graduate lectures (organic synthesis in water)

Organic Synthesis in Water

Kinetics, Mechanism and Synthesis

Graduate Lecture Series

Lecture 1

Dr Anthony Coyne(anthony.g.coyne@gmail.com)

Outline

Lecture 1 – Kinetics, Mechanism and Synthesis

• Background

• Mechanistic aspects

• Influence on rate of reaction

• Organic Synthesis

• Diels-Alder [4+2] cycloaddition reaction

• Huisgen [3+2] cycloaddition reaction

• Claisen rearrangement

• Epoxide ring opening

Lecture 2 – Emerging areas of research

• Recap of Lecture 1

• Organic Synthesis

Emerging metal catalysed reactions

• Olefin metathesis

• Cyclopropanation reactions

• Chemical Biology Applications

• CuAAC reactions

• SPAAC reactions

• Sonogashira coupling

• Suzuki coupling

Why water as a reaction solvent?

Background

Acetonitrile (2009)

While acetonitrile is not a key solvent in organic synthesis it is just a matter of time that there will be a shortage

of a solvent that is used day to day

Background

Why water as a solvent for organic reactions?

Water is the universal solvent in Nature

Non-toxic

Non-flammable

Cheap and readily available

Can have interesting acceleration effects for certain reactions

Can be used in conjunction with some organic solvents

Applicable to a wide range of reaction types

Green Chemistry

Difficult to remove water from reactions

Solubility (not always a problem)

Not suitable for all organic reactions

Waste streams need to be treated

Pros

Cons

Background – Reactions using water as a solvent

Typically how have reactions been carried out using water as a solvent

Background – In the beginning

1828 – Friedrich Wöhler

1931 – Otto Diels and Kurt Alder

1948 – Robert Burns Woodward

Diels, O.; Alder, K. Justus Liebigs Ann. Chem. 1931, 490, 243

Woodward, R. B.; Baer, H. J. Am. Chem. Soc. 1948, 70, 1161

Wöhler, F. Annalen der Physik und Chemie. 1828, 88(2), 253

Background

1980 – Ronald Breslow – Columbia University

Rideout, D, Breslow, R, J. Am. Chem. Soc., 1980, 7816

Ph.D Harvard University

(R. B Woodward)

PostDoc – University of

Cambridge (Lord Todd)

Solvent k2 x 105 M-1s-1

Isooctane 5.94

Methanol 75.5

H2O 4400

Solvent k2 x 105 M-1s-1

Isooctane 1.90

Methanol 4.0

H2O 59.3

The reaction of cyclopentadiene and methyl vinyl ketone is over 700 times faster in water than in isooctane.

The corresponding reaction with acrylonitrile is only 30 times faster. Why is this?

k2 isooctane

k2 Water= 740

k2 isooctane

k2 Water= 31

Background

1996 – Jan Engberts – University of GroningenPhD. University of

Groningen

PostDoc – University of

Amsterdam

Solvent Additive k2 (M-1s-1)

Acetonitrile - 1.4 x 10-5

Water - 4.02 x 10-3

Acetonitrile Cu(NO3)2 0.472

Water Cu(NO3)2 1.11

k2 Acetonitrile

k2 Water = 287k2 Acetonitrile

k2 Water= 5.4

k2 Acetonitrile

k2 Water(Cu )= 79285

Otto, S., Bertonicin F., Engberts, J.B.F.N., J. Am. Chem. Soc., 1996,118, 7702

2+

Uncatalysed Cu2+ catalysed

Reaction is accelerated 287 times faster in H2O compared to MeCN. When a Lewis acid (Cu(NO3)2) was added a large

rate acceleration observed however the reaction using water does not have a large rate acceleration as observed with the

uncatalysed reaction

Catalysis using water as a solvent possible however mechanistically can be difficult to study

Klign, J. E., Engberts, J.B.F.N. Nature. 2005, 435, 746

Background

2005 – K. Barry Sharpless – Scripps Research Institute

Narayan, S., Muldoon, J., Finn, M.G., et al. Angew. Chem. Int. Ed., 2005, 44, 3275

Solvent Conc (M) Time to completion

Toluene 2 > 120 h

Methanol 2 18 h

H2O 4.53 10 min

These reactions were classed as ‘on-water’ as they were seen to float on water surface

Background

2005 – K. Barry Sharpless

Narayan, S., Muldoon, J., Finn, M.G., et al. Angew. Chem. Int. Ed., 2005, 44, 3275

PhD. Stanford University

(E.E. Van Tamelen)

PostDoc – Stanford

University and Harvard

Solvent Reaction Time

Neat 36 h

H2O 3 h

Solvent Conc (M) Reaction

Time

Yield (%)

Toluene 1 144 79

Neat 3.69 10 82

H2O 3.69 8 81

Both reactants are liquids so there is not mixing issues

associated with neat reactions

The reaction ‘on-water’ is faster than the neat reaction.

No large rate acceleration observed with these

reactions. TSRI TSRI TSRI

Background – What is so significant about the rate acceleration using water?

A key aspect of the initial studies where water has been used as a solvent has focused on cycloaddition reactions.

