William A. Goddard, III, [email protected]

EEWS-90.502-Goddard-L15 1© copyright 2009 William A. Goddard III, all rights reserved

Nature of the Chemical Bond with applications to catalysis, materials

science, nanotechnology, surface science, bioinorganic chemistry, and energy

William A. Goddard, III, [email protected] Professor at EEWS-KAIST and

Charles and Mary Ferkel Professor of Chemistry, Materials Science, and Applied Physics,

California Institute of Technology

Course number: KAIST EEWS 80.502 Room E11-101Hours: 0900-1030 Tuesday and Thursday

Senior Assistant: Dr. Hyungjun Kim: [email protected] of Center for Materials Simulation and Design (CMSD)

Teaching Assistant: Ms. Ga In Lee: [email protected] assistant: Tod Pascal:[email protected]

Lecture 26, December 3, 2009

mailto:[email protected]


Schedule changesDec. 3, Thursday, 9am, L26, as scheduledDec. 7-10 wag in Pasadena; no lectures,Dec. 14, Monday, 2pm, L27, additional lecture, room 101Dec. 15, Final exam 9am-noon, room 101


Last time


Bonding in metallic solids

Mosty of the systems discussed so far in this course have been covalent, with the number of bonds related to the number of valence electrons.

Thus we have discussed the bonding of molecules such as CH4, benzene, O2, and Ozone.. The solids such as diamond, silicon, GaAs, are generally insulators or semiconductors

We have also considered covalent bonds to metals such as FeH+, (PH3)2Pt(CH3)2, (bpym)Pt(Cl)(CH3), The Grubbs Ru catalysts

We have also discussed the bonding in ionic materials such as (NaCl)n, NaCl crystal, and BaTiO3, where the atoms are best modeled as ions with the bonding dominated by electrostatics

Next we consider the bonding in bulk metals, such as iron, Pt, Li, etc. where there is little connection between the number of bonds and the number of valence electrons.


Bringing atoms together to form the solidAs we bring atoms together to form the solid, the levels broaden into energy bands, which may overlap . Thus for Cu we obtain

Energy

Density states

Fermi energy (HOMO and LUMO

Thus we can obtain

systems with no band gap.


Metals vs inulators


conductivity


The elements leading to metallic binding

There is not yet a conceptual description for metals of a quality comparable to that for non-metals. However there are some trends, as will be described


Body centered cubic (bcc), A2

A2


Face-centered cubic (fcc), A1


Alternative view of fcc


Closest packing layer


Stacking of 2 closest packed layers


Hexagaonal closest packed

(hcp) structure, A3


Cubic closest packing


Double hcp

The hexagonal lanthanides mostly exhibit a packing of closest packed layers in the sequence

ABAC ABAC ABAC

This is called the double hcp structure


bcc

hcp

fcc

mis

Structures of elemental metals

some correlation of structure with number of

valence electrons


Binding in metalsLi has the bcc structure with 8 nearest neighbor atoms, but there is only one valence electron per atom. Similarly fcc and hcp have 12 nearest neighbor atoms, but Al has only three valence electrons per atom. Clearly the bonding is very different than covalentOne model (Pauling) resonating valence bondsProblem is energetics:Li2 bond energy = 24 kcal/mol 12 kcal/mol per valence electronCohesive energy of Li (energy to atomize the crystal is 37.7 kcal/mol per valence electron. Too much to explain with resonance

New paradigm: Interstitial electron model (IEM). Each valence electron localizes in a tetrahedron between four Li nuclei.

Bonding like in Li2+, which is 33.7 kcal/mol per valence electron


GVB orbitals of ring M10 molecules

Get 10 valence electrons each localized in a bond midpoint

Calculations treated all 11 valence electrons of Cu, Ag, Au using effective core potential.

All electrons for H and Li

R=2 a0









New


Hypervalent compounds

It was quite a surprize to most chemists in 1962 when Neil bartlett reported the formation of a compound involving Xe-F bonds. But this was quickly folllowed by the synthesis of XeF4 (from Xe and F2 at high temperature and XeF2 in 1962 and later XeF6.Indeed Pauling had predicted in 1933 that XeF6 would be stable, but noone tried to make it.

