arXiv subjects

Markus Reiher

Publications and source records attributed to Markus Reiher.

At least 37 records · Page 2Linked to original sources

arXiv2025

QCMaquis 4.0: Multi-Purpose Electronic, Vibrational, and Vibronic Structure and Dynamics Calculations with the Density Matrix Renormalization Group

QCMaquis is a quantum chemistry software package for general molecular structure calculations in a matrix product state/matrix product operator formalism of the density matrix renormalization group (DMRG). It supports a wide range of features for electronic structure, multi-component (pre-Born-Oppenheimer), anharmonic vibrational structure, and vibronic calculations. In addition to the ground and excited state solvers, QCMaquis allows for time propagation of matrix product states based on the tangent-space formulation of time-dependent DMRG. The latest developments include transcorrelated electronic structure calculations, very recent vibrational and vibronic models, and a convenient Python wrapper, facilitating the interface with external libraries. This paper reviews all the new features of QCMaquis and demonstrates them with new results.

physics.comp-ph↗

arXiv2025

Molecular Similarity in Machine Learning of Energies in Chemical Reaction Networks

Machine learning has emerged as a powerful tool for predicting molecular properties in chemical reaction networks with reduced computational cost. However, accurately predicting energies of transition state (TS) structures remains a challenge due to their distinct electronic characteristics compared to stable intermediates. In this work, we investigate the limitations of structural descriptors in capturing electronic differences between minima and TS structures. We explore $Δ$-machine learning approaches to predict correlation energy corrections using both Hartree-Fock (HF) and density functional theory (DFT) as reference methods. Our results demonstrate that learning the energy difference between DFT and coupled cluster methods outperforms direct learning and HF-based $Δ$-learning. We also assess the effectiveness of combining electronic descriptors with structural ones but find that simple electronic features do not significantly enhance the prediction of TS energies. These findings highlight the need for more sophisticated descriptors or integrated approaches to accurately predict the electronic energies of TS structures within chemical reaction networks.

physics.chem-ph↗

arXiv2025

Machine Learning Enhanced Calculation of Quantum-Classical Binding Free Energies

Binding free energies are a key element in understanding and predicting the strength of protein--drug interactions. While classical free energy simulations yield good results for many purely organic ligands, drugs including transition metal atoms often require quantum chemical methods for an accurate description. We propose a general and automated workflow that samples the potential energy surface with hybrid quantum mechanics/molecular mechanics (QM/MM) calculations and trains a machine learning (ML) potential on the QM energies and forces to enable efficient alchemical free energy simulations. To represent systems including many different chemical elements efficiently and to account for the different description of QM and MM atoms, we propose an extension of element-embracing atom-centered symmetry functions for QM/MM data as an ML descriptor. The ML potential approach takes electrostatic embedding and long-range electrostatics into account. We demonstrate the applicability of the workflow on the well-studied protein--ligand complex of myeloid cell leukemia 1 and the inhibitor 19G and on the anti-cancer drug NKP1339 acting on the glucose-regulated protein 78.

physics.chem-ph↗

arXiv2025

Hierarchical quantum embedding by machine learning for large molecular assemblies

We present a quantum-in-quantum embedding strategy coupled to machine learning potentials to improve on the accuracy of quantum-classical hybrid models for the description of large molecules. In such hybrid models, relevant structural regions (such as those around reaction centers or pockets for binding of host molecules) can be described by a quantum model that is then embedded into a classical molecular-mechanics environment. However, this quantum region may become so large that only approximate electronic structure models are applicable. To then restore accuracy in the quantum description, we here introduce the concept of quantum cores within the quantum region that are amenable to accurate electronic structure models due to their limited size. Huzinaga-type projection-based embedding, for example, can deliver accurate electronic energies obtained with advanced electronic structure methods. The resulting total electronic energies are then fed into a transfer learning approach that efficiently exploits the higher-accuracy data to improve on a machine learning potential obtained for the original quantum-classical hybrid approach. We explore the potential of this approach in the context of a well-studied protein-ligand complex for which we calculate the free energy of binding using alchemical free energy and non-equilibrium switching simulations.