Huisgen, R. Pure Appl Chem. 1980, 52, 2283

Huisgen, R., Seidel, H, Brüning, I, Chem. Ber. 1969, 102, 1102

Why are there large rate accelerations observed using water as a reaction solvent

and what is causing these?

The rate on going

from toluene to

ethanol only changes

by a factor of 5.6

This is because these reactions are solvent insensitive

Why are there large rate accelerations using water as a solvent?

Not fully understood however various theories have been put forward

Mechanistic Aspects – Hydrophobic Effect (Breslow)

k2 isooctane

k2 Water= 740

k2 isooctane

k2 Water= 31

Breslow and Rideout proposed that the rate acceleration observed for the reactions was due to the hydrophobic

effect.

Hydrophobic effect found widespread in nature and is important in

protein structure.

However this does not take into account the difference in rate between the reaction with methyl vinyl

ketone and acrylonitrile.

Rideout, D, Breslow, R, J. Am. Chem. Soc., 1980, 7816

Jorgensen and co-workers examined

the reaction using computational

methods and suggested that the large

accelerations observed with vinyl

ketones was due to a significant

Hydrogen bonding effects

Jorgensen calculated that the rate

acceleration was due to approximately

90% H-bonding with 10% from

hydrophobic effects

Mechanism similar to H-bonding

organocatalysis

k2 isooctane

k2 Water= 740

k2 isooctane

k2 Water= 31

Mechanistic Aspects – H-Bonding Effects (Jorgensen)

Rideout, D, Breslow, R, J. Am. Chem. Soc., 1980, 7816

Jorgensen, W.L., J. Org. Chem., 1994, 59, 803

PhD Harvard

University

(E.J. Corey)

H-bonding occurs with the vinyl ketone however

not with the acrylonitrile

Mechanistic Aspects – ‘On-water’ Effect (Sharpless and Marcus)

Toluene: >120 h

H2O: 10 mins

The ‘on-water’ is so named because the organic reactions are ‘floated’ on water

Marcus and co-workers examined this reaction from a computational aspect . The large rate accelerations were

proposed to be due to the favorable H-bonding interactions to the transition state. The H-bonding was at the oil

water/interface where a proton protrudes into the ‘oil’ phase which acts as the catalyst.

These reactions are very difficult to examine experimentally in order to explore the on-water effect.

Jung, Y, Marcus, R.A, J. Am Chem. Soc., 2007, 129, 5492

Jung, Y, Marcus, R.A, J. Chem. Phys. Cond Matt., 2010, 284117

PhD. McGill University

Nobel Prize: 1992

(Electron transfer

reactions)

Mechanistic Aspects – Influence on the rate of the reaction

k2 Toluene

k2 Water= 40.9

1998 – M.R Gholami

k2 Acetonitrile

k2 Water= 164

2004 – R.N. Butler

k2 Acetonitrile

k2 Water= 15.3

1982 – R. Breslow

k2 Acetonitrile

k2 Water= 211

Rideout, D, Breslow, R, J. Am. Chem. Soc., 1980, 7816

Gholami, M. R.; J. Chem. Res (S), 1999, 226

Butler, R.N. et al., J Chem. Soc Perkin Trans 2, 2002, 1807

In all of the above cases the reactants are soluble in water and the

kinetics can be measured

(‘in-water’ reactions)

‘In-water’ versus ‘On-water’ – What is the difference?

‘In-water’ ‘On-water’

Water is the only reaction medium - no

organic co-solvents are used.

Reactions use insoluble substrates and

suspensions are observed.

Typically reactants are present in

concentrations >0.1M or above.

Mechanistically very difficult to study

Large rate accelerations observed can be

substrate and reaction specific.

Water is generally the reaction medium -

organic co-solvents are used to solubilise

reactants although significantly effects rate

acceleration.

Reactions use soluble substrates

Typically reactants are present in

concentrations < 0.1M or below.

Mechanistically as reactants are in solution

these are easier to study

Large rate accelerations observed can be

substrate and reaction specific.

Distinguishing between in-water and on water is very difficult however concentration of reactants and

solubility can be used as a guide

Mechanistic Aspects

Model Reactions using water as a solvent

Increase in rate of reaction

Increase in stereoselectivity

These can both be rationalized through various mechanisms

Exact mechanism is unknown and needs further research

What happens when you move to more complex reaction systems?

Pericyclic Reactions – Cycloaddition reactions

Concerted reactions and solvent insensitive

Key reactions in multi-step synthesis

Highly regio- and stereospecific

Can generate up to 4 new sterocentres in one synthetic step

Large number of diene/1,3-dipoles and diene/dipolarophiles available

Wide structural diversity

Diels-Alder [4+2] Cycloaddition Reaction

Huisgen [3+2] Cycloaddition Reaction

Mechanistic Aspects – Influence on the stereoselectivity

Solvent Dienophile endo/exo

Cyclopentadiene (excess) Methyl vinyl ketone 3.85:1

Methyl acrylate 2.9:1

Ethanol Methyl vinyl ketone 8.5:1

Methyl acrylate 5.2:1

Water (0.15M) Methyl vinyl ketone 21.4:1

Methyl acrylate 9.3:1

Water (0.30M) Methyl vinyl ketone 18.6:1

Methyl acrylate 5.9:1

How can water be useful as a reaction solvent in organic synthesis?

