What can a synthetic chemist learn from charge density? · P. Coppens, X-ray Charge Densities and Chemical Bonding, IUCr texts on Crystallography, Oxford Univ. Press, 1997. The atomic

What can a synthetic chemistlearn from charge density?

Dietmar StalkeInstitut für Anorganische Chemie der Universität Göttingen

What can a synthetic chemistWhat can a synthetic chemistlearn from charge density?learn from charge density?

Dietmar StalkeDietmar StalkeInstitut fInstitut füür Anorganische Chemie der Universitr Anorganische Chemie der Universitäät Gt Gööttingenttingen

What can a synthetic chemistlearn from charge density?

Dietmar StalkeInstitut für Anorganische Chemie der Universität Göttingen

What can a synthetic chemistWhat can a synthetic chemistlearn from charge density?learn from charge density?

Dietmar StalkeDietmar StalkeInstitut fInstitut füür Anorganische Chemie der Universitr Anorganische Chemie der Universitäät Gt Gööttingenttingen

Natureof a chemical bond

Hypervalencycentral atom exceeds

the noble gas configuration Single or double bond

Structure/Reactivitybond formation or cleavage

A B A B

Bond or topological connectivity ?Bond or topological connectivity ?Bond or topological connectivity ?

T. Stey, D. Stalke Lead structures in lithium organic chemistry in The Chemistry of Organolithium Compounds, eds. Z. Rappoport, I. Marek, John Wiley & Sons New York, 2004, 47-120.

[(RLi)4]n - Tetrahedra[(RLi)[(RLi)44]]nn -- TetrahedraTetrahedra

[(EtLi)4] [(MeLi)4] [(t BuLi)4]

Li - Cα 228 226 225 pm Li - Cβ 250 (236) 237 pm Li ... Li 253 259 241 pm

H. J. Dietrich, J. Organomet. Chem. 1981, 205, 291.

E. Weiss et al., Chem. Ber. 1990, 123, 79.

D. Stalke et al., Angew. Chem. Int. Ed. 1993, 32, 580.

Experimental charge densityExperimental charge densityExperimental charge density

Analyses according to Bader‘s

„Atoms in Molecules“ (AIM) formalism

High resolution diffraction data (2Θ = 3-110° (MoKα ))

Standard structure determination

Multipole refinement

Crystallization

Inert gas and low temperature crystal application

T. Kottke, D. Stalke, J. Appl. Crystallogr. 1993, 26, 615.

Bruker TXS and INCOATEC Mo mirrorsBruker TXS and INCOATEC Mo mirrorsBruker TXS and INCOATEC Mo mirrors

Beware: Burning crystalBeware: Burning crystalBeware: Burning crystal

Exquisite data from the Bruker TXSExquisite data from the Bruker TXSExquisite data from the Bruker TXS

0.420.540.620.680.740.780.830.880.930.961.001.041.091.111.141.19

36.1346.3353.7060.1665.1069.7375.1579.8685.3089.4394.0699.32105.38108.79112.51121.18

2 θ(MoKα)

0.05030.0126

0.05700.0201

16.3743.86

3.507.67

91.995.4

0.52 - 0.42Inf - 0.42

0.00470.00580.00720.01330.01500.01600.01290.01680.02170.02910.03900.04910.05330.05770.06670.0817

0.01590.01940.02370.02220.02480.02860.03280.03950.03930.03820.04790.05720.06280.06580.07330.0770

145.11117.9497.2652.8246.5245.9155.2944.2035.1626.9620.8716.9515.5714.7112.8210.64

22.4323.0920.166.435.876.51

10.009.236.114.163.753.733.753.593.432.13

99.8100.0100.099.699.098.598.197.697.494.993.194.894.992.594.775.3

Inf - 1.181.18 - 0.930.93 - 0.810.81 - 0.730.73 - 0.680.68 - 0.640.64 - 0.600.60 - 0.570.57 - 0.540.54 - 0.520.52 - 0.500.50 - 0.480.48 - 0.460.46 - 0.450.45 - 0.440.44 - 0.42