physics.chem-ph↗

arXiv2025

Complete Active Space Iterative Coupled Cluster Theory

In this work, we investigate the possibility of improving multireference-driven coupled cluster (CC) approaches with an algorithm that iteratively combines complete active space (CAS) calculations with tailored CC and externally corrected CC. This is accomplished by establishing a feedback loop between the CC and CAS parts of a calculation through similarity transformation of the Hamiltonian with those CC amplitudes that are not encompassed by the active space. We denote this approach the complete active space iterative coupled cluster (CASiCC) ansatz. We investigate its efficiency and accuracy in the singles and doubles approximation by studying the prototypical molecules H4, H8, H2O, and N2. Our results demonstrate that CASiCC systematically improves on the single-reference CCSD and the ecCCSD methods across entire potential energy curves, while retaining modest computational costs. However, the tailored coupled cluster method shows superior performance in the strong correlation regime suggesting that its accuracy is based on error compensation. We find that the iterative version of externally corrected and tailored coupled cluster methods converge to the same results.

physics.chem-ph↗

arXiv2025

Renormalized Internally-Contracted Multireference Coupled Cluster with Perturbative Triples

In this work, we combine the many-body formulation of the internally contracted multireference coupled cluster (ic-MRCC) method with Evangelista's multireference formulation of the driven similarity renormalization group (DSRG). The DSRG method can be viewed as a unitary multireference coupled cluster theory, which renormalizes the amplitudes based on a flow equation approach to eliminate numerical instabilities. We extend this approach by demonstrating that the unitary flow equation approach can be adapted for nonunitary transformations, rationalizing the renormalization of ic-MRCC amplitudes. We denote the new approach, the renormalized ic-MRCC (ric-MRCC) method. To achieve high accuracy with a reasonable computational cost, we introduce a new approximation to the Baker-Campbell-Hausdorff expansion. We fully consider the linear commutator while approximating the quadratic commutator, for which we neglect specific contractions involving amplitudes with active indices. Moreover, we introduce approximate perturbative triples to obtain the ric-MRCCSD[T] method. We demonstrate the accuracy of our approaches in comparison to advanced multireference methods for the potential energy curves of H8, F2, H2O, N2, and Cr2. Additionally, we show that ric-MRCCSD and ric-MRCSSD[T] match the accuracy of CCSD(T) for evaluating spectroscopic constants and of full configuration interaction energies for a set of small molecules.

physics.chem-ph↗

arXiv2025

Heron: Visualizing and Controlling Chemical Reaction Explorations and Networks

Automated and high-throughput quantum chemical investigations into chemical processes have become feasible in great detail and broad scope. This results in an increase in complexity of the tasks and in the amount of generated data. An efficient and intuitive way for an operator to interact with these data and to steer virtual experiments is required. Here, we introduce Heron, a graphical user interface that allows for advanced human-machine interactions with quantum chemical exploration campaigns into molecular structure and reactivity. Heron offers access to interactive and automated explorations of chemical reactions with standard electronic structure modules, haptic force feedback, microkinetic modeling, and refinement of data by automated correlated calculations including black-box complete active space calculations. It is tailored to the exploration and analysis of vast chemical reaction networks. We show how interoperable modules enable advanced workflows and pave the way for routine low-entrance-barrier access to advanced modeling techniques.

physics.chem-ph↗

arXiv2025

NEAR: A Training-Free Pre-Estimator of Machine Learning Model Performance

Artificial neural networks have been shown to be state-of-the-art machine learning models in a wide variety of applications, including natural language processing and image recognition. However, building a performant neural network is a laborious task and requires substantial computing power. Neural Architecture Search (NAS) addresses this issue by an automatic selection of the optimal network from a set of potential candidates. While many NAS methods still require training of (some) neural networks, zero-cost proxies promise to identify the optimal network without training. In this work, we propose the zero-cost proxy \textit{Network Expressivity by Activation Rank} (NEAR). It is based on the effective rank of the pre- and post-activation matrix, i.e., the values of a neural network layer before and after applying its activation function. We demonstrate the cutting-edge correlation between this network score and the model accuracy on NAS-Bench-101 and NATS-Bench-SSS/TSS. In addition, we present a simple approach to estimate the optimal layer sizes in multi-layer perceptrons. Furthermore, we show that this score can be utilized to select hyperparameters such as the activation function and the neural network weight initialization scheme.