1982 – Ronald Breslow

Enhancement of the endo/exo ratio and this is more pronounced in the cases of the vinyl ketones. Useful in organic

synthesis step where the endo isomer is required. Concentration of the reactants has some effect on endo:exo ratio

Breslow, R. Maitra, U, Rideout, D, Tet. Lett, 1984, 25(12), 1239

Pericyclic Reactions – Diels-Alder Cycloaddition reactions

Solvent Time (hr) Yield (%)

Toluene 168 Trace

Water 1 77

The cis isomer is formed however this isomerises to the trans isomer

Addition of THF, MeOH or 1,4-Dioxane causes a fall off in the rate of reaction

Reaction has excess diene present and the concentration of this is maintained at 1.0M

Increase in concentration of diene gives a fall off in rate of reaction

Reaction needs to be stirred vigorously

The use of the sodium salt adds an extra step to convert to the methyl ester

Grieco, P.A. et al, J. Org. Chem, 1983, 48, 3139

What about in more complex cases?

Pericyclic Reactions – Diels-Alder [4+2] cycloaddition reaction

Quassinoid natural product

R Solvent Diene conc t (h) Yield (%) endo:exo

Et Benzene 1M 288 52 0.85:1

Et H2O 1M 168 82 1.3:1

Na H2O 1M 8 83 2.0:1

Na H2O 2M 5 100 3.0:1

Grieco, P.A. et al, Tet Lett, 1983, 24, 1897

Concentration critical for these type of reactions

Significant increase in rate stereoselectivity in comparison to the reaction in organic solvents

Pericyclic Reactions – Diels-Alder [4+2] Intramolecular cycloaddition reaction

Solvent Temp (oC) Ratio

Toluene 90 75:25

Water 90 40:60

Reaction in water shows different selectivity

compared to toluene.

Solvent Reaction Time

Chloroform 10 days

Water 2 days

Williams, D.R. et al, Tetrahedron Lett, 1985, 26, 1362

Lovastatin

Witter, D.J., Vederas, J.C., J. Org. Chem, 1996, 61, 2613

Reaction accelerated on going from chloroform to water.

No change in stereoselectivity

Possible assembly for lovastatin core by Aspergillus terrus MF 4845

Pericyclic Reactions – Huisgen [3+2] cycloaddition reaction

Mechanistically identical to the Diels-Alder [4+2] cycloaddition reaction

Typically 1,3-Dipoles are highly unstable and need to be generated in-situ

There are some 1,3-dipoles that are stable at room temperature

This makes carrying out reactions using water as a reaction solvent more difficult and exploring the

mechanistic aspects

Pericyclic Reactions – Huisgen [3+2] cycloaddition reaction

Dipolarophile Solvent Yield endo/exo

Acetonitrile 96 3:1

Water 95 7:1

Acetonitrile 80 3:1

Water 95 16:1

Acetonitrile 65 8:1

Water 91 10:1

Unusually these 1,3-dipoles are highly stable and can be isolated and stored.

Stability is due to the electron withdrawing nature of the two cyano groups

Reaction with vinyl ketones is highly endo selective using water a a reaction solvent

(Same trend as observed with cyclopentadiene)

Azomethine ylides

Butler, R.N. et al, J. Chem. Soc. Perkin Trans 2, 2002, 1807

Pericyclic Reactions – Huisgen [3+2] cycloaddition reaction - Azides

Thermal cycloaddition

Cu and Ru Catalysed (CuAAC and RuAAC)

Strain Promoted cycloaddition (SPAAC) – Lecture 2

1,4 and 1,5 isomer formed in a 1:1

ratio. Need to be heated over 80oC

Cu - 1,4-isomer

Ru - 1,5-isomer

Strain of the double or triple bond of the

dipolarophiles gives rise to a rate increase for

the reaction. No metal or heat required for the

reaction.

Azide chemistry has undergone a renaissance with the advent of the CuAAC, RuAAC and SPAAC

(Sharpess, Fokin, Meldal and Bertozzi)

Azides Kinetics – Engberts

Pericyclic Reactions – Huisgen [3+2] cycloaddition reaction

Novartis – Rufinamide synthesis

Solvent k rel

Hexane 1

EtOH 1.6

H2O/NCP (99:1) 53.2

Solvent Temp (oC) Yield (%)

Neat 80 72

N-Heptane 80 46

EtOH 77 40

H2O 80 98

The cycloaddition reaction was found to be over 50 times faster in water than in hexane. 1% NCP was added to help

solubilise the azide

HCl is a side product of this reaction. In

organic solvents this polymerises the

chloroacrylonitrile. In water a two phase

system is observed where the HCl is dissolved

in the water layer

Engberts, J.B.F.N et al., Tet. Lett., 1995, 36, 5389

Portmann, R., WO98022423, 1998

Pericyclic Reactions – Huisgen [3+2] cycloaddition reaction

Synthesis of Biotin – De Clercq

Monomeric streptavidin and bound

biotin

(KD = 10-14 M)

The cycloaddition precursor was synthesized from L-cysteine.

When heated in water this undergoes cycloaddition reaction followed by elimination of N2

The seven membered ring opens up using water to form the N-benzylated biotin.

