Chemist
Team Lead, Chemical Physics Theory Team A
Chemist
Team Lead, Chemical Physics Theory Team A

Biography

Marcel Baer is a chemist at Pacific Northwest National Laboratory, where he leads the Chemical Physics Theory Team A. His research sits at the interface of physical chemistry, biology, and materials science. Using ab initio molecular dynamics, density functional theory, classical simulation, and, increasingly, machine learning and agentic AI, he builds molecular-level, predictive pictures of how structure, solvation, and dynamics shape chemical behavior in complex environments. His work spans ion pairing at aqueous interfaces, enzyme mechanisms in plant biology, and the design and self-assembly of bio-inspired polymers.

As Principal Investigator of a 2021 Department of Energy Early Career Research Program award in the BES Biomaterials Program, Baer leads a five-year effort to develop computational methods for designing sequence-defined polymers, including peptoids and triazine-based polymers, that bind and stabilize the metal clusters responsible for nature’s most important electron-transfer and catalytic reactions. The aim is synthetic materials that perform these reactions with enzyme-like selectivity but across a far broader range of temperatures, solvents, and operating conditions than biology allows.

Baer earned his PhD in Chemistry from Ruhr-Universität Bochum in 2010 with a thesis on the theoretical vibrational spectroscopy of protonated water networks in the gas phase and in bacteriorhodopsin, an early signal of the biological and biophysical themes that animate his current program. He joined PNNL as a Linus Pauling Distinguished Postdoctoral Fellow.

Current Research

DOE Early Career Research Program — BES Biomaterials (FY21–present). Principal Investigator of a five-year DOE Office of Science award developing the computational framework needed to design sequence-defined biomolecular materials. The project combines first-principles simulations, force-field development, and machine learning to model peptoid and triazine-based polymer scaffolds hosting functional metal clusters in non-natural environments.

Genie-CAT (2025–present). Co-developer of Genie-CAT, an agentic large language model framework for mechanistic protein and enzyme design, with lead responsibility for the AI/ML components. The platform integrates literature-grounded retrieval-augmented reasoning, structural analysis of PDB files, electrostatic-potential calculations, and machine-learning prediction of redox properties into a single interpretable workflow—demonstrated on [Fe–S]-cluster metalloproteins such as ferredoxins. See: Beyond Protein Language Models: An Agentic LLM Framework for Mechanistic Enzyme Design (arXiv:2511.19423, 2025).

STEPs and STEPs-SOL. Leads the development of STEPs, a systematic first-principles workflow for force-field parameterization of noncanonical biomolecular systems, and its solvent-aware extension STEPs-SOL. The framework currently provides validated parameters for 70 peptoid side chains and enables scalable molecular simulation of sequence-defined materials that fall outside the coverage of standard biomolecular force fields. See: Development of a Systematic and Extensible Force Field for Peptoids (STEPs), J. Phys. Chem. B, 2023; and STEPs-SOL, a Peptoid Force Field Parameterization to Include Solvent Effects, J. Phys. Chem. B, 2025.

Research Interests

Bridging physical chemistry, biology, and materials science through theory, simulation, and AI:

  • Computational design of bio-inspired, sequence-defined polymers (peptoids, triazine-based polymers)
  • Electronic structure and stabilization of functional metal clusters in synthetic scaffolds
  • Machine learning and agentic AI for mechanistic molecular design
  • First-principles force-field development for noncanonical biomolecular systems
  • Enzyme mechanisms and protein dynamics (acyl carrier proteins, fatty-acid desaturases, bacteriorhodopsin)
  • Self-assembly and structural dynamics of peptoid-based biomimetic materials
  • Ab initio molecular dynamics of aqueous solutions and interfaces
  • Ion hydration, ion pairing, and specific-ion (Hofmeister) effects
  • Classical and quantum descriptions of water and aqueous electrolytes
  • Free energy methods, transition-state theory, and Marcus theory for condensed-phase reactions

