Collaboration with ACDLabs
The Department of Chemistry, UWI, Mona Campus, JAMAICA is pleased
to acknowledge assistance from Advanced Chemistry Development (ACDLabs)
in relation to service provision of software.
Since June 1999, I have been using the SpecManagement suite and
all staff together with our undergraduate and postgraduate
students have access to the ChemSketch program.
ChemSketch vs 5
The major difference between the free version and the full
version appears to be the absence of the ACD dictionary and the
presence of the products poster advertisements display at startup
(less than 10 seconds).
On running the program it initially begins in structure mode.
From here it is possible to assemble a 2D molecular display
and/or to copy from the templates available such as: aminoacids,
aromatics, carbohydrates, phosphorus compounds, steroids, sugars
(which can be shown as Haworth Formulae, stereo or Fischer
projections or chair presentations), terpenes, carotenes,
orbitals, N-containing molecules or N-rings etc.
Once a molecule is completed, it is then possible to look for the
existence of tautomers and run the clean and optimisation
routines to check and highlight problems. For example, drawing
2-hydroxypyridine will return the information that this is likely
to be the minor form and offer to replace the structure with
2-pyridone. To view the molecule in 3D, the ACD/Labs menu item 3D
viewer is selected. This quickly and conveniently moves the
molecule into a new window where further optimisation is
possible. From here the display can be viewed in a variety of
modes including wireframe, stick or spacefill. It can be printed
or copied to the clipboard for use in reports as well. To save,
the only format available is ACDLabs own .S3D format.
From ChemSketch, saving the 2D information is possible as an
ACDLabs .SK2 file or by exporting as MDL .MOL, ISIS .SKC or
ChemDraw .CHM files. Alternatively it is possible to export an
image as a bitmap (e.g. .BMP or .GIF etc.). Once a structure has
been optimised in ChemSketch so that 3D coordinates are
calculated, it is then possible to export a 3D structure, again
as MDL .MOL file etc. From vs 5.0 export as PDF, CML or SMILES string
is possible.
Naming a molecule was added to vs 5.0. Either via the ACD/Name
freeware button or built into the commercial package. This returns
the IUPAC name very quickly and we have been unable to fault the
responses received so far.
The calculation of RMM (molecular weight) and the goodies buttons
for determining the correct amount of substance to weigh out in
preparing solutions are handy add-ins for laboratory classes (now
included in the ChemBasic package).
We have found the program to be quite intuitive to use and
within a short time our students have become adept in mastering
it and their reports are beginning to look so much more
professional.
NMR software
The commercial NMR package (5.0) contains the proton and carbon
predictors, spectra manager and spectral database modules. The
free versions consist of the spectral viewer (experimental data)
and the viewers for predicted proton and carbon spectra. That is,
three separate programs are needed to view the experimental and
predicted data.
At present, our postgraduate students get access to Bruker 200
and 500 MHz NMRs. These are controlled by PC's running
Bruker software that produce proprietary binary files for the FID
or 1r etc data.
ACD Labs Specmanager 5.0 is able to read the Bruker FID and
generate the spectrum for printing and interpretation. The
Fourier transform and phase correction have proved to be
extremely quick and efficient.
The free ACDLabs Spec Viewer (4+) only reads JCAMP-DX, ASCII and
SPC files. It is necessary therefore to convert the Bruker files
to one of these formats first before they can be viewed with the
free software. There is no provision for saving files.
Annotation of spectra is straightforward and adding a molecular
structure is conveniently done with ChemSketch since the programs
all work together and are a simple mouse click away on the status
line.
A new feature of the H and C viewers (4.5), that read predicted
spectra, is to allow for export of a JCAMP-DX file. ACDLabs has
been responsive to this request from us primarily so that we
would be able to generate a library of "spectra" for lab classes.
In this way, we can draw a molecule in ChemSketch, use the H or C
predictor program to simulate a "spectrum" and then using the
viewers now save the "spectrum" for later use. To ensure that
there is no confusion between simulated and actual spectra we
have used a non-standard operating frequency like 555 or 666
MHz!
Over the years, ACDLabs has grown to be one of the de
facto standards in the Chemistry software industry and have
made a substantial contribution to how chemists operate and can
improve their productivity. We hope to be able to continue the
collaboration for years to come.
Copyright © 2005 by Robert John Lancashire,
all rights reserved.
Created and maintained by Prof. Robert J.
Lancashire,
The Department of Chemistry, University of the West Indies,
Mona Campus, Kingston 7, Jamaica.
Created June 2000. Links checked and/or last
modified 11th January 2005.
URL:
http://wwwchem.uwimona.edu.jm/ACDLabs.html
