Making an overview presentation of the scaling relations

The following video-presentation – for the CHEAC Summer school 2025 – retells our review on the scaling relations electrocatalysis https://chemrxiv.org/engage/chemrxiv/article-details/67ed469081d2151a02b33a98

The final video

From the beginning I decided to try AI to prepare the presentation. Eventually the only to record the video turned out to be by the traditional way. Together with co-authors Ritums and Nadezda, we used PowerPoint with its slide-by-slide recording feature. As we were in 3 different locations, we exchanged the presentation several time while recording. I used chatgpt 4o and 5 to write lecturer’s notes for every slide. In particular, I gave the chat our article’s pdf-file and then discussed every slide-text using canvas-feature to polish it iteratively. Nadezda also used chatgpt to refined her slides before reading them aloud. Overall, I have spend over two weeks planning the presentation. Then a week polishing the slides. Then several days to record and re-record slides. And finally I have got this the final video-presentation.

Adding voice to a ready presentation

app.pictory.ai does a relatively good job on reading the lecturer’s notes in a ready presentation. Thought, it reads “Jan” and “OOH” in a funny way. And it adds a lot of 10–20 second pauses. Also the slide numbering is off as well as all animation. The picture is also cut from below. But overall, it takes around 2 hours to generate this voiced video and process it.

Use NotebookLM to make a podcast

In the prompt I have specified to avoid banned tells, see https://doublelayer.eu/vilab/2024/12/17/list-of-banned-tells-for-gpt/ Well, I have forbidden to use “pivotal”, but AI still uses “pivotal”.

I am not responsible for the result 🙂 I have heard it and it sounds OK-ish.

Using Gemini in Google Slides

Does not work for me. Gemini wants to draw images. I just want to enter my own figures.

All I need is to convert Figures to Slides

https://www.magicslides.app promises to do exactly that but I failed with a notice that below 5 Mb files are allowed.

SlideAI extension also does not do what I want.

Ufff … manual upload is still the fastest and most robust. Well, it is not so simple, as most of my figures are in pdf, so I wrote this script to convert everything to png. When it took me 2 mins to drag-and-drop all png figure to my presentation. Hurray!

#!/bin/bash

# Create output folder
mkdir -p png

# List of input files
files=(
"Figure 1 mechanisms.png"
"Figure 18 Timeline.png"
"FIgure 14 distances.pdf"
"Figure 11 relative.pdf"
"Figure 6 3dvolcano_withscaling.pdf"
"Figure 2 publications.pdf"
"Figure 5 3dvolcano.pdf"
"Figure 17 perspectives.pdf"
"Figure 16 O_bypassing.pdf"
"Figure 15 O_pushing.pdf"
"Figure 12 O_breaking.pdf"
"Figure 13 O_switching.png"
"Figure 10 O_tuning.pdf"
"Figure 7 projection_potential.pdf"
"Figure 9 projection_ads.pdf"
"Figure 8 timeline.pdf"
"Figure 3 ass_diss.png"
"Figure 4 scalings.png"
)

# Loop through files
for f in "${files[@]}"; do
  base=$(basename "$f")
  name="${base%.*}"
  ext="${base##*.}"
  
  if [[ "$ext" == "pdf" ]]; then
    convert -density 300 "$f" -quality 100 "png/${name}.png"
  elif [[ "$ext" == "png" ]]; then
    cp "$f" "png/${name}.png"
  else
    echo "Unsupported file type: $f"
  fi
done

Use NotebookLM to create FAQ

Pretty cool – NotebookLM make a FAQ.

What are scaling relations in electrocatalysis, and why are they important?

Scaling relations are correlations between the adsorption energies of reaction intermediates on a catalyst’s surface. They are crucial in multi-step electrocatalytic reactions, such as the oxygen reduction reaction (ORR), carbon dioxide reduction (CO2R), and nitrogen reduction (N2RR). The concept emerged in 2005 with the discovery of linear relations between adsorption energies of intermediates like OH, OOH, and O on metal surfaces. Understanding these relations is vital because they define fundamental chemical limitations in electrocatalytic reactions, impacting the design of more efficient catalysts for energy conversion technologies like electrolysers, fuel cells, and metal-air batteries.