Disciplines and Skills

  • Density functional theory and ab initio molecular dynamics
  • Classical molecular dynamics and enhanced-sampling techniques (metadynamics, umbrella sampling, committor analysis)
  • Machine learning and agentic AI workflows for computational chemistry and materials design
  • First-principles force-field development and automated parameterization pipelines
  • Multiscale modeling combining quantum-mechanical and empirical descriptions
  • Free energy calculations and rate-theory analysis of condensed-phase reactions
  • Protein structure prediction and biomolecular docking
  • Simulation–experiment integration for X-ray absorption and scattering data
  • High-performance computing workflows for large-scale molecular simulation
  • Simulation packages: CP2K, ORCA, GROMACS, LAMMPS, PyRosetta, HADDOCK

Education

  • PhD in Chemistry, Ruhr-Universität Bochum
  • MS in Chemistry, Ruhr-Universität Bochum
  • BS in Chemistry, Ruhr-Universität Bochum

Affiliations and Professional Service

  • Member, American Chemical Society
  • Advisory Board, 13th Peptoid Summit (2026) — abstract evaluation and program development

Awards and Recognitions

  • Department of Energy Early Career Research Program Award (2021)
  • Linus Pauling Distinguished Postdoctoral Research Fellowship, Pacific Northwest National Laboratory.

Publications

2022

  • Baer M.D., E. Whittle, J. Chai, X. Yu, S. Raugei, and J. Shankline. 2022. "Regioselectivity mechanism of the Thunbergia alata Delta(6)-16:0-acyl carrier protein desaturase." Plant Physiology 188, no. 3:1537 - 1549. PNNL-SA-166222. doi:10.1093/plphys/kiab577
  • Johnson S., M.D. Baer, and S. Raugei. 2022. "Protonation of Serine In Gas, Condensed and Microsolvated States In Aqueous Solution." Journal of Physical Chemistry A 126, no. 1:44-52. PNNL-SA-167114. doi:10.1021/acs.jpca.1c08795

2021

  • Baer M.D., J. Shankline, and S. Raugei. 2021. "Atomistic insight on Structure and Dynamics of Spinach Acyl Carrier Protein with Substrate Length." Biophysical Journal 120, no. 17:3841-3853. PNNL-SA-155027. doi:10.1016/j.bpj.2020.12.036
  • Hammons J.A., M.D. Baer, T. Jian, J.R. Lee, T.M. Weiss, J.J. De Yoreo, and A. Noy, et al. 2021. "Early-Stage Aggregation and Crystalline Interactions of Peptoid Nanomembranes." The Journal of Physical Chemistry Letters 12, no. 26:6126-6133. PNNL-SA-163392. doi:10.1021/acs.jpclett.1c01033
  • Song Y., M. Wang, S. Akkineni, W. Yang, J.J. Hettige, H. Jin, and Z. Liao, et al. 2021. "Highly bright and photostable two-dimensional nanomaterials assembled from sequence-defined peptoids." ACS Materials Letters 3, no. 4:420-427. PNNL-SA-160450. doi:10.1021/acsmaterialslett.1c00110
  • Vasquez de Vasquez M.G., B.A. Wellen Rudd, M.D. Baer, E.E. Beasley, and H.C. Allen. 2021. "Role of Hydration in Magnesium versus Calcium Ion Pairing with Carboxylate: Solution and the Aqueous Interface." Journal of Physical Chemistry B 125, no. 40:11308–11319. PNNL-SA-166343. doi:10.1021/acs.jpcb.1c06108

