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# Bader Analysis: Calculating the Charge on Individual Atoms in Molecules & Crystals

by Egill Sklason

## Protonated water-layer : q = + 0.64 e Pt(111) + 7/6 ML Hads : q = - 0.64 e

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

## Mulliken Analysis Comparison Between Different Schemes

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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

## and others based on only the charge density:

Bader analysis Hirshfeld analysis
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## Electron Density of Ethene

Plane containing the 2 C and 4 H nuclei
H C=C H H H

cusp

Contour Map

## Portrayed as a projection in the third dimension

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.

## Critical Points and Hessian of

Critical points of (r): maximum, minimum or saddle where the gradient of (r) vanish ((rc) = 0), where
2 2 2 xy x 2 2 A( rc ) = yx y 2 2 2 zx zy 2 xz 2 yz 2 z 2 r = r c

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.

## Classification of the Critical Points

CPs are labeled: (rank, signature) Only 4 possible signature values for critical points of rank = 3 : (3, -3) : Nuclear Attractor (NA) (3, -1) : Bond Critical Point (BCP) (3, +1) : Ring Critical Point (RCP) (3, +3) : Cage Critical Point (CCP)
RCP CCP

NA

B2H6

BCP

C4H4
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## Gradient Vector Field of the Electron Density

Vector pointing in the direction of maximum increase in One makes an infinitesimal step in this direction and then recalculates the gradient to obtain the new direction By continued repetition of the process, one traces out a trajectory of (r) Sets of trajectories terminate where the density is at maximum (each nucleus) The space of the molecule is partitioned into basins (atoms)

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.

## Contour map of NaCl overlaid with trajectories of

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

## Laplacian of and the Lewis & VSEPR Models

Topology of : atoms, bonds and structure. No indication of maxima in corresponding to the electron pairs of the Lewis model The Laplacian of recovers the shell structure of an atom (in agreement with Lewis Octet Theory) Laplacian: 2 = 2/ x2+ 2/y2 + 2/ z2
F: 2 quantum shells Cl: 3 quantum shells

2 Lone pairs

## Equatorial plane of ClF3

- 2
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

## Laplacian of and Lewis Acid & Base

A local charge concentration is a Lewis base or a nucleophile A local charge depletion is a Lewis acid or an electrophile Zero envelope of 2

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

## Algorithms for Bader Analysis

Commonly used implementations involve:
Finding the CPs (accurately) of the charge density where = 0 (can involve interpolations between grid points and solving nonlinear equations, e.g. Newtons method or Bisection) Construction of the zero-flux surfaces explicitly (expensive) Integration of the electron density within each region (e.g. 3D integration from the nucleus) Packages: AIM2000, TopMoD, InteGriTy, Extreme 94 & MORPHY Usually these programs have a nice interface where one can get nice figures of the electronic density, the gradient vector field, the Laplacian, IAS, CPs etc.

However, these algorithms are known to have convergence problems in some cases
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## Fast and Robust Algorithm for Bader Decomposition of Charge Density

Code: http://theory.cm.utexas.edu/bader/ Forum: http://theory.cm.utexas.edu/forum/

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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## Fast and Robust Algorithm for Bader Decomposition of Charge Density

No effort in trying to find CPs of or the accurate shape of the IAS. No 3D integration (only summation of the charge density on the grid points for each region) Only searching for the local maximum in on the 3D grid. One can get e.g. partial charges and dipole moments of individual atoms in molecules or crystals. Although the dividing surfaces are not found explicitly, it is easy to render them for visualization after the analysis is complete. The algorithm scales linearly with number of grid points, (not with e.g. number of atoms or CPs)
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## Results: Water Molecule

Charge density: aug-cc-pVDZ basis, Gaussian 98, MP2 level 3 Bader regions found, each containing one atom

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## Results: Boron Clusters in Silicon Crystals

Charge density: DFT, plane wave basis, VASP, ultra-soft PsP, PW91 62 Si, 3 B, extra electron added Total charge of the B3-cluster: 10.5 eOverall charge of the cluster is -1.5 e Single B atom in Si crystal has -0.9 e Formation of B3 clusters reduces boron electronic activity by ca. 50%

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## G. Henkelman et al., Comp. Mat. Sc. (2006)

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

## Scales linearly with number of grid points

G. Henkelman et al., Comp. Mat. Sc. (2006)

## Bader Analysis at CAMP

(from e.g. Dacapo, Siesta or Grid-PAW)
from Dacapo import Dacapo from ASE.IO.Cube import * atoms = Dacapo.ReadAtoms('filename.nc') calc = atoms.GetCalculator() dens = calc.GetDensityArray() density = dens * (0.529177)**3 WriteCube(atoms, density, 'filename.cube') Bader filename.cube

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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## Bader Analysis from Dacapo Calculations

Problems with Bader analysis on O-H groups in pseudopotential codes
All electron code (Gaussian): Partial Charge: O: - 1.16 H: + 0.58 9.16 ePseudopotential code (Dacapo): Partial Charge: O: - 2.00 H: + 1.00 8.00 e-

## O 0.42 eH H 0.42 eG. Henkelman et al., Comp. Mat. Sc. (2006)

O 0.00 e- H H 0.00 e-

## We could use Grid-PAW in near future to solve this problem

However, Protonated water-layer : q = + 0.64 Hontop : 1.17 ePt(111) + 7/6 ML Hads : q = - 0.64
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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

## Charge Analysis with Hirshfeld, Mulliken & Bader

Data points: Series of organic molecules, all values in |e|

Usually the points are located in the (-, -) and (+, +) quadrants of the graphs Atomic charges: Hirshfeld < Mulliken < Bader

Bader

## Charge Analysis with Hirshfeld, Mulliken & Bader

Selected number of hypervalent compounds, all values in |e|
Hirshfeld Bader

## 22 De Proft et al, Vol. 23, No. 12, J.Comp. Chem. (2002)

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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## Masunov et al., J. Phys. Chem. A, Vol. 105, No. 19, 2001

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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