updating the UgiWorkflows tables

[Jean-Claude Bradley]

Ajay started to update the UgiWorkflows tables and had some questions. 
For links to the tables see:
http://usefulchem.wikispaces.com/combiugi

I am continuing the discussion on the mailing list because it is likely many other students have similar questions:

I did 8 and 9 on the spreadsheet. I was hoping you could have a look at
them.

I had a few questions though:

I interpreted the numbers to be the amount of vortex time. I just added
on the time onto the initial from amine to aldehyde etc. Is that what
it should be?
No, in the table times(min) all the numbers refer to the number of minutes after the start of the experiment when an action took place.  Generally the addition of solvent is the first step and I have put 1 min for this to avoid misinterpreting entries with blanks (which might be considered zero) at the start of the experiment.  So in EXP151 ( http://usefulchem.wikispaces.com/Exp151 ) check the log and you'll see that the experiment started at 14:30 and the aldehyde was added at 14:32 so you would put 2 under the aldehyde column.

How can I link the pictures to your flickr account?
From EXP151 http://usefulchem.wikispaces.com/Exp151 right click and save images on your desktop then upload them on your Flickr account.  You may have to crop them using Paint or Photoshop if there are multiple vials in the image or if there is too much background wasting space.  Make sure to tag all pics with "UsefulChem" and "EXP151" and place a link to http://usefulchem.wikispaces.com/Exp151 .  Also very important some of the pics are not named correctly - rename them so that they have the same name as their tag in the wiki. e.g. EXP151-1-A in this experiment

What exactly are the result numbers? Are those from the CombiugiResults
table?
If you mean the ResultID column - you have them correctly labeled - same name as in the wiki

--
Jean-Claude Bradley, Ph. D.
E-Learning Coordinator for the College of Arts and Sciences
Associate Professor of Chemistry
Drexel University

http://drexel-coas-elearning.blogspot.com
http://drexel-coas-talks-mp3-podcast.blogspot.com/
http://usefulchem.blogspot.com

[jcb]

Ajay will no longer be working in our group this term. I have
highlighted the cells for his entries that are incomplete. Although
it is preferable for everyone to update their own experiments (and
this is a component of your evaluation if taking research for credit),
we really can't wait too long to get these tables current. Anyone
coming across an experiment completed for more than a week please go
ahead and update the Master and Workflow tables, even if it is not
your own. In fact there are many experiments done by students no
longer in the group that need to be processed.

As you can see from the discussion on other threads by Egon and
Rajarshi, our collaborators need the experiments processed in table
format to plug into their models to predict precipitation of the Ugi
products.

In the past few days Emily has done a great job in finding one
reaction that precipitates (and taking good pics to prove it)
http://usefulchem.wikispaces.com/Exp156

and one that does not (although check again in a few days just to make
sure)
http://usefulchem.wikispaces.com/Exp155

So Emily you need to update the tables and the Result script pages as
outlined here:
http://usefulchem.wikispaces.com/combiugi

Emily you also need to correct and complete a few things on your
experiment pages - tags, links to correct molecules on ChemSpider,
naming your pics (155A, 155B) and centrifuge 156 to isolate the Ugi
product and characterize with NMR

To clarify any of that use the mailing list so all our lab members can
learn how to do these things.



On Jan 7, 6:48 am, "Jean-Claude Bradley"

<jeanclaude.brad...@gmail.com> wrote:
> Ajay started to update the UgiWorkflows tables and had some questions.
> For links to the tables see:http://usefulchem.wikispaces.com/combiugi
>
> I am continuing the discussion on the mailing list because it is likely many
> other students have similar questions:
>
> I did 8 and 9 on the spreadsheet. I was hoping you could have a look at
> them.
>
> I had a few questions though:
>

> *I interpreted the numbers to be the amount of vortex time. I just added

> on the time onto the initial from amine to aldehyde etc. Is that what

> it should be?*

> No, in the table times(min) all the numbers refer to the number of minutes
> after the start of the experiment when an action took place. Generally the
> addition of solvent is the first step and I have put 1 min for this to avoid
> misinterpreting entries with blanks (which might be considered zero) at the

> start of the experiment. So in EXP151 (http://usefulchem.wikispaces.com/Exp151) check the log and you'll see that

> the experiment started at 14:30 and the aldehyde was added at 14:32 so you
> would put 2 under the aldehyde column.

