(file: ACD 01 How To by RAK 10/29/2011)
How to use ACD software for basic 1D NMR Processing:
a tutorial manual for users familiar with vnmr and NMR processing generally.
GOALS: Manual Processing: choosing FT, zerofilling, line broadening
Manual phasing (mouse phasing)
Baseline correction:
Exporting spectra images to documents or powerpoint.
Conventions in these notes:
Normal (Times) font for my words and descriptions;
Ariel font for menu commands (e.g. File > Import > From1D )
Courier font for commands you type on command line
-- Getting Started
The free academic version is available from:
http://www.acdlabs.com/resources/freeware/index.php
the “Quickstart” guide can be found at:
http://nuweb2.neu.edu/barnett/nmr/ssh.htm
basically says to clickthe “Shortcut” button to have the wizards to autoprocess data.
The ACD program family is designed for a broad range of analytical tasks, beyond
routine 1D NMR processing (see http://www.acdlabs.com/). It offers buttons for
preparing and printing reports, including tables of peaks and integrals. But the
Documentation fails to open with a concrete statement of what or whom the program is
for and how it should be approached (which I am still determining). The documentation
is also inaccurate and spotty: For example, details of manual processing are referred to
the ACD/1D NMR Processor Reference Manual. which can allegedly be found from the
Processor window (Help>Documents>1D NMR>Reference Manual), but there is no
“Documents” under help. Also, their Help Topics menu seems to be for a different
program or previous version -- It sometimes refers to buttons we don’t see in our
academic version (“FourierTr”, “Wfunction”), and not to the buttons we have
(“Interactive FT”, nor “AutoSimple”, “AutoBL Opt”, nor “Auto Symm”). Help doesn’t
explain mouse phasing. A half-hour of looking couldn’t find how to set the scale to Hz
instead of ppm, or measure the width of a peak.
Opening a Spectrum
(The “Open” option is only for ACD .esp files)
Navigate to your data directory (a .fid folder); open it,
Choose the file .fid, then double-click it or click “open”.
This should display an FID
You can expand and position the FID using mouse wheel and slider bar to right of
window.
File > Import > From 1DNMR Directory
Fourier Transform and Processing
(You can click the Shortcut button on the Operation Toolbar. It guesses at the LB,
zero-filling, phasing, baseline correction, and solvent peaks. It might work for you, but
you’ll probably want to process manually. )
Click Interactive FT button on Operation Toolbar
(It shows a preview of the FID, you can optimize your parameters on)
Zero Filling: increase “Final FT”; or
Linear Prediction > Forward > to final FT size (16384 or 32768)
Line Broadening: click “Window Function” to open it;
Change “default” to “user” in drop-down;
Choose e.g. LB and set to 1 Hz.
Phasing: accept the numbers (from saved file); mouse phase on the preview
Mouse Phasing picks the biggest peak (or drag red line to another peak). Drag left
button up&down to phase biggest peak; right button phases spectrum, such that
phase at biggest peak stays constant. Note “Fine Adjustment” button.
Autophasing: There are three buttons:
“Auto Simple”: phases leftmost peak.
“Auto BL Opt” autophasing by baseline optimization
“Auto Symm” autophasing by symmetrical lines.
Click OK when ready.
-- Expansions and Zooming
Vertical scale - mouse wheel
Vertical position – slider at right of window
Zooming: Use buttons on second menu bar (icon toolbar).
-- Baseline Correction
click Baseline button .
(best do full spectrum; can left-click and drag across region to baseline correct. )
Options (or rightclick and choose it):
Change Cubic Splines (too aggressive; unrealistic) to 5th order polynomial
Click: Auto chooses peaks and draws a red line across them.
Set Points” lets you drag points off of peaks; add new ones by dragging the red line
itself. (You can drag points to where baseline ought to be, below peaks -- they don’t
have to be on the spectrum). There’s some voodoo about whether it uses straight lines
between points, or fits a curve through them; let me know if you figure it out.
(SetPoints without Auto gives a number of points at zero; which you can drag
individually to spectrum, but end points remain at zero).
“Result” applies correction (appears to be cubic spline?)
Click green checkmark to apply correction and exit the BC routine.
