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Gilles Peslherbe, PhD

Professor, Chemistry and Biochemistry
Professor (cross-appointed), Physics
Professor (cross-appointed), Chemical and Materials Engineering
Centre for Research in Molecular Modeling (CERMM)



Education

Diplôme d'Ingénieur Chimiste (Ecole Supérieure de Chimie Industrielle de Lyon, France)
PhD in Physical Chemistry with Minor in Computer Engineering (Wayne State University, USA)

Research interests

Physical, Theoretical and Computational Chemistry; Biophysical Chemistry; Chemical Physics and Biology; Materials Science and Engineering


Teaching

CHEM 235 - Kinetics of Chemical Reactions
CHEM 333 - Introduction to Quantum Theory
CHEM 431/631 - Computational Chemistry for Chemists and Biochemists
CHEM 498Q/630Q - Statistical Mechanics

For additional information, see course websites on  Moodle
(registered students and users only)


Research activities

Chemical Modeling in the Materials, Life and Environmental Sciences

Ongoing advances and breakthroughs in synthesis and experimental characterization techniques yield increasing detailed molecular-level information about chemical processes that is becoming increasingly difficult to decipher without the guidance of modeling. Computer simulations have thus rapidly been permeating all branches of chemistry, not only because they may help interpret convoluted experimental data, but also because they ultimately allow for further educated experimental design over time-consuming and costly trial-and-error approaches. Our research program centers on the development and application of state-of-the-art molecular dynamics and quantum chemistry techniques for realistic simulations of chemical processes, enabled by high-performance computing and typically validated against top-notch experiments. Our research in chemical modeling across the materials, life and environmental sciences entails applications such as wear-resistant transition metal-nitride thin films and nanoparticles for opto-electronics, carbon-based molecular electronics, magnetic materials for spin catalysis, guest molecule encapsulation, membrane permeation, delivery of ligands to porous protein active sites, protein dynamics and reactions, small-molecule structure and reactivity, RNA structure fundamentals, photochemistry of ionic clusters as precursors of the solvated electron or models for DNA radiation damage, structure and formation thermodynamics of seeded droplets, toxic metal atmospheric chemistry, geochemistry. We maintain intensive collaboration with renown experimentalists worldwide, as connection with experiment is crucial for assessing the reliability of our computer simulations and theoretical models, which, in turn can be used to improve our fundamental understanding of chemistry.

Areas of method development and application:

• Nanomaterials and materials science
• Photochemistry and ultrasfast spectroscopy
• Water structure and solvation effects on chemical structure and reactivity
• Chemical biology
• First-principles, approximate and efficient molecular dynamics simulations

Selected on-going research projects:

• Carbon chemistry, encapsulation and spin catalysis
• Dense transition metal nitride nanoparticles and materials
• Cluster materials and amorphous materials (such as glasses)
• Catalysis of chemical reactions by clusters, surfaces and organic/inorganic frameworks
• Advanced materials for electrochemistry

• Chemistry in extreme conditions (high-pressure, high-temperature, cluster impact)
• Charge-transfer-to-solvent phenomena in clusters
• Excited-state electron and molecular dynamics and femtosecond spectroscopy
• Water in confined environments
• Microsolvation in chemical reaction dynamics
• Solvation structure of molecular ions, thermodynamics and spectroscopy
• Molecular ions at interfaces and their effects on phase behavior and role in biology
• Diffusion and reaction of small molecules in proteins (myoglobin, hemoglobin, GAPDH)
• Enhanced sampling molecular dynamics simulations of proteins
• Small-molecule permeation of lipid bilayers

• Protein-protein interactions

• Nucleic acid assemblies, structure and function
• Advanced therapeutics, drug and vaccine design


Publications

Selected Refereed Journal Articles

  • Hang Hu* and Gilles H. Peslherbe, “Accurate Mechanical and Electronic Properties of Spinel Nitrides from Density-Functional Theory”, Journal of Physical Chemistry C 125, XXXX-XXXX (2021).

  • Siyuan Huang, Yong-Kai Wei, SatyavaniKaliamurthi, Yanghui Cao, Asma S Nangraj, Xin Sui, Dan Chu, Huan Wang,Dong-Qing Wei, Gilles H. Peslherbe, Gurudeeban Selvaraj and Jiang Shi,“Circulating miR-1246 Targeting UBE2C, TNNI3, TRAIP, UCHL1 Genes, and Key Pathways as a Potential Biomarker for Lung Adenocarcinoma: Integrated Biological Network Analysis”, Journal of Personalized Medicine 10, 162 (2020).

  • Esam Orabi* and Gilles H. Peslherbe, “Computational Insight into Hydrogen Persulfide and a New Additive Model for Chemical and Biological Simulations”, Physical Chemistry Chemical Physics 21, 15988-16004 (2019). Selected for the 2019 PCCP HOT Articles thematic issue.

