Timothy Berkelbach
· Associate Professor of ChemistryVerifiedColumbia University · Joint Programs
Active 2009–2026
Research topics
- Computer Science
- Programming language
- Software engineering
- Engineering
- Physics
- Chemistry
- Database
- Molecular physics
- Computational science
- Systems engineering
- Atomic physics
- Quantum mechanics
Selected publications
ArXiv.org · 2026-03-23
articleOpen accessSenior authorFor ethylene carbonate on the (100) surface of lithium, we calculate the adsorption energy in two binding motifs as well as the barrier height for a ring-opening decomposition reaction. We validate a scheme for producing results in the thermodynamic limit by correcting results obtained on finite lithium clusters containing only 40-100 atoms, which enables the use of hybrid density functionals, the random-phase approximation, and correlated wavefunction theories such as coupled-cluster theory and auxiliary-field quantum Monte Carlo. We find that the high-level theories agree to within 2-5 kcal/mol and can therefore serve as benchmarks for more affordable methods. Using our reference data, we demonstrate that generalized gradient approximation functionals, such as PBE, are not sufficiently accurate for reaction barrier heights, and we identify $ω$B97X-V as an especially promising functional for the interfacial chemistry of electrolyte solvents at lithium metal anodes.
The Python Simulations of Chemistry Framework: 10 years of an open-source quantum chemistry project
arXiv (Cornell University) · 2026-03-14
articleOpen accessOver the past decade, the Python-based Simulations of Chemistry Framework (PySCF) has developed into a widely used open-source platform for electronic structure theory and quantum chemical method development. This article reviews the major advances since the previous overview in 2020, covering new modules and methodology, infrastructure changes, and performance benchmarks.
Markov State Models for Tracking Reaction Dynamics on Catalytic Nanoparticles
Journal of Chemical Theory and Computation · 2026-04-16
articleOpen accessMarkov state models (MSMs) are a powerful tool to analyze and coarse-grain complex dynamical data into interpretable kinetic processes. This capability is particularly important in heterogeneous catalysis, where a medley of reactants and intermediates interact on surfaces that might simultaneously experience structural fluctuations. For these very complex systems, standard transition state theory (TST) approaches are no longer appropriate, motivating alternative approaches that can retain dynamical complexity while providing physical insight. With machine-learned interatomic potentials being more and more ubiquitous, directly simulating complex catalytic systems with molecular dynamics (MD) is becoming increasingly feasible. Extending MSMs to dynamically coarse-grain MD simulation data of catalytic processes, we analyze hydrogen dynamics on rhodium catalysts with slab and nanoparticle geometries over a range of hydrogen surface concentrations. Nanoparticle features, such as corners and edges, effectively slow down the association/dissociation process, and the cooperative behavior of hydrogen-hydrogen interactions leads to a nonmonotonic concentration dependence of the rates, which would not be predicted with standard TST.
Size-Consistent Adiabatic Connection Functionals via Orbital-Based Matrix Interpolation
Journal of Chemical Theory and Computation · 2026-01-08 · 1 citations
articleSenior authorCorrespondingWe introduce a size-consistent and orbital-invariant formalism for constructing correlation functionals based on the adiabatic connection for density functional theory (DFT). By constructing correlation energy matrices for the weak and strong correlation limits in the space of occupied orbitals, our method, which we call orbital-based size-consistent matrix interpolation (OSMI), avoids previous difficulties in the construction of size-consistent adiabatic connection functionals. We design a simple, nonempirical adiabatic connection and a one-parameter strong-interaction limit functional, and we show that the resulting method reproduces the correlation energy of the uniform electron gas over a wide range of densities. When applied to subsets of the GMTKN55 thermochemistry database, OSMI is more accurate on average than MP2 and nonempirical density functionals. Most notably, OSMI provides excellent predictions of the barrier heights we tested, with average errors of less than 2 kcal mol–1. Finally, we find that OSMI improves the trade-off between fractional spin and fractional charge errors for bond dissociation curves compared to DFT and MP2. The fact that OSMI provides a good description of molecular systems and the uniform electron gas, while also maintaining low self-interaction error and size-consistency, suggests that it could provide a framework for studying heterogeneous chemical systems.
Markov State Models for Tracking Reaction Dynamics on Catalytic Nanoparticles
ArXiv.org · 2026-02-12
articleOpen accessMarkov state models (MSMs) are a powerful tool to analyze and coarse-grain complex dynamical data into interpretable kinetic processes. This capability is particularly important in heterogeneous catalysis, where a medley of reactants and intermediates interact on surfaces that might simultaneously experience structural fluctuations. For these very complex systems, standard transition state theory (TST) approaches are no longer appropriate, motivating alternative approaches that can retain dynamical complexity while providing physical insight. With machine learned interatomic potentials being more and more ubiquitous, directly simulating complex catalytic systems with molecular dynamics (MD) is becoming increasingly feasible. Extending MSMs to dynamically coarse grain MD simulation data of catalytic processes, we analyze hydrogen dynamics on rhodium catalysts with slab and nanoparticle geometries over a range of hydrogen surface concentrations. Somewhat counterintuitively, nanoparticle features, such as corners and edges, effectively slow down the association/dissociation process, and the cooperative behavior of hydrogen-hydrogen interactions leads to a non-monotonic concentration dependence of the rates, which would not be predicted with standard TST.