2020

  • Duignan T.T., G.K. Schenter, J.L. Fulton, T. Huthwelker, M. Balasubramanian, M. Galib, and M.D. Baer, et al. 2020. "Quantifying the hydration structure of sodium and potassium ions: Taking additional steps on Jacob's Ladder." Physical Chemistry Chemical Physics. PCCP 22, no. 19:10641-10652. PNNL-SA-140415. doi:10.1039/c9cp06161d
  • Legg B.A., M.D. Baer, J. Chun, G.K. Schenter, S. Huang, Y. Zhang, and Y. Min, et al. 2020. "Visualization of Aluminum Ions at the Mica Water Interface Links Hydrolysis State-to-Surface Potential and Particle Adhesion." Journal of the American Chemical Society 142, no. 13:6093-6102. PNNL-SA-153730. doi:10.1021/jacs.9b12530
  • Leitold C., C.J. Mundy, M.D. Baer, G.K. Schenter, and B. Peters. 2020. "Solvent reaction coordinate for an SN2 reaction." Journal of Chemical Physics 153, no. 2:Article No. 024103. PNNL-SA-151167. doi:10.1063/5.0002766
  • Manookian B., E.D. Hernandez, M.D. Baer, C.J. Mundy, F.C. Jentoft, and S.M. Auerbach. 2020. "Experimental and DFT Calculated IR Spectra of Guests in Zeolites: Acyclic Olefins and Host-Guest Interactions." Journal of Physical Chemistry C 124, no. 19:10561-10572. PNNL-SA-151187. doi:10.1021/acs.jpcc.0c01225
  • Roy S., G.K. Schenter, J.A. Napoli, M.D. Baer, T.E. Markland, and C.J. Mundy. 2020. "Resolving Heterogeneous Dynamics of Excess Protons in Aqueous Solution with Rate Theory." Journal of Physical Chemistry B 124, no. 27:5665-5675. PNNL-SA-153399. doi:10.1021/acs.jpcb.0c02649

2019

  • Denton J., P.J. Kelleher, M.A. Johnson, M.D. Baer, S.M. Kathmann, C.J. Mundy, and B.A. Wellen Rudd, et al. 2019. "Molecular-level origin of the carboxylate head group response to divalent metal ion complexation at the air-water interface." Proceedings of the National Academy of Sciences of the United States of America 116, no. 30:14874-14880. PNNL-SA-138980. doi:10.1073/pnas.1818600116
  • Zdrali E., M.D. Baer, H.I. Okur, C.J. Mundy, and S. Roke. 2019. "The Diverse Nature of Ion Speciation at the Nanoscale Hydrophobic/Water Interface." Journal of Physical Chemistry B 123, no. 10:2397-2404. PNNL-SA-130894. doi:10.1021/acs.jpcb.8b10207

2018

  • Duignan T.T., M. Peng, A.V. Nguyen, X. Zhao, M.D. Baer, and C.J. Mundy. 2018. "Detecting the undetectable: The role of trace surfactant in the Jones-Ray effect." Journal of Chemical Physics 149, no. 19:194702. PNNL-SA-136999. doi:10.1063/1.5050421
  • Duignan T.T., M.D. Baer, and C.J. Mundy. 2018. "Understanding the Scale of the Single Ion Free Energy: A Critical Test of the Tetra-Phenyl Arsonium and Tetra-Phenyl Borate Assumption." Journal of Chemical Physics 148, no. 22:222819. PNNL-SA-132440. doi:10.1063/1.5020171
  • Henzler K., E. Fetisov, M. Galib, M.D. Baer, B.A. Legg, C. Borca, and J.M. Xto, et al. 2018. "Supersaturated calcium carbonate solutions are classical." Science Advances 4, no. 1:eaao6283. PNNL-SA-128147. doi:10.1126/sciadv.aao6283
  • Prakash A., M.D. Baer, C.J. Mundy, and W.J. Pfaendtner. 2018. "Peptoid backbone flexibilility dictates its interaction with water and surfaces: A molecular dynamics investigation." Biomacromolecules 19, no. 3:1006-1015. PNNL-SA-132333. doi:10.1021/acs.biomac.7b01813
  • Remsing R.C., T. Duignan, M.D. Baer, G.K. Schenter, C.J. Mundy, and J.D. Weeks. 2018. "Water Lone Pair Delocalization in Classical and Quantum Descriptions of the Hydration of Model Ions." Journal of Physical Chemistry B 122, no. 13:3519-3527. PNNL-SA-130323. doi:10.1021/acs.jpcb.7b10722

