I have been working in the cylindrospermopsin structure using chemfig. The structure is:enter image description here

I draw it with te following code:

\documentclass[12pt, border={10pt 10pt 10pt 10pt}]{standalone}
\usepackage[utf8]{inputenc}%Para copiar caracteres especiais como ç, á, à
\usepackage[T1]{fontenc}%Para copiar caracteres especiais como ç, á, à

The result is:

enter image description here

My questions:

  1. How can I put the positive charge out the structure, like the example?
  2. How can I draw the double bonds with one dashed line between N, NH1 and NH2?
  3. How can I link the NH2 atom correctly with the hydrogen outside?
  4. How can I put HN instead of M? I've been trying, but the bounds link in the H atom

Any help, indication, suggestion?

  • 1
    For the positive charge (1) I'd use an invisible bond: tex.stackexchange.com/q/267684 For the atom groups and the bonds (3 & 4) I'd use the departure/arrival option: tex.stackexchange.com/q/327278
    – cgnieder
    May 28, 2017 at 16:16
  • 1
    For the delocalized double bond (2) have a look in the chemfig manual section Delocalized double bonds
    – cgnieder
    May 28, 2017 at 16:19
  • @clemens I'm not understandig how works the delocalized double bonds. I pasted the code from the manual and it is not working. The message isInvalid code (1000), should be in the range 0..15. \catcode‘\@ Missing $ inserted. \catcode‘\@ Missing number, treated as zero. \catcode‘ Missing number, treated as zero. \catcode‘ You can't use `\spacefactor' in math mode. \catcode‘\@ Package pgfkeys Error: I do not know the key '/tikz/decoration', to which you May 28, 2017 at 19:38
  • 1
    @DanielValencia You need to change to ` (backtick)
    – Troy
    May 29, 2017 at 2:56
  • @ DanielValencia errors without examples to reproduce them are often impossible to debug. I would have added an answer but @Troy already did, so…
    – cgnieder
    May 29, 2017 at 7:30

1 Answer 1

\documentclass[12pt, border=3mm,tikz]{standalone}
\usepackage[utf8]{inputenc}%Para copiar caracteres especiais como ç, á, à
\usepackage[T1]{fontenc}%Para copiar caracteres especiais como ç, á, à
\usetikzlibrary{decorations.markings} % You need this for q2

% From package documentation, pg 29, change ‘ to ` (2 instances)
    ddbond/.style args={#1}{
            mark=at position 0 with {
                \coordinate (CF@startdeloc) at (0,\dimexpr#1\CF@double@sep/2)
                coordinate (CF@startaxis) at (0,\dimexpr-#1\CF@double@sep/2);
            mark=at position 1 with {
                \coordinate (CF@enddeloc) at (0,\dimexpr#1\CF@double@sep/2)
                coordinate (CF@endaxis) at (0,\dimexpr-#1\CF@double@sep/2);
                \draw[dash pattern=on 2pt off 1.5pt] (CF@startdeloc)--(CF@enddeloc);
                \draw (CF@startaxis)--(CF@endaxis);



Just some small notes on each question. The very well-written package documentation goes into more details, I'll just point you to what's relevant.

  1. with -[7,0.2,,,draw=none]{\scriptstyle+}: This draws a + at the end of an invisible bond, drawn -45deg from the C atom (that's what the 7 means), 0.2*bond length away.

  2. with -[,,,,ddbond={+/-}]: this is taken from the chemfig documentation, pg 29. You need to use \usetikzlibrary{decorations.markings} in the preamble for this to work, and add the relevant part in the preamble. Then just add the ddbond={+} or ddbond={-} option to the relevant bonds (after 4 commas in the optional argument).

  3. with -[:-108,,,1]N?[a]H2: This bond is drawn from the + to the NH2, so set its arrival atom to 1 explicitly, which is the N atom. (Try removing the 1 in the argument, note what you get).

  4. with -[,,,2]HN instead of -M Similar with question 3, set the arrival atom to the second atom (the N), by passing 2 to the fourth optional argument.


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  • The LaTeX versions of \catcode`\@=11 and \catcode`\@=12 are \makeatletter and \makeatother
    – cgnieder
    May 29, 2017 at 7:28
  • I have recently been trying to use delocalized bonds and have copied the code from pg 30 character for character but I am getting an error {! Undefined control sequence.<argument> 0,\dimexpr +\CF_doublesep/2'}. The error is basically saying it needs a number rather than a {+} or a {-} in the ddbond={+/-}. Can anyone else repeat this and get the same issue?
    – Leeser
    Jan 27, 2020 at 16:03

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