cs.LG↗

arXiv2025

Non-iterative Triples for Transcorrelated Coupled Cluster Theory

We present an implementation of a perturbative triples correction for the coupled cluster ansatz including single and double excitations based on the transcorrelated Hamiltonian. Transcorrelation introduces explicit electron correlation in the electronic Hamiltonian through similarity transformation with a correlation factor. Due to this transformation, the transcorrelated Hamiltonian includes up to three-body couplings and becomes non-Hermitian. Since the conventional coupled cluster equations are solved by projection, it is well suited to harbor non-Hermitian Hamiltonians. The arising three-body operator, however, creates a huge memory bottleneck and increases the runtime scaling of the coupled cluster equations. As it has been shown that the three-body operator can be approximated, by expressing the Hamiltonian in the normal-ordered form, we investigate this approximation for the perturbative triples correction. Results are compared with a code-generation based transcorrelated coupled cluster implementation up to quadruple excitations.

physics.chem-ph↗

arXiv2025

High ground state overlap via quantum embedding methods

Quantum computers can accurately compute ground state energies using phase estimation, but this requires a guiding state that has significant overlap with the true ground state. For large molecules and extended materials, it becomes difficult to find guiding states with good ground state overlap for growing molecule sizes. Additionally, the required number of qubits and quantum gates may become prohibitively large. One approach for dealing with these challenges is to use a quantum embedding method, which allows a reduction to one or multiple smaller quantum cores embedded in a larger quantum region. In such situations it is unclear how the embedding method affects the hardness of constructing good guiding states. In this work, we therefore investigate the preparation of guiding states in the context of quantum embedding methods. We extend previous work on quantum impurity problems, a framework in which we can rigorously analyze the embedding of a subset of orbitals. While there exist results for optimal active orbital space selection in terms of energy minimization, we rigorously demonstrate how the same principles can be used to define selected orbital spaces for state preparation in terms of the overlap with the ground state. Moreover, we perform numerical studies of molecular systems relevant to biochemistry, one field in which quantum embedding methods are required due to the large size of biomacromolecules such as proteins and nucleic acids. We investigate two different embedding strategies which can exhibit qualitatively different orbital entanglement. In all cases we demonstrate that the easy-to-obtain mean-field state will have a sufficiently high overlap with the target state to perform quantum phase estimation.

quant-ph↗

arXiv2025

Automated Microsolvation for Minimum Energy Path Construction in Solution

Describing chemical reactions in solution on a molecular level is a challenging task due to the high mobility of weakly interacting solvent molecules which requires configurational sampling. For instance, polar and protic solvents can interact strongly with solutes and may interfere in reactions. However, to define and identify representative arrangements of solvent molecules modulating a transition state is a non-trivial task. Here, we propose to monitor their active participation in the decaying normal mode at a transition state, which defines active solvent molecules. Moreover, it is desirable to prepare a low-dimensional microsolvation model in a well-defined, fully automated, high-throughput, and easy-to-deploy fashion, which we propose to derive in a stepwise protocol. First, transition state structures are optimized in a sufficiently solvated quantum-classical hybrid model, which are then subjected to a re-definition of a then reduced quantum region. From the reduced model, minimally microsolvated structures are extracted that contain only active solvent molecules. Modeling the remaining solvation effects is deferred to a continuum model. To establish an easy-to-use free-energy model, we combine the standard thermochemical gas-phase model with a correction for the cavity entropy in solution. We assess our microsolvation and free-energy models for methanediol formation from formaldehyde, for the hydration of carbon dioxide (which we consider in a solvent mixture to demonstrate the versatility of our approach), and, finally, for the chlorination of phenol with hypochlorous acid.

