Wow, fantastic vid! :D Really cool to see people putting out such great in depth tutorials. I wanted to clarify one small thing; when you use the 'track orbital' function in IboView, it;s not the energy of the orbital that is being plotted. It's the 'orbital change' i.e. how the centre of charge of the orbital is displaced through space.
4 ปีที่แล้ว +5
Thanks for sharing! Excellent video, very explanatory and interesting.
That’s a great question. One could theoretically test the proposed product of a reaction by guessing at the reaction mechanism and product structure, running transition state calculations for each guess, and identifying the pathway with the lowest TS energy, which would be the most likely reaction pathway and thus the most likely product.
Amazing! I am running an aldolic condensation folloing this tutorial and looks great, Can you explain how to increase the number of interpolations to achieve a graph like image 10 from the notes document? thank you again!!!!
Hi there! If your .interp file output from the NEB doesn't happen to have enough steps to provide a smooth graph like the bottom half of image 10, I would recommend dividing the path calculation into smaller fragments, then combining the interp results. So run the NEB between your starting configuration and an intermediary configuration, then again from the intermediate to the finish. Divide into as many chunks as is needed for the desired effect for the energy vs reaction pathway graph. Hope this helps!
Hi, Kate! You mentioned that you optimized both reactants separately and then you brought them together in a single file and optimized them again. Could you tell me how that is done? Thank you and I love the video!
Hello, If you take a look at the walkthrough in the description (also here: docs.google.com/document/d/1YK3ojoLP4Ks7XkJ1ykbOYY7Bsdc66EHvk81AEhAC4Ck/edit?usp=sharing) on page 10 there's a description on how to do geometry optimizations in Avogadro. Also, IaNiusha has a nice video walkthrough on the subject: th-cam.com/video/Y1l1PK45Rsg/w-d-xo.html Hope this helps!
@@kateboyd1989 I do know how to optimize structures but I was wondering how you can combine single xyz files into one file that allows you to view multiple molecules in one Avogadro window, if that is even possible. I hope that makes sense lol Thank you for your response! It is highly appreciated 😊
@@Liza-gb9mv Oh, gotcha! In Avogadro you can open your two files in separate windows, then use the selection tool (the one that looks like a mouse) to highlight the structure of one of your molecules. Once highlighted, you can copy with crtl+C, head over to the other window, and crtl+V, aka copy/paste. Then you can spend time moving molecules around if you like, or a geometry optimization at that point will move them around for you. Best of luck!
Good evening madam, I have the same problem as you because it did not take long for the neb to converge. When I use %geom maxIter 500 end , it's the same as the first output and then I use maxiter 2000 same again... please help me and please show me, how do you change the file.inp? thank you Ms
Thanks so much for the explanation. I am new to these topics but I am very interested in what I am doing research work. Do you carry out consulting? I really appreciate your response. Miguel from Perú
Hi, you have opened image because it was in xyz format but when i tried i got these images in gbw format it's not opening can you please tell how can i see?
Hi, your video is quite interesting and clear, but I have a question about the path you describe. During the search process, NEB finds possible "intermediate minima" in different images, and even other "climbing images", what is observed as a second maximum in the image of your path. My question is, can such points be considered additional intermediates and transition states since your reaction is "complex" or is it best to consider a simple scheme containing a single reavtive, product and TS?
Does anyone have a method of converting Gaussian 16 IRC or opt=modredundant potential energy surface scan to visualize the structures with IboView? Think we really just need a script to convert the structures in the .log file to the combined .xyz trajectory file. In the meantime.... i'll make one
Hi Dr. Kate Boyd. Thank you so much for your training video, very helpful with me. If possible, could you give me your email? I would like to contact you about some of my problems in the TS search mode of ORCA. Now I'm studying a Master's course in Korea about Nanomaterials and I'm a beginner with Computational Chemistry. I hope your reply soon! Thank you so much!
Wow, fantastic vid! :D Really cool to see people putting out such great in depth tutorials. I wanted to clarify one small thing; when you use the 'track orbital' function in IboView, it;s not the energy of the orbital that is being plotted. It's the 'orbital change' i.e. how the centre of charge of the orbital is displaced through space.
Thanks for sharing! Excellent video, very explanatory and interesting.
Thanks Kate for the information, I've got a 10/10 in mi reserch project for Graduation!
Although I use Gaussian, it is a very helpful and interesting video. thank you so much.
