eReaxFF: Electron transfer in MD
********************************

ReaxFF Batteries Charge transfer eReaxFF ACKS2 Molecular Dynamics


Overview
========

The novel eReaxFF method is an extension to the well-known reactive
force field ReaxFF. It allows for the simulation of explicit electrons
within the ReaxFF framework. Those electrons are treated in a
pseudoclassical manner that is orders of magnitude faster than any
quantum chemical methods.

[image]

In this tutorial, eReaxFF is used to simulate the dynamics of an
electron transferring through a hydrocarbon radical. A detailed
description of the eReaxFF method and the carbanion (explicit electron
+ hydrocarbon radical) are given in:

Md Mahbubul Islam, Grigory Kolesov, Toon Verstraelen, Efthimios
Kaxiras, and Adri C. T. van Duin, eReaxFF: A Pseudoclassical Treatment
of Explicit Electrons within Reactive Force Field Simulations. , J.
Chem. Theory Comput. **2016**, 12, 8, 3463–3472.

This tutorial was also featured in our video tip of the week series

This tutorial assumes a basic familiarity with the GUI. If you are not
familiar with using the GUI yet, you might take a look at the GUI
introduction tutorials before continuing.


The System
==========

The hydrocarbon radical C_12H_19• is the base used to construct an
anion with one explicit electron. This radical consists of both a
conjugated (polyacetylene) and an aliphatic part. In addition, a
radical site has been placed on the end of the aliphatic part (labeled
CH_2in the below image).

[image]

An excited anion is generated by inserting one explicit electron into
the conjugated part of the radical. From there the electron can
diffuse through the chain until eventually settling at the radical
site. Once the electron settles at the radical site, the ground state
of the anion, a primary carbanion, is reached.

[image]


Setting up the MD simulation
============================

Begin by importing the radical structure into AMSinput

   **1.** Download the file C12H19.xyz "here"
   **2.** In AMSinput: **File → Import Coordinates**
   **3.** Select the XYZ file you just downloaded using the file dialogue window
   **4.** Change to the ReaxFF panel, [image: ReaxFFPanel][image]
 [image]

Next, add the explicit electron to the system

   **1.** Click on the Element tool [image: XTool][image]
   **2.** From the periodic table, select **El**
 [image]

   **1.** Place the electron next to the radical
 [image]

Before placing the electron in its final position, create a new region
and add only the electron to that region.

   **1.** Go to **Model  → Regions**
   **2.** Select the electron in the view panel
   **3.** Click on the Add button [image: AddButton][image]
   **4.** Name the region 'El'
 [image]

Using the newly created region (El), define a charge constraint that
will ensure the electron particle remains its charge of -1 throughout
the charge equilibration scheme

   **1.** Go to **Model  → Charge constraints**
   **2.** Click on the Add button, [image: AddButton][image]
   **3.** Select the region **El** and enter "-1" into the **Charge** field.
 [image]

Next, move the electron particle onto its final starting position,
which is very close (5 pm) to carbon atom #3.

[image]

Placing the electron and carbon atom almost on top of each other at a
defined distance is best done by using the distance slider of the GUI.

   **1.** Select the electron in the view panel
   **2.** Hold down the SHIFT key and select carbon atom #3
   **3.** Use the distance slider or the entry field to set a distance of "5" pm
 [image]

Now, only the general ReaxFF and MD settings need to be setup.

   **1.** In the **Main** panel
   **2.** Set **Total charge** to "-1"
   **3.** In the **Force field** drop-down, select **CHONSMgPNaFBLi-e.ff**.
 [image]

Move on to the general MD settings

   **1.** Click on [image: MoreBtn][image] next to **Task: Molecular Dynamics**
   **2.** Enter **Number of steps** "750000"
   **3.** Enter **Time step** "0.1" fs
   **4.** Enter **Sample frequency** "500"
 [image]

And finally, define the thermostat and start the calculation.

   **1.** Click on [image: MoreBtn][image] next to **Thermostat**
   **2.** Click on the [image: AddButton][image]
   **3.** Select **Thermostat → Berendsen**
   **4.** Set **Temperature** to "600"
   **5.** Set **Damping constant** to "100" fs
   **6.** Save and Run. (Ignore a potential warning about atoms being too close.)
 [image]

The progress of the simulation can be followed in AMSmovie.


Analyzing the results
=====================

Note:

  This simulation depends on random numbers, therefore your results
  may differ from the ones discussed here. The general trend should be
  reproduced. More information on the results are found in Md Mahbubul
  Islam, Grigory Kolesov, Toon Verstraelen, Efthimios Kaxiras, and
  Adri C. T. van Duin, eReaxFF: A Pseudoclassical Treatment of
  Explicit Electrons within Reactive Force Field Simulations. , J.
  Chem. Theory Comput. **2016**, 12, 8, 3463–3472.

The qualitative analysis of the results can easily be done in
AMSmovie:

   **1.** Click on the SCM menu [image: SCMMenu][image] and select **Movie**
   **2.** Start the playback by clicking on the play button

You should see the electron diffusing through the hydrocarbon radical.
The electron diffuses rather effortlessly through the conjugated
chain, while the intersection between the aliphatic and conjugated
parts is a point with slightly higher stability. This slightly higher
stability is the reason why the electron is often seen in the vicinity
of this region.

[image]

Eventually, the electron will be able to escape the small well at the
intersection region and diffuse to the radical site. The arrival at
the radical site, i.e. ground state, is clearly visible as a drop in
the total energy of the system.

[image]

In the present case the electron transfer to the radical site took
around 275 frames which correspond to 13.75ps. Compared to the
literature reference this is faster than average but as mentioned in
the beginning of this section, different runs will yield different
results due to the use of random numbers.

A more quantitative analysis can be carried out by comparing transfer
rates at different temperatures and/or calculating a time averaged
position of the electron along the atoms of the chain. The transfer
times can simply be extracted from the movies of different
trajectories, while the calculation of averaged positions is easily
done with the help of the PLAMS python library shipped with AMS
