Easy way to draw atomic orbitals and integrate them into ChemFig structures
10
I'm looking for a method to draw molecules as skeleton structures via chemfig and include some atomic orbitals (i.e. s, p and d orbitals and some sp-hybrid orbitals too) into them (at positions where chemfig places atomlabels, i.e. at the ends of bonds). I give you an example:
The shapes needed for the different orbitals essentially boil down to the following
The right appearence would then be achieved by rotating and scaling these orbitals. This should ideally work with a simple command which tells chemfig to insert an orbital of a certain type (i.e. s, p, d, ...) at an atomic position and how this orbital shall be rotated, scaled or colored and which phase it should have. Is this doable? Or is there a package out there which provides such a functionality?
tikz-pgf chemfig
asked Jun 21 '12 at 15:15
Philipp
2,38531645
add a comment |
10
I'm looking for a method to draw molecules as skeleton structures via chemfig and include some atomic orbitals (i.e. s, p and d orbitals and some sp-hybrid orbitals too) into them (at positions where chemfig places atomlabels, i.e. at the ends of bonds). I give you an example:
The shapes needed for the different orbitals essentially boil down to the following
The right appearence would then be achieved by rotating and scaling these orbitals. This should ideally work with a simple command which tells chemfig to insert an orbital of a certain type (i.e. s, p, d, ...) at an atomic position and how this orbital shall be rotated, scaled or colored and which phase it should have. Is this doable? Or is there a package out there which provides such a functionality?
tikz-pgf chemfig
asked Jun 21 '12 at 15:15
Philipp
2,38531645
add a comment |
10
10
10
2
I'm looking for a method to draw molecules as skeleton structures via chemfig and include some atomic orbitals (i.e. s, p and d orbitals and some sp-hybrid orbitals too) into them (at positions where chemfig places atomlabels, i.e. at the ends of bonds). I give you an example:
The shapes needed for the different orbitals essentially boil down to the following
The right appearence would then be achieved by rotating and scaling these orbitals. This should ideally work with a simple command which tells chemfig to insert an orbital of a certain type (i.e. s, p, d, ...) at an atomic position and how this orbital shall be rotated, scaled or colored and which phase it should have. Is this doable? Or is there a package out there which provides such a functionality?
tikz-pgf chemfig
asked Jun 21 '12 at 15:15
Philipp
2,38531645
I'm looking for a method to draw molecules as skeleton structures via chemfig and include some atomic orbitals (i.e. s, p and d orbitals and some sp-hybrid orbitals too) into them (at positions where chemfig places atomlabels, i.e. at the ends of bonds). I give you an example:
The shapes needed for the different orbitals essentially boil down to the following
The right appearence would then be achieved by rotating and scaling these orbitals. This should ideally work with a simple command which tells chemfig to insert an orbital of a certain type (i.e. s, p, d, ...) at an atomic position and how this orbital shall be rotated, scaled or colored and which phase it should have. Is this doable? Or is there a package out there which provides such a functionality?
tikz-pgf chemfig
tikz-pgf chemfig
asked Jun 21 '12 at 15:15
Philipp
2,38531645
asked Jun 21 '12 at 15:15
Philipp
2,38531645
asked Jun 21 '12 at 15:15
Philipp
2,38531645
asked Jun 21 '12 at 15:15
Philipp
2,38531645
asked Jun 21 '12 at 15:15
Philipp
2,38531645
2,38531645
add a comment |
add a comment |
2 Answers
2
active
oldest
votes
11
The chemmacros package offers s,p and sp-hybrid orbitals (based on TikZ), d orbitals are missing (for now). These are examples from the documentation:
documentclass{article}
usepackage{chemfig,chemmacros}
begin{document}
setbondoffset{0pt}
chemsetup[orbital]{
overlay ,
opacity = .75 ,
p/scale = 1.6 ,
s/color = blue!50 ,
s/scale = 1.6
}
chemfig{orbital{s}-[:-20]{orbital[scale=2]{p}}{orbital[half,angle=0]{p}}{orbital[angle=170,half]{p}}{orbital[angle=-150,half]{p}}(-[:-150]orbital{s})-orbital{s}}
end{document}
documentclass{article}
usepackage{chemfig,chemmacros}
begin{document}
chemsetup[orbital]{
overlay,
p/color = black!70
}
setbondoffset{0pt}
chemfig{?orbital{p}-[,1.3]{orbital[phase=-]{p}}-[:30,1.1]orbital{p}-[:150,.9]{orbital[phase=-]{p}}-[4,1.3]orbital{p}-[:-150,1.1]{orbital[phase=-]{p}}?}
end{document}
answered Jun 21 '12 at 15:37
clemens
51k5129277
Thank you. That's an awesome package. That mostly solves my problem. There is only one tiny drawback: it includes s, p and sp-hybrid orbitals but no d orbitals. Is there also a solution for that? Or could you include them in a future version ofchemmacros?
