A Research Project in the Second Semester Organic Chemistry Laboratory

A Research Project in the Second Semester Organic Chemistry Laboratory

Timm A. Knoerzer

Nazareth College

NERM 2004

Rochester, NY

The Problem Students are usually not engaged in problem

solving or critical thinking while in the laboratory No connection of work from week to week (does

not simulate the real world; the “one and done” scenario)

Chemistry not done in context (scientifically relevant)

Student do not always learn about modern chemical techniques and reactions

Limited integration of technology Little exposure to structurally sophisticated

molecules

The Objectives

Do what real organic chemists do (perform a multi-step, multi-week project that requires students to plan, adapt, modify, improvise)

Learn modern/advanced chemical techniques Use technology to support and explain

experimental outcomes Learn relevant chemistry (connected to what

students are learning in class and are interested in) Summarize and communicate the work (report and

poster)

Provide students with an opportunity to:

Synopsis of The Project Objective: To generate a diverse small molecule

library of benzothiazine/amino acid/isothiocyanate hybrids

Context: Students are active participants in generating new compounds and in rehearsing critical synthetic transformations

Novelty: Synthesize a heterocycle that has limited precedence in the chemical literature (unknown utility)

Relevance: To ultimately explore the binding potential of these compounds toward various molecular recognition targets (receptors, enzymes, and other proteins) = bioorganic chemistry

Synopsis of The Project

Strategy: Combinatorial chemistry in conjunction with the synthesis of key nitrocinnamic acid starting materials

Schedule: Spring semester -- Begins in week 5; ends in week 14 (total of 9 weeks)

Topics: carbonyl addition, NAcS, SN2 (Mitsunobu), peptide synthesis, NArS, synthesis of ethers, enolates, use of protecting groups, spectroscopy, molecular modeling, scientific communication – parallels the chemistry introduced in class

Our target

H2N NH

O HN

R1 O NS

HN

R2

R3

linker

diversification #1: amino acids

diversification #2: nitrocinnamic acids

diversification #3: phenyl isothiocyanates

**

R4

Combinatorial strategy

OH

AA1

AA2

AA3

attach linker split #1NCA1

NCA2

split #2I1

I2

SCN1

SCN2

I3split #3

T1

Total AA = 3, total NCA = 2, total SCN = 2

3 x 2 x 2 = 12 total compounds in this library

Solid-phase parallel synthesis

Synthesis

OHH2N NH2

N N

O

N N

(CDI)

O NH

O

NH2HO

ONH

R1

O

O

HOBt, HBTU, Hunig's base

DMFWang Resin (1.1mmol/gram)

O NH

O

NH

O HN

R1

fmoc20% piperidine

DMF

HO

O

O2NR2

R3

DCC, HOBt, Et3N

DMF

O NH

O

NH

OHN

R1 O NO2

R2

R3

DMF

SnCl2

Synthesis

O NH

O

NH

OHN

R1 O NH2

R2

R3NCS

DMF

R

H2N NH

O HN

R1 O NS

HN

R2

R3

R4

O NH

O

NH

O HN

R1 O NH

R2

R3

S

HN

50% TFA, CH2Cl2

R4

Nitrocinnamic Acid Synthesis

H

O

H3CO

H3CO NO2

HH3CO

H3CO NO2

OO

HO2C CO2H

HHO

H3CO NO2

OOH

RO

H3CO NO2

OO

HO OH

R OH

HRO

H3CO NO2

ORO

H3CO NO2

O

OH

pTSA, toluene

20% aq. KOH

dioxanereflux reflux

10% aq. HCl

piperidine, pyridine

PPh3, DIAD

acetone, heat

We have used this scheme to construct 13 novel substituted 2-nitrocinnamic acidsMcDonald, E; Suksamrarn, A. J. Chem. Soc., Perkin Trans. 1 1978, 440-446.

Project Design PowerPoint introduction to project Students select synthetic units:

(2-3) amino acids (2) nitrocinnamic acids (1-2) phenyl isothiocyanates may also select linker

Students are responsible for generating enough synthetic material to complete project (need ~20 mg of the final compound)

Students are responsible for using analytical and spectroscopic methods to confirm products

Students must decide if synthetic products are pure enough to continue – if not they must purify (e.g. chromatography)

Technology Connection #1

HH3CO

H3CO NO2

OO

HHO

H3CO NO2

OO20% aq. KOH

dioxanereflux

1. Is this pathway SN2 or NArS?2. Why does the conversion occur para to the nitro group

rather than meta upon exposure of the starting 4,5-dimethoxy compound to 20% KOH (aq)?

Molecular Modeling (Spartan)The red line represents the energy of the transition state (kcal/mol) and the green line represents the charge on the incoming OH nucleophile.

More Modeling ResultsHere surface value = +20 in range of –60 to +26

Here surface value = +13 in range of –60 to +26

Technology Connection #2

How can you confirm the identity/purity of your products?

NMR

Mass Spec LC

Example NMR data

1.00 1.23

0.99

5.60

2.95

1.92

2.23

3.19

8 7 6 5 4 3 2 1 ppm

O

O

O

O NO2

CH3

NMR Expansions

2.0 1.8 1.6 1.4 1.2 1.0 ppm

4.3 4.2 4.1 4.0 3.9 3.8 3.7 3.6 ppm

O

O

O

O NO2

CH3

a

b

b

c

d

e

f

Example Mass Spec and LC data

H2N NH

OHN

O NH2

O

OMe

H2N

M+1 at 478.4 amu

More Mass Spec and LC data

H2N NH

OHN

O N

H2N

S

HNPh

M+1 at 483.2 amu

“391” = loss of NH-Ph“348” = leftover starting material (incomplete rxn)

Further Study and Extensions Design TLC system to monitor the course of

the Mitsunobu reaction and to perform subsequent column chromatographic purification

Determine how to obtain solid products that are free of solvent

Further confirmation of products by 13C-NMR, 13C-DEPT, and 1H-1H-COSY

Adjust # of equivalents and observe changes MECHANISMS Must determine how much analysis is to be

completed for “publication”

Communicating results

Poster

Formal Report

Questions to Ponder

Pictures

Pictures

Acknowledgements

Dr. Benjamin Miller (U of R Medical School Center for Future Health)

Dr. Paula Satterly-Childs Nazareth College summer research students

(Jessica Goodman, Jennifer Cahoon, Christina Gallis, Ed O’Neil, Ashanti Tolbert)

Graduate students in the the Miller group Terry O’Connell Organic chemistry students 2002-2004