RσRintMean

I/σRed.% CompleteResolutionλθ sin

QUADRUPOLE

HEXADECAPOLE

M1

O0

D1+D1-D0

Q0

H0

Q1- Q1+ Q2- Q2+

O1- O1+ O2- O2+ O3- O3+

H2-H1- H1+ H3-H2+ H4-H3+ H4+

MONOPOL

DIPOLE

OCTAPOLE

( ) ( )∑∑−=

⎟⎠⎞

⎜⎝⎛⋅′′=′

l

lmlmlm

lld r

YPrR rr κκκρ 3

Multipole structure refinementMultipole structure refinementMultipole structure refinement

P. Coppens, X-ray Charge Densities and Chemical Bonding, IUCr texts on Crystallography, Oxford Univ. Press, 1997.

The atomic density is modelled along spherical harmonics

The gradient vector field of methyl carbamide:

P. Coppens, X-ray Charge Densities and Chemical Bonding, IUCr texts on Crystallography, Oxford Univ. Press, 1997.

Structure topologyStructure topologyStructure topology

)f(ρondistributi density Charge r=

Charge density and derivativesCharge density and derivativesCharge density and derivatives

R. J. Gillespie, E. A. Robinson, Angew. Chem. Int. Ed. Engl. 1996, 35, 495.

Charge density and derivativesCharge density and derivativesCharge density and derivatives

d)

2

22

d)f(dρLaplacian

rr

−=∇−)f(ρondistributi density Charge r=

R. J. Gillespie, E. A. Robinson, Angew. Chem. Int. Ed. Engl. 1996, 35, 495.

Hypervalency ??Hypervalency ??Hypervalency ??

P

F

F

FF

FS

O O

O

SiFF

FF

F

F

2

The usual suspects: third (or higher) period central atoms,

dnspm hybridized,

no formal charges.

Independent atom model vs. multipole modelIndependent Independent atomatom modelmodel vs. vs. multipole multipole modelmodel

Si

N

N

OF

OF

N

N

CH3CH3

H3CH3C

N. Kocher, J. Henn, B. Gostevskii, D. Kost, I. Kalikhman, B. Engels, D. Stalke, J. Am. Chem. Soc. 2004, 126, 5563.

Si←N Si—N Si═N

197 pm 174 pm 157 pm

CCDC 2005 Wiberg et al. 1986


Independent Atom Model

(IAM)Multipole Model


Si

N

N

OF

OF

N

N

CH3CH3

H3CH3C





Si

N

N

OF

OF

N

N

CH3CH3

H3CH3C





Si

N

N

OF

OF

N

N

CH3CH3

H3CH3C

Δρ(stat.)

Topology of the Si—E-bonding (E = N, O, F)Topology of the SiTopology of the Si——EE--bonding (E = N, O, F)bonding (E = N, O, F)

Si

N

N

OF

OF

N

N

CH3CH3

H3CH3C


∇2ρ(r)

Topology of the Si—E-bonding (E = N, O, F)Topology of the SiTopology of the Si——EE--bonding (E = N, O, F)bonding (E = N, O, F)

A–B bond path ρ(rBCP) ∇2ρ(rBCP) charge (B) NBO-

charge (B)

Si–N 197.03 0.501(16) 7.755(32) – 0.78 – 0.43

Si–O 177.89 0.766(13) 7.373(29) – 1.21 – 0.81

Si–F 163.97 1.015(13) 13.472(33) – 0.80 – 0.66

Si

N

N

OF

OF

N

N

CH3CH3

H3CH3C

Si: + 2.78 (exp.); + 2.27 (NBO)


∇2ρ(r)

Classical chelating ligandsasymmetrical, chiral, hemilabile

M[L]n

Janus-Head ligandsσ/π coordination via the

ligand periphery

M[L]n

M'[L]n

Reviews: L. Mahalakshmi, D. Stalke, In Structure and Bonding, Springer Verlag Heidelberg, 2002, 103, 85.D. Stalke et al., J. Organomet. Chem. 2002, 661, 111.

Phosphorus centred Janus-Head ligandsPhosphorus Phosphorus centredcentred JanusJanus--HeadHead ligandsligands

N

P

N

N

P

N

NMe3Si N SiMe3

Phosphorus centred Janus-Head ligandsPhosphorus Phosphorus centredcentred JanusJanus--HeadHead ligandsligands

Reviews: L. Mahalakshmi, D. Stalke, In Structure and Bonding, Springer Verlag Heidelberg, 2002, 103, 85.D. Stalke et al., J. Organomet. Chem. 2002, 661, 111.

