arXiv subjects

Todd J. Martínez

Publications and source records attributed to Todd J. Martínez.

At least 19 recordsLinked to original sources

arXiv2026

libterachem.py: Modular development of electronic structure methods with graphical processing units

We present libterachem.py, a Python interface and method framework that facilitates development and prototyping of electronic structure methods while leveraging TeraChem's optimized graphical processing unit (GPU) operations. Direct access to these building blocks and their intermediate quantities allows users to assemble and modify methods within Python while reusing the underlying GPU implementations. A layered architecture, programmable at both the operation level and the method level, supports numerical experimentation, composition of complete electronic structure methods with interchangeable components, and integration with external scientific libraries. We illustrate operation-level use with grid pruning for least-squares tensor hypercontraction and with exchange--correlation functionals supplied through LibXC and by the machine-learned Skala functional. We illustrate method-level use with dispersion corrections, periodic calculations, and geometry optimization with an external optimizer. Python-driven self-consistent-field calculations using libterachem.py incur no significant computational overhead compared to native TeraChem and preserve its multi-GPU scaling. A photoactive yellow protein QM/MM molecular dynamics application further demonstrates throughput comparable to native TeraChem in a workflow composed with external simulation libraries. These results establish libterachem.py as a platform for method development and interoperable molecular simulation that retains the performance of TeraChem's GPU operations.

physics.chem-ph↗

arXiv2026

Latent unified smooth Hamiltonians for excited state chemistry

We describe a neural network architecture and training procedure designed to model electronic ground and excited states of arbitrary molecular systems. By indirectly learning a latent, implicit basis representation of the electronic-state Hamiltonian, the model offers a unified treatment of multiple electronic states, conical intersections, and non-adiabatic couplings. The formalism can be further extended to learn consistent latent representations of additional operators such as transition dipole moments, for example. To demonstrate the general capabilities of our architecture, we train and evaluate networks on two realistic photochemical systems, thymine and azobenzene. The resulting models accurately reproduce energies and oscillator strengths for the ground- and low-lying excited states relevant to the photochemistry of these systems. We highlight the performance of the trained networks by studying critical molecular geometries, including conical intersections and excited state minima. By construction, the proposed framework also recovers the emergence of Berry phase accumulation around conical intersections. By pairing key mathematical structure from quantum chemistry with the representation learning power of transformers, the presented architecture offers a qualitatively new path toward fast and accurate ground- and excited-state simulations.

physics.chem-ph↗

arXiv2026

Spectroscopic photorelaxation signatures in pyrazine from nonadiabatic dynamics simulations with coupled cluster theory

Despite extensive theoretical and experimental efforts, the mechanisms underlying the ultrafast relaxation of pyrazine after photoexcitation remain challenging to disentangle. Recently, theoretical investigations have been converging towards a three-state mechanism, with an ultrafast decay of the bright ${}^{1}B_{2u}$ state followed by beats in the populations of the low-lying ${}^{1}B_{3u}$ and ${}^{1}A_u$ states. However, a clear agreement between the experimental results and the corresponding theoretical predictions remains elusive. Here, we present a high-level simulation of the ultrafast excited states dynamics of pyrazine using coupled cluster theory with single and double excitations and ab initio multiple spawning, together with predictions of the time-resolved photoelectron spectrum and X-ray absorption spectra at the nitrogen and carbon edges. This is made possible by using a newly developed multistate implementation of similarity constrained coupled cluster theory. We find quantitative agreement with the experimental signature of the ${}^{1}B_{2u}$ decay in the photoelectron spectrum, and qualitative agreement with the available experimental X-ray absorption spectra. Moreover, we detail spectroscopic signatures that should be verifiable in experiments with sufficient resolution in the time and frequency domains. Compared to previous theoretical studies, we provide further detailed insight into the interplay of the states involved in the photorelaxation.