How do scaling relations limit the efficiency of oxygen electrocatalysis?

In oxygen electrocatalysis, particularly the oxygen reduction reaction (ORR), the adsorption energies of key intermediates (OOH, OH, O) are correlated by scaling relations. These correlations constrain the achievable catalytic activity, often visualised on “volcano plots.” The OOH-OH and O-OH scaling relations, for instance, mean that if a catalyst binds one intermediate optimally, it might bind another too strongly or too weakly, preventing it from reaching the ideal catalytic activity (the “volcano top”). This limitation is significant, as experimental results have shown catalytic overpotentials converging to a limit set by these relations for over two decades, hindering progress in sustainable energy solutions.

What are the main reaction mechanisms in oxygen electrocatalysis, and how does catalyst geometry influence them?

Oxygen electrocatalysis primarily proceeds via two mechanisms: associative and dissociative. The associative mechanism, which dominates most known catalysts, involves intermediates like OOH, OH, and O adsorbing at a single active site. Geometrically, this requires only one atom in the active site. The dissociative mechanism, conversely, requires at least two neighbouring atoms to accommodate dissociation products (O and OH). On metal surfaces, a spatial mismatch often prevents the dissociative mechanism, as O preferentially adsorbs on hollow sites and OH on top sites. However, dual-atom site catalysts (DACs) can facilitate dissociative pathways by providing two adjacent sites, allowing for the adsorption of dissociation products. The inter-atomic distance within these active sites is a critical geometric parameter that influences the energy barrier for dissociation, balancing thermodynamics and kinetics.

What is the “volcano plot” in electrocatalysis, and how do scaling relations affect it?

The “volcano plot” is a theoretical framework used to understand electrocatalysis, typically representing overpotential or activity as an “altitude” against adsorption energy descriptors. For ORR, it correlates adsorption energies with deviations from the thermodynamic equilibrium potential. Scaling relations define the “paths” or “fixed climbing routes” on this volcano plot that are accessible to catalysts. For example, the OOH-OH scaling relation appears as a plane on the three-dimensional volcano, and catalysts following this relation are confined to a specific line on the volcano’s surface. This means that while an “ideal catalyst” (the volcano’s apex) might exist theoretically, scaling relations prevent most catalysts from reaching it, limiting the search for optimal catalysts to a two-dimensional projection.

What are the five general strategies for “manipulating” scaling relations in electrocatalysis?

The review outlines five general strategies for manipulating scaling relations to enhance electrocatalytic performance:

  1. Tuning: Adjusting the adsorption energy of a key intermediate (e.g., ∆GOH) to optimise catalyst performance within the constraints of an existing scaling relation, adhering to the Sabatier principle.
  2. Breaking: Decreasing the intercept (β) of a scaling relation by selectively stabilising one intermediate over another (e.g., OOH relative to OH), often by introducing spectator groups that induce stabilising interactions.
  3. Switching: Changing the slope (α) of a scaling relation by enabling an alternative reaction mechanism (e.g., switching from an associative to a dissociative mechanism in ORR) to avoid problematic intermediates. This usually requires dual active sites.
  4. Pushing: A combined strategy that changes the slope and adjusts the intercept, simultaneously switching to an alternative mechanism and using stabilising interactions (similar to breaking).
  5. Bypassing: Completely decoupling adsorption energies by switching between two distinct states of the catalyst (e.g., geometric or electronic) during the reaction cycle, with each state having optimal adsorption energies for specific intermediates. This strategy aims to eliminate all scaling relation constraints.

How does the “breaking” strategy specifically aim to overcome the OOH-OH scaling relation?

