This suite of activities can be used as a unit exploring the use of small molecule models and biophysical techniques to illuminate complicated biomolecules. The Parent LO: Modeling the FeB center in bacterial Nitric Oxide reductase is a short, data-filled and well-written article that is approachable with an undergraduate's level of understanding.
This is an in-class PDB exercise based on the paper "Mechanisms Controlling the Cellular Metal Economy" by Gilston and O'Halloran. Students are asked to visualize the metal binding sites of several proteins discussed in the paper, highlighting unusual metal geometries. After identifying the amino acid residues involved in metal binding, students will discuss the bond structure in terms of HSAB theory.
In this experiment, students will synthesize a cobalt Schiff base complex with varying axial ligands ([Co(acacen)L2]+). They will characterize the complex using various techniques, and may perform computational modeling to predict spectroscopic properties.
This activity is designed to give students a deeper understanding of what post-translational modification does in a metalloenzyme using nitrile hydratase (NHase) as a model system. The metallo-active site of NHase contains a cobalt(III) center that is bound to an unusual coodination sphere containing bis-amidate, cysteinate, sulfenate (RSO-), and sulfinate (RSO2-) ligands.
This experiment involves the preparation of a key starting reactant in high purity and yield for an ongoing research project, specifically for the development of potential photodynamic therapy (PDT) agents. The students synthesize [ReO2(py)4]Cl.2H2O using standard inorganic synthesis techniques. The students visualize the vibrations and electronic properties (e.g. molecular orbitals) of the compound using output files generated from density functional theory (DFT).
A guided-inquiry activity for the interactive PhET simuation "Molecules and Light" was created to introduce upper-level inorganic laboratory students to inorganic spectroscopy. The activity included here is the first part of a two-day discussion. This activity instructs students to use the PhET simulation "Molecules and Light" to explore how various molecules interact with different energies of electromagnetic radiation (microwave, infrared, visible, ultraviolet). This activity can also be used in a general chemistry setting as the topics discussed are very basic.
Having been inspired by a number of wonderful LOs, I introduced group theory in my 'sophomore' inorganic class this spring. In addition to learning to determine the point group of a molecule, students were taught how to construct a qualitative MO diagram though the use of LGOs. While this course can be taken with or without the laboratory component, it seemed only natural to include a lab on this material. A previous lab had introduced the students to computational methods for geometry optimization.
Students construct computer models of two transition metal complexes, solve their electronic structures, and inspect the resulting d-type molecular orbitals to identify which are non-bonding, sigma* antibonding, or pi* antibonding. After constructing a molecular orbital diagram, they determine which of the two complexes is likely to absorb light at a longer wavelength.
During my junior/senior level inorganic course, we did several guided literature discussions over the course of the semester where the students read papers and answered a series of questions based on them (some from this site!). As part of my take home final exam, I gave the students an open choice literature analysis question where they had the chance to integrate topics from the semester into their interpretation of a recent paper of their own choice from Inorganic Chemistry, this time with limited guidance.
Chimera is a program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can also be generated. Chimera includes documentation and tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use. Chimera was developed at UCSF and was funded by the National Institute of Health.