arXiv subjects

Elvar Ö. Jónsson

Publications and source records attributed to Elvar Ö. Jónsson.

14 recordsLinked to original sources

arXiv2026

Polaron Conductivity in $α$-Fe2O3 Quenched by Adsorbed NO2

Polaron-mediated charge transport in α-Fe2O3 plays a central role in its performance as a gas-sensing material, yet the atomistic interaction between surface adsorbates and polarons remains insufficiently understood. Here, density functional theory with Hubbard-U correction (DFT+U) combined with nudged elastic band calculations is used to investigate polaron formation, migration, and quenching at the Fe-terminated α-Fe2O3 (0001) surface. The calculated activation energy for small-polaron hopping in bulk α-Fe2O3 is found to be 0.12 eV, in excellent agreement with experimental measurements, confirming the validity of the computational approach. Slab calculations show that migration of the polaron from bulk to the surface lowers the energy by 0.12 eV, indicating preferential localization of charge carriers at the gas-solid interface. Adsorption of NO2 induces substantial electron transfer (0.72 e-) from the oxide to the molecule, eliminating the localized Fe2+ polaron state and thereby suppressing polaronic conductivity. These results provide a direct microscopic explanation for the resistance increase of hematite-based sensors upon exposure to oxidizing gases. More broadly, the study establishes how surface adsorption can modulate charge transport α-Fe2O3 through control of polaron populations, offering design principles for improved iron oxide gas sensors.

cond-mat.mtrl-sci↗

arXiv2026

ChemFit: A framework for automated high-dimensional model parameter optimization

The parameterization of simulation-based models is a central yet laborious task in computational chemistry and physics, often driven by human intuition and manual iteration. Automating this task necessitates the definition of suitable objective functions, which tend to be expensive to evaluate, noisy, non-differentiable, or composed of heterogeneous contributions originating from separate sets of simulations. Gradient-free and black-box optimization algorithms are powerful tools which are particularly well-suited to minimizing such objective functions. Here, we introduce ChemFit, a flexible Python framework for the definition, composition, and massively concurrent evaluation of simulation-based objective functions, which is designed to operate in conjunction with these algorithms. We demonstrate the broad applicability of this approach by using ChemFit for three representative examples of increasing complexity and real-world relevance. First, we obtain the parameters of the Lennard-Jones potential for liquid argon from experimental measurements of the density. Second, we parameterize a polarizable and flexible potential energy function to reproduce the structure of small H$_2$O clusters obtained from density functional theory calculations. Finally, we tune a small subset of the parameters of a residue-level coarse-grained protein force-field, with the goal to reproduce the experimental critical solution temperature of the low complexity domain of the wild-type hnRNPA1 sequence and an arginine-enriched mutant of this protein. hnRNPA1 is an RNA-binding protein linked to amyotrophic lateral sclerosis. Together, these examples illustrate how ChemFit enables scalable, reproducible, and optimizer-agnostic parameter fitting for broadly applicable multiscale models.

physics.chem-ph↗

arXiv2026

Orbital Optimization and Neural-Network-Assisted Configuration Interaction Calculations of Rydberg States

Rydberg excited states of molecules pose a challenge for electronic structure calculations because of their highly diffuse electron distribution. Even large and elaborate atomic basis sets tend to underrepresent the long-range tail, overly confining the Rydberg state. An approach is presented here where the molecular orbitals are variationally optimized for the excited state using a plane wave basis set in a Hartree-Fock calculation, followed by a configuration interaction calculation. The use of excited state optimized orbitals greatly enhances the convergence of the many-body calculation, as illustrated by a full configuration interaction calculation of the $2s$ Rydberg state of H$_2$. A neural-network-based selective configuration interaction approach is then applied to calculations of $3s$ and $3p$ states of H$_2$O and NH$_3$. The obtained values of excitation energy are in close agreement with experimental measurements as well as previous many-body calculations where sufficiently diffuse atomic basis sets were used. Calculations using atomic basis sets lacking extra diffuse functions, such as aug-cc-pVTZ, give significantly higher estimates due to confinement of the Rydberg states.

