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by Egill Sklason
Overview
Introduction Electron Density Bader Analysis
Critical Points in and their Classification Gradient Vector Field of and Zero-flux Surfaces Laplacian of and the Lewis and VSEPR Models Algorithms and Applications
Introduction
Atomic charges in molecules or solids are not observables and, therefore, not defined by quantum mechanical theory. The output of quantum mechanical calculations is continuous electronic charge density and it is not clear how one should partition electrons amongst fragments of the system such as atoms or molecules. Many different schemes have been proposed, some based on electronic orbitals:
Mulliken population analysis Density matrix based normal population analysis
cusp
Contour Map
Similar features of the electron density are observed for crystals as for molecules
http://www.chemistry.mcmaster.ca/faculty/bader/aim/aim_1.html
Bader Analysis
The electron density, (x, y, z), of materials is analyzed. Critical points of (x, y, z) are determined and classified. The 3D space is divided into subsystems, each usually containing 1 nucleus (but sometimes none). The subsystems are separated by zero-flux surfaces: (rs) n(rs) = 0 for every point rs on the surface S(rs)
where n(rs) is the unit vector normal to the surface at rs The electron density can either be from experimental data (e.g. X-ray crystallography) or from theoretical data (e.g. ab initio calculations).
4 R.F.W. Bader, Atoms in Molecules - A quantum theory, Oxford University Press, New York, 1990.
Hessian of at a critical point: The Hessian matrix is real and symmetric => we can put it in a diagonal form: eigenvalues = curvatures of
2 2 x = 0 0
0 2 y 2 0
0 1 0 0 0 = 0 2 0 0 0 3 2 z 2 r = r c
R.F.W. Bader, Atoms in Molecules - A quantum theory, Oxford University Press, New York, 1990.
NA
B2H6
BCP
C4H4
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Ethene
H C=C H H H
7 http://www.chemistry.mcmaster.ca/faculty/bader/aim/aim_1.html
Zero-flux Surfaces
An atom can be defined as a region of real space bounded by surfaces through which there is no flux in the gradient vector field of , meaning that the surface is not crossed by any trajectories of (rs) An interatomic surface (IAS) satisfies the zero-flux boundary condition: (rs) n(rs) = 0 for every point rs on the surface S(rs)
where n(rs) is the unit vector normal to the surface at rs At a point on a dividing surface the gradient of the electron density has no component normal to the surface.
R.F.W. Bader, Atoms in Molecules A quantum theory, Oxford University Press, New York, 1990.
Interatomic Surfaces
The Bader atoms consist of regions where there is no flux in the gradient vector field of the electronic density. Fig: The 2nd-row hydrides; AHn where A = Li, Be, B, C, N, O and F.
Note the change in the size and form of the H atom, from the hydride ion in Li+H- to the positively charged one in H+F9 http://www.chemistry.mcmaster.ca/faculty/bader/aim/aim_3.html
2 Lone pairs
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VSEPR: All electron pairs repel each other. Bonding and lone pairs push apart as far as possible. The Laplacian of the electron density provides evidence for the localized lone pairs of the VSEPR model 2 < 0 : locally concentrated 2 > 0 : locally depleted
10 chemistry.mcmaster.ca/faculty/bader/aim/aim_5.html
A chemical reaction corresponds to the combination of a lump in the VSCC of the base combining with the hole in the VSCC of the acid
O=C
Non-bonded charge on C (Lewis base)
BH3
Hole on B (Lewis acid)
11 chemistry.mcmaster.ca/faculty/bader/aim/aim_5.html
However, these algorithms are known to have convergence problems in some cases
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Charge density grid -> Steepest ascent path -> Bader region -> Sum up
2D : 8 neighboring grid points 3D : 26 neighboring grid points Steepest ascent move to max :
di, dj, dk are each assigned the values {-1, 0, 1} but excluding di = dj = dk = 0 Change in density :
Change in distance :
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Scaling of Effort
Data: Boron cluster in silicon with different number of grid points Time: 3 - 45 sec on 1.8 GHz Athlon based computer. 3 atom H2O system required the same computational effort as the 65 atom B-Si system with similar grid size. -> The computer time neither depends upon the number of atoms in the system nor the bonding topology. 17
One gets e.g. Charges on each atom Dipole moment on each atom Bader volume around each atom Bader maxima for each atom etc.
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O 0.00 e- H H 0.00 e-
Mulliken Method
Can be applied when basis functions centered on atoms are used in the calculation of the electronic wavefunction of the system. The charge associated with the basis functions centered on a particular atom is then assigned to that atom. This can be a fast and useful way of determining partial charges on atoms but it has the major drawback that the analysis is sensitive to the choice of basis set. Mulliken analysis is e.g. used in the Gaussian and the Siesta codes.
Output from Siesta calculations on CO molecule:
mulliken: Atomic and Orbital Populations: Species: C
Atom 1 Qatom Qorb 1.822 2s -0.027 2s 0.504 2py 0.504 2pz 1.006 2px 0.072 2py 0.072 2pz 0.193 2px 0.054 2Pdxy 0.000 2Pdyz 0.011 2Pdz2 0.054 2Pdxz 0.034
4.300
Qatom
Species: O
Atom 2 Qorb 1.039 2s 0.506 2s 1.164 2py 1.164 2pz 1.067 2px 0.191 2py 0.191 2pz 0.340 2px 0.014 2Pdxy 0.000 2Pdyz 0.002 2Pdz2 0.014 2Pdxz 0.007
5.700
mulliken: Qtot =
10.000
Usually the points are located in the (-, -) and (+, +) quadrants of the graphs Atomic charges: Hirshfeld < Mulliken < Bader
Bader
Charge Analysis with Mulliken, NBO & Bader as a Function of Applied Field
The charge on the H-atom in HCN is almost the same by all three methods at zero applied field.
Bader
The sensitivity of the charge on the H-atom to the change in applied field follows the order: Bader > Mulliken > NBO
Fig: Charge on the H atom of HCN (calculated using three different conventions) as a function of the applied electric field.
GAMESS (HF/D95** level): optimize the geometries in a dipolar electric field
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Summary
The main features of the Bader analysis Atoms in Molecules have been presented. An example of a simple, fast and robust Bader analysis algorithm has been given. People at CAMP can start using that Bader analysis algorithm on their systems. A comparison of different charge analysis schemes was presented.
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