Later compounds such as ClF3 and ClF5 were synthesized

These compounds violate simple octet rules and are call hypervalent


Noble gas dimers

Recall from L17 that there is no chemical bonding in He2, Ne2 etc

This is explained in VB theory as due to repulsive Pauli repulsion from the overlap of doubly occupied orbitals

(g)2(u)2

It is explained in MO theory as due to filled bonding and antibonding orbitals


Noble gas dimer positive ions

On the other hand the positive ions are strongly bound (L17)

This is explained in MO theory as due to one less antibonding electron than bonding, leading to a three electron bond for He2

+ of 2.5 eV, the same strength as the one electron bond of H2

+ (g)2(u)1

-

The VB explanation is a little less straightforward. Here we consider that there are two equivalent VB structures neither of which leads to much bonding, but superimposing them leads to resonance stabilization

Using (g) = L+R and (u)=L-R

Leads to (with negative sign


Re-examine the bonding of HeH

Why not describe HeH as (g)2(u)1 where (g) = L+R and (u)=L-RWould this lead to bonding?The answer is no, as easily seen with the VB form where the right structure is 23.9 eV above the left. Thus the energy for the (g)2(u)1 state would be +12.0 – 2.5 = 9.5 eV unbound at R=∞Adding in ionic stabilization lowers the energy by 14.4/2.0 = 7.2 eV (too big because of shielding) , still unbound by 2.3 eV

-

He H He+H-

IP=+24.6 eV EA = 0.7 eV


Examine the bonding of XeF

Xe Xe+

The energy to form Xe+ F- can be estimated from

Consider the energy to form the charge transfer complex

Using IP(Xe)=12.13eV, EA(F)=3.40eV, and R(IF)=1.98 A, we get

E(Xe+ F-)=1.45eV

Thus there is no covalent bond for XeF, which has a weak bond of ~ 0.1 eV and a long bond


Examine the bonding in XeF2

We saw that the energy to form Xe+F-, now consider, the impact of putting a 2nd F on the back side of the Xe+ Xe+

Since Xe+ has a singly occupied pz orbital pointing directly at this 2nd F, we can now form a bond to it?How strong would the bond be?Probably the same as for IF, which is 2.88 eV.Thus we expect F--Xe+F- to have a bond strength of ~2.88 – 1.45 = 1.43 eV!Of course for FXeF we can also form an equivalent bond for F-Xe+--F. Thus we get a resonance

We will denote this 3 center – 4 electron charge transfer bond asFXeF


Stability of XeF2

Ignoring resonance we predict that XeF2 is stable by 1.43 eV. In fact the experimental bond energy is 2.69 eV suggesting that the resonance energy is ~ 1.3 eV.

The XeF2 molecule is stable by 2.7 eV with respect to Xe + F2

But to assess where someone could make and store XeF2, say in a bottle, we have to consider other modes of decomposition.

The most likely might be that light or surfaces might generate F atoms, which could then decompose XeF2 by the chain reaction

XeF2 + F {XeF + F2} Xe + F2 + F

Since the bond energy of F2 is 1.6 eV, this reaction is endothermic by 2.7-1.6 = 1.1 eV, suggesting the XeF2 is relatively stable. Indeed it is used with F2 to synthesize XeF4 and XeF6.


The VB analysis would indicate that the stability for XeF4 relative to XeF2 should be ~ 2.7 eV, but maybe a bit weaker due to the increased IP of the Xe due to the first hypervalent bond and because of some possible F---F steric interactions.

There is a report that the bond energy is 6 eV, which seems too high, compared to our estimate of 5.4 eV.

XeF4

Putting 2 additional F to overlap the Xe py pair leads to the square planar structure, which allows 3 center – 4 electron charge transfer bonds in both the x and y directions, leading to a square planar structure


XeF6

Since XeF4 still has a pz pair, we can form a third hypervalent bond in this direction to obtain an octahedral XeF6 molecule.

