About Me
- Reactivity: mechanism, thermodynamics & kinetics
- Condensed phase & Interfaces (Solid Liquid/Liquid-Gas)
- Solvent / Solutes / Ions interactions
- Spectroscopies (IR, vSFG)
- Dialogue theory experience in the field of reactivity and spectroscopy
- Machine Learning for Chemistry (Neural Network-based reactive Force-Fields (NNP) & generation of data)
- Main instigator of the ArcaNN project https://github.com/arcann-chem
- Enhanced Sampling & Free Energy Calculations
- Code development (Analysis, spectroscopy, AI)
- Transition Path Sampling (TPS)
- Density Functional Theory (DFT)
- Molecular Dynamics (MD)
- Quantum Mechanics/Molecular Mechanics (QM/MM)
Research Experiences
Post-doctoral researcher
École Normale Supérieure - Paris Sciences et Lettres (Paris, France) Institut de Biologie Physico-Chimique (Paris, France)
November 2022 - July 2024 (21 months)
Laboratoire Pasteur - Pôle Théorie
Development and uses of Machine Learning for Reactivity
Previously at the Laboratoire de Biochimie Théorique
Supervisor: Dr. Guillaume Stirnemann
- Study of phosphoester bond formation in aqueous media
- Use of AI for the design of reaction coordinates for complex reactivity
- Combined use of NNP and TPS to study reactive mechanisms
- Development of machine learning programs/codes
Post-doctoral researcher
École Normale Supérieure - Paris Sciences et Lettres (Paris, France)
January 2021 - September 2022 (21 months)
Laboratoire Pasteur - Pôle Théorie
Simulation of prebiotic chemical reactions catalyzed by aqueous aerosols
Supervisor: Dr. Damien Laage
- Study of peptide bond formation in bulk water and at the air-water interface
- Study of acidity difference between bulk water and air-water interface
- Development of Combined use of NNP and TPS to study reactive mechanisms
- Development of machine learning and interfaces programs/codes
Post-doctoral researcher
Louisiana State University (Baton-Rouge, USA)
2018-2020 (3 years)
Departement of Chemistry - Kumar's Group
Interfaces solid-liquid and their properties: spectroscopy & reactivity
Supervisor: Pr. Revati Kumar
- Study of the graphene oxide and its properties/reactivity in aqueous media and its spectroscopic signatures (vSFG)
- Study of peptoids in aqueous media and their micellar structures
- Study of ion pairing in HCl-water clusters
- Study of electrolytes in glymes and their non-vehicular diffusion
- Development of codes for analysis/spectroscopy of sold/liquid and air/water interfaces and new force-fields
PhD student
Université Grenoble-Alpes (Grenoble, France)
2014-2017 (3 years)
Département de Chimie Moleculaire
Protonation pathways and reactivity of metalloenzymes
Also with the Laboratoire Chimie et Biologie des Métaux
Supervisors: Pr. Anne Milet, Dr. Yohann Moreau
- Study of a protonation step and reactivity of a metalloenzyme using QM/MM
- Study of transition metal complexes for catalysis
- Use of hybrid-DFT/MM and metadynamics
Awards & Distinctions
- Discussion Leader of the GRS session Chemistry and Physics of Liquids, Holderness, US, August 3-4th 2019
- Chairman of a PHYS session at the 257th ACS National Meeting “Chemistry for New Frontiers”, Orlando, US, March/April 31-4th, 2019
- Invited talk at the 257th ACS National Meeting “Chemistry for New Frontiers”, Orlando, US, March/April 31-4th, 2019
- 1st prize poster at Journée de printemps SCF Rhône-Alpes 2016, Grenoble, FR, June 9th, 2016
- 1st prize poster at the 7th Modeling Interactions in Biomolecules, Prague, CZ, September 14-18th, 2015
Scientific Production
Publications (21 with 6 as first author and 2 in preparation as corresponding author/first author)
P1. David, R.*; de la Puente, M.; Gomez, A.; Anton, O.; Stirnemann, G.; Laage, D. ArcaNN: automated enhanced sampling generation of training sets for chemically reactive machine learning interatomic potentials. Submitted.
arXiv: https://doi.org/10.48550/arXiv.2407.07751
P2. Golam, A.; Milet, A.; David, R.*; Kumar, R.* From Graphene Oxide to Graphene: Changes in Interfacial Water Structure and Reactivity. Submitted.
