Dummkopf, wo hast du die lone-pairs hingepackt? *

A survey of halogens

Peter W Kenny

AstraZeneca

* Idiot, where have you put the lone pairs? (PWK thanks Ulrich Zachariae for essential linguistic assistance)

‘In 1839 Bouchardat, a medical writer in Paris, recounts that, when dogs were being surreptitiously poisoned with strychnine in Paris, and an antidote was asked for, first Guibourt recommended powdered galls, and then Donné asked for iodine tincture, whereupon Bouchardat himself, approving the use of iodine, said that they should use it in potassium iodide solution.’

A.B. Prescott The Periodides, JACS, 1895, 17, 775-781.

Halogen chemistry teaser

I2(s) + I-(aq) I3-(aq)

Scifinder free energy

Plot of date of first preparation for halogen fluorides as function of atomic number of halogen

BrF7 has been claimed in a patent; BrF, IF & IF3 appear to be unstable with respect to disproportionation

X C-X BDE/kJmol-1 O-X BDE/kJmol-1

H 338 430

F 514 220

Cl 394 267

Br 318 238

I 253 240

CRC Handbook of Chemistry and Physics, 88th edition, 2007-2008

More Halogen Chemistry

Bond dissociation energies for diatomic molecules

CF3: Nitro without tears?

Three fluorine atoms can be easily accommodated on a single tetrahedral carbon atom. Try this with oxygen or nitrogen! Nitro (sm = 0.71; sp = 0.78); CF3 (sm = 0.43; sp = 0.54)

Bonus question: Against what sort of fire would you not want to deploy a halon extinquisher?

Halogens in Medicinal Chemistry

Hydrophobicité, Stabilité, Electronégativité

• Tune potency & lipophilicity

– Cl most commonly used for this purpose

• Block phase 1 (oxidative) metabolism

– F most commonly used but Cl also works

• Electronegative substituent

– Tune pKa (usually of bases)

– Increase electrophilicity (e.g. CF3 ketones as serine protease inhibitors)

– CF3 can be placed next to heteroaromatic nitrogen without reactivty risks associated with chloro.

Halogens, lipophilicity & hydrogen bonding

Structure logPoct/wat logPalk/wat logP 2H

2.13 0 2.24 -0.11 0.14

2.27 0.14 2.46 -0.19 0.10

2.84 0.71 2.93 -0.09 0.09

2.99 0.86 3.10 -0.11 0.09

3.25 1.12 3.33 -0.08 0.09

1.56 -0.57 0.96 0.60 0.42

1.85 -0.28 1.44 0.41 0.34

0.64 -1.49 -0.48 1.12 0.62

N

O

O

N

I

Br

Cl

F

N

Direct interactions Indirect interactions

Non-classicale.g. heavy

halogen

Electrostatice.g. hydrogen

bonding

Dispersionforces

Steric clash Hydrophobic Conformational strain & entropy

Non-covalent interactions

A taxonomy of non-covalent interactions

Organic Fluorine Hardly Ever Accepts Hydrogen Bonds

J.D. Dunitz and R. Taylor

Chem. Eur.J. 1997, 3, 89-98

Jawohl!

Contacts between fluorine & hydogen bond donors in

PTP-1B complex with dianionic difluorophosphonate

P

F F

O

O

O

33mM

F to H: 3500mM

F to H: 315mM

AstraZeneca in house crystal structure; IC50 values from Kotoris et al, JCS Perkin 1, 2000, 1271-1281

Inductive effect (electronegativity) of fluorine feeds off concentrated of negative charge of dianionic phosphonate: A perfect storm?

Evidence for C-F….C=O Interactions?

Olsen et al, Angew. Chem. 2003, 42, 2507-2511

Ar Ki pKi

Phenyl 0.31 6.51

2-Fluorophenyl 0.50 6.30

3-Fluorophenyl 0.36 6.44

4-Fluorophenyl 0.06 7.24

N

NN

O

O

N

Ar

Nein!

Cl…O=C Br…O=C

X

O

Halogen bonding: Close contacts between carbonyl

oxygen & halogens observed in crystal structures

Lommerse et al, JACS, 1996, 118, 3108-3116

ar

a

r

a

r

Riley & Merz, J. Phys Chem. A, 2007, 111, 1688-1694

Halogen bonding studied by QM calculations on halobenzene-formaldehyde dimers. Complex stability increases with atomic number of halogen. Read this if you thought BSSE was a particularly unpleasant form of mad cow disease.

Clark et al, J. Mol. Model., 2007, 13, 291-296

The s-hole and halogen binding. Electrostatic potential computed on molecular surface for CF4, CF3Cl, CF3Br & CF3I.

Lommerse et al, JACS, 1996, 118, 3108-3116

Includes InterMolecular Perturbation Theory calculations in addition to analysis of crystal structures

Halogen bonding & computational chemistry

Dimethylamino group splayed inward reflecting incipient nucleophilic addition to carbonyl group. Halogen chemistry indicates increased ability to expand valence shell going down group

Schweizer et al, Helv Chim Acta 61, 2783-2808 (1978)

Partial bond formation

Is this the basis for heavy halogen interactions?

Covalency is simply a continuation of polarisation by other means

Clausewitz on covalency

Minimised electrostatic potential (Vmin) for

halobenzenes & hydrogen bond acceptors

Vmin has been shown to be a useful predictor for hydrogen bond bascity. See Murray & Politzer, JOC, 1991, 56, 3734-3739 and Kenny, JCS Perkin 2, 1994, 199-202

Electrostatic potential on C-X axis for

fluorobenzene, chlorobenzene & aza analogs

F

ArF ArCl

ArCl

r

A view of the s-hole for 5-chloropyrimidine

N

N

Cl

x

z

y

See also Clark et al, J. Mol. Model., 2007, 13, 291-296

Some questions

• Are VDW (or similar) radii relevant to aqueous solvation or hydrogen bonding?

• Are halogens the problem or should we look to the left (on the periodic table)?

• Are halogens as boring as their location in the periodic table would suggest?

• Is anybody other than Bismarck looking for lone pairs?

• Will we ever get Ant onto facebook?

It’s the robot!

Dr Head tenders incorrect response to question:

Which ‘Lost in Space’ character is most like Ant?

The correct answer is of course Dr Zachary Smith

Hold still Gabri, and I’ll have that ear wax out faster than

you can say ‘Vlad the Impaler’

Documentary evidence that Tudor is a real medical doctor

Please come back next year to find out about the lanthanides!