How to connect structures in Avogadro at certain angles?

Question

I am working with this carbon nano-structure in Avogadro and the junction between my two nano-structures I try to join never seems to be aligned well. It always seems to be off kilter, which is most likely due to how I move the junction into position (manually dragging).

I posted a picture of my issue above. Where the two white arrows are is what is bothering me. I would like those to be as vertical as possible but I do not know of ways to do this aside from manually adjusting the atoms/bonds, which I assume would not get them to align exactly.

UPDATE:

As per khaverim's advice, I followed his first instructions, using MMFF94 instead of UFF (forgot to change it and my structure is large so it takes a while to optmize, will try with UFF later), and got the following structure:

I am pretty sure they are all equal angled, at least they look to be so, so thanks.

If you don't mind, please share a link to the .xyz file of your system. — khaverim, Commented Mar 6, 2017 at 3:55
I'm afraid I don't think this is at all possible with Avogardo. I personally have little to no experience with the program itself, as I find it especially tedious to build a molecule with symmetric features there. As far as I know, it only has drag and drop tools to manipulate the geometry. If you open up your question to suggest alternative programs, you probably get a workable solution. I'd think it would be quite easy with ChemCraft which is unfortunately not free. — Martin - マーチン, Commented Mar 6, 2017 at 5:35
I do not have access to it right now, but the build tool of Turbomole (as bundled with TmoleX) is free for academic or personal use and cross-platform. I shall endeavour to post a picture of its application later, given that the only available answer thus far resorts to outside programs. — TAR86, Commented Mar 6, 2017 at 6:05
@Martin-マーチン How can I edit the bounty to allow for your response. Also, would the trial version of ChemCraft allow me to do this? — Ro Siv, Commented Mar 6, 2017 at 14:42
@khaverim I would need to ask my advisor for permission to link the .xyz file sorry. — Ro Siv, Commented Mar 6, 2017 at 14:43

khaverim · Accepted Answer · 2017-03-07 14:29:11Z

Did you try a (Universal Force-Field) geometry optimization? I would:

Select all atoms
Deselect (hold Ctrl + click) the 4 (6? 8?) carbons of interest
Click Extensions -> Molecular Mechanics -> Ignore Selection
Click Extensions -> Optimize Geometry

Alternatively, you could optimize a few more atoms around/in the bridge while the others are constrained. The G.O. algorithm is pretty robust and handles many systems quite well. A simple example of hand-drawn cyclohexane:

I got a result like this by making 2 nanotubes with chiral index (4,4), drawing 6 bonds and optimizing the bridge:

If this is ineffective, I would resort to:

Change the 4 carbons to different elements e.g.

$\ce{O H}$

$\ce{N S}$

(like the arrangement you have in the picture, so you can identify them later)

Click File -> Save As... and save the file as an .xyz
Calculate the O-N and H-S distance by $r_{ij} = \sqrt{\Delta x^2 + \Delta y^2 + \Delta z^2}$ from the coordinates in the .xyz file.
Ideally, Avogadro saved the .xyz coordinates aligned in z (which is default when you draw molecules without rotating the initial view).
(Even if not,) re-write the coordinates of the atoms aligned in x and z, e.g. $\ce{O}$ at $(x, y, z)$; $\ce{N}$ at $(x, y-r, z)$.
Or (yikes) write a quick program to generate possible systems with the fixed $r$ you calculated, name them system-000.xyz, system-001.xyz, system-002.xyz, etc., and view the "trajectory" frames until you find one pleasing. (Viewing can be made much easier with VMD, e.g. vmd system-*.xyz).

Avoiding Avogadro: If you use Molden and load your system (as an .xyz, .car, .pdb etc.), you can use the ZMAT-editor to manually change bond angles and dihedrals:

Finally, if all else fails, it may be time to consider a full quantum-mechanical treatment of the system (if you're familiar with High Performance Computing) with a free (for academia!) program like Orca (where one can constrain certain atoms during the optimization). An example input would be:

! hf 6-31g* opt  # or copt, for cartesian optimization

%pal
nprocs 128   # num. processors
end

%scf
maxiter 2000 # max self-consistent field iterations
end

%geom
Constraints # atoms to keep fixed starting at index 0
{C 61 C}
{C 62 C}
{C 290 C}
{C 291 C}
{C 292 C}
end
end


*xyz 0 1  # charge=0; mult=2S+1 = 1 (closed shell)
  C      -1.306743      4.170005      1.012072
  C      -0.042414      3.718873      0.686759
  C       0.210647      2.367809      0.785537
  C      -2.267754      3.271952      1.435683
  C      -2.920909      0.889649      1.948837
  C      -4.153277      1.187877      2.498723
  C      -4.989183      0.155126      2.896328
  C      -4.571713     -1.152339      2.735382
  C      -3.332221     -1.380404      2.172864
....... etc.
*

