SwePub - sökning: WFRF:(Lindh Roland Professor 1...

Numrering	Referens	Omslagsbild	Hitta
1.	Stegeby, Henrik, 1979- (författare) MATTER-ANTIMATTER INTERACTIONS : The hydrogen-antihydrogen system and antiproton-matter interactions 2018 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Ever since antiparticles were discovered their nature has been something of a mystery. They were postulated to be identical to regular particles except for having opposite charge, but this would imply that an equal amount of antiparticles and particles should have been created at the beginning of time. However, everywhere we look the Universe seems to be constituted of regular particles, giving rise to the question whether there is something else that differentiates antiparticles from regular particles, or if there is something amiss in the Standard Model of particle physics.This thesis focuses on a central system of study in this field, the hydrogen-antihydrogen system and the theory surrounding it, as well as an expansion into systems with an antiproton interacting with small molecules, bridging the fields of quantum physics and quantum chemistry.Methods expanding on the Born-Oppenheimer approximation for the interaction between the two atoms are presented. The resulting 2-body interaction potential is then used for creating a part of the basis in a non-adiabatic 4-body method in order to look for resonance states whose existence could impact cross-sections of hydrogen-antihydrogen scattering. The eigenfunctions obtained from the non-adiabatic method are used by extracting the 2-body hadronic density function and comparing it to the adiabatic wave function, for measuring the adiabaticity of the hydrogen-antihydrogen system.The antiproton-matter interaction is first investigated by a quantum dynamical approach of an antiproton scattering on molecular hydrogen, common products in high-energy collision experiments, continued by a study of the potential energy surfaces of an antiproton interacting with a range of functional groups present in the human body.
2.	Aquilante, Francesco, et al. (författare) Modern quantum chemistry with [Open]Molcas 2020 Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21 Tidskriftsartikel (refereegranskat)abstract MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
3.	Aurbakken, Einar, et al. (författare) Transient spectroscopy from time-dependent electronic-structure theory without multipole expansions 2024 Ingår i: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - : American Physical Society. - 2469-9926 .- 2469-9934. ; 109:1 Tidskriftsartikel (refereegranskat)abstract Based on the work done by an electromagnetic field on an atomic or molecular electronic system, a general gauge-invariant formulation of transient absorption spectroscopy is presented within the semiclassical approximation. Avoiding multipole expansions, a computationally viable expression for the spectral response function is derived from the minimal-coupling Hamiltonian of an electronic system interacting with one or more laser pulses described by a source-free, enveloped electromagnetic vector potential. With a fixed-basis expansion of the electronic wave function, the computational cost of simulations of laser-driven electron dynamics beyond the dipole approximation is the same as simulations adopting the dipole approximation. We illustrate the theory by time-dependent configuration interaction and coupled-cluster simulations of core-level absorption and circular dichroism spectra.
4.	Bao, Jie J., et al. (författare) Analytic gradients for compressed multistate pair-density functional theory 2022 Ingår i: Molecular Physics. - : Taylor & Francis Group. - 0026-8976 .- 1362-3028. ; 120:19-20 Tidskriftsartikel (refereegranskat)abstract Photochemical reactions often involve states that are closely coupled due to near degeneracies, for example by proximity to conical intersections. Therefore, a multistate method is used to accurately describe these states; for example, ordinary perturbation theory is replaced by quasidegenerate perturbation theory. Multiconfiguration pair-density functional theory (MC-PDFT) provides an efficient way to approximate the full dynamical correlation energy of strongly correlated systems, and we recently proposed compressed multistate pair-density functional theory (CMS-PDFT) to treat closely coupled states. In the present paper, we report the implementation of analytic gradients for CMS-PDFT in both OpenMolcas and PySCF, and we illustrate the use of these gradients by applying the method to the excited states of formaldehyde and phenol.
