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Jónsson, Hannes

Publications and source records attributed to Jónsson, Hannes.

15 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Characterization of Deformational Isomerization Potential and Interconversion Dynamics with Ultrafast X-ray Solution Scattering

Dimeric complexes composed of d 8 square planar metal centers and rigid bridging ligands provide model systems to understand the interplay between attractive dispersion forces and steric strain in order to assist the development of reliable methods to model metal dimer complexes more broadly. [Ir 2 (dimen) 4 ] 2+ (dimen = para-diisocyanomenthane) presents a unique case study for such phenomena, as distortions of the optimal structure of a ligand with limited conformational flexibility counteract the attractive dispersive forces from the metal and ligand to yield a complex with two ground state deformational isomers. Here, in this work, we use ultrafast X-ray solution scattering (XSS) and optical transient absorption spectroscopy (OTAS) to reveal the nature of the equilibrium distribution and the exchange rate between the deformational isomers. The two ground state isomers have spectrally distinct electronic excitations that enable the selective excitation of one isomer or the other using a femtosecond duration pulse of visible light. We then track the dynamics of the nonequilibrium depletion of the electronic ground state population—often termed the ground state hole—with ultrafast XSS and OTAS, revealing a restoration of the ground state equilibrium in 2.3 ps. This combined experimental and theoretical study provides a critical test of various density functional approximations in the description of bridged d 8 –d 8 metal complexes. The results show that density functional theory calculations can reproduce the primary experimental observations if dispersion interactions are added, and a hybrid functional, which includes exact exchange, is used.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

GPAW: An open Python package for electronic structure calculations

We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for the implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE), providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe–Salpeter Equation, variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn–Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support for graphics processing unit (GPU) acceleration has been achieved with minor modifications to the GPAW code thanks to the CuPy library. We end the review with an outlook, describing some future plans for GPAW.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Complex Orbitals, Multiple Local Minima, and Symmetry Breaking in Perdew–Zunger Self-Interaction Corrected Density Functional Theory Calculations

Implentation of seminumerical stability analysis for calculations using the Perdew-Zunger self-interaction correction is described. It is shown that real-valued solutions of the Perdew-Zunger equations for gas phase atoms are unstable with respect to imaginary orbital rotations, confirming that a proper implementation of the correction requires complex-valued orbitals. The orbital density dependence of the self-interaction corrected functional is found to lead to multiple local minima in the case of the acrylic acid, H 6 , and benzene molecules. Finally, in the case of benzene, symmetry breaking that results in incorrect ground state geometry is found to occur, erroneously leading to alternating bond lengths in the molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Towards an Optimal Gradient-dependent Energy Functional of the PZ-SIC Form

Results of Perdew–Zunger self-interaction corrected (PZ-SIC) density functional theory calculations of the atomization energy of 35 molecules are compared to those of high-level quantum chemistry calculations. While the PBE functional, which is commonly used in calculations of condensed matter, is known to predict on average too high atomization energy (overbinding of the molecules), the application of PZ-SIC gives a large overcorrection and leads to significant underestimation of the atomization energy. The exchange enhancement factor that is optimal for the generalized gradient approximation within the Kohn-Sham (KS) approach may not be optimal for the self-interaction corrected functional. The PBEsol functional, where the exchange enhancement factor was optimized for solids, gives poor results for molecules in KS but turns out to work better than PBE in PZ-SIC calculations. The exchange enhancement is weaker in PBEsol and the functional is closer to the local density approximation. Furthermore, the drop in the exchange enhancement factor for increasing reduced gradient in the PW91 functional gives more accurate results than the plateaued enhancement in the PBE functional. A step towards an optimal exchange enhancement factor for a gradient dependent functional of the PZ-SIC form is taken by constructing an exchange enhancement factor that mimics PBEsol for small values of the reduced gradient, and PW91 for large values. The average atomization energy is then in closer agreement with the high-level quantum chemistry calculations, but the variance is still large, the F 2 molecule being a notable outlier.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Self-interaction corrected density functional calculations of Rydberg states of molecular clusters: N,N-dimethylisopropylamine

