Timeline for How can I determine if there are π-π interactions between an amide and an aromatic ring in a protein?
Current License: CC BY-SA 4.0
13 events
| when toggle format | what | by | license | comment | |
|---|---|---|---|---|---|
| Dec 25, 2018 at 13:36 | history | edited | orthocresol | CC BY-SA 4.0 |
deleted 83 characters in body
|
| Jun 19, 2015 at 15:38 | comment | added | diffracteD | Actually I'm dealing with full amino acid chain from protein crystal structure. That's why I ask, if I truncate the whole thing except the particular section I'm intending to find i.e. N-H...O-C, then would it serve well ? (the example I put on there was just an analogy) | |
| Jun 19, 2015 at 15:33 | comment | added | LordStryker | Is your system an entire crystal structure or protein? No its not though given the location of your comment it was easy for me to assume this. Your system is small enough you would not have to cap anything and I would recommend that you characterize the full thing. | |
| Jun 19, 2015 at 15:31 | comment | added | diffracteD | If I got a structure(chain) looks like, say, H3C-CH2-N-H...O-C-CH(CH3)-CH3. And if I want to get the energy between N-H...O-C. Then is it sensible to use only that concerned part(i.e. N-H...O-C) with the strict-geometry I have ? | |
| Jun 19, 2015 at 15:26 | comment | added | LordStryker | You cannot model an entire crystal structure, protein, etc. with a method that can reasonably quantify $\pi$-$\pi$ interactions with acceptable accuracy as this would be computationally intractable. You would have to cap your system somewhere. | |
| Jun 19, 2015 at 15:23 | comment | added | diffracteD | explanation is highly motivating. But I got some basic query. What if I use only the aromatic geometry here and truncate everything else, i mean why I need to cap ? Given that this is an amino acid chain, polarizibility won't be so high in this case may be. | |
| Jun 17, 2015 at 16:01 | history | edited | LordStryker | CC BY-SA 3.0 |
minor tweaks
|
| Apr 26, 2012 at 19:52 | history | edited | LordStryker | CC BY-SA 3.0 |
added 203 characters in body
|
| Apr 26, 2012 at 2:12 | history | edited | LordStryker | CC BY-SA 3.0 |
added 1 characters in body
|
| Apr 25, 2012 at 21:12 | history | edited | LordStryker | CC BY-SA 3.0 |
added 437 characters in body
|
| Apr 25, 2012 at 21:00 | history | edited | LordStryker | CC BY-SA 3.0 |
Forgot to mention basis sets.
|
| Apr 25, 2012 at 20:54 | history | edited | LordStryker | CC BY-SA 3.0 |
Forgot to mention basis sets.
|
| Apr 25, 2012 at 20:48 | history | answered | LordStryker | CC BY-SA 3.0 |