Frequently Asked Questions

"Smartness" of Algorithms

• I'd like to be able to send an email from a spectrometer...
• Solvent effects (HNMR).
• Specifying solvent by menu (CNMR, HNMR).
• Sources of data (general).
• Confidence limits (CNMR, HNMR).
• What should I do if NMR Experiment/Manager cannot read my FID? (NMR Manager)
• Can I view the experimental spectrum on the same screen as ACD/Labs' predicted spectrum?
• Carbon-phosphorus, carbon-fluorine splitting (CNMR).
• Distinction between axial and equatorial hydrogens (CNMR, HNMR).
• Using 3D structures optimized in other software (HNMR Predictor).
• Stereochemistry in IUPAC name (Name).

 

Q:

I'd like to be able to send an email from a spectrometer when an experiment has finished, so that when a link is double-clicked, NMR Manager starts, and imports the filename specified. We use Outlook as the PC mail client.

A:

This is the same, by analogy, as sending a *.doc file as an e-mail attachment. Right now, if a colleague sends you file1.doc in Outlook and you double-click on the icon, MS Word starts up, right? This is because the "Open with" setting means the application WINWORD.EXE will begin when a filename extension of *.doc is double-clicked.       What happens on this same system if you RIGHT-click on file1.fid? You should get a pop-up menu that says "Open" or "Open with" as the top item.       If the pop-up menu shows "Open with" as the top item, this means that you can specify a new route. Just select "Open with", type in a description such as "Raw NMR Spectrum", mark the "Always open" check-box, and then click on the "Other" button. This will open a dialog box where you can point and click your way to the SPECMAN.EXE program. Click "Open" and then "OK". Once you exit the "Open with" dialog, you can test this by double-clicking on the file and watching SpecManager open up with the fid in it.       If the pop-up menu shows "Open" as the top item, this means that you will have to CHANGE the route from the application that used to open *.fid to the new one, SpecManager. As described in Windows Online Help, double-click on Your Computer, choose View/Options/File Type. In File Type, add "ACD Spectrum" by clicking on the "New Type" button. The extension will be "*.fid". Just below the "Actions" box click "New". In the "New Action" dialog box, type in "open with" for the action, and then click on the "Browse" button so that you can point and click your way to the location of SPECMAN.EXE. There are three "OK" buttons to click after this. Again, a test should open the file in SpecManager just by double-clicking on it.       Once your "Open" or "Open With" is in order, then any file of that extension sent through Outlook should open properly when double-clicked.

 

Q:

Does ACD/HNMR take solvent effects into account when generating predicted spectra?

A:

ACD/HNMR calculations assume an aprotic/non-polar, non-aromatic solvent (e.g. CCl4, CDCl3). This is because our calculations involve algorithms based on large numbers of compiled spectral data drawn from the public domain. Unfortunately, not enough published data for structures in polar, protic and aromatic solvents (e.g. C6D6, CD3OD) exists for us to produce accurate enough algorithms. As we compile more data this may change with time.

 

Q:

How come there is a drop-down menu that allows me to specify a particular solvent for calculations in ACD/CNMR but not in ACD/HNMR?

A:

As solvents used in C13 experiments contain carbons they always add lines to the spectrum and always at the same positions. It is therefore easy to provide the exact lines for these solvents in our predicted spectrum. It should be noted that even though we provide these typical solvent lines ACD/CNMR is not calculating the actual solvent effect on the solute. In H1 experiments solvents are deuterated and as they should not contain protons, theoretically, should not add lines to the spectrum which is why we do not provide these in a drop-down menu (in practice residual proton resonances are observed due to small impurities in the solvent; ACD/HNMR does not provide these lines). Solvents do however affect the positions of the shifts for the actual solute. These solvent effects are very difficult to predict in the absence of large amounts of published data that we normally require for writing algorithms. Therefore ACD/HNMR always assumes an aprotic/non-polar, non-aromatic solvent (e.g. CCl4, CDCl3).

 

Q:

What are the sources of data from which your database is constructed?

A:

The data which are used in constructing the database come from appropriate literature sources (including several leading journals: Tetrahedron, the Journal of the American Chemical Society, the Journal of Organic Chemistry, Magn. Reson. Chem. and review articles) as well as collaborative partners from a number of academic and industrial laboratories. During our data entry we have adopted stringent procedures by which to screen the data prior to database inclusion.

Q:	Do you have a sample HNMR calculation showing the difference between axial vs. equatorial protons?
A:	Yes, check out the following. Note the use of wedge bonds to designate explicit stereochemistry. If stereobonds are not explicitly shown, the position of substituents is ambiguous, and HNMR will not make a distinction between axial and equatorial protons.

Q:	Why doesn't ACD/Name give a stereochemical name for bromo(chloro)methanol?
A:	It will, but you must (a) have the Name Preferences for stereochemistry toggled on; and (b) use the stereo bond tool ("wedge tool") to indicate explicitly the stereochemistry. Otherwise, ACD/Name will ignore the asymmetric centers.

Further questions?