Theoretical calculations of Rydberg excited states of molecular clusters consisting of N,N-dimethylisopropylamine molecules using a Perdew-Zunger self-interaction corrected energy functional are presented and compared with results of resonant multiphoton ionization measurements. The binding energy of the Rydberg electron in the monomer is calculated to be 2.79 eV and 2.27 eV in the 3s and 3p state, respectively, which compares well with measured values of 2.88 eV and 2.21 eV. Three different stable configurations of the dimer in the ground state were found using an energy functional that includes van der Waals interaction. The lowest ground state energy conformation has the two N-atoms widely separated, by 6.2 Å, while the Rydberg state energy is lowest for a configuration where the N-atoms of the two molecules come close together, separated by 3.7 Å. This conformational change is found to lower the Rydberg electron binding energy by 0.2 eV. The self-interaction corrected functional gives a highly localized hole on one of the two molecules, unlike results obtained using the PBE functional or the hybrid B3LYP functional which give a delocalized hole. For the trimer, the self-interaction corrected calculation gives a Rydberg electron binding energy lowered further by 0.13 eV as compared with the dimer. The calculated results compare well with trends observed in experimental measurements. The reduction of the Rydberg electron binding energy with cluster size can be ascribed to an effective delocalization of the positive charge of the hole by the induced and permanent dipole moments of the neighboring molecules. A further decrease observed to occur on a time scale of tens of ps can be ascribed to a structural rearrangement of the clusters in the Rydberg state where molecules rotate to orient their dipoles in response to the formation of the localized hole.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Molecular reordering processes on ice (0001) surfaces from long timescale simulations

We report results of long timescale adaptive kinetic Monte Carlo simulations aimed at identifying possible molecular reordering processes on both proton-disordered and ordered (Fletcher) basal plane (0001) surfaces of hexagonal ice. The simulations are based on a force field for flexible molecules and span a time interval of up to 50 μs at a temperature of 100 K, which represents a lower bound to the temperature range of earth's atmosphere. Additional calculations using both density functional theory and an ab initio based polarizable potential function are performed to test and refine the force field predictions. Several distinct processes are found to occur readily even at this low temperature, including concerted reorientation (flipping) of neighboring surface molecules, which changes the pattern of dangling H-atoms, and the formation of interstitial defects by the downwards motion of upper-bilayer molecules. On the proton-disordered surface, one major surface roughening process is observed that significantly disrupts the crystalline structure. Despite much longer simulation time, such roughening processes are not observed on the highly ordered Fletcher surface which is energetically more stable because of smaller repulsive interaction between neighboring dangling H-atoms. However, a more localized process takes place on the Fletcher surface involving a surface molecule transiently leaving its lattice site. The flipping process provides a facile pathway of increasing proton-order and stabilizing the surface, supporting a predominantly Fletcher-like ordering of low-temperature ice surfaces. Our simulations also show that eventual proton-disordered patches on the surface may induce significant local reconstructions. Further, a subset of the molecules on the Fletcher surface are susceptible to forming interstitial defects which might provide active sites for various chemical reactions in the atmosphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Improved initial guess for minimum energy path calculations

A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Polymer escape from a confining potential

The rate of escape of polymers from a two-dimensionally confining potential well has been evaluated using self-avoiding as well as ideal chain representations of varying length, up to 80 beads. Long timescale Langevin trajectories were calculated using the path integral hyperdynamics method to evaluate the escape rate. A minimum is found in the rate for self-avoiding polymers of intermediate length while the escape rate decreases monotonically with polymer length for ideal polymers. The increase in the rate for long, self-avoiding polymers is ascribed to crowding in the potential well which reduces the free energy escape barrier. An effective potential curve obtained using the centroid as an independent variable was evaluated by thermodynamic averaging and Kramers rate theory then applied to estimate the escape rate. While the qualitative features are well reproduced by this approach, it significantly overestimates the rate, especially for the longer polymers. The reason for this is illustrated by constructing a two-dimensional effective energy surface using the radius of gyration as well as the centroid as controlled variables. This shows that the description of a transition state dividing surface using only the centroid fails to confine the system to the region corresponding to the free energy barrier and this problem becomes more pronounced the longer the polymer is. A proper definition of a transition state for polymer escape needs to take into account the shape as well as the location of the polymer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Self-interaction corrected density functional calculations of molecular Rydberg states