AminoiminophosphoranesAminoiminophosphoranesAminoiminophosphoranes

Inorg. Chem. 1993, 32, 1977; Inorg. Chem. 1997, 36, 2413; J. Am. Chem. Soc. 2001, 123, 1381.

N

P

NN

N

SiMe3

SiMe3

N

P

NN

N

Me3Si

Me3Si[M]Me3

N

PPy

NNSi

Me3SiZn

N

PPy

N

NSi

SiMe3

Me3

+ MeLi+ [Li{N(SiMe3)2}]

+ R2Zn+ RM

Ar = Py Ar = Py

[M] = Sr, BaAr = Py

Ar = Py

Ar = Ph

P

NNLi

N

P

N

N

N

P

N

N

Li

LiSiMe3

Me3Si

PhP

Ph

N

N

SiMe3

SiMe3

[M]

ArP

Ar

N

N

SiMe3

SiMe3

H

AminoiminophosphoranesAminoiminophosphoranesAminoiminophosphoranes

Inorg. Chem. 1993, 32, 1977; Inorg. Chem. 1997, 36, 2413; J. Am. Chem. Soc. 2001, 123, 1381.

N

P

NN

N

SiMe3

SiMe3

N

P

NN

N

Me3Si

Me3Si[M]Me3

N

PPy

NNSi

Me3SiZn

N

PPy

N

NSi

SiMe3

Me3

+ MeLi+ [Li{N(SiMe3)2}]

+ R2Zn+ RM

Ar = Py Ar = Py

[M] = Sr, BaAr = Py

Ar = Py

Ar = Ph

P

NNLi

N

P

N

N

N

P

N

N

Li

LiSiMe3

Me3Si

PhP

Ph

N

N

SiMe3

SiMe3

[M]

ArP

Ar

N

N

SiMe3

SiMe3

H

single P=N-bond cleavage

dual P=N-bond cleavage

Important new synthetic route

P=N double bond ??P=N double P=N double bondbond ????

- N2N

Ph2P

NMe3Si

Ph2PCH2Py + N3SiMe3reflux

N. Kocher, D. Leusser, A. Murso, D. Stalke, Chem. Eur. J. 2004, 10, 3622.


- N2N

Ph2P

NMe3Si


- HN(SiMe3)2

hexane / Et2O NLi

NP

H

PhPh

Me3SiOEt2

+ [LiN(SiMe3)2



- N2N

Ph2P

NMe3Si


- HN(SiMe3)2

hexane / Et2O NLi

NP

H

PhPh

Me3SiOEt2

+ [LiN(SiMe3)2


N

PPhPh

NMe3Si

H

[M]N

PPhPh

NMe3Si

H

[M]N

PPhPh

NMe3Si

H

[M]N

PPhPh

NMe3Si

H

[M]

“delocalised”amide,olefin

amide, ylene

carbanion, ylide

All canonical forms would require hypervalent phosphorus

in P─C or P─N multiple bonding.

No double bonds at phosphorusNo double bonds at phosphorusNo double bonds at phosphorus

bond path [Å]P E = Cipso, C1, N1

P-NP-C1

P-Cipso

P-Cipso

∇ 2

[eÅ-5]


refluxPh2PCH2Py + N3SiMe3

NPh2P

NMe3Si

- HN(SiMe3)2

hexane / Et2O NLi

NP

H

PhPh

Me3SiOEt2

+ [LiN(SiMe3)2]

- N2

No double bonds at phosphorusNo dNo doouubbllee bboonnddss at phosphorusat phosphorus

bond path [Å]P E = Cipso, C1, N1

P-NP-C1

P-Cipso

P-Cipso

∇ 2

[eÅ-5]


refluxPh2PCH2Py + N3SiMe3

NPh2P

NMe3Si

- HN(SiMe3)2

hexane / Et2O NLi

NP

H

PhPh

Me3SiOEt2

+ [LiN(SiMe3)2]

- N2

No double bonds at phosphorusNo dNo doouubbllee bboonnddss at phosphorusat phosphorus


N

PPhPh

NMe3Si

H H

N

PPhPh

NMe3Si

H

[M]

4 e─ donorJanus-Head ligands4 e4 e── ddonoronorJanusJanus--HeadHead ligandsligands