DeClercq, P. J., et al, Tetrahedron Lett., 1994, 35, 2615

Pericyclic Reactions – Claisen [3,3] sigmatropic rearrangement

Concerted reactions and solvent insensitive

Key reactions in multi-step synthesis

A number of different variants – N (azaClaisen), S (thiaClaisen)

Claisen

Aza-Claisen

Thia-Claisen

Typically require high temperatures which can lead to decomposition products

Substitution on the substrate can lower the activation energy for reaction.

In Nature

Chorismate to Prephenate- enzyme catalysed by

Chorismate mutase

kcat= 106

kuncat

Chorismate mutase

Pericyclic Reactions – Claisen [3,3] sigmatropic rearrangement

Reaction is water at 75oC at pH 5 has a t1/2 of 10

mins

k(H2O)/k(MeOH) = 100

This Claisen rearrangement occurs at a much faster rate in

water in comparison to methanol.

This reaction occurs even without the presence of the

enzyme Chorismate mutase

Reaction with no enzyme

Andrews, P.R., et al, Biochemistry, 1973, 12, 3492

Pericyclic Reactions – Claisen [3,3] sigmatropic rearrangement

Brandes, E. et al., J. Org. Chem., 1989, 54, 515

Rearrangement of allyl vinyl ethers – effect of water on the rate of reaction.

R Solvent Rate

(k x 10-5s-1)

Yield

(%)

Na H2O 18 85

Na MeOH 0.79 -

Me C6H12 0.084 -

The Claisen rearrangement of the sodium carboxylate allyl vinyl ether is over 200 times faster that the corresponding

reaction in cyclohexane (methyl ester)

Rearrangement of naphthyl ethers – effect of water on the rate of reaction.

Solvent Yield (%)

Toluene 16

DMF 21

MeOH 56 (+14%)

neat 73

H2O 100

Narayan, S., Muldoon, J., Finn, M.G., et al. Angew. Chem. Int. Ed., 2005, 44, 3275

‘On-water’ reaction is faster than other polar solvents. Product

can be filtered off when water is used

No large rate accelerations observed as in the case of

quadricyclane and DEAD

Claisen Rearrangement

This Claisen rearrangement occurs at a much faster rate in water in comparison to toluene.

The corresponding a-anomeric reaction occurs in a similar time.

When the reaction was carried out in toluene only decomposition products were observed. The NaBH4 was added

to reduce the aldehyde.

Lubineau, A., et al, J. Chem. Soc. Perkin Trans 1, 1992, 1631

Lubineau, A. et al., Tetrahedron Lett., 1990, 31, 4147

Rearrangement of allyl vinyl ethers – effect of water solubilising groups

Claisen Rearrangement

Gambogin

Solvent T (oC) t (h) Conversion (%)

Ethanol 65 4 0

Methanol 65 4 0

MeOH/H2O (1:1) 65 4.0 100

MeOH/H2O (1:2) 100 0.5 100

H2O - - ppt of SM

Synthesis of Gambogin (Nicolaou)

First isolated in 1996 from

Gamboge resin from

Garcinia hamburgi

MIC (Hela) = 6.25 mg/mL

MIC (HLA) = 3.13 mg/mL

Organic co-solvent

present as reaction in

pure water causes

precipitation of the

starting material

Nucleophilic Ring Opening

Epoxides and aziridines are excellent synthetic intermediates

Readily converted to other functional groups such as diols, aminoalcohols and diamines

Can be done enantioselectively

Could also be described as a ‘Click’ reaction as they are highly efficient and give high yields

In Nature nucleophilic ring opening has been proposed as a key biosynthetic step in the formation of

some natural products

Epoxides

Aziridines

Nucleophilic Ring Opening

Cane, Celmer, Westley Proposed Mechanism

Monensin Brevetoxin

Jamison T.J. et al, Mar. Drugs, 2010, 8, 763

Nucleophilic Ring Opening – Epoxides (water as a nucleophile)

What happened when you heat an epoxide in water?

Monoepoxide

Bisepoxide

Qu, J et al, J Org Chem, 2008, 73, 2270

Could this be a competing pathway in epoxide ring opening with other nucleophiles in water?

Nucleophilic Ring Opening – Epoxides (Other nucleophiles)

Monoepoxide

No reaction occurred in either toluene or diethylether

Bonollo et al, Green Chem, 2006, 8, 960

Nucleophilic Ring Opening – Cascade Sequence

Kolb, H.C.; Finn, M.G.; Sharpless, K.B. Angew Chem. Int. Ed.,

2001, 40, 2004

Cited 5609 times (Dec 2014)

Rostovtsev, V.V.; Green, L.G.; Fokin, V.V; Sharpless, K.B.

Angew Chem. Int. Ed., 2002, 41, 2596

Cited 4971 times (Dec 2014)

Epoxide Ring Opening – Biomimetic Approach

Conditions Ratio (endo: exo)

Cs2CO3, MeOH 1:2.7

AcOH, Toluene 1.6:1

Ethylene glycol 9:1

Methanol 8:1

Water > 10:1

Brevetoxin B Ph.D Harvard University

(Stuart Schreiber)

PostDoc Harvard University

(Eric Jacobsen)

Jamison T.J. et al, Science, 2007, 317, 1189

Epoxide Ring Opening

Triepoxide and Bisepoxide

Where next for this methodology?