-- Referencing
Expand the peak you will reference on (e.g. TMS, DMSO, CDCl3)
Click “Reference” on ribbon menu.
Left click the peak center. If the scale is about right, it will offer you the correct solvent
option, and you can choose it.
If the scale is far off, or you don’t see the correct solvent option, then right-click the peak,
choose “Options”, then choose the relevant solvent, then OK.
Then you can left-click the peak and set the reference.
Printing, and Graphics for MS Word
ACD will print to the default printer. (Whatever the default printer was when you opened
ACD).
File > Print > Standard
Accept its defaults for your first print. Based on what you see, you can turn off the
tables and other annotations in the “Report Page Setup” which appears (View tab). I
keep only Horizontal Scale and Spectrum Labels. The Text tab lets you input another
name, or reference and description.
I recommend saving spectra as a pdf, making “Adobe pdf” the default printer (in Start >
Devices and Printers). If you have to close & re-open ACD, save the spectrum in the
ACD default format ( .esp ), so your processing, baseline, phasing, and reference will be
saved.
ACD saves pdf’s in a very good and compact way, which also lets you generate
graphics for Word or Powerpoint, at any time in the future, at any resolution you want at
the time. ACD saves the spectrum in the pdf as “vector graphics”, here meaning a list
of all the x,y datapoints. Many other (especially older) programs use “bitmap graphics”,
which records the pattern of dots at screen resolution (70 dpi) or printer resolution (300
dpi). An alternative quick & dirty method is to use Screen Capture (ctrl-PrintScreen)
and pasting into documents. It’s fine if you are doing a 1-minute summary email to your
boss, but the resolution is inadequate for anything more than reminding you what the
spectrum roughly looked like.
To make nice graphics files you can put into MS Word or Powerpoint, open the pdf, in
Adobe Acrobat. In recent versions choose File > Save As > Image > Tiff. Under
“Settings”, “Resolution” at bottom choose 300 dpi, or higher if you need it. At top,
under File Settings, Monochrome be sure it has CCITT4. Previous versions of Acrobat
have used “Export” or something instead of “Print”, but there’s an option to output tif in
every version.
I recommend you crop the tif image in a photo editor if you are going to put it in
powerpoint. Because of the red text at the top, it will be about 500kb; if you crop it down
to just the spectrum, it will be under 50 kb. If you don’t crop them, a powerpoint will be
too big to email -- over 5 Mb -- if it has 10 images in it.
I recommend .tif over .jpg for NMR spectra (or any other black-and-white line art).
Jpg’s give ghosty haloes around any sharp edges or lines. Tif files use the same
compression that fax machines use, which is lossless and a tenth the size of a jpg. But
always check the settings. Tif is a “container” file format that can record data using
many different kinds of compression. Most programs detect line art and use fax
compression (CCITT 4), but some photo editors default to color images like jpg or even
uncompressed color bitmaps.
-- Putting NMR Data into Documents
You can copy and paste the current spectrum graphics into MS Word documents,
or into a picture-editing program like PaintShop, Paint, or Photoshop.
Resolution issues:
Displaying full-screen and taking screenshots was the quickest.
Using cut&paste, the image will be at half of screen resolution, 658 x 454 pixels –
(If you paste into Word, text is not pixellated; into PaintShop, text is pixillated)
(Into Word, the spectrum is diagonal lines; into PaintShop, pixillation is worse)
If you print the image, the printed page will be at about twice screen resolution.
Screenshot of ACD display
Printed and Scanned
Pasted into MS Word
Pasted into PaintShop
Pixelation is less of an issue for detailed expansions when you can see the digital
resolution of the data at screen or printer resolution:
Screenshot of ACD display
Pasted into MS Word
Pasted into PaintShop
Printed and Scanned
has four options (not relevant to routine chemistry NMR users):
.esp file
ACD spectrum format
.txt
ascii – tab-delimited text file of numbers (can import to spreadsheet)
.spc file
“Galactic” format
.jdx or .dx file
JCAMP file (originally an IR spectrum data format).
File > Export
--- Measuring Chemical Shifts and Linewidths
ppm is given by cursor at bottom. How to see Hz?
? How to display in Hz, so we can measure linewidths?
?! “Help” says to PeakPicking > Options > Preferences > Peaks tab
but there is no such menu.