physics.chem-ph↗

arXiv2026

Perspective on a challenge: predicting the photochemistry of cyclobutanone

This Perspective is part of a Special Topic that explored the maturity of nonadiabatic molecular dynamics for predicting photochemical processes. In 2023, a prediction challenge was issued to the community of computational photochemists to simulate the photochemistry of cyclobutanone, photoexcited at 200 nm, and the resulting time-resolved MeV-UED signal. The challenge attracted 15 theoretical predictions from more than 70 researchers, employing a wide range of strategies for electronic structure and nonadiabatic molecular dynamics to predict the time-resolved MeV-UED signal before the experiment had been conducted at SLAC (Stanford, USA). The MeV-UED instrument at Shanghai Jiao Tong University was also used to provide a second independent time-resolved MeV-UED signal for the photochemistry of cyclobutanone. This Perspective discusses the various approaches and strategies used by the participants to predict the photochemistry of cyclobutanone. This work also summarizes the strengths and weaknesses of various methods used for photoexcitation, electronic structure, nonadiabatic dynamics, and calculation of observables, as agreed by the participants during a CECAM workshop dedicated to the results of the challenge and organized in Lausanne in April 2025. This Perspective also collects all the predicted time-resolved MeV-UED signals into a single figure, together with the experimental signal. This challenge (i) demonstrated the qualitative predictive power of nonadiabatic molecular dynamics and (ii) underscore the impact of electronic-structure theory on the outcome of the excited-state dynamics and the need for its careful benchmarking. This effort allowed the community to share practical strategies to perform nonadiabatic dynamics (discussed in the present Perspective) and constitutes a 'calibration' exercise for computational photochemistry.

physics.chem-ph↗

arXiv2026

Non-Negative Least Squares Reweighting and Pruning of Quadrature Grids for Tensor Hypercontraction

Tensor hypercontraction provides an attractive four-center two-electron repulsion integral format that can lower the scaling of many electronic structure methods while only requiring O(N^2) memory. However, in its grid-based least-squares incarnation, tensor hypercontraction requires the tedious design of compact spatial quadrature grids to achieve efficiency and accuracy, representing a bottleneck for widespread application. To simplify grid generation, we devise a reweighting scheme in which the grid weights are optimized to ensure accurate reproduction of the atomic orbital overlap matrix by numerical integration. By casting this fitting task as a non-negative least-squares problem, we obtain a black-box methodology that not only yields robust grids for tensor hypercontraction as well as numerical integration of other integrals but also prunes the grids by zeroing quadrature weights for insignificant points.

physics.chem-ph↗

arXiv2025

Accelerating CCSD(T) on Graphical Processing Units (GPUs)

Coupled cluster with singles, doubles and perturbative triples (CCSD(T)) often provides ground state correlation energies within "chemical accuracy," but suffers from high computational cost and steep scaling with system size. We present a GPU-accelerated implementation of CCSD(T) in the TeraChem software package. The new implementation achieves state-of-the-art performance, enabling the calculation of the (T) correction for a system with 63 atoms and more than 1000 basis functions in a little under 8 hours on a single node. Additionally, we demonstrate the utility of our optimized implementation for the rapid calculation of full CCSD(T)/CBS stacking energies for all ten unique DNA base pair stacked tetramers. We expect that the TeraChem CCSD(T) implementation will enable the rapid calculation of high-level data that was not previously accessible in a reasonable timeframe.

physics.chem-ph↗

arXiv2025

Accelerating Hartree-Fock and Density Functional Theory Calculations using Tensor Hypercontraction

With the widespread use of self-consistent field methods, including Hartree-Fock and Density Functional Theory, the implications of accelerating these methods are immense. To this end, we develop a tensor hypercontraction construction with $O(N^3)$ formal scaling that can accelerate self-consistent field calculations. Using tensor hypercontraction, we implement an empirically $O(N^2)$ scaling Fock matrix construction that is 2-4$\times$ faster than existing integral-direct methods, as it avoids the repeated recalculation of two-electron repulsion integrals. In combination with a density-difference ansatz, our tensor hypercontraction self-consistent field implementation tests show errors below $7.0 x 10^{-3} E_h$ for relative energies on protein systems containing up to 3000 basis functions.

