Module Descriptions

UREICA Module Descriptions

Module 1 Fundamentals of Spectroscopy (5.351)

This experimental module provides an introduction to the fundamental principles of the most common types of spectroscopy, including UV-visible absorption and fluorescence, infrared, and nuclear magnetic resonance. Emphasis is on the principles of how light interacts with matter, a fundamental and hands-on understanding of how spectrometers work, and what can be learned through spectroscopy about prototype molecules and materials. Spectra of small organic molecules, native and denatured proteins, semiconductor quantum dots, and laser crystals are recorded and analyzed.

*Based on the research of Professor Keith Nelson
Offered Fall and Spring; Prerequisites: 5.111, 5.112, or 3.091; 4 units; 1/2 Institute Lab

Module 2 Synthesis of Coordination Compounds and Kinetics (5.352)

This experiment is an introduction to the synthesis of simple coordination compounds and chemical kinetics. Cobalt coordination chemistry and its transformations are illustrated in the preparation of [Co(NH3)4(CO3)]NO3 and [Co(NH3)5Cl]Cl2, followed by the aquation of [Co(NH3)5Cl]2+ to yield [Co(NH3)5(H2O)]3+, as detected by visible spectroscopy. Isosbestic points are observed in visible spectra, the rate and rate law is determined, the rate constant is measured at several temperatures, and the activation energy is derived for the aquation reaction.

*Similar to the research of Professor Richard Schrock
Offered Fall and Spring; Prerequisites: 5.111, 5.112, or 3.091; Corequisite: Module 1 (5.351); 4 units; 1/2 Institute Lab

Module 3 Late-Stage Drug Modification and Selective Delivery (5.353)

This experiment will introduce students to a modern strategy used to improve the performance of pharmaceuticals, which will teach experimental techniques from synthetic organic chemistry and organic materials science. First, a biologically active small molecule will be selectively modified to introduce new reactive functional groups at two distinct molecular positions. These chemical handles will be used to incorporate the small molecule into a number of polymer nanoparticles with different microstructures, and the rate of drug release under model physiological conditions will be monitored. Students will be exposed to several types of reactions, including free-radical chemistry and metathesis polymerization. Fundamental laboratory techniques including the standard handling of organic and inorganic chemicals, purification by acid-base extraction and recrystallization, monitoring of reaction kinetics by UV/Visible spectrophotometry, and identification of product isomers by NMR spectrometry will be introduced.

*Developed by Professor Jeffrey Van Humbeck and based on the research of Professors Jeffrey Van Humbeck and Jeremiah Johnson
Offered Fall and Spring; Corequisites: 5.12 and Module 2 (5.352); 4 units; 1/2 Institute Lab

Module 4 Expression and Purification of Enzyme Mutants (5.361)

In this experiment, students will use biochemical techniques for protein expression and DNA manipulation of Bcr-Abl kinase, which is inhibited by the blockbuster drug Gleevec in the treatment of chronic myelogenous leukemia. The kinase domain of the recombinant Abl enzyme will be expressed in E. coli and then purified and analyzed using nickel affinity chromatography, polyacrylamide gel electrophoresis, UV-Vis spectroscopy, and BSA assays. In addition, the DNA of selected Abl mutants identified in Gleevec-resistant cancer patients will be constructed using site-directed mutagenesis, which will include DNA primer design and agarose-gel electrophoresis.

*Developed by Dr. Elizabeth Vogel Taylor and Professor Catherine L. Drennan and based on the research of Professor Alice Ting
Offered in Spring; Must be taken simultaneously with Module 5 (5.362); Prerequisites: 5.07 or 7.05; Module 2 (5.352) or 5.310; Corequisite: Module 5 (5.362); 3 units

Module 5 Kinetics of Enzyme Inhibition (5.362)

In this experiment, students will study the activity and structure of the domains developed in Module 4 to understand the role of mutations in the development of resistance to Gleevec. Both mutant and wild-type Abl kinase domains will be assayed for phosphorylation activity to determine enzyme kinetics and the inhibition efficacy of Gleevec. The kinase activity of Gleevec-resistant mutants will be further tested in the presence of other potential inhibitors. The use of structure-viewing programs will enable analysis of the mechanistic basis of Bcr-Abl inhibition and Gleevec-resistance.