Could this be used in the synthesis of brevetoxin or larger polyether natural products such as Maitotoxin?

Jamison T.J. et al, Science, 2007, 317, 1189

Lecture 1 - Overview

Large rate accelerations and increase in stereoselectivites observed using water as

a reaction solvent which are not found using organic solvents.

The reasons for these accelerations are not fully understood and need further

mechanistic study

Can be applied to more complex systems

Organic Synthesis in Water

Emerging Areas of Research

Graduate Lecture Series

Lecture 2

Dr Anthony Coyne(anthony.g.coyne@gmail.com)

Outline

Lecture 1 – Kinetics, Mechanism and Synthesis

• Background

• Mechanistic aspects

• Influence on rate of reaction

• Organic Synthesis

• Diels-Alder [4+2] cycloaddition reaction

• Huisgen [3+2] cycloaddition reaction

• Claisen rearrangement

• Epoxide ring opening

Lecture 2 – Emerging areas of research

• Recap of Lecture 1

• Organic Synthesis:

Emerging metal catalysed reactions

• Olefin metathesis

• Cyclopropanation reactions

• Chemical Biology Applications

• CuAAC reactions

• SPAAC reactions

• Sonogashira coupling

• Suzuki coupling

Complexity of reactions using water as a solvent

Level of

complexity

Claisen Rearrangement

(1 reactant)

Lecture 1

Diels-Alder Reaction

(2 reactants)

Lecture 1

Olefin Metathesis (Cross Metathesis)

(2 reactants and catalyst)

Lecture 2

Suzuki Reaction

(2 reactants and catalyst, ligand, base)

Lecture 2

Diels-Alder Reaction – Cu catalysed

Solvent Additive k2 (M-1s-1)

Acetonitrile - 1.4 x 10-5

Water - 4.02 x 10-3

Acetonitrile Cu(NO3)2 0.472

Water Cu(NO3)2 1.11

Otto, S., Bertonicin F., Engberts, J.B.F.N., J. Am. Chem. Soc., 1996,118, 7702

Reactions using catalysis are more complex to understand when water is used as a reaction

solvent

Lecture 1

Uncatalysed Reaction

Increase in rate of reaction when water is used as

the solvent

Cu catalysed Reaction

No large rate increase is observed on

changing to water as a solvent.

Lewis acid catalysis predominates?

Olefin Metathesis

Ruthenium Catalysts (Grubbs and Hoyveda) Robert Grubbs

Ph.D Columbia University

(Ron Breslow)

PostDoc Stanford

University

(James Collman)

Amir Hoyveda

Ph.D Yale University

(Stuart Schreiber)

PostDoc Harvard

University

(David Evans)

Olefin Metathesis

Ruthenium Catalysts - Modified with water solubilizing groups

In many cases catalysts have been modified where one of the ligands was appended with a water solubilizing

group.

Where the catalyst is modified using a PEG chain the molecular weight can be up to 5000 g/mol

Catalysts are only used in simple reactions and major focus of research has been focused on the catalysts and

not on reactions

Still an emerging area of research

Insoluble in water

Olefin Metathesis

Ring Closing Metathesis – Water soluble catalysts

Grubbs R.H et al, J. Org. Chem. 1998, 63, 9904

Solvent Catalyst

(mol%)

Conversion

(%)

MeOH 5 90

H2O 5 60

H2O 10 90

No reaction was observed with the diallylmalonate due to methylidene instability

When substituted with a phenyl ring the reaction goes in high conversion

The catalysts were shown to be stable in water over a number of days

Olefin Metathesis

CM and ROMP – Water soluble catalysts

Ring Opening Metathesis Polymerisation (ROMP) Cross Metathesis (CM)

Hoyveda-Grubbs type catalyst

This catalyst is highly versatile and can be used sucessfully in CM, ROMP and RCM reactions

Attempts to synthesis the phosphine derived catalyst was not possible (Grubbs I)

Grubbs R.H et al, J. Am. Chem. Soc. 2006, 128, 3509

Catalyst synthesis is straightforward

Olefin Metathesis

Dimerisation of Vancomycin– Grubbs I Catalyst

Nicolaou, K.C., et al, Chem.. Eur. J., 2001, 7, 3824

Using a modified Vancomycin it was possible to

homodimerise this using olefin metathesis

Typically the yields for this reaction were 30-60% with

the only product formed is the homodimer

No other side reactions observed even though there is

a large number of different functional groups on the

vancomycin scaffold

Grubbs I catalyst was used without any

modification

Olefin Metathesis

CM in Biological Systems

A surface cysteine residue undergoes a dethiolation to give a dehydroalanine. This can undergo

conjugate addition reactions with thiols. This can also undergo reaction with allylmercaptan to give a

double bond which is an effective substrate for olefin metathesis

No modified catalyst used,

t-Butanol needed for solubility,

Cysteine needs to be on the surface of the protein

Uses natural amino acids

Davis, B.G.; Bernardes, G.J.L, et al, J. Am Chem Soc,. 2008, 130, 9642

Davis, B.G.; Bernardes, G.J.L, et al, J. Am Chem Soc., 2008, 130, 5052

Metal catalysed cyclopropanation

Key Reaction

Carbenes generally unstable in water but when stabailzed by complexation to a transition metal

this increases their lifetime

Diazo compounds can be either generated in situ, synthesised or in some cases be purchased

