CHEM G8316.001 : Supramolecular Organic Chemistry
Taught by Nicholas Turro
| Course Information | Syllabus | Reading Materials | Broadcasts | |
General Course Information

Supramolecular Organic Chemistry
MW 10:35A-11:50A
Havemeyer 320

Instructor Information:
Nicholas J. Turro
njt3@columbia.edu

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Chem G8316: "Supramolecular Aspects of Organic Chemistry"

Supramolecular organic chemistry can be broadly defined as chemistry of the non-covalent bond. The course will explore the field of supramolecular organic chemistry through exemplars in organic photochemistry and photophysics. Examples of the control of photochemical reactions through the use of supramolecular structure will be described and discussed. Examples will be given the strategy for the development of photo-luminescent sensors of supramolecular structure and dynamics. Readings from the current literature dealing with supramolecular chemistry and supramolecular photochemistry will be assigned and discussed.

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G8316 Course Syllabus

During the 20th century the science of molecular chemistry was developed as chemists established a mastery of the understanding of atomic valence and the covalent bond between atoms; During the 21st century chemists are attempting to develop a mastery of intermolecular bonds and molecule valence, establishing a new field of supramolecular chemistry. The course will involve a survey of organic supramolecular chemistry emphasizing the enzyme guest@host model as a basis for modeling systems such as micelles, dendrimers, zeolites, and DNA molecules. Examples of the use of photoluminescence and photochemistry to characterize and exploit supramolecular systems will be presented.

Molecular Biology has been at the center of one of the great intellectual scientific revolutions of the last and current centuries. Chemistry has been an important component of this revolution with the promise of reducing the enormous complexity of biological systems from knowledge of molecular structure and interactions and is at the core of a relatively new field termed Chemical Biology. Many important biological processes operate on the basis of a common chemical event that can be termed molecular recognition, the highly selective recognition of a molecule or molecular fragment by another molecule from a complex mixture due to non-covalent interactions. Understanding the basis of molecular recognition is a major concern of current chemistry. It appears that in order to acquire this understanding, it will be necessary to extend our knowledge of chemistry that is based on covalent bonds, "molecular chemistry", to embrace a chemistry based on non-covalent bonds, "supramolecular chemistry." Molecular chemistry has been successful in achieving selectivity with systems possessing a relatively small valence (small number of strong bonds), whereas the supramolecular chemistry of biological systems achieves selectivity through polyvalence (a large numbers of relatively weak non-covalent bond).

The course content will involve the following:

  1. Reading reviews and the primary literature on supramolecular chemistry.
  2. Using organic supramolecular photochemistry and photophysics as exemplars of supramolecular systems.
  3. Describing the use of supramolecular systems to control photochemical reactions; describing photophysics as a probe of the structure and dynamics of supramolecular systems.
  4. Supramolecular systems to be discussed will include:
    • Synthetic systems: Micelles, Dendrimers, DNA, Fullerenes, Zeolites, Cyclodextrins, Nanoparticles, Molecular Beacons, Molecular Carcerands, Molecular Capsules
    • Biological systems: DNA, proteins, membranes
  5. Students will present a discussion of a selected supramolecular system to the class and then submit a written report on the topic. The grade in the course will be determined by the presentation, the written report and individual participation in class discussions.

The class will experiment with internet connections with groups at other universities that are interested in supramolecular organic chemistry.

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Reading materials

Reading materials will be provided as downloads of pdfs sent by email or made available on courseworks.


Course Reserve Books

Hardcopies of the following books will be placed on reserve in the Math Library. Electronic version of books are indicated by a blue title. To access the electronic copy just click on the title below:

  1. Israelachvili, Jacob N., "Intermolecular and surface forces", 2nd ed., London ; San Diego : Academic Press, 1991.
    On reserve in the Math Library

  2. Israelachvili, Jacob N., "Intermolecular and surface forces : with applications to colloidal and biological systems", London ; Orlando, FL: Academic Press, 1987.
    Recalled - coming soon

  3. Fendler, Janos H.. "Catalysis in micellar and macromolecular systems", New York : Academic Press, 1975.
    On reserve in the Math Library

  4. Jean-Marie Lehn, "Supramolecular Chemistry" VCH, New York, 1995.
    On reserve in the Math Library

  5. J. Steed and J. L. Atwood, "Supramolecular Chemistry", Wiley, NY, 2000.
    On reserve in the Math Library

  6. Donald J. Cram and Jane M. Cram., "Container molecules and their guests" [alternate URL], Cambridge : Royal Society of Chemistry, 1994.
    Available online [link above]

  7. Dodziuk, Helena, "Introduction to supramolecular chemistry" [alternate URL], Boston : Kluwer Academic Publishers, 2002.
    Available online [link above]
    Note: Users are limited to printing 10 pages per hour through the NetLibrary.

