Please prepare energy plot, frequencies, finding torsion angles and editing of bond angles of prepared molecules using wxMacMolPlt since Avagadro is not running on some desktops due to software issues.
IaNiusha, what about the double bonds of the ring? They converted into single bond. Could you tell how to avoid such situation while optimising the geomety. Is the bond order alterations affect the MO calculation?
You should not be mistaken by some visualization tools, especially when it comes to displaying bonds. Generally, they contain kind of built-in threshold values in terms of distances between connected atoms which tell them whether a bond should be displayed as single or double. But this is not always reliable. Some software even completely ignore this aspect by displaying all the bonds as single sticks (single bonds). Very often, you will come across situations where the bond has been omitted. This can happen when the bond was stretched a lot in the attempt of the optimization algorithm to locate the desired stationary point. Among approaches that can reliably tell you the nature of a chemical bond are those theoretical / computational tools based on the analysis of the electron density of the system (NBO,QTAIM,etc).
Please prepare energy plot, frequencies, finding torsion angles and editing of bond angles of prepared molecules using wxMacMolPlt since Avagadro is not running on some desktops due to software issues.
Très bon tutoriel. Merci beaucoup!
IaNiusha
you are great. Thank you so much :-)
Awsome, thank you so much for this!
Very helpful, thank you.
Dr. IaNiusha,
What kind of software to view the result ?
I'am using Ubuntu.
IaNiusha, what about the double bonds of the ring? They converted into single bond.
Could you tell how to avoid such situation while optimising the geomety. Is the bond order alterations affect the MO calculation?
You should not be mistaken by some visualization tools, especially when it comes to displaying bonds. Generally, they contain kind of built-in threshold values in terms of distances between connected atoms which tell them whether a bond should be displayed as single or double. But this is not always reliable. Some software even completely ignore this aspect by displaying all the bonds as single sticks (single bonds). Very often, you will come across situations where the bond has been omitted. This can happen when the bond was stretched a lot in the attempt of the optimization algorithm to locate the desired stationary point. Among approaches that can reliably tell you the nature of a chemical bond are those theoretical / computational tools based on the analysis of the electron density of the system (NBO,QTAIM,etc).
a nice video can you make a video about dalton software?
Thank you
Hi IaNiusha, is there any way to find the conduction band energy on GAMESS?
Does number of processors mean the same as number of cores or threads?
i can use the open enhanend console here and the console say me that phyntom are not ejecutable ,i have already pyntom but i can do it helpme please
for some reason in the end I click on the log file (output) and dont open at all and I have the macmol bla bla bla
Hi IaNiusha, could you please tell me how to open .log file in 3D? What software. you have used to see the charge surface?
MacmolPlt should open log files
Another suggestion is to create an input GAMESS file with GabEdit program, for instance: th-cam.com/video/8ZRuB5JkA0c/w-d-xo.html
sure, I just don't like GabEdit =)