> *
> How can I link the pictures to your flickr account?*
> From EXP151http://usefulchem.wikispaces.com/Exp151right click and save

> images on your desktop then upload them on your Flickr account. You may
> have to crop them using Paint or Photoshop if there are multiple vials in
> the image or if there is too much background wasting space. Make sure to

> tag all pics with "UsefulChem" and "EXP151" and place a link tohttp://usefulchem.wikispaces.com/Exp151. Also very important some of the

> pics are not named correctly - rename them so that they have the same name
> as their tag in the wiki. e.g. EXP151-1-A in this experiment
>

> *What exactly are the result numbers? Are those from the CombiugiResults
> table?
> *If you mean the ResultID column - you have them correctly labeled - same

[jcb]

Shannon writes:
I was trying to update the Workflows and I am a bit confused...is
there some system or other chart dictating which workflow number is
assigned to which experiment number? and how are the times/duration
measured? and I see that the amounts are mmol which makes sense for
the 4 components but I don't understand where the numbers for the
solvent and centrifuge/decant/add solvent columns come from.

I also have not centrifuged my compound yet, I was looking at your
comments on the wiki on my exp157 and I will probably redo it to make
sure that I let it fully dissolve, but from what I saw it dissolved
because there was a distinct change in the color and consistency as I
vortexed the vial, but it also seemed to precipitate almost
immediately, which is what I believe the solid in the initial pictures
of the experiment are. I think this is supported by when I went and
looked at it this evening there was an increased amount of precipitate
and it was extremely fine crystals, which is consistent with rapid
crystallization.

Response:
1) There is no correlation between the workflow number and experiment
number - just create the next workflow number and link it to the
experiment that it comes from in the appropriate column.
2) The times (always in minutes) are measured from the log when the
experiment was started (adding methanol to the vial). The durations
are also in minutes and apply to actions like vortexing and
centrifuging.
3) The numbers for centrifuge/decant/add solvent only arise when you
have a result that included these actions. In your first pictures,
you have not done any of that so leave those cells blank.
4) There should not be an immediate precipitate after adding the last
component. If it is not a clear solution after vortexing for several
minutes after adding the last component, you have a solubility
problem. You should abort the experiment at that point but still
record the workflows for the pictures you did take.
5) Each pic you took is a separate workflow leading to a single result
- that is why you must record the time you took the picture and name
it in the log (e.g. 157A)

Quick link to workflow tables:
http://usefulchem.wikispaces.com/combiugi

[jcb]

Shannon - I saw your updates for workflows 10-12
http://spreadsheets.google.com/pub?key=plwwufp30hfrgkmcd6n_1AA

and I noticed that at least your total solvent mmol number is
incorrect for workflow 12
You are also missing the "Take Result" time for all those workflows.

I flagged a few of these by marking the cells in red but please double
check all your values.

Exp162 (workflow 12)
http://usefulchem.wikispaces.com/Exp162

is an example of why we still need to do Result script pages, e.g.
http://usefulchem.wikispaces.com/RESULT0001

because there a second dilution with methanol which is not captured in
the workflow table.

The table is still useful for comparing results but we'll have to keep
in mind that some information is lost from the lab notebook page to
the table in some cases.

[soseback]

Dr Bradley, Where is a list of the existing results script pages so I
know what to number the result page and where to add a link to it, I
can't seem to find where they are on the wiki.

On Jan 24, 10:12 am, jcb <jeanclaude.brad...@gmail.com> wrote:
> Shannon - I saw your updates for workflows 10-12http://spreadsheets.google.com/pub?key=plwwufp30hfrgkmcd6n_1AA

>
> and I noticed that at least your total solvent mmol number is
> incorrect for workflow 12
> You are also missing the "Take Result" time for all those workflows.
>
> I flagged a few of these by marking the cells in red but please double
> check all your values.
>

> Exp162 (workflow 12)http://usefulchem.wikispaces.com/Exp162
> is an example of why we still need to do Result script pages, e.g.http://usefulchem.wikispaces.com/RESULT0001

[Jean-Claude Bradley]

There is no separate page to list them - they should just have the same numbers as the Ugi workflows
http://spreadsheets.google.com/pub?key=plwwufp30hfrgkmcd6n_1AA&gid=0