  8. J. L. Atwood, J. E. D. Davies, D. D. MacNicol, F. Voetle and J. M. Lehn, "Comprehansive Supramolecular Chemistry", Pergamon, Oxford, 1996.
    QD411 C66 1996 - Chemistry Reference Collection: Chemistry Library.
    Note: These are shelved on one of the tables in the reference section, not on the shelves along the wall.

  9. "Perspectives in Supramolecular Chemistry", Book series, vol. 1, 2004, Wiley, Chichester.
    Rush ordered - coming soon

  10. L. F. Lindoy and I. M. Atkinson, "Self-Assembly in Supramolecular Systems", The Royal Society of Chemistry: Cambridge, 2000.
    Available online [link above]

  11. "Encyclopedia of Supramolecular Chemistry", Vols 1 and 2, J. L. Atwood and J. W. Steed, eds., Marcel Dekker, Inc.: New York, 2004.
    On reserve in the Math Library

  12. V. Balzani and F. Scandola, "Supramolecular Photochemistry", Ellis Horwood Limited: Chichester, 1991.
    On reserve in the Math Library

  13. "Frontiers in Supramolecular Organic Chemistry and Photochemistry", H.-J. Schneider and H. Durr, eds., VCH Publishers: New York, 1991.
    On reserve in the Math Library

  14. N. J. Turro, V. Ramamurthy and J. C. Scaiano, "Modern Molecular Photochemistry of Organic Molecules", University Science Books, ISBN-978-1-891389-25-2.
    Rush ordered - coming soon

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Broadcasts, etc.

Broadcast27: G8316_10_Presentations

Dear Class,

Some further comments on presentations.

I have modified the tentative schedule to produce the attached schedule. If you would like to switch with a class mate and can work it out, please let me know. The schedule is flexible. However, I would like all changes to be make by tomorrow at 5 PM.

The ordering of the presentations is alphabetical on each day unless there has been a request to switch which I have approved.

In order to be sure that we don't spend time finding out problems with your ppt, I'd like to have a copy of whatever you have by 8 PM on the day before the presentation is due. So for the presentations on Monday, March 1, those giving the presentation should send me their ppt by 8 PM on Sunday, February 28. I will go over the ppt and let you know if I have any comments and will be able to check the ppt for compatibility with my computer. On the day of your presentation, please bring it on a flash drive so we can put all five talks on my computer.

I'll be available for any questions on Friday and all weekend by email or Skype. The latter is a free download compatible with Mac or PC that allows free audio or audio video connections via the internet. I recommend that you all download it and give it a try. My Skype address is nickturro.

Best for a snowy prequel to the weekend. I'm looking forward to the start of the presentations on Monday.        


Broadcast26: G8316_10_Information on presentations. Readings

Dear All,

Attached please find some suggested guidelines for preparing your powerpoint presentation.  Also attached is a copy of a paper mentioned by Professor Tomalia on his ideas concerning a systematic outline for nanoscience and a paper referred to by Professor Tomalia on "There's Plenty of Room at the Bottom".        


Broadcast25: G8316_10_Tentative presentation schedule

Dear Class,

Attached is a tentative schedule of presentations based on your responses.        


Broadcast24: G8316_10_Selection of date for presentation

Dear Class,

If you have a preferred day (M March 1, W March 3 or M March 8) for your presentation, please let me know by 9 PM this evening. I will try to provide you with your preferred day if at all possible. If you don't respond I'll organize a schedule and send it out on Tuesday.        


Broadcast23: G8316_10_Check out broadcasts on labeling reports as a guide for making your outlines.

