Molecular orbital calculation by using free chemical software
on Windows95 &98.
Outline
Recently chemical calculation software that can be acquired on the Web has increased.Some of them,though it is freeware,isn't inferior to the commercial one.Here is a report that shows an example of their usage for the molecular orbital calculation of organic compounds with Windows PC.
The software used is the following.
The procedure is described below.
1.Drawing
MOLDA for Windows ver6.4 is used for molecular drawing.This is able to draw the molcular structure itself and also to import "mol"and "PDB"file.γ-Butyrolactone was drawn as an example.
The method to make a MOPAC input file after drawing is as follows.
Select "Data conversion/MOLDA→MOPAC".
Input keyword for the MOPAC calculation.
Save it as the name of "FOR005"
2.Calculation
MOPAC7 for MS-DOS is used for the molecular orbital calculation.Put "GO.EXE", "MOPAC7.SML"or"MOPAC7.BIG", and "FOR005"made above on the same directory,then start the MOPAC by inputting the command line "go.exe mopac7.sml" or "go.exe mopac7.big" on the MS-DOS WINDOW(prompt mode).The output file"FOR006"is made after the termination of calculation.It is comfortable that these operations are doing with the batch file.Moreover,when"GRAPH"keyword of MOPAC is used,"FOR013"output file is made,too.
3.Display
Well,Molden ver3.6 for Windows is convenient for display of the calculation results.This can express the vibration mode,the shape of HOMO,LUMO etc. On Windows platform X-server program is needed for it.Though the combination of Cygwin and X-server is available,"WeirdX" working on Java is adopted.
Modify "WeirdX-JAVA2.bat" and "prop"file.(*1)
WeirdX is started.
The output display for molden is set.(*2)
Molden is started.
Read "FOR006"or"FOR013"MOPAC output file.
The shape of HOMO of γ-butyrolactone was drawn as an example.
Neither the energy level of molecular orbit,the coefficient of eigenvector,nor the value of the dipole moment are displayed.Let's take it out directly from "FOR006".
And Molden is possible to output vrml file(*.wrl).By using this,3D model can be shown at the cosiderable high speed on the Web browser.
Footnote
(*1)
If the installation directory of Java2 and WeirdX is "C:\jdk1.2",and "C:\WeirdX" respectively,the following parts of original "WierdX-JAVA2.bat"file should be changed in this mammer.
*original
rem set WEIRDX_HOME=\tmp\weirdx\misc
if "%WEIRDX_HOME%" == "" set WEIRDX_HOME=.
java -classpath ".;%WEIRDX_HOME%\weirdx.jar" com.jcraft.weirdx.WeirdX
*changed
set PATH=c:\jdk1.2\bin ....this line was added.
set WEIRDX_HOME=c:\weirdx\misc
if "%WEIRDX_HOME%" == "" set WEIRDX_HOME=.
java -classpath ".;%WEIRDX_HOME%\weirdx.jar" com.jcraft.weirdx.WeirdX
A partial change in "Prop"file was two places.
#Weirdx.windowmode=InBrowser
Weirdx.windowmode=MultiWindow ....MultiWindow was adopted.
# xdmcp
# At present, any authorization mechanism has not been
# implemented. So please use this functionality with your own risk.
#Weirdx.xdmcp.mode=query
Weirdx.xdmcp.mode=boradcast ....Boradcast was adopted.
Weirdx.xdmcp.address=127.0.0.1:2.0 ....default must be this.
(*2)
It is necessary to specify the X-server as the output of Molden.
Therefore,it is convenient that Molden is started with batch file of the following content.
set DISPLAY=127.0.0.1:2.0
molden.exe
Please look at the paragraph of "runnig molden...." in the manual of "molden3.6for MS Windows 95,98,and NT4.0" in detail.
Acknowledgment
It did not at least cost money to the application.I will sincerely express my gratitude to the people who make these software and open to the public without charge.
2001.01.02 last update
1.Drawing
