Computer Programs:  Chemistry

 

These programs were designed as instructional material for university chemistry instruction and were distributed commercially by Trinity Software, which is now out of business.  I am now offering these Windows programs as freeware from this website.  Some have also been written for the Mac; if you are interested, email your request.

 

NameIt contains the rules for assigning chemical names to organic chemical compounds.  The program contains a library of named structures, and the program can be used in two modes:

1) A name is displayed, and the student is asked to draw the structure attached to the name using structure-drawing tools offered by the program.  The program has the smarts to check the structure and let the student know where his/her drawing deviates from the correct representation.

2) A structure is displayed, and the user is asked to type in the systematic chemical name of the structure.  The student’s input is analyzed by the program (including punctuation), and an error message appears if correction is required.

Zipped file is 823 KB. Download NameIt

 

HMO computes electron distributions using a first approximation based on Hueckel Molecular Orbitals, a basic quantum mechanical computation.  The electronic distributions are shown graphically along with tables of numerical results.  A number of models that use different parameter sets are available in the program.  An editing program, HMOedit, allows the user to create his own parameter set.

Zipped file is 537 KB.Download HMO

 

 

MassSpec is a program that assists in the interpretation of mass spectra.  Mass spectroscopy is a useful tool in chemistry for establishing chemical structure.  It is based on fragmentation of a compound in vacuo by a beam of high energy electrons, separation of the resulting (charged) fragments according to mass by an intense  magnetic field, and recording of the relative amounts of each mass. also known as a  “mass spectrum.”  The distribution of masses in the spectrum can be related to the original structure of the compound. 

The computer program, MassSpec, simulates the fragmentation of a compound.  Using structure-building tools supplied by the program, the user creates a chemical structure on the screen.  Code simulating fragmentation produces a (very) large collection of fragments (substructures), which are sorted by mass.  Some rules—based on event restrictions that actually pertain in a mass spectrometer—are incorporated that restrict fragment generation in order to limit the population to fragments that might actually appear in practice.  The results of fragmentation are presented in a table according to mass.  The user can click on a table entry, and the structure of the fragment is delineated by red highlighting on the input structure.  In the event that more than one fragment corresponds to the selected mass, the user can scroll through those fragments.  This operation of assigning substructures to the observed masses in a mass spectrum is an essential tool in structure assignment.  For example, if a mass appears in a mass spectrum to which no correspondent substructure can be found based on the hypothetical input structure, then the hypothetical structure must be incorrect (or, a good possibility, the original compound that gave the spectrum was impure. 

Zipped file is 594 KB.Download MassSpec

 

Top of Page

SynTree is probably the most complex program I have ever written (aside from some diffusion cum reaction simulations for Eastman Kodak).  It is actually a suite of three programs containing SynTree (the basic program), IPLists, and TransformSynTree accepts a chemical structure input by user as a goal, and, using a database of known organic chemical reactions, produces an output list of possible precursors that could lead in a single step to the goal structure.  Thus, the program runs chemical synthesis backwards, from complex to simpler structures, a route known as “retrosynthesis.”  One of the precursors can then be selected as the goal, and the program applied to it, producing a still simpler precursor.  It is apparent that continued application of this routine should generate a tree of simpler and simpler starting materials until some common and readily available precursor appears.  Looking at this reaction chain in reverse, one will have generated a possible route from simplest starting material to final product.  The heart of this program is discovering substructures contained in the goal structure that lend themselves to the chemical manipulations built into the database.  The database supplied with the program contains most of the common reactions found in elementary organic chemistry. 

Synthetic schemes are often plagued by side reactions owing to the presence of more than one reactive center in a structure.  For a particular desired outcome, the presence of a second reactive center constitutes an interference in the reaction.  Syntree has an accompanying program called IPLists that can be used to specify chemical structures that might constitute interferences and to select the chemical reactions  in which these structures would function as interferences. 

The Transform program included in the Syntree suite allows the user to add his own reactions (aka “transforms”) to the database.  It accepts a goal structure (actually a substructure) representing a reactive unit and tools that can be applied to the goal that transform it into a precursor structure.  The tools are basic operations that add or remove atoms, change the order of bonds, and alter the hydrogen count at an atom.  These elemental steps taken together constitute a conversion of goal to precursor structure.  The allowed conversions are not arbitrary but correspond to some known chemistry.  As the user applies these tools, the computer records the successive applications and the final, collected result comprises the transform.

  An old version of SynTree is not available.  It has been replaced by a new, much improved version of the same program.   Download SynTree for Mac v1.0

Download SynTree for Windows

top of page