2017

  • Duignan T., M.D. Baer, G.K. Schenter, and C.J. Mundy. 2017. "Real single ion solvation free energies with quantum mechanical simulation." Chemical Science 8, no. 9:6131-6140. PNNL-SA-123711. doi:10.1039/c7sc02138k
  • Galib M., M.D. Baer, L.B. Skinner, C.J. Mundy, T. Huthwelker, G.K. Schenter, and C.J. Benmore, et al. 2017. "Revisiting the hydration structure of aqueous Na+." Journal of Chemical Physics 146, no. 8:084504. PNNL-SA-122600. doi:10.1063/1.4975608
  • Galib M., T. Duignan, Y.B. Misteli, M.D. Baer, G.K. Schenter, J. Hutter, and C.J. Mundy. 2017. "Mass Density Fluctuations in Quantum and Classical descriptions of Liquid Water." Journal of Chemical Physics 146, no. 24:244501. PNNL-SA-124698. doi:10.1063/1.4986284
  • Roy S., M.D. Baer, C.J. Mundy, and G.K. Schenter. 2017. "Marcus Theory of Ion-Pairing." Journal of Chemical Theory and Computation 13, no. 8:3470-3477. PNNL-SA-124513. doi:10.1021/acs.jctc.7b00332

2016

  • Baer M.D., and C.J. Mundy. 2016. "Local Aqueous Solvation Structure Around Ca2+ During Ca2+---Cl- Pair Formation." Journal of Physical Chemistry B 120, no. 8:1885-1893. PNNL-SA-113515. doi:10.1021/acs.jpcb.5b09579
  • Daily M.D., M.D. Baer, and C.J. Mundy. 2016. "Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer." Journal of Physical Chemistry B 120, no. 9:2198-2208. PNNL-SA-115083. doi:10.1021/acs.jpcb.5b12277
  • Duignan T., M.D. Baer, and C.J. Mundy. 2016. "Ions Interacting in Solution: Moving from Intrinsic to Collective Properties." Current Opinion in Colloid & Interface Science 23. PNNL-SA-115774. doi:10.1016/j.cocis.2016.05.009
  • Jin H., F. Jiao, M.D. Daily, Y. Chen, F. Yan, Y. Ding, and X. Zhang, et al. 2016. "Highly stable and self-repairing membrane-mimetic 2D nanomaterials assembled from lipid-like peptoids." Nature Communications 7. PNNL-SA-112006. doi:10.1038/ncomms12252
  • Pluharova E., M.D. Baer, G.K. Schenter, P. Jungwirth, and C.J. Mundy. 2016. "Dependence of the rate of LiF ion pairing on the description of molecular interaction." Journal of Physical Chemistry B 120, no. 8:1749-1758. PNNL-SA-113233. doi:10.1021/acs.jpcb.5b09344
  • Roy S., M.D. Baer, C.J. Mundy, and G.K. Schenter. 2016. "Reaction Rate Theory in Coordination Number Space: An Application to Ion Solvation." Journal of Physical Chemistry C 120, no. 14:7597-7605. PNNL-SA-115065. doi:10.1021/acs.jpcc.6b00443

2014

  • Baer M.D., I.W. Kuo, D.J. Tobias, and C.J. Mundy. 2014. "Toward a unified picture of the water self-ions at the air-water interface: a density functional theory perspective." Journal of Physical Chemistry B 118, no. 28:8364-8372. PNNL-SA-101070. doi:10.1021/jp501854h
  • Baer M.D., J.L. Fulton, M. Balasubramanian, G.K. Schenter, and C.J. Mundy. 2014. "Persistent Ion Pairing in Aqueous Hydrochloric Acid." Journal of Physical Chemistry B 118, no. 26:7211-7220. PNNL-SA-97211. doi:10.1021/jp501091h
  • Pluharova E., M.D. Baer, C.J. Mundy, B. Schmidt, and P. Jungwirth. 2014. "Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics." The Journal of Physical Chemistry Letters 5, no. 13:2235-2240. PNNL-SA-102863. doi:10.1021/jz500976m
  • Remsing R.C., M.D. Baer, G.K. Schenter, C.J. Mundy, and J.D. Weeks. 2014. "The role of broken symmetry in solvation of a spherical cavity in classical and quantum water models." The Journal of Physical Chemistry Letters 5, no. 16:2767-2774. PNNL-SA-102866. doi:10.1021/jz501067w