5.	Battaglia, Stefano, et al. (författare) Extended Dynamically Weighted CASPT2 : The Best of Two Worlds 2020 Ingår i: Journal of Chemical Theory and Computation. - : AMER CHEMICAL SOC. - 1549-9618 .- 1549-9626. ; 16:3, s. 1555-1567 Tidskriftsartikel (refereegranskat)abstract We introduce a new variant of the complete active A space second-order perturbation theory (CASPT2) method that performs similarly to multistate CASPT2 (MS-CASPT2) in regions of the potential energy surface where the electronic states are energetically well separated and is akin to extended MS-CASPT2 (XMS-CASPT2) in case the underlying zeroth-order references are near-degenerate. Our approach follows a recipe analogous to that of XMS-CASPT2 to ensure approximate invariance under unitary transformations of the model states and a dynamic weighting scheme to smoothly interpolate the Fock operator between state-specific and state-average regimes. The resulting extended dynamically weighted CASPT2 (XDW-CASPT2) methodology possesses the most desirable features of both MS-CASPT2 and XMS-CASPT2, that is, the ability to provide accurate transition energies and correctly describe avoided crossings and conical intersections. The reliability of XDW-CASPT2 is assessed on a number of molecular systems. First, we consider the dissociation of lithium fluoride, highlighting the distinctive characteristics of the new approach. Second, the invariance of the theory is investigated by studying the conical intersection of the distorted allene molecule. Finally, the relative accuracy in the calculation of vertical excitation energies is benchmarked on a set of 26 organic compounds. We found that XDW-CASPT2, albeit being only approximately invariant, produces smooth potential energy surfaces around conical intersections and avoided crossings, performing equally well to the strictly invariant XMS-CASPT2 method. The accuracy of vertical transition energies is almost identical to MS-CASPT2, with a mean absolute deviation of 0.01-0.02 eV, in contrast to 0.12 eV for XMS-CASPT2.
6.	Battaglia, Stefano, et al. (författare) On the role of symmetry in XDW-CASPT2 2021 Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 154:3 Tidskriftsartikel (refereegranskat)abstract Herewith, we propose two new exponents for the recently introduced XDW-CASPT2 method [S. Battaglia and R. Lindh, J. Chem. Theory Comput. 16, 1555-1567 (2020)], which fix one of the largest issues hindering this approach. By using the first-order effective Hamiltonian coupling elements, the weighting scheme implicitly takes into account the symmetry of the states, thereby averaging Fock operators only if the zeroth-order wave functions interact with each other. The use of Hamiltonian couplings also provides a physically sounder approach to quantitate the relative weights; however, it introduces new difficulties when these rapidly die off to zero. The improved XDW-CASPT2 method is critically tested on several systems of photochemical relevance, and it is shown that it succeeds in its original intent of maintaining MS-CASPT2 accuracy for the evaluation of transition energies and at the same time providing smooth potential energy surfaces around near-degenerate points akin to XMS-CASPT2.
7.	Battaglia, Stefano, et al. (författare) Regularized CASPT2 : an Intruder-State-Free Approach 2022 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 18:8, s. 4814-4825 Tidskriftsartikel (refereegranskat)abstract In this work we present a new approach to fix the intruder-state problem (ISP) in CASPT2 based on sigma p regularization. The resulting sigma(p)-CASPT2 method is compared to previous techniques, namely, the real and imaginary level shifts, on a theoretical basis and by performing a series of systematic calculations. The analysis is focused on two aspects, the effectiveness of sigma(p)-CASPT2 in removing the ISP and the sensitivity of the approach with respect to the input parameter. We found that sigma p- CASPT2 compares favorably with respect to previous approaches and that different versions, sigma(1)-CASPT2 and sigma(2)-CASPT2, have different potential application domains. This analysis also reveals the unsuitability of the real level shift technique as a general way to avoid the intruder-state problem.
8.	Calio, Paul B., et al. (författare) Minimum-Energy Conical Intersections by Compressed Multistate Pair-Density Functional Theory 2024 Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 128:9, s. 1698-1706 Tidskriftsartikel (refereegranskat)abstract Compressed multistate pair-density functional theory (CMS-PDFT) is a multistate version of multiconfiguration pair-density functional theory that can capture the correct topology of coupled potential energy surfaces (PESs) around conical intersections. In this work, we develop interstate coupling vectors (ISCs) for CMS-PDFT in the OpenMolcas and PySCF/mrh electronic structure packages. Yet, the main focus of this work is using ISCs to calculate minimum-energy conical intersections (MECIs) by CMS-PDFT. This is performed using the projected constrained optimization method in OpenMolcas, which uses ISCs to restrain the iterations to the conical intersection seam. We optimize the S1/S0 MECIs for ethylene, butadiene, and benzene and show that CMS-PDFT gives smooth PESs in the vicinities of the MECIs. Furthermore, the CMS-PDFT MECIs are in good agreement with the MECI calculated by the more expensive XMS-CASPT2 method.
9.	Cuéllar-Zuquin, Juliana, et al. (författare) Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size 2023 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:22, s. 8258-8272 Tidskriftsartikel (refereegranskat)abstract We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1nO/Nπ* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.