physics.chem-ph↗

arXiv2025

Natural-Orbital-Based Neural Network Configuration Interaction

Selective configuration interaction methods approximate correlated molecular ground- and excited states by considering only the most relevant Slater determinants in the expansion. While a recently proposed neural-network-assisted approach efficiently identifies such determinants, the procedure typically relies on canonical Hartree-Fock orbitals, which are optimized only at the mean-field level. Here we assess approximate natural orbitals - eigenfunctions of the one-particle density matrix computed from intermediate many-body eigenstates - as an alternative. Across our benchmarks for H$_2$O, NH$_3$, CO, and C$_3$H$_8$ we see a consistent reduction in the required determinants for a given accuracy of the computed correlation energy compared to full configuration interaction calculations. Our results confirm that even approximate natural orbitals constitute a simple yet powerful strategy to enhance the efficiency of neural-network-assisted configuration interaction calculations.

physics.chem-ph↗

arXiv2025

Multiple Adsorption of CO Molecules on Transition Metal Substitutional Impurities in Copper Surfaces

Copper-based catalysts are of particular interest for electrochemical reduction of CO$_2$ (CO2RR) as products beyond CO can form. To improve activity and selectivity, several studies have focused on the addition of other elements as substitutional impurities. Although the adsorption of a single CO molecule has often been used as a descriptor for CO2RR activity, our recent calculations using the RPBE functional showed that multiple CO molecules can bind to first-row transition metal impurities. Here, we extend the study to second-row transition metals and also to a functional that explicitly includes dispersion interaction, BEEF-vdW. The binding energy of the first CO molecule on the impurity atom is found to be significantly larger than on the clean Cu(111) and Cu(100) surfaces, but the differential binding energy generally drops as more CO molecules adsorb. The dispersion interaction is found to make a significant contribution to the binding energy, in particular for the last and weakest bound CO molecule, the one that is most likely to participate in CO2RR. In some cases, four CO admolecules can bind more strongly on the impurity atom than on the clean copper surface. The adsorption of CO causes the position of the impurity atom to shift outwards and in some cases, even escape from the surface layer. The C-O stretch frequencies are calculated in order to identify possible experimental signatures of multiple CO adsorption.

cond-mat.mtrl-sci↗

arXiv2025

Localised and Delocalised Charge Distribution in a Diamine Cation and Rydberg Excited State: A Challenging Test for Density Functionals

The balance between localised and delocalised electron distribution in the N,N'-dimethylpiperazine (DMP) molecule in the 3s Rydberg excited state and in the fully ionised DMP$^+$ provides a valuable test of density functionals, in particular the weight of Fock exchange (FE) in hybrid functionals and the scaling of explicit orbital-based self-interaction correction (SIC) applied to less elaborate functionals. We present results of calculations using density functionals of all rungs of Jacob's ladder, ranging from LDA to the DM21 machine learned local hybrid as well as double hybrids. For DMP$^+$, the commonly used hybrid functionals, such as PBE0(.25) with FE weight of 0.25, as well as PBE0(.32) with a weight of 0.32 only produce the more delocalised charge. The latter mimics the DM21 energy surface well. However, hybrid functionals with stronger FE, such as BHLYP and PBE0(.50) as well as some double hybrid functionals, also produce local energy minima corresponding to localised charge. When full SIC is applied to the PBE functional, an energy surface analogous to hybrid functionals with FE weight of 0.50 is obtained, while the scaling of SIC by 0.50, which has previously been shown to give improved atomisation energy and band gap of solids, only produces the more delocalised charge. For the 3s Rydberg excited state of DMP, two types of configurations with a localised hole are obtained in calculations using the PBE0(.32) functional, in addition to the delocalised hole, but only the latter is found with the PBE functional, showing that a significant reduction of the self-interaction error is needed in order to obtain agreement between density functional calculations and experimental measurements of the Rydberg state

physics.chem-ph↗

arXiv2025

Single Atom Substituents in Copper Surfaces May Adsorb Multiple CO Molecules

Copper is a good CO2 electroreduction catalyst as products beyond CO form, but efficiency and selectivity is low. Experiments have shown that admixture of other elements can help, and computational screening studies have pointed out various promising candidates based on the adsorption of a single CO molecule as a descriptor. Our calculations of CO adsorption on surfaces where a first row transition metal atom replaces a Cu atom show that multiple CO molecules, not just one, bind to the substitutional atom. For Fe, Co, and Ni atoms, a decrease in binding energy is found, but the reverse trend, namely increasing bond strength, is found for V, Cr, and Mn and the first three CO molecules. Magnetic moment, charge, and position of the substitutional atom are also strongly affected by the CO adsorption in most cases. Magnetic moment is stepwise reduced to zero, and the outward displacement of the substitutional atom increased.

