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Physics

Using chemfig I was able to represent DPPC (Dipalmitoylphosphatidylcholine) and other lipids in Latex by using the following code

\newcommand\setpolymerdelim[2]{\def\delimleft{#1}\def\delimright{#2}}
\def\makebraces[#1,#2]#3#4#5{%
\edef\delimhalfdim{\the\dimexpr(#1+#2)/2}%
\edef\delimvshift{\the\dimexpr(#1-#2)/2}%
\chemmove{%
\node[at=(#4),yshift=(\delimvshift)]
{$\left\delimleft\vrule height\delimhalfdim depth\delimhalfdim
width0pt\right.$};%
\node[at=(#5),yshift=(\delimvshift)]
{$\left.\vrule height\delimhalfdim depth\delimhalfdim
width0pt\right\delimright_{\rlap{$\scriptstyle#3$}}$};}}
\setpolymerdelim[]


\begin{figure}
\small
\setatomsep{1.5em}
\chemfig{N^+(-[:180,1.1]H_3C)(-[:90,1.3]CH_3)(-[:270,1.3]CH_3)(-[:-30]-[:30]-[:-30]O-[:30,1.3]P^+(<[:50,1.5]O\rlap{${}^-$})(<:[:130,1.5]O\rlap{${}^-$})(-#(1pt,)[:330,1.3]O-[:30]-[:-30](-[:270]O-[:-30](=[:270]O)(-[@{downleft,0.8}:30]CH_2-#(1pt,1pt)[@{downright,0.3}:-30,1.2]CH_3))(-[:30]-[:-30]O-[:30](=[:90]O)(-[@{upleft,0.8}:-30]CH_2-#(1pt,1pt)[@{upright,0.3}:30,1.2]CH_3))))}
\makebraces[10pt,13pt]{n}{downleft}{downright}
\makebraces[6pt,15pt]{n}{upleft}{upright}
\label{fig:lipids}
\end{figure}

The crucial line is:
\chemfig{N^+(-[:180,1.1]H_3C)(-[:90,1.3]CH_3)(-[:270,1.3]CH_3)(-[:-30]-[:30]-[:-30]O-[:30,1.3]P^+(<[:50,1.5]O\rlap{${}^-$})(<:[:130,1.5]O\rlap{${}^-$})(-#(1pt,)[:330,1.3]O-[:30]-[:-30](-[:270]O-[:-30](=[:270]O)(-[@{downleft,0.8}:30]CH_2-#(1pt,1pt)[@{downright,0.3}:-30,1.2]CH_3))(-[:30]-[:-30]O-[:30](=[:90]O)(-[@{upleft,0.8}:-30]CH_2-#(1pt,1pt)[@{upright,0.3}:30,1.2]CH_3))))}

You’ll also need to include the following in the preamble

\usepackage{chemfig}

Which produces something that looks like this:

Image

Thermo Scientific NanoDrop range of UV/Vis spectrophotometers (http://www.nanodrop.com/Absorbance.aspx) seem to be pretty good to me — apart from their terrible software.

I used the NanoDrop 1000 Spectrophotometer, and found the software to be so unintuitive that I had to read the entirety of the manual for the sections I used (which can be found at http://goo.gl/smXCT). The two main points I would note are:

  • The data can be exported from the report – select ‘Show report’->’Save report’->’Full report’  which will save a .ndv file of all the spectra taken in the current session.
  • The absorbance data at 0.2mm (NB on the report it is shown for 0.1mm so you can visually confirm it is a tenth of the 1mm absorbance, see the wikipedia page on the Beer-Lambert law for an explanation of this linearity) is stored in C:\NanoDrop Data\User name\ HiAbs — there is no other way to get to it.

The .ndv files saved are tab-delimited files which you can load into spreadsheet software to manipulate and plot. As I wanted to do further spectral analysis this was a bit useless to me, so I wrote a quick perl script to convert these files into a set of .csv files (one for each spectrum listed in the .ndv file).

This is available at my other site (for now, this link will expire in July 2013) at http://users.ox.ac.uk/~ball3126/ndv-converter.pl and is also listed below. Run ‘ndv-converter.pl –help’ for a usage guide. The default behaviour is to convert all .ndv files in the current working directory

ndv-converter code listing (pdf)