10.	Delcey, Mickael G., et al. (författare) Exact semi-classical light-matter interaction operator applied to two-photon processes with strong relativistic effects 2020 Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 153:2 Tidskriftsartikel (refereegranskat)abstract X-ray processes involve interactions with high-energy photons. For these short wavelengths, the perturbing field cannot be treated as constant, and there is a need to go beyond the electric-dipole approximation. The exact semi-classical light-matter interaction operator offers several advantages compared to the multipole expansion such as improved stability and ease of implementation. Here, the exact operator is used to model x-ray scattering in metal K pre-edges. This is a relativistic two-photon process where absorption is dominated by electric-dipole forbidden transitions. With the restricted active space state-interaction approach, spectra can be calculated even for the multiconfigurational wavefunctions including second-order perturbation. However, as the operator itself depends on the transition energy, the cost for evaluating integrals for hundreds of thousands unique transitions becomes a bottleneck. Here, this is solved by calculating the integrals in a molecular-orbital basis that only runs over the active space, combined with a grouping scheme where the operator is the same for close-lying transitions. This speeds up the calculations of single-photon processes and is critical for the modeling of two-photon scattering processes. The new scheme is used to model Kα resonant inelastic x-ray scattering of iron-porphyrin complexes with relevance to studies of heme enzymes, for which the total computational time is reduced by several orders of magnitude with an effect on transition intensities of 0.1% or less.
11.	Fernández Galván, Ignacio, 1977-, et al. (författare) Restricted-Variance Constrained, Reaction Path, and Transition State Molecular Optimizations Using Gradient-Enhanced Kriging 2021 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 17:1, s. 571-582 Tidskriftsartikel (refereegranskat)abstract Gaussian process regression has recently been explored as an alternative to standard surrogate models in molecular equilibrium geometry optimization. In particular, the gradient-enhanced Kriging approach in association with internal coordinates, restricted-variance optimization, and an efficient and fast estimate of hyperparameters has demonstrated performance on par or better than standard methods. In this report, we extend the approach to constrained optimizations and transition states and benchmark it for a set of reactions. We compare the performance of the newly developed method with the standard techniques in the location of transition states and in constrained optimizations, both isolated and in the context of reaction path computation. The results show that the method outperforms the current standard in efficiency as well as in robustness.
12.	Fernández Galván, Ignacio, 1977-, et al. (författare) Smooth Things Come in Threes : A Diabatic Surrogate Model for Conical Intersection Optimization 2023 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:11, s. 3418-3427 Tidskriftsartikel (refereegranskat)abstract The optimization of conical intersection structures iscomplicatedby the nondifferentiability of the adiabatic potential energy surfaces.In this work, we build a pseudodiabatic surrogate model, based onGaussian process regression, formed by three smooth and differentiablesurfaces that can adequately reproduce the adiabatic surfaces. Usingthis model with the restricted variance optimization method resultsin a notable decrease of the overall computational effort requiredto obtain minimum energy crossing points.
13.	Galván, Ignacio Fdez., et al. (författare) OpenMolcas : From Source Code to Insight 2019 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:11, s. 5925-5964 Tidskriftsartikel (refereegranskat)abstract In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.
14.	Giussani, Angelo, et al. (författare) Molecular Basis of the Chemiluminescence Mechanism of Luminol 2019 Ingår i: Chemistry - A European Journal. - : WILEY-V C H VERLAG GMBH. - 0947-6539 .- 1521-3765. ; 25:20, s. 5202-5213 Tidskriftsartikel (refereegranskat)abstract Light emission from luminol is probably one of the most popular chemiluminescence reactions due to its use in forensic science, and has recently displayed promising applications for the treatment of cancer in deep tissues. The mechanism is, however, very complex and distinct possibilities have been proposed. By efficiently combining DFT and CASPT2 methodologies, the chemiluminescence mechanism has been studied in three steps: 1)luminol oxygenation to generate the chemiluminophore, 2)a chemiexcitation step, and 3)generation of the light emitter. The findings demonstrate that the luminol double-deprotonated dianion activates molecular oxygen, diazaquinone is not formed, and the chemiluminophore is formed through the concerted addition of oxygen and concerted elimination of nitrogen. The peroxide bond, in comparison to other isoelectronic chemical functionalities (-NH-NH-, -N--N--, and -S-S-), is found to have the best chemiexcitation efficiency, which allows the oxygenation requirement to be rationalized and establishes general design principles for the chemiluminescence efficiency. Electron transfer from the aniline ring to the OO bond promotes the excitation process to create an excited state that is not the chemiluminescent species. To produce the light emitter, proton transfer between the amino and carbonyl groups must occur; this requires highly localized vibrational energy during chemiexcitation.