– Philipp
Jun 21 '12 at 15:46
@Philipp I have that on my TODO list for a while now. Maybe I can put it a bit higher on my list, though.
– clemens
Jun 21 '12 at 15:48
Sorry, I seem to have skipped the sentence where you alread wrote that there are no d orbitals included in the package. I guess I got distracted by the stunning pictures ;) It's nice to hear that it is already on your TODO list. Until then I will try to get by with ChemDraw when I have to draw something with d orbitals.
– Philipp
Jun 21 '12 at 15:54
The only real problem is thed$_z$orbital. The others could be modelled by using 4 timesorbital[half]{p}with appropriate angles and colors...
– clemens
Jun 21 '12 at 16:38
I guess it is the torus contained in the $mathrm{d}_{z^2}$ orbital which makes things complicated. Would it make things easier to build the orbital from two half p orbitals sandwiching an ellipse between them (like in the pictures contained in my question) or can't this be handled properly when it comes to rotation, scaling etc.?
– Philipp
Jun 22 '12 at 11:29
|
show 5 more comments
0
I have used your suggestion
chemsetup[orbital]{
overlay,
p/color = black!40
}
setbondoffset{0pt}
chemfig{?orbital{s}}
to draw an S orbital, but the figure appears too small. How can I turn it greater? Thanks.
edited 3 mins ago
Kurt
35.1k847158
answered 33 mins ago
Décio Krause
1
New contributor
Décio Krause is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
1
Welcome, please ask a new question. This does not answer the question at the very top.
– Johannes_B
30 mins ago
add a comment |
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2 Answers
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11
The chemmacros package offers s,p and sp-hybrid orbitals (based on TikZ), d orbitals are missing (for now). These are examples from the documentation:
documentclass{article}
usepackage{chemfig,chemmacros}
begin{document}
setbondoffset{0pt}
chemsetup[orbital]{
overlay ,
opacity = .75 ,
p/scale = 1.6 ,
s/color = blue!50 ,
s/scale = 1.6
}
chemfig{orbital{s}-[:-20]{orbital[scale=2]{p}}{orbital[half,angle=0]{p}}{orbital[angle=170,half]{p}}{orbital[angle=-150,half]{p}}(-[:-150]orbital{s})-orbital{s}}
end{document}
documentclass{article}
usepackage{chemfig,chemmacros}
begin{document}
chemsetup[orbital]{
overlay,
p/color = black!70
}
setbondoffset{0pt}
chemfig{?orbital{p}-[,1.3]{orbital[phase=-]{p}}-[:30,1.1]orbital{p}-[:150,.9]{orbital[phase=-]{p}}-[4,1.3]orbital{p}-[:-150,1.1]{orbital[phase=-]{p}}?}
end{document}
answered Jun 21 '12 at 15:37
clemens
51k5129277
Thank you. That's an awesome package. That mostly solves my problem. There is only one tiny drawback: it includes s, p and sp-hybrid orbitals but no d orbitals. Is there also a solution for that? Or could you include them in a future version ofchemmacros?
– Philipp
Jun 21 '12 at 15:46
@Philipp I have that on my TODO list for a while now. Maybe I can put it a bit higher on my list, though.
– clemens
Jun 21 '12 at 15:48
Sorry, I seem to have skipped the sentence where you alread wrote that there are no d orbitals included in the package. I guess I got distracted by the stunning pictures ;) It's nice to hear that it is already on your TODO list. Until then I will try to get by with ChemDraw when I have to draw something with d orbitals.
– Philipp
Jun 21 '12 at 15:54
The only real problem is thed$_z$orbital. The others could be modelled by using 4 timesorbital[half]{p}with appropriate angles and colors...
– clemens
Jun 21 '12 at 16:38
I guess it is the torus contained in the $mathrm{d}_{z^2}$ orbital which makes things complicated. Would it make things easier to build the orbital from two half p orbitals sandwiching an ellipse between them (like in the pictures contained in my question) or can't this be handled properly when it comes to rotation, scaling etc.?