P1S1

N2

C8

H2

S2

N1

C1

1. Li / THF2. H2O

- 1/2 (bth)2- LiOH

N

SP

3

N

S

N

SP

H

T. Stey, J. Henn, D. Stalke, Chem. Commun. 2007, 413.


P1S1

N2

C8

H2

S2

N1

C1

1. Li / THF2. H2O

- 1/2 (bth)2- LiOH

N

SP

3

N

S

N

SP

H

N

S

N

S P

H

N

S

N

S P

H




P1S1

N2

C8

H2

S2

N1

C1

1. Li / THF2. H2O

- 1/2 (bth)2- LiOH

N

SP

3

N

S

N

SP

H

∇2ρ(r)


1. Li / THF2. H2O

- 1/2 (bth)2- LiOH

N

SP

3

N

S

N

SP

H

T. Stey, M. Pfeiffer, J. Henn, S. K. Pandey, D. Stalke, Chem. Eur. J. 2007, DOI: 10.1002/Chem200601221.

n / 2 H2

n2

78 °C / n CsN

S

PCs


1. Li / THF2. H2O

- 1/2 (bth)2- LiOH

N

SP

3

N

S

N

SP

H

T. Stey, M. Pfeiffer, J. Henn, S. K. Pandey, D. Stalke, Chem. Eur. J. 2007, DOI: 10.1002/Chem200601221.

n / 2 H2

n2

78 °C / n CsN

S

PCs


PS

ON

Mn

Li

O

Mn

CpMn(CO)2(THF)

- THF- Et2OLi

N

S P

N

S

Et2O OEt2

n

LiN

S P

N

S

O OCC

MnMnCO

LiN

S P

N

S

OC


d-Block metal─metal bondsdd--Block metalBlock metal──metal bondsmetal bonds

Review: P. Macchi, A. Sironi, Coord. Chem. Rev. 2003, 238, 383.Chemical Bonds without "Chemical Bonding"? L. J. Farrugia, C. Evans, M. Tegel, J. Phys. Chem. A 2006, 110, 7952.

OC

Mn Mn

CO

CO

CO

CO

OCOC

OC

CO

COC

Fe Fe

CO

OC

OC

CO

OC

COCOOC O

252 pm290 pm

F. A. Cotton et al. Dalton Trans. 1974, 800.

G. Bianchi et al. Inorg. Chem. 2000, 39, 2360.

P. Macchi et al. J. Am. Chem. Soc. 1998, 120, 13429.

L. J. Farrugia et al. Acta Crystallogr. Sect. B 2003, 59, 234.


Review: P. Macchi, A. Sironi, Coord. Chem. Rev. 2003, 238, 383.Chemical Bonds without "Chemical Bonding"? L. J. Farrugia, C. Evans, M. Tegel, J. Phys. Chem. A 2006, 110, 7952.

OC

Mn Mn

CO

CO

CO

CO

OCOC

OC

CO

COC

Fe Fe

CO

OC

OC

CO

OC

COCOOC O

252 pm290 pm

F. A. Cotton et al. Dalton Trans. 1974, 800.

Mn Mn

B

CpCp

COOC COOC

But

H. Braunschweig et al. Angew. Chem. Int. Ed. 2006, 45, 4352.

G. Bianchi et al. Inorg. Chem. 2000, 39, 2360.

P. Macchi et al. J. Am. Chem. Soc. 1998, 120, 13429.

L. J. Farrugia et al. Acta Crystallogr. Sect. B 2003, 59, 234.

U. Flierler, J. Henn, M. Burzler, H. Braunschweig, H. Ott, D. Leusser, D. Stalke, in preparation.

53.85Nrefl. / Nparam.

23961 / 0.0203 / 0.0126no. of unique reflections / Rint / Rsigma

0.0162 / 0.0281 (w = 1/σ2)R1 (I>3σ(I)) / wR2 (I>3σ(I)) after multipole ref. to sin θ/λ max = 1.187 [Å]



14.8440.9821.784501.7850(3)Mn─C2.9040.6172.02172.0215(3)Mn─B(1.415)(0.213)-2.7820(8)Mn…Mn

∇2ρ(rBCP)ρ(rBCP)bond pathsbond lengthsA─B



Δρ(stat.)

Δρ(stat.)

∇2ρ(r)

∇2ρ(r)

ρ(r)


static deformation

density

Δρ(stat.)