Dear All,

If you have not yet submitted the outline of your reports, I suggest that you check out Broadcast 3, Broadcast 16 and Broadcast 22 on the course home page.        


Broadcast22: G8316_10_Important: labeling files sent to me

Dear Class,

Please review the required labeling for any files sent to me. Use as the keywords G8316_10_ReportOutline.        

IMPORTANT: LABELING FILES AND REPORTS

It's important for all of you to use the same format for labeling electronic and hard copy files that you send me or print out. It is very important to follow this format in order for me to keep track of what you send me.

For any electronic file, please use initials of your first and last name, then an underscore, a key word or two indicating the nature of the file, then an underscore or a name that I have indicated that you should use, then an underscore, and the date with two numbers for the month, date and year. Always use the proper extension for the file (.doc, .ppt, etc.).

In the first page of any documents that you send me be sure to include your name at the top of the first page.

Example: NT_Assignment1_012010.doc.


Broadcast21: G8316_10: Q and A and tweeting

Dear Class,

Below is a question from the member of the class and my response.        

I'd like to continue to experiment with available internet resources for the remainder of class.  When a question is sent to me, I'd like to see how twitter works to get the class to receive the method an possibly get involved in the discussion.        

Until then, I'll sent broadcasts of any questions and my repsonses and also post them on our home page.        

We'll discuss your opinions on this experiment at the end of class on Monday.

Prof Turro, There seems to be some confusion amongst the students on whether the report is a presentation of existing research or an original research proposal.  Can you clear this up for us? -Thanks, XX

Dear XX, The report should be a presentation of existing research.  Some original research can be presented for extra credit.

Here would be the tweet:

Q: Is the report a presentation of existing research or an original research proposal?

A: Existing reported research. Some original research can be included for extra credit.


Broadcast20: G8316_10_pdf of Monday's lecture on a framework for unifying nanoscience

Dear Class,

A pdf of the lecture on Monday by Professor Tomalia is available for download at http://turroserver.chem.columbia.edu/supramolecular/documents/G8316_10_Tomalia_Lecture.pdf and is also on CourseWorks under Broadcast 19.      

Have a nice weekend and see you Monday.


Broadcast19: G8316_Tomalia ppt

Dear Class,

You can download a ppt of Professor Tomalia's lecture for Monday by going to CourseWorks and checking Broadcast 18 and clicking on Lecture 10 (full .pdf).        

Best for the weekend.


Broadcast18: G8316_10_ppt for lecture on Monday by Prof. Donald Tomalia

Dear All,

Lecture 10 (full .pdf) on Monday will be given by Professor Donald Tomalia of Central Michigan University. Professor Tomalia has been the leader in the development of dendrimers in the 1990-present. He'll discuss some ideas that he is formulation on producing "a periodic table for nanoscience" that are very relevant to supramolecular chemistry.

You may want to consider a topic based on the ppt.

Let me know if you have any questions on finding materials to determine the scope of your topic.


Broadcast17: G8316_10_Lecture9

Dear All,

Attached is a pdf of today's Lecture 9.


Broadcast16: G8316_10_Report/presentation Topics

Dear Class,

I've received all of your tentative topics and responded by email concerning their suitability for the report/presentation.

Please send me an outline of the topic and how you plan to structure your report by next Sunday at 5 PM. We can meet to discuss or you can send me material that we can discuss by email. Another possibility is to get together by Skype.

There are numerous ways for you to search the hard copy and electronic literature to narrow down your topic and proposal the more defined version of the topic for us to discuss.

Here are some tried and true ways to proceed, but there are many other possibilities.

(1) The gold standards for searching the electronic literature are SciFinder and Web Of Science (Citation Index).

(2) You can search each by key words, authors, etc.

(3) For the first cut you can search for reviews.

(4) Or you can find a paper that we have discussed and find the article in Web Of Science. The article will have references that you can search of other relevant papers dealing with the topic. In addition, you can search all the new articles that have cited the article. This method leads to a branching that could quickly allow you to find out whether the topic is really what you had in mind or whether there is a reasonable scope that you can cover.

We will discuss further in class on Wednesday.


Broadcast15: G8316_Lecture8

Dear All,

Attached is a pdf of Lecture 8.