– Philipp
Jun 22 '12 at 11:29
|
show 5 more comments
11
The chemmacros package offers s,p and sp-hybrid orbitals (based on TikZ), d orbitals are missing (for now). These are examples from the documentation:
documentclass{article}
usepackage{chemfig,chemmacros}
begin{document}
setbondoffset{0pt}
chemsetup[orbital]{
overlay ,
opacity = .75 ,
p/scale = 1.6 ,
s/color = blue!50 ,
s/scale = 1.6
}
chemfig{orbital{s}-[:-20]{orbital[scale=2]{p}}{orbital[half,angle=0]{p}}{orbital[angle=170,half]{p}}{orbital[angle=-150,half]{p}}(-[:-150]orbital{s})-orbital{s}}
end{document}
documentclass{article}
usepackage{chemfig,chemmacros}
begin{document}
chemsetup[orbital]{
overlay,
p/color = black!70
}
setbondoffset{0pt}
chemfig{?orbital{p}-[,1.3]{orbital[phase=-]{p}}-[:30,1.1]orbital{p}-[:150,.9]{orbital[phase=-]{p}}-[4,1.3]orbital{p}-[:-150,1.1]{orbital[phase=-]{p}}?}
end{document}
answered Jun 21 '12 at 15:37
clemens
51k5129277
Thank you. That's an awesome package. That mostly solves my problem. There is only one tiny drawback: it includes s, p and sp-hybrid orbitals but no d orbitals. Is there also a solution for that? Or could you include them in a future version ofchemmacros?
– Philipp
Jun 21 '12 at 15:46
@Philipp I have that on my TODO list for a while now. Maybe I can put it a bit higher on my list, though.
– clemens
Jun 21 '12 at 15:48
Sorry, I seem to have skipped the sentence where you alread wrote that there are no d orbitals included in the package. I guess I got distracted by the stunning pictures ;) It's nice to hear that it is already on your TODO list. Until then I will try to get by with ChemDraw when I have to draw something with d orbitals.
– Philipp
Jun 21 '12 at 15:54
The only real problem is thed$_z$orbital. The others could be modelled by using 4 timesorbital[half]{p}with appropriate angles and colors...
– clemens
Jun 21 '12 at 16:38
I guess it is the torus contained in the $mathrm{d}_{z^2}$ orbital which makes things complicated. Would it make things easier to build the orbital from two half p orbitals sandwiching an ellipse between them (like in the pictures contained in my question) or can't this be handled properly when it comes to rotation, scaling etc.?
– Philipp
Jun 22 '12 at 11:29
|
show 5 more comments
11
11
11
The chemmacros package offers s,p and sp-hybrid orbitals (based on TikZ), d orbitals are missing (for now). These are examples from the documentation:
documentclass{article}
usepackage{chemfig,chemmacros}
begin{document}
setbondoffset{0pt}
chemsetup[orbital]{
overlay ,
opacity = .75 ,
p/scale = 1.6 ,
s/color = blue!50 ,
s/scale = 1.6
}
chemfig{orbital{s}-[:-20]{orbital[scale=2]{p}}{orbital[half,angle=0]{p}}{orbital[angle=170,half]{p}}{orbital[angle=-150,half]{p}}(-[:-150]orbital{s})-orbital{s}}
end{document}
documentclass{article}
usepackage{chemfig,chemmacros}
begin{document}
chemsetup[orbital]{
overlay,
p/color = black!70
}
setbondoffset{0pt}
chemfig{?orbital{p}-[,1.3]{orbital[phase=-]{p}}-[:30,1.1]orbital{p}-[:150,.9]{orbital[phase=-]{p}}-[4,1.3]orbital{p}-[:-150,1.1]{orbital[phase=-]{p}}?}
end{document}
answered Jun 21 '12 at 15:37
clemens
51k5129277
The chemmacros package offers s,p and sp-hybrid orbitals (based on TikZ), d orbitals are missing (for now). These are examples from the documentation:
documentclass{article}
usepackage{chemfig,chemmacros}
begin{document}
setbondoffset{0pt}
chemsetup[orbital]{
overlay ,
opacity = .75 ,
p/scale = 1.6 ,
s/color = blue!50 ,
s/scale = 1.6
}
chemfig{orbital{s}-[:-20]{orbital[scale=2]{p}}{orbital[half,angle=0]{p}}{orbital[angle=170,half]{p}}{orbital[angle=-150,half]{p}}(-[:-150]orbital{s})-orbital{s}}
end{document}
documentclass{article}
usepackage{chemfig,chemmacros}
begin{document}
chemsetup[orbital]{
overlay,
p/color = black!70
}
setbondoffset{0pt}
chemfig{?orbital{p}-[,1.3]{orbital[phase=-]{p}}-[:30,1.1]orbital{p}-[:150,.9]{orbital[phase=-]{p}}-[4,1.3]orbital{p}-[:-150,1.1]{orbital[phase=-]{p}}?}
end{document}
answered Jun 21 '12 at 15:37
clemens
51k5129277
answered Jun 21 '12 at 15:37
clemens
51k5129277
answered Jun 21 '12 at 15:37
clemens
51k5129277
answered Jun 21 '12 at 15:37
clemens
51k5129277
51k5129277
Thank you. That's an awesome package. That mostly solves my problem. There is only one tiny drawback: it includes s, p and sp-hybrid orbitals but no d orbitals. Is there also a solution for that? Or could you include them in a future version ofchemmacros?