  • Bilkiss Issack* and Gilles H. Peslherbe, “Accuracy and Precision of Simulated Free Energies: Water Permeation of Hydrated DPPC Bilayers as a Paradigm”, invited article in the Water special issue, Molecular Simulation 45,466-473 (2019).

  • Jithin J. Varghese, Bharathi Saravanan, Holger Vach, Gilles H. Peslherbe,Samir H. Mushrif, “First-Principles Investigation of the Coupling-Induced Dissociation of Methane and its Transformation to Ethane and Ethylene”, Chemical Physics Letters 708, 21-27 (2018).

  • Lauralicia Sacre, Derek K. O’Flaherty, Philippe Archambault,* William Copp,Gilles H. Peslherbe, Heidi M. Muchall and Christopher J. Wilds,“O4-Alkylated-2-deoxyuridine Repair by O6-alkylguanine DNA Alkyltransferase is Augmented by a C5-Fluorine Modification”, ChemBioChem 19, 575-582 (2018).

  • Soran Jahangiri,* Qadir K. Timerghazin,* HengJiang, Gilles H. Peslherbe and Ann M. English, "Dramatic C-C Bond Activation on Protonation of the Persistent Nitroxyl Radical TEMPO•", invited article for the Terry McMahon special issue of the International Journal of Mass Spectrometry 429,182-188 (2018).

  • Grygoriy A. Dolgonos* and Gilles H. Peslherbe, “Can two H2 Molecules be Inserted into C60 - an Accurate First-Principles Exploration of Structural, Energetic and Vibrational Properties of the 2H2@C60 Complex”, Chemical Physics Letters 663, 104-110 (2016).

  • Oleksiy V. Khavryuchenko* and Gilles H. Peslherbe, “Spin Catalysis over Conductive Solids: Enhancing the Rate of Model C-C Bond Cracking over Carbon Nanoparticles, ChemCatChem 8, 3156-3160 (2016).

  • Anthony A. Noce* and Gilles H. Peslherbe, “Transitioning to a Hydrogen Economy: Kinetic Isotope Effects of Stratospheric Monodeuterated Hydrogen Accumulation”, International Journal of Hydrogen Energy 41, 15373–15387 (2016).

  • Maria Shadrina,* Ann M. English and Gilles H. Peslherbe, “Benchmarking Rapid TLES Simulations of Gas Diffusion in Proteins: Mapping O2 Migration and Escape in Myoglobin as a Case Study”, Journal of Chemical Theory and Computation 12, 2038-2046 (2016).

  • Maria Shadrina,* Gilles H. Peslherbe and Ann M. English, “Quaternary-Linked Changes in Structure and Dynamics That Modulate O2 Migration within Hemoglobin's Gas Diffusion Tunnels”, Biochemistry 54, 5268-5278 (2015).

  • Bilkiss B. Issack* and Gilles H. Peslherbe, “Effect of Cholesterol on the Thermodynamics and Kinetics of Passive Transport of Water through Lipid Membranes”, special issue honoring Branka Ladanyi, Journal of Physical Chemistry B 119, 9391-9400 (2015).

  • Oleksiy V. Khavryuchenko,* Gilles H. Peslherbe and Frank Hagelberg, “A Spin Filter Circuit Design Based on a Finite Single-Walled Carbon Nanotube of the Zigzag Type”, Journal of Physical Chemistry C 119, 3740–3745 (2015).

  • Soran Jahangiri,* Valéry Legris-Falardeau* and Gilles H. Peslherbe, “Computational Investigation of the Hydration of Alkyl Diammonium Cations in Water Clusters”, Chemical Physics Letters 621, 85-90 (2015).

  • Soran Jahangiri,* Lemin Cai* and Gilles H. Peslherbe, “Performance of Density-Functional Tight-Binding Models in Describing Hydrogen-Bonded Anionic-Water Clusters”, Journal of Computational Chemistry 35, 1707-1715 (2014). Made the cover of the journal issue.

  • Oleksiy V. Khavryuchenko,* Volodymyr D. Khavryuchenko and Gilles H. Peslherbe, “Density Functional Theory versus Complete Active Space Self-Consistent Field Investigation of the Half-Metallic Character of Graphite-Like and Amorphous Carbon Nanoparticles”, Journal of Physical Chemistry A 118, 7052-7057 (2014).

  • Chun C. Mak* and Gilles H. Peslherbe, “Relaxation Pathways of Photoexcited Iodide-Methanol Clusters: A Computational Investigation”, Journal of Physical Chemistry A 118, 4494-4501 (2014).

  • Soran Jahangiri,* Grygoriy A. Dolgonos,* Thomas Frauenheim and Gilles H. Peslherbe, “Parameterization of New Elements for Self-Consistent-Charge Density-Functional Tight-Binding: Investigation of Halide Hydration”, Journal of Chemical Theory and Computation 9, 3321-3332 (2013).

