Sample Learning Goals. Recognize the difference between electron and molecular geometry. Name molecule and electron geometries for molecules with up to six electron groups surrounding a central atom. Compare bond angle predictions from the VSEPR-based model to real molecules. Describe how lone pairs affect bond angles in real molecules. Sample Learning Goals. Describe the differences between an atom and a molecule. Construct simple molecules from atoms. Recognize that the subscript in the molecular formula indicates the number of that atom in the molecule. Recognize that the coefficient indicates the total number of molecules. Associate common molecule names with multiple representations.
Purpose:When wefirst consider the structure of organic molecules, most of us realize thatthree-dimensional structure is both supremely important and sometimes hard tovisualize.Once upon a time, everyorganic chemistry student was encouraged to buy a small set of molecular models(wood, metal or plastic) to help learn the characteristic shapes of all thosecurious combinations of sp2 and sp3 hybridizations.Biochemists built elaborate (and sometimesquite lovely) 3D models of their favorite proteins.Nowadays, molecular modeling software isavailable for the same purposes.
Molecular viewing software should allow you to easily createmolecules (or load them from a variety of file formats), optimize the geometryif needed, then display the structures in a variety of formats: “ball andstick” and “wire frame” mimic some of the older wooden and metal models, whilesemi-transparent electron density formats provide information not availablefrom physical model kits.Most packagesalso allow the color coding or labeling of atoms (or residues) and automaticrotation of the image to fool the eye into seeing 3 dimensions on a flatdisplay screen.
Recommended:Forbuilding, optimizing and displaying small molecules quickly, the ACD/3D viewersoftware from Advanced Chemistry Development is hard to beat.It is an‘add-on’ to their invaluable ChemSketch 12.0 molecular drawing software, which is why they are downloaded from the same page. Switching between drawing (2D) and viewing (3D) modes is quick and painless, and the viewer offers six customizable displayformats, automatic rotation, and (limited) imports of other file formats.Strongly recommended for students of organicchemistry who are still learning to see molecules in their mind’s eye. A short demonstration video is available for download below. ACD/3D viewer, like ChemSketch, runs in Windows and Linux but not on the MacOS. On the other hand, if you want to look at larger molecules, the Molegro Molecular Viewer from Molegro Bioinformatics is a good choice. Like ChemSketch, the Molegro viewer is commercial freeware with an easy-to-use interface and good quality graphics. It cannot be used to build molecules, but macromolecules can be imported using a variety of file formats, including MDL, Sybyl and protein data bank (.pdb). Since the viewer is designed to help analyze interactions between small molecules (ligands) and macromolecules, it should be especially useful for drug interactions and docking. The Molegro viewer is available for Windows, Mac and Linux operating systems.
Two other programs which may be useful to more advanced students are the open source molecular viewer and editor Avogadro and the more advanced commercial freeware program Discovery Studio Visualizer. Additional information on these programs can be found in the Resource pdf attachment (below).
Last updated July 18,2011
A full featured chemical editor for making science accessible on all platforms
Marvin suite is a chemically intelligent desktop toolkit built to help you draw, edit, publish, render, import and export your chemical structures and as well as allowing you to convert between various chemical and graphical file formats. It is free for individual, academic and non-commercial use.
MarvinSketch - Create and Design
MarvinSketch features an extensive set of functionalities to enable the fast and accurate drawing of chemical compounds, reactions, Markush structures and query molecules. Furthermore, MarvinSketch has built-in structure and valence checkers to provide guidance, and integrated property calculators to pull live results - upon your request. Not only does MarvinSketch translate chemistry into a digital environment, it also supports the widest selection of industrially acknowledged standard chemical file formats. For chemical drawing on the web, please also check our browser component Marvin JS.
MarvinView - View your molecules
MarvinView is an advanced chemical viewer for single and multiple 2D/3D chemical structures, queries, reactions and their associated data. This lightweight renderer can display even thousands of molecules in a matrix or spreadsheet view along with the on-the-fly calculated fields, like molecule name, generated IUPAC name and SMILES strings. It supports all common chemistry file formats as well as some document formats, if you use Document to Structure license. These filetypes include .doc and .pdf, where chemical text names and context are extracted into a MarvinView table.
Read more about MarvinView in the documentation.
Read more about MarvinView in the documentation.
Molconvert - Convert between chemical file formats
Molconvert is a highly flexible command line program for batch chemical file format conversion and image creation. Read more about Molconvert in the documentation.