cond-mat.mtrl-sci↗

arXiv2025

A Neural-Network-Based Selective Configuration Interaction Approach to Molecular Electronic Structure

By combining Hartree-Fock with a neural-network-supported quantum-cluster solver proposed recently in the context of solid-state lattice models, we formulate a scheme for selective neural-network configuration interaction (NNCI) calculations and implement it with various options for the type of basis set and boundary conditions. The method's performance is evaluated in studies of several small molecules as a step toward calculations of larger systems. In particular, the correlation energy in the N$_2$ molecule is compared with published full CI calculations that included nearly $10^{10}$ Slater determinants, and the results are reproduced with only $4\cdot10^{5}$ determinants using NNCI. A clear advantage is seen from increasing the set of orbitals included rather than approaching full CI for a smaller set. The method's high efficiency and implementation in a condensed matter simulation software expands the applicability of CI calculations to a wider range of problems, even extended systems through an embedding approach.

physics.chem-ph↗

arXiv2024

Evidence of sharp transitions between octahedral and capped trigonal prism states of the solvation shell of Fe$^{+3}$(aq)

The structure of the solvation shell of aqueous Fe$^{+3}$ ion has been a subject of controversy due to discrepancies between experiments and different levels of theory. We address this issue by performing simulations for a wide range of ion concentrations, using various empirical potential energy functions, as well as density functional theory calculations of selected configurations. The solvation shell undergoes abrupt transitions between two states: an octahedral (OH) state with 6-fold coordination, and a capped trigonal prism (CTP) state with 7-fold coordination. The lifetime of these states is concentration dependent. In dilute $\mathrm{FeCl_3}$ solutions, the lifetime of the two states is similar ($\approx 1$ ns). However, the lifetime of the OH state increases with ion concentration, while that of the CTP state decreases slightly. When a uniform negative background charge is used instead of explicit counterions, the lifetime of the OH state is greatly overestimated. These findings underscore the need for further experimental measurements as well as high-level simulations over sufficiently long timescales and low concentration.

physics.chem-ph↗

arXiv2023

Variational Density Functional Calculations of Excited States: Conical Intersection and Avoided Crossing in Ethylene Bond Twisting

Theoretical studies of photochemical processes require a description of the energy surfaces of excited electronic states, especially near degeneracies, where transitions between states are most likely. Systems relevant to photochemical applications are typically too large for high-level multireference methods, and while time-dependent density functional theory (TDDFT) is efficient, it can fail to provide the required accuracy. A variational, time-independent density functional approach is applied to the twisting of the double bond and pyramidal distortion in ethylene, the quintessential model for photochemical studies. By allowing for symmetry breaking, the calculated energy surfaces exhibit the correct topology around the twisted-pyramidalized conical intersection even when using a semilocal functional approximation, and by including explicit self-interaction correction, the torsional energy curves are in close agreement with published multireference results. The findings of the present work point to the possibility of using a single determinant time-independent density functional approach to simulate nonadiabatic dynamics, even for large systems where multireference methods are impractical and TDDFT is often not accurate enough.

physics.chem-ph↗

arXiv2021

Direct Energy Minimization Based on Exponential Transformation in Density Functional Calculations of Finite and Extended Systems

The energy minimization involved in density functional calculations of electronic systems can be carried out using an exponential transformation that preserves the orthonormality of the orbitals. The energy of the system is then represented as a function of the elements of a skew-Hermitian matrix that can be optimized directly using unconstrained minimization methods. An implementation based on the limited memory Broyden-Fletcher-Goldfarb-Shanno approach with inexact line search and a preconditioner is presented and the performance compared with that of the commonly used self-consistent field approach. Results are presented for the G2 set of 148 molecules, liquid water configurations with up to 576 molecules and some insulating crystals. A general preconditioner is presented that is applicable to systems with fractional orbital occupation as is, for example, needed in the k-point sampling for periodic systems. This exponential transformation direct minimization approach is found to outperform the standard implementation of the self-consistent field approach in that all the calculations converge with the same set of parameter values and it requires less computational effort on average. The formulation of the exponential transformation and the gradients of the energy presented here are quite general and can be applied to energy functionals that are not unitary invariant such as self-interaction corrected functionals.

