used in the treatment of various types of cancer. Furthermore, we aim to synthesize a library of Etoposide analogs and screen them for activity.

Synthetic Studies Towards the Total Synthesis of Etoposide

Aβ-42 is an amyloidogenic protein linked with the progression of Alzheimer's disease. This project, in conjunction with the Brah research group, uses a combined computational-synthesis approach. Molecular dynamics simulations are used to gauge inhibitor binding, while the modeled inhibitors are synthesized using natural product precursors.

Synthesis of Aggregation Inhibitors of Aβ-42 

This research project aims to understand the effect of solvents and nonideal solutes on the stability, structure, and biophysical properties of sodium dodecyl sulfate (SDS) micelles. We utilize cylic voltammetry, spectroscopy, and fluorescent probes to eludicate the physical constraints within micellular systems. 

Solvent Effect Stabilization of SDS Micelles

Lactase is an enzyme common to many mammals that catalyzes the hydrolysis of 1,4-β-glycosidic bonds in lactose. In collaboration with the Brah research group, we investigate the efficacy of a library of synthetic glycoside acetal analogs in affecting the action of lactase, and the specific roles of individual amino acid residues in disacchariade binding. 

Synthesis and Competitve Inhibition Action of Glycoside Acetals on Lactases 

The effect of the ligand field on electronic structure of transition metal complexes is investigated using cyclic voltammetry and DFT calculations, towards the purpose of the development of efficient catalysts for synthesis, and for altering the electrochemical properties of the metal towards materials. 

Taming the First Transition: Development of Dicarbonyl Ligands for First-Transition Metal Applications in Electrochemistry & Catalysis

With continual development of drug resistance, there is a continual need to develop new and novel antibiotics. We are interested in the green, scalable semisynthesis of a diverse class of aminoglycoside compounds with potential antimicrobial activity derived from natural products such as glucosamine. 

Synthesis and Antimicrobial Activity of Natural Product Aminoglycoside Derivatives

Research

 

Past Work

 

Adrian, M.; Gowda, A.; Sharma, A.; & Wei, R. (2018). The Theoretical-Empirical Role of Transition Metals Fe3+ , Cu2+, and Ni2+ in the Efficiency of Nucleophilic Addition of Salicylic Acid to Acetic Anhydride. ASDRP Communications 1(1), 63-68.

Anna, A.; Cen, L.; & Guo, C. (2018). Combinatorial Synthesis and Characterization of Azo Dyes: A Dual Experimental-Theoretical Approach. ASDRP Communications 1(1), 17-37.

Balu, N.; Chang, W.; Huang, J.; & Yallampalli, H. (2018). Synthesis and Antibiotic Efficacy of p-(N,N-dimethyl) and 4-hydroxy-3-methoxy hydrazone Compounds. ASDRP Communications 1(1), 2-11.

Boominathan, A. & Xie, M. (2018). Mechanistic Studies of Azo Dye Oxidation via Hypochlorite and Persulfate. ASDRP Communications 1(1), 38-53.

Chou, H. & Wu, J. (2018). Thermodynamics of Ligand Exchange in Transition Metal Complexes: A Comparison of Experimental and Time Dependent-Density Functional Theoretical Calculations. ASDRP Communications 1(1), 76-87.

Dong, A.; Nayak, A.; & Rajaram, V. (2018). Synthesis and Combustion Efficiency of Trans-esterified Methyl Ester Biodiesels. ASDRP Communications 1(1), 93-98.

Han, A. Merugulmala, H.; Ramapriyan, G.; & Yelugoti, S.G. (2018). Synthesis, Characterization, and Antibiotic Efficacy of a Combinatorial Library of Commercially-Relevant Esters. ASDRP Communications 1(1), 69-75.

Jain, T., Murali, M.; Shah, A.; & Yu, A. (2018). The Small Molecule Inhibition of Alpha-Amylase: Mechanistic Studies in Michaelis-Menten Kinetics. ASDRP Communications 1(1), 12-16.