Laplacians

∇2ρ(r)



Chemical bonds without "chemical bonding"Chemical Chemical bonds without "chemical bonding"bonds without "chemical bonding"

J. Henn, D. Stalke, J. Comput. Chem., submitted.

O

HC

S

HH

C

HH

C

S

HH

C

H

S

H

S

H

C

S

HH

C

H

S

H

C

S

HH

C

H

S

H

C

H

C

HH

b

c d

a



S

H

C

S

HH

C

H

187 pm

147 pm

192 pm

85 % in NRT

O

HC

S

HH

C

HH

C

S

HH

C

H

S

H

S

H

C

S

HH

C

H

S

H

C

S

HH

C

H

S

H

C

H

C

HH

b

c d

a



S

H

C

S

HH

C

H

187 pm

147 pm

192 pm

85 % in NRTBCPs VSCCs

in QTAIM

O

HC

S

HH

C

HH

C

S

HH

C

H

S

H

S

H

C

S

HH

C

H

S

H

C

S

HH

C

H

S

H

C

H

C

HH

b

c d

a



Lithium organics or lithium amidesLithium organics or lithium amidesLithium organics or lithium amides

According to the literature it is impossible to metalate pyridine directly with n-butyllithium, because this base acts as a nucleophileand the ring substitution is in favor of the deprotonation.

B. J. Wakefield, The Chemistry of Organolithium Compounds, Pergamon Press 1974.D. R. Armstrong, R. E. Mulvey, D. Barr, R. Snaith, D. Reed, J. Organomet. Chem. 1988, 350, 191.

T. Lauterbach, K.-J. Niehues, Butyllithium-Eigenschaften und Anwendungen, CHEMETALL.


According to the literature it is impossible to metalate pyridine directly with n-butyllithium, because this base acts as a nucleophileand the ring substitution is in favor of the deprotonation.

B. J. Wakefield, The Chemistry of Organolithium Compounds, Pergamon Press 1974.D. R. Armstrong, R. E. Mulvey, D. Barr, R. Snaith, D. Reed, J. Organomet. Chem. 1988, 350, 191.

T. Lauterbach, K.-J. Niehues, Butyllithium-Eigenschaften und Anwendungen, CHEMETALL.


H. Ott, J. Henn, D. Leusser, D. Stalke, in preparation.

2 + nBuLi [H4C5NCH2Li · NC5H4Me] + BuHEt2O- 78 °C

N Me



24.08Nrefl. / Nparam.

13125 / 0.0202 / 0.0092no. of unique reflections / Rint / Rsigma

0.0244 / 0.0417 (w = 1/σ2)R1 (I>3σ(I)) / wR2 (I>3σ(I)) after multipole ref. to sin θ/λ max = 1.136 [Å]



2.4378(5)Li─C4.4350.1532.03372.0337(4)Li…N(donor)

3.6150.1232.05062.0489(4)Li(allyl)─N(carb.)

4.8990.1671.97891.9788(4)Li─N(carb.)

∇2ρ(rBCP)ρ(rBCP)bond pathsbond lengthsA─B



Liamid

Liallyl

N1C1 back

top facing Li

C6

Li

N2 C7

Laplacians

∇2ρ(r)



H. Ott, U. Flierler, I. Dix, M. Ruf, G. M. Sheldrick, D. Stalke, in preparation.

Cubic insulinC257H387N65O66S6 + soup

a = 77.8 Å

V = 470.140 Å3

space group = I 213

size = 0.30 x 0.31 x 0.38 mm

detector dist. = 75 mm

MoKα TXS in life scienceMoKMoKαα TXS in life scienceTXS in life science

Cubic insulinC257H387N65O66S6 + soup

a = 77.8 Å

V = 470.140 Å3

space group = I 213

size = 0.30 x 0.31 x 0.38 mm

detector dist. = 75 mm





AcknowledgementAcknowledgementAcknowledgement

Finances:ExpED priority program 1178 of the DFGGraduiertenkolleg 690 of the DFGDeutscher Akademischer Austauschdienst (ARC, INIDA, PROCOP)German-Israeli FoundationCHEMETALL GmbH / Frankfurt

Documents

What can a synthetic chemist learn from charge density? · P. Coppens, X-ray Charge Densities and Chemical Bonding, IUCr texts on Crystallography, Oxford Univ. Press, 1997. The atomic