physics.comp-ph↗

arXiv2021

Method for Calculating Excited Electronic States Using Density Functionals and Direct Orbital Optimization with Real Space Grid or Plane Wave Basis Set

A direct orbital optimization method is presented for density functional calculations of excited electronic states using either a real space grid or a plane wave basis set. The method is variational, provides atomic forces in the excited states, and can be applied to Kohn-Sham (KS) functionals as well as orbital-density dependent functionals (ODD) including explicit self-interaction correction. The implementation for KS functionals involves two nested loops: (1) An inner loop for finding a stationary point in a subspace spanned by the occupied and a few virtual orbitals corresponding to the excited state; (2) an outer loop for minimizing the energy in a tangential direction in the space of the orbitals. For ODD functionals, a third loop is used to find the unitary transformation that minimizes the energy functional among occupied orbitals only. Combined with the maximum overlap method, the algorithm converges in challenging cases where conventional self-consistent field algorithms tend to fail. The benchmark tests presented include two charge-transfer excitations in nitrobenzene and an excitation of CO to degenerate $π^\ast$ orbitals where the importance of complex orbitals is illustrated. An application of the method to several metal-to-ligand charge-transfer and metal-centred excited states of an Fe$^{\rm II}$ photosensitizer complex is described and the results compared to reported experimental estimates. The method is also used to study the effect of Perdew-Zunger self-interaction correction on valence and Rydberg excited states of several molecules, both singlet and triplet states, and the performance compared to semilocal and hybrid functionals.

physics.comp-ph↗

arXiv2021

Mn Dimer can be Described Accurately with Density Functional Calculations when Self-interaction Correction is Applied

Qualitatively incorrect results are obtained for the Mn dimer in density functional theory calculations using the generalized gradient approximation (GGA) and similar results are obtained from local density and meta-GGA functionals. The coupling is predicted to be ferromagnetic rather than antiferromagnetic and the bond between the atoms is predicted to be an order of magnitude too strong and about an Ångstrøm too short. Explicit, self-interaction correction (SIC) applied to a commonly used GGA energy functional, however, provides close agreement with both experimental data and high-level, multi-reference wave function calculations. These results show that the failure is not due to strong correlation but rather the single electron self-interaction that is necessarily introduced in estimates of the classical Coulomb and exchange-correlation energy when only the total electron density is used as input. The corrected functional depends explicitly on the orbital densities and can, therefore, avoid the introduction of self-Coulomb interaction. The error arises because of over-stabilization of bonding $d$-states in the minority spin channel resulting from an overestimate of the $d$-electron self-interaction in the semi-local exchange-correlation functionals. Since the computational effort in the self-interaction corrected calculations scales with system size in the same way as for regular semi-local functional calculations, this approach provides a way to calculate properties of Mn nanoclusters as well as biomolecules and extended solids where Mn dimers and larger cluster are present, while multi-reference wave function calculations can only be applied to small systems.

physics.chem-ph↗

arXiv2017

Theory and applications of generalized Pipek--Mezey Wannier functions

The theory for the generation of Wannier functions within the generalized Pipek--Mezey approach [Lehtola, S.; Jónsson, H. J. Chem. Theory Comput. 2014, 10, 642] is presented and an implementation thereof is described. Results are presented for systems with periodicity in one, two and three dimensions as well as isolated molecules. The generalized Pipek--Mezey Wannier functions (PMWF) are highly localized orbitals consistent with chemical intuition where a distinction is maintained between σ- and π-orbitals. The PMWF method is compared with the so-called maximally localized Wannier functions (MLWF) that are frequently used for the analysis of condensed matter calculations. Whereas PMWFs maximize the localization criterion of Pipek and Mezey, MLWFs maximize that of Foster and Boys and have the disadvantage of mixing σ- and π-orbitals in many cases. The PMWF orbitals turn out to be as localized as the MLWF orbitals as evidenced by cross-comparison of the values of the PMWF and MLWF objective functions for the two types of orbitals. Our implementation in the atomic simulation environment (ASE) is compatible with various representations of the wave function, including real-space grids, plane waves and linear combinations of atomic orbitals. The projector augmented wave formalism for the representation of atomic core electrons is also supported. Results of calculations with the GPAW software are described here, but our implementation can also use output from other electronic structure software such as ABINIT, NWChem and VASP.

cond-mat.mtrl-sci↗