– Philipp
Jun 21 '12 at 15:46
@Philipp I have that on my TODO list for a while now. Maybe I can put it a bit higher on my list, though.
– clemens
Jun 21 '12 at 15:48
Sorry, I seem to have skipped the sentence where you alread wrote that there are no d orbitals included in the package. I guess I got distracted by the stunning pictures ;) It's nice to hear that it is already on your TODO list. Until then I will try to get by with ChemDraw when I have to draw something with d orbitals.
– Philipp
Jun 21 '12 at 15:54
The only real problem is thed$_z$orbital. The others could be modelled by using 4 timesorbital[half]{p}with appropriate angles and colors...
– clemens
Jun 21 '12 at 16:38
I guess it is the torus contained in the $mathrm{d}_{z^2}$ orbital which makes things complicated. Would it make things easier to build the orbital from two half p orbitals sandwiching an ellipse between them (like in the pictures contained in my question) or can't this be handled properly when it comes to rotation, scaling etc.?
– Philipp
Jun 22 '12 at 11:29
|
show 5 more comments
Thank you. That's an awesome package. That mostly solves my problem. There is only one tiny drawback: it includes s, p and sp-hybrid orbitals but no d orbitals. Is there also a solution for that? Or could you include them in a future version ofchemmacros?
– Philipp
Jun 21 '12 at 15:46
@Philipp I have that on my TODO list for a while now. Maybe I can put it a bit higher on my list, though.
– clemens
Jun 21 '12 at 15:48
Sorry, I seem to have skipped the sentence where you alread wrote that there are no d orbitals included in the package. I guess I got distracted by the stunning pictures ;) It's nice to hear that it is already on your TODO list. Until then I will try to get by with ChemDraw when I have to draw something with d orbitals.
– Philipp
Jun 21 '12 at 15:54
The only real problem is thed$_z$orbital. The others could be modelled by using 4 timesorbital[half]{p}with appropriate angles and colors...
– clemens
Jun 21 '12 at 16:38
I guess it is the torus contained in the $mathrm{d}_{z^2}$ orbital which makes things complicated. Would it make things easier to build the orbital from two half p orbitals sandwiching an ellipse between them (like in the pictures contained in my question) or can't this be handled properly when it comes to rotation, scaling etc.?
– Philipp
Jun 22 '12 at 11:29
Thank you. That's an awesome package. That mostly solves my problem. There is only one tiny drawback: it includes s, p and sp-hybrid orbitals but no d orbitals. Is there also a solution for that? Or could you include them in a future version of
chemmacros?– Philipp
Jun 21 '12 at 15:46
Thank you. That's an awesome package. That mostly solves my problem. There is only one tiny drawback: it includes s, p and sp-hybrid orbitals but no d orbitals. Is there also a solution for that? Or could you include them in a future version of
chemmacros?– Philipp
Jun 21 '12 at 15:46
@Philipp I have that on my TODO list for a while now. Maybe I can put it a bit higher on my list, though.
– clemens
Jun 21 '12 at 15:48
@Philipp I have that on my TODO list for a while now. Maybe I can put it a bit higher on my list, though.