The “breaking” strategy focuses on reducing the intercept of the OOH-OH scaling relation (from approximately 3.2 eV to an ideal value of 2.46 eV) by selectively stabilising the OOH intermediate relative to OH. This typically involves introducing spectator groups or a second adsorption site near the active site. These spectators can form hydrogen bonds or other stabilising interactions with OOH, effectively shifting its adsorption energy without proportionally affecting OH. While challenging to achieve experimentally, this strategy has been demonstrated in oxygen evolution reactions (OER) and more recently in ORR using dual-atom catalysts (DACs) with specific active sites like PN3FeN3, where the phosphorus acts as a spectator to stabilise OOH through hydrogen bonding.

What role do Single-Atom Site Catalysts (SACs) and Dual-Atom Site Catalysts (DACs) play in manipulating scaling relations?

Single-Atom Site Catalysts (SACs) and Dual-Atom Site Catalysts (DACs) are crucial in manipulating scaling relations due to their distinct geometric and electronic properties. SACs typically allow for “on-top” adsorption, primarily favouring the associative mechanism in ORR. DACs, with their two neighbouring active sites, offer the possibility of accommodating two dissociation products simultaneously, thereby enabling the dissociative mechanism. This ability to switch mechanisms is key to the “switching” strategy, where DACs can replace the OOH intermediate with two distinct O and OH intermediates adsorbed at separate sites. Furthermore, the precise control over inter-atomic distances and curvature in DACs allows for fine-tuning of electronic structures and promoting specific interactions (like hydrogen bonding), contributing to “breaking” and “pushing” strategies.

What is the ultimate goal of manipulating scaling relations, and how does the “bypassing” strategy contribute to this vision?

The ultimate goal of manipulating scaling relations is to achieve ideal catalyst performance, ideally with zero overpotential, by overcoming the fundamental limitations imposed by these correlations. The “bypassing” strategy represents the most ambitious approach towards this goal. It seeks to completely decouple the adsorption energies of reaction intermediates by allowing the catalyst to switch between two or more distinct states (e.g., geometric, electronic, or photonic) during the reaction cycle. Each state would be optimally configured to bind specific intermediates at the ideal energy values required for efficient catalysis. While seemingly challenging in practice, this concept, inspired by natural enzymes like cytochrome c oxidase, offers a theoretical pathway to eliminate all scaling constraints and achieve the theoretical apex of the volcano plot, pushing the boundaries of what is currently achievable in electrocatalysis.

Playing with GPAW in colab

To play with GPAW in colab “sandbox” install it like that:

!apt install libxc-dev
!pip install gpaw
!echo "y" | gpaw install-data /usr/local/pkgs/gpaw-data-0.9.20000/
setup_paths = ['/usr/local/pkgs/gpaw-data-0.9.20000/gpaw-setups-24.11.0/']

Showing difference in files

We are submitting the review “Twenty Years After: Scaling Relations in Oxygen Electrocatalysis and Beyond

I have made so many changes to the LaTeX code that latexdiff gives 99+ errors. UPDATE: the errors were related to table and equations. To fix them I played with –math-markup=none and –add-to-config PICTURENEV=tabular, but eventually just fixed the Tables and specific errors.

In search for an alternative, have tested DiffPDF and Meld. The result looks useful, yet unsuitable for submitting them to the editor. So, this post should have a label “do not know how” instead of usual “know-how”. Still, fun.

To make the last printscreen, I did the following.