P3. David, R.; Tuñón, I.; Laage, D.* Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling. J. Am. Chem. Soc. 2024, 146 (20), 14213–14224. https://doi.org/10.1021/jacs.4c03445.
ChemRxiv: https://doi.org/10.26434/chemrxiv-2024-tfk5v
P4. Gomez, A.†; de la Puente, M.†; David, R.; Laage, D.* Neural network potentials for exploring condensed phase chemical reactivity. C. R. Chim. 2024. https://doi.org/10.5802/crchim.315. († contributed equally)
ChemRxiv: https://doi.org/10.26434/chemrxiv-2024-9j85m-v2
P5. Benayad, Z.†; David, R.†; Stirnemann G.* Prebiotic Chemical Reactivity in Solution with Quantum Accuracy and Microsecond Sampling Using Neural Network Potentials. Proc. Natl. Acad. Sci. 2024, 121 (23), e2322040121. https://doi.org/10.1073/pnas.2322040121). († contributed equally)
ChemRxiv: https://doi.org/10.26434/chemrxiv-2023-8c1mt
P6. Subasinghege Don, V.; Kim, L.; David, R.; Nauman, J. A.; Kumar, R.* Adsorption Studies at the Graphene Oxide – Liquid Interface: A Molecular Dynamics Study. J. Phys. Chem. C 2023, 127, 5920−5930 https://doi.org/10.1021/acs.jpcc.2c07080.
P7. Tsai, E.; Gallage Dona, H. K.; Tong, X.; Du, P.; Novak, B.; David, R.; Rick, S. W.; Zhang, D.; Kumar, R.* Unraveling the Role of Charge Patterning in the Micellar Structure of Sequence-Defined Amphiphilic Peptoid Oligomers by Molecular Dynamics Simulations. Macromolecules 2022, 55 (12), 5197–5212 https://doi.org/10.1021/acs.macromol.2c00141.
P8. de la Puente, M.; David, R.; Gomez, A.; Laage, D.* Acids at the Edge: Why Nitric and Formic Acid Dissociations at Air–Water Interfaces Depend on Depth and on Interface Specific Area. J. Am. Chem. Soc. 2022, 144 (23), 10524–10529. https://doi.org/10.1021/jacs.2c03099.
P9. Sun, L.; Adam, S. M.; Mokdad, W.; David, R.; Milet, A.; Artero, V.*; Duboc, C.* A Bio-Inspired Heterodinuclear CoFe Complex of the Hydrogenases. Faraday Discuss. 2022 234, 34–41. https://doi.org/10.1039/D1FD00085C.
P10. David, R.; Kumar, R.* Reactive Events at the Graphene Oxide–Water Interface. Chem. Commun. 2021, 57 (88), 11697–11700. https://doi.org/10.1039/D1CC04589J.
P11. Li, K.; Subasinghege Don, V.; Gupta, C. S.; David, R.; Kumar, R.* Effect of Anion Identity on Ion Association and Dynamics of Sodium Ions in Non-Aqueous Glyme Based Electrolytes—OTf vs TFSI. J. Chem. Phys. 2021, 154 (18), 184505 https://doi.org/10.1063/5.0046073.
P12. David, R.; Tuladhar, A.*; Zhang, L.; Arges, C.; Kumar, R.* Effect of Oxidation Level on the Interfacial Water at the Graphene Oxide–Water Interface: From Spectroscopic Signatures to Hydrogen-Bonding Environment. J. Phys. Chem. B 2020, 124 (37), 8167–8178. https://doi.org/10.1021/acs.jpcb.0c05282.
P13. Bresnahan, C. G.; David, R.; Milet, A.; Kumar, R.* Ion Pairing in HCl–Water Clusters: From Electronic Structure Investigations to Multiconfigurational Force-Field Development. J. Phys. Chem. A 2019, 123 (43), 9371–9381. https://doi.org/10.1021/acs.jpca.9b07775.
