Ed's Computers in Chemistry Homepage

The use of computers in chemistry has become widespread whether as an aid to visualization of 3-dimensional structures or in the ability of the computer to handle large sets of data and perform rigorous calculations.

This Web site is an introduction to the use of computers in chemistry and the increasing role they have in chemical research.

Molecular Modeling

Molecular modeling involves the use of computational methods for simulating/predicting the three-dimensional structures and physicochemical properties of molecules. Molecular modeling can be divided into two levels of theory: Empirical Calculations (Molecular mechanics) and Quantum Calculations.

Empirical Calculations are based on a ball and spring approach where atoms are described in terms of balls of different sizes, and the interaction between atoms is described as a spring. A set of potential functions are are set up to describe bond stretching, angle bending, torsional angle bending, and even non-bonded interactions. These potential functions are used to construct a force field and the goal of Molecular mechanics is to minimize the strain energy of a particular structure.

Quantum Calculations explicitly describe the interactions between electrons, and of course are based on Quantum Mechanical principles. Semi-empirical calculations rely on some experimental data to solve for Schrodeinger's equation, but ab initio calculations do not use any experimental data at all. Ab initio, latin for from the beginning, solves schroedinger's equation from scratch. However one should note that the absolute solution to Schroedinger's equation is impossible beyond a two body system. Although ab initio calculations solve Schroedinger's equation from scratch, the set up of the equation itself is only an approximation.

The NIH Guide to Molecular Modeling is an excellent site for information on computational engines and the underlying theories that these engines are based on. This site is a part of the NIH Center for Molecular Modeling site which also has sites for Research Tools on the Network and Molecular Modeling Software Tools The following computer programs and applications are only a small slice of the actual tools available from this site.

Spartan is a molecular modeling package for computation chemistry applications produced by Wavefunction. Spartan can compute molecular energies using three different methods: Molecular Modeling, SemiEmpirical and ab initio. Spartan has a very friendly graphical user interface, and creating molecules is very easy. This program is by far the easiest to use for computational chemistry.

Here is an image of Spartan's friendly GUI. The builder is located on the right. The menu bar across the top allows you to manipulate a structure.



MOPAC unlike SPARTAN, can do semiempirical calculations only. It also has a fortran input/output interface, which is much more difficult to use than SPARTAN's friendly graphical user interface. MOPAC also requires the user to input the Z-matrix of a molecule. A Z-matrix is a convenient way of describing the 3-dimensional structure of a molecule based on its chemical bonding.

GAUSSIAN is a series of electronic structure programs. It is designed to model a broad range of molecular systems under a variety of conditions, performing its computations starting from the basic laws of quantum mechanics. Like MOPAC, Gaussian also requires you to specify the Z matrix of a molecule.

Here are results obtained from using SPARTAN to compute semiempirical and ab initio calculations on 1-cyclopropenamine. The PDB files can be viewed using Rasmol or Chime, two visualization programs described in the next section.

Ab Initio Results

PDB file for 1-cyclopropenamine
Output file for 1-cyclopropenamine

Semiempirical Results
PDB file for 1-cyclopropenamine
Output file for 1-cyclopropenamine

Summary of Results

Molecular Formula: C₃H₄N

Symmetry: C_s

Heat of Formation:

Molecular Mechanics:	69.712 kcal/mol
Semi-Empirical:	68.752 kcal/mol
Ab-initio:	68.732 kcal/mol

Degrees of Freedom in System: 14

Vibrational Frequencies from semi-empirical results (cm^-1):

-888.35	329.40	368.71
398.58	743.50	829.06
881.16	971.39	1005.76
1060.90	1130.46	1268.09
2054.31	3041.61	3089.49
3310.61	3512.17	3563.09

Molecular Surfaces:

HOMO - Highest Occupied Molecular Orbital	LUMO - Lowest Unoccupied Molecular Orbital

Visualization Programs

ChemDraw is a product that provides specialized tools which allow you to create 2 dimensional chemical drawings for publication. This program allows you to communicate structures and mechanisms with easy point and click options utilizing your mouse.

1-cyclopropenamine drawn with ChemDraw

Rasmol is a helper application that allows you to view and rotate three dimensional chemical structures. Download Rasmol, then all you need to do is download PDB files and you can view them in the program. PDB files contain information related to the chemical structure of a molecule and specify the atoms and connectivity of the molecule.

Rasmol allows you to explore and manipulate the structure and put together package demonstrations. It also has a second command line window that displays additional information.

After you've downloaded Rasmol, take a look at the PDB files for 1-cyclopropenamine. 1-cyclopropenamine is a relatively simple molecule to practice with. Once you've learned some of the basic functions of Rasmol, try viewing the dimeric form of Diphtheria Toxin (4 character code 1DDT)

Chime is a program similar to Rasmol but Chime is able to show the molecule directly within the Web Page. Chime is a plug in that downloads itself directly into the directory tree of your Internet browser. Like Rasmol, Chime also reads files of PDB format. Download Chime, then you can right click the Chime image below to rotate and animate the structures.

1-cyclopropenamine

Diphtheria Toxin (1DDT)


Mage is a program that allows you to view and explore kinemages (kinetic images). A kinemage is a scientific illustration presented as an interactive computer display. Kinemages can be rotated and animated.

WebLab ViewerPro is a software tool that allows you to construct three dimensional graphical models. You can visualize structures, create stunning reports, web pages and presentations.

Molecular Arts Corporation is a software company whose products range from simple 2D chemical diagrams to programs that are able to create 3D virtual worlds.

Rotating buckeyball provided by software from Molecular Arts.

Data Acquisition Instrument Control "Virtual Instruments"

LabVIEW is a software package developed by National Instruments that allows you to create virtual instruments without having to do any low level programming. Since interfacing instruments to computers is inherently difficult to begin with, LabVIEW takes an object oriented approach in interfacing the instrument to the computer to eliminate any artificial difficulty.

VRML - Virtual Reality Modeling Language

VRML is for 3-D what HTML is for 2-D. VRML is a language authors can use to describe 3D objects fro the Internet. With VRML, authors can construct entire "virtual worlds" with infinite space and depth. Objects in this virtual world can be links to text, audio, video, HTML files or sites, and links to other VRML virtual worlds.
VRML Players

Cosmo Player is a free VRML 2.0 client that allows you to maneuver in an interactive, 3-D environment.

WorldView 2.0 claims to be the fastest 3D plugin for Netscape Navigator and Microsoft Internet Explorer.

Once you have downloaded a VRML 2.0 Player, visit the WebMolecules site to view thousands of molecules in full 3D.

R. Stanley Williams is a Chemistry professor at UCLA involved in the development of a high end VRML program. In collaboration with Warren Robinett, he aided in the development of the nanoManipulator interface.

Data Processing Software

Mathematica marked the beginning of modern technical computing. This program evaluates integrals, solves complicated algebraic computations, can deal with digits of arbitrary precision, plots data graphically and does a number of other specialized functions that is used throughout the sciences. Mathematica is high level software and in no way should be thought of as a glorified calculator.

Matlab is a language for technical computing that combines numeric computation, advanced graphics and visualization, and a high level programming language. Some features of Matlab include matrix analysis and manipulation, all forms of 3-D plots, and friendly graphical user interface tools.

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Chemistry related sites:

Department of Chemistry and Biochemistry at UCLA GO BRUINS!

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[ Molecular Modeling | Computational Chemistry Programs | Spartan Excercise | Visualization Tools ]
[ Virtual Instruments | VRML | Data Processing Software | Related Links ]

Copyright © 1999 Ed Chung