Guide for newcomer and current members of Compchem@MU

🛠️🚧🚧 Under construction 🚧🚧🛠️

Welcome to the Compchem@MU! You will be working under Prof. Panida for here on. Trust me, she is a kind-soul and you will not find yourself under a better supervisor 😊.

You will also get a lot of opportunities to collaborate with others, inside and outside the university as she has a pretty good networking. Particularly, with the Japaneses, under the Sakura exchange program 🌸 and others. So if you adore JP stuffs like me ⸂⸂⸜(രᴗര๑)⸝⸃⸃, again, there is no better advisor than her.

DISCLAIMER You don't need to be familiar with everything mentioned below. Proficiency in first-principle calculations, especially DFT, is sufficient for conducting research in our group. However, I highly recommend diving into advanced topics, especially coding skills to automate routine tasks. In today's age of digitalization and the increasing importance of big data and machine learning, you'll find these advanced skills becoming increasingly relevant to your work. Besides, it is just more elegant to work more efficiently by having automated workflow/pipeline in your projects. 💻📈🤖

How to use this guide

Essential stuffs are on the main page here.

For the advanced topics, you can find them in the respective folders.

• coding: coding skills
• AQC: automated quantum-chemical calculations
• quantum_machine_learning: quantum-chemical machine learning
• chem_design: chemical design

If you may still find coding irrelevance to your work, at least check out the AQC folder. It will save you a lot of time and effort in the long run.

If you have any questions, feel free to reach out to me via thanapat142@gmail.com or thanapat.worakul@epfl.ch

General research topics

1. Homogenous catalytic reactions:

• Mechanistic study of catalytic reactions: to reveal the free energy profile
• Electronic structure elucidation: to rationalize the reactivity and selectivity
• Catalyst design and substrate scope
  • virtual screening over a library of catalysts or substrates
  • machine learning
  • exploration of chemical compound space

2. Photochemical and photophysical properties

Mostly collaboration with experimentalists to validate their experimental results and to provide a theoretical explanation.

Typical Quantum-Chemical Calculations

DFT calculation

• Geometry optimization
• Frequency calculation
• Single point energy calculation
• Transition state search
  • saddle point optimization
  • QST2/QST3
  • IRC calculation
• TD-DFT calculation
• NBO analysis
• Energy decomposition analysis

Semiempirical Tight Binding (xTB)

With xTB, you can obtain a better guess geometry for optimization at DFT later, possible making the calculation more efficient. You can also do various stuffs with xTB. Check out xTB tutorial to learn more and AQC folder for more examples of usage.

Essential Skills and Knowledge

Theory stuff

1. Basic theoretical background behind the electronic structure methods and able to apply a right method to a specific problem

   • Hartree-Fock theory
   • Density functional theory
   • Post-HF methods
     • Moller-Plesset perturbation theory (MP)
     • Coupled cluster theory (CC)
     • Configuration interaction theory (CI)
     • Complete active space self-consistent field theory (CASSCF)
     • Complete active space second-order perturbation theory (CASPT2)
   • Basis set
   • Semiempirical methods
   • Solvation models

2. Theoretical background and ability to apply electronic wavefunction analysis methods

   • Natural bond orbital (NBO) analysis
   • Energy decomposition analysis (EDA)
   • Quantum theory of atoms in molecules (QTAIM)
   • and many more (please refer to Multiwfn)

3. Chemistry

   • organic chemistry: structure and reactivity
   • organometallic chemistry
   • catalysis

4. Data science (optional, advanced topic, see quantum_machine_learning folder for more detail)

5. Chemoinformatics (optional, advanced topic, see quantum_machine_learning folder for more detail)

6. Chemical design (optional, advanced topic, see chem_design folder for more detail)

Practical stuff

0. OS (that you will probably use)

   • Linux: 🐧
     • WSL (Windows Subsystem for Linux)
     • Ubuntu (If you hate Windows)
     • CentOS (our servers)
   • Windows (preferably Windows 11)

1. Basic Linux commands

2. Quantum-chemical calculations, particularly

   • xTB (semiempirical, free)
   • Gaussian16/09 (most used, household program here)
   • ORCA (used sometimes, CASSCF, CASPT2, complicate spin stuffs)
   • GAMESS (for NEDA)
   • pySCF (python-based, free)

3. Analysis and Visualization of molecular structures and orbitals

   • Multiwfn [extremely powerful, and versatile. MUST LEARN]
   • NBO6 [MUST LEARN as boss uses it a lot to rationalize the reactivity and selectivity]
   • ArgusLab/Molden (╯ ͠° ͟ʖ ͡°)╯┻━┻
   • GaussView: ( ͡° ͜ʖ ͡°)
   • Avogadro
   • VMD: most elegant and most beautiful
   • Jimp2: maybe easiest to use but not so beautiful