Broadcast14: G8316_10 More on Topics for report and presentation and Lecture8

Dear All,

I hope that you all have had a pleasant weekend.

I would like to have your tentative topics for your presentation/reports by 5 PM on Monday, Feb. 15. Those of you who have already submitted possible topics don't have to sent anything further, unless you want to update or modify what you have sent.

On Wed we'll discuss the report topics and begin to arrange for email or personal sessions to refine the possible topics to a tentative topic.

The remaining 7 classes will cover the following topics:

(1) The use of supramolecular chemistry to sequence the genome using fluorescence sensors (attached is a review on this topic: ACR_ASAP_SeqBySynthesis.pdf).

(2) The concept of a "solid" surface as a supramolecular host and the use of ESR into the characterization of the surface of a zeolite external surface as a host (attached is a relevant paper dealing with the subject: JACS_130_11344_08_DBK_MFI_External.pdf).

(3) Toward the development of a "periodic table for nanoscience". Prof. Donald Tomalia of the Nanotechnology Center, Central Michigan University, will present an iLecture to the class on this topic on Monday, February 22. We will discuss this topic briefly on this Wed., February 17. A discussion of the topic is attached (JNR_11_1251_09_NanoPeriodicTable.pdf).

This is a long paper, but it will be worth your effort to go through it and see if there are some possible areas for your report/presentation.

(4) If time allows, we'll discuss endofullerenes, complexes that contain atoms or molecules inside a C60 or derivative of C60.

(5) The presentations will be give on Monday, March 1, Wed. March 3 and Monday, March 8.

See you in class tomorrow.


Broadcast13: G8316_10_Lecture7 and information on the reports and presentation

Dear All,

Attached is a pdf of today's lecture.        

You need to start thinking about a possible topic for your report and presentation.  Both can be on the same topic or each can be on a separate topic.  Attached are Guidelines for writing the report and giving the presentation.        

I need to approve your topics for the report and the presentation.  By next Monday at 9 AM you need to send me one or more topics that your are considering.  You need to connect your topic to some aspect of supramolecular organic chemistry.  You decide how to make the connection and then present the topics to me and we'll discuss either by email or face to face of some combination.  If you pick more than one topic, we'll discuss and determine the best one.        

So by next Monday at 9 AM, please send me some questions if you have them and the topics that you want to consider.  Candidates are topics covered in the lecture so far.  The remaining lectures will cover endofullerenes and interfaces as hosts and possibly some other topics depending on the time available.        

Thanks for coming to class this morning.  I hope that it was worth the effort.


Broadcast12: G8316_Lecture6

Dear Class,

A pdf of Lecture 6. It's a big file. If you can't get it let me know and I'll figure out a way to get it to you later this afternoon.


Broadcast11: G8316_Readings for Lecture 6

Dear Class,

Lecture 6 on Monday will deal with guest@carcerands (guest@carcerplexes). We'll discuss electronic energy transfer, photoinduced spin tranfer and photoinduced electron transfer of guest@carcerand systems. We'll then move on to discuss the use of fluorescence energy transfer as a tool to investigate biomolecules in vitro and in vivo.

Two brief readings on the two major mechanisms for energy transfer are attached along with a review of an article dealing with the use of fluorescence resonance energy transfer to probe DNA and mRNA.

Dipole-dipole_EnergyTransfer.pdf

ElectronExchangeEnergyTransfer.pdf

ACR_40_402_07_Biosensors.pdf


Broadcast10 G8316: Student questions and answers

Dear All,

Students from U Miami have kindly submitted some questions on the materials presented in Lecture 4. Attached are my responses to the questions (.doc) and a detailed description of CIDNP for those interested.


Broadcast9 G8316: pdf of Lecture 5

Dear All,

pdf of lecture 5 attached.


Broadcast8: G8316 Readings for Lecture 5

Dear All,

Readings for Lecture 5 (alternate for Adobe Reader 5+):

Section 13.9: General principles of supramolecular control, p. 954.
Section 13.10: Room temperature phosphorescence, p. 955-959.
Section 13.11: Excimer formation and bimolecular interactions, p. 959-961.


Broadcast 7: G8316_Lecture 4

Dear Class,

Attached is a pdf of Lecture 4.