15.	Hase, Florian, et al. (författare) Machine learning for analysing ab initio molecular dynamics simulations 2020 Ingår i: 31St International Conference On Photonic, Electronic And Atomic Collisions (Icpeac Xxxi). - : IOP PUBLISHING LTD. Konferensbidrag (refereegranskat)abstract Post-calculation analyses are often required to extract physical insights from ab initio molecular dynamics simulations. In the present work, we use different machine learning classifiers to take a new perspective on the decomposition reaction of dioxetane. Upon thermally activated decomposition, dioxetane can form products in an electronically excited state and can thus chemiluminesce. Simulated dynamics trajectories exhibit both successful and frustrated dissociations. As an exhaustive and systematic study of the decomposition mechanism "by hand" is beyond feasibility, machine learning models have been employed to study the relevant nuclear distortions governing molecular dissociation. According to all classifiers used in the study, the two sets of geometries differ by the in-phase planarisation of the two formaldehyde moieties. New insights are obtained from this analysis: if both moieties are not planar enough when the dissociation is attempted, it is frustrated and the molecule remains trapped. The postponing of the decomposition reaction by the so-called entropic trap enhances the chemiexcitation efficiency.
16.	Jeong, WooSeok, et al. (författare) Automation of Active Space Selection for Multireference Methods via Machine Learning on Chemical Bond Dissociation 2020 Ingår i: Journal of Chemical Theory and Computation. - : AMER CHEMICAL SOC. - 1549-9618 .- 1549-9626. ; 16:4, s. 2389-2399 Tidskriftsartikel (refereegranskat)abstract Predicting and understanding the chemical bond is one of the major challenges of computational quantum chemistry. Kohn-Sham density functional theory (KS-DFT) is the most common method, but approximate density functionals may not be able to describe systems where multiple electronic configurations are equally important. Multiconfigurational wave functions, on the other hand, can provide a detailed understanding of the electronic structures and chemical bonds of such systems. In the complete active space self-consistent field (CASSCF) method, one performs a full configuration interaction calculation in an active space consisting of active electrons and active orbitals. However, CASSCF and its variants require the selection of these active spaces. This choice is not black box; it requires significant experience and testing by the user, and thus active space methods are not considered particularly user-friendly and are employed only by a minority of quantum chemists. Our goal is to popularize these methods by making it easier to make good active space choices. We present a machine learning protocol that performs an automated selection of active spaces for chemical bond dissociation calculations of main group diatomic molecules. The protocol shows high prediction performance for a given target system as long as a properly correlated system is chosen for training. Good active spaces are correctly predicted with a considerably better success rate than random guess (larger than 80% precision for most systems studied). Our automated machine learning protocol shows that a "black-box" mode is possible for facilitating and accelerating the large-scale calculations on multireference systems where single-reference methods such as KS-DFT cannot be applied.
17.	Kamerlin, Natasha, et al. (författare) Unravelling the mechanism of pH-regulation in dinoflagellate luciferase 2020 Ingår i: International Journal of Biological Macromolecules. - : Elsevier BV. - 0141-8130 .- 1879-0003. ; 164, s. 2671-2680 Tidskriftsartikel (refereegranskat)abstract Dinoflagellates are the dominant source of bioluminescence in coastal waters. The luminescence reaction involves the oxidation of luciferin by a luciferase enzyme, which only takes place at low pH. The pH-dependence has previously been linked to four conserved histidines. It has been suggested that their protonation might induce a conformational change in the enzyme, thereby allowing substrate access to the binding pocket. Yet, the precise mechanism of luciferase activation has remained elusive. Here, we use computational tools to predict the open structure of the luciferase in Lingulodinium polyedra and to decipher the nature of the opening mechanism. Through accelerated molecular dynamics simulations, we demonstrate that the closed-open conformational change likely takes place via a tilt of the pH-regulatory helix-loop-helix domain. Moreover, we propose that the molecular basis for the transition is electrostatic repulsion between histidine-cation pairs, which destabilizes the closed conformation at low pH. Finally, by simulating truncated mutants, we show that eliminating the C-terminus alters the shape of the active site, effectively inactivating the luciferase.
