Thursday, February 01, 2007

Horizontal vs. Vertical Integrals

This subject was already treated inside an old post. That time horizontal were the winners. Today I witnessed the revenge. I also heard for the first times that there are still ogres in America (I already knew about Shrek, of course, yet I was convinced it was an isolated case).

V. writes to G.

Also, is there some way to get the integrations to be displayed vertically instead of horizontally?

At this point G. copies and pastes the content of the blog:

The integrals are written horizontally. You also wrote your e-mail horizontally. Why do you want to write vertically? It's more difficult to read. Your eyes will soon get tired. There are many tricks to avoid overcrowding of integrals:
reduce the number of digits.
set 1 proton = 100 integral units and you can do without decimal digits.
enlarge some integrals to the right or to the left: the number will be displaced accordingly.
change the font.
use the cutter tool to remove non-interesting regions.
print on larger sheets of paper (we in Europe have the A3 format).
you can merge two integral regions; you will only read the sum, yet it's usually trivial to estimate by eye the contributions of each peak.

and V. demolishes them one by one:

From the tone of your response to the vertical integration request, it seems to me that you have received this request on more than one occasion. Let me try to delineate why... Some of the seven things that you suggest are just not feasible for an organic chemistry grad student, post-doc (such as myself), or faculty member. The size of the paper is dictated by that which the advisor or journal chooses and cannot be modified. Furthermore, some advisors and many referees want to see the exact scale for every spectrum. If you cut part of it out, they will wonder what it is that are you hiding and may reject the submission if it is for a well respected journal. Most organic chemists want to see separate integrations for every identifiable proton signal anything less, and again people wonder what you are hiding... We want to be certain that every single proton integrates accurately within acceptable margins of error. The Ogre at the graduate school in some instances will reject the document if it is not written in a single font style. As for the whole number integrations... we as organic chemists have a convention. It is a widely accepted one, and one that we are unlikely to change. We want to see the integrations represent the exact number of protons with two decimal places, period. The vertical integrations keep the values neatly stacked side by side, like the Rockettes. If you have a spectrum with closely spaced signals, the horizontal integrations take up more space, and when they overlap they become difficult to read.

The last defense of G. was:

I object one main thing: cuts are good. You can't say thay cuts hide the spectrum. Let's say that you print all your 1-H spectra from 0 to 10 ppm. I can argue that you are hiding me some peaks at 11 ppm ! If what you write is valid, the consequence would be that all spectra should be printed from -5 to 15 ppm ! And, even in this case, there is a program, ACD NMR-processor, that lets you easily clean the spectrum from any peak you like...
Nothing prevents you, however, to print a panoramic copy of the spectrum (without integrals) and a fragmented copy with integrals. Also consider the creation of insets.
You are probably the third person to ask me the vertical integrals, and certainly the first one I could not convince to forget them. I had my answer prepared mainly because of my long-term experience with NMR (16 years as spectroscopist into a pharmaceutical industry). I could always print my spectra into an A4 sheet, with horizontal integrals.
Let me clarify one more thing: when I wrote to hide the decimal digit, I mean: first multiply by 100, then truncate.
For example: 1.00 takes more space than 100, but the precision is the same.

V. strikes with a new weapon: the picture

For terpenoids, most impurities will not occur outside of the 0-10 range, they occur within it. For a thesis or supporting material, there should never be any cuts within the 0-10 area where almost all signals are going to occur. Although it does not go to 10 like it should, in my example spectrum you will see two labeled impurity signals. If I cut that portion out, I could claim that my material was pure. The other portion of the spectrum that is labeled contains three closely spaced signals that, if written horizontally, would most certainly overlap. They are clearly three separate signals and should be integrated as such. The use of 1.00 vs 100 is again, a convention. Advisors and referees are creatures of convention and habit. They don't want to see 100, they want to see 1.00. Sure the precision is the same, but trying to get your peers to accept it would take some force. I am not familiar with the ACD NMR-processor and its capabilities, and so I cannot comment on it.
Oh, and the strangely large margin requirements displayed on the attached spectrum are part of the rules to publish a thesis here in the states... Again, this is not something that a grad student has control over, the Ogre at the grad school would reject the thesis if any little portion of your spectrum went into the margin area. The truncation at 8 ppm was a decision based on the small area given to display the spectrum, and the fact that no impurity for this compound should occur downfield of 8 ppm.

G. admits the defeat:

your picture is enough of a convincing proof. Luckily I have no experience with ogres and could always avoid bureaucratic issues. Yours seems to be a nice 500 MHz spectrum, at it is certainly a great experience to see it into the 20" monitor of an iMac, at full screen and possibly with cuts. Don't they even allow insets? These requirements seem so strict that, by this point, they could even specify which software to use.
My conclusion is that certainly vertical integrals allow for more crowding (almost unlimited), but horizontal integrals are more readable. They enter into my eyes and brain without effort. If it was not for bureaucracy, horizontal integrals would be better.

V., however, is not in the mood of celebrating his victory:

Now I hope that you a little better understanding for the plight of the piddley org. chem. grad student. Everyone has all these requirements, but no one wants to make it easy to meet them. Some people still take their spectra tape on the label and scan them... imagine how long that takes when you are dealing with 300 pages of spectra...


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