A method is presented for calculating the wave function and energy of Rydberg excited states of molecules. A good estimate of the Rydberg state orbital is obtained using ground state density functional theory including Perdew-Zunger self-interaction correction and an optimized effective potential. The total energy of the excited molecule is obtained using the Delta Self-Consistent Field method where an electron is removed from the highest occupied orbital and placed in the Rydberg orbital. Results are presented for the first few Rydberg states of NH{sub 3}, H{sub 2}O, H{sub 2}CO, C{sub 2}H{sub 4}, and N(CH{sub 3}){sub 3}. The mean absolute error in the energy of the 33 molecular Rydberg states presented here is 0.18 eV. The orbitals are represented on a real space grid, avoiding the dependence on diffuse atomic basis sets. As in standard density functional theory calculations, the computational effort scales as NM{sup 2} where N is the number of orbitals and M is the number of grid points included in the calculation. Due to the slow scaling of the computational effort with system size and the high level of parallelism in the real space grid approach, the method presented here makes it possible to estimate Rydberg electron binding energy in large molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Hydrogen adsorption and desorption at the Pt(110)-(1×2) surface: experimental and theoretical study

The interaction of hydrogen with the Pt(110)-(1×2) surface is studied using temperature programmed desorption (TPD) measurements and density functional theory (DFT) calculations. The ridges in this surface resemble edges between micro-facets of Pt nano-particle catalysts used for hydrogen evolution (HER) and hydrogen oxidation reactions (HOR). The binding energy and activation energy for desorption are found to depend strongly on hydrogen coverage. At low coverage, the strongest binding sites are found to be the low coordination bridge sites at the edge and this is shown to agree well with the He-atom interaction and work function change which have been reported previously. At higher hydrogen coverage, the higher coordination sites on the micro-facet and in the trough get populated. The simulated TPD spectra based on the DFT results are in close agreement with our experimental spectra and provide microscopic interpretation of the three measured peaks. The lowest temperature peak obtained from the surface with highest hydrogen coverage does not correspond to desorption directly from the weakest binding sites, the trough sites, but is due to desorption from the ridge sites, followed by subsequent, thermally activated rearrangement of the H-adatoms. The reason is low catalytic activity of the Pt-atoms at the trough sites and large reduction in the binding energy at the ridge sites at high coverage. The intermediate temperature peak corresponds to desorption from the micro-facet. The highest temperature peak again corresponds to desorption from the ridge sites, giving rise to a re-entrant mechanism for the thermal desorption.

Gudmundsdóttir, Sigrídur↗
DOE OSTI2012

The effect of coadsorbed water on the stability, configuration and interconversion of formyl (HCO) and hydroxymethylidyne (COH) on platinum (111)

Two forms of the methanol electro-oxidation intermediate with stoichiometry C:H:O, COH (hydroxymethylidyne) and HCO (formyl), on Pt (11 1) with and without coadsorbed water were studied using density functional theory calculations. The structure, adsorption energy and stability with respect to dissociation were calculated. Both HC=O and C–OH were stable on clean Pt (11 1) and with a single coadsorbed water molecule, while only the HCO configuration was stable in the presence of a whole water layer. The vibrational modes of HC=O on a bridge site showed no mode around 1700 cm-1 characteristic of C=O stretch making it hard to distinguish it from C–OH.

36 MATERIALS SCIENCE↗