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F.A.Q.

Frequently Asked Questions

I get loads of emails from you lovely people, and try to answer them all, but sometimes I can’t really be bothered writing the same replies over and over again. So here’s some specimen answers – but to email me if you want to! ts (at) totallysynthetic.com

Q. Your chemical diagrams are scrumpteous – how can I draw mine like that too?

A. Well, I draw mine by hand, and scan them in, of course, but here’s a good guide to doing to otherwise.

*NEW* ChemDraw Document Setting download

You can now download the Tot. Syn. document settings for ChemDraw. Place this file in the appropriate location in your ChemDraw directory (eg. “C:\Program Files\CambridgeSoft\ChemOffice2006\ChemDraw\ChemDraw Items”).

Alternatively, you can do a bit of DIY…

Two methods. Either own ChemOffice 2005* or later (automatically antialiased structures) or do the following:

1. Draw your sketch as a normal ACS settings scheme, and change to the following settings:

Line Width = 0.04cm, Bold width – 0.08cm.

I find this makes the structures clearer.

2. Double the size to 200%, so everything is too large.
3. Save this as a jpeg/bmp/gif or whatever, or do a screen grab (Print Scrn button on your keyboard)
4. Take this ugly, oversized file into Photoshop (or whatever image editor you like).
5. Do a resize down to 50%, which will bring back your scheme to a normal size. There should be an option to do a “smooth” (antialiased) resize, which will give you a nice, clean image.
6. Bask in awe at your creation.

*BTW, if you have an older version of ChemDraw, you can use the free version of ChemDraw Net Plugin to render your previously created schemes in all-singing-all-dancing antialiased-o-vision.

Q. I saw this great paper in Tet. Lett. from three months back; can you do a post on it?

A. I’m only covering the best of what’s happening now. It might be a great paper, but I don’t have time to write about it, so why don’t you? Add it to the forums…

Q. Why not add some methodology papers?

A. Nope. This is TotallySynthetic, not TotallyEverything. For every great total synthesis, there are several interesting methodology papers, and it’s just too much work to write about them. However, most good methodology ends up in a total synthesis at some point, so perhaps you’ll see it soon.

Q. Can you link to our ecommerce site? We sell really cool stuff.

A. Buy some Google Ads, cheap-ass.

Q. I dissagree with some of the comments on your site, can you do something about it?

A. Yes, I can suggest you write a reply to said comment, and tell them your opinion. I’m not responsible for the comments made by other users.

Q. Can I syndicate your blog onto my site?

A. Ask me first, please.

Q. My comment hasn’t turned up on your site. Where’s it gone?

A. It’s been eaten by my spam-devourer. I’ll get it to regurgitate your comment soon.

Q. Well sell really great V A I G R A softtabbsss buy now from our P F H A R M A C C Y.

A. You are the spawn of satan. Die, please.

23 Comments

  • [...] Now check out a slide that I may have used at my last ACS meeting. HOT! Note the bold lines in the structure. You accomplish them in ChemDraw by highlighting your structure, selecting “object settings” and adjusting the line thickness to .018in. Then you save it as a 600 dpi .png and import it as an image into PowerPoint. Your structures will be hot. Also notice the pretty blue bar. Nice but not ostentatious. Of course, if you really want to be awesome, you can follow Paul Docherty’s formula for generating awesome pics. But… no matter what… do not just copy right out of chemdraw! Your structures look like garbage and I will hate you and shit in your face if I see you. The resolution is too low. Cutting and pasting feature of Chemdraw is for Word documents only. [...]

  • npsynthesis says:

    paul, there is a new tamiflu synthesis in JOC ASAP if you missed it.

    Not sure that it is blog worthy..several of the same set backs the first few synthesies had — namely the use of hazardous azide chemistry and they employ the rare and expensive shikimic acid as starting material.

    John

  • Paul, I am interested in exchanging links with you. We are company that deals in aluminas, silicas, TLC plates, etc. If you could respond to me and let me know if this is possible, I would greatly appreciate it. Also, our toll free # is 866-314-7672.

  • Jax says:

    Sorry, I am new to this site. I searched for the answer on the net….But to no avail.

    What does “RBF” mean?

  • John Wood says:

    round bottom flask

  • Karl Collins says:

    Hi,

    This probably is not the right place to ask but I am stuck. I’m looking for 2nd year opportunities to present a poster and am struggling to find much. Does anybody know of any or a decent place to start looking?

