Orbital Viewer (http://www.orbitals.com/orb/ov.htm) is a PC-based program that shows electron density calculated from the Schrodinger equation for atoms and molecules. Results can be shown as probability densities or probability surfaces.
Orbital Viewer Program copyright 1986-2004 by David Manthey
The Materials Project is part of the Materials Genome Initiative that uses high-througput computing to uncover the properties of inorganic materials.
It's possible to search for materials and their properties
It employs high-throughput computation approaches and IT to create a system that can be used to predict properties and construct phase diagrams andPourbaix diagrams.
Hilary first higlighted this resource as a news item before we had a web resource category. I'd like to bring it back to people's attention as a web resource because of its value.
Students use a Java-based website to explore the faujasite zeolite structure. The activity questions guide them through identifying different atomic positions within the structure, and orienting the zeolite pores and "cages" relative to the crystal axes.
In this activity, students will compare and contrast two closely related structures, [Pd(dcpf)PR3]2+ (dcpf = 1,1'-bis(dicyclohexylphosphino)ferrocene; R = Me or Ph). They will be required to obtain the cif files from the supporting information of a paper. They will then make a variety of measurments in the two stuctures. These measurements can be made using a variety of different freely available programs. Instructions are provided for Mercury 3.3 and Olex2. Finally, students will be required to provide a rationale for the differences in the two structures.
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.