Sista, S. & Lee, T. (2018). Theoretical and Empirical Spectroscopic Studies of Solvent Effects and Fish Oil ⍵-6/⍵-3 Ratio Effects in Fluorescence Quantum Yields. ASDRP Communications 1(1), 88-92.

Tools & Techniques

 

Targeted Organic Synthesis of Bioactive Molecules

Our research centers around organic synthesis and understanding the utility of various synthetic and semisynthetic molecules in biological contexts. We are also interested in the development of green, scalable synthetic routes using readily available feedstocks.

Nuclear Magnetic Resonance (NMR) Spectroscopy

We utilize nuclear magnetic resonance (NMR) spectroscopy for a variety of functionalities, including characterization of synthesis products, identification of intermediates, detection of trace compounds, and solvent effects on chemical equilibria.

UV-Visible & Fluorescence Spectroscopy

We are fascinated by the photochemical behavior of various compounds and extensively use UV-VIS & fluorescence spectroscopy to probe electronic structure. Further, we are interested in the development of novel chromophoic materials

Chemical Biology: Enzyme Kinetics & Ligand Interactions

Several of our research projects are oriented around enzymology and interactions between protein structure and ligand binding. We have several collaborations with the Brah lab in order to investigate the role of small molecules on biological systems.

Computational Chemistry: Density Functional Theory

We utilize ORCA, a semi-empirical, ab initio density functional theory package that allows for computational analysis at various levels of theory. We use DFT for excited electronic state predictions, vibrational analysis, and energy topography screening.

Organometallic Catalysis & Ligand Field Theory

Our research harnesses the catalytic capabilities of complexes of first-transition metals such as copper, nickel, iron, and cobalt to drive site-directed functionalization. Specifically, we are focused on iron-arene complexes and their role in driving Lewis-acid catalyzed oxidation.

Collaborations

 

Sulfhydryl proteases use a cysteine (R = -CH2SH) as a catalytic residue in the hydrolysis of bonds. Here, we screen small molecules for inhibitory activity on two common sulfhydryl proteases, and investigate the effect of thiol functionalization on the activity of the active site residues. 

Small Molecule Inhibition of Sulfhydryl Proteases via Thiol Functionalization

Aβ-42 is an amyloidogenic protein linked with the progression of Alzheimer's disease. This project, in conjunction with the Brah research group, uses a combined computational-synthesis approach. Molecular dynamics simulations are used to gauge inhibitor binding, while the modeled inhibitors are synthesized using natural product precursors.

Synthesis of Aggregation Inhibitors of Aβ-42 

This research project aims to understand the effect of solvents and nonideal solutes on the stability, structure, and biophysical properties of sodium dodecyl sulfate (SDS) micelles. We utilize cylic voltammetry, spectroscopy, and fluorescent probes to eludicate the physical constraints within micellular systems. 

Solvent Effect Stabilization of SDS Micelles

Lactase is an enzyme common to many mammals that catalyzes the hydrolysis of 1,4-β-glycosidic bonds in lactose. In collaboration with the Brah research group, we investigate the efficacy of a library of synthetic glycoside acetal analogs in affecting the action of lactase, and the specific roles of individual amino acid residues in disacchariade binding. 

Synthesis and Competitve Inhibition Action of Glycoside Acetals on Lactases 

With continual development of drug resistance, there is a continual need to develop new and novel antibiotics. We are interested in the green, scalable semisynthesis of a diverse class of aminoglycoside compounds with potential antimicrobial activity derived from natural products such as glucosamine. 

Synthesis and Antimicrobial Activity of Natural Product Aminoglycoside Derivatives

Our collaboration with the Gupta lab focuses on the derivation of fluorescein and rhodamine B analogs for the selective fluorescent probing of cells using chromophoric dyes. We are interested in scalable synthesis, selectivity of fluorescent tagging, biocompatability of dyes, and improved sensitivity in UV-fluorescence microscopy of cell cultures that is potentially relevant in translational medicine.

Fluorescent Derivatives of Rhodamine for Selective Cellular Imaging