physics.chem-ph↗

arXiv2025

Shadow excited state molecular dynamics with the \DeltaSCF method

We present an extension of the shadow extended Lagrangian Born-Oppenheimer molecular dynamics (XL-BOMD) method to excited state molecular dynamics (ESMD) in the context of \DeltaSCF Kohn-Sham density functional theory, with demonstrations performed using self-consistent charge density functional tight binding (SCC-DFTB) theory. In this shadow ESMD approach, the approximate iterative solution to the exact potential in conventional ESMD is replaced by an exact single-step solution to an approximate shadow excited-state potential. We show that in addition to offering significant improvement in computational cost relative to direct ESMD, our shadow ESMD method provides enhanced stability and robustness relative to its 'exact' counterpart. Our implementation is carried out in the context of SCC-DFTB theory but should be broadly generalizable, both to {\textit{ab initio}} electronic structure methods and to other semi-empirical quantum chemistry approaches.

physics.chem-ph↗

arXiv2025

Locating Ab Initio Transition States via Approximate Geodesics on Machine Learned Potential Energy Surfaces

Efficient and reliable identification and optimization of transition state structures is a longstanding challenge in computational chemistry. Popular chain-of-states methods require hundreds if not thousands of ab initio calculations to generate initial guesses for local quasi-Newton optimizers, with persistent risk of collapse to an alternative stationary point on the potential energy surface (PES). Here, we show that high-quality guess structures for transition state optimization can be obtained by constructing the geodesic path between reactant and product structures on the PES generated by machine learning potentials (MLPs). We present an algorithm for optimization of such geodesic paths, as well as the associated codebase. We demonstrate effectiveness of this approach using the recent eSEN-sm-cons MLP. On average, the highest-energy point along these MLP geodesics requires 30% fewer quasi-Newton optimization steps to converge to the transition state compared to guesses from the fully ab initio frozen string method. Our approach therefore completely eliminates the need for ab initio calculations for generation of transition state guesses and considerably speeds up subsequent structural optimization. Geodesic construction on ML PES thus promises to be a useful approach for efficient computational elucidation of complex chemical reaction networks.

physics.chem-ph↗

arXiv2024

Fast and Scalable GPU-Accelerated Quantum Chemistry for Periodic Systems with Gaussian Orbitals: Implementation and Hybrid Density Functional Theory Calculations

Efficient hybrid DFT simulations of solid state materials would be extremely beneficial for computational chemistry and materials science, but is presently bottlenecked by difficulties in computing Hartree-Fock (HF) exchange with plane wave orbital bases. We present a GPU-accelerated, Gaussian orbital based integral algorithm for systems with periodic boundary conditions, which takes advantage of Ewald summation to efficiently compute electrostatic interactions. We have implemented this approach into the TeraChem software package within the $Γ$ point approximation, enabling simulation of unit cells with hundreds or thousands of atoms at the HF or hybrid DFT level on a single GPU card. Our implementation readily parallelizes over multiple GPUs and paves the road to accurate simulation of the properties and dynamics of extended materials in both the ground and excited states.

physics.chem-ph↗

arXiv2024

Extending GPU-Accelerated Gaussian Integrals in the TeraChem Software Package to f Type Orbitals: Implementation and Applications

The increasing availability of GPUs for scientific computing has prompted interest in accelerating quantum chemical calculations through their use. The complexity of integral kernels for high angular momentum basis functions however often limits the utility of GPU implementations with large basis sets or for metal containing systems. In this work, we report implementation of $f$ function support in the GPU-accelerated TeraChem software package through the development of efficient kernels for the evaluation of Hamiltonian integrals. The high efficiency of the resulting code is demonstrated through density functional theory (DFT) calculations on increasingly large organic molecules and transition metal complexes, as well as coupled cluster singles and doubles (CCSD) calculations on water clusters. Preliminary investigations into Ni(I) catalysis with DFT and the photochemistry of MnH(CH$_3$) with complete active space self-consistent field (CASSCF) are also carried out. Overall, our GPU-accelerated software appears to be well-suited for fast simulation of large transition metal containing systems, as well as organic molecules.