physics.chem-ph↗

arXiv2024

More quantum chemistry with fewer qubits

Quantum computation is one of the most promising new paradigms for the simulation of physical systems composed of electrons and atomic nuclei, with applications in chemistry, solid-state physics, materials science, and molecular biology. This requires a truncated representation of the electronic structure Hamiltonian using a finite number of orbitals. While it is, in principle, obvious how to improve on the representation by including more orbitals, this is usually unfeasible in practice (e.g., because of the limited number of qubits available) and severely compromises the accuracy of the obtained results. Here, we propose a quantum algorithm that improves on the representation of the physical problem by virtue of second-order perturbation theory. In particular, our quantum algorithm evaluates the second-order energy correction through a series of time-evolution steps under the unperturbed Hamiltonian. An important application is to go beyond the active-space approximation, allowing to include corrections of virtual orbitals, known as multireference perturbation theory. Here, we exploit that the unperturbed Hamiltonian is diagonal for virtual orbitals and show that the number of qubits is independent of the number of virtual orbitals. This gives rise to more accurate energy estimates without increasing the number of qubits. Moreover, we demonstrate numerically for realistic chemical systems that the total runtime has highly favorable scaling in the number of virtual orbitals compared to previous work. Numerical calculations confirm the necessity of the multireference perturbation theory energy corrections to reach accurate ground state energy estimates. Our perturbation theory quantum algorithm can also be applied to symmetry-adapted perturbation theory. As such, we demonstrate that perturbation theory can help to reduce the quantum hardware requirements for quantum chemistry.

quant-ph↗

arXiv2024

Classification of electronic structures and state preparation for quantum computation of reaction chemistry

Quantum computation for chemical problems will require the construction of guiding states with sufficient overlap with a target state. Since easily available and initializable mean-field states are characterized by an overlap that is reduced for multi-configurational electronic structures and even vanishes with growing system size, we here investigate the severity of state preparation for reaction chemistry. We emphasize weaknesses in current traditional approaches (even for weakly correlated molecules) and highlight the advantage of quantum phase estimation algorithms. An important result is the introduction of a new classification scheme for electronic structures based on orbital entanglement information. We identify two categories of multi-configurational molecules. Whereas class-1 molecules are dominated by very few determinants and often found in reaction chemistry, class-2 molecules do not allow one to single out a reasonably sized number of important determinants. The latter are particularly hard for traditional approaches and an ultimate target for quantum computation. Some open-shell iron-sulfur clusters belong to class 2. We discuss the role of the molecular orbital basis set and show that true class-2 molecules remain in this class independent of the choice of the orbital basis, with the iron-molybdenum cofactor of nitrogenase being a prototypical example. We stress that class-2 molecules can be build in a systematic fashion from open-shell centers or unsaturated carbon atoms. Our key result is that it will always be possible to initialize a guiding state for chemical reaction chemistry in the ground state based on initial low-cost approximate electronic structure information, which is facilitated by the finite size of the atomistic structures to be considered.

physics.comp-ph↗

arXiv2024

SCINE -- Software for Chemical Interaction Networks

The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum chemical calculations on molecular structures to a new level. While calculations on individual structures as well as on simple relations between them e.g., as given by an intrinsic reaction coordinate) have become routine in chemistry, new developments have pushed the frontier in the field to high-throughput calculations. Chemical relations may be created by a search for specific molecular properties in a molecular design attempt or they can be defined by a set of elementary reaction steps that form a chemical reaction network. The software modules of SCINE have been designed to facilitate such studies. The features of the modules are (i) general applicability of the applied methodologies ranging from electronic structure (no restriction to specific elements of the periodic table) to microkinetic modeling (with little restrictions on molecularity), full modularity so that SCINE modules can also be applied as stand-alone programs or be exchanged for external software packages that fulfill a similar purpose (to increase options for computational campaigns and to provide alternatives in case of tasks that are hard or impossible to accomplish with certain programs), (ii) high stability and autonomous operations so that control and steering by an operator is as easy as possible, and (iii) easy embedding into complex heterogeneous environments for molecular structures taken individually or in the context of a reaction network. A graphical user interface unites all modules and ensures interoperability. All components of the software have been made available open source and free of charge.

