January 19, 2022, 03:23:27 AM
Forum Rules: Read This Before Posting


Topic: Reading synthetic organic research papers  (Read 4606 times)

0 Members and 1 Guest are viewing this topic.

Offline davidenarb

  • Full Member
  • ****
  • Posts: 133
  • Mole Snacks: +0/-1
Reading synthetic organic research papers
« on: August 06, 2014, 09:47:42 AM »
Hi all,

I finished reading an entire classic organic chemistry textbook, and I tried to begin by reading some papers in synthetic organic chemistry, and I find some difficulties in understanding the paper.

Any tips or advices?

Thank you

Offline clarkstill

  • Chemist
  • Full Member
  • *
  • Posts: 456
  • Mole Snacks: +74/-4
Re: Reading synthetic organic research papers
« Reply #1 on: August 06, 2014, 10:03:44 AM »
What difficulties are you having?

If you want to get a general overview of a paper, read the abstract, introduction and conclusions, and look at the figures/schemes.  The main body of the paper is where the technical details reside, and they might be daunting for the un-initiated...

Offline PhDoc

  • Full Member
  • ****
  • Posts: 133
  • Mole Snacks: +22/-0
  • O-Chem Prof
    • PH.D. Organic Chemistry Tutor
Re: Reading synthetic organic research papers
« Reply #2 on: August 06, 2014, 10:37:27 PM »
David,

Everyone experiences varying levels of challenge when transitioning from organic chemistry textbooks to more advanced journal articles, sometime due to topics, whilst other times due to writing styles. Please keep in mind o-chem textbooks are written to be understood by undergraduates, whereas o-chem research papers are written to be understood by other professionals.

Just keep doing it. Eventually the lightbulb will turn on!
O-Chem Prof

Offline davidenarb

  • Full Member
  • ****
  • Posts: 133
  • Mole Snacks: +0/-1
Re: Reading synthetic organic research papers
« Reply #3 on: August 07, 2014, 06:43:49 AM »
What difficulties are you having?

If you want to get a general overview of a paper, read the abstract, introduction and conclusions, and look at the figures/schemes.  The main body of the paper is where the technical details reside, and they might be daunting for the un-initiated...

David,

Everyone experiences varying levels of challenge when transitioning from organic chemistry textbooks to more advanced journal articles, sometime due to topics, whilst other times due to writing styles. Please keep in mind o-chem textbooks are written to be understood by undergraduates, whereas o-chem research papers are written to be understood by other professionals.

Just keep doing it. Eventually the lightbulb will turn on!


Thank you very much for you support; I understand that the key is apparently the perseverance.

Offline davidenarb

  • Full Member
  • ****
  • Posts: 133
  • Mole Snacks: +0/-1
Re: Reading synthetic organic research papers
« Reply #4 on: August 07, 2014, 06:46:03 AM »
One of the major difficulties that I find is, for instance, I cannot find the reaction provided in the journal in my textbook; somtimes the reagents are different...etc

Offline Ben Bob2

  • Regular Member
  • ***
  • Posts: 83
  • Mole Snacks: +22/-0
  • Gender: Male
  • Undergraduate Chemist
    • Ben's Chemistry Page
Re: Reading synthetic organic research papers
« Reply #5 on: August 07, 2014, 10:51:54 AM »
I find it helpful to paste an article into a word document, and write my own very brief summary of each paragraph as I read. It's slow work, but is also enjoyable in a way.
Change and decay in all around I see;
O Thou who changest not, abide with me

2014 Eisenhower Fellow
2015 GRO Fellow

Offline davidenarb

  • Full Member
  • ****
  • Posts: 133
  • Mole Snacks: +0/-1
Re: Reading synthetic organic research papers
« Reply #6 on: August 07, 2014, 11:10:42 AM »
I find it helpful to paste an article into a word document, and write my own very brief summary of each paragraph as I read. It's slow work, but is also enjoyable in a way.

That sounds helpful. Thanks !

what about this ?
One of the major difficulties that I find is, for instance, I cannot find the reaction provided in the journal in my textbook; somtimes the reagents are different...etc

Offline clarkstill

  • Chemist
  • Full Member
  • *
  • Posts: 456
  • Mole Snacks: +74/-4
Re: Reading synthetic organic research papers
« Reply #7 on: August 07, 2014, 11:20:10 AM »
If it's a reasonably standard reaction but using reagents you don't recognise then just google the reagents and take a look at their structure and properties.  If they are related to the reagents you are familiar with, then chances are the mechanism is the same. e.g. for Pd-catalyzed cross-coupling reactions there are hundreds of phosphine ligands people choose to use, but generally speaking they serve the same purpose in the reaction, so you don't need to worry too much about the minutiae of the specific one being used.