P14. Subasinghege Don, V.†; David, R.†; Du, P.; Milet, A.; Kumar, R.* Interfacial Water at Graphene Oxide Surface: Ordered or Disordered? J. Phys. Chem. B 2019, 123 (7), 1636–1649. https://doi.org/10.1021/acs.jpcb.8b10987. († contributed equally)
P15. Isaac, J. A.; Mansour, A.-T.; David, R.; Kochem, A.; Philouze, C.; Demeshko, S.; Meyer, F.; Réglier, M.; Simaan, A. J.; Caldarelli, S.; Yemloul, M.; Jamet, H.; Thibon-Pourret, A.; Belle, C.* Tetranuclear and Dinuclear Phenoxido Bridged Copper Complexes Based on Unsymmetrical Thiosemicarbazone Ligands. Dalt. Trans. 2018, 47 (29), 9665–9676. https://doi.org/10.1039/C8DT02452A.
P16. Thibon-Pourret, A.*; Gennarini, F.; David, R.; Isaac, J. A.; Lopez, I.; Gellon, G.; Molton, F.; Wojcik, L.; Philouze, C.; Flot, D.; Le Mest, Y.; Réglier, M.; Le Poul, N.; Jamet, H.; Belle, C. Effect of Monoelectronic Oxidation of an Unsymmetrical Phenoxido-Hydroxido Bridged Dicopper(II) Complex. Inorg. Chem. 2018, 57 (19), 12364–12375. https://doi.org/10.1021/acs.inorgchem.8b02127.
P17. David, R.; Jamet, H.; Nivière, V.; Moreau, Y.; Milet, A.* Iron Hydroperoxide Intermediate in Superoxide Reductase: Protonation or Dissociation First? MM Dynamics and QM/MM Metadynamics Study. J. Chem. Theory Comput. 2017, 13 (6), 2987–3004. https://doi.org/10.1021/acs.jctc.7b00126.
P18. Gennarini, F.; David, R.; López, I.; Le Mest, Y.; Réglier, M.; Belle, C.; Thibon-Pourret, A.; Jamet, H.*; Le Poul, N.* Influence of Asymmetry on the Redox Properties of Phenoxo- and Hydroxo-Bridged Dicopper Complexes: Spectroelectrochemical and Theoretical Studies. Inorg. Chem. 2017, 56 (14), 7707–7719. https://doi.org/10.1021/acs.inorgchem.7b00338.
P19. Lalaoui, N.; David, R.; Jamet, H.; Holzinger, M.; Le Goff, A.*; Cosnier, S. Hosting Adamantane in the Substrate Pocket of Laccase: Direct Bioelectrocatalytic Reduction of O2on Functionalized Carbon Nanotubes. ACS Catal. 2016, 6 (7), 4259–4264. https://doi.org/10.1021/acscatal.6b00797.
P20. Isaac, J. A.; Gennarini, F.; López, I.; Thibon-Pourret, A.; David, R.; Gellon, G.; Gennaro, B.; Philouze, C.; Meyer, F.; Demeshko, S.; Le Mest, Y.; Réglier, M.; Jamet, H.; Le Poul, N.*; Belle, C.* Room-Temperature Characterization of a Mixed-Valent μ-Hydroxodicopper(II,III) Complex. Inorg. Chem. 2016, 55 (17), 8263–8266. https://doi.org/10.1021/acs.inorgchem.6b01504.
P21. Rao, K. V. R.; Caiveau, N.; David, R.; Shalayel, I.; Milet, A.; Vallée, Y.* Theoretical Study, Synthesis, and Reactivity of Five-Membered-Ring Acyl Sulfonium Cations. European J. Org. Chem. 2015, 2015 (28), 6125–6129. https://doi.org/10.1002/ejoc.201500749.