18.	Khamesian, Marjan, et al. (författare) Spectroscopy of linear and circular polarized light with the exact semiclassical light–matter interaction 2019 Ingår i: Annual Reports in Computational Chemistry. - : Elsevier Ltd. - 1574-1400. - 9780128171196 ; , s. 39-76 Bokkapitel (refereegranskat)abstract We present the theory and the analytical and numerical solution for the calculation of the oscillator and rotatory strengths of molecular systems using a state-specific formalism. For a start, this is done in the context of the exact semiclassical light–matter interaction in association with electronic wave functions expanded in a Gaussian basis. The reader is guided through the standard approximations of the field, e.g., the use of commutators, truncation of Taylor expansions, and the implications of these are discussed in parallel. Expressions for the isotropically averaged values are derived, recovering the isotropic oscillator strength in terms of the transition electric-dipole moment, and the isotropic rotatory strength in terms of the transition electric-dipole and magnetic-dipole moments. This chapter gives a detailed description of the computation of the integrals over the plane wave in association with Gaussian one-particle basis sets. Finally, a brief description is given of how the computed oscillator and rotatory strengths are related to the quantities commonly used and discussed in experimental studies.
19.	Källman, Erik, PhD, et al. (författare) Quantifying similarity for spectra with a large number of overlapping transitions : Examples from soft X-ray spectroscopy 2020 Ingår i: Chemical Physics. - : ELSEVIER. - 0301-0104 .- 1873-4421. ; 535 Tidskriftsartikel (refereegranskat)abstract Theoretical simulations are frequently used to assign electronic and geometric structure from spectral fingerprints. However, such assignments are prone to expectation bias. Bias can be reduced by using numerical measures of the similarity between calculated and experimental spectra. However, the commonly used pointwise comparisons cannot handle larger deviations in peak position. Here a weighted cross-correlation function is used to evaluate similarity scores for soft X-ray spectra of first-row transition metals. These spectra consist of hundreds of overlapping resonances, which makes spectral decomposition difficult. They are also challenging to model, leading to significant errors in both peak position and intensity. It is first shown how the choice of weight-function width can be related to the modeling errors. The method is then applied to evaluate the sensitivity of multiconfigurational wavefunction and charge-transfer multiplet simulations to model choices. The approach makes it possible to assess the reliability of assignments from spectral fingerprinting.
20.	Källman, Erik, PhD, et al. (författare) Simulations of valence excited states in coordination complexes reached through hard X-ray scattering 2020 Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 22:16, s. 8325-8335 Tidskriftsartikel (refereegranskat)abstract Hard X-ray spectroscopy selectively probes metal sites in complex environments. Resonant inelastic X-ray scattering (RIXS) makes it is possible to directly study metal-ligand interactions through local valence excitations. Here multiconfigurational wavefunction simulations are used to model valence K pre-edge RIXS for three metal-hexacyanide complexes by coupling the electric dipole-forbidden excitations with dipole-allowed valence-to-core emission. Comparisons between experimental and simulated spectra makes it possible to evaluate the simulation accuracy and establish a best-modeling practice. The calculations give correct descriptions of all LMCT excitations in the spectra, although energies and intensities are sensitive to the description of dynamical electron correlation. The consistent treatment of all complexes shows that simulations can rationalize spectral features. The dispersion in the manganese(iii) spectrum comes from unresolved multiple resonances rather than fluorescence, and the splitting is mainly caused by differences in spatial orientation between holes and electrons. The simulations predict spectral features that cannot be resolved in current experimental data sets and the potential for observing d-d excitations is also explored. The latter can be of relevance for non-centrosymmetric systems with more intense K pre-edges. These ab initio simulations can be used to both design and interpret high-resolution X-ray scattering experiments.
21.	Manni, Giovanni Li, et al. (författare) The OpenMolcas Web : A Community-Driven Approach to Advancing Computational Chemistry 2023 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:20, s. 6933-6991 Tidskriftsartikel (refereegranskat)abstract The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.