Installed packages in Linux/Ubuntu/WSL2.

sudo apt-get -y install meld calibre parallel

Saved the following code in a file named “diffdoc” (with no extensions) inside directory “/usr/local/bin”.

usage="
*** usage:

diffepub - compare text in two files. Valid format for input files are:
MOBI, LIT, PRC, EPUB, ODT, HTML, CBR, CBZ, RTF, TXT, PDF and LRS.

diffepub -h | FILE1 FILE2

-h print this message

Example:
diffepub my_file1.pdf my_file2.pdf
diffepub my_file1.epub my_file2.epub

v0.2 (added parallel and 3 files processing)
"

#parse command line options
while getopts "h" OPTIONS ; do
  case ${OPTIONS} in
    h|-help) echo "${usage}"; exit;;
  esac
done
shift $(($OPTIND - 1))

#check if first 2 command line arguments are files
if [ -z "$1" ] || [ -z "$2" ] || [ ! -f "$1" ] || [ ! -f "$2" ]
then
  echo "ERROR: input files do not exist."
  echo
  echo "$usage"
  exit
fi



#create temporary files (first & last 10 characters of
# input files w/o extension)
file1=`basename "$1" | sed -r -e '
s/\..*$//                     #strip file extension
s/(^.{1,10}).*(.{10})/\1__\2/ #take first-last 10 chars
s/$/_XXX.txt/                 #add tmp file extension
'`
TMPFILE1=$(mktemp --tmpdir "$file1")

file2=`basename "$2" | sed -r -e '
s/\..*$//                     #strip file extension
s/(^.{1,10}).*(.{10})/\1__\2/ #take first-last 10 chars
s/$/_XXX.txt/                 #add tmp file extension
'`
TMPFILE2=$(mktemp --tmpdir "$file2")

if [ "$#" -gt 2 ] 
then
  file3=`basename "$3" | sed -r -e '
  s/\..*$//                     #strip file extension
  s/(^.{1,10}).*(.{10})/\1__\2/ #take first-last 10 chars
  s/$/_XXX.txt/                 #add tmp file extension
  '`
  TMPFILE3=$(mktemp --tmpdir "$file3")
fi

#convert to txt and compare using meld
doit(){ #to solve __space__ between filenames and parallel
  ebook-convert $1
}
export -f doit
if [ "$#" -gt 2 ] 
then
  (parallel doit ::: "$1 $TMPFILE1" \
                     "$2 $TMPFILE2" \
                     "$3 $TMPFILE3" ) &&
  (meld "$TMPFILE1" "$TMPFILE2" "$TMPFILE3")
else
  (parallel doit ::: "$1 $TMPFILE1" \
                     "$2 $TMPFILE2" ) &&
  (meld "$TMPFILE1" "$TMPFILE2")
fi

Made sure the owner is me and it has execution permissions:

sudo chown $USER:$USER /usr/local/bin/diffepub
sudo chmod 700 /usr/local/bin/diffepub

Run it on two pdf files:

diffdoc FILE1.pdf FILE2.pdf

Playing with new xTB

https://chemrxiv.org/engage/chemrxiv/article-details/685434533ba0887c335fc974

# login to HPC
wget https://github.com/grimme-lab/g-xtb/archive/refs/tags/v1.0.0.tar.gz
tar -xvf v1.0.0.tar.gz
nano ~/.bashrc
add "export PATH=~/g-xtb-1.0.0/binary:$PATH"
exit .bashrc
source ~/.bashrc
cp -r ~/g-xtb-1.0.0/parameters/ ~/
# create a new conda environment
conda create gxtb
conda activate gxtb
conda install -c conda-forge libgfortran=14.2.0
conda install -c conda-forge xtb
# run
xtb example.xyz --driver "gxtb -grad -c xtbdriver.xyz" --optA quick test of g-xTB

Reconnecting colab

Recently I noticed that my colab notebooks get too often disconnected. Yes, their run takes over an hour, which is a usual timing for a seminar. I just want to test that they run by executing all cells and leaving my workplace.