physics.chem-ph↗

arXiv2024

Vibrational Entanglement through the Lens of Quantum Information Measures

We introduce a quantum information analysis of vibrational wave functions to understand complex vibrational spectra of molecules with strong anharmonic couplings and vibrational resonances. For this purpose, we define one- and two-modal entropies to guide the identification of strongly coupled vibrational modes and to characterize correlations within modal basis sets. We evaluate these descriptors for multi-configurational vibrational wave functions which we calculate with the n-mode vibrational density matrix renormalization group algorithm. Based on the quantum information measures, we present a vibrational entanglement analysis of the vibrational ground and excited states of CO2, which display strong anharmonic effects due to the symmetry-induced and accidental (near-) degeneracies. We investigate the entanglement signature of the Fermi resonance and discuss the maximally entangled state arising from the two degenerate bending modes.

physics.chem-ph↗

arXiv2024

Striking the Right Balance of Encoding Electron Correlation in the Hamiltonian and the Wavefunction Ansatz

Multi-configurational electronic structure theory delivers the most versatile approximations to many-electron wavefunctions, flexible enough to deal with all sorts of transformations, ranging from electronic excitations, to open-shell molecules and chemical reactions. Multi-configurational models are therefore essential to establish universally applicable, predictive ab initio methods for chemistry. Here, we present a discussion of explicit correlation approaches which address the nagging problem of dealing with static and dynamic electron correlation in multi-configurational active-space approaches. We review the latest developments and then point to their key obstacles. Our discussion is supported by new data obtained with tensor network methods. We argue in favor of simple electrons-only correlator expressions that may allow one to define transcorrelated models in which the correlator does not bear a dependence on molecular structure.

physics.chem-ph↗

arXiv2024

Automated Preparation of Nanoscopic Structures: Graph-Based Sequence Analysis, Mismatch Detection, and pH-Consistent Protonation with Uncertainty Estimates

Structure and function in nanoscale atomistic assemblies are tightly coupled, and every atom with its specific position and even every electron will have a decisive effect on the electronic structure, and hence, on the molecular properties. Molecular simulations of nanoscopic atomistic structures therefore require accurately resolved three-dimensional input structures. If extracted from experiment, these structures often suffer from severe uncertainties, of which the lack of information on hydrogen atoms is a prominent example. Hence, experimental structures require careful review and curation, which is a time-consuming and error-prone process. Here, we present a fast and robust protocol for the automated structure analysis, and pH-consistent protonation, in short, ASAP. For biomolecules as a target, the ASAP protocol integrates sequence analysis and error assessment of a given input structure. ASAP allows for pKa prediction from reference data through Gaussian process regression including uncertainty estimation and connects to system-focused atomistic modeling described in (J. Chem. Theory Comput. 16, 2020, 1646). Although focused on biomolecules, ASAP can be extended to other nanoscopic objects, because most of its design elements rely on a general graph-based foundation guaranteeing transferability. The modular character of the underlying pipeline supports different degrees of automation, which allows for (i) efficient feedback loops for human-machine interaction with a low entrance barrier and for (ii) integration into autonomous procedures such as automated force field parametrizations. This facilitates fast switching of the pH-state through on-the-fly system-focused reparametrization during a molecular simulation at virtually no extra computational cost.

physics.chem-ph↗

arXiv2024

CoRe Optimizer: An All-in-One Solution for Machine Learning

The optimization algorithm and its hyperparameters can significantly affect the training speed and resulting model accuracy in machine learning applications. The wish list for an ideal optimizer includes fast and smooth convergence to low error, low computational demand, and general applicability. Our recently introduced continual resilient (CoRe) optimizer has shown superior performance compared to other state-of-the-art first-order gradient-based optimizers for training lifelong machine learning potentials. In this work we provide an extensive performance comparison of the CoRe optimizer and nine other optimization algorithms including the Adam optimizer and resilient backpropagation (RPROP) for diverse machine learning tasks. We analyze the influence of different hyperparameters and provide generally applicable values. The CoRe optimizer yields best or competitive performance in every investigated application, while only one hyperparameter needs to be changed depending on mini-batch or batch learning.

cs.LG↗