physics.chem-ph↗

arXiv2024

Attosecond Probing of Coherent Vibrational Dynamics in CBr$_4$

A coherent vibrational wavepacket is launched and manipulated in the symmetric stretch (a$_1$) mode of CBr$_4$, by impulsive stimulated Raman scattering from non-resonant 400 nm laser pump pulses with various peak intensities on the order of tens of 10$^{12}$ W/cm$^2$. Extreme ultraviolet (XUV) attosecond transient absorption spectroscopy (ATAS) records the wavepacket dynamics as temporal oscillations in XUV absorption energy at the bromine M$_{4,5}$ 3d$_{3/2,5/2}$ edges around 70 eV. The results are augmented by nuclear time-dependent Schrödinger equation simulations. Slopes of the (Br-3d$_{3/2,5/2}$)$^{-1}$10a$_1^*$ core-excited state potential energy surface (PES) along the a$_1$ mode are calculated to be -9.4 eV/Å from restricted open-shell Kohn-Sham calculations. Using analytical relations derived for the small-displacement limit with the calculated slopes of the core-excited state PES, a deeper insight into the vibrational dynamics is obtained by retrieving the experimental excursion amplitude of the vibrational wavepacket and the amount of population transferred to the vibrational first-excited state, as a function of pump-pulse peak intensity. Experimentally, the results show that XUV ATAS is capable of easily resolving oscillations in the XUV absorption energy on the order of few to tens of meV and tens of femtosecond time precision, limited only by the averaging times in the experimental scans. This corresponds to oscillations of C-Br bond length on the order of 10$^{-4}$ to 10$^{-3}$ Å. The results and the analytic relationships offer a clear physical picture, on multiple levels of understanding, for how the pump-pulse intensity controls the vibrational dynamics launched by non-resonant ISRS in the small-displacement limit.

physics.chem-ph↗

arXiv2024

Unexpected hydrogen dissociation in thymine: predictions from a novel coupled cluster theory

The fate of thymine upon excitation by ultraviolet radiation has been the subject of intense debate over the past three decades. Today, it is widely believed that its ultrafast excited state decay stems from a radiationless transition from the bright $ππ^*$ state to a dark $nπ^*$ state. However, conflicting theoretical predictions have made the experimental data difficult to interpret. Here we simulate the ultrafast dynamics in thymine at the highest level of theory to date, performing wavepacket dynamics with a new coupled cluster method. Our simulation confirms an ultrafast $ππ^*$ to $nπ^*$ transition ($τ = 41 \pm 14$ fs). Furthermore, the predicted oxygen-edge X-ray absorption spectra agree quantitatively with the experimental results. Our simulation also predicts an as-yet uncharacterized photochemical pathway: a $πσ^*$ channel that leads to hydrogen dissociation at one of the two N-H bonds in thymine. Similar behavior has been identified in other heteroaromatic compounds, including adenine, and several authors have speculated that a similar pathway may exist in thymine. However, this was never confirmed theoretically or experimentally. This prediction calls for renewed efforts to experimentally identify or exclude the presence of this channel.

physics.chem-ph↗

arXiv2022

Rehybridization dynamics into the pericyclic minimum of an electrcyclic reaction imaged in real-time

Electrocyclic reactions are characterized by the concerted formation and cleavage of both σ and π bonds through a cyclic structure. This structure is known as a pericyclic transition state for thermal reactions and a pericyclic minimum in the excited state for photochemical reactions. However, the structure of the pericyclic geometry has yet to be observed experimentally. We use a combination of ultrafast electron diffraction and excited state wavepacket simulations to image structural dynamics through the pericyclic minimum of a photochemical electrocyclic ring-opening reaction in the molecule α-terpinene. The structural motion into the pericyclic minimum is dominated by rehybridization of two carbon atoms, which is required for the transformation from two to three conjugated π bonds. The σ bond dissociation largely happens after internal conversion from the pericyclic minimum to the electronic ground state. These findings may be transferrable to electrocyclic reactions in general.

