By Audrey Ngambia ([email protected]) and Valentina Erastova ([email protected]), University of Edinburgh

Please cite as:

A. Ngambia, O. Masek, V. Erastova, Development of biochar molecular models with controlled porosity. https://doi.org/10.48550/....

The structure of the shared files as follows:

Model_BCMA - BCMA model, using uniform sizes of building blocks

• model.gro - gromacs structure
• topol.top- full OPLS-AA topology, including all building blocks assigned with PolyParGen

Model_BCMB - BCMB model, using two types of building blocks with different sizes

• model_II.gro - gromacs structure
• topol.top- full OPLS-AA topology, including all building blocks assigned with PolyParGen

Model_BCMA_V10 - BCMA model simulated with virtual atom V10-6

• model_with_VA.gro - gromacs structure, including VAs.
• model_VA_removed.gro - gromacs structure generated with VAs, with VAs removed.
• topol_with_VA.top- full OPLS-AA topology, including VAs.

Model_BCMA_V30 - BCMA model simulated with virtual atom V30-6

• model_with_VA.gro - gromacs structure, including VAs.
• model_VA_removed.gro - gromacs structure generated with VAs, with VAs removed.
• topol_with_VA.top- full OPLS-AA topology, including VAs.

Model_BCMB_V10 - BCMB model simulated with virtual atom V10-6

• model_with_VA.gro - gromacs structure, including VAs.
• model_VA_removed.gro - gromacs structure generated with VAs, with VAs removed.
• topol_with_VA.top- full OPLS-AA topology, including VAs.

Model_BCMB_V30 - BCMB model simulated with virtual atom V30-6

• model_with_VA.gro - gromacs structure, including VAs.
• model_VA_removed.gro - gromacs structure generated with VAs, with VAs removed.
• topol_with_VA.top- full OPLS-AA topology, including VAs.

Please note that the VA V10-6 and V30-6 in the manuscript correspond to V4 and V14, respectively, in the these shared structures.

--> To simulate the models without VAs, comment out the corresponding line in the .top file, i.e.:

[ molecules ]
; Compound        #mols
# VS                49
B_14              280
8G11C             120 

--> To model a surface-exposed biochar, extend the simulation box of a bulk system in one of the directions (typically z-direction) by creating an empty space above/below the layer of biochar. Make sure to run the simulation with semi-isotropic pressure coupling to allow de-coupling of z-direction from the xy-plane.

--> If you would like to set up your own biochar models following our approach:

The data collection of experimental measures and a selection of molecular building blocks are given at: github.com/Erastova-group/Biochar_MolecularModels

For more information on the set-up of biochar molecular models, please see the following publications.

• R. Wood, O. Masek, V. Erastova, Biochars at the molecular level. Part 1 -- Insights into the molecular structures within biochars. https://doi.org/10.48550/arXiv.2303.09661

• R. Wood, O. Masek, V. Erastova, Biochars at the molecular level. Part 2 -- Development of realistic molecular models of biochars. https://doi.org/10.48550/arXiv.2303.09907

• A. Ngambia, O. Masek, V. Erastova, Development of biochar molecular models with controlled porosity. https://doi.org/10.48550/....