4. Pre- and post-processing of quantum-chemical calculations (optional, see AQC folder)

5. Coding skills (optional, see coding folder)

6. Presentation skills

   • Sadly, people would rarely care about your work, so you need to captivate their attention.
   • please use LaTex more Overleaf, better for collaboration, more elegant and all. Nowadays, it has become much easier also. (Well, except you are working with the experimentalists)
   • able to make attention-grabbing figures
     • matplotlib and seaborn
     • Inkscape or others
     • Blender

Resource

Our lab has a lot of books, check out

• Introduction to Computational Chemistry: classic
• Exploring Chemistry with Electronic Structure Methods: some guides on how to use g09/g16
• there are as well chemistry books like organometallics and catalysis, check them out if you are interested

Quantum-chemical calculations

• Computational Chemistry from Laptop to HPC
• Best-Practice DFT Protocols for Basic Molecular Computational Chemistry
• Perspective: Fifty years of density-functional theory in chemical physics
• Jacob’s ladder of density functional approximations for the exchange-correlation energy
• A Chemist's Guide to Density Functional Theory
• Modern Quantum Chemistry

Electronic wavefunction analysis methods

• Multiwfn: read the manual which contains both theory and practical stuffs
• Read NBO tutorial here
• What is NBO analysis and how is it useful?
• Natural bond orbital analysis: A critical overview of relationships to alternative bonding perspectives
• Natural bond orbital methods
• The Chemical Bond: Fundamental Aspects of Chemical Bonding
• The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design

Free real estate

• Materials Cloud Archive: a repository for computational materials science
• Github: please start to use it
• zenodo: for archiving your data/code and get others
• The Cambridge Structural Database | CCDC: for mining and extracting crystallographic data
• Scihub ( ͡° ͜ʖ ͡°)
• ChemRxiv, Arxiv: latest, hot, frontier stuffs, also publish your preprint here.
• Journal of Cheminformatics, ACS Central Science, Chemical Science, Communications Chemistry

Our previous notable work

Mechanistic study of organometallic-catalyzed reactions

Mostly Ni-NHC catalysts.

1. C-F bond

   • Mechanisms of the Ruthenium Sulfur Complex in Generation and Stabilization of Silicon and Aluminum Electrophile for C(sp³)−F Bond Activation

   • Computational Design of Transition Metal Catalysts for Hydrodefluorination of Trifluoromethylarenes using Hydrosilanes: COMING OUT SOON

2. C-H bond

   • Insights into the Regioselectivity of Hydroheteroarylation of Allylbenzene with Pyridine Catalyzed by Ni/AlMe₃ with N‑Heterocyclic Carbene: The Concerted Hydrogen Transfer Mechanism

3. C-O bond

   • Mechanism of Ni N-heterocyclic carbene catalys for C–O bond hydrogenolysis of diphenyl ether: a density functional study
   • Density Functional Study of Nickel N‑Heterocyclic Carbene Catalyzed C−O Bond Hydrogenolysis of Methyl Phenyl Ether: The Concerted β‑H Transfer Mechanism
   • Aryl C–O oxidative addition of phenol derivatives to nickel supported by an N-heterocyclic carbene via a Ni(0) five-centered complex

4. H-H bond

   • Mechanisms for dehydrogenation and hydrogenation of N-heterocycles using PNP-pincer-supported iron catalysts: a density functional study
   • Insights into H₂ Activation and Styrene Hydrogenation by Nickel−Borane and Nickel−Alane Bifunctional Catalysts

5. CO₂ activation

   • Mechanistic insights into HCO₂H dehydrogenation and CO₂ hydrogenation catalyzed by Ir(Cp*) containing tetrahydroxy bipyrimidine ligand: the role of sodium and proton shuttle
   • Understanding the reactivity of geminal P/B and P/Al frustrated Lewis pairs in CO₂ addition and H₂ activation

6. O₂ activation

   • Proton-Coupled Electron Transfer and Adduct Configuration Are Important for C4a-Hydroperoxyflavin Formation and Stabilization in Flavoenzyme

   • Mechanism of Oxygen Activation in a Flavin-Dependent Monooxygenase: A Nearly Barrierless Formation of C4a-Hydroperoxyflavin via Proton-Coupled Electron Transfer

Catalyst design

1. Elucidating structure-activity relationships for Metal-catalyzed Hydrodefluorination of Trifluoromethylarenes using Hydrosilanes: COMING OUT SOON
2. Computational Design of Ni catalyst for C-H Activation and Hydroarylation of Alkenes: : COMING OUT SOON