Utilizing the PDB and HSAB theory to understand metal specificity in trafficking proteins

Submitted by EGunn / Simmons College on Thu, 07/17/2014 - 15:19

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. 

Exploring Post-Translational Modification with DFT

Submitted by Gerard Rowe / University of South Carolina Aiken on Thu, 07/17/2014 - 12:52

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.

The Synthesis and Characterization of a trans-Dioxorhenium(V) Complex

Submitted by Sibrina Collins / Marburger STEM Center (MSC) at Lawrence Technological University on Mon, 07/14/2014 - 12:31

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).

Inorganic Spectroscopy Introduced Using an Interactive PhET Simulation (Part 1)

Submitted by Alycia Palmer / The Ohio State University on Wed, 04/30/2014 - 20:49

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.

'Sophomore' symmetry: Computational analysis

Submitted by Chip Nataro / Lafayette College on Tue, 03/25/2014 - 17:34

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.

Molecular Orbital of Transition Metal Complexes

Submitted by Steven Neshyba / University of Puget Sound on Wed, 02/05/2014 - 21:39

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.

Student choice literature-based take home exam question

Submitted by Hilary Eppley / DePauw University on Fri, 01/24/2014 - 15:27

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 - A Molecular Modeling Program

Submitted by Walter Flomer / St. Andrew's University on Wed, 06/26/2013 - 06:54

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.

Trends in Measured Redox Potentials and Computed Molecular Orbital Energies of Derivatized Buckminsterfullerenes

Submitted by Robert Q. Topper / Cooper Union on Tue, 06/25/2013 - 01:55

In this project students are asked to reproduce published calculations of molecular orbital energies of a series of derivatized fullerenes and correlate them with published reduction and oxidation potentials obtained from cyclic voltammetry. The particular subset of the derivatives to be studied are chosen by the student and this choice is part of the learning activity. The students then carry out additional calculations using other theoretical models to see whether they improve the correlation between computed and experimental properties.