– clemens
Jun 21 '12 at 15:48
Sorry, I seem to have skipped the sentence where you alread wrote that there are no d orbitals included in the package. I guess I got distracted by the stunning pictures ;) It's nice to hear that it is already on your TODO list. Until then I will try to get by with ChemDraw when I have to draw something with d orbitals.
– Philipp
Jun 21 '12 at 15:54
Sorry, I seem to have skipped the sentence where you alread wrote that there are no d orbitals included in the package. I guess I got distracted by the stunning pictures ;) It's nice to hear that it is already on your TODO list. Until then I will try to get by with ChemDraw when I have to draw something with d orbitals.
– Philipp
Jun 21 '12 at 15:54
The only real problem is the
d$_z$ orbital. The others could be modelled by using 4 times orbital[half]{p} with appropriate angles and colors...– clemens
Jun 21 '12 at 16:38
The only real problem is the
d$_z$ orbital. The others could be modelled by using 4 times orbital[half]{p} with appropriate angles and colors...– clemens
Jun 21 '12 at 16:38
I guess it is the torus contained in the $mathrm{d}_{z^2}$ orbital which makes things complicated. Would it make things easier to build the orbital from two half p orbitals sandwiching an ellipse between them (like in the pictures contained in my question) or can't this be handled properly when it comes to rotation, scaling etc.?
– Philipp
Jun 22 '12 at 11:29
I guess it is the torus contained in the $mathrm{d}_{z^2}$ orbital which makes things complicated. Would it make things easier to build the orbital from two half p orbitals sandwiching an ellipse between them (like in the pictures contained in my question) or can't this be handled properly when it comes to rotation, scaling etc.?
– Philipp
Jun 22 '12 at 11:29
|
show 5 more comments
0
I have used your suggestion
chemsetup[orbital]{
overlay,
p/color = black!40
}
setbondoffset{0pt}
chemfig{?orbital{s}}
to draw an S orbital, but the figure appears too small. How can I turn it greater? Thanks.
edited 3 mins ago
Kurt
35.1k847158
answered 33 mins ago
Décio Krause
1
New contributor
Décio Krause is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
1
Welcome, please ask a new question. This does not answer the question at the very top.
– Johannes_B
30 mins ago
add a comment |
0
I have used your suggestion
chemsetup[orbital]{
overlay,
p/color = black!40
}
setbondoffset{0pt}
chemfig{?orbital{s}}
to draw an S orbital, but the figure appears too small. How can I turn it greater? Thanks.
edited 3 mins ago
Kurt
35.1k847158
answered 33 mins ago
Décio Krause
1
New contributor
Décio Krause is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
1
Welcome, please ask a new question. This does not answer the question at the very top.
– Johannes_B
30 mins ago
add a comment |
0
0
0
I have used your suggestion
chemsetup[orbital]{
overlay,
p/color = black!40
}
setbondoffset{0pt}
chemfig{?orbital{s}}
to draw an S orbital, but the figure appears too small. How can I turn it greater? Thanks.
edited 3 mins ago
Kurt
35.1k847158
answered 33 mins ago
Décio Krause
1
New contributor
Décio Krause is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
I have used your suggestion
chemsetup[orbital]{
overlay,
p/color = black!40
}
setbondoffset{0pt}
chemfig{?orbital{s}}
to draw an S orbital, but the figure appears too small. How can I turn it greater? Thanks.
edited 3 mins ago
Kurt
35.1k847158
answered 33 mins ago
Décio Krause
1
New contributor
Décio Krause is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
edited 3 mins ago
Kurt
35.1k847158
edited 3 mins ago
Kurt
35.1k847158
edited 3 mins ago
Kurt
35.1k847158
35.1k847158
answered 33 mins ago
Décio Krause
1
New contributor
Décio Krause is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
answered 33 mins ago
Décio Krause
1
answered 33 mins ago
Décio Krause
1
1
New contributor
Décio Krause is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
Décio Krause is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Décio Krause is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
1
Welcome, please ask a new question. This does not answer the question at the very top.
– Johannes_B
30 mins ago
add a comment |
1
Welcome, please ask a new question. This does not answer the question at the very top.
– Johannes_B
30 mins ago
1
1
Welcome, please ask a new question. This does not answer the question at the very top.
– Johannes_B
30 mins ago
Welcome, please ask a new question. This does not answer the question at the very top.
– Johannes_B
30 mins ago
add a comment |
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