22.	Pedersen, Thomas Bondo, et al. (författare) The versatility of the Cholesky decomposition in electronic structure theory 2024 Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : John Wiley & Sons. - 1759-0876 .- 1759-0884. ; 14:1 Tidskriftsartikel (refereegranskat)abstract The resolution-of-the-identity (RI) or density fitting (DF) approximation for the electron repulsion integrals (ERIs) has become a standard component of accelerated and reduced-scaling implementations of first-principles Gaussian-type orbital electronic-structure methods. The Cholesky decomposition (CD) of the ERIs has also become increasingly deployed across quantum chemistry packages in the last decade, even though its early applications were mostly limited to high-accuracy methods such as coupled-cluster theory and multiconfigurational approaches. Starting with a summary of the basic theory underpinning both the CD and RI/DF approximations, thus underlining the extremely close relation of the CD and RI/DF techniques, we provide a brief and largely chronological review of the evolution of the CD approach from its birth in 1977 to its current state. In addition to being a purely numerical procedure for handling ERIs, thus providing robust and computationally efficient approximations to the exact ERIs that have been found increasingly useful on modern computer platforms, CD also offers highly accurate approaches for generating auxiliary basis sets for the RI/DF approximation on the fly due to the deep mathematical connection between the two approaches. In this review, we aim to provide a concise reference of the main techniques employed in various CD approaches in electronic structure theory, to exemplify the connection between the CD and RI/DF approaches, and to clarify the state of the art to guide new implementations of CD approaches across electronic structure programs.
23.	Raggi, Gerardo, et al. (författare) Restricted-Variance Molecular Geometry Optimization Based on Gradient-Enhanced Kriging 2020 Ingår i: Journal of Chemical Theory and Computation. - : AMER CHEMICAL SOC. - 1549-9618 .- 1549-9626. ; 16:6, s. 3989-4001 Tidskriftsartikel (refereegranskat)abstract Machine learning techniques, specifically gradient-enhanced Kriging (GEK), have been implemented for molecular geometry optimization. GEK-based optimization has many advantages compared to conventional-step-restricted second-order truncated expansion-molecular optimization methods. In particular, the surrogate model given by GEK can have multiple stationary points, will smoothly converge to the exact model as the number of sample points increases, and contains an explicit expression for the expected error of the model function at an arbitrary point. Machine learning is, however, associated with abundance of data, contrary to the situation desired for efficient geometry optimizations. In this paper, we demonstrate how the GEK procedure can be utilized in a fashion such that in the presence of few data points, the surrogate surface will in a robust way guide the optimization to a minimum of a potential energy surface. In this respect, the GEK procedure will be used to mimic the behavior of a conventional second-order scheme but retaining the flexibility of the superior machine learning approach. Moreover, the expected error will be used in the optimizations to facilitate restricted-variance optimizations. A procedure which relates the eigenvalues of the approximate guessed Hessian with the individual characteristic lengths, used in the GEK model, reduces the number of empirical parameters to optimize to two: the value of the trend function and the maximum allowed variance. These parameters are determined using the extended Baker (e-Baker) and part of the Baker transition-state (Baker-TS) test suites as a training set. The so-created optimization procedure is tested using the e-Baker, full Baker-TS, and S22 test suites, at the density functional theory and second-order Moller-Plesset levels of approximation. The results show that the new method is generally of similar or better performance than a state-of-the-art conventional method, even for cases where no significant improvement was expected.
24.	Reiersolmoen, Ann Christin, et al. (författare) Symmetry of three-center, four-electron bonds 2020 Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 11:30, s. 7979-7990 Tidskriftsartikel (refereegranskat)abstract Three-center, four-electron bonds provide unusually strong interactions; however, their nature remains ununderstood. Investigations of the strength, symmetry and the covalentversuselectrostatic character of three-center hydrogen bonds have vastly contributed to the understanding of chemical bonding, whereas the assessments of the analogous three-center halogen, chalcogen, tetrel and metallic & xe111;-type long bonding are still lagging behind. Herein, we disclose the X-ray crystallographic, NMR spectroscopic and computational investigation of three-center, four-electron [D-X-D](+)bonding for a variety of cations (X+= H+, Li+, Na+, F+, Cl+, Br+, I+, Ag(+)and Au+) using a benchmark bidentate model system. Formation of a three-center bond, [D-X-D](+)is accompanied by an at least 30% shortening of the D-X bonds. We introduce a numerical index that correlates symmetry to the ionic size and the electron affinity of the central cation, X+. Providing an improved understanding of the fundamental factors determining bond symmetry on a comprehensive level is expected to facilitate future developments and applications of secondary bonding and hypervalent chemistry.