Practical and accurate density functionals for transition-metal heterogeneous catalysis
Open MIND · 2026-02-16
preprintSenior authorDensity functional theory (DFT) underpins modern atomistic simulations of transition-metal surfaces. It can predict key properties linked to catalytic performance, such as adsorption energies and barrier heights, enabling new paradigms in rational catalyst design. These applications require reliable density functionals, however achieving transition-metal chemical accuracy (13 kJ/mol) on these properties remains challenging. We introduce a framework for designing new functionals tailored to catalytic processes on transition-metal surfaces, building on recent non-self-consistent approaches. Within this framework, we develop a hybrid and a double-hybrid functional that achieve unprecedented accuracy, with the latter reaching transition-metal chemical accuracy on average across 39 experimental adsorption reactions. In addition, both functionals demonstrate balanced performance for 17 barrier heights and correct qualitative failures of standard functionals, including CO adsorption on Pt(111) and graphene on Ni(111). They are computationally efficient, readily integrated into existing DFT codes, and supported by open-source workflows to facilitate adoption. More broadly, this framework provides a systematic route towards improved functionals for heterogeneous catalysis and complex materials.
Markov State Models for Tracking Reaction Dynamics on Catalytic Nanoparticles
Open MIND · 2026-02-12
preprintMarkov state models (MSMs) are a powerful tool to analyze and coarse-grain complex dynamical data into interpretable kinetic processes. This capability is particularly important in heterogeneous catalysis, where a medley of reactants and intermediates interact on surfaces that might simultaneously experience structural fluctuations. For these very complex systems, standard transition state theory (TST) approaches are no longer appropriate, motivating alternative approaches that can retain dynamical complexity while providing physical insight. With machine learned interatomic potentials being more and more ubiquitous, directly simulating complex catalytic systems with molecular dynamics (MD) is becoming increasingly feasible. Extending MSMs to dynamically coarse grain MD simulation data of catalytic processes, we analyze hydrogen dynamics on rhodium catalysts with slab and nanoparticle geometries over a range of hydrogen surface concentrations. Somewhat counterintuitively, nanoparticle features, such as corners and edges, effectively slow down the association/dissociation process, and the cooperative behavior of hydrogen-hydrogen interactions leads to a non-monotonic concentration dependence of the rates, which would not be predicted with standard TST.
Practical and accurate density functionals for transition-metal heterogeneous catalysis
ArXiv.org · 2026-02-16
articleOpen accessSenior authorDensity functional theory (DFT) underpins modern atomistic simulations of transition-metal surfaces. It can predict key properties linked to catalytic performance, such as adsorption energies and barrier heights, enabling new paradigms in rational catalyst design. These applications require reliable density functionals, however achieving transition-metal chemical accuracy (13 kJ/mol) on these properties remains challenging. We introduce a framework for designing new functionals tailored to catalytic processes on transition-metal surfaces, building on recent non-self-consistent approaches. Within this framework, we develop a hybrid and a double-hybrid functional that achieve unprecedented accuracy, with the latter reaching transition-metal chemical accuracy on average across 39 experimental adsorption reactions. In addition, both functionals demonstrate balanced performance for 17 barrier heights and correct qualitative failures of standard functionals, including CO adsorption on Pt(111) and graphene on Ni(111). They are computationally efficient, readily integrated into existing DFT codes, and supported by open-source workflows to facilitate adoption. More broadly, this framework provides a systematic route towards improved functionals for heterogeneous catalysis and complex materials.
Strong anharmonicity dictates ultralow thermal conductivities of type-I clathrates
Physical review. B./Physical review. B · 2025-06-25 · 3 citations
articleSenior authorDiabatic States of Charge Transfer with Constrained Charge Equilibration
Journal of Chemical Theory and Computation · 2025-03-21 · 1 citations
articleSenior authorCorrespondingCharge transfer (CT) processes that are electronically nonadiabatic are ubiquitous in chemistry, biology, and materials science, but their theoretical description requires diabatic states or adiabatic excited states. For complex systems, these latter states are more difficult to calculate than the adiabatic ground state. Here, we propose a simple method to obtain diabatic states, including energies and charges, by constraining the atomic charges within the charge equilibration framework. For two-state systems, the exact diabatic coupling can be determined, from which the adiabatic excited-state energy can also be calculated. The method can be viewed as an affordable alternative to constrained density functional theory (CDFT), and so we call it constrained charge equilibration (CQEq). We test the CQEq method on the anthracene-tetracyanoethylene CT complex and the reductive decomposition of ethylene carbonate on a lithium metal surface. We find that CQEq predicts diabatic energies, charges, and adiabatic excitation energies in good agreement with CDFT, and we propose that CQEq is promising for combination with machine learning force fields to study nonadiabatic CT in the condensed phase.
Recent grants
Frequent coauthors
- 46 shared
Jonathan Weare
- 44 shared
Robert J. Webber
California Institute of Technology
- 43 shared
Hong‐Zhou Ye
Columbia University
- 34 shared
David R. Reichman
Columbia University
- 29 shared
Samuel M. Greene
- 28 shared
Tony F. Heinz
- 27 shared
Yeongsu Cho
- 26 shared
Alexey Chernikov
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