  • Soran Jahangiri,* Sean M. Mercer, Philip G. Jessop and Gilles H. Peslherbe, “Computational Investigation of the Hydration of Alkyl Diammonium Chlorides and their Effect on THF/Water Phase Separation”, Journal of Physical Chemistry B 26, 8010-8017 (2013).

  • Oleksiy V. Khavryuchenko,* Nataliya V. Stus and Gilles H. Peslherbe, “Structural and Spin Properties of (PO2)4(WO3)8 Model Bronzes from Density-Functional Theory Calculations”, Solid State Communications 152, 2138-2141 (2012).

  • Maria Shadrina,* Ann M. English and Gilles H. Peslherbe, “Effective Simulations of Gas Diffusion Through Kinetically Accessible Tunnels in Multisubunit Proteins: O2 Pathways and Escape Routes in T-state Deoxyhemoglobin”, Journal of the American Chemical Society 134, 11177–11184 (2012).

  • Chun C. Mak,* Qadir K. Timerghazin* and Gilles H. Peslherbe, “Photoinduced Electron Transfer and Solvation Dynamics in Aqueous Clusters: Comparison of the Photoexcited Iodide-Water Pentamer and the Water Pentamer Anion”, special issue on Ultrafast Chemical Dynamics, Physical Chemistry Chemical Physics 14, 6250-6258 (2012).

  • Sean M. Mercer, Tobias Robert, Daniel V. Dixon, Chien-Shun Chen, Zahra G. Rahami, Jitendra R. Harjani, Soran Jahangiri,* Gilles H. Peslherbe and Philip G. Jessop, “Design, Synthesis, and Solution Behavior of Small Polyamines as Switchable Water Additives”, Green Chemistry 14, 832-839 (2012).

  • Qadir K. Timerghazin,* Inessa Rizvi* and Gilles H. Peslherbe, “Can a Dipole-Bound Electron Form a Pseudo-Atom? An Atoms-In-Molecules Study of the Hydrated Electron”, special issue honoring Richard Bader, Journal of Physical Chemistry A 115, 13201–13209 (2011).

  • Tao-Nhan V. Nguyen,* Qadir K. Timerghazin,* Holger Vach and Gilles H. Peslherbe, “Mechanically-Induced Generation of Highly Reactive Excited-State Oxygen Molecules in Clusters”, Journal of Chemical Physics 134, 064305 (2011).

  • Lei Zhang,* Gilles H. Peslherbe and Heidi M. Muchall, “A General Measure of Conjugation in Biphenyls and Their Radical Cations”, special issue Honoring Russ Boyd, Canadian Journal of Chemistry 88, 1175-1185 (2010).

  • Samir H. Mushrif,* Alejandro D. Rey and Gilles H. Peslherbe, “Energetics and Dynamics of Hydrogen Adsorption, Desorption and Migration on a Carbon-Supported Palladium Cluster”, Journal of Materials Chemistry 20, 10503-10510 (2010).

  • Lisandro Hernández de la Peña* and Gilles H. Peslherbe, “Quantum Effects on the Free Energy of Ionic Aqueous Clusters Evaluated by Nonequilibrium Computational Methods”, Journal of Physical Chemistry B 114, 5404-5411 (2010).

Selected Refereed Articles in Conference Proceedings

  • Lei Zhang,* Gilles H. Peslherbe and Heidi M. Muchall, “Issues with Computational Studies of Photo-induced Degradations of Lignin Model Compounds”, Proceedings of the Third Fundamental and Applied Pulp & Paper Molecular Modeling Symposium, edited by Roger Gaudreault and Michael A. Whitehead, Cascades Inc., 2012.

  • Chun C. Mak,* Denise M. Koch* and Gilles H. Peslherbe, “Large-Scale First-Principles Molecular Dynamics Simulations: Application to the Microsolvation of Biologically-Relevant Ions in Aqueous Clusters”, Proceedings of the 25th High-Performance Computing Symposium, Journal of Physics Conference Series 341, 012010, 2012.

Selected Refereed Book Chapters and Invited Review Articles

  • Chun C. Mak* and Gilles H. Peslherbe, “New Developments in First-Principles Excited-State Dynamics Simulations: Unveiling the Solvent-Specificity of Excited Anionic Cluster Relaxation and Electron Solvation”, in Recent Advances in the Molecular Simulation of Chemical Reactions, special issue of Molecular Simulation, Taylor and Francis, 2014. DOI: 10.1080/08927022.2014.945083

  • Samir H. Mushrif,* Gilles H. Peslherbe and Alejandro D. Rey. “Molecular Modeling: Application to Hydrogen Interaction with Carbon–Supported Transition Metal Systems”. in Chemical Sensors: Simulation and Modeling – Vol. 3, edited by Ghenadii Korotcenkov, Momentum Press, New York, 2012.

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