25.	Sankari, Anna, et al. (författare) Non-radiative decay and fragmentation in water molecules after 1a1-14a1 excitation and core ionization studied by electron-energy-resolved electron–ion coincidence spectroscopy 2020 Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:7 Tidskriftsartikel (refereegranskat)abstract In this paper, we examine decay and fragmentation of core-excited and core-ionized water molecules combining quantum chemical calculations and electron-energy-resolved electron–ion coincidence spectroscopy. The experimental technique allows us to connect electronic decay from core-excited states, electronic transitions between ionic states, and dissociation of the molecular ion. To this end, we calculate the minimum energy dissociation path of the core-excited molecule and the potential energy surfaces of the molecular ion. Our measurements highlight the role of ultra-fast nuclear motion in the 1a1-14a1 core-excited molecule in the production of fragment ions. OH+ fragments dominate for spectator Auger decay. Complete atomization after sequential fragmentation is also evident through detection of slow H+ fragments. Additional measurements of the non-resonant Auger decay of the core-ionized molecule (1a1-1) to the lower-energy dication states show that the formation of the OH+ + H+ ion pair dominates, whereas sequential fragmentation OH+ + H+ → O + H+ + H+ is observed for transitions to higher dication states, supporting previous theoretical investigations.
26.	Scott, Thais R., et al. (författare) Analytic gradients for multiconfiguration pair-density functional theory with density fitting : Development and application to geometry optimization in the ground and excited states 2021 Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 154:7 Tidskriftsartikel (refereegranskat)abstract Density fitting reduces the computational cost of both energy and gradient calculations by avoiding the computation and manipulation of four-index electron repulsion integrals. With this algorithm, one can efficiently optimize the geometries of large systems with an accurate multireference treatment. Here, we present the derivation of multiconfiguration pair-density functional theory for energies and analytic gradients with density fitting. Six systems are studied, and the results are compared to those obtained with no approximation to the electron repulsion integrals and to the results obtained by complete active space second-order perturbation theory. With the new approach, there is an increase in the speed of computation with a negligible loss in accuracy. Smaller grid sizes have also been used to reduce the computational cost of multiconfiguration pair-density functional theory with little effect on the optimized geometries and gradient values.
27.	Sethio, Daniel, et al. (författare) A Story of Three Levels of Sophistication in SCF/KS-DFT Orbital Optimization Procedures 2024 Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 128:12, s. 2472-2486 Tidskriftsartikel (refereegranskat)abstract In this work, three versions of self-consistent field/Kohn-Sham density functional theory (SCF/KS-DFT) orbital optimization are described and benchmarked. The methods are a modified version of the geometry version of the direct inversion in the iterative subspace approach (which we call r-GDIIS), the modified restricted step rational function optimization method (RS-RFO), and the novel subspace gradient-enhanced Kriging method combined with restricted variance optimization (S-GEK/RVO). The modifications introduced are aimed at improving the robustness and computational scaling of the procedures. In particular, the subspace approach in S-GEK/RVO allows the application to SCF/KS-DFT optimization of a machine learning technique that has proven to be successful in geometry optimizations. The performance of the three methods is benchmarked for a large number of small- to medium-sized organic molecules, at equilibrium structures and close to a transition state, and a second set of molecules containing closed- and open-shell transition metals. The results indicate the importance of the resetting technique in boosting the performance of the r-GDIIS procedure. Moreover, it is demonstrated that already at the inception of the subspace version of GEK to optimize SCF wave functions, it displays superior and robust convergence properties as compared to those of the standard state-of-the-art SCF/KS-DFT optimization methods.
28.	Sethio, Daniel, et al. (författare) Halogen bond of halonium ions : Benchmarking DFT methods for the description of NMR chemical shifts 2020 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 16:12, s. 7690-7701 Tidskriftsartikel (refereegranskat)abstract Because of their anisotropic electron distribution and electron deficiency, halonium ions are unusually strong halogen-bond donors that form strong and directional three-center, four-electron halogen bonds. These halogen bonds have received considerable attention owing to their applicability in supramolecular and synthetic chemistry and have been intensely studied using spectroscopic and crystallographic techniques over the past decade. Their computational treatment faces different challenges to those of conventional weak and neutral halogen bonds. Literature studies have used a variety of wave functions and DFT functionals for prediction of their geometries and NMR chemical shifts, however, without any systematic evaluation of the accuracy of these methods being available. In order to provide guidance for future studies, we present the assessment of the accuracy of 12 common DFT functionals along with the Hartree–Fock (HF) and the second-order Møller–Plesset perturbation theory (MP2) methods, selected from an initial set of 36 prescreened functionals, for the prediction of 1H, 13C, and 15N NMR chemical shifts of [N–X–N]+ halogen-bond complexes, where X = F, Cl, Br, and I. Using a benchmark set of 14 complexes, providing 170 high-quality experimental chemical shifts, we show that the choice of the DFT functional is more important than that of the basis set. The M06 functional in combination with the aug-cc-pVTZ basis set is demonstrated to provide the overall most accurate NMR chemical shifts, whereas LC-ωPBE, ωB97X-D, LC-TPSS, CAM-B3LYP, and B3LYP to show acceptable performance. Our results are expected to provide a guideline to facilitate future developments and applications of the [N–X–N]+ halogen bond.
