VCD using

ab initio
Molecular
Dynamics
Review of the last
2 VCD using ab initio Molecular Dynamics - Presentation.nb

Review of the last

presentation

IR using dipole moments

Dipole Moments
and
 VCD using ab initio Molecular Dynamics - Presentation.nb 3

Dipole Moments
and
Polarizabilities

Maximally Localized Wannier

Functions
The dipole moment is easily computed as
the expectation value of the dipole
operator after the wave function is
known by the electronic structure
method.
 operator after the wave function is
4 VCD using ab initio Molecular Dynamics - Presentation.nb

known by the electronic structure

method.

This approach works very well for

isolated molecules in the gas phase, and
it is available in most quantum chemistry
software packages.

An AIMD simulation of a liquid, however,

suffers from the problem that the
standard dipole operator is ill-defined
when periodic boundary conditions are
applied.

In many applications, it is desirable to

assign an individual dipole moment to
each molecule of the system.

By a unitary transformation of the

occupied Kohn–Sham orbitals, a set of
localized Wannier orbitals is created . The
 VCD using ab initio Molecular Dynamics - Presentation.nb 5

By a unitary transformation of the

occupied Kohn–Sham orbitals, a set of
localized Wannier orbitals is created . The
particular form of this transformation is
chosen in such a way that a specfic
spread functional of the Wannier orbitals
(see the references for details) is
minimized .

The position expectation values ri of

these Wannier orbitals are called Wannier
function centers, and they can be
interpreted in a chemical sense as the
locations of electron pairs .
6 VCD using ab initio Molecular Dynamics - Presentation.nb

The Wannier localization itself is required

to be performed by the simulation
software package while Travis takes the
resulting Wannier function centers as
input to carry out the assignment to the
molecules and to calculate the dipole
moments.

Voronoi Tessellation of the

Electron Density
Voronoi Tessellation of the VCD using ab initio Molecular Dynamics - Presentation.nb 7

Electron Density
It is sufficient to know the total electron
density to calculate the dipole moment
by integration according to
the classical definition.

The Wannier function centers allow to

assign each orbital to
a molecule, but this is actually
unnecessary, as it is only needed to
divide the total
electron density into molecular
contributions
8 VCD using ab initio Molecular Dynamics - Presentation.nb

{p = RandomReal[{-1, 1}, {12, 2}]},

In[ ]:= DynamicModule[

LocatorPane[Dynamic @ p,
Dynamic @ VoronoiMesh[p],
LocatorAutoCreate  True]]

Out[]=
In[ ]:= o = RandomReal[1, {100, 2}];
VCD using ab initio Molecular Dynamics - Presentation.nb 9

v = VoronoiMesh[o];
edges = MeshPrimitives[v, 1] /.
Line[{a_, b_}] 

weights = edges /. UndirectedEdge 

UndirectedEdge[a, b];

g = Graph[edges, EdgeWeight  weights];

EuclideanDistance;

nf = Composition[
First, Nearest[VertexList[g]]];
DynamicModule[ ]
10 VCD using ab initio Molecular Dynamics - Presentation.nb

Out[]=

Problem of Chemical Intuition

for Radii
Problem of Vertex Error
 VCD using ab initio Molecular Dynamics - Presentation.nb 11

Problem of Vertex Error

The Solution : the radical
Voronoi tessellation
12 VCD using ab initio Molecular Dynamics - Presentation.nb

Some issues
1. accuracy of the integration depends on
the
 VCD using ab initio Molecular Dynamics - Presentation.nb 13

accuracy of the integration depends on

the
grid spacing

2. integral shows finite jumps over time

3. many grid points might be close to cell

faces

4. For the dipole moment, it is important to

note that it generally depends on the
reference point

5. how the radii for the radical Voronoi

tessellation should be
chosen
1.
 tessellation should be
14 VCD using ab initio Molecular Dynamics - Presentation.nb

chosen

Magnetic
Moments and
Vibrational
Circular Dichroism

5.
 VCD using ab initio Molecular Dynamics - Presentation.nb 15

Computing atomic partial charges drops

information that is actually present

The charges always depend on the

method chosen for the population
analysis

In the Wannier center approach, dipole

moments are calculated by a classical
sum over point charges

These can readily be computed by finite

difference derivation of the Wannier
16 VCD using ab initio Molecular Dynamics - Presentation.nb

These can readily be computed by finite

difference derivation of the Wannier
center coordinates ri analogous to the
nuclear velocities

This is hampered by the fact that there is

no specific ordering of the Wannier
centers, so they are arbitrarily mixed in
each step of the trajectory

A reasonable criterion for this purpose is

that the sum of the squared distances
between the Wannier centers in two
subsequent steps should become
minimal

Another issue is the jumping of the

Wannier centers in certain cases . In
aromatic rings, e . g ., the Wannier
localization produces an alternating
Another issue is the jumping of the
VCD using ab initio Molecular Dynamics - Presentation.nb 17

Wannier centers in certain cases . In

aromatic rings, e . g ., the Wannier
localization produces an alternating
pattern of single and double bonds .
Switching between the two possible ways
to form this pattern yields large velocities
of the corresponding Wannier centers,
leading to unphysically large magnetic
moments

A model for magnetic moments

in AIMD that directly relies on
the electron density

j(r) is the electric current density

18 VCD using ab initio Molecular Dynamics - Presentation.nb

j(r) is the electric current density

If the electric current density is known,

molecular magnetic moments can be
calculated in the same manner as
molecular
dipole moments by integration over
Voronoi cells

If the electron density is saved in each

snapshot of the trajectory, the time
derivative can be calculated by finite
difference derivation after the simulation

It is closely related to the

abovementioned jumping of the Wannier
 VCD using ab initio Molecular Dynamics - Presentation.nb 19

It is closely related to the

abovementioned jumping of the Wannier
centers, e . g ., the switching of the
Wannier localization between the two
patterns of alternating single and double
bonds in an aromatic ring is just a
particular eddy current

An issue occurs in regions with vanishing

electron density . In principle, α(r) can
take arbitrary values there without
 An issue occurs in regions with vanishing
electron density . In principle, α(r) can
20 VCD using ab initio Molecular Dynamics - Presentation.nb

take arbitrary values there without

violating the differential equation (3.92) .
To improve the stability of the solution
algorithm in this case, the Travis
implementation provides the possibility
to add a constant background electron
density .

Analogous to the dipole moment, the

magnetic moment depends on the choice
of the reference point . However, not only
the position of the reference point, but
also its velocity are important.
 VCD using ab initio Molecular Dynamics - Presentation.nb 21

Experimental Results