Atoms in Molecules

Ruud Visser
July 6, 2005
vrije Universiteit amsterdam
Department of Theoretical Chemistry
Outline
Introduction to AIM
Electron density
Critical points, gradient paths
Atoms
Bonds and their properties
Charge
Summary and conclusions
Introduction to AIM
Classical chemistry:
molecule = atoms + bonds
Quantum mechanics:
molecule = nuclei + electrons
Atoms in molecules (AIM):
molecule = nuclei + electrons
molecule = atoms + bonds
Wave function ( or )
Schrdinger:
H4=E4
Born-Oppenheimer:
nuclei fixed, consider only
Problem: many-dimensional,
difficult to visualize, interpret
Electron density ()

p: 3-dimensional, easier to
visualize, interpret than
p directly derived from :
no loss of information
( ) ( )

=
spins
3 2
d d d N
N
r
Gradient of
Gradient: first derivative

p=0: critical point (CP)

( )
z

k j i r + + =
Critical points in 2D
Gradient paths in 2D
GP example: formaldehyde
Hessian of
Hessian: second derivative

( )

=
2
2 2 2
2
2
2 2
2 2
2
2

z y z x z
z y y x y
z x y x x



r
( ) 3 , 2 , 1 = = i
i i i
u u
Characterization of CPs
Rank (r): # of A
i
=0
Signature (s):
# of A
i
>0 minus # of A
i
<0
r s Name .
3 -3 Nuclear attractor (NA)
3 -1 Bond critical point (BCP)
3 +1 Ring critical point (RCP)
3 +3 Cage critical point (CCP)
0 0 Critical point at infinity
Bond critical point (BCP)
Ring critical point (RCP)
Overview of CPs and GPs
Interatomic surface (IAS)
IAS = BCP + bundle of GPs
IAS is zero-flux surface (ZFS):
Problem: m number of ZFSs
( ) ( ) ( ) r r r n r S = 0
Zero-flux surfaces
Solutions to problem of ZFSs
Cusp?
Exclude surfaces with NA?
Boundary conditions?
Definition of an atom
NA: terminus for bundle of GPs,
together defining an atomic basin
Atom = nucleus + atomic basin
Atom = subspace bounded by ZFS
Beware: non-nuclear attractors
NNA example: Li
2
NNA example: Na
8
(SiAlO
4
)
6
Definition of a bond
Bond path (BP) =
AIL in equilibrium geometry
Not every BP is a bond,
not every bond is a BP
BPbond example: phenanthrene
BPbond example: He@adam
He@adam(g) He (g) + adam(g): AE =-645 kJ/mol
Laplacian of
Laplacian: second derivative

At BCP: A
3
>0, (along AIL)
At BCP: A
1
A
2
<0 (along AIS)
( )
3 2 1
2
2
2
2
2
2
2

+ + =
+ + =
z y x
r
Bond characterization by
2

L() =-
2
p
L
BCP
p
BCP
Type .
0 ~0.1 Shared (covalent, polar)
0 ~0.01 Closed- shell
(ionic, hydrogen, van der Waals)
~0 any Intermediate
More bond properties
Ellipticity: c =(A
1
/A
2
) -1
Bond order: n=e
A(p
BCP
-B)
Bond path length vs.
internuclear distance
Bond path angle vs.
geometrical bond angle
BCP properties: CC bonds
Bond L
BCP
p
BCP
c n
CH
3
CH
2
-CH
2
CH
3
0.51 0.24 0.01 1.0
CH
2
=CH
2
1.20 0.36 0.30 2.0
CHCH 1.46 0.43 0.00 3.0
C-C in benzene 0.94 0.32 0.18 1.6
CH
2
CH-CHCH
2
0.68 0.27 0.07 1.2
CH
2
=CHCHCH
2
1.19 0.36 0.29 2.0
CH
3
-CHCH
2
0.67 0.27 0.03 1.2
CH
3
-C
6
H
5
0.93 0.32 0.19 1.6
C-C in c- C
3
H
6
0.42 0.24 0.42 1.0
CH
3
-C
3
H
5
0.54 0.25 0.02 1.1
Atomic charge
Too large: bonds too ionic
(e.g. CH
3
Li, HCN, CO)
Worse: Mulliken, Weinhold/NPA
Better: Hirshfeld, VDD, "AIMDD
What AIM can and cannot do
Can do:
Bond order (C, N, O)
Conjugation
Hyperconjugation
Three-membered rings
Cannot do well:
Atomic charge
Atomic energy
Summary and conclusions
Atoms in molecules (AIM)
Partitioning of molecule into atoms
based on gradient of p
Not omnipotent, not without flaws:
useful, but use with caution
Important references
R.F.W. Bader, Atoms in Molecules: A Quantum
Theory; Clarendon Press: Oxford,
P.L.A. Popelier, Atoms in Molecules: An Introduction;
Prentice Hall: Essex,
R.F.W. Bader, Chem. Rev. , 91, 893-928
R.F.W. Bader, Int. J. Quantum Chem. , 49,
299-308
P. Cassam-Chena & D. Jayatilaka, Theor. Chem.
Acc. , 105, 213-218
Finally... questions?