    Thanks,

    Karl

  • allan says:

    Hi Paul,

    Can i bother you with something? I would like to ask if you have come across with any methods of olefinating or methylenating C=O’s of C-5 substituted gamma hydroxybutenolides (GHBs). I have browsed the literature and have found that GHBs are in equilibrium with its (open) 5-keto 1-carboxyl form. Is there any way to supress this like perhaps protecting the OH group with Me or Ac? Or there is a direct way to olefinate the carbonyl grp without adding such protective step? Maybe you have some tricky ideas?

    I would appreaciate it very much if you could help me. Thanks!!!

    Allan

    PS. the e-mail add indicated above does not work. my msg bounced back.

  • [...] Sorry the .gif looks a little grody. Even the tried and true Tot. Syn method produced weird lookin’ results… Just give it a click, I promise it looks [...]

  • Peter Bladon says:

    Hi
    I liked the reference to “golden age of steroid synthesis” in your piece about Cephalostatin 1. However, it is a pity that the reference used “et al” and so failed to mention Ivor Williams and William McMeekin who did the “heroic work” all those years ago. “Heroic” is perhaps a better adjective because in those days H$S did not rule.

    What is interesting about the original paper in JACS (in particular the supporting information) is the lack of any crystalline compounds.

    Cheers

    Peter Bladon

  • Tim says:

    Hi
    have subscribed for a year or so but last updating entry is 29 Dec and IE8 now has feed errors and cannot update. I remove and re-add your feed and it says RSS2 feed errors in code (text dump at bottom) can you fix as really love this blog.
    Cheers Tim
    PS if add it as “totallysynthetic.com/blog/?feed=rss” not rss2 (eg no pics) all is OK

    An invalid character was found in text content.
    Line: 248 Character: 709

    Y’know, I was kinda hoping for a bit of break between blog-posts this winter, as the amount of online publications tends to tail-off around the year-end. However, not only have the publications been thick-’n’-fast (got quite a lot of material to get through), but up pops palau’amine. I really did think that Angewandte would hold-off until sometime in early 2010, but here it is – and it lives up to Baran’s reputation. I mean that in every sense, as in some ways there’s a slight dissapointment, as he has a way of making the synthesis look to obivious, too easy. However, it was undoubtedly a challenge; Baran states that ‘the synthesis of palau’amine has thus far eluded organic chemists despite the dozens of Ph.D. theses… Many well-founded and logical plans to secure the peculiar trans-5,5 core of [palau'amine] in our laboratory resulted in unfortunate outcomes‘. This goes some-way to explaining the brevity of this blog post, but I intend to follow-up this post with a quick review of other routes that have been attempted in other labs.

  • suku says:

    i am new to this website

  • Jobde says:

    Also agree with the author, all true.

  • Michelle says:

    I’m an English professor at Auburn University in Alabama, and I’m writing a book about Science 2.0. My second chapter includes a case study of Totally Synthetic as an example of how blogs and other social networking sites are challenging traditional scientific publication practices.

    If you are willing, I’d like to ask you a few questions at your convenience.

  • Freuts says:

    Add to favorites, I’ll use it.

  • Mark says:

    Wow. Paul, you have a seriously impressive blog. Is this the way of the future??? to blogging about your work??? I like it. Well, it does look like you have been at it for several years now. I work as an industrial chemist and would blog about mine too if I hadn’t signed off on a privatization clause. I work for a fortune 500 industrial gases company that fails to see the value in publishing advances on a continual basis.

    Keep it up…:)

    Mark

  • [...] totally synthetic ????????????????????????????????????? faq ????????? [...]

  • Manuel says:

    Hi Paul
    I would love to know how you did the “totally synthetic” banner. I’ve tried so many thing but nothing worked.
    Maybe you cold tell me the software and the used tools.

    sincerely,
    manuel

    • Tot. Syn. says:

      Manuel,

      I used ChemDraw to draw the structures, then saved the sketch as a PDF file. I imported this into PhotoShop and converted them into a selection. I drew the blue rectangle as a layer, and then ‘cut’ out the sketch. I did the same with the text. I then took the blue rectangle layer and applied a shadow to give the ‘template’ feel.

      I think that’s what I did- it was a few years ago now!

      Paul

  • [...] of ChemDraw.  This works well enough for publications, but for presentations and the web I prefer Totally Synthetic’s style sheet, available on his blog.  The bonds are thicker, and on a screen everything looks just a little [...]

  • In case anyone was wondering how to add this into ChemDraw (2012 in my case) under Windows 8, the new location for the ChemDraw Items folder is: C:\ProgramData\CambridgeSoft\ChemOffice2012\ChemDraw\

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