Oral Communications (12 with three invited talks)
T1. “Streamlining the training and the chemical space exploration of neural network potential based force-fields” at: ACS National Meeting “Many Flavors of Chemistry”, New Orleans, US, March 17-21st, 2024
T2. “Combining the power of Neural Network Potentials with Transition Path Sampling to study complex chemical processes” at: Laboratoire de Chimie Théorique - IBPC, Paris, FR, March 7th, 2024 (invited talk)
T3. “Combining the power of Neural Network Potentials with Transition Path Sampling to study complex chemical processes” at: Statistical Thermodynamics & Molecular Simulations Seminar Series, Virtual, February 23rd, 2024 (invited talk)
T4. “L’Intelligence Artificielle (IA) pour la réactivité en chimie” at: Journée CECIC (Local Chemistry-HPC community), Grenoble, FR, July 13th, 2023 (invited talk)
T5. “Reactivity of graphene oxide in aqueous media” at TSRC “Interfacial Molecular and Electronic Structure and Dynamics”, Virtual, June 15-19th, 2020
T6. “Computational studies of an acidic proton at the graphene oxide ‑ water interface” at 257th ACS National Meeting “Chemistry for New Frontiers”, Orlando, US, March/April 31/4th, 2019 (invited talk + chaired a session of the physical chemistry section)
T7. “Mutations on the superoxide reductase: A theoretical study of the 2nd coordination sphere and formation of an oxo-iron” at 255th ACS National Meeting “Nexus of Food, Energy & Water”, New Orleans, US, March 18-22nd, 2018
T8. “Formation of H2O2 in Superoxide Reductase: Protonation or Dissociation First?” at CIMENT (Regional HPC community) Users day, Grenoble, FR, June 1st, 2017
T9. “Formation of H2O2 in Superoxide Reductase: Protonation or Dissociation First?” at Event LABEX ARCANE, Grenoble, FR, October 18th, 2016
T10. “Understanding the formation of H2O2 in superoxide reductase: A metadynamic QM/MM study” at 15th Rencontres de Chimistes Théoriciens Francophones, Lyon, FR, June/July 27-1st, 2016
T11. “Understanding the formation of H2O2 in superoxide reductase: A metadynamic QM/MM study” at 9th Journée de Chimie de Coordination en Rhône-Alpes, Grenoble, FR, April 7th, 2016
T12. “Understanding the formation of H2O2 in superoxide reductase: A metadynamic QM/MM study” at 251st ACS National Meeting “Computers in Chemistry”, San Diego, US, March 14-17th, 2016
Poster Communications (9 with 2 winning prize)
Po1. “Role of environment in the abiotic peptide bond formation” at 17th Rencontres de Chimistes Théoriciens Francophones, Bordeaux, FR, June/July 27-1st, 2022
Po2. “Role of environment in the abiotic peptide bond formation” at Journées GDR SolvATE 2022, Paris, FR, May 30-31st, 2022
Po3. “Simulations of the graphene oxide water interface: hydrogen bonding and spectroscopy” at Journées “Théorie, Modélisation et Simulation 2020”, Virtual, FR, November 2-6th, 2020
Po4. “Reactivity at the graphene-oxide – acidic aqueous solution interface” at 6th Annual International LSU Research Fair, Baton Rouge, US, November 20th, 2019
Po5. “Reactivity at the graphene-oxide – acidic aqueous solution interface” at 27th Current Trends in Computational Chemistry, Jackson, US, November 8-9th, 2019
Po6. “Reactivity at the graphene-oxide – acidic aqueous solution interface” at GRS/GRC “Chemistry and Physics of Liquids”, Holderness, US, August 3-9th, 2019
Po7. “Understanding the formation of hydrogen peroxide in superoxide reductase: a QM/MM study” at Journée de printemps SCF Rhône-Alpes 2016, Grenoble, FR, June 9th, 2016 (Poster won first prize)
Po8. “Understanding the formation of hydrogen peroxide in superoxide reductase: a QM/MM study” at 10th Journée Scientifique de l’IMBG, Autrans, FR, May 19-20th, 2016
Po9. “Understanding the formation of hydrogen peroxide in superoxide reductase: a QM/MM study” at 7th Modeling Interactions in Biomolecules, Prague, CZ, September 14-18th, 2015 (Poster won first prize)