• Like
  • Save
A survey of halogens (2008 EuroCUP)
Upcoming SlideShare
Loading in...5

A survey of halogens (2008 EuroCUP)



Slides from my presentation at OpenEye's 2008 EuroCUP meeting. Halogen bonding has been around for a lot longer than people think.

Slides from my presentation at OpenEye's 2008 EuroCUP meeting. Halogen bonding has been around for a lot longer than people think.



Total Views
Views on SlideShare
Embed Views



1 Embed 1

https://twitter.com 1



Upload Details

Uploaded via as Adobe PDF

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
Post Comment
Edit your comment

    A survey of halogens (2008 EuroCUP) A survey of halogens (2008 EuroCUP) Presentation Transcript

    • 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 2 H 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-classical e.g. heavy halogen Electrostatic e.g. hydrogen bonding Dispersion forces 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 N N 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 a r 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!