Even though I like Molden a lot, it often has problems finding a good z-matrix to manipulate for complex systems. Changing one angle can easily ruin the whole molecule depending on how the relative connections are defined. However, I kind of agree that this task needs a different program than Avogadro. — Martin - マーチン, Commented Mar 6, 2017 at 5:40
@Martin-マーチン Or "simple" systems with high symmetry. — LordStryker, Commented Mar 6, 2017 at 14:27
@LordStryker Indeed. So far I only know that ChemCraft handles symmetry well. — Martin - マーチン, Commented Mar 6, 2017 at 15:09
@khaverim In your latest picture you made a bridge, even though I wanted pentagons to compose the bridge only, and it appears you have squares, which molecules did you select before optimizing the bridge? Only the ones within the bridge? And then did you ignore the rest of the selection before optimizing? Also, as an aside why use UFF as opposed to other optimizations? Thanks. — Ro Siv, Commented Mar 6, 2017 at 15:44
@RoSiv to clarify: you want 5 bonds linking the two tubes? It looks like an even number in your picture, like 4 maybe. I did the procedure in the first part of my answer: select all, deselect bonding atoms (which is 6 in my example), ignore selection, optimize. I say UFF because sometimes it is necessary if you have a large system. Otherwise Avogadro defaults to a better force-field. (The program usually gives you the option if the system is too big to handle with non-UFF) — khaverim, Commented Mar 6, 2017 at 15:55

Community · Accepted Answer · 2020-06-11 10:20:38Z

I don't know if you can do it with Avogadro, since I have no extended experience with the program. As far as I can see, there is no possibility to edit bond lengths/ angles/ dihedral angles directly. It provides a cartesian coordinate editor, but that's as tedious to manipulate your structure with as it is by doing it by hand.

I assume your problem is quite simple to be solved with ChemCraft. This program provides the tool to merge and align two structures from two different windows. This allows you to easily combine pre-computed fragments without loosing symmetry and not doing any calculations by hand.

Since I have no access to any of your structures, I am going to run you through it with an example. I am going to cup a $\ce{C70}$ nano-tube fragment with a $\ce{C40}$ buckminster fullerene, twice. Both fragments have (at least) $C_5$ symmentry, but this is no necessity. At the end we will produce a Fullerene with $D_\mathrm{5h}$ symmetry. For reasons of spacing this post, I'll include the coordinates at the end. (I am using build 485 currently, but the updated versions should still be able to perform this.)

You start with opening two instances of ChemCraft and loading each fragment into one. You want the parts to be aligned facing each other. In my layout I am modifying the $\ce{C70}$ fragment on the left, while the window on the right provides me with the fragments I use (not that it matters in this context). After this is done, you select the atoms you want to align in each window. The more atoms you select, the more input you provide for the program to align structures. Your display should look somewhat like below:

In the left window you choose "Tools > Structure combiner > Merge two structures from two Chemcraft windows by selected subunits". Because of the high symmetry the algorithm might get the orientation wrong. It is then best to try selecting (one or two) fewer atoms.

The right window should now look like below. Obviously the atoms you have taken to align are double in the mix. In some structures you can easily select them and delete them, when they are matching too well, you can switch between displays.

If you decide to "show erasen atoms" they will be displayed as dummies; after you click apply those will disappear and the program will re-bond you molecule.
Now one side is successfully capped, and I'll proceed with adding the second cup. We have created a nice little nano-pill. From the menu, you can choose to symmetrise the molecule. Ideally in this case it should already be very, very close to $D_\mathrm{5h}$. Cartesian space will obviously introduce some artefacts. Coose "Edit > Set point group ... > Auto" to let the program determine it for you.

Indeed there is a slight variation for the point group. Fortunately the program can also correct for it.

You don't need to stop there. ChameCraft comes with a xyz/ distance/ angle/ dihedral editor on the lower left corner of the window, dpending on how many atoms you select. You can choose whether you want to average the structure or only move the last selected atom. If the atoms are not connected with visible bonds, it will manipulate the whole fragment accordingly. With this feature you can fine tune everything, but then you might need your pen, paper and calculator again.

As I don't know the context of your research, it should suffice to say that these are techniques for creating suitable input geometries for more advanced calculation programs, of which there are quite a few. A well designed geometry might take crucial optimisation time off your hands. I am not sure how well suited force field methods are for nanotubes, and while Avogadro provides methodology for simple organic molecules, projects like this might just be too complex for it to be reasonable. As far as I know, Avogadro has no symmetry recognition.