29.	Sethio, Daniel, et al. (författare) Simulation Reveals the Chameleonic Behavior of Macrocycles 2023 Ingår i: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 63:1, s. 138-146 Tidskriftsartikel (refereegranskat)abstract Conformational analysis is central to the design of bioactive molecules. It is particularly challenging for macrocycles due to noncovalent transannular interactions, steric interactions, and ring strain that are often coupled. Herein, we simulated the conformations of five macrocycles designed to express a progression of increasing complexity in environment-dependent intramolecular interactions and verified the results against NMR measurements in chloroform and dimethyl sulfoxide. Molecular dynamics using an explicit solvent model, but not the Monte Carlo method with implicit solvation, handled both solvents correctly. Refinement of conformations at the ab initio level was fundamental to reproducing the experimental observations-standard state-of-the-art molecular mechanics force fields were insufficient. Our simulations correctly predicted the intramolecular interactions between side chains and the macrocycle and revealed an unprecedented solvent-induced conformational switch of the macrocyclic ring. Our results provide a platform for the rational, prospective design of molecular chameleons that adapt to the properties of the environment.
30.	Slanina, Tomáš, et al. (författare) Impact of Excited-State Antiaromaticity Relief in a Fundamental Benzene Photoreaction Leading to Substituted Bicyclo[3.1.0]hexenes 2020 Ingår i: Journal of the American Chemical Society. - : American Chemical Society. - 0002-7863 .- 1520-5126. ; 142:25, s. 10942-10954 Tidskriftsartikel (refereegranskat)abstract Benzene exhibits a rich photochemistry which can provide access to complex molecular scaffolds that are difficult to access with reactions in the electronic ground state. While benzene is aromatic in its ground state, it is antiaromatic in its lowest ππ∗ excited states. Herein, we clarify to what extent relief of excited-state antiaromaticity (ESAA) triggers a fundamental benzene photoreaction: the photoinitiated nucleophilic addition of solvent to benzene in acidic media leading to substituted bicyclo[3.1.0]hex-2-enes. The reaction scope was probed experimentally, and it was found that silyl-substituted benzenes provide the most rapid access to bicyclo[3.1.0]hexene derivatives, formed as single isomers with three stereogenic centers in yields up to 75% in one step. Two major mechanism hypotheses, both involving ESAA relief, were explored through quantum chemical calculations and experiments. The first mechanism involves protonation of excited-state benzene and subsequent rearrangement to bicyclo[3.1.0]hexenium cation, trapped by a nucleophile, while the second involves photorearrangement of benzene to benzvalene followed by protonation and nucleophilic addition. Our studies reveal that the second mechanism is operative. We also clarify that similar ESAA relief leads to puckering of S1-state silabenzene and pyridinium ion, where the photorearrangement of the latter is of established synthetic utility. Finally, we identified causes for the limitations of the reaction, information that should be valuable in explorations of similar photoreactions. Taken together, we reveal how the ESAA in benzene and 6π-electron heterocycles trigger photochemical distortions that provide access to complex three-dimensional molecular scaffolds from simple reactants.
31.	Wilcox, Scott, 1993-, et al. (författare) Do 2-coordinate iodine(i) and silver(i) complexes form nucleophilic iodonium interactions (NIIs) in solution? 2022 Ingår i: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1359-7345 .- 1364-548X. ; 58:32, s. 4977-4980 Tidskriftsartikel (refereegranskat)abstract The interaction of a [bis(pyridine)iodine(i)](+) cation with a [bis(pyridine)silver(i)](+) cation, in which an iodonium ion acts as a nucleophile by transferring electron density to the silver(i) cation, is reinvestigated herein. No measurable interaction is observed between the cationic species in solution by NMR; DFT reveals that if there is an attractive interaction between these complexes in solution, it is dominantly the pi-pi interaction of pyridines.

Skapa referenser, mejla, bekava och länka

Länka till träfflistan

Träfflista för sökning "WFRF:(Lindh Roland Professor 1958 ) "

Avgränsa träffmängd

År