2013

  • Baer M.D., and C.J. Mundy. 2013. "An ab initio approach to understanding the specific ion effect." Faraday Discussions 160, no. 0:89-101. PNNL-SA-88317. doi:10.1039/C2FD20113E
  • Devanathan R., N.B. Idupulapati, M.D. Baer, C.J. Mundy, and M. Dupuis. 2013. "Ab initio molecular dynamics simulation of proton hopping in a model polymer membrane." Journal of Physical Chemistry B 117, no. 51:16522-16529. PNNL-SA-98829. doi:10.1021/jp410229u
  • Stern A.C., M.D. Baer, C.J. Mundy, and D.J. Tobias. 2013. "Thermodynamics of Iodide Adsorption at the Instantaneous Air-Water Interface." Journal of Chemical Physics 138, no. 11:114709. PNNL-SA-87976. doi:10.1063/1.4794688
  • Tobias D.J., A.C. Stern, M.D. Baer, Y. Levin, and C.J. Mundy. 2013. "Simulation and Theory of Ions at Atmospherically Relevant Aqueous Liquid-Air Interfaces." Annual Review of Physical Chemistry 64. PNNL-SA-89705. doi:10.1146/annurev-physchem-040412-110049

2012

  • Baer M.D., A.C. Stern, Y. Levin, D.J. Tobias, and C.J. Mundy. 2012. "Electrochemical Surface Potential due to Classical Point Charge Models Drives Anion Adsorption to the Air-Water Interface." The Journal of Physical Chemistry Letters 3, no. 11:1565-1570. PNNL-SA-85917. doi:10.1021/jz300302t
  • Kimmel G.A., M.D. Baer, N.G. Petrik, J. VandeVondele, R.J. Rousseau, and C.J. Mundy. 2012. "Polarization- and Azimuth-Resolved Infrared Spectroscopy of Water on TiO2(110): Anisotropy and the Hydrogen-Bonding Network." The Journal of Physical Chemistry Letters 3, no. 6:778-784. PNNL-SA-85286. doi:10.1021/jz3001079

2011

  • Baer M.D., and C.J. Mundy. 2011. "Toward an Understanding of the Specific Ion Effect using Density Functional Theory." The Journal of Physical Chemistry Letters 2, no. 9:1088-1093. PNNL-SA-78516. doi:10.1021/jz200333b
  • Baer M.D., C.J. Mundy, M.J. McGrath, I.W. Kuo, J.I. Siepmann, and D.J. Tobias. 2011. "Re-Examining the Properties of the Aqueous Vapor-Liquid Interface Using Dispersion Corrected Density Functional Theory." Journal of Chemical Physics 135, no. 12:Article No. 124712. PNNL-SA-79783. doi:10.1063/1.3633239
  • Baer M.D., T.V. Pham, J.L. Fulton, G.K. Schenter, M. Balasubramanian, and C.J. Mundy. 2011. "Is Iodate a Strongly Hydrated Cation?." The Journal of Physical Chemistry Letters 2, no. 20:2650-2654. PNNL-SA-81565. doi:10.1021/jz2011435
  • Lewis T., B. Winter, A.C. Stern, M.D. Baer, C.J. Mundy, D.J. Tobias, and J.C. Hemminger. 2011. "Dissociation of strong acid revisited: X-ray photoelectron spectroscopy and molecular dynamics simulations of HNO3 in water." Journal of Physical Chemistry B 115, no. 30:9445-9451. PNNL-SA-78514. doi:10.1021/jp205510q
  • Lewis T., B. Winter, A.C. Stern, M.D. Baer, C.J. Mundy, D.J. Tobias, and J.C. Hemminger. 2011. "Does Nitric Acid Dissociate at the Aqueous Solution Surface?." Journal of Physical Chemistry C 115, no. 43:21183-21190. PNNL-SA-82030. doi:10.1021/jp205842w