*Developed by Dr. Elizabeth Vogel Taylor and Professor Catherine L. Drennan and similar to the research of Professor Joanne Stubbe
Offered in Spring; Must be taken simultaneously with Module 4; (5.361) Prerequisites: 5.07 or 7.05; Module 2 (5.352) or 5.310; Corequisite: Module 4 (5.361); 5 units; CI-M

Module 6 Organic Structure Determination (5.363)

The objective of this experiment is to introduce students to modern methods for the elucidation of the structure of organic compounds. Students will carry out transition metal-catalyzed coupling reactions based on chemistry developed in the Fu and Buchwald laboratories using reactants of unknown structure. Full spectroscopic characterization, by proton and carbon NMR, IR, and mass spectrometry of the reactants and the coupling products will be carried out in order to identify the structures of each compound. Other techniques taught are transfer and manipulation of organic and organometallic reagents and compounds, separation by extraction, and purification by column chromatography.

*Developed by Professor Rick Danheiser and based on the research of Professors Steve Buchwald and Greg Fu
Offered in Fall; Prerequisite: 5.12; Corequisite: 5.13; 4 units; 1/2 Institute Lab

Module 7 Continuous Flow Chemistry:  Sustainable Conversion of Reclaimed Vegetable Oil into Biodiesel (5.371)

Students will learn the theoretical and practical fundamentals of continuous flow synthesis, wherein pumps, tubes, and connectors are used to conduct chemical reactions instead of flasks, beakers, etc.  The focus will be a catalytic reaction that converts natural vegetable oil into biodiesel that can be used in a variety of combustion engines.  Given the low cost and small footprint of the equipment used and minimal energy requirements, this approach is sustainable and amenable to use in the developing world.  Students will learn several important organic chemistry experimental techniques, including purification by extraction, rotary evaporation, acid-base titration, gas chromatography (GC), and 1H NMR.

*Based on the research of Professor Tim Jamison
Offered in Spring; Prerequisites: 5.13 and Module 6 (5.363); 4 units

Module 8 Chemistry of Renewable Energy (5.372)

Students are exposed to the electrochemical processes that underlie renewable energy storage and recovery. They will investigate charge transfer reactions at electrode surfaces that are critical to the operation of advanced batteries, fuel cells, and electrolyzers. The basic theory behind inner- and outer-sphere charge transfer reactions at interfaces will be developed and applied to construct mechanistic models for important energy conversion reactions including the reduction of O2 to water and the reduction of protons to H2. Students will also synthesize new catalytic materials for these reactions and investigate their relative performance.

*Based on the research of Professor Yogesh Surendranath
Offered in Fall; Prerequisites: 5.03 and Module 2 (5.352); 4 units

Module 9 Dinitrogen Cleavage (5.373)

An introduction to the research area of small-molecule activation by transition-element complexes. A three-coordinate molybdenum(III) complex is synthesized and its NaH-catalyzed six-electron reductive cleavage of the dinitrogen molecule is investigated. The techniques covered in this module include glove-box methods for synthesis for exclusion of oxygen and water; filtration, reaction mixture concentration, and recrystallization under a dinitrogen atmosphere and under static vacuum. Characterization methods include proton NMR spectroscopy of both paramagnetic and diamagnetic systems, Evans’ method magnetic susceptibility measurement, UV-Vis spectroscopy, and infrared spectroscopy of a metal-nitrogen triple bond system.

*Based on the research of Professor Kit Cummins
Offered in Fall: Prerequisites: 5.03 and Module 6 (5.363); Corequisite: 5.61; 4 units

Module 10 Quantum Dots (5.381)

Synthesis of a discrete size series of quantum dots, followed by synthesis of a single size of core-shell quantum dots utilizing air free Schlenk manipulations of precursors. Characterization by absorption spectroscopy and fluorescence will be used to rationalize the compositional/size dependence of the shell on the electronic structure of the quantum dot as well as the phenomena of "blinking". Fluorescence resonance energy transfer between quantum dot/dye conjugates.

*Based on the research of Professor Moungi Bawendi
Offered in Spring; Prerequisites: 5.61 and Module 3 (5.353); 3 units

Module 11 Time and Frequency Resolved Spectroscopy of Photosynthesis (5.382)

Time and frequency resolved fluorescence measurements are used to investigate photosynthetic light harvesting and energy transfer.

*Based on the research of Professor Gabriela Schlau-Cohen
Offered in Spring; Prerequisites: 5.61; 5.07 or 7.05; Corequisite: Module 4 (5.361); 5 units; CI-M

Module 12 Fast Flow Peptide and Protein Synthesis (5.383)

This module aims to teach students both the theory and practice of some fundamental techniques in biological chemistry, which include chemical reactivity (amide-bond formation, solid phase synthesis, disulfide bond formation, and protecting group chemistry), separation science for purification and analysis such as preparative HPLC and MALDI-TOF MS, and protein structure-function relationships (protein folding and binding). For part of this module, visitors from the local biotech research community will give guest lectures to describe how this module has practical applications in industry.

*Based on the research of Professor Brad Pentelute
Offered in Spring; Prerequisites: 5.07 or 7.05; Module 6 (5.363); 4 units