Thank you very much please send us more videos
Very nice presentation
thank you for the excellent video, can you make a video for radical reaction, what like any compound attack by a OH radical
This is really helpful for me, thank u so much for sharing
this is visually very interesting video.
Well explained! Thumbs up
Thanks, love the explanation
Fascinating.
Excellent tutorial, During implementing it in my project I found some issues. I know the mechanism. Looking forward if u assist me to solve the issue.
Very nice explanation!!! Can we predict the product of a chemical reaction?
That’s a great question. One could theoretically test the proposed product of a reaction by guessing at the reaction mechanism and product structure, running transition state calculations for each guess, and identifying the pathway with the lowest TS energy, which would be the most likely reaction pathway and thus the most likely product.
Amazing! I am running an aldolic condensation folloing this tutorial and looks great, Can you explain how to increase the number of interpolations to achieve a graph like image 10 from the notes document? thank you again!!!!
Hi there! If your .interp file output from the NEB doesn't happen to have enough steps to provide a smooth graph like the bottom half of image 10, I would recommend dividing the path calculation into smaller fragments, then combining the interp results. So run the NEB between your starting configuration and an intermediary configuration, then again from the intermediate to the finish. Divide into as many chunks as is needed for the desired effect for the energy vs reaction pathway graph. Hope this helps!
Hi, Kate! You mentioned that you optimized both reactants separately and then you brought them together in a single file and optimized them again. Could you tell me how that is done? Thank you and I love the video!
Hello,
If you take a look at the walkthrough in the description (also here: docs.google.com/document/d/1YK3ojoLP4Ks7XkJ1ykbOYY7Bsdc66EHvk81AEhAC4Ck/edit?usp=sharing) on page 10 there's a description on how to do geometry optimizations in Avogadro. Also, IaNiusha has a nice video walkthrough on the subject: th-cam.com/video/Y1l1PK45Rsg/w-d-xo.html
Hope this helps!
@@kateboyd1989 I do know how to optimize structures but I was wondering how you can combine single xyz files into one file that allows you to view multiple molecules in one Avogadro window, if that is even possible. I hope that makes sense lol
Thank you for your response! It is highly appreciated 😊
@@Liza-gb9mv Oh, gotcha! In Avogadro you can open your two files in separate windows, then use the selection tool (the one that looks like a mouse) to highlight the structure of one of your molecules. Once highlighted, you can copy with crtl+C, head over to the other window, and crtl+V, aka copy/paste. Then you can spend time moving molecules around if you like, or a geometry optimization at that point will move them around for you. Best of luck!
Can transition State for hantzsch thiazole synthesis is find out by using this?
Good evening madam, I have the same problem as you because it did not take long for the neb to converge. When I use %geom maxIter 500 end , it's the same as the first output and then I use maxiter 2000 same again... please help me and please show me, how do you change the file.inp? thank you Ms
If you have a metal complex and it is undergoing ligand rearrangement along with change in spin state then can NEB be used?
Thanks so much for the explanation. I am new to these topics but I am very interested in what I am doing research work. Do you carry out consulting? I really appreciate your response.
Miguel from Perú
I wanna learn orca for organic chemistry please suggest something...
Hi, you have opened image because it was in xyz format but when i tried i got these images in gbw format it's not opening can you please tell how can i see?
Hi, I got same situation, how did you do in this case? Were did you able to fix the file o what did you do to get xyz files? Thank u in advace! :D
Hi, your video is quite interesting and clear, but I have a question about the path you describe. During the search process, NEB finds possible "intermediate minima" in different images, and even other "climbing images", what is observed as a second maximum in the image of your path. My question is, can such points be considered additional intermediates and transition states since your reaction is "complex" or is it best to consider a simple scheme containing a single reavtive, product and TS?
Hello Madam, How can I get connect to you? Its too urgent.
Hi Kate I can't download the file from google drive it say that the file does not exist ..can you update the url file to download it please !!!
Looks like the old Google Drive file expired. Replaced it with a PDF link. Happy modeling!
Does anyone have a method of converting Gaussian 16 IRC or opt=modredundant potential energy surface scan to visualize the structures with IboView? Think we really just need a script to convert the structures in the .log file to the combined .xyz trajectory file. In the meantime.... i'll make one
Hi Dr. Kate Boyd. Thank you so much for your training video, very helpful with me. If possible, could you give me your email? I would like to contact you about some of my problems in the TS search mode of ORCA. Now I'm studying a Master's course in Korea about Nanomaterials and I'm a beginner with Computational Chemistry. I hope your reply soon! Thank you so much!