Appendix

The $\ce{C70}$ fragment has the following coordinates (in angstrom):

70
symmetry c1
C        1.385307752     -3.115487343     -5.540304632
C        2.534920901     -2.280244499     -5.540304632
C        3.391088177      0.354767430     -5.540304632
C        2.951975027      1.706218740     -5.540304632
C        0.710500000      3.334745672     -5.540304632
C       -0.710500000      3.334745672     -5.540304632
C       -2.951975027      1.706218740     -5.540304632
C       -3.391088176      0.354767430     -5.540304632
C       -2.534920901     -2.280244499     -5.540304632
C       -1.385307752     -3.115487343     -5.540304632
C       -0.710500000     -3.334745672     -4.309125825
C        0.710500000     -3.334745672     -4.309125825
C        1.385307752     -3.115487343     -3.077947018
C        2.534920901     -2.280244499     -3.077947018
C        2.951975027     -1.706218740     -4.309125825
C        3.391088177     -0.354767430     -4.309125825
C        3.391088177      0.354767430     -3.077947018
C        2.951975027      1.706218740     -3.077947018
C        2.534920901      2.280244499     -4.309125825
C        1.385307752      3.115487343     -4.309125825
C        0.710500000      3.334745672     -3.077947018
C       -0.710500000      3.334745672     -3.077947018
C       -1.385307752      3.115487343     -4.309125825
C       -2.534920901      2.280244499     -4.309125825
C       -2.951975027      1.706218740     -3.077947018
C       -3.391088176      0.354767430     -3.077947018
C       -3.391088176     -0.354767430     -4.309125825
C       -2.951975027     -1.706218740     -4.309125825
C       -2.534920901     -2.280244499     -3.077947018
C       -1.385307752     -3.115487343     -3.077947018
C       -0.710500000     -3.334745672     -1.846768211
C        0.710500000     -3.334745672     -1.846768211
C        1.385307752     -3.115487343     -0.615589404
C        2.534920901     -2.280244499     -0.615589404
C        2.951975027     -1.706218740     -1.846768211
C        3.391088176     -0.354767430     -1.846768211
C        3.391088176      0.354767430     -0.615589404
C        2.951975027      1.706218740     -0.615589404
C        2.534920901      2.280244499     -1.846768211
C        1.385307752      3.115487343     -1.846768211
C        0.710500000      3.334745672     -0.615589404
C       -0.710500000      3.334745672     -0.615589404
C       -1.385307752      3.115487343     -1.846768211
C       -2.534920901      2.280244499     -1.846768211
C       -2.951975027      1.706218740     -0.615589404
C       -3.391088176      0.354767430     -0.615589404
C       -3.391088176     -0.354767430     -1.846768211
C       -2.951975027     -1.706218740     -1.846768211
C       -2.534920901     -2.280244499     -0.615589404
C       -1.385307752     -3.115487343     -0.615589404
C       -0.710500000     -3.334745672      0.615589404
C        0.710500000     -3.334745672      0.615589404
C        1.385307752     -3.115487343      1.846768211
C        2.534920901     -2.280244499      1.846768211
C        2.951975027     -1.706218740      0.615589404
C        3.391088176     -0.354767430      0.615589404
C        3.391088176      0.354767430      1.846768211
C        2.951975027      1.706218740      1.846768211
C        2.534920901      2.280244499      0.615589404
C        1.385307752      3.115487343      0.615589404
C        0.710500000      3.334745672      1.846768211
C       -0.710500000      3.334745672      1.846768211
C       -1.385307752      3.115487343      0.615589404
C       -2.534920901      2.280244499      0.615589404
C       -2.951975027      1.706218740      1.846768211
C       -3.391088176      0.354767430      1.846768211
C       -3.391088176     -0.354767430      0.615589404
C       -2.951975027     -1.706218740      0.615589404
C       -2.534920901     -2.280244499      1.846768211
C       -1.385307752     -3.115487343      1.846768211

The $\ce{C40}$ fragment has the following coordinates:

40
symmetry c1
C       -0.004840185     -3.437248260     -1.231937277
C       -1.267748660     -3.000481413     -1.692390182
C       -2.250219438     -2.561103110     -0.763208689
C       -3.030739803     -1.417632648     -1.047784233
C       -2.833456162     -0.706703611     -2.263242764
C       -2.833456162      0.706703611     -2.263242764
C       -3.030739803      1.417632648     -1.047784233
C       -2.250219438      2.561103110     -0.763208689
C       -1.267748660      3.000481413     -1.692390182
C       -0.004840185      3.437248260     -1.231937277
C        0.283148522      3.437248269      0.160450194
C        1.546056995      3.000481414      0.620903095
C        2.528527766      2.561103104     -0.308278399
C        3.309048125      1.417632641     -0.023702855
C        3.111764498      0.706703610      1.191755677
C        3.111764498     -0.706703610      1.191755677
C        3.309048125     -1.417632641     -0.023702855
C        2.528527766     -2.561103104     -0.308278399
C        1.546056995     -3.000481414      0.620903095
C        0.283148522     -3.437248269      0.160450194
C       -0.693482914     -3.000481414      1.084109073
C       -1.963942392     -2.561103104      0.620903094
C       -2.567533811     -1.417632641      1.191755675
C       -3.226850870     -0.710929034      0.160450192
C       -3.226850870      0.710929034      0.160450192
C       -2.567533811      1.417632641      1.191755675
C       -1.963942392      2.561103104      0.620903094
C       -0.693482914      3.000481414      1.084109073
C       -0.034165862      2.293777797      2.115414553
C        1.349945920      2.293777797      1.829137515
C        2.135133060      1.143470461      2.115414554
C        1.531541637      0.000000000      2.686267134
C        2.135133060     -1.143470461      2.115414554
C        1.349945920     -2.293777797      1.829137515
C       -0.034165862     -2.293777797      2.115414553
C       -0.641366192     -1.143470461      2.689680299
C       -1.904274667     -0.706703610      2.229227401
C       -1.904274667      0.706703610      2.229227401
C       -0.641366192      1.143470461      2.689680299
C        0.139154169      0.000000000      2.974255840

Final $\ce{C130}$ nano-pill:

130
symmetry d5h
C        3.334745673     -0.710500000     -2.462357615
C        3.334745673      0.710500000     -2.462357615
C        3.115487344      1.385307752     -1.231178807
C        2.280244500      2.534920901     -1.231178807
C        1.706218741      2.951975027     -2.462357615
C        0.354767431      3.391088176     -2.462357615
C       -0.354767429      3.391088176     -1.231178807
C       -1.706218739      2.951975027     -1.231178807
C       -2.280244498      2.534920901     -2.462357615
C       -3.115487342      1.385307752     -2.462357615
C       -3.334745671      0.710500000     -1.231178807
C       -3.334745671     -0.710500000     -1.231178807
C       -3.115487342     -1.385307752     -2.462357615
C       -2.280244498     -2.534920901     -2.462357615
C       -1.706218739     -2.951975027     -1.231178807
C       -0.354767429     -3.391088176     -1.231178807
C        0.354767431     -3.391088176     -2.462357615
C        1.706218741     -2.951975027     -2.462357615
C        2.280244500     -2.534920901     -1.231178807
C        3.115487344     -1.385307752     -1.231178807
C        3.334745673     -0.710500000      0.000000000
C        3.334745673      0.710500000      0.000000000
C        3.115487344      1.385307752      1.231178807
C        2.280244500      2.534920901      1.231178807
C        1.706218741      2.951975027      0.000000000
C        0.354767431      3.391088176      0.000000000
C       -0.354767429      3.391088176      1.231178807
C       -1.706218739      2.951975027      1.231178807
C       -2.280244498      2.534920901      0.000000000
C       -3.115487342      1.385307752      0.000000000
C       -3.334745671      0.710500000      1.231178807
C       -3.334745671     -0.710500000      1.231178807
C       -3.115487342     -1.385307752      0.000000000
C       -2.280244498     -2.534920901      0.000000000
C       -1.706218739     -2.951975027      1.231178807
C       -0.354767429     -3.391088176      1.231178807
C        0.354767431     -3.391088176      0.000000000
C        1.706218741     -2.951975027      0.000000000
C        2.280244500     -2.534920901      1.231178807
C        3.115487344     -1.385307752      1.231178807
C        3.334745673     -0.710500000      2.462357615
C        3.334745673      0.710500000      2.462357615
C        1.706218741      2.951975027      2.462357615
C        0.354767431      3.391088176      2.462357615
C       -2.280244498      2.534920901      2.462357615
C       -3.115487342      1.385307752      2.462357615
C       -3.115487342     -1.385307752      2.462357615
C       -2.280244498     -2.534920901      2.462357615
C        0.354767431     -3.391088176      2.462357615
C        1.706218741     -2.951975027      2.462357615
C       -1.717973404      3.000456514      3.693536421
C       -0.373754410      3.437219745      3.693536421
C        0.373754411      3.437219749      4.903041136
C        1.717973407      3.000456525      4.903041139
C        2.322720745      2.561081857      3.693536424
C        3.153493774      1.417620883      3.693536424
C        3.384486708      0.706697748      4.903041140
C        3.384486708     -0.706697748      4.903041140
C        3.153493774     -1.417620883      3.693536424
C        2.322720745     -2.561081857      3.693536424
C        1.717973407     -3.000456525      4.903041139
C        0.373754411     -3.437219749      4.903041136
C       -0.373754410     -3.437219745      3.693536421
C       -1.717973404     -3.000456514      3.693536421
C       -2.322720749     -2.561081859      4.903041134
C       -3.153493775     -1.417620884      4.903041132
C       -3.384486697     -0.706697747      3.693536419
C       -3.384486697      0.706697747      3.693536419
C       -3.153493775      1.417620884      4.903041132
C       -2.322720749      2.561081859      4.903041134
C       -1.579654762      2.561081856      6.105357127
C       -0.227398602      3.000456514      6.105357127
C        0.745287399      2.293758766      6.848429277
C        1.947593421      2.293758772      6.105357132
C        2.783333689      1.143460975      6.105357132
C        2.411800691      0.000000000      6.848429279
C        2.783333689     -1.143460975      6.105357132
C        1.947593421     -2.293758772      6.105357132
C        0.745287399     -2.293758766      6.848429277
C       -0.227398602     -3.000456514      6.105357127
C       -1.579654762     -2.561081857      6.105357127
C       -1.951187752     -1.417620880      6.848429274
C       -2.923873754     -0.710923134      6.105357124
C       -2.923873754      0.710923134      6.105357124
C       -1.951187752      1.417620880      6.848429274
C       -0.972686005      0.706697746      7.595944297
C        0.371532989      1.143460974      7.595944302
C        1.202306016      0.000000000      7.595944306
C        0.371532989     -1.143460974      7.595944302
C       -0.972686005     -0.706697746      7.595944297
C       -1.717973404     -3.000456514     -3.693536421
C       -0.373754410     -3.437219745     -3.693536421
C        0.373754411     -3.437219749     -4.903041136
C        1.717973407     -3.000456525     -4.903041139
C        2.322720745     -2.561081857     -3.693536424
C        3.153493774     -1.417620883     -3.693536424
C        3.384486708     -0.706697748     -4.903041140
C        3.384486708      0.706697748     -4.903041140
C        3.153493774      1.417620883     -3.693536424
C        2.322720745      2.561081857     -3.693536424
C        1.717973407      3.000456525     -4.903041139
C        0.373754411      3.437219749     -4.903041136
C       -0.373754410      3.437219745     -3.693536421
C       -1.717973404      3.000456514     -3.693536421
C       -2.322720749      2.561081859     -4.903041134
C       -3.153493775      1.417620884     -4.903041132
C       -3.384486697      0.706697747     -3.693536419
C       -3.384486697     -0.706697747     -3.693536419
C       -3.153493775     -1.417620884     -4.903041132
C       -2.322720749     -2.561081859     -4.903041134
C       -1.579654762     -2.561081857     -6.105357127
C       -0.227398602     -3.000456514     -6.105357127
C        0.745287399     -2.293758766     -6.848429277
C        1.947593421     -2.293758772     -6.105357132
C        2.783333689     -1.143460975     -6.105357132
C        2.411800691      0.000000000     -6.848429279
C        2.783333689      1.143460975     -6.105357132
C        1.947593421      2.293758772     -6.105357132
C        0.745287399      2.293758766     -6.848429277
C       -0.227398602      3.000456514     -6.105357127
C       -1.579654762      2.561081856     -6.105357127
C       -1.951187752      1.417620880     -6.848429274
C       -2.923873754      0.710923134     -6.105357124
C       -2.923873754     -0.710923134     -6.105357124
C       -1.951187752     -1.417620880     -6.848429274
C       -0.972686005     -0.706697746     -7.595944297
C        0.371532989     -1.143460974     -7.595944302
C        1.202306016      0.000000000     -7.595944306
C        0.371532989      1.143460974     -7.595944302
C       -0.972686005      0.706697746     -7.595944297

This method actually worked better than the first answer, as I got weird angles on one part of the joining nanotube when just using Avogadro. Is there a way to split the bounty between you and khaverim? — Ro Siv, Commented Mar 9, 2017 at 17:18
@RoSiv No, there is no way to split the bounty, but that is okay. I am happy to help and I really don't need more reputation. After all, your question gave me some nice opportunity to play with my toys :D — Martin - マーチン, Commented Mar 10, 2017 at 10:14

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How to connect structures in Avogadro at certain angles?

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How to connect structures in Avogadro at certain angles?

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