physics.chem-ph↗

arXiv2018

Reaction dynamics of cyanohydrins with hydrosulfide in water

We studied the reaction dynamics of a proposed prebiotic reaction theoretically. The chemical process involves acetone cyanohydrin or formalcyanohydrin reacting with hydrosulfide in an aqueous environment. Rate constants and populations of reactant and product bimolecular geometric orientations for the reactions were obtained by using density functional theory for the energies, transition state theory for the rates and matrix exponentiation as well as the hybrid tau-leaping algorithm for the population dynamics. The role of including the solvent explicitly versus implicitly was also investigated. We found that adding water or hydrogen sulfide molecules explicitly lowers the activation energy barrier and leads to a more efficient reaction pathway. In particular, hydrogen sulfide was a better proton donor. Further, when adding the solvent explicitly a synchronous reaction mechanism was observed while a concerted reaction mechanism was seen when using an implicit solvent model. Finally, we studied the role of including more than one reactant and product bimolecular orientation geometry in the dynamics. Including all pathways, reactant to reactant, product to product, reactant to product and product to reactant reduced the reaction half-time by two orders of magnitude and was therefore determined to be fundamental for an accurate description of the dynamics. Overall, we found that most reactions which involve formalcyanohydrin occur more rapidly or at the same speed as reactions which involve acetone cyanohydrin at room temperature.

physics.chem-ph↗

arXiv2015

Quantum Chemistry for Solvated Molecules on Graphical Processing Units (GPUs)using Polarizable Continuum Models

The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale biomolecular systems can be limited by computational expense of both the gas phase electronic structure and the solvation interaction. We have previously used graphical processing units (GPUs) to accelerate the first of these steps. Here, we extend the use of GPUs to accelerate electronic structure calculations including C-PCM solvation. Implementation on the GPU leads to significant acceleration of the generation of the required integrals for C-PCM. We further propose two strategies to improve the solution of the required linear equations: a dynamic convergence threshold and a randomized block-Jacobi preconditioner. These strategies are not specific to GPUs and are expected to be beneficial for both CPU and GPU implementations. We benchmark the performance of the new implementation using over 20 small proteins in solvent environment. Using a single GPU, our method evaluates the C-PCM related integrals and their derivatives more than 10X faster than a conventional CPU based implementation. Our improvements to the linear solver provide a further 3X acceleration. The overall calculations including C-PCM solvation require typically 20-40% more effort than their gas phase counterparts for moderate basis set and molecule surface discretization level. The relative cost of the C-PCM solvation correction decreases as the basis sets and/or cavity radii increase. Therefore description of solvation with this model should be routine. We also discuss applications to the study of the conformational landscape of an amyloid fibril.

physics.chem-ph↗

arXiv2013

Relation of exact Gaussian basis methods to the dephasing representation: Theory and application to time-resolved electronic spectra

We recently showed that the Dephasing Representation (DR) provides an efficient tool for computing ultrafast electronic spectra and that further acceleration is possible with cellularization [M. Šulc and J. Vaníček, Mol. Phys. 110, 945 (2012)]. Here we focus on increasing the accuracy of this approximation by first implementing an exact Gaussian basis method, which benefits from the accuracy of quantum dynamics and efficiency of classical dynamics. Starting from this exact method, the DR is derived together with ten other methods for computing time-resolved spectra with intermediate accuracy and efficiency. These methods include the Gaussian DR, an exact generalization of the DR, in which trajectories are replaced by communicating frozen Gaussian basis functions evolving classically with an average Hamiltonian. The newly obtained methods are tested numerically on time correlation functions and time-resolved stimulated emission spectra in the harmonic potential, pyrazine S0/S1 model, and quartic oscillator. Numerical results confirm that both the Gaussian basis method and the Gaussian DR increase the accuracy of the DR. Surprisingly, in chaotic systems the Gaussian DR can outperform the presumably more accurate Gaussian basis method, in which the two bases are evolved separately.

physics.chem-ph↗

arXiv2009

A note on the role of charge conservation in electronegativity equalization and its implications for the translational symmetries of electrostatic properties in fluctuating-charge models

An analytical solution of fluctuating-charge models using Gaussian elimination allows us to isolate the contribution of charge conservation effects in determining the charge distribution. We use this analytical solution to calculate dipole moments and polarizabilities and show that charge conservation plays a critical role in maintaining the correct translational properties of the electrostatic properties predicted by these models.

physics.chem-ph↗