Orbital visualization programs

The JME Editor is a Java program which allows one to draw, edit, and display molecules and reactions directly within a web page and may also be used as an application in a stand-alone mode. The editor was originally developed for use in an in-house web-based chemoinformatics system but because of many requests it was released to the public. The JME currently is probably the most popular molecule entry system written in Java. Internet sites that use the JME applet include several structure databases, property prediction services, various chemoinformatics tools (such as for generation of 3D structures or molecular orbital visualization), and interactive sites focused on chemistry education [209]. 

Three tools are provided on the CD-ROM for your use. Orbital Viewer Is a program for viewing representations of atomic and molecular orbitals. ISIS /Draw Is a chemical drawing program. WebLab VfewerUte Is a molecular visualization program that will convert the 2-dimensional structures created by ISIS/Draw Into Interactive 3-dimenslonal representations. 

Orbdraw is a visualization program for displaying molecular orbital and electron density data from Mopac, AMPAC, Gaussian, PSGVB, and HONDO calculations. Version 2 of Orbdraw can read the standard output file of a Mopac or... 

Wave functions can be visualized as the total electron density, orbital densities, electrostatic potential, atomic densities, or the Laplacian of the electron density. The program computes the data from the basis functions and molecular orbital coefficients. Thus, it does not need a large amount of disk space to store data, but the computation can be time-consuming. Molden can also compute electrostatic charges from the wave function. Several visualization modes are available, including contour plots, three-dimensional isosurfaces, and data slices. 

It is now possible to "see" the spatial nature of molecular orbitals (10). This information has always been available in the voluminous output from quantum mechanics programs, but it can be discerned much more rapidly when presented in visual form. Chemical reactivity is often governed by the nature of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). Spectroscopic phenomena usually depend on the HOMO and higher energy unoccupied states, all of which can be displayed and examined in detail. 

Roald Hoffmann, a former coworker of R.B. Woodward and Nobel Prize as well for his contribution to the frontier orbital theory (the famous Woodward-Hoffmann rules concerning the conservation of molecular orbital symmetry), has also emphasised the artistic aspects of organic synthesis "The making of molecules puts chemistry very close to the arts. We create the objects that we or others then study or appreciate. That s exactly what writers, visual artists and composers do" [15a]. Nevertheless, Hoffmann also recognises the logic content of synthesis that "has inspired people to write computer programs to emulate the mind of a synthetic chemist, to suggest new syntheses". 

Art Program We have revised almost every figure in the textbook to better serve visual learners. Most of the glassware, orbitals, graphs, and flowcharts have been redrawn. 

Quantum mechanics computer programs can calculate heats of formation and the energies of fransifion sfafes. The shapes of orbitals can be displayed in three dimensions. Important properties can be mapped onto the surface of a molecule. Wifh fhese programs, fhe chemist can visualize concepts and properties in a way that the mind cannot readily imagine. Often this visualization is the key to understanding or to solving a problem. 

In this study, most of the molecular orbital calculations were carried out using a MOPAC (Stewart, version 6.0), a packaged program of the semi-empirical molecular orbital method. A molgraph (Daikin Co. Ltd.) was used for the visualization of the calculation results. 

One can almost marvel at the ability and way of those who worked on molecular orbitals to make sense of the molecular spectral data. And, yet, the apparently simplistic approach to "duplicate" Bohr s aufbau program for molecules turned out to be a great success. Furthermore, it adhered to a basic chemical characteristic that of being visualizable. The molecule conceived as "united atoms" helped in visualizing the new bonding mechanisms. Notably, one did not need to make use of the Schrodinger equation, even though the Pauli principle was absolutely crucial. 

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