In the more difficult examples, where you aren't familiar with the reaction at all, sometimes you will need to follow a reference given in the paper for that step (often this is in the supporting information file).  If they don't give a reference, try just googling all of the reagents as a single search (e.g. if you search for "PPh3 CCl4" you will find that these relate to the Appel reaction). The organic chemistry portal (http://www.organic-chemistry.org/) is also a good resource for summarizing the features of reactions, and providing references for further reading.

Offline orgopete

  • Chemist
  • Sr. Member
  • *
  • Posts: 2636
  • Mole Snacks: +213/-71
    • Curved Arrow Press
Re: Reading synthetic organic research papers
« Reply #8 on: August 08, 2014, 08:24:59 AM »
Hi all,

I finished reading an entire classic organic chemistry textbook, and I tried to begin by reading some papers in synthetic organic chemistry, and I find some difficulties in understanding the paper.

Any tips or advices?

Thank you

I would suggest dropping back a step. There are any number of advanced organic chemistry books available that will explain the mechanisms. I suggest it will be easier and more productive to start there. That way, if you don't know a mechanism, you won't have to go searching for one. If you are learning French and just read Le Petit Prince and thought, okay, I know French, and picked up a copy of Le Monde, you may be similarly frustrated. Language is learned on context. You need to have enough understanding at each level for this to occur. Reading a newspaper to a baby will not teach a baby that language because the baby would not know enough words to assimilate them. This should be your objective.
Author of a multi-tiered example based workbook for learning organic chemistry mechanisms.

Offline davidenarb

  • Full Member
  • ****
  • Posts: 133
  • Mole Snacks: +0/-1
Re: Reading synthetic organic research papers
« Reply #9 on: August 08, 2014, 09:07:37 AM »
If it's a reasonably standard reaction but using reagents you don't recognise then just google the reagents and take a look at their structure and properties.  If they are related to the reagents you are familiar with, then chances are the mechanism is the same. e.g. for Pd-catalyzed cross-coupling reactions there are hundreds of phosphine ligands people choose to use, but generally speaking they serve the same purpose in the reaction, so you don't need to worry too much about the minutiae of the specific one being used.

In the more difficult examples, where you aren't familiar with the reaction at all, sometimes you will need to follow a reference given in the paper for that step (often this is in the supporting information file).  If they don't give a reference, try just googling all of the reagents as a single search (e.g. if you search for "PPh3 CCl4" you will find that these relate to the Appel reaction). The organic chemistry portal (http://www.organic-chemistry.org/) is also a good resource for summarizing the features of reactions, and providing references for further reading.

Thank you. I will do my best :)

Offline davidenarb

  • Full Member
  • ****
  • Posts: 133
  • Mole Snacks: +0/-1
Re: Reading synthetic organic research papers
« Reply #10 on: August 08, 2014, 09:08:04 AM »
Hi all,

I finished reading an entire classic organic chemistry textbook, and I tried to begin by reading some papers in synthetic organic chemistry, and I find some difficulties in understanding the paper.

Any tips or advices?

Thank you

I would suggest dropping back a step. There are any number of advanced organic chemistry books available that will explain the mechanisms. I suggest it will be easier and more productive to start there. That way, if you don't know a mechanism, you won't have to go searching for one. If you are learning French and just read Le Petit Prince and thought, okay, I know French, and picked up a copy of Le Monde, you may be similarly frustrated. Language is learned on context. You need to have enough understanding at each level for this to occur. Reading a newspaper to a baby will not teach a baby that language because the baby would not know enough words to assimilate them. This should be your objective.

Thanks

Offline millsware

  • New Member
  • **
  • Posts: 5
  • Mole Snacks: +0/-0
Re: Reading synthetic organic research papers
« Reply #11 on: August 26, 2014, 10:36:08 AM »
I would agree that there is a big gap between 'textbook chemistry' and hands-on synthetic chemistry.  The textbooks generally give very little detail, while synthetic papers assume that the reader is fluent in many techniques and reagents.  If you have access to a chemical search engine like scifinder or reaxys, it is helpful to plug in some of the reagents or structures to find similar reactions.  For example, there are many different kinds of carbodiimides used for amide coupling, but they all work in essentially the same way.  Also, different journals require different levels of detail in their experimental sections, so it helps to check different journals. 

Sponsored Links