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I was able to draw using \chemmove, remember picture and @{} syntax for naming atoms and links. \documentclass[varwidth,border=50]{standalone} \usepackage{tikz} \usepackage{chemfig} \begin{document} \begin{tikzpicture}[remember picture, node distance=0] \node (foo){}; \node (a) [draw,minimum height=0.5cm,minimum width = 0.7cm, above of = foo, node ...


I cobbled this together using the example in the chemfig package (section 12.7). Edit: I also added a plain label (without arrows) next to the bond. I think this looks better because the line with arrows is not quite parallel to the line indicating the bond. \documentclass[a4paper, 12pt, twocolumn]{article} \usepackage[utf8]{inputenc} ...


A straightforward solution is to "bind" the submolecules, i.e., replace your code: \chemfig{ !{Val1} !{ala2} !{Phe1} !{Phe2} !{gly1} } by for example (some tweaking would be probably necessary): \chemfig{ !{Val1}-[,0.3,,,draw=none] !{ala2}-[,0.3,,,draw=none] !{Phe1}-[,0.3,,,draw=none] !{Phe2}-[,0.3,,,draw=none] !{gly1} }


Edit: A new answer, after changes in the question. This is an exemplary solution. The idea is clear: let all atoms have the same length. In place of width of Mn there may be some fixed length, in our small example length of Cl would be enough. Changing \setatomsep to a suitable value is left to you. \documentclass{article} \usepackage{chemfig} ...


As for the alignment question, here is a "tricky" solution: \definesubmol\nobond{-[,0.2,,,draw=none]} \begin{equation} \mbox{Preceding text:} \schemestart[][185] \chemfig[][scale=0.4]{[:-30]*6(=-(!\nobond\vphantom{\bullet})=(-*6(-=-=-=))-(!\nobond\bullet)=-)} \arrow{0}[,0]\+ \chemfig{C_2H_2} \arrow ...


As for your second question, you have it basically ok. Just modify these lines as following (treat them as submolecules): \path node(A){\chemfig{ !{\sera{1}}-[,0.3,,,draw=none] !{\serb{2}}-[,0.3,,,draw=none] !{\sera{3}}-[,0.3,,,draw=none] }}; Compiling it with pdflatex should do the work.

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