Here is how to set up an automatic reconnect using javascript functions that one can enter to the browser console:

function ConnectButton() {console.log("Working");document.querySelector("#connect").click()}
setInterval(ConnectButton,600000);

Uni-, false, and true bifunctional oxygen catalysis

Publishing as chapters in books does now always attract the deserved attention. That might be the case with a chapter I co-authored: R. Cepitis, A. Kosimov, V. Ivaništšev, and N. Kongi, in Multi-functional ElectrocatalystsFundamentals and Applications, ed. V. S. Saji and V. K. Pillai, Royal Society of Chemistry, 2024, vol. 46, ch. 13, pp. 357-374. https://drive.google.com/file/u/0/d/1_oLCbMU6vxPsQe93HitgP-rm6bFSvED_/view

It is worth reading for at least two reasons. First it gives a nice overview of uni-, false, and true bifunctional oxygen catalysis in just one Figure:

Second, it provides a dictionary for theoreticians and experimentalists to allow them to talk about workflows in electrocatalysis:

Colors in ASE

Updated colors for atoms in ASE in 2024 look like this:

For POV rendering there are several options: ASE2, ASE3, Glass, Glass2, Intermediate, JMOL, Pale, Simple, VMD. I like intermediate because it does not have an reflection and glare.

List of banned tells for GPT

1) Just watched Andy Stapleton youtube-video about echo technique for working with chatGPT. After that I have made my list of banned tells for GPT. Here it is.

You must not use these words and phrases: Vibrant, Bustling, Vital, Out of the box, Underscores, Dive into, Reverberate, Delve, Hustle and bustle, Foster, Labyrinthine, Moist, Remnant, Nestled, Game changer, Symphony, Gossamer, Enigma, A testament to, Indelible, Meticulous, Meticulously, Navigating, Complexities, Realm, Tailored, Underpins, Everchanging, Ever-evolving, Not only, Embark, Designed to enhance, It is advisable, Daunting,  In the realm of, Unlock the secrets, Unveil the secrets, Diving, Unleash, Harness, Tapestry, Take a dive into, Leverage, Metropolis, Unless, Arguably, To put it simply, Promptly, In today's digital era. Avoid analogies and ambiguity in wording. Avoid using gerunds, mdash, and other ways of extending sentences; instead split a sentence and consider removing the unnecessary second part. Avoid words that non-native speakers may not understand. Avoid jargon, but do keep all my terms – do not substitute technical terms with analogies. Avoid comparative adjectives and remove adjectives that do not shape the meaning. 

2) Previously I also used this prompt for working with LaTeX codes, but now I simply use texGPT in overleaf for quick drafting.
Start every sentence on a new line. Add line breaks after every 60 characters to make the text easier to read, but do not add these breaks within commented text. Preserve all original comments exactly as written, and do not delete anything unless explicitly instructed.

3) When working within a project, I define instructions like this:

Prohibited words and phrases: You must not use these words and phrases: Vibrant, Bustling, Vital, Out of the box, Underscores, Dive into, Reverberate, Delve, Hustle and bustle, Foster, Labyrinthine, Moist, Remnant, Nestled, Game changer, Symphony, Gossamer, Enigma, A testament to, Indelible, Meticulous, Meticulously, Navigating, Complexities, Realm, Tailored, Underpins, Everchanging, Ever-evolving, Not only, Embark, Designed to enhance, It is advisable, Daunting,  In the realm of, Unlock the secrets, Unveil the secrets, Diving, Unleash, Harness, Tapestry, Take a dive into, Leverage, Metropolis, Unless, Arguably, To put it simply, Promptly, In today's digital era. Avoid analogies and ambiguity in wording. Avoid using gerunds, mdash, and other ways of extending sentences; instead split a sentence and consider removing the unnecessary second part. Avoid words that non-native speakers may not understand. Avoid jargon, but do keep all my terms – do not substitute technical terms with analogies. Avoid comparative adjectives and remove adjectives that do not shape the meaning. 
You must avoid using "potential" in the sense of showing the capacity to develop into something in the future, because "electric potential" is a physical quantity. you must avoid "framework" in the sense of a basic structure underlying a computations, because "organic framework" is a term in material science. You must avoid using "capacity" and "capacitance" in sense of ability to do something, because similar terms are used in electrochemistry. You must avoid using "generation" in sense of production.