Broadcast6: G8316_Readings for Lecture 4

Dear Class,

Attached are some readings that will prepare you for Lecture 4 on Monday.

We'll start with a discussion of supramolecular effects on the competition between Type I and Type II reactions and then we'll launch into a discussion of spin effects in supramolecular systems with micelles as an exemplar host.

Please make a note of any questions that you have as you do the reading.

21_ACR_13_369_80_DBK_Micelle_Spin_Review.pdf

22_JACS_103_4200_81_EXB_Micelles_Spin.pdf

23_JACS_105_1572_83_MicellePoly_Spin.pdf

24_JACS_105_1861_83_DBK_MicelleCage_Spin.pdf


Broadcast5: pdf of lecture 3

Dear iClass,

Attached please find a pdf of Lecture 3.


Broadcast4: PDF of lecture 2 and some readings.

Dear Class,

A pdf of Lecture 2 is attached. Please let me know if you have any questions.

There are a list of reserve books dealing with various aspects of supramolecular organic chemistry and related materials that has been put on the Course home page on courseworks.

Books 6, 7 and 10 are electronic and can be viewed on the web. The others are on Reserve in the Math Library.

Some readings related to Wednesday's lecture 3 which will be on supramolecular photochemistry and photophysics in micelles are also attached:

297_JACS_105_1861_Weed.pdf

305_JACS_105_6347_MicelleExit.pdf

256_JACS_103_4200_81_DBZ.pdf


Broadcast3: G8316_Assignment 2

Thanks for the excellent discussion today. I'm attaching a powerpoint (ppt) summarizing Lecture 1 and some readings related to the Lecture.

(1) G8316_10_Lecture1_011910 is pdf of the material covered in the lecture given on Wed. January 20.

(2) G8316_Ch13_SupramolecularPhotochem is a pdf of Chapter 13 of the book "Modern Molecular Photochemistry of Organic Molecules" This book has just been published and the library has requested a copy that will be put on reserve as soon as it arrives. This chapter will be the basis for the lectures of the course. Please read pages: Section 13.1-13.5, pages 925-937 and Section 13.6, pages 941-948.

(3) JPCC_112_8046_08 is a pdf that shows how a guest@host complex is a true supramolecular system for which the guest properties, as determined by IR spectroscopy, are systematically related to a changing host structure, in this case micelles of different size.

(4) CC_2279_02_ZeoliteRev.pdf is a review of photochemistry of molecules adsorbed on the external or internal surface of zeolites. We'll be discussing some exemplar photochemical reactions on Monday.

Please come in with questions on any of these readings on Monday.

IMPORTANT: LABELING FILES AND REPORTS

It's important for all of you to use the same format for labeling electronic and hard copy files that you send me or print out. It is very important to follow this format in order for me to keep track of what you send me.

For any electronic file, please use initials of your first and last name, then an underscore, a key word or two indicating the nature of the file, then an underscore or a name that I have indicated that you should use, then an underscore, and the date with two numbers for the month, date and year. Always use the proper extension for the file (.doc, .ppt, etc.).

In the first page of any documents that you send me be sure to include your name at the top of the first page.

Example: NT_Assignment1_012010.doc.

Note the labeling system for references and see if you can figure it out.

We'll go over this in Class on Monday.

Best,

NJT


Broadcast2: G8316_Assignment 1

Dear Class,

During the first class we will discuss the possible meanings of the words (1) supramolecular chemistry, (2) supermolecule, (3) molecular complex, (4) molecular recognition.

Assignment 1 involves your views of the meaning of these words. Please bring to class a print out of your definitions of each of the above together with examples. We will have a class discussion based on these definitions.

See you Wednesday, at 10:35 AM in 320 Havemeyer.

NJT


Broadcast1: G8316_SUPRAMOLECULAR_ORGANIC_CHEMISTRY

Dear Class,

Welcome to G8316_SUPRAMOLECULAR_ORGANIC_CHEMISTRY.

The first class meeting will be held in 320 Havemeyer at 10:35 AM on Wednesday, January. A copy of the class syllabus is attached (see above).

I look forward to meeting you next Wed.

Best for the weekend,

NJT


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