The formation of both trans and cis cyclopropanes are passible and if a chiral ligand is used then this

reaction can be carries out enantioselectively

Cyclopropane containing natural products

Metal catalysed cyclopropanation

Rhodium(II) catalysed cyclopropanation – Water soluble catalysts

[Rh(OAc)2]2

Catalyst Yield (%) dr (trans/cis)

[Rh(OAc)2]2 26 1.6:1

[Rh(O2C tBu)2]2 61 1.5:1

[Rh(O2C(CH2)6Me)2]2 72 1.5:1

Water soluble catalysts gave low yields and poor

diastereoselectivity

This is due to [Rh(OAc)2]2 having a preference for

the aqueous layer and not dissolving in the

‘organic’ layer

Water insoluble catalysts gave higher yields

than water soluble catalysts

There is a biphasic system (due to 2 eq of

styrene) where the water insoluble catalysts go

into the organic layer

No change in diastereoselectivity

Wurz, R. P., Charette, A. B., Org Lett., 2002, 4, 4531

Metal catalysed cyclopropanation

Rhodium(II) catalysed cyclopropanation – Water soluble catalysts

Run Conversion (%) Yield (%) dr (trans/cis)

1 100 90 10:1

4 90 88 9:1

When the catalyst is recycled for a 4th time there is a negligible drop

in yield and diastereoselectivity

Water soluble catalysts gave excellent yields and trans diastereoselectivity

The porphyrin catalyst was modified using four sugar functional group which aided water solubility.

The catalyst could be recycled

Loading of 1 mol% is high as the catalyst has a molecular weight of 1450 (C73H80N4O21Ru)

Che, C-M et al., J. Am. Chem. Soc, 2010, 132, 1886

Metal catalysed cyclopropanation

Rhodium(II) catalysed cyclopropanation – Water soluble catalysts

55%

Uses natural amino acid

Incorporation of an alkene possible onto

Ubiquitin as lysine can be tethered using a N-

hydroxysuccinimide ester

Subsequent cyclopropanation using a diazo

modified dansyl tag carried out in 55% yield

using the water soluble Ru-porphyrin catalyst

Che, C-M et al., J. Am. Chem. Soc, 2010, 132, 1886

Metal catalysed cyclopropanation

From synthetic porphyrin to natural porphyrin systems

Porphyrins are found in cytochrome P450s (CYPs) which catalyse a wide range of oxidations such as

hydroxylations, epoxidations and heteroatom oxidation.

Could Iron be used as a metal for the generation of the carbene intermediate?

Carriera and co-workers showed that simple substrates can undergo cyclopropanation using iron catalyst

Typically enzymes are highly specific for substrates and how can this be overcome?

1450 Da 106169 Da (P450BM3)

Carriera, E. M et al., Org Lett, 2012, 14, 2162

Metal catalysed cyclopropanation

Cytochrome P450’s as cyclopropanation catalysts (Frances Arnold) B.S: Mechanical and Aerospace

Engineering (Princeton)

PhD: Chemical Engineering (Berkeley)

Post Doc: Biophysical Chemistry

(Caltech)

cis

trans

92 P450BM3 variants screened with this reaction

Catalyst Yield (%) dr (trans/cis) ee cis ee trans

P450BM3 1 63:37 27 2

H2-5-F10 59 84:16 41 63

H2A10 33 40:60 95 78

By making mutations this can greatly enhance the reactivity and selectivity of these enzymes

Amount of enzyme used needs to be reduced from 0.2 mol%

Arnold, F.H. et al., Science., 2013, 339, 307

Metal catalysed cyclopropanation

Cytochrome P450’ BM3 as cyclopropanation catalysts (Frances Arnold)

BM3-Hstar (T268A-C400H-L437W-V78M-L181V)

Arnold, F.H. et al., CatSciTech, 2014, 339, 307

By making five mutations this can greatly enhance

the reactivity and selectivity of these enzymes.

A noticeable mutation was on the cysteine where

this was mutated to a a histidine.This gave improved

rates for in vivo reactions

Levomilnacipran

Metal catalysed reactions

It is possible to carry metal-catalysed reactions using water as a reaction solvent.

These can be applied to complex reaction systems

The solubility of the catalyst/ligand combination can play a major part in the outcome of the reaction.

Typically the rate acceleration and enhanced stereoselectivity observed with pericyclic

reaction is not observed in metal catalysed reactions.

Still an emerging area of research

Can organic reactions be carried out in biological systems?

Bioorthogonal chemistry

Bioorthogonal Reactions

What are bioorthogonal reactions?

The term bioorthogonal chemistry refers to a chemical reaction that can occur inside of living systems without

interfering with native biochemical processes

Carolyn Bertozzi

University of Califonia, Berkeley

Joseph Fox

University of Delaware

Scott Hilderbrandt

Harvard Medical School

Azide-Alkyne cycloadditon (CuAAC/SPAAC)

1,2,4,5-Tetrazine-Alkyne cycloaddition

Ralph Weissleder

Harvard Medical School

Bioorthogonal Reactions

Bioorthogonal reactions requirements

Water as a solvent

Ambient temperature

Fast reaction kinetics

Synthetically accessible functionalities

Non-toxic reagents

No cross reactivity

Stable reactants and products

Stable at physiological pH

Cell permeable reagents

Bioorthogonal Reactions

Solvent k rel

Hexane 1

EtOH 1.6

H2O/NCP (99:1) 53.2

Azide-Norbornene cycloaddition (Engberts)

Engberts, J.B.F.N et al., Tet. Lett., 1995, 36, 5389

Solvent k rel

Toluene 1

EtOH 2.0

H2O/tBuOH (0.95 MF) 60.9

1,2,4,5-Tetrazine-styrene cycloaddition (Engberts)

Engberts, J.B.F.N et al., J Org. Chem, 1996, 61, 2001

Key observations from kinetic studies (Lecture 1)

Cu Catalysed azide-alkyne cycloaddition

(CuAAC) Sharpless, Fokin and Meldal (2002)

Strain Promoted cycloaddition (SPAAC)

Bertozzi (2004)

Solubility is an issue

Bioorthogonal Reactions – SPAAC

Influence of strain on reactivity?

Significant development carried out on a number of strained cyclooctynes.

Different substitution patterns on the ring can increase the rate of reaction

However in many cases the rates of the reactions have been determined in mixed organic and aqueous solvents.

There is the question as to whether this gives an adequate indication of the rate in the biological system

Solubility is a major issue in the development of strained ring systems

Using a strained dienophile/dipolarophile can have a significant effect on the rate of reaction

Bioorthogonal Reactions – Azides versus Tetrazines

Not present in biological systems

Possesses orthogonal reactivity to most biological

groups

Is a small functional group (only three atoms)

Does not have appreciable reactivity with water

Triazole products are stable

Why use azide and tetrazines in bioorthogonal reactions?

Not present in biological systems

Possesses orthogonal reactivity to most biological

groups

Very fast kinetics for inverse electron demand

cycloadditions (IED)

No metals needed

Bigger functional group and needs to be stabilized

with an aryl ring

Bioorthogonal Reactions –Azides versus Tetrazines

Selectivity of Bioorthogonal Reactions – Inverse electron demand cycloaddition reactions

Houk, K.N., et al., J. Am Chem. Soc., 2012, 134, 17904

k2 = 0.0064 M-1s-1 k2 = 210 M-1s-1

k2 = 2.10 M-1s-1

k2 Azide

k2 Tetrazine= 32000

1,2,4,5-tetrazine does not

react with the cyclooctyne

trans-cyclooctene reacts over 32000 faster with the 1,2,4,5-tetrazine over the azide. However in the case of

cyclooctyne no reaction was observed with 1,2,4,5-tetrazine

The difference in reactivity between azides and tetrazines with various diene/dipolarophiles means that in

biological environments more than one tag/probe can introduced using a specific bioorthogonal reaction

Bioorthogonal Reactions –Azides versus Tetrazines

Reactivities of Strain Promoted Dienophile/Dipolarophiles

Dienophiles reported for their reactivity towards

1,2,4,5-Tetrazines

Dipolarophiles reported for their reactivity towards azides.

(Rates are measured in MeOH or MeCN)

There has been a wide range of different dipolarophile and dienophiles discovered for the strain-promoted

bioorthogoanal reactions.

Very much an active area of research however need further reliable rate data in water as this would reflect the

rates in biological systems

King, M, Wagner, A, Bioconjugate Chem., 2014, 25, 825

Bioorthogonal Reactions – SPAAC

Strained dipolarophiles - PEGylation of CalB

Van Delft, F. L., et al., Chem Comm., 2010, 46 97

CalB expressed with azidohomoalanine residues (5)

with one surface exposed residue

Cyclooctyne (DIBAC) synthesized in 10 steps

Corresponding tagging carried out under Cu(I)

conditions took 1-3 days and with no full conversion

observed (CuAAC).

Under SPAAC conditions the conversion was

complete after 3 hours

Solvent k (M-1 s-1)

CD3OD 0.31

D2O 0.36

Bioorthogonal Reactions – Azides

Strained dipolarophiles - In vivo imaging (Glycan Trafficking)

Bertozzi, C.R., et al., Proc. Nat Acad. Sci., 2007, 104, 16793

Visualization of dynamic processes in

living cells is possible

The visualization of the azidosugar

metabolism is possible using the

fluorescent tags

Both the azide sugar and strained alkyne

do not fluoresce but upon SPAAC reaction

the localization of these in a cell can be

visualized

Bioorthogonal Reactions – Azides

Strained dipolarophiles - In vivo imaging (Zebrafish)

Bertozzi, C.R., et al., Science., 2008, 320, 664

Scheme From – D. A Nagib, MacMillan Group, Princeton

Metabolic labeling was observed, similar to that of mammalian cells

Interestingly there was no observed toxicity resulting from use with Ac4GalNAz or DIFO reagents.

Organic reactions using water as a solvent in a living system

Bioorthogonal Reactions – 1,2,4,5-Tetrazines

Tetrazines in bioorthogonal reactions - Tetradoxin

12014 Da12222 Da

100% Conversion

(5 mins)

Fox, J.F., et al., J. Am. Chem. Soc, 2008, 130, 13518

Tetradoxin is labelled with a maleimide derived trans-cyclooctene though coupling onto a cysteine residue on the surface

of the protein

Subsequent reaction with a 1,2,4,5-tetrazine led to complete conversion in 5 mins.

Reaction can be carried out in organic sovlents, water, cell lysate with identical results

Stability of the trans-cyclooctene over prolonged time is an issue so the reaction has to be quick

Other Metal catalysed reactions

Palladium Catalysed Reactions – Sonogashira (GFP)

No ligand

Sonogashira coupling carried out to label alkyne encoded GFP

with a rhodamine conjugated phenyl iodide.

Pd(NO3)2 did not have any effect on the cells over 1 hour

Using a ligands gave poorer yields

This is an interesting reaction as there are only a handful of

Sonogashira reactions carried out using water as a reaction

solvent

95%

Chen et al., J. Am. Chem. Soc, 2013, 135, 7330

Other Metal catalysed reactions

Palladium Catalysed Reactions – Suzuki Coupling (OmpC)

OmpC contained a genetically modified p-iodophenylalanine

OmpC is a membrane protein on the surface of E.coli

This modified OmpC was reacted with a boronic acid-fluorescein which was

carried out in 1hr using the palladium catalyst.

Suzuki reactions generally have water present as a co-solvent.

Davis, B.G. et al., J. Am. Chem. Soc, 2012, 134, 800

Bioorthogonal Reactions – Where next?

Within 8 years from the reporting of the first ‘click’ reaction there has been the application of this

methodology in living systems

The number of reactions in the bioorthogonal toolbox is increasing however there is the need for new

reaction types

Use of natural amino acids is key

A key aspect of this methodology is the discovery of new reactions that can be carried out using

water as a solvent

2002Sharpless

FokinMeldal

2007 2008 2010

Conclusions

Organic reactions are possible using water as a solvent.

In some cases there are large rate accelerations observed however these can

be reaction and substrate specific.

Mechanistically the rationale for these accelerations is not fully understood

In the last decade a major application of organic reactions using water as a

solvent has been to bioorthogonal chemistry

Not discussed in these lectures

(NDI)3 (NDI)4

AO10 Dynamic Covalent Chemistry: A Tool For Synthesis, Molecular Recognition And Understanding Systems Behavior

(2L): Professor Jeremy Sanders (January 2015)

Dynamic Covalent Chemistry

Micellar Additives

Bruce Lipshutz

University of Califonia,

Santa Barbara

Reactions explored using water as a solvent

General References

D. Burtscher, K. Grela, Angew. Chem. Int. Ed., 2009, 48,

442 (Olefin Metathesis)

S. Otto, J.B.F.N. Engberts, Org Biomol. Chem., 2003, 1(16),

2809

C-J. Li, Chem. Rev., 2005, 105, 3095–3166 (General)

A. Chandra, V.V. Fokin, Chem. Rev., 2009, 109, 725

(General)

D. Dallinger, C. Oliver Kappe, Chem Rev, 2007, 107, 2563

(Microwave synthesis in water)

U. M. Lindström, Chem. Rev, 2002, 102, 2751

(Stereoselective reactions)

M. Raj, V. K. Singh, Chem. Comm., 2009, 6687

(Organocatalysis)

J. Paradowska, M. Stodulski, J. Mlynarski, Angew. Chem.

Int. Ed., 2009, 48, 4288 (Organocatalysis)

H. Hailes, Org. Proc. Res. Dev., 2007, 11, 114 (General)

‘Organic Reactions in water’ U. Marcus Lindströhm Ed.,

Blackwell Publishing, 2007

Science of Synthesis: Water in Organic Synthesis,

Shu Kobayshi Ed, Thieme, 2012

Organic Synthesis in Water, Paul A. Grieco Ed.,

Springer, 1999.

Aqueous Phase Organometallic Catalysis – Concepts

and Applications Boy Cornlis and Wolfgang Herrmann

Ed, Wiley, 1998 G. Molteni, Heterocycles, 2006, 68(10), 2177 (Huisgen

cycloaddition reactions)

R.N. Butler, A.G. Coyne, Chem. Rev., 2010, 110, 6302

(General – in-water/on-water)

Books

B. H. Lipshutz, S. Ghorai, Green Chem, 2014, 16, 3660

(General and Stereoselective reactions)

Water is the solvent used by nature for biological chemistry. Considering the enormous variety of biological

pathways and the complicated molecular structures and materials, including precise arrangements of multitudes of

asymmetric centers, which are found in biological systems, It is remarkable that up until recently organic synthesis has

mainly shunned water. In recent years there has been a resurgence in the use of water as a solvent in a wide variety of

reaction types.

The aim of these two lectures will be to explore these reactions where water has been applied as a solvent. The

initial focus will be the investigation of the kinetics of these reactions where interesting rate effects have been observed.

The focus will then move onto a range of reaction types such as the Diels-Alder [4+2] and Huisgen [3+2] cycloaddition

reactions, Claisen rearrangement, epoxide ring openings, olefin metathesis and cyclopropanation reactions. The final

part of this lecture series will focus on the development and application of biorthogonal reactions where the use of water

as the solvent is crucial.