Here we expect a stability a little less than 8.1 eV.

Pauling in 1933 suggested that XeF6 would be stabile, 30 years in advance of the experiments.

He also suggested that XeF8 is stable. However this prediction is wrong


Estimated stability of other Nobel gas fluorides (eV)

Using the same method as for XeF2, we can estimate the binding energies for the other Noble metals.

Here we see that KrF2 is predicted to be stable by 0.7 eV, which makes it susceptible to decomposition by F radicals

1.3 1.3 1.3 1.3 1.3 1.32.71.0 3.9-5.3-2.9 -0.1

RnF2 is quite stable, by 3.6 eV, but I do not know if it has been observed


XeCl2

Since EA(Cl)=3.615 eV and R(XeCl+)=2.32A and De(XeCl+)=2.15eV, can estimate that XeCl2 is stable by 1.14 eV with respect to Xe + Cl2.

However since the bond energy of Cl2 is 2.48 eV, the energetics of the chain dempostion process are exothermic by 1.34 eV, suggesting at most a small barrier

Thus XeCl2 would be difficult to observe


Halogen Fluorides, ClFn

The IP of ClF is 12.66 eV which compares well to the IP of 12.13 for Xe.

This suggests that the px and py pairs of Cl could be used to form hypervalent bonds leading to ClF3 and ClF5.

Indeed these estimates suggest that ClF3 and ClF5 are stable.

Indeed the experiment energy for ClF3 ClF +F2 is 2.6 eV, quite similar to XeF2.











Julius Su and William A. Goddard IIIMaterials and Process Simulation Center,

California Institute of Technology

Origin of reactivity in the hypervalentreagent o-iodoxybenzoic acid (IBX)


Hypervalent iodine assumes many metallic personalities

IOH

O O

O

I

OAc

OAc

I

OH

OTs

I

O

Oxidations

Radicalcyclizations

CC bondformation

Electrophilicalkene activation

CrO3/H2SO4

Pd(OAc)2

SnBu3Cl

HgCl2

Can we understand iodine as we understand metals?Martin, J. C. organo-nonmetallic chemistry – Science 1983 221(4610):509-514


Practical benefits of hypervalent iodine reagents

Cheap, non-toxic, and environmentally friendly.

$/molI 2

Pd 1,300Os 2,300Ir 2,700Pt 2,400Rh 19,500

oral rat LD50 (mg/kg)

I2 14,000OsO4 162SeO2 68

Variants possible:water solublepolymer supportednon-explosive mixture


S

SOH

S

SO

NH

O

N

O

OH

t-Bu

O

t-Bu

O

O O

CHO

IBX, a single reagent withmany roles 78%

IOH

O O

O

1.1 eq IBX

25oC

CHXH oxidationsphenols to quinones unsaturationallylic oxidationradical cyclization

What is the origin of its diverse reactivity?

85%

99% conv

Solvents are DMSO mixtures or CHCl3.Taken from Palmisano, Nicolaou, McFadden.

86%

85%

1 eq IBX

23oC

2 eq IBX

75oC

3 eq IBX

85oC

2 eq IBX

90oC


Theoretical methods

Density functional theoryHarmonic frequenciesSingle point continuum solvent

Added d and f functions on INeeded for correct bond length andenergy, even for covalent iodine bonds

Alternative functionalMPW1PW91 for better descriptionof long range binding

mpwb

pw


Validation against experiment and more accurate theory

-20

-10

0

10

20

30

40

50

60

70

IF ICl IBr I2 IOH ICH3 XeF+ XeF2 XeF4 XeF6 XeO XeO3 XeO4

reference

our method

Includes atom spin-orbit effects,zero point energy, and BSSE

Systematic underestimation of bond energies,but relative energies are accurate.

Ener

gy p

er b

ond

(kca

l/mol

)


Nature of the hypervalent bond


Multicenter bonds go beyond the covalent bond

H

H

H

H

H H

H

HH

H

HH

Multicenter 6c-6eDepends on out-of-plane bend too

Covalent 2c-2eStrength depends on length only

60o bend, 114 kcal/mol

bend (degrees)

ener

gy

Bond angles and torsions change multicenter bonds.Dijkstra, F. et al. bent benzene – Int J. Quan. Chem 1999 74:213-221


Electron rich or poor multicenter bonds: allyl variations

Electrostatics makes charged bonds especially stiff.

H

H

H

HH

H

H

H

HH

H

H

H

HH

38 13 33Etwist(kcal/mol)

bonding

antibonding

nonbonding

MO stabilizations are similar but twisting localizes charge

Gobbi et al. allyl resonance – J. Am. Chem. Soc. 1994 116:9275-9286

HH

HH

H

H

H

HH

H

localized charge,less stable


Hypervalent bonds as 3c-4e bonds

Resonance stabilized 180o pairs

Xe

F Xe F F Xe F

F

F

F Xe F

F

F

F

F+ F2

h

valence bond picture molecular orbital picture

Each lone pair can bondtwo fluorines (3c-4e bond)


Valence bond explanation of hypervalent bond strengths

E = 2 • (½ covalent + ½ ionic) + resonance

covalent = D(XeF+) = 38 kcal/molionic = IP(Xe) – EA(F) – 1/R = +35 kcal/molresonance = E(180o) – E(90o) = 71 kcal/moltotal = –74 kcal/mol vs. –62 kcal/mol (expt)

Majority of energy comes from resonance stabilization


I Xe

O

Xe

F

Fcovalent dative

hypervalent

Combining different ligand typescr

ysta

l str

uctu

res

Occupy octahedralpositions


Lower symmetry structure becomes more stable.

High symmetry structure has 2nd order Jahn-Teller distortion

e

e*a LUMO

Higher order multicenter bonds as transition states

F I F

F F

FFI

3c4e 4c6e

‡

E = 15.5 kcal/mol


Valence bond comparison of IF3 geometries

To a first approximation, both geometries have the same energy.

In both cases, E = 2 • covalent + ionic + resonance


VB explanation of C2v vs. D3h energy difference

90o 120oangle bending

electrostatic repulsionbetween ligands

E(bend) E(elec) sum DFT

ClF3 4.0 12.3 16.3 16.7BrF3 5.0 12.0 17.0 17.2IF3 6.4 11.4 17.7 15.4

Accounts for allobserved energydifference

energies in kcal/mol


Rules of hypervalent reactivity


Folk notion of hypervalent bonds as weak and reactive

Xe FFEatom = 62 kcal/mol, or31 kcal/mol per bond

breaking in oxidation

creating anionic fragment

single electronacceptor

Proposed mechanisms focus on reactivity of hypervalent bonds


Rule 1. Individual hypervalent bonds are strong

Xe FF FF Xe + F Xe F+ +

+51 kcal/mol +8 kcal/mol

3e- 2 center bond,resonance lost.

The first bond is strong,since breaking it createsunstable fragments.


Rule 2: Bonds next to hypervalent bonds are weakened

Adjacent bond weakened byhypervalent hyperconjugation3e-, 2 center

bond isparticularlystable

44 kcal/mol 41 13

Hypervalent oxo bond isparticularly effective at weakening neighboring bond


Rule 3. Twist switches hypervalent and covalent ligands

hypervalentbonds circled

Twist proceeds viaD3h transition state,E‡ = 15.5 kcal/mol

3c-4e 3c-4e4c-6e: promotion tohigher order hypervalentbond.


IBX oxidation of alcohols


NMR kinetics study of alcohol oxidation

IOH

O O

O

IO

O O

O

H2O

IOH

O O

R'R

H

HOR'

RH

O R'

R

fast slow

De Munari et al, kinetics study – J. Org. Chem. 1996 61(26):9272-9276

Fast ligand exchangefollowed by slow oxidation

Large alcohols oxidize fasterthan small alcohols

axial geometry


DFT supports ligand exchange preequilibrium

0.00

1.00

2.00

3.00

4.00

5.00

0 0.02 0.04 0.06Experimental Keq

Cal

cula

ted

dG (k

cal/m

ol)

Low barrier pathway found,and good correlation between G (theory) and Keq (expt)

methanol, isopropanol, t-BuOHbenzyl alcohol, etc.

IOH2

O O

O

HOCH3

I OH2O O

O

HOCH3

IOH2

O O

OOCH3H

protonated IBX internal ligand rotationE‡ = 7.2 kcal/mol

swapped ligand

+


-1

-0.8

-0.6

-0.4

-0.2

0

0.2

0.4

0.6

0.8

1

0 0.5 1

measured chemical shift (ppm)

calc

. N

MR

shi

eldi

ng

-1

-0.8

-0.6

-0.4

-0.2

0

0.2

0.4

0.6

0.8

1

0 0.2 0.4 0.6 0.8 1

axial geometry equatorial geometry

Theoretical prediction of alcohol NMR shifts

Confirms that axial species predominates in solution


An oxidation mechanism with a twist

IOH

O O

O

IO

O O

O

HH

H

IO

O O

OH

HH

IOH

O O

O

H

H

-H2O

+CH3OH

hypervalent twist

axial

equatorial

Complex must twist for oxidation to happen


Twisting switches strong and weak bonds

We find activating reactivity by twisting to be a common theme


IOH

O O

O

IO

O O

O

HH

H

IO

O O

OH

HH

IOH

O O

O

H

H

-H2O

+CH3OH

Twisting9.9 kcal/mol

Oxidation2.6 kcal/molLigand exchange

7.2 kcal/mol (with H+)

Hypervalent twisting is rate-limiting


Size selectivity explained, and an improved reagent?

Large alcohols oxidize fasterbecause they twist more easily.

IOR

O O

OR' An ortho group shouldaccelerate twisting further.

repulsionrelieved


B(Ome)2

B(OH)2

tBu

iPA

Et

Ph

Cl

F

Me

H

-0.5

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

-7.0 -6.0 -5.0 -4.0 -3.0 -2.0 -1.0 0.0

best Large enough to favor twisted structure

O

I

OHO

O

R'

Medium-sized aliphatics (Me, Et, i-Pr) best

But not so large it hinders alcohol/water exchange

better alcohol/waterexchange

better twisting

Screening for an optimal ortho substituent


et

ipaiso

neo2,4

ph

-1

0

1

2

3

4

5

6

-1 0 1 2

measured log(kalc/kMeOH)

pred

icte

d lo

g(ka

lc/k

MeO

H)

100xfasterrate!

OI O

HO

O

ligandexchange

twisting

rate-limiting OI O

HO

O

H3C

Predicted rate acceleration for ortho-methyl IBX

Up to 100x faster,then limited byligand exchange rate


Other predictions

IO

O O

O nn Etwist

‡ Eelim‡

2 - 21.93 - 12.84 5.9 4.85 5.5 3.8

Minimum chain length needed for oxidation

group Gtwist‡

none 12.1o-CH3 9.7

o-F 12.1m-CH3 13.8

m-F 13.9

Meta substituents inhibittwisting, for unknown reasons


Other reactions of IBX


More complex reactions of IBX

Can we explain mechanism and reagent scope?Nicolaou, K. C. et al, allylic oxidation – J. Am. Chem. Soc. 2001 123:2183-3185Nicolaou, K. C. et al, HIO3 reactivity – Angew. Chem. Int. Ed. 2002 41:1386-1388

H

O

O O

NH

O

N

O

OH O

IBX

HIO3•DMSO


Evidence for a single-electron-transfer mechanism

O

HPh

Ph Ph

Ph

O

HO

HPh

Ph

IBX

Radical clock moiety fragments:

Hammett plot mildly e deficient resonance-stabilized TS:

IBX-mediatedcyclization, = –1.4

But EA(IBX-OMe) = 14 kcal/mol,while IP(substrate) = 187 kcal/mol

Experiments suggest yes,but theory says no.

Nicolaou, K. C. et al, SET model – J. Am. Chem. Soc. 2002 124(10):2245-2258


Proposed mechanism for phenol oxidation

IO

O O

OI O

O O

OMe

OMeO

H

I OO O

OMeHOB

IO OHO

OMeO

B[2,3]firstoxidation

secondoxidation

variant trappedas Diels-Alderadduct

breaking bothhypervalent bonds at onceis okay

OH

MeO

O

MeO

O

IBX

Diels-Alder adduct strongly suggests [2,3] involved.Magdziak, D. et al, phenol oxidation – Org. Lett. 2002 4(2):285-288


With theory, IBX adducts readily undergo [2,3]

E‡ = 3.0 kcal/mol E‡ = 5.5 kcal/mol

Twisting and [2,3]rearrangement occursin one step.

Transition states:

[2,3]

twist


OMe

Et

F

ClNO2

-1.5

-1

-0.5

0

0.5

1

1.5

2

2.5

-1 -0.5 0 0.5 1

Theoretical Hammett analysis of [2,3]/twist step

log (k/k0)

p+

RHO

experiment, THF -1.4theory, gas phase -1.7

theory, THF -2.1

typical SN2 -2.8

typical cation -4.5

Small negative equally well supports [2,3]/twist

Small negative mildly electron deficientresonance stabilized

IO

O O

O

R

IO

O O

O

R[2,3]/twist SET


Proposed mechanisms for IBX reactions

Alcohol oxidation

, oxidation

Radical cyclization


Can now explain most known IBX reactions

Key step is either twist + elimination or twist/[2,3]


Reagent scope of IBX versus HIO3•DMSO explained

can twistno twist possible,only free rotation

can perform

HIO3 cannot twist, so is limited to [2,3]/twist reactions

alcohol oxidationallylic oxidationdehydrogenationradical cyclization

doesn’t need twist

dehydrogenationradical cyclization (predicted)

needstwist


Allylic oxidation

IO

O OOH

IO

O O+ OH

IBX may generate hydroxy radical in situ:

performsallylic oxidations?

stable, like nitroso

Otherwise, we still cannot explain this reactionNicolaou, K. C. et al, allylic oxidation – J. Am. Chem. Soc. 2001 123:2183-3185

Me CHO3 eq IBX

12 h/85oCDMSO

85% yield,similar results with25 substrates.


A new IBX reaction?


IBX as a generator of alkoxy radicals

BDE (kcal/mol)IBX-OMe (untwisted) 60IBX-OMe (twisted) 33HO-OH 49AcO-OAc 38HO-ONO 22

When no hydrogens ordouble bonds are available,

we predict thermal homolysiscan occur to generate radicals.

Homolysis only favored inthe twisted form of IBX.


Propose experiments to detect or trap alkoxy radical

Spin trapping with PhNO, EPR detection IO

O O

OtBu

Catch radical in fastestmanner possible: I

O

O O

O

O O

(most direct)

Cyclization with substratefree from other side rxns:

HO O

Looking for way to exploit or clearly demonstrate this pathway


Anticancer warheads cause dsDNA damage

Bleomycin A2 Dynemicin

Propose one based on distortions of hypervalent bonds


A warhead that releases alkoxy radicals when triggered

iminehydrolysis

cleavable tether

no hydrogensor unsaturation

+

Cleaving tether enables twistand homolysis


Conclusions

Hypervalent bonds are strong, and weaken adjacent bonds

Twisting allows the interchange of hypervalent and adjacent bonds, and is the rate-limiting step in manyreactions.

In IBX reactions, -elimination or [2,3] rearrangementis the key step.


Acknowledgements

Prof. William A. Goddard III

Prof. Brian